diff --git a/.gitignore b/.gitignore index 434f20f..6fcce67 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,5 @@ build +html *.so *.o *.pyc @@ -7,6 +8,8 @@ build *.a *.log *.status +*.dSYM +*.nc bathy_smoother/Python/ examples/Yellow_Sea/Inputs/Initial/compute_remap_weights_in examples/Yellow_Sea/YELLOW_grd_v1.nc @@ -36,3 +39,4 @@ pyroms/external/scrip/source/makefile2 pyroms/external/scrip/source/scrip pyroms/external/scrip/source/scrip_test pyroms_toolbox/Python/ +mask_change.txt diff --git a/README b/README index a65d23d..228e86a 100644 --- a/README +++ b/README @@ -10,16 +10,11 @@ rough around the edges. Prerequisites ------------- -Meanwhile, you can prepare by installing Enthought Python -(http://www.enthought.com/) or by this collection of packages: +Now using Anaconda python to download python 3.x and a bunch of other stuff: - * Python itself. You will need a version that's at least 2.4 and - less than 3.0. + * Python itself. You will need a version that's at least 3.4. - * numpy. Get a version that's reasonably new, don't count on the - version 1.0.1 that you found already on the system. How do you - tell the version? At the interactive prompt from python, type - "import numpy" then "numpy.__version__". + * numpy. * scipy. @@ -39,10 +34,15 @@ Meanwhile, you can prepare by installing Enthought Python interactive fun. It preloads both numpy and the matplotlib pylab package. -We may also add pyngl and pynio from NCAR to this list. Or ESMPy. -Or Python 3... + * natgrid from http://github.com/matplotlib/natgrid for at least + one of the examples. -If you want a package manager for these bits, check out Anaconda. +Planning to move to ESMF. Download it with: + + conda install --channel https://conda.anaconda.org/conda-forge esmf + +We may also add pyngl and pynio from NCAR to this list. +Or jupyter. Installing ---------- @@ -53,31 +53,40 @@ setup.py scripts for each, plus an examples directory. For now, - cd pyroms_toolbox; python setup.py build --fcompiler=gnu95; + cd pyroms_toolbox; python setup.py build python setup.py install --prefix=xxx; cd .. -The above may or may not need something along these lines: -setenv LDFLAGS '-L/usr/local/pkg/python/python-2.7.2/lib -shared' - cd bathy_smoother; python setup.py build; python setup.py install --prefix=xxx; cd .. cd pyroms; check the paths in the install script and see if it runs... + Maybe cut and paste from it into a bash shell. + +I had to hack the scrip makefile for the fortran90 netcdf stuff. The +anaconda netcdf-fortran reports: + nf-config not yet implemented for cmake builds + +A note on the .so files from fortran: They might now end up with names like: -If you needed the LDFLAGS above, you'll need to add it to the -install script too, at least for the build of scrip. + scrip.cpython-35m-x86_64-linux-gnu.so -I'm getting inconsistent results with where the .so files need to be. Best -results for me are if I go to the site-packages directory where pycnal -got installed and copy all the .so files: +It's OK - they'll load as long as they are in your PYTHONPATH. You might +also need libgu.so to be in your LD_LIBRARY_PATH. I'm getting inconsistent +results with where the .so files need to be. Best results for me are if I go +to the site-packages directory where pyroms got installed and copy all the +.so files: - cp pycnal/*.so . - cp pycnal_toolbox/*.so . + cp pyroms/*.so . + cp pyroms_toolbox/*.so . cp bathy_smoother/*.so . -Make sure this site-packages directory is in your PYTHONPATH. +Make sure this site-packages directory is in your PYTHONPATH. As for +libgu.so, it went into $DESTDIR/lib, for me $HOME/python/lib - that's +what needs to be in the LD_LIBRARY_PATH. +Also, f2py may or may not be called f2py3, depending. It's listed explicitly +in the scrip makefile and under pyroms_toolbox/pyroms_toolbox/src/makefile. Running ------- @@ -86,3 +95,11 @@ We have a gridid.txt file that's pointed to by the PYROMS_GRIDID_FILE environment variable. If you are operating on files containing sufficient grid information already, you won't need to use this. An example is provided in the examples directory. + + +Doxygen +------- + +Running "doxygen .doxygen" in any of pyroms, pyroms_toolbox or +bathy_smoother will generate doxygen files. Edit the .doxygen files to +specify html vs. some other output format. diff --git a/bathy_smoother/.doxygen b/bathy_smoother/.doxygen new file mode 100644 index 0000000..3d79969 --- /dev/null +++ b/bathy_smoother/.doxygen @@ -0,0 +1,1519 @@ +# Doxyfile 1.6.1 + +# This file describes the settings to be used by the documentation system +# doxygen (www.doxygen.org) for a project +# +# All text after a hash (#) is considered a comment and will be ignored +# The format is: +# TAG = value [value, ...] +# For lists items can also be appended using: +# TAG += value [value, ...] +# Values that contain spaces should be placed between quotes (" ") + +#--------------------------------------------------------------------------- +# Project related configuration options +#--------------------------------------------------------------------------- + +# This tag specifies the encoding used for all characters in the config file +# that follow. The default is UTF-8 which is also the encoding used for all +# text before the first occurrence of this tag. Doxygen uses libiconv (or the +# iconv built into libc) for the transcoding. See +# http://www.gnu.org/software/libiconv for the list of possible encodings. + +DOXYFILE_ENCODING = UTF-8 + +# The PROJECT_NAME tag is a single word (or a sequence of words surrounded +# by quotes) that should identify the project. + +PROJECT_NAME = bathy_smoother + +# The PROJECT_NUMBER tag can be used to enter a project or revision number. +# This could be handy for archiving the generated documentation or +# if some version control system is used. + +PROJECT_NUMBER = + +# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) +# base path where the generated documentation will be put. +# If a relative path is entered, it will be relative to the location +# where doxygen was started. If left blank the current directory will be used. + +OUTPUT_DIRECTORY = + +# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create +# 4096 sub-directories (in 2 levels) under the output directory of each output +# format and will distribute the generated files over these directories. +# Enabling this option can be useful when feeding doxygen a huge amount of +# source files, where putting all generated files in the same directory would +# otherwise cause performance problems for the file system. + +CREATE_SUBDIRS = YES + +# The OUTPUT_LANGUAGE tag is used to specify the language in which all +# documentation generated by doxygen is written. Doxygen will use this +# information to generate all constant output in the proper language. +# The default language is English, other supported languages are: +# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional, +# Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German, +# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English +# messages), Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian, +# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrilic, Slovak, +# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese. + +OUTPUT_LANGUAGE = English + +# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will +# include brief member descriptions after the members that are listed in +# the file and class documentation (similar to JavaDoc). +# Set to NO to disable this. + +BRIEF_MEMBER_DESC = YES + +# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend +# the brief description of a member or function before the detailed description. +# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the +# brief descriptions will be completely suppressed. + +REPEAT_BRIEF = YES + +# This tag implements a quasi-intelligent brief description abbreviator +# that is used to form the text in various listings. Each string +# in this list, if found as the leading text of the brief description, will be +# stripped from the text and the result after processing the whole list, is +# used as the annotated text. Otherwise, the brief description is used as-is. +# If left blank, the following values are used ("$name" is automatically +# replaced with the name of the entity): "The $name class" "The $name widget" +# "The $name file" "is" "provides" "specifies" "contains" +# "represents" "a" "an" "the" + +ABBREVIATE_BRIEF = + +# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then +# Doxygen will generate a detailed section even if there is only a brief +# description. + +ALWAYS_DETAILED_SEC = NO + +# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all +# inherited members of a class in the documentation of that class as if those +# members were ordinary class members. Constructors, destructors and assignment +# operators of the base classes will not be shown. + +INLINE_INHERITED_MEMB = NO + +# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full +# path before files name in the file list and in the header files. If set +# to NO the shortest path that makes the file name unique will be used. + +FULL_PATH_NAMES = YES + +# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag +# can be used to strip a user-defined part of the path. Stripping is +# only done if one of the specified strings matches the left-hand part of +# the path. The tag can be used to show relative paths in the file list. +# If left blank the directory from which doxygen is run is used as the +# path to strip. + +STRIP_FROM_PATH = + +# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of +# the path mentioned in the documentation of a class, which tells +# the reader which header file to include in order to use a class. +# If left blank only the name of the header file containing the class +# definition is used. Otherwise one should specify the include paths that +# are normally passed to the compiler using the -I flag. + +STRIP_FROM_INC_PATH = + +# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter +# (but less readable) file names. This can be useful is your file systems +# doesn't support long names like on DOS, Mac, or CD-ROM. + +SHORT_NAMES = NO + +# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen +# will interpret the first line (until the first dot) of a JavaDoc-style +# comment as the brief description. If set to NO, the JavaDoc +# comments will behave just like regular Qt-style comments +# (thus requiring an explicit @brief command for a brief description.) + +JAVADOC_AUTOBRIEF = NO + +# If the QT_AUTOBRIEF tag is set to YES then Doxygen will +# interpret the first line (until the first dot) of a Qt-style +# comment as the brief description. If set to NO, the comments +# will behave just like regular Qt-style comments (thus requiring +# an explicit \brief command for a brief description.) + +QT_AUTOBRIEF = NO + +# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen +# treat a multi-line C++ special comment block (i.e. a block of //! or /// +# comments) as a brief description. This used to be the default behaviour. +# The new default is to treat a multi-line C++ comment block as a detailed +# description. Set this tag to YES if you prefer the old behaviour instead. + +MULTILINE_CPP_IS_BRIEF = NO + +# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented +# member inherits the documentation from any documented member that it +# re-implements. + +INHERIT_DOCS = YES + +# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce +# a new page for each member. If set to NO, the documentation of a member will +# be part of the file/class/namespace that contains it. + +SEPARATE_MEMBER_PAGES = NO + +# The TAB_SIZE tag can be used to set the number of spaces in a tab. +# Doxygen uses this value to replace tabs by spaces in code fragments. + +TAB_SIZE = 8 + +# This tag can be used to specify a number of aliases that acts +# as commands in the documentation. An alias has the form "name=value". +# For example adding "sideeffect=\par Side Effects:\n" will allow you to +# put the command \sideeffect (or @sideeffect) in the documentation, which +# will result in a user-defined paragraph with heading "Side Effects:". +# You can put \n's in the value part of an alias to insert newlines. + +ALIASES = + +# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C +# sources only. Doxygen will then generate output that is more tailored for C. +# For instance, some of the names that are used will be different. The list +# of all members will be omitted, etc. + +OPTIMIZE_OUTPUT_FOR_C = NO + +# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java +# sources only. Doxygen will then generate output that is more tailored for +# Java. For instance, namespaces will be presented as packages, qualified +# scopes will look different, etc. + +OPTIMIZE_OUTPUT_JAVA = YES + +# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran +# sources only. Doxygen will then generate output that is more tailored for +# Fortran. + +OPTIMIZE_FOR_FORTRAN = NO + +# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL +# sources. Doxygen will then generate output that is tailored for +# VHDL. + +OPTIMIZE_OUTPUT_VHDL = NO + +# Doxygen selects the parser to use depending on the extension of the files it parses. +# With this tag you can assign which parser to use for a given extension. +# Doxygen has a built-in mapping, but you can override or extend it using this tag. +# The format is ext=language, where ext is a file extension, and language is one of +# the parsers supported by doxygen: IDL, Java, Javascript, C#, C, C++, D, PHP, +# Objective-C, Python, Fortran, VHDL, C, C++. For instance to make doxygen treat +# .inc files as Fortran files (default is PHP), and .f files as C (default is Fortran), +# use: inc=Fortran f=C. Note that for custom extensions you also need to set FILE_PATTERNS otherwise the files are not read by doxygen. + +EXTENSION_MAPPING = + +# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want +# to include (a tag file for) the STL sources as input, then you should +# set this tag to YES in order to let doxygen match functions declarations and +# definitions whose arguments contain STL classes (e.g. func(std::string); v.s. +# func(std::string) {}). This also make the inheritance and collaboration +# diagrams that involve STL classes more complete and accurate. + +BUILTIN_STL_SUPPORT = NO + +# If you use Microsoft's C++/CLI language, you should set this option to YES to +# enable parsing support. + +CPP_CLI_SUPPORT = NO + +# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only. +# Doxygen will parse them like normal C++ but will assume all classes use public +# instead of private inheritance when no explicit protection keyword is present. + +SIP_SUPPORT = NO + +# For Microsoft's IDL there are propget and propput attributes to indicate getter +# and setter methods for a property. Setting this option to YES (the default) +# will make doxygen to replace the get and set methods by a property in the +# documentation. This will only work if the methods are indeed getting or +# setting a simple type. If this is not the case, or you want to show the +# methods anyway, you should set this option to NO. + +IDL_PROPERTY_SUPPORT = YES + +# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC +# tag is set to YES, then doxygen will reuse the documentation of the first +# member in the group (if any) for the other members of the group. By default +# all members of a group must be documented explicitly. + +DISTRIBUTE_GROUP_DOC = NO + +# Set the SUBGROUPING tag to YES (the default) to allow class member groups of +# the same type (for instance a group of public functions) to be put as a +# subgroup of that type (e.g. under the Public Functions section). Set it to +# NO to prevent subgrouping. Alternatively, this can be done per class using +# the \nosubgrouping command. + +SUBGROUPING = YES + +# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum +# is documented as struct, union, or enum with the name of the typedef. So +# typedef struct TypeS {} TypeT, will appear in the documentation as a struct +# with name TypeT. When disabled the typedef will appear as a member of a file, +# namespace, or class. And the struct will be named TypeS. This can typically +# be useful for C code in case the coding convention dictates that all compound +# types are typedef'ed and only the typedef is referenced, never the tag name. + +TYPEDEF_HIDES_STRUCT = NO + +# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to +# determine which symbols to keep in memory and which to flush to disk. +# When the cache is full, less often used symbols will be written to disk. +# For small to medium size projects (<1000 input files) the default value is +# probably good enough. For larger projects a too small cache size can cause +# doxygen to be busy swapping symbols to and from disk most of the time +# causing a significant performance penality. +# If the system has enough physical memory increasing the cache will improve the +# performance by keeping more symbols in memory. Note that the value works on +# a logarithmic scale so increasing the size by one will rougly double the +# memory usage. The cache size is given by this formula: +# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0, +# corresponding to a cache size of 2^16 = 65536 symbols + +SYMBOL_CACHE_SIZE = 0 + +#--------------------------------------------------------------------------- +# Build related configuration options +#--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in +# documentation are documented, even if no documentation was available. +# Private class members and static file members will be hidden unless +# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES + +EXTRACT_ALL = YES + +# If the EXTRACT_PRIVATE tag is set to YES all private members of a class +# will be included in the documentation. + +EXTRACT_PRIVATE = YES + +# If the EXTRACT_STATIC tag is set to YES all static members of a file +# will be included in the documentation. + +EXTRACT_STATIC = YES + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) +# defined locally in source files will be included in the documentation. +# If set to NO only classes defined in header files are included. + +EXTRACT_LOCAL_CLASSES = YES + +# This flag is only useful for Objective-C code. When set to YES local +# methods, which are defined in the implementation section but not in +# the interface are included in the documentation. +# If set to NO (the default) only methods in the interface are included. + +EXTRACT_LOCAL_METHODS = YES + +# If this flag is set to YES, the members of anonymous namespaces will be +# extracted and appear in the documentation as a namespace called +# 'anonymous_namespace{file}', where file will be replaced with the base +# name of the file that contains the anonymous namespace. By default +# anonymous namespace are hidden. + +EXTRACT_ANON_NSPACES = NO + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all +# undocumented members of documented classes, files or namespaces. +# If set to NO (the default) these members will be included in the +# various overviews, but no documentation section is generated. +# This option has no effect if EXTRACT_ALL is enabled. + +HIDE_UNDOC_MEMBERS = NO + +# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. +# If set to NO (the default) these classes will be included in the various +# overviews. This option has no effect if EXTRACT_ALL is enabled. + +HIDE_UNDOC_CLASSES = NO + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all +# friend (class|struct|union) declarations. +# If set to NO (the default) these declarations will be included in the +# documentation. + +HIDE_FRIEND_COMPOUNDS = NO + +# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any +# documentation blocks found inside the body of a function. +# If set to NO (the default) these blocks will be appended to the +# function's detailed documentation block. + +HIDE_IN_BODY_DOCS = NO + +# The INTERNAL_DOCS tag determines if documentation +# that is typed after a \internal command is included. If the tag is set +# to NO (the default) then the documentation will be excluded. +# Set it to YES to include the internal documentation. + +INTERNAL_DOCS = YES + +# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate +# file names in lower-case letters. If set to YES upper-case letters are also +# allowed. This is useful if you have classes or files whose names only differ +# in case and if your file system supports case sensitive file names. Windows +# and Mac users are advised to set this option to NO. + +CASE_SENSE_NAMES = YES + +# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen +# will show members with their full class and namespace scopes in the +# documentation. If set to YES the scope will be hidden. + +HIDE_SCOPE_NAMES = NO + +# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen +# will put a list of the files that are included by a file in the documentation +# of that file. + +SHOW_INCLUDE_FILES = YES + +# If the INLINE_INFO tag is set to YES (the default) then a tag [inline] +# is inserted in the documentation for inline members. + +INLINE_INFO = YES + +# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen +# will sort the (detailed) documentation of file and class members +# alphabetically by member name. If set to NO the members will appear in +# declaration order. + +SORT_MEMBER_DOCS = YES + +# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the +# brief documentation of file, namespace and class members alphabetically +# by member name. If set to NO (the default) the members will appear in +# declaration order. + +SORT_BRIEF_DOCS = NO + +# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the (brief and detailed) documentation of class members so that constructors and destructors are listed first. If set to NO (the default) the constructors will appear in the respective orders defined by SORT_MEMBER_DOCS and SORT_BRIEF_DOCS. This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO. + +SORT_MEMBERS_CTORS_1ST = NO + +# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the +# hierarchy of group names into alphabetical order. If set to NO (the default) +# the group names will appear in their defined order. + +SORT_GROUP_NAMES = NO + +# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be +# sorted by fully-qualified names, including namespaces. If set to +# NO (the default), the class list will be sorted only by class name, +# not including the namespace part. +# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. +# Note: This option applies only to the class list, not to the +# alphabetical list. + +SORT_BY_SCOPE_NAME = NO + +# The GENERATE_TODOLIST tag can be used to enable (YES) or +# disable (NO) the todo list. This list is created by putting \todo +# commands in the documentation. + +GENERATE_TODOLIST = YES + +# The GENERATE_TESTLIST tag can be used to enable (YES) or +# disable (NO) the test list. This list is created by putting \test +# commands in the documentation. + +GENERATE_TESTLIST = YES + +# The GENERATE_BUGLIST tag can be used to enable (YES) or +# disable (NO) the bug list. This list is created by putting \bug +# commands in the documentation. + +GENERATE_BUGLIST = YES + +# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or +# disable (NO) the deprecated list. This list is created by putting +# \deprecated commands in the documentation. + +GENERATE_DEPRECATEDLIST= YES + +# The ENABLED_SECTIONS tag can be used to enable conditional +# documentation sections, marked by \if sectionname ... \endif. + +ENABLED_SECTIONS = + +# The MAX_INITIALIZER_LINES tag determines the maximum number of lines +# the initial value of a variable or define consists of for it to appear in +# the documentation. If the initializer consists of more lines than specified +# here it will be hidden. Use a value of 0 to hide initializers completely. +# The appearance of the initializer of individual variables and defines in the +# documentation can be controlled using \showinitializer or \hideinitializer +# command in the documentation regardless of this setting. + +MAX_INITIALIZER_LINES = 30 + +# Set the SHOW_USED_FILES tag to NO to disable the list of files generated +# at the bottom of the documentation of classes and structs. If set to YES the +# list will mention the files that were used to generate the documentation. + +SHOW_USED_FILES = YES + +# If the sources in your project are distributed over multiple directories +# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy +# in the documentation. The default is NO. + +SHOW_DIRECTORIES = YES + +# Set the SHOW_FILES tag to NO to disable the generation of the Files page. +# This will remove the Files entry from the Quick Index and from the +# Folder Tree View (if specified). The default is YES. + +SHOW_FILES = YES + +# Set the SHOW_NAMESPACES tag to NO to disable the generation of the +# Namespaces page. +# This will remove the Namespaces entry from the Quick Index +# and from the Folder Tree View (if specified). The default is YES. + +SHOW_NAMESPACES = YES + +# The FILE_VERSION_FILTER tag can be used to specify a program or script that +# doxygen should invoke to get the current version for each file (typically from +# the version control system). Doxygen will invoke the program by executing (via +# popen()) the command , where is the value of +# the FILE_VERSION_FILTER tag, and is the name of an input file +# provided by doxygen. Whatever the program writes to standard output +# is used as the file version. See the manual for examples. + +FILE_VERSION_FILTER = + +# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed by +# doxygen. The layout file controls the global structure of the generated output files +# in an output format independent way. The create the layout file that represents +# doxygen's defaults, run doxygen with the -l option. You can optionally specify a +# file name after the option, if omitted DoxygenLayout.xml will be used as the name +# of the layout file. + +LAYOUT_FILE = + +#--------------------------------------------------------------------------- +# configuration options related to warning and progress messages +#--------------------------------------------------------------------------- + +# The QUIET tag can be used to turn on/off the messages that are generated +# by doxygen. Possible values are YES and NO. If left blank NO is used. + +QUIET = NO + +# The WARNINGS tag can be used to turn on/off the warning messages that are +# generated by doxygen. Possible values are YES and NO. If left blank +# NO is used. + +WARNINGS = YES + +# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings +# for undocumented members. If EXTRACT_ALL is set to YES then this flag will +# automatically be disabled. + +WARN_IF_UNDOCUMENTED = YES + +# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for +# potential errors in the documentation, such as not documenting some +# parameters in a documented function, or documenting parameters that +# don't exist or using markup commands wrongly. + +WARN_IF_DOC_ERROR = YES + +# This WARN_NO_PARAMDOC option can be abled to get warnings for +# functions that are documented, but have no documentation for their parameters +# or return value. If set to NO (the default) doxygen will only warn about +# wrong or incomplete parameter documentation, but not about the absence of +# documentation. + +WARN_NO_PARAMDOC = NO + +# The WARN_FORMAT tag determines the format of the warning messages that +# doxygen can produce. The string should contain the $file, $line, and $text +# tags, which will be replaced by the file and line number from which the +# warning originated and the warning text. Optionally the format may contain +# $version, which will be replaced by the version of the file (if it could +# be obtained via FILE_VERSION_FILTER) + +WARN_FORMAT = "$file:$line: $text" + +# The WARN_LOGFILE tag can be used to specify a file to which warning +# and error messages should be written. If left blank the output is written +# to stderr. + +WARN_LOGFILE = doxygen.log + +#--------------------------------------------------------------------------- +# configuration options related to the input files +#--------------------------------------------------------------------------- + +# The INPUT tag can be used to specify the files and/or directories that contain +# documented source files. You may enter file names like "myfile.cpp" or +# directories like "/usr/src/myproject". Separate the files or directories +# with spaces. + +INPUT = bathy_smoother + +# This tag can be used to specify the character encoding of the source files +# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is +# also the default input encoding. Doxygen uses libiconv (or the iconv built +# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for +# the list of possible encodings. + +INPUT_ENCODING = UTF-8 + +# If the value of the INPUT tag contains directories, you can use the +# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank the following patterns are tested: +# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx +# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90 + +FILE_PATTERNS = + +# The RECURSIVE tag can be used to turn specify whether or not subdirectories +# should be searched for input files as well. Possible values are YES and NO. +# If left blank NO is used. + +RECURSIVE = YES + +# The EXCLUDE tag can be used to specify files and/or directories that should +# excluded from the INPUT source files. This way you can easily exclude a +# subdirectory from a directory tree whose root is specified with the INPUT tag. + +EXCLUDE = + +# The EXCLUDE_SYMLINKS tag can be used select whether or not files or +# directories that are symbolic links (a Unix filesystem feature) are excluded +# from the input. + +EXCLUDE_SYMLINKS = NO + +# If the value of the INPUT tag contains directories, you can use the +# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude +# certain files from those directories. Note that the wildcards are matched +# against the file with absolute path, so to exclude all test directories +# for example use the pattern */test/* + +EXCLUDE_PATTERNS = + +# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names +# (namespaces, classes, functions, etc.) that should be excluded from the +# output. The symbol name can be a fully qualified name, a word, or if the +# wildcard * is used, a substring. Examples: ANamespace, AClass, +# AClass::ANamespace, ANamespace::*Test + +EXCLUDE_SYMBOLS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or +# directories that contain example code fragments that are included (see +# the \include command). + +EXAMPLE_PATH = + +# If the value of the EXAMPLE_PATH tag contains directories, you can use the +# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank all files are included. + +EXAMPLE_PATTERNS = + +# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be +# searched for input files to be used with the \include or \dontinclude +# commands irrespective of the value of the RECURSIVE tag. +# Possible values are YES and NO. If left blank NO is used. + +EXAMPLE_RECURSIVE = NO + +# The IMAGE_PATH tag can be used to specify one or more files or +# directories that contain image that are included in the documentation (see +# the \image command). + +IMAGE_PATH = + +# The INPUT_FILTER tag can be used to specify a program that doxygen should +# invoke to filter for each input file. Doxygen will invoke the filter program +# by executing (via popen()) the command , where +# is the value of the INPUT_FILTER tag, and is the name of an +# input file. Doxygen will then use the output that the filter program writes +# to standard output. +# If FILTER_PATTERNS is specified, this tag will be +# ignored. + +INPUT_FILTER = + +# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern +# basis. +# Doxygen will compare the file name with each pattern and apply the +# filter if there is a match. +# The filters are a list of the form: +# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further +# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER +# is applied to all files. + +FILTER_PATTERNS = + +# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using +# INPUT_FILTER) will be used to filter the input files when producing source +# files to browse (i.e. when SOURCE_BROWSER is set to YES). + +FILTER_SOURCE_FILES = NO + +#--------------------------------------------------------------------------- +# configuration options related to source browsing +#--------------------------------------------------------------------------- + +# If the SOURCE_BROWSER tag is set to YES then a list of source files will +# be generated. Documented entities will be cross-referenced with these sources. +# Note: To get rid of all source code in the generated output, make sure also +# VERBATIM_HEADERS is set to NO. + +SOURCE_BROWSER = YES + +# Setting the INLINE_SOURCES tag to YES will include the body +# of functions and classes directly in the documentation. + +INLINE_SOURCES = YES + +# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct +# doxygen to hide any special comment blocks from generated source code +# fragments. Normal C and C++ comments will always remain visible. + +STRIP_CODE_COMMENTS = NO + +# If the REFERENCED_BY_RELATION tag is set to YES +# then for each documented function all documented +# functions referencing it will be listed. + +REFERENCED_BY_RELATION = YES + +# If the REFERENCES_RELATION tag is set to YES +# then for each documented function all documented entities +# called/used by that function will be listed. + +REFERENCES_RELATION = YES + +# If the REFERENCES_LINK_SOURCE tag is set to YES (the default) +# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from +# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will +# link to the source code. +# Otherwise they will link to the documentation. + +REFERENCES_LINK_SOURCE = YES + +# If the USE_HTAGS tag is set to YES then the references to source code +# will point to the HTML generated by the htags(1) tool instead of doxygen +# built-in source browser. The htags tool is part of GNU's global source +# tagging system (see http://www.gnu.org/software/global/global.html). You +# will need version 4.8.6 or higher. + +USE_HTAGS = NO + +# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen +# will generate a verbatim copy of the header file for each class for +# which an include is specified. Set to NO to disable this. + +VERBATIM_HEADERS = YES + +#--------------------------------------------------------------------------- +# configuration options related to the alphabetical class index +#--------------------------------------------------------------------------- + +# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index +# of all compounds will be generated. Enable this if the project +# contains a lot of classes, structs, unions or interfaces. + +ALPHABETICAL_INDEX = YES + +# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then +# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns +# in which this list will be split (can be a number in the range [1..20]) + +COLS_IN_ALPHA_INDEX = 5 + +# In case all classes in a project start with a common prefix, all +# classes will be put under the same header in the alphabetical index. +# The IGNORE_PREFIX tag can be used to specify one or more prefixes that +# should be ignored while generating the index headers. + +IGNORE_PREFIX = + +#--------------------------------------------------------------------------- +# configuration options related to the HTML output +#--------------------------------------------------------------------------- + +# If the GENERATE_HTML tag is set to YES (the default) Doxygen will +# generate HTML output. + +GENERATE_HTML = YES + +# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `html' will be used as the default path. + +HTML_OUTPUT = html + +# The HTML_FILE_EXTENSION tag can be used to specify the file extension for +# each generated HTML page (for example: .htm,.php,.asp). If it is left blank +# doxygen will generate files with .html extension. + +HTML_FILE_EXTENSION = .html + +# The HTML_HEADER tag can be used to specify a personal HTML header for +# each generated HTML page. If it is left blank doxygen will generate a +# standard header. + +HTML_HEADER = + +# The HTML_FOOTER tag can be used to specify a personal HTML footer for +# each generated HTML page. If it is left blank doxygen will generate a +# standard footer. + +HTML_FOOTER = + +# If the HTML_TIMESTAMP tag is set to YES then the generated HTML +# documentation will contain the timesstamp. + +HTML_TIMESTAMP = NO + +# The HTML_STYLESHEET tag can be used to specify a user-defined cascading +# style sheet that is used by each HTML page. It can be used to +# fine-tune the look of the HTML output. If the tag is left blank doxygen +# will generate a default style sheet. Note that doxygen will try to copy +# the style sheet file to the HTML output directory, so don't put your own +# stylesheet in the HTML output directory as well, or it will be erased! + +HTML_STYLESHEET = + +# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, +# files or namespaces will be aligned in HTML using tables. If set to +# NO a bullet list will be used. + +HTML_ALIGN_MEMBERS = YES + +# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML +# documentation will contain sections that can be hidden and shown after the +# page has loaded. For this to work a browser that supports +# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox +# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari). + +HTML_DYNAMIC_SECTIONS = NO + +# If the GENERATE_DOCSET tag is set to YES, additional index files +# will be generated that can be used as input for Apple's Xcode 3 +# integrated development environment, introduced with OSX 10.5 (Leopard). +# To create a documentation set, doxygen will generate a Makefile in the +# HTML output directory. Running make will produce the docset in that +# directory and running "make install" will install the docset in +# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find +# it at startup. +# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html for more information. + +GENERATE_DOCSET = NO + +# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the +# feed. A documentation feed provides an umbrella under which multiple +# documentation sets from a single provider (such as a company or product suite) +# can be grouped. + +DOCSET_FEEDNAME = "Doxygen generated docs" + +# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that +# should uniquely identify the documentation set bundle. This should be a +# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen +# will append .docset to the name. + +DOCSET_BUNDLE_ID = org.doxygen.Project + +# If the GENERATE_HTMLHELP tag is set to YES, additional index files +# will be generated that can be used as input for tools like the +# Microsoft HTML help workshop to generate a compiled HTML help file (.chm) +# of the generated HTML documentation. + +GENERATE_HTMLHELP = NO + +# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can +# be used to specify the file name of the resulting .chm file. You +# can add a path in front of the file if the result should not be +# written to the html output directory. + +CHM_FILE = + +# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can +# be used to specify the location (absolute path including file name) of +# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run +# the HTML help compiler on the generated index.hhp. + +HHC_LOCATION = + +# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag +# controls if a separate .chi index file is generated (YES) or that +# it should be included in the master .chm file (NO). + +GENERATE_CHI = NO + +# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING +# is used to encode HtmlHelp index (hhk), content (hhc) and project file +# content. + +CHM_INDEX_ENCODING = + +# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag +# controls whether a binary table of contents is generated (YES) or a +# normal table of contents (NO) in the .chm file. + +BINARY_TOC = NO + +# The TOC_EXPAND flag can be set to YES to add extra items for group members +# to the contents of the HTML help documentation and to the tree view. + +TOC_EXPAND = NO + +# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and QHP_VIRTUAL_FOLDER +# are set, an additional index file will be generated that can be used as input for +# Qt's qhelpgenerator to generate a Qt Compressed Help (.qch) of the generated +# HTML documentation. + +GENERATE_QHP = NO + +# If the QHG_LOCATION tag is specified, the QCH_FILE tag can +# be used to specify the file name of the resulting .qch file. +# The path specified is relative to the HTML output folder. + +QCH_FILE = + +# The QHP_NAMESPACE tag specifies the namespace to use when generating +# Qt Help Project output. For more information please see +# http://doc.trolltech.com/qthelpproject.html#namespace + +QHP_NAMESPACE = + +# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating +# Qt Help Project output. For more information please see +# http://doc.trolltech.com/qthelpproject.html#virtual-folders + +QHP_VIRTUAL_FOLDER = doc + +# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to add. +# For more information please see +# http://doc.trolltech.com/qthelpproject.html#custom-filters + +QHP_CUST_FILTER_NAME = + +# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the custom filter to add.For more information please see +# Qt Help Project / Custom Filters. + +QHP_CUST_FILTER_ATTRS = + +# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this project's +# filter section matches. +# Qt Help Project / Filter Attributes. + +QHP_SECT_FILTER_ATTRS = + +# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can +# be used to specify the location of Qt's qhelpgenerator. +# If non-empty doxygen will try to run qhelpgenerator on the generated +# .qhp file. + +QHG_LOCATION = + +# The DISABLE_INDEX tag can be used to turn on/off the condensed index at +# top of each HTML page. The value NO (the default) enables the index and +# the value YES disables it. + +DISABLE_INDEX = NO + +# This tag can be used to set the number of enum values (range [1..20]) +# that doxygen will group on one line in the generated HTML documentation. + +ENUM_VALUES_PER_LINE = 4 + +# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index +# structure should be generated to display hierarchical information. +# If the tag value is set to YES, a side panel will be generated +# containing a tree-like index structure (just like the one that +# is generated for HTML Help). For this to work a browser that supports +# JavaScript, DHTML, CSS and frames is required (i.e. any modern browser). +# Windows users are probably better off using the HTML help feature. + +GENERATE_TREEVIEW = YES + +# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories, +# and Class Hierarchy pages using a tree view instead of an ordered list. + +USE_INLINE_TREES = NO + +# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be +# used to set the initial width (in pixels) of the frame in which the tree +# is shown. + +TREEVIEW_WIDTH = 250 + +# Use this tag to change the font size of Latex formulas included +# as images in the HTML documentation. The default is 10. Note that +# when you change the font size after a successful doxygen run you need +# to manually remove any form_*.png images from the HTML output directory +# to force them to be regenerated. + +FORMULA_FONTSIZE = 10 + +# When the SEARCHENGINE tag is enable doxygen will generate a search box for the HTML output. The underlying search engine uses javascript +# and DHTML and should work on any modern browser. Note that when using HTML help (GENERATE_HTMLHELP) or Qt help (GENERATE_QHP) +# there is already a search function so this one should typically +# be disabled. + +SEARCHENGINE = YES + +#--------------------------------------------------------------------------- +# configuration options related to the LaTeX output +#--------------------------------------------------------------------------- + +# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will +# generate Latex output. + +GENERATE_LATEX = NO + +# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `latex' will be used as the default path. + +LATEX_OUTPUT = latex + +# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be +# invoked. If left blank `latex' will be used as the default command name. + +LATEX_CMD_NAME = latex + +# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to +# generate index for LaTeX. If left blank `makeindex' will be used as the +# default command name. + +MAKEINDEX_CMD_NAME = makeindex + +# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact +# LaTeX documents. This may be useful for small projects and may help to +# save some trees in general. + +COMPACT_LATEX = NO + +# The PAPER_TYPE tag can be used to set the paper type that is used +# by the printer. Possible values are: a4, a4wide, letter, legal and +# executive. If left blank a4wide will be used. + +PAPER_TYPE = letter + +# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX +# packages that should be included in the LaTeX output. + +EXTRA_PACKAGES = + +# The LATEX_HEADER tag can be used to specify a personal LaTeX header for +# the generated latex document. The header should contain everything until +# the first chapter. If it is left blank doxygen will generate a +# standard header. Notice: only use this tag if you know what you are doing! + +LATEX_HEADER = + +# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated +# is prepared for conversion to pdf (using ps2pdf). The pdf file will +# contain links (just like the HTML output) instead of page references +# This makes the output suitable for online browsing using a pdf viewer. + +PDF_HYPERLINKS = YES + +# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of +# plain latex in the generated Makefile. Set this option to YES to get a +# higher quality PDF documentation. + +USE_PDFLATEX = YES + +# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. +# command to the generated LaTeX files. This will instruct LaTeX to keep +# running if errors occur, instead of asking the user for help. +# This option is also used when generating formulas in HTML. + +LATEX_BATCHMODE = NO + +# If LATEX_HIDE_INDICES is set to YES then doxygen will not +# include the index chapters (such as File Index, Compound Index, etc.) +# in the output. + +LATEX_HIDE_INDICES = NO + +# If LATEX_SOURCE_CODE is set to YES then doxygen will include source code with syntax highlighting in the LaTeX output. Note that which sources are shown also depends on other settings such as SOURCE_BROWSER. + +LATEX_SOURCE_CODE = NO + +#--------------------------------------------------------------------------- +# configuration options related to the RTF output +#--------------------------------------------------------------------------- + +# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output +# The RTF output is optimized for Word 97 and may not look very pretty with +# other RTF readers or editors. + +GENERATE_RTF = NO + +# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `rtf' will be used as the default path. + +RTF_OUTPUT = rtf + +# If the COMPACT_RTF tag is set to YES Doxygen generates more compact +# RTF documents. This may be useful for small projects and may help to +# save some trees in general. + +COMPACT_RTF = NO + +# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated +# will contain hyperlink fields. The RTF file will +# contain links (just like the HTML output) instead of page references. +# This makes the output suitable for online browsing using WORD or other +# programs which support those fields. +# Note: wordpad (write) and others do not support links. + +RTF_HYPERLINKS = NO + +# Load stylesheet definitions from file. Syntax is similar to doxygen's +# config file, i.e. a series of assignments. You only have to provide +# replacements, missing definitions are set to their default value. + +RTF_STYLESHEET_FILE = + +# Set optional variables used in the generation of an rtf document. +# Syntax is similar to doxygen's config file. + +RTF_EXTENSIONS_FILE = + +#--------------------------------------------------------------------------- +# configuration options related to the man page output +#--------------------------------------------------------------------------- + +# If the GENERATE_MAN tag is set to YES (the default) Doxygen will +# generate man pages + +GENERATE_MAN = NO + +# The MAN_OUTPUT tag is used to specify where the man pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `man' will be used as the default path. + +MAN_OUTPUT = man + +# The MAN_EXTENSION tag determines the extension that is added to +# the generated man pages (default is the subroutine's section .3) + +MAN_EXTENSION = .3 + +# If the MAN_LINKS tag is set to YES and Doxygen generates man output, +# then it will generate one additional man file for each entity +# documented in the real man page(s). These additional files +# only source the real man page, but without them the man command +# would be unable to find the correct page. The default is NO. + +MAN_LINKS = NO + +#--------------------------------------------------------------------------- +# configuration options related to the XML output +#--------------------------------------------------------------------------- + +# If the GENERATE_XML tag is set to YES Doxygen will +# generate an XML file that captures the structure of +# the code including all documentation. + +GENERATE_XML = NO + +# The XML_OUTPUT tag is used to specify where the XML pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `xml' will be used as the default path. + +XML_OUTPUT = xml + +# The XML_SCHEMA tag can be used to specify an XML schema, +# which can be used by a validating XML parser to check the +# syntax of the XML files. + +XML_SCHEMA = + +# The XML_DTD tag can be used to specify an XML DTD, +# which can be used by a validating XML parser to check the +# syntax of the XML files. + +XML_DTD = + +# If the XML_PROGRAMLISTING tag is set to YES Doxygen will +# dump the program listings (including syntax highlighting +# and cross-referencing information) to the XML output. Note that +# enabling this will significantly increase the size of the XML output. + +XML_PROGRAMLISTING = YES + +#--------------------------------------------------------------------------- +# configuration options for the AutoGen Definitions output +#--------------------------------------------------------------------------- + +# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will +# generate an AutoGen Definitions (see autogen.sf.net) file +# that captures the structure of the code including all +# documentation. Note that this feature is still experimental +# and incomplete at the moment. + +GENERATE_AUTOGEN_DEF = NO + +#--------------------------------------------------------------------------- +# configuration options related to the Perl module output +#--------------------------------------------------------------------------- + +# If the GENERATE_PERLMOD tag is set to YES Doxygen will +# generate a Perl module file that captures the structure of +# the code including all documentation. Note that this +# feature is still experimental and incomplete at the +# moment. + +GENERATE_PERLMOD = NO + +# If the PERLMOD_LATEX tag is set to YES Doxygen will generate +# the necessary Makefile rules, Perl scripts and LaTeX code to be able +# to generate PDF and DVI output from the Perl module output. + +PERLMOD_LATEX = NO + +# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be +# nicely formatted so it can be parsed by a human reader. +# This is useful +# if you want to understand what is going on. +# On the other hand, if this +# tag is set to NO the size of the Perl module output will be much smaller +# and Perl will parse it just the same. + +PERLMOD_PRETTY = YES + +# The names of the make variables in the generated doxyrules.make file +# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. +# This is useful so different doxyrules.make files included by the same +# Makefile don't overwrite each other's variables. + +PERLMOD_MAKEVAR_PREFIX = + +#--------------------------------------------------------------------------- +# Configuration options related to the preprocessor +#--------------------------------------------------------------------------- + +# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will +# evaluate all C-preprocessor directives found in the sources and include +# files. + +ENABLE_PREPROCESSING = YES + +# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro +# names in the source code. If set to NO (the default) only conditional +# compilation will be performed. Macro expansion can be done in a controlled +# way by setting EXPAND_ONLY_PREDEF to YES. + +MACRO_EXPANSION = NO + +# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES +# then the macro expansion is limited to the macros specified with the +# PREDEFINED and EXPAND_AS_DEFINED tags. + +EXPAND_ONLY_PREDEF = NO + +# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files +# in the INCLUDE_PATH (see below) will be search if a #include is found. + +SEARCH_INCLUDES = YES + +# The INCLUDE_PATH tag can be used to specify one or more directories that +# contain include files that are not input files but should be processed by +# the preprocessor. + +INCLUDE_PATH = + +# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard +# patterns (like *.h and *.hpp) to filter out the header-files in the +# directories. If left blank, the patterns specified with FILE_PATTERNS will +# be used. + +INCLUDE_FILE_PATTERNS = + +# The PREDEFINED tag can be used to specify one or more macro names that +# are defined before the preprocessor is started (similar to the -D option of +# gcc). The argument of the tag is a list of macros of the form: name +# or name=definition (no spaces). If the definition and the = are +# omitted =1 is assumed. To prevent a macro definition from being +# undefined via #undef or recursively expanded use the := operator +# instead of the = operator. + +PREDEFINED = + +# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then +# this tag can be used to specify a list of macro names that should be expanded. +# The macro definition that is found in the sources will be used. +# Use the PREDEFINED tag if you want to use a different macro definition. + +EXPAND_AS_DEFINED = + +# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then +# doxygen's preprocessor will remove all function-like macros that are alone +# on a line, have an all uppercase name, and do not end with a semicolon. Such +# function macros are typically used for boiler-plate code, and will confuse +# the parser if not removed. + +SKIP_FUNCTION_MACROS = YES + +#--------------------------------------------------------------------------- +# Configuration::additions related to external references +#--------------------------------------------------------------------------- + +# The TAGFILES option can be used to specify one or more tagfiles. +# Optionally an initial location of the external documentation +# can be added for each tagfile. The format of a tag file without +# this location is as follows: +# +# TAGFILES = file1 file2 ... +# Adding location for the tag files is done as follows: +# +# TAGFILES = file1=loc1 "file2 = loc2" ... +# where "loc1" and "loc2" can be relative or absolute paths or +# URLs. If a location is present for each tag, the installdox tool +# does not have to be run to correct the links. +# Note that each tag file must have a unique name +# (where the name does NOT include the path) +# If a tag file is not located in the directory in which doxygen +# is run, you must also specify the path to the tagfile here. + +TAGFILES = + +# When a file name is specified after GENERATE_TAGFILE, doxygen will create +# a tag file that is based on the input files it reads. + +GENERATE_TAGFILE = + +# If the ALLEXTERNALS tag is set to YES all external classes will be listed +# in the class index. If set to NO only the inherited external classes +# will be listed. + +ALLEXTERNALS = NO + +# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed +# in the modules index. If set to NO, only the current project's groups will +# be listed. + +EXTERNAL_GROUPS = YES + +# The PERL_PATH should be the absolute path and name of the perl script +# interpreter (i.e. the result of `which perl'). + +PERL_PATH = /usr/bin/perl + +#--------------------------------------------------------------------------- +# Configuration options related to the dot tool +#--------------------------------------------------------------------------- + +# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will +# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base +# or super classes. Setting the tag to NO turns the diagrams off. Note that +# this option is superseded by the HAVE_DOT option below. This is only a +# fallback. It is recommended to install and use dot, since it yields more +# powerful graphs. + +CLASS_DIAGRAMS = YES + +# You can define message sequence charts within doxygen comments using the \msc +# command. Doxygen will then run the mscgen tool (see +# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the +# documentation. The MSCGEN_PATH tag allows you to specify the directory where +# the mscgen tool resides. If left empty the tool is assumed to be found in the +# default search path. + +MSCGEN_PATH = + +# If set to YES, the inheritance and collaboration graphs will hide +# inheritance and usage relations if the target is undocumented +# or is not a class. + +HIDE_UNDOC_RELATIONS = YES + +# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is +# available from the path. This tool is part of Graphviz, a graph visualization +# toolkit from AT&T and Lucent Bell Labs. The other options in this section +# have no effect if this option is set to NO (the default) + +HAVE_DOT = YES + +# By default doxygen will write a font called FreeSans.ttf to the output +# directory and reference it in all dot files that doxygen generates. This +# font does not include all possible unicode characters however, so when you need +# these (or just want a differently looking font) you can specify the font name +# using DOT_FONTNAME. You need need to make sure dot is able to find the font, +# which can be done by putting it in a standard location or by setting the +# DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory +# containing the font. + +DOT_FONTNAME = FreeSans + +# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs. +# The default size is 10pt. + +DOT_FONTSIZE = 10 + +# By default doxygen will tell dot to use the output directory to look for the +# FreeSans.ttf font (which doxygen will put there itself). If you specify a +# different font using DOT_FONTNAME you can set the path where dot +# can find it using this tag. + +DOT_FONTPATH = + +# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for each documented class showing the direct and +# indirect inheritance relations. 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Note that enabling this option will significantly increase +# the time of a run. So in most cases it will be better to enable call graphs +# for selected functions only using the \callgraph command. + +CALL_GRAPH = NO + +# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then +# doxygen will generate a caller dependency graph for every global function +# or class method. Note that enabling this option will significantly increase +# the time of a run. So in most cases it will be better to enable caller +# graphs for selected functions only using the \callergraph command. + +CALLER_GRAPH = NO + +# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen +# will graphical hierarchy of all classes instead of a textual one. + +GRAPHICAL_HIERARCHY = YES + +# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES +# then doxygen will show the dependencies a directory has on other directories +# in a graphical way. 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Note that doxygen if the +# number of direct children of the root node in a graph is already larger than +# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note +# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH. + +DOT_GRAPH_MAX_NODES = 50 + +# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the +# graphs generated by dot. A depth value of 3 means that only nodes reachable +# from the root by following a path via at most 3 edges will be shown. Nodes +# that lay further from the root node will be omitted. Note that setting this +# option to 1 or 2 may greatly reduce the computation time needed for large +# code bases. Also note that the size of a graph can be further restricted by +# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction. + +MAX_DOT_GRAPH_DEPTH = 0 + +# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent +# background. This is disabled by default, because dot on Windows does not +# seem to support this out of the box. Warning: Depending on the platform used, +# enabling this option may lead to badly anti-aliased labels on the edges of +# a graph (i.e. they become hard to read). + +DOT_TRANSPARENT = NO + +# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output +# files in one run (i.e. multiple -o and -T options on the command line). This +# makes dot run faster, but since only newer versions of dot (>1.8.10) +# support this, this feature is disabled by default. + +DOT_MULTI_TARGETS = NO + +# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will +# generate a legend page explaining the meaning of the various boxes and +# arrows in the dot generated graphs. + +GENERATE_LEGEND = YES + +# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will +# remove the intermediate dot files that are used to generate +# the various graphs. + +DOT_CLEANUP = YES diff --git a/bathy_smoother/bathy_smoother/LP_bathy_smoothing.py b/bathy_smoother/bathy_smoother/LP_bathy_smoothing.py index e974233..d18c745 100644 --- a/bathy_smoother/bathy_smoother/LP_bathy_smoothing.py +++ b/bathy_smoother/bathy_smoother/LP_bathy_smoothing.py @@ -62,7 +62,7 @@ def LP_smoothing_rx0(MSK, Hobs, rx0max, SignConst, AmpConst): ValueFct, ValueVar, testfeasibility = LP_tools.SolveLinearProgram(iList, jList, sList, Constant, ObjectiveFct) if (testfeasibility == 0): NewBathy = NaN * np.ones((eta_rho,xi_rho)) - raise ValueError, 'Feasibility test failed. testfeasibility = 0.' + raise ValueError('Feasibility test failed. testfeasibility = 0.') correctionBathy = np.zeros((eta_rho,xi_rho)) nbVert = 0 @@ -75,7 +75,7 @@ def LP_smoothing_rx0(MSK, Hobs, rx0max, SignConst, AmpConst): NewBathy = Hobs + correctionBathy RMat = bathy_tools.RoughnessMatrix(NewBathy, MSK) MaxRx0 = RMat.max() - print 'rx0max = ', rx0max, ' MaxRx0 = ', MaxRx0 + print('rx0max = ', rx0max, ' MaxRx0 = ', MaxRx0) return NewBathy @@ -124,7 +124,7 @@ def LP_smoothing_rx0_heuristic(MSK, Hobs, rx0max, SignConst, AmpConst): Kbad = np.where(MSKbad == 1) nbKbad = np.size(Kbad,1) ListIdx = np.zeros((eta_rho,xi_rho), dtype=np.int) - ListIdx[Kbad] = range(nbKbad) + ListIdx[Kbad] = list(range(nbKbad)) ListEdges = [] nbEdge = 0 @@ -146,11 +146,11 @@ def LP_smoothing_rx0_heuristic(MSK, Hobs, rx0max, SignConst, AmpConst): NewBathy = Hobs.copy() for iColor in range(1,nbColor+1): - print '---------------------------------------------------------------' + print('---------------------------------------------------------------') MSKcolor = np.zeros((eta_rho, xi_rho)) K = np.where(ListVertexStatus == iColor) nbK = np.size(K,1) - print 'iColor = ', iColor, ' nbK = ', nbK + print('iColor = ', iColor, ' nbK = ', nbK) for iVertex in range(nbKbad): if (ListVertexStatus[iVertex,0] == iColor): iEta, iXi = Kbad[0][iVertex], Kbad[1][iVertex] @@ -166,10 +166,10 @@ def LP_smoothing_rx0_heuristic(MSK, Hobs, rx0max, SignConst, AmpConst): TheNewBathy = LP_smoothing_rx0(MSKcolor, MSKHobs, rx0max, SignConst, AmpConst) NewBathy[K] = TheNewBathy[K].copy() - print 'Final obtained bathymetry' + print('Final obtained bathymetry') RMat = bathy_tools.RoughnessMatrix(NewBathy, MSK) MaxRx0 = RMat.max() - print 'rx0max = ', rx0max, ' MaxRx0 = ', MaxRx0 + print('rx0max = ', rx0max, ' MaxRx0 = ', MaxRx0) return NewBathy diff --git a/bathy_smoother/bathy_smoother/LP_bathy_tools.py b/bathy_smoother/bathy_smoother/LP_bathy_tools.py index 15b69a2..1fbdbff 100644 --- a/bathy_smoother/bathy_smoother/LP_bathy_tools.py +++ b/bathy_smoother/bathy_smoother/LP_bathy_tools.py @@ -12,7 +12,7 @@ def GetIJS_rx0(MSK, DEP, r): eta_rho, xi_rho = DEP.shape - print 'eta_rho = ', eta_rho, ' xi_rho = ', xi_rho + print('eta_rho = ', eta_rho, ' xi_rho = ', xi_rho) nbVert = 0 ListCoord = np.zeros((eta_rho, xi_rho)) @@ -23,8 +23,8 @@ def GetIJS_rx0(MSK, DEP, r): ListCoord[iEta,iXi] = nbVert TotalNbVert = nbVert - print 'ListCoord built' - print 'Computing inequalities for r = ', r + print('ListCoord built') + print('Computing inequalities for r = ', r) TotalNbConstant = 0 TotalNbEntry = 0 @@ -80,7 +80,7 @@ def GetIJS_rx0(MSK, DEP, r): sList[nbEntry,0] = 1-r nbEntry = nbEntry + 1 - print 'Inequalities for dh(iEta,iXi) and dh(iEta+1,iXi)' + print('Inequalities for dh(iEta,iXi) and dh(iEta+1,iXi)') for iEta in range(eta_rho): for iXi in range(xi_rho-1): @@ -112,7 +112,7 @@ def GetIJS_rx0(MSK, DEP, r): sList[nbEntry,0] = 1-r nbEntry = nbEntry + 1 - print 'Inequalities for dh(iEta,iXi) and dh(iEta,iXi+1)' + print('Inequalities for dh(iEta,iXi) and dh(iEta,iXi+1)') for iEta in range(eta_rho): for iXi in range(xi_rho): @@ -141,16 +141,16 @@ def GetIJS_rx0(MSK, DEP, r): sList[nbEntry,0] = -1 nbEntry = nbEntry + 1 - print 'Inequalities dh <= ad and -dh <= ad' + print('Inequalities dh <= ad and -dh <= ad') - print 'rx0: nbEntry = ', nbEntry, ' nbConst = ', nbConst - print ' ' + print('rx0: nbEntry = ', nbEntry, ' nbConst = ', nbConst) + print(' ') if (abs(nbEntry - TotalNbEntry) > 0): - raise ValueError, 'We have a coding inconsistency for nbEntry. Please correct' + raise ValueError('We have a coding inconsistency for nbEntry. Please correct') if (abs(nbConst - TotalNbConstant) > 0): - raise ValueError, 'We have a coding inconsistency for nbConst. Please correct' + raise ValueError('We have a coding inconsistency for nbConst. Please correct') return iList, jList, sList, Constant @@ -161,7 +161,7 @@ def GetIJS_maxamp(MSK, DEP, AmpConst): eta_rho, xi_rho = DEP.shape - print 'eta_rho = ', eta_rho, ' xi_rho = ', xi_rho + print('eta_rho = ', eta_rho, ' xi_rho = ', xi_rho) nbVert = 0 ListCoord = np.zeros((eta_rho, xi_rho)) @@ -178,8 +178,8 @@ def GetIJS_maxamp(MSK, DEP, AmpConst): if (MSK[iEta,iXi] == 1): alpha = AmpConst[iEta,iXi] if (alpha < 9999): - TotalNbConstant = TotalNbConstant + 2 - TotalNbEntry = TotalNbEntry + 2 + TotalNbConstant = TotalNbConstant + 2 + TotalNbEntry = TotalNbEntry + 2 nbConst = 0 nbEntry = 0 @@ -195,29 +195,29 @@ def GetIJS_maxamp(MSK, DEP, AmpConst): alpha = AmpConst[iEta,iXi] if (alpha < 9999): - Constant[nbConst,0] = alpha * DEP[iEta,iXi] - iList[nbEntry,0] = nbConst + 1 - jList[nbEntry,0] = idx - sList[nbEntry,0] = -1 - nbConst = nbConst + 1 + Constant[nbConst,0] = alpha * DEP[iEta,iXi] + iList[nbEntry,0] = nbConst + 1 + jList[nbEntry,0] = idx + sList[nbEntry,0] = -1 + nbConst = nbConst + 1 nbEntry = nbEntry + 1 - Constant[nbConst,0] = alpha * DEP[iEta,iXi] - iList[nbEntry,0] = nbConst + 1 - jList[nbEntry,0] = idx - sList[nbEntry,0] = 1 - nbConst = nbConst + 1 - nbEntry = nbEntry + 1 + Constant[nbConst,0] = alpha * DEP[iEta,iXi] + iList[nbEntry,0] = nbConst + 1 + jList[nbEntry,0] = idx + sList[nbEntry,0] = 1 + nbConst = nbConst + 1 + nbEntry = nbEntry + 1 - print 'Inequalities |h^{new} - h^{old}| <= alpha h^{old}' - print 'maxamp: nbEntry = ', nbEntry, ' nbConst = ', nbConst - print ' ' + print('Inequalities |h^{new} - h^{old}| <= alpha h^{old}') + print('maxamp: nbEntry = ', nbEntry, ' nbConst = ', nbConst) + print(' ') if (abs(nbEntry - TotalNbEntry) > 0): - raise ValueError, 'We have a coding inconsistency for nbEntry. Please correct' + raise ValueError('We have a coding inconsistency for nbEntry. Please correct') if (abs(nbConst - TotalNbConstant) > 0): - raise ValueError, 'We have a coding inconsistency for nbConst. Please correct' + raise ValueError('We have a coding inconsistency for nbConst. Please correct') return iList, jList, sList, Constant @@ -227,7 +227,7 @@ def GetIJS_maxamp(MSK, DEP, AmpConst): def GetIJS_signs(MSK, SignConst): eta_rho, xi_rho = MSK.shape - print 'eta_rho = ', eta_rho, ' xi_rho = ', xi_rho + print('eta_rho = ', eta_rho, ' xi_rho = ', xi_rho) nbVert = 0 ListCoord = np.zeros((eta_rho, xi_rho)) @@ -242,8 +242,8 @@ def GetIJS_signs(MSK, SignConst): for iEta in range(eta_rho): for iXi in range(xi_rho): if (MSK[iEta,iXi] == 1 and SignConst[iEta,iXi] != 0): - TotalNbConstant = TotalNbConstant + 1 - TotalNbEntry = TotalNbEntry + 1 + TotalNbConstant = TotalNbConstant + 1 + TotalNbEntry = TotalNbEntry + 1 nbConst = 0 nbEntry = 0 @@ -267,18 +267,18 @@ def GetIJS_signs(MSK, SignConst): elif (SignConst[iEta, iXi] == -1): sList[nbEntry,0] = 1 else: - raise ValueError, 'Wrong assigning please check SignConst' + raise ValueError('Wrong assigning please check SignConst') nbEntry = nbEntry + 1 - print 'Inequalities dh >= 0 or dh <= 0' - print 'signs: nbEntry = ', nbEntry, ' nbConst = ', nbConst - print ' ' + print('Inequalities dh >= 0 or dh <= 0') + print('signs: nbEntry = ', nbEntry, ' nbConst = ', nbConst) + print(' ') if (abs(nbEntry - TotalNbEntry) > 0): - raise ValueError, 'We have a coding inconsistency for nbEntry. Please correct' + raise ValueError('We have a coding inconsistency for nbEntry. Please correct') if (abs(nbConst - TotalNbConstant) > 0): - raise ValueError, 'We have a coding inconsistency for nbConst. Please correct' + raise ValueError('We have a coding inconsistency for nbConst. Please correct') return iList, jList, sList, Constant @@ -348,9 +348,9 @@ def Neighborhood(MSK, iEta, iXi, Kdist): nbPt = 1 List4dir = np.array([[1, 0], - [0, 1], - [-1, 0], - [0, -1]]) + [0, 1], + [-1, 0], + [0, -1]]) for iK in range(1,Kdist+1): nbPtOld = nbPt @@ -359,7 +359,7 @@ def Neighborhood(MSK, iEta, iXi, Kdist): iEta = ListNeigh[iPt,0] iXi = ListNeigh[iPt,1] for ineigh in range(4): - iEtaN = iEta + List4dir[ineigh,0] + iEtaN = iEta + List4dir[ineigh,0] iXiN = iXi + List4dir[ineigh,1] if (iEtaN <= eta_rho-1 and iEtaN >= 0 and iXiN <= xi_rho-1 \ and iXiN >= 0 and MSK[iEtaN,iXiN] == 1): @@ -399,7 +399,7 @@ def ConnectedComponent(ListEdges, nbVert): ListAdjacency[eVert,eDeg-1] = fVert ListAdjacency[fVert,fDeg-1] = eVert - + MaxDeg = ListDegree.max() ListAdjacency = ListAdjacency[:,:MaxDeg] @@ -424,7 +424,7 @@ def ConnectedComponent(ListEdges, nbVert): for iH in range(np.size(H, 1)): eVert = H[0][iH] for iV in range(ListDegree[eVert, 0]): - ListNewHot[ListAdjacency[eVert, iV],0] = 1 + ListNewHot[ListAdjacency[eVert, iV],0] = 1 ListHot = ListNotDone * ListNewHot SumH = sum(ListHot) diff --git a/bathy_smoother/bathy_smoother/LP_tools.py b/bathy_smoother/bathy_smoother/LP_tools.py index 4cd41e8..2217bf4 100644 --- a/bathy_smoother/bathy_smoother/LP_tools.py +++ b/bathy_smoother/bathy_smoother/LP_tools.py @@ -5,8 +5,8 @@ try: from lpsolve55 import * except: - print 'lpsolve55.so not found.' - print 'Linear programming method will not be available.' + print('lpsolve55.so not found.') + print('Linear programming method will not be available.') # This code is adapted from the matlab code @@ -24,9 +24,9 @@ def WriteLinearProgram(FileName, iList, jList, sList, Constant, ObjectiveFct): nbVar = ObjectiveFct.shape[0] nbConst = Constant.shape[0] - print 'Write linear program' - print 'nbvar = ', nbVar, ' nbConst = ', nbConst - print ' ' + print('Write linear program') + print('nbvar = ', nbVar, ' nbConst = ', nbConst) + print(' ') f = open(FileName,'w') @@ -62,7 +62,7 @@ def WriteLinearProgram(FileName, iList, jList, sList, Constant, ObjectiveFct): if (Constant[iConst,0] < -tolCrit): testfeasibility = 0 return testfeasibility - + else: string = 'row%s: ' %str(iConst+1) f.write(string) @@ -71,9 +71,9 @@ def WriteLinearProgram(FileName, iList, jList, sList, Constant, ObjectiveFct): sL = sList[H[iH],0] string = '%.2f X%d ' %(sL, jL) if (sL > 0): - add='+' + add='+' else: - add='' + add='' string = '%s%s' %(add, string) f.write(string) @@ -105,7 +105,7 @@ def SolveLinearProgram(iList, jList, sList, Constant, ObjectiveFct): nbVar = ObjectiveFct.shape[0] nbConstraint = Constant.shape[0] - print 'Solving a linear program of ', nbVar, ' variables and ', nbConstraint, ' Constraints' + print('Solving a linear program of ', nbVar, ' variables and ', nbConstraint, ' Constraints') while(1): H = localtime() @@ -120,20 +120,20 @@ def SolveLinearProgram(iList, jList, sList, Constant, ObjectiveFct): if (os.path.exists(FileInput) is False and os.path.exists(FileOutput) is False): break - print 'We failed with FileInput = ', FileInput + print('We failed with FileInput = ', FileInput) testfeasibility = WriteLinearProgram(FileInput, iList, jList, sList, Constant, ObjectiveFct) if (testfeasibility == 0): - raise ValueError, 'Feasibility test failed. testfeasibility = 0.' + raise ValueError('Feasibility test failed. testfeasibility = 0.') - print 'Linear program written in FileOutput=', FileOutput + print('Linear program written in FileOutput=', FileOutput) lp_handle = lpsolve('read_lp_file', FileInput) result = lpsolve('solve', lp_handle) obj, ValueVar, ValueFct, testfeasibility = lpsolve('get_solution', result) lpsolve('delete_lp', result) - print 'Linear program solved' + print('Linear program solved') return ValueFct, ValueVar, testfeasibility diff --git a/bathy_smoother/bathy_smoother/__init__.py b/bathy_smoother/bathy_smoother/__init__.py index c86fae9..fe325df 100644 --- a/bathy_smoother/bathy_smoother/__init__.py +++ b/bathy_smoother/bathy_smoother/__init__.py @@ -4,11 +4,11 @@ (ripped from matlab script LP_bathymetry) ''' -import bathy_smoothing -import bathy_tools -import LP_bathy_smoothing -import LP_bathy_tools -import LP_tools +from . import bathy_smoothing +from . import bathy_tools +from . import LP_bathy_smoothing +from . import LP_bathy_tools +from . import LP_tools __authors__ = ['Frederic Castruccio '] diff --git a/bathy_smoother/bathy_smoother/bathy_smoothing.py b/bathy_smoother/bathy_smoother/bathy_smoothing.py index a30c84d..0e9c3f6 100644 --- a/bathy_smoother/bathy_smoother/bathy_smoothing.py +++ b/bathy_smoother/bathy_smoother/bathy_smoothing.py @@ -27,9 +27,9 @@ def smoothing_Positive_rx0(MSK, Hobs, rx0max): eta_rho, xi_rho = Hobs.shape ListNeigh = np.array([[1, 0], - [0, 1], - [-1, 0], - [0, -1]]) + [0, 1], + [-1, 0], + [0, -1]]) RetBathy = Hobs.copy() @@ -41,21 +41,21 @@ def smoothing_Positive_rx0(MSK, Hobs, rx0max): for iEta in range(eta_rho): for iXi in range(xi_rho): if (MSK[iEta,iXi] == 1): - for ineigh in range(4): - iEtaN = iEta + ListNeigh[ineigh,0] - iXiN = iXi + ListNeigh[ineigh,1] + for ineigh in range(4): + iEtaN = iEta + ListNeigh[ineigh,0] + iXiN = iXi + ListNeigh[ineigh,1] if (iEtaN <= eta_rho-1 and iEtaN >= 0 and iXiN <= xi_rho-1 \ and iXiN >= 0 and MSK[iEtaN,iXiN] == 1): - LowerBound = RetBathy[iEtaN,iXiN] * (1-rx0max)/(1+rx0max) - if ((RetBathy[iEta,iXi] - LowerBound) < -tol): - IsFinished = 0 - RetBathy[iEta,iXi] = LowerBound - nbModif = nbModif + 1 + LowerBound = RetBathy[iEtaN,iXiN] * (1-rx0max)/(1+rx0max) + if ((RetBathy[iEta,iXi] - LowerBound) < -tol): + IsFinished = 0 + RetBathy[iEta,iXi] = LowerBound + nbModif = nbModif + 1 if (IsFinished == 1): break - print ' nbModif=', nbModif + print(' nbModif=', nbModif) return RetBathy @@ -63,8 +63,8 @@ def smoothing_Positive_rx0(MSK, Hobs, rx0max): def smoothing_Negative_rx0(MSK, Hobs, rx0max): """ - This program use an opposite methode to the direct iterative method from - Martinho and Batteen (2006). This program optimizes the bathymetry for + This program use an opposite methode to the direct iterative method from + Martinho and Batteen (2006). This program optimizes the bathymetry for a given rx0 factor by decreasing it. Usage: @@ -80,9 +80,9 @@ def smoothing_Negative_rx0(MSK, Hobs, rx0max): eta_rho, xi_rho = Hobs.shape ListNeigh = np.array([[1, 0], - [0, 1], - [-1, 0], - [0, -1]]) + [0, 1], + [-1, 0], + [0, -1]]) RetBathy = Hobs.copy() @@ -94,21 +94,21 @@ def smoothing_Negative_rx0(MSK, Hobs, rx0max): for iEta in range(eta_rho): for iXi in range(xi_rho): if (MSK[iEta, iXi] == 1): - for ineigh in range(4): - iEtaN = iEta + ListNeigh[ineigh,0] - iXiN = iXi + ListNeigh[ineigh,1] + for ineigh in range(4): + iEtaN = iEta + ListNeigh[ineigh,0] + iXiN = iXi + ListNeigh[ineigh,1] if (iEtaN <= eta_rho-1 and iEtaN >= 0 and iXiN <= xi_rho-1 \ and iXiN >= 0 and MSK[iEtaN,iXiN] == 1): - UpperBound = RetBathy[iEtaN, iXiN] * (1+rx0max)/(1-rx0max) - if (RetBathy[iEta,iXi] > (UpperBound + tol)): - IsFinished = 0 - RetBathy[iEta, iXi] = UpperBound - nbModif = nbModif + 1 + UpperBound = RetBathy[iEtaN, iXiN] * (1+rx0max)/(1-rx0max) + if (RetBathy[iEta,iXi] > (UpperBound + tol)): + IsFinished = 0 + RetBathy[iEta, iXi] = UpperBound + nbModif = nbModif + 1 if (IsFinished == 1): break - print ' nbModif=', nbModif + print(' nbModif=', nbModif) return RetBathy @@ -117,8 +117,8 @@ def smoothing_Negative_rx0(MSK, Hobs, rx0max): def smoothing_PositiveVolume_rx0(MSK, Hobs, rx0max, AreaMatrix): """ This program use the direct iterative method from Martinho and Batteen (2006) - The bathymetry is optimized for a given rx0 factor by increasing it. All depth - are then multiplied by the coeficient K = Vol_init/Vol_final in order to + The bathymetry is optimized for a given rx0 factor by increasing it. All depth + are then multiplied by the coeficient K = Vol_init/Vol_final in order to insure volume conservation. Usage: @@ -136,9 +136,9 @@ def smoothing_PositiveVolume_rx0(MSK, Hobs, rx0max, AreaMatrix): eta_rho, xi_rho = Hobs.shape ListNeigh = np.array([[1, 0], - [0, 1], - [-1, 0], - [0, -1]]) + [0, 1], + [-1, 0], + [0, -1]]) WorkBathy = Hobs.copy() @@ -150,21 +150,21 @@ def smoothing_PositiveVolume_rx0(MSK, Hobs, rx0max, AreaMatrix): for iEta in range(eta_rho): for iXi in range(xi_rho): if (MSK[iEta, iXi] == 1): - for ineigh in range(4): - iEtaN = iEta + ListNeigh[ineigh,0] - iXiN = iXi + ListNeigh[ineigh,1] + for ineigh in range(4): + iEtaN = iEta + ListNeigh[ineigh,0] + iXiN = iXi + ListNeigh[ineigh,1] if (iEtaN <= eta_rho-1 and iEtaN >= 0 and iXiN <= xi_rho-1 \ and iXiN >= 0 and MSK[iEtaN,iXiN] == 1): - LowerBound = RetBathy[iEtaN, iXiN] * (1-rx0max)/(1+rx0max) - if ((WorkBathy[iEta,iXi] - LowerBound) < -tol): - IsFinished = 0 - WorkBathy[iEta, iXi] = LowerBound - nbModif = nbModif + 1 + LowerBound = RetBathy[iEtaN, iXiN] * (1-rx0max)/(1+rx0max) + if ((WorkBathy[iEta,iXi] - LowerBound) < -tol): + IsFinished = 0 + WorkBathy[iEta, iXi] = LowerBound + nbModif = nbModif + 1 if (IsFinished == 1): break - print ' nbModif=', nbModif + print(' nbModif=', nbModif) VolOrig=0 VolWork=0 @@ -182,9 +182,9 @@ def smoothing_PositiveVolume_rx0(MSK, Hobs, rx0max, AreaMatrix): def smoothing_NegativeVolume_rx0(MSK, Hobs, rx0maxi, AreaMatrix): """ - This program use an opposite methode to the direct iterative method from - Martinho and Batteen (2006). This program optimizes the bathymetry for - a given rx0 factor by decreasing it. All depth are then multiplied by + This program use an opposite methode to the direct iterative method from + Martinho and Batteen (2006). This program optimizes the bathymetry for + a given rx0 factor by decreasing it. All depth are then multiplied by the coeficient K = Vol_init/Vol_final in order to insure volume conservation. Usage: @@ -202,9 +202,9 @@ def smoothing_NegativeVolume_rx0(MSK, Hobs, rx0maxi, AreaMatrix): eta_rho, xi_rho = Hobs.shape ListNeigh = np.array([[1, 0], - [0, 1], - [-1, 0], - [0, -1]]) + [0, 1], + [-1, 0], + [0, -1]]) WorkBathy = Hobs.copy() @@ -216,21 +216,21 @@ def smoothing_NegativeVolume_rx0(MSK, Hobs, rx0maxi, AreaMatrix): for iEta in range(eta_rho): for iXi in range(xi_rho): if (MSK[iEta, iXi] == 1): - for ineigh in range(4): - iEtaN = iEta + ListNeigh[ineigh,0] - iXiN = iXi + ListNeigh[ineigh,1] + for ineigh in range(4): + iEtaN = iEta + ListNeigh[ineigh,0] + iXiN = iXi + ListNeigh[ineigh,1] if (iEtaN <= eta_rho-1 and iEtaN >= 0 and iXiN <= xi_rho-1 \ and iXiN >= 0 and MSK[iEtaN,iXiN] == 1): - UpperBound = RetBathy[iEtaN, iXiN] * (1+rx0max)/(1-rx0max) - if (WorkBathy[iEta,iXi] > (UpperBound + tol)): - IsFinished = 0 - WorkBathy[iEta, iXi] = UpperBound - nbModif = nbModif + 1 + UpperBound = RetBathy[iEtaN, iXiN] * (1+rx0max)/(1-rx0max) + if (WorkBathy[iEta,iXi] > (UpperBound + tol)): + IsFinished = 0 + WorkBathy[iEta, iXi] = UpperBound + nbModif = nbModif + 1 if (IsFinished == 1): break - print ' nbModif=', nbModif + print(' nbModif=', nbModif) VolOrig=0 VolWork=0 @@ -267,9 +267,9 @@ def smoothing_PlusMinus_rx0(MSK, Hobs, rx0max, AreaMatrix): eta_rho, xi_rho = Hobs.shape ListNeigh = np.array([[1, 0], - [0, 1], - [-1, 0], - [0, -1]]) + [0, 1], + [-1, 0], + [0, -1]]) RetBathy = Hobs.copy() @@ -283,15 +283,15 @@ def smoothing_PlusMinus_rx0(MSK, Hobs, rx0max, AreaMatrix): for iEta in range(eta_rho): for iXi in range(xi_rho): if (MSK[iEta, iXi] == 1): - Area = AreaMatrix[iEta, iXi] - for ineigh in range(4): - iEtaN = iEta + ListNeigh[ineigh,0] - iXiN = iXi + ListNeigh[ineigh,1] + Area = AreaMatrix[iEta, iXi] + for ineigh in range(4): + iEtaN = iEta + ListNeigh[ineigh,0] + iXiN = iXi + ListNeigh[ineigh,1] if (iEtaN <= eta_rho-1 and iEtaN >= 0 and iXiN <= xi_rho-1 \ and iXiN >= 0 and MSK[iEtaN,iXiN] == 1): - AreaN = AreaMatrix[iEtaN,iXiN] - LowerBound = RetBathy[iEtaN,iXiN] * TheMultiplier - if ((RetBathy[iEta,iXi] - LowerBound) < -tol): + AreaN = AreaMatrix[iEtaN,iXiN] + LowerBound = RetBathy[iEtaN,iXiN] * TheMultiplier + if ((RetBathy[iEta,iXi] - LowerBound) < -tol): IsFinished = 0 h = (TheMultiplier * RetBathy[iEtaN,iXiN] - RetBathy[iEta,iXi]) \ / (AreaN + TheMultiplier * Area) @@ -308,7 +308,7 @@ def smoothing_PlusMinus_rx0(MSK, Hobs, rx0max, AreaMatrix): H = AreaMatrix * RetBathy * MSK TheBathymetry2 = H.sum() DeltaBathymetry = TheBathymetry1 - TheBathymetry2 - print 'DeltaBathymetry = ', DeltaBathymetry + print('DeltaBathymetry = ', DeltaBathymetry) return RetBathy, HmodifVal, ValueFct @@ -332,9 +332,9 @@ def smoothing_Laplacian_rx0(MSK, Hobs, rx0max): eta_rho, xi_rho = Hobs.shape ListNeigh = np.array([[1, 0], - [0, 1], - [-1, 0], - [0, -1]]) + [0, 1], + [-1, 0], + [0, -1]]) RetBathy = Hobs.copy() @@ -344,8 +344,8 @@ def smoothing_Laplacian_rx0(MSK, Hobs, rx0max): for iXi in range(xi_rho): WeightSum = 0 for ineigh in range(4): - iEtaN = iEta + ListNeigh[ineigh,0] - iXiN = iXi + ListNeigh[ineigh,1] + iEtaN = iEta + ListNeigh[ineigh,0] + iXiN = iXi + ListNeigh[ineigh,1] if (iEtaN <= eta_rho-1 and iEtaN >= 0 and iXiN <= xi_rho-1 \ and iXiN >= 0 and MSK[iEtaN,iXiN] == 1): WeightSum = WeightSum + 1 @@ -364,7 +364,7 @@ def smoothing_Laplacian_rx0(MSK, Hobs, rx0max): nbPointMod = 0 AdditionalDone = np.zeros((eta_rho, xi_rho)) for iEta in range(eta_rho): - for iXi in range(xi_rho): + for iXi in range(xi_rho): Weight = 0 WeightSum = 0 for ineigh in range(4): @@ -378,17 +378,17 @@ def smoothing_Laplacian_rx0(MSK, Hobs, rx0max): TheWeight = WeightMatrix[iEta,iXi] WeDo = 0 if TheWeight > tol: - if RoughMat[iEta,iXi] > rx0max: - WeDo = 1 + if RoughMat[iEta,iXi] > rx0max: + WeDo = 1 if NumberDones[iEta,iXi] > 0: - WeDo = 1 + WeDo = 1 if WeDo == 1: - IsFinished = 0 - TheDelta = (Weight - TheWeight * RetBathy[iEta,iXi]) / (2 * TheWeight) - TheCorrect[iEta,iXi] = TheCorrect[iEta,iXi] + TheDelta - nbPointMod = nbPointMod + 1 - NumberDones[iEta,iXi] = 1 + IsFinished = 0 + TheDelta = (Weight - TheWeight * RetBathy[iEta,iXi]) / (2 * TheWeight) + TheCorrect[iEta,iXi] = TheCorrect[iEta,iXi] + TheDelta + nbPointMod = nbPointMod + 1 + NumberDones[iEta,iXi] = 1 NumberDones = NumberDones + AdditionalDone RetBathy = RetBathy + TheCorrect @@ -403,13 +403,13 @@ def smoothing_Laplacian_rx0(MSK, Hobs, rx0max): eStr=''; NumberDones = np.zeros((eta_rho, xi_rho)) - print 'Iteration #', Iter - print 'current r=', realR, ' nbPointMod=', nbPointMod, eStr - print ' ' + print('Iteration #', Iter) + print('current r=', realR, ' nbPointMod=', nbPointMod, eStr) + print(' ') Iter = Iter + 1 if (IsFinished == 1): break - + return RetBathy diff --git a/bathy_smoother/bathy_smoother/bathy_tools.py b/bathy_smoother/bathy_smoother/bathy_tools.py index 58126c8..cc298ba 100644 --- a/bathy_smoother/bathy_smoother/bathy_tools.py +++ b/bathy_smoother/bathy_smoother/bathy_tools.py @@ -19,9 +19,9 @@ def RoughnessMatrix(DEP, MSK): eta_rho, xi_rho = DEP.shape Umat = np.array([[0, 1], - [1, 0], - [0, -1], - [-1, 0]]) + [1, 0], + [0, -1], + [-1, 0]]) RoughMat = np.zeros(DEP.shape) diff --git a/bathy_smoother/docs/api-objects.txt b/bathy_smoother/docs/api-objects.txt deleted file mode 100644 index 34b58b9..0000000 --- a/bathy_smoother/docs/api-objects.txt +++ /dev/null @@ -1,151 +0,0 @@ -bathy_smoother bathy_smoother-module.html -bathy_smoother.LP_bathy_smoothing bathy_smoother.LP_bathy_smoothing-module.html -bathy_smoother.LP_bathy_smoothing.LP_smoothing_rx0 bathy_smoother.LP_bathy_smoothing-module.html#LP_smoothing_rx0 -bathy_smoother.LP_bathy_smoothing.LP_smoothing_rx0_heuristic bathy_smoother.LP_bathy_smoothing-module.html#LP_smoothing_rx0_heuristic -bathy_smoother.LP_bathy_tools bathy_smoother.LP_bathy_tools-module.html -bathy_smoother.LP_bathy_tools.MergeIJS_listings bathy_smoother.LP_bathy_tools-module.html#MergeIJS_listings -bathy_smoother.LP_bathy_tools.ConnectedComponent 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Package bathy_smoother

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ROMS_bathy_smoother is a toolkit for working with ROMS bathymetry - (ripped from matlab script LP_bathymetry)

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Version: - 0.1 -

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Author: - Frederic Castruccio <frederic@marine.rutgers.edu> -

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- 1  # encoding: utf-8 
- 2  '''  
- 3  ROMS_bathy_smoother is a toolkit for working with ROMS bathymetry 
- 4  (ripped from matlab script LP_bathymetry) 
- 5  ''' 
- 6   
- 7  import bathy_smoothing 
- 8  import bathy_tools 
- 9  import LP_bathy_smoothing 
-10  import LP_bathy_tools 
-11  import LP_tools 
-12   
-13  __authors__ = ['Frederic Castruccio <frederic@marine.rutgers.edu>'] 
-14   
-15  __version__ = '0.1' 
-16   
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Module LP_bathy_smoothing

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LP_smoothing_rx0(MSK, - Hobs, - rx0max, - SignConst, - AmpConst)
- This program perform a linear programming method in order to -optimize the bathymetry for a fixed factor r.		 - source code - -
- -
-   - - - - - - -
LP_smoothing_rx0_heuristic(MSK, - Hobs, - rx0max, - SignConst, - AmpConst)
- This program perform a linear programming method in order to -optimize the bathymetry for a fixed factor r.		 - source code - -
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Function Details[hide private]
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LP_smoothing_rx0(MSK, - Hobs, - rx0max, - SignConst, - AmpConst) -

- 		source code  -
- - 
-
-This program perform a linear programming method in order to 
-optimize the bathymetry for a fixed factor r.
-The inequality |H(e)-H(e')| / (H(e)-H(e')) <= r where H(e)=h(e)+dh(e) 
-can be rewritten as two linear inequalities on dh(e) and dh(e'). 
-The optimal bathymetry is obtain by minimising the perturbation
-P = sum_e(|dh(e)| under the above inequalitie constraintes.
-
-Usage:
-NewBathy = LP_smoothing_rx0(MSK, Hobs, rx0max, SignConst, AmpConst)
-
----MSK(eta_rho,xi_rho) is the mask of the grd
-     1 for sea
-     0 for land
----Hobs(eta_rho,xi_rho) is the raw depth of the grid
----rx0max is the target rx0 roughness factor
----SignConst(eta_rho,xi_rho) matrix of 0, +1, -1
-     +1  only bathymetry increase are allowed.
-     -1  only bathymetry decrease are allowed.
-     0   increase and decrease are allowed.
-     (put 0 if you are indifferent)
----AmpConst(eta_rho,xi_rho)  matrix of reals.
-     coefficient alpha such that the new bathymetry should
-     satisfy to  |h^{new} - h^{raw}| <= alpha h^{raw}
-     (put 10000 if you are indifferent)
-
-
-
-
-
-
- -
- -
- - -
-

LP_smoothing_rx0_heuristic(MSK, - Hobs, - rx0max, - SignConst, - AmpConst) -

- 		source code  -
- - 
-
-This program perform a linear programming method in order to 
-optimize the bathymetry for a fixed factor r.
-The inequality |H(e)-H(e')| / (H(e)-H(e')) <= r where H(e)=h(e)+dh(e) 
-can be rewritten as two linear inequalities on dh(e) and dh(e'). 
-The optimal bathymetry is obtain by minimising the perturbation
-P = sum_e(|dh(e)| under the above inequalitie constraintes.
-In order to reduce the computation time, an heurastic method is
-used.
-
-Usage:
-NewBathy = LP_smoothing_rx0_heuristic(MSK, Hobs, rx0max, SignConst, AmpConst)
-
----MSK(eta_rho,xi_rho) is the mask of the grd
-     1 for sea
-     0 for land
----Hobs(eta_rho,xi_rho) is the raw depth of the grid
----rx0max is the target rx0 roughness factor
----SignConst(eta_rho,xi_rho) matrix of 0, +1, -1
-     +1  only bathymetry increase are allowed.
-     -1  only bathymetry decrease are allowed.
-     0   increase and decrease are allowed.
-     (put 0 if you are indifferent)
----AmpConst(eta_rho,xi_rho)  matrix of reals.
-     coefficient alpha such that the new bathymetry should
-     satisfy to  |h^{new} - h^{raw}| <= alpha h^{raw}
-     (put 10000 if you are indifferent)
-
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Source Code for Module bathy_smoother.LP_bathy_smoothing

-
-  1  import numpy as np 
-  2  from ROMS_bathy_smoother import LP_bathy_tools 
-  3  from ROMS_bathy_smoother import LP_tools 
-  4  from ROMS_bathy_smoother import bathy_tools 
-  5   
-  6  import matplotlib.pyplot as plt 
-  7   
-  8   
-
  9 -def LP_smoothing_rx0(MSK, Hobs, rx0max, SignConst, AmpConst): 
-
 10      """ 
- 11      This program perform a linear programming method in order to  
- 12      optimize the bathymetry for a fixed factor r. 
- 13      The inequality |H(e)-H(e')| / (H(e)-H(e')) <= r where H(e)=h(e)+dh(e)  
- 14      can be rewritten as two linear inequalities on dh(e) and dh(e').  
- 15      The optimal bathymetry is obtain by minimising the perturbation 
- 16      P = sum_e(|dh(e)| under the above inequalitie constraintes. 
- 17   
- 18      Usage: 
- 19      NewBathy = LP_smoothing_rx0(MSK, Hobs, rx0max, SignConst, AmpConst) 
- 20      
- 21      ---MSK(eta_rho,xi_rho) is the mask of the grd 
- 22           1 for sea 
- 23           0 for land 
- 24      ---Hobs(eta_rho,xi_rho) is the raw depth of the grid 
- 25      ---rx0max is the target rx0 roughness factor 
- 26      ---SignConst(eta_rho,xi_rho) matrix of 0, +1, -1 
- 27           +1  only bathymetry increase are allowed. 
- 28           -1  only bathymetry decrease are allowed. 
- 29           0   increase and decrease are allowed. 
- 30           (put 0 if you are indifferent) 
- 31      ---AmpConst(eta_rho,xi_rho)  matrix of reals. 
- 32           coefficient alpha such that the new bathymetry should 
- 33           satisfy to  |h^{new} - h^{raw}| <= alpha h^{raw} 
- 34           (put 10000 if you are indifferent) 
- 35      """ 
- 36   
- 37      eta_rho, xi_rho = MSK.shape 
- 38   
- 39      iList, jList, sList, Constant = LP_bathy_tools.GetIJS_rx0(MSK, Hobs, rx0max) 
- 40   
- 41      iListApp, jListApp, sListApp, ConstantApp = LP_bathy_tools.GetIJS_maxamp(MSK, Hobs, AmpConst) 
- 42   
- 43      iList, jList, sList, Constant = LP_bathy_tools.MergeIJS_listings(iList, jList, sList, Constant, iListApp, jListApp, sListApp, ConstantApp) 
- 44   
- 45      iListApp, jListApp, sListApp, ConstantApp = LP_bathy_tools.GetIJS_signs(MSK, SignConst) 
- 46   
- 47      iList, jList, sList, Constant = LP_bathy_tools.MergeIJS_listings(iList, jList, sList, Constant, iListApp, jListApp, sListApp, ConstantApp) 
- 48   
- 49      TotalNbVert = int(MSK.sum()) 
- 50   
- 51      ObjectiveFct = np.zeros((2*TotalNbVert,1)) 
- 52      for iVert in range(TotalNbVert): 
- 53          ObjectiveFct[TotalNbVert+iVert,0] = 1 
- 54   
- 55      ValueFct, ValueVar, testfeasibility = LP_tools.SolveLinearProgram(iList, jList, sList, Constant, ObjectiveFct) 
- 56      if (testfeasibility == 0): 
- 57          NewBathy = NaN * np.ones((eta_rho,xi_rho)) 
- 58          raise ValueError, 'Feasibility test failed. testfeasibility = 0.' 
- 59   
- 60      correctionBathy = np.zeros((eta_rho,xi_rho)) 
- 61      nbVert = 0 
- 62      for iEta in range(eta_rho): 
- 63          for iXi in range(xi_rho): 
- 64              if (MSK[iEta,iXi] == 1): 
- 65                  correctionBathy[iEta,iXi] = ValueVar[nbVert] 
- 66                  nbVert = nbVert + 1 
- 67   
- 68      NewBathy = Hobs + correctionBathy 
- 69      RMat = bathy_tools.RoughnessMatrix(NewBathy, MSK) 
- 70      MaxRx0 = RMat.max() 
- 71      print 'rx0max = ', rx0max, '  MaxRx0 = ', MaxRx0 
- 72   
- 73      return NewBathy 
-
 74   
- 75   
- 76   
- 77   
- 78   
-
 79 -def LP_smoothing_rx0_heuristic(MSK, Hobs, rx0max, SignConst, AmpConst): 
-
 80      """ 
- 81      This program perform a linear programming method in order to  
- 82      optimize the bathymetry for a fixed factor r. 
- 83      The inequality |H(e)-H(e')| / (H(e)-H(e')) <= r where H(e)=h(e)+dh(e)  
- 84      can be rewritten as two linear inequalities on dh(e) and dh(e').  
- 85      The optimal bathymetry is obtain by minimising the perturbation 
- 86      P = sum_e(|dh(e)| under the above inequalitie constraintes. 
- 87      In order to reduce the computation time, an heurastic method is 
- 88      used. 
- 89   
- 90      Usage: 
- 91      NewBathy = LP_smoothing_rx0_heuristic(MSK, Hobs, rx0max, SignConst, AmpConst) 
- 92       
- 93      ---MSK(eta_rho,xi_rho) is the mask of the grd 
- 94           1 for sea 
- 95           0 for land 
- 96      ---Hobs(eta_rho,xi_rho) is the raw depth of the grid 
- 97      ---rx0max is the target rx0 roughness factor 
- 98      ---SignConst(eta_rho,xi_rho) matrix of 0, +1, -1 
- 99           +1  only bathymetry increase are allowed. 
-100           -1  only bathymetry decrease are allowed. 
-101           0   increase and decrease are allowed. 
-102           (put 0 if you are indifferent) 
-103      ---AmpConst(eta_rho,xi_rho)  matrix of reals. 
-104           coefficient alpha such that the new bathymetry should 
-105           satisfy to  |h^{new} - h^{raw}| <= alpha h^{raw} 
-106           (put 10000 if you are indifferent) 
-107      """ 
-108   
-109   
-110      # the points that need to be modified 
-111      MSKbad = LP_bathy_tools.GetBadPoints(MSK, Hobs, rx0max) 
-112   
-113      eta_rho, xi_rho = MSK.shape 
-114   
-115      Kdist = 5 
-116   
-117      Kbad = np.where(MSKbad == 1) 
-118      nbKbad = np.size(Kbad,1) 
-119      ListIdx = np.zeros((eta_rho,xi_rho), dtype=np.int) 
-120      ListIdx[Kbad] = range(nbKbad) 
-121   
-122      ListEdges = [] 
-123      nbEdge = 0 
-124      for iK in range(nbKbad): 
-125          iEta, iXi = Kbad[0][iK], Kbad[1][iK] 
-126          ListNeigh = LP_bathy_tools.Neighborhood(MSK, iEta, iXi, 2*Kdist+1) 
-127          nbNeigh = np.size(ListNeigh, 0) 
-128          for iNeigh in range(nbNeigh): 
-129              iEtaN, iXiN = ListNeigh[iNeigh] 
-130              if (MSKbad[iEtaN,iXiN] == 1): 
-131                  idx = ListIdx[iEtaN,iXiN] 
-132                  if (idx > iK): 
-133                      nbEdge = nbEdge + 1 
-134                      ListEdges.append([iK, idx]) 
-135   
-136      ListEdges = np.array(ListEdges) 
-137      ListVertexStatus = LP_bathy_tools.ConnectedComponent(ListEdges, nbKbad) 
-138      nbColor = ListVertexStatus.max() 
-139   
-140      NewBathy = Hobs.copy() 
-141      for iColor in range(1,nbColor+1): 
-142          print '---------------------------------------------------------------' 
-143          MSKcolor = np.zeros((eta_rho, xi_rho)) 
-144          K = np.where(ListVertexStatus == iColor) 
-145          nbK = np.size(K,1) 
-146          print 'iColor = ', iColor, '  nbK = ', nbK 
-147          for iVertex in range(nbKbad): 
-148              if (ListVertexStatus[iVertex,0] == iColor): 
-149                  iEta, iXi = Kbad[0][iVertex], Kbad[1][iVertex] 
-150                  MSKcolor[iEta, iXi] = 1 
-151                  ListNeigh = LP_bathy_tools.Neighborhood(MSK, iEta, iXi, Kdist) 
-152                  nbNeigh = np.size(ListNeigh, 0) 
-153                  for iNeigh in range(nbNeigh): 
-154                      iEtaN, iXiN = ListNeigh[iNeigh] 
-155                      MSKcolor[iEtaN,iXiN] = 1 
-156          K = np.where(MSKcolor == 1) 
-157          MSKHobs = np.zeros((eta_rho, xi_rho)) 
-158          MSKHobs[K] = Hobs[K].copy() 
-159          TheNewBathy = LP_smoothing_rx0(MSKcolor, MSKHobs, rx0max, SignConst, AmpConst) 
-160          NewBathy[K] = TheNewBathy[K].copy() 
-161   
-162      print 'Final obtained bathymetry' 
-163      RMat = bathy_tools.RoughnessMatrix(NewBathy, MSK) 
-164      MaxRx0 = RMat.max() 
-165      print 'rx0max = ', rx0max, '  MaxRx0 = ', MaxRx0 
-166   
-167      return NewBathy 
-
168   
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Module LP_bathy_tools

source code

- - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - -
Functions[hide private]
-
-   - - - - - - -
GetIJS_rx0(MSK, - DEP, - r) - source code - -
- -
-   - - - - - - -
GetIJS_maxamp(MSK, - DEP, - AmpConst) - source code - -
- -
-   - - - - - - -
GetIJS_signs(MSK, - SignConst) - source code - -
- -
-   - - - - - - -
MergeIJS_listings(iList1, - jList1, - sList1, - Constant1, - iList2, - jList2, - sList2, - Constant2) - source code - -
- -
-   - - - - - - -
GetBadPoints(MSK, - DEP, - rx0max) - source code - -
- -
-   - - - - - - -
Neighborhood(MSK, - iEta, - iXi, - Kdist) - source code - -
- -
-   - - - - - - -
ConnectedComponent(ListEdges, - nbVert)
- compute the vector of connected component belonging using a - representation and an algorithm well suited for sparse graphs.		 - source code - -
- -
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Source Code for Module bathy_smoother.LP_bathy_tools

-
-  1  import numpy as np 
-  2  from ROMS_bathy_smoother import bathy_smoothing 
-  3   
-
  4 -def GetIJS_rx0(MSK, DEP, r): 
-
  5   
-  6      eta_rho, xi_rho = DEP.shape 
-  7      print 'eta_rho = ', eta_rho, '  xi_rho = ', xi_rho 
-  8   
-  9      nbVert = 0 
- 10      ListCoord = np.zeros((eta_rho, xi_rho)) 
- 11      for iEta in range(eta_rho): 
- 12         for iXi in range(xi_rho): 
- 13             if (MSK[iEta,iXi] == 1): 
- 14                 nbVert = nbVert + 1 
- 15                 ListCoord[iEta,iXi] = nbVert 
- 16   
- 17      TotalNbVert = nbVert 
- 18      print 'ListCoord built' 
- 19      print 'Computing inequalities for r = ', r 
- 20   
- 21      TotalNbConstant = 0 
- 22      TotalNbEntry = 0 
- 23      for iEta in range(eta_rho-1): 
- 24         for iXi in range(xi_rho): 
- 25              if (MSK[iEta,iXi] == 1 and MSK[iEta+1,iXi] == 1): 
- 26                  TotalNbConstant = TotalNbConstant + 2 
- 27                  TotalNbEntry = TotalNbEntry + 4 
- 28   
- 29      for iEta in range(eta_rho): 
- 30         for iXi in range(xi_rho-1): 
- 31              if (MSK[iEta,iXi] == 1 and MSK[iEta,iXi+1] == 1): 
- 32                  TotalNbConstant = TotalNbConstant + 2 
- 33                  TotalNbEntry = TotalNbEntry + 4 
- 34   
- 35      TotalNbConstant = TotalNbConstant + 2 * TotalNbVert 
- 36      TotalNbEntry = TotalNbEntry + 4 * TotalNbVert 
- 37   
- 38      Constant = np.zeros((TotalNbConstant,1)) 
- 39      iList = np.zeros((TotalNbEntry,1)) 
- 40      jList=np.zeros((TotalNbEntry,1)) 
- 41      sList=np.zeros((TotalNbEntry,1)) 
- 42   
- 43      nbConst=0; 
- 44      nbEntry=0; 
- 45      for iEta in range(eta_rho-1): 
- 46         for iXi in range(xi_rho): 
- 47              if (MSK[iEta,iXi] == 1 and MSK[iEta+1,iXi] == 1): 
- 48                  idx1 = ListCoord[iEta,iXi] 
- 49                  idx2 = ListCoord[iEta+1,iXi] 
- 50   
- 51                  CST = (1+r) * DEP[iEta+1,iXi] + (-1+r) * DEP[iEta,iXi] 
- 52                  Constant[nbConst,0] = CST 
- 53                  nbConst = nbConst + 1 
- 54                  iList[nbEntry,0] = nbConst 
- 55                  jList[nbEntry,0] = idx2 
- 56                  sList[nbEntry,0] = -1-r 
- 57                  nbEntry = nbEntry + 1 
- 58                  iList[nbEntry,0] = nbConst 
- 59                  jList[nbEntry,0] = idx1 
- 60                  sList[nbEntry,0] = 1-r 
- 61                  nbEntry = nbEntry + 1 
- 62   
- 63                  CST = (1+r) * DEP[iEta,iXi] + (-1+r) * DEP[iEta+1,iXi] 
- 64                  Constant[nbConst,0] = CST 
- 65                  nbConst = nbConst + 1 
- 66                  iList[nbEntry,0] = nbConst 
- 67                  jList[nbEntry,0] = idx1 
- 68                  sList[nbEntry,0] = -r-1 
- 69                  nbEntry = nbEntry + 1 
- 70                  iList[nbEntry,0] = nbConst 
- 71                  jList[nbEntry,0] = idx2 
- 72                  sList[nbEntry,0] = 1-r 
- 73                  nbEntry = nbEntry + 1 
- 74   
- 75      print 'Inequalities for dh(iEta,iXi) and dh(iEta+1,iXi)' 
- 76   
- 77      for iEta in range(eta_rho): 
- 78          for iXi in range(xi_rho-1): 
- 79              if (MSK[iEta,iXi] == 1 and MSK[iEta, iXi+1] == 1): 
- 80                  idx1 = ListCoord[iEta,iXi] 
- 81                  idx2 = ListCoord[iEta,iXi+1] 
- 82   
- 83                  CST = (1+r) * DEP[iEta,iXi+1] + (r-1) * DEP[iEta,iXi] 
- 84                  Constant[nbConst,0] = CST 
- 85                  nbConst = nbConst + 1 
- 86                  iList[nbEntry,0] = nbConst 
- 87                  jList[nbEntry,0] = idx2 
- 88                  sList[nbEntry,0] = -r-1 
- 89                  nbEntry = nbEntry + 1 
- 90                  iList[nbEntry,0] = nbConst 
- 91                  jList[nbEntry,0] = idx1 
- 92                  sList[nbEntry,0] = 1-r 
- 93                  nbEntry = nbEntry + 1 
- 94   
- 95                  CST = (1+r) * DEP[iEta,iXi] + (r-1) * DEP[iEta,iXi+1] 
- 96                  Constant[nbConst,0] = CST 
- 97                  nbConst = nbConst + 1 
- 98                  iList[nbEntry,0] = nbConst 
- 99                  jList[nbEntry,0] = idx1 
-100                  sList[nbEntry,0] = -r-1 
-101                  nbEntry = nbEntry + 1 
-102                  iList[nbEntry,0] = nbConst 
-103                  jList[nbEntry,0] = idx2 
-104                  sList[nbEntry,0] = 1-r 
-105                  nbEntry = nbEntry + 1 
-106   
-107      print 'Inequalities for dh(iEta,iXi) and dh(iEta,iXi+1)' 
-108   
-109      for iEta in range(eta_rho): 
-110          for iXi in range(xi_rho): 
-111              if (MSK[iEta,iXi] == 1): 
-112                  idx = ListCoord[iEta,iXi] 
-113   
-114                  Constant[nbConst,0] = 0 
-115                  nbConst = nbConst + 1 
-116                  iList[nbEntry,0] = nbConst 
-117                  jList[nbEntry,0] = TotalNbVert + idx 
-118                  sList[nbEntry,0] = -1 
-119                  nbEntry = nbEntry + 1 
-120                  iList[nbEntry,0] = nbConst 
-121                  jList[nbEntry,0] = idx 
-122                  sList[nbEntry,0] = 1 
-123                  nbEntry = nbEntry + 1 
-124   
-125                  Constant[nbConst,0] = 0 
-126                  nbConst = nbConst + 1 
-127                  iList[nbEntry,0] = nbConst 
-128                  jList[nbEntry,0] = TotalNbVert+idx 
-129                  sList[nbEntry,0] = -1 
-130                  nbEntry = nbEntry + 1 
-131                  iList[nbEntry,0] = nbConst 
-132                  jList[nbEntry,0] = idx 
-133                  sList[nbEntry,0] = -1 
-134                  nbEntry = nbEntry + 1 
-135   
-136      print 'Inequalities dh <= ad and -dh <= ad' 
-137   
-138      print 'rx0: nbEntry = ', nbEntry, '  nbConst = ', nbConst 
-139      print ' ' 
-140   
-141      if (abs(nbEntry - TotalNbEntry) > 0): 
-142          raise ValueError, 'We have a coding inconsistency for nbEntry. Please correct' 
-143   
-144      if (abs(nbConst - TotalNbConstant) > 0): 
-145          raise ValueError, 'We have a coding inconsistency for nbConst. Please correct' 
-146   
-147   
-148      return iList, jList, sList, Constant 
-
149   
-150   
-151   
-
152 -def GetIJS_maxamp(MSK, DEP, AmpConst): 
-
153   
-154   
-155      eta_rho, xi_rho = DEP.shape 
-156      print 'eta_rho = ', eta_rho, '  xi_rho = ', xi_rho 
-157   
-158      nbVert = 0 
-159      ListCoord = np.zeros((eta_rho, xi_rho)) 
-160      for iEta in range(eta_rho): 
-161         for iXi in range(xi_rho): 
-162             if (MSK[iEta,iXi] == 1): 
-163                 nbVert = nbVert + 1 
-164                 ListCoord[iEta,iXi] = nbVert 
-165   
-166      TotalNbConstant = 0 
-167      TotalNbEntry = 0 
-168      for iEta in range(eta_rho): 
-169         for iXi in range(xi_rho): 
-170             if (MSK[iEta,iXi] == 1): 
-171                  alpha = AmpConst[iEta,iXi] 
-172                  if (alpha < 9999): 
-173                      TotalNbConstant = TotalNbConstant + 2 
-174                      TotalNbEntry = TotalNbEntry + 2 
-175   
-176      nbConst = 0 
-177      nbEntry = 0 
-178      Constant = np.zeros((TotalNbConstant,1)) 
-179      iList = np.zeros((TotalNbEntry,1)) 
-180      jList = np.zeros((TotalNbEntry,1)) 
-181      sList = np.zeros((TotalNbEntry,1)) 
-182   
-183      for iEta in range(eta_rho): 
-184         for iXi in range(xi_rho): 
-185             if (MSK[iEta,iXi] == 1): 
-186                  idx = ListCoord[iEta,iXi] 
-187                  alpha = AmpConst[iEta,iXi] 
-188   
-189                  if (alpha < 9999): 
-190                      Constant[nbConst,0] = alpha * DEP[iEta,iXi] 
-191                      iList[nbEntry,0] = nbConst + 1 
-192                      jList[nbEntry,0] = idx 
-193                      sList[nbEntry,0] = -1 
-194                      nbConst = nbConst + 1 
-195                      nbEntry = nbEntry + 1 
-196   
-197                      Constant[nbConst,0] = alpha * DEP[iEta,iXi] 
-198                      iList[nbEntry,0] = nbConst + 1 
-199                      jList[nbEntry,0] = idx 
-200                      sList[nbEntry,0] = 1 
-201                      nbConst = nbConst + 1 
-202                      nbEntry = nbEntry + 1 
-203   
-204      print 'Inequalities |h^{new} - h^{old}| <= alpha h^{old}' 
-205      print 'maxamp: nbEntry = ', nbEntry, '  nbConst = ', nbConst 
-206      print ' ' 
-207   
-208      if (abs(nbEntry - TotalNbEntry) > 0): 
-209          raise ValueError, 'We have a coding inconsistency for nbEntry. Please correct' 
-210   
-211      if (abs(nbConst - TotalNbConstant) > 0): 
-212          raise ValueError, 'We have a coding inconsistency for nbConst. Please correct' 
-213   
-214   
-215      return iList, jList, sList, Constant 
-
216   
-217   
-218   
-
219 -def GetIJS_signs(MSK, SignConst): 
-
220   
-221      eta_rho, xi_rho = MSK.shape 
-222      print 'eta_rho = ', eta_rho, '  xi_rho = ', xi_rho 
-223   
-224      nbVert = 0 
-225      ListCoord = np.zeros((eta_rho, xi_rho)) 
-226      for iEta in range(eta_rho): 
-227         for iXi in range(xi_rho): 
-228             if (MSK[iEta,iXi] == 1): 
-229                 nbVert = nbVert + 1 
-230                 ListCoord[iEta,iXi] = nbVert 
-231   
-232      TotalNbConstant = 0 
-233      TotalNbEntry = 0 
-234      for iEta in range(eta_rho): 
-235         for iXi in range(xi_rho): 
-236             if (MSK[iEta,iXi] == 1 and SignConst[iEta,iXi] != 0): 
-237                  TotalNbConstant = TotalNbConstant + 1 
-238                  TotalNbEntry = TotalNbEntry + 1 
-239   
-240      nbConst = 0 
-241      nbEntry = 0 
-242      Constant = np.zeros((TotalNbConstant,1)) 
-243      iList = np.zeros((TotalNbEntry,1)) 
-244      jList = np.zeros((TotalNbEntry,1)) 
-245      sList = np.zeros((TotalNbEntry,1)) 
-246   
-247   
-248      for iEta in range(eta_rho): 
-249         for iXi in range(xi_rho): 
-250             if (MSK[iEta,iXi] == 1 and SignConst[iEta,iXi] != 0): 
-251                 idx = ListCoord[iEta,iXi] 
-252   
-253                 Constant[nbConst,0] = 0 
-254                 nbConst = nbConst + 1 
-255                 iList[nbEntry,0] = nbConst 
-256                 jList[nbEntry,0] = idx 
-257                 if (SignConst[iEta,iXi] == 1): 
-258                     sList[nbEntry,0] = -1 
-259                 elif (SignConst[iEta, iXi] == -1): 
-260                     sList[nbEntry,0] = 1 
-261                 else: 
-262                     raise ValueError, 'Wrong assigning please check SignConst' 
-263                 nbEntry = nbEntry + 1 
-264   
-265      print 'Inequalities dh >= 0 or dh <= 0' 
-266      print 'signs: nbEntry = ', nbEntry, '  nbConst = ', nbConst 
-267      print ' ' 
-268   
-269      if (abs(nbEntry - TotalNbEntry) > 0): 
-270          raise ValueError, 'We have a coding inconsistency for nbEntry. Please correct' 
-271   
-272      if (abs(nbConst - TotalNbConstant) > 0): 
-273          raise ValueError, 'We have a coding inconsistency for nbConst. Please correct' 
-274   
-275   
-276      return iList, jList, sList, Constant 
-
277   
-278   
-279   
-
280 -def MergeIJS_listings(iList1, jList1, sList1, Constant1, iList2, jList2, sList2, Constant2): 
-
281   
-282      # Suppose we have two sets of inequalities for two linear programs 
-283      # with the same set of variables presented in sparse form. 
-284      # The two descriptions are merge. 
-285   
-286      nbConst1 = Constant1.shape[0] 
-287      nbConst2 = Constant2.shape[0] 
-288      nbEnt1 = iList1.shape[0] 
-289      nbEnt2 = iList2.shape[0] 
-290   
-291      Constant = np.zeros((nbConst1+nbConst2,1)) 
-292      iList = np.zeros((nbEnt1+nbEnt2,1)) 
-293      jList = np.zeros((nbEnt1+nbEnt2,1)) 
-294      sList = np.zeros((nbEnt1+nbEnt2,1)) 
-295   
-296      for iCons in range(nbConst1): 
-297          Constant[iCons,0] = Constant1[iCons,0] 
-298   
-299      for iCons in range(nbConst2): 
-300          Constant[nbConst1+iCons,0] = Constant2[iCons,0] 
-301   
-302      for iEnt in range(nbEnt1): 
-303          iList[iEnt,0] = iList1[iEnt,0] 
-304          jList[iEnt,0] = jList1[iEnt,0] 
-305          sList[iEnt,0] = sList1[iEnt,0] 
-306   
-307      for iEnt in range(nbEnt2): 
-308          iList[nbEnt1+iEnt,0] = nbConst1 + iList2[iEnt,0] 
-309          jList[nbEnt1+iEnt,0] = jList2[iEnt,0] 
-310          sList[nbEnt1+iEnt,0] = sList2[iEnt,0] 
-311   
-312      return iList, jList, sList, Constant 
-
313   
-314   
-
315 -def GetBadPoints(MSK, DEP, rx0max): 
-
316   
-317      RetBathy = bathy_smoothing.smoothing_Positive_rx0(MSK, DEP, rx0max) 
-318      K1 = np.where(RetBathy != DEP) 
-319   
-320      eta_rho, xi_rho = MSK.shape 
-321      MSKbad = np.zeros((eta_rho,xi_rho)) 
-322      MSKbad[K1] = 1 
-323   
-324      return MSKbad 
-
325   
-326   
-
327 -def Neighborhood(MSK, iEta, iXi, Kdist): 
-
328   
-329      eta_rho, xi_rho = MSK.shape 
-330      MaxSiz = (2 * Kdist + 1) * (2 * Kdist + 1) 
-331      ListNeigh = np.zeros((MaxSiz,2), dtype=np.int) 
-332      ListStatus = -1 * np.ones((MaxSiz,1), dtype=np.int) 
-333      ListKeys = np.zeros((MaxSiz,1), dtype=np.int) 
-334   
-335      eKey = iEta + (eta_rho+1) * iXi 
-336      ListNeigh[0,0] = iEta 
-337      ListNeigh[0,1] = iXi 
-338      ListStatus[0,0] = 0 
-339      ListKeys[0,0] = eKey 
-340      nbPt = 1 
-341   
-342      List4dir = np.array([[1, 0], 
-343                            [0, 1], 
-344                            [-1, 0], 
-345                            [0, -1]]) 
-346   
-347      for iK in range(1,Kdist+1): 
-348          nbPtOld = nbPt 
-349          for iPt in range(nbPtOld): 
-350              if (ListStatus[iPt,0] == iK-1): 
-351                  iEta = ListNeigh[iPt,0] 
-352                  iXi = ListNeigh[iPt,1] 
-353                  for ineigh in range(4): 
-354                      iEtaN = iEta + List4dir[ineigh,0] 
-355                      iXiN = iXi + List4dir[ineigh,1] 
-356                      if (iEtaN <= eta_rho-1 and iEtaN >= 0 and iXiN <= xi_rho-1 \ 
-357                              and iXiN >= 0 and MSK[iEtaN,iXiN] == 1): 
-358                          eKeyN = iEtaN + (eta_rho+1)*iXiN 
-359                          Kf = np.where(ListKeys == eKeyN) 
-360                          nbKf = np.size(Kf,1) 
-361                          if (nbKf == 0): 
-362                              ListNeigh[nbPt,0] = iEtaN 
-363                              ListNeigh[nbPt,1] = iXiN 
-364                              ListStatus[nbPt,0] = iK 
-365                              ListKeys[nbPt,0] = eKeyN 
-366                              nbPt = nbPt + 1 
-367   
-368      ListNeighRet = ListNeigh[1:nbPt,:] 
-369   
-370      return ListNeighRet 
-
371   
-372   
-
373 -def ConnectedComponent(ListEdges, nbVert): 
-
374      """ 
-375      compute the vector of connected component belonging 
-376      using a representation and an algorithm well suited 
-377      for sparse graphs. 
-378      """ 
-379   
-380      nbEdge = np.size(ListEdges, 0) 
-381      ListDegree = np.zeros((nbVert,1), dtype=np.int) 
-382      ListAdjacency = np.zeros((nbVert,10000), dtype=np.int) 
-383   
-384      for iEdge in range(nbEdge): 
-385          eVert = ListEdges[iEdge,0] 
-386          fVert = ListEdges[iEdge,1] 
-387          eDeg = ListDegree[eVert,0] + 1 
-388          fDeg = ListDegree[fVert,0] + 1 
-389          ListDegree[eVert,0] = eDeg 
-390          ListDegree[fVert,0] = fDeg 
-391          ListAdjacency[eVert,eDeg-1] = fVert 
-392          ListAdjacency[fVert,fDeg-1] = eVert 
-393   
-394       
-395      MaxDeg = ListDegree.max() 
-396      ListAdjacency = ListAdjacency[:,:MaxDeg] 
-397   
-398      ListVertexStatus = np.zeros((nbVert,1)) 
-399      ListHot = np.zeros((nbVert,1)) 
-400      ListNotDone = np.ones((nbVert,1)) 
-401   
-402      iComp = 0 
-403      while(1): 
-404          H = np.where(ListNotDone == 1) 
-405          nb = np.size(H, 1) 
-406          if (nb == 0): 
-407              break; 
-408   
-409          iComp = iComp + 1 
-410          ListVertexStatus[H[0][0],0] = iComp 
-411          ListHot[H[0][0],0] = 1 
-412          while(1): 
-413              H = np.where(ListHot == 1) 
-414              ListNotDone[H] = 0 
-415              ListNewHot = np.zeros((nbVert,1)) 
-416              for iH in range(np.size(H, 1)): 
-417                  eVert = H[0][iH] 
-418                  for iV in range(ListDegree[eVert, 0]): 
-419                      ListNewHot[ListAdjacency[eVert, iV],0] = 1 
-420   
-421              ListHot = ListNotDone * ListNewHot 
-422              SumH = sum(ListHot) 
-423              if (SumH == 0): 
-424                  break 
-425   
-426              H2 = np.where(ListHot == 1) 
-427              ListVertexStatus[H2] = iComp 
-428   
-429   
-430      return ListVertexStatus 
-
431   
-
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- - Package bathy_smoother :: - Module LP_tools - - - - - - -
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Module LP_tools

source code

- - - - - - - - - - - - -
- - - - - -
Functions[hide private]
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-   - - - - - - -
WriteLinearProgram(FileName, - iList, - jList, - sList, - Constant, - ObjectiveFct) - source code - -
- -
-   - - - - - - -
SolveLinearProgram(iList, - jList, - sList, - Constant, - ObjectiveFct) - source code - -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Variables[hide private]
-
-   - - ANTIDEGEN_BOUNDFLIP = 512 -
-   - - ANTIDEGEN_COLUMNCHECK = 2 -
-   - - ANTIDEGEN_DURINGBB = 128 -
-   - - ANTIDEGEN_DYNAMIC = 64 -
-   - - ANTIDEGEN_FIXEDVARS = 1 -
-   - - ANTIDEGEN_INFEASIBLE = 32 -
-   - - ANTIDEGEN_LOSTFEAS = 16 -
-   - - ANTIDEGEN_NONE = 0 -
-   - - ANTIDEGEN_NUMFAILURE = 8 -
-   - - ANTIDEGEN_RHSPERTURB = 256 -
-   - - ANTIDEGEN_STALLING = 4 -
-   - - BRANCH_AUTOMATIC = 2 -
-   - - BRANCH_CEILING = 0 -
-   - - BRANCH_FLOOR = 1 -
-   - - CRASH_LEASTDEGENERATE = 3 -
-   - - CRASH_MOSTFEASIBLE = 2 -
-   - - CRASH_NONE = 0 -
-   - - CRITICAL = 1 -
-   - - DEGENERATE = 4 -
-   - - DETAILED = 5 -
-   - - EQ = 3 -
-   - - FEASFOUND = 12 -
-   - - FR = 0 -
-   - - FULL = 6 -
-   - - GE = 2 -
-   - - IMPORTANT = 3 -
-   - - IMPROVE_BBSIMPLEX = 8 -
-   - - IMPROVE_DUALFEAS = 2 -
-   - - IMPROVE_NONE = 0 -
-   - - IMPROVE_SOLUTION = 1 -
-   - - IMPROVE_THETAGAP = 4 -
-   - - INFEASIBLE = 2 -
-   - - Infinite = 1e+30 -
-   - - LE = 1 -
-   - - MSG_LPFEASIBLE = 8 -
-   - - MSG_LPOPTIMAL = 16 -
-   - - MSG_MILPBETTER = 512 -
-   - - MSG_MILPEQUAL = 256 -
-   - - MSG_MILPFEASIBLE = 128 -
-   - - MSG_PRESOLVE = 1 -
-   - - NEUTRAL = 0 -
-   - - NODE_AUTOORDER = 8192 -
-   - - NODE_BRANCHREVERSEMODE = 16 -
-   - - NODE_BREADTHFIRSTMODE = 4096 -
-   - - NODE_DEPTHFIRSTMODE = 128 -
-   - - NODE_DYNAMICMODE = 1024 -
-   - - NODE_FIRSTSELECT = 0 -
-   - - NODE_FRACTIONSELECT = 3 -
-   - - NODE_GAPSELECT = 1 -
-   - - NODE_GREEDYMODE = 32 -
-   - - NODE_GUBMODE = 512 -
-   - - NODE_PSEUDOCOSTMODE = 64 -
-   - - NODE_PSEUDOCOSTSELECT = 4 -
-   - - NODE_PSEUDONONINTSELECT = 5 -
-   - - NODE_PSEUDORATIOSELECT = 6 -
-   - - NODE_RANDOMIZEMODE = 256 -
-   - - NODE_RANGESELECT = 2 -
-   - - NODE_RCOSTFIXING = 16384 -
-   - - NODE_RESTARTMODE = 2048 -
-   - - NODE_STRONGINIT = 32768 -
-   - - NODE_USERSELECT = 7 -
-   - - NODE_WEIGHTREVERSEMODE = 8 -
-   - - NOFEASFOUND = 13 -
-   - - NOMEMORY = -2 -
-   - - NORMAL = 4 -
-   - - NUMFAILURE = 5 -
-   - - OPTIMAL = 0 -
-   - - PRESOLVE_BOUNDS = 262144 -
-   - - PRESOLVE_COLDOMINATE = 16384 -
-   - - PRESOLVE_COLFIXDUAL = 131072 -
-   - - PRESOLVE_COLS = 2 -
-   - - PRESOLVE_DUALS = 524288 -
-   - - PRESOLVE_ELIMEQ2 = 256 -
-   - - PRESOLVE_IMPLIEDFREE = 512 -
-   - - PRESOLVE_IMPLIEDSLK = 65536 -
-   - - PRESOLVE_KNAPSACK = 128 -
-   - - PRESOLVE_LINDEP = 4 -
-   - - PRESOLVE_MERGEROWS = 32768 -
-   - - PRESOLVE_NONE = 0 -
-   - - PRESOLVE_PROBEFIX = 2048 -
-   - - PRESOLVE_PROBEREDUCE = 4096 -
-   - - PRESOLVE_REDUCEGCD = 1024 -
-   - - PRESOLVE_REDUCEMIP = 64 -
-   - - PRESOLVE_ROWDOMINATE = 8192 -
-   - - PRESOLVE_ROWS = 1 -
-   - - PRESOLVE_SENSDUALS = 1048576 -
-   - - PRESOLVE_SOS = 32 -
-   - - PRICER_DANTZIG = 1 -
-   - - PRICER_DEVEX = 2 -
-   - - PRICER_FIRSTINDEX = 0 -
-   - - PRICER_STEEPESTEDGE = 3 -
-   - - PRICE_ADAPTIVE = 32 -
-   - - PRICE_AUTOPARTIAL = 256 -
-   - - PRICE_HARRISTWOPASS = 4096 -
-   - - PRICE_LOOPALTERNATE = 2048 -
-   - - PRICE_LOOPLEFT = 1024 -
-   - - PRICE_MULTIPLE = 8 -
-   - - PRICE_PARTIAL = 16 -
-   - - PRICE_PRIMALFALLBACK = 4 -
-   - - PRICE_RANDOMIZE = 128 -
-   - - PRICE_TRUENORMINIT = 16384 -
-   - - PROCBREAK = 11 -
-   - - PROCFAIL = 10 -
-   - - SCALE_COLSONLY = 1024 -
-   - - SCALE_CURTISREID = 7 -
-   - - SCALE_DYNUPDATE = 256 -
-   - - SCALE_EQUILIBRATE = 64 -
-   - - SCALE_EXTREME = 1 -
-   - - SCALE_GEOMETRIC = 4 -
-   - - SCALE_INTEGERS = 128 -
-   - - SCALE_LOGARITHMIC = 16 -
-   - - SCALE_MEAN = 3 -
-   - - SCALE_NONE = 0 -
-   - - SCALE_POWER2 = 32 -
-   - - SCALE_QUADRATIC = 8 -
-   - - SCALE_RANGE = 2 -
-   - - SCALE_ROWSONLY = 512 -
-   - - SCALE_USERWEIGHT = 31 -
-   - - SEVERE = 2 -
-   - - SIMPLEX_DUAL_DUAL = 10 -
-   - - SIMPLEX_DUAL_PRIMAL = 6 -
-   - - SIMPLEX_PRIMAL_DUAL = 9 -
-   - - SIMPLEX_PRIMAL_PRIMAL = 5 -
-   - - SUBOPTIMAL = 1 -
-   - - TIMEOUT = 7 -
-   - - UNBOUNDED = 3 -
-   - - USERABORT = 6 -
- - - - - - - - - - - - - - - - - -
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- - - - - -
- Generated by Epydoc 3.0.1 on Thu Apr 22 11:29:10 2010 - - http://epydoc.sourceforge.net -
- - - - diff --git a/bathy_smoother/docs/bathy_smoother.LP_tools-pysrc.html b/bathy_smoother/docs/bathy_smoother.LP_tools-pysrc.html deleted file mode 100644 index 4d51485..0000000 --- a/bathy_smoother/docs/bathy_smoother.LP_tools-pysrc.html +++ /dev/null @@ -1,243 +0,0 @@ - - - - - bathy_smoother.LP_tools - - - - - - - - - - - - - - - - - - - - - - -
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- - - - - -
- - Package bathy_smoother :: - Module LP_tools - - - - - - -
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-
-

Source Code for Module bathy_smoother.LP_tools

-
-  1  import numpy as np 
-  2  from numpy.random import random 
-  3  from time import localtime 
-  4  import os 
-  5  try: 
-  6      from lpsolve55 import * 
-  7  except: 
-  8      print 'lpsolve55.so not found.' 
-  9      print 'Linear programming method will not be available.' 
- 10   
- 11   
- 12   
-
 13 -def WriteLinearProgram(FileName, iList, jList, sList, Constant, ObjectiveFct): 
-
 14   
- 15      # Do not remove the test of feasibility ! 
- 16      # It is a preliminary check and it is actually useful. 
- 17   
- 18      nbVar = ObjectiveFct.shape[0] 
- 19      nbConst = Constant.shape[0] 
- 20      print 'Write linear program' 
- 21      print 'nbvar = ', nbVar, ' nbConst = ', nbConst 
- 22      print ' ' 
- 23   
- 24      f = open(FileName,'w') 
- 25   
- 26      # write the function to minimise 
- 27      # we want to minimize the perturbation P = sum_e(|dh(e)| 
- 28      # as the absolute value is not a linear function, we use a trick: 
- 29      # we introduce an additional variable ad(e) satisfying +/- dh(e) <= ad(e) 
- 30      # and we minimize sum_e(ad(e)) 
- 31      f.write('min: ') 
- 32      for iVar in range(nbVar): 
- 33          eVal = ObjectiveFct[iVar,0] 
- 34          if (eVal != 0): 
- 35              if (eVal > 0): 
- 36                  add='+' 
- 37              else: 
- 38                  add='' 
- 39   
- 40              string = '%s%f X%d ' %(add,eVal,iVar+1) 
- 41              f.write(string) 
- 42          else: 
- 43              string = '+0 X%d ' %(iVar+1) 
- 44              f.write(string) 
- 45   
- 46      f.write(';\n') 
- 47      f.write('\n') 
- 48   
- 49      #write the inequality constraintes 
- 50      tolCrit = 1e-6 
- 51      for iConst in range(nbConst): 
- 52          H = np.where(iList == iConst+1)[0] 
- 53          nbH = H.shape[0] 
- 54          if (nbH == 0): 
- 55              if (Constant[iConst,0] < -tolCrit): 
- 56                  testfeasibility = 0 
- 57                  return testfeasibility 
- 58    
- 59          else: 
- 60              string = 'row%s: ' %str(iConst+1) 
- 61              f.write(string) 
- 62              for iH in range(nbH): 
- 63                  jL = jList[H[iH],0] 
- 64                  sL = sList[H[iH],0] 
- 65                  string = '%.2f X%d ' %(sL, jL) 
- 66                  if (sL > 0): 
- 67                      add='+' 
- 68                  else: 
- 69                      add='' 
- 70   
- 71                  string = '%s%s' %(add, string) 
- 72                  f.write(string) 
- 73   
- 74              string = '<= %.8e ;\n' %Constant[iConst,0] 
- 75              f.write(string) 
- 76   
- 77      f.write('\n') 
- 78   
- 79      # the free command does not seem to work as advertised 
- 80      f.write('free') 
- 81      for iVar in range(nbVar): 
- 82          if (iVar+1 > 1): 
- 83              f.write(',') 
- 84   
- 85          string = ' X%d' %(iVar+1) 
- 86          f.write(string) 
- 87   
- 88      f.write(';\n') 
- 89      f.close() 
- 90      testfeasibility = 1 
- 91   
- 92   
- 93      return testfeasibility 
-
 94   
- 95   
- 96   
-
 97 -def SolveLinearProgram(iList, jList, sList, Constant, ObjectiveFct): 
-
 98   
- 99      nbVar = ObjectiveFct.shape[0] 
-100      nbConstraint = Constant.shape[0] 
-101      print 'Solving a linear program of ', nbVar, ' variables and ', nbConstraint, ' Constraints' 
-102   
-103      while(1): 
-104          H = localtime() 
-105          V0 = H[3] 
-106          V1 = H[4] 
-107          V2 = np.floor(H[5]) 
-108          V3 = np.ceil(10 * random()) 
-109          Prefix = '/tmp/lp_%s_%s_%s_%s' %(str(V0),str(V1),str(V2),str(V3)) 
-110   
-111          FileInput = '%s_input.lp' %Prefix 
-112          FileOutput = '%s_output.lp' %Prefix 
-113          if (os.path.exists(FileInput) is False and os.path.exists(FileOutput) is False): 
-114              break 
-115   
-116          print 'We failed with FileInput = ', FileInput 
-117   
-118      testfeasibility = WriteLinearProgram(FileInput, iList, jList, sList, Constant, ObjectiveFct) 
-119      if (testfeasibility == 0): 
-120          raise ValueError, 'Feasibility test failed. testfeasibility = 0.' 
-121   
-122      print 'Linear program written in FileOutput=', FileOutput 
-123   
-124      lp_handle = lpsolve('read_lp_file', FileInput) 
-125      result = lpsolve('solve', lp_handle) 
-126      obj, ValueVar, ValueFct, testfeasibility = lpsolve('get_solution', result) 
-127      lpsolve('delete_lp', result) 
-128   
-129      print 'Linear program solved' 
-130   
-131   
-132      return ValueFct, ValueVar, testfeasibility 
-
133   
-
-
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- Generated by Epydoc 3.0.1 on Thu Apr 22 11:29:10 2010 - - http://epydoc.sourceforge.net -
- - - - diff --git a/bathy_smoother/docs/bathy_smoother.bathy_smoothing-module.html b/bathy_smoother/docs/bathy_smoother.bathy_smoothing-module.html deleted file mode 100644 index c2916d3..0000000 --- a/bathy_smoother/docs/bathy_smoother.bathy_smoothing-module.html +++ /dev/null @@ -1,488 +0,0 @@ - - - - - bathy_smoother.bathy_smoothing - - - - - - - - - - - - - - - - - - - - - - -
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- - - - - -
- - Package bathy_smoother :: - Module bathy_smoothing - - - - - - -
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-
- -

Module bathy_smoothing

source code

- - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - -
Functions[hide private]
-
-   - - - - - - -
smoothing_Positive_rx0(MSK, - Hobs, - rx0max)
- This program use the direct iterative method from Martinho and Batteen (2006) -The bathymetry is optimized for a given rx0 factor by increasing it.		 - source code - -
- -
-   - - - - - - -
smoothing_Negative_rx0(MSK, - Hobs, - rx0max)
- This program use an opposite methode to the direct iterative method from -Martinho and Batteen (2006).		 - source code - -
- -
-   - - - - - - -
smoothing_PositiveVolume_rx0(MSK, - Hobs, - rx0max, - AreaMatrix)
- This program use the direct iterative method from Martinho and Batteen (2006) -The bathymetry is optimized for a given rx0 factor by increasing it.		 - source code - -
- -
-   - - - - - - -
smoothing_NegativeVolume_rx0(MSK, - Hobs, - rx0maxi, - AreaMatrix)
- This program use an opposite methode to the direct iterative method from -Martinho and Batteen (2006).		 - source code - -
- -
-   - - - - - - -
smoothing_PlusMinus_rx0(MSK, - Hobs, - rx0max, - AreaMatrix)
- This program use the Mellor-Ezer-Oey method (Mellor et al., 1994).		 - source code - -
- -
-   - - - - - - -
smoothing_Laplacian_rx0(MSK, - Hobs, - rx0max)
- This program use Laplacian filter.		 - source code - -
- -
- - - - - - -
- - - - - -
Function Details[hide private]
-
- -
- -
- - -
-

smoothing_Positive_rx0(MSK, - Hobs, - rx0max) -

- 		source code  -
- - 
-
-This program use the direct iterative method from Martinho and Batteen (2006)
-The bathymetry is optimized for a given rx0 factor by increasing it.
-
-Usage:
-RetBathy = smoothing_Positive_rx0(MSK, Hobs, rx0max)
-
----MSK(eta_rho,xi_rho) is the mask of the grid
-     1 for sea
-     0 for land
----Hobs(eta_rho,xi_rho) is the raw depth of the grid
----rx0max is the target rx0 roughness factor
-
-
-
-
-
-
- -
- -
- - -
-

smoothing_Negative_rx0(MSK, - Hobs, - rx0max) -

- 		source code  -
- - 
-
-This program use an opposite methode to the direct iterative method from 
-Martinho and Batteen (2006). This program optimizes the bathymetry for 
-a given rx0 factor by decreasing it.
-
-Usage:
-RetBathy = smoothing_Negative_rx0(MSK, Hobs, rx0max)
-
----MSK(eta_rho,xi_rho) is the mask of the grid
-     1 for sea
-     0 for land
----Hobs(eta_rho,xi_rho) is the raw depth of the grid
----rx0max is the target rx0 roughness factor
-
-
-
-
-
-
- -
- -
- - -
-

smoothing_PositiveVolume_rx0(MSK, - Hobs, - rx0max, - AreaMatrix) -

- 		source code  -
- - 
-
-This program use the direct iterative method from Martinho and Batteen (2006)
-The bathymetry is optimized for a given rx0 factor by increasing it. All depth 
-are then multiplied by the coeficient K = Vol_init/Vol_final in order to 
-insure volume conservation.
-
-Usage:
-RetBathy = smoothing_Positive_rx0(MSK, Hobs, rx0max, AreaMatrix)
-
----MSK(eta_rho,xi_rho) is the mask of the grid
-     1 for sea
-     0 for land
----Hobs(eta_rho,xi_rho) is the raw depth of the grid
----rx0max is the target rx0 roughness factor
----AreaMatrix(eta_rho,xi_rho) is the matrix of areas at
-   rho point
-
-
-
-
-
-
- -
- -
- - -
-

smoothing_NegativeVolume_rx0(MSK, - Hobs, - rx0maxi, - AreaMatrix) -

- 		source code  -
- - 
-
-This program use an opposite methode to the direct iterative method from 
-Martinho and Batteen (2006). This program optimizes the bathymetry for 
-a given rx0 factor by decreasing it. All depth are then multiplied by 
-the coeficient K = Vol_init/Vol_final in order to insure volume conservation.
-
-Usage:
-RetBathy = smoothing_Negative_rx0(MSK, Hobs, rx0max, AreaMatrix)
-
----MSK(eta_rho,xi_rho) is the mask of the grid
-     1 for sea
-     0 for land
----Hobs(eta_rho,xi_rho) is the raw depth of the grid
----rx0max is the target rx0 roughness factor
----AreaMatrix(eta_rho,xi_rho) is the matrix of areas at
-   rho point
-
-
-
-
-
-
- -
- -
- - -
-

smoothing_PlusMinus_rx0(MSK, - Hobs, - rx0max, - AreaMatrix) -

- 		source code  -
- - 
-
-This program use the Mellor-Ezer-Oey method (Mellor et al., 1994).
-The bathymetry is optimized for a given rx0 factor by doing a sequence
-of increase/decrease at adjacent cells.
-
-Usage:
-RetBathy, HmodifVal, ValueFct = smoothing_PlusMinus_rx0(MSK, Hobs, rx0max, AreaMatrix)
-
----MSK(eta_rho,xi_rho) is the mask of the grid
-     1 for sea
-     0 for land
----Hobs(eta_rho,xi_rho) is the raw depth of the grid
----rx0max is the target rx0 roughness factor
----AreaMatrix(eta_rho,xi_rho) is the matrix of areas at
-   rho-points.
-
-
-
-
-
-
- -
- -
- - -
-

smoothing_Laplacian_rx0(MSK, - Hobs, - rx0max) -

- 		source code  -
- - 
-
-This program use Laplacian filter.
-The bathymetry is optimized for a given rx0 factor by doing an iterated
-sequence of Laplacian filterings.
-
-Usage:
-RetBathy = smoothing_Laplacian_rx0(MSK, Hobs, rx0max)
-
----MSK(eta_rho,xi_rho) is the mask of the grid
-     1 for sea
-     0 for land
----Hobs(eta_rho,xi_rho) is the raw depth of the grid
----rx0max is the target rx0 roughness factor
-
-
-
-
-
-
-
- - - - - - - - - - - - - - - - - -
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- - - - - -
- Generated by Epydoc 3.0.1 on Thu Apr 22 11:29:10 2010 - - http://epydoc.sourceforge.net -
- - - - diff --git a/bathy_smoother/docs/bathy_smoother.bathy_smoothing-pysrc.html b/bathy_smoother/docs/bathy_smoother.bathy_smoothing-pysrc.html deleted file mode 100644 index 418e6a1..0000000 --- a/bathy_smoother/docs/bathy_smoother.bathy_smoothing-pysrc.html +++ /dev/null @@ -1,519 +0,0 @@ - - - - - bathy_smoother.bathy_smoothing - - - - - - - - - - - - - - - - - - - - - - -
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- - - - - -
- - Package bathy_smoother :: - Module bathy_smoothing - - - - - - -
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-
-

Source Code for Module bathy_smoother.bathy_smoothing

-
-  1  import numpy as np 
-  2  from ROMS_bathy_smoother import bathy_tools 
-  3   
-  4   
-
  5 -def smoothing_Positive_rx0(MSK, Hobs, rx0max): 
-
  6      """ 
-  7      This program use the direct iterative method from Martinho and Batteen (2006) 
-  8      The bathymetry is optimized for a given rx0 factor by increasing it. 
-  9   
- 10      Usage: 
- 11      RetBathy = smoothing_Positive_rx0(MSK, Hobs, rx0max) 
- 12   
- 13      ---MSK(eta_rho,xi_rho) is the mask of the grid 
- 14           1 for sea 
- 15           0 for land 
- 16      ---Hobs(eta_rho,xi_rho) is the raw depth of the grid 
- 17      ---rx0max is the target rx0 roughness factor 
- 18      """ 
- 19   
- 20      eta_rho, xi_rho = Hobs.shape 
- 21   
- 22      ListNeigh = np.array([[1, 0], 
- 23                            [0, 1], 
- 24                            [-1, 0], 
- 25                            [0, -1]]) 
- 26   
- 27      RetBathy = Hobs.copy() 
- 28   
- 29      nbModif = 0 
- 30      tol = 0.000001 
- 31   
- 32      while(True): 
- 33          IsFinished = 1 
- 34          for iEta in range(eta_rho): 
- 35              for iXi in range(xi_rho): 
- 36                  if (MSK[iEta,iXi] == 1): 
- 37                      for ineigh in range(4): 
- 38                          iEtaN = iEta + ListNeigh[ineigh,0] 
- 39                          iXiN = iXi + ListNeigh[ineigh,1] 
- 40                          if (iEtaN <= eta_rho-1 and iEtaN >= 0 and iXiN <= xi_rho-1 \ 
- 41                                  and iXiN >= 0 and MSK[iEtaN,iXiN] == 1): 
- 42                              LowerBound = RetBathy[iEtaN,iXiN] * (1-rx0max)/(1+rx0max) 
- 43                              if ((RetBathy[iEta,iXi] - LowerBound) < -tol): 
- 44                                  IsFinished = 0 
- 45                                  RetBathy[iEta,iXi] = LowerBound 
- 46                                  nbModif = nbModif + 1 
- 47   
- 48          if (IsFinished == 1): 
- 49              break 
- 50   
- 51      print '     nbModif=', nbModif 
- 52   
- 53      return RetBathy 
-
 54   
- 55   
- 56   
-
 57 -def smoothing_Negative_rx0(MSK, Hobs, rx0max): 
-
 58      """ 
- 59      This program use an opposite methode to the direct iterative method from  
- 60      Martinho and Batteen (2006). This program optimizes the bathymetry for  
- 61      a given rx0 factor by decreasing it. 
- 62   
- 63      Usage: 
- 64      RetBathy = smoothing_Negative_rx0(MSK, Hobs, rx0max) 
- 65   
- 66      ---MSK(eta_rho,xi_rho) is the mask of the grid 
- 67           1 for sea 
- 68           0 for land 
- 69      ---Hobs(eta_rho,xi_rho) is the raw depth of the grid 
- 70      ---rx0max is the target rx0 roughness factor 
- 71      """ 
- 72   
- 73      eta_rho, xi_rho = Hobs.shape 
- 74   
- 75      ListNeigh = np.array([[1, 0], 
- 76                            [0, 1], 
- 77                            [-1, 0], 
- 78                            [0, -1]]) 
- 79   
- 80      RetBathy = Hobs.copy() 
- 81   
- 82      nbModif = 0 
- 83      tol = 0.000001 
- 84   
- 85      while(True): 
- 86          IsFinished = 1 
- 87          for iEta in range(eta_rho): 
- 88              for iXi in range(xi_rho): 
- 89                  if (MSK[iEta, iXi] == 1): 
- 90                      for ineigh in range(4): 
- 91                          iEtaN = iEta + ListNeigh[ineigh,0] 
- 92                          iXiN = iXi + ListNeigh[ineigh,1] 
- 93                          if (iEtaN <= eta_rho-1 and iEtaN >= 0 and iXiN <= xi_rho-1 \ 
- 94                                  and iXiN >= 0 and MSK[iEtaN,iXiN] == 1): 
- 95                              UpperBound = RetBathy[iEtaN, iXiN] * (1+rx0max)/(1-rx0max) 
- 96                              if (RetBathy[iEta,iXi] > (UpperBound + tol)): 
- 97                                  IsFinished = 0 
- 98                                  RetBathy[iEta, iXi] = UpperBound 
- 99                                  nbModif = nbModif + 1 
-100   
-101          if (IsFinished == 1): 
-102              break 
-103   
-104      print '     nbModif=', nbModif 
-105   
-106      return RetBathy 
-
107   
-108   
-109   
-
110 -def smoothing_PositiveVolume_rx0(MSK, Hobs, rx0max, AreaMatrix): 
-
111      """ 
-112      This program use the direct iterative method from Martinho and Batteen (2006) 
-113      The bathymetry is optimized for a given rx0 factor by increasing it. All depth  
-114      are then multiplied by the coeficient K = Vol_init/Vol_final in order to  
-115      insure volume conservation. 
-116   
-117      Usage: 
-118      RetBathy = smoothing_Positive_rx0(MSK, Hobs, rx0max, AreaMatrix) 
-119   
-120      ---MSK(eta_rho,xi_rho) is the mask of the grid 
-121           1 for sea 
-122           0 for land 
-123      ---Hobs(eta_rho,xi_rho) is the raw depth of the grid 
-124      ---rx0max is the target rx0 roughness factor 
-125      ---AreaMatrix(eta_rho,xi_rho) is the matrix of areas at 
-126         rho point 
-127      """ 
-128   
-129      eta_rho, xi_rho = Hobs.shape 
-130   
-131      ListNeigh = np.array([[1, 0], 
-132                            [0, 1], 
-133                            [-1, 0], 
-134                            [0, -1]]) 
-135   
-136      WorkBathy = Hobs.copy() 
-137   
-138      nbModif = 0 
-139      tol = 0.000001 
-140   
-141      while(True): 
-142          IsFinished = 1 
-143          for iEta in range(eta_rho): 
-144              for iXi in range(xi_rho): 
-145                  if (MSK[iEta, iXi] == 1): 
-146                      for ineigh in range(4): 
-147                          iEtaN = iEta + ListNeigh[ineigh,0] 
-148                          iXiN = iXi + ListNeigh[ineigh,1] 
-149                          if (iEtaN <= eta_rho-1 and iEtaN >= 0 and iXiN <= xi_rho-1 \ 
-150                                  and iXiN >= 0 and MSK[iEtaN,iXiN] == 1): 
-151                              LowerBound = RetBathy[iEtaN, iXiN] * (1-rx0max)/(1+rx0max) 
-152                              if ((WorkBathy[iEta,iXi] - LowerBound) < -tol): 
-153                                  IsFinished = 0 
-154                                  WorkBathy[iEta, iXi] = LowerBound 
-155                                  nbModif = nbModif + 1 
-156   
-157          if (IsFinished == 1): 
-158              break 
-159   
-160      print '     nbModif=', nbModif 
-161   
-162      VolOrig=0 
-163      VolWork=0 
-164      for iEta in range(eta_rho): 
-165          for iXi in range(xi_rho): 
-166              if (MSK[iEta, iXi] == 1): 
-167                  VolOrig = VolOrig + AreaMatrix[iEta,iXi] * Hobs[iEta,iXi] 
-168                  VolWork = VolWork + AreaMatrix[iEta,iXi] * WorkBathy[iEta,iXi] 
-169   
-170      RetBathy = WorkBathy * (VolOrig / VolWork) 
-171   
-172      return RetBathy 
-
173   
-174   
-175   
-
176 -def smoothing_NegativeVolume_rx0(MSK, Hobs, rx0maxi, AreaMatrix): 
-
177      """ 
-178      This program use an opposite methode to the direct iterative method from  
-179      Martinho and Batteen (2006). This program optimizes the bathymetry for  
-180      a given rx0 factor by decreasing it. All depth are then multiplied by  
-181      the coeficient K = Vol_init/Vol_final in order to insure volume conservation. 
-182   
-183      Usage: 
-184      RetBathy = smoothing_Negative_rx0(MSK, Hobs, rx0max, AreaMatrix) 
-185   
-186      ---MSK(eta_rho,xi_rho) is the mask of the grid 
-187           1 for sea 
-188           0 for land 
-189      ---Hobs(eta_rho,xi_rho) is the raw depth of the grid 
-190      ---rx0max is the target rx0 roughness factor 
-191      ---AreaMatrix(eta_rho,xi_rho) is the matrix of areas at 
-192         rho point 
-193      """ 
-194   
-195      eta_rho, xi_rho = Hobs.shape 
-196   
-197      ListNeigh = np.array([[1, 0], 
-198                            [0, 1], 
-199                            [-1, 0], 
-200                            [0, -1]]) 
-201   
-202      WorkBathy = Hobs.copy() 
-203   
-204      nbModif = 0 
-205      tol = 0.000001 
-206   
-207      while(True): 
-208          IsFinished = 1 
-209          for iEta in range(eta_rho): 
-210              for iXi in range(xi_rho): 
-211                  if (MSK[iEta, iXi] == 1): 
-212                      for ineigh in range(4): 
-213                          iEtaN = iEta + ListNeigh[ineigh,0] 
-214                          iXiN = iXi + ListNeigh[ineigh,1] 
-215                          if (iEtaN <= eta_rho-1 and iEtaN >= 0 and iXiN <= xi_rho-1 \ 
-216                                  and iXiN >= 0 and MSK[iEtaN,iXiN] == 1): 
-217                              UpperBound = RetBathy[iEtaN, iXiN] * (1+rx0max)/(1-rx0max) 
-218                              if (WorkBathy[iEta,iXi] > (UpperBound + tol)): 
-219                                  IsFinished = 0 
-220                                  WorkBathy[iEta, iXi] = UpperBound 
-221                                  nbModif = nbModif + 1 
-222   
-223          if (IsFinished == 1): 
-224              break 
-225   
-226      print '     nbModif=', nbModif 
-227   
-228      VolOrig=0 
-229      VolWork=0 
-230      for iEta in range(eta_rho): 
-231          for iXi in range(xi_rho): 
-232              if (MSK[iEta, iXi] == 1): 
-233                  VolOrig = VolOrig + AreaMatrix[iEta,iXi] * Hobs[iEta,iXi] 
-234                  VolWork = VolWork + AreaMatrix[iEta,iXi] * WorkBathy[iEta,iXi] 
-235   
-236      RetBathy = WorkBathy * (VolOrig / VolWork) 
-237   
-238      return RetBathy 
-
239   
-240   
-241   
-
242 -def smoothing_PlusMinus_rx0(MSK, Hobs, rx0max, AreaMatrix): 
-
243      """ 
-244      This program use the Mellor-Ezer-Oey method (Mellor et al., 1994). 
-245      The bathymetry is optimized for a given rx0 factor by doing a sequence 
-246      of increase/decrease at adjacent cells. 
-247   
-248      Usage: 
-249      RetBathy, HmodifVal, ValueFct = smoothing_PlusMinus_rx0(MSK, Hobs, rx0max, AreaMatrix) 
-250   
-251      ---MSK(eta_rho,xi_rho) is the mask of the grid 
-252           1 for sea 
-253           0 for land 
-254      ---Hobs(eta_rho,xi_rho) is the raw depth of the grid 
-255      ---rx0max is the target rx0 roughness factor 
-256      ---AreaMatrix(eta_rho,xi_rho) is the matrix of areas at 
-257         rho-points. 
-258      """ 
-259   
-260      eta_rho, xi_rho = Hobs.shape 
-261   
-262      ListNeigh = np.array([[1, 0], 
-263                            [0, 1], 
-264                            [-1, 0], 
-265                            [0, -1]]) 
-266   
-267      RetBathy = Hobs.copy() 
-268   
-269      HmodifVal = 0 
-270      TheMultiplier = (1 - rx0max) / (1 + rx0max) 
-271      tol = 0.000001 
-272      ValueFct = 0 
-273   
-274      while(True): 
-275          IsFinished = 1 
-276          for iEta in range(eta_rho): 
-277              for iXi in range(xi_rho): 
-278                  if (MSK[iEta, iXi] == 1): 
-279                      Area = AreaMatrix[iEta, iXi] 
-280                      for ineigh in range(4): 
-281                          iEtaN = iEta + ListNeigh[ineigh,0] 
-282                          iXiN = iXi + ListNeigh[ineigh,1] 
-283                          if (iEtaN <= eta_rho-1 and iEtaN >= 0 and iXiN <= xi_rho-1 \ 
-284                              and iXiN >= 0 and MSK[iEtaN,iXiN] == 1): 
-285                              AreaN = AreaMatrix[iEtaN,iXiN] 
-286                              LowerBound = RetBathy[iEtaN,iXiN] * TheMultiplier 
-287                              if ((RetBathy[iEta,iXi] - LowerBound) < -tol): 
-288                                  IsFinished = 0 
-289                                  h = (TheMultiplier * RetBathy[iEtaN,iXiN] - RetBathy[iEta,iXi]) \ 
-290                                           / (AreaN + TheMultiplier * Area) 
-291                                  RetBathy[iEta,iXi] = RetBathy[iEta,iXi] + AreaN * h 
-292                                  RetBathy[iEtaN,iXiN] = RetBathy[iEtaN,iXiN] - Area * h 
-293                                  HmodifVal = HmodifVal + abs(h) 
-294                                  ValueFct = ValueFct + abs(h) * (Area + AreaN) 
-295   
-296          if (IsFinished == 1): 
-297              break 
-298   
-299      H = AreaMatrix * Hobs * MSK 
-300      TheBathymetry1 = H.sum() 
-301      H = AreaMatrix * RetBathy * MSK 
-302      TheBathymetry2 = H.sum() 
-303      DeltaBathymetry = TheBathymetry1 - TheBathymetry2 
-304      print 'DeltaBathymetry = ', DeltaBathymetry 
-305   
-306      return RetBathy, HmodifVal, ValueFct 
-
307   
-308   
-
309 -def smoothing_Laplacian_rx0(MSK, Hobs, rx0max): 
-
310      """ 
-311      This program use Laplacian filter. 
-312      The bathymetry is optimized for a given rx0 factor by doing an iterated 
-313      sequence of Laplacian filterings. 
-314   
-315      Usage: 
-316      RetBathy = smoothing_Laplacian_rx0(MSK, Hobs, rx0max) 
-317   
-318      ---MSK(eta_rho,xi_rho) is the mask of the grid 
-319           1 for sea 
-320           0 for land 
-321      ---Hobs(eta_rho,xi_rho) is the raw depth of the grid 
-322      ---rx0max is the target rx0 roughness factor 
-323      """ 
-324   
-325      eta_rho, xi_rho = Hobs.shape 
-326   
-327      ListNeigh = np.array([[1, 0], 
-328                            [0, 1], 
-329                            [-1, 0], 
-330                            [0, -1]]) 
-331   
-332      RetBathy = Hobs.copy() 
-333   
-334      tol = 0.00001 
-335      WeightMatrix = np.zeros((eta_rho, xi_rho)) 
-336      for iEta in range(eta_rho): 
-337          for iXi in range(xi_rho): 
-338              WeightSum = 0 
-339              for ineigh in range(4): 
-340                  iEtaN = iEta + ListNeigh[ineigh,0] 
-341                  iXiN = iXi + ListNeigh[ineigh,1] 
-342                  if (iEtaN <= eta_rho-1 and iEtaN >= 0 and iXiN <= xi_rho-1 \ 
-343                        and iXiN >= 0 and MSK[iEtaN,iXiN] == 1): 
-344                      WeightSum = WeightSum + 1 
-345   
-346              WeightMatrix[iEta,iXi] = WeightSum 
-347   
-348      Iter = 1 
-349      NumberDones = np.zeros((eta_rho, xi_rho)) 
-350      while(True): 
-351          RoughMat = bathy_tools.RoughnessMatrix(RetBathy, MSK) 
-352          Kbefore = np.where(RoughMat > rx0max) 
-353          nbPtBefore = np.size(Kbefore, 1) 
-354          realR = RoughMat.max() 
-355          TheCorrect = np.zeros((eta_rho,xi_rho)) 
-356          IsFinished = 1 
-357          nbPointMod = 0 
-358          AdditionalDone = np.zeros((eta_rho, xi_rho)) 
-359          for iEta in range(eta_rho): 
-360              for iXi in range(xi_rho):   
-361                  Weight = 0 
-362                  WeightSum = 0 
-363                  for ineigh in range(4): 
-364                      iEtaN = iEta + ListNeigh[ineigh,0] 
-365                      iXiN = iXi + ListNeigh[ineigh,1] 
-366                      if (iEtaN <= eta_rho-1 and iEtaN >= 0 and iXiN <= xi_rho-1 \ 
-367                            and iXiN >= 0 and MSK[iEtaN,iXiN] == 1): 
-368                          Weight = Weight + RetBathy[iEtaN,iXiN] 
-369                          AdditionalDone[iEtaN,iXiN] = AdditionalDone[iEtaN,iXiN] + NumberDones[iEta,iXi] 
-370   
-371                  TheWeight = WeightMatrix[iEta,iXi] 
-372                  WeDo = 0 
-373                  if TheWeight > tol: 
-374                      if RoughMat[iEta,iXi] > rx0max: 
-375                          WeDo = 1 
-376                      if NumberDones[iEta,iXi] > 0: 
-377                          WeDo = 1 
-378   
-379                  if WeDo == 1: 
-380                      IsFinished = 0 
-381                      TheDelta = (Weight - TheWeight * RetBathy[iEta,iXi]) / (2 * TheWeight) 
-382                      TheCorrect[iEta,iXi] = TheCorrect[iEta,iXi] + TheDelta 
-383                      nbPointMod = nbPointMod + 1 
-384                      NumberDones[iEta,iXi] = 1 
-385   
-386          NumberDones = NumberDones + AdditionalDone 
-387          RetBathy = RetBathy + TheCorrect 
-388          NewRoughMat = bathy_tools.RoughnessMatrix(RetBathy, MSK) 
-389          Kafter = np.where(NewRoughMat > rx0max) 
-390          nbPtAfter = np.size(Kafter, 1) 
-391          TheProd = (RoughMat > rx0max) * (NewRoughMat > rx0max) 
-392          nbPtInt = TheProd.sum() 
-393          if (nbPtInt == nbPtAfter and nbPtBefore == nbPtAfter): 
-394              eStr=' no erase' 
-395          else: 
-396              eStr=''; 
-397              NumberDones = np.zeros((eta_rho, xi_rho)) 
-398   
-399          print 'Iteration #', Iter 
-400          print 'current r=', realR, '  nbPointMod=', nbPointMod, eStr 
-401          print ' ' 
-402   
-403          Iter = Iter + 1 
-404   
-405          if (IsFinished == 1): 
-406              break 
-407    
-408      return RetBathy 
-
409   
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Module bathy_tools

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Functions[hide private]
-
-   - - - - - - -
RoughnessMatrix(DEP, - MSK)
- RoughMat=GRID_RoughnessMatrix(DEP, MSK)		 - source code - -
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RoughnessMatrix(DEP, - MSK) -

- 		source code  -
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RoughMat=GRID_RoughnessMatrix(DEP, MSK)

-

---DEP is the bathymetry of the grid ---MSK is the mask of the - grid

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Source Code for Module bathy_smoother.bathy_tools

-
- 1  import numpy as np 
- 2   
- 3   
-
 4 -def RoughnessMatrix(DEP, MSK): 
-
 5      """ 
- 6      RoughMat=GRID_RoughnessMatrix(DEP, MSK) 
- 7   
- 8      ---DEP is the bathymetry of the grid 
- 9      ---MSK is the mask of the grid 
-10      """ 
-11   
-12      eta_rho, xi_rho = DEP.shape 
-13   
-14      Umat = np.array([[0, 1], 
-15                      [1, 0], 
-16                      [0, -1], 
-17                      [-1, 0]]) 
-18   
-19      RoughMat = np.zeros(DEP.shape) 
-20   
-21      for iEta in range(1,eta_rho-1): 
-22          for iXi in range(1,xi_rho-1): 
-23              if (MSK[iEta,iXi] == 1): 
-24                  rough = 0 
-25                  for i in range(4): 
-26                      iEtaB = iEta + Umat[i,0] 
-27                      iXiB = iXi + Umat[i,1] 
-28                      if (MSK[iEtaB,iXiB] == 1): 
-29                          dep1 = DEP[iEta,iXi] 
-30                          dep2 = DEP[iEtaB,iXiB] 
-31                          delta = abs((dep1 - dep2) / (dep1 + dep2)) 
-32                          rough = np.maximum(rough, delta) 
-33   
-34                  RoughMat[iEta,iXi] = rough 
-35   
-36   
-37      return RoughMat 
-
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The page title may be followed by a link to the - * corresponding source code (using 'span.codelink'). - * - The footer consists of a navigation bar, a timestamp, and a - * pointer to epydoc's homepage. - */ -h1.epydoc { margin: 0; font-size: +140%; font-weight: bold; } -h2.epydoc { font-size: +130%; font-weight: bold; } -h3.epydoc { font-size: +115%; font-weight: bold; - margin-top: 0.2em; } -td h3.epydoc { font-size: +115%; font-weight: bold; - margin-bottom: 0; } -table.navbar { background: #a0c0ff; color: #000000; - border: 2px groove #c0d0d0; } -table.navbar table { color: #000000; } -th.navbar-select { background: #70b0ff; - color: #000000; } -table.navbar a { text-decoration: none; } -table.navbar a:link { color: #0000ff; } -table.navbar a:visited { color: #204080; } -span.breadcrumbs { font-size: 85%; font-weight: bold; } -span.options { font-size: 70%; } -span.codelink { font-size: 85%; } -td.footer { font-size: 85%; } - -/* Table Headers - * - Each summary table and details section begins with a 'header' - * row. This row contains a section title (marked by - * 'span.table-header') as well as a show/hide private link - * (marked by 'span.options', defined above). - * - Summary tables that contain user-defined groups mark those - * groups using 'group header' rows. - */ -td.table-header { background: #70b0ff; color: #000000; - border: 1px solid #608090; } -td.table-header table { color: #000000; } -td.table-header table a:link { color: #0000ff; } -td.table-header table a:visited { color: #204080; } -span.table-header { font-size: 120%; font-weight: bold; } -th.group-header { background: #c0e0f8; color: #000000; - text-align: left; font-style: italic; - font-size: 115%; - border: 1px solid #608090; } - -/* Summary Tables (functions, variables, etc) - * - Each object is described by a single row of the table with - * two cells. The left cell gives the object's type, and is - * marked with 'code.summary-type'. 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The width of this box is - * restricted to 80 chars; if the value's repr is longer than - * this it will be wrapped, using a backslash marked with - * class 'variable-linewrap'. 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Store - // their old text in "cmd," so we will know what action to - // take; and change their text to the opposite action. - var cmd = "?"; - var elts = document.getElementsByTagName("a"); - for(var i=0; i...
"; - elt.innerHTML = s; - } -} - -function toggle(id) { - elt = document.getElementById(id+"-toggle"); - if (elt.innerHTML == "-") - collapse(id); - else - expand(id); - return false; -} - -function highlight(id) { - var elt = document.getElementById(id+"-def"); - if (elt) elt.className = "py-highlight-hdr"; - var elt = document.getElementById(id+"-expanded"); - if (elt) elt.className = "py-highlight"; - var elt = document.getElementById(id+"-collapsed"); - if (elt) elt.className = "py-highlight"; -} - -function num_lines(s) { - var n = 1; - var pos = s.indexOf("\n"); - while ( pos > 0) { - n += 1; - pos = s.indexOf("\n", pos+1); - } - return n; -} - -// Collapse all blocks that mave more than `min_lines` lines. -function collapse_all(min_lines) { - var elts = document.getElementsByTagName("div"); - for (var i=0; i 0) - if (elt.id.substring(split, elt.id.length) == "-expanded") - if (num_lines(elt.innerHTML) > min_lines) - collapse(elt.id.substring(0, split)); - } -} - -function expandto(href) { - var start = href.indexOf("#")+1; - if (start != 0 && start != href.length) { - if (href.substring(start, href.length) != "-") { - collapse_all(4); - pos = href.indexOf(".", start); - while (pos != -1) { - var id = href.substring(start, pos); - expand(id); - pos = href.indexOf(".", pos+1); - } - var id = href.substring(start, href.length); - expand(id); - highlight(id); - } - } -} - -function kill_doclink(id) { - var parent = document.getElementById(id); - parent.removeChild(parent.childNodes.item(0)); -} -function auto_kill_doclink(ev) { - if (!ev) var ev = window.event; - if (!this.contains(ev.toElement)) { - var parent = document.getElementById(this.parentID); - parent.removeChild(parent.childNodes.item(0)); - } -} - -function doclink(id, name, targets_id) { - var elt = document.getElementById(id); - - // If we already opened the box, then destroy it. - // (This case should never occur, but leave it in just in case.) - if (elt.childNodes.length > 1) { - elt.removeChild(elt.childNodes.item(0)); - } - else { - // The outer box: relative + inline positioning. - var box1 = document.createElement("div"); - box1.style.position = "relative"; - box1.style.display = "inline"; - box1.style.top = 0; - box1.style.left = 0; - - // A shadow for fun - var shadow = document.createElement("div"); - shadow.style.position = "absolute"; - shadow.style.left = "-1.3em"; - shadow.style.top = "-1.3em"; - shadow.style.background = "#404040"; - - // The inner box: absolute positioning. - var box2 = document.createElement("div"); - box2.style.position = "relative"; - box2.style.border = "1px solid #a0a0a0"; - box2.style.left = "-.2em"; - box2.style.top = "-.2em"; - box2.style.background = "white"; - box2.style.padding = ".3em .4em .3em .4em"; - box2.style.fontStyle = "normal"; - box2.onmouseout=auto_kill_doclink; - box2.parentID = id; - - // Get the targets - var targets_elt = document.getElementById(targets_id); - var targets = targets_elt.getAttribute("targets"); - var links = ""; - target_list = targets.split(","); - for (var i=0; i" + - target[0] + ""; - } - - // Put it all together. - elt.insertBefore(box1, elt.childNodes.item(0)); - //box1.appendChild(box2); - box1.appendChild(shadow); - shadow.appendChild(box2); - box2.innerHTML = - "Which "+name+" do you want to see documentation for?" + - ""; - } - return false; -} - -function get_anchor() { - var href = location.href; - var start = href.indexOf("#")+1; - if ((start != 0) && (start != href.length)) - return href.substring(start, href.length); - } -function redirect_url(dottedName) { - // Scan through each element of the "pages" list, and check - // if "name" matches with any of them. - for (var i=0; i-m" or "-c"; - // extract the portion & compare it to dottedName. - var pagename = pages[i].substring(0, pages[i].length-2); - if (pagename == dottedName.substring(0,pagename.length)) { - - // We've found a page that matches `dottedName`; - // construct its URL, using leftover `dottedName` - // content to form an anchor. - var pagetype = pages[i].charAt(pages[i].length-1); - var url = pagename + ((pagetype=="m")?"-module.html": - "-class.html"); - if (dottedName.length > pagename.length) - url += "#" + dottedName.substring(pagename.length+1, - dottedName.length); - return url; - } - } - } diff --git a/bathy_smoother/docs/frames.html b/bathy_smoother/docs/frames.html deleted file mode 100644 index e2d082b..0000000 --- a/bathy_smoother/docs/frames.html +++ /dev/null @@ -1,17 +0,0 @@ - - - - - API Documentation - - - - - - - - - diff --git a/bathy_smoother/docs/help.html b/bathy_smoother/docs/help.html deleted file mode 100644 index 27fd225..0000000 --- a/bathy_smoother/docs/help.html +++ /dev/null @@ -1,268 +0,0 @@ - - - - - Help - - - - - - - - - - - - - - - - - - - - - - -
   Home      Trees      Indices      Help   
- - - - - -
  - - - - -
[hide private]
[frames] | no frames]
-
- -

API Documentation

- -

This document contains the API (Application Programming Interface) -documentation for this project. Documentation for the Python -objects defined by the project is divided into separate pages for each -package, module, and class. The API documentation also includes two -pages containing information about the project as a whole: a trees -page, and an index page.

- -

Object Documentation

- -

Each Package Documentation page contains:

-
    -
  • A description of the package.
    • -
  • A list of the modules and sub-packages contained by the - package.
    • -
  • A summary of the classes defined by the package.
    • -
  • A summary of the functions defined by the package.
    • -
  • A summary of the variables defined by the package.
    • -
  • A detailed description of each function defined by the - package.
    • -
  • A detailed description of each variable defined by the - package.
    • -
- -

Each Module Documentation page contains:

-
    -
  • A description of the module.
    • -
  • A summary of the classes defined by the module.
    • -
  • A summary of the functions defined by the module.
    • -
  • A summary of the variables defined by the module.
    • -
  • A detailed description of each function defined by the - module.
    • -
  • A detailed description of each variable defined by the - module.
    • -
- -

Each Class Documentation page contains:

-
    -
  • A class inheritance diagram.
    • -
  • A list of known subclasses.
    • -
  • A description of the class.
    • -
  • A summary of the methods defined by the class.
    • -
  • A summary of the instance variables defined by the class.
    • -
  • A summary of the class (static) variables defined by the - class.
    • -
  • A detailed description of each method defined by the - class.
    • -
  • A detailed description of each instance variable defined by the - class.
    • -
  • A detailed description of each class (static) variable defined - by the class.
    • -
- -

Project Documentation

- -

The Trees page contains the module and class hierarchies:

-
    -
  • The module hierarchy lists every package and module, with - modules grouped into packages. At the top level, and within each - package, modules and sub-packages are listed alphabetically.
    • -
  • The class hierarchy lists every class, grouped by base - class. If a class has more than one base class, then it will be - listed under each base class. At the top level, and under each base - class, classes are listed alphabetically.
    • -
- -

The Index page contains indices of terms and - identifiers:

-
    -
  • The term index lists every term indexed by any object's - documentation. For each term, the index provides links to each - place where the term is indexed.
    • -
  • The identifier index lists the (short) name of every package, - module, class, method, function, variable, and parameter. For each - identifier, the index provides a short description, and a link to - its documentation.
    • -
- -

The Table of Contents

- -

The table of contents occupies the two frames on the left side of -the window. The upper-left frame displays the project -contents, and the lower-left frame displays the module -contents:

- - - - - - - - - -
- Project
Contents
...		 - API
Documentation
Frame


-
- Module
Contents
 
...
  -

- -

The project contents frame contains a list of all packages -and modules that are defined by the project. Clicking on an entry -will display its contents in the module contents frame. Clicking on a -special entry, labeled "Everything," will display the contents of -the entire project.

- -

The module contents frame contains a list of every -submodule, class, type, exception, function, and variable defined by a -module or package. Clicking on an entry will display its -documentation in the API documentation frame. Clicking on the name of -the module, at the top of the frame, will display the documentation -for the module itself.

- -

The "frames" and "no frames" buttons below the top -navigation bar can be used to control whether the table of contents is -displayed or not.

- -

The Navigation Bar

- -

A navigation bar is located at the top and bottom of every page. -It indicates what type of page you are currently viewing, and allows -you to go to related pages. The following table describes the labels -on the navigation bar. Note that not some labels (such as -[Parent]) are not displayed on all pages.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -
LabelHighlighted when...Links to...
[Parent](never highlighted) the parent of the current package
[Package]viewing a packagethe package containing the current object -
[Module]viewing a modulethe module containing the current object -
[Class]viewing a class the class containing the current object
[Trees]viewing the trees page the trees page
[Index]viewing the index page the index page
[Help]viewing the help page the help page
- -

The "show private" and "hide private" buttons below -the top navigation bar can be used to control whether documentation -for private objects is displayed. Private objects are usually defined -as objects whose (short) names begin with a single underscore, but do -not end with an underscore. For example, "_x", -"__pprint", and "epydoc.epytext._tokenize" -are private objects; but "re.sub", -"__init__", and "type_" are not. However, -if a module defines the "__all__" variable, then its -contents are used to decide which objects are private.

- -

A timestamp below the bottom navigation bar indicates when each -page was last updated.

- - - - - - - - - - - - - - - - - -
   Home      Trees      Indices      Help   
- - - - - -
- Generated by Epydoc 3.0.1 on Thu Apr 22 11:29:10 2010 - - http://epydoc.sourceforge.net -
- - - - diff --git a/bathy_smoother/docs/identifier-index.html b/bathy_smoother/docs/identifier-index.html deleted file mode 100644 index cf1afac..0000000 --- a/bathy_smoother/docs/identifier-index.html +++ /dev/null @@ -1,666 +0,0 @@ - - - - - Identifier Index - - - - - - - - - - - - - - - - - - - - - - -
   Home      Trees      Indices      Help   
- - - - - -
  - - - - -
[hide private]
[frames] | no frames]
-
- -
-

Identifier Index

-		 -[ - A - B - C - D - E - F - G - H - I - J - K - L - M - N - O - P - Q - R - S - T - U - V - W - X - Y - Z - _ -] -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

A

 - - - - - - - - - - - - - - - - - - - - - -
ANTIDEGEN_BOUNDFLIP
-(in bathy_smoother.LP_tools)		ANTIDEGEN_FIXEDVARS
-(in bathy_smoother.LP_tools)		ANTIDEGEN_NUMFAILURE
-(in bathy_smoother.LP_tools)
ANTIDEGEN_COLUMNCHECK
-(in bathy_smoother.LP_tools)		ANTIDEGEN_INFEASIBLE
-(in bathy_smoother.LP_tools)		ANTIDEGEN_RHSPERTURB
-(in bathy_smoother.LP_tools)
ANTIDEGEN_DURINGBB
-(in bathy_smoother.LP_tools)		ANTIDEGEN_LOSTFEAS
-(in bathy_smoother.LP_tools)		ANTIDEGEN_STALLING
-(in bathy_smoother.LP_tools)
ANTIDEGEN_DYNAMIC
-(in bathy_smoother.LP_tools)		ANTIDEGEN_NONE
-(in bathy_smoother.LP_tools)		 
-

B

 - - - - - - - - - - - -
bathy_smootherbathy_tools
-(in bathy_smoother)		BRANCH_CEILING
-(in bathy_smoother.LP_tools)
bathy_smoothing
-(in bathy_smoother)		BRANCH_AUTOMATIC
-(in bathy_smoother.LP_tools)		BRANCH_FLOOR
-(in bathy_smoother.LP_tools)
-

C

 - - - - - - - - - - - -
ConnectedComponent()
-(in bathy_smoother.LP_bathy_tools)		CRASH_MOSTFEASIBLE
-(in bathy_smoother.LP_tools)		CRITICAL
-(in bathy_smoother.LP_tools)
CRASH_LEASTDEGENERATE
-(in bathy_smoother.LP_tools)		CRASH_NONE
-(in bathy_smoother.LP_tools)		 
-

D

 - - - - - - - -
DEGENERATE
-(in bathy_smoother.LP_tools)		DETAILED
-(in bathy_smoother.LP_tools)		 
   
-

E

 - - - - - - - -
EQ
-(in bathy_smoother.LP_tools)		  
   
-

F

 - - - - - - - -
FEASFOUND
-(in bathy_smoother.LP_tools)		FR
-(in bathy_smoother.LP_tools)		FULL
-(in bathy_smoother.LP_tools)
   
-

G

 - - - - - - - - - - - -
GE
-(in bathy_smoother.LP_tools)		GetIJS_maxamp()
-(in bathy_smoother.LP_bathy_tools)		GetIJS_signs()
-(in bathy_smoother.LP_bathy_tools)
GetBadPoints()
-(in bathy_smoother.LP_bathy_tools)		GetIJS_rx0()
-(in bathy_smoother.LP_bathy_tools)		 
-

I

 - - - - - - - - - - - - - - - - -
IMPORTANT
-(in bathy_smoother.LP_tools)		IMPROVE_NONE
-(in bathy_smoother.LP_tools)		INFEASIBLE
-(in bathy_smoother.LP_tools)
IMPROVE_BBSIMPLEX
-(in bathy_smoother.LP_tools)		IMPROVE_SOLUTION
-(in bathy_smoother.LP_tools)		Infinite
-(in bathy_smoother.LP_tools)
IMPROVE_DUALFEAS
-(in bathy_smoother.LP_tools)		IMPROVE_THETAGAP
-(in bathy_smoother.LP_tools)		 
-

L

 - - - - - - - - - - - -
LE
-(in bathy_smoother.LP_tools)		LP_bathy_tools
-(in bathy_smoother)		LP_smoothing_rx0_heuristic()
-(in bathy_smoother.LP_bathy_smoothing)
LP_bathy_smoothing
-(in bathy_smoother)		LP_smoothing_rx0()
-(in bathy_smoother.LP_bathy_smoothing)		LP_tools
-(in bathy_smoother)
-

M

 - - - - - - - - - - - - - - - - -
MergeIJS_listings()
-(in bathy_smoother.LP_bathy_tools)		MSG_MILPBETTER
-(in bathy_smoother.LP_tools)		MSG_PRESOLVE
-(in bathy_smoother.LP_tools)
MSG_LPFEASIBLE
-(in bathy_smoother.LP_tools)		MSG_MILPEQUAL
-(in bathy_smoother.LP_tools)		 
MSG_LPOPTIMAL
-(in bathy_smoother.LP_tools)		MSG_MILPFEASIBLE
-(in bathy_smoother.LP_tools)		 
-

N

 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Neighborhood()
-(in bathy_smoother.LP_bathy_tools)		NODE_GAPSELECT
-(in bathy_smoother.LP_tools)		NODE_RCOSTFIXING
-(in bathy_smoother.LP_tools)
NEUTRAL
-(in bathy_smoother.LP_tools)		NODE_GREEDYMODE
-(in bathy_smoother.LP_tools)		NODE_RESTARTMODE
-(in bathy_smoother.LP_tools)
NODE_AUTOORDER
-(in bathy_smoother.LP_tools)		NODE_GUBMODE
-(in bathy_smoother.LP_tools)		NODE_STRONGINIT
-(in bathy_smoother.LP_tools)
NODE_BRANCHREVERSEMODE
-(in bathy_smoother.LP_tools)		NODE_PSEUDOCOSTMODE
-(in bathy_smoother.LP_tools)		NODE_USERSELECT
-(in bathy_smoother.LP_tools)
NODE_BREADTHFIRSTMODE
-(in bathy_smoother.LP_tools)		NODE_PSEUDOCOSTSELECT
-(in bathy_smoother.LP_tools)		NODE_WEIGHTREVERSEMODE
-(in bathy_smoother.LP_tools)
NODE_DEPTHFIRSTMODE
-(in bathy_smoother.LP_tools)		NODE_PSEUDONONINTSELECT
-(in bathy_smoother.LP_tools)		NOFEASFOUND
-(in bathy_smoother.LP_tools)
NODE_DYNAMICMODE
-(in bathy_smoother.LP_tools)		NODE_PSEUDORATIOSELECT
-(in bathy_smoother.LP_tools)		NOMEMORY
-(in bathy_smoother.LP_tools)
NODE_FIRSTSELECT
-(in bathy_smoother.LP_tools)		NODE_RANDOMIZEMODE
-(in bathy_smoother.LP_tools)		NORMAL
-(in bathy_smoother.LP_tools)
NODE_FRACTIONSELECT
-(in bathy_smoother.LP_tools)		NODE_RANGESELECT
-(in bathy_smoother.LP_tools)		NUMFAILURE
-(in bathy_smoother.LP_tools)
-

O

 - - - - - - - -
OPTIMAL
-(in bathy_smoother.LP_tools)		  
   
-

P

 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
PRESOLVE_BOUNDS
-(in bathy_smoother.LP_tools)		PRESOLVE_PROBEFIX
-(in bathy_smoother.LP_tools)		PRICE_LOOPLEFT
-(in bathy_smoother.LP_tools)
PRESOLVE_COLDOMINATE
-(in bathy_smoother.LP_tools)		PRESOLVE_PROBEREDUCE
-(in bathy_smoother.LP_tools)		PRICE_MULTIPLE
-(in bathy_smoother.LP_tools)
PRESOLVE_COLFIXDUAL
-(in bathy_smoother.LP_tools)		PRESOLVE_REDUCEGCD
-(in bathy_smoother.LP_tools)		PRICE_PARTIAL
-(in bathy_smoother.LP_tools)
PRESOLVE_COLS
-(in bathy_smoother.LP_tools)		PRESOLVE_REDUCEMIP
-(in bathy_smoother.LP_tools)		PRICE_PRIMALFALLBACK
-(in bathy_smoother.LP_tools)
PRESOLVE_DUALS
-(in bathy_smoother.LP_tools)		PRESOLVE_ROWDOMINATE
-(in bathy_smoother.LP_tools)		PRICE_RANDOMIZE
-(in bathy_smoother.LP_tools)
PRESOLVE_ELIMEQ2
-(in bathy_smoother.LP_tools)		PRESOLVE_ROWS
-(in bathy_smoother.LP_tools)		PRICE_TRUENORMINIT
-(in bathy_smoother.LP_tools)
PRESOLVE_IMPLIEDFREE
-(in bathy_smoother.LP_tools)		PRESOLVE_SENSDUALS
-(in bathy_smoother.LP_tools)		PRICER_DANTZIG
-(in bathy_smoother.LP_tools)
PRESOLVE_IMPLIEDSLK
-(in bathy_smoother.LP_tools)		PRESOLVE_SOS
-(in bathy_smoother.LP_tools)		PRICER_DEVEX
-(in bathy_smoother.LP_tools)
PRESOLVE_KNAPSACK
-(in bathy_smoother.LP_tools)		PRICE_ADAPTIVE
-(in bathy_smoother.LP_tools)		PRICER_FIRSTINDEX
-(in bathy_smoother.LP_tools)
PRESOLVE_LINDEP
-(in bathy_smoother.LP_tools)		PRICE_AUTOPARTIAL
-(in bathy_smoother.LP_tools)		PRICER_STEEPESTEDGE
-(in bathy_smoother.LP_tools)
PRESOLVE_MERGEROWS
-(in bathy_smoother.LP_tools)		PRICE_HARRISTWOPASS
-(in bathy_smoother.LP_tools)		PROCBREAK
-(in bathy_smoother.LP_tools)
PRESOLVE_NONE
-(in bathy_smoother.LP_tools)		PRICE_LOOPALTERNATE
-(in bathy_smoother.LP_tools)		PROCFAIL
-(in bathy_smoother.LP_tools)
-

R

 - - - - - - - -
RoughnessMatrix()
-(in bathy_smoother.bathy_tools)		  
   
-

S

 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
SCALE_COLSONLY
-(in bathy_smoother.LP_tools)		SCALE_POWER2
-(in bathy_smoother.LP_tools)		smoothing_Laplacian_rx0()
-(in bathy_smoother.bathy_smoothing)
SCALE_CURTISREID
-(in bathy_smoother.LP_tools)		SCALE_QUADRATIC
-(in bathy_smoother.LP_tools)		smoothing_Negative_rx0()
-(in bathy_smoother.bathy_smoothing)
SCALE_DYNUPDATE
-(in bathy_smoother.LP_tools)		SCALE_RANGE
-(in bathy_smoother.LP_tools)		smoothing_NegativeVolume_rx0()
-(in bathy_smoother.bathy_smoothing)
SCALE_EQUILIBRATE
-(in bathy_smoother.LP_tools)		SCALE_ROWSONLY
-(in bathy_smoother.LP_tools)		smoothing_PlusMinus_rx0()
-(in bathy_smoother.bathy_smoothing)
SCALE_EXTREME
-(in bathy_smoother.LP_tools)		SCALE_USERWEIGHT
-(in bathy_smoother.LP_tools)		smoothing_Positive_rx0()
-(in bathy_smoother.bathy_smoothing)
SCALE_GEOMETRIC
-(in bathy_smoother.LP_tools)		SEVERE
-(in bathy_smoother.LP_tools)		smoothing_PositiveVolume_rx0()
-(in bathy_smoother.bathy_smoothing)
SCALE_INTEGERS
-(in bathy_smoother.LP_tools)		SIMPLEX_DUAL_DUAL
-(in bathy_smoother.LP_tools)		SolveLinearProgram()
-(in bathy_smoother.LP_tools)
SCALE_LOGARITHMIC
-(in bathy_smoother.LP_tools)		SIMPLEX_DUAL_PRIMAL
-(in bathy_smoother.LP_tools)		SUBOPTIMAL
-(in bathy_smoother.LP_tools)
SCALE_MEAN
-(in bathy_smoother.LP_tools)		SIMPLEX_PRIMAL_DUAL
-(in bathy_smoother.LP_tools)		 
SCALE_NONE
-(in bathy_smoother.LP_tools)		SIMPLEX_PRIMAL_PRIMAL
-(in bathy_smoother.LP_tools)		 
-

T

 - - - - - - - -
TIMEOUT
-(in bathy_smoother.LP_tools)		  
   
-

U

 - - - - - - - -
UNBOUNDED
-(in bathy_smoother.LP_tools)		USERABORT
-(in bathy_smoother.LP_tools)		 
   
-

W

 - - - - - - - -
WriteLinearProgram()
-(in bathy_smoother.LP_tools)		  
   
-
-

- - - - - - - - - - - - - - - - -
   Home      Trees      Indices      Help   
- - - - - -
- Generated by Epydoc 3.0.1 on Thu Apr 22 11:29:10 2010 - - http://epydoc.sourceforge.net -
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   Home      Trees      Indices      Help   
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Module Hierarchy

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- - - - - -
- Generated by Epydoc 3.0.1 on Thu Apr 22 11:29:10 2010 - - http://epydoc.sourceforge.net -
- - - - diff --git a/bathy_smoother/docs/redirect.html b/bathy_smoother/docs/redirect.html deleted file mode 100644 index e39aca5..0000000 --- a/bathy_smoother/docs/redirect.html +++ /dev/null @@ -1,38 +0,0 @@ -Epydoc Redirect Page - - - - - - - - -

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- - - - - diff --git a/bathy_smoother/docs/toc-bathy_smoother-module.html b/bathy_smoother/docs/toc-bathy_smoother-module.html deleted file mode 100644 index c3977c6..0000000 --- a/bathy_smoother/docs/toc-bathy_smoother-module.html +++ /dev/null @@ -1,29 +0,0 @@ - - - - - bathy_smoother - - - - - -

Module bathy_smoother

-
-
-[hide private] - - - - diff --git a/bathy_smoother/docs/toc-bathy_smoother.LP_bathy_smoothing-module.html b/bathy_smoother/docs/toc-bathy_smoother.LP_bathy_smoothing-module.html deleted file mode 100644 index f585bf5..0000000 --- a/bathy_smoother/docs/toc-bathy_smoother.LP_bathy_smoothing-module.html +++ /dev/null @@ -1,32 +0,0 @@ - - - - - LP_bathy_smoothing - - - - - -

Module LP_bathy_smoothing

-
-

Functions

- LP_smoothing_rx0
LP_smoothing_rx0_heuristic
-[hide private] - - - - diff --git a/bathy_smoother/docs/toc-bathy_smoother.LP_bathy_tools-module.html b/bathy_smoother/docs/toc-bathy_smoother.LP_bathy_tools-module.html deleted file mode 100644 index 1762839..0000000 --- a/bathy_smoother/docs/toc-bathy_smoother.LP_bathy_tools-module.html +++ /dev/null @@ -1,37 +0,0 @@ - - - - - LP_bathy_tools - - - - - -

Module LP_bathy_tools

-
-

Functions

- ConnectedComponent
GetBadPoints
GetIJS_maxamp
GetIJS_rx0
GetIJS_signs
MergeIJS_listings
Neighborhood
-[hide private] - - - - diff --git a/bathy_smoother/docs/toc-bathy_smoother.LP_tools-module.html b/bathy_smoother/docs/toc-bathy_smoother.LP_tools-module.html deleted file mode 100644 index 558e180..0000000 --- a/bathy_smoother/docs/toc-bathy_smoother.LP_tools-module.html +++ /dev/null @@ -1,160 +0,0 @@ - - - - - LP_tools - - - - - -

Module LP_tools

-
-

Functions

- SolveLinearProgram
WriteLinearProgram

Variables

- ANTIDEGEN_BOUNDFLIP
ANTIDEGEN_COLUMNCHECK
ANTIDEGEN_DURINGBB
ANTIDEGEN_DYNAMIC
ANTIDEGEN_FIXEDVARS
ANTIDEGEN_INFEASIBLE
ANTIDEGEN_LOSTFEAS
ANTIDEGEN_NONE
ANTIDEGEN_NUMFAILURE
ANTIDEGEN_RHSPERTURB
ANTIDEGEN_STALLING
BRANCH_AUTOMATIC
BRANCH_CEILING
BRANCH_FLOOR
CRASH_LEASTDEGENERATE
CRASH_MOSTFEASIBLE
CRASH_NONE
CRITICAL
DEGENERATE
DETAILED
EQ
FEASFOUND
FR
FULL
GE
IMPORTANT
IMPROVE_BBSIMPLEX
IMPROVE_DUALFEAS
IMPROVE_NONE
IMPROVE_SOLUTION
IMPROVE_THETAGAP
INFEASIBLE
Infinite
LE
MSG_LPFEASIBLE
MSG_LPOPTIMAL
MSG_MILPBETTER
MSG_MILPEQUAL
MSG_MILPFEASIBLE
MSG_PRESOLVE
NEUTRAL
NODE_AUTOORDER
NODE_BRANCHREVERSEMODE
NODE_BREADTHFIRSTMODE
NODE_DEPTHFIRSTMODE
NODE_DYNAMICMODE
NODE_FIRSTSELECT
NODE_FRACTIONSELECT
NODE_GAPSELECT
NODE_GREEDYMODE
NODE_GUBMODE
NODE_PSEUDOCOSTMODE
NODE_PSEUDOCOSTSELECT
NODE_PSEUDONONINTSELECT
NODE_PSEUDORATIOSELECT
NODE_RANDOMIZEMODE
NODE_RANGESELECT
NODE_RCOSTFIXING
NODE_RESTARTMODE
NODE_STRONGINIT
NODE_USERSELECT
NODE_WEIGHTREVERSEMODE
NOFEASFOUND
NOMEMORY
NORMAL
NUMFAILURE
OPTIMAL
PRESOLVE_BOUNDS
PRESOLVE_COLDOMINATE
PRESOLVE_COLFIXDUAL
PRESOLVE_COLS
PRESOLVE_DUALS
PRESOLVE_ELIMEQ2
PRESOLVE_IMPLIEDFREE
PRESOLVE_IMPLIEDSLK
PRESOLVE_KNAPSACK
PRESOLVE_LINDEP
PRESOLVE_MERGEROWS
PRESOLVE_NONE
PRESOLVE_PROBEFIX
PRESOLVE_PROBEREDUCE
PRESOLVE_REDUCEGCD
PRESOLVE_REDUCEMIP
PRESOLVE_ROWDOMINATE
PRESOLVE_ROWS
PRESOLVE_SENSDUALS
PRESOLVE_SOS
PRICER_DANTZIG
PRICER_DEVEX
PRICER_FIRSTINDEX
PRICER_STEEPESTEDGE
PRICE_ADAPTIVE
PRICE_AUTOPARTIAL
PRICE_HARRISTWOPASS
PRICE_LOOPALTERNATE
PRICE_LOOPLEFT
PRICE_MULTIPLE
PRICE_PARTIAL
PRICE_PRIMALFALLBACK
PRICE_RANDOMIZE
PRICE_TRUENORMINIT
PROCBREAK
PROCFAIL
SCALE_COLSONLY
SCALE_CURTISREID
SCALE_DYNUPDATE
SCALE_EQUILIBRATE
SCALE_EXTREME
SCALE_GEOMETRIC
SCALE_INTEGERS
SCALE_LOGARITHMIC
SCALE_MEAN
SCALE_NONE
SCALE_POWER2
SCALE_QUADRATIC
SCALE_RANGE
SCALE_ROWSONLY
SCALE_USERWEIGHT
SEVERE
SIMPLEX_DUAL_DUAL
SIMPLEX_DUAL_PRIMAL
SIMPLEX_PRIMAL_DUAL
SIMPLEX_PRIMAL_PRIMAL
SUBOPTIMAL
TIMEOUT
UNBOUNDED
USERABORT
-[hide private] - - - - diff --git a/bathy_smoother/docs/toc-bathy_smoother.bathy_smoothing-module.html b/bathy_smoother/docs/toc-bathy_smoother.bathy_smoothing-module.html deleted file mode 100644 index 5f38659..0000000 --- a/bathy_smoother/docs/toc-bathy_smoother.bathy_smoothing-module.html +++ /dev/null @@ -1,36 +0,0 @@ - - - - - bathy_smoothing - - - - - -

Module bathy_smoothing

-
-

Functions

- smoothing_Laplacian_rx0
smoothing_NegativeVolume_rx0
smoothing_Negative_rx0
smoothing_PlusMinus_rx0
smoothing_PositiveVolume_rx0
smoothing_Positive_rx0
-[hide private] - - - - diff --git a/bathy_smoother/docs/toc-bathy_smoother.bathy_tools-module.html b/bathy_smoother/docs/toc-bathy_smoother.bathy_tools-module.html deleted file mode 100644 index e64a5b1..0000000 --- a/bathy_smoother/docs/toc-bathy_smoother.bathy_tools-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - bathy_tools - - - - - -

Module bathy_tools

-
-

Functions

- RoughnessMatrix
-[hide private] - - - - diff --git a/bathy_smoother/docs/toc-everything.html b/bathy_smoother/docs/toc-everything.html deleted file mode 100644 index 5f9ba1f..0000000 --- a/bathy_smoother/docs/toc-everything.html +++ /dev/null @@ -1,176 +0,0 @@ - - - - - Everything - - - - - -

Everything

-
-

All Functions

- bathy_smoother.LP_bathy_smoothing.LP_smoothing_rx0
bathy_smoother.LP_bathy_smoothing.LP_smoothing_rx0_heuristic
bathy_smoother.LP_bathy_tools.ConnectedComponent
bathy_smoother.LP_bathy_tools.GetBadPoints
bathy_smoother.LP_bathy_tools.GetIJS_maxamp
bathy_smoother.LP_bathy_tools.GetIJS_rx0
bathy_smoother.LP_bathy_tools.GetIJS_signs
bathy_smoother.LP_bathy_tools.MergeIJS_listings
bathy_smoother.LP_bathy_tools.Neighborhood
bathy_smoother.LP_tools.SolveLinearProgram
bathy_smoother.LP_tools.WriteLinearProgram
bathy_smoother.bathy_smoothing.smoothing_Laplacian_rx0
bathy_smoother.bathy_smoothing.smoothing_NegativeVolume_rx0
bathy_smoother.bathy_smoothing.smoothing_Negative_rx0
bathy_smoother.bathy_smoothing.smoothing_PlusMinus_rx0
bathy_smoother.bathy_smoothing.smoothing_PositiveVolume_rx0
bathy_smoother.bathy_smoothing.smoothing_Positive_rx0
bathy_smoother.bathy_tools.RoughnessMatrix

All Variables

- bathy_smoother.LP_tools.ANTIDEGEN_BOUNDFLIP
bathy_smoother.LP_tools.ANTIDEGEN_COLUMNCHECK
bathy_smoother.LP_tools.ANTIDEGEN_DURINGBB
bathy_smoother.LP_tools.ANTIDEGEN_DYNAMIC
bathy_smoother.LP_tools.ANTIDEGEN_FIXEDVARS
bathy_smoother.LP_tools.ANTIDEGEN_INFEASIBLE
bathy_smoother.LP_tools.ANTIDEGEN_LOSTFEAS
bathy_smoother.LP_tools.ANTIDEGEN_NONE
bathy_smoother.LP_tools.ANTIDEGEN_NUMFAILURE
bathy_smoother.LP_tools.ANTIDEGEN_RHSPERTURB
bathy_smoother.LP_tools.ANTIDEGEN_STALLING
bathy_smoother.LP_tools.BRANCH_AUTOMATIC
bathy_smoother.LP_tools.BRANCH_CEILING
bathy_smoother.LP_tools.BRANCH_FLOOR
bathy_smoother.LP_tools.CRASH_LEASTDEGENERATE
bathy_smoother.LP_tools.CRASH_MOSTFEASIBLE
bathy_smoother.LP_tools.CRASH_NONE
bathy_smoother.LP_tools.CRITICAL
bathy_smoother.LP_tools.DEGENERATE
bathy_smoother.LP_tools.DETAILED
bathy_smoother.LP_tools.EQ
bathy_smoother.LP_tools.FEASFOUND
bathy_smoother.LP_tools.FR
bathy_smoother.LP_tools.FULL
bathy_smoother.LP_tools.GE
bathy_smoother.LP_tools.IMPORTANT
bathy_smoother.LP_tools.IMPROVE_BBSIMPLEX
bathy_smoother.LP_tools.IMPROVE_DUALFEAS
bathy_smoother.LP_tools.IMPROVE_NONE
bathy_smoother.LP_tools.IMPROVE_SOLUTION
bathy_smoother.LP_tools.IMPROVE_THETAGAP
bathy_smoother.LP_tools.INFEASIBLE
bathy_smoother.LP_tools.Infinite
bathy_smoother.LP_tools.LE
bathy_smoother.LP_tools.MSG_LPFEASIBLE
bathy_smoother.LP_tools.MSG_LPOPTIMAL
bathy_smoother.LP_tools.MSG_MILPBETTER
bathy_smoother.LP_tools.MSG_MILPEQUAL
bathy_smoother.LP_tools.MSG_MILPFEASIBLE
bathy_smoother.LP_tools.MSG_PRESOLVE
bathy_smoother.LP_tools.NEUTRAL
bathy_smoother.LP_tools.NODE_AUTOORDER
bathy_smoother.LP_tools.NODE_BRANCHREVERSEMODE
bathy_smoother.LP_tools.NODE_BREADTHFIRSTMODE
bathy_smoother.LP_tools.NODE_DEPTHFIRSTMODE
bathy_smoother.LP_tools.NODE_DYNAMICMODE
bathy_smoother.LP_tools.NODE_FIRSTSELECT
bathy_smoother.LP_tools.NODE_FRACTIONSELECT
bathy_smoother.LP_tools.NODE_GAPSELECT
bathy_smoother.LP_tools.NODE_GREEDYMODE
bathy_smoother.LP_tools.NODE_GUBMODE
bathy_smoother.LP_tools.NODE_PSEUDOCOSTMODE
bathy_smoother.LP_tools.NODE_PSEUDOCOSTSELECT
bathy_smoother.LP_tools.NODE_PSEUDONONINTSELECT
bathy_smoother.LP_tools.NODE_PSEUDORATIOSELECT
bathy_smoother.LP_tools.NODE_RANDOMIZEMODE
bathy_smoother.LP_tools.NODE_RANGESELECT
bathy_smoother.LP_tools.NODE_RCOSTFIXING
bathy_smoother.LP_tools.NODE_RESTARTMODE
bathy_smoother.LP_tools.NODE_STRONGINIT
bathy_smoother.LP_tools.NODE_USERSELECT
bathy_smoother.LP_tools.NODE_WEIGHTREVERSEMODE
bathy_smoother.LP_tools.NOFEASFOUND
bathy_smoother.LP_tools.NOMEMORY
bathy_smoother.LP_tools.NORMAL
bathy_smoother.LP_tools.NUMFAILURE
bathy_smoother.LP_tools.OPTIMAL
bathy_smoother.LP_tools.PRESOLVE_BOUNDS
bathy_smoother.LP_tools.PRESOLVE_COLDOMINATE
bathy_smoother.LP_tools.PRESOLVE_COLFIXDUAL
bathy_smoother.LP_tools.PRESOLVE_COLS
bathy_smoother.LP_tools.PRESOLVE_DUALS
bathy_smoother.LP_tools.PRESOLVE_ELIMEQ2
bathy_smoother.LP_tools.PRESOLVE_IMPLIEDFREE
bathy_smoother.LP_tools.PRESOLVE_IMPLIEDSLK
bathy_smoother.LP_tools.PRESOLVE_KNAPSACK
bathy_smoother.LP_tools.PRESOLVE_LINDEP
bathy_smoother.LP_tools.PRESOLVE_MERGEROWS
bathy_smoother.LP_tools.PRESOLVE_NONE
bathy_smoother.LP_tools.PRESOLVE_PROBEFIX
bathy_smoother.LP_tools.PRESOLVE_PROBEREDUCE
bathy_smoother.LP_tools.PRESOLVE_REDUCEGCD
bathy_smoother.LP_tools.PRESOLVE_REDUCEMIP
bathy_smoother.LP_tools.PRESOLVE_ROWDOMINATE
bathy_smoother.LP_tools.PRESOLVE_ROWS
bathy_smoother.LP_tools.PRESOLVE_SENSDUALS
bathy_smoother.LP_tools.PRESOLVE_SOS
bathy_smoother.LP_tools.PRICER_DANTZIG
bathy_smoother.LP_tools.PRICER_DEVEX
bathy_smoother.LP_tools.PRICER_FIRSTINDEX
bathy_smoother.LP_tools.PRICER_STEEPESTEDGE
bathy_smoother.LP_tools.PRICE_ADAPTIVE
bathy_smoother.LP_tools.PRICE_AUTOPARTIAL
bathy_smoother.LP_tools.PRICE_HARRISTWOPASS
bathy_smoother.LP_tools.PRICE_LOOPALTERNATE
bathy_smoother.LP_tools.PRICE_LOOPLEFT
bathy_smoother.LP_tools.PRICE_MULTIPLE
bathy_smoother.LP_tools.PRICE_PARTIAL
bathy_smoother.LP_tools.PRICE_PRIMALFALLBACK
bathy_smoother.LP_tools.PRICE_RANDOMIZE
bathy_smoother.LP_tools.PRICE_TRUENORMINIT
bathy_smoother.LP_tools.PROCBREAK
bathy_smoother.LP_tools.PROCFAIL
bathy_smoother.LP_tools.SCALE_COLSONLY
bathy_smoother.LP_tools.SCALE_CURTISREID
bathy_smoother.LP_tools.SCALE_DYNUPDATE
bathy_smoother.LP_tools.SCALE_EQUILIBRATE
bathy_smoother.LP_tools.SCALE_EXTREME
bathy_smoother.LP_tools.SCALE_GEOMETRIC
bathy_smoother.LP_tools.SCALE_INTEGERS
bathy_smoother.LP_tools.SCALE_LOGARITHMIC
bathy_smoother.LP_tools.SCALE_MEAN
bathy_smoother.LP_tools.SCALE_NONE
bathy_smoother.LP_tools.SCALE_POWER2
bathy_smoother.LP_tools.SCALE_QUADRATIC
bathy_smoother.LP_tools.SCALE_RANGE
bathy_smoother.LP_tools.SCALE_ROWSONLY
bathy_smoother.LP_tools.SCALE_USERWEIGHT
bathy_smoother.LP_tools.SEVERE
bathy_smoother.LP_tools.SIMPLEX_DUAL_DUAL
bathy_smoother.LP_tools.SIMPLEX_DUAL_PRIMAL
bathy_smoother.LP_tools.SIMPLEX_PRIMAL_DUAL
bathy_smoother.LP_tools.SIMPLEX_PRIMAL_PRIMAL
bathy_smoother.LP_tools.SUBOPTIMAL
bathy_smoother.LP_tools.TIMEOUT
bathy_smoother.LP_tools.UNBOUNDED
bathy_smoother.LP_tools.USERABORT
-[hide private] - - - - diff --git a/bathy_smoother/docs/toc.html b/bathy_smoother/docs/toc.html deleted file mode 100644 index f10d6dd..0000000 --- a/bathy_smoother/docs/toc.html +++ /dev/null @@ -1,38 +0,0 @@ - - - - - Table of Contents - - - - - -

Table of Contents

-
- Everything -
-

Modules

- bathy_smoother
bathy_smoother.LP_bathy_smoothing
bathy_smoother.LP_bathy_tools
bathy_smoother.LP_tools
bathy_smoother.bathy_smoothing
bathy_smoother.bathy_tools
- [hide private] - - - - diff --git a/bathy_smoother/external/lp_solve_5.5/extra/Python/lp_maker.pyc b/bathy_smoother/external/lp_solve_5.5/extra/Python/lp_maker.pyc deleted file mode 100644 index 720f8c8..0000000 Binary files a/bathy_smoother/external/lp_solve_5.5/extra/Python/lp_maker.pyc and /dev/null differ diff --git a/bathy_smoother/external/lp_solve_5.5/extra/Python/pyhelp.py b/bathy_smoother/external/lp_solve_5.5/extra/Python/pyhelp.py index 03e569d..de9ca0a 100644 --- a/bathy_smoother/external/lp_solve_5.5/extra/Python/pyhelp.py +++ b/bathy_smoother/external/lp_solve_5.5/extra/Python/pyhelp.py @@ -18,4 +18,4 @@ setupfile.close() output.close() - + diff --git a/bathy_smoother/setup.py b/bathy_smoother/setup.py index 497f913..f469f44 100644 --- a/bathy_smoother/setup.py +++ b/bathy_smoother/setup.py @@ -1,6 +1,6 @@ """ bathy_smoother is a suite of tools for working with ROMS bathymetry. -(ripped from matlab script LP_bathymetry) +(ripped from matlab script LP_bathymetry) Requires: NumPy (http://numpy.scipy.org) @@ -84,9 +84,7 @@ def configuration(parent_package='',top_path=None): version = '0.1', description = doclines[0], long_description = "\n".join(doclines[2:]), - author = "Frederic Castruccio", - author_email = "frederic@marine.rutgers.edu", - url = 'https://github.com/kshedstrom/pyroms', + url = 'https://github.com/ESMG/pyroms', license = 'BSD', platforms = ["any"], configuration=configuration, diff --git a/examples/Arctic2/make_bdry_file.py b/examples/Arctic2/make_bdry_file.py index 4722a37..502dfd8 100644 --- a/examples/Arctic2/make_bdry_file.py +++ b/examples/Arctic2/make_bdry_file.py @@ -68,9 +68,9 @@ def do_file(file, src_grd, dst_grd): lst = lst.split() lst_file = lst_file + lst -print 'Build OBC file from the following file list:' -print lst_file -print ' ' +print('Build OBC file from the following file list:') +print(lst_file) +print(' ') src_grd_file = data_dir + 'SODA_grid.cdf' src_grd = pyroms_toolbox.BGrid_SODA.get_nc_BGrid_SODA(src_grd_file, name='SODA_2.1.6_ARCTIC2', area='npolar', ystart=240) diff --git a/examples/Arctic2/make_clm_file.py b/examples/Arctic2/make_clm_file.py index 0d0efd6..714ce0f 100644 --- a/examples/Arctic2/make_clm_file.py +++ b/examples/Arctic2/make_clm_file.py @@ -73,9 +73,9 @@ def do_file(file, src_grd, dst_grd): lst = lst.split() lst_file = lst_file + lst -print 'Build CLM file from the following file list:' -print lst_file -print ' ' +print('Build CLM file from the following file list:') +print(lst_file) +print(' ') src_grd_file = data_dir + '../SODA_grid.cdf' src_grd = pyroms_toolbox.BGrid_SODA.get_nc_BGrid_SODA(src_grd_file, name='SODA_2.1.6_ARCTIC2', area='npolar', ystart=240) diff --git a/examples/Arctic2/make_ic_file.py b/examples/Arctic2/make_ic_file.py index ce64f24..e8d8099 100644 --- a/examples/Arctic2/make_ic_file.py +++ b/examples/Arctic2/make_ic_file.py @@ -2,7 +2,7 @@ matplotlib.use('Agg') import subprocess import os -import commands +import subprocess import numpy as np import pyroms @@ -15,9 +15,9 @@ file = '/nfs/P1/Data/SODA/SODA_2.1.6/SODA_2.1.6_20031231-20040105.cdf' dst_dir='./' -print 'Build IC file from the following file:' -print file -print ' ' +print('Build IC file from the following file:') +print(file) +print(' ') src_grd = pyroms_toolbox.BGrid_SODA.get_nc_BGrid_SODA('/nfs/P1/Data/SODA/SODA_2.1.6/SODA_grid.cdf', name='SODA_2.1.6', area='npolar', ystart=240) dst_grd = pyroms.grid.get_ROMS_grid('ARCTIC2') diff --git a/examples/Arctic2/make_remap_weights_file.py b/examples/Arctic2/make_remap_weights_file.py index 3348b98..2afa1c2 100644 --- a/examples/Arctic2/make_remap_weights_file.py +++ b/examples/Arctic2/make_remap_weights_file.py @@ -26,7 +26,7 @@ pyroms.remapping.compute_remap_weights(grid1_file, grid2_file, \ interp_file1, interp_file2, map1_name, \ map2_name, num_maps, map_method, \ - grid1_periodic='.true.', grid2_periodic='.true.') + grid1_periodic='.true.', grid2_periodic='.true.') # compute remap weights @@ -43,7 +43,7 @@ pyroms.remapping.compute_remap_weights(grid1_file, grid2_file, \ interp_file1, interp_file2, map1_name, \ map2_name, num_maps, map_method, \ - grid1_periodic='.true.', grid2_periodic='.true.') + grid1_periodic='.true.', grid2_periodic='.true.') # compute remap weights @@ -60,7 +60,7 @@ pyroms.remapping.compute_remap_weights(grid1_file, grid2_file, \ interp_file1, interp_file2, map1_name, \ map2_name, num_maps, map_method, \ - grid1_periodic='.true.', grid2_periodic='.true.') + grid1_periodic='.true.', grid2_periodic='.true.') # compute remap weights @@ -77,5 +77,5 @@ pyroms.remapping.compute_remap_weights(grid1_file, grid2_file, \ interp_file1, interp_file2, map1_name, \ map2_name, num_maps, map_method, \ - grid1_periodic='.true.', grid2_periodic='.true.') + grid1_periodic='.true.', grid2_periodic='.true.') diff --git a/examples/Arctic2/remap.py b/examples/Arctic2/remap.py index ecdbad0..092bf50 100644 --- a/examples/Arctic2/remap.py +++ b/examples/Arctic2/remap.py @@ -47,7 +47,7 @@ def remap(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_d # create IC file dst_file = src_file.rsplit('/')[-1] dst_file = dst_dir + dst_file[:-4] + '_' + src_varname + '_ic_' + dst_grd.name + '.nc' - print '\nCreating file', dst_file + print('\nCreating file', dst_file) if os.path.exists(dst_file) is True: os.remove(dst_file) pyroms_toolbox.nc_create_roms_file(dst_file, dst_grd, nctime) @@ -107,7 +107,7 @@ def remap(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_d units = 'PSU' field = 'salinity, scalar, series' else: - raise ValueError, 'Undefined src_varname' + raise ValueError('Undefined src_varname') if ndim == 3: @@ -119,7 +119,7 @@ def remap(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_d # create variable in file - print 'Creating variable', dst_varname + print('Creating variable', dst_varname) nc.createVariable(dst_varname, 'f8', dimensions, fill_value=spval) nc.variables[dst_varname].long_name = long_name nc.variables[dst_varname].units = units @@ -127,34 +127,34 @@ def remap(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_d # remapping - print 'remapping', dst_varname, 'from', src_grd.name, \ - 'to', dst_grd.name - print 'time =', time + print('remapping', dst_varname, 'from', src_grd.name, \ + 'to', dst_grd.name) + print('time =', time) if ndim == 3: # flood the grid - print 'flood the grid' + print('flood the grid') src_varz = pyroms_toolbox.BGrid_SODA.flood(src_var, src_grd, Bpos=Bpos, spval=spval, \ dmax=dmax, cdepth=cdepth, kk=kk) else: src_varz = src_var # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_varz = pyroms.remapping.remap(src_varz, wts_file, \ spval=spval) if ndim == 3: # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_var = pyroms.remapping.z2roms(dst_varz[::-1,:,:], dst_grdz, \ dst_grd, Cpos=Cpos, spval=spval, flood=False) else: dst_var = dst_varz # write data in destination file - print 'write data in destination file' + print('write data in destination file') nc.variables['ocean_time'][0] = time nc.variables[dst_varname][0] = dst_var diff --git a/examples/Arctic2/remap_bdry.py b/examples/Arctic2/remap_bdry.py index 57328f6..b3fce57 100644 --- a/examples/Arctic2/remap_bdry.py +++ b/examples/Arctic2/remap_bdry.py @@ -38,7 +38,7 @@ def remap_bdry(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, # create boundary file dst_file = src_file.rsplit('/')[-1] dst_file = dst_dir + dst_file[:-4] + '_' + src_varname + '_bdry_' + dst_grd.name + '.nc' - print '\nCreating boundary file', dst_file + print('\nCreating boundary file', dst_file) if os.path.exists(dst_file) is True: os.remove(dst_file) pyroms_toolbox.nc_create_roms_file(dst_file, dst_grd, nctime) @@ -139,7 +139,7 @@ def remap_bdry(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, field_west = 'salt_west, scalar, series' units = 'PSU' else: - raise ValueError, 'Undefined src_varname' + raise ValueError('Undefined src_varname') if ndim == 3: @@ -151,25 +151,25 @@ def remap_bdry(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, # create variable in boudary file - print 'Creating variable', dst_varname_north + print('Creating variable', dst_varname_north) nc.createVariable(dst_varname_north, 'f8', dimensions_north, fill_value=spval) nc.variables[dst_varname_north].long_name = long_name_north nc.variables[dst_varname_north].units = units nc.variables[dst_varname_north].field = field_north - print 'Creating variable', dst_varname_south + print('Creating variable', dst_varname_south) nc.createVariable(dst_varname_south, 'f8', dimensions_south, fill_value=spval) nc.variables[dst_varname_south].long_name = long_name_south nc.variables[dst_varname_south].units = units nc.variables[dst_varname_south].field = field_south - print 'Creating variable', dst_varname_east + print('Creating variable', dst_varname_east) nc.createVariable(dst_varname_east, 'f8', dimensions_east, fill_value=spval) nc.variables[dst_varname_east].long_name = long_name_east nc.variables[dst_varname_east].units = units nc.variables[dst_varname_east].field = field_east - print 'Creating variable', dst_varname_west + print('Creating variable', dst_varname_west) nc.createVariable(dst_varname_west, 'f8', dimensions_west, fill_value=spval) nc.variables[dst_varname_west].long_name = long_name_west nc.variables[dst_varname_west].units = units @@ -177,28 +177,28 @@ def remap_bdry(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, # remapping - print 'remapping', dst_varname, 'from', src_grd.name, \ - 'to', dst_grd.name - print 'time =', time + print('remapping', dst_varname, 'from', src_grd.name, \ + 'to', dst_grd.name) + print('time =', time) if ndim == 3: # flood the grid - print 'flood the grid' - print src_var.shape - print src_grd.z_t.shape + print('flood the grid') + print(src_var.shape) + print(src_grd.z_t.shape) src_varz = pyroms_toolbox.BGrid_SODA.flood(src_var, src_grd, Bpos=Bpos, spval=spval, \ dmax=dmax, cdepth=cdepth, kk=kk) else: src_varz = src_var # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_varz = pyroms.remapping.remap(src_varz, wts_file, spval=spval) if ndim == 3: # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_var_north = pyroms.remapping.z2roms(dst_varz[::-1, Mp-1:Mp, 0:Lp], \ dst_grdz, dst_grd, Cpos=Cpos, spval=spval, \ flood=False, irange=(0,Lp), jrange=(Mp-1,Mp)) @@ -218,7 +218,7 @@ def remap_bdry(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_var_west = dst_varz[:, 0] # write data in destination file - print 'write data in destination file' + print('write data in destination file') nc.variables['ocean_time'][0] = time nc.variables[dst_varname_north][0] = np.squeeze(dst_var_north) nc.variables[dst_varname_south][0] = np.squeeze(dst_var_south) diff --git a/examples/Arctic2/remap_bdry_uv.py b/examples/Arctic2/remap_bdry_uv.py index eee6eac..51c1f13 100644 --- a/examples/Arctic2/remap_bdry_uv.py +++ b/examples/Arctic2/remap_bdry_uv.py @@ -42,12 +42,12 @@ def remap_bdry_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='. # create destination file dst_file = src_file.rsplit('/')[-1] dst_fileu = dst_dir + dst_file[:-4] + '_u_bdry_' + dst_grd.name + '.nc' - print '\nCreating destination file', dst_fileu + print('\nCreating destination file', dst_fileu) if os.path.exists(dst_fileu) is True: os.remove(dst_fileu) pyroms_toolbox.nc_create_roms_file(dst_fileu, dst_grd, nctime) dst_filev = dst_dir + dst_file[:-4] + '_v_bdry_' + dst_grd.name + '.nc' - print 'Creating destination file', dst_filev + print('Creating destination file', dst_filev) if os.path.exists(dst_filev) is True: os.remove(dst_filev) pyroms_toolbox.nc_create_roms_file(dst_filev, dst_grd, nctime) @@ -80,87 +80,87 @@ def remap_bdry_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='. dst_grdz = pyroms.grid.ROMS_Grid(dst_grd.name+'_Z', dst_grd.hgrid, dst_zcoord) # create variable in destination file - print 'Creating variable u_north' + print('Creating variable u_north') ncu.createVariable('u_north', 'f8', ('ocean_time', 's_rho', 'xi_u'), fill_value=spval) ncu.variables['u_north'].long_name = '3D u-momentum north boundary condition' ncu.variables['u_north'].units = 'meter second-1' ncu.variables['u_north'].field = 'u_north, scalar, series' - print 'Creating variable u_south' + print('Creating variable u_south') ncu.createVariable('u_south', 'f8', ('ocean_time', 's_rho', 'xi_u'), fill_value=spval) ncu.variables['u_south'].long_name = '3D u-momentum south boundary condition' ncu.variables['u_south'].units = 'meter second-1' ncu.variables['u_south'].field = 'u_south, scalar, series' - print 'Creating variable u_east' + print('Creating variable u_east') ncu.createVariable('u_east', 'f8', ('ocean_time', 's_rho', 'eta_u'), fill_value=spval) ncu.variables['u_east'].long_name = '3D u-momentum east boundary condition' ncu.variables['u_east'].units = 'meter second-1' ncu.variables['u_east'].field = 'u_east, scalar, series' - print 'Creating variable u_west' + print('Creating variable u_west') ncu.createVariable('u_west', 'f8', ('ocean_time', 's_rho', 'eta_u'), fill_value=spval) ncu.variables['u_west'].long_name = '3D u-momentum west boundary condition' ncu.variables['u_west'].units = 'meter second-1' ncu.variables['u_west'].field = 'u_east, scalar, series' # create variable in destination file - print 'Creating variable ubar_north' + print('Creating variable ubar_north') ncu.createVariable('ubar_north', 'f8', ('ocean_time', 'xi_u'), fill_value=spval) ncu.variables['ubar_north'].long_name = '2D u-momentum north boundary condition' ncu.variables['ubar_north'].units = 'meter second-1' ncu.variables['ubar_north'].field = 'ubar_north, scalar, series' - print 'Creating variable ubar_south' + print('Creating variable ubar_south') ncu.createVariable('ubar_south', 'f8', ('ocean_time', 'xi_u'), fill_value=spval) ncu.variables['ubar_south'].long_name = '2D u-momentum south boundary condition' ncu.variables['ubar_south'].units = 'meter second-1' ncu.variables['ubar_south'].field = 'ubar_south, scalar, series' - print 'Creating variable ubar_east' + print('Creating variable ubar_east') ncu.createVariable('ubar_east', 'f8', ('ocean_time', 'eta_u'), fill_value=spval) ncu.variables['ubar_east'].long_name = '2D u-momentum east boundary condition' ncu.variables['ubar_east'].units = 'meter second-1' ncu.variables['ubar_east'].field = 'ubar_east, scalar, series' - print 'Creating variable ubar_west' + print('Creating variable ubar_west') ncu.createVariable('ubar_west', 'f8', ('ocean_time', 'eta_u'), fill_value=spval) ncu.variables['ubar_west'].long_name = '2D u-momentum west boundary condition' ncu.variables['ubar_west'].units = 'meter second-1' ncu.variables['ubar_west'].field = 'ubar_east, scalar, series' - print 'Creating variable v_north' + print('Creating variable v_north') ncv.createVariable('v_north', 'f8', ('ocean_time', 's_rho', 'xi_v'), fill_value=spval) ncv.variables['v_north'].long_name = '3D v-momentum north boundary condition' ncv.variables['v_north'].units = 'meter second-1' ncv.variables['v_north'].field = 'v_north, scalar, series' - print 'Creating variable v_south' + print('Creating variable v_south') ncv.createVariable('v_south', 'f8', ('ocean_time', 's_rho', 'xi_v'), fill_value=spval) ncv.variables['v_south'].long_name = '3D v-momentum south boundary condition' ncv.variables['v_south'].units = 'meter second-1' ncv.variables['v_south'].field = 'v_south, scalar, series' - print 'Creating variable v_east' + print('Creating variable v_east') ncv.createVariable('v_east', 'f8', ('ocean_time', 's_rho', 'eta_v'), fill_value=spval) ncv.variables['v_east'].long_name = '3D v-momentum east boundary condition' ncv.variables['v_east'].units = 'meter second-1' ncv.variables['v_east'].field = 'v_east, scalar, series' - print 'Creating variable v_west' + print('Creating variable v_west') ncv.createVariable('v_west', 'f8', ('ocean_time', 's_rho', 'eta_v'), fill_value=spval) ncv.variables['v_west'].long_name = '3D v-momentum west boundary condition' ncv.variables['v_west'].units = 'meter second-1' ncv.variables['v_west'].field = 'v_east, scalar, series' - print 'Creating variable vbar_north' + print('Creating variable vbar_north') ncv.createVariable('vbar_north', 'f8', ('ocean_time', 'xi_v'), fill_value=spval) ncv.variables['vbar_north'].long_name = '2D v-momentum north boundary condition' ncv.variables['vbar_north'].units = 'meter second-1' ncv.variables['vbar_north'].field = 'vbar_north, scalar, series' - print 'Creating variable vbar_south' + print('Creating variable vbar_south') ncv.createVariable('vbar_south', 'f8', ('ocean_time', 'xi_v'), fill_value=spval) ncv.variables['vbar_south'].long_name = '2D v-momentum south boundary condition' ncv.variables['vbar_south'].units = 'meter second-1' ncv.variables['vbar_south'].field = 'vbar_south, scalar, series' - print 'Creating variable vbar_east' + print('Creating variable vbar_east') ncv.createVariable('vbar_east', 'f8', ('ocean_time', 'eta_v'), fill_value=spval) ncv.variables['vbar_east'].long_name = '2D v-momentum east boundary condition' ncv.variables['vbar_east'].units = 'meter second-1' ncv.variables['vbar_east'].field = 'vbar_east, scalar, series' - print 'Creating variable vbar_west' + print('Creating variable vbar_west') ncv.createVariable('vbar_west', 'f8', ('ocean_time', 'eta_v'), fill_value=spval) ncv.variables['vbar_west'].long_name = '2D v-momentum west boundary condition' ncv.variables['vbar_west'].units = 'meter second-1' @@ -169,27 +169,27 @@ def remap_bdry_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='. # remaping - print 'remapping and rotating u and v from', src_grd.name, \ - 'to', dst_grd.name - print 'time =', time + print('remapping and rotating u and v from', src_grd.name, \ + 'to', dst_grd.name) + print('time =', time) # flood the grid - print 'flood the grid' + print('flood the grid') src_uz = pyroms_toolbox.BGrid_SODA.flood(src_varu, src_grd, Bpos='uv', \ spval=spval, dmax=dmax, cdepth=cdepth, kk=kk) src_vz = pyroms_toolbox.BGrid_SODA.flood(src_varv, src_grd, Bpos='uv', \ spval=spval, dmax=dmax, cdepth=cdepth, kk=kk) # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_uz = pyroms.remapping.remap(src_uz, wts_file, \ spval=spval) dst_vz = pyroms.remapping.remap(src_vz, wts_file, \ spval=spval) # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_u_north = pyroms.remapping.z2roms(dst_uz[::-1, Mp-2:Mp, 0:Lp], \ dst_grdz, dst_grd, Cpos='rho', spval=spval, \ flood=False, irange=(0,Lp), jrange=(Mp-2,Mp)) @@ -320,7 +320,7 @@ def remap_bdry_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='. dst_vbar_west = np.ma.masked_where(dst_grd.hgrid.mask_v[:,0] == 0, dst_vbar_west) # write data in destination file - print 'write data in destination file' + print('write data in destination file') ncu.variables['ocean_time'][0] = time ncu.variables['u_north'][0] = dst_u_north ncu.variables['u_south'][0] = dst_u_south diff --git a/examples/Arctic2/remap_clm.py b/examples/Arctic2/remap_clm.py index 5f6c69a..3bf9589 100644 --- a/examples/Arctic2/remap_clm.py +++ b/examples/Arctic2/remap_clm.py @@ -47,7 +47,7 @@ def remap_clm(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, d # create IC file dst_file = src_file.rsplit('/')[-1] dst_file = dst_dir + dst_file[:-3] + '_' + src_varname + '_clim_' + dst_grd.name + '.nc' - print '\nCreating file', dst_file + print('\nCreating file', dst_file) if os.path.exists(dst_file) is True: os.remove(dst_file) pyroms_toolbox.nc_create_roms_file(dst_file, dst_grd, nctime) @@ -110,7 +110,7 @@ def remap_clm(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, d field = 'salinity, scalar, series' vartime = 'ocean_time' else: - raise ValueError, 'Undefined src_varname' + raise ValueError('Undefined src_varname') if ndim == 3: @@ -122,7 +122,7 @@ def remap_clm(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, d # create variable in file - print 'Creating variable', dst_varname + print('Creating variable', dst_varname) nc.createVariable(dst_varname, 'f8', dimensions, fill_value=spval) nc.variables[dst_varname].long_name = long_name nc.variables[dst_varname].units = units @@ -131,34 +131,34 @@ def remap_clm(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, d # remapping - print 'remapping', dst_varname, 'from', src_grd.name, \ - 'to', dst_grd.name - print 'time =', time + print('remapping', dst_varname, 'from', src_grd.name, \ + 'to', dst_grd.name) + print('time =', time) if ndim == 3: # flood the grid - print 'flood the grid' + print('flood the grid') src_varz = pyroms_toolbox.BGrid_SODA.flood(src_var, src_grd, Bpos=Bpos, spval=spval, \ dmax=dmax, cdepth=cdepth, kk=kk) else: src_varz = src_var # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_varz = pyroms.remapping.remap(src_varz, wts_file, \ spval=spval) if ndim == 3: # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_var = pyroms.remapping.z2roms(dst_varz[::-1,:,:], dst_grdz, \ dst_grd, Cpos=Cpos, spval=spval, flood=False) else: dst_var = dst_varz # write data in destination file - print 'write data in destination file' + print('write data in destination file') nc.variables['ocean_time'][0] = time nc.variables[dst_varname][0] = dst_var diff --git a/examples/Arctic2/remap_clm_uv.py b/examples/Arctic2/remap_clm_uv.py index 0d10c7a..980b813 100644 --- a/examples/Arctic2/remap_clm_uv.py +++ b/examples/Arctic2/remap_clm_uv.py @@ -48,12 +48,12 @@ def remap_clm_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./ # create destination file dst_file = src_file.rsplit('/')[-1] dst_fileu = dst_dir + dst_file[:-3] + '_u_clim_' + dst_grd.name + '.nc' - print '\nCreating destination file', dst_fileu + print('\nCreating destination file', dst_fileu) if os.path.exists(dst_fileu) is True: os.remove(dst_fileu) pyroms_toolbox.nc_create_roms_file(dst_fileu, dst_grd, nctime) dst_filev = dst_dir + dst_file[:-3] + '_v_clim_' + dst_grd.name + '.nc' - print 'Creating destination file', dst_filev + print('Creating destination file', dst_filev) if os.path.exists(dst_filev) is True: os.remove(dst_filev) pyroms_toolbox.nc_create_roms_file(dst_filev, dst_grd, nctime) @@ -86,27 +86,27 @@ def remap_clm_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./ dst_grdz = pyroms.grid.ROMS_Grid(dst_grd.name+'_Z', dst_grd.hgrid, dst_zcoord) # create variable in destination file - print 'Creating variable u' + print('Creating variable u') ncu.createVariable('u', 'f8', ('ocean_time', 's_rho', 'eta_u', 'xi_u'), fill_value=spval) ncu.variables['u'].long_name = '3D u-momentum component' ncu.variables['u'].units = 'meter second-1' ncu.variables['u'].field = 'u-velocity, scalar, series' ncu.variables['u'].time = 'ocean_time' # create variable in destination file - print 'Creating variable ubar' + print('Creating variable ubar') ncu.createVariable('ubar', 'f8', ('ocean_time', 'eta_u', 'xi_u'), fill_value=spval) ncu.variables['ubar'].long_name = '2D u-momentum component' ncu.variables['ubar'].units = 'meter second-1' ncu.variables['ubar'].field = 'ubar-velocity,, scalar, series' ncu.variables['ubar'].time = 'ocean_time' - print 'Creating variable v' + print('Creating variable v') ncv.createVariable('v', 'f8', ('ocean_time', 's_rho', 'eta_v', 'xi_v'), fill_value=spval) ncv.variables['v'].long_name = '3D v-momentum component' ncv.variables['v'].units = 'meter second-1' ncv.variables['v'].field = 'v-velocity, scalar, series' ncv.variables['v'].time = 'ocean_time' - print 'Creating variable vbar' + print('Creating variable vbar') ncv.createVariable('vbar', 'f8', ('ocean_time', 'eta_v', 'xi_v'), fill_value=spval) ncv.variables['vbar'].long_name = '2D v-momentum component' ncv.variables['vbar'].units = 'meter second-1' @@ -115,27 +115,27 @@ def remap_clm_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./ # remaping - print 'remapping and rotating u and v from', src_grd.name, \ - 'to', dst_grd.name - print 'time =', time + print('remapping and rotating u and v from', src_grd.name, \ + 'to', dst_grd.name) + print('time =', time) # flood the grid - print 'flood the grid' + print('flood the grid') src_uz = pyroms_toolbox.BGrid_SODA.flood(src_varu, src_grd, Bpos='uv', \ spval=spval, dmax=dmax, cdepth=cdepth, kk=kk) src_vz = pyroms_toolbox.BGrid_SODA.flood(src_varv, src_grd, Bpos='uv', \ spval=spval, dmax=dmax, cdepth=cdepth, kk=kk) # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_uz = pyroms.remapping.remap(src_uz, wts_file, \ spval=spval) dst_vz = pyroms.remapping.remap(src_vz, wts_file, \ spval=spval) # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_u = pyroms.remapping.z2roms(dst_uz[::-1,:,:], dst_grdz, \ dst_grd, Cpos='rho', spval=spval, flood=False) dst_v = pyroms.remapping.z2roms(dst_vz[::-1,:,:], dst_grdz, \ @@ -187,7 +187,7 @@ def remap_clm_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./ dst_vbar[idxv[0], idxv[1]] = spval # write data in destination file - print 'write data in destination file' + print('write data in destination file') ncu.variables['ocean_time'][0] = time ncu.variables['u'][0] = dst_u ncu.variables['ubar'][0] = dst_ubar @@ -196,10 +196,10 @@ def remap_clm_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./ ncv.variables['v'][0] = dst_v ncv.variables['vbar'][0] = dst_vbar - print dst_u.shape - print dst_ubar.shape - print dst_v.shape - print dst_vbar.shape + print(dst_u.shape) + print(dst_ubar.shape) + print(dst_v.shape) + print(dst_vbar.shape) # close destination file ncu.close() diff --git a/examples/Arctic2/remap_uv.py b/examples/Arctic2/remap_uv.py index 1cf7765..fd218fa 100644 --- a/examples/Arctic2/remap_uv.py +++ b/examples/Arctic2/remap_uv.py @@ -40,12 +40,12 @@ def remap_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): # create destination file dst_file = src_file.rsplit('/')[-1] dst_fileu = dst_dir + dst_file[:-4] + '_u_ic_' + dst_grd.name + '.nc' - print '\nCreating destination file', dst_fileu + print('\nCreating destination file', dst_fileu) if os.path.exists(dst_fileu) is True: os.remove(dst_fileu) pyroms_toolbox.nc_create_roms_file(dst_fileu, dst_grd, nctime) dst_filev = dst_dir + dst_file[:-4] + '_v_ic_' + dst_grd.name + '.nc' - print 'Creating destination file', dst_filev + print('Creating destination file', dst_filev) if os.path.exists(dst_filev) is True: os.remove(dst_filev) pyroms_toolbox.nc_create_roms_file(dst_filev, dst_grd, nctime) @@ -78,24 +78,24 @@ def remap_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): dst_grdz = pyroms.grid.ROMS_Grid(dst_grd.name+'_Z', dst_grd.hgrid, dst_zcoord) # create variable in destination file - print 'Creating variable u' + print('Creating variable u') ncu.createVariable('u', 'f8', ('ocean_time', 's_rho', 'eta_u', 'xi_u'), fill_value=spval) ncu.variables['u'].long_name = '3D u-momentum component' ncu.variables['u'].units = 'meter second-1' ncu.variables['u'].field = 'u-velocity, scalar, series' # create variable in destination file - print 'Creating variable ubar' + print('Creating variable ubar') ncu.createVariable('ubar', 'f8', ('ocean_time', 'eta_u', 'xi_u'), fill_value=spval) ncu.variables['ubar'].long_name = '2D u-momentum component' ncu.variables['ubar'].units = 'meter second-1' ncu.variables['ubar'].field = 'ubar-velocity,, scalar, series' - print 'Creating variable v' + print('Creating variable v') ncv.createVariable('v', 'f8', ('ocean_time', 's_rho', 'eta_v', 'xi_v'), fill_value=spval) ncv.variables['v'].long_name = '3D v-momentum component' ncv.variables['v'].units = 'meter second-1' ncv.variables['v'].field = 'v-velocity, scalar, series' - print 'Creating variable vbar' + print('Creating variable vbar') ncv.createVariable('vbar', 'f8', ('ocean_time', 'eta_v', 'xi_v'), fill_value=spval) ncv.variables['vbar'].long_name = '2D v-momentum component' ncv.variables['vbar'].units = 'meter second-1' @@ -103,27 +103,27 @@ def remap_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): # remaping - print 'remapping and rotating u and v from', src_grd.name, \ - 'to', dst_grd.name - print 'time =', time + print('remapping and rotating u and v from', src_grd.name, \ + 'to', dst_grd.name) + print('time =', time) # flood the grid - print 'flood the grid' + print('flood the grid') src_uz = pyroms_toolbox.BGrid_SODA.flood(src_varu, src_grd, Bpos='uv', \ spval=spval, dmax=dmax, cdepth=cdepth, kk=kk) src_vz = pyroms_toolbox.BGrid_SODA.flood(src_varv, src_grd, Bpos='uv', \ spval=spval, dmax=dmax, cdepth=cdepth, kk=kk) # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_uz = pyroms.remapping.remap(src_uz, wts_file, \ spval=spval) dst_vz = pyroms.remapping.remap(src_vz, wts_file, \ spval=spval) # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_u = pyroms.remapping.z2roms(dst_uz[::-1,:,:], dst_grdz, \ dst_grd, Cpos='rho', spval=spval, flood=False) dst_v = pyroms.remapping.z2roms(dst_vz[::-1,:,:], dst_grdz, \ @@ -175,7 +175,7 @@ def remap_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): dst_vbar[idxv[0], idxv[1]] = spval # write data in destination file - print 'write data in destination file' + print('write data in destination file') ncu.variables['ocean_time'][0] = time ncu.variables['u'][0] = dst_u ncu.variables['ubar'][0] = dst_ubar @@ -184,10 +184,10 @@ def remap_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): ncv.variables['v'][0] = dst_v ncv.variables['vbar'][0] = dst_vbar - print dst_u.shape - print dst_ubar.shape - print dst_v.shape - print dst_vbar.shape + print(dst_u.shape) + print(dst_ubar.shape) + print(dst_v.shape) + print(dst_vbar.shape) # close destination file ncu.close() diff --git a/examples/Arctic_GLORYS/fixpole.py b/examples/Arctic_GLORYS/fixpole.py index e58988a..8d8e8ca 100644 --- a/examples/Arctic_GLORYS/fixpole.py +++ b/examples/Arctic_GLORYS/fixpole.py @@ -10,26 +10,26 @@ h = nc.variables['hice'][0,759:762,277:281] a = nc.variables['aice'][0,759:762,277:281] -print 'temp shape', t.shape +print('temp shape', t.shape) t1 = (t[:,0,1] + t[:,1,0] + t[:,2,2] + t[:,2,1] + t[:,0,2] + t[:,1,3])/6. s1 = (s[:,0,1] + s[:,1,0] + s[:,2,2] + s[:,2,1] + s[:,0,2] + s[:,1,3])/6. h1 = (h[0,1] + h[1,0] + h[2,2] + h[2,1] + h[0,2] + h[1,3])/6. a1 = (a[0,1] + a[1,0] + a[2,2] + a[2,1] + a[0,2] + a[1,3])/6. -print 'temp 0', t[:,1,1] -print 'temp 0a', t[:,1,2] -print 'temp 1', t[:,1,0] -print 'temp 2', t1 -print 'salt 0', s[:,1,1] -print 'salt 1', s[:,1,0] -print 'salt 2', s1 +print('temp 0', t[:,1,1]) +print('temp 0a', t[:,1,2]) +print('temp 1', t[:,1,0]) +print('temp 2', t1) +print('salt 0', s[:,1,1]) +print('salt 1', s[:,1,0]) +print('salt 2', s1) -print 'hice 0', h[1,1] -print 'hice 0a', h[1,2] -print 'hice 1', h[1,0] -print 'hice 2', h1 -print 'aice 0', a[1,1] -print 'aice 1', a[1,0] -print 'aice 2', a1 +print('hice 0', h[1,1]) +print('hice 0a', h[1,2]) +print('hice 1', h[1,0]) +print('hice 2', h1) +print('aice 0', a[1,1]) +print('aice 1', a[1,0]) +print('aice 2', a1) nc.variables['temp'][0,:,760,278] = t1 nc.variables['salt'][0,:,760,278] = s1 diff --git a/examples/Arctic_GLORYS/make_ic_file.py b/examples/Arctic_GLORYS/make_ic_file.py old mode 100755 new mode 100644 index 268022b..b304d18 --- a/examples/Arctic_GLORYS/make_ic_file.py +++ b/examples/Arctic_GLORYS/make_ic_file.py @@ -2,7 +2,7 @@ matplotlib.use('Agg') import subprocess import os -import commands +import subprocess import numpy as np import pyroms @@ -15,9 +15,9 @@ dst_dir='./' -print 'Build IC file from the following file:' -print file -print ' ' +print('Build IC file from the following file:') +print(file) +print(' ') src_grd = pyroms_toolbox.CGrid_GLORYS.get_nc_CGrid_GLORYS('/archive/u1/uaf/kate/GLORYS/GL2V1_mesh_mask_new.nc', name='GLORYS', area='npolar', ystart=690) dst_grd = pyroms.grid.get_ROMS_grid('ARCTIC2') diff --git a/examples/Arctic_GLORYS/make_remap_weights_file.py b/examples/Arctic_GLORYS/make_remap_weights_file.py old mode 100755 new mode 100644 index 669e1ab..a6b7fab --- a/examples/Arctic_GLORYS/make_remap_weights_file.py +++ b/examples/Arctic_GLORYS/make_remap_weights_file.py @@ -32,7 +32,7 @@ pyroms.remapping.compute_remap_weights(grid1_file, grid2_file, \ interp_file1, interp_file2, map1_name, \ map2_name, num_maps, map_method, \ - grid1_periodic='.true.', grid2_periodic='.true.') + grid1_periodic='.true.', grid2_periodic='.true.') # compute remap weights @@ -49,7 +49,7 @@ pyroms.remapping.compute_remap_weights(grid1_file, grid2_file, \ interp_file1, interp_file2, map1_name, \ map2_name, num_maps, map_method, \ - grid1_periodic='.true.', grid2_periodic='.true.') + grid1_periodic='.true.', grid2_periodic='.true.') # compute remap weights @@ -66,7 +66,7 @@ pyroms.remapping.compute_remap_weights(grid1_file, grid2_file, \ interp_file1, interp_file2, map1_name, \ map2_name, num_maps, map_method, \ - grid1_periodic='.true.', grid2_periodic='.true.') + grid1_periodic='.true.', grid2_periodic='.true.') # compute remap weights @@ -83,7 +83,7 @@ pyroms.remapping.compute_remap_weights(grid1_file, grid2_file, \ interp_file1, interp_file2, map1_name, \ map2_name, num_maps, map_method, \ - grid1_periodic='.true.', grid2_periodic='.true.') + grid1_periodic='.true.', grid2_periodic='.true.') # compute remap weights @@ -100,5 +100,5 @@ pyroms.remapping.compute_remap_weights(grid1_file, grid2_file, \ interp_file1, interp_file2, map1_name, \ map2_name, num_maps, map_method, \ - grid1_periodic='.true.', grid2_periodic='.true.') + grid1_periodic='.true.', grid2_periodic='.true.') diff --git a/examples/Arctic_GLORYS/remap.py b/examples/Arctic_GLORYS/remap.py old mode 100755 new mode 100644 index 3aeedfd..f8b2171 --- a/examples/Arctic_GLORYS/remap.py +++ b/examples/Arctic_GLORYS/remap.py @@ -28,7 +28,7 @@ def remap(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_d ref = date2num(ref) # For IC tag = src_file.rsplit('/')[-1].rsplit('_')[2] - print("date string:", tag) + print(("date string:", tag)) year = int(tag[:4]) month = int(tag[4:6]) day = int(tag[6:]) @@ -40,7 +40,7 @@ def remap(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_d # create IC file dst_file = src_file.rsplit('/')[-1] dst_file = dst_dir + dst_file[:-4] + '_' + src_varname + '_ic_' + dst_grd.name + '.nc' - print '\nCreating file', dst_file + print('\nCreating file', dst_file) if os.path.exists(dst_file) is True: os.remove(dst_file) pyroms_toolbox.nc_create_roms_file(dst_file, dst_grd, nctime) @@ -74,7 +74,7 @@ def remap(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_d elif ndim == 2: src_var = src_var[:] src_var = src_var[np.r_[ystart:np.size(src_var,0),-1],:] - print "dimensions:", src_var.shape, ndim + print("dimensions:", src_var.shape, ndim) if src_varname == 'sossheig': Bpos = 't' @@ -143,7 +143,7 @@ def remap(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_d units = 'PSU' field = 'salinity, scalar, series' else: - raise ValueError, 'Undefined src_varname' + raise ValueError('Undefined src_varname') if ndim == 3: @@ -155,7 +155,7 @@ def remap(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_d # create variable in file - print 'Creating variable', dst_varname + print('Creating variable', dst_varname) nc.createVariable(dst_varname, 'f8', dimensions, fill_value=spval) nc.variables[dst_varname].long_name = long_name nc.variables[dst_varname].units = units @@ -163,36 +163,36 @@ def remap(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_d # remapping - print 'remapping', dst_varname, 'from', src_grd.name, \ - 'to', dst_grd.name - print 'time =', time + print('remapping', dst_varname, 'from', src_grd.name, \ + 'to', dst_grd.name) + print('time =', time) if ndim == 3: # flood the grid - print 'flood the grid' + print('flood the grid') src_varz = pyroms_toolbox.CGrid_GLORYS.flood(src_var, src_grd, Cpos=Bpos, spval=spval, \ dmax=dmax, cdepth=cdepth, kk=kk) - print 'flooded the grid', src_varz[:,-1,189] - print 'flooded the grid', src_varz[:,-1,277] + print('flooded the grid', src_varz[:,-1,189]) + print('flooded the grid', src_varz[:,-1,277]) else: src_varz = src_var # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_varz = pyroms.remapping.remap(src_varz, wts_file, \ spval=spval) if ndim == 3: # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_var = pyroms.remapping.z2roms(dst_varz[::-1,:,:], dst_grdz, \ dst_grd, Cpos=Cpos, spval=spval, flood=False) else: dst_var = dst_varz # write data in destination file - print 'write data in destination file' + print('write data in destination file') nc.variables['ocean_time'][0] = time nc.variables[dst_varname][0] = dst_var diff --git a/examples/Arctic_GLORYS/remap_bdry.py b/examples/Arctic_GLORYS/remap_bdry.py old mode 100755 new mode 100644 index f87f88d..4941bfa --- a/examples/Arctic_GLORYS/remap_bdry.py +++ b/examples/Arctic_GLORYS/remap_bdry.py @@ -27,7 +27,7 @@ def remap_bdry(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, ref = datetime(1900, 1, 1, 0, 0, 0) ref = date2num(ref) tag = src_file.rsplit('/')[-1].rsplit('_')[2] - print("date string:", tag) + print(("date string:", tag)) year = int(tag[:4]) month = int(tag[4:6]) day = int(tag[6:]) @@ -39,7 +39,7 @@ def remap_bdry(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, # create boundary file dst_file = src_file.rsplit('/')[-1] dst_file = dst_dir + dst_file[:-4] + '_' + src_varname + '_bdry_' + dst_grd.name + '.nc' - print '\nCreating boundary file', dst_file + print('\nCreating boundary file', dst_file) if os.path.exists(dst_file) is True: os.remove(dst_file) pyroms_toolbox.nc_create_roms_file(dst_file, dst_grd, nctime) @@ -149,7 +149,7 @@ def remap_bdry(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, field_west = 'salt_west, scalar, series' units = 'PSU' else: - raise ValueError, 'Undefined src_varname' + raise ValueError('Undefined src_varname') if ndim == 3: @@ -161,25 +161,25 @@ def remap_bdry(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, # create variable in boudary file - print 'Creating variable', dst_varname_north + print('Creating variable', dst_varname_north) nc.createVariable(dst_varname_north, 'f8', dimensions_north, fill_value=spval) nc.variables[dst_varname_north].long_name = long_name_north nc.variables[dst_varname_north].units = units nc.variables[dst_varname_north].field = field_north - print 'Creating variable', dst_varname_south + print('Creating variable', dst_varname_south) nc.createVariable(dst_varname_south, 'f8', dimensions_south, fill_value=spval) nc.variables[dst_varname_south].long_name = long_name_south nc.variables[dst_varname_south].units = units nc.variables[dst_varname_south].field = field_south - print 'Creating variable', dst_varname_east + print('Creating variable', dst_varname_east) nc.createVariable(dst_varname_east, 'f8', dimensions_east, fill_value=spval) nc.variables[dst_varname_east].long_name = long_name_east nc.variables[dst_varname_east].units = units nc.variables[dst_varname_east].field = field_east - print 'Creating variable', dst_varname_west + print('Creating variable', dst_varname_west) nc.createVariable(dst_varname_west, 'f8', dimensions_west, fill_value=spval) nc.variables[dst_varname_west].long_name = long_name_west nc.variables[dst_varname_west].units = units @@ -187,26 +187,26 @@ def remap_bdry(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, # remapping - print 'remapping', dst_varname, 'from', src_grd.name, \ - 'to', dst_grd.name - print 'time =', time + print('remapping', dst_varname, 'from', src_grd.name, \ + 'to', dst_grd.name) + print('time =', time) if ndim == 3: # flood the grid - print 'flood the grid' + print('flood the grid') src_varz = pyroms_toolbox.CGrid_GLORYS.flood(src_var, src_grd, Cpos=Bpos, spval=spval, \ dmax=dmax, cdepth=cdepth, kk=kk) else: src_varz = src_var # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_varz = pyroms.remapping.remap(src_varz, wts_file, spval=spval) if ndim == 3: # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_var_north = pyroms.remapping.z2roms(dst_varz[::-1, Mp-1:Mp, 0:Lp], \ dst_grdz, dst_grd, Cpos=Cpos, spval=spval, \ flood=False, irange=(0,Lp), jrange=(Mp-1,Mp)) @@ -226,7 +226,7 @@ def remap_bdry(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_var_west = dst_varz[:, 0] # write data in destination file - print 'write data in destination file' + print('write data in destination file') nc.variables['ocean_time'][0] = time nc.variables[dst_varname_north][0] = np.squeeze(dst_var_north) nc.variables[dst_varname_south][0] = np.squeeze(dst_var_south) diff --git a/examples/Arctic_GLORYS/remap_bdry_uv.py b/examples/Arctic_GLORYS/remap_bdry_uv.py old mode 100755 new mode 100644 index bca375e..611875d --- a/examples/Arctic_GLORYS/remap_bdry_uv.py +++ b/examples/Arctic_GLORYS/remap_bdry_uv.py @@ -28,7 +28,7 @@ def remap_bdry_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='. ref = datetime(1900, 1, 1, 0, 0, 0) ref = date2num(ref) tag = src_file.rsplit('/')[-1].rsplit('_')[2] - print("tag:", tag) + print(("tag:", tag)) year = int(tag[:4]) month = int(tag[4:6]) day = int(tag[6:]) @@ -43,12 +43,12 @@ def remap_bdry_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='. # create destination file dst_file = src_file.rsplit('/')[-1] dst_fileu = dst_dir + dst_file[:-4] + '_u_bdry_' + dst_grd.name + '.nc' - print '\nCreating destination file', dst_fileu + print('\nCreating destination file', dst_fileu) if os.path.exists(dst_fileu) is True: os.remove(dst_fileu) pyroms_toolbox.nc_create_roms_file(dst_fileu, dst_grd, nctime) dst_filev = dst_dir + dst_file[:-4] + '_v_bdry_' + dst_grd.name + '.nc' - print 'Creating destination file', dst_filev + print('Creating destination file', dst_filev) if os.path.exists(dst_filev) is True: os.remove(dst_filev) pyroms_toolbox.nc_create_roms_file(dst_filev, dst_grd, nctime) @@ -68,13 +68,13 @@ def remap_bdry_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='. # ARCTIC2 grid sub-sample src_varu = src_varu[:] src_varv = src_varv[:] - print "shape 1", src_varu.shape, src_varv.shape + print("shape 1", src_varu.shape, src_varv.shape) src_varu = np.squeeze(src_varu) src_varv = np.squeeze(src_varv) - print "shape 2", src_varu.shape, src_varv.shape + print("shape 2", src_varu.shape, src_varv.shape) src_varu = src_varu[:,np.r_[ystart:np.size(src_varu,1),-1],:] src_varv = src_varv[:,np.r_[ystart:np.size(src_varv,1),-1],:] - print "shape 3", src_varu.shape, src_varv.shape + print("shape 3", src_varu.shape, src_varv.shape) # get weights file wts_file_a = 'remap_weights_GLORYS_to_ARCTIC2_bilinear_t_to_rho.nc' @@ -88,87 +88,87 @@ def remap_bdry_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='. dst_grdz = pyroms.grid.ROMS_Grid(dst_grd.name+'_Z', dst_grd.hgrid, dst_zcoord) # create variable in destination file - print 'Creating variable u_north' + print('Creating variable u_north') ncu.createVariable('u_north', 'f8', ('ocean_time', 's_rho', 'xi_u'), fill_value=spval) ncu.variables['u_north'].long_name = '3D u-momentum north boundary condition' ncu.variables['u_north'].units = 'meter second-1' ncu.variables['u_north'].field = 'u_north, scalar, series' - print 'Creating variable u_south' + print('Creating variable u_south') ncu.createVariable('u_south', 'f8', ('ocean_time', 's_rho', 'xi_u'), fill_value=spval) ncu.variables['u_south'].long_name = '3D u-momentum south boundary condition' ncu.variables['u_south'].units = 'meter second-1' ncu.variables['u_south'].field = 'u_south, scalar, series' - print 'Creating variable u_east' + print('Creating variable u_east') ncu.createVariable('u_east', 'f8', ('ocean_time', 's_rho', 'eta_u'), fill_value=spval) ncu.variables['u_east'].long_name = '3D u-momentum east boundary condition' ncu.variables['u_east'].units = 'meter second-1' ncu.variables['u_east'].field = 'u_east, scalar, series' - print 'Creating variable u_west' + print('Creating variable u_west') ncu.createVariable('u_west', 'f8', ('ocean_time', 's_rho', 'eta_u'), fill_value=spval) ncu.variables['u_west'].long_name = '3D u-momentum west boundary condition' ncu.variables['u_west'].units = 'meter second-1' ncu.variables['u_west'].field = 'u_east, scalar, series' # create variable in destination file - print 'Creating variable ubar_north' + print('Creating variable ubar_north') ncu.createVariable('ubar_north', 'f8', ('ocean_time', 'xi_u'), fill_value=spval) ncu.variables['ubar_north'].long_name = '2D u-momentum north boundary condition' ncu.variables['ubar_north'].units = 'meter second-1' ncu.variables['ubar_north'].field = 'ubar_north, scalar, series' - print 'Creating variable ubar_south' + print('Creating variable ubar_south') ncu.createVariable('ubar_south', 'f8', ('ocean_time', 'xi_u'), fill_value=spval) ncu.variables['ubar_south'].long_name = '2D u-momentum south boundary condition' ncu.variables['ubar_south'].units = 'meter second-1' ncu.variables['ubar_south'].field = 'ubar_south, scalar, series' - print 'Creating variable ubar_east' + print('Creating variable ubar_east') ncu.createVariable('ubar_east', 'f8', ('ocean_time', 'eta_u'), fill_value=spval) ncu.variables['ubar_east'].long_name = '2D u-momentum east boundary condition' ncu.variables['ubar_east'].units = 'meter second-1' ncu.variables['ubar_east'].field = 'ubar_east, scalar, series' - print 'Creating variable ubar_west' + print('Creating variable ubar_west') ncu.createVariable('ubar_west', 'f8', ('ocean_time', 'eta_u'), fill_value=spval) ncu.variables['ubar_west'].long_name = '2D u-momentum west boundary condition' ncu.variables['ubar_west'].units = 'meter second-1' ncu.variables['ubar_west'].field = 'ubar_east, scalar, series' - print 'Creating variable v_north' + print('Creating variable v_north') ncv.createVariable('v_north', 'f8', ('ocean_time', 's_rho', 'xi_v'), fill_value=spval) ncv.variables['v_north'].long_name = '3D v-momentum north boundary condition' ncv.variables['v_north'].units = 'meter second-1' ncv.variables['v_north'].field = 'v_north, scalar, series' - print 'Creating variable v_south' + print('Creating variable v_south') ncv.createVariable('v_south', 'f8', ('ocean_time', 's_rho', 'xi_v'), fill_value=spval) ncv.variables['v_south'].long_name = '3D v-momentum south boundary condition' ncv.variables['v_south'].units = 'meter second-1' ncv.variables['v_south'].field = 'v_south, scalar, series' - print 'Creating variable v_east' + print('Creating variable v_east') ncv.createVariable('v_east', 'f8', ('ocean_time', 's_rho', 'eta_v'), fill_value=spval) ncv.variables['v_east'].long_name = '3D v-momentum east boundary condition' ncv.variables['v_east'].units = 'meter second-1' ncv.variables['v_east'].field = 'v_east, scalar, series' - print 'Creating variable v_west' + print('Creating variable v_west') ncv.createVariable('v_west', 'f8', ('ocean_time', 's_rho', 'eta_v'), fill_value=spval) ncv.variables['v_west'].long_name = '3D v-momentum west boundary condition' ncv.variables['v_west'].units = 'meter second-1' ncv.variables['v_west'].field = 'v_east, scalar, series' - print 'Creating variable vbar_north' + print('Creating variable vbar_north') ncv.createVariable('vbar_north', 'f8', ('ocean_time', 'xi_v'), fill_value=spval) ncv.variables['vbar_north'].long_name = '2D v-momentum north boundary condition' ncv.variables['vbar_north'].units = 'meter second-1' ncv.variables['vbar_north'].field = 'vbar_north, scalar, series' - print 'Creating variable vbar_south' + print('Creating variable vbar_south') ncv.createVariable('vbar_south', 'f8', ('ocean_time', 'xi_v'), fill_value=spval) ncv.variables['vbar_south'].long_name = '2D v-momentum south boundary condition' ncv.variables['vbar_south'].units = 'meter second-1' ncv.variables['vbar_south'].field = 'vbar_south, scalar, series' - print 'Creating variable vbar_east' + print('Creating variable vbar_east') ncv.createVariable('vbar_east', 'f8', ('ocean_time', 'eta_v'), fill_value=spval) ncv.variables['vbar_east'].long_name = '2D v-momentum east boundary condition' ncv.variables['vbar_east'].units = 'meter second-1' ncv.variables['vbar_east'].field = 'vbar_east, scalar, series' - print 'Creating variable vbar_west' + print('Creating variable vbar_west') ncv.createVariable('vbar_west', 'f8', ('ocean_time', 'eta_v'), fill_value=spval) ncv.variables['vbar_west'].long_name = '2D v-momentum west boundary condition' ncv.variables['vbar_west'].units = 'meter second-1' @@ -177,27 +177,27 @@ def remap_bdry_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='. # remaping - print 'remapping and rotating u and v from', src_grd.name, \ - 'to', dst_grd.name - print 'time =', time + print('remapping and rotating u and v from', src_grd.name, \ + 'to', dst_grd.name) + print('time =', time) # flood the grid - print 'flood the grid' + print('flood the grid') src_uz = pyroms_toolbox.CGrid_GLORYS.flood(src_varu, src_grd, Cpos='u', \ spval=spval, dmax=dmax, cdepth=cdepth, kk=kk) src_vz = pyroms_toolbox.CGrid_GLORYS.flood(src_varv, src_grd, Cpos='v', \ spval=spval, dmax=dmax, cdepth=cdepth, kk=kk) # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_uz = pyroms.remapping.remap(src_uz, wts_file_u, \ spval=spval) dst_vz = pyroms.remapping.remap(src_vz, wts_file_v, \ spval=spval) # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_u_north = pyroms.remapping.z2roms(dst_uz[::-1, Mp-2:Mp, 0:Lp], \ dst_grdz, dst_grd, Cpos='rho', spval=spval, \ flood=False, irange=(0,Lp), jrange=(Mp-2,Mp)) @@ -329,7 +329,7 @@ def remap_bdry_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='. dst_vbar_west = np.ma.masked_where(dst_grd.hgrid.mask_v[:,0] == 0, dst_vbar_west) # write data in destination file - print 'write data in destination file' + print('write data in destination file') ncu.variables['ocean_time'][0] = time ncu.variables['u_north'][0] = dst_u_north ncu.variables['u_south'][0] = dst_u_south diff --git a/examples/Arctic_GLORYS/remap_uv.py b/examples/Arctic_GLORYS/remap_uv.py old mode 100755 new mode 100644 index a7cb5f6..de156fa --- a/examples/Arctic_GLORYS/remap_uv.py +++ b/examples/Arctic_GLORYS/remap_uv.py @@ -26,7 +26,7 @@ def remap_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): ref = datetime(1900, 1, 1, 0, 0, 0) ref = date2num(ref) tag = src_file.rsplit('/')[-1].rsplit('_')[2] - print("tag:", tag) + print(("tag:", tag)) year = int(tag[:4]) month = int(tag[4:6]) day = int(tag[6:]) @@ -41,12 +41,12 @@ def remap_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): # create destination file dst_file = src_file.rsplit('/')[-1] dst_fileu = dst_dir + dst_file[:-4] + '_u_ic_' + dst_grd.name + '.nc' - print '\nCreating destination file', dst_fileu + print('\nCreating destination file', dst_fileu) if os.path.exists(dst_fileu) is True: os.remove(dst_fileu) pyroms_toolbox.nc_create_roms_file(dst_fileu, dst_grd, nctime) dst_filev = dst_dir + dst_file[:-4] + '_v_ic_' + dst_grd.name + '.nc' - print 'Creating destination file', dst_filev + print('Creating destination file', dst_filev) if os.path.exists(dst_filev) is True: os.remove(dst_filev) pyroms_toolbox.nc_create_roms_file(dst_filev, dst_grd, nctime) @@ -59,7 +59,7 @@ def remap_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): cdf = netCDF.Dataset(src_file) src_varu = cdf.variables['vozocrtx'] src_varv = cdf.variables['vomecrty'] - print "dims", src_varu.dimensions, src_varv.dimensions + print("dims", src_varu.dimensions, src_varv.dimensions) #get missing value spval = src_varu._FillValue @@ -67,13 +67,13 @@ def remap_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): # ARCTIC grid sub-sample src_varu = src_varu[:] src_varv = src_varv[:] - print "shape 1", src_varu.shape, src_varv.shape + print("shape 1", src_varu.shape, src_varv.shape) src_varu = np.squeeze(src_varu) src_varv = np.squeeze(src_varv) - print "shape 2", src_varu.shape, src_varv.shape + print("shape 2", src_varu.shape, src_varv.shape) src_varu = src_varu[:,np.r_[ystart:np.size(src_varu,1),-1],:] src_varv = src_varv[:,np.r_[ystart:np.size(src_varv,1),-1],:] - print "shape 3", src_varu.shape, src_varv.shape + print("shape 3", src_varu.shape, src_varv.shape) # get weights file wts_file_a = 'remap_weights_GLORYS_to_ARCTIC2_bilinear_t_to_rho.nc' @@ -87,24 +87,24 @@ def remap_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): dst_grdz = pyroms.grid.ROMS_Grid(dst_grd.name+'_Z', dst_grd.hgrid, dst_zcoord) # create variable in destination file - print 'Creating variable u' + print('Creating variable u') ncu.createVariable('u', 'f8', ('ocean_time', 's_rho', 'eta_u', 'xi_u'), fill_value=spval) ncu.variables['u'].long_name = '3D u-momentum component' ncu.variables['u'].units = 'meter second-1' ncu.variables['u'].field = 'u-velocity, scalar, series' # create variable in destination file - print 'Creating variable ubar' + print('Creating variable ubar') ncu.createVariable('ubar', 'f8', ('ocean_time', 'eta_u', 'xi_u'), fill_value=spval) ncu.variables['ubar'].long_name = '2D u-momentum component' ncu.variables['ubar'].units = 'meter second-1' ncu.variables['ubar'].field = 'ubar-velocity,, scalar, series' - print 'Creating variable v' + print('Creating variable v') ncv.createVariable('v', 'f8', ('ocean_time', 's_rho', 'eta_v', 'xi_v'), fill_value=spval) ncv.variables['v'].long_name = '3D v-momentum component' ncv.variables['v'].units = 'meter second-1' ncv.variables['v'].field = 'v-velocity, scalar, series' - print 'Creating variable vbar' + print('Creating variable vbar') ncv.createVariable('vbar', 'f8', ('ocean_time', 'eta_v', 'xi_v'), fill_value=spval) ncv.variables['vbar'].long_name = '2D v-momentum component' ncv.variables['vbar'].units = 'meter second-1' @@ -112,27 +112,27 @@ def remap_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): # remaping - print 'remapping and rotating u and v from', src_grd.name, \ - 'to', dst_grd.name - print 'time =', time + print('remapping and rotating u and v from', src_grd.name, \ + 'to', dst_grd.name) + print('time =', time) # flood the grid - print 'flood the grid', src_varu.shape + print('flood the grid', src_varu.shape) src_uz = pyroms_toolbox.CGrid_GLORYS.flood(src_varu, src_grd, Cpos='u', \ spval=spval, dmax=dmax, cdepth=cdepth, kk=kk) src_vz = pyroms_toolbox.CGrid_GLORYS.flood(src_varv, src_grd, Cpos='v', \ spval=spval, dmax=dmax, cdepth=cdepth, kk=kk) # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_uz = pyroms.remapping.remap(src_uz, wts_file_u, \ spval=spval) dst_vz = pyroms.remapping.remap(src_vz, wts_file_v, \ spval=spval) # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_u = pyroms.remapping.z2roms(dst_uz[::-1,:,:], dst_grdz, \ dst_grd, Cpos='rho', spval=spval, flood=False) dst_v = pyroms.remapping.z2roms(dst_vz[::-1,:,:], dst_grdz, \ @@ -185,7 +185,7 @@ def remap_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): dst_vbar[idxv[0], idxv[1]] = spval # write data in destination file - print 'write data in destination file' + print('write data in destination file') ncu.variables['ocean_time'][0] = time ncu.variables['u'][0] = dst_u ncu.variables['ubar'][0] = dst_ubar @@ -194,10 +194,10 @@ def remap_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): ncv.variables['v'][0] = dst_v ncv.variables['vbar'][0] = dst_vbar - print dst_u.shape - print dst_ubar.shape - print dst_v.shape - print dst_vbar.shape + print(dst_u.shape) + print(dst_ubar.shape) + print(dst_v.shape) + print(dst_vbar.shape) # close destination file ncu.close() diff --git a/examples/Arctic_HYCOM/fixt.py b/examples/Arctic_HYCOM/fixt.py index 3214db9..86d50c9 100644 --- a/examples/Arctic_HYCOM/fixt.py +++ b/examples/Arctic_HYCOM/fixt.py @@ -41,13 +41,13 @@ for i in range(706,898): if np.fabs(ubar[0,j,i]) > 10: if np.fabs(ubar[0,j,i+1]) > 10: - ubar[0,j,i] = 2/3.0*ubar[0,j,i-1]+1/3.0*ubar[0,j,i+2] - ubar[0,j,i+1] = 1/3.0*ubar[0,j,i-1]+2/3.0*ubar[0,j,i+2] - u[0,:,j,i] = 2/3.0*u[0,:,j,i-1]+1/3.0*u[0,:,j,i+2] - u[0,:,j,i+1] = 1/3.0*u[0,:,j,i-1]+2/3.0*u[0,:,j,i+2] - else: - ubar[0,j,i] = 0.5*(ubar[0,j,i-1]+ubar[0,j,i+1]) - u[0,:,j,i] = 0.5*(u[0,:,j,i-1]+u[0,:,j,i+1]) + ubar[0,j,i] = 2/3.0*ubar[0,j,i-1]+1/3.0*ubar[0,j,i+2] + ubar[0,j,i+1] = 1/3.0*ubar[0,j,i-1]+2/3.0*ubar[0,j,i+2] + u[0,:,j,i] = 2/3.0*u[0,:,j,i-1]+1/3.0*u[0,:,j,i+2] + u[0,:,j,i+1] = 1/3.0*u[0,:,j,i-1]+2/3.0*u[0,:,j,i+2] + else: + ubar[0,j,i] = 0.5*(ubar[0,j,i-1]+ubar[0,j,i+1]) + u[0,:,j,i] = 0.5*(u[0,:,j,i-1]+u[0,:,j,i+1]) vbar = root.variables['vbar'][:] @@ -66,13 +66,13 @@ for i in range(708,900): if np.fabs(vbar[0,j,i]) > 10: if np.fabs(vbar[0,j,i+1]) > 10: - vbar[0,j,i] = 2/3.0*vbar[0,j,i-1]+1/3.0*vbar[0,j,i+2] - vbar[0,j,i+1] = 1/3.0*vbar[0,j,i-1]+2/3.0*vbar[0,j,i+2] - v[0,:,j,i] = 2/3.0*v[0,:,j,i-1]+1/3.0*v[0,:,j,i+2] - v[0,:,j,i+1] = 1/3.0*v[0,:,j,i-1]+2/3.0*v[0,:,j,i+2] - else: - vbar[0,j,i] = 0.5*(vbar[0,j,i-1]+vbar[0,j,i+1]) - v[0,:,j,i] = 0.5*(v[0,:,j,i-1]+v[0,:,j,i+1]) + vbar[0,j,i] = 2/3.0*vbar[0,j,i-1]+1/3.0*vbar[0,j,i+2] + vbar[0,j,i+1] = 1/3.0*vbar[0,j,i-1]+2/3.0*vbar[0,j,i+2] + v[0,:,j,i] = 2/3.0*v[0,:,j,i-1]+1/3.0*v[0,:,j,i+2] + v[0,:,j,i+1] = 1/3.0*v[0,:,j,i-1]+2/3.0*v[0,:,j,i+2] + else: + vbar[0,j,i] = 0.5*(vbar[0,j,i-1]+vbar[0,j,i+1]) + v[0,:,j,i] = 0.5*(v[0,:,j,i-1]+v[0,:,j,i+1]) root.variables['ubar'][:] = ubar root.variables['u'][:] = u diff --git a/examples/Arctic_HYCOM/get_hycom_GLBa0.08_salt_2014.py b/examples/Arctic_HYCOM/get_hycom_GLBa0.08_salt_2014.py index 294f6a3..257a231 100644 --- a/examples/Arctic_HYCOM/get_hycom_GLBa0.08_salt_2014.py +++ b/examples/Arctic_HYCOM/get_hycom_GLBa0.08_salt_2014.py @@ -12,7 +12,7 @@ def create_HYCOM_file(name, time, lon, lat, z, var): - print 'Write with file %s' %name + print('Write with file %s' %name) #create netCDF file nc = netCDF4.Dataset(name, 'w', format='NETCDF3_64BIT') @@ -57,7 +57,7 @@ def create_HYCOM_file(name, time, lon, lat, z, var): nc.close() - print 'Done with file %s' %name + print('Done with file %s' %name) @@ -92,7 +92,7 @@ def create_HYCOM_file(name, time, lon, lat, z, var): daysinyear = 94 for day in range(1,daysinyear+1): #for day in range(95,daysinyear+1): - print 'Processing file for %s, day %03d, year %04d' %(invarname, day, year) + print('Processing file for %s, day %03d, year %04d' %(invarname, day, year)) url='http://tds.hycom.org/thredds/dodsC/datasets/GLBa0.08/expt_91.0/2014/salt/archv.%04d_%03d_00_3zs.nc' %(year,day) # url='http://tds.hycom.org/thredds/dodsC/datasets/GLBa0.08/expt_91.1/2014/salt/archv.%04d_%03d_00_3zs.nc' %(year,day) #get data from server @@ -101,9 +101,9 @@ def create_HYCOM_file(name, time, lon, lat, z, var): var = dataset.variables[invarname][0,:,2100:,550:4040] spval = var.get_fill_value() dataset.close() - print 'Got %s from server...' %invarname + print('Got %s from server...' %invarname) except: - print 'No file on the server... We skip this day.' + print('No file on the server... We skip this day.') retry_day.append(day) continue @@ -115,10 +115,10 @@ def create_HYCOM_file(name, time, lon, lat, z, var): if retry == 'True': if len(retry_day) != 0: - print "Some file have not been downloded... Let's try again" + print("Some file have not been downloded... Let's try again") while len(retry_day) != 0: for day in retry_day: - print 'Retry file for %s, day %03d, year %04d' %(invarname, day, year) + print('Retry file for %s, day %03d, year %04d' %(invarname, day, year)) url='http://tds.hycom.org/thredds/dodsC/datasets/GLBa0.08/expt_91.0/2014/salt/archv.%04d_%03d_00_3zs.nc' %(year,day) # url='http://tds.hycom.org/thredds/dodsC/datasets/GLBa0.08/expt_91.1/2014/salt/archv.%04d_%03d_00_3zs.nc' %(year,day) #get data from server @@ -127,9 +127,9 @@ def create_HYCOM_file(name, time, lon, lat, z, var): var = dataset.variables[invarname][0,:,2100:,550:4040] spval = var.get_fill_value() dataset.close() - print 'Got %s from server...' %invarname + print('Got %s from server...' %invarname) except: - print 'No file on the server... We skip this day.' + print('No file on the server... We skip this day.') continue #create netCDF file diff --git a/examples/Arctic_HYCOM/get_hycom_GLBa0.08_ssh_2014.py b/examples/Arctic_HYCOM/get_hycom_GLBa0.08_ssh_2014.py index 086ed6d..5958b2e 100644 --- a/examples/Arctic_HYCOM/get_hycom_GLBa0.08_ssh_2014.py +++ b/examples/Arctic_HYCOM/get_hycom_GLBa0.08_ssh_2014.py @@ -48,7 +48,7 @@ def create_HYCOM_file(name, time, lon, lat, var): nc.close() - print 'Done with file %s' %name + print('Done with file %s' %name) @@ -82,7 +82,7 @@ def create_HYCOM_file(name, time, lon, lat, var): daysinyear = 94 for day in range(1,daysinyear+1): #for day in range(95,daysinyear+1): - print 'Processing file for day %03d, year %04d' %(day, year) + print('Processing file for day %03d, year %04d' %(day, year)) url='http://tds.hycom.org/thredds/dodsC/datasets/GLBa0.08/expt_91.0/2014/2d/archv.%04d_%03d_00_2d.nc' %(year,day) # url='http://tds.hycom.org/thredds/dodsC/datasets/GLBa0.08/expt_91.1/2014/2d/archv.%04d_%03d_00_2d.nc' %(year,day) #get data from server @@ -92,7 +92,7 @@ def create_HYCOM_file(name, time, lon, lat, var): spval = var.get_fill_value() dataset.close() except: - print 'No file on the server... We skip this day.' + print('No file on the server... We skip this day.') retry_day.append(day) continue @@ -104,10 +104,10 @@ def create_HYCOM_file(name, time, lon, lat, var): if retry == 'True': if len(retry_day) != 0: - print "Some file have not been downloded... Let's try again" + print("Some file have not been downloded... Let's try again") while len(retry_day) != 0: for day in retry_day: - print 'Retry file for day %03d, year %04d' %(day, year) + print('Retry file for day %03d, year %04d' %(day, year)) url='http://tds.hycom.org/thredds/dodsC/datasets/GLBa0.08/expt_91.0/2014/2d/archv.%04d_%03d_00_2d.nc' %(year,day) # url='http://tds.hycom.org/thredds/dodsC/datasets/GLBa0.08/expt_91.1/2014/2d/archv.%04d_%03d_00_2d.nc' %(year,day) #get data from server @@ -117,7 +117,7 @@ def create_HYCOM_file(name, time, lon, lat, var): spval = var.get_fill_value() dataset.close() except: - print 'No file on the server... We skip this day.' + print('No file on the server... We skip this day.') continue #create netCDF file diff --git a/examples/Arctic_HYCOM/get_hycom_GLBa0.08_temp_2014.py b/examples/Arctic_HYCOM/get_hycom_GLBa0.08_temp_2014.py index 3af6443..09969cb 100644 --- a/examples/Arctic_HYCOM/get_hycom_GLBa0.08_temp_2014.py +++ b/examples/Arctic_HYCOM/get_hycom_GLBa0.08_temp_2014.py @@ -12,7 +12,7 @@ def create_HYCOM_file(name, time, lon, lat, z, var): - print 'Write with file %s' %name + print('Write with file %s' %name) #create netCDF file nc = netCDF4.Dataset(name, 'w', format='NETCDF3_64BIT') @@ -57,7 +57,7 @@ def create_HYCOM_file(name, time, lon, lat, z, var): nc.close() - print 'Done with file %s' %name + print('Done with file %s' %name) @@ -92,7 +92,7 @@ def create_HYCOM_file(name, time, lon, lat, z, var): daysinyear = 94 for day in range(1,daysinyear+1): #for day in range(95,daysinyear+1): - print 'Processing file for %s, day %03d, year %04d' %(invarname, day, year) + print('Processing file for %s, day %03d, year %04d' %(invarname, day, year)) url='http://tds.hycom.org/thredds/dodsC/datasets/GLBa0.08/expt_91.0/2014/temp/archv.%04d_%03d_00_3zt.nc' %(year,day) # url='http://tds.hycom.org/thredds/dodsC/datasets/GLBa0.08/expt_91.1/2014/temp/archv.%04d_%03d_00_3zt.nc' %(year,day) #get data from server @@ -101,9 +101,9 @@ def create_HYCOM_file(name, time, lon, lat, z, var): var = dataset.variables[invarname][0,:,2100:,550:4040] spval = var.get_fill_value() dataset.close() - print 'Got %s from server...' %invarname + print('Got %s from server...' %invarname) except: - print 'No file on the server... We skip this day.' + print('No file on the server... We skip this day.') retry_day.append(day) continue @@ -115,10 +115,10 @@ def create_HYCOM_file(name, time, lon, lat, z, var): if retry == 'True': if len(retry_day) != 0: - print "Some file have not been downloded... Let's try again" + print("Some file have not been downloded... Let's try again") while len(retry_day) != 0: for day in retry_day: - print 'Retry file for %s, day %03d, year %04d' %(invarname, day, year) + print('Retry file for %s, day %03d, year %04d' %(invarname, day, year)) url='http://tds.hycom.org/thredds/dodsC/datasets/GLBa0.08/expt_91.0/2014/temp/archv.%04d_%03d_00_3zt.nc' %(year,day) # url='http://tds.hycom.org/thredds/dodsC/datasets/GLBa0.08/expt_91.1/2014/temp/archv.%04d_%03d_00_3zt.nc' %(year,day) #get data from server @@ -127,9 +127,9 @@ def create_HYCOM_file(name, time, lon, lat, z, var): var = dataset.variables[invarname][0,:,2100:,550:4040] spval = var.get_fill_value() dataset.close() - print 'Got %s from server...' %invarname + print('Got %s from server...' %invarname) except: - print 'No file on the server... We skip this day.' + print('No file on the server... We skip this day.') continue #create netCDF file diff --git a/examples/Arctic_HYCOM/get_hycom_GLBa0.08_u_2014.py b/examples/Arctic_HYCOM/get_hycom_GLBa0.08_u_2014.py index 682e00d..bf7813e 100644 --- a/examples/Arctic_HYCOM/get_hycom_GLBa0.08_u_2014.py +++ b/examples/Arctic_HYCOM/get_hycom_GLBa0.08_u_2014.py @@ -12,7 +12,7 @@ def create_HYCOM_file(name, time, lon, lat, z, var): - print 'Write with file %s' %name + print('Write with file %s' %name) #create netCDF file nc = netCDF4.Dataset(name, 'w', format='NETCDF3_64BIT') @@ -57,7 +57,7 @@ def create_HYCOM_file(name, time, lon, lat, z, var): nc.close() - print 'Done with file %s' %name + print('Done with file %s' %name) @@ -92,7 +92,7 @@ def create_HYCOM_file(name, time, lon, lat, z, var): daysinyear = 94 for day in range(1,daysinyear+1): #for day in range(95,daysinyear+1): - print 'Processing file for %s, day %03d, year %04d' %(invarname, day, year) + print('Processing file for %s, day %03d, year %04d' %(invarname, day, year)) url='http://tds.hycom.org/thredds/dodsC/datasets/GLBa0.08/expt_91.0/2014/uvel/archv.%04d_%03d_00_3zu.nc' %(year,day) # url='http://tds.hycom.org/thredds/dodsC/datasets/GLBa0.08/expt_91.1/2014/uvel/archv.%04d_%03d_00_3zu.nc' %(year,day) #get data from server @@ -101,9 +101,9 @@ def create_HYCOM_file(name, time, lon, lat, z, var): var = dataset.variables[invarname][0,:,2100:,550:4040] spval = var.get_fill_value() dataset.close() - print 'Got %s from server...' %invarname + print('Got %s from server...' %invarname) except: - print 'No file on the server... We skip this day.' + print('No file on the server... We skip this day.') retry_day.append(day) continue @@ -115,10 +115,10 @@ def create_HYCOM_file(name, time, lon, lat, z, var): if retry == 'True': if len(retry_day) != 0: - print "Some file have not been downloded... Let's try again" + print("Some file have not been downloded... Let's try again") while len(retry_day) != 0: for day in retry_day: - print 'Retry file for %s, day %03d, year %04d' %(invarname, day, year) + print('Retry file for %s, day %03d, year %04d' %(invarname, day, year)) url='http://tds.hycom.org/thredds/dodsC/datasets/GLBa0.08/expt_91.0/2014/uvel/archv.%04d_%03d_00_3zu.nc' %(year,day) # url='http://tds.hycom.org/thredds/dodsC/datasets/GLBa0.08/expt_91.1/2014/uvel/archv.%04d_%03d_00_3zu.nc' %(year,day) #get data from server @@ -127,9 +127,9 @@ def create_HYCOM_file(name, time, lon, lat, z, var): var = dataset.variables[invarname][0,:,2100:,550:4040] spval = var.get_fill_value() dataset.close() - print 'Got %s from server...' %invarname + print('Got %s from server...' %invarname) except: - print 'No file on the server... We skip this day.' + print('No file on the server... We skip this day.') continue #create netCDF file diff --git a/examples/Arctic_HYCOM/get_hycom_GLBa0.08_v_2014.py b/examples/Arctic_HYCOM/get_hycom_GLBa0.08_v_2014.py index 122675f..abbb7d2 100644 --- a/examples/Arctic_HYCOM/get_hycom_GLBa0.08_v_2014.py +++ b/examples/Arctic_HYCOM/get_hycom_GLBa0.08_v_2014.py @@ -12,7 +12,7 @@ def create_HYCOM_file(name, time, lon, lat, z, var): - print 'Write with file %s' %name + print('Write with file %s' %name) #create netCDF file nc = netCDF4.Dataset(name, 'w', format='NETCDF3_64BIT') @@ -57,7 +57,7 @@ def create_HYCOM_file(name, time, lon, lat, z, var): nc.close() - print 'Done with file %s' %name + print('Done with file %s' %name) @@ -92,7 +92,7 @@ def create_HYCOM_file(name, time, lon, lat, z, var): daysinyear = 94 for day in range(1,daysinyear+1): #for day in range(95,daysinyear+1): - print 'Processing file for %s, day %03d, year %04d' %(invarname, day, year) + print('Processing file for %s, day %03d, year %04d' %(invarname, day, year)) url='http://tds.hycom.org/thredds/dodsC/datasets/GLBa0.08/expt_91.0/2014/vvel/archv.%04d_%03d_00_3zv.nc' %(year,day) # url='http://tds.hycom.org/thredds/dodsC/datasets/GLBa0.08/expt_91.1/2014/vvel/archv.%04d_%03d_00_3zv.nc' %(year,day) #get data from server @@ -101,9 +101,9 @@ def create_HYCOM_file(name, time, lon, lat, z, var): var = dataset.variables[invarname][0,:,2100:,550:4040] spval = var.get_fill_value() dataset.close() - print 'Got %s from server...' %invarname + print('Got %s from server...' %invarname) except: - print 'No file on the server... We skip this day.' + print('No file on the server... We skip this day.') retry_day.append(day) continue @@ -115,10 +115,10 @@ def create_HYCOM_file(name, time, lon, lat, z, var): if retry == 'True': if len(retry_day) != 0: - print "Some file have not been downloded... Let's try again" + print("Some file have not been downloded... Let's try again") while len(retry_day) != 0: for day in retry_day: - print 'Retry file for %s, day %03d, year %04d' %(invarname, day, year) + print('Retry file for %s, day %03d, year %04d' %(invarname, day, year)) url='http://tds.hycom.org/thredds/dodsC/datasets/GLBa0.08/expt_91.0/2014/vvel/archv.%04d_%03d_00_3zv.nc' %(year,day) # url='http://tds.hycom.org/thredds/dodsC/datasets/GLBa0.08/expt_91.1/2014/vvel/archv.%04d_%03d_00_3zv.nc' %(year,day) #get data from server @@ -127,9 +127,9 @@ def create_HYCOM_file(name, time, lon, lat, z, var): var = dataset.variables[invarname][0,:,2100:,550:4040] spval = var.get_fill_value() dataset.close() - print 'Got %s from server...' %invarname + print('Got %s from server...' %invarname) except: - print 'No file on the server... We skip this day.' + print('No file on the server... We skip this day.') continue #create netCDF file diff --git a/examples/Arctic_HYCOM/make_bdry_file.py b/examples/Arctic_HYCOM/make_bdry_file.py index 8028fa8..d1b5512 100644 --- a/examples/Arctic_HYCOM/make_bdry_file.py +++ b/examples/Arctic_HYCOM/make_bdry_file.py @@ -4,7 +4,7 @@ import subprocess import os import sys -import commands +import subprocess import numpy as np from multiprocessing import Pool #import pdb @@ -29,14 +29,14 @@ for year in lst_year: # lst = commands.getoutput('ls ' + data_dir + 'HYCOM_GLBa0.08_' + year + '*') - lst = commands.getoutput('ls ' + data_dir + 'HYCOM_GLBa0.08_' + year + '_0*') + lst = subprocess.getoutput('ls ' + data_dir + 'HYCOM_GLBa0.08_' + year + '_0*') # lst = commands.getoutput('ls ' + data_dir + 'HYCOM_GLBa0.08_' + year + '_0[4-9]*') lst = lst.split() lst_file = lst_file + lst -print 'Build OBC file from the following file list:' -print lst_file -print ' ' +print('Build OBC file from the following file list:') +print(lst_file) +print(' ') src_grd_file = data_dir + '../HYCOM_GLBa0.08_North_grid2.nc' src_grd = pyroms_toolbox.Grid_HYCOM.get_nc_Grid_HYCOM(src_grd_file) diff --git a/examples/Arctic_HYCOM/make_clm_file.py b/examples/Arctic_HYCOM/make_clm_file.py index b4afc36..8de0bc9 100644 --- a/examples/Arctic_HYCOM/make_clm_file.py +++ b/examples/Arctic_HYCOM/make_clm_file.py @@ -1,7 +1,7 @@ import subprocess import os import sys -import commands +import subprocess import numpy as np from datetime import datetime import matplotlib @@ -23,13 +23,13 @@ for year in lst_year: year = np.str(year) # lst = commands.getoutput('ls ' + data_dir + 'SODA_2.1.6_' + year + '_0*') - lst = commands.getoutput('ls ' + data_dir + '*' + year + '*') + lst = subprocess.getoutput('ls ' + data_dir + '*' + year + '*') lst = lst.split() lst_file = lst_file + lst -print 'Build CLM file from the following file list:' -print lst_file -print ' ' +print('Build CLM file from the following file list:') +print(lst_file) +print(' ') src_grd = pyroms_toolbox.Grid_HYCOM.get_nc_Grid_HYCOM('/archive/u1/uaf/kate/HYCOM/Svalbard/HYCOM_GLBa0.08_North_grid2.nc') dst_grd = pyroms.grid.get_ROMS_grid('ARCTIC2') @@ -47,26 +47,26 @@ out_file = dst_dir + file.rsplit('/')[-1][:-3] + '_ssh_clim_' + dst_grd.name + '.nc' command = ('ncks', '-a', '-O', out_file, clim_file) - print command + print(command) subprocess.check_call(command) os.remove(out_file) out_file = dst_dir + file.rsplit('/')[-1][:-3] + '_temp_clim_' + dst_grd.name + '.nc' command = ('ncks', '-a', '-A', out_file, clim_file) - print command + print(command) subprocess.check_call(command) os.remove(out_file) out_file = dst_dir + file.rsplit('/')[-1][:-3] + '_salt_clim_' + dst_grd.name + '.nc' command = ('ncks', '-a', '-A', out_file, clim_file) - print command + print(command) subprocess.check_call(command) os.remove(out_file) out_file = dst_dir + file.rsplit('/')[-1][:-3] + '_u_clim_' + dst_grd.name + '.nc' command = ('ncks', '-a', '-A', out_file, clim_file) - print command + print(command) subprocess.check_call(command) os.remove(out_file) out_file = dst_dir + file.rsplit('/')[-1][:-3] + '_v_clim_' + dst_grd.name + '.nc' command = ('ncks', '-a', '-A', out_file, clim_file) - print command + print(command) subprocess.check_call(command) os.remove(out_file) diff --git a/examples/Arctic_HYCOM/make_ic_file.py b/examples/Arctic_HYCOM/make_ic_file.py index a4f2c45..55d2ac2 100644 --- a/examples/Arctic_HYCOM/make_ic_file.py +++ b/examples/Arctic_HYCOM/make_ic_file.py @@ -1,6 +1,6 @@ import subprocess import os -import commands +import subprocess import numpy as np import matplotlib matplotlib.use('Agg') @@ -15,9 +15,9 @@ file = '/archive/u1/uaf/kate/HYCOM/Svalbard/data/HYCOM_GLBa0.08_2009_001.nc' dst_dir='./' -print 'Build IC file from the following file:' -print file -print ' ' +print('Build IC file from the following file:') +print(file) +print(' ') src_grd = pyroms_toolbox.Grid_HYCOM.get_nc_Grid_HYCOM('/archive/u1/uaf/kate/HYCOM/Svalbard/HYCOM_GLBa0.08_North_grid2.nc') dst_grd = pyroms.grid.get_ROMS_grid('ARCTIC2') @@ -34,26 +34,26 @@ out_file = dst_dir + file.rsplit('/')[-1][:-3] + '_ssh_ic_' + dst_grd.name + '.nc' command = ('ncks', '-a', '-O', out_file, ic_file) -print command +print(command) subprocess.check_call(command) os.remove(out_file) out_file = dst_dir + file.rsplit('/')[-1][:-3] + '_temp_ic_' + dst_grd.name + '.nc' command = ('ncks', '-a', '-A', out_file, ic_file) -print command +print(command) subprocess.check_call(command) os.remove(out_file) out_file = dst_dir + file.rsplit('/')[-1][:-3] + '_salt_ic_' + dst_grd.name + '.nc' command = ('ncks', '-a', '-A', out_file, ic_file) -print command +print(command) subprocess.check_call(command) os.remove(out_file) out_file = dst_dir + file.rsplit('/')[-1][:-3] + '_u_ic_' + dst_grd.name + '.nc' command = ('ncks', '-a', '-A', out_file, ic_file) -print command +print(command) subprocess.check_call(command) os.remove(out_file) out_file = dst_dir + file.rsplit('/')[-1][:-3] + '_v_ic_' + dst_grd.name + '.nc' command = ('ncks', '-a', '-A', out_file, ic_file) -print command +print(command) subprocess.check_call(command) os.remove(out_file) diff --git a/examples/Arctic_HYCOM/remap.py b/examples/Arctic_HYCOM/remap.py index 38e9238..55560dd 100644 --- a/examples/Arctic_HYCOM/remap.py +++ b/examples/Arctic_HYCOM/remap.py @@ -41,7 +41,7 @@ def remap(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, dst_d # create IC file dst_file = src_file.rsplit('/')[-1] dst_file = dst_dir + dst_file[:-3] + '_' + src_varname + '_ic_' + dst_grd.name + '.nc' - print '\nCreating file', dst_file + print('\nCreating file', dst_file) if os.path.exists(dst_file) is True: os.remove(dst_file) pyroms_toolbox.nc_create_roms_file(dst_file, dst_grd, nctime) @@ -95,7 +95,7 @@ def remap(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, dst_d units = 'PSU' field = 'salinity, scalar, series' else: - raise ValueError, 'Undefined src_varname' + raise ValueError('Undefined src_varname') if ndim == 3: @@ -107,7 +107,7 @@ def remap(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, dst_d # create variable in file - print 'Creating variable', dst_varname + print('Creating variable', dst_varname) nc.createVariable(dst_varname, 'f8', dimensions, fill_value=spval) nc.variables[dst_varname].long_name = long_name nc.variables[dst_varname].units = units @@ -115,34 +115,34 @@ def remap(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, dst_d # remapping - print 'remapping', dst_varname, 'from', src_grd.name, \ - 'to', dst_grd.name - print 'time =', time + print('remapping', dst_varname, 'from', src_grd.name, \ + 'to', dst_grd.name) + print('time =', time) if ndim == 3: # flood the grid - print 'flood the grid' + print('flood the grid') src_varz = pyroms_toolbox.Grid_HYCOM.flood_fast(src_var, src_grd, pos=pos, spval=spval, \ dxy=dxy, cdepth=cdepth, kk=kk) else: src_varz = src_var # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_varz = pyroms.remapping.remap(src_varz, wts_file, \ spval=spval) if ndim == 3: # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_var = pyroms.remapping.z2roms(dst_varz[::-1,:,:], dst_grdz, \ dst_grd, Cpos=Cpos, spval=spval, flood=False) else: dst_var = dst_varz # write data in destination file - print 'write data in destination file' + print('write data in destination file') nc.variables['ocean_time'][0] = time nc.variables[dst_varname][0] = dst_var diff --git a/examples/Arctic_HYCOM/remap_bdry.py b/examples/Arctic_HYCOM/remap_bdry.py index 8ff2232..62d2d31 100644 --- a/examples/Arctic_HYCOM/remap_bdry.py +++ b/examples/Arctic_HYCOM/remap_bdry.py @@ -18,7 +18,7 @@ class nctime(object): def remap_bdry(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=2, dst_dir='./'): - print src_file + print(src_file) # get time nctime.long_name = 'time' @@ -27,7 +27,7 @@ def remap_bdry(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=2, # create boundary file dst_file = src_file.rsplit('/')[-1] dst_file = dst_dir + dst_file[:-3] + '_' + src_varname + '_bdry_' + dst_grd.name + '.nc' - print '\nCreating boundary file', dst_file + print('\nCreating boundary file', dst_file) if os.path.exists(dst_file) is True: os.remove(dst_file) pyroms_toolbox.nc_create_roms_bdry_file(dst_file, dst_grd, nctime) @@ -39,7 +39,7 @@ def remap_bdry(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=2, cdf = netCDF.Dataset(src_file) src_var = cdf.variables[src_varname] time = cdf.variables['ocean_time'][0] - print time + print(time) #get missing value spval = src_var._FillValue @@ -124,7 +124,7 @@ def remap_bdry(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=2, field_west = 'salt_west, scalar, series' units = 'PSU' else: - raise ValueError, 'Undefined src_varname' + raise ValueError('Undefined src_varname') if ndim == 3: @@ -136,25 +136,25 @@ def remap_bdry(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=2, # create variable in boudary file - print 'Creating variable', dst_varname_north + print('Creating variable', dst_varname_north) nc.createVariable(dst_varname_north, 'f8', dimensions_north, fill_value=spval) nc.variables[dst_varname_north].long_name = long_name_north nc.variables[dst_varname_north].units = units nc.variables[dst_varname_north].field = field_north - print 'Creating variable', dst_varname_south + print('Creating variable', dst_varname_south) nc.createVariable(dst_varname_south, 'f8', dimensions_south, fill_value=spval) nc.variables[dst_varname_south].long_name = long_name_south nc.variables[dst_varname_south].units = units nc.variables[dst_varname_south].field = field_south - print 'Creating variable', dst_varname_east + print('Creating variable', dst_varname_east) nc.createVariable(dst_varname_east, 'f8', dimensions_east, fill_value=spval) nc.variables[dst_varname_east].long_name = long_name_east nc.variables[dst_varname_east].units = units nc.variables[dst_varname_east].field = field_east - print 'Creating variable', dst_varname_west + print('Creating variable', dst_varname_west) nc.createVariable(dst_varname_west, 'f8', dimensions_west, fill_value=spval) nc.variables[dst_varname_west].long_name = long_name_west nc.variables[dst_varname_west].units = units @@ -162,26 +162,26 @@ def remap_bdry(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=2, # remapping - print 'remapping', dst_varname, 'from', src_grd.name, \ - 'to', dst_grd.name - print 'time =', time + print('remapping', dst_varname, 'from', src_grd.name, \ + 'to', dst_grd.name) + print('time =', time) if ndim == 3: # flood the grid - print 'flood the grid' + print('flood the grid') src_varz = pyroms_toolbox.Grid_HYCOM.flood_fast(src_var, src_grd, pos=pos, spval=spval, \ dxy=dxy, cdepth=cdepth, kk=kk) else: src_varz = src_var # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_varz = pyroms.remapping.remap(src_varz, wts_file, spval=spval) if ndim == 3: # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_var_north = pyroms.remapping.z2roms(dst_varz[::-1, Mp-1:Mp, :], \ dst_grdz, dst_grd, Cpos=Cpos, spval=spval, \ flood=False, irange=(0,Lp), jrange=(Mp-1,Mp)) @@ -201,7 +201,7 @@ def remap_bdry(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=2, dst_var_west = dst_varz[:, 0] # write data in destination file - print 'write data in destination file' + print('write data in destination file') nc.variables['ocean_time'][0] = time nc.variables[dst_varname_north][0] = np.squeeze(dst_var_north) nc.variables[dst_varname_south][0] = np.squeeze(dst_var_south) diff --git a/examples/Arctic_HYCOM/remap_bdry_uv.py b/examples/Arctic_HYCOM/remap_bdry_uv.py index 5bf4c69..ad093f8 100644 --- a/examples/Arctic_HYCOM/remap_bdry_uv.py +++ b/examples/Arctic_HYCOM/remap_bdry_uv.py @@ -28,12 +28,12 @@ def remap_bdry_uv(src_file, src_grd, dst_grd, dxy=20, cdepth=0, kk=2, dst_dir='. # create destination file dst_file = src_file.rsplit('/')[-1] dst_fileu = dst_dir + dst_file[:-3] + '_u_bdry_' + dst_grd.name + '.nc' - print '\nCreating destination file', dst_fileu + print('\nCreating destination file', dst_fileu) if os.path.exists(dst_fileu) is True: os.remove(dst_fileu) pyroms_toolbox.nc_create_roms_file(dst_fileu, dst_grd, nctime) dst_filev = dst_dir + dst_file[:-3] + '_v_bdry_' + dst_grd.name + '.nc' - print 'Creating destination file', dst_filev + print('Creating destination file', dst_filev) if os.path.exists(dst_filev) is True: os.remove(dst_filev) pyroms_toolbox.nc_create_roms_file(dst_filev, dst_grd, nctime) @@ -64,95 +64,95 @@ def remap_bdry_uv(src_file, src_grd, dst_grd, dxy=20, cdepth=0, kk=2, dst_dir='. dst_grdz = pyroms.grid.ROMS_Grid(dst_grd.name+'_Z', dst_grd.hgrid, dst_zcoord) # create variable in destination file - print 'Creating variable u_north' + print('Creating variable u_north') ncu.createVariable('u_north', 'f8', ('ocean_time', 's_rho', 'xi_u'), fill_value=spval) ncu.variables['u_north'].long_name = '3D u-momentum north boundary condition' ncu.variables['u_north'].units = 'meter second-1' ncu.variables['u_north'].field = 'u_north, scalar, series' - print 'Creating variable u_south' + print('Creating variable u_south') ncu.createVariable('u_south', 'f8', ('ocean_time', 's_rho', 'xi_u'), fill_value=spval) ncu.variables['u_south'].long_name = '3D u-momentum south boundary condition' ncu.variables['u_south'].units = 'meter second-1' ncu.variables['u_south'].field = 'u_south, scalar, series' - print 'Creating variable u_east' + print('Creating variable u_east') ncu.createVariable('u_east', 'f8', ('ocean_time', 's_rho', 'eta_u'), fill_value=spval) ncu.variables['u_east'].long_name = '3D u-momentum east boundary condition' ncu.variables['u_east'].units = 'meter second-1' ncu.variables['u_east'].field = 'u_east, scalar, series' - print 'Creating variable u_west' + print('Creating variable u_west') ncu.createVariable('u_west', 'f8', ('ocean_time', 's_rho', 'eta_u'), fill_value=spval) ncu.variables['u_west'].long_name = '3D u-momentum west boundary condition' ncu.variables['u_west'].units = 'meter second-1' ncu.variables['u_west'].field = 'u_east, scalar, series' # create variable in destination file - print 'Creating variable ubar_north' + print('Creating variable ubar_north') ncu.createVariable('ubar_north', 'f8', ('ocean_time', 'xi_u'), fill_value=spval) ncu.variables['ubar_north'].long_name = '2D u-momentum north boundary condition' ncu.variables['ubar_north'].units = 'meter second-1' ncu.variables['ubar_north'].field = 'ubar_north, scalar, series' - print 'Creating variable ubar_south' + print('Creating variable ubar_south') ncu.createVariable('ubar_south', 'f8', ('ocean_time', 'xi_u'), fill_value=spval) ncu.variables['ubar_south'].long_name = '2D u-momentum south boundary condition' ncu.variables['ubar_south'].units = 'meter second-1' ncu.variables['ubar_south'].field = 'ubar_south, scalar, series' - print 'Creating variable ubar_east' + print('Creating variable ubar_east') ncu.createVariable('ubar_east', 'f8', ('ocean_time', 'eta_u'), fill_value=spval) ncu.variables['ubar_east'].long_name = '2D u-momentum east boundary condition' ncu.variables['ubar_east'].units = 'meter second-1' ncu.variables['ubar_east'].field = 'ubar_east, scalar, series' - print 'Creating variable ubar_west' + print('Creating variable ubar_west') ncu.createVariable('ubar_west', 'f8', ('ocean_time', 'eta_u'), fill_value=spval) ncu.variables['ubar_west'].long_name = '2D u-momentum west boundary condition' ncu.variables['ubar_west'].units = 'meter second-1' ncu.variables['ubar_west'].field = 'ubar_east, scalar, series' - print 'Creating variable v_north' + print('Creating variable v_north') ncv.createVariable('v_north', 'f8', ('ocean_time', 's_rho', 'xi_v'), fill_value=spval) ncv.variables['v_north'].long_name = '3D v-momentum north boundary condition' ncv.variables['v_north'].units = 'meter second-1' ncv.variables['v_north'].field = 'v_north, scalar, series' - print 'Creating variable v_south' + print('Creating variable v_south') ncv.createVariable('v_south', 'f8', ('ocean_time', 's_rho', 'xi_v'), fill_value=spval) ncv.variables['v_south'].long_name = '3D v-momentum south boundary condition' ncv.variables['v_south'].units = 'meter second-1' ncv.variables['v_south'].field = 'v_south, scalar, series' - print 'Creating variable v_east' + print('Creating variable v_east') ncv.createVariable('v_east', 'f8', ('ocean_time', 's_rho', 'eta_v'), fill_value=spval) ncv.variables['v_east'].long_name = '3D v-momentum east boundary condition' ncv.variables['v_east'].units = 'meter second-1' ncv.variables['v_east'].field = 'v_east, scalar, series' - print 'Creating variable v_west' + print('Creating variable v_west') ncv.createVariable('v_west', 'f8', ('ocean_time', 's_rho', 'eta_v'), fill_value=spval) ncv.variables['v_west'].long_name = '3D v-momentum west boundary condition' ncv.variables['v_west'].units = 'meter second-1' ncv.variables['v_west'].field = 'v_east, scalar, series' - print 'Creating variable vbar_north' + print('Creating variable vbar_north') ncv.createVariable('vbar_north', 'f8', ('ocean_time', 'xi_v'), fill_value=spval) ncv.variables['vbar_north'].long_name = '2D v-momentum north boundary condition' ncv.variables['vbar_north'].units = 'meter second-1' ncv.variables['vbar_north'].field = 'vbar_north, scalar, series' - print 'Creating variable vbar_south' + print('Creating variable vbar_south') ncv.createVariable('vbar_south', 'f8', ('ocean_time', 'xi_v'), fill_value=spval) ncv.variables['vbar_south'].long_name = '2D v-momentum south boundary condition' ncv.variables['vbar_south'].units = 'meter second-1' ncv.variables['vbar_south'].field = 'vbar_south, scalar, series' - print 'Creating variable vbar_east' + print('Creating variable vbar_east') ncv.createVariable('vbar_east', 'f8', ('ocean_time', 'eta_v'), fill_value=spval) ncv.variables['vbar_east'].long_name = '2D v-momentum east boundary condition' ncv.variables['vbar_east'].units = 'meter second-1' ncv.variables['vbar_east'].field = 'vbar_east, scalar, series' - print 'Creating variable vbar_west' + print('Creating variable vbar_west') ncv.createVariable('vbar_west', 'f8', ('ocean_time', 'eta_v'), fill_value=spval) ncv.variables['vbar_west'].long_name = '2D v-momentum west boundary condition' ncv.variables['vbar_west'].units = 'meter second-1' @@ -161,27 +161,27 @@ def remap_bdry_uv(src_file, src_grd, dst_grd, dxy=20, cdepth=0, kk=2, dst_dir='. # remaping - print 'remapping and rotating u and v from', src_grd.name, \ - 'to', dst_grd.name - print 'time =', time + print('remapping and rotating u and v from', src_grd.name, \ + 'to', dst_grd.name) + print('time =', time) # flood the grid - print 'flood the grid' + print('flood the grid') src_uz = pyroms_toolbox.Grid_HYCOM.flood_fast(src_varu, src_grd, pos='t', \ spval=spval, dxy=dxy, cdepth=cdepth, kk=kk) src_vz = pyroms_toolbox.Grid_HYCOM.flood_fast(src_varv, src_grd, pos='t', \ spval=spval, dxy=dxy, cdepth=cdepth, kk=kk) # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_uz = pyroms.remapping.remap(src_uz, wts_file, \ spval=spval) dst_vz = pyroms.remapping.remap(src_vz, wts_file, \ spval=spval) # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_u_north = pyroms.remapping.z2roms(dst_uz[::-1, Mp-2:Mp, 0:Lp], \ dst_grdz, dst_grd, Cpos='rho', spval=spval, \ flood=False, irange=(0,Lp), jrange=(Mp-2,Mp)) @@ -325,7 +325,7 @@ def remap_bdry_uv(src_file, src_grd, dst_grd, dxy=20, cdepth=0, kk=2, dst_dir='. dst_vbar_west = np.ma.masked_where(dst_grd.hgrid.mask_v[:,0] == 0, dst_vbar_west) # write data in destination file - print 'write data in destination file' + print('write data in destination file') ncu.variables['ocean_time'][0] = time ncu.variables['u_north'][0] = dst_u_north ncu.variables['u_south'][0] = dst_u_south diff --git a/examples/Arctic_HYCOM/remap_clm.py b/examples/Arctic_HYCOM/remap_clm.py index c5aafe5..3505435 100644 --- a/examples/Arctic_HYCOM/remap_clm.py +++ b/examples/Arctic_HYCOM/remap_clm.py @@ -41,7 +41,7 @@ def remap_clm(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, d # create IC file dst_file = src_file.rsplit('/')[-1] dst_file = dst_dir + dst_file[:-3] + '_' + src_varname + '_clim_' + dst_grd.name + '.nc' - print '\nCreating file', dst_file + print('\nCreating file', dst_file) if os.path.exists(dst_file) is True: os.remove(dst_file) pyroms_toolbox.nc_create_roms_file(dst_file, dst_grd, nctime) @@ -72,7 +72,7 @@ def remap_clm(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, d long_name = 'free-surface' units = 'meter' field = 'free-surface, scalar, series' - vartime = 'ocean_time' + vartime = 'ocean_time' elif src_varname == 'temp': pos = 't' Cpos = 'rho' @@ -84,7 +84,7 @@ def remap_clm(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, d long_name = 'potential temperature' units = 'Celsius' field = 'temperature, scalar, series' - vartime = 'ocean_time' + vartime = 'ocean_time' elif src_varname == 'salt': pos = 't' Cpos = 'rho' @@ -96,9 +96,9 @@ def remap_clm(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, d long_name = 'salinity' units = 'PSU' field = 'salinity, scalar, series' - vartime = 'ocean_time' + vartime = 'ocean_time' else: - raise ValueError, 'Undefined src_varname' + raise ValueError('Undefined src_varname') if ndim == 3: @@ -110,7 +110,7 @@ def remap_clm(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, d # create variable in file - print 'Creating variable', dst_varname + print('Creating variable', dst_varname) nc.createVariable(dst_varname, 'f8', dimensions, fill_value=spval) nc.variables[dst_varname].long_name = long_name nc.variables[dst_varname].units = units @@ -119,34 +119,34 @@ def remap_clm(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, d # remapping - print 'remapping', dst_varname, 'from', src_grd.name, \ - 'to', dst_grd.name - print 'time =', time + print('remapping', dst_varname, 'from', src_grd.name, \ + 'to', dst_grd.name) + print('time =', time) if ndim == 3: # flood the grid - print 'flood the grid' + print('flood the grid') src_varz = pyroms_toolbox.Grid_HYCOM.flood_fast(src_var, src_grd, pos=pos, spval=spval, \ dxy=dxy, cdepth=cdepth, kk=kk) else: src_varz = src_var # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_varz = pyroms.remapping.remap(src_varz, wts_file, \ spval=spval) if ndim == 3: # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_var = pyroms.remapping.z2roms(dst_varz[::-1,:,:], dst_grdz, \ dst_grd, Cpos=Cpos, spval=spval, flood=False) else: dst_var = dst_varz # write data in destination file - print 'write data in destination file' + print('write data in destination file') nc.variables['ocean_time'][0] = time nc.variables[dst_varname][0] = dst_var diff --git a/examples/Arctic_HYCOM/remap_clm_uv.py b/examples/Arctic_HYCOM/remap_clm_uv.py index ede5f9a..e91f265 100644 --- a/examples/Arctic_HYCOM/remap_clm_uv.py +++ b/examples/Arctic_HYCOM/remap_clm_uv.py @@ -43,12 +43,12 @@ def remap_clm_uv(src_file, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, dst_dir='./ # create destination file dst_file = src_file.rsplit('/')[-1] dst_fileu = dst_dir + dst_file[:-3] + '_u_clim_' + dst_grd.name + '.nc' - print '\nCreating destination file', dst_fileu + print('\nCreating destination file', dst_fileu) if os.path.exists(dst_fileu) is True: os.remove(dst_fileu) pyroms_toolbox.nc_create_roms_file(dst_fileu, dst_grd, nctime) dst_filev = dst_dir + dst_file[:-3] + '_v_clim_' + dst_grd.name + '.nc' - print 'Creating destination file', dst_filev + print('Creating destination file', dst_filev) if os.path.exists(dst_filev) is True: os.remove(dst_filev) pyroms_toolbox.nc_create_roms_file(dst_filev, dst_grd, nctime) @@ -77,27 +77,27 @@ def remap_clm_uv(src_file, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, dst_dir='./ dst_grdz = pyroms.grid.ROMS_Grid(dst_grd.name+'_Z', dst_grd.hgrid, dst_zcoord) # create variable in destination file - print 'Creating variable u' + print('Creating variable u') ncu.createVariable('u', 'f8', ('ocean_time', 's_rho', 'eta_u', 'xi_u'), fill_value=spval) ncu.variables['u'].long_name = '3D u-momentum component' ncu.variables['u'].units = 'meter second-1' ncu.variables['u'].field = 'u-velocity, scalar, series' ncu.variables['u'].time = 'ocean_time' # create variable in destination file - print 'Creating variable ubar' + print('Creating variable ubar') ncu.createVariable('ubar', 'f8', ('ocean_time', 'eta_u', 'xi_u'), fill_value=spval) ncu.variables['ubar'].long_name = '2D u-momentum component' ncu.variables['ubar'].units = 'meter second-1' ncu.variables['ubar'].field = 'ubar-velocity,, scalar, series' ncu.variables['ubar'].time = 'ocean_time' - print 'Creating variable v' + print('Creating variable v') ncv.createVariable('v', 'f8', ('ocean_time', 's_rho', 'eta_v', 'xi_v'), fill_value=spval) ncv.variables['v'].long_name = '3D v-momentum component' ncv.variables['v'].units = 'meter second-1' ncv.variables['v'].field = 'v-velocity, scalar, series' ncv.variables['v'].time = 'ocean_time' - print 'Creating variable vbar' + print('Creating variable vbar') ncv.createVariable('vbar', 'f8', ('ocean_time', 'eta_v', 'xi_v'), fill_value=spval) ncv.variables['vbar'].long_name = '2D v-momentum component' ncv.variables['vbar'].units = 'meter second-1' @@ -106,27 +106,27 @@ def remap_clm_uv(src_file, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, dst_dir='./ # remaping - print 'remapping and rotating u and v from', src_grd.name, \ - 'to', dst_grd.name - print 'time =', time + print('remapping and rotating u and v from', src_grd.name, \ + 'to', dst_grd.name) + print('time =', time) # flood the grid - print 'flood the grid' + print('flood the grid') src_uz = pyroms_toolbox.Grid_HYCOM.flood_fast(src_varu, src_grd, pos='t', \ spval=spval, dxy=dxy, cdepth=cdepth, kk=kk) src_vz = pyroms_toolbox.Grid_HYCOM.flood_fast(src_varv, src_grd, pos='t', \ spval=spval, dxy=dxy, cdepth=cdepth, kk=kk) # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_uz = pyroms.remapping.remap(src_uz, wts_file, \ spval=spval) dst_vz = pyroms.remapping.remap(src_vz, wts_file, \ spval=spval) # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_u = pyroms.remapping.z2roms(dst_uz[::-1,:,:], dst_grdz, \ dst_grd, Cpos='rho', spval=spval, flood=False) dst_v = pyroms.remapping.z2roms(dst_vz[::-1,:,:], dst_grdz, \ @@ -181,7 +181,7 @@ def remap_clm_uv(src_file, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, dst_dir='./ dst_vbar[idxv[0], idxv[1]] = spval # write data in destination file - print 'write data in destination file' + print('write data in destination file') ncu.variables['ocean_time'][0] = time ncu.variables['u'][0] = dst_u ncu.variables['ubar'][0] = dst_ubar diff --git a/examples/Arctic_HYCOM/remap_uv.py b/examples/Arctic_HYCOM/remap_uv.py index 0d48fc3..1c871c9 100644 --- a/examples/Arctic_HYCOM/remap_uv.py +++ b/examples/Arctic_HYCOM/remap_uv.py @@ -43,12 +43,12 @@ def remap_uv(src_file, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, dst_dir='./'): # create destination file dst_file = src_file.rsplit('/')[-1] dst_fileu = dst_dir + dst_file[:-3] + '_u_ic_' + dst_grd.name + '.nc' - print '\nCreating destination file', dst_fileu + print('\nCreating destination file', dst_fileu) if os.path.exists(dst_fileu) is True: os.remove(dst_fileu) pyroms_toolbox.nc_create_roms_file(dst_fileu, dst_grd, nctime) dst_filev = dst_dir + dst_file[:-3] + '_v_ic_' + dst_grd.name + '.nc' - print 'Creating destination file', dst_filev + print('Creating destination file', dst_filev) if os.path.exists(dst_filev) is True: os.remove(dst_filev) pyroms_toolbox.nc_create_roms_file(dst_filev, dst_grd, nctime) @@ -77,24 +77,24 @@ def remap_uv(src_file, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, dst_dir='./'): dst_grdz = pyroms.grid.ROMS_Grid(dst_grd.name+'_Z', dst_grd.hgrid, dst_zcoord) # create variable in destination file - print 'Creating variable u' + print('Creating variable u') ncu.createVariable('u', 'f8', ('ocean_time', 's_rho', 'eta_u', 'xi_u'), fill_value=spval) ncu.variables['u'].long_name = '3D u-momentum component' ncu.variables['u'].units = 'meter second-1' ncu.variables['u'].field = 'u-velocity, scalar, series' # create variable in destination file - print 'Creating variable ubar' + print('Creating variable ubar') ncu.createVariable('ubar', 'f8', ('ocean_time', 'eta_u', 'xi_u'), fill_value=spval) ncu.variables['ubar'].long_name = '2D u-momentum component' ncu.variables['ubar'].units = 'meter second-1' ncu.variables['ubar'].field = 'ubar-velocity,, scalar, series' - print 'Creating variable v' + print('Creating variable v') ncv.createVariable('v', 'f8', ('ocean_time', 's_rho', 'eta_v', 'xi_v'), fill_value=spval) ncv.variables['v'].long_name = '3D v-momentum component' ncv.variables['v'].units = 'meter second-1' ncv.variables['v'].field = 'v-velocity, scalar, series' - print 'Creating variable vbar' + print('Creating variable vbar') ncv.createVariable('vbar', 'f8', ('ocean_time', 'eta_v', 'xi_v'), fill_value=spval) ncv.variables['vbar'].long_name = '2D v-momentum component' ncv.variables['vbar'].units = 'meter second-1' @@ -102,27 +102,27 @@ def remap_uv(src_file, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, dst_dir='./'): # remaping - print 'remapping and rotating u and v from', src_grd.name, \ - 'to', dst_grd.name - print 'time =', time + print('remapping and rotating u and v from', src_grd.name, \ + 'to', dst_grd.name) + print('time =', time) # flood the grid - print 'flood the grid' + print('flood the grid') src_uz = pyroms_toolbox.Grid_HYCOM.flood_fast(src_varu, src_grd, pos='t', \ spval=spval, dxy=dxy, cdepth=cdepth, kk=kk) src_vz = pyroms_toolbox.Grid_HYCOM.flood_fast(src_varv, src_grd, pos='t', \ spval=spval, dxy=dxy, cdepth=cdepth, kk=kk) # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_uz = pyroms.remapping.remap(src_uz, wts_file, \ spval=spval) dst_vz = pyroms.remapping.remap(src_vz, wts_file, \ spval=spval) # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_u = pyroms.remapping.z2roms(dst_uz[::-1,:,:], dst_grdz, \ dst_grd, Cpos='rho', spval=spval, flood=False) dst_v = pyroms.remapping.z2roms(dst_vz[::-1,:,:], dst_grdz, \ @@ -177,7 +177,7 @@ def remap_uv(src_file, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, dst_dir='./'): dst_vbar[idxv[0], idxv[1]] = spval # write data in destination file - print 'write data in destination file' + print('write data in destination file') ncu.variables['ocean_time'][0] = time ncu.variables['u'][0] = dst_u ncu.variables['ubar'][0] = dst_ubar diff --git a/examples/Arctic_SODA3.3.1/make_bdry_file.py b/examples/Arctic_SODA3.3.1/make_bdry_file.py new file mode 100644 index 0000000..1821570 --- /dev/null +++ b/examples/Arctic_SODA3.3.1/make_bdry_file.py @@ -0,0 +1,71 @@ +import matplotlib +matplotlib.use('Agg') +import subprocess +import os +import sys +import commands +import numpy as np + +#increase the maximum number of open files allowed +#import resource +#resource.setrlimit(resource.RLIMIT_NOFILE, (3000,-1)) + +import pyroms +import pyroms_toolbox + +from remap_bdry import remap_bdry +from remap_bdry_uv import remap_bdry_uv + +my_year=int(sys.argv[-1]) + +data_dir = '/archive/u1/uaf/AKWATERS/kshedstrom/SODA/' +data_dir_year = data_dir + str(my_year) + '/' +dst_dir='bdry/' + +filelst = subprocess.check_output(['ls', data_dir_year]).replace('/n',' ').split() + +#src_grd = pyroms_toolbox.BGrid_GFDL.get_nc_BGrid_GFDL(data_dir + 'grid/SODA3_0.5deg_grid.nc', name='SODA3.3.1', xrange=(285, 500), yrange=(180, 300) ) +#src_grd = pyroms_toolbox.BGrid_GFDL.get_nc_BGrid_GFDL(data_dir + 'grid/SODA3_0.5deg_grid.nc', name='SODA3.3.1', area=npolar, ystart=236) +src_grd = pyroms_toolbox.BGrid_GFDL.get_nc_BGrid_GFDL(data_dir + 'SODA3_0.5deg_grid.nc', name='SODA3.3.1', area='npolar') +dst_grd = pyroms.grid.get_ROMS_grid('ARCTIC4') + +for filein in filelst: + tag=filein.replace('soda3.3.1_5dy_ocean_reg_','').replace('.nc','') + print '\nBuild OBC file for time %s' %filein + zeta_dst_file = dst_dir + dst_grd.name + '_bdry_zeta_' + tag + '_' + src_grd.name + '.nc' + temp_dst_file = dst_dir + dst_grd.name + '_bdry_temp_' + tag + '_' + src_grd.name + '.nc' + salt_dst_file = dst_dir + dst_grd.name + '_bdry_salt_' + tag + '_' + src_grd.name + '.nc' + u_dst_file = dst_dir + dst_grd.name + '_bdry_u_' + tag + '_' + src_grd.name + '.nc' + v_dst_file = dst_dir + dst_grd.name + '_bdry_v_' + tag + '_' + src_grd.name + '.nc' + + # remap ssh + zeta = remap_bdry('ssh', data_dir_year + filein, src_grd, dst_grd, zeta_dst_file, dst_dir=dst_dir) + + # reload grid with zeta (more accurate) + dst_grd = pyroms.grid.get_ROMS_grid('ARCTIC4', zeta=zeta) + + # regrid temp, salt and velocities + remap_bdry('temp',data_dir_year + filein, src_grd, dst_grd, temp_dst_file, dst_dir=dst_dir) + remap_bdry('salt',data_dir_year + filein, src_grd, dst_grd, salt_dst_file, dst_dir=dst_dir) + remap_bdry_uv(data_dir_year + filein, src_grd, dst_grd, u_dst_file, v_dst_file, dst_dir=dst_dir) + + # merge file + bdry_file = dst_dir + dst_grd.name + '_bdry_' + tag + '_' + src_grd.name + '.nc' + + command1 = 'mv ' + zeta_dst_file + ' ' + bdry_file + command2 = 'ncks -A ' + temp_dst_file + ' -o ' + bdry_file + command3 = 'ncks -A ' + salt_dst_file + ' -o ' + bdry_file + command4 = 'ncks -A ' + u_dst_file + ' -o ' + bdry_file + command5 = 'ncks -A ' + v_dst_file + ' -o ' + bdry_file + + subprocess.call(command1,shell=True) + subprocess.call(command2,shell=True) + subprocess.call(command3,shell=True) + subprocess.call(command4,shell=True) + subprocess.call(command5,shell=True) + + # clean up + os.remove(temp_dst_file) + os.remove(salt_dst_file) + os.remove(u_dst_file) + os.remove(v_dst_file) diff --git a/examples/Arctic_SODA3.3.1/make_clm_file.py b/examples/Arctic_SODA3.3.1/make_clm_file.py new file mode 100644 index 0000000..8787185 --- /dev/null +++ b/examples/Arctic_SODA3.3.1/make_clm_file.py @@ -0,0 +1,75 @@ +import matplotlib +matplotlib.use('Agg') +import subprocess +import os +import sys +import commands +import numpy as np + +#increase the maximum number of open files allowed +#import resource +#resource.setrlimit(resource.RLIMIT_NOFILE, (3000,-1)) + +import pyroms +import pyroms_toolbox + +from remap import remap +from remap_uv import remap_uv + +my_year=int(sys.argv[-1]) + +data_dir = '/archive/u1/uaf/AKWATERS/kshedstrom/SODA/' +data_dir_year = data_dir + '/monthly/*' + str(my_year) + '*' +dst_dir='clm/' + +filelst = commands.getoutput('ls ' + data_dir_year) +filelst = filelst.split() +#filelst = subprocess.check_output(['ls', data_dir_year]).replace('/n',' ').split() + +#src_grd = pyroms_toolbox.BGrid_GFDL.get_nc_BGrid_GFDL(data_dir + 'grid/SODA3_0.5deg_grid.nc', name='SODA3.3.1', xrange=(285, 500), yrange=(180, 300) ) +#src_grd = pyroms_toolbox.BGrid_GFDL.get_nc_BGrid_GFDL(data_dir + 'grid/SODA3_0.5deg_grid.nc', name='SODA3.3.1', area=npolar, ystart=236) +src_grd = pyroms_toolbox.BGrid_GFDL.get_nc_BGrid_GFDL(data_dir + 'SODA3_0.5deg_grid.nc', name='SODA3.3.1', area='npolar') +dst_grd = pyroms.grid.get_ROMS_grid('ARCTIC4') +print src_grd.name +print dst_grd.name + +for filein in filelst: + tag=filein.replace(data_dir+'/monthly/','').replace('soda3.3.1_monthly_ocean_reg_','').replace('.nc','') + print '\nBuild OBC file for time %s' %tag + zeta_dst_file = dst_dir + dst_grd.name + '_clm_zeta_' + tag + '_' + src_grd.name + '.nc' + temp_dst_file = dst_dir + dst_grd.name + '_clm_temp_' + tag + '_' + src_grd.name + '.nc' + salt_dst_file = dst_dir + dst_grd.name + '_clm_salt_' + tag + '_' + src_grd.name + '.nc' + u_dst_file = dst_dir + dst_grd.name + '_clm_u_' + tag + '_' + src_grd.name + '.nc' + v_dst_file = dst_dir + dst_grd.name + '_clm_v_' + tag + '_' + src_grd.name + '.nc' + + # remap ssh + zeta = remap('ssh', filein, src_grd, dst_grd, zeta_dst_file, dst_dir=dst_dir) + + # reload grid with zeta (more accurate) + dst_grd = pyroms.grid.get_ROMS_grid('ARCTIC4', zeta=zeta) + + # regrid temp, salt and velocities + remap('temp', filein, src_grd, dst_grd, temp_dst_file, dst_dir=dst_dir) + remap('salt', filein, src_grd, dst_grd, salt_dst_file, dst_dir=dst_dir) + remap_uv(filein, src_grd, dst_grd, u_dst_file, v_dst_file, dst_dir=dst_dir) + + # merge file + clm_file = dst_dir + dst_grd.name + '_clm_' + tag + '_' + src_grd.name + '.nc' + + command1 = 'mv ' + zeta_dst_file + ' ' + clm_file + command2 = 'ncks -A ' + temp_dst_file + ' -o ' + clm_file + command3 = 'ncks -A ' + salt_dst_file + ' -o ' + clm_file + command4 = 'ncks -A ' + u_dst_file + ' -o ' + clm_file + command5 = 'ncks -A ' + v_dst_file + ' -o ' + clm_file + + subprocess.call(command1,shell=True) + subprocess.call(command2,shell=True) + subprocess.call(command3,shell=True) + subprocess.call(command4,shell=True) + subprocess.call(command5,shell=True) + + # clean up + os.remove(temp_dst_file) + os.remove(salt_dst_file) + os.remove(u_dst_file) + os.remove(v_dst_file) diff --git a/examples/Arctic_SODA3.3.1/make_ini_file.py b/examples/Arctic_SODA3.3.1/make_ini_file.py new file mode 100644 index 0000000..951f7f3 --- /dev/null +++ b/examples/Arctic_SODA3.3.1/make_ini_file.py @@ -0,0 +1,76 @@ +import matplotlib +matplotlib.use('Agg') +import subprocess +import os +import sys +import commands +import numpy as np + +#increase the maximum number of open files allowed +#import resource +#resource.setrlimit(resource.RLIMIT_NOFILE, (3000,-1)) + +import pyroms +import pyroms_toolbox + +from remap import remap +from remap_uv import remap_uv + +#my_year=int(sys.argv[-1]) +my_year = '2010' + +data_dir = '/archive/AKWATERS/kshedstrom/SODA/' +data_dir_year = data_dir + '/' + str(my_year) + '/soda3.3.1_5dy_ocean_reg_2010_12_26.nc' +dst_dir='./' + +filelst = commands.getoutput('ls ' + data_dir_year) +filelst = filelst.split() +#filelst = subprocess.check_output(['ls', data_dir_year]).replace('/n',' ').split() + +#src_grd = pyroms_toolbox.BGrid_GFDL.get_nc_BGrid_GFDL(data_dir + 'grid/SODA3_0.5deg_grid.nc', name='SODA3.3.1', xrange=(285, 500), yrange=(180, 300) ) +#src_grd = pyroms_toolbox.BGrid_GFDL.get_nc_BGrid_GFDL(data_dir + 'grid/SODA3_0.5deg_grid.nc', name='SODA3.3.1', area=npolar, ystart=236) +src_grd = pyroms_toolbox.BGrid_GFDL.get_nc_BGrid_GFDL(data_dir + 'SODA3_0.5deg_grid.nc', name='SODA3.3.1', area='npolar') +dst_grd = pyroms.grid.get_ROMS_grid('ARCTIC4') +print src_grd.name +print dst_grd.name + +for filein in filelst: + tag=filein.replace(data_dir+'/'+my_year+'/','').replace('soda3.3.1_5dy_ocean_reg_','').replace('.nc','') + print '\nBuild OBC file for time %s' %tag + zeta_dst_file = dst_dir + dst_grd.name + '_IC_zeta_' + tag + '_' + src_grd.name + '.nc' + temp_dst_file = dst_dir + dst_grd.name + '_IC_temp_' + tag + '_' + src_grd.name + '.nc' + salt_dst_file = dst_dir + dst_grd.name + '_IC_salt_' + tag + '_' + src_grd.name + '.nc' + u_dst_file = dst_dir + dst_grd.name + '_IC_u_' + tag + '_' + src_grd.name + '.nc' + v_dst_file = dst_dir + dst_grd.name + '_IC_v_' + tag + '_' + src_grd.name + '.nc' + + # remap ssh + zeta = remap('ssh', filein, src_grd, dst_grd, zeta_dst_file, dst_dir=dst_dir) + + # reload grid with zeta (more accurate) + dst_grd = pyroms.grid.get_ROMS_grid('ARCTIC4', zeta=zeta) + + # regrid temp, salt and velocities + remap('temp', filein, src_grd, dst_grd, temp_dst_file, dst_dir=dst_dir) + remap('salt', filein, src_grd, dst_grd, salt_dst_file, dst_dir=dst_dir) + remap_uv(filein, src_grd, dst_grd, u_dst_file, v_dst_file, dst_dir=dst_dir) + + # merge file + IC_file = dst_dir + dst_grd.name + '_IC_' + tag + '_' + src_grd.name + '.nc' + + command1 = 'mv ' + zeta_dst_file + ' ' + IC_file + command2 = 'ncks -A ' + temp_dst_file + ' -o ' + IC_file + command3 = 'ncks -A ' + salt_dst_file + ' -o ' + IC_file + command4 = 'ncks -A ' + u_dst_file + ' -o ' + IC_file + command5 = 'ncks -A ' + v_dst_file + ' -o ' + IC_file + + subprocess.call(command1,shell=True) + subprocess.call(command2,shell=True) + subprocess.call(command3,shell=True) + subprocess.call(command4,shell=True) + subprocess.call(command5,shell=True) + + # clean up + os.remove(temp_dst_file) + os.remove(salt_dst_file) + os.remove(u_dst_file) + os.remove(v_dst_file) diff --git a/examples/Arctic_SODA3.3.1/make_remap_weights_file.py b/examples/Arctic_SODA3.3.1/make_remap_weights_file.py new file mode 100644 index 0000000..eb884e6 --- /dev/null +++ b/examples/Arctic_SODA3.3.1/make_remap_weights_file.py @@ -0,0 +1,83 @@ +import pyroms +import pyroms_toolbox + +# load the grid +#srcgrd = pyroms_toolbox.BGrid_GFDL.get_nc_BGrid_GFDL('/Volumes/P1/Data/SODA/SODA_3.3.1/grid/SODA3_0.5deg_grid.nc', name='SODA3.3.1', xrange=(285, 500), yrange=(180, 300)) +srcgrd = pyroms_toolbox.BGrid_GFDL.get_nc_BGrid_GFDL('/archive/u1/uaf/AKWATERS/kshedstrom/SODA/SODA3_0.5deg_grid.nc', \ + name='SODA3.3.1', area='npolar', ystart=235) +dstgrd = pyroms.grid.get_ROMS_grid('ARCTIC4') + +# make remap grid file for scrip +pyroms_toolbox.BGrid_GFDL.make_remap_grid_file(srcgrd, Bpos='t') +pyroms_toolbox.BGrid_GFDL.make_remap_grid_file(srcgrd, Bpos='uv') +pyroms.remapping.make_remap_grid_file(dstgrd, Cpos='rho') +pyroms.remapping.make_remap_grid_file(dstgrd, Cpos='u') +pyroms.remapping.make_remap_grid_file(dstgrd, Cpos='v') + +# compute remap weights +# input namelist variables for bilinear remapping at rho points +grid1_file = 'remap_grid_' + srcgrd.name + '_t.nc' +grid2_file = 'remap_grid_' + dstgrd.name + '_rho.nc' +interp_file1 = 'remap_weights_' + srcgrd.name + '_to_' + dstgrd.name + '_bilinear_t_to_rho.nc' +interp_file2 = 'remap_weights_' + dstgrd.name + '_to_' + srcgrd.name + '_bilinear_rho_to_t.nc' +map1_name = srcgrd.name + ' to ' + dstgrd.name + ' Bilinear Mapping' +map2_name = dstgrd.name + ' to ' + srcgrd.name + ' Bilinear Mapping' +num_maps = 1 +map_method = 'bilinear' + +pyroms.remapping.compute_remap_weights(grid1_file, grid2_file, \ + interp_file1, interp_file2, map1_name, \ + map2_name, num_maps, map_method, \ + grid1_periodic='.true.', grid2_periodic='.true.') + + +# compute remap weights +# input namelist variables for bilinear remapping at rho points +grid1_file = 'remap_grid_' + srcgrd.name + '_uv.nc' +grid2_file = 'remap_grid_' + dstgrd.name + '_rho.nc' +interp_file1 = 'remap_weights_' + srcgrd.name + '_to_' + dstgrd.name + '_bilinear_uv_to_rho.nc' +interp_file2 = 'remap_weights_' + dstgrd.name + '_to_' + srcgrd.name + '_bilinear_rho_to_uv.nc' +map1_name = srcgrd.name + ' to ' + dstgrd.name + ' Bilinear Mapping' +map2_name = dstgrd.name + ' to ' + srcgrd.name + ' Bilinear Mapping' +num_maps = 1 +map_method = 'bilinear' + +pyroms.remapping.compute_remap_weights(grid1_file, grid2_file, \ + interp_file1, interp_file2, map1_name, \ + map2_name, num_maps, map_method, \ + grid1_periodic='.true.', grid2_periodic='.true.') + + +# compute remap weights +# input namelist variables for bilinear remapping at rho points +grid1_file = 'remap_grid_' + srcgrd.name + '_t.nc' +grid2_file = 'remap_grid_' + dstgrd.name + '_u.nc' +interp_file1 = 'remap_weights_' + srcgrd.name + '_to_' + dstgrd.name + '_bilinear_t_to_u.nc' +interp_file2 = 'remap_weights_' + dstgrd.name + '_to_' + srcgrd.name + '_bilinear_u_to_t.nc' +map1_name = srcgrd.name + ' to ' + dstgrd.name + ' Bilinear Mapping' +map2_name = dstgrd.name + ' to ' + srcgrd.name + ' Bilinear Mapping' +num_maps = 1 +map_method = 'bilinear' + +pyroms.remapping.compute_remap_weights(grid1_file, grid2_file, \ + interp_file1, interp_file2, map1_name, \ + map2_name, num_maps, map_method, \ + grid1_periodic='.true.', grid2_periodic='.true.') + + +# compute remap weights +# input namelist variables for bilinear remapping at rho points +grid1_file = 'remap_grid_' + srcgrd.name + '_t.nc' +grid2_file = 'remap_grid_' + dstgrd.name + '_v.nc' +interp_file1 = 'remap_weights_' + srcgrd.name + '_to_' + dstgrd.name + '_bilinear_t_to_v.nc' +interp_file2 = 'remap_weights_' + dstgrd.name + '_to_' + srcgrd.name + '_bilinear_v_to_t.nc' +map1_name = srcgrd.name + ' to ' + dstgrd.name + ' Bilinear Mapping' +map2_name = dstgrd.name + ' to ' + srcgrd.name + ' Bilinear Mapping' +num_maps = 1 +map_method = 'bilinear' + +pyroms.remapping.compute_remap_weights(grid1_file, grid2_file, \ + interp_file1, interp_file2, map1_name, \ + map2_name, num_maps, map_method, \ + grid1_periodic='.true.', grid2_periodic='.true.') + diff --git a/examples/Arctic_SODA3.3.1/remap.py b/examples/Arctic_SODA3.3.1/remap.py new file mode 100644 index 0000000..ee0daa5 --- /dev/null +++ b/examples/Arctic_SODA3.3.1/remap.py @@ -0,0 +1,165 @@ +import numpy as np +import os +try: + import netCDF4 as netCDF +except: + import netCDF3 as netCDF +import matplotlib.pyplot as plt +import time +import datetime as dt +from matplotlib.dates import date2num, num2date + +import pyroms +import pyroms_toolbox +import _remapping + +class nctime(object): + pass + +def remap(src_varname, src_file, src_grd, dst_grd, dst_file, dmax=0, cdepth=0, kk=0, dst_dir='./'): + + # ARCTIC4 grid sub-sample +# xrange=src_grd.xrange; yrange=src_grd.yrange + ystart=235 + + # get time + nctime.long_name = 'time' + nctime.units = 'days since 1900-01-01 00:00:00' + + # create IC/CLM file + print 'Creating ROMS file', dst_file + if os.path.exists(dst_file) is True: + os.remove(dst_file) + pyroms_toolbox.nc_create_roms_file(dst_file, dst_grd, nctime) + + # open IC file + nc = netCDF.Dataset(dst_file, 'a', format='NETCDF3_64BIT') + + #load var + cdf = netCDF.Dataset(src_file) + src_var = cdf.variables[src_varname] + + tmp = cdf.variables['time'][:] + if len(tmp) > 1: + print 'error : multiple frames in input file' ; exit() + else: + time = tmp[0] + + # we need to correct the time axis + ref_soda = dt.datetime(1980,1,1,0,0) + ref_roms = dt.datetime(1900,1,1,0,0) + ndays = (ref_soda - ref_roms).days + time = time + ndays + + #get missing value + spval = src_var.missing_value + + # determine variable dimension + ndim = len(src_var.dimensions) - 1 + + # ARCTIC4 grid sub-sample + if ndim == 3: +# src_var = src_var[0,:, yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] + print 'subgrid 3d', src_var.shape + src_var = np.squeeze(src_var, axis=(0,)) + src_var = src_var[:,np.r_[ystart:np.size(src_var,1),-1],:] + print 'subgrid 3d', src_var.shape + elif ndim == 2: +# src_var = src_var[0,yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] + print 'subgrid 2d', src_var.shape + src_var = np.squeeze(src_var, axis=(0,)) + src_var = src_var[np.r_[ystart:np.size(src_var,0),-1],:] + print 'subgrid 2d', src_var.shape + + + vartime = 'ocean_time' + if src_varname == 'ssh': + Bpos = 't' + Cpos = 'rho' + z = src_grd.z_t + Mp, Lp = dst_grd.hgrid.mask_rho.shape + wts_file = 'remap_weights_' + src_grd.name + '_to_' + dst_grd.name + '_bilinear_t_to_rho.nc' + dst_varname = 'zeta' + dimensions = ('ocean_time', 'eta_rho', 'xi_rho') + long_name = 'free-surface' + units = 'meter' + field = 'zeta, scalar, series' + elif src_varname == 'temp': + src_var = src_var + Bpos = 't' + Cpos = 'rho' + z = src_grd.z_t + Mp, Lp = dst_grd.hgrid.mask_rho.shape + wts_file = 'remap_weights_' + src_grd.name + '_to_' + dst_grd.name + '_bilinear_t_to_rho.nc' + dst_varname = 'temp' + dimensions = ('ocean_time', 's_rho', 'eta_rho', 'xi_rho') + long_name = 'potential temperature' + units = 'Celsius' + field = 'temp, scalar, series' + elif src_varname == 'salt': + Bpos = 't' + Cpos = 'rho' + z = src_grd.z_t + Mp, Lp = dst_grd.hgrid.mask_rho.shape + wts_file = 'remap_weights_' + src_grd.name + '_to_' + dst_grd.name + '_bilinear_t_to_rho.nc' + dst_varname = 'salt' + dimensions = ('ocean_time', 's_rho', 'eta_rho', 'xi_rho') + long_name = 'salinity' + units = 'none' + field = 'salt_north, scalar, series' + else: + raise ValueError, 'Undefined src_varname' + + + if ndim == 3: + # build intermediate zgrid + zlevel = -z[::-1] + nzlevel = len(zlevel) + dst_zcoord = pyroms.vgrid.z_coordinate(dst_grd.vgrid.h, zlevel, nzlevel) + dst_grdz = pyroms.grid.ROMS_Grid(dst_grd.name+'_Z', dst_grd.hgrid, dst_zcoord) + + + # create variable in file + print 'Creating variable', dst_varname + nc.createVariable(dst_varname, 'f8', dimensions, fill_value=spval) + nc.variables[dst_varname].long_name = long_name + nc.variables[dst_varname].units = units + nc.variables[dst_varname].field = field + nc.variables[dst_varname].time = 'ocean_time' + + # remapping + print 'remapping', dst_varname, 'from', src_grd.name, \ + 'to', dst_grd.name + + if ndim == 3: + # flood the grid + print 'flood the grid' + src_varz = pyroms_toolbox.BGrid_GFDL.flood(src_var, src_grd, Bpos=Bpos, spval=spval, \ + dmax=dmax, cdepth=cdepth, kk=kk) + else: + src_varz = src_var + + # horizontal interpolation using scrip weights + print 'horizontal interpolation using scrip weights' + dst_varz = pyroms.remapping.remap(src_varz, wts_file, spval=spval) + + if ndim == 3: + # vertical interpolation from standard z level to sigma + print 'vertical interpolation from standard z level to sigma' + dst_var= pyroms.remapping.z2roms(dst_varz[::-1, :, :], \ + dst_grdz, dst_grd, Cpos=Cpos, spval=spval, \ + flood=False, irange=(0,Lp), jrange=(0,Mp)) + else: + dst_var = dst_varz + + # write data in destination file + print 'write data in destination file\n' + nc.variables['ocean_time'][0] = time + nc.variables[dst_varname][0] = np.squeeze(dst_var) + + # close file + nc.close() + cdf.close() + + if src_varname == 'ssh': + return dst_varz diff --git a/examples/Arctic_SODA3.3.1/remap_bdry.py b/examples/Arctic_SODA3.3.1/remap_bdry.py new file mode 100644 index 0000000..241c941 --- /dev/null +++ b/examples/Arctic_SODA3.3.1/remap_bdry.py @@ -0,0 +1,241 @@ +import numpy as np +import os +try: + import netCDF4 as netCDF +except: + import netCDF3 as netCDF +import matplotlib.pyplot as plt +import time +import datetime as dt +from matplotlib.dates import date2num, num2date + +import pyroms +import pyroms_toolbox +import _remapping + +class nctime(object): + pass + +def remap_bdry(src_varname, src_file, src_grd, dst_grd, dst_file, dmax=0, cdepth=0, kk=0, dst_dir='./'): + + # ARCTIC4 grid sub-sample + ystart=235 +# xrange=src_grd.xrange; yrange=src_grd.yrange + + # get time + nctime.long_name = 'time' + nctime.units = 'days since 1900-01-01 00:00:00' + + # create boundary file + print 'Creating boundary file', dst_file + if os.path.exists(dst_file) is True: + os.remove(dst_file) + pyroms_toolbox.nc_create_roms_bdry_file(dst_file, dst_grd, nctime) + + # open boundary file + nc = netCDF.Dataset(dst_file, 'a', format='NETCDF3_64BIT') + + #load var + #load var + cdf = netCDF.Dataset(src_file) + src_var = cdf.variables[src_varname] + + tmp = cdf.variables['time'][:] + if len(tmp) > 1: + print 'error : multiple frames in input file' ; exit() + else: + time = tmp[0] + + # we need to correct the time axis + ref_soda = dt.datetime(1980,1,1,0,0) + ref_roms = dt.datetime(1900,1,1,0,0) + ndays = (ref_soda - ref_roms).days + time = time + ndays + + #get missing value + spval = src_var.missing_value + + # determine variable dimension + ndim = len(src_var.dimensions) - 1 + + # ARCTIC4 grid sub-sample + if ndim == 3: +# src_var = src_var[0,:, yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] + print 'subgrid 3d', src_var.shape + src_var = np.squeeze(src_var, axis=(0,)) + src_var = src_var[:,np.r_[ystart:np.size(src_var,1),-1],:] + print 'subgrid 3d', src_var.shape + elif ndim == 2: +# src_var = src_var[0,yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] + print 'subgrid 2d', src_var.shape + src_var = np.squeeze(src_var, axis=(0,)) + src_var = src_var[np.r_[ystart:np.size(src_var,0),-1],:] + print 'subgrid 2d', src_var.shape + + if src_varname == 'ssh': + Bpos = 't' + Cpos = 'rho' + z = src_grd.z_t + Mp, Lp = dst_grd.hgrid.mask_rho.shape + wts_file = 'remap_weights_' + src_grd.name + '_to_' + dst_grd.name + '_bilinear_t_to_rho.nc' + dst_varname = 'zeta' + dimensions = ('ocean_time', 'eta_rho', 'xi_rho') + long_name = 'free-surface' + dst_varname_north = 'zeta_north' + dimensions_north = ('ocean_time', 'xi_rho') + long_name_north = 'free-surface north boundary condition' + field_north = 'zeta_north, scalar, series' + dst_varname_south = 'zeta_south' + dimensions_south = ('ocean_time', 'xi_rho') + long_name_south = 'free-surface south boundary condition' + field_south = 'zeta_south, scalar, series' + dst_varname_east = 'zeta_east' + dimensions_east = ('ocean_time', 'eta_rho') + long_name_east = 'free-surface east boundary condition' + field_east = 'zeta_east, scalar, series' + dst_varname_west = 'zeta_west' + dimensions_west = ('ocean_time', 'eta_rho') + long_name_west = 'free-surface west boundary condition' + field_west = 'zeta_west, scalar, series' + units = 'meter' + elif src_varname == 'temp': + src_var = src_var + Bpos = 't' + Cpos = 'rho' + z = src_grd.z_t + Mp, Lp = dst_grd.hgrid.mask_rho.shape + wts_file = 'remap_weights_' + src_grd.name + '_to_' + dst_grd.name + '_bilinear_t_to_rho.nc' + dst_varname = 'temperature' + dst_varname_north = 'temp_north' + dimensions_north = ('ocean_time', 's_rho', 'xi_rho') + long_name_north = 'potential temperature north boundary condition' + field_north = 'temp_north, scalar, series' + dst_varname_south = 'temp_south' + dimensions_south = ('ocean_time', 's_rho', 'xi_rho') + long_name_south = 'potential temperature south boundary condition' + field_south = 'temp_south, scalar, series' + dst_varname_east = 'temp_east' + dimensions_east = ('ocean_time', 's_rho', 'eta_rho') + long_name_east = 'potential temperature east boundary condition' + field_east = 'temp_east, scalar, series' + dst_varname_west = 'temp_west' + dimensions_west = ('ocean_time', 's_rho', 'eta_rho') + long_name_west = 'potential temperature west boundary condition' + field_west = 'temp_west, scalar, series' + units = 'Celsius' + elif src_varname == 'salt': + Bpos = 't' + Cpos = 'rho' + z = src_grd.z_t + Mp, Lp = dst_grd.hgrid.mask_rho.shape + wts_file = 'remap_weights_' + src_grd.name + '_to_' + dst_grd.name + '_bilinear_t_to_rho.nc' + dst_varname = 'salinity' + dst_varname_north = 'salt_north' + dimensions_north = ('ocean_time', 's_rho', 'xi_rho') + long_name_north = 'salinity north boundary condition' + field_north = 'salt_north, scalar, series' + dst_varname_south = 'salt_south' + dimensions_south = ('ocean_time', 's_rho', 'xi_rho') + long_name_south = 'salinity south boundary condition' + field_south = 'salt_south, scalar, series' + dst_varname_east = 'salt_east' + dimensions_east = ('ocean_time', 's_rho', 'eta_rho') + long_name_east = 'salinity east boundary condition' + field_east = 'salt_east, scalar, series' + dst_varname_west = 'salt_west' + dimensions_west = ('ocean_time', 's_rho', 'eta_rho') + long_name_west = 'salinity west boundary condition' + field_west = 'salt_west, scalar, series' + units = 'PSU' + else: + raise ValueError, 'Undefined src_varname' + + + if ndim == 3: + # build intermediate zgrid + zlevel = -z[::-1] + nzlevel = len(zlevel) + dst_zcoord = pyroms.vgrid.z_coordinate(dst_grd.vgrid.h, zlevel, nzlevel) + dst_grdz = pyroms.grid.ROMS_Grid(dst_grd.name+'_Z', dst_grd.hgrid, dst_zcoord) + + + # create variable in boudary file + print 'Creating variable', dst_varname_north + nc.createVariable(dst_varname_north, 'f8', dimensions_north, fill_value=spval) + nc.variables[dst_varname_north].long_name = long_name_north + nc.variables[dst_varname_north].units = units + nc.variables[dst_varname_north].field = field_north + nc.variables[dst_varname_north].time = 'ocean_time' + + print 'Creating variable', dst_varname_south + nc.createVariable(dst_varname_south, 'f8', dimensions_south, fill_value=spval) + nc.variables[dst_varname_south].long_name = long_name_south + nc.variables[dst_varname_south].units = units + nc.variables[dst_varname_south].field = field_south + nc.variables[dst_varname_south].time = 'ocean_time' + + print 'Creating variable', dst_varname_east + nc.createVariable(dst_varname_east, 'f8', dimensions_east, fill_value=spval) + nc.variables[dst_varname_east].long_name = long_name_east + nc.variables[dst_varname_east].units = units + nc.variables[dst_varname_east].field = field_east + nc.variables[dst_varname_east].time = 'ocean_time' + + print 'Creating variable', dst_varname_west + nc.createVariable(dst_varname_west, 'f8', dimensions_west, fill_value=spval) + nc.variables[dst_varname_west].long_name = long_name_west + nc.variables[dst_varname_west].units = units + nc.variables[dst_varname_west].field = field_west + nc.variables[dst_varname_west].time = 'ocean_time' + + # remapping + print 'remapping', dst_varname, 'from', src_grd.name, \ + 'to', dst_grd.name + + if ndim == 3: + # flood the grid + print 'flood the grid', src_var.shape + src_varz = pyroms_toolbox.BGrid_GFDL.flood(src_var, src_grd, Bpos=Bpos, spval=spval, \ + dmax=dmax, cdepth=cdepth, kk=kk) + else: + src_varz = src_var + + # horizontal interpolation using scrip weights + print 'horizontal interpolation using scrip weights' + dst_varz = pyroms.remapping.remap(src_varz, wts_file, spval=spval) + + if ndim == 3: + # vertical interpolation from standard z level to sigma + print 'vertical interpolation from standard z level to sigma' + dst_var_north = pyroms.remapping.z2roms(dst_varz[::-1, Mp-1:Mp, 0:Lp], \ + dst_grdz, dst_grd, Cpos=Cpos, spval=spval, \ + flood=False, irange=(0,Lp), jrange=(Mp-1,Mp)) + dst_var_south = pyroms.remapping.z2roms(dst_varz[::-1, 0:1, :], \ + dst_grdz, dst_grd, Cpos=Cpos, spval=spval, \ + flood=False, irange=(0,Lp), jrange=(0,1)) + dst_var_east = pyroms.remapping.z2roms(dst_varz[::-1, :, Lp-1:Lp], \ + dst_grdz, dst_grd, Cpos=Cpos, spval=spval, \ + flood=False, irange=(Lp-1,Lp), jrange=(0,Mp)) + dst_var_west = pyroms.remapping.z2roms(dst_varz[::-1, :, 0:1], \ + dst_grdz, dst_grd, Cpos=Cpos, spval=spval, \ + flood=False, irange=(0,1), jrange=(0,Mp)) + else: + dst_var_north = dst_varz[-1, :] + dst_var_south = dst_varz[0, :] + dst_var_east = dst_varz[:, -1] + dst_var_west = dst_varz[:, 0] + + # write data in destination file + print 'write data in destination file\n' + nc.variables['ocean_time'][0] = time + nc.variables[dst_varname_north][0] = np.squeeze(dst_var_north) + nc.variables[dst_varname_south][0] = np.squeeze(dst_var_south) + nc.variables[dst_varname_east][0] = np.squeeze(dst_var_east) + nc.variables[dst_varname_west][0] = np.squeeze(dst_var_west) + + # close file + nc.close() + cdf.close() + + if src_varname == 'ssh': + return dst_varz diff --git a/examples/Arctic_SODA3.3.1/remap_bdry_uv.py b/examples/Arctic_SODA3.3.1/remap_bdry_uv.py new file mode 100644 index 0000000..7a73f17 --- /dev/null +++ b/examples/Arctic_SODA3.3.1/remap_bdry_uv.py @@ -0,0 +1,375 @@ +import numpy as np +import os +try: + import netCDF4 as netCDF +except: + import netCDF3 as netCDF +import matplotlib.pyplot as plt +import time +import datetime as dt +from matplotlib.dates import date2num, num2date + +import pyroms +import pyroms_toolbox +import _remapping + +class nctime(object): + pass + +def remap_bdry_uv(src_fileuv, src_grd, dst_grd, dst_fileu, dst_filev, dmax=0, cdepth=0, kk=0, dst_dir='./'): + + # ARCTIC4 grid sub-sample +# xrange=src_grd.xrange; yrange=src_grd.yrange + ystart=235 + + # get time + nctime.long_name = 'time' + nctime.units = 'days since 1900-01-01 00:00:00' + + # get dimensions + Mp, Lp = dst_grd.hgrid.mask_rho.shape + + # create destination file + print '\nCreating destination file', dst_fileu + if os.path.exists(dst_fileu) is True: + os.remove(dst_fileu) + pyroms_toolbox.nc_create_roms_file(dst_fileu, dst_grd, nctime) + print 'Creating destination file', dst_filev + if os.path.exists(dst_filev) is True: + os.remove(dst_filev) + pyroms_toolbox.nc_create_roms_bdry_file(dst_filev, dst_grd, nctime) + + # open destination file + ncu = netCDF.Dataset(dst_fileu, 'a', format='NETCDF3_64BIT') + ncv = netCDF.Dataset(dst_filev, 'a', format='NETCDF3_64BIT') + + #load var + cdfuv = netCDF.Dataset(src_fileuv) + src_varu = cdfuv.variables['u'] + src_varv = cdfuv.variables['v'] + + tmp = cdfuv.variables['time'][:] + if len(tmp) > 1: + print 'error : multiple frames in input file' ; exit() + else: + time = tmp[0] + + # we need to correct the time axis + ref_soda = dt.datetime(1980,1,1,0,0) + ref_roms = dt.datetime(1900,1,1,0,0) + ndays = (ref_soda - ref_roms).days + time = time + ndays + + #get missing value + spval = src_varu.missing_value + + # ARCTIC4 grid sub-sample +# src_varu = src_varu[0,:, yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] + src_varu = np.squeeze(src_varu, axis=(0,)) + src_varu = src_varu[:,np.r_[ystart:np.size(src_varu,1),-1],:] + print 'subgrid 3d', src_varu.shape +# src_varv = src_varv[0,:, yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] + src_varv = np.squeeze(src_varv, axis=(0,)) + src_varv = src_varv[:,np.r_[ystart:np.size(src_varv,1),-1],:] + print 'subgrid 3d', src_varv.shape + + # get weights file + wts_file = 'remap_weights_' + src_grd.name + '_to_' + dst_grd.name + '_bilinear_uv_to_rho.nc' + + # build intermediate zgrid + zlevel = -src_grd.z_t[::-1] + nzlevel = len(zlevel) + dst_zcoord = pyroms.vgrid.z_coordinate(dst_grd.vgrid.h, zlevel, nzlevel) + dst_grdz = pyroms.grid.ROMS_Grid(dst_grd.name+'_Z', dst_grd.hgrid, dst_zcoord) + + # create variable in destination file + print 'Creating variable u_north' + ncu.createVariable('u_north', 'f8', ('ocean_time', 's_rho', 'xi_u'), fill_value=spval) + ncu.variables['u_north'].long_name = '3D u-momentum north boundary condition' + ncu.variables['u_north'].units = 'meter second-1' + ncu.variables['u_north'].field = 'u_north, scalar, series' + ncu.variables['u_north'].time = 'ocean_time' + + print 'Creating variable u_south' + ncu.createVariable('u_south', 'f8', ('ocean_time', 's_rho', 'xi_u'), fill_value=spval) + ncu.variables['u_south'].long_name = '3D u-momentum south boundary condition' + ncu.variables['u_south'].units = 'meter second-1' + ncu.variables['u_south'].field = 'u_south, scalar, series' + ncu.variables['u_south'].time = 'ocean_time' + + print 'Creating variable u_east' + ncu.createVariable('u_east', 'f8', ('ocean_time', 's_rho', 'eta_u'), fill_value=spval) + ncu.variables['u_east'].long_name = '3D u-momentum east boundary condition' + ncu.variables['u_east'].units = 'meter second-1' + ncu.variables['u_east'].field = 'u_east, scalar, series' + ncu.variables['u_east'].time = 'ocean_time' + + print 'Creating variable u_west' + ncu.createVariable('u_west', 'f8', ('ocean_time', 's_rho', 'eta_u'), fill_value=spval) + ncu.variables['u_west'].long_name = '3D u-momentum west boundary condition' + ncu.variables['u_west'].units = 'meter second-1' + ncu.variables['u_west'].field = 'u_east, scalar, series' + ncu.variables['u_west'].time = 'ocean_time' + + # create variable in destination file + print 'Creating variable ubar_north' + ncu.createVariable('ubar_north', 'f8', ('ocean_time', 'xi_u'), fill_value=spval) + ncu.variables['ubar_north'].long_name = '2D u-momentum north boundary condition' + ncu.variables['ubar_north'].units = 'meter second-1' + ncu.variables['ubar_north'].field = 'ubar_north, scalar, series' + ncu.variables['ubar_north'].time = 'ocean_time' + + print 'Creating variable ubar_south' + ncu.createVariable('ubar_south', 'f8', ('ocean_time', 'xi_u'), fill_value=spval) + ncu.variables['ubar_south'].long_name = '2D u-momentum south boundary condition' + ncu.variables['ubar_south'].units = 'meter second-1' + ncu.variables['ubar_south'].field = 'ubar_south, scalar, series' + ncu.variables['ubar_south'].time = 'ocean_time' + + print 'Creating variable ubar_east' + ncu.createVariable('ubar_east', 'f8', ('ocean_time', 'eta_u'), fill_value=spval) + ncu.variables['ubar_east'].long_name = '2D u-momentum east boundary condition' + ncu.variables['ubar_east'].units = 'meter second-1' + ncu.variables['ubar_east'].field = 'ubar_east, scalar, series' + ncu.variables['ubar_east'].time = 'ocean_time' + + print 'Creating variable ubar_west' + ncu.createVariable('ubar_west', 'f8', ('ocean_time', 'eta_u'), fill_value=spval) + ncu.variables['ubar_west'].long_name = '2D u-momentum west boundary condition' + ncu.variables['ubar_west'].units = 'meter second-1' + ncu.variables['ubar_west'].field = 'ubar_east, scalar, series' + ncu.variables['ubar_west'].time = 'ocean_time' + + print 'Creating variable v_north' + ncv.createVariable('v_north', 'f8', ('ocean_time', 's_rho', 'xi_v'), fill_value=spval) + ncv.variables['v_north'].long_name = '3D v-momentum north boundary condition' + ncv.variables['v_north'].units = 'meter second-1' + ncv.variables['v_north'].field = 'v_north, scalar, series' + ncv.variables['v_north'].time = 'ocean_time' + + print 'Creating variable v_south' + ncv.createVariable('v_south', 'f8', ('ocean_time', 's_rho', 'xi_v'), fill_value=spval) + ncv.variables['v_south'].long_name = '3D v-momentum south boundary condition' + ncv.variables['v_south'].units = 'meter second-1' + ncv.variables['v_south'].field = 'v_south, scalar, series' + ncv.variables['v_south'].time = 'ocean_time' + + print 'Creating variable v_east' + ncv.createVariable('v_east', 'f8', ('ocean_time', 's_rho', 'eta_v'), fill_value=spval) + ncv.variables['v_east'].long_name = '3D v-momentum east boundary condition' + ncv.variables['v_east'].units = 'meter second-1' + ncv.variables['v_east'].field = 'v_east, scalar, series' + ncv.variables['v_east'].time = 'ocean_time' + + print 'Creating variable v_west' + ncv.createVariable('v_west', 'f8', ('ocean_time', 's_rho', 'eta_v'), fill_value=spval) + ncv.variables['v_west'].long_name = '3D v-momentum west boundary condition' + ncv.variables['v_west'].units = 'meter second-1' + ncv.variables['v_west'].field = 'v_east, scalar, series' + ncv.variables['v_west'].time = 'ocean_time' + + print 'Creating variable vbar_north' + ncv.createVariable('vbar_north', 'f8', ('ocean_time', 'xi_v'), fill_value=spval) + ncv.variables['vbar_north'].long_name = '2D v-momentum north boundary condition' + ncv.variables['vbar_north'].units = 'meter second-1' + ncv.variables['vbar_north'].field = 'vbar_north, scalar, series' + ncv.variables['vbar_north'].time = 'ocean_time' + + print 'Creating variable vbar_south' + ncv.createVariable('vbar_south', 'f8', ('ocean_time', 'xi_v'), fill_value=spval) + ncv.variables['vbar_south'].long_name = '2D v-momentum south boundary condition' + ncv.variables['vbar_south'].units = 'meter second-1' + ncv.variables['vbar_south'].field = 'vbar_south, scalar, series' + ncv.variables['vbar_south'].time = 'ocean_time' + + print 'Creating variable vbar_east' + ncv.createVariable('vbar_east', 'f8', ('ocean_time', 'eta_v'), fill_value=spval) + ncv.variables['vbar_east'].long_name = '2D v-momentum east boundary condition' + ncv.variables['vbar_east'].units = 'meter second-1' + ncv.variables['vbar_east'].field = 'vbar_east, scalar, series' + ncv.variables['vbar_east'].time = 'ocean_time' + + print 'Creating variable vbar_west' + ncv.createVariable('vbar_west', 'f8', ('ocean_time', 'eta_v'), fill_value=spval) + ncv.variables['vbar_west'].long_name = '2D v-momentum west boundary condition' + ncv.variables['vbar_west'].units = 'meter second-1' + ncv.variables['vbar_west'].field = 'vbar_east, scalar, series' + ncv.variables['vbar_west'].time = 'ocean_time' + + + # remaping + print 'remapping and rotating u and v from', src_grd.name, \ + 'to', dst_grd.name + print 'time =', time + + # flood the grid + print 'flood the grid' + src_uz = pyroms_toolbox.BGrid_GFDL.flood(src_varu, src_grd, Bpos='uv', \ + spval=spval, dmax=dmax, cdepth=cdepth, kk=kk) + src_vz = pyroms_toolbox.BGrid_GFDL.flood(src_varv, src_grd, Bpos='uv', \ + spval=spval, dmax=dmax, cdepth=cdepth, kk=kk) + + # horizontal interpolation using scrip weights + print 'horizontal interpolation using scrip weights' + dst_uz = pyroms.remapping.remap(src_uz, wts_file, \ + spval=spval) + dst_vz = pyroms.remapping.remap(src_vz, wts_file, \ + spval=spval) + + # vertical interpolation from standard z level to sigma + print 'vertical interpolation from standard z level to sigma' + dst_u_north = pyroms.remapping.z2roms(dst_uz[::-1, Mp-2:Mp, 0:Lp], \ + dst_grdz, dst_grd, Cpos='rho', spval=spval, \ + flood=False, irange=(0,Lp), jrange=(Mp-2,Mp)) + dst_u_south = pyroms.remapping.z2roms(dst_uz[::-1, 0:2, 0:Lp], \ + dst_grdz, dst_grd, Cpos='rho', spval=spval, \ + flood=False, irange=(0,Lp), jrange=(0,2)) + dst_u_east = pyroms.remapping.z2roms(dst_uz[::-1, 0:Mp, Lp-2:Lp], \ + dst_grdz, dst_grd, Cpos='rho', spval=spval, \ + flood=False, irange=(Lp-2,Lp), jrange=(0,Mp)) + dst_u_west = pyroms.remapping.z2roms(dst_uz[::-1, 0:Mp, 0:2], \ + dst_grdz, dst_grd, Cpos='rho', spval=spval, \ + flood=False, irange=(0,2), jrange=(0,Mp)) + + dst_v_north = pyroms.remapping.z2roms(dst_vz[::-1, Mp-2:Mp, 0:Lp], \ + dst_grdz, dst_grd, Cpos='rho', spval=spval, \ + flood=False, irange=(0,Lp), jrange=(Mp-2,Mp)) + dst_v_south = pyroms.remapping.z2roms(dst_vz[::-1, 0:2, 0:Lp], \ + dst_grdz, dst_grd, Cpos='rho', spval=spval, \ + flood=False, irange=(0,Lp), jrange=(0,2)) + dst_v_east = pyroms.remapping.z2roms(dst_vz[::-1, 0:Mp, Lp-2:Lp], \ + dst_grdz, dst_grd, Cpos='rho', spval=spval, \ + flood=False, irange=(Lp-2,Lp), jrange=(0,Mp)) + dst_v_west = pyroms.remapping.z2roms(dst_vz[::-1, 0:Mp, 0:2], \ + dst_grdz, dst_grd, Cpos='rho', spval=spval, \ + flood=False, irange=(0,2), jrange=(0,Mp)) + + + # rotate u,v fields + src_angle = np.zeros(dst_grd.hgrid.angle_rho.shape) + dst_angle = dst_grd.hgrid.angle_rho + angle = dst_angle - src_angle + angle = np.tile(angle, (dst_grd.vgrid.N, 1, 1)) + + U_north = dst_u_north + dst_v_north*1j + eitheta_north = np.exp(-1j*angle[:,Mp-2:Mp, 0:Lp]) + U_north = U_north * eitheta_north + dst_u_north = np.real(U_north) + dst_v_north = np.imag(U_north) + + U_south = dst_u_south + dst_v_south*1j + eitheta_south = np.exp(-1j*angle[:,0:2, 0:Lp]) + U_south = U_south * eitheta_south + dst_u_south = np.real(U_south) + dst_v_south = np.imag(U_south) + + U_east = dst_u_east + dst_v_east*1j + eitheta_east = np.exp(-1j*angle[:,0:Mp, Lp-2:Lp]) + U_east = U_east * eitheta_east + dst_u_east = np.real(U_east) + dst_v_east = np.imag(U_east) + + U_west = dst_u_west + dst_v_west*1j + eitheta_west = np.exp(-1j*angle[:,0:Mp, 0:2]) + U_west = U_west * eitheta_west + dst_u_west = np.real(U_west) + dst_v_west = np.imag(U_west) + + # move back to u,v points + dst_u_north = 0.5 * np.squeeze(dst_u_north[:,-1,:-1] + dst_u_north[:,-1,1:]) + dst_v_north = 0.5 * np.squeeze(dst_v_north[:,:-1,:] + dst_v_north[:,1:,:]) + dst_u_south = 0.5 * np.squeeze(dst_u_south[:,0,:-1] + dst_u_south[:,0,1:]) + dst_v_south = 0.5 * np.squeeze(dst_v_south[:,:-1,:] + dst_v_south[:,1:,:]) + dst_u_east = 0.5 * np.squeeze(dst_u_east[:,:,:-1] + dst_u_east[:,:,1:]) + dst_v_east = 0.5 * np.squeeze(dst_v_east[:,:-1,-1] + dst_v_east[:,1:,-1]) + dst_u_west = 0.5 * np.squeeze(dst_u_west[:,:,:-1] + dst_u_west[:,:,1:]) + dst_v_west = 0.5 * np.squeeze(dst_v_west[:,:-1,0] + dst_v_west[:,1:,0]) + + # spval + idxu_north = np.where(dst_grd.hgrid.mask_u[-1,:] == 0) + idxv_north = np.where(dst_grd.hgrid.mask_v[-1,:] == 0) + idxu_south = np.where(dst_grd.hgrid.mask_u[0,:] == 0) + idxv_south = np.where(dst_grd.hgrid.mask_v[0,:] == 0) + idxu_east = np.where(dst_grd.hgrid.mask_u[:,-1] == 0) + idxv_east = np.where(dst_grd.hgrid.mask_v[:,-1] == 0) + idxu_west = np.where(dst_grd.hgrid.mask_u[:,0] == 0) + idxv_west = np.where(dst_grd.hgrid.mask_v[:,0] == 0) + for n in range(dst_grd.vgrid.N): + dst_u_north[n, idxu_north[0]] = spval + dst_v_north[n, idxv_north[0]] = spval + dst_u_south[n, idxu_south[0]] = spval + dst_v_south[n, idxv_south[0]] = spval + dst_u_east[n, idxu_east[0]] = spval + dst_v_east[n, idxv_east[0]] = spval + dst_u_west[n, idxu_west[0]] = spval + dst_v_west[n, idxv_west[0]] = spval + + # compute depth average velocity ubar and vbar + # get z at the right position + z_u_north = 0.5 * (dst_grd.vgrid.z_w[0,:,-1,:-1] + dst_grd.vgrid.z_w[0,:,-1,1:]) + z_v_north = 0.5 * (dst_grd.vgrid.z_w[0,:,-1,:] + dst_grd.vgrid.z_w[0,:,-2,:]) + z_u_south = 0.5 * (dst_grd.vgrid.z_w[0,:,0,:-1] + dst_grd.vgrid.z_w[0,:,0,1:]) + z_v_south = 0.5 * (dst_grd.vgrid.z_w[0,:,0,:] + dst_grd.vgrid.z_w[0,:,1,:]) + z_u_east = 0.5 * (dst_grd.vgrid.z_w[0,:,:,-1] + dst_grd.vgrid.z_w[0,:,:,-2]) + z_v_east = 0.5 * (dst_grd.vgrid.z_w[0,:,:-1,-1] + dst_grd.vgrid.z_w[0,:,1:,-1]) + z_u_west = 0.5 * (dst_grd.vgrid.z_w[0,:,:,0] + dst_grd.vgrid.z_w[0,:,:,1]) + z_v_west = 0.5 * (dst_grd.vgrid.z_w[0,:,:-1,0] + dst_grd.vgrid.z_w[0,:,1:,0]) + + dst_ubar_north = np.zeros(dst_u_north.shape[1]) + dst_ubar_south = np.zeros(dst_u_south.shape[1]) + dst_ubar_east = np.zeros(dst_u_east.shape[1]) + dst_ubar_west = np.zeros(dst_u_west.shape[1]) + dst_vbar_north = np.zeros(dst_v_north.shape[1]) + dst_vbar_south = np.zeros(dst_v_south.shape[1]) + dst_vbar_east = np.zeros(dst_v_east.shape[1]) + dst_vbar_west = np.zeros(dst_v_west.shape[1]) + + for i in range(dst_u_north.shape[1]): + dst_ubar_north[i] = (dst_u_north[:,i] * np.diff(z_u_north[:,i])).sum() / -z_u_north[0,i] + dst_ubar_south[i] = (dst_u_south[:,i] * np.diff(z_u_south[:,i])).sum() / -z_u_south[0,i] + for i in range(dst_v_north.shape[1]): + dst_vbar_north[i] = (dst_v_north[:,i] * np.diff(z_v_north[:,i])).sum() / -z_v_north[0,i] + dst_vbar_south[i] = (dst_v_south[:,i] * np.diff(z_v_south[:,i])).sum() / -z_v_south[0,i] + for j in range(dst_u_east.shape[1]): + dst_ubar_east[j] = (dst_u_east[:,j] * np.diff(z_u_east[:,j])).sum() / -z_u_east[0,j] + dst_ubar_west[j] = (dst_u_west[:,j] * np.diff(z_u_west[:,j])).sum() / -z_u_west[0,j] + for j in range(dst_v_east.shape[1]): + dst_vbar_east[j] = (dst_v_east[:,j] * np.diff(z_v_east[:,j])).sum() / -z_v_east[0,j] + dst_vbar_west[j] = (dst_v_west[:,j] * np.diff(z_v_west[:,j])).sum() / -z_v_west[0,j] + + #mask + dst_ubar_north = np.ma.masked_where(dst_grd.hgrid.mask_u[-1,:] == 0, dst_ubar_north) + dst_ubar_south = np.ma.masked_where(dst_grd.hgrid.mask_u[0,:] == 0, dst_ubar_south) + dst_ubar_east = np.ma.masked_where(dst_grd.hgrid.mask_u[:,-1] == 0, dst_ubar_east) + dst_ubar_west = np.ma.masked_where(dst_grd.hgrid.mask_u[:,0] == 0, dst_ubar_west) + dst_vbar_north = np.ma.masked_where(dst_grd.hgrid.mask_v[-1,:] == 0, dst_vbar_north) + dst_vbar_south = np.ma.masked_where(dst_grd.hgrid.mask_v[0,:] == 0, dst_vbar_south) + dst_vbar_east = np.ma.masked_where(dst_grd.hgrid.mask_v[:,-1] == 0, dst_vbar_east) + dst_vbar_west = np.ma.masked_where(dst_grd.hgrid.mask_v[:,0] == 0, dst_vbar_west) + + # write data in destination file + print 'write data in destination file' + ncu.variables['ocean_time'][0] = time + ncu.variables['u_north'][0] = dst_u_north + ncu.variables['u_south'][0] = dst_u_south + ncu.variables['u_east'][0] = dst_u_east + ncu.variables['u_west'][0] = dst_u_west + ncu.variables['ubar_north'][0] = dst_ubar_north + ncu.variables['ubar_south'][0] = dst_ubar_south + ncu.variables['ubar_east'][0] = dst_ubar_east + ncu.variables['ubar_west'][0] = dst_ubar_west + + ncv.variables['ocean_time'][0] = time + ncv.variables['v_north'][0] = dst_v_north + ncv.variables['v_south'][0] = dst_v_south + ncv.variables['v_east'][0] = dst_v_east + ncv.variables['v_west'][0] = dst_v_west + ncv.variables['vbar_north'][0] = dst_vbar_north + ncv.variables['vbar_south'][0] = dst_vbar_south + ncv.variables['vbar_east'][0] = dst_vbar_east + ncv.variables['vbar_west'][0] = dst_vbar_west + + # close file + ncu.close() + ncv.close() + cdfuv.close() diff --git a/examples/Arctic_SODA3.3.1/remap_uv.py b/examples/Arctic_SODA3.3.1/remap_uv.py new file mode 100644 index 0000000..e7ad132 --- /dev/null +++ b/examples/Arctic_SODA3.3.1/remap_uv.py @@ -0,0 +1,206 @@ +import numpy as np +import os +try: + import netCDF4 as netCDF +except: + import netCDF3 as netCDF +import matplotlib.pyplot as plt +import time +import datetime as dt +from matplotlib.dates import date2num, num2date + +import pyroms +import pyroms_toolbox +import _remapping + +class nctime(object): + pass + +def remap_uv(src_fileuv, src_grd, dst_grd, dst_fileu, dst_filev, dmax=0, cdepth=0, kk=0, dst_dir='./'): + + # ARCTIC4 grid sub-sample +# xrange=src_grd.xrange; yrange=src_grd.yrange + ystart=235 + + # get time + nctime.long_name = 'time' + nctime.units = 'days since 1900-01-01 00:00:00' + + # get dimensions + Mp, Lp = dst_grd.hgrid.mask_rho.shape + + # create destination file + print '\nCreating destination file', dst_fileu + if os.path.exists(dst_fileu) is True: + os.remove(dst_fileu) + pyroms_toolbox.nc_create_roms_file(dst_fileu, dst_grd, nctime) + print 'Creating destination file', dst_filev + if os.path.exists(dst_filev) is True: + os.remove(dst_filev) + pyroms_toolbox.nc_create_roms_file(dst_filev, dst_grd, nctime) + + # open destination file + ncu = netCDF.Dataset(dst_fileu, 'a', format='NETCDF3_64BIT') + ncv = netCDF.Dataset(dst_filev, 'a', format='NETCDF3_64BIT') + + #load var + cdfuv = netCDF.Dataset(src_fileuv) + src_varu = cdfuv.variables['u'] + src_varv = cdfuv.variables['v'] + + tmp = cdfuv.variables['time'][:] + if len(tmp) > 1: + print 'error : multiple frames in input file' ; exit() + else: + time = tmp[0] + + # we need to correct the time axis + ref_soda = dt.datetime(1980,1,1,0,0) + ref_roms = dt.datetime(1900,1,1,0,0) + ndays = (ref_soda - ref_roms).days + time = time + ndays + + #get missing value + spval = src_varu.missing_value + + # ARCTIC4 grid sub-sample +# src_varu = src_varu[0,:, yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] + print 'subgrid u', src_varu.shape + src_varu = np.squeeze(src_varu, axis=(0,)) + src_varu = src_varu[:,np.r_[ystart:np.size(src_varu,1),-1],:] + print 'subgrid u', src_varu.shape +# src_varv = src_varv[0,:, yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] + print 'subgrid v', src_varv.shape + src_varv = np.squeeze(src_varv, axis=(0,)) + src_varv = src_varv[:,np.r_[ystart:np.size(src_varv,1),-1],:] + print 'subgrid v', src_varv.shape + + # get weights file + wts_file = 'remap_weights_' + src_grd.name + '_to_' + dst_grd.name + '_bilinear_uv_to_rho.nc' + + # build intermediate zgrid + zlevel = -src_grd.z_t[::-1] + nzlevel = len(zlevel) + dst_zcoord = pyroms.vgrid.z_coordinate(dst_grd.vgrid.h, zlevel, nzlevel) + dst_grdz = pyroms.grid.ROMS_Grid(dst_grd.name+'_Z', dst_grd.hgrid, dst_zcoord) + + # create variable in destination file + print 'Creating variable u' + ncu.createVariable('u', 'f8', ('ocean_time', 's_rho', 'eta_u', 'xi_u'), fill_value=spval) + ncu.variables['u'].long_name = '3D u-momentum component' + ncu.variables['u'].units = 'meter second-1' + ncu.variables['u'].field = 'u, scalar, series' + ncu.variables['u'].time = 'ocean_time' + + # create variable in destination file + print 'Creating variable ubar' + ncu.createVariable('ubar', 'f8', ('ocean_time', 'eta_u', 'xi_u'), fill_value=spval) + ncu.variables['ubar'].long_name = '2D u-momentum component' + ncu.variables['ubar'].units = 'meter second-1' + ncu.variables['ubar'].field = 'ubar, scalar, series' + ncu.variables['ubar'].time = 'ocean_time' + + print 'Creating variable v' + ncv.createVariable('v', 'f8', ('ocean_time', 's_rho', 'eta_v', 'xi_v'), fill_value=spval) + ncv.variables['v'].long_name = '3D v-momentum component' + ncv.variables['v'].units = 'meter second-1' + ncv.variables['v'].field = 'v, scalar, series' + ncv.variables['v'].time = 'ocean_time' + + print 'Creating variable vbar' + ncv.createVariable('vbar', 'f8', ('ocean_time', 'eta_v', 'xi_v'), fill_value=spval) + ncv.variables['vbar'].long_name = '2D v-momentum component' + ncv.variables['vbar'].units = 'meter second-1' + ncv.variables['vbar'].field = 'vbar, scalar, series' + ncv.variables['vbar'].time = 'ocean_time' + + + # remaping + print 'remapping and rotating u and v from', src_grd.name, \ + 'to', dst_grd.name + + # flood the grid + print 'flood the grid' + src_uz = pyroms_toolbox.BGrid_GFDL.flood(src_varu, src_grd, Bpos='uv', \ + spval=spval, dmax=dmax, cdepth=cdepth, kk=kk) + src_vz = pyroms_toolbox.BGrid_GFDL.flood(src_varv, src_grd, Bpos='uv', \ + spval=spval, dmax=dmax, cdepth=cdepth, kk=kk) + + # horizontal interpolation using scrip weights + print 'horizontal interpolation using scrip weights' + dst_uz = pyroms.remapping.remap(src_uz, wts_file, \ + spval=spval) + dst_vz = pyroms.remapping.remap(src_vz, wts_file, \ + spval=spval) + + # vertical interpolation from standard z level to sigma + print 'vertical interpolation from standard z level to sigma' + dst_u = pyroms.remapping.z2roms(dst_uz[::-1,:,:], dst_grdz, \ + dst_grd, Cpos='rho', spval=spval, flood=False) + dst_v = pyroms.remapping.z2roms(dst_vz[::-1,:,:], dst_grdz, \ + dst_grd, Cpos='rho', spval=spval, flood=False) +# dst_u = pyroms.remapping.z2roms(dst_uz[::-1, :, :], \ +# dst_grdz, dst_grd, Cpos='rho', spval=spval, \ +# flood=False, irange=(0,Lp), jrange=(0,Mp)) + +# dst_v = pyroms.remapping.z2roms(dst_vz[::-1, :, :], \ +# dst_grdz, dst_grd, Cpos='rho', spval=spval, \ +# flood=False, irange=(0,Lp), jrange=(0,Mp)) + + # rotate u,v fields + src_angle = np.zeros(dst_grd.hgrid.angle_rho.shape) + dst_angle = dst_grd.hgrid.angle_rho + angle = dst_angle - src_angle + angle = np.tile(angle, (dst_grd.vgrid.N, 1, 1)) + + U = dst_u + dst_v*1j + eitheta = np.exp(-1j*angle[:,:,:]) + U = U * eitheta + dst_u = np.real(U) + dst_v = np.imag(U) + + # move back to u,v points + dst_u = 0.5 * np.squeeze(dst_u[:,:,:-1] + dst_u[:,:,1:]) + dst_v = 0.5 * np.squeeze(dst_v[:,:-1,:] + dst_v[:,1:,:]) + + # spval + idxu = np.where(dst_grd.hgrid.mask_u == 0) + idxv = np.where(dst_grd.hgrid.mask_v == 0) + for n in range(dst_grd.vgrid.N): + dst_u[n, idxu[0], idxu[1]] = spval + dst_v[n, idxv[0], idxv[1]] = spval + + # compute depth average velocity ubar and vbar + # get z at the right position + z_u = 0.5 * (dst_grd.vgrid.z_w[0,:,:,:-1] + dst_grd.vgrid.z_w[0,:,:,1:]) + z_v = 0.5 * (dst_grd.vgrid.z_w[0,:,:-1,:] + dst_grd.vgrid.z_w[0,:,1:,:]) + + print 'shapes', dst_u.shape, dst_v.shape + dst_ubar = np.zeros([dst_u.shape[1], dst_u.shape[2]]) + dst_vbar = np.zeros([dst_v.shape[1], dst_v.shape[2]]) + + for i in range(dst_ubar.shape[1]): + for j in range(dst_ubar.shape[0]): + dst_ubar[j,i] = (dst_u[:,j,i] * np.diff(z_u[:,j,i])).sum() / -z_u[0,j,i] + for i in range(dst_vbar.shape[1]): + for j in range(dst_vbar.shape[0]): + dst_vbar[j,i] = (dst_v[:,j,i] * np.diff(z_v[:,j,i])).sum() / -z_v[0,j,i] + + #mask + dst_ubar = np.ma.masked_where(dst_grd.hgrid.mask_u == 0, dst_ubar) + dst_vbar = np.ma.masked_where(dst_grd.hgrid.mask_v == 0, dst_vbar) + + # write data in destination file + print 'write data in destination file' + ncu.variables['ocean_time'][0] = time + ncu.variables['u'][0] = dst_u + ncu.variables['ubar'][0] = dst_ubar + + ncv.variables['ocean_time'][0] = time + ncv.variables['v'][0] = dst_v + ncv.variables['vbar'][0] = dst_vbar + + # close file + ncu.close() + ncv.close() + cdfuv.close() diff --git a/examples/Arctic_runoff/addto_runoff_file.py b/examples/Arctic_runoff/addto_runoff_file.py index d550df4..79610ae 100644 --- a/examples/Arctic_runoff/addto_runoff_file.py +++ b/examples/Arctic_runoff/addto_runoff_file.py @@ -14,7 +14,7 @@ # load 2-dimentional interannual discharge data # from 1948-2007. See Dai and Trenberth (2002) and Dai et al. (2009) -print 'Load interannual discharge data' +print('Load interannual discharge data') nc_data = netCDF.Dataset('/archive/u1/uaf/kate/CORE2/runoff.daitren.iaf.10FEB2011.nc', 'r') data = nc_data.variables['runoff'][:] # time with leap year @@ -112,7 +112,7 @@ nct=0 for t in range(374,376): #for t in range(nt): - print 'Remapping runoff for time %f' %time[t] + print('Remapping runoff for time %f' %time[t]) # conservative horizontal interpolation using scrip runoff_raw = pyroms.remapping.remap(data[t,:,:], wts_file, \ spval=spval) @@ -125,8 +125,8 @@ runoff_spread = np.zeros((Mp,Lp)) idx = np.where(runoff != 0) for p in range(np.size(idx,1)): - j = range(max(0,idx[0][p]-rspread), min(Mp-1,idx[0][p]+rspread+1)) - i = range(max(0,idx[1][p]-rspread), min(Lp-1,idx[1][p]+rspread+1)) + j = list(range(max(0,idx[0][p]-rspread), min(Mp-1,idx[0][p]+rspread+1))) + i = list(range(max(0,idx[1][p]-rspread), min(Lp-1,idx[1][p]+rspread+1))) ji = np.meshgrid(j,i) sidx = np.where(maskl[ji] == 1) nbpt = np.size(sidx) / 2 diff --git a/examples/Arctic_runoff/compute_daitren_remap_weights.py b/examples/Arctic_runoff/compute_daitren_remap_weights.py index aaf799e..ad252b5 100644 --- a/examples/Arctic_runoff/compute_daitren_remap_weights.py +++ b/examples/Arctic_runoff/compute_daitren_remap_weights.py @@ -8,7 +8,7 @@ ## load 2-dimentional interannual discharge data ## from 1948-2007. See Dai and Trenberth (2002) and Dai et al. (2009) -print 'Load interannual discharge data' +print('Load interannual discharge data') nc_data = netCDF.Dataset('/archive/u1/uaf/kate/CORE2/runoff.daitren.iaf.10FEB2011.nc', 'r') runoff = nc_data.variables['runoff'][:] lon = nc_data.variables['xc'][:] @@ -18,7 +18,7 @@ mask = nc_data.variables['mask'][:] ## create data remap file for scrip -print 'Create remap grid file for Dai and Trenberth runoff' +print('Create remap grid file for Dai and Trenberth runoff') remap_filename = 'remap_grid_daitren.nc' nc = netCDF.Dataset(remap_filename, 'w', format='NETCDF3_CLASSIC') nc.Description = 'remap grid file for Dai and Trenberth runoff data' @@ -84,14 +84,14 @@ ## create Arctic2 remap file for scrip -print 'Create remap grid file for Arctic2 grid' +print('Create remap grid file for Arctic2 grid') dstgrd = pyroms.grid.get_ROMS_grid('ARCTIC2') dstgrd.hgrid.mask_rho = np.ones(dstgrd.hgrid.mask_rho.shape) pyroms.remapping.make_remap_grid_file(dstgrd, Cpos='rho') ## compute remap weights -print 'compute remap weights using scrip' +print('compute remap weights using scrip') # input namelist variables for conservative remapping at rho points grid1_file = 'remap_grid_daitren.nc' grid2_file = 'remap_grid_ARCTIC2_rho.nc' diff --git a/examples/Arctic_runoff/make_runoff_clim.py b/examples/Arctic_runoff/make_runoff_clim.py index a28752a..20d8ff5 100644 --- a/examples/Arctic_runoff/make_runoff_clim.py +++ b/examples/Arctic_runoff/make_runoff_clim.py @@ -8,7 +8,7 @@ # load 2-dimentional interannual discharge data # from 1948-2007. See Dai and Trenberth (2002) and Dai et al. (2009) -print 'Load interannual discharge data' +print('Load interannual discharge data') nc_data = netCDF.Dataset('/archive/u1/uaf/kate/CORE2/runoff.daitren.clim.10FEB2011.nc', 'r') data = nc_data.variables['runoff'][:] @@ -92,7 +92,7 @@ nct=0 for t in range(nt): - print 'Remapping runoff for time %f' %time[nct] + print('Remapping runoff for time %f' %time[nct]) # conservative horizontal interpolation using scrip runoff_raw = pyroms.remapping.remap(data[t,:,:], wts_file, \ spval=spval) @@ -105,8 +105,8 @@ runoff_spread = np.zeros((Mp,Lp)) idx = np.where(runoff != 0) for p in range(np.size(idx,1)): - j = range(max(0,idx[0][p]-rspread), min(Mp-1,idx[0][p]+rspread+1)) - i = range(max(0,idx[1][p]-rspread), min(Lp-1,idx[1][p]+rspread+1)) + j = list(range(max(0,idx[0][p]-rspread), min(Mp-1,idx[0][p]+rspread+1))) + i = list(range(max(0,idx[1][p]-rspread), min(Lp-1,idx[1][p]+rspread+1))) ji = np.meshgrid(j,i) sidx = np.where(maskl[ji] == 1) nbpt = np.size(sidx) / 2 diff --git a/examples/Arctic_runoff/make_runoff_file.py b/examples/Arctic_runoff/make_runoff_file.py index 69cf30f..7fd52fd 100644 --- a/examples/Arctic_runoff/make_runoff_file.py +++ b/examples/Arctic_runoff/make_runoff_file.py @@ -14,7 +14,7 @@ # load 2-dimentional interannual discharge data # from 1948-2007. See Dai and Trenberth (2002) and Dai et al. (2009) -print 'Load interannual discharge data' +print('Load interannual discharge data') nc_data = netCDF.Dataset('/archive/u1/uaf/kate/CORE2/runoff.daitren.iaf.10FEB2011.nc', 'r') data = nc_data.variables['runoff'][:] # time with leap year @@ -111,7 +111,7 @@ nct=0 for t in range(nt): - print 'Remapping runoff for time %f' %time[nct] + print('Remapping runoff for time %f' %time[nct]) # conservative horizontal interpolation using scrip runoff_raw = pyroms.remapping.remap(data[t,:,:], wts_file, \ spval=spval) @@ -124,8 +124,8 @@ runoff_spread = np.zeros((Mp,Lp)) idx = np.where(runoff != 0) for p in range(np.size(idx,1)): - j = range(max(0,idx[0][p]-rspread), min(Mp-1,idx[0][p]+rspread+1)) - i = range(max(0,idx[1][p]-rspread), min(Lp-1,idx[1][p]+rspread+1)) + j = list(range(max(0,idx[0][p]-rspread), min(Mp-1,idx[0][p]+rspread+1))) + i = list(range(max(0,idx[1][p]-rspread), min(Lp-1,idx[1][p]+rspread+1))) ji = np.meshgrid(j,i) sidx = np.where(maskl[ji] == 1) nbpt = np.size(sidx) / 2 diff --git a/examples/BC_from_sta/make_bry_file.py b/examples/BC_from_sta/make_bry_file.py index 74d7148..b6bfb73 100644 --- a/examples/BC_from_sta/make_bry_file.py +++ b/examples/BC_from_sta/make_bry_file.py @@ -8,14 +8,14 @@ import pyroms from station_bound import * -import commands +import subprocess import pdb irange = None jrange = None def do_file(file): - print 'file is: ' + file + print('file is: ' + file) var_list = ['u', 'v', 'temp', 'salt', 'zeta'] # pdb.set_trace() dst_var = station_bound(var_list, file,\ @@ -23,7 +23,7 @@ def do_file(file): # Change src_filename to your directory for the file's containing variable data data_dir = '/archive/u1/uaf/kate/NGOA/run05/' -lst = commands.getoutput('ls ' + data_dir + 'nwgoa_sta.nc') +lst = subprocess.getoutput('ls ' + data_dir + 'nwgoa_sta.nc') lst_file = lst.split() src_grd = pyroms.sta_grid.get_Stations_grid('NWGOA3', lst_file[0]) diff --git a/examples/BC_from_sta/station_bound.py b/examples/BC_from_sta/station_bound.py index 7ce754c..2464510 100644 --- a/examples/BC_from_sta/station_bound.py +++ b/examples/BC_from_sta/station_bound.py @@ -78,14 +78,14 @@ def station_bound(varname, srcfile, srcgrd, dst_grd, \ varname = [varname] nvar = len(varname) else: - raise ValueError, 'varname must be a str or a list of str' + raise ValueError('varname must be a str or a list of str') # if we're working on u and v, we'll compute ubar,vbar afterwards compute_ubar = False if (varname.__contains__('u') == 1 and varname.__contains__('v') == 1) or \ (varname.__contains__('u_eastward') == 1 and varname.__contains__('v_northward') == 1): compute_ubar = True - print 'ubar/vbar to be computed from u/v' + print('ubar/vbar to be computed from u/v') if varname.__contains__('ubar'): varname.remove('ubar') nvar = nvar-1 @@ -96,8 +96,8 @@ def station_bound(varname, srcfile, srcgrd, dst_grd, \ # if rotate_uv=True, check that u and v are in varname if rotate_uv is True: if varname.__contains__(uvar) == 0 or varname.__contains__(vvar) == 0: - raise Warning, 'varname must include uvar and vvar in order to' \ - + ' rotate the velocity field' + raise Warning('varname must include uvar and vvar in order to' \ + + ' rotate the velocity field') else: varname.remove(uvar) varname.remove(vvar) @@ -110,7 +110,7 @@ def station_bound(varname, srcfile, srcgrd, dst_grd, \ srcfile = sorted(glob.glob(srcfile)) nfile = len(srcfile) else: - raise ValueError, 'src_srcfile must be a str or a list of str' + raise ValueError('src_srcfile must be a str or a list of str') sides = ['_west','_east','_north','_south'] long = {'_west':'Western', '_east':'Eastern', \ @@ -121,7 +121,7 @@ def station_bound(varname, srcfile, srcgrd, dst_grd, \ nctidx = 0 # loop over the srcfile for nf in range(nfile): - print 'Working with file', srcfile[nf], '...' + print('Working with file', srcfile[nf], '...') # get time ocean_time = pyroms.utility.get_nc_var('ocean_time', srcfile[nf]) @@ -129,14 +129,14 @@ def station_bound(varname, srcfile, srcgrd, dst_grd, \ # trange argument if trange is None: - trange = range(ntime) + trange = list(range(ntime)) # create destination file if nctidx == 0: dstfile = dstdir + os.path.basename(srcfile[nf])[:-3] + '_' \ + dst_grd.name + '_bdry.nc' if os.path.exists(dstfile) is False: - print 'Creating destination file', dstfile + print('Creating destination file', dstfile) pyroms_toolbox.nc_create_roms_file(dstfile, dst_grd, \ ocean_time, lgrid=False) @@ -150,10 +150,10 @@ def station_bound(varname, srcfile, srcgrd, dst_grd, \ # loop over variable for nv in range(nvar): - print ' ' - print 'extracting', varname[nv], 'from', srcgrd.name, \ - 'to', dst_grd.name - print 'time =', ocean_time[nt] + print(' ') + print('extracting', varname[nv], 'from', srcgrd.name, \ + 'to', dst_grd.name) + print('time =', ocean_time[nt]) Mp, Lp = dst_grd.hgrid.mask_rho.shape if varname[nv] == uvar: Lp = Lp-1 @@ -170,7 +170,7 @@ def station_bound(varname, srcfile, srcgrd, dst_grd, \ try: spval = src_var._FillValue except: - print Warning, 'Did not find a _FillValue attribute.' + print(Warning, 'Did not find a _FillValue attribute.') # srange if srange is None: @@ -181,14 +181,14 @@ def station_bound(varname, srcfile, srcgrd, dst_grd, \ # determine where on the C-grid these variable lies Cpos='rho' - print 'Arakawa C-grid position is', Cpos + print('Arakawa C-grid position is', Cpos) # create variable in _destination file if nctidx == 0: for sid in sides: varn = varname[nv]+str(sid) dimens = [i for i in src_var.dimensions] - print 'dimens', dimens, len(dimens) + print('dimens', dimens, len(dimens)) if len(dimens) == 3: dimens = ['ocean_time', 's_rho', \ dimincl[sid]] @@ -200,15 +200,15 @@ def station_bound(varname, srcfile, srcgrd, dst_grd, \ if varname[nv] == vvar: foo = dimens[-1].replace('rho', 'v') dimens[-1] = foo - print 'Creating variable', varn, dimens + print('Creating variable', varn, dimens) nc.createVariable(varn, 'f8', dimens, \ fill_value=spval) nc.variables[varn].long_name = varname[nv] + \ - ' ' + long[sid] + ' boundary condition' + ' ' + int[sid] + ' boundary condition' try: nc.variables[varn].units = src_var.units except: - print varn+' has no units' + print(varn+' has no units') nc.variables[varn].time = src_var.time nc.variables[varn].coordinates = \ str(dimens.reverse()) @@ -216,7 +216,7 @@ def station_bound(varname, srcfile, srcgrd, dst_grd, \ if ndim == 2: # vertical interpolation from sigma to standard z level - print 'vertical interpolation from sigma to standard z level' + print('vertical interpolation from sigma to standard z level') src_varz = pyroms.remapping.sta2z( \ src_var[nt,:,ssrange[0]:ssrange[1]], \ srcgrd, srcgrdz, Cpos=Cpos, spval=spval, \ @@ -273,7 +273,7 @@ def station_bound(varname, srcfile, srcgrd, dst_grd, \ dst_varz[44:79, 0] = src_varz[0:35] dst_varz[0, 56:87] = src_varz[35:] - print datetime.datetime.now() + print(datetime.datetime.now()) # horizontal placement of stations into target grid. if ndim == 2: @@ -313,7 +313,7 @@ def station_bound(varname, srcfile, srcgrd, dst_grd, \ # print datetime.datetime.now() # write data in destination file - print 'write data in destination file' + print('write data in destination file') sid = '_west' varn = varname[nv]+str(sid) nc.variables[varn][nctidx] = np.squeeze(dst_var_west) @@ -332,9 +332,9 @@ def station_bound(varname, srcfile, srcgrd, dst_grd, \ # rotate the velocity field if requested if rotate_uv is True: - print ' ' - print 'remapping and rotating u and v from', srcgrd.name, \ - 'to', dst_grd.name + print(' ') + print('remapping and rotating u and v from', srcgrd.name, \ + 'to', dst_grd.name) # get source data src_u = pyroms.utility.get_nc_var(uvar, srcfile[nf]) @@ -344,16 +344,16 @@ def station_bound(varname, srcfile, srcgrd, dst_grd, \ try: spval = src_v._FillValue except: - print Warning, 'Did not find a _FillValue attribute.' + print(Warning, 'Did not find a _FillValue attribute.') if rotate_part: ndim = len(src_u.dimensions)-1 ind = uvar.find('_eastward') uvar_out = uvar[0:ind] - print "Warning: renaming uvar to", uvar_out + print("Warning: renaming uvar to", uvar_out) ind = vvar.find('_northward') vvar_out = vvar[0:ind] - print "Warning: renaming vvar to", vvar_out + print("Warning: renaming vvar to", vvar_out) if ndim == 3: dimens_u = ['ocean_time', 's_rho', 'eta_u', 'xi_u'] dimens_v = ['ocean_time', 's_rho', 'eta_v', 'xi_v'] @@ -369,10 +369,10 @@ def station_bound(varname, srcfile, srcgrd, dst_grd, \ # create variable in destination file if nctidx == 0: - print 'Creating boundary variables for '+uvar + print('Creating boundary variables for '+uvar) for sid in sides: varn = uvar_out+str(sid) - print 'Creating variable', varn + print('Creating variable', varn) dimens = list(dimens_u) # for dim in dimens: # if re.match(dimexcl[sid],dim): @@ -380,19 +380,19 @@ def station_bound(varname, srcfile, srcgrd, dst_grd, \ nc.createVariable(varn, 'f8', dimens, \ fill_value=spval) nc.variables[varn].long_name = uvar_out + \ - ' ' + long[sid] + ' boundary condition' + ' ' + int[sid] + ' boundary condition' try: nc.variables[varn].units = src_u.units except: - print varn+' has no units' + print(varn+' has no units') nc.variables[varn].time = src_u.time nc.variables[varn].coordinates = \ str(dimens.reverse()) nc.variables[varn].field = src_u.field - print 'Creating boundary variables for '+vvar + print('Creating boundary variables for '+vvar) for sid in sides: varn = vvar_out+str(sid) - print 'Creating variable', varn + print('Creating variable', varn) dimens = list(dimens_v) for dim in dimens: if re.match(dimexcl[sid],dim): @@ -400,11 +400,11 @@ def station_bound(varname, srcfile, srcgrd, dst_grd, \ nc.createVariable(varn, 'f8', dimens, \ fill_value=spval) nc.variables[varn].long_name = vvar_out + \ - ' ' + long[sid] + ' boundary condition' + ' ' + int[sid] + ' boundary condition' try: nc.variables[varn].units = src_v.units except: - print varn+' has no units' + print(varn+' has no units') nc.variables[varn].time = src_v.time nc.variables[varn].coordinates = \ str(dimens.reverse()) @@ -433,7 +433,7 @@ def station_bound(varname, srcfile, srcgrd, dst_grd, \ ndim = len(src_v.dimensions)-1 if ndim == 3: - print 'vertical interpolation from sigma to standard z level' + print('vertical interpolation from sigma to standard z level') src_uz = pyroms.remapping.sta2z( \ src_u[nt,:,ssrange[0]:ssrange[1]], \ srcgrd, srcgrdz, Cpos=Cpos_u, spval=spval, \ @@ -464,7 +464,7 @@ def station_bound(varname, srcfile, srcgrd, dst_grd, \ if ndim == 3: # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_u_north = pyroms.remapping.z2roms(dst_uz[:, Mp-2:Mp, 0:Lp], \ dst_grdz, dst_grd, Cpos='rho', spval=spval, \ flood=False, irange=(0,Lp), jrange=(Mp-2,Mp)) @@ -610,7 +610,7 @@ def station_bound(varname, srcfile, srcgrd, dst_grd, \ dst_v_west[idxv_west[0]] = spval # write data in destination file - print 'write data in destination file' + print('write data in destination file') sid = '_west' varn = uvar_out+str(sid) nc.variables[varn][nctidx] = dst_u_west @@ -637,7 +637,7 @@ def station_bound(varname, srcfile, srcgrd, dst_grd, \ if compute_ubar: if nctidx == 0: - print 'Creating variable ubar_north' + print('Creating variable ubar_north') nc.createVariable('ubar_north', 'f8', \ ('ocean_time', 'xi_u'), fill_value=spval) nc.variables['ubar_north'].long_name = \ @@ -646,7 +646,7 @@ def station_bound(varname, srcfile, srcgrd, dst_grd, \ nc.variables['ubar_north'].time = 'ocean_time' nc.variables['ubar_north'].coordinates = 'xi_u ocean_time' nc.variables['ubar_north'].field = 'ubar_north, scalar, series' - print 'Creating variable vbar_north' + print('Creating variable vbar_north') nc.createVariable('vbar_north', 'f8', \ ('ocean_time', 'xi_v'), fill_value=spval) nc.variables['vbar_north'].long_name = \ @@ -656,7 +656,7 @@ def station_bound(varname, srcfile, srcgrd, dst_grd, \ nc.variables['vbar_north'].coordinates = 'xi_v ocean_time' nc.variables['vbar_north'].field = 'vbar_north,, scalar, series' - print 'Creating variable ubar_south' + print('Creating variable ubar_south') nc.createVariable('ubar_south', 'f8', \ ('ocean_time', 'xi_u'), fill_value=spval) nc.variables['ubar_south'].long_name = \ @@ -665,7 +665,7 @@ def station_bound(varname, srcfile, srcgrd, dst_grd, \ nc.variables['ubar_south'].time = 'ocean_time' nc.variables['ubar_south'].coordinates = 'xi_u ocean_time' nc.variables['ubar_south'].field = 'ubar_south, scalar, series' - print 'Creating variable vbar_south' + print('Creating variable vbar_south') nc.createVariable('vbar_south', 'f8', \ ('ocean_time', 'xi_v'), fill_value=spval) nc.variables['vbar_south'].long_name = \ @@ -674,7 +674,7 @@ def station_bound(varname, srcfile, srcgrd, dst_grd, \ nc.variables['vbar_south'].time = 'ocean_time' nc.variables['vbar_south'].coordinates = 'xi_v ocean_time' - print 'Creating variable ubar_west' + print('Creating variable ubar_west') nc.createVariable('ubar_west', 'f8', \ ('ocean_time', 'eta_u'), fill_value=spval) nc.variables['ubar_west'].long_name = \ @@ -683,7 +683,7 @@ def station_bound(varname, srcfile, srcgrd, dst_grd, \ nc.variables['ubar_west'].time = 'ocean_time' nc.variables['ubar_west'].coordinates = 'eta_u ocean_time' nc.variables['ubar_west'].field = 'ubar_west, scalar, series' - print 'Creating variable vbar_west' + print('Creating variable vbar_west') nc.createVariable('vbar_west', 'f8', \ ('ocean_time', 'eta_v'), fill_value=spval) nc.variables['vbar_west'].long_name = \ @@ -692,7 +692,7 @@ def station_bound(varname, srcfile, srcgrd, dst_grd, \ nc.variables['vbar_west'].time = 'ocean_time' nc.variables['vbar_west'].coordinates = 'eta_v ocean_time' - print 'Creating variable ubar_east' + print('Creating variable ubar_east') nc.createVariable('ubar_east', 'f8', \ ('ocean_time', 'eta_u'), fill_value=spval) nc.variables['ubar_east'].long_name = \ @@ -701,7 +701,7 @@ def station_bound(varname, srcfile, srcgrd, dst_grd, \ nc.variables['ubar_east'].time = 'ocean_time' nc.variables['ubar_east'].coordinates = 'eta_u ocean_time' nc.variables['ubar_east'].field = 'ubar_east, scalar, series' - print 'Creating variable vbar_east' + print('Creating variable vbar_east') nc.createVariable('vbar_east', 'f8', \ ('ocean_time', 'eta_v'), fill_value=spval) nc.variables['vbar_east'].long_name = \ @@ -712,7 +712,7 @@ def station_bound(varname, srcfile, srcgrd, dst_grd, \ # compute depth average velocity ubar and vbar # get z at the right position - print 'Computing ubar/vbar from u/v' + print('Computing ubar/vbar from u/v') z_u_north = 0.5 * (dst_grd.vgrid.z_w[0,:,-1,:-1] + dst_grd.vgrid.z_w[0,:,-1, 1:]) z_v_north = 0.5 * (dst_grd.vgrid.z_w[0,:,-1,:] + @@ -800,7 +800,7 @@ def station_bound(varname, srcfile, srcgrd, dst_grd, \ nc.variables['vbar_west'][nctidx] = dst_vbar_west nctidx = nctidx + 1 - print 'ADDING to nctidx ', nctidx + print('ADDING to nctidx ', nctidx) nc.sync() # close files here? how? diff --git a/examples/Beaufort/make_clm_file.py b/examples/Beaufort/make_clm_file.py index eee8219..2d00509 100644 --- a/examples/Beaufort/make_clm_file.py +++ b/examples/Beaufort/make_clm_file.py @@ -9,7 +9,7 @@ import pyroms import pyroms_toolbox -import commands +import subprocess irange=(370,580) jrange=(460,580) diff --git a/examples/Beaufort/make_ice_bdry_file.py b/examples/Beaufort/make_ice_bdry_file.py index 55eb33f..d2a246a 100644 --- a/examples/Beaufort/make_ice_bdry_file.py +++ b/examples/Beaufort/make_ice_bdry_file.py @@ -33,7 +33,7 @@ def do_file(month): src_filename = part_filename + month + '*.nc' lcopy = list(src_varname) - print 'working on file '+src_filename + print('working on file '+src_filename) # didn't work even with processes=1 # pdb.set_trace() dst_var = pyroms_toolbox.remapping_bound(lcopy, src_filename,\ diff --git a/examples/Beaufort/make_weight_files.py b/examples/Beaufort/make_weight_files.py index 19f532c..766314e 100644 --- a/examples/Beaufort/make_weight_files.py +++ b/examples/Beaufort/make_weight_files.py @@ -30,7 +30,7 @@ num_maps = 1 map_method = 'bilinear' - print "Making "+str(interp_file1)+"..." + print("Making "+str(interp_file1)+"...") pyroms.remapping.compute_remap_weights(grid1_file,grid2_file,\ interp_file1,interp_file2,map1_name,\ diff --git a/examples/Bering/make_weight_files.py b/examples/Bering/make_weight_files.py index decb20e..c8db342 100644 --- a/examples/Bering/make_weight_files.py +++ b/examples/Bering/make_weight_files.py @@ -23,7 +23,7 @@ num_maps = 1 map_method = 'bilinear' - print "Making "+str(interp_file1)+"..." + print("Making "+str(interp_file1)+"...") pyroms.remapping.compute_remap_weights(grid1_file,grid2_file,\ interp_file1,interp_file2,map1_name,\ diff --git a/examples/CCS1_SODA3.3.1/Boundary/make_bdry_file.py b/examples/CCS1_SODA3.3.1/Boundary/make_bdry_file.py index 0f4b26c..b984a32 100644 --- a/examples/CCS1_SODA3.3.1/Boundary/make_bdry_file.py +++ b/examples/CCS1_SODA3.3.1/Boundary/make_bdry_file.py @@ -1,7 +1,7 @@ import subprocess import os import sys -import commands +import subprocess import numpy as np #increase the maximum number of open files allowed @@ -27,7 +27,7 @@ for filein in filelst: tag=filein.replace('soda3.3.1_5dy_ocean_reg_','').replace('.nc','') - print '\nBuild OBC file for time %s' %filein + print('\nBuild OBC file for time %s' %filein) zeta_dst_file = dst_dir + dst_grd.name + '_bdry_zeta_' + tag + '_' + src_grd.name + '.nc' temp_dst_file = dst_dir + dst_grd.name + '_bdry_temp_' + tag + '_' + src_grd.name + '.nc' salt_dst_file = dst_dir + dst_grd.name + '_bdry_salt_' + tag + '_' + src_grd.name + '.nc' diff --git a/examples/CCS1_SODA3.3.1/Boundary/remap_bdry.py b/examples/CCS1_SODA3.3.1/Boundary/remap_bdry.py index a8b8451..1a8a76d 100644 --- a/examples/CCS1_SODA3.3.1/Boundary/remap_bdry.py +++ b/examples/CCS1_SODA3.3.1/Boundary/remap_bdry.py @@ -26,7 +26,7 @@ def remap_bdry(src_varname, src_file, src_grd, dst_grd, dst_file, dmax=0, cdepth nctime.units = 'days since 1900-01-01 00:00:00' # create boundary file - print 'Creating boundary file', dst_file + print('Creating boundary file', dst_file) if os.path.exists(dst_file) is True: os.remove(dst_file) pyroms_toolbox.nc_create_roms_bdry_file(dst_file, dst_grd, nctime) @@ -41,7 +41,7 @@ def remap_bdry(src_varname, src_file, src_grd, dst_grd, dst_file, dmax=0, cdepth tmp = cdf.variables['time'][:] if len(tmp) > 1: - print 'error : multiple frames in input file' ; exit() + print('error : multiple frames in input file') ; exit() else: time = tmp[0] @@ -128,7 +128,7 @@ def remap_bdry(src_varname, src_file, src_grd, dst_grd, dst_file, dmax=0, cdepth field_west = 'salt_west, scalar, series' units = 'PSU' else: - raise ValueError, 'Undefined src_varname' + raise ValueError('Undefined src_varname') if ndim == 3: @@ -140,21 +140,21 @@ def remap_bdry(src_varname, src_file, src_grd, dst_grd, dst_file, dmax=0, cdepth # create variable in boudary file - print 'Creating variable', dst_varname_north + print('Creating variable', dst_varname_north) nc.createVariable(dst_varname_north, 'f8', dimensions_north, fill_value=spval) nc.variables[dst_varname_north].long_name = long_name_north nc.variables[dst_varname_north].units = units nc.variables[dst_varname_north].field = field_north #nc.variables[dst_varname_north]._FillValue = spval - print 'Creating variable', dst_varname_south + print('Creating variable', dst_varname_south) nc.createVariable(dst_varname_south, 'f8', dimensions_south, fill_value=spval) nc.variables[dst_varname_south].long_name = long_name_south nc.variables[dst_varname_south].units = units nc.variables[dst_varname_south].field = field_south #nc.variables[dst_varname_south]._FillValue = spval - print 'Creating variable', dst_varname_west + print('Creating variable', dst_varname_west) nc.createVariable(dst_varname_west, 'f8', dimensions_west, fill_value=spval) nc.variables[dst_varname_west].long_name = long_name_west nc.variables[dst_varname_west].units = units @@ -162,24 +162,24 @@ def remap_bdry(src_varname, src_file, src_grd, dst_grd, dst_file, dmax=0, cdepth #nc.variables[dst_varname_west]._FillValue = spval # remapping - print 'remapping', dst_varname, 'from', src_grd.name, \ - 'to', dst_grd.name + print('remapping', dst_varname, 'from', src_grd.name, \ + 'to', dst_grd.name) if ndim == 3: # flood the grid - print 'flood the grid' + print('flood the grid') src_varz = pyroms_toolbox.BGrid_SODA.flood(src_var, src_grd, Bpos=Bpos, spval=spval, \ dmax=dmax, cdepth=cdepth, kk=kk) else: src_varz = src_var # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_varz = pyroms.remapping.remap(src_varz, wts_file, spval=spval) if ndim == 3: # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_var_north = pyroms.remapping.z2roms(dst_varz[::-1, Mp-1:Mp, 0:Lp], \ dst_grdz, dst_grd, Cpos=Cpos, spval=spval, \ flood=False, irange=(0,Lp), jrange=(Mp-1,Mp)) @@ -195,7 +195,7 @@ def remap_bdry(src_varname, src_file, src_grd, dst_grd, dst_file, dmax=0, cdepth dst_var_west = dst_varz[:, 0] # write data in destination file - print 'write data in destination file\n' + print('write data in destination file\n') nc.variables['ocean_time'][0] = time nc.variables[dst_varname_north][0] = np.squeeze(dst_var_north) nc.variables[dst_varname_south][0] = np.squeeze(dst_var_south) diff --git a/examples/CCS1_SODA3.3.1/Boundary/remap_bdry_uv.py b/examples/CCS1_SODA3.3.1/Boundary/remap_bdry_uv.py index 309ed8a..c2516cf 100644 --- a/examples/CCS1_SODA3.3.1/Boundary/remap_bdry_uv.py +++ b/examples/CCS1_SODA3.3.1/Boundary/remap_bdry_uv.py @@ -29,11 +29,11 @@ def remap_bdry_uv(src_fileuv, src_grd, dst_grd, dst_fileu, dst_filev, dmax=0, cd Mp, Lp = dst_grd.hgrid.mask_rho.shape # create destination file - print '\nCreating destination file', dst_fileu + print('\nCreating destination file', dst_fileu) if os.path.exists(dst_fileu) is True: os.remove(dst_fileu) pyroms_toolbox.nc_create_roms_file(dst_fileu, dst_grd, nctime) - print 'Creating destination file', dst_filev + print('Creating destination file', dst_filev) if os.path.exists(dst_filev) is True: os.remove(dst_filev) pyroms_toolbox.nc_create_roms_bdry_file(dst_filev, dst_grd, nctime) @@ -49,7 +49,7 @@ def remap_bdry_uv(src_fileuv, src_grd, dst_grd, dst_fileu, dst_filev, dmax=0, cd tmp = cdfuv.variables['time'][:] if len(tmp) > 1: - print 'error : multiple frames in input file' ; exit() + print('error : multiple frames in input file') ; exit() else: time = tmp[0] @@ -76,19 +76,19 @@ def remap_bdry_uv(src_fileuv, src_grd, dst_grd, dst_fileu, dst_filev, dmax=0, cd dst_grdz = pyroms.grid.ROMS_Grid(dst_grd.name+'_Z', dst_grd.hgrid, dst_zcoord) # create variable in destination file - print 'Creating variable u_north' + print('Creating variable u_north') ncu.createVariable('u_north', 'f8', ('ocean_time', 's_rho', 'xi_u'), fill_value=spval) ncu.variables['u_north'].long_name = '3D u-momentum north boundary condition' ncu.variables['u_north'].units = 'meter second-1' ncu.variables['u_north'].field = 'u_north, scalar, series' #ncu.variables['u_north']._FillValue = spval - print 'Creating variable u_south' + print('Creating variable u_south') ncu.createVariable('u_south', 'f8', ('ocean_time', 's_rho', 'xi_u'), fill_value=spval) ncu.variables['u_south'].long_name = '3D u-momentum south boundary condition' ncu.variables['u_south'].units = 'meter second-1' ncu.variables['u_south'].field = 'u_south, scalar, series' #ncu.variables['u_south']._FillValue = spval - print 'Creating variable u_west' + print('Creating variable u_west') ncu.createVariable('u_west', 'f8', ('ocean_time', 's_rho', 'eta_u'), fill_value=spval) ncu.variables['u_west'].long_name = '3D u-momentum west boundary condition' ncu.variables['u_west'].units = 'meter second-1' @@ -96,57 +96,57 @@ def remap_bdry_uv(src_fileuv, src_grd, dst_grd, dst_fileu, dst_filev, dmax=0, cd #ncu.variables['u_west']._FillValue = spval # create variable in destination file - print 'Creating variable ubar_north' + print('Creating variable ubar_north') ncu.createVariable('ubar_north', 'f8', ('ocean_time', 'xi_u'), fill_value=spval) ncu.variables['ubar_north'].long_name = '2D u-momentum north boundary condition' ncu.variables['ubar_north'].units = 'meter second-1' ncu.variables['ubar_north'].field = 'ubar_north, scalar, series' #ncu.variables['ubar_north']._FillValue = spval - print 'Creating variable ubar_south' + print('Creating variable ubar_south') ncu.createVariable('ubar_south', 'f8', ('ocean_time', 'xi_u'), fill_value=spval) ncu.variables['ubar_south'].long_name = '2D u-momentum south boundary condition' ncu.variables['ubar_south'].units = 'meter second-1' ncu.variables['ubar_south'].field = 'ubar_south, scalar, series' #ncu.variables['ubar_south']._FillValue = spval - print 'Creating variable ubar_west' + print('Creating variable ubar_west') ncu.createVariable('ubar_west', 'f8', ('ocean_time', 'eta_u'), fill_value=spval) ncu.variables['ubar_west'].long_name = '2D u-momentum west boundary condition' ncu.variables['ubar_west'].units = 'meter second-1' ncu.variables['ubar_west'].field = 'ubar_east, scalar, series' #ncu.variables['ubar_west']._FillValue = spval - print 'Creating variable v_north' + print('Creating variable v_north') ncv.createVariable('v_north', 'f8', ('ocean_time', 's_rho', 'xi_v'), fill_value=spval) ncv.variables['v_north'].long_name = '3D v-momentum north boundary condition' ncv.variables['v_north'].units = 'meter second-1' ncv.variables['v_north'].field = 'v_north, scalar, series' #ncv.variables['v_north']._FillValue = spval - print 'Creating variable v_south' + print('Creating variable v_south') ncv.createVariable('v_south', 'f8', ('ocean_time', 's_rho', 'xi_v'), fill_value=spval) ncv.variables['v_south'].long_name = '3D v-momentum south boundary condition' ncv.variables['v_south'].units = 'meter second-1' ncv.variables['v_south'].field = 'v_south, scalar, series' #ncv.variables['v_south']._FillValue = spval - print 'Creating variable v_west' + print('Creating variable v_west') ncv.createVariable('v_west', 'f8', ('ocean_time', 's_rho', 'eta_v'), fill_value=spval) ncv.variables['v_west'].long_name = '3D v-momentum west boundary condition' ncv.variables['v_west'].units = 'meter second-1' ncv.variables['v_west'].field = 'v_east, scalar, series' #ncv.variables['v_west']._FillValue = spval - print 'Creating variable vbar_north' + print('Creating variable vbar_north') ncv.createVariable('vbar_north', 'f8', ('ocean_time', 'xi_v'), fill_value=spval) ncv.variables['vbar_north'].long_name = '2D v-momentum north boundary condition' ncv.variables['vbar_north'].units = 'meter second-1' ncv.variables['vbar_north'].field = 'vbar_north, scalar, series' #ncv.variables['vbar_north']._FillValue = spval - print 'Creating variable vbar_south' + print('Creating variable vbar_south') ncv.createVariable('vbar_south', 'f8', ('ocean_time', 'xi_v'), fill_value=spval) ncv.variables['vbar_south'].long_name = '2D v-momentum south boundary condition' ncv.variables['vbar_south'].units = 'meter second-1' ncv.variables['vbar_south'].field = 'vbar_south, scalar, series' #ncv.variables['vbar_south']._FillValue = spval - print 'Creating variable vbar_west' + print('Creating variable vbar_west') ncv.createVariable('vbar_west', 'f8', ('ocean_time', 'eta_v'), fill_value=spval) ncv.variables['vbar_west'].long_name = '2D v-momentum west boundary condition' ncv.variables['vbar_west'].units = 'meter second-1' @@ -156,25 +156,25 @@ def remap_bdry_uv(src_fileuv, src_grd, dst_grd, dst_fileu, dst_filev, dmax=0, cd # remaping - print 'remapping and rotating u and v from', src_grd.name, \ - 'to', dst_grd.name + print('remapping and rotating u and v from', src_grd.name, \ + 'to', dst_grd.name) # flood the grid - print 'flood the grid' + print('flood the grid') src_uz = pyroms_toolbox.BGrid_SODA.flood(src_varu, src_grd, Bpos='uv', \ spval=spval, dmax=dmax, cdepth=cdepth, kk=kk) src_vz = pyroms_toolbox.BGrid_SODA.flood(src_varv, src_grd, Bpos='uv', \ spval=spval, dmax=dmax, cdepth=cdepth, kk=kk) # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_uz = pyroms.remapping.remap(src_uz, wts_file, \ spval=spval) dst_vz = pyroms.remapping.remap(src_vz, wts_file, \ spval=spval) # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_u_north = pyroms.remapping.z2roms(dst_uz[::-1, Mp-2:Mp, 0:Lp], \ dst_grdz, dst_grd, Cpos='rho', spval=spval, \ flood=False, irange=(0,Lp), jrange=(Mp-2,Mp)) @@ -278,7 +278,7 @@ def remap_bdry_uv(src_fileuv, src_grd, dst_grd, dst_fileu, dst_filev, dmax=0, cd dst_vbar_west = np.ma.masked_where(dst_grd.hgrid.mask_v[:,0] == 0, dst_vbar_west) # write data in destination file - print 'write data in destination file' + print('write data in destination file') ncu.variables['ocean_time'][0] = time ncu.variables['u_north'][0] = dst_u_north ncu.variables['u_south'][0] = dst_u_south diff --git a/examples/CCS1_SODA3.3.1/Clim/make_clim_file.py b/examples/CCS1_SODA3.3.1/Clim/make_clim_file.py index 0a2157b..cf6e4c0 100644 --- a/examples/CCS1_SODA3.3.1/Clim/make_clim_file.py +++ b/examples/CCS1_SODA3.3.1/Clim/make_clim_file.py @@ -1,7 +1,7 @@ import subprocess import os import sys -import commands +import subprocess import numpy as np #increase the maximum number of open files allowed @@ -24,15 +24,15 @@ filelstyear = [] for ff in filelst: - if ff.find(str(my_year)) > 0: - filelstyear.append(ff) + if ff.find(str(my_year)) > 0: + filelstyear.append(ff) src_grd = pyroms_toolbox.BGrid_GFDL.get_nc_BGrid_GFDL(data_dir + 'grid/SODA3_0.5deg_grid.nc', name='SODA3.3.1', xrange=(400, 500), yrange=(180, 280) ) dst_grd = pyroms.grid.get_ROMS_grid('CCS') for filein in filelstyear: tag=filein.replace('soda3.3.1_monthly_ocean_reg_','').replace('.nc','') - print '\nBuild OBC file for time %s' %filein + print('\nBuild OBC file for time %s' %filein) zeta_dst_file = dst_dir + dst_grd.name + '_clim_zeta_' + tag + '_' + src_grd.name + '.nc' temp_dst_file = dst_dir + dst_grd.name + '_clim_temp_' + tag + '_' + src_grd.name + '.nc' salt_dst_file = dst_dir + dst_grd.name + '_clim_salt_' + tag + '_' + src_grd.name + '.nc' diff --git a/examples/CCS1_SODA3.3.1/Clim/remap.py b/examples/CCS1_SODA3.3.1/Clim/remap.py index 7231c91..59aba44 100644 --- a/examples/CCS1_SODA3.3.1/Clim/remap.py +++ b/examples/CCS1_SODA3.3.1/Clim/remap.py @@ -26,7 +26,7 @@ def remap(src_varname, src_file, src_grd, dst_grd, dst_file, dmax=0, cdepth=0, k nctime.units = 'days since 1900-01-01 00:00:00' # create IC file - print '\nCreating initial condition file', dst_file + print('\nCreating initial condition file', dst_file) if os.path.exists(dst_file) is True: os.remove(dst_file) pyroms_toolbox.nc_create_roms_file(dst_file, dst_grd, nctime) @@ -40,7 +40,7 @@ def remap(src_varname, src_file, src_grd, dst_grd, dst_file, dmax=0, cdepth=0, k tmp = cdf.variables['time'][:] if len(tmp) > 1: - print 'error : multiple frames in input file' ; exit() + print('error : multiple frames in input file') ; exit() else: time = tmp[0] @@ -98,7 +98,7 @@ def remap(src_varname, src_file, src_grd, dst_grd, dst_file, dmax=0, cdepth=0, k units = 'PSU' field = 'salinity, scalar, series' else: - raise ValueError, 'Undefined src_varname' + raise ValueError('Undefined src_varname') if ndim == 3: @@ -110,7 +110,7 @@ def remap(src_varname, src_file, src_grd, dst_grd, dst_file, dmax=0, cdepth=0, k # create variable in file - print 'Creating variable', dst_varname + print('Creating variable', dst_varname) nc.createVariable(dst_varname, 'f8', dimensions, fill_value=spval) nc.variables[dst_varname].long_name = long_name nc.variables[dst_varname].units = units @@ -119,31 +119,31 @@ def remap(src_varname, src_file, src_grd, dst_grd, dst_file, dmax=0, cdepth=0, k # remapping - print 'remapping', dst_varname, 'from', src_grd.name, \ - 'to', dst_grd.name + print('remapping', dst_varname, 'from', src_grd.name, \ + 'to', dst_grd.name) if ndim == 3: # flood the grid - print 'flood the grid' + print('flood the grid') src_varz = pyroms_toolbox.BGrid_SODA.flood(src_var, src_grd, Bpos=Bpos, spval=spval, \ dmax=dmax, cdepth=cdepth, kk=kk) else: src_varz = src_var # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_varz = pyroms.remapping.remap(src_varz, wts_file, spval=spval) if ndim == 3: # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_var = pyroms.remapping.z2roms(dst_varz[::-1,:,:], dst_grdz, \ dst_grd, Cpos=Cpos, spval=spval, flood=False) else: dst_var = dst_varz # write data in destination file - print 'write data in destination file\n' + print('write data in destination file\n') nc.variables['ocean_time'][0] = time nc.variables[dst_varname][0] = dst_var diff --git a/examples/CCS1_SODA3.3.1/Clim/remap_uv.py b/examples/CCS1_SODA3.3.1/Clim/remap_uv.py index 14f7a7c..5819eb6 100644 --- a/examples/CCS1_SODA3.3.1/Clim/remap_uv.py +++ b/examples/CCS1_SODA3.3.1/Clim/remap_uv.py @@ -29,11 +29,11 @@ def remap_uv(src_fileuv, src_grd, dst_grd, dst_fileu, dst_filev, dmax=0, cdepth= Mp, Lp = dst_grd.hgrid.mask_rho.shape # create destination file - print '\nCreating destination file', dst_fileu + print('\nCreating destination file', dst_fileu) if os.path.exists(dst_fileu) is True: os.remove(dst_fileu) pyroms_toolbox.nc_create_roms_file(dst_fileu, dst_grd, nctime) - print 'Creating destination file', dst_filev + print('Creating destination file', dst_filev) if os.path.exists(dst_filev) is True: os.remove(dst_filev) pyroms_toolbox.nc_create_roms_file(dst_filev, dst_grd, nctime) @@ -49,7 +49,7 @@ def remap_uv(src_fileuv, src_grd, dst_grd, dst_fileu, dst_filev, dmax=0, cdepth= tmp = cdfuv.variables['time'][:] if len(tmp) > 1: - print 'error : multiple frames in input file' ; exit() + print('error : multiple frames in input file') ; exit() else: time = tmp[0] @@ -76,27 +76,27 @@ def remap_uv(src_fileuv, src_grd, dst_grd, dst_fileu, dst_filev, dmax=0, cdepth= dst_grdz = pyroms.grid.ROMS_Grid(dst_grd.name+'_Z', dst_grd.hgrid, dst_zcoord) # create variable in destination file - print 'Creating variable u' + print('Creating variable u') ncu.createVariable('u', 'f8', ('ocean_time', 's_rho', 'eta_u', 'xi_u'), fill_value=spval) ncu.variables['u'].long_name = '3D u-momentum component' ncu.variables['u'].units = 'meter second-1' ncu.variables['u'].field = 'u-velocity, scalar, series' #ncu.variables['u_north']._FillValue = spval # create variable in destination file - print 'Creating variable ubar' + print('Creating variable ubar') ncu.createVariable('ubar', 'f8', ('ocean_time', 'eta_u', 'xi_u'), fill_value=spval) ncu.variables['ubar'].long_name = '2D u-momentum component' ncu.variables['ubar'].units = 'meter second-1' ncu.variables['ubar'].field = 'ubar-velocity,, scalar, series' #ncu.variables['ubar_north']._FillValue = spval - print 'Creating variable v' + print('Creating variable v') ncv.createVariable('v', 'f8', ('ocean_time', 's_rho', 'eta_v', 'xi_v'), fill_value=spval) ncv.variables['v'].long_name = '3D v-momentum component' ncv.variables['v'].units = 'meter second-1' ncv.variables['v'].field = 'v-velocity, scalar, series' #ncv.variables['v_north']._FillValue = spval - print 'Creating variable vbar' + print('Creating variable vbar') ncv.createVariable('vbar', 'f8', ('ocean_time', 'eta_v', 'xi_v'), fill_value=spval) ncv.variables['vbar'].long_name = '2D v-momentum component' ncv.variables['vbar'].units = 'meter second-1' @@ -105,25 +105,25 @@ def remap_uv(src_fileuv, src_grd, dst_grd, dst_fileu, dst_filev, dmax=0, cdepth= # remaping - print 'remapping and rotating u and v from', src_grd.name, \ - 'to', dst_grd.name + print('remapping and rotating u and v from', src_grd.name, \ + 'to', dst_grd.name) # flood the grid - print 'flood the grid' + print('flood the grid') src_uz = pyroms_toolbox.BGrid_SODA.flood(src_varu, src_grd, Bpos='uv', \ spval=spval, dmax=dmax, cdepth=cdepth, kk=kk) src_vz = pyroms_toolbox.BGrid_SODA.flood(src_varv, src_grd, Bpos='uv', \ spval=spval, dmax=dmax, cdepth=cdepth, kk=kk) # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_uz = pyroms.remapping.remap(src_uz, wts_file, \ spval=spval) dst_vz = pyroms.remapping.remap(src_vz, wts_file, \ spval=spval) # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_u = pyroms.remapping.z2roms(dst_uz[::-1,:,:], dst_grdz, \ dst_grd, Cpos='rho', spval=spval, flood=False) dst_v = pyroms.remapping.z2roms(dst_vz[::-1,:,:], dst_grdz, \ @@ -175,7 +175,7 @@ def remap_uv(src_fileuv, src_grd, dst_grd, dst_fileu, dst_filev, dmax=0, cdepth= dst_vbar[idxv[0], idxv[1]] = spval # write data in destination file - print 'write data in destination file\n' + print('write data in destination file\n') ncu.variables['ocean_time'][0] = time ncu.variables['u'][0] = dst_u ncu.variables['ubar'][0] = dst_ubar diff --git a/examples/CCS1_SODA3.3.1/Initial/make_ic_file.py b/examples/CCS1_SODA3.3.1/Initial/make_ic_file.py index 06821b2..a15568f 100644 --- a/examples/CCS1_SODA3.3.1/Initial/make_ic_file.py +++ b/examples/CCS1_SODA3.3.1/Initial/make_ic_file.py @@ -1,7 +1,7 @@ import subprocess import os import sys -import commands +import subprocess import numpy as np import pyroms import pyroms_toolbox @@ -10,17 +10,17 @@ from remap_uv import remap_uv #date to remap -data_dir = '/Volumes/P1/Data/SODA/SODA_3.3.1/' +data_dir = '/import/archive/u1/uaf/AKWATERS/kshedstrom/SODA/' dst_dir='./' -tag='1980_01_08' +tag='2010_12_26' filein=data_dir + 'soda3.3.1_5dy_ocean_reg_' + tag + '.nc' # load grids -src_grd = pyroms_toolbox.BGrid_GFDL.get_nc_BGrid_GFDL(data_dir + 'grid/SODA3_0.5deg_grid.nc', name='SODA3.3.1', xrange=(400, 500), yrange=(180, 280)) -dst_grd = pyroms.grid.get_ROMS_grid('CCS') +src_grd = pyroms_toolbox.BGrid_GFDL.get_nc_BGrid_GFDL(data_dir + 'SODA3_0.5deg_grid.nc', name='SODA3.3.1', xrange=(400, 500), yrange=(180, 280)) +dst_grd = pyroms.grid.get_ROMS_grid('CCS_10') -print '\nBuild IC file from %s' %filein +print('\nBuild IC file from %s' %filein) zeta_dst_file = dst_dir + dst_grd.name + '_ic_zeta_' + tag + '_' + src_grd.name + '.nc' temp_dst_file = dst_dir + dst_grd.name + '_ic_temp_' + tag + '_' + src_grd.name + '.nc' @@ -32,7 +32,7 @@ zeta = remap('ssh', filein, src_grd, dst_grd, zeta_dst_file, dst_dir=dst_dir) # reload grid with zeta (more accurate) -dst_grd = pyroms.grid.get_ROMS_grid('CCS', zeta=zeta) +dst_grd = pyroms.grid.get_ROMS_grid('CCS_10', zeta=zeta) # regrid temp, salt and velocities remap('temp',filein, src_grd, dst_grd, temp_dst_file, dst_dir=dst_dir) diff --git a/examples/CCS1_SODA3.3.1/Initial/make_remap_weights_file.py b/examples/CCS1_SODA3.3.1/Initial/make_remap_weights_file.py index 11043ba..df8780b 100644 --- a/examples/CCS1_SODA3.3.1/Initial/make_remap_weights_file.py +++ b/examples/CCS1_SODA3.3.1/Initial/make_remap_weights_file.py @@ -2,8 +2,8 @@ import pyroms_toolbox # load the grid -srcgrd = pyroms_toolbox.BGrid_GFDL.get_nc_BGrid_GFDL('/Volumes/P1/Data/SODA/SODA_3.3.1/grid/SODA3_0.5deg_grid.nc', name='SODA3.3.1', xrange=(400, 500), yrange=(180, 280)) -dstgrd = pyroms.grid.get_ROMS_grid('CCS') +srcgrd = pyroms_toolbox.BGrid_GFDL.get_nc_BGrid_GFDL('/import/archive/u1/uaf/AKWATERS/kshedstrom/SODA/SODA3_0.5deg_grid.nc', name='SODA3.3.1', xrange=(400, 500), yrange=(180, 280)) +dstgrd = pyroms.grid.get_ROMS_grid('CCS_10') # make remap grid file for scrip pyroms_toolbox.BGrid_GFDL.make_remap_grid_file(srcgrd, Bpos='t') diff --git a/examples/CCS1_SODA3.3.1/Initial/remap.py b/examples/CCS1_SODA3.3.1/Initial/remap.py index 7231c91..59aba44 100644 --- a/examples/CCS1_SODA3.3.1/Initial/remap.py +++ b/examples/CCS1_SODA3.3.1/Initial/remap.py @@ -26,7 +26,7 @@ def remap(src_varname, src_file, src_grd, dst_grd, dst_file, dmax=0, cdepth=0, k nctime.units = 'days since 1900-01-01 00:00:00' # create IC file - print '\nCreating initial condition file', dst_file + print('\nCreating initial condition file', dst_file) if os.path.exists(dst_file) is True: os.remove(dst_file) pyroms_toolbox.nc_create_roms_file(dst_file, dst_grd, nctime) @@ -40,7 +40,7 @@ def remap(src_varname, src_file, src_grd, dst_grd, dst_file, dmax=0, cdepth=0, k tmp = cdf.variables['time'][:] if len(tmp) > 1: - print 'error : multiple frames in input file' ; exit() + print('error : multiple frames in input file') ; exit() else: time = tmp[0] @@ -98,7 +98,7 @@ def remap(src_varname, src_file, src_grd, dst_grd, dst_file, dmax=0, cdepth=0, k units = 'PSU' field = 'salinity, scalar, series' else: - raise ValueError, 'Undefined src_varname' + raise ValueError('Undefined src_varname') if ndim == 3: @@ -110,7 +110,7 @@ def remap(src_varname, src_file, src_grd, dst_grd, dst_file, dmax=0, cdepth=0, k # create variable in file - print 'Creating variable', dst_varname + print('Creating variable', dst_varname) nc.createVariable(dst_varname, 'f8', dimensions, fill_value=spval) nc.variables[dst_varname].long_name = long_name nc.variables[dst_varname].units = units @@ -119,31 +119,31 @@ def remap(src_varname, src_file, src_grd, dst_grd, dst_file, dmax=0, cdepth=0, k # remapping - print 'remapping', dst_varname, 'from', src_grd.name, \ - 'to', dst_grd.name + print('remapping', dst_varname, 'from', src_grd.name, \ + 'to', dst_grd.name) if ndim == 3: # flood the grid - print 'flood the grid' + print('flood the grid') src_varz = pyroms_toolbox.BGrid_SODA.flood(src_var, src_grd, Bpos=Bpos, spval=spval, \ dmax=dmax, cdepth=cdepth, kk=kk) else: src_varz = src_var # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_varz = pyroms.remapping.remap(src_varz, wts_file, spval=spval) if ndim == 3: # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_var = pyroms.remapping.z2roms(dst_varz[::-1,:,:], dst_grdz, \ dst_grd, Cpos=Cpos, spval=spval, flood=False) else: dst_var = dst_varz # write data in destination file - print 'write data in destination file\n' + print('write data in destination file\n') nc.variables['ocean_time'][0] = time nc.variables[dst_varname][0] = dst_var diff --git a/examples/CCS1_SODA3.3.1/Initial/remap_uv.py b/examples/CCS1_SODA3.3.1/Initial/remap_uv.py index 14f7a7c..5819eb6 100644 --- a/examples/CCS1_SODA3.3.1/Initial/remap_uv.py +++ b/examples/CCS1_SODA3.3.1/Initial/remap_uv.py @@ -29,11 +29,11 @@ def remap_uv(src_fileuv, src_grd, dst_grd, dst_fileu, dst_filev, dmax=0, cdepth= Mp, Lp = dst_grd.hgrid.mask_rho.shape # create destination file - print '\nCreating destination file', dst_fileu + print('\nCreating destination file', dst_fileu) if os.path.exists(dst_fileu) is True: os.remove(dst_fileu) pyroms_toolbox.nc_create_roms_file(dst_fileu, dst_grd, nctime) - print 'Creating destination file', dst_filev + print('Creating destination file', dst_filev) if os.path.exists(dst_filev) is True: os.remove(dst_filev) pyroms_toolbox.nc_create_roms_file(dst_filev, dst_grd, nctime) @@ -49,7 +49,7 @@ def remap_uv(src_fileuv, src_grd, dst_grd, dst_fileu, dst_filev, dmax=0, cdepth= tmp = cdfuv.variables['time'][:] if len(tmp) > 1: - print 'error : multiple frames in input file' ; exit() + print('error : multiple frames in input file') ; exit() else: time = tmp[0] @@ -76,27 +76,27 @@ def remap_uv(src_fileuv, src_grd, dst_grd, dst_fileu, dst_filev, dmax=0, cdepth= dst_grdz = pyroms.grid.ROMS_Grid(dst_grd.name+'_Z', dst_grd.hgrid, dst_zcoord) # create variable in destination file - print 'Creating variable u' + print('Creating variable u') ncu.createVariable('u', 'f8', ('ocean_time', 's_rho', 'eta_u', 'xi_u'), fill_value=spval) ncu.variables['u'].long_name = '3D u-momentum component' ncu.variables['u'].units = 'meter second-1' ncu.variables['u'].field = 'u-velocity, scalar, series' #ncu.variables['u_north']._FillValue = spval # create variable in destination file - print 'Creating variable ubar' + print('Creating variable ubar') ncu.createVariable('ubar', 'f8', ('ocean_time', 'eta_u', 'xi_u'), fill_value=spval) ncu.variables['ubar'].long_name = '2D u-momentum component' ncu.variables['ubar'].units = 'meter second-1' ncu.variables['ubar'].field = 'ubar-velocity,, scalar, series' #ncu.variables['ubar_north']._FillValue = spval - print 'Creating variable v' + print('Creating variable v') ncv.createVariable('v', 'f8', ('ocean_time', 's_rho', 'eta_v', 'xi_v'), fill_value=spval) ncv.variables['v'].long_name = '3D v-momentum component' ncv.variables['v'].units = 'meter second-1' ncv.variables['v'].field = 'v-velocity, scalar, series' #ncv.variables['v_north']._FillValue = spval - print 'Creating variable vbar' + print('Creating variable vbar') ncv.createVariable('vbar', 'f8', ('ocean_time', 'eta_v', 'xi_v'), fill_value=spval) ncv.variables['vbar'].long_name = '2D v-momentum component' ncv.variables['vbar'].units = 'meter second-1' @@ -105,25 +105,25 @@ def remap_uv(src_fileuv, src_grd, dst_grd, dst_fileu, dst_filev, dmax=0, cdepth= # remaping - print 'remapping and rotating u and v from', src_grd.name, \ - 'to', dst_grd.name + print('remapping and rotating u and v from', src_grd.name, \ + 'to', dst_grd.name) # flood the grid - print 'flood the grid' + print('flood the grid') src_uz = pyroms_toolbox.BGrid_SODA.flood(src_varu, src_grd, Bpos='uv', \ spval=spval, dmax=dmax, cdepth=cdepth, kk=kk) src_vz = pyroms_toolbox.BGrid_SODA.flood(src_varv, src_grd, Bpos='uv', \ spval=spval, dmax=dmax, cdepth=cdepth, kk=kk) # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_uz = pyroms.remapping.remap(src_uz, wts_file, \ spval=spval) dst_vz = pyroms.remapping.remap(src_vz, wts_file, \ spval=spval) # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_u = pyroms.remapping.z2roms(dst_uz[::-1,:,:], dst_grdz, \ dst_grd, Cpos='rho', spval=spval, flood=False) dst_v = pyroms.remapping.z2roms(dst_vz[::-1,:,:], dst_grdz, \ @@ -175,7 +175,7 @@ def remap_uv(src_fileuv, src_grd, dst_grd, dst_fileu, dst_filev, dmax=0, cdepth= dst_vbar[idxv[0], idxv[1]] = spval # write data in destination file - print 'write data in destination file\n' + print('write data in destination file\n') ncu.variables['ocean_time'][0] = time ncu.variables['u'][0] = dst_u ncu.variables['ubar'][0] = dst_ubar diff --git a/examples/CCS1_SODA3.3.1/make_SODA3_grid.py b/examples/CCS1_SODA3.3.1/make_SODA3_grid.py index d5bc98c..e4ee835 100644 --- a/examples/CCS1_SODA3.3.1/make_SODA3_grid.py +++ b/examples/CCS1_SODA3.3.1/make_SODA3_grid.py @@ -56,26 +56,26 @@ kmt = np.empty((ny,nx)) ht = np.empty((ny,nx)) for ky in np.arange(ny): - for kx in np.arange(nx): - indlist = np.where(mask_t[:,ky,kx] == 1)[0] - if len(indlist) == 0: - kmt[ky,kx] = 0 - ht[ky,kx] = 0 - else: - kmt[ky,kx] = indlist.max() + 1 - ht[ky,kx] = st_edges_ocean[indlist.max() + 1] + for kx in np.arange(nx): + indlist = np.where(mask_t[:,ky,kx] == 1)[0] + if len(indlist) == 0: + kmt[ky,kx] = 0 + ht[ky,kx] = 0 + else: + kmt[ky,kx] = indlist.max() + 1 + ht[ky,kx] = st_edges_ocean[indlist.max() + 1] kmt[np.where(kmt == 0)] = spval ht[np.where(ht == 0)] = spval kmu = np.empty((ny,nx)) for ky in np.arange(ny): - for kx in np.arange(nx): - indlist = np.where(mask_u[:,ky,kx] == 1)[0] - if len(indlist) == 0: - kmu[ky,kx] = 0 - else: - kmu[ky,kx] = indlist.max() + 1 + for kx in np.arange(nx): + indlist = np.where(mask_u[:,ky,kx] == 1)[0] + if len(indlist) == 0: + kmu[ky,kx] = 0 + else: + kmu[ky,kx] = indlist.max() + 1 kmu[np.where(kmu == 0)] = spval diff --git a/examples/MERRA-2/get_MERRA_Pair_from_nasa_opendap_3hours.py b/examples/MERRA-2/get_MERRA_Pair_from_nasa_opendap_3hours.py index aa66dfa..0cf48c6 100644 --- a/examples/MERRA-2/get_MERRA_Pair_from_nasa_opendap_3hours.py +++ b/examples/MERRA-2/get_MERRA_Pair_from_nasa_opendap_3hours.py @@ -6,9 +6,9 @@ import pyroms import pyroms_toolbox -import cookielib +import http.cookiejar import netrc -import urllib2 +import urllib.request, urllib.error, urllib.parse import re import pydap.lib from pydap.exceptions import ClientError @@ -25,26 +25,26 @@ def install_basic_client(uri='', user='', passwd='', use_netrc=True): # Create special opener with support for Cookies - cj = cookielib.CookieJar() + cj = http.cookiejar.CookieJar() # Create the password manager and load with the credentials using - pwMgr = urllib2.HTTPPasswordMgrWithDefaultRealm() + pwMgr = urllib.request.HTTPPasswordMgrWithDefaultRealm() # Get passwords from the .netrc file nless use_netrc is False if use_netrc: logins = netrc.netrc() accounts = logins.hosts # a dist of hosts and tuples - for host, info in accounts.iteritems(): + for host, info in accounts.items(): login, account, password = info # log.debug('Host: %s; login: %s; account: %s; password: %s' % (host, login, account, password)) pwMgr.add_password(None, host, login, password) if uri and user and passwd: pwMgr.add_password(None, uri, user, passwd) - opener = urllib2.build_opener(urllib2.HTTPBasicAuthHandler(pwMgr), urllib2.HTTPCookieProcessor(cj)) + opener = urllib.request.build_opener(urllib.request.HTTPBasicAuthHandler(pwMgr), urllib.request.HTTPCookieProcessor(cj)) opener.addheaders = [('User-agent', pydap.lib.USER_AGENT)] - urllib2.install_opener(opener) + urllib.request.install_opener(opener) def new_request(url): if url[-1] is '&': url = url[0:-1] # log.debug('Opening %s (install_basic_client)' % url) - r = urllib2.urlopen(url) + r = urllib.request.urlopen(url) resp = r.headers.dict resp['status'] = str(r.code) data = r.read() diff --git a/examples/MERRA-2/get_MERRA_Qair_from_nasa_opendap_3hours.py b/examples/MERRA-2/get_MERRA_Qair_from_nasa_opendap_3hours.py index f9d9abe..f44119d 100644 --- a/examples/MERRA-2/get_MERRA_Qair_from_nasa_opendap_3hours.py +++ b/examples/MERRA-2/get_MERRA_Qair_from_nasa_opendap_3hours.py @@ -6,9 +6,9 @@ import pyroms import pyroms_toolbox -import cookielib +import http.cookiejar import netrc -import urllib2 +import urllib.request, urllib.error, urllib.parse import re import pydap.lib from pydap.exceptions import ClientError @@ -25,26 +25,26 @@ def install_basic_client(uri='', user='', passwd='', use_netrc=True): # Create special opener with support for Cookies - cj = cookielib.CookieJar() + cj = http.cookiejar.CookieJar() # Create the password manager and load with the credentials using - pwMgr = urllib2.HTTPPasswordMgrWithDefaultRealm() + pwMgr = urllib.request.HTTPPasswordMgrWithDefaultRealm() # Get passwords from the .netrc file nless use_netrc is False if use_netrc: logins = netrc.netrc() accounts = logins.hosts # a dist of hosts and tuples - for host, info in accounts.iteritems(): + for host, info in accounts.items(): login, account, password = info # log.debug('Host: %s; login: %s; account: %s; password: %s' % (host, login, account, password)) pwMgr.add_password(None, host, login, password) if uri and user and passwd: pwMgr.add_password(None, uri, user, passwd) - opener = urllib2.build_opener(urllib2.HTTPBasicAuthHandler(pwMgr), urllib2.HTTPCookieProcessor(cj)) + opener = urllib.request.build_opener(urllib.request.HTTPBasicAuthHandler(pwMgr), urllib.request.HTTPCookieProcessor(cj)) opener.addheaders = [('User-agent', pydap.lib.USER_AGENT)] - urllib2.install_opener(opener) + urllib.request.install_opener(opener) def new_request(url): if url[-1] is '&': url = url[0:-1] # log.debug('Opening %s (install_basic_client)' % url) - r = urllib2.urlopen(url) + r = urllib.request.urlopen(url) resp = r.headers.dict resp['status'] = str(r.code) data = r.read() diff --git a/examples/MERRA-2/get_MERRA_Tair_from_nasa_opendap_3hours.py b/examples/MERRA-2/get_MERRA_Tair_from_nasa_opendap_3hours.py index fe68e94..c436d22 100644 --- a/examples/MERRA-2/get_MERRA_Tair_from_nasa_opendap_3hours.py +++ b/examples/MERRA-2/get_MERRA_Tair_from_nasa_opendap_3hours.py @@ -6,9 +6,9 @@ import pyroms import pyroms_toolbox -import cookielib +import http.cookiejar import netrc -import urllib2 +import urllib.request, urllib.error, urllib.parse import re import pydap.lib from pydap.exceptions import ClientError @@ -25,26 +25,26 @@ def install_basic_client(uri='', user='', passwd='', use_netrc=True): # Create special opener with support for Cookies - cj = cookielib.CookieJar() + cj = http.cookiejar.CookieJar() # Create the password manager and load with the credentials using - pwMgr = urllib2.HTTPPasswordMgrWithDefaultRealm() + pwMgr = urllib.request.HTTPPasswordMgrWithDefaultRealm() # Get passwords from the .netrc file nless use_netrc is False if use_netrc: logins = netrc.netrc() accounts = logins.hosts # a dist of hosts and tuples - for host, info in accounts.iteritems(): + for host, info in accounts.items(): login, account, password = info # log.debug('Host: %s; login: %s; account: %s; password: %s' % (host, login, account, password)) pwMgr.add_password(None, host, login, password) if uri and user and passwd: pwMgr.add_password(None, uri, user, passwd) - opener = urllib2.build_opener(urllib2.HTTPBasicAuthHandler(pwMgr), urllib2.HTTPCookieProcessor(cj)) + opener = urllib.request.build_opener(urllib.request.HTTPBasicAuthHandler(pwMgr), urllib.request.HTTPCookieProcessor(cj)) opener.addheaders = [('User-agent', pydap.lib.USER_AGENT)] - urllib2.install_opener(opener) + urllib.request.install_opener(opener) def new_request(url): if url[-1] is '&': url = url[0:-1] # log.debug('Opening %s (install_basic_client)' % url) - r = urllib2.urlopen(url) + r = urllib.request.urlopen(url) resp = r.headers.dict resp['status'] = str(r.code) data = r.read() diff --git a/examples/MERRA-2/get_MERRA_Uwind_from_nasa_opendap_3hours.py b/examples/MERRA-2/get_MERRA_Uwind_from_nasa_opendap_3hours.py index 623e4eb..4aebbf2 100644 --- a/examples/MERRA-2/get_MERRA_Uwind_from_nasa_opendap_3hours.py +++ b/examples/MERRA-2/get_MERRA_Uwind_from_nasa_opendap_3hours.py @@ -6,9 +6,9 @@ import pyroms import pyroms_toolbox -import cookielib +import http.cookiejar import netrc -import urllib2 +import urllib.request, urllib.error, urllib.parse import re import pydap.lib from pydap.exceptions import ClientError @@ -25,26 +25,26 @@ def install_basic_client(uri='', user='', passwd='', use_netrc=True): # Create special opener with support for Cookies - cj = cookielib.CookieJar() + cj = http.cookiejar.CookieJar() # Create the password manager and load with the credentials using - pwMgr = urllib2.HTTPPasswordMgrWithDefaultRealm() + pwMgr = urllib.request.HTTPPasswordMgrWithDefaultRealm() # Get passwords from the .netrc file nless use_netrc is False if use_netrc: logins = netrc.netrc() accounts = logins.hosts # a dist of hosts and tuples - for host, info in accounts.iteritems(): + for host, info in accounts.items(): login, account, password = info # log.debug('Host: %s; login: %s; account: %s; password: %s' % (host, login, account, password)) pwMgr.add_password(None, host, login, password) if uri and user and passwd: pwMgr.add_password(None, uri, user, passwd) - opener = urllib2.build_opener(urllib2.HTTPBasicAuthHandler(pwMgr), urllib2.HTTPCookieProcessor(cj)) + opener = urllib.request.build_opener(urllib.request.HTTPBasicAuthHandler(pwMgr), urllib.request.HTTPCookieProcessor(cj)) opener.addheaders = [('User-agent', pydap.lib.USER_AGENT)] - urllib2.install_opener(opener) + urllib.request.install_opener(opener) def new_request(url): if url[-1] is '&': url = url[0:-1] # log.debug('Opening %s (install_basic_client)' % url) - r = urllib2.urlopen(url) + r = urllib.request.urlopen(url) resp = r.headers.dict resp['status'] = str(r.code) data = r.read() diff --git a/examples/MERRA-2/get_MERRA_Vwind_from_nasa_opendap_3hours.py b/examples/MERRA-2/get_MERRA_Vwind_from_nasa_opendap_3hours.py index 5d46c48..bcde044 100644 --- a/examples/MERRA-2/get_MERRA_Vwind_from_nasa_opendap_3hours.py +++ b/examples/MERRA-2/get_MERRA_Vwind_from_nasa_opendap_3hours.py @@ -6,9 +6,9 @@ import pyroms import pyroms_toolbox -import cookielib +import http.cookiejar import netrc -import urllib2 +import urllib.request, urllib.error, urllib.parse import re import pydap.lib from pydap.exceptions import ClientError @@ -25,26 +25,26 @@ def install_basic_client(uri='', user='', passwd='', use_netrc=True): # Create special opener with support for Cookies - cj = cookielib.CookieJar() + cj = http.cookiejar.CookieJar() # Create the password manager and load with the credentials using - pwMgr = urllib2.HTTPPasswordMgrWithDefaultRealm() + pwMgr = urllib.request.HTTPPasswordMgrWithDefaultRealm() # Get passwords from the .netrc file nless use_netrc is False if use_netrc: logins = netrc.netrc() accounts = logins.hosts # a dist of hosts and tuples - for host, info in accounts.iteritems(): + for host, info in accounts.items(): login, account, password = info # log.debug('Host: %s; login: %s; account: %s; password: %s' % (host, login, account, password)) pwMgr.add_password(None, host, login, password) if uri and user and passwd: pwMgr.add_password(None, uri, user, passwd) - opener = urllib2.build_opener(urllib2.HTTPBasicAuthHandler(pwMgr), urllib2.HTTPCookieProcessor(cj)) + opener = urllib.request.build_opener(urllib.request.HTTPBasicAuthHandler(pwMgr), urllib.request.HTTPCookieProcessor(cj)) opener.addheaders = [('User-agent', pydap.lib.USER_AGENT)] - urllib2.install_opener(opener) + urllib.request.install_opener(opener) def new_request(url): if url[-1] is '&': url = url[0:-1] # log.debug('Opening %s (install_basic_client)' % url) - r = urllib2.urlopen(url) + r = urllib.request.urlopen(url) resp = r.headers.dict resp['status'] = str(r.code) data = r.read() diff --git a/examples/MERRA-2/get_MERRA_albedo_from_nasa_opendap_daily.py b/examples/MERRA-2/get_MERRA_albedo_from_nasa_opendap_daily.py index e9cb33e..cebfccf 100644 --- a/examples/MERRA-2/get_MERRA_albedo_from_nasa_opendap_daily.py +++ b/examples/MERRA-2/get_MERRA_albedo_from_nasa_opendap_daily.py @@ -6,9 +6,9 @@ import pyroms import pyroms_toolbox -import cookielib +import http.cookiejar import netrc -import urllib2 +import urllib.request, urllib.error, urllib.parse import re import pydap.lib from pydap.exceptions import ClientError @@ -25,26 +25,26 @@ def install_basic_client(uri='', user='', passwd='', use_netrc=True): # Create special opener with support for Cookies - cj = cookielib.CookieJar() + cj = http.cookiejar.CookieJar() # Create the password manager and load with the credentials using - pwMgr = urllib2.HTTPPasswordMgrWithDefaultRealm() + pwMgr = urllib.request.HTTPPasswordMgrWithDefaultRealm() # Get passwords from the .netrc file nless use_netrc is False if use_netrc: logins = netrc.netrc() accounts = logins.hosts # a dist of hosts and tuples - for host, info in accounts.iteritems(): + for host, info in accounts.items(): login, account, password = info # log.debug('Host: %s; login: %s; account: %s; password: %s' % (host, login, account, password)) pwMgr.add_password(None, host, login, password) if uri and user and passwd: pwMgr.add_password(None, uri, user, passwd) - opener = urllib2.build_opener(urllib2.HTTPBasicAuthHandler(pwMgr), urllib2.HTTPCookieProcessor(cj)) + opener = urllib.request.build_opener(urllib.request.HTTPBasicAuthHandler(pwMgr), urllib.request.HTTPCookieProcessor(cj)) opener.addheaders = [('User-agent', pydap.lib.USER_AGENT)] - urllib2.install_opener(opener) + urllib.request.install_opener(opener) def new_request(url): if url[-1] is '&': url = url[0:-1] # log.debug('Opening %s (install_basic_client)' % url) - r = urllib2.urlopen(url) + r = urllib.request.urlopen(url) resp = r.headers.dict resp['status'] = str(r.code) data = r.read() diff --git a/examples/MERRA-2/get_MERRA_cloud_from_nasa_opendap_3hours.py b/examples/MERRA-2/get_MERRA_cloud_from_nasa_opendap_3hours.py index 51c4092..c407e33 100644 --- a/examples/MERRA-2/get_MERRA_cloud_from_nasa_opendap_3hours.py +++ b/examples/MERRA-2/get_MERRA_cloud_from_nasa_opendap_3hours.py @@ -6,9 +6,9 @@ import pyroms import pyroms_toolbox -import cookielib +import http.cookiejar import netrc -import urllib2 +import urllib.request, urllib.error, urllib.parse import re import pydap.lib from pydap.exceptions import ClientError @@ -25,26 +25,26 @@ def install_basic_client(uri='', user='', passwd='', use_netrc=True): # Create special opener with support for Cookies - cj = cookielib.CookieJar() + cj = http.cookiejar.CookieJar() # Create the password manager and load with the credentials using - pwMgr = urllib2.HTTPPasswordMgrWithDefaultRealm() + pwMgr = urllib.request.HTTPPasswordMgrWithDefaultRealm() # Get passwords from the .netrc file nless use_netrc is False if use_netrc: logins = netrc.netrc() accounts = logins.hosts # a dist of hosts and tuples - for host, info in accounts.iteritems(): + for host, info in accounts.items(): login, account, password = info # log.debug('Host: %s; login: %s; account: %s; password: %s' % (host, login, account, password)) pwMgr.add_password(None, host, login, password) if uri and user and passwd: pwMgr.add_password(None, uri, user, passwd) - opener = urllib2.build_opener(urllib2.HTTPBasicAuthHandler(pwMgr), urllib2.HTTPCookieProcessor(cj)) + opener = urllib.request.build_opener(urllib.request.HTTPBasicAuthHandler(pwMgr), urllib.request.HTTPCookieProcessor(cj)) opener.addheaders = [('User-agent', pydap.lib.USER_AGENT)] - urllib2.install_opener(opener) + urllib.request.install_opener(opener) def new_request(url): if url[-1] is '&': url = url[0:-1] # log.debug('Opening %s (install_basic_client)' % url) - r = urllib2.urlopen(url) + r = urllib.request.urlopen(url) resp = r.headers.dict resp['status'] = str(r.code) data = r.read() diff --git a/examples/MERRA-2/get_MERRA_lwrad_down_from_nasa_opendap_3hours.py b/examples/MERRA-2/get_MERRA_lwrad_down_from_nasa_opendap_3hours.py index d859190..ce63195 100644 --- a/examples/MERRA-2/get_MERRA_lwrad_down_from_nasa_opendap_3hours.py +++ b/examples/MERRA-2/get_MERRA_lwrad_down_from_nasa_opendap_3hours.py @@ -6,9 +6,9 @@ import pyroms import pyroms_toolbox -import cookielib +import http.cookiejar import netrc -import urllib2 +import urllib.request, urllib.error, urllib.parse import re import pydap.lib from pydap.exceptions import ClientError @@ -25,26 +25,26 @@ def install_basic_client(uri='', user='', passwd='', use_netrc=True): # Create special opener with support for Cookies - cj = cookielib.CookieJar() + cj = http.cookiejar.CookieJar() # Create the password manager and load with the credentials using - pwMgr = urllib2.HTTPPasswordMgrWithDefaultRealm() + pwMgr = urllib.request.HTTPPasswordMgrWithDefaultRealm() # Get passwords from the .netrc file nless use_netrc is False if use_netrc: logins = netrc.netrc() accounts = logins.hosts # a dist of hosts and tuples - for host, info in accounts.iteritems(): + for host, info in accounts.items(): login, account, password = info # log.debug('Host: %s; login: %s; account: %s; password: %s' % (host, login, account, password)) pwMgr.add_password(None, host, login, password) if uri and user and passwd: pwMgr.add_password(None, uri, user, passwd) - opener = urllib2.build_opener(urllib2.HTTPBasicAuthHandler(pwMgr), urllib2.HTTPCookieProcessor(cj)) + opener = urllib.request.build_opener(urllib.request.HTTPBasicAuthHandler(pwMgr), urllib.request.HTTPCookieProcessor(cj)) opener.addheaders = [('User-agent', pydap.lib.USER_AGENT)] - urllib2.install_opener(opener) + urllib.request.install_opener(opener) def new_request(url): if url[-1] is '&': url = url[0:-1] # log.debug('Opening %s (install_basic_client)' % url) - r = urllib2.urlopen(url) + r = urllib.request.urlopen(url) resp = r.headers.dict resp['status'] = str(r.code) data = r.read() diff --git a/examples/MERRA-2/get_MERRA_rain_from_nasa_opendap_3hours.py b/examples/MERRA-2/get_MERRA_rain_from_nasa_opendap_3hours.py index 49dcb14..4c8ace6 100644 --- a/examples/MERRA-2/get_MERRA_rain_from_nasa_opendap_3hours.py +++ b/examples/MERRA-2/get_MERRA_rain_from_nasa_opendap_3hours.py @@ -6,9 +6,9 @@ import pyroms import pyroms_toolbox -import cookielib +import http.cookiejar import netrc -import urllib2 +import urllib.request, urllib.error, urllib.parse import re import pydap.lib from pydap.exceptions import ClientError @@ -25,26 +25,26 @@ def install_basic_client(uri='', user='', passwd='', use_netrc=True): # Create special opener with support for Cookies - cj = cookielib.CookieJar() + cj = http.cookiejar.CookieJar() # Create the password manager and load with the credentials using - pwMgr = urllib2.HTTPPasswordMgrWithDefaultRealm() + pwMgr = urllib.request.HTTPPasswordMgrWithDefaultRealm() # Get passwords from the .netrc file nless use_netrc is False if use_netrc: logins = netrc.netrc() accounts = logins.hosts # a dist of hosts and tuples - for host, info in accounts.iteritems(): + for host, info in accounts.items(): login, account, password = info # log.debug('Host: %s; login: %s; account: %s; password: %s' % (host, login, account, password)) pwMgr.add_password(None, host, login, password) if uri and user and passwd: pwMgr.add_password(None, uri, user, passwd) - opener = urllib2.build_opener(urllib2.HTTPBasicAuthHandler(pwMgr), urllib2.HTTPCookieProcessor(cj)) + opener = urllib.request.build_opener(urllib.request.HTTPBasicAuthHandler(pwMgr), urllib.request.HTTPCookieProcessor(cj)) opener.addheaders = [('User-agent', pydap.lib.USER_AGENT)] - urllib2.install_opener(opener) + urllib.request.install_opener(opener) def new_request(url): if url[-1] is '&': url = url[0:-1] # log.debug('Opening %s (install_basic_client)' % url) - r = urllib2.urlopen(url) + r = urllib.request.urlopen(url) resp = r.headers.dict resp['status'] = str(r.code) data = r.read() diff --git a/examples/MERRA-2/get_MERRA_snow_from_nasa_opendap_3hours.py b/examples/MERRA-2/get_MERRA_snow_from_nasa_opendap_3hours.py index 6996d5a..cfd9af4 100644 --- a/examples/MERRA-2/get_MERRA_snow_from_nasa_opendap_3hours.py +++ b/examples/MERRA-2/get_MERRA_snow_from_nasa_opendap_3hours.py @@ -6,9 +6,9 @@ import pyroms import pyroms_toolbox -import cookielib +import http.cookiejar import netrc -import urllib2 +import urllib.request, urllib.error, urllib.parse import re import pydap.lib from pydap.exceptions import ClientError @@ -25,26 +25,26 @@ def install_basic_client(uri='', user='', passwd='', use_netrc=True): # Create special opener with support for Cookies - cj = cookielib.CookieJar() + cj = http.cookiejar.CookieJar() # Create the password manager and load with the credentials using - pwMgr = urllib2.HTTPPasswordMgrWithDefaultRealm() + pwMgr = urllib.request.HTTPPasswordMgrWithDefaultRealm() # Get passwords from the .netrc file nless use_netrc is False if use_netrc: logins = netrc.netrc() accounts = logins.hosts # a dist of hosts and tuples - for host, info in accounts.iteritems(): + for host, info in accounts.items(): login, account, password = info # log.debug('Host: %s; login: %s; account: %s; password: %s' % (host, login, account, password)) pwMgr.add_password(None, host, login, password) if uri and user and passwd: pwMgr.add_password(None, uri, user, passwd) - opener = urllib2.build_opener(urllib2.HTTPBasicAuthHandler(pwMgr), urllib2.HTTPCookieProcessor(cj)) + opener = urllib.request.build_opener(urllib.request.HTTPBasicAuthHandler(pwMgr), urllib.request.HTTPCookieProcessor(cj)) opener.addheaders = [('User-agent', pydap.lib.USER_AGENT)] - urllib2.install_opener(opener) + urllib.request.install_opener(opener) def new_request(url): if url[-1] is '&': url = url[0:-1] # log.debug('Opening %s (install_basic_client)' % url) - r = urllib2.urlopen(url) + r = urllib.request.urlopen(url) resp = r.headers.dict resp['status'] = str(r.code) data = r.read() diff --git a/examples/MERRA-2/get_MERRA_swrad_from_nasa_opendap_3hours.py b/examples/MERRA-2/get_MERRA_swrad_from_nasa_opendap_3hours.py index 972edb8..ca2e385 100644 --- a/examples/MERRA-2/get_MERRA_swrad_from_nasa_opendap_3hours.py +++ b/examples/MERRA-2/get_MERRA_swrad_from_nasa_opendap_3hours.py @@ -6,9 +6,9 @@ import pyroms import pyroms_toolbox -import cookielib +import http.cookiejar import netrc -import urllib2 +import urllib.request, urllib.error, urllib.parse import re import pydap.lib from pydap.exceptions import ClientError @@ -25,26 +25,26 @@ def install_basic_client(uri='', user='', passwd='', use_netrc=True): # Create special opener with support for Cookies - cj = cookielib.CookieJar() + cj = http.cookiejar.CookieJar() # Create the password manager and load with the credentials using - pwMgr = urllib2.HTTPPasswordMgrWithDefaultRealm() + pwMgr = urllib.request.HTTPPasswordMgrWithDefaultRealm() # Get passwords from the .netrc file nless use_netrc is False if use_netrc: logins = netrc.netrc() accounts = logins.hosts # a dist of hosts and tuples - for host, info in accounts.iteritems(): + for host, info in accounts.items(): login, account, password = info # log.debug('Host: %s; login: %s; account: %s; password: %s' % (host, login, account, password)) pwMgr.add_password(None, host, login, password) if uri and user and passwd: pwMgr.add_password(None, uri, user, passwd) - opener = urllib2.build_opener(urllib2.HTTPBasicAuthHandler(pwMgr), urllib2.HTTPCookieProcessor(cj)) + opener = urllib.request.build_opener(urllib.request.HTTPBasicAuthHandler(pwMgr), urllib.request.HTTPCookieProcessor(cj)) opener.addheaders = [('User-agent', pydap.lib.USER_AGENT)] - urllib2.install_opener(opener) + urllib.request.install_opener(opener) def new_request(url): if url[-1] is '&': url = url[0:-1] # log.debug('Opening %s (install_basic_client)' % url) - r = urllib2.urlopen(url) + r = urllib.request.urlopen(url) resp = r.headers.dict resp['status'] = str(r.code) data = r.read() diff --git a/examples/NWGOA3/Fetch_Pacific/get_pacific_3d.py b/examples/NWGOA3/Fetch_Pacific/get_pacific_3d.py index a336406..08e94ff 100644 --- a/examples/NWGOA3/Fetch_Pacific/get_pacific_3d.py +++ b/examples/NWGOA3/Fetch_Pacific/get_pacific_3d.py @@ -21,7 +21,7 @@ def create_HYCOM_file(name): global nc - print 'Creating file %s' %name + print('Creating file %s' %name) #create netCDF file nc = netCDF4.Dataset(name, 'w', format='NETCDF3_64BIT') @@ -79,7 +79,7 @@ def create_HYCOM_file(name): nc.variables[outvarname].coordinates = 'ocean_time s_rho lon_rho lat_rho' - print 'Done with header for file %s' %name + print('Done with header for file %s' %name) @@ -118,15 +118,15 @@ def create_HYCOM_file(name): create_HYCOM_file(outfile) day_out = 0 for day in range(rec_start,rec_end): - print 'Processing file for %s, day %d, year %04d' %(invarname, day_out*3, year) + print('Processing file for %s, day %d, year %04d' %(invarname, day_out*3, year)) #get data from server try: var = dataset.variables[invarname][day,:,170:215,195:265] # spval = var.get_fill_value() # dataset.close() - print 'Got %s from server...' %invarname + print('Got %s from server...' %invarname) except: - print 'No file on the server... We skip this day.' + print('No file on the server... We skip this day.') retry_day.append((day,day_out)) continue @@ -139,17 +139,17 @@ def create_HYCOM_file(name): if retry == 'True': if len(retry_day) != 0: - print "Some file have not been downloded... Let's try again" + print("Some file have not been downloded... Let's try again") while len(retry_day) != 0: for (day,day_out) in retry_day: - print 'Retry file for %s, day %03d, year %04d' %(invarname, day_out, year) + print('Retry file for %s, day %03d, year %04d' %(invarname, day_out, year)) #get data from server try: var = dataset.variables[invarname][day,:,170:215,195:265] # spval = var.get_fill_value() - print 'Got %s from server...' %invarname + print('Got %s from server...' %invarname) except: - print 'No file on the server... We skip this day.' + print('No file on the server... We skip this day.') continue #create netCDF file diff --git a/examples/NWGOA3/Fetch_Pacific/get_pacific_u.py b/examples/NWGOA3/Fetch_Pacific/get_pacific_u.py index e35181b..d969dbe 100644 --- a/examples/NWGOA3/Fetch_Pacific/get_pacific_u.py +++ b/examples/NWGOA3/Fetch_Pacific/get_pacific_u.py @@ -13,7 +13,7 @@ def create_HYCOM_file(name): global nc - print 'Creating file %s' %name + print('Creating file %s' %name) #create netCDF file nc = netCDF4.Dataset(name, 'w', format='NETCDF3_64BIT') @@ -72,7 +72,7 @@ def create_HYCOM_file(name): nc.variables[outvarname].coordinates = 'ocean_time s_rho lon_u lat_u' - print 'Done with header for file %s' %name + print('Done with header for file %s' %name) @@ -113,15 +113,15 @@ def create_HYCOM_file(name): create_HYCOM_file(outfile) day_out = 0 for day in range(rec_start,rec_end): - print 'Processing file for %s, day %d, year %04d' %(invarname, day_out*3, year) + print('Processing file for %s, day %d, year %04d' %(invarname, day_out*3, year)) #get data from server try: var = dataset.variables[invarname][day,:,170:215,195:265-1] # spval = var.get_fill_value() # dataset.close() - print 'Got %s from server...' %invarname + print('Got %s from server...' %invarname) except: - print 'No file on the server... We skip this day.' + print('No file on the server... We skip this day.') retry_day.append((day,day_out)) continue @@ -134,17 +134,17 @@ def create_HYCOM_file(name): if retry == 'True': if len(retry_day) != 0: - print "Some file have not been downloded... Let's try again" + print("Some file have not been downloded... Let's try again") while len(retry_day) != 0: for (day,day_out) in retry_day: - print 'Retry file for %s, day %03d, year %04d' %(invarname, day_out, year) + print('Retry file for %s, day %03d, year %04d' %(invarname, day_out, year)) #get data from server try: var = dataset.variables[invarname][day,:,170:215,195:265-1] #spval = var.get_fill_value() - print 'Got %s from server...' %invarname + print('Got %s from server...' %invarname) except: - print 'No file on the server... We skip this day.' + print('No file on the server... We skip this day.') continue #create netCDF file diff --git a/examples/NWGOA3/Fetch_Pacific/get_pacific_v.py b/examples/NWGOA3/Fetch_Pacific/get_pacific_v.py index 0d892c8..55da7d8 100644 --- a/examples/NWGOA3/Fetch_Pacific/get_pacific_v.py +++ b/examples/NWGOA3/Fetch_Pacific/get_pacific_v.py @@ -13,7 +13,7 @@ def create_HYCOM_file(name): global nc - print 'Creating file %s' %name + print('Creating file %s' %name) #create netCDF file nc = netCDF4.Dataset(name, 'w', format='NETCDF3_64BIT') @@ -72,7 +72,7 @@ def create_HYCOM_file(name): nc.variables[outvarname].coordinates = 'ocean_time s_rho lon_v lat_v' - print 'Done with header for file %s' %name + print('Done with header for file %s' %name) @@ -113,15 +113,15 @@ def create_HYCOM_file(name): create_HYCOM_file(outfile) day_out = 0 for day in range(rec_start,rec_end): - print 'Processing file for %s, day %d, year %04d' %(invarname, day_out*3, year) + print('Processing file for %s, day %d, year %04d' %(invarname, day_out*3, year)) #get data from server try: var = dataset.variables[invarname][day,:,170:215-1,195:265] # spval = var.get_fill_value() # dataset.close() - print 'Got %s from server...' %invarname + print('Got %s from server...' %invarname) except: - print 'No file on the server... We skip this day.' + print('No file on the server... We skip this day.') retry_day.append((day,day_out)) continue @@ -134,17 +134,17 @@ def create_HYCOM_file(name): if retry == 'True': if len(retry_day) != 0: - print "Some file have not been downloded... Let's try again" + print("Some file have not been downloded... Let's try again") while len(retry_day) != 0: for (day,day_out) in retry_day: - print 'Retry file for %s, day %03d, year %04d' %(invarname, day_out, year) + print('Retry file for %s, day %03d, year %04d' %(invarname, day_out, year)) #get data from server try: var = dataset.variables[invarname][day,:,170:215-1,195:265] # spval = var.get_fill_value() - print 'Got %s from server...' %invarname + print('Got %s from server...' %invarname) except: - print 'No file on the server... We skip this day.' + print('No file on the server... We skip this day.') continue #create netCDF file diff --git a/examples/NWGOA3/Fetch_Pacific/get_pacific_zeta.py b/examples/NWGOA3/Fetch_Pacific/get_pacific_zeta.py index 4a3536c..34a65fa 100644 --- a/examples/NWGOA3/Fetch_Pacific/get_pacific_zeta.py +++ b/examples/NWGOA3/Fetch_Pacific/get_pacific_zeta.py @@ -13,7 +13,7 @@ def create_HYCOM_file(name): global nc - print 'Creating file %s' %name + print('Creating file %s' %name) #create netCDF file nc = netCDF4.Dataset(name, 'w', format='NETCDF3_64BIT') @@ -71,7 +71,7 @@ def create_HYCOM_file(name): nc.variables[outvarname].coordinates = 'ocean_time lon_rho lat_rho' - print 'Done with header for file %s' %name + print('Done with header for file %s' %name) @@ -113,15 +113,15 @@ def create_HYCOM_file(name): create_HYCOM_file(outfile) day_out = 0 for day in range(rec_start,rec_end): - print 'Processing file for %s, day %d, year %04d' %(invarname, day_out*3, year) + print('Processing file for %s, day %d, year %04d' %(invarname, day_out*3, year)) #get data from server try: var = dataset.variables[invarname][day,170:215,195:265] # spval = var.get_fill_value() # dataset.close() - print 'Got %s from server...' %invarname + print('Got %s from server...' %invarname) except: - print 'No file on the server... We skip this day.' + print('No file on the server... We skip this day.') retry_day.append((day,day_out)) continue @@ -134,17 +134,17 @@ def create_HYCOM_file(name): if retry == 'True': if len(retry_day) != 0: - print "Some file have not been downloded... Let's try again" + print("Some file have not been downloded... Let's try again") while len(retry_day) != 0: for (day,day_out) in retry_day: - print 'Retry file for %s, day %03d, year %04d' %(invarname, day_out, year) + print('Retry file for %s, day %03d, year %04d' %(invarname, day_out, year)) #get data from server try: var = dataset.variables[invarname][day,170:215,195:265] # spval = var.get_fill_value() - print 'Got %s from server...' %invarname + print('Got %s from server...' %invarname) except: - print 'No file on the server... We skip this day.' + print('No file on the server... We skip this day.') continue #create netCDF file diff --git a/examples/NWGOA3/Fetch_Pacific/make_months.py b/examples/NWGOA3/Fetch_Pacific/make_months.py index 0b67eae..47d1f7d 100644 --- a/examples/NWGOA3/Fetch_Pacific/make_months.py +++ b/examples/NWGOA3/Fetch_Pacific/make_months.py @@ -4,7 +4,7 @@ import subprocess import os import sys -import commands +import subprocess import numpy as np from multiprocessing import Pool @@ -19,7 +19,7 @@ dst_dir='./months/' -lst = commands.getoutput('ls ' + data_dir + 'Pacific_*' + year + '.nc') +lst = subprocess.getoutput('ls ' + data_dir + 'Pacific_*' + year + '.nc') lst_file = lst.split() #print 'Make monthly average files from the following file list:' @@ -33,46 +33,46 @@ def do_file(file): # print 'Output filename ', outfile, index command = ('ncra', '-d', 'ocean_time,0,9', file, outfile+'.01') - print 'ncra -d ocean_time,0,9', file, outfile+'.01' + print('ncra -d ocean_time,0,9', file, outfile+'.01') # subprocess.check_call(command) command = ('ncra', '-d', 'ocean_time,10,19', file, outfile+'.02') - print 'ncra -d ocean_time,10,19', file, outfile+'.02' + print('ncra -d ocean_time,10,19', file, outfile+'.02') # subprocess.check_call(command) command = ('ncra', '-d', 'ocean_time,20,29', file, outfile+'.03') - print 'ncra -d ocean_time,20,29', file, outfile+'.03' + print('ncra -d ocean_time,20,29', file, outfile+'.03') # subprocess.check_call(command) command = ('ncra', '-d', 'ocean_time,30,39', file, outfile+'.04') - print 'ncra -d ocean_time,30,39', file, outfile+'.04' + print('ncra -d ocean_time,30,39', file, outfile+'.04') # subprocess.check_call(command) command = ('ncra', '-d', 'ocean_time,40,49', file, outfile+'.05') - print 'ncra -d ocean_time,40,49', file, outfile+'.05' + print('ncra -d ocean_time,40,49', file, outfile+'.05') # subprocess.check_call(command) command = ('ncra', '-d', 'ocean_time,50,59', file, outfile+'.06') - print 'ncra -d ocean_time,50,59', file, outfile+'.06' + print('ncra -d ocean_time,50,59', file, outfile+'.06') # subprocess.check_call(command) command = ('ncra', '-d', 'ocean_time,60,69', file, outfile+'.07') - print 'ncra -d ocean_time,60,69', file, outfile+'.07' + print('ncra -d ocean_time,60,69', file, outfile+'.07') # subprocess.check_call(command) command = ('ncra', '-d', 'ocean_time,70,79', file, outfile+'.08') - print 'ncra -d ocean_time,70,79', file, outfile+'.08' + print('ncra -d ocean_time,70,79', file, outfile+'.08') # subprocess.check_call(command) command = ('ncra', '-d', 'ocean_time,80,89', file, outfile+'.09') - print 'ncra -d ocean_time,80,89', file, outfile+'.09' + print('ncra -d ocean_time,80,89', file, outfile+'.09') # subprocess.check_call(command) command = ('ncra', '-d', 'ocean_time,90,99', file, outfile+'.10') - print 'ncra -d ocean_time,90,99', file, outfile+'.10' + print('ncra -d ocean_time,90,99', file, outfile+'.10') # subprocess.check_call(command) command = ('ncra', '-d', 'ocean_time,100,109', file, outfile+'.11') - print 'ncra -d ocean_time,100,109', file, outfile+'.11' + print('ncra -d ocean_time,100,109', file, outfile+'.11') # subprocess.check_call(command) command = ('ncra', '-d', 'ocean_time,110,119', file, outfile+'.12') - print 'ncra -d ocean_time,110,119', file, outfile+'.12' + print('ncra -d ocean_time,110,119', file, outfile+'.12') # subprocess.check_call(command) command = ('ncrcat', outfile+'.*', outfile) - print 'ncrcat', outfile+'.*', outfile + print('ncrcat', outfile+'.*', outfile) # subprocess.check_call(command) command = ('rm', outfile+'.*') - print 'rm', outfile+'.*' + print('rm', outfile+'.*') # subprocess.check_call(command) processes = 1 diff --git a/examples/NWGOA3/make_bry_file.py b/examples/NWGOA3/make_bry_file.py index a6e1187..eff1784 100644 --- a/examples/NWGOA3/make_bry_file.py +++ b/examples/NWGOA3/make_bry_file.py @@ -9,17 +9,17 @@ import pyroms import pyroms_toolbox -import commands +import subprocess irange = None jrange = None def do_file(file): - print 'file is: ' + file + print('file is: ' + file) start = string.find(file,'_') end = string.find(file,'_',start+1) var = file[start+1:end] - print 'var is: ' + var + print('var is: ' + var) if var == 'uv': dst_var = pyroms_toolbox.remapping_bound(['u', 'v'], file,\ wts_file,src_grd,dst_grd,rotate_uv=True,\ @@ -34,7 +34,7 @@ def do_file(file): data_dir = '/archive/u1/uaf/kate/COSINE/data/' #lst = commands.getoutput('ls ' + data_dir + '*_1979.nc') #lst = commands.getoutput('ls ' + data_dir + 'Pacific_s?o[n4]_1979.nc') -lst = commands.getoutput('ls ' + data_dir + 'Pacific_[tuvz]*_1979.nc') +lst = subprocess.getoutput('ls ' + data_dir + 'Pacific_[tuvz]*_1979.nc') lst = lst.split() lst_file = lst_file + lst diff --git a/examples/NWGOA3/make_clm_file.py b/examples/NWGOA3/make_clm_file.py index 5aecad1..bcfe5e7 100644 --- a/examples/NWGOA3/make_clm_file.py +++ b/examples/NWGOA3/make_clm_file.py @@ -9,17 +9,17 @@ import pyroms import pyroms_toolbox -import commands +import subprocess irange = None jrange = None def do_file(file): - print 'file is: ' + file + print('file is: ' + file) start = string.find(file,'_') end = string.find(file,'_',start+1) var = file[start+1:end] - print 'var is: ' + var + print('var is: ' + var) if var == 'uv': dst_var = pyroms_toolbox.remapping(['u', 'v'], file,\ wts_file,src_grd,dst_grd,rotate_uv=True,\ @@ -32,7 +32,7 @@ def do_file(file): # Change src_filename to your directory for the file's containing variable data data_dir = '/archive/u1/uaf/kate/COSINE/months/' -lst = commands.getoutput('ls ' + data_dir + 'Pac*_2008.nc') +lst = subprocess.getoutput('ls ' + data_dir + 'Pac*_2008.nc') #lst = commands.getoutput('ls ' + data_dir + 'Pacific_z*2_1987.nc') #lst = commands.getoutput('ls ' + data_dir + 'Pacific_[tuvz]*_2008.nc') lst = lst.split() diff --git a/examples/NWGOA3/make_ini_file.py b/examples/NWGOA3/make_ini_file.py index 46f323b..7fb8fc8 100644 --- a/examples/NWGOA3/make_ini_file.py +++ b/examples/NWGOA3/make_ini_file.py @@ -7,10 +7,10 @@ #src_varname = ['u', 'v'] src_varname = ['zeta', 'temp', 'salt', 'u', 'v', 'bac', 'c1', 'c2', 'c3', \ 'chl1', 'chl2', 'chl3', 'cldoc', 'csdoc', 'ddc', 'ddca', \ - 'ddn', 'ddsi', 'ldoc', 'ldon', 'nh4', 'no3', 'ox', 'po4', \ + 'ddn', 'ddsi', 'ldoc', 'ldon', 'nh4', 'no3', 'ox', 'po4', \ 's1', 's2', 's3', 'sdoc', 'sdon', 'sio4', 'talk', 'tco2', \ - 'zz1', 'zz2', 'zzc1', 'zzc2'] -print 'Number of variables', len(src_varname) + 'zz1', 'zz2', 'zzc1', 'zzc2'] +print('Number of variables', len(src_varname)) irange = None jrange = None diff --git a/examples/Palau_HYCOM/get_hycom_GLBa0.08_salt_2015.py b/examples/Palau_HYCOM/get_hycom_GLBa0.08_salt_2015.py index 994fe36..1027593 100644 --- a/examples/Palau_HYCOM/get_hycom_GLBa0.08_salt_2015.py +++ b/examples/Palau_HYCOM/get_hycom_GLBa0.08_salt_2015.py @@ -12,7 +12,7 @@ def create_HYCOM_file(name, time, lon, lat, z, var): - print 'Write with file %s' %name + print('Write with file %s' %name) #create netCDF file nc = netCDF4.Dataset(name, 'w', format='NETCDF3_64BIT') @@ -57,7 +57,7 @@ def create_HYCOM_file(name, time, lon, lat, z, var): nc.close() - print 'Done with file %s' %name + print('Done with file %s' %name) @@ -91,7 +91,7 @@ def create_HYCOM_file(name, time, lon, lat, z, var): # daysinyear = 365 daysinyear = 32 for day in range(1,daysinyear+1): - print 'Processing file for %s, day %03d, year %04d' %(invarname, day, year) + print('Processing file for %s, day %03d, year %04d' %(invarname, day, year)) url='http://tds.hycom.org/thredds/dodsC/datasets/GLBa0.08/expt_91.1/2015/salt/archv.%04d_%03d_00_3zs.nc' %(year,day) #get data from server try: @@ -99,9 +99,9 @@ def create_HYCOM_file(name, time, lon, lat, z, var): var = dataset.variables[invarname][0,:,1500-9:1800,600:940] spval = var.get_fill_value() dataset.close() - print 'Got %s from server...' %invarname + print('Got %s from server...' %invarname) except: - print 'No file on the server... We skip this day.' + print('No file on the server... We skip this day.') retry_day.append(day) continue @@ -113,10 +113,10 @@ def create_HYCOM_file(name, time, lon, lat, z, var): if retry == 'True': if len(retry_day) != 0: - print "Some file have not been downloded... Let's try again" + print("Some file have not been downloded... Let's try again") while len(retry_day) != 0: for day in retry_day: - print 'Retry file for %s, day %03d, year %04d' %(invarname, day, year) + print('Retry file for %s, day %03d, year %04d' %(invarname, day, year)) url='http://tds.hycom.org/thredds/dodsC/datasets/GLBa0.08/expt_91.1/2015/salt/archv.%04d_%03d_00_3zs.nc' %(year,day) #get data from server try: @@ -124,9 +124,9 @@ def create_HYCOM_file(name, time, lon, lat, z, var): var = dataset.variables[invarname][0,:,1500-9:1800,600:940] spval = var.get_fill_value() dataset.close() - print 'Got %s from server...' %invarname + print('Got %s from server...' %invarname) except: - print 'No file on the server... We skip this day.' + print('No file on the server... We skip this day.') continue #create netCDF file diff --git a/examples/Palau_HYCOM/get_hycom_GLBa0.08_ssh_2015.py b/examples/Palau_HYCOM/get_hycom_GLBa0.08_ssh_2015.py index 254cb0b..0f1a834 100644 --- a/examples/Palau_HYCOM/get_hycom_GLBa0.08_ssh_2015.py +++ b/examples/Palau_HYCOM/get_hycom_GLBa0.08_ssh_2015.py @@ -48,7 +48,7 @@ def create_HYCOM_file(name, time, lon, lat, var): nc.close() - print 'Done with file %s' %name + print('Done with file %s' %name) @@ -81,7 +81,7 @@ def create_HYCOM_file(name, time, lon, lat, var): # daysinyear = 365 daysinyear = 32 for day in range(1,daysinyear+1): - print 'Processing file for day %03d, year %04d' %(day, year) + print('Processing file for day %03d, year %04d' %(day, year)) url='http://tds.hycom.org/thredds/dodsC/datasets/GLBa0.08/expt_91.1/2015/2d/archv.%04d_%03d_00_2d.nc' %(year,day) #get data from server try: @@ -90,7 +90,7 @@ def create_HYCOM_file(name, time, lon, lat, var): spval = var.get_fill_value() dataset.close() except: - print 'No file on the server... We skip this day.' + print('No file on the server... We skip this day.') retry_day.append(day) continue @@ -102,10 +102,10 @@ def create_HYCOM_file(name, time, lon, lat, var): if retry == 'True': if len(retry_day) != 0: - print "Some files have not been downloded... Let's try again" + print("Some files have not been downloded... Let's try again") while len(retry_day) != 0: for day in retry_day: - print 'Retry file for day %03d, year %04d' %(day, year) + print('Retry file for day %03d, year %04d' %(day, year)) url='http://tds.hycom.org/thredds/dodsC/datasets/GLBa0.08/expt_91.1/2015/2d/archv.%04d_%03d_00_2d.nc' %(year,day) #get data from server try: @@ -114,7 +114,7 @@ def create_HYCOM_file(name, time, lon, lat, var): spval = var.get_fill_value() dataset.close() except: - print 'No file on the server... We skip this day.' + print('No file on the server... We skip this day.') continue #create netCDF file diff --git a/examples/Palau_HYCOM/get_hycom_GLBa0.08_temp_2015.py b/examples/Palau_HYCOM/get_hycom_GLBa0.08_temp_2015.py index deaadc8..ba72307 100644 --- a/examples/Palau_HYCOM/get_hycom_GLBa0.08_temp_2015.py +++ b/examples/Palau_HYCOM/get_hycom_GLBa0.08_temp_2015.py @@ -12,7 +12,7 @@ def create_HYCOM_file(name, time, lon, lat, z, var): - print 'Write with file %s' %name + print('Write with file %s' %name) #create netCDF file nc = netCDF4.Dataset(name, 'w', format='NETCDF3_64BIT') @@ -57,7 +57,7 @@ def create_HYCOM_file(name, time, lon, lat, z, var): nc.close() - print 'Done with file %s' %name + print('Done with file %s' %name) @@ -91,7 +91,7 @@ def create_HYCOM_file(name, time, lon, lat, z, var): # daysinyear = 365 daysinyear = 32 for day in range(1,daysinyear+1): - print 'Processing file for %s, day %03d, year %04d' %(invarname, day, year) + print('Processing file for %s, day %03d, year %04d' %(invarname, day, year)) url='http://tds.hycom.org/thredds/dodsC/datasets/GLBa0.08/expt_91.1/2015/temp/archv.%04d_%03d_00_3zt.nc' %(year,day) #get data from server try: @@ -99,9 +99,9 @@ def create_HYCOM_file(name, time, lon, lat, z, var): var = dataset.variables[invarname][0,:,1500-9:1800,600:940] spval = var.get_fill_value() dataset.close() - print 'Got %s from server...' %invarname + print('Got %s from server...' %invarname) except: - print 'No file on the server... We skip this day.' + print('No file on the server... We skip this day.') retry_day.append(day) continue @@ -113,10 +113,10 @@ def create_HYCOM_file(name, time, lon, lat, z, var): if retry == 'True': if len(retry_day) != 0: - print "Some file have not been downloded... Let's try again" + print("Some file have not been downloded... Let's try again") while len(retry_day) != 0: for day in retry_day: - print 'Retry file for %s, day %03d, year %04d' %(invarname, day, year) + print('Retry file for %s, day %03d, year %04d' %(invarname, day, year)) url='http://tds.hycom.org/thredds/dodsC/datasets/GLBa0.08/expt_91.1/2015/temp/archv.%04d_%03d_00_3zt.nc' %(year,day) #get data from server try: @@ -124,10 +124,10 @@ def create_HYCOM_file(name, time, lon, lat, z, var): var = dataset.variables[invarname][0,:,1500-9:1800,600:940] spval = var.get_fill_value() dataset.close() - print 'Got %s from server...' %invarname + print('Got %s from server...' %invarname) except: - print 'No file on the server... We skip this day.' + print('No file on the server... We skip this day.') continue #create netCDF file diff --git a/examples/Palau_HYCOM/get_hycom_GLBa0.08_u_2015.py b/examples/Palau_HYCOM/get_hycom_GLBa0.08_u_2015.py index 3315ec2..27a9352 100644 --- a/examples/Palau_HYCOM/get_hycom_GLBa0.08_u_2015.py +++ b/examples/Palau_HYCOM/get_hycom_GLBa0.08_u_2015.py @@ -12,7 +12,7 @@ def create_HYCOM_file(name, time, lon, lat, z, var): - print 'Write with file %s' %name + print('Write with file %s' %name) #create netCDF file nc = netCDF4.Dataset(name, 'w', format='NETCDF3_64BIT') @@ -57,7 +57,7 @@ def create_HYCOM_file(name, time, lon, lat, z, var): nc.close() - print 'Done with file %s' %name + print('Done with file %s' %name) @@ -93,7 +93,7 @@ def create_HYCOM_file(name, time, lon, lat, z, var): # daysinyear = 365 daysinyear = 32 for day in range(1,daysinyear+1): - print 'Processing file for %s, day %03d, year %04d' %(invarname, day, year) + print('Processing file for %s, day %03d, year %04d' %(invarname, day, year)) url='http://tds.hycom.org/thredds/dodsC/datasets/GLBa0.08/expt_91.1/2015/uvel/archv.%04d_%03d_00_3zu.nc' %(year,day) #get data from server try: @@ -101,9 +101,9 @@ def create_HYCOM_file(name, time, lon, lat, z, var): var = dataset.variables[invarname][0,:,1500-9:1800,600:940] spval = var.get_fill_value() dataset.close() - print 'Got %s from server...' %invarname + print('Got %s from server...' %invarname) except: - print 'No file on the server... We skip this day.' + print('No file on the server... We skip this day.') retry_day.append(day) continue @@ -115,10 +115,10 @@ def create_HYCOM_file(name, time, lon, lat, z, var): if retry == 'True': if len(retry_day) != 0: - print "Some file have not been downloded... Let's try again" + print("Some file have not been downloded... Let's try again") while len(retry_day) != 0: for day in retry_day: - print 'Retry file for %s, day %03d, year %04d' %(invarname, day, year) + print('Retry file for %s, day %03d, year %04d' %(invarname, day, year)) url='http://tds.hycom.org/thredds/dodsC/datasets/GLBa0.08/expt_91.1/2015/uvel/archv.%04d_%03d_00_3zu.nc' %(year,day) #get data from server try: @@ -126,9 +126,9 @@ def create_HYCOM_file(name, time, lon, lat, z, var): var = dataset.variables[invarname][0,:,1500-9:1800,600:940] spval = var.get_fill_value() dataset.close() - print 'Got %s from server...' %invarname + print('Got %s from server...' %invarname) except: - print 'No file on the server... We skip this day.' + print('No file on the server... We skip this day.') continue #create netCDF file diff --git a/examples/Palau_HYCOM/get_hycom_GLBa0.08_v_2015.py b/examples/Palau_HYCOM/get_hycom_GLBa0.08_v_2015.py index c7acc44..818bee7 100644 --- a/examples/Palau_HYCOM/get_hycom_GLBa0.08_v_2015.py +++ b/examples/Palau_HYCOM/get_hycom_GLBa0.08_v_2015.py @@ -12,7 +12,7 @@ def create_HYCOM_file(name, time, lon, lat, z, var): - print 'Write with file %s' %name + print('Write with file %s' %name) #create netCDF file nc = netCDF4.Dataset(name, 'w', format='NETCDF3_64BIT') @@ -57,7 +57,7 @@ def create_HYCOM_file(name, time, lon, lat, z, var): nc.close() - print 'Done with file %s' %name + print('Done with file %s' %name) @@ -91,7 +91,7 @@ def create_HYCOM_file(name, time, lon, lat, z, var): # daysinyear = 365 daysinyear = 32 for day in range(1,daysinyear+1): - print 'Processing file for %s, day %03d, year %04d' %(invarname, day, year) + print('Processing file for %s, day %03d, year %04d' %(invarname, day, year)) url='http://tds.hycom.org/thredds/dodsC/datasets/GLBa0.08/expt_91.1/2015/vvel/archv.%04d_%03d_00_3zv.nc' %(year,day) #get data from server try: @@ -99,9 +99,9 @@ def create_HYCOM_file(name, time, lon, lat, z, var): var = dataset.variables[invarname][0,:,1500-9:1800,600:940] spval = var.get_fill_value() dataset.close() - print 'Got %s from server...' %invarname + print('Got %s from server...' %invarname) except: - print 'No file on the server... We skip this day.' + print('No file on the server... We skip this day.') retry_day.append(day) continue @@ -113,10 +113,10 @@ def create_HYCOM_file(name, time, lon, lat, z, var): if retry == 'True': if len(retry_day) != 0: - print "Some file have not been downloded... Let's try again" + print("Some file have not been downloded... Let's try again") while len(retry_day) != 0: for day in retry_day: - print 'Retry file for %s, day %03d, year %04d' %(invarname, day, year) + print('Retry file for %s, day %03d, year %04d' %(invarname, day, year)) url='http://tds.hycom.org/thredds/dodsC/datasets/GLBa0.08/expt_91.1/2015/vvel/archv.%04d_%03d_00_3zv.nc' %(year,day) #get data from server try: @@ -124,9 +124,9 @@ def create_HYCOM_file(name, time, lon, lat, z, var): var = dataset.variables[invarname][0,:,1500-9:1800,600:940] spval = var.get_fill_value() dataset.close() - print 'Got %s from server...' %invarname + print('Got %s from server...' %invarname) except: - print 'No file on the server... We skip this day.' + print('No file on the server... We skip this day.') continue #create netCDF file diff --git a/examples/Palau_HYCOM/make_bdry_file.py b/examples/Palau_HYCOM/make_bdry_file.py index c625057..cfefa37 100644 --- a/examples/Palau_HYCOM/make_bdry_file.py +++ b/examples/Palau_HYCOM/make_bdry_file.py @@ -66,9 +66,9 @@ def do_file(file, src_grd, dst_grd): lst = lst.split() lst_file = lst_file + lst -print 'Build OBC file from the following file list:' -print lst_file -print ' ' +print('Build OBC file from the following file list:') +print(lst_file) +print(' ') src_grd_file = data_dir + '../HYCOM_GLBa0.08_PALAU_grid.nc' src_grd = pyroms_toolbox.Grid_HYCOM.get_nc_Grid_HYCOM(src_grd_file) diff --git a/examples/Palau_HYCOM/make_clm_file.py b/examples/Palau_HYCOM/make_clm_file.py index b8e3aea..8009a30 100644 --- a/examples/Palau_HYCOM/make_clm_file.py +++ b/examples/Palau_HYCOM/make_clm_file.py @@ -1,7 +1,7 @@ import subprocess import os import sys -import commands +import subprocess import numpy as np from datetime import datetime import matplotlib @@ -23,13 +23,13 @@ for year in lst_year: year = np.str(year) # lst = commands.getoutput('ls ' + data_dir + 'SODA_2.1.6_' + year + '_0*') - lst = commands.getoutput('ls ' + data_dir + '*' + year + '*') + lst = subprocess.getoutput('ls ' + data_dir + '*' + year + '*') lst = lst.split() lst_file = lst_file + lst -print 'Build CLM file from the following file list:' -print lst_file -print ' ' +print('Build CLM file from the following file list:') +print(lst_file) +print(' ') src_grd = pyroms_toolbox.Grid_HYCOM.get_nc_Grid_HYCOM('/archive/u1/uaf/kate/HYCOM/Svalbard/HYCOM_GLBa0.08_North_grid2.nc') dst_grd = pyroms.grid.get_ROMS_grid('ARCTIC2') @@ -47,26 +47,26 @@ out_file = dst_dir + file.rsplit('/')[-1][:-3] + '_ssh_clim_' + dst_grd.name + '.nc' command = ('ncks', '-a', '-O', out_file, clim_file) - print command + print(command) subprocess.check_call(command) os.remove(out_file) out_file = dst_dir + file.rsplit('/')[-1][:-3] + '_temp_clim_' + dst_grd.name + '.nc' - command = ('ncks', '-a', '-A', out_file, clim_file) - print command + command = ('ncks', '-a', '-A', out_file, clim_file) + print(command) subprocess.check_call(command) os.remove(out_file) out_file = dst_dir + file.rsplit('/')[-1][:-3] + '_salt_clim_' + dst_grd.name + '.nc' - command = ('ncks', '-a', '-A', out_file, clim_file) - print command + command = ('ncks', '-a', '-A', out_file, clim_file) + print(command) subprocess.check_call(command) os.remove(out_file) out_file = dst_dir + file.rsplit('/')[-1][:-3] + '_u_clim_' + dst_grd.name + '.nc' - command = ('ncks', '-a', '-A', out_file, clim_file) - print command + command = ('ncks', '-a', '-A', out_file, clim_file) + print(command) subprocess.check_call(command) os.remove(out_file) out_file = dst_dir + file.rsplit('/')[-1][:-3] + '_v_clim_' + dst_grd.name + '.nc' - command = ('ncks', '-a', '-A', out_file, clim_file) - print command + command = ('ncks', '-a', '-A', out_file, clim_file) + print(command) subprocess.check_call(command) os.remove(out_file) diff --git a/examples/Palau_HYCOM/make_ic_file.py b/examples/Palau_HYCOM/make_ic_file.py index 6da1876..6abc88b 100644 --- a/examples/Palau_HYCOM/make_ic_file.py +++ b/examples/Palau_HYCOM/make_ic_file.py @@ -1,6 +1,6 @@ import subprocess import os -import commands +import subprocess import numpy as np import matplotlib matplotlib.use('Agg') @@ -16,9 +16,9 @@ data_dir = '/archive/u1/uaf/kate/HYCOM/SCS/data/' dst_dir='./' -print 'Build IC file from the following file:' -print file -print ' ' +print('Build IC file from the following file:') +print(file) +print(' ') src_grd_file = data_dir + '../HYCOM_GLBa0.08_PALAU_grid.nc' src_grd = pyroms_toolbox.Grid_HYCOM.get_nc_Grid_HYCOM(src_grd_file) @@ -36,26 +36,26 @@ out_file = dst_dir + file.rsplit('/')[-1][:-3] + '_ssh_ic_' + dst_grd.name + '.nc' command = ('ncks', '-a', '-O', out_file, ic_file) -print command +print(command) subprocess.check_call(command) os.remove(out_file) out_file = dst_dir + file.rsplit('/')[-1][:-3] + '_temp_ic_' + dst_grd.name + '.nc' command = ('ncks', '-a', '-A', out_file, ic_file) -print command +print(command) subprocess.check_call(command) os.remove(out_file) out_file = dst_dir + file.rsplit('/')[-1][:-3] + '_salt_ic_' + dst_grd.name + '.nc' command = ('ncks', '-a', '-A', out_file, ic_file) -print command +print(command) subprocess.check_call(command) os.remove(out_file) out_file = dst_dir + file.rsplit('/')[-1][:-3] + '_u_ic_' + dst_grd.name + '.nc' command = ('ncks', '-a', '-A', out_file, ic_file) -print command +print(command) subprocess.check_call(command) os.remove(out_file) out_file = dst_dir + file.rsplit('/')[-1][:-3] + '_v_ic_' + dst_grd.name + '.nc' command = ('ncks', '-a', '-A', out_file, ic_file) -print command +print(command) subprocess.check_call(command) os.remove(out_file) diff --git a/examples/Palau_HYCOM/remap.py b/examples/Palau_HYCOM/remap.py index 7e410f9..3296416 100644 --- a/examples/Palau_HYCOM/remap.py +++ b/examples/Palau_HYCOM/remap.py @@ -41,7 +41,7 @@ def remap(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, dst_d # create IC file dst_file = src_file.rsplit('/')[-1] dst_file = dst_dir + dst_file[:-3] + '_' + src_varname + '_ic_' + dst_grd.name + '.nc' - print '\nCreating file', dst_file + print('\nCreating file', dst_file) if os.path.exists(dst_file) is True: os.remove(dst_file) pyroms_toolbox.nc_create_roms_file(dst_file, dst_grd, nctime) @@ -95,7 +95,7 @@ def remap(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, dst_d units = 'PSU' field = 'salinity, scalar, series' else: - raise ValueError, 'Undefined src_varname' + raise ValueError('Undefined src_varname') if ndim == 3: @@ -107,7 +107,7 @@ def remap(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, dst_d # create variable in file - print 'Creating variable', dst_varname + print('Creating variable', dst_varname) nc.createVariable(dst_varname, 'f8', dimensions, fill_value=spval) nc.variables[dst_varname].long_name = long_name nc.variables[dst_varname].units = units @@ -115,36 +115,36 @@ def remap(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, dst_d # remapping - print 'remapping', dst_varname, 'from', src_grd.name, \ - 'to', dst_grd.name - print 'time =', time + print('remapping', dst_varname, 'from', src_grd.name, \ + 'to', dst_grd.name) + print('time =', time) if ndim == 3: # flood the grid - print 'flood the grid' + print('flood the grid') src_varz = pyroms_toolbox.Grid_HYCOM.flood_fast(src_var, src_grd, pos=pos, spval=spval, \ dxy=dxy, cdepth=cdepth, kk=kk) else: src_varz = src_var # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' - print 'about to call remap ' + wts_file - print src_varz.shape + print('horizontal interpolation using scrip weights') + print('about to call remap ' + wts_file) + print(src_varz.shape) dst_varz = pyroms.remapping.remap(src_varz, wts_file, \ spval=spval) if ndim == 3: # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_var = pyroms.remapping.z2roms(dst_varz[::-1,:,:], dst_grdz, \ dst_grd, Cpos=Cpos, spval=spval, flood=False) else: dst_var = dst_varz # write data in destination file - print 'write data in destination file' + print('write data in destination file') nc.variables['ocean_time'][0] = time nc.variables[dst_varname][0] = dst_var diff --git a/examples/Palau_HYCOM/remap_bdry.py b/examples/Palau_HYCOM/remap_bdry.py index 559860d..a28d554 100644 --- a/examples/Palau_HYCOM/remap_bdry.py +++ b/examples/Palau_HYCOM/remap_bdry.py @@ -18,7 +18,7 @@ class nctime(object): def remap_bdry(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=2, dst_dir='./'): - print src_file + print(src_file) # get time nctime.long_name = 'time' @@ -27,7 +27,7 @@ def remap_bdry(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=2, # create boundary file dst_file = src_file.rsplit('/')[-1] dst_file = dst_dir + dst_file[:-3] + '_' + src_varname + '_bdry_' + dst_grd.name + '.nc' - print '\nCreating boundary file', dst_file + print('\nCreating boundary file', dst_file) if os.path.exists(dst_file) is True: os.remove(dst_file) pyroms_toolbox.nc_create_roms_bdry_file(dst_file, dst_grd, nctime) @@ -39,7 +39,7 @@ def remap_bdry(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=2, cdf = netCDF.Dataset(src_file) src_var = cdf.variables[src_varname] time = cdf.variables['ocean_time'][0] - print time + print(time) #get missing value spval = src_var._FillValue @@ -124,7 +124,7 @@ def remap_bdry(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=2, field_west = 'salt_west, scalar, series' units = 'PSU' else: - raise ValueError, 'Undefined src_varname' + raise ValueError('Undefined src_varname') if ndim == 3: @@ -136,25 +136,25 @@ def remap_bdry(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=2, # create variable in boudary file - print 'Creating variable', dst_varname_north + print('Creating variable', dst_varname_north) nc.createVariable(dst_varname_north, 'f8', dimensions_north, fill_value=spval) nc.variables[dst_varname_north].long_name = long_name_north nc.variables[dst_varname_north].units = units nc.variables[dst_varname_north].field = field_north - print 'Creating variable', dst_varname_south + print('Creating variable', dst_varname_south) nc.createVariable(dst_varname_south, 'f8', dimensions_south, fill_value=spval) nc.variables[dst_varname_south].long_name = long_name_south nc.variables[dst_varname_south].units = units nc.variables[dst_varname_south].field = field_south - print 'Creating variable', dst_varname_east + print('Creating variable', dst_varname_east) nc.createVariable(dst_varname_east, 'f8', dimensions_east, fill_value=spval) nc.variables[dst_varname_east].long_name = long_name_east nc.variables[dst_varname_east].units = units nc.variables[dst_varname_east].field = field_east - print 'Creating variable', dst_varname_west + print('Creating variable', dst_varname_west) nc.createVariable(dst_varname_west, 'f8', dimensions_west, fill_value=spval) nc.variables[dst_varname_west].long_name = long_name_west nc.variables[dst_varname_west].units = units @@ -162,26 +162,26 @@ def remap_bdry(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=2, # remapping - print 'remapping', dst_varname, 'from', src_grd.name, \ - 'to', dst_grd.name - print 'time =', time + print('remapping', dst_varname, 'from', src_grd.name, \ + 'to', dst_grd.name) + print('time =', time) if ndim == 3: # flood the grid - print 'flood the grid' + print('flood the grid') src_varz = pyroms_toolbox.Grid_HYCOM.flood_fast(src_var, src_grd, pos=pos, spval=spval, \ dxy=dxy, cdepth=cdepth, kk=kk) else: src_varz = src_var # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_varz = pyroms.remapping.remap(src_varz, wts_file, spval=spval) if ndim == 3: # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_var_north = pyroms.remapping.z2roms(dst_varz[::-1, Mp-1:Mp, :], \ dst_grdz, dst_grd, Cpos=Cpos, spval=spval, \ flood=False, irange=(0,Lp), jrange=(Mp-1,Mp)) @@ -201,7 +201,7 @@ def remap_bdry(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=2, dst_var_west = dst_varz[:, 0] # write data in destination file - print 'write data in destination file' + print('write data in destination file') nc.variables['ocean_time'][0] = time nc.variables[dst_varname_north][0] = np.squeeze(dst_var_north) nc.variables[dst_varname_south][0] = np.squeeze(dst_var_south) diff --git a/examples/Palau_HYCOM/remap_bdry_uv.py b/examples/Palau_HYCOM/remap_bdry_uv.py index 20379ab..315d73b 100644 --- a/examples/Palau_HYCOM/remap_bdry_uv.py +++ b/examples/Palau_HYCOM/remap_bdry_uv.py @@ -28,12 +28,12 @@ def remap_bdry_uv(src_file, src_grd, dst_grd, dxy=20, cdepth=0, kk=2, dst_dir='. # create destination file dst_file = src_file.rsplit('/')[-1] dst_fileu = dst_dir + dst_file[:-3] + '_u_bdry_' + dst_grd.name + '.nc' - print '\nCreating destination file', dst_fileu + print('\nCreating destination file', dst_fileu) if os.path.exists(dst_fileu) is True: os.remove(dst_fileu) pyroms_toolbox.nc_create_roms_file(dst_fileu, dst_grd, nctime) dst_filev = dst_dir + dst_file[:-3] + '_v_bdry_' + dst_grd.name + '.nc' - print 'Creating destination file', dst_filev + print('Creating destination file', dst_filev) if os.path.exists(dst_filev) is True: os.remove(dst_filev) pyroms_toolbox.nc_create_roms_file(dst_filev, dst_grd, nctime) @@ -64,95 +64,95 @@ def remap_bdry_uv(src_file, src_grd, dst_grd, dxy=20, cdepth=0, kk=2, dst_dir='. dst_grdz = pyroms.grid.ROMS_Grid(dst_grd.name+'_Z', dst_grd.hgrid, dst_zcoord) # create variable in destination file - print 'Creating variable u_north' + print('Creating variable u_north') ncu.createVariable('u_north', 'f8', ('ocean_time', 's_rho', 'xi_u'), fill_value=spval) ncu.variables['u_north'].long_name = '3D u-momentum north boundary condition' ncu.variables['u_north'].units = 'meter second-1' ncu.variables['u_north'].field = 'u_north, scalar, series' - print 'Creating variable u_south' + print('Creating variable u_south') ncu.createVariable('u_south', 'f8', ('ocean_time', 's_rho', 'xi_u'), fill_value=spval) ncu.variables['u_south'].long_name = '3D u-momentum south boundary condition' ncu.variables['u_south'].units = 'meter second-1' ncu.variables['u_south'].field = 'u_south, scalar, series' - print 'Creating variable u_east' + print('Creating variable u_east') ncu.createVariable('u_east', 'f8', ('ocean_time', 's_rho', 'eta_u'), fill_value=spval) ncu.variables['u_east'].long_name = '3D u-momentum east boundary condition' ncu.variables['u_east'].units = 'meter second-1' ncu.variables['u_east'].field = 'u_east, scalar, series' - print 'Creating variable u_west' + print('Creating variable u_west') ncu.createVariable('u_west', 'f8', ('ocean_time', 's_rho', 'eta_u'), fill_value=spval) ncu.variables['u_west'].long_name = '3D u-momentum west boundary condition' ncu.variables['u_west'].units = 'meter second-1' ncu.variables['u_west'].field = 'u_east, scalar, series' # create variable in destination file - print 'Creating variable ubar_north' + print('Creating variable ubar_north') ncu.createVariable('ubar_north', 'f8', ('ocean_time', 'xi_u'), fill_value=spval) ncu.variables['ubar_north'].long_name = '2D u-momentum north boundary condition' ncu.variables['ubar_north'].units = 'meter second-1' ncu.variables['ubar_north'].field = 'ubar_north, scalar, series' - print 'Creating variable ubar_south' + print('Creating variable ubar_south') ncu.createVariable('ubar_south', 'f8', ('ocean_time', 'xi_u'), fill_value=spval) ncu.variables['ubar_south'].long_name = '2D u-momentum south boundary condition' ncu.variables['ubar_south'].units = 'meter second-1' ncu.variables['ubar_south'].field = 'ubar_south, scalar, series' - print 'Creating variable ubar_east' + print('Creating variable ubar_east') ncu.createVariable('ubar_east', 'f8', ('ocean_time', 'eta_u'), fill_value=spval) ncu.variables['ubar_east'].long_name = '2D u-momentum east boundary condition' ncu.variables['ubar_east'].units = 'meter second-1' ncu.variables['ubar_east'].field = 'ubar_east, scalar, series' - print 'Creating variable ubar_west' + print('Creating variable ubar_west') ncu.createVariable('ubar_west', 'f8', ('ocean_time', 'eta_u'), fill_value=spval) ncu.variables['ubar_west'].long_name = '2D u-momentum west boundary condition' ncu.variables['ubar_west'].units = 'meter second-1' ncu.variables['ubar_west'].field = 'ubar_east, scalar, series' - print 'Creating variable v_north' + print('Creating variable v_north') ncv.createVariable('v_north', 'f8', ('ocean_time', 's_rho', 'xi_v'), fill_value=spval) ncv.variables['v_north'].long_name = '3D v-momentum north boundary condition' ncv.variables['v_north'].units = 'meter second-1' ncv.variables['v_north'].field = 'v_north, scalar, series' - print 'Creating variable v_south' + print('Creating variable v_south') ncv.createVariable('v_south', 'f8', ('ocean_time', 's_rho', 'xi_v'), fill_value=spval) ncv.variables['v_south'].long_name = '3D v-momentum south boundary condition' ncv.variables['v_south'].units = 'meter second-1' ncv.variables['v_south'].field = 'v_south, scalar, series' - print 'Creating variable v_east' + print('Creating variable v_east') ncv.createVariable('v_east', 'f8', ('ocean_time', 's_rho', 'eta_v'), fill_value=spval) ncv.variables['v_east'].long_name = '3D v-momentum east boundary condition' ncv.variables['v_east'].units = 'meter second-1' ncv.variables['v_east'].field = 'v_east, scalar, series' - print 'Creating variable v_west' + print('Creating variable v_west') ncv.createVariable('v_west', 'f8', ('ocean_time', 's_rho', 'eta_v'), fill_value=spval) ncv.variables['v_west'].long_name = '3D v-momentum west boundary condition' ncv.variables['v_west'].units = 'meter second-1' ncv.variables['v_west'].field = 'v_east, scalar, series' - print 'Creating variable vbar_north' + print('Creating variable vbar_north') ncv.createVariable('vbar_north', 'f8', ('ocean_time', 'xi_v'), fill_value=spval) ncv.variables['vbar_north'].long_name = '2D v-momentum north boundary condition' ncv.variables['vbar_north'].units = 'meter second-1' ncv.variables['vbar_north'].field = 'vbar_north, scalar, series' - print 'Creating variable vbar_south' + print('Creating variable vbar_south') ncv.createVariable('vbar_south', 'f8', ('ocean_time', 'xi_v'), fill_value=spval) ncv.variables['vbar_south'].long_name = '2D v-momentum south boundary condition' ncv.variables['vbar_south'].units = 'meter second-1' ncv.variables['vbar_south'].field = 'vbar_south, scalar, series' - print 'Creating variable vbar_east' + print('Creating variable vbar_east') ncv.createVariable('vbar_east', 'f8', ('ocean_time', 'eta_v'), fill_value=spval) ncv.variables['vbar_east'].long_name = '2D v-momentum east boundary condition' ncv.variables['vbar_east'].units = 'meter second-1' ncv.variables['vbar_east'].field = 'vbar_east, scalar, series' - print 'Creating variable vbar_west' + print('Creating variable vbar_west') ncv.createVariable('vbar_west', 'f8', ('ocean_time', 'eta_v'), fill_value=spval) ncv.variables['vbar_west'].long_name = '2D v-momentum west boundary condition' ncv.variables['vbar_west'].units = 'meter second-1' @@ -161,27 +161,27 @@ def remap_bdry_uv(src_file, src_grd, dst_grd, dxy=20, cdepth=0, kk=2, dst_dir='. # remaping - print 'remapping and rotating u and v from', src_grd.name, \ - 'to', dst_grd.name - print 'time =', time + print('remapping and rotating u and v from', src_grd.name, \ + 'to', dst_grd.name) + print('time =', time) # flood the grid - print 'flood the grid' + print('flood the grid') src_uz = pyroms_toolbox.Grid_HYCOM.flood_fast(src_varu, src_grd, pos='t', \ spval=spval, dxy=dxy, cdepth=cdepth, kk=kk) src_vz = pyroms_toolbox.Grid_HYCOM.flood_fast(src_varv, src_grd, pos='t', \ spval=spval, dxy=dxy, cdepth=cdepth, kk=kk) # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_uz = pyroms.remapping.remap(src_uz, wts_file, \ spval=spval) dst_vz = pyroms.remapping.remap(src_vz, wts_file, \ spval=spval) # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_u_north = pyroms.remapping.z2roms(dst_uz[::-1, Mp-2:Mp, 0:Lp], \ dst_grdz, dst_grd, Cpos='rho', spval=spval, \ flood=False, irange=(0,Lp), jrange=(Mp-2,Mp)) @@ -325,7 +325,7 @@ def remap_bdry_uv(src_file, src_grd, dst_grd, dxy=20, cdepth=0, kk=2, dst_dir='. dst_vbar_west = np.ma.masked_where(dst_grd.hgrid.mask_v[:,0] == 0, dst_vbar_west) # write data in destination file - print 'write data in destination file' + print('write data in destination file') ncu.variables['ocean_time'][0] = time ncu.variables['u_north'][0] = dst_u_north ncu.variables['u_south'][0] = dst_u_south diff --git a/examples/Palau_HYCOM/remap_clm.py b/examples/Palau_HYCOM/remap_clm.py index af74e1d..c6e24c9 100644 --- a/examples/Palau_HYCOM/remap_clm.py +++ b/examples/Palau_HYCOM/remap_clm.py @@ -41,7 +41,7 @@ def remap_clm(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, d # create IC file dst_file = src_file.rsplit('/')[-1] dst_file = dst_dir + dst_file[:-3] + '_' + src_varname + '_clim_' + dst_grd.name + '.nc' - print '\nCreating file', dst_file + print('\nCreating file', dst_file) if os.path.exists(dst_file) is True: os.remove(dst_file) pyroms_toolbox.nc_create_roms_file(dst_file, dst_grd, nctime) @@ -72,7 +72,7 @@ def remap_clm(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, d long_name = 'free-surface' units = 'meter' field = 'free-surface, scalar, series' - vartime = 'ocean_time' + vartime = 'ocean_time' elif src_varname == 'temp': pos = 't' Cpos = 'rho' @@ -84,7 +84,7 @@ def remap_clm(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, d long_name = 'potential temperature' units = 'Celsius' field = 'temperature, scalar, series' - vartime = 'ocean_time' + vartime = 'ocean_time' elif src_varname == 'salt': pos = 't' Cpos = 'rho' @@ -96,9 +96,9 @@ def remap_clm(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, d long_name = 'salinity' units = 'PSU' field = 'salinity, scalar, series' - vartime = 'ocean_time' + vartime = 'ocean_time' else: - raise ValueError, 'Undefined src_varname' + raise ValueError('Undefined src_varname') if ndim == 3: @@ -110,7 +110,7 @@ def remap_clm(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, d # create variable in file - print 'Creating variable', dst_varname + print('Creating variable', dst_varname) nc.createVariable(dst_varname, 'f8', dimensions, fill_value=spval) nc.variables[dst_varname].long_name = long_name nc.variables[dst_varname].units = units @@ -119,34 +119,34 @@ def remap_clm(src_file, src_varname, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, d # remapping - print 'remapping', dst_varname, 'from', src_grd.name, \ - 'to', dst_grd.name - print 'time =', time + print('remapping', dst_varname, 'from', src_grd.name, \ + 'to', dst_grd.name) + print('time =', time) if ndim == 3: # flood the grid - print 'flood the grid' + print('flood the grid') src_varz = pyroms_toolbox.Grid_HYCOM.flood_fast(src_var, src_grd, pos=pos, spval=spval, \ dxy=dxy, cdepth=cdepth, kk=kk) else: src_varz = src_var # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_varz = pyroms.remapping.remap(src_varz, wts_file, \ spval=spval) if ndim == 3: # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_var = pyroms.remapping.z2roms(dst_varz[::-1,:,:], dst_grdz, \ dst_grd, Cpos=Cpos, spval=spval, flood=False) else: dst_var = dst_varz # write data in destination file - print 'write data in destination file' + print('write data in destination file') nc.variables['ocean_time'][0] = time nc.variables[dst_varname][0] = dst_var diff --git a/examples/Palau_HYCOM/remap_clm_uv.py b/examples/Palau_HYCOM/remap_clm_uv.py index f8aa116..d3e06ff 100644 --- a/examples/Palau_HYCOM/remap_clm_uv.py +++ b/examples/Palau_HYCOM/remap_clm_uv.py @@ -43,12 +43,12 @@ def remap_clm_uv(src_file, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, dst_dir='./ # create destination file dst_file = src_file.rsplit('/')[-1] dst_fileu = dst_dir + dst_file[:-3] + '_u_clim_' + dst_grd.name + '.nc' - print '\nCreating destination file', dst_fileu + print('\nCreating destination file', dst_fileu) if os.path.exists(dst_fileu) is True: os.remove(dst_fileu) pyroms_toolbox.nc_create_roms_file(dst_fileu, dst_grd, nctime) dst_filev = dst_dir + dst_file[:-3] + '_v_clim_' + dst_grd.name + '.nc' - print 'Creating destination file', dst_filev + print('Creating destination file', dst_filev) if os.path.exists(dst_filev) is True: os.remove(dst_filev) pyroms_toolbox.nc_create_roms_file(dst_filev, dst_grd, nctime) @@ -77,27 +77,27 @@ def remap_clm_uv(src_file, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, dst_dir='./ dst_grdz = pyroms.grid.ROMS_Grid(dst_grd.name+'_Z', dst_grd.hgrid, dst_zcoord) # create variable in destination file - print 'Creating variable u' + print('Creating variable u') ncu.createVariable('u', 'f8', ('ocean_time', 's_rho', 'eta_u', 'xi_u'), fill_value=spval) ncu.variables['u'].long_name = '3D u-momentum component' ncu.variables['u'].units = 'meter second-1' ncu.variables['u'].field = 'u-velocity, scalar, series' ncu.variables['u'].time = 'ocean_time' # create variable in destination file - print 'Creating variable ubar' + print('Creating variable ubar') ncu.createVariable('ubar', 'f8', ('ocean_time', 'eta_u', 'xi_u'), fill_value=spval) ncu.variables['ubar'].long_name = '2D u-momentum component' ncu.variables['ubar'].units = 'meter second-1' ncu.variables['ubar'].field = 'ubar-velocity,, scalar, series' ncu.variables['ubar'].time = 'ocean_time' - print 'Creating variable v' + print('Creating variable v') ncv.createVariable('v', 'f8', ('ocean_time', 's_rho', 'eta_v', 'xi_v'), fill_value=spval) ncv.variables['v'].long_name = '3D v-momentum component' ncv.variables['v'].units = 'meter second-1' ncv.variables['v'].field = 'v-velocity, scalar, series' ncv.variables['v'].time = 'ocean_time' - print 'Creating variable vbar' + print('Creating variable vbar') ncv.createVariable('vbar', 'f8', ('ocean_time', 'eta_v', 'xi_v'), fill_value=spval) ncv.variables['vbar'].long_name = '2D v-momentum component' ncv.variables['vbar'].units = 'meter second-1' @@ -106,27 +106,27 @@ def remap_clm_uv(src_file, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, dst_dir='./ # remaping - print 'remapping and rotating u and v from', src_grd.name, \ - 'to', dst_grd.name - print 'time =', time + print('remapping and rotating u and v from', src_grd.name, \ + 'to', dst_grd.name) + print('time =', time) # flood the grid - print 'flood the grid' + print('flood the grid') src_uz = pyroms_toolbox.Grid_HYCOM.flood_fast(src_varu, src_grd, pos='t', \ spval=spval, dxy=dxy, cdepth=cdepth, kk=kk) src_vz = pyroms_toolbox.Grid_HYCOM.flood_fast(src_varv, src_grd, pos='t', \ spval=spval, dxy=dxy, cdepth=cdepth, kk=kk) # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_uz = pyroms.remapping.remap(src_uz, wts_file, \ spval=spval) dst_vz = pyroms.remapping.remap(src_vz, wts_file, \ spval=spval) # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_u = pyroms.remapping.z2roms(dst_uz[::-1,:,:], dst_grdz, \ dst_grd, Cpos='rho', spval=spval, flood=False) dst_v = pyroms.remapping.z2roms(dst_vz[::-1,:,:], dst_grdz, \ @@ -181,7 +181,7 @@ def remap_clm_uv(src_file, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, dst_dir='./ dst_vbar[idxv[0], idxv[1]] = spval # write data in destination file - print 'write data in destination file' + print('write data in destination file') ncu.variables['ocean_time'][0] = time ncu.variables['u'][0] = dst_u ncu.variables['ubar'][0] = dst_ubar diff --git a/examples/Palau_HYCOM/remap_uv.py b/examples/Palau_HYCOM/remap_uv.py index b2b786e..6185243 100644 --- a/examples/Palau_HYCOM/remap_uv.py +++ b/examples/Palau_HYCOM/remap_uv.py @@ -43,12 +43,12 @@ def remap_uv(src_file, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, dst_dir='./'): # create destination file dst_file = src_file.rsplit('/')[-1] dst_fileu = dst_dir + dst_file[:-3] + '_u_ic_' + dst_grd.name + '.nc' - print '\nCreating destination file', dst_fileu + print('\nCreating destination file', dst_fileu) if os.path.exists(dst_fileu) is True: os.remove(dst_fileu) pyroms_toolbox.nc_create_roms_file(dst_fileu, dst_grd, nctime) dst_filev = dst_dir + dst_file[:-3] + '_v_ic_' + dst_grd.name + '.nc' - print 'Creating destination file', dst_filev + print('Creating destination file', dst_filev) if os.path.exists(dst_filev) is True: os.remove(dst_filev) pyroms_toolbox.nc_create_roms_file(dst_filev, dst_grd, nctime) @@ -77,24 +77,24 @@ def remap_uv(src_file, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, dst_dir='./'): dst_grdz = pyroms.grid.ROMS_Grid(dst_grd.name+'_Z', dst_grd.hgrid, dst_zcoord) # create variable in destination file - print 'Creating variable u' + print('Creating variable u') ncu.createVariable('u', 'f8', ('ocean_time', 's_rho', 'eta_u', 'xi_u'), fill_value=spval) ncu.variables['u'].long_name = '3D u-momentum component' ncu.variables['u'].units = 'meter second-1' ncu.variables['u'].field = 'u-velocity, scalar, series' # create variable in destination file - print 'Creating variable ubar' + print('Creating variable ubar') ncu.createVariable('ubar', 'f8', ('ocean_time', 'eta_u', 'xi_u'), fill_value=spval) ncu.variables['ubar'].long_name = '2D u-momentum component' ncu.variables['ubar'].units = 'meter second-1' ncu.variables['ubar'].field = 'ubar-velocity,, scalar, series' - print 'Creating variable v' + print('Creating variable v') ncv.createVariable('v', 'f8', ('ocean_time', 's_rho', 'eta_v', 'xi_v'), fill_value=spval) ncv.variables['v'].long_name = '3D v-momentum component' ncv.variables['v'].units = 'meter second-1' ncv.variables['v'].field = 'v-velocity, scalar, series' - print 'Creating variable vbar' + print('Creating variable vbar') ncv.createVariable('vbar', 'f8', ('ocean_time', 'eta_v', 'xi_v'), fill_value=spval) ncv.variables['vbar'].long_name = '2D v-momentum component' ncv.variables['vbar'].units = 'meter second-1' @@ -102,27 +102,27 @@ def remap_uv(src_file, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, dst_dir='./'): # remaping - print 'remapping and rotating u and v from', src_grd.name, \ - 'to', dst_grd.name - print 'time =', time + print('remapping and rotating u and v from', src_grd.name, \ + 'to', dst_grd.name) + print('time =', time) # flood the grid - print 'flood the grid' + print('flood the grid') src_uz = pyroms_toolbox.Grid_HYCOM.flood_fast(src_varu, src_grd, pos='t', \ spval=spval, dxy=dxy, cdepth=cdepth, kk=kk) src_vz = pyroms_toolbox.Grid_HYCOM.flood_fast(src_varv, src_grd, pos='t', \ spval=spval, dxy=dxy, cdepth=cdepth, kk=kk) # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_uz = pyroms.remapping.remap(src_uz, wts_file, \ spval=spval) dst_vz = pyroms.remapping.remap(src_vz, wts_file, \ spval=spval) # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_u = pyroms.remapping.z2roms(dst_uz[::-1,:,:], dst_grdz, \ dst_grd, Cpos='rho', spval=spval, flood=False) dst_v = pyroms.remapping.z2roms(dst_vz[::-1,:,:], dst_grdz, \ @@ -177,7 +177,7 @@ def remap_uv(src_file, src_grd, dst_grd, dxy=20, cdepth=0, kk=0, dst_dir='./'): dst_vbar[idxv[0], idxv[1]] = spval # write data in destination file - print 'write data in destination file' + print('write data in destination file') ncu.variables['ocean_time'][0] = time ncu.variables['u'][0] = dst_u ncu.variables['ubar'][0] = dst_ubar diff --git a/examples/README b/examples/README index e61181d..f6762a6 100644 --- a/examples/README +++ b/examples/README @@ -23,6 +23,8 @@ INTERPOLATING FROM SODA: conditions and climatology files - be sure to set the number of processes desired. + Added a couple of SODA3 examples, but the Arctic isn't working yet. + INTERPOLATING FROM LARGER ROMS DOMAINS: For creating initial and boundary files from larger ROMS grids, diff --git a/examples/Yellow_Sea/Inputs/Boundary/make_bdry_file.py b/examples/Yellow_Sea/Inputs/Boundary/make_bdry_file.py index ccdad52..6cf071f 100644 --- a/examples/Yellow_Sea/Inputs/Boundary/make_bdry_file.py +++ b/examples/Yellow_Sea/Inputs/Boundary/make_bdry_file.py @@ -1,7 +1,7 @@ import subprocess import os import sys -import commands +import subprocess import numpy as np import pyroms @@ -20,13 +20,13 @@ for year in lst_year: year = np.str(year) - lst = commands.getoutput('ls ' + data_dir + 'SODA_2.1.6_' + year + '*') + lst = subprocess.getoutput('ls ' + data_dir + 'SODA_2.1.6_' + year + '*') lst = lst.split() lst_file = lst_file + lst -print 'Build OBC file from the following file list:' -print lst_file -print ' ' +print('Build OBC file from the following file list:') +print(lst_file) +print(' ') src_grd_file = data_dir + 'SODA_grid.cdf' src_grd = pyroms_toolbox.BGrid_SODA.get_nc_BGrid_SODA('/Volumes/R1/DATA/SODA_2.1.6/SODA_grid.cdf', name='SODA_2.1.6_YELLOW', xrange=(225, 275), yrange=(190, 240)) diff --git a/examples/Yellow_Sea/Inputs/Boundary/remap_bdry.py b/examples/Yellow_Sea/Inputs/Boundary/remap_bdry.py index 4165d19..aac2f31 100644 --- a/examples/Yellow_Sea/Inputs/Boundary/remap_bdry.py +++ b/examples/Yellow_Sea/Inputs/Boundary/remap_bdry.py @@ -39,7 +39,7 @@ def remap_bdry(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, # create boundary file dst_file = src_file.rsplit('/')[-1] dst_file = dst_dir + dst_file[:-4] + '_' + src_varname + '_bdry_' + dst_grd.name + '.nc' - print '\nCreating boundary file', dst_file + print('\nCreating boundary file', dst_file) if os.path.exists(dst_file) is True: os.remove(dst_file) pyroms_toolbox.nc_create_roms_file(dst_file, dst_grd, nctime, Lgrid=False) @@ -139,7 +139,7 @@ def remap_bdry(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, field_west = 'salt_west, scalar, series' units = 'PSU' else: - raise ValueError, 'Undefined src_varname' + raise ValueError('Undefined src_varname') if ndim == 3: @@ -151,25 +151,25 @@ def remap_bdry(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, # create variable in boudary file - print 'Creating variable', dst_varname_north + print('Creating variable', dst_varname_north) nc.createVariable(dst_varname_north, 'f8', dimensions_north, fill_value=spval) nc.variables[dst_varname_north].long_name = long_name_north nc.variables[dst_varname_north].units = units nc.variables[dst_varname_north].field = field_north - print 'Creating variable', dst_varname_south + print('Creating variable', dst_varname_south) nc.createVariable(dst_varname_south, 'f8', dimensions_south, fill_value=spval) nc.variables[dst_varname_south].long_name = long_name_south nc.variables[dst_varname_south].units = units nc.variables[dst_varname_south].field = field_south - print 'Creating variable', dst_varname_east + print('Creating variable', dst_varname_east) nc.createVariable(dst_varname_east, 'f8', dimensions_east, fill_value=spval) nc.variables[dst_varname_east].long_name = long_name_east nc.variables[dst_varname_east].units = units nc.variables[dst_varname_east].field = field_east - print 'Creating variable', dst_varname_west + print('Creating variable', dst_varname_west) nc.createVariable(dst_varname_west, 'f8', dimensions_west, fill_value=spval) nc.variables[dst_varname_west].long_name = long_name_west nc.variables[dst_varname_west].units = units @@ -177,26 +177,26 @@ def remap_bdry(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, # remapping - print 'remapping', dst_varname, 'from', src_grd.name, \ - 'to', dst_grd.name - print 'time =', time + print('remapping', dst_varname, 'from', src_grd.name, \ + 'to', dst_grd.name) + print('time =', time) if ndim == 3: # flood the grid - print 'flood the grid' + print('flood the grid') src_varz = pyroms_toolbox.BGrid_SODA.flood(src_var, src_grd, Bpos=Bpos, spval=spval, \ dmax=dmax, cdepth=cdepth, kk=kk) else: src_varz = src_var # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_varz = pyroms.remapping.remap(src_varz, wts_file, spval=spval) if ndim == 3: # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_var_north = pyroms.remapping.z2roms(dst_varz[::-1, Mp-1:Mp, 0:Lp], \ dst_grdz, dst_grd, Cpos=Cpos, spval=spval, \ flood=False, irange=(0,Lp), jrange=(Mp-1,Mp)) @@ -216,7 +216,7 @@ def remap_bdry(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_var_west = dst_varz[:, 0] # write data in destination file - print 'write data in destination file' + print('write data in destination file') nc.variables['ocean_time'][0] = time nc.variables[dst_varname_north][0] = np.squeeze(dst_var_north) nc.variables[dst_varname_south][0] = np.squeeze(dst_var_south) diff --git a/examples/Yellow_Sea/Inputs/Boundary/remap_bdry_uv.py b/examples/Yellow_Sea/Inputs/Boundary/remap_bdry_uv.py index c5966d8..97eb9e2 100644 --- a/examples/Yellow_Sea/Inputs/Boundary/remap_bdry_uv.py +++ b/examples/Yellow_Sea/Inputs/Boundary/remap_bdry_uv.py @@ -42,12 +42,12 @@ def remap_bdry_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='. # create destination file dst_file = src_file.rsplit('/')[-1] dst_fileu = dst_dir + dst_file[:-4] + '_u_bdry_' + dst_grd.name + '.nc' - print '\nCreating destination file', dst_fileu + print('\nCreating destination file', dst_fileu) if os.path.exists(dst_fileu) is True: os.remove(dst_fileu) pyroms_toolbox.nc_create_roms_file(dst_fileu, dst_grd, nctime) dst_filev = dst_dir + dst_file[:-4] + '_v_bdry_' + dst_grd.name + '.nc' - print 'Creating destination file', dst_filev + print('Creating destination file', dst_filev) if os.path.exists(dst_filev) is True: os.remove(dst_filev) pyroms_toolbox.nc_create_roms_file(dst_filev, dst_grd, nctime) @@ -78,87 +78,87 @@ def remap_bdry_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='. dst_grdz = pyroms.grid.ROMS_Grid(dst_grd.name+'_Z', dst_grd.hgrid, dst_zcoord) # create variable in destination file - print 'Creating variable u_north' + print('Creating variable u_north') ncu.createVariable('u_north', 'f8', ('ocean_time', 's_rho', 'xi_u'), fill_value=spval) ncu.variables['u_north'].long_name = '3D u-momentum north boundary condition' ncu.variables['u_north'].units = 'meter second-1' ncu.variables['u_north'].field = 'u_north, scalar, series' - print 'Creating variable u_south' + print('Creating variable u_south') ncu.createVariable('u_south', 'f8', ('ocean_time', 's_rho', 'xi_u'), fill_value=spval) ncu.variables['u_south'].long_name = '3D u-momentum south boundary condition' ncu.variables['u_south'].units = 'meter second-1' ncu.variables['u_south'].field = 'u_south, scalar, series' - print 'Creating variable u_east' + print('Creating variable u_east') ncu.createVariable('u_east', 'f8', ('ocean_time', 's_rho', 'eta_u'), fill_value=spval) ncu.variables['u_east'].long_name = '3D u-momentum east boundary condition' ncu.variables['u_east'].units = 'meter second-1' ncu.variables['u_east'].field = 'u_east, scalar, series' - print 'Creating variable u_west' + print('Creating variable u_west') ncu.createVariable('u_west', 'f8', ('ocean_time', 's_rho', 'eta_u'), fill_value=spval) ncu.variables['u_west'].long_name = '3D u-momentum west boundary condition' ncu.variables['u_west'].units = 'meter second-1' ncu.variables['u_west'].field = 'u_east, scalar, series' # create variable in destination file - print 'Creating variable ubar_north' + print('Creating variable ubar_north') ncu.createVariable('ubar_north', 'f8', ('ocean_time', 'xi_u'), fill_value=spval) ncu.variables['ubar_north'].long_name = '2D u-momentum north boundary condition' ncu.variables['ubar_north'].units = 'meter second-1' ncu.variables['ubar_north'].field = 'ubar_north, scalar, series' - print 'Creating variable ubar_south' + print('Creating variable ubar_south') ncu.createVariable('ubar_south', 'f8', ('ocean_time', 'xi_u'), fill_value=spval) ncu.variables['ubar_south'].long_name = '2D u-momentum south boundary condition' ncu.variables['ubar_south'].units = 'meter second-1' ncu.variables['ubar_south'].field = 'ubar_south, scalar, series' - print 'Creating variable ubar_east' + print('Creating variable ubar_east') ncu.createVariable('ubar_east', 'f8', ('ocean_time', 'eta_u'), fill_value=spval) ncu.variables['ubar_east'].long_name = '2D u-momentum east boundary condition' ncu.variables['ubar_east'].units = 'meter second-1' ncu.variables['ubar_east'].field = 'ubar_east, scalar, series' - print 'Creating variable ubar_west' + print('Creating variable ubar_west') ncu.createVariable('ubar_west', 'f8', ('ocean_time', 'eta_u'), fill_value=spval) ncu.variables['ubar_west'].long_name = '2D u-momentum west boundary condition' ncu.variables['ubar_west'].units = 'meter second-1' ncu.variables['ubar_west'].field = 'ubar_east, scalar, series' - print 'Creating variable v_north' + print('Creating variable v_north') ncv.createVariable('v_north', 'f8', ('ocean_time', 's_rho', 'xi_v'), fill_value=spval) ncv.variables['v_north'].long_name = '3D v-momentum north boundary condition' ncv.variables['v_north'].units = 'meter second-1' ncv.variables['v_north'].field = 'v_north, scalar, series' - print 'Creating variable v_south' + print('Creating variable v_south') ncv.createVariable('v_south', 'f8', ('ocean_time', 's_rho', 'xi_v'), fill_value=spval) ncv.variables['v_south'].long_name = '3D v-momentum south boundary condition' ncv.variables['v_south'].units = 'meter second-1' ncv.variables['v_south'].field = 'v_south, scalar, series' - print 'Creating variable v_east' + print('Creating variable v_east') ncv.createVariable('v_east', 'f8', ('ocean_time', 's_rho', 'eta_v'), fill_value=spval) ncv.variables['v_east'].long_name = '3D v-momentum east boundary condition' ncv.variables['v_east'].units = 'meter second-1' ncv.variables['v_east'].field = 'v_east, scalar, series' - print 'Creating variable v_west' + print('Creating variable v_west') ncv.createVariable('v_west', 'f8', ('ocean_time', 's_rho', 'eta_v'), fill_value=spval) ncv.variables['v_west'].long_name = '3D v-momentum west boundary condition' ncv.variables['v_west'].units = 'meter second-1' ncv.variables['v_west'].field = 'v_east, scalar, series' - print 'Creating variable vbar_north' + print('Creating variable vbar_north') ncv.createVariable('vbar_north', 'f8', ('ocean_time', 'xi_v'), fill_value=spval) ncv.variables['vbar_north'].long_name = '2D v-momentum north boundary condition' ncv.variables['vbar_north'].units = 'meter second-1' ncv.variables['vbar_north'].field = 'vbar_north, scalar, series' - print 'Creating variable vbar_south' + print('Creating variable vbar_south') ncv.createVariable('vbar_south', 'f8', ('ocean_time', 'xi_v'), fill_value=spval) ncv.variables['vbar_south'].long_name = '2D v-momentum south boundary condition' ncv.variables['vbar_south'].units = 'meter second-1' ncv.variables['vbar_south'].field = 'vbar_south, scalar, series' - print 'Creating variable vbar_east' + print('Creating variable vbar_east') ncv.createVariable('vbar_east', 'f8', ('ocean_time', 'eta_v'), fill_value=spval) ncv.variables['vbar_east'].long_name = '2D v-momentum east boundary condition' ncv.variables['vbar_east'].units = 'meter second-1' ncv.variables['vbar_east'].field = 'vbar_east, scalar, series' - print 'Creating variable vbar_west' + print('Creating variable vbar_west') ncv.createVariable('vbar_west', 'f8', ('ocean_time', 'eta_v'), fill_value=spval) ncv.variables['vbar_west'].long_name = '2D v-momentum west boundary condition' ncv.variables['vbar_west'].units = 'meter second-1' @@ -167,27 +167,27 @@ def remap_bdry_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='. # remaping - print 'remapping and rotating u and v from', src_grd.name, \ - 'to', dst_grd.name - print 'time =', time + print('remapping and rotating u and v from', src_grd.name, \ + 'to', dst_grd.name) + print('time =', time) # flood the grid - print 'flood the grid' + print('flood the grid') src_uz = pyroms_toolbox.BGrid_SODA.flood(src_varu, src_grd, Bpos='uv', \ spval=spval, dmax=dmax, cdepth=cdepth, kk=kk) src_vz = pyroms_toolbox.BGrid_SODA.flood(src_varv, src_grd, Bpos='uv', \ spval=spval, dmax=dmax, cdepth=cdepth, kk=kk) # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_uz = pyroms.remapping.remap(src_uz, wts_file, \ spval=spval) dst_vz = pyroms.remapping.remap(src_vz, wts_file, \ spval=spval) # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_u_north = pyroms.remapping.z2roms(dst_uz[::-1, Mp-2:Mp, 0:Lp], \ dst_grdz, dst_grd, Cpos='rho', spval=spval, \ flood=False, irange=(0,Lp), jrange=(Mp-2,Mp)) @@ -319,7 +319,7 @@ def remap_bdry_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='. dst_vbar_west = np.ma.masked_where(dst_grd.hgrid.mask_v[:,0] == 0, dst_vbar_west) # write data in destination file - print 'write data in destination file' + print('write data in destination file') ncu.variables['ocean_time'][0] = time ncu.variables['u_north'][0] = dst_u_north ncu.variables['u_south'][0] = dst_u_south diff --git a/examples/Yellow_Sea/Inputs/Initial/make_ic_file.py b/examples/Yellow_Sea/Inputs/Initial/make_ic_file.py index 4831e95..55e6dbe 100644 --- a/examples/Yellow_Sea/Inputs/Initial/make_ic_file.py +++ b/examples/Yellow_Sea/Inputs/Initial/make_ic_file.py @@ -1,6 +1,6 @@ import subprocess import os -import commands +import subprocess import _iso import numpy as np @@ -14,9 +14,9 @@ file = '/center/w/kate/SODA/SODA_2.1.6_20071230-20080104.cdf' dst_dir='./' -print 'Build IC file from the following file:' -print file -print ' ' +print('Build IC file from the following file:') +print(file) +print(' ') src_grd = pyroms_toolbox.BGrid_SODA.get_nc_BGrid_SODA('/center/w/SODA/SODA_grid.cdf', name='SODA_2.1.6_YELLOW', xrange=(225, 275), yrange=(190, 240)) dst_grd = pyroms.grid.get_ROMS_grid('YELLOW') diff --git a/examples/Yellow_Sea/Inputs/Initial/remap.py b/examples/Yellow_Sea/Inputs/Initial/remap.py index a77504c..c20c5b6 100644 --- a/examples/Yellow_Sea/Inputs/Initial/remap.py +++ b/examples/Yellow_Sea/Inputs/Initial/remap.py @@ -39,7 +39,7 @@ def remap(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_d # create IC file dst_file = src_file.rsplit('/')[-1] dst_file = dst_dir + dst_file[:-4] + '_' + src_varname + '_ic_' + dst_grd.name + '.nc' - print '\nCreating file', dst_file + print('\nCreating file', dst_file) if os.path.exists(dst_file) is True: os.remove(dst_file) pyroms_toolbox.nc_create_roms_file(dst_file, dst_grd, nctime) @@ -98,7 +98,7 @@ def remap(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_d units = 'PSU' field = 'salinity, scalar, series' else: - raise ValueError, 'Undefined src_varname' + raise ValueError('Undefined src_varname') if ndim == 3: @@ -110,7 +110,7 @@ def remap(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_d # create variable in file - print 'Creating variable', dst_varname + print('Creating variable', dst_varname) nc.createVariable(dst_varname, 'f8', dimensions, fill_value=spval) nc.variables[dst_varname].long_name = long_name nc.variables[dst_varname].units = units @@ -118,34 +118,34 @@ def remap(src_file, src_varname, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_d # remapping - print 'remapping', dst_varname, 'from', src_grd.name, \ - 'to', dst_grd.name - print 'time =', time + print('remapping', dst_varname, 'from', src_grd.name, \ + 'to', dst_grd.name) + print('time =', time) if ndim == 3: # flood the grid - print 'flood the grid' + print('flood the grid') src_varz = pyroms_toolbox.BGrid_SODA.flood(src_var, src_grd, Bpos=Bpos, spval=spval, \ dmax=dmax, cdepth=cdepth, kk=kk) else: src_varz = src_var # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_varz = pyroms.remapping.remap(src_varz, wts_file, \ spval=spval) if ndim == 3: # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_var = pyroms.remapping.z2roms(dst_varz[::-1,:,:], dst_grdz, \ dst_grd, Cpos=Cpos, spval=spval, flood=False) else: dst_var = dst_varz # write data in destination file - print 'write data in destination file' + print('write data in destination file') nc.variables['ocean_time'][0] = time nc.variables[dst_varname][0] = dst_var diff --git a/examples/Yellow_Sea/Inputs/Initial/remap_uv.py b/examples/Yellow_Sea/Inputs/Initial/remap_uv.py index 04bd2f0..b79ad1f 100644 --- a/examples/Yellow_Sea/Inputs/Initial/remap_uv.py +++ b/examples/Yellow_Sea/Inputs/Initial/remap_uv.py @@ -42,12 +42,12 @@ def remap_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): # create destination file dst_file = src_file.rsplit('/')[-1] dst_fileu = dst_dir + dst_file[:-4] + '_u_ic_' + dst_grd.name + '.nc' - print '\nCreating destination file', dst_fileu + print('\nCreating destination file', dst_fileu) if os.path.exists(dst_fileu) is True: os.remove(dst_fileu) pyroms_toolbox.nc_create_roms_file(dst_fileu, dst_grd, nctime) dst_filev = dst_dir + dst_file[:-4] + '_v_ic_' + dst_grd.name + '.nc' - print 'Creating destination file', dst_filev + print('Creating destination file', dst_filev) if os.path.exists(dst_filev) is True: os.remove(dst_filev) pyroms_toolbox.nc_create_roms_file(dst_filev, dst_grd, nctime) @@ -78,24 +78,24 @@ def remap_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): dst_grdz = pyroms.grid.ROMS_Grid(dst_grd.name+'_Z', dst_grd.hgrid, dst_zcoord) # create variable in destination file - print 'Creating variable u' + print('Creating variable u') ncu.createVariable('u', 'f8', ('ocean_time', 's_rho', 'eta_u', 'xi_u'), fill_value=spval) ncu.variables['u'].long_name = '3D u-momentum component' ncu.variables['u'].units = 'meter second-1' ncu.variables['u'].field = 'u-velocity, scalar, series' # create variable in destination file - print 'Creating variable ubar' + print('Creating variable ubar') ncu.createVariable('ubar', 'f8', ('ocean_time', 'eta_u', 'xi_u'), fill_value=spval) ncu.variables['ubar'].long_name = '2D u-momentum component' ncu.variables['ubar'].units = 'meter second-1' ncu.variables['ubar'].field = 'ubar-velocity,, scalar, series' - print 'Creating variable v' + print('Creating variable v') ncv.createVariable('v', 'f8', ('ocean_time', 's_rho', 'eta_v', 'xi_v'), fill_value=spval) ncv.variables['v'].long_name = '3D v-momentum component' ncv.variables['v'].units = 'meter second-1' ncv.variables['v'].field = 'v-velocity, scalar, series' - print 'Creating variable vbar' + print('Creating variable vbar') ncv.createVariable('vbar', 'f8', ('ocean_time', 'eta_v', 'xi_v'), fill_value=spval) ncv.variables['vbar'].long_name = '2D v-momentum component' ncv.variables['vbar'].units = 'meter second-1' @@ -103,27 +103,27 @@ def remap_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): # remaping - print 'remapping and rotating u and v from', src_grd.name, \ - 'to', dst_grd.name - print 'time =', time + print('remapping and rotating u and v from', src_grd.name, \ + 'to', dst_grd.name) + print('time =', time) # flood the grid - print 'flood the grid' + print('flood the grid') src_uz = pyroms_toolbox.BGrid_SODA.flood(src_varu, src_grd, Bpos='uv', \ spval=spval, dmax=dmax, cdepth=cdepth, kk=kk) src_vz = pyroms_toolbox.BGrid_SODA.flood(src_varv, src_grd, Bpos='uv', \ spval=spval, dmax=dmax, cdepth=cdepth, kk=kk) # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_uz = pyroms.remapping.remap(src_uz, wts_file, \ spval=spval) dst_vz = pyroms.remapping.remap(src_vz, wts_file, \ spval=spval) # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_u = pyroms.remapping.z2roms(dst_uz[::-1,:,:], dst_grdz, \ dst_grd, Cpos='rho', spval=spval, flood=False) dst_v = pyroms.remapping.z2roms(dst_vz[::-1,:,:], dst_grdz, \ @@ -176,7 +176,7 @@ def remap_uv(src_file, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): dst_vbar[idxv[0], idxv[1]] = spval # write data in destination file - print 'write data in destination file' + print('write data in destination file') ncu.variables['ocean_time'][0] = time ncu.variables['u'][0] = dst_u ncu.variables['ubar'][0] = dst_ubar diff --git a/examples/Yellow_Sea/make_YELLOW_grd_v1.py b/examples/Yellow_Sea/make_YELLOW_grd_v1.py index f679fbf..d98510a 100644 --- a/examples/Yellow_Sea/make_YELLOW_grd_v1.py +++ b/examples/Yellow_Sea/make_YELLOW_grd_v1.py @@ -35,7 +35,7 @@ #bry = pyroms.hgrid.BoundaryInteractor(xp, yp, beta, shp=(Mm+3,Lm+3), proj=map) #hgrd=bry.grd -lonv, latv = map(hgrd.x_vert, hgrd.y_vert, inverse=True) +lonv, latv = list(map(hgrd.x_vert, hgrd.y_vert, inverse=True)) hgrd = pyroms.grid.CGrid_geo(lonv, latv, map) # generate the mask @@ -94,7 +94,7 @@ # check bathymetry roughness RoughMat = bathy_tools.RoughnessMatrix(h, hgrd.mask_rho) -print 'Max Roughness value is: ', RoughMat.max() +print('Max Roughness value is: ', RoughMat.max()) # smooth the raw bathy using the direct iterative method from Martinho and Batteen (2006) rx0_max = 0.35 @@ -102,7 +102,7 @@ # check bathymetry roughness again RoughMat = bathy_tools.RoughnessMatrix(h, hgrd.mask_rho) -print 'Max Roughness value is: ', RoughMat.max() +print('Max Roughness value is: ', RoughMat.max()) # vertical coordinate theta_b = 2 diff --git a/examples/Yellow_Sea/make_YELLOW_grd_v2.py b/examples/Yellow_Sea/make_YELLOW_grd_v2.py index 9d9f355..4026d93 100644 --- a/examples/Yellow_Sea/make_YELLOW_grd_v2.py +++ b/examples/Yellow_Sea/make_YELLOW_grd_v2.py @@ -129,10 +129,10 @@ # smooth the raw bathy using the direct iterative method from Martinho and Batteen (2006) RoughMat = bathy_tools.RoughnessMatrix(h, hgrd.mask_rho) -print 'Max Roughness value is: ', RoughMat.max() +print('Max Roughness value is: ', RoughMat.max()) hsmooth = bathy_smoothing.smoothing_Positive_rx0(hgrd.mask_rho, h, 0.3) RoughMat = bathy_tools.RoughnessMatrix(hsmooth, hgrd.mask_rho) -print 'Max Roughness value is: ', RoughMat.max() +print('Max Roughness value is: ', RoughMat.max()) # insure that depth is always deeper than hmin h = pyroms_toolbox.change(h, '<', hmin, hmin) diff --git a/examples/cobalt-preproc/Arctic/fix_pole.py b/examples/cobalt-preproc/Arctic/fix_pole.py new file mode 100644 index 0000000..7e8aedf --- /dev/null +++ b/examples/cobalt-preproc/Arctic/fix_pole.py @@ -0,0 +1,54 @@ +import subprocess +import os +import sys +import subprocess +import numpy as np +import netCDF4 as nc + +dst_dir='./' + +ic_file = dst_dir + 'ARCTIC4_ic_bio_GFDL-APR.nc' +fidic = nc.Dataset(ic_file,'a') +Cs_r = fidic.variables['Cs_r'] +nz = Cs_r.shape[0] + +# define all tracer stuff +list_tracer = ['alk', 'cadet_arag', 'cadet_calc', 'dic', 'fed', 'fedet', 'fedi', 'felg', 'fesm', 'ldon', 'ldop', 'lith', 'lithdet', 'nbact', 'ndet', 'ndi', 'nlg', 'nsm', 'nh4', 'no3', 'o2', 'pdet', 'po4', 'srdon', 'srdop', 'sldon', 'sldop', 'sidet', 'silg', 'sio4', 'nsmz', 'nmdz', 'nlgz','cased','chl','irr_mem','htotal','co3_ion'] + + +print('\nFixing a north pole problem') +for tr in list_tracer: + print('for variable', tr) + tracer = fidic.variables[tr][:] + mysum = np.zeros((nz)) + count = 0 + for j in range(753,768): + for i in range(271,287): + if tracer[0,0,j,i] != 0: + count += 1 + mysum += tracer[0,:,j,i] + print('count', count) + mysum = mysum/count + print('mysum', mysum) + for j in range(753,768): + for i in range(271,287): + if tracer[0,0,j,i] == 0: + tracer[0,:,j,i] = mysum + fidic.variables[tr][:] = tracer + +# These two tracers contain zeros, leading to nans. +tracer = fidic.variables['cased'][:] +mysum = 0.25*(tracer[0,:,752,279] + tracer[0,:,768,279] + tracer[0,:,760,270] + tracer[0,:,602,287]) +for j in range(753,768): + for i in range(271,287): + tracer[0,:,j,i] = mysum +fidic.variables['cased'][:] = tracer + +tracer = fidic.variables['irr_mem'][:] +mysum = 0.25*(tracer[0,:,752,279] + tracer[0,:,768,279] + tracer[0,:,760,270] + tracer[0,:,602,287]) +for j in range(753,768): + for i in range(271,287): + tracer[0,:,j,i] = mysum +fidic.variables['irr_mem'][:] = tracer + +fidic.close() diff --git a/examples/cobalt-preproc/Arctic/make_ic_file_bio.py b/examples/cobalt-preproc/Arctic/make_ic_file_bio.py new file mode 100644 index 0000000..f470721 --- /dev/null +++ b/examples/cobalt-preproc/Arctic/make_ic_file_bio.py @@ -0,0 +1,75 @@ +import subprocess +import os +import sys +import subprocess +import numpy as np +import netCDF4 as nc + +import pyroms +import pyroms_toolbox + +from remap_bio import remap_bio + +#build list of date to remap +tag = 'y1988-2007m04' + +data_dir = '/archive/AKWATERS/kshedstrom/COBALT/' +dst_dir='./' + +src_grd = pyroms_toolbox.BGrid_GFDL.get_nc_BGrid_GFDL('/archive/AKWATERS/kshedstrom/COBALT/GFDL_CM2.1_grid.nc', \ + name='ESM2M_ARCTIC4', area='tripole', ystart=150) +dst_grd = pyroms.grid.get_ROMS_grid('ARCTIC4') + +# define all tracer stuff +list_tracer = ['alk', 'cadet_arag', 'cadet_calc', 'dic', 'fed', 'fedet', 'fedi', 'felg', 'fesm', 'ldon', 'ldop', 'lith', 'lithdet', 'nbact', 'ndet', 'ndi', 'nlg', 'nsm', 'nh4', 'no3', 'o2', 'pdet', 'po4', 'srdon', 'srdop', 'sldon', 'sldop', 'sidet', 'silg', 'sio4', 'nsmz', 'nmdz', 'nlgz','cased','chl','irr_mem','htotal','co3_ion'] + +tracer_longname = ['Alkalinity', 'Detrital CaCO3', 'Detrital CaCO3', 'Dissolved Inorganic Carbon', 'Dissolved Iron', 'Detrital Iron', 'Diazotroph Iron', 'Large Phytoplankton Iron', 'Small Phytoplankton Iron', 'labile DON', 'labile DOP', 'Lithogenic Aluminosilicate', 'lithdet', 'bacterial', 'ndet', 'Diazotroph Nitrogen', 'Large Phytoplankton Nitrogen', 'Small Phytoplankton Nitrogen', 'Ammonia', 'Nitrate', 'Oxygen', 'Detrital Phosphorus', 'Phosphate', 'Semi-Refractory DON', 'Semi-Refractory DOP', 'Semilabile DON', 'Semilabile DOP', 'Detrital Silicon', 'Large Phytoplankton Silicon', 'Silicate', 'Small Zooplankton Nitrogen', 'Medium-sized zooplankton Nitrogen', 'large Zooplankton Nitrogen','Sediment CaCO3','Cholorophyll','Irradiance Memory','Total H+','Carbonate ion'] + +tracer_units = ['mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'g/kg', 'g/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg','mol.m-3','ug.kg-1','W.m-2','mol/kg','mol/kg'] + + + +print('\nBuild IC file for time %s' %tag) +for ktr in np.arange(len(list_tracer)): + mydict = {'tracer':list_tracer[ktr],'longname':tracer_longname[ktr],'units':tracer_units[ktr], \ + 'file':data_dir + 'ocean_cobalt_tracers.1988-2007.01_12.nc', 'nframe':3} + remap_bio(mydict, src_grd, dst_grd, dst_dir=dst_dir) + +## merge file +ic_file = dst_dir + dst_grd.name + '_ic_bio_GFDL-APR.nc' +out_file = dst_dir + dst_grd.name + '_ic_bio_' + list_tracer[0] + '.nc' +command = ('ncks', '-a', '-O', out_file, ic_file) +subprocess.check_call(command) +os.remove(out_file) + +for ktr in np.arange(1,len(list_tracer)): + out_file = dst_dir + dst_grd.name + '_ic_bio_' + list_tracer[ktr] + '.nc' + command = ('ncks', '-a', '-A', out_file, ic_file) + subprocess.check_call(command) + os.remove(out_file) + + +#------------------ Add additional zeros fields ---------------------------------- + +fidic = nc.Dataset(ic_file,'a',format='NETCDF3_64BIT') + +fidic.createVariable('mu_mem_lg', 'f8', ('ocean_time', 's_rho', 'eta_rho', 'xi_rho',) ) +fidic.variables['mu_mem_lg'].long_name = 'large phytoplankton aggregation memory' +fidic.variables['mu_mem_lg'].units = '' +fidic.variables['mu_mem_lg'].field = 'mu_mem_lg, scalar, series' + +fidic.createVariable('mu_mem_di', 'f8', ('ocean_time', 's_rho', 'eta_rho', 'xi_rho',) ) +fidic.variables['mu_mem_di'].long_name = 'medium phytoplankton aggregation memory' +fidic.variables['mu_mem_di'].units = '' +fidic.variables['mu_mem_di'].field = 'mu_mem_di, scalar, series' + +fidic.createVariable('mu_mem_sm', 'f8', ('ocean_time', 's_rho', 'eta_rho', 'xi_rho',) ) +fidic.variables['mu_mem_sm'].long_name = 'small phytoplankton aggregation memory' +fidic.variables['mu_mem_sm'].units = '' +fidic.variables['mu_mem_sm'].field = 'mu_mem_sm, scalar, series' + +fidic.variables['mu_mem_lg'][0,:,:,:] = 0. +fidic.variables['mu_mem_di'][0,:,:,:] = 0. +fidic.variables['mu_mem_sm'][0,:,:,:] = 0. + +fidic.close() diff --git a/examples/cobalt-preproc/Arctic/make_ic_file_bio_addons.py b/examples/cobalt-preproc/Arctic/make_ic_file_bio_addons.py new file mode 100644 index 0000000..9c083c3 --- /dev/null +++ b/examples/cobalt-preproc/Arctic/make_ic_file_bio_addons.py @@ -0,0 +1,83 @@ +import subprocess +import os +import sys +import subprocess +import numpy as np + +import pyroms +import pyroms_toolbox + +from remap_bio_woa import remap_bio_woa +from remap_bio_glodap import remap_bio_glodap + +data_dir_woa = '/archive/AKWATERS/kshedstrom/COBALT/' +data_dir_glodap = '/archive/AKWATERS/kshedstrom/COBALT/' +dst_dir='./' + +src_grd = pyroms_toolbox.BGrid_GFDL.get_nc_BGrid_GFDL('/archive/AKWATERS/kshedstrom/COBALT/GFDL_CM2.1_grid.nc', \ + name='ESM2M_ARCTIC4', area='tripole', ystart=150) +dst_grd = pyroms.grid.get_ROMS_grid('ARCTIC4') + +# tracer informations +list_tracer = ['alk', 'cadet_arag', 'cadet_calc', 'dic', 'fed', 'fedet', 'fedi', 'felg', 'fesm', 'ldon', 'ldop', 'lith', 'lithdet', 'nbact', 'ndet', 'ndi', 'nlg', 'nsm', 'nh4', 'no3', 'o2', 'pdet', 'po4', 'srdon', 'srdop', 'sldon', 'sldop', 'sidet', 'silg', 'sio4', 'nsmz', 'nmdz', 'nlgz','cased','chl','irr_mem','htotal','co3_ion'] + +tracer_longname = ['Alkalinity', 'Detrital CaCO3', 'Detrital CaCO3', 'Dissolved Inorganic Carbon', 'Dissolved Iron', 'Detrital Iron', 'Diazotroph Iron', 'Large Phytoplankton Iron', 'Small Phytoplankton Iron', 'labile DON', 'labile DOP', 'Lithogenic Aluminosilicate', 'lithdet', 'bacterial', 'ndet', 'Diazotroph Nitrogen', 'Large Phytoplankton Nitrogen', 'Small Phytoplankton Nitrogen', 'Ammonia', 'Nitrate', 'Oxygen', 'Detrital Phosphorus', 'Phosphate', 'Semi-Refractory DON', 'Semi-Refractory DOP', 'Semilabile DON', 'Semilabile DOP', 'Detrital Silicon', 'Large Phytoplankton Silicon', 'Silicate', 'Small Zooplankton Nitrogen', 'Medium-sized zooplankton Nitrogen', 'large Zooplankton Nitrogen','Sediment CaCO3','Cholorophyll','Irradiance Memory','Total H+','Carbonate ion'] + +tracer_units = ['mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'g/kg', 'g/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg','mol.m-3','ug.kg-1','W.m-2','mol/kg','mol/kg'] + + +ic_file = dst_dir + dst_grd.name + '_ic_bio_GFDL-APR.nc' + +#------- WOA13 --------------------------------- +id_tracer_update_woa = [19,20,22,29] +list_tracer_update_woa = [] +tracer_longname_update_woa = [] +tracer_units_update_woa = [] + +for idtra in id_tracer_update_woa: + print(list_tracer[idtra]) + +for idtra in id_tracer_update_woa: + # add to tracer update + list_tracer_update_woa.append(list_tracer[idtra]) + tracer_longname_update_woa.append(tracer_longname[idtra]) + tracer_units_update_woa.append(tracer_units[idtra]) + +for ktr in np.arange(len(list_tracer_update_woa)): + ctra = list_tracer_update_woa[ktr] + if ctra == 'sio4': + ctra = 'si' + mydict = {'tracer':list_tracer_update_woa[ktr],'longname':tracer_longname_update_woa[ktr],'units':tracer_units_update_woa[ktr],'file':data_dir_woa + ctra + '_WOA13-CM2.1_monthly.nc', \ + 'nframe':3} + remap_bio_woa(mydict, src_grd, dst_grd, dst_dir=dst_dir) + out_file = dst_dir + dst_grd.name + '_ic_bio_' + list_tracer_update_woa[ktr] + '.nc' + command = ('ncks', '-a', '-A', out_file, ic_file) + subprocess.check_call(command) + os.remove(out_file) + +#--------- GLODAP ------------------------------- +id_tracer_update_glodap = [0,3] +list_tracer_update_glodap = [] +tracer_longname_update_glodap = [] +tracer_units_update_glodap = [] + +for idtra in id_tracer_update_glodap: + print(list_tracer[idtra]) + +for idtra in id_tracer_update_glodap: + # add to tracer update + list_tracer_update_glodap.append(list_tracer[idtra]) + tracer_longname_update_glodap.append(tracer_longname[idtra]) + tracer_units_update_glodap.append(tracer_units[idtra]) + +for ktr in np.arange(len(list_tracer_update_glodap)): + ctra = list_tracer_update_glodap[ktr] + mydict = {'tracer':list_tracer_update_glodap[ktr],'longname':tracer_longname_update_glodap[ktr],'units':tracer_units_update_glodap[ktr],'file':data_dir_glodap + ctra + '_GLODAP-ESM2M_annual.nc', \ + 'nframe':0} + remap_bio_glodap(mydict, src_grd, dst_grd, dst_dir=dst_dir) + out_file = dst_dir + dst_grd.name + '_ic_bio_' + list_tracer_update_glodap[ktr] + '.nc' + command = ('ncks', '-a', '-A', out_file, ic_file) + subprocess.check_call(command) + os.remove(out_file) + + diff --git a/examples/cobalt-preproc/Arctic/make_remap_weights_file.py b/examples/cobalt-preproc/Arctic/make_remap_weights_file.py new file mode 100644 index 0000000..e236766 --- /dev/null +++ b/examples/cobalt-preproc/Arctic/make_remap_weights_file.py @@ -0,0 +1,83 @@ +import pyroms +import pyroms_toolbox + +# load the grid +srcgrd = pyroms_toolbox.BGrid_GFDL.get_nc_BGrid_GFDL('/import/archive/AKWATERS/kshedstrom/COBALT/GFDL_CM2.1_grid.nc', \ + name='ESM2M_ARCTIC4', area='tripole', ystart=150) +dstgrd = pyroms.grid.get_ROMS_grid('ARCTIC4') +dstgrd.hgrid.lon_rho = dstgrd.hgrid.lon_rho - 360. +dstgrd.hgrid.lon_u = dstgrd.hgrid.lon_u - 360. +dstgrd.hgrid.lon_v = dstgrd.hgrid.lon_v - 360. +dstgrd.hgrid.lon_psi = dstgrd.hgrid.lon_psi - 360. +dstgrd.hgrid.lon_vert = dstgrd.hgrid.lon_vert - 360. + +# make remap grid file for scrip +pyroms_toolbox.BGrid_GFDL.make_remap_grid_file(srcgrd, Bpos='t') +pyroms_toolbox.BGrid_GFDL.make_remap_grid_file(srcgrd, Bpos='uv') +pyroms.remapping.make_remap_grid_file(dstgrd, Cpos='rho') +pyroms.remapping.make_remap_grid_file(dstgrd, Cpos='u') +pyroms.remapping.make_remap_grid_file(dstgrd, Cpos='v') + +# compute remap weights +# input namelist variables for bilinear remapping at rho points +grid1_file = 'remap_grid_ESM2M_ARCTIC4_t.nc' +grid2_file = 'remap_grid_ARCTIC4_rho.nc' +interp_file1 = 'remap_weights_ESM2M_to_ARCTIC4_bilinear_t_to_rho.nc' +interp_file2 = 'remap_weights_ARCTIC4_to_ESM2M_bilinear_rho_to_t.nc' +map1_name = 'ESM2M to ARCTIC4 Bilinear Mapping' +map2_name = 'ARCTIC4 to ESM2M Bilinear Mapping' +num_maps = 1 +map_method = 'bilinear' + +pyroms.remapping.compute_remap_weights(grid1_file, grid2_file, \ + interp_file1, interp_file2, map1_name, \ + map2_name, num_maps, map_method) + + +# compute remap weights +# input namelist variables for bilinear remapping at rho points +grid1_file = 'remap_grid_ESM2M_ARCTIC4_uv.nc' +grid2_file = 'remap_grid_ARCTIC4_rho.nc' +interp_file1 = 'remap_weights_ESM2M_to_ARCTIC4_bilinear_uv_to_rho.nc' +interp_file2 = 'remap_weights_ARCTIC4_to_ESM2M_bilinear_rho_to_uv.nc' +map1_name = 'ESM2M to ARCTIC4 Bilinear Mapping' +map2_name = 'ARCTIC4 to ESM2M Bilinear Mapping' +num_maps = 1 +map_method = 'bilinear' + +pyroms.remapping.compute_remap_weights(grid1_file, grid2_file, \ + interp_file1, interp_file2, map1_name, \ + map2_name, num_maps, map_method) + + +# compute remap weights +# input namelist variables for bilinear remapping at rho points +grid1_file = 'remap_grid_ESM2M_ARCTIC4_t.nc' +grid2_file = 'remap_grid_ARCTIC4_u.nc' +interp_file1 = 'remap_weights_ESM2M_to_ARCTIC4_bilinear_t_to_u.nc' +interp_file2 = 'remap_weights_ARCTIC4_to_ESM2M_bilinear_u_to_t.nc' +map1_name = 'ESM2M to ARCTIC4 Bilinear Mapping' +map2_name = 'ARCTIC4 to ESM2M Bilinear Mapping' +num_maps = 1 +map_method = 'bilinear' + +pyroms.remapping.compute_remap_weights(grid1_file, grid2_file, \ + interp_file1, interp_file2, map1_name, \ + map2_name, num_maps, map_method) + + +# compute remap weights +# input namelist variables for bilinear remapping at rho points +grid1_file = 'remap_grid_ESM2M_ARCTIC4_t.nc' +grid2_file = 'remap_grid_ARCTIC4_v.nc' +interp_file1 = 'remap_weights_ESM2M_to_ARCTIC4_bilinear_t_to_v.nc' +interp_file2 = 'remap_weights_ARCTIC4_to_ESM2M_bilinear_v_to_t.nc' +map1_name = 'ESM2M to ARCTIC4 Bilinear Mapping' +map2_name = 'ARCTIC4 to ESM2M Bilinear Mapping' +num_maps = 1 +map_method = 'bilinear' + +pyroms.remapping.compute_remap_weights(grid1_file, grid2_file, \ + interp_file1, interp_file2, map1_name, \ + map2_name, num_maps, map_method) + diff --git a/examples/cobalt-preproc/Arctic/remap_bio.py b/examples/cobalt-preproc/Arctic/remap_bio.py new file mode 100644 index 0000000..cafdcd6 --- /dev/null +++ b/examples/cobalt-preproc/Arctic/remap_bio.py @@ -0,0 +1,143 @@ +import numpy as np +import os +try: + import netCDF4 as netCDF +except: + import netCDF3 as netCDF +import matplotlib.pyplot as plt +import time +from datetime import datetime +from matplotlib.dates import date2num, num2date + +import pyroms +import pyroms_toolbox +import _remapping + +class nctime(object): + pass + +def remap_bio(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): + + # ARCTIC4 grid sub-sample +# xrange=src_grd.xrange; yrange=src_grd.yrange + ystart = 150 + + src_varname = argdict['tracer'] + tracer = src_varname + src_file = argdict['file'] + units = argdict['units'] + longname = argdict['longname'] + nframe = argdict['nframe'] + + # get time + nctime.long_name = 'time' + nctime.units = 'days since 1900-01-01 00:00:00' + + # create clim file + dst_file = tracer + '.nc' + dst_file = dst_dir + dst_grd.name + '_ic_bio_' + dst_file + print('Creating clim file', dst_file) + if os.path.exists(dst_file) is True: + os.remove(dst_file) + pyroms_toolbox.nc_create_roms_file(dst_file, dst_grd, nctime) + + # open clim file + nc = netCDF.Dataset(dst_file, 'a', format='NETCDF3_64BIT') + + #load var + cdf = netCDF.Dataset(src_file) + src_var = cdf.variables[src_varname] + + time = cdf.variables['time'][nframe] + + # to be in sync with physics, add +0.5 day + #time = time + 0.5 + # time will be given by physics anyway + + #get missing value + spval = src_var._FillValue + + # determine variable dimension + ndim = len(src_var.dimensions) - 1 + print('ndim', ndim, src_var.dimensions) + + # ARCTIC4 grid sub-sample + if ndim == 3: +# src_var = src_var[nframe,:, yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] + src_var = src_var[nframe,:,:,:] + print('subgrid 3d', src_var.shape) +# src_var = np.squeeze(src_var, axis=(0,)) + src_var = src_var[:,np.r_[ystart:np.size(src_var,1),-1],:] + print('subgrid 3d', src_var.shape) + elif ndim == 2: +# src_var = src_var[nframe,yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] + src_var = src_var[nframe,:,:] + print('subgrid 2d', src_var.shape) +# src_var = np.squeeze(src_var, axis=(0,)) + src_var = src_var[np.r_[ystart:np.size(src_var,0),-1],:] + print('subgrid 2d', src_var.shape) + + + Bpos = 't' + Cpos = 'rho' + z = src_grd.z_t + Mp, Lp = dst_grd.hgrid.mask_rho.shape + wts_file = 'remap_weights_ESM2M_to_ARCTIC4_bilinear_t_to_rho.nc' + dst_varname = tracer + dimensions = ('ocean_time', 's_rho', 'eta_rho', 'xi_rho') + long_name = longname + field = tracer + ', scalar, series' + units = units + + if ndim == 3: + # build intermediate zgrid + zlevel = -z[::-1] + nzlevel = len(zlevel) + dst_zcoord = pyroms.vgrid.z_coordinate(dst_grd.vgrid.h, zlevel, nzlevel) + dst_grdz = pyroms.grid.ROMS_Grid(dst_grd.name+'_Z', dst_grd.hgrid, dst_zcoord) + + + # create variable in file + print('Creating variable', dst_varname) + nc.createVariable(dst_varname, 'f8', dimensions, fill_value=spval) + nc.variables[dst_varname].long_name = long_name + nc.variables[dst_varname].units = units + nc.variables[dst_varname].field = field + #nc.variables[dst_varname_north]._FillValue = spval + + + # remapping + print('remapping', dst_varname, 'from', src_grd.name, \ + 'to', dst_grd.name) + + if ndim == 3: + # flood the grid + print('flood the grid') + src_varz = pyroms_toolbox.BGrid_GFDL.flood(src_var, src_grd, Bpos=Bpos, spval=spval, \ + dmax=dmax, cdepth=cdepth, kk=kk) + else: + src_varz = src_var + + # horizontal interpolation using scrip weights + print('horizontal interpolation using scrip weights') + dst_varz = pyroms.remapping.remap(src_varz, wts_file, spval=spval) + + if ndim == 3: + # vertical interpolation from standard z level to sigma + print('vertical interpolation from standard z level to sigma') + dst_var = pyroms.remapping.z2roms(dst_varz[::-1,:,:], dst_grdz, \ + dst_grd, Cpos=Cpos, spval=spval, flood=False) + else: + dst_var = dst_varz + + # write data in destination file + print('write data in destination file\n') + nc.variables['ocean_time'][0] = time + nc.variables[dst_varname][0] = dst_var + + # close file + nc.close() + cdf.close() + + if src_varname == 'eta': + return dst_varz diff --git a/examples/cobalt-preproc/Arctic/remap_bio_glodap.py b/examples/cobalt-preproc/Arctic/remap_bio_glodap.py new file mode 100644 index 0000000..bead4b9 --- /dev/null +++ b/examples/cobalt-preproc/Arctic/remap_bio_glodap.py @@ -0,0 +1,162 @@ +import numpy as np +import os +try: + import netCDF4 as netCDF +except: + import netCDF3 as netCDF +import matplotlib.pyplot as plt +import time +from datetime import datetime +from matplotlib.dates import date2num, num2date + +import pyroms +import pyroms_toolbox +import _remapping + +class nctime(object): + pass + +def remap_bio_glodap(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): + + # ARCTIC4 grid sub-sample + ystart = 150 +# xrange=src_grd.xrange; yrange=src_grd.yrange + + src_varname = argdict['tracer'] + tracer = src_varname + src_file = argdict['file'] + units = argdict['units'] + longname = argdict['longname'] + nframe = argdict['nframe'] + + # get time + nctime.long_name = 'time' + nctime.units = 'days since 1900-01-01 00:00:00' + + # create clim file + dst_file = tracer + '.nc' + dst_file = dst_dir + dst_grd.name + '_ic_bio_' + dst_file + print('Creating clim file', dst_file) + if os.path.exists(dst_file) is True: + os.remove(dst_file) + pyroms_toolbox.nc_create_roms_file(dst_file, dst_grd, nctime) + + # open clim file + nc = netCDF.Dataset(dst_file, 'a', format='NETCDF3_64BIT') + + #load var + cdf = netCDF.Dataset(src_file) + src_var = cdf.variables[src_varname] + + tmp = cdf.variables['time'][nframe] + #if len(tmp) > 1: + # print 'error : multiple frames in input file' ; exit() + #else: + # time = tmp[0] + + # to be in sync with physics, add +0.5 day + #time = time + 0.5 + # time will be given by physics anyway + time = 0. + + #get missing value + spval = src_var._FillValue + + spval2 = -1.0e+10 + + # determine variable dimension + ndim = len(src_var.dimensions) - 1 + + # ARCTIC4 grid sub-sample + if ndim == 3: +# src_var = src_var[nframe,:, yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] + src_var = src_var[nframe, :, :, :] + print('subgrid 3d', src_var.shape) +# src_var = np.squeeze(src_var, axis=(0,)) + src_var = src_var[:,np.r_[ystart:np.size(src_var,1),-1],:] + print('subgrid 3d', src_var.shape) + elif ndim == 2: +# src_var = src_var[nframe,yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] + src_var = src_var[nframe, :, :] + print('subgrid 2d', src_var.shape) +# src_var = np.squeeze(src_var, axis=(0,)) + src_var = src_var[np.r_[ystart:np.size(src_var,0),-1],:] + print('subgrid 2d', src_var.shape) + + if tracer == 'alk': + unit_conversion = 1. / 1e6 + elif tracer == 'dic': + unit_conversion = 1. / 1e6 + + src_var = src_var * unit_conversion + + + Bpos = 't' + Cpos = 'rho' + z = src_grd.z_t + Mp, Lp = dst_grd.hgrid.mask_rho.shape + wts_file = 'remap_weights_ESM2M_to_ARCTIC4_bilinear_t_to_rho.nc' + dst_varname = tracer + dimensions = ('ocean_time', 's_rho', 'eta_rho', 'xi_rho') + long_name = longname + field = tracer + ', scalar, series' + units = units + + if ndim == 3: + # build intermediate zgrid + zlevel = -z[::-1] + nzlevel = len(zlevel) + dst_zcoord = pyroms.vgrid.z_coordinate(dst_grd.vgrid.h, zlevel, nzlevel) + dst_grdz = pyroms.grid.ROMS_Grid(dst_grd.name+'_Z', dst_grd.hgrid, dst_zcoord) + + + # create variable in file + print('Creating variable', dst_varname) + nc.createVariable(dst_varname, 'f8', dimensions, fill_value=spval2) + nc.variables[dst_varname].long_name = long_name + nc.variables[dst_varname].units = units + nc.variables[dst_varname].field = field + #nc.variables[dst_varname_north]._FillValue = spval + + + # remapping + print('remapping', dst_varname, 'from', src_grd.name, \ + 'to', dst_grd.name) + + if ndim == 3: + # flood the grid + print('flood the grid') + src_varz = pyroms_toolbox.BGrid_GFDL.flood(src_var, src_grd, Bpos=Bpos, spval=spval, \ + dmax=dmax, cdepth=cdepth, kk=kk) + else: + src_varz = src_var + + # horizontal interpolation using scrip weights + print('horizontal interpolation using scrip weights') + dst_varz = pyroms.remapping.remap(src_varz, wts_file, spval=spval) + + if ndim == 3: + # vertical interpolation from standard z level to sigma + print('vertical interpolation from standard z level to sigma') + dst_var = pyroms.remapping.z2roms(dst_varz[::-1,:,:], dst_grdz, \ + dst_grd, Cpos=Cpos, spval=spval, flood=False) + else: + dst_var = dst_varz + + if ndim == 3: + for kz in np.arange(dst_grd.vgrid.N): + tmp = dst_var[kz,:,:].copy() + tmp[np.where(dst_grd.hgrid.mask_rho == 0)] = spval2 + dst_var[kz,:,:] = tmp.copy() + + # write data in destination file + print('write data in destination file\n') + nc.variables['ocean_time'][0] = time + nc.variables[dst_varname][0] = dst_var + + # close file + nc.close() + cdf.close() + + if src_varname == 'eta': + return dst_varz diff --git a/examples/cobalt-preproc/Arctic/remap_bio_woa.py b/examples/cobalt-preproc/Arctic/remap_bio_woa.py new file mode 100644 index 0000000..e273581 --- /dev/null +++ b/examples/cobalt-preproc/Arctic/remap_bio_woa.py @@ -0,0 +1,166 @@ +import numpy as np +import os +try: + import netCDF4 as netCDF +except: + import netCDF3 as netCDF +import matplotlib.pyplot as plt +import time +from datetime import datetime +from matplotlib.dates import date2num, num2date + +import pyroms +import pyroms_toolbox +import _remapping + +class nctime(object): + pass + +def remap_bio_woa(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): + + # ARCTIC4 grid sub-sample +# xrange=src_grd.xrange; yrange=src_grd.yrange + ystart = 150 + + src_varname = argdict['tracer'] + tracer = src_varname + src_file = argdict['file'] + units = argdict['units'] + longname = argdict['longname'] + nframe = argdict['nframe'] + + if src_varname == 'sio4': + src_varname = 'si' + + # get time + nctime.long_name = 'time' + nctime.units = 'days since 1900-01-01 00:00:00' + + # create clim file + dst_file = tracer + '.nc' + dst_file = dst_dir + dst_grd.name + '_ic_bio_' + dst_file + print('Creating clim file', dst_file) + if os.path.exists(dst_file) is True: + os.remove(dst_file) + pyroms_toolbox.nc_create_roms_file(dst_file, dst_grd, nctime) + + # open clim file + nc = netCDF.Dataset(dst_file, 'a', format='NETCDF3_64BIT') + + #load var + cdf = netCDF.Dataset(src_file) + src_var = cdf.variables[src_varname] + + + tmp = cdf.variables['time'][nframe] + + # to be in sync with physics, add +0.5 day + #time = time + 0.5 + # time will be given by physics anyway + time = 0. + + #get missing value + spval = src_var._FillValue + + spval2 = -1.0e+10 + + # determine variable dimension + ndim = len(src_var.dimensions) - 1 + + # ARCTIC4 grid sub-sample + if ndim == 3: +# src_var = src_var[nframe,:, yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] + src_var = src_var[nframe, :, :, :] + print('subgrid 3d', src_var.shape) +# src_var = np.squeeze(src_var, axis=(0,)) + src_var = src_var[:,np.r_[ystart:np.size(src_var,1),-1],:] + print('subgrid 3d', src_var.shape) + elif ndim == 2: +# src_var = src_var[nframe,yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] + src_var = src_var[nframe, :, :] + print('subgrid 2d', src_var.shape) +# src_var = np.squeeze(src_var, axis=(0,)) + src_var = src_var[np.r_[ystart:np.size(src_var,0),-1],:] + print('subgrid 2d', src_var.shape) + + + if tracer == 'no3': + unit_conversion = 1. / 1e6 / 1.035 + elif tracer == 'po4': + unit_conversion = 1. / 1e6 / 1.035 + elif tracer == 'o2': + unit_conversion = 1. / 1035 / 22391.6 * 1000.0 + elif tracer == 'sio4': + unit_conversion = 1. / 1e6 / 1.035 + + src_var = src_var * unit_conversion + + Bpos = 't' + Cpos = 'rho' + z = src_grd.z_t + Mp, Lp = dst_grd.hgrid.mask_rho.shape + wts_file = 'remap_weights_ESM2M_to_ARCTIC4_bilinear_t_to_rho.nc' + dst_varname = tracer + dimensions = ('ocean_time', 's_rho', 'eta_rho', 'xi_rho') + long_name = longname + field = tracer + ', scalar, series' + units = units + + if ndim == 3: + # build intermediate zgrid + zlevel = -z[::-1] + nzlevel = len(zlevel) + dst_zcoord = pyroms.vgrid.z_coordinate(dst_grd.vgrid.h, zlevel, nzlevel) + dst_grdz = pyroms.grid.ROMS_Grid(dst_grd.name+'_Z', dst_grd.hgrid, dst_zcoord) + + + # create variable in file + print('Creating variable', dst_varname) + nc.createVariable(dst_varname, 'f8', dimensions, fill_value=spval2) + nc.variables[dst_varname].long_name = long_name + nc.variables[dst_varname].units = units + nc.variables[dst_varname].field = field + #nc.variables[dst_varname_north]._FillValue = spval + + + # remapping + print('remapping', dst_varname, 'from', src_grd.name, \ + 'to', dst_grd.name) + + if ndim == 3: + # flood the grid + print('flood the grid') + src_varz = pyroms_toolbox.BGrid_GFDL.flood(src_var, src_grd, Bpos=Bpos, spval=spval, \ + dmax=dmax, cdepth=cdepth, kk=kk) + else: + src_varz = src_var + + # horizontal interpolation using scrip weights + print('horizontal interpolation using scrip weights') + dst_varz = pyroms.remapping.remap(src_varz, wts_file, spval=spval) + + if ndim == 3: + # vertical interpolation from standard z level to sigma + print('vertical interpolation from standard z level to sigma') + dst_var = pyroms.remapping.z2roms(dst_varz[::-1,:,:], dst_grdz, \ + dst_grd, Cpos=Cpos, spval=spval, flood=False) + else: + dst_var = dst_varz + + if ndim == 3: + for kz in np.arange(dst_grd.vgrid.N): + tmp = dst_var[kz,:,:].copy() + tmp[np.where(dst_grd.hgrid.mask_rho == 0)] = spval2 + dst_var[kz,:,:] = tmp.copy() + + # write data in destination file + print('write data in destination file\n') + nc.variables['ocean_time'][0] = time + nc.variables[dst_varname][0] = dst_var + + # close file + nc.close() + cdf.close() + + if src_varname == 'eta': + return dst_varz diff --git a/examples/cobalt-preproc/Boundary_bio/make_bdry_file_bio_GFDLclimato.py b/examples/cobalt-preproc/Boundary_bio/make_bdry_file_bio_GFDLclimato.py index 248698a..d77fd9d 100644 --- a/examples/cobalt-preproc/Boundary_bio/make_bdry_file_bio_GFDLclimato.py +++ b/examples/cobalt-preproc/Boundary_bio/make_bdry_file_bio_GFDLclimato.py @@ -1,7 +1,7 @@ import subprocess import os import sys -import commands +import subprocess import numpy as np import pyroms @@ -23,7 +23,7 @@ tracer_units = ['mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'g/kg', 'g/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg'] for mm in np.arange(12): - print '\nBuild OBC file for month', mm + print('\nBuild OBC file for month', mm) for ktr in np.arange(len(list_tracer)): mydict = {'tracer':list_tracer[ktr],'longname':tracer_longname[ktr],'units':tracer_units[ktr],'file':data_dir + 'ocean_cobalt_tracers.1988-2007.01_12.nc','frame':mm} remap_bdry_bio(mydict, src_grd, dst_grd, dst_dir=dst_dir) diff --git a/examples/cobalt-preproc/Boundary_bio/make_bdry_file_bio_addons.py b/examples/cobalt-preproc/Boundary_bio/make_bdry_file_bio_addons.py index fd8ed17..45a448f 100644 --- a/examples/cobalt-preproc/Boundary_bio/make_bdry_file_bio_addons.py +++ b/examples/cobalt-preproc/Boundary_bio/make_bdry_file_bio_addons.py @@ -1,7 +1,7 @@ import subprocess import os import sys -import commands +import subprocess import numpy as np import pyroms @@ -34,7 +34,7 @@ tracer_units_update_woa = [] for idtra in id_tracer_update_woa: - print list_tracer[idtra] + print(list_tracer[idtra]) for idtra in id_tracer_update_woa: # add to tracer update @@ -44,7 +44,7 @@ for mm in np.arange(12): bdry_file = dst_dir + dst_grd.name + '_bdry_bio_GFDL+WOA+GLODAP_m' + str(mm+1).zfill(2) + '.nc' - print '\nBuild OBC file for month', mm + print('\nBuild OBC file for month', mm) for ktr in np.arange(len(list_tracer_update_woa)): ctra = list_tracer_update_woa[ktr] if ctra == 'sio4': @@ -65,7 +65,7 @@ tracer_units_update_glodap = [] for idtra in id_tracer_update_glodap: - print list_tracer[idtra] + print(list_tracer[idtra]) for idtra in id_tracer_update_glodap: # add to tracer update @@ -75,7 +75,7 @@ for mm in np.arange(12): bdry_file = dst_dir + dst_grd.name + '_bdry_bio_GFDL+WOA+GLODAP_m' + str(mm+1).zfill(2) + '.nc' - print '\nBuild OBC file for month', mm + print('\nBuild OBC file for month', mm) for ktr in np.arange(len(list_tracer_update_glodap)): ctra = list_tracer_update_glodap[ktr] if ctra == 'sio4': diff --git a/examples/cobalt-preproc/Boundary_bio/remap_bdry_bio.py b/examples/cobalt-preproc/Boundary_bio/remap_bdry_bio.py index e72f6cb..1b88ff8 100644 --- a/examples/cobalt-preproc/Boundary_bio/remap_bdry_bio.py +++ b/examples/cobalt-preproc/Boundary_bio/remap_bdry_bio.py @@ -17,7 +17,7 @@ class nctime(object): pass def remap_bdry_bio(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): - + # NWGOA3 grid sub-sample xrange=src_grd.xrange; yrange=src_grd.yrange src_varname = argdict['tracer'] @@ -35,7 +35,7 @@ def remap_bdry_bio(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='. # create boundary file dst_file = tracer + '.nc' dst_file = dst_dir + dst_grd.name + '_bdry_bio_' + dst_file - print 'Creating boundary file', dst_file + print('Creating boundary file', dst_file) if os.path.exists(dst_file) is True: os.remove(dst_file) pyroms_toolbox.nc_create_roms_bdry_file(dst_file, dst_grd, nctime) @@ -44,7 +44,7 @@ def remap_bdry_bio(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='. nc = netCDF.Dataset(dst_file, 'a', format='NETCDF3_64BIT') #load var - cdf = netCDF.Dataset(src_file) + cdf = netCDF.Dataset(src_file) src_var = cdf.variables[src_varname] # correct time to some classic value @@ -98,25 +98,25 @@ def remap_bdry_bio(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='. # create variable in boudary file - print 'Creating variable', dst_varname_north + print('Creating variable', dst_varname_north) nc.createVariable(dst_varname_north, 'f8', dimensions_north, fill_value=spval) nc.variables[dst_varname_north].long_name = long_name_north nc.variables[dst_varname_north].units = units nc.variables[dst_varname_north].field = field_north - print 'Creating variable', dst_varname_south + print('Creating variable', dst_varname_south) nc.createVariable(dst_varname_south, 'f8', dimensions_south, fill_value=spval) nc.variables[dst_varname_south].long_name = long_name_south nc.variables[dst_varname_south].units = units nc.variables[dst_varname_south].field = field_south - print 'Creating variable', dst_varname_west + print('Creating variable', dst_varname_west) nc.createVariable(dst_varname_west, 'f8', dimensions_west, fill_value=spval) nc.variables[dst_varname_west].long_name = long_name_west nc.variables[dst_varname_west].units = units nc.variables[dst_varname_west].field = field_west - print 'Creating variable', dst_varname_east + print('Creating variable', dst_varname_east) nc.createVariable(dst_varname_east, 'f8', dimensions_east, fill_value=spval) nc.variables[dst_varname_east].long_name = long_name_east nc.variables[dst_varname_east].units = units @@ -124,31 +124,31 @@ def remap_bdry_bio(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='. # remapping - print 'remapping', dst_varname, 'from', src_grd.name, \ - 'to', dst_grd.name + print('remapping', dst_varname, 'from', src_grd.name, \ + 'to', dst_grd.name) if ndim == 3: # flood the grid - print 'flood the grid' + print('flood the grid') src_varz = pyroms_toolbox.BGrid_GFDL.flood(src_var, src_grd, Bpos=Bpos, spval=spval, \ dmax=dmax, cdepth=cdepth, kk=kk) else: src_varz = src_var # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_varz = pyroms.remapping.remap(src_varz, wts_file, spval=spval) if ndim == 3: # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_var_north = pyroms.remapping.z2roms(dst_varz[::-1, Mp-1:Mp, 0:Lp], \ dst_grdz, dst_grd, Cpos=Cpos, spval=spval, \ flood=False, irange=(0,Lp), jrange=(Mp-1,Mp)) dst_var_south = pyroms.remapping.z2roms(dst_varz[::-1, 0:1, :], \ dst_grdz, dst_grd, Cpos=Cpos, spval=spval, \ flood=False, irange=(0,Lp), jrange=(0,1)) - dst_var_east = pyroms.remapping.z2roms(dst_varz[::-1, :, Lp-1:Lp], \ + dst_var_east = pyroms.remapping.z2roms(dst_varz[::-1, :, Lp-1:Lp], \ dst_grdz, dst_grd, Cpos=Cpos, spval=spval, \ flood=False, irange=(Lp-1,Lp), jrange=(0,Mp)) dst_var_west = pyroms.remapping.z2roms(dst_varz[::-1, :, 0:1], \ @@ -157,11 +157,11 @@ def remap_bdry_bio(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='. else: dst_var_north = dst_varz[-1, :] dst_var_south = dst_varz[0, :] - dst_var_east = dst_varz[:, -1] + dst_var_east = dst_varz[:, -1] dst_var_west = dst_varz[:, 0] # write data in destination file - print 'write data in destination file\n' + print('write data in destination file\n') nc.variables['ocean_time'][0] = time nc.variables['ocean_time'].cycle_length = 365.25 nc.variables[dst_varname_north][0] = np.squeeze(dst_var_north) diff --git a/examples/cobalt-preproc/Boundary_bio/remap_bdry_bio_glodap.py b/examples/cobalt-preproc/Boundary_bio/remap_bdry_bio_glodap.py index 86e0144..0471946 100644 --- a/examples/cobalt-preproc/Boundary_bio/remap_bdry_bio_glodap.py +++ b/examples/cobalt-preproc/Boundary_bio/remap_bdry_bio_glodap.py @@ -17,7 +17,7 @@ class nctime(object): pass def remap_bdry_bio_glodap(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): - + # NWGOA3 grid sub-sample xrange=src_grd.xrange; yrange=src_grd.yrange src_varname = argdict['tracer'] @@ -35,7 +35,7 @@ def remap_bdry_bio_glodap(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst # create boundary file dst_file = tracer + '.nc' dst_file = dst_dir + dst_grd.name + '_bdry_bio_' + dst_file - print 'Creating boundary file', dst_file + print('Creating boundary file', dst_file) if os.path.exists(dst_file) is True: os.remove(dst_file) pyroms_toolbox.nc_create_roms_bdry_file(dst_file, dst_grd, nctime) @@ -44,7 +44,7 @@ def remap_bdry_bio_glodap(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst nc = netCDF.Dataset(dst_file, 'a', format='NETCDF3_64BIT') #load var - cdf = netCDF.Dataset(src_file) + cdf = netCDF.Dataset(src_file) src_var = cdf.variables[src_varname] # correct time to some classic value @@ -65,9 +65,9 @@ def remap_bdry_bio_glodap(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst src_var = src_var[0,yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] if tracer == 'alk': - unit_conversion = 1. / 1e6 + unit_conversion = 1. / 1e6 elif tracer == 'dic': - unit_conversion = 1. / 1e6 + unit_conversion = 1. / 1e6 src_var = src_var * unit_conversion @@ -105,25 +105,25 @@ def remap_bdry_bio_glodap(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst # create variable in boudary file - print 'Creating variable', dst_varname_north + print('Creating variable', dst_varname_north) nc.createVariable(dst_varname_north, 'f8', dimensions_north, fill_value=spval2) nc.variables[dst_varname_north].long_name = long_name_north nc.variables[dst_varname_north].units = units nc.variables[dst_varname_north].field = field_north - print 'Creating variable', dst_varname_south + print('Creating variable', dst_varname_south) nc.createVariable(dst_varname_south, 'f8', dimensions_south, fill_value=spval2) nc.variables[dst_varname_south].long_name = long_name_south nc.variables[dst_varname_south].units = units nc.variables[dst_varname_south].field = field_south - print 'Creating variable', dst_varname_west + print('Creating variable', dst_varname_west) nc.createVariable(dst_varname_west, 'f8', dimensions_west, fill_value=spval2) nc.variables[dst_varname_west].long_name = long_name_west nc.variables[dst_varname_west].units = units nc.variables[dst_varname_west].field = field_west - print 'Creating variable', dst_varname_east + print('Creating variable', dst_varname_east) nc.createVariable(dst_varname_east, 'f8', dimensions_east, fill_value=spval2) nc.variables[dst_varname_east].long_name = long_name_east nc.variables[dst_varname_east].units = units @@ -131,31 +131,31 @@ def remap_bdry_bio_glodap(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst # remapping - print 'remapping', dst_varname, 'from', src_grd.name, \ - 'to', dst_grd.name + print('remapping', dst_varname, 'from', src_grd.name, \ + 'to', dst_grd.name) if ndim == 3: # flood the grid - print 'flood the grid' + print('flood the grid') src_varz = pyroms_toolbox.BGrid_GFDL.flood(src_var, src_grd, Bpos=Bpos, spval=spval, \ dmax=dmax, cdepth=cdepth, kk=kk) else: src_varz = src_var # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_varz = pyroms.remapping.remap(src_varz, wts_file, spval=spval) if ndim == 3: # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_var_north = pyroms.remapping.z2roms(dst_varz[::-1, Mp-1:Mp, 0:Lp], \ dst_grdz, dst_grd, Cpos=Cpos, spval=spval, \ flood=False, irange=(0,Lp), jrange=(Mp-1,Mp)) dst_var_south = pyroms.remapping.z2roms(dst_varz[::-1, 0:1, :], \ dst_grdz, dst_grd, Cpos=Cpos, spval=spval, \ flood=False, irange=(0,Lp), jrange=(0,1)) - dst_var_east = pyroms.remapping.z2roms(dst_varz[::-1, :, Lp-1:Lp], \ + dst_var_east = pyroms.remapping.z2roms(dst_varz[::-1, :, Lp-1:Lp], \ dst_grdz, dst_grd, Cpos=Cpos, spval=spval, \ flood=False, irange=(Lp-1,Lp), jrange=(0,Mp)) dst_var_west = pyroms.remapping.z2roms(dst_varz[::-1, :, 0:1], \ @@ -164,7 +164,7 @@ def remap_bdry_bio_glodap(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst else: dst_var_north = dst_varz[-1, :] dst_var_south = dst_varz[0, :] - dst_var_east = dst_varz[:, -1] + dst_var_east = dst_varz[:, -1] dst_var_west = dst_varz[:, 0] dst_var_north[np.where(dst_var_north == spval)] = spval2 @@ -173,7 +173,7 @@ def remap_bdry_bio_glodap(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst dst_var_west[np.where(dst_var_west == spval)] = spval2 # write data in destination file - print 'write data in destination file\n' + print('write data in destination file\n') nc.variables['ocean_time'][0] = time nc.variables['ocean_time'].cycle_length = 365.25 nc.variables[dst_varname_north][0] = np.squeeze(dst_var_north) diff --git a/examples/cobalt-preproc/Boundary_bio/remap_bdry_bio_woa.py b/examples/cobalt-preproc/Boundary_bio/remap_bdry_bio_woa.py index 5ed4a38..1e1e98c 100644 --- a/examples/cobalt-preproc/Boundary_bio/remap_bdry_bio_woa.py +++ b/examples/cobalt-preproc/Boundary_bio/remap_bdry_bio_woa.py @@ -17,7 +17,7 @@ class nctime(object): pass def remap_bdry_bio_woa(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): - + # NWGOA3 grid sub-sample xrange=src_grd.xrange; yrange=src_grd.yrange src_varname = argdict['tracer'] @@ -38,7 +38,7 @@ def remap_bdry_bio_woa(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_di # create boundary file dst_file = tracer + '.nc' dst_file = dst_dir + dst_grd.name + '_bdry_bio_' + dst_file - print 'Creating boundary file', dst_file + print('Creating boundary file', dst_file) if os.path.exists(dst_file) is True: os.remove(dst_file) pyroms_toolbox.nc_create_roms_bdry_file(dst_file, dst_grd, nctime) @@ -47,7 +47,7 @@ def remap_bdry_bio_woa(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_di nc = netCDF.Dataset(dst_file, 'a', format='NETCDF3_64BIT') #load var - cdf = netCDF.Dataset(src_file) + cdf = netCDF.Dataset(src_file) src_var = cdf.variables[src_varname] # correct time to some classic value @@ -112,25 +112,25 @@ def remap_bdry_bio_woa(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_di # create variable in boudary file - print 'Creating variable', dst_varname_north + print('Creating variable', dst_varname_north) nc.createVariable(dst_varname_north, 'f8', dimensions_north, fill_value=spval2) nc.variables[dst_varname_north].long_name = long_name_north nc.variables[dst_varname_north].units = units nc.variables[dst_varname_north].field = field_north - print 'Creating variable', dst_varname_south + print('Creating variable', dst_varname_south) nc.createVariable(dst_varname_south, 'f8', dimensions_south, fill_value=spval2) nc.variables[dst_varname_south].long_name = long_name_south nc.variables[dst_varname_south].units = units nc.variables[dst_varname_south].field = field_south - print 'Creating variable', dst_varname_west + print('Creating variable', dst_varname_west) nc.createVariable(dst_varname_west, 'f8', dimensions_west, fill_value=spval2) nc.variables[dst_varname_west].long_name = long_name_west nc.variables[dst_varname_west].units = units nc.variables[dst_varname_west].field = field_west - print 'Creating variable', dst_varname_east + print('Creating variable', dst_varname_east) nc.createVariable(dst_varname_east, 'f8', dimensions_east, fill_value=spval2) nc.variables[dst_varname_east].long_name = long_name_east nc.variables[dst_varname_east].units = units @@ -138,31 +138,31 @@ def remap_bdry_bio_woa(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_di # remapping - print 'remapping', dst_varname, 'from', src_grd.name, \ - 'to', dst_grd.name + print('remapping', dst_varname, 'from', src_grd.name, \ + 'to', dst_grd.name) if ndim == 3: # flood the grid - print 'flood the grid' + print('flood the grid') src_varz = pyroms_toolbox.BGrid_GFDL.flood(src_var, src_grd, Bpos=Bpos, spval=spval, \ dmax=dmax, cdepth=cdepth, kk=kk) else: src_varz = src_var # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_varz = pyroms.remapping.remap(src_varz, wts_file, spval=spval) if ndim == 3: # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_var_north = pyroms.remapping.z2roms(dst_varz[::-1, Mp-1:Mp, 0:Lp], \ dst_grdz, dst_grd, Cpos=Cpos, spval=spval, \ flood=False, irange=(0,Lp), jrange=(Mp-1,Mp)) dst_var_south = pyroms.remapping.z2roms(dst_varz[::-1, 0:1, :], \ dst_grdz, dst_grd, Cpos=Cpos, spval=spval, \ flood=False, irange=(0,Lp), jrange=(0,1)) - dst_var_east = pyroms.remapping.z2roms(dst_varz[::-1, :, Lp-1:Lp], \ + dst_var_east = pyroms.remapping.z2roms(dst_varz[::-1, :, Lp-1:Lp], \ dst_grdz, dst_grd, Cpos=Cpos, spval=spval, \ flood=False, irange=(Lp-1,Lp), jrange=(0,Mp)) dst_var_west = pyroms.remapping.z2roms(dst_varz[::-1, :, 0:1], \ @@ -171,7 +171,7 @@ def remap_bdry_bio_woa(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_di else: dst_var_north = dst_varz[-1, :] dst_var_south = dst_varz[0, :] - dst_var_east = dst_varz[:, -1] + dst_var_east = dst_varz[:, -1] dst_var_west = dst_varz[:, 0] dst_var_north[np.where(dst_var_north == spval)] = spval2 @@ -180,7 +180,7 @@ def remap_bdry_bio_woa(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_di dst_var_west[np.where(dst_var_west == spval)] = spval2 # write data in destination file - print 'write data in destination file\n' + print('write data in destination file\n') nc.variables['ocean_time'][0] = time nc.variables['ocean_time'].cycle_length = 365.25 nc.variables[dst_varname_north][0] = np.squeeze(dst_var_north) diff --git a/examples/cobalt-preproc/Clim_bio/make_clim_file_bio_addons.py b/examples/cobalt-preproc/Clim_bio/make_clim_file_bio_addons.py index 7ca04aa..c28b579 100644 --- a/examples/cobalt-preproc/Clim_bio/make_clim_file_bio_addons.py +++ b/examples/cobalt-preproc/Clim_bio/make_clim_file_bio_addons.py @@ -1,7 +1,7 @@ import subprocess import os import sys -import commands +import subprocess import numpy as np import pyroms @@ -32,7 +32,7 @@ tracer_units_update_woa = [] for idtra in id_tracer_update_woa: - print list_tracer[idtra] + print(list_tracer[idtra]) for idtra in id_tracer_update_woa: # add to tracer update @@ -42,7 +42,7 @@ for mm in np.arange(12): clim_file = dst_dir + dst_grd.name + '_clim_bio_GFDL+WOA+GLODAP_m' + str(mm+1).zfill(2) + '.nc' - print '\nBuild CLIM file for month', mm + print('\nBuild CLIM file for month', mm) for ktr in np.arange(len(list_tracer_update_woa)): ctra = list_tracer_update_woa[ktr] if ctra == 'sio4': @@ -62,7 +62,7 @@ tracer_units_update_glodap = [] for idtra in id_tracer_update_glodap: - print list_tracer[idtra] + print(list_tracer[idtra]) for idtra in id_tracer_update_glodap: # add to tracer update @@ -72,7 +72,7 @@ for mm in np.arange(12): clim_file = dst_dir + dst_grd.name + '_clim_bio_GFDL+WOA+GLODAP_m' + str(mm+1).zfill(2) + '.nc' - print '\nBuild CLIM file for month', mm + print('\nBuild CLIM file for month', mm) for ktr in np.arange(len(list_tracer_update_glodap)): ctra = list_tracer_update_glodap[ktr] mydict = {'tracer':list_tracer_update_glodap[ktr],'longname':tracer_longname_update_glodap[ktr],'units':tracer_units_update_glodap[ktr],'file':data_dir_glodap + ctra + '_GLODAP-ESM2M_annual.nc', \ diff --git a/examples/cobalt-preproc/Clim_bio/make_clim_file_bio_gfdl-climato.py b/examples/cobalt-preproc/Clim_bio/make_clim_file_bio_gfdl-climato.py index 2983a22..a248a9c 100644 --- a/examples/cobalt-preproc/Clim_bio/make_clim_file_bio_gfdl-climato.py +++ b/examples/cobalt-preproc/Clim_bio/make_clim_file_bio_gfdl-climato.py @@ -1,7 +1,7 @@ import subprocess import os import sys -import commands +import subprocess import numpy as np import pyroms @@ -23,7 +23,7 @@ tracer_units = ['mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'g/kg', 'g/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg', 'mol/kg'] for mm in np.arange(12): - print '\nBuild clim file for month ', mm + print('\nBuild clim file for month ', mm) for ktr in np.arange(len(list_tracer)): mydict = {'tracer':list_tracer[ktr],'longname':tracer_longname[ktr],'units':tracer_units[ktr],'file':data_dir + 'ocean_cobalt_tracers.1988-2007.01_12.nc','frame':mm} remap_bio(mydict, src_grd, dst_grd, dst_dir=dst_dir) diff --git a/examples/cobalt-preproc/Clim_bio/remap_bio.py b/examples/cobalt-preproc/Clim_bio/remap_bio.py index 55c7016..6d7d4b3 100644 --- a/examples/cobalt-preproc/Clim_bio/remap_bio.py +++ b/examples/cobalt-preproc/Clim_bio/remap_bio.py @@ -35,7 +35,7 @@ def remap_bio(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): # create clim file dst_file = tracer + '.nc' dst_file = dst_dir + dst_grd.name + '_clim_bio_' + dst_file - print 'Creating clim file', dst_file + print('Creating clim file', dst_file) if os.path.exists(dst_file) is True: os.remove(dst_file) pyroms_toolbox.nc_create_roms_file(dst_file, dst_grd, nctime) @@ -85,38 +85,38 @@ def remap_bio(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): # create variable in file - print 'Creating variable', dst_varname + print('Creating variable', dst_varname) nc.createVariable(dst_varname, 'f8', dimensions, fill_value=spval) nc.variables[dst_varname].long_name = long_name nc.variables[dst_varname].units = units nc.variables[dst_varname].field = field # remapping - print 'remapping', dst_varname, 'from', src_grd.name, \ - 'to', dst_grd.name + print('remapping', dst_varname, 'from', src_grd.name, \ + 'to', dst_grd.name) if ndim == 3: # flood the grid - print 'flood the grid' + print('flood the grid') src_varz = pyroms_toolbox.BGrid_GFDL.flood(src_var, src_grd, Bpos=Bpos, spval=spval, \ dmax=dmax, cdepth=cdepth, kk=kk) else: src_varz = src_var # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_varz = pyroms.remapping.remap(src_varz, wts_file, spval=spval) if ndim == 3: # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_var = pyroms.remapping.z2roms(dst_varz[::-1,:,:], dst_grdz, \ dst_grd, Cpos=Cpos, spval=spval, flood=False) else: dst_var = dst_varz # write data in destination file - print 'write data in destination file\n' + print('write data in destination file\n') nc.variables['ocean_time'][0] = time nc.variables['ocean_time'].cycle_length = 365.25 nc.variables[dst_varname][0] = dst_var diff --git a/examples/cobalt-preproc/Clim_bio/remap_bio_glodap.py b/examples/cobalt-preproc/Clim_bio/remap_bio_glodap.py index 7a0fd97..d431436 100644 --- a/examples/cobalt-preproc/Clim_bio/remap_bio_glodap.py +++ b/examples/cobalt-preproc/Clim_bio/remap_bio_glodap.py @@ -35,7 +35,7 @@ def remap_bio_glodap(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir= # create clim file dst_file = tracer + '.nc' dst_file = dst_dir + dst_grd.name + '_clim_bio_' + dst_file - print 'Creating clim file', dst_file + print('Creating clim file', dst_file) if os.path.exists(dst_file) is True: os.remove(dst_file) pyroms_toolbox.nc_create_roms_file(dst_file, dst_grd, nctime) @@ -93,7 +93,7 @@ def remap_bio_glodap(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir= # create variable in file - print 'Creating variable', dst_varname + print('Creating variable', dst_varname) nc.createVariable(dst_varname, 'f8', dimensions, fill_value=spval2) nc.variables[dst_varname].long_name = long_name nc.variables[dst_varname].units = units @@ -102,24 +102,24 @@ def remap_bio_glodap(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir= # remapping - print 'remapping', dst_varname, 'from', src_grd.name, \ - 'to', dst_grd.name + print('remapping', dst_varname, 'from', src_grd.name, \ + 'to', dst_grd.name) if ndim == 3: # flood the grid - print 'flood the grid' + print('flood the grid') src_varz = pyroms_toolbox.BGrid_GFDL.flood(src_var, src_grd, Bpos=Bpos, spval=spval, \ dmax=dmax, cdepth=cdepth, kk=kk) else: src_varz = src_var # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_varz = pyroms.remapping.remap(src_varz, wts_file, spval=spval) if ndim == 3: # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_var = pyroms.remapping.z2roms(dst_varz[::-1,:,:], dst_grdz, \ dst_grd, Cpos=Cpos, spval=spval, flood=False) else: @@ -132,7 +132,7 @@ def remap_bio_glodap(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir= dst_var[kz,:,:] = tmp.copy() # write data in destination file - print 'write data in destination file\n' + print('write data in destination file\n') nc.variables['ocean_time'][0] = time nc.variables[dst_varname][0] = dst_var diff --git a/examples/cobalt-preproc/Clim_bio/remap_bio_woa.py b/examples/cobalt-preproc/Clim_bio/remap_bio_woa.py index 3c0d3ba..aee0a78 100644 --- a/examples/cobalt-preproc/Clim_bio/remap_bio_woa.py +++ b/examples/cobalt-preproc/Clim_bio/remap_bio_woa.py @@ -17,7 +17,7 @@ class nctime(object): pass def remap_bio_woa(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): - + # NWGOA3 grid sub-sample xrange=src_grd.xrange; yrange=src_grd.yrange @@ -38,7 +38,7 @@ def remap_bio_woa(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./ # create clim file dst_file = tracer + '.nc' dst_file = dst_dir + dst_grd.name + '_clim_bio_' + dst_file - print 'Creating clim file', dst_file + print('Creating clim file', dst_file) if os.path.exists(dst_file) is True: os.remove(dst_file) pyroms_toolbox.nc_create_roms_file(dst_file, dst_grd, nctime) @@ -47,7 +47,7 @@ def remap_bio_woa(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./ nc = netCDF.Dataset(dst_file, 'a', format='NETCDF3_64BIT') #load var - cdf = netCDF.Dataset(src_file) + cdf = netCDF.Dataset(src_file) src_var = cdf.variables[src_varname] # correct time to some classic value @@ -100,7 +100,7 @@ def remap_bio_woa(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./ # create variable in file - print 'Creating variable', dst_varname + print('Creating variable', dst_varname) nc.createVariable(dst_varname, 'f8', dimensions, fill_value=spval2) nc.variables[dst_varname].long_name = long_name nc.variables[dst_varname].units = units @@ -109,24 +109,24 @@ def remap_bio_woa(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./ # remapping - print 'remapping', dst_varname, 'from', src_grd.name, \ - 'to', dst_grd.name + print('remapping', dst_varname, 'from', src_grd.name, \ + 'to', dst_grd.name) if ndim == 3: # flood the grid - print 'flood the grid' + print('flood the grid') src_varz = pyroms_toolbox.BGrid_GFDL.flood(src_var, src_grd, Bpos=Bpos, spval=spval, \ dmax=dmax, cdepth=cdepth, kk=kk) else: src_varz = src_var # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_varz = pyroms.remapping.remap(src_varz, wts_file, spval=spval) if ndim == 3: # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_var = pyroms.remapping.z2roms(dst_varz[::-1,:,:], dst_grdz, \ dst_grd, Cpos=Cpos, spval=spval, flood=False) else: @@ -135,11 +135,11 @@ def remap_bio_woa(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./ if ndim == 3: for kz in np.arange(dst_grd.vgrid.N): tmp = dst_var[kz,:,:].copy() - tmp[np.where(dst_grd.hgrid.mask_rho == 0)] = spval2 + tmp[np.where(dst_grd.hgrid.mask_rho == 0)] = spval2 dst_var[kz,:,:] = tmp.copy() # write data in destination file - print 'write data in destination file\n' + print('write data in destination file\n') nc.variables['ocean_time'][0] = time nc.variables[dst_varname][0] = dst_var diff --git a/examples/cobalt-preproc/Initial_bio/make_ic_file_bio.py b/examples/cobalt-preproc/Initial_bio/make_ic_file_bio.py index bd58f86..b95fe5b 100644 --- a/examples/cobalt-preproc/Initial_bio/make_ic_file_bio.py +++ b/examples/cobalt-preproc/Initial_bio/make_ic_file_bio.py @@ -1,7 +1,7 @@ import subprocess import os import sys -import commands +import subprocess import numpy as np import netCDF4 as nc @@ -28,20 +28,21 @@ -print '\nBuild IC file for time %s' %tag +print('\nBuild IC file for time %s' %tag) for ktr in np.arange(len(list_tracer)): - mydict = {'tracer':list_tracer[ktr],'longname':tracer_longname[ktr],'units':tracer_units[ktr],'file':data_dir + 'ocean_cobalt_tracers.1988-2007.01.nc'} + mydict = {'tracer':list_tracer[ktr],'longname':tracer_longname[ktr],'units':tracer_units[ktr], \ + 'file':data_dir + 'ocean_cobalt_tracers.1988-2007.01_12.nc', 'nframe':0} remap_bio(mydict, src_grd, dst_grd, dst_dir=dst_dir) ## merge file -ic_file = dst_dir + dst_grd.name + '_ic_bio_GFDL-JAN.nc' -out_file = dst_dir + dst_grd.name + '_ic_bio_' + list_tracer[0] + '.nc' +ic_file = dst_dir + dst_grd.name + '_ic_bio_GFDL-JAN.nc' +out_file = dst_dir + dst_grd.name + '_ic_bio_' + list_tracer[0] + '.nc' command = ('ncks', '-a', '-O', out_file, ic_file) subprocess.check_call(command) os.remove(out_file) for ktr in np.arange(1,len(list_tracer)): - out_file = dst_dir + dst_grd.name + '_ic_bio_' + list_tracer[ktr] + '.nc' + out_file = dst_dir + dst_grd.name + '_ic_bio_' + list_tracer[ktr] + '.nc' command = ('ncks', '-a', '-A', out_file, ic_file) subprocess.check_call(command) os.remove(out_file) diff --git a/examples/cobalt-preproc/Initial_bio/make_ic_file_bio_addons.py b/examples/cobalt-preproc/Initial_bio/make_ic_file_bio_addons.py index e2a5f40..437c82a 100644 --- a/examples/cobalt-preproc/Initial_bio/make_ic_file_bio_addons.py +++ b/examples/cobalt-preproc/Initial_bio/make_ic_file_bio_addons.py @@ -1,7 +1,7 @@ import subprocess import os import sys -import commands +import subprocess import numpy as np import pyroms @@ -34,7 +34,7 @@ tracer_units_update_woa = [] for idtra in id_tracer_update_woa: - print list_tracer[idtra] + print(list_tracer[idtra]) for idtra in id_tracer_update_woa: # add to tracer update @@ -61,7 +61,7 @@ tracer_units_update_glodap = [] for idtra in id_tracer_update_glodap: - print list_tracer[idtra] + print(list_tracer[idtra]) for idtra in id_tracer_update_glodap: # add to tracer update diff --git a/examples/cobalt-preproc/Initial_bio/remap_bio.py b/examples/cobalt-preproc/Initial_bio/remap_bio.py index 713a1d7..4cf740e 100644 --- a/examples/cobalt-preproc/Initial_bio/remap_bio.py +++ b/examples/cobalt-preproc/Initial_bio/remap_bio.py @@ -17,7 +17,7 @@ class nctime(object): pass def remap_bio(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): - + # NWGOA3 grid sub-sample xrange=src_grd.xrange; yrange=src_grd.yrange @@ -26,6 +26,7 @@ def remap_bio(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): src_file = argdict['file'] units = argdict['units'] longname = argdict['longname'] + nframe = argdict['nframe'] # get time nctime.long_name = 'time' @@ -34,7 +35,7 @@ def remap_bio(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): # create clim file dst_file = tracer + '.nc' dst_file = dst_dir + dst_grd.name + '_ic_bio_' + dst_file - print 'Creating clim file', dst_file + print('Creating clim file', dst_file) if os.path.exists(dst_file) is True: os.remove(dst_file) pyroms_toolbox.nc_create_roms_file(dst_file, dst_grd, nctime) @@ -43,19 +44,14 @@ def remap_bio(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): nc = netCDF.Dataset(dst_file, 'a', format='NETCDF3_64BIT') #load var - cdf = netCDF.Dataset(src_file) + cdf = netCDF.Dataset(src_file) src_var = cdf.variables[src_varname] - tmp = cdf.variables['time'][:] - if len(tmp) > 1: - print 'error : multiple frames in input file' ; exit() - else: - time = tmp[0] + time = cdf.variables['time'][nframe] # to be in sync with physics, add +0.5 day #time = time + 0.5 # time will be given by physics anyway - time = 0. #get missing value spval = src_var._FillValue @@ -65,9 +61,9 @@ def remap_bio(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): # NWGOA3 grid sub-sample if ndim == 3: - src_var = src_var[0,:, yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] + src_var = src_var[nframe,:, yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] elif ndim == 2: - src_var = src_var[0,yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] + src_var = src_var[nframe,yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] Bpos = 't' @@ -90,7 +86,7 @@ def remap_bio(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): # create variable in file - print 'Creating variable', dst_varname + print('Creating variable', dst_varname) nc.createVariable(dst_varname, 'f8', dimensions, fill_value=spval) nc.variables[dst_varname].long_name = long_name nc.variables[dst_varname].units = units @@ -99,31 +95,31 @@ def remap_bio(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): # remapping - print 'remapping', dst_varname, 'from', src_grd.name, \ - 'to', dst_grd.name + print('remapping', dst_varname, 'from', src_grd.name, \ + 'to', dst_grd.name) if ndim == 3: # flood the grid - print 'flood the grid' + print('flood the grid') src_varz = pyroms_toolbox.BGrid_GFDL.flood(src_var, src_grd, Bpos=Bpos, spval=spval, \ dmax=dmax, cdepth=cdepth, kk=kk) else: src_varz = src_var # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_varz = pyroms.remapping.remap(src_varz, wts_file, spval=spval) if ndim == 3: # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_var = pyroms.remapping.z2roms(dst_varz[::-1,:,:], dst_grdz, \ dst_grd, Cpos=Cpos, spval=spval, flood=False) else: dst_var = dst_varz # write data in destination file - print 'write data in destination file\n' + print('write data in destination file\n') nc.variables['ocean_time'][0] = time nc.variables[dst_varname][0] = dst_var diff --git a/examples/cobalt-preproc/Initial_bio/remap_bio_glodap.py b/examples/cobalt-preproc/Initial_bio/remap_bio_glodap.py index 3b8ef00..bb9242f 100644 --- a/examples/cobalt-preproc/Initial_bio/remap_bio_glodap.py +++ b/examples/cobalt-preproc/Initial_bio/remap_bio_glodap.py @@ -35,7 +35,7 @@ def remap_bio_glodap(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir= # create clim file dst_file = tracer + '.nc' dst_file = dst_dir + dst_grd.name + '_ic_bio_' + dst_file - print 'Creating clim file', dst_file + print('Creating clim file', dst_file) if os.path.exists(dst_file) is True: os.remove(dst_file) pyroms_toolbox.nc_create_roms_file(dst_file, dst_grd, nctime) @@ -100,7 +100,7 @@ def remap_bio_glodap(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir= # create variable in file - print 'Creating variable', dst_varname + print('Creating variable', dst_varname) nc.createVariable(dst_varname, 'f8', dimensions, fill_value=spval2) nc.variables[dst_varname].long_name = long_name nc.variables[dst_varname].units = units @@ -109,24 +109,24 @@ def remap_bio_glodap(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir= # remapping - print 'remapping', dst_varname, 'from', src_grd.name, \ - 'to', dst_grd.name + print('remapping', dst_varname, 'from', src_grd.name, \ + 'to', dst_grd.name) if ndim == 3: # flood the grid - print 'flood the grid' + print('flood the grid') src_varz = pyroms_toolbox.BGrid_GFDL.flood(src_var, src_grd, Bpos=Bpos, spval=spval, \ dmax=dmax, cdepth=cdepth, kk=kk) else: src_varz = src_var # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_varz = pyroms.remapping.remap(src_varz, wts_file, spval=spval) if ndim == 3: # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_var = pyroms.remapping.z2roms(dst_varz[::-1,:,:], dst_grdz, \ dst_grd, Cpos=Cpos, spval=spval, flood=False) else: @@ -139,7 +139,7 @@ def remap_bio_glodap(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir= dst_var[kz,:,:] = tmp.copy() # write data in destination file - print 'write data in destination file\n' + print('write data in destination file\n') nc.variables['ocean_time'][0] = time nc.variables[dst_varname][0] = dst_var diff --git a/examples/cobalt-preproc/Initial_bio/remap_bio_woa.py b/examples/cobalt-preproc/Initial_bio/remap_bio_woa.py index 08c4173..5744c66 100644 --- a/examples/cobalt-preproc/Initial_bio/remap_bio_woa.py +++ b/examples/cobalt-preproc/Initial_bio/remap_bio_woa.py @@ -17,7 +17,7 @@ class nctime(object): pass def remap_bio_woa(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./'): - + # NWGOA3 grid sub-sample xrange=src_grd.xrange; yrange=src_grd.yrange @@ -38,7 +38,7 @@ def remap_bio_woa(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./ # create clim file dst_file = tracer + '.nc' dst_file = dst_dir + dst_grd.name + '_ic_bio_' + dst_file - print 'Creating clim file', dst_file + print('Creating clim file', dst_file) if os.path.exists(dst_file) is True: os.remove(dst_file) pyroms_toolbox.nc_create_roms_file(dst_file, dst_grd, nctime) @@ -47,15 +47,11 @@ def remap_bio_woa(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./ nc = netCDF.Dataset(dst_file, 'a', format='NETCDF3_64BIT') #load var - cdf = netCDF.Dataset(src_file) + cdf = netCDF.Dataset(src_file) src_var = cdf.variables[src_varname] tmp = cdf.variables['time'][nframe] - #if len(tmp) > 1: - # print 'error : multiple frames in input file' ; exit() - #else: - # time = tmp[0] # to be in sync with physics, add +0.5 day #time = time + 0.5 @@ -72,9 +68,9 @@ def remap_bio_woa(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./ # NWGOA3 grid sub-sample if ndim == 3: - src_var = src_var[0,:, yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] + src_var = src_var[nframe,:, yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] elif ndim == 2: - src_var = src_var[0,yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] + src_var = src_var[nframe,yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] if tracer == 'no3': @@ -108,7 +104,7 @@ def remap_bio_woa(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./ # create variable in file - print 'Creating variable', dst_varname + print('Creating variable', dst_varname) nc.createVariable(dst_varname, 'f8', dimensions, fill_value=spval2) nc.variables[dst_varname].long_name = long_name nc.variables[dst_varname].units = units @@ -117,24 +113,24 @@ def remap_bio_woa(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./ # remapping - print 'remapping', dst_varname, 'from', src_grd.name, \ - 'to', dst_grd.name + print('remapping', dst_varname, 'from', src_grd.name, \ + 'to', dst_grd.name) if ndim == 3: # flood the grid - print 'flood the grid' + print('flood the grid') src_varz = pyroms_toolbox.BGrid_GFDL.flood(src_var, src_grd, Bpos=Bpos, spval=spval, \ dmax=dmax, cdepth=cdepth, kk=kk) else: src_varz = src_var # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_varz = pyroms.remapping.remap(src_varz, wts_file, spval=spval) if ndim == 3: # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_var = pyroms.remapping.z2roms(dst_varz[::-1,:,:], dst_grdz, \ dst_grd, Cpos=Cpos, spval=spval, flood=False) else: @@ -143,11 +139,11 @@ def remap_bio_woa(argdict, src_grd, dst_grd, dmax=0, cdepth=0, kk=0, dst_dir='./ if ndim == 3: for kz in np.arange(dst_grd.vgrid.N): tmp = dst_var[kz,:,:].copy() - tmp[np.where(dst_grd.hgrid.mask_rho == 0)] = spval2 + tmp[np.where(dst_grd.hgrid.mask_rho == 0)] = spval2 dst_var[kz,:,:] = tmp.copy() # write data in destination file - print 'write data in destination file\n' + print('write data in destination file\n') nc.variables['ocean_time'][0] = time nc.variables[dst_varname][0] = dst_var diff --git a/examples/cobalt-preproc/README b/examples/cobalt-preproc/README new file mode 100644 index 0000000..418b44a --- /dev/null +++ b/examples/cobalt-preproc/README @@ -0,0 +1,10 @@ +Most of these are suitable for a mid-latitude domain with xrange, +yrange. The Arctic had some issues with the tripole source grid, so I +hacked in a tripole option, but there are still remnant pole problems, +needing the fix_pole.py routine. It only matters for the initial +file - the Arctic directory is a copy of Initial_bio. + +The climatology we were given did not contain the coastal diatom +fields (medium phyto). I was told that to create appropriate files, +split the large phyto into large and medium phyto. The scripts in +the diatoms directory do just that. diff --git a/examples/cobalt-preproc/Runoff_bio/make_runoff_bio_file.py b/examples/cobalt-preproc/Runoff_bio/make_runoff_bio_file.py index 810027b..5ada844 100644 --- a/examples/cobalt-preproc/Runoff_bio/make_runoff_bio_file.py +++ b/examples/cobalt-preproc/Runoff_bio/make_runoff_bio_file.py @@ -1,7 +1,7 @@ import subprocess import os import sys -import commands +import subprocess import numpy as np from datetime import * @@ -29,53 +29,53 @@ tracer_longname = [] tracer_units = [] for kt in list_tracer: - tracer_longname.append(kt.lower() + ' river source') - tracer_units.append('mol.m-2.s-1') + tracer_longname.append(kt.lower() + ' river source') + tracer_units.append('mol.m-2.s-1') for ktr in np.arange(len(list_tracer)): - dst_varname = 'river_' + list_tracer[ktr].lower() - # create output file - dst_file = dst_dir + grd.name + '_' + dst_varname + '_runoff_bio_NEWS.nc' - fid_o = nc.Dataset(dst_file, 'w', format='NETCDF3_64BIT') - fid_o.Description = 'ROMS file' - fid_o.Author = 'pyroms_toolbox.nc_create_roms_file' - fid_o.Created = datetime.now().strftime("%Y-%m-%d %H:%M:%S") - fid_o.title = 'ROMS file' + dst_varname = 'river_' + list_tracer[ktr].lower() + # create output file + dst_file = dst_dir + grd.name + '_' + dst_varname + '_runoff_bio_NEWS.nc' + fid_o = nc.Dataset(dst_file, 'w', format='NETCDF3_64BIT') + fid_o.Description = 'ROMS file' + fid_o.Author = 'pyroms_toolbox.nc_create_roms_file' + fid_o.Created = datetime.now().strftime("%Y-%m-%d %H:%M:%S") + fid_o.title = 'ROMS file' + + fid_o.createDimension('xi_rho', np.size(grd.hgrid.mask_rho,1)) + fid_o.createDimension('xi_u', np.size(grd.hgrid.mask_u,1)) + fid_o.createDimension('xi_v', np.size(grd.hgrid.mask_v,1)) + fid_o.createDimension('xi_psi', np.size(grd.hgrid.mask_psi,1)) + fid_o.createDimension('eta_rho', np.size(grd.hgrid.mask_rho,0)) + fid_o.createDimension('eta_u', np.size(grd.hgrid.mask_u,0)) + fid_o.createDimension('eta_v', np.size(grd.hgrid.mask_v,0)) + fid_o.createDimension('eta_psi', np.size(grd.hgrid.mask_psi,0)) + fid_o.createDimension('s_rho', grd.vgrid.N) + fid_o.createDimension('s_w', grd.vgrid.Np) + fid_o.createDimension('runoff_time', None) + fid_o.createVariable('runoff_time', 'f8', ('runoff_time')) + fid_o.variables['runoff_time'].long_name = 'runoff_time' + fid_o.variables['runoff_time'].units = 'days since 1900-01-01 00:00:00' + fid_o.variables['runoff_time'][:] = nctime - fid_o.createDimension('xi_rho', np.size(grd.hgrid.mask_rho,1)) - fid_o.createDimension('xi_u', np.size(grd.hgrid.mask_u,1)) - fid_o.createDimension('xi_v', np.size(grd.hgrid.mask_v,1)) - fid_o.createDimension('xi_psi', np.size(grd.hgrid.mask_psi,1)) - fid_o.createDimension('eta_rho', np.size(grd.hgrid.mask_rho,0)) - fid_o.createDimension('eta_u', np.size(grd.hgrid.mask_u,0)) - fid_o.createDimension('eta_v', np.size(grd.hgrid.mask_v,0)) - fid_o.createDimension('eta_psi', np.size(grd.hgrid.mask_psi,0)) - fid_o.createDimension('s_rho', grd.vgrid.N) - fid_o.createDimension('s_w', grd.vgrid.Np) - fid_o.createDimension('runoff_time', None) - fid_o.createVariable('runoff_time', 'f8', ('runoff_time')) - fid_o.variables['runoff_time'].long_name = 'runoff_time' - fid_o.variables['runoff_time'].units = 'days since 1900-01-01 00:00:00' - fid_o.variables['runoff_time'][:] = nctime + spval = 1.0e+15 + dimensions = ('runoff_time', 'eta_rho', 'xi_rho') + long_name = tracer_longname[ktr] + field = dst_varname + ', scalar, series' + units = tracer_units[ktr] + fid_o.createVariable(dst_varname, 'f8', dimensions, fill_value=spval) + fid_o.variables[dst_varname].long_name = long_name + fid_o.variables[dst_varname].units = units + fid_o.variables[dst_varname].field = field + conc = fid_n.variables[list_tracer[ktr]][:] + for kt in np.arange(nt): + print('working on timestep', kt) + runoff = fid_r.variables['Runoff'][kt,:,:] + river_input = conc * runoff / 1000. + fid_o.variables[dst_varname][kt,:,:] = river_input - spval = 1.0e+15 - dimensions = ('runoff_time', 'eta_rho', 'xi_rho') - long_name = tracer_longname[ktr] - field = dst_varname + ', scalar, series' - units = tracer_units[ktr] - fid_o.createVariable(dst_varname, 'f8', dimensions, fill_value=spval) - fid_o.variables[dst_varname].long_name = long_name - fid_o.variables[dst_varname].units = units - fid_o.variables[dst_varname].field = field - conc = fid_n.variables[list_tracer[ktr]][:] - for kt in np.arange(nt): - print 'working on timestep', kt - runoff = fid_r.variables['Runoff'][kt,:,:] - river_input = conc * runoff / 1000. - fid_o.variables[dst_varname][kt,:,:] = river_input - - fid_o.close() + fid_o.close() fid_r.close() fid_n.close() diff --git a/examples/cobalt-preproc/diatoms/split_bdry_diatom.py b/examples/cobalt-preproc/diatoms/split_bdry_diatom.py new file mode 100644 index 0000000..56c96b5 --- /dev/null +++ b/examples/cobalt-preproc/diatoms/split_bdry_diatom.py @@ -0,0 +1,147 @@ +import numpy as np +import netCDF4 +import sys + +# This program splits the large phytoplankton into large and medium. +# True for nitrogen, iron, and silicon. +# Copy the original file before running this, then operate on the copy. +# Could probably do this with ncap2 instead. +# +ncfile = sys.argv[1] +nc = netCDF4.Dataset(ncfile, 'a', format='NETCDF3_CLASSIC') +spval = -10000000000. + +nlg = nc.variables['nlg_north'][:] +nlg *= 0.5 +nc.variables['nlg_north'][:] = nlg + +nc.createVariable('nmd_north', 'f8', ('ocean_time', 's_rho', 'xi_rho'), fill_value=spval) +nc.variables['nmd_north'].long_name = 'Medium Phytoplankton Nitrogen north boundary condition' +nc.variables['nmd_north'].units = 'mol/kg' +nc.variables['nmd_north'].time = 'ocean_time' +nc.variables['nmd_north'].field = 'nmd_north, scalar, series' +nc.variables['nmd_north'][:] = nlg + +felg = nc.variables['felg_north'][:] +felg *= 0.5 +nc.variables['felg_north'][:] = felg + +nc.createVariable('femd_north', 'f8', ('ocean_time', 's_rho', 'xi_rho'), fill_value=spval) +nc.variables['femd_north'].long_name = 'Medium Phytoplankton Iron north boundary condition' +nc.variables['femd_north'].units = 'mol/kg' +nc.variables['femd_north'].time = 'ocean_time' +nc.variables['femd_north'].field = 'femd_north, scalar, series' +nc.variables['femd_north'][:] = felg + +silg = nc.variables['silg_north'][:] +silg *= 0.5 +nc.variables['silg_north'][:] = silg + +nc.createVariable('simd_north', 'f8', ('ocean_time', 's_rho', 'xi_rho'), fill_value=spval) +nc.variables['simd_north'].long_name = 'Medium Phytoplankton Silicon north boundary condition' +nc.variables['simd_north'].units = 'mol/kg' +nc.variables['simd_north'].time = 'ocean_time' +nc.variables['simd_north'].field = 'simd_north, scalar, series' +nc.variables['simd_north'][:] = silg + + +nlg = nc.variables['nlg_south'][:] +nlg *= 0.5 +nc.variables['nlg_south'][:] = nlg + +nc.createVariable('nmd_south', 'f8', ('ocean_time', 's_rho', 'xi_rho'), fill_value=spval) +nc.variables['nmd_south'].long_name = 'Medium Phytoplankton Nitrogen south boundary condition' +nc.variables['nmd_south'].units = 'mol/kg' +nc.variables['nmd_south'].time = 'ocean_time' +nc.variables['nmd_south'].field = 'nmd_south, scalar, series' +nc.variables['nmd_south'][:] = nlg + +felg = nc.variables['felg_south'][:] +felg *= 0.5 +nc.variables['felg_south'][:] = felg + +nc.createVariable('femd_south', 'f8', ('ocean_time', 's_rho', 'xi_rho'), fill_value=spval) +nc.variables['femd_south'].long_name = 'Medium Phytoplankton Iron south boundary condition' +nc.variables['femd_south'].units = 'mol/kg' +nc.variables['femd_south'].time = 'ocean_time' +nc.variables['femd_south'].field = 'femd_south, scalar, series' +nc.variables['femd_south'][:] = felg + +silg = nc.variables['silg_south'][:] +silg *= 0.5 +nc.variables['silg_south'][:] = silg + +nc.createVariable('simd_south', 'f8', ('ocean_time', 's_rho', 'xi_rho'), fill_value=spval) +nc.variables['simd_south'].long_name = 'Medium Phytoplankton Silicon south boundary condition' +nc.variables['simd_south'].units = 'mol/kg' +nc.variables['simd_south'].time = 'ocean_time' +nc.variables['simd_south'].field = 'simd_south, scalar, series' +nc.variables['simd_south'][:] = silg + +nlg = nc.variables['nlg_west'][:] +nlg *= 0.5 +nc.variables['nlg_west'][:] = nlg + +nc.createVariable('nmd_west', 'f8', ('ocean_time', 's_rho', 'eta_rho'), fill_value=spval) +nc.variables['nmd_west'].long_name = 'Medium Phytoplankton Nitrogen west boundary condition' +nc.variables['nmd_west'].units = 'mol/kg' +nc.variables['nmd_west'].time = 'ocean_time' +nc.variables['nmd_west'].field = 'nmd_west, scalar, series' +nc.variables['nmd_west'][:] = nlg + +felg = nc.variables['felg_west'][:] +felg *= 0.5 +nc.variables['felg_west'][:] = felg + +nc.createVariable('femd_west', 'f8', ('ocean_time', 's_rho', 'eta_rho'), fill_value=spval) +nc.variables['femd_west'].long_name = 'Medium Phytoplankton Iron west boundary condition' +nc.variables['femd_west'].units = 'mol/kg' +nc.variables['femd_west'].time = 'ocean_time' +nc.variables['femd_west'].field = 'femd_west, scalar, series' +nc.variables['femd_west'][:] = felg + +silg = nc.variables['silg_west'][:] +silg *= 0.5 +nc.variables['silg_west'][:] = silg + +nc.createVariable('simd_west', 'f8', ('ocean_time', 's_rho', 'eta_rho'), fill_value=spval) +nc.variables['simd_west'].long_name = 'Medium Phytoplankton Silicon west boundary condition' +nc.variables['simd_west'].units = 'mol/kg' +nc.variables['simd_west'].time = 'ocean_time' +nc.variables['simd_west'].field = 'simd_west, scalar, series' +nc.variables['simd_west'][:] = silg + +nlg = nc.variables['nlg_east'][:] +nlg *= 0.5 +nc.variables['nlg_east'][:] = nlg + +nc.createVariable('nmd_east', 'f8', ('ocean_time', 's_rho', 'eta_rho'), fill_value=spval) +nc.variables['nmd_east'].long_name = 'Medium Phytoplankton Nitrogen east boundary condition' +nc.variables['nmd_east'].units = 'mol/kg' +nc.variables['nmd_east'].time = 'ocean_time' +nc.variables['nmd_east'].field = 'nmd_east, scalar, series' +nc.variables['nmd_east'][:] = nlg + +felg = nc.variables['felg_east'][:] +felg *= 0.5 +nc.variables['felg_east'][:] = felg + +nc.createVariable('femd_east', 'f8', ('ocean_time', 's_rho', 'eta_rho'), fill_value=spval) +nc.variables['femd_east'].long_name = 'Medium Phytoplankton Iron east boundary condition' +nc.variables['femd_east'].units = 'mol/kg' +nc.variables['femd_east'].time = 'ocean_time' +nc.variables['femd_east'].field = 'femd_east, scalar, series' +nc.variables['femd_east'][:] = felg + +silg = nc.variables['silg_east'][:] +silg *= 0.5 +nc.variables['silg_east'][:] = silg + +nc.createVariable('simd_east', 'f8', ('ocean_time', 's_rho', 'eta_rho'), fill_value=spval) +nc.variables['simd_east'].long_name = 'Medium Phytoplankton Silicon east boundary condition' +nc.variables['simd_east'].units = 'mol/kg' +nc.variables['simd_east'].time = 'ocean_time' +nc.variables['simd_east'].field = 'simd_east, scalar, series' +nc.variables['simd_east'][:] = silg + +nc.close() diff --git a/examples/cobalt-preproc/diatoms/split_diatom.py b/examples/cobalt-preproc/diatoms/split_diatom.py new file mode 100644 index 0000000..a1fd080 --- /dev/null +++ b/examples/cobalt-preproc/diatoms/split_diatom.py @@ -0,0 +1,73 @@ +import numpy as np +import netCDF4 +import sys + +# This program splits the large phytoplankton into large and medium. +# True for nitrogen, iron, and silicon. +# Copy the original file before running this, then operate on the copy. +# Could probably do this with ncap2 instead. +# +ncfile = sys.argv[1] +nc = netCDF4.Dataset(ncfile, 'a', format='NETCDF3_CLASSIC') +spval = 1.e+37 + +nlg = nc.variables['nlg'][:] +nlg *= 0.5 +nc.variables['nlg'][:] = nlg + +nc.createVariable('nmd', 'f8', ('ocean_time', 's_rho', 'eta_rho', 'xi_rho'), fill_value=spval) +#nc.createVariable('nmd', 'f8', ('ocean_time', 'two', 's_rho', 'eta_rho', 'xi_rho'), fill_value=spval) +nc.variables['nmd'].long_name = 'Medium Phytoplankton Nitrogen' +nc.variables['nmd'].units = 'mol/kg' +nc.variables['nmd'].time = 'ocean_time' +nc.variables['nmd'].field = 'nmd, scalar, series' +nc.variables['nmd'].grid = 'grid' +nc.variables['nmd'].location = 'face' +nc.variables['nmd'].coordinates = 'lon_rho lat_rho s_rho ocean_time' +nc.variables['nmd'][:] = nlg + +felg = nc.variables['felg'][:] +felg *= 0.5 +nc.variables['felg'][:] = felg + +nc.createVariable('femd', 'f8', ('ocean_time', 's_rho', 'eta_rho', 'xi_rho'), fill_value=spval) +#nc.createVariable('femd', 'f8', ('ocean_time', 'two', 's_rho', 'eta_rho', 'xi_rho'), fill_value=spval) +nc.variables['femd'].long_name = 'Medium Phytoplankton Iron' +nc.variables['femd'].units = 'mol/kg' +nc.variables['femd'].time = 'ocean_time' +nc.variables['femd'].field = 'femd, scalar, series' +nc.variables['femd'].grid = 'grid' +nc.variables['femd'].location = 'face' +nc.variables['femd'].coordinates = 'lon_rho lat_rho s_rho ocean_time' +nc.variables['femd'][:] = felg + +silg = nc.variables['silg'][:] +silg *= 0.5 +nc.variables['silg'][:] = silg + +nc.createVariable('simd', 'f8', ('ocean_time', 's_rho', 'eta_rho', 'xi_rho'), fill_value=spval) +#nc.createVariable('simd', 'f8', ('ocean_time', 'two', 's_rho', 'eta_rho', 'xi_rho'), fill_value=spval) +nc.variables['simd'].long_name = 'Medium Phytoplankton Silicon' +nc.variables['simd'].units = 'mol/kg' +nc.variables['simd'].time = 'ocean_time' +nc.variables['simd'].field = 'simd, scalar, series' +nc.variables['simd'].grid = 'grid' +nc.variables['simd'].location = 'face' +nc.variables['simd'].coordinates = 'lon_rho lat_rho s_rho ocean_time' +nc.variables['simd'][:] = silg + +mu_mem_lg = nc.variables['mu_mem_lg'][:] +mu_mem_lg *= 0.5 +nc.variables['mu_mem_lg'][:] = mu_mem_lg + +nc.createVariable('mu_mem_md', 'f8', ('two', 's_rho', 'eta_rho', 'xi_rho'), fill_value=spval) +nc.variables['mu_mem_md'].long_name = 'Medium Phytoplankton Silicon' +nc.variables['mu_mem_md'].units = 'mol/kg' +nc.variables['mu_mem_md'].time = 'ocean_time' +nc.variables['mu_mem_md'].field = 'mu_mem_md, scalar, series' +nc.variables['mu_mem_md'].grid = 'grid' +nc.variables['mu_mem_md'].location = 'face' +nc.variables['mu_mem_md'].coordinates = 'lon_rho lat_rho s_rho ocean_time' +nc.variables['mu_mem_md'][:] = mu_mem_lg + +nc.close() diff --git a/examples/cobalt-preproc/diatoms/split_restart_diatom.py b/examples/cobalt-preproc/diatoms/split_restart_diatom.py new file mode 100644 index 0000000..0874b02 --- /dev/null +++ b/examples/cobalt-preproc/diatoms/split_restart_diatom.py @@ -0,0 +1,73 @@ +import numpy as np +import netCDF4 +import sys + +# This program splits the large phytoplankton into large and medium. +# True for nitrogen, iron, and silicon. +# Copy the original file before running this, then operate on the copy. +# Could probably do this with ncap2 instead. +# +ncfile = sys.argv[1] +nc = netCDF4.Dataset(ncfile, 'a', format='NETCDF3_CLASSIC') +spval = 1.e+37 + +nlg = nc.variables['nlg'][:] +nlg *= 0.5 +nc.variables['nlg'][:] = nlg + +#nc.createVariable('nmd', 'f8', ('ocean_time', 'two', 's_rho', 'eta_rho', 'xi_rho'), fill_value=spval) +nc.createVariable('nmd', 'f8', ('ocean_time', 's_rho', 'eta_rho', 'xi_rho'), fill_value=spval) +nc.variables['nmd'].long_name = 'Medium Phytoplankton Nitrogen' +nc.variables['nmd'].units = 'mol/kg' +nc.variables['nmd'].time = 'ocean_time' +nc.variables['nmd'].field = 'nmd, scalar, series' +nc.variables['nmd'].grid = 'grid' +nc.variables['nmd'].location = 'face' +nc.variables['nmd'].coordinates = 'lon_rho lat_rho s_rho ocean_time' +nc.variables['nmd'][:] = nlg + +felg = nc.variables['felg'][:] +felg *= 0.5 +nc.variables['felg'][:] = felg + +#nc.createVariable('femd', 'f8', ('ocean_time', 'two', 's_rho', 'eta_rho', 'xi_rho'), fill_value=spval) +nc.createVariable('femd', 'f8', ('ocean_time', 's_rho', 'eta_rho', 'xi_rho'), fill_value=spval) +nc.variables['femd'].long_name = 'Medium Phytoplankton Iron' +nc.variables['femd'].units = 'mol/kg' +nc.variables['femd'].time = 'ocean_time' +nc.variables['femd'].field = 'femd, scalar, series' +nc.variables['femd'].grid = 'grid' +nc.variables['femd'].location = 'face' +nc.variables['femd'].coordinates = 'lon_rho lat_rho s_rho ocean_time' +nc.variables['femd'][:] = felg + +silg = nc.variables['silg'][:] +silg *= 0.5 +nc.variables['silg'][:] = silg + +#nc.createVariable('simd', 'f8', ('ocean_time', 'two', 's_rho', 'eta_rho', 'xi_rho'), fill_value=spval) +nc.createVariable('simd', 'f8', ('ocean_time', 's_rho', 'eta_rho', 'xi_rho'), fill_value=spval) +nc.variables['simd'].long_name = 'Medium Phytoplankton Silicon' +nc.variables['simd'].units = 'mol/kg' +nc.variables['simd'].time = 'ocean_time' +nc.variables['simd'].field = 'simd, scalar, series' +nc.variables['simd'].grid = 'grid' +nc.variables['simd'].location = 'face' +nc.variables['simd'].coordinates = 'lon_rho lat_rho s_rho ocean_time' +nc.variables['simd'][:] = silg + +mu_mem_lg = nc.variables['mu_mem_lg'][:] +mu_mem_lg *= 0.5 +nc.variables['mu_mem_lg'][:] = mu_mem_lg + +nc.createVariable('mu_mem_md', 'f8', ('two', 's_rho', 'eta_rho', 'xi_rho'), fill_value=spval) +nc.variables['mu_mem_md'].long_name = 'Medium Phytoplankton Silicon' +nc.variables['mu_mem_md'].units = 'mol/kg' +nc.variables['mu_mem_md'].time = 'ocean_time' +nc.variables['mu_mem_md'].field = 'mu_mem_md, scalar, series' +nc.variables['mu_mem_md'].grid = 'grid' +nc.variables['mu_mem_md'].location = 'face' +nc.variables['mu_mem_md'].coordinates = 'lon_rho lat_rho s_rho ocean_time' +nc.variables['mu_mem_md'][:] = mu_mem_lg + +nc.close() diff --git a/examples/cobalt-preproc/iron_coastal/create_zero_iron_coastal_file.py b/examples/cobalt-preproc/iron_coastal/create_zero_iron_coastal_file.py index 14fe0c8..8a3f333 100644 --- a/examples/cobalt-preproc/iron_coastal/create_zero_iron_coastal_file.py +++ b/examples/cobalt-preproc/iron_coastal/create_zero_iron_coastal_file.py @@ -8,114 +8,114 @@ class iron_coastal(): - def __init__(self,domain): - self.grd = pyroms.grid.get_ROMS_grid(domain) - self.fileout = 'iron_nofecoast_' + domain + '.nc' - self.ny, self.nx = self.grd.hgrid.lon_rho.shape - self.spval = 1.0e+15 - return None - - def __call__(self,mom_grid_file): - self.maskcoast = self.create_mask_coast_MOM(mom_grid_file) - if self.grd.name == 'NWGOA3': - self.ana_iron_ccs1() - else: - print 'domain not supported' ; pass - self.write_nc_file(self) - return None - - def create_mask_coast_MOM(self,mom_grid_file): - fidmask = nc.Dataset(mom_grid_file,'r') - kmt = fidmask.variables['kmt'][:].squeeze() - lon_mom = fidmask.variables['geolon_t'][:].squeeze() - lat_mom = fidmask.variables['geolat_t'][:].squeeze() - fidmask.close() - - if self.grd.name == 'NWGOA3': - lon_mom = lon_mom + 360. - - mask = np.zeros(kmt.shape) - mask[np.where(kmt.mask)] = 1 - #plt.figure() ; plt.pcolormesh(mask) ; plt.colorbar() - - mask_reduced = morph.binary_erosion(mask, structure=None, iterations=1, mask=None, output=None, border_value=0, origin=0, brute_force=False) - mask_extended = morph.binary_dilation(mask, structure=None, iterations=1, mask=None, output=None, border_value=0, origin=0, brute_force=False) - mask_coast = mask_extended - mask_reduced - #plt.figure() ; plt.pcolormesh(mask_coast) ; plt.colorbar() - - # interpolate mask to target grid - nymom, nxmom = lon_mom.shape - - sizetot_ini = nymom * nxmom - position_ini = np.zeros((sizetot_ini ,2)) - - a = lon_mom.flat - b = lat_mom.flat - - for k in np.arange(sizetot_ini): - position_ini[k,0] = a[k] - position_ini[k,1] = b[k] - - sizetot_final = self.grd.hgrid.lon_rho.shape[0]*self.grd.hgrid.lon_rho.shape[1] - position_final = np.zeros((sizetot_final ,2)) - - c = self.grd.hgrid.lon_rho.flat - d = self.grd.hgrid.lat_rho.flat - - for k in np.arange(sizetot_final): - position_final[k,0] = c[k] - position_final[k,1] = d[k] - - tmp = scipyint.griddata(position_ini,mask_coast.flat,position_final,method='nearest') - mask_coast_interp = np.reshape(tmp,self.grd.hgrid.lon_rho.shape) - - #plt.figure() ; plt.pcolormesh(mask_coast_interp) ; plt.colorbar() ; plt.show() - return mask_coast_interp - - def ana_iron_ccs1(self): - h = self.grd.vgrid.h - one_fe_coast = h.copy() - # set to constant value everywhere - one_fe_coast = 0.0e-11 # mol Fe m kg-1 s-1 - # mask the array - one_fe_coast = one_fe_coast * self.maskcoast * self.grd.hgrid.mask_rho - one_fe_coast[np.where( self.grd.hgrid.mask_rho == 0)] = self.spval - #plt.figure() ; plt.pcolormesh(one_fe_coast) ; plt.colorbar() ; plt.show() - # - self.fe_coast = np.zeros((12,self.ny,self.nx)) - for kt in np.arange(12): - self.fe_coast[kt,:,:] = one_fe_coast[:,:] - return None - - def write_nc_file(self,fileout): - fid = nc.Dataset(self.fileout, 'w', format='NETCDF3_CLASSIC') - fid.description = 'Iron coastal source file (raphael@esm.rutgers.edu)' - # dimensions - fid.createDimension('lat', self.ny) - fid.createDimension('lon', self.nx) - fid.createDimension('fecoast_time', None) - # variables - latitudes = fid.createVariable('lat', 'f4', ('lat','lon',)) - longitudes = fid.createVariable('lon', 'f4', ('lat','lon',)) - times = fid.createVariable('fecoast_time', 'f4', ('fecoast_time',)) - times.units = "days since 1900-01-01 00:00" - times.cycle_length = 365.25 - - variable = fid.createVariable('fecoast', 'f8', ('fecoast_time','lat','lon',),fill_value=self.spval) - variable.coordinates="lon lat fecoast_time" - variable.missing_value = 1e+15 - variable.time ="fecoast_time" - variable.units = "mol Fe m kg-1 s-1" - variable.long_name = "iron coastal source" - - # data - latitudes[:,:] = self.grd.hgrid.lat_rho - longitudes[:,:] = self.grd.hgrid.lon_rho - times[:] = [15.5, 45, 74.5, 105, 135.5, 166, 196.5, 227.5, 258, 288.5, 319, 349.5] - variable[:,:,:] = self.fe_coast - # close - fid.close() - return None + def __init__(self,domain): + self.grd = pyroms.grid.get_ROMS_grid(domain) + self.fileout = 'iron_nofecoast_' + domain + '.nc' + self.ny, self.nx = self.grd.hgrid.lon_rho.shape + self.spval = 1.0e+15 + return None + + def __call__(self,mom_grid_file): + self.maskcoast = self.create_mask_coast_MOM(mom_grid_file) + if self.grd.name == 'NWGOA3': + self.ana_iron_ccs1() + else: + print('domain not supported') ; pass + self.write_nc_file(self) + return None + + def create_mask_coast_MOM(self,mom_grid_file): + fidmask = nc.Dataset(mom_grid_file,'r') + kmt = fidmask.variables['kmt'][:].squeeze() + lon_mom = fidmask.variables['geolon_t'][:].squeeze() + lat_mom = fidmask.variables['geolat_t'][:].squeeze() + fidmask.close() + + if self.grd.name == 'NWGOA3': + lon_mom = lon_mom + 360. + + mask = np.zeros(kmt.shape) + mask[np.where(kmt.mask)] = 1 + #plt.figure() ; plt.pcolormesh(mask) ; plt.colorbar() + + mask_reduced = morph.binary_erosion(mask, structure=None, iterations=1, mask=None, output=None, border_value=0, origin=0, brute_force=False) + mask_extended = morph.binary_dilation(mask, structure=None, iterations=1, mask=None, output=None, border_value=0, origin=0, brute_force=False) + mask_coast = mask_extended - mask_reduced + #plt.figure() ; plt.pcolormesh(mask_coast) ; plt.colorbar() + + # interpolate mask to target grid + nymom, nxmom = lon_mom.shape + + sizetot_ini = nymom * nxmom + position_ini = np.zeros((sizetot_ini ,2)) + + a = lon_mom.flat + b = lat_mom.flat + + for k in np.arange(sizetot_ini): + position_ini[k,0] = a[k] + position_ini[k,1] = b[k] + + sizetot_final = self.grd.hgrid.lon_rho.shape[0]*self.grd.hgrid.lon_rho.shape[1] + position_final = np.zeros((sizetot_final ,2)) + + c = self.grd.hgrid.lon_rho.flat + d = self.grd.hgrid.lat_rho.flat + + for k in np.arange(sizetot_final): + position_final[k,0] = c[k] + position_final[k,1] = d[k] + + tmp = scipyint.griddata(position_ini,mask_coast.flat,position_final,method='nearest') + mask_coast_interp = np.reshape(tmp,self.grd.hgrid.lon_rho.shape) + + #plt.figure() ; plt.pcolormesh(mask_coast_interp) ; plt.colorbar() ; plt.show() + return mask_coast_interp + + def ana_iron_ccs1(self): + h = self.grd.vgrid.h + one_fe_coast = h.copy() + # set to constant value everywhere + one_fe_coast = 0.0e-11 # mol Fe m kg-1 s-1 + # mask the array + one_fe_coast = one_fe_coast * self.maskcoast * self.grd.hgrid.mask_rho + one_fe_coast[np.where( self.grd.hgrid.mask_rho == 0)] = self.spval + #plt.figure() ; plt.pcolormesh(one_fe_coast) ; plt.colorbar() ; plt.show() + # + self.fe_coast = np.zeros((12,self.ny,self.nx)) + for kt in np.arange(12): + self.fe_coast[kt,:,:] = one_fe_coast[:,:] + return None + + def write_nc_file(self,fileout): + fid = nc.Dataset(self.fileout, 'w', format='NETCDF3_CLASSIC') + fid.description = 'Iron coastal source file (raphael@esm.rutgers.edu)' + # dimensions + fid.createDimension('lat', self.ny) + fid.createDimension('lon', self.nx) + fid.createDimension('fecoast_time', None) + # variables + latitudes = fid.createVariable('lat', 'f4', ('lat','lon',)) + longitudes = fid.createVariable('lon', 'f4', ('lat','lon',)) + times = fid.createVariable('fecoast_time', 'f4', ('fecoast_time',)) + times.units = "days since 1900-01-01 00:00" + times.cycle_length = 365.25 + + variable = fid.createVariable('fecoast', 'f8', ('fecoast_time','lat','lon',),fill_value=self.spval) + variable.coordinates="lon lat fecoast_time" + variable.missing_value = 1e+15 + variable.time ="fecoast_time" + variable.units = "mol Fe m kg-1 s-1" + variable.long_name = "iron coastal source" + + # data + latitudes[:,:] = self.grd.hgrid.lat_rho + longitudes[:,:] = self.grd.hgrid.lon_rho + times[:] = [15.5, 45, 74.5, 105, 135.5, 166, 196.5, 227.5, 258, 288.5, 319, 349.5] + variable[:,:,:] = self.fe_coast + # close + fid.close() + return None #------------------------------------------------------------------------------- # iron coastal source for NWGOA3 diff --git a/examples/cobalt-preproc/iron_sediment/create_iron_sediment_file.py b/examples/cobalt-preproc/iron_sediment/create_iron_sediment_file.py index 0e141c5..c3cf0a2 100644 --- a/examples/cobalt-preproc/iron_sediment/create_iron_sediment_file.py +++ b/examples/cobalt-preproc/iron_sediment/create_iron_sediment_file.py @@ -4,71 +4,69 @@ class iron_sediment(): - def __init__(self,domain): - self.grd = pyroms.grid.get_ROMS_grid(domain) - self.fileout = 'iron_sediment_' + domain + '.nc' - self.ny, self.nx = self.grd.hgrid.lon_rho.shape - return None + def __init__(self,domain): + self.grd = pyroms.grid.get_ROMS_grid(domain) + self.fileout = 'iron_sediment_' + domain + '.nc' + self.ny, self.nx = self.grd.hgrid.lon_rho.shape + return None - def __call__(self): - if self.grd.name == 'NWGOA3': - self.ana_iron_ccs1() - else: - print 'domain not supported' ; pass - self.write_nc_file(self) - return None + def __call__(self): + if self.grd.name == 'NWGOA3': + self.ana_iron_ccs1() + else: + print('domain not supported') ; pass + self.write_nc_file(self) + return None - def ana_iron_ccs1(self): - h = self.grd.vgrid.h - iron_sed = h.copy() - # set to constant value everywhere - # jk moore et al., global BGC cycles, 2004 - # suggest a value of 5 micromol/m2/day for california shelf - iron_sed[:,:] = 0e-6 / 86400. # mol/m2/s -# iron_sed[:,:] = 5e-6 / 86400. # mol/m2/s - # set to zero deeper than cutoff depth - iron_sed[npy.where( h > 1100. ) ] = 0. - # mask the array - iron_sed = iron_sed * self.grd.hgrid.mask_rho - # - self.iron_flx = npy.zeros((12,self.ny,self.nx)) - print self.iron_flx.shape - for kt in npy.arange(12): - self.iron_flx[kt,:,:] = iron_sed[:,:] - return None + def ana_iron_ccs1(self): + h = self.grd.vgrid.h + iron_sed = h.copy() + # set to constant value everywhere + # jk moore et al., global BGC cycles, 2004 + # suggest a value of 5 micromol/m2/day for california shelf + iron_sed[:,:] = 0e-6 / 86400. # mol/m2/s +# iron_sed[:,:] = 5e-6 / 86400. # mol/m2/s + # set to zero deeper than cutoff depth + iron_sed[npy.where( h > 1100. ) ] = 0. + # mask the array + iron_sed = iron_sed * self.grd.hgrid.mask_rho + # + self.iron_flx = npy.zeros((12,self.ny,self.nx)) + print(self.iron_flx.shape) + for kt in npy.arange(12): + self.iron_flx[kt,:,:] = iron_sed[:,:] + return None - def write_nc_file(self,fileout): - fid = nc.Dataset(self.fileout, 'w', format='NETCDF3_CLASSIC') - fid.description = 'Iron flux from sediment file (raphael@esm.rutgers.edu)' - # dimensions - fid.createDimension('lat', self.ny) - fid.createDimension('lon', self.nx) - fid.createDimension('ironsed_time', None) - # variables - latitudes = fid.createVariable('lat', 'f4', ('lat','lon',)) - longitudes = fid.createVariable('lon', 'f4', ('lat','lon',)) - times = fid.createVariable('ironsed_time', 'f4', ('ironsed_time',)) - times.units = "days since 1900-01-01 00:00" - times.cycle_length = 365.25 - - variable = fid.createVariable('ironsed', 'f8', ('ironsed_time','lat','lon',)) - variable.coordinates="lon lat ironsed" - variable.missing_value = 1e+15 - variable.time ="ironsed_time" - variable.units = "mol/m2/s" - variable.long_name = "iron flux from sediments" - - # data - latitudes[:,:] = self.grd.hgrid.lat_rho - longitudes[:,:] = self.grd.hgrid.lon_rho - times[:] = [15.5, 45, 74.5, 105, 135.5, 166, 196.5, 227.5, 258, 288.5, 319, 349.5] - variable[:,:,:] = self.iron_flx - # close - fid.close() - return None + def write_nc_file(self,fileout): + fid = nc.Dataset(self.fileout, 'w', format='NETCDF3_CLASSIC') + fid.description = 'Iron flux from sediment file (raphael@esm.rutgers.edu)' + # dimensions + fid.createDimension('lat', self.ny) + fid.createDimension('lon', self.nx) + fid.createDimension('ironsed_time', None) + # variables + latitudes = fid.createVariable('lat', 'f4', ('lat','lon',)) + longitudes = fid.createVariable('lon', 'f4', ('lat','lon',)) + times = fid.createVariable('ironsed_time', 'f4', ('ironsed_time',)) + times.units = "days since 1900-01-01 00:00" + times.cycle_length = 365.25 + variable = fid.createVariable('ironsed', 'f8', ('ironsed_time','lat','lon',)) + variable.coordinates="lon lat ironsed" + variable.missing_value = 1e+15 + variable.time ="ironsed_time" + variable.units = "mol/m2/s" + variable.long_name = "iron flux from sediments" + # data + latitudes[:,:] = self.grd.hgrid.lat_rho + longitudes[:,:] = self.grd.hgrid.lon_rho + times[:] = [15.5, 45, 74.5, 105, 135.5, 166, 196.5, 227.5, 258, 288.5, 319, 349.5] + variable[:,:,:] = self.iron_flx + # close + fid.close() + return None #------------------------------------------------------------------------------- diff --git a/examples/cobalt-preproc/nudging_coef/lib_nudgcoef.py b/examples/cobalt-preproc/nudging_coef/lib_nudgcoef.py index 85f2c2e..202126e 100644 --- a/examples/cobalt-preproc/nudging_coef/lib_nudgcoef.py +++ b/examples/cobalt-preproc/nudging_coef/lib_nudgcoef.py @@ -3,181 +3,181 @@ import pyroms class nudgcoef(): - ''' A class to write the Nudging coeficient file for ROMS ''' - - def __init__(self,roms_grid): - ''' init an object of the class with the pyroms grid ID ''' - self.grd = pyroms.grid.get_ROMS_grid(roms_grid) - return None - - def __call__(self,east_dict,west_dict,north_dict,south_dict,tracer_timescales,foutname='./nudging_coef.nc'): - ''' call with following dictionaries : - 4 boundaries dict + tracer timescales - for example : - east_dict = {'nudge':True,'factor': 1,'width':50,'transition':'linear'} - west_dict = {'nudge':True,'factor': 1,'width':50,'transition':'linear'} - north_dict = {'nudge':True,'factor': 1,'width':50,'transition':'linear'} - south_dict = {'nudge':True,'factor': 1,'width':50,'transition':'linear'} - tracer_timescales = {'M2':30,'M3':30,'temp':30,'salt':30,'tracer':30} - tips: - * nudge = True if open boundary, False otherwise - * factor allows to have different timescales at each boundary - * width is in grid points - * transition shapes how timescale varies spatially - * tracer timescales are in days - ''' - self.east_dict = east_dict - self.west_dict = west_dict - self.north_dict = north_dict - self.south_dict = south_dict - self.tra_ts = tracer_timescales - self.foutname = foutname - # create 2d coef - self.nud2 = self._create_nudgcoef_2d() - # create 3d coef - self.nud3 = self._create_nudgcoef_3d() - # write to netcdf - self._write_nc_file() - return None - - def _create_nudgcoef_3d(self): - ''' expand 2d coef along the vertical ''' - # RD: later we could imagine multiplying by - # a vertical profile if needed - ny, nx = self.grd.hgrid.mask_rho.shape - nz = self.grd.vgrid.N - nudgcoef = npy.zeros((nz,ny,nx)) - for kz in npy.arange(nz): - nudgcoef[kz,:,:] = self.nud2[:,:] - return nudgcoef - - def _create_nudgcoef_2d(self): - ''' create the 2d nudging coef from dictionaries ''' - ny, nx = self.grd.hgrid.mask_rho.shape - nudgcoef_west = npy.zeros((ny,nx)) - nudgcoef_east = npy.zeros((ny,nx)) - nudgcoef_north = npy.zeros((ny,nx)) - nudgcoef_south = npy.zeros((ny,nx)) - nudgcoef = npy.zeros((ny,nx)) - mask = self.grd.hgrid.mask_rho - # west boundary - if self.west_dict['nudge'] is True: - fc = self.west_dict['factor'] - wd = self.west_dict['width'] - tr = self.west_dict['transition'] - if tr == 'linear': - for ji in npy.arange(0,wd): - nudgcoef_west[:,ji] = fc * (wd-ji) / float(wd) - elif tr == 'linear_nocoast': - for ji in npy.arange(0,wd): - nudgcoef_west[:,ji] = mask[:,0] * fc * (wd-ji) / float(wd) - else: - print 'transition not coded' ; pass - # east boundary - if self.east_dict['nudge'] is True: - fc = self.east_dict['factor'] - wd = self.east_dict['width'] - tr = self.east_dict['transition'] - if tr == 'linear': - for ji in npy.arange(nx-wd,nx): - nudgcoef_east[:,ji] = fc * (wd-nx+ji) / float(wd) - elif tr == 'linear_nocoast': - for ji in npy.arange(nx-wd,nx): - nudgcoef_east[:,ji] = mask[:,-1] * fc * (wd-nx+ji) / float(wd) - else: - print 'transition not coded' ; pass - # south boundary - if self.south_dict['nudge'] is True: - fc = self.south_dict['factor'] - wd = self.south_dict['width'] - tr = self.south_dict['transition'] - if tr == 'linear': - for jj in npy.arange(0,wd): - nudgcoef_south[jj,:] = fc * (wd-jj) / float(wd) - if tr == 'linear_nocoast': - for jj in npy.arange(0,wd): - nudgcoef_south[jj,:] = mask[0,:] * fc * (wd-jj) / float(wd) - else: - print 'transition not coded' ; pass - # north boundary - if self.north_dict['nudge'] is True: - fc = self.north_dict['factor'] - wd = self.north_dict['width'] - tr = self.north_dict['transition'] - if tr == 'linear': - for jj in npy.arange(ny-wd,ny): - nudgcoef_south[jj,:] = fc * (wd-ny+jj) / float(wd) - if tr == 'linear_nocoast': - for jj in npy.arange(ny-wd,ny): - nudgcoef_south[jj,:] = mask[-1,:] * fc * (wd-ny+jj) / float(wd) - else: - print 'transition not coded' ; pass - - - # create the total coefficient by combining all 4 fields - # the max functions is useful to make nice corners when - # individual field overlap - # maybe not the most efficient but short and readable - for jj in npy.arange(ny): - for ji in npy.arange(nx): - nudgcoef[jj,ji] = max(nudgcoef_west[jj,ji], \ - nudgcoef_east[jj,ji],nudgcoef_north[jj,ji],nudgcoef_south[jj,ji]) - return nudgcoef - - def _write_nc_file(self): - ''' writing to netcdf and multiplying by inverse timescales ''' - ncfile = self.foutname - fid = nc.Dataset(ncfile, 'w', format='NETCDF3_CLASSIC') - - # dimensions - fid.createDimension('xi_rho', npy.size(self.grd.hgrid.mask_rho,1)) - fid.createDimension('eta_rho', npy.size(self.grd.hgrid.mask_rho,0)) - fid.createDimension('s_rho', self.grd.vgrid.N) - fid.createDimension('s_w', self.grd.vgrid.Np) - fid.description = 'Nudging coefficients for grid' + self.grd.name - # vertical coordinate - fid.createVariable('s_rho', 'f8', ('s_rho')) - fid.variables['s_rho'].long_name = 'S-coordinate at RHO-points' - fid.variables['s_rho'].valid_min = '-1' - fid.variables['s_rho'].valid_max = '0' - fid.variables['s_rho'].field = 's_rho,scalar' - fid.variables['s_rho'][:] = self.grd.vgrid.s_rho - - # variables - O_M2_NudgeCoef = fid.createVariable('M2_NudgeCoef', 'f8', ('eta_rho','xi_rho',)) - O_M3_NudgeCoef = fid.createVariable('M3_NudgeCoef', 'f8', ('s_rho','eta_rho','xi_rho',)) - O_temp_NudgeCoef = fid.createVariable('temp_NudgeCoef', 'f8', ('s_rho','eta_rho','xi_rho',)) - O_salt_NudgeCoef = fid.createVariable('salt_NudgeCoef', 'f8', ('s_rho','eta_rho','xi_rho',)) - O_tracer_NudgeCoef = fid.createVariable('tracer_NudgeCoef', 'f8', ('s_rho','eta_rho','xi_rho',)) - # data - O_M2_NudgeCoef[:,:] = (1./self.tra_ts['M2']) * self.nud2 - O_M3_NudgeCoef[:,:,:] = (1./self.tra_ts['M3']) * self.nud3 - O_temp_NudgeCoef[:,:,:] = (1./self.tra_ts['temp']) * self.nud3 - O_salt_NudgeCoef[:,:,:] = (1./self.tra_ts['salt']) * self.nud3 - O_tracer_NudgeCoef[:,:,:] = (1./self.tra_ts['tracer']) * self.nud3 - # attributes - O_M2_NudgeCoef.long_name = '2D momentum inverse nudging coefficients' - O_M2_NudgeCoef.units = 'days-1' - O_M2_NudgeCoef.coordinates = 'xi_rho eta_rho' - - O_M3_NudgeCoef.long_name = '3D momentum inverse nudging coefficients' - O_M3_NudgeCoef.units = 'days-1' - O_M3_NudgeCoef.coordinates = 'xi_rho eta_rho s_rho' - - O_temp_NudgeCoef.long_name = 'temp inverse nudging coefficients' - O_temp_NudgeCoef.units = 'days-1' - O_temp_NudgeCoef.coordinates = 'xi_rho eta_rho s_rho' - - O_salt_NudgeCoef.long_name = 'salt inverse nudging coefficients' - O_salt_NudgeCoef.units = 'days-1' - O_salt_NudgeCoef.coordinates = 'xi_rho eta_rho s_rho' - - O_tracer_NudgeCoef.long_name = 'generic tracer inverse nudging coefficients' - O_tracer_NudgeCoef.units = 'days-1' - O_tracer_NudgeCoef.coordinates = 'xi_rho eta_rho s_rho' - # close - fid.close() - return None + ''' A class to write the Nudging coeficient file for ROMS ''' + + def __init__(self,roms_grid): + ''' init an object of the class with the pyroms grid ID ''' + self.grd = pyroms.grid.get_ROMS_grid(roms_grid) + return None + + def __call__(self,east_dict,west_dict,north_dict,south_dict,tracer_timescales,foutname='./nudging_coef.nc'): + ''' call with following dictionaries : + 4 boundaries dict + tracer timescales + for example : + east_dict = {'nudge':True,'factor': 1,'width':50,'transition':'linear'} + west_dict = {'nudge':True,'factor': 1,'width':50,'transition':'linear'} + north_dict = {'nudge':True,'factor': 1,'width':50,'transition':'linear'} + south_dict = {'nudge':True,'factor': 1,'width':50,'transition':'linear'} + tracer_timescales = {'M2':30,'M3':30,'temp':30,'salt':30,'tracer':30} + tips: + * nudge = True if open boundary, False otherwise + * factor allows to have different timescales at each boundary + * width is in grid points + * transition shapes how timescale varies spatially + * tracer timescales are in days + ''' + self.east_dict = east_dict + self.west_dict = west_dict + self.north_dict = north_dict + self.south_dict = south_dict + self.tra_ts = tracer_timescales + self.foutname = foutname + # create 2d coef + self.nud2 = self._create_nudgcoef_2d() + # create 3d coef + self.nud3 = self._create_nudgcoef_3d() + # write to netcdf + self._write_nc_file() + return None + + def _create_nudgcoef_3d(self): + ''' expand 2d coef along the vertical ''' + # RD: later we could imagine multiplying by + # a vertical profile if needed + ny, nx = self.grd.hgrid.mask_rho.shape + nz = self.grd.vgrid.N + nudgcoef = npy.zeros((nz,ny,nx)) + for kz in npy.arange(nz): + nudgcoef[kz,:,:] = self.nud2[:,:] + return nudgcoef + + def _create_nudgcoef_2d(self): + ''' create the 2d nudging coef from dictionaries ''' + ny, nx = self.grd.hgrid.mask_rho.shape + nudgcoef_west = npy.zeros((ny,nx)) + nudgcoef_east = npy.zeros((ny,nx)) + nudgcoef_north = npy.zeros((ny,nx)) + nudgcoef_south = npy.zeros((ny,nx)) + nudgcoef = npy.zeros((ny,nx)) + mask = self.grd.hgrid.mask_rho + # west boundary + if self.west_dict['nudge'] is True: + fc = self.west_dict['factor'] + wd = self.west_dict['width'] + tr = self.west_dict['transition'] + if tr == 'linear': + for ji in npy.arange(0,wd): + nudgcoef_west[:,ji] = fc * (wd-ji) / float(wd) + elif tr == 'linear_nocoast': + for ji in npy.arange(0,wd): + nudgcoef_west[:,ji] = mask[:,0] * fc * (wd-ji) / float(wd) + else: + print('transition not coded') ; pass + # east boundary + if self.east_dict['nudge'] is True: + fc = self.east_dict['factor'] + wd = self.east_dict['width'] + tr = self.east_dict['transition'] + if tr == 'linear': + for ji in npy.arange(nx-wd,nx): + nudgcoef_east[:,ji] = fc * (wd-nx+ji) / float(wd) + elif tr == 'linear_nocoast': + for ji in npy.arange(nx-wd,nx): + nudgcoef_east[:,ji] = mask[:,-1] * fc * (wd-nx+ji) / float(wd) + else: + print('transition not coded') ; pass + # south boundary + if self.south_dict['nudge'] is True: + fc = self.south_dict['factor'] + wd = self.south_dict['width'] + tr = self.south_dict['transition'] + if tr == 'linear': + for jj in npy.arange(0,wd): + nudgcoef_south[jj,:] = fc * (wd-jj) / float(wd) + if tr == 'linear_nocoast': + for jj in npy.arange(0,wd): + nudgcoef_south[jj,:] = mask[0,:] * fc * (wd-jj) / float(wd) + else: + print('transition not coded') ; pass + # north boundary + if self.north_dict['nudge'] is True: + fc = self.north_dict['factor'] + wd = self.north_dict['width'] + tr = self.north_dict['transition'] + if tr == 'linear': + for jj in npy.arange(ny-wd,ny): + nudgcoef_south[jj,:] = fc * (wd-ny+jj) / float(wd) + if tr == 'linear_nocoast': + for jj in npy.arange(ny-wd,ny): + nudgcoef_south[jj,:] = mask[-1,:] * fc * (wd-ny+jj) / float(wd) + else: + print('transition not coded') ; pass + + + # create the total coefficient by combining all 4 fields + # the max functions is useful to make nice corners when + # individual field overlap + # maybe not the most efficient but short and readable + for jj in npy.arange(ny): + for ji in npy.arange(nx): + nudgcoef[jj,ji] = max(nudgcoef_west[jj,ji], \ + nudgcoef_east[jj,ji],nudgcoef_north[jj,ji],nudgcoef_south[jj,ji]) + return nudgcoef + + def _write_nc_file(self): + ''' writing to netcdf and multiplying by inverse timescales ''' + ncfile = self.foutname + fid = nc.Dataset(ncfile, 'w', format='NETCDF3_CLASSIC') + + # dimensions + fid.createDimension('xi_rho', npy.size(self.grd.hgrid.mask_rho,1)) + fid.createDimension('eta_rho', npy.size(self.grd.hgrid.mask_rho,0)) + fid.createDimension('s_rho', self.grd.vgrid.N) + fid.createDimension('s_w', self.grd.vgrid.Np) + fid.description = 'Nudging coefficients for grid' + self.grd.name + # vertical coordinate + fid.createVariable('s_rho', 'f8', ('s_rho')) + fid.variables['s_rho'].long_name = 'S-coordinate at RHO-points' + fid.variables['s_rho'].valid_min = '-1' + fid.variables['s_rho'].valid_max = '0' + fid.variables['s_rho'].field = 's_rho,scalar' + fid.variables['s_rho'][:] = self.grd.vgrid.s_rho + + # variables + O_M2_NudgeCoef = fid.createVariable('M2_NudgeCoef', 'f8', ('eta_rho','xi_rho',)) + O_M3_NudgeCoef = fid.createVariable('M3_NudgeCoef', 'f8', ('s_rho','eta_rho','xi_rho',)) + O_temp_NudgeCoef = fid.createVariable('temp_NudgeCoef', 'f8', ('s_rho','eta_rho','xi_rho',)) + O_salt_NudgeCoef = fid.createVariable('salt_NudgeCoef', 'f8', ('s_rho','eta_rho','xi_rho',)) + O_tracer_NudgeCoef = fid.createVariable('tracer_NudgeCoef', 'f8', ('s_rho','eta_rho','xi_rho',)) + # data + O_M2_NudgeCoef[:,:] = (1./self.tra_ts['M2']) * self.nud2 + O_M3_NudgeCoef[:,:,:] = (1./self.tra_ts['M3']) * self.nud3 + O_temp_NudgeCoef[:,:,:] = (1./self.tra_ts['temp']) * self.nud3 + O_salt_NudgeCoef[:,:,:] = (1./self.tra_ts['salt']) * self.nud3 + O_tracer_NudgeCoef[:,:,:] = (1./self.tra_ts['tracer']) * self.nud3 + # attributes + O_M2_NudgeCoef.long_name = '2D momentum inverse nudging coefficients' + O_M2_NudgeCoef.units = 'days-1' + O_M2_NudgeCoef.coordinates = 'xi_rho eta_rho' + + O_M3_NudgeCoef.long_name = '3D momentum inverse nudging coefficients' + O_M3_NudgeCoef.units = 'days-1' + O_M3_NudgeCoef.coordinates = 'xi_rho eta_rho s_rho' + + O_temp_NudgeCoef.long_name = 'temp inverse nudging coefficients' + O_temp_NudgeCoef.units = 'days-1' + O_temp_NudgeCoef.coordinates = 'xi_rho eta_rho s_rho' + + O_salt_NudgeCoef.long_name = 'salt inverse nudging coefficients' + O_salt_NudgeCoef.units = 'days-1' + O_salt_NudgeCoef.coordinates = 'xi_rho eta_rho s_rho' + + O_tracer_NudgeCoef.long_name = 'generic tracer inverse nudging coefficients' + O_tracer_NudgeCoef.units = 'days-1' + O_tracer_NudgeCoef.coordinates = 'xi_rho eta_rho s_rho' + # close + fid.close() + return None #---------------------------------------------------------------------------- diff --git a/examples/make_tide/CGrid_TPXO8/__init__.py b/examples/make_tide/CGrid_TPXO8/__init__.py index 6501d0e..2de9184 100644 --- a/examples/make_tide/CGrid_TPXO8/__init__.py +++ b/examples/make_tide/CGrid_TPXO8/__init__.py @@ -2,9 +2,9 @@ TPXO8 module """ -from CGrid_TPXO8 import CGrid_TPXO8 -from get_nc_CGrid_TPXO8 import get_nc_CGrid_TPXO8 -from make_remap_grid_file import make_remap_grid_file -from flood import flood -from remap import remap -from tidal_ellipse import * +from .CGrid_TPXO8 import CGrid_TPXO8 +from .get_nc_CGrid_TPXO8 import get_nc_CGrid_TPXO8 +from .make_remap_grid_file import make_remap_grid_file +from .flood import flood +from .remap import remap +from .tidal_ellipse import * diff --git a/examples/make_tide/CGrid_TPXO8/get_nc_CGrid_TPXO8.py b/examples/make_tide/CGrid_TPXO8/get_nc_CGrid_TPXO8.py index 9300b3d..53dc4cb 100644 --- a/examples/make_tide/CGrid_TPXO8/get_nc_CGrid_TPXO8.py +++ b/examples/make_tide/CGrid_TPXO8/get_nc_CGrid_TPXO8.py @@ -1,6 +1,6 @@ import numpy as np import pyroms -from CGrid_TPXO8 import CGrid_TPXO8 +from .CGrid_TPXO8 import CGrid_TPXO8 def get_nc_CGrid_TPXO8(grdfile, name='TPXO8', \ diff --git a/examples/make_tide/CGrid_TPXO8/remap.py b/examples/make_tide/CGrid_TPXO8/remap.py index abc1c37..c8ccbf4 100644 --- a/examples/make_tide/CGrid_TPXO8/remap.py +++ b/examples/make_tide/CGrid_TPXO8/remap.py @@ -23,7 +23,7 @@ def remap(src_varname, src_file, src_grd, dst_grd, dst_file, dmax=0, cdepth=0, k nctime.units = 'days since 1900-01-01 00:00:00' # create tide file - print '\nCreating tide file', dst_file + print('\nCreating tide file', dst_file) if os.path.exists(dst_file) is True: os.remove(dst_file) pyroms_toolbox.nc_create_roms_file(dst_file, dst_grd, nctime) @@ -96,10 +96,10 @@ def remap(src_varname, src_file, src_grd, dst_grd, dst_file, dmax=0, cdepth=0, k field = 'y-velocity, scalar, series' else: - raise ValueError, 'Undefined src_varname' + raise ValueError('Undefined src_varname') # create variable in file - print 'Creating variable', dst_varname + print('Creating variable', dst_varname) nc.createVariable(dst_varname, 'f8', dimensions, fill_value=spval) # nc.createVariable(dst_varname, 'f8', dimensions) nc.variables[dst_varname].long_name = long_name @@ -107,15 +107,15 @@ def remap(src_varname, src_file, src_grd, dst_grd, dst_file, dmax=0, cdepth=0, k nc.variables[dst_varname].field = field # remapping - print 'remapping', dst_varname, 'from', src_grd.name, \ - 'to', dst_grd.name + print('remapping', dst_varname, 'from', src_grd.name, \ + 'to', dst_grd.name) # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_var = pyroms.remapping.remap(src_var, wts_file, spval=spval) # write data in destination file - print 'write data in destination file\n' + print('write data in destination file\n') nc.variables[dst_varname][:] = dst_var # close file diff --git a/examples/make_tide/CGrid_TPXO8/tidal_ellipse.py b/examples/make_tide/CGrid_TPXO8/tidal_ellipse.py index 86ab81f..b99092a 100644 --- a/examples/make_tide/CGrid_TPXO8/tidal_ellipse.py +++ b/examples/make_tide/CGrid_TPXO8/tidal_ellipse.py @@ -603,11 +603,11 @@ def prep_plot(SEMA, ECC, INC, PHA): rAu, rPhi_u, rAv, rPhi_v, rw = ep2ap(SEMA, ECC, INC, PHA, [2, 3, 1]) # Check if ep2ap has recovered Au, Phi_u, Av, Phi_v - print(np.max(np.abs(rAu - Au).flatten())) # = 9.9920e-16, = 2.22044604925e-16 - print(np.max(np.abs(rAv - Av).flatten())) # = 6.6613e-16, = 7.77156117238e-16 - print(np.max(np.abs(rPhi_u - Phi_u).flatten())) # = 4.4764e-13, = 1.70530256582e-13 - print(np.max(np.abs(rPhi_v - Phi_v).flatten())) # = 1.1369e-13, = 2.27373675443e-13 - print(np.max(np.max(np.abs(w - rw).flatten()))) # = 1.3710e-15, = 1.1322097734e-15 + print((np.max(np.abs(rAu - Au).flatten()))) # = 9.9920e-16, = 2.22044604925e-16 + print((np.max(np.abs(rAv - Av).flatten()))) # = 6.6613e-16, = 7.77156117238e-16 + print((np.max(np.abs(rPhi_u - Phi_u).flatten()))) # = 4.4764e-13, = 1.70530256582e-13 + print((np.max(np.abs(rPhi_v - Phi_v).flatten()))) # = 1.1369e-13, = 2.27373675443e-13 + print((np.max(np.max(np.abs(w - rw).flatten())))) # = 1.3710e-15, = 1.1322097734e-15 # For the random realization I (Zhigang Xu) had, the differences are listed # on the right hand of the above column. I (Pierre Cazenave) got the second # column with the Python version. What are yours? diff --git a/examples/make_tide/make_remap_weights_file.py b/examples/make_tide/make_remap_weights_file.py old mode 100755 new mode 100644 diff --git a/examples/rivers/add_remap.py b/examples/rivers/add_remap.py index 4d7dea1..aa05c44 100644 --- a/examples/rivers/add_remap.py +++ b/examples/rivers/add_remap.py @@ -12,32 +12,32 @@ def add_to_lists(pairs, i, j, sign, dir): for it in range(1,len(pairs)): x2, y2 = pairs[it] - if x2 > x1: - # negative v-velocity - i.append(x1) - j.append(y1) - sign.append(-1) - dir.append(1) - elif x1 > x2: - # positive v-velocity - i.append(x2) - j.append(y1) - sign.append(1) - dir.append(1) - elif y2 > y1: - # positive u-velocity - i.append(x1) - j.append(y1) - sign.append(1) - dir.append(0) - elif y1 > y2: - # negative u-velocity - i.append(x1) - j.append(y2) - sign.append(-1) - dir.append(0) - x1 = x2 - y1 = y2 + if x2 > x1: + # negative v-velocity + i.append(x1) + j.append(y1) + sign.append(-1) + dir.append(1) + elif x1 > x2: + # positive v-velocity + i.append(x2) + j.append(y1) + sign.append(1) + dir.append(1) + elif y2 > y1: + # positive u-velocity + i.append(x1) + j.append(y1) + sign.append(1) + dir.append(0) + elif y1 > y2: + # negative u-velocity + i.append(x1) + j.append(y2) + sign.append(-1) + dir.append(0) + x1 = x2 + y1 = y2 #outfile = sys.argv[1] outfile = 'remap_grid_CI_rivers.nc' @@ -65,15 +65,15 @@ def add_to_lists(pairs, i, j, sign, dir): for line in f: a, b, c = re.split('\s+', line) if a=='-10': - # wrap up object - add_to_lists(pairs, i, j, sign, dir) + # wrap up object + add_to_lists(pairs, i, j, sign, dir) elif (a=='-1' or a=='-3'): - # wrap up object - add_to_lists(pairs, i, j, sign, dir) - # start new object + # wrap up object + add_to_lists(pairs, i, j, sign, dir) + # start new object pairs = [] else: - pairs.append([int(a),int(b)]) + pairs.append([int(a),int(b)]) # set up grid coords grd = pyroms.grid.get_ROMS_grid('COOK_INLET_LYON') diff --git a/examples/rivers/add_rivers.py b/examples/rivers/add_rivers.py index d206b2f..fa9f6f5 100644 --- a/examples/rivers/add_rivers.py +++ b/examples/rivers/add_rivers.py @@ -10,32 +10,32 @@ def add_to_lists(pairs, i, j, sign, dir): for it in range(1,len(pairs)): x2, y2 = pairs[it] - if x2 > x1: - # negative v-velocity - i.append(x1) - j.append(y1) - sign.append(-1) - dir.append(1) - elif x1 > x2: - # positive v-velocity - i.append(x2) - j.append(y1) - sign.append(1) - dir.append(1) - elif y2 > y1: - # positive u-velocity - i.append(x1) - j.append(y1) - sign.append(1) - dir.append(0) - elif y1 > y2: - # negative u-velocity - i.append(x1) - j.append(y2) - sign.append(-1) - dir.append(0) - x1 = x2 - y1 = y2 + if x2 > x1: + # negative v-velocity + i.append(x1) + j.append(y1) + sign.append(-1) + dir.append(1) + elif x1 > x2: + # positive v-velocity + i.append(x2) + j.append(y1) + sign.append(1) + dir.append(1) + elif y2 > y1: + # positive u-velocity + i.append(x1) + j.append(y1) + sign.append(1) + dir.append(0) + elif y1 > y2: + # negative u-velocity + i.append(x1) + j.append(y2) + sign.append(-1) + dir.append(0) + x1 = x2 + y1 = y2 outfile = sys.argv[1] @@ -62,15 +62,15 @@ def add_to_lists(pairs, i, j, sign, dir): for line in f: a, b, c = re.split('\s+', line) if a=='-10': - # wrap up object - add_to_lists(pairs, i, j, sign, dir) + # wrap up object + add_to_lists(pairs, i, j, sign, dir) elif (a=='-1' or a=='-3'): - # wrap up object - add_to_lists(pairs, i, j, sign, dir) - # start new object + # wrap up object + add_to_lists(pairs, i, j, sign, dir) + # start new object pairs = [] else: - pairs.append([int(a),int(b)]) + pairs.append([int(a),int(b)]) # create file with all the objects out = netCDF4.Dataset(outfile, 'w', format='NETCDF3_64BIT') @@ -90,7 +90,7 @@ def add_to_lists(pairs, i, j, sign, dir): river = out.createVariable('river', 'i4', ('river')) river.long_name = 'river runoff identification number' -out.variables['river'][:] = range(1,len(i)+1) +out.variables['river'][:] = list(range(1,len(i)+1)) flag = out.createVariable('river_sign', 'f8', ('river')) flag.long_name = 'river directional sign' diff --git a/examples/rivers/compute_daitren_remap_weights.py b/examples/rivers/compute_daitren_remap_weights.py index 629abbc..9fee80a 100644 --- a/examples/rivers/compute_daitren_remap_weights.py +++ b/examples/rivers/compute_daitren_remap_weights.py @@ -8,7 +8,7 @@ ## load 2-dimentional interannual discharge data ## from 1948-2007. See Dai and Trenberth (2002) and Dai et al. (2009) -print 'Load interannual discharge data' +print('Load interannual discharge data') nc_data = netCDF.Dataset('/archive/u1/uaf/kate/CORE2/runoff.daitren.iaf.10FEB2011.nc', 'r') runoff = nc_data.variables['runoff'][:] lon = nc_data.variables['xc'][:] @@ -18,7 +18,7 @@ mask = nc_data.variables['mask'][:] ## create data remap file for scrip -print 'Create remap grid file for Dai and Trenberth runoff' +print('Create remap grid file for Dai and Trenberth runoff') remap_filename = 'remap_grid_daitren.nc' nc = netCDF.Dataset(remap_filename, 'w', format='NETCDF3_CLASSIC') nc.Description = 'remap grid file for Dai and Trenberth runoff data' @@ -84,14 +84,14 @@ ## create NWGOA remap file for scrip -print 'Create remap grid file for NWGOA grid' +print('Create remap grid file for NWGOA grid') dstgrd = pyroms.grid.get_ROMS_grid('NWGOA') dstgrd.hgrid.mask_rho = np.ones(dstgrd.hgrid.mask_rho.shape) pyroms.remapping.make_remap_grid_file(dstgrd, Cpos='rho') ## compute remap weights -print 'compute remap weights using scrip' +print('compute remap weights using scrip') # input namelist variables for conservative remapping at rho points grid1_file = 'remap_grid_daitren.nc' grid2_file = 'remap_grid_NWGOA_rho.nc' diff --git a/examples/rivers/compute_hill_remap_weights.py b/examples/rivers/compute_hill_remap_weights.py index cc1ba66..ef3ddfa 100644 --- a/examples/rivers/compute_hill_remap_weights.py +++ b/examples/rivers/compute_hill_remap_weights.py @@ -99,14 +99,14 @@ # create CI remap file for scrip -print 'Create remap grid file for CI grid' +print('Create remap grid file for CI grid') dstgrd = pyroms.grid.get_ROMS_grid('COOK_INLET_LYON') dstgrd.hgrid.mask_rho = np.ones(dstgrd.hgrid.mask_rho.shape) pyroms.remapping.make_remap_grid_file(dstgrd, Cpos='rho') ## compute remap weights -print 'compute remap weights using scrip' +print('compute remap weights using scrip') # input namelist variables for conservative remapping at rho points grid1_file = '../version1/remap_grid_runoff.nc' grid2_file = 'remap_grid_COOK_INLET_LYON_rho.nc' diff --git a/examples/rivers/compute_hill_remap_weights_2.py b/examples/rivers/compute_hill_remap_weights_2.py index d3a2c47..965a350 100644 --- a/examples/rivers/compute_hill_remap_weights_2.py +++ b/examples/rivers/compute_hill_remap_weights_2.py @@ -15,7 +15,7 @@ # # ### compute remap weights -print 'compute remap weights using scrip' +print('compute remap weights using scrip') # input namelist variables for conservative remapping at rho points grid1_file = '../version1/remap_grid_runoff.nc' grid2_file = 'remap_grid_CI_rho.nc' diff --git a/examples/rivers/hack_runoff_clim.py b/examples/rivers/hack_runoff_clim.py index 6435c83..b770c2a 100644 --- a/examples/rivers/hack_runoff_clim.py +++ b/examples/rivers/hack_runoff_clim.py @@ -8,7 +8,7 @@ # load 2-dimentional interannual discharge data # from 1948-2007. See Dai and Trenberth (2002) and Dai et al. (2009) -print 'Load interannual discharge data' +print('Load interannual discharge data') runoff_file = 'NWGOA_runoff.nc' nc = netCDF.Dataset(runoff_file, 'a', format='NETCDF3_64BIT') @@ -18,16 +18,16 @@ raw_180 = runoff_raw[180,:,:] runoff_180 = runoff[180,:,:] -print 'Sum 1', np.sum(raw_180) -print 'Sum 2', np.sum(runoff_180) +print('Sum 1', np.sum(raw_180)) +print('Sum 2', np.sum(runoff_180)) susitna = runoff[:,349,590] copper = runoff[:,158,688] copper2 = runoff[:,157,688] -print 'copper', copper[180] -print 'copper2', copper2[180] -print 'susitna', susitna[180] +print('copper', copper[180]) +print('copper2', copper2[180]) +print('susitna', susitna[180]) runoff[:,350,591] += susitna/3.0 runoff[:,348,590] += susitna/3.0 @@ -38,11 +38,11 @@ runoff[:,158,688] = copper/3.0 runoff_180 = runoff[180,:,:] -print 'Sum 3', np.sum(runoff_180) +print('Sum 3', np.sum(runoff_180)) -print 'copper', copper[180] -print 'copper2', copper2[180] -print 'susitna', susitna[180] +print('copper', copper[180]) +print('copper2', copper2[180]) +print('susitna', susitna[180]) nc.variables['Runoff'][:] = runoff diff --git a/examples/rivers/latlon_to_nc.py b/examples/rivers/latlon_to_nc.py index 9445c75..601c441 100644 --- a/examples/rivers/latlon_to_nc.py +++ b/examples/rivers/latlon_to_nc.py @@ -17,7 +17,7 @@ lon2 = np.zeros(lat.shape) numy, numx = lat.shape -print numy, numx +print(numy, numx) for j in range(numy): lat2[j,:] = lat[numy-1-j,:] diff --git a/examples/rivers/make_river_clim.py b/examples/rivers/make_river_clim.py index 1487e09..aa10175 100644 --- a/examples/rivers/make_river_clim.py +++ b/examples/rivers/make_river_clim.py @@ -6,8 +6,8 @@ import pyroms_toolbox -# load 2-dimentional discharge data -print 'Load discharge data' +# load 2-dimentional discharge data +print('Load discharge data') nc_data = netCDF.Dataset('CI_runoff.nc', 'r') nc_rivers = netCDF.Dataset('Cook_Inlet_rivers.nc', 'a') data = nc_data.variables['Runoff'][:] @@ -36,25 +36,25 @@ for k in range(Nr): if (sign[k]==1): count[eta[k],xi[k]] += 1 - rivers[eta[k],xi[k]].append(k) + rivers[eta[k],xi[k]].append(k) elif (sign[k]==-1 and dir[k]==0): count[eta[k],xi[k]-1] += 1 - rivers[eta[k],xi[k]-1].append(k) + rivers[eta[k],xi[k]-1].append(k) elif (sign[k]==-1 and dir[k]==1): count[eta[k]-1,xi[k]] += 1 - rivers[eta[k]-1,xi[k]].append(k) + rivers[eta[k]-1,xi[k]].append(k) nct=0 for t in range(nt): - print 'Remapping runoff for time %f' %time[t] + print('Remapping runoff for time %f' %time[t]) for j in range(Mp): for i in range(Lp): - for n in range(count[j,i]): - frac = 1.0/count[j,i] - k = rivers[j,i][n] - runoff[k] = frac*data[t,j,i] - + for n in range(count[j,i]): + frac = 1.0/count[j,i] + k = rivers[j,i][n] + runoff[k] = frac*data[t,j,i] + if t==180: sum180 = np.sum(runoff) @@ -69,4 +69,4 @@ # close netcdf file nc_rivers.close() -print 'sum 4', sum180 +print('sum 4', sum180) diff --git a/examples/rivers/make_runoff_clim.py b/examples/rivers/make_runoff_clim.py index 2d17556..96c2e07 100644 --- a/examples/rivers/make_runoff_clim.py +++ b/examples/rivers/make_runoff_clim.py @@ -8,7 +8,7 @@ # load 2-dimentional interannual discharge data # from Hill and Beamer. -print 'Load interannual discharge data' +print('Load interannual discharge data') nc_data = netCDF.Dataset('runoff.nc', 'r') time = nc_data.variables['time'][:] data = nc_data.variables['runoff'][:] @@ -95,7 +95,7 @@ #for t in range(nt): for t in range(nt-243,nt): flow = np.sum(data[t,280:600,160:460]) - print nct+1, 'Remapping runoff for time %f' %time[t] + print(nct+1, 'Remapping runoff for time %f' %time[t]) # print 'Remapping runoff for time %f' %time[nct] # conservative horizontal interpolation using scrip runoff_raw = pyroms.remapping.remap(data[t,:,:], wts_file, \ @@ -115,17 +115,17 @@ # HACK nc.variables['runoff_time'][nct] = time[nct] if t==180: - print 'Sum 2', np.sum(runoff_raw) - print 'Sum 3', np.sum(runoff) + print('Sum 2', np.sum(runoff_raw)) + print('Sum 3', np.sum(runoff)) if nct==180: - print 'Sum 2 new 180', np.sum(runoff_raw) - print 'Sum 3 new 180', np.sum(runoff) + print('Sum 2 new 180', np.sum(runoff_raw)) + print('Sum 3 new 180', np.sum(runoff)) nct = nct + 1 # Get rest of year for t in range(nt-243): flow = np.sum(data[t,280:600,160:460]) - print nct+1, 'Remapping runoff for time %f' %time[t] + print(nct+1, 'Remapping runoff for time %f' %time[t]) # conservative horizontal interpolation using scrip runoff_raw = pyroms.remapping.remap(data[t,:,:], wts_file, \ @@ -145,8 +145,8 @@ nct = nct + 1 if t==180: - print 'Sum 2', np.sum(runoff_raw) - print 'Sum 3', np.sum(runoff) + print('Sum 2', np.sum(runoff_raw)) + print('Sum 3', np.sum(runoff)) # close netcdf file nc.close() diff --git a/examples/rivers/mask_flow.py b/examples/rivers/mask_flow.py index 9ab16aa..d6b46fb 100644 --- a/examples/rivers/mask_flow.py +++ b/examples/rivers/mask_flow.py @@ -36,7 +36,7 @@ if it == 180: raw_180 = runoff[280:600,160:460] -print 'Sum 1', np.sum(raw_180) +print('Sum 1', np.sum(raw_180)) nc.close() mc.close() diff --git a/examples/rivers/maskedge.py b/examples/rivers/maskedge.py index 9401f24..14aa726 100644 --- a/examples/rivers/maskedge.py +++ b/examples/rivers/maskedge.py @@ -1,4 +1,4 @@ -from __future__ import print_function + import numpy as np import netCDF4 import sys @@ -50,13 +50,13 @@ def flood_fill_water(imask, i, j, ii): (j,i) = llist.pop() imask[j,i] = ii if ( imask[j,i-1] == jj and i > 1 ): - llist.append((j, i-1)) + llist.append((j, i-1)) if ( imask[j-1,i] == jj and j > 1 ): - llist.append((j-1, i)) + llist.append((j-1, i)) if ( imask[j,i+1] == jj and i < Lm ): - llist.append((j, i+1)) + llist.append((j, i+1)) if ( imask[j+1,i] == jj and j < Mm ): - llist.append((j+1, i)) + llist.append((j+1, i)) def flood_fill_land(imask, i, j, ii): """ @@ -75,29 +75,29 @@ def flood_fill_land(imask, i, j, ii): (j,i) = llist.pop() imask[j,i] = ii if ( imask[j,i-1] == jj and i > 1 ): - llist.append((j, i-1)) + llist.append((j, i-1)) if ( imask[j-1,i] == jj and j > 1 ): - llist.append((j-1, i)) + llist.append((j-1, i)) if ( imask[j,i+1] == jj and i < Lm ): - llist.append((j, i+1)) + llist.append((j, i+1)) if ( imask[j+1,i] == jj and j < Mm ): - llist.append((j+1, i)) + llist.append((j+1, i)) # now do the diagonals if ( imask[j-1,i-1] == jj and i > 1 ): - llist.append((j-1, i-1)) + llist.append((j-1, i-1)) if ( imask[j-1,i+1] == jj and j > 1 ): - llist.append((j-1, i+1)) + llist.append((j-1, i+1)) if ( imask[j+1,i+1] == jj and i < Lm ): - llist.append((j+1, i+1)) + llist.append((j+1, i+1)) if ( imask[j+1,i-1] == jj and j < Mm ): - llist.append((j+1, i-1)) + llist.append((j+1, i-1)) def set_values(imask, k, val): """ Set all k values to val""" Mp, Lp = imask.shape for j in range(1,Mp-1): for i in range(1,Lp-1): - if (imask[j,i] == k): imask[j,i] = val + if (imask[j,i] == k): imask[j,i] = val def warning(*objs): print("STDERR: ", *objs, file=sys.stderr) @@ -110,8 +110,8 @@ def color_water(imask): Mp, Lp = imask.shape for j in range(1,Mp-1): for i in range(1,Lp-1): - if (imask[j,i] == 1): - flood_fill_water(imask, i, j, count) + if (imask[j,i] == 1): + flood_fill_water(imask, i, j, count) warning("New body!", i, j) count += 1 @@ -132,13 +132,13 @@ def peninsula(imask, plist, i, j, dir, iwat, iland): plist.append(p) if (dir == 'east'): - seed = (i,j) + seed = (i,j) elif (dir == 'west'): - seed = (i-1,j-1) + seed = (i-1,j-1) elif (dir == 'south'): - seed = (i,j-1) + seed = (i,j-1) elif (dir == 'north'): - seed = (i-1,j) + seed = (i-1,j) # warning("Peninsula at", seed, dir) # Trace the edge of the peninsula, keeping track of the psi @@ -147,61 +147,61 @@ def peninsula(imask, plist, i, j, dir, iwat, iland): # value. while True: if (dir == 'east'): - i += 1 + i += 1 p = (i,j) - if ((imask[j-1,i] == iland) and (imask[j-1,i-1] == iwat)): - dir = 'south' - elif ((imask[j,i] == iland) and (imask[j-1,i] == iwat)): - dir = 'east' - elif ((imask[j,i-1] == iland) and (imask[j,i] == iwat)): - dir = 'north' - elif (i==1 or j==1 or i==Lp-1 or j==Mp-1): - break - else: - warning("Problem in peninsula at ", i, j) - exit(1) + if ((imask[j-1,i] == iland) and (imask[j-1,i-1] == iwat)): + dir = 'south' + elif ((imask[j,i] == iland) and (imask[j-1,i] == iwat)): + dir = 'east' + elif ((imask[j,i-1] == iland) and (imask[j,i] == iwat)): + dir = 'north' + elif (i==1 or j==1 or i==Lp-1 or j==Mp-1): + break + else: + warning("Problem in peninsula at ", i, j) + exit(1) elif (dir == 'north'): - j += 1 + j += 1 p = (i,j) - if ((imask[j,i] == iland) and (imask[j-1,i] == iwat)): - dir = 'east' - elif ((imask[j,i-1] == iland) and (imask[j,i] == iwat)): - dir = 'north' - elif ((imask[j-1,i-1] == iland) and (imask[j,i-1] == iwat)): - dir = 'west' - elif (i==1 or j==1 or i==Lp-1 or j==Mp-1): - break - else: - warning("Problem in peninsula at ", i, j) - exit(1) + if ((imask[j,i] == iland) and (imask[j-1,i] == iwat)): + dir = 'east' + elif ((imask[j,i-1] == iland) and (imask[j,i] == iwat)): + dir = 'north' + elif ((imask[j-1,i-1] == iland) and (imask[j,i-1] == iwat)): + dir = 'west' + elif (i==1 or j==1 or i==Lp-1 or j==Mp-1): + break + else: + warning("Problem in peninsula at ", i, j) + exit(1) elif (dir == 'west'): - i -= 1 + i -= 1 p = (i,j) - if ((imask[j,i-1] == iland) and (imask[j,i] == iwat)): - dir = 'north' - elif ((imask[j-1,i-1] == iland) and (imask[j,i-1] == iwat)): - dir = 'west' - elif ((imask[j-1,i] == iland) and (imask[j-1,i-1] == iwat)): - dir = 'south' - elif (i==1 or j==1 or i==Lp-1 or j==Mp-1): - break - else: - warning("Problem in peninsula at ", i, j) - exit(1) + if ((imask[j,i-1] == iland) and (imask[j,i] == iwat)): + dir = 'north' + elif ((imask[j-1,i-1] == iland) and (imask[j,i-1] == iwat)): + dir = 'west' + elif ((imask[j-1,i] == iland) and (imask[j-1,i-1] == iwat)): + dir = 'south' + elif (i==1 or j==1 or i==Lp-1 or j==Mp-1): + break + else: + warning("Problem in peninsula at ", i, j) + exit(1) elif (dir == 'south'): - j -= 1 + j -= 1 p = (i,j) - if ((imask[j-1,i-1] == iland) and (imask[j,i-1] == iwat)): - dir = 'west' - elif ((imask[j-1,i] == iland) and (imask[j-1,i-1] == iwat)): - dir = 'south' - elif ((imask[j,i] == iland) and (imask[j-1,i] == iwat)): - dir = 'east' - elif (i==1 or j==1 or i==Lp-1 or j==Mp-1): - break - else: - warning("Problem in peninsula at ", i, j) - exit(1) + if ((imask[j-1,i-1] == iland) and (imask[j,i-1] == iwat)): + dir = 'west' + elif ((imask[j-1,i] == iland) and (imask[j-1,i-1] == iwat)): + dir = 'south' + elif ((imask[j,i] == iland) and (imask[j-1,i] == iwat)): + dir = 'east' + elif (i==1 or j==1 or i==Lp-1 or j==Mp-1): + break + else: + warning("Problem in peninsula at ", i, j) + exit(1) plist.append(p) plist.append(p) @@ -227,13 +227,13 @@ def island(imask, ilist, i, j, dir, iwat, iland): p = (0,0) if (dir == 'east'): - seed = (i,j) + seed = (i,j) elif (dir == 'west'): - seed = (i-1,j-1) + seed = (i-1,j-1) elif (dir == 'south'): - seed = (i,j-1) + seed = (i,j-1) elif (dir == 'north'): - seed = (i-1,j) + seed = (i-1,j) # warning("Island at", seed, dir) # Trace the edge of the island, keeping track of the psi @@ -241,56 +241,56 @@ def island(imask, ilist, i, j, dir, iwat, iland): # edge segments so that we can later change the peninsula mask # points to water. while True: - if (p == pstart): - break + if (p == pstart): + break if (dir == 'east'): - i += 1 + i += 1 p = (i,j) - if ((imask[j-1,i] == iland) and (imask[j-1,i-1] == iwat)): - dir = 'south' - elif ((imask[j,i] == iland) and (imask[j-1,i] == iwat)): - dir = 'east' - elif ((imask[j,i-1] == iland) and (imask[j,i] == iwat)): - dir = 'north' - else: - warning("Problem in island at ", i, j) - exit(1) + if ((imask[j-1,i] == iland) and (imask[j-1,i-1] == iwat)): + dir = 'south' + elif ((imask[j,i] == iland) and (imask[j-1,i] == iwat)): + dir = 'east' + elif ((imask[j,i-1] == iland) and (imask[j,i] == iwat)): + dir = 'north' + else: + warning("Problem in island at ", i, j) + exit(1) elif (dir == 'north'): - j += 1 + j += 1 p = (i,j) - if ((imask[j,i] == iland) and (imask[j-1,i] == iwat)): - dir = 'east' - elif ((imask[j,i-1] == iland) and (imask[j,i] == iwat)): - dir = 'north' - elif ((imask[j-1,i-1] == iland) and (imask[j,i-1] == iwat)): - dir = 'west' - else: - warning("Problem in island at ", i, j) - exit(1) + if ((imask[j,i] == iland) and (imask[j-1,i] == iwat)): + dir = 'east' + elif ((imask[j,i-1] == iland) and (imask[j,i] == iwat)): + dir = 'north' + elif ((imask[j-1,i-1] == iland) and (imask[j,i-1] == iwat)): + dir = 'west' + else: + warning("Problem in island at ", i, j) + exit(1) elif (dir == 'west'): - i -= 1 + i -= 1 p = (i,j) - if ((imask[j,i-1] == iland) and (imask[j,i] == iwat)): - dir = 'north' - elif ((imask[j-1,i-1] == iland) and (imask[j,i-1] == iwat)): - dir = 'west' - elif ((imask[j-1,i] == iland) and (imask[j-1,i-1] == iwat)): - dir = 'south' - else: - warning("Problem in island at ", i, j) - exit(1) + if ((imask[j,i-1] == iland) and (imask[j,i] == iwat)): + dir = 'north' + elif ((imask[j-1,i-1] == iland) and (imask[j,i-1] == iwat)): + dir = 'west' + elif ((imask[j-1,i] == iland) and (imask[j-1,i-1] == iwat)): + dir = 'south' + else: + warning("Problem in island at ", i, j) + exit(1) elif (dir == 'south'): - j -= 1 + j -= 1 p = (i,j) - if ((imask[j-1,i-1] == iland) and (imask[j,i-1] == iwat)): - dir = 'west' - elif ((imask[j-1,i] == iland) and (imask[j-1,i-1] == iwat)): - dir = 'south' - elif ((imask[j,i] == iland) and (imask[j-1,i] == iwat)): - dir = 'east' - else: - warning("Problem in island at ", i, j) - exit(1) + if ((imask[j-1,i-1] == iland) and (imask[j,i-1] == iwat)): + dir = 'west' + elif ((imask[j-1,i] == iland) and (imask[j-1,i-1] == iwat)): + dir = 'south' + elif ((imask[j,i] == iland) and (imask[j-1,i] == iwat)): + dir = 'east' + else: + warning("Problem in island at ", i, j) + exit(1) ilist.append(p) @@ -310,10 +310,10 @@ def edges(imask, plist, iwat, iland): for i in range(1,Lp-2): if ((imask[Mp-2,i] == iwat) and (imask[Mp-2,i+1] == iland)): peninsula(imask, plist, i+1, Mp-1, 'south', iwat, iland) - for j in list(reversed(range(2,Mp-1))): + for j in list(reversed(list(range(2,Mp-1)))): if ((imask[j,Lp-2] == iwat) and (imask[j-1,Lp-2] == iland)): peninsula(imask, plist, Lp-1, j, 'west', iwat, iland) - for i in list(reversed(range(2,Lp-1))): + for i in list(reversed(list(range(2,Lp-1)))): if ((imask[1,i] == iwat) and (imask[1,i-1] == iland)): peninsula(imask, plist, i, 1, 'north', iwat, iland) @@ -325,7 +325,7 @@ def interior(imask, ilist, iwat, iland): for i in range(2,Lp-2): for j in range(2,Mp-2): if ((imask[j,i] == iwat) and (imask[j+1,i] == iland)): - island(imask, ilist, i, j+1, 'east', iwat, iland) + island(imask, ilist, i, j+1, 'east', iwat, iland) def main(): ncfile = sys.argv[1] @@ -347,16 +347,16 @@ def main(): # Ngl.contour(wks,imask,res) interior(imask, ipoints, iwat, iland) # Ngl.contour(wks,imask,res) - set_values(imask, iland, iwat) + set_values(imask, iland, iwat) # Ngl.contour(wks,imask,res) - iland = iwat + iland = iwat # Islands first, then peninsulas for point in ipoints: - i,j = point + i,j = point print(i, j) for point in lpoints: - i,j = point + i,j = point print(i, j) print(-10, -10) # Ngl.end() diff --git a/examples/rivers/mat_to_nc.py b/examples/rivers/mat_to_nc.py index 260d21e..496cebd 100644 --- a/examples/rivers/mat_to_nc.py +++ b/examples/rivers/mat_to_nc.py @@ -14,7 +14,7 @@ coast_cells = np.where(np.isnan(coast_cells),nine,coast_cells) numy, numx = coast_cells.shape -print numy, numx +print(numy, numx) ntime = 1 out.createDimension('x', numx) diff --git a/examples/rivers/set_vshape.py b/examples/rivers/set_vshape.py index 41d3937..e7f942c 100644 --- a/examples/rivers/set_vshape.py +++ b/examples/rivers/set_vshape.py @@ -18,7 +18,7 @@ area = sum(vshape[:,0]) vshape = (1.0/area)*vshape -print vshape[:,0] +print(vshape[:,0]) vshape2 = np.zeros([N]) for k in range(N): @@ -26,7 +26,7 @@ area = sum(vshape2[:]) vshape2 = (1.0/area)*vshape2 -print vshape2 +print(vshape2) # Copper River #for k in range(5490,5497): diff --git a/examples/rivers/squeeze_rivers.py b/examples/rivers/squeeze_rivers.py index 8735c18..9c465b2 100644 --- a/examples/rivers/squeeze_rivers.py +++ b/examples/rivers/squeeze_rivers.py @@ -20,7 +20,7 @@ time = nc_rivers.variables['river_time'][:] run_280 = np.abs(runoff[280,:]) -print 'Sum 5', np.sum(run_280) +print('Sum 5', np.sum(run_280)) Nr = sign.shape[0] Nt = time.shape[0] @@ -28,7 +28,7 @@ year_sum = np.sum(runoff, axis=0) all_sum = np.sum(np.abs(year_sum)) -print year_sum.shape, all_sum +print(year_sum.shape, all_sum) for i in range(Nr): if np.abs(year_sum[i]) > 0.: @@ -44,7 +44,7 @@ salt2 = np.zeros((Nt)) temp2 = temp -print 'Squeezing down to', count, 'rivers' +print('Squeezing down to', count, 'rivers') it = 0 for i in range(Nr): if np.abs(year_sum[i]) > 0.: @@ -120,10 +120,10 @@ out.variables['river_time'][:] = time run_280 = np.abs(runoff2[280,:]) -print 'Sum 6', np.sum(run_280) +print('Sum 6', np.sum(run_280)) year_sum = np.sum(runoff2, axis=0) all_sum = np.sum(np.abs(year_sum)) -print year_sum.shape, all_sum +print(year_sum.shape, all_sum) out.close() diff --git a/examples/rivers/view_temp.py b/examples/rivers/view_temp.py index abd3283..8980a16 100644 --- a/examples/rivers/view_temp.py +++ b/examples/rivers/view_temp.py @@ -25,7 +25,7 @@ temp.append(float(b)) salt.append(0.0) -print temp +print(temp) # create file with all the objects out = netCDF4.Dataset(outfile, 'a', format='NETCDF3_64BIT') diff --git a/examples/runoff/compute_daitren_remap_weights.py b/examples/runoff/compute_daitren_remap_weights.py new file mode 100644 index 0000000..3750f4f --- /dev/null +++ b/examples/runoff/compute_daitren_remap_weights.py @@ -0,0 +1,107 @@ +import numpy as np +from datetime import datetime +import netCDF4 as netCDF + +import pyroms +import pyroms_toolbox + + +## load 2-dimentional interannual discharge data +## from 1948-2007. See Dai and Trenberth (2002) and Dai et al. (2009) +print('Load interannual discharge data') +nc_data = netCDF.Dataset('/archive/u1/uaf/kate/CORE2/runoff.daitren.iaf.10FEB2011.nc', 'r') +runoff = nc_data.variables['runoff'][:] +lon = nc_data.variables['xc'][:] +lat = nc_data.variables['yc'][:] +lon_corner = nc_data.variables['xv'][:] +lat_corner = nc_data.variables['yv'][:] +mask = nc_data.variables['mask'][:] + +## create data remap file for scrip +print('Create remap grid file for Dai and Trenberth runoff') +remap_filename = 'remap_grid_daitren.nc' +nc = netCDF.Dataset(remap_filename, 'w', format='NETCDF3_CLASSIC') +nc.Description = 'remap grid file for Dai and Trenberth runoff data' +nc.Author = 'build_runoff' +nc.Created = datetime.now().strftime("%Y-%m-%d %H:%M:%S") +nc.title = 'Dai and Trenberth runoff' + +grid_center_lon = lon.flatten() +grid_center_lat = lat.flatten() +Mp, Lp = lon.shape +grid_imask = mask.flatten() +grid_size = Lp * Mp +grid_corner_lon = np.zeros((grid_size, 4)) +grid_corner_lat = np.zeros((grid_size, 4)) +k = 0 +for j in range(Mp): + for i in range(Lp): + grid_corner_lon[k,0] = lon_corner[0,j,i] + grid_corner_lat[k,0] = lat_corner[0,j,i] + grid_corner_lon[k,1] = lon_corner[1,j,i] + grid_corner_lat[k,1] = lat_corner[1,j,i] + grid_corner_lon[k,2] = lon_corner[2,j,i] + grid_corner_lat[k,2] = lat_corner[2,j,i] + grid_corner_lon[k,3] = lon_corner[3,j,i] + grid_corner_lat[k,3] = lat_corner[3,j,i] + k = k + 1 + +nc.createDimension('grid_size', grid_size) +nc.createDimension('grid_corners', 4) +nc.createDimension('grid_rank', 2) + +nc.createVariable('grid_dims', 'i4', ('grid_rank')) +nc.variables['grid_dims'].long_name = 'grid size along x and y axis' +nc.variables['grid_dims'].units = 'None' +nc.variables['grid_dims'][:] = [(Lp, Mp)] + +nc.createVariable('grid_center_lon', 'f8', ('grid_size')) +nc.variables['grid_center_lon'].long_name = 'longitude of cell center' +nc.variables['grid_center_lon'].units = 'degrees' +nc.variables['grid_center_lon'][:] = grid_center_lon + +nc.createVariable('grid_center_lat', 'f8', ('grid_size')) +nc.variables['grid_center_lat'].long_name = 'latitude of cell center' +nc.variables['grid_center_lat'].units = 'degrees' +nc.variables['grid_center_lat'][:] = grid_center_lat + +nc.createVariable('grid_imask', 'i4', ('grid_size')) +nc.variables['grid_imask'].long_name = 'mask' +nc.variables['grid_imask'].units = 'None' +nc.variables['grid_imask'][:] = grid_imask + +nc.createVariable('grid_corner_lon', 'f8', ('grid_size', 'grid_corners')) +nc.variables['grid_corner_lon'].long_name = 'longitude of cell corner' +nc.variables['grid_corner_lon'].units = 'degrees' +nc.variables['grid_corner_lon'][:] = grid_corner_lon + +nc.createVariable('grid_corner_lat', 'f8', ('grid_size', 'grid_corners')) +nc.variables['grid_corner_lat'].long_name = 'latitude of cell corner' +nc.variables['grid_corner_lat'].units = 'degrees' +nc.variables['grid_corner_lat'][:] = grid_corner_lat + +nc.close() + + +## create SCS remap file for scrip +print('Create remap grid file for SCS grid') +dstgrd = pyroms.grid.get_ROMS_grid('SCS') +dstgrd.hgrid.mask_rho = np.ones(dstgrd.hgrid.mask_rho.shape) +pyroms.remapping.make_remap_grid_file(dstgrd, Cpos='rho') + + +## compute remap weights +print('compute remap weights using scrip') +# input namelist variables for conservative remapping at rho points +grid1_file = 'remap_grid_daitren.nc' +grid2_file = 'remap_grid_SCS_rho.nc' +interp_file1 = 'remap_weights_daitren_to_SCS_conservative_nomask.nc' +interp_file2 = 'remap_weights_SCS_to_daitren_conservative_nomask.nc' +map1_name = 'daitren to SCS conservative Mapping' +map2_name = 'SCS to daitren conservative Mapping' +num_maps = 1 +map_method = 'conservative' + +pyroms.remapping.compute_remap_weights(grid1_file, grid2_file, \ + interp_file1, interp_file2, map1_name, \ + map2_name, num_maps, map_method) diff --git a/examples/runoff/make_SCS_runoff_clim.py b/examples/runoff/make_SCS_runoff_clim.py new file mode 100644 index 0000000..1aa9062 --- /dev/null +++ b/examples/runoff/make_SCS_runoff_clim.py @@ -0,0 +1,132 @@ +import numpy as np +import netCDF4 as netCDF +from datetime import datetime + +import pyroms +import pyroms_toolbox + + +# load 2-dimentional interannual discharge data +# from 1948-2007. See Dai and Trenberth (2002) and Dai et al. (2009) +print('Load interannual discharge data') +nc_data = netCDF.Dataset('/archive/u1/uaf/kate/CORE2/runoff.daitren.clim.10FEB2011.nc', 'r') +data = nc_data.variables['runoff'][:] + +# time: cyclic year (365.25 days) +time = np.array([15.21875, 45.65625, 76.09375, 106.53125, 136.96875, 167.40625, \ + 197.84375, 228.28125, 258.71875, 289.15625, 319.59375, 350.03125]) + + +# load SCS grid object +grd = pyroms.grid.get_ROMS_grid('SCS') + + +# define some variables +wts_file = 'remap_weights_daitren_to_SCS_conservative_nomask.nc' +nt = data.shape[0] +Mp, Lp = grd.hgrid.mask_rho.shape +spval = -1e30 +runoff_raw = np.zeros((Mp,Lp)) +runoff = np.zeros((Mp,Lp)) +rspread = 6 + +# create runoff file +#runoff_file = 'runoff_SCS_daitren_inter_annual_2002-2004.nc' +runoff_file = 'runoff_SCS_daitren_clim.nc' +nc = netCDF.Dataset(runoff_file, 'w', format='NETCDF3_64BIT') +nc.Description = 'Dai & Trenberth monthly climatology river discharge' +nc.Author = 'make_SCS_runoff.py' +nc.Created = datetime.now().strftime("%Y-%m-%d %H:%M:%S") +nc.title = 'Dai & Trenberth river discharge' + +# creat dimensions and variables +nc.createDimension('xi_rho', np.size(grd.hgrid.mask_rho,1)) +nc.createDimension('eta_rho', np.size(grd.hgrid.mask_rho,0)) +nc.createDimension('runoff_time', (12)) + +nc.createVariable('lon_rho', 'f8', ('eta_rho', 'xi_rho')) +nc.variables['lon_rho'].long_name = 'longitude of RHO-points' +nc.variables['lon_rho'].units = 'degree_east' +nc.variables['lon_rho'].field = 'lon_rho, scalar' +nc.variables['lon_rho'][:] = grd.hgrid.lon_rho + +nc.createVariable('lat_rho', 'f8', ('eta_rho', 'xi_rho')) +nc.variables['lat_rho'].long_name = 'latitude of RHO-points' +nc.variables['lat_rho'].units = 'degree_north' +nc.variables['lat_rho'].field = 'lat_rho, scalar' +nc.variables['lat_rho'][:] = grd.hgrid.lat_rho + +nc.createVariable('runoff_time', 'f8', ('runoff_time')) +nc.variables['runoff_time'].long_name = 'time' +nc.variables['runoff_time'].units = 'days since 1900-01-01 00:00:00' +nc.variables['runoff_time'].cycle_length = 365.25 +nc.variables['runoff_time'][:] = time + +nc.createVariable('Runoff_raw', 'f8', ('runoff_time', 'eta_rho', 'xi_rho')) +nc.variables['Runoff_raw'].long_name = 'Dai_Trenberth River Runoff raw' +nc.variables['Runoff_raw'].missing_value = str(spval) +nc.variables['Runoff_raw'].units = 'kg/s/m^2' + +nc.createVariable('Runoff', 'f8', ('runoff_time', 'eta_rho', 'xi_rho')) +nc.variables['Runoff'].long_name = 'Dai_Trenberth River Runoff' +nc.variables['Runoff'].missing_value = str(spval) +nc.variables['Runoff'].units = 'kg/s/m^2' + + +# get littoral (here 4 cells width) +width = 4 +idx = [] +idy = [] +maskl = grd.hgrid.mask_rho.copy() +for w in range(width): + lit = pyroms_toolbox.get_littoral(maskl) + idx.extend(lit[0]) + idy.extend(lit[1]) + maskl[lit] = 0 + +littoral_idx = (np.array(idx), np.array(idy)) +maskl = np.zeros(grd.hgrid.mask_rho.shape) +maskl[littoral_idx] = 1 + +mask_idx = np.where(grd.hgrid.mask_rho == 0) + +nct=0 +for t in range(nt): + print('Remapping runoff for time %f' %time[nct]) + # conservative horizontal interpolation using scrip + runoff_raw = pyroms.remapping.remap(data[t,:,:], wts_file, \ + spval=spval) + idx = np.where(runoff_raw != 0) + runoff = pyroms_toolbox.move_runoff(runoff_raw, \ + np.array(idx).T + 1, np.array(littoral_idx).T + 1, maskl, \ + grd.hgrid.x_rho, grd.hgrid.y_rho, grd.hgrid.dx, grd.hgrid.dy) + + # spread the runoff within the littoral band + runoff_spread = np.zeros((Mp,Lp)) + idx = np.where(runoff != 0) + for p in range(np.size(idx,1)): + j = list(range(max(0,idx[0][p]-rspread), min(Mp-1,idx[0][p]+rspread+1))) + i = list(range(max(0,idx[1][p]-rspread), min(Lp-1,idx[1][p]+rspread+1))) + ji = np.meshgrid(j,i) + sidx = np.where(maskl[ji] == 1) + nbpt = np.size(sidx) / 2 + rpt = runoff[idx[0][p],idx[1][p]] * grd.hgrid.dx[idx[0][p],idx[1][p]] * grd.hgrid.dy[idx[0][p],idx[1][p]] + rpt = rpt / nbpt + for pa in range(nbpt): + pai = sidx[0][pa] + ji[1].min() + paj = sidx[1][pa] + ji[0].min() + runoff_spread[paj, pai] = runoff_spread[paj, pai] + \ + rpt / (grd.hgrid.dx[paj, pai] * grd.hgrid.dy[paj, pai]) + + + # spval + runoff_spread[mask_idx] = spval + + # write data in destination file + nc.variables['Runoff'][nct] = runoff_spread + nc.variables['Runoff_raw'][nct] = runoff_raw + + nct = nct + 1 + +# close netcdf file +nc.close() diff --git a/examples/stuff/aice.py b/examples/stuff/aice.py index 7bbba1f..50357f8 100644 --- a/examples/stuff/aice.py +++ b/examples/stuff/aice.py @@ -27,10 +27,10 @@ # "(/1.,.42,.42/)", "(/1.,.30,.30/)", \ # "(/1., 0., 0./)", "(/.85,0., 0./)"] cmap = ["white", "black", \ - "(/0., 0.,.85/)", "(/ 0., 0.,1./)", "(/.30,.30,1./)", \ - "(/.42,.42,1./)", "(/.55,.55,1./)", \ - "(/.64,.64,1./)", "(/.72,.72,1./)", "(/.80,.80,1./)", \ - "(/.88,.88,1./)", "(/.9, .9, .9/)", "burlywood"] + "(/0., 0.,.85/)", "(/ 0., 0.,1./)", "(/.30,.30,1./)", \ + "(/.42,.42,1./)", "(/.55,.55,1./)", \ + "(/.64,.64,1./)", "(/.72,.72,1./)", "(/.80,.80,1./)", \ + "(/.88,.88,1./)", "(/.9, .9, .9/)", "burlywood"] rlist = Ngl.Resources() rlist.wkColorMap = cmap @@ -116,13 +116,13 @@ txres.txFontHeightF = 0.015 for file in lst_file: - print "Plotting "+file + print("Plotting "+file) nc = netCDF4.Dataset(file, "r") aice = nc.variables["aice"][0,:,:] time = nc.variables["ocean_time"][0] myday = jday2date(time/86400.) date_tag = myday.strftime('%d %B %Y') - print date_tag + print(date_tag) plot = Ngl.contour_map(wks, aice, res) Ngl.text_ndc(wks, date_tag, 0.85, 0.94, txres) nc.close() diff --git a/examples/stuff/caldate.py b/examples/stuff/caldate.py index 470b41a..0843b1c 100644 --- a/examples/stuff/caldate.py +++ b/examples/stuff/caldate.py @@ -78,13 +78,13 @@ def caldate_1900(Julian): min = floor((sec%3600)/60) sec = round(sec%60) - print "Year: "+str(yr) - print "Year Day: "+str(yday) - print "Month: "+str(mo) - print "Day: "+str(d) - print "Hour: "+str(hour) - print "Min: "+str(min) - print "Sec: "+str(sec) + print("Year: "+str(yr)) + print("Year Day: "+str(yday)) + print("Month: "+str(mo)) + print("Day: "+str(d)) + print("Hour: "+str(hour)) + print("Min: "+str(min)) + print("Sec: "+str(sec)) cal = {'year':yr,'yearday':yday,'month':mo,'day':d,\ 'hour':hour,'minute':min,'second':sec} diff --git a/examples/stuff/make_grid.py b/examples/stuff/make_grid.py index 131330a..4483944 100644 --- a/examples/stuff/make_grid.py +++ b/examples/stuff/make_grid.py @@ -1,3 +1,6 @@ +# This file is designed to be cut and pasted into an ipython --pylab +# session. Otherwise, you'll need to "import numpy as np" then +# convert "array" to "np.array". import os from mpl_toolkits.basemap import Basemap, shiftgrid import matplotlib.colors as colors @@ -6,7 +9,7 @@ import pyroms import pyroms_toolbox -from ROMS_bathy_smoother import * +from bathy_smoother import * #Grid dimension @@ -55,7 +58,7 @@ #hgrd = bry.grd -lonv, latv = map(hgrd.x_vert, hgrd.y_vert, inverse=True) +lonv, latv = list(map(hgrd.x_vert, hgrd.y_vert, inverse=True)) hgrd = pyroms.grid.CGrid_geo(lonv, latv, map) # generate the mask @@ -77,7 +80,7 @@ # read in topo data (on a regular lat/lon grid) # this topo come with basemap so you should have it on your laptop. # just update datadir with the appropriate path -# you can get this data from matplolib svn with +# you can get this data from matplolib svn with # svn co https://matplotlib.svn.sourceforge.net/svnroot/matplotlib/trunk/htdocs/screenshots/data/" datadir = '/home/frederic/python/basemap-0.99.4/examples/' topo = np.loadtxt(os.path.join(datadir, 'etopo20data.gz')) @@ -108,7 +111,7 @@ # check bathymetry roughness RoughMat = bathy_tools.RoughnessMatrix(h, hgrd.mask_rho) -print 'Max Roughness value is: ', RoughMat.max() +print('Max Roughness value is: ', RoughMat.max()) # smooth the raw bathy using the direct iterative method from Martinho and Batteen (2006) rx0_max = 0.35 @@ -116,7 +119,7 @@ # check bathymetry roughness again RoughMat = bathy_tools.RoughnessMatrix(h, hgrd.mask_rho) -print 'Max Roughness value is: ', RoughMat.max() +print('Max Roughness value is: ', RoughMat.max()) hgrd.h = h diff --git a/examples/stuff/make_scgrid.py b/examples/stuff/make_scgrid.py index d22fe3e..2dd696e 100644 --- a/examples/stuff/make_scgrid.py +++ b/examples/stuff/make_scgrid.py @@ -6,7 +6,7 @@ import pyroms import pyroms_toolbox -from ROMS_bathy_smoother import * +from bathy_smoother import * #Grid dimension @@ -19,7 +19,7 @@ lon1=0. ; lat1=0. lon2=10. ; lat2=0. lon3=40. ; lat3=4.724700232622634 -lon4=40. ; lat3=30. +lon4=40. ; lat4=30. #define map projection (here mercator) lon_min = min(lon0,lon1,lon2,lon3,lon4) @@ -49,7 +49,7 @@ #hgrd = bry.grd -lonv, latv = map(hgrd.x_vert, hgrd.y_vert, inverse=True) +lonv, latv = list(map(hgrd.x_vert, hgrd.y_vert, inverse=True)) hgrd = pyroms.grid.CGrid_geo(lonv, latv, map) # generate the mask @@ -63,7 +63,7 @@ # read in topo data (on a regular lat/lon grid) # this topo come with basemap so you should have it on your laptop. # just update datadir with the appropriate path -# you can get this data from matplolib svn with +# you can get this data from matplolib svn with # svn co https://matplotlib.svn.sourceforge.net/svnroot/matplotlib/trunk/htdocs/screenshots/data/" datadir = '/home/frederic/python/basemap-0.99.4/examples/' topo = np.loadtxt(os.path.join(datadir, 'etopo20data.gz')) @@ -94,7 +94,7 @@ # check bathymetry roughness RoughMat = bathy_tools.RoughnessMatrix(h, hgrd.mask_rho) -print 'Max Roughness value is: ', RoughMat.max() +print('Max Roughness value is: ', RoughMat.max()) # smooth the raw bathy using the direct iterative method from Martinho and Batteen (2006) rx0_max = 0.35 @@ -102,7 +102,7 @@ # check bathymetry roughness again RoughMat = bathy_tools.RoughnessMatrix(h, hgrd.mask_rho) -print 'Max Roughness value is: ', RoughMat.max() +print('Max Roughness value is: ', RoughMat.max()) hgrd.h = h diff --git a/examples/stuff/rename_file.py b/examples/stuff/rename_file.py index 1ac73a2..5405451 100644 --- a/examples/stuff/rename_file.py +++ b/examples/stuff/rename_file.py @@ -5,77 +5,78 @@ class tagfile(): - def __init__(self,filename): - self.filein = filename - return None + def __init__(self,filename): + self.filein = filename + return None - def __call__(self): - # read time in netcdf - time, timeunits = self.read_time() - # create the date tag - tag = self.create_tag(time, timeunits) - # define a new filename - self.create_new_filename(tag) - # rename file - self.rename_file() - return None + def __call__(self): + # read time in netcdf + time, timeunits = self.read_time() + # create the date tag + tag = self.create_tag(time, timeunits) + # define a new filename + self.create_new_filename(tag) + # rename file + self.rename_file() + return None - def read_time(self): - ''' read ocean_time variable and units in netcdf file''' - fid = nc.Dataset(self.filein,'r') - time = fid.variables['ocean_time'][:] - timeunits = fid.variables['ocean_time'].units - fid.close() - if len(time) > 1: + def read_time(self): + ''' read ocean_time variable and units in netcdf file''' + fid = nc.Dataset(self.filein,'r') + time = fid.variables['ocean_time'][:] + timeunits = fid.variables['ocean_time'].units + fid.close() + if len(time) > 1: # print 'error : multiple values in time array' ; exit() ntim = len(time) - time = time[ntim-1] - else: - time = time[0] - return time, timeunits + time = time[ntim-1] + else: + time = time[0] + return time, timeunits - def create_tag(self,time, timeunits): - ''' create a datetime object from reference date and ocean_time''' - # ugly part to get reference date from units string - units_wrk = timeunits.replace(':',' ').replace('-',' ').split() - delta_type = units_wrk[0] - year_ref = int(units_wrk[2]) - month_ref = int(units_wrk[3]) - day_ref = int(units_wrk[4]) - hour_ref = int(units_wrk[5]) - min_ref = int(units_wrk[6]) - sec_ref = int(units_wrk[7]) - # create datetime object for reference date - dateref = dt.datetime(year_ref,month_ref,day_ref,hour_ref,min_ref,sec_ref) - # create a datetime object for current time - if delta_type == 'seconds': - tag = dateref + dt.timedelta(seconds=time) - return tag + def create_tag(self,time, timeunits): + ''' create a datetime object from reference date and ocean_time''' + # ugly part to get reference date from units string + units_wrk = timeunits.replace(':',' ').replace('-',' ').split() + delta_type = units_wrk[0] + year_ref = int(units_wrk[2]) + month_ref = int(units_wrk[3]) + day_ref = int(units_wrk[4]) + hour_ref = int(units_wrk[5]) + min_ref = int(units_wrk[6]) + sec_ref = int(units_wrk[7]) + # create datetime object for reference date + dateref = dt.datetime(year_ref,month_ref,day_ref,hour_ref,min_ref,sec_ref) + # create a datetime object for current time + if delta_type == 'seconds': + tag = dateref + dt.timedelta(seconds=time) + return tag - def create_new_filename(self,tag): - ''' based on tag, generate a new filename ''' - # get rid of full path (if any) - filein = self.filein.replace('/',' ').split()[-1] - # get the pieces we want to keep in filename - filein_wrk = filein.replace('_',' ').split() - runname = filein_wrk[0] - filetype = filein_wrk[1] - # write our new filename - self.fileout = runname + '_' + filetype + '_' + tag.isoformat() + '.nc' - return None + def create_new_filename(self,tag): + ''' based on tag, generate a new filename ''' + # get rid of full path (if any) + filein = self.filein.replace('/',' ').split()[-1] + # get the pieces we want to keep in filename + filein_wrk = filein.replace('_',' ').split() + runname = filein_wrk[0] + filetype = filein_wrk[1] + # write our new filename + self.fileout = runname + '_' + filetype + '_' + tag.isoformat() + '.nc' + self.fileout = self.fileout.replace(':00:00','') + return None - def rename_file(self): - ''' call unix command mv ''' - # remove filein from full path - wrk = self.filein.replace('/',' ').split()[0:-1] - # re-create path - path = '.' - for part in wrk: - path = path + '/' + part - # rename file - subprocess.call('mv ' + self.filein + ' ' + path + '/' + self.fileout, shell=True) - return None + def rename_file(self): + ''' call unix command mv ''' + # remove filein from full path + wrk = self.filein.replace('/',' ').split()[0:-1] + # re-create path + path = '.' + for part in wrk: + path = path + '/' + part + # rename file + subprocess.call('mv ' + self.filein + ' ' + path + '/' + self.fileout, shell=True) + return None #---------------------------------------------------------------------------------------------- @@ -85,6 +86,7 @@ def rename_file(self): lis = lis.split() for file in lis: + file = str(file).replace("b'","").replace("'","") print(file) mytag = tagfile(file) mytag() diff --git a/examples/stuff/restart.py b/examples/stuff/restart.py index 559d8a6..616dd5e 100644 --- a/examples/stuff/restart.py +++ b/examples/stuff/restart.py @@ -2,10 +2,10 @@ import os.path import netCDF4 -num = raw_input("Restart number? ") +num = input("Restart number? ") file_path = "$ARCHIVE/Arctic2/run45/restart_" + num if os.path.exists(file_path): - print "directory exists already:", file_path + print("directory exists already:", file_path) exit() else: cmd = "mkdir " + file_path @@ -16,7 +16,7 @@ fh = netCDF4.Dataset("arctic2_flt.nc", "r") nt = len(fh.dimensions['ocean_time']) nt = str(nt-1) -print nt +print(nt) fh.close() cmd = "mv -i arctic2_flt.nc arctic2_flt_" + num + ".nc" subprocess.call([cmd], shell=True) diff --git a/examples/stuff/slice.py b/examples/stuff/slice.py index 387076e..06eba7b 100644 --- a/examples/stuff/slice.py +++ b/examples/stuff/slice.py @@ -2,7 +2,7 @@ import netCDF4 import os import sys -import commands +import subprocess #import Ngl import pyroms from pyroms_toolbox import jday2date @@ -16,8 +16,8 @@ #for year in lst_year: # year = np.str(year) -#lst = commands.getoutput('ls averages/*74??.nc') -lst = commands.getoutput('ls months/*.nc') +#lst = subprocess.getoutput('ls averages/*74??.nc') +lst = subprocess.getoutput('ls months/*.nc') lst = lst.split() lst_file = lst_file + lst @@ -26,103 +26,20 @@ #clat = grd.hgrid.lat_rho #clon = grd.hgrid.lon_rho -#******************************************** -#wks = Ngl.open_wks("ncgm", "aice") # open workstation -#cmap = ["white", "black", \ -# "(/0., 0.,.85/)", "(/ 0., 0.,1./)", "(/.30,.30,1./)", \ -# "(/.42,.42,1./)", "(/.55,.55,1./)", \ -# "(/.64,.64,1./)", "(/.72,.72,1./)", "(/.80,.80,1./)", \ -# "(/.88,.88,1./)", "(/.9, .9, .9/)", "burlywood"] - -#rlist = Ngl.Resources() -#rlist.wkColorMap = cmap -#Ngl.set_values(wks, rlist) - -#ncolors = len(cmap) - 3 -#print ncolors -#; gsn_define_colormap(wks, cmap) -# -#zmin = 0.0 -#zmax = 1.0 -#cnLevels = np.zeros(ncolors-1) -#for i in range(ncolors-1): -# cnLevels[i] = zmin + (zmax-zmin)*(i+1)/ncolors -#spcng = (zmax-zmin)/ncolors - -# -#; Names is used when drawing the labelbar -#; names = new(dimsizes(cnLevels), string) -#; do i=0,dimsizes(cnLevels)-1 -#; names(i) = sprintf("%5.1f", doubletofloat(cnLevels(i))) -#; end do - -#i = NhlNewColor(wks,0.8,0.8,0.8) #; add gray to colormap - -#res = Ngl.Resources() #; plot mods desired -#res.nglMaximize = True -#res.sfXArray = clon -#res.sfYArray = clat -# -#res.cnFillOn = True #; color fill -#res.cnLinesOn = True #; no contour lines -#res.cnLineLabelsOn = False # ; no contour labels -#res.cnFillDrawOrder = "PreDraw" # ; put continents on top -# -##res.gsnSpreadColors = True # ; use total colormap -##res.gsnSpreadColorEnd = -3 -## res.cnInfoLabelOn = False ; no contour info label -#res.cnLevelSelectionMode = "ManualLevels" -#res.cnMinLevelValF = cnLevels[0] -#res.cnMaxLevelValF = cnLevels[ncolors-2] -#res.cnLevelSpacingF = spcng - -## Chukchi plot parameters -#res.mpProjection = "Stereographic" -#res.mpCenterLatF = 90 -#res.mpCenterLonF = 205 -# -#res.mpLimitMode = "Corners" -#res.mpLeftCornerLatF = 60.0 -#res.mpLeftCornerLonF = 180.0 -#res.mpRightCornerLatF = 74. -#res.mpRightCornerLonF = 250.0 -#res.mpDataBaseVersion = "MediumRes" -# -#res.mpFillOn = True -#res.mpFillColors = ["background","transparent","burlywood","transparent"] -# -#res.nglFrame = False # we can attach some text. -#res.tiMainString = "ROMS Arctic Simulation" -#res.tiMainOffsetYF = 0.04 -#res.tiMainFontHeightF = 0.02 -#res.nglSpreadColorEnd = -2 -#res.lbOrientation = "Horizontal" -#res.lbTitleString = "Sea Ice Concentration" -#res.lbTitleFontHeightF = 0.012 -#res.lbLabelFontHeightF = 0.015 -#res.pmLabelBarOrthogonalPosF = +0.02 -#res.pmLabelBarHeightF = 0.1 -#res.pmLabelBarWidthF = 0.6 -# -#txres = Ngl.Resources() # Text resources desired -#txres.txFontHeightF = 0.015 - -#txres.txFontColor = "OrangeRed" - istart = 356 jstart = 373 iend = 387 jend = 411 for file in lst_file: - print "Plotting "+file + print("Plotting "+file) nc = netCDF4.Dataset(file, "r") temp = nc.variables["temp"][0,:,:,:] time = nc.variables["ocean_time"][0] myday = jday2date(time/86400.) # date_tag = myday.strftime('%d %B %Y') date_tag = myday.strftime('%Y_%m_%d') - print date_tag + print(date_tag) plotout = date_tag + '.png' # plot = Ngl.contour_map(wks, aice, res) # Ngl.text_ndc(wks, date_tag, 0.85, 0.84, txres) diff --git a/pyroms/.doxygen b/pyroms/.doxygen new file mode 100644 index 0000000..b32a83a --- /dev/null +++ b/pyroms/.doxygen @@ -0,0 +1,1519 @@ +# Doxyfile 1.6.1 + +# This file describes the settings to be used by the documentation system +# doxygen (www.doxygen.org) for a project +# +# All text after a hash (#) is considered a comment and will be ignored +# The format is: +# TAG = value [value, ...] +# For lists items can also be appended using: +# TAG += value [value, ...] +# Values that contain spaces should be placed between quotes (" ") + +#--------------------------------------------------------------------------- +# Project related configuration options +#--------------------------------------------------------------------------- + +# This tag specifies the encoding used for all characters in the config file +# that follow. The default is UTF-8 which is also the encoding used for all +# text before the first occurrence of this tag. Doxygen uses libiconv (or the +# iconv built into libc) for the transcoding. See +# http://www.gnu.org/software/libiconv for the list of possible encodings. + +DOXYFILE_ENCODING = UTF-8 + +# The PROJECT_NAME tag is a single word (or a sequence of words surrounded +# by quotes) that should identify the project. + +PROJECT_NAME = pycnal + +# The PROJECT_NUMBER tag can be used to enter a project or revision number. +# This could be handy for archiving the generated documentation or +# if some version control system is used. + +PROJECT_NUMBER = + +# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) +# base path where the generated documentation will be put. +# If a relative path is entered, it will be relative to the location +# where doxygen was started. If left blank the current directory will be used. + +OUTPUT_DIRECTORY = + +# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create +# 4096 sub-directories (in 2 levels) under the output directory of each output +# format and will distribute the generated files over these directories. +# Enabling this option can be useful when feeding doxygen a huge amount of +# source files, where putting all generated files in the same directory would +# otherwise cause performance problems for the file system. + +CREATE_SUBDIRS = YES + +# The OUTPUT_LANGUAGE tag is used to specify the language in which all +# documentation generated by doxygen is written. Doxygen will use this +# information to generate all constant output in the proper language. +# The default language is English, other supported languages are: +# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional, +# Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German, +# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English +# messages), Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian, +# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrilic, Slovak, +# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese. + +OUTPUT_LANGUAGE = English + +# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will +# include brief member descriptions after the members that are listed in +# the file and class documentation (similar to JavaDoc). +# Set to NO to disable this. + +BRIEF_MEMBER_DESC = YES + +# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend +# the brief description of a member or function before the detailed description. +# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the +# brief descriptions will be completely suppressed. + +REPEAT_BRIEF = YES + +# This tag implements a quasi-intelligent brief description abbreviator +# that is used to form the text in various listings. Each string +# in this list, if found as the leading text of the brief description, will be +# stripped from the text and the result after processing the whole list, is +# used as the annotated text. Otherwise, the brief description is used as-is. +# If left blank, the following values are used ("$name" is automatically +# replaced with the name of the entity): "The $name class" "The $name widget" +# "The $name file" "is" "provides" "specifies" "contains" +# "represents" "a" "an" "the" + +ABBREVIATE_BRIEF = + +# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then +# Doxygen will generate a detailed section even if there is only a brief +# description. + +ALWAYS_DETAILED_SEC = NO + +# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all +# inherited members of a class in the documentation of that class as if those +# members were ordinary class members. Constructors, destructors and assignment +# operators of the base classes will not be shown. + +INLINE_INHERITED_MEMB = NO + +# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full +# path before files name in the file list and in the header files. If set +# to NO the shortest path that makes the file name unique will be used. + +FULL_PATH_NAMES = YES + +# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag +# can be used to strip a user-defined part of the path. Stripping is +# only done if one of the specified strings matches the left-hand part of +# the path. The tag can be used to show relative paths in the file list. +# If left blank the directory from which doxygen is run is used as the +# path to strip. + +STRIP_FROM_PATH = + +# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of +# the path mentioned in the documentation of a class, which tells +# the reader which header file to include in order to use a class. +# If left blank only the name of the header file containing the class +# definition is used. Otherwise one should specify the include paths that +# are normally passed to the compiler using the -I flag. + +STRIP_FROM_INC_PATH = + +# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter +# (but less readable) file names. This can be useful is your file systems +# doesn't support long names like on DOS, Mac, or CD-ROM. + +SHORT_NAMES = NO + +# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen +# will interpret the first line (until the first dot) of a JavaDoc-style +# comment as the brief description. If set to NO, the JavaDoc +# comments will behave just like regular Qt-style comments +# (thus requiring an explicit @brief command for a brief description.) + +JAVADOC_AUTOBRIEF = NO + +# If the QT_AUTOBRIEF tag is set to YES then Doxygen will +# interpret the first line (until the first dot) of a Qt-style +# comment as the brief description. If set to NO, the comments +# will behave just like regular Qt-style comments (thus requiring +# an explicit \brief command for a brief description.) + +QT_AUTOBRIEF = NO + +# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen +# treat a multi-line C++ special comment block (i.e. a block of //! or /// +# comments) as a brief description. This used to be the default behaviour. +# The new default is to treat a multi-line C++ comment block as a detailed +# description. Set this tag to YES if you prefer the old behaviour instead. + +MULTILINE_CPP_IS_BRIEF = NO + +# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented +# member inherits the documentation from any documented member that it +# re-implements. + +INHERIT_DOCS = YES + +# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce +# a new page for each member. If set to NO, the documentation of a member will +# be part of the file/class/namespace that contains it. + +SEPARATE_MEMBER_PAGES = NO + +# The TAB_SIZE tag can be used to set the number of spaces in a tab. +# Doxygen uses this value to replace tabs by spaces in code fragments. + +TAB_SIZE = 8 + +# This tag can be used to specify a number of aliases that acts +# as commands in the documentation. An alias has the form "name=value". +# For example adding "sideeffect=\par Side Effects:\n" will allow you to +# put the command \sideeffect (or @sideeffect) in the documentation, which +# will result in a user-defined paragraph with heading "Side Effects:". +# You can put \n's in the value part of an alias to insert newlines. + +ALIASES = + +# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C +# sources only. Doxygen will then generate output that is more tailored for C. +# For instance, some of the names that are used will be different. The list +# of all members will be omitted, etc. + +OPTIMIZE_OUTPUT_FOR_C = NO + +# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java +# sources only. Doxygen will then generate output that is more tailored for +# Java. For instance, namespaces will be presented as packages, qualified +# scopes will look different, etc. + +OPTIMIZE_OUTPUT_JAVA = YES + +# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran +# sources only. Doxygen will then generate output that is more tailored for +# Fortran. + +OPTIMIZE_FOR_FORTRAN = NO + +# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL +# sources. Doxygen will then generate output that is tailored for +# VHDL. + +OPTIMIZE_OUTPUT_VHDL = NO + +# Doxygen selects the parser to use depending on the extension of the files it parses. +# With this tag you can assign which parser to use for a given extension. +# Doxygen has a built-in mapping, but you can override or extend it using this tag. +# The format is ext=language, where ext is a file extension, and language is one of +# the parsers supported by doxygen: IDL, Java, Javascript, C#, C, C++, D, PHP, +# Objective-C, Python, Fortran, VHDL, C, C++. For instance to make doxygen treat +# .inc files as Fortran files (default is PHP), and .f files as C (default is Fortran), +# use: inc=Fortran f=C. Note that for custom extensions you also need to set FILE_PATTERNS otherwise the files are not read by doxygen. + +EXTENSION_MAPPING = + +# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want +# to include (a tag file for) the STL sources as input, then you should +# set this tag to YES in order to let doxygen match functions declarations and +# definitions whose arguments contain STL classes (e.g. func(std::string); v.s. +# func(std::string) {}). This also make the inheritance and collaboration +# diagrams that involve STL classes more complete and accurate. + +BUILTIN_STL_SUPPORT = NO + +# If you use Microsoft's C++/CLI language, you should set this option to YES to +# enable parsing support. + +CPP_CLI_SUPPORT = NO + +# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only. +# Doxygen will parse them like normal C++ but will assume all classes use public +# instead of private inheritance when no explicit protection keyword is present. + +SIP_SUPPORT = NO + +# For Microsoft's IDL there are propget and propput attributes to indicate getter +# and setter methods for a property. Setting this option to YES (the default) +# will make doxygen to replace the get and set methods by a property in the +# documentation. This will only work if the methods are indeed getting or +# setting a simple type. If this is not the case, or you want to show the +# methods anyway, you should set this option to NO. + +IDL_PROPERTY_SUPPORT = YES + +# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC +# tag is set to YES, then doxygen will reuse the documentation of the first +# member in the group (if any) for the other members of the group. By default +# all members of a group must be documented explicitly. + +DISTRIBUTE_GROUP_DOC = NO + +# Set the SUBGROUPING tag to YES (the default) to allow class member groups of +# the same type (for instance a group of public functions) to be put as a +# subgroup of that type (e.g. under the Public Functions section). Set it to +# NO to prevent subgrouping. Alternatively, this can be done per class using +# the \nosubgrouping command. + +SUBGROUPING = YES + +# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum +# is documented as struct, union, or enum with the name of the typedef. So +# typedef struct TypeS {} TypeT, will appear in the documentation as a struct +# with name TypeT. When disabled the typedef will appear as a member of a file, +# namespace, or class. And the struct will be named TypeS. This can typically +# be useful for C code in case the coding convention dictates that all compound +# types are typedef'ed and only the typedef is referenced, never the tag name. + +TYPEDEF_HIDES_STRUCT = NO + +# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to +# determine which symbols to keep in memory and which to flush to disk. +# When the cache is full, less often used symbols will be written to disk. +# For small to medium size projects (<1000 input files) the default value is +# probably good enough. For larger projects a too small cache size can cause +# doxygen to be busy swapping symbols to and from disk most of the time +# causing a significant performance penality. +# If the system has enough physical memory increasing the cache will improve the +# performance by keeping more symbols in memory. Note that the value works on +# a logarithmic scale so increasing the size by one will rougly double the +# memory usage. The cache size is given by this formula: +# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0, +# corresponding to a cache size of 2^16 = 65536 symbols + +SYMBOL_CACHE_SIZE = 0 + +#--------------------------------------------------------------------------- +# Build related configuration options +#--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in +# documentation are documented, even if no documentation was available. +# Private class members and static file members will be hidden unless +# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES + +EXTRACT_ALL = YES + +# If the EXTRACT_PRIVATE tag is set to YES all private members of a class +# will be included in the documentation. + +EXTRACT_PRIVATE = YES + +# If the EXTRACT_STATIC tag is set to YES all static members of a file +# will be included in the documentation. + +EXTRACT_STATIC = YES + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) +# defined locally in source files will be included in the documentation. +# If set to NO only classes defined in header files are included. + +EXTRACT_LOCAL_CLASSES = YES + +# This flag is only useful for Objective-C code. When set to YES local +# methods, which are defined in the implementation section but not in +# the interface are included in the documentation. +# If set to NO (the default) only methods in the interface are included. + +EXTRACT_LOCAL_METHODS = YES + +# If this flag is set to YES, the members of anonymous namespaces will be +# extracted and appear in the documentation as a namespace called +# 'anonymous_namespace{file}', where file will be replaced with the base +# name of the file that contains the anonymous namespace. By default +# anonymous namespace are hidden. + +EXTRACT_ANON_NSPACES = NO + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all +# undocumented members of documented classes, files or namespaces. +# If set to NO (the default) these members will be included in the +# various overviews, but no documentation section is generated. +# This option has no effect if EXTRACT_ALL is enabled. + +HIDE_UNDOC_MEMBERS = NO + +# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. +# If set to NO (the default) these classes will be included in the various +# overviews. This option has no effect if EXTRACT_ALL is enabled. + +HIDE_UNDOC_CLASSES = NO + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all +# friend (class|struct|union) declarations. +# If set to NO (the default) these declarations will be included in the +# documentation. + +HIDE_FRIEND_COMPOUNDS = NO + +# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any +# documentation blocks found inside the body of a function. +# If set to NO (the default) these blocks will be appended to the +# function's detailed documentation block. + +HIDE_IN_BODY_DOCS = NO + +# The INTERNAL_DOCS tag determines if documentation +# that is typed after a \internal command is included. If the tag is set +# to NO (the default) then the documentation will be excluded. +# Set it to YES to include the internal documentation. + +INTERNAL_DOCS = YES + +# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate +# file names in lower-case letters. If set to YES upper-case letters are also +# allowed. This is useful if you have classes or files whose names only differ +# in case and if your file system supports case sensitive file names. Windows +# and Mac users are advised to set this option to NO. + +CASE_SENSE_NAMES = YES + +# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen +# will show members with their full class and namespace scopes in the +# documentation. If set to YES the scope will be hidden. + +HIDE_SCOPE_NAMES = NO + +# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen +# will put a list of the files that are included by a file in the documentation +# of that file. + +SHOW_INCLUDE_FILES = YES + +# If the INLINE_INFO tag is set to YES (the default) then a tag [inline] +# is inserted in the documentation for inline members. + +INLINE_INFO = YES + +# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen +# will sort the (detailed) documentation of file and class members +# alphabetically by member name. If set to NO the members will appear in +# declaration order. + +SORT_MEMBER_DOCS = YES + +# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the +# brief documentation of file, namespace and class members alphabetically +# by member name. If set to NO (the default) the members will appear in +# declaration order. + +SORT_BRIEF_DOCS = NO + +# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the (brief and detailed) documentation of class members so that constructors and destructors are listed first. If set to NO (the default) the constructors will appear in the respective orders defined by SORT_MEMBER_DOCS and SORT_BRIEF_DOCS. This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO. + +SORT_MEMBERS_CTORS_1ST = NO + +# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the +# hierarchy of group names into alphabetical order. If set to NO (the default) +# the group names will appear in their defined order. + +SORT_GROUP_NAMES = NO + +# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be +# sorted by fully-qualified names, including namespaces. If set to +# NO (the default), the class list will be sorted only by class name, +# not including the namespace part. +# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. +# Note: This option applies only to the class list, not to the +# alphabetical list. + +SORT_BY_SCOPE_NAME = NO + +# The GENERATE_TODOLIST tag can be used to enable (YES) or +# disable (NO) the todo list. This list is created by putting \todo +# commands in the documentation. + +GENERATE_TODOLIST = YES + +# The GENERATE_TESTLIST tag can be used to enable (YES) or +# disable (NO) the test list. This list is created by putting \test +# commands in the documentation. + +GENERATE_TESTLIST = YES + +# The GENERATE_BUGLIST tag can be used to enable (YES) or +# disable (NO) the bug list. This list is created by putting \bug +# commands in the documentation. + +GENERATE_BUGLIST = YES + +# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or +# disable (NO) the deprecated list. This list is created by putting +# \deprecated commands in the documentation. + +GENERATE_DEPRECATEDLIST= YES + +# The ENABLED_SECTIONS tag can be used to enable conditional +# documentation sections, marked by \if sectionname ... \endif. + +ENABLED_SECTIONS = + +# The MAX_INITIALIZER_LINES tag determines the maximum number of lines +# the initial value of a variable or define consists of for it to appear in +# the documentation. If the initializer consists of more lines than specified +# here it will be hidden. Use a value of 0 to hide initializers completely. +# The appearance of the initializer of individual variables and defines in the +# documentation can be controlled using \showinitializer or \hideinitializer +# command in the documentation regardless of this setting. + +MAX_INITIALIZER_LINES = 30 + +# Set the SHOW_USED_FILES tag to NO to disable the list of files generated +# at the bottom of the documentation of classes and structs. If set to YES the +# list will mention the files that were used to generate the documentation. + +SHOW_USED_FILES = YES + +# If the sources in your project are distributed over multiple directories +# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy +# in the documentation. The default is NO. + +SHOW_DIRECTORIES = YES + +# Set the SHOW_FILES tag to NO to disable the generation of the Files page. +# This will remove the Files entry from the Quick Index and from the +# Folder Tree View (if specified). The default is YES. + +SHOW_FILES = YES + +# Set the SHOW_NAMESPACES tag to NO to disable the generation of the +# Namespaces page. +# This will remove the Namespaces entry from the Quick Index +# and from the Folder Tree View (if specified). The default is YES. + +SHOW_NAMESPACES = YES + +# The FILE_VERSION_FILTER tag can be used to specify a program or script that +# doxygen should invoke to get the current version for each file (typically from +# the version control system). Doxygen will invoke the program by executing (via +# popen()) the command , where is the value of +# the FILE_VERSION_FILTER tag, and is the name of an input file +# provided by doxygen. Whatever the program writes to standard output +# is used as the file version. See the manual for examples. + +FILE_VERSION_FILTER = + +# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed by +# doxygen. The layout file controls the global structure of the generated output files +# in an output format independent way. The create the layout file that represents +# doxygen's defaults, run doxygen with the -l option. You can optionally specify a +# file name after the option, if omitted DoxygenLayout.xml will be used as the name +# of the layout file. + +LAYOUT_FILE = + +#--------------------------------------------------------------------------- +# configuration options related to warning and progress messages +#--------------------------------------------------------------------------- + +# The QUIET tag can be used to turn on/off the messages that are generated +# by doxygen. Possible values are YES and NO. If left blank NO is used. + +QUIET = NO + +# The WARNINGS tag can be used to turn on/off the warning messages that are +# generated by doxygen. Possible values are YES and NO. If left blank +# NO is used. + +WARNINGS = YES + +# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings +# for undocumented members. If EXTRACT_ALL is set to YES then this flag will +# automatically be disabled. + +WARN_IF_UNDOCUMENTED = YES + +# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for +# potential errors in the documentation, such as not documenting some +# parameters in a documented function, or documenting parameters that +# don't exist or using markup commands wrongly. + +WARN_IF_DOC_ERROR = YES + +# This WARN_NO_PARAMDOC option can be abled to get warnings for +# functions that are documented, but have no documentation for their parameters +# or return value. If set to NO (the default) doxygen will only warn about +# wrong or incomplete parameter documentation, but not about the absence of +# documentation. + +WARN_NO_PARAMDOC = NO + +# The WARN_FORMAT tag determines the format of the warning messages that +# doxygen can produce. The string should contain the $file, $line, and $text +# tags, which will be replaced by the file and line number from which the +# warning originated and the warning text. Optionally the format may contain +# $version, which will be replaced by the version of the file (if it could +# be obtained via FILE_VERSION_FILTER) + +WARN_FORMAT = "$file:$line: $text" + +# The WARN_LOGFILE tag can be used to specify a file to which warning +# and error messages should be written. If left blank the output is written +# to stderr. + +WARN_LOGFILE = doxygen.log + +#--------------------------------------------------------------------------- +# configuration options related to the input files +#--------------------------------------------------------------------------- + +# The INPUT tag can be used to specify the files and/or directories that contain +# documented source files. You may enter file names like "myfile.cpp" or +# directories like "/usr/src/myproject". Separate the files or directories +# with spaces. + +INPUT = pycnal + +# This tag can be used to specify the character encoding of the source files +# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is +# also the default input encoding. Doxygen uses libiconv (or the iconv built +# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for +# the list of possible encodings. + +INPUT_ENCODING = UTF-8 + +# If the value of the INPUT tag contains directories, you can use the +# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank the following patterns are tested: +# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx +# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90 + +FILE_PATTERNS = + +# The RECURSIVE tag can be used to turn specify whether or not subdirectories +# should be searched for input files as well. Possible values are YES and NO. +# If left blank NO is used. + +RECURSIVE = YES + +# The EXCLUDE tag can be used to specify files and/or directories that should +# excluded from the INPUT source files. This way you can easily exclude a +# subdirectory from a directory tree whose root is specified with the INPUT tag. + +EXCLUDE = + +# The EXCLUDE_SYMLINKS tag can be used select whether or not files or +# directories that are symbolic links (a Unix filesystem feature) are excluded +# from the input. + +EXCLUDE_SYMLINKS = NO + +# If the value of the INPUT tag contains directories, you can use the +# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude +# certain files from those directories. Note that the wildcards are matched +# against the file with absolute path, so to exclude all test directories +# for example use the pattern */test/* + +EXCLUDE_PATTERNS = + +# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names +# (namespaces, classes, functions, etc.) that should be excluded from the +# output. The symbol name can be a fully qualified name, a word, or if the +# wildcard * is used, a substring. Examples: ANamespace, AClass, +# AClass::ANamespace, ANamespace::*Test + +EXCLUDE_SYMBOLS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or +# directories that contain example code fragments that are included (see +# the \include command). + +EXAMPLE_PATH = + +# If the value of the EXAMPLE_PATH tag contains directories, you can use the +# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank all files are included. + +EXAMPLE_PATTERNS = + +# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be +# searched for input files to be used with the \include or \dontinclude +# commands irrespective of the value of the RECURSIVE tag. +# Possible values are YES and NO. If left blank NO is used. + +EXAMPLE_RECURSIVE = NO + +# The IMAGE_PATH tag can be used to specify one or more files or +# directories that contain image that are included in the documentation (see +# the \image command). + +IMAGE_PATH = + +# The INPUT_FILTER tag can be used to specify a program that doxygen should +# invoke to filter for each input file. Doxygen will invoke the filter program +# by executing (via popen()) the command , where +# is the value of the INPUT_FILTER tag, and is the name of an +# input file. Doxygen will then use the output that the filter program writes +# to standard output. +# If FILTER_PATTERNS is specified, this tag will be +# ignored. + +INPUT_FILTER = + +# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern +# basis. +# Doxygen will compare the file name with each pattern and apply the +# filter if there is a match. +# The filters are a list of the form: +# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further +# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER +# is applied to all files. + +FILTER_PATTERNS = + +# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using +# INPUT_FILTER) will be used to filter the input files when producing source +# files to browse (i.e. when SOURCE_BROWSER is set to YES). + +FILTER_SOURCE_FILES = NO + +#--------------------------------------------------------------------------- +# configuration options related to source browsing +#--------------------------------------------------------------------------- + +# If the SOURCE_BROWSER tag is set to YES then a list of source files will +# be generated. Documented entities will be cross-referenced with these sources. +# Note: To get rid of all source code in the generated output, make sure also +# VERBATIM_HEADERS is set to NO. + +SOURCE_BROWSER = YES + +# Setting the INLINE_SOURCES tag to YES will include the body +# of functions and classes directly in the documentation. + +INLINE_SOURCES = YES + +# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct +# doxygen to hide any special comment blocks from generated source code +# fragments. Normal C and C++ comments will always remain visible. + +STRIP_CODE_COMMENTS = NO + +# If the REFERENCED_BY_RELATION tag is set to YES +# then for each documented function all documented +# functions referencing it will be listed. + +REFERENCED_BY_RELATION = YES + +# If the REFERENCES_RELATION tag is set to YES +# then for each documented function all documented entities +# called/used by that function will be listed. + +REFERENCES_RELATION = YES + +# If the REFERENCES_LINK_SOURCE tag is set to YES (the default) +# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from +# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will +# link to the source code. +# Otherwise they will link to the documentation. + +REFERENCES_LINK_SOURCE = YES + +# If the USE_HTAGS tag is set to YES then the references to source code +# will point to the HTML generated by the htags(1) tool instead of doxygen +# built-in source browser. The htags tool is part of GNU's global source +# tagging system (see http://www.gnu.org/software/global/global.html). You +# will need version 4.8.6 or higher. + +USE_HTAGS = NO + +# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen +# will generate a verbatim copy of the header file for each class for +# which an include is specified. Set to NO to disable this. + +VERBATIM_HEADERS = YES + +#--------------------------------------------------------------------------- +# configuration options related to the alphabetical class index +#--------------------------------------------------------------------------- + +# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index +# of all compounds will be generated. Enable this if the project +# contains a lot of classes, structs, unions or interfaces. + +ALPHABETICAL_INDEX = YES + +# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then +# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns +# in which this list will be split (can be a number in the range [1..20]) + +COLS_IN_ALPHA_INDEX = 5 + +# In case all classes in a project start with a common prefix, all +# classes will be put under the same header in the alphabetical index. +# The IGNORE_PREFIX tag can be used to specify one or more prefixes that +# should be ignored while generating the index headers. + +IGNORE_PREFIX = + +#--------------------------------------------------------------------------- +# configuration options related to the HTML output +#--------------------------------------------------------------------------- + +# If the GENERATE_HTML tag is set to YES (the default) Doxygen will +# generate HTML output. + +GENERATE_HTML = YES + +# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `html' will be used as the default path. + +HTML_OUTPUT = html + +# The HTML_FILE_EXTENSION tag can be used to specify the file extension for +# each generated HTML page (for example: .htm,.php,.asp). If it is left blank +# doxygen will generate files with .html extension. + +HTML_FILE_EXTENSION = .html + +# The HTML_HEADER tag can be used to specify a personal HTML header for +# each generated HTML page. If it is left blank doxygen will generate a +# standard header. + +HTML_HEADER = + +# The HTML_FOOTER tag can be used to specify a personal HTML footer for +# each generated HTML page. If it is left blank doxygen will generate a +# standard footer. + +HTML_FOOTER = + +# If the HTML_TIMESTAMP tag is set to YES then the generated HTML +# documentation will contain the timesstamp. + +HTML_TIMESTAMP = NO + +# The HTML_STYLESHEET tag can be used to specify a user-defined cascading +# style sheet that is used by each HTML page. It can be used to +# fine-tune the look of the HTML output. If the tag is left blank doxygen +# will generate a default style sheet. Note that doxygen will try to copy +# the style sheet file to the HTML output directory, so don't put your own +# stylesheet in the HTML output directory as well, or it will be erased! + +HTML_STYLESHEET = + +# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, +# files or namespaces will be aligned in HTML using tables. If set to +# NO a bullet list will be used. + +HTML_ALIGN_MEMBERS = YES + +# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML +# documentation will contain sections that can be hidden and shown after the +# page has loaded. For this to work a browser that supports +# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox +# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari). + +HTML_DYNAMIC_SECTIONS = NO + +# If the GENERATE_DOCSET tag is set to YES, additional index files +# will be generated that can be used as input for Apple's Xcode 3 +# integrated development environment, introduced with OSX 10.5 (Leopard). +# To create a documentation set, doxygen will generate a Makefile in the +# HTML output directory. Running make will produce the docset in that +# directory and running "make install" will install the docset in +# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find +# it at startup. +# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html for more information. + +GENERATE_DOCSET = NO + +# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the +# feed. A documentation feed provides an umbrella under which multiple +# documentation sets from a single provider (such as a company or product suite) +# can be grouped. + +DOCSET_FEEDNAME = "Doxygen generated docs" + +# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that +# should uniquely identify the documentation set bundle. This should be a +# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen +# will append .docset to the name. + +DOCSET_BUNDLE_ID = org.doxygen.Project + +# If the GENERATE_HTMLHELP tag is set to YES, additional index files +# will be generated that can be used as input for tools like the +# Microsoft HTML help workshop to generate a compiled HTML help file (.chm) +# of the generated HTML documentation. + +GENERATE_HTMLHELP = NO + +# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can +# be used to specify the file name of the resulting .chm file. You +# can add a path in front of the file if the result should not be +# written to the html output directory. + +CHM_FILE = + +# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can +# be used to specify the location (absolute path including file name) of +# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run +# the HTML help compiler on the generated index.hhp. + +HHC_LOCATION = + +# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag +# controls if a separate .chi index file is generated (YES) or that +# it should be included in the master .chm file (NO). + +GENERATE_CHI = NO + +# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING +# is used to encode HtmlHelp index (hhk), content (hhc) and project file +# content. + +CHM_INDEX_ENCODING = + +# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag +# controls whether a binary table of contents is generated (YES) or a +# normal table of contents (NO) in the .chm file. + +BINARY_TOC = NO + +# The TOC_EXPAND flag can be set to YES to add extra items for group members +# to the contents of the HTML help documentation and to the tree view. + +TOC_EXPAND = NO + +# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and QHP_VIRTUAL_FOLDER +# are set, an additional index file will be generated that can be used as input for +# Qt's qhelpgenerator to generate a Qt Compressed Help (.qch) of the generated +# HTML documentation. + +GENERATE_QHP = NO + +# If the QHG_LOCATION tag is specified, the QCH_FILE tag can +# be used to specify the file name of the resulting .qch file. +# The path specified is relative to the HTML output folder. + +QCH_FILE = + +# The QHP_NAMESPACE tag specifies the namespace to use when generating +# Qt Help Project output. For more information please see +# http://doc.trolltech.com/qthelpproject.html#namespace + +QHP_NAMESPACE = + +# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating +# Qt Help Project output. For more information please see +# http://doc.trolltech.com/qthelpproject.html#virtual-folders + +QHP_VIRTUAL_FOLDER = doc + +# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to add. +# For more information please see +# http://doc.trolltech.com/qthelpproject.html#custom-filters + +QHP_CUST_FILTER_NAME = + +# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the custom filter to add.For more information please see +# Qt Help Project / Custom Filters. + +QHP_CUST_FILTER_ATTRS = + +# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this project's +# filter section matches. +# Qt Help Project / Filter Attributes. + +QHP_SECT_FILTER_ATTRS = + +# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can +# be used to specify the location of Qt's qhelpgenerator. +# If non-empty doxygen will try to run qhelpgenerator on the generated +# .qhp file. + +QHG_LOCATION = + +# The DISABLE_INDEX tag can be used to turn on/off the condensed index at +# top of each HTML page. The value NO (the default) enables the index and +# the value YES disables it. + +DISABLE_INDEX = NO + +# This tag can be used to set the number of enum values (range [1..20]) +# that doxygen will group on one line in the generated HTML documentation. + +ENUM_VALUES_PER_LINE = 4 + +# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index +# structure should be generated to display hierarchical information. +# If the tag value is set to YES, a side panel will be generated +# containing a tree-like index structure (just like the one that +# is generated for HTML Help). For this to work a browser that supports +# JavaScript, DHTML, CSS and frames is required (i.e. any modern browser). +# Windows users are probably better off using the HTML help feature. + +GENERATE_TREEVIEW = YES + +# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories, +# and Class Hierarchy pages using a tree view instead of an ordered list. + +USE_INLINE_TREES = NO + +# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be +# used to set the initial width (in pixels) of the frame in which the tree +# is shown. + +TREEVIEW_WIDTH = 250 + +# Use this tag to change the font size of Latex formulas included +# as images in the HTML documentation. The default is 10. Note that +# when you change the font size after a successful doxygen run you need +# to manually remove any form_*.png images from the HTML output directory +# to force them to be regenerated. + +FORMULA_FONTSIZE = 10 + +# When the SEARCHENGINE tag is enable doxygen will generate a search box for the HTML output. The underlying search engine uses javascript +# and DHTML and should work on any modern browser. Note that when using HTML help (GENERATE_HTMLHELP) or Qt help (GENERATE_QHP) +# there is already a search function so this one should typically +# be disabled. + +SEARCHENGINE = YES + +#--------------------------------------------------------------------------- +# configuration options related to the LaTeX output +#--------------------------------------------------------------------------- + +# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will +# generate Latex output. + +GENERATE_LATEX = NO + +# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `latex' will be used as the default path. + +LATEX_OUTPUT = latex + +# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be +# invoked. If left blank `latex' will be used as the default command name. + +LATEX_CMD_NAME = latex + +# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to +# generate index for LaTeX. If left blank `makeindex' will be used as the +# default command name. + +MAKEINDEX_CMD_NAME = makeindex + +# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact +# LaTeX documents. This may be useful for small projects and may help to +# save some trees in general. + +COMPACT_LATEX = NO + +# The PAPER_TYPE tag can be used to set the paper type that is used +# by the printer. Possible values are: a4, a4wide, letter, legal and +# executive. If left blank a4wide will be used. + +PAPER_TYPE = letter + +# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX +# packages that should be included in the LaTeX output. + +EXTRA_PACKAGES = + +# The LATEX_HEADER tag can be used to specify a personal LaTeX header for +# the generated latex document. The header should contain everything until +# the first chapter. If it is left blank doxygen will generate a +# standard header. Notice: only use this tag if you know what you are doing! + +LATEX_HEADER = + +# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated +# is prepared for conversion to pdf (using ps2pdf). The pdf file will +# contain links (just like the HTML output) instead of page references +# This makes the output suitable for online browsing using a pdf viewer. + +PDF_HYPERLINKS = YES + +# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of +# plain latex in the generated Makefile. Set this option to YES to get a +# higher quality PDF documentation. + +USE_PDFLATEX = YES + +# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. +# command to the generated LaTeX files. This will instruct LaTeX to keep +# running if errors occur, instead of asking the user for help. +# This option is also used when generating formulas in HTML. + +LATEX_BATCHMODE = NO + +# If LATEX_HIDE_INDICES is set to YES then doxygen will not +# include the index chapters (such as File Index, Compound Index, etc.) +# in the output. + +LATEX_HIDE_INDICES = NO + +# If LATEX_SOURCE_CODE is set to YES then doxygen will include source code with syntax highlighting in the LaTeX output. Note that which sources are shown also depends on other settings such as SOURCE_BROWSER. + +LATEX_SOURCE_CODE = NO + +#--------------------------------------------------------------------------- +# configuration options related to the RTF output +#--------------------------------------------------------------------------- + +# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output +# The RTF output is optimized for Word 97 and may not look very pretty with +# other RTF readers or editors. + +GENERATE_RTF = NO + +# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `rtf' will be used as the default path. + +RTF_OUTPUT = rtf + +# If the COMPACT_RTF tag is set to YES Doxygen generates more compact +# RTF documents. This may be useful for small projects and may help to +# save some trees in general. + +COMPACT_RTF = NO + +# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated +# will contain hyperlink fields. The RTF file will +# contain links (just like the HTML output) instead of page references. +# This makes the output suitable for online browsing using WORD or other +# programs which support those fields. +# Note: wordpad (write) and others do not support links. + +RTF_HYPERLINKS = NO + +# Load stylesheet definitions from file. Syntax is similar to doxygen's +# config file, i.e. a series of assignments. You only have to provide +# replacements, missing definitions are set to their default value. + +RTF_STYLESHEET_FILE = + +# Set optional variables used in the generation of an rtf document. +# Syntax is similar to doxygen's config file. + +RTF_EXTENSIONS_FILE = + +#--------------------------------------------------------------------------- +# configuration options related to the man page output +#--------------------------------------------------------------------------- + +# If the GENERATE_MAN tag is set to YES (the default) Doxygen will +# generate man pages + +GENERATE_MAN = NO + +# The MAN_OUTPUT tag is used to specify where the man pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `man' will be used as the default path. + +MAN_OUTPUT = man + +# The MAN_EXTENSION tag determines the extension that is added to +# the generated man pages (default is the subroutine's section .3) + +MAN_EXTENSION = .3 + +# If the MAN_LINKS tag is set to YES and Doxygen generates man output, +# then it will generate one additional man file for each entity +# documented in the real man page(s). These additional files +# only source the real man page, but without them the man command +# would be unable to find the correct page. The default is NO. + +MAN_LINKS = NO + +#--------------------------------------------------------------------------- +# configuration options related to the XML output +#--------------------------------------------------------------------------- + +# If the GENERATE_XML tag is set to YES Doxygen will +# generate an XML file that captures the structure of +# the code including all documentation. + +GENERATE_XML = NO + +# The XML_OUTPUT tag is used to specify where the XML pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. 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Note that +# enabling this will significantly increase the size of the XML output. + +XML_PROGRAMLISTING = YES + +#--------------------------------------------------------------------------- +# configuration options for the AutoGen Definitions output +#--------------------------------------------------------------------------- + +# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will +# generate an AutoGen Definitions (see autogen.sf.net) file +# that captures the structure of the code including all +# documentation. 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If left blank, the patterns specified with FILE_PATTERNS will +# be used. + +INCLUDE_FILE_PATTERNS = + +# The PREDEFINED tag can be used to specify one or more macro names that +# are defined before the preprocessor is started (similar to the -D option of +# gcc). The argument of the tag is a list of macros of the form: name +# or name=definition (no spaces). If the definition and the = are +# omitted =1 is assumed. To prevent a macro definition from being +# undefined via #undef or recursively expanded use the := operator +# instead of the = operator. + +PREDEFINED = + +# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then +# this tag can be used to specify a list of macro names that should be expanded. +# The macro definition that is found in the sources will be used. +# Use the PREDEFINED tag if you want to use a different macro definition. + +EXPAND_AS_DEFINED = + +# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then +# doxygen's preprocessor will remove all function-like macros that are alone +# on a line, have an all uppercase name, and do not end with a semicolon. Such +# function macros are typically used for boiler-plate code, and will confuse +# the parser if not removed. + +SKIP_FUNCTION_MACROS = YES + +#--------------------------------------------------------------------------- +# Configuration::additions related to external references +#--------------------------------------------------------------------------- + +# The TAGFILES option can be used to specify one or more tagfiles. +# Optionally an initial location of the external documentation +# can be added for each tagfile. The format of a tag file without +# this location is as follows: +# +# TAGFILES = file1 file2 ... +# Adding location for the tag files is done as follows: +# +# TAGFILES = file1=loc1 "file2 = loc2" ... +# where "loc1" and "loc2" can be relative or absolute paths or +# URLs. If a location is present for each tag, the installdox tool +# does not have to be run to correct the links. +# Note that each tag file must have a unique name +# (where the name does NOT include the path) +# If a tag file is not located in the directory in which doxygen +# is run, you must also specify the path to the tagfile here. + +TAGFILES = + +# When a file name is specified after GENERATE_TAGFILE, doxygen will create +# a tag file that is based on the input files it reads. + +GENERATE_TAGFILE = + +# If the ALLEXTERNALS tag is set to YES all external classes will be listed +# in the class index. If set to NO only the inherited external classes +# will be listed. + +ALLEXTERNALS = NO + +# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed +# in the modules index. If set to NO, only the current project's groups will +# be listed. + +EXTERNAL_GROUPS = YES + +# The PERL_PATH should be the absolute path and name of the perl script +# interpreter (i.e. the result of `which perl'). + +PERL_PATH = /usr/bin/perl + +#--------------------------------------------------------------------------- +# Configuration options related to the dot tool +#--------------------------------------------------------------------------- + +# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will +# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base +# or super classes. Setting the tag to NO turns the diagrams off. Note that +# this option is superseded by the HAVE_DOT option below. This is only a +# fallback. It is recommended to install and use dot, since it yields more +# powerful graphs. + +CLASS_DIAGRAMS = YES + +# You can define message sequence charts within doxygen comments using the \msc +# command. Doxygen will then run the mscgen tool (see +# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the +# documentation. The MSCGEN_PATH tag allows you to specify the directory where +# the mscgen tool resides. If left empty the tool is assumed to be found in the +# default search path. + +MSCGEN_PATH = + +# If set to YES, the inheritance and collaboration graphs will hide +# inheritance and usage relations if the target is undocumented +# or is not a class. + +HIDE_UNDOC_RELATIONS = YES + +# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is +# available from the path. This tool is part of Graphviz, a graph visualization +# toolkit from AT&T and Lucent Bell Labs. The other options in this section +# have no effect if this option is set to NO (the default) + +HAVE_DOT = YES + +# By default doxygen will write a font called FreeSans.ttf to the output +# directory and reference it in all dot files that doxygen generates. This +# font does not include all possible unicode characters however, so when you need +# these (or just want a differently looking font) you can specify the font name +# using DOT_FONTNAME. You need need to make sure dot is able to find the font, +# which can be done by putting it in a standard location or by setting the +# DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory +# containing the font. + +DOT_FONTNAME = FreeSans + +# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs. +# The default size is 10pt. + +DOT_FONTSIZE = 10 + +# By default doxygen will tell dot to use the output directory to look for the +# FreeSans.ttf font (which doxygen will put there itself). If you specify a +# different font using DOT_FONTNAME you can set the path where dot +# can find it using this tag. + +DOT_FONTPATH = + +# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for each documented class showing the direct and +# indirect inheritance relations. Setting this tag to YES will force the +# the CLASS_DIAGRAMS tag to NO. + +CLASS_GRAPH = YES + +# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for each documented class showing the direct and +# indirect implementation dependencies (inheritance, containment, and +# class references variables) of the class with other documented classes. + +COLLABORATION_GRAPH = YES + +# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for groups, showing the direct groups dependencies + +GROUP_GRAPHS = YES + +# If the UML_LOOK tag is set to YES doxygen will generate inheritance and +# collaboration diagrams in a style similar to the OMG's Unified Modeling +# Language. + +UML_LOOK = NO + +# If set to YES, the inheritance and collaboration graphs will show the +# relations between templates and their instances. + +TEMPLATE_RELATIONS = NO + +# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT +# tags are set to YES then doxygen will generate a graph for each documented +# file showing the direct and indirect include dependencies of the file with +# other documented files. + +INCLUDE_GRAPH = YES + +# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and +# HAVE_DOT tags are set to YES then doxygen will generate a graph for each +# documented header file showing the documented files that directly or +# indirectly include this file. + +INCLUDED_BY_GRAPH = YES + +# If the CALL_GRAPH and HAVE_DOT options are set to YES then +# doxygen will generate a call dependency graph for every global function +# or class method. Note that enabling this option will significantly increase +# the time of a run. So in most cases it will be better to enable call graphs +# for selected functions only using the \callgraph command. + +CALL_GRAPH = NO + +# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then +# doxygen will generate a caller dependency graph for every global function +# or class method. Note that enabling this option will significantly increase +# the time of a run. So in most cases it will be better to enable caller +# graphs for selected functions only using the \callergraph command. + +CALLER_GRAPH = NO + +# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen +# will graphical hierarchy of all classes instead of a textual one. + +GRAPHICAL_HIERARCHY = YES + +# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES +# then doxygen will show the dependencies a directory has on other directories +# in a graphical way. The dependency relations are determined by the #include +# relations between the files in the directories. + +DIRECTORY_GRAPH = YES + +# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images +# generated by dot. Possible values are png, jpg, or gif +# If left blank png will be used. + +DOT_IMAGE_FORMAT = png + +# The tag DOT_PATH can be used to specify the path where the dot tool can be +# found. If left blank, it is assumed the dot tool can be found in the path. + +DOT_PATH = + +# The DOTFILE_DIRS tag can be used to specify one or more directories that +# contain dot files that are included in the documentation (see the +# \dotfile command). + +DOTFILE_DIRS = + +# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of +# nodes that will be shown in the graph. If the number of nodes in a graph +# becomes larger than this value, doxygen will truncate the graph, which is +# visualized by representing a node as a red box. Note that doxygen if the +# number of direct children of the root node in a graph is already larger than +# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note +# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH. + +DOT_GRAPH_MAX_NODES = 50 + +# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the +# graphs generated by dot. A depth value of 3 means that only nodes reachable +# from the root by following a path via at most 3 edges will be shown. Nodes +# that lay further from the root node will be omitted. Note that setting this +# option to 1 or 2 may greatly reduce the computation time needed for large +# code bases. Also note that the size of a graph can be further restricted by +# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction. + +MAX_DOT_GRAPH_DEPTH = 0 + +# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent +# background. This is disabled by default, because dot on Windows does not +# seem to support this out of the box. Warning: Depending on the platform used, +# enabling this option may lead to badly anti-aliased labels on the edges of +# a graph (i.e. they become hard to read). + +DOT_TRANSPARENT = NO + +# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output +# files in one run (i.e. multiple -o and -T options on the command line). 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The 'nomargin' class is used to remove both the - * top and bottom margin (but not the left or right margin -- - * for lists, that would cause the bullets to disappear.) - */ -p.indent-wrapped-lines { padding: 0 0 0 7em; text-indent: -7em; - margin: 0; } -.nomargin-top { margin-top: 0; } -.nomargin { margin-top: 0; margin-bottom: 0; } - -/* HTML Log */ -div.log-block { padding: 0; margin: .5em 0 .5em 0; - background: #e8f0f8; color: #000000; - border: 1px solid #000000; } -div.log-error { padding: .1em .3em .1em .3em; margin: 4px; - background: #ffb0b0; color: #000000; - border: 1px solid #000000; } -div.log-warning { padding: .1em .3em .1em .3em; margin: 4px; - background: #ffffb0; color: #000000; - border: 1px solid #000000; } -div.log-info { padding: .1em .3em .1em .3em; margin: 4px; - background: #b0ffb0; color: #000000; - border: 1px solid #000000; } -h2.log-hdr { background: #70b0ff; color: #000000; - margin: 0; padding: 0em 0.5em 0em 0.5em; - border-bottom: 1px solid #000000; font-size: 110%; } -p.log { font-weight: bold; margin: .5em 0 .5em 0; } -tr.opt-changed { color: #000000; font-weight: bold; } -tr.opt-default { color: #606060; } -pre.log { margin: 0; padding: 0; padding-left: 1em; } diff --git a/pyroms/docs/epydoc.js b/pyroms/docs/epydoc.js deleted file mode 100644 index e787dbc..0000000 --- a/pyroms/docs/epydoc.js +++ /dev/null @@ -1,293 +0,0 @@ -function toggle_private() { - // Search for any private/public links on this page. Store - // their old text in "cmd," so we will know what action to - // take; and change their text to the opposite action. - var cmd = "?"; - var elts = document.getElementsByTagName("a"); - for(var i=0; i...
"; - elt.innerHTML = s; - } -} - -function toggle(id) { - elt = document.getElementById(id+"-toggle"); - if (elt.innerHTML == "-") - collapse(id); - else - expand(id); - return false; -} - -function highlight(id) { - var elt = document.getElementById(id+"-def"); - if (elt) elt.className = "py-highlight-hdr"; - var elt = document.getElementById(id+"-expanded"); - if (elt) elt.className = "py-highlight"; - var elt = document.getElementById(id+"-collapsed"); - if (elt) elt.className = "py-highlight"; -} - -function num_lines(s) { - var n = 1; - var pos = s.indexOf("\n"); - while ( pos > 0) { - n += 1; - pos = s.indexOf("\n", pos+1); - } - return n; -} - -// Collapse all blocks that mave more than `min_lines` lines. -function collapse_all(min_lines) { - var elts = document.getElementsByTagName("div"); - for (var i=0; i 0) - if (elt.id.substring(split, elt.id.length) == "-expanded") - if (num_lines(elt.innerHTML) > min_lines) - collapse(elt.id.substring(0, split)); - } -} - -function expandto(href) { - var start = href.indexOf("#")+1; - if (start != 0 && start != href.length) { - if (href.substring(start, href.length) != "-") { - collapse_all(4); - pos = href.indexOf(".", start); - while (pos != -1) { - var id = href.substring(start, pos); - expand(id); - pos = href.indexOf(".", pos+1); - } - var id = href.substring(start, href.length); - expand(id); - highlight(id); - } - } -} - -function kill_doclink(id) { - var parent = document.getElementById(id); - parent.removeChild(parent.childNodes.item(0)); -} -function auto_kill_doclink(ev) { - if (!ev) var ev = window.event; - if (!this.contains(ev.toElement)) { - var parent = document.getElementById(this.parentID); - parent.removeChild(parent.childNodes.item(0)); - } -} - -function doclink(id, name, targets_id) { - var elt = document.getElementById(id); - - // If we already opened the box, then destroy it. - // (This case should never occur, but leave it in just in case.) - if (elt.childNodes.length > 1) { - elt.removeChild(elt.childNodes.item(0)); - } - else { - // The outer box: relative + inline positioning. - var box1 = document.createElement("div"); - box1.style.position = "relative"; - box1.style.display = "inline"; - box1.style.top = 0; - box1.style.left = 0; - - // A shadow for fun - var shadow = document.createElement("div"); - shadow.style.position = "absolute"; - shadow.style.left = "-1.3em"; - shadow.style.top = "-1.3em"; - shadow.style.background = "#404040"; - - // The inner box: absolute positioning. - var box2 = document.createElement("div"); - box2.style.position = "relative"; - box2.style.border = "1px solid #a0a0a0"; - box2.style.left = "-.2em"; - box2.style.top = "-.2em"; - box2.style.background = "white"; - box2.style.padding = ".3em .4em .3em .4em"; - box2.style.fontStyle = "normal"; - box2.onmouseout=auto_kill_doclink; - box2.parentID = id; - - // Get the targets - var targets_elt = document.getElementById(targets_id); - var targets = targets_elt.getAttribute("targets"); - var links = ""; - target_list = targets.split(","); - for (var i=0; i" + - target[0] + ""; - } - - // Put it all together. - elt.insertBefore(box1, elt.childNodes.item(0)); - //box1.appendChild(box2); - box1.appendChild(shadow); - shadow.appendChild(box2); - box2.innerHTML = - "Which "+name+" do you want to see documentation for?" + - ""; - } - return false; -} - -function get_anchor() { - var href = location.href; - var start = href.indexOf("#")+1; - if ((start != 0) && (start != href.length)) - return href.substring(start, href.length); - } -function redirect_url(dottedName) { - // Scan through each element of the "pages" list, and check - // if "name" matches with any of them. - for (var i=0; i-m" or "-c"; - // extract the portion & compare it to dottedName. - var pagename = pages[i].substring(0, pages[i].length-2); - if (pagename == dottedName.substring(0,pagename.length)) { - - // We've found a page that matches `dottedName`; - // construct its URL, using leftover `dottedName` - // content to form an anchor. - var pagetype = pages[i].charAt(pages[i].length-1); - var url = pagename + ((pagetype=="m")?"-module.html": - "-class.html"); - if (dottedName.length > pagename.length) - url += "#" + dottedName.substring(pagename.length+1, - dottedName.length); - return url; - } - } - } diff --git a/pyroms/docs/frames.html b/pyroms/docs/frames.html deleted file mode 100644 index 0baa165..0000000 --- a/pyroms/docs/frames.html +++ /dev/null @@ -1,17 +0,0 @@ - - - - - API Documentation - - - - - - - - - diff --git a/pyroms/docs/help.html b/pyroms/docs/help.html deleted file mode 100644 index 9545651..0000000 --- a/pyroms/docs/help.html +++ /dev/null @@ -1,268 +0,0 @@ - - - - - Help - - - - - - - - - - - - - - - - - - - - - - -
   Home      Trees      Indices      Help   
- - - - - -
  - - - - -
[hide private]
[frames] | no frames]
-
- -

API Documentation

- -

This document contains the API (Application Programming Interface) -documentation for this project. Documentation for the Python -objects defined by the project is divided into separate pages for each -package, module, and class. The API documentation also includes two -pages containing information about the project as a whole: a trees -page, and an index page.

- -

Object Documentation

- -

Each Package Documentation page contains:

-
    -
  • A description of the package.
    • -
  • A list of the modules and sub-packages contained by the - package.
    • -
  • A summary of the classes defined by the package.
    • -
  • A summary of the functions defined by the package.
    • -
  • A summary of the variables defined by the package.
    • -
  • A detailed description of each function defined by the - package.
    • -
  • A detailed description of each variable defined by the - package.
    • -
- -

Each Module Documentation page contains:

-
    -
  • A description of the module.
    • -
  • A summary of the classes defined by the module.
    • -
  • A summary of the functions defined by the module.
    • -
  • A summary of the variables defined by the module.
    • -
  • A detailed description of each function defined by the - module.
    • -
  • A detailed description of each variable defined by the - module.
    • -
- -

Each Class Documentation page contains:

-
    -
  • A class inheritance diagram.
    • -
  • A list of known subclasses.
    • -
  • A description of the class.
    • -
  • A summary of the methods defined by the class.
    • -
  • A summary of the instance variables defined by the class.
    • -
  • A summary of the class (static) variables defined by the - class.
    • -
  • A detailed description of each method defined by the - class.
    • -
  • A detailed description of each instance variable defined by the - class.
    • -
  • A detailed description of each class (static) variable defined - by the class.
    • -
- -

Project Documentation

- -

The Trees page contains the module and class hierarchies:

-
    -
  • The module hierarchy lists every package and module, with - modules grouped into packages. At the top level, and within each - package, modules and sub-packages are listed alphabetically.
    • -
  • The class hierarchy lists every class, grouped by base - class. If a class has more than one base class, then it will be - listed under each base class. At the top level, and under each base - class, classes are listed alphabetically.
    • -
- -

The Index page contains indices of terms and - identifiers:

-
    -
  • The term index lists every term indexed by any object's - documentation. For each term, the index provides links to each - place where the term is indexed.
    • -
  • The identifier index lists the (short) name of every package, - module, class, method, function, variable, and parameter. For each - identifier, the index provides a short description, and a link to - its documentation.
    • -
- -

The Table of Contents

- -

The table of contents occupies the two frames on the left side of -the window. The upper-left frame displays the project -contents, and the lower-left frame displays the module -contents:

- - - - - - - - - -
- Project
Contents
...		 - API
Documentation
Frame


-
- Module
Contents
 
...
  -

- -

The project contents frame contains a list of all packages -and modules that are defined by the project. Clicking on an entry -will display its contents in the module contents frame. Clicking on a -special entry, labeled "Everything," will display the contents of -the entire project.

- -

The module contents frame contains a list of every -submodule, class, type, exception, function, and variable defined by a -module or package. Clicking on an entry will display its -documentation in the API documentation frame. Clicking on the name of -the module, at the top of the frame, will display the documentation -for the module itself.

- -

The "frames" and "no frames" buttons below the top -navigation bar can be used to control whether the table of contents is -displayed or not.

- -

The Navigation Bar

- -

A navigation bar is located at the top and bottom of every page. -It indicates what type of page you are currently viewing, and allows -you to go to related pages. The following table describes the labels -on the navigation bar. Note that not some labels (such as -[Parent]) are not displayed on all pages.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -
LabelHighlighted when...Links to...
[Parent](never highlighted) the parent of the current package
[Package]viewing a packagethe package containing the current object -
[Module]viewing a modulethe module containing the current object -
[Class]viewing a class the class containing the current object
[Trees]viewing the trees page the trees page
[Index]viewing the index page the index page
[Help]viewing the help page the help page
- -

The "show private" and "hide private" buttons below -the top navigation bar can be used to control whether documentation -for private objects is displayed. Private objects are usually defined -as objects whose (short) names begin with a single underscore, but do -not end with an underscore. For example, "_x", -"__pprint", and "epydoc.epytext._tokenize" -are private objects; but "re.sub", -"__init__", and "type_" are not. However, -if a module defines the "__all__" variable, then its -contents are used to decide which objects are private.

- -

A timestamp below the bottom navigation bar indicates when each -page was last updated.

- - - - - - - - - - - - - - - - - -
   Home      Trees      Indices      Help   
- - - - - -
- Generated by Epydoc 3.0.1 on Mon Sep 27 11:31:38 2010 - - http://epydoc.sourceforge.net -
- - - - diff --git a/pyroms/docs/identifier-index.html b/pyroms/docs/identifier-index.html deleted file mode 100644 index 6bba8e5..0000000 --- a/pyroms/docs/identifier-index.html +++ /dev/null @@ -1,1183 +0,0 @@ - - - - - Identifier Index - - - - - - - - - - - - - - - - - - - - - - -
   Home      Trees      Indices      Help   
- - - - - -
  - - - - -
[hide private]
[frames] | no frames]
-
- -
-

Identifier Index

-		 -[ - A - B - C - D - E - F - G - H - I - J - K - L - M - N - O - P - Q - R - S - T - U - V - W - X - Y - Z - _ -] -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

A

 - - - - - - - - - - - - - - - - -
ABSENT
-(in pyroms.extern.pupynere)		add_focus_y()
-(in Focus)		arg_nearest_date()
-(in time)
add_focus_x()
-(in Focus)		add_focus_y()
-(in Focus)		 
add_focus_x()
-(in Focus)		arg_nearest()
-(in time)		 
-

B

 - - - - - - - -
BoundaryInteractor
-(in pyroms.hgrid)		BoundaryInteractor
-(in pyroms.hgrid_old)		 
   
-

C

 - - - - - - - - - - - - - - - - - - - - - -
calculate_orthogonality()
-(in CGrid)		CGrid
-(in pyroms.hgrid_old)		compute_remap_weights'
-(in pyroms.remapping)
calculate_orthogonality()
-(in CGrid)		CGrid_geo
-(in pyroms.hgrid)		compute_remap_weights()
-(in pyroms.remapping.compute_remap_weights')
cf
-(in pyroms)		CGrid_geo
-(in pyroms.hgrid_old)		count_neighbors()
-(in KDTree)
CGrid
-(in pyroms.hgrid)		close()
-(in NetCDFFile)		 
-

D

 - - - - - - - - - - - -
Dataset()
-(in pyroms.io)		days
-(in time)		 
dates
-(in time)		distance_matrix()
-(in pyroms.extern.kdtree)		 
-

E

 - - - - - - - -
edit_mask_mesh
-(in pyroms.hgrid)		edit_mask_mesh
-(in pyroms.hgrid_old)		extern
-(in pyroms)
   
-

F

 - - - - - - - - - - - -
find_nearestgridpoints()
-(in pyroms.utility)		flood()
-(in pyroms.remapping.flood')		Focus
-(in pyroms.hgrid_old)
flood'
-(in pyroms.remapping)		Focus
-(in pyroms.hgrid)		 
-

G

 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
generate_grid()
-(in Gridgen)		get_minutes()
-(in time)		get_ydata()
-(in BoundaryInteractor)
generate_grid()
-(in Gridgen)		get_nc_var()
-(in pyroms.utility)		get_ydata()
-(in BoundaryInteractor)
get_bottom()
-(in pyroms.utility)		get_position_from_map
-(in pyroms.hgrid)		getValue()
-(in NetCDFVariable)
get_date_tag()
-(in pyroms.utility)		get_position_from_map
-(in pyroms.hgrid_old)		greatcircle
-(in pyroms.extern)
get_dates()
-(in time)		get_ROMS_grid()
-(in pyroms.grid)		GreatCircle
-(in pyroms.extern.greatcircle)
get_days()
-(in time)		get_ROMS_hgrid()
-(in pyroms.grid)		grid
-(in pyroms)
get_grid_proj()
-(in pyroms.utility)		get_ROMS_vgrid()
-(in pyroms.grid)		Gridgen
-(in pyroms.hgrid)
get_hours()
-(in time)		get_seconds()
-(in time)		Gridgen
-(in pyroms.hgrid_old)
get_ij()
-(in pyroms.utility)		get_surface()
-(in pyroms.utility)		gridid_dictionary
-(in pyroms.grid)
get_jd()
-(in time)		get_xdata()
-(in BoundaryInteractor)		 
get_lonlat()
-(in pyroms.utility)		get_xdata()
-(in BoundaryInteractor)		 
-

H

 - - - - - - - -
hgrid
-(in pyroms)		hgrid_old
-(in pyroms)		hours
-(in time)
   
-

I

 - - - - - - - - - - - -
innernode
-(in KDTree)		io
-(in pyroms)		isoslice()
-(in pyroms.tools)
interm_pt()
-(in pyroms.tools)		islice()
-(in pyroms.tools)		 
-

J

 - - - - - - - -
jd
-(in time)		jslice()
-(in pyroms.tools)		 
   
-

K

 - - - - - - - -
kdtree
-(in pyroms.extern)		KDTree
-(in pyroms.extern.kdtree)		 
   
-

L

 - - - - - - - - - - - - - - - - - - - - - -
lat
-(in CGrid_geo)		list_ROMS_gridid()
-(in pyroms.grid)		lon
-(in CGrid_geo)
lat
-(in CGrid_geo)		load_bry()
-(in BoundaryInteractor)		lonslice()
-(in pyroms.tools)
latslice()
-(in pyroms.tools)		load_bry()
-(in BoundaryInteractor)		 
leafnode
-(in KDTree)		lon
-(in CGrid_geo)		 
-

M

 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
make_remap_grid_file'
-(in pyroms.remapping)		mask_psi
-(in CGrid)		MFDataset()
-(in pyroms.io)
make_remap_grid_file()
-(in pyroms.remapping.make_remap_grid_file')		mask_psi
-(in CGrid)		min_distance_point()
-(in Rectangle)
mask
-(in CGrid)		mask_u
-(in CGrid)		min_distance_rectangle()
-(in Rectangle)
mask
-(in CGrid)		mask_u
-(in CGrid)		minkowski_distance()
-(in pyroms.extern.kdtree)
mask_polygon()
-(in CGrid)		mask_v
-(in CGrid)		minkowski_distance_p()
-(in pyroms.extern.kdtree)
mask_polygon()
-(in CGrid)		mask_v
-(in CGrid)		minutes
-(in time)
mask_polygon_geo()
-(in CGrid_geo)		max_distance_point()
-(in Rectangle)		move2grid()
-(in pyroms.utility)
mask_polygon_geo()
-(in CGrid_geo)		max_distance_rectangle()
-(in Rectangle)		 
-

N

 - - - - - - - - - - - - - - - - - - - - - - - - - - -
NC_ATTRIBUTE
-(in pyroms.extern.pupynere)		NC_FLOAT
-(in pyroms.extern.pupynere)		nearest_date()
-(in time)
NC_BYTE
-(in pyroms.extern.pupynere)		NC_INT
-(in pyroms.extern.pupynere)		NetCDFFile
-(in pyroms.extern.pupynere)
NC_CHAR
-(in pyroms.extern.pupynere)		NC_SHORT
-(in pyroms.extern.pupynere)		NetCDFVariable
-(in pyroms.extern.pupynere)
NC_DIMENSION
-(in pyroms.extern.pupynere)		NC_VARIABLE
-(in pyroms.extern.pupynere)		node
-(in KDTree)
NC_DOUBLE
-(in pyroms.extern.pupynere)		nearest()
-(in time)		 
-

P

 - - - - - - - - - - - -
points()
-(in GreatCircle)		pupynere
-(in pyroms.extern)		 
print_ROMS_gridinfo()
-(in pyroms.grid)		pyroms 
-

Q

 - - - - - - - -
query()
-(in KDTree)		query_ball_point()
-(in KDTree)		query_ball_tree()
-(in KDTree)
   
-

R

 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
read()
-(in NetCDFFile)		remove_grid()
-(in BoundaryInteractor)		roms2z()
-(in pyroms.remapping.roms2z')
Rectangle
-(in pyroms.extern.kdtree)		rho_to_vert()
-(in pyroms.hgrid)		ROMS_Grid
-(in pyroms.grid)
remap'
-(in pyroms.remapping)		rho_to_vert()
-(in pyroms.hgrid_old)		ROMS_gridinfo
-(in pyroms.grid)
remap()
-(in pyroms.remapping.remap')		rho_to_vert_geo()
-(in pyroms.hgrid)		roms_varlist()
-(in pyroms.utility)
remapping
-(in pyroms)		rho_to_vert_geo()
-(in pyroms.hgrid_old)		 
remove_grid()
-(in BoundaryInteractor)		roms2z'
-(in pyroms.remapping)		 
-

S

 - - - - - - - - - - - - - - - - - - - - - -
s_coordinate
-(in pyroms.vgrid)		save_grid()
-(in BoundaryInteractor)		split()
-(in Rectangle)
s_coordinate_2
-(in pyroms.vgrid)		save_grid()
-(in BoundaryInteractor)		sslice()
-(in pyroms.tools)
save_bry()
-(in BoundaryInteractor)		seconds
-(in time)		 
save_bry()
-(in BoundaryInteractor)		section_transport()
-(in pyroms.tools)		 
-

T

 - - - - - - - - - - - -
test_remap_weights'
-(in pyroms.remapping)		time
-(in pyroms.cf)		transect()
-(in pyroms.tools)
test_remap_weights()
-(in pyroms.remapping.test_remap_weights')		tools
-(in pyroms)		typecode()
-(in NetCDFVariable)
-

U

 - - - - - - - -
utility
-(in pyroms)		uvp_masks()
-(in pyroms.hgrid)		uvp_masks()
-(in pyroms.hgrid_old)
   
-

V

 - - - - - - - - - - - -
verts
-(in BoundaryInteractor)		vgrid
-(in pyroms)		vinc_pt()
-(in pyroms.extern.greatcircle)
verts
-(in BoundaryInteractor)		vinc_dist()
-(in pyroms.extern.greatcircle)		volume()
-(in Rectangle)
-

W

 - - - - - - - -
write_ROMS_grid()
-(in pyroms.grid)		  
   
-

X

 - - - - - - - - - - - -
x
-(in BoundaryInteractor)		x
-(in BoundaryInteractor)		 
x
-(in CGrid)		x
-(in CGrid)		 
-

Y

 - - - - - - - - - - - -
y
-(in BoundaryInteractor)		y
-(in BoundaryInteractor)		 
y
-(in CGrid)		y
-(in CGrid)		 
-

Z

 - - - - - - - - - - - - - - - - -
z2roms'
-(in pyroms.remapping)		z_r
-(in pyroms.vgrid)		zslice()
-(in pyroms.tools)
z2roms()
-(in pyroms.remapping.z2roms')		z_w
-(in pyroms.vgrid)		 
z_coordinate
-(in pyroms.vgrid)		ZERO
-(in pyroms.extern.pupynere)		 
-

_

 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
__array_finalize__()
-(in time)		__query()
-(in KDTree)		_get_mask_u()
-(in CGrid)
__build()
-(in KDTree)		__query_ball_point()
-(in KDTree)		_get_mask_v()
-(in CGrid)
__call__()
-(in Focus)		__repr__()
-(in Rectangle)		_get_mask_v()
-(in CGrid)
__call__()
-(in _Focus_x)		_approximate_erf()
-(in pyroms.hgrid)		_get_s_rho()
-(in s_coordinate)
__call__()
-(in _Focus_y)		_approximate_erf()
-(in pyroms.hgrid_old)		_get_s_rho()
-(in s_coordinate_2)
__call__()
-(in Focus)		_att_array()
-(in NetCDFFile)		_get_s_w()
-(in s_coordinate)
__call__()
-(in _Focus_x)		_button_press_callback()
-(in BoundaryInteractor)		_get_s_w()
-(in s_coordinate_2)
__call__()
-(in _Focus_y)		_button_press_callback()
-(in BoundaryInteractor)		_get_verts()
-(in BoundaryInteractor)
__del__()
-(in Gridgen)		_button_release_callback()
-(in BoundaryInteractor)		_get_verts()
-(in BoundaryInteractor)
__del__()
-(in Gridgen)		_button_release_callback()
-(in BoundaryInteractor)		_key_press_callback()
-(in BoundaryInteractor)
__getitem__()
-(in NetCDFVariable)		_calculate_angle()
-(in CGrid)		_key_press_callback()
-(in BoundaryInteractor)
__getitem__()
-(in z_r)		_calculate_angle()
-(in CGrid)		_motion_notify_callback()
-(in BoundaryInteractor)
__getitem__()
-(in z_w)		_calculate_angle_rho()
-(in CGrid)		_motion_notify_callback()
-(in BoundaryInteractor)
__init__()
-(in GreatCircle)		_calculate_angle_rho()
-(in CGrid_geo)		_numrecs()
-(in NetCDFFile)
__init__()
-(in KDTree)		_calculate_angle_rho()
-(in CGrid)		_on_click()
-(in edit_mask_mesh)
__init__()
-(in innernode)		_calculate_angle_rho()
-(in CGrid_geo)		_on_click()
-(in get_position_from_map)
__init__()
-(in leafnode)		_calculate_derivative_metrics()
-(in CGrid)		_on_click()
-(in edit_mask_mesh)
__init__()
-(in Rectangle)		_calculate_derivative_metrics()
-(in CGrid_geo)		_on_click()
-(in get_position_from_map)
__init__()
-(in NetCDFFile)		_calculate_derivative_metrics()
-(in CGrid)		_on_key()
-(in edit_mask_mesh)
__init__()
-(in NetCDFVariable)		_calculate_derivative_metrics()
-(in CGrid_geo)		_on_key()
-(in get_position_from_map)
__init__()
-(in ROMS_Grid)		_calculate_metrics()
-(in CGrid)		_on_key()
-(in edit_mask_mesh)
__init__()
-(in ROMS_gridinfo)		_calculate_metrics()
-(in CGrid_geo)		_on_key()
-(in get_position_from_map)
__init__()
-(in BoundaryInteractor)		_calculate_metrics()
-(in CGrid)		_parse()
-(in NetCDFFile)
__init__()
-(in CGrid)		_calculate_metrics()
-(in CGrid_geo)		_poly_changed()
-(in BoundaryInteractor)
__init__()
-(in CGrid_geo)		_calculate_subgrids()
-(in CGrid)		_poly_changed()
-(in BoundaryInteractor)
__init__()
-(in Focus)		_calculate_subgrids()
-(in CGrid)		_read_recsize()
-(in NetCDFFile)
__init__()
-(in Gridgen)		_dim_array()
-(in NetCDFFile)		_read_string()
-(in NetCDFFile)
__init__()
-(in _Focus_x)		_draw_callback()
-(in BoundaryInteractor)		_read_values()
-(in NetCDFFile)
__init__()
-(in _Focus_y)		_draw_callback()
-(in BoundaryInteractor)		_read_var()
-(in NetCDFFile)
__init__()
-(in edit_mask_mesh)		_epsilon
-(in BoundaryInteractor)		_sec2unit
-(in time)
__init__()
-(in get_position_from_map)		_epsilon
-(in BoundaryInteractor)		_set_mask_rho()
-(in CGrid)
__init__()
-(in BoundaryInteractor)		_Focus_x
-(in pyroms.hgrid)		_set_mask_rho()
-(in CGrid)
__init__()
-(in CGrid)		_Focus_x
-(in pyroms.hgrid_old)		_showbetas
-(in BoundaryInteractor)
__init__()
-(in CGrid_geo)		_Focus_y
-(in pyroms.hgrid)		_showbetas
-(in BoundaryInteractor)
__init__()
-(in Focus)		_Focus_y
-(in pyroms.hgrid_old)		_showgrid
-(in BoundaryInteractor)
__init__()
-(in Gridgen)		_gatt_array()
-(in NetCDFFile)		_showgrid
-(in BoundaryInteractor)
__init__()
-(in _Focus_x)		_get_Cs_r()
-(in s_coordinate)		_showverts
-(in BoundaryInteractor)
__init__()
-(in _Focus_y)		_get_Cs_r()
-(in s_coordinate_2)		_showverts
-(in BoundaryInteractor)
__init__()
-(in edit_mask_mesh)		_get_Cs_w()
-(in s_coordinate)		_test()
-(in pyroms.extern.pupynere)
__init__()
-(in get_position_from_map)		_get_Cs_w()
-(in s_coordinate_2)		_unit2sec
-(in time)
__init__()
-(in s_coordinate)		_get_grid_info()
-(in ROMS_gridinfo)		_unpack_int()
-(in NetCDFFile)
__init__()
-(in s_coordinate_2)		_get_ind_under_point()
-(in BoundaryInteractor)		_unpack_int64()
-(in NetCDFFile)
__init__()
-(in z_coordinate)		_get_ind_under_point()
-(in BoundaryInteractor)		_update_beta_lines()
-(in BoundaryInteractor)
__init__()
-(in z_r)		_get_mask_psi()
-(in CGrid)		_update_beta_lines()
-(in BoundaryInteractor)
__init__()
-(in z_w)		_get_mask_psi()
-(in CGrid)		_var_array()
-(in NetCDFFile)
__new__()
-(in time)		_get_mask_u()
-(in CGrid)		 
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Package pyroms

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-

PYROMS is a toolkit for working with ROMS ocean models

-

pyroms is based on the python/numpy/matplotlib scientific python - suite. NetCDF I/O is based on the NetCDF4-python package. The toolkit - contains general modeling tools for dealing with arrays, diagnosing - standard properties, curvilinear grid generation, and interpolation.

- -
-

Version: - 0.1.0 -

-

Author: - Frederic Castruccio (frederic@marine.rutgers.edu) -

-
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Source Code for Package pyroms

-
- 1  # encoding: utf-8 
- 2  '''  
- 3  PYROMS is a toolkit for working with ROMS ocean models 
- 4   
- 5  pyroms is based on the python/numpy/matplotlib scientific python suite.  
- 6  NetCDF I/O is based on the NetCDF4-python package. The toolkit contains  
- 7  general modeling tools for dealing with arrays, diagnosing standard  
- 8  properties, curvilinear grid generation, and interpolation. 
- 9  ''' 
-10   
-11  import cf 
-12  import vgrid 
-13  import extern 
-14  import hgrid 
-15  import grid 
-16  import io 
-17  import tools 
-18  import remapping 
-19  import utility 
-20   
-21  __authors__ = ['Frederic Castruccio (frederic@marine.rutgers.edu)'] 
-22                  
-23  __version__ = '0.1.0' 
-24   
-
-
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Module cf

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-
-cf.py - classes around CF compliant files
-
-The cf module is made for reading CF-compliant datasets,
-knowing data, its structure, units and conversions
-between units afterwards.
-
-Dependencies:
-=============
-numpy
-netcdftime (packaged in netcdf4-python)
-
-
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-   - - time
- Return time object from netCDF file -
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Source Code for Module pyroms.cf

-
-  1  # encoding: utf-8 
-  2  """ 
-  3  cf.py - classes around CF compliant files 
-  4   
-  5  The cf module is made for reading CF-compliant datasets, 
-  6  knowing data, its structure, units and conversions 
-  7  between units afterwards. 
-  8   
-  9  Dependencies: 
- 10  ============= 
- 11  numpy 
- 12  netcdftime (packaged in netcdf4-python) 
- 13  """ 
- 14  __docformat__ = "restructuredtext en" 
- 15   
- 16  import numpy as np 
- 17   
- 18  import netcdftime 
- 19   
- 20  import pyroms.io 
- 21   
-
 22 -class time (np.ndarray): 
-
 23      """Return time object from netCDF file 
- 24       
- 25      Parameters 
- 26      ---------- 
- 27      nc : netCDF3/4 object or filename 
- 28          Time information will be read from this netCDF3/4 file. 
- 29      name : string, optional 
- 30          The name of the the variable. 
- 31      units : string, optional 
- 32          The name of the variable units. 
- 33      calendar : string, optional 
- 34          A string representing the calandar to use. See netcdftime 
- 35          documentation for possible values. 
- 36       
- 37      Returns 
- 38      ------- 
- 39      nctime : ndarray 
- 40          A subclass of numpy.ndarray with values equal to the time variable in 
- 41          the netCDF file referenced with nc. 
- 42       
- 43      """ 
- 44       
- 45      _unit2sec={'seconds' : 1.0, 
- 46                 'minutes' : 60.0, 
- 47                 'hours'   : 3600.0, 
- 48                 'days'    : 3600.0*24.0, 
- 49                 'weeks'   : 3600.0*24.0*7.0, 
- 50                 'years'   : 3600.0*24.0*365.242198781} #ref to udunits 
- 51   
- 52      _sec2unit={'seconds' : 1.0, 
- 53                 'minutes' : 1.0/60.0, 
- 54                 'hours'   : 1.0/3600.0, 
- 55                 'days'    : 1.0/(24.0*3600.0)} 
- 56   
-
 57 -    def __new__(self, ncfile, name='time', units=None, calendar='standard'): 
-
 58          self._nc = pyroms.io.Dataset(ncfile) 
- 59          data = self._nc.variables[name][:] 
- 60          data = data.view(time) 
- 61          if units == None: 
- 62              units = self._nc.variables[name].units 
- 63          data.utime = netcdftime.utime(units, calendar=calendar) 
- 64          return data 
-
 65       
-
 66 -    def __array_finalize__(self, obj): 
-
 67          self.utime = getattr(obj, 'utime', {}) 
-
 68       
-
 69 -    def arg_nearest_date(self, dateo): 
-
 70          """Return index of date nearest to query date. 
- 71           
- 72          Prameters 
- 73          --------- 
- 74          dateo : datetime object 
- 75              The query date 
- 76           
- 77          Returns 
- 78          ------- 
- 79          idx : integer 
- 80              The index of the date closest to dateo. If two dates are 
- 81              equidistant, the smaller is returned. 
- 82           
- 83          """ 
- 84          to = self.utime.date2num(dateo) 
- 85          return np.min(np.where(np.abs(self-to) == \ 
- 86                  np.min(np.abs(self-to)))[0]) 
-
 87       
-
 88 -    def nearest_date(self, dateo): 
-
 89          """Return the nearest date to query date. 
- 90           
- 91          Prameters 
- 92          --------- 
- 93          dateo : datetime object 
- 94              The query date 
- 95           
- 96          Returns 
- 97          ------- 
- 98          nearest_date : datetime object 
- 99              A datetime object of the date closest to dateo. If two dates are 
-100              equidistant, the smaller is returned. 
-101           
-102          """ 
-103          idx = np.where(np.abs(self.dates-dateo) == \ 
-104                  np.min(np.abs(self.dates-dateo)))[0] 
-105          idx = np.min(idx) 
-106          return self.dates[idx] 
-
107       
-
108 -    def arg_nearest(self, to, units=None): 
-
109          """Return index of time nearest to query time. 
-110           
-111          Prameters 
-112          --------- 
-113          to : float 
-114              The query time. 
-115          units : string, optional 
-116              The units of the reference time. Defaults to the reference time 
-117              string 'units' in the netcdf oject. 
-118           
-119          Returns 
-120          ------- 
-121          idx : integer 
-122              The index of the date closest to to. If two times are equidistant, 
-123              the smaller is returned. 
-124           
-125          """ 
-126          if units is not None: 
-127              to *= self._unit2sec[units] * self._sec2unit[self.utime.units] 
-128          return np.min(np.where(np.abs(self-to) == np.min(np.abs(self-to)))[0]) 
-
129       
-
130 -    def nearest(self, to, units=None): 
-
131          """Return time nearest to time query. 
-132           
-133          Prameters 
-134          --------- 
-135          to : float 
-136              The query time. 
-137          units : string, optional 
-138              The units of the reference time. Defaults to the reference time 
-139              string 'units' in the netcdf oject. 
-140           
-141          Returns 
-142          ------- 
-143          idx : integer 
-144              The index of the date closest to to. If two times are equidistant, 
-145              the smaller is returned. 
-146           
-147          """ 
-148          if units is not None: 
-149              to *= self._unit2sec[units] * self._sec2unit[self.utime.units] 
-150          idx = np.where(np.abs(self-to) == np.min(np.abs(self-to)))[0] 
-151          idx = np.min(idx) 
-152          return self[idx] 
-
153       
-
154 -    def get_seconds(self): 
-
155          fac = self._unit2sec[self.utime.units] * self._sec2unit['seconds'] 
-156          return self*fac 
-
157       
-
158 -    def get_minutes(self): 
-
159          fac = self._unit2sec[self.utime.units] * self._sec2unit['minutes'] 
-160          return self*fac 
-
161   
-
162 -    def get_hours(self): 
-
163          fac = self._unit2sec[self.utime.units] * self._sec2unit['hours'] 
-164          return self*fac 
-
165       
-
166 -    def get_days(self): 
-
167          fac = self._unit2sec[self.utime.units] * self._sec2unit['days'] 
-168          return np.asarray(self,dtype='float64')*fac 
-
169       
-
170 -    def get_jd(self): 
-
171          utime = netcdftime.utime('days since 0001-01-01 00:00:00', \ 
-172                                   calendar='proleptic_gregorian') 
-173          return utime.date2num(self.dates) 
-
174   
-
175 -    def get_dates(self): 
-
176          return np.array([self.utime.num2date(tval) for tval in self]) 
-
177           
-178      jd = property(get_jd, None, doc="Julian day, for plotting in pylab") 
-179      seconds = property(get_seconds, None, doc="seconds") 
-180      minutes = property(get_minutes, None, doc="minutes") 
-181      hours = property(get_hours, None, doc="hours") 
-182      days = property(get_days, None, doc="days") 
-183      dates = property(get_dates, None, doc="datetime objects") 
-
184   
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Class time

source code

-
-   object --+    
-            |    
-numpy.ndarray --+
-                |
-               time
-
- -
-
-Return time object from netCDF file
-
-Parameters
-----------
-nc : netCDF3/4 object or filename
-    Time information will be read from this netCDF3/4 file.
-name : string, optional
-    The name of the the variable.
-units : string, optional
-    The name of the variable units.
-calendar : string, optional
-    A string representing the calandar to use. See netcdftime
-    documentation for possible values.
-
-Returns
--------
-nctime : ndarray
-    A subclass of numpy.ndarray with values equal to the time variable in
-    the netCDF file referenced with nc.
-
-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
-   - - - - - - -
__array_finalize__(self, - obj)
- None.		 - source code - -
- -
-   - - - - - - -
arg_nearest_date(self, - dateo)
- Return index of date nearest to query date.		 - source code - -
- -
-   - - - - - - -
nearest_date(self, - dateo)
- Return the nearest date to query date.		 - source code - -
- -
-   - - - - - - -
arg_nearest(self, - to, - units=None)
- Return index of time nearest to query time.		 - source code - -
- -
-   - - - - - - -
nearest(self, - to, - units=None)
- Return time nearest to time query.		 - source code - -
- -
-   - - - - - - -
get_seconds(self) - source code - -
- -
-   - - - - - - -
get_minutes(self) - source code - -
- -
-   - - - - - - -
get_hours(self) - source code - -
- -
-   - - - - - - -
get_days(self) - source code - -
- -
-   - - - - - - -
get_jd(self) - source code - -
- -
-   - - - - - - -
get_dates(self) - source code - -
- -
-

Inherited from numpy.ndarray: - __abs__, - __add__, - __and__, - __array__, - __array_wrap__, - __contains__, - __copy__, - __deepcopy__, - __delitem__, - __delslice__, - __div__, - __divmod__, - __eq__, - __float__, - __floordiv__, - __ge__, - __getitem__, - __getslice__, - __gt__, - __hex__, - __iadd__, - __iand__, - __idiv__, - __ifloordiv__, - __ilshift__, - __imod__, - __imul__, - __index__, - __int__, - __invert__, - __ior__, - __ipow__, - __irshift__, - __isub__, - __iter__, - __itruediv__, - __ixor__, - __le__, - __len__, - __long__, - __lshift__, - __lt__, - __mod__, - __mul__, - __ne__, - __neg__, - __nonzero__, - __oct__, - __or__, - __pos__, - __pow__, - __radd__, - __rand__, - __rdiv__, - __rdivmod__, - __reduce__, - __repr__, - __rfloordiv__, - __rlshift__, - __rmod__, - __rmul__, - __ror__, - __rpow__, - __rrshift__, - __rshift__, - __rsub__, - __rtruediv__, - __rxor__, - __setitem__, - __setslice__, - __setstate__, - __str__, - __sub__, - __truediv__, - __xor__, - all, - any, - argmax, - argmin, - argsort, - astype, - byteswap, - choose, - clip, - compress, - conj, - conjugate, - copy, - cumprod, - cumsum, - diagonal, - dump, - dumps, - fill, - flatten, - getfield, - item, - itemset, - max, - mean, - min, - newbyteorder, - nonzero, - prod, - ptp, - put, - ravel, - repeat, - reshape, - resize, - round, - searchsorted, - setfield, - setflags, - sort, - squeeze, - std, - sum, - swapaxes, - take, - tofile, - tolist, - tostring, - trace, - transpose, - var, - view -

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Inherited from numpy.ndarray: - T, - __array_interface__, - __array_priority__, - __array_struct__, - base, - ctypes, - data, - dtype, - flags, - flat, - imag, - itemsize, - nbytes, - ndim, - real, - shape, - size, - strides -

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-    The query time.
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-    The query time.
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-{'days': 86400.0,
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- 'years': 31556925.9747}
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-{'days': 1.15740740741e-05,
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- 'minutes': 0.0166666666667,
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jd

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get_jd(self) -
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seconds

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dates

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-datetime objects
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Package extern

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Source Code for Package pyroms.extern

-
- 1  'External packages' 
- 2   
- 3  # from an old version Jeff Whitaker's Basemap 
- 4  from greatcircle import GreatCircle 
- 5   
- 6  # from Roberto De Almeida <rob@pydap.org> 
- 7  import pupynere 
- 8   
- 9  # from Anne M. Archibald's scipy.spatial.kdtree pure python code 
-10  from kdtree import KDTree 
-11   
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Module greatcircle

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Version: - 1.0.1 -

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Classes[hide private]
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-   - - GreatCircle
- formula for perfect sphere from Ed Williams' 'Aviation Formulary' - (http://williams.best.vwh.net/avform.htm) -
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- - - - - -
Functions[hide private]
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vinc_dist(f, - a, - phi1, - lembda1, - phi2, - lembda2)
- Returns the distance between two geographic points on the ellipsoid - and the forward and reverse azimuths between these points.		 - source code - -
- -
-   - - - - - - -
vinc_pt(f, - a, - phi1, - lembda1, - alpha12, - s)
- Returns the lat and long of projected point and reverse azimuth given - a reference point and a distance and azimuth to project.		 - source code - -
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Function Details[hide private]
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vinc_dist(f, - a, - phi1, - lembda1, - phi2, - lembda2) -

- 		source code  -
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Returns the distance between two geographic points on the ellipsoid - and the forward and reverse azimuths between these points. lats, longs - and azimuths are in radians, distance in metres

-

Returns ( s, alpha12, alpha21 ) as a tuple

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vinc_pt(f, - a, - phi1, - lembda1, - alpha12, - s) -

- 		source code  -
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Returns the lat and long of projected point and reverse azimuth given - a reference point and a distance and azimuth to project. lats, longs and - azimuths are passed in decimal degrees

-

Returns ( phi2, lambda2, alpha21 ) as a tuple

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Source Code for Module pyroms.extern.greatcircle

-
-  1  import numpy as NX 
-  2  import math 
-  3   
-  4  __version__ = '1.0.1' 
-
  5 -class GreatCircle(object): 
-
  6      """ 
-  7      formula for perfect sphere from Ed Williams' 'Aviation Formulary' 
-  8      (http://williams.best.vwh.net/avform.htm) 
-  9        
- 10      code for ellipsoid posted to GMT mailing list by Jim Leven in Dec 1999 
- 11   
- 12      Contact: Jeff Whitaker <jeffrey.s.whitaker@noaa.gov> 
- 13      """ 
- 14   
- 15   
-
 16 -    def __init__(self,rmajor,rminor,lon1,lat1,lon2,lat2): 
-
 17          """ 
- 18          Define a great circle by specifying: 
- 19          rmajor - radius of major axis of ellipsoid 
- 20          rminor - radius of minor axis of ellipsoid. 
- 21          lon1 - starting longitude of great circle 
- 22          lat1 - starting latitude 
- 23          lon2 - ending longitude 
- 24          lat2 - ending latitude 
- 25          All must be given in degrees. 
- 26   
- 27          Instance variables: 
- 28          distance - distance along great circle in radians. 
- 29          lon1,lat1,lon2,lat2 - start and end points (in radians). 
- 30          """ 
- 31          # convert to radians from degrees. 
- 32          lat1 = math.radians(lat1) 
- 33          lon1 = math.radians(lon1) 
- 34          lat2 = math.radians(lat2) 
- 35          lon2 = math.radians(lon2) 
- 36          self.a = rmajor 
- 37          self.f = (rmajor-rminor)/rmajor 
- 38          self.lat1 = lat1 
- 39          self.lat2 = lat2 
- 40          self.lon1 = lon1 
- 41          self.lon2 = lon2 
- 42          # distance along geodesic in meters. 
- 43          d,a12,a21 = vinc_dist(self.f,  self.a,  lat1,  lon1,  lat2,  lon2 )  
- 44          self.distance = d 
- 45          self.azimuth12 = a12 
- 46          self.azimuth21 = a21 
- 47          # great circle arc-length distance (in radians). 
- 48          self.gcarclen = 2.*math.asin(math.sqrt((math.sin((lat1-lat2)/2))**2+\ 
- 49          math.cos(lat1)*math.cos(lat2)*(math.sin((lon1-lon2)/2))**2)) 
- 50          # check to see if points are antipodal (if so, route is undefined). 
- 51          if self.gcarclen == math.pi: 
- 52              self.antipodal = True 
- 53          else: 
- 54              self.antipodal = False 
-
 55   
-
 56 -    def points(self,npoints): 
-
 57          """ 
- 58          compute arrays of npoints equally spaced 
- 59          intermediate points along the great circle. 
- 60   
- 61          input parameter npoints is the number of points 
- 62          to compute. 
- 63   
- 64          Returns lons, lats (lists with longitudes and latitudes 
- 65          of intermediate points in degrees). 
- 66   
- 67          For example npoints=10 will return arrays lons,lats of 10 
- 68          equally spaced points along the great circle. 
- 69          """ 
- 70          # must ask for at least 2 points. 
- 71          if npoints <= 1: 
- 72              raise ValueError,'npoints must be greater than 1' 
- 73          elif npoints == 2: 
- 74              return [math.degrees(self.lon1),math.degrees(self.lon2)],[math.degrees(self.lat1),math.degrees(self.lat2)] 
- 75          # can't do it if endpoints are antipodal, since 
- 76          # route is undefined. 
- 77          if self.antipodal: 
- 78              raise ValueError,'cannot compute intermediate points on a great circle whose endpoints are antipodal' 
- 79          d = self.gcarclen 
- 80          delta = 1.0/(npoints-1) 
- 81          f = delta*NX.arange(npoints) # f=0 is point 1, f=1 is point 2. 
- 82          incdist = self.distance/(npoints-1) 
- 83          lat1 = self.lat1 
- 84          lat2 = self.lat2 
- 85          lon1 = self.lon1 
- 86          lon2 = self.lon2 
- 87          # perfect sphere, use great circle formula 
- 88          if self.f == 0.: 
- 89              A = NX.sin((1-f)*d)/math.sin(d) 
- 90              B = NX.sin(f*d)/math.sin(d) 
- 91              x = A*math.cos(lat1)*math.cos(lon1)+B*math.cos(lat2)*math.cos(lon2) 
- 92              y = A*math.cos(lat1)*math.sin(lon1)+B*math.cos(lat2)*math.sin(lon2) 
- 93              z = A*math.sin(lat1)               +B*math.sin(lat2) 
- 94              lats=NX.arctan2(z,NX.sqrt(x**2+y**2)) 
- 95              lons=NX.arctan2(y,x) 
- 96              lons = map(math.degrees,lons.tolist()) 
- 97              lats = map(math.degrees,lats.tolist()) 
- 98          # use ellipsoid formulas 
- 99          else: 
-100              latpt = self.lat1 
-101              lonpt = self.lon1 
-102              azimuth = self.azimuth12 
-103              lons = [math.degrees(lonpt)] 
-104              lats = [math.degrees(latpt)] 
-105              for n in range(npoints-2): 
-106                  latptnew,lonptnew,alpha21=vinc_pt(self.f,self.a,latpt,lonpt,azimuth,incdist)  
-107                  d,azimuth,a21=vinc_dist(self.f,self.a,latptnew,lonptnew,lat2,lon2)  
-108                  lats.append(math.degrees(latptnew)) 
-109                  lons.append(math.degrees(lonptnew)) 
-110                  latpt = latptnew; lonpt = lonptnew 
-111              lons.append(math.degrees(self.lon2)) 
-112              lats.append(math.degrees(self.lat2)) 
-113          return lons,lats 
-
114  # 
-115  # ---------------------------------------------------------------------  
-116  # |                                                                    | 
-117  # |     geodetic.py -  a collection of geodetic functions              | 
-118  # |                                                                    | 
-119  # ---------------------------------------------------------------------  
-120  #  
-121  #  
-122  # ---------------------------------------------------------------------- 
-123  # | Algrothims from Geocentric Datum of Australia Technical Manual      | 
-124  # |                                                                     | 
-125  # | http://www.anzlic.org.au/icsm/gdatum/chapter4.html                  | 
-126  # |                                                                     | 
-127  # | This page last updated 11 May 1999                                  | 
-128  # |                                                                     | 
-129  # | Computations on the Ellipsoid                                       | 
-130  # |                                                                     | 
-131  # | There are a number of formulae that are available                   | 
-132  # | to calculate accurate geodetic positions,                           | 
-133  # | azimuths and distances on the ellipsoid.                            | 
-134  # |                                                                     | 
-135  # | Vincenty's formulae (Vincenty, 1975) may be used                    | 
-136  # | for lines ranging from a few cm to nearly 20,000 km,                | 
-137  # | with millimetre accuracy.                                           | 
-138  # | The formulae have been extensively tested                           | 
-139  # | for the Australian region, by comparison with results               | 
-140  # | from other formulae (Rainsford, 1955 & Sodano, 1965).               | 
-141  # |                                                                     | 
-142  # | * Inverse problem: azimuth and distance from known                  | 
-143  # |                     latitudes and longitudes                        | 
-144  # | * Direct problem: Latitude and longitude from known                 | 
-145  # |                     position, azimuth and distance.                 | 
-146  # | * Sample data                                                       | 
-147  # | * Excel spreadsheet                                                 | 
-148  # |                                                                     | 
-149  # | Vincenty's Inverse formulae                                         | 
-150  # | Given: latitude and longitude of two points                         | 
-151  # |                     (phi1, lembda1 and phi2, lembda2),              | 
-152  # | Calculate: the ellipsoidal distance (s) and                         | 
-153  # | forward and reverse azimuths between the points (alpha12, alpha21). | 
-154  # |                                                                     | 
-155  # ----------------------------------------------------------------------  
-156   
-
157 -def vinc_dist(  f,  a,  phi1,  lembda1,  phi2,  lembda2 ) : 
-
158          """  
-159   
-160          Returns the distance between two geographic points on the ellipsoid 
-161          and the forward and reverse azimuths between these points. 
-162          lats, longs and azimuths are in radians, distance in metres  
-163   
-164          Returns ( s, alpha12,  alpha21 ) as a tuple 
-165   
-166          """ 
-167   
-168          if (abs( phi2 - phi1 ) < 1e-8) and ( abs( lembda2 - lembda1) < 1e-8 ) : 
-169            return 0.0, 0.0, 0.0 
-170     
-171          two_pi = 2.0*math.pi 
-172   
-173          b = a * (1.0 - f) 
-174   
-175          TanU1 = (1-f) * math.tan( phi1 ) 
-176          TanU2 = (1-f) * math.tan( phi2 ) 
-177           
-178          U1 = math.atan(TanU1) 
-179          U2 = math.atan(TanU2) 
-180   
-181          lembda = lembda2 - lembda1 
-182          last_lembda = -4000000.0                # an impossibe value 
-183          omega = lembda 
-184   
-185          # Iterate the following equations,  
-186          #  until there is no significant change in lembda  
-187           
-188          while ( last_lembda < -3000000.0 or lembda != 0 and abs( (last_lembda - lembda)/lembda) > 1.0e-9 ) : 
-189           
-190            sqr_sin_sigma = pow( math.cos(U2) * math.sin(lembda), 2) + \ 
-191                  pow( (math.cos(U1) * math.sin(U2) - \ 
-192                  math.sin(U1) *  math.cos(U2) * math.cos(lembda) ), 2 ) 
-193   
-194            Sin_sigma = math.sqrt( sqr_sin_sigma ) 
-195             
-196            Cos_sigma = math.sin(U1) * math.sin(U2) + math.cos(U1) * math.cos(U2) * math.cos(lembda) 
-197             
-198            sigma = math.atan2( Sin_sigma, Cos_sigma ) 
-199   
-200            Sin_alpha = math.cos(U1) * math.cos(U2) * math.sin(lembda) / math.sin(sigma) 
-201            alpha = math.asin( Sin_alpha ) 
-202             
-203            Cos2sigma_m = math.cos(sigma) - (2 * math.sin(U1) * math.sin(U2) / pow(math.cos(alpha), 2) ) 
-204             
-205            C = (f/16) * pow(math.cos(alpha), 2) * (4 + f * (4 - 3 * pow(math.cos(alpha), 2))) 
-206             
-207            last_lembda = lembda 
-208             
-209            lembda = omega + (1-C) * f * math.sin(alpha) * (sigma + C * math.sin(sigma) * \ 
-210                  (Cos2sigma_m + C * math.cos(sigma) * (-1 + 2 * pow(Cos2sigma_m, 2) ))) 
-211           
-212   
-213          u2 = pow(math.cos(alpha),2) * (a*a-b*b) / (b*b) 
-214           
-215          A = 1 + (u2/16384) * (4096 + u2 * (-768 + u2 * (320 - 175 * u2))) 
-216           
-217          B = (u2/1024) * (256 + u2 * (-128+ u2 * (74 - 47 * u2))) 
-218           
-219          delta_sigma = B * Sin_sigma * (Cos2sigma_m + (B/4) * \ 
-220                  (Cos_sigma * (-1 + 2 * pow(Cos2sigma_m, 2) ) - \ 
-221                  (B/6) * Cos2sigma_m * (-3 + 4 * sqr_sin_sigma) * \ 
-222                  (-3 + 4 * pow(Cos2sigma_m,2 ) ))) 
-223           
-224          s = b * A * (sigma - delta_sigma) 
-225           
-226          alpha12 = math.atan2( (math.cos(U2) * math.sin(lembda)), \ 
-227                  (math.cos(U1) * math.sin(U2) - math.sin(U1) * math.cos(U2) * math.cos(lembda))) 
-228           
-229          alpha21 = math.atan2( (math.cos(U1) * math.sin(lembda)), \ 
-230                  (-math.sin(U1) * math.cos(U2) + math.cos(U1) * math.sin(U2) * math.cos(lembda))) 
-231   
-232          if ( alpha12 < 0.0 ) :  
-233                  alpha12 =  alpha12 + two_pi 
-234          if ( alpha12 > two_pi ) :  
-235                  alpha12 = alpha12 - two_pi 
-236   
-237          alpha21 = alpha21 + two_pi / 2.0 
-238          if ( alpha21 < 0.0 ) :  
-239                  alpha21 = alpha21 + two_pi 
-240          if ( alpha21 > two_pi ) :  
-241                  alpha21 = alpha21 - two_pi 
-242   
-243          return s, alpha12,  alpha21  
-
244   
-245     # END of Vincenty's Inverse formulae  
-246   
-247   
-248  #---------------------------------------------------------------------------- 
-249  # Vincenty's Direct formulae                                                | 
-250  # Given: latitude and longitude of a point (phi1, lembda1) and              | 
-251  # the geodetic azimuth (alpha12)                                            | 
-252  # and ellipsoidal distance in metres (s) to a second point,                 | 
-253  #                                                                           | 
-254  # Calculate: the latitude and longitude of the second point (phi2, lembda2) | 
-255  # and the reverse azimuth (alpha21).                                        | 
-256  #                                                                           | 
-257  #---------------------------------------------------------------------------- 
-258   
-
259 -def  vinc_pt( f, a, phi1, lembda1, alpha12, s ) : 
-
260          """ 
-261   
-262          Returns the lat and long of projected point and reverse azimuth 
-263          given a reference point and a distance and azimuth to project. 
-264          lats, longs and azimuths are passed in decimal degrees 
-265   
-266          Returns ( phi2,  lambda2,  alpha21 ) as a tuple  
-267   
-268          """ 
-269   
-270   
-271          two_pi = 2.0*math.pi 
-272   
-273          if ( alpha12 < 0.0 ) :  
-274                  alpha12 = alpha12 + two_pi 
-275          if ( alpha12 > two_pi ) :  
-276                  alpha12 = alpha12 - two_pi 
-277   
-278           
-279          b = a * (1.0 - f) 
-280   
-281          TanU1 = (1-f) * math.tan(phi1) 
-282          U1 = math.atan( TanU1 ) 
-283          sigma1 = math.atan2( TanU1, math.cos(alpha12) ) 
-284          Sinalpha = math.cos(U1) * math.sin(alpha12) 
-285          cosalpha_sq = 1.0 - Sinalpha * Sinalpha 
-286           
-287          u2 = cosalpha_sq * (a * a - b * b ) / (b * b) 
-288          A = 1.0 + (u2 / 16384) * (4096 + u2 * (-768 + u2 * \ 
-289                  (320 - 175 * u2) ) ) 
-290          B = (u2 / 1024) * (256 + u2 * (-128 + u2 * (74 - 47 * u2) ) ) 
-291           
-292          # Starting with the approximation 
-293          sigma = (s / (b * A)) 
-294   
-295          last_sigma = 2.0 * sigma + 2.0  # something impossible 
-296           
-297          # Iterate the following three equations  
-298          # until there is no significant change in sigma  
-299   
-300          # two_sigma_m , delta_sigma 
-301   
-302          while ( abs( (last_sigma - sigma) / sigma) > 1.0e-9 ) : 
-303   
-304             two_sigma_m = 2 * sigma1 + sigma 
-305              
-306             delta_sigma = B * math.sin(sigma) * ( math.cos(two_sigma_m) \ 
-307                          + (B/4) * (math.cos(sigma) * \ 
-308                          (-1 + 2 * math.pow( math.cos(two_sigma_m), 2 ) -  \ 
-309                          (B/6) * math.cos(two_sigma_m) * \ 
-310                          (-3 + 4 * math.pow(math.sin(sigma), 2 )) *  \ 
-311                          (-3 + 4 * math.pow( math.cos (two_sigma_m), 2 ))))) \ 
-312              
-313             last_sigma = sigma 
-314             sigma = (s / (b * A)) + delta_sigma 
-315           
-316           
-317          phi2 = math.atan2 ( (math.sin(U1) * math.cos(sigma) + math.cos(U1) * math.sin(sigma) * math.cos(alpha12) ), \ 
-318                  ((1-f) * math.sqrt( math.pow(Sinalpha, 2) +  \ 
-319                  pow(math.sin(U1) * math.sin(sigma) - math.cos(U1) * math.cos(sigma) * math.cos(alpha12), 2)))) 
-320           
-321   
-322          lembda = math.atan2( (math.sin(sigma) * math.sin(alpha12 )), (math.cos(U1) * math.cos(sigma) -  \ 
-323                  math.sin(U1) *  math.sin(sigma) * math.cos(alpha12))) 
-324           
-325          C = (f/16) * cosalpha_sq * (4 + f * (4 - 3 * cosalpha_sq )) 
-326           
-327          omega = lembda - (1-C) * f * Sinalpha *  \ 
-328                  (sigma + C * math.sin(sigma) * (math.cos(two_sigma_m) + \ 
-329                  C * math.cos(sigma) * (-1 + 2 * math.pow(math.cos(two_sigma_m),2) ))) 
-330           
-331          lembda2 = lembda1 + omega 
-332           
-333          alpha21 = math.atan2 ( Sinalpha, (-math.sin(U1) * math.sin(sigma) +  \ 
-334                  math.cos(U1) * math.cos(sigma) * math.cos(alpha12))) 
-335   
-336          alpha21 = alpha21 + two_pi / 2.0 
-337          if ( alpha21 < 0.0 ) : 
-338                  alpha21 = alpha21 + two_pi 
-339          if ( alpha21 > two_pi ) : 
-340                  alpha21 = alpha21 - two_pi 
-341   
-342   
-343          return phi2,  lembda2,  alpha21  
-
344   
-345     # END of Vincenty's Direct formulae 
-346   
-347  ##--------------------------------------------------------------------------- 
-348  # Notes:  
-349  #  
-350  # * "The inverse formulae may give no solution over a line  
-351  #       between two nearly antipodal points. This will occur when  
-352  #       lembda ... is greater than pi in absolute value". (Vincenty, 1975) 
-353  #   
-354  # * In Vincenty (1975) L is used for the difference in longitude,  
-355  #       however for consistency with other formulae in this Manual,  
-356  #       omega is used here.  
-357  #  
-358  # * Variables specific to Vincenty's formulae are shown below,  
-359  #       others common throughout the manual are shown in the Glossary.  
-360  #  
-361  #  
-362  # alpha = Azimuth of the geodesic at the equator 
-363  # U = Reduced latitude 
-364  # lembda = Difference in longitude on an auxiliary sphere (lembda1 & lembda2  
-365  #               are the geodetic longitudes of points 1 & 2) 
-366  # sigma = Angular distance on a sphere, from point 1 to point 2 
-367  # sigma1 = Angular distance on a sphere, from the equator to point 1 
-368  # sigma2 = Angular distance on a sphere, from the equator to point 2 
-369  # sigma_m = Angular distance on a sphere, from the equator to the  
-370  #               midpoint of the line from point 1 to point 2 
-371  # u, A, B, C = Internal variables 
-372  #  
-373  #  
-374  # Sample Data 
-375  #  
-376  # Flinders Peak 
-377  # -37o57'03.72030" 
-378  # 144o25'29.52440" 
-379  # Buninyong 
-380  # -37o39'10.15610" 
-381  # 143o55'35.38390" 
-382  # Ellipsoidal Distance 
-383  # 54,972.271 m 
-384  #   
-385  # Forward Azimuth 
-386  # 306o52'05.37" 
-387  #   
-388  # Reverse Azimuth 
-389  # 127o10'25.07" 
-390  #  
-391  #  
-392  ##******************************************************************* 
-393   
-394  # Test driver 
-395   
-396  if __name__ == "__main__" : 
-397   
-398     # WGS84 
-399   
-400     a = 6378137.0 
-401     b = 6356752.3142 
-402     f = (a-b)/a 
-403   
-404     print  "\n Ellipsoidal major axis =  %12.3f metres\n" % ( a ) 
-405     print  "\n Inverse flattening     =  %15.9f\n" % ( 1.0/f ) 
-406   
-407     print "\n Test Flinders Peak to Buninyon" 
-408     print "\n ****************************** \n" 
-409     phi1 = -(( 3.7203 / 60. + 57) / 60. + 37 ) 
-410     lembda1 = ( 29.5244 / 60. + 25) / 60. + 144 
-411     print "\n Flinders Peak = %12.6f, %13.6f \n" % ( phi1, lembda1 ) 
-412     deg = int(phi1) 
-413     minn = int(abs( ( phi1 - deg) * 60.0 )) 
-414     sec = abs(phi1 * 3600 - deg * 3600) - minn * 60 
-415     print " Flinders Peak =   %3i\xF8%3i\' %6.3f\",  " % ( deg, minn, sec ), 
-416     deg = int(lembda1) 
-417     minn = int(abs( ( lembda1 - deg) * 60.0 )) 
-418     sec = abs(lembda1 * 3600 - deg * 3600) - minn * 60 
-419     print " %3i\xF8%3i\' %6.3f\" \n" % ( deg, minn, sec ) 
-420   
-421     phi2 = -(( 10.1561 / 60. + 39) / 60. + 37 ) 
-422     lembda2 = ( 35.3839 / 60. + 55) / 60. + 143 
-423     print "\n Buninyon      = %12.6f, %13.6f \n" % ( phi2, lembda2 ) 
-424   
-425     deg = int(phi2) 
-426     minn = int(abs( ( phi2 - deg) * 60.0 )) 
-427     sec = abs(phi2 * 3600 - deg * 3600) - minn * 60 
-428     print " Buninyon      =   %3i\xF8%3i\' %6.3f\",  " % ( deg, minn, sec ), 
-429     deg = int(lembda2) 
-430     minn = int(abs( ( lembda2 - deg) * 60.0 )) 
-431     sec = abs(lembda2 * 3600 - deg * 3600) - minn * 60 
-432     print " %3i\xF8%3i\' %6.3f\" \n" % ( deg, minn, sec ) 
-433   
-434     dist, alpha12, alpha21   = vinc_dist  ( f, a, math.radians(phi1), math.radians(lembda1), math.radians(phi2),  math.radians(lembda2) ) 
-435   
-436     alpha12 = math.degrees(alpha12) 
-437     alpha21 = math.degrees(alpha21) 
-438   
-439     print "\n Ellipsoidal Distance = %15.3f metres\n            should be         54972.271 m\n" % ( dist ) 
-440     print "\n Forward and back azimuths = %15.6f, %15.6f \n" % ( alpha12, alpha21 ) 
-441     deg = int(alpha12) 
-442     minn =int( abs(( alpha12 - deg) * 60.0 ) ) 
-443     sec = abs(alpha12 * 3600 - deg * 3600) - minn * 60 
-444     print " Forward azimuth = %3i\xF8%3i\' %6.3f\"\n" % ( deg, minn, sec ) 
-445     deg = int(alpha21) 
-446     minn =int(abs( ( alpha21 - deg) * 60.0 )) 
-447     sec = abs(alpha21 * 3600 - deg * 3600) - minn * 60 
-448     print " Reverse azimuth = %3i\xF8%3i\' %6.3f\"\n" % ( deg, minn, sec ) 
-449   
-450   
-451     # Test the direct function */ 
-452     phi1 = -(( 3.7203 / 60. + 57) / 60. + 37 ) 
-453     lembda1 = ( 29.5244 / 60. + 25) / 60. + 144 
-454     dist = 54972.271 
-455     alpha12 = ( 5.37 / 60. + 52) / 60. + 306 
-456     phi2 = lembda2 = 0.0 
-457     alpha21 = 0.0 
-458   
-459     phi2, lembda2, alpha21 = vinc_pt (  f, a, math.radians(phi1), math.radians(lembda1), math.radians(alpha12), dist ) 
-460   
-461     phi2 = math.degrees(phi2) 
-462     lembda2 = math.degrees(lembda2) 
-463     alpha21 = math.degrees(alpha21) 
-464   
-465     print "\n Projected point =%11.6f, %13.6f \n" % ( phi2, lembda2 ) 
-466     deg = int(phi2) 
-467     minn =int(abs( ( phi2 - deg) * 60.0 )) 
-468     sec = abs( phi2 * 3600 - deg * 3600) - minn * 60 
-469     print " Projected Point = %3i\xF8%3i\' %6.3f\", " % ( deg, minn, sec ), 
-470     deg = int(lembda2) 
-471     minn =int(abs( ( lembda2 - deg) * 60.0 )) 
-472     sec = abs(lembda2 * 3600 - deg * 3600) - minn * 60 
-473     print "  %3i\xF8%3i\' %6.3f\"\n" % ( deg, minn, sec ) 
-474     print " Should be Buninyon \n"  
-475     print "\n Reverse azimuth = %10.6f \n" % ( alpha21 ) 
-476     deg = int(alpha21) 
-477     minn =int(abs( ( alpha21 - deg) * 60.0 )) 
-478     sec = abs(alpha21 * 3600 - deg * 3600) - minn * 60 
-479     print " Reverse azimuth = %3i\xF8%3i\' %6.3f\"\n\n" % ( deg, minn, sec ) 
-480   
-481     # lat/lon of New York 
-482     lat1 = 40.78 
-483     lon1 = -73.98 
-484     # lat/lon of London. 
-485     lat2 = 51.53 
-486     lon2 = 0.08 
-487     print 'New York to London:' 
-488     gc = GreatCircle((2*a+b)/3.,(2*a+b)/3.,lon1,lat1,lon2,lat2) 
-489     print 'geodesic distance using a sphere with WGS84 mean radius = ',gc.distance 
-490     print 'lon/lat for 10 equally spaced points along geodesic:' 
-491     lons,lats = gc.points(10) 
-492     for lon,lat in zip(lons,lats): 
-493         print lon,lat 
-494     gc = GreatCircle(a,b,lon1,lat1,lon2,lat2) 
-495     print 'geodesic distance using WGS84 ellipsoid = ',gc.distance 
-496     print 'lon/lat for 10 equally spaced points along geodesic:' 
-497     lons,lats = gc.points(10) 
-498     for lon,lat in zip(lons,lats): 
-499         print lon,lat 
-500   
-
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- - Package pyroms :: - Package extern :: - Module greatcircle :: - Class GreatCircle - - - - - - -
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-
- -

Class GreatCircle

source code

-
-object --+
-         |
-        GreatCircle
-
- -
-

formula for perfect sphere from Ed Williams' 'Aviation Formulary' - (http://williams.best.vwh.net/avform.htm)

-

code for ellipsoid posted to GMT mailing list by Jim Leven in Dec - 1999

-

Contact: Jeff Whitaker <jeffrey.s.whitaker@noaa.gov>

- - - - - - - - - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
-   - - - - - - -
__init__(self, - rmajor, - rminor, - lon1, - lat1, - lon2, - lat2)
- Define a great circle by specifying: rmajor - radius of major axis of - ellipsoid rminor - radius of minor axis of ellipsoid.		 - source code - -
- -
-   - - - - - - -
points(self, - npoints)
- compute arrays of npoints equally spaced intermediate points along - the great circle.		 - source code - -
- -
-

Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

-
- - - - - - - - - -
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Properties[hide private]
-
-

Inherited from object: - __class__ -

-
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- - - - - -
Method Details[hide private]
-
- -
- -
- - -
-

__init__(self, - rmajor, - rminor, - lon1, - lat1, - lon2, - lat2) -
(Constructor) -

- 		source code  -
- -

Define a great circle by specifying: rmajor - radius of major axis of - ellipsoid rminor - radius of minor axis of ellipsoid. lon1 - starting - longitude of great circle lat1 - starting latitude lon2 - ending - longitude lat2 - ending latitude All must be given in degrees.

-

Instance variables: distance - distance along great circle in radians. - lon1,lat1,lon2,lat2 - start and end points (in radians).

-
-
Overrides: - object.__init__ -
-
-
-
- -
- -
- - -
-

points(self, - npoints) -

- 		source code  -
- -

compute arrays of npoints equally spaced intermediate points along the - great circle.

-

input parameter npoints is the number of points to compute.

-

Returns lons, lats (lists with longitudes and latitudes of - intermediate points in degrees).

-

For example npoints=10 will return arrays lons,lats of 10 equally - spaced points along the great circle.

-
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Module kdtree

source code

- - - - - - - - - - - - -
- - - - - -
Classes[hide private]
-
-   - - Rectangle
- Hyperrectangle class. -
-   - - KDTree
- kd-tree for quick nearest-neighbor lookup -
- - - - - - - - - - - - - - - -
- - - - - -
Functions[hide private]
-
-   - - - - - - -
minkowski_distance_p(x, - y, - p=2)
- Compute the pth power of the L**p distance between x and y		 - source code - -
- -
-   - - - - - - -
minkowski_distance(x, - y, - p=2)
- Compute the L**p distance between x and y		 - source code - -
- -
-   - - - - - - -
distance_matrix(x, - y, - p=2, - threshold=1000000)
- Compute the distance matrix.		 - source code - -
- -
- - - - - - -
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Function Details[hide private]
-
- -
- -
- - -
-

minkowski_distance_p(x, - y, - p=2) -

- 		source code  -
- -

Compute the pth power of the L**p distance between x and y

-

For efficiency, this function computes the L**p distance but does not - extract the pth root. If p is 1 or infinity, this is equal to the actual - L**p distance.

-
-
-
-
- -
- -
- - -
-

distance_matrix(x, - y, - p=2, - threshold=1000000) -

- 		source code  -
- - 
-Compute the distance matrix.
-
-Computes the matrix of all pairwise distances.
-
-Parameters
-==========
-
-x : array-like, m by k
-y : array-like, n by k
-p : float 1<=p<=infinity
-    Which Minkowski p-norm to use.
-threshold : positive integer
-    If m*n*k>threshold use a python loop instead of creating
-    a very large temporary.
-
-Returns
-=======
-
-result : array-like, m by n
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Source Code for Module pyroms.extern.kdtree

-
-  1  # Copyright Anne M. Archibald 2008 
-  2  # Released under the scipy license 
-  3  import numpy as np 
-  4  from heapq import heappush, heappop 
-  5  #  import scipy.sparse  ### removed method that uses this -rdh 
-  6   
-
  7 -def minkowski_distance_p(x,y,p=2): 
-
  8      """Compute the pth power of the L**p distance between x and y 
-  9   
- 10      For efficiency, this function computes the L**p distance but does 
- 11      not extract the pth root. If p is 1 or infinity, this is equal to 
- 12      the actual L**p distance. 
- 13      """ 
- 14      x = np.asarray(x) 
- 15      y = np.asarray(y) 
- 16      if p==np.inf: 
- 17          return np.amax(np.abs(y-x),axis=-1) 
- 18      elif p==1: 
- 19          return np.sum(np.abs(y-x),axis=-1) 
- 20      else: 
- 21          return np.sum(np.abs(y-x)**p,axis=-1) 
-
 22 -def minkowski_distance(x,y,p=2): 
-
 23      """Compute the L**p distance between x and y""" 
- 24      x = np.asarray(x) 
- 25      y = np.asarray(y) 
- 26      if p==np.inf or p==1: 
- 27          return minkowski_distance_p(x,y,p) 
- 28      else: 
- 29          return minkowski_distance_p(x,y,p)**(1./p) 
-
 30   
-
 31 -class Rectangle(object): 
-
 32      """Hyperrectangle class. 
- 33   
- 34      Represents a Cartesian product of intervals. 
- 35      """ 
-
 36 -    def __init__(self, maxes, mins): 
-
 37          """Construct a hyperrectangle.""" 
- 38          self.maxes = np.maximum(maxes,mins).astype(np.float) 
- 39          self.mins = np.minimum(maxes,mins).astype(np.float) 
- 40          self.m, = self.maxes.shape 
-
 41   
-
 42 -    def __repr__(self): 
-
 43          return "<Rectangle %s>" % zip(self.mins, self.maxes) 
-
 44   
-
 45 -    def volume(self): 
-
 46          """Total volume.""" 
- 47          return np.prod(self.maxes-self.mins) 
-
 48   
-
 49 -    def split(self, d, split): 
-
 50          """Produce two hyperrectangles by splitting along axis d. 
- 51   
- 52          In general, if you need to compute maximum and minimum 
- 53          distances to the children, it can be done more efficiently 
- 54          by updating the maximum and minimum distances to the parent. 
- 55          """ # FIXME: do this 
- 56          mid = np.copy(self.maxes) 
- 57          mid[d] = split 
- 58          less = Rectangle(self.mins, mid) 
- 59          mid = np.copy(self.mins) 
- 60          mid[d] = split 
- 61          greater = Rectangle(mid, self.maxes) 
- 62          return less, greater 
-
 63   
-
 64 -    def min_distance_point(self, x, p=2.): 
-
 65          """Compute the minimum distance between x and a point in the hyperrectangle.""" 
- 66          return minkowski_distance(0, np.maximum(0,np.maximum(self.mins-x,x-self.maxes)),p) 
-
 67   
-
 68 -    def max_distance_point(self, x, p=2.): 
-
 69          """Compute the maximum distance between x and a point in the hyperrectangle.""" 
- 70          return minkowski_distance(0, np.maximum(self.maxes-x,x-self.mins),p) 
-
 71   
-
 72 -    def min_distance_rectangle(self, other, p=2.): 
-
 73          """Compute the minimum distance between points in the two hyperrectangles.""" 
- 74          return minkowski_distance(0, np.maximum(0,np.maximum(self.mins-other.maxes,other.mins-self.maxes)),p) 
-
 75   
-
 76 -    def max_distance_rectangle(self, other, p=2.): 
-
 77          """Compute the maximum distance between points in the two hyperrectangles.""" 
- 78          return minkowski_distance(0, np.maximum(self.maxes-other.mins,other.maxes-self.mins),p) 
-
 79   
- 80   
-
 81 -class KDTree(object): 
-
 82      """kd-tree for quick nearest-neighbor lookup 
- 83   
- 84      This class provides an index into a set of k-dimensional points 
- 85      which can be used to rapidly look up the nearest neighbors of any 
- 86      point. 
- 87   
- 88      The algorithm used is described in Maneewongvatana and Mount 1999. 
- 89      The general idea is that the kd-tree is a binary trie, each of whose 
- 90      nodes represents an axis-aligned hyperrectangle. Each node specifies 
- 91      an axis and splits the set of points based on whether their coordinate 
- 92      along that axis is greater than or less than a particular value. 
- 93   
- 94      During construction, the axis and splitting point are chosen by the 
- 95      "sliding midpoint" rule, which ensures that the cells do not all 
- 96      become long and thin. 
- 97   
- 98      The tree can be queried for the r closest neighbors of any given point 
- 99      (optionally returning only those within some maximum distance of the 
-100      point). It can also be queried, with a substantial gain in efficiency, 
-101      for the r approximate closest neighbors. 
-102   
-103      For large dimensions (20 is already large) do not expect this to run 
-104      significantly faster than brute force. High-dimensional nearest-neighbor 
-105      queries are a substantial open problem in computer science. 
-106   
-107      The tree also supports all-neighbors queries, both with arrays of points 
-108      and with other kd-trees. These do use a reasonably efficient algorithm, 
-109      but the kd-tree is not necessarily the best data structure for this 
-110      sort of calculation. 
-111      """ 
-112   
-
113 -    def __init__(self, data, leafsize=10): 
-
114          """Construct a kd-tree. 
-115   
-116          Parameters: 
-117          =========== 
-118   
-119          data : array-like, shape (n,k) 
-120              The data points to be indexed. This array is not copied, and 
-121              so modifying this data will result in bogus results. 
-122          leafsize : positive integer 
-123              The number of points at which the algorithm switches over to 
-124              brute-force. 
-125          """ 
-126          self.data = np.asarray(data) 
-127          self.n, self.m = np.shape(self.data) 
-128          self.leafsize = int(leafsize) 
-129          if self.leafsize<1: 
-130              raise ValueError("leafsize must be at least 1") 
-131          self.maxes = np.amax(self.data,axis=0) 
-132          self.mins = np.amin(self.data,axis=0) 
-133   
-134          self.tree = self.__build(np.arange(self.n), self.maxes, self.mins) 
-
135   
-
136 -    class node(object): 
-
137          pass 
-
138 -    class leafnode(node): 
-
139 -        def __init__(self, idx): 
-
140              self.idx = idx 
-141              self.children = len(idx) 
-
142 -    class innernode(node): 
-
143 -        def __init__(self, split_dim, split, less, greater): 
-
144              self.split_dim = split_dim 
-145              self.split = split 
-146              self.less = less 
-147              self.greater = greater 
-148              self.children = less.children+greater.children 
-
149   
-
150 -    def __build(self, idx, maxes, mins): 
-
151          if len(idx)<=self.leafsize: 
-152              return KDTree.leafnode(idx) 
-153          else: 
-154              data = self.data[idx] 
-155              #maxes = np.amax(data,axis=0) 
-156              #mins = np.amin(data,axis=0) 
-157              d = np.argmax(maxes-mins) 
-158              maxval = maxes[d] 
-159              minval = mins[d] 
-160              if maxval==minval: 
-161                  # all points are identical; warn user? 
-162                  return KDTree.leafnode(idx) 
-163              data = data[:,d] 
-164   
-165              # sliding midpoint rule; see Maneewongvatana and Mount 1999 
-166              # for arguments that this is a good idea. 
-167              split = (maxval+minval)/2 
-168              less_idx = np.nonzero(data<=split)[0] 
-169              greater_idx = np.nonzero(data>split)[0] 
-170              if len(less_idx)==0: 
-171                  split = np.amin(data) 
-172                  less_idx = np.nonzero(data<=split)[0] 
-173                  greater_idx = np.nonzero(data>split)[0] 
-174              if len(greater_idx)==0: 
-175                  split = np.amax(data) 
-176                  less_idx = np.nonzero(data<split)[0] 
-177                  greater_idx = np.nonzero(data>=split)[0] 
-178              if len(less_idx)==0: 
-179                  # _still_ zero? all must have the same value 
-180                  assert np.all(data==data[0]), "Troublesome data array: %s" % data 
-181                  split = data[0] 
-182                  less_idx = np.arange(len(data)-1) 
-183                  greater_idx = np.array([len(data)-1]) 
-184   
-185              lessmaxes = np.copy(maxes) 
-186              lessmaxes[d] = split 
-187              greatermins = np.copy(mins) 
-188              greatermins[d] = split 
-189              return KDTree.innernode(d, split, 
-190                      self.__build(idx[less_idx],lessmaxes,mins), 
-191                      self.__build(idx[greater_idx],maxes,greatermins)) 
-
192   
-
193 -    def __query(self, x, k=1, eps=0, p=2, distance_upper_bound=np.inf): 
-
194   
-195          side_distances = np.maximum(0,np.maximum(x-self.maxes,self.mins-x)) 
-196          if p!=np.inf: 
-197              side_distances**=p 
-198              min_distance = np.sum(side_distances) 
-199          else: 
-200              min_distance = np.amax(side_distances) 
-201   
-202          # priority queue for chasing nodes 
-203          # entries are: 
-204          #  minimum distance between the cell and the target 
-205          #  distances between the nearest side of the cell and the target 
-206          #  the head node of the cell 
-207          q = [(min_distance, 
-208                tuple(side_distances), 
-209                self.tree)] 
-210          # priority queue for the nearest neighbors 
-211          # furthest known neighbor first 
-212          # entries are (-distance**p, i) 
-213          neighbors = [] 
-214   
-215          if eps==0: 
-216              epsfac=1 
-217          elif p==np.inf: 
-218              epsfac = 1/(1+eps) 
-219          else: 
-220              epsfac = 1/(1+eps)**p 
-221   
-222          if p!=np.inf and distance_upper_bound!=np.inf: 
-223              distance_upper_bound = distance_upper_bound**p 
-224   
-225          while q: 
-226              min_distance, side_distances, node = heappop(q) 
-227              if isinstance(node, KDTree.leafnode): 
-228                  # brute-force 
-229                  data = self.data[node.idx] 
-230                  ds = minkowski_distance_p(data,x[np.newaxis,:],p) 
-231                  for i in range(len(ds)): 
-232                      if ds[i]<distance_upper_bound: 
-233                          if len(neighbors)==k: 
-234                              heappop(neighbors) 
-235                          heappush(neighbors, (-ds[i], node.idx[i])) 
-236                          if len(neighbors)==k: 
-237                              distance_upper_bound = -neighbors[0][0] 
-238              else: 
-239                  # we don't push cells that are too far onto the queue at all, 
-240                  # but since the distance_upper_bound decreases, we might get 
-241                  # here even if the cell's too far 
-242                  if min_distance>distance_upper_bound*epsfac: 
-243                      # since this is the nearest cell, we're done, bail out 
-244                      break 
-245                  # compute minimum distances to the children and push them on 
-246                  if x[node.split_dim]<node.split: 
-247                      near, far = node.less, node.greater 
-248                  else: 
-249                      near, far = node.greater, node.less 
-250   
-251                  # near child is at the same distance as the current node 
-252                  heappush(q,(min_distance, side_distances, near)) 
-253   
-254                  # far child is further by an amount depending only 
-255                  # on the split value 
-256                  sd = list(side_distances) 
-257                  if p == np.inf: 
-258                      min_distance = max(min_distance, abs(node.split-x[node.split_dim])) 
-259                  elif p == 1: 
-260                      sd[node.split_dim] = np.abs(node.split-x[node.split_dim]) 
-261                      min_distance = min_distance - side_distances[node.split_dim] + sd[node.split_dim] 
-262                  else: 
-263                      sd[node.split_dim] = np.abs(node.split-x[node.split_dim])**p 
-264                      min_distance = min_distance - side_distances[node.split_dim] + sd[node.split_dim] 
-265   
-266                  # far child might be too far, if so, don't bother pushing it 
-267                  if min_distance<=distance_upper_bound*epsfac: 
-268                      heappush(q,(min_distance, tuple(sd), far)) 
-269   
-270          if p==np.inf: 
-271              return sorted([(-d,i) for (d,i) in neighbors]) 
-272          else: 
-273              return sorted([((-d)**(1./p),i) for (d,i) in neighbors]) 
-
274   
-
275 -    def query(self, x, k=1, eps=0, p=2, distance_upper_bound=np.inf): 
-
276          """query the kd-tree for nearest neighbors 
-277   
-278          Parameters: 
-279          =========== 
-280   
-281          x : array-like, last dimension self.m 
-282              An array of points to query. 
-283          k : integer 
-284              The number of nearest neighbors to return. 
-285          eps : nonnegative float 
-286              Return approximate nearest neighbors; the kth returned value 
-287              is guaranteed to be no further than (1+eps) times the 
-288              distance to the real kth nearest neighbor. 
-289          p : float, 1<=p<=infinity 
-290              Which Minkowski p-norm to use. 
-291              1 is the sum-of-absolute-values "Manhattan" distance 
-292              2 is the usual Euclidean distance 
-293              infinity is the maximum-coordinate-difference distance 
-294          distance_upper_bound : nonnegative float 
-295              Return only neighbors within this distance. This is used to prune 
-296              tree searches, so if you are doing a series of nearest-neighbor 
-297              queries, it may help to supply the distance to the nearest neighbor 
-298              of the most recent point. 
-299   
-300          Returns: 
-301          ======== 
-302   
-303          d : array of floats 
-304              The distances to the nearest neighbors. 
-305              If x has shape tuple+(self.m,), then d has shape tuple if 
-306              k is one, or tuple+(k,) if k is larger than one.  Missing 
-307              neighbors are indicated with infinite distances.  If k is None, 
-308              then d is an object array of shape tuple, containing lists 
-309              of distances. In either case the hits are sorted by distance 
-310              (nearest first). 
-311          i : array of integers 
-312              The locations of the neighbors in self.data. i is the same 
-313              shape as d. 
-314          """ 
-315          x = np.asarray(x) 
-316          if np.shape(x)[-1] != self.m: 
-317              raise ValueError("x must consist of vectors of length %d but has shape %s" % (self.m, np.shape(x))) 
-318          if p<1: 
-319              raise ValueError("Only p-norms with 1<=p<=infinity permitted") 
-320          retshape = np.shape(x)[:-1] 
-321          if retshape!=(): 
-322              if k>1: 
-323                  dd = np.empty(retshape+(k,),dtype=np.float) 
-324                  dd.fill(np.inf) 
-325                  ii = np.empty(retshape+(k,),dtype=np.int) 
-326                  ii.fill(self.n) 
-327              elif k==1: 
-328                  dd = np.empty(retshape,dtype=np.float) 
-329                  dd.fill(np.inf) 
-330                  ii = np.empty(retshape,dtype=np.int) 
-331                  ii.fill(self.n) 
-332              elif k is None: 
-333                  dd = np.empty(retshape,dtype=np.object) 
-334                  ii = np.empty(retshape,dtype=np.object) 
-335              else: 
-336                  raise ValueError("Requested %s nearest neighbors; acceptable numbers are integers greater than or equal to one, or None") 
-337              for c in np.ndindex(retshape): 
-338                  hits = self.__query(x[c], k=k, p=p, distance_upper_bound=distance_upper_bound) 
-339                  if k>1: 
-340                      for j in range(len(hits)): 
-341                          dd[c+(j,)], ii[c+(j,)] = hits[j] 
-342                  elif k==1: 
-343                      if len(hits)>0: 
-344                          dd[c], ii[c] = hits[0] 
-345                      else: 
-346                          dd[c] = np.inf 
-347                          ii[c] = self.n 
-348                  elif k is None: 
-349                      dd[c] = [d for (d,i) in hits] 
-350                      ii[c] = [i for (d,i) in hits] 
-351              return dd, ii 
-352          else: 
-353              hits = self.__query(x, k=k, p=p, distance_upper_bound=distance_upper_bound) 
-354              if k==1: 
-355                  if len(hits)>0: 
-356                      return hits[0] 
-357                  else: 
-358                      return np.inf, self.n 
-359              elif k>1: 
-360                  dd = np.empty(k,dtype=np.float) 
-361                  dd.fill(np.inf) 
-362                  ii = np.empty(k,dtype=np.int) 
-363                  ii.fill(self.n) 
-364                  for j in range(len(hits)): 
-365                      dd[j], ii[j] = hits[j] 
-366                  return dd, ii 
-367              elif k is None: 
-368                  return [d for (d,i) in hits], [i for (d,i) in hits] 
-369              else: 
-370                  raise ValueError("Requested %s nearest neighbors; acceptable numbers are integers greater than or equal to one, or None") 
-
371   
-372   
-
373 -    def __query_ball_point(self, x, r, p=2., eps=0): 
-
374          R = Rectangle(self.maxes, self.mins) 
-375   
-376          def traverse_checking(node, rect): 
-377              if rect.min_distance_point(x,p)>=r/(1.+eps): 
-378                  return [] 
-379              elif rect.max_distance_point(x,p)<r*(1.+eps): 
-380                  return traverse_no_checking(node) 
-381              elif isinstance(node, KDTree.leafnode): 
-382                  d = self.data[node.idx] 
-383                  return node.idx[minkowski_distance(d,x,p)<=r].tolist() 
-384              else: 
-385                  less, greater = rect.split(node.split_dim, node.split) 
-386                  return traverse_checking(node.less, less)+traverse_checking(node.greater, greater) 
-
387          def traverse_no_checking(node): 
-388              if isinstance(node, KDTree.leafnode): 
-389   
-390                  return node.idx.tolist() 
-391              else: 
-392                  return traverse_no_checking(node.less)+traverse_no_checking(node.greater) 
-
393   
-394          return traverse_checking(self.tree, R) 
-395   
-
396 -    def query_ball_point(self, x, r, p=2., eps=0): 
-
397          """Find all points within r of x 
-398   
-399          Parameters 
-400          ========== 
-401   
-402          x : array_like, shape tuple + (self.m,) 
-403              The point or points to search for neighbors of 
-404          r : positive float 
-405              The radius of points to return 
-406          p : float 1<=p<=infinity 
-407              Which Minkowski p-norm to use 
-408          eps : nonnegative float 
-409              Approximate search. Branches of the tree are not explored 
-410              if their nearest points are further than r/(1+eps), and branches 
-411              are added in bulk if their furthest points are nearer than r*(1+eps). 
-412   
-413          Returns 
-414          ======= 
-415   
-416          results : list or array of lists 
-417              If x is a single point, returns a list of the indices of the neighbors 
-418              of x. If x is an array of points, returns an object array of shape tuple 
-419              containing lists of neighbors. 
-420   
-421   
-422          Note: if you have many points whose neighbors you want to find, you may save 
-423          substantial amounts of time by putting them in a KDTree and using query_ball_tree. 
-424          """ 
-425          x = np.asarray(x) 
-426          if x.shape[-1]!=self.m: 
-427              raise ValueError("Searching for a %d-dimensional point in a %d-dimensional KDTree" % (x.shape[-1],self.m)) 
-428          if len(x.shape)==1: 
-429              return self.__query_ball_point(x,r,p,eps) 
-430          else: 
-431              retshape = x.shape[:-1] 
-432              result = np.empty(retshape,dtype=np.object) 
-433              for c in np.ndindex(retshape): 
-434                  result[c] = self.__query_ball_point(x[c], r, p=p, eps=eps) 
-435              return result 
-
436   
-
437 -    def query_ball_tree(self, other, r, p=2., eps=0): 
-
438          """Find all pairs of points whose distance is at most r 
-439   
-440          Parameters 
-441          ========== 
-442   
-443          other : KDTree 
-444              The tree containing points to search against 
-445          r : positive float 
-446              The maximum distance 
-447          p : float 1<=p<=infinity 
-448              Which Minkowski norm to use 
-449          eps : nonnegative float 
-450              Approximate search. Branches of the tree are not explored 
-451              if their nearest points are further than r/(1+eps), and branches 
-452              are added in bulk if their furthest points are nearer than r*(1+eps). 
-453   
-454          Returns 
-455          ======= 
-456   
-457          results : list of lists 
-458              For each element self.data[i] of this tree, results[i] is a list of the 
-459              indices of its neighbors in other.data. 
-460          """ 
-461          results = [[] for i in range(self.n)] 
-462          def traverse_checking(node1, rect1, node2, rect2): 
-463              if rect1.min_distance_rectangle(rect2, p)>r/(1.+eps): 
-464                  return 
-465              elif rect1.max_distance_rectangle(rect2, p)<r*(1.+eps): 
-466                  traverse_no_checking(node1, node2) 
-467              elif isinstance(node1, KDTree.leafnode): 
-468                  if isinstance(node2, KDTree.leafnode): 
-469                      d = other.data[node2.idx] 
-470                      for i in node1.idx: 
-471                          results[i] += node2.idx[minkowski_distance(d,self.data[i],p)<=r].tolist() 
-472                  else: 
-473                      less, greater = rect2.split(node2.split_dim, node2.split) 
-474                      traverse_checking(node1,rect1,node2.less,less) 
-475                      traverse_checking(node1,rect1,node2.greater,greater) 
-476              elif isinstance(node2, KDTree.leafnode): 
-477                  less, greater = rect1.split(node1.split_dim, node1.split) 
-478                  traverse_checking(node1.less,less,node2,rect2) 
-479                  traverse_checking(node1.greater,greater,node2,rect2) 
-480              else: 
-481                  less1, greater1 = rect1.split(node1.split_dim, node1.split) 
-482                  less2, greater2 = rect2.split(node2.split_dim, node2.split) 
-483                  traverse_checking(node1.less,less1,node2.less,less2) 
-484                  traverse_checking(node1.less,less1,node2.greater,greater2) 
-485                  traverse_checking(node1.greater,greater1,node2.less,less2) 
-486                  traverse_checking(node1.greater,greater1,node2.greater,greater2) 
-
487   
-488          def traverse_no_checking(node1, node2): 
-489              if isinstance(node1, KDTree.leafnode): 
-490                  if isinstance(node2, KDTree.leafnode): 
-491                      for i in node1.idx: 
-492                          results[i] += node2.idx.tolist() 
-493                  else: 
-494                      traverse_no_checking(node1, node2.less) 
-495                      traverse_no_checking(node1, node2.greater) 
-496              else: 
-497                  traverse_no_checking(node1.less, node2) 
-498                  traverse_no_checking(node1.greater, node2) 
-499   
-500          traverse_checking(self.tree, Rectangle(self.maxes, self.mins), 
-501                            other.tree, Rectangle(other.maxes, other.mins)) 
-502          return results 
-503   
-504   
-
505 -    def count_neighbors(self, other, r, p=2.): 
-
506          """Count how many nearby pairs can be formed. 
-507   
-508          Count the number of pairs (x1,x2) can be formed, with x1 drawn 
-509          from self and x2 drawn from other, and where distance(x1,x2,p)<=r. 
-510          This is the "two-point correlation" described in Gray and Moore 2000, 
-511          "N-body problems in statistical learning", and the code here is based 
-512          on their algorithm. 
-513   
-514          Parameters 
-515          ========== 
-516   
-517          other : KDTree 
-518   
-519          r : float or one-dimensional array of floats 
-520              The radius to produce a count for. Multiple radii are searched with a single 
-521              tree traversal. 
-522          p : float, 1<=p<=infinity 
-523              Which Minkowski p-norm to use 
-524   
-525          Returns 
-526          ======= 
-527   
-528          result : integer or one-dimensional array of integers 
-529              The number of pairs. Note that this is internally stored in a numpy int, 
-530              and so may overflow if very large (two billion). 
-531          """ 
-532   
-533          def traverse(node1, rect1, node2, rect2, idx): 
-534              min_r = rect1.min_distance_rectangle(rect2,p) 
-535              max_r = rect1.max_distance_rectangle(rect2,p) 
-536              c_greater = r[idx]>max_r 
-537              result[idx[c_greater]] += node1.children*node2.children 
-538              idx = idx[(min_r<=r[idx]) & (r[idx]<=max_r)] 
-539              if len(idx)==0: 
-540                  return 
-541   
-542              if isinstance(node1,KDTree.leafnode): 
-543                  if isinstance(node2,KDTree.leafnode): 
-544                      ds = minkowski_distance(self.data[node1.idx][:,np.newaxis,:], 
-545                                    other.data[node2.idx][np.newaxis,:,:], 
-546                                    p).ravel() 
-547                      ds.sort() 
-548                      result[idx] += np.searchsorted(ds,r[idx],side='right') 
-549                  else: 
-550                      less, greater = rect2.split(node2.split_dim, node2.split) 
-551                      traverse(node1, rect1, node2.less, less, idx) 
-552                      traverse(node1, rect1, node2.greater, greater, idx) 
-553              else: 
-554                  if isinstance(node2,KDTree.leafnode): 
-555                      less, greater = rect1.split(node1.split_dim, node1.split) 
-556                      traverse(node1.less, less, node2, rect2, idx) 
-557                      traverse(node1.greater, greater, node2, rect2, idx) 
-558                  else: 
-559                      less1, greater1 = rect1.split(node1.split_dim, node1.split) 
-560                      less2, greater2 = rect2.split(node2.split_dim, node2.split) 
-561                      traverse(node1.less,less1,node2.less,less2,idx) 
-562                      traverse(node1.less,less1,node2.greater,greater2,idx) 
-563                      traverse(node1.greater,greater1,node2.less,less2,idx) 
-564                      traverse(node1.greater,greater1,node2.greater,greater2,idx) 
-
565          R1 = Rectangle(self.maxes, self.mins) 
-566          R2 = Rectangle(other.maxes, other.mins) 
-567          if np.shape(r) == (): 
-568              r = np.array([r]) 
-569              result = np.zeros(1,dtype=int) 
-570              traverse(self.tree, R1, other.tree, R2, np.arange(1)) 
-571              return result[0] 
-572          elif len(np.shape(r))==1: 
-573              r = np.asarray(r) 
-574              n, = r.shape 
-575              result = np.zeros(n,dtype=int) 
-576              traverse(self.tree, R1, other.tree, R2, np.arange(n)) 
-577              return result 
-578          else: 
-579              raise ValueError("r must be either a single value or a one-dimensional array of values") 
-580   
-581      ############################################################### 
-582      # Commented this routine out because of scipy.sparse dependence 
-583      #       -rdh 
-584      ############################################################### 
-585      # def sparse_distance_matrix(self, other, max_distance, p=2.): 
-586      #     """Compute a sparse distance matrix 
-587      #  
-588      #     Computes a distance matrix between two KDTrees, leaving as zero 
-589      #     any distance greater than max_distance. 
-590      #  
-591      #     Parameters 
-592      #     ========== 
-593      #  
-594      #     other : KDTree 
-595      #  
-596      #     max_distance : positive float 
-597      #  
-598      #     Returns 
-599      #     ======= 
-600      #  
-601      #     result : dok_matrix 
-602      #         Sparse matrix representing the results in "dictionary of keys" format. 
-603      #     """ 
-604      #     result = scipy.sparse.dok_matrix((self.n,other.n)) 
-605      #  
-606      #     def traverse(node1, rect1, node2, rect2): 
-607      #         if rect1.min_distance_rectangle(rect2, p)>max_distance: 
-608      #             return 
-609      #         elif isinstance(node1, KDTree.leafnode): 
-610      #             if isinstance(node2, KDTree.leafnode): 
-611      #                 for i in node1.idx: 
-612      #                     for j in node2.idx: 
-613      #                         d = minkowski_distance(self.data[i],other.data[j],p) 
-614      #                         if d<=max_distance: 
-615      #                             result[i,j] = d 
-616      #             else: 
-617      #                 less, greater = rect2.split(node2.split_dim, node2.split) 
-618      #                 traverse(node1,rect1,node2.less,less) 
-619      #                 traverse(node1,rect1,node2.greater,greater) 
-620      #         elif isinstance(node2, KDTree.leafnode): 
-621      #             less, greater = rect1.split(node1.split_dim, node1.split) 
-622      #             traverse(node1.less,less,node2,rect2) 
-623      #             traverse(node1.greater,greater,node2,rect2) 
-624      #         else: 
-625      #             less1, greater1 = rect1.split(node1.split_dim, node1.split) 
-626      #             less2, greater2 = rect2.split(node2.split_dim, node2.split) 
-627      #             traverse(node1.less,less1,node2.less,less2) 
-628      #             traverse(node1.less,less1,node2.greater,greater2) 
-629      #             traverse(node1.greater,greater1,node2.less,less2) 
-630      #             traverse(node1.greater,greater1,node2.greater,greater2) 
-631      #     traverse(self.tree, Rectangle(self.maxes, self.mins), 
-632      #              other.tree, Rectangle(other.maxes, other.mins)) 
-633      #  
-634      #     return result 
-635   
-636   
-
637 -def distance_matrix(x,y,p=2,threshold=1000000): 
-
638      """Compute the distance matrix. 
-639   
-640      Computes the matrix of all pairwise distances. 
-641   
-642      Parameters 
-643      ========== 
-644   
-645      x : array-like, m by k 
-646      y : array-like, n by k 
-647      p : float 1<=p<=infinity 
-648          Which Minkowski p-norm to use. 
-649      threshold : positive integer 
-650          If m*n*k>threshold use a python loop instead of creating 
-651          a very large temporary. 
-652   
-653      Returns 
-654      ======= 
-655   
-656      result : array-like, m by n 
-657   
-658   
-659      """ 
-660   
-661      x = np.asarray(x) 
-662      m, k = x.shape 
-663      y = np.asarray(y) 
-664      n, kk = y.shape 
-665   
-666      if k != kk: 
-667          raise ValueError("x contains %d-dimensional vectors but y contains %d-dimensional vectors" % (k, kk)) 
-668   
-669      if m*n*k <= threshold: 
-670          return minkowski_distance(x[:,np.newaxis,:],y[np.newaxis,:,:],p) 
-671      else: 
-672          result = np.empty((m,n),dtype=np.float) #FIXME: figure out the best dtype 
-673          if m<n: 
-674              for i in range(m): 
-675                  result[i,:] = minkowski_distance(x[i],y,p) 
-676          else: 
-677              for j in range(n): 
-678                  result[:,j] = minkowski_distance(x,y[j],p) 
-679          return result 
-
680   
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- - Package pyroms :: - Package extern :: - Module kdtree :: - Class KDTree - - - - - - -
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Class KDTree

source code

-
-object --+
-         |
-        KDTree
-
- -
-

kd-tree for quick nearest-neighbor lookup

-

This class provides an index into a set of k-dimensional points which - can be used to rapidly look up the nearest neighbors of any point.

-

The algorithm used is described in Maneewongvatana and Mount 1999. The - general idea is that the kd-tree is a binary trie, each of whose nodes - represents an axis-aligned hyperrectangle. Each node specifies an axis - and splits the set of points based on whether their coordinate along that - axis is greater than or less than a particular value.

-

During construction, the axis and splitting point are chosen by the - "sliding midpoint" rule, which ensures that the cells do not - all become long and thin.

-

The tree can be queried for the r closest neighbors of any given point - (optionally returning only those within some maximum distance of the - point). It can also be queried, with a substantial gain in efficiency, - for the r approximate closest neighbors.

-

For large dimensions (20 is already large) do not expect this to run - significantly faster than brute force. High-dimensional nearest-neighbor - queries are a substantial open problem in computer science.

-

The tree also supports all-neighbors queries, both with arrays of - points and with other kd-trees. These do use a reasonably efficient - algorithm, but the kd-tree is not necessarily the best data structure for - this sort of calculation.

- - - - - - - - - - - - - - - - -
- - - - - -
Nested Classes[hide private]
-
-   - - node -
-   - - leafnode -
-   - - innernode -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
-   - - - - - - -
__init__(self, - data, - leafsize=10)
- Construct a kd-tree.		 - source code - -
- -
-   - - - - - - -
__build(self, - idx, - maxes, - mins) - source code - -
- -
-   - - - - - - -
__query(self, - x, - k=1, - eps=0, - p=2, - distance_upper_bound=inf) - source code - -
- -
-   - - - - - - -
query(self, - x, - k=1, - eps=0, - p=2, - distance_upper_bound=inf)
- query the kd-tree for nearest neighbors		 - source code - -
- -
-   - - - - - - -
__query_ball_point(self, - x, - r, - p=2.0, - eps=0) - source code - -
- -
-   - - - - - - -
query_ball_point(self, - x, - r, - p=2.0, - eps=0)
- Find all points within r of x		 - source code - -
- -
-   - - - - - - -
query_ball_tree(self, - other, - r, - p=2.0, - eps=0)
- Find all pairs of points whose distance is at most r		 - source code - -
- -
-   - - - - - - -
count_neighbors(self, - other, - r, - p=2.0)
- Count how many nearby pairs can be formed.		 - source code - -
- -
-

Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

-
- - - - - - - - - -
- - - - - -
Properties[hide private]
-
-

Inherited from object: - __class__ -

-
- - - - - - -
- - - - - -
Method Details[hide private]
-
- -
- -
- - -
-

__init__(self, - data, - leafsize=10) -
(Constructor) -

- 		source code  -
- - 
-Construct a kd-tree.
-
-Parameters:
-===========
-
-data : array-like, shape (n,k)
-    The data points to be indexed. This array is not copied, and
-    so modifying this data will result in bogus results.
-leafsize : positive integer
-    The number of points at which the algorithm switches over to
-    brute-force.
-
-
-
-
Overrides: - object.__init__ -
-
-
-
- -
- -
- - -
-

query(self, - x, - k=1, - eps=0, - p=2, - distance_upper_bound=inf) -

- 		source code  -
- - 
-query the kd-tree for nearest neighbors
-
-Parameters:
-===========
-
-x : array-like, last dimension self.m
-    An array of points to query.
-k : integer
-    The number of nearest neighbors to return.
-eps : nonnegative float
-    Return approximate nearest neighbors; the kth returned value
-    is guaranteed to be no further than (1+eps) times the
-    distance to the real kth nearest neighbor.
-p : float, 1<=p<=infinity
-    Which Minkowski p-norm to use.
-    1 is the sum-of-absolute-values "Manhattan" distance
-    2 is the usual Euclidean distance
-    infinity is the maximum-coordinate-difference distance
-distance_upper_bound : nonnegative float
-    Return only neighbors within this distance. This is used to prune
-    tree searches, so if you are doing a series of nearest-neighbor
-    queries, it may help to supply the distance to the nearest neighbor
-    of the most recent point.
-
-Returns:
-========
-
-d : array of floats
-    The distances to the nearest neighbors.
-    If x has shape tuple+(self.m,), then d has shape tuple if
-    k is one, or tuple+(k,) if k is larger than one.  Missing
-    neighbors are indicated with infinite distances.  If k is None,
-    then d is an object array of shape tuple, containing lists
-    of distances. In either case the hits are sorted by distance
-    (nearest first).
-i : array of integers
-    The locations of the neighbors in self.data. i is the same
-    shape as d.
-
-
-
-
-
-
- -
- -
- - -
-

query_ball_point(self, - x, - r, - p=2.0, - eps=0) -

- 		source code  -
- - 
-Find all points within r of x
-
-Parameters
-==========
-
-x : array_like, shape tuple + (self.m,)
-    The point or points to search for neighbors of
-r : positive float
-    The radius of points to return
-p : float 1<=p<=infinity
-    Which Minkowski p-norm to use
-eps : nonnegative float
-    Approximate search. Branches of the tree are not explored
-    if their nearest points are further than r/(1+eps), and branches
-    are added in bulk if their furthest points are nearer than r*(1+eps).
-
-Returns
-=======
-
-results : list or array of lists
-    If x is a single point, returns a list of the indices of the neighbors
-    of x. If x is an array of points, returns an object array of shape tuple
-    containing lists of neighbors.
-
-
-Note: if you have many points whose neighbors you want to find, you may save
-substantial amounts of time by putting them in a KDTree and using query_ball_tree.
-
-
-
-
-
-
- -
- -
- - -
-

query_ball_tree(self, - other, - r, - p=2.0, - eps=0) -

- 		source code  -
- - 
-Find all pairs of points whose distance is at most r
-
-Parameters
-==========
-
-other : KDTree
-    The tree containing points to search against
-r : positive float
-    The maximum distance
-p : float 1<=p<=infinity
-    Which Minkowski norm to use
-eps : nonnegative float
-    Approximate search. Branches of the tree are not explored
-    if their nearest points are further than r/(1+eps), and branches
-    are added in bulk if their furthest points are nearer than r*(1+eps).
-
-Returns
-=======
-
-results : list of lists
-    For each element self.data[i] of this tree, results[i] is a list of the
-    indices of its neighbors in other.data.
-
-
-
-
-
-
- -
- -
- - -
-

count_neighbors(self, - other, - r, - p=2.0) -

- 		source code  -
- - 
-Count how many nearby pairs can be formed.
-
-Count the number of pairs (x1,x2) can be formed, with x1 drawn
-from self and x2 drawn from other, and where distance(x1,x2,p)<=r.
-This is the "two-point correlation" described in Gray and Moore 2000,
-"N-body problems in statistical learning", and the code here is based
-on their algorithm.
-
-Parameters
-==========
-
-other : KDTree
-
-r : float or one-dimensional array of floats
-    The radius to produce a count for. Multiple radii are searched with a single
-    tree traversal.
-p : float, 1<=p<=infinity
-    Which Minkowski p-norm to use
-
-Returns
-=======
-
-result : integer or one-dimensional array of integers
-    The number of pairs. Note that this is internally stored in a numpy int,
-    and so may overflow if very large (two billion).
-
-
-
-
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Class innernode

source code

-
- object --+    
-          |    
-KDTree.node --+
-              |
-             KDTree.innernode
-
- -
- - - - - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
-   - - - - - - -
__init__(self, - split_dim, - split, - less, - greater)
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature		 - source code - -
- -
-

Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

-
- - - - - - - - - -
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Properties[hide private]
-
-

Inherited from object: - __class__ -

-
- - - - - - -
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Method Details[hide private]
-
- -
- -
- - -
-

__init__(self, - split_dim, - split, - less, - greater) -
(Constructor) -

- 		source code  -
- -

x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

-
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Overrides: - object.__init__ -
(inherited documentation)
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Class leafnode

source code

-
- object --+    
-          |    
-KDTree.node --+
-              |
-             KDTree.leafnode
-
- -
- - - - - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
-   - - - - - - -
__init__(self, - idx)
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature		 - source code - -
- -
-

Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

-
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Inherited from object: - __class__ -

-
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Method Details[hide private]
-
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- -
- - -
-

__init__(self, - idx) -
(Constructor) -

- 		source code  -
- -

x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

-
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Overrides: - object.__init__ -
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Class node

source code

-
-object --+
-         |
-        KDTree.node
-
- -
Known Subclasses:
-
- -
- -
- - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
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Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __init__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

-
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Class Rectangle

source code

-
-object --+
-         |
-        Rectangle
-
- -
-

Hyperrectangle class.

-

Represents a Cartesian product of intervals.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
-   - - - - - - -
__init__(self, - maxes, - mins)
- Construct a hyperrectangle.		 - source code - -
- -
-   - - - - - - -
__repr__(self)
- repr(x)		 - source code - -
- -
-   - - - - - - -
volume(self)
- Total volume.		 - source code - -
- -
-   - - - - - - -
split(self, - d, - split)
- Produce two hyperrectangles by splitting along axis d.		 - source code - -
- -
-   - - - - - - -
min_distance_point(self, - x, - p=2.0)
- Compute the minimum distance between x and a point in the - hyperrectangle.		 - source code - -
- -
-   - - - - - - -
max_distance_point(self, - x, - p=2.0)
- Compute the maximum distance between x and a point in the - hyperrectangle.		 - source code - -
- -
-   - - - - - - -
min_distance_rectangle(self, - other, - p=2.0)
- Compute the minimum distance between points in the two - hyperrectangles.		 - source code - -
- -
-   - - - - - - -
max_distance_rectangle(self, - other, - p=2.0)
- Compute the maximum distance between points in the two - hyperrectangles.		 - source code - -
- -
-

Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __setattr__, - __str__ -

-
- - - - - - - - - -
- - - - - -
Properties[hide private]
-
-

Inherited from object: - __class__ -

-
- - - - - - -
- - - - - -
Method Details[hide private]
-
- -
- -
- - -
-

__init__(self, - maxes, - mins) -
(Constructor) -

- 		source code  -
- -

Construct a hyperrectangle.

-
-
Overrides: - object.__init__ -
-
-
-
- -
- -
- - -
-

__repr__(self) -
(Representation operator) -

- 		source code  -
- -

repr(x)

-
-
Overrides: - object.__repr__ -
(inherited documentation)
- -
-
-
- -
- -
- - -
-

split(self, - d, - split) -

- 		source code  -
- -

Produce two hyperrectangles by splitting along axis d.

-

In general, if you need to compute maximum and minimum distances to - the children, it can be done more efficiently by updating the maximum and - minimum distances to the parent.

-
-
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Module pupynere

source code

-

NetCDF reader.

-

Pupynere implements a PUre PYthon NEtcdf REader.

- -
-

Author: - Roberto De Almeida <rob@pydap.org> -

-
- - - - - - - - - - - -
- - - - - -
Classes[hide private]
-
-   - - NetCDFFile
- A NetCDF file parser. -
-   - - NetCDFVariable -
- - - - - - - - - -
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Functions[hide private]
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- - - - - -
Variables[hide private]
-
-   - - ABSENT = '\x00\x00\x00\x00\x00\x00\x00\x00' -
-   - - ZERO = '\x00\x00\x00\x00' -
-   - - NC_BYTE = '\x00\x00\x00\x01' -
-   - - NC_CHAR = '\x00\x00\x00\x02' -
-   - - NC_SHORT = '\x00\x00\x00\x03' -
-   - - NC_INT = '\x00\x00\x00\x04' -
-   - - NC_FLOAT = '\x00\x00\x00\x05' -
-   - - NC_DOUBLE = '\x00\x00\x00\x06' -
-   - - NC_DIMENSION = '\x00\x00\x00\n' -
-   - - NC_VARIABLE = '\x00\x00\x00\x0b' -
-   - - NC_ATTRIBUTE = '\x00\x00\x00\x0c' -
- - - - - - - - - - - - - - - - - -
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- Generated by Epydoc 3.0.1 on Mon Sep 27 11:31:38 2010 - - http://epydoc.sourceforge.net -
- - - - diff --git a/pyroms/docs/pyroms.extern.pupynere-pysrc.html b/pyroms/docs/pyroms.extern.pupynere-pysrc.html deleted file mode 100644 index 8d08cb5..0000000 --- a/pyroms/docs/pyroms.extern.pupynere-pysrc.html +++ /dev/null @@ -1,365 +0,0 @@ - - - - - pyroms.extern.pupynere - - - - - - - - - - - - - - - - - - - - - - -
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- - - - - -
- - Package pyroms :: - Package extern :: - Module pupynere - - - - - - -
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-

Source Code for Module pyroms.extern.pupynere

-
-  1  """NetCDF reader. 
-  2   
-  3  Pupynere implements a PUre PYthon NEtcdf REader. 
-  4  """ 
-  5   
-  6  __author__ = "Roberto De Almeida <rob@pydap.org>" 
-  7   
-  8   
-  9  import struct 
- 10  import itertools 
- 11  import mmap 
- 12   
- 13  from numpy import ndarray, zeros, array 
- 14   
- 15   
- 16  ABSENT       = '\x00' * 8 
- 17  ZERO         = '\x00' * 4 
- 18  NC_BYTE      = '\x00\x00\x00\x01'  
- 19  NC_CHAR      = '\x00\x00\x00\x02' 
- 20  NC_SHORT     = '\x00\x00\x00\x03' 
- 21  NC_INT       = '\x00\x00\x00\x04' 
- 22  NC_FLOAT     = '\x00\x00\x00\x05' 
- 23  NC_DOUBLE    = '\x00\x00\x00\x06' 
- 24  NC_DIMENSION = '\x00\x00\x00\n' 
- 25  NC_VARIABLE  = '\x00\x00\x00\x0b' 
- 26  NC_ATTRIBUTE = '\x00\x00\x00\x0c' 
- 27   
- 28   
-
 29 -class NetCDFFile(object): 
-
 30      """A NetCDF file parser.""" 
- 31   
-
 32 -    def __init__(self, file): 
-
 33          self._buffer = open(file, 'rb') 
- 34          self._parse() 
-
 35   
-
 36 -    def read(self, size=-1): 
-
 37          """Alias for reading the file buffer.""" 
- 38          return self._buffer.read(size) 
-
 39   
-
 40 -    def _parse(self): 
-
 41          """Initial parsing of the header.""" 
- 42          # Check magic bytes. 
- 43          assert self.read(3) == 'CDF' 
- 44   
- 45          # Read version byte. 
- 46          byte = self.read(1) 
- 47          self.version_byte = struct.unpack('>b', byte)[0] 
- 48   
- 49          # Read header info. 
- 50          self._numrecs() 
- 51          self._dim_array() 
- 52          self._gatt_array() 
- 53          self._var_array() 
-
 54   
-
 55 -    def _numrecs(self): 
-
 56          """Read number of records.""" 
- 57          self._nrecs = self._unpack_int() 
-
 58   
-
 59 -    def _dim_array(self): 
-
 60          """Read a dict with dimensions names and sizes.""" 
- 61          assert self.read(4) in [ZERO, NC_DIMENSION] 
- 62          count = self._unpack_int() 
- 63   
- 64          self.dimensions = {} 
- 65          self._dims = [] 
- 66          for dim in range(count): 
- 67              name = self._read_string() 
- 68              length = self._unpack_int() 
- 69              if length == 0: length = None # record dimension 
- 70              self.dimensions[name] = length 
- 71              self._dims.append(name)  # preserve dim order 
-
 72   
-
 73 -    def _gatt_array(self): 
-
 74          """Read global attributes.""" 
- 75          self.attributes = self._att_array() 
- 76   
- 77          # Update __dict__ for compatibility with S.IO.N 
- 78          self.__dict__.update(self.attributes) 
-
 79   
-
 80 -    def _att_array(self): 
-
 81          """Read a dict with attributes.""" 
- 82          assert self.read(4) in [ZERO, NC_ATTRIBUTE] 
- 83          count = self._unpack_int() 
- 84   
- 85          # Read attributes. 
- 86          attributes = {} 
- 87          for attribute in range(count): 
- 88              name = self._read_string() 
- 89              nc_type = self._unpack_int() 
- 90              n = self._unpack_int() 
- 91   
- 92              # Read value for attributes. 
- 93              attributes[name] = self._read_values(n, nc_type) 
- 94   
- 95          return attributes 
-
 96   
-
 97 -    def _var_array(self): 
-
 98          """Read all variables.""" 
- 99          assert self.read(4) in [ZERO, NC_VARIABLE] 
-100   
-101          # Read size of each record, in bytes. 
-102          self._read_recsize() 
-103   
-104          # Read variables. 
-105          self.variables = {} 
-106          count = self._unpack_int() 
-107          for variable in range(count): 
-108              name = self._read_string() 
-109              self.variables[name] = self._read_var() 
-
110   
-
111 -    def _read_recsize(self): 
-
112          """Read all variables and compute record bytes.""" 
-113          pos = self._buffer.tell() 
-114           
-115          recsize = 0 
-116          count = self._unpack_int() 
-117          for variable in range(count): 
-118              name = self._read_string() 
-119              n = self._unpack_int() 
-120              isrec = False 
-121              for i in range(n): 
-122                  dimid = self._unpack_int() 
-123                  name = self._dims[dimid] 
-124                  dim = self.dimensions[name] 
-125                  if dim is None and i == 0: 
-126                      isrec = True 
-127              attributes = self._att_array() 
-128              nc_type = self._unpack_int() 
-129              vsize = self._unpack_int() 
-130              begin = [self._unpack_int, self._unpack_int64][self.version_byte-1]() 
-131   
-132              if isrec: recsize += vsize 
-133   
-134          self._recsize = recsize 
-135          self._buffer.seek(pos) 
-
136   
-
137 -    def _read_var(self): 
-
138          dimensions = [] 
-139          shape = [] 
-140          n = self._unpack_int() 
-141          isrec = False 
-142          for i in range(n): 
-143              dimid = self._unpack_int() 
-144              name = self._dims[dimid] 
-145              dimensions.append(name) 
-146              dim = self.dimensions[name] 
-147              if dim is None and i == 0: 
-148                  dim = self._nrecs 
-149                  isrec = True 
-150              shape.append(dim) 
-151          dimensions = tuple(dimensions) 
-152          shape = tuple(shape) 
-153   
-154          attributes = self._att_array() 
-155          nc_type = self._unpack_int() 
-156          vsize = self._unpack_int() 
-157           
-158          # Read offset. 
-159          begin = [self._unpack_int, self._unpack_int64][self.version_byte-1]() 
-160   
-161          return NetCDFVariable(self._buffer.fileno(), nc_type, vsize, begin, shape, dimensions, attributes, isrec, self._recsize) 
-
162   
-
163 -    def _read_values(self, n, nc_type): 
-
164          bytes = [1, 1, 2, 4, 4, 8] 
-165          typecodes = ['b', 'c', 'h', 'i', 'f', 'd'] 
-166           
-167          count = n * bytes[nc_type-1] 
-168          values = self.read(count) 
-169          padding = self.read((4 - (count % 4)) % 4) 
-170           
-171          typecode = typecodes[nc_type-1] 
-172          if nc_type != 2:  # not char  
-173              values = struct.unpack('>%s' % (typecode * n), values) 
-174              values = array(values, dtype=typecode)  
-175          else: 
-176              # Remove EOL terminator. 
-177              if values.endswith('\x00'): values = values[:-1] 
-178   
-179          return values 
-
180   
-
181 -    def _unpack_int(self): 
-
182          return struct.unpack('>i', self.read(4))[0] 
-
183      _unpack_int32 = _unpack_int 
-184   
-
185 -    def _unpack_int64(self): 
-
186          return struct.unpack('>q', self.read(8))[0] 
-
187   
-
188 -    def _read_string(self): 
-
189          count = struct.unpack('>i', self.read(4))[0] 
-190          s = self.read(count) 
-191          # Remove EOL terminator. 
-192          if s.endswith('\x00'): s = s[:-1] 
-193          padding = self.read((4 - (count % 4)) % 4) 
-194          return s 
-
195   
-
196 -    def close(self): 
-
197          self._buffer.close() 
-
198   
-199   
-
200 -class NetCDFVariable(object): 
-
201 -    def __init__(self, fileno, nc_type, vsize, begin, shape, dimensions, attributes, isrec=False, recsize=0): 
-
202          self._nc_type = nc_type 
-203          self._vsize = vsize 
-204          self._begin = begin 
-205          self.shape = shape 
-206          self.dimensions = dimensions 
-207          self.attributes = attributes  # for ``dap.plugins.netcdf`` 
-208          self.__dict__.update(attributes) 
-209          self._is_record = isrec 
-210   
-211          # Number of bytes and type. 
-212          self._bytes = [1, 1, 2, 4, 4, 8][self._nc_type-1] 
-213          type_ = ['i', 'S', 'i', 'i', 'f', 'f'][self._nc_type-1] 
-214          dtype = '>%s%d' % (type_, self._bytes) 
-215          bytes = self._begin + self._vsize  
-216   
-217          if isrec: 
-218              # Record variables are not stored contiguosly on disk, so we  
-219              # need to create a separate array for each record. 
-220              self.__array_data__ = zeros(shape, dtype) 
-221              bytes += (shape[0] - 1) * recsize 
-222              for n in range(shape[0]): 
-223                  offset = self._begin + (n * recsize) 
-224                  mm = mmap.mmap(fileno, bytes, access=mmap.ACCESS_READ) 
-225                  self.__array_data__[n] = ndarray.__new__(ndarray, shape[1:], dtype=dtype, buffer=mm, offset=offset, order=0) 
-226          else: 
-227              # Create buffer and data. 
-228              mm = mmap.mmap(fileno, bytes, access=mmap.ACCESS_READ) 
-229              self.__array_data__ = ndarray.__new__(ndarray, shape, dtype=dtype, buffer=mm, offset=self._begin, order=0) 
-230   
-231          # N-D array interface 
-232          self.__array_interface__ = {'shape'  : shape, 
-233                                      'typestr': dtype, 
-234                                      'data'   : self.__array_data__, 
-235                                      'version': 3, 
-236                                     } 
-
237   
-
238 -    def __getitem__(self, index): 
-
239          return self.__array_data__.__getitem__(index) 
-
240   
-
241 -    def getValue(self): 
-
242          """For scalars.""" 
-243          return self.__array_data__.item() 
-
244   
-
245 -    def typecode(self): 
-
246          return ['b', 'c', 'h', 'i', 'f', 'd'][self._nc_type-1] 
-
247   
-248               
-
249 -def _test(): 
-
250      import doctest 
-251      doctest.testmod() 
-
252   
-
-
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- Generated by Epydoc 3.0.1 on Mon Sep 27 11:31:40 2010 - - http://epydoc.sourceforge.net -
- - - - diff --git a/pyroms/docs/pyroms.extern.pupynere.NetCDFFile-class.html b/pyroms/docs/pyroms.extern.pupynere.NetCDFFile-class.html deleted file mode 100644 index 76a14d0..0000000 --- a/pyroms/docs/pyroms.extern.pupynere.NetCDFFile-class.html +++ /dev/null @@ -1,487 +0,0 @@ - - - - - pyroms.extern.pupynere.NetCDFFile - - - - - - - - - - - - - - - - - - - - - - -
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- - Package pyroms :: - Package extern :: - Module pupynere :: - Class NetCDFFile - - - - - - -
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-
- -

Class NetCDFFile

source code

-
-object --+
-         |
-        NetCDFFile
-
- -
-

A NetCDF file parser.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
-   - - - - - - -
__init__(self, - file)
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature		 - source code - -
- -
-   - - - - - - -
read(self, - size=-1)
- Alias for reading the file buffer.		 - source code - -
- -
-   - - - - - - -
_parse(self)
- Initial parsing of the header.		 - source code - -
- -
-   - - - - - - -
_numrecs(self)
- Read number of records.		 - source code - -
- -
-   - - - - - - -
_dim_array(self)
- Read a dict with dimensions names and sizes.		 - source code - -
- -
-   - - - - - - -
_gatt_array(self)
- Read global attributes.		 - source code - -
- -
-   - - - - - - -
_att_array(self)
- Read a dict with attributes.		 - source code - -
- -
-   - - - - - - -
_var_array(self)
- Read all variables.		 - source code - -
- -
-   - - - - - - -
_read_recsize(self)
- Read all variables and compute record bytes.		 - source code - -
- -
-   - - - - - - -
_read_var(self) - source code - -
- -
-   - - - - - - -
_read_values(self, - n, - nc_type) - source code - -
- -
-   - - - - - - -
_unpack_int(self) - source code - -
- -
-   - - - - - - -
_unpack_int32(self) - source code - -
- -
-   - - - - - - -
_unpack_int64(self) - source code - -
- -
-   - - - - - - -
_read_string(self) - source code - -
- -
-   - - - - - - -
close(self) - source code - -
- -
-

Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

-
- - - - - - - - - -
- - - - - -
Properties[hide private]
-
-

Inherited from object: - __class__ -

-
- - - - - - -
- - - - - -
Method Details[hide private]
-
- -
- -
- - -
-

__init__(self, - file) -
(Constructor) -

- 		source code  -
- -

x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

-
-
Overrides: - object.__init__ -
(inherited documentation)
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- Generated by Epydoc 3.0.1 on Mon Sep 27 11:31:39 2010 - - http://epydoc.sourceforge.net -
- - - - diff --git a/pyroms/docs/pyroms.extern.pupynere.NetCDFVariable-class.html b/pyroms/docs/pyroms.extern.pupynere.NetCDFVariable-class.html deleted file mode 100644 index c558a8f..0000000 --- a/pyroms/docs/pyroms.extern.pupynere.NetCDFVariable-class.html +++ /dev/null @@ -1,300 +0,0 @@ - - - - - pyroms.extern.pupynere.NetCDFVariable - - - - - - - - - - - - - - - - - - - - - - -
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- - Package pyroms :: - Package extern :: - Module pupynere :: - Class NetCDFVariable - - - - - - -
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-
- -

Class NetCDFVariable

source code

-
-object --+
-         |
-        NetCDFVariable
-
- -
- - - - - - - - - - - - - - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
-   - - - - - - -
__init__(self, - fileno, - nc_type, - vsize, - begin, - shape, - dimensions, - attributes, - isrec=False, - recsize=0)
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature		 - source code - -
- -
-   - - - - - - -
__getitem__(self, - index) - source code - -
- -
-   - - - - - - -
getValue(self)
- For scalars.		 - source code - -
- -
-   - - - - - - -
typecode(self) - source code - -
- -
-

Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

-
- - - - - - - - - -
- - - - - -
Properties[hide private]
-
-

Inherited from object: - __class__ -

-
- - - - - - -
- - - - - -
Method Details[hide private]
-
- -
- -
- - -
-

__init__(self, - fileno, - nc_type, - vsize, - begin, - shape, - dimensions, - attributes, - isrec=False, - recsize=0) -
(Constructor) -

- 		source code  -
- -

x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

-
-
Overrides: - object.__init__ -
(inherited documentation)
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- Generated by Epydoc 3.0.1 on Mon Sep 27 11:31:39 2010 - - http://epydoc.sourceforge.net -
- - - - diff --git a/pyroms/docs/pyroms.grid-module.html b/pyroms/docs/pyroms.grid-module.html deleted file mode 100644 index 9aa9774..0000000 --- a/pyroms/docs/pyroms.grid-module.html +++ /dev/null @@ -1,404 +0,0 @@ - - - - - pyroms.grid - - - - - - - - - - - - - - - - - - - - - - -
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- - Package pyroms :: - Module grid - - - - - - -
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-
- -

Module grid

source code

- - - - - - - - - - - - -
- - - - - -
Classes[hide private]
-
-   - - ROMS_Grid
- grd = ROMS_Grid(hgrid, vgrid) -
-   - - ROMS_gridinfo
- gridinfo = ROMS_gridinfo(gridid,grid_file=None,hist_file=None) -
- - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - -
Functions[hide private]
-
-   - - - - - - -
print_ROMS_gridinfo(gridid)
- return the grid information for gridid		 - source code - -
- -
-   - - - - - - -
list_ROMS_gridid()
- return the list of the defined gridid		 - source code - -
- -
-   - - - - - - -
get_ROMS_hgrid(gridid)
- hgrid = get_ROMS_hgrid(gridid)		 - source code - -
- -
-   - - - - - - -
get_ROMS_vgrid(gridid, - zeta=None)
- vgrid = get_ROMS_vgrid(gridid)		 - source code - -
- -
-   - - - - - - -
get_ROMS_grid(gridid, - zeta=None, - hist_file=None, - grid_file=None)
- grd = get_ROMS_grid(gridid,hist_file=None,grid_file=None)		 - source code - -
- -
-   - - - - - - -
write_ROMS_grid(grd, - filename='ocean_grd.nc')
- Write ROMS_CGrid class on a NetCDF file.		 - source code - -
- -
- - - - - - - - - -
- - - - - -
Variables[hide private]
-
-   - - gridid_dictionary = {} -
- - - - - - -
- - - - - -
Function Details[hide private]
-
- -
- -
- - -
-

get_ROMS_hgrid(gridid) -

- 		source code  -
- -

hgrid = get_ROMS_hgrid(gridid)

-

Load ROMS horizontal grid object

-
-
-
-
- -
- -
- - -
-

get_ROMS_vgrid(gridid, - zeta=None) -

- 		source code  -
- -

vgrid = get_ROMS_vgrid(gridid)

-

Load ROMS vertical grid object. vgrid is a s_coordinate or a - z_coordinate object, depending on gridid.grdtype. vgrid.z_r and vgrid.z_w - (vgrid.z for a z_coordinate object) can be indexed in order to retreive - the actual depths. The free surface time serie zeta can be provided as an - optional argument. Note that the values of zeta are not calculated until - z is indexed, so a netCDF variable for zeta may be passed, even if the - file is large, as only the values that are required will be retrieved - from the file.

-
-
-
-
- -
- -
- - -
-

get_ROMS_grid(gridid, - zeta=None, - hist_file=None, - grid_file=None) -

- 		source code  -
- - 
-
-grd = get_ROMS_grid(gridid,hist_file=None,grid_file=None)
-
-Load ROMS grid object.
-
-gridid is a string with the name of the grid in it.  If hist_file
-   and grid_file are not passed into the function, or are set to
-   None, then gridid is used to get the grid data from the
-   gridid.txt file.
-
-   if hist_file and grid_file are given, and they are the file
-   paths to a ROMS history file and grid file respectively, the
-   grid information will be extracted from those files, and gridid
-   will be used to name that grid for the rest of the python
-   session.
-
-grd.vgrid is a s_coordinate or
-a z_coordinate object, depending on gridid.grdtype.
-grd.vgrid.z_r and grd.vgrid.z_w (grd.vgrid.z for a 
-z_coordinate object) can be indexed in order to retreive the 
-actual depths. The free surface time serie zeta can be provided 
-as an optional argument. Note that the values of zeta are not 
-calculated until z is indexed, so a netCDF variable for zeta may 
-be passed, even if the file is large, as only the values that 
-are required will be retrieved from the file.
-
-
-
-
-
-
-
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Source Code for Module pyroms.grid

-
-  1  # encoding: utf-8 
-  2   
-  3  import sys 
-  4  import os 
-  5  import numpy as np 
-  6  from mpl_toolkits.basemap import Basemap 
-  7  from datetime import datetime 
-  8  try: 
-  9    import netCDF4 as netCDF 
- 10  except: 
- 11    import netCDF3 as netCDF 
- 12   
- 13  import pyroms 
- 14  from pyroms.hgrid import * 
- 15  from pyroms.vgrid import * 
- 16  from pyroms.grid import * 
- 17  from pyroms import io 
- 18   
- 19  #define a dictionary that will remember gridid's that are defined from 
- 20  #a history and grid file. Because this is defined in this models name 
- 21  #space, it will remain persistent.  They keys are the gridid, and the 
- 22  #values are ROMS_gridinfo objects. 
- 23  gridid_dictionary={} 
- 24   
-
 25 -class ROMS_Grid(object): 
-
 26      """ 
- 27      grd = ROMS_Grid(hgrid, vgrid) 
- 28   
- 29      ROMS Grid object combining horizontal and vertical grid 
- 30      """ 
- 31   
-
 32 -    def __init__(self, name, hgrid=CGrid, vgrid=s_coordinate): 
-
 33          self.name = name 
- 34          self.hgrid = hgrid 
- 35          self.vgrid = vgrid 
-
 36   
- 37   
-
 38 -class ROMS_gridinfo(object): 
-
 39      ''' 
- 40      gridinfo = ROMS_gridinfo(gridid,grid_file=None,hist_file=None) 
- 41   
- 42      Return an object with grid information for gridid. 
- 43   
- 44      There are two ways to define the grid information.  If grid_file 
- 45      and hist_file are not passed to the object when it is created, the 
- 46      information is retrieved from gridid.txt.   
- 47      To add new grid please edit your gridid.txt. You need to define  
- 48      an environment variable PYROMS_GRIDID_FILE pointing to your  
- 49      gridid.txt file. Just copy an existing grid and modify the  
- 50      definition accordingly to your case (Be carefull with 
- 51      space and blank line). 
- 52   
- 53      If grid_file is the path to a ROMS grid file, and hist_file is the 
- 54      path to a ROMS history file, then the grid information will be 
- 55      read from those files.  Gridid can then be used to refer to this 
- 56      grid information so that the grid and history files do not be 
- 57      included in subsequent calls. 
- 58      ''' 
- 59   
-
 60 -    def __init__(self, gridid,grid_file=None,hist_file=None): 
-
 61        #first determine if the information for the gridid has already been obtained. 
- 62        if gridid in gridid_dictionary: 
- 63          #print 'CJMP> gridid found in gridid_dictionary, grid retrieved from dictionary' 
- 64          saved_self=gridid_dictionary[gridid] 
- 65          for attrib in saved_self.__dict__.keys(): 
- 66            setattr(self,attrib,getattr(saved_self,attrib)) 
- 67        else: 
- 68          #nope, we need to get the information from gridid.txt or from 
- 69          #the grid and history files from the model 
- 70          self.id = gridid 
- 71          self._get_grid_info(grid_file,hist_file) 
- 72           
- 73          #now save the data in the dictionary, so we don't need to get it again 
- 74          gridid_dictionary[gridid]=self 
-
 75   
-
 76 -    def _get_grid_info(self,grid_file,hist_file): 
-
 77   
- 78        #check if the grid_file and hist_files are both null; if so get data from gridid.txt 
- 79        if (type(grid_file)==type(None))&(type(hist_file)==type(None)): 
- 80          #print 'CJMP> gridid not in dictionary, data will be retrieved from gridid.txt' 
- 81          gridid_file =  os.getenv("PYROMS_GRIDID_FILE") 
- 82          data = open(gridid_file,'r') 
- 83          lines = data.readlines() 
- 84          data.close() 
- 85   
- 86          line_nb = 0 
- 87          info = [] 
- 88          for line in lines: 
- 89              s = line.split() 
- 90              if s[0] == 'id': 
- 91                  if s[2] == self.id: 
- 92                      for l in range(line_nb, line_nb+5): 
- 93                          s = lines[l].split() 
- 94                          info.append(s[2]) 
- 95                          line_nb = line_nb + 1 
- 96                      if info[4] == 'roms': 
- 97                          for l in range(line_nb, line_nb+4): 
- 98                              s = lines[l].split() 
- 99                              info.append(s[2]) 
-100                      if info[4] == 'z': 
-101                          s = lines[line_nb].split() 
-102                          info.append(s[3:-1]) 
-103                          while s[-1:] == ['\\']: 
-104                              line_nb = line_nb + 1 
-105                              s = lines[line_nb].split() 
-106                              info.append(s[:-1]) 
-107              line_nb = line_nb + 1 
-108   
-109          if info == []: 
-110              raise ValueError, 'Unknow gridid. Please check your gridid.txt file' 
-111   
-112          if info[4] == 'roms': 
-113              self.name     =          info[1] 
-114              self.grdfile  =          info[2] 
-115              self.N        =   np.int(info[3]) 
-116              self.grdtype  =          info[4] 
-117              self.Vtrans   =   np.int(info[5]) 
-118              self.theta_s  = np.float(info[6]) 
-119              self.theta_b  = np.float(info[7]) 
-120              self.Tcline   = np.float(info[8]) 
-121   
-122          elif info[4] == 'z':   
-123              nline = len(info) 
-124              dep = info[5] 
-125              for line in range(6,nline): 
-126                  dep = dep + info[line] 
-127              dep = np.array(dep, dtype=np.float) 
-128   
-129              self.name    =        info[1] 
-130              self.grdfile =        info[2] 
-131              self.N       = np.int(info[3]) 
-132              self.grdtype =        info[4] 
-133              self.depth   = dep 
-134   
-135          else: 
-136              raise ValueError, 'Unknow grid type. Please check your gridid.txt file' 
-137   
-138        else: #lets get the grid information from the history and grid files 
-139          #print 'CJMP> getting grid info from ROMS history and grid files' 
-140          assert type(grid_file)!=type(None), 'if specify history file you must specify grid file' 
-141          assert type(hist_file)!=type(None), 'if specify grid file you must specify history file' 
-142   
-143          #open history file and get necessary grid information from it.  
-144          hist=netCDF.Dataset(hist_file,'r') 
-145   
-146          #put data into ROMS_gridinfo object 
-147          self.name=self.id 
-148          self.grdfile=grid_file 
-149          self.N=len(hist.dimensions['s_rho']) 
-150          self.grdtype='roms' 
-151   
-152          #now write this to deal with both ROMS 3 and 2 
-153          try: 
-154            self.Vtrans=np.float(hist.Vtransform) 
-155            self.theta_s=np.float(hist.theta_s) 
-156            self.theta_b=np.float(hist.theta_b) 
-157            self.Tcline=np.float(hist.Tcline) 
-158          except AttributeError: 
-159            try: 
-160              self.Vtrans=np.float(hist.variables['Vtransform'][:]) 
-161            except: 
-162              print 'variable Vtransform not found in history file. Defaulting to Vtranform=1' 
-163              self.Vtrans=1 
-164            self.theta_s=np.float(hist.variables['theta_s'][:]) 
-165            self.theta_b=np.float(hist.variables['theta_b'][:]) 
-166            self.Tcline=np.float(hist.variables['Tcline'][:]) 
-
167             
-168   
-192   
-193   
-
194 -def list_ROMS_gridid(): 
-
195      """ 
-196      list_ROMS_gridid() 
-197   
-198      return the list of the defined gridid 
-199      """ 
-200   
-201      gridid_file = os.getenv("PYROMS_GRIDID_FILE") 
-202      data = open(gridid_file,'r') 
-203      lines = data.readlines() 
-204      data.close() 
-205       
-206      gridid_list = [] 
-207      for line in lines: 
-208          s = line.split() 
-209          if s[0] == 'id': 
-210              gridid_list.append(s[2]) 
-211   
-212      print 'List of defined gridid : ', gridid_list 
-
213   
-214   
-
215 -def get_ROMS_hgrid(gridid): 
-
216      """ 
-217      hgrid = get_ROMS_hgrid(gridid) 
-218   
-219      Load ROMS horizontal grid object 
-220      """ 
-221   
-222      gridinfo = ROMS_gridinfo(gridid) 
-223      grdfile = gridinfo.grdfile 
-224   
-225      nc = io.Dataset(grdfile) 
-226   
-227      #Check for cartesian or geographical grid 
-228      spherical = nc.variables['spherical'][:] 
-229   
-230      #Get horizontal grid  
-231      if spherical == 'F': 
-232          #cartesian grid 
-233          print 'Load cartesian grid from file' 
-234          if 'x_vert' in nc.variables.keys() and 'y_vert' in nc.variables.keys(): 
-235              x_vert = nc.variables['x_vert'][:] 
-236              y_vert = nc.variables['y_vert'][:] 
-237          elif 'x_rho' in nc.variables.keys() and 'y_rho' in nc.variables.keys() \ 
-238                   and 'pm' in nc.variables.keys() and 'pn' in nc.variables.keys(): 
-239              x_rho = nc.variables['x_rho'][:] 
-240              y_rho = nc.variables['y_rho'][:] 
-241              pm = nc.variables['pm'][:] 
-242              pn = nc.variables['pn'][:] 
-243              try: angle = nc.variables['angle'][:] 
-244              except: angle = np.zeros(x_rho.shape) 
-245              #compute verts from rho point, pm, pn, angle 
-246              x_vert, y_vert = rho_to_vert(x_rho, y_rho, pm, pn, angle) 
-247          else: 
-248              raise ValueError, 'NetCDF file must contain x_vert and y_vert \ 
-249                       or x_rho, y_rho, pm, pn and angle for a cartesian grid' 
-250   
-251          if 'x_rho' in nc.variables.keys() and 'y_rho' in nc.variables.keys() and \ 
-252               'x_u' in nc.variables.keys() and 'y_u' in nc.variables.keys() and \ 
-253               'x_v' in nc.variables.keys() and 'y_v' in nc.variables.keys() and \ 
-254               'x_psi' in nc.variables.keys() and 'y_psi' in nc.variables.keys(): 
-255              x_rho = nc.variables['x_rho'][:] 
-256              y_rho = nc.variables['y_rho'][:] 
-257              x_u = nc.variables['x_u'][:] 
-258              y_u = nc.variables['y_u'][:] 
-259              x_v = nc.variables['x_v'][:] 
-260              y_v = nc.variables['y_v'][:] 
-261              x_psi = nc.variables['x_psi'][:] 
-262              y_psi = nc.variables['y_psi'][:] 
-263          else: 
-264              x_rho = None 
-265              y_rho = None 
-266              x_u = None 
-267              y_u = None 
-268              x_v = None 
-269              y_v = None 
-270              x_psi = None 
-271              y_psi = None 
-272   
-273          if 'pm' in nc.variables.keys() and 'pn' in nc.variables.keys(): 
-274              pm = nc.variables['pm'][:] 
-275              dx = 1. / pm 
-276              pn = nc.variables['pn'][:] 
-277              dy = 1. / pn 
-278          else: 
-279              dx = None 
-280              dy = None 
-281   
-282          if 'dndx' in nc.variables.keys() and 'dmde' in nc.variables.keys(): 
-283              dndx = nc.variables['dndx'][:] 
-284              dmde = nc.variables['dmde'][:] 
-285          else: 
-286              dndx = None 
-287              dmde = None 
-288   
-289          if 'angle' in nc.variables.keys(): 
-290              angle = nc.variables['angle'][:] 
-291          else: 
-292              angle = None 
-293   
-294          #Get cartesian grid 
-295          hgrd = CGrid(x_vert, y_vert, x_rho=x_rho, y_rho=y_rho, \ 
-296                       x_u=x_u, y_u=y_u, x_v=x_v, y_v=y_v, \ 
-297                       x_psi=x_psi, y_psi=y_psi, dx=dx, dy=dy, \ 
-298                       dndx=dndx, dmde=dmde, angle_rho=angle) 
-299   
-300      else: 
-301          #geographical grid 
-302          print 'Load geographical grid from file' 
-303          proj = Basemap(projection='merc', resolution=None, lat_0=0, lon_0=0) 
-304          if 'lon_vert' in nc.variables.keys() and 'lat_vert' in nc.variables.keys(): 
-305              lon_vert = nc.variables['lon_vert'][:] 
-306              lat_vert = nc.variables['lat_vert'][:] 
-307          elif 'lon_rho' in nc.variables.keys() and 'lon_rho' in nc.variables.keys() \ 
-308                  and 'lon_psi' in nc.variables.keys() and 'lat_psi' in nc.variables.keys(): 
-309              lon_rho = nc.variables['lon_rho'][:] 
-310              lat_rho = nc.variables['lat_rho'][:] 
-311              lon_psi = nc.variables['lon_psi'][:] 
-312              lat_psi = nc.variables['lat_psi'][:] 
-313              #compute verts from rho and psi point 
-314              lon_vert, lat_vert = rho_to_vert_geo(lon_rho, lat_rho, lon_psi, lat_psi) 
-315          else: 
-316              raise ValueError, 'NetCDF file must contain lon_vert and lat_vert \ 
-317                    or lon_rho, lat_rho, lon_psi, lat_psi for a geographical grid' 
-318   
-319          if 'lon_rho' in nc.variables.keys() and 'lat_rho' in nc.variables.keys() and \ 
-320                'lon_u' in nc.variables.keys() and 'lat_u' in nc.variables.keys() and \ 
-321                'lon_v' in nc.variables.keys() and 'lat_v' in nc.variables.keys() and \ 
-322                'lon_psi' in nc.variables.keys() and 'lat_psi' in nc.variables.keys(): 
-323              lon_rho = nc.variables['lon_rho'][:] 
-324              lat_rho = nc.variables['lat_rho'][:] 
-325              lon_u = nc.variables['lon_u'][:] 
-326              lat_u = nc.variables['lat_u'][:] 
-327              lon_v = nc.variables['lon_v'][:] 
-328              lat_v = nc.variables['lat_v'][:] 
-329              lon_psi = nc.variables['lon_psi'][:] 
-330              lat_psi = nc.variables['lat_psi'][:] 
-331          else: 
-332              lon_rho = None 
-333              lat_rho = None 
-334              lon_u = None 
-335              lat_u = None 
-336              lon_v = None 
-337              lat_v = None 
-338              lon_psi = None 
-339              lat_psi = None 
-340   
-341          if 'pm' in nc.variables.keys() and 'pn' in nc.variables.keys(): 
-342              pm = nc.variables['pm'][:] 
-343              dx = 1. / pm 
-344              pn = nc.variables['pn'][:] 
-345              dy = 1. / pn 
-346          else: 
-347              dx = None 
-348              dy = None 
-349   
-350          if 'dndx' in nc.variables.keys() and 'dmde' in nc.variables.keys(): 
-351              dndx = nc.variables['dndx'][:] 
-352              dmde = nc.variables['dmde'][:] 
-353          else: 
-354              dndx = None 
-355              dmde = None 
-356   
-357          if 'angle' in nc.variables.keys(): 
-358              angle = nc.variables['angle'][:] 
-359          else: 
-360              angle = None 
-361   
-362          #Get geographical grid    
-363          hgrd = CGrid_geo(lon_vert, lat_vert, proj, \ 
-364                           lon_rho=lon_rho, lat_rho=lat_rho, \ 
-365                           lon_u=lon_u, lat_u=lat_u, lon_v=lon_v, lat_v=lat_v, \ 
-366                           lon_psi=lon_psi, lat_psi=lat_psi, dx=dx, dy=dy, \ 
-367                           dndx=dndx, dmde=dmde, angle_rho=angle) 
-368   
-369      #load the mask 
-370      try:  
-371          hgrd.mask_rho = np.array(nc.variables['mask_rho'][:]) 
-372      except:  
-373          hgrd.mask_rho = np.ones(hgrd.mask_rho.shape) 
-374   
-375      return hgrd 
-
376   
-377   
-
378 -def get_ROMS_vgrid(gridid, zeta=None): 
-
379      """ 
-380      vgrid = get_ROMS_vgrid(gridid) 
-381   
-382      Load ROMS vertical grid object. vgrid is a s_coordinate or 
-383      a z_coordinate object, depending on gridid.grdtype. 
-384      vgrid.z_r and vgrid.z_w (vgrid.z for a z_coordinate object) 
-385      can be indexed in order to retreive the actual depths. The  
-386      free surface time serie zeta can be provided as an optional  
-387      argument. Note that the values of zeta are not calculated  
-388      until z is indexed, so a netCDF variable for zeta may be passed,  
-389      even if the file is large, as only the values that are required  
-390      will be retrieved from the file. 
-391      """ 
-392   
-393      gridinfo = ROMS_gridinfo(gridid) 
-394      grdfile = gridinfo.grdfile 
-395   
-396      nc = io.Dataset(grdfile) 
-397   
-398      #Get vertical grid 
-399      try: 
-400          h = nc.variables['h'][:] 
-401      except: 
-402          raise ValueError, 'NetCDF file must contain the bathymetry h' 
-403   
-404      if gridinfo.grdtype == 'roms': 
-405          Vtrans = gridinfo.Vtrans 
-406          theta_b = gridinfo.theta_b 
-407          theta_s = gridinfo.theta_s 
-408          Tcline = gridinfo.Tcline 
-409          N = gridinfo.N 
-410          if Vtrans == 1: 
-411              vgrid = s_coordinate(h, theta_b, theta_s, Tcline, N, zeta=zeta) 
-412          elif Vtrans == 2: 
-413              vgrid = s_coordinate_2(h, theta_b, theta_s, Tcline, N, zeta=zeta) 
-414          else: 
-415              raise Warning, 'Unknow vertical transformation Vtrans' 
-416   
-417      elif  gridinfo.grdtype == 'z': 
-418          N = gridinfo.N 
-419          depth = gridinfo.depth 
-420          vgrid = z_coordinate(h, depth, N) 
-421   
-422      else: 
-423          raise ValueError, 'Unknow grid type' 
-424   
-425      return vgrid 
-
426   
-427   
-
428 -def get_ROMS_grid(gridid, zeta=None, hist_file=None,grid_file=None): 
-
429      """ 
-430      grd = get_ROMS_grid(gridid,hist_file=None,grid_file=None) 
-431   
-432      Load ROMS grid object. 
-433   
-434      gridid is a string with the name of the grid in it.  If hist_file 
-435         and grid_file are not passed into the function, or are set to 
-436         None, then gridid is used to get the grid data from the 
-437         gridid.txt file. 
-438   
-439         if hist_file and grid_file are given, and they are the file 
-440         paths to a ROMS history file and grid file respectively, the 
-441         grid information will be extracted from those files, and gridid 
-442         will be used to name that grid for the rest of the python 
-443         session. 
-444    
-445      grd.vgrid is a s_coordinate or 
-446      a z_coordinate object, depending on gridid.grdtype. 
-447      grd.vgrid.z_r and grd.vgrid.z_w (grd.vgrid.z for a  
-448      z_coordinate object) can be indexed in order to retreive the  
-449      actual depths. The free surface time serie zeta can be provided  
-450      as an optional argument. Note that the values of zeta are not  
-451      calculated until z is indexed, so a netCDF variable for zeta may  
-452      be passed, even if the file is large, as only the values that  
-453      are required will be retrieved from the file. 
-454      """ 
-455   
-456      #in this first call to ROMS_gridinfo, we pass in the history file 
-457      #and gridfile info.  If hist_file and grid_file are defined, the 
-458      #grid info will be extracted from those files and will able to be 
-459      #accessed later by gridid 
-460      gridinfo = ROMS_gridinfo(gridid,hist_file=hist_file,grid_file=grid_file) 
-461      name = gridinfo.name 
-462   
-463      #we need not pass in hist_file and grid_file here, because the 
-464      #gridinfo file will already have been initialized by the call to 
-465      #ROMS_gridinfo above. 
-466      hgrd = get_ROMS_hgrid(gridid) 
-467      vgrid = get_ROMS_vgrid(gridid, zeta=zeta) 
-468   
-469      #Get ROMS grid 
-470      return ROMS_Grid(name, hgrd, vgrid) 
-
471   
-472   
-
473 -def write_ROMS_grid(grd, filename='ocean_grd.nc'): 
-
474      """ 
-475      write_ROMS_grid(grd, filename) 
-476   
-477      Write ROMS_CGrid class on a NetCDF file. 
-478      """ 
-479   
-480      if grd.hgrid.lon_rho is not None: 
-481          Mm, Lm = grd.hgrid.lon_rho.shape 
-482      else: 
-483          Mm, Lm = grd.hgrid.x_rho.shape 
-484   
-485       
-486      # Write ROMS grid to file 
-487      nc = netCDF.Dataset(filename, 'w', format='NETCDF3_CLASSIC') 
-488      nc.Description = 'ROMS grid' 
-489      nc.Author = 'pyroms.grid.write_grd' 
-490      nc.Created = datetime.now().isoformat() 
-491      nc.type = 'ROMS grid file' 
-492   
-493      nc.createDimension('xi_rho', Lm) 
-494      nc.createDimension('xi_u', Lm-1) 
-495      nc.createDimension('xi_v', Lm) 
-496      nc.createDimension('xi_psi', Lm-1) 
-497       
-498      nc.createDimension('eta_rho', Mm) 
-499      nc.createDimension('eta_u', Mm) 
-500      nc.createDimension('eta_v', Mm-1) 
-501      nc.createDimension('eta_psi', Mm-1) 
-502   
-503      if grd.hgrid.x_vert is not None: 
-504          nc.createDimension('xi_vert', Lm+1) 
-505          nc.createDimension('eta_vert', Mm+1) 
-506   
-507      if hasattr(grd.vgrid, 's_rho') is True and grd.vgrid.s_rho is not None: 
-508          N, = grd.vgrid.s_rho.shape 
-509          nc.createDimension('s_rho', N) 
-510          nc.createDimension('s_w', N+1) 
-511   
-512   
-513      def write_nc_var(var, name, dimensions, long_name=None, units=None): 
-514          nc.createVariable(name, 'f8', dimensions) 
-515          if long_name is not None: 
-516              nc.variables[name].long_name = long_name 
-517          if units is not None: 
-518              nc.variables[name].units = units 
-519          nc.variables[name][:] = var 
-520          print ' ... wrote ', name 
-
521   
-522      if hasattr(grd.vgrid, 's_rho') is True and grd.vgrid.s_rho is not None: 
-523          write_nc_var(grd.vgrid.theta_s, 'theta_s', (), 'S-coordinate surface control parameter') 
-524          write_nc_var(grd.vgrid.theta_b, 'theta_b', (), 'S-coordinate bottom control parameter') 
-525          write_nc_var(grd.vgrid.Tcline, 'Tcline', (), 'S-coordinate surface/bottom layer width', 'meter') 
-526          write_nc_var(grd.vgrid.hc, 'hc', (), 'S-coordinate parameter, critical depth', 'meter') 
-527          write_nc_var(grd.vgrid.s_rho, 's_rho', ('s_rho'), 'S-coordinate at RHO-points') 
-528          write_nc_var(grd.vgrid.s_w, 's_w', ('s_w'), 'S-coordinate at W-points') 
-529          write_nc_var(grd.vgrid.Cs_r, 'Cs_r', ('s_rho'), 'S-coordinate stretching curves at RHO-points') 
-530          write_nc_var(grd.vgrid.Cs_w, 'Cs_w', ('s_w'), 'S-coordinate stretching curves at W-points') 
-531   
-532      write_nc_var(grd.vgrid.h, 'h', ('eta_rho', 'xi_rho'), 'bathymetry at RHO-points', 'meter') 
-533      write_nc_var(grd.hgrid.f, 'f', ('eta_rho', 'xi_rho'), 'Coriolis parameter at RHO-points', 'second-1') 
-534      write_nc_var(1./grd.hgrid.dx, 'pm', ('eta_rho', 'xi_rho'), 'curvilinear coordinate metric in XI', 'meter-1') 
-535      write_nc_var(1./grd.hgrid.dy, 'pn', ('eta_rho', 'xi_rho'), 'curvilinear coordinate metric in ETA', 'meter-1') 
-536      write_nc_var(grd.hgrid.dmde, 'dmde', ('eta_rho', 'xi_rho'), 'XI derivative of inverse metric factor pn', 'meter') 
-537      write_nc_var(grd.hgrid.dndx, 'dndx', ('eta_rho', 'xi_rho'), 'ETA derivative of inverse metric factor pm', 'meter') 
-538      write_nc_var(grd.hgrid.xl, 'xl', (), 'domain length in the XI-direction', 'meter') 
-539      write_nc_var(grd.hgrid.el, 'el', (), 'domain length in the ETA-direction', 'meter') 
-540   
-541      if grd.hgrid.x_rho is not None: 
-542          write_nc_var(grd.hgrid.x_rho, 'x_rho', ('eta_rho', 'xi_rho'), 'x location of RHO-points', 'meter') 
-543          write_nc_var(grd.hgrid.x_rho, 'y_rho', ('eta_rho', 'xi_rho'), 'y location of RHO-points', 'meter') 
-544          write_nc_var(grd.hgrid.x_u, 'x_u', ('eta_u', 'xi_u'), 'x location of U-points', 'meter') 
-545          write_nc_var(grd.hgrid.x_u, 'y_u', ('eta_u', 'xi_u'), 'y location of U-points', 'meter') 
-546          write_nc_var(grd.hgrid.x_v, 'x_v', ('eta_v', 'xi_v'), 'x location of V-points', 'meter') 
-547          write_nc_var(grd.hgrid.x_v, 'y_v', ('eta_v', 'xi_v'), 'y location of V-points', 'meter') 
-548          write_nc_var(grd.hgrid.x_psi, 'x_psi', ('eta_psi', 'xi_psi'), 'x location of PSI-points', 'meter') 
-549          write_nc_var(grd.hgrid.x_psi, 'y_psi', ('eta_psi', 'xi_psi'), 'y location of PSI-points', 'meter') 
-550   
-551      if grd.hgrid.lon_rho is not None: 
-552          write_nc_var(grd.hgrid.lon_rho, 'lon_rho', ('eta_rho', 'xi_rho'), 'longitude of RHO-points', 'degree_east') 
-553          write_nc_var(grd.hgrid.lat_rho, 'lat_rho', ('eta_rho', 'xi_rho'), 'latitude of RHO-points', 'degree_north') 
-554          write_nc_var(grd.hgrid.lon_u, 'lon_u', ('eta_u', 'xi_u'), 'longitude of U-points', 'degree_east') 
-555          write_nc_var(grd.hgrid.lat_u, 'lat_u', ('eta_u', 'xi_u'), 'latitude of U-points', 'degree_north') 
-556          write_nc_var(grd.hgrid.lon_v, 'lon_v', ('eta_v', 'xi_v'), 'longitude of V-points', 'degree_east') 
-557          write_nc_var(grd.hgrid.lat_v, 'lat_v', ('eta_v', 'xi_v'), 'latitude of V-points', 'degree_north') 
-558          write_nc_var(grd.hgrid.lon_psi, 'lon_psi', ('eta_psi', 'xi_psi'), 'longitude of PSI-points', 'degree_east') 
-559          write_nc_var(grd.hgrid.lat_psi, 'lat_psi', ('eta_psi', 'xi_psi'), 'latitude of PSI-points', 'degree_north') 
-560   
-561      if grd.hgrid.x_vert is not None: 
-562          write_nc_var(grd.hgrid.x_vert, 'x_vert', ('eta_vert', 'xi_vert'), 'x location of cell verticies', 'meter') 
-563          write_nc_var(grd.hgrid.y_vert, 'y_vert', ('eta_vert', 'xi_vert'), 'y location of cell verticies', 'meter') 
-564   
-565      if grd.hgrid.lon_vert is not None: 
-566          write_nc_var(grd.hgrid.lon_vert, 'lon_vert', ('eta_vert', 'xi_vert'), 'longitude of cell verticies', 'degree_east') 
-567          write_nc_var(grd.hgrid.lat_vert, 'lat_vert', ('eta_vert', 'xi_vert'), 'latitude of cell verticies', 'degree_north') 
-568   
-569      nc.createVariable('spherical', 'c') 
-570      nc.variables['spherical'].long_name = 'Grid type logical switch' 
-571      nc.variables['spherical'][:] = grd.hgrid.spherical 
-572      print ' ... wrote ', 'spherical' 
-573   
-574      write_nc_var(grd.hgrid.angle_rho, 'angle', ('eta_rho', 'xi_rho'), 'angle between XI-axis and EAST', 'radians') 
-575   
-576      write_nc_var(grd.hgrid.mask_rho, 'mask_rho', ('eta_rho', 'xi_rho'), 'mask on RHO-points') 
-577      write_nc_var(grd.hgrid.mask_u, 'mask_u', ('eta_u', 'xi_u'), 'mask on U-points') 
-578      write_nc_var(grd.hgrid.mask_v, 'mask_v', ('eta_v', 'xi_v'), 'mask on V-points') 
-579      write_nc_var(grd.hgrid.mask_psi, 'mask_psi', ('eta_psi', 'xi_psi'), 'mask on psi-points') 
-580   
-581      nc.close() 
-582   
-
-
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- Generated by Epydoc 3.0.1 on Mon Sep 27 11:31:39 2010 - - http://epydoc.sourceforge.net -
- - - - diff --git a/pyroms/docs/pyroms.grid.ROMS_Grid-class.html b/pyroms/docs/pyroms.grid.ROMS_Grid-class.html deleted file mode 100644 index 8fa9b59..0000000 --- a/pyroms/docs/pyroms.grid.ROMS_Grid-class.html +++ /dev/null @@ -1,240 +0,0 @@ - - - - - pyroms.grid.ROMS_Grid - - - - - - - - - - - - - - - - - - - - - - -
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- - Package pyroms :: - Module grid :: - Class ROMS_Grid - - - - - - -
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-
- -

Class ROMS_Grid

source code

-
-object --+
-         |
-        ROMS_Grid
-
- -
-

grd = ROMS_Grid(hgrid, vgrid)

-

ROMS Grid object combining horizontal and vertical grid

- - - - - - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
-   - - - - - - -
__init__(self, - name, - hgrid=<class 'pyroms.hgrid.CGrid'>, - vgrid=<class 'pyroms.vgrid.s_coordinate'>)
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature		 - source code - -
- -
-

Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

-
- - - - - - - - - -
- - - - - -
Properties[hide private]
-
-

Inherited from object: - __class__ -

-
- - - - - - -
- - - - - -
Method Details[hide private]
-
- -
- -
- - -
-

__init__(self, - name, - hgrid=<class 'pyroms.hgrid.CGrid'>, - vgrid=<class 'pyroms.vgrid.s_coordinate'>) -
(Constructor) -

- 		source code  -
- -

x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

-
-
Overrides: - object.__init__ -
(inherited documentation)
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- - Package pyroms :: - Module grid :: - Class ROMS_gridinfo - - - - - - -
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-
- -

Class ROMS_gridinfo

source code

-
-object --+
-         |
-        ROMS_gridinfo
-
- -
-

gridinfo = ROMS_gridinfo(gridid,grid_file=None,hist_file=None)

-

Return an object with grid information for gridid.

-

There are two ways to define the grid information. If grid_file and - hist_file are not passed to the object when it is created, the - information is retrieved from gridid.txt. To add new grid please edit - your gridid.txt. You need to define an environment variable - PYROMS_GRIDID_FILE pointing to your gridid.txt file. Just copy an - existing grid and modify the definition accordingly to your case (Be - carefull with space and blank line).

-

If grid_file is the path to a ROMS grid file, and hist_file is the - path to a ROMS history file, then the grid information will be read from - those files. Gridid can then be used to refer to this grid information - so that the grid and history files do not be included in subsequent - calls.

- - - - - - - - - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
-   - - - - - - -
__init__(self, - gridid, - grid_file=None, - hist_file=None)
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature		 - source code - -
- -
-   - - - - - - -
_get_grid_info(self, - grid_file, - hist_file) - source code - -
- -
-

Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

-
- - - - - - - - - -
- - - - - -
Properties[hide private]
-
-

Inherited from object: - __class__ -

-
- - - - - - -
- - - - - -
Method Details[hide private]
-
- -
- -
- - -
-

__init__(self, - gridid, - grid_file=None, - hist_file=None) -
(Constructor) -

- 		source code  -
- -

x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

-
-
Overrides: - object.__init__ -
(inherited documentation)
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- Generated by Epydoc 3.0.1 on Mon Sep 27 11:31:39 2010 - - http://epydoc.sourceforge.net -
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- - Package pyroms :: - Module hgrid - - - - - - -
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Module hgrid

source code

-
-Tools for creating and working with Arikawa C-Grids
-
-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - -
Classes[hide private]
-
-   - - BoundaryInteractor
- Interactive grid creation -
-   - - _Focus_x
- Return a transformed, uniform grid, focused in the x-direction -
-   - - _Focus_y
- Return a transformed, uniform grid, focused in the y-direction -
-   - - Focus
- Return a container for a sequence of Focus objects -
-   - - CGrid
- Curvilinear Arakawa C-Grid -
-   - - CGrid_geo
- Curvilinear Arakawa C-grid defined in geographic coordinates -
-   - - Gridgen
- docstring for Gridgen -
-   - - edit_mask_mesh
- Interactive mask editor -
-   - - get_position_from_map
- Get cell index position Interactively -
- - - - - - - - - - - - - - - - - - -
- - - - - -
Functions[hide private]
-
-   - - - - - - -
_approximate_erf(x)
- Return approximate solution to error function...		 - source code - -
- -
-   - - - - - - -
rho_to_vert(xr, - yr, - pm, - pn, - ang) - source code - -
- -
-   - - - - - - -
rho_to_vert_geo(lonr, - latr, - lonp, - latp) - source code - -
- -
-   - - - - - - -
uvp_masks(rmask)
- return u-, v-, and psi-masks based on input rho-mask		 - source code - -
- -
- - - - - - -
- - - - - -
Function Details[hide private]
-
- -
- -
- - -
-

_approximate_erf(x) -

- 		source code  -
- - 
-
-Return approximate solution to error function
-see http://en.wikipedia.org/wiki/Error_function
-
-
-
-
-
-
- -
- -
- - -
-

uvp_masks(rmask) -

- 		source code  -
- - 
-
-return u-, v-, and psi-masks based on input rho-mask
-
-Parameters
-----------
-
-rmask : ndarray
-    mask at CGrid rho-points
-
-Returns
--------
-(umask, vmask, pmask) : ndarrays
-    masks at u-, v-, and psi-points
-
-
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Source Code for Module pyroms.hgrid

-
-   1  # encoding: utf-8 
-   2  '''Tools for creating and working with Arikawa C-Grids''' 
-   3  __docformat__ = "restructuredtext en" 
-   4   
-   5  import os 
-   6  import sys 
-   7  import ctypes 
-   8  import cPickle 
-   9  from warnings import warn 
-  10  from copy import deepcopy 
-  11   
-  12  import numpy as np 
-  13  import matplotlib.pyplot as plt 
-  14  from matplotlib.artist import Artist 
-  15  from matplotlib.patches import Polygon, CirclePolygon 
-  16  from matplotlib.lines import Line2D 
-  17  #from matplotlib.numerix.mlab import amin 
-  18  from matplotlib.mlab import dist_point_to_segment 
-  19  from matplotlib.nxutils import points_inside_poly 
-  20   
-  21  from mpl_toolkits.basemap import Basemap 
-  22  from mpl_toolkits.basemap import pyproj 
-  23   
-  24  try: 
-  25      import scipy.spatial.cKDTree as KDTree 
-  26  except: 
-  27      #  no scipy 
-  28      from pyroms.extern import KDTree 
-  29   
-  30  import pyroms 
-  31  from pyroms.vgrid import * 
-  32  from pyroms.extern import GreatCircle 
-  33   
-
  34 -class BoundaryInteractor(object): 
-
  35      """ 
-  36      Interactive grid creation 
-  37           
-  38      bry = BoundaryClick(x=[], y=[], beta=None, ax=gca(), **gridgen_options) 
-  39       
-  40      The initial boundary polygon points (x and y) are 
-  41      counterclockwise, starting in the upper left corner of the 
-  42      boundary.  
-  43       
-  44      Key commands: 
-  45           
-  46          t : toggle visibility of verticies 
-  47          d : delete a vertex 
-  48          i : insert a vertex at a point on the polygon line 
-  49           
-  50          p : set vertex as beta=1 (a Positive turn, marked with green triangle) 
-  51          m : set vertex as beta=1 (a Negative turn, marked with red triangle) 
-  52          z : set vertex as beta=0 (no corner, marked with a black dot) 
-  53           
-  54          G : generate grid from the current boundary using gridgen 
-  55          T : toggle visability of the current grid 
-  56       
-  57      Methods: 
-  58       
-  59          bry.dump(bry_file) 
-  60              Write the current boundary informtion (bry.x, bry.y, bry.beta) to 
-  61              a cPickle file bry_file. 
-  62           
-  63          bry.load(bry_file) 
-  64              Read in boundary informtion (x, y, beta) from the cPickle file 
-  65              bry_file. 
-  66           
-  67          bry.remove_grid()   
-  68              Remove gridlines from axes. 
-  69       
-  70      Attributes: 
-  71          bry.x : the X boundary points 
-  72          bry.y : the Y boundary points 
-  73          bry.verts : the verticies of the grid 
-  74          bry.grd : the CGrid object 
-  75           
-  76      """ 
-  77       
-  78      _showverts = True 
-  79      _showbetas = True 
-  80      _showgrid = True 
-  81      _epsilon = 5  # max pixel distance to count as a vertex hit 
-  82       
-
  83 -    def _update_beta_lines(self): 
-
  84          """Update m/pline by finding the points where self.beta== -/+ 1""" 
-  85          x, y = zip(*self._poly.xy) 
-  86          num_points = len(x)-1  # the first and last point are repeated 
-  87           
-  88          xp = [x[n] for n in range(num_points) if self.beta[n]==1] 
-  89          yp = [y[n] for n in range(num_points) if self.beta[n]==1] 
-  90          self._pline.set_data(xp, yp) 
-  91           
-  92          xm = [x[n] for n in range(num_points) if self.beta[n]==-1] 
-  93          ym = [y[n] for n in range(num_points) if self.beta[n]==-1] 
-  94          self._mline.set_data(xm, ym) 
-  95           
-  96          xz = [x[n] for n in range(num_points) if self.beta[n]==0] 
-  97          yz = [y[n] for n in range(num_points) if self.beta[n]==0] 
-  98          self._zline.set_data(xz, yz) 
-  99           
- 100          if len(x)-1 < self.gridgen_options['ul_idx']: 
- 101              self.gridgen_options['ul_idx'] = len(x)-1 
- 102          xs = x[self.gridgen_options['ul_idx']] 
- 103          ys = y[self.gridgen_options['ul_idx']] 
- 104          self._sline.set_data(xs, ys) 
-
 105       
-
 106 -    def remove_grid(self): 
-
 107          """Remove a generated grid from the BoundaryClick figure""" 
- 108          if hasattr(self, '_gridlines'): 
- 109              for line in self._gridlines: 
- 110                  self._ax.lines.remove(line) 
- 111              delattr(self, '_gridlines') 
-
 112       
-
 113 -    def _draw_callback(self, event): 
-
 114          self._background = self._canvas.copy_from_bbox(self._ax.bbox) 
- 115          self._ax.draw_artist(self._poly) 
- 116          self._ax.draw_artist(self._pline) 
- 117          self._ax.draw_artist(self._mline) 
- 118          self._ax.draw_artist(self._zline) 
- 119          self._ax.draw_artist(self._sline) 
- 120          self._ax.draw_artist(self._line) 
- 121          self._canvas.blit(self._ax.bbox) 
-
 122       
-
 123 -    def _poly_changed(self, poly): 
-
 124          'this method is called whenever the polygon object is called' 
- 125          # only copy the artist props to the line (except visibility) 
- 126          vis = self._line.get_visible() 
- 127          Artist.update_from(self._line, poly) 
- 128          self._line.set_visible(vis)  # don't use the poly visibility state 
-
 129       
-
 130 -    def _get_ind_under_point(self, event): 
-
 131          'get the index of the vertex under point if within epsilon tolerance' 
- 132          try: 
- 133              x, y = zip(*self._poly.xy) 
- 134               
- 135              # display coords 
- 136              xt, yt = self._poly.get_transform().numerix_x_y(x, y) 
- 137              d = np.sqrt((xt-event.x)**2 + (yt-event.y)**2) 
- 138              indseq = np.nonzero(np.equal(d, np.amin(d))) 
- 139              ind = indseq[0] 
- 140           
- 141              if d[ind]>=self._epsilon: 
- 142                  ind = None 
- 143           
- 144              return ind 
- 145          except: 
- 146              # display coords 
- 147              xy = np.asarray(self._poly.xy) 
- 148              xyt = self._poly.get_transform().transform(xy) 
- 149              xt, yt = xyt[:, 0], xyt[:, 1] 
- 150              d = np.sqrt((xt-event.x)**2 + (yt-event.y)**2) 
- 151              indseq = np.nonzero(np.equal(d, np.amin(d)))[0] 
- 152              ind = indseq[0] 
- 153               
- 154              if d[ind]>=self._epsilon: 
- 155                  ind = None 
- 156               
- 157              return ind 
-
 158       
-
 159 -    def _button_press_callback(self, event): 
-
 160          'whenever a mouse button is pressed' 
- 161          # if not self._showverts: return 
- 162          if event.inaxes==None: return 
- 163          if event.button != 1: return 
- 164          self._ind = self._get_ind_under_point(event) 
-
 165       
-
 166 -    def _button_release_callback(self, event): 
-
 167          'whenever a mouse button is released' 
- 168          # if not self._showverts: return 
- 169          if event.button != 1: return 
- 170          self._ind = None 
-
 171       
-
 172 -    def _key_press_callback(self, event): 
-
 173          'whenever a key is pressed' 
- 174          if not event.inaxes: return 
- 175          if event.key=='shift': return 
- 176           
- 177          if event.key=='t': 
- 178              self._showbetas = not self._showbetas 
- 179              self._line.set_visible(self._showbetas) 
- 180              self._pline.set_visible(self._showbetas) 
- 181              self._mline.set_visible(self._showbetas) 
- 182              self._zline.set_visible(self._showbetas) 
- 183              self._sline.set_visible(self._showbetas) 
- 184          elif event.key=='d': 
- 185              ind = self._get_ind_under_point(event) 
- 186              if ind is not None: 
- 187                  self._poly.xy = [tup for i,tup in enumerate(self._poly.xy) \ 
- 188                                   if i!=ind] 
- 189                  self._line.set_data(zip(*self._poly.xy)) 
- 190                  self.beta = [beta for i,beta in enumerate(self.beta) \ 
- 191                               if i!=ind] 
- 192          elif event.key=='p': 
- 193              ind = self._get_ind_under_point(event) 
- 194              if ind is not None: 
- 195                  self.beta[ind] = 1.0 
- 196          elif event.key=='m': 
- 197              ind = self._get_ind_under_point(event) 
- 198              if ind is not None: 
- 199                  self.beta[ind] = -1.0 
- 200          elif event.key=='z': 
- 201              ind = self._get_ind_under_point(event) 
- 202              if ind is not None: 
- 203                  self.beta[ind] = 0.0 
- 204          elif event.key=='s': 
- 205              ind = self._get_ind_under_point(event) 
- 206              if ind is not None: 
- 207                  self.gridgen_options['ul_idx'] = ind 
- 208          elif event.key=='i': 
- 209              xys = self._poly.get_transform().transform(self._poly.xy) 
- 210              p = event.x, event.y # display coords 
- 211              for i in range(len(xys)-1): 
- 212                  s0 = xys[i] 
- 213                  s1 = xys[i+1] 
- 214                  d = dist_point_to_segment(p, s0, s1) 
- 215                  if d<=self._epsilon: 
- 216                      self._poly.xy = np.array( 
- 217                          list(self._poly.xy[:i+1]) + 
- 218                          [(event.xdata, event.ydata)] + 
- 219                          list(self._poly.xy[i+1:])) 
- 220                      self._line.set_data(zip(*self._poly.xy)) 
- 221                      self.beta.insert(i+1, 0) 
- 222                      break 
- 223              s0 = xys[-1] 
- 224              s1 = xys[0] 
- 225              d = dist_point_to_segment(p, s0, s1) 
- 226              if d<=self._epsilon: 
- 227                  self._poly.xy = np.array( 
- 228                      list(self._poly.xy) + 
- 229                      [(event.xdata, event.ydata)]) 
- 230                  self._line.set_data(zip(*self._poly.xy)) 
- 231                  self.beta.append(0) 
- 232          elif event.key=='G' or event.key == '1': 
- 233              options = deepcopy(self.gridgen_options) 
- 234              shp = options.pop('shp') 
- 235              if self.proj is None: 
- 236                  x = self.x 
- 237                  y = self.y 
- 238                  self.grd = Gridgen(x, y, self.beta, shp, 
- 239                                     proj=self.proj, **options) 
- 240              else: 
- 241                  lon, lat = self.proj(self.x, self.y, inverse=True) 
- 242                  self.grd = Gridgen(lon, lat, self.beta, shp,  
- 243                                     proj=self.proj, **options) 
- 244              self.remove_grid() 
- 245              self._showgrid = True 
- 246              gridlineprops = {'linestyle':'-', 'color':'k', 'lw':0.2} 
- 247              self._gridlines = [] 
- 248              for line in self._ax._get_lines(*(self.grd.x, self.grd.y), 
- 249                                              **gridlineprops): 
- 250                  self._ax.add_line(line) 
- 251                  self._gridlines.append(line) 
- 252              for line in self._ax._get_lines(*(self.grd.x.T, self.grd.y.T), 
- 253                                              **gridlineprops): 
- 254                  self._ax.add_line(line) 
- 255                  self._gridlines.append(line) 
- 256          elif event.key=='T' or event.key == '2': 
- 257              self._showgrid = not self._showgrid 
- 258              if hasattr(self, '_gridlines'): 
- 259                  for line in self._gridlines: 
- 260                      line.set_visible(self._showgrid) 
- 261           
- 262          self._update_beta_lines() 
- 263          self._draw_callback(event) 
- 264          self._canvas.draw() 
-
 265       
-
 266 -    def _motion_notify_callback(self, event): 
-
 267          'on mouse movement' 
- 268          # if not self._showverts: return 
- 269          if self._ind is None: return 
- 270          if event.inaxes is None: return 
- 271          if event.button != 1: return 
- 272          x,y = event.xdata, event.ydata 
- 273          self._poly.xy[self._ind] = x, y 
- 274          if self._ind == 0: 
- 275              self._poly.xy[-1] = x, y 
- 276           
- 277          x, y = zip(*self._poly.xy) 
- 278          self._line.set_data(x[:-1], y[:-1]) 
- 279          self._update_beta_lines() 
- 280           
- 281          self._canvas.restore_region(self._background) 
- 282          self._ax.draw_artist(self._poly) 
- 283          self._ax.draw_artist(self._pline) 
- 284          self._ax.draw_artist(self._mline) 
- 285          self._ax.draw_artist(self._zline) 
- 286          self._ax.draw_artist(self._sline) 
- 287          self._ax.draw_artist(self._line) 
- 288          self._canvas.blit(self._ax.bbox) 
-
 289       
- 290       
-
 291 -    def __init__(self, x, y=None, beta=None, ax=None, proj=None,  
- 292                   **gridgen_options): 
-
 293           
- 294          if isinstance(x, str): 
- 295              bry_dict = np.load(x) 
- 296              x = bry_dict['x'] 
- 297              y = bry_dict['y'] 
- 298              beta = bry_dict['beta'] 
- 299           
- 300          assert len(x) >= 4, 'Boundary must have at least four points.' 
- 301           
- 302          if ax is None:  
- 303              ax = plt.gca() 
- 304           
- 305          self._ax = ax 
- 306           
- 307          self.proj = proj 
- 308           
- 309          # Set default gridgen option, and copy over specified options. 
- 310          self.gridgen_options = {'ul_idx': 0, 'shp': (32, 32)} 
- 311           
- 312          for key, value in gridgen_options.iteritems(): 
- 313              self.gridgen_options[key] = gridgen_options[key] 
- 314           
- 315          x = list(x); y = list(y) 
- 316          assert len(x)==len(y), 'arrays must be equal length' 
- 317           
- 318          if beta is None: 
- 319              self.beta = [0 for xi in x] 
- 320          else: 
- 321              assert len(x)==len(beta), 'beta must have same length as x and y' 
- 322              self.beta = list(beta) 
- 323           
- 324          self._line = Line2D(x, y, animated=True,  
- 325                              ls='-', color='k', alpha=0.5, lw=1) 
- 326          self._ax.add_line(self._line) 
- 327           
- 328          self._canvas = self._line.figure.canvas         
- 329           
- 330          self._poly = Polygon(self.verts, alpha=0.1, fc='k', animated=True) 
- 331          self._ax.add_patch(self._poly) 
- 332           
- 333          # Link in the lines that will show the beta values 
- 334          # pline for positive turns, mline for negative (minus) turns 
- 335          # otherwize zline (zero) for straight sections 
- 336          self._pline = Line2D([], [], marker='^', ms=12, mfc='g',\ 
- 337                               animated=True, lw=0) 
- 338          self._mline = Line2D([], [], marker='v', ms=12, mfc='r',\ 
- 339                               animated=True, lw=0) 
- 340          self._zline = Line2D([], [], marker='o', mfc='k', animated=True, lw=0) 
- 341          self._sline = Line2D([], [], marker='s', mfc='k', animated=True, lw=0) 
- 342           
- 343          self._update_beta_lines() 
- 344          self._ax.add_artist(self._pline) 
- 345          self._ax.add_artist(self._mline) 
- 346          self._ax.add_artist(self._zline) 
- 347          self._ax.add_artist(self._sline) 
- 348           
- 349          # get the canvas and connect the callback events 
- 350          cid = self._poly.add_callback(self._poly_changed) 
- 351          self._ind = None # the active vert 
- 352           
- 353          self._canvas.mpl_connect('draw_event', self._draw_callback) 
- 354          self._canvas.mpl_connect('button_press_event',\ 
- 355                                   self._button_press_callback) 
- 356          self._canvas.mpl_connect('key_press_event', self._key_press_callback) 
- 357          self._canvas.mpl_connect('button_release_event',\ 
- 358                                   self._button_release_callback) 
- 359          self._canvas.mpl_connect('motion_notify_event',\ 
- 360                                   self._motion_notify_callback) 
-
 361       
-
 362 -    def save_bry(self, bry_file='bry.pickle'): 
-
 363          f = open(bry_file, 'wb') 
- 364          bry_dict = {'x': self.x, 'y': self.y, 'beta': self.beta} 
- 365          cPickle.dump(bry_dict, f, protocol=-1) 
- 366          f.close() 
-
 367       
-
 368 -    def load_bry(self, bry_file='bry.pickle'): 
-
 369          bry_dict = np.load(bry_file) 
- 370          x = bry_dict['x'] 
- 371          y = bry_dict['y'] 
- 372          self._line.set_data(x, y) 
- 373          self.beta = bry_dict['beta'] 
- 374          if hasattr(self, '_poly'): 
- 375              self._poly.xy = zip(x, y) 
- 376              self._update_beta_lines() 
- 377              self._draw_callback(None) 
- 378              self._canvas.draw() 
-
 379       
-
 380 -    def save_grid(self, grid_file='grid.pickle'): 
-
 381          f = open(grid_file, 'wb') 
- 382          cPickle.dump(self.grd, f, protocol=-1) 
- 383          f.close() 
-
 384       
-
 385 -    def _get_verts(self): return zip(self.x, self.y) 
-
 386      verts = property(_get_verts)     
-
 387 -    def get_xdata(self): return self._line.get_xdata() 
-
 388      x = property(get_xdata) 
-
 389 -    def get_ydata(self): return self._line.get_ydata() 
-
 390      y = property(get_ydata) 
-
 391       
- 392   
- 393   
-
 394 -def _approximate_erf(x): 
-
 395      ''' 
- 396      Return approximate solution to error function 
- 397      see http://en.wikipedia.org/wiki/Error_function 
- 398      ''' 
- 399      a = -(8*(np.pi-3.0)/(3.0*np.pi*(np.pi-4.0))) 
- 400      return np.sign(x) * \ 
- 401             np.sqrt(1.0 - np.exp( -x**2*(4.0/np.pi+a*x*x)/(1.0+a*x*x) )) 
-
 402       
- 403   
-
 404 -class _Focus_x(object): 
-
 405      """ 
- 406      Return a transformed, uniform grid, focused in the x-direction 
- 407       
- 408      This class may be called with a uniform grid, with limits from [0, 1], to 
- 409      create a focused grid in the x-directions centered about xo. The output 
- 410      grid is also uniform from [0, 1] in both x and y. 
- 411       
- 412      Parameters 
- 413      ---------- 
- 414      xo : float 
- 415          Location about which to focus grid 
- 416      factor : float 
- 417          amount to focus grid. Creates cell sizes that are factor smaller in 
- 418          the focused 
- 419          region. 
- 420      Rx : float 
- 421          Lateral extent of focused region, similar to a lateral spatial scale 
- 422          for the focusing region. 
- 423       
- 424      Returns 
- 425      ------- 
- 426      foc : class 
- 427          The class may be called with arguments of a grid. The returned 
- 428          transformed grid (x, y) will be focused as per the parameters above. 
- 429      """ 
- 430       
-
 431 -    def __init__(self, xo, factor=2.0, Rx=0.1): 
-
 432          self.xo = xo 
- 433          self.factor = factor 
- 434          self.Rx = Rx 
-
 435       
-
 436 -    def __call__(self, x, y): 
-
 437          x = np.asarray(x) 
- 438          y = np.asarray(y) 
- 439          assert not np.any(x>1.0) or not np.any(x<0.0)  \ 
- 440              or not np.any(y>1.0) or not np.any(x<0.0), \ 
- 441                  'x and y must both be within the range [0, 1].' 
- 442           
- 443          alpha = 1.0 - 1.0/self.factor 
- 444          def xf(x): 
- 445              return x - 0.5*( np.sqrt(np.pi)*self.Rx*alpha 
- 446                              *_approximate_erf((x-self.xo)/self.Rx) ) 
-
 447           
- 448          xf0 = xf(0.0); xf1 = xf(1.0) 
- 449           
- 450          return (xf(x)-xf0)/(xf1-xf0), y 
-
 451   
-
 452 -class _Focus_y(object): 
-
 453      """ 
- 454      Return a transformed, uniform grid, focused in the y-direction 
- 455       
- 456      This class may be called with a uniform grid, with limits from [0, 1],  
- 457      to create a focused grid in the y-directions centered about yo.  
- 458      The output grid is also uniform from [0, 1] in both x and y. 
- 459       
- 460      Parameters 
- 461      ---------- 
- 462      yo : float 
- 463          Location about which to focus grid 
- 464      factor : float 
- 465          amount to focus grid. Creates cell sizes that are factor  
- 466          smaller in the focused region. 
- 467      Ry : float 
- 468          Lateral extent of focused region, similar to a lateral  
- 469          spatial scale for the focusing region. 
- 470       
- 471      Returns 
- 472      ------- 
- 473      foc : class 
- 474          The class may be called with arguments of a grid. The returned  
- 475          transformed grid (x, y) will be focused as per the parameters above. 
- 476      """ 
- 477       
-
 478 -    def __init__(self, yo, factor=2.0, Ry=0.1): 
-
 479          self.yo = yo 
- 480          self.factor = factor 
- 481          self.Ry = Ry 
-
 482       
-
 483 -    def __call__(self, x, y): 
-
 484          x = np.asarray(x) 
- 485          y = np.asarray(y) 
- 486          assert not np.any(x>1.0) or not np.any(x<0.0)  \ 
- 487              or not np.any(y>1.0) or not np.any(x<0.0), \ 
- 488                  'x and y must both be within the range [0, 1].' 
- 489           
- 490          alpha = 1.0 - 1.0/self.factor 
- 491           
- 492          def yf(y): 
- 493              return y - 0.5*( np.sqrt(np.pi)*self.Ry*alpha  
- 494                              *_approximate_erf((y-self.yo)/self.Ry) ) 
-
 495           
- 496          yf0 = yf(0.0); yf1 = yf(1.0) 
- 497           
- 498          return x, (yf(y)-yf0)/(yf1-yf0) 
-
 499   
-
 500 -class Focus(object): 
-
 501      """ 
- 502      Return a container for a sequence of Focus objects 
- 503       
- 504      foc = Focus() 
- 505       
- 506      The sequence is populated by using the 'add_focus_x' and 'add_focus_y' 
- 507      methods. These methods define a point ('xo' or 'yo'), around witch to 
- 508      focus, a focusing factor of 'focus', and x and y extent of focusing given 
- 509      by Rx or Ry. The region of focusing will be approximately Gausian, and the 
- 510      resolution will be increased by approximately the value of factor. 
- 511       
- 512      Methods 
- 513      ------- 
- 514      foc.add_focus_x(xo, factor=2.0, Rx=0.1) 
- 515      foc.add_focus_y(yo, factor=2.0, Ry=0.1) 
- 516       
- 517      Calls to the object return transformed coordinates: 
- 518          xf, yf = foc(x, y) 
- 519      where x and y must be within [0, 1], and are typically a uniform, 
- 520      normalized grid. The focused grid will be the result of applying each of 
- 521      the focus elements in the sequence they are added to the series. 
- 522       
- 523       
- 524      EXAMPLES 
- 525      -------- 
- 526       
- 527      >>> foc = pyroms.grid.Focus() 
- 528      >>> foc.add_focus_x(0.2, factor=3.0, Rx=0.2) 
- 529      >>> foc.add_focus_y(0.6, factor=5.0, Ry=0.35) 
- 530       
- 531      >>> x, y = np.mgrid[0:1:3j,0:1:3j] 
- 532      >>> xf, yf = foc(x, y) 
- 533       
- 534      >>> print xf 
- 535      [[ 0.          0.          0.        ] 
- 536       [ 0.36594617  0.36594617  0.36594617] 
- 537       [ 1.          1.          1.        ]] 
- 538      >>> print yf 
- 539      [[ 0.          0.62479833  1.        ] 
- 540       [ 0.          0.62479833  1.        ] 
- 541       [ 0.          0.62479833  1.        ]] 
- 542      """ 
-
 543 -    def __init__(self): 
-
 544          self._focuspoints = [] 
-
 545       
-
 546 -    def add_focus_x(self, xo, factor=2.0, Rx=0.1): 
-
 547          """docstring for add_point""" 
- 548          self._focuspoints.append(_Focus_x(xo, factor, Rx)) 
-
 549       
-
 550 -    def add_focus_y(self, yo, factor=2.0, Ry=0.1): 
-
 551          """docstring for add_point""" 
- 552          self._focuspoints.append(_Focus_y(yo, factor, Ry)) 
-
 553       
-
 554 -    def __call__(self, x, y): 
-
 555          """docstring for __call__""" 
- 556          for focuspoint in self._focuspoints: 
- 557              x, y = focuspoint(x, y) 
- 558          return x, y 
-
 559   
- 560   
- 561   
-
 562 -class CGrid(object): 
-
 563      """ 
- 564      Curvilinear Arakawa C-Grid 
- 565        
- 566      The basis for the CGrid class are two arrays defining the verticies of the 
- 567      grid in Cartesian (for geographic coordinates, see CGrid_geo). An optional 
- 568      mask may be defined on the cell centers. Other Arakawa C-grid properties, 
- 569      such as the locations of the cell centers (rho-points), cell edges (u and 
- 570      v velocity points), cell widths (dx and dy) and other metrics (angle, 
- 571      dmde, and dndx) are all calculated internally from the vertex points. 
- 572        
- 573      Input vertex arrays may be either type np.array or np.ma.MaskedArray. If 
- 574      masked arrays are used, the mask will be a combination of the specified 
- 575      mask (if given) and the masked locations. 
- 576        
- 577      EXAMPLES: 
- 578      -------- 
- 579        
- 580      >>> x, y = mgrid[0.0:7.0, 0.0:8.0] 
- 581      >>> x = np.ma.masked_where( (x<3) & (y<3), x) 
- 582      >>> y = np.ma.MaskedArray(y, x.mask) 
- 583      >>> grd = pyroms.grid.CGrid(x, y) 
- 584      >>> print grd.x_rho 
- 585      [[-- -- -- 0.5 0.5 0.5 0.5] 
- 586       [-- -- -- 1.5 1.5 1.5 1.5] 
- 587       [-- -- -- 2.5 2.5 2.5 2.5] 
- 588       [3.5 3.5 3.5 3.5 3.5 3.5 3.5] 
- 589       [4.5 4.5 4.5 4.5 4.5 4.5 4.5] 
- 590       [5.5 5.5 5.5 5.5 5.5 5.5 5.5]] 
- 591      >>> print grd.mask 
- 592      [[ 0.  0.  0.  1.  1.  1.  1.] 
- 593       [ 0.  0.  0.  1.  1.  1.  1.] 
- 594       [ 0.  0.  0.  1.  1.  1.  1.] 
- 595       [ 1.  1.  1.  1.  1.  1.  1.] 
- 596       [ 1.  1.  1.  1.  1.  1.  1.] 
- 597       [ 1.  1.  1.  1.  1.  1.  1.]] 
- 598      """ 
- 599       
-
 600 -    def __init__(self, x_vert, y_vert, x_rho=None, y_rho=None, x_u=None, y_u=None, x_v=None, y_v=None, \ 
- 601                      x_psi=None, y_psi=None, dx=None, dy=None, dndx=None, dmde=None, angle_rho=None): 
-
 602                   
- 603          assert np.ndim(x_vert)==2 and np.ndim(y_vert)==2 and np.shape(x_vert)==np.shape(y_vert), \ 
- 604              'x and y must be 2D arrays of the same size.' 
- 605           
- 606          if np.any(np.isnan(x_vert)) or np.any(np.isnan(y_vert)): 
- 607              x_vert = np.ma.masked_where( (isnan(x_vert)) | (isnan(y_vert)) , x_vert) 
- 608              y_vert = np.ma.masked_where( (isnan(x_vert)) | (isnan(y_vert)) , y_vert) 
- 609               
- 610          self.x_vert = x_vert 
- 611          self.y_vert = y_vert 
- 612   
- 613          self.f = None 
- 614          self.spherical = 'F' 
- 615           
- 616          mask_shape = tuple([n-1 for n in self.x_vert.shape]) 
- 617          self.mask_rho = np.ones(mask_shape, dtype='d') 
- 618           
- 619          # If maskedarray is given for verticies, modify the mask such that  
- 620          # non-existant grid points are masked.  A cell requires all four 
- 621          # verticies to be defined as a water point. 
- 622          if isinstance(self.x_vert, np.ma.MaskedArray): 
- 623              mask = (self.x_vert.mask[:-1,:-1] | self.x_vert.mask[1:,:-1] | \ 
- 624                      self.x_vert.mask[:-1,1:] | self.x_vert.mask[1:,1:]) 
- 625              self.mask_rho = np.asarray(~(~np.bool_(self.mask_rho) | mask), dtype='d') 
- 626           
- 627          if isinstance(self.y_vert, np.ma.MaskedArray): 
- 628              mask = (self.y_vert.mask[:-1,:-1] | self.y_vert.mask[1:,:-1] | \ 
- 629                      self.y_vert.mask[:-1,1:] | self.y_vert.mask[1:,1:]) 
- 630              self.mask_rho = np.asarray(~(~np.bool_(self.mask_rho) | mask), dtype='d') 
- 631   
- 632          if x_rho is None or y_rho is None or x_u is None or y_u is None or \ 
- 633              x_v is None or y_v is None or x_psi is None or y_psi is None: 
- 634              self._calculate_subgrids() 
- 635          else: 
- 636              self.x_rho = x_rho 
- 637              self.y_rho = y_rho 
- 638              self.x_u = x_u 
- 639              self.y_u = y_u 
- 640              self.x_v = x_v 
- 641              self.y_v = y_v 
- 642              self.x_psi = x_psi 
- 643              self.y_psi = y_psi 
- 644   
- 645          if dx is None or dy is None: 
- 646              self._calculate_metrics() 
- 647          else: 
- 648              self.dx = dx 
- 649              self.dy = dy 
- 650   
- 651          self.xl = np.maximum(self.dx[0,:].sum(), self.dx[-1,:].sum()) 
- 652          self.el = np.maximum(self.dy[:,0].sum(), self.dy[:,-1].sum()) 
- 653   
- 654          if dndx is None or dmde is None: 
- 655              self._calculate_derivative_metrics() 
- 656          else: 
- 657              self.dndx = dndx 
- 658              self.dmde = dmde 
- 659   
- 660          if angle_rho is None: 
- 661              self._calculate_angle_rho() 
- 662          else: 
- 663              self.angle_rho = angle_rho 
- 664   
- 665          self._calculate_angle() 
-
 666      
- 667       
-
 668 -    def _calculate_subgrids(self): 
-
 669          self.x_rho = 0.25*(self.x_vert[1:,1:]+self.x_vert[1:,:-1]+ \ 
- 670                             self.x_vert[:-1,1:]+self.x_vert[:-1,:-1]) 
- 671          self.y_rho = 0.25*(self.y_vert[1:,1:]+self.y_vert[1:,:-1]+ \ 
- 672                             self.y_vert[:-1,1:]+self.y_vert[:-1,:-1]) 
- 673          self.x_u = 0.5*(self.x_vert[:-1,1:-1] + self.x_vert[1:,1:-1]) 
- 674          self.y_u = 0.5*(self.y_vert[:-1,1:-1] + self.y_vert[1:,1:-1]) 
- 675          self.x_v = 0.5*(self.x_vert[1:-1,:-1] + self.x_vert[1:-1,1:]) 
- 676          self.y_v = 0.5*(self.y_vert[1:-1,:-1] + self.y_vert[1:-1,1:]) 
- 677          self.x_psi = self.x_vert[1:-1,1:-1] 
- 678          self.y_psi = self.y_vert[1:-1,1:-1] 
-
 679       
-
 680 -    def _calculate_metrics(self): 
-
 681          'Calculates pm, pn, dndx, dmde from x_vert and y_vert' 
- 682          x_temp = 0.5*(self.x_vert[1:,:]+self.x_vert[:-1,:]) 
- 683          y_temp = 0.5*(self.y_vert[1:,:]+self.y_vert[:-1,:]) 
- 684          self.dx = np.sqrt(np.diff(x_temp, axis=1)**2 + np.diff(y_temp, axis=1)**2) 
- 685          x_temp = 0.5*(self.x_vert[:,1:]+self.x_vert[:,:-1]) 
- 686          y_temp = 0.5*(self.y_vert[:,1:]+self.y_vert[:,:-1]) 
- 687          self.dy = np.sqrt(np.diff(x_temp, axis=0)**2 + np.diff(y_temp, axis=0)**2) 
-
 688   
- 690          if isinstance(self.dy, np.ma.MaskedArray): 
- 691              self.dndx = np.ma.zeros(self.x_rho.shape, dtype='d') 
- 692          else: 
- 693              self.dndx = np.zeros(self.x_rho.shape, dtype='d') 
- 694           
- 695          if isinstance(self.dx, np.ma.MaskedArray): 
- 696              self.dmde = np.ma.zeros(self.x_rho.shape, dtype='d') 
- 697          else: 
- 698              self.dmde = np.zeros(self.x_rho.shape, dtype='d') 
- 699           
- 700          self.dndx[1:-1,1:-1] = 0.5*(self.dy[1:-1,2:] - self.dy[1:-1,:-2]) 
- 701          self.dmde[1:-1,1:-1] = 0.5*(self.dx[2:,1:-1] - self.dx[:-2,1:-1]) 
-
 702   
-
 703 -    def _calculate_angle(self):      
-
 704          if isinstance(self.x_vert, np.ma.MaskedArray) or \ 
- 705             isinstance(self.y_vert, np.ma.MaskedArray): 
- 706              self.angle = np.ma.zeros(self.x_vert.shape, dtype='d') 
- 707          else: 
- 708              self.angle = np.zeros(self.x_vert.shape, dtype='d') 
- 709           
- 710          angle_ud = np.arctan2(np.diff(self.y_vert, axis=1), np.diff(self.x_vert, axis=1)) 
- 711          angle_lr = np.arctan2(np.diff(self.y_vert, axis=0), np.diff(self.x_vert, axis=0)) - np.pi/2.0         
- 712          # domain center 
- 713          self.angle[1:-1,1:-1] = 0.25*(angle_ud[1:-1,1:]+angle_ud[1:-1,:-1]\ 
- 714                                       +angle_lr[1:,1:-1]+angle_lr[:-1,1:-1]) 
- 715          # edges 
- 716          self.angle[0,1:-1] = (1.0/3.0)*(angle_lr[0,1:-1]+angle_ud[0,1:]+angle_ud[0,:-1]) 
- 717          self.angle[-1,1:-1] = (1.0/3.0)*(angle_lr[-1,1:-1]+angle_ud[-1,1:]+angle_ud[-1,:-1]) 
- 718          self.angle[1:-1,0] = (1.0/3.0)*(angle_ud[1:-1,0]+angle_lr[1:,0]+angle_lr[:-1,0]) 
- 719          self.angle[1:-1,-1] = (1.0/3.0)*(angle_ud[1:-1,-1]+angle_lr[1:,-1]+angle_lr[:-1,-1]) 
- 720          #conrers 
- 721          self.angle[0,0] = 0.5*(angle_lr[0,0]+angle_ud[0,0]) 
- 722          self.angle[0,-1] = 0.5*(angle_lr[0,-1]+angle_ud[0,-1]) 
- 723          self.angle[-1,0] = 0.5*(angle_lr[-1,0]+angle_ud[-1,0]) 
- 724          self.angle[-1,-1] = 0.5*(angle_lr[-1,-1]+angle_ud[-1,-1]) 
- 725           
-
 726 -    def _calculate_angle_rho(self):  
-
 727          self.angle_rho = np.arctan2(np.diff(0.5*(self.y_vert[1:,:]+self.y_vert[:-1,:])), \ 
- 728                                      np.diff(0.5*(self.x_vert[1:,:]+self.x_vert[:-1,:])))         
- 729       
-
 730 -    def calculate_orthogonality(self): 
-
 731          ''' 
- 732          Calculate orthogonality error in radians 
- 733          ''' 
- 734          z = self.x_vert + 1j*self.y_vert 
- 735          du = np.diff(z, axis=1); du = (du/abs(du))[:-1,:] 
- 736          dv = np.diff(z, axis=0); dv = (dv/abs(dv))[:,:-1] 
- 737          ang1 = np.arccos(du.real*dv.real + du.imag*dv.imag) 
- 738          du = np.diff(z, axis=1); du = (du/abs(du))[1:,:] 
- 739          dv = np.diff(z, axis=0); dv = (dv/abs(dv))[:,:-1] 
- 740          ang2 = np.arccos(du.real*dv.real + du.imag*dv.imag) 
- 741          du = np.diff(z, axis=1); du = (du/abs(du))[:-1,:] 
- 742          dv = np.diff(z, axis=0); dv = (dv/abs(dv))[:,1:] 
- 743          ang3 = np.arccos(du.real*dv.real + du.imag*dv.imag) 
- 744          du = np.diff(z, axis=1); du = (du/abs(du))[1:,:] 
- 745          dv = np.diff(z, axis=0); dv = (dv/abs(dv))[:,1:] 
- 746          ang4 = np.arccos(du.real*dv.real + du.imag*dv.imag) 
- 747          ang = np.mean([abs(ang1), abs(ang2), abs(ang3), abs(ang4)], axis=0) 
- 748          ang = (ang-np.pi/2.0) 
- 749          return ang 
-
 750       
-
 751 -    def mask_polygon(self, polyverts, mask_value=0.0): 
-
 752          """ 
- 753          Mask Cartesian points contained within the polygon defined by polyverts 
- 754           
- 755          A cell is masked if the cell center (x_rho, y_rho) is within the 
- 756          polygon. Other sub-masks (mask_u, mask_v, and mask_psi) are updated 
- 757          automatically. 
- 758           
- 759          mask_value [=0.0] may be specified to alter the value of the mask set 
- 760          within the polygon.  E.g., mask_value=1 for water points. 
- 761          """ 
- 762           
- 763          polyverts = np.asarray(polyverts) 
- 764          assert polyverts.ndim == 2, \ 
- 765              'polyverts must be a 2D array, or a similar sequence' 
- 766          assert polyverts.shape[1] == 2, \ 
- 767              'polyverts must be two columns of points' 
- 768          assert polyverts.shape[0] > 2, \ 
- 769              'polyverts must contain at least 3 points' 
- 770           
- 771          mask = self.mask_rho 
- 772          inside = points_inside_poly( 
- 773              np.vstack( (self.x_rho.flatten(), self.y_rho.flatten()) ).T, 
- 774              polyverts) 
- 775          if np.any(inside): 
- 776              self.mask_rho.flat[inside] = mask_value 
-
 777       
-
 778 -    def _get_mask_u(self): 
-
 779          return self.mask_rho[:,1:]*self.mask_rho[:,:-1] 
-
 780       
-
 781 -    def _get_mask_v(self): 
-
 782          return self.mask_rho[1:,:]*self.mask_rho[:-1,:] 
-
 783       
-
 784 -    def _get_mask_psi(self): 
-
 785          return self.mask_rho[1:,1:]*self.mask_rho[:-1,1:]* \ 
- 786                 self.mask_rho[1:,:-1]*self.mask_rho[:-1,:-1] 
-
 787   
-
 788 -    def _set_mask_rho(self, mask_rho): 
-
 789          self.mask_rho = mask_rho 
-
 790    
- 791      x = property(lambda self: self.x_vert, None, None, 'Return x_vert') 
- 792      y = property(lambda self: self.y_vert, None, None, 'Return x_vert') 
- 793      mask = property(lambda self: self.mask_rho, _set_mask_rho, None, 'Return mask_rho') 
- 794      mask_u   = property(_get_mask_u, None, None, 'Return mask_u') 
- 795      mask_v   = property(_get_mask_v, None, None, 'Return mask_v') 
- 796      mask_psi = property(_get_mask_psi, None, None, 'Return mask_psi') 
- 797   
- 798   
-
 799 -class CGrid_geo(CGrid): 
-
 800      """ 
- 801      Curvilinear Arakawa C-grid defined in geographic coordinates 
- 802       
- 803      For a geographic grid, a projection may be specified, or The default 
- 804      projection for will be defined by the matplotlib.toolkits.Basemap 
- 805      projection: 
- 806       
- 807      proj = Basemap(projection='merc', resolution=None, lat_ts=0.0) 
- 808       
- 809      For a geographic grid, the cell widths are determined by the great 
- 810      circle distances. Angles, however, are defined using the projected 
- 811      coordinates, so a projection that conserves angles must be used. This 
- 812      means typically either Mercator (projection='merc') or Lambert 
- 813      Conformal Conic (projection='lcc'). 
- 814      """ 
-
 815 -    def _calculate_metrics(self): 
-
 816          # calculate metrics based on x and y grid 
- 817          super(CGrid_geo, self)._calculate_metrics() 
- 818   
- 819          # optionally calculate dx and dy based on great circle distances 
- 820          # for more accurate cell sizes. 
- 821          if self.use_gcdist: 
- 822              geod = pyproj.Geod(ellps=self.ellipse) 
- 823              az_forward, az_back, dx = geod.inv(self.lon[:,1:],  self.lat[:,1:], \ 
- 824                                                 self.lon[:,:-1], self.lat[:,:-1]) 
- 825              self.dx = 0.5*(dx[1:,:]+dx[:-1,:]) 
- 826              self.pm = 1.0/self.dx 
- 827              az_forward, az_back, dy = geod.inv(self.lon[1:,:],  self.lat[1:,:], \ 
- 828                                                 self.lon[:-1,:], self.lat[:-1,:]) 
- 829              self.dy = 0.5*(dy[:,1:]+dy[:,:-1]) 
- 830              self.pn = 1.0/self.dy 
-
 831   
- 832   
-
 834          if isinstance(self.dy, np.ma.MaskedArray): 
- 835              self.dndx = np.ma.zeros(self.dy.shape, dtype='d') 
- 836          else: 
- 837              self.dndx = np.zeros(self.dy.shape, dtype='d') 
- 838           
- 839          if isinstance(self.dx, np.ma.MaskedArray): 
- 840              self.dmde = np.ma.zeros(self.dx.shape, dtype='d') 
- 841          else: 
- 842              self.dmde = np.zeros(self.dx.shape, dtype='d') 
- 843           
- 844          self.dndx[1:-1,1:-1] = 0.5*(self.dy[1:-1,2:] - self.dy[1:-1,:-2]) 
- 845          self.dmde[1:-1,1:-1] = 0.5*(self.dx[2:,1:-1] - self.dx[:-2,1:-1]) 
-
 846           
-
 847 -    def _calculate_angle_rho(self): 
-
 848          if isinstance(self.lon, np.ma.MaskedArray) or \ 
- 849             isinstance(self.lat, np.ma.MaskedArray): 
- 850              self.angle_rho = np.ma.zeros(self.lon.shape, dtype='d') 
- 851          else: 
- 852              self.angle_rho = np.zeros(self.lon.shape, dtype='d') 
- 853   
- 854          # calculate metrics based on x and y grid 
- 855          super(CGrid_geo, self)._calculate_angle_rho() 
- 856   
- 857          # optionally calculate dx and dy based on great circle distances 
- 858          # for more accurate cell sizes. 
- 859          if self.use_gcdist: 
- 860              geod = pyproj.Geod(ellps=self.ellipse) 
- 861              az_forward, az_back, dx = geod.inv(self.lon[:,:-1], self.lat[:,:-1], \ 
- 862                                                 self.lon[:,1:], self.lat[:,1:]) 
- 863   
- 864              angle = 0.5 * (az_forward[1:,:] + az_forward[:-1,:]) 
- 865              self.angle_rho = (90 - angle) * np.pi/180. 
-
 866   
- 867   
-
 868 -    def __init__(self, lon_vert, lat_vert, proj, use_gcdist=True, ellipse='WGS84', \ 
- 869                      lon_rho=None, lat_rho=None, lon_u=None, lat_u=None, \ 
- 870                      lon_v=None, lat_v=None, lon_psi=None, lat_psi=None, dx=None, dy=None, \ 
- 871                      dndx=None, dmde=None, angle_rho=None): 
-
 872   
- 873          x, y = proj(lon_vert, lat_vert) 
- 874          self.lon_vert = lon_vert 
- 875          self.lat_vert = lat_vert 
- 876          self.proj = proj 
- 877   
- 878          self.use_gcdist = use_gcdist 
- 879          self.ellipse = ellipse 
- 880   
- 881          if lon_rho is None or lat_rho is None or lon_u is None or lat_u is None or \ 
- 882               lon_v is None or lat_v is None or lon_psi is None or lat_psi is None: 
- 883   
- 884              super(CGrid_geo, self).__init__(x, y) 
- 885   
- 886              self.lon_rho, self.lat_rho = self.proj(self.x_rho, self.y_rho, 
- 887                                                     inverse=True) 
- 888              self.lon_u, self.lat_u = self.proj(self.x_u, self.y_u, inverse=True) 
- 889              self.lon_v, self.lat_v = self.proj(self.x_v, self.y_v, inverse=True) 
- 890              self.lon_psi, self.lat_psi = self.proj(self.x_psi, self.y_psi, 
- 891                                                     inverse=True) 
- 892          else: 
- 893              self.lon_rho = lon_rho 
- 894              self.lat_rho = lat_rho 
- 895              self.lon_u = lon_u 
- 896              self.lat_u = lat_u 
- 897              self.lon_v = lon_v 
- 898              self.lat_v = lat_v 
- 899              self.lon_psi = lon_psi 
- 900              self.lat_psi = lat_psi 
- 901              #calculate cartesian position 
- 902              self.x_vert, self.y_vert = proj(lon_vert, lat_vert) 
- 903              self.x_rho, self.y_rho = proj(lon_rho, lat_rho) 
- 904              self.x_u, self.y_u = proj(lon_u, lat_u) 
- 905              self.x_v, self.y_v = proj(lon_v, lat_v) 
- 906              self.x_psi, self.y_psi = proj(lon_psi, lat_psi) 
- 907   
- 908          if dx is None or dy is None: 
- 909              self._calculate_metrics() 
- 910          else: 
- 911              self.dx = dx 
- 912              self.dy = dy 
- 913   
- 914          self.xl = np.maximum(self.dx[0,:].sum(), self.dx[-1,:].sum()) 
- 915          self.el = np.maximum(self.dy[:,0].sum(), self.dy[:,-1].sum()) 
- 916   
- 917          if dndx is None or dmde is None: 
- 918              self._calculate_derivative_metrics() 
- 919          else: 
- 920              self.dndx = dndx 
- 921              self.dmde = dmde 
- 922   
- 923          if angle_rho is None: 
- 924              self._calculate_angle_rho() 
- 925          else: 
- 926              self.angle_rho = angle_rho 
- 927   
- 928          self.f = 2.0 * 7.29e-5 * np.sin(self.lat_rho * np.pi / 180.0) 
- 929          self.spherical = 'T' 
-
 930   
- 931   
-
 932 -    def mask_polygon_geo(lonlat_verts, mask_value=0.0): 
-
 933          lon, lat = zip(*lonlat_verts) 
- 934          x, y = proj(lon, lat, inverse=True) 
- 935          self.mask_polygon(zip(x, y), mask_value) 
-
 936       
- 937      lon = property(lambda self: self.lon_vert, None, None, 'Shorthand for lon_vert') 
- 938      lat = property(lambda self: self.lat_vert, None, None, 'Shorthand for lat_vert') 
-
 939           
- 940   
- 941   
-
 942 -class Gridgen(CGrid): 
-
 943      """ 
- 944      docstring for Gridgen 
- 945      """ 
- 946   
- 947       
-
 948 -    def generate_grid(self): 
-
 949           
- 950          if self._gn is not None: 
- 951              self._libgridgen.gridnodes_destroy(self._gn) 
- 952           
- 953          nbry = len(self.xbry) 
- 954           
- 955          nsigmas = ctypes.c_int(0) 
- 956          sigmas = ctypes.c_void_p(0) 
- 957          nrect = ctypes.c_int(0) 
- 958          xrect =  ctypes.c_void_p(0) 
- 959          yrect = ctypes.c_void_p(0) 
- 960           
- 961          if self.focus is None: 
- 962              ngrid = ctypes.c_int(0) 
- 963              xgrid = ctypes.POINTER(ctypes.c_double)() 
- 964              ygrid = ctypes.POINTER(ctypes.c_double)() 
- 965          else: 
- 966              y, x =  np.mgrid[0:1:self.ny*1j, 0:1:self.nx*1j] 
- 967              xgrid, ygrid = self.focus(x, y) 
- 968              ngrid = ctypes.c_int(xgrid.size) 
- 969              xgrid = (ctypes.c_double * xgrid.size)(*xgrid.flatten()) 
- 970              ygrid = (ctypes.c_double * ygrid.size)(*ygrid.flatten()) 
- 971           
- 972          self._gn = self._libgridgen.gridgen_generategrid2( 
- 973               ctypes.c_int(nbry),  
- 974               (ctypes.c_double * nbry)(*self.xbry),  
- 975               (ctypes.c_double * nbry)(*self.ybry),  
- 976               (ctypes.c_double * nbry)(*self.beta), 
- 977               ctypes.c_int(self.ul_idx),  
- 978               ctypes.c_int(self.nx),  
- 979               ctypes.c_int(self.ny),  
- 980               ngrid,  
- 981               xgrid,  
- 982               ygrid, 
- 983               ctypes.c_int(self.nnodes),  
- 984               ctypes.c_int(self.newton),  
- 985               ctypes.c_double(self.precision), 
- 986               ctypes.c_int(self.checksimplepoly),  
- 987               ctypes.c_int(self.thin),  
- 988               ctypes.c_int(self.nppe), 
- 989               ctypes.c_int(self.verbose), 
- 990               ctypes.byref(nsigmas),  
- 991               ctypes.byref(sigmas),  
- 992               ctypes.byref(nrect), 
- 993               ctypes.byref(xrect),  
- 994               ctypes.byref(yrect) ) 
- 995           
- 996          x = self._libgridgen.gridnodes_getx(self._gn) 
- 997          x = np.asarray([x[0][i] for i in range(self.ny*self.nx)]) 
- 998          # x = np.asarray([x[j][i] for j in range(self.ny) for i in range(self.nx)]) 
- 999          x.shape = (self.ny, self.nx) 
-1000           
-1001          y = self._libgridgen.gridnodes_gety(self._gn)     
-1002          y = np.asarray([y[0][i] for i in range(self.ny*self.nx)])             
-1003          # y = np.asarray([y[j][i] for j in range(self.ny) for i in range(self.nx)]) 
-1004          y.shape = (self.ny, self.nx) 
-1005           
-1006          if np.any(np.isnan(x)) or np.any(np.isnan(y)): 
-1007              x = np.ma.masked_where(np.isnan(x), x) 
-1008              y = np.ma.masked_where(np.isnan(y), y) 
-1009           
-1010          # if self.proj is not None: 
-1011          #     lon, lat = self.proj(x, y, inverse=True) 
-1012          #     super(Gridgen, self).__init__(lon, lat, proj=self.proj) 
-1013          # else: 
-1014          super(Gridgen, self).__init__(x, y) 
-
1015   
-1016   
-1017   
-
1018 -    def __init__(self, xbry, ybry, beta, shape, ul_idx=0, \ 
-1019                   focus=None, proj=None, \ 
-1020                   nnodes=14, precision=1.0e-12, nppe=3, \ 
-1021                   newton=True, thin=True, checksimplepoly=True, verbose=False): 
-
1022   
-1023          #self._libgridgen = np.ctypeslib.load_library('libgridgen',__file__) 
-1024          self._libgridgen = np.ctypeslib.load_library('libgridgen', pyroms.__path__[0]) 
-1025   
-1026          # In MacOSX, use of c_void_p does not return proper structure. 
-1027          # (An integer address is returned and subsequent use results in a  
-1028          #   Segmentation Fault) 
-1029          # All structures have to be declared.   
-1030   
-1031          # NODETYPE is enum(erated) 
-1032          (NT_NONE, NT_DD, NT_CEN, NT_COR) = (0, 1, 2, 3) 
-1033           
-1034          class GRIDSTATS(ctypes.Structure): 
-1035            _fields_ = [ 
-1036              ("mdo", ctypes.c_double), 
-1037              ("imdo", ctypes.c_int), 
-1038              ("jmdo", ctypes.c_int), 
-1039              ("ado", ctypes.c_double), 
-1040              ("mar", ctypes.c_double), 
-1041              ("aar", ctypes.c_double) 
-1042            ] 
-
1043           
-1044          class GRIDNODES(ctypes.Structure): 
-1045            _fields_ = [ 
-1046              ("nx", ctypes.c_int), 
-1047              ("ny", ctypes.c_int), 
-1048              ("gx", ctypes.POINTER(ctypes.POINTER(ctypes.c_double))), 
-1049              ("gy", ctypes.POINTER(ctypes.POINTER(ctypes.c_double))), 
-1050              ("type", ctypes.c_int), 
-1051              ("validated", ctypes.c_int), 
-1052              ("stats", ctypes.POINTER(GRIDSTATS)), 
-1053              ("nextpoint", ctypes.c_int) 
-1054            ] 
-
1055           
-1056          class EXTENT(ctypes.Structure): 
-1057            _fields_ = [ 
-1058              ("xmin", ctypes.c_double), 
-1059              ("xmax", ctypes.c_double), 
-1060              ("ymin", ctypes.c_double), 
-1061              ("ymax", ctypes.c_double) 
-1062            ] 
-1063           
-1064          class POLY(ctypes.Structure): 
-1065            _fields_ = [ 
-1066              ("n", ctypes.c_int), 
-1067              ("nallocated", ctypes.c_int), 
-1068              ("e", EXTENT), 
-1069              ("x", ctypes.POINTER(ctypes.c_double)), 
-1070              ("y", ctypes.POINTER(ctypes.c_double)) 
-1071            ] 
-1072           
-1073          # SUBGRID 
-1074          # A forward declaration of this structure is used 
-1075          # (1) Defined it first with pass 
-1076          # (2) Define the fields next 
-1077           
-1078          # SUBGRID (1) 
-1079          class SUBGRID(ctypes.Structure): 
-1080            pass 
-1081           
-1082          class GRIDMAP(ctypes.Structure): 
-1083            _fields_ = [ 
-1084              ("bound", ctypes.POINTER(POLY)), 
-1085              ("trunk", ctypes.POINTER(SUBGRID)), 
-1086              ("nleaves", ctypes.c_int), 
-1087              ("nce1", ctypes.c_int), 
-1088              ("nce2", ctypes.c_int), 
-1089              ("gx", ctypes.POINTER(ctypes.POINTER(ctypes.c_double))), 
-1090              ("gy", ctypes.POINTER(ctypes.POINTER(ctypes.c_double))), 
-1091              ("sign", ctypes.c_int) 
-1092            ] 
-1093           
-1094          # SUBGRID (2) 
-1095          SUBGRID._fields_ = [ 
-1096              ("gmap", ctypes.POINTER(GRIDMAP)), 
-1097              ("bound", ctypes.POINTER(POLY)), 
-1098              ("mini", ctypes.c_int), 
-1099              ("maxi", ctypes.c_int), 
-1100              ("minj", ctypes.c_int), 
-1101              ("maxj", ctypes.c_int), 
-1102              ("half1", ctypes.POINTER(SUBGRID)), 
-1103              ("half2", ctypes.POINTER(SUBGRID)) 
-1104          ] 
-1105                   
-1106          #self._libgridgen.gridgen_generategrid2.restype = ctypes.c_void_p 
-1107          self._libgridgen.gridgen_generategrid2.restype = ctypes.POINTER(GRIDNODES) 
-1108          self._libgridgen.gridnodes_getx.restype = ctypes.POINTER(ctypes.POINTER(ctypes.c_double)) 
-1109          self._libgridgen.gridnodes_gety.restype = ctypes.POINTER(ctypes.POINTER(ctypes.c_double)) 
-1110          self._libgridgen.gridnodes_getnce1.restype = ctypes.c_int 
-1111          self._libgridgen.gridnodes_getnce2.restype = ctypes.c_int 
-1112          #self._libgridgen.gridmap_build.restype = ctypes.c_void_p 
-1113          self._libgridgen.gridmap_build.restype = ctypes.POINTER(GRIDMAP) 
-1114           
-1115          self.xbry = np.asarray(xbry, dtype='d') 
-1116          self.ybry = np.asarray(ybry, dtype='d') 
-1117          self.beta = np.asarray(beta, dtype='d') 
-1118          assert self.beta.sum() == 4.0, 'sum of beta must be 4.0' 
-1119          self.shape = shape 
-1120          self.ny = shape[0] 
-1121          self.nx = shape[1] 
-1122          self.ul_idx = ul_idx 
-1123          self.focus = focus 
-1124          self.nnodes = nnodes 
-1125          self.precision = precision 
-1126          self.nppe = nppe 
-1127          self.newton = newton 
-1128          self.thin = thin 
-1129          self.checksimplepoly = checksimplepoly 
-1130          self.verbose = verbose 
-1131           
-1132          self.proj = proj 
-1133          if self.proj is not None: 
-1134              self.xbry, self.ybry = proj(self.xbry, self.ybry) 
-1135           
-1136          self._gn = None 
-1137          self.generate_grid() 
-1138       
-
1139 -    def __del__(self): 
-
1140          """delete gridnode object upon deletion""" 
-1141          self._libgridgen.gridnodes_destroy(self._gn) 
-
1142   
-1143   
-
1144 -def rho_to_vert(xr, yr, pm, pn, ang): 
-
1145      Mp, Lp = xr.shape 
-1146      x = np.empty((Mp+1, Lp+1), dtype='d') 
-1147      y = np.empty((Mp+1, Lp+1), dtype='d') 
-1148      x[1:-1, 1:-1] = 0.25*(xr[1:,1:]+xr[1:,:-1]+xr[:-1,1:]+xr[:-1,:-1]) 
-1149      y[1:-1, 1:-1] = 0.25*(yr[1:,1:]+yr[1:,:-1]+yr[:-1,1:]+yr[:-1,:-1]) 
-1150       
-1151      # east side 
-1152      theta = 0.5*(ang[:-1,-1]+ang[1:,-1]) 
-1153      dx = 0.5*(1.0/pm[:-1,-1]+1.0/pm[1:,-1]) 
-1154      dy = 0.5*(1.0/pn[:-1,-1]+1.0/pn[1:,-1]) 
-1155      x[1:-1,-1] = x[1:-1,-2] + dx*np.cos(theta) 
-1156      y[1:-1,-1] = y[1:-1,-2] + dx*np.sin(theta) 
-1157       
-1158      # west side 
-1159      theta = 0.5*(ang[:-1,0]+ang[1:,0]) 
-1160      dx = 0.5*(1.0/pm[:-1,0]+1.0/pm[1:,0]) 
-1161      dy = 0.5*(1.0/pn[:-1,0]+1.0/pn[1:,0]) 
-1162      x[1:-1,0] = x[1:-1,1] - dx*np.cos(theta) 
-1163      y[1:-1,0] = y[1:-1,1] - dx*np.sin(theta) 
-1164       
-1165      # north side 
-1166      theta = 0.5*(ang[-1,:-1]+ang[-1,1:]) 
-1167      dx = 0.5*(1.0/pm[-1,:-1]+1.0/pm[-1,1:]) 
-1168      dy = 0.5*(1.0/pn[-1,:-1]+1.0/pn[-1,1:]) 
-1169      x[-1,1:-1] = x[-2,1:-1] - dy*np.sin(theta) 
-1170      y[-1,1:-1] = y[-2,1:-1] + dy*np.cos(theta) 
-1171       
-1172      # here we are now going to the south side.. 
-1173      theta = 0.5*(ang[0,:-1]+ang[0,1:]) 
-1174      dx = 0.5*(1.0/pm[0,:-1]+1.0/pm[0,1:]) 
-1175      dy = 0.5*(1.0/pn[0,:-1]+1.0/pn[0,1:]) 
-1176      x[0,1:-1] = x[1,1:-1] + dy*np.sin(theta) 
-1177      y[0,1:-1] = y[1,1:-1] - dy*np.cos(theta) 
-1178       
-1179      #Corners 
-1180      x[0,0] = 4.0*xr[0,0]-x[1,0]-x[0,1]-x[1,1] 
-1181      x[-1,0] = 4.0*xr[-1,0]-x[-2,0]-x[-1,1]-x[-2,1] 
-1182      x[0,-1] = 4.0*xr[0,-1]-x[0,-2]-x[1,-1]-x[1,-2] 
-1183      x[-1,-1] = 4.0*xr[-1,-1]-x[-2,-2]-x[-2,-1]-x[-1,-2] 
-1184       
-1185      y[0,0] = 4.0*yr[0,0]-y[1,0]-y[0,1]-y[1,1] 
-1186      y[-1,0] = 4.0*yr[-1,0]-y[-2,0]-y[-1,1]-y[-2,1] 
-1187      y[0,-1] = 4.0*yr[0,-1]-y[0,-2]-y[1,-1]-y[1,-2] 
-1188      y[-1,-1] = 4.0*yr[-1,-1]-y[-2,-2]-y[-2,-1]-y[-1,-2] 
-1189       
-1190      return x, y 
-
1191   
-1192   
-
1193 -def rho_to_vert_geo(lonr, latr, lonp, latp): 
-
1194      Mm, Lm = lonr.shape 
-1195      lon = np.zeros((Mm+1,Lm+1)) 
-1196      lat = np.zeros((Mm+1,Lm+1)) 
-1197   
-1198      lon[1:-1, 1:-1] = lonp[:,:] 
-1199      lat[1:-1, 1:-1] = latp[:,:] 
-1200   
-1201      #North edge 
-1202      lon[Mm,0:-2] = lonr[Mm-1,0:-1] - ( lonp[Mm-2,:] - lonr[Mm-1,0:-1] ) 
-1203      lon[Mm,-2:] = lonr[Mm-1,-2:] - ( lonp[Mm-2,-2:] - lonr[Mm-1,-2:] ) 
-1204      lat[Mm,0:-2] = latr[Mm-1,0:-1] - ( latp[Mm-2,:] - latr[Mm-1,0:-1] ) 
-1205      lat[Mm,-2:] = latr[Mm-1,-2:] - ( latp[Mm-2,-2:] - latr[Mm-1,-2:] ) 
-1206           
-1207      #South edge 
-1208      lon[0,0:-2] = lonr[0,0:-1] - ( lonp[0,:] - lonr[0,0:-1] ) 
-1209      lon[0,-2:] = lonr[0,-2:] - ( lonp[0,-2:] - lonr[0,-2:] ) 
-1210      lat[0,0:-2] = latr[0,0:-1] - ( latp[0,:] - latr[0,0:-1] ) 
-1211      lat[0,-2:] = latr[0,-2:] - ( latp[0,-2:] - latr[0,-2:] ) 
-1212   
-1213      #East edge 
-1214      lon[0:-2,Lm] = lonr[0:-1,Lm-1] - ( lonp[:,Lm-2] - lonr[0:-1,Lm-1] ) 
-1215      lon[-2:,Lm] = lonr[-2:,Lm-1] - ( lonp[-2:,Lm-2] - lonr[-2:,Lm-1] ) 
-1216      lat[0:-2,Lm] = latr[0:-1,Lm-1] - ( latp[:,Lm-2] - latr[0:-1,Lm-1] ) 
-1217      lat[-2:,Lm] = latr[-2:,Lm-1] - ( latp[-2:,Lm-2] - latr[-2:,Lm-1] ) 
-1218   
-1219      #West edge 
-1220      lon[0:-2,0] = lonr[0:-1,0] - ( lonp[:,0] - lonr[0:-1,0] ) 
-1221      lon[-2:,0] = lonr[-2:,0] - ( lonp[-2:,0] - lonr[-2:,0] ) 
-1222      lat[0:-2,0] = latr[0:-1,0] - ( latp[:,0] - latr[0:-1,0] ) 
-1223      lat[-2:,0] = latr[-2:,0] - ( latp[-2:,0] - latr[-2:,0] ) 
-1224   
-1225      return lon, lat 
-
1226   
-1227   
-
1228 -class edit_mask_mesh(object): 
-
1229      """ 
-1230      Interactive mask editor 
-1231   
-1232      edit_mask_mesh(grd, proj) 
-1233   
-1234      Edit grd mask. Mask/Unsmask cell by a simple click on the cell. 
-1235      Mask modification are store in mask_change.txt for further use. 
-1236   
-1237      Key commands: 
-1238          e : toggle between Editing/Viewing mode 
-1239      """ 
-1240       
-
1241 -    def _on_key(self, event): 
-
1242          if event.key == 'e': 
-1243              self._clicking = not self._clicking 
-1244              plt.title('Editing %s -- click "e" to toggle' % self._clicking) 
-1245              plt.draw() 
-
1246       
-
1247 -    def _on_click(self, event): 
-
1248          x, y = event.xdata, event.ydata 
-1249          if event.button==1 and event.inaxes is not None and self._clicking == True: 
-1250              d = (x-self._xc)**2 + (y-self._yc)**2 
-1251              if isinstance(self.xv, np.ma.MaskedArray): 
-1252                  idx = np.argwhere(d[~self._xc.mask] == d.min()) 
-1253              else: 
-1254                  idx = np.argwhere(d.flatten() == d.min()) 
-1255              self._mask[idx] = float(not self._mask[idx]) 
-1256              i, j = np.argwhere(d == d.min())[0] 
-1257              self.mask[i, j] = float(not self.mask[i, j]) 
-1258              #open output file 
-1259              f = open('mask_change.txt','a') 
-1260              value = (i, j, self.mask[i, j]) 
-1261              s = str(value) 
-1262              f.write(s + '\n') 
-1263              #close file 
-1264              f.close() 
-1265              self._pc.set_array(self._mask) 
-1266              self._pc.changed() 
-1267              plt.draw() 
-
1268       
-
1269 -    def __init__(self, grd, proj=None, **kwargs): 
-
1270   
-1271          if type(grd).__name__ == 'ROMS_Grid': 
-1272              try: 
-1273                  xv = grd.hgrid.lon_vert 
-1274                  yv = grd.hgrid.lat_vert 
-1275                  mask = grd.hgrid.mask_rho 
-1276              except: 
-1277                  xv = grd.hgrid.x_vert 
-1278                  yv = grd.hgrid.y_vert 
-1279                  mask = grd.hgrid.mask_rho 
-1280   
-1281          if type(grd).__name__ == 'CGrid_geo': 
-1282              try: 
-1283                  xv = grd.lon_vert 
-1284                  yv = grd.lat_vert 
-1285                  mask = grd.mask_rho 
-1286              except: 
-1287                  xv = grd.x_vert 
-1288                  yv = grd.y_vert 
-1289                  mask = grd.mask_rho 
-1290   
-1291          assert xv.shape == yv.shape, 'xv and yv must have the same shape' 
-1292          for dx, dq in zip(xv.shape, mask.shape): 
-1293               assert dx==dq+1, \ 
-1294               '''xv and yv must be cell verticies 
-1295               (i.e., one cell bigger in each dimension)''' 
-1296           
-1297          self.xv = xv 
-1298          self.yv = yv 
-1299           
-1300          self.mask = mask 
-1301   
-1302          self.proj = proj 
-1303           
-1304          land_color = kwargs.pop('land_color', (0.6, 1.0, 0.6)) 
-1305          sea_color = kwargs.pop('sea_color', (0.6, 0.6, 1.0)) 
-1306   
-1307          cm = plt.matplotlib.colors.ListedColormap([land_color, sea_color],  
-1308                                                   name='land/sea') 
-1309   
-1310          if self.proj is None: 
-1311              self._pc = plt.pcolor(xv, yv, mask, cmap=cm, vmin=0, vmax=1, edgecolor='k', **kwargs) 
-1312          else: 
-1313              xv, yv = self.proj(xv, yv) 
-1314              self._pc = Basemap.pcolor(self.proj, xv, yv, mask, cmap=cm, vmin=0, vmax=1, edgecolor='k', **kwargs) 
-1315              self.proj.drawcoastlines() 
-1316   
-1317          self._xc = 0.25*(xv[1:,1:]+xv[1:,:-1]+xv[:-1,1:]+xv[:-1,:-1]) 
-1318          self._yc = 0.25*(yv[1:,1:]+yv[1:,:-1]+yv[:-1,1:]+yv[:-1,:-1]) 
-1319           
-1320          if isinstance(self.xv, np.ma.MaskedArray): 
-1321              self._mask = mask[~self._xc.mask] 
-1322          else: 
-1323              self._mask = mask.flatten() 
-1324           
-1325          plt.connect('button_press_event', self._on_click) 
-1326          plt.connect('key_press_event', self._on_key) 
-1327          self._clicking = False 
-1328          plt.title('Editing %s -- click "e" to toggle' % self._clicking) 
-1329          plt.draw() 
-
1330   
-1331   
-
1332 -def uvp_masks(rmask): 
-
1333      ''' 
-1334      return u-, v-, and psi-masks based on input rho-mask 
-1335       
-1336      Parameters 
-1337      ---------- 
-1338       
-1339      rmask : ndarray 
-1340          mask at CGrid rho-points 
-1341       
-1342      Returns 
-1343      ------- 
-1344      (umask, vmask, pmask) : ndarrays 
-1345          masks at u-, v-, and psi-points 
-1346      ''' 
-1347      rmask = np.asarray(rmask) 
-1348      assert rmask.ndim == 2, 'rmask must be a 2D array' 
-1349      assert np.all((rmask==0)|(rmask==1)), 'rmask array must contain only ones and zeros.' 
-1350   
-1351      umask = rmask[:, :-1] * rmask[:, 1:] 
-1352      vmask = rmask[:-1, :] * rmask[1:, :] 
-1353      pmask = rmask[:-1, :-1] * rmask[:-1, 1:] * rmask[1:, :-1] * rmask[1:, 1:] 
-1354   
-1355      return umask, vmask, pmask 
-
1356   
-1357   
-1358   
-1359  if __name__ == '__main__': 
-1360      geographic = False 
-1361      if geographic: 
-1362          from mpl_toolkits.basemap import Basemap 
-1363          proj = Basemap(projection='lcc', 
-1364                         resolution='i', 
-1365                         llcrnrlon=-72.0, 
-1366                         llcrnrlat= 40.0, 
-1367                         urcrnrlon=-63.0, 
-1368                         urcrnrlat=47.0, 
-1369                         lat_0=43.0, 
-1370                         lon_0=-62.5) 
-1371           
-1372          lon = (-71.977385177601761, -70.19173825913137, 
-1373                 -63.045075098584945,-64.70104074097425) 
-1374          lat = (42.88215610827428, 41.056141745853786, 
-1375                 44.456701607935841, 46.271758064353897) 
-1376          beta = [1.0, 1.0, 1.0, 1.0] 
-1377   
-1378          grd = Gridgen(lon, lat, beta, (32, 32), proj=proj) 
-1379           
-1380          for seg in proj.coastsegs: 
-1381              grd.mask_polygon(seg) 
-1382           
-1383          plt.pcolor(grd.x, grd.y, grd.mask) 
-1384          plt.show() 
-1385      else: 
-1386          x = [0.2, 0.85, 0.9, 0.82, 0.23] 
-1387          y = [0.2, 0.25, 0.5, 0.82, .83] 
-1388          beta = [1.0, 1.0, 0.0, 1.0, 1.0] 
-1389           
-1390          grd = Gridgen(x, y, beta, (32, 32)) 
-1391           
-1392          ax = plt.subplot(111) 
-1393          BoundaryInteractor(x, y, beta) 
-1394          plt.show() 
-1395   
-1396   
-1397   
-
1398 -class get_position_from_map(object): 
-
1399      """ 
-1400      Get cell index position Interactively 
-1401   
-1402      get_position_from_map(grd, proj) 
-1403   
-1404      Get index i, j as well as lon, lat coordinates for one cell 
-1405      simply by clicking on the cell. 
-1406   
-1407      Key commands: 
-1408          i : toggle between Interactive/Viewing mode 
-1409      """ 
-
1410 -    def _on_key(self, event): 
-
1411          if event.key == 'i': 
-1412              self._clicking = not self._clicking 
-1413              plt.title('Interactive %s -- click "i" to toggle' % self._clicking) 
-1414              plt.draw() 
-
1415   
-
1416 -    def _on_click(self, event): 
-
1417          x, y = event.xdata, event.ydata 
-1418          if event.button==1 and event.inaxes is not None and self._clicking == True: 
-1419              d = (x-self._xc)**2 + (y-self._yc)**2 
-1420              if isinstance(self.xv, np.ma.MaskedArray): 
-1421                  idx = np.argwhere(d[~self._xc.mask] == d.min()) 
-1422              else: 
-1423                  idx = np.argwhere(d.flatten() == d.min()) 
-1424              j, i = np.argwhere(d == d.min())[0] 
-1425              print 'Position on the grid (rho point): i =', i, ', j =', j 
-1426              if self.proj is not None: 
-1427                  lon, lat = self.proj(self._xc[j,i], self._yc[j,i], inverse=True) 
-1428                  print 'corresponding geographical position : lon = ', lon, ', lat =', lat 
-1429              else: 
-1430                  print 'corresponding cartesian position : x = ', self._xc[j,i], ', y =', self._yc[j,i] 
-
1431       
-
1432 -    def __init__(self, grd, proj=None, **kwargs): 
-
1433   
-1434          try: 
-1435              xv = grd.hgrid.lon_vert 
-1436              yv = grd.hgrid.lat_vert 
-1437              mask = grd.hgrid.mask_rho 
-1438          except: 
-1439              xv = grd.hgrid.x_vert 
-1440              yv = grd.hgrid.y_vert 
-1441              mask = grd.hgrid.mask_rho 
-1442             
-1443          assert xv.shape == yv.shape, 'xv and yv must have the same shape' 
-1444          for dx, dq in zip(xv.shape, mask.shape): 
-1445               assert dx==dq+1, \ 
-1446               '''xv and yv must be cell verticies 
-1447               (i.e., one cell bigger in each dimension)''' 
-1448           
-1449          self.xv = xv 
-1450          self.yv = yv 
-1451           
-1452          self.mask = mask 
-1453   
-1454          self.proj = proj 
-1455           
-1456          land_color = kwargs.pop('land_color', (0.6, 1.0, 0.6)) 
-1457          sea_color = kwargs.pop('sea_color', (0.6, 0.6, 1.0)) 
-1458   
-1459          cm = plt.matplotlib.colors.ListedColormap([land_color, sea_color],  
-1460                                                   name='land/sea') 
-1461   
-1462          if self.proj is None: 
-1463              self._pc = plt.pcolor(xv, yv, mask, cmap=cm, vmin=0, vmax=1, edgecolor='k', **kwargs) 
-1464   
-1465          else: 
-1466              xv, yv = self.proj(xv, yv) 
-1467              self._pc = Basemap.pcolor(self.proj, xv, yv, mask, cmap=cm, vmin=0, vmax=1, edgecolor='k', **kwargs) 
-1468              self.proj.drawcoastlines() 
-1469   
-1470          self._xc = 0.25*(xv[1:,1:]+xv[1:,:-1]+xv[:-1,1:]+xv[:-1,:-1]) 
-1471          self._yc = 0.25*(yv[1:,1:]+yv[1:,:-1]+yv[:-1,1:]+yv[:-1,:-1]) 
-1472           
-1473          plt.connect('button_press_event', self._on_click) 
-1474          plt.connect('key_press_event', self._on_key) 
-1475          self._clicking = False 
-1476          plt.title('Interactive %s -- click "i" to toggle' % self._clicking) 
-1477          plt.draw() 
-
1478       
-1479   
-1480  if __name__ == '__main__': 
-1481      geographic = False 
-1482      if geographic: 
-1483          from mpl_toolkits.basemap import Basemap 
-1484          proj = Basemap(projection='lcc', 
-1485                         resolution='i', 
-1486                         llcrnrlon=-72.0, 
-1487                         llcrnrlat= 40.0, 
-1488                         urcrnrlon=-63.0, 
-1489                         urcrnrlat=47.0, 
-1490                         lat_0=43.0, 
-1491                         lon_0=-62.5) 
-1492           
-1493          lon = (-71.977385177601761, -70.19173825913137, 
-1494                 -63.045075098584945,-64.70104074097425) 
-1495          lat = (42.88215610827428, 41.056141745853786, 
-1496                 44.456701607935841, 46.271758064353897) 
-1497          beta = [1.0, 1.0, 1.0, 1.0] 
-1498   
-1499          grd = Gridgen(lon, lat, beta, (32, 32), proj=proj) 
-1500           
-1501          for seg in proj.coastsegs: 
-1502              grd.mask_polygon(seg) 
-1503           
-1504          plt.pcolor(grd.x, grd.y, grd.mask) 
-1505          plt.show() 
-1506      else: 
-1507          x = [0.2, 0.85, 0.9, 0.82, 0.23] 
-1508          y = [0.2, 0.25, 0.5, 0.82, .83] 
-1509          beta = [1.0, 1.0, 0.0, 1.0, 1.0] 
-1510           
-1511          grd = Gridgen(x, y, beta, (32, 32)) 
-1512           
-1513          ax = plt.subplot(111) 
-1514          BoundaryInteractor(x, y, beta) 
-1515          plt.show() 
-1516   
-
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- Generated by Epydoc 3.0.1 on Mon Sep 27 11:31:40 2010 - - http://epydoc.sourceforge.net -
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- - Package pyroms :: - Module hgrid :: - Class BoundaryInteractor - - - - - - -
[hide private]
[frames] | no frames]
-
- -

Class BoundaryInteractor

source code

-
-object --+
-         |
-        BoundaryInteractor
-
- -
-
-
-Interactive grid creation
-    
-bry = BoundaryClick(x=[], y=[], beta=None, ax=gca(), **gridgen_options)
-
-The initial boundary polygon points (x and y) are
-counterclockwise, starting in the upper left corner of the
-boundary. 
-
-Key commands:
-    
-    t : toggle visibility of verticies
-    d : delete a vertex
-    i : insert a vertex at a point on the polygon line
-    
-    p : set vertex as beta=1 (a Positive turn, marked with green triangle)
-    m : set vertex as beta=1 (a Negative turn, marked with red triangle)
-    z : set vertex as beta=0 (no corner, marked with a black dot)
-    
-    G : generate grid from the current boundary using gridgen
-    T : toggle visability of the current grid
-
-Methods:
-
-    bry.dump(bry_file)
-        Write the current boundary informtion (bry.x, bry.y, bry.beta) to
-        a cPickle file bry_file.
-    
-    bry.load(bry_file)
-        Read in boundary informtion (x, y, beta) from the cPickle file
-        bry_file.
-    
-    bry.remove_grid()  
-        Remove gridlines from axes.
-
-Attributes:
-    bry.x : the X boundary points
-    bry.y : the Y boundary points
-    bry.verts : the verticies of the grid
-    bry.grd : the CGrid object
-    
-
-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
-   - - - - - - -
_update_beta_lines(self)
- Update m/pline by finding the points where self.beta== -/+ 1		 - source code - -
- -
-   - - - - - - -
remove_grid(self)
- Remove a generated grid from the BoundaryClick figure		 - source code - -
- -
-   - - - - - - -
_draw_callback(self, - event) - source code - -
- -
-   - - - - - - -
_poly_changed(self, - poly)
- this method is called whenever the polygon object is called		 - source code - -
- -
-   - - - - - - -
_get_ind_under_point(self, - event)
- get the index of the vertex under point if within epsilon tolerance		 - source code - -
- -
-   - - - - - - -
_button_press_callback(self, - event)
- whenever a mouse button is pressed		 - source code - -
- -
-   - - - - - - -
_button_release_callback(self, - event)
- whenever a mouse button is released		 - source code - -
- -
-   - - - - - - -
_key_press_callback(self, - event)
- whenever a key is pressed		 - source code - -
- -
-   - - - - - - -
_motion_notify_callback(self, - event)
- on mouse movement		 - source code - -
- -
-   - - - - - - -
__init__(self, - x, - y=None, - beta=None, - ax=None, - proj=None, - **gridgen_options)
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature		 - source code - -
- -
-   - - - - - - -
save_bry(self, - bry_file='bry.pickle') - source code - -
- -
-   - - - - - - -
load_bry(self, - bry_file='bry.pickle') - source code - -
- -
-   - - - - - - -
save_grid(self, - grid_file='grid.pickle') - source code - -
- -
-   - - - - - - -
_get_verts(self) - source code - -
- -
-   - - - - - - -
get_xdata(self) - source code - -
- -
-   - - - - - - -
get_ydata(self) - source code - -
- -
-

Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

-
- - - - - - - - - - - - - - - - - - -
- - - - - -
Class Variables[hide private]
-
-   - - _showverts = True -
-   - - _showbetas = True -
-   - - _showgrid = True -
-   - - _epsilon = 5 -
- - - - - - - - - - - - - - - - - - -
- - - - - -
Properties[hide private]
-
-   - - verts -
-   - - x -
-   - - y -
-

Inherited from object: - __class__ -

-
- - - - - - -
- - - - - -
Method Details[hide private]
-
- -
- -
- - -
-

__init__(self, - x, - y=None, - beta=None, - ax=None, - proj=None, - **gridgen_options) -
(Constructor) -

- 		source code  -
- -

x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

-
-
Overrides: - object.__init__ -
(inherited documentation)
- -
-
-
-
- - - - - - -
- - - - - -
Property Details[hide private]
-
- -
- -
-

verts

- -
-
Get Method:
-
_get_verts(self) -
-
-
-
- -
- -
-

x

- -
-
Get Method:
-
get_xdata(self) -
-
-
-
- -
- -
-

y

- -
-
Get Method:
-
get_ydata(self) -
-
-
-
-
- - - - - - - - - - - - - - - - - -
   Home      Trees      Indices      Help   
- - - - - -
- Generated by Epydoc 3.0.1 on Mon Sep 27 11:31:39 2010 - - http://epydoc.sourceforge.net -
- - - - diff --git a/pyroms/docs/pyroms.hgrid.CGrid-class.html b/pyroms/docs/pyroms.hgrid.CGrid-class.html deleted file mode 100644 index 9024e09..0000000 --- a/pyroms/docs/pyroms.hgrid.CGrid-class.html +++ /dev/null @@ -1,693 +0,0 @@ - - - - - pyroms.hgrid.CGrid - - - - - - - - - - - - - - - - - - - - - - -
   Home      Trees      Indices      Help   
- - - - - -
- - Package pyroms :: - Module hgrid :: - Class CGrid - - - - - - -
[hide private]
[frames] | no frames]
-
- -

Class CGrid

source code

-
-object --+
-         |
-        CGrid
-
- -
Known Subclasses:
-
- -
- -
-
-
-Curvilinear Arakawa C-Grid
- 
-The basis for the CGrid class are two arrays defining the verticies of the
-grid in Cartesian (for geographic coordinates, see CGrid_geo). An optional
-mask may be defined on the cell centers. Other Arakawa C-grid properties,
-such as the locations of the cell centers (rho-points), cell edges (u and
-v velocity points), cell widths (dx and dy) and other metrics (angle,
-dmde, and dndx) are all calculated internally from the vertex points.
- 
-Input vertex arrays may be either type np.array or np.ma.MaskedArray. If
-masked arrays are used, the mask will be a combination of the specified
-mask (if given) and the masked locations.
- 
-EXAMPLES:
---------
- 
->>> x, y = mgrid[0.0:7.0, 0.0:8.0]
->>> x = np.ma.masked_where( (x<3) & (y<3), x)
->>> y = np.ma.MaskedArray(y, x.mask)
->>> grd = pyroms.grid.CGrid(x, y)
->>> print grd.x_rho
-[[-- -- -- 0.5 0.5 0.5 0.5]
- [-- -- -- 1.5 1.5 1.5 1.5]
- [-- -- -- 2.5 2.5 2.5 2.5]
- [3.5 3.5 3.5 3.5 3.5 3.5 3.5]
- [4.5 4.5 4.5 4.5 4.5 4.5 4.5]
- [5.5 5.5 5.5 5.5 5.5 5.5 5.5]]
->>> print grd.mask
-[[ 0.  0.  0.  1.  1.  1.  1.]
- [ 0.  0.  0.  1.  1.  1.  1.]
- [ 0.  0.  0.  1.  1.  1.  1.]
- [ 1.  1.  1.  1.  1.  1.  1.]
- [ 1.  1.  1.  1.  1.  1.  1.]
- [ 1.  1.  1.  1.  1.  1.  1.]]
-
-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
-   - - - - - - -
__init__(self, - x_vert, - y_vert, - x_rho=None, - y_rho=None, - x_u=None, - y_u=None, - x_v=None, - y_v=None, - x_psi=None, - y_psi=None, - dx=None, - dy=None, - dndx=None, - dmde=None, - angle_rho=None)
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature		 - source code - -
- -
-   - - - - - - -
_calculate_subgrids(self) - source code - -
- -
-   - - - - - - -
_calculate_metrics(self)
- Calculates pm, pn, dndx, dmde from x_vert and y_vert		 - source code - -
- -
-   - - - - - - -
_calculate_derivative_metrics(self) - source code - -
- -
-   - - - - - - -
_calculate_angle(self) - source code - -
- -
-   - - - - - - -
_calculate_angle_rho(self) - source code - -
- -
-   - - - - - - -
calculate_orthogonality(self)
- Calculate orthogonality error in radians		 - source code - -
- -
-   - - - - - - -
mask_polygon(self, - polyverts, - mask_value=0.0)
- Mask Cartesian points contained within the polygon defined by polyverts		 - source code - -
- -
-   - - - - - - -
_get_mask_u(self) - source code - -
- -
-   - - - - - - -
_get_mask_v(self) - source code - -
- -
-   - - - - - - -
_get_mask_psi(self) - source code - -
- -
-   - - - - - - -
_set_mask_rho(self, - mask_rho) - source code - -
- -
-

Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

-
- - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - -
Properties[hide private]
-
-   - - x
- Return x_vert -
-   - - y
- Return x_vert -
-   - - mask
- Return mask_rho -
-   - - mask_u
- Return mask_u -
-   - - mask_v
- Return mask_v -
-   - - mask_psi
- Return mask_psi -
-

Inherited from object: - __class__ -

-
- - - - - - -
- - - - - -
Method Details[hide private]
-
- -
- -
- - -
-

__init__(self, - x_vert, - y_vert, - x_rho=None, - y_rho=None, - x_u=None, - y_u=None, - x_v=None, - y_v=None, - x_psi=None, - y_psi=None, - dx=None, - dy=None, - dndx=None, - dmde=None, - angle_rho=None) -
(Constructor) -

- 		source code  -
- -

x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

-
-
Overrides: - object.__init__ -
(inherited documentation)
- -
-
-
- -
- -
- - -
-

mask_polygon(self, - polyverts, - mask_value=0.0) -

- 		source code  -
- - 
-
-Mask Cartesian points contained within the polygon defined by polyverts
-
-A cell is masked if the cell center (x_rho, y_rho) is within the
-polygon. Other sub-masks (mask_u, mask_v, and mask_psi) are updated
-automatically.
-
-mask_value [=0.0] may be specified to alter the value of the mask set
-within the polygon.  E.g., mask_value=1 for water points.
-
-
-
-
-
-
-
- - - - - - -
- - - - - -
Property Details[hide private]
-
- -
- -
-

x

- 
-Return x_vert
-
-
-
-
Get Method:
-
unreachable(self) -
-
-
-
- -
- -
-

y

- 
-Return x_vert
-
-
-
-
Get Method:
-
unreachable(self) -
-
-
-
- -
- -
-

mask

- 
-Return mask_rho
-
-
-
-
Get Method:
-
unreachable(self) -
-
Set Method:
-
_set_mask_rho(self, - mask_rho) -
-
-
-
- -
- -
-

mask_u

- 
-Return mask_u
-
-
-
-
Get Method:
-
_get_mask_u(self) -
-
-
-
- -
- -
-

mask_v

- 
-Return mask_v
-
-
-
-
Get Method:
-
_get_mask_v(self) -
-
-
-
- -
- -
-

mask_psi

- 
-Return mask_psi
-
-
-
-
Get Method:
-
_get_mask_psi(self) -
-
-
-
-
- - - - - - - - - - - - - - - - - -
   Home      Trees      Indices      Help   
- - - - - -
- Generated by Epydoc 3.0.1 on Mon Sep 27 11:31:39 2010 - - http://epydoc.sourceforge.net -
- - - - diff --git a/pyroms/docs/pyroms.hgrid.CGrid_geo-class.html b/pyroms/docs/pyroms.hgrid.CGrid_geo-class.html deleted file mode 100644 index c6aaf9a..0000000 --- a/pyroms/docs/pyroms.hgrid.CGrid_geo-class.html +++ /dev/null @@ -1,512 +0,0 @@ - - - - - pyroms.hgrid.CGrid_geo - - - - - - - - - - - - - - - - - - - - - - -
   Home      Trees      Indices      Help   
- - - - - -
- - Package pyroms :: - Module hgrid :: - Class CGrid_geo - - - - - - -
[hide private]
[frames] | no frames]
-
- -

Class CGrid_geo

source code

-
-object --+    
-         |    
-     CGrid --+
-             |
-            CGrid_geo
-
- -
-
-
-Curvilinear Arakawa C-grid defined in geographic coordinates
-
-For a geographic grid, a projection may be specified, or The default
-projection for will be defined by the matplotlib.toolkits.Basemap
-projection:
-
-proj = Basemap(projection='merc', resolution=None, lat_ts=0.0)
-
-For a geographic grid, the cell widths are determined by the great
-circle distances. Angles, however, are defined using the projected
-coordinates, so a projection that conserves angles must be used. This
-means typically either Mercator (projection='merc') or Lambert
-Conformal Conic (projection='lcc').
-
-
- - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
-   - - - - - - -
_calculate_metrics(self)
- Calculates pm, pn, dndx, dmde from x_vert and y_vert		 - source code - -
- -
-   - - - - - - -
_calculate_derivative_metrics(self) - source code - -
- -
-   - - - - - - -
_calculate_angle_rho(self) - source code - -
- -
-   - - - - - - -
__init__(self, - lon_vert, - lat_vert, - proj, - use_gcdist=True, - ellipse='WGS84', - lon_rho=None, - lat_rho=None, - lon_u=None, - lat_u=None, - lon_v=None, - lat_v=None, - lon_psi=None, - lat_psi=None, - dx=None, - dy=None, - dndx=None, - dmde=None, - angle_rho=None)
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature		 - source code - -
- -
-   - - - - - - -
mask_polygon_geo(lonlat_verts, - mask_value=0.0) - source code - -
- -
-

Inherited from CGrid: - calculate_orthogonality, - mask_polygon -

-

Inherited from CGrid (private): - _calculate_angle, - _calculate_subgrids, - _get_mask_psi, - _get_mask_u, - _get_mask_v, - _set_mask_rho -

-

Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

-
- - - - - - - - - - - - - - - -
- - - - - -
Properties[hide private]
-
-   - - lon
- Shorthand for lon_vert -
-   - - lat
- Shorthand for lat_vert -
-

Inherited from CGrid: - mask, - mask_psi, - mask_u, - mask_v, - x, - y -

-

Inherited from object: - __class__ -

-
- - - - - - -
- - - - - -
Method Details[hide private]
-
- -
- -
- - -
-

_calculate_metrics(self) -

- 		source code  -
- - 
-Calculates pm, pn, dndx, dmde from x_vert and y_vert
-
-
-
-
Overrides: - CGrid._calculate_metrics -
(inherited documentation)
- -
-
-
- -
- -
- - -
-

_calculate_derivative_metrics(self) -

- 		source code  -
- - -
-
Overrides: - CGrid._calculate_derivative_metrics -
-
-
-
- -
- -
- - -
-

_calculate_angle_rho(self) -

- 		source code  -
- - -
-
Overrides: - CGrid._calculate_angle_rho -
-
-
-
- -
- -
- - -
-

__init__(self, - lon_vert, - lat_vert, - proj, - use_gcdist=True, - ellipse='WGS84', - lon_rho=None, - lat_rho=None, - lon_u=None, - lat_u=None, - lon_v=None, - lat_v=None, - lon_psi=None, - lat_psi=None, - dx=None, - dy=None, - dndx=None, - dmde=None, - angle_rho=None) -
(Constructor) -

- 		source code  -
- -

x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

-
-
Overrides: - object.__init__ -
(inherited documentation)
- -
-
-
-
- - - - - - -
- - - - - -
Property Details[hide private]
-
- -
- -
-

lon

- 
-Shorthand for lon_vert
-
-
-
-
Get Method:
-
unreachable(self) -
-
-
-
- -
- -
-

lat

- 
-Shorthand for lat_vert
-
-
-
-
Get Method:
-
unreachable(self) -
-
-
-
-
- - - - - - - - - - - - - - - - - -
   Home      Trees      Indices      Help   
- - - - - -
- Generated by Epydoc 3.0.1 on Mon Sep 27 11:31:39 2010 - - http://epydoc.sourceforge.net -
- - - - diff --git a/pyroms/docs/pyroms.hgrid.Focus-class.html b/pyroms/docs/pyroms.hgrid.Focus-class.html deleted file mode 100644 index 1d6ccb0..0000000 --- a/pyroms/docs/pyroms.hgrid.Focus-class.html +++ /dev/null @@ -1,335 +0,0 @@ - - - - - pyroms.hgrid.Focus - - - - - - - - - - - - - - - - - - - - - - -
   Home      Trees      Indices      Help   
- - - - - -
- - Package pyroms :: - Module hgrid :: - Class Focus - - - - - - -
[hide private]
[frames] | no frames]
-
- -

Class Focus

source code

-
-object --+
-         |
-        Focus
-
- -
-
-
-Return a container for a sequence of Focus objects
-
-foc = Focus()
-
-The sequence is populated by using the 'add_focus_x' and 'add_focus_y'
-methods. These methods define a point ('xo' or 'yo'), around witch to
-focus, a focusing factor of 'focus', and x and y extent of focusing given
-by Rx or Ry. The region of focusing will be approximately Gausian, and the
-resolution will be increased by approximately the value of factor.
-
-Methods
--------
-foc.add_focus_x(xo, factor=2.0, Rx=0.1)
-foc.add_focus_y(yo, factor=2.0, Ry=0.1)
-
-Calls to the object return transformed coordinates:
-    xf, yf = foc(x, y)
-where x and y must be within [0, 1], and are typically a uniform,
-normalized grid. The focused grid will be the result of applying each of
-the focus elements in the sequence they are added to the series.
-
-
-EXAMPLES
---------
-
->>> foc = pyroms.grid.Focus()
->>> foc.add_focus_x(0.2, factor=3.0, Rx=0.2)
->>> foc.add_focus_y(0.6, factor=5.0, Ry=0.35)
-
->>> x, y = np.mgrid[0:1:3j,0:1:3j]
->>> xf, yf = foc(x, y)
-
->>> print xf
-[[ 0.          0.          0.        ]
- [ 0.36594617  0.36594617  0.36594617]
- [ 1.          1.          1.        ]]
->>> print yf
-[[ 0.          0.62479833  1.        ]
- [ 0.          0.62479833  1.        ]
- [ 0.          0.62479833  1.        ]]
-
-
- - - - - - - - - - - - - - - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
-   - - - - - - -
__init__(self)
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature		 - source code - -
- -
-   - - - - - - -
add_focus_x(self, - xo, - factor=2.0, - Rx=0.1)
- docstring for add_point		 - source code - -
- -
-   - - - - - - -
add_focus_y(self, - yo, - factor=2.0, - Ry=0.1)
- docstring for add_point		 - source code - -
- -
-   - - - - - - -
__call__(self, - x, - y)
- docstring for __call__		 - source code - -
- -
-

Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

-
- - - - - - - - - -
- - - - - -
Properties[hide private]
-
-

Inherited from object: - __class__ -

-
- - - - - - -
- - - - - -
Method Details[hide private]
-
- -
- -
- - -
-

__init__(self) -
(Constructor) -

- 		source code  -
- -

x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

-
-
Overrides: - object.__init__ -
(inherited documentation)
- -
-
-
-
- - - - - - - - - - - - - - - - - -
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- - - - - -
- Generated by Epydoc 3.0.1 on Mon Sep 27 11:31:39 2010 - - http://epydoc.sourceforge.net -
- - - - diff --git a/pyroms/docs/pyroms.hgrid.Gridgen-class.html b/pyroms/docs/pyroms.hgrid.Gridgen-class.html deleted file mode 100644 index bc2614c..0000000 --- a/pyroms/docs/pyroms.hgrid.Gridgen-class.html +++ /dev/null @@ -1,323 +0,0 @@ - - - - - pyroms.hgrid.Gridgen - - - - - - - - - - - - - - - - - - - - - - -
   Home      Trees      Indices      Help   
- - - - - -
- - Package pyroms :: - Module hgrid :: - Class Gridgen - - - - - - -
[hide private]
[frames] | no frames]
-
- -

Class Gridgen

source code

-
-object --+    
-         |    
-     CGrid --+
-             |
-            Gridgen
-
- -
-
-
-docstring for Gridgen
-
-
- - - - - - - - - - - - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
-   - - - - - - -
generate_grid(self) - source code - -
- -
-   - - - - - - -
__init__(self, - xbry, - ybry, - beta, - shape, - ul_idx=0, - focus=None, - proj=None, - nnodes=14, - precision=1e-12, - nppe=3, - newton=True, - thin=True, - checksimplepoly=True, - verbose=False)
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature		 - source code - -
- -
-   - - - - - - -
__del__(self)
- delete gridnode object upon deletion		 - source code - -
- -
-

Inherited from CGrid: - calculate_orthogonality, - mask_polygon -

-

Inherited from CGrid (private): - _calculate_angle, - _calculate_angle_rho, - _calculate_derivative_metrics, - _calculate_metrics, - _calculate_subgrids, - _get_mask_psi, - _get_mask_u, - _get_mask_v, - _set_mask_rho -

-

Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

-
- - - - - - - - - -
- - - - - -
Properties[hide private]
-
-

Inherited from CGrid: - mask, - mask_psi, - mask_u, - mask_v, - x, - y -

-

Inherited from object: - __class__ -

-
- - - - - - -
- - - - - -
Method Details[hide private]
-
- -
- -
- - -
-

__init__(self, - xbry, - ybry, - beta, - shape, - ul_idx=0, - focus=None, - proj=None, - nnodes=14, - precision=1e-12, - nppe=3, - newton=True, - thin=True, - checksimplepoly=True, - verbose=False) -
(Constructor) -

- 		source code  -
- -

x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

-
-
Overrides: - object.__init__ -
(inherited documentation)
- -
-
-
-
- - - - - - - - - - - - - - - - - -
   Home      Trees      Indices      Help   
- - - - - -
- Generated by Epydoc 3.0.1 on Mon Sep 27 11:31:39 2010 - - http://epydoc.sourceforge.net -
- - - - diff --git a/pyroms/docs/pyroms.hgrid._Focus_x-class.html b/pyroms/docs/pyroms.hgrid._Focus_x-class.html deleted file mode 100644 index 1ae8c75..0000000 --- a/pyroms/docs/pyroms.hgrid._Focus_x-class.html +++ /dev/null @@ -1,283 +0,0 @@ - - - - - pyroms.hgrid._Focus_x - - - - - - - - - - - - - - - - - - - - - - -
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Class _Focus_x

source code

-
-object --+
-         |
-        _Focus_x
-
- -
-
-
-Return a transformed, uniform grid, focused in the x-direction
-
-This class may be called with a uniform grid, with limits from [0, 1], to
-create a focused grid in the x-directions centered about xo. The output
-grid is also uniform from [0, 1] in both x and y.
-
-Parameters
-----------
-xo : float
-    Location about which to focus grid
-factor : float
-    amount to focus grid. Creates cell sizes that are factor smaller in
-    the focused
-    region.
-Rx : float
-    Lateral extent of focused region, similar to a lateral spatial scale
-    for the focusing region.
-
-Returns
--------
-foc : class
-    The class may be called with arguments of a grid. The returned
-    transformed grid (x, y) will be focused as per the parameters above.
-
-
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Instance Methods[hide private]
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-   - - - - - - -
__init__(self, - xo, - factor=2.0, - Rx=0.1)
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature		 - source code - -
- -
-   - - - - - - -
__call__(self, - x, - y) - source code - -
- -
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Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

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__init__(self, - xo, - factor=2.0, - Rx=0.1) -
(Constructor) -

- 		source code  -
- -

x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

-
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- - Package pyroms :: - Module hgrid :: - Class _Focus_y - - - - - - -
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Class _Focus_y

source code

-
-object --+
-         |
-        _Focus_y
-
- -
-
-
-Return a transformed, uniform grid, focused in the y-direction
-
-This class may be called with a uniform grid, with limits from [0, 1], 
-to create a focused grid in the y-directions centered about yo. 
-The output grid is also uniform from [0, 1] in both x and y.
-
-Parameters
-----------
-yo : float
-    Location about which to focus grid
-factor : float
-    amount to focus grid. Creates cell sizes that are factor 
-    smaller in the focused region.
-Ry : float
-    Lateral extent of focused region, similar to a lateral 
-    spatial scale for the focusing region.
-
-Returns
--------
-foc : class
-    The class may be called with arguments of a grid. The returned 
-    transformed grid (x, y) will be focused as per the parameters above.
-
-
- - - - - - - - - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
-   - - - - - - -
__init__(self, - yo, - factor=2.0, - Ry=0.1)
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature		 - source code - -
- -
-   - - - - - - -
__call__(self, - x, - y) - source code - -
- -
-

Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

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__init__(self, - yo, - factor=2.0, - Ry=0.1) -
(Constructor) -

- 		source code  -
- -

x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

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Class edit_mask_mesh

source code

-
-object --+
-         |
-        edit_mask_mesh
-
- -
-
-
-Interactive mask editor
-
-edit_mask_mesh(grd, proj)
-
-Edit grd mask. Mask/Unsmask cell by a simple click on the cell.
-Mask modification are store in mask_change.txt for further use.
-
-Key commands:
-    e : toggle between Editing/Viewing mode
-
-
- - - - - - - - - - - - - - - - - - - -
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Instance Methods[hide private]
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_on_key(self, - event) - source code - -
- -
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_on_click(self, - event) - source code - -
- -
-   - - - - - - -
__init__(self, - grd, - proj=None, - **kwargs)
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature		 - source code - -
- -
-

Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

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__init__(self, - grd, - proj=None, - **kwargs) -
(Constructor) -

- 		source code  -
- -

x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

-
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Class edit_mask_mesh_ij

source code

-
-object --+
-         |
-        edit_mask_mesh_ij
-
- -
-
-
-Interactive mask editor
-
-edit_mask_mesh_ij(grd)
-
-Edit grd mask. Mask/Unsmask cell by a simple click on the cell.
-Mask modification are store in mask_change.txt for further use.
-
-Key commands:
-    e : toggle between Editing/Viewing mode
-
-
- - - - - - - - - - - - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
-   - - - - - - -
_on_key(self, - event) - source code - -
- -
-   - - - - - - -
_on_click(self, - event) - source code - -
- -
-   - - - - - - -
__init__(self, - grd, - coast=None, - **kwargs)
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature		 - source code - -
- -
-

Inherited from object: - __delattr__, - __format__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __sizeof__, - __str__, - __subclasshook__ -

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__init__(self, - grd, - coast=None, - **kwargs) -
(Constructor) -

- 		source code  -
- -

x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

-
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Class get_position_from_map

source code

-
-object --+
-         |
-        get_position_from_map
-
- -
-
-
-Get cell index position Interactively
-
-get_position_from_map(grd, proj)
-
-Get index i, j as well as lon, lat coordinates for one cell
-simply by clicking on the cell.
-
-Key commands:
-    i : toggle between Interactive/Viewing mode
-
-
- - - - - - - - - - - - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
-   - - - - - - -
_on_key(self, - event) - source code - -
- -
-   - - - - - - -
_on_click(self, - event) - source code - -
- -
-   - - - - - - -
__init__(self, - grd, - proj=None, - **kwargs)
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature		 - source code - -
- -
-

Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

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Inherited from object: - __class__ -

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-

__init__(self, - grd, - proj=None, - **kwargs) -
(Constructor) -

- 		source code  -
- -

x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

-
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Overrides: - object.__init__ -
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Module hgrid_old

source code

-
-Tools for creating and working with Arikawa C-Grids
-
-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - -
Classes[hide private]
-
-   - - BoundaryInteractor
- Interactive grid creation -
-   - - _Focus_x
- Return a transformed, uniform grid, focused in the x-direction -
-   - - _Focus_y
- Return a transformed, uniform grid, focused in the y-direction -
-   - - Focus
- Return a container for a sequence of Focus objects -
-   - - CGrid
- Curvilinear Arakawa C-Grid -
-   - - CGrid_geo
- Curvilinear Arakawa C-grid defined in geographic coordinates -
-   - - Gridgen
- docstring for Gridgen -
-   - - edit_mask_mesh
- Interactive mask editor -
-   - - get_position_from_map
- Get cell index position Interactively -
- - - - - - - - - - - - - - - - - - -
- - - - - -
Functions[hide private]
-
-   - - - - - - -
_approximate_erf(x)
- Return approximate solution to error function...		 - source code - -
- -
-   - - - - - - -
rho_to_vert(xr, - yr, - pm, - pn, - ang) - source code - -
- -
-   - - - - - - -
rho_to_vert_geo(lonr, - latr, - lonp, - latp) - source code - -
- -
-   - - - - - - -
uvp_masks(rmask)
- return u-, v-, and psi-masks based on input rho-mask		 - source code - -
- -
- - - - - - -
- - - - - -
Function Details[hide private]
-
- -
- -
- - -
-

_approximate_erf(x) -

- 		source code  -
- - 
-
-Return approximate solution to error function
-see http://en.wikipedia.org/wiki/Error_function
-
-
-
-
-
-
- -
- -
- - -
-

uvp_masks(rmask) -

- 		source code  -
- - 
-
-return u-, v-, and psi-masks based on input rho-mask
-
-Parameters
-----------
-
-rmask : ndarray
-    mask at CGrid rho-points
-
-Returns
--------
-(umask, vmask, pmask) : ndarrays
-    masks at u-, v-, and psi-points
-
-
-
-
-
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Source Code for Module pyroms.hgrid_old

-
-   1  # encoding: utf-8 
-   2  '''Tools for creating and working with Arikawa C-Grids''' 
-   3  __docformat__ = "restructuredtext en" 
-   4   
-   5  import os 
-   6  import sys 
-   7  import ctypes 
-   8  import cPickle 
-   9  from warnings import warn 
-  10  from copy import deepcopy 
-  11   
-  12  import numpy as np 
-  13  import matplotlib.pyplot as plt 
-  14  from matplotlib.artist import Artist 
-  15  from matplotlib.patches import Polygon, CirclePolygon 
-  16  from matplotlib.lines import Line2D 
-  17  #from matplotlib.numerix.mlab import amin 
-  18  from matplotlib.mlab import dist_point_to_segment 
-  19  from matplotlib.nxutils import points_inside_poly 
-  20   
-  21  from mpl_toolkits.basemap import Basemap 
-  22  from mpl_toolkits.basemap import pyproj 
-  23   
-  24  try: 
-  25      import scipy.spatial.cKDTree as KDTree 
-  26  except: 
-  27      #  no scipy 
-  28      from pyroms.extern import KDTree 
-  29   
-  30  import pyroms 
-  31  from pyroms.vgrid import * 
-  32  from pyroms.extern import GreatCircle 
-  33   
-
  34 -class BoundaryInteractor(object): 
-
  35      """ 
-  36      Interactive grid creation 
-  37           
-  38      bry = BoundaryClick(x=[], y=[], beta=None, ax=gca(), **gridgen_options) 
-  39       
-  40      The initial boundary polygon points (x and y) are 
-  41      counterclockwise, starting in the upper left corner of the 
-  42      boundary.  
-  43       
-  44      Key commands: 
-  45           
-  46          t : toggle visibility of verticies 
-  47          d : delete a vertex 
-  48          i : insert a vertex at a point on the polygon line 
-  49           
-  50          p : set vertex as beta=1 (a Positive turn, marked with green triangle) 
-  51          m : set vertex as beta=1 (a Negative turn, marked with red triangle) 
-  52          z : set vertex as beta=0 (no corner, marked with a black dot) 
-  53           
-  54          G : generate grid from the current boundary using gridgen 
-  55          T : toggle visability of the current grid 
-  56       
-  57      Methods: 
-  58       
-  59          bry.dump(bry_file) 
-  60              Write the current boundary informtion (bry.x, bry.y, bry.beta) to 
-  61              a cPickle file bry_file. 
-  62           
-  63          bry.load(bry_file) 
-  64              Read in boundary informtion (x, y, beta) from the cPickle file 
-  65              bry_file. 
-  66           
-  67          bry.remove_grid()   
-  68              Remove gridlines from axes. 
-  69       
-  70      Attributes: 
-  71          bry.x : the X boundary points 
-  72          bry.y : the Y boundary points 
-  73          bry.verts : the verticies of the grid 
-  74          bry.grd : the CGrid object 
-  75           
-  76      """ 
-  77       
-  78      _showverts = True 
-  79      _showbetas = True 
-  80      _showgrid = True 
-  81      _epsilon = 5  # max pixel distance to count as a vertex hit 
-  82       
-
  83 -    def _update_beta_lines(self): 
-
  84          """Update m/pline by finding the points where self.beta== -/+ 1""" 
-  85          x, y = zip(*self._poly.xy) 
-  86          num_points = len(x)-1  # the first and last point are repeated 
-  87           
-  88          xp = [x[n] for n in range(num_points) if self.beta[n]==1] 
-  89          yp = [y[n] for n in range(num_points) if self.beta[n]==1] 
-  90          self._pline.set_data(xp, yp) 
-  91           
-  92          xm = [x[n] for n in range(num_points) if self.beta[n]==-1] 
-  93          ym = [y[n] for n in range(num_points) if self.beta[n]==-1] 
-  94          self._mline.set_data(xm, ym) 
-  95           
-  96          xz = [x[n] for n in range(num_points) if self.beta[n]==0] 
-  97          yz = [y[n] for n in range(num_points) if self.beta[n]==0] 
-  98          self._zline.set_data(xz, yz) 
-  99           
- 100          if len(x)-1 < self.gridgen_options['ul_idx']: 
- 101              self.gridgen_options['ul_idx'] = len(x)-1 
- 102          xs = x[self.gridgen_options['ul_idx']] 
- 103          ys = y[self.gridgen_options['ul_idx']] 
- 104          self._sline.set_data(xs, ys) 
-
 105       
-
 106 -    def remove_grid(self): 
-
 107          """Remove a generated grid from the BoundaryClick figure""" 
- 108          if hasattr(self, '_gridlines'): 
- 109              for line in self._gridlines: 
- 110                  self._ax.lines.remove(line) 
- 111              delattr(self, '_gridlines') 
-
 112       
-
 113 -    def _draw_callback(self, event): 
-
 114          self._background = self._canvas.copy_from_bbox(self._ax.bbox) 
- 115          self._ax.draw_artist(self._poly) 
- 116          self._ax.draw_artist(self._pline) 
- 117          self._ax.draw_artist(self._mline) 
- 118          self._ax.draw_artist(self._zline) 
- 119          self._ax.draw_artist(self._sline) 
- 120          self._ax.draw_artist(self._line) 
- 121          self._canvas.blit(self._ax.bbox) 
-
 122       
-
 123 -    def _poly_changed(self, poly): 
-
 124          'this method is called whenever the polygon object is called' 
- 125          # only copy the artist props to the line (except visibility) 
- 126          vis = self._line.get_visible() 
- 127          Artist.update_from(self._line, poly) 
- 128          self._line.set_visible(vis)  # don't use the poly visibility state 
-
 129       
-
 130 -    def _get_ind_under_point(self, event): 
-
 131          'get the index of the vertex under point if within epsilon tolerance' 
- 132          try: 
- 133              x, y = zip(*self._poly.xy) 
- 134               
- 135              # display coords 
- 136              xt, yt = self._poly.get_transform().numerix_x_y(x, y) 
- 137              d = np.sqrt((xt-event.x)**2 + (yt-event.y)**2) 
- 138              indseq = np.nonzero(np.equal(d, np.amin(d))) 
- 139              ind = indseq[0] 
- 140           
- 141              if d[ind]>=self._epsilon: 
- 142                  ind = None 
- 143           
- 144              return ind 
- 145          except: 
- 146              # display coords 
- 147              xy = np.asarray(self._poly.xy) 
- 148              xyt = self._poly.get_transform().transform(xy) 
- 149              xt, yt = xyt[:, 0], xyt[:, 1] 
- 150              d = np.sqrt((xt-event.x)**2 + (yt-event.y)**2) 
- 151              indseq = np.nonzero(np.equal(d, np.amin(d)))[0] 
- 152              ind = indseq[0] 
- 153               
- 154              if d[ind]>=self._epsilon: 
- 155                  ind = None 
- 156               
- 157              return ind 
-
 158       
-
 159 -    def _button_press_callback(self, event): 
-
 160          'whenever a mouse button is pressed' 
- 161          # if not self._showverts: return 
- 162          if event.inaxes==None: return 
- 163          if event.button != 1: return 
- 164          self._ind = self._get_ind_under_point(event) 
-
 165       
-
 166 -    def _button_release_callback(self, event): 
-
 167          'whenever a mouse button is released' 
- 168          # if not self._showverts: return 
- 169          if event.button != 1: return 
- 170          self._ind = None 
-
 171       
-
 172 -    def _key_press_callback(self, event): 
-
 173          'whenever a key is pressed' 
- 174          if not event.inaxes: return 
- 175          if event.key=='shift': return 
- 176           
- 177          if event.key=='t': 
- 178              self._showbetas = not self._showbetas 
- 179              self._line.set_visible(self._showbetas) 
- 180              self._pline.set_visible(self._showbetas) 
- 181              self._mline.set_visible(self._showbetas) 
- 182              self._zline.set_visible(self._showbetas) 
- 183              self._sline.set_visible(self._showbetas) 
- 184          elif event.key=='d': 
- 185              ind = self._get_ind_under_point(event) 
- 186              if ind is not None: 
- 187                  self._poly.xy = [tup for i,tup in enumerate(self._poly.xy) \ 
- 188                                   if i!=ind] 
- 189                  self._line.set_data(zip(*self._poly.xy)) 
- 190                  self.beta = [beta for i,beta in enumerate(self.beta) \ 
- 191                               if i!=ind] 
- 192          elif event.key=='p': 
- 193              ind = self._get_ind_under_point(event) 
- 194              if ind is not None: 
- 195                  self.beta[ind] = 1.0 
- 196          elif event.key=='m': 
- 197              ind = self._get_ind_under_point(event) 
- 198              if ind is not None: 
- 199                  self.beta[ind] = -1.0 
- 200          elif event.key=='z': 
- 201              ind = self._get_ind_under_point(event) 
- 202              if ind is not None: 
- 203                  self.beta[ind] = 0.0 
- 204          elif event.key=='s': 
- 205              ind = self._get_ind_under_point(event) 
- 206              if ind is not None: 
- 207                  self.gridgen_options['ul_idx'] = ind 
- 208          elif event.key=='i': 
- 209              xys = self._poly.get_transform().transform(self._poly.xy) 
- 210              p = event.x, event.y # display coords 
- 211              for i in range(len(xys)-1): 
- 212                  s0 = xys[i] 
- 213                  s1 = xys[i+1] 
- 214                  d = dist_point_to_segment(p, s0, s1) 
- 215                  if d<=self._epsilon: 
- 216                      self._poly.xy = np.array( 
- 217                          list(self._poly.xy[:i+1]) + 
- 218                          [(event.xdata, event.ydata)] + 
- 219                          list(self._poly.xy[i+1:])) 
- 220                      self._line.set_data(zip(*self._poly.xy)) 
- 221                      self.beta.insert(i+1, 0) 
- 222                      break 
- 223              s0 = xys[-1] 
- 224              s1 = xys[0] 
- 225              d = dist_point_to_segment(p, s0, s1) 
- 226              if d<=self._epsilon: 
- 227                  self._poly.xy = np.array( 
- 228                      list(self._poly.xy) + 
- 229                      [(event.xdata, event.ydata)]) 
- 230                  self._line.set_data(zip(*self._poly.xy)) 
- 231                  self.beta.append(0) 
- 232          elif event.key=='G' or event.key == '1': 
- 233              options = deepcopy(self.gridgen_options) 
- 234              shp = options.pop('shp') 
- 235              if self.proj is None: 
- 236                  x = self.x 
- 237                  y = self.y 
- 238                  self.grd = Gridgen(x, y, self.beta, shp, 
- 239                                     proj=self.proj, **options) 
- 240              else: 
- 241                  lon, lat = self.proj(self.x, self.y, inverse=True) 
- 242                  self.grd = Gridgen(lon, lat, self.beta, shp,  
- 243                                     proj=self.proj, **options) 
- 244              self.remove_grid() 
- 245              self._showgrid = True 
- 246              gridlineprops = {'linestyle':'-', 'color':'k', 'lw':0.2} 
- 247              self._gridlines = [] 
- 248              for line in self._ax._get_lines(*(self.grd.x, self.grd.y), 
- 249                                              **gridlineprops): 
- 250                  self._ax.add_line(line) 
- 251                  self._gridlines.append(line) 
- 252              for line in self._ax._get_lines(*(self.grd.x.T, self.grd.y.T), 
- 253                                              **gridlineprops): 
- 254                  self._ax.add_line(line) 
- 255                  self._gridlines.append(line) 
- 256          elif event.key=='T' or event.key == '2': 
- 257              self._showgrid = not self._showgrid 
- 258              if hasattr(self, '_gridlines'): 
- 259                  for line in self._gridlines: 
- 260                      line.set_visible(self._showgrid) 
- 261           
- 262          self._update_beta_lines() 
- 263          self._draw_callback(event) 
- 264          self._canvas.draw() 
-
 265       
-
 266 -    def _motion_notify_callback(self, event): 
-
 267          'on mouse movement' 
- 268          # if not self._showverts: return 
- 269          if self._ind is None: return 
- 270          if event.inaxes is None: return 
- 271          if event.button != 1: return 
- 272          x,y = event.xdata, event.ydata 
- 273          self._poly.xy[self._ind] = x, y 
- 274          if self._ind == 0: 
- 275              self._poly.xy[-1] = x, y 
- 276           
- 277          x, y = zip(*self._poly.xy) 
- 278          self._line.set_data(x[:-1], y[:-1]) 
- 279          self._update_beta_lines() 
- 280           
- 281          self._canvas.restore_region(self._background) 
- 282          self._ax.draw_artist(self._poly) 
- 283          self._ax.draw_artist(self._pline) 
- 284          self._ax.draw_artist(self._mline) 
- 285          self._ax.draw_artist(self._zline) 
- 286          self._ax.draw_artist(self._sline) 
- 287          self._ax.draw_artist(self._line) 
- 288          self._canvas.blit(self._ax.bbox) 
-
 289       
- 290       
-
 291 -    def __init__(self, x, y=None, beta=None, ax=None, proj=None,  
- 292                   **gridgen_options): 
-
 293           
- 294          if isinstance(x, str): 
- 295              bry_dict = np.load(x) 
- 296              x = bry_dict['x'] 
- 297              y = bry_dict['y'] 
- 298              beta = bry_dict['beta'] 
- 299           
- 300          assert len(x) >= 4, 'Boundary must have at least four points.' 
- 301           
- 302          if ax is None:  
- 303              ax = plt.gca() 
- 304           
- 305          self._ax = ax 
- 306           
- 307          self.proj = proj 
- 308           
- 309          # Set default gridgen option, and copy over specified options. 
- 310          self.gridgen_options = {'ul_idx': 0, 'shp': (32, 32)} 
- 311           
- 312          for key, value in gridgen_options.iteritems(): 
- 313              self.gridgen_options[key] = gridgen_options[key] 
- 314           
- 315          x = list(x); y = list(y) 
- 316          assert len(x)==len(y), 'arrays must be equal length' 
- 317           
- 318          if beta is None: 
- 319              self.beta = [0 for xi in x] 
- 320          else: 
- 321              assert len(x)==len(beta), 'beta must have same length as x and y' 
- 322              self.beta = list(beta) 
- 323           
- 324          self._line = Line2D(x, y, animated=True,  
- 325                              ls='-', color='k', alpha=0.5, lw=1) 
- 326          self._ax.add_line(self._line) 
- 327           
- 328          self._canvas = self._line.figure.canvas         
- 329           
- 330          self._poly = Polygon(self.verts, alpha=0.1, fc='k', animated=True) 
- 331          self._ax.add_patch(self._poly) 
- 332           
- 333          # Link in the lines that will show the beta values 
- 334          # pline for positive turns, mline for negative (minus) turns 
- 335          # otherwize zline (zero) for straight sections 
- 336          self._pline = Line2D([], [], marker='^', ms=12, mfc='g',\ 
- 337                               animated=True, lw=0) 
- 338          self._mline = Line2D([], [], marker='v', ms=12, mfc='r',\ 
- 339                               animated=True, lw=0) 
- 340          self._zline = Line2D([], [], marker='o', mfc='k', animated=True, lw=0) 
- 341          self._sline = Line2D([], [], marker='s', mfc='k', animated=True, lw=0) 
- 342           
- 343          self._update_beta_lines() 
- 344          self._ax.add_artist(self._pline) 
- 345          self._ax.add_artist(self._mline) 
- 346          self._ax.add_artist(self._zline) 
- 347          self._ax.add_artist(self._sline) 
- 348           
- 349          # get the canvas and connect the callback events 
- 350          cid = self._poly.add_callback(self._poly_changed) 
- 351          self._ind = None # the active vert 
- 352           
- 353          self._canvas.mpl_connect('draw_event', self._draw_callback) 
- 354          self._canvas.mpl_connect('button_press_event',\ 
- 355                                   self._button_press_callback) 
- 356          self._canvas.mpl_connect('key_press_event', self._key_press_callback) 
- 357          self._canvas.mpl_connect('button_release_event',\ 
- 358                                   self._button_release_callback) 
- 359          self._canvas.mpl_connect('motion_notify_event',\ 
- 360                                   self._motion_notify_callback) 
-
 361       
-
 362 -    def save_bry(self, bry_file='bry.pickle'): 
-
 363          f = open(bry_file, 'wb') 
- 364          bry_dict = {'x': self.x, 'y': self.y, 'beta': self.beta} 
- 365          cPickle.dump(bry_dict, f, protocol=-1) 
- 366          f.close() 
-
 367       
-
 368 -    def load_bry(self, bry_file='bry.pickle'): 
-
 369          bry_dict = np.load(bry_file) 
- 370          x = bry_dict['x'] 
- 371          y = bry_dict['y'] 
- 372          self._line.set_data(x, y) 
- 373          self.beta = bry_dict['beta'] 
- 374          if hasattr(self, '_poly'): 
- 375              self._poly.xy = zip(x, y) 
- 376              self._update_beta_lines() 
- 377              self._draw_callback(None) 
- 378              self._canvas.draw() 
-
 379       
-
 380 -    def save_grid(self, grid_file='grid.pickle'): 
-
 381          f = open(grid_file, 'wb') 
- 382          cPickle.dump(self.grd, f, protocol=-1) 
- 383          f.close() 
-
 384       
-
 385 -    def _get_verts(self): return zip(self.x, self.y) 
-
 386      verts = property(_get_verts)     
-
 387 -    def get_xdata(self): return self._line.get_xdata() 
-
 388      x = property(get_xdata) 
-
 389 -    def get_ydata(self): return self._line.get_ydata() 
-
 390      y = property(get_ydata) 
-
 391       
- 392   
- 393   
-
 394 -def _approximate_erf(x): 
-
 395      ''' 
- 396      Return approximate solution to error function 
- 397      see http://en.wikipedia.org/wiki/Error_function 
- 398      ''' 
- 399      a = -(8*(np.pi-3.0)/(3.0*np.pi*(np.pi-4.0))) 
- 400      return np.sign(x) * \ 
- 401             np.sqrt(1.0 - np.exp( -x**2*(4.0/np.pi+a*x*x)/(1.0+a*x*x) )) 
-
 402       
- 403   
-
 404 -class _Focus_x(object): 
-
 405      """ 
- 406      Return a transformed, uniform grid, focused in the x-direction 
- 407       
- 408      This class may be called with a uniform grid, with limits from [0, 1], to 
- 409      create a focused grid in the x-directions centered about xo. The output 
- 410      grid is also uniform from [0, 1] in both x and y. 
- 411       
- 412      Parameters 
- 413      ---------- 
- 414      xo : float 
- 415          Location about which to focus grid 
- 416      factor : float 
- 417          amount to focus grid. Creates cell sizes that are factor smaller in 
- 418          the focused 
- 419          region. 
- 420      Rx : float 
- 421          Lateral extent of focused region, similar to a lateral spatial scale 
- 422          for the focusing region. 
- 423       
- 424      Returns 
- 425      ------- 
- 426      foc : class 
- 427          The class may be called with arguments of a grid. The returned 
- 428          transformed grid (x, y) will be focused as per the parameters above. 
- 429      """ 
- 430       
-
 431 -    def __init__(self, xo, factor=2.0, Rx=0.1): 
-
 432          self.xo = xo 
- 433          self.factor = factor 
- 434          self.Rx = Rx 
-
 435       
-
 436 -    def __call__(self, x, y): 
-
 437          x = np.asarray(x) 
- 438          y = np.asarray(y) 
- 439          assert not np.any(x>1.0) or not np.any(x<0.0)  \ 
- 440              or not np.any(y>1.0) or not np.any(x<0.0), \ 
- 441                  'x and y must both be within the range [0, 1].' 
- 442           
- 443          alpha = 1.0 - 1.0/self.factor 
- 444          def xf(x): 
- 445              return x - 0.5*( np.sqrt(np.pi)*self.Rx*alpha 
- 446                              *_approximate_erf((x-self.xo)/self.Rx) ) 
-
 447           
- 448          xf0 = xf(0.0); xf1 = xf(1.0) 
- 449           
- 450          return (xf(x)-xf0)/(xf1-xf0), y 
-
 451   
-
 452 -class _Focus_y(object): 
-
 453      """ 
- 454      Return a transformed, uniform grid, focused in the y-direction 
- 455       
- 456      This class may be called with a uniform grid, with limits from [0, 1],  
- 457      to create a focused grid in the y-directions centered about yo.  
- 458      The output grid is also uniform from [0, 1] in both x and y. 
- 459       
- 460      Parameters 
- 461      ---------- 
- 462      yo : float 
- 463          Location about which to focus grid 
- 464      factor : float 
- 465          amount to focus grid. Creates cell sizes that are factor  
- 466          smaller in the focused region. 
- 467      Ry : float 
- 468          Lateral extent of focused region, similar to a lateral  
- 469          spatial scale for the focusing region. 
- 470       
- 471      Returns 
- 472      ------- 
- 473      foc : class 
- 474          The class may be called with arguments of a grid. The returned  
- 475          transformed grid (x, y) will be focused as per the parameters above. 
- 476      """ 
- 477       
-
 478 -    def __init__(self, yo, factor=2.0, Ry=0.1): 
-
 479          self.yo = yo 
- 480          self.factor = factor 
- 481          self.Ry = Ry 
-
 482       
-
 483 -    def __call__(self, x, y): 
-
 484          x = np.asarray(x) 
- 485          y = np.asarray(y) 
- 486          assert not np.any(x>1.0) or not np.any(x<0.0)  \ 
- 487              or not np.any(y>1.0) or not np.any(x<0.0), \ 
- 488                  'x and y must both be within the range [0, 1].' 
- 489           
- 490          alpha = 1.0 - 1.0/self.factor 
- 491           
- 492          def yf(y): 
- 493              return y - 0.5*( np.sqrt(np.pi)*self.Ry*alpha  
- 494                              *_approximate_erf((y-self.yo)/self.Ry) ) 
-
 495           
- 496          yf0 = yf(0.0); yf1 = yf(1.0) 
- 497           
- 498          return x, (yf(y)-yf0)/(yf1-yf0) 
-
 499   
-
 500 -class Focus(object): 
-
 501      """ 
- 502      Return a container for a sequence of Focus objects 
- 503       
- 504      foc = Focus() 
- 505       
- 506      The sequence is populated by using the 'add_focus_x' and 'add_focus_y' 
- 507      methods. These methods define a point ('xo' or 'yo'), around witch to 
- 508      focus, a focusing factor of 'focus', and x and y extent of focusing given 
- 509      by Rx or Ry. The region of focusing will be approximately Gausian, and the 
- 510      resolution will be increased by approximately the value of factor. 
- 511       
- 512      Methods 
- 513      ------- 
- 514      foc.add_focus_x(xo, factor=2.0, Rx=0.1) 
- 515      foc.add_focus_y(yo, factor=2.0, Ry=0.1) 
- 516       
- 517      Calls to the object return transformed coordinates: 
- 518          xf, yf = foc(x, y) 
- 519      where x and y must be within [0, 1], and are typically a uniform, 
- 520      normalized grid. The focused grid will be the result of applying each of 
- 521      the focus elements in the sequence they are added to the series. 
- 522       
- 523       
- 524      EXAMPLES 
- 525      -------- 
- 526       
- 527      >>> foc = pyroms.grid.Focus() 
- 528      >>> foc.add_focus_x(0.2, factor=3.0, Rx=0.2) 
- 529      >>> foc.add_focus_y(0.6, factor=5.0, Ry=0.35) 
- 530       
- 531      >>> x, y = np.mgrid[0:1:3j,0:1:3j] 
- 532      >>> xf, yf = foc(x, y) 
- 533       
- 534      >>> print xf 
- 535      [[ 0.          0.          0.        ] 
- 536       [ 0.36594617  0.36594617  0.36594617] 
- 537       [ 1.          1.          1.        ]] 
- 538      >>> print yf 
- 539      [[ 0.          0.62479833  1.        ] 
- 540       [ 0.          0.62479833  1.        ] 
- 541       [ 0.          0.62479833  1.        ]] 
- 542      """ 
-
 543 -    def __init__(self): 
-
 544          self._focuspoints = [] 
-
 545       
-
 546 -    def add_focus_x(self, xo, factor=2.0, Rx=0.1): 
-
 547          """docstring for add_point""" 
- 548          self._focuspoints.append(_Focus_x(xo, factor, Rx)) 
-
 549       
-
 550 -    def add_focus_y(self, yo, factor=2.0, Ry=0.1): 
-
 551          """docstring for add_point""" 
- 552          self._focuspoints.append(_Focus_y(yo, factor, Ry)) 
-
 553       
-
 554 -    def __call__(self, x, y): 
-
 555          """docstring for __call__""" 
- 556          for focuspoint in self._focuspoints: 
- 557              x, y = focuspoint(x, y) 
- 558          return x, y 
-
 559   
- 560   
- 561   
-
 562 -class CGrid(object): 
-
 563      """ 
- 564      Curvilinear Arakawa C-Grid 
- 565        
- 566      The basis for the CGrid class are two arrays defining the verticies of the 
- 567      grid in Cartesian (for geographic coordinates, see CGrid_geo). An optional 
- 568      mask may be defined on the cell centers. Other Arakawa C-grid properties, 
- 569      such as the locations of the cell centers (rho-points), cell edges (u and 
- 570      v velocity points), cell widths (dx and dy) and other metrics (angle, 
- 571      dmde, and dndx) are all calculated internally from the vertex points. 
- 572        
- 573      Input vertex arrays may be either type np.array or np.ma.MaskedArray. If 
- 574      masked arrays are used, the mask will be a combination of the specified 
- 575      mask (if given) and the masked locations. 
- 576        
- 577      EXAMPLES: 
- 578      -------- 
- 579        
- 580      >>> x, y = mgrid[0.0:7.0, 0.0:8.0] 
- 581      >>> x = np.ma.masked_where( (x<3) & (y<3), x) 
- 582      >>> y = np.ma.MaskedArray(y, x.mask) 
- 583      >>> grd = pyroms.grid.CGrid(x, y) 
- 584      >>> print grd.x_rho 
- 585      [[-- -- -- 0.5 0.5 0.5 0.5] 
- 586       [-- -- -- 1.5 1.5 1.5 1.5] 
- 587       [-- -- -- 2.5 2.5 2.5 2.5] 
- 588       [3.5 3.5 3.5 3.5 3.5 3.5 3.5] 
- 589       [4.5 4.5 4.5 4.5 4.5 4.5 4.5] 
- 590       [5.5 5.5 5.5 5.5 5.5 5.5 5.5]] 
- 591      >>> print grd.mask 
- 592      [[ 0.  0.  0.  1.  1.  1.  1.] 
- 593       [ 0.  0.  0.  1.  1.  1.  1.] 
- 594       [ 0.  0.  0.  1.  1.  1.  1.] 
- 595       [ 1.  1.  1.  1.  1.  1.  1.] 
- 596       [ 1.  1.  1.  1.  1.  1.  1.] 
- 597       [ 1.  1.  1.  1.  1.  1.  1.]] 
- 598      """ 
- 599       
-
 600 -    def __init__(self, x_vert, y_vert, x_rho=None, y_rho=None, x_u=None, y_u=None, x_v=None, y_v=None, \ 
- 601                      x_psi=None, y_psi=None, dx=None, dy=None, dndx=None, dmde=None, angle_rho=None): 
-
 602                   
- 603          assert np.ndim(x_vert)==2 and np.ndim(y_vert)==2 and np.shape(x_vert)==np.shape(y_vert), \ 
- 604              'x and y must be 2D arrays of the same size.' 
- 605           
- 606          if np.any(np.isnan(x_vert)) or np.any(np.isnan(y_vert)): 
- 607              x_vert = np.ma.masked_where( (isnan(x_vert)) | (isnan(y_vert)) , x_vert) 
- 608              y_vert = np.ma.masked_where( (isnan(x_vert)) | (isnan(y_vert)) , y_vert) 
- 609               
- 610          self.x_vert = x_vert 
- 611          self.y_vert = y_vert 
- 612   
- 613          self.f = None 
- 614          self.spherical = 'F' 
- 615           
- 616          mask_shape = tuple([n-1 for n in self.x_vert.shape]) 
- 617          self.mask_rho = np.ones(mask_shape, dtype='d') 
- 618           
- 619          # If maskedarray is given for verticies, modify the mask such that  
- 620          # non-existant grid points are masked.  A cell requires all four 
- 621          # verticies to be defined as a water point. 
- 622          if isinstance(self.x_vert, np.ma.MaskedArray): 
- 623              mask = (self.x_vert.mask[:-1,:-1] | self.x_vert.mask[1:,:-1] | \ 
- 624                      self.x_vert.mask[:-1,1:] | self.x_vert.mask[1:,1:]) 
- 625              self.mask_rho = np.asarray(~(~np.bool_(self.mask_rho) | mask), dtype='d') 
- 626           
- 627          if isinstance(self.y_vert, np.ma.MaskedArray): 
- 628              mask = (self.y_vert.mask[:-1,:-1] | self.y_vert.mask[1:,:-1] | \ 
- 629                      self.y_vert.mask[:-1,1:] | self.y_vert.mask[1:,1:]) 
- 630              self.mask_rho = np.asarray(~(~np.bool_(self.mask_rho) | mask), dtype='d') 
- 631   
- 632          if x_rho is None or y_rho is None or x_u is None or y_u is None or \ 
- 633              x_v is None or y_v is None or x_psi is None or y_psi is None: 
- 634              self._calculate_subgrids() 
- 635          else: 
- 636              self.x_rho = x_rho 
- 637              self.y_rho = y_rho 
- 638              self.x_u = x_u 
- 639              self.y_u = y_u 
- 640              self.x_v = x_v 
- 641              self.y_v = y_v 
- 642              self.x_psi = x_psi 
- 643              self.y_psi = y_psi 
- 644   
- 645          if dx is None or dy is None: 
- 646              self._calculate_metrics() 
- 647          else: 
- 648              self.dx = dx 
- 649              self.dy = dy 
- 650   
- 651          self.xl = np.maximum(self.dx[0,:].sum(), self.dx[-1,:].sum()) 
- 652          self.el = np.maximum(self.dy[:,0].sum(), self.dy[:,-1].sum()) 
- 653   
- 654          if dndx is None or dmde is None: 
- 655              self._calculate_derivative_metrics() 
- 656          else: 
- 657              self.dndx = dndx 
- 658              self.dmde = dmde 
- 659   
- 660          if angle_rho is None: 
- 661              self._calculate_angle_rho() 
- 662          else: 
- 663              self.angle_rho = angle_rho 
- 664   
- 665          self._calculate_angle() 
-
 666      
- 667       
-
 668 -    def _calculate_subgrids(self): 
-
 669          self.x_rho = 0.25*(self.x_vert[1:,1:]+self.x_vert[1:,:-1]+ \ 
- 670                             self.x_vert[:-1,1:]+self.x_vert[:-1,:-1]) 
- 671          self.y_rho = 0.25*(self.y_vert[1:,1:]+self.y_vert[1:,:-1]+ \ 
- 672                             self.y_vert[:-1,1:]+self.y_vert[:-1,:-1]) 
- 673          self.x_u = 0.5*(self.x_vert[:-1,1:-1] + self.x_vert[1:,1:-1]) 
- 674          self.y_u = 0.5*(self.y_vert[:-1,1:-1] + self.y_vert[1:,1:-1]) 
- 675          self.x_v = 0.5*(self.x_vert[1:-1,:-1] + self.x_vert[1:-1,1:]) 
- 676          self.y_v = 0.5*(self.y_vert[1:-1,:-1] + self.y_vert[1:-1,1:]) 
- 677          self.x_psi = self.x_vert[1:-1,1:-1] 
- 678          self.y_psi = self.y_vert[1:-1,1:-1] 
-
 679       
-
 680 -    def _calculate_metrics(self): 
-
 681          'Calculates pm, pn, dndx, dmde from x_vert and y_vert' 
- 682          x_temp = 0.5*(self.x_vert[1:,:]+self.x_vert[:-1,:]) 
- 683          y_temp = 0.5*(self.y_vert[1:,:]+self.y_vert[:-1,:]) 
- 684          self.dx = np.sqrt(np.diff(x_temp, axis=1)**2 + np.diff(y_temp, axis=1)**2) 
- 685          x_temp = 0.5*(self.x_vert[:,1:]+self.x_vert[:,:-1]) 
- 686          y_temp = 0.5*(self.y_vert[:,1:]+self.y_vert[:,:-1]) 
- 687          self.dy = np.sqrt(np.diff(x_temp, axis=0)**2 + np.diff(y_temp, axis=0)**2) 
-
 688   
- 690          if isinstance(self.dy, np.ma.MaskedArray): 
- 691              self.dndx = np.ma.zeros(self.x_rho.shape, dtype='d') 
- 692          else: 
- 693              self.dndx = np.zeros(self.x_rho.shape, dtype='d') 
- 694           
- 695          if isinstance(self.dx, np.ma.MaskedArray): 
- 696              self.dmde = np.ma.zeros(self.x_rho.shape, dtype='d') 
- 697          else: 
- 698              self.dmde = np.zeros(self.x_rho.shape, dtype='d') 
- 699           
- 700          self.dndx[1:-1,1:-1] = 0.5*(self.dy[1:-1,2:] - self.dy[1:-1,:-2]) 
- 701          self.dmde[1:-1,1:-1] = 0.5*(self.dx[2:,1:-1] - self.dx[:-2,1:-1]) 
-
 702   
-
 703 -    def _calculate_angle(self):      
-
 704          if isinstance(self.x_vert, np.ma.MaskedArray) or \ 
- 705             isinstance(self.y_vert, np.ma.MaskedArray): 
- 706              self.angle = np.ma.zeros(self.x_vert.shape, dtype='d') 
- 707          else: 
- 708              self.angle = np.zeros(self.x_vert.shape, dtype='d') 
- 709           
- 710          angle_ud = np.arctan2(np.diff(self.y_vert, axis=1), np.diff(self.x_vert, axis=1)) 
- 711          angle_lr = np.arctan2(np.diff(self.y_vert, axis=0), np.diff(self.x_vert, axis=0)) - np.pi/2.0         
- 712          # domain center 
- 713          self.angle[1:-1,1:-1] = 0.25*(angle_ud[1:-1,1:]+angle_ud[1:-1,:-1]\ 
- 714                                       +angle_lr[1:,1:-1]+angle_lr[:-1,1:-1]) 
- 715          # edges 
- 716          self.angle[0,1:-1] = (1.0/3.0)*(angle_lr[0,1:-1]+angle_ud[0,1:]+angle_ud[0,:-1]) 
- 717          self.angle[-1,1:-1] = (1.0/3.0)*(angle_lr[-1,1:-1]+angle_ud[-1,1:]+angle_ud[-1,:-1]) 
- 718          self.angle[1:-1,0] = (1.0/3.0)*(angle_ud[1:-1,0]+angle_lr[1:,0]+angle_lr[:-1,0]) 
- 719          self.angle[1:-1,-1] = (1.0/3.0)*(angle_ud[1:-1,-1]+angle_lr[1:,-1]+angle_lr[:-1,-1]) 
- 720          #conrers 
- 721          self.angle[0,0] = 0.5*(angle_lr[0,0]+angle_ud[0,0]) 
- 722          self.angle[0,-1] = 0.5*(angle_lr[0,-1]+angle_ud[0,-1]) 
- 723          self.angle[-1,0] = 0.5*(angle_lr[-1,0]+angle_ud[-1,0]) 
- 724          self.angle[-1,-1] = 0.5*(angle_lr[-1,-1]+angle_ud[-1,-1]) 
- 725           
-
 726 -    def _calculate_angle_rho(self):  
-
 727          self.angle_rho = np.arctan2(np.diff(0.5*(self.y_vert[1:,:]+self.y_vert[:-1,:])), \ 
- 728                                      np.diff(0.5*(self.x_vert[1:,:]+self.x_vert[:-1,:])))         
- 729       
-
 730 -    def calculate_orthogonality(self): 
-
 731          ''' 
- 732          Calculate orthogonality error in radians 
- 733          ''' 
- 734          z = self.x_vert + 1j*self.y_vert 
- 735          du = np.diff(z, axis=1); du = (du/abs(du))[:-1,:] 
- 736          dv = np.diff(z, axis=0); dv = (dv/abs(dv))[:,:-1] 
- 737          ang1 = np.arccos(du.real*dv.real + du.imag*dv.imag) 
- 738          du = np.diff(z, axis=1); du = (du/abs(du))[1:,:] 
- 739          dv = np.diff(z, axis=0); dv = (dv/abs(dv))[:,:-1] 
- 740          ang2 = np.arccos(du.real*dv.real + du.imag*dv.imag) 
- 741          du = np.diff(z, axis=1); du = (du/abs(du))[:-1,:] 
- 742          dv = np.diff(z, axis=0); dv = (dv/abs(dv))[:,1:] 
- 743          ang3 = np.arccos(du.real*dv.real + du.imag*dv.imag) 
- 744          du = np.diff(z, axis=1); du = (du/abs(du))[1:,:] 
- 745          dv = np.diff(z, axis=0); dv = (dv/abs(dv))[:,1:] 
- 746          ang4 = np.arccos(du.real*dv.real + du.imag*dv.imag) 
- 747          ang = np.mean([abs(ang1), abs(ang2), abs(ang3), abs(ang4)], axis=0) 
- 748          ang = (ang-np.pi/2.0) 
- 749          return ang 
-
 750       
-
 751 -    def mask_polygon(self, polyverts, mask_value=0.0): 
-
 752          """ 
- 753          Mask Cartesian points contained within the polygon defined by polyverts 
- 754           
- 755          A cell is masked if the cell center (x_rho, y_rho) is within the 
- 756          polygon. Other sub-masks (mask_u, mask_v, and mask_psi) are updated 
- 757          automatically. 
- 758           
- 759          mask_value [=0.0] may be specified to alter the value of the mask set 
- 760          within the polygon.  E.g., mask_value=1 for water points. 
- 761          """ 
- 762           
- 763          polyverts = np.asarray(polyverts) 
- 764          assert polyverts.ndim == 2, \ 
- 765              'polyverts must be a 2D array, or a similar sequence' 
- 766          assert polyverts.shape[1] == 2, \ 
- 767              'polyverts must be two columns of points' 
- 768          assert polyverts.shape[0] > 2, \ 
- 769              'polyverts must contain at least 3 points' 
- 770           
- 771          mask = self.mask_rho 
- 772          inside = points_inside_poly( 
- 773              np.vstack( (self.x_rho.flatten(), self.y_rho.flatten()) ).T, 
- 774              polyverts) 
- 775          if np.any(inside): 
- 776              self.mask_rho.flat[inside] = mask_value 
-
 777       
-
 778 -    def _get_mask_u(self): 
-
 779          return self.mask_rho[:,1:]*self.mask_rho[:,:-1] 
-
 780       
-
 781 -    def _get_mask_v(self): 
-
 782          return self.mask_rho[1:,:]*self.mask_rho[:-1,:] 
-
 783       
-
 784 -    def _get_mask_psi(self): 
-
 785          return self.mask_rho[1:,1:]*self.mask_rho[:-1,1:]* \ 
- 786                 self.mask_rho[1:,:-1]*self.mask_rho[:-1,:-1] 
-
 787   
-
 788 -    def _set_mask_rho(self, mask_rho): 
-
 789          self.mask_rho = mask_rho 
-
 790    
- 791      x = property(lambda self: self.x_vert, None, None, 'Return x_vert') 
- 792      y = property(lambda self: self.y_vert, None, None, 'Return x_vert') 
- 793      mask = property(lambda self: self.mask_rho, _set_mask_rho, None, 'Return mask_rho') 
- 794      mask_u   = property(_get_mask_u, None, None, 'Return mask_u') 
- 795      mask_v   = property(_get_mask_v, None, None, 'Return mask_v') 
- 796      mask_psi = property(_get_mask_psi, None, None, 'Return mask_psi') 
- 797   
- 798   
-
 799 -class CGrid_geo(CGrid): 
-
 800      """ 
- 801      Curvilinear Arakawa C-grid defined in geographic coordinates 
- 802       
- 803      For a geographic grid, a projection may be specified, or The default 
- 804      projection for will be defined by the matplotlib.toolkits.Basemap 
- 805      projection: 
- 806       
- 807      proj = Basemap(projection='merc', resolution=None, lat_ts=0.0) 
- 808       
- 809      For a geographic grid, the cell widths are determined by the great 
- 810      circle distances. Angles, however, are defined using the projected 
- 811      coordinates, so a projection that conserves angles must be used. This 
- 812      means typically either Mercator (projection='merc') or Lambert 
- 813      Conformal Conic (projection='lcc'). 
- 814      """ 
-
 815 -    def _calculate_metrics(self): 
-
 816          # calculate metrics based on x and y grid 
- 817          super(CGrid_geo, self)._calculate_metrics() 
- 818   
- 819          # optionally calculate dx and dy based on great circle distances 
- 820          # for more accurate cell sizes. 
- 821          if self.use_gcdist: 
- 822              geod = pyproj.Geod(ellps=self.ellipse) 
- 823              az_forward, az_back, dx = geod.inv(self.lon[:,1:],  self.lat[:,1:], \ 
- 824                                                 self.lon[:,:-1], self.lat[:,:-1]) 
- 825              self.dx = 0.5*(dx[1:,:]+dx[:-1,:]) 
- 826              self.pm = 1.0/self.dx 
- 827              az_forward, az_back, dy = geod.inv(self.lon[1:,:],  self.lat[1:,:], \ 
- 828                                                 self.lon[:-1,:], self.lat[:-1,:]) 
- 829              self.dy = 0.5*(dy[:,1:]+dy[:,:-1]) 
- 830              self.pn = 1.0/self.dy 
-
 831   
- 832   
-
 834          if isinstance(self.dy, np.ma.MaskedArray): 
- 835              self.dndx = np.ma.zeros(self.dy.shape, dtype='d') 
- 836          else: 
- 837              self.dndx = np.zeros(self.dy.shape, dtype='d') 
- 838           
- 839          if isinstance(self.dx, np.ma.MaskedArray): 
- 840              self.dmde = np.ma.zeros(self.dx.shape, dtype='d') 
- 841          else: 
- 842              self.dmde = np.zeros(self.dx.shape, dtype='d') 
- 843           
- 844          self.dndx[1:-1,1:-1] = 0.5*(self.dy[1:-1,2:] - self.dy[1:-1,:-2]) 
- 845          self.dmde[1:-1,1:-1] = 0.5*(self.dx[2:,1:-1] - self.dx[:-2,1:-1]) 
-
 846           
-
 847 -    def _calculate_angle_rho(self): 
-
 848          if isinstance(self.lon, np.ma.MaskedArray) or \ 
- 849             isinstance(self.lat, np.ma.MaskedArray): 
- 850              self.angle_rho = np.ma.zeros(self.lon.shape, dtype='d') 
- 851          else: 
- 852              self.angle_rho = np.zeros(self.lon.shape, dtype='d') 
- 853   
- 854          # calculate metrics based on x and y grid 
- 855          super(CGrid_geo, self)._calculate_angle_rho() 
- 856   
- 857          # optionally calculate dx and dy based on great circle distances 
- 858          # for more accurate cell sizes. 
- 859          if self.use_gcdist: 
- 860              geod = pyproj.Geod(ellps=self.ellipse) 
- 861              az_forward, az_back, dx = geod.inv(self.lon[:,:-1], self.lat[:,:-1], \ 
- 862                                                 self.lon[:,1:], self.lat[:,1:]) 
- 863   
- 864              angle = 0.5 * (az_forward[1:,:] + az_forward[:-1,:]) 
- 865              self.angle_rho = (90 - angle) * np.pi/180. 
-
 866   
- 867   
-
 868 -    def __init__(self, lon_vert, lat_vert, proj, use_gcdist=True, ellipse='WGS84', \ 
- 869                      lon_rho=None, lat_rho=None, lon_u=None, lat_u=None, \ 
- 870                      lon_v=None, lat_v=None, lon_psi=None, lat_psi=None, dx=None, dy=None, \ 
- 871                      dndx=None, dmde=None, angle_rho=None): 
-
 872   
- 873          x, y = proj(lon_vert, lat_vert) 
- 874          self.lon_vert = lon_vert 
- 875          self.lat_vert = lat_vert 
- 876          self.proj = proj 
- 877   
- 878          self.use_gcdist = use_gcdist 
- 879          self.ellipse = ellipse 
- 880   
- 881          if lon_rho is None or lat_rho is None or lon_u is None or lat_u is None or \ 
- 882               lon_v is None or lat_v is None or lon_psi is None or lat_psi is None: 
- 883   
- 884              super(CGrid_geo, self).__init__(x, y) 
- 885   
- 886              self.lon_rho, self.lat_rho = self.proj(self.x_rho, self.y_rho, 
- 887                                                     inverse=True) 
- 888              self.lon_u, self.lat_u = self.proj(self.x_u, self.y_u, inverse=True) 
- 889              self.lon_v, self.lat_v = self.proj(self.x_v, self.y_v, inverse=True) 
- 890              self.lon_psi, self.lat_psi = self.proj(self.x_psi, self.y_psi, 
- 891                                                     inverse=True) 
- 892          else: 
- 893              self.lon_rho = lon_rho 
- 894              self.lat_rho = lat_rho 
- 895              self.lon_u = lon_u 
- 896              self.lat_u = lat_u 
- 897              self.lon_v = lon_v 
- 898              self.lat_v = lat_v 
- 899              self.lon_psi = lon_psi 
- 900              self.lat_psi = lat_psi 
- 901              #calculate cartesian position 
- 902              self.x_vert, self.y_vert = proj(lon_vert, lat_vert) 
- 903              self.x_rho, self.y_rho = proj(lon_rho, lat_rho) 
- 904              self.x_u, self.y_u = proj(lon_u, lat_u) 
- 905              self.x_v, self.y_v = proj(lon_v, lat_v) 
- 906              self.x_psi, self.y_psi = proj(lon_psi, lat_psi) 
- 907   
- 908          if dx is None or dy is None: 
- 909              self._calculate_metrics() 
- 910          else: 
- 911              self.dx = dx 
- 912              self.dy = dy 
- 913   
- 914          self.xl = np.maximum(self.dx[0,:].sum(), self.dx[-1,:].sum()) 
- 915          self.el = np.maximum(self.dy[:,0].sum(), self.dy[:,-1].sum()) 
- 916   
- 917          if dndx is None or dmde is None: 
- 918              self._calculate_derivative_metrics() 
- 919          else: 
- 920              self.dndx = dndx 
- 921              self.dmde = dmde 
- 922   
- 923          if angle_rho is None: 
- 924              self._calculate_angle_rho() 
- 925          else: 
- 926              self.angle_rho = angle_rho 
- 927   
- 928          self.f = 2.0 * 7.29e-5 * np.sin(self.lat_rho * np.pi / 180.0) 
- 929          self.spherical = 'T' 
-
 930   
- 931   
-
 932 -    def mask_polygon_geo(lonlat_verts, mask_value=0.0): 
-
 933          lon, lat = zip(*lonlat_verts) 
- 934          x, y = proj(lon, lat, inverse=True) 
- 935          self.mask_polygon(zip(x, y), mask_value) 
-
 936       
- 937      lon = property(lambda self: self.lon_vert, None, None, 'Shorthand for lon_vert') 
- 938      lat = property(lambda self: self.lat_vert, None, None, 'Shorthand for lat_vert') 
-
 939           
- 940   
- 941   
-
 942 -class Gridgen(CGrid): 
-
 943      """ 
- 944      docstring for Gridgen 
- 945      """ 
- 946   
- 947       
-
 948 -    def generate_grid(self): 
-
 949           
- 950          if self._gn is not None: 
- 951              self._libgridgen.gridnodes_destroy(self._gn) 
- 952           
- 953          nbry = len(self.xbry) 
- 954           
- 955          nsigmas = ctypes.c_int(0) 
- 956          sigmas = ctypes.c_void_p(0) 
- 957          nrect = ctypes.c_int(0) 
- 958          xrect =  ctypes.c_void_p(0) 
- 959          yrect = ctypes.c_void_p(0) 
- 960           
- 961          if self.focus is None: 
- 962              ngrid = ctypes.c_int(0) 
- 963              xgrid = ctypes.POINTER(ctypes.c_double)() 
- 964              ygrid = ctypes.POINTER(ctypes.c_double)() 
- 965          else: 
- 966              y, x =  np.mgrid[0:1:self.ny*1j, 0:1:self.nx*1j] 
- 967              xgrid, ygrid = self.focus(x, y) 
- 968              ngrid = ctypes.c_int(xgrid.size) 
- 969              xgrid = (ctypes.c_double * xgrid.size)(*xgrid.flatten()) 
- 970              ygrid = (ctypes.c_double * ygrid.size)(*ygrid.flatten()) 
- 971           
- 972          self._gn = self._libgridgen.gridgen_generategrid2( 
- 973               ctypes.c_int(nbry),  
- 974               (ctypes.c_double * nbry)(*self.xbry),  
- 975               (ctypes.c_double * nbry)(*self.ybry),  
- 976               (ctypes.c_double * nbry)(*self.beta), 
- 977               ctypes.c_int(self.ul_idx),  
- 978               ctypes.c_int(self.nx),  
- 979               ctypes.c_int(self.ny),  
- 980               ngrid,  
- 981               xgrid,  
- 982               ygrid, 
- 983               ctypes.c_int(self.nnodes),  
- 984               ctypes.c_int(self.newton),  
- 985               ctypes.c_double(self.precision), 
- 986               ctypes.c_int(self.checksimplepoly),  
- 987               ctypes.c_int(self.thin),  
- 988               ctypes.c_int(self.nppe), 
- 989               ctypes.c_int(self.verbose), 
- 990               ctypes.byref(nsigmas),  
- 991               ctypes.byref(sigmas),  
- 992               ctypes.byref(nrect), 
- 993               ctypes.byref(xrect),  
- 994               ctypes.byref(yrect) ) 
- 995           
- 996          x = self._libgridgen.gridnodes_getx(self._gn) 
- 997          x = np.asarray([x[0][i] for i in range(self.ny*self.nx)]) 
- 998          # x = np.asarray([x[j][i] for j in range(self.ny) for i in range(self.nx)]) 
- 999          x.shape = (self.ny, self.nx) 
-1000           
-1001          y = self._libgridgen.gridnodes_gety(self._gn)     
-1002          y = np.asarray([y[0][i] for i in range(self.ny*self.nx)])             
-1003          # y = np.asarray([y[j][i] for j in range(self.ny) for i in range(self.nx)]) 
-1004          y.shape = (self.ny, self.nx) 
-1005           
-1006          if np.any(np.isnan(x)) or np.any(np.isnan(y)): 
-1007              x = np.ma.masked_where(np.isnan(x), x) 
-1008              y = np.ma.masked_where(np.isnan(y), y) 
-1009           
-1010          # if self.proj is not None: 
-1011          #     lon, lat = self.proj(x, y, inverse=True) 
-1012          #     super(Gridgen, self).__init__(lon, lat, proj=self.proj) 
-1013          # else: 
-1014          super(Gridgen, self).__init__(x, y) 
-
1015   
-1016   
-1017   
-
1018 -    def __init__(self, xbry, ybry, beta, shape, ul_idx=0, \ 
-1019                   focus=None, proj=None, \ 
-1020                   nnodes=14, precision=1.0e-12, nppe=3, \ 
-1021                   newton=True, thin=True, checksimplepoly=True, verbose=False): 
-
1022   
-1023          #self._libgridgen = np.ctypeslib.load_library('libgridgen',__file__) 
-1024          self._libgridgen = np.ctypeslib.load_library('libgridgen', pyroms.__path__[0]) 
-1025           
-1026          self._libgridgen.gridgen_generategrid2.restype = ctypes.c_void_p 
-1027          self._libgridgen.gridnodes_getx.restype = ctypes.POINTER(ctypes.POINTER(ctypes.c_double)) 
-1028          self._libgridgen.gridnodes_gety.restype = ctypes.POINTER(ctypes.POINTER(ctypes.c_double)) 
-1029          self._libgridgen.gridnodes_getnce1.restype = ctypes.c_int 
-1030          self._libgridgen.gridnodes_getnce2.restype = ctypes.c_int 
-1031          self._libgridgen.gridmap_build.restype = ctypes.c_void_p 
-1032           
-1033          self.xbry = np.asarray(xbry, dtype='d') 
-1034          self.ybry = np.asarray(ybry, dtype='d') 
-1035          self.beta = np.asarray(beta, dtype='d') 
-1036          assert self.beta.sum() == 4.0, 'sum of beta must be 4.0' 
-1037          self.shape = shape 
-1038          self.ny = shape[0] 
-1039          self.nx = shape[1] 
-1040          self.ul_idx = ul_idx 
-1041          self.focus = focus 
-1042          self.nnodes = nnodes 
-1043          self.precision = precision 
-1044          self.nppe = nppe 
-1045          self.newton = newton 
-1046          self.thin = thin 
-1047          self.checksimplepoly = checksimplepoly 
-1048          self.verbose = verbose 
-1049           
-1050          self.proj = proj 
-1051          if self.proj is not None: 
-1052              self.xbry, self.ybry = proj(self.xbry, self.ybry) 
-1053           
-1054          self._gn = None 
-1055          self.generate_grid() 
-
1056       
-
1057 -    def __del__(self): 
-
1058          """delete gridnode object upon deletion""" 
-1059          self._libgridgen.gridnodes_destroy(self._gn) 
-
1060   
-1061   
-
1062 -def rho_to_vert(xr, yr, pm, pn, ang): 
-
1063      Mp, Lp = xr.shape 
-1064      x = np.empty((Mp+1, Lp+1), dtype='d') 
-1065      y = np.empty((Mp+1, Lp+1), dtype='d') 
-1066      x[1:-1, 1:-1] = 0.25*(xr[1:,1:]+xr[1:,:-1]+xr[:-1,1:]+xr[:-1,:-1]) 
-1067      y[1:-1, 1:-1] = 0.25*(yr[1:,1:]+yr[1:,:-1]+yr[:-1,1:]+yr[:-1,:-1]) 
-1068       
-1069      # east side 
-1070      theta = 0.5*(ang[:-1,-1]+ang[1:,-1]) 
-1071      dx = 0.5*(1.0/pm[:-1,-1]+1.0/pm[1:,-1]) 
-1072      dy = 0.5*(1.0/pn[:-1,-1]+1.0/pn[1:,-1]) 
-1073      x[1:-1,-1] = x[1:-1,-2] + dx*np.cos(theta) 
-1074      y[1:-1,-1] = y[1:-1,-2] + dx*np.sin(theta) 
-1075       
-1076      # west side 
-1077      theta = 0.5*(ang[:-1,0]+ang[1:,0]) 
-1078      dx = 0.5*(1.0/pm[:-1,0]+1.0/pm[1:,0]) 
-1079      dy = 0.5*(1.0/pn[:-1,0]+1.0/pn[1:,0]) 
-1080      x[1:-1,0] = x[1:-1,1] - dx*np.cos(theta) 
-1081      y[1:-1,0] = y[1:-1,1] - dx*np.sin(theta) 
-1082       
-1083      # north side 
-1084      theta = 0.5*(ang[-1,:-1]+ang[-1,1:]) 
-1085      dx = 0.5*(1.0/pm[-1,:-1]+1.0/pm[-1,1:]) 
-1086      dy = 0.5*(1.0/pn[-1,:-1]+1.0/pn[-1,1:]) 
-1087      x[-1,1:-1] = x[-2,1:-1] - dy*np.sin(theta) 
-1088      y[-1,1:-1] = y[-2,1:-1] + dy*np.cos(theta) 
-1089       
-1090      # here we are now going to the south side.. 
-1091      theta = 0.5*(ang[0,:-1]+ang[0,1:]) 
-1092      dx = 0.5*(1.0/pm[0,:-1]+1.0/pm[0,1:]) 
-1093      dy = 0.5*(1.0/pn[0,:-1]+1.0/pn[0,1:]) 
-1094      x[0,1:-1] = x[1,1:-1] + dy*np.sin(theta) 
-1095      y[0,1:-1] = y[1,1:-1] - dy*np.cos(theta) 
-1096       
-1097      #Corners 
-1098      x[0,0] = 4.0*xr[0,0]-x[1,0]-x[0,1]-x[1,1] 
-1099      x[-1,0] = 4.0*xr[-1,0]-x[-2,0]-x[-1,1]-x[-2,1] 
-1100      x[0,-1] = 4.0*xr[0,-1]-x[0,-2]-x[1,-1]-x[1,-2] 
-1101      x[-1,-1] = 4.0*xr[-1,-1]-x[-2,-2]-x[-2,-1]-x[-1,-2] 
-1102       
-1103      y[0,0] = 4.0*yr[0,0]-y[1,0]-y[0,1]-y[1,1] 
-1104      y[-1,0] = 4.0*yr[-1,0]-y[-2,0]-y[-1,1]-y[-2,1] 
-1105      y[0,-1] = 4.0*yr[0,-1]-y[0,-2]-y[1,-1]-y[1,-2] 
-1106      y[-1,-1] = 4.0*yr[-1,-1]-y[-2,-2]-y[-2,-1]-y[-1,-2] 
-1107       
-1108      return x, y 
-
1109   
-1110   
-
1111 -def rho_to_vert_geo(lonr, latr, lonp, latp): 
-
1112      Mm, Lm = lonr.shape 
-1113      lon = np.zeros((Mm+1,Lm+1)) 
-1114      lat = np.zeros((Mm+1,Lm+1)) 
-1115   
-1116      lon[1:-1, 1:-1] = lonp[:,:] 
-1117      lat[1:-1, 1:-1] = latp[:,:] 
-1118   
-1119      #North edge 
-1120      lon[Mm,0:-2] = lonr[Mm-1,0:-1] - ( lonp[Mm-2,:] - lonr[Mm-1,0:-1] ) 
-1121      lon[Mm,-2:] = lonr[Mm-1,-2:] - ( lonp[Mm-2,-2:] - lonr[Mm-1,-2:] ) 
-1122      lat[Mm,0:-2] = latr[Mm-1,0:-1] - ( latp[Mm-2,:] - latr[Mm-1,0:-1] ) 
-1123      lat[Mm,-2:] = latr[Mm-1,-2:] - ( latp[Mm-2,-2:] - latr[Mm-1,-2:] ) 
-1124           
-1125      #South edge 
-1126      lon[0,0:-2] = lonr[0,0:-1] - ( lonp[0,:] - lonr[0,0:-1] ) 
-1127      lon[0,-2:] = lonr[0,-2:] - ( lonp[0,-2:] - lonr[0,-2:] ) 
-1128      lat[0,0:-2] = latr[0,0:-1] - ( latp[0,:] - latr[0,0:-1] ) 
-1129      lat[0,-2:] = latr[0,-2:] - ( latp[0,-2:] - latr[0,-2:] ) 
-1130   
-1131      #East edge 
-1132      lon[0:-2,Lm] = lonr[0:-1,Lm-1] - ( lonp[:,Lm-2] - lonr[0:-1,Lm-1] ) 
-1133      lon[-2:,Lm] = lonr[-2:,Lm-1] - ( lonp[-2:,Lm-2] - lonr[-2:,Lm-1] ) 
-1134      lat[0:-2,Lm] = latr[0:-1,Lm-1] - ( latp[:,Lm-2] - latr[0:-1,Lm-1] ) 
-1135      lat[-2:,Lm] = latr[-2:,Lm-1] - ( latp[-2:,Lm-2] - latr[-2:,Lm-1] ) 
-1136   
-1137      #West edge 
-1138      lon[0:-2,0] = lonr[0:-1,0] - ( lonp[:,0] - lonr[0:-1,0] ) 
-1139      lon[-2:,0] = lonr[-2:,0] - ( lonp[-2:,0] - lonr[-2:,0] ) 
-1140      lat[0:-2,0] = latr[0:-1,0] - ( latp[:,0] - latr[0:-1,0] ) 
-1141      lat[-2:,0] = latr[-2:,0] - ( latp[-2:,0] - latr[-2:,0] ) 
-1142   
-1143      return lon, lat 
-
1144   
-1145   
-
1146 -class edit_mask_mesh(object): 
-
1147      """ 
-1148      Interactive mask editor 
-1149   
-1150      edit_mask_mesh(grd, proj) 
-1151   
-1152      Edit grd mask. Mask/Unsmask cell by a simple click on the cell. 
-1153      Mask modification are store in mask_change.txt for further use. 
-1154   
-1155      Key commands: 
-1156          e : toggle between Editing/Viewing mode 
-1157      """ 
-1158       
-
1159 -    def _on_key(self, event): 
-
1160          if event.key == 'e': 
-1161              self._clicking = not self._clicking 
-1162              plt.title('Editing %s -- click "e" to toggle' % self._clicking) 
-1163              plt.draw() 
-
1164       
-
1165 -    def _on_click(self, event): 
-
1166          x, y = event.xdata, event.ydata 
-1167          if event.button==1 and event.inaxes is not None and self._clicking == True: 
-1168              d = (x-self._xc)**2 + (y-self._yc)**2 
-1169              if isinstance(self.xv, np.ma.MaskedArray): 
-1170                  idx = np.argwhere(d[~self._xc.mask] == d.min()) 
-1171              else: 
-1172                  idx = np.argwhere(d.flatten() == d.min()) 
-1173              self._mask[idx] = float(not self._mask[idx]) 
-1174              i, j = np.argwhere(d == d.min())[0] 
-1175              self.mask[i, j] = float(not self.mask[i, j]) 
-1176              #open output file 
-1177              f = open('mask_change.txt','a') 
-1178              value = (i, j, self.mask[i, j]) 
-1179              s = str(value) 
-1180              f.write(s + '\n') 
-1181              #close file 
-1182              f.close() 
-1183              self._pc.set_array(self._mask) 
-1184              self._pc.changed() 
-1185              plt.draw() 
-
1186       
-
1187 -    def __init__(self, grd, proj=None, **kwargs): 
-
1188   
-1189          if type(grd).__name__ == 'ROMS_Grid': 
-1190              try: 
-1191                  xv = grd.hgrid.lon_vert 
-1192                  yv = grd.hgrid.lat_vert 
-1193                  mask = grd.hgrid.mask_rho 
-1194              except: 
-1195                  xv = grd.hgrid.x_vert 
-1196                  yv = grd.hgrid.y_vert 
-1197                  mask = grd.hgrid.mask_rho 
-1198   
-1199          if type(grd).__name__ == 'CGrid_geo': 
-1200              try: 
-1201                  xv = grd.lon_vert 
-1202                  yv = grd.lat_vert 
-1203                  mask = grd.mask_rho 
-1204              except: 
-1205                  xv = grd.x_vert 
-1206                  yv = grd.y_vert 
-1207                  mask = grd.mask_rho 
-1208   
-1209          assert xv.shape == yv.shape, 'xv and yv must have the same shape' 
-1210          for dx, dq in zip(xv.shape, mask.shape): 
-1211               assert dx==dq+1, \ 
-1212               '''xv and yv must be cell verticies 
-1213               (i.e., one cell bigger in each dimension)''' 
-1214           
-1215          self.xv = xv 
-1216          self.yv = yv 
-1217           
-1218          self.mask = mask 
-1219   
-1220          self.proj = proj 
-1221           
-1222          land_color = kwargs.pop('land_color', (0.6, 1.0, 0.6)) 
-1223          sea_color = kwargs.pop('sea_color', (0.6, 0.6, 1.0)) 
-1224   
-1225          cm = plt.matplotlib.colors.ListedColormap([land_color, sea_color],  
-1226                                                   name='land/sea') 
-1227   
-1228          if self.proj is None: 
-1229              self._pc = plt.pcolor(xv, yv, mask, cmap=cm, vmin=0, vmax=1, edgecolor='k', **kwargs) 
-1230          else: 
-1231              xv, yv = self.proj(xv, yv) 
-1232              self._pc = Basemap.pcolor(self.proj, xv, yv, mask, cmap=cm, vmin=0, vmax=1, edgecolor='k', **kwargs) 
-1233              self.proj.drawcoastlines() 
-1234   
-1235          self._xc = 0.25*(xv[1:,1:]+xv[1:,:-1]+xv[:-1,1:]+xv[:-1,:-1]) 
-1236          self._yc = 0.25*(yv[1:,1:]+yv[1:,:-1]+yv[:-1,1:]+yv[:-1,:-1]) 
-1237           
-1238          if isinstance(self.xv, np.ma.MaskedArray): 
-1239              self._mask = mask[~self._xc.mask] 
-1240          else: 
-1241              self._mask = mask.flatten() 
-1242           
-1243          plt.connect('button_press_event', self._on_click) 
-1244          plt.connect('key_press_event', self._on_key) 
-1245          self._clicking = False 
-1246          plt.title('Editing %s -- click "e" to toggle' % self._clicking) 
-1247          plt.draw() 
-
1248   
-1249   
-
1250 -def uvp_masks(rmask): 
-
1251      ''' 
-1252      return u-, v-, and psi-masks based on input rho-mask 
-1253       
-1254      Parameters 
-1255      ---------- 
-1256       
-1257      rmask : ndarray 
-1258          mask at CGrid rho-points 
-1259       
-1260      Returns 
-1261      ------- 
-1262      (umask, vmask, pmask) : ndarrays 
-1263          masks at u-, v-, and psi-points 
-1264      ''' 
-1265      rmask = np.asarray(rmask) 
-1266      assert rmask.ndim == 2, 'rmask must be a 2D array' 
-1267      assert np.all((rmask==0)|(rmask==1)), 'rmask array must contain only ones and zeros.' 
-1268   
-1269      umask = rmask[:, :-1] * rmask[:, 1:] 
-1270      vmask = rmask[:-1, :] * rmask[1:, :] 
-1271      pmask = rmask[:-1, :-1] * rmask[:-1, 1:] * rmask[1:, :-1] * rmask[1:, 1:] 
-1272   
-1273      return umask, vmask, pmask 
-
1274   
-1275   
-1276   
-1277  if __name__ == '__main__': 
-1278      geographic = False 
-1279      if geographic: 
-1280          from mpl_toolkits.basemap import Basemap 
-1281          proj = Basemap(projection='lcc', 
-1282                         resolution='i', 
-1283                         llcrnrlon=-72.0, 
-1284                         llcrnrlat= 40.0, 
-1285                         urcrnrlon=-63.0, 
-1286                         urcrnrlat=47.0, 
-1287                         lat_0=43.0, 
-1288                         lon_0=-62.5) 
-1289           
-1290          lon = (-71.977385177601761, -70.19173825913137, 
-1291                 -63.045075098584945,-64.70104074097425) 
-1292          lat = (42.88215610827428, 41.056141745853786, 
-1293                 44.456701607935841, 46.271758064353897) 
-1294          beta = [1.0, 1.0, 1.0, 1.0] 
-1295   
-1296          grd = Gridgen(lon, lat, beta, (32, 32), proj=proj) 
-1297           
-1298          for seg in proj.coastsegs: 
-1299              grd.mask_polygon(seg) 
-1300           
-1301          plt.pcolor(grd.x, grd.y, grd.mask) 
-1302          plt.show() 
-1303      else: 
-1304          x = [0.2, 0.85, 0.9, 0.82, 0.23] 
-1305          y = [0.2, 0.25, 0.5, 0.82, .83] 
-1306          beta = [1.0, 1.0, 0.0, 1.0, 1.0] 
-1307           
-1308          grd = Gridgen(x, y, beta, (32, 32)) 
-1309           
-1310          ax = plt.subplot(111) 
-1311          BoundaryInteractor(x, y, beta) 
-1312          plt.show() 
-1313   
-1314   
-1315   
-
1316 -class get_position_from_map(object): 
-
1317      """ 
-1318      Get cell index position Interactively 
-1319   
-1320      get_position_from_map(grd, proj) 
-1321   
-1322      Get index i, j as well as lon, lat coordinates for one cell 
-1323      simply by clicking on the cell. 
-1324   
-1325      Key commands: 
-1326          i : toggle between Interactive/Viewing mode 
-1327      """ 
-
1328 -    def _on_key(self, event): 
-
1329          if event.key == 'i': 
-1330              self._clicking = not self._clicking 
-1331              plt.title('Interactive %s -- click "i" to toggle' % self._clicking) 
-1332              plt.draw() 
-
1333   
-
1334 -    def _on_click(self, event): 
-
1335          x, y = event.xdata, event.ydata 
-1336          if event.button==1 and event.inaxes is not None and self._clicking == True: 
-1337              d = (x-self._xc)**2 + (y-self._yc)**2 
-1338              if isinstance(self.xv, np.ma.MaskedArray): 
-1339                  idx = np.argwhere(d[~self._xc.mask] == d.min()) 
-1340              else: 
-1341                  idx = np.argwhere(d.flatten() == d.min()) 
-1342              j, i = np.argwhere(d == d.min())[0] 
-1343              print 'Position on the grid (rho point): i =', i, ', j =', j 
-1344              if self.proj is not None: 
-1345                  lon, lat = self.proj(self._xc[j,i], self._yc[j,i], inverse=True) 
-1346                  print 'corresponding geographical position : lon = ', lon, ', lat =', lat 
-1347              else: 
-1348                  print 'corresponding cartesian position : x = ', self._xc[j,i], ', y =', self._yc[j,i] 
-
1349       
-
1350 -    def __init__(self, grd, proj=None, **kwargs): 
-
1351   
-1352          try: 
-1353              xv = grd.hgrid.lon_vert 
-1354              yv = grd.hgrid.lat_vert 
-1355              mask = grd.hgrid.mask_rho 
-1356          except: 
-1357              xv = grd.hgrid.x_vert 
-1358              yv = grd.hgrid.y_vert 
-1359              mask = grd.hgrid.mask_rho 
-1360             
-1361          assert xv.shape == yv.shape, 'xv and yv must have the same shape' 
-1362          for dx, dq in zip(xv.shape, mask.shape): 
-1363               assert dx==dq+1, \ 
-1364               '''xv and yv must be cell verticies 
-1365               (i.e., one cell bigger in each dimension)''' 
-1366           
-1367          self.xv = xv 
-1368          self.yv = yv 
-1369           
-1370          self.mask = mask 
-1371   
-1372          self.proj = proj 
-1373           
-1374          land_color = kwargs.pop('land_color', (0.6, 1.0, 0.6)) 
-1375          sea_color = kwargs.pop('sea_color', (0.6, 0.6, 1.0)) 
-1376   
-1377          cm = plt.matplotlib.colors.ListedColormap([land_color, sea_color],  
-1378                                                   name='land/sea') 
-1379   
-1380          if self.proj is None: 
-1381              self._pc = plt.pcolor(xv, yv, mask, cmap=cm, vmin=0, vmax=1, edgecolor='k', **kwargs) 
-1382   
-1383          else: 
-1384              xv, yv = self.proj(xv, yv) 
-1385              self._pc = Basemap.pcolor(self.proj, xv, yv, mask, cmap=cm, vmin=0, vmax=1, edgecolor='k', **kwargs) 
-1386              self.proj.drawcoastlines() 
-1387   
-1388          self._xc = 0.25*(xv[1:,1:]+xv[1:,:-1]+xv[:-1,1:]+xv[:-1,:-1]) 
-1389          self._yc = 0.25*(yv[1:,1:]+yv[1:,:-1]+yv[:-1,1:]+yv[:-1,:-1]) 
-1390           
-1391          plt.connect('button_press_event', self._on_click) 
-1392          plt.connect('key_press_event', self._on_key) 
-1393          self._clicking = False 
-1394          plt.title('Interactive %s -- click "i" to toggle' % self._clicking) 
-1395          plt.draw() 
-
1396       
-1397   
-1398  if __name__ == '__main__': 
-1399      geographic = False 
-1400      if geographic: 
-1401          from mpl_toolkits.basemap import Basemap 
-1402          proj = Basemap(projection='lcc', 
-1403                         resolution='i', 
-1404                         llcrnrlon=-72.0, 
-1405                         llcrnrlat= 40.0, 
-1406                         urcrnrlon=-63.0, 
-1407                         urcrnrlat=47.0, 
-1408                         lat_0=43.0, 
-1409                         lon_0=-62.5) 
-1410           
-1411          lon = (-71.977385177601761, -70.19173825913137, 
-1412                 -63.045075098584945,-64.70104074097425) 
-1413          lat = (42.88215610827428, 41.056141745853786, 
-1414                 44.456701607935841, 46.271758064353897) 
-1415          beta = [1.0, 1.0, 1.0, 1.0] 
-1416   
-1417          grd = Gridgen(lon, lat, beta, (32, 32), proj=proj) 
-1418           
-1419          for seg in proj.coastsegs: 
-1420              grd.mask_polygon(seg) 
-1421           
-1422          plt.pcolor(grd.x, grd.y, grd.mask) 
-1423          plt.show() 
-1424      else: 
-1425          x = [0.2, 0.85, 0.9, 0.82, 0.23] 
-1426          y = [0.2, 0.25, 0.5, 0.82, .83] 
-1427          beta = [1.0, 1.0, 0.0, 1.0, 1.0] 
-1428           
-1429          grd = Gridgen(x, y, beta, (32, 32)) 
-1430           
-1431          ax = plt.subplot(111) 
-1432          BoundaryInteractor(x, y, beta) 
-1433          plt.show() 
-1434   
-
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- - - - - -
- - Package pyroms :: - Module hgrid_old :: - Class BoundaryInteractor - - - - - - -
[hide private]
[frames] | no frames]
-
- -

Class BoundaryInteractor

source code

-
-object --+
-         |
-        BoundaryInteractor
-
- -
-
-
-Interactive grid creation
-    
-bry = BoundaryClick(x=[], y=[], beta=None, ax=gca(), **gridgen_options)
-
-The initial boundary polygon points (x and y) are
-counterclockwise, starting in the upper left corner of the
-boundary. 
-
-Key commands:
-    
-    t : toggle visibility of verticies
-    d : delete a vertex
-    i : insert a vertex at a point on the polygon line
-    
-    p : set vertex as beta=1 (a Positive turn, marked with green triangle)
-    m : set vertex as beta=1 (a Negative turn, marked with red triangle)
-    z : set vertex as beta=0 (no corner, marked with a black dot)
-    
-    G : generate grid from the current boundary using gridgen
-    T : toggle visability of the current grid
-
-Methods:
-
-    bry.dump(bry_file)
-        Write the current boundary informtion (bry.x, bry.y, bry.beta) to
-        a cPickle file bry_file.
-    
-    bry.load(bry_file)
-        Read in boundary informtion (x, y, beta) from the cPickle file
-        bry_file.
-    
-    bry.remove_grid()  
-        Remove gridlines from axes.
-
-Attributes:
-    bry.x : the X boundary points
-    bry.y : the Y boundary points
-    bry.verts : the verticies of the grid
-    bry.grd : the CGrid object
-    
-
-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
-   - - - - - - -
_update_beta_lines(self)
- Update m/pline by finding the points where self.beta== -/+ 1		 - source code - -
- -
-   - - - - - - -
remove_grid(self)
- Remove a generated grid from the BoundaryClick figure		 - source code - -
- -
-   - - - - - - -
_draw_callback(self, - event) - source code - -
- -
-   - - - - - - -
_poly_changed(self, - poly)
- this method is called whenever the polygon object is called		 - source code - -
- -
-   - - - - - - -
_get_ind_under_point(self, - event)
- get the index of the vertex under point if within epsilon tolerance		 - source code - -
- -
-   - - - - - - -
_button_press_callback(self, - event)
- whenever a mouse button is pressed		 - source code - -
- -
-   - - - - - - -
_button_release_callback(self, - event)
- whenever a mouse button is released		 - source code - -
- -
-   - - - - - - -
_key_press_callback(self, - event)
- whenever a key is pressed		 - source code - -
- -
-   - - - - - - -
_motion_notify_callback(self, - event)
- on mouse movement		 - source code - -
- -
-   - - - - - - -
__init__(self, - x, - y=None, - beta=None, - ax=None, - proj=None, - **gridgen_options)
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature		 - source code - -
- -
-   - - - - - - -
save_bry(self, - bry_file='bry.pickle') - source code - -
- -
-   - - - - - - -
load_bry(self, - bry_file='bry.pickle') - source code - -
- -
-   - - - - - - -
save_grid(self, - grid_file='grid.pickle') - source code - -
- -
-   - - - - - - -
_get_verts(self) - source code - -
- -
-   - - - - - - -
get_xdata(self) - source code - -
- -
-   - - - - - - -
get_ydata(self) - source code - -
- -
-

Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

-
- - - - - - - - - - - - - - - - - - -
- - - - - -
Class Variables[hide private]
-
-   - - _showverts = True -
-   - - _showbetas = True -
-   - - _showgrid = True -
-   - - _epsilon = 5 -
- - - - - - - - - - - - - - - - - - -
- - - - - -
Properties[hide private]
-
-   - - verts -
-   - - x -
-   - - y -
-

Inherited from object: - __class__ -

-
- - - - - - -
- - - - - -
Method Details[hide private]
-
- -
- -
- - -
-

__init__(self, - x, - y=None, - beta=None, - ax=None, - proj=None, - **gridgen_options) -
(Constructor) -

- 		source code  -
- -

x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

-
-
Overrides: - object.__init__ -
(inherited documentation)
- -
-
-
-
- - - - - - -
- - - - - -
Property Details[hide private]
-
- -
- -
-

verts

- -
-
Get Method:
-
_get_verts(self) -
-
-
-
- -
- -
-

x

- -
-
Get Method:
-
get_xdata(self) -
-
-
-
- -
- -
-

y

- -
-
Get Method:
-
get_ydata(self) -
-
-
-
-
- - - - - - - - - - - - - - - - - -
   Home      Trees      Indices      Help   
- - - - - -
- Generated by Epydoc 3.0.1 on Mon Sep 27 11:31:39 2010 - - http://epydoc.sourceforge.net -
- - - - diff --git a/pyroms/docs/pyroms.hgrid_old.CGrid-class.html b/pyroms/docs/pyroms.hgrid_old.CGrid-class.html deleted file mode 100644 index 2536121..0000000 --- a/pyroms/docs/pyroms.hgrid_old.CGrid-class.html +++ /dev/null @@ -1,693 +0,0 @@ - - - - - pyroms.hgrid_old.CGrid - - - - - - - - - - - - - - - - - - - - - - -
   Home      Trees      Indices      Help   
- - - - - -
- - Package pyroms :: - Module hgrid_old :: - Class CGrid - - - - - - -
[hide private]
[frames] | no frames]
-
- -

Class CGrid

source code

-
-object --+
-         |
-        CGrid
-
- -
Known Subclasses:
-
- -
- -
-
-
-Curvilinear Arakawa C-Grid
- 
-The basis for the CGrid class are two arrays defining the verticies of the
-grid in Cartesian (for geographic coordinates, see CGrid_geo). An optional
-mask may be defined on the cell centers. Other Arakawa C-grid properties,
-such as the locations of the cell centers (rho-points), cell edges (u and
-v velocity points), cell widths (dx and dy) and other metrics (angle,
-dmde, and dndx) are all calculated internally from the vertex points.
- 
-Input vertex arrays may be either type np.array or np.ma.MaskedArray. If
-masked arrays are used, the mask will be a combination of the specified
-mask (if given) and the masked locations.
- 
-EXAMPLES:
---------
- 
->>> x, y = mgrid[0.0:7.0, 0.0:8.0]
->>> x = np.ma.masked_where( (x<3) & (y<3), x)
->>> y = np.ma.MaskedArray(y, x.mask)
->>> grd = pyroms.grid.CGrid(x, y)
->>> print grd.x_rho
-[[-- -- -- 0.5 0.5 0.5 0.5]
- [-- -- -- 1.5 1.5 1.5 1.5]
- [-- -- -- 2.5 2.5 2.5 2.5]
- [3.5 3.5 3.5 3.5 3.5 3.5 3.5]
- [4.5 4.5 4.5 4.5 4.5 4.5 4.5]
- [5.5 5.5 5.5 5.5 5.5 5.5 5.5]]
->>> print grd.mask
-[[ 0.  0.  0.  1.  1.  1.  1.]
- [ 0.  0.  0.  1.  1.  1.  1.]
- [ 0.  0.  0.  1.  1.  1.  1.]
- [ 1.  1.  1.  1.  1.  1.  1.]
- [ 1.  1.  1.  1.  1.  1.  1.]
- [ 1.  1.  1.  1.  1.  1.  1.]]
-
-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
-   - - - - - - -
__init__(self, - x_vert, - y_vert, - x_rho=None, - y_rho=None, - x_u=None, - y_u=None, - x_v=None, - y_v=None, - x_psi=None, - y_psi=None, - dx=None, - dy=None, - dndx=None, - dmde=None, - angle_rho=None)
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature		 - source code - -
- -
-   - - - - - - -
_calculate_subgrids(self) - source code - -
- -
-   - - - - - - -
_calculate_metrics(self)
- Calculates pm, pn, dndx, dmde from x_vert and y_vert		 - source code - -
- -
-   - - - - - - -
_calculate_derivative_metrics(self) - source code - -
- -
-   - - - - - - -
_calculate_angle(self) - source code - -
- -
-   - - - - - - -
_calculate_angle_rho(self) - source code - -
- -
-   - - - - - - -
calculate_orthogonality(self)
- Calculate orthogonality error in radians		 - source code - -
- -
-   - - - - - - -
mask_polygon(self, - polyverts, - mask_value=0.0)
- Mask Cartesian points contained within the polygon defined by polyverts		 - source code - -
- -
-   - - - - - - -
_get_mask_u(self) - source code - -
- -
-   - - - - - - -
_get_mask_v(self) - source code - -
- -
-   - - - - - - -
_get_mask_psi(self) - source code - -
- -
-   - - - - - - -
_set_mask_rho(self, - mask_rho) - source code - -
- -
-

Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

-
- - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - -
Properties[hide private]
-
-   - - x
- Return x_vert -
-   - - y
- Return x_vert -
-   - - mask
- Return mask_rho -
-   - - mask_u
- Return mask_u -
-   - - mask_v
- Return mask_v -
-   - - mask_psi
- Return mask_psi -
-

Inherited from object: - __class__ -

-
- - - - - - -
- - - - - -
Method Details[hide private]
-
- -
- -
- - -
-

__init__(self, - x_vert, - y_vert, - x_rho=None, - y_rho=None, - x_u=None, - y_u=None, - x_v=None, - y_v=None, - x_psi=None, - y_psi=None, - dx=None, - dy=None, - dndx=None, - dmde=None, - angle_rho=None) -
(Constructor) -

- 		source code  -
- -

x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

-
-
Overrides: - object.__init__ -
(inherited documentation)
- -
-
-
- -
- -
- - -
-

mask_polygon(self, - polyverts, - mask_value=0.0) -

- 		source code  -
- - 
-
-Mask Cartesian points contained within the polygon defined by polyverts
-
-A cell is masked if the cell center (x_rho, y_rho) is within the
-polygon. Other sub-masks (mask_u, mask_v, and mask_psi) are updated
-automatically.
-
-mask_value [=0.0] may be specified to alter the value of the mask set
-within the polygon.  E.g., mask_value=1 for water points.
-
-
-
-
-
-
-
- - - - - - -
- - - - - -
Property Details[hide private]
-
- -
- -
-

x

- 
-Return x_vert
-
-
-
-
Get Method:
-
unreachable(self) -
-
-
-
- -
- -
-

y

- 
-Return x_vert
-
-
-
-
Get Method:
-
unreachable(self) -
-
-
-
- -
- -
-

mask

- 
-Return mask_rho
-
-
-
-
Get Method:
-
unreachable(self) -
-
Set Method:
-
_set_mask_rho(self, - mask_rho) -
-
-
-
- -
- -
-

mask_u

- 
-Return mask_u
-
-
-
-
Get Method:
-
_get_mask_u(self) -
-
-
-
- -
- -
-

mask_v

- 
-Return mask_v
-
-
-
-
Get Method:
-
_get_mask_v(self) -
-
-
-
- -
- -
-

mask_psi

- 
-Return mask_psi
-
-
-
-
Get Method:
-
_get_mask_psi(self) -
-
-
-
-
- - - - - - - - - - - - - - - - - -
   Home      Trees      Indices      Help   
- - - - - -
- Generated by Epydoc 3.0.1 on Mon Sep 27 11:31:39 2010 - - http://epydoc.sourceforge.net -
- - - - diff --git a/pyroms/docs/pyroms.hgrid_old.CGrid_geo-class.html b/pyroms/docs/pyroms.hgrid_old.CGrid_geo-class.html deleted file mode 100644 index d56fea2..0000000 --- a/pyroms/docs/pyroms.hgrid_old.CGrid_geo-class.html +++ /dev/null @@ -1,512 +0,0 @@ - - - - - pyroms.hgrid_old.CGrid_geo - - - - - - - - - - - - - - - - - - - - - - -
   Home      Trees      Indices      Help   
- - - - - -
- - Package pyroms :: - Module hgrid_old :: - Class CGrid_geo - - - - - - -
[hide private]
[frames] | no frames]
-
- -

Class CGrid_geo

source code

-
-object --+    
-         |    
-     CGrid --+
-             |
-            CGrid_geo
-
- -
-
-
-Curvilinear Arakawa C-grid defined in geographic coordinates
-
-For a geographic grid, a projection may be specified, or The default
-projection for will be defined by the matplotlib.toolkits.Basemap
-projection:
-
-proj = Basemap(projection='merc', resolution=None, lat_ts=0.0)
-
-For a geographic grid, the cell widths are determined by the great
-circle distances. Angles, however, are defined using the projected
-coordinates, so a projection that conserves angles must be used. This
-means typically either Mercator (projection='merc') or Lambert
-Conformal Conic (projection='lcc').
-
-
- - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
-   - - - - - - -
_calculate_metrics(self)
- Calculates pm, pn, dndx, dmde from x_vert and y_vert		 - source code - -
- -
-   - - - - - - -
_calculate_derivative_metrics(self) - source code - -
- -
-   - - - - - - -
_calculate_angle_rho(self) - source code - -
- -
-   - - - - - - -
__init__(self, - lon_vert, - lat_vert, - proj, - use_gcdist=True, - ellipse='WGS84', - lon_rho=None, - lat_rho=None, - lon_u=None, - lat_u=None, - lon_v=None, - lat_v=None, - lon_psi=None, - lat_psi=None, - dx=None, - dy=None, - dndx=None, - dmde=None, - angle_rho=None)
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature		 - source code - -
- -
-   - - - - - - -
mask_polygon_geo(lonlat_verts, - mask_value=0.0) - source code - -
- -
-

Inherited from CGrid: - calculate_orthogonality, - mask_polygon -

-

Inherited from CGrid (private): - _calculate_angle, - _calculate_subgrids, - _get_mask_psi, - _get_mask_u, - _get_mask_v, - _set_mask_rho -

-

Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

-
- - - - - - - - - - - - - - - -
- - - - - -
Properties[hide private]
-
-   - - lon
- Shorthand for lon_vert -
-   - - lat
- Shorthand for lat_vert -
-

Inherited from CGrid: - mask, - mask_psi, - mask_u, - mask_v, - x, - y -

-

Inherited from object: - __class__ -

-
- - - - - - -
- - - - - -
Method Details[hide private]
-
- -
- -
- - -
-

_calculate_metrics(self) -

- 		source code  -
- - 
-Calculates pm, pn, dndx, dmde from x_vert and y_vert
-
-
-
-
Overrides: - CGrid._calculate_metrics -
(inherited documentation)
- -
-
-
- -
- -
- - -
-

_calculate_derivative_metrics(self) -

- 		source code  -
- - -
-
Overrides: - CGrid._calculate_derivative_metrics -
-
-
-
- -
- -
- - -
-

_calculate_angle_rho(self) -

- 		source code  -
- - -
-
Overrides: - CGrid._calculate_angle_rho -
-
-
-
- -
- -
- - -
-

__init__(self, - lon_vert, - lat_vert, - proj, - use_gcdist=True, - ellipse='WGS84', - lon_rho=None, - lat_rho=None, - lon_u=None, - lat_u=None, - lon_v=None, - lat_v=None, - lon_psi=None, - lat_psi=None, - dx=None, - dy=None, - dndx=None, - dmde=None, - angle_rho=None) -
(Constructor) -

- 		source code  -
- -

x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

-
-
Overrides: - object.__init__ -
(inherited documentation)
- -
-
-
-
- - - - - - -
- - - - - -
Property Details[hide private]
-
- -
- -
-

lon

- 
-Shorthand for lon_vert
-
-
-
-
Get Method:
-
unreachable(self) -
-
-
-
- -
- -
-

lat

- 
-Shorthand for lat_vert
-
-
-
-
Get Method:
-
unreachable(self) -
-
-
-
-
- - - - - - - - - - - - - - - - - -
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- - - - - -
- Generated by Epydoc 3.0.1 on Mon Sep 27 11:31:39 2010 - - http://epydoc.sourceforge.net -
- - - - diff --git a/pyroms/docs/pyroms.hgrid_old.Focus-class.html b/pyroms/docs/pyroms.hgrid_old.Focus-class.html deleted file mode 100644 index 142d4d5..0000000 --- a/pyroms/docs/pyroms.hgrid_old.Focus-class.html +++ /dev/null @@ -1,335 +0,0 @@ - - - - - pyroms.hgrid_old.Focus - - - - - - - - - - - - - - - - - - - - - - -
   Home      Trees      Indices      Help   
- - - - - -
- - Package pyroms :: - Module hgrid_old :: - Class Focus - - - - - - -
[hide private]
[frames] | no frames]
-
- -

Class Focus

source code

-
-object --+
-         |
-        Focus
-
- -
-
-
-Return a container for a sequence of Focus objects
-
-foc = Focus()
-
-The sequence is populated by using the 'add_focus_x' and 'add_focus_y'
-methods. These methods define a point ('xo' or 'yo'), around witch to
-focus, a focusing factor of 'focus', and x and y extent of focusing given
-by Rx or Ry. The region of focusing will be approximately Gausian, and the
-resolution will be increased by approximately the value of factor.
-
-Methods
--------
-foc.add_focus_x(xo, factor=2.0, Rx=0.1)
-foc.add_focus_y(yo, factor=2.0, Ry=0.1)
-
-Calls to the object return transformed coordinates:
-    xf, yf = foc(x, y)
-where x and y must be within [0, 1], and are typically a uniform,
-normalized grid. The focused grid will be the result of applying each of
-the focus elements in the sequence they are added to the series.
-
-
-EXAMPLES
---------
-
->>> foc = pyroms.grid.Focus()
->>> foc.add_focus_x(0.2, factor=3.0, Rx=0.2)
->>> foc.add_focus_y(0.6, factor=5.0, Ry=0.35)
-
->>> x, y = np.mgrid[0:1:3j,0:1:3j]
->>> xf, yf = foc(x, y)
-
->>> print xf
-[[ 0.          0.          0.        ]
- [ 0.36594617  0.36594617  0.36594617]
- [ 1.          1.          1.        ]]
->>> print yf
-[[ 0.          0.62479833  1.        ]
- [ 0.          0.62479833  1.        ]
- [ 0.          0.62479833  1.        ]]
-
-
- - - - - - - - - - - - - - - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
-   - - - - - - -
__init__(self)
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature		 - source code - -
- -
-   - - - - - - -
add_focus_x(self, - xo, - factor=2.0, - Rx=0.1)
- docstring for add_point		 - source code - -
- -
-   - - - - - - -
add_focus_y(self, - yo, - factor=2.0, - Ry=0.1)
- docstring for add_point		 - source code - -
- -
-   - - - - - - -
__call__(self, - x, - y)
- docstring for __call__		 - source code - -
- -
-

Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

-
- - - - - - - - - -
- - - - - -
Properties[hide private]
-
-

Inherited from object: - __class__ -

-
- - - - - - -
- - - - - -
Method Details[hide private]
-
- -
- -
- - -
-

__init__(self) -
(Constructor) -

- 		source code  -
- -

x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

-
-
Overrides: - object.__init__ -
(inherited documentation)
- -
-
-
-
- - - - - - - - - - - - - - - - - -
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- - - - - -
- Generated by Epydoc 3.0.1 on Mon Sep 27 11:31:39 2010 - - http://epydoc.sourceforge.net -
- - - - diff --git a/pyroms/docs/pyroms.hgrid_old.Gridgen-class.html b/pyroms/docs/pyroms.hgrid_old.Gridgen-class.html deleted file mode 100644 index 009ebb7..0000000 --- a/pyroms/docs/pyroms.hgrid_old.Gridgen-class.html +++ /dev/null @@ -1,323 +0,0 @@ - - - - - pyroms.hgrid_old.Gridgen - - - - - - - - - - - - - - - - - - - - - - -
   Home      Trees      Indices      Help   
- - - - - -
- - Package pyroms :: - Module hgrid_old :: - Class Gridgen - - - - - - -
[hide private]
[frames] | no frames]
-
- -

Class Gridgen

source code

-
-object --+    
-         |    
-     CGrid --+
-             |
-            Gridgen
-
- -
-
-
-docstring for Gridgen
-
-
- - - - - - - - - - - - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
-   - - - - - - -
generate_grid(self) - source code - -
- -
-   - - - - - - -
__init__(self, - xbry, - ybry, - beta, - shape, - ul_idx=0, - focus=None, - proj=None, - nnodes=14, - precision=1e-12, - nppe=3, - newton=True, - thin=True, - checksimplepoly=True, - verbose=False)
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature		 - source code - -
- -
-   - - - - - - -
__del__(self)
- delete gridnode object upon deletion		 - source code - -
- -
-

Inherited from CGrid: - calculate_orthogonality, - mask_polygon -

-

Inherited from CGrid (private): - _calculate_angle, - _calculate_angle_rho, - _calculate_derivative_metrics, - _calculate_metrics, - _calculate_subgrids, - _get_mask_psi, - _get_mask_u, - _get_mask_v, - _set_mask_rho -

-

Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

-
- - - - - - - - - -
- - - - - -
Properties[hide private]
-
-

Inherited from CGrid: - mask, - mask_psi, - mask_u, - mask_v, - x, - y -

-

Inherited from object: - __class__ -

-
- - - - - - -
- - - - - -
Method Details[hide private]
-
- -
- -
- - -
-

__init__(self, - xbry, - ybry, - beta, - shape, - ul_idx=0, - focus=None, - proj=None, - nnodes=14, - precision=1e-12, - nppe=3, - newton=True, - thin=True, - checksimplepoly=True, - verbose=False) -
(Constructor) -

- 		source code  -
- -

x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

-
-
Overrides: - object.__init__ -
(inherited documentation)
- -
-
-
-
- - - - - - - - - - - - - - - - - -
   Home      Trees      Indices      Help   
- - - - - -
- Generated by Epydoc 3.0.1 on Mon Sep 27 11:31:39 2010 - - http://epydoc.sourceforge.net -
- - - - diff --git a/pyroms/docs/pyroms.hgrid_old._Focus_x-class.html b/pyroms/docs/pyroms.hgrid_old._Focus_x-class.html deleted file mode 100644 index 34a4fd2..0000000 --- a/pyroms/docs/pyroms.hgrid_old._Focus_x-class.html +++ /dev/null @@ -1,283 +0,0 @@ - - - - - pyroms.hgrid_old._Focus_x - - - - - - - - - - - - - - - - - - - - - - -
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- - Package pyroms :: - Module hgrid_old :: - Class _Focus_x - - - - - - -
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-
- -

Class _Focus_x

source code

-
-object --+
-         |
-        _Focus_x
-
- -
-
-
-Return a transformed, uniform grid, focused in the x-direction
-
-This class may be called with a uniform grid, with limits from [0, 1], to
-create a focused grid in the x-directions centered about xo. The output
-grid is also uniform from [0, 1] in both x and y.
-
-Parameters
-----------
-xo : float
-    Location about which to focus grid
-factor : float
-    amount to focus grid. Creates cell sizes that are factor smaller in
-    the focused
-    region.
-Rx : float
-    Lateral extent of focused region, similar to a lateral spatial scale
-    for the focusing region.
-
-Returns
--------
-foc : class
-    The class may be called with arguments of a grid. The returned
-    transformed grid (x, y) will be focused as per the parameters above.
-
-
- - - - - - - - - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
-   - - - - - - -
__init__(self, - xo, - factor=2.0, - Rx=0.1)
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature		 - source code - -
- -
-   - - - - - - -
__call__(self, - x, - y) - source code - -
- -
-

Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

-
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Inherited from object: - __class__ -

-
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- - - - - -
Method Details[hide private]
-
- -
- -
- - -
-

__init__(self, - xo, - factor=2.0, - Rx=0.1) -
(Constructor) -

- 		source code  -
- -

x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

-
-
Overrides: - object.__init__ -
(inherited documentation)
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Class _Focus_y

source code

-
-object --+
-         |
-        _Focus_y
-
- -
-
-
-Return a transformed, uniform grid, focused in the y-direction
-
-This class may be called with a uniform grid, with limits from [0, 1], 
-to create a focused grid in the y-directions centered about yo. 
-The output grid is also uniform from [0, 1] in both x and y.
-
-Parameters
-----------
-yo : float
-    Location about which to focus grid
-factor : float
-    amount to focus grid. Creates cell sizes that are factor 
-    smaller in the focused region.
-Ry : float
-    Lateral extent of focused region, similar to a lateral 
-    spatial scale for the focusing region.
-
-Returns
--------
-foc : class
-    The class may be called with arguments of a grid. The returned 
-    transformed grid (x, y) will be focused as per the parameters above.
-
-
- - - - - - - - - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
-   - - - - - - -
__init__(self, - yo, - factor=2.0, - Ry=0.1)
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature		 - source code - -
- -
-   - - - - - - -
__call__(self, - x, - y) - source code - -
- -
-

Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

-
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Inherited from object: - __class__ -

-
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- - - - - -
Method Details[hide private]
-
- -
- -
- - -
-

__init__(self, - yo, - factor=2.0, - Ry=0.1) -
(Constructor) -

- 		source code  -
- -

x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

-
-
Overrides: - object.__init__ -
(inherited documentation)
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- - Package pyroms :: - Module hgrid_old :: - Class edit_mask_mesh - - - - - - -
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-
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Class edit_mask_mesh

source code

-
-object --+
-         |
-        edit_mask_mesh
-
- -
-
-
-Interactive mask editor
-
-edit_mask_mesh(grd, proj)
-
-Edit grd mask. Mask/Unsmask cell by a simple click on the cell.
-Mask modification are store in mask_change.txt for further use.
-
-Key commands:
-    e : toggle between Editing/Viewing mode
-
-
- - - - - - - - - - - - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
-   - - - - - - -
_on_key(self, - event) - source code - -
- -
-   - - - - - - -
_on_click(self, - event) - source code - -
- -
-   - - - - - - -
__init__(self, - grd, - proj=None, - **kwargs)
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature		 - source code - -
- -
-

Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

-
- - - - - - - - - -
- - - - - -
Properties[hide private]
-
-

Inherited from object: - __class__ -

-
- - - - - - -
- - - - - -
Method Details[hide private]
-
- -
- -
- - -
-

__init__(self, - grd, - proj=None, - **kwargs) -
(Constructor) -

- 		source code  -
- -

x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

-
-
Overrides: - object.__init__ -
(inherited documentation)
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- - - - diff --git a/pyroms/docs/pyroms.hgrid_old.get_position_from_map-class.html b/pyroms/docs/pyroms.hgrid_old.get_position_from_map-class.html deleted file mode 100644 index fd6f6f7..0000000 --- a/pyroms/docs/pyroms.hgrid_old.get_position_from_map-class.html +++ /dev/null @@ -1,285 +0,0 @@ - - - - - pyroms.hgrid_old.get_position_from_map - - - - - - - - - - - - - - - - - - - - - - -
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-
- -

Class get_position_from_map

source code

-
-object --+
-         |
-        get_position_from_map
-
- -
-
-
-Get cell index position Interactively
-
-get_position_from_map(grd, proj)
-
-Get index i, j as well as lon, lat coordinates for one cell
-simply by clicking on the cell.
-
-Key commands:
-    i : toggle between Interactive/Viewing mode
-
-
- - - - - - - - - - - - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
-   - - - - - - -
_on_key(self, - event) - source code - -
- -
-   - - - - - - -
_on_click(self, - event) - source code - -
- -
-   - - - - - - -
__init__(self, - grd, - proj=None, - **kwargs)
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature		 - source code - -
- -
-

Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

-
- - - - - - - - - -
- - - - - -
Properties[hide private]
-
-

Inherited from object: - __class__ -

-
- - - - - - -
- - - - - -
Method Details[hide private]
-
- -
- -
- - -
-

__init__(self, - grd, - proj=None, - **kwargs) -
(Constructor) -

- 		source code  -
- -

x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

-
-
Overrides: - object.__init__ -
(inherited documentation)
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- - - - diff --git a/pyroms/docs/pyroms.io-module.html b/pyroms/docs/pyroms.io-module.html deleted file mode 100644 index ad3b34f..0000000 --- a/pyroms/docs/pyroms.io-module.html +++ /dev/null @@ -1,320 +0,0 @@ - - - - - pyroms.io - - - - - - - - - - - - - - - - - - - - - - -
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- - Package pyroms :: - Module io - - - - - - -
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-
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Module io

source code

-
-A thin wrapper for netCDF4.Dataset and netCDF4.MFDataset
-
-This module provides two functions, Dataset and MFDataset, that are similar to the
-netCDF[3/4] functions of the same name. This package is a thin wrapper around these
-functions, and provides two services. First of all, it will use either netCDF3 or
-netCDF4 (prefering the later), so that the netCDF package does not need to be changed
-on different systems that only have one or the other. Second, it will pass through
-netCDF[3/4] objects unchanged, so that netCDF objects, filenames, lists of files, or
-strings with wildcards can be passed to the function indescriminately.
-
-Examples of usage
------------------
-
-with an input of a string:
-    # returns netCDF4.Dataset object based on file
-    nc = pyroms.io.Dataset(file) 
-  
-    # returns MFnetCDF4.Dataset object based on file (with wildcard chars)
-    nc = pyroms.io.MFDataset(file) 
-
-with an input of a list of files:
-    # returns MFDataset object based on list of files
-    nc = pyroms.io.Dataset(files) 
-    
-    # returns MFDataset object based on list of files
-    nc = pyroms.io.MFDataset(files)
-
-with an input of a netCDF4.Dataset or MFnetCDF4.Dataset object:
-    # passes through netCDF4.Dataset or MFnetCDF4.Dataset object
-    nc = pyroms.io.Dataset(nc)
-    
-    # passes through MFDataset object based on file (with wildcard chars)
-    nc = pyroms.io.MFDataset(nc)
-
-
- - - - - - - - - - - - - -
- - - - - -
Functions[hide private]
-
-   - - - - - - -
MFDataset(ncfile)
- A thin wrapper for netCDF4.Dataset and netCDF4.MFDataset		 - source code - -
- -
-   - - - - - - -
Dataset(ncfile)
- A thin wrapper for netCDF4.Dataset and netCDF4.MFDataset		 - source code - -
- -
- - - - - - -
- - - - - -
Function Details[hide private]
-
- -
- -
- - -
-

MFDataset(ncfile) -

- 		source code  -
- - 
-A thin wrapper for netCDF4.Dataset and netCDF4.MFDataset
-
-This module provides two functions, Dataset and MFDataset, that are similar to the
-netCDF[3/4] functions of the same name. This package is a thin wrapper around these
-functions, and provides two services. First of all, it will use either netCDF3 or
-netCDF4 (prefering the later), so that the netCDF package does not need to be changed
-on different systems that only have one or the other. Second, it will pass through
-netCDF[3/4] objects unchanged, so that netCDF objects, filenames, lists of files, or
-strings with wildcards can be passed to the function indescriminately.
-
-Examples of usage
------------------
-
-with an input of a string:
-    # returns netCDF4.Dataset object based on file
-    nc = pyroms.io.Dataset(file) 
-  
-    # returns MFnetCDF4.Dataset object based on file (with wildcard chars)
-    nc = pyroms.io.MFDataset(file) 
-
-with an input of a list of files:
-    # returns MFDataset object based on list of files
-    nc = pyroms.io.Dataset(files) 
-    
-    # returns MFDataset object based on list of files
-    nc = pyroms.io.MFDataset(files)
-
-with an input of a netCDF4.Dataset or MFnetCDF4.Dataset object:
-    # passes through netCDF4.Dataset or MFnetCDF4.Dataset object
-    nc = pyroms.io.Dataset(nc)
-    
-    # passes through MFDataset object based on file (with wildcard chars)
-    nc = pyroms.io.MFDataset(nc)
-
-
-
-
-
-
- -
- -
- - -
-

Dataset(ncfile) -

- 		source code  -
- - 
-A thin wrapper for netCDF4.Dataset and netCDF4.MFDataset
-
-This module provides two functions, Dataset and MFDataset, that are similar to the
-netCDF[3/4] functions of the same name. This package is a thin wrapper around these
-functions, and provides two services. First of all, it will use either netCDF3 or
-netCDF4 (prefering the later), so that the netCDF package does not need to be changed
-on different systems that only have one or the other. Second, it will pass through
-netCDF[3/4] objects unchanged, so that netCDF objects, filenames, lists of files, or
-strings with wildcards can be passed to the function indescriminately.
-
-Examples of usage
------------------
-
-with an input of a string:
-    # returns netCDF4.Dataset object based on file
-    nc = pyroms.io.Dataset(file) 
-  
-    # returns MFnetCDF4.Dataset object based on file (with wildcard chars)
-    nc = pyroms.io.MFDataset(file) 
-
-with an input of a list of files:
-    # returns MFDataset object based on list of files
-    nc = pyroms.io.Dataset(files) 
-    
-    # returns MFDataset object based on list of files
-    nc = pyroms.io.MFDataset(files)
-
-with an input of a netCDF4.Dataset or MFnetCDF4.Dataset object:
-    # passes through netCDF4.Dataset or MFnetCDF4.Dataset object
-    nc = pyroms.io.Dataset(nc)
-    
-    # passes through MFDataset object based on file (with wildcard chars)
-    nc = pyroms.io.MFDataset(nc)
-
-
-
-
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Source Code for Module pyroms.io

-
-  1  # encoding: utf-8 
-  2  '''A thin wrapper for netCDF4.Dataset and netCDF4.MFDataset 
-  3   
-  4  This module provides two functions, Dataset and MFDataset, that are similar to the 
-  5  netCDF[3/4] functions of the same name. This package is a thin wrapper around these 
-  6  functions, and provides two services. First of all, it will use either netCDF3 or 
-  7  netCDF4 (prefering the later), so that the netCDF package does not need to be changed 
-  8  on different systems that only have one or the other. Second, it will pass through 
-  9  netCDF[3/4] objects unchanged, so that netCDF objects, filenames, lists of files, or 
- 10  strings with wildcards can be passed to the function indescriminately. 
- 11   
- 12  Examples of usage 
- 13  ----------------- 
- 14   
- 15  with an input of a string: 
- 16      # returns netCDF4.Dataset object based on file 
- 17      nc = pyroms.io.Dataset(file)  
- 18     
- 19      # returns MFnetCDF4.Dataset object based on file (with wildcard chars) 
- 20      nc = pyroms.io.MFDataset(file)  
- 21   
- 22  with an input of a list of files: 
- 23      # returns MFDataset object based on list of files 
- 24      nc = pyroms.io.Dataset(files)  
- 25       
- 26      # returns MFDataset object based on list of files 
- 27      nc = pyroms.io.MFDataset(files) 
- 28   
- 29  with an input of a netCDF4.Dataset or MFnetCDF4.Dataset object: 
- 30      # passes through netCDF4.Dataset or MFnetCDF4.Dataset object 
- 31      nc = pyroms.io.Dataset(nc) 
- 32       
- 33      # passes through MFDataset object based on file (with wildcard chars) 
- 34      nc = pyroms.io.MFDataset(nc) 
- 35  ''' 
- 36  __docformat__ = "restructuredtext en" 
- 37   
- 38  from glob import glob 
- 39   
- 40  try: 
- 41      try: 
- 42          import netCDF4 as netCDF 
- 43      except: 
- 44          import netCDF3 as netCDF 
- 45       
-
 46 -    def Dataset(ncfile): 
-
 47          """Return an appropriate netcdf object: 
- 48                  netCDF4 object given a file string 
- 49                  MFnetCDF4 object given a list of files 
- 50               
- 51              A netCDF4 or MFnetCDF4 object returns itself.""" 
- 52          if isinstance(ncfile, str): 
- 53              return netCDF.Dataset(ncfile, 'r') 
- 54          elif isinstance(ncfile, list) or isinstance(ncfile, tuple): 
- 55              return netCDF.MFDataset(sorted(ncfile)) 
- 56          elif hasattr(ncfile, 'variables'):  # accept any oject with a variables attribute 
- 57              assert isinstance(ncfile.variables, dict), \ 
- 58                     'variables attribute must be a dictionary' 
- 59              return ncfile 
- 60          else: 
- 61              raise TypeError, 'type %s not supported' % type(ncfile) 
-
 62       
- 63      Dataset.__doc__ = __doc__ 
- 64   
-
 65 -    def MFDataset(ncfile): 
-
 66          """Return an MFnetCDF4 object given a string or list.  A string is expanded 
- 67             with wildcards using glob.  A netCDF4 or MFnetCDF4 object returns itself.""" 
- 68          if isinstance(ncfile, str): 
- 69              ncfiles = glob(ncfile) 
- 70              return netCDF.MFDataset(sorted(ncfiles)) 
- 71          elif isinstance(ncfile, list) or isinstance(ncfile, tuple): 
- 72              return netCDF.MFDataset(sorted(ncfile)) 
- 73          elif hasattr(ncfile, 'variables'):  # accept any oject with a variables attribute 
- 74              assert isinstance(ncfile.variables, dict), \ 
- 75                     'variables attribute must be a dictionary' 
- 76              return ncfile 
- 77          else: 
- 78              raise TypeError, 'type %s not supported' % type(ncfile) 
- 79              return MFnetCDF4.Dataset(files) 
-
 80       
- 81      MFDataset.__doc__ = __doc__ 
- 82   
- 83  except: 
- 84      import pyroms.extern.pupynere 
- 85      import warnings 
- 86       
- 87      warnings.warn('netCDF[3/4] not found -- using pupynere.') 
- 88       
-
 89 -    def Dataset(ncfile): 
-
 90          if isinstance(ncfile, str): 
- 91              return pupynere.NetCDFFile(ncfile) 
- 92          elif isinstance(ncfile, pupynere.NetCDFFile): 
- 93              return ncfile 
- 94          else: 
- 95              raise TypeError, 'type %s not supported' % type(ncfile) 
-
 96       
- 97      Dataset.__doc__ = __doc__ 
- 98   
- 99   
-100  if __name__ == '__main__': 
-101      pass 
-102   
-
-
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Package remapping

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-

A set of tools for remapping

- - - - - - - - -
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Source Code for Package pyroms.remapping

-
- 1  # encoding: utf-8 
- 2  '''  
- 3  A set of tools for remapping 
- 4  ''' 
- 5   
- 6  from make_remap_grid_file import make_remap_grid_file 
- 7  from compute_remap_weights import compute_remap_weights 
- 8  from test_remap_weights import test_remap_weights 
- 9  from remap import remap 
-10  try: 
-11      import scrip 
-12  except: 
-13      print 'scrip.so not found. Remapping function will not be available' 
-14  from roms2z import roms2z 
-15  from z2roms import z2roms 
-16  from flood import flood 
-17   
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Module compute_remap_weights'

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Functions[hide private]
-
-   - - - - - - -
compute_remap_weights(grid1_file, - grid2_file, - interp_file1, - interp_file2, - map1_name, - map2_name, - num_maps, - map_method, - luse_grid1_area='.false.', - luse_grid2_area='.false.', - normalize_opt='fracarea', - output_opt='scrip', - restrict_type='latitude', - num_srch_bins='90', - grid1_periodic='.false.', - grid2_periodic='.false.')
- compute remap weights and addresses		 - source code - -
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Source Code for Module pyroms.remapping.compute_remap_weights'

-
- 1  import os 
- 2  import pyroms 
- 3   
- 4   
-
 5 -def compute_remap_weights(grid1_file, grid2_file, \ 
- 6         interp_file1, interp_file2, map1_name, \ 
- 7         map2_name, num_maps, map_method, \ 
- 8         luse_grid1_area='.false.', luse_grid2_area='.false.', \ 
- 9         normalize_opt='fracarea', output_opt='scrip', \ 
-10         restrict_type='latitude', num_srch_bins='90', \ 
-11         grid1_periodic='.false.', grid2_periodic='.false.'): 
-
12      ''' 
-13      compute remap weights and addresses 
-14      ''' 
-15   
-16      # write namelist file 
-17      f = open('compute_remap_weights_in','w') 
-18   
-19      f.write('&remap_inputs' + '\n') 
-20      f.write('    num_maps = ' + str(num_maps) + '\n') 
-21      f.write('    grid1_file = \'' + str(grid1_file) + '\'\n') 
-22      f.write('    grid2_file = \'' + str(grid2_file) + '\'\n') 
-23      f.write('    interp_file1 = \'' + str(interp_file1) + '\'\n') 
-24      f.write('    interp_file2 = \'' + str(interp_file2) + '\'\n') 
-25      f.write('    map1_name = \'' + str(map1_name) + '\'\n') 
-26      f.write('    map2_name = \'' + str(map2_name) + '\'\n') 
-27      f.write('    map_method = \'' + str(map_method) + '\'\n') 
-28      f.write('    normalize_opt = \'' + str(normalize_opt) + '\'\n') 
-29      f.write('    output_opt = \'' + str(output_opt) + '\'\n') 
-30      f.write('    restrict_type = \'' + str(restrict_type) + '\'\n') 
-31      f.write('    num_srch_bins = ' + str(num_srch_bins) + '\n') 
-32      f.write('    luse_grid1_area = ' + str(luse_grid1_area) + '\n') 
-33      f.write('    luse_grid2_area = ' + str(luse_grid2_area) + '\n') 
-34      f.write('    grid1_periodic = ' + str(grid1_periodic) + '\n') 
-35      f.write('    grid2_periodic = ' + str(grid2_periodic) + '\n') 
-36      f.write('/\n') 
-37   
-38      f.close() 
-39   
-40      # compute weights 
-41      pyroms.remapping.scrip.compute_remap_weights('compute_remap_weights_in') 
-42   
-43      # clean 
-44      os.remove('compute_remap_weights_in') 
-
45   
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Module compute_remap_weights

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Functions[hide private]
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compute_remap_weights(grid1_file, - grid2_file, - interp_file1, - interp_file2, - map1_name, - map2_name, - num_maps, - map_method, - luse_grid1_area='.false.', - luse_grid2_area='.false.', - normalize_opt='fracarea', - output_opt='scrip', - restrict_type='latitude', - num_srch_bins='90', - grid1_periodic='.false.', - grid2_periodic='.false.')
- compute remap weights and addresses		 - source code - -
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Source Code for Module pyroms.remapping.compute_remap_weights

-
- 1  import os 
- 2  import pyroms 
- 3   
- 4   
-
 5 -def compute_remap_weights(grid1_file, grid2_file, \ 
- 6         interp_file1, interp_file2, map1_name, \ 
- 7         map2_name, num_maps, map_method, \ 
- 8         luse_grid1_area='.false.', luse_grid2_area='.false.', \ 
- 9         normalize_opt='fracarea', output_opt='scrip', \ 
-10         restrict_type='latitude', num_srch_bins='90', \ 
-11         grid1_periodic='.false.', grid2_periodic='.false.'): 
-
12      ''' 
-13      compute remap weights and addresses 
-14      ''' 
-15   
-16      # write namelist file 
-17      f = open('compute_remap_weights_in','w') 
-18   
-19      f.write('&remap_inputs' + '\n') 
-20      f.write('    num_maps = ' + str(num_maps) + '\n') 
-21      f.write('    grid1_file = \'' + str(grid1_file) + '\'\n') 
-22      f.write('    grid2_file = \'' + str(grid2_file) + '\'\n') 
-23      f.write('    interp_file1 = \'' + str(interp_file1) + '\'\n') 
-24      f.write('    interp_file2 = \'' + str(interp_file2) + '\'\n') 
-25      f.write('    map1_name = \'' + str(map1_name) + '\'\n') 
-26      f.write('    map2_name = \'' + str(map2_name) + '\'\n') 
-27      f.write('    map_method = \'' + str(map_method) + '\'\n') 
-28      f.write('    normalize_opt = \'' + str(normalize_opt) + '\'\n') 
-29      f.write('    output_opt = \'' + str(output_opt) + '\'\n') 
-30      f.write('    restrict_type = \'' + str(restrict_type) + '\'\n') 
-31      f.write('    num_srch_bins = ' + str(num_srch_bins) + '\n') 
-32      f.write('    luse_grid1_area = ' + str(luse_grid1_area) + '\n') 
-33      f.write('    luse_grid2_area = ' + str(luse_grid2_area) + '\n') 
-34      f.write('    grid1_periodic = ' + str(grid1_periodic) + '\n') 
-35      f.write('    grid2_periodic = ' + str(grid2_periodic) + '\n') 
-36      f.write('/\n') 
-37   
-38      f.close() 
-39   
-40      # compute weights 
-41      pyroms.remapping.scrip.compute_remap_weights('compute_remap_weights_in') 
-42   
-43      # clean 
-44      os.remove('compute_remap_weights_in') 
-
45   
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Module flood'

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Functions[hide private]
-
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flood(varz, - grdz, - Cpos='rho', - irange=None, - jrange=None, - spval=1e+37, - dmax=0, - cdepth=0, - kk=0)
- var = flood(var, grdz)		 - source code - -
- -
- - - - - - -
- - - - - -
Function Details[hide private]
-
- -
- -
- - -
-

flood(varz, - grdz, - Cpos='rho', - irange=None, - jrange=None, - spval=1e+37, - dmax=0, - cdepth=0, - kk=0) -

- 		source code  -
- -

var = flood(var, grdz)

-

optional switch:

-
    -
  • - Cpos='rho', 'u' or 'v' specify the C-grid position where the - variable rely -
    • -
  • - irange specify grid sub-sample for i direction -
    • -
  • - jrange specify grid sub-sample for j direction -
    • -
  • - spval=1e37 define spval value -
    • -
  • - dmax=0 if dmax>0, maximum horizontal - flooding distance -
    • -
  • - cdepth=0 critical depth for flooding if - depth<cdepth => no flooding -
    • -
  • - kk -
    • -
-

Flood varz on gridz

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Source Code for Module pyroms.remapping.flood'

-
-  1  # encoding: utf-8 
-  2   
-  3  import numpy as np 
-  4  import _remapping 
-  5   
-  6  import pyroms 
-  7   
-
  8 -def flood(varz, grdz, Cpos='rho', irange=None, jrange=None, \ 
-  9            spval=1e37, dmax=0, cdepth=0, kk=0): 
-
 10      """ 
- 11      var = flood(var, grdz) 
- 12   
- 13      optional switch: 
- 14        - Cpos='rho', 'u' or 'v'       specify the C-grid position where  
- 15                                       the variable rely 
- 16        - irange                       specify grid sub-sample for i direction 
- 17        - jrange                       specify grid sub-sample for j direction 
- 18        - spval=1e37                   define spval value 
- 19        - dmax=0                       if dmax>0, maximum horizontal  
- 20                                       flooding distance 
- 21        - cdepth=0                     critical depth for flooding 
- 22                                       if depth<cdepth => no flooding 
- 23        - kk 
- 24   
- 25      Flood varz on gridz 
- 26      """ 
- 27   
- 28      varz = varz.copy() 
- 29      varz = np.array(varz) 
- 30   
- 31      assert len(varz.shape) == 3, 'var must be 3D' 
- 32   
- 33      # replace spval by nan 
- 34      idx = np.where(abs((varz-spval)/spval)<=1e-5) 
- 35      varz[idx] = np.nan 
- 36   
- 37      if Cpos is 'rho': 
- 38          x = grdz.hgrid.lon_rho 
- 39          y = grdz.hgrid.lat_rho 
- 40          z = grdz.vgrid.z[:] 
- 41          h = grdz.vgrid.h 
- 42          mask = grdz.hgrid.mask_rho 
- 43      elif Cpos is 'u': 
- 44          x = grdz.hgrid.lon_u 
- 45          y = grdz.hgrid.lat_u 
- 46          z = 0.5 * (grdz.vgrid.z[:,:,:-1] + grdz.vgrid.z[:,:,1:]) 
- 47          h = 0.5 * (grdz.vgrid.h[:,:-1] + grdz.vgrid.h[:,1:]) 
- 48          mask = grdz.hgrid.mask_u 
- 49      elif Cpos is 'v': 
- 50          x = grdz.hgrid.lon_v 
- 51          y = grdz.hgrid.lat_v 
- 52          z = 0.5 * (grdz.vgrid.z[:,:-1,:] + grdz.vgrid.z[:,1:,:]) 
- 53          h = 0.5 * (grdz.vgrid.h[:-1,:] + grdz.vgrid.h[1:,:]) 
- 54          mask = grdz.hgrid.mask_v 
- 55      elif Cpos is 'w': 
- 56          x = grdz.hgrid.lon_rho 
- 57          y = grdz.hgrid.lat_rho 
- 58          z = grdz.vgrid.z[:] 
- 59          h = grdz.vgrid.h 
- 60          mask = grdz.hgrid.mask_rho 
- 61      else: 
- 62          raise Warning, '%s bad position. Use depth at Arakawa-C rho points instead.' % Cpos 
- 63   
- 64      nlev, Mm, Lm = varz.shape 
- 65   
- 66      if irange is None: 
- 67          irange = (0,Lm) 
- 68      else: 
- 69          assert varz.shape[2] == irange[1]-irange[0], \ 
- 70                 'var shape and irange must agreed' 
- 71   
- 72      if jrange is None: 
- 73          jrange = (0,Mm) 
- 74      else: 
- 75          assert varz.shape[1] == jrange[1]-jrange[0], \ 
- 76                 'var shape and jrange must agreed' 
- 77   
- 78      x = x[jrange[0]:jrange[1], irange[0]:irange[1]] 
- 79      y = y[jrange[0]:jrange[1], irange[0]:irange[1]] 
- 80      z = z[:,jrange[0]:jrange[1], irange[0]:irange[1]] 
- 81      h = h[jrange[0]:jrange[1], irange[0]:irange[1]] 
- 82      mask = mask[jrange[0]:jrange[1], irange[0]:irange[1]] 
- 83   
- 84      # Finding nearest values in horizontal 
- 85      # critical deph => no change if depth is less than specified value 
- 86      cdepth = abs(cdepth) 
- 87      if cdepth != 0: 
- 88          idx = np.where(h >= cdepth) 
- 89          msk = np.zeros(mask.shape) 
- 90          msk[idx] = 1 
- 91      else: 
- 92          msk = mask.copy() 
- 93      for k in range(nlev-1): 
- 94          c1 = np.array(msk, dtype=bool) 
- 95          c2 = np.isnan(varz[k,:,:]) == 1 
- 96          if kk == 0: 
- 97              c3 = np.ones(mask.shape).astype(bool) 
- 98          else: 
- 99              c3 = np.isnan(varz[min(k+kk,nlev-1),:,:]) == 0 
-100          c = c1 & c2 & c3 
-101          idxnan = np.where(c == True) 
-102          idx = np.where(c2 == False) 
-103          if list(idx[0]): 
-104              wet = np.zeros((len(idx[0]),2)) 
-105              dry = np.zeros((len(idxnan[0]),2)) 
-106              wet[:,0] = idx[0]+1 
-107              wet[:,1] = idx[1]+1 
-108              dry[:,0] = idxnan[0]+1 
-109              dry[:,1] = idxnan[1]+1 
-110   
-111              varz[k,:] = _remapping.flood(varz[k,:], wet, dry, x, y, dmax) 
-112   
-113      # drop the deepest values down 
-114      idx = np.where(np.isnan(varz) == 1) 
-115      varz[idx] = spval 
-116      bottom = pyroms.utility.get_bottom(varz, mask, spval=spval) 
-117      surface = pyroms.utility.get_surface(varz, mask, spval=spval) 
-118      for i in range(Lm): 
-119          for j in range(Mm): 
-120              if mask[j,i] == 1: 
-121                  varz[:bottom[j,i],j,i] = varz[bottom[j,i],j,i] 
-122                  varz[surface[j,i]:,j,i] = varz[surface[j,i],j,i] 
-123   
-124      return varz 
-
125   
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Module flood

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Functions[hide private]
-
-   - - - - - - -
flood(varz, - grdz, - Cpos='rho', - irange=None, - jrange=None, - spval=1e37, - dmax=0, - cdepth=0, - kk=0)
- var = flood(var, grdz)		 - source code - -
- -
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Function Details[hide private]
-
- -
- -
- - -
-

flood(varz, - grdz, - Cpos='rho', - irange=None, - jrange=None, - spval=1e37, - dmax=0, - cdepth=0, - kk=0) -

- 		source code  -
- -

var = flood(var, grdz)

-

optional switch:

-
    -
  • - Cpos='rho', 'u' or 'v' specify the C-grid position where the - variable rely -
    • -
  • - irange specify grid sub-sample for i direction -
    • -
  • - jrange specify grid sub-sample for j direction -
    • -
  • - spval=1e37 define spval value -
    • -
  • - dmax=0 if dmax>0, maximum horizontal - flooding distance -
    • -
  • - cdepth=0 critical depth for flooding if - depth<cdepth => no flooding -
    • -
  • - kk -
    • -
-

Flood varz on gridz

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Source Code for Module pyroms.remapping.flood

-
-  1  # encoding: utf-8 
-  2   
-  3  import numpy as np 
-  4  import _remapping 
-  5   
-  6  import pyroms 
-  7   
-
  8 -def flood(varz, grdz, Cpos='rho', irange=None, jrange=None, \ 
-  9            spval=1e37, dmax=0, cdepth=0, kk=0): 
-
 10      """ 
- 11      var = flood(var, grdz) 
- 12   
- 13      optional switch: 
- 14        - Cpos='rho', 'u' or 'v'       specify the C-grid position where  
- 15                                       the variable rely 
- 16        - irange                       specify grid sub-sample for i direction 
- 17        - jrange                       specify grid sub-sample for j direction 
- 18        - spval=1e37                   define spval value 
- 19        - dmax=0                       if dmax>0, maximum horizontal  
- 20                                       flooding distance 
- 21        - cdepth=0                     critical depth for flooding 
- 22                                       if depth<cdepth => no flooding 
- 23        - kk 
- 24   
- 25      Flood varz on gridz 
- 26      """ 
- 27   
- 28      varz = varz.copy() 
- 29      varz = np.array(varz) 
- 30   
- 31      assert len(varz.shape) == 3, 'var must be 3D' 
- 32   
- 33      # replace spval by nan 
- 34      idx = np.where(abs((varz-spval)/spval)<=1e-5) 
- 35      varz[idx] = np.nan 
- 36   
- 37      if Cpos is 'rho': 
- 38          x = grdz.hgrid.lon_rho 
- 39          y = grdz.hgrid.lat_rho 
- 40          z = grdz.vgrid.z[:] 
- 41          h = grdz.vgrid.h 
- 42          mask = grdz.hgrid.mask_rho 
- 43      elif Cpos is 'u': 
- 44          x = grdz.hgrid.lon_u 
- 45          y = grdz.hgrid.lat_u 
- 46          z = 0.5 * (grdz.vgrid.z[:,:,:-1] + grdz.vgrid.z[:,:,1:]) 
- 47          h = 0.5 * (grdz.vgrid.h[:,:-1] + grdz.vgrid.h[:,1:]) 
- 48          mask = grdz.hgrid.mask_u 
- 49      elif Cpos is 'v': 
- 50          x = grdz.hgrid.lon_v 
- 51          y = grdz.hgrid.lat_v 
- 52          z = 0.5 * (grdz.vgrid.z[:,:-1,:] + grdz.vgrid.z[:,1:,:]) 
- 53          h = 0.5 * (grdz.vgrid.h[:-1,:] + grdz.vgrid.h[1:,:]) 
- 54          mask = grdz.hgrid.mask_v 
- 55      elif Cpos is 'w': 
- 56          x = grdz.hgrid.lon_rho 
- 57          y = grdz.hgrid.lat_rho 
- 58          z = grdz.vgrid.z[:] 
- 59          h = grdz.vgrid.h 
- 60          mask = grdz.hgrid.mask_rho 
- 61      else: 
- 62          raise Warning, '%s bad position. Use depth at Arakawa-C rho points instead.' % Cpos 
- 63   
- 64      nlev, Mm, Lm = varz.shape 
- 65   
- 66      if irange is None: 
- 67          irange = (0,Lm) 
- 68      else: 
- 69          assert varz.shape[2] == irange[1]-irange[0], \ 
- 70                 'var shape and irange must agreed' 
- 71   
- 72      if jrange is None: 
- 73          jrange = (0,Mm) 
- 74      else: 
- 75          assert varz.shape[1] == jrange[1]-jrange[0], \ 
- 76                 'var shape and jrange must agreed' 
- 77   
- 78      x = x[jrange[0]:jrange[1], irange[0]:irange[1]] 
- 79      y = y[jrange[0]:jrange[1], irange[0]:irange[1]] 
- 80      z = z[:,jrange[0]:jrange[1], irange[0]:irange[1]] 
- 81      h = h[jrange[0]:jrange[1], irange[0]:irange[1]] 
- 82      mask = mask[jrange[0]:jrange[1], irange[0]:irange[1]] 
- 83   
- 84      # Finding nearest values in horizontal 
- 85      # critical deph => no change if depth is less than specified value 
- 86      cdepth = abs(cdepth) 
- 87      if cdepth != 0: 
- 88          idx = np.where(h >= cdepth) 
- 89          msk = np.zeros(mask.shape) 
- 90          msk[idx] = 1 
- 91      else: 
- 92          msk = mask.copy() 
- 93      for k in range(nlev-1): 
- 94          c1 = np.array(msk, dtype=bool) 
- 95          c2 = np.isnan(varz[k,:,:]) == 1 
- 96          if kk == 0: 
- 97              c3 = np.ones(mask.shape).astype(bool) 
- 98          else: 
- 99              c3 = np.isnan(varz[min(k+kk,nlev-1),:,:]) == 0 
-100          c = c1 & c2 & c3 
-101          idxnan = np.where(c == True) 
-102          idx = np.where(c2 == False) 
-103          if list(idx[0]): 
-104              wet = np.zeros((len(idx[0]),2)) 
-105              dry = np.zeros((len(idxnan[0]),2)) 
-106              wet[:,0] = idx[0]+1 
-107              wet[:,1] = idx[1]+1 
-108              dry[:,0] = idxnan[0]+1 
-109              dry[:,1] = idxnan[1]+1 
-110   
-111              varz[k,:] = _remapping.flood(varz[k,:], wet, dry, x, y, dmax) 
-112   
-113      # drop the deepest values down 
-114      idx = np.where(np.isnan(varz) == 1) 
-115      varz[idx] = spval 
-116      bottom = pyroms.utility.get_bottom(varz, mask, spval=spval) 
-117      surface = pyroms.utility.get_surface(varz, mask, spval=spval) 
-118      for i in range(Lm): 
-119          for j in range(Mm): 
-120              if mask[j,i] == 1: 
-121                  varz[:bottom[j,i],j,i] = varz[bottom[j,i],j,i] 
-122                  varz[surface[j,i]:,j,i] = varz[surface[j,i],j,i] 
-123   
-124      return varz 
-
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Module make_remap_grid_file'

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make_remap_grid_file(grid)
- generate grid file to be used with scrip to compute the weights for - remapping.		 - source code - -
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Source Code for Module pyroms.remapping.make_remap_grid_file'

-
-  1  import numpy as np 
-  2  from datetime import datetime 
-  3  try: 
-  4    import netCDF4 as netCDF 
-  5  except: 
-  6    import netCDF3 as netCDF 
-  7  import pyroms 
-  8   
-  9   
-
 10 -def make_remap_grid_file(grid, Cpos='rho'): 
-
 11      ''' 
- 12      make_remap_grid_file(grid) 
- 13   
- 14      generate grid file to be used with scrip to compute 
- 15      the weights for remapping. 
- 16      ''' 
- 17   
- 18      # get grid 
- 19      if type(grid).__name__ == 'ROMS_Grid': 
- 20          grd = grid 
- 21      else: 
- 22          grd = pyroms.grid.get_ROMS_grid(grid) 
- 23   
- 24      #create remap file 
- 25      remap_filename = 'remap_grid_' + grd.name + '_' + Cpos + '.nc' 
- 26      nc = netCDF.Dataset(remap_filename, 'w', format='NETCDF3_CLASSIC') 
- 27      nc.Description = 'remap grid file on' + Cpos + 'points' 
- 28      nc.Author = 'pyroms.remapping.make_remap_grid_file' 
- 29      nc.Created = datetime.now().strftime("%Y-%m-%d %H:%M:%S") 
- 30      nc.title = grd.name 
- 31   
- 32      if Cpos == 'rho': 
- 33          lon_corner = grd.hgrid.lon_vert 
- 34          lat_corner = grd.hgrid.lat_vert 
- 35          grid_center_lon = grd.hgrid.lon_rho.flatten() 
- 36          grid_center_lat = grd.hgrid.lat_rho.flatten() 
- 37          grid_imask = grd.hgrid.mask_rho.flatten() 
- 38          Mp, Lp = grd.hgrid.mask_rho.shape 
- 39      elif Cpos == 'u': 
- 40          lon_corner = 0.5 * (grd.hgrid.lon_vert[:,:-1] + \ 
- 41                              grd.hgrid.lon_vert[:,1:]) 
- 42          lat_corner = 0.5 * (grd.hgrid.lat_vert[:,:-1] + \ 
- 43                              grd.hgrid.lat_vert[:,1:]) 
- 44          grid_center_lon = grd.hgrid.lon_u.flatten() 
- 45          grid_center_lat = grd.hgrid.lat_u.flatten() 
- 46          grid_imask = grd.hgrid.mask_u.flatten() 
- 47          Mp, Lp = grd.hgrid.mask_u.shape 
- 48      elif Cpos == 'v': 
- 49          lon_corner = 0.5 * (grd.hgrid.lon_vert[:-1,:] + \ 
- 50                              grd.hgrid.lon_vert[1:,:]) 
- 51          lat_corner = 0.5 * (grd.hgrid.lat_vert[:-1,:] + \ 
- 52                              grd.hgrid.lat_vert[1:,:]) 
- 53          grid_center_lon = grd.hgrid.lon_v.flatten() 
- 54          grid_center_lat = grd.hgrid.lat_v.flatten() 
- 55          grid_imask = grd.hgrid.mask_v.flatten() 
- 56          Mp, Lp = grd.hgrid.mask_v.shape 
- 57      else: 
- 58          raise ValueError, 'Cpos must be rho, u or v' 
- 59   
- 60      grid_size = Lp * Mp 
- 61   
- 62      grid_corner_lon = np.zeros((grid_size, 4)) 
- 63      grid_corner_lat = np.zeros((grid_size, 4)) 
- 64      k = 0 
- 65      for j in range(Mp): 
- 66          for i in range(Lp): 
- 67              grid_corner_lon[k,0] = lon_corner[j,i] 
- 68              grid_corner_lat[k,0] = lat_corner[j,i] 
- 69              grid_corner_lon[k,1] = lon_corner[j,i+1] 
- 70              grid_corner_lat[k,1] = lat_corner[j,i+1] 
- 71              grid_corner_lon[k,2] = lon_corner[j+1,i+1] 
- 72              grid_corner_lat[k,2] = lat_corner[j+1,i+1] 
- 73              grid_corner_lon[k,3] = lon_corner[j+1,i] 
- 74              grid_corner_lat[k,3] = lat_corner[j+1,i] 
- 75              k = k + 1 
- 76   
- 77      #Write netcdf file 
- 78      nc.createDimension('grid_size', grid_size) 
- 79      nc.createDimension('grid_corners', 4) 
- 80      nc.createDimension('grid_rank', 2) 
- 81   
- 82      nc.createVariable('grid_dims', 'i4', ('grid_rank')) 
- 83      nc.variables['grid_dims'].long_name = 'grid size along x and y axis' 
- 84      nc.variables['grid_dims'].units = 'None' 
- 85      nc.variables['grid_dims'][:] = [(Lp, Mp)] 
- 86   
- 87      nc.createVariable('grid_center_lon', 'f8', ('grid_size')) 
- 88      nc.variables['grid_center_lon'].long_name = 'longitude of cell center' 
- 89      nc.variables['grid_center_lon'].units = 'degrees' 
- 90      nc.variables['grid_center_lon'][:] = grid_center_lon 
- 91   
- 92      nc.createVariable('grid_center_lat', 'f8', ('grid_size')) 
- 93      nc.variables['grid_center_lat'].long_name = 'latitude of cell center' 
- 94      nc.variables['grid_center_lat'].units = 'degrees' 
- 95      nc.variables['grid_center_lat'][:] = grid_center_lat 
- 96   
- 97      nc.createVariable('grid_imask', 'i4', ('grid_size')) 
- 98      nc.variables['grid_imask'].long_name = 'mask' 
- 99      nc.variables['grid_imask'].units = 'None' 
-100      nc.variables['grid_imask'][:] = grid_imask 
-101   
-102      nc.createVariable('grid_corner_lon', 'f8', ('grid_size', 'grid_corners')) 
-103      nc.variables['grid_corner_lon'].long_name = 'longitude of cell corner' 
-104      nc.variables['grid_corner_lon'].units = 'degrees' 
-105      nc.variables['grid_corner_lon'][:] = grid_corner_lon 
-106   
-107      nc.createVariable('grid_corner_lat', 'f8', ('grid_size', 'grid_corners')) 
-108      nc.variables['grid_corner_lat'].long_name = 'latitude of cell corner' 
-109      nc.variables['grid_corner_lat'].units = 'degrees' 
-110      nc.variables['grid_corner_lat'][:] = grid_corner_lat 
-111   
-112      nc.close() 
-
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Module make_remap_grid_file

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make_remap_grid_file(grid)
- generate grid file to be used with scrip to compute the weights for - remapping.		 - source code - -
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Source Code for Module pyroms.remapping.make_remap_grid_file

-
-  1  import numpy as np 
-  2  from datetime import datetime 
-  3  try: 
-  4    import netCDF4 as netCDF 
-  5  except: 
-  6    import netCDF3 as netCDF 
-  7  import pyroms 
-  8   
-  9   
-
 10 -def make_remap_grid_file(grid, Cpos='rho'): 
-
 11      ''' 
- 12      make_remap_grid_file(grid) 
- 13   
- 14      generate grid file to be used with scrip to compute 
- 15      the weights for remapping. 
- 16      ''' 
- 17   
- 18      # get grid 
- 19      if type(grid).__name__ == 'ROMS_Grid': 
- 20          grd = grid 
- 21      else: 
- 22          grd = pyroms.grid.get_ROMS_grid(grid) 
- 23   
- 24      #create remap file 
- 25      remap_filename = 'remap_grid_' + grd.name + '_' + Cpos + '.nc' 
- 26      nc = netCDF.Dataset(remap_filename, 'w', format='NETCDF3_CLASSIC') 
- 27      nc.Description = 'remap grid file on' + Cpos + 'points' 
- 28      nc.Author = 'pyroms.remapping.make_remap_grid_file' 
- 29      nc.Created = datetime.now().strftime("%Y-%m-%d %H:%M:%S") 
- 30      nc.title = grd.name 
- 31   
- 32      if Cpos == 'rho': 
- 33          lon_corner = grd.hgrid.lon_vert 
- 34          lat_corner = grd.hgrid.lat_vert 
- 35          grid_center_lon = grd.hgrid.lon_rho.flatten() 
- 36          grid_center_lat = grd.hgrid.lat_rho.flatten() 
- 37          grid_imask = grd.hgrid.mask_rho.flatten() 
- 38          Mp, Lp = grd.hgrid.mask_rho.shape 
- 39      elif Cpos == 'u': 
- 40          lon_corner = 0.5 * (grd.hgrid.lon_vert[:,:-1] + \ 
- 41                              grd.hgrid.lon_vert[:,1:]) 
- 42          lat_corner = 0.5 * (grd.hgrid.lat_vert[:,:-1] + \ 
- 43                              grd.hgrid.lat_vert[:,1:]) 
- 44          grid_center_lon = grd.hgrid.lon_u.flatten() 
- 45          grid_center_lat = grd.hgrid.lat_u.flatten() 
- 46          grid_imask = grd.hgrid.mask_u.flatten() 
- 47          Mp, Lp = grd.hgrid.mask_u.shape 
- 48      elif Cpos == 'v': 
- 49          lon_corner = 0.5 * (grd.hgrid.lon_vert[:-1,:] + \ 
- 50                              grd.hgrid.lon_vert[1:,:]) 
- 51          lat_corner = 0.5 * (grd.hgrid.lat_vert[:-1,:] + \ 
- 52                              grd.hgrid.lat_vert[1:,:]) 
- 53          grid_center_lon = grd.hgrid.lon_v.flatten() 
- 54          grid_center_lat = grd.hgrid.lat_v.flatten() 
- 55          grid_imask = grd.hgrid.mask_v.flatten() 
- 56          Mp, Lp = grd.hgrid.mask_v.shape 
- 57      else: 
- 58          raise ValueError, 'Cpos must be rho, u or v' 
- 59   
- 60      grid_size = Lp * Mp 
- 61   
- 62      grid_corner_lon = np.zeros((grid_size, 4)) 
- 63      grid_corner_lat = np.zeros((grid_size, 4)) 
- 64      k = 0 
- 65      for j in range(Mp): 
- 66          for i in range(Lp): 
- 67              grid_corner_lon[k,0] = lon_corner[j,i] 
- 68              grid_corner_lat[k,0] = lat_corner[j,i] 
- 69              grid_corner_lon[k,1] = lon_corner[j,i+1] 
- 70              grid_corner_lat[k,1] = lat_corner[j,i+1] 
- 71              grid_corner_lon[k,2] = lon_corner[j+1,i+1] 
- 72              grid_corner_lat[k,2] = lat_corner[j+1,i+1] 
- 73              grid_corner_lon[k,3] = lon_corner[j+1,i] 
- 74              grid_corner_lat[k,3] = lat_corner[j+1,i] 
- 75              k = k + 1 
- 76   
- 77      #Write netcdf file 
- 78      nc.createDimension('grid_size', grid_size) 
- 79      nc.createDimension('grid_corners', 4) 
- 80      nc.createDimension('grid_rank', 2) 
- 81   
- 82      nc.createVariable('grid_dims', 'i4', ('grid_rank')) 
- 83      nc.variables['grid_dims'].long_name = 'grid size along x and y axis' 
- 84      nc.variables['grid_dims'].units = 'None' 
- 85      nc.variables['grid_dims'][:] = [(Lp, Mp)] 
- 86   
- 87      nc.createVariable('grid_center_lon', 'f8', ('grid_size')) 
- 88      nc.variables['grid_center_lon'].long_name = 'longitude of cell center' 
- 89      nc.variables['grid_center_lon'].units = 'degrees' 
- 90      nc.variables['grid_center_lon'][:] = grid_center_lon 
- 91   
- 92      nc.createVariable('grid_center_lat', 'f8', ('grid_size')) 
- 93      nc.variables['grid_center_lat'].long_name = 'latitude of cell center' 
- 94      nc.variables['grid_center_lat'].units = 'degrees' 
- 95      nc.variables['grid_center_lat'][:] = grid_center_lat 
- 96   
- 97      nc.createVariable('grid_imask', 'i4', ('grid_size')) 
- 98      nc.variables['grid_imask'].long_name = 'mask' 
- 99      nc.variables['grid_imask'].units = 'None' 
-100      nc.variables['grid_imask'][:] = grid_imask 
-101   
-102      nc.createVariable('grid_corner_lon', 'f8', ('grid_size', 'grid_corners')) 
-103      nc.variables['grid_corner_lon'].long_name = 'longitude of cell corner' 
-104      nc.variables['grid_corner_lon'].units = 'degrees' 
-105      nc.variables['grid_corner_lon'][:] = grid_corner_lon 
-106   
-107      nc.createVariable('grid_corner_lat', 'f8', ('grid_size', 'grid_corners')) 
-108      nc.variables['grid_corner_lat'].long_name = 'latitude of cell corner' 
-109      nc.variables['grid_corner_lat'].units = 'degrees' 
-110      nc.variables['grid_corner_lat'][:] = grid_corner_lat 
-111   
-112      nc.close() 
-
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remap(src_array, - remap_file, - src_grad1=None, - src_grad2=None, - src_grad3=None, - spval=1e+37, - verbose=False)
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Source Code for Module pyroms.remapping.remap'

-
-  1  import numpy as np 
-  2  try: 
-  3      import netCDF4 as netCDF 
-  4  except: 
-  5      import netCDF3 as netCDF 
-  6  import pyroms 
-  7   
-  8   
-
  9 -def remap(src_array, remap_file, src_grad1=None, src_grad2=None, \ 
- 10               src_grad3=None, spval=1e37, verbose=False): 
-
 11      ''' 
- 12      remap based on addresses and weights computed in a setup phase 
- 13      ''' 
- 14   
- 15      # get info from remap_file 
- 16      data = netCDF.Dataset(remap_file, 'r') 
- 17      title = data.title 
- 18      map_method = data.map_method 
- 19      normalization = data.normalization 
- 20      src_grid_name = data.source_grid 
- 21      dst_grid_name = data.dest_grid 
- 22      src_grid_size = len(data.dimensions['src_grid_size']) 
- 23      dst_grid_size = len(data.dimensions['dst_grid_size']) 
- 24      num_links = len(data.dimensions['num_links']) 
- 25      src_grid_dims = data.variables['src_grid_dims'] 
- 26      dst_grid_dims = data.variables['dst_grid_dims']     
- 27   
- 28      # get weights and addresses from remap_file 
- 29      map_wts = data.variables['remap_matrix'][:] 
- 30      dst_add = data.variables['dst_address'][:] 
- 31      src_add = data.variables['src_address'][:] 
- 32   
- 33      # get destination mask 
- 34      dst_mask = data.variables['dst_grid_imask'][:] 
- 35   
- 36      # remap from src grid to dst grid 
- 37      if src_grad1 is not None: 
- 38          iorder = 2 
- 39      else: 
- 40          iorder = 1 
- 41   
- 42      if verbose is True: 
- 43          print 'Reading remapping: ', title 
- 44          print 'From file: ', remap_file 
- 45          print ' ' 
- 46          print 'Remapping between:' 
- 47          print src_grid_name 
- 48          print 'and'  
- 49          print dst_grid_name 
- 50          print 'Remapping method: ', map_method 
- 51   
- 52      ndim = len(src_array.squeeze().shape) 
- 53       
- 54      if (ndim == 2): 
- 55          tmp_dst_array = np.zeros((dst_grid_size)) 
- 56          tmp_src_array = src_array.flatten() 
- 57   
- 58          if iorder == 1: 
- 59              # first order remapping 
- 60              # insure that map_wts is a (num_links,4) array 
- 61              tmp_map_wts = np.zeros((num_links,4)) 
- 62              tmp_map_wts[:,0] = map_wts[:,0].copy() 
- 63              map_wts = tmp_map_wts 
- 64              pyroms.remapping.scrip.remap(tmp_dst_array, map_wts, \ 
- 65                                           dst_add, src_add, tmp_src_array) 
- 66   
- 67          if iorder == 2: 
- 68              # second order remapping 
- 69              if map_method == 'conservative': 
- 70                  # insure that map_wts is a (num_links,4) array 
- 71                  tmp_map_wts = np.zeros((num_links,4)) 
- 72                  tmp_map_wts[:,0:2] = map_wts[:,0:2].copy() 
- 73                  map_wts = tmp_map_wts 
- 74                  tmp_src_grad1 = src_grad1.flatten() 
- 75                  tmp_src_grad2 = src_grad2.flatten() 
- 76                  pyroms.remapping.scrip.remap(tmp_dst_array, map_wts, \ 
- 77                                               dst_add, src_add, tmp_src_array, \ 
- 78                                               tmp_src_grad1, tmp_src_grad2) 
- 79              elif map_method == 'bicubic': 
- 80                  tmp_src_grad1 = src_grad1.flatten() 
- 81                  tmp_src_grad2 = src_grad2.flatten() 
- 82                  tmp_src_grad3 = src_grad3.flatten() 
- 83                  pyroms.remapping.scrip.remap(tmp_dst_array, map_wts, \ 
- 84                                               dst_add, src_add, tmp_src_array, \ 
- 85                                               tmp_src_grad1, tmp_src_grad2, \ 
- 86                                               tmp_src_grad3) 
- 87              else: 
- 88                  raise ValueError, 'Unknow method'                 
- 89   
- 90          # mask dst_array 
- 91          idx = np.where(dst_mask == 0) 
- 92          tmp_dst_array[idx] = spval 
- 93          tmp_dst_array = np.ma.masked_values(tmp_dst_array, spval) 
- 94   
- 95          # reshape 
- 96          dst_array = np.reshape(tmp_dst_array, (dst_grid_dims[1], \ 
- 97                                 dst_grid_dims[0])) 
- 98   
- 99      elif (ndim == 3): 
-100   
-101          nlev = src_array.shape[0] 
-102          dst_array = np.zeros((nlev, dst_grid_dims[1], dst_grid_dims[0])) 
-103   
-104          # loop over vertical level 
-105          for k in range(nlev): 
-106   
-107              tmp_src_array = src_array[k,:,:].flatten() 
-108              tmp_dst_array = np.zeros((dst_grid_size)) 
-109   
-110              if iorder == 1: 
-111                  # first order remapping 
-112                  # insure that map_wts is a (num_links,4) array 
-113                  tmp_map_wts = np.zeros((num_links,4)) 
-114                  tmp_map_wts[:,0] = map_wts[:,0].copy() 
-115                  map_wts = tmp_map_wts 
-116                  pyroms.remapping.scrip.remap(tmp_dst_array, map_wts, \ 
-117                                               dst_add, src_add, tmp_src_array) 
-118   
-119              if iorder == 2: 
-120                  # second order remapping 
-121                  if map_method == 'conservative': 
-122                      tmp_src_grad1 = src_grad1.flatten() 
-123                      tmp_src_grad2 = src_grad2.flatten() 
-124                      pyroms.remapping.scrip.remap(tmp_dst_array, map_wts, \ 
-125                                                   dst_add, src_add, tmp_src_array, \ 
-126                                                   tmp_src_grad1, tmp_src_grad2) 
-127                  elif map_method == 'bicubic': 
-128                      tmp_src_grad1 = src_grad1.flatten() 
-129                      tmp_src_grad2 = src_grad2.flatten() 
-130                      tmp_src_grad3 = src_grad3.flatten() 
-131                      pyroms.remapping.scrip.remap(tmp_dst_array, map_wts, \ 
-132                                                   dst_add, src_add, tmp_src_array, \ 
-133                                                   tmp_src_grad1, tmp_src_grad2, \ 
-134                                                   tmp_src_grad3) 
-135                  else: 
-136                      raise ValueError, 'Unknow method'                 
-137   
-138   
-139              # mask dst_array 
-140              idx = np.where(dst_mask == 0) 
-141              tmp_dst_array[idx] = spval 
-142              tmp_dst_array = np.ma.masked_values(tmp_dst_array, spval) 
-143   
-144              # reshape 
-145              dst_array[k,:,:] = np.reshape(tmp_dst_array, (dst_grid_dims[1], \ 
-146                                            dst_grid_dims[0])) 
-147   
-148      else: 
-149          raise ValueError, 'src_array must have two or three dimensions' 
-150   
-151   
-152      # close data file 
-153      data.close() 
-154   
-155      return dst_array 
-
156   
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Module remap

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Functions[hide private]
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remap(src_array, - remap_file, - src_grad1=None, - src_grad2=None, - src_grad3=None, - spval=1e37, - verbose=False)
- remap based on addresses and weights computed in a setup phase		 - source code - -
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Source Code for Module pyroms.remapping.remap

-
-  1  import numpy as np 
-  2  try: 
-  3      import netCDF4 as netCDF 
-  4  except: 
-  5      import netCDF3 as netCDF 
-  6  import pyroms 
-  7   
-  8   
-
  9 -def remap(src_array, remap_file, src_grad1=None, src_grad2=None, \ 
- 10               src_grad3=None, spval=1e37, verbose=False): 
-
 11      ''' 
- 12      remap based on addresses and weights computed in a setup phase 
- 13      ''' 
- 14   
- 15      # get info from remap_file 
- 16      data = netCDF.Dataset(remap_file, 'r') 
- 17      title = data.title 
- 18      map_method = data.map_method 
- 19      normalization = data.normalization 
- 20      src_grid_name = data.source_grid 
- 21      dst_grid_name = data.dest_grid 
- 22      src_grid_size = len(data.dimensions['src_grid_size']) 
- 23      dst_grid_size = len(data.dimensions['dst_grid_size']) 
- 24      num_links = len(data.dimensions['num_links']) 
- 25      src_grid_dims = data.variables['src_grid_dims'] 
- 26      dst_grid_dims = data.variables['dst_grid_dims']     
- 27   
- 28      # get weights and addresses from remap_file 
- 29      map_wts = data.variables['remap_matrix'][:] 
- 30      dst_add = data.variables['dst_address'][:] 
- 31      src_add = data.variables['src_address'][:] 
- 32   
- 33      # get destination mask 
- 34      dst_mask = data.variables['dst_grid_imask'][:] 
- 35   
- 36      # remap from src grid to dst grid 
- 37      if src_grad1 is not None: 
- 38          iorder = 2 
- 39      else: 
- 40          iorder = 1 
- 41   
- 42      if verbose is True: 
- 43          print 'Reading remapping: ', title 
- 44          print 'From file: ', remap_file 
- 45          print ' ' 
- 46          print 'Remapping between:' 
- 47          print src_grid_name 
- 48          print 'and'  
- 49          print dst_grid_name 
- 50          print 'Remapping method: ', map_method 
- 51   
- 52      ndim = len(src_array.squeeze().shape) 
- 53       
- 54      if (ndim == 2): 
- 55          tmp_dst_array = np.zeros((dst_grid_size)) 
- 56          tmp_src_array = src_array.flatten() 
- 57   
- 58          if iorder == 1: 
- 59              # first order remapping 
- 60              # insure that map_wts is a (num_links,4) array 
- 61              tmp_map_wts = np.zeros((num_links,4)) 
- 62              tmp_map_wts[:,0] = map_wts[:,0].copy() 
- 63              map_wts = tmp_map_wts 
- 64              pyroms.remapping.scrip.remap(tmp_dst_array, map_wts, \ 
- 65                                           dst_add, src_add, tmp_src_array) 
- 66   
- 67          if iorder == 2: 
- 68              # second order remapping 
- 69              if map_method == 'conservative': 
- 70                  # insure that map_wts is a (num_links,4) array 
- 71                  tmp_map_wts = np.zeros((num_links,4)) 
- 72                  tmp_map_wts[:,0:2] = map_wts[:,0:2].copy() 
- 73                  map_wts = tmp_map_wts 
- 74                  tmp_src_grad1 = src_grad1.flatten() 
- 75                  tmp_src_grad2 = src_grad2.flatten() 
- 76                  pyroms.remapping.scrip.remap(tmp_dst_array, map_wts, \ 
- 77                                               dst_add, src_add, tmp_src_array, \ 
- 78                                               tmp_src_grad1, tmp_src_grad2) 
- 79              elif map_method == 'bicubic': 
- 80                  tmp_src_grad1 = src_grad1.flatten() 
- 81                  tmp_src_grad2 = src_grad2.flatten() 
- 82                  tmp_src_grad3 = src_grad3.flatten() 
- 83                  pyroms.remapping.scrip.remap(tmp_dst_array, map_wts, \ 
- 84                                               dst_add, src_add, tmp_src_array, \ 
- 85                                               tmp_src_grad1, tmp_src_grad2, \ 
- 86                                               tmp_src_grad3) 
- 87              else: 
- 88                  raise ValueError, 'Unknow method'                 
- 89   
- 90          # mask dst_array 
- 91          idx = np.where(dst_mask == 0) 
- 92          tmp_dst_array[idx] = spval 
- 93          tmp_dst_array = np.ma.masked_values(tmp_dst_array, spval) 
- 94   
- 95          # reshape 
- 96          dst_array = np.reshape(tmp_dst_array, (dst_grid_dims[1], \ 
- 97                                 dst_grid_dims[0])) 
- 98   
- 99      elif (ndim == 3): 
-100   
-101          nlev = src_array.shape[0] 
-102          dst_array = np.zeros((nlev, dst_grid_dims[1], dst_grid_dims[0])) 
-103   
-104          # loop over vertical level 
-105          for k in range(nlev): 
-106   
-107              tmp_src_array = src_array[k,:,:].flatten() 
-108              tmp_dst_array = np.zeros((dst_grid_size)) 
-109   
-110              if iorder == 1: 
-111                  # first order remapping 
-112                  # insure that map_wts is a (num_links,4) array 
-113                  tmp_map_wts = np.zeros((num_links,4)) 
-114                  tmp_map_wts[:,0] = map_wts[:,0].copy() 
-115                  map_wts = tmp_map_wts 
-116                  pyroms.remapping.scrip.remap(tmp_dst_array, map_wts, \ 
-117                                               dst_add, src_add, tmp_src_array) 
-118   
-119              if iorder == 2: 
-120                  # second order remapping 
-121                  if map_method == 'conservative': 
-122                      tmp_src_grad1 = src_grad1.flatten() 
-123                      tmp_src_grad2 = src_grad2.flatten() 
-124                      pyroms.remapping.scrip.remap(tmp_dst_array, map_wts, \ 
-125                                                   dst_add, src_add, tmp_src_array, \ 
-126                                                   tmp_src_grad1, tmp_src_grad2) 
-127                  elif map_method == 'bicubic': 
-128                      tmp_src_grad1 = src_grad1.flatten() 
-129                      tmp_src_grad2 = src_grad2.flatten() 
-130                      tmp_src_grad3 = src_grad3.flatten() 
-131                      pyroms.remapping.scrip.remap(tmp_dst_array, map_wts, \ 
-132                                                   dst_add, src_add, tmp_src_array, \ 
-133                                                   tmp_src_grad1, tmp_src_grad2, \ 
-134                                                   tmp_src_grad3) 
-135                  else: 
-136                      raise ValueError, 'Unknow method'                 
-137   
-138   
-139              # mask dst_array 
-140              idx = np.where(dst_mask == 0) 
-141              tmp_dst_array[idx] = spval 
-142              tmp_dst_array = np.ma.masked_values(tmp_dst_array, spval) 
-143   
-144              # reshape 
-145              dst_array[k,:,:] = np.reshape(tmp_dst_array, (dst_grid_dims[1], \ 
-146                                            dst_grid_dims[0])) 
-147   
-148      else: 
-149          raise ValueError, 'src_array must have two or three dimensions' 
-150   
-151   
-152      # close data file 
-153      data.close() 
-154   
-155      return dst_array 
-
156   
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Module roms2z'

source code

- - - - - - - - - -
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Functions[hide private]
-
-   - - - - - - -
roms2z(var, - grd, - grdz, - Cpos='rho', - irange=None, - jrange=None, - spval=1e+37, - mode='linear')
- varz = roms2z(var, grd, grdz)		 - source code - -
- -
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Function Details[hide private]
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- -
- - -
-

roms2z(var, - grd, - grdz, - Cpos='rho', - irange=None, - jrange=None, - spval=1e+37, - mode='linear') -

- 		source code  -
- -

varz = roms2z(var, grd, grdz)

-

optional switch:

-
    -
  • - Cpos='rho', 'u' 'v' or 'w' specify the C-grid position where the - variable rely -
    • -
  • - irange specify grid sub-sample for i direction -
    • -
  • - jrange specify grid sub-sample for j direction -
    • -
  • - spval=1e37 define spval value -
    • -
  • - mode='linear' or 'spline' specify the type of interpolation -
    • -
-

Interpolate the variable from ROMS grid grd to z vertical grid - grdz

-
-
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Source Code for Module pyroms.remapping.roms2z'

-
- 1  # encoding: utf-8 
- 2   
- 3  import numpy as np 
- 4  import _interp 
- 5   
-
 6 -def roms2z(var, grd, grdz, Cpos='rho', irange=None, jrange=None, \ 
- 7             spval=1e37, mode='linear'): 
-
 8      """ 
- 9      varz = roms2z(var, grd, grdz) 
-10   
-11      optional switch: 
-12        - Cpos='rho', 'u' 'v' or 'w'   specify the C-grid position where  
-13                                       the variable rely 
-14        - irange                       specify grid sub-sample for i direction 
-15        - jrange                       specify grid sub-sample for j direction 
-16        - spval=1e37                   define spval value 
-17        - mode='linear' or 'spline'    specify the type of interpolation 
-18   
-19      Interpolate the variable from ROMS grid grd to z vertical grid grdz 
-20      """ 
-21   
-22      var = var.copy() 
-23   
-24      assert len(var.shape) == 3, 'var must be 3D' 
-25   
-26      if mode=='linear': 
-27          imode=0 
-28      elif mode=='spline': 
-29          imode=1 
-30      else: 
-31          imode=0 
-32          raise Warning, '%s not supported, defaulting to linear' % mode 
-33   
-34   
-35      if Cpos is 'rho': 
-36          z = grd.vgrid.z_r[0,:] 
-37          depth = grdz.vgrid.z 
-38          mask = grd.hgrid.mask_rho 
-39      elif Cpos is 'u': 
-40          z = 0.5 * (grd.vgrid.z_r[0,:,:,:-1] + grd.vgrid.z_r[0,:,:,1:]) 
-41          depth = 0.5 * (grdz.vgrid.z[:,:,:-1] + grdz.vgrid.z[:,:,1:]) 
-42          mask = grd.hgrid.mask_u 
-43      elif Cpos is 'v': 
-44          z = 0.5 * (grd.vgrid.z_r[0,:,:-1,:] + grd.vgrid.z_r[0,:,1:,:]) 
-45          depth = 0.5 * (grdz.vgrid.z[:,:-1,:] + grdz.vgrid.z[:,1:,:]) 
-46          mask = grd.hgrid.mask_v 
-47      elif Cpos is 'w': 
-48          z = grd.vgrid.z_w[0,:] 
-49          depth = grdz.vgrid.z 
-50          mask = grd.hgrid.mask_rho 
-51      else: 
-52          raise Warning, '%s unknown position. Cpos must be rho, u, v or w.' % Cpos 
-53   
-54      Nm, Mm, Lm = var.shape 
-55      nlev = grdz.vgrid.N 
-56   
-57      var = np.concatenate((var, var[-2:-1,:,:]), 0) 
-58      z = np.concatenate((z, 100*np.ones((1,z.shape[1], z.shape[2]))), 0) 
-59   
-60      if irange is None: 
-61          irange = (0,Lm) 
-62      else: 
-63          assert var.shape[2] == irange[1]-irange[0], \ 
-64                 'var shape and irange must agreed' 
-65   
-66      if jrange is None: 
-67          jrange = (0,Mm) 
-68      else: 
-69          assert var.shape[1] == jrange[1]-jrange[0], \ 
-70                 'var shape and jrange must agreed' 
-71   
-72      varz = np.zeros((nlev, jrange[1]-jrange[0], irange[1]-irange[0])) 
-73   
-74      for k in range(nlev): 
-75          varz[k,:,:] = _interp.xhslice(var, \ 
-76                          z[:,jrange[0]:jrange[1], irange[0]:irange[1]], \ 
-77                          depth[k,jrange[0]:jrange[1], irange[0]:irange[1]], \ 
-78                          mask[jrange[0]:jrange[1], irange[0]:irange[1]], \ 
-79                          imode, spval) 
-80   
-81      #mask 
-82      idx = np.where(abs((varz-spval)/spval)<=1e-5) 
-83      varz[idx] = spval 
-84      #varz = np.ma.masked_values(varz, spval, rtol=1e-5) 
-85       
-86      return varz 
-
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Module roms2z

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Functions[hide private]
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roms2z(var, - grd, - grdz, - Cpos='rho', - irange=None, - jrange=None, - spval=1e37, - mode='linear')
- varz = roms2z(var, grd, grdz)		 - source code - -
- -
- - - - - - -
- - - - - -
Function Details[hide private]
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- - -
-

roms2z(var, - grd, - grdz, - Cpos='rho', - irange=None, - jrange=None, - spval=1e37, - mode='linear') -

- 		source code  -
- -

varz = roms2z(var, grd, grdz)

-

optional switch:

-
    -
  • - Cpos='rho', 'u' 'v' or 'w' specify the C-grid position where the - variable rely -
    • -
  • - irange specify grid sub-sample for i direction -
    • -
  • - jrange specify grid sub-sample for j direction -
    • -
  • - spval=1e37 define spval value -
    • -
  • - mode='linear' or 'spline' specify the type of interpolation -
    • -
-

Interpolate the variable from ROMS grid grd to z vertical grid - grdz

-
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Source Code for Module pyroms.remapping.roms2z

-
- 1  # encoding: utf-8 
- 2   
- 3  import numpy as np 
- 4  import _interp 
- 5   
-
 6 -def roms2z(var, grd, grdz, Cpos='rho', irange=None, jrange=None, \ 
- 7             spval=1e37, mode='linear'): 
-
 8      """ 
- 9      varz = roms2z(var, grd, grdz) 
-10   
-11      optional switch: 
-12        - Cpos='rho', 'u' 'v' or 'w'   specify the C-grid position where  
-13                                       the variable rely 
-14        - irange                       specify grid sub-sample for i direction 
-15        - jrange                       specify grid sub-sample for j direction 
-16        - spval=1e37                   define spval value 
-17        - mode='linear' or 'spline'    specify the type of interpolation 
-18   
-19      Interpolate the variable from ROMS grid grd to z vertical grid grdz 
-20      """ 
-21   
-22      var = var.copy() 
-23   
-24      assert len(var.shape) == 3, 'var must be 3D' 
-25   
-26      if mode=='linear': 
-27          imode=0 
-28      elif mode=='spline': 
-29          imode=1 
-30      else: 
-31          imode=0 
-32          raise Warning, '%s not supported, defaulting to linear' % mode 
-33   
-34   
-35      if Cpos is 'rho': 
-36          z = grd.vgrid.z_r[0,:] 
-37          depth = grdz.vgrid.z 
-38          mask = grd.hgrid.mask_rho 
-39      elif Cpos is 'u': 
-40          z = 0.5 * (grd.vgrid.z_r[0,:,:,:-1] + grd.vgrid.z_r[0,:,:,1:]) 
-41          depth = 0.5 * (grdz.vgrid.z[:,:,:-1] + grdz.vgrid.z[:,:,1:]) 
-42          mask = grd.hgrid.mask_u 
-43      elif Cpos is 'v': 
-44          z = 0.5 * (grd.vgrid.z_r[0,:,:-1,:] + grd.vgrid.z_r[0,:,1:,:]) 
-45          depth = 0.5 * (grdz.vgrid.z[:,:-1,:] + grdz.vgrid.z[:,1:,:]) 
-46          mask = grd.hgrid.mask_v 
-47      elif Cpos is 'w': 
-48          z = grd.vgrid.z_w[0,:] 
-49          depth = grdz.vgrid.z 
-50          mask = grd.hgrid.mask_rho 
-51      else: 
-52          raise Warning, '%s unknown position. Cpos must be rho, u, v or w.' % Cpos 
-53   
-54      Nm, Mm, Lm = var.shape 
-55      nlev = grdz.vgrid.N 
-56   
-57      var = np.concatenate((var, var[-2:-1,:,:]), 0) 
-58      z = np.concatenate((z, 100*np.ones((1,z.shape[1], z.shape[2]))), 0) 
-59   
-60      if irange is None: 
-61          irange = (0,Lm) 
-62      else: 
-63          assert var.shape[2] == irange[1]-irange[0], \ 
-64                 'var shape and irange must agreed' 
-65   
-66      if jrange is None: 
-67          jrange = (0,Mm) 
-68      else: 
-69          assert var.shape[1] == jrange[1]-jrange[0], \ 
-70                 'var shape and jrange must agreed' 
-71   
-72      varz = np.zeros((nlev, jrange[1]-jrange[0], irange[1]-irange[0])) 
-73   
-74      for k in range(nlev): 
-75          varz[k,:,:] = _interp.xhslice(var, \ 
-76                          z[:,jrange[0]:jrange[1], irange[0]:irange[1]], \ 
-77                          depth[k,jrange[0]:jrange[1], irange[0]:irange[1]], \ 
-78                          mask[jrange[0]:jrange[1], irange[0]:irange[1]], \ 
-79                          imode, spval) 
-80   
-81      #mask 
-82      idx = np.where(abs((varz-spval)/spval)<=1e-5) 
-83      varz[idx] = spval 
-84      #varz = np.ma.masked_values(varz, spval, rtol=1e-5) 
-85       
-86      return varz 
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Module test_remap_weights'

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test_remap_weights(field_choice, - interp_file, - output_file)
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Source Code for Module pyroms.remapping.test_remap_weights'

-
- 1  import os 
- 2  import pyroms 
- 3   
- 4   
-
 5 -def test_remap_weights(field_choice, interp_file, output_file):  
-
 6      ''' 
- 7      test addresses and weights computed in a setup phase 
- 8      ''' 
- 9   
-10      # write test namelist file 
-11      f = open('test_remap_weights_in','w') 
-12   
-13      f.write('&remap_inputs' + '\n') 
-14      f.write('    field_choice = ' + str(field_choice) + '\n') 
-15      f.write('    interp_file = \'' + str(interp_file) + '\'\n') 
-16      f.write('    output_file = \'' + str(output_file) + '\'\n') 
-17      f.write('/') 
-18   
-19      f.close() 
-20   
-21      # run test weights 
-22      pyroms.remapping.scrip.test_remap_weights('test_remap_weights_in') 
-23   
-24      # clean 
-25      os.remove('test_remap_weights_in') 
-26   
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Module test_remap_weights

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Functions[hide private]
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test_remap_weights(field_choice, - interp_file, - output_file)
- test addresses and weights computed in a setup phase		 - source code - -
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Source Code for Module pyroms.remapping.test_remap_weights

-
- 1  import os 
- 2  import pyroms 
- 3   
- 4   
-
 5 -def test_remap_weights(field_choice, interp_file, output_file):  
-
 6      ''' 
- 7      test addresses and weights computed in a setup phase 
- 8      ''' 
- 9   
-10      # write test namelist file 
-11      f = open('test_remap_weights_in','w') 
-12   
-13      f.write('&remap_inputs' + '\n') 
-14      f.write('    field_choice = ' + str(field_choice) + '\n') 
-15      f.write('    interp_file = \'' + str(interp_file) + '\'\n') 
-16      f.write('    output_file = \'' + str(output_file) + '\'\n') 
-17      f.write('/') 
-18   
-19      f.close() 
-20   
-21      # run test weights 
-22      pyroms.remapping.scrip.test_remap_weights('test_remap_weights_in') 
-23   
-24      # clean 
-25      os.remove('test_remap_weights_in') 
-26   
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Module z2roms'

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- - - - - - - - - -
- - - - - -
Functions[hide private]
-
-   - - - - - - -
z2roms(varz, - grdz, - grd, - Cpos='rho', - irange=None, - jrange=None, - spval=1e+37, - flood=True, - dmax=0, - cdepth=0, - kk=0, - mode='linear')
- var = z2roms(var, grdz, grd)		 - source code - -
- -
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Function Details[hide private]
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z2roms(varz, - grdz, - grd, - Cpos='rho', - irange=None, - jrange=None, - spval=1e+37, - flood=True, - dmax=0, - cdepth=0, - kk=0, - mode='linear') -

- 		source code  -
- -

var = z2roms(var, grdz, grd)

-

optional switch:

-
    -
  • - Cpos='rho', 'u' or 'v' specify the C-grid position where the - variable rely -
    • -
  • - irange specify grid sub-sample for i direction -
    • -
  • - jrange specify grid sub-sample for j direction -
    • -
  • - spval=1e37 define spval value -
    • -
  • - dmax=0 if dmax>0, maximum horizontal - flooding distance -
    • -
  • - cdepth=0 critical depth for flooding if - depth<cdepth => no flooding -
    • -
  • - kk -
    • -
  • - mode='linear' or 'spline' specify the type of interpolation -
    • -
-

Interpolate the variable from z vertical grid grdz to ROMS grid - grd

-
-
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Source Code for Module pyroms.remapping.z2roms'

-
-  1  # encoding: utf-8 
-  2   
-  3  import numpy as np 
-  4  import _interp 
-  5  import _remapping 
-  6   
-  7  import pyroms 
-  8   
-
  9 -def z2roms(varz, grdz, grd, Cpos='rho', irange=None, jrange=None, \ 
- 10             spval=1e37, flood=True, dmax=0, cdepth=0, kk=0, \ 
- 11             mode='linear'): 
-
 12      """ 
- 13      var = z2roms(var, grdz, grd) 
- 14   
- 15      optional switch: 
- 16        - Cpos='rho', 'u' or 'v'       specify the C-grid position where  
- 17                                       the variable rely 
- 18        - irange                       specify grid sub-sample for i direction 
- 19        - jrange                       specify grid sub-sample for j direction 
- 20        - spval=1e37                   define spval value 
- 21        - dmax=0                       if dmax>0, maximum horizontal  
- 22                                       flooding distance 
- 23        - cdepth=0                     critical depth for flooding 
- 24                                       if depth<cdepth => no flooding 
- 25        - kk 
- 26        - mode='linear' or 'spline'    specify the type of interpolation 
- 27   
- 28      Interpolate the variable from z vertical grid grdz to ROMS grid grd 
- 29      """ 
- 30   
- 31      varz = varz.copy() 
- 32   
- 33      assert len(varz.shape) == 3, 'var must be 3D' 
- 34   
- 35      if mode=='linear': 
- 36          imode=0 
- 37      elif mode=='spline': 
- 38          imode=1 
- 39      else: 
- 40          raise Warning, '%s not supported, defaulting to linear' % mode 
- 41   
- 42      if Cpos is 'rho': 
- 43          z = grdz.vgrid.z[:] 
- 44          depth = grd.vgrid.z_r[0,:] 
- 45          mask = grd.hgrid.mask_rho 
- 46      elif Cpos is 'u': 
- 47          z = 0.5 * (grdz.vgrid.z[:,:,:-1] + grdz.vgrid.z[:,:,1:]) 
- 48          depth = 0.5 * (grd.vgrid.z_r[0,:,:,:-1] + grd.vgrid.z_r[0,:,:,1:]) 
- 49          mask = grd.hgrid.mask_u 
- 50      elif Cpos is 'v': 
- 51          z = 0.5 * (grdz.vgrid.z[:,:-1,:] + grdz.vgrid.z[:,1:,:]) 
- 52          depth = 0.5 * (grd.vgrid.z_r[0,:,:-1,:] + grd.vgrid.z_r[0,:,1:,:]) 
- 53          mask = grd.hgrid.mask_v 
- 54      elif Cpos is 'w': 
- 55          z = grdz.vgrid.z[:] 
- 56          depth = grd.vgrid.z_w[0,:] 
- 57          mask = grd.hgrid.mask_rho 
- 58      else: 
- 59          raise Warning, '%s bad position. Use depth at Arakawa-C \ 
- 60                               rho points instead.' % Cpos 
- 61   
- 62      nlev, Mm, Lm = varz.shape 
- 63      Nm = depth.shape[0] 
- 64   
- 65      if irange is None: 
- 66          irange = (0,Lm) 
- 67      else: 
- 68          assert varz.shape[2] == irange[1]-irange[0], \ 
- 69                 'var shape and irange must agreed' 
- 70   
- 71      if jrange is None: 
- 72          jrange = (0,Mm) 
- 73      else: 
- 74          assert varz.shape[1] == jrange[1]-jrange[0], \ 
- 75                 'var shape and jrange must agreed' 
- 76   
- 77      # flood varz if requested 
- 78      if flood is True: 
- 79          varz = pyroms.remapping.flood(varz, grdz, Cpos=Cpos, \ 
- 80                   irange=irange, jrange=jrange, spval=spval, \ 
- 81                   dmax=dmax, cdepth=cdepth, kk=kk) 
- 82   
- 83      varz = np.concatenate((varz[0:1,:,:], varz, varz[-1:,:,:]), 0) 
- 84      z = np.concatenate((-9999*np.ones((1,z.shape[1], z.shape[2])), \ 
- 85             z, \ 
- 86             100*np.ones((1,z.shape[1], z.shape[2]))), 0) 
- 87       
- 88      var = np.ma.zeros((Nm, Mm, Lm)) 
- 89   
- 90      for k in range(Nm): 
- 91          var[k,:,:] = _interp.xhslice(varz, \ 
- 92                        z[:,jrange[0]:jrange[1], irange[0]:irange[1]], \ 
- 93                        depth[k,jrange[0]:jrange[1], irange[0]:irange[1]], \ 
- 94                        mask[jrange[0]:jrange[1], irange[0]:irange[1]], \ 
- 95                        imode, spval) 
- 96          #mask 
- 97          var = np.ma.masked_values(var, spval, rtol=1e-5) 
- 98          #var[k,:,:] = np.ma.masked_where(mask == 0, var[k,:,:]) 
- 99       
-100      return var 
-
101   
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Module z2roms

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Functions[hide private]
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z2roms(varz, - grdz, - grd, - Cpos='rho', - irange=None, - jrange=None, - spval=1e37, - flood=True, - dmax=0, - cdepth=0, - kk=0, - mode='linear')
- var = z2roms(var, grdz, grd)		 - source code - -
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Function Details[hide private]
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- - -
-

z2roms(varz, - grdz, - grd, - Cpos='rho', - irange=None, - jrange=None, - spval=1e37, - flood=True, - dmax=0, - cdepth=0, - kk=0, - mode='linear') -

- 		source code  -
- -

var = z2roms(var, grdz, grd)

-

optional switch:

-
    -
  • - Cpos='rho', 'u' or 'v' specify the C-grid position where the - variable rely -
    • -
  • - irange specify grid sub-sample for i direction -
    • -
  • - jrange specify grid sub-sample for j direction -
    • -
  • - spval=1e37 define spval value -
    • -
  • - dmax=0 if dmax>0, maximum horizontal - flooding distance -
    • -
  • - cdepth=0 critical depth for flooding if - depth<cdepth => no flooding -
    • -
  • - kk -
    • -
  • - mode='linear' or 'spline' specify the type of interpolation -
    • -
-

Interpolate the variable from z vertical grid grdz to ROMS grid - grd

-
-
-
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Source Code for Module pyroms.remapping.z2roms

-
-  1  # encoding: utf-8 
-  2   
-  3  import numpy as np 
-  4  import _interp 
-  5  import _remapping 
-  6   
-  7  import pyroms 
-  8   
-
  9 -def z2roms(varz, grdz, grd, Cpos='rho', irange=None, jrange=None, \ 
- 10             spval=1e37, flood=True, dmax=0, cdepth=0, kk=0, \ 
- 11             mode='linear'): 
-
 12      """ 
- 13      var = z2roms(var, grdz, grd) 
- 14   
- 15      optional switch: 
- 16        - Cpos='rho', 'u' or 'v'       specify the C-grid position where  
- 17                                       the variable rely 
- 18        - irange                       specify grid sub-sample for i direction 
- 19        - jrange                       specify grid sub-sample for j direction 
- 20        - spval=1e37                   define spval value 
- 21        - dmax=0                       if dmax>0, maximum horizontal  
- 22                                       flooding distance 
- 23        - cdepth=0                     critical depth for flooding 
- 24                                       if depth<cdepth => no flooding 
- 25        - kk 
- 26        - mode='linear' or 'spline'    specify the type of interpolation 
- 27   
- 28      Interpolate the variable from z vertical grid grdz to ROMS grid grd 
- 29      """ 
- 30   
- 31      varz = varz.copy() 
- 32   
- 33      assert len(varz.shape) == 3, 'var must be 3D' 
- 34   
- 35      if mode=='linear': 
- 36          imode=0 
- 37      elif mode=='spline': 
- 38          imode=1 
- 39      else: 
- 40          raise Warning, '%s not supported, defaulting to linear' % mode 
- 41   
- 42      if Cpos is 'rho': 
- 43          z = grdz.vgrid.z[:] 
- 44          depth = grd.vgrid.z_r[0,:] 
- 45          mask = grd.hgrid.mask_rho 
- 46      elif Cpos is 'u': 
- 47          z = 0.5 * (grdz.vgrid.z[:,:,:-1] + grdz.vgrid.z[:,:,1:]) 
- 48          depth = 0.5 * (grd.vgrid.z_r[0,:,:,:-1] + grd.vgrid.z_r[0,:,:,1:]) 
- 49          mask = grd.hgrid.mask_u 
- 50      elif Cpos is 'v': 
- 51          z = 0.5 * (grdz.vgrid.z[:,:-1,:] + grdz.vgrid.z[:,1:,:]) 
- 52          depth = 0.5 * (grd.vgrid.z_r[0,:,:-1,:] + grd.vgrid.z_r[0,:,1:,:]) 
- 53          mask = grd.hgrid.mask_v 
- 54      elif Cpos is 'w': 
- 55          z = grdz.vgrid.z[:] 
- 56          depth = grd.vgrid.z_w[0,:] 
- 57          mask = grd.hgrid.mask_rho 
- 58      else: 
- 59          raise Warning, '%s bad position. Use depth at Arakawa-C \ 
- 60                               rho points instead.' % Cpos 
- 61   
- 62      nlev, Mm, Lm = varz.shape 
- 63      Nm = depth.shape[0] 
- 64   
- 65      if irange is None: 
- 66          irange = (0,Lm) 
- 67      else: 
- 68          assert varz.shape[2] == irange[1]-irange[0], \ 
- 69                 'var shape and irange must agreed' 
- 70   
- 71      if jrange is None: 
- 72          jrange = (0,Mm) 
- 73      else: 
- 74          assert varz.shape[1] == jrange[1]-jrange[0], \ 
- 75                 'var shape and jrange must agreed' 
- 76   
- 77      # flood varz if requested 
- 78      if flood is True: 
- 79          varz = pyroms.remapping.flood(varz, grdz, Cpos=Cpos, \ 
- 80                   irange=irange, jrange=jrange, spval=spval, \ 
- 81                   dmax=dmax, cdepth=cdepth, kk=kk) 
- 82   
- 83      varz = np.concatenate((varz[0:1,:,:], varz, varz[-1:,:,:]), 0) 
- 84      z = np.concatenate((-9999*np.ones((1,z.shape[1], z.shape[2])), \ 
- 85             z, \ 
- 86             100*np.ones((1,z.shape[1], z.shape[2]))), 0) 
- 87       
- 88      var = np.ma.zeros((Nm, Mm, Lm)) 
- 89   
- 90      for k in range(Nm): 
- 91          var[k,:,:] = _interp.xhslice(varz, \ 
- 92                        z[:,jrange[0]:jrange[1], irange[0]:irange[1]], \ 
- 93                        depth[k,jrange[0]:jrange[1], irange[0]:irange[1]], \ 
- 94                        mask[jrange[0]:jrange[1], irange[0]:irange[1]], \ 
- 95                        imode, spval) 
- 96          #mask 
- 97          var = np.ma.masked_values(var, spval, rtol=1e-5) 
- 98          #var[k,:,:] = np.ma.masked_where(mask == 0, var[k,:,:]) 
- 99       
-100      return var 
-
101   
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Module tools

source code

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - -
Functions[hide private]
-
-   - - - - - - -
zslice(var, - depth, - grd, - Cpos='rho', - vert=False, - mode='linear')
- zslice, lon, lat = zslice(var, depth, grd)		 - source code - -
- -
-   - - - - - - -
sslice(var, - sindex, - grd, - Cpos='rho', - vert=False)
- sslice, lon, lat = sslice(var, sindex, grd)		 - source code - -
- -
-   - - - - - - -
islice(var, - iindex, - grd, - Cpos='rho', - vert=False)
- islice, z, lon, lat = islice(var, iindex, grd)		 - source code - -
- -
-   - - - - - - -
jslice(var, - jindex, - grd, - Cpos='rho', - vert=False)
- jslice, z, lon, lat = jslice(var, jindex, grd)		 - source code - -
- -
-   - - - - - - -
isoslice(var, - prop, - isoval, - grd, - Cpos='rho', - masking=True, - vert=False)
- isoslice, lon, lat = isoslice(variable,property, isoval, grd)		 - source code - -
- -
-   - - - - - - -
transect(var, - istart, - iend, - jstart, - jend, - grd, - Cpos='rho', - vert=False, - spval=1e+37)
- transect, z, lon, lat = transect(var, istart, iend, jstart, jend, - grd)		 - source code - -
- -
-   - - - - - - -
lonslice(var, - longitude, - grd, - Cpos='rho', - vert=False, - spval=1e+37)
- lonslice, z, lon, lat = lonslice(var, longitude, grd)		 - source code - -
- -
-   - - - - - - -
latslice(var, - latitude, - grd, - Cpos='rho', - vert=False, - spval=1e+37)
- latslice, z, lon, lat = latslice(var, latitude, grd)		 - source code - -
- -
-   - - - - - - -
section_transport(u, - v, - istart, - iend, - jstart, - jend, - grd)
- transpu, transpv = section_transport(u, v, istart, iend, jstart, - jend, grd)		 - source code - -
- -
-   - - - - - - -
interm_pt(pnear, - pk, - pai, - pbi, - paj, - pbj) - source code - -
- -
- - - - - - -
- - - - - -
Function Details[hide private]
-
- -
- -
- - -
-

zslice(var, - depth, - grd, - Cpos='rho', - vert=False, - mode='linear') -

- 		source code  -
- -

zslice, lon, lat = zslice(var, depth, grd)

-

optional switch:

-
    -
  • - Cpos='rho', 'u', 'v' or 'w' specify the C-grid position where the - variable rely -
    • -
  • - vert=True/False If True, return the position of the - verticies -
    • -
  • - mode='linear' or 'spline' specify the type of interpolation -
    • -
-

return a constant-z slice at depth depth from 3D variable var lon and - lat contain the C-grid position of the slice for plotting. If vert=True, - lon and lat contain contain the position of the verticies (to be used - with pcolor)

-
-
-
-
- -
- -
- - -
-

sslice(var, - sindex, - grd, - Cpos='rho', - vert=False) -

- 		source code  -
- -

sslice, lon, lat = sslice(var, sindex, grd)

-

optional switch:

-
    -
  • - Cpos='rho', 'u' or 'v' specify the C-grid position where the - variable rely -
    • -
  • - vert=True/False If True, return the position of the - verticies -
    • -
  • - mode='linear' or 'spline' specify the type of interpolation -
    • -
-

return a constant-s slice at index sindex from 3D variable var lon and - lat contain the C-grid position of the slice for plotting. If vert=True, - lon and lat contain contain the position of the verticies (to be used - with pcolor)

-
-
-
-
- -
- -
- - -
-

islice(var, - iindex, - grd, - Cpos='rho', - vert=False) -

- 		source code  -
- -

islice, z, lon, lat = islice(var, iindex, grd)

-

optional switch:

-
    -
  • - Cpos='rho', 'u', 'v' or 'w' specify the C-grid position where the - variable rely -
    • -
  • - vert=True/False If True, return the position of the - verticies -
    • -
-

return a constant-i slice at index iindex from 3D variable var lon, - lat and z contain the C-grid position of the slice for plotting. If - vert=True, lon, lat and z contain contain the position of the verticies - (to be used with pcolor)

-
-
-
-
- -
- -
- - -
-

jslice(var, - jindex, - grd, - Cpos='rho', - vert=False) -

- 		source code  -
- -

jslice, z, lon, lat = jslice(var, jindex, grd)

-

optional switch:

-
    -
  • - Cpos='rho', 'u', 'v' or 'w' specify the C-grid position where the - variable rely -
    • -
  • - vert=True/False If True, return the position of the - verticies -
    • -
-

return a constant-j slice at index jindex from 3D variable var lon, - lat and z contain the C-grid position of the slice for plotting. If - vert=True, lon, lat and z contain contain the position of the verticies - (to be used with pcolor)

-
-
-
-
- -
- -
- - -
-

isoslice(var, - prop, - isoval, - grd, - Cpos='rho', - masking=True, - vert=False) -

- 		source code  -
- -

isoslice, lon, lat = isoslice(variable,property, isoval, grd)

-

optional switch:

-
    -
  • - Cpos='rho', 'u' or 'v' specify the C-grid position where the - variable rely -
    • -
  • - masking=True mask the output if True -
    • -
  • - vert=True/False If True, return the position of the - verticies -
    • -
  • - mode='linear' or 'spline' specify the type of interpolation -
    • -
-

result is a projection of variable at property == isoval in the first - nonsingleton dimension. In the case when there is more than one zero - crossing, the results are averaged. lon, and lat contain the C-grid - position of the slice for plotting. If vert=True, lon and lat and z - contain contain the position of the verticies (to be used with - pcolor)

-

EXAMPLE: s_at_m5 = isoslice(s,z,-5); # s at z == -5 h_at_s30 = - isoslice(z,s,30); # z at s == 30

-
-
-
-
- -
- -
- - -
-

transect(var, - istart, - iend, - jstart, - jend, - grd, - Cpos='rho', - vert=False, - spval=1e+37) -

- 		source code  -
- -

transect, z, lon, lat = transect(var, istart, iend, jstart, jend, - grd)

-

optional switch:

-
    -
  • - Cpos='rho', 'u' or 'v' specify the C-grid position where the - variable rely -
    • -
  • - vert=True/False If True, return the position of the - verticies -
    • -
  • - spval special value -
    • -
  • - rtol tolerance parameter -
    • -
-

return a vertical transect between the points P1=(istart, jstart) and - P2=(iend, jend) from 3D variable var lon, lat and z contain the C-grid - position of the section for plotting. If vert=True, lon, lat and z - contain contain the position of the verticies (to be used with - pcolor)

-
-
-
-
- -
- -
- - -
-

lonslice(var, - longitude, - grd, - Cpos='rho', - vert=False, - spval=1e+37) -

- 		source code  -
- -

lonslice, z, lon, lat = lonslice(var, longitude, grd)

-

optional switch:

-
    -
  • - Cpos='rho', 'u' or 'v' specify the C-grid position where the - variable rely -
    • -
  • - vert=True/False If True, return the position of the - verticies -
    • -
  • - spval special value -
    • -
  • - rtol tolerance parameter -
    • -
-

return a longitudinal slice along longitude=longitude from 3D variable - var lon, lat and z contain the C-grid position of the section for - plotting. If vert=True, lon, lat and z contain contain the position of - the verticies (to be used with pcolor) Returns a longitudinal slice of - the grid

-
-
-
-
- -
- -
- - -
-

latslice(var, - latitude, - grd, - Cpos='rho', - vert=False, - spval=1e+37) -

- 		source code  -
- -

latslice, z, lon, lat = latslice(var, latitude, grd)

-

optional switch:

-
    -
  • - Cpos='rho', 'u' or 'v' specify the C-grid position where the - variable rely -
    • -
  • - vert=True/False If True, return the position of the - verticies -
    • -
  • - spval special value -
    • -
  • - rtol tolerance parameter -
    • -
-

return a latitudinal slice along latitude=latitude from 3D variable - var lon, lat and z contain the C-grid position of the section for - plotting. If vert=True, lon, lat and z contain contain the position of - the verticies (to be used with pcolor) Returns a longitudinal slice of - the grid

-
-
-
-
- -
- -
- - -
-

section_transport(u, - v, - istart, - iend, - jstart, - jend, - grd) -

- 		source code  -
- -

transpu, transpv = section_transport(u, v, istart, iend, jstart, jend, - grd)

-

compute the transport through the section defined between the point P1 - (istart,jstart) and P2 (iend, jend). P1 and P2 are Arakawa-C psi points. - The transpot is positive right handside of the section.

-
-
-
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Source Code for Module pyroms.tools

-
-   1  # encoding: utf-8 
-   2   
-   3  import numpy as np 
-   4  import _iso 
-   5   
-   6  import pyroms 
-   7   
-   8   
-
   9 -def zslice(var, depth, grd, Cpos='rho', vert=False, mode='linear'): 
-
  10      """  
-  11      zslice, lon, lat = zslice(var, depth, grd) 
-  12   
-  13      optional switch: 
-  14        - Cpos='rho', 'u', 'v' or 'w'  specify the C-grid position where  
-  15                                       the variable rely 
-  16        - vert=True/False              If True, return the position of  
-  17                                       the verticies 
-  18        - mode='linear' or 'spline'    specify the type of interpolation 
-  19   
-  20      return a constant-z slice at depth depth from 3D variable var 
-  21      lon and lat contain the C-grid position of the slice for plotting. 
-  22      If vert=True, lon and lat contain contain the position of the  
-  23      verticies (to be used with pcolor) 
-  24      """ 
-  25     
-  26      if mode=='linear': 
-  27          imode=0 
-  28      elif mode=='spline': 
-  29          imode=1 
-  30      else: 
-  31          imode=0 
-  32          raise Warning, '%s not supported, defaulting to linear' % mode 
-  33           
-  34   
-  35      # compute the depth on Arakawa-C grid position 
-  36   
-  37      if Cpos is 'u': 
-  38          # average z_r at Arakawa-C u points 
-  39          z = 0.5 * (grd.vgrid.z_r[0,:,:,:-1] + grd.vgrid.z_r[0,:,:,1:]) 
-  40          if vert == True:  
-  41              lon = 0.5 * (grd.hgrid.lon_vert[:,:-1] + grd.hgrid.lon_vert[:,1:]) 
-  42              lat = 0.5 * (grd.hgrid.lat_vert[:,:-1] + grd.hgrid.lat_vert[:,1:]) 
-  43          else: 
-  44              lon = grd.hgrid.lon_u[:] 
-  45              lat = grd.hgrid.lat_u[:] 
-  46          mask = grd.hgrid.mask_u[:] 
-  47   
-  48      elif Cpos is 'v': 
-  49          # average z_r at Arakawa-C v points 
-  50          z = 0.5 * (grd.vgrid.z_r[0,:,:-1,:] + grd.vgrid.z_r[0,:,1:,:]) 
-  51          if vert == True:  
-  52              lon = 0.5 * (grd.hgrid.lon_vert[:-1,:] + grd.hgrid.lon_vert[1:,:]) 
-  53              lat = 0.5 * (grd.hgrid.lat_vert[:-1,:] + grd.hgrid.lat_vert[1:,:]) 
-  54          else: 
-  55              lon = grd.hgrid.lon_v[:] 
-  56              lat = grd.hgrid.lat_v[:] 
-  57          mask = grd.hgrid.mask_v[:] 
-  58   
-  59      elif Cpos is 'w': 
-  60          # for temp, salt, rho 
-  61          z = grd.vgrid.z_w[0,:] 
-  62          if vert == True: 
-  63              lon = grd.hgrid.lon_vert[:] 
-  64              lat = grd.hgrid.lat_vert[:] 
-  65          else: 
-  66              lon = grd.hgrid.lon_rho[:] 
-  67              lat = grd.hgrid.lat_rho[:] 
-  68          mask = grd.hgrid.mask_rho[:] 
-  69   
-  70      elif Cpos is 'rho': 
-  71          # for temp, salt, rho 
-  72          z = grd.vgrid.z_r[0,:] 
-  73          if vert == True:  
-  74              lon = grd.hgrid.lon_vert[:] 
-  75              lat = grd.hgrid.lat_vert[:] 
-  76          else: 
-  77              lon = grd.hgrid.lon_rho[:] 
-  78              lat = grd.hgrid.lat_rho[:] 
-  79          mask = grd.hgrid.mask_rho[:] 
-  80   
-  81      else: 
-  82          raise Warning, '%s bad position. Valid Arakawa-C are \ 
-  83                             rho, u or v.' % Cpos 
-  84   
-  85      assert len(z.shape) == 3, 'z must be 3D' 
-  86      assert len(var.shape) == 3, 'var must be 3D' 
-  87      assert z.shape == var.shape, 'data and prop must be the same size' 
-  88   
-  89      depth = -abs(depth) 
-  90      depth = depth * np.ones(z.shape[1:]) 
-  91       
-  92      zslice = _iso.zslice(z, var, depth, imode) 
-  93   
-  94      # mask land 
-  95      zslice = np.ma.masked_where(mask == 0, zslice) 
-  96      # mask region with shalower depth than requisted depth 
-  97      zslice = np.ma.masked_where(zslice == 1e20, zslice) 
-  98   
-  99      return zslice, lon, lat 
-
 100   
- 101   
-
 102 -def sslice(var, sindex, grd, Cpos='rho', vert=False): 
-
 103      """  
- 104      sslice, lon, lat = sslice(var, sindex, grd) 
- 105   
- 106      optional switch: 
- 107        - Cpos='rho', 'u' or 'v'       specify the C-grid position where  
- 108                                       the variable rely 
- 109        - vert=True/False              If True, return the position of  
- 110                                       the verticies 
- 111        - mode='linear' or 'spline'    specify the type of interpolation 
- 112   
- 113      return a constant-s slice at index sindex from 3D variable var 
- 114      lon and lat contain the C-grid position of the slice for plotting. 
- 115      If vert=True, lon and lat contain contain the position of the  
- 116      verticies (to be used with pcolor) 
- 117      """ 
- 118   
- 119      # compute the depth on Arakawa-C grid position 
- 120   
- 121      if Cpos is 'u': 
- 122          # average z_r at Arakawa-C u points 
- 123          z = 0.5 * (grd.vgrid.z_r[0,:,:,:-1] + grd.vgrid.z_r[0,:,:,1:]) 
- 124          if vert == True:  
- 125              lon = 0.5 * (grd.hgrid.lon_vert[:,:-1] + grd.hgrid.lon_vert[:,1:]) 
- 126              lat = 0.5 * (grd.hgrid.lat_vert[:,:-1] + grd.hgrid.lat_vert[:,1:]) 
- 127          else: 
- 128              lon = grd.hgrid.lon_u[:] 
- 129              lat = grd.hgrid.lat_u[:] 
- 130          mask = grd.hgrid.mask_u[:] 
- 131   
- 132      elif Cpos is 'v': 
- 133          # average z_r at Arakawa-C v points 
- 134          z = 0.5 * (grd.vgrid.z_r[0,:,:-1,:] + grd.vgrid.z_r[0,:,1:,:]) 
- 135          if vert == True:  
- 136              lon = 0.5 * (grd.hgrid.lon_vert[:-1,:] + grd.hgrid.lon_vert[1:,:]) 
- 137              lat = 0.5 * (grd.hgrid.lat_vert[:-1,:] + grd.hgrid.lat_vert[1:,:]) 
- 138          else: 
- 139              lon = grd.hgrid.lon_v[:] 
- 140              lat = grd.hgrid.lat_v[:] 
- 141          mask = grd.hgrid.mask_v[:] 
- 142   
- 143      elif Cpos is 'rho': 
- 144          # for temp, salt, rho, w 
- 145          z = grd.vgrid.z_r[0,:] 
- 146          if vert == True:  
- 147              lon = grd.hgrid.lon_vert[:] 
- 148              lat = grd.hgrid.lat_vert[:] 
- 149          else: 
- 150              lon = grd.hgrid.lon_rho[:] 
- 151              lat = grd.hgrid.lat_rho[:] 
- 152          mask = grd.hgrid.mask_rho[:] 
- 153   
- 154      else: 
- 155          raise Warning, '%s bad position. Valid Arakawa-C are \ 
- 156                             rho, u or v.' % Cpos 
- 157   
- 158      assert len(var.shape) == 3, 'var must be 3D' 
- 159   
- 160      sslice = var[sindex,:,:] 
- 161   
- 162      # mask land 
- 163      sslice = np.ma.masked_where(mask == 0, sslice) 
- 164       
- 165      return sslice, lon, lat 
-
 166   
- 167   
- 168   
-
 169 -def islice(var, iindex, grd, Cpos='rho', vert=False): 
-
 170      """ 
- 171      islice, z, lon, lat = islice(var, iindex, grd) 
- 172   
- 173      optional switch: 
- 174        - Cpos='rho', 'u', 'v' or 'w'  specify the C-grid position where  
- 175                                       the variable rely 
- 176        - vert=True/False              If True, return the position of  
- 177                                       the verticies 
- 178   
- 179   
- 180      return a constant-i slice at index iindex from 3D variable var 
- 181      lon, lat and z contain the C-grid position of the slice for plotting. 
- 182      If vert=True, lon, lat and z contain contain the position of the  
- 183      verticies (to be used with pcolor) 
- 184      """ 
- 185   
- 186      # compute the depth on Arakawa-C grid position 
- 187   
- 188      if Cpos is 'u': 
- 189          # average z_r at Arakawa-C u points 
- 190          if vert == True:  
- 191              z = grd.vgrid.z_w[0,:] 
- 192              z = 0.5 * (z[:,:,:-1] + z[:,:,1:]) 
- 193              z = 0.5 * (z[:,:-1,:] + z[:,1:,:]) 
- 194              z = np.concatenate((z[:,0:1,:], z, z[:,-2:-1,:]), 1) 
- 195              lon = grd.hgrid.lon_vert[:,1:-1] 
- 196              lat = grd.hgrid.lat_vert[:,1:-1] 
- 197          else: 
- 198              z = grd.vgrid.z_r[0,:] 
- 199              z = 0.5 * (z[:,:,:-1] + z[:,:,1:]) 
- 200              lon = grd.hgrid.lon_u[:] 
- 201              lat = grd.hgrid.lat_u[:]          
- 202          mask = grd.hgrid.mask_u[:] 
- 203   
- 204      elif Cpos is 'v': 
- 205          # average z_r at Arakawa-C v points 
- 206          if vert == True:  
- 207              z = grd.vgrid.z_w[0,:] 
- 208              lon = grd.hgrid.lon_rho 
- 209              lat = grd.hgrid.lat_rho 
- 210          else: 
- 211              z = grd.vgrid.z_r[0,:] 
- 212              z = 0.5 * (z[:,:-1,:] + z[:,1:,:]) 
- 213              lon = grd.hgrid.lon_v[:] 
- 214              lat = grd.hgrid.lat_v[:] 
- 215          mask = grd.hgrid.mask_v[:] 
- 216   
- 217      elif Cpos is 'w': 
- 218          # for w, AKt, ... 
- 219          if vert == True: 
- 220              z = grd.vgrid.z_w[0,:] 
- 221              z = 0.5 * (z[:-1,:,:] + z[1:,:,:]) 
- 222              z = np.concatenate((np.array(grd.vgrid.z_w[0,0,:,:], ndmin=3), \ 
- 223                                  z, \ 
- 224                                  np.array(grd.vgrid.z_w[0,-1,:,:], ndmin=3)), 0) 
- 225              z = 0.5 * (z[:,:,:-1] + z[:,:,1:]) 
- 226              z = np.concatenate((z[:,:,0:1], z, z[:,:,-2:-1]), 2) 
- 227              lon = 0.5 * (grd.hgrid.lon_vert[:-1,:] + grd.hgrid.lon_vert[1:,:]) 
- 228              lat = 0.5 * (grd.hgrid.lat_vert[:-1,:] + grd.hgrid.lat_vert[1:,:]) 
- 229          else: 
- 230              z = grd.vgrid.z_w[0,:] 
- 231              lon = grd.hgrid.lon_rho[:] 
- 232              lat = grd.hgrid.lat_rho[:] 
- 233          mask = grd.hgrid.mask_rho[:] 
- 234   
- 235   
- 236      elif Cpos is 'rho': 
- 237          # for temp, salt, rho, ... 
- 238          if vert == True:  
- 239              z = grd.vgrid.z_w[0,:] 
- 240              z = 0.5 * (z[:,:-1,:] + z[:,1:,:]) 
- 241              z = np.concatenate((z[:,0:1,:], z, z[:,-2:-1,:]), 1) 
- 242              lon = 0.5 * (grd.hgrid.lon_vert[:,:-1] + grd.hgrid.lon_vert[:,1:]) 
- 243              lat = 0.5 * (grd.hgrid.lat_vert[:,:-1] + grd.hgrid.lat_vert[:,1:]) 
- 244          else: 
- 245              z = grd.vgrid.z_r[0,:] 
- 246              lon = grd.hgrid.lon_rho[:] 
- 247              lat = grd.hgrid.lat_rho[:]       
- 248          mask = grd.hgrid.mask_rho[:] 
- 249   
- 250      else: 
- 251          raise Warning, '%s bad position. Valid Arakawa-C are \ 
- 252                             rho, u or v.' % Cpos 
- 253   
- 254      # get constant-i slice 
- 255      vari = var[:,:,iindex] 
- 256      zi = z[:,:,iindex] 
- 257      loni = np.tile(lon[:,iindex], (zi.shape[0], 1)) 
- 258      lati = np.tile(lat[:,iindex], (zi.shape[0], 1)) 
- 259   
- 260      # land/sea mask 
- 261      maski = np.tile(mask[:,iindex], (vari.shape[0], 1)) 
- 262      vari = np.ma.masked_where(maski[:,:] == 0, vari[:,:]) 
- 263   
- 264      return vari, zi, loni, lati 
-
 265       
- 266   
-
 267 -def jslice(var, jindex, grd, Cpos='rho', vert=False): 
-
 268      """ 
- 269      jslice, z, lon, lat = jslice(var, jindex, grd) 
- 270   
- 271      optional switch: 
- 272        - Cpos='rho', 'u', 'v' or 'w'  specify the C-grid position where  
- 273                                       the variable rely 
- 274        - vert=True/False              If True, return the position of  
- 275                                       the verticies 
- 276   
- 277   
- 278      return a constant-j slice at index jindex from 3D variable var 
- 279      lon, lat and z contain the C-grid position of the slice for plotting. 
- 280      If vert=True, lon, lat and z contain contain the position of the  
- 281      verticies (to be used with pcolor) 
- 282      """ 
- 283   
- 284      # compute the depth on Arakawa-C grid position 
- 285   
- 286      if Cpos is 'u': 
- 287          # average z_r at Arakawa-C u points 
- 288          if vert == True:  
- 289              z = grd.vgrid.z_w[0,:] 
- 290              lon = grd.hgrid.lon_rho 
- 291              lat = grd.hgrid.lat_rho 
- 292          else: 
- 293              z = grd.vgrid.z_r[0,:] 
- 294              z = 0.5 * (z[:,:,:-1] + z[:,:,1:]) 
- 295              lon = grd.hgrid.lon_u[:] 
- 296              lat = grd.hgrid.lat_u[:]          
- 297          mask = grd.hgrid.mask_u[:] 
- 298   
- 299      elif Cpos is 'v': 
- 300          # average z_r at Arakawa-C v points 
- 301          if vert == True:  
- 302              z = grd.vgrid.z_w[0,:] 
- 303              z = 0.5 * (z[:,:-1,:] + z[:,1:,:]) 
- 304              z = 0.5 * (z[:,:,:-1] + z[:,:,1:]) 
- 305              z = np.concatenate((z[:,:,0:1], z, z[:,:,-2:-1]), 2) 
- 306              lon = grd.hgrid.lon_vert[1:-1,:] 
- 307              lat = grd.hgrid.lat_vert[1:-1,:] 
- 308          else: 
- 309              z = grd.vgrid.z_r[0,:] 
- 310              z = 0.5 * (z[:,:-1,:] + z[:,1:,:]) 
- 311              lon = grd.hgrid.lon_v[:] 
- 312              lat = grd.hgrid.lat_v[:] 
- 313          mask = grd.hgrid.mask_v[:] 
- 314   
- 315      elif Cpos is 'w': 
- 316          # for w, AKt, ... 
- 317          if vert == True: 
- 318              z = grd.vgrid.z_w[0,:] 
- 319              z = 0.5 * (z[:-1,:,:] + z[1:,:,:]) 
- 320              z = np.concatenate((np.array(grd.vgrid.z_w[0,0,:,:], ndmin=3), \ 
- 321                                  z, \ 
- 322                                  np.array(grd.vgrid.z_w[0,-1,:,:], ndmin=3)), 0) 
- 323              z = 0.5 * (z[:,:,:-1] + z[:,:,1:]) 
- 324              z = np.concatenate((z[:,:,0:1], z, z[:,:,-2:-1]), 2) 
- 325              lon = 0.5 * (grd.hgrid.lon_vert[:-1,:] + grd.hgrid.lon_vert[1:,:]) 
- 326              lat = 0.5 * (grd.hgrid.lat_vert[:-1,:] + grd.hgrid.lat_vert[1:,:]) 
- 327          else: 
- 328              z = grd.vgrid.z_w[0,:] 
- 329              lon = grd.hgrid.lon_rho[:] 
- 330              lat = grd.hgrid.lat_rho[:] 
- 331          mask = grd.hgrid.mask_rho[:] 
- 332   
- 333      elif Cpos is 'rho': 
- 334          # for temp, salt, rho, ... 
- 335          if vert == True:  
- 336              z = grd.vgrid.z_w[0,:] 
- 337              z = 0.5 * (z[:,:,:-1] + z[:,:,1:]) 
- 338              z = np.concatenate((z[:,:,0:1], z, z[:,:,-2:-1]), 2) 
- 339              lon = 0.5 * (grd.hgrid.lon_vert[:-1,:] + grd.hgrid.lon_vert[1:,:]) 
- 340              lat = 0.5 * (grd.hgrid.lat_vert[:-1,:] + grd.hgrid.lat_vert[1:,:]) 
- 341          else: 
- 342              z = grd.vgrid.z_r[0,:] 
- 343              lon = grd.hgrid.lon_rho[:] 
- 344              lat = grd.hgrid.lat_rho[:]       
- 345          mask = grd.hgrid.mask_rho[:] 
- 346   
- 347      else: 
- 348          raise Warning, '%s bad position. Valid Arakawa-C are \ 
- 349                             rho, u or v.' % Cpos 
- 350   
- 351      # get constant-j slice 
- 352      varj = var[:,jindex,:] 
- 353      zj = z[:,jindex,:] 
- 354      lonj = np.tile(lon[jindex,:], (zj.shape[0], 1)) 
- 355      latj = np.tile(lat[jindex,:], (zj.shape[0], 1)) 
- 356   
- 357      # land/sea mask 
- 358      maskj = np.tile(mask[jindex,:], (varj.shape[0], 1)) 
- 359      varj = np.ma.masked_where(maskj[:,:] == 0, varj[:,:]) 
- 360   
- 361      return varj, zj, lonj, latj 
-
 362   
- 363   
- 364   
-
 365 -def isoslice(var,prop,isoval, grd, Cpos='rho', masking=True, vert=False): 
-
 366      """ 
- 367      isoslice, lon, lat = isoslice(variable,property, isoval, grd) 
- 368   
- 369      optional switch: 
- 370        - Cpos='rho', 'u' or 'v'       specify the C-grid position where  
- 371                                       the variable rely 
- 372        - masking=True                 mask the output if True 
- 373        - vert=True/False              If True, return the position of  
- 374                                       the verticies 
- 375        - mode='linear' or 'spline'    specify the type of interpolation 
- 376   
- 377       
- 378      result is a projection of variable at property == isoval in the first 
- 379      nonsingleton dimension.  In the case when there is more than one zero 
- 380      crossing, the results are averaged. 
- 381      lon, and lat contain the C-grid position of the slice for plotting. 
- 382      If vert=True, lon and lat and z contain contain the position of the  
- 383      verticies (to be used with pcolor)     
- 384   
- 385      EXAMPLE: 
- 386      s_at_m5  = isoslice(s,z,-5);        # s at z == -5 
- 387      h_at_s30 = isoslice(z,s,30);        # z at s == 30 
- 388      """ 
- 389      if (len(var.squeeze().shape)<=2): 
- 390          raise ValueError, 'variable must have at least two dimensions' 
- 391      if not prop.shape == var.shape: 
- 392          raise ValueError, 'dimension of var and prop must be identical' 
- 393   
- 394      # compute the depth on Arakawa-C grid position 
- 395      if Cpos is 'u': 
- 396          # average z_r at Arakawa-C u points 
- 397          z = 0.5 * (grd.vgrid.z_r[0,:,:,:-1] + grd.vgrid.z_r[0,:,:,1:]) 
- 398          if vert == True:  
- 399              lon = 0.5 * (grd.hgrid.lon_vert[:,:-1] + grd.hgrid.lon_vert[:,1:]) 
- 400              lat = 0.5 * (grd.hgrid.lat_vert[:,:-1] + grd.hgrid.lat_vert[:,1:]) 
- 401          else: 
- 402              lon = grd.hgrid.lon_u[:] 
- 403              lat = grd.hgrid.lat_u[:] 
- 404          mask = grd.hgrid.mask_u[:] 
- 405   
- 406      elif Cpos is 'v': 
- 407          # average z_r at Arakawa-C v points 
- 408          z = 0.5 * (grd.vgrid.z_r[0,:,:-1,:] + grd.vgrid.z_r[0,:,1:,:]) 
- 409          if vert == True:  
- 410              lon = 0.5 * (grd.hgrid.lon_vert[:-1,:] + grd.hgrid.lon_vert[1:,:]) 
- 411              lat = 0.5 * (grd.hgrid.lat_vert[:-1,:] + grd.hgrid.lat_vert[1:,:]) 
- 412          else: 
- 413              lon = grd.hgrid.lon_v[:] 
- 414              lat = grd.hgrid.lat_v[:] 
- 415          mask = grd.hgrid.mask_v[:] 
- 416   
- 417      elif Cpos is 'rho': 
- 418          # for temp, salt, rho, w 
- 419          z = grd.vgrid.z_r[0,:] 
- 420          if vert == True:  
- 421              lon = grd.hgrid.lon_vert[:] 
- 422              lat = grd.hgrid.lat_vert[:] 
- 423          else: 
- 424              lon = grd.hgrid.lon_rho[:] 
- 425              lat = grd.hgrid.lat_rho[:] 
- 426          mask = grd.hgrid.mask_rho[:] 
- 427   
- 428      else: 
- 429          raise Warning, '%s bad position. Valid Arakawa-C are \ 
- 430                             rho, u or v.' % Cpos 
- 431      
- 432      prop = prop-isoval 
- 433      sz = np.shape(var) 
- 434      var = var.reshape(sz[0],-1) 
- 435      prop = prop.reshape(sz[0],-1) 
- 436      #find zero-crossings (zc == 1) 
- 437      zc =  np.where( (prop[:-1,:] * prop[1:,:])<0 ,1., 0.) 
- 438      varl = var[:-1,:] * zc 
- 439      varh = var[1:,:] * zc 
- 440      propl = prop[:-1,:] * zc 
- 441      proph = prop[1:,:] * zc 
- 442      isoslice = varl - propl * (varh - varl) / (proph - propl) 
- 443      isoslice = np.where(zc==1., isoslice, 0.) 
- 444      szc = zc.sum(axis=0) 
- 445      szc = np.where(szc==0., 1, szc) 
- 446      isoslice = isoslice.sum(axis=0)/szc 
- 447      if masking: 
- 448          isoslice = np.ma.masked_where(zc.sum(axis=0)==0, isoslice) 
- 449          if all(isoslice.mask): 
- 450              raise Warning, 'property==%f out of range (%f, %f)' % \ 
- 451                             (isoval, (prop+isoval).min(), (prop+isoval).max()) 
- 452      isoslice = isoslice.reshape(sz[1:]) 
- 453   
- 454      # mask land 
- 455      isoslice = np.ma.masked_where(mask == 0, isoslice) 
- 456   
- 457      return isoslice, lon, lat 
-
 458   
- 459   
- 460   
-
 461 -def transect(var, istart, iend, jstart, jend, grd, Cpos='rho', vert=False, \ 
- 462              spval=1e37): 
-
 463      """ 
- 464      transect, z, lon, lat = transect(var, istart, iend, jstart, jend, grd) 
- 465   
- 466      optional switch: 
- 467        - Cpos='rho', 'u' or 'v'       specify the C-grid position where  
- 468                                       the variable rely 
- 469        - vert=True/False              If True, return the position of  
- 470                                       the verticies 
- 471        - spval                        special value 
- 472        - rtol                         tolerance parameter 
- 473   
- 474   
- 475      return a vertical transect between the points P1=(istart, jstart) 
- 476      and P2=(iend, jend) from 3D variable var 
- 477      lon, lat and z contain the C-grid position of the section for plotting. 
- 478      If vert=True, lon, lat and z contain contain the position of the  
- 479      verticies (to be used with pcolor) 
- 480      """ 
- 481   
- 482      # compute the depth on Arakawa-C grid position and get grid information 
- 483   
- 484      if Cpos is 'u': 
- 485          # average z_r and z_w at Arakawa-C u points 
- 486          if vert == True: 
- 487              z = grd.vgrid.z_w[0,:] 
- 488              z = 0.5 * (z[:,:-1,:] + z[:,1:,:]) 
- 489              z = np.concatenate((z[:,0:1,:], z, z[:,-2:-1,:]), 1) 
- 490              lon = 0.5 * (grd.hgrid.lon_vert[:,:-1] + grd.hgrid.lon_vert[:,1:]) 
- 491              lat = 0.5 * (grd.hgrid.lat_vert[:,:-1] + grd.hgrid.lat_vert[:,1:]) 
- 492          else: 
- 493              z = grd.vgrid.z_r[0,:] 
- 494              z = 0.5 * (z[:,:,:-1] + z[:,:,1:]) 
- 495              lon = grd.hgrid.lon_u[:] 
- 496              lat = grd.hgrid.lat_u[:] 
- 497          mask = grd.hgrid.mask_u[:] 
- 498   
- 499      elif Cpos is 'v': 
- 500          # average z_r and z_w at Arakawa-C v points 
- 501          if vert == True: 
- 502              z = grd.vgrid.z_w[0,:] 
- 503              z = 0.5 * (z[:,:,:-1] + z[:,:,1:]) 
- 504              z = np.concatenate((z[:,:,0:1], z, z[:,:,-2:-1]), 2) 
- 505              lon = 0.5 * (grd.hgrid.lon_vert[:-1,:] + grd.hgrid.lon_vert[1:,:]) 
- 506              lat = 0.5 * (grd.hgrid.lat_vert[:-1,:] + grd.hgrid.lat_vert[1:,:]) 
- 507          else: 
- 508              z = grd.vgrid.z_r[0,:] 
- 509              z = 0.5 * (z[:,-1:,:] + z[:,1:,:]) 
- 510              lon = grd.hgrid.lon_v[:] 
- 511              lat = grd.hgrid.lat_v[:] 
- 512          mask = grd.hgrid.mask_v[:] 
- 513   
- 514      elif Cpos is 'rho': 
- 515          # for temp, salt, rho 
- 516          if vert == True: 
- 517              z = grd.vgrid.z_w[0,:] 
- 518              z = 0.5 * (z[:,:,:-1] + z[:,:,1:]) 
- 519              z = 0.5 * (z[:,:-1,:] + z[:,1:,:]) 
- 520              z = np.concatenate((z[:,:,0:1], z, z[:,:,-2:-1]), 2) 
- 521              z = np.concatenate((z[:,0:1,:], z, z[:,-2:-1,:]), 1) 
- 522              lon = grd.hgrid.lon_vert[:] 
- 523              lat = grd.hgrid.lat_vert[:] 
- 524          else: 
- 525              z = grd.vgrid.z_r[0,:] 
- 526              lon = grd.hgrid.lon_rho[:] 
- 527              lat = grd.hgrid.lat_rho[:] 
- 528          mask = grd.hgrid.mask_rho[:] 
- 529   
- 530      else: 
- 531          raise Warning, '%s bad position. Valid Arakawa-C are \ 
- 532                             rho, u or v.' % Cpos 
- 533   
- 534   
- 535      # Find the nearest point between P1 (imin,jmin) and P2 (imax, jmax) 
- 536      # ----------------------------------------------------------------- 
- 537      # Initialization 
- 538      i0=istart; j0=jstart; i1=iend;  j1=jend 
- 539      istart = float(istart); iend = float(iend) 
- 540      jstart = float(jstart); jend = float(jend) 
- 541   
- 542      # Compute equation:  j = aj i + bj 
- 543      if istart != iend: 
- 544          aj = (jend - jstart ) / (iend - istart) 
- 545          bj = jstart - aj * istart 
- 546      else: 
- 547          aj=10000. 
- 548          bj=0. 
- 549   
- 550      # Compute equation:  i = ai j + bi 
- 551      if jstart != jend: 
- 552          ai = (iend - istart ) / ( jend - jstart ) 
- 553          bi = istart - ai * jstart 
- 554      else: 
- 555          ai=10000. 
- 556          bi=0. 
- 557        
- 558      # Compute the integer pathway: 
- 559      # Chose the strait line with the smallest slope 
- 560      if (abs(aj) <=  1 ): 
- 561          # Here, the best line is y(x) 
- 562          print 'Here, the best line is y(x)' 
- 563          # If i1 < i0 swap points and remember it has been swapped 
- 564          if (i1 <  i0 ): 
- 565              i  = i0 ; j  = j0 
- 566              i0 = i1 ; j0 = j1 
- 567              i1 = i  ; j1 = j 
- 568   
- 569          # compute the nearest j point on the line crossing at i 
- 570          n=0 
- 571          near = np.zeros(((i1-i0+1),4)) 
- 572          for i in range(i0,i1+1): 
- 573              jj = aj*i + bj 
- 574              near[n,0] = i 
- 575              near[n,1] = jj 
- 576              near[n,2] = np.floor(jj) 
- 577              near[n,3] = np.ceil(jj) 
- 578              n = n + 1 
- 579           
- 580          if vert == False: 
- 581              nearp = np.zeros(((i1-i0+1),4)) 
- 582              nearp = near 
- 583          else:    
- 584              # compute the nearest j vert point on the line crossing at i 
- 585              n=0 
- 586              nearp = np.zeros(((i1-i0+2),4)) 
- 587              for i in range(i0,i1+2): 
- 588                  jj = aj*(i-0.5) + bj 
- 589                  nearp[n,0] = i 
- 590                  nearp[n,1] = jj 
- 591                  nearp[n,2] = np.floor(jj) 
- 592                  nearp[n,3] = np.ceil(jj) 
- 593                  n = n + 1 
- 594              
- 595      else: 
- 596          # Here, the best line is x(y) 
- 597          print 'Here, the best line is x(y)' 
- 598          # If j1 < j0 swap points and remember it has been swapped 
- 599          if (j1 <  j0 ): 
- 600              i  = i0 ; j  = j0 
- 601              i0 = i1 ; j0 = j1 
- 602              i1 = i  ; j1 = j 
- 603   
- 604          # compute the nearest i point on the line crossing at j 
- 605          n=0 
- 606          near = np.zeros(((j1-j0+1),4)) 
- 607          for j in range(j0,j1+1): 
- 608              ii = ai*j + bi 
- 609              near[n,0] = j 
- 610              near[n,1] = ii 
- 611              near[n,2] = np.floor(ii) 
- 612              near[n,3] = np.ceil(ii) 
- 613              n = n + 1 
- 614   
- 615          if vert == False: 
- 616              nearp = np.zeros(((j1-j0+1),4)) 
- 617              nearp = near 
- 618          else: 
- 619              # compute the nearest i vert point on the line crossing at j 
- 620              n=0 
- 621              nearp = np.zeros(((j1-j0+2),4)) 
- 622              for j in range(j0,j1+2): 
- 623                  ii = ai*(j-0.5) + bi 
- 624                  nearp[n,0] = j 
- 625                  nearp[n,1] = ii 
- 626                  nearp[n,2] = np.floor(ii) 
- 627                  nearp[n,3] = np.ceil(ii) 
- 628                  n = n + 1 
- 629   
- 630       
- 631      # Now interpolate between the nearest point through the section 
- 632      # ------------------------------------------------------------- 
- 633      # Initialize output variables 
- 634      nlev = z.shape[0] 
- 635   
- 636      transect = np.zeros((grd.vgrid.N, near.shape[0])) 
- 637      zs = np.zeros((nlev, nearp.shape[0])) 
- 638      lons = np.zeros((nlev, nearp.shape[0])) 
- 639      lats = np.zeros((nlev, nearp.shape[0])) 
- 640   
- 641      # mask variable 
- 642      for k in range(var.shape[0]): 
- 643          var[k,:,:] = np.ma.masked_where(mask == 0, var[k,:,:]) 
- 644   
- 645      for n in range(near.shape[0]): 
- 646          if (abs(aj) <=  1 ): 
- 647              # check if our position match a grid cell 
- 648              if (near[n,2] == near[n,3]): 
- 649                  transect[:,n] = var[:, near[n,2], near[n,0]] 
- 650              else: 
- 651                  if mask[near[n,3], near[n,0]] == 0 or mask[near[n,2], near[n,0]] == 0: 
- 652                      transect[:,n] = spval 
- 653                  else: 
- 654                      transect[:,n] = (near[n,1] - near[n,2]) * var[:, near[n,3], near[n,0]] + \ 
- 655                                     (near[n,3] - near[n,1]) * var[:, near[n,2], near[n,0]] 
- 656          else: 
- 657              # check if our position match a grid cell 
- 658              if (near[n,2] == near[n,3]): 
- 659                  transect[:,n] = var[:, near[n,0], near[n,2]] 
- 660              else: 
- 661                  if mask[near[n,0], near[n,3]] == 0 or mask[near[n,0], near[n,2]] == 0: 
- 662                      transect[:,n] = spval 
- 663                  else: 
- 664                      transect[:,n] = (near[n,1] - near[n,2]) * var[:, near[n,0], near[n,3]] + \ 
- 665                                     (near[n,3] - near[n,1]) * var[:, near[n,0], near[n,2]] 
- 666   
- 667      for n in range(nearp.shape[0]): 
- 668          if (abs(aj) <=  1 ): 
- 669              # check if our position match a grid cell 
- 670              if (nearp[n,2] == nearp[n,3]): 
- 671                  zs[:,n] = z[:, nearp[n,2], nearp[n,0]] 
- 672                  lons[:,n] = lon[nearp[n,2], nearp[n,0]] 
- 673                  lats[:,n] = lat[nearp[n,2], nearp[n,0]] 
- 674              else: 
- 675                  zs[:,n] = (nearp[n,1] - nearp[n,2]) * z[:, nearp[n,3], nearp[n,0]] + \ 
- 676                            (nearp[n,3] - nearp[n,1]) * z[:, nearp[n,2], nearp[n,0]] 
- 677                  lons[:,n] = (nearp[n,1] - nearp[n,2]) * lon[nearp[n,3], nearp[n,0]] + \ 
- 678                              (nearp[n,3] - nearp[n,1]) * lon[nearp[n,2], nearp[n,0]] 
- 679                  lats[:,n] = (nearp[n,1] - nearp[n,2]) * lat[nearp[n,3], nearp[n,0]] + \ 
- 680                              (nearp[n,3] - nearp[n,1]) * lat[nearp[n,2], nearp[n,0]] 
- 681          else: 
- 682              # check if our position match a grid cell 
- 683              if (nearp[n,2] == nearp[n,3]): 
- 684                  zs[:,n] = z[:, nearp[n,0], nearp[n,2]] 
- 685                  lons[:,n] = lon[nearp[n,0], nearp[n,2]] 
- 686                  lats[:,n] = lat[nearp[n,0], nearp[n,2]] 
- 687              else: 
- 688                  zs[:,n] = (nearp[n,1] - nearp[n,2]) * z[:, nearp[n,0], nearp[n,3]] + \ 
- 689                            (nearp[n,3] - nearp[n,1]) * z[:, nearp[n,0], nearp[n,2]] 
- 690                  lons[:,n] = (nearp[n,1] - nearp[n,2]) * lon[nearp[n,0], nearp[n,3]] + \ 
- 691                              (nearp[n,3] - nearp[n,1]) * lon[nearp[n,0], nearp[n,2]] 
- 692                  lats[:,n] = (nearp[n,1] - nearp[n,2]) * lat[nearp[n,0], nearp[n,3]] + \ 
- 693                              (nearp[n,3] - nearp[n,1]) * lat[nearp[n,0], nearp[n,2]] 
- 694   
- 695      # mask transect 
- 696      transect = np.ma.masked_values(transect, spval) 
- 697   
- 698   
- 699      return transect, zs, lons, lats 
-
 700               
- 701   
- 702               
- 703   
-
 704 -def lonslice(var, longitude, grd, Cpos='rho', vert=False, spval=1e37): 
-
 705      """ 
- 706      lonslice, z, lon, lat = lonslice(var, longitude, grd) 
- 707   
- 708      optional switch: 
- 709        - Cpos='rho', 'u' or 'v'       specify the C-grid position where  
- 710                                       the variable rely 
- 711        - vert=True/False              If True, return the position of  
- 712                                       the verticies 
- 713        - spval                        special value 
- 714        - rtol                         tolerance parameter 
- 715   
- 716   
- 717      return a longitudinal slice along longitude=longitude from 3D variable var 
- 718      lon, lat and z contain the C-grid position of the section for plotting. 
- 719      If vert=True, lon, lat and z contain contain the position of the  
- 720      verticies (to be used with pcolor) 
- 721      Returns a longitudinal slice of the grid 
- 722      """ 
- 723   
- 724      if Cpos == 'u': 
- 725          lon = grd.hgrid.lon_u 
- 726          lat = grd.hgrid.lat_u 
- 727      elif Cpos == 'v': 
- 728          lon = grd.hgrid.lon_v 
- 729          lat = grd.hgrid.lat_v 
- 730      elif Cpos == 'rho': 
- 731          lon = grd.hgrid.lon_rho 
- 732          lat = grd.hgrid.lat_rho 
- 733      else: 
- 734          raise Warning, '%s bad position. Valid Arakawa-C are \ 
- 735                             rho, u or v.' % Cpos 
- 736   
- 737      edge = np.concatenate((lon[1,1:-1], \ 
- 738                             lon[1:-1,-2], \ 
- 739                             lon[-2,-2:0:-1], \ 
- 740                             lon[-2:0:-1,1])) 
- 741      idx =  np.concatenate((range(1,lon[0,:].shape[0]-1), \ 
- 742                             range(1,lon[:,-1].shape[0]-1), \ 
- 743                             range(1,lon[-1,::-1].shape[0]-1)[::-1], \ 
- 744                             range(1,lon[::-1,0].shape[0]-1)[::-1])) 
- 745   
- 746      d = np.zeros(edge.shape) 
- 747      for i in range (edge.shape[0]): 
- 748          d[i] = edge[i] - longitude 
- 749          d[i] = d[i] / abs(d[i]) 
- 750      d = np.diff(d) 
- 751   
- 752      pt_idx = np.where(d != 0)[0] 
- 753   
- 754      Mp, Lp = lon.shape 
- 755   
- 756      if len(pt_idx) != 2: 
- 757          raise ValueError, 'this function only works for simple quadrangle' 
- 758   
- 759      # determine is latitude ligne is crossing a i or j edge 
- 760      side = np.zeros(2) 
- 761      if pt_idx[0] < Lp: side[0] = 1 
- 762      if pt_idx[0] >= Lp and pt_idx[0] < Lp+Mp: side[0] = 2 
- 763      if pt_idx[0] >= Lp+Mp and pt_idx[0] < Lp+Mp+Lp: side[0] = 3 
- 764      if pt_idx[0] >= Lp+Mp+Lp: side[0] = 4 
- 765      if pt_idx[1] < Lp: side[1] = 1 
- 766      if pt_idx[1] >= Lp and pt_idx[1] < Lp+Mp: side[1] = 2 
- 767      if pt_idx[1] >= Lp+Mp and pt_idx[1] < Lp+Mp+Lp: side[1] = 3 
- 768      if pt_idx[1] >= Lp+Mp+Lp: side[1] = 4 
- 769   
- 770   
- 771      if side[0] == 1 and side[1] == 2: 
- 772          lonslice, z, lon, lat = pyroms.tools.section(var, \ 
- 773                                  idx[pt_idx[0]], Lp-2, \ 
- 774                                  1, idx[pt_idx[1]], \ 
- 775                                  grd, Cpos=Cpos, vert=vert, spval=spval) 
- 776      elif side[0] == 1 and side[1] == 3: 
- 777          lonslice, z, lon, lat = pyroms.tools.section(var, \ 
- 778                                  idx[pt_idx[0]], idx[pt_idx[1]], \ 
- 779                                  1, Mp-2, \ 
- 780                                  grd, Cpos=Cpos, vert=vert, spval=spval) 
- 781      elif side[0] == 1 and side[1] == 4: 
- 782          lonslice, z, lon, lat = pyroms.tools.section(var, \ 
- 783                                  idx[pt_idx[0]], 1, \ 
- 784                                  1, idx[pt_idx[1]], \ 
- 785                                  grd, Cpos=Cpos, vert=vert, spval=spval) 
- 786      elif side[0] == 2 and side[1] == 3: 
- 787          lonslice, z, lon, lat = pyroms.tools.section(var, \ 
- 788                                  Lp-2, idx[pt_idx[1]], \ 
- 789                                  idx[pt_idx[0]], Mp-2, \ 
- 790                                  grd, Cpos=Cpos, vert=vert, spval=spval) 
- 791      elif side[0] == 2 and side[1] == 4: 
- 792          lonslice, z, lon, lat = pyroms.tools.section(var, \ 
- 793                                  Lp-2, 1, \ 
- 794                                  idx[pt_idx[0]], idx[pt_idx[0]], \ 
- 795                                  grd, Cpos=Cpos, vert=vert, spval=spval) 
- 796      elif side[0] == 3 and side[1] == 4: 
- 797          lonslice, z, lon, lat = pyroms.tools.section(var, \ 
- 798                                  idx[pt_idx[0]], 1, \ 
- 799                                  Mp-2, idx[pt_idx[1]], \ 
- 800                                  grd, Cpos=Cpos, vert=vert, spval=spval) 
- 801   
- 802   
- 803      return lonslice, z, lon, lat 
-
 804   
- 805   
- 806   
-
 807 -def latslice(var, latitude, grd, Cpos='rho', vert=False, spval=1e37): 
-
 808      """ 
- 809      latslice, z, lon, lat = latslice(var, latitude, grd) 
- 810   
- 811      optional switch: 
- 812        - Cpos='rho', 'u' or 'v'       specify the C-grid position where  
- 813                                       the variable rely 
- 814        - vert=True/False              If True, return the position of  
- 815                                       the verticies 
- 816        - spval                        special value 
- 817        - rtol                         tolerance parameter 
- 818   
- 819   
- 820      return a latitudinal slice along latitude=latitude from 3D variable var 
- 821      lon, lat and z contain the C-grid position of the section for plotting. 
- 822      If vert=True, lon, lat and z contain contain the position of the  
- 823      verticies (to be used with pcolor) 
- 824      Returns a longitudinal slice of the grid 
- 825      """ 
- 826   
- 827      if Cpos == 'u': 
- 828          lon = grd.hgrid.lon_u 
- 829          lat = grd.hgrid.lat_u 
- 830      elif Cpos == 'v': 
- 831          lon = grd.hgrid.lon_v 
- 832          lat = grd.hgrid.lat_v 
- 833      elif Cpos == 'rho': 
- 834          lon = grd.hgrid.lon_rho 
- 835          lat = grd.hgrid.lat_rho 
- 836      else: 
- 837          raise Warning, '%s bad position. Valid Arakawa-C are \ 
- 838                             rho, u or v.' % Cpos 
- 839   
- 840      edge = np.concatenate((lat[1,1:-1], \ 
- 841                             lat[1:-1,-2], \ 
- 842                             lat[-2,-2:0:-1], \ 
- 843                             lat[-2:0:-1,1])) 
- 844      idx =  np.concatenate((range(1,lat[0,:].shape[0]-1), \ 
- 845                             range(1,lat[:,-1].shape[0]-1), \ 
- 846                             range(1,lat[-1,::-1].shape[0]-1)[::-1], \ 
- 847                             range(1,lat[::-1,0].shape[0]-1)[::-1])) 
- 848   
- 849      d = np.zeros(edge.shape) 
- 850      for i in range (edge.shape[0]): 
- 851          d[i] = edge[i] - latitude 
- 852          d[i] = d[i] / abs(d[i]) 
- 853      d = np.diff(d) 
- 854   
- 855      pt_idx = np.where(d != 0)[0] 
- 856   
- 857      Mp, Lp = lon.shape 
- 858   
- 859      if len(pt_idx) != 2: 
- 860          raise ValueError, 'this function only works for simple quadrangle' 
- 861   
- 862      # determine is latitude ligne is crossing a i or j edge 
- 863      side = np.zeros(2) 
- 864      if pt_idx[0] < Lp: side[0] = 1 
- 865      if pt_idx[0] >= Lp and pt_idx[0] < Lp+Mp: side[0] = 2 
- 866      if pt_idx[0] >= Lp+Mp and pt_idx[0] < Lp+Mp+Lp: side[0] = 3 
- 867      if pt_idx[0] >= Lp+Mp+Lp: side[0] = 4 
- 868      if pt_idx[1] < Lp: side[1] = 1 
- 869      if pt_idx[1] >= Lp and pt_idx[1] < Lp+Mp: side[1] = 2 
- 870      if pt_idx[1] >= Lp+Mp and pt_idx[1] < Lp+Mp+Lp: side[1] = 3 
- 871      if pt_idx[1] >= Lp+Mp+Lp: side[1] = 4 
- 872   
- 873   
- 874      if side[0] == 1 and side[1] == 2: 
- 875          latslice, z, lon, lat = pyroms.tools.section(var, \ 
- 876                                  idx[pt_idx[0]], Lp-2, \ 
- 877                                  1, idx[pt_idx[1]], \ 
- 878                                  grd, Cpos=Cpos, vert=vert, spval=spval) 
- 879      elif side[0] == 1 and side[1] == 3: 
- 880          latslice, z, lon, lat = pyroms.tools.section(var, \ 
- 881                                  idx[pt_idx[0]], idx[pt_idx[1]], \ 
- 882                                  1, Mp-2, \ 
- 883                                  grd, Cpos=Cpos, vert=vert, spval=spval) 
- 884      elif side[0] == 1 and side[1] == 4: 
- 885          latslice, z, lon, lat = pyroms.tools.section(var, \ 
- 886                                  idx[pt_idx[0]], 1, \ 
- 887                                  1, idx[pt_idx[1]], \ 
- 888                                  grd, Cpos=Cpos, vert=vert, spval=spval) 
- 889      elif side[0] == 2 and side[1] == 3: 
- 890          latslice, z, lon, lat = pyroms.tools.section(var, \ 
- 891                                  Lp-2, idx[pt_idx[1]], \ 
- 892                                  idx[pt_idx[0]], Mp-2, \ 
- 893                                  grd, Cpos=Cpos, vert=vert, spval=spval) 
- 894      elif side[0] == 2 and side[1] == 4: 
- 895          latslice, z, lon, lat = pyroms.tools.section(var, \ 
- 896                                  Lp-2, 1, \ 
- 897                                  idx[pt_idx[0]], idx[pt_idx[0]], \ 
- 898                                  grd, Cpos=Cpos, vert=vert, spval=spval) 
- 899      elif side[0] == 3 and side[1] == 4: 
- 900          latslice, z, lon, lat = pyroms.tools.section(var, \ 
- 901                                  idx[pt_idx[0]], 1, \ 
- 902                                  Mp-2, idx[pt_idx[1]], \ 
- 903                                  grd, Cpos=Cpos, vert=vert, spval=spval) 
- 904   
- 905      return latslice, z, lon, lat 
-
 906   
- 907   
- 908   
-
 909 -def section_transport(u, v, istart, iend, jstart, jend, grd): 
-
 910      """ 
- 911      transpu, transpv = section_transport(u, v, istart, iend, jstart, jend, grd) 
- 912   
- 913      compute the transport through the section defined between  
- 914      the point P1 (istart,jstart) and P2 (iend, jend). 
- 915      P1 and P2 are Arakawa-C psi points. 
- 916      The transpot is positive right handside of the section. 
- 917      """                            
- 918           
- 919   
- 920      # Find the nearest point between P1 (imin,jmin) and P2 (imax, jmax) 
- 921      # ----------------------------------------------------------------- 
- 922      # Initialization 
- 923      i0=istart; j0=jstart; i1=iend;  j1=jend 
- 924      istart = float(istart); iend = float(iend) 
- 925      jstart = float(jstart); jend = float(jend) 
- 926   
- 927      # Compute equation:  j = aj i + bj 
- 928      if istart != iend: 
- 929          aj = (jend - jstart ) / (iend - istart) 
- 930          bj = jstart - aj * istart 
- 931      else: 
- 932          aj=10000. 
- 933          bj=0. 
- 934   
- 935      # Compute equation:  i = ai j + bi 
- 936      if jstart != jend: 
- 937          ai = (iend - istart ) / ( jend - jstart ) 
- 938          bi = istart - ai * jstart 
- 939      else: 
- 940          ai=10000. 
- 941          bi=0. 
- 942        
- 943      # Compute the integer pathway: 
- 944      # Chose the strait line with the smallest slope 
- 945      if (abs(aj) <=  1 ): 
- 946          # Here, the best line is y(x) 
- 947          print 'Here, the best line is y(x)' 
- 948          # If i1 < i0 swap points and remember it has been swapped 
- 949          if i1 <  i0: 
- 950              i  = i0 ; j  = j0 
- 951              i0 = i1 ; j0 = j1 
- 952              i1 = i  ; j1 = j 
- 953              norm = -1 
- 954          else: 
- 955              norm = 1 
- 956   
- 957          if j1 >= j0: 
- 958              ist = 1; jst = 1 
- 959              norm_u = 1; norm_v = -1 
- 960          else: 
- 961              ist = 1; jst = 0 
- 962              norm_u = -1; norm_v = -1 
- 963   
- 964          near = [] 
- 965          # compute the nearest j point on the line crossing at i 
- 966          for i in range(i0,i1+1): 
- 967              j = aj*i + bj 
- 968              near.append(i + round(j)*1j) 
- 969              
- 970      else: 
- 971          # Here, the best line is x(y) 
- 972          print 'Here, the best line is x(y)' 
- 973          # If j1 < j0 swap points and remember it has been swapped 
- 974          if j1 <  j0: 
- 975              i  = i0 ; j  = j0 
- 976              i0 = i1 ; j0 = j1 
- 977              i1 = i  ; j1 = j 
- 978              norm = -1 
- 979          else: 
- 980              norm = 1 
- 981   
- 982          if i1 >= i0: 
- 983              ist = 1; jst = 1 
- 984              norm_u = 1; norm_v = -1 
- 985          else: 
- 986              ist = 0; jst = 1 
- 987              norm_u = 1; norm_v = 1 
- 988   
- 989          near = [] 
- 990          # compute the nearest i point on the line crossing at j 
- 991          for j in range(j0,j1+1): 
- 992              i = ai*j + bi 
- 993              near.append(round(i) + j*1j) 
- 994   
- 995   
- 996      # Look for intermediate points to be added 
- 997      # ------------------------------------------------------------- 
- 998   
- 999      inear = copy(near) 
-1000   
-1001      n = len(near) 
-1002      nn=1 
-1003   
-1004      for k in range(1,n): 
-1005          # distance between 2 neighbour points 
-1006          d = abs(inear[k] - inear[k-1]) 
-1007                   
-1008          if ( d > 1 ): 
-1009              # intermediate points required if d>1 
-1010              neari = interm_pt(inear, k, ai, bi, aj, bj) 
-1011              near.insert(nn,neari) 
-1012              nn=nn+1 
-1013           
-1014          nn=nn+1 
-1015   
-1016   
-1017      # Now extract the transport through a section 
-1018      # ------------------------------------------- 
-1019   
-1020      #get metrics 
-1021      dx = grd.hgrid.dx 
-1022      dy = grd.hgrid.dy 
-1023      # average z_w at Arakawa-C u points                                             
-1024      zu = 0.5 * (grd.vgrid.z_w[:,:,:-1] + grd.vgrid.z_w[:,:,1:])                                     
-1025      dzu = zu[1:,:,:] - zu[:-1,:,:] 
-1026      # average z_w at Arakawa-C v points 
-1027      zv = 0.5 * (grd.vgrid.z_w[:,:-1,:] + grd.vgrid.z_w[:,1:,:]) 
-1028      dzv = zv[1:,:,:] - zv[:-1,:,:] 
-1029   
-1030      #set u and v to zero where u and v are masked for the sum 
-1031      for k in range(u.shape[0]): 
-1032          u[k,:] = np.where(grd.hgrid.mask_u == 1, u[k,:], 0) 
-1033          v[k,:] = np.where(grd.hgrid.mask_v == 1, v[k,:], 0) 
-1034   
-1035      n = len(near) 
-1036      transpu = 0 
-1037      transpv = 0 
-1038   
-1039      for l in range(0,n-1): 
-1040          ii = int(real(near[l])); jj = int(imag(near[l])) 
-1041          for k in range(0, dzu.shape[0]): 
-1042              if real(near[l]) == real(near[l+1]): 
-1043                  trans = u[k, jj+jst, ii] * dy[jj+jst, ii] * \ 
-1044                          dzu[k, jj+jst, ii] * norm_u * norm 
-1045                  transpu = transpu + trans 
-1046   
-1047              elif imag(near[l]) == imag(near[l+1]): 
-1048                  trans = v[k, jj, ii+ist] * dx[jj, ii+ist] * \ 
-1049                          dzv[k, jj, ii+ist] * norm_v * norm 
-1050                  transpv = transpv + trans 
-1051   
-1052   
-1053      return transpu, transpv 
-
1054   
-1055   
-
1056 -def interm_pt(pnear, pk, pai, pbi, paj, pbj): 
-
1057      ### FIND THE BEST INTERMEDIATE POINT ON A PATHWAY 
-1058      #           ----------------------------- 
-1059      #   pnear   : vector of the position of the nearest point 
-1060      #   pk      : current working index 
-1061      #   pai, pbi: slope and original ordinate of x(y) 
-1062      #   paj, pbj: slope and original ordinate of y(x) 
-1063      #   pneari  : vector holding the position of intermediate point 
-1064      #           ----------------------------- 
-1065       
-1066      # 1 - Compute intermediate point 
-1067       
-1068      # Determine whether we use y(x) or x(y): 
-1069      if (abs(paj) <= 1): 
-1070          # y(x) 
-1071          # possible intermediate point 
-1072          ylptmp1 = pnear[pk-1] + 1 
-1073          ylptmp2 = pnear[pk-1] + (paj/abs(paj))*1j 
-1074          # M is the candidate point: 
-1075          zxm = real(ylptmp1) 
-1076          zym = imag(ylptmp1) 
-1077          za0 = paj 
-1078          zb0 = pbj 
-1079          # 
-1080          za1 = -1./za0 
-1081          zb1 = zym-za1*zxm 
-1082          # P is the projection of M in the strait line 
-1083          zxp = -(zb1-zb0)/(za1-za0) 
-1084          zyp = za0*zxp+zb0 
-1085          # zd1 is the distance MP 
-1086          zd1 = (zxm-zxp) * (zxm-zxp) + (zym-zyp) * (zym-zyp) 
-1087          # 
-1088          # M is the candidate point: 
-1089          zxm = real(ylptmp2) 
-1090          zym = imag(ylptmp2) 
-1091          za1 = -1./za0 
-1092          zb1 = zym-za1*zxm 
-1093          # P is the projection of M in the strait line 
-1094          zxp = -(zb1-zb0)/(za1-za0) 
-1095          zyp = za0*zxp+zb0 
-1096          # zd1 is the distance MP 
-1097          zd2 = (zxm-zxp) * (zxm-zxp) + (zym-zyp) * (zym-zyp) 
-1098          # 
-1099          # choose the smallest (zd1,zd2) 
-1100          if (zd2 <= zd1): 
-1101              pneari = ylptmp2 
-1102          else: 
-1103              pneari = ylptmp1 
-1104          #        
-1105      else: 
-1106          # x(y) 
-1107          ylptmp1 = pnear[pk-1] + (pai/abs(pai)) 
-1108          ylptmp2 = pnear[pk-1] + 1*1j 
-1109          # M is the candidate point: 
-1110          zxm = real(ylptmp1) 
-1111          zym = imag(ylptmp1) 
-1112          za0 = pai 
-1113          zb0 = pbi 
-1114          # 
-1115          za1 = -1./za0 
-1116          zb1 = zxm-za1*zym 
-1117          # P is the projection of M in the strait line 
-1118          zyp = -(zb1-zb0)/(za1-za0) 
-1119          zxp = za0*zyp+zb0 
-1120          # zd1 is the distance MP 
-1121          zd1 = (zxm-zxp) * (zxm-zxp) + (zym-zyp) * (zym-zyp) 
-1122          # 
-1123          # M is the candidate point: 
-1124          zxm = real(ylptmp2) 
-1125          zym = imag(ylptmp2) 
-1126          za1 = -1./za0 
-1127          zb1 = zxm-za1*zym 
-1128          # P is the projection of M in the strait line 
-1129          zyp = -(zb1-zb0)/(za1-za0) 
-1130          zxp = za0*zyp+zb0 
-1131          # zd2 is the distance MP 
-1132          zd2 = (zxm-zxp) * (zxm-zxp) + (zym-zyp) * (zym-zyp) 
-1133          # 
-1134          # choose the smallest (zd1,zd2) 
-1135          if (zd2 <= zd1): 
-1136              pneari = ylptmp2 
-1137          else: 
-1138              pneari = ylptmp1 
-1139           
-1140      return pneari 
-
1141   
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Module utility

source code

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Functions[hide private]
-
-   - - - - - - -
get_lonlat(iindex, - jindex, - grd, - Cpos='rho')
- lon, lat = get_lonlat(iindex, jindex, grd)		 - source code - -
- -
-   - - - - - - -
get_ij(longitude, - latitude, - grd, - Cpos='rho')
- i, j = get_ij(longitude, latitude, grd)		 - source code - -
- -
-   - - - - - - -
find_nearestgridpoints(longitude, - latitude, - grd, - Cpos='rho') - source code - -
- -
-   - - - - - - -
get_grid_proj(grd, - type='merc', - resolution='h')
- map = get_grid_proj(grd)		 - source code - -
- -
-   - - - - - - -
get_nc_var(varname, - filename)
- var = roms_nc_var(varname, filename)		 - source code - -
- -
-   - - - - - - -
roms_varlist(option)
- varlist = roms_varlist(option)		 - source code - -
- -
-   - - - - - - -
get_bottom(varz, - mask, - spval=1e+37) - source code - -
- -
-   - - - - - - -
get_surface(varz, - mask, - spval=1e+37) - source code - -
- -
-   - - - - - - -
move2grid(varin, - init_grid, - final_grid)
- tempu = move2grid(temp, 'rho', 'u')		 - source code - -
- -
-   - - - - - - -
get_date_tag(roms_time, - ref=(2006, 1, 1), - format='%d %b %Y at %H:%M:%S')
- tag = get_date_tag(roms_time)		 - source code - -
- -
- - - - - - -
- - - - - -
Function Details[hide private]
-
- -
- -
- - -
-

get_lonlat(iindex, - jindex, - grd, - Cpos='rho') -

- 		source code  -
- -

lon, lat = get_lonlat(iindex, jindex, grd)

-

return the longitude (degree east) and latitude (degree north) for - grid point (iindex, jindex)

-
-
-
-
- -
- -
- - -
-

get_ij(longitude, - latitude, - grd, - Cpos='rho') -

- 		source code  -
- -

i, j = get_ij(longitude, latitude, grd)

-

return the index of the closest point on the grid from the point - (longitude,latitude) in degree

-
-
-
-
- -
- -
- - -
-

get_grid_proj(grd, - type='merc', - resolution='h') -

- 		source code  -
- -

map = get_grid_proj(grd)

-

optional arguments:

-
    -
  • - type set projection type (default is merc) -
    • -
  • - resolution set resolution parameter (default is high) -
    • -
-

return a Basemap object that can be use for plotting

-
-
-
-
- -
- -
- - -
-

get_nc_var(varname, - filename) -

- 		source code  -
- -

var = roms_nc_var(varname, filename)

-

a simple wraper for netCDF4

-
-
-
-
- -
- -
- - -
-

roms_varlist(option) -

- 		source code  -
- -

varlist = roms_varlist(option)

-

Return ROMS varlist.

-
-
-
-
- -
- -
- - -
-

move2grid(varin, - init_grid, - final_grid) -

- 		source code  -
- -

tempu = move2grid(temp, 'rho', 'u')

-

Move var from init_grid to final_grid.

-
-
-
-
- -
- -
- - -
-

get_date_tag(roms_time, - ref=(2006, 1, 1), - format='%d %b %Y at %H:%M:%S') -

- 		source code  -
- -

tag = get_date_tag(roms_time)

-

return date tag for roms_time (in second since initialisation). - default reference time is January 1st 2006.

-
-
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Source Code for Module pyroms.utility

-
-  1  #encoding: utf-8 
-  2   
-  3  import sys 
-  4  import numpy as np 
-  5  from mpl_toolkits.basemap import Basemap 
-  6  import time 
-  7  from datetime import datetime 
-  8  from matplotlib.nxutils import pnpoly 
-  9   
- 10  from pyroms import io 
- 11  import _interp 
- 12   
- 13   
-
 14 -def get_lonlat(iindex, jindex, grd, Cpos='rho'): 
-
 15      """  
- 16      lon, lat = get_lonlat(iindex, jindex, grd) 
- 17   
- 18      return the longitude (degree east) and latitude (degree north) 
- 19      for grid point (iindex, jindex) 
- 20      """ 
- 21   
- 22      if Cpos is 'u': 
- 23          lon = grd.hgrid.lon_u[:,:] 
- 24          lat = grd.hgrid.lat_u[:,:] 
- 25      elif Cpos is 'v': 
- 26          lon = grd.hgrid.lon_v[:,:] 
- 27          lat = grd.hgrid.lat_v[:,:] 
- 28      elif Cpos is 'rho': 
- 29          lon = grd.hgrid.lon_rho[:,:] 
- 30          lat = grd.hgrid.lat_rho[:,:]    
- 31      else: 
- 32          raise Warning, '%s bad position. Cpos must be rho, u or v.' % Cpos 
- 33   
- 34      return lon[jindex, iindex], lat[jindex, iindex] 
-
 35   
- 36   
-
 37 -def get_ij(longitude, latitude, grd, Cpos='rho'): 
-
 38      """  
- 39      i, j = get_ij(longitude, latitude, grd) 
- 40   
- 41      return the index of the closest point on the grid from the  
- 42      point (longitude,latitude) in degree 
- 43      """ 
- 44   
- 45      if Cpos is 'u': 
- 46          lon = grd.hgrid.lon_u[:,:] 
- 47          lat = grd.hgrid.lat_u[:,:] 
- 48      elif Cpos is 'v': 
- 49          lon = grd.hgrid.lon_v[:,:] 
- 50          lat = grd.hgrid.lat_v[:,:] 
- 51      elif Cpos is 'rho': 
- 52          lon = grd.hgrid.lon_rho[:,:] 
- 53          lat = grd.hgrid.lat_rho[:,:]    
- 54      else: 
- 55          raise Warning, '%s bad position. Cpos must be rho, u or v.' % Cpos 
- 56   
- 57      lon = lon[:,:] - longitude 
- 58      lat = lat[:,:] - latitude 
- 59   
- 60      diff = (lon * lon) + (lat * lat) 
- 61   
- 62      jindex, iindex = np.where(diff==diff.min()) 
- 63       
- 64      return iindex[0], jindex[0] 
-
 65   
- 66   
- 67   
-
 68 -def find_nearestgridpoints(longitude, latitude, grd, Cpos='rho'): 
-
 69   
- 70      if Cpos is 'u': 
- 71          lon = grd.hgrid.lon_u[:,:] 
- 72          lat = grd.hgrid.lat_u[:,:] 
- 73      elif Cpos is 'v': 
- 74          lon = grd.hgrid.lon_v[:,:] 
- 75          lat = grd.hgrid.lat_v[:,:] 
- 76      elif Cpos is 'rho': 
- 77          lon = grd.hgrid.lon_rho[:,:] 
- 78          lat = grd.hgrid.lat_rho[:,:] 
- 79      else: 
- 80          raise Warning, '%s bad position. Cpos must be rho, u or v.' % Cpos 
- 81   
- 82      dlon = lon[:,:] - longitude 
- 83      dlat = lat[:,:] - latitude 
- 84   
- 85      diff = (dlon * dlon) + (dlat * dlat) 
- 86   
- 87      jidx, iidx = np.where(diff==diff.min()) 
- 88   
- 89      iidx = iidx[0] # take element 1 in case min dist is not unique 
- 90      jidx = jidx[0] 
- 91   
- 92      try: 
- 93   
- 94          iindex = [iidx, iidx+1, iidx+1, iidx] 
- 95          jindex = [jidx, jidx, jidx+1, jidx+1] 
- 96          xp = lon[jindex, iindex] 
- 97          yp = lat[jindex, iindex] 
- 98          verts = [] 
- 99          for n in range(4): 
-100              verts.append([xp[n], yp[n]]) 
-101          inside = pnpoly(longitude, latitude, verts) 
-102   
-103          if inside == 0: 
-104              iindex = [iidx, iidx+1, iidx+1, iidx] 
-105              jindex = [jidx-1, jidx-1, jidx, jidx] 
-106              xp = lon[jindex, iindex] 
-107              yp = lat[jindex, iindex] 
-108              verts = [] 
-109              for n in range(4): 
-110                  verts.append([xp[n], yp[n]]) 
-111              inside = pnpoly(longitude, latitude, verts) 
-112   
-113              if inside == 0: 
-114                  iindex = [iidx-1, iidx, iidx, iidx-1] 
-115                  jindex = [jidx-1, jidx-1, jidx, jidx] 
-116                  xp = lon[jindex, iindex] 
-117                  yp = lat[jindex, iindex] 
-118                  verts = [] 
-119                  for n in range(4): 
-120                      verts.append([xp[n], yp[n]]) 
-121                  inside = pnpoly(longitude, latitude, verts) 
-122   
-123                  if inside == 0: 
-124                      iindex = [iidx-1, iidx, iidx, iidx-1] 
-125                      jindex = [jidx, jidx, jidx+1, jidx+1] 
-126                      xp = lon[jindex, iindex] 
-127                      yp = lat[jindex, iindex] 
-128                      verts = [] 
-129                      for n in range(4): 
-130                          verts.append([xp[n], yp[n]]) 
-131                      inside = pnpoly(longitude, latitude, verts) 
-132   
-133                      if inside == 0: 
-134                          raise ValueError, 'well where is it then?' 
-135   
-136          iindex = iindex[:2] 
-137          jindex = jindex[1:3] 
-138   
-139      except: 
-140          print 'point (%f, %f) is not in the grid' %(longitude, latitude) 
-141          iindex = [] 
-142          jindex = [] 
-143           
-144      return iindex, jindex 
-
145       
-146   
-
147 -def get_grid_proj(grd, type='merc', resolution='h'): 
-
148      """ 
-149      map = get_grid_proj(grd) 
-150   
-151      optional arguments: 
-152        - type           set projection type (default is merc) 
-153        - resolution     set resolution parameter (default is high) 
-154   
-155      return a Basemap object that can be use for plotting 
-156      """ 
-157   
-158      lon_min = grd.hgrid.lon_vert.min() 
-159      lon_max = grd.hgrid.lon_vert.max() 
-160      lon_0 = (lon_min + lon_max) / 2. 
-161   
-162      lat_min = grd.hgrid.lat_vert.min() 
-163      lat_max = grd.hgrid.lat_vert.max() 
-164      lat_0 = (lat_min + lat_max) / 2. 
-165   
-166      map = Basemap(projection=type, llcrnrlon=lon_min, llcrnrlat=lat_min, \ 
-167           urcrnrlon=lon_max, urcrnrlat=lat_max, lat_0=lat_0, lon_0=lon_0, \ 
-168           resolution=resolution) 
-169   
-170      return map 
-
171   
-172   
-
173 -def get_nc_var(varname, filename): 
-
174      """ 
-175      var = roms_nc_var(varname, filename) 
-176   
-177      a simple wraper for netCDF4 
-178      """ 
-179   
-180      data = io.MFDataset(filename) 
-181      var = data.variables[varname] 
-182   
-183      return var 
-
184   
-185   
-
186 -def roms_varlist(option): 
-
187      """ 
-188      varlist = roms_varlist(option) 
-189   
-190      Return ROMS varlist. 
-191      """ 
-192   
-193      if option == 'physics': 
-194          varlist = (['temp','salt','u','v','ubar','vbar','zeta']) 
-195      elif option == 'physics2d': 
-196          varlist = (['ubar','vbar','zeta']) 
-197      elif option == 'physics3d': 
-198          varlist = (['temp','salt','u','v']) 
-199      elif option == 'mixing3d': 
-200          varlist = (['AKv','AKt','AKs']) 
-201      elif option == 's-param': 
-202          varlist = (['theta_s','theta_b','Tcline','hc']) 
-203      elif option == 's-coord': 
-204          varlist = (['s_rho','s_w','Cs_r','Cs_w']) 
-205      elif option == 'coord': 
-206          varlist = (['lon_rho','lat_rho','lon_u','lat_u','lon_v','lat_v']) 
-207      elif option == 'grid': 
-208          varlist = (['h','f','pm','pn','angle','lon_rho','lat_rho', \ 
-209            'lon_u','lat_u','lon_v','lat_v','lon_psi','lat_psi', \ 
-210            'mask_rho','mask_u','mask_v','mask_psi']) 
-211      elif option == 'hgrid': 
-212          varlist = (['f','dx','dy','angle_rho','lon_rho','lat_rho', \ 
-213            'lon_u','lat_u','lon_v','lat_v','lon_psi','lat_psi', \ 
-214            'mask_rho','mask_u','mask_v','mask_psi']) 
-215      elif option == 'vgrid': 
-216          varlist = (['h','s_rho','s_w','Cs_r','Cs_w', \ 
-217            'theta_s','theta_b','Tcline','hc']) 
-218      else: 
-219          raise Warning, 'Unknow varlist id' 
-220   
-221      return varlist 
-
222   
-223   
-
224 -def get_bottom(varz, mask, spval=1e37): 
-
225   
-226      assert len(varz.shape) == 3, 'var must be 3D' 
-227   
-228      N = varz.shape[0] 
-229      jj = varz.shape[1] 
-230      ii = varz.shape[2] 
-231   
-232      bottom = spval * np.ones((jj, ii)) 
-233   
-234      bottom[:,:] = _interp.get_bottom(varz,mask,spval) 
-235   
-236      return bottom 
-
237   
-238   
-
239 -def get_surface(varz, mask, spval=1e37): 
-
240   
-241      assert len(varz.shape) == 3, 'var must be 3D' 
-242   
-243      N = varz.shape[0] 
-244      jj = varz.shape[1] 
-245      ii = varz.shape[2] 
-246   
-247      surface = spval * np.ones((jj, ii)) 
-248   
-249      surface[:,:] = _interp.get_surface(varz,mask,spval) 
-250   
-251      return surface 
-
252   
-253   
-
254 -def move2grid(varin, init_grid, final_grid): 
-
255      ''' 
-256      tempu = move2grid(temp, 'rho', 'u') 
-257   
-258      Move var from init_grid to final_grid. 
-259      ''' 
-260   
-261      ndim = len(varin.shape) 
-262   
-263      if ndim == 2: 
-264   
-265          if (init_grid == 'rho' and final_grid == 'u'): 
-266              varout = 0.5 * (varin[:,1:] + varin[:,:-1]) 
-267          elif (init_grid == 'rho' and final_grid == 'v'): 
-268              varout = 0.5 * (varin[1:,:] + varin[:-1,:]) 
-269          elif (init_grid == 'rho' and final_grid == 'psi'): 
-270              varout = 0.25 * (varin[1:,1:] + varin[:-1,:-1] + \ 
-271                               varin[1:,:-1] + varin[:-1,1:]) 
-272          elif (init_grid == 'u' and final_grid == 'psi'): 
-273              varout = 0.5 * (varin[1:,:] + varin[:-1,:]) 
-274          elif (init_grid == 'v' and final_grid == 'psi'): 
-275              varout = 0.5 * (varin[:,1:] + varin[:,:-1]) 
-276          else: 
-277              raise ValueError, 'Undefined combination for init_grid and final_grid' 
-278   
-279      elif ndim == 3: 
-280   
-281          if (init_grid == 'rho' and final_grid == 'u'): 
-282              varout = 0.5 * (varin[:,:,1:] + varin[:,:,:-1]) 
-283          elif (init_grid == 'rho' and final_grid == 'v'): 
-284              varout = 0.5 * (varin[:,1:,:] + varin[:,:-1,:]) 
-285          elif (init_grid == 'rho' and final_grid == 'psi'): 
-286              varout = 0.25 * (varin[:,1:,1:] + varin[:,:-1,:-1] + \ 
-287                               varin[:,1:,:-1] + varin[:,:-1,1:]) 
-288          elif (init_grid == 'u' and final_grid == 'psi'): 
-289              varout = 0.5 * (varin[:,1:,:] + varin[:,:-1,:]) 
-290          elif (init_grid == 'v' and final_grid == 'psi'): 
-291              varout = 0.5 * (varin[:,:,1:] + varin[:,:,:-1]) 
-292          else: 
-293              raise ValueError, 'Undefined combination for init_grid and final_grid' 
-294   
-295      else: 
-296          raise ValueError, 'varin must be 2D or 3D' 
-297   
-298      return varout 
-
299   
-300   
-
301 -def get_date_tag(roms_time, ref=(2006, 01, 01), format="%d %b %Y at %H:%M:%S"): 
-
302      ''' 
-303      tag = get_date_tag(roms_time) 
-304   
-305      return date tag for roms_time (in second since initialisation). 
-306      default reference time is January 1st 2006.  
-307      ''' 
-308   
-309      ref = time.mktime(datetime(ref[0], ref[1], ref[2]).timetuple()) 
-310      timestamp = ref + roms_time 
-311      tag = datetime.fromtimestamp(timestamp).strftime(format) 
-312   
-313      return tag 
-
314   
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Module vgrid

source code

-
-
-Various vertical coordinates
-
-Presently, only ocean s-coordinates are supported. Future plans will be to
-include all of the vertical coordinate systems defined by the CF conventions.
-
-
- - - - - - - - - - - - - - - - - - - - - - -
- - - - - -
Classes[hide private]
-
-   - - s_coordinate
- Original vertical coordinate transformation (Vtransform=1) -
-   - - s_coordinate_2
- New vertical coordinate transformation (Vtransform=2) -
-   - - z_r
- return an object that can be indexed to return depths of rho point -
-   - - z_w
- return an object that can be indexed to return depths of w point -
-   - - z_coordinate
- return an object that can be indexed to return depths -
- - - - - - - - - - - - - - - - - -
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- Generated by Epydoc 3.0.1 on Mon Sep 27 11:31:38 2010 - - http://epydoc.sourceforge.net -
- - - - diff --git a/pyroms/docs/pyroms.vgrid-pysrc.html b/pyroms/docs/pyroms.vgrid-pysrc.html deleted file mode 100644 index 61fbf31..0000000 --- a/pyroms/docs/pyroms.vgrid-pysrc.html +++ /dev/null @@ -1,408 +0,0 @@ - - - - - pyroms.vgrid - - - - - - - - - - - - - - - - - - - - - - -
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- - Package pyroms :: - Module vgrid - - - - - - -
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Source Code for Module pyroms.vgrid

-
-  1  # encoding: utf-8 
-  2  ''' 
-  3  Various vertical coordinates 
-  4   
-  5  Presently, only ocean s-coordinates are supported. Future plans will be to 
-  6  include all of the vertical coordinate systems defined by the CF conventions. 
-  7  ''' 
-  8   
-  9  __docformat__ = "restructuredtext en" 
- 10   
- 11  import numpy as np 
- 12  import warnings 
- 13   
- 14   
-
 15 -class s_coordinate(object): 
-
 16      """ 
- 17      Original vertical coordinate transformation (Vtransform=1) 
- 18       
- 19      return an object that can be indexed to return depths 
- 20   
- 21      s = s_coordinate(h, theta_b, theta_s, Tcline, N) 
- 22      """ 
- 23   
-
 24 -    def __init__(self, h, theta_b, theta_s, Tcline, N, zeta=None): 
-
 25          self.h = np.asarray(h) 
- 26          self.hmin = h.min() 
- 27          self.theta_b = theta_b 
- 28          self.theta_s = theta_s 
- 29          self.Tcline = Tcline 
- 30          self.N = int(N) 
- 31          self.Np = self.N+1 
- 32   
- 33          self.hc = min(self.hmin, self.Tcline) 
- 34   
- 35          self.Vtrans = 1 
- 36   
- 37          #assert self.Tcline <= self.hmin, 'Vertical transformation parameters definition error: \n Tcline = %d and hmin = %d. \n You need to make sure that Tcline <= hmin when using the transformation (1).' %(self.Tcline,self.hmin) 
- 38          if (self.Tcline > self.hmin): 
- 39              warnings.warn('Vertical transformation parameters are not defined correctly in either gridid.txt or in the history files: \n Tcline = %d and hmin = %d. \n You need to make sure that Tcline <= hmin when using transformation 1.' %(self.Tcline,self.hmin)) 
- 40   
- 41   
- 42          self.c1 = 1.0 
- 43          self.c2 = 2.0 
- 44          self.p5 = 0.5        
- 45   
- 46          if zeta is None: 
- 47              self.zeta = np.zeros(h.shape) 
- 48          else: 
- 49              self.zeta = zeta 
- 50           
- 51          self._get_s_rho() 
- 52          self._get_s_w() 
- 53          self._get_Cs_r() 
- 54          self._get_Cs_w() 
- 55   
- 56          self.z_r = z_r(self.h, self.hc, self.N, self.s_rho, self.Cs_r, self.zeta, self.Vtrans) 
- 57          self.z_w = z_w(self.h, self.hc, self.Np, self.s_w, self.Cs_w, self.zeta, self.Vtrans) 
-
 58   
- 59   
-
 60 -    def _get_s_rho(self): 
-
 61          lev = np.arange(1,self.N+1,1) 
- 62          ds = 1.0 / self.N 
- 63          self.s_rho = -self.c1 + (lev - self.p5) * ds 
-
 64   
-
 65 -    def _get_s_w(self): 
-
 66          lev = np.arange(0,self.Np,1) 
- 67          ds = 1.0 / (self.Np-1) 
- 68          self.s_w = -self.c1 + lev * ds 
-
 69   
-
 70 -    def _get_Cs_r(self): 
-
 71          if (self.theta_s >= 0): 
- 72              Ptheta = np.sinh(self.theta_s * self.s_rho) / np.sinh(self.theta_s) 
- 73              Rtheta = np.tanh(self.theta_s * (self.s_rho + self.p5)) / \ 
- 74                        (self.c2 * np.tanh(self.p5 * self.theta_s)) - self.p5 
- 75              self.Cs_r = (self.c1 - self.theta_b) * Ptheta + self.theta_b * Rtheta 
- 76          else: 
- 77              self.Cs_r = self.s_rho 
-
 78   
-
 79 -    def _get_Cs_w(self): 
-
 80          if (self.theta_s >= 0): 
- 81              Ptheta = np.sinh(self.theta_s * self.s_w) / np.sinh(self.theta_s) 
- 82              Rtheta = np.tanh(self.theta_s * (self.s_w + self.p5)) / \ 
- 83                        (self.c2 * np.tanh(self.p5 * self.theta_s)) - self.p5 
- 84              self.Cs_w = (self.c1 - self.theta_b) * Ptheta + self.theta_b * Rtheta 
- 85          else: 
- 86              self.Cs_w = self.s_w 
-
 87   
- 88   
- 89   
-
 90 -class s_coordinate_2(s_coordinate): 
-
 91      """ 
- 92      New vertical coordinate transformation (Vtransform=2) 
- 93       
- 94      return an object that can be indexed to return depths 
- 95   
- 96      s = s_coordinate_2(h, theta_b, theta_s, Tcline, N) 
- 97      """ 
- 98   
-
 99 -    def __init__(self, h, theta_b, theta_s, Tcline, N, zeta=None): 
-
100   
-101          self.Aweight = 1.0 
-102          self.Bweight = 1.0 
-103   
-104          super(s_coordinate_2, self).__init__( h, theta_b, theta_s, Tcline, N, zeta) 
-105   
-106          self.Vtrans = 2 
-
107   
-
108 -    def _get_s_rho(self): 
-
109          super(s_coordinate_2, self)._get_s_rho() 
-
110   
-
111 -    def _get_s_w(self): 
-
112          super(s_coordinate_2, self)._get_s_w() 
-
113   
-
114 -    def _get_Cs_r(self): 
-
115          if (self.theta_s >= 0): 
-116              Csur = (self.c1 - np.cosh(self.theta_s * self.s_rho)) / \ 
-117                       (np.cosh(self.theta_s) - self.c1) 
-118              if (self.theta_b >= 0): 
-119                  Cbot = np.sinh(self.theta_b * (self.s_rho + self.c1)) / \ 
-120                         np.sinh(self.theta_b) - self.c1 
-121                  Cweight = (self.s_rho + self.c1)**self.Aweight * \ 
-122                            (self.c1 + (self.Aweight / self.Bweight) * \ 
-123                            (self.c1 - (self.s_rho + self.c1)**self.Bweight)) 
-124                  self.Cs_r = Cweight * Csur + (self.c1 - Cweight) * Cbot 
-125              else: 
-126                  self.Cs_r = Csur 
-127          else: 
-128              self.Cs_r = self.s_rho  
-
129         
-
130 -    def _get_Cs_w(self): 
-
131          if (self.theta_s >= 0): 
-132              Csur = (self.c1 - np.cosh(self.theta_s * self.s_w)) / \ 
-133                       (np.cosh(self.theta_s) - self.c1) 
-134              if (self.theta_b >= 0): 
-135                  Cbot = np.sinh(self.theta_b * (self.s_w + self.c1)) / \ 
-136                         np.sinh(self.theta_b) - self.c1 
-137                  Cweight = (self.s_w + self.c1)**self.Aweight * \ 
-138                            (self.c1 + (self.Aweight / self.Bweight) * \ 
-139                            (self.c1 - (self.s_w + self.c1)**self.Bweight)) 
-140                  self.Cs_w = Cweight * Csur + (self.c1 - Cweight) * Cbot 
-141              else: 
-142                  self.Cs_w = Csur 
-143          else: 
-144              self.Cs_w = self.s_w 
-
145   
-146   
-147   
-
148 -class z_r(object): 
-
149      """ 
-150      return an object that can be indexed to return depths of rho point 
-151   
-152      z_r = z_r(h, hc, N, s_rho, Cs_r, zeta, Vtrans) 
-153      """ 
-154   
-
155 -    def __init__(self, h, hc, N, s_rho, Cs_r, zeta, Vtrans): 
-
156          self.h = h 
-157          self.hc = hc 
-158          self.N = N 
-159          self.s_rho = s_rho 
-160          self.Cs_r = Cs_r 
-161          self.zeta = zeta 
-162          self.Vtrans = Vtrans 
-
163   
-
164 -    def __getitem__(self, key): 
-
165   
-166          if isinstance(key, tuple) and len(self.zeta.shape) > len(self.h.shape): 
-167              zeta = self.zeta[key[0]] 
-168              res_index = (slice(None),) + key[1:] 
-169          elif len(self.zeta.shape) > len(self.h.shape): 
-170              zeta = self.zeta[key] 
-171              res_index = slice(None) 
-172          else: 
-173              zeta = self.zeta 
-174              res_index = key 
-175        
-176          if self.h.ndim == zeta.ndim:       # Assure a time-dimension exists 
-177              zeta = zeta[np.newaxis, :] 
-178         
-179          ti = zeta.shape[0] 
-180          z_r = np.empty((ti, self.N) + self.h.shape, 'd') 
-181          if self.Vtrans == 1: 
-182              for n in range(ti): 
-183                  for  k in range(self.N): 
-184                      z0 = self.hc * self.s_rho[k] + (self.h - self.hc) * self.Cs_r[k] 
-185                      z_r[n,k,:] = z0 + zeta[n,:] * (1.0 + z0 / self.h) 
-186          elif self.Vtrans == 2: 
-187              for n in range(ti): 
-188                  for  k in range(self.N): 
-189                      z0 = (self.hc * self.s_rho[k] + self.h * self.Cs_r[k]) / \ 
-190                            (self.hc + self.h) 
-191                      z_r[n,k,:] = zeta[n,:] + (zeta[n,:] + self.h * z0) 
-192   
-193          return np.squeeze(z_r[res_index]) 
-
194   
-195   
-
196 -class z_w(object): 
-
197      """ 
-198      return an object that can be indexed to return depths of w point 
-199   
-200      z_w = z_w(h, hc, Np, s_w, Cs_w, zeta, Vtrans) 
-201      """ 
-202   
-
203 -    def __init__(self, h, hc, Np, s_w, Cs_w, zeta, Vtrans): 
-
204          self.h = h 
-205          self.hc = hc 
-206          self.Np = Np 
-207          self.s_w = s_w 
-208          self.Cs_w = Cs_w 
-209          self.zeta = zeta 
-210          self.Vtrans = Vtrans 
-
211   
-
212 -    def __getitem__(self, key): 
-
213   
-214          if isinstance(key, tuple) and len(self.zeta.shape) > len(self.h.shape): 
-215              zeta = self.zeta[key[0]] 
-216              res_index = (slice(None),) + key[1:] 
-217          elif len(self.zeta.shape) > len(self.h.shape): 
-218              zeta = self.zeta[key] 
-219              res_index = slice(None) 
-220          else: 
-221              zeta = self.zeta 
-222              res_index = key 
-223        
-224          if self.h.ndim == zeta.ndim:       # Assure a time-dimension exists 
-225              zeta = zeta[np.newaxis, :] 
-226         
-227          ti = zeta.shape[0] 
-228          z_w = np.empty((ti, self.Np) + self.h.shape, 'd') 
-229          if self.Vtrans == 1: 
-230              for n in range(ti): 
-231                  for  k in range(self.Np): 
-232                      z0 = self.hc * self.s_w[k] + (self.h - self.hc) * self.Cs_w[k] 
-233                      z_w[n,k,:] = z0 + zeta[n,:] * (1.0 + z0 / self.h) 
-234          elif self.Vtrans == 2: 
-235              for n in range(ti): 
-236                  for  k in range(self.Np): 
-237                      z0 = (self.hc * self.s_w[k] + self.h * self.Cs_w[k]) / \ 
-238                            (self.hc + self.h) 
-239                      z_w[n,k,:] = zeta[n,:] + (zeta[n,:] + self.h * z0) 
-240   
-241          return np.squeeze(z_w[res_index]) 
-
242   
-243   
-244   
-
245 -class z_coordinate(object): 
-
246      """ 
-247      return an object that can be indexed to return depths 
-248   
-249      z = z_coordinate(h, depth, N) 
-250      """ 
-251   
-
252 -    def __init__(self, h, depth, N): 
-
253          self.h = np.asarray(h) 
-254          self.N = int(N) 
-255   
-256          Mm, Lm = h.shape 
-257   
-258          self.z = np.zeros((N, Mm, Lm)) 
-259          for k in range(N): 
-260              self.z[k,:] = depth[k] 
-
261   
-
-
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- Generated by Epydoc 3.0.1 on Mon Sep 27 11:31:39 2010 - - http://epydoc.sourceforge.net -
- - - - diff --git a/pyroms/docs/pyroms.vgrid.s_coordinate-class.html b/pyroms/docs/pyroms.vgrid.s_coordinate-class.html deleted file mode 100644 index 822bcd7..0000000 --- a/pyroms/docs/pyroms.vgrid.s_coordinate-class.html +++ /dev/null @@ -1,323 +0,0 @@ - - - - - pyroms.vgrid.s_coordinate - - - - - - - - - - - - - - - - - - - - - - -
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- - Package pyroms :: - Module vgrid :: - Class s_coordinate - - - - - - -
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-
- -

Class s_coordinate

source code

-
-object --+
-         |
-        s_coordinate
-
- -
Known Subclasses:
-
- -
- -
-
-
-Original vertical coordinate transformation (Vtransform=1)
-
-return an object that can be indexed to return depths
-
-s = s_coordinate(h, theta_b, theta_s, Tcline, N)
-
-
- - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
-   - - - - - - -
__init__(self, - h, - theta_b, - theta_s, - Tcline, - N, - zeta=None)
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature		 - source code - -
- -
-   - - - - - - -
_get_s_rho(self) - source code - -
- -
-   - - - - - - -
_get_s_w(self) - source code - -
- -
-   - - - - - - -
_get_Cs_r(self) - source code - -
- -
-   - - - - - - -
_get_Cs_w(self) - source code - -
- -
-

Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

-
- - - - - - - - - -
- - - - - -
Properties[hide private]
-
-

Inherited from object: - __class__ -

-
- - - - - - -
- - - - - -
Method Details[hide private]
-
- -
- -
- - -
-

__init__(self, - h, - theta_b, - theta_s, - Tcline, - N, - zeta=None) -
(Constructor) -

- 		source code  -
- -

x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

-
-
Overrides: - object.__init__ -
(inherited documentation)
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- - Package pyroms :: - Module vgrid :: - Class s_coordinate_2 - - - - - - -
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-
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Class s_coordinate_2

source code

-
-  object --+    
-           |    
-s_coordinate --+
-               |
-              s_coordinate_2
-
- -
-
-
-New vertical coordinate transformation (Vtransform=2)
-
-return an object that can be indexed to return depths
-
-s = s_coordinate_2(h, theta_b, theta_s, Tcline, N)
-
-
- - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
-   - - - - - - -
__init__(self, - h, - theta_b, - theta_s, - Tcline, - N, - zeta=None)
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature		 - source code - -
- -
-   - - - - - - -
_get_s_rho(self) - source code - -
- -
-   - - - - - - -
_get_s_w(self) - source code - -
- -
-   - - - - - - -
_get_Cs_r(self) - source code - -
- -
-   - - - - - - -
_get_Cs_w(self) - source code - -
- -
-

Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

-
- - - - - - - - - -
- - - - - -
Properties[hide private]
-
-

Inherited from object: - __class__ -

-
- - - - - - -
- - - - - -
Method Details[hide private]
-
- -
- -
- - -
-

__init__(self, - h, - theta_b, - theta_s, - Tcline, - N, - zeta=None) -
(Constructor) -

- 		source code  -
- -

x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

-
-
Overrides: - object.__init__ -
(inherited documentation)
- -
-
-
- -
- -
- - -
-

_get_s_rho(self) -

- 		source code  -
- - -
-
Overrides: - s_coordinate._get_s_rho -
-
-
-
- -
- -
- - -
-

_get_s_w(self) -

- 		source code  -
- - -
-
Overrides: - s_coordinate._get_s_w -
-
-
-
- -
- -
- - -
-

_get_Cs_r(self) -

- 		source code  -
- - -
-
Overrides: - s_coordinate._get_Cs_r -
-
-
-
- -
- -
- - -
-

_get_Cs_w(self) -

- 		source code  -
- - -
-
Overrides: - s_coordinate._get_Cs_w -
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- - Package pyroms :: - Module vgrid :: - Class z_coordinate - - - - - - -
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Class z_coordinate

source code

-
-object --+
-         |
-        z_coordinate
-
- -
-
-
-return an object that can be indexed to return depths
-
-z = z_coordinate(h, depth, N)
-
-
- - - - - - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
-   - - - - - - -
__init__(self, - h, - depth, - N)
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature		 - source code - -
- -
-

Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

-
- - - - - - - - - -
- - - - - -
Properties[hide private]
-
-

Inherited from object: - __class__ -

-
- - - - - - -
- - - - - -
Method Details[hide private]
-
- -
- -
- - -
-

__init__(self, - h, - depth, - N) -
(Constructor) -

- 		source code  -
- -

x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

-
-
Overrides: - object.__init__ -
(inherited documentation)
- -
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- - - - diff --git a/pyroms/docs/pyroms.vgrid.z_r-class.html b/pyroms/docs/pyroms.vgrid.z_r-class.html deleted file mode 100644 index 1d9ee6f..0000000 --- a/pyroms/docs/pyroms.vgrid.z_r-class.html +++ /dev/null @@ -1,270 +0,0 @@ - - - - - pyroms.vgrid.z_r - - - - - - - - - - - - - - - - - - - - - - -
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- - Package pyroms :: - Module vgrid :: - Class z_r - - - - - - -
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Class z_r

source code

-
-object --+
-         |
-        z_r
-
- -
-
-
-return an object that can be indexed to return depths of rho point
-
-z_r = z_r(h, hc, N, s_rho, Cs_r, zeta, Vtrans)
-
-
- - - - - - - - - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
-   - - - - - - -
__init__(self, - h, - hc, - N, - s_rho, - Cs_r, - zeta, - Vtrans)
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature		 - source code - -
- -
-   - - - - - - -
__getitem__(self, - key) - source code - -
- -
-

Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

-
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Properties[hide private]
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Inherited from object: - __class__ -

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Method Details[hide private]
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__init__(self, - h, - hc, - N, - s_rho, - Cs_r, - zeta, - Vtrans) -
(Constructor) -

- 		source code  -
- -

x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

-
-
Overrides: - object.__init__ -
(inherited documentation)
- -
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- Generated by Epydoc 3.0.1 on Mon Sep 27 11:31:39 2010 - - http://epydoc.sourceforge.net -
- - - - diff --git a/pyroms/docs/pyroms.vgrid.z_w-class.html b/pyroms/docs/pyroms.vgrid.z_w-class.html deleted file mode 100644 index c2cc04d..0000000 --- a/pyroms/docs/pyroms.vgrid.z_w-class.html +++ /dev/null @@ -1,270 +0,0 @@ - - - - - pyroms.vgrid.z_w - - - - - - - - - - - - - - - - - - - - - - -
   Home      Trees      Indices      Help   
- - - - - -
- - Package pyroms :: - Module vgrid :: - Class z_w - - - - - - -
[hide private]
[frames] | no frames]
-
- -

Class z_w

source code

-
-object --+
-         |
-        z_w
-
- -
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-
-return an object that can be indexed to return depths of w point
-
-z_w = z_w(h, hc, Np, s_w, Cs_w, zeta, Vtrans)
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Instance Methods[hide private]
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-   - - - - - - -
__init__(self, - h, - hc, - Np, - s_w, - Cs_w, - zeta, - Vtrans)
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature		 - source code - -
- -
-   - - - - - - -
__getitem__(self, - key) - source code - -
- -
-

Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

-
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Inherited from object: - __class__ -

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Method Details[hide private]
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-

__init__(self, - h, - hc, - Np, - s_w, - Cs_w, - zeta, - Vtrans) -
(Constructor) -

- 		source code  -
- -

x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

-
-
Overrides: - object.__init__ -
(inherited documentation)
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- Generated by Epydoc 3.0.1 on Mon Sep 27 11:31:39 2010 - - http://epydoc.sourceforge.net -
- - - - diff --git a/pyroms/docs/redirect.html b/pyroms/docs/redirect.html deleted file mode 100644 index 07d64ad..0000000 --- a/pyroms/docs/redirect.html +++ /dev/null @@ -1,38 +0,0 @@ -Epydoc Redirect Page - - - - - - - - -

Epydoc Auto-redirect page

- -

When javascript is enabled, this page will redirect URLs of -the form redirect.html#dotted.name to the -documentation for the object with the given fully-qualified -dotted name.

-

 

- - - - - diff --git a/pyroms/docs/toc-everything.html b/pyroms/docs/toc-everything.html deleted file mode 100644 index 7bdcf0b..0000000 --- a/pyroms/docs/toc-everything.html +++ /dev/null @@ -1,141 +0,0 @@ - - - - - Everything - - - - - -

Everything

-
-

All Classes

- pyroms.cf.time
pyroms.extern.greatcircle.GreatCircle
pyroms.extern.kdtree.KDTree
pyroms.extern.kdtree.KDTree.innernode
pyroms.extern.kdtree.KDTree.leafnode
pyroms.extern.kdtree.KDTree.node
pyroms.extern.kdtree.Rectangle
pyroms.extern.pupynere.NetCDFFile
pyroms.extern.pupynere.NetCDFVariable
pyroms.grid.ROMS_Grid
pyroms.grid.ROMS_gridinfo
pyroms.hgrid.BoundaryInteractor
pyroms.hgrid.CGrid
pyroms.hgrid.CGrid_geo
pyroms.hgrid.Focus
pyroms.hgrid.Gridgen
- pyroms.hgrid._Focus_x
-
- pyroms.hgrid._Focus_y
- pyroms.hgrid.edit_mask_mesh
pyroms.hgrid.get_position_from_map
pyroms.hgrid_old.BoundaryInteractor
pyroms.hgrid_old.CGrid
pyroms.hgrid_old.CGrid_geo
pyroms.hgrid_old.Focus
pyroms.hgrid_old.Gridgen
- pyroms.hgrid_old._Focus_x
-
- pyroms.hgrid_old._Focus_y
- pyroms.hgrid_old.edit_mask_mesh
pyroms.hgrid_old.get_position_from_map
pyroms.vgrid.s_coordinate
pyroms.vgrid.s_coordinate_2
pyroms.vgrid.z_coordinate
pyroms.vgrid.z_r
pyroms.vgrid.z_w

All Functions

- pyroms.extern.greatcircle.vinc_dist
pyroms.extern.greatcircle.vinc_pt
pyroms.extern.kdtree.distance_matrix
pyroms.extern.kdtree.minkowski_distance
pyroms.extern.kdtree.minkowski_distance_p
- pyroms.extern.pupynere._test
- pyroms.grid.get_ROMS_grid
pyroms.grid.get_ROMS_hgrid
pyroms.grid.get_ROMS_vgrid
pyroms.grid.list_ROMS_gridid
pyroms.grid.print_ROMS_gridinfo
pyroms.grid.write_ROMS_grid
- pyroms.hgrid._approximate_erf
- pyroms.hgrid.rho_to_vert
pyroms.hgrid.rho_to_vert_geo
pyroms.hgrid.uvp_masks
- pyroms.hgrid_old._approximate_erf
- pyroms.hgrid_old.rho_to_vert
pyroms.hgrid_old.rho_to_vert_geo
pyroms.hgrid_old.uvp_masks
pyroms.io.Dataset
pyroms.io.MFDataset
pyroms.remapping.compute_remap_weights'.compute_remap_weights
pyroms.remapping.flood'.flood
pyroms.remapping.make_remap_grid_file'.make_remap_grid_file
pyroms.remapping.remap'.remap
pyroms.remapping.roms2z'.roms2z
pyroms.remapping.test_remap_weights'.test_remap_weights
pyroms.remapping.z2roms'.z2roms
pyroms.tools.interm_pt
pyroms.tools.islice
pyroms.tools.isoslice
pyroms.tools.jslice
pyroms.tools.latslice
pyroms.tools.lonslice
pyroms.tools.section_transport
pyroms.tools.sslice
pyroms.tools.transect
pyroms.tools.zslice
pyroms.utility.find_nearestgridpoints
pyroms.utility.get_bottom
pyroms.utility.get_date_tag
pyroms.utility.get_grid_proj
pyroms.utility.get_ij
pyroms.utility.get_lonlat
pyroms.utility.get_nc_var
pyroms.utility.get_surface
pyroms.utility.move2grid
pyroms.utility.roms_varlist

All Variables

- pyroms.extern.pupynere.ABSENT
pyroms.extern.pupynere.NC_ATTRIBUTE
pyroms.extern.pupynere.NC_BYTE
pyroms.extern.pupynere.NC_CHAR
pyroms.extern.pupynere.NC_DIMENSION
pyroms.extern.pupynere.NC_DOUBLE
pyroms.extern.pupynere.NC_FLOAT
pyroms.extern.pupynere.NC_INT
pyroms.extern.pupynere.NC_SHORT
pyroms.extern.pupynere.NC_VARIABLE
pyroms.extern.pupynere.ZERO
pyroms.grid.gridid_dictionary
-[hide private] - - - - diff --git a/pyroms/docs/toc-pyroms-module.html b/pyroms/docs/toc-pyroms-module.html deleted file mode 100644 index f29427e..0000000 --- a/pyroms/docs/toc-pyroms-module.html +++ /dev/null @@ -1,29 +0,0 @@ - - - - - pyroms - - - - - -

Module pyroms

-
-
-[hide private] - - - - diff --git a/pyroms/docs/toc-pyroms.cf-module.html b/pyroms/docs/toc-pyroms.cf-module.html deleted file mode 100644 index 2515160..0000000 --- a/pyroms/docs/toc-pyroms.cf-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - cf - - - - - -

Module cf

-
-

Classes

- time
-[hide private] - - - - diff --git a/pyroms/docs/toc-pyroms.extern-module.html b/pyroms/docs/toc-pyroms.extern-module.html deleted file mode 100644 index 21ec307..0000000 --- a/pyroms/docs/toc-pyroms.extern-module.html +++ /dev/null @@ -1,29 +0,0 @@ - - - - - extern - - - - - -

Module extern

-
-
-[hide private] - - - - diff --git a/pyroms/docs/toc-pyroms.extern.greatcircle-module.html b/pyroms/docs/toc-pyroms.extern.greatcircle-module.html deleted file mode 100644 index e2ea65e..0000000 --- a/pyroms/docs/toc-pyroms.extern.greatcircle-module.html +++ /dev/null @@ -1,34 +0,0 @@ - - - - - greatcircle - - - - - -

Module greatcircle

-
-

Classes

- GreatCircle

Functions

- vinc_dist
vinc_pt
-[hide private] - - - - diff --git a/pyroms/docs/toc-pyroms.extern.kdtree-module.html b/pyroms/docs/toc-pyroms.extern.kdtree-module.html deleted file mode 100644 index 8bdb620..0000000 --- a/pyroms/docs/toc-pyroms.extern.kdtree-module.html +++ /dev/null @@ -1,36 +0,0 @@ - - - - - kdtree - - - - - -

Module kdtree

-
-

Classes

- KDTree
Rectangle

Functions

- distance_matrix
minkowski_distance
minkowski_distance_p
-[hide private] - - - - diff --git a/pyroms/docs/toc-pyroms.extern.pupynere-module.html b/pyroms/docs/toc-pyroms.extern.pupynere-module.html deleted file mode 100644 index 70a7795..0000000 --- a/pyroms/docs/toc-pyroms.extern.pupynere-module.html +++ /dev/null @@ -1,48 +0,0 @@ - - - - - pupynere - - - - - -

Module pupynere

-
-

Classes

- NetCDFFile
NetCDFVariable

Functions

-
- _test
-

Variables

- ABSENT
NC_ATTRIBUTE
NC_BYTE
NC_CHAR
NC_DIMENSION
NC_DOUBLE
NC_FLOAT
NC_INT
NC_SHORT
NC_VARIABLE
ZERO
-[hide private] - - - - diff --git a/pyroms/docs/toc-pyroms.grid-module.html b/pyroms/docs/toc-pyroms.grid-module.html deleted file mode 100644 index 51ebc2f..0000000 --- a/pyroms/docs/toc-pyroms.grid-module.html +++ /dev/null @@ -1,41 +0,0 @@ - - - - - grid - - - - - -

Module grid

-
-

Classes

- ROMS_Grid
ROMS_gridinfo

Functions

- get_ROMS_grid
get_ROMS_hgrid
get_ROMS_vgrid
list_ROMS_gridid
print_ROMS_gridinfo
write_ROMS_grid

Variables

- gridid_dictionary
-[hide private] - - - - diff --git a/pyroms/docs/toc-pyroms.hgrid-module.html b/pyroms/docs/toc-pyroms.hgrid-module.html deleted file mode 100644 index cafd89e..0000000 --- a/pyroms/docs/toc-pyroms.hgrid-module.html +++ /dev/null @@ -1,50 +0,0 @@ - - - - - hgrid - - - - - -

Module hgrid

-
-

Classes

- BoundaryInteractor
CGrid
CGrid_geo
Focus
Gridgen
- _Focus_x
-
- _Focus_y
- edit_mask_mesh
get_position_from_map

Functions

-
- _approximate_erf
- rho_to_vert
rho_to_vert_geo
uvp_masks
-[hide private] - - - - diff --git a/pyroms/docs/toc-pyroms.hgrid_old-module.html b/pyroms/docs/toc-pyroms.hgrid_old-module.html deleted file mode 100644 index 1735f9e..0000000 --- a/pyroms/docs/toc-pyroms.hgrid_old-module.html +++ /dev/null @@ -1,50 +0,0 @@ - - - - - hgrid_old - - - - - -

Module hgrid_old

-
-

Classes

- BoundaryInteractor
CGrid
CGrid_geo
Focus
Gridgen
- _Focus_x
-
- _Focus_y
- edit_mask_mesh
get_position_from_map

Functions

-
- _approximate_erf
- rho_to_vert
rho_to_vert_geo
uvp_masks
-[hide private] - - - - diff --git a/pyroms/docs/toc-pyroms.io-module.html b/pyroms/docs/toc-pyroms.io-module.html deleted file mode 100644 index d501d91..0000000 --- a/pyroms/docs/toc-pyroms.io-module.html +++ /dev/null @@ -1,32 +0,0 @@ - - - - - io - - - - - -

Module io

-
-

Functions

- Dataset
MFDataset
-[hide private] - - - - diff --git a/pyroms/docs/toc-pyroms.remapping-module.html b/pyroms/docs/toc-pyroms.remapping-module.html deleted file mode 100644 index 852c7a9..0000000 --- a/pyroms/docs/toc-pyroms.remapping-module.html +++ /dev/null @@ -1,29 +0,0 @@ - - - - - remapping - - - - - -

Module remapping

-
-
-[hide private] - - - - diff --git a/pyroms/docs/toc-pyroms.remapping.compute_remap_weights'-module.html b/pyroms/docs/toc-pyroms.remapping.compute_remap_weights'-module.html deleted file mode 100644 index fc2c3fc..0000000 --- a/pyroms/docs/toc-pyroms.remapping.compute_remap_weights'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - compute_remap_weights' - - - - - -

Module compute_remap_weights'

-
-

Functions

- compute_remap_weights
-[hide private] - - - - diff --git a/pyroms/docs/toc-pyroms.remapping.compute_remap_weights-module.html b/pyroms/docs/toc-pyroms.remapping.compute_remap_weights-module.html deleted file mode 100644 index 9b9d24a..0000000 --- a/pyroms/docs/toc-pyroms.remapping.compute_remap_weights-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - compute_remap_weights - - - - - -

Module compute_remap_weights

-
-

Functions

- compute_remap_weights
-[hide private] - - - - diff --git a/pyroms/docs/toc-pyroms.remapping.flood'-module.html b/pyroms/docs/toc-pyroms.remapping.flood'-module.html deleted file mode 100644 index fd9a91c..0000000 --- a/pyroms/docs/toc-pyroms.remapping.flood'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - flood' - - - - - -

Module flood'

-
-

Functions

- flood
-[hide private] - - - - diff --git a/pyroms/docs/toc-pyroms.remapping.flood-module.html b/pyroms/docs/toc-pyroms.remapping.flood-module.html deleted file mode 100644 index 5acb3c6..0000000 --- a/pyroms/docs/toc-pyroms.remapping.flood-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - flood - - - - - -

Module flood

-
-

Functions

- flood
-[hide private] - - - - diff --git a/pyroms/docs/toc-pyroms.remapping.make_remap_grid_file'-module.html b/pyroms/docs/toc-pyroms.remapping.make_remap_grid_file'-module.html deleted file mode 100644 index f4371ad..0000000 --- a/pyroms/docs/toc-pyroms.remapping.make_remap_grid_file'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - make_remap_grid_file' - - - - - -

Module make_remap_grid_file'

-
-

Functions

- make_remap_grid_file
-[hide private] - - - - diff --git a/pyroms/docs/toc-pyroms.remapping.make_remap_grid_file-module.html b/pyroms/docs/toc-pyroms.remapping.make_remap_grid_file-module.html deleted file mode 100644 index dd1dbdd..0000000 --- a/pyroms/docs/toc-pyroms.remapping.make_remap_grid_file-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - make_remap_grid_file - - - - - -

Module make_remap_grid_file

-
-

Functions

- make_remap_grid_file
-[hide private] - - - - diff --git a/pyroms/docs/toc-pyroms.remapping.remap'-module.html b/pyroms/docs/toc-pyroms.remapping.remap'-module.html deleted file mode 100644 index 91c39c8..0000000 --- a/pyroms/docs/toc-pyroms.remapping.remap'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - remap' - - - - - -

Module remap'

-
-

Functions

- remap
-[hide private] - - - - diff --git a/pyroms/docs/toc-pyroms.remapping.remap-module.html b/pyroms/docs/toc-pyroms.remapping.remap-module.html deleted file mode 100644 index a148963..0000000 --- a/pyroms/docs/toc-pyroms.remapping.remap-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - remap - - - - - -

Module remap

-
-

Functions

- remap
-[hide private] - - - - diff --git a/pyroms/docs/toc-pyroms.remapping.roms2z'-module.html b/pyroms/docs/toc-pyroms.remapping.roms2z'-module.html deleted file mode 100644 index cafed66..0000000 --- a/pyroms/docs/toc-pyroms.remapping.roms2z'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - roms2z' - - - - - -

Module roms2z'

-
-

Functions

- roms2z
-[hide private] - - - - diff --git a/pyroms/docs/toc-pyroms.remapping.roms2z-module.html b/pyroms/docs/toc-pyroms.remapping.roms2z-module.html deleted file mode 100644 index e23f39a..0000000 --- a/pyroms/docs/toc-pyroms.remapping.roms2z-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - roms2z - - - - - -

Module roms2z

-
-

Functions

- roms2z
-[hide private] - - - - diff --git a/pyroms/docs/toc-pyroms.remapping.test_remap_weights'-module.html b/pyroms/docs/toc-pyroms.remapping.test_remap_weights'-module.html deleted file mode 100644 index 9f20263..0000000 --- a/pyroms/docs/toc-pyroms.remapping.test_remap_weights'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - test_remap_weights' - - - - - -

Module test_remap_weights'

-
-

Functions

- test_remap_weights
-[hide private] - - - - diff --git a/pyroms/docs/toc-pyroms.remapping.test_remap_weights-module.html b/pyroms/docs/toc-pyroms.remapping.test_remap_weights-module.html deleted file mode 100644 index 90d2828..0000000 --- a/pyroms/docs/toc-pyroms.remapping.test_remap_weights-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - test_remap_weights - - - - - -

Module test_remap_weights

-
-

Functions

- test_remap_weights
-[hide private] - - - - diff --git a/pyroms/docs/toc-pyroms.remapping.z2roms'-module.html b/pyroms/docs/toc-pyroms.remapping.z2roms'-module.html deleted file mode 100644 index b6613ec..0000000 --- a/pyroms/docs/toc-pyroms.remapping.z2roms'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - z2roms' - - - - - -

Module z2roms'

-
-

Functions

- z2roms
-[hide private] - - - - diff --git a/pyroms/docs/toc-pyroms.remapping.z2roms-module.html b/pyroms/docs/toc-pyroms.remapping.z2roms-module.html deleted file mode 100644 index 064c690..0000000 --- a/pyroms/docs/toc-pyroms.remapping.z2roms-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - z2roms - - - - - -

Module z2roms

-
-

Functions

- z2roms
-[hide private] - - - - diff --git a/pyroms/docs/toc-pyroms.tools-module.html b/pyroms/docs/toc-pyroms.tools-module.html deleted file mode 100644 index bfdbef4..0000000 --- a/pyroms/docs/toc-pyroms.tools-module.html +++ /dev/null @@ -1,40 +0,0 @@ - - - - - tools - - - - - -

Module tools

-
-

Functions

- interm_pt
islice
isoslice
jslice
latslice
lonslice
section_transport
sslice
transect
zslice
-[hide private] - - - - diff --git a/pyroms/docs/toc-pyroms.utility-module.html b/pyroms/docs/toc-pyroms.utility-module.html deleted file mode 100644 index 4964fd8..0000000 --- a/pyroms/docs/toc-pyroms.utility-module.html +++ /dev/null @@ -1,40 +0,0 @@ - - - - - utility - - - - - -

Module utility

-
-

Functions

- find_nearestgridpoints
get_bottom
get_date_tag
get_grid_proj
get_ij
get_lonlat
get_nc_var
get_surface
move2grid
roms_varlist
-[hide private] - - - - diff --git a/pyroms/docs/toc-pyroms.vgrid-module.html b/pyroms/docs/toc-pyroms.vgrid-module.html deleted file mode 100644 index ce00f12..0000000 --- a/pyroms/docs/toc-pyroms.vgrid-module.html +++ /dev/null @@ -1,35 +0,0 @@ - - - - - vgrid - - - - - -

Module vgrid

-
-

Classes

- s_coordinate
s_coordinate_2
z_coordinate
z_r
z_w
-[hide private] - - - - diff --git a/pyroms/docs/toc.html b/pyroms/docs/toc.html deleted file mode 100644 index acd5924..0000000 --- a/pyroms/docs/toc.html +++ /dev/null @@ -1,53 +0,0 @@ - - - - - Table of Contents - - - - - -

Table of Contents

-
- Everything -
-

Modules

- pyroms
pyroms.cf
pyroms.extern
pyroms.extern.greatcircle
pyroms.extern.kdtree
pyroms.extern.pupynere
pyroms.grid
pyroms.hgrid
pyroms.hgrid_old
pyroms.io
pyroms.remapping
pyroms.remapping.compute_remap_weights'
pyroms.remapping.flood'
pyroms.remapping.make_remap_grid_file'
pyroms.remapping.remap'
pyroms.remapping.roms2z'
pyroms.remapping.test_remap_weights'
pyroms.remapping.z2roms'
pyroms.tools
pyroms.utility
pyroms.vgrid
- [hide private] - - - - diff --git a/pyroms/external/csa/makefile b/pyroms/external/csa/makefile index 72674db..cb29d86 100644 --- a/pyroms/external/csa/makefile +++ b/pyroms/external/csa/makefile @@ -6,11 +6,11 @@ SHELL = /bin/sh #### Start of system configuration section. #### -prefix = /u1/uaf/kshedstrom/python +prefix = /home/kshedstrom/python exec_prefix = ${prefix} bindir = ${exec_prefix}/bin -libdir = /u1/uaf/kshedstrom/python/lib +libdir = /home/kshedstrom/python/lib includedir = ${prefix}/include INSTALLDIRS =\ @@ -27,8 +27,8 @@ INSTALL_DATA = ${INSTALL} -m 644 #### End of system configuration section. #### CC = gcc -CFLAGS = -I/u1/uaf/kshedstrom/python/include -LDFLAGS = -L$DESTDIR/lib +CFLAGS = -g -O2 -Wall -pedantic +LDFLAGS = AR = ar ARFLAGS = cru diff --git a/pyroms/external/gridgen/makefile b/pyroms/external/gridgen/makefile index ae57fce..95963f5 100644 --- a/pyroms/external/gridgen/makefile +++ b/pyroms/external/gridgen/makefile @@ -6,11 +6,11 @@ SHELL = /bin/sh #### Start of system configuration section. #### -prefix = /u1/uaf/kshedstrom/python +prefix = /home/kshedstrom/python exec_prefix = ${prefix} bindir = ${exec_prefix}/bin -libdir = /u1/uaf/kshedstrom/python/lib +libdir = /home/kshedstrom/python/lib includedir = ${prefix}/include INSTALLDIRS =\ @@ -24,18 +24,18 @@ INSTALL = /usr/bin/install -c INSTALL_PROGRAM = ${INSTALL} INSTALL_DATA = ${INSTALL} -m 644 -NOCOMPLEX = -HAVE_GRIDNODES_H = +NOCOMPLEX = +HAVE_GRIDNODES_H = CC = gcc -CFLAGS = -I/u1/uaf/kshedstrom/python/include -CFLAGS_TRIANGLE = -I/u1/uaf/kshedstrom/python/include -w -ffloat-store -LDFLAGS = -L$DESTDIR/lib +CFLAGS = -I/home/kshedstrom/python/include +CFLAGS_TRIANGLE = -I/home/kshedstrom/python/include -w -ffloat-store +LDFLAGS = -L/home/kshedstrom/python/lib AR = ar ARFLAGS = cru -LIBS = -lm +LIBS = -lgu -lm MLIB = -lm diff --git a/pyroms/external/gridutils/makefile b/pyroms/external/gridutils/makefile index 053ff82..c91fb29 100644 --- a/pyroms/external/gridutils/makefile +++ b/pyroms/external/gridutils/makefile @@ -7,11 +7,11 @@ SHELL = /bin/sh #### Start of system configuration section. #### -prefix = /u1/uaf/kshedstrom/python +prefix = /home/kshedstrom/python exec_prefix = ${prefix} bindir = ${exec_prefix}/bin -libdir = /u1/uaf/kshedstrom/python/lib +libdir = /home/kshedstrom/python/lib includedir = ${prefix}/include INSTALLDIRS =\ @@ -28,9 +28,9 @@ INSTALL_DATA = ${INSTALL} -m 644 #### End of system configuration section. #### CC = gcc -CFLAGS = -I/u1/uaf/kshedstrom/python/include -LDFLAGS = -L$DESTDIR/lib -CPPFLAGS = -I/u1/uaf/kshedstrom/python/include +CFLAGS = -I/home/kshedstrom/python/include +LDFLAGS = -L/home/kshedstrom/python/lib +CPPFLAGS = -I/home/kshedstrom/python/include AR = ar ARFLAGS = cru diff --git a/pyroms/external/nn/makefile b/pyroms/external/nn/makefile index 008c6b5..e21ba3a 100644 --- a/pyroms/external/nn/makefile +++ b/pyroms/external/nn/makefile @@ -1,9 +1,9 @@ SHELL = /bin/sh -prefix = /u1/uaf/kshedstrom/python +prefix = /home/kshedstrom/python exec_prefix = ${prefix} bindir = ${exec_prefix}/bin -libdir = /u1/uaf/kshedstrom/python/lib +libdir = /home/kshedstrom/python/lib includedir = ${prefix}/include INSTALLDIRS =\ @@ -18,10 +18,10 @@ INSTALL_PROGRAM = ${INSTALL} INSTALL_DATA = ${INSTALL} -m 644 CC = gcc -CFLAGS = -I/u1/uaf/kshedstrom/python/include -CFLAGS_TRIANGLE = -I/u1/uaf/kshedstrom/python/include -w -ffloat-store +CFLAGS = -g -O2 -Wall -pedantic +CFLAGS_TRIANGLE = -g -O2 -Wall -pedantic -w -ffloat-store CFLAGS_VULNERABLE = -ffloat-store -LDFLAGS = -L$DESTDIR/lib +LDFLAGS = AR = ar ARFLAGS = cru diff --git a/pyroms/external/scrip/source/makefile b/pyroms/external/scrip/source/makefile index 4a2f85c..3336cc1 100644 --- a/pyroms/external/scrip/source/makefile +++ b/pyroms/external/scrip/source/makefile @@ -9,7 +9,7 @@ # SVN $URL$ #=============================================================================== -NC_CONFIG = nc-config +NC_CONFIG = nf-config LIBDIR = $(shell $(NC_CONFIG) --prefix)/lib INCDIR = $(shell $(NC_CONFIG) --prefix)/include SRCDIR = . @@ -125,7 +125,7 @@ remap_read.o: $(SRCDIR)/remap_read.f kinds_mod.o constants.o netcdf.o \ remap_vars.o grids.o $(COMPILE) $(FLAGS) $(INCLUDE) -c $(SRCDIR)/remap_read.f -remap.o: $(SRCDIR)/remap.f kinds_mod.o constants.o +remap.o: $(SRCDIR)/remap.f kinds_mod.o constants.o $(COMPILE) $(FLAGS) -c $(SRCDIR)/remap.f scrip.o: $(SRCDIR)/scrip.f kinds_mod.o constants.o iounits.o timers.o \ @@ -152,7 +152,7 @@ $(SRCDIR)/scrip.so: $(SRCDIR)/pyscrip.f90 $(OBJF2PY) install: /bin/cp $(SRCDIR)/scrip $(PREFIX)/bin /bin/cp $(SRCDIR)/scrip_test $(PREFIX)/bin - /bin/cp $(SRCDIR)/scrip.so $(PREFIX)/lib + /bin/cp $(SRCDIR)/scrip*.so $(PREFIX)/lib -clean: +clean: /bin/rm *.o *.mod *.so scrip scrip_test diff --git a/pyroms/install_pyroms.sh b/pyroms/install_pyroms.sh index ce50074..91e7aae 100755 --- a/pyroms/install_pyroms.sh +++ b/pyroms/install_pyroms.sh @@ -1,13 +1,9 @@ #!/bin/sh #DESTDIR=/usr/local -DESTDIR=/u1/uaf/kshedstrom/python +DESTDIR=$HOME/python +PYROMS_PATH=$DESTDIR/lib/python3.6/site-packages/pyroms CURDIR=`pwd` -export CPPFLAGS=-I$DESTDIR/include -export LDFLAGS='-L$DESTDIR/lib' -#export LDFLAGS='-L$DESTDIR/lib -L/usr/local/pkg/python/python-2.7.2/lib -shared' -export CFLAGS=-I$DESTDIR/include -export SHLIBS=-L$DESTDIR/lib echo echo "installing pyroms..." @@ -23,24 +19,27 @@ cd $CURDIR/external/csa ./configure --prefix=$DESTDIR make install cd $CURDIR/external/gridutils -./configure --prefix=$DESTDIR +./configure CPPFLAGS=-I$DESTDIR/include LDFLAGS=-L$DESTDIR/lib CFLAGS=-I$DESTDIR/include --prefix=$DESTDIR make install cd $CURDIR/external/gridgen -./configure --prefix=$DESTDIR +export SHLIBS=-L$DESTDIR/lib +./configure CPPFLAGS=-I$DESTDIR/include LDFLAGS=-L$DESTDIR/lib CFLAGS=-I$DESTDIR/include --prefix=$DESTDIR make make lib make shlib make install -PYROMS_PATH=`python -c 'import pyroms ; print pyroms.__path__[0]'` +# Now setting this above because this gave me an error: +#PYROMS_PATH=`python -c 'import pyroms ; print pyroms.__path__[0]'` +# $ echo $PYROMS_PATH cp libgridgen.so $PYROMS_PATH -#cp $LOCALDIR/lib/libgridgen.so $PYROMS_PATH echo "installing scrip..." cd $CURDIR/external/scrip/source perl -pe "s#\/usr\/local#$DESTDIR#" makefile > makefile2 make -f makefile2 make -f makefile2 f2py make -f makefile2 install -cp scrip.so $PYROMS_PATH ++# Write it this way for Darwin... +cp -r scrip*.so* $PYROMS_PATH cd $CURDIR echo echo "Done installing pyroms..." diff --git a/pyroms/pyroms/__init__.py b/pyroms/pyroms/__init__.py index b18fb4e..83b61b9 100644 --- a/pyroms/pyroms/__init__.py +++ b/pyroms/pyroms/__init__.py @@ -1,25 +1,25 @@ # encoding: utf-8 -''' +''' PYROMS is a toolkit for working with ROMS ocean models -pyroms is based on the python/numpy/matplotlib scientific python suite. -NetCDF I/O is based on the NetCDF4-python package. The toolkit contains -general modeling tools for dealing with arrays, diagnosing standard +pyroms is based on the python/numpy/matplotlib scientific python suite. +NetCDF I/O is based on the NetCDF4-python package. The toolkit contains +general modeling tools for dealing with arrays, diagnosing standard properties, curvilinear grid generation, and interpolation. ''' -import cf -import vgrid -import extern -import hgrid -import grid -import io -import sta_hgrid -import sta_grid -import tools -import remapping -import utility +from . import cf +from . import vgrid +from . import extern +from . import hgrid +from . import grid +from . import io +from . import sta_hgrid +from . import sta_grid +from . import tools +from . import remapping +from . import utility __authors__ = ['Frederic Castruccio (frederic@marine.rutgers.edu)'] - + __version__ = '0.1.0' diff --git a/pyroms/pyroms/cf.py b/pyroms/pyroms/cf.py index ea9e3c8..472e122 100644 --- a/pyroms/pyroms/cf.py +++ b/pyroms/pyroms/cf.py @@ -15,13 +15,16 @@ import numpy as np -import netcdftime +try: + import cftime +except: + import netcdftime import pyroms.io class time (np.ndarray): """Return time object from netCDF file - + Parameters ---------- nc : netCDF3/4 object or filename @@ -33,15 +36,15 @@ class time (np.ndarray): calendar : string, optional A string representing the calandar to use. See netcdftime documentation for possible values. - + Returns ------- nctime : ndarray A subclass of numpy.ndarray with values equal to the time variable in the netCDF file referenced with nc. - + """ - + _unit2sec={'seconds' : 1.0, 'minutes' : 60.0, 'hours' : 3600.0, @@ -62,52 +65,52 @@ def __new__(self, ncfile, name='time', units=None, calendar='standard'): units = self._nc.variables[name].units data.utime = netcdftime.utime(units, calendar=calendar) return data - + def __array_finalize__(self, obj): self.utime = getattr(obj, 'utime', {}) - + def arg_nearest_date(self, dateo): """Return index of date nearest to query date. - + Prameters --------- dateo : datetime object The query date - + Returns ------- idx : integer The index of the date closest to dateo. If two dates are equidistant, the smaller is returned. - + """ to = self.utime.date2num(dateo) return np.min(np.where(np.abs(self-to) == \ np.min(np.abs(self-to)))[0]) - + def nearest_date(self, dateo): """Return the nearest date to query date. - + Prameters --------- dateo : datetime object The query date - + Returns ------- nearest_date : datetime object A datetime object of the date closest to dateo. If two dates are equidistant, the smaller is returned. - + """ idx = np.where(np.abs(self.dates-dateo) == \ np.min(np.abs(self.dates-dateo)))[0] idx = np.min(idx) return self.dates[idx] - + def arg_nearest(self, to, units=None): """Return index of time nearest to query time. - + Prameters --------- to : float @@ -115,21 +118,21 @@ def arg_nearest(self, to, units=None): units : string, optional The units of the reference time. Defaults to the reference time string 'units' in the netcdf oject. - + Returns ------- idx : integer The index of the date closest to to. If two times are equidistant, the smaller is returned. - + """ if units is not None: to *= self._unit2sec[units] * self._sec2unit[self.utime.units] return np.min(np.where(np.abs(self-to) == np.min(np.abs(self-to)))[0]) - + def nearest(self, to, units=None): """Return time nearest to time query. - + Prameters --------- to : float @@ -137,24 +140,24 @@ def nearest(self, to, units=None): units : string, optional The units of the reference time. Defaults to the reference time string 'units' in the netcdf oject. - + Returns ------- idx : integer The index of the date closest to to. If two times are equidistant, the smaller is returned. - + """ if units is not None: to *= self._unit2sec[units] * self._sec2unit[self.utime.units] idx = np.where(np.abs(self-to) == np.min(np.abs(self-to)))[0] idx = np.min(idx) return self[idx] - + def get_seconds(self): fac = self._unit2sec[self.utime.units] * self._sec2unit['seconds'] return self*fac - + def get_minutes(self): fac = self._unit2sec[self.utime.units] * self._sec2unit['minutes'] return self*fac @@ -162,11 +165,11 @@ def get_minutes(self): def get_hours(self): fac = self._unit2sec[self.utime.units] * self._sec2unit['hours'] return self*fac - + def get_days(self): fac = self._unit2sec[self.utime.units] * self._sec2unit['days'] return np.asarray(self,dtype='float64')*fac - + def get_jd(self): utime = netcdftime.utime('days since 0001-01-01 00:00:00', \ calendar='proleptic_gregorian') @@ -174,7 +177,7 @@ def get_jd(self): def get_dates(self): return np.array([self.utime.num2date(tval) for tval in self]) - + jd = property(get_jd, None, doc="Julian day, for plotting in pylab") seconds = property(get_seconds, None, doc="seconds") minutes = property(get_minutes, None, doc="minutes") diff --git a/pyroms/pyroms/extern/__init__.py b/pyroms/pyroms/extern/__init__.py index 232d736..602f809 100644 --- a/pyroms/pyroms/extern/__init__.py +++ b/pyroms/pyroms/extern/__init__.py @@ -1,10 +1,10 @@ 'External packages' # from an old version Jeff Whitaker's Basemap -from greatcircle import GreatCircle +from .greatcircle import GreatCircle # from Roberto De Almeida -import pupynere +from . import pupynere # from Anne M. Archibald's scipy.spatial.kdtree pure python code -from kdtree import KDTree \ No newline at end of file +from .kdtree import KDTree \ No newline at end of file diff --git a/pyroms/pyroms/extern/greatcircle.py b/pyroms/pyroms/extern/greatcircle.py index c6f2037..81a958f 100644 --- a/pyroms/pyroms/extern/greatcircle.py +++ b/pyroms/pyroms/extern/greatcircle.py @@ -6,7 +6,7 @@ class GreatCircle(object): """ formula for perfect sphere from Ed Williams' 'Aviation Formulary' (http://williams.best.vwh.net/avform.htm) - + code for ellipsoid posted to GMT mailing list by Jim Leven in Dec 1999 Contact: Jeff Whitaker @@ -40,7 +40,7 @@ def __init__(self,rmajor,rminor,lon1,lat1,lon2,lat2): self.lon1 = lon1 self.lon2 = lon2 # distance along geodesic in meters. - d,a12,a21 = vinc_dist(self.f, self.a, lat1, lon1, lat2, lon2 ) + d,a12,a21 = vinc_dist(self.f, self.a, lat1, lon1, lat2, lon2 ) self.distance = d self.azimuth12 = a12 self.azimuth21 = a21 @@ -69,13 +69,13 @@ def points(self,npoints): """ # must ask for at least 2 points. if npoints <= 1: - raise ValueError,'npoints must be greater than 1' + raise ValueError('npoints must be greater than 1') elif npoints == 2: return [math.degrees(self.lon1),math.degrees(self.lon2)],[math.degrees(self.lat1),math.degrees(self.lat2)] # can't do it if endpoints are antipodal, since # route is undefined. if self.antipodal: - raise ValueError,'cannot compute intermediate points on a great circle whose endpoints are antipodal' + raise ValueError('cannot compute intermediate points on a great circle whose endpoints are antipodal') d = self.gcarclen delta = 1.0/(npoints-1) f = delta*NX.arange(npoints) # f=0 is point 1, f=1 is point 2. @@ -93,8 +93,8 @@ def points(self,npoints): z = A*math.sin(lat1) +B*math.sin(lat2) lats=NX.arctan2(z,NX.sqrt(x**2+y**2)) lons=NX.arctan2(y,x) - lons = map(math.degrees,lons.tolist()) - lats = map(math.degrees,lats.tolist()) + lons = list(map(math.degrees,lons.tolist())) + lats = list(map(math.degrees,lats.tolist())) # use ellipsoid formulas else: latpt = self.lat1 @@ -103,8 +103,8 @@ def points(self,npoints): lons = [math.degrees(lonpt)] lats = [math.degrees(latpt)] for n in range(npoints-2): - latptnew,lonptnew,alpha21=vinc_pt(self.f,self.a,latpt,lonpt,azimuth,incdist) - d,azimuth,a21=vinc_dist(self.f,self.a,latptnew,lonptnew,lat2,lon2) + latptnew,lonptnew,alpha21=vinc_pt(self.f,self.a,latpt,lonpt,azimuth,incdist) + d,azimuth,a21=vinc_dist(self.f,self.a,latptnew,lonptnew,lat2,lon2) lats.append(math.degrees(latptnew)) lons.append(math.degrees(lonptnew)) latpt = latptnew; lonpt = lonptnew @@ -112,13 +112,13 @@ def points(self,npoints): lats.append(math.degrees(self.lat2)) return lons,lats # -# --------------------------------------------------------------------- +# --------------------------------------------------------------------- # | | # | geodetic.py - a collection of geodetic functions | # | | -# --------------------------------------------------------------------- -# -# +# --------------------------------------------------------------------- +# +# # ---------------------------------------------------------------------- # | Algrothims from Geocentric Datum of Australia Technical Manual | # | | @@ -152,14 +152,14 @@ def points(self,npoints): # | Calculate: the ellipsoidal distance (s) and | # | forward and reverse azimuths between the points (alpha12, alpha21). | # | | -# ---------------------------------------------------------------------- +# ---------------------------------------------------------------------- def vinc_dist( f, a, phi1, lembda1, phi2, lembda2 ) : - """ + """ Returns the distance between two geographic points on the ellipsoid and the forward and reverse azimuths between these points. - lats, longs and azimuths are in radians, distance in metres + lats, longs and azimuths are in radians, distance in metres Returns ( s, alpha12, alpha21 ) as a tuple @@ -167,14 +167,14 @@ def vinc_dist( f, a, phi1, lembda1, phi2, lembda2 ) : if (abs( phi2 - phi1 ) < 1e-8) and ( abs( lembda2 - lembda1) < 1e-8 ) : return 0.0, 0.0, 0.0 - + two_pi = 2.0*math.pi b = a * (1.0 - f) TanU1 = (1-f) * math.tan( phi1 ) TanU2 = (1-f) * math.tan( phi2 ) - + U1 = math.atan(TanU1) U2 = math.atan(TanU2) @@ -182,67 +182,67 @@ def vinc_dist( f, a, phi1, lembda1, phi2, lembda2 ) : last_lembda = -4000000.0 # an impossibe value omega = lembda - # Iterate the following equations, - # until there is no significant change in lembda - + # Iterate the following equations, + # until there is no significant change in lembda + while ( last_lembda < -3000000.0 or lembda != 0 and abs( (last_lembda - lembda)/lembda) > 1.0e-9 ) : - + sqr_sin_sigma = pow( math.cos(U2) * math.sin(lembda), 2) + \ pow( (math.cos(U1) * math.sin(U2) - \ math.sin(U1) * math.cos(U2) * math.cos(lembda) ), 2 ) Sin_sigma = math.sqrt( sqr_sin_sigma ) - + Cos_sigma = math.sin(U1) * math.sin(U2) + math.cos(U1) * math.cos(U2) * math.cos(lembda) - + sigma = math.atan2( Sin_sigma, Cos_sigma ) Sin_alpha = math.cos(U1) * math.cos(U2) * math.sin(lembda) / math.sin(sigma) alpha = math.asin( Sin_alpha ) - + Cos2sigma_m = math.cos(sigma) - (2 * math.sin(U1) * math.sin(U2) / pow(math.cos(alpha), 2) ) - + C = (f/16) * pow(math.cos(alpha), 2) * (4 + f * (4 - 3 * pow(math.cos(alpha), 2))) - + last_lembda = lembda - + lembda = omega + (1-C) * f * math.sin(alpha) * (sigma + C * math.sin(sigma) * \ (Cos2sigma_m + C * math.cos(sigma) * (-1 + 2 * pow(Cos2sigma_m, 2) ))) - + u2 = pow(math.cos(alpha),2) * (a*a-b*b) / (b*b) - + A = 1 + (u2/16384) * (4096 + u2 * (-768 + u2 * (320 - 175 * u2))) - + B = (u2/1024) * (256 + u2 * (-128+ u2 * (74 - 47 * u2))) - + delta_sigma = B * Sin_sigma * (Cos2sigma_m + (B/4) * \ (Cos_sigma * (-1 + 2 * pow(Cos2sigma_m, 2) ) - \ (B/6) * Cos2sigma_m * (-3 + 4 * sqr_sin_sigma) * \ (-3 + 4 * pow(Cos2sigma_m,2 ) ))) - + s = b * A * (sigma - delta_sigma) - + alpha12 = math.atan2( (math.cos(U2) * math.sin(lembda)), \ (math.cos(U1) * math.sin(U2) - math.sin(U1) * math.cos(U2) * math.cos(lembda))) - + alpha21 = math.atan2( (math.cos(U1) * math.sin(lembda)), \ (-math.sin(U1) * math.cos(U2) + math.cos(U1) * math.sin(U2) * math.cos(lembda))) - if ( alpha12 < 0.0 ) : + if ( alpha12 < 0.0 ) : alpha12 = alpha12 + two_pi - if ( alpha12 > two_pi ) : + if ( alpha12 > two_pi ) : alpha12 = alpha12 - two_pi alpha21 = alpha21 + two_pi / 2.0 - if ( alpha21 < 0.0 ) : + if ( alpha21 < 0.0 ) : alpha21 = alpha21 + two_pi - if ( alpha21 > two_pi ) : + if ( alpha21 > two_pi ) : alpha21 = alpha21 - two_pi - return s, alpha12, alpha21 + return s, alpha12, alpha21 - # END of Vincenty's Inverse formulae + # END of Vincenty's Inverse formulae #---------------------------------------------------------------------------- @@ -263,19 +263,19 @@ def vinc_pt( f, a, phi1, lembda1, alpha12, s ) : given a reference point and a distance and azimuth to project. lats, longs and azimuths are passed in decimal degrees - Returns ( phi2, lambda2, alpha21 ) as a tuple + Returns ( phi2, lambda2, alpha21 ) as a tuple """ two_pi = 2.0*math.pi - if ( alpha12 < 0.0 ) : + if ( alpha12 < 0.0 ) : alpha12 = alpha12 + two_pi - if ( alpha12 > two_pi ) : + if ( alpha12 > two_pi ) : alpha12 = alpha12 - two_pi - + b = a * (1.0 - f) TanU1 = (1-f) * math.tan(phi1) @@ -283,53 +283,53 @@ def vinc_pt( f, a, phi1, lembda1, alpha12, s ) : sigma1 = math.atan2( TanU1, math.cos(alpha12) ) Sinalpha = math.cos(U1) * math.sin(alpha12) cosalpha_sq = 1.0 - Sinalpha * Sinalpha - + u2 = cosalpha_sq * (a * a - b * b ) / (b * b) A = 1.0 + (u2 / 16384) * (4096 + u2 * (-768 + u2 * \ (320 - 175 * u2) ) ) B = (u2 / 1024) * (256 + u2 * (-128 + u2 * (74 - 47 * u2) ) ) - + # Starting with the approximation sigma = (s / (b * A)) last_sigma = 2.0 * sigma + 2.0 # something impossible - - # Iterate the following three equations - # until there is no significant change in sigma + + # Iterate the following three equations + # until there is no significant change in sigma # two_sigma_m , delta_sigma while ( abs( (last_sigma - sigma) / sigma) > 1.0e-9 ) : two_sigma_m = 2 * sigma1 + sigma - + delta_sigma = B * math.sin(sigma) * ( math.cos(two_sigma_m) \ + (B/4) * (math.cos(sigma) * \ (-1 + 2 * math.pow( math.cos(two_sigma_m), 2 ) - \ (B/6) * math.cos(two_sigma_m) * \ (-3 + 4 * math.pow(math.sin(sigma), 2 )) * \ (-3 + 4 * math.pow( math.cos (two_sigma_m), 2 ))))) \ - + last_sigma = sigma sigma = (s / (b * A)) + delta_sigma - - + + phi2 = math.atan2 ( (math.sin(U1) * math.cos(sigma) + math.cos(U1) * math.sin(sigma) * math.cos(alpha12) ), \ ((1-f) * math.sqrt( math.pow(Sinalpha, 2) + \ pow(math.sin(U1) * math.sin(sigma) - math.cos(U1) * math.cos(sigma) * math.cos(alpha12), 2)))) - + lembda = math.atan2( (math.sin(sigma) * math.sin(alpha12 )), (math.cos(U1) * math.cos(sigma) - \ math.sin(U1) * math.sin(sigma) * math.cos(alpha12))) - + C = (f/16) * cosalpha_sq * (4 + f * (4 - 3 * cosalpha_sq )) - + omega = lembda - (1-C) * f * Sinalpha * \ (sigma + C * math.sin(sigma) * (math.cos(two_sigma_m) + \ C * math.cos(sigma) * (-1 + 2 * math.pow(math.cos(two_sigma_m),2) ))) - + lembda2 = lembda1 + omega - + alpha21 = math.atan2 ( Sinalpha, (-math.sin(U1) * math.sin(sigma) + \ math.cos(U1) * math.cos(sigma) * math.cos(alpha12))) @@ -340,39 +340,39 @@ def vinc_pt( f, a, phi1, lembda1, alpha12, s ) : alpha21 = alpha21 - two_pi - return phi2, lembda2, alpha21 + return phi2, lembda2, alpha21 # END of Vincenty's Direct formulae ##--------------------------------------------------------------------------- -# Notes: -# -# * "The inverse formulae may give no solution over a line -# between two nearly antipodal points. This will occur when +# Notes: +# +# * "The inverse formulae may give no solution over a line +# between two nearly antipodal points. This will occur when # lembda ... is greater than pi in absolute value". (Vincenty, 1975) -# -# * In Vincenty (1975) L is used for the difference in longitude, -# however for consistency with other formulae in this Manual, -# omega is used here. -# -# * Variables specific to Vincenty's formulae are shown below, -# others common throughout the manual are shown in the Glossary. -# -# +# +# * In Vincenty (1975) L is used for the difference in longitude, +# however for consistency with other formulae in this Manual, +# omega is used here. +# +# * Variables specific to Vincenty's formulae are shown below, +# others common throughout the manual are shown in the Glossary. +# +# # alpha = Azimuth of the geodesic at the equator # U = Reduced latitude -# lembda = Difference in longitude on an auxiliary sphere (lembda1 & lembda2 +# lembda = Difference in longitude on an auxiliary sphere (lembda1 & lembda2 # are the geodetic longitudes of points 1 & 2) # sigma = Angular distance on a sphere, from point 1 to point 2 # sigma1 = Angular distance on a sphere, from the equator to point 1 # sigma2 = Angular distance on a sphere, from the equator to point 2 -# sigma_m = Angular distance on a sphere, from the equator to the +# sigma_m = Angular distance on a sphere, from the equator to the # midpoint of the line from point 1 to point 2 # u, A, B, C = Internal variables -# -# +# +# # Sample Data -# +# # Flinders Peak # -37o57'03.72030" # 144o25'29.52440" @@ -381,14 +381,14 @@ def vinc_pt( f, a, phi1, lembda1, alpha12, s ) : # 143o55'35.38390" # Ellipsoidal Distance # 54,972.271 m -# +# # Forward Azimuth # 306o52'05.37" -# +# # Reverse Azimuth # 127o10'25.07" -# -# +# +# ##******************************************************************* # Test driver @@ -401,51 +401,51 @@ def vinc_pt( f, a, phi1, lembda1, alpha12, s ) : b = 6356752.3142 f = (a-b)/a - print "\n Ellipsoidal major axis = %12.3f metres\n" % ( a ) - print "\n Inverse flattening = %15.9f\n" % ( 1.0/f ) + print("\n Ellipsoidal major axis = %12.3f metres\n" % ( a )) + print("\n Inverse flattening = %15.9f\n" % ( 1.0/f )) - print "\n Test Flinders Peak to Buninyon" - print "\n ****************************** \n" + print("\n Test Flinders Peak to Buninyon") + print("\n ****************************** \n") phi1 = -(( 3.7203 / 60. + 57) / 60. + 37 ) lembda1 = ( 29.5244 / 60. + 25) / 60. + 144 - print "\n Flinders Peak = %12.6f, %13.6f \n" % ( phi1, lembda1 ) + print("\n Flinders Peak = %12.6f, %13.6f \n" % ( phi1, lembda1 )) deg = int(phi1) minn = int(abs( ( phi1 - deg) * 60.0 )) sec = abs(phi1 * 3600 - deg * 3600) - minn * 60 - print " Flinders Peak = %3i\xF8%3i\' %6.3f\", " % ( deg, minn, sec ), + print(" Flinders Peak = %3i\xF8%3i\' %6.3f\", " % ( deg, minn, sec )) deg = int(lembda1) minn = int(abs( ( lembda1 - deg) * 60.0 )) sec = abs(lembda1 * 3600 - deg * 3600) - minn * 60 - print " %3i\xF8%3i\' %6.3f\" \n" % ( deg, minn, sec ) + print(" %3i\xF8%3i\' %6.3f\" \n" % ( deg, minn, sec )) phi2 = -(( 10.1561 / 60. + 39) / 60. + 37 ) lembda2 = ( 35.3839 / 60. + 55) / 60. + 143 - print "\n Buninyon = %12.6f, %13.6f \n" % ( phi2, lembda2 ) + print("\n Buninyon = %12.6f, %13.6f \n" % ( phi2, lembda2 )) deg = int(phi2) minn = int(abs( ( phi2 - deg) * 60.0 )) sec = abs(phi2 * 3600 - deg * 3600) - minn * 60 - print " Buninyon = %3i\xF8%3i\' %6.3f\", " % ( deg, minn, sec ), + print(" Buninyon = %3i\xF8%3i\' %6.3f\", " % ( deg, minn, sec )) deg = int(lembda2) minn = int(abs( ( lembda2 - deg) * 60.0 )) sec = abs(lembda2 * 3600 - deg * 3600) - minn * 60 - print " %3i\xF8%3i\' %6.3f\" \n" % ( deg, minn, sec ) + print(" %3i\xF8%3i\' %6.3f\" \n" % ( deg, minn, sec )) dist, alpha12, alpha21 = vinc_dist ( f, a, math.radians(phi1), math.radians(lembda1), math.radians(phi2), math.radians(lembda2) ) alpha12 = math.degrees(alpha12) alpha21 = math.degrees(alpha21) - print "\n Ellipsoidal Distance = %15.3f metres\n should be 54972.271 m\n" % ( dist ) - print "\n Forward and back azimuths = %15.6f, %15.6f \n" % ( alpha12, alpha21 ) + print("\n Ellipsoidal Distance = %15.3f metres\n should be 54972.271 m\n" % ( dist )) + print("\n Forward and back azimuths = %15.6f, %15.6f \n" % ( alpha12, alpha21 )) deg = int(alpha12) minn =int( abs(( alpha12 - deg) * 60.0 ) ) sec = abs(alpha12 * 3600 - deg * 3600) - minn * 60 - print " Forward azimuth = %3i\xF8%3i\' %6.3f\"\n" % ( deg, minn, sec ) + print(" Forward azimuth = %3i\xF8%3i\' %6.3f\"\n" % ( deg, minn, sec )) deg = int(alpha21) minn =int(abs( ( alpha21 - deg) * 60.0 )) sec = abs(alpha21 * 3600 - deg * 3600) - minn * 60 - print " Reverse azimuth = %3i\xF8%3i\' %6.3f\"\n" % ( deg, minn, sec ) + print(" Reverse azimuth = %3i\xF8%3i\' %6.3f\"\n" % ( deg, minn, sec )) # Test the direct function */ @@ -462,21 +462,21 @@ def vinc_pt( f, a, phi1, lembda1, alpha12, s ) : lembda2 = math.degrees(lembda2) alpha21 = math.degrees(alpha21) - print "\n Projected point =%11.6f, %13.6f \n" % ( phi2, lembda2 ) + print("\n Projected point =%11.6f, %13.6f \n" % ( phi2, lembda2 )) deg = int(phi2) minn =int(abs( ( phi2 - deg) * 60.0 )) sec = abs( phi2 * 3600 - deg * 3600) - minn * 60 - print " Projected Point = %3i\xF8%3i\' %6.3f\", " % ( deg, minn, sec ), + print(" Projected Point = %3i\xF8%3i\' %6.3f\", " % ( deg, minn, sec )) deg = int(lembda2) minn =int(abs( ( lembda2 - deg) * 60.0 )) sec = abs(lembda2 * 3600 - deg * 3600) - minn * 60 - print " %3i\xF8%3i\' %6.3f\"\n" % ( deg, minn, sec ) - print " Should be Buninyon \n" - print "\n Reverse azimuth = %10.6f \n" % ( alpha21 ) + print(" %3i\xF8%3i\' %6.3f\"\n" % ( deg, minn, sec )) + print(" Should be Buninyon \n") + print("\n Reverse azimuth = %10.6f \n" % ( alpha21 )) deg = int(alpha21) minn =int(abs( ( alpha21 - deg) * 60.0 )) sec = abs(alpha21 * 3600 - deg * 3600) - minn * 60 - print " Reverse azimuth = %3i\xF8%3i\' %6.3f\"\n\n" % ( deg, minn, sec ) + print(" Reverse azimuth = %3i\xF8%3i\' %6.3f\"\n\n" % ( deg, minn, sec )) # lat/lon of New York lat1 = 40.78 @@ -484,16 +484,16 @@ def vinc_pt( f, a, phi1, lembda1, alpha12, s ) : # lat/lon of London. lat2 = 51.53 lon2 = 0.08 - print 'New York to London:' + print('New York to London:') gc = GreatCircle((2*a+b)/3.,(2*a+b)/3.,lon1,lat1,lon2,lat2) - print 'geodesic distance using a sphere with WGS84 mean radius = ',gc.distance - print 'lon/lat for 10 equally spaced points along geodesic:' + print('geodesic distance using a sphere with WGS84 mean radius = ',gc.distance) + print('lon/lat for 10 equally spaced points along geodesic:') lons,lats = gc.points(10) for lon,lat in zip(lons,lats): - print lon,lat + print(lon,lat) gc = GreatCircle(a,b,lon1,lat1,lon2,lat2) - print 'geodesic distance using WGS84 ellipsoid = ',gc.distance - print 'lon/lat for 10 equally spaced points along geodesic:' + print('geodesic distance using WGS84 ellipsoid = ',gc.distance) + print('lon/lat for 10 equally spaced points along geodesic:') lons,lats = gc.points(10) for lon,lat in zip(lons,lats): - print lon,lat + print(lon,lat) diff --git a/pyroms/pyroms/extern/kdtree.py b/pyroms/pyroms/extern/kdtree.py index 05350ef..eabc28f 100644 --- a/pyroms/pyroms/extern/kdtree.py +++ b/pyroms/pyroms/extern/kdtree.py @@ -40,7 +40,7 @@ def __init__(self, maxes, mins): self.m, = self.maxes.shape def __repr__(self): - return "" % zip(self.mins, self.maxes) + return "" % list(zip(self.mins, self.maxes)) def volume(self): """Total volume.""" diff --git a/pyroms/pyroms/grid.py b/pyroms/pyroms/grid.py index eb1bc66..32a1a45 100644 --- a/pyroms/pyroms/grid.py +++ b/pyroms/pyroms/grid.py @@ -43,10 +43,10 @@ class ROMS_gridinfo(object): There are two ways to define the grid information. If grid_file and hist_file are not passed to the object when it is created, the - information is retrieved from gridid.txt. - To add new grid please edit your gridid.txt. You need to define - an environment variable PYROMS_GRIDID_FILE pointing to your - gridid.txt file. Just copy an existing grid and modify the + information is retrieved from gridid.txt. + To add new grid please edit your gridid.txt. You need to define + an environment variable PYROMS_GRIDID_FILE pointing to your + gridid.txt file. Just copy an existing grid and modify the definition accordingly to your case (Be carefull with space and blank line). @@ -62,14 +62,14 @@ def __init__(self, gridid,grid_file=None,hist_file=None): if gridid in gridid_dictionary: #print 'CJMP> gridid found in gridid_dictionary, grid retrieved from dictionary' saved_self=gridid_dictionary[gridid] - for attrib in saved_self.__dict__.keys(): + for attrib in list(saved_self.__dict__.keys()): setattr(self,attrib,getattr(saved_self,attrib)) else: #nope, we need to get the information from gridid.txt or from #the grid and history files from the model self.id = gridid self._get_grid_info(grid_file,hist_file) - + #now save the data in the dictionary, so we don't need to get it again gridid_dictionary[gridid]=self @@ -107,7 +107,7 @@ def _get_grid_info(self,grid_file,hist_file): line_nb = line_nb + 1 if info == []: - raise ValueError, 'Unknow gridid. Please check your gridid.txt file' + raise ValueError('Unknown gridid. Please check your gridid.txt file') if info[4] == 'roms': self.name = info[1] @@ -119,7 +119,7 @@ def _get_grid_info(self,grid_file,hist_file): self.theta_b = np.float(info[7]) self.Tcline = np.float(info[8]) - elif info[4] == 'z': + elif info[4] == 'z': nline = len(info) dep = info[5] for line in range(6,nline): @@ -133,14 +133,14 @@ def _get_grid_info(self,grid_file,hist_file): self.depth = dep else: - raise ValueError, 'Unknow grid type. Please check your gridid.txt file' + raise ValueError('Unknown grid type. Please check your gridid.txt file') else: #lets get the grid information from the history and grid files #print 'CJMP> getting grid info from ROMS history and grid files' assert type(grid_file)!=type(None), 'if specify history file you must specify grid file' assert type(hist_file)!=type(None), 'if specify grid file you must specify history file' - #open history file and get necessary grid information from it. + #open history file and get necessary grid information from it. hist=netCDF.Dataset(hist_file,'r') #put data into ROMS_gridinfo object @@ -159,12 +159,12 @@ def _get_grid_info(self,grid_file,hist_file): try: self.Vtrans=np.float(hist.variables['Vstretching'][:]) except: - print 'variable Vtransform not found in history file. Defaulting to Vtrans=1' + print('variable Vtransform not found in history file. Defaulting to Vtrans=1') self.Vtrans=1 self.theta_s=np.float(hist.variables['theta_s'][:]) self.theta_b=np.float(hist.variables['theta_b'][:]) self.Tcline=np.float(hist.variables['Tcline'][:]) - + def print_ROMS_gridinfo(gridid): """ @@ -175,20 +175,20 @@ def print_ROMS_gridinfo(gridid): gridinfo = ROMS_gridinfo(gridid) - print ' ' - print 'grid information for gridid ', gridinfo.id, ':' - print ' ' - print 'grid name : ', gridinfo.name - print 'grid file path : ', gridinfo.grdfile - print 'number of vertical level : ', gridinfo.N - print 'grid type : ', gridinfo.grdtype + print(' ') + print('grid information for gridid ', gridinfo.id, ':') + print(' ') + print('grid name : ', gridinfo.name) + print('grid file path : ', gridinfo.grdfile) + print('number of vertical level : ', gridinfo.N) + print('grid type : ', gridinfo.grdtype) if gridinfo.grdtype == 'roms': - print 'theta_s = ', gridinfo.theta_s - print 'theta_b = ', gridinfo.theta_b - print 'Tcline = ', gridinfo.Tcline + print('theta_s = ', gridinfo.theta_s) + print('theta_b = ', gridinfo.theta_b) + print('Tcline = ', gridinfo.Tcline) #print 'hc = ', gridinfo.hc elif gridinfo.grdtype == 'z': - print 'depth = ', gridinfo.depth + print('depth = ', gridinfo.depth) def list_ROMS_gridid(): @@ -202,14 +202,14 @@ def list_ROMS_gridid(): data = open(gridid_file,'r') lines = data.readlines() data.close() - + gridid_list = [] for line in lines: s = line.split() if s[0] == 'id': gridid_list.append(s[2]) - print 'List of defined gridid : ', gridid_list + print('List of defined gridid : ', gridid_list) def get_ROMS_hgrid(gridid): @@ -225,17 +225,23 @@ def get_ROMS_hgrid(gridid): nc = io.Dataset(grdfile) #Check for cartesian or geographical grid - spherical = nc.variables['spherical'][:] + spherical = nc.variables['spherical'][0] + + #if it is type byte, then convert to string + try: + spherical=spherical.decode('utf8') + except: + print('Assuming spherical is integer',spherical, type(spherical)) - #Get horizontal grid + #Get horizontal grid if ((spherical == 0) or (spherical == 'F')): #cartesian grid - print 'Load cartesian grid from file' - if 'x_vert' in nc.variables.keys() and 'y_vert' in nc.variables.keys(): + print('Load cartesian grid from file') + if 'x_vert' in list(nc.variables.keys()) and 'y_vert' in list(nc.variables.keys()): x_vert = nc.variables['x_vert'][:] y_vert = nc.variables['y_vert'][:] - elif 'x_rho' in nc.variables.keys() and 'y_rho' in nc.variables.keys() \ - and 'pm' in nc.variables.keys() and 'pn' in nc.variables.keys(): + elif 'x_rho' in list(nc.variables.keys()) and 'y_rho' in list(nc.variables.keys()) \ + and 'pm' in list(nc.variables.keys()) and 'pn' in list(nc.variables.keys()): x_rho = nc.variables['x_rho'][:] y_rho = nc.variables['y_rho'][:] pm = nc.variables['pm'][:] @@ -245,13 +251,13 @@ def get_ROMS_hgrid(gridid): #compute verts from rho point, pm, pn, angle x_vert, y_vert = rho_to_vert(x_rho, y_rho, pm, pn, angle) else: - raise ValueError, 'NetCDF file must contain x_vert and y_vert \ - or x_rho, y_rho, pm, pn and angle for a cartesian grid' + raise ValueError('NetCDF file must contain x_vert and y_vert \ + or x_rho, y_rho, pm, pn and angle for a cartesian grid') - if 'x_rho' in nc.variables.keys() and 'y_rho' in nc.variables.keys() and \ - 'x_u' in nc.variables.keys() and 'y_u' in nc.variables.keys() and \ - 'x_v' in nc.variables.keys() and 'y_v' in nc.variables.keys() and \ - 'x_psi' in nc.variables.keys() and 'y_psi' in nc.variables.keys(): + if 'x_rho' in list(nc.variables.keys()) and 'y_rho' in list(nc.variables.keys()) and \ + 'x_u' in list(nc.variables.keys()) and 'y_u' in list(nc.variables.keys()) and \ + 'x_v' in list(nc.variables.keys()) and 'y_v' in list(nc.variables.keys()) and \ + 'x_psi' in list(nc.variables.keys()) and 'y_psi' in list(nc.variables.keys()): x_rho = nc.variables['x_rho'][:] y_rho = nc.variables['y_rho'][:] x_u = nc.variables['x_u'][:] @@ -270,7 +276,7 @@ def get_ROMS_hgrid(gridid): x_psi = None y_psi = None - if 'pm' in nc.variables.keys() and 'pn' in nc.variables.keys(): + if 'pm' in list(nc.variables.keys()) and 'pn' in list(nc.variables.keys()): pm = nc.variables['pm'][:] dx = 1. / pm pn = nc.variables['pn'][:] @@ -279,14 +285,14 @@ def get_ROMS_hgrid(gridid): dx = None dy = None - if 'dndx' in nc.variables.keys() and 'dmde' in nc.variables.keys(): + if 'dndx' in list(nc.variables.keys()) and 'dmde' in list(nc.variables.keys()): dndx = nc.variables['dndx'][:] dmde = nc.variables['dmde'][:] else: dndx = None dmde = None - if 'angle' in nc.variables.keys(): + if 'angle' in list(nc.variables.keys()): angle = nc.variables['angle'][:] else: angle = None @@ -297,15 +303,21 @@ def get_ROMS_hgrid(gridid): x_psi=x_psi, y_psi=y_psi, dx=dx, dy=dy, \ dndx=dndx, dmde=dmde, angle_rho=angle) + #load the mask + try: + hgrd.mask_rho = np.array(nc.variables['mask_rho'][:]) + except: + hgrd.mask_rho = np.ones(hgrd.x_rho.shape) + else: #geographical grid - print 'Load geographical grid from file' + print('Load geographical grid from file') proj = Basemap(projection='merc', resolution=None, lat_0=0, lon_0=0) - if 'lon_vert' in nc.variables.keys() and 'lat_vert' in nc.variables.keys(): + if 'lon_vert' in list(nc.variables.keys()) and 'lat_vert' in list(nc.variables.keys()): lon_vert = nc.variables['lon_vert'][:] lat_vert = nc.variables['lat_vert'][:] - elif 'lon_rho' in nc.variables.keys() and 'lat_rho' in nc.variables.keys() \ - and 'lon_psi' in nc.variables.keys() and 'lat_psi' in nc.variables.keys(): + elif 'lon_rho' in list(nc.variables.keys()) and 'lat_rho' in list(nc.variables.keys()) \ + and 'lon_psi' in list(nc.variables.keys()) and 'lat_psi' in list(nc.variables.keys()): lon_rho = nc.variables['lon_rho'][:] lat_rho = nc.variables['lat_rho'][:] lon_psi = nc.variables['lon_psi'][:] @@ -313,13 +325,13 @@ def get_ROMS_hgrid(gridid): #compute verts from rho and psi point lon_vert, lat_vert = rho_to_vert_geo(lon_rho, lat_rho, lon_psi, lat_psi) else: - raise ValueError, 'NetCDF file must contain lon_vert and lat_vert \ - or lon_rho, lat_rho, lon_psi, lat_psi for a geographical grid' + raise ValueError('NetCDF file must contain lon_vert and lat_vert \ + or lon_rho, lat_rho, lon_psi, lat_psi for a geographical grid') - if 'lon_rho' in nc.variables.keys() and 'lat_rho' in nc.variables.keys() and \ - 'lon_u' in nc.variables.keys() and 'lat_u' in nc.variables.keys() and \ - 'lon_v' in nc.variables.keys() and 'lat_v' in nc.variables.keys() and \ - 'lon_psi' in nc.variables.keys() and 'lat_psi' in nc.variables.keys(): + if 'lon_rho' in list(nc.variables.keys()) and 'lat_rho' in list(nc.variables.keys()) and \ + 'lon_u' in list(nc.variables.keys()) and 'lat_u' in list(nc.variables.keys()) and \ + 'lon_v' in list(nc.variables.keys()) and 'lat_v' in list(nc.variables.keys()) and \ + 'lon_psi' in list(nc.variables.keys()) and 'lat_psi' in list(nc.variables.keys()): lon_rho = nc.variables['lon_rho'][:] lat_rho = nc.variables['lat_rho'][:] lon_u = nc.variables['lon_u'][:] @@ -338,7 +350,7 @@ def get_ROMS_hgrid(gridid): lon_psi = None lat_psi = None - if 'pm' in nc.variables.keys() and 'pn' in nc.variables.keys(): + if 'pm' in list(nc.variables.keys()) and 'pn' in list(nc.variables.keys()): pm = nc.variables['pm'][:] dx = 1. / pm pn = nc.variables['pn'][:] @@ -347,30 +359,30 @@ def get_ROMS_hgrid(gridid): dx = None dy = None - if 'dndx' in nc.variables.keys() and 'dmde' in nc.variables.keys(): + if 'dndx' in list(nc.variables.keys()) and 'dmde' in list(nc.variables.keys()): dndx = nc.variables['dndx'][:] dmde = nc.variables['dmde'][:] else: dndx = None dmde = None - if 'angle' in nc.variables.keys(): + if 'angle' in list(nc.variables.keys()): angle = nc.variables['angle'][:] else: angle = None - #Get geographical grid + #Get geographical grid hgrd = CGrid_geo(lon_vert, lat_vert, proj, \ lon_rho=lon_rho, lat_rho=lat_rho, \ lon_u=lon_u, lat_u=lat_u, lon_v=lon_v, lat_v=lat_v, \ lon_psi=lon_psi, lat_psi=lat_psi, dx=dx, dy=dy, \ dndx=dndx, dmde=dmde, angle_rho=angle) - #load the mask - try: - hgrd.mask_rho = np.array(nc.variables['mask_rho'][:]) - except: - hgrd.mask_rho = np.ones(hgrd.lat_rho.shape) + #load the mask + try: + hgrd.mask_rho = np.array(nc.variables['mask_rho'][:]) + except: + hgrd.mask_rho = np.ones(hgrd.lat_rho.shape) return hgrd @@ -382,11 +394,11 @@ def get_ROMS_vgrid(gridid, zeta=None): Load ROMS vertical grid object. vgrid is a s_coordinate or a z_coordinate object, depending on gridid.grdtype. vgrid.z_r and vgrid.z_w (vgrid.z for a z_coordinate object) - can be indexed in order to retreive the actual depths. The - free surface time serie zeta can be provided as an optional - argument. Note that the values of zeta are not calculated - until z is indexed, so a netCDF variable for zeta may be passed, - even if the file is large, as only the values that are required + can be indexed in order to retreive the actual depths. The + free surface time serie zeta can be provided as an optional + argument. Note that the values of zeta are not calculated + until z is indexed, so a netCDF variable for zeta may be passed, + even if the file is large, as only the values that are required will be retrieved from the file. """ @@ -399,7 +411,7 @@ def get_ROMS_vgrid(gridid, zeta=None): try: h = nc.variables['h'][:] except: - raise ValueError, 'NetCDF file must contain the bathymetry h' + raise ValueError('NetCDF file must contain the bathymetry h') try: hraw = nc.variables['hraw'][:] @@ -418,8 +430,10 @@ def get_ROMS_vgrid(gridid, zeta=None): vgrid = s_coordinate_2(h, theta_b, theta_s, Tcline, N, hraw=hraw, zeta=zeta) elif Vtrans == 4: vgrid = s_coordinate_4(h, theta_b, theta_s, Tcline, N, hraw=hraw, zeta=zeta) + elif Vtrans == 5: + vgrid = s_coordinate_5(h, theta_b, theta_s, Tcline, N, hraw=hraw, zeta=zeta) else: - raise Warning, 'Unknow vertical transformation Vtrans' + raise Warning('Unknown vertical transformation Vtrans') elif gridinfo.grdtype == 'z': N = gridinfo.N @@ -427,7 +441,7 @@ def get_ROMS_vgrid(gridid, zeta=None): vgrid = z_coordinate(h, depth, N) else: - raise ValueError, 'Unknow grid type' + raise ValueError('Unknown grid type') return vgrid @@ -448,15 +462,15 @@ def get_ROMS_grid(gridid, zeta=None, hist_file=None,grid_file=None): grid information will be extracted from those files, and gridid will be used to name that grid for the rest of the python session. - + grd.vgrid is a s_coordinate or a z_coordinate object, depending on gridid.grdtype. - grd.vgrid.z_r and grd.vgrid.z_w (grd.vgrid.z for a - z_coordinate object) can be indexed in order to retreive the - actual depths. The free surface time serie zeta can be provided - as an optional argument. Note that the values of zeta are not - calculated until z is indexed, so a netCDF variable for zeta may - be passed, even if the file is large, as only the values that + grd.vgrid.z_r and grd.vgrid.z_w (grd.vgrid.z for a + z_coordinate object) can be indexed in order to retreive the + actual depths. The free surface time serie zeta can be provided + as an optional argument. Note that the values of zeta are not + calculated until z is indexed, so a netCDF variable for zeta may + be passed, even if the file is large, as only the values that are required will be retrieved from the file. """ @@ -486,7 +500,7 @@ def write_ROMS_grid(grd, filename='roms_grd.nc'): Mm, Lm = grd.hgrid.x_rho.shape - + # Write ROMS grid to file nc = netCDF.Dataset(filename, 'w', format='NETCDF3_64BIT') nc.Description = 'ROMS grid' @@ -498,7 +512,7 @@ def write_ROMS_grid(grd, filename='roms_grd.nc'): nc.createDimension('xi_u', Lm-1) nc.createDimension('xi_v', Lm) nc.createDimension('xi_psi', Lm-1) - + nc.createDimension('eta_rho', Mm) nc.createDimension('eta_u', Mm) nc.createDimension('eta_v', Mm-1) @@ -521,7 +535,7 @@ def write_nc_var(var, name, dimensions, long_name=None, units=None): if units is not None: nc.variables[name].units = units nc.variables[name][:] = var - print ' ... wrote ', name + print(' ... wrote ', name) if hasattr(grd.vgrid, 's_rho') is True and grd.vgrid.s_rho is not None: write_nc_var(grd.vgrid.theta_s, 'theta_s', (), 'S-coordinate surface control parameter') @@ -575,7 +589,7 @@ def write_nc_var(var, name, dimensions, long_name=None, units=None): nc.createVariable('spherical', 'c') nc.variables['spherical'].long_name = 'Grid type logical switch' nc.variables['spherical'][:] = grd.hgrid.spherical - print ' ... wrote ', 'spherical' + print(' ... wrote ', 'spherical') write_nc_var(grd.hgrid.angle_rho, 'angle', ('eta_rho', 'xi_rho'), 'angle between XI-axis and EAST', 'radians') diff --git a/pyroms/pyroms/hgrid.py b/pyroms/pyroms/hgrid.py index 9ae98ee..94432d6 100644 --- a/pyroms/pyroms/hgrid.py +++ b/pyroms/pyroms/hgrid.py @@ -5,7 +5,7 @@ import os import sys import ctypes -import cPickle +import pickle from warnings import warn from copy import deepcopy @@ -84,7 +84,7 @@ class BoundaryInteractor(object): def _update_beta_lines(self): """Update m/pline by finding the points where self.beta== -/+ 1""" - x, y = zip(*self._poly.xy) + x, y = list(zip(*self._poly.xy)) num_points = len(x)-1 # the first and last point are repeated xp = [x[n] for n in range(num_points) if self.beta[n]==1] @@ -132,7 +132,7 @@ def _poly_changed(self, poly): def _get_ind_under_point(self, event): 'get the index of the vertex under point if within epsilon tolerance' try: - x, y = zip(*self._poly.xy) + x, y = list(zip(*self._poly.xy)) # display coords xt, yt = self._poly.get_transform().numerix_x_y(x, y) @@ -188,7 +188,7 @@ def _key_press_callback(self, event): if ind is not None: self._poly.xy = [tup for i,tup in enumerate(self._poly.xy) \ if i!=ind] - self._line.set_data(zip(*self._poly.xy)) + self._line.set_data(list(zip(*self._poly.xy))) self.beta = [beta for i,beta in enumerate(self.beta) \ if i!=ind] elif event.key=='p': @@ -219,7 +219,7 @@ def _key_press_callback(self, event): list(self._poly.xy[:i+1]) + [(event.xdata, event.ydata)] + list(self._poly.xy[i+1:])) - self._line.set_data(zip(*self._poly.xy)) + self._line.set_data(list(zip(*self._poly.xy))) self.beta.insert(i+1, 0) break s0 = xys[-1] @@ -229,7 +229,7 @@ def _key_press_callback(self, event): self._poly.xy = np.array( list(self._poly.xy) + [(event.xdata, event.ydata)]) - self._line.set_data(zip(*self._poly.xy)) + self._line.set_data(list(zip(*self._poly.xy))) self.beta.append(0) elif event.key=='G' or event.key == '1': options = deepcopy(self.gridgen_options) @@ -276,7 +276,7 @@ def _motion_notify_callback(self, event): if self._ind == 0: self._poly.xy[-1] = x, y - x, y = zip(*self._poly.xy) + x, y = list(zip(*self._poly.xy)) self._line.set_data(x[:-1], y[:-1]) self._update_beta_lines() @@ -311,7 +311,7 @@ def __init__(self, x, y=None, beta=None, ax=None, proj=None, # Set default gridgen option, and copy over specified options. self.gridgen_options = {'ul_idx': 0, 'shp': (32, 32)} - for key, value in gridgen_options.iteritems(): + for key, value in gridgen_options.items(): self.gridgen_options[key] = gridgen_options[key] x = list(x); y = list(y) @@ -364,7 +364,7 @@ def __init__(self, x, y=None, beta=None, ax=None, proj=None, def save_bry(self, bry_file='bry.pickle'): f = open(bry_file, 'wb') bry_dict = {'x': self.x, 'y': self.y, 'beta': self.beta} - cPickle.dump(bry_dict, f, protocol=-1) + pickle.dump(bry_dict, f, protocol=-1) f.close() def load_bry(self, bry_file='bry.pickle'): @@ -374,17 +374,17 @@ def load_bry(self, bry_file='bry.pickle'): self._line.set_data(x, y) self.beta = bry_dict['beta'] if hasattr(self, '_poly'): - self._poly.xy = zip(x, y) + self._poly.xy = list(zip(x, y)) self._update_beta_lines() self._draw_callback(None) self._canvas.draw() def save_grid(self, grid_file='grid.pickle'): f = open(grid_file, 'wb') - cPickle.dump(self.grd, f, protocol=-1) + pickle.dump(self.grd, f, protocol=-1) f.close() - def _get_verts(self): return zip(self.x, self.y) + def _get_verts(self): return list(zip(self.x, self.y)) verts = property(_get_verts) def get_xdata(self): return self._line.get_xdata() x = property(get_xdata) @@ -934,9 +934,9 @@ def __init__(self, lon_vert, lat_vert, proj, use_gcdist=True, ellipse='WGS84', \ def mask_polygon_geo(lonlat_verts, mask_value=0.0): - lon, lat = zip(*lonlat_verts) + lon, lat = list(zip(*lonlat_verts)) x, y = proj(lon, lat, inverse=True) - self.mask_polygon(zip(x, y), mask_value) + self.mask_polygon(list(zip(x, y)), mask_value) lon = property(lambda self: self.lon_vert, None, None, 'Shorthand for lon_vert') lat = property(lambda self: self.lat_vert, None, None, 'Shorthand for lat_vert') @@ -1376,25 +1376,25 @@ def __init__(self, grd, coast=None, **kwargs): if type(grd).__name__ == 'ROMS_Grid': try: - x = range(grd.hgrid.lon_vert.shape[1]) - y = range(grd.hgrid.lat_vert.shape[0]) + x = list(range(grd.hgrid.lon_vert.shape[1])) + y = list(range(grd.hgrid.lat_vert.shape[0])) xv, yv = np.meshgrid(x,y) mask = grd.hgrid.mask_rho except: - x = range(grd.hgrid.x_vert.shape[1]) - y = range(grd.hgrid.y_vert.shape[0]) + x = list(range(grd.hgrid.x_vert.shape[1])) + y = list(range(grd.hgrid.y_vert.shape[0])) xv, yv = np.meshgrid(x,y) mask = grd.hgrid.mask_rho if type(grd).__name__ == 'CGrid_geo': try: - x = range(grd.lon_vert.shape[1]) - y = range(grd.lat_vert.shape[0]) + x = list(range(grd.lon_vert.shape[1])) + y = list(range(grd.lat_vert.shape[0])) xv, yv = np.meshgrid(x,y) mask = grd.mask_rho except: - x = range(grd.x_vert.shape[1]) - y = range(grd.y_vert.shape[0]) + x = list(range(grd.x_vert.shape[1])) + y = list(range(grd.y_vert.shape[0])) xv, yv = np.meshgrid(x,y) mask = grd.mask_rho @@ -1498,12 +1498,12 @@ def _on_click(self, event): else: idx = np.argwhere(d.flatten() == d.min()) j, i = np.argwhere(d == d.min())[0] - print 'Position on the grid (rho point): i =', i, ', j =', j + print('Position on the grid (rho point): i =', i, ', j =', j) if self.proj is not None: lon, lat = self.proj(self._xc[j,i], self._yc[j,i], inverse=True) - print 'corresponding geographical position : lon = ', lon, ', lat =', lat + print('corresponding geographical position : lon = ', lon, ', lat =', lat) else: - print 'corresponding cartesian position : x = ', self._xc[j,i], ', y =', self._yc[j,i] + print('corresponding cartesian position : x = ', self._xc[j,i], ', y =', self._yc[j,i]) def __init__(self, grd, proj=None, **kwargs): diff --git a/pyroms/pyroms/io.py b/pyroms/pyroms/io.py index b796a21..2254159 100644 --- a/pyroms/pyroms/io.py +++ b/pyroms/pyroms/io.py @@ -14,22 +14,22 @@ with an input of a string: # returns netCDF4.Dataset object based on file - nc = pyroms.io.Dataset(file) - + nc = pyroms.io.Dataset(file) + # returns MFnetCDF4.Dataset object based on file (with wildcard chars) - nc = pyroms.io.MFDataset(file) + nc = pyroms.io.MFDataset(file) with an input of a list of files: # returns MFDataset object based on list of files - nc = pyroms.io.Dataset(files) - + nc = pyroms.io.Dataset(files) + # returns MFDataset object based on list of files nc = pyroms.io.MFDataset(files) with an input of a netCDF4.Dataset or MFnetCDF4.Dataset object: # passes through netCDF4.Dataset or MFnetCDF4.Dataset object nc = pyroms.io.Dataset(nc) - + # passes through MFDataset object based on file (with wildcard chars) nc = pyroms.io.MFDataset(nc) ''' @@ -42,12 +42,12 @@ import netCDF4 as netCDF except: import netCDF3 as netCDF - + def Dataset(ncfile): """Return an appropriate netcdf object: netCDF4 object given a file string MFnetCDF4 object given a list of files - + A netCDF4 or MFnetCDF4 object returns itself.""" if isinstance(ncfile, str): return netCDF.Dataset(ncfile, 'r') @@ -58,8 +58,8 @@ def Dataset(ncfile): 'variables attribute must be a dictionary' return ncfile else: - raise TypeError, 'type %s not supported' % type(ncfile) - + raise TypeError('type %s not supported' % type(ncfile)) + Dataset.__doc__ = __doc__ def MFDataset(ncfile): @@ -75,29 +75,29 @@ def MFDataset(ncfile): 'variables attribute must be a dictionary' return ncfile else: - raise TypeError, 'type %s not supported' % type(ncfile) + raise TypeError('type %s not supported' % type(ncfile)) return MFnetCDF4.Dataset(files) - + MFDataset.__doc__ = __doc__ except: import pyroms.extern.pupynere import warnings - + warnings.warn('netCDF[3/4] not found -- using pupynere.') - + def Dataset(ncfile): if isinstance(ncfile, str): return pupynere.NetCDFFile(ncfile) elif isinstance(ncfile, pupynere.NetCDFFile): return ncfile else: - raise TypeError, 'type %s not supported' % type(ncfile) - + raise TypeError('type %s not supported' % type(ncfile)) + Dataset.__doc__ = __doc__ if __name__ == '__main__': pass - + diff --git a/pyroms/pyroms/remapping/__init__.py b/pyroms/pyroms/remapping/__init__.py index 80077f9..1836723 100644 --- a/pyroms/pyroms/remapping/__init__.py +++ b/pyroms/pyroms/remapping/__init__.py @@ -3,18 +3,18 @@ A set of tools for remapping ''' -from make_remap_grid_file import make_remap_grid_file -from compute_remap_weights import compute_remap_weights -from test_remap_weights import test_remap_weights -from remap import remap -from remap2 import remap2 +from .make_remap_grid_file import make_remap_grid_file +from .compute_remap_weights import compute_remap_weights +from .test_remap_weights import test_remap_weights +from .remap import remap +from .remap2 import remap2 try: import scrip except: - print 'scrip.so not found. Remapping function will not be available' -from roms2z import roms2z -from sta2z import sta2z -from z2roms import z2roms -from flood import flood -from flood2d import flood2d + print('scrip.so not found. Remapping function will not be available') +from .roms2z import roms2z +from .sta2z import sta2z +from .z2roms import z2roms +from .flood import flood +from .flood2d import flood2d diff --git a/pyroms/pyroms/remapping/flood.py b/pyroms/pyroms/remapping/flood.py index 4d9e066..1690620 100644 --- a/pyroms/pyroms/remapping/flood.py +++ b/pyroms/pyroms/remapping/flood.py @@ -11,12 +11,12 @@ def flood(varz, grdz, Cpos='rho', irange=None, jrange=None, \ var = flood(var, grdz) optional switch: - - Cpos='rho', 'u' or 'v' specify the C-grid position where - the variable rely + - Cpos='rho', 'u' or 'v' specify the C-grid position where + the variable rely - irange specify grid sub-sample for i direction - jrange specify grid sub-sample for j direction - spval=1e37 define spval value - - dmax=0 if dmax>0, maximum horizontal + - dmax=0 if dmax>0, maximum horizontal flooding distance - cdepth=0 critical depth for flooding if depth no flooding @@ -59,7 +59,7 @@ def flood(varz, grdz, Cpos='rho', irange=None, jrange=None, \ h = grdz.vgrid.h mask = grdz.hgrid.mask_rho else: - raise Warning, '%s bad position. Use depth at Arakawa-C rho points instead.' % Cpos + raise Warning('%s bad position. Use depth at Arakawa-C rho points instead.' % Cpos) nlev, Mm, Lm = varz.shape @@ -118,7 +118,7 @@ def flood(varz, grdz, Cpos='rho', irange=None, jrange=None, \ for i in range(Lm): for j in range(Mm): if mask[j,i] == 1: - varz[:bottom[j,i],j,i] = varz[bottom[j,i],j,i] - varz[surface[j,i]:,j,i] = varz[surface[j,i],j,i] + varz[:int(bottom[j,i]),j,i] = varz[int(bottom[j,i]),j,i] + varz[int(surface[j,i]):,j,i] = varz[int(surface[j,i]),j,i] return varz diff --git a/pyroms/pyroms/remapping/flood2d.py b/pyroms/pyroms/remapping/flood2d.py index a2b5671..80d2a72 100644 --- a/pyroms/pyroms/remapping/flood2d.py +++ b/pyroms/pyroms/remapping/flood2d.py @@ -3,20 +3,18 @@ import numpy as np import _remapping -import pyroms - def flood2d(varz, grdz, Cpos='rho', irange=None, jrange=None, \ spval=1e37, dmax=0, cdepth=0, kk=0): """ var = flood(var, grdz) optional switch: - - Cpos='rho', 'u' or 'v' specify the C-grid position where - the variable rely + - Cpos='rho', 'u' or 'v' specify the C-grid position where + the variable rely - irange specify grid sub-sample for i direction - jrange specify grid sub-sample for j direction - spval=1e37 define spval value - - dmax=0 if dmax>0, maximum horizontal + - dmax=0 if dmax>0, maximum horizontal flooding distance Flood varz on gridz """ @@ -51,7 +49,7 @@ def flood2d(varz, grdz, Cpos='rho', irange=None, jrange=None, \ z = grdz.vgrid.z[:] mask = grdz.hgrid.mask_rho else: - raise Warning, '%s bad position. Use depth at Arakawa-C rho points instead.' % Cpos + raise Warning('%s bad position. Use depth at Arakawa-C rho points instead.' % Cpos) Mm, Lm = varz.shape @@ -82,7 +80,7 @@ def flood2d(varz, grdz, Cpos='rho', irange=None, jrange=None, \ idxnan = np.where(c2 == True) idx = np.where(c2 == False) if list(idx[0]): -# print "inside test", len(idx[0]), len(idxnan[0]) +# print "inside test", len(idx[0]), len(idxnan[0]) wet = np.zeros((len(idx[0]),2)) dry = np.zeros((len(idxnan[0]),2)) wet[:,0] = idx[0]+1 diff --git a/pyroms/pyroms/remapping/make_remap_grid_file.py b/pyroms/pyroms/remapping/make_remap_grid_file.py index 76ccf19..001dfe6 100644 --- a/pyroms/pyroms/remapping/make_remap_grid_file.py +++ b/pyroms/pyroms/remapping/make_remap_grid_file.py @@ -45,17 +45,17 @@ def make_remap_grid_file(grid, Cpos='rho', irange=None, jrange=None): if Cpos == 'rho': if jrange != (0,Mp-1) or irange != (0,Lp-1): lon_corner = grd.hgrid.lon_vert[jrange[0]:jrange[1]+1, \ - irange[0]:irange[1]+1] + irange[0]:irange[1]+1] lat_corner = grd.hgrid.lat_vert[jrange[0]:jrange[1]+1, \ - irange[0]:irange[1]+1] + irange[0]:irange[1]+1] grid_center_lon = grd.hgrid.lon_rho[jrange[0]:jrange[1], \ - irange[0]:irange[1]].flatten() + irange[0]:irange[1]].flatten() grid_center_lat = grd.hgrid.lat_rho[jrange[0]:jrange[1], \ - irange[0]:irange[1]].flatten() + irange[0]:irange[1]].flatten() grid_imask = grd.hgrid.mask_rho[jrange[0]:jrange[1], \ - irange[0]:irange[1]].flatten() - Lp = irange[1] - irange[0] - Mp = jrange[1] - jrange[0] + irange[0]:irange[1]].flatten() + Lp = irange[1] - irange[0] + Mp = jrange[1] - jrange[0] else: lon_corner = grd.hgrid.lon_vert lat_corner = grd.hgrid.lat_vert @@ -66,20 +66,20 @@ def make_remap_grid_file(grid, Cpos='rho', irange=None, jrange=None): elif Cpos == 'u': if jrange != (0,Mp-1) or irange != (0,Lp-1): lon_corner = 0.5 * \ - (grd.hgrid.lon_vert[jrange[0]:jrange[1]+1,irange[0]:irange[1]] + \ + (grd.hgrid.lon_vert[jrange[0]:jrange[1]+1,irange[0]:irange[1]] + \ grd.hgrid.lon_vert[jrange[0]:jrange[1]+1,1+irange[0]:irange[1]+1]) lat_corner = 0.5 * \ - (grd.hgrid.lat_vert[jrange[0]:jrange[1]+1,irange[0]:irange[1]] + \ + (grd.hgrid.lat_vert[jrange[0]:jrange[1]+1,irange[0]:irange[1]] + \ grd.hgrid.lat_vert[jrange[0]:jrange[1]+1,1+irange[0]:irange[1]+1]) grid_center_lon = grd.hgrid.lon_u[jrange[0]:jrange[1], \ - irange[0]:irange[1]-1].flatten() + irange[0]:irange[1]-1].flatten() grid_center_lat = grd.hgrid.lat_u[jrange[0]:jrange[1], \ - irange[0]:irange[1]-1].flatten() + irange[0]:irange[1]-1].flatten() grid_imask = grd.hgrid.mask_u[jrange[0]:jrange[1], \ - irange[0]:irange[1]-1].flatten() - Lp = irange[1] - irange[0] - 1 - Mp = jrange[1] - jrange[0] - else: + irange[0]:irange[1]-1].flatten() + Lp = irange[1] - irange[0] - 1 + Mp = jrange[1] - jrange[0] + else: lon_corner = 0.5 * (grd.hgrid.lon_vert[:,:-1] + \ grd.hgrid.lon_vert[:,1:]) lat_corner = 0.5 * (grd.hgrid.lat_vert[:,:-1] + \ @@ -91,20 +91,20 @@ def make_remap_grid_file(grid, Cpos='rho', irange=None, jrange=None): elif Cpos == 'v': if jrange != (0,Mp-1) or irange != (0,Lp-1): lon_corner = 0.5 * \ - (grd.hgrid.lon_vert[jrange[0]:jrange[1],irange[0]:irange[1]+1] + \ + (grd.hgrid.lon_vert[jrange[0]:jrange[1],irange[0]:irange[1]+1] + \ grd.hgrid.lon_vert[1+jrange[0]:jrange[1]+1,irange[0]:irange[1]+1]) lat_corner = 0.5 * \ - (grd.hgrid.lat_vert[jrange[0]:jrange[1],irange[0]:irange[1]+1] + \ + (grd.hgrid.lat_vert[jrange[0]:jrange[1],irange[0]:irange[1]+1] + \ grd.hgrid.lat_vert[1+jrange[0]:jrange[1]+1,irange[0]:irange[1]+1]) grid_center_lon = grd.hgrid.lon_v[jrange[0]:jrange[1]-1, \ - irange[0]:irange[1]].flatten() + irange[0]:irange[1]].flatten() grid_center_lat = grd.hgrid.lat_v[jrange[0]:jrange[1]-1, \ - irange[0]:irange[1]].flatten() + irange[0]:irange[1]].flatten() grid_imask = grd.hgrid.mask_v[jrange[0]:jrange[1]-1, \ - irange[0]:irange[1]].flatten() - Lp = irange[1] - irange[0] - Mp = jrange[1] - jrange[0] - 1 - else: + irange[0]:irange[1]].flatten() + Lp = irange[1] - irange[0] + Mp = jrange[1] - jrange[0] - 1 + else: lon_corner = 0.5 * (grd.hgrid.lon_vert[:-1,:] + \ grd.hgrid.lon_vert[1:,:]) lat_corner = 0.5 * (grd.hgrid.lat_vert[:-1,:] + \ @@ -114,10 +114,10 @@ def make_remap_grid_file(grid, Cpos='rho', irange=None, jrange=None): grid_imask = grd.hgrid.mask_v.flatten() Mp, Lp = grd.hgrid.mask_v.shape else: - raise ValueError, 'Cpos must be rho, u or v' + raise ValueError('Cpos must be rho, u or v') grid_size = Lp * Mp - print 'grid shape', Mp, Lp + print('grid shape', Mp, Lp) grid_corner_lon = np.zeros((grid_size, 4)) grid_corner_lat = np.zeros((grid_size, 4)) diff --git a/pyroms/pyroms/remapping/remap.py b/pyroms/pyroms/remapping/remap.py index 734b5c8..a936055 100644 --- a/pyroms/pyroms/remapping/remap.py +++ b/pyroms/pyroms/remapping/remap.py @@ -40,14 +40,14 @@ def remap(src_array, remap_file, src_grad1=None, src_grad2=None, \ iorder = 1 if verbose is True: - print 'Reading remapping: ', title - print 'From file: ', remap_file - print ' ' - print 'Remapping between:' - print src_grid_name - print 'and' - print dst_grid_name - print 'Remapping method: ', map_method + print('Reading remapping: ', title) + print('From file: ', remap_file) + print(' ') + print('Remapping between:') + print(src_grid_name) + print('and') + print(dst_grid_name) + print('Remapping method: ', map_method) ndim = len(src_array.squeeze().shape) @@ -85,7 +85,7 @@ def remap(src_array, remap_file, src_grad1=None, src_grad2=None, \ tmp_src_grad1, tmp_src_grad2, \ tmp_src_grad3) else: - raise ValueError, 'Unknown method' + raise ValueError('Unknown method') # mask dst_array idx = np.where(dst_mask == 0) @@ -133,7 +133,7 @@ def remap(src_array, remap_file, src_grad1=None, src_grad2=None, \ tmp_src_grad1, tmp_src_grad2, \ tmp_src_grad3) else: - raise ValueError, 'Unknown method' + raise ValueError('Unknown method') # mask dst_array @@ -146,7 +146,7 @@ def remap(src_array, remap_file, src_grad1=None, src_grad2=None, \ dst_grid_dims[0])) else: - raise ValueError, 'src_array must have two or three dimensions' + raise ValueError('src_array must have two or three dimensions') # close data file diff --git a/pyroms/pyroms/remapping/remap2.py b/pyroms/pyroms/remapping/remap2.py index 38a08e1..953da18 100644 --- a/pyroms/pyroms/remapping/remap2.py +++ b/pyroms/pyroms/remapping/remap2.py @@ -40,17 +40,17 @@ def remap2(src_array, remap_file, src_grad1=None, src_grad2=None, \ iorder = 1 if verbose is True: - print 'Reading remapping: ', title - print 'From file: ', remap_file - print ' ' - print 'Remapping between:' - print src_grid_name - print 'and' - print dst_grid_name - print 'Remapping method: ', map_method + print('Reading remapping: ', title) + print('From file: ', remap_file) + print(' ') + print('Remapping between:') + print(src_grid_name) + print('and') + print(dst_grid_name) + print('Remapping method: ', map_method) ndim = len(src_array.squeeze().shape) - + if (ndim == 2): tmp_dst_array = np.zeros((dst_grid_size)) tmp_src_array = src_array.flatten() @@ -85,7 +85,7 @@ def remap2(src_array, remap_file, src_grad1=None, src_grad2=None, \ tmp_src_grad1, tmp_src_grad2, \ tmp_src_grad3) else: - raise ValueError, 'Unknown method' + raise ValueError('Unknown method') # mask dst_array idx = np.where(dst_mask == 0) @@ -95,7 +95,7 @@ def remap2(src_array, remap_file, src_grad1=None, src_grad2=None, \ # reshape # dst_array = np.reshape(tmp_dst_array, (dst_grid_dims[1], \ # dst_grid_dims[0])) - dst_array = tmp_dst_array + dst_array = tmp_dst_array elif (ndim == 3): @@ -134,7 +134,7 @@ def remap2(src_array, remap_file, src_grad1=None, src_grad2=None, \ tmp_src_grad1, tmp_src_grad2, \ tmp_src_grad3) else: - raise ValueError, 'Unknow method' + raise ValueError('Unknown method') # mask dst_array @@ -147,7 +147,7 @@ def remap2(src_array, remap_file, src_grad1=None, src_grad2=None, \ dst_grid_dims[0])) else: - raise ValueError, 'src_array must have two or three dimensions' + raise ValueError('src_array must have two or three dimensions') # close data file diff --git a/pyroms/pyroms/remapping/roms2z.py b/pyroms/pyroms/remapping/roms2z.py index a911f87..da6d38d 100644 --- a/pyroms/pyroms/remapping/roms2z.py +++ b/pyroms/pyroms/remapping/roms2z.py @@ -9,8 +9,8 @@ def roms2z(var, grd, grdz, Cpos='rho', irange=None, jrange=None, \ varz = roms2z(var, grd, grdz) optional switch: - - Cpos='rho', 'u' 'v' or 'w' specify the C-grid position where - the variable rely + - Cpos='rho', 'u' 'v' or 'w' specify the C-grid position where + the variable rely - irange specify grid sub-sample for i direction - jrange specify grid sub-sample for j direction - spval=1e37 define spval value @@ -29,7 +29,7 @@ def roms2z(var, grd, grdz, Cpos='rho', irange=None, jrange=None, \ imode=1 else: imode=0 - raise Warning, '%s not supported, defaulting to linear' % mode + raise Warning('%s not supported, defaulting to linear' % mode) if Cpos is 'rho': @@ -49,7 +49,7 @@ def roms2z(var, grd, grdz, Cpos='rho', irange=None, jrange=None, \ depth = grdz.vgrid.z mask = grd.hgrid.mask_rho else: - raise Warning, '%s unknown position. Cpos must be rho, u, v or w.' % Cpos + raise Warning('%s unknown position. Cpos must be rho, u, v or w.' % Cpos) Nm, Mm, Lm = var.shape nlev = grdz.vgrid.N @@ -82,5 +82,5 @@ def roms2z(var, grd, grdz, Cpos='rho', irange=None, jrange=None, \ idx = np.where(abs((varz-spval)/spval)<=1e-5) varz[idx] = spval #varz = np.ma.masked_values(varz, spval, rtol=1e-5) - + return varz diff --git a/pyroms/pyroms/remapping/sta2z.py b/pyroms/pyroms/remapping/sta2z.py index 451f8d4..3a94184 100644 --- a/pyroms/pyroms/remapping/sta2z.py +++ b/pyroms/pyroms/remapping/sta2z.py @@ -28,7 +28,7 @@ def sta2z(var, grd, grdz, Cpos='rho', srange=None, \ imode=1 else: imode=0 - raise Warning, '%s not supported, defaulting to linear' % mode + raise Warning('%s not supported, defaulting to linear' % mode) if Cpos is 'rho': z = grd.vgrid.z_r[0,:] @@ -37,7 +37,7 @@ def sta2z(var, grd, grdz, Cpos='rho', srange=None, \ z = grd.vgrid.z_w[0,:] depth = grdz.vgrid.z else: - raise Warning, '%s unknown position. Cpos must be rho or w.' % Cpos + raise Warning('%s unknown position. Cpos must be rho or w.' % Cpos) var = var.T Nm, Sm = var.shape diff --git a/pyroms/pyroms/remapping/z2roms.py b/pyroms/pyroms/remapping/z2roms.py index 2a72842..1a4f241 100644 --- a/pyroms/pyroms/remapping/z2roms.py +++ b/pyroms/pyroms/remapping/z2roms.py @@ -13,12 +13,12 @@ def z2roms(varz, grdz, grd, Cpos='rho', irange=None, jrange=None, \ var = z2roms(var, grdz, grd) optional switch: - - Cpos='rho', 'u' or 'v' specify the C-grid position where - the variable rely + - Cpos='rho', 'u' or 'v' specify the C-grid position where + the variable rely - irange specify grid sub-sample for i direction - jrange specify grid sub-sample for j direction - spval=1e37 define spval value - - dmax=0 if dmax>0, maximum horizontal + - dmax=0 if dmax>0, maximum horizontal flooding distance - cdepth=0 critical depth for flooding if depth no flooding @@ -37,7 +37,7 @@ def z2roms(varz, grdz, grd, Cpos='rho', irange=None, jrange=None, \ elif mode=='spline': imode=1 else: - raise Warning, '%s not supported, defaulting to linear' % mode + raise Warning('%s not supported, defaulting to linear' % mode) if Cpos is 'rho': z = grdz.vgrid.z[:] @@ -56,8 +56,8 @@ def z2roms(varz, grdz, grd, Cpos='rho', irange=None, jrange=None, \ depth = grd.vgrid.z_w[0,:] mask = grd.hgrid.mask_rho else: - raise Warning, '%s bad position. Use depth at Arakawa-C \ - rho points instead.' % Cpos + raise Warning('%s bad position. Use depth at Arakawa-C \ + rho points instead.' % Cpos) nlev, Mm, Lm = varz.shape Nm = depth.shape[0] @@ -84,7 +84,7 @@ def z2roms(varz, grdz, grd, Cpos='rho', irange=None, jrange=None, \ z = np.concatenate((-9999*np.ones((1,z.shape[1], z.shape[2])), \ z, \ 100*np.ones((1,z.shape[1], z.shape[2]))), 0) - + var = np.ma.zeros((Nm, Mm, Lm)) for k in range(Nm): @@ -96,5 +96,5 @@ def z2roms(varz, grdz, grd, Cpos='rho', irange=None, jrange=None, \ #mask var = np.ma.masked_values(var, spval, rtol=1e-5) #var[k,:,:] = np.ma.masked_where(mask == 0, var[k,:,:]) - + return var diff --git a/pyroms/pyroms/sandbox/googleearth.py b/pyroms/pyroms/sandbox/googleearth.py index 0103176..dfaac56 100644 --- a/pyroms/pyroms/sandbox/googleearth.py +++ b/pyroms/pyroms/sandbox/googleearth.py @@ -15,6 +15,7 @@ import pylab import zipfile import octant +import pyroms import os kml_preamble = ''' @@ -68,15 +69,15 @@ def kmz_anim(lon, lat, time, prop, **kwargs): lon = asarray(lon) lat = asarray(lat) - + jd = pylab.date2num(time) - jd_edges = hstack((1.5*jd[0]-0.5*jd[1], - 0.5*(jd[1:]+jd[:-1]), + jd_edges = hstack((1.5*jd[0]-0.5*jd[1], + 0.5*(jd[1:]+jd[:-1]), 1.5*jd[-1]-0.5*jd[-2])) time_edges = pylab.num2date(jd_edges) time_starts = time_edges[:-1] time_stops = time_edges[1:] - + name = kwargs.pop('name', 'overlay') color = kwargs.pop('color', '9effffff') visibility = str( kwargs.pop('visibility', 1) ) @@ -87,29 +88,29 @@ def kmz_anim(lon, lat, time, prop, **kwargs): kwargs['vmax'] = vmax vmin = kwargs.pop('vmin', prop.min()) kwargs['vmin'] = vmin - + geo_aspect = cos(lat.mean()*pi/180.0) xsize = lon.ptp()*geo_aspect ysize = lat.ptp() - + aspect = ysize/xsize if aspect > 1.0: figsize = (10.0/aspect, 10.0) else: figsize = (10.0, 10.0*aspect) - + kml_text = kml_preamble - + ioff() fig = figure(figsize=figsize, dpi=pixels//10, facecolor=None, frameon=False) ax = fig.add_axes([0, 0, 1, 1]) - + f = zipfile.ZipFile(kmzfile, 'w') - + for frame in range(prop.shape[0]): tstart = time_starts[frame] tstop = time_stops[frame] - print 'Writing frame ', frame, tstart.isoformat(), tstop.isoformat() + print('Writing frame ', frame, tstart.isoformat(), tstop.isoformat()) ax.cla() pc = ax.pcolor(lon, lat, prop[frame], **kwargs) ax.set_xlim(lon.min(), lon.max()) @@ -127,10 +128,10 @@ def kmz_anim(lon, lat, time, prop, **kwargs): .replace('__FRAME__', icon)\ .replace('__TIMEBEGIN__', tstart.isoformat())\ .replace('__TIMEEND__', tstop.isoformat()) - + f.write(icon) os.remove(icon) - + # legend fig = figure(figsize=(1.0, 4.0), facecolor=None, frameon=False) cax = fig.add_axes([0.0, 0.05, 0.2, 0.90]) @@ -138,13 +139,13 @@ def kmz_anim(lon, lat, time, prop, **kwargs): cb.set_label(units, color='0.9') for lab in cb.ax.get_yticklabels(): setp(lab, 'color', '0.9') - + savefig('legend.png') f.write('legend.png') os.remove('legend.png') - + kml_text += kml_legend - + kml_text += kml_closing f.writestr('overlay.kml', kml_text) f.close() @@ -153,21 +154,21 @@ def kmz_anim(lon, lat, time, prop, **kwargs): if __name__ == '__main__': ncll = octant.io.Dataset('/Users/rob/Archive/GWB/bodden/latlon.nc') nc = octant.io.Dataset('/Users/rob/Archive/GWB/bodden/bsh_elev_2001-10.nc') - + lat = ncll.variables['lat'][:] lon = ncll.variables['lon'][:] - + lon, lat = meshgrid(lon, lat) - + time = octant.ocean_time(nc, name='time')[:200:4] - + propname = 'elev' - + prop = nc.variables[propname][:200:4] mask = prop == nc.variables[propname].missing_value prop = ma.masked_where(mask, prop) - - kmz_anim(lon, lat, time.dates, prop, kmzfile='bsh_anim.kmz', + + kmz_anim(lon, lat, time.dates, prop, kmzfile='bsh_anim.kmz', name='BSH model -- sea surface height', units='sea surface height [m]') @@ -207,7 +208,7 @@ def kmz_anim(lon, lat, time, prop, **kwargs): def geo_pcolor(lon, lat, prop, **kwargs): """docstring for geo_pcolor""" - + name = kwargs.pop('name', 'overlay') color = kwargs.pop('color', '9effffff') visibility = str( kwargs.pop('visibility', 1) ) @@ -218,17 +219,17 @@ def geo_pcolor(lon, lat, prop, **kwargs): kwargs['vmax'] = vmax vmin = kwargs.pop('vmin', prop.min()) kwargs['vmin'] = vmin - + geo_aspect = cos(lat.mean()*pi/180.0) xsize = lon.ptp()*geo_aspect ysize = lat.ptp() - + aspect = ysize/xsize if aspect > 1.0: figsize = (10.0/aspect, 10.0) else: figsize = (10.0, 10.0*aspect) - + ioff() fig = figure(figsize=figsize, facecolor=None, frameon=False, dpi=pixels//10) ax = fig.add_axes([0, 0, 1, 1]) @@ -237,7 +238,7 @@ def geo_pcolor(lon, lat, prop, **kwargs): ax.set_ylim(lat.min(), lat.max()) ax.set_axis_off() savefig('overlay.png') - + f = zipfile.ZipFile(kmzfile, 'w') f.writestr('overlay.kml', kml_groundoverlay.replace('__NAME__', name)\ .replace('__COLOR__', color)\ @@ -248,35 +249,35 @@ def geo_pcolor(lon, lat, prop, **kwargs): .replace('__WEST__', str(lon.min()))) f.write('overlay.png') os.remove('overlay.png') - + fig = figure(figsize=(1.0, 4.0), facecolor=None, frameon=False) ax = fig.add_axes([0.0, 0.05, 0.2, 0.9]) cb = colorbar(pc, cax=ax) cb.set_label(units, color='0.9') for lab in cb.ax.get_yticklabels(): setp(lab, 'color', '0.9') - + savefig('legend.png') f.write('legend.png') - os.remove('legend.png') + os.remove('legend.png') f.close() if __name__ == '__main__': ncll = pyroms.Dataset('/Users/rob/Archive/GWB/bodden/latlon.nc') nc = pyroms.Dataset('/Users/rob/Archive/GWB/bodden/bsh_elev_2001-10.nc') - + lat = ncll.variables['lat'][:] lon = ncll.variables['lon'][:] - + lon, lat = meshgrid(lon, lat) - + propname = 'elev' - + prop = nc.variables[propname][-1] mask = prop == nc.variables[propname].missing_value prop = ma.masked_where(mask, prop) - + geo_pcolor(lon, lat, prop, kmzfile='bsh.kmz', \ name='BSH model -- sea surface height',\ units='sea surface height [m]') diff --git a/pyroms/pyroms/sandbox/sea_level.py b/pyroms/pyroms/sandbox/sea_level.py index b346b19..e3c385b 100644 --- a/pyroms/pyroms/sandbox/sea_level.py +++ b/pyroms/pyroms/sandbox/sea_level.py @@ -2,7 +2,7 @@ # sample url #http://tidesandcurrents.noaa.gov/data_listing.shtml?bdate=20080323&edate=20080423&datum=6&unit=0&shift=g&stn=8762075&type=Tide%20Data&format=View+Data&listing=1 -import urllib2 +import urllib.request, urllib.error, urllib.parse from datetime import datetime import numpy as np @@ -28,8 +28,8 @@ def __init__(self, station_id, start_date, end_date=None): self.data_dict['stn'] = str(station_id) url = self.root + '&'.join([ '='.join(keyval) for (keyval) in - self.data_dict.iteritems()]) - lines = urllib2.urlopen(url).readlines() + self.data_dict.items()]) + lines = urllib.request.urlopen(url).readlines() pr = False date = [] @@ -54,6 +54,6 @@ def __init__(self, station_id, start_date, end_date=None): sl = sea_level('8762075', 'foo') -print sl.date -print sl.ssh +print(sl.date) +print(sl.ssh) \ No newline at end of file diff --git a/pyroms/pyroms/setup.py b/pyroms/pyroms/setup.py index aab68fc..d0ea53e 100644 --- a/pyroms/pyroms/setup.py +++ b/pyroms/pyroms/setup.py @@ -33,14 +33,14 @@ get_ROMS_hgrid get_ROMS_vgrid get_ROMS_grid - write_ROMS_grid + write_ROMS_grid io - wrapper for netCDF4 Dataset MFDataset cf - CF compliant files tools - time + time tools - Tools specific to the Regional Ocean Modeling System roms2z @@ -55,7 +55,7 @@ latslice section_transport - utility - Some basic tools + utility - Some basic tools get_lonlat get_ij roms_varlist @@ -95,14 +95,12 @@ version = '0.1.0', description = doclines[0], long_description = "\n".join(doclines[2:]), - author = "Frederic Castruccio", - author_email = "frederic@marine.rutgers.edu", - url = "ftp://marine.rutgers.edu/pub/frederic/pyroms/", + url = "https://github.com/ESMG/pyroms", packages = ['pyroms', 'pyroms.remapping', 'pyroms.extern'], license = 'BSD', platforms = ["any"], ext_modules = [iso,interp,remapping], - classifiers = filter(None, classifiers.split("\n")), + classifiers = [_f for _f in classifiers.split("\n") if _f], ) diff --git a/pyroms/pyroms/src/interp.f b/pyroms/pyroms/src/interp.f index b80277a..fbd7c79 100644 --- a/pyroms/pyroms/src/interp.f +++ b/pyroms/pyroms/src/interp.f @@ -3,7 +3,6 @@ ! SUBROUTINE xhslice (f2d,f3d,z,depth,mask,im,jm,km,vintrp,spval) ! -!svn $Id: xhslice.F 159 2008-03-05 18:02:32Z arango $ !================================================== Hernan G. Arango === ! Copyright (c) 2002-2008 The ROMS/TOMS Group ! ! Licensed under a MIT/X style license ! @@ -86,7 +85,9 @@ SUBROUTINE xhslice (f2d,f3d,z,depth,mask,im,jm,km,vintrp,spval) real*8 f3d(km,jm,im), z(km,jm,im) real*8 depth(jm,im), mask(jm,im) real*8 f2d(jm,im) -cf2py intent(out) f2d +!f2py intent(out) f2d +!f2py intent(hide) im +!f2py intent(hide) jm real*8 fk(NK), zk(NK), wk(NK) parameter (der1=c1ep30,derkm=c1ep30) ! @@ -140,7 +141,6 @@ SUBROUTINE xhslice (f2d,f3d,z,depth,mask,im,jm,km,vintrp,spval) ! SUBROUTINE lintrp (n,x,y,ni,xi,yi) ! -!svn $Id: lintrp.F 159 2008-03-05 18:02:32Z arango $ !================================================== Hernan G. Arango === ! Copyright (c) 2002-2008 The ROMS/TOMS Group ! ! Licensed under a MIT/X style license ! @@ -162,6 +162,9 @@ SUBROUTINE lintrp (n,x,y,ni,xi,yi) integer i, ii, j, n, ni real*8 d1, d2 real*8 x(n), y(n), xi(ni), yi(ni) +!f2py intent(out) yi +!f2py intent(hide) n +!f2py intent(hide) ni ! !----------------------------------------------------------------------- ! Begin executable code. @@ -195,7 +198,6 @@ SUBROUTINE lintrp (n,x,y,ni,xi,yi) ! SUBROUTINE spline (x,y,n,yp1,ypn,y2) ! -!svn $Id: spline.F 159 2008-03-05 18:02:32Z arango $ !================================================== Hernan G. Arango === ! Copyright (c) 2002-2008 The ROMS/TOMS Group ! ! Licensed under a MIT/X style license ! @@ -268,6 +270,8 @@ SUBROUTINE spline (x,y,n,yp1,ypn,y2) parameter (nmax=10000) real*8 p, qn, sig, un, ypn, yp1 real*8 x(n), y(n), y2(n), u(nmax) +!f2py intent(out) :: y2 +!f2py intent(hide) :: n ! !----------------------------------------------------------------------- ! Begin excutable code. @@ -329,7 +333,6 @@ SUBROUTINE spline (x,y,n,yp1,ypn,y2) ! SUBROUTINE splint (x,y,y2,n,xx,yy,dydx) ! -!svn $Id: splint.F 159 2008-03-05 18:02:32Z arango $ !================================================== Hernan G. Arango === ! Copyright (c) 2002-2008 The ROMS/TOMS Group ! ! Licensed under a MIT/X style license ! @@ -400,6 +403,8 @@ SUBROUTINE splint (x,y,y2,n,xx,yy,dydx) integer k, khi, klo, n real*8 a, b, c, d, dydx, e, f, h, xx, yy real*8 x(n), y(n), y2(n) +!f2py intent(out) :: yy +!f2py intent(hide) :: n ! !----------------------------------------------------------------------- ! Begin executable code. @@ -454,7 +459,9 @@ SUBROUTINE get_bottom (bottom,var,mask,im,jm,km,spval) real*8 spval, bot real*8 var(km,jm,im) real*8 mask(jm,im), bottom(jm,im) -cf2py intent(out) bottom +!f2py intent(out) bottom +!f2py intent(hide) :: jm +!f2py intent(hide) :: im DO j=1,jm DO i=1,im @@ -490,7 +497,9 @@ SUBROUTINE get_surface (surface,var,mask,im,jm,km,spval) real*8 spval, surf real*8 var(km,jm,im) real*8 mask(jm,im), surface(jm,im) -cf2py intent(out) surface +!f2py intent(out) surface +!f2py intent(hide) :: jm +!f2py intent(hide) :: im DO j=1,jm DO i=1,im diff --git a/pyroms/pyroms/src/iso.f b/pyroms/pyroms/src/iso.f index 4a045d5..a5a515f 100644 --- a/pyroms/pyroms/src/iso.f +++ b/pyroms/pyroms/src/iso.f @@ -1,8 +1,8 @@ -ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc -c SUBROUTINE INTEGRATE -ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc +!cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc +! SUBROUTINE INTEGRATE +!cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc subroutine integrate(z_w,q,z_iso,iqu,iql,L,M,N) - + implicit none integer L, M, N real*8 z_w(N+1,M,L) @@ -10,12 +10,15 @@ subroutine integrate(z_w,q,z_iso,iqu,iql,L,M,N) real*8 q(N,M,L) real*8 iqu(M,L) real*8 iql(M,L) -cf2py intent(out) iqu -cf2py intent(out) iql +!f2py intent(out) iqu +!f2py intent(out) iql +!f2py intent(hide) :: L +!f2py intent(hide) :: M +!f2py intent(hide) :: N integer i, j, k real*8 dz(N) real*8 dzp - + do i=1,L do j=1,M do k=1,N @@ -37,27 +40,30 @@ subroutine integrate(z_w,q,z_iso,iqu,iql,L,M,N) enddo enddo enddo - + return end -ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc -c SUBROUTINE SURFACE -ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc +!cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc +! SUBROUTINE SURFACE +!cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc subroutine surface(z, q, q0, z_iso, L, M, N) -c Assume q is sorted - +! Assume q is sorted + implicit none integer L, M, N real*8 z(N,M,L) real*8 q(N,M,L) real*8 q0(M,L) real*8 z_iso(M,L) -cf2py intent(out) z_iso +!f2py intent(out) z_iso +!f2py intent(hide) :: L +!f2py intent(hide) :: M +!f2py intent(hide) :: N integer i, j, k real*8 dz, dq, dq0 - + do i=1,L do j=1,M z_iso(j,i)=1.0d20 ! default value - isoline not in profile @@ -72,26 +78,29 @@ subroutine surface(z, q, q0, z_iso, L, M, N) enddo enddo enddo - + return end -cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc -c SUBROUTINE ZSLICE -cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc +!ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc +! SUBROUTINE ZSLICE +!ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc subroutine zslice (z,f3d,depths,f2d,vinterp,L,M,N) - + implicit none integer L, M, N, vinterp real*8 depths(M,L) real*8 f3d(N,M,L), z(N,M,L) real*8 f2d(M,L) -cf2py intent(out) f2d +!f2py intent(out) f2d +!f2py intent(hide) :: L +!f2py intent(hide) :: M +!f2py intent(hide) :: N integer i, j, k real*8 zk(N), fk(N) real*8 wk(N), dfdz(N) - -c Linear Interpolation. + +! Linear Interpolation. if (vinterp.eq.0) then do i=1,L do j=1,M @@ -106,7 +115,7 @@ subroutine zslice (z,f3d,depths,f2d,vinterp,L,M,N) endif enddo enddo -c Cubic spline interpolation. +! Cubic spline interpolation. else if (vinterp.eq.1) then do i=1,L do j=1,M @@ -123,39 +132,42 @@ subroutine zslice (z,f3d,depths,f2d,vinterp,L,M,N) enddo enddo endif - + return end - - - - + + + + subroutine lintrp (n,x,y,ni,xi,yi) -c -c======================================================================= -c Copyright (c) 1996 Rutgers University === -c======================================================================= -c === -c Given arrays X and Y of length N, which tabulate a function, === -c Y = F(X), with the Xs in ascending order, and given array === -c XI of lenght NI, this routine returns a linear interpolated === -c array YI. === -c === -c======================================================================= -c -c----------------------------------------------------------------------- -c Define local variable. -c----------------------------------------------------------------------- -c +! +!======================================================================= +! Copyright (c) 1996 Rutgers University === +!======================================================================= +! === +! Given arrays X and Y of length N, which tabulate a function, === +! Y = F(X), with the Xs in ascending order, and given array === +! XI of lenght NI, this routine returns a linear interpolated === +! array YI. === +! === +!======================================================================= +! +!----------------------------------------------------------------------- +! Define local variable. +!----------------------------------------------------------------------- +! implicit none integer i, ii, j, n, ni real*8 d1, d2 real*8 x(n), y(n), xi(ni), yi(ni) -c -c----------------------------------------------------------------------- -c Begin executable code. -c----------------------------------------------------------------------- -c +!f2py intent(out) yi +!f2py intent(hide) n +!f2py intent(hide) ni +! +!----------------------------------------------------------------------- +! Begin executable code. +!----------------------------------------------------------------------- +! do 30 j=1,ni if (xi(j).le.x(1)) then ii=1 @@ -179,41 +191,41 @@ subroutine lintrp (n,x,y,ni,xi,yi) subroutine spline (x,y,n,yp1,ypn,y2) -c -c======================================================================= -c Copyright (c) 1996 Rutgers University === -c======================================================================= -c === -c Given X, Y of length N containing a tabulated function, Y=f(X), === -c with the Xs in ascending order, and given values Yp1 and Ypn === -c for the first derivative of the interpolating function at points === -c 1 and N, respectively this routine returns an array Y2 of length === -c N which contains the second derivatives of the interpolating === -c function at the tabulated points X. If Yp1 and/or Ypn are equal === -c to 1.0E+30 or larger, the routine is signalled to set the === -c corresponding boundary condition for a natural spline, with zero === -c second derivative on that boundary. === -c === -c Reference : === -c === -c Press, W.H, B.P. Flannery, S.A. Teukolsky, and W.T. Vetterling, === -c 1986: Numerical Recipes, the art of scientific computing. === -c Cambridge University Press. === -c === -c======================================================================= -c -c----------------------------------------------------------------------- -c Define global data. -c----------------------------------------------------------------------- -c - real*8 cm1,cm3,c0,c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,c11,c20,c25,c50, +! +!======================================================================= +! Copyright (c) 1996 Rutgers University === +!======================================================================= +! === +! Given X, Y of length N containing a tabulated function, Y=f(X), === +! with the Xs in ascending order, and given values Yp1 and Ypn === +! for the first derivative of the interpolating function at points === +! 1 and N, respectively this routine returns an array Y2 of length === +! N which contains the second derivatives of the interpolating === +! function at the tabulated points X. If Yp1 and/or Ypn are equal === +! to 1.0E+30 or larger, the routine is signalled to set the === +! corresponding boundary condition for a natural spline, with zero === +! second derivative on that boundary. === +! === +! Reference : === +! === +! Press, W.H, B.P. Flannery, S.A. Teukolsky, and W.T. Vetterling, === +! 1986: Numerical Recipes, the art of scientific computing. === +! Cambridge University Press. === +! === +!======================================================================= +! +!----------------------------------------------------------------------- +! Define global data. +!----------------------------------------------------------------------- +! + real*8 cm1,cm3,c0,c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,c11,c20,c25,c50, & c90,c100,c180,c200,c255,c300,c360,c366,c500,c1000,c5000, & c10000,c1em9,c1em10,c1em12,c1em20,c1ep30,p006,p009,p035, & p015,p012,p08,p06,p5,p25,p75,p98,r3,r10,r20,r33,r35,r40, & r50,r80,r100,r200,r250,r400,r1000 real*8 day2sec,deg2rad,grav,cm2m,m2cm,m2km,pi,rad2deg,re,root2, & sec2day,spval0,spval1,spval2,spvgeo -c +! parameter (cm1=-1.0,cm3=-3.0,c0=0.0,c1=1.0,c2=2.0,c3=3.0,c4=4.0, & c5=5.0,c6=6.0,c7=7.0,c8=8.0,c9=9.0,c10=10,c11=11.0, & c20=20.0,c25=25.0,c50=50.0,c90=90.0,c100=100.0, @@ -233,30 +245,32 @@ subroutine spline (x,y,n,yp1,ypn,y2) & spval2=0.99e+30) parameter (deg2rad=pi/c180,rad2deg=c180/pi) -c -c----------------------------------------------------------------------- -c Define local data. Change NMAX as desired to be the largest -c anticipated value of N. -c----------------------------------------------------------------------- -c +! +!----------------------------------------------------------------------- +! Define local data. Change NMAX as desired to be the largest +! anticipated value of N. +!----------------------------------------------------------------------- +! integer i, k, n, nmax parameter (nmax=10000) real*8 p, qn, sig, un, ypn, yp1 real*8 x(n), y(n), y2(n), u(nmax) -c -c----------------------------------------------------------------------- -c Begin excutable code. -c----------------------------------------------------------------------- -c +!f2py intent(out) :: y2 +!f2py intent(hide) :: n +! +!----------------------------------------------------------------------- +! Begin excutable code. +!----------------------------------------------------------------------- +! if (n.gt.nmax) then print 10, n,nmax 10 format(/' SPLINE: underdimensioned array, N, NMAX = ',2i5) call crash ('SPLINE',1) endif -c -c The lower boundary condition is set either to be "natural" or else -c to have a specified first derivative. -c +! +! The lower boundary condition is set either to be "natural" or else +! to have a specified first derivative. +! if (yp1.gt.spval2) then y2(1)=c0 u(1)=c0 @@ -264,10 +278,10 @@ subroutine spline (x,y,n,yp1,ypn,y2) y2(1)=-p5 u(1)=(c3/(x(2)-x(1)))*((y(2)-y(1))/(x(2)-x(1))-yp1) endif -c -c This is the decomposition loop of the tridiagonal algorithm. Y2 and -c U are used for temporary storage of the decomposition factors. -c +! +! This is the decomposition loop of the tridiagonal algorithm. Y2 and +! U are used for temporary storage of the decomposition factors. +! do i=2,n-1 sig=(x(i)-x(i-1))/(x(i+1)-x(i-1)) p=sig*y2(i-1)+c2 @@ -276,10 +290,10 @@ subroutine spline (x,y,n,yp1,ypn,y2) & (y(i)-y(i-1))/(x(i)-x(i-1)))/ & (x(i+1)-x(i-1))-sig*u(i-1))/p enddo -c -c The upper boundary condition is set either to be "natural" or else -c to have a specified first derivative. -c +! +! The upper boundary condition is set either to be "natural" or else +! to have a specified first derivative. +! if (ypn.gt.spval2) then qn=c0 un=c0 @@ -288,9 +302,9 @@ subroutine spline (x,y,n,yp1,ypn,y2) un=(c3/(x(n)-x(n-1)))*(ypn-(y(n)-y(n-1))/(x(n)-x(n-1))) endif y2(n)=(un-qn*u(n-1))/(qn*y2(n-1)+c1) -c -c This is the back-substitution loop of the tridiagonal algorithm. -c +! +! This is the back-substitution loop of the tridiagonal algorithm. +! do k=n-1,1,-1 y2(k)=y2(k)*y2(k+1)+u(k) enddo @@ -298,33 +312,33 @@ subroutine spline (x,y,n,yp1,ypn,y2) end subroutine splint (x,y,y2,n,xx,yy,dydx) -c -c======================================================================= -c Copyright (c) 1996 Rutgers University === -c======================================================================= -c === -c Given arrays X and Y of length N, which tabulate a function, === -c Y=f(X), with the Xs in ascending order, and given the array === -c Y2 which contains the second derivative of the interpolating === -c function at the tabulated points X as computed by routine === -c SPLINE, and given a value XX, this routine returns a cubic- === -c spline interpolated value YY. === -c === -c Reference : === -c === -c Press, W.H, B.P. Flannery, S.A. Teukolsky, and W.T. Vetterling, === -c 1986: Numerical Recipes, the art of scientific computing. === -c Cambridge University Press. === -c === -c Modified by H.G. Arango (1989) to output the first derivative === -c DYDX at a given value XX. === -c === -c======================================================================= -c -c----------------------------------------------------------------------- -c Define global data. -c----------------------------------------------------------------------- -c +! +!======================================================================= +! Copyright (c) 1996 Rutgers University === +!======================================================================= +! === +! Given arrays X and Y of length N, which tabulate a function, === +! Y=f(X), with the Xs in ascending order, and given the array === +! Y2 which contains the second derivative of the interpolating === +! function at the tabulated points X as computed by routine === +! SPLINE, and given a value XX, this routine returns a cubic- === +! spline interpolated value YY. === +! === +! Reference : === +! === +! Press, W.H, B.P. Flannery, S.A. Teukolsky, and W.T. Vetterling, === +! 1986: Numerical Recipes, the art of scientific computing. === +! Cambridge University Press. === +! === +! Modified by H.G. Arango (1989) to output the first derivative === +! DYDX at a given value XX. === +! === +!======================================================================= +! +!----------------------------------------------------------------------- +! Define global data. +!----------------------------------------------------------------------- +! implicit none real*8 cm1,cm3,c0,c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,c11,c20,c25,c50, & c90,c100,c180,c200,c255,c300,c360,c366,c500,c1000,c5000, @@ -333,7 +347,7 @@ subroutine splint (x,y,y2,n,xx,yy,dydx) & r50,r80,r100,r200,r250,r400,r1000 real*8 day2sec,deg2rad,grav,cm2m,m2cm,m2km,pi,rad2deg,re,root2, & sec2day,spval0,spval1,spval2,spvgeo -c +! parameter (cm1=-1.0,cm3=-3.0,c0=0.0,c1=1.0,c2=2.0,c3=3.0,c4=4.0, & c5=5.0,c6=6.0,c7=7.0,c8=8.0,c9=9.0,c10=10,c11=11.0, & c20=20.0,c25=25.0,c50=50.0,c90=90.0,c100=100.0, @@ -353,21 +367,23 @@ subroutine splint (x,y,y2,n,xx,yy,dydx) & spval2=0.99e+30) parameter (deg2rad=pi/c180,rad2deg=c180/pi) -c -c----------------------------------------------------------------------- -c Define local data. -c----------------------------------------------------------------------- -c +! +!----------------------------------------------------------------------- +! Define local data. +!----------------------------------------------------------------------- +! integer k, khi, klo, n real*8 a, b, c, d, dydx, e, f, h, xx, yy real*8 x(n), y(n), y2(n) -c -c----------------------------------------------------------------------- -c Begin executable code. -c----------------------------------------------------------------------- -c -c Found the right place of XX in the table by means of bisection. -c +!f2py intent(out) :: yy +!f2py intent(hide) :: n +! +!----------------------------------------------------------------------- +! Begin executable code. +!----------------------------------------------------------------------- +! +! Found the right place of XX in the table by means of bisection. +! klo=1 khi=n 10 if ((khi-klo).gt.1) then @@ -379,17 +395,17 @@ subroutine splint (x,y,y2,n,xx,yy,dydx) endif goto 10 endif -c -c KLO and KHI now bracket the input value XX. -c +! +! KLO and KHI now bracket the input value XX. +! h=x(khi)-x(klo) if (h.eq.c0) then print *, ' SPLINT: bad X input, they must be distinct.' call crash ('SPLINT',1) endif -c -c Evaluate cubic spline polynomial. -c +! +! Evaluate cubic spline polynomial. +! a=(x(khi)-xx)/h b=(xx-x(klo))/h c=(a*a*a-a)*(h*h)/c6 @@ -400,7 +416,7 @@ subroutine splint (x,y,y2,n,xx,yy,dydx) dydx=(y(khi)-y(klo))/h-e*y2(klo)+f*y2(khi) return end - + subroutine crash (string,ierr) integer ierr character*(*) string diff --git a/pyroms/pyroms/sta_grid.py b/pyroms/pyroms/sta_grid.py index 7a0e6dd..327ea7c 100644 --- a/pyroms/pyroms/sta_grid.py +++ b/pyroms/pyroms/sta_grid.py @@ -47,20 +47,20 @@ def get_Stations_hgrid(gridid, sta_file): #Get horizontal grid if ((spherical == 0) or (spherical == 'F')): #cartesian grid - print 'Load cartesian grid from file' - if 'x_rho' in nc.variables.keys() and 'y_rho' in nc.variables.keys(): + print('Load cartesian grid from file') + if 'x_rho' in list(nc.variables.keys()) and 'y_rho' in list(nc.variables.keys()): x_rho = nc.variables['x_rho'][:] y_rho = nc.variables['y_rho'][:] try: angle = nc.variables['angle'][:] except: angle = np.zeros(x_rho.shape) else: - raise ValueError, 'NetCDF file must contain x_rho and y_rho \ - and possibly angle for a cartesian grid' + raise ValueError('NetCDF file must contain x_rho and y_rho \ + and possibly angle for a cartesian grid') x_rho = nc.variables['x_rho'][:] y_rho = nc.variables['y_rho'][:] - if 'angle' in nc.variables.keys(): + if 'angle' in list(nc.variables.keys()): angle = nc.variables['angle'][:] else: angle = None @@ -70,19 +70,19 @@ def get_Stations_hgrid(gridid, sta_file): else: #geographical grid - print 'Load geographical grid from file' + print('Load geographical grid from file') proj = Basemap(projection='merc', resolution=None, lat_0=0, lon_0=0) - if 'lon_rho' in nc.variables.keys() and 'lat_rho' in nc.variables.keys(): + if 'lon_rho' in list(nc.variables.keys()) and 'lat_rho' in list(nc.variables.keys()): lon_rho = nc.variables['lon_rho'][:] lat_rho = nc.variables['lat_rho'][:] else: - raise ValueError, 'NetCDF file must contain lon_rho and lat_rho \ - for a geographical grid' + raise ValueError('NetCDF file must contain lon_rho and lat_rho \ + for a geographical grid') lon_rho = nc.variables['lon_rho'][:] lat_rho = nc.variables['lat_rho'][:] - if 'angle' in nc.variables.keys(): + if 'angle' in list(nc.variables.keys()): angle = nc.variables['angle'][:] else: angle = None @@ -156,7 +156,7 @@ def write_nc_var(var, name, dimensions, long_name=None, units=None): if units is not None: nc.variables[name].units = units nc.variables[name][:] = var - print ' ... wrote ', name + print(' ... wrote ', name) if hasattr(grd.vgrid, 's_rho') is True and grd.vgrid.s_rho is not None: write_nc_var(grd.vgrid.theta_s, 'theta_s', (), 'S-coordinate surface control parameter') @@ -179,7 +179,7 @@ def write_nc_var(var, name, dimensions, long_name=None, units=None): nc.createVariable('spherical', 'c') nc.variables['spherical'].long_name = 'Grid type logical switch' nc.variables['spherical'][:] = grd.hgrid.spherical - print ' ... wrote ', 'spherical' + print(' ... wrote ', 'spherical') write_nc_var(grd.hgrid.angle_rho, 'angle', ('station'), 'angle between XI-axis and EAST', 'radians') diff --git a/pyroms/pyroms/sta_hgrid.py b/pyroms/pyroms/sta_hgrid.py index 8e84d83..b8e1b3a 100644 --- a/pyroms/pyroms/sta_hgrid.py +++ b/pyroms/pyroms/sta_hgrid.py @@ -5,7 +5,7 @@ import os import sys import ctypes -import cPickle +import pickle from warnings import warn from copy import deepcopy @@ -18,38 +18,38 @@ class Sta_CGrid(object): """ Stations Grid - + EXAMPLES: -------- - + >>> x = arange(8) >>> y = arange(8)*2-1 >>> grd = pyroms.grid.StaGrid(x, y) >>> print grd.x_rho [4.5 4.5 4.5 4.5 4.5 4.5 4.5] """ - + def __init__(self, x_rho, y_rho, angle_rho=None): - + assert np.ndim(x_rho)==1 and np.ndim(y_rho)==1 and \ - np.shape(x_rho)==np.shape(y_rho), \ + np.shape(x_rho)==np.shape(y_rho), \ 'x and y must be 2D arrays of the same size.' - + if np.any(np.isnan(x_rho)) or np.any(np.isnan(y_rho)): x_rho = np.ma.masked_where( (isnan(x_rho)) | (isnan(y_rho)) , x_rho) y_rho = np.ma.masked_where( (isnan(x_rho)) | (isnan(y_rho)) , y_rho) - + self.x_rho = x_rho self.y_rho = y_rho self.spherical = 'F' - + if angle_rho is None: self.angle_rho = np.zeros(len(self.y_rho)) else: self.angle_rho = angle_rho - + x = property(lambda self: self.x_rho, None, None, 'Return x_rho') y = property(lambda self: self.y_rho, None, None, 'Return y_rho') @@ -57,11 +57,11 @@ def __init__(self, x_rho, y_rho, angle_rho=None): class Sta_CGrid_geo(Sta_CGrid): """ Curvilinear Arakawa C-grid defined in geographic coordinates - + For a geographic grid, a projection may be specified, or The default projection for will be defined by the matplotlib.toolkits.Basemap projection: - + proj = Basemap(projection='merc', resolution=None, lat_ts=0.0) """ diff --git a/pyroms/pyroms/tools.py b/pyroms/pyroms/tools.py index a468015..69153f8 100644 --- a/pyroms/pyroms/tools.py +++ b/pyroms/pyroms/tools.py @@ -13,7 +13,7 @@ def zslice(var, depth, grd, Cpos='rho', vert=False, mode='linear'): optional switch: - Cpos='rho', 'u', 'v' or 'w' specify the C-grid position where - the variable rely + the variable rely - vert=True/False If True, return the position of the verticies - mode='linear' or 'spline' specify the type of interpolation @@ -30,7 +30,7 @@ def zslice(var, depth, grd, Cpos='rho', vert=False, mode='linear'): imode=1 else: imode=0 - raise Warning, '%s not supported, defaulting to linear' % mode + raise Warning('%s not supported, defaulting to linear' % mode) # compute the depth on Arakawa-C grid position @@ -111,8 +111,8 @@ def zslice(var, depth, grd, Cpos='rho', vert=False, mode='linear'): mask = grd.hgrid.mask_rho[:] else: - raise Warning, '%s bad position. Valid Arakawa-C are \ - rho, u or v.' % Cpos + raise Warning('%s bad position. Valid Arakawa-C are \ + rho, u or v.' % Cpos) assert len(z.shape) == 3, 'z must be 3D' assert len(var.shape) == 3, 'var must be 3D' @@ -136,8 +136,8 @@ def sslice(var, sindex, grd, Cpos='rho', vert=False): sslice, lon, lat = sslice(var, sindex, grd) optional switch: - - Cpos='rho', 'u' or 'v' specify the C-grid position where - the variable rely + - Cpos='rho', 'u' or 'v' specify the C-grid position where + the variable rely - vert=True/False If True, return the position of the verticies - mode='linear' or 'spline' specify the type of interpolation @@ -226,8 +226,8 @@ def sslice(var, sindex, grd, Cpos='rho', vert=False): mask = grd.hgrid.mask_rho[:] else: - raise Warning, '%s bad position. Valid Arakawa-C are \ - rho, u or v.' % Cpos + raise Warning('%s bad position. Valid Arakawa-C are \ + rho, u or v.' % Cpos) assert len(var.shape) == 3, 'var must be 3D' @@ -246,7 +246,7 @@ def islice(var, iindex, grd, Cpos='rho', vert=False): optional switch: - Cpos='rho', 'u', 'v' or 'w' specify the C-grid position where - the variable rely + the variable rely - vert=True/False If True, return the position of the verticies @@ -352,8 +352,8 @@ def islice(var, iindex, grd, Cpos='rho', vert=False): mask = grd.hgrid.mask_rho[:] else: - raise Warning, '%s bad position. Valid Arakawa-C are \ - rho, u or v.' % Cpos + raise Warning('%s bad position. Valid Arakawa-C are \ + rho, u or v.' % Cpos) # get constant-i slice vari = var[:,:,iindex] @@ -374,7 +374,7 @@ def jslice(var, jindex, grd, Cpos='rho', vert=False): optional switch: - Cpos='rho', 'u', 'v' or 'w' specify the C-grid position where - the variable rely + the variable rely - vert=True/False If True, return the position of the verticies @@ -479,8 +479,8 @@ def jslice(var, jindex, grd, Cpos='rho', vert=False): mask = grd.hgrid.mask_rho[:] else: - raise Warning, '%s bad position. Valid Arakawa-C are \ - rho, u or v.' % Cpos + raise Warning('%s bad position. Valid Arakawa-C are \ + rho, u or v.' % Cpos) # get constant-j slice varj = var[:,jindex,:] @@ -501,8 +501,8 @@ def isoslice(var,prop,isoval, grd, Cpos='rho', masking=True, vert=False): isoslice, lon, lat = isoslice(variable,property, isoval, grd) optional switch: - - Cpos='rho', 'u' or 'v' specify the C-grid position where - the variable rely + - Cpos='rho', 'u' or 'v' specify the C-grid position where + the variable rely - masking=True mask the output if True - vert=True/False If True, return the position of the verticies @@ -521,9 +521,9 @@ def isoslice(var,prop,isoval, grd, Cpos='rho', masking=True, vert=False): h_at_s30 = isoslice(z,s,30); # z at s == 30 """ if (len(var.squeeze().shape)<=2): - raise ValueError, 'variable must have at least two dimensions' + raise ValueError('variable must have at least two dimensions') if not prop.shape == var.shape: - raise ValueError, 'dimension of var and prop must be identical' + raise ValueError('dimension of var and prop must be identical') # compute the depth on Arakawa-C grid position @@ -603,8 +603,8 @@ def isoslice(var,prop,isoval, grd, Cpos='rho', masking=True, vert=False): mask = grd.hgrid.mask_rho[:] else: - raise Warning, '%s bad position. Valid Arakawa-C are \ - rho, u or v.' % Cpos + raise Warning('%s bad position. Valid Arakawa-C are \ + rho, u or v.' % Cpos) prop = prop-isoval sz = np.shape(var) @@ -624,8 +624,8 @@ def isoslice(var,prop,isoval, grd, Cpos='rho', masking=True, vert=False): if masking: isoslice = np.ma.masked_where(zc.sum(axis=0)==0, isoslice) if all(isoslice.mask): - raise Warning, 'property==%f out of range (%f, %f)' % \ - (isoval, (prop+isoval).min(), (prop+isoval).max()) + raise Warning('property==%f out of range (%f, %f)' % \ + (isoval, (prop+isoval).min(), (prop+isoval).max())) isoslice = isoslice.reshape(sz[1:]) # mask land @@ -641,8 +641,8 @@ def transect(var, istart, iend, jstart, jend, grd, Cpos='rho', vert=False, \ transect, z, lon, lat = transect(var, istart, iend, jstart, jend, grd) optional switch: - - Cpos='rho', 'u' or 'v' specify the C-grid position where - the variable rely + - Cpos='rho', 'u' or 'v' specify the C-grid position where + the variable rely - vert=True/False If True, return the position of the verticies - spval special value @@ -727,8 +727,8 @@ def transect(var, istart, iend, jstart, jend, grd, Cpos='rho', vert=False, \ mask = grd.hgrid.mask_rho[:] else: - raise Warning, '%s bad position. Valid Arakawa-C are \ - rho, u or v.' % Cpos + raise Warning('%s bad position. Valid Arakawa-C are \ + rho, u or v.' % Cpos) # Find the nearest point between P1 (imin,jmin) and P2 (imax, jmax) @@ -758,7 +758,7 @@ def transect(var, istart, iend, jstart, jend, grd, Cpos='rho', vert=False, \ # Chose the strait line with the smallest slope if (abs(aj) <= 1 ): # Here, the best line is y(x) - print 'Here, the best line is y(x)' + print('Here, the best line is y(x)') # If i1 < i0 swap points and remember it has been swapped if (i1 < i0 ): i = i0 ; j = j0 @@ -793,7 +793,7 @@ def transect(var, istart, iend, jstart, jend, grd, Cpos='rho', vert=False, \ else: # Here, the best line is x(y) - print 'Here, the best line is x(y)' + print('Here, the best line is x(y)') # If j1 < j0 swap points and remember it has been swapped if (j1 < j0 ): i = i0 ; j = j0 @@ -905,8 +905,8 @@ def lonslice(var, longitude, grd, Cpos='rho', vert=False, spval=1e37): lonslice, z, lon, lat = lonslice(var, longitude, grd) optional switch: - - Cpos='rho', 'u' or 'v' specify the C-grid position where - the variable rely + - Cpos='rho', 'u' or 'v' specify the C-grid position where + the variable rely - vert=True/False If True, return the position of the verticies - spval special value @@ -930,17 +930,17 @@ def lonslice(var, longitude, grd, Cpos='rho', vert=False, spval=1e37): lon = grd.hgrid.lon_rho lat = grd.hgrid.lat_rho else: - raise Warning, '%s bad position. Valid Arakawa-C are \ - rho, u or v.' % Cpos + raise Warning('%s bad position. Valid Arakawa-C are \ + rho, u or v.' % Cpos) edge = np.concatenate((lon[1,1:-1], \ lon[1:-1,-2], \ lon[-2,-2:0:-1], \ lon[-2:0:-1,1])) - idx = np.concatenate((range(1,lon[0,:].shape[0]-1), \ - range(1,lon[:,-1].shape[0]-1), \ - range(1,lon[-1,::-1].shape[0]-1)[::-1], \ - range(1,lon[::-1,0].shape[0]-1)[::-1])) + idx = np.concatenate((list(range(1,lon[0,:].shape[0]-1)), \ + list(range(1,lon[:,-1].shape[0]-1)), \ + list(range(1,lon[-1,::-1].shape[0]-1))[::-1], \ + list(range(1,lon[::-1,0].shape[0]-1))[::-1])) d = np.zeros(edge.shape) for i in range (edge.shape[0]): @@ -953,7 +953,7 @@ def lonslice(var, longitude, grd, Cpos='rho', vert=False, spval=1e37): Mp, Lp = lon.shape if len(pt_idx) != 2: - raise ValueError, 'this function only works for simple quadrangle' + raise ValueError('this function only works for simple quadrangle') # determine is latitude ligne is crossing a i or j edge side = np.zeros(2) @@ -1008,8 +1008,8 @@ def latslice(var, latitude, grd, Cpos='rho', vert=False, spval=1e37): latslice, z, lon, lat = latslice(var, latitude, grd) optional switch: - - Cpos='rho', 'u' or 'v' specify the C-grid position where - the variable rely + - Cpos='rho', 'u' or 'v' specify the C-grid position where + the variable rely - vert=True/False If True, return the position of the verticies - spval special value @@ -1033,17 +1033,17 @@ def latslice(var, latitude, grd, Cpos='rho', vert=False, spval=1e37): lon = grd.hgrid.lon_rho lat = grd.hgrid.lat_rho else: - raise Warning, '%s bad position. Valid Arakawa-C are \ - rho, u or v.' % Cpos + raise Warning('%s bad position. Valid Arakawa-C are \ + rho, u or v.' % Cpos) edge = np.concatenate((lat[1,1:-1], \ lat[1:-1,-2], \ lat[-2,-2:0:-1], \ lat[-2:0:-1,1])) - idx = np.concatenate((range(1,lat[0,:].shape[0]-1), \ - range(1,lat[:,-1].shape[0]-1), \ - range(1,lat[-1,::-1].shape[0]-1)[::-1], \ - range(1,lat[::-1,0].shape[0]-1)[::-1])) + idx = np.concatenate((list(range(1,lat[0,:].shape[0]-1)), \ + list(range(1,lat[:,-1].shape[0]-1)), \ + list(range(1,lat[-1,::-1].shape[0]-1))[::-1], \ + list(range(1,lat[::-1,0].shape[0]-1))[::-1])) d = np.zeros(edge.shape) for i in range (edge.shape[0]): @@ -1056,7 +1056,7 @@ def latslice(var, latitude, grd, Cpos='rho', vert=False, spval=1e37): Mp, Lp = lon.shape if len(pt_idx) != 2: - raise ValueError, 'this function only works for simple quadrangle' + raise ValueError('this function only works for simple quadrangle') # determine is latitude ligne is crossing a i or j edge side = np.zeros(2) @@ -1169,8 +1169,8 @@ def zlayer(var, grd, h1=None, h2=None, Cpos='rho', vert=False): mask = grd.hgrid.mask_rho[:] else: - raise Warning, '%s bad position. Valid Arakawa-C are \ - rho, u or v.' % Cpos + raise Warning('%s bad position. Valid Arakawa-C are \ + rho, u or v.' % Cpos) @@ -1247,7 +1247,7 @@ def section_transport(u, v, grd, istart, iend, jstart, jend): # Chose the strait line with the smallest slope if (abs(aj) <= 1 ): # Here, the best line is y(x) - print 'Here, the best line is y(x)' + print('Here, the best line is y(x)') # If i1 < i0 swap points and remember it has been swapped if i1 < i0: i = i0 ; j = j0 @@ -1272,7 +1272,7 @@ def section_transport(u, v, grd, istart, iend, jstart, jend): else: # Here, the best line is x(y) - print 'Here, the best line is x(y)' + print('Here, the best line is x(y)') # If j1 < j0 swap points and remember it has been swapped if j1 < j0: i = i0 ; j = j0 @@ -1308,9 +1308,9 @@ def section_transport(u, v, grd, istart, iend, jstart, jend): # distance between 2 neighbour points d = abs(inear[k] - inear[k-1]) - if ( d > 1 ): + if ( d > 1 ): # intermediate points required if d>1 - neari = interm_pt(inear, k, ai, bi, aj, bj) + neari = interm_pt(inear, k, ai, bi, aj, bj) near.insert(nn,neari) nn=nn+1 @@ -1395,7 +1395,7 @@ def section_transport_z(u, v, grd, istart, iend, jstart, jend, h1=None, h2=None) # Chose the strait line with the smallest slope if (abs(aj) <= 1 ): # Here, the best line is y(x) - print 'Here, the best line is y(x)' + print('Here, the best line is y(x)') # If i1 < i0 swap points and remember it has been swapped if i1 < i0: i = i0 ; j = j0 @@ -1420,7 +1420,7 @@ def section_transport_z(u, v, grd, istart, iend, jstart, jend, h1=None, h2=None) else: # Here, the best line is x(y) - print 'Here, the best line is x(y)' + print('Here, the best line is x(y)') # If j1 < j0 swap points and remember it has been swapped if j1 < j0: i = i0 ; j = j0 @@ -1456,9 +1456,9 @@ def section_transport_z(u, v, grd, istart, iend, jstart, jend, h1=None, h2=None) # distance between 2 neighbour points d = abs(inear[k] - inear[k-1]) - if ( d > 1 ): + if ( d > 1 ): # intermediate points required if d>1 - neari = interm_pt(inear, k, ai, bi, aj, bj) + neari = interm_pt(inear, k, ai, bi, aj, bj) near.insert(nn,neari) nn=nn+1 @@ -1573,7 +1573,7 @@ def section_tracer_transport_z(u, v, tracer, grd, istart, iend, jstart, jend, h1 # Chose the strait line with the smallest slope if (abs(aj) <= 1 ): # Here, the best line is y(x) - print 'Here, the best line is y(x)' + print('Here, the best line is y(x)') # If i1 < i0 swap points and remember it has been swapped if i1 < i0: i = i0 ; j = j0 @@ -1598,7 +1598,7 @@ def section_tracer_transport_z(u, v, tracer, grd, istart, iend, jstart, jend, h1 else: # Here, the best line is x(y) - print 'Here, the best line is x(y)' + print('Here, the best line is x(y)') # If j1 < j0 swap points and remember it has been swapped if j1 < j0: i = i0 ; j = j0 @@ -1634,9 +1634,9 @@ def section_tracer_transport_z(u, v, tracer, grd, istart, iend, jstart, jend, h1 # distance between 2 neighbour points d = abs(inear[k] - inear[k-1]) - if ( d > 1 ): + if ( d > 1 ): # intermediate points required if d>1 - neari = interm_pt(inear, k, ai, bi, aj, bj) + neari = interm_pt(inear, k, ai, bi, aj, bj) near.insert(nn,neari) nn=nn+1 @@ -1724,88 +1724,88 @@ def section_tracer_transport_z(u, v, tracer, grd, istart, iend, jstart, jend, h1 def interm_pt(pnear, pk, pai, pbi, paj, pbj): ### FIND THE BEST INTERMEDIATE POINT ON A PATHWAY - # ----------------------------- - # pnear : vector of the position of the nearest point - # pk : current working index - # pai, pbi: slope and original ordinate of x(y) - # paj, pbj: slope and original ordinate of y(x) - # pneari : vector holding the position of intermediate point - # ----------------------------- + # ----------------------------- + # pnear : vector of the position of the nearest point + # pk : current working index + # pai, pbi: slope and original ordinate of x(y) + # paj, pbj: slope and original ordinate of y(x) + # pneari : vector holding the position of intermediate point + # ----------------------------- # 1 - Compute intermediate point # Determine whether we use y(x) or x(y): if (abs(paj) <= 1): # y(x) - # possible intermediate point - ylptmp1 = pnear[pk-1] + 1 - ylptmp2 = pnear[pk-1] + (paj/abs(paj))*1j - # M is the candidate point: - zxm = np.real(ylptmp1) - zym = np.imag(ylptmp1) - za0 = paj - zb0 = pbj - # - za1 = -1./za0 - zb1 = zym-za1*zxm - # P is the projection of M in the strait line - zxp = -(zb1-zb0)/(za1-za0) - zyp = za0*zxp+zb0 - # zd1 is the distance MP - zd1 = (zxm-zxp) * (zxm-zxp) + (zym-zyp) * (zym-zyp) + # possible intermediate point + ylptmp1 = pnear[pk-1] + 1 + ylptmp2 = pnear[pk-1] + (paj/abs(paj))*1j + # M is the candidate point: + zxm = np.real(ylptmp1) + zym = np.imag(ylptmp1) + za0 = paj + zb0 = pbj # - # M is the candidate point: - zxm = np.real(ylptmp2) - zym = np.imag(ylptmp2) - za1 = -1./za0 - zb1 = zym-za1*zxm - # P is the projection of M in the strait line - zxp = -(zb1-zb0)/(za1-za0) - zyp = za0*zxp+zb0 - # zd1 is the distance MP - zd2 = (zxm-zxp) * (zxm-zxp) + (zym-zyp) * (zym-zyp) + za1 = -1./za0 + zb1 = zym-za1*zxm + # P is the projection of M in the strait line + zxp = -(zb1-zb0)/(za1-za0) + zyp = za0*zxp+zb0 + # zd1 is the distance MP + zd1 = (zxm-zxp) * (zxm-zxp) + (zym-zyp) * (zym-zyp) + # + # M is the candidate point: + zxm = np.real(ylptmp2) + zym = np.imag(ylptmp2) + za1 = -1./za0 + zb1 = zym-za1*zxm + # P is the projection of M in the strait line + zxp = -(zb1-zb0)/(za1-za0) + zyp = za0*zxp+zb0 + # zd1 is the distance MP + zd2 = (zxm-zxp) * (zxm-zxp) + (zym-zyp) * (zym-zyp) + # + # choose the smallest (zd1,zd2) + if (zd2 <= zd1): + pneari = ylptmp2 + else: + pneari = ylptmp1 # - # choose the smallest (zd1,zd2) - if (zd2 <= zd1): - pneari = ylptmp2 - else: - pneari = ylptmp1 - # else: # x(y) - ylptmp1 = pnear[pk-1] + (pai/abs(pai)) - ylptmp2 = pnear[pk-1] + 1*1j - # M is the candidate point: - zxm = np.real(ylptmp1) - zym = np.imag(ylptmp1) - za0 = pai - zb0 = pbi - # - za1 = -1./za0 - zb1 = zxm-za1*zym - # P is the projection of M in the strait line - zyp = -(zb1-zb0)/(za1-za0) - zxp = za0*zyp+zb0 - # zd1 is the distance MP - zd1 = (zxm-zxp) * (zxm-zxp) + (zym-zyp) * (zym-zyp) + ylptmp1 = pnear[pk-1] + (pai/abs(pai)) + ylptmp2 = pnear[pk-1] + 1*1j + # M is the candidate point: + zxm = np.real(ylptmp1) + zym = np.imag(ylptmp1) + za0 = pai + zb0 = pbi # - # M is the candidate point: - zxm = np.real(ylptmp2) - zym = np.imag(ylptmp2) - za1 = -1./za0 - zb1 = zxm-za1*zym - # P is the projection of M in the strait line - zyp = -(zb1-zb0)/(za1-za0) - zxp = za0*zyp+zb0 - # zd2 is the distance MP - zd2 = (zxm-zxp) * (zxm-zxp) + (zym-zyp) * (zym-zyp) + za1 = -1./za0 + zb1 = zxm-za1*zym + # P is the projection of M in the strait line + zyp = -(zb1-zb0)/(za1-za0) + zxp = za0*zyp+zb0 + # zd1 is the distance MP + zd1 = (zxm-zxp) * (zxm-zxp) + (zym-zyp) * (zym-zyp) # - # choose the smallest (zd1,zd2) - if (zd2 <= zd1): - pneari = ylptmp2 - else: - pneari = ylptmp1 - + # M is the candidate point: + zxm = np.real(ylptmp2) + zym = np.imag(ylptmp2) + za1 = -1./za0 + zb1 = zxm-za1*zym + # P is the projection of M in the strait line + zyp = -(zb1-zb0)/(za1-za0) + zxp = za0*zyp+zb0 + # zd2 is the distance MP + zd2 = (zxm-zxp) * (zxm-zxp) + (zym-zyp) * (zym-zyp) + # + # choose the smallest (zd1,zd2) + if (zd2 <= zd1): + pneari = ylptmp2 + else: + pneari = ylptmp1 + return pneari @@ -1828,8 +1828,8 @@ def hindices(lon, lat, grd, Cpos='rho', rectangular=0, spval=1e37): latg = grd.hgrid.lat_rho angle = grd.hgrid.angle_rho else: - raise Warning, '%s bad position. Valid Arakawa-C are \ - rho, u or v.' % Cpos + raise Warning('%s bad position. Valid Arakawa-C are \ + rho, u or v.' % Cpos) if type(grd).__name__ == 'CGrid_geo': spherical = grd.spherical @@ -1846,8 +1846,8 @@ def hindices(lon, lat, grd, Cpos='rho', rectangular=0, spval=1e37): latg = grd.lat_rho angle = grd.angle_rho else: - raise Warning, '%s bad position. Valid Arakawa-C are \ - rho, u or v.' % Cpos + raise Warning('%s bad position. Valid Arakawa-C are \ + rho, u or v.' % Cpos) lon = np.matrix(lon) diff --git a/pyroms/pyroms/utility.py b/pyroms/pyroms/utility.py index 4f98d03..a58d578 100644 --- a/pyroms/pyroms/utility.py +++ b/pyroms/pyroms/utility.py @@ -34,7 +34,7 @@ def get_lonlat(iindex, jindex, grd, Cpos='rho'): lon = grd.hgrid.lon_psi[:,:] lat = grd.hgrid.lat_psi[:,:] else: - raise Warning, '%s bad position. Cpos must be rho, psi, u or v.' % Cpos + raise Warning('%s bad position. Cpos must be rho, psi, u or v.' % Cpos) return lon[jindex, iindex], lat[jindex, iindex] @@ -60,7 +60,7 @@ def get_ij(longitude, latitude, grd, Cpos='rho'): lon = grd.hgrid.lon_psi[:,:] lat = grd.hgrid.lat_psi[:,:] else: - raise Warning, '%s bad position. Cpos must be rho, psi, u or v.' % Cpos + raise Warning('%s bad position. Cpos must be rho, psi, u or v.' % Cpos) lon = lon[:,:] - longitude lat = lat[:,:] - latitude @@ -91,7 +91,7 @@ def find_nearestgridpoints(longitude, latitude, grd, Cpos='rho'): lon = grd.hgrid.lon_vert[:,:] lat = grd.hgrid.lat_vert[:,:] else: - raise Warning, '%s bad position. Cpos must be rho, u or v.' % Cpos + raise Warning('%s bad position. Cpos must be rho, u or v.' % Cpos) if type(grd).__name__ == 'CGrid_geo': @@ -109,7 +109,7 @@ def find_nearestgridpoints(longitude, latitude, grd, Cpos='rho'): lon = grd.lon_vert[:,:] lat = grd.lat_vert[:,:] else: - raise Warning, '%s bad position. Cpos must be rho, u or v.' % Cpos + raise Warning('%s bad position. Cpos must be rho, u or v.' % Cpos) dlon = lon[:,:] - longitude @@ -168,7 +168,7 @@ def find_nearestgridpoints(longitude, latitude, grd, Cpos='rho'): inside = mpl.path.Path(verts).contains_point([longitude, latitude]) if inside == 0: - raise ValueError, 'well where is it then?' + raise ValueError('well where is it then?') iindex = iindex[:2] jindex = jindex[1:3] @@ -190,7 +190,7 @@ def get_coast_from_map(map): for k in range(kk): ll = len(map.coastsegs[k]) for l in range(ll): - c = map(map.coastsegs[k][l][0], map.coastsegs[k][l][1], inverse=True) + c = list(map(map.coastsegs[k][l][0], map.coastsegs[k][l][1], inverse=True)) coast.append(c) coast.append((np.nan, np.nan)) @@ -326,7 +326,7 @@ def roms_varlist(option): varlist = (['h','s_rho','s_w','Cs_r','Cs_w', \ 'theta_s','theta_b','Tcline','hc']) else: - raise Warning, 'Unknow varlist id' + raise Warning('Unknow varlist id') return varlist @@ -343,7 +343,7 @@ def get_bottom(varz, mask, spval=1e37): bottom[:,:] = _interp.get_bottom(varz,mask,spval) - return np.int(bottom) + return bottom def get_surface(varz, mask, spval=1e37): @@ -384,7 +384,7 @@ def move2grid(varin, init_grid, final_grid): elif (init_grid == 'v' and final_grid == 'psi'): varout = 0.5 * (varin[:,1:] + varin[:,:-1]) else: - raise ValueError, 'Undefined combination for init_grid and final_grid' + raise ValueError('Undefined combination for init_grid and final_grid') elif ndim == 3: @@ -400,15 +400,15 @@ def move2grid(varin, init_grid, final_grid): elif (init_grid == 'v' and final_grid == 'psi'): varout = 0.5 * (varin[:,:,1:] + varin[:,:,:-1]) else: - raise ValueError, 'Undefined combination for init_grid and final_grid' + raise ValueError('Undefined combination for init_grid and final_grid') else: - raise ValueError, 'varin must be 2D or 3D' + raise ValueError('varin must be 2D or 3D') return varout -def get_date_tag(roms_time, ref=(2006, 01, 01), format="%d %b %Y at %H:%M:%S"): +def get_date_tag(roms_time, ref=(2006, 0o1, 0o1), format="%d %b %Y at %H:%M:%S"): ''' tag = get_date_tag(roms_time) diff --git a/pyroms/pyroms/vgrid.py b/pyroms/pyroms/vgrid.py index c09f21a..152df3b 100644 --- a/pyroms/pyroms/vgrid.py +++ b/pyroms/pyroms/vgrid.py @@ -289,21 +289,17 @@ def __init__(self, h, theta_b, theta_s, Tcline, N, hraw=None, zeta=None): self.z_r = z_r(self.h, self.hc, self.N, self.s_rho, self.Cs_r, self.zeta, self.Vtrans) self.z_w = z_w(self.h, self.hc, self.Np, self.s_w, self.Cs_w, self.zeta, self.Vtrans) - def _get_s_rho(self): - lev = np.arange(1,self.N+1,1) - s = -(lev * lev - 2 * lev * self.N + lev + self.N * self.N - self.N) / \ - (self.N * self.N - self.N) - \ - 0.01 * (lev * lev - lev * self.N) / (self.c1 - self.N) -# (self.c1 * self.N * self.N - self.N) - \ - self.s_rho = s + lev = np.arange(1, self.N+1) - .5 + self.s_rho = -(lev * lev - 2 * lev * self.N + lev + self.N * self.N - self.N) / \ + (1.0 * self.N * self.N - self.N) - \ + 0.01 * (lev * lev - lev * self.N) / (1.0 - self.N) def _get_s_w(self): lev = np.arange(0,self.Np,1) s = -(lev * lev - 2 * lev * self.N + lev + self.N * self.N - self.N) / \ (self.N * self.N - self.N) - \ 0.01 * (lev * lev - lev * self.N) / (self.c1 - self.N) -# (self.c1 * self.N * self.N - self.N) - \ self.s_w = s def _get_Cs_r(self): @@ -417,7 +413,7 @@ def __getitem__(self, key): for k in range(self.Np): z0 = self.hc * self.s_w[k] + (self.h - self.hc) * self.Cs_w[k] z_w[n,k,:] = z0 + zeta[n,:] * (1.0 + z0 / self.h) - elif self.Vtrans == 2 or self.Vtrans == 4: + elif self.Vtrans == 2 or self.Vtrans == 4 or self.Vtrans == 5: for n in range(ti): for k in range(self.Np): z0 = (self.hc * self.s_w[k] + self.h * self.Cs_w[k]) / \ @@ -440,7 +436,7 @@ def __init__(self, h, depth, N): self.N = int(N) ndim = len(h.shape) -# print h.shape, ndim +# print(h.shape, ndim) if ndim == 2: Mm, Lm = h.shape diff --git a/pyroms/setup.py b/pyroms/setup.py index 92ba2d1..3f9739a 100644 --- a/pyroms/setup.py +++ b/pyroms/setup.py @@ -33,14 +33,14 @@ get_ROMS_hgrid get_ROMS_vgrid get_ROMS_grid - write_ROMS_grid + write_ROMS_grid io - wrapper for netCDF4 Dataset MFDataset cf - CF compliant files tools - time + time tools - Tools specific to the Regional Ocean Modeling System roms2z @@ -55,7 +55,7 @@ latslice section_transport - utility - Some basic tools + utility - Some basic tools get_lonlat get_ij roms_varlist @@ -76,25 +76,16 @@ Topic :: Software Development :: Libraries :: Python Modules """ -from numpy.distutils.core import Extension - -iso = Extension(name = '_iso', - sources = ['pyroms/src/iso.f']) - -interp = Extension(name = '_interp', - sources = ['pyroms/src/interp.f']) - -obs_interp = Extension(name = '_obs_interp', - sources = ['pyroms/src/obs_interp.f']) - -remapping = Extension(name = '_remapping', - sources = ['pyroms/src/remapping.f']) - -remapping_fast = Extension(name = '_remapping_fast', - sources = ['pyroms/src/remapping_fast.f']) - -remapping_fast_weighted = Extension(name = '_remapping_fast_weighted', - sources = ['pyroms/src/remapping_fast_weighted.f']) +def configuration(parent_package='', top_path=None): + from numpy.distutils.misc_util import Configuration + config = Configuration('pyroms', parent_package, top_path) + config.add_extension('_interp', sources = ['pyroms/src/interp.f']) + config.add_extension('_obs_interp', sources = ['pyroms/src/obs_interp.f']) + config.add_extension('_remapping', sources = ['pyroms/src/remapping.f']) + config.add_extension('_remapping_fast', sources = ['pyroms/src/remapping_fast.f']) + config.add_extension('_remapping_fast_weighted', sources = ['pyroms/src/remapping_fast_weighted.f']) + config.add_extension('_iso', sources = ['pyroms/src/iso.f']) + return config doclines = __doc__.split("\n") @@ -104,14 +95,11 @@ version = '0.1.0', description = doclines[0], long_description = "\n".join(doclines[2:]), - author = "Frederic Castruccio", - author_email = "frederic@marine.rutgers.edu", - url = "ftp://marine.rutgers.edu/pub/frederic/pyroms/", + url = "https://github.com/ESMG/", packages = ['pyroms', 'pyroms.remapping', 'pyroms.extern'], license = 'BSD', platforms = ["any"], - ext_modules = [iso, interp, obs_interp, remapping, remapping_fast, remapping_fast_weighted], - classifiers = filter(None, classifiers.split("\n")), ) + setup(**configuration(top_path='').todict()) diff --git a/pyroms_toolbox/.doxygen b/pyroms_toolbox/.doxygen new file mode 100644 index 0000000..b87a94b --- /dev/null +++ b/pyroms_toolbox/.doxygen @@ -0,0 +1,1519 @@ +# Doxyfile 1.6.1 + +# This file describes the settings to be used by the documentation system +# doxygen (www.doxygen.org) for a project +# +# All text after a hash (#) is considered a comment and will be ignored +# The format is: +# TAG = value [value, ...] +# For lists items can also be appended using: +# TAG += value [value, ...] +# Values that contain spaces should be placed between quotes (" ") + +#--------------------------------------------------------------------------- +# Project related configuration options +#--------------------------------------------------------------------------- + +# This tag specifies the encoding used for all characters in the config file +# that follow. The default is UTF-8 which is also the encoding used for all +# text before the first occurrence of this tag. Doxygen uses libiconv (or the +# iconv built into libc) for the transcoding. See +# http://www.gnu.org/software/libiconv for the list of possible encodings. + +DOXYFILE_ENCODING = UTF-8 + +# The PROJECT_NAME tag is a single word (or a sequence of words surrounded +# by quotes) that should identify the project. + +PROJECT_NAME = pycnal_toolbox + +# The PROJECT_NUMBER tag can be used to enter a project or revision number. +# This could be handy for archiving the generated documentation or +# if some version control system is used. + +PROJECT_NUMBER = + +# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) +# base path where the generated documentation will be put. +# If a relative path is entered, it will be relative to the location +# where doxygen was started. If left blank the current directory will be used. + +OUTPUT_DIRECTORY = + +# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create +# 4096 sub-directories (in 2 levels) under the output directory of each output +# format and will distribute the generated files over these directories. +# Enabling this option can be useful when feeding doxygen a huge amount of +# source files, where putting all generated files in the same directory would +# otherwise cause performance problems for the file system. + +CREATE_SUBDIRS = YES + +# The OUTPUT_LANGUAGE tag is used to specify the language in which all +# documentation generated by doxygen is written. Doxygen will use this +# information to generate all constant output in the proper language. +# The default language is English, other supported languages are: +# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional, +# Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German, +# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English +# messages), Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian, +# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrilic, Slovak, +# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese. + +OUTPUT_LANGUAGE = English + +# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will +# include brief member descriptions after the members that are listed in +# the file and class documentation (similar to JavaDoc). +# Set to NO to disable this. + +BRIEF_MEMBER_DESC = YES + +# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend +# the brief description of a member or function before the detailed description. +# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the +# brief descriptions will be completely suppressed. + +REPEAT_BRIEF = YES + +# This tag implements a quasi-intelligent brief description abbreviator +# that is used to form the text in various listings. Each string +# in this list, if found as the leading text of the brief description, will be +# stripped from the text and the result after processing the whole list, is +# used as the annotated text. Otherwise, the brief description is used as-is. +# If left blank, the following values are used ("$name" is automatically +# replaced with the name of the entity): "The $name class" "The $name widget" +# "The $name file" "is" "provides" "specifies" "contains" +# "represents" "a" "an" "the" + +ABBREVIATE_BRIEF = + +# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then +# Doxygen will generate a detailed section even if there is only a brief +# description. + +ALWAYS_DETAILED_SEC = NO + +# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all +# inherited members of a class in the documentation of that class as if those +# members were ordinary class members. Constructors, destructors and assignment +# operators of the base classes will not be shown. + +INLINE_INHERITED_MEMB = NO + +# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full +# path before files name in the file list and in the header files. If set +# to NO the shortest path that makes the file name unique will be used. + +FULL_PATH_NAMES = YES + +# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag +# can be used to strip a user-defined part of the path. Stripping is +# only done if one of the specified strings matches the left-hand part of +# the path. The tag can be used to show relative paths in the file list. +# If left blank the directory from which doxygen is run is used as the +# path to strip. + +STRIP_FROM_PATH = + +# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of +# the path mentioned in the documentation of a class, which tells +# the reader which header file to include in order to use a class. +# If left blank only the name of the header file containing the class +# definition is used. Otherwise one should specify the include paths that +# are normally passed to the compiler using the -I flag. + +STRIP_FROM_INC_PATH = + +# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter +# (but less readable) file names. This can be useful is your file systems +# doesn't support long names like on DOS, Mac, or CD-ROM. + +SHORT_NAMES = NO + +# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen +# will interpret the first line (until the first dot) of a JavaDoc-style +# comment as the brief description. If set to NO, the JavaDoc +# comments will behave just like regular Qt-style comments +# (thus requiring an explicit @brief command for a brief description.) + +JAVADOC_AUTOBRIEF = NO + +# If the QT_AUTOBRIEF tag is set to YES then Doxygen will +# interpret the first line (until the first dot) of a Qt-style +# comment as the brief description. If set to NO, the comments +# will behave just like regular Qt-style comments (thus requiring +# an explicit \brief command for a brief description.) + +QT_AUTOBRIEF = NO + +# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen +# treat a multi-line C++ special comment block (i.e. a block of //! or /// +# comments) as a brief description. This used to be the default behaviour. +# The new default is to treat a multi-line C++ comment block as a detailed +# description. Set this tag to YES if you prefer the old behaviour instead. + +MULTILINE_CPP_IS_BRIEF = NO + +# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented +# member inherits the documentation from any documented member that it +# re-implements. + +INHERIT_DOCS = YES + +# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce +# a new page for each member. If set to NO, the documentation of a member will +# be part of the file/class/namespace that contains it. + +SEPARATE_MEMBER_PAGES = NO + +# The TAB_SIZE tag can be used to set the number of spaces in a tab. +# Doxygen uses this value to replace tabs by spaces in code fragments. + +TAB_SIZE = 8 + +# This tag can be used to specify a number of aliases that acts +# as commands in the documentation. An alias has the form "name=value". +# For example adding "sideeffect=\par Side Effects:\n" will allow you to +# put the command \sideeffect (or @sideeffect) in the documentation, which +# will result in a user-defined paragraph with heading "Side Effects:". +# You can put \n's in the value part of an alias to insert newlines. + +ALIASES = + +# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C +# sources only. Doxygen will then generate output that is more tailored for C. +# For instance, some of the names that are used will be different. The list +# of all members will be omitted, etc. + +OPTIMIZE_OUTPUT_FOR_C = NO + +# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java +# sources only. Doxygen will then generate output that is more tailored for +# Java. For instance, namespaces will be presented as packages, qualified +# scopes will look different, etc. + +OPTIMIZE_OUTPUT_JAVA = YES + +# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran +# sources only. Doxygen will then generate output that is more tailored for +# Fortran. + +OPTIMIZE_FOR_FORTRAN = NO + +# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL +# sources. Doxygen will then generate output that is tailored for +# VHDL. + +OPTIMIZE_OUTPUT_VHDL = NO + +# Doxygen selects the parser to use depending on the extension of the files it parses. +# With this tag you can assign which parser to use for a given extension. +# Doxygen has a built-in mapping, but you can override or extend it using this tag. +# The format is ext=language, where ext is a file extension, and language is one of +# the parsers supported by doxygen: IDL, Java, Javascript, C#, C, C++, D, PHP, +# Objective-C, Python, Fortran, VHDL, C, C++. For instance to make doxygen treat +# .inc files as Fortran files (default is PHP), and .f files as C (default is Fortran), +# use: inc=Fortran f=C. Note that for custom extensions you also need to set FILE_PATTERNS otherwise the files are not read by doxygen. + +EXTENSION_MAPPING = + +# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want +# to include (a tag file for) the STL sources as input, then you should +# set this tag to YES in order to let doxygen match functions declarations and +# definitions whose arguments contain STL classes (e.g. func(std::string); v.s. +# func(std::string) {}). This also make the inheritance and collaboration +# diagrams that involve STL classes more complete and accurate. + +BUILTIN_STL_SUPPORT = NO + +# If you use Microsoft's C++/CLI language, you should set this option to YES to +# enable parsing support. + +CPP_CLI_SUPPORT = NO + +# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only. +# Doxygen will parse them like normal C++ but will assume all classes use public +# instead of private inheritance when no explicit protection keyword is present. + +SIP_SUPPORT = NO + +# For Microsoft's IDL there are propget and propput attributes to indicate getter +# and setter methods for a property. Setting this option to YES (the default) +# will make doxygen to replace the get and set methods by a property in the +# documentation. This will only work if the methods are indeed getting or +# setting a simple type. If this is not the case, or you want to show the +# methods anyway, you should set this option to NO. + +IDL_PROPERTY_SUPPORT = YES + +# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC +# tag is set to YES, then doxygen will reuse the documentation of the first +# member in the group (if any) for the other members of the group. By default +# all members of a group must be documented explicitly. + +DISTRIBUTE_GROUP_DOC = NO + +# Set the SUBGROUPING tag to YES (the default) to allow class member groups of +# the same type (for instance a group of public functions) to be put as a +# subgroup of that type (e.g. under the Public Functions section). Set it to +# NO to prevent subgrouping. Alternatively, this can be done per class using +# the \nosubgrouping command. + +SUBGROUPING = YES + +# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum +# is documented as struct, union, or enum with the name of the typedef. So +# typedef struct TypeS {} TypeT, will appear in the documentation as a struct +# with name TypeT. When disabled the typedef will appear as a member of a file, +# namespace, or class. And the struct will be named TypeS. This can typically +# be useful for C code in case the coding convention dictates that all compound +# types are typedef'ed and only the typedef is referenced, never the tag name. + +TYPEDEF_HIDES_STRUCT = NO + +# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to +# determine which symbols to keep in memory and which to flush to disk. +# When the cache is full, less often used symbols will be written to disk. +# For small to medium size projects (<1000 input files) the default value is +# probably good enough. For larger projects a too small cache size can cause +# doxygen to be busy swapping symbols to and from disk most of the time +# causing a significant performance penality. +# If the system has enough physical memory increasing the cache will improve the +# performance by keeping more symbols in memory. Note that the value works on +# a logarithmic scale so increasing the size by one will rougly double the +# memory usage. The cache size is given by this formula: +# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0, +# corresponding to a cache size of 2^16 = 65536 symbols + +SYMBOL_CACHE_SIZE = 0 + +#--------------------------------------------------------------------------- +# Build related configuration options +#--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in +# documentation are documented, even if no documentation was available. +# Private class members and static file members will be hidden unless +# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES + +EXTRACT_ALL = YES + +# If the EXTRACT_PRIVATE tag is set to YES all private members of a class +# will be included in the documentation. + +EXTRACT_PRIVATE = YES + +# If the EXTRACT_STATIC tag is set to YES all static members of a file +# will be included in the documentation. + +EXTRACT_STATIC = YES + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) +# defined locally in source files will be included in the documentation. +# If set to NO only classes defined in header files are included. + +EXTRACT_LOCAL_CLASSES = YES + +# This flag is only useful for Objective-C code. When set to YES local +# methods, which are defined in the implementation section but not in +# the interface are included in the documentation. +# If set to NO (the default) only methods in the interface are included. + +EXTRACT_LOCAL_METHODS = YES + +# If this flag is set to YES, the members of anonymous namespaces will be +# extracted and appear in the documentation as a namespace called +# 'anonymous_namespace{file}', where file will be replaced with the base +# name of the file that contains the anonymous namespace. By default +# anonymous namespace are hidden. + +EXTRACT_ANON_NSPACES = NO + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all +# undocumented members of documented classes, files or namespaces. +# If set to NO (the default) these members will be included in the +# various overviews, but no documentation section is generated. +# This option has no effect if EXTRACT_ALL is enabled. + +HIDE_UNDOC_MEMBERS = NO + +# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. +# If set to NO (the default) these classes will be included in the various +# overviews. This option has no effect if EXTRACT_ALL is enabled. + +HIDE_UNDOC_CLASSES = NO + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all +# friend (class|struct|union) declarations. +# If set to NO (the default) these declarations will be included in the +# documentation. + +HIDE_FRIEND_COMPOUNDS = NO + +# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any +# documentation blocks found inside the body of a function. +# If set to NO (the default) these blocks will be appended to the +# function's detailed documentation block. + +HIDE_IN_BODY_DOCS = NO + +# The INTERNAL_DOCS tag determines if documentation +# that is typed after a \internal command is included. If the tag is set +# to NO (the default) then the documentation will be excluded. +# Set it to YES to include the internal documentation. + +INTERNAL_DOCS = YES + +# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate +# file names in lower-case letters. If set to YES upper-case letters are also +# allowed. This is useful if you have classes or files whose names only differ +# in case and if your file system supports case sensitive file names. Windows +# and Mac users are advised to set this option to NO. + +CASE_SENSE_NAMES = YES + +# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen +# will show members with their full class and namespace scopes in the +# documentation. If set to YES the scope will be hidden. + +HIDE_SCOPE_NAMES = NO + +# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen +# will put a list of the files that are included by a file in the documentation +# of that file. + +SHOW_INCLUDE_FILES = YES + +# If the INLINE_INFO tag is set to YES (the default) then a tag [inline] +# is inserted in the documentation for inline members. + +INLINE_INFO = YES + +# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen +# will sort the (detailed) documentation of file and class members +# alphabetically by member name. If set to NO the members will appear in +# declaration order. + +SORT_MEMBER_DOCS = YES + +# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the +# brief documentation of file, namespace and class members alphabetically +# by member name. If set to NO (the default) the members will appear in +# declaration order. + +SORT_BRIEF_DOCS = NO + +# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the (brief and detailed) documentation of class members so that constructors and destructors are listed first. If set to NO (the default) the constructors will appear in the respective orders defined by SORT_MEMBER_DOCS and SORT_BRIEF_DOCS. This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO. + +SORT_MEMBERS_CTORS_1ST = NO + +# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the +# hierarchy of group names into alphabetical order. If set to NO (the default) +# the group names will appear in their defined order. + +SORT_GROUP_NAMES = NO + +# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be +# sorted by fully-qualified names, including namespaces. If set to +# NO (the default), the class list will be sorted only by class name, +# not including the namespace part. +# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. +# Note: This option applies only to the class list, not to the +# alphabetical list. + +SORT_BY_SCOPE_NAME = NO + +# The GENERATE_TODOLIST tag can be used to enable (YES) or +# disable (NO) the todo list. This list is created by putting \todo +# commands in the documentation. + +GENERATE_TODOLIST = YES + +# The GENERATE_TESTLIST tag can be used to enable (YES) or +# disable (NO) the test list. This list is created by putting \test +# commands in the documentation. + +GENERATE_TESTLIST = YES + +# The GENERATE_BUGLIST tag can be used to enable (YES) or +# disable (NO) the bug list. This list is created by putting \bug +# commands in the documentation. + +GENERATE_BUGLIST = YES + +# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or +# disable (NO) the deprecated list. This list is created by putting +# \deprecated commands in the documentation. + +GENERATE_DEPRECATEDLIST= YES + +# The ENABLED_SECTIONS tag can be used to enable conditional +# documentation sections, marked by \if sectionname ... \endif. + +ENABLED_SECTIONS = + +# The MAX_INITIALIZER_LINES tag determines the maximum number of lines +# the initial value of a variable or define consists of for it to appear in +# the documentation. If the initializer consists of more lines than specified +# here it will be hidden. Use a value of 0 to hide initializers completely. +# The appearance of the initializer of individual variables and defines in the +# documentation can be controlled using \showinitializer or \hideinitializer +# command in the documentation regardless of this setting. + +MAX_INITIALIZER_LINES = 30 + +# Set the SHOW_USED_FILES tag to NO to disable the list of files generated +# at the bottom of the documentation of classes and structs. If set to YES the +# list will mention the files that were used to generate the documentation. + +SHOW_USED_FILES = YES + +# If the sources in your project are distributed over multiple directories +# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy +# in the documentation. The default is NO. + +SHOW_DIRECTORIES = YES + +# Set the SHOW_FILES tag to NO to disable the generation of the Files page. +# This will remove the Files entry from the Quick Index and from the +# Folder Tree View (if specified). The default is YES. + +SHOW_FILES = YES + +# Set the SHOW_NAMESPACES tag to NO to disable the generation of the +# Namespaces page. +# This will remove the Namespaces entry from the Quick Index +# and from the Folder Tree View (if specified). The default is YES. + +SHOW_NAMESPACES = YES + +# The FILE_VERSION_FILTER tag can be used to specify a program or script that +# doxygen should invoke to get the current version for each file (typically from +# the version control system). Doxygen will invoke the program by executing (via +# popen()) the command , where is the value of +# the FILE_VERSION_FILTER tag, and is the name of an input file +# provided by doxygen. Whatever the program writes to standard output +# is used as the file version. See the manual for examples. + +FILE_VERSION_FILTER = + +# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed by +# doxygen. The layout file controls the global structure of the generated output files +# in an output format independent way. The create the layout file that represents +# doxygen's defaults, run doxygen with the -l option. You can optionally specify a +# file name after the option, if omitted DoxygenLayout.xml will be used as the name +# of the layout file. + +LAYOUT_FILE = + +#--------------------------------------------------------------------------- +# configuration options related to warning and progress messages +#--------------------------------------------------------------------------- + +# The QUIET tag can be used to turn on/off the messages that are generated +# by doxygen. Possible values are YES and NO. If left blank NO is used. + +QUIET = NO + +# The WARNINGS tag can be used to turn on/off the warning messages that are +# generated by doxygen. Possible values are YES and NO. If left blank +# NO is used. + +WARNINGS = YES + +# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings +# for undocumented members. If EXTRACT_ALL is set to YES then this flag will +# automatically be disabled. + +WARN_IF_UNDOCUMENTED = YES + +# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for +# potential errors in the documentation, such as not documenting some +# parameters in a documented function, or documenting parameters that +# don't exist or using markup commands wrongly. + +WARN_IF_DOC_ERROR = YES + +# This WARN_NO_PARAMDOC option can be abled to get warnings for +# functions that are documented, but have no documentation for their parameters +# or return value. If set to NO (the default) doxygen will only warn about +# wrong or incomplete parameter documentation, but not about the absence of +# documentation. + +WARN_NO_PARAMDOC = NO + +# The WARN_FORMAT tag determines the format of the warning messages that +# doxygen can produce. The string should contain the $file, $line, and $text +# tags, which will be replaced by the file and line number from which the +# warning originated and the warning text. Optionally the format may contain +# $version, which will be replaced by the version of the file (if it could +# be obtained via FILE_VERSION_FILTER) + +WARN_FORMAT = "$file:$line: $text" + +# The WARN_LOGFILE tag can be used to specify a file to which warning +# and error messages should be written. If left blank the output is written +# to stderr. + +WARN_LOGFILE = doxygen.log + +#--------------------------------------------------------------------------- +# configuration options related to the input files +#--------------------------------------------------------------------------- + +# The INPUT tag can be used to specify the files and/or directories that contain +# documented source files. You may enter file names like "myfile.cpp" or +# directories like "/usr/src/myproject". Separate the files or directories +# with spaces. + +INPUT = pycnal_toolbox + +# This tag can be used to specify the character encoding of the source files +# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is +# also the default input encoding. Doxygen uses libiconv (or the iconv built +# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for +# the list of possible encodings. + +INPUT_ENCODING = UTF-8 + +# If the value of the INPUT tag contains directories, you can use the +# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank the following patterns are tested: +# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx +# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90 + +FILE_PATTERNS = + +# The RECURSIVE tag can be used to turn specify whether or not subdirectories +# should be searched for input files as well. Possible values are YES and NO. +# If left blank NO is used. + +RECURSIVE = YES + +# The EXCLUDE tag can be used to specify files and/or directories that should +# excluded from the INPUT source files. This way you can easily exclude a +# subdirectory from a directory tree whose root is specified with the INPUT tag. + +EXCLUDE = + +# The EXCLUDE_SYMLINKS tag can be used select whether or not files or +# directories that are symbolic links (a Unix filesystem feature) are excluded +# from the input. + +EXCLUDE_SYMLINKS = NO + +# If the value of the INPUT tag contains directories, you can use the +# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude +# certain files from those directories. Note that the wildcards are matched +# against the file with absolute path, so to exclude all test directories +# for example use the pattern */test/* + +EXCLUDE_PATTERNS = + +# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names +# (namespaces, classes, functions, etc.) that should be excluded from the +# output. The symbol name can be a fully qualified name, a word, or if the +# wildcard * is used, a substring. Examples: ANamespace, AClass, +# AClass::ANamespace, ANamespace::*Test + +EXCLUDE_SYMBOLS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or +# directories that contain example code fragments that are included (see +# the \include command). + +EXAMPLE_PATH = + +# If the value of the EXAMPLE_PATH tag contains directories, you can use the +# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank all files are included. + +EXAMPLE_PATTERNS = + +# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be +# searched for input files to be used with the \include or \dontinclude +# commands irrespective of the value of the RECURSIVE tag. +# Possible values are YES and NO. If left blank NO is used. + +EXAMPLE_RECURSIVE = NO + +# The IMAGE_PATH tag can be used to specify one or more files or +# directories that contain image that are included in the documentation (see +# the \image command). + +IMAGE_PATH = + +# The INPUT_FILTER tag can be used to specify a program that doxygen should +# invoke to filter for each input file. Doxygen will invoke the filter program +# by executing (via popen()) the command , where +# is the value of the INPUT_FILTER tag, and is the name of an +# input file. Doxygen will then use the output that the filter program writes +# to standard output. +# If FILTER_PATTERNS is specified, this tag will be +# ignored. + +INPUT_FILTER = + +# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern +# basis. +# Doxygen will compare the file name with each pattern and apply the +# filter if there is a match. +# The filters are a list of the form: +# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further +# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER +# is applied to all files. + +FILTER_PATTERNS = + +# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using +# INPUT_FILTER) will be used to filter the input files when producing source +# files to browse (i.e. when SOURCE_BROWSER is set to YES). + +FILTER_SOURCE_FILES = NO + +#--------------------------------------------------------------------------- +# configuration options related to source browsing +#--------------------------------------------------------------------------- + +# If the SOURCE_BROWSER tag is set to YES then a list of source files will +# be generated. Documented entities will be cross-referenced with these sources. +# Note: To get rid of all source code in the generated output, make sure also +# VERBATIM_HEADERS is set to NO. + +SOURCE_BROWSER = YES + +# Setting the INLINE_SOURCES tag to YES will include the body +# of functions and classes directly in the documentation. + +INLINE_SOURCES = YES + +# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct +# doxygen to hide any special comment blocks from generated source code +# fragments. Normal C and C++ comments will always remain visible. + +STRIP_CODE_COMMENTS = NO + +# If the REFERENCED_BY_RELATION tag is set to YES +# then for each documented function all documented +# functions referencing it will be listed. + +REFERENCED_BY_RELATION = YES + +# If the REFERENCES_RELATION tag is set to YES +# then for each documented function all documented entities +# called/used by that function will be listed. + +REFERENCES_RELATION = YES + +# If the REFERENCES_LINK_SOURCE tag is set to YES (the default) +# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from +# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will +# link to the source code. +# Otherwise they will link to the documentation. + +REFERENCES_LINK_SOURCE = YES + +# If the USE_HTAGS tag is set to YES then the references to source code +# will point to the HTML generated by the htags(1) tool instead of doxygen +# built-in source browser. The htags tool is part of GNU's global source +# tagging system (see http://www.gnu.org/software/global/global.html). You +# will need version 4.8.6 or higher. + +USE_HTAGS = NO + +# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen +# will generate a verbatim copy of the header file for each class for +# which an include is specified. Set to NO to disable this. + +VERBATIM_HEADERS = YES + +#--------------------------------------------------------------------------- +# configuration options related to the alphabetical class index +#--------------------------------------------------------------------------- + +# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index +# of all compounds will be generated. Enable this if the project +# contains a lot of classes, structs, unions or interfaces. + +ALPHABETICAL_INDEX = YES + +# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then +# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns +# in which this list will be split (can be a number in the range [1..20]) + +COLS_IN_ALPHA_INDEX = 5 + +# In case all classes in a project start with a common prefix, all +# classes will be put under the same header in the alphabetical index. +# The IGNORE_PREFIX tag can be used to specify one or more prefixes that +# should be ignored while generating the index headers. + +IGNORE_PREFIX = + +#--------------------------------------------------------------------------- +# configuration options related to the HTML output +#--------------------------------------------------------------------------- + +# If the GENERATE_HTML tag is set to YES (the default) Doxygen will +# generate HTML output. + +GENERATE_HTML = YES + +# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `html' will be used as the default path. + +HTML_OUTPUT = html + +# The HTML_FILE_EXTENSION tag can be used to specify the file extension for +# each generated HTML page (for example: .htm,.php,.asp). If it is left blank +# doxygen will generate files with .html extension. + +HTML_FILE_EXTENSION = .html + +# The HTML_HEADER tag can be used to specify a personal HTML header for +# each generated HTML page. If it is left blank doxygen will generate a +# standard header. + +HTML_HEADER = + +# The HTML_FOOTER tag can be used to specify a personal HTML footer for +# each generated HTML page. If it is left blank doxygen will generate a +# standard footer. + +HTML_FOOTER = + +# If the HTML_TIMESTAMP tag is set to YES then the generated HTML +# documentation will contain the timesstamp. + +HTML_TIMESTAMP = NO + +# The HTML_STYLESHEET tag can be used to specify a user-defined cascading +# style sheet that is used by each HTML page. It can be used to +# fine-tune the look of the HTML output. If the tag is left blank doxygen +# will generate a default style sheet. Note that doxygen will try to copy +# the style sheet file to the HTML output directory, so don't put your own +# stylesheet in the HTML output directory as well, or it will be erased! + +HTML_STYLESHEET = + +# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, +# files or namespaces will be aligned in HTML using tables. If set to +# NO a bullet list will be used. + +HTML_ALIGN_MEMBERS = YES + +# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML +# documentation will contain sections that can be hidden and shown after the +# page has loaded. For this to work a browser that supports +# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox +# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari). + +HTML_DYNAMIC_SECTIONS = NO + +# If the GENERATE_DOCSET tag is set to YES, additional index files +# will be generated that can be used as input for Apple's Xcode 3 +# integrated development environment, introduced with OSX 10.5 (Leopard). +# To create a documentation set, doxygen will generate a Makefile in the +# HTML output directory. Running make will produce the docset in that +# directory and running "make install" will install the docset in +# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find +# it at startup. +# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html for more information. + +GENERATE_DOCSET = NO + +# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the +# feed. A documentation feed provides an umbrella under which multiple +# documentation sets from a single provider (such as a company or product suite) +# can be grouped. + +DOCSET_FEEDNAME = "Doxygen generated docs" + +# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that +# should uniquely identify the documentation set bundle. This should be a +# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen +# will append .docset to the name. + +DOCSET_BUNDLE_ID = org.doxygen.Project + +# If the GENERATE_HTMLHELP tag is set to YES, additional index files +# will be generated that can be used as input for tools like the +# Microsoft HTML help workshop to generate a compiled HTML help file (.chm) +# of the generated HTML documentation. + +GENERATE_HTMLHELP = NO + +# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can +# be used to specify the file name of the resulting .chm file. You +# can add a path in front of the file if the result should not be +# written to the html output directory. + +CHM_FILE = + +# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can +# be used to specify the location (absolute path including file name) of +# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run +# the HTML help compiler on the generated index.hhp. + +HHC_LOCATION = + +# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag +# controls if a separate .chi index file is generated (YES) or that +# it should be included in the master .chm file (NO). + +GENERATE_CHI = NO + +# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING +# is used to encode HtmlHelp index (hhk), content (hhc) and project file +# content. + +CHM_INDEX_ENCODING = + +# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag +# controls whether a binary table of contents is generated (YES) or a +# normal table of contents (NO) in the .chm file. + +BINARY_TOC = NO + +# The TOC_EXPAND flag can be set to YES to add extra items for group members +# to the contents of the HTML help documentation and to the tree view. + +TOC_EXPAND = NO + +# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and QHP_VIRTUAL_FOLDER +# are set, an additional index file will be generated that can be used as input for +# Qt's qhelpgenerator to generate a Qt Compressed Help (.qch) of the generated +# HTML documentation. + +GENERATE_QHP = NO + +# If the QHG_LOCATION tag is specified, the QCH_FILE tag can +# be used to specify the file name of the resulting .qch file. +# The path specified is relative to the HTML output folder. + +QCH_FILE = + +# The QHP_NAMESPACE tag specifies the namespace to use when generating +# Qt Help Project output. For more information please see +# http://doc.trolltech.com/qthelpproject.html#namespace + +QHP_NAMESPACE = + +# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating +# Qt Help Project output. For more information please see +# http://doc.trolltech.com/qthelpproject.html#virtual-folders + +QHP_VIRTUAL_FOLDER = doc + +# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to add. +# For more information please see +# http://doc.trolltech.com/qthelpproject.html#custom-filters + +QHP_CUST_FILTER_NAME = + +# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the custom filter to add.For more information please see +# Qt Help Project / Custom Filters. + +QHP_CUST_FILTER_ATTRS = + +# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this project's +# filter section matches. +# Qt Help Project / Filter Attributes. + +QHP_SECT_FILTER_ATTRS = + +# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can +# be used to specify the location of Qt's qhelpgenerator. +# If non-empty doxygen will try to run qhelpgenerator on the generated +# .qhp file. + +QHG_LOCATION = + +# The DISABLE_INDEX tag can be used to turn on/off the condensed index at +# top of each HTML page. The value NO (the default) enables the index and +# the value YES disables it. + +DISABLE_INDEX = NO + +# This tag can be used to set the number of enum values (range [1..20]) +# that doxygen will group on one line in the generated HTML documentation. + +ENUM_VALUES_PER_LINE = 4 + +# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index +# structure should be generated to display hierarchical information. +# If the tag value is set to YES, a side panel will be generated +# containing a tree-like index structure (just like the one that +# is generated for HTML Help). For this to work a browser that supports +# JavaScript, DHTML, CSS and frames is required (i.e. any modern browser). +# Windows users are probably better off using the HTML help feature. + +GENERATE_TREEVIEW = YES + +# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories, +# and Class Hierarchy pages using a tree view instead of an ordered list. + +USE_INLINE_TREES = NO + +# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be +# used to set the initial width (in pixels) of the frame in which the tree +# is shown. + +TREEVIEW_WIDTH = 250 + +# Use this tag to change the font size of Latex formulas included +# as images in the HTML documentation. The default is 10. Note that +# when you change the font size after a successful doxygen run you need +# to manually remove any form_*.png images from the HTML output directory +# to force them to be regenerated. + +FORMULA_FONTSIZE = 10 + +# When the SEARCHENGINE tag is enable doxygen will generate a search box for the HTML output. The underlying search engine uses javascript +# and DHTML and should work on any modern browser. Note that when using HTML help (GENERATE_HTMLHELP) or Qt help (GENERATE_QHP) +# there is already a search function so this one should typically +# be disabled. + +SEARCHENGINE = YES + +#--------------------------------------------------------------------------- +# configuration options related to the LaTeX output +#--------------------------------------------------------------------------- + +# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will +# generate Latex output. + +GENERATE_LATEX = NO + +# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `latex' will be used as the default path. + +LATEX_OUTPUT = latex + +# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be +# invoked. If left blank `latex' will be used as the default command name. + +LATEX_CMD_NAME = latex + +# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to +# generate index for LaTeX. If left blank `makeindex' will be used as the +# default command name. + +MAKEINDEX_CMD_NAME = makeindex + +# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact +# LaTeX documents. This may be useful for small projects and may help to +# save some trees in general. + +COMPACT_LATEX = NO + +# The PAPER_TYPE tag can be used to set the paper type that is used +# by the printer. Possible values are: a4, a4wide, letter, legal and +# executive. If left blank a4wide will be used. + +PAPER_TYPE = letter + +# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX +# packages that should be included in the LaTeX output. + +EXTRA_PACKAGES = + +# The LATEX_HEADER tag can be used to specify a personal LaTeX header for +# the generated latex document. The header should contain everything until +# the first chapter. If it is left blank doxygen will generate a +# standard header. Notice: only use this tag if you know what you are doing! + +LATEX_HEADER = + +# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated +# is prepared for conversion to pdf (using ps2pdf). The pdf file will +# contain links (just like the HTML output) instead of page references +# This makes the output suitable for online browsing using a pdf viewer. + +PDF_HYPERLINKS = YES + +# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of +# plain latex in the generated Makefile. Set this option to YES to get a +# higher quality PDF documentation. + +USE_PDFLATEX = YES + +# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. +# command to the generated LaTeX files. This will instruct LaTeX to keep +# running if errors occur, instead of asking the user for help. +# This option is also used when generating formulas in HTML. + +LATEX_BATCHMODE = NO + +# If LATEX_HIDE_INDICES is set to YES then doxygen will not +# include the index chapters (such as File Index, Compound Index, etc.) +# in the output. + +LATEX_HIDE_INDICES = NO + +# If LATEX_SOURCE_CODE is set to YES then doxygen will include source code with syntax highlighting in the LaTeX output. Note that which sources are shown also depends on other settings such as SOURCE_BROWSER. + +LATEX_SOURCE_CODE = NO + +#--------------------------------------------------------------------------- +# configuration options related to the RTF output +#--------------------------------------------------------------------------- + +# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output +# The RTF output is optimized for Word 97 and may not look very pretty with +# other RTF readers or editors. + +GENERATE_RTF = NO + +# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `rtf' will be used as the default path. + +RTF_OUTPUT = rtf + +# If the COMPACT_RTF tag is set to YES Doxygen generates more compact +# RTF documents. This may be useful for small projects and may help to +# save some trees in general. + +COMPACT_RTF = NO + +# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated +# will contain hyperlink fields. The RTF file will +# contain links (just like the HTML output) instead of page references. +# This makes the output suitable for online browsing using WORD or other +# programs which support those fields. +# Note: wordpad (write) and others do not support links. + +RTF_HYPERLINKS = NO + +# Load stylesheet definitions from file. Syntax is similar to doxygen's +# config file, i.e. a series of assignments. You only have to provide +# replacements, missing definitions are set to their default value. + +RTF_STYLESHEET_FILE = + +# Set optional variables used in the generation of an rtf document. +# Syntax is similar to doxygen's config file. + +RTF_EXTENSIONS_FILE = + +#--------------------------------------------------------------------------- +# configuration options related to the man page output +#--------------------------------------------------------------------------- + +# If the GENERATE_MAN tag is set to YES (the default) Doxygen will +# generate man pages + +GENERATE_MAN = NO + +# The MAN_OUTPUT tag is used to specify where the man pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `man' will be used as the default path. + +MAN_OUTPUT = man + +# The MAN_EXTENSION tag determines the extension that is added to +# the generated man pages (default is the subroutine's section .3) + +MAN_EXTENSION = .3 + +# If the MAN_LINKS tag is set to YES and Doxygen generates man output, +# then it will generate one additional man file for each entity +# documented in the real man page(s). These additional files +# only source the real man page, but without them the man command +# would be unable to find the correct page. The default is NO. + +MAN_LINKS = NO + +#--------------------------------------------------------------------------- +# configuration options related to the XML output +#--------------------------------------------------------------------------- + +# If the GENERATE_XML tag is set to YES Doxygen will +# generate an XML file that captures the structure of +# the code including all documentation. + +GENERATE_XML = NO + +# The XML_OUTPUT tag is used to specify where the XML pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `xml' will be used as the default path. + +XML_OUTPUT = xml + +# The XML_SCHEMA tag can be used to specify an XML schema, +# which can be used by a validating XML parser to check the +# syntax of the XML files. + +XML_SCHEMA = + +# The XML_DTD tag can be used to specify an XML DTD, +# which can be used by a validating XML parser to check the +# syntax of the XML files. + +XML_DTD = + +# If the XML_PROGRAMLISTING tag is set to YES Doxygen will +# dump the program listings (including syntax highlighting +# and cross-referencing information) to the XML output. Note that +# enabling this will significantly increase the size of the XML output. + +XML_PROGRAMLISTING = YES + +#--------------------------------------------------------------------------- +# configuration options for the AutoGen Definitions output +#--------------------------------------------------------------------------- + +# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will +# generate an AutoGen Definitions (see autogen.sf.net) file +# that captures the structure of the code including all +# documentation. Note that this feature is still experimental +# and incomplete at the moment. + +GENERATE_AUTOGEN_DEF = NO + +#--------------------------------------------------------------------------- +# configuration options related to the Perl module output +#--------------------------------------------------------------------------- + +# If the GENERATE_PERLMOD tag is set to YES Doxygen will +# generate a Perl module file that captures the structure of +# the code including all documentation. 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Note that doxygen if the +# number of direct children of the root node in a graph is already larger than +# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note +# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH. + +DOT_GRAPH_MAX_NODES = 50 + +# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the +# graphs generated by dot. A depth value of 3 means that only nodes reachable +# from the root by following a path via at most 3 edges will be shown. Nodes +# that lay further from the root node will be omitted. Note that setting this +# option to 1 or 2 may greatly reduce the computation time needed for large +# code bases. Also note that the size of a graph can be further restricted by +# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction. + +MAX_DOT_GRAPH_DEPTH = 0 + +# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent +# background. This is disabled by default, because dot on Windows does not +# seem to support this out of the box. Warning: Depending on the platform used, +# enabling this option may lead to badly anti-aliased labels on the edges of +# a graph (i.e. they become hard to read). + +DOT_TRANSPARENT = NO + +# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output +# files in one run (i.e. multiple -o and -T options on the command line). 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Line numbers are displayed with 'span.py-lineno'. - * The expand/collapse block toggle button is displayed with - * 'a.py-toggle' (Note: the CSS style for 'a.py-toggle' should not - * modify the font size of the text.) - * - If a source code page is opened with an anchor, then the - * corresponding code block will be highlighted. 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Store - // their old text in "cmd," so we will know what action to - // take; and change their text to the opposite action. - var cmd = "?"; - var elts = document.getElementsByTagName("a"); - for(var i=0; i...
"; - elt.innerHTML = s; - } -} - -function toggle(id) { - elt = document.getElementById(id+"-toggle"); - if (elt.innerHTML == "-") - collapse(id); - else - expand(id); - return false; -} - -function highlight(id) { - var elt = document.getElementById(id+"-def"); - if (elt) elt.className = "py-highlight-hdr"; - var elt = document.getElementById(id+"-expanded"); - if (elt) elt.className = "py-highlight"; - var elt = document.getElementById(id+"-collapsed"); - if (elt) elt.className = "py-highlight"; -} - -function num_lines(s) { - var n = 1; - var pos = s.indexOf("\n"); - while ( pos > 0) { - n += 1; - pos = s.indexOf("\n", pos+1); - } - return n; -} - -// Collapse all blocks that mave more than `min_lines` lines. -function collapse_all(min_lines) { - var elts = document.getElementsByTagName("div"); - for (var i=0; i 0) - if (elt.id.substring(split, elt.id.length) == "-expanded") - if (num_lines(elt.innerHTML) > min_lines) - collapse(elt.id.substring(0, split)); - } -} - -function expandto(href) { - var start = href.indexOf("#")+1; - if (start != 0 && start != href.length) { - if (href.substring(start, href.length) != "-") { - collapse_all(4); - pos = href.indexOf(".", start); - while (pos != -1) { - var id = href.substring(start, pos); - expand(id); - pos = href.indexOf(".", pos+1); - } - var id = href.substring(start, href.length); - expand(id); - highlight(id); - } - } -} - -function kill_doclink(id) { - var parent = document.getElementById(id); - parent.removeChild(parent.childNodes.item(0)); -} -function auto_kill_doclink(ev) { - if (!ev) var ev = window.event; - if (!this.contains(ev.toElement)) { - var parent = document.getElementById(this.parentID); - parent.removeChild(parent.childNodes.item(0)); - } -} - -function doclink(id, name, targets_id) { - var elt = document.getElementById(id); - - // If we already opened the box, then destroy it. - // (This case should never occur, but leave it in just in case.) - if (elt.childNodes.length > 1) { - elt.removeChild(elt.childNodes.item(0)); - } - else { - // The outer box: relative + inline positioning. - var box1 = document.createElement("div"); - box1.style.position = "relative"; - box1.style.display = "inline"; - box1.style.top = 0; - box1.style.left = 0; - - // A shadow for fun - var shadow = document.createElement("div"); - shadow.style.position = "absolute"; - shadow.style.left = "-1.3em"; - shadow.style.top = "-1.3em"; - shadow.style.background = "#404040"; - - // The inner box: absolute positioning. - var box2 = document.createElement("div"); - box2.style.position = "relative"; - box2.style.border = "1px solid #a0a0a0"; - box2.style.left = "-.2em"; - box2.style.top = "-.2em"; - box2.style.background = "white"; - box2.style.padding = ".3em .4em .3em .4em"; - box2.style.fontStyle = "normal"; - box2.onmouseout=auto_kill_doclink; - box2.parentID = id; - - // Get the targets - var targets_elt = document.getElementById(targets_id); - var targets = targets_elt.getAttribute("targets"); - var links = ""; - target_list = targets.split(","); - for (var i=0; i" + - target[0] + ""; - } - - // Put it all together. - elt.insertBefore(box1, elt.childNodes.item(0)); - //box1.appendChild(box2); - box1.appendChild(shadow); - shadow.appendChild(box2); - box2.innerHTML = - "Which "+name+" do you want to see documentation for?" + - ""; - } - return false; -} - -function get_anchor() { - var href = location.href; - var start = href.indexOf("#")+1; - if ((start != 0) && (start != href.length)) - return href.substring(start, href.length); - } -function redirect_url(dottedName) { - // Scan through each element of the "pages" list, and check - // if "name" matches with any of them. - for (var i=0; i-m" or "-c"; - // extract the portion & compare it to dottedName. - var pagename = pages[i].substring(0, pages[i].length-2); - if (pagename == dottedName.substring(0,pagename.length)) { - - // We've found a page that matches `dottedName`; - // construct its URL, using leftover `dottedName` - // content to form an anchor. - var pagetype = pages[i].charAt(pages[i].length-1); - var url = pagename + ((pagetype=="m")?"-module.html": - "-class.html"); - if (dottedName.length > pagename.length) - url += "#" + dottedName.substring(pagename.length+1, - dottedName.length); - return url; - } - } - } diff --git a/pyroms_toolbox/docs/frames.html b/pyroms_toolbox/docs/frames.html deleted file mode 100644 index 7e651fc..0000000 --- a/pyroms_toolbox/docs/frames.html +++ /dev/null @@ -1,17 +0,0 @@ - - - - - API Documentation - - - - - - - - - diff --git a/pyroms_toolbox/docs/help.html b/pyroms_toolbox/docs/help.html deleted file mode 100644 index f621b39..0000000 --- a/pyroms_toolbox/docs/help.html +++ /dev/null @@ -1,268 +0,0 @@ - - - - - Help - - - - - - - - - - - - - - - - - - - - - - -
   Home      Trees      Indices      Help   
- - - - - -
  - - - - -
[hide private]
[frames] | no frames]
-
- -

API Documentation

- -

This document contains the API (Application Programming Interface) -documentation for this project. Documentation for the Python -objects defined by the project is divided into separate pages for each -package, module, and class. The API documentation also includes two -pages containing information about the project as a whole: a trees -page, and an index page.

- -

Object Documentation

- -

Each Package Documentation page contains:

-
    -
  • A description of the package.
    • -
  • A list of the modules and sub-packages contained by the - package.
    • -
  • A summary of the classes defined by the package.
    • -
  • A summary of the functions defined by the package.
    • -
  • A summary of the variables defined by the package.
    • -
  • A detailed description of each function defined by the - package.
    • -
  • A detailed description of each variable defined by the - package.
    • -
- -

Each Module Documentation page contains:

-
    -
  • A description of the module.
    • -
  • A summary of the classes defined by the module.
    • -
  • A summary of the functions defined by the module.
    • -
  • A summary of the variables defined by the module.
    • -
  • A detailed description of each function defined by the - module.
    • -
  • A detailed description of each variable defined by the - module.
    • -
- -

Each Class Documentation page contains:

-
    -
  • A class inheritance diagram.
    • -
  • A list of known subclasses.
    • -
  • A description of the class.
    • -
  • A summary of the methods defined by the class.
    • -
  • A summary of the instance variables defined by the class.
    • -
  • A summary of the class (static) variables defined by the - class.
    • -
  • A detailed description of each method defined by the - class.
    • -
  • A detailed description of each instance variable defined by the - class.
    • -
  • A detailed description of each class (static) variable defined - by the class.
    • -
- -

Project Documentation

- -

The Trees page contains the module and class hierarchies:

-
    -
  • The module hierarchy lists every package and module, with - modules grouped into packages. At the top level, and within each - package, modules and sub-packages are listed alphabetically.
    • -
  • The class hierarchy lists every class, grouped by base - class. If a class has more than one base class, then it will be - listed under each base class. At the top level, and under each base - class, classes are listed alphabetically.
    • -
- -

The Index page contains indices of terms and - identifiers:

-
    -
  • The term index lists every term indexed by any object's - documentation. For each term, the index provides links to each - place where the term is indexed.
    • -
  • The identifier index lists the (short) name of every package, - module, class, method, function, variable, and parameter. For each - identifier, the index provides a short description, and a link to - its documentation.
    • -
- -

The Table of Contents

- -

The table of contents occupies the two frames on the left side of -the window. The upper-left frame displays the project -contents, and the lower-left frame displays the module -contents:

- - - - - - - - - -
- Project
Contents
...		 - API
Documentation
Frame


-
- Module
Contents
 
...
  -

- -

The project contents frame contains a list of all packages -and modules that are defined by the project. Clicking on an entry -will display its contents in the module contents frame. Clicking on a -special entry, labeled "Everything," will display the contents of -the entire project.

- -

The module contents frame contains a list of every -submodule, class, type, exception, function, and variable defined by a -module or package. Clicking on an entry will display its -documentation in the API documentation frame. Clicking on the name of -the module, at the top of the frame, will display the documentation -for the module itself.

- -

The "frames" and "no frames" buttons below the top -navigation bar can be used to control whether the table of contents is -displayed or not.

- -

The Navigation Bar

- -

A navigation bar is located at the top and bottom of every page. -It indicates what type of page you are currently viewing, and allows -you to go to related pages. The following table describes the labels -on the navigation bar. Note that not some labels (such as -[Parent]) are not displayed on all pages.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -
LabelHighlighted when...Links to...
[Parent](never highlighted) the parent of the current package
[Package]viewing a packagethe package containing the current object -
[Module]viewing a modulethe module containing the current object -
[Class]viewing a class the class containing the current object
[Trees]viewing the trees page the trees page
[Index]viewing the index page the index page
[Help]viewing the help page the help page
- -

The "show private" and "hide private" buttons below -the top navigation bar can be used to control whether documentation -for private objects is displayed. Private objects are usually defined -as objects whose (short) names begin with a single underscore, but do -not end with an underscore. For example, "_x", -"__pprint", and "epydoc.epytext._tokenize" -are private objects; but "re.sub", -"__init__", and "type_" are not. However, -if a module defines the "__all__" variable, then its -contents are used to decide which objects are private.

- -

A timestamp below the bottom navigation bar indicates when each -page was last updated.

- - - - - - - - - - - - - - - - - -
   Home      Trees      Indices      Help   
- - - - - -
- Generated by Epydoc 3.0.1 on Mon Sep 27 11:35:23 2010 - - http://epydoc.sourceforge.net -
- - - - diff --git a/pyroms_toolbox/docs/identifier-index.html b/pyroms_toolbox/docs/identifier-index.html deleted file mode 100644 index b386910..0000000 --- a/pyroms_toolbox/docs/identifier-index.html +++ /dev/null @@ -1,944 +0,0 @@ - - - - - Identifier Index - - - - - - - - - - - - - - - - - - - - - - -
   Home      Trees      Indices      Help   
- - - - - -
  - - - - -
[hide private]
[frames] | no frames]
-
- -
-

Identifier Index

-		 -[ - A - B - C - D - E - F - G - H - I - J - K - L - M - N - O - P - Q - R - S - T - U - V - W - X - Y - Z - _ -] -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

A

 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
absolute
-(in pyroms_toolbox.quiver')		arccosh
-(in pyroms_toolbox.quiver')		average'
-(in pyroms_toolbox)
add
-(in pyroms_toolbox.quiver')		arcsin
-(in pyroms_toolbox.quiver')		average()
-(in pyroms_toolbox.average')
adtgrad()
-(in pyroms_toolbox.seawater.heat)		arcsinh
-(in pyroms_toolbox.quiver')		avg
-(in pyroms_toolbox.average')
ALLOW_THREADS
-(in pyroms_toolbox.quiver')		arctan
-(in pyroms_toolbox.quiver')		avg2d
-(in pyroms_toolbox._average)
alpha()
-(in pyroms_toolbox.seawater.density)		arctan2
-(in pyroms_toolbox.quiver')		avg3d
-(in pyroms_toolbox._average)
arccos
-(in pyroms_toolbox.quiver')		arctanh
-(in pyroms_toolbox.quiver')		avg_obj
-(in pyroms_toolbox.average')
-

B

 - - - - - - - - - - - - - - - - - - - - - -
beta()
-(in pyroms_toolbox.seawater.density)		BGrid_GFDL'
-(in pyroms_toolbox.BGrid_GFDL)		bitwise_or
-(in pyroms_toolbox.quiver')
BGrid_GFDL
-(in pyroms_toolbox)		BGrid_GFDL_full
-(in pyroms_toolbox.BGrid_GFDL)		bitwise_xor
-(in pyroms_toolbox.quiver')
BGrid_GFDL
-(in pyroms_toolbox.BGrid_GFDL.BGrid_GFDL')		bitwise_and
-(in pyroms_toolbox.quiver')		BUFSIZE
-(in pyroms_toolbox.quiver')
BGrid_GFDL
-(in pyroms_toolbox.BGrid_GFDL.BGrid_GFDL_full)		bitwise_not
-(in pyroms_toolbox.quiver')		 
-

C

 - - - - - - - - - - - - - - - - - - - - - -
c_
-(in pyroms_toolbox.quiver')		change()
-(in pyroms_toolbox.change')		conjugate
-(in pyroms_toolbox.quiver')
cast
-(in pyroms_toolbox.quiver')		CLIP
-(in pyroms_toolbox.quiver')		cos
-(in pyroms_toolbox.quiver')
ceil
-(in pyroms_toolbox.quiver')		cond()
-(in pyroms_toolbox.seawater.salinity)		cosh
-(in pyroms_toolbox.quiver')
change'
-(in pyroms_toolbox)		conj
-(in pyroms_toolbox.quiver')		 
-

D

 - - - - - - - - - - - - - - - - -
deg2rad
-(in pyroms_toolbox.quiver')		density
-(in pyroms_toolbox.seawater)		drhods()
-(in pyroms_toolbox.seawater.density)
degrees
-(in pyroms_toolbox.quiver')		depth()
-(in pyroms_toolbox.seawater.misc)		drhodt()
-(in pyroms_toolbox.seawater.density)
dens()
-(in pyroms_toolbox.seawater.density)		divide
-(in pyroms_toolbox.quiver')		 
-

E

 - - - - - - - - - - - - - - - - - - - - - - - - - - -
e
-(in pyroms_toolbox.quiver')		ERR_IGNORE
-(in pyroms_toolbox.quiver')		exp
-(in pyroms_toolbox.quiver')
equal
-(in pyroms_toolbox.quiver')		ERR_LOG
-(in pyroms_toolbox.quiver')		exp2
-(in pyroms_toolbox.quiver')
ERR_CALL
-(in pyroms_toolbox.quiver')		ERR_PRINT
-(in pyroms_toolbox.quiver')		expm1
-(in pyroms_toolbox.quiver')
ERR_DEFAULT
-(in pyroms_toolbox.quiver')		ERR_RAISE
-(in pyroms_toolbox.quiver')		 
ERR_DEFAULT2
-(in pyroms_toolbox.quiver')		ERR_WARN
-(in pyroms_toolbox.quiver')		 
-

F

 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
fabs
-(in pyroms_toolbox.quiver')		floor_divide
-(in pyroms_toolbox.quiver')		FPE_OVERFLOW
-(in pyroms_toolbox.quiver')
False_
-(in pyroms_toolbox.quiver')		fmax
-(in pyroms_toolbox.quiver')		FPE_UNDERFLOW
-(in pyroms_toolbox.quiver')
FLOATING_POINT_SUPPORT
-(in pyroms_toolbox.quiver')		fmin
-(in pyroms_toolbox.quiver')		freezept()
-(in pyroms_toolbox.seawater.misc)
flood'
-(in pyroms_toolbox.BGrid_GFDL)		fmod
-(in pyroms_toolbox.quiver')		frexp
-(in pyroms_toolbox.quiver')
flood()
-(in pyroms_toolbox.BGrid_GFDL.flood')		FPE_DIVIDEBYZERO
-(in pyroms_toolbox.quiver')		 
floor
-(in pyroms_toolbox.quiver')		FPE_INVALID
-(in pyroms_toolbox.quiver')		 
-

G

 - - - - - - - - - - - - - - - - - - - - - -
get_Bgrid_proj'
-(in pyroms_toolbox.BGrid_GFDL)		get_coast_line()
-(in pyroms_toolbox.BGrid_GFDL.get_coast_line')		get_nc_BGrid_GFDL()
-(in pyroms_toolbox.BGrid_GFDL.get_nc_BGrid_GFDL')
get_Bgrid_proj()
-(in pyroms_toolbox.BGrid_GFDL.get_Bgrid_proj')		get_coast_line()
-(in pyroms_toolbox.get_coast_line')		greater
-(in pyroms_toolbox.quiver')
get_coast_line'
-(in pyroms_toolbox.BGrid_GFDL)		get_nc_BGrid_GFDL'
-(in pyroms_toolbox.BGrid_GFDL)		greater_equal
-(in pyroms_toolbox.quiver')
get_coast_line'
-(in pyroms_toolbox)		get_nc_BGrid_GFDL()
-(in pyroms_toolbox.BGrid_GFDL.BGrid_GFDL_full)		 
-

H

 - - - - - - - -
heat
-(in pyroms_toolbox.seawater)		heatcap()
-(in pyroms_toolbox.seawater.heat)		hypot
-(in pyroms_toolbox.quiver')
   
-

I

 - - - - - - - - - - - - - - - - - - - - - - - - - - -
index_exp
-(in pyroms_toolbox.quiver')		invert
-(in pyroms_toolbox.quiver')		isoview()
-(in pyroms_toolbox.isoview')
Inf
-(in pyroms_toolbox.quiver')		isfinite
-(in pyroms_toolbox.quiver')		iview'
-(in pyroms_toolbox)
inf
-(in pyroms_toolbox.quiver')		isinf
-(in pyroms_toolbox.quiver')		iview()
-(in pyroms_toolbox.iview')
Infinity
-(in pyroms_toolbox.quiver')		isnan
-(in pyroms_toolbox.quiver')		 
infty
-(in pyroms_toolbox.quiver')		isoview'
-(in pyroms_toolbox)		 
-

J

 - - - - - - - -
jview'
-(in pyroms_toolbox)		jview()
-(in pyroms_toolbox.jview')		 
   
-

L

 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
latview'
-(in pyroms_toolbox)		log
-(in pyroms_toolbox.quiver')		logical_or
-(in pyroms_toolbox.quiver')
latview()
-(in pyroms_toolbox.latview')		log10
-(in pyroms_toolbox.quiver')		logical_xor
-(in pyroms_toolbox.quiver')
ldexp
-(in pyroms_toolbox.quiver')		log1p
-(in pyroms_toolbox.quiver')		lonview'
-(in pyroms_toolbox)
left_shift
-(in pyroms_toolbox.quiver')		logaddexp
-(in pyroms_toolbox.quiver')		lonview()
-(in pyroms_toolbox.lonview')
less
-(in pyroms_toolbox.quiver')		logaddexp2
-(in pyroms_toolbox.quiver')		lsq_phase_amplitude'
-(in pyroms_toolbox)
less_equal
-(in pyroms_toolbox.quiver')		logical_and
-(in pyroms_toolbox.quiver')		lsq_phase_amplitude()
-(in pyroms_toolbox.lsq_phase_amplitude')
little_endian
-(in pyroms_toolbox.quiver')		logical_not
-(in pyroms_toolbox.quiver')		 
-

M

 - - - - - - - - - - - - - - - - - - - - - -
make_remap_BGrid_GFDL_file()
-(in pyroms_toolbox.BGrid_GFDL.BGrid_GFDL_full)		maximum
-(in pyroms_toolbox.quiver')		mod
-(in pyroms_toolbox.quiver')
make_remap_grid_file'
-(in pyroms_toolbox.BGrid_GFDL)		mgrid
-(in pyroms_toolbox.quiver')		modf
-(in pyroms_toolbox.quiver')
make_remap_grid_file()
-(in pyroms_toolbox.BGrid_GFDL.make_remap_grid_file')		minimum
-(in pyroms_toolbox.quiver')		multiply
-(in pyroms_toolbox.quiver')
MAXDIMS
-(in pyroms_toolbox.quiver')		misc
-(in pyroms_toolbox.seawater)		 
-

N

 - - - - - - - - - - - - - - - - - - - - - - - - - - -
N2'
-(in pyroms_toolbox)		nbytes
-(in pyroms_toolbox.quiver')		negative
-(in pyroms_toolbox.quiver')
N2()
-(in pyroms_toolbox.N2')		nc_create_roms_bdry_file'
-(in pyroms_toolbox)		newaxis
-(in pyroms_toolbox.quiver')
NAN
-(in pyroms_toolbox.quiver')		nc_create_roms_bdry_file()
-(in pyroms_toolbox.nc_create_roms_bdry_file')		NINF
-(in pyroms_toolbox.quiver')
NaN
-(in pyroms_toolbox.quiver')		nc_create_roms_file'
-(in pyroms_toolbox)		not_equal
-(in pyroms_toolbox.quiver')
nan
-(in pyroms_toolbox.quiver')		nc_create_roms_file()
-(in pyroms_toolbox.nc_create_roms_file')		NZERO
-(in pyroms_toolbox.quiver')
-

O

 - - - - - - - - - - - -
O2_saturation'
-(in pyroms_toolbox)		ogrid
-(in pyroms_toolbox.quiver')		OutOfRangeError
-(in pyroms_toolbox.seawater)
O2_saturation()
-(in pyroms_toolbox.O2_saturation')		ones_like
-(in pyroms_toolbox.quiver')		 
-

P

 - - - - - - - - - - - - - - - - - - - - - -
pi
-(in pyroms_toolbox.quiver')		plot_coast_line()
-(in pyroms_toolbox.BGrid_GFDL.plot_coast_line')		power
-(in pyroms_toolbox.quiver')
PINF
-(in pyroms_toolbox.quiver')		plot_coast_line()
-(in pyroms_toolbox.plot_coast_line')		pyroms_toolbox
plot_coast_line'
-(in pyroms_toolbox.BGrid_GFDL)		plot_mask'
-(in pyroms_toolbox)		PZERO
-(in pyroms_toolbox.quiver')
plot_coast_line'
-(in pyroms_toolbox)		plot_mask()
-(in pyroms_toolbox.plot_mask')		 
-

Q

 - - - - - - - -
quiver'
-(in pyroms_toolbox)		quiver()
-(in pyroms_toolbox.quiver')		 
   
-

R

 - - - - - - - - - - - - - - - - - - - - - - - - - - -
r_
-(in pyroms_toolbox.quiver')		remainder
-(in pyroms_toolbox.quiver')		right_shift
-(in pyroms_toolbox.quiver')
rad2deg
-(in pyroms_toolbox.quiver')		remapping'
-(in pyroms_toolbox)		rint
-(in pyroms_toolbox.quiver')
radians
-(in pyroms_toolbox.quiver')		remapping()
-(in pyroms_toolbox.remapping')		rvalue'
-(in pyroms_toolbox)
RAISE
-(in pyroms_toolbox.quiver')		rfactor'
-(in pyroms_toolbox)		rvalue()
-(in pyroms_toolbox.rvalue')
reciprocal
-(in pyroms_toolbox.quiver')		rfactor()
-(in pyroms_toolbox.rfactor')		 
-

S

 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
s_
-(in pyroms_toolbox.quiver')		shapiro2()
-(in pyroms_toolbox.shapiro_filter)		sin
-(in pyroms_toolbox.quiver')
salinity
-(in pyroms_toolbox.seawater)		shapiro_filter
-(in pyroms_toolbox)		sinh
-(in pyroms_toolbox.quiver')
salt()
-(in pyroms_toolbox.seawater.salinity)		SHIFT_DIVIDEBYZERO
-(in pyroms_toolbox.quiver')		soundvel()
-(in pyroms_toolbox.seawater.misc)
ScalarType
-(in pyroms_toolbox.quiver')		SHIFT_INVALID
-(in pyroms_toolbox.quiver')		sqrt
-(in pyroms_toolbox.quiver')
sctypeDict
-(in pyroms_toolbox.quiver')		SHIFT_OVERFLOW
-(in pyroms_toolbox.quiver')		square
-(in pyroms_toolbox.quiver')
sctypeNA
-(in pyroms_toolbox.quiver')		SHIFT_UNDERFLOW
-(in pyroms_toolbox.quiver')		subtract
-(in pyroms_toolbox.quiver')
sctypes
-(in pyroms_toolbox.quiver')		sigma()
-(in pyroms_toolbox.seawater.density)		svan()
-(in pyroms_toolbox.seawater.density)
seawater
-(in pyroms_toolbox)		sign
-(in pyroms_toolbox.quiver')		sview'
-(in pyroms_toolbox)
shapiro1()
-(in pyroms_toolbox.shapiro_filter)		signbit
-(in pyroms_toolbox.quiver')		sview()
-(in pyroms_toolbox.sview')
-

T

 - - - - - - - - - - - - - - - - - - - - - - - - - - -
tan
-(in pyroms_toolbox.quiver')		transectview'
-(in pyroms_toolbox)		twoDview'
-(in pyroms_toolbox)
tanh
-(in pyroms_toolbox.quiver')		transectview()
-(in pyroms_toolbox.transectview')		twoDview()
-(in pyroms_toolbox.twoDview')
temppot()
-(in pyroms_toolbox.seawater.heat)		True_
-(in pyroms_toolbox.quiver')		typecodes
-(in pyroms_toolbox.quiver')
temppot0()
-(in pyroms_toolbox.seawater.heat)		true_divide
-(in pyroms_toolbox.quiver')		typeDict
-(in pyroms_toolbox.quiver')
test
-(in pyroms_toolbox.seawater)		trunc
-(in pyroms_toolbox.quiver')		typeNA
-(in pyroms_toolbox.quiver')
-

U

 - - - - - - - -
UFUNC_BUFSIZE_DEFAULT
-(in pyroms_toolbox.quiver')		UFUNC_PYVALS_NAME
-(in pyroms_toolbox.quiver')		 
   
-

W

 - - - - - - - -
WRAP
-(in pyroms_toolbox.quiver')		  
   
-

Z

 - - - - - - - -
zview'
-(in pyroms_toolbox)		zview()
-(in pyroms_toolbox.zview')		 
   
-

_

 - - - - - - - - - - - - - - - - - - - - - - - - - - -
__init__()
-(in BGrid_GFDL)		_c()
-(in pyroms_toolbox.seawater.salinity)		_dens0()
-(in pyroms_toolbox.seawater.density)
__init__()
-(in BGrid_GFDL)		_calculate_grid_angle()
-(in BGrid_GFDL)		_dsal()
-(in pyroms_toolbox.seawater.salinity)
_a()
-(in pyroms_toolbox.seawater.salinity)		_calculate_grid_angle()
-(in BGrid_GFDL)		_rt()
-(in pyroms_toolbox.seawater.salinity)
_average
-(in pyroms_toolbox)		_calculate_t_vert()
-(in BGrid_GFDL)		_sal()
-(in pyroms_toolbox.seawater.salinity)
_b()
-(in pyroms_toolbox.seawater.salinity)		_calculate_uv_vert()
-(in BGrid_GFDL)		_seck()
-(in pyroms_toolbox.seawater.density)
-
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Module Hierarchy

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Package pyroms_toolbox

source code

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PYROMS_TOOLBOX is a toolbox for working with ROMS ocean models - input/output files based on PYROMS

-

pyroms and pyroms_toolbox are based on the python/numpy/matplotlib - scientific python suite. NetCDF I/O is based on the NetCDF4-python - package.

- -
-

Version: - 0.1.0 -

-

Author: - Frederic Castruccio (frederic@marine.rutgers.edu) -

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Source Code for Package pyroms_toolbox

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- 1  #!/usr/bin/env python 
- 2  ''' 
- 3  PYROMS_TOOLBOX is a toolbox for working with ROMS  
- 4  ocean models input/output files based on PYROMS 
- 5   
- 6  pyroms and pyroms_toolbox are based on the  
- 7  python/numpy/matplotlib scientific python suite.  
- 8  NetCDF I/O is based on the NetCDF4-python package. 
- 9  ''' 
-10   
-11   
-12  from iview import iview 
-13  from jview import jview 
-14  from lonview import lonview 
-15  from latview import latview 
-16  from sview import sview 
-17  from zview import zview 
-18  from isoview import isoview 
-19  from twoDview import twoDview 
-20  from transectview import transectview 
-21  from quiver import quiver 
-22  import seawater 
-23  from N2 import N2 
-24  from O2_saturation import O2_saturation 
-25  from shapiro_filter import * 
-26  from change import change 
-27  from rfactor import rfactor 
-28  from rvalue import rvalue 
-29  from get_coast_line import get_coast_line 
-30  from plot_coast_line import plot_coast_line 
-31  from lsq_phase_amplitude import lsq_phase_amplitude 
-32  from remapping import remapping 
-33  from nc_create_roms_file import nc_create_roms_file 
-34  from nc_create_roms_bdry_file import nc_create_roms_bdry_file 
-35  from average import average 
-36  from plot_mask import plot_mask 
-37  import BGrid_GFDL 
-38   
-39  __authors__ = ['Frederic Castruccio (frederic@marine.rutgers.edu)'] 
-40   
-41  __version__ = '0.1.0' 
-42   
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Package BGrid_GFDL

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BGrid_GFDL module

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Source Code for Package pyroms_toolbox.BGrid_GFDL

-
- 1  """ 
- 2  BGrid_GFDL module 
- 3  """ 
- 4   
- 5  from BGrid_GFDL import BGrid_GFDL 
- 6  from get_nc_BGrid_GFDL import get_nc_BGrid_GFDL 
- 7  from make_remap_grid_file import make_remap_grid_file 
- 8  from get_coast_line import get_coast_line 
- 9  from plot_coast_line import plot_coast_line 
-10  from get_Bgrid_proj import get_Bgrid_proj 
-11  from flood import flood 
-12   
-
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Module BGrid_GFDL'

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- Arakawa B-Grid for GFDL CM2.1 -
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Source Code for Module pyroms_toolbox.BGrid_GFDL.BGrid_GFDL'

-
- 1  import numpy as np 
- 2  from mpl_toolkits.basemap import pyproj 
- 3  from datetime import datetime 
- 4  try: 
- 5    import netCDF4 as netCDF 
- 6  except: 
- 7    import netCDF3 as netCDF 
- 8  import pyroms 
- 9   
-10   
-11   
-
12 -class BGrid_GFDL(object): 
-
13      """ 
-14      Arakawa B-Grid for GFDL CM2.1 
-15      """ 
-16   
-17   
-
18 -    def __init__(self, lon_t, lat_t, lon_uv, lat_uv, \ 
-19                         mask_t, mask_uv, h, z_t, z_t_edges, \ 
-20                         z_uv, z_uv_edges, f, name, xrange, yrange): 
-
21   
-22          self.name = name 
-23   
-24          self.xrange = xrange 
-25          self.yrange = yrange 
-26   
-27          self.lon_t = lon_t[yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] 
-28          self.lat_t = lat_t[yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] 
-29          self.lon_uv = lon_uv[yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] 
-30          self.lat_uv = lat_uv[yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] 
-31          self.mask_t = mask_t[:,yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] 
-32          self.mask_uv = mask_uv[:,yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] 
-33          self.h = h[yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] 
-34          self.z_t = z_t 
-35          self.z_t_edges = z_t_edges 
-36          self.z_uv = z_uv 
-37          self.z_uv_edges = z_uv_edges 
-38          self.f = f[yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] 
-39   
-40          self.lon_t_vert = lon_uv[yrange[0]-1:yrange[1]+1, xrange[0]-1:xrange[1]+1] 
-41          self.lat_t_vert = lat_uv[yrange[0]-1:yrange[1]+1, xrange[0]-1:xrange[1]+1] 
-42   
-43          self.lon_uv_vert = lon_t[yrange[0]:yrange[1]+2, xrange[0]:xrange[1]+2] 
-44          self.lat_uv_vert = lat_t[yrange[0]:yrange[1]+2, xrange[0]:xrange[1]+2] 
-45   
-46          self._calculate_grid_angle() 
-
47   
-48   
-
49 -    def _calculate_grid_angle(self): 
-
50          geod = pyproj.Geod(ellps='WGS84') 
-51          az_forward, az_back, dx = geod.inv(self.lon_t_vert[:,:-1], self.lat_t_vert[:,:-1], \ 
-52                                             self.lon_t_vert[:,1:], self.lat_t_vert[:,1:]) 
-53   
-54          angle = 0.5 * (az_forward[1:,:] + az_forward[:-1,:]) 
-55          self.angle = (90 - angle) * np.pi/180. 
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56   
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Class BGrid_GFDL

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-object --+
-         |
-        BGrid_GFDL
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-

Arakawa B-Grid for GFDL CM2.1

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Instance Methods[hide private]
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__init__(self, - lon_t, - lat_t, - lon_uv, - lat_uv, - mask_t, - mask_uv, - h, - z_t, - z_t_edges, - z_uv, - z_uv_edges, - f, - name, - xrange, - yrange)
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature		 - source code - -
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-   - - - - - - -
_calculate_grid_angle(self) - source code - -
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Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

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Properties[hide private]
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Inherited from object: - __class__ -

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Method Details[hide private]
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__init__(self, - lon_t, - lat_t, - lon_uv, - lat_uv, - mask_t, - mask_uv, - h, - z_t, - z_t_edges, - z_uv, - z_uv_edges, - f, - name, - xrange, - yrange) -
(Constructor) -

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x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

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Module BGrid_GFDL_full

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Classes[hide private]
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-   - - BGrid_GFDL
- Arakawa B-Grid for GFDL CM2.1 -
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Functions[hide private]
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get_nc_BGrid_GFDL(grdfile)
- Bgrd = get_nc_BGrid_GFDL(grdfile)		 - source code - -
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make_remap_BGrid_GFDL_file(Bgrd, - Bpos='t') - source code - -
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Function Details[hide private]
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get_nc_BGrid_GFDL(grdfile) -

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Bgrd = get_nc_BGrid_GFDL(grdfile)

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Load B-Grid grid object for GFDL CM2.1 from netCDF grid file

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Source Code for Module pyroms_toolbox.BGrid_GFDL.BGrid_GFDL_full

-
-  1  import numpy as np 
-  2  from mpl_toolkits.basemap import pyproj 
-  3  from datetime import datetime 
-  4  try: 
-  5    import netCDF4 as netCDF 
-  6  except: 
-  7    import netCDF3 as netCDF 
-  8  import pyroms 
-  9   
- 10   
- 11   
-
 12 -class BGrid_GFDL(object): 
-
 13      """ 
- 14      Arakawa B-Grid for GFDL CM2.1 
- 15      """ 
- 16   
- 17   
-
 18 -    def __init__(self, lon_t, lat_t, lon_uv, lat_uv, \ 
- 19                         mask_t, mask_uv, h, z_t, z_t_edges, \ 
- 20                         z_uv, z_uv_edges, f): 
-
 21   
- 22          self.name = 'GFDL_CM2.1' 
- 23          self.lon_t = lon_t 
- 24          self.lat_t = lat_t 
- 25          self.lon_uv = lon_uv 
- 26          self.lat_uv = lat_uv 
- 27          self.mask_t = mask_t 
- 28          self.mask_uv = mask_uv 
- 29          self.h = h 
- 30          self.z_t = z_t 
- 31          self.z_t_edges = z_t_edges 
- 32          self.z_uv = z_uv 
- 33          self.z_uv_edges = z_uv_edges 
- 34          self.f = f 
- 35   
- 36          self._calculate_t_vert() 
- 37          self._calculate_uv_vert() 
- 38          self._calculate_grid_angle() 
-
 39   
- 40   
-
 41 -    def _calculate_t_vert(self): 
-
 42          Mm, Lm = self.lon_t.shape 
- 43          lon = np.zeros((Mm+1,Lm+1)) 
- 44          lat = np.zeros((Mm+1,Lm+1)) 
- 45   
- 46          lon[1:, 1:] = self.lon_uv[:,:] 
- 47          lat[1:, 1:] = self.lat_uv[:,:] 
- 48   
- 49          #South edge 
- 50          lon[0,0:-1] = self.lon_t[0,:] - ( self.lon_uv[0,:] - self.lon_t[0,:] ) 
- 51          lon[0,-1] = self.lon_t[0,-1] - ( self.lon_uv[0,-2] - self.lon_t[0,-1] ) 
- 52          lat[0,0:-1] = self.lat_t[0,:] - ( self.lat_uv[0,:] - self.lat_t[0,:] ) 
- 53          lat[0,-1] = self.lat_t[0,-1] - ( self.lat_uv[0,-2] - self.lat_t[0,-1] ) 
- 54   
- 55          #West edge 
- 56          lon[0:-1,0] = self.lon_t[:,0] - ( self.lon_uv[:,0] - self.lon_t[:,0] ) 
- 57          lon[-1,0] = self.lon_t[-1,0] - ( self.lon_uv[-2,0] - self.lon_t[-1,0] ) 
- 58          lat[0:-1,0] = self.lat_t[:,0] - ( self.lat_uv[:,0] - self.lat_t[:,0] ) 
- 59          lat[-1,0] = self.lat_t[-1,0] - ( self.lat_uv[-2,0] - self.lat_t[-1,0] ) 
- 60   
- 61          self.lon_t_vert = lon 
- 62          self.lat_t_vert = lat 
-
 63   
- 64   
-
 65 -    def _calculate_uv_vert(self): 
-
 66          Mm, Lm = self.lon_uv.shape 
- 67          lon = np.zeros((Mm+1,Lm+1)) 
- 68          lat = np.zeros((Mm+1,Lm+1)) 
- 69   
- 70          lon[:-1, :-1] = self.lon_t[:,:] 
- 71          lat[:-1, :-1] = self.lat_t[:,:] 
- 72   
- 73          #North edge 
- 74          lon[-1,0:-2] = self.lon_uv[-1,:-1] - ( self.lon_t[-1,1:] - self.lon_uv[-1,:-1] ) 
- 75          lon[-1,-2:] = self.lon_uv[-1,-2:] - ( self.lon_t[-1,-2:] - self.lon_uv[-1,-2:] ) 
- 76          lat[-1,0:-2] = self.lat_uv[-1,:-1] - ( self.lat_t[-1,1:] - self.lat_uv[-1,:-1] ) 
- 77          lat[-1,-2:] = self.lat_uv[-1,-2:] - ( self.lat_t[-1,-2:] - self.lat_uv[-1,-2:] ) 
- 78   
- 79          #East edge 
- 80          lon[0:-2,-1] = self.lon_uv[:-1,-1] - ( self.lon_t[1:,-1] - self.lon_uv[:-1,-1] ) 
- 81          lon[-2,-1] = self.lon_uv[-2:-1,-1] - ( self.lon_t[-2:-1,-1] - self.lon_uv[-2:-1,-1] ) 
- 82          lat[0:-2,-1] = self.lat_uv[:-1,-1] - ( self.lat_t[1:,-1] - self.lat_uv[:-1,-1] ) 
- 83          lat[-2,-1] = self.lat_uv[-2:-1,-1] - ( self.lat_t[-2:-1,-1] - self.lat_uv[-2:-1,-1] ) 
- 84   
- 85          self.lon_uv_vert = lon 
- 86          self.lat_uv_vert = lat 
-
 87   
- 88   
-
 89 -    def _calculate_grid_angle(self): 
-
 90          geod = pyproj.Geod(ellps='WGS84') 
- 91          az_forward, az_back, dx = geod.inv(self.lon_t[:,:-1], self.lat_t[:,:-1], \ 
- 92                                             self.lon_t[:,1:], self.lat_t[:,1:]) 
- 93   
- 94          angle = 0.5 * (az_forward[1:,:] + az_forward[:-1,:]) 
- 95          self.angle = (90 - angle) * np.pi/180. 
-
 96           
- 97   
- 98   
-
 99 -def get_nc_BGrid_GFDL(grdfile): 
-
100      """ 
-101      Bgrd = get_nc_BGrid_GFDL(grdfile) 
-102   
-103      Load B-Grid grid object for GFDL CM2.1 from netCDF grid file 
-104      """ 
-105   
-106      nc = pyroms.io.Dataset(grdfile) 
-107   
-108      lon_t = nc.variables['geolon_t'][:] 
-109      lat_t = nc.variables['geolat_t'][:] 
-110      lon_uv = nc.variables['geolon_c'][:] 
-111      lat_uv = nc.variables['geolat_c'][:] 
-112   
-113      h = nc.variables['ht'][:] 
-114   
-115      f = nc.variables['coriolis_param'][:] 
-116   
-117      kmt = nc.variables['kmt'][:] 
-118      z_t = nc.variables['st_ocean'][:] 
-119      z_t_edges = nc.variables['st_edges_ocean'][:] 
-120   
-121      kmu = nc.variables['kmu'][:] 
-122      z_uv = nc.variables['sw_ocean'][:] 
-123      z_uv_edges = nc.variables['sw_edges_ocean'][:] 
-124   
-125      # compute mask at t-point 
-126      M_t, L_t = kmt.shape 
-127      N_t = z_t.shape[0] 
-128      mask_t = np.zeros((N_t, M_t, L_t)) 
-129      for j in range(M_t): 
-130          for i in range(L_t): 
-131              try: 
-132                  mask_t[0:kmt[j,i], j,i] = 1 
-133              except: 
-134                  mask_t[:, j,i] = 0 
-135   
-136      # compute mask at uv-point 
-137      M_uv, L_uv = kmu.shape 
-138      N_uv = z_uv.shape[0] 
-139      mask_uv = np.zeros((N_uv, M_uv, L_uv)) 
-140      for j in range(M_uv): 
-141          for i in range(L_uv): 
-142              try: 
-143                  mask_uv[0:kmt[j,i], j,i] = 1 
-144              except: 
-145                  mask_uv[:, j,i] = 0 
-146   
-147      return BGrid_GFDL(lon_t, lat_t, lon_uv, lat_uv, \ 
-148                         mask_t, mask_uv, h, z_t, z_t_edges, \ 
-149                         z_uv, z_uv_edges, f) 
-
150   
-151   
-152   
-
153 -def make_remap_BGrid_GFDL_file(Bgrd, Bpos='t'): 
-
154   
-155      #create remap file 
-156      remap_filename = 'remap_grid_' + Bgrd.name + '_' + Bpos + '.nc' 
-157      nc = netCDF.Dataset(remap_filename, 'w', format='NETCDF3_CLASSIC') 
-158      nc.Description = 'remap grid file on' + Bpos + 'points' 
-159      nc.Author = 'pyroms.remapping.make_remap_grid_file' 
-160      nc.Created = datetime.now().strftime("%Y-%m-%d %H:%M:%S") 
-161      nc.title = Bgrd.name 
-162   
-163      if Bpos == 't': 
-164          lon_corner = Bgrd.lon_t_vert 
-165          lat_corner = Bgrd.lat_t_vert 
-166          grid_center_lon = Bgrd.lon_t.flatten() 
-167          grid_center_lat = Bgrd.lat_t.flatten() 
-168          grid_imask = Bgrd.mask_t[0,:].flatten() 
-169          Mp, Lp = Bgrd.lon_t.shape 
-170      elif Bpos == 'uv': 
-171          lon_corner = Bgrd.lon_uv_vert 
-172          lat_corner = Bgrd.lat_uv_vert 
-173          grid_center_lon = Bgrd.lon_uv.flatten() 
-174          grid_center_lat = Bgrd.lat_uv.flatten() 
-175          grid_imask = Bgrd.mask_uv[0,:].flatten() 
-176          Mp, Lp = Bgrd.lon_uv.shape 
-177      else: 
-178          raise ValueError, 'Bpos must be t or uv' 
-179   
-180      grid_size = Lp * Mp 
-181   
-182      grid_corner_lon = np.zeros((grid_size, 4)) 
-183      grid_corner_lat = np.zeros((grid_size, 4)) 
-184      k = 0 
-185      for j in range(Mp): 
-186          for i in range(Lp): 
-187              grid_corner_lon[k,0] = lon_corner[j,i] 
-188              grid_corner_lat[k,0] = lat_corner[j,i] 
-189              grid_corner_lon[k,1] = lon_corner[j,i+1] 
-190              grid_corner_lat[k,1] = lat_corner[j,i+1] 
-191              grid_corner_lon[k,2] = lon_corner[j+1,i+1] 
-192              grid_corner_lat[k,2] = lat_corner[j+1,i+1] 
-193              grid_corner_lon[k,3] = lon_corner[j+1,i] 
-194              grid_corner_lat[k,3] = lat_corner[j+1,i] 
-195              k = k + 1 
-196   
-197      #Write netcdf file 
-198      nc.createDimension('grid_size', grid_size) 
-199      nc.createDimension('grid_corners', 4) 
-200      nc.createDimension('grid_rank', 2) 
-201   
-202      nc.createVariable('grid_dims', 'i4', ('grid_rank')) 
-203      nc.variables['grid_dims'].long_name = 'grid size along x and y axis' 
-204      nc.variables['grid_dims'].units = 'None' 
-205      nc.variables['grid_dims'][:] = [(Lp, Mp)] 
-206   
-207      nc.createVariable('grid_center_lon', 'f8', ('grid_size')) 
-208      nc.variables['grid_center_lon'].long_name = 'longitude of cell center' 
-209      nc.variables['grid_center_lon'].units = 'degrees' 
-210      nc.variables['grid_center_lon'][:] = grid_center_lon 
-211   
-212      nc.createVariable('grid_center_lat', 'f8', ('grid_size')) 
-213      nc.variables['grid_center_lat'].long_name = 'latitude of cell center' 
-214      nc.variables['grid_center_lat'].units = 'degrees' 
-215      nc.variables['grid_center_lat'][:] = grid_center_lat 
-216   
-217      nc.createVariable('grid_imask', 'i4', ('grid_size')) 
-218      nc.variables['grid_imask'].long_name = 'mask' 
-219      nc.variables['grid_imask'].units = 'None' 
-220      nc.variables['grid_imask'][:] = grid_imask 
-221   
-222      nc.createVariable('grid_corner_lon', 'f8', ('grid_size', 'grid_corners')) 
-223      nc.variables['grid_corner_lon'].long_name = 'longitude of cell corner' 
-224      nc.variables['grid_corner_lon'].units = 'degrees' 
-225      nc.variables['grid_corner_lon'][:] = grid_corner_lon 
-226   
-227      nc.createVariable('grid_corner_lat', 'f8', ('grid_size', 'grid_corners')) 
-228      nc.variables['grid_corner_lat'].long_name = 'latitude of cell corner' 
-229      nc.variables['grid_corner_lat'].units = 'degrees' 
-230      nc.variables['grid_corner_lat'][:] = grid_corner_lat 
-231   
-232      nc.close() 
-
233   
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Class BGrid_GFDL

source code

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Arakawa B-Grid for GFDL CM2.1

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Instance Methods[hide private]
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__init__(self, - lon_t, - lat_t, - lon_uv, - lat_uv, - mask_t, - mask_uv, - h, - z_t, - z_t_edges, - z_uv, - z_uv_edges, - f)
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_calculate_t_vert(self) - source code - -
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_calculate_uv_vert(self) - source code - -
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_calculate_grid_angle(self) - source code - -
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Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

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Properties[hide private]
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Inherited from object: - __class__ -

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Method Details[hide private]
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__init__(self, - lon_t, - lat_t, - lon_uv, - lat_uv, - mask_t, - mask_uv, - h, - z_t, - z_t_edges, - z_uv, - z_uv_edges, - f) -
(Constructor) -

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x.__init__(...) initializes x; see x.__class__.__doc__ for - signature

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Module flood'

source code

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Functions[hide private]
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flood(varz, - Bgrdz, - Bpos='t', - irange=None, - jrange=None, - spval=-10000000000.0, - dmax=0, - cdepth=0, - kk=0)
- var = flood(var, Bgrdz)		 - source code - -
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flood(varz, - Bgrdz, - Bpos='t', - irange=None, - jrange=None, - spval=-10000000000.0, - dmax=0, - cdepth=0, - kk=0) -

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var = flood(var, Bgrdz)

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optional switch:

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  • - Bpos='t', 'uv' specify the B-grid position where the - variable rely -
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  • - irange specify grid sub-sample for i direction -
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  • - jrange specify grid sub-sample for j direction -
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  • - spval=1e35 define spval value -
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  • - dmax=0 if dmax>0, maximum horizontal - flooding distance -
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  • - cdepth=0 critical depth for flooding if - depth<cdepth => no flooding -
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  • - kk -
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Flood varz on gridz

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Source Code for Module pyroms_toolbox.BGrid_GFDL.flood'

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-  1  # encoding: utf-8 
-  2   
-  3  import numpy as np 
-  4  import _remapping 
-  5   
-  6  import pyroms 
-  7   
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  8 -def flood(varz, Bgrdz, Bpos='t', irange=None, jrange=None, \ 
-  9            spval=-1.e10, dmax=0, cdepth=0, kk=0): 
-
 10      """ 
- 11      var = flood(var, Bgrdz) 
- 12   
- 13      optional switch: 
- 14        - Bpos='t', 'uv'               specify the B-grid position where  
- 15                                       the variable rely 
- 16        - irange                       specify grid sub-sample for i direction 
- 17        - jrange                       specify grid sub-sample for j direction 
- 18        - spval=1e35                   define spval value 
- 19        - dmax=0                       if dmax>0, maximum horizontal  
- 20                                       flooding distance 
- 21        - cdepth=0                     critical depth for flooding 
- 22                                       if depth<cdepth => no flooding 
- 23        - kk 
- 24   
- 25      Flood varz on gridz 
- 26      """ 
- 27   
- 28      varz = varz.copy() 
- 29      varz = np.array(varz) 
- 30   
- 31      assert len(varz.shape) == 3, 'var must be 3D' 
- 32   
- 33      # replace spval by nan 
- 34      idx = np.where(abs((varz-spval)/spval)<=1e-5) 
- 35      varz[idx] = np.nan 
- 36   
- 37      if Bpos is 't': 
- 38          x = Bgrdz.lon_t 
- 39          y = Bgrdz.lat_t 
- 40          h = Bgrdz.h 
- 41          mask = Bgrdz.mask_t[0,:,:] 
- 42      elif Bpos is 'uv': 
- 43          x = Bgrdz.lon_uv 
- 44          y = Bgrdz.lat_uv 
- 45          h = Bgrdz.h 
- 46          mask = Bgrdz.mask_uv[0,:,:] 
- 47      else: 
- 48          raise Warning, '%s bad position. Bpos must be t or uv' % Bpos 
- 49   
- 50      nlev, Mm, Lm = varz.shape 
- 51   
- 52      if irange is None: 
- 53          irange = (0,Lm) 
- 54      else: 
- 55          assert varz.shape[2] == irange[1]-irange[0], \ 
- 56                 'var shape and irange must agreed' 
- 57   
- 58      if jrange is None: 
- 59          jrange = (0,Mm) 
- 60      else: 
- 61          assert varz.shape[1] == jrange[1]-jrange[0], \ 
- 62                 'var shape and jrange must agreed' 
- 63   
- 64      x = x[jrange[0]:jrange[1], irange[0]:irange[1]] 
- 65      y = y[jrange[0]:jrange[1], irange[0]:irange[1]] 
- 66      h = h[jrange[0]:jrange[1], irange[0]:irange[1]] 
- 67      mask = mask[jrange[0]:jrange[1], irange[0]:irange[1]] 
- 68   
- 69      # Finding nearest values in horizontal 
- 70      # critical deph => no change if depth is less than specified value 
- 71      cdepth = abs(cdepth) 
- 72      if cdepth != 0: 
- 73          idx = np.where(h >= cdepth) 
- 74          msk = np.zeros(mask.shape) 
- 75          msk[idx] = 1 
- 76      else: 
- 77          msk = mask.copy() 
- 78      for k in range(nlev-1,0,-1): 
- 79          c1 = np.array(msk, dtype=bool) 
- 80          c2 = np.isnan(varz[k,:,:]) == 1 
- 81          if kk == 0: 
- 82              c3 = np.ones(mask.shape).astype(bool) 
- 83          else: 
- 84              c3 = np.isnan(varz[min(k-kk,0),:,:]) == 0 
- 85          c = c1 & c2 & c3 
- 86          idxnan = np.where(c == True) 
- 87          idx = np.where(c2 == False) 
- 88          if list(idx[0]): 
- 89              wet = np.zeros((len(idx[0]),2)) 
- 90              dry = np.zeros((len(idxnan[0]),2)) 
- 91              wet[:,0] = idx[0]+1 
- 92              wet[:,1] = idx[1]+1 
- 93              dry[:,0] = idxnan[0]+1 
- 94              dry[:,1] = idxnan[1]+1 
- 95   
- 96              varz[k,:] = _remapping.flood(varz[k,:], wet, dry, x, y, dmax) 
- 97   
- 98      # drop the deepest values down 
- 99      idx = np.where(np.isnan(varz) == 1) 
-100      varz[idx] = spval 
-101      bottom = pyroms.utility.get_bottom(varz[::-1,:,:], mask, spval=spval) 
-102      bottom = (nlev-1) - bottom 
-103      for i in range(Lm): 
-104          for j in range(Mm): 
-105              if mask[j,i] == 1: 
-106                  varz[bottom[j,i]:,j,i] = varz[bottom[j,i],j,i] 
-107   
-108      return varz 
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Module get_Bgrid_proj'

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Functions[hide private]
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get_Bgrid_proj(Bgrd, - type='merc', - resolution='h')
- map = get_Bgrid_proj(Bgrd)		 - source code - -
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Function Details[hide private]
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get_Bgrid_proj(Bgrd, - type='merc', - resolution='h') -

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map = get_Bgrid_proj(Bgrd)

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optional arguments:

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  • - resolution set resolution parameter (default is high) -
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return a Basemap object that can be use for plotting

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Source Code for Module pyroms_toolbox.BGrid_GFDL.get_Bgrid_proj'

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- 1  from mpl_toolkits.basemap import Basemap 
- 2   
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 3 -def get_Bgrid_proj(Bgrd, type='merc', resolution='h'): 
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 4      """ 
- 5      map = get_Bgrid_proj(Bgrd) 
- 6   
- 7      optional arguments: 
- 8        - type           set projection type (default is merc) 
- 9        - resolution     set resolution parameter (default is high) 
-10   
-11      return a Basemap object that can be use for plotting 
-12      """ 
-13   
-14      lon_min = Bgrd.lon_t_vert.min() 
-15      lon_max = Bgrd.lon_t_vert.max() 
-16      lon_0 = (lon_min + lon_max) / 2. 
-17   
-18      lat_min = Bgrd.lat_t_vert.min() 
-19      lat_max = Bgrd.lat_t_vert.max() 
-20      lat_0 = (lat_min + lat_max) / 2. 
-21   
-22      map = Basemap(projection=type, llcrnrlon=lon_min, llcrnrlat=lat_min, \ 
-23           urcrnrlon=lon_max, urcrnrlat=lat_max, lat_0=lat_0, lon_0=lon_0, \ 
-24           resolution=resolution) 
-25   
-26      return map 
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Module get_coast_line'

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Functions[hide private]
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get_coast_line(Bgrd)
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get_coast_line(Bgrd) -

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coast = get_coast_line(grd)

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return the coastline from the grid object grid

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Source Code for Module pyroms_toolbox.BGrid_GFDL.get_coast_line'

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- 1  import numpy as np 
- 2   
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 3 -def get_coast_line(Bgrd): 
-
 4      ''' 
- 5      coast = get_coast_line(grd) 
- 6   
- 7      return the coastline from the grid object grid  
- 8      ''' 
- 9   
-10      #get data 
-11      lon = Bgrd.lon_t_vert 
-12      lat = Bgrd.lat_t_vert 
-13      mask = Bgrd.mask_t[0,:] 
-14   
-15      #get land point 
-16      jidx, iidx = np.where(mask == 0) 
-17   
-18      coast = [] 
-19   
-20      for i in range(iidx.shape[0]): 
-21          if jidx[i] != mask.shape[0]-1: 
-22              if mask[jidx[i], iidx[i]] != mask[jidx[i]+1, iidx[i]]: 
-23                  lonc = ([lon[jidx[i]+1,iidx[i]], lon[jidx[i]+1,iidx[i]+1]]) 
-24                  latc = ([lat[jidx[i]+1,iidx[i]], lat[jidx[i]+1,iidx[i]+1]]) 
-25                  seg = zip(lonc,latc) 
-26                  coast.append(seg) 
-27   
-28          if jidx[i] != 0: 
-29              if mask[jidx[i], iidx[i]] != mask[jidx[i]-1, iidx[i]]: 
-30                  lonc = ([lon[jidx[i],iidx[i]], lon[jidx[i],iidx[i]+1]]) 
-31                  latc = ([lat[jidx[i],iidx[i]], lat[jidx[i],iidx[i]+1]]) 
-32                  seg = zip(lonc,latc) 
-33                  coast.append(seg) 
-34   
-35          if iidx[i] != mask.shape[1]-1: 
-36              if mask[jidx[i], iidx[i]] != mask[jidx[i], iidx[i]+1]: 
-37                  lonc = ([lon[jidx[i],iidx[i]+1], lon[jidx[i]+1,iidx[i]+1]]) 
-38                  latc = ([lat[jidx[i],iidx[i]+1], lat[jidx[i]+1,iidx[i]+1]]) 
-39                  seg = zip(lonc,latc) 
-40                  coast.append(seg) 
-41   
-42          if iidx[i] != 0: 
-43              if mask[jidx[i], iidx[i]] != mask[jidx[i], iidx[i]-1]: 
-44                  lonc = ([lon[jidx[i],iidx[i]], lon[jidx[i]+1,iidx[i]]]) 
-45                  latc = ([lat[jidx[i],iidx[i]], lat[jidx[i]+1,iidx[i]]]) 
-46                  seg = zip(lonc,latc) 
-47                  coast.append(seg) 
-48   
-49      return coast 
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Module get_nc_BGrid_GFDL'

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Functions[hide private]
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get_nc_BGrid_GFDL(grdfile, - name='GFDL_CM2.1_North_Pacific', - xrange=(60, 175), - yrange=(120, 190))
- Bgrd = get_nc_BGrid_GFDL(grdfile)		 - source code - -
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get_nc_BGrid_GFDL(grdfile, - name='GFDL_CM2.1_North_Pacific', - xrange=(60, 175), - yrange=(120, 190)) -

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Bgrd = get_nc_BGrid_GFDL(grdfile)

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Load B-Grid grid object for GFDL CM2.1 from netCDF grid file

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Source Code for Module pyroms_toolbox.BGrid_GFDL.get_nc_BGrid_GFDL'

-
- 1  import numpy as np 
- 2  import pyroms 
- 3  from pyroms_toolbox.BGrid_GFDL import BGrid_GFDL 
- 4   
- 5   
-
 6 -def get_nc_BGrid_GFDL(grdfile, name='GFDL_CM2.1_North_Pacific', \ 
- 7  #                             xrange=(80,189), yrange=(96,198)): 
- 8                               xrange=(60,175), yrange=(120, 190)): 
-
 9      """ 
-10      Bgrd = get_nc_BGrid_GFDL(grdfile) 
-11   
-12      Load B-Grid grid object for GFDL CM2.1 from netCDF grid file 
-13      """ 
-14   
-15      nc = pyroms.io.Dataset(grdfile) 
-16   
-17      lon_t = nc.variables['geolon_t'][:] 
-18      lat_t = nc.variables['geolat_t'][:] 
-19      lon_uv = nc.variables['geolon_c'][:] 
-20      lat_uv = nc.variables['geolat_c'][:] 
-21   
-22      h = nc.variables['ht'][:] 
-23   
-24      f = nc.variables['coriolis_param'][:] 
-25   
-26      kmt = nc.variables['kmt'][:] 
-27      z_t = nc.variables['st_ocean'][:] 
-28      z_t_edges = nc.variables['st_edges_ocean'][:] 
-29   
-30      kmu = nc.variables['kmu'][:] 
-31      z_uv = nc.variables['sw_ocean'][:] 
-32      z_uv_edges = nc.variables['sw_edges_ocean'][:] 
-33   
-34      # compute mask at t-point 
-35      M_t, L_t = kmt.shape 
-36      N_t = z_t.shape[0] 
-37      mask_t = np.zeros((N_t, M_t, L_t)) 
-38      for j in range(M_t): 
-39          for i in range(L_t): 
-40              try: 
-41                  mask_t[0:kmt[j,i], j,i] = 1 
-42              except: 
-43                  mask_t[:, j,i] = 0 
-44   
-45      # compute mask at uv-point 
-46      M_uv, L_uv = kmu.shape 
-47      N_uv = z_uv.shape[0] 
-48      mask_uv = np.zeros((N_uv, M_uv, L_uv)) 
-49      for j in range(M_uv): 
-50          for i in range(L_uv): 
-51              try: 
-52                  mask_uv[0:kmu[j,i], j,i] = 1 
-53              except: 
-54                  mask_uv[:, j,i] = 0 
-55   
-56      return BGrid_GFDL(lon_t, lat_t, lon_uv, lat_uv, \ 
-57                         mask_t, mask_uv, h, z_t, z_t_edges, \ 
-58                         z_uv, z_uv_edges, f, \ 
-59                         name, xrange=xrange, yrange=yrange) 
-
60   
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Source Code for Module pyroms_toolbox.BGrid_GFDL.make_remap_grid_file'

-
- 1  import numpy as np 
- 2  from mpl_toolkits.basemap import pyproj 
- 3  from datetime import datetime 
- 4  try: 
- 5    import netCDF4 as netCDF 
- 6  except: 
- 7    import netCDF3 as netCDF 
- 8  import pyroms 
- 9   
-10   
-
11 -def make_remap_grid_file(Bgrd, Bpos='t'): 
-
12   
-13      #create remap file 
-14      remap_filename = 'remap_grid_' + Bgrd.name + '_' + Bpos + '.nc' 
-15      nc = netCDF.Dataset(remap_filename, 'w', format='NETCDF3_CLASSIC') 
-16      nc.Description = 'remap grid file on' + Bpos + 'points' 
-17      nc.Author = 'pyroms.remapping.make_remap_grid_file' 
-18      nc.Created = datetime.now().strftime("%Y-%m-%d %H:%M:%S") 
-19      nc.title = Bgrd.name 
-20   
-21      if Bpos == 't': 
-22          lon_corner = Bgrd.lon_t_vert 
-23          lat_corner = Bgrd.lat_t_vert 
-24          grid_center_lon = Bgrd.lon_t.flatten() 
-25          grid_center_lat = Bgrd.lat_t.flatten() 
-26          grid_imask = Bgrd.mask_t[0,:].flatten() 
-27          Mp, Lp = Bgrd.lon_t.shape 
-28      elif Bpos == 'uv': 
-29          lon_corner = Bgrd.lon_uv_vert 
-30          lat_corner = Bgrd.lat_uv_vert 
-31          grid_center_lon = Bgrd.lon_uv.flatten() 
-32          grid_center_lat = Bgrd.lat_uv.flatten() 
-33          grid_imask = Bgrd.mask_uv[0,:].flatten() 
-34          Mp, Lp = Bgrd.lon_uv.shape 
-35      else: 
-36          raise ValueError, 'Bpos must be t or uv' 
-37   
-38      grid_size = Lp * Mp 
-39   
-40      grid_corner_lon = np.zeros((grid_size, 4)) 
-41      grid_corner_lat = np.zeros((grid_size, 4)) 
-42      k = 0 
-43      for j in range(Mp): 
-44          for i in range(Lp): 
-45              grid_corner_lon[k,0] = lon_corner[j,i] 
-46              grid_corner_lat[k,0] = lat_corner[j,i] 
-47              grid_corner_lon[k,1] = lon_corner[j,i+1] 
-48              grid_corner_lat[k,1] = lat_corner[j,i+1] 
-49              grid_corner_lon[k,2] = lon_corner[j+1,i+1] 
-50              grid_corner_lat[k,2] = lat_corner[j+1,i+1] 
-51              grid_corner_lon[k,3] = lon_corner[j+1,i] 
-52              grid_corner_lat[k,3] = lat_corner[j+1,i] 
-53              k = k + 1 
-54   
-55      #Write netcdf file 
-56      nc.createDimension('grid_size', grid_size) 
-57      nc.createDimension('grid_corners', 4) 
-58      nc.createDimension('grid_rank', 2) 
-59   
-60      nc.createVariable('grid_dims', 'i4', ('grid_rank')) 
-61      nc.variables['grid_dims'].long_name = 'grid size along x and y axis' 
-62      nc.variables['grid_dims'].units = 'None' 
-63      nc.variables['grid_dims'][:] = [(Lp, Mp)] 
-64   
-65      nc.createVariable('grid_center_lon', 'f8', ('grid_size')) 
-66      nc.variables['grid_center_lon'].long_name = 'longitude of cell center' 
-67      nc.variables['grid_center_lon'].units = 'degrees' 
-68      nc.variables['grid_center_lon'][:] = grid_center_lon 
-69   
-70      nc.createVariable('grid_center_lat', 'f8', ('grid_size')) 
-71      nc.variables['grid_center_lat'].long_name = 'latitude of cell center' 
-72      nc.variables['grid_center_lat'].units = 'degrees' 
-73      nc.variables['grid_center_lat'][:] = grid_center_lat 
-74   
-75      nc.createVariable('grid_imask', 'i4', ('grid_size')) 
-76      nc.variables['grid_imask'].long_name = 'mask' 
-77      nc.variables['grid_imask'].units = 'None' 
-78      nc.variables['grid_imask'][:] = grid_imask 
-79   
-80      nc.createVariable('grid_corner_lon', 'f8', ('grid_size', 'grid_corners')) 
-81      nc.variables['grid_corner_lon'].long_name = 'longitude of cell corner' 
-82      nc.variables['grid_corner_lon'].units = 'degrees' 
-83      nc.variables['grid_corner_lon'][:] = grid_corner_lon 
-84   
-85      nc.createVariable('grid_corner_lat', 'f8', ('grid_size', 'grid_corners')) 
-86      nc.variables['grid_corner_lat'].long_name = 'latitude of cell corner' 
-87      nc.variables['grid_corner_lat'].units = 'degrees' 
-88      nc.variables['grid_corner_lat'][:] = grid_corner_lat 
-89   
-90      nc.close() 
-
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plot_coast_line(grd, {proj})

-

plot the coastline from the object grid. proj=map (optional) is a - Basemap object for projection.

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-
- 1  import numpy as np 
- 2  import matplotlib.pyplot as plt 
- 3  import matplotlib.collections as collections 
- 4  from pyroms_toolbox.BGrid_GFDL import get_coast_line 
- 5   
- 6   
-
 7 -def plot_coast_line(grd, proj=None): 
-
 8      ''' 
- 9      plot_coast_line(grd, {proj}) 
-10   
-11      plot the coastline from the object grid.  
-12      proj=map (optional) is a Basemap object for 
-13      projection. 
-14      '''  
-15   
-16   
-17      a = plt.gca() 
-18   
-19      coast = get_coast_line(grd) 
-20      c = np.array(coast) 
-21   
-22      if proj is None: 
-23          col = collections.LineCollection(c) 
-24      else: 
-25          cp = np.zeros(c.shape) 
-26          for i in range(c.shape[0]): 
-27              cp[i,:,0], cp[i,:,1] = proj(c[i,:,0], c[i,:,1]) 
-28   
-29          col = collections.LineCollection(cp) 
-30   
-31    
-32      a.add_collection(col, autolim=True) 
-33      col.set_color('k') 
-
34      #a.autoscale_view() 
-35   
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Module N2'

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N2(rho, - z, - rho_0=1000.0)
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N2(rho, - z, - rho_0=1000.0) -

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-Return the stratification frequency
-
-Parameters
-----------
-rho : array_like
-    density [kg/m^3]
-z : array_like
-    depths [m] (positive upward)
-
-Returns
--------
-N2 : array_like
-    Stratification frequency [1/s], where the vertical dimension (the
-    first dimension) is one less than the input arrays.    
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-
-
 1 -def N2(rho, z, rho_0=1000.0): 
-
 2      ''' 
- 3      Return the stratification frequency 
- 4       
- 5      Parameters 
- 6      ---------- 
- 7      rho : array_like 
- 8          density [kg/m^3] 
- 9      z : array_like 
-10          depths [m] (positive upward) 
-11       
-12      Returns 
-13      ------- 
-14      N2 : array_like 
-15          Stratification frequency [1/s], where the vertical dimension (the 
-16          first dimension) is one less than the input arrays.     
-17      ''' 
-18      rho = np.asarray(rho) 
-19      z = np.asarray(z) 
-20      assert rho.shape == z.shape, 'rho and z must have the same shape.' 
-21      r_z = np.diff(rho, axis=0) / np.diff(z, axis=0) 
-22      return -(9.8 / rho_0) * r_z 
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O2_saturation(T, - S)
- Return saturation value of oxygen.		 - source code - -
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O2_saturation(T, - S) -

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-Return saturation value of oxygen.
-
-Parameters
-----------
-T : array_like
-    Temperature (ËšC)
-S : array_like
-    Salinity (PSU)
-
-Returns
--------
-O2_sat : array_like
-    concentrations of O2 [ millimole O2 / m3 ] for a given temperature and
-    salinity (at STP)
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Source Code for Module pyroms_toolbox.O2_saturation'

-
- 1  # encoding: utf-8 
- 2   
-
 3 -def O2_saturation(T,S): 
-
 4      """ 
- 5      Return saturation value of oxygen. 
- 6       
- 7      Parameters 
- 8      ---------- 
- 9      T : array_like 
-10          Temperature (˚C) 
-11      S : array_like 
-12          Salinity (PSU) 
-13       
-14      Returns 
-15      ------- 
-16      O2_sat : array_like 
-17          concentrations of O2 [ millimole O2 / m3 ] for a given temperature and 
-18          salinity (at STP) 
-19      """ 
-20   
-21      A1 = -173.4292 
-22      A2 =  249.6339 
-23      A3 =  143.3483 
-24      A4 =  -21.8492 
-25      B1 =   -0.033096 
-26      B2 =    0.014259 
-27      B3 =   -0.0017000 
-28      # Convert T to deg. C to deg. K 
-29      T = T + 273.15 
-30      # O2 Concentration in mg/l 
-31      # [from Millero and Sohn, Chemical Oceanography, CRC Press, 1992] 
-32      O = np.exp(A1 + A2*(100.0/T) + A3*np.log(T/100.0) + A4*(T/100.0) + \ 
-33              S*(B1 + B2*(T/100.0) + B3*((T/100.0)**2)) ) 
-34      # Convert to mmol/m3 
-35      #  mmol/m3 = 44.66 ml/l 
-36      #  mg/l = ml/l * 1.42903 mg/ml 
-37      return O*(44.66*1.42903) 
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Module _average

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-Functions:
-  avg = avg3d(dataset,incavg,counter,spval,dim1=shape(dataset,0),dim2=shape(dataset,1),dim3=shape(dataset,2))
-  avg = avg2d(dataset,incavg,counter,spval,dim1=shape(dataset,0),dim2=shape(dataset,1))
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-   - - - - - - -
average(var, - ncfiles, - trange=None, - avgfile=None, - spval=1e+37, - timevar='ocean_time')
- This function computes the temporal average of a given variable or set of -variables.		 - source code - -
- -
- - - - - - - - - -
- - - - - -
Variables[hide private]
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-   - - avg = <pyroms_toolbox.average.avg_obj object at 0x329db90> -
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Function Details[hide private]
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average(var, - ncfiles, - trange=None, - avgfile=None, - spval=1e+37, - timevar='ocean_time') -

- 		source code  -
- - 
-
-
-This function computes the temporal average of a given variable or set of
-variables. It uses a shared library object created using f2py to
-calculate this average. Creates a netCDF file if avgfile does not
-equal None, or returns an object containing all of the averages if
-avgfile is equal to None.
-
-List of Arguments:
-
-var        - Either a string or list of strings relating to variable
-             names in the netCDF files
-
-ncfiles    - This variable can be one of three types: a string containing
-             the path to a netCDF file, a string with a Unix wildcard indicator,
-             or a list of strings containing netCDF files.
-
-             E.g. 1) ncfiles = '/path/to/ncfile.nc'
-                  2) ncfiles = '/path/to/nc*.nc'
-                  3) ncfiles = ['/path/to/ncfile1.nc','/path/to/ncfile2.nc',...]
-
-trange      - time range index for ocean time dimension, used if you want to compute
-             average over a given time range.
-
-             E.g. trange = (10,40)
-
-avgfile    - A string used for naming a new netCDF file containing only the
-             averages from the variables after being computed.
-
-timevar    - time variable name. Default is ROMS time variable name "ocean_time".
-
-
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Source Code for Module pyroms_toolbox.average'

-
-  1  # encoding: utf-8 
-  2   
-  3  import _average 
-  4  import types 
-  5  import pyroms 
-  6  import numpy as np 
-  7  import netCDF4 
-  8  from datetime import datetime 
-  9   
- 10  # defined an avg_obj object 
-
 11 -class avg_obj(object): 
-
 12      pass 
-
 13   
- 14  avg = avg_obj() 
- 15   
-
 16 -def average(var, ncfiles, trange=None, avgfile=None, spval=1e37, timevar='ocean_time'): 
-
 17      """ 
- 18   
- 19      This function computes the temporal average of a given variable or set of 
- 20      variables. It uses a shared library object created using f2py to 
- 21      calculate this average. Creates a netCDF file if avgfile does not 
- 22      equal None, or returns an object containing all of the averages if 
- 23      avgfile is equal to None. 
- 24   
- 25      List of Arguments: 
- 26   
- 27      var        - Either a string or list of strings relating to variable 
- 28                   names in the netCDF files 
- 29   
- 30      ncfiles    - This variable can be one of three types: a string containing 
- 31                   the path to a netCDF file, a string with a Unix wildcard indicator, 
- 32                   or a list of strings containing netCDF files. 
- 33   
- 34                   E.g. 1) ncfiles = '/path/to/ncfile.nc' 
- 35                        2) ncfiles = '/path/to/nc*.nc' 
- 36                        3) ncfiles = ['/path/to/ncfile1.nc','/path/to/ncfile2.nc',...] 
- 37   
- 38      trange      - time range index for ocean time dimension, used if you want to compute 
- 39                   average over a given time range. 
- 40   
- 41                   E.g. trange = (10,40) 
- 42   
- 43      avgfile    - A string used for naming a new netCDF file containing only the 
- 44                   averages from the variables after being computed. 
- 45   
- 46      timevar    - time variable name. Default is ROMS time variable name "ocean_time". 
- 47      """ 
- 48   
- 49      if type(var).__name__ == 'list': 
- 50          nvar = len(var) 
- 51      elif type(var).__name__ == 'str': 
- 52          var = [var] 
- 53          nvar = len(var) 
- 54      else: 
- 55          raise ValueError, 'var must be a str or a list of str' 
- 56   
- 57      avg.ncfiles = pyroms.io.MFDataset(ncfiles) 
- 58   
- 59      ocean_time = pyroms.utility.get_nc_var(timevar, avg.ncfiles) 
- 60      Nt = len(ocean_time[:])    
- 61   
- 62      if trange is None: 
- 63          start = 0 
- 64          end = Nt 
- 65      else: 
- 66          if trange[0] >= 0 and trange[1] <= Nt: 
- 67              start = trange[0] 
- 68              end = min(trange[1]+1, Nt) 
- 69          else: 
- 70              raise ValueError, 'trange must be within interval [0, %s].' %Nt 
- 71   
- 72      print range(start,end) 
- 73   
- 74      for varname in var: 
- 75          name = varname 
- 76          vble = pyroms.utility.get_nc_var(varname,avg.ncfiles) 
- 77          vsh = vble.shape 
- 78          leng = len(vsh) 
- 79   
- 80          # if variable is 4D, enters this conditional 
- 81          if leng is 4: 
- 82              # create an empty numpy array with dimensions equal to shape of the 
- 83              # shape of the variable minus the ocean_time dimension 
- 84              incavg = np.zeros((vsh[1],vsh[2],vsh[3])) 
- 85   
- 86              ii = 0 
- 87              for i in range(start,end): 
- 88                  ii = ii + 1 
- 89                  #calls Fortran function avg3d to perform an incremental average 
- 90                  incavg = _average.avg3d(vble[i,:],incavg,ii,spval) 
- 91              # mask 
- 92              incavg = np.ma.masked_values(incavg, spval) 
- 93              #sets attribute of avg object to the final temporal average 
- 94              setattr(avg, varname, incavg[:]) 
- 95   
- 96          # if variable is 3D, enters this conditional 
- 97          elif leng is 3: 
- 98              # create an empty numpy array with dimensions equal to shape of the 
- 99              # shape of the variable minus the ocean_time dimension 
-100              incavg = np.zeros((vsh[1],vsh[2])) 
-101   
-102              ii = 0 
-103              for i in range(start,end): 
-104                  ii = ii + 1 
-105                  #calls Fortran function avg2d to perform an incremental average 
-106                  incavg = _average.avg2d(vble[i,:],incavg,ii,spval) 
-107              # mask 
-108              incavg = np.ma.masked_values(incavg, spval) 
-109              #sets attribute of avg object to the final temporal average 
-110              setattr(avg, varname, incavg[:]) 
-111   
-112          else: 
-113              raise ValueError, 'Variable must be 3D (time + 2 spacial dims) or \ 
-114  4D (time + 3 spacial dims)' 
-115   
-116   
-117      # if avgfile is defined, enter this conditional and begin creating a new netCDF file 
-118      if avgfile is not None: 
-119          # if avgfile is a string, enter this conditional 
-120          if type(avgfile).__name__ == 'str': 
-121              # if original name of avgfile left off .nc in the filename, append it to the string 
-122              if avgfile.find('.nc') == -1: 
-123                  avgfile = avgfile+'.nc' 
-124   
-125              # creates netCDF file 
-126              nc = netCDF4.Dataset(avgfile, 'w', format='NETCDF3_CLASSIC') 
-127              nc.Description = 'Variable Average File' 
-128              nc.Author = 'pyroms_toolbox.average' 
-129              nc.Created = datetime.now().strftime("%Y-%m-%d %H:%M:%S") 
-130              nc.Files = ", ".join(avg.ncfiles._files) 
-131   
-132              print 'Writing '+str(avgfile)+'...' 
-133   
-134              # for each dimension in original netCDF files, recreate the dimensions in the new netCDF file 
-135              for newdim in avg.ncfiles.dimensions.keys(): 
-136                  if avg.ncfiles.dimensions[newdim].isunlimited(): 
-137                      nc.createDimension(newdim,None) 
-138                  else: 
-139                      nc.createDimension(newdim,len(avg.ncfiles.dimensions[newdim])) 
-140   
-141              tdims = avg.ncfiles.variables[timevar].dimensions 
-142              nc.createVariable(timevar, 'f8', (tdims)) 
-143              nc.variables[timevar].long_name = 'averaged time since initialization' 
-144              try: 
-145                  nc.variables[timevar].units = avg.ncfiles.variables[timevar].units 
-146                  nc.variables[timevar].field = avg.ncfiles.variables[timevar].field 
-147              except: 
-148                  nc.variables[timevar].units = 'N/A' 
-149                  nc.variables[timevar].field = 'N/A' 
-150              nc.variables[timevar][0] =  ocean_time[start:end].mean() 
-151   
-152              # for each variable in var, create a new variable with all dimensions associated with that 
-153              # variable except ocean_time 
-154              for varname in var: 
-155                  print '  writting %s...' %varname 
-156   
-157                  vardims = avg.ncfiles.variables[varname].dimensions 
-158   
-159                  nc.createVariable(varname, 'f8', (vardims)) 
-160                  nc.variables[varname].long_name = 'Temporal average of variable '+str(varname) 
-161   
-162                  # try to pull the units from the original netCDF variable 
-163                  try: 
-164                      nc.variables[varname].units = avg.ncfiles.variables[varname].units 
-165                      nc.variables[varname].field = avg.ncfiles.variables[varname].field 
-166                  # mark as N/A if no units were given to this particular variable 
-167                  except: 
-168                      nc.variables[varname].units = 'N/A' 
-169                      nc.variables[varname].field = 'N/A' 
-170   
-171                  nc.variables[varname]._FillValue = str(spval) 
-172                  nc.variables[varname][0] = avg.__getattribute__(varname) 
-173              nc.close() 
-174          else: 
-175              print "avgfile must be a string that equates to the path where this netCDF file is to be placed." 
-176          return 
-177      else: 
-178          print "Returning average object..." 
-179          return avg 
-
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Class avg_obj

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-
-object --+
-         |
-        avg_obj
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Instance Methods[hide private]
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Inherited from object: - __delattr__, - __getattribute__, - __hash__, - __init__, - __new__, - __reduce__, - __reduce_ex__, - __repr__, - __setattr__, - __str__ -

-
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Properties[hide private]
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Inherited from object: - __class__ -

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Module change'

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Functions[hide private]
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change(old, - relation, - flag, - value)
- Change values in a matrix		 - source code - -
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Source Code for Module pyroms_toolbox.change'

-
- 1  import numpy as np 
- 2   
-
 3 -def change(old,relation,flag,value): 
-
 4      """  
- 5      Change values in a matrix 
- 6      """ 
- 7   
- 8      if relation != '==' and relation != '!=' and relation != '>' and relation != '<' and \ 
- 9           relation != '!=' and relation != '>=' and relation != '<=': 
-10          raise ValueError, 'Relation {%s} not valid' % relation 
-11   
-12      if np.isnan(flag): 
-13          if relation == '==': 
-14              replace = np.where(np.isnan(old) == True) 
-15          elif relation == '!=': 
-16              replace = np.where(np.isnan(old) == False) 
-17          else: 
-18              raise ValueError, 'Relation should be == or ~= to compare to NaN' 
-19   
-20      else: 
-21          if relation == '==': 
-22              replace = np.where(old == flag) 
-23          elif relation == '>': 
-24              replace = np.where(old > flag) 
-25          elif relation == '<': 
-26              replace = np.where(old < flag) 
-27          elif relation == '!=': 
-28              replace = np.where(old != flag) 
-29          elif relation == '>=': 
-30              replace = np.where(old >= flag) 
-31          elif relation == '<=': 
-32              replace = np.where(old <= flag) 
-33   
-34      new = old.copy() 
-35      new[replace] = value 
-36   
-37      return new 
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Module get_coast_line'

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Functions[hide private]
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get_coast_line(grd)
- coast = get_coast_line(grd)		 - source code - -
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Function Details[hide private]
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get_coast_line(grd) -

- 		source code  -
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coast = get_coast_line(grd)

-

return the coastline from the grid object grid

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Source Code for Module pyroms_toolbox.get_coast_line'

-
- 1  import numpy as np 
- 2   
-
 3 -def get_coast_line(grd): 
-
 4      ''' 
- 5      coast = get_coast_line(grd) 
- 6   
- 7      return the coastline from the grid object grid  
- 8      ''' 
- 9   
-10      #get land point 
-11      jidx, iidx = np.where(grd.hgrid.mask_rho == 0) 
-12   
-13      lon = grd.hgrid.lon_vert 
-14      lat = grd.hgrid.lat_vert 
-15      mask = grd.hgrid.mask_rho 
-16   
-17      coast = [] 
-18   
-19      for i in range(iidx.shape[0]): 
-20          if jidx[i] != mask.shape[0]-1: 
-21              if mask[jidx[i], iidx[i]] != mask[jidx[i]+1, iidx[i]]: 
-22                  lonc = ([lon[jidx[i]+1,iidx[i]], lon[jidx[i]+1,iidx[i]+1]]) 
-23                  latc = ([lat[jidx[i]+1,iidx[i]], lat[jidx[i]+1,iidx[i]+1]]) 
-24                  seg = zip(lonc,latc) 
-25                  coast.append(seg) 
-26   
-27          if jidx[i] != 0: 
-28              if mask[jidx[i], iidx[i]] != mask[jidx[i]-1, iidx[i]]: 
-29                  lonc = ([lon[jidx[i],iidx[i]], lon[jidx[i],iidx[i]+1]]) 
-30                  latc = ([lat[jidx[i],iidx[i]], lat[jidx[i],iidx[i]+1]]) 
-31                  seg = zip(lonc,latc) 
-32                  coast.append(seg) 
-33   
-34          if iidx[i] != mask.shape[1]-1: 
-35              if mask[jidx[i], iidx[i]] != mask[jidx[i], iidx[i]+1]: 
-36                  lonc = ([lon[jidx[i],iidx[i]+1], lon[jidx[i]+1,iidx[i]+1]]) 
-37                  latc = ([lat[jidx[i],iidx[i]+1], lat[jidx[i]+1,iidx[i]+1]]) 
-38                  seg = zip(lonc,latc) 
-39                  coast.append(seg) 
-40   
-41          if iidx[i] != 0: 
-42              if mask[jidx[i], iidx[i]] != mask[jidx[i], iidx[i]-1]: 
-43                  lonc = ([lon[jidx[i],iidx[i]], lon[jidx[i]+1,iidx[i]]]) 
-44                  latc = ([lat[jidx[i],iidx[i]], lat[jidx[i]+1,iidx[i]]]) 
-45                  seg = zip(lonc,latc) 
-46                  coast.append(seg) 
-47   
-48      return coast 
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Module isoview'

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Functions[hide private]
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isoview(var, - prop, - tindex, - isoval, - grid, - filename=None, - cmin=None, - cmax=None, - clev=None, - fill=False, - contour=False, - d=4, - range=None, - fts=None, - title=None, - clb=True, - pal=None, - proj='merc', - fill_land=False, - outfile=None)
- map = isoview(var, prop, tindex, isoval, grid, {optional switch})		 - source code - -
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Function Details[hide private]
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isoview(var, - prop, - tindex, - isoval, - grid, - filename=None, - cmin=None, - cmax=None, - clev=None, - fill=False, - contour=False, - d=4, - range=None, - fts=None, - title=None, - clb=True, - pal=None, - proj='merc', - fill_land=False, - outfile=None) -

- 		source code  -
- -

map = isoview(var, prop, tindex, isoval, grid, {optional switch})

-

optional switch:

-
    -
  • - filename if defined, load the variable from file -
    • -
  • - cmin set color minimum limit -
    • -
  • - cmax set color maximum limit -
    • -
  • - clev set the number of color step -
    • -
  • - fill use contourf instead of pcolor -
    • -
  • - contour overlay contour (request fill=True) -
    • -
  • - d contour density (default d=4) -
    • -
  • - range set axis limit -
    • -
  • - fts set font size (default: 12) -
    • -
  • - title add title to the plot -
    • -
  • - clb add colorbar (defaul: True) -
    • -
  • - pal set color map (default: cm.jet) -
    • -
  • - proj set projection type (default: merc) -
    • -
  • - fill_land fill land masked area with gray (defaul: True) -
    • -
  • - outfile if defined, write figure to file -
    • -
-

plot a projection of variable at property == isoval. If filename is - provided, var and prop must be a strings and the variables will be load - from the file. grid can be a grid object or a gridid. In the later case, - the grid object correponding to the provided gridid will be loaded. If - proj is not None, return a Basemap object to be used with quiver for - example.

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- - - - diff --git a/pyroms_toolbox/docs/pyroms_toolbox.isoview'-pysrc.html b/pyroms_toolbox/docs/pyroms_toolbox.isoview'-pysrc.html deleted file mode 100644 index 65b9242..0000000 --- a/pyroms_toolbox/docs/pyroms_toolbox.isoview'-pysrc.html +++ /dev/null @@ -1,332 +0,0 @@ - - - - - pyroms_toolbox.isoview' - - - - - - - - - - - - - - - - - - - - - - -
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Source Code for Module pyroms_toolbox.isoview'

-
-  1  import numpy as np 
-  2  import matplotlib.pyplot as plt 
-  3  from  matplotlib import cm, colors 
-  4  from mpl_toolkits.basemap import Basemap 
-  5  import pyroms 
-  6  import pyroms_toolbox 
-  7   
-  8   
-
  9 -def isoview(var, prop, tindex, isoval, grid, filename=None, \ 
- 10            cmin=None, cmax=None, clev=None, fill=False, \ 
- 11            contour=False, d=4, range=None, fts=None, \ 
- 12            title=None, clb=True, pal=None, proj='merc', \ 
- 13            fill_land=False, outfile=None): 
-
 14      """ 
- 15      map = isoview(var, prop, tindex, isoval, grid, {optional switch}) 
- 16   
- 17      optional switch: 
- 18        - filename         if defined, load the variable from file 
- 19        - cmin             set color minimum limit 
- 20        - cmax             set color maximum limit 
- 21        - clev             set the number of color step 
- 22        - fill             use contourf instead of pcolor 
- 23        - contour          overlay contour (request fill=True) 
- 24        - d                contour density (default d=4)  
- 25        - range            set axis limit 
- 26        - fts              set font size (default: 12) 
- 27        - title            add title to the plot 
- 28        - clb              add colorbar (defaul: True) 
- 29        - pal              set color map (default: cm.jet) 
- 30        - proj             set projection type (default: merc) 
- 31        - fill_land        fill land masked area with gray (defaul: True) 
- 32        - outfile          if defined, write figure to file 
- 33   
- 34      plot a projection of variable at property == isoval. If filename  
- 35      is provided, var and prop must be a strings and the variables will  
- 36      be load from the file. 
- 37      grid can be a grid object or a gridid. In the later case, the grid 
- 38      object correponding to the provided gridid will be loaded. 
- 39      If proj is not None, return a Basemap object to be used with quiver  
- 40      for example.  
- 41      """ 
- 42   
- 43      # get grid 
- 44      if type(grid).__name__ == 'ROMS_Grid': 
- 45          grd = grid 
- 46      else: 
- 47          grd = pyroms.grid.get_ROMS_grid(grid) 
- 48   
- 49   
- 50      # get variable 
- 51      if filename == None: 
- 52          var = var 
- 53          prop = prop 
- 54      else: 
- 55          data = pyroms.io.Dataset(filename) 
- 56          var = data.variables[var] 
- 57          prop = data.variables[prop] 
- 58   
- 59      Np, Mp, Lp = grd.vgrid.z_r[0,:].shape 
- 60   
- 61      if tindex is not -1: 
- 62          assert len(var.shape) == 4, 'var must be 4D (time plus space).' 
- 63          K, N, M, L = var.shape 
- 64      else: 
- 65          assert len(var.shape) == 3, 'var must be 3D (no time dependency).' 
- 66          N, M, L = var.shape 
- 67   
- 68      # determine where on the C-grid these variable lies 
- 69      if N == Np and M == Mp and L == Lp: 
- 70          Cpos='rho' 
- 71          mask = grd.hgrid.mask_rho 
- 72   
- 73      if N == Np and M == Mp and L == Lp-1: 
- 74          Cpos='u' 
- 75          mask = grd.hgrid.mask_u 
- 76   
- 77      if N == Np and M == Mp-1 and L == Lp: 
- 78          Cpos='v' 
- 79          mask = grd.hgrid.mask_v 
- 80   
- 81      # get constante-iso slice 
- 82      if tindex == -1: 
- 83          var = var[:,:,:] 
- 84          prop = prop[:,:,:] 
- 85      else: 
- 86          var = var[tindex,:,:,:] 
- 87          prop = prop[tindex,:,:,:] 
- 88   
- 89      if fill == True: 
- 90          isoslice, lon, lat = pyroms.tools.isoslice(var, prop, isoval, \ 
- 91                                               grd, Cpos=Cpos) 
- 92      else: 
- 93          isoslice, lon, lat = pyroms.tools.isoslice(var, prop, isoval, \ 
- 94                                               grd, Cpos=Cpos, vert=True) 
- 95   
- 96      # plot 
- 97      if cmin is None: 
- 98          cmin = isoslice.min() 
- 99      else: 
-100          cmin = float(cmin) 
-101   
-102      if cmax is None: 
-103          cmax = isoslice.max() 
-104      else: 
-105          cmax = float(cmax) 
-106   
-107      if clev is None: 
-108          clev = 100. 
-109      else: 
-110          clev = float(clev) 
-111   
-112      dc = (cmax - cmin)/clev ; vc = np.arange(cmin,cmax+dc,dc) 
-113   
-114      if pal is None: 
-115          pal = cm.jet 
-116      else: 
-117          pal = pal 
-118   
-119      if fts is None: 
-120          fts = 12 
-121      else: 
-122          fts = fts 
-123   
-124      #pal.set_over('w', 1.0) 
-125      #pal.set_under('w', 1.0) 
-126      #pal.set_bad('w', 1.0) 
-127   
-128      pal_norm = colors.BoundaryNorm(vc,ncolors=256, clip = False) 
-129   
-130      if range is None: 
-131          lon_min = lon.min() 
-132          lon_max = lon.max() 
-133          lon_0 = (lon_min + lon_max) / 2. 
-134          lat_min = lat.min() 
-135          lat_max = lat.max()      
-136          lat_0 = (lat_min + lat_max) / 2. 
-137      else: 
-138          lon_min = range[0] 
-139          lon_max = range[1] 
-140          lon_0 = (lon_min + lon_max) / 2. 
-141          lat_min = range[2] 
-142          lat_max = range[3] 
-143          lat_0 = (lat_min + lat_max) / 2. 
-144   
-145      # clear figure 
-146      #plt.clf() 
-147   
-148      if proj is not None: 
-149          map = Basemap(projection=proj, llcrnrlon=lon_min, llcrnrlat=lat_min, \ 
-150                urcrnrlon=lon_max, urcrnrlat=lat_max, lat_0=lat_0, lon_0=lon_0, \ 
-151                   resolution='h', area_thresh=5.) 
-152          x, y = map(lon,lat) 
-153       
-154      if fill_land is True and proj is not None: 
-155          # fill land and draw coastlines 
-156          map.drawcoastlines() 
-157          map.fillcontinents(color='grey') 
-158      else: 
-159          if proj is not None:  
-160              Basemap.pcolor(map, x, y, mask, vmin=-2, cmap=cm.gray) 
-161              pyroms_toolbox.plot_coast_line(grd, map) 
-162          else:  
-163              plt.pcolor(lon, lat, mask, vmin=-2, cmap=cm.gray) 
-164              pyroms_toolbox.plot_coast_line(grd) 
-165       
-166      if fill is True: 
-167          if proj is not None:  
-168              cf = Basemap.contourf(map, x, y, isoslice, vc, cmap = pal, \ 
-169                                    norm = pal_norm) 
-170          else:  
-171              cf = plt.contourf(lon, lat, isoslice, vc, cmap = pal, \ 
-172                                norm = pal_norm) 
-173      else: 
-174          if proj is not None:  
-175              cf = Basemap.pcolor(map, x, y, isoslice, cmap = pal, norm = pal_norm) 
-176          else:  
-177              cf = plt.pcolor(lon, lat, isoslice, cmap = pal, norm = pal_norm) 
-178   
-179      if clb is True: 
-180          clb = plt.colorbar(cf, fraction=0.075,format='%.2f') 
-181          for t in clb.ax.get_yticklabels(): 
-182              t.set_fontsize(fts) 
-183   
-184      if contour is True: 
-185          if fill is not True: 
-186              raise Warning, 'Please run again with fill=True to overlay contour.' 
-187          else: 
-188              if proj is not None: 
-189                  Basemap.contour(map, x, y, isoslice, vc[::d], colors='k', linewidths=0.5, linestyles='solid') 
-190              else:  
-191                  plt.contour(lon, lat, isoslice, vc[::d], colors='k', linewidths=0.5, linestyles='solid') 
-192   
-193      if proj is None and range is not None: 
-194          plt.axis(range)  
-195   
-196   
-197      if title is not None: 
-198              plt.title(title, fontsize=fts+4) 
-199   
-200      if proj is not None: 
-201          map.drawmeridians(np.arange(lon_min,lon_max, (lon_max-lon_min)/5.), \ 
-202                            labels=[0,0,0,1], fmt='%.1f') 
-203          map.drawparallels(np.arange(lat_min,lat_max, (lat_max-lat_min)/5.), \ 
-204                            labels=[1,0,0,0], fmt='%.1f') 
-205   
-206      if outfile is not None: 
-207          if outfile.find('.png') != -1 or outfile.find('.svg') != -1 or \ 
-208             outfile.find('.eps') != -1: 
-209              print 'Write figure to file', outfile 
-210              plt.savefig(outfile, dpi=200, facecolor='w', edgecolor='w', \ 
-211                          orientation='portrait') 
-212          else: 
-213              print 'Unrecognized file extension. Please use .png, .svg or .eps file extension.'    
-214   
-215   
-216      if proj is None: 
-217          return 
-218      else: 
-219          return map 
-
220   
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Module iview'

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- - - - - - - - - -
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Functions[hide private]
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-   - - - - - - -
iview(var, - tindex, - iindex, - gridid, - filename=None, - cmin=None, - cmax=None, - clev=None, - clbformat='%.2f', - fill=False, - contour=False, - d=4, - jrange=None, - hrange=None, - fts=None, - title=None, - map=False, - pal=None, - clb=True, - outfile=None)
- iview(var, tindex, iindex, gridid, {optional switch})		 - source code - -
- -
- - - - - - -
- - - - - -
Function Details[hide private]
-
- -
- -
- - -
-

iview(var, - tindex, - iindex, - gridid, - filename=None, - cmin=None, - cmax=None, - clev=None, - clbformat='%.2f', - fill=False, - contour=False, - d=4, - jrange=None, - hrange=None, - fts=None, - title=None, - map=False, - pal=None, - clb=True, - outfile=None) -

- 		source code  -
- -

iview(var, tindex, iindex, gridid, {optional switch})

-

optional switch:

-
    -
  • - filename if defined, load the variable from file -
    • -
  • - cmin set color minimum limit -
    • -
  • - cmax set color maximum limit -
    • -
  • - clev set the number of color step -
    • -
  • - fill use contourf instead of pcolor -
    • -
  • - contour overlay contour (request fill=True) -
    • -
  • - d contour density (default d=4) -
    • -
  • - jrange j range -
    • -
  • - hrange h range -
    • -
  • - fts set font size (default: 12) -
    • -
  • - title add title to the plot -
    • -
  • - map if True, draw a map showing islice location -
    • -
  • - pal set color map (default: cm.jet) -
    • -
  • - clb add colorbar (defaul: True) -
    • -
  • - outfile if defined, write figure to file -
    • -
-

plot a constante-i slice of variable var. If filename is provided, var - must be a string and the variable will be load from the file. grid can be - a grid object or a gridid. In the later case, the grid object - correponding to the provided gridid will be loaded.

-
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Source Code for Module pyroms_toolbox.iview'

-
-  1  import numpy as np 
-  2  import matplotlib.pyplot as plt 
-  3  from  matplotlib import cm, colors 
-  4  from mpl_toolkits.basemap import Basemap 
-  5  import pyroms 
-  6   
-  7   
-
  8 -def iview(var, tindex, iindex, gridid, filename=None, \ 
-  9            cmin=None, cmax=None, clev=None, clbformat='%.2f', \ 
- 10            fill=False, contour=False, d=4, jrange=None, \ 
- 11            hrange=None, fts=None, title=None, map=False, \ 
- 12            pal=None, clb=True, outfile=None): 
-
 13      """ 
- 14      iview(var, tindex, iindex, gridid, {optional switch}) 
- 15   
- 16      optional switch: 
- 17        - filename         if defined, load the variable from file 
- 18        - cmin             set color minimum limit 
- 19        - cmax             set color maximum limit 
- 20        - clev             set the number of color step 
- 21        - fill             use contourf instead of pcolor 
- 22        - contour          overlay contour (request fill=True) 
- 23        - d                contour density (default d=4)  
- 24        - jrange           j range 
- 25        - hrange           h range 
- 26        - fts              set font size (default: 12) 
- 27        - title            add title to the plot 
- 28        - map              if True, draw a map showing islice location 
- 29        - pal              set color map (default: cm.jet) 
- 30        - clb              add colorbar (defaul: True) 
- 31        - outfile          if defined, write figure to file 
- 32   
- 33      plot a constante-i slice of variable var. If filename is provided, 
- 34      var must be a string and the variable will be load from the file. 
- 35      grid can be a grid object or a gridid. In the later case, the grid 
- 36      object correponding to the provided gridid will be loaded. 
- 37      """ 
- 38   
- 39      # get grid 
- 40      if type(gridid).__name__ == 'ROMS_Grid': 
- 41          grd = gridid 
- 42      else: 
- 43          grd = pyroms.grid.get_ROMS_grid(gridid) 
- 44   
- 45      # get variable 
- 46      if filename == None: 
- 47          var = var 
- 48      else: 
- 49          data = pyroms.io.Dataset(filename) 
- 50   
- 51          var = data.variables[var] 
- 52   
- 53      Np, Mp, Lp = grd.vgrid.z_r[0,:].shape 
- 54   
- 55      if tindex is not -1: 
- 56          assert len(var.shape) == 4, 'var must be 4D (time plus space).' 
- 57          K, N, M, L = var.shape 
- 58      else: 
- 59          assert len(var.shape) == 3, 'var must be 3D (no time dependency).' 
- 60          N, M, L = var.shape 
- 61   
- 62      # determine where on the C-grid these variable lies 
- 63      if N == Np and M == Mp and L == Lp: 
- 64          Cpos='rho' 
- 65          lon = grd.hgrid.lon_vert 
- 66          lat = grd.hgrid.lat_vert 
- 67          mask = grd.hgrid.mask_rho 
- 68   
- 69      if N == Np and M == Mp and L == Lp-1: 
- 70          Cpos='u' 
- 71          lon = 0.5 * (grd.hgrid.lon_vert[:,:-1] + grd.hgrid.lon_vert[:,1:]) 
- 72          lat = 0.5 * (grd.hgrid.lat_vert[:,:-1] + grd.hgrid.lat_vert[:,1:]) 
- 73          mask = grd.hgrid.mask_u 
- 74   
- 75      if N == Np and M == Mp-1 and L == Lp: 
- 76          Cpos='v' 
- 77          lon = 0.5 * (grd.hgrid.lon_vert[:-1,:] + grd.hgrid.lon_vert[1:,:]) 
- 78          lat = 0.5 * (grd.hgrid.lat_vert[:-1,:] + grd.hgrid.lat_vert[1:,:]) 
- 79          mask = grd.hgrid.mask_v 
- 80   
- 81      if N == Np+1 and M == Mp and L == Lp: 
- 82          Cpos='w' 
- 83          lon = grd.hgrid.lon_vert 
- 84          lat = grd.hgrid.lat_vert 
- 85          mask = grd.hgrid.mask_rho 
- 86   
- 87      # get constante-j slice 
- 88      if tindex == -1: 
- 89          var = var[:,:,:] 
- 90      else: 
- 91          var = var[tindex,:,:,:] 
- 92   
- 93      if fill == True: 
- 94          islice, zi, loni, lati, = pyroms.tools.islice(var, iindex, grd, \ 
- 95                                      Cpos) 
- 96      else: 
- 97          islice, zi, loni, lati, = pyroms.tools.islice(var, iindex, grd, \ 
- 98                                      Cpos, vert=True) 
- 99   
-100   
-101      # plot 
-102      if cmin is None: 
-103          cmin = islice.min() 
-104      else: 
-105          cmin = float(cmin) 
-106   
-107      if cmax is None: 
-108          cmax = islice.max() 
-109      else: 
-110          cmax = float(cmax) 
-111   
-112      if clev is None: 
-113          clev = 100. 
-114      else: 
-115          clev = float(clev) 
-116   
-117      dc = (cmax - cmin)/clev ; vc = np.arange(cmin,cmax+dc,dc) 
-118   
-119      if pal is None: 
-120          pal = cm.jet 
-121      else: 
-122          pal = pal 
-123   
-124      if fts is None: 
-125          fts = 12 
-126      else: 
-127          fts = fts 
-128   
-129      #pal.set_over('w', 1.0) 
-130      #pal.set_under('w', 1.0) 
-131      #pal.set_bad('w', 1.0) 
-132   
-133      pal_norm = colors.BoundaryNorm(vc,ncolors=256, clip = False) 
-134       
-135      # clear figure 
-136      #plt.clf() 
-137   
-138      if map is True: 
-139          # set axes for the main plot in order to keep space for the map        
-140          if fts < 12: 
-141              ax=None 
-142          else: 
-143              ax = plt.axes([0.15, 0.08, 0.8, 0.65])        
-144      else:        
-145          if fts < 12: 
-146              ax=None 
-147          else: 
-148              ax=plt.axes([0.15, 0.1, 0.8, 0.8]) 
-149   
-150   
-151      if fill is True: 
-152          cf = plt.contourf(lati, zi, islice, vc, cmap = pal, norm = pal_norm, axes=ax) 
-153      else: 
-154          cf = plt.pcolor(lati, zi, islice, cmap = pal, norm = pal_norm, axes=ax) 
-155   
-156      if clb is True: 
-157          clb = plt.colorbar(cf, fraction=0.075,format=clbformat) 
-158          for t in clb.ax.get_yticklabels(): 
-159              t.set_fontsize(fts) 
-160   
-161      if contour is True: 
-162          if fill is not True: 
-163              raise Warning, 'Please run again with fill=True for overlay contour.' 
-164          else: 
-165              plt.contour(lati, zi, islice, vc[::d], colors='k', linewidths=0.5, linestyles='solid', axes=ax) 
-166   
-167   
-168      if jrange is not None: 
-169          plt.xlim(jrange) 
-170   
-171      if hrange is not None: 
-172          plt.ylim(hrange) 
-173   
-174      if title is not None: 
-175          if map is True: 
-176              # move the title on the right 
-177              xmin, xmax = ax.get_xlim() 
-178              ymin, ymax = ax.get_ylim() 
-179              xt = xmin - (xmax-xmin)/9. 
-180              yt = ymax + (ymax-ymin)/7. 
-181              plt.text(xt, yt, title, fontsize=fts+4) 
-182          else: 
-183              plt.title(title, fontsize=fts+4) 
-184   
-185      plt.xlabel('Latitude', fontsize=fts) 
-186      plt.ylabel('Depth', fontsize=fts) 
-187   
-188      if map is True: 
-189          # draw a map with constant-i slice location 
-190          ax_map = plt.axes([0.4, 0.76, 0.2, 0.23]) 
-191          varm = np.ma.masked_where(mask[:,:] == 0, var[var.shape[0]-1,:,:])         
-192          xmin, xmax = ax.get_xlim()       
-193          dd = (lat[:,iindex] - xmin) * (lat[:,iindex] - xmin) 
-194          start = np.where(dd == dd.min()) 
-195          dd = (lat[:,iindex] - xmax) * (lat[:,iindex] - xmax) 
-196          end = np.where(dd == dd.min()) 
-197          lon_min = lon.min() 
-198          lon_max = lon.max() 
-199          lon_0 = (lon_min + lon_max) / 2. 
-200          lat_min = lat.min() 
-201          lat_max = lat.max()      
-202          lat_0 = (lat_min + lat_max) / 2. 
-203          map = Basemap(projection='merc', llcrnrlon=lon_min, llcrnrlat=lat_min, \ 
-204                   urcrnrlon=lon_max, urcrnrlat=lat_max, lat_0=lat_0, lon_0=lon_0, \ 
-205                   resolution='i', area_thresh=10.) 
-206          x, y = map(lon,lat) 
-207          # fill land and draw coastlines 
-208          map.drawcoastlines() 
-209          map.fillcontinents(color='grey') 
-210          #map.drawmapboundary() 
-211          Basemap.pcolor(map, x, y, varm, axes=ax_map) 
-212          Basemap.plot(map, x[start[0]:end[0],iindex], y[start[0]:end[0],iindex], \ 
-213                         'k-', linewidth=3, axes=ax_map) 
-214   
-215   
-216      if outfile is not None: 
-217          if outfile.find('.png') != -1 or outfile.find('.svg') != -1 or outfile.find('.eps') != -1: 
-218              print 'Write figure to file', outfile 
-219              plt.savefig(outfile, dpi=200, facecolor='w', edgecolor='w', orientation='portrait') 
-220          else: 
-221              print 'Unrecognized file extension. Please use .png, .svg or .eps file extension.'    
-222   
-223   
-224      return 
-
225   
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Module jview'

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- - - - - - - - - -
- - - - - -
Functions[hide private]
-
-   - - - - - - -
jview(var, - tindex, - jindex, - gridid, - filename=None, - cmin=None, - cmax=None, - clev=None, - clbformat='%.2f', - fill=False, - contour=False, - d=4, - irange=None, - hrange=None, - fts=None, - title=None, - map=False, - pal=None, - clb=True, - outfile=None)
- jview(var, tindex, jindex, gridid, {optional switch})		 - source code - -
- -
- - - - - - -
- - - - - -
Function Details[hide private]
-
- -
- -
- - -
-

jview(var, - tindex, - jindex, - gridid, - filename=None, - cmin=None, - cmax=None, - clev=None, - clbformat='%.2f', - fill=False, - contour=False, - d=4, - irange=None, - hrange=None, - fts=None, - title=None, - map=False, - pal=None, - clb=True, - outfile=None) -

- 		source code  -
- -

jview(var, tindex, jindex, gridid, {optional switch})

-

optional switch:

-
    -
  • - filename if defined, load the variable from file -
    • -
  • - cmin set color minimum limit -
    • -
  • - cmax set color maximum limit -
    • -
  • - clev set the number of color step -
    • -
  • - fill use contourf instead of pcolor -
    • -
  • - contour overlay contour (request fill=True) -
    • -
  • - d contour density (default d=4) -
    • -
  • - irange i range -
    • -
  • - hrange h range -
    • -
  • - fts set font size (default: 12) -
    • -
  • - title add title to the plot -
    • -
  • - map if True, draw a map showing islice location -
    • -
  • - pal set color map (default: cm.jet) -
    • -
  • - clb add colorbar (defaul: True) -
    • -
  • - outfile if defined, write figure to file -
    • -
-

plot a constante-j slice of variable var. If filename is provided, var - must be a string and the variable will be load from the file. grid can be - a grid object or a gridid. In the later case, the grid object - correponding to the provided gridid will be loaded.

-
-
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- Generated by Epydoc 3.0.1 on Mon Sep 27 11:35:24 2010 - - http://epydoc.sourceforge.net -
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Source Code for Module pyroms_toolbox.jview'

-
-  1  import numpy as np 
-  2  import matplotlib.pyplot as plt 
-  3  from  matplotlib import cm, colors 
-  4  from mpl_toolkits.basemap import Basemap 
-  5  import pyroms 
-  6   
-  7   
-
  8 -def jview(var, tindex, jindex, gridid, filename=None, \ 
-  9            cmin=None, cmax=None, clev=None, clbformat='%.2f', \ 
- 10            fill=False, contour=False, d=4, irange=None, \ 
- 11            hrange=None, fts=None, title=None, map=False, \ 
- 12            pal=None, clb=True, outfile=None): 
-
 13      """ 
- 14      jview(var, tindex, jindex, gridid, {optional switch}) 
- 15   
- 16      optional switch: 
- 17        - filename         if defined, load the variable from file 
- 18        - cmin             set color minimum limit 
- 19        - cmax             set color maximum limit 
- 20        - clev             set the number of color step 
- 21        - fill             use contourf instead of pcolor 
- 22        - contour          overlay contour (request fill=True) 
- 23        - d                contour density (default d=4)  
- 24        - irange           i range 
- 25        - hrange           h range 
- 26        - fts              set font size (default: 12) 
- 27        - title            add title to the plot 
- 28        - map              if True, draw a map showing islice location 
- 29        - pal              set color map (default: cm.jet) 
- 30        - clb              add colorbar (defaul: True) 
- 31        - outfile          if defined, write figure to file 
- 32   
- 33      plot a constante-j slice of variable var. If filename is provided, 
- 34      var must be a string and the variable will be load from the file. 
- 35      grid can be a grid object or a gridid. In the later case, the grid 
- 36      object correponding to the provided gridid will be loaded. 
- 37      """ 
- 38   
- 39      # get grid 
- 40      if type(gridid).__name__ == 'ROMS_Grid': 
- 41          grd = gridid 
- 42      else: 
- 43          grd = pyroms.grid.get_ROMS_grid(gridid) 
- 44   
- 45      # get variable 
- 46      if filename == None: 
- 47          var = var 
- 48      else: 
- 49          data = pyroms.io.Dataset(filename) 
- 50   
- 51          var = data.variables[var] 
- 52   
- 53      Np, Mp, Lp = grd.vgrid.z_r[0,:].shape 
- 54   
- 55      if tindex is not -1: 
- 56          assert len(var.shape) == 4, 'var must be 4D (time plus space).' 
- 57          K, N, M, L = var.shape 
- 58      else: 
- 59          assert len(var.shape) == 3, 'var must be 3D (no time dependency).' 
- 60          N, M, L = var.shape 
- 61   
- 62      # determine where on the C-grid these variable lies 
- 63      if N == Np and M == Mp and L == Lp: 
- 64          Cpos='rho' 
- 65          lon = grd.hgrid.lon_vert 
- 66          lat = grd.hgrid.lat_vert 
- 67          mask = grd.hgrid.mask_rho 
- 68   
- 69      if N == Np and M == Mp and L == Lp-1: 
- 70          Cpos='u' 
- 71          lon = 0.5 * (grd.hgrid.lon_vert[:,:-1] + grd.hgrid.lon_vert[:,1:]) 
- 72          lat = 0.5 * (grd.hgrid.lat_vert[:,:-1] + grd.hgrid.lat_vert[:,1:]) 
- 73          mask = grd.hgrid.mask_u 
- 74   
- 75      if N == Np and M == Mp-1 and L == Lp: 
- 76          Cpos='v' 
- 77          lon = 0.5 * (grd.hgrid.lon_vert[:-1,:] + grd.hgrid.lon_vert[1:,:]) 
- 78          lat = 0.5 * (grd.hgrid.lat_vert[:-1,:] + grd.hgrid.lat_vert[1:,:]) 
- 79          mask = grd.hgrid.mask_v 
- 80   
- 81      if N == Np+1 and M == Mp and L == Lp: 
- 82          Cpos='w' 
- 83          lon = grd.hgrid.lon_vert 
- 84          lat = grd.hgrid.lat_vert 
- 85          mask = grd.hgrid.mask_rho 
- 86   
- 87      # get constante-j slice 
- 88      if tindex == -1: 
- 89          var = var[:,:,:] 
- 90      else: 
- 91          var = var[tindex,:,:,:] 
- 92   
- 93      if fill == True: 
- 94          jslice, zj, lonj, latj, = pyroms.tools.jslice(var, jindex, grd, \ 
- 95                                      Cpos) 
- 96      else: 
- 97          jslice, zj, lonj, latj, = pyroms.tools.jslice(var, jindex, grd, \ 
- 98                                      Cpos, vert=True) 
- 99   
-100      # plot 
-101      if cmin is None: 
-102          cmin = jslice.min() 
-103      else: 
-104          cmin = float(cmin) 
-105   
-106      if cmax is None: 
-107          cmax = jslice.max() 
-108      else: 
-109          cmax = float(cmax) 
-110   
-111      if clev is None: 
-112          clev = 100. 
-113      else: 
-114          clev = float(clev) 
-115   
-116      dc = (cmax - cmin)/clev ; vc = np.arange(cmin,cmax+dc,dc) 
-117   
-118      if pal is None: 
-119          pal = cm.jet 
-120      else: 
-121          pal = pal 
-122   
-123      if fts is None: 
-124          fts = 12 
-125      else: 
-126          fts = fts 
-127   
-128      #pal.set_over('w', 1.0) 
-129      #pal.set_under('w', 1.0) 
-130      #pal.set_bad('w', 1.0) 
-131   
-132      pal_norm = colors.BoundaryNorm(vc,ncolors=256, clip = False) 
-133       
-134      # clear figure 
-135      #plt.clf() 
-136   
-137      if map is True: 
-138          # set axes for the main plot in order to keep space for the map        
-139          if fts < 12: 
-140              ax=None 
-141          else: 
-142              ax = plt.axes([0.15, 0.08, 0.8, 0.65])        
-143      else:        
-144          if fts < 12: 
-145              ax=None 
-146          else: 
-147              ax=plt.axes([0.15, 0.1, 0.8, 0.8]) 
-148   
-149   
-150      if fill is True: 
-151          cf = plt.contourf(lonj, zj, jslice, vc, cmap = pal, norm = pal_norm, axes=ax) 
-152      else: 
-153          cf = plt.pcolor(lonj, zj, jslice, cmap = pal, norm = pal_norm, axes=ax) 
-154   
-155      if clb is True: 
-156          clb = plt.colorbar(cf, fraction=0.075,format=clbformat) 
-157          for t in clb.ax.get_yticklabels(): 
-158              t.set_fontsize(fts) 
-159   
-160      if contour is True: 
-161          if fill is not True: 
-162              raise Warning, 'Please run again with fill=True for overlay contour.' 
-163          else: 
-164              plt.contour(lonj, zj, jslice, vc[::d], colors='k', linewidths=0.5, linestyles='solid', axes=ax) 
-165   
-166   
-167      if irange is not None: 
-168          plt.xlim(irange) 
-169   
-170      if hrange is not None: 
-171          plt.ylim(hrange) 
-172   
-173      if title is not None: 
-174          if map is True: 
-175              # move the title on the right 
-176              xmin, xmax = ax.get_xlim() 
-177              ymin, ymax = ax.get_ylim() 
-178              xt = xmin - (xmax-xmin)/9. 
-179              yt = ymax + (ymax-ymin)/7. 
-180              plt.text(xt, yt, title, fontsize=fts+4) 
-181          else: 
-182              plt.title(title, fontsize=fts+4) 
-183   
-184      plt.xlabel('Latitude', fontsize=fts) 
-185      plt.ylabel('Depth', fontsize=fts) 
-186   
-187      if map is True: 
-188          # draw a map with constant-i slice location 
-189          ax_map = plt.axes([0.4, 0.76, 0.2, 0.23]) 
-190          varm = np.ma.masked_where(mask[:,:] == 0, var[var.shape[0]-1,:,:])         
-191          xmin, xmax = ax.get_xlim()       
-192          dd = (lon[jindex,:] - xmin) * (lon[jindex,:] - xmin) 
-193          start = np.where(dd == dd.min()) 
-194          dd = (lon[jindex,:] - xmax) * (lon[jindex,:] - xmax) 
-195          end = np.where(dd == dd.min()) 
-196          lon_min = lon.min() 
-197          lon_max = lon.max() 
-198          lon_0 = (lon_min + lon_max) / 2. 
-199          lat_min = lat.min() 
-200          lat_max = lat.max()      
-201          lat_0 = (lat_min + lat_max) / 2. 
-202          map = Basemap(projection='merc', llcrnrlon=lon_min, llcrnrlat=lat_min, \ 
-203                   urcrnrlon=lon_max, urcrnrlat=lat_max, lat_0=lat_0, lon_0=lon_0, \ 
-204                   resolution='i', area_thresh=10.) 
-205          x, y = map(lon,lat) 
-206          # fill land and draw coastlines 
-207          map.drawcoastlines() 
-208          map.fillcontinents(color='grey') 
-209          #map.drawmapboundary() 
-210          Basemap.pcolor(map, x, y, varm, axes=ax_map) 
-211          Basemap.plot(map, x[jindex,start[0]:end[0]], y[jindex,start[0]:end[0]], \ 
-212                         'k-', linewidth=3, axes=ax_map) 
-213   
-214   
-215      if outfile is not None: 
-216          if outfile.find('.png') != -1 or outfile.find('.svg') != -1 or outfile.find('.eps') != -1: 
-217              print 'Write figure to file', outfile 
-218              plt.savefig(outfile, dpi=200, facecolor='w', edgecolor='w', orientation='portrait') 
-219          else: 
-220              print 'Unrecognized file extension. Please use .png, .svg or .eps file extension.'    
-221   
-222   
-223      return 
-
224   
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- Generated by Epydoc 3.0.1 on Mon Sep 27 11:35:25 2010 - - http://epydoc.sourceforge.net -
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- - Package pyroms_toolbox :: - Module latview' - - - - - - -
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Module latview'

source code

- - - - - - - - - -
- - - - - -
Functions[hide private]
-
-   - - - - - - -
latview(var, - tindex, - latitude, - gridid, - filename=None, - cmin=None, - cmax=None, - clev=None, - fill=False, - contour=False, - d=4, - lonrange=None, - hrange=None, - fts=None, - title=None, - map=False, - pal=None, - clb=True, - outfile=None)
- latview(var, tindex, latitude, gridid, {optional switch})		 - source code - -
- -
- - - - - - -
- - - - - -
Function Details[hide private]
-
- -
- -
- - -
-

latview(var, - tindex, - latitude, - gridid, - filename=None, - cmin=None, - cmax=None, - clev=None, - fill=False, - contour=False, - d=4, - lonrange=None, - hrange=None, - fts=None, - title=None, - map=False, - pal=None, - clb=True, - outfile=None) -

- 		source code  -
- -

latview(var, tindex, latitude, gridid, {optional switch})

-

optional switch:

-
    -
  • - filename if defined, load the variable from file -
    • -
  • - cmin set color minimum limit -
    • -
  • - cmax set color maximum limit -
    • -
  • - clev set the number of color step -
    • -
  • - fill use contourf instead of pcolor -
    • -
  • - contour overlay contour (request fill=True) -
    • -
  • - d contour density (default d=4) -
    • -
  • - lonrange longitude range -
    • -
  • - hrange h range -
    • -
  • - fts set font size (default: 12) -
    • -
  • - title add title to the plot -
    • -
  • - map if True, draw a map showing islice location -
    • -
  • - pal set color map (default: cm.jet) -
    • -
  • - clb add colorbar (defaul: True) -
    • -
  • - outfile if defined, write figure to file -
    • -
-

plot a constante-latitudinal slice of variable var. If filename is - provided, var must be a string and the variable will be load from the - file. grid can be a grid object or a gridid. In the later case, the grid - object correponding to the provided gridid will be loaded.

-
-
-
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-
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- Generated by Epydoc 3.0.1 on Mon Sep 27 11:35:24 2010 - - http://epydoc.sourceforge.net -
- - - - diff --git a/pyroms_toolbox/docs/pyroms_toolbox.latview'-pysrc.html b/pyroms_toolbox/docs/pyroms_toolbox.latview'-pysrc.html deleted file mode 100644 index 385af21..0000000 --- a/pyroms_toolbox/docs/pyroms_toolbox.latview'-pysrc.html +++ /dev/null @@ -1,330 +0,0 @@ - - - - - pyroms_toolbox.latview' - - - - - - - - - - - - - - - - - - - - - - -
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Source Code for Module pyroms_toolbox.latview'

-
-  1  import numpy as np 
-  2  import matplotlib.pyplot as plt 
-  3  from  matplotlib import cm, colors 
-  4  from mpl_toolkits.basemap import Basemap 
-  5  import pyroms 
-  6   
-  7   
-
  8 -def latview(var, tindex, latitude, gridid, filename=None, \ 
-  9              cmin=None, cmax=None, clev=None, fill=False, \ 
- 10              contour=False, d=4, lonrange=None, hrange=None,\ 
- 11              fts=None, title=None, map=False, \ 
- 12              pal=None, clb=True, outfile=None): 
-
 13      """ 
- 14      latview(var, tindex, latitude, gridid, {optional switch}) 
- 15   
- 16      optional switch: 
- 17        - filename         if defined, load the variable from file 
- 18        - cmin             set color minimum limit 
- 19        - cmax             set color maximum limit 
- 20        - clev             set the number of color step 
- 21        - fill             use contourf instead of pcolor 
- 22        - contour          overlay contour (request fill=True) 
- 23        - d                contour density (default d=4)  
- 24        - lonrange         longitude range 
- 25        - hrange           h range 
- 26        - fts              set font size (default: 12) 
- 27        - title            add title to the plot 
- 28        - map              if True, draw a map showing islice location 
- 29        - pal              set color map (default: cm.jet) 
- 30        - clb              add colorbar (defaul: True) 
- 31        - outfile          if defined, write figure to file 
- 32   
- 33      plot a constante-latitudinal slice of variable var. If filename  
- 34      is provided, var must be a string and the variable will be load  
- 35      from the file. 
- 36      grid can be a grid object or a gridid. In the later case, the grid 
- 37      object correponding to the provided gridid will be loaded. 
- 38      """ 
- 39   
- 40      # get grid 
- 41      if type(gridid).__name__ == 'ROMS_Grid': 
- 42          grd = gridid 
- 43      else: 
- 44          grd = pyroms.grid.get_ROMS_grid(gridid) 
- 45   
- 46      # get variable 
- 47      if filename == None: 
- 48          var = var 
- 49      else: 
- 50          data = pyroms.io.Dataset(filename) 
- 51   
- 52          var = data.variables[var] 
- 53   
- 54      Np, Mp, Lp = grd.vgrid.z_r[0,:].shape 
- 55   
- 56      if tindex is not -1: 
- 57          assert len(var.shape) == 4, 'var must be 4D (time plus space).' 
- 58          K, N, M, L = var.shape 
- 59      else: 
- 60          assert len(var.shape) == 3, 'var must be 3D (no time dependency).' 
- 61          N, M, L = var.shape 
- 62   
- 63      # determine where on the C-grid these variable lies 
- 64      if N == Np and M == Mp and L == Lp: 
- 65          Cpos='rho' 
- 66          lon = grd.hgrid.lon_vert 
- 67          lat = grd.hgrid.lat_vert 
- 68          mask = grd.hgrid.mask_rho 
- 69   
- 70      if N == Np and M == Mp and L == Lp-1: 
- 71          Cpos='u' 
- 72          lon = 0.5 * (grd.hgrid.lon_vert[:,:-1] + grd.hgrid.lon_vert[:,1:]) 
- 73          lat = 0.5 * (grd.hgrid.lat_vert[:,:-1] + grd.hgrid.lat_vert[:,1:]) 
- 74          mask = grd.hgrid.mask_u 
- 75   
- 76      if N == Np and M == Mp-1 and L == Lp: 
- 77          Cpos='v' 
- 78          lon = 0.5 * (grd.hgrid.lon_vert[:-1,:] + grd.hgrid.lon_vert[1:,:]) 
- 79          lat = 0.5 * (grd.hgrid.lat_vert[:-1,:] + grd.hgrid.lat_vert[1:,:]) 
- 80          mask = grd.hgrid.mask_v 
- 81   
- 82      # get constante-lat slice 
- 83      if tindex == -1: 
- 84          var = var[:,:,:] 
- 85      else: 
- 86          var = var[tindex,:,:,:] 
- 87   
- 88      if fill == True: 
- 89          latslice, zs, lons, lats, = pyroms.tools.latslice(var, latitude, grd, Cpos) 
- 90      else: 
- 91          latslice, zs, lons, lats, = pyroms.tools.latslice(var, latitude, grd, Cpos, vert=True) 
- 92   
- 93   
- 94      # plot 
- 95      if cmin is None: 
- 96          cmin = latslice.min() 
- 97      else: 
- 98          cmin = float(cmin) 
- 99   
-100      if cmax is None: 
-101          cmax = latslice.max() 
-102      else: 
-103          cmax = float(cmax) 
-104   
-105      if clev is None: 
-106          clev = 100. 
-107      else: 
-108          clev = float(clev) 
-109   
-110      dc = (cmax - cmin)/clev ; vc = np.arange(cmin,cmax+dc,dc) 
-111   
-112      if pal is None: 
-113          pal = cm.jet 
-114      else: 
-115          pal = pal 
-116   
-117      if fts is None: 
-118          fts = 12 
-119      else: 
-120          fts = fts 
-121   
-122      #pal.set_over('w', 1.0) 
-123      #pal.set_under('w', 1.0) 
-124      #pal.set_bad('w', 1.0) 
-125   
-126      pal_norm = colors.BoundaryNorm(vc,ncolors=256, clip = False) 
-127       
-128      # clear figure 
-129      #plt.clf() 
-130   
-131      if map is True: 
-132          # set axes for the main plot in order to keep space for the map        
-133          if fts < 12: 
-134              ax=None 
-135          else: 
-136              ax = plt.axes([0.15, 0.08, 0.8, 0.65])        
-137      else:        
-138          if fts < 12: 
-139              ax=None 
-140          else: 
-141              ax=plt.axes([0.15, 0.1, 0.8, 0.8]) 
-142   
-143   
-144      if fill is True: 
-145          cf = plt.contourf(lons, zs, latslice, vc, cmap = pal, norm = pal_norm, axes=ax) 
-146      else: 
-147          cf = plt.pcolor(lons, zs, latslice, cmap = pal, norm = pal_norm, axes=ax) 
-148   
-149      if clb is True: 
-150          clb = plt.colorbar(cf, fraction=0.075,format='%.2f') 
-151          for t in clb.ax.get_yticklabels(): 
-152              t.set_fontsize(fts) 
-153   
-154      if contour is True: 
-155          if fill is not True: 
-156              raise Warning, 'Please run again with fill=True for overlay contour.' 
-157          else: 
-158              plt.contour(lons, zs, latslice, vc[::d], colors='k', linewidths=0.5, linestyles='solid', axes=ax) 
-159   
-160   
-161      if lonrange is not None: 
-162          plt.xlim(lonrange) 
-163   
-164      if hrange is not None: 
-165          plt.ylim(hrange) 
-166   
-167      if title is not None: 
-168          if map is True: 
-169              # move the title on the right 
-170              xmin, xmax = ax.get_xlim() 
-171              ymin, ymax = ax.get_ylim() 
-172              xt = xmin - (xmax-xmin)/9. 
-173              yt = ymax + (ymax-ymin)/7. 
-174              plt.text(xt, yt, title, fontsize=fts+4) 
-175          else: 
-176              plt.title(title, fontsize=fts+4) 
-177   
-178      plt.xlabel('Latitude', fontsize=fts) 
-179      plt.ylabel('Depth', fontsize=fts) 
-180   
-181      if map is True: 
-182          # draw a map with constant-i slice location 
-183          ax_map = plt.axes([0.4, 0.76, 0.2, 0.23]) 
-184          varm = np.ma.masked_where(mask[:,:] == 0, var[var.shape[0]-1,:,:])         
-185          lon_min = lon.min() 
-186          lon_max = lon.max() 
-187          lon_0 = (lon_min + lon_max) / 2. 
-188          lat_min = lat.min() 
-189          lat_max = lat.max()      
-190          lat_0 = (lat_min + lat_max) / 2. 
-191          map = Basemap(projection='merc', llcrnrlon=lon_min, llcrnrlat=lat_min, \ 
-192                   urcrnrlon=lon_max, urcrnrlat=lat_max, lat_0=lat_0, lon_0=lon_0, \ 
-193                   resolution='i', area_thresh=10.) 
-194          x, y = map(lon,lat) 
-195          if lonrange is None: 
-196              xs, ys = map(lons[0,:],lats[0,:]) 
-197          else: 
-198              c1 = lats[0,:] >= lonrange[0] 
-199              c2 = lats[0,:] <= lonrange[1] 
-200              c = c1 & c2 
-201              idx = np.where(c == True) 
-202              xs, ys = map(lons[0,idx[0]],lats[0,idx[0]]) 
-203          # fill land and draw coastlines 
-204          map.drawcoastlines() 
-205          map.fillcontinents(color='grey') 
-206          #map.drawmapboundary() 
-207          Basemap.pcolor(map, x, y, varm, axes=ax_map) 
-208          Basemap.plot(map, xs, ys, 'k-', linewidth=3, axes=ax_map) 
-209   
-210   
-211      if outfile is not None: 
-212          if outfile.find('.png') != -1 or outfile.find('.svg') != -1 or outfile.find('.eps') != -1: 
-213              print 'Write figure to file', outfile 
-214              plt.savefig(outfile, dpi=200, facecolor='w', edgecolor='w', orientation='portrait') 
-215          else: 
-216              print 'Unrecognized file extension. Please use .png, .svg or .eps file extension.'    
-217   
-218   
-219      return 
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220   
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Module lonview'

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Functions[hide private]
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lonview(var, - tindex, - longitude, - gridid, - filename=None, - cmin=None, - cmax=None, - clev=None, - fill=False, - contour=False, - d=4, - latrange=None, - hrange=None, - fts=None, - title=None, - map=False, - pal=None, - clb=True, - outfile=None)
- lonview(var, tindex, longitude, gridid, {optional switch})		 - source code - -
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Function Details[hide private]
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lonview(var, - tindex, - longitude, - gridid, - filename=None, - cmin=None, - cmax=None, - clev=None, - fill=False, - contour=False, - d=4, - latrange=None, - hrange=None, - fts=None, - title=None, - map=False, - pal=None, - clb=True, - outfile=None) -

- 		source code  -
- -

lonview(var, tindex, longitude, gridid, {optional switch})

-

optional switch:

-
    -
  • - filename if defined, load the variable from file -
    • -
  • - cmin set color minimum limit -
    • -
  • - cmax set color maximum limit -
    • -
  • - clev set the number of color step -
    • -
  • - fill use contourf instead of pcolor -
    • -
  • - contour overlay contour (request fill=True) -
    • -
  • - d contour density (default d=4) -
    • -
  • - latrange latitude range -
    • -
  • - hrange h range -
    • -
  • - fts set font size (default: 12) -
    • -
  • - title add title to the plot -
    • -
  • - map if True, draw a map showing islice location -
    • -
  • - pal set color map (default: cm.jet) -
    • -
  • - clb add colorbar (defaul: True) -
    • -
  • - outfile if defined, write figure to file -
    • -
-

plot a constante-longitudinal slice of variable var. If filename is - provided, var must be a string and the variable will be load from the - file. grid can be a grid object or a gridid. In the later case, the grid - object correponding to the provided gridid will be loaded.

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Source Code for Module pyroms_toolbox.lonview'

-
-  1  import numpy as np 
-  2  import matplotlib.pyplot as plt 
-  3  from  matplotlib import cm, colors 
-  4  from mpl_toolkits.basemap import Basemap 
-  5  import pyroms 
-  6   
-  7   
-
  8 -def lonview(var, tindex, longitude, gridid, filename=None, \ 
-  9              cmin=None, cmax=None, clev=None, fill=False, \ 
- 10              contour=False, d=4, latrange=None, hrange=None,\ 
- 11              fts=None, title=None, map=False, \ 
- 12              pal=None, clb=True, outfile=None): 
-
 13      """ 
- 14      lonview(var, tindex, longitude, gridid, {optional switch}) 
- 15   
- 16      optional switch: 
- 17        - filename         if defined, load the variable from file 
- 18        - cmin             set color minimum limit 
- 19        - cmax             set color maximum limit 
- 20        - clev             set the number of color step 
- 21        - fill             use contourf instead of pcolor 
- 22        - contour          overlay contour (request fill=True) 
- 23        - d                contour density (default d=4)  
- 24        - latrange         latitude range 
- 25        - hrange           h range 
- 26        - fts              set font size (default: 12) 
- 27        - title            add title to the plot 
- 28        - map              if True, draw a map showing islice location 
- 29        - pal              set color map (default: cm.jet) 
- 30        - clb              add colorbar (defaul: True) 
- 31        - outfile          if defined, write figure to file 
- 32   
- 33      plot a constante-longitudinal slice of variable var. If filename  
- 34      is provided, var must be a string and the variable will be load  
- 35      from the file. 
- 36      grid can be a grid object or a gridid. In the later case, the grid 
- 37      object correponding to the provided gridid will be loaded. 
- 38      """ 
- 39   
- 40      # get grid 
- 41      if type(gridid).__name__ == 'ROMS_Grid': 
- 42          grd = gridid 
- 43      else: 
- 44          grd = pyroms.grid.get_ROMS_grid(gridid) 
- 45   
- 46      # get variable 
- 47      if filename == None: 
- 48          var = var 
- 49      else: 
- 50          data = pyroms.io.Dataset(filename) 
- 51   
- 52          var = data.variables[var] 
- 53   
- 54      Np, Mp, Lp = grd.vgrid.z_r[0,:].shape 
- 55   
- 56      if tindex is not -1: 
- 57          assert len(var.shape) == 4, 'var must be 4D (time plus space).' 
- 58          K, N, M, L = var.shape 
- 59      else: 
- 60          assert len(var.shape) == 3, 'var must be 3D (no time dependency).' 
- 61          N, M, L = var.shape 
- 62   
- 63      # determine where on the C-grid these variable lies 
- 64      if N == Np and M == Mp and L == Lp: 
- 65          Cpos='rho' 
- 66          lon = grd.hgrid.lon_vert 
- 67          lat = grd.hgrid.lat_vert 
- 68          mask = grd.hgrid.mask_rho 
- 69   
- 70      if N == Np and M == Mp and L == Lp-1: 
- 71          Cpos='u' 
- 72          lon = 0.5 * (grd.hgrid.lon_vert[:,:-1] + grd.hgrid.lon_vert[:,1:]) 
- 73          lat = 0.5 * (grd.hgrid.lat_vert[:,:-1] + grd.hgrid.lat_vert[:,1:]) 
- 74          mask = grd.hgrid.mask_u 
- 75   
- 76      if N == Np and M == Mp-1 and L == Lp: 
- 77          Cpos='v' 
- 78          lon = 0.5 * (grd.hgrid.lon_vert[:-1,:] + grd.hgrid.lon_vert[1:,:]) 
- 79          lat = 0.5 * (grd.hgrid.lat_vert[:-1,:] + grd.hgrid.lat_vert[1:,:]) 
- 80          mask = grd.hgrid.mask_v 
- 81   
- 82      # get constante-lon slice 
- 83      if tindex == -1: 
- 84          var = var[:,:,:] 
- 85      else: 
- 86          var = var[tindex,:,:,:] 
- 87   
- 88      if fill == True: 
- 89          lonslice, zs, lons, lats, = pyroms.tools.lonslice(var, longitude, grd, Cpos) 
- 90      else: 
- 91          lonslice, zs, lons, lats, = pyroms.tools.lonslice(var, longitude, grd, Cpos, vert=True) 
- 92   
- 93   
- 94      # plot 
- 95      if cmin is None: 
- 96          cmin = lonslice.min() 
- 97      else: 
- 98          cmin = float(cmin) 
- 99   
-100      if cmax is None: 
-101          cmax = lonslice.max() 
-102      else: 
-103          cmax = float(cmax) 
-104   
-105      if clev is None: 
-106          clev = 100. 
-107      else: 
-108          clev = float(clev) 
-109   
-110      dc = (cmax - cmin)/clev ; vc = np.arange(cmin,cmax+dc,dc) 
-111   
-112      if pal is None: 
-113          pal = cm.jet 
-114      else: 
-115          pal = pal 
-116   
-117      if fts is None: 
-118          fts = 12 
-119      else: 
-120          fts = fts 
-121   
-122      #pal.set_over('w', 1.0) 
-123      #pal.set_under('w', 1.0) 
-124      #pal.set_bad('w', 1.0) 
-125   
-126      pal_norm = colors.BoundaryNorm(vc,ncolors=256, clip = False) 
-127       
-128      # clear figure 
-129      #plt.clf() 
-130   
-131      if map is True: 
-132          # set axes for the main plot in order to keep space for the map        
-133          if fts < 12: 
-134              ax=None 
-135          else: 
-136              ax = plt.axes([0.15, 0.08, 0.8, 0.65])        
-137      else:        
-138          if fts < 12: 
-139              ax=None 
-140          else: 
-141              ax=plt.axes([0.15, 0.1, 0.8, 0.8]) 
-142   
-143   
-144      if fill is True: 
-145          cf = plt.contourf(lats, zs, lonslice, vc, cmap = pal, norm = pal_norm, axes=ax) 
-146      else: 
-147          cf = plt.pcolor(lats, zs, lonslice, cmap = pal, norm = pal_norm, axes=ax) 
-148   
-149      if clb is True: 
-150          clb = plt.colorbar(cf, fraction=0.075,format='%.2f') 
-151          for t in clb.ax.get_yticklabels(): 
-152              t.set_fontsize(fts) 
-153   
-154      if contour is True: 
-155          if fill is not True: 
-156              raise Warning, 'Please run again with fill=True for overlay contour.' 
-157          else: 
-158              plt.contour(lats, zs, lonslice, vc[::d], colors='k', linewidths=0.5, linestyles='solid', axes=ax) 
-159   
-160   
-161      if latrange is not None: 
-162          plt.xlim(latrange) 
-163   
-164      if hrange is not None: 
-165          plt.ylim(hrange) 
-166   
-167      if title is not None: 
-168          if map is True: 
-169              # move the title on the right 
-170              xmin, xmax = ax.get_xlim() 
-171              ymin, ymax = ax.get_ylim() 
-172              xt = xmin - (xmax-xmin)/9. 
-173              yt = ymax + (ymax-ymin)/7. 
-174              plt.text(xt, yt, title, fontsize=fts+4) 
-175          else: 
-176              plt.title(title, fontsize=fts+4) 
-177   
-178      plt.xlabel('Latitude', fontsize=fts) 
-179      plt.ylabel('Depth', fontsize=fts) 
-180   
-181      if map is True: 
-182          # draw a map with constant-i slice location 
-183          ax_map = plt.axes([0.4, 0.76, 0.2, 0.23]) 
-184          varm = np.ma.masked_where(mask[:,:] == 0, var[var.shape[0]-1,:,:])         
-185          lon_min = lon.min() 
-186          lon_max = lon.max() 
-187          lon_0 = (lon_min + lon_max) / 2. 
-188          lat_min = lat.min() 
-189          lat_max = lat.max()      
-190          lat_0 = (lat_min + lat_max) / 2. 
-191          map = Basemap(projection='merc', llcrnrlon=lon_min, llcrnrlat=lat_min, \ 
-192                   urcrnrlon=lon_max, urcrnrlat=lat_max, lat_0=lat_0, lon_0=lon_0, \ 
-193                   resolution='i', area_thresh=10.) 
-194          x, y = map(lon,lat) 
-195          if latrange is None: 
-196              xs, ys = map(lons[0,:],lats[0,:]) 
-197          else: 
-198              c1 = lats[0,:] >= latrange[0] 
-199              c2 = lats[0,:] <= latrange[1] 
-200              c = c1 & c2 
-201              idx = np.where(c == True) 
-202              xs, ys = map(lons[0,idx[0]],lats[0,idx[0]]) 
-203          # fill land and draw coastlines 
-204          map.drawcoastlines() 
-205          map.fillcontinents(color='grey') 
-206          #map.drawmapboundary() 
-207          Basemap.pcolor(map, x, y, varm, axes=ax_map) 
-208          Basemap.plot(map, xs, ys, 'k-', linewidth=3, axes=ax_map) 
-209   
-210   
-211      if outfile is not None: 
-212          if outfile.find('.png') != -1 or outfile.find('.svg') != -1 or outfile.find('.eps') != -1: 
-213              print 'Write figure to file', outfile 
-214              plt.savefig(outfile, dpi=200, facecolor='w', edgecolor='w', orientation='portrait') 
-215          else: 
-216              print 'Unrecognized file extension. Please use .png, .svg or .eps file extension.'    
-217   
-218   
-219      return 
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Module lsq_phase_amplitude'

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lsq_phase_amplitude(omega, - ue, - un, - t)
- Amp, Pha = lsq_phase_amplitude(omega,ue,un,t)		 - source code - -
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Source Code for Module pyroms_toolbox.lsq_phase_amplitude'

-
- 1  import numpy as np 
- 2  import matplotlib.pyplot as plt 
- 3   
- 4   
-
 5 -def lsq_phase_amplitude(omega,ue,un,t): 
-
 6      ''' 
- 7      Amp, Pha = lsq_phase_amplitude(omega,ue,un,t) 
- 8      ''' 
- 9      nc = omega.shape[0] 
-10      m = 1 + 2*nc 
-11   
-12      # Build Matrix 
-13      c = np.ones((m,t.shape[0])) 
-14      for i in range(nc): 
-15          c[2*i+1,:]   =  np.cos(omega[i]*t) 
-16          c[2*i+2,:] =  np.sin(omega[i]*t) 
-17   
-18      A = np.zeros((m,m)) 
-19      for i in range(m): 
-20          for j in range(m): 
-21              A[i,j] = np.mean(c[i,:] * c[j,:]) 
-22   
-23      b1 = np.zeros(m) 
-24      b2 = np.zeros(m) 
-25      for i in range(m): 
-26          b1[i] = np.mean(ue * c[i,:]) 
-27          b2[i] = np.mean(un * c[i,:]) 
-28   
-29   
-30      # Get solution  
-31      x1 = np.linalg.solve(A,b1) 
-32      x2 = np.linalg.solve(A,b2) 
-33   
-34      C = x1[1:2*nc:2]; D = x1[2:2*nc+1:2] 
-35   
-36      Amp = np.sqrt(C*C + D*D) 
-37      Pha = 180*np.arctan2(C,D)/np.pi 
-38   
-39      for i in range(nc): 
-40          if Pha[i] < 0: 
-41              Pha[i] = Pha[i] + 360 
-42   
-43      return Amp, Pha 
-
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Source Code for Module pyroms_toolbox.nc_create_roms_bdry_file'

-
- 1  import numpy as np 
- 2  from datetime import datetime 
- 3  try: 
- 4    import netCDF4 as netCDF 
- 5  except: 
- 6    import netCDF3 as netCDF 
- 7   
- 8   
-
 9 -def nc_create_roms_bdry_file(filename, grd, ocean_time): 
-
10   
-11      # create file 
-12      nc = netCDF.Dataset(filename, 'w', format='NETCDF3_CLASSIC') 
-13      nc.Description = 'ROMS file' 
-14      nc.Author = 'pyroms_toolbox.nc_create_roms_file' 
-15      nc.Created = datetime.now().strftime("%Y-%m-%d %H:%M:%S") 
-16      nc.title = 'ROMS file' 
-17   
-18      nc.createDimension('xi_rho', np.size(grd.hgrid.mask_rho,1)) 
-19      nc.createDimension('xi_u', np.size(grd.hgrid.mask_u,1)) 
-20      nc.createDimension('xi_v', np.size(grd.hgrid.mask_v,1)) 
-21      nc.createDimension('xi_psi', np.size(grd.hgrid.mask_psi,1)) 
-22      nc.createDimension('eta_rho', np.size(grd.hgrid.mask_rho,0)) 
-23      nc.createDimension('eta_u', np.size(grd.hgrid.mask_u,0)) 
-24      nc.createDimension('eta_v', np.size(grd.hgrid.mask_v,0)) 
-25      nc.createDimension('eta_psi', np.size(grd.hgrid.mask_psi,0)) 
-26      nc.createDimension('s_rho', grd.vgrid.N) 
-27      nc.createDimension('s_w', grd.vgrid.Np) 
-28      nc.createDimension('ocean_time', None) 
-29   
-30      # write time and grid information 
-31      nc.createVariable('theta_s', 'f8', ()) 
-32      nc.variables['theta_s'].long_name = 'S-coordinate surface control parameter' 
-33      nc.variables['theta_s'][:] = grd.vgrid.theta_s 
-34   
-35      nc.createVariable('theta_b', 'f8', ()) 
-36      nc.variables['theta_b'].long_name = 'S-coordinate bottom control parameter' 
-37      nc.variables['theta_b'][:] = grd.vgrid.theta_b 
-38   
-39      nc.createVariable('Tcline', 'f8', ()) 
-40      nc.variables['Tcline'].long_name = 'S-cordinate surface/bottom layer width' 
-41      nc.variables['Tcline'].units = 'meter' 
-42      nc.variables['Tcline'][:] = grd.vgrid.Tcline 
-43   
-44      nc.createVariable('hc', 'f8', ()) 
-45      nc.variables['hc'].long_name = 'S-coordinate parameter, critical depth' 
-46      nc.variables['hc'].units = 'meter' 
-47      nc.variables['hc'][:] = grd.vgrid.hc 
-48   
-49      nc.createVariable('s_rho', 'f8', ('s_rho')) 
-50      nc.variables['s_rho'].long_name = 'S-coordinate at RHO-points' 
-51      nc.variables['s_rho'].valid_min = '-1' 
-52      nc.variables['s_rho'].valid_max = '0' 
-53      nc.variables['s_rho'].field = 's_rho,scalar' 
-54      nc.variables['s_rho'][:] = grd.vgrid.s_rho 
-55   
-56      nc.createVariable('s_w', 'f8', ('s_w')) 
-57      nc.variables['s_w'].long_name = 'S-coordinate at W-points' 
-58      nc.variables['s_w'].valid_min = '-1' 
-59      nc.variables['s_w'].valid_max = '0' 
-60      nc.variables['s_w'].field = 's_w,scalar' 
-61      nc.variables['s_w'][:] = grd.vgrid.s_w 
-62   
-63      nc.createVariable('Cs_r', 'f8', ('s_rho')) 
-64      nc.variables['Cs_r'].long_name = 'S-coordinate stretching curves at RHO-points' 
-65      nc.variables['Cs_r'].valid_min = '-1' 
-66      nc.variables['Cs_r'].valid_max = '0' 
-67      nc.variables['Cs_r'].field = 'Cs_r,scalar' 
-68      nc.variables['Cs_r'][:] = grd.vgrid.Cs_r 
-69   
-70      nc.createVariable('Cs_w', 'f8', ('s_w')) 
-71      nc.variables['Cs_w'].long_name = 'S-coordinate stretching curves at W-points' 
-72      nc.variables['Cs_w'].valid_min = '-1' 
-73      nc.variables['Cs_w'].valid_max = '0' 
-74      nc.variables['Cs_w'].field = 'Cs_w,scalar' 
-75      nc.variables['Cs_w'][:] = grd.vgrid.Cs_w 
-76   
-77      nc.createVariable('h', 'f8', ('eta_rho', 'xi_rho')) 
-78      nc.variables['h'].long_name = 'bathymetry at RHO-points' 
-79      nc.variables['h'].units ='meter' 
-80      nc.variables['h'].coordinates = 'lon_rho lat_rho' 
-81      nc.variables['h'].field = 'bath, scalar' 
-82      nc.variables['h'][:] = grd.vgrid.h 
-83   
-84   
-85      nc.createVariable('ocean_time', 'f8', ('ocean_time')) 
-86      nc.variables['ocean_time'].long_name = ocean_time.long_name 
-87      nc.variables['ocean_time'].units = ocean_time.units 
-88      try: 
-89          nc.variables['ocean_time'].field = ocean_time.field 
-90      except: 
-91          nc.variables['ocean_time'].field = ' ' 
-92   
-93      nc.close() 
-
94   
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Module nc_create_roms_file'

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Source Code for Module pyroms_toolbox.nc_create_roms_file'

-
-  1  import numpy as np 
-  2  from datetime import datetime 
-  3  try: 
-  4    import netCDF4 as netCDF 
-  5  except: 
-  6    import netCDF3 as netCDF 
-  7   
-  8   
-
  9 -def nc_create_roms_file(filename, grd, ocean_time): 
-
 10   
- 11      # create file 
- 12      nc = netCDF.Dataset(filename, 'w', format='NETCDF3_CLASSIC') 
- 13      nc.Description = 'ROMS file' 
- 14      nc.Author = 'pyroms_toolbox.nc_create_roms_file' 
- 15      nc.Created = datetime.now().strftime("%Y-%m-%d %H:%M:%S") 
- 16      nc.title = 'ROMS file' 
- 17   
- 18      nc.createDimension('xi_rho', np.size(grd.hgrid.mask_rho,1)) 
- 19      nc.createDimension('xi_u', np.size(grd.hgrid.mask_u,1)) 
- 20      nc.createDimension('xi_v', np.size(grd.hgrid.mask_v,1)) 
- 21      nc.createDimension('xi_psi', np.size(grd.hgrid.mask_psi,1)) 
- 22      nc.createDimension('eta_rho', np.size(grd.hgrid.mask_rho,0)) 
- 23      nc.createDimension('eta_u', np.size(grd.hgrid.mask_u,0)) 
- 24      nc.createDimension('eta_v', np.size(grd.hgrid.mask_v,0)) 
- 25      nc.createDimension('eta_psi', np.size(grd.hgrid.mask_psi,0)) 
- 26      nc.createDimension('s_rho', grd.vgrid.N) 
- 27      nc.createDimension('s_w', grd.vgrid.Np) 
- 28      nc.createDimension('ocean_time', None) 
- 29   
- 30      # write time and grid information 
- 31      nc.createVariable('theta_s', 'f8', ()) 
- 32      nc.variables['theta_s'].long_name = 'S-coordinate surface control parameter' 
- 33      nc.variables['theta_s'][:] = grd.vgrid.theta_s 
- 34   
- 35      nc.createVariable('theta_b', 'f8', ()) 
- 36      nc.variables['theta_b'].long_name = 'S-coordinate bottom control parameter' 
- 37      nc.variables['theta_b'][:] = grd.vgrid.theta_b 
- 38   
- 39      nc.createVariable('Tcline', 'f8', ()) 
- 40      nc.variables['Tcline'].long_name = 'S-cordinate surface/bottom layer width' 
- 41      nc.variables['Tcline'].units = 'meter' 
- 42      nc.variables['Tcline'][:] = grd.vgrid.Tcline 
- 43   
- 44      nc.createVariable('hc', 'f8', ()) 
- 45      nc.variables['hc'].long_name = 'S-coordinate parameter, critical depth' 
- 46      nc.variables['hc'].units = 'meter' 
- 47      nc.variables['hc'][:] = grd.vgrid.hc 
- 48   
- 49      nc.createVariable('s_rho', 'f8', ('s_rho')) 
- 50      nc.variables['s_rho'].long_name = 'S-coordinate at RHO-points' 
- 51      nc.variables['s_rho'].valid_min = '-1' 
- 52      nc.variables['s_rho'].valid_max = '0' 
- 53      nc.variables['s_rho'].field = 's_rho,scalar' 
- 54      nc.variables['s_rho'][:] = grd.vgrid.s_rho 
- 55   
- 56      nc.createVariable('s_w', 'f8', ('s_w')) 
- 57      nc.variables['s_w'].long_name = 'S-coordinate at W-points' 
- 58      nc.variables['s_w'].valid_min = '-1' 
- 59      nc.variables['s_w'].valid_max = '0' 
- 60      nc.variables['s_w'].field = 's_w,scalar' 
- 61      nc.variables['s_w'][:] = grd.vgrid.s_w 
- 62   
- 63      nc.createVariable('Cs_r', 'f8', ('s_rho')) 
- 64      nc.variables['Cs_r'].long_name = 'S-coordinate stretching curves at RHO-points' 
- 65      nc.variables['Cs_r'].valid_min = '-1' 
- 66      nc.variables['Cs_r'].valid_max = '0' 
- 67      nc.variables['Cs_r'].field = 'Cs_r,scalar' 
- 68      nc.variables['Cs_r'][:] = grd.vgrid.Cs_r 
- 69   
- 70      nc.createVariable('Cs_w', 'f8', ('s_w')) 
- 71      nc.variables['Cs_w'].long_name = 'S-coordinate stretching curves at W-points' 
- 72      nc.variables['Cs_w'].valid_min = '-1' 
- 73      nc.variables['Cs_w'].valid_max = '0' 
- 74      nc.variables['Cs_w'].field = 'Cs_w,scalar' 
- 75      nc.variables['Cs_w'][:] = grd.vgrid.Cs_w 
- 76   
- 77      nc.createVariable('h', 'f8', ('eta_rho', 'xi_rho')) 
- 78      nc.variables['h'].long_name = 'bathymetry at RHO-points' 
- 79      nc.variables['h'].units ='meter' 
- 80      nc.variables['h'].coordinates = 'lon_rho lat_rho' 
- 81      nc.variables['h'].field = 'bath, scalar' 
- 82      nc.variables['h'][:] = grd.vgrid.h 
- 83   
- 84      nc.createVariable('pm', 'f8', ('eta_rho', 'xi_rho')) 
- 85      nc.variables['pm'].long_name = 'curvilinear coordinate metric in XI' 
- 86      nc.variables['pm'].units ='meter-1' 
- 87      nc.variables['pm'].coordinates = 'lon_rho lat_rho' 
- 88      nc.variables['pm'].field = 'pm, scalar' 
- 89      nc.variables['pm'][:] = 1. / grd.hgrid.dx 
- 90   
- 91      nc.createVariable('pn', 'f8', ('eta_rho', 'xi_rho')) 
- 92      nc.variables['pn'].long_name = 'curvilinear coordinate metric in ETA' 
- 93      nc.variables['pn'].units ='meter-1' 
- 94      nc.variables['pn'].coordinates = 'lon_rho lat_rho' 
- 95      nc.variables['pn'].field = 'pn, scalar' 
- 96      nc.variables['pn'][:] = 1. / grd.hgrid.dy 
- 97   
- 98      nc.createVariable('lon_rho', 'f8', ('eta_rho', 'xi_rho')) 
- 99      nc.variables['lon_rho'].long_name = 'longitude of RHO-points' 
-100      nc.variables['lon_rho'].units = 'degree_east' 
-101      nc.variables['lon_rho'].field = 'lon_rho, scalar' 
-102      nc.variables['lon_rho'][:] = grd.hgrid.lon_rho 
-103   
-104      nc.createVariable('lat_rho', 'f8', ('eta_rho', 'xi_rho')) 
-105      nc.variables['lat_rho'].long_name = 'latitude of RHO-points' 
-106      nc.variables['lat_rho'].units = 'degree_north' 
-107      nc.variables['lat_rho'].field = 'lat_rho, scalar' 
-108      nc.variables['lat_rho'][:] = grd.hgrid.lat_rho 
-109   
-110      nc.createVariable('lon_u', 'f8', ('eta_u', 'xi_u')) 
-111      nc.variables['lon_u'].long_name = 'longitude of U-points' 
-112      nc.variables['lon_u'].units = 'degree_east' 
-113      nc.variables['lon_u'].field = 'lon_u, scalar' 
-114      nc.variables['lon_u'][:] = grd.hgrid.lon_u 
-115   
-116      nc.createVariable('lat_u', 'f8', ('eta_u', 'xi_u')) 
-117      nc.variables['lat_u'].long_name = 'latitude of U-points' 
-118      nc.variables['lat_u'].units = 'degree_north' 
-119      nc.variables['lat_u'].field = 'lat_u, scalar' 
-120      nc.variables['lat_u'][:] = grd.hgrid.lat_u 
-121   
-122      nc.createVariable('lon_v', 'f8', ('eta_v', 'xi_v')) 
-123      nc.variables['lon_v'].long_name = 'longitude of V-points' 
-124      nc.variables['lon_v'].units = 'degree_east' 
-125      nc.variables['lon_v'].field = 'lon_v, scalar' 
-126      nc.variables['lon_v'][:] = grd.hgrid.lon_v 
-127   
-128      nc.createVariable('lat_v', 'f8', ('eta_v', 'xi_v')) 
-129      nc.variables['lat_v'].long_name = 'latitude of V-points' 
-130      nc.variables['lat_v'].units = 'degree_north' 
-131      nc.variables['lat_v'].field = 'lat_v, scalar' 
-132      nc.variables['lat_v'][:] = grd.hgrid.lat_v 
-133   
-134      nc.createVariable('lon_psi', 'f8', ('eta_psi', 'xi_psi')) 
-135      nc.variables['lon_psi'].long_name = 'longitude of PSI-points' 
-136      nc.variables['lon_psi'].units = 'degree_east' 
-137      nc.variables['lon_psi'].field = 'lon_psi, scalar' 
-138      nc.variables['lon_psi'][:] = grd.hgrid.lon_psi 
-139   
-140      nc.createVariable('lat_psi', 'f8', ('eta_psi', 'xi_psi')) 
-141      nc.variables['lat_psi'].long_name = 'latitude of PSI-points' 
-142      nc.variables['lat_psi'].units = 'degree_north' 
-143      nc.variables['lat_psi'].field = 'lat_psi, scalar' 
-144      nc.variables['lat_psi'][:] = grd.hgrid.lat_psi 
-145   
-146      nc.createVariable('angle', 'f8', ('eta_rho', 'xi_rho')) 
-147      nc.variables['angle'].long_name = 'angle between XI-axis and EAST' 
-148      nc.variables['angle'].units = 'radians' 
-149      nc.variables['angle'].coordinates = 'lon_rho lat_rho' 
-150      nc.variables['angle'].field = 'angle, scalar' 
-151      nc.variables['angle'][:] = grd.hgrid.angle_rho 
-152   
-153      nc.createVariable('mask_rho', 'f8', ('eta_rho', 'xi_rho')) 
-154      nc.variables['mask_rho'].long_name = 'mask on RHO-points' 
-155      nc.variables['mask_rho'].option_0 = 'land' 
-156      nc.variables['mask_rho'].option_1 = 'water' 
-157      nc.variables['mask_rho'].coordinates = 'lon_rho lat_rho' 
-158      nc.variables['mask_rho'][:] = grd.hgrid.mask_rho 
-159   
-160      nc.createVariable('mask_u', 'f8', ('eta_u', 'xi_u')) 
-161      nc.variables['mask_u'].long_name = 'mask on U-points' 
-162      nc.variables['mask_u'].option_0 = 'land' 
-163      nc.variables['mask_u'].option_1 = 'water' 
-164      nc.variables['mask_u'].coordinates = 'lon_u lat_u' 
-165      nc.variables['mask_u'][:] = grd.hgrid.mask_u 
-166   
-167      nc.createVariable('mask_v', 'f8', ('eta_v', 'xi_v')) 
-168      nc.variables['mask_v'].long_name = 'mask on V-points' 
-169      nc.variables['mask_v'].option_0 = 'land' 
-170      nc.variables['mask_v'].option_1 = 'water' 
-171      nc.variables['mask_v'].coordinates = 'lon_v lat_v' 
-172      nc.variables['mask_v'][:] = grd.hgrid.mask_v 
-173   
-174      nc.createVariable('mask_psi', 'f8', ('eta_psi', 'xi_psi')) 
-175      nc.variables['mask_psi'].long_name = 'mask on PSI-points' 
-176      nc.variables['mask_psi'].option_0 = 'land' 
-177      nc.variables['mask_psi'].option_1 = 'water' 
-178      nc.variables['mask_psi'].coordinates = 'lon_psi lat_psi' 
-179      nc.variables['mask_psi'][:] = grd.hgrid.mask_psi 
-180   
-181      nc.createVariable('ocean_time', 'f8', ('ocean_time')) 
-182      nc.variables['ocean_time'].long_name = ocean_time.long_name 
-183      nc.variables['ocean_time'].units = ocean_time.units 
-184      try: 
-185          nc.variables['ocean_time'].field = ocean_time.field 
-186      except: 
-187          nc.variables['ocean_time'].field = ' ' 
-188   
-189      nc.close() 
-
190   
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Module plot_coast_line'

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plot_coast_line(grd, - proj=None)
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plot_coast_line(grd, - proj=None) -

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plot_coast_line(grd, {proj})

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plot the coastline from the object grid. proj=map (optional) is a - Basemap object for projection.

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Source Code for Module pyroms_toolbox.plot_coast_line'

-
- 1  import numpy as np 
- 2  import matplotlib.pyplot as plt 
- 3  import matplotlib.collections as collections 
- 4  from pyroms_toolbox import get_coast_line 
- 5   
- 6   
-
 7 -def plot_coast_line(grd, proj=None): 
-
 8      ''' 
- 9      plot_coast_line(grd, {proj}) 
-10   
-11      plot the coastline from the object grid.  
-12      proj=map (optional) is a Basemap object for 
-13      projection. 
-14      '''  
-15   
-16   
-17      a = plt.gca() 
-18   
-19      coast = get_coast_line(grd) 
-20      c = np.array(coast) 
-21   
-22      if proj is None: 
-23          col = collections.LineCollection(c) 
-24      else: 
-25          cp = np.zeros(c.shape) 
-26          for i in range(c.shape[0]): 
-27              cp[i,:,0], cp[i,:,1] = proj(c[i,:,0], c[i,:,1]) 
-28   
-29          col = collections.LineCollection(cp) 
-30   
-31    
-32      a.add_collection(col, autolim=True) 
-33      col.set_color('k') 
-
34      #a.autoscale_view() 
-35   
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Module plot_mask'

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- - - - - - - - - -
- - - - - -
Functions[hide private]
-
-   - - - - - - -
plot_mask(gridid, - Cpos='rho', - proj=None, - **kwargs) - source code - -
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- Generated by Epydoc 3.0.1 on Mon Sep 27 11:35:24 2010 - - http://epydoc.sourceforge.net -
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Source Code for Module pyroms_toolbox.plot_mask'

-
- 1  import numpy as np 
- 2  import matplotlib.pyplot as plt 
- 3  from mpl_toolkits.basemap import Basemap 
- 4  import pyroms 
- 5  import pyroms_toolbox 
- 6   
- 7   
-
 8 -def plot_mask(gridid, Cpos='rho', proj=None, **kwargs): 
-
 9   
-10   
-11      # get grid 
-12      if type(gridid).__name__ == 'ROMS_Grid': 
-13          grd = gridid 
-14      else: 
-15          grd = pyroms.grid.get_ROMS_grid(gridid) 
-16   
-17      Cpos = str(Cpos) 
-18      print Cpos 
-19   
-20      # get grid information 
-21      if Cpos == 'rho': 
-22          lon = grd.hgrid.lon_vert 
-23          lat = grd.hgrid.lat_vert 
-24          mask = grd.hgrid.mask_rho 
-25   
-26      elif Cpos == 'u': 
-27          lon = 0.5 * (grd.hgrid.lon_vert[:,:-1] + grd.hgrid.lon_vert[:,1:]) 
-28          lat = 0.5 * (grd.hgrid.lat_vert[:,:-1] + grd.hgrid.lat_vert[:,1:]) 
-29          mask = grd.hgrid.mask_u 
-30   
-31      elif Cpos == 'v': 
-32          lon = 0.5 * (grd.hgrid.lon_vert[:-1,:] + grd.hgrid.lon_vert[1:,:]) 
-33          lat = 0.5 * (grd.hgrid.lat_vert[:-1,:] + grd.hgrid.lat_vert[1:,:]) 
-34          mask = grd.hgrid.mask_v 
-35   
-36      else: 
-37          raise Warning, 'Cpos must be rho, u or v' 
-38   
-39      # defined color map 
-40      land_color = kwargs.pop('land_color', (0.6, 1.0, 0.6)) 
-41      sea_color = kwargs.pop('sea_color', (0.6, 0.6, 1.0)) 
-42   
-43      cm = plt.matplotlib.colors.ListedColormap([land_color, sea_color], 
-44                                               name='land/sea') 
-45   
-46   
-47   
-48      if proj is None: 
-49          plt.pcolor(lon, lat, mask, cmap=cm, vmin=0, vmax=1, \ 
-50                     edgecolor='k', **kwargs) 
-51          pyroms_toolbox.plot_coast_line(grd) 
-52      else: 
-53          x, y = proj(lon, lat) 
-54          Basemap.pcolor(proj, x, y, mask, cmap=cm, vmin=0, vmax=1, \ 
-55                         edgecolor='k', **kwargs) 
-56          pyroms_toolbox.plot_coast_line(grd, proj=proj) 
-57   
-58          lon_min = lon.min() 
-59          lon_max = lon.max() 
-60          lat_min = lat.min() 
-61          lat_max = lat.max() 
-62   
-63          proj.drawmeridians(np.arange(lon_min,lon_max,(lon_max-lon_min)/5.001), \ 
-64                            labels=[0,0,0,1], fmt='%.1f') 
-65          proj.drawparallels(np.arange(lat_min,lat_max,(lat_max-lat_min)/5.001), \ 
-66                            labels=[1,0,0,0], fmt='%.1f') 
-
67   
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- Generated by Epydoc 3.0.1 on Mon Sep 27 11:35:25 2010 - - http://epydoc.sourceforge.net -
- - - - diff --git a/pyroms_toolbox/docs/pyroms_toolbox.quiver'-module.html b/pyroms_toolbox/docs/pyroms_toolbox.quiver'-module.html deleted file mode 100644 index 1183589..0000000 --- a/pyroms_toolbox/docs/pyroms_toolbox.quiver'-module.html +++ /dev/null @@ -1,1547 +0,0 @@ - - - - - pyroms_toolbox.quiver' - - - - - - - - - - - - - - - - - - - - - - -
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- - Package pyroms_toolbox :: - Module quiver' - - - - - - -
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-
- -

Module quiver'

source code

-
-

Version: - 1.3.0 -

-
- - - - - - - - -
- - - - - -
Functions[hide private]
-
-   - - - - - - -
quiver(uvar, - vvar, - tindex, - depth, - gridid)
- optional switch:		 - source code - -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - -
Variables[hide private]
-
-   - - ALLOW_THREADS = 1 -
-   - - BUFSIZE = 10000 -
-   - - CLIP = 0 -
-   - - ERR_CALL = 3 -
-   - - ERR_DEFAULT = 0 -
-   - - ERR_DEFAULT2 = 2084 -
-   - - ERR_IGNORE = 0 -
-   - - ERR_LOG = 5 -
-   - - ERR_PRINT = 4 -
-   - - ERR_RAISE = 2 -
-   - - ERR_WARN = 1 -
-   - - FLOATING_POINT_SUPPORT = 1 -
-   - - FPE_DIVIDEBYZERO = 1 -
-   - - FPE_INVALID = 8 -
-   - - FPE_OVERFLOW = 2 -
-   - - FPE_UNDERFLOW = 4 -
-   - - False_ = False -
-   - - Inf = inf -
-   - - Infinity = inf -
-   - - MAXDIMS = 32 -
-   - - NAN = nan -
-   - - NINF = -inf -
-   - - NZERO = -0.0 -
-   - - NaN = nan -
-   - - PINF = inf -
-   - - PZERO = 0.0 -
-   - - RAISE = 2 -
-   - - SHIFT_DIVIDEBYZERO = 0 -
-   - - SHIFT_INVALID = 9 -
-   - - SHIFT_OVERFLOW = 3 -
-   - - SHIFT_UNDERFLOW = 6 -
-   - - ScalarType = (<type 'int'>, <type 'float'>, <type 'complex'>, ... -
-   - - True_ = True -
-   - - UFUNC_BUFSIZE_DEFAULT = 10000 -
-   - - UFUNC_PYVALS_NAME = 'UFUNC_PYVALS' -
-   - - WRAP = 1 -
-   - - absolute = <ufunc 'absolute'> -
-   - - add = <ufunc 'add'> -
-   - - arccos = <ufunc 'arccos'> -
-   - - arccosh = <ufunc 'arccosh'> -
-   - - arcsin = <ufunc 'arcsin'> -
-   - - arcsinh = <ufunc 'arcsinh'> -
-   - - arctan = <ufunc 'arctan'> -
-   - - arctan2 = <ufunc 'arctan2'> -
-   - - arctanh = <ufunc 'arctanh'> -
-   - - bitwise_and = <ufunc 'bitwise_and'> -
-   - - bitwise_not = <ufunc 'invert'> -
-   - - bitwise_or = <ufunc 'bitwise_or'> -
-   - - bitwise_xor = <ufunc 'bitwise_xor'> -
-   - - c_ = <numpy.lib.index_tricks.CClass object at 0x7fcf4da53050> -
-   - - cast = {<type 'numpy.int64'>: <function <lambda> at 0x7fcf4f4e... -
-   - - ceil = <ufunc 'ceil'> -
-   - - conj = <ufunc 'conjugate'> -
-   - - conjugate = <ufunc 'conjugate'> -
-   - - cos = <ufunc 'cos'> -
-   - - cosh = <ufunc 'cosh'> -
-   - - deg2rad = <ufunc 'deg2rad'> -
-   - - degrees = <ufunc 'degrees'> -
-   - - divide = <ufunc 'divide'> -
-   - - e = 2.71828182846 -
-   - - equal = <ufunc 'equal'> -
-   - - exp = <ufunc 'exp'> -
-   - - exp2 = <ufunc 'exp2'> -
-   - - expm1 = <ufunc 'expm1'> -
-   - - fabs = <ufunc 'fabs'> -
-   - - floor = <ufunc 'floor'> -
-   - - floor_divide = <ufunc 'floor_divide'> -
-   - - fmax = <ufunc 'fmax'> -
-   - - fmin = <ufunc 'fmin'> -
-   - - fmod = <ufunc 'fmod'> -
-   - - frexp = <ufunc 'frexp'> -
-   - - greater = <ufunc 'greater'> -
-   - - greater_equal = <ufunc 'greater_equal'> -
-   - - hypot = <ufunc 'hypot'> -
-   - - index_exp = <numpy.lib.index_tricks.IndexExpression object at ... -
-   - - inf = inf -
-   - - infty = inf -
-   - - invert = <ufunc 'invert'> -
-   - - isfinite = <ufunc 'isfinite'> -
-   - - isinf = <ufunc 'isinf'> -
-   - - isnan = <ufunc 'isnan'> -
-   - - ldexp = <ufunc 'ldexp'> -
-   - - left_shift = <ufunc 'left_shift'> -
-   - - less = <ufunc 'less'> -
-   - - less_equal = <ufunc 'less_equal'> -
-   - - little_endian = True -
-   - - log = <ufunc 'log'> -
-   - - log10 = <ufunc 'log10'> -
-   - - log1p = <ufunc 'log1p'> -
-   - - logaddexp = <ufunc 'logaddexp'> -
-   - - logaddexp2 = <ufunc 'logaddexp2'> -
-   - - logical_and = <ufunc 'logical_and'> -
-   - - logical_not = <ufunc 'logical_not'> -
-   - - logical_or = <ufunc 'logical_or'> -
-   - - logical_xor = <ufunc 'logical_xor'> -
-   - - maximum = <ufunc 'maximum'> -
-   - - mgrid = <numpy.lib.index_tricks.nd_grid object at 0x7fcf4decbe90> -
-   - - minimum = <ufunc 'minimum'> -
-   - - mod = <ufunc 'remainder'> -
-   - - modf = <ufunc 'modf'> -
-   - - multiply = <ufunc 'multiply'> -
-   - - nan = nan -
-   - - nbytes = {<type 'numpy.int64'>: 8, <type 'numpy.int16'>: 2, <t... -
-   - - negative = <ufunc 'negative'> -
-   - - newaxis = None -
-   - - not_equal = <ufunc 'not_equal'> -
-   - - ogrid = <numpy.lib.index_tricks.nd_grid object at 0x7fcf4decbed0> -
-   - - ones_like = <ufunc 'ones_like'> -
-   - - pi = 3.14159265359 -
-   - - power = <ufunc 'power'> -
-   - - r_ = <numpy.lib.index_tricks.RClass object at 0x7fcf4decbf90> -
-   - - rad2deg = <ufunc 'rad2deg'> -
-   - - radians = <ufunc 'radians'> -
-   - - reciprocal = <ufunc 'reciprocal'> -
-   - - remainder = <ufunc 'remainder'> -
-   - - right_shift = <ufunc 'right_shift'> -
-   - - rint = <ufunc 'rint'> -
-   - - s_ = <numpy.lib.index_tricks.IndexExpression object at 0x7fcf4... -
-   - - sctypeDict = {0: <type 'numpy.bool_'>, 1: <type 'numpy.int8'>,... -
-   - - sctypeNA = {'?': 'Bool', 'B': 'UInt8', 'Bool': <type 'numpy.bo... -
-   - - sctypes = {'complex': [<type 'numpy.complex64'>, <type 'numpy.... -
-   - - sign = <ufunc 'sign'> -
-   - - signbit = <ufunc 'signbit'> -
-   - - sin = <ufunc 'sin'> -
-   - - sinh = <ufunc 'sinh'> -
-   - - sqrt = <ufunc 'sqrt'> -
-   - - square = <ufunc 'square'> -
-   - - subtract = <ufunc 'subtract'> -
-   - - tan = <ufunc 'tan'> -
-   - - tanh = <ufunc 'tanh'> -
-   - - true_divide = <ufunc 'true_divide'> -
-   - - trunc = <ufunc 'trunc'> -
-   - - typeDict = {0: <type 'numpy.bool_'>, 1: <type 'numpy.int8'>, 2... -
-   - - typeNA = {'?': 'Bool', 'B': 'UInt8', 'Bool': <type 'numpy.bool... -
-   - - typecodes = {'All': '?bhilqpBHILQPfdgFDGSUVO', 'AllFloat': 'fd... -
- - - - - - -
- - - - - -
Function Details[hide private]
-
- -
- -
- - -
-

quiver(uvar, - vvar, - tindex, - depth, - gridid) -

- 		source code  -
- -

optional switch:

-
    -
  • - filename if defined, load the variable from file -
    • -
  • - proj Basemap object returned by sview, zview, ... -
    • -
  • - d arrow density parameter -
    • -
  • - uscale data units per arrow length unit parameter -
    • -
  • - xkey x location of the key -
    • -
  • - ykey y location of the key -
    • -
  • - ukey length of the key -
    • -
  • - outfile if defined, write figure to file -
    • -
-

overlay a 2-D field of arrows for velocity (uvar, vvar) above an - existing horizontal 2D plot. If filename is provided, uvar and vvar must - be strings and the variables will be load from the file. grid can be a - grid object or a gridid. In the later case, the grid object correponding - to the provided gridid will be loaded. For projection, use proj=map, map - being the Basemap object returned by sview, zview, ...

-

Note: if quiver is called before any other part of the plot has been - created, you must create an axis which covers the region to be plotted. - to do this, you can call - axis([Longitude_min,Longitude_max,Latitude_min,Latitude_max] where - Longitude_min, etc, are replaced with the appropriate longitudes and - latitudes.

-
-
-
-
-
- - - - - - -
- - - - - -
Variables Details[hide private]
-
- -
- -
-

ScalarType

- -
-
-
-
Value:
- 
-(<type 'int'>,
- <type 'float'>,
- <type 'complex'>,
- <type 'long'>,
- <type 'bool'>,
- <type 'str'>,
- <type 'unicode'>,
- <type 'buffer'>,
-...
-
-
-
-
-
- -
- -
-

cast

- -
-
-
-
Value:
- 
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- <lambda> at 0x7fcf4f4e99b0>, <type 'numpy.uint32'>: <function <lambda\
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-...
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-

index_exp

- -
-
-
-
Value:
- 
-<numpy.lib.index_tricks.IndexExpression object at 0x7fcf4da53150>
-
-
-
-
-
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-

nbytes

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s_

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-{0: <type 'numpy.bool_'>,
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- 'Integer': 'bhilqp',
- 'UnsignedInteger': 'BHILQP'}
-
-
-
-
-
-
- - - - - - - - - - - - - - - - - -
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- - - - - -
- Generated by Epydoc 3.0.1 on Mon Sep 27 11:35:24 2010 - - http://epydoc.sourceforge.net -
- - - - diff --git a/pyroms_toolbox/docs/pyroms_toolbox.quiver'-pysrc.html b/pyroms_toolbox/docs/pyroms_toolbox.quiver'-pysrc.html deleted file mode 100644 index b5d3e4a..0000000 --- a/pyroms_toolbox/docs/pyroms_toolbox.quiver'-pysrc.html +++ /dev/null @@ -1,231 +0,0 @@ - - - - - pyroms_toolbox.quiver' - - - - - - - - - - - - - - - - - - - - - - -
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- - Package pyroms_toolbox :: - Module quiver' - - - - - - -
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-
-

Source Code for Module pyroms_toolbox.quiver'

-
-  1  from numpy import * 
-  2  import matplotlib.pyplot as plt 
-  3  from mpl_toolkits.basemap import Basemap 
-  4  import pyroms 
-  5   
-  6   
-
  7 -def quiver(uvar, vvar, tindex, depth, gridid, \ 
-  8             filename=None, proj=None, d=2, uscale=None, \ 
-  9             xkey=0.9, ykey=0.1, ukey=1, outfile=None): 
-
 10      """ 
- 11      quiver(uvar, vvar, tindex, depth, gridid) 
- 12   
- 13      optional switch: 
- 14        - filename         if defined, load the variable from file 
- 15        - proj             Basemap object returned by sview, zview, ... 
- 16        - d                arrow density parameter 
- 17        - uscale           data units per arrow length unit parameter 
- 18        - xkey             x location of the key 
- 19        - ykey             y location of the key 
- 20        - ukey             length of the key 
- 21        - outfile          if defined, write figure to file 
- 22   
- 23   
- 24      overlay a 2-D field of arrows for velocity (uvar, vvar) above an  
- 25      existing horizontal 2D plot. If filename is provided, uvar and vvar  
- 26      must be strings and the variables will be load from the file.  
- 27      grid can be a grid object or a gridid. In the later case, the grid  
- 28      object correponding to the provided gridid will be loaded.  
- 29      For projection, use proj=map, map being the Basemap object returned  
- 30      by sview, zview, ... 
- 31   
- 32      Note: if quiver is called before any other part of the plot has been 
- 33      created, you must create an axis which covers the region to be plotted. 
- 34      to do this, you can call axis([Longitude_min,Longitude_max,Latitude_min,Latitude_max] 
- 35      where Longitude_min, etc, are replaced with the appropriate longitudes and latitudes. 
- 36      """ 
- 37   
- 38   
- 39      # get grid 
- 40      if type(gridid).__name__ == 'ROMS_Grid': 
- 41          grd = gridid 
- 42      else: 
- 43          grd = pyroms.grid.get_ROMS_grid(gridid) 
- 44      lon = grd.hgrid.lon_rho 
- 45      lat = grd.hgrid.lat_rho 
- 46      mask = grd.hgrid.mask_rho     
- 47   
- 48      # get u and v 
- 49      if filename == None: 
- 50          u = uvar[tindex,:,:,:] 
- 51          v = vvar[tindex,:,:,:] 
- 52      else: 
- 53          data = pyroms.io.Dataset(filename) 
- 54          u = data.variables[uvar][tindex,:,:,:] 
- 55          v = data.variables[vvar][tindex,:,:,:] 
- 56   
- 57      # get u and v slice at requested depth 
- 58      zsliceu, lonu, latu = pyroms.tools.zslice(u, depth, grd, Cpos='u') 
- 59      zslicev, lonv, latv = pyroms.tools.zslice(v, depth, grd, Cpos='v') 
- 60    
- 61      # average field at rho point position 
- 62      zsliceu = 0.5 * (zsliceu[:,:-1] + zsliceu[:,1:])     
- 63      zslicev = 0.5 * (zslicev[:-1,:] + zslicev[1:,:])        
- 64   
- 65      # correct dimension with zeros at edges 
- 66      zsliceu = concatenate((zeros((zsliceu.shape[0],1)), zsliceu, \ 
- 67                             zeros((zsliceu.shape[0],1))),1) 
- 68      zsliceu = ma.masked_where(mask == 0, zsliceu) 
- 69      zsliceu = ma.masked_where(zsliceu >= 1000, zsliceu) 
- 70      zslicev = concatenate((zeros((1,zslicev.shape[1])), zslicev, \ 
- 71                             zeros((1,zslicev.shape[1]))),0) 
- 72      zslicev = ma.masked_where(mask == 0, zslicev) 
- 73      zslicev = ma.masked_where(zslicev >= 1000, zslicev) 
- 74   
- 75      # rotate velocity vector according to grid angle 
- 76      rotzsliceu = zsliceu * cos(grd.hgrid.angle_rho) - \ 
- 77                   zslicev * sin(grd.hgrid.angle_rho) 
- 78      rotzslicev = zsliceu * sin(grd.hgrid.angle_rho) + \ 
- 79                   zslicev * cos(grd.hgrid.angle_rho) 
- 80   
- 81      # plot 
- 82      if proj is not None: 
- 83          x, y = proj(lon,lat) 
- 84      else: 
- 85          range = plt.axis() 
- 86   
- 87      if uscale is None: 
- 88          if proj is not None:  
- 89              qv = Basemap.quiver(proj, x[::d,::d], y[::d,::d], \ 
- 90                                  rotzsliceu[::d,::d], rotzslicev[::d,::d], \ 
- 91                                  linewidths=0.01) 
- 92          else:  
- 93              qv = plt.quiver(lon[::d,::d], lat[::d,::d], \ 
- 94                              rotzsliceu[::d,::d], rotzslicev[::d,::d], \ 
- 95                              linewidths=0.01) 
- 96      else: 
- 97          if proj is not None: 
- 98              qv = Basemap.quiver(proj, x[::d,::d], y[::d,::d], \ 
- 99                                        rotzsliceu[::d,::d], rotzslicev[::d,::d], \ 
-100                                       scale=uscale, linewidths=0.01) 
-101          else: 
-102              qv = plt.quiver(lon[::d,::d], lat[::d,::d], \ 
-103                              rotzsliceu[::d,::d], rotzslicev[::d,::d], \ 
-104                              scale=uscale, linewidths=0.01) 
-105   
-106      if proj is None: 
-107          plt.axis(range) 
-108   
-109      plt.quiverkey(qv, xkey, ykey, ukey, str(ukey) + ' ms$^{-1}$') 
-110   
-111      if outfile is not None: 
-112          if outfile.find('.png') != -1 or outfile.find('.svg') != -1 or \ 
-113             outfile.find('.eps') != -1: 
-114              print 'Write figure to file', outfile 
-115              plt.savefig(outfile, dpi=100, facecolor='w', edgecolor='w', \ 
-116                          orientation='portrait') 
-117          else: 
-118              print 'Unrecognized file extension. Please use .png, .svg or .eps file extension.' 
-119   
-120      return 
-
121   
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Module remapping'

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Functions[hide private]
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remapping(varname, - srcfile, - wts_files, - srcgrd, - dstgrd, - rotate_uv=False, - trange=None, - irange=None, - jrange=None, - dstdir='./', - zlevel=None, - dmax=0, - cdepth=0, - kk=0)
- A remaping function to go from a ROMS grid to another ROMS grid.		 - source code - -
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Source Code for Module pyroms_toolbox.remapping'

-
-  1  # encoding: utf-8 
-  2   
-  3  import os 
-  4  import numpy as np 
-  5  import glob 
-  6  try: 
-  7    import netCDF4 as netCDF 
-  8  except: 
-  9    import netCDF3 as netCDF 
- 10   
- 11  import pyroms 
- 12  import pyroms_toolbox 
- 13  import _remapping 
- 14   
- 15  import matplotlib.pyplot as plt 
- 16   
- 17  import datetime 
- 18   
-
 19 -def remapping(varname, srcfile, wts_files, srcgrd, dstgrd, \ 
- 20                rotate_uv=False, trange=None, irange=None, jrange=None, \ 
- 21                dstdir='./' ,zlevel=None, dmax=0, cdepth=0, kk=0): 
-
 22      ''' 
- 23      A remaping function to go from a ROMS grid to another ROMS grid. 
- 24      ''' 
- 25   
- 26      # get input and output grid 
- 27      if type(srcgrd).__name__ == 'ROMS_Grid': 
- 28          srcgrd = srcgrd 
- 29      else: 
- 30          srcgrd = pyroms.grid.get_ROMS_grid(srcgrd) 
- 31      if type(dstgrd).__name__ == 'ROMS_Grid': 
- 32          dstgrd = dstgrd 
- 33      else: 
- 34          dstgrd = pyroms.grid.get_ROMS_grid(dstgrd) 
- 35   
- 36      # build intermediaire zgrid 
- 37      if zlevel is None: 
- 38          zlevel = np.array([-4500.,-4000.,-3500.,-3000.,-2500.,-2000.,-1750.,\ 
- 39                     -1500.,-1250.,-1000.,-900.,-800.,-700.,-600.,-500.,\ 
- 40                     -400.,-300.,-250.,-200.,-175.,-150.,-125.,-100.,-90.,\ 
- 41                     -80.,-70.,-60.,-50.,-45.,-40.,-35.,-30.,-25.,-20.,-17.5,\ 
- 42                     -15.,-12.5,-10.,-7.5,-5.,-2.5,0.]) 
- 43      else: 
- 44          zlevel = np.sort(-abs(zlevel)) 
- 45      nzlevel = len(zlevel) 
- 46      src_zcoord = pyroms.vgrid.z_coordinate(srcgrd.vgrid.h, zlevel, nzlevel) 
- 47      dst_zcoord = pyroms.vgrid.z_coordinate(dstgrd.vgrid.h, zlevel, nzlevel) 
- 48      srcgrdz = pyroms.grid.ROMS_Grid(srcgrd.name+'_Z', srcgrd.hgrid, src_zcoord) 
- 49      dstgrdz = pyroms.grid.ROMS_Grid(dstgrd.name+'_Z', dstgrd.hgrid, dst_zcoord) 
- 50   
- 51      # varname argument 
- 52      if type(varname).__name__ == 'list': 
- 53          nvar = len(varname) 
- 54      elif type(varname).__name__ == 'str': 
- 55          varname = [varname] 
- 56          nvar = len(varname) 
- 57      else: 
- 58          raise ValueError, 'varname must be a str or a list of str' 
- 59      # if rotate_uv=True, check that u and v are in varname 
- 60      if rotate_uv is True: 
- 61          if varname.__contains__('u') == 0 or varname.__contains__('v') == 0: 
- 62              raise Warning, 'varname must include u and v in order to rotate \ 
- 63  the velocity field' 
- 64          else: 
- 65              varname.remove('u') 
- 66              varname.remove('v') 
- 67              nvar = nvar-2 
- 68   
- 69      # srcfile argument 
- 70      if type(srcfile).__name__ == 'list': 
- 71          nfile = len(srcfile) 
- 72      elif type(srcfile).__name__ == 'str': 
- 73          srcfile = sorted(glob.glob(srcfile)) 
- 74          nfile = len(srcfile) 
- 75      else: 
- 76          raise ValueError, 'src_srcfile must be a str or a list of str' 
- 77   
- 78      # get wts_file 
- 79      if type(wts_files).__name__ == 'str': 
- 80          wts_files = sorted(glob.glob(wts_files)) 
- 81    
- 82      # loop over the srcfile 
- 83      for nf in range(nfile): 
- 84          print 'Working with file', srcfile[nf], '...' 
- 85   
- 86          # get time  
- 87          ocean_time = pyroms.utility.get_nc_var('ocean_time', srcfile[nf]) 
- 88          ntime = len(ocean_time[:]) 
- 89   
- 90          # trange argument 
- 91          if trange is None: 
- 92              trange = range(ntime) 
- 93          else: 
- 94              trange = range(trange[0], trange[1]+1) 
- 95   
- 96          # create destination file 
- 97          dstfile = dstdir + os.path.basename(srcfile[nf])[:-3] + '_' + dstgrd.name + '.nc' 
- 98          print 'Creating destination file', dstfile 
- 99          if os.path.exists(dstfile) is True: 
-100              os.remove(dstfile)  
-101          pyroms_toolbox.nc_create_roms_file(dstfile, dstgrd, ocean_time) 
-102   
-103          # open destination file 
-104          nc = netCDF.Dataset(dstfile, 'a', format='NETCDF3_CLASSIC') 
-105   
-106   
-107          nctidx = 0 
-108          # loop over time 
-109          for nt in trange: 
-110   
-111              nc.variables['ocean_time'][nctidx] = ocean_time[nt] 
-112   
-113              # loop over variable 
-114              for nv in range(nvar): 
-115                  print ' ' 
-116                  print 'remapping', varname[nv], 'from', srcgrd.name, \ 
-117                        'to', dstgrd.name 
-118                  print 'time =', ocean_time[nt]    
-119   
-120                  # get source data 
-121                  src_var = pyroms.utility.get_nc_var(varname[nv], srcfile[nf]) 
-122   
-123                  # determine variable dimension 
-124                  ndim = len(src_var.dimensions)-1 
-125   
-126                  # get spval 
-127                  try: 
-128                      spval = src_var._FillValue 
-129                  except: 
-130                      raise Warning, 'Did not find a _FillValue attribute.'  
-131   
-132                  # irange 
-133                  if irange is None: 
-134                      iirange = (0,src_var._shape()[-1]) 
-135                  else: 
-136                      iirange = irange 
-137   
-138                  # jrange 
-139                  if jrange is None: 
-140                      jjrange = (0,src_var._shape()[-2]) 
-141                  else: 
-142                      jjrange = jrange 
-143   
-144                  # determine where on the C-grid these variable lies 
-145                  if src_var.dimensions[2].find('_rho') != -1: 
-146                      Cpos='rho' 
-147                  if src_var.dimensions[2].find('_u') != -1: 
-148                      Cpos='u' 
-149                  if src_var.dimensions[2].find('_v') != -1: 
-150                      Cpos='v' 
-151                  if src_var.dimensions[1].find('_w') != -1: 
-152                      Cpos='w' 
-153   
-154                  print 'Arakawa C-grid position is', Cpos 
-155   
-156                  # create variable in _destination file 
-157                  if nt == trange[0]: 
-158                      print 'Creating variable', varname[nv] 
-159                      nc.createVariable(varname[nv], 'f8', src_var.dimensions) 
-160                      nc.variables[varname[nv]].long_name = src_var.long_name 
-161                      if varname[nv] != 'salt': 
-162                          nc.variables[varname[nv]].units = src_var.units 
-163                      nc.variables[varname[nv]].field = src_var.field 
-164                      nc.variables[varname[nv]]._FillValue = spval 
-165   
-166                  # get the right remap weights file 
-167                  for s in range(len(wts_files)): 
-168                      if wts_files[s].__contains__(Cpos+'_to_'+Cpos+'.nc'): 
-169                          wts_file = wts_files[s] 
-170                          break 
-171                      else: 
-172                          if s == len(wts_files) - 1: 
-173                              raise ValueError, 'Did not find the appropriate remap weights file' 
-174   
-175                  if ndim == 3: 
-176                      # vertical interpolation from sigma to standard z level 
-177                      print 'vertical interpolation from sigma to standard z level' 
-178                      src_varz = pyroms.remapping.roms2z( \ 
-179                                   src_var[nt,:,jjrange[0]:jjrange[1],iirange[0]:iirange[1]], \ 
-180                                   srcgrd, srcgrdz, Cpos=Cpos, spval=spval, \ 
-181                                   irange=iirange, jrange=jjrange) 
-182   
-183                      # flood the grid 
-184                      print 'flood the grid' 
-185                      src_varz = pyroms.remapping.flood(src_varz, srcgrdz, Cpos=Cpos, \ 
-186                                        irange=iirange, jrange=jjrange, spval=spval, \ 
-187                                        dmax=dmax, cdepth=cdepth, kk=kk) 
-188   
-189                      tmp_src_varz = np.zeros((nzlevel, src_var[:].shape[-2], src_var[:].shape[-1])) 
-190                      tmp_src_varz[:,jjrange[0]:jjrange[1],iirange[0]:iirange[1]] = src_varz 
-191                  else: 
-192                      src_varz = src_var[nt,jjrange[0]:jjrange[1],iirange[0]:iirange[1]] 
-193                      tmp_src_varz = np.zeros(src_var[nt,:].shape) 
-194                      tmp_src_varz[jjrange[0]:jjrange[1],iirange[0]:iirange[1]] = src_varz 
-195   
-196                  print datetime.datetime.now() 
-197                  # horizontal interpolation using scrip weights 
-198                  print 'horizontal interpolation using scrip weights' 
-199                  dst_varz = pyroms.remapping.remap(tmp_src_varz, wts_file, \ 
-200                                                    spval=spval) 
-201   
-202                  print datetime.datetime.now() 
-203   
-204                  if ndim == 3: 
-205                      # vertical interpolation from standard z level to sigma 
-206                      print 'vertical interpolation from standard z level to sigma' 
-207                      dst_var = pyroms.remapping.z2roms(dst_varz, dstgrdz, dstgrd, \ 
-208                                       Cpos=Cpos, spval=spval, flood=False) 
-209                  else: 
-210                      dst_var = dst_varz 
-211   
-212                  # write data in destination file 
-213                  print 'write data in destination file' 
-214                  nc.variables[varname[nv]][nctidx] = dst_var 
-215   
-216   
-217              # rotate the velocity field if requested 
-218              if rotate_uv is True: 
-219                  print ' '  
-220                  print 'remapping and rotating u and v from', srcgrd.name, \ 
-221                        'to', dstgrd.name 
-222   
-223                  # get source data 
-224                  src_u = pyroms.utility.get_nc_var('u', srcfile[nf]) 
-225                  src_v = pyroms.utility.get_nc_var('v', srcfile[nf]) 
-226   
-227                  # create variable in destination file 
-228                  print 'Creating variable u' 
-229                  nc.createVariable('u', 'f8', src_u.dimensions) 
-230                  nc.variables['u'].long_name = src_u.long_name 
-231                  nc.variables['u'].units = src_u.units 
-232                  nc.variables['u'].field = src_u.field 
-233                  nc.variables['u']._FillValue = spval 
-234                  print 'Creating variable v' 
-235                  nc.createVariable('v', 'f8', src_v.dimensions) 
-236                  nc.variables['v'].long_name = src_v.long_name 
-237                  nc.variables['v'].units = src_v.units 
-238                  nc.variables['v'].field = src_v.field 
-239                  nc.variables['v']._FillValue = spval 
-240   
-241                  # get the right remap weights file 
-242                  for s in range(len(wts_files)): 
-243                      if wts_files[s].__contains__('u_to_rho.nc'): 
-244                          wts_file_u = wts_files[s] 
-245                      if wts_files[s].__contains__('v_to_rho.nc'): 
-246                          wts_file_v = wts_files[s] 
-247   
-248                  # vertical interpolation from sigma to standard z level 
-249                  print 'vertical interpolation from sigma to standard z level' 
-250                  src_uz = pyroms.remapping.roms2z( \ 
-251                              src_u[nt,:,jjrange[0]:jjrange[1],iirange[0]:iirange[1]], \ 
-252                              srcgrd, srcgrdz, Cpos='u', irange=iirange, jrange=jjrange) 
-253                  src_vz = pyroms.remapping.roms2z( \ 
-254                              src_v[nt,:,jjrange[0]:jjrange[1],iirange[0]:iirange[1]], \ 
-255                              srcgrd, srcgrdz, Cpos='v', irange=iirange, jrange=jjrange) 
-256   
-257                  # flood the grid 
-258                  print 'flood the grid' 
-259                  src_uz = pyroms.remapping.flood(src_uz, srcgrdz, Cpos='u', \ 
-260                                    irange=iirange, jrange=jjrange, \ 
-261                                    spval=spval, dmax=dmax, cdepth=cdepth, kk=kk) 
-262                  src_vz = pyroms.remapping.flood(src_vz, srcgrdz, Cpos='v', \ 
-263                                    irange=iirange, jrange=jjrange, \ 
-264                                    spval=spval, dmax=dmax, cdepth=cdepth, kk=kk) 
-265   
-266                  # horizontal interpolation using scrip weights 
-267                  print 'horizontal interpolation using scrip weights' 
-268                  dst_uz = pyroms.remapping.remap(src_uz, wts_file_u, \ 
-269                                                    spval=spval) 
-270                  dst_vz = pyroms.remapping.remap(src_vz, wts_file_v, \ 
-271                                                    spval=spval) 
-272   
-273                  # vertical interpolation from standard z level to sigma 
-274                  print 'vertical interpolation from standard z level to sigma' 
-275                  dst_u = pyroms.remapping.z2roms(dst_uz, dstgrdz, dstgrd, \ 
-276                                   Cpos='rho', spval=spval, flood=False) 
-277                  dst_v = pyroms.remapping.z2roms(dst_vz, dstgrdz, dstgrd, \ 
-278                                   Cpos='rho', spval=spval, flood=False) 
-279   
-280                  # rotate u,v fields 
-281                  for s in range(len(wts_files)): 
-282                      if wts_files[s].__contains__('rho_to_rho.nc'): 
-283                          wts_file = wts_files[s] 
-284                  src_angle = pyroms.remapping.remap(srcgrd.hgrid.angle_rho, wts_file) 
-285                  dst_angle = dstgrd.hgrid.angle_rho 
-286                  angle = dst_angle - src_angle 
-287                  angle = np.tile(angle, (dstgrd.vgrid.N, 1, 1)) 
-288   
-289                  U = dst_u + dst_v*1j 
-290                  eitheta = np.exp(-1j*angle) 
-291                  U = U * eitheta 
-292   
-293                  dst_u = np.real(U) 
-294                  dst_v = np.imag(U) 
-295   
-296                  # move back to u,v points 
-297                  dst_u = 0.5 * (dst_u[:,:,:-1] + dst_u[:,:,1:]) 
-298                  dst_v = 0.5 * (dst_v[:,:-1,:] + dst_v[:,1:,:]) 
-299   
-300                  # write data in destination file 
-301                  print 'write data in destination file' 
-302                  nc.variables['u'][nctidx] = dst_u 
-303                  nc.variables['v'][nctidx] = dst_v 
-304   
-305          nctidx = nctidx + 1 
-306    
-307      # close destination file 
-308      nc.close() 
-309   
-310      return 
-
311   
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Module rfactor'

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rfactor(h, - rmask)
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Function Details[hide private]
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rfactor(h, - rmask) -

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-
-function r = rfactor(h,rmask)
-
-This function computes the bathymetry slope from a SCRUM NetCDF file.
-
-On Input:
-   h           bathymetry at RHO-points.
-   rmask       Land/Sea masking at RHO-points.
-
-On Output:
-   r           R-factor.
-
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- - Package pyroms_toolbox :: - Module rfactor' - - - - - - -
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Source Code for Module pyroms_toolbox.rfactor'

-
-
 1 -def rfactor(h,rmask): 
-
 2      """ 
- 3      function r = rfactor(h,rmask) 
- 4    
- 5      This function computes the bathymetry slope from a SCRUM NetCDF file. 
- 6   
- 7      On Input: 
- 8         h           bathymetry at RHO-points. 
- 9         rmask       Land/Sea masking at RHO-points. 
-10    
-11      On Output: 
-12         r           R-factor. 
-13      """ 
-14   
-15      Lp, Mp = h.shape 
-16      L=Lp-1 
-17      M=Mp-1 
-18   
-19      #  Land/Sea mask on U-points. 
-20      umask = np.zeros((L,Mp)) 
-21      for j in range(Mp): 
-22          for i in range(1,Lp): 
-23              umask[i-1,j] = rmask[i,j] * rmask[i-1,j] 
-24   
-25      #  Land/Sea mask on V-points. 
-26      vmask = np.zeros((Lp,M)) 
-27      for j in range(1,Mp): 
-28          for i in range(Lp): 
-29              vmask[i,j-1] = rmask[i,j] * rmask[i,j-1] 
-30   
-31      #------------------------------------------------------------------- 
-32      #  Compute R-factor. 
-33      #------------------------------------------------------------------- 
-34   
-35      hx = np.zeros((L,Mp)) 
-36      hy = np.zeros((Lp,M)) 
-37   
-38      hx = abs(h[1:,:] - h[:-1,:]) / (h[1:,:] + h[:-1,:]) 
-39      hy = abs(h[:,1:] - h[:,:-1]) / (h[:,1:] + h[:,:-1]) 
-40   
-41      hx = hx * umask 
-42      hy = hy * vmask 
-43   
-44      r = np.zeros((L,M)) 
-45   
-46      r = np.maximum(np.maximum(hx[:,:-1],hx[:,1:]), np.maximum(hy[:-1,:],hy[1:,:])) 
-47   
-48      rmin = r.min() 
-49      rmax = r.max() 
-50      ravg = r.mean() 
-51      rmed = np.median(r) 
-52   
-53      print '  ' 
-54      print 'Minimum r-value = ', rmin 
-55      print 'Maximum r-value = ', rmax 
-56      print 'Mean    r-value = ', ravg 
-57      print 'Median  r-value = ', rmed 
-58   
-59      return r 
-
60   
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Module rvalue'

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Functions[hide private]
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rvalue(h)
- function rv = rvalue(h)		 - source code - -
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Function Details[hide private]
-
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- -
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rvalue(h) -

- 		source code  -
- - 
-
-function rv = rvalue(h)
-
-This function compute ROMS stiffness parameter 
-(ripped from John Wilkin rvalue.m)
-
-On Input:
-   h           bathymetry at RHO-points.
-
-On Output:
-   rv          ROMS stiffness parameter.
-
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Source Code for Module pyroms_toolbox.rvalue'

-
-
 1 -def rvalue(h): 
-
 2      """ 
- 3      function rv = rvalue(h) 
- 4   
- 5      This function compute ROMS stiffness parameter  
- 6      (ripped from John Wilkin rvalue.m) 
- 7   
- 8      On Input: 
- 9         h           bathymetry at RHO-points. 
-10    
-11      On Output: 
-12         rv          ROMS stiffness parameter. 
-13      """ 
-14      #check that h is 2D 
-15      if (len(h.squeeze().shape)!=2): 
-16          raise ValueError, 'h must be two dimensions' 
-17   
-18      #check whether h contains any NaNs 
-19      if np.isnan(h).any(): raise Warning, 'the height array contains NaNs' 
-20   
-21      #compute  diff(h)/2*mean(h) at each velocity grid point 
-22      dhdx_u = np.diff(h, axis=1) 
-23      dhdy_v = np.diff(h, axis=0) 
-24      th_u = 2 * 0.5*(h[:,1:] + h[:,:-1]) 
-25      th_v = 2 * 0.5*(h[1:,:] + h[:-1,:]) 
-26      r_u = abs(dhdx_u / th_u) 
-27      r_v = abs(dhdy_v / th_v) 
-28   
-29      #for each rho point, find the maximum rvalue at the 4  
-30      #surrounding u,v points 
-31      r_u = np.maximum(r_u[:,1:],r_u[:,:-1]) 
-32      r_v = np.maximum(r_v[1:,:],r_v[:-1,:]) 
-33   
-34      # pad rows and columns to give a result the same size as the input h 
-35      r_u = np.c_[r_u[:,0], r_u, r_u[:,-1]] 
-36      r_v = np.r_[np.tile(r_v[0,:], (1, 1)), r_v, np.tile(r_v[-1,:], (1, 1))] 
-37   
-38      rv = np.maximum(r_u,r_v) 
-39   
-40      return rv 
-
41   
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- - - - diff --git a/pyroms_toolbox/docs/pyroms_toolbox.seawater-module.html b/pyroms_toolbox/docs/pyroms_toolbox.seawater-module.html deleted file mode 100644 index 88cdfb5..0000000 --- a/pyroms_toolbox/docs/pyroms_toolbox.seawater-module.html +++ /dev/null @@ -1,211 +0,0 @@ - - - - - pyroms_toolbox.seawater - - - - - - - - - - - - - - - - - - - - - - -
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Package seawater

source code

-
-
-Seawater -- Python functions for properties of sea water
-   Bjørn Ådlandsvik <bjorn@imr.no>,
-   Institute of Marine Research,
-   Version 1.1, 13 November 2002
-
-Public functions:
-Density related
-  dens(S,T,P)           Density of sea water              kg/m**3
-  delta(S,T,P)          Specific volume anomaly           m**3/kg
-  sigma(S,T,P)          Density anomaly                   kg/m**3
-  drhodt(S,T,P)         Temperature derivative of density kg/(K*m**3)
-  alpha(S,T,P)          Thermal expansion coefficient     1/K 
-  drhods(S,T,P)         Salinity derivative of density    kg/m**3
-  beta(S,T,P)           Salinity expansion coefficient
-  
-Salinity related
-  salt(R,T,P)           Salinity
-  cond(S,T,P)           Conductivity ratio
-
-Heat related
-  heatcap(S,T,P)        Heat capacity                     J/(kg*K)
-  adtgrad(S,T,P)        Adiabatic lapse rate              K/dbar
-  temppot(S,T,P,Pref)   Potential temperature             °C
-  temppot0(S,T,P)       Potential temperature             °C
-  
-Miscellaneous
-  freezept(S,P)         Freezing point                    °C
-  soundvel(S,T,P)       Sound velocity                    m/s
-  depth(P,lat)          Depth                             m
-
-Arguments:
-  S     = Salinity                 
-  T     = Temperature               °C
-  P     = Pressure                  dbar 
-  R     = Conductivity ratio
-  Pref  = Reference pressure        dbar
-  lat   = Latitude                  deg
-
-References:
-  [Bryden 1973], New polynomials for thermal expansion, adiabatic
-  temperature gradient and potential temperature gradient of sea water
-  Deep-Sea Res. 20, 401-408
-
-  [UNESCO 1981], Tenth report of the joint panel on oceanographic
-  tables and standards, Unesco technical papers in marine science 36.
-
-  [UNESCO 1983], N.P. Fofonoff and R.C. Millard Jr., Algorithms for
-  computation of fundamental properties of seawater, Unesco technical
-  papers in marine science 44.
-
-
- - - - - - - - -
- - - - - -
Submodules[hide private]
-
-
- -
- - - - - - - - - -
- - - - - -
Classes[hide private]
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Source Code for Package pyroms_toolbox.seawater

-
- 1  # --- encoding: iso-8859-1 --- 
- 2   
- 3  """ 
- 4   Seawater -- Python functions for properties of sea water 
- 5      Bjørn Ådlandsvik <bjorn@imr.no>, 
- 6      Institute of Marine Research, 
- 7      Version 1.1, 13 November 2002 
- 8   
- 9   Public functions: 
-10   Density related 
-11     dens(S,T,P)           Density of sea water              kg/m**3 
-12     delta(S,T,P)          Specific volume anomaly           m**3/kg 
-13     sigma(S,T,P)          Density anomaly                   kg/m**3 
-14     drhodt(S,T,P)         Temperature derivative of density kg/(K*m**3) 
-15     alpha(S,T,P)          Thermal expansion coefficient     1/K  
-16     drhods(S,T,P)         Salinity derivative of density    kg/m**3 
-17     beta(S,T,P)           Salinity expansion coefficient 
-18      
-19   Salinity related 
-20     salt(R,T,P)           Salinity 
-21     cond(S,T,P)           Conductivity ratio 
-22   
-23   Heat related 
-24     heatcap(S,T,P)        Heat capacity                     J/(kg*K) 
-25     adtgrad(S,T,P)        Adiabatic lapse rate              K/dbar 
-26     temppot(S,T,P,Pref)   Potential temperature             °C 
-27     temppot0(S,T,P)       Potential temperature             °C 
-28      
-29   Miscellaneous 
-30     freezept(S,P)         Freezing point                    °C 
-31     soundvel(S,T,P)       Sound velocity                    m/s 
-32     depth(P,lat)          Depth                             m 
-33   
-34   Arguments: 
-35     S     = Salinity                  
-36     T     = Temperature               °C 
-37     P     = Pressure                  dbar  
-38     R     = Conductivity ratio 
-39     Pref  = Reference pressure        dbar 
-40     lat   = Latitude                  deg 
-41   
-42   References: 
-43     [Bryden 1973], New polynomials for thermal expansion, adiabatic 
-44     temperature gradient and potential temperature gradient of sea water 
-45     Deep-Sea Res. 20, 401-408 
-46   
-47     [UNESCO 1981], Tenth report of the joint panel on oceanographic 
-48     tables and standards, Unesco technical papers in marine science 36. 
-49   
-50     [UNESCO 1983], N.P. Fofonoff and R.C. Millard Jr., Algorithms for 
-51     computation of fundamental properties of seawater, Unesco technical 
-52     papers in marine science 44. 
-53   
-54  """ 
-55   
-56  # --- Exceptions --- 
-
57 -class OutOfRangeError(Exception): pass 
-
58   
-59  from density import dens, svan, sigma, drhodt, alpha, drhods, beta 
-60  from salinity import salt, cond 
-61  from heat import heatcap, adtgrad, temppot, temppot0 
-62  from misc import freezept, soundvel, depth 
-63   
-
-
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- - - - diff --git a/pyroms_toolbox/docs/pyroms_toolbox.seawater.OutOfRangeError-class.html b/pyroms_toolbox/docs/pyroms_toolbox.seawater.OutOfRangeError-class.html deleted file mode 100644 index 81944e6..0000000 --- a/pyroms_toolbox/docs/pyroms_toolbox.seawater.OutOfRangeError-class.html +++ /dev/null @@ -1,186 +0,0 @@ - - - - - pyroms_toolbox.seawater.OutOfRangeError - - - - - - - - - - - - - - - - - - - - - - -
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Class OutOfRangeError

source code

-
-              object --+        
-                       |        
-exceptions.BaseException --+    
-                           |    
-        exceptions.Exception --+
-                               |
-                              OutOfRangeError
-
- -
- - - - - - - - - -
- - - - - -
Instance Methods[hide private]
-
-

Inherited from exceptions.Exception: - __init__, - __new__ -

-

Inherited from exceptions.BaseException: - __delattr__, - __getattribute__, - __getitem__, - __getslice__, - __reduce__, - __repr__, - __setattr__, - __setstate__, - __str__ -

-

Inherited from object: - __hash__, - __reduce_ex__ -

-
- - - - - - - - - -
- - - - - -
Properties[hide private]
-
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Inherited from exceptions.BaseException: - args, - message -

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Inherited from object: - __class__ -

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Module density

source code

-

Seawater density module

-

dens(S, T[, P]) -- Density svan(S, T[, P]) -- Specific volume - anomaly sigma(S, T[, P]) -- Density anomaly drhodt(S, T[, P]) -- - Temperature derivative of density alpha(S, T[, P]) -- Thermal expansion - coefficient drhods(S, T[, P]) -- Salinity derivative of density beta(S, - T[, P]) -- Saline expansion coefficient

-

Bjørn Ådlandsvik <bjorn@imr.no>, 07 November 2004

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - -
Functions[hide private]
-
-   - - - - - - -
_dens0(S, - T)
- Density of seawater at zero pressure		 - source code - -
- -
-   - - - - - - -
_seck(S, - T, - P=0)
- Secant bulk modulus		 - source code - -
- -
-   - - - - - - -
dens(S, - T, - P=0)
- Compute density of seawater from salinity, temperature, and pressure		 - source code - -
- -
-   - - - - - - -
svan(S, - T, - P=0)
- Compute specific volume anomaly		 - source code - -
- -
-   - - - - - - -
sigma(S, - T, - P=0)
- Compute density anomaly, sigma-T		 - source code - -
- -
-   - - - - - - -
drhodt(S, - T, - P=0)
- Compute temperature derivative of density		 - source code - -
- -
-   - - - - - - -
alpha(S, - T, - P=0)
- Compute thermal expansion coefficient		 - source code - -
- -
-   - - - - - - -
drhods(S, - T, - P=0)
- Compute salinity derivative of density		 - source code - -
- -
-   - - - - - - -
beta(S, - T, - P=0)
- Compute saline expansion coefficient		 - source code - -
- -
- - - - - - -
- - - - - -
Function Details[hide private]
-
- -
- -
- - -
-

dens(S, - T, - P=0) -

- 		source code  -
- - 
-Compute density of seawater from salinity, temperature, and pressure
-
-Usage: dens(S, T, [P])
-
-Input:               
-    S = Salinity,     [PSS-78]
-    T = Temperature,  [°C]
-    P = Pressure,     [dbar = 10**4 Pa]
-P is optional, with default value zero
-
-Output:
-    Density,          [kg/m**3]
-
-Algorithm: UNESCO 1983
-
-
-
-
-
-
- -
- -
- - -
-

svan(S, - T, - P=0) -

- 		source code  -
- - 
-Compute specific volume anomaly
-
-Usage: svan(S, T, [P])
-
-Input:
-    S = Salinity,     [PSS-78]
-    T = Temperature,  [°C]
-    P = Pressure,     [dbar]
-P is optional, with a default value = zero
-
-Output:
-    Specific volume anomaly  [m**3/kg]
-
-
-
-
-
-
- -
- -
- - -
-

sigma(S, - T, - P=0) -

- 		source code  -
- - 
-Compute density anomaly, sigma-T
-
-Usage: sigma(S, T, [P])
-
-Input:
-    S = Salinity,     [PSS-78]
-    T = Temperature,  [°C]
-    P = Pressure,     [dbar]
-P is optional, with a default value = zero
-
-Output:
-   Density anomaly,  [kg/m**3]
-
-
-
-
-
-
- -
- -
- - -
-

drhodt(S, - T, - P=0) -

- 		source code  -
- - 
-Compute temperature derivative of density
-
-Usage: drhodt(S, T, [P])
-
-Input:
-    S = Salinity,     [PSS-78]
-    T = Temperature,  [°C]
-    P = Pressure,     [dbar]
-P is optional, with a default value = zero
-
-Output:
-    Temperature derivative of density  [kg /(K m**3)]
-
-
-
-
-
-
- -
- -
- - -
-

alpha(S, - T, - P=0) -

- 		source code  -
- - 
-Compute thermal expansion coefficient
-
-Usage: alpha(S, T, [P])
-
-Input:
-    S = Salinity,     [PSS-78]
-    T = Temperature,  [°C]
-    P = Pressure,     [dbar]
-P is optional, with a default value = zero
-
-Output:
-    Thermal expansion coefficient,  [1/K]
-
-
-
-
-
-
- -
- -
- - -
-

drhods(S, - T, - P=0) -

- 		source code  -
- - 
-Compute salinity derivative of density
-
-Usage: drhodt(S, T, [P])
-
-Input:
-    S = Salinity,     [PSS-78]
-    T = Temperature,  [°C]
-    P = Pressure,     [dbar]
-P is optional, with a default value = zero
-
-Output:
-    Salinity derivative of density [kg/m**3]
-
-
-
-
-
-
- -
- -
- - -
-

beta(S, - T, - P=0) -

- 		source code  -
- - 
-Compute saline expansion coefficient
-
-Usage: alpha(S, T, [P])
-
-Input:
-    S = Salinity,     [PSS-78]
-    T = Temperature,  [°C]
-    P = Pressure,     [dbar]
-P is optional, with a default value = zero
-
-Output:
-    Saline expansion coefficient
-
-
-
-
-
-
-
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Source Code for Module pyroms_toolbox.seawater.density

-
-  1  # --- encoding: iso-8859-1 --- 
-  2   
-  3  """Seawater density module 
-  4   
-  5  dens(S, T[, P])   -- Density 
-  6  svan(S, T[, P])   -- Specific volume anomaly 
-  7  sigma(S, T[, P])  -- Density anomaly 
-  8  drhodt(S, T[, P]) -- Temperature derivative of density 
-  9  alpha(S, T[, P])  -- Thermal expansion coefficient 
- 10  drhods(S, T[, P]) -- Salinity derivative of density 
- 11  beta(S, T[, P])   -- Saline expansion coefficient 
- 12   
- 13  Bjørn Ådlandsvik <bjorn@imr.no>, 07 November 2004 
- 14   
- 15  """ 
- 16   
- 17  # ----------------------------------------------- 
- 18   
-
 19 -def _dens0(S,T): 
-
 20      """Density of seawater at zero pressure""" 
- 21   
- 22      # --- Define constants --- 
- 23      a0 = 999.842594 
- 24      a1 =   6.793952e-2 
- 25      a2 =  -9.095290e-3 
- 26      a3 =   1.001685e-4 
- 27      a4 =  -1.120083e-6 
- 28      a5 =   6.536332e-9 
- 29   
- 30      b0 =   8.24493e-1 
- 31      b1 =  -4.0899e-3 
- 32      b2 =   7.6438e-5 
- 33      b3 =  -8.2467e-7 
- 34      b4 =   5.3875e-9 
- 35   
- 36      c0 =  -5.72466e-3 
- 37      c1 =   1.0227e-4 
- 38      c2 =  -1.6546e-6 
- 39   
- 40      d0 =   4.8314e-4 
- 41   
- 42      # --- Computations --- 
- 43      # Density of pure water 
- 44      SMOW = a0 + (a1 + (a2 + (a3 + (a4 + a5*T)*T)*T)*T)*T 
- 45   
- 46      # More temperature polynomials 
- 47      RB = b0 + (b1 + (b2 + (b3 + b4*T)*T)*T)*T 
- 48      RC = c0 + (c1 + c2*T)*T 
- 49       
- 50      return SMOW + RB*S + RC*(S**1.5) + d0*S*S  
-
 51          
- 52  # ----------------------------------------------------------------- 
- 53   
-
 54 -def _seck(S, T, P=0): 
-
 55      """Secant bulk modulus""" 
- 56     
- 57      # --- Pure water terms --- 
- 58   
- 59      h0 =  3.239908   
- 60      h1 =  1.43713E-3 
- 61      h2 =  1.16092E-4 
- 62      h3 = -5.77905E-7 
- 63      AW = h0 + (h1 + (h2 + h3*T)*T)*T 
- 64   
- 65      k0 =  8.50935E-5   
- 66      k1 = -6.12293E-6 
- 67      k2 =  5.2787E-8 
- 68      BW = k0 + (k1 + k2*T)*T 
- 69   
- 70      e0 = 19652.21 
- 71      e1 = 148.4206 
- 72      e2 = -2.327105 
- 73      e3 =  1.360477E-2 
- 74      e4 = -5.155288E-5 
- 75      KW = e0 + (e1 + (e2 + (e3 + e4*T)*T)*T)*T   
- 76   
- 77      # --- seawater, P = 0 --- 
- 78   
- 79      SR = S**0.5 
- 80   
- 81      i0 =  2.2838E-3 
- 82      i1 = -1.0981E-5 
- 83      i2 = -1.6078E-6 
- 84      j0 =  1.91075E-4 
- 85      A  = AW + (i0 + (i1 + i2*T)*T + j0*SR)*S  
- 86   
- 87      f0 = 54.6746 
- 88      f1 = -0.603459 
- 89      f2 =  1.09987E-2 
- 90      f3 = -6.1670E-5 
- 91      g0 =  7.944E-2 
- 92      g1 =  1.6483E-2 
- 93      g2 = -5.3009E-4 
- 94      K0 = KW + (f0 + (f1 + (f2 + f3*T)*T)*T  \ 
- 95              + (g0 + (g1 + g2*T)*T)*SR)*S    
- 96   
- 97      # --- General expression --- 
- 98       
- 99      m0 = -9.9348E-7 
-100      m1 =  2.0816E-8 
-101      m2 =  9.1697E-10 
-102      B = BW + (m0 + (m1 + m2*T)*T)*S   
-103   
-104      K = K0 + (A + B*P)*P  
-105   
-106      return K 
-
107    
-108  # ---------------------------------------------- 
-109   
-
110 -def dens(S, T, P=0): 
-
111      """Compute density of seawater from salinity, temperature, and pressure 
-112   
-113      Usage: dens(S, T, [P]) 
-114    
-115      Input:                
-116          S = Salinity,     [PSS-78] 
-117          T = Temperature,  [°C] 
-118          P = Pressure,     [dbar = 10**4 Pa] 
-119      P is optional, with default value zero 
-120   
-121      Output: 
-122          Density,          [kg/m**3] 
-123    
-124      Algorithm: UNESCO 1983 
-125   
-126      """ 
-127   
-128      P = 0.1*P # Convert to bar 
-129      return _dens0(S,T)/(1 - P/_seck(S,T,P)) 
-
130   
-131  # ------------------------------------------- 
-132   
-
133 -def svan(S,T,P=0): 
-
134      """Compute specific volume anomaly 
-135   
-136      Usage: svan(S, T, [P]) 
-137   
-138      Input: 
-139          S = Salinity,     [PSS-78] 
-140          T = Temperature,  [°C] 
-141          P = Pressure,     [dbar] 
-142      P is optional, with a default value = zero 
-143   
-144      Output: 
-145          Specific volume anomaly  [m**3/kg] 
-146   
-147      """ 
-148      return 1.0/dens(S,T,P) - 1.0/dens(35,0,P) 
-
149   
-150  # ----------------------------------------------- 
-151   
-
152 -def sigma(S,T,P=0): 
-
153      """Compute density anomaly, sigma-T 
-154   
-155      Usage: sigma(S, T, [P]) 
-156   
-157      Input: 
-158          S = Salinity,     [PSS-78] 
-159          T = Temperature,  [°C] 
-160          P = Pressure,     [dbar] 
-161      P is optional, with a default value = zero 
-162   
-163      Output: 
-164         Density anomaly,  [kg/m**3] 
-165   
-166      """ 
-167      return dens(S,T,P) - 1000.0 
-
168   
-169  # ---------------------------------------------- 
-170   
-
171 -def drhodt(S,T,P=0): 
-
172      """Compute temperature derivative of density 
-173       
-174      Usage: drhodt(S, T, [P]) 
-175   
-176      Input: 
-177          S = Salinity,     [PSS-78] 
-178          T = Temperature,  [°C] 
-179          P = Pressure,     [dbar] 
-180      P is optional, with a default value = zero 
-181   
-182      Output: 
-183          Temperature derivative of density  [kg /(K m**3)] 
-184   
-185      """ 
-186   
-187      a1 =  6.793952e-2 
-188      a2 = -1.819058e-2 
-189      a3 =  3.005055e-4 
-190      a4 = -4.480332e-6 
-191      a5 =  3.268166e-8 
-192   
-193      b1 = -4.0899e-3 
-194      b2 =  1.52876e-4 
-195      b3 = -2.47401e-6 
-196      b4 =  2.155e-8  
-197   
-198      c1 =  1.0227e-4 
-199      c2 = -3.3092e-6 
-200   
-201      e1 =  148.4206 
-202      e2 = -4.65421 
-203      e3 =  4.081431e-2 
-204      e4 = -2.0621152e-4 
-205   
-206      f1 = -0.603459 
-207      f2 =  2.19974e-2 
-208      f3 = -1.8501e-4 
-209     
-210      g1 =  1.6483e-2 
-211      g2 = -1.06018e-3 
-212   
-213      h1 =  1.43713e-3 
-214      h2 =  2.32184e-4 
-215      h3 = -1.733715e-6 
-216    
-217      i1 = -1.0981e-5 
-218      i2 = -3.2156e-6 
-219   
-220      k1 = -6.12293e-6 
-221      k2 =  1.05574e-7 
-222     
-223      m1 = 2.0816e-8 
-224      m2 = 1.83394e-9 
-225   
-226      P = P/10.0 
-227   
-228      DSMOV = a1 + (a2 + (a3 + (a4 + a5*T)*T)*T)*T 
-229      DRHO0 = DSMOV + (b1 + (b2 + (b3 + b4*T)*T)*T)*S + (c1 + c2*T)*S**1.5 
-230   
-231      DAW = h1 + (h2 + h3*T) 
-232      DA  = DAW + (i1 + i2*T)*S 
-233        
-234   
-235      DBW = k1 + k2*T 
-236      DB  = DBW + (m1 + m2*T)*S 
-237   
-238      DKW = e1 + (e2 + (e3 + e4*T)*T)*T 
-239      DK0 = DKW + (f1 + (f2 + f3*T)*T)*S + (g1 + g2*T)*S**1.5 
-240      DK  = DK0 + (DA + DB*P)*P 
-241   
-242      K    = _seck(S,T,P) 
-243      RHO0 = _dens0(S,T)  
-244      denom  = 1. - P/K 
-245      return (DRHO0 * denom - RHO0 * P * DK / (K*K)) / (denom*denom) 
-
246   
-247  # ----------------------------------------------- 
-248   
-
249 -def alpha(S,T,P=0): 
-
250      """Compute thermal expansion coefficient 
-251   
-252      Usage: alpha(S, T, [P]) 
-253   
-254      Input: 
-255          S = Salinity,     [PSS-78] 
-256          T = Temperature,  [°C] 
-257          P = Pressure,     [dbar] 
-258      P is optional, with a default value = zero 
-259   
-260      Output: 
-261          Thermal expansion coefficient,  [1/K] 
-262   
-263      """ 
-264       
-265      ALPHA = - drhodt(S,T,P) / dens(S,T,P) 
-266      return ALPHA 
-
267   
-268  # ------------------------------------------------ 
-269   
-
270 -def drhods(S,T,P=0): 
-
271      """Compute salinity derivative of density 
-272       
-273      Usage: drhodt(S, T, [P]) 
-274   
-275      Input: 
-276          S = Salinity,     [PSS-78] 
-277          T = Temperature,  [°C] 
-278          P = Pressure,     [dbar] 
-279      P is optional, with a default value = zero 
-280   
-281      Output: 
-282          Salinity derivative of density [kg/m**3] 
-283   
-284      """ 
-285       
-286      b0 =  8.24493e-1 
-287      b1 = -4.0899e-3 
-288      b2 =  7.6438e-5 
-289      b3 = -8.2467e-7 
-290      b4 =  5.3875e-9 
-291   
-292      c0 = -5.72466e-3 
-293      c1 =  1.0227e-4 
-294      c2 = -1.6546e-6 
-295   
-296      d0 =  9.6628e-4 
-297   
-298      f0 = 54.6746 
-299      f1 = -0.603459 
-300      f2 =  1.09987e-2 
-301      f3 = -6.1670e-5 
-302   
-303      g0 =  7.944e-2 
-304      g1 =  1.6483e-2 
-305      g2 = -5.3009e-4 
-306   
-307      i0 =  2.2838e-3 
-308      i1 = -1.0981e-5 
-309      i2 = -1.6078e-6 
-310   
-311      j0 =  2.866125e-4 
-312   
-313      m0 = -9.9348e-7 
-314      m1 =  2.0816e-8 
-315      m2 =  9.1697e-10 
-316   
-317      P = 0.1*P # Convert to bar 
-318   
-319      DRHO0 = b0 + T*(b1 + T*(b2 + T*(b3 + T*b4))) +   \ 
-320             1.5*S**0.5*(c0 + T*(c1 + T*c2)) + S*d0 
-321      DK0 = f0 + T*(f1 + T*(f2 + T*f3)) +              \ 
-322             1.5*S**0.5*(g0 + T*(g1 + T*g2)) 
-323      DA = i0 + T*(i1 + T*i2) + j0*S**0.5 
-324      DB = m0 + T*(m1 + T*m2) 
-325      DK = DK0 + P*(DA + P*DB) 
-326      RHO0 = _dens0(S,T) 
-327      K = _seck(S,T,P) 
-328      denom  = 1. - P/K 
-329      DRHO = (DRHO0 * denom - RHO0 * P * DK / (K*K)) / (denom*denom) 
-330      return DRHO 
-
331   
-332  # ------------------------------------------------------ 
-333   
-
334 -def beta(S,T,P=0): 
-
335      """Compute saline expansion coefficient 
-336   
-337      Usage: alpha(S, T, [P]) 
-338   
-339      Input: 
-340          S = Salinity,     [PSS-78] 
-341          T = Temperature,  [°C] 
-342          P = Pressure,     [dbar] 
-343      P is optional, with a default value = zero 
-344   
-345      Output: 
-346          Saline expansion coefficient 
-347   
-348      """ 
-349   
-350      BETA = drhods(S,T,P) / dens(S,T,P) 
-351      return BETA 
-
352   
-353   
-354  ### SALINITY FUNCTIONS ################################# 
-355   
-356  ## def _sal(XR,XT): 
-357       
-358  ##     a0 =  0.0080 
-359  ##     a1 = -0.1692 
-360  ##     a2 = 25.3851 
-361  ##     a3 = 14.0941 
-362  ##     a4 = -7.0261 
-363  ##     a5 =  2.7081 
-364       
-365  ##     b0 =  0.0005 
-366  ##     b1 = -0.0056 
-367  ##     b2 = -0.0066 
-368  ##     b3 = -0.0375 
-369  ##     b4 =  0.0636 
-370  ##     b5 = -0.0144 
-371       
-372  ##     k  =  0.0162 
-373   
-374  ##     DS = (XT / (1+k*XT) ) *        \ 
-375  ##          (b0 + (b1 + (b2 + (b3 + (b4 + b5*XR)*XR)*XR)*XR)*XR) 
-376   
-377  ##     return a0 + (a1 + (a2 + (a3 + (a4 + a5*XR)*XR)*XR)*XR)*XR + DS 
-378   
-379  ## # --------------------------------------------------- 
-380   
-381  ## def _dsal(XR,XT): 
-382       
-383  ##     a1 = -0.1692 
-384  ##     a2 = 25.3851 
-385  ##     a3 = 14.0941 
-386  ##     a4 = -7.0261 
-387  ##     a5 =  2.7081 
-388   
-389  ##     b1 = -0.0056 
-390  ##     b2 = -0.0066 
-391  ##     b3 = -0.0375 
-392  ##     b4 =  0.0636 
-393  ##     b5 = -0.0144 
-394   
-395  ##     k  =  0.0162 
-396       
-397  ##     dDS = (XT / (1+k*XT) ) *      \ 
-398  ##           (b1 + (b2*2 + (b3*3 + (b4*4 + b5*5*XR)*XR)*XR)*XR) 
-399       
-400  ##     return a1 + (a2*2 + (a3*3 + (a4*4 + a5*5*XR)*XR)*XR)*XR + dDS 
-401   
-402  ## # --------------------------------------------- 
-403   
-404  ## def _rt(T): 
-405       
-406  ##     c0 =  0.6766097 
-407  ##     c1 =  2.00564e-2 
-408  ##     c2 =  1.104259e-4 
-409  ##     c3 = -6.9698e-7 
-410  ##     c4 =  1.0031e-9 
-411       
-412  ##     return c0 + (c1 + (c2 + (c3 + c4*T)*T)*T)*T 
-413   
-414  ## # --------------------------------------------------- 
-415   
-416  ## def _c(P): 
-417       
-418  ##     e1 =  2.070e-5 
-419  ##     e2 = -6.370e-10 
-420  ##     e3 =  3.989e-15 
-421       
-422  ##     return (e1 + (e2 + e3*P)*P)*P 
-423   
-424  ## # --------------------------------------------------- 
-425   
-426  ## def _b(T): 
-427       
-428  ##     d1 =  3.426e-2 
-429  ##     d2 =  4.464e-4 
-430       
-431  ##     return 1.0 + (d1 + d2*T)*T 
-432   
-433  ## # --------------------------------------------------- 
-434   
-435  ## def _a(T): 
-436       
-437  ##     d3 =  4.215e-1 
-438  ##     d4 = -3.107e-3     
-439  ##     return d3 + d4*T 
-440   
-
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Module heat

source code

-

Seawater heat module

-

heatcap(S, T[, P]) -- Heat capacity adtgrad(S, T[, P]) -- - Adiabatic temperature gradiente temppot(S, T, P[, Pref]) -- Potential - temperature temppot0(S, T, P) -- Potential temperature, relative - to surface

-

Bjørn Ådlandsvik, <bjorn@imr.no>, 07 November 2004

- - - - - - - - - - - - - - - - - - - -
- - - - - -
Functions[hide private]
-
-   - - - - - - -
heatcap(S, - T, - P=0)
- Compute heat capacity		 - source code - -
- -
-   - - - - - - -
adtgrad(S, - T, - P=0)
- Compute adiabatic temperature gradient		 - source code - -
- -
-   - - - - - - -
temppot(S, - T, - P, - Pref=0)
- Compute potential temperature		 - source code - -
- -
-   - - - - - - -
temppot0(S, - T, - P)
- Compute potential temperature relative to surface		 - source code - -
- -
- - - - - - -
- - - - - -
Function Details[hide private]
-
- -
- -
- - -
-

heatcap(S, - T, - P=0) -

- 		source code  -
- - 
-Compute heat capacity
-
-Usage: heatcap(S, T, [P])
-
-Input:
-    S = Salinity,     [PSS-78]
-    T = Temperature,  [°C]
-    P = Pressure,     [dbar]
-P is optional, with a default value = zero
-
-Output:
-    Heat capacity  [J/(kg*K)]
-
-Algorithm: UNESCO 1983
-
-
-
-
-
-
- -
- -
- - -
-

adtgrad(S, - T, - P=0) -

- 		source code  -
- - 
-Compute adiabatic temperature gradient
-
-Usage: adtgrad(S, T, [P])
-
-Input:
-    S = Salinity,     [PSS-78]
-    T = Temperature,  [°C]
-    P = Pressure,     [dbar]
-P is optional, with a default value = zero
-
-Output:
-    Adiabatic temperature gradient,  [K/dbar]
-
-Algorithm: UNESCO 1983
-
-
-
-
-
-
- -
- -
- - -
-

temppot(S, - T, - P, - Pref=0) -

- 		source code  -
- - 
-Compute potential temperature
-
-Usage: temppot(S, T, P, [Pref])
-
-Input:
-    S = Salinity,                [PSS-78]
-    T = Temperature,             [°C]
-    P = Pressure,                [dbar]
-    Pref = Reference pressure,   [dbar]
-Pref is optional, with a default value = zero
-
-Output:
-    Potential temperature,  [°C]
-
-Algorithm: UNESCO 1983
-
-
-
-
-
-
- -
- -
- - -
-

temppot0(S, - T, - P) -

- 		source code  -
- - 
-Compute potential temperature relative to surface
-
-Usage: temppot0(S, T, P)
-
-Input:
-    S = Salinity,                [PSS-78]
-    T = Temperature,             [°C]
-    P = Pressure,                [dbar]
-
-Output:
-    Potential temperature,       [°C]
-
-Algorithm: Bryden 1973
-
-Note: Due to different algorithms,
-    temppot0(S, T, P) != tempot(S, T, P, Pref=0)
-
-
-
-
-
-
-
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Source Code for Module pyroms_toolbox.seawater.heat

-
-  1  # --- encoding: iso-8859-1 --- 
-  2   
-  3  """Seawater heat module 
-  4   
-  5  heatcap(S, T[, P])       -- Heat capacity 
-  6  adtgrad(S, T[, P])       -- Adiabatic temperature gradiente 
-  7  temppot(S, T, P[, Pref]) -- Potential temperature 
-  8  temppot0(S, T, P)        -- Potential temperature, relative to surface 
-  9   
- 10  Bjørn Ådlandsvik, <bjorn@imr.no>, 07 November 2004 
- 11   
- 12  """ 
- 13   
- 14  # ------------------------------------------------- 
- 15   
-
 16 -def heatcap(S, T, P=0): 
-
 17      """Compute heat capacity 
- 18   
- 19      Usage: heatcap(S, T, [P]) 
- 20   
- 21      Input: 
- 22          S = Salinity,     [PSS-78] 
- 23          T = Temperature,  [°C] 
- 24          P = Pressure,     [dbar] 
- 25      P is optional, with a default value = zero 
- 26   
- 27      Output: 
- 28          Heat capacity  [J/(kg*K)] 
- 29   
- 30      Algorithm: UNESCO 1983 
- 31   
- 32      """ 
- 33       
- 34      P = 0.1*P  # Conversion to bar 
- 35   
- 36      # - Temperatur dependence 
- 37      c0 =  4217.4 
- 38      c1 = -3.720283 
- 39      c2 =  0.1412855 
- 40      c3 = -2.654387e-3 
- 41      c4 =  2.093236e-5 
- 42   
- 43      a0 = -7.64357 
- 44      a1 =  0.1072763 
- 45      a2 = -1.38385e-3 
- 46   
- 47      b0 =  0.1770383 
- 48      b1 = -4.07718e-3 
- 49      b2 =  5.148e-5 
- 50   
- 51      CP0 =  c0 + c1*T + c2*T**2 + c3*T**3 + c4*T**4  \ 
- 52            + (a0 + a1*T + a2*T**2)*S \ 
- 53            + (b0 + b1*T + b2*T**2)*S**1.5 
- 54   
- 55      # - Pressure dependence     
- 56      a0 = -4.9592e-1 
- 57      a1 =  1.45747e-2 
- 58      a2 = -3.13885e-4 
- 59      a3 =  2.0357e-6 
- 60      a4 =  1.7168e-8 
- 61   
- 62      b0 =  2.4931e-4 
- 63      b1 = -1.08645e-5 
- 64      b2 =  2.87533e-7 
- 65      b3 = -4.0027e-9 
- 66      b4 =  2.2956e-11 
- 67   
- 68      c0 = -5.422e-8 
- 69      c1 =  2.6380e-9 
- 70      c2 = -6.5637e-11 
- 71      c3 =  6.136e-13 
- 72   
- 73      CP1 = (a0 + a1*T + a2*T**2 + a3*T**3 + a4*T**4)*P  \ 
- 74                + (b0 + b1*T + b2*T**2 + b3*T**3 + b4*T**4)*P**2 \ 
- 75                + (c0 + c1*T + c2*T**2 + c3*T**3)*P**3 
- 76   
- 77      # - Salinity dependence     
- 78      d0 =  4.9247e-3 
- 79      d1 = -1.28315e-4 
- 80      d2 =  9.802e-7 
- 81      d3 =  2.5941e-8 
- 82      d4 = -2.9179e-10 
- 83   
- 84      e0 = -1.2331e-4 
- 85      e1 = -1.517e-6 
- 86      e2 =  3.122e-8 
- 87   
- 88      f0 = -2.9558e-6 
- 89      f1 =  1.17054e-7 
- 90      f2 = -2.3905e-9 
- 91      f3 =  1.8448e-11 
- 92   
- 93      g0 =  9.971e-8 
- 94    
- 95      h0 =  5.540e-10 
- 96      h1 = -1.7682e-11 
- 97      h2 =  3.513e-13 
- 98   
- 99      j1 = -1.4300e-12 
-100      S3_2  = S**1.5 
-101   
-102      CP2 = ((d0 + d1*T + d2*T**2 + d3*T**3 + d4*T**4)*S \ 
-103             + (e0 + e1*T + e2*T**2)*S3_2)*P  \ 
-104             + ((f0 + f1*T + f2*T**2 + f3*T**3)*S  \ 
-105             +   g0*S3_2)*P**2 \ 
-106             + ((h0 + h1*T + h2*T**2)*S + j1*T*S3_2)*P**3 
-107        
-108   
-109      return CP0 + CP1 + CP2 
-
110   
-111  # -------------------------------------------------------------- 
-112   
-
113 -def adtgrad(S, T, P=0): 
-
114      """Compute adiabatic temperature gradient 
-115   
-116      Usage: adtgrad(S, T, [P]) 
-117   
-118      Input: 
-119          S = Salinity,     [PSS-78] 
-120          T = Temperature,  [°C] 
-121          P = Pressure,     [dbar] 
-122      P is optional, with a default value = zero 
-123   
-124      Output: 
-125          Adiabatic temperature gradient,  [K/dbar] 
-126   
-127      Algorithm: UNESCO 1983 
-128   
-129      """ 
-130       
-131      a0 =  3.5803e-5 
-132      a1 = +8.5258e-6 
-133      a2 = -6.836e-8 
-134      a3 =  6.6228e-10 
-135   
-136      b0 = +1.8932e-6 
-137      b1 = -4.2393e-8 
-138   
-139      c0 = +1.8741e-8 
-140      c1 = -6.7795e-10 
-141      c2 = +8.733e-12 
-142      c3 = -5.4481e-14 
-143   
-144      d0 = -1.1351e-10 
-145      d1 =  2.7759e-12 
-146   
-147      e0 = -4.6206e-13 
-148      e1 = +1.8676e-14 
-149      e2 = -2.1687e-16 
-150   
-151      return  a0 + (a1 + (a2 + a3*T)*T)*T  \ 
-152           + (b0 + b1*T)*(S-35)  \ 
-153           + ( (c0 + (c1 + (c2 + c3*T)*T)*T) \ 
-154           +   (d0 + d1*T)*(S-35) )*P \ 
-155           + (e0 + (e1 + e2*T)*T )*P*P 
-
156   
-157  # --------------------------------------------------------------- 
-158   
-
159 -def temppot(S, T, P, Pref=0): 
-
160      """Compute potential temperature 
-161   
-162      Usage: temppot(S, T, P, [Pref]) 
-163   
-164      Input: 
-165          S = Salinity,                [PSS-78] 
-166          T = Temperature,             [°C] 
-167          P = Pressure,                [dbar] 
-168          Pref = Reference pressure,   [dbar] 
-169      Pref is optional, with a default value = zero 
-170   
-171      Output: 
-172          Potential temperature,  [°C] 
-173   
-174      Algorithm: UNESCO 1983 
-175   
-176      """ 
-177       
-178      H = Pref-P 
-179      XK = H*adtgrad(S,T,P) 
-180   
-181      T = T + 0.5*XK 
-182      Q = XK 
-183      P = P + 0.5*H 
-184      XK = H*adtgrad(S,T,P) 
-185   
-186      T = T + 0.29289322*(XK-Q) 
-187      Q = 0.58578644*XK + 0.121320344*Q 
-188      XK = H*adtgrad(S,T,P) 
-189       
-190      T = T + 1.707106781*(XK-Q) 
-191      Q = 3.414213562*XK - 4.121320344*Q 
-192      P = P + 0.5*H 
-193      XK = H*adtgrad(S,T,P) 
-194       
-195      return T + (XK-2.0*Q)/6.0     
-
196       
-197   
-198  # ------------------------------------------------------ 
-199   
-
200 -def temppot0(S,T,P): 
-
201      """Compute potential temperature relative to surface 
-202   
-203      Usage: temppot0(S, T, P) 
-204   
-205      Input: 
-206          S = Salinity,                [PSS-78] 
-207          T = Temperature,             [°C] 
-208          P = Pressure,                [dbar] 
-209    
-210      Output: 
-211          Potential temperature,       [°C] 
-212   
-213      Algorithm: Bryden 1973 
-214   
-215      Note: Due to different algorithms, 
-216          temppot0(S, T, P) != tempot(S, T, P, Pref=0) 
-217     
-218      """ 
-219   
-220      P = P/10  # Conversion from dbar 
-221   
-222      a0 =  3.6504e-4 
-223      a1 =  8.3198e-5 
-224      a2 = -5.4065e-7 
-225      a3 =  4.0274e-9 
-226   
-227      b0 =  1.7439e-5 
-228      b1 = -2.9778e-7 
-229   
-230      c0 =  8.9309e-7 
-231      c1 = -3.1628e-8 
-232      c2 =  2.1987e-10 
-233   
-234      d0 =  4.1057e-9 
-235   
-236      e0 = -1.6056e-10 
-237      e1 =  5.0484e-12 
-238   
-239      S0 = S - 35.0 
-240   
-241      return  T - (a0 + (a1 + (a2 + a3*T)*T)*T)*P  \ 
-242                - (b0 + b1*T)*P*S0                 \ 
-243                - (c0 + (c1 + c2*T)*T)*P*P         \ 
-244                + d0*S0*P*P                        \ 
-245                - (e0 + e1*T)*P*P*P 
-
246   
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Module misc

source code

-

Miscellaneous sea water functions

-

freezept(S[, P]) -- Freezing point soundvel(S, T[, P]) -- Sound - velocity depth(P, lat) -- Depth from pressure

-

Bjørn Ådlandsvik, <bjorn@imr.no> 07 November 2004

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Functions[hide private]
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freezept(S, - P=0)
- Compute freezing temperature of sea water		 - source code - -
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soundvel(S, - T, - P=0)
- Compute velocity of sound		 - source code - -
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depth(P, - lat)
- Compute depth from pressure and latitude		 - source code - -
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Function Details[hide private]
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freezept(S, - P=0) -

- 		source code  -
- - 
-Compute freezing temperature of sea water
-
-Usage: freezept(S, [P])
-
-Input:               
-    S = Salinity,      [psu]
-    P = Pressure,      [dbar]
-P is optional, with a default value = 0
-
-Output:
-    T = Freezing point,   [°C]
-
-Algorithm: UNESCO 1983 
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-
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soundvel(S, - T, - P=0) -

- 		source code  -
- - 
-Compute velocity of sound
-
-Usage: soundvel(S, T, [P])
-
-Input:
-    S = Salinity,     [PSS-78]
-    T = Temperature,  [°C]
-    P = Pressure,     [dbar]
-P is optional, with a default value = zero
-
-Output:
-    Sound velocity,  [m/s]
-
-Algorithm: UNESCO 1983 
-
-
-
-
-
-
- -
- -
- - -
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depth(P, - lat) -

- 		source code  -
- - 
-Compute depth from pressure and latitude
-
-Usage: depth(P, lat)
-
-Input:
-    P = Pressure,     [dbar]
-    lat = Latitude    [deg]
-
-Output:
-    Depth             [m]
-
-Algorithm: UNESCO 1983 
-
-
-
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Source Code for Module pyroms_toolbox.seawater.misc

-
-  1  # --- encoding: iso-8859-1 --- 
-  2   
-  3  """Miscellaneous sea water functions 
-  4   
-  5  freezept(S[, P])    -- Freezing point 
-  6  soundvel(S, T[, P]) -- Sound velocity 
-  7  depth(P, lat)       -- Depth from pressure 
-  8   
-  9  Bjørn Ådlandsvik, <bjorn@imr.no>  07 November 2004 
- 10   
- 11  """ 
- 12   
- 13  # ---------------------------------------------------------- 
- 14   
-
 15 -def freezept(S, P=0): 
-
 16   
- 17      """Compute freezing temperature of sea water 
- 18   
- 19      Usage: freezept(S, [P]) 
- 20    
- 21      Input:                
- 22          S = Salinity,      [psu] 
- 23          P = Pressure,      [dbar] 
- 24      P is optional, with a default value = 0 
- 25   
- 26      Output: 
- 27          T = Freezing point,   [°C] 
- 28   
- 29      Algorithm: UNESCO 1983  
- 30   
- 31      """ 
- 32       
- 33      a0 = -0.0575 
- 34      a1 =  1.710523e-3 
- 35      a2 = -2.154996e-4 
- 36      b  = -7.53e-4 
- 37   
- 38      Tf = a0*S + a1*S**1.5 + a2*S**2 + b*P 
- 39      return Tf 
-
 40   
- 41  # ---------------------------------------------------------------- 
- 42   
-
 43 -def soundvel(S, T, P=0): 
-
 44      """Compute velocity of sound 
- 45   
- 46      Usage: soundvel(S, T, [P]) 
- 47   
- 48      Input: 
- 49          S = Salinity,     [PSS-78] 
- 50          T = Temperature,  [°C] 
- 51          P = Pressure,     [dbar] 
- 52      P is optional, with a default value = zero 
- 53   
- 54      Output: 
- 55          Sound velocity,  [m/s] 
- 56   
- 57      Algorithm: UNESCO 1983  
- 58   
- 59      """ 
- 60   
- 61      P = 0.1*P  # Conversion to bar 
- 62   
- 63      c00 = 1402.388 
- 64      c01 =  5.03711 
- 65      c02 = -5.80852e-2 
- 66      c03 =  3.3420e-4 
- 67      c04 = -1.47800e-6 
- 68      c05 =  3.1464e-9 
- 69   
- 70      c10 =  0.153563 
- 71      c11 =  6.8982e-4 
- 72      c12 = -8.1788e-6 
- 73      c13 =  1.3621e-7 
- 74      c14 = -6.1185e-10 
- 75   
- 76      c20 =  3.1260e-5 
- 77      c21 = -1.7107e-6 
- 78      c22 =  2.5974e-8 
- 79      c23 = -2.5335e-10 
- 80      c24 =  1.0405e-12 
- 81   
- 82      c30 = -9.7729e-9 
- 83      c31 =  3.8504e-10 
- 84      c32 = -2.3643e-12 
- 85    
- 86      P2 = P*P 
- 87      P3 = P2*P 
- 88      Cw =  c00 + (c01 + (c02 + (c03 + (c04 + c05*T)*T)*T)*T)*T   \ 
- 89         + (c10 + (c11 + (c12 + (c13 + c14*T)*T)*T)*T)*P          \ 
- 90         + (c20 + (c21 + (c22 + (c23 + c24*T)*T)*T)*T)*P2         \ 
- 91         + (c30 + (c31 + c32*T)*T)*P3 
- 92    
- 93      a00 =  1.389 
- 94      a01 = -1.262e-2 
- 95      a02 =  7.164e-5 
- 96      a03 =  2.006e-6 
- 97      a04 = -3.21e-8 
- 98   
- 99      a10 =  9.4742e-5 
-100      a11 = -1.2580e-5 
-101      a12 = -6.4885e-8 
-102      a13 =  1.0507e-8 
-103      a14 = -2.0122e-10 
-104   
-105      a20 = -3.9064e-7 
-106      a21 =  9.1041e-9 
-107      a22 = -1.6002e-10 
-108      a23 =  7.988e-12 
-109   
-110      a30 =  1.100e-10 
-111      a31 =  6.649e-12 
-112      a32 = -3.389e-13 
-113   
-114      A =  a00 + (a01 + (a02 + (a03 + a04*T)*T)*T)*T      \ 
-115        + (a10 + (a11 + (a12 + (a13 + a14*T)*T)*T)*T)*P   \ 
-116        + (a20 + (a21 + (a22 + a23*T)*T)*T)*P2            \ 
-117        + (a30 + (a31 + a32*T)*T)*P3 
-118   
-119      b00 = -1.922e-2 
-120      b01 = -4.42e-5 
-121      b10 =  7.3637e-5 
-122      b11 =  1.7945e-7 
-123   
-124      B = b00 + b01*T + (b10 + b11*T)*P 
-125   
-126      d00 =  1.727e-3 
-127      d10 = -7.9836e-6 
-128   
-129      D = d00 + d10*P 
-130   
-131      return Cw + A*S + B*S**1.5 + D*S**2 
-
132   
-133  # ---------------------------------------------------------------- 
-134   
-
135 -def depth(P, lat): 
-
136      """Compute depth from pressure and latitude 
-137   
-138      Usage: depth(P, lat) 
-139   
-140      Input: 
-141          P = Pressure,     [dbar] 
-142          lat = Latitude    [deg] 
-143   
-144      Output: 
-145          Depth             [m] 
-146   
-147      Algorithm: UNESCO 1983  
-148   
-149      """ 
-150       
-151      # Use Numeric for trigonometry if present 
-152      try: 
-153          from Numeric import sin, pi 
-154      except: 
-155          from math import sin, pi 
-156       
-157      a1 =  9.72659 
-158      a2 = -2.2512e-5 
-159      a3 =  2.279e-10 
-160      a4 = -1.82e-15 
-161   
-162      b  =  1.092e-6 
-163   
-164      g0 =  9.780318 
-165      g1 =  5.2788e-3 
-166      g2 =  2.36e-5 
-167   
-168      rad = pi / 180. 
-169   
-170      X = sin(lat*rad) 
-171      X = X*X 
-172      grav = g0 * (1.0 + (g1 + g2*X)*X) + b*P 
-173      nom = (a1 + (a2 + (a3 + a4*P)*P)*P)*P 
-174   
-175      return nom / grav 
-
176   
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Module salinity

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-
-Seawater salinity module, providing salt and cond functions
-
-S = salt(R, T[, P]) -- Salinity    
-R = cond(S, T[, P]) -- Conductivity ratio
-
-Arguments:
-    R = Conductivity ratio
-    S = Salinity
-    T = Temperature         [°C]
-    P = Pressure,           [dbar = 10**4 Pa]
-
-Bjørn Ådlandsvik <bjorn@imr.no>, 07 November 2004
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_sal(XR, - XT) - source code - -
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_rt(T) - source code - -
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_c(P) - source code - -
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_b(T) - source code - -
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_a(T) - source code - -
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salt(R, - T, - P)
- Compute salinity from conductivity, temperature, and pressure		 - source code - -
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cond(S, - T, - P)
- Compute conductivity ratio from salinity, temperature, and pressure		 - source code - -
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Function Details[hide private]
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salt(R, - T, - P) -

- 		source code  -
- - 
-Compute salinity from conductivity, temperature, and pressure
-
-Usage: salt(R, T, [P])
-
-Input:
-    R = Conductivity ratio
-    T = Temperature        [°C]
-    P = Pressure,          [dbar = 10**4 Pa]
-P is optional, with default value zero
-  
-Output:
-    S = Salinity           [PSS-78]
-
-
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cond(S, - T, - P) -

- 		source code  -
- - 
-Compute conductivity ratio from salinity, temperature, and pressure
-
-Usage: cond(S, T, [P])
-
-Input:
-    S = Salinity      [PSS-78]
-    T = Temperature   [°C]
-    P = Pressure,     [dbar = 10**4 Pa]
-P is optional, with default value zero
-  
-Output:
-    R = Conductivity ratio
-
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Source Code for Module pyroms_toolbox.seawater.salinity

-
-  1  # --- encoding: iso-8859-1 --- 
-  2   
-  3  """Seawater salinity module, providing salt and cond functions 
-  4   
-  5  S = salt(R, T[, P]) -- Salinity     
-  6  R = cond(S, T[, P]) -- Conductivity ratio 
-  7   
-  8  Arguments: 
-  9      R = Conductivity ratio 
- 10      S = Salinity 
- 11      T = Temperature         [°C] 
- 12      P = Pressure,           [dbar = 10**4 Pa] 
- 13   
- 14  Bjørn Ådlandsvik <bjorn@imr.no>, 07 November 2004 
- 15   
- 16  """ 
- 17   
- 18  # ------------------------------------------------------- 
- 19   
-
 20 -def _sal(XR,XT): 
-
 21       
- 22      a0 =  0.0080 
- 23      a1 = -0.1692 
- 24      a2 = 25.3851 
- 25      a3 = 14.0941 
- 26      a4 = -7.0261 
- 27      a5 =  2.7081 
- 28       
- 29      b0 =  0.0005 
- 30      b1 = -0.0056 
- 31      b2 = -0.0066 
- 32      b3 = -0.0375 
- 33      b4 =  0.0636 
- 34      b5 = -0.0144 
- 35       
- 36      k  =  0.0162 
- 37   
- 38      DS = (XT / (1+k*XT) ) *        \ 
- 39           (b0 + (b1 + (b2 + (b3 + (b4 + b5*XR)*XR)*XR)*XR)*XR) 
- 40   
- 41      return a0 + (a1 + (a2 + (a3 + (a4 + a5*XR)*XR)*XR)*XR)*XR + DS 
-
 42   
- 43  # --------------------------------------------------- 
- 44   
-
 45 -def _dsal(XR,XT): 
-
 46       
- 47      a1 = -0.1692 
- 48      a2 = 25.3851 
- 49      a3 = 14.0941 
- 50      a4 = -7.0261 
- 51      a5 =  2.7081 
- 52   
- 53      b1 = -0.0056 
- 54      b2 = -0.0066 
- 55      b3 = -0.0375 
- 56      b4 =  0.0636 
- 57      b5 = -0.0144 
- 58   
- 59      k  =  0.0162 
- 60       
- 61      dDS = (XT / (1+k*XT) ) *      \ 
- 62            (b1 + (b2*2 + (b3*3 + (b4*4 + b5*5*XR)*XR)*XR)*XR) 
- 63       
- 64      return a1 + (a2*2 + (a3*3 + (a4*4 + a5*5*XR)*XR)*XR)*XR + dDS 
-
 65   
- 66  # --------------------------------------------- 
- 67   
-
 68 -def _rt(T): 
-
 69       
- 70      c0 =  0.6766097 
- 71      c1 =  2.00564e-2 
- 72      c2 =  1.104259e-4 
- 73      c3 = -6.9698e-7 
- 74      c4 =  1.0031e-9 
- 75       
- 76      return c0 + (c1 + (c2 + (c3 + c4*T)*T)*T)*T 
-
 77   
- 78  # --------------------------------------------------- 
- 79   
-
 80 -def _c(P): 
-
 81       
- 82      e1 =  2.070e-5 
- 83      e2 = -6.370e-10 
- 84      e3 =  3.989e-15 
- 85       
- 86      return (e1 + (e2 + e3*P)*P)*P 
-
 87   
- 88  # --------------------------------------------------- 
- 89   
-
 90 -def _b(T): 
-
 91       
- 92      d1 =  3.426e-2 
- 93      d2 =  4.464e-4 
- 94       
- 95      return 1.0 + (d1 + d2*T)*T 
-
 96   
- 97  # --------------------------------------------------- 
- 98   
-
 99 -def _a(T): 
-
100       
-101      d3 =  4.215e-1 
-102      d4 = -3.107e-3 
-103       
-104      return d3 + d4*T 
-
105   
-106  # -------------------------------------------------- 
-107   
-
108 -def salt(R, T, P): 
-
109      """Compute salinity from conductivity, temperature, and pressure 
-110   
-111      Usage: salt(R, T, [P]) 
-112   
-113      Input: 
-114          R = Conductivity ratio 
-115          T = Temperature        [°C] 
-116          P = Pressure,          [dbar = 10**4 Pa] 
-117      P is optional, with default value zero 
-118         
-119      Output: 
-120          S = Salinity           [PSS-78] 
-121   
-122      """ 
-123       
-124      DT = T - 15.0 
-125      RT = R/(_rt(T)*(1.0 + _c(P)/(_b(T) + _a(T)*R))) 
-126      RT = abs(RT)**0.5 
-127       
-128      return _sal(RT,DT) 
-
129   
-130  # ------------------------------------------------- 
-131   
-
132 -def cond(S, T, P): 
-
133      """Compute conductivity ratio from salinity, temperature, and pressure 
-134   
-135      Usage: cond(S, T, [P]) 
-136   
-137      Input: 
-138          S = Salinity      [PSS-78] 
-139          T = Temperature   [°C] 
-140          P = Pressure,     [dbar = 10**4 Pa] 
-141      P is optional, with default value zero 
-142         
-143      Output: 
-144          R = Conductivity ratio 
-145   
-146  """ 
-147       
-148      DT = T-15.0 
-149      RT = (S/35.0)**0.5 
-150      SI = _sal(RT,DT) 
-151      # Iteration 
-152      for n in xrange(100): 
-153          RT = RT + (S-SI)/_dsal(RT,DT) 
-154          SI = _sal(RT,DT) 
-155          try: 
-156              DELS = max(abs(SI-S)) 
-157          except TypeError: # Not sequence, i.e. scalar S 
-158              DELS = abs(SI-S) 
-159          if (DELS < 1.0E-4): 
-160              break 
-161   
-162      RTT = _rt(T)*RT*RT 
-163      AT = _a(T) 
-164      BT = _b(T) 
-165      CP = _c(P) 
-166      CP = RTT*(CP + BT) 
-167      BT = BT - RTT*AT 
-168   
-169      R = abs(BT*BT + 4.0*AT*CP)**0.5 - BT 
-170       
-171      return 0.5*R/AT 
-
172   
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Source Code for Module pyroms_toolbox.seawater.test

-
- 1                                         
- 2  ### TEST-CODE ##################################### 
- 3   
- 4  if __name__ == '__main__': 
- 5   
- 6      format1 = "Computed: %25s = " 
- 7      format2 = "Check value                         = " 
- 8       
- 9      print 
-10      # Check value from UNESCO 1983, p. 20 
-11      print "Checking svan" 
-12      print 
-13      print "S = 40, T = 40 °C, P = 10000 dbar" 
-14      print format1 % "svan(40, 40, 10000)", svan(40, 40, 10000) 
-15      print format2, "981.30210E-8" 
-16   
-17      print 
-18      # Check value from UNESCO 1983, p. 20 
-19      print "Checking sigma" 
-20      print 
-21      print "S = 40, T = 40 °C, P = 10000 dbar" 
-22      print format1 % "sigma(40, 40, 10000)", sigma(40, 40, 10000) 
-23      print format2, 59.82037 
-24   
-25      print 
-26      # Check value from UNESCO 1983, p. 11 
-27      print "Checking salt" 
-28      print 
-29      print "Salinity = 40.0000" 
-30      print "cond = 1.888091, T = 40 °C, P = 10000 dbar" 
-31      print format1 % "salt(1.888091, 40, 10000)", salt(1.888091, 40, 10000) 
-32      print format2, 40.0000 
-33   
-34      print 
-35      # Check value from UNESCO 1983, p. 11 
-36      print "Checking cond" 
-37      print 
-38      print "S = 40, T = 40 °C, P = 10000 dbar" 
-39      print format1 % "cond(40, 40, 10000)", cond(40, 40, 10000) 
-40      print format2, 1.888091 
-41   
-42      print 
-43      # Check value from UNESCO 1983, p. 35 
-44      print "Checking heatcap" 
-45      print 
-46      print "S = 40, T = 40 °C, P = 10000 dbar" 
-47      print format1 % "heatcap(40, 40, 10000)", heatcap(40, 40, 10000) 
-48      print format2, "3849.500"  
-49   
-50      print 
-51      # Check value from UNESCO 1983, p. 36 
-52      print "Checking adtgrad" 
-53      print 
-54      print "S = 40, T = 40 °C, P = 10000 dbar" 
-55      print format1 % "adtgrad(40, 40, 10000)", adtgrad(40, 40, 10000) 
-56      print format2, "3.255976E-4" 
-57   
-58      print 
-59      # Check value from UNESCO 1983, p. 44 
-60      print "Checking temppot" 
-61      print  
-62      print "S = 40, T = 40 °C, P = 10000 dbar, Pref = 0" 
-63      print format1 % "temppot(40, 40, 10000)", temppot(40, 40, 10000) 
-64      print format2, 36.89073 
-65   
-66      print 
-67      # Check value from UNESCO 1983, p. 30 
-68      print "Checking freezept" 
-69      print 
-70      print "S = 40, p = 500 dbar" 
-71      print format1 % "freezept(40, 500)", freezept(40, 500) 
-72      print format2, -2.588567 
-73   
-74      print 
-75      # Check value from UNESCO 1983, p. 49 
-76      print "Checking soundvel" 
-77      print  
-78      print "S = 40, T = 40 °C,  P = 10000 dbar" 
-79      print format1 % "soundvel(40, 40, 10000)", soundvel(40, 40, 10000) 
-80      print format2, 1731.995 
-81   
-82      print 
-83      # Check value from UNESCO 1983, p. 28 
-84      print "Checking depth" 
-85      print 
-86      print "P = 10000 dbar, latitude = 30 degrees" 
-87      print format1 % "depth(10000, 30)", depth(10000, 30) 
-88      print format2, 9712.653 
-89   
-90  # ---------------------------------------------------------------- 
-91   
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Module shapiro_filter

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Functions[hide private]
-
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shapiro1(Finp, - order, - scheme=1)
- This function applies a 1D shapiro filter to input 1D field.		 - source code - -
- -
-   - - - - - - -
shapiro2(Finp, - order, - scheme=1, - napp=1)
- This function applies a 2D shapiro filter to input 2D field.		 - source code - -
- -
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Function Details[hide private]
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- -
- - -
-

shapiro1(Finp, - order, - scheme=1) -

- 		source code  -
- - 
-
-This function applies a 1D shapiro filter to input 1D field.
-(ripped from Hernan G. Arango shapiro1.m)
-
- On Input:
-
-     Finp        Field be filtered (1D array).
-     order       Order of the Shapiro filter (2,4,8,16,...).
-     scheme      Switch indicating the type of boundary scheme to use:
-                     scheme = 1  =>  No change at wall, constant order.
-                     scheme = 2  =>  Smoothing at wall, constant order.
-                     scheme = 3  =>  No change at wall, reduced order.
-                     scheme = 4  =>  Smoothing at wall, reduced order.
-                     scheme = 5  =>  Periodic, constant order.
-
-
-
-
-
-
- -
- -
- - -
-

shapiro2(Finp, - order, - scheme=1, - napp=1) -

- 		source code  -
- - 
-
-This function applies a 2D shapiro filter to input 2D field.
-(ripped from Hernan G. Arango shapiro2.m)
-
- On Input:
-
-     Finp        Field be filtered (2D array).
-     order       Order of the Shapiro filter (2,4,8,16,...).
-     scheme      Switch indicating the type of boundary scheme to use:
-                     scheme = 1  =>  No change at wall, constant order.
-                     scheme = 2  =>  Smoothing at wall, constant order.
-                     scheme = 3  =>  No change at wall, reduced order.
-                     scheme = 4  =>  Smoothing at wall, reduced order.
-                     scheme = 5  =>  Periodic, constant order.
-     napp        Number of Shapiro filter applications (optional). 
-
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Source Code for Module pyroms_toolbox.shapiro_filter

-
-
  1 -def shapiro1(Finp,order,scheme=1): 
-
  2      ''' 
-  3      This function applies a 1D shapiro filter to input 1D field. 
-  4      (ripped from Hernan G. Arango shapiro1.m) 
-  5   
-  6       On Input: 
-  7   
-  8           Finp        Field be filtered (1D array). 
-  9           order       Order of the Shapiro filter (2,4,8,16,...). 
- 10           scheme      Switch indicating the type of boundary scheme to use: 
- 11                           scheme = 1  =>  No change at wall, constant order. 
- 12                           scheme = 2  =>  Smoothing at wall, constant order. 
- 13                           scheme = 3  =>  No change at wall, reduced order. 
- 14                           scheme = 4  =>  Smoothing at wall, reduced order. 
- 15                           scheme = 5  =>  Periodic, constant order. 
- 16      ''' 
- 17   
- 18      fourk=np.array([2.500000e-1,   6.250000e-2,    1.562500e-2,    3.906250e-3, \ 
- 19                      9.765625e-4,   2.44140625e-4,  6.103515625e-5, 1.5258789063e-5, \ 
- 20                      3.814697e-6,   9.536743e-7,    2.384186e-7,    5.960464e-8, \ 
- 21                      1.490116e-8,   3.725290e-9,    9.313226e-10,   2.328306e-10, \ 
- 22                      5.820766e-11,  1.455192e-11,   3.637979e-12,   9.094947e-13]) 
- 23   
- 24   
- 25      Im = Finp.shape[0] 
- 26      order2 = np.int(np.floor(order/2)) 
- 27   
- 28      cor=np.zeros((Im)) 
- 29      Fcor=np.zeros((Im)) 
- 30   
- 31      #Compute filter correction. 
- 32   
- 33      if (scheme == 1): 
- 34          #Scheme 1:  constant order and no change at wall. 
- 35          for n in range(order2): 
- 36              if n != order2: 
- 37                  cor[0] = 2. * (Finp[0] - Finp[1]) 
- 38                  cor[Im-1] = 2. * (Finp[Im-1] - Finp[Im-2]) 
- 39              else: 
- 40                  cor[0] = 0. 
- 41                  cor[Im-1] = 0. 
- 42   
- 43              cor[1:-1] = 2. * Finp[1:-1] - Finp[0:-2] - Finp[2:] 
- 44   
- 45          Fcor= cor * fourk[order2-1] 
- 46   
- 47      elif scheme == 2: 
- 48          #Scheme 2:  constant order, smoothed at edges. 
- 49          for n in range(order2): 
- 50              cor[0] = 2. * (Finp[0] - Finp[1]) 
- 51              cor[Im-1] = 2. * (Finp[Im-1] - Finp[Im-2]) 
- 52              cor[1:-1] = 2. * Finp[1:-1] - Finp[0:-2] - Finp[2:] 
- 53               
- 54          Fcor= cor * fourk[order2-1] 
- 55   
- 56      elif scheme == 3: 
- 57          #Scheme 3:  reduced order and no change at wall. 
- 58          for n in range(order2): 
- 59              Istr = n 
- 60              Iend = Im-k+1 
- 61              if n == 1: 
- 62                  cor[0] = 2. * (Finp[0] - Finp[1]) 
- 63                  cor[Im-1] = 2. * (Finp[Im-1] - Finp[Im-2]) 
- 64                  cor[1:-1] = 2. * Finp[1:-1] - Finp[0:-2] - Finp[2:] 
- 65              else: 
- 66                  cor[Istr:Iend] = 2. * Finp[Istr:Iend] - Finp[Istr-1:Iend-1] - Finp[Istr+1:Iend+1] 
- 67   
- 68              Fcor[Istr] = cor[Istr] * fourk[n] 
- 69              Fcor[Iend] = cor[Iend] * fourk[n] 
- 70   
- 71          Fcor[0] = 0. 
- 72          Fcor[Istr:Iend] = cor[Istr:Iend] * fourk[order2] 
- 73          Fcor[Im] = 0. 
- 74   
- 75      elif scheme == 4: 
- 76          #Scheme 4:  reduced order, smoothed at edges. 
- 77          for n in range(order2): 
- 78              Istr = n 
- 79              Iend = Im-k+1 
- 80              if n == 1: 
- 81                  cor[0] = 2. * (Finp[0] - Finp[1]) 
- 82                  cor[Im-1] = 2. * (Finp[Im-1] - Finp[Im-2]) 
- 83                  cor[1:-1] = 2. * Finp[1:-1] - Finp[0:-2] - Finp[2:] 
- 84              else: 
- 85                  cor[Istr:Iend] = 2. * Finp[Istr:Iend] - Finp[Istr-1:Iend-1] - Finp[Istr+1:Iend+1] 
- 86   
- 87              Fcor[Istr] = cor[Istr] * fourk[n] 
- 88              Fcor[Iend] = cor[Iend] * fourk[n] 
- 89   
- 90          Fcor[Istr:Iend] = cor[Istr:Iend] * fourk[order2] 
- 91   
- 92      elif scheme == 5: 
- 93          #Scheme 5:  constant order, periodic. 
- 94          for n in range(order2): 
- 95              cor[0] = Finp[Im-2] 
- 96              cor[Im-1] = Finp[1] 
- 97              cor[1:-1] = 2. * Finp[1:-1] - Finp[0:-2] - Finp[2:] 
- 98               
- 99          Fcor= cor * fourk[order2-1] 
-100   
-101      #Apply correction. 
-102      Fout = Finp - Fcor 
-103   
-104      return Fout 
-
105   
-106   
-107   
-
108 -def shapiro2(Finp,order,scheme=1,napp=1): 
-
109      ''' 
-110      This function applies a 2D shapiro filter to input 2D field. 
-111      (ripped from Hernan G. Arango shapiro2.m) 
-112   
-113       On Input: 
-114   
-115           Finp        Field be filtered (2D array). 
-116           order       Order of the Shapiro filter (2,4,8,16,...). 
-117           scheme      Switch indicating the type of boundary scheme to use: 
-118                           scheme = 1  =>  No change at wall, constant order. 
-119                           scheme = 2  =>  Smoothing at wall, constant order. 
-120                           scheme = 3  =>  No change at wall, reduced order. 
-121                           scheme = 4  =>  Smoothing at wall, reduced order. 
-122                           scheme = 5  =>  Periodic, constant order. 
-123           napp        Number of Shapiro filter applications (optional).  
-124      ''' 
-125   
-126      Im, Jm = Finp.shape 
-127   
-128      F=Finp.copy() 
-129      Fout = np.zeros((Im, Jm)) 
-130   
-131      for n in range(napp): 
-132     
-133          #Filter all rows. 
-134          for j in range(Jm): 
-135              Fraw = np.squeeze(F[:,j]) 
-136              Fraw = Fraw.T 
-137              Fwrk = shapiro1(Fraw,order,scheme) 
-138              Fout[:,j] = Fwrk.T 
-139   
-140          #Filter all columns. 
-141          for i in range(Im): 
-142              Fraw = np.squeeze(Fout[i,:]) 
-143              Fwrk = shapiro1(Fraw,order,scheme) 
-144              Fout[i,:] = Fwrk 
-145     
-146      return Fout 
-
147   
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Module sview'

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Functions[hide private]
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sview(var, - tindex, - sindex, - grid, - filename=None, - cmin=None, - cmax=None, - clev=None, - fill=False, - contour=False, - d=4, - range=None, - fts=None, - title=None, - clb=True, - pal=None, - proj='merc', - fill_land=False, - outfile=None)
- map = sview(var, tindex, sindex, grid, {optional switch})		 - source code - -
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Function Details[hide private]
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sview(var, - tindex, - sindex, - grid, - filename=None, - cmin=None, - cmax=None, - clev=None, - fill=False, - contour=False, - d=4, - range=None, - fts=None, - title=None, - clb=True, - pal=None, - proj='merc', - fill_land=False, - outfile=None) -

- 		source code  -
- -

map = sview(var, tindex, sindex, grid, {optional switch})

-

optional switch:

-
    -
  • - filename if defined, load the variable from file -
    • -
  • - cmin set color minimum limit -
    • -
  • - cmax set color maximum limit -
    • -
  • - clev set the number of color step -
    • -
  • - fill use contourf instead of pcolor -
    • -
  • - contour overlay contour (request fill=True) -
    • -
  • - d contour density (default d=4) -
    • -
  • - range set axis limit -
    • -
  • - fts set font size (default: 12) -
    • -
  • - title add title to the plot -
    • -
  • - clb add colorbar (defaul: True) -
    • -
  • - pal set color map (default: cm.jet) -
    • -
  • - proj set projection type (default: merc) -
    • -
  • - fill_land fill land masked area with gray (defaul: True) -
    • -
  • - outfile if defined, write figure to file -
    • -
-

plot a constante-sigma slice of variable var. If filename is provided, - var must be a string and the variable will be load from the file. grid - can be a grid object or a gridid. In the later case, the grid object - correponding to the provided gridid will be loaded. If proj is not None, - return a Basemap object to be used with quiver for example.

-
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Source Code for Module pyroms_toolbox.sview'

-
-  1  import numpy as np 
-  2  import matplotlib.pyplot as plt 
-  3  from  matplotlib import cm, colors 
-  4  from mpl_toolkits.basemap import Basemap 
-  5  import pyroms 
-  6  import pyroms_toolbox 
-  7   
-  8   
-
  9 -def sview(var, tindex, sindex, grid, filename=None, \ 
- 10            cmin=None, cmax=None, clev=None, \ 
- 11            fill=False, contour=False, d=4, range=None, fts=None, \ 
- 12            title=None, clb=True, pal=None, proj='merc', \ 
- 13            fill_land=False, outfile=None): 
-
 14      """ 
- 15      map = sview(var, tindex, sindex, grid, {optional switch}) 
- 16   
- 17      optional switch: 
- 18        - filename         if defined, load the variable from file 
- 19        - cmin             set color minimum limit 
- 20        - cmax             set color maximum limit 
- 21        - clev             set the number of color step 
- 22        - fill             use contourf instead of pcolor 
- 23        - contour          overlay contour (request fill=True) 
- 24        - d                contour density (default d=4)  
- 25        - range            set axis limit 
- 26        - fts              set font size (default: 12) 
- 27        - title            add title to the plot 
- 28        - clb              add colorbar (defaul: True) 
- 29        - pal              set color map (default: cm.jet) 
- 30        - proj             set projection type (default: merc) 
- 31        - fill_land        fill land masked area with gray (defaul: True) 
- 32        - outfile          if defined, write figure to file 
- 33   
- 34      plot a constante-sigma slice of variable var. If filename is provided, 
- 35      var must be a string and the variable will be load from the file. 
- 36      grid can be a grid object or a gridid. In the later case, the grid 
- 37      object correponding to the provided gridid will be loaded. 
- 38      If proj is not None, return a Basemap object to be used with quiver  
- 39      for example.  
- 40      """ 
- 41   
- 42      # get grid 
- 43      if type(grid).__name__ == 'ROMS_Grid': 
- 44          grd = grid 
- 45      else: 
- 46          grd = pyroms.grid.get_ROMS_grid(grid) 
- 47   
- 48   
- 49      # get variable 
- 50      if filename == None: 
- 51          var = var 
- 52      else: 
- 53          data = pyroms.io.Dataset(filename) 
- 54   
- 55          var = data.variables[var] 
- 56   
- 57      Np, Mp, Lp = grd.vgrid.z_r[0,:].shape 
- 58   
- 59      if tindex is not -1: 
- 60          assert len(var.shape) == 4, 'var must be 4D (time plus space).' 
- 61          K, N, M, L = var.shape 
- 62      else: 
- 63          assert len(var.shape) == 3, 'var must be 3D (no time dependency).' 
- 64          N, M, L = var.shape 
- 65   
- 66      # determine where on the C-grid these variable lies 
- 67      if N == Np and M == Mp and L == Lp: 
- 68          Cpos='rho' 
- 69          mask = grd.hgrid.mask_rho 
- 70   
- 71      if N == Np and M == Mp and L == Lp-1: 
- 72          Cpos='u' 
- 73          mask = grd.hgrid.mask_u 
- 74   
- 75      if N == Np and M == Mp-1 and L == Lp: 
- 76          Cpos='v' 
- 77          mask = grd.hgrid.mask_v 
- 78   
- 79      # get constante-s slice 
- 80      if tindex == -1: 
- 81          var = var[:,:,:] 
- 82      else: 
- 83          var = var[tindex,:,:,:] 
- 84   
- 85      if fill == True: 
- 86          sslice, lon, lat = pyroms.tools.sslice(var, sindex, grd, \ 
- 87                                    Cpos=Cpos) 
- 88      else: 
- 89          sslice, lon, lat = pyroms.tools.sslice(var, sindex, grd, \ 
- 90                                    Cpos=Cpos, vert=True) 
- 91   
- 92      # plot 
- 93      if cmin is None: 
- 94          cmin = sslice.min() 
- 95      else: 
- 96          cmin = float(cmin) 
- 97   
- 98      if cmax is None: 
- 99          cmax = sslice.max() 
-100      else: 
-101          cmax = float(cmax) 
-102   
-103      if clev is None: 
-104          clev = 100. 
-105      else: 
-106          clev = float(clev) 
-107   
-108      dc = (cmax - cmin)/clev ; vc = np.arange(cmin,cmax+dc,dc) 
-109   
-110      if pal is None: 
-111          pal = cm.jet 
-112      else: 
-113          pal = pal 
-114   
-115      if fts is None: 
-116          fts = 12 
-117      else: 
-118          fts = fts 
-119   
-120      #pal.set_over('w', 1.0) 
-121      #pal.set_under('w', 1.0) 
-122      #pal.set_bad('w', 1.0) 
-123   
-124      pal_norm = colors.BoundaryNorm(vc,ncolors=256, clip = False) 
-125   
-126      if range is None: 
-127          lon_min = lon.min() 
-128          lon_max = lon.max() 
-129          lon_0 = (lon_min + lon_max) / 2. 
-130          lat_min = lat.min() 
-131          lat_max = lat.max()      
-132          lat_0 = (lat_min + lat_max) / 2. 
-133      else: 
-134          lon_min = range[0] 
-135          lon_max = range[1] 
-136          lon_0 = (lon_min + lon_max) / 2. 
-137          lat_min = range[2] 
-138          lat_max = range[3] 
-139          lat_0 = (lat_min + lat_max) / 2. 
-140   
-141      # clear figure 
-142      #plt.clf() 
-143   
-144      if proj is not None: 
-145          map = Basemap(projection=proj, llcrnrlon=lon_min, llcrnrlat=lat_min, \ 
-146                urcrnrlon=lon_max, urcrnrlat=lat_max, lat_0=lat_0, lon_0=lon_0, \ 
-147                   resolution='h', area_thresh=5.) 
-148          x, y = map(lon,lat) 
-149       
-150      if fill_land is True and proj is not None: 
-151          # fill land and draw coastlines 
-152          map.drawcoastlines() 
-153          map.fillcontinents(color='grey') 
-154      else: 
-155          if proj is not None:  
-156              Basemap.pcolor(map, x, y, mask, vmin=-2, cmap=cm.gray) 
-157              pyroms_toolbox.plot_coast_line(grd, map) 
-158          else:  
-159              plt.pcolor(lon, lat, mask, vmin=-2, cmap=cm.gray) 
-160              pyroms_toolbox.plot_coast_line(grd) 
-161       
-162      if fill is True: 
-163          if proj is not None:  
-164              cf = Basemap.contourf(map, x, y, sslice, vc, cmap = pal, \ 
-165                                    norm = pal_norm) 
-166          else:  
-167              cf = plt.contourf(lon, lat, sslice, vc, cmap = pal, \ 
-168                                norm = pal_norm) 
-169      else: 
-170          if proj is not None:  
-171              cf = Basemap.pcolor(map, x, y, sslice, cmap = pal, norm = pal_norm) 
-172          else:  
-173              cf = plt.pcolor(lon, lat, sslice, cmap = pal, norm = pal_norm) 
-174   
-175      if clb is True: 
-176          clb = plt.colorbar(cf, fraction=0.075,format='%.2f') 
-177          for t in clb.ax.get_yticklabels(): 
-178              t.set_fontsize(fts) 
-179   
-180      if contour is True: 
-181          if fill is not True: 
-182              raise Warning, 'Please run again with fill=True to overlay contour.' 
-183          else: 
-184              if proj is not None: 
-185                  Basemap.contour(map, x, y, sslice, vc[::d], colors='k', linewidths=0.5, linestyles='solid') 
-186              else:  
-187                  plt.contour(lon, lat, sslice, vc[::d], colors='k', linewidths=0.5, linestyles='solid') 
-188   
-189      if proj is None and range is not None: 
-190          plt.axis(range)  
-191   
-192   
-193      if title is not None: 
-194              plt.title(title, fontsize=fts+4) 
-195   
-196      if proj is not None: 
-197          map.drawmeridians(np.arange(lon_min,lon_max, (lon_max-lon_min)/5.), \ 
-198                            labels=[0,0,0,1], fmt='%.1f') 
-199          map.drawparallels(np.arange(lat_min,lat_max, (lat_max-lat_min)/5.), \ 
-200                            labels=[1,0,0,0], fmt='%.1f') 
-201   
-202      if outfile is not None: 
-203          if outfile.find('.png') != -1 or outfile.find('.svg') != -1 or \ 
-204             outfile.find('.eps') != -1: 
-205              print 'Write figure to file', outfile 
-206              plt.savefig(outfile, dpi=200, facecolor='w', edgecolor='w', \ 
-207                          orientation='portrait') 
-208          else: 
-209              print 'Unrecognized file extension. Please use .png, .svg or .eps file extension.'    
-210   
-211   
-212      if proj is None: 
-213          return 
-214      else: 
-215          return map 
-
216   
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Module transectview'

source code

- - - - - - - - - -
- - - - - -
Functions[hide private]
-
-   - - - - - - -
transectview(var, - tindex, - istart, - iend, - jstart, - jend, - gridid, - filename=None, - spval=1e+37, - cmin=None, - cmax=None, - clev=None, - fill=False, - contour=False, - d=4, - jrange=None, - hrange=None, - fts=None, - title=None, - map=False, - pal=None, - clb=True, - xaxis='lon', - outfile=None)
- transectview(var, tindex, istart, iend, jstart, jend, gridid, - {optional switch})		 - source code - -
- -
- - - - - - -
- - - - - -
Function Details[hide private]
-
- -
- -
- - -
-

transectview(var, - tindex, - istart, - iend, - jstart, - jend, - gridid, - filename=None, - spval=1e+37, - cmin=None, - cmax=None, - clev=None, - fill=False, - contour=False, - d=4, - jrange=None, - hrange=None, - fts=None, - title=None, - map=False, - pal=None, - clb=True, - xaxis='lon', - outfile=None) -

- 		source code  -
- - 
-
-transectview(var, tindex, istart, iend, jstart, jend, gridid, 
-             {optional switch})
-
-optional switch:
-  - filename         if defined, load the variable from file
-  - spval            specify spval
-  - cmin             set color minimum limit
-  - cmax             set color maximum limit
-  - clev             set the number of color step
-  - fill             use contourf instead of pcolor
-  - contour          overlay contour (request fill=True)
-  - d                contour density (default d=4) 
-  - jrange           j range
-  - hrange           h range
-  - fts              set font size (default: 12)
-  - title            add title to the plot
-  - map              if True, draw a map showing transect location
-  - pal              set color map (default: cm.jet)
-  - clb              add colorbar (defaul: True)
-  - xaxis            use lon or lat for x axis
-  - outfile          if defined, write figure to file
-
-plot vertical transect between the points P1=(istart, jstart)
-and P2=(iend, jend) from 3D variable var. If filename is provided,
-var must be a string and the variable will be load from the file.
-grid can be a grid object or a gridid. In the later case, the grid
-object correponding to the provided gridid will be loaded.
-
-
-
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Source Code for Module pyroms_toolbox.transectview'

-
-  1  import numpy as np 
-  2  import matplotlib.pyplot as plt 
-  3  from  matplotlib import cm, colors 
-  4  from mpl_toolkits.basemap import Basemap 
-  5  import pyroms 
-  6   
-  7   
-
  8 -def transectview(var, tindex, istart, iend, jstart, jend, gridid, \ 
-  9            filename=None, spval=1e37, cmin=None, cmax=None, clev=None, \ 
- 10            fill=False, contour=False, d=4, jrange=None, hrange=None,\ 
- 11            fts=None, title=None, map=False, \ 
- 12            pal=None, clb=True, xaxis='lon', outfile=None): 
-
 13      """ 
- 14      transectview(var, tindex, istart, iend, jstart, jend, gridid,  
- 15                   {optional switch}) 
- 16   
- 17      optional switch: 
- 18        - filename         if defined, load the variable from file 
- 19        - spval            specify spval 
- 20        - cmin             set color minimum limit 
- 21        - cmax             set color maximum limit 
- 22        - clev             set the number of color step 
- 23        - fill             use contourf instead of pcolor 
- 24        - contour          overlay contour (request fill=True) 
- 25        - d                contour density (default d=4)  
- 26        - jrange           j range 
- 27        - hrange           h range 
- 28        - fts              set font size (default: 12) 
- 29        - title            add title to the plot 
- 30        - map              if True, draw a map showing transect location 
- 31        - pal              set color map (default: cm.jet) 
- 32        - clb              add colorbar (defaul: True) 
- 33        - xaxis            use lon or lat for x axis 
- 34        - outfile          if defined, write figure to file 
- 35   
- 36      plot vertical transect between the points P1=(istart, jstart) 
- 37      and P2=(iend, jend) from 3D variable var. If filename is provided, 
- 38      var must be a string and the variable will be load from the file. 
- 39      grid can be a grid object or a gridid. In the later case, the grid 
- 40      object correponding to the provided gridid will be loaded. 
- 41      """ 
- 42   
- 43      # get grid 
- 44      if type(gridid).__name__ == 'ROMS_Grid': 
- 45          grd = gridid 
- 46      else: 
- 47          grd = pyroms.grid.get_ROMS_grid(gridid) 
- 48   
- 49      # get variable 
- 50      if filename == None: 
- 51          var = var 
- 52      else: 
- 53          data = pyroms.io.Dataset(filename) 
- 54   
- 55          var = data.variables[var] 
- 56   
- 57      Np, Mp, Lp = grd.vgrid.z_r[0,:].shape 
- 58   
- 59      if tindex is not -1: 
- 60          assert len(var.shape) == 4, 'var must be 4D (time plus space).' 
- 61          K, N, M, L = var.shape 
- 62      else: 
- 63          assert len(var.shape) == 3, 'var must be 3D (no time dependency).' 
- 64          N, M, L = var.shape 
- 65   
- 66      # determine where on the C-grid these variable lies 
- 67      if N == Np and M == Mp and L == Lp: 
- 68          Cpos='rho' 
- 69          lon = grd.hgrid.lon_vert 
- 70          lat = grd.hgrid.lat_vert 
- 71          mask = grd.hgrid.mask_rho 
- 72   
- 73      if N == Np and M == Mp and L == Lp-1: 
- 74          Cpos='u' 
- 75          lon = 0.5 * (grd.hgrid.lon_vert[:,:-1] + grd.hgrid.lon_vert[:,1:]) 
- 76          lat = 0.5 * (grd.hgrid.lat_vert[:,:-1] + grd.hgrid.lat_vert[:,1:]) 
- 77          mask = grd.hgrid.mask_u 
- 78   
- 79      if N == Np and M == Mp-1 and L == Lp: 
- 80          Cpos='v' 
- 81          lon = 0.5 * (grd.hgrid.lon_vert[:-1,:] + grd.hgrid.lon_vert[1:,:]) 
- 82          lat = 0.5 * (grd.hgrid.lat_vert[:-1,:] + grd.hgrid.lat_vert[1:,:]) 
- 83          mask = grd.hgrid.mask_v 
- 84   
- 85      # get transect 
- 86      if tindex == -1: 
- 87          var = var[:,:,:] 
- 88      else: 
- 89          var = var[tindex,:,:,:] 
- 90   
- 91      if fill == True: 
- 92          transect, zt, lont, latt, = pyroms.tools.transect(var, istart, iend, \ 
- 93                                       jstart, jend, grd, Cpos, spval=spval) 
- 94      else: 
- 95          transect, zt, lont, latt, = pyroms.tools.transect(var, istart, iend, \ 
- 96                                       jstart, jend, grd, Cpos, vert=True, spval=spval) 
- 97   
- 98      if xaxis == 'lon': 
- 99          xt = lont 
-100      elif xaxis == 'lat': 
-101          xt = latt 
-102   
-103      # plot 
-104      if cmin is None: 
-105          cmin = transect.min() 
-106      else: 
-107          cmin = float(cmin) 
-108   
-109      if cmax is None: 
-110          cmax = transect.max() 
-111      else: 
-112          cmax = float(cmax) 
-113   
-114      if clev is None: 
-115          clev = 100. 
-116      else: 
-117          clev = float(clev) 
-118   
-119      dc = (cmax - cmin)/clev ; vc = np.arange(cmin,cmax+dc,dc) 
-120   
-121      if pal is None: 
-122          pal = cm.jet 
-123      else: 
-124          pal = pal 
-125   
-126      if fts is None: 
-127          fts = 12 
-128      else: 
-129          fts = fts 
-130   
-131      #pal.set_over('w', 1.0) 
-132      #pal.set_under('w', 1.0) 
-133      #pal.set_bad('w', 1.0) 
-134   
-135      pal_norm = colors.BoundaryNorm(vc,ncolors=256, clip = False) 
-136       
-137      # clear figure 
-138      #plt.clf() 
-139   
-140      if map is True: 
-141          # set axes for the main plot in order to keep space for the map        
-142          if fts < 12: 
-143              ax=None 
-144          else: 
-145              ax = plt.axes([0.15, 0.08, 0.8, 0.65])        
-146      else:        
-147          if fts < 12: 
-148              ax=None 
-149          else: 
-150              ax=plt.axes([0.15, 0.1, 0.8, 0.8]) 
-151   
-152   
-153      if fill is True: 
-154          cf = plt.contourf(xt, zt, transect, vc, cmap = pal, norm = pal_norm, axes=ax) 
-155      else: 
-156          cf = plt.pcolor(xt, zt, transect, cmap = pal, norm = pal_norm, axes=ax) 
-157   
-158      if clb is True: 
-159          clb = plt.colorbar(cf, fraction=0.075,format='%.2f') 
-160          for t in clb.ax.get_yticklabels(): 
-161              t.set_fontsize(fts) 
-162   
-163      if contour is True: 
-164          if fill is not True: 
-165              raise Warning, 'Please run again with fill=True for overlay contour.' 
-166          else: 
-167              plt.contour(xt, zt, transect, vc[::d], colors='k', linewidths=0.5, linestyles='solid', axes=ax) 
-168   
-169   
-170      if jrange is not None: 
-171          plt.xlim(jrange) 
-172   
-173      if hrange is not None: 
-174          plt.ylim(hrange) 
-175   
-176      if title is not None: 
-177          if map is True: 
-178              # move the title on the right 
-179              xmin, xmax = ax.get_xlim() 
-180              ymin, ymax = ax.get_ylim() 
-181              xt = xmin - (xmax-xmin)/9. 
-182              yt = ymax + (ymax-ymin)/7. 
-183              plt.text(xt, yt, title, fontsize=fts+4) 
-184          else: 
-185              plt.title(title, fontsize=fts+4) 
-186   
-187      plt.xlabel('Latitude', fontsize=fts) 
-188      plt.ylabel('Depth', fontsize=fts) 
-189   
-190      if map is True: 
-191          # draw a map with constant-i slice location 
-192          ax_map = plt.axes([0.4, 0.76, 0.2, 0.23]) 
-193          varm = np.ma.masked_where(mask[:,:] == 0, var[var.shape[0]-1,:,:])         
-194          lon_min = lon.min() 
-195          lon_max = lon.max() 
-196          lon_0 = (lon_min + lon_max) / 2. 
-197          lat_min = lat.min() 
-198          lat_max = lat.max()      
-199          lat_0 = (lat_min + lat_max) / 2. 
-200          map = Basemap(projection='merc', llcrnrlon=lon_min, llcrnrlat=lat_min, \ 
-201                   urcrnrlon=lon_max, urcrnrlat=lat_max, lat_0=lat_0, lon_0=lon_0, \ 
-202                   resolution='i', area_thresh=10.) 
-203          x, y = map(lon,lat) 
-204          xt, yt = map(lont[0,:],latt[0,:]) 
-205          # fill land and draw coastlines 
-206          map.drawcoastlines() 
-207          map.fillcontinents(color='grey') 
-208          #map.drawmapboundary() 
-209          Basemap.pcolor(map, x, y, varm, axes=ax_map) 
-210          Basemap.plot(map, xt, yt, 'k-', linewidth=3, axes=ax_map) 
-211   
-212   
-213      if outfile is not None: 
-214          if outfile.find('.png') != -1 or outfile.find('.svg') != -1 or outfile.find('.eps') != -1: 
-215              print 'Write figure to file', outfile 
-216              plt.savefig(outfile, dpi=200, facecolor='w', edgecolor='w', orientation='portrait') 
-217          else: 
-218              print 'Unrecognized file extension. Please use .png, .svg or .eps file extension.'    
-219   
-220   
-221      return 
-
222   
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Module twoDview'

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Functions[hide private]
-
-   - - - - - - -
twoDview(var, - tindex, - grid, - filename=None, - cmin=None, - cmax=None, - clev=None, - fill=False, - contour=False, - d=4, - range=None, - fts=None, - title=None, - clb=True, - pal=None, - proj='merc', - fill_land=False, - outfile=None)
- map = twoDview(var, tindex, grid, {optional switch})		 - source code - -
- -
- - - - - - -
- - - - - -
Function Details[hide private]
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- -
- -
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twoDview(var, - tindex, - grid, - filename=None, - cmin=None, - cmax=None, - clev=None, - fill=False, - contour=False, - d=4, - range=None, - fts=None, - title=None, - clb=True, - pal=None, - proj='merc', - fill_land=False, - outfile=None) -

- 		source code  -
- -

map = twoDview(var, tindex, grid, {optional switch})

-

optional switch:

-
    -
  • - filename if defined, load the variable from file -
    • -
  • - cmin set color minimum limit -
    • -
  • - cmax set color maximum limit -
    • -
  • - clev set the number of color step -
    • -
  • - fill use contourf instead of pcolor -
    • -
  • - contour overlay contour (request fill=True) -
    • -
  • - d contour density (default d=4) -
    • -
  • - range set axis limit -
    • -
  • - fts set font size (default: 12) -
    • -
  • - title add title to the plot -
    • -
  • - clb add colorbar (defaul: True) -
    • -
  • - pal set color map (default: cm.jet) -
    • -
  • - proj set projection type (default: merc) -
    • -
  • - fill_land fill land masked area with gray (defaul: True) -
    • -
  • - outfile if defined, write figure to file -
    • -
-

plot 2-dimensions variable var. If filename is provided, var must be a - string and the variable will be load from the file. grid can be a grid - object or a gridid. In the later case, the grid object correponding to - the provided gridid will be loaded. If proj is not None, return a Basemap - object to be used with quiver for example.

-
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Source Code for Module pyroms_toolbox.twoDview'

-
-  1  import numpy as np 
-  2  import matplotlib.pyplot as plt 
-  3  from  matplotlib import cm, colors 
-  4  from mpl_toolkits.basemap import Basemap 
-  5  import pyroms 
-  6  import pyroms_toolbox 
-  7   
-  8   
-
  9 -def twoDview(var, tindex, grid, filename=None, \ 
- 10            cmin=None, cmax=None, clev=None, fill=False, \ 
- 11            contour=False, d=4, range=None, fts=None, \ 
- 12            title=None, clb=True, pal=None, proj='merc', \ 
- 13            fill_land=False, outfile=None): 
-
 14      """ 
- 15      map = twoDview(var, tindex, grid, {optional switch}) 
- 16   
- 17      optional switch: 
- 18        - filename         if defined, load the variable from file 
- 19        - cmin             set color minimum limit 
- 20        - cmax             set color maximum limit 
- 21        - clev             set the number of color step 
- 22        - fill             use contourf instead of pcolor 
- 23        - contour          overlay contour (request fill=True) 
- 24        - d                contour density (default d=4)  
- 25        - range            set axis limit 
- 26        - fts              set font size (default: 12) 
- 27        - title            add title to the plot 
- 28        - clb              add colorbar (defaul: True) 
- 29        - pal              set color map (default: cm.jet) 
- 30        - proj             set projection type (default: merc) 
- 31        - fill_land        fill land masked area with gray (defaul: True) 
- 32        - outfile          if defined, write figure to file 
- 33   
- 34      plot 2-dimensions variable var. If filename is provided, 
- 35      var must be a string and the variable will be load from the file. 
- 36      grid can be a grid object or a gridid. In the later case, the grid 
- 37      object correponding to the provided gridid will be loaded. 
- 38      If proj is not None, return a Basemap object to be used with quiver  
- 39      for example.  
- 40      """ 
- 41   
- 42      # get grid 
- 43      if type(grid).__name__ == 'ROMS_Grid': 
- 44          grd = grid 
- 45      else: 
- 46          grd = pyroms.grid.get_ROMS_grid(grid) 
- 47   
- 48   
- 49      # get variable 
- 50      if filename == None: 
- 51          var = var 
- 52      else: 
- 53          data = pyroms.io.Dataset(filename) 
- 54   
- 55          var = data.variables[var] 
- 56   
- 57   
- 58      Np, Mp, Lp = grd.vgrid.z_r[0,:].shape 
- 59   
- 60      if tindex is not -1: 
- 61          assert len(var.shape) == 3, 'var must be 3D (time plus space).' 
- 62          K, M, L = var.shape 
- 63      else: 
- 64          assert len(var.shape) == 2, 'var must be 2D (no time dependency).' 
- 65          M, L = var.shape 
- 66   
- 67      # determine where on the C-grid these variable lies 
- 68      if M == Mp and L == Lp: 
- 69          Cpos='rho' 
- 70          if fill == True: 
- 71              lon = grd.hgrid.lon_rho 
- 72              lat = grd.hgrid.lat_rho 
- 73          else: 
- 74              lon = grd.hgrid.lon_vert 
- 75              lat = grd.hgrid.lat_vert 
- 76          mask = grd.hgrid.mask_rho 
- 77   
- 78      if M == Mp and L == Lp-1: 
- 79          Cpos='u' 
- 80          if fill == True: 
- 81              lon = grd.hgrid.lon_u 
- 82              lat = grd.hgrid.lat_u 
- 83          else: 
- 84              lon = 0.5 * (grd.hgrid.lon_vert[:,:-1] + grd.hgrid.lon_vert[:,1:]) 
- 85              lat = 0.5 * (grd.hgrid.lat_vert[:,:-1] + grd.hgrid.lat_vert[:,1:]) 
- 86          mask = grd.hgrid.mask_u 
- 87   
- 88      if M == Mp-1 and L == Lp: 
- 89          Cpos='v' 
- 90          if fill == True: 
- 91              lon = grd.hgrid.lon_v 
- 92              lat = grd.hgrid.lat_v 
- 93          else: 
- 94              lon = 0.5 * (grd.hgrid.lon_vert[:-1,:] + grd.hgrid.lon_vert[1:,:]) 
- 95              lat = 0.5 * (grd.hgrid.lat_vert[:-1,:] + grd.hgrid.lat_vert[1:,:]) 
- 96          mask = grd.hgrid.mask_v 
- 97   
- 98      # get 2D var 
- 99      if tindex == -1: 
-100          var = var[:,:] 
-101      else: 
-102          var = var[tindex,:,:] 
-103   
-104      # mask 
-105      var = np.ma.masked_where(mask == 0, var) 
-106   
-107      # plot 
-108      if cmin is None: 
-109          cmin = var.min() 
-110      else: 
-111          cmin = float(cmin) 
-112   
-113      if cmax is None: 
-114          cmax = var.max() 
-115      else: 
-116          cmax = float(cmax) 
-117   
-118      if clev is None: 
-119          clev = 100. 
-120      else: 
-121          clev = float(clev) 
-122   
-123      dc = (cmax - cmin)/clev ; vc = np.arange(cmin,cmax+dc,dc) 
-124   
-125      if pal is None: 
-126          pal = cm.jet 
-127      else: 
-128          pal = pal 
-129   
-130      if fts is None: 
-131          fts = 12 
-132      else: 
-133          fts = fts 
-134   
-135      #pal.set_over('w', 1.0) 
-136      #pal.set_under('w', 1.0) 
-137      #pal.set_bad('w', 1.0) 
-138   
-139      pal_norm = colors.BoundaryNorm(vc,ncolors=256, clip = False) 
-140   
-141      if range is None: 
-142          lon_min = lon.min() 
-143          lon_max = lon.max() 
-144          lon_0 = (lon_min + lon_max) / 2. 
-145          lat_min = lat.min() 
-146          lat_max = lat.max()      
-147          lat_0 = (lat_min + lat_max) / 2. 
-148      else: 
-149          lon_min = range[0] 
-150          lon_max = range[1] 
-151          lon_0 = (lon_min + lon_max) / 2. 
-152          lat_min = range[2] 
-153          lat_max = range[3] 
-154          lat_0 = (lat_min + lat_max) / 2. 
-155   
-156      # clear figure 
-157      #plt.clf() 
-158   
-159      if proj is not None: 
-160          map = Basemap(projection=proj, llcrnrlon=lon_min, llcrnrlat=lat_min, \ 
-161                urcrnrlon=lon_max, urcrnrlat=lat_max, lat_0=lat_0, lon_0=lon_0, \ 
-162                   resolution='h', area_thresh=5.) 
-163          x, y = map(lon,lat) 
-164       
-165      if fill_land is True and proj is not None: 
-166          # fill land and draw coastlines 
-167          map.drawcoastlines() 
-168          map.fillcontinents(color='grey') 
-169      else: 
-170          if proj is not None:  
-171              Basemap.pcolor(map, x, y, mask, vmin=-2, cmap=cm.gray) 
-172              pyroms_toolbox.plot_coast_line(grd, map) 
-173          else:  
-174              plt.pcolor(lon, lat, mask, vmin=-2, cmap=cm.gray) 
-175              pyroms_toolbox.plot_coast_line(grd) 
-176       
-177      if fill is True: 
-178          if proj is not None:  
-179              cf = Basemap.contourf(map, x, y, var, vc, cmap = pal, \ 
-180                                    norm = pal_norm) 
-181          else:  
-182              cf = plt.contourf(lon, lat, var, vc, cmap = pal, \ 
-183                                norm = pal_norm) 
-184      else: 
-185          if proj is not None:  
-186              cf = Basemap.pcolor(map, x, y, var, cmap = pal, norm = pal_norm) 
-187          else:  
-188              cf = plt.pcolor(lon, lat, var, cmap = pal, norm = pal_norm) 
-189   
-190      if clb is True: 
-191          clb = plt.colorbar(cf, fraction=0.075,format='%.2f') 
-192          for t in clb.ax.get_yticklabels(): 
-193              t.set_fontsize(fts) 
-194   
-195      if contour is True: 
-196          if fill is not True: 
-197              raise Warning, 'Please run again with fill=True to overlay contour.' 
-198          else: 
-199              if proj is not None: 
-200                  Basemap.contour(map, x, y, var, vc[::d], colors='k', linewidths=0.5, linestyles='solid') 
-201              else:  
-202                  plt.contour(lon, lat, var, vc[::d], colors='k', linewidths=0.5, linestyles='solid') 
-203   
-204      if proj is None and range is not None: 
-205          plt.axis(range)  
-206   
-207   
-208      if title is not None: 
-209              plt.title(title, fontsize=fts+4) 
-210   
-211      if proj is not None: 
-212          map.drawmeridians(np.arange(lon_min,lon_max, (lon_max-lon_min)/5.), \ 
-213                            labels=[0,0,0,1], fmt='%.1f') 
-214          map.drawparallels(np.arange(lat_min,lat_max, (lat_max-lat_min)/5.), \ 
-215                            labels=[1,0,0,0], fmt='%.1f') 
-216   
-217      if outfile is not None: 
-218          if outfile.find('.png') != -1 or outfile.find('.svg') != -1 or \ 
-219             outfile.find('.eps') != -1: 
-220              print 'Write figure to file', outfile 
-221              plt.savefig(outfile, dpi=200, facecolor='w', edgecolor='w', \ 
-222                          orientation='portrait') 
-223          else: 
-224              print 'Unrecognized file extension. Please use .png, .svg or .eps file extension.'    
-225   
-226   
-227      if proj is None: 
-228          return 
-229      else: 
-230          return map 
-
231   
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Module zview'

source code

- - - - - - - - - -
- - - - - -
Functions[hide private]
-
-   - - - - - - -
zview(var, - tindex, - depth, - grid, - filename=None, - cmin=None, - cmax=None, - clev=None, - clb_format='%.2f', - fill=False, - contour=False, - d=4, - range=None, - fts=None, - title=None, - clb=True, - pal=None, - proj='merc', - fill_land=False, - outfile=None)
- map = zview(var, tindex, depth, grid, {optional switch})		 - source code - -
- -
- - - - - - -
- - - - - -
Function Details[hide private]
-
- -
- -
- - -
-

zview(var, - tindex, - depth, - grid, - filename=None, - cmin=None, - cmax=None, - clev=None, - clb_format='%.2f', - fill=False, - contour=False, - d=4, - range=None, - fts=None, - title=None, - clb=True, - pal=None, - proj='merc', - fill_land=False, - outfile=None) -

- 		source code  -
- -

map = zview(var, tindex, depth, grid, {optional switch})

-

optional switch:

-
    -
  • - filename if defined, load the variable from file -
    • -
  • - cmin set color minimum limit -
    • -
  • - cmax set color maximum limit -
    • -
  • - clev set the number of color step -
    • -
  • - fill use contourf instead of pcolor -
    • -
  • - contour overlay contour (request fill=True) -
    • -
  • - range set axis limit -
    • -
  • - fts set font size (default: 12) -
    • -
  • - title add title to the plot -
    • -
  • - clb add colorbar (defaul: True) -
    • -
  • - pal set color map (default: cm.jet) -
    • -
  • - proj set projection type (default: merc) -
    • -
  • - fill_land fill land masked area with gray (defaul: True) -
    • -
  • - outfile if defined, write figure to file -
    • -
-

plot a constante-z slice of variable var. If filename is provided, var - must be a string and the variable will be load from the file. grid can be - a grid object or a gridid. In the later case, the grid object - correponding to the provided gridid will be loaded. If proj is not None, - return a Basemap object to be used with quiver for example.

-
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Source Code for Module pyroms_toolbox.zview'

-
-  1  import numpy as np 
-  2  import matplotlib.pyplot as plt 
-  3  from  matplotlib import cm, colors 
-  4  from mpl_toolkits.basemap import Basemap 
-  5  import pyroms 
-  6  import pyroms_toolbox 
-  7   
-  8   
-
  9 -def zview(var, tindex, depth, grid, filename=None, \ 
- 10            cmin=None, cmax=None, clev=None, clb_format='%.2f', \ 
- 11            fill=False, contour=False, d=4, range=None, fts=None, \ 
- 12            title=None, clb=True, pal=None, proj='merc', \ 
- 13            fill_land=False, outfile=None): 
-
 14      """ 
- 15      map = zview(var, tindex, depth, grid, {optional switch}) 
- 16   
- 17      optional switch: 
- 18        - filename         if defined, load the variable from file 
- 19        - cmin             set color minimum limit 
- 20        - cmax             set color maximum limit 
- 21        - clev             set the number of color step 
- 22        - fill             use contourf instead of pcolor 
- 23        - contour          overlay contour (request fill=True) 
- 24        - range            set axis limit 
- 25        - fts              set font size (default: 12) 
- 26        - title            add title to the plot 
- 27        - clb              add colorbar (defaul: True) 
- 28        - pal              set color map (default: cm.jet) 
- 29        - proj             set projection type (default: merc) 
- 30        - fill_land        fill land masked area with gray (defaul: True) 
- 31        - outfile          if defined, write figure to file 
- 32   
- 33      plot a constante-z slice of variable var. If filename is provided, 
- 34      var must be a string and the variable will be load from the file. 
- 35      grid can be a grid object or a gridid. In the later case, the grid 
- 36      object correponding to the provided gridid will be loaded. 
- 37      If proj is not None, return a Basemap object to be used with quiver  
- 38      for example.  
- 39      """ 
- 40   
- 41      # get grid 
- 42      if type(grid).__name__ == 'ROMS_Grid': 
- 43          grd = grid 
- 44      else: 
- 45          grd = pyroms.grid.get_ROMS_grid(grid) 
- 46   
- 47   
- 48      # get variable 
- 49      if filename == None: 
- 50          var = var 
- 51      else: 
- 52          data = pyroms.io.Dataset(filename) 
- 53   
- 54          var = data.variables[var] 
- 55   
- 56      Np, Mp, Lp = grd.vgrid.z_r[0,:].shape 
- 57   
- 58      if tindex is not -1: 
- 59          assert len(var.shape) == 4, 'var must be 4D (time plus space).' 
- 60          K, N, M, L = var.shape 
- 61      else: 
- 62          assert len(var.shape) == 3, 'var must be 3D (no time dependency).' 
- 63          N, M, L = var.shape 
- 64   
- 65      # determine where on the C-grid these variable lies 
- 66      if N == Np and M == Mp and L == Lp: 
- 67          Cpos='rho' 
- 68          mask = grd.hgrid.mask_rho 
- 69   
- 70      if N == Np and M == Mp and L == Lp-1: 
- 71          Cpos='u' 
- 72          mask = grd.hgrid.mask_u 
- 73   
- 74      if N == Np and M == Mp-1 and L == Lp: 
- 75          Cpos='v' 
- 76          mask = grd.hgrid.mask_v 
- 77   
- 78      # get constante-z slice 
- 79      if tindex == -1: 
- 80          var = var[:,:,:] 
- 81      else: 
- 82          var = var[tindex,:,:,:] 
- 83   
- 84      depth = -abs(depth) 
- 85      if fill == True: 
- 86          zslice, lon, lat = pyroms.tools.zslice(var, depth, grd, \ 
- 87                                    Cpos=Cpos) 
- 88      else: 
- 89          zslice, lon, lat = pyroms.tools.zslice(var, depth, grd, \ 
- 90                                    Cpos=Cpos, vert=True) 
- 91   
- 92      # plot 
- 93      if cmin is None: 
- 94          cmin = zslice.min() 
- 95      else: 
- 96          cmin = float(cmin) 
- 97   
- 98      if cmax is None: 
- 99          cmax = zslice.max() 
-100      else: 
-101          cmax = float(cmax) 
-102   
-103      if clev is None: 
-104          clev = 100. 
-105      else: 
-106          clev = float(clev) 
-107   
-108      dc = (cmax - cmin)/clev ; vc = np.arange(cmin,cmax+dc,dc) 
-109   
-110      if pal is None: 
-111          pal = cm.jet 
-112      else: 
-113          pal = pal 
-114   
-115      if fts is None: 
-116          fts = 12 
-117      else: 
-118          fts = fts 
-119   
-120      #pal.set_over('w', 1.0) 
-121      #pal.set_under('w', 1.0) 
-122      #pal.set_bad('w', 1.0) 
-123   
-124      pal_norm = colors.BoundaryNorm(vc,ncolors=256, clip = False) 
-125   
-126      if range is None: 
-127          lon_min = lon.min() 
-128          lon_max = lon.max() 
-129          lon_0 = (lon_min + lon_max) / 2. 
-130          lat_min = lat.min() 
-131          lat_max = lat.max()      
-132          lat_0 = (lat_min + lat_max) / 2. 
-133      else: 
-134          lon_min = range[0] 
-135          lon_max = range[1] 
-136          lon_0 = (lon_min + lon_max) / 2. 
-137          lat_min = range[2] 
-138          lat_max = range[3] 
-139          lat_0 = (lat_min + lat_max) / 2. 
-140   
-141      # clear figure 
-142      #plt.clf() 
-143   
-144      if proj is not None: 
-145          map = Basemap(projection=proj, llcrnrlon=lon_min, llcrnrlat=lat_min, \ 
-146                   urcrnrlon=lon_max, urcrnrlat=lat_max, lat_0=lat_0, lon_0=lon_0, \ 
-147                   resolution='h', area_thresh=5.) 
-148          x, y = map(lon,lat) 
-149       
-150      if fill_land is True and proj is not None: 
-151          # fill land and draw coastlines 
-152          map.drawcoastlines() 
-153          map.fillcontinents(color='grey') 
-154      else: 
-155          if proj is not None:  
-156              Basemap.pcolor(map, x, y, mask, vmin=-2, cmap=cm.gray) 
-157              pyroms_toolbox.plot_coast_line(grd, map) 
-158          else:  
-159              plt.pcolor(lon, lat, mask, vmin=-2, cmap=cm.gray) 
-160              pyroms_toolbox.plot_coast_line(grd) 
-161       
-162      if fill is True: 
-163          if proj is not None:  
-164              cf = Basemap.contourf(map, x, y, zslice, vc, cmap = pal, \ 
-165                                    norm = pal_norm) 
-166          else:  
-167              cf = plt.contourf(lon, lat, zslice, vc, cmap = pal, \ 
-168                                norm = pal_norm) 
-169      else: 
-170          if proj is not None:  
-171              cf = Basemap.pcolor(map, x, y, zslice, cmap = pal, norm = pal_norm) 
-172          else:  
-173              cf = plt.pcolor(lon, lat, zslice, cmap = pal, norm = pal_norm) 
-174   
-175      if clb is True: 
-176          clb = plt.colorbar(cf, fraction=0.075,format=clb_format) 
-177          for t in clb.ax.get_yticklabels(): 
-178              t.set_fontsize(fts) 
-179   
-180      if contour is True: 
-181          if fill is not True: 
-182              raise Warning, 'Please run again with fill=True to overlay contour.' 
-183          else: 
-184              if proj is not None: 
-185                  Basemap.contour(map, x, y, zslice, vc[::d], colors='k', linewidths=0.5, linestyles='solid') 
-186              else:  
-187                  plt.contour(lon, lat, zslice, vc[::d], colors='k', linewidths=0.5, linestyles='solid') 
-188   
-189      if proj is None and range is not None: 
-190          plt.axis(range)  
-191   
-192   
-193      if title is not None: 
-194              plt.title(title, fontsize=fts+4) 
-195   
-196      if proj is not None: 
-197          map.drawmeridians(np.arange(lon_min,lon_max, (lon_max-lon_min)/5.001), \ 
-198                            labels=[0,0,0,1], fmt='%.1f') 
-199          map.drawparallels(np.arange(lat_min,lat_max, (lat_max-lat_min)/5.001), \ 
-200                            labels=[1,0,0,0], fmt='%.1f') 
-201   
-202      if outfile is not None: 
-203          if outfile.find('.png') != -1 or outfile.find('.svg') != -1 or \ 
-204             outfile.find('.eps') != -1: 
-205              print 'Write figure to file', outfile 
-206              plt.savefig(outfile, dpi=200, facecolor='w', edgecolor='w', \ 
-207                          orientation='portrait') 
-208          else: 
-209              print 'Unrecognized file extension. Please use .png, .svg or .eps file extension.'    
-210   
-211   
-212      if proj is None: 
-213          return 
-214      else: 
-215          return map 
-
216   
-
-
- - - - - - - - - - - - - - - - - -
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- - - - - diff --git a/pyroms_toolbox/docs/toc-everything.html b/pyroms_toolbox/docs/toc-everything.html deleted file mode 100644 index ae6421d..0000000 --- a/pyroms_toolbox/docs/toc-everything.html +++ /dev/null @@ -1,251 +0,0 @@ - - - - - Everything - - - - - -

Everything

-
-

All Classes

- pyroms_toolbox.BGrid_GFDL.BGrid_GFDL'.BGrid_GFDL
pyroms_toolbox.BGrid_GFDL.BGrid_GFDL_full.BGrid_GFDL
pyroms_toolbox.average'.avg_obj
pyroms_toolbox.seawater.OutOfRangeError

All Functions

- pyroms_toolbox.BGrid_GFDL.BGrid_GFDL_full.get_nc_BGrid_GFDL
pyroms_toolbox.BGrid_GFDL.BGrid_GFDL_full.make_remap_BGrid_GFDL_file
pyroms_toolbox.BGrid_GFDL.flood'.flood
pyroms_toolbox.BGrid_GFDL.get_Bgrid_proj'.get_Bgrid_proj
pyroms_toolbox.BGrid_GFDL.get_coast_line'.get_coast_line
pyroms_toolbox.BGrid_GFDL.get_nc_BGrid_GFDL'.get_nc_BGrid_GFDL
pyroms_toolbox.BGrid_GFDL.make_remap_grid_file'.make_remap_grid_file
pyroms_toolbox.BGrid_GFDL.plot_coast_line'.plot_coast_line
pyroms_toolbox.N2'.N2
pyroms_toolbox.O2_saturation'.O2_saturation
pyroms_toolbox.average'.average
pyroms_toolbox.change'.change
pyroms_toolbox.get_coast_line'.get_coast_line
pyroms_toolbox.isoview'.isoview
pyroms_toolbox.iview'.iview
pyroms_toolbox.jview'.jview
pyroms_toolbox.latview'.latview
pyroms_toolbox.lonview'.lonview
pyroms_toolbox.lsq_phase_amplitude'.lsq_phase_amplitude
pyroms_toolbox.nc_create_roms_bdry_file'.nc_create_roms_bdry_file
pyroms_toolbox.nc_create_roms_file'.nc_create_roms_file
pyroms_toolbox.plot_coast_line'.plot_coast_line
pyroms_toolbox.plot_mask'.plot_mask
pyroms_toolbox.quiver'.quiver
pyroms_toolbox.remapping'.remapping
pyroms_toolbox.rfactor'.rfactor
pyroms_toolbox.rvalue'.rvalue
- pyroms_toolbox.seawater.density._dens0
-
- pyroms_toolbox.seawater.density._seck
- pyroms_toolbox.seawater.density.alpha
pyroms_toolbox.seawater.density.beta
pyroms_toolbox.seawater.density.dens
pyroms_toolbox.seawater.density.drhods
pyroms_toolbox.seawater.density.drhodt
pyroms_toolbox.seawater.density.sigma
pyroms_toolbox.seawater.density.svan
pyroms_toolbox.seawater.heat.adtgrad
pyroms_toolbox.seawater.heat.heatcap
pyroms_toolbox.seawater.heat.temppot
pyroms_toolbox.seawater.heat.temppot0
pyroms_toolbox.seawater.misc.depth
pyroms_toolbox.seawater.misc.freezept
pyroms_toolbox.seawater.misc.soundvel
- pyroms_toolbox.seawater.salinity._a
-
- pyroms_toolbox.seawater.salinity._b
-
- pyroms_toolbox.seawater.salinity._c
-
- pyroms_toolbox.seawater.salinity._dsal
-
- pyroms_toolbox.seawater.salinity._rt
-
- pyroms_toolbox.seawater.salinity._sal
- pyroms_toolbox.seawater.salinity.cond
pyroms_toolbox.seawater.salinity.salt
pyroms_toolbox.shapiro_filter.shapiro1
pyroms_toolbox.shapiro_filter.shapiro2
pyroms_toolbox.sview'.sview
pyroms_toolbox.transectview'.transectview
pyroms_toolbox.twoDview'.twoDview
pyroms_toolbox.zview'.zview

All Variables

-
- pyroms_toolbox._average.avg2d
-
- pyroms_toolbox._average.avg3d
- pyroms_toolbox.average'.avg
pyroms_toolbox.quiver'.ALLOW_THREADS
pyroms_toolbox.quiver'.BUFSIZE
pyroms_toolbox.quiver'.CLIP
pyroms_toolbox.quiver'.ERR_CALL
pyroms_toolbox.quiver'.ERR_DEFAULT
pyroms_toolbox.quiver'.ERR_DEFAULT2
pyroms_toolbox.quiver'.ERR_IGNORE
pyroms_toolbox.quiver'.ERR_LOG
pyroms_toolbox.quiver'.ERR_PRINT
pyroms_toolbox.quiver'.ERR_RAISE
pyroms_toolbox.quiver'.ERR_WARN
pyroms_toolbox.quiver'.FLOATING_POINT_SUPPORT
pyroms_toolbox.quiver'.FPE_DIVIDEBYZERO
pyroms_toolbox.quiver'.FPE_INVALID
pyroms_toolbox.quiver'.FPE_OVERFLOW
pyroms_toolbox.quiver'.FPE_UNDERFLOW
pyroms_toolbox.quiver'.False_
pyroms_toolbox.quiver'.Inf
pyroms_toolbox.quiver'.Infinity
pyroms_toolbox.quiver'.MAXDIMS
pyroms_toolbox.quiver'.NAN
pyroms_toolbox.quiver'.NINF
pyroms_toolbox.quiver'.NZERO
pyroms_toolbox.quiver'.NaN
pyroms_toolbox.quiver'.PINF
pyroms_toolbox.quiver'.PZERO
pyroms_toolbox.quiver'.RAISE
pyroms_toolbox.quiver'.SHIFT_DIVIDEBYZERO
pyroms_toolbox.quiver'.SHIFT_INVALID
pyroms_toolbox.quiver'.SHIFT_OVERFLOW
pyroms_toolbox.quiver'.SHIFT_UNDERFLOW
pyroms_toolbox.quiver'.ScalarType
pyroms_toolbox.quiver'.True_
pyroms_toolbox.quiver'.UFUNC_BUFSIZE_DEFAULT
pyroms_toolbox.quiver'.UFUNC_PYVALS_NAME
pyroms_toolbox.quiver'.WRAP
pyroms_toolbox.quiver'.absolute
pyroms_toolbox.quiver'.add
pyroms_toolbox.quiver'.arccos
pyroms_toolbox.quiver'.arccosh
pyroms_toolbox.quiver'.arcsin
pyroms_toolbox.quiver'.arcsinh
pyroms_toolbox.quiver'.arctan
pyroms_toolbox.quiver'.arctan2
pyroms_toolbox.quiver'.arctanh
pyroms_toolbox.quiver'.bitwise_and
pyroms_toolbox.quiver'.bitwise_not
pyroms_toolbox.quiver'.bitwise_or
pyroms_toolbox.quiver'.bitwise_xor
pyroms_toolbox.quiver'.c_
pyroms_toolbox.quiver'.cast
pyroms_toolbox.quiver'.ceil
pyroms_toolbox.quiver'.conj
pyroms_toolbox.quiver'.conjugate
pyroms_toolbox.quiver'.cos
pyroms_toolbox.quiver'.cosh
pyroms_toolbox.quiver'.deg2rad
pyroms_toolbox.quiver'.degrees
pyroms_toolbox.quiver'.divide
pyroms_toolbox.quiver'.e
pyroms_toolbox.quiver'.equal
pyroms_toolbox.quiver'.exp
pyroms_toolbox.quiver'.exp2
pyroms_toolbox.quiver'.expm1
pyroms_toolbox.quiver'.fabs
pyroms_toolbox.quiver'.floor
pyroms_toolbox.quiver'.floor_divide
pyroms_toolbox.quiver'.fmax
pyroms_toolbox.quiver'.fmin
pyroms_toolbox.quiver'.fmod
pyroms_toolbox.quiver'.frexp
pyroms_toolbox.quiver'.greater
pyroms_toolbox.quiver'.greater_equal
pyroms_toolbox.quiver'.hypot
pyroms_toolbox.quiver'.index_exp
pyroms_toolbox.quiver'.inf
pyroms_toolbox.quiver'.infty
pyroms_toolbox.quiver'.invert
pyroms_toolbox.quiver'.isfinite
pyroms_toolbox.quiver'.isinf
pyroms_toolbox.quiver'.isnan
pyroms_toolbox.quiver'.ldexp
pyroms_toolbox.quiver'.left_shift
pyroms_toolbox.quiver'.less
pyroms_toolbox.quiver'.less_equal
pyroms_toolbox.quiver'.little_endian
pyroms_toolbox.quiver'.log
pyroms_toolbox.quiver'.log10
pyroms_toolbox.quiver'.log1p
pyroms_toolbox.quiver'.logaddexp
pyroms_toolbox.quiver'.logaddexp2
pyroms_toolbox.quiver'.logical_and
pyroms_toolbox.quiver'.logical_not
pyroms_toolbox.quiver'.logical_or
pyroms_toolbox.quiver'.logical_xor
pyroms_toolbox.quiver'.maximum
pyroms_toolbox.quiver'.mgrid
pyroms_toolbox.quiver'.minimum
pyroms_toolbox.quiver'.mod
pyroms_toolbox.quiver'.modf
pyroms_toolbox.quiver'.multiply
pyroms_toolbox.quiver'.nan
pyroms_toolbox.quiver'.nbytes
pyroms_toolbox.quiver'.negative
pyroms_toolbox.quiver'.newaxis
pyroms_toolbox.quiver'.not_equal
pyroms_toolbox.quiver'.ogrid
pyroms_toolbox.quiver'.ones_like
pyroms_toolbox.quiver'.pi
pyroms_toolbox.quiver'.power
pyroms_toolbox.quiver'.r_
pyroms_toolbox.quiver'.rad2deg
pyroms_toolbox.quiver'.radians
pyroms_toolbox.quiver'.reciprocal
pyroms_toolbox.quiver'.remainder
pyroms_toolbox.quiver'.right_shift
pyroms_toolbox.quiver'.rint
pyroms_toolbox.quiver'.s_
pyroms_toolbox.quiver'.sctypeDict
pyroms_toolbox.quiver'.sctypeNA
pyroms_toolbox.quiver'.sctypes
pyroms_toolbox.quiver'.sign
pyroms_toolbox.quiver'.signbit
pyroms_toolbox.quiver'.sin
pyroms_toolbox.quiver'.sinh
pyroms_toolbox.quiver'.sqrt
pyroms_toolbox.quiver'.square
pyroms_toolbox.quiver'.subtract
pyroms_toolbox.quiver'.tan
pyroms_toolbox.quiver'.tanh
pyroms_toolbox.quiver'.true_divide
pyroms_toolbox.quiver'.trunc
pyroms_toolbox.quiver'.typeDict
pyroms_toolbox.quiver'.typeNA
pyroms_toolbox.quiver'.typecodes
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox-module.html deleted file mode 100644 index 977f80f..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox-module.html +++ /dev/null @@ -1,29 +0,0 @@ - - - - - pyroms_toolbox - - - - - -

Module pyroms_toolbox

-
-
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.BGrid_GFDL-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.BGrid_GFDL-module.html deleted file mode 100644 index 7571d9e..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.BGrid_GFDL-module.html +++ /dev/null @@ -1,29 +0,0 @@ - - - - - BGrid_GFDL - - - - - -

Module BGrid_GFDL

-
-
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.BGrid_GFDL.BGrid_GFDL'-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.BGrid_GFDL.BGrid_GFDL'-module.html deleted file mode 100644 index 9081b4a..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.BGrid_GFDL.BGrid_GFDL'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - BGrid_GFDL' - - - - - -

Module BGrid_GFDL'

-
-

Classes

- BGrid_GFDL
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.BGrid_GFDL.BGrid_GFDL_full-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.BGrid_GFDL.BGrid_GFDL_full-module.html deleted file mode 100644 index 0c73ae4..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.BGrid_GFDL.BGrid_GFDL_full-module.html +++ /dev/null @@ -1,34 +0,0 @@ - - - - - BGrid_GFDL_full - - - - - -

Module BGrid_GFDL_full

-
-

Classes

- BGrid_GFDL

Functions

- get_nc_BGrid_GFDL
make_remap_BGrid_GFDL_file
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.BGrid_GFDL.flood'-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.BGrid_GFDL.flood'-module.html deleted file mode 100644 index bb84d39..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.BGrid_GFDL.flood'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - flood' - - - - - -

Module flood'

-
-

Functions

- flood
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.BGrid_GFDL.get_Bgrid_proj'-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.BGrid_GFDL.get_Bgrid_proj'-module.html deleted file mode 100644 index 1709b7e..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.BGrid_GFDL.get_Bgrid_proj'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - get_Bgrid_proj' - - - - - -

Module get_Bgrid_proj'

-
-

Functions

- get_Bgrid_proj
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.BGrid_GFDL.get_coast_line'-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.BGrid_GFDL.get_coast_line'-module.html deleted file mode 100644 index fa5d843..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.BGrid_GFDL.get_coast_line'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - get_coast_line' - - - - - -

Module get_coast_line'

-
-

Functions

- get_coast_line
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.BGrid_GFDL.get_nc_BGrid_GFDL'-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.BGrid_GFDL.get_nc_BGrid_GFDL'-module.html deleted file mode 100644 index ce5b3cf..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.BGrid_GFDL.get_nc_BGrid_GFDL'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - get_nc_BGrid_GFDL' - - - - - -

Module get_nc_BGrid_GFDL'

-
-

Functions

- get_nc_BGrid_GFDL
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.BGrid_GFDL.make_remap_grid_file'-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.BGrid_GFDL.make_remap_grid_file'-module.html deleted file mode 100644 index fdb4f5c..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.BGrid_GFDL.make_remap_grid_file'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - make_remap_grid_file' - - - - - -

Module make_remap_grid_file'

-
-

Functions

- make_remap_grid_file
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.BGrid_GFDL.plot_coast_line'-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.BGrid_GFDL.plot_coast_line'-module.html deleted file mode 100644 index a6b5067..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.BGrid_GFDL.plot_coast_line'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - plot_coast_line' - - - - - -

Module plot_coast_line'

-
-

Functions

- plot_coast_line
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.N2'-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.N2'-module.html deleted file mode 100644 index 4363a42..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.N2'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - N2' - - - - - -

Module N2'

-
-

Functions

- N2
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.O2_saturation'-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.O2_saturation'-module.html deleted file mode 100644 index 267d1e1..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.O2_saturation'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - O2_saturation' - - - - - -

Module O2_saturation'

-
-

Functions

- O2_saturation
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox._average-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox._average-module.html deleted file mode 100644 index b0f96ea..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox._average-module.html +++ /dev/null @@ -1,36 +0,0 @@ - - - - - _average - - - - - -

Module _average

-
-

Variables

-
- avg2d
-
- avg3d
-
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.average'-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.average'-module.html deleted file mode 100644 index 3f1e4f1..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.average'-module.html +++ /dev/null @@ -1,35 +0,0 @@ - - - - - average' - - - - - -

Module average'

-
-

Classes

- avg_obj

Functions

- average

Variables

- avg
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.change'-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.change'-module.html deleted file mode 100644 index 3580647..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.change'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - change' - - - - - -

Module change'

-
-

Functions

- change
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.get_coast_line'-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.get_coast_line'-module.html deleted file mode 100644 index 87ebd0d..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.get_coast_line'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - get_coast_line' - - - - - -

Module get_coast_line'

-
-

Functions

- get_coast_line
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.isoview'-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.isoview'-module.html deleted file mode 100644 index 60ec608..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.isoview'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - isoview' - - - - - -

Module isoview'

-
-

Functions

- isoview
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.iview'-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.iview'-module.html deleted file mode 100644 index 247ea3b..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.iview'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - iview' - - - - - -

Module iview'

-
-

Functions

- iview
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.jview'-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.jview'-module.html deleted file mode 100644 index 58f5e4a..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.jview'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - jview' - - - - - -

Module jview'

-
-

Functions

- jview
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.latview'-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.latview'-module.html deleted file mode 100644 index 706debb..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.latview'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - latview' - - - - - -

Module latview'

-
-

Functions

- latview
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.lonview'-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.lonview'-module.html deleted file mode 100644 index 9398ddd..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.lonview'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - lonview' - - - - - -

Module lonview'

-
-

Functions

- lonview
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.lsq_phase_amplitude'-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.lsq_phase_amplitude'-module.html deleted file mode 100644 index 541ff8d..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.lsq_phase_amplitude'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - lsq_phase_amplitude' - - - - - -

Module lsq_phase_amplitude'

-
-

Functions

- lsq_phase_amplitude
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.nc_create_roms_bdry_file'-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.nc_create_roms_bdry_file'-module.html deleted file mode 100644 index b5e5862..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.nc_create_roms_bdry_file'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - nc_create_roms_bdry_file' - - - - - -

Module nc_create_roms_bdry_file'

-
-

Functions

- nc_create_roms_bdry_file
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.nc_create_roms_file'-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.nc_create_roms_file'-module.html deleted file mode 100644 index 6c9c3b8..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.nc_create_roms_file'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - nc_create_roms_file' - - - - - -

Module nc_create_roms_file'

-
-

Functions

- nc_create_roms_file
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.plot_coast_line'-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.plot_coast_line'-module.html deleted file mode 100644 index 70a048b..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.plot_coast_line'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - plot_coast_line' - - - - - -

Module plot_coast_line'

-
-

Functions

- plot_coast_line
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.plot_mask'-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.plot_mask'-module.html deleted file mode 100644 index 7764b08..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.plot_mask'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - plot_mask' - - - - - -

Module plot_mask'

-
-

Functions

- plot_mask
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.quiver'-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.quiver'-module.html deleted file mode 100644 index 4e2beb9..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.quiver'-module.html +++ /dev/null @@ -1,167 +0,0 @@ - - - - - quiver' - - - - - -

Module quiver'

-
-

Functions

- quiver

Variables

- ALLOW_THREADS
BUFSIZE
CLIP
ERR_CALL
ERR_DEFAULT
ERR_DEFAULT2
ERR_IGNORE
ERR_LOG
ERR_PRINT
ERR_RAISE
ERR_WARN
FLOATING_POINT_SUPPORT
FPE_DIVIDEBYZERO
FPE_INVALID
FPE_OVERFLOW
FPE_UNDERFLOW
False_
Inf
Infinity
MAXDIMS
NAN
NINF
NZERO
NaN
PINF
PZERO
RAISE
SHIFT_DIVIDEBYZERO
SHIFT_INVALID
SHIFT_OVERFLOW
SHIFT_UNDERFLOW
ScalarType
True_
UFUNC_BUFSIZE_DEFAULT
UFUNC_PYVALS_NAME
WRAP
absolute
add
arccos
arccosh
arcsin
arcsinh
arctan
arctan2
arctanh
bitwise_and
bitwise_not
bitwise_or
bitwise_xor
c_
cast
ceil
conj
conjugate
cos
cosh
deg2rad
degrees
divide
e
equal
exp
exp2
expm1
fabs
floor
floor_divide
fmax
fmin
fmod
frexp
greater
greater_equal
hypot
index_exp
inf
infty
invert
isfinite
isinf
isnan
ldexp
left_shift
less
less_equal
little_endian
log
log10
log1p
logaddexp
logaddexp2
logical_and
logical_not
logical_or
logical_xor
maximum
mgrid
minimum
mod
modf
multiply
nan
nbytes
negative
newaxis
not_equal
ogrid
ones_like
pi
power
r_
rad2deg
radians
reciprocal
remainder
right_shift
rint
s_
sctypeDict
sctypeNA
sctypes
sign
signbit
sin
sinh
sqrt
square
subtract
tan
tanh
true_divide
trunc
typeDict
typeNA
typecodes
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.remapping'-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.remapping'-module.html deleted file mode 100644 index 3f11c1e..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.remapping'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - remapping' - - - - - -

Module remapping'

-
-

Functions

- remapping
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.rfactor'-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.rfactor'-module.html deleted file mode 100644 index fa72dfd..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.rfactor'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - rfactor' - - - - - -

Module rfactor'

-
-

Functions

- rfactor
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.rvalue'-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.rvalue'-module.html deleted file mode 100644 index fbbf158..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.rvalue'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - rvalue' - - - - - -

Module rvalue'

-
-

Functions

- rvalue
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.seawater-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.seawater-module.html deleted file mode 100644 index 5d1c171..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.seawater-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - seawater - - - - - -

Module seawater

-
-

Classes

- OutOfRangeError
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.seawater.density-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.seawater.density-module.html deleted file mode 100644 index 0631e38..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.seawater.density-module.html +++ /dev/null @@ -1,43 +0,0 @@ - - - - - density - - - - - -

Module density

-
-

Functions

-
- _dens0
-
- _seck
- alpha
beta
dens
drhods
drhodt
sigma
svan
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.seawater.heat-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.seawater.heat-module.html deleted file mode 100644 index 4d83c93..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.seawater.heat-module.html +++ /dev/null @@ -1,34 +0,0 @@ - - - - - heat - - - - - -

Module heat

-
-

Functions

- adtgrad
heatcap
temppot
temppot0
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.seawater.misc-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.seawater.misc-module.html deleted file mode 100644 index c0e8677..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.seawater.misc-module.html +++ /dev/null @@ -1,33 +0,0 @@ - - - - - misc - - - - - -

Module misc

-
-

Functions

- depth
freezept
soundvel
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.seawater.salinity-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.seawater.salinity-module.html deleted file mode 100644 index 426d15d..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.seawater.salinity-module.html +++ /dev/null @@ -1,50 +0,0 @@ - - - - - salinity - - - - - -

Module salinity

-
-

Functions

-
- _a
-
- _b
-
- _c
-
- _dsal
-
- _rt
-
- _sal
- cond
salt
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.seawater.test-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.seawater.test-module.html deleted file mode 100644 index 850ba19..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.seawater.test-module.html +++ /dev/null @@ -1,29 +0,0 @@ - - - - - test - - - - - -

Module test

-
-
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.shapiro_filter-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.shapiro_filter-module.html deleted file mode 100644 index 61c0a3f..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.shapiro_filter-module.html +++ /dev/null @@ -1,32 +0,0 @@ - - - - - shapiro_filter - - - - - -

Module shapiro_filter

-
-

Functions

- shapiro1
shapiro2
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.sview'-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.sview'-module.html deleted file mode 100644 index 1c7d77a..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.sview'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - sview' - - - - - -

Module sview'

-
-

Functions

- sview
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.transectview'-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.transectview'-module.html deleted file mode 100644 index a80bfc5..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.transectview'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - transectview' - - - - - -

Module transectview'

-
-

Functions

- transectview
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.twoDview'-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.twoDview'-module.html deleted file mode 100644 index 9bd4c24..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.twoDview'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - twoDview' - - - - - -

Module twoDview'

-
-

Functions

- twoDview
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc-pyroms_toolbox.zview'-module.html b/pyroms_toolbox/docs/toc-pyroms_toolbox.zview'-module.html deleted file mode 100644 index 45a194a..0000000 --- a/pyroms_toolbox/docs/toc-pyroms_toolbox.zview'-module.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - - zview' - - - - - -

Module zview'

-
-

Functions

- zview
-[hide private] - - - - diff --git a/pyroms_toolbox/docs/toc.html b/pyroms_toolbox/docs/toc.html deleted file mode 100644 index 2f2ad50..0000000 --- a/pyroms_toolbox/docs/toc.html +++ /dev/null @@ -1,75 +0,0 @@ - - - - - Table of Contents - - - - - -

Table of Contents

-
- Everything -
-

Modules

- pyroms_toolbox
pyroms_toolbox.BGrid_GFDL
pyroms_toolbox.BGrid_GFDL.BGrid_GFDL'
pyroms_toolbox.BGrid_GFDL.BGrid_GFDL_full
pyroms_toolbox.BGrid_GFDL.flood'
pyroms_toolbox.BGrid_GFDL.get_Bgrid_proj'
pyroms_toolbox.BGrid_GFDL.get_coast_line'
pyroms_toolbox.BGrid_GFDL.get_nc_BGrid_GFDL'
pyroms_toolbox.BGrid_GFDL.make_remap_grid_file'
pyroms_toolbox.BGrid_GFDL.plot_coast_line'
pyroms_toolbox.N2'
pyroms_toolbox.O2_saturation'
- pyroms_toolbox._average
- pyroms_toolbox.average'
pyroms_toolbox.change'
pyroms_toolbox.get_coast_line'
pyroms_toolbox.isoview'
pyroms_toolbox.iview'
pyroms_toolbox.jview'
pyroms_toolbox.latview'
pyroms_toolbox.lonview'
pyroms_toolbox.lsq_phase_amplitude'
pyroms_toolbox.nc_create_roms_bdry_file'
pyroms_toolbox.nc_create_roms_file'
pyroms_toolbox.plot_coast_line'
pyroms_toolbox.plot_mask'
pyroms_toolbox.quiver'
pyroms_toolbox.remapping'
pyroms_toolbox.rfactor'
pyroms_toolbox.rvalue'
pyroms_toolbox.seawater
pyroms_toolbox.seawater.density
pyroms_toolbox.seawater.heat
pyroms_toolbox.seawater.misc
pyroms_toolbox.seawater.salinity
pyroms_toolbox.seawater.test
pyroms_toolbox.shapiro_filter
pyroms_toolbox.sview'
pyroms_toolbox.transectview'
pyroms_toolbox.twoDview'
pyroms_toolbox.zview'
- [hide private] - - - - diff --git a/pyroms_toolbox/pyroms_toolbox/BGrid_GFDL/BGrid_GFDL.py b/pyroms_toolbox/pyroms_toolbox/BGrid_GFDL/BGrid_GFDL.py index 2f9f798..2473d69 100644 --- a/pyroms_toolbox/pyroms_toolbox/BGrid_GFDL/BGrid_GFDL.py +++ b/pyroms_toolbox/pyroms_toolbox/BGrid_GFDL/BGrid_GFDL.py @@ -5,7 +5,6 @@ import netCDF4 as netCDF except: import netCDF3 as netCDF -import pyroms @@ -48,8 +47,20 @@ def __init__(self, lon_t, lat_t, lon_uv, lat_uv, \ def _calculate_grid_angle(self): geod = pyproj.Geod(ellps='WGS84') - az_forward, az_back, dx = geod.inv(self.lon_t_vert[:,:-1], self.lat_t_vert[:,:-1], \ - self.lon_t_vert[:,1:], self.lat_t_vert[:,1:]) + # This is how it used to be, but it fails for some reason. +# az_forward, az_back, dx = geod.inv(self.lon_t_vert[:,:-1], self.lat_t_vert[:,:-1], \ +# self.lon_t_vert[:,1:], self.lat_t_vert[:,1:]) +# angle = 0.5 * (az_forward[1:,:] + az_forward[:-1,:]) - angle = 0.5 * (az_forward[1:,:] + az_forward[:-1,:]) + # Seems to work... + sizey, sizex = self.lon_t_vert.shape + angle = np.zeros(self.h.shape) + + for i in range(sizex-1): + az_forward, az_back, dx = geod.inv(self.lon_t_vert[:,i], self.lat_t_vert[:,i], \ + self.lon_t_vert[:,i+1], self.lat_t_vert[:,i+1]) + + angle[:,i] = 0.5 * (az_forward[1:] + az_forward[:-1]) + + # part of original code self.angle = (90 - angle) * np.pi/180. diff --git a/pyroms_toolbox/pyroms_toolbox/BGrid_GFDL/BGrid_GFDL_full.py b/pyroms_toolbox/pyroms_toolbox/BGrid_GFDL/BGrid_GFDL_full.py index 11e669e..db5a90a 100644 --- a/pyroms_toolbox/pyroms_toolbox/BGrid_GFDL/BGrid_GFDL_full.py +++ b/pyroms_toolbox/pyroms_toolbox/BGrid_GFDL/BGrid_GFDL_full.py @@ -59,7 +59,7 @@ def _calculate_t_vert(self): lat[-1,0] = self.lat_t[-1,0] - ( self.lat_uv[-2,0] - self.lat_t[-1,0] ) self.lon_t_vert = lon - self.lat_t_vert = lat + self.lat_t_vert = lat def _calculate_uv_vert(self): @@ -93,7 +93,7 @@ def _calculate_grid_angle(self): angle = 0.5 * (az_forward[1:,:] + az_forward[:-1,:]) self.angle = (90 - angle) * np.pi/180. - + def get_nc_BGrid_GFDL(grdfile): @@ -175,7 +175,7 @@ def make_remap_BGrid_GFDL_file(Bgrd, Bpos='t'): grid_imask = Bgrd.mask_uv[0,:].flatten() Mp, Lp = Bgrd.lon_uv.shape else: - raise ValueError, 'Bpos must be t or uv' + raise ValueError('Bpos must be t or uv') grid_size = Lp * Mp diff --git a/pyroms_toolbox/pyroms_toolbox/BGrid_GFDL/__init__.py b/pyroms_toolbox/pyroms_toolbox/BGrid_GFDL/__init__.py index 77fb113..7151993 100644 --- a/pyroms_toolbox/pyroms_toolbox/BGrid_GFDL/__init__.py +++ b/pyroms_toolbox/pyroms_toolbox/BGrid_GFDL/__init__.py @@ -2,11 +2,11 @@ BGrid_GFDL module """ -from BGrid_GFDL import BGrid_GFDL -from get_nc_BGrid_GFDL import get_nc_BGrid_GFDL -from make_remap_grid_file import make_remap_grid_file -from get_coast_line import get_coast_line -from plot_coast_line import plot_coast_line -from get_Bgrid_proj import get_Bgrid_proj -from flood import flood +from .BGrid_GFDL import BGrid_GFDL +from .get_nc_BGrid_GFDL import get_nc_BGrid_GFDL +from .make_remap_grid_file import make_remap_grid_file +from .get_coast_line import get_coast_line +from .plot_coast_line import plot_coast_line +from .get_Bgrid_proj import get_Bgrid_proj +from .flood import flood diff --git a/pyroms_toolbox/pyroms_toolbox/BGrid_GFDL/flood.py b/pyroms_toolbox/pyroms_toolbox/BGrid_GFDL/flood.py index c7acb86..ae33da7 100644 --- a/pyroms_toolbox/pyroms_toolbox/BGrid_GFDL/flood.py +++ b/pyroms_toolbox/pyroms_toolbox/BGrid_GFDL/flood.py @@ -11,12 +11,12 @@ def flood(varz, Bgrdz, Bpos='t', irange=None, jrange=None, \ var = flood(var, Bgrdz) optional switch: - - Bpos='t', 'uv' specify the B-grid position where - the variable rely + - Bpos='t', 'uv' specify the B-grid position where + the variable rely - irange specify grid sub-sample for i direction - jrange specify grid sub-sample for j direction - spval=1e35 define spval value - - dmax=0 if dmax>0, maximum horizontal + - dmax=0 if dmax>0, maximum horizontal flooding distance - cdepth=0 critical depth for flooding if depth no flooding @@ -45,7 +45,7 @@ def flood(varz, Bgrdz, Bpos='t', irange=None, jrange=None, \ h = Bgrdz.h mask = Bgrdz.mask_uv[0,:,:] else: - raise Warning, '%s bad position. Bpos must be t or uv' % Bpos + raise Warning('%s bad position. Bpos must be t or uv' % Bpos) nlev, Mm, Lm = varz.shape @@ -103,6 +103,6 @@ def flood(varz, Bgrdz, Bpos='t', irange=None, jrange=None, \ for i in range(Lm): for j in range(Mm): if mask[j,i] == 1: - varz[bottom[j,i]:,j,i] = varz[bottom[j,i],j,i] + varz[int(bottom[j,i]):,j,i] = varz[int(bottom[j,i]),j,i] return varz diff --git a/pyroms_toolbox/pyroms_toolbox/BGrid_GFDL/get_coast_line.py b/pyroms_toolbox/pyroms_toolbox/BGrid_GFDL/get_coast_line.py index eb6ae60..1f7d2ac 100644 --- a/pyroms_toolbox/pyroms_toolbox/BGrid_GFDL/get_coast_line.py +++ b/pyroms_toolbox/pyroms_toolbox/BGrid_GFDL/get_coast_line.py @@ -22,28 +22,28 @@ def get_coast_line(Bgrd): if mask[jidx[i], iidx[i]] != mask[jidx[i]+1, iidx[i]]: lonc = ([lon[jidx[i]+1,iidx[i]], lon[jidx[i]+1,iidx[i]+1]]) latc = ([lat[jidx[i]+1,iidx[i]], lat[jidx[i]+1,iidx[i]+1]]) - seg = zip(lonc,latc) + seg = list(zip(lonc,latc)) coast.append(seg) if jidx[i] != 0: if mask[jidx[i], iidx[i]] != mask[jidx[i]-1, iidx[i]]: lonc = ([lon[jidx[i],iidx[i]], lon[jidx[i],iidx[i]+1]]) latc = ([lat[jidx[i],iidx[i]], lat[jidx[i],iidx[i]+1]]) - seg = zip(lonc,latc) + seg = list(zip(lonc,latc)) coast.append(seg) if iidx[i] != mask.shape[1]-1: if mask[jidx[i], iidx[i]] != mask[jidx[i], iidx[i]+1]: lonc = ([lon[jidx[i],iidx[i]+1], lon[jidx[i]+1,iidx[i]+1]]) latc = ([lat[jidx[i],iidx[i]+1], lat[jidx[i]+1,iidx[i]+1]]) - seg = zip(lonc,latc) + seg = list(zip(lonc,latc)) coast.append(seg) if iidx[i] != 0: if mask[jidx[i], iidx[i]] != mask[jidx[i], iidx[i]-1]: lonc = ([lon[jidx[i],iidx[i]], lon[jidx[i]+1,iidx[i]]]) latc = ([lat[jidx[i],iidx[i]], lat[jidx[i]+1,iidx[i]]]) - seg = zip(lonc,latc) + seg = list(zip(lonc,latc)) coast.append(seg) return coast diff --git a/pyroms_toolbox/pyroms_toolbox/BGrid_GFDL/get_nc_BGrid_GFDL.py b/pyroms_toolbox/pyroms_toolbox/BGrid_GFDL/get_nc_BGrid_GFDL.py index 715302a..c72a7cb 100644 --- a/pyroms_toolbox/pyroms_toolbox/BGrid_GFDL/get_nc_BGrid_GFDL.py +++ b/pyroms_toolbox/pyroms_toolbox/BGrid_GFDL/get_nc_BGrid_GFDL.py @@ -4,7 +4,7 @@ def get_nc_BGrid_GFDL(grdfile, name='GFDL_CM2.1_North_Pacific', area='regional', \ - xrange=(60,175), yrange=(120, 190), ystart=235)): + xrange=(60,175), yrange=(120, 190), ystart=235): """ Bgrd = get_nc_BGrid_GFDL(grdfile) @@ -37,7 +37,7 @@ def get_nc_BGrid_GFDL(grdfile, name='GFDL_CM2.1_North_Pacific', area='regional', for j in range(M_t): for i in range(L_t): try: - mask_t[0:kmt[j,i], j,i] = 1 + mask_t[0:int(kmt[j,i]), j,i] = 1 except: mask_t[:, j,i] = 0 @@ -48,22 +48,86 @@ def get_nc_BGrid_GFDL(grdfile, name='GFDL_CM2.1_North_Pacific', area='regional', for j in range(M_uv): for i in range(L_uv): try: - mask_uv[0:kmu[j,i], j,i] = 1 + mask_uv[0:int(kmu[j,i]), j,i] = 1 except: mask_uv[:, j,i] = 0 if area == 'npolar': - #add one row in the north and the south - lon_t = lon_t[np.r_[0,:len(lon_t),-1]] - lon_t[0] = lon_t[1] - (lon_t[2]-lon_t[1]) - lon_t[-1] = lon_t[-2] + (lon_t[-2]-lon_t[-3]) - lat_t = lat_t[np.r_[0,0,:len(lat_t),-1,-1]] - lat_t[0] = -85 - lat_t[1] = -80 - lat_t[-2] = 90 - lat_t[-1] = 91 - lon_uv = lon_t - lat_uv = lat_t + #add two rows in the north and the south + lon_t = lon_t[np.r_[0,0,:np.size(lon_t,0),-1,-1]] + lon_t = lon_t[:,np.r_[0,:np.size(lon_t,1),-1]] + lon_t[:,0] = lon_t[:,1] - (lon_t[:,2]-lon_t[:,1]) + lon_t[:,-1] = lon_t[:,-2] + (lon_t[:,-2]-lon_t[:,-3]) + lat_t = lat_t[np.r_[0,0,:np.size(lat_t,0),-1,-1]] + lat_t = lat_t[:,np.r_[0,:np.size(lat_t,1),-1]] + lat_t[0,:] = -85 + lat_t[1,:] = -80 + lat_t[-2,:] = 90 + lat_t[-1,:] = 91 + lon_uv = lon_uv[np.r_[0,0,:np.size(lon_uv,0),-1,-1]] + lon_uv = lon_uv[:,np.r_[0,:np.size(lon_uv,1),-1]] + lon_uv[:,0] = lon_uv[:,1] - (lon_uv[:,2]-lon_t[:,1]) + lon_uv[:,-1] = lon_uv[:,-2] + (lon_uv[:,-2]-lon_uv[:,-3]) + lat_uv = lat_uv[np.r_[0,0,:np.size(lat_uv,0),-1,-1]] + lat_uv = lat_uv[:,np.r_[0,:np.size(lat_uv,1),-1]] + lat_uv[0,:] = -85 + lat_uv[1,:] = -80 + lat_uv[-2,:] = 90 + lat_uv[-1,:] = 91 + mask_t = mask_t[:,np.r_[0,0,:np.size(mask_t,1),-1,-1],:] + mask_t = mask_t[:,:,np.r_[0,:np.size(mask_t,2),-1]] + mask_t[:,:,0] = mask_t[:,:,-2] + mask_t[:,:,-1] = mask_t[:,:,1] + mask_uv = mask_uv[:,np.r_[0,0,:np.size(mask_uv,1),-1,-1],:] + mask_uv = mask_uv[:,:,np.r_[0,:np.size(mask_uv,2),-1]] + mask_uv[:,:,0] = mask_uv[:,:,-2] + mask_uv[:,:,-1] = mask_uv[:,:,1] + h = h[np.r_[0,0,:np.size(h,0),-1,-1]] + h = h[:,np.r_[0,:np.size(h,1),-1]] + h[:,0] = h[:,-2] + h[:,-1] = h[:,1] + f = f[np.r_[0,0,:np.size(f,0),-1,-1]] + f = f[:,np.r_[0,:np.size(f,1),-1]] + f[:,0] = f[:,-2] + f[:,-1] = f[:,1] + m,l = h.shape + xrange=(1,l-2) + yrange=(ystart+2,m-2) + + if area == 'tripole': + #add two rows in the north and the south + fold1 = L_t//2 + lon_t = lon_t[np.r_[0,0,:np.size(lon_t,0),-1,-1]] + lon_t[-2,:fold1] = lon_t[-3,L_t:fold1-1:-1] + lon_t[-2,L_t:fold1-1:-1] = lon_t[-3,:fold1] + lon_t[-1,:fold1] = lon_t[-4,L_t:fold1-1:-1] + lon_t[-1,L_t:fold1-1:-1] = lon_t[-4,:fold1] + + lon_t = lon_t[:,np.r_[0,:np.size(lon_t,1),-1]] + lon_t[:,0] = lon_t[:,1] - (lon_t[:,2]-lon_t[:,1]) + lon_t[:,-1] = lon_t[:,-2] + (lon_t[:,-2]-lon_t[:,-3]) + lat_t = lat_t[np.r_[0,0,:np.size(lat_t,0),-1,-1]] + lat_t = lat_t[:,np.r_[0,:np.size(lat_t,1),-1]] + lat_t[0,:] = -85 + lat_t[1,:] = -80 + lat_t[-2,:] = lat_t[-3,:] + lat_t[-1,:] = lat_t[-4,:] + lon_uv = lon_uv[np.r_[0,0,:np.size(lon_uv,0),-1,-1]] + + lon_uv[-2,:fold1] = lon_uv[-4,L_t:fold1-1:-1] + lon_uv[-2,L_t:fold1-1:-1] = lon_uv[-4,:fold1] + lon_uv[-1,:fold1] = lon_uv[-5,L_t:fold1-1:-1] + lon_uv[-1,L_t:fold1-1:-1] = lon_uv[-5,:fold1] + + lon_uv = lon_uv[:,np.r_[0,:np.size(lon_uv,1),-1]] + lon_uv[:,0] = lon_uv[:,1] - (lon_uv[:,2]-lon_t[:,1]) + lon_uv[:,-1] = lon_uv[:,-2] + (lon_uv[:,-2]-lon_uv[:,-3]) + lat_uv = lat_uv[np.r_[0,0,:np.size(lat_uv,0),-1,-1]] + lat_uv = lat_uv[:,np.r_[0,:np.size(lat_uv,1),-1]] + lat_uv[0,:] = -85 + lat_uv[1,:] = -80 + lat_uv[-2,:] = lat_uv[-3,:] + lat_uv[-1,:] = lat_uv[-4,:] mask_t = mask_t[:,np.r_[0,0,:np.size(mask_t,1),-1,-1],:] mask_t = mask_t[:,:,np.r_[0,:np.size(mask_t,2),-1]] mask_t[:,:,0] = mask_t[:,:,-2] diff --git a/pyroms_toolbox/pyroms_toolbox/BGrid_GFDL/make_remap_grid_file.py b/pyroms_toolbox/pyroms_toolbox/BGrid_GFDL/make_remap_grid_file.py index ef56fe5..e574730 100644 --- a/pyroms_toolbox/pyroms_toolbox/BGrid_GFDL/make_remap_grid_file.py +++ b/pyroms_toolbox/pyroms_toolbox/BGrid_GFDL/make_remap_grid_file.py @@ -33,7 +33,7 @@ def make_remap_grid_file(Bgrd, Bpos='t'): grid_imask = Bgrd.mask_uv[0,:].flatten() Mp, Lp = Bgrd.lon_uv.shape else: - raise ValueError, 'Bpos must be t or uv' + raise ValueError('Bpos must be t or uv') grid_size = Lp * Mp diff --git a/pyroms_toolbox/pyroms_toolbox/BGrid_POP/__init__.py b/pyroms_toolbox/pyroms_toolbox/BGrid_POP/__init__.py index 5279852..21bfe6a 100644 --- a/pyroms_toolbox/pyroms_toolbox/BGrid_POP/__init__.py +++ b/pyroms_toolbox/pyroms_toolbox/BGrid_POP/__init__.py @@ -2,7 +2,7 @@ POP module """ -from BGrid_POP import BGrid_POP -from get_nc_BGrid_POP import get_nc_BGrid_POP -from make_remap_grid_file import make_remap_grid_file -from flood import flood +from .BGrid_POP import BGrid_POP +from .get_nc_BGrid_POP import get_nc_BGrid_POP +from .make_remap_grid_file import make_remap_grid_file +from .flood import flood diff --git a/pyroms_toolbox/pyroms_toolbox/BGrid_POP/flood.py b/pyroms_toolbox/pyroms_toolbox/BGrid_POP/flood.py index 9f7ba56..134a669 100644 --- a/pyroms_toolbox/pyroms_toolbox/BGrid_POP/flood.py +++ b/pyroms_toolbox/pyroms_toolbox/BGrid_POP/flood.py @@ -12,11 +12,11 @@ def flood(varz, Bgrd, Bpos='t', irange=None, jrange=None, \ optional switch: - Bpos='t', 'u' specify the grid position where - the variable rely + the variable rely - irange specify grid sub-sample for i direction - jrange specify grid sub-sample for j direction - spval=1e35 define spval value - - dmax=0 if dmax>0, maximum horizontal + - dmax=0 if dmax>0, maximum horizontal flooding distance - cdepth=0 critical depth for flooding if depth no flooding @@ -101,6 +101,6 @@ def flood(varz, Bgrd, Bpos='t', irange=None, jrange=None, \ for i in range(Lm): for j in range(Mm): if mask[j,i] == 1: - varz[bottom[j,i]:,j,i] = varz[bottom[j,i],j,i] + varz[int(bottom[j,i]):,j,i] = varz[int(bottom[j,i]),j,i] return varz diff --git a/pyroms_toolbox/pyroms_toolbox/BGrid_SODA/BGrid_SODA.py b/pyroms_toolbox/pyroms_toolbox/BGrid_SODA/BGrid_SODA.py index 02f564b..54e3746 100644 --- a/pyroms_toolbox/pyroms_toolbox/BGrid_SODA/BGrid_SODA.py +++ b/pyroms_toolbox/pyroms_toolbox/BGrid_SODA/BGrid_SODA.py @@ -5,7 +5,7 @@ import netCDF4 as netCDF except: import netCDF3 as netCDF - import pyroms +import pyroms class BGrid_SODA(object): """ diff --git a/pyroms_toolbox/pyroms_toolbox/BGrid_SODA/__init__.py b/pyroms_toolbox/pyroms_toolbox/BGrid_SODA/__init__.py index 5e710a7..0291486 100644 --- a/pyroms_toolbox/pyroms_toolbox/BGrid_SODA/__init__.py +++ b/pyroms_toolbox/pyroms_toolbox/BGrid_SODA/__init__.py @@ -2,7 +2,7 @@ SODA module """ -from BGrid_SODA import BGrid_SODA -from get_nc_BGrid_SODA import get_nc_BGrid_SODA -from make_remap_grid_file import make_remap_grid_file -from flood import flood +from .BGrid_SODA import BGrid_SODA +from .get_nc_BGrid_SODA import get_nc_BGrid_SODA +from .make_remap_grid_file import make_remap_grid_file +from .flood import flood diff --git a/pyroms_toolbox/pyroms_toolbox/BGrid_SODA/flood.py b/pyroms_toolbox/pyroms_toolbox/BGrid_SODA/flood.py index 853623f..c56986f 100644 --- a/pyroms_toolbox/pyroms_toolbox/BGrid_SODA/flood.py +++ b/pyroms_toolbox/pyroms_toolbox/BGrid_SODA/flood.py @@ -12,11 +12,11 @@ def flood(varz, Bgrd, Bpos='t', irange=None, jrange=None, \ optional switch: - Bpos='t', 'uv' specify the grid position where - the variable rely + the variable rely - irange specify grid sub-sample for i direction - jrange specify grid sub-sample for j direction - spval=1e35 define spval value - - dmax=0 if dmax>0, maximum horizontal + - dmax=0 if dmax>0, maximum horizontal flooding distance - cdepth=0 critical depth for flooding if depth no flooding @@ -98,6 +98,6 @@ def flood(varz, Bgrd, Bpos='t', irange=None, jrange=None, \ for i in range(Lm): for j in range(Mm): if mask[j,i] == 1: - varz[bottom[j,i]:,j,i] = varz[bottom[j,i],j,i] + varz[int(bottom[j,i]):,j,i] = varz[int(bottom[j,i]),j,i] return varz diff --git a/pyroms_toolbox/pyroms_toolbox/BGrid_SODA/get_nc_BGrid_SODA.py b/pyroms_toolbox/pyroms_toolbox/BGrid_SODA/get_nc_BGrid_SODA.py index 4ce3fa2..74bf368 100644 --- a/pyroms_toolbox/pyroms_toolbox/BGrid_SODA/get_nc_BGrid_SODA.py +++ b/pyroms_toolbox/pyroms_toolbox/BGrid_SODA/get_nc_BGrid_SODA.py @@ -42,7 +42,7 @@ def get_nc_BGrid_SODA(grdfile, name='SODA_2.1.6_CORAL', area='regional', \ for i in range(mask_t[0,:].shape[1]): for j in range(mask_t[0,:].shape[0]): if mask_t[0,j,i] == 1: - h[j,i] = depth_bnds[bottom[j,i]] + h[j,i] = depth_bnds[int(bottom[j,i])] if area == 'global': #add one row in the north and the south diff --git a/pyroms_toolbox/pyroms_toolbox/BGrid_SODA/make_remap_grid_file.py b/pyroms_toolbox/pyroms_toolbox/BGrid_SODA/make_remap_grid_file.py index f568124..1496275 100644 --- a/pyroms_toolbox/pyroms_toolbox/BGrid_SODA/make_remap_grid_file.py +++ b/pyroms_toolbox/pyroms_toolbox/BGrid_SODA/make_remap_grid_file.py @@ -5,7 +5,6 @@ import netCDF4 as netCDF except: import netCDF3 as netCDF -import pyroms def make_remap_grid_file(Bgrd, Bpos='t'): diff --git a/pyroms_toolbox/pyroms_toolbox/CGrid_GLORYS/CGrid_GLORYS.py b/pyroms_toolbox/pyroms_toolbox/CGrid_GLORYS/CGrid_GLORYS.py index a671a18..bad9c5e 100644 --- a/pyroms_toolbox/pyroms_toolbox/CGrid_GLORYS/CGrid_GLORYS.py +++ b/pyroms_toolbox/pyroms_toolbox/CGrid_GLORYS/CGrid_GLORYS.py @@ -53,12 +53,12 @@ def __init__(self, lon_t, lat_t, lon_u, lat_u, lon_v, lat_v, mask_t, mask_u, mas ones = np.ones(self.h.shape) a1 = lat_u[yrange[0]:yrange[1]+1, xrange[0]+1:xrange[1]+2] - \ - lat_u[yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] + lat_u[yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] a2 = lon_u[yrange[0]:yrange[1]+1, xrange[0]+1:xrange[1]+2] - \ - lon_u[yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] + lon_u[yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1] a3 = 0.5*(lat_u[yrange[0]:yrange[1]+1, xrange[0]+1:xrange[1]+2] + \ - lat_u[yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1]) - a2 = np.where(a2 > 180*ones, a2 - 360*ones, a2) - a2 = np.where(a2 < -180*ones, a2 + 360*ones, a2) - a2 = a2 * np.cos(np.pi/180.*a3) - self.angle = np.arctan2(a1, a2) + lat_u[yrange[0]:yrange[1]+1, xrange[0]:xrange[1]+1]) + a2 = np.where(a2 > 180*ones, a2 - 360*ones, a2) + a2 = np.where(a2 < -180*ones, a2 + 360*ones, a2) + a2 = a2 * np.cos(np.pi/180.*a3) + self.angle = np.arctan2(a1, a2) diff --git a/pyroms_toolbox/pyroms_toolbox/CGrid_GLORYS/__init__.py b/pyroms_toolbox/pyroms_toolbox/CGrid_GLORYS/__init__.py index b7511ff..35a4c6a 100644 --- a/pyroms_toolbox/pyroms_toolbox/CGrid_GLORYS/__init__.py +++ b/pyroms_toolbox/pyroms_toolbox/CGrid_GLORYS/__init__.py @@ -2,7 +2,7 @@ GLORYS module """ -from CGrid_GLORYS import CGrid_GLORYS -from get_nc_CGrid_GLORYS import get_nc_CGrid_GLORYS -from make_remap_grid_file import make_remap_grid_file -from flood import flood +from .CGrid_GLORYS import CGrid_GLORYS +from .get_nc_CGrid_GLORYS import get_nc_CGrid_GLORYS +from .make_remap_grid_file import make_remap_grid_file +from .flood import flood diff --git a/pyroms_toolbox/pyroms_toolbox/CGrid_GLORYS/flood.py b/pyroms_toolbox/pyroms_toolbox/CGrid_GLORYS/flood.py index 8980dab..0725c2f 100644 --- a/pyroms_toolbox/pyroms_toolbox/CGrid_GLORYS/flood.py +++ b/pyroms_toolbox/pyroms_toolbox/CGrid_GLORYS/flood.py @@ -16,7 +16,7 @@ def flood(varz, Cgrd, Cpos='t', irange=None, jrange=None, \ - irange specify grid sub-sample for i direction - jrange specify grid sub-sample for j direction - spval=1e35 define spval value - - dmax=0 if dmax>0, maximum horizontal + - dmax=0 if dmax>0, maximum horizontal flooding distance - cdepth=0 critical depth for flooding if depth no flooding @@ -100,6 +100,6 @@ def flood(varz, Cgrd, Cpos='t', irange=None, jrange=None, \ for i in range(Lm): for j in range(Mm): if mask[j,i] == 1: - varz[bottom[j,i]:,j,i] = varz[bottom[j,i],j,i] + varz[int(bottom[j,i]):,j,i] = varz[int(bottom[j,i]),j,i] return varz diff --git a/pyroms_toolbox/pyroms_toolbox/CGrid_GLORYS/get_nc_CGrid_GLORYS.py b/pyroms_toolbox/pyroms_toolbox/CGrid_GLORYS/get_nc_CGrid_GLORYS.py index fd5f033..43e8226 100644 --- a/pyroms_toolbox/pyroms_toolbox/CGrid_GLORYS/get_nc_CGrid_GLORYS.py +++ b/pyroms_toolbox/pyroms_toolbox/CGrid_GLORYS/get_nc_CGrid_GLORYS.py @@ -45,7 +45,7 @@ def get_nc_CGrid_GLORYS(grdfile, name='GLORYS_CORAL', area='regional', \ for i in range(mask_t[0,:].shape[1]): for j in range(mask_t[0,:].shape[0]): if mask_t[0,j,i] == 1: - h[j,i] = depth_bnds[bottom[j,i]] + h[j,i] = depth_bnds[int(bottom[j,i])] if area == 'global': #add rows in the north and the south, east and west diff --git a/pyroms_toolbox/pyroms_toolbox/CGrid_GLORYS/make_remap_grid_file.py b/pyroms_toolbox/pyroms_toolbox/CGrid_GLORYS/make_remap_grid_file.py index 666f6ed..5e66dbe 100644 --- a/pyroms_toolbox/pyroms_toolbox/CGrid_GLORYS/make_remap_grid_file.py +++ b/pyroms_toolbox/pyroms_toolbox/CGrid_GLORYS/make_remap_grid_file.py @@ -5,7 +5,6 @@ import netCDF4 as netCDF except: import netCDF3 as netCDF -import pyroms def make_remap_grid_file(Cgrd, Cpos='t'): diff --git a/pyroms_toolbox/pyroms_toolbox/Grid_HYCOM/__init__.py b/pyroms_toolbox/pyroms_toolbox/Grid_HYCOM/__init__.py index 7e04c5b..805da8e 100644 --- a/pyroms_toolbox/pyroms_toolbox/Grid_HYCOM/__init__.py +++ b/pyroms_toolbox/pyroms_toolbox/Grid_HYCOM/__init__.py @@ -2,9 +2,9 @@ HYCOM module """ -from Grid_HYCOM import Grid_HYCOM -from get_nc_Grid_HYCOM import get_nc_Grid_HYCOM -from make_remap_grid_file import make_remap_grid_file -from flood import flood -from flood_fast import flood_fast -from flood_fast_weighted import flood_fast_weighted +from .Grid_HYCOM import Grid_HYCOM +from .get_nc_Grid_HYCOM import get_nc_Grid_HYCOM +from .make_remap_grid_file import make_remap_grid_file +from .flood import flood +from .flood_fast import flood_fast +from .flood_fast_weighted import flood_fast_weighted diff --git a/pyroms_toolbox/pyroms_toolbox/Grid_HYCOM/flood.py b/pyroms_toolbox/pyroms_toolbox/Grid_HYCOM/flood.py index 73b885c..6ea4964 100644 --- a/pyroms_toolbox/pyroms_toolbox/Grid_HYCOM/flood.py +++ b/pyroms_toolbox/pyroms_toolbox/Grid_HYCOM/flood.py @@ -12,11 +12,11 @@ def flood(varz, grd, pos='t', irange=None, jrange=None, \ optional switch: - Bpos='t' specify the grid position where - the variable rely + the variable rely - irange specify grid sub-sample for i direction - jrange specify grid sub-sample for j direction - spval=1e35 define spval value - - dmax=0 if dmax>0, maximum horizontal + - dmax=0 if dmax>0, maximum horizontal flooding distance - cdepth=0 critical depth for flooding if depth no flooding @@ -95,6 +95,6 @@ def flood(varz, grd, pos='t', irange=None, jrange=None, \ for i in range(Lm): for j in range(Mm): if mask[j,i] == 1: - varz[bottom[j,i]:,j,i] = varz[bottom[j,i],j,i] + varz[int(bottom[j,i]):,j,i] = varz[int(bottom[j,i]),j,i] return varz diff --git a/pyroms_toolbox/pyroms_toolbox/Grid_HYCOM/flood_fast.py b/pyroms_toolbox/pyroms_toolbox/Grid_HYCOM/flood_fast.py index 6db3706..4cfc5c1 100644 --- a/pyroms_toolbox/pyroms_toolbox/Grid_HYCOM/flood_fast.py +++ b/pyroms_toolbox/pyroms_toolbox/Grid_HYCOM/flood_fast.py @@ -15,11 +15,11 @@ def flood_fast(varz, grd, pos='t', irange=None, jrange=None, \ optional switch: - Bpos='t' specify the grid position where - the variable rely + the variable rely - irange specify grid sub-sample for i direction - jrange specify grid sub-sample for j direction - spval=1e35 define spval value - - dmax=0 if dmax>0, maximum horizontal + - dmax=0 if dmax>0, maximum horizontal flooding distance - cdepth=0 critical depth for flooding if depth no flooding @@ -92,9 +92,9 @@ def flood_fast(varz, grd, pos='t', irange=None, jrange=None, \ varz[k][idx] = spval # RD: #varz[k,:] = _remapping_fast.flood(varz[k,:], dry, wet_mask, dxy) - print 'RD new flooding' + print('RD new flooding') varz[k,:] = creep.cslf(varz[k,:],spval,-200.,200.) - print varz[k,:].min() , varz[k,:].max() + print(varz[k,:].min() , varz[k,:].max()) # drop the deepest values down idx = np.where(np.isnan(varz) == 1) @@ -104,6 +104,6 @@ def flood_fast(varz, grd, pos='t', irange=None, jrange=None, \ for i in range(Lm): for j in range(Mm): if mask[j,i] == 1: - varz[bottom[j,i]:,j,i] = varz[bottom[j,i],j,i] + varz[int(bottom[j,i]):,j,i] = varz[int(bottom[j,i]),j,i] return varz diff --git a/pyroms_toolbox/pyroms_toolbox/Grid_HYCOM/flood_fast_weighted.py b/pyroms_toolbox/pyroms_toolbox/Grid_HYCOM/flood_fast_weighted.py index 6e00e24..19ca8e1 100644 --- a/pyroms_toolbox/pyroms_toolbox/Grid_HYCOM/flood_fast_weighted.py +++ b/pyroms_toolbox/pyroms_toolbox/Grid_HYCOM/flood_fast_weighted.py @@ -12,11 +12,11 @@ def flood_fast_weighted(varz, grd, pos='t', irange=None, jrange=None, \ optional switch: - Bpos='t' specify the grid position where - the variable rely + the variable rely - irange specify grid sub-sample for i direction - jrange specify grid sub-sample for j direction - spval=1e35 define spval value - - dmax=0 if dmax>0, maximum horizontal + - dmax=0 if dmax>0, maximum horizontal flooding distance - cdepth=0 critical depth for flooding if depth no flooding @@ -97,6 +97,6 @@ def flood_fast_weighted(varz, grd, pos='t', irange=None, jrange=None, \ for i in range(Lm): for j in range(Mm): if mask[j,i] == 1: - varz[bottom[j,i]:,j,i] = varz[bottom[j,i],j,i] + varz[int(bottom[j,i]):,j,i] = varz[int(bottom[j,i]),j,i] return varz diff --git a/pyroms_toolbox/pyroms_toolbox/Grid_HYCOM/get_nc_Grid_HYCOM.py b/pyroms_toolbox/pyroms_toolbox/Grid_HYCOM/get_nc_Grid_HYCOM.py index 5d948f9..277ea5d 100644 --- a/pyroms_toolbox/pyroms_toolbox/Grid_HYCOM/get_nc_Grid_HYCOM.py +++ b/pyroms_toolbox/pyroms_toolbox/Grid_HYCOM/get_nc_Grid_HYCOM.py @@ -45,7 +45,7 @@ def get_nc_Grid_HYCOM(grdfile, name='GLBa0.08_NEP'): for i in range(mask_t[0,:].shape[1]): for j in range(mask_t[0,:].shape[0]): if mask_t[0,j,i] == 1: - h[j,i] = depth_bnds[bottom[j,i]+1] + h[j,i] = depth_bnds[int(bottom[j,i])+1] geod = pyproj.Geod(ellps='WGS84') diff --git a/pyroms_toolbox/pyroms_toolbox/Grid_HYCOM/make_remap_grid_file.py b/pyroms_toolbox/pyroms_toolbox/Grid_HYCOM/make_remap_grid_file.py index f05d3e7..f75f433 100644 --- a/pyroms_toolbox/pyroms_toolbox/Grid_HYCOM/make_remap_grid_file.py +++ b/pyroms_toolbox/pyroms_toolbox/Grid_HYCOM/make_remap_grid_file.py @@ -5,7 +5,6 @@ import netCDF4 as netCDF except: import netCDF3 as netCDF -import pyroms def make_remap_grid_file(grd): diff --git a/pyroms_toolbox/pyroms_toolbox/PCA.py b/pyroms_toolbox/pyroms_toolbox/PCA.py index 5ce9bb7..81d137c 100644 --- a/pyroms_toolbox/pyroms_toolbox/PCA.py +++ b/pyroms_toolbox/pyroms_toolbox/PCA.py @@ -73,7 +73,7 @@ def GetPSD(self, blocks_length=0, fs=1, window='boxcar', overlap=0): window_vector = get_window(window, blocks_length) PSD = np.zeros((nECs, blocks_length/2+1)) freq = np.zeros((nECs, blocks_length/2+1)) - for n in xrange(nECs): + for n in range(nECs): P, f = psd(self.ECs[n], NFFT=blocks_length, Fs=fs, window=window_vector, noverlap=overlap) PSD[n] = np.squeeze(P) freq[n] = f @@ -87,7 +87,7 @@ def pack(self, dataset): npt = np.sum(~mask) packedata = np.zeros((nt,npt)) - for t in xrange(nt): + for t in range(nt): packedata[t] = np.ma.compressed(dataset[t]) return packedata, mask @@ -108,7 +108,7 @@ def unpack(self, packedeofs, mask): eofs = np.ma.masked_all((neof,dims)) - for n in xrange(neof): + for n in range(neof): eofs[n,~mask.flatten()] = packedeofs[:,n] if len(mask.shape) == 2: diff --git a/pyroms_toolbox/pyroms_toolbox/TS_diagram.py b/pyroms_toolbox/pyroms_toolbox/TS_diagram.py index 6de7c85..0515657 100644 --- a/pyroms_toolbox/pyroms_toolbox/TS_diagram.py +++ b/pyroms_toolbox/pyroms_toolbox/TS_diagram.py @@ -5,13 +5,13 @@ import pyroms_toolbox -def TS_diagram(temp, salt, depth=None, dens_lev=None, marker_size=2, fmt='%2.2f', pal=cm.spectral, \ +def TS_diagram(temp, salt, depth=None, dens_lev=None, marker_size=2, fmt='%2.2f', pal=cm.Spectral, \ tlim='None', slim='None', outfile=None): if dens_lev is None: dens_lev = np.arange(10,36,1) - if depth is None: + if depth is None: diag = plt.scatter(salt.flatten(), temp.flatten(), s=marker_size, edgecolors='none') else: diag = plt.scatter(salt.flatten(), temp.flatten(), c=depth.flatten(), \ @@ -36,12 +36,12 @@ def TS_diagram(temp, salt, depth=None, dens_lev=None, marker_size=2, fmt='%2.2f' ax.set_xlim(slim) ax.set_ylim(tlim) - + if outfile is not None: if outfile.find('.png') != -1 or outfile.find('.svg') != -1 or \ outfile.find('.eps') != -1: - print 'Write figure to file', outfile + print('Write figure to file', outfile) plt.savefig(outfile, dpi=200, facecolor='w', edgecolor='w', \ orientation='portrait') else: - print 'Unrecognized file extension. Please use .png, .svg or .eps file extension.' + print('Unrecognized file extension. Please use .png, .svg or .eps file extension.') diff --git a/pyroms_toolbox/pyroms_toolbox/__init__.py b/pyroms_toolbox/pyroms_toolbox/__init__.py index 0d0f565..9b9eb87 100644 --- a/pyroms_toolbox/pyroms_toolbox/__init__.py +++ b/pyroms_toolbox/pyroms_toolbox/__init__.py @@ -1,75 +1,76 @@ #!/usr/bin/env python ''' -PYROMS_TOOLBOX is a toolbox for working with ROMS +PYROMS_TOOLBOX is a toolbox for working with ROMS ocean models input/output files based on PYROMS -pyroms and pyroms_toolbox are based on the -python/numpy/matplotlib scientific python suite. +pyroms and pyroms_toolbox are based on the +python/numpy/matplotlib scientific python suite. NetCDF I/O is based on the NetCDF4-python package. ''' -from iview import iview -from jview import jview -from lonview import lonview -from latview import latview -from sview import sview -from zview import zview -from isoview import isoview -from twoDview import twoDview -from transectview import transectview -from quiver import quiver -import seawater -from N2 import N2 -from O2_saturation import O2_saturation -import shapiro_filter -from change import change -from rx0 import rx0 -from rx1 import rx1 -from rvalue import rvalue -from get_coast_line import get_coast_line -from get_coast_line_from_mask import get_coast_line_from_mask -from get_ijcoast_line import get_ijcoast_line -from plot_coast_line import plot_coast_line -from plot_coast_line_from_mask import plot_coast_line_from_mask -from plot_ijcoast_line import plot_ijcoast_line -from lsq_phase_amplitude import lsq_phase_amplitude -from remapping import remapping -from remapping_bound import remapping_bound -from remapping_bound_sig import remapping_bound_sig -from remapping_tensor import remapping_tensor -from nc_create_roms_file import nc_create_roms_file -from nc_create_roms_bdry_file import nc_create_roms_bdry_file -from average import average -from plot_mask import plot_mask -import BGrid_GFDL -from smooth_1D import smooth_1D -import BGrid_SODA -from get_littoral import get_littoral -from get_littoral2 import get_littoral2 -from _move_runoff import move_runoff -from _move_river_t import move_river_t -from TS_diagram import TS_diagram -from date2jday import date2jday -from jday2date import jday2date -from iso2gregorian import iso2gregorian -from gregorian2iso import gregorian2iso -import BGrid_POP -from low_pass_filter import low_pass_filter -from PCA import PCA, center, standardize -from compute_eke import compute_eke -from compute_moc import compute_moc +from .iview import iview +from .jview import jview +from .lonview import lonview +from .latview import latview +from .sview import sview +from .zview import zview +from .isoview import isoview +from .twoDview import twoDview +from .transectview import transectview +from .quiver import quiver +from . import seawater +from .N2 import N2 +from .O2_saturation import O2_saturation +from . import shapiro_filter +from .change import change +from .rx0 import rx0 +from .rx1 import rx1 +from .rvalue import rvalue +from .get_coast_line import get_coast_line +from .get_coast_line_from_mask import get_coast_line_from_mask +from .get_ijcoast_line import get_ijcoast_line +from .plot_coast_line import plot_coast_line +from .plot_coast_line_from_mask import plot_coast_line_from_mask +from .plot_ijcoast_line import plot_ijcoast_line +from .lsq_phase_amplitude import lsq_phase_amplitude +from .remapping import remapping +from .remapping_bound import remapping_bound +from .remapping_bound_sig import remapping_bound_sig +from .remapping_tensor import remapping_tensor +from .nc_create_roms_file import nc_create_roms_file +from .nc_create_roms_bdry_file import nc_create_roms_bdry_file +from .average import average +from .plot_mask import plot_mask +from . import BGrid_GFDL +from .smooth_1D import smooth_1D +from . import BGrid_SODA +from .get_littoral import get_littoral +from .get_littoral2 import get_littoral2 +from ._move_runoff import move_runoff +from ._move_river_t import move_river_t +from .TS_diagram import TS_diagram +from .date2jday import date2jday +from .jday2date import jday2date +from .iso2gregorian import iso2gregorian +from .gregorian2iso import gregorian2iso +from . import BGrid_POP +from .low_pass_filter import low_pass_filter +from .PCA import PCA, center, standardize +from .compute_eke import compute_eke +from .compute_moc import compute_moc #from plot_Robinson_pyngl import plot_Robinson_pyngl -from get_cell_area import get_cell_area -from laplacian import laplacian -from vorticity import vorticity -from strain_norm import strain_norm -from strain_norm_old import strain_norm_old -from shift_SODA_data import shift_SODA_data -import Grid_HYCOM -from mld_from_temp import mld_from_temp -from mld_from_dens import mld_from_dens -from ocean_in import ocean_in +from .get_cell_area import get_cell_area +from .laplacian import laplacian +from .vorticity import vorticity +from .strain_norm import strain_norm +from .strain_norm_old import strain_norm_old +from .shift_SODA_data import shift_SODA_data +from . import Grid_HYCOM +from . import CGrid_GLORYS +from .mld_from_temp import mld_from_temp +from .mld_from_dens import mld_from_dens +from .ocean_in import ocean_in diff --git a/pyroms_toolbox/pyroms_toolbox/average.py b/pyroms_toolbox/pyroms_toolbox/average.py index 79759f1..5843345 100644 --- a/pyroms_toolbox/pyroms_toolbox/average.py +++ b/pyroms_toolbox/pyroms_toolbox/average.py @@ -52,7 +52,7 @@ def average(var, ncfiles, trange=None, avgfile=None, spval=1e37, timevar='ocean_ var = [var] nvar = len(var) else: - raise ValueError, 'var must be a str or a list of str' + raise ValueError('var must be a str or a list of str') avg.ncfiles = pyroms.io.MFDataset(ncfiles) @@ -67,9 +67,9 @@ def average(var, ncfiles, trange=None, avgfile=None, spval=1e37, timevar='ocean_ start = trange[0] end = min(trange[1]+1, Nt) else: - raise ValueError, 'trange must be within interval [0, %s].' %Nt + raise ValueError('trange must be within interval [0, %s].' %Nt) - print range(start,end) + print(list(range(start,end))) for varname in var: name = varname @@ -110,8 +110,8 @@ def average(var, ncfiles, trange=None, avgfile=None, spval=1e37, timevar='ocean_ setattr(avg, varname, incavg[:]) else: - raise ValueError, 'Variable must be 3D (time + 2 spacial dims) or \ -4D (time + 3 spacial dims)' + raise ValueError('Variable must be 3D (time + 2 spacial dims) or \ +4D (time + 3 spacial dims)') # if avgfile is defined, enter this conditional and begin creating a new netCDF file @@ -129,10 +129,10 @@ def average(var, ncfiles, trange=None, avgfile=None, spval=1e37, timevar='ocean_ nc.Created = datetime.now().strftime("%Y-%m-%d %H:%M:%S") nc.Files = ", ".join(avg.ncfiles._files) - print 'Writing '+str(avgfile)+'...' + print('Writing '+str(avgfile)+'...') # for each dimension in original netCDF files, recreate the dimensions in the new netCDF file - for newdim in avg.ncfiles.dimensions.keys(): + for newdim in list(avg.ncfiles.dimensions.keys()): if avg.ncfiles.dimensions[newdim].isunlimited(): nc.createDimension(newdim,None) else: @@ -152,7 +152,7 @@ def average(var, ncfiles, trange=None, avgfile=None, spval=1e37, timevar='ocean_ # for each variable in var, create a new variable with all dimensions associated with that # variable except ocean_time for varname in var: - print ' writting %s...' %varname + print(' writting %s...' %varname) vardims = avg.ncfiles.variables[varname].dimensions @@ -172,9 +172,9 @@ def average(var, ncfiles, trange=None, avgfile=None, spval=1e37, timevar='ocean_ avg.ncfiles.close() nc.close() else: - print "avgfile must be a string that equates to the path where this netCDF file is to be placed." + print("avgfile must be a string that equates to the path where this netCDF file is to be placed.") return else: avg.ncfiles.close() - print "Returning average object..." + print("Returning average object...") return avg diff --git a/pyroms_toolbox/pyroms_toolbox/change.py b/pyroms_toolbox/pyroms_toolbox/change.py index ccfc9b3..5ac3bec 100644 --- a/pyroms_toolbox/pyroms_toolbox/change.py +++ b/pyroms_toolbox/pyroms_toolbox/change.py @@ -7,7 +7,7 @@ def change(old,relation,flag,value): if relation != '==' and relation != '!=' and relation != '>' and relation != '<' and \ relation != '!=' and relation != '>=' and relation != '<=': - raise ValueError, 'Relation {%s} not valid' % relation + raise ValueError('Relation {%s} not valid' % relation) if np.isnan(flag): if relation == '==': @@ -15,7 +15,7 @@ def change(old,relation,flag,value): elif relation == '!=': replace = np.where(np.isnan(old) == False) else: - raise ValueError, 'Relation should be == or ~= to compare to NaN' + raise ValueError('Relation should be == or ~= to compare to NaN') else: if relation == '==': diff --git a/pyroms_toolbox/pyroms_toolbox/compute_eke.py b/pyroms_toolbox/pyroms_toolbox/compute_eke.py index c9abaa8..5bcb57d 100644 --- a/pyroms_toolbox/pyroms_toolbox/compute_eke.py +++ b/pyroms_toolbox/pyroms_toolbox/compute_eke.py @@ -1,5 +1,4 @@ import numpy as np -import pyroms def compute_eke(u, v): diff --git a/pyroms_toolbox/pyroms_toolbox/get_coast_line.py b/pyroms_toolbox/pyroms_toolbox/get_coast_line.py index 56bb61a..189f79e 100644 --- a/pyroms_toolbox/pyroms_toolbox/get_coast_line.py +++ b/pyroms_toolbox/pyroms_toolbox/get_coast_line.py @@ -24,8 +24,8 @@ def get_coast_line(grd, Cpos='rho'): lat = grd.hgrid.lat_rho mask = grd.hgrid.mask_psi else: - raise Warning, '%s bad position. Valid Arakawa-C are \ - rho, u or v.' % Cpos + raise Warning('%s bad position. Valid Arakawa-C are \ + rho, u or v.' % Cpos) jidx, iidx = np.where(mask == 0) @@ -36,28 +36,28 @@ def get_coast_line(grd, Cpos='rho'): if mask[jidx[i], iidx[i]] != mask[jidx[i]+1, iidx[i]]: lonc = ([lon[jidx[i]+1,iidx[i]], lon[jidx[i]+1,iidx[i]+1]]) latc = ([lat[jidx[i]+1,iidx[i]], lat[jidx[i]+1,iidx[i]+1]]) - seg = zip(lonc,latc) + seg = list(zip(lonc,latc)) coast.append(seg) if jidx[i] != 0: if mask[jidx[i], iidx[i]] != mask[jidx[i]-1, iidx[i]]: lonc = ([lon[jidx[i],iidx[i]], lon[jidx[i],iidx[i]+1]]) latc = ([lat[jidx[i],iidx[i]], lat[jidx[i],iidx[i]+1]]) - seg = zip(lonc,latc) + seg = list(zip(lonc,latc)) coast.append(seg) if iidx[i] != mask.shape[1]-1: if mask[jidx[i], iidx[i]] != mask[jidx[i], iidx[i]+1]: lonc = ([lon[jidx[i],iidx[i]+1], lon[jidx[i]+1,iidx[i]+1]]) latc = ([lat[jidx[i],iidx[i]+1], lat[jidx[i]+1,iidx[i]+1]]) - seg = zip(lonc,latc) + seg = list(zip(lonc,latc)) coast.append(seg) if iidx[i] != 0: if mask[jidx[i], iidx[i]] != mask[jidx[i], iidx[i]-1]: lonc = ([lon[jidx[i],iidx[i]], lon[jidx[i]+1,iidx[i]]]) latc = ([lat[jidx[i],iidx[i]], lat[jidx[i]+1,iidx[i]]]) - seg = zip(lonc,latc) + seg = list(zip(lonc,latc)) coast.append(seg) return np.array(coast) diff --git a/pyroms_toolbox/pyroms_toolbox/get_coast_line_from_mask.py b/pyroms_toolbox/pyroms_toolbox/get_coast_line_from_mask.py index 8735888..4a9c207 100644 --- a/pyroms_toolbox/pyroms_toolbox/get_coast_line_from_mask.py +++ b/pyroms_toolbox/pyroms_toolbox/get_coast_line_from_mask.py @@ -19,28 +19,28 @@ def get_coast_line_from_mask(msk, lon, lat): if mask[jidx[i], iidx[i]] != mask[jidx[i]+1, iidx[i]]: lonc = ([lon[jidx[i]+1,iidx[i]], lon[jidx[i]+1,iidx[i]+1]]) latc = ([lat[jidx[i]+1,iidx[i]], lat[jidx[i]+1,iidx[i]+1]]) - seg = zip(lonc,latc) + seg = list(zip(lonc,latc)) coast.append(seg) if jidx[i] != 0: if mask[jidx[i], iidx[i]] != mask[jidx[i]-1, iidx[i]]: lonc = ([lon[jidx[i],iidx[i]], lon[jidx[i],iidx[i]+1]]) latc = ([lat[jidx[i],iidx[i]], lat[jidx[i],iidx[i]+1]]) - seg = zip(lonc,latc) + seg = list(zip(lonc,latc)) coast.append(seg) if iidx[i] != mask.shape[1]-1: if mask[jidx[i], iidx[i]] != mask[jidx[i], iidx[i]+1]: lonc = ([lon[jidx[i],iidx[i]+1], lon[jidx[i]+1,iidx[i]+1]]) latc = ([lat[jidx[i],iidx[i]+1], lat[jidx[i]+1,iidx[i]+1]]) - seg = zip(lonc,latc) + seg = list(zip(lonc,latc)) coast.append(seg) if iidx[i] != 0: if mask[jidx[i], iidx[i]] != mask[jidx[i], iidx[i]-1]: lonc = ([lon[jidx[i],iidx[i]], lon[jidx[i]+1,iidx[i]]]) latc = ([lat[jidx[i],iidx[i]], lat[jidx[i]+1,iidx[i]]]) - seg = zip(lonc,latc) + seg = list(zip(lonc,latc)) coast.append(seg) return np.array(coast) diff --git a/pyroms_toolbox/pyroms_toolbox/get_ijcoast_line.py b/pyroms_toolbox/pyroms_toolbox/get_ijcoast_line.py index 24177c1..7041dc6 100644 --- a/pyroms_toolbox/pyroms_toolbox/get_ijcoast_line.py +++ b/pyroms_toolbox/pyroms_toolbox/get_ijcoast_line.py @@ -17,28 +17,28 @@ def get_ijcoast_line(mask): if mask[jidx[i], iidx[i]] != mask[jidx[i]+1, iidx[i]]: ic = ([iidx[i]-0.5, iidx[i]+1-0.5]) jc = ([jidx[i]+1-0.5, jidx[i]+1-0.5]) - seg = zip(ic,jc) + seg = list(zip(ic,jc)) ijcoast.append(seg) if jidx[i] != 0: if mask[jidx[i], iidx[i]] != mask[jidx[i]-1, iidx[i]]: ic = ([iidx[i]-0.5, iidx[i]+1-0.5]) jc = ([jidx[i]-0.5, jidx[i]-0.5]) - seg = zip(ic,jc) + seg = list(zip(ic,jc)) ijcoast.append(seg) if iidx[i] != mask.shape[1]-1: if mask[jidx[i], iidx[i]] != mask[jidx[i], iidx[i]+1]: ic = ([iidx[i]+1-0.5, iidx[i]+1-0.5]) jc = ([jidx[i]-0.5, jidx[i]+1-0.5]) - seg = zip(ic,jc) + seg = list(zip(ic,jc)) ijcoast.append(seg) if iidx[i] != 0: if mask[jidx[i], iidx[i]] != mask[jidx[i], iidx[i]-1]: ic = ([iidx[i]-0.5, iidx[i]-0.5]) jc = ([jidx[i]-0.5, jidx[i]+1-0.5]) - seg = zip(ic,jc) + seg = list(zip(ic,jc)) ijcoast.append(seg) return np.array(ijcoast) diff --git a/pyroms_toolbox/pyroms_toolbox/isoview.py b/pyroms_toolbox/pyroms_toolbox/isoview.py index c3592bb..3e1045e 100644 --- a/pyroms_toolbox/pyroms_toolbox/isoview.py +++ b/pyroms_toolbox/pyroms_toolbox/isoview.py @@ -15,29 +15,29 @@ def isoview(var, prop, tindex, isoval, grid, filename=None, \ map = isoview(var, prop, tindex, isoval, grid, {optional switch}) optional switch: - - filename if defined, load the variable from file - - cmin set color minimum limit - - cmax set color maximum limit - - clev set the number of color step - - fill use contourf instead of pcolor - - contour overlay contour (request fill=True) - - d contour density (default d=4) - - range set axis limit - - fts set font size (default: 12) - - title add title to the plot - - clb add colorbar (defaul: True) - - pal set color map (default: cm.jet) - - proj set projection type (default: merc) - - fill_land fill land masked area with gray (defaul: True) - - outfile if defined, write figure to file - - plot a projection of variable at property == isoval. If filename - is provided, var and prop must be a strings and the variables will + - filename if defined, load the variable from file + - cmin set color minimum limit + - cmax set color maximum limit + - clev set the number of color step + - fill use contourf instead of pcolor + - contour overlay contour (request fill=True) + - d contour density (default d=4) + - range set axis limit + - fts set font size (default: 12) + - title add title to the plot + - clb add colorbar (defaul: True) + - pal set color map (default: cm.jet) + - proj set projection type (default: merc) + - fill_land fill land masked area with gray (defaul: True) + - outfile if defined, write figure to file + + plot a projection of variable at property == isoval. If filename + is provided, var and prop must be a strings and the variables will be load from the file. grid can be a grid object or a gridid. In the later case, the grid object correponding to the provided gridid will be loaded. - If proj is not None, return a Basemap object to be used with quiver - for example. + If proj is not None, return a Basemap object to be used with quiver + for example. """ # get grid @@ -81,10 +81,10 @@ def isoview(var, prop, tindex, isoval, grid, filename=None, \ # get constante-iso slice if tindex == -1: var = var[:,:,:] - prop = prop[:,:,:] + prop = prop[:,:,:] else: var = var[tindex,:,:,:] - prop = prop[tindex,:,:,:] + prop = prop[tindex,:,:,:] if fill == True: isoslice, lon, lat = pyroms.tools.isoslice(var, prop, isoval, \ @@ -132,7 +132,7 @@ def isoview(var, prop, tindex, isoval, grid, filename=None, \ lon_max = lon.max() lon_0 = (lon_min + lon_max) / 2. lat_min = lat.min() - lat_max = lat.max() + lat_max = lat.max() lat_0 = (lat_min + lat_max) / 2. else: lon_min = range[0] @@ -150,49 +150,49 @@ def isoview(var, prop, tindex, isoval, grid, filename=None, \ urcrnrlon=lon_max, urcrnrlat=lat_max, lat_0=lat_0, lon_0=lon_0, \ resolution='h', area_thresh=5.) #map = pyroms.utility.get_grid_proj(grd, type=proj) - x, y = map(lon,lat) - + x, y = list(map(lon,lat)) + if fill_land is True and proj is not None: # fill land and draw coastlines map.drawcoastlines() map.fillcontinents(color='grey') else: - if proj is not None: + if proj is not None: Basemap.pcolor(map, x, y, mask, vmin=-2, cmap=cm.gray) pyroms_toolbox.plot_coast_line(grd, map) - else: + else: plt.pcolor(lon, lat, mask, vmin=-2, cmap=cm.gray) pyroms_toolbox.plot_coast_line(grd) - + if fill is True: - if proj is not None: + if proj is not None: cf = Basemap.contourf(map, x, y, isoslice, vc, cmap = pal, \ norm = pal_norm) - else: + else: cf = plt.contourf(lon, lat, isoslice, vc, cmap = pal, \ norm = pal_norm) else: - if proj is not None: + if proj is not None: cf = Basemap.pcolor(map, x, y, isoslice, cmap = pal, norm = pal_norm) - else: + else: cf = plt.pcolor(lon, lat, isoslice, cmap = pal, norm = pal_norm) if clb is True: - clb = plt.colorbar(cf, fraction=0.075,format='%.2f') - for t in clb.ax.get_yticklabels(): - t.set_fontsize(fts) + clb = plt.colorbar(cf, fraction=0.075,format='%.2f') + for t in clb.ax.get_yticklabels(): + t.set_fontsize(fts) if contour is True: if fill is not True: - raise Warning, 'Please run again with fill=True to overlay contour.' + raise Warning('Please run again with fill=True to overlay contour.') else: if proj is not None: Basemap.contour(map, x, y, isoslice, vc[::d], colors='k', linewidths=0.5, linestyles='solid') - else: + else: plt.contour(lon, lat, isoslice, vc[::d], colors='k', linewidths=0.5, linestyles='solid') if proj is None and range is not None: - plt.axis(range) + plt.axis(range) if title is not None: @@ -207,11 +207,11 @@ def isoview(var, prop, tindex, isoval, grid, filename=None, \ if outfile is not None: if outfile.find('.png') != -1 or outfile.find('.svg') != -1 or \ outfile.find('.eps') != -1: - print 'Write figure to file', outfile + print('Write figure to file', outfile) plt.savefig(outfile, dpi=200, facecolor='w', edgecolor='w', \ orientation='portrait') else: - print 'Unrecognized file extension. Please use .png, .svg or .eps file extension.' + print('Unrecognized file extension. Please use .png, .svg or .eps file extension.') if proj is None: diff --git a/pyroms_toolbox/pyroms_toolbox/iview.py b/pyroms_toolbox/pyroms_toolbox/iview.py index 17813ff..6df0eac 100644 --- a/pyroms_toolbox/pyroms_toolbox/iview.py +++ b/pyroms_toolbox/pyroms_toolbox/iview.py @@ -20,7 +20,7 @@ def iview(var, tindex, iindex, gridid, filename=None, \ - clev set the number of color step - fill use contourf instead of pcolor - contour overlay contour (request fill=True) - - d contour density (default d=4) + - d contour density (default d=4) - jrange j range - hrange h range - fts set font size (default: 12) @@ -131,21 +131,21 @@ def iview(var, tindex, iindex, gridid, filename=None, \ #pal.set_bad('w', 1.0) pal_norm = colors.BoundaryNorm(vc,ncolors=256, clip = False) - + # clear figure #plt.clf() if map is True: - # set axes for the main plot in order to keep space for the map - if fts < 12: - ax=None - else: - ax = plt.axes([0.15, 0.08, 0.8, 0.65]) - else: - if fts < 12: - ax=None - else: - ax=plt.axes([0.15, 0.1, 0.8, 0.8]) + # set axes for the main plot in order to keep space for the map + if fts < 12: + ax=None + else: + ax = plt.axes([0.15, 0.08, 0.8, 0.65]) + else: + if fts < 12: + ax=None + else: + ax=plt.axes([0.15, 0.1, 0.8, 0.8]) if fill is True: @@ -154,13 +154,13 @@ def iview(var, tindex, iindex, gridid, filename=None, \ cf = plt.pcolor(lati, zi, islice, cmap = pal, norm = pal_norm, axes=ax) if clb is True: - clb = plt.colorbar(cf, fraction=0.075,format=clbformat) - for t in clb.ax.get_yticklabels(): - t.set_fontsize(fts) + clb = plt.colorbar(cf, fraction=0.075,format=clbformat) + for t in clb.ax.get_yticklabels(): + t.set_fontsize(fts) if contour is True: if fill is not True: - raise Warning, 'Please run again with fill=True for overlay contour.' + raise Warning('Please run again with fill=True for overlay contour.') else: plt.contour(lati, zi, islice, vc[::d], colors='k', linewidths=0.5, linestyles='solid', axes=ax) @@ -188,8 +188,8 @@ def iview(var, tindex, iindex, gridid, filename=None, \ if map is True: # draw a map with constant-i slice location ax_map = plt.axes([0.4, 0.76, 0.2, 0.23]) - varm = np.ma.masked_where(mask[:,:] == 0, var[var.shape[0]-1,:,:]) - xmin, xmax = ax.get_xlim() + varm = np.ma.masked_where(mask[:,:] == 0, var[var.shape[0]-1,:,:]) + xmin, xmax = ax.get_xlim() dd = (lat[:,iindex] - xmin) * (lat[:,iindex] - xmin) start = np.where(dd == dd.min()) dd = (lat[:,iindex] - xmax) * (lat[:,iindex] - xmax) @@ -198,12 +198,12 @@ def iview(var, tindex, iindex, gridid, filename=None, \ lon_max = lon.max() lon_0 = (lon_min + lon_max) / 2. lat_min = lat.min() - lat_max = lat.max() + lat_max = lat.max() lat_0 = (lat_min + lat_max) / 2. map = Basemap(projection='merc', llcrnrlon=lon_min, llcrnrlat=lat_min, \ urcrnrlon=lon_max, urcrnrlat=lat_max, lat_0=lat_0, lon_0=lon_0, \ resolution='i', area_thresh=10.) - x, y = map(lon,lat) + x, y = list(map(lon,lat)) # fill land and draw coastlines map.drawcoastlines() map.fillcontinents(color='grey') @@ -215,10 +215,10 @@ def iview(var, tindex, iindex, gridid, filename=None, \ if outfile is not None: if outfile.find('.png') != -1 or outfile.find('.svg') != -1 or outfile.find('.eps') != -1: - print 'Write figure to file', outfile + print('Write figure to file', outfile) plt.savefig(outfile, dpi=200, facecolor='w', edgecolor='w', orientation='portrait') else: - print 'Unrecognized file extension. Please use .png, .svg or .eps file extension.' + print('Unrecognized file extension. Please use .png, .svg or .eps file extension.') return diff --git a/pyroms_toolbox/pyroms_toolbox/jday2date.py b/pyroms_toolbox/pyroms_toolbox/jday2date.py index 8c5c95b..1b16630 100644 --- a/pyroms_toolbox/pyroms_toolbox/jday2date.py +++ b/pyroms_toolbox/pyroms_toolbox/jday2date.py @@ -22,18 +22,18 @@ def jday2date(jday): for t in range(nt): j = int(np.floor(jday[t])) + 32044 + jd0 - g = j / 146097 + g = j // 146097 dg = j % 146097 - c = (dg / 36524 + 1) * 3 / 4 + c = (dg // 36524 + 1) * 3 // 4 dc = dg - c * 36524 - b = dc / 1461 + b = dc // 1461 db = dc % 1461 - a = (db / 365 + 1) * 3 / 4 + a = (db // 365 + 1) * 3 // 4 da = db - a * 365 y = g * 400 + c * 100 + b * 4 + a - m = (da * 5 + 308) / 153 - 2 - d = da - (m + 4) * 153 / 5 + 122 - Y = y - 4800 + (m + 2) / 12 + m = (da * 5 + 308) // 153 - 2 + d = da - (m + 4) * 153 // 5 + 122 + Y = y - 4800 + (m + 2) // 12 M = (m + 2) % 12 + 1 D = d + 1 diff --git a/pyroms_toolbox/pyroms_toolbox/jview.py b/pyroms_toolbox/pyroms_toolbox/jview.py index 66fc00c..e5406e6 100644 --- a/pyroms_toolbox/pyroms_toolbox/jview.py +++ b/pyroms_toolbox/pyroms_toolbox/jview.py @@ -20,7 +20,7 @@ def jview(var, tindex, jindex, gridid, filename=None, \ - clev set the number of color step - fill use contourf instead of pcolor - contour overlay contour (request fill=True) - - d contour density (default d=4) + - d contour density (default d=4) - irange i range - hrange h range - fts set font size (default: 12) @@ -130,21 +130,21 @@ def jview(var, tindex, jindex, gridid, filename=None, \ #pal.set_bad('w', 1.0) pal_norm = colors.BoundaryNorm(vc,ncolors=256, clip = False) - + # clear figure #plt.clf() if map is True: - # set axes for the main plot in order to keep space for the map - if fts < 12: - ax=None - else: - ax = plt.axes([0.15, 0.08, 0.8, 0.65]) - else: - if fts < 12: - ax=None - else: - ax=plt.axes([0.15, 0.1, 0.8, 0.8]) + # set axes for the main plot in order to keep space for the map + if fts < 12: + ax=None + else: + ax = plt.axes([0.15, 0.08, 0.8, 0.65]) + else: + if fts < 12: + ax=None + else: + ax=plt.axes([0.15, 0.1, 0.8, 0.8]) if fill is True: @@ -153,13 +153,13 @@ def jview(var, tindex, jindex, gridid, filename=None, \ cf = plt.pcolor(lonj, zj, jslice, cmap = pal, norm = pal_norm, axes=ax) if clb is True: - clb = plt.colorbar(cf, fraction=0.075,format=clbformat) - for t in clb.ax.get_yticklabels(): - t.set_fontsize(fts) + clb = plt.colorbar(cf, fraction=0.075,format=clbformat) + for t in clb.ax.get_yticklabels(): + t.set_fontsize(fts) if contour is True: if fill is not True: - raise Warning, 'Please run again with fill=True for overlay contour.' + raise Warning('Please run again with fill=True for overlay contour.') else: plt.contour(lonj, zj, jslice, vc[::d], colors='k', linewidths=0.5, linestyles='solid', axes=ax) @@ -187,8 +187,8 @@ def jview(var, tindex, jindex, gridid, filename=None, \ if map is True: # draw a map with constant-i slice location ax_map = plt.axes([0.4, 0.76, 0.2, 0.23]) - varm = np.ma.masked_where(mask[:,:] == 0, var[var.shape[0]-1,:,:]) - xmin, xmax = ax.get_xlim() + varm = np.ma.masked_where(mask[:,:] == 0, var[var.shape[0]-1,:,:]) + xmin, xmax = ax.get_xlim() dd = (lon[jindex,:] - xmin) * (lon[jindex,:] - xmin) start = np.where(dd == dd.min()) dd = (lon[jindex,:] - xmax) * (lon[jindex,:] - xmax) @@ -197,12 +197,12 @@ def jview(var, tindex, jindex, gridid, filename=None, \ lon_max = lon.max() lon_0 = (lon_min + lon_max) / 2. lat_min = lat.min() - lat_max = lat.max() + lat_max = lat.max() lat_0 = (lat_min + lat_max) / 2. map = Basemap(projection='merc', llcrnrlon=lon_min, llcrnrlat=lat_min, \ urcrnrlon=lon_max, urcrnrlat=lat_max, lat_0=lat_0, lon_0=lon_0, \ resolution='i', area_thresh=10.) - x, y = map(lon,lat) + x, y = list(map(lon,lat)) # fill land and draw coastlines map.drawcoastlines() map.fillcontinents(color='grey') @@ -214,10 +214,10 @@ def jview(var, tindex, jindex, gridid, filename=None, \ if outfile is not None: if outfile.find('.png') != -1 or outfile.find('.svg') != -1 or outfile.find('.eps') != -1: - print 'Write figure to file', outfile + print('Write figure to file', outfile) plt.savefig(outfile, dpi=200, facecolor='w', edgecolor='w', orientation='portrait') else: - print 'Unrecognized file extension. Please use .png, .svg or .eps file extension.' + print('Unrecognized file extension. Please use .png, .svg or .eps file extension.') return diff --git a/pyroms_toolbox/pyroms_toolbox/latview.py b/pyroms_toolbox/pyroms_toolbox/latview.py index 05e4bff..2937ce0 100644 --- a/pyroms_toolbox/pyroms_toolbox/latview.py +++ b/pyroms_toolbox/pyroms_toolbox/latview.py @@ -20,7 +20,7 @@ def latview(var, tindex, latitude, gridid, filename=None, \ - clev set the number of color step - fill use contourf instead of pcolor - contour overlay contour (request fill=True) - - d contour density (default d=4) + - d contour density (default d=4) - lonrange longitude range - hrange h range - fts set font size (default: 12) @@ -30,8 +30,8 @@ def latview(var, tindex, latitude, gridid, filename=None, \ - clb add colorbar (defaul: True) - outfile if defined, write figure to file - plot a constante-latitudinal slice of variable var. If filename - is provided, var must be a string and the variable will be load + plot a constante-latitudinal slice of variable var. If filename + is provided, var must be a string and the variable will be load from the file. grid can be a grid object or a gridid. In the later case, the grid object correponding to the provided gridid will be loaded. @@ -124,21 +124,21 @@ def latview(var, tindex, latitude, gridid, filename=None, \ #pal.set_bad('w', 1.0) pal_norm = colors.BoundaryNorm(vc,ncolors=256, clip = False) - + # clear figure #plt.clf() if map is True: - # set axes for the main plot in order to keep space for the map - if fts < 12: - ax=None - else: - ax = plt.axes([0.15, 0.08, 0.8, 0.65]) - else: - if fts < 12: - ax=None - else: - ax=plt.axes([0.15, 0.1, 0.8, 0.8]) + # set axes for the main plot in order to keep space for the map + if fts < 12: + ax=None + else: + ax = plt.axes([0.15, 0.08, 0.8, 0.65]) + else: + if fts < 12: + ax=None + else: + ax=plt.axes([0.15, 0.1, 0.8, 0.8]) if fill is True: @@ -147,13 +147,13 @@ def latview(var, tindex, latitude, gridid, filename=None, \ cf = plt.pcolor(lons, zs, latslice, cmap = pal, norm = pal_norm, axes=ax) if clb is True: - clb = plt.colorbar(cf, fraction=0.075,format='%.2f') - for t in clb.ax.get_yticklabels(): - t.set_fontsize(fts) + clb = plt.colorbar(cf, fraction=0.075,format='%.2f') + for t in clb.ax.get_yticklabels(): + t.set_fontsize(fts) if contour is True: if fill is not True: - raise Warning, 'Please run again with fill=True for overlay contour.' + raise Warning('Please run again with fill=True for overlay contour.') else: plt.contour(lons, zs, latslice, vc[::d], colors='k', linewidths=0.5, linestyles='solid', axes=ax) @@ -181,25 +181,25 @@ def latview(var, tindex, latitude, gridid, filename=None, \ if map is True: # draw a map with constant-i slice location ax_map = plt.axes([0.4, 0.76, 0.2, 0.23]) - varm = np.ma.masked_where(mask[:,:] == 0, var[var.shape[0]-1,:,:]) + varm = np.ma.masked_where(mask[:,:] == 0, var[var.shape[0]-1,:,:]) lon_min = lon.min() lon_max = lon.max() lon_0 = (lon_min + lon_max) / 2. lat_min = lat.min() - lat_max = lat.max() + lat_max = lat.max() lat_0 = (lat_min + lat_max) / 2. map = Basemap(projection='merc', llcrnrlon=lon_min, llcrnrlat=lat_min, \ urcrnrlon=lon_max, urcrnrlat=lat_max, lat_0=lat_0, lon_0=lon_0, \ resolution='i', area_thresh=10.) - x, y = map(lon,lat) + x, y = list(map(lon,lat)) if lonrange is None: - xs, ys = map(lons[0,:],lats[0,:]) + xs, ys = list(map(lons[0,:],lats[0,:])) else: c1 = lats[0,:] >= lonrange[0] c2 = lats[0,:] <= lonrange[1] c = c1 & c2 idx = np.where(c == True) - xs, ys = map(lons[0,idx[0]],lats[0,idx[0]]) + xs, ys = list(map(lons[0,idx[0]],lats[0,idx[0]])) # fill land and draw coastlines map.drawcoastlines() map.fillcontinents(color='grey') @@ -210,10 +210,10 @@ def latview(var, tindex, latitude, gridid, filename=None, \ if outfile is not None: if outfile.find('.png') != -1 or outfile.find('.svg') != -1 or outfile.find('.eps') != -1: - print 'Write figure to file', outfile + print('Write figure to file', outfile) plt.savefig(outfile, dpi=200, facecolor='w', edgecolor='w', orientation='portrait') else: - print 'Unrecognized file extension. Please use .png, .svg or .eps file extension.' + print('Unrecognized file extension. Please use .png, .svg or .eps file extension.') return diff --git a/pyroms_toolbox/pyroms_toolbox/lonview.py b/pyroms_toolbox/pyroms_toolbox/lonview.py index 989e465..0861f26 100644 --- a/pyroms_toolbox/pyroms_toolbox/lonview.py +++ b/pyroms_toolbox/pyroms_toolbox/lonview.py @@ -20,7 +20,7 @@ def lonview(var, tindex, longitude, gridid, filename=None, \ - clev set the number of color step - fill use contourf instead of pcolor - contour overlay contour (request fill=True) - - d contour density (default d=4) + - d contour density (default d=4) - latrange latitude range - hrange h range - fts set font size (default: 12) @@ -30,8 +30,8 @@ def lonview(var, tindex, longitude, gridid, filename=None, \ - clb add colorbar (defaul: True) - outfile if defined, write figure to file - plot a constant-longitudinal slice of variable var. If filename - is provided, var must be a string and the variable will be load + plot a constant-longitudinal slice of variable var. If filename + is provided, var must be a string and the variable will be load from the file. grid can be a grid object or a gridid. In the later case, the grid object correponding to the provided gridid will be loaded. @@ -124,21 +124,21 @@ def lonview(var, tindex, longitude, gridid, filename=None, \ #pal.set_bad('w', 1.0) pal_norm = colors.BoundaryNorm(vc,ncolors=256, clip = False) - + # clear figure #plt.clf() if map is True: - # set axes for the main plot in order to keep space for the map - if fts < 12: - ax=None - else: - ax = plt.axes([0.15, 0.08, 0.8, 0.65]) - else: - if fts < 12: - ax=None - else: - ax=plt.axes([0.15, 0.1, 0.8, 0.8]) + # set axes for the main plot in order to keep space for the map + if fts < 12: + ax=None + else: + ax = plt.axes([0.15, 0.08, 0.8, 0.65]) + else: + if fts < 12: + ax=None + else: + ax=plt.axes([0.15, 0.1, 0.8, 0.8]) if fill is True: @@ -147,13 +147,13 @@ def lonview(var, tindex, longitude, gridid, filename=None, \ cf = plt.pcolor(lats, zs, lonslice, cmap = pal, norm = pal_norm, axes=ax) if clb is True: - clb = plt.colorbar(cf, fraction=0.075,format='%.2f') - for t in clb.ax.get_yticklabels(): - t.set_fontsize(fts) + clb = plt.colorbar(cf, fraction=0.075,format='%.2f') + for t in clb.ax.get_yticklabels(): + t.set_fontsize(fts) if contour is True: if fill is not True: - raise Warning, 'Please run again with fill=True for overlay contour.' + raise Warning('Please run again with fill=True for overlay contour.') else: plt.contour(lats, zs, lonslice, vc[::d], colors='k', linewidths=0.5, linestyles='solid', axes=ax) @@ -181,25 +181,25 @@ def lonview(var, tindex, longitude, gridid, filename=None, \ if map is True: # draw a map with constant-i slice location ax_map = plt.axes([0.4, 0.76, 0.2, 0.23]) - varm = np.ma.masked_where(mask[:,:] == 0, var[var.shape[0]-1,:,:]) + varm = np.ma.masked_where(mask[:,:] == 0, var[var.shape[0]-1,:,:]) lon_min = lon.min() lon_max = lon.max() lon_0 = (lon_min + lon_max) / 2. lat_min = lat.min() - lat_max = lat.max() + lat_max = lat.max() lat_0 = (lat_min + lat_max) / 2. map = Basemap(projection='merc', llcrnrlon=lon_min, llcrnrlat=lat_min, \ urcrnrlon=lon_max, urcrnrlat=lat_max, lat_0=lat_0, lon_0=lon_0, \ resolution='i', area_thresh=10.) - x, y = map(lon,lat) + x, y = list(map(lon,lat)) if latrange is None: - xs, ys = map(lons[0,:],lats[0,:]) + xs, ys = list(map(lons[0,:],lats[0,:])) else: c1 = lats[0,:] >= latrange[0] c2 = lats[0,:] <= latrange[1] c = c1 & c2 idx = np.where(c == True) - xs, ys = map(lons[0,idx[0]],lats[0,idx[0]]) + xs, ys = list(map(lons[0,idx[0]],lats[0,idx[0]])) # fill land and draw coastlines map.drawcoastlines() map.fillcontinents(color='grey') @@ -210,10 +210,10 @@ def lonview(var, tindex, longitude, gridid, filename=None, \ if outfile is not None: if outfile.find('.png') != -1 or outfile.find('.svg') != -1 or outfile.find('.eps') != -1: - print 'Write figure to file', outfile + print('Write figure to file', outfile) plt.savefig(outfile, dpi=200, facecolor='w', edgecolor='w', orientation='portrait') else: - print 'Unrecognized file extension. Please use .png, .svg or .eps file extension.' + print('Unrecognized file extension. Please use .png, .svg or .eps file extension.') return diff --git a/pyroms_toolbox/pyroms_toolbox/low_pass_filter.py b/pyroms_toolbox/pyroms_toolbox/low_pass_filter.py index 45b5702..5a60a76 100644 --- a/pyroms_toolbox/pyroms_toolbox/low_pass_filter.py +++ b/pyroms_toolbox/pyroms_toolbox/low_pass_filter.py @@ -20,7 +20,7 @@ def low_pass_filter(data, window_size=3): low_passed_data = np.zeros(data.shape) if np.abs(window_size) % 2 != 1: - raise ValueError, 'window_size must be odd.' + raise ValueError('window_size must be odd.') win2 = (window_size - 1) / 2 diff --git a/pyroms_toolbox/pyroms_toolbox/nc_create_roms_file.py b/pyroms_toolbox/pyroms_toolbox/nc_create_roms_file.py index 879877d..7227245 100644 --- a/pyroms_toolbox/pyroms_toolbox/nc_create_roms_file.py +++ b/pyroms_toolbox/pyroms_toolbox/nc_create_roms_file.py @@ -48,29 +48,29 @@ def nc_create_roms_file(filename, grd, ocean_time, lgrid=True): nc.createVariable('s_rho', 'f8', ('s_rho')) nc.variables['s_rho'].long_name = 'S-coordinate at RHO-points' - nc.variables['s_rho'].valid_min = '-1' - nc.variables['s_rho'].valid_max = '0' + nc.variables['s_rho'].valid_min = '-1.0' + nc.variables['s_rho'].valid_max = '0.0' nc.variables['s_rho'].field = 's_rho,scalar' nc.variables['s_rho'][:] = grd.vgrid.s_rho nc.createVariable('s_w', 'f8', ('s_w')) nc.variables['s_w'].long_name = 'S-coordinate at W-points' - nc.variables['s_w'].valid_min = '-1' - nc.variables['s_w'].valid_max = '0' + nc.variables['s_w'].valid_min = '-1.0' + nc.variables['s_w'].valid_max = '0.0' nc.variables['s_w'].field = 's_w,scalar' nc.variables['s_w'][:] = grd.vgrid.s_w nc.createVariable('Cs_r', 'f8', ('s_rho')) nc.variables['Cs_r'].long_name = 'S-coordinate stretching curves at RHO-points' - nc.variables['Cs_r'].valid_min = '-1' - nc.variables['Cs_r'].valid_max = '0' + nc.variables['Cs_r'].valid_min = '-1.0' + nc.variables['Cs_r'].valid_max = '0.0' nc.variables['Cs_r'].field = 'Cs_r,scalar' nc.variables['Cs_r'][:] = grd.vgrid.Cs_r nc.createVariable('Cs_w', 'f8', ('s_w')) nc.variables['Cs_w'].long_name = 'S-coordinate stretching curves at W-points' - nc.variables['Cs_w'].valid_min = '-1' - nc.variables['Cs_w'].valid_max = '0' + nc.variables['Cs_w'].valid_min = '-1.0' + nc.variables['Cs_w'].valid_max = '0.0' nc.variables['Cs_w'].field = 'Cs_w,scalar' nc.variables['Cs_w'][:] = grd.vgrid.Cs_w diff --git a/pyroms_toolbox/pyroms_toolbox/ocean_in.py b/pyroms_toolbox/pyroms_toolbox/ocean_in.py index d638a7b..7871528 100644 --- a/pyroms_toolbox/pyroms_toolbox/ocean_in.py +++ b/pyroms_toolbox/pyroms_toolbox/ocean_in.py @@ -8,7 +8,7 @@ """ Some tools for parsing the ROMS ocean.in file, saving it to JSON and/or -writing it back out to ocean.in format. The Python format is a list and +writing it back out to ocean.in format. The Python format is a list and a dictionary. The dictionary has the settable variables such as 'Ngrids' as keys, the values as values in string form. The list is more complex, containing one element for comment lines and blank lines and up to four @@ -27,18 +27,18 @@ class Line: """ def __init__(self, text, ngrids=False, pos=0, comment="", extra=[]): """(Line, str, bool, int, str) -> NoneType - Constructor for line with ROMS variable name. + Constructor for line with ROMS variable name. - text - String with ROMS variable name. - ngrids - One value per grid (True) or one for all grids (False) - pos - Position of first = in file. + text - String with ROMS variable name. + ngrids - One value per grid (True) or one for all grids (False) + pos - Position of first = in file. comment - String containing a final comment (if any) - """ - self.text = text - self.ngrids = ngrids - self.pos = pos - self.comment = comment - self.extra = extra + """ + self.text = text + self.ngrids = ngrids + self.pos = pos + self.comment = comment + self.extra = extra class ocean_in: @@ -51,35 +51,35 @@ class ocean_in: def do_lines(self, line_list): # Private helper function for dealing with continuation lines first = line_list.pop(0) - extra = [] + extra = [] if len(first) > 1: extra.append(first[1]) else: extra.append("") p = re.compile('([^=]+)(=+)([^=!]+)') try: - eq_pos = first[0].find('=') + eq_pos = first[0].find('=') m = p.match(first[0]) key = m.group(1) eq = m.group(2) value = m.group(3) - key = key.strip() - value = value.lstrip() + key = key.strip() + value = value.lstrip() except: - print("trouble!", first) + print(("trouble!", first)) exit() key = key.strip() value_list = [value] for item in line_list: - line = item[0] + line = item[0] line = line.strip() value_list.append(line) if len(item) > 1: extra.append(item[1]) else: extra.append("") - ngrids = False - if eq == "==": ngrids = True + ngrids = False + if eq == "==": ngrids = True my_list = Line(key, ngrids=ngrids, pos=eq_pos, extra = extra) self.var_list.append(my_list) self.var_dict[key] = value_list @@ -98,12 +98,12 @@ def __init__(self, fname): fh = open(fname) for line in fh: - # Handle blank lines and lines starting with ! - line = line.rstrip() + # Handle blank lines and lines starting with ! + line = line.rstrip() if len(line) == 0 or line[0] == '!': line_list = Line(line) self.var_list.append(line_list) - continue + continue # Look for comments after the assignment and stash them away p = re.compile('(.*\S)( *!.*)') @@ -135,7 +135,7 @@ def __init__(self, fname): eq = m.group(2) value = m.group(3) except: - print("trouble with line:", line) + print(("trouble with line:", line)) exit() key = key.strip() value = [value.strip()] @@ -155,69 +155,69 @@ def write_ocean_in(self, fname): try: fh = open(fname, 'w') except: - print('trouble opening file', fname) + print(('trouble opening file', fname)) exit() for item in self.var_list: # Deal with non-var lines first - if item.pos == 0: + if item.pos == 0: fh.write(item.text) fh.write("\n") - continue - + continue + varname = item.text - eq = "=" - if item.ngrids: eq = "==" - value = self.var_dict[varname] + eq = "=" + if item.ngrids: eq = "==" + value = self.var_dict[varname] string = ' '.join(value) string = item.text + ' ' + eq + ' ' + string - if item.comment: + if item.comment: string += item.comment - index = string.find('=') - # We might need pos below. - pos = item.pos + index = string.find('=') + # We might need pos below. + pos = item.pos if pos > index: - string = ' '*(item.pos-index) + string + string = ' '*(item.pos-index) + string - # Look for continuation lines and split them up - first = True + # Look for continuation lines and split them up + first = True p = re.compile('(\\\\|\|)') m = p.findall(string) - if m: - # All continuation chunks should have an "extra" - # except after a merge - extra = item.extra - count = 0 + if m: + # All continuation chunks should have an "extra" + # except after a merge + extra = item.extra + count = 0 for match in m: index = string.find(match) part = string[0:index+len(match)] - if len(extra) > count and extra[count]: + if len(extra) > count and extra[count]: part += extra[count] - count += 1 + count += 1 string = string[index+len(match):] - # Add space to front of trailing lines - if first: - first = False - else: + # Add space to front of trailing lines + if first: + first = False + else: p = re.compile('([^ ])') - m = p.search(part) - index = part.find(m.group(1)) - part = ' '*(pos-index + 3) + part + m = p.search(part) + index = part.find(m.group(1)) + part = ' '*(pos-index + 3) + part fh.write(part) fh.write("\n") - # Get the last continued line and pad it too + # Get the last continued line and pad it too p = re.compile('([^ ])') - m = p.search(string) - index = string.find(m.group(1)) - string = ' '*(pos-index + 3) + string - if len(extra) > count and extra[count]: + m = p.search(string) + index = string.find(m.group(1)) + string = ' '*(pos-index + 3) + string + if len(extra) > count and extra[count]: string += extra[count] fh.write(string) fh.write("\n") - else: + else: fh.write(string) fh.write("\n") @@ -243,28 +243,28 @@ def merge_dicts(self, my_ocn_list): my_ocn_list - a list of dictionaries to add to self. Given a ROMS ocean_in object, merge the dictionaries from one or - more other grids to create a multi-grid ocean_in. + more other grids to create a multi-grid ocean_in. """ # Copy here in case we're adding this object to itself t_dict = copy.deepcopy(self.var_dict) num_lists = len(my_ocn_list) for i in range(num_lists): - new_dict = my_ocn_list[i].var_dict + new_dict = my_ocn_list[i].var_dict for it in self.var_list: - var = it.text - if it.ngrids: - try: + var = it.text + if it.ngrids: + try: # If the first string ends in "\" or "|", it is likely to be # a set of long filenames for which we need to add "\" before appending - first = t_dict[var][0] - if first[-1] == '|' or first[-1] == '\\': - t_dict[var][-1] += ' \\' - t_dict[var] = t_dict[var] + new_dict[var] + first = t_dict[var][0] + if first[-1] == '|' or first[-1] == '\\': + t_dict[var][-1] += ' \\' + t_dict[var] = t_dict[var] + new_dict[var] except: - print("List", i, "is missing variable", var) + print(("List", i, "is missing variable", var)) t_dict['Ngrids'][0] = str(int(t_dict['Ngrids'][0]) + \ - int(new_dict['Ngrids'][0])) + int(new_dict['Ngrids'][0])) self.var_dict = t_dict def main(): diff --git a/pyroms_toolbox/pyroms_toolbox/plot_Robinson_pyngl.py b/pyroms_toolbox/pyroms_toolbox/plot_Robinson_pyngl.py index 9a78178..fbbb215 100644 --- a/pyroms_toolbox/pyroms_toolbox/plot_Robinson_pyngl.py +++ b/pyroms_toolbox/pyroms_toolbox/plot_Robinson_pyngl.py @@ -28,7 +28,7 @@ def plot_Robinson_pyngl(var,lon,lat,wks_name='plot', clim=None, cspace=None, cma try: Ngl.define_colormap(wks,mycmap) except: - raise Warning, 'Unknown colormap' + raise Warning('Unknown colormap') # # The next set of resources will apply to the contour plot and the labelbar. diff --git a/pyroms_toolbox/pyroms_toolbox/plot_mask.py b/pyroms_toolbox/pyroms_toolbox/plot_mask.py index d09e3ab..4fa4568 100644 --- a/pyroms_toolbox/pyroms_toolbox/plot_mask.py +++ b/pyroms_toolbox/pyroms_toolbox/plot_mask.py @@ -15,7 +15,7 @@ def plot_mask(gridid, Cpos='rho', proj=None, **kwargs): grd = pyroms.grid.get_ROMS_grid(gridid) Cpos = str(Cpos) - print Cpos + print(Cpos) # get grid information if Cpos == 'rho': @@ -34,7 +34,7 @@ def plot_mask(gridid, Cpos='rho', proj=None, **kwargs): mask = grd.hgrid.mask_v else: - raise Warning, 'Cpos must be rho, u or v' + raise Warning('Cpos must be rho, u or v') # defined color map land_color = kwargs.pop('land_color', (0.6, 1.0, 0.6)) diff --git a/pyroms_toolbox/pyroms_toolbox/quiver.py b/pyroms_toolbox/pyroms_toolbox/quiver.py index 679de67..511a57c 100644 --- a/pyroms_toolbox/pyroms_toolbox/quiver.py +++ b/pyroms_toolbox/pyroms_toolbox/quiver.py @@ -124,10 +124,10 @@ def quiver(uvar, vvar, tindex, depth, gridid, \ if outfile is not None: if outfile.find('.png') != -1 or outfile.find('.svg') != -1 or \ outfile.find('.eps') != -1: - print 'Write figure to file', outfile + print('Write figure to file', outfile) plt.savefig(outfile, dpi=100, facecolor='w', edgecolor='w', \ orientation='portrait') else: - print 'Unrecognized file extension. Please use .png, .svg or .eps file extension.' + print('Unrecognized file extension. Please use .png, .svg or .eps file extension.') return diff --git a/pyroms_toolbox/pyroms_toolbox/remapping.py b/pyroms_toolbox/pyroms_toolbox/remapping.py index b7e5446..8bd8ccf 100644 --- a/pyroms_toolbox/pyroms_toolbox/remapping.py +++ b/pyroms_toolbox/pyroms_toolbox/remapping.py @@ -15,8 +15,6 @@ import matplotlib.pyplot as plt -import datetime - def remapping(varname, srcfile, wts_files, srcgrd, dstgrd, \ rotate_uv=False, trange=None, irange=None, jrange=None, \ dstdir='./' ,zlevel=None, dmax=0, cdepth=0, kk=0, \ @@ -60,14 +58,14 @@ def remapping(varname, srcfile, wts_files, srcgrd, dstgrd, \ varname = [varname] nvar = len(varname) else: - raise ValueError, 'varname must be a str or a list of str' + raise ValueError('varname must be a str or a list of str') # if we're working on u and v, we'll compute ubar,vbar afterwards compute_ubar = False if (varname.__contains__('u') == 1 and varname.__contains__('v') == 1) or \ (varname.__contains__('u_eastward') == 1 and varname.__contains__('v_northward') == 1): compute_ubar = True - print 'ubar/vbar to be computed from u/v' + print('ubar/vbar to be computed from u/v') if varname.__contains__('ubar'): varname.remove('ubar') nvar = nvar-1 @@ -78,23 +76,23 @@ def remapping(varname, srcfile, wts_files, srcgrd, dstgrd, \ # if rotate_uv=True, check that u and v are in varname if rotate_uv is True: if varname.__contains__(uvar) == 0 or varname.__contains__(vvar) == 0: - raise Warning, 'varname must include uvar and vvar in order to' \ - + ' rotate the velocity field' + raise Warning('varname must include uvar and vvar in order to' \ + + ' rotate the velocity field') else: varname.remove(uvar) varname.remove(vvar) nvar = nvar-2 # srcfile argument - print 'files', srcfile + print('files', srcfile) if type(srcfile).__name__ == 'list': nfile = len(srcfile) elif type(srcfile).__name__ == 'str': srcfile = sorted(glob.glob(srcfile)) nfile = len(srcfile) else: - raise ValueError, 'src_srcfile must be a str or a list of str' - print 'number of files', nfile, srcfile + raise ValueError('src_srcfile must be a str or a list of str') + print('number of files', nfile, srcfile) # get wts_file if type(wts_files).__name__ == 'str': @@ -103,7 +101,7 @@ def remapping(varname, srcfile, wts_files, srcgrd, dstgrd, \ nctidx = 0 # loop over the srcfile for nf in range(nfile): - print 'Working with file', srcfile[nf], '...' + print('Working with file', srcfile[nf], '...') # get time ocean_time = pyroms.utility.get_nc_var('ocean_time', srcfile[nf]) @@ -111,14 +109,14 @@ def remapping(varname, srcfile, wts_files, srcgrd, dstgrd, \ # trange argument if trange is None: - trange = range(ntime) + trange = list(range(ntime)) # create destination file if nctidx == 0: dstfile = dstdir + os.path.basename(srcfile[nf])[:-3] + '_' \ + dstgrd.name + '.nc' if os.path.exists(dstfile) is False: - print 'Creating destination file', dstfile + print('Creating destination file', dstfile) pyroms_toolbox.nc_create_roms_file(dstfile, dstgrd, ocean_time) # open destination file @@ -131,10 +129,10 @@ def remapping(varname, srcfile, wts_files, srcgrd, dstgrd, \ # loop over variable for nv in range(nvar): - print ' ' - print 'remapping', varname[nv], 'from', srcgrd.name, \ - 'to', dstgrd.name - print 'time =', ocean_time[nt] + print(' ') + print('remapping', varname[nv], 'from', srcgrd.name, \ + 'to', dstgrd.name) + print('time =', ocean_time[nt]) # get source data src_var = pyroms.utility.get_nc_var(varname[nv], srcfile[nf]) @@ -146,8 +144,8 @@ def remapping(varname, srcfile, wts_files, srcgrd, dstgrd, \ try: spval = src_var._FillValue except: -# raise Warning, 'Did not find a _FillValue attribute.' - print 'Warning, Did not find a _FillValue attribute.' +# raise Warning, 'Did not find a _FillValue attribute.' + print('Warning, Did not find a _FillValue attribute.') spval = 1.e37 # irange @@ -172,17 +170,17 @@ def remapping(varname, srcfile, wts_files, srcgrd, dstgrd, \ if src_var.dimensions[1].find('_w') != -1: Cpos='w' - print 'Arakawa C-grid position is', Cpos + print('Arakawa C-grid position is', Cpos) # create variable in _destination file if nctidx == 0: - print 'Creating variable', varname[nv] + print('Creating variable', varname[nv]) nc.createVariable(varname[nv], 'f8', src_var.dimensions, fill_value=spval) nc.variables[varname[nv]].long_name = src_var.long_name try: nc.variables[varname[nv]].units = src_var.units except: - print varname[nv]+' has no units' + print(varname[nv]+' has no units') nc.variables[varname[nv]].time = src_var.time nc.variables[varname[nv]].coordinates = \ src_var.coordinates @@ -195,18 +193,18 @@ def remapping(varname, srcfile, wts_files, srcgrd, dstgrd, \ break else: if s == len(wts_files) - 1: - raise ValueError, 'Did not find the appropriate remap weights file' + raise ValueError('Did not find the appropriate remap weights file') if ndim == 3: # vertical interpolation from sigma to standard z level - print 'vertical interpolation from sigma to standard z level' + print('vertical interpolation from sigma to standard z level') src_varz = pyroms.remapping.roms2z( \ src_var[nt,:,jjrange[0]:jjrange[1],iirange[0]:iirange[1]], \ srcgrd, srcgrdz, Cpos=Cpos, spval=spval, \ irange=iirange, jrange=jjrange) # flood the grid - print 'flood the grid' + print('flood the grid') src_varz = pyroms.remapping.flood(src_varz, srcgrdz, Cpos=Cpos, \ irange=iirange, jrange=jjrange, spval=spval, \ dmax=dmax, cdepth=cdepth, kk=kk) @@ -214,32 +212,35 @@ def remapping(varname, srcfile, wts_files, srcgrd, dstgrd, \ else: src_varz = src_var[nt,jjrange[0]:jjrange[1],iirange[0]:iirange[1]] -# print datetime.datetime.now() # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_varz = pyroms.remapping.remap(src_varz, wts_file, \ spval=spval) -# print datetime.datetime.now() if ndim == 3: # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_var = pyroms.remapping.z2roms(dst_varz, dstgrdz, dstgrd, \ Cpos=Cpos, spval=spval, flood=False) else: dst_var = dst_varz + if varname[nv] == 'u': + dst_u = dst_var + if varname[nv] == 'v': + dst_v = dst_var + # write data in destination file - print 'write data in destination file' + print('write data in destination file') nc.variables[varname[nv]][nctidx] = dst_var # rotate the velocity field if requested if rotate_uv is True: - print ' ' - print 'remapping and rotating', uvar, 'and', vvar, 'from', \ - srcgrd.name, 'to', dstgrd.name + print(' ') + print('remapping and rotating', uvar, 'and', vvar, 'from', \ + srcgrd.name, 'to', dstgrd.name) # get source data src_u = pyroms.utility.get_nc_var(uvar, srcfile[nf]) @@ -249,18 +250,18 @@ def remapping(varname, srcfile, wts_files, srcgrd, dstgrd, \ try: spval = src_v._FillValue except: - raise Warning, 'Did not find a _FillValue attribute.' + raise Warning('Did not find a _FillValue attribute.') if rotate_part: ndim = len(src_u.dimensions)-1 ind = uvar.find('_eastward') uvar_out = uvar[0:ind] - print "Warning: renaming uvar to", uvar_out - print "uvar dims:", src_u.dimensions + print("Warning: renaming uvar to", uvar_out) +# print("uvar dims:", src_u.dimensions) ind = vvar.find('_northward') vvar_out = vvar[0:ind] - print "Warning: renaming vvar to", vvar_out - print "uvar dims:", src_v.dimensions + print("Warning: renaming vvar to", vvar_out) +# print("vvar dims:", src_v.dimensions) if ndim == 3: dimens_u = ['ocean_time', 's_rho', 'eta_u', 'xi_u'] dimens_v = ['ocean_time', 's_rho', 'eta_v', 'xi_v'] @@ -276,7 +277,7 @@ def remapping(varname, srcfile, wts_files, srcgrd, dstgrd, \ # create variable in destination file if nctidx == 0: - print 'Creating variable '+uvar_out + print('Creating variable '+uvar_out) nc.createVariable(uvar_out, 'f8', dimens_u, fill_value=spval) nc.variables[uvar_out].long_name = src_u.long_name nc.variables[uvar_out].units = src_u.units @@ -284,7 +285,7 @@ def remapping(varname, srcfile, wts_files, srcgrd, dstgrd, \ nc.variables[uvar_out].coordinates = \ str(dimens_u.reverse()) nc.variables[uvar_out].field = src_u.field - print 'Creating variable '+vvar_out + print('Creating variable '+vvar_out) nc.createVariable(vvar_out, 'f8', dimens_v, fill_value=spval) nc.variables[vvar_out].long_name = src_v.long_name nc.variables[vvar_out].units = src_v.units @@ -301,24 +302,28 @@ def remapping(varname, srcfile, wts_files, srcgrd, dstgrd, \ wts_file_v = wts_files[s] Cpos_u = 'rho' Cpos_v = 'rho' + else: + for s in range(len(wts_files)): + if wts_files[s].__contains__('u_to_rho.nc'): + wts_file_u = wts_files[s] + if wts_files[s].__contains__('v_to_rho.nc'): + wts_file_v = wts_files[s] + Cpos_u = 'u' + Cpos_v = 'v' + + # get the right ranges + if rotate_part: # irange if irange is None: iirange = (0,src_u.shape[-1]) else: - iirange = iirange + iirange = irange # jrange if jrange is None: jjrange = (0,src_u.shape[-2]) else: jjrange = jrange else: - for s in range(len(wts_files)): - if wts_files[s].__contains__('u_to_rho.nc'): - wts_file_u = wts_files[s] - if wts_files[s].__contains__('v_to_rho.nc'): - wts_file_v = wts_files[s] - Cpos_u = 'u' - Cpos_v = 'v' # irange if irange is None: iirange = (0,src_u.shape[-1]) @@ -334,13 +339,13 @@ def remapping(varname, srcfile, wts_files, srcgrd, dstgrd, \ ndim = len(src_v.dimensions)-1 if ndim == 3: - print 'vertical interpolation from sigma to standard z level' + print('vertical interpolation from sigma to standard z level') src_uz = pyroms.remapping.roms2z( \ src_u[nt,:,jjrange[0]:jjrange[1],iirange[0]:iirange[1]], \ srcgrd, srcgrdz, Cpos=Cpos_u, spval=spval, \ irange=iirange, jrange=jjrange) # flood the grid - print 'flood the u grid' + print('flood the u grid') src_uz = pyroms.remapping.flood(src_uz, srcgrdz, Cpos=Cpos_u, \ irange=iirange, jrange=jjrange, \ spval=spval, dmax=dmax, cdepth=cdepth, kk=kk) @@ -356,7 +361,7 @@ def remapping(varname, srcfile, wts_files, srcgrd, dstgrd, \ if irange is None: iirange = (0,src_v.shape[-1]) else: - iirange = iirange + iirange = irange # jrange if jrange is None: jjrange = (0,src_v.shape[-2]) @@ -381,7 +386,7 @@ def remapping(varname, srcfile, wts_files, srcgrd, dstgrd, \ irange=iirange, jrange=jjrange) # flood the grid - print 'flood the v grid' + print('flood the v grid') src_vz = pyroms.remapping.flood(src_vz, srcgrdz, Cpos=Cpos_v, \ irange=iirange, jrange=jjrange, \ spval=spval, dmax=dmax, cdepth=cdepth, kk=kk) @@ -392,7 +397,7 @@ def remapping(varname, srcfile, wts_files, srcgrd, dstgrd, \ dmax=dmax) # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_uz = pyroms.remapping.remap(src_uz, wts_file_u, \ spval=spval) dst_vz = pyroms.remapping.remap(src_vz, wts_file_v, \ @@ -400,7 +405,7 @@ def remapping(varname, srcfile, wts_files, srcgrd, dstgrd, \ if ndim == 3: # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_u = pyroms.remapping.z2roms(dst_uz, dstgrdz, dstgrd, \ Cpos='rho', spval=spval, flood=False) dst_v = pyroms.remapping.z2roms(dst_vz, dstgrdz, dstgrd, \ @@ -442,20 +447,20 @@ def remapping(varname, srcfile, wts_files, srcgrd, dstgrd, \ for n in range(dstgrd.vgrid.N): dst_u[n,idxu[0], idxu[1]] = spval dst_v[n,idxv[0], idxv[1]] = spval - else: + else: dst_u = 0.5 * (dst_u[:,:-1] + dst_u[:,1:]) dst_v = 0.5 * (dst_v[:-1,:] + dst_v[1:,:]) dst_u[idxu[0], idxu[1]] = spval dst_v[idxv[0], idxv[1]] = spval # write data in destination file - print 'write data in destination file' + print('write data in destination file') nc.variables[uvar_out][nctidx] = dst_u nc.variables[vvar_out][nctidx] = dst_v if compute_ubar: if nctidx == 0: - print 'Creating variable ubar' + print('Creating variable ubar') nc.createVariable('ubar', 'f8', \ ('ocean_time', 'eta_u', 'xi_u'), fill_value=spval) nc.variables['ubar'].long_name = '2D u-momentum component' @@ -463,7 +468,7 @@ def remapping(varname, srcfile, wts_files, srcgrd, dstgrd, \ nc.variables['ubar'].time = 'ocean_time' nc.variables['ubar'].coordinates = 'xi_u eta_u ocean_time' nc.variables['ubar'].field = 'ubar-velocity,, scalar, series' - print 'Creating variable vbar' + print('Creating variable vbar') nc.createVariable('vbar', 'f8', \ ('ocean_time', 'eta_v', 'xi_v'), fill_value=spval) nc.variables['vbar'].long_name = '2D v-momentum component' @@ -502,9 +507,9 @@ def remapping(varname, srcfile, wts_files, srcgrd, dstgrd, \ nc.variables['vbar'][nctidx] = dst_vbar nctidx = nctidx + 1 - print 'ADDING to nctidx ', nctidx + print('ADDING to nctidx ', nctidx) nc.sync() - + # close destination file nc.close() diff --git a/pyroms_toolbox/pyroms_toolbox/remapping_bound.py b/pyroms_toolbox/pyroms_toolbox/remapping_bound.py index 43e4f45..d81ccfa 100644 --- a/pyroms_toolbox/pyroms_toolbox/remapping_bound.py +++ b/pyroms_toolbox/pyroms_toolbox/remapping_bound.py @@ -60,14 +60,14 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ varname = [varname] nvar = len(varname) else: - raise ValueError, 'varname must be a str or a list of str' + raise ValueError('varname must be a str or a list of str') # if we're working on u and v, we'll compute ubar,vbar afterwards compute_ubar = False if (varname.__contains__('u') == 1 and varname.__contains__('v') == 1) or \ (varname.__contains__('u_eastward') == 1 and varname.__contains__('v_northward') == 1): compute_ubar = True - print 'ubar/vbar to be computed from u/v' + print('ubar/vbar to be computed from u/v') if varname.__contains__('ubar'): varname.remove('ubar') nvar = nvar-1 @@ -78,8 +78,8 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ # if rotate_uv=True, check that u and v are in varname if rotate_uv is True: if varname.__contains__(uvar) == 0 or varname.__contains__(vvar) == 0: - raise Warning, 'varname must include uvar and vvar in order to' \ - + ' rotate the velocity field' + raise Warning('varname must include uvar and vvar in order to' \ + + ' rotate the velocity field') else: varname.remove(uvar) varname.remove(vvar) @@ -92,7 +92,7 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ srcfile = sorted(glob.glob(srcfile)) nfile = len(srcfile) else: - raise ValueError, 'src_srcfile must be a str or a list of str' + raise ValueError('src_srcfile must be a str or a list of str') # get wts_file if type(wts_files).__name__ == 'str': @@ -107,7 +107,7 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ nctidx = 0 # loop over the srcfile for nf in range(nfile): - print 'Working with file', srcfile[nf], '...' + print('Working with file', srcfile[nf], '...') # get time ocean_time = pyroms.utility.get_nc_var('ocean_time', srcfile[nf]) @@ -115,14 +115,14 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ # trange argument if trange is None: - trange = range(ntime) + trange = list(range(ntime)) # create destination file if nctidx == 0: dstfile = dstdir + os.path.basename(srcfile[nf])[:-3] + '_' \ + dst_grd.name + '_bdry.nc' if os.path.exists(dstfile) is False: - print 'Creating destination file', dstfile + print('Creating destination file', dstfile) pyroms_toolbox.nc_create_roms_file(dstfile, dst_grd, \ ocean_time, lgrid=False) @@ -136,10 +136,10 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ # loop over variable for nv in range(nvar): - print ' ' - print 'remapping', varname[nv], 'from', srcgrd.name, \ - 'to', dst_grd.name - print 'time =', ocean_time[nt] + print(' ') + print('remapping', varname[nv], 'from', srcgrd.name, \ + 'to', dst_grd.name) + print('time =', ocean_time[nt]) Mp, Lp = dst_grd.hgrid.mask_rho.shape # get source data @@ -152,7 +152,7 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ try: spval = src_var._FillValue except: - raise Warning, 'Did not find a _FillValue attribute.' + raise Warning('Did not find a _FillValue attribute.') # irange if irange is None: @@ -182,7 +182,7 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ if src_var.dimensions[1].find('_w') != -1: Cpos='w' - print 'Arakawa C-grid position is', Cpos + print('Arakawa C-grid position is', Cpos) # create variable in _destination file if nctidx == 0: @@ -192,7 +192,7 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ for dim in dimens: if re.match(dimexcl[sid],dim): dimens.remove(dim) - print 'Creating variable', varn, dimens + print('Creating variable', varn, dimens) nc.createVariable(varn, 'f8', dimens, \ fill_value=spval) nc.variables[varn].long_name = varname[nv] + \ @@ -200,7 +200,7 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ try: nc.variables[varn].units = src_var.units except: - print varn+' has no units' + print(varn+' has no units') nc.variables[varn].time = src_var.time nc.variables[varn].coordinates = \ str(dimens.reverse()) @@ -213,18 +213,18 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ break else: if s == len(wts_files) - 1: - raise ValueError, 'Did not find the appropriate remap weights file' + raise ValueError('Did not find the appropriate remap weights file') if ndim == 3: # vertical interpolation from sigma to standard z level - print 'vertical interpolation from sigma to standard z level' + print('vertical interpolation from sigma to standard z level') src_varz = pyroms.remapping.roms2z( \ src_var[nt,:,jjrange[0]:jjrange[1],iirange[0]:iirange[1]], \ srcgrd, srcgrdz, Cpos=Cpos, spval=spval, \ irange=iirange, jrange=jjrange) # flood the grid - print 'flood the grid' + print('flood the grid') src_varz = pyroms.remapping.flood(src_varz, srcgrdz, Cpos=Cpos, \ irange=iirange, jrange=jjrange, spval=spval, \ dmax=dmax, cdepth=cdepth, kk=kk) @@ -232,9 +232,9 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ else: src_varz = src_var[nt,jjrange[0]:jjrange[1],iirange[0]:iirange[1]] - print datetime.datetime.now() + print(datetime.datetime.now()) # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_varz = pyroms.remapping.remap(src_varz, wts_file, \ spval=spval) @@ -275,7 +275,7 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ # print datetime.datetime.now() # write data in destination file - print 'write data in destination file' + print('write data in destination file') sid = '_west' varn = varname[nv]+str(sid) nc.variables[varn][nctidx] = np.squeeze(dst_var_west) @@ -294,9 +294,9 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ # rotate the velocity field if requested if rotate_uv is True: - print ' ' - print 'remapping and rotating u and v from', srcgrd.name, \ - 'to', dst_grd.name + print(' ') + print('remapping and rotating u and v from', srcgrd.name, \ + 'to', dst_grd.name) # get source data src_u = pyroms.utility.get_nc_var(uvar, srcfile[nf]) @@ -306,16 +306,16 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ try: spval = src_v._FillValue except: - raise Warning, 'Did not find a _FillValue attribute.' + raise Warning('Did not find a _FillValue attribute.') if rotate_part: ndim = len(src_u.dimensions)-1 ind = uvar.find('_eastward') uvar_out = uvar[0:ind] - print "Warning: renaming uvar to", uvar_out + print("Warning: renaming uvar to", uvar_out) ind = vvar.find('_northward') vvar_out = vvar[0:ind] - print "Warning: renaming vvar to", vvar_out + print("Warning: renaming vvar to", vvar_out) if ndim == 3: dimens_u = ['ocean_time', 's_rho', 'eta_u', 'xi_u'] dimens_v = ['ocean_time', 's_rho', 'eta_v', 'xi_v'] @@ -331,10 +331,10 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ # create variable in destination file if nctidx == 0: - print 'Creating boundary variables for '+uvar + print('Creating boundary variables for '+uvar) for sid in sides: varn = uvar_out+str(sid) - print 'Creating variable', varn + print('Creating variable', varn) dimens = list(dimens_u) for dim in dimens: if re.match(dimexcl[sid],dim): @@ -346,15 +346,15 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ try: nc.variables[varn].units = src_u.units except: - print varn+' has no units' + print(varn+' has no units') nc.variables[varn].time = src_u.time nc.variables[varn].coordinates = \ str(dimens.reverse()) nc.variables[varn].field = src_u.field - print 'Creating boundary variables for '+vvar + print('Creating boundary variables for '+vvar) for sid in sides: varn = vvar_out+str(sid) - print 'Creating variable', varn + print('Creating variable', varn) dimens = list(dimens_v) for dim in dimens: if re.match(dimexcl[sid],dim): @@ -366,7 +366,7 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ try: nc.variables[varn].units = src_v.units except: - print varn+' has no units' + print(varn+' has no units') nc.variables[varn].time = src_v.time nc.variables[varn].coordinates = \ str(dimens.reverse()) @@ -380,6 +380,16 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ wts_file_v = wts_files[s] Cpos_u = 'rho' Cpos_v = 'rho' + else: + for s in range(len(wts_files)): + if wts_files[s].__contains__('u_to_rho.nc'): + wts_file_u = wts_files[s] + if wts_files[s].__contains__('v_to_rho.nc'): + wts_file_v = wts_files[s] + Cpos_u = 'u' + Cpos_v = 'v' + + if rotate_part: # irange if irange is None: iirange = (0,src_u.shape[-1]) @@ -391,13 +401,6 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ else: jjrange = jrange else: - for s in range(len(wts_files)): - if wts_files[s].__contains__('u_to_rho.nc'): - wts_file_u = wts_files[s] - if wts_files[s].__contains__('v_to_rho.nc'): - wts_file_v = wts_files[s] - Cpos_u = 'u' - Cpos_v = 'v' # irange if irange is None: iirange = (0,src_u.shape[-1]) @@ -410,16 +413,15 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ jjrange = jrange # vertical interpolation from sigma to standard z level - ndim = len(src_v.dimensions)-1 if ndim == 3: - print 'vertical interpolation from sigma to standard z level' + print('vertical interpolation from sigma to standard z level') src_uz = pyroms.remapping.roms2z( \ src_u[nt,:,jjrange[0]:jjrange[1],iirange[0]:iirange[1]], \ srcgrd, srcgrdz, Cpos=Cpos_u, spval=spval, \ irange=iirange, jrange=jjrange) # flood the grid - print 'flood the u grid' + print('flood the u grid') src_uz = pyroms.remapping.flood(src_uz, srcgrdz, Cpos=Cpos_u, \ irange=iirange, jrange=jjrange, \ spval=spval, dmax=dmax, cdepth=cdepth, kk=kk) @@ -429,7 +431,6 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ irange=iirange, jrange=jjrange, spval=spval, \ dmax=dmax) - # get the right ranges if rotate_part: # irange if irange is None: @@ -460,7 +461,7 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ irange=iirange, jrange=jjrange) # flood the grid - print 'flood the v grid' + print('flood the v grid') src_vz = pyroms.remapping.flood(src_vz, srcgrdz, Cpos=Cpos_v, \ irange=iirange, jrange=jjrange, \ spval=spval, dmax=dmax, cdepth=cdepth, kk=kk) @@ -471,7 +472,7 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ dmax=dmax) # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_uz = pyroms.remapping.remap(src_uz, wts_file_u, \ spval=spval) dst_vz = pyroms.remapping.remap(src_vz, wts_file_v, \ @@ -480,7 +481,7 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ if ndim == 3: # vertical interpolation from standard z level to sigma - print 'vertical interpolation from standard z level to sigma' + print('vertical interpolation from standard z level to sigma') dst_u_north = pyroms.remapping.z2roms(dst_uz[:, Mp-2:Mp, 0:Lp], \ dst_grdz, dst_grd, Cpos='rho', spval=spval, \ flood=False, irange=(0,Lp), jrange=(Mp-2,Mp)) @@ -630,7 +631,7 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ dst_v_west[idxv_west[0]] = spval # write data in destination file - print 'write data in destination file' + print('write data in destination file') sid = '_west' varn = uvar_out+str(sid) nc.variables[varn][nctidx] = dst_u_west @@ -657,7 +658,7 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ if compute_ubar: if nctidx == 0: - print 'Creating variable ubar_north' + print('Creating variable ubar_north') nc.createVariable('ubar_north', 'f8', \ ('ocean_time', 'xi_u'), fill_value=spval) nc.variables['ubar_north'].long_name = \ @@ -666,7 +667,7 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ nc.variables['ubar_north'].time = 'ocean_time' nc.variables['ubar_north'].coordinates = 'xi_u ocean_time' nc.variables['ubar_north'].field = 'ubar_north, scalar, series' - print 'Creating variable vbar_north' + print('Creating variable vbar_north') nc.createVariable('vbar_north', 'f8', \ ('ocean_time', 'xi_v'), fill_value=spval) nc.variables['vbar_north'].long_name = \ @@ -676,7 +677,7 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ nc.variables['vbar_north'].coordinates = 'xi_v ocean_time' nc.variables['vbar_north'].field = 'vbar_north,, scalar, series' - print 'Creating variable ubar_south' + print('Creating variable ubar_south') nc.createVariable('ubar_south', 'f8', \ ('ocean_time', 'xi_u'), fill_value=spval) nc.variables['ubar_south'].long_name = \ @@ -685,7 +686,7 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ nc.variables['ubar_south'].time = 'ocean_time' nc.variables['ubar_south'].coordinates = 'xi_u ocean_time' nc.variables['ubar_south'].field = 'ubar_south, scalar, series' - print 'Creating variable vbar_south' + print('Creating variable vbar_south') nc.createVariable('vbar_south', 'f8', \ ('ocean_time', 'xi_v'), fill_value=spval) nc.variables['vbar_south'].long_name = \ @@ -694,7 +695,7 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ nc.variables['vbar_south'].time = 'ocean_time' nc.variables['vbar_south'].coordinates = 'xi_v ocean_time' - print 'Creating variable ubar_west' + print('Creating variable ubar_west') nc.createVariable('ubar_west', 'f8', \ ('ocean_time', 'eta_u'), fill_value=spval) nc.variables['ubar_west'].long_name = \ @@ -703,7 +704,7 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ nc.variables['ubar_west'].time = 'ocean_time' nc.variables['ubar_west'].coordinates = 'eta_u ocean_time' nc.variables['ubar_west'].field = 'ubar_west, scalar, series' - print 'Creating variable vbar_west' + print('Creating variable vbar_west') nc.createVariable('vbar_west', 'f8', \ ('ocean_time', 'eta_v'), fill_value=spval) nc.variables['vbar_west'].long_name = \ @@ -712,7 +713,7 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ nc.variables['vbar_west'].time = 'ocean_time' nc.variables['vbar_west'].coordinates = 'eta_v ocean_time' - print 'Creating variable ubar_east' + print('Creating variable ubar_east') nc.createVariable('ubar_east', 'f8', \ ('ocean_time', 'eta_u'), fill_value=spval) nc.variables['ubar_east'].long_name = \ @@ -721,7 +722,7 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ nc.variables['ubar_east'].time = 'ocean_time' nc.variables['ubar_east'].coordinates = 'eta_u ocean_time' nc.variables['ubar_east'].field = 'ubar_east, scalar, series' - print 'Creating variable vbar_east' + print('Creating variable vbar_east') nc.createVariable('vbar_east', 'f8', \ ('ocean_time', 'eta_v'), fill_value=spval) nc.variables['vbar_east'].long_name = \ @@ -732,7 +733,7 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ # compute depth average velocity ubar and vbar # get z at the right position - print 'Computing ubar/vbar from u/v' + print('Computing ubar/vbar from u/v') z_u_north = 0.5 * (dst_grd.vgrid.z_w[0,:,-1,:-1] + dst_grd.vgrid.z_w[0,:,-1, 1:]) z_v_north = 0.5 * (dst_grd.vgrid.z_w[0,:,-1,:] + @@ -820,7 +821,7 @@ def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \ nc.variables['vbar_west'][nctidx] = dst_vbar_west nctidx = nctidx + 1 - print 'ADDING to nctidx ', nctidx + print('ADDING to nctidx ', nctidx) nc.sync() # close files here? how? diff --git a/pyroms_toolbox/pyroms_toolbox/remapping_bound_sig.py b/pyroms_toolbox/pyroms_toolbox/remapping_bound_sig.py index 5282784..058fd3c 100644 --- a/pyroms_toolbox/pyroms_toolbox/remapping_bound_sig.py +++ b/pyroms_toolbox/pyroms_toolbox/remapping_bound_sig.py @@ -43,7 +43,7 @@ def remapping_bound_sig(varname, srcfile, wts_files, srcgrd, dst_grd, \ varname = [varname] nvar = len(varname) else: - raise ValueError, 'varname must be a str or a list of str' + raise ValueError('varname must be a str or a list of str') # srcfile argument if type(srcfile).__name__ == 'list': @@ -52,12 +52,12 @@ def remapping_bound_sig(varname, srcfile, wts_files, srcgrd, dst_grd, \ srcfile = sorted(glob.glob(srcfile)) nfile = len(srcfile) else: - raise ValueError, 'src_srcfile must be a str or a list of str' + raise ValueError('src_srcfile must be a str or a list of str') # get wts_file if type(wts_files).__name__ == 'str': wts_files = sorted(glob.glob(wts_files)) - + sides = ['_west','_east','_north','_south'] long = {'_west':'Western', '_east':'Eastern', \ '_north':'Northern', '_south':'Southern'} @@ -67,22 +67,22 @@ def remapping_bound_sig(varname, srcfile, wts_files, srcgrd, dst_grd, \ nctidx = 0 # loop over the srcfile for nf in range(nfile): - print 'Working with file', srcfile[nf], '...' + print('Working with file', srcfile[nf], '...') - # get time + # get time ocean_time = pyroms.utility.get_nc_var('ocean_time', srcfile[nf]) ntime = len(ocean_time[:]) # trange argument if trange is None: - trange = range(ntime) + trange = list(range(ntime)) # create destination file if nctidx == 0: dstfile = dstdir + os.path.basename(srcfile[nf])[:-3] + '_' \ + dst_grd.name + '_bdry.nc' if os.path.exists(dstfile) is False: - print 'Creating destination file', dstfile + print('Creating destination file', dstfile) pyroms_toolbox.nc_create_roms_file(dstfile, dst_grd, \ ocean_time, lgrid=False) @@ -96,10 +96,10 @@ def remapping_bound_sig(varname, srcfile, wts_files, srcgrd, dst_grd, \ # loop over variable for nv in range(nvar): - print ' ' - print 'remapping', varname[nv], 'from', srcgrd.name, \ - 'to', dst_grd.name - print 'time =', ocean_time[nt] + print(' ') + print('remapping', varname[nv], 'from', srcgrd.name, \ + 'to', dst_grd.name) + print('time =', ocean_time[nt]) Mp, Lp = dst_grd.hgrid.mask_rho.shape # get source data @@ -109,7 +109,7 @@ def remapping_bound_sig(varname, srcfile, wts_files, srcgrd, dst_grd, \ try: spval = src_var._FillValue except: - raise Warning, 'Did not find a _FillValue attribute.' + raise Warning('Did not find a _FillValue attribute.') # irange if irange is None: @@ -127,15 +127,15 @@ def remapping_bound_sig(varname, srcfile, wts_files, srcgrd, dst_grd, \ if src_var.dimensions[2].find('_rho') != -1: Cpos='rho' else: - print "Sigma should be on rho points" + print("Sigma should be on rho points") - print 'Arakawa C-grid position is', Cpos + print('Arakawa C-grid position is', Cpos) # create variable in _destination file if nctidx == 0: for sid in sides: varn = varname[nv]+str(sid) - print 'Creating variable', varn + print('Creating variable', varn) dimens = [i for i in src_var.dimensions] for dim in dimens: if re.match(dimexcl[sid],dim): @@ -147,7 +147,7 @@ def remapping_bound_sig(varname, srcfile, wts_files, srcgrd, dst_grd, \ try: nc.variables[varn].units = src_var.units except: - print varn+' has no units' + print(varn+' has no units') nc.variables[varn].time = src_var.time nc.variables[varn].coordinates = \ str(dimens.reverse()) @@ -160,7 +160,7 @@ def remapping_bound_sig(varname, srcfile, wts_files, srcgrd, dst_grd, \ break else: if s == len(wts_files) - 1: - raise ValueError, 'Did not find the appropriate remap weights file' + raise ValueError('Did not find the appropriate remap weights file') # print datetime.datetime.now() # horizontal interpolation using scrip weights @@ -175,7 +175,7 @@ def remapping_bound_sig(varname, srcfile, wts_files, srcgrd, dst_grd, \ dst_var_west = dst_var[:, 0] # write data in destination file - print 'write data in destination file' + print('write data in destination file') sid = '_west' varn = varname[nv]+str(sid) nc.variables[varn][nctidx] = np.squeeze(dst_var_west) @@ -194,9 +194,9 @@ def remapping_bound_sig(varname, srcfile, wts_files, srcgrd, dst_grd, \ # rotate the velocity field if requested if rotate_sig: - print ' ' - print 'remapping and rotating sigma from', srcgrd.name, \ - 'to', dst_grd.name + print(' ') + print('remapping and rotating sigma from', srcgrd.name, \ + 'to', dst_grd.name) # get source data src_11 = pyroms.utility.get_nc_var(varname[0], srcfile[nf]) @@ -204,7 +204,7 @@ def remapping_bound_sig(varname, srcfile, wts_files, srcgrd, dst_grd, \ try: spval = src_11._FillValue except: - raise Warning, 'Did not find a _FillValue attribute.' + raise Warning('Did not find a _FillValue attribute.') src_11 = src_11[nt,jjrange[0]:jjrange[1],iirange[0]:iirange[1]] @@ -216,7 +216,7 @@ def remapping_bound_sig(varname, srcfile, wts_files, srcgrd, dst_grd, \ # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_11 = pyroms.remapping.remap(src_11, wts_file, \ spval=spval) dst_22 = pyroms.remapping.remap(src_22, wts_file, \ @@ -253,7 +253,7 @@ def remapping_bound_sig(varname, srcfile, wts_files, srcgrd, dst_grd, \ sin_ang = np.sin(angle) Lp = cos_ang.shape[-1] Mp = cos_ang.shape[-2] - print "Lp, Mp", Lp, Mp + print("Lp, Mp", Lp, Mp) if rotate_sig: # North @@ -329,7 +329,7 @@ def remapping_bound_sig(varname, srcfile, wts_files, srcgrd, dst_grd, \ dst_12_west[idx_west[0]] = spval # write data in destination file - print 'write data in destination file' + print('write data in destination file') sid = '_west' varn = 'sig11'+str(sid) nc.variables[varn][nctidx] = dst_11_west @@ -365,7 +365,7 @@ def remapping_bound_sig(varname, srcfile, wts_files, srcgrd, dst_grd, \ nctidx = nctidx + 1 nc.sync() # close files here? how? - + # close destination file nc.close() diff --git a/pyroms_toolbox/pyroms_toolbox/remapping_tensor.py b/pyroms_toolbox/pyroms_toolbox/remapping_tensor.py index 654ce68..03dda27 100644 --- a/pyroms_toolbox/pyroms_toolbox/remapping_tensor.py +++ b/pyroms_toolbox/pyroms_toolbox/remapping_tensor.py @@ -42,7 +42,7 @@ def remapping_tensor(varname, srcfile, wts_files, srcgrd, dstgrd, \ varname = [varname] nvar = len(varname) else: - raise ValueError, 'varname must be a str or a list of str' + raise ValueError('varname must be a str or a list of str') # srcfile argument if type(srcfile).__name__ == 'list': @@ -51,7 +51,7 @@ def remapping_tensor(varname, srcfile, wts_files, srcgrd, dstgrd, \ srcfile = sorted(glob.glob(srcfile)) nfile = len(srcfile) else: - raise ValueError, 'src_srcfile must be a str or a list of str' + raise ValueError('src_srcfile must be a str or a list of str') # get wts_file if type(wts_files).__name__ == 'str': @@ -59,7 +59,7 @@ def remapping_tensor(varname, srcfile, wts_files, srcgrd, dstgrd, \ # loop over the srcfile for nf in range(nfile): - print 'Working with file', srcfile[nf], '...' + print('Working with file', srcfile[nf], '...') # get time ocean_time = pyroms.utility.get_nc_var('ocean_time', srcfile[nf]) @@ -67,12 +67,12 @@ def remapping_tensor(varname, srcfile, wts_files, srcgrd, dstgrd, \ # trange argument if trange is None: - trange = range(ntime) + trange = list(range(ntime)) # create destination file dstfile = dstdir + os.path.basename(srcfile[nf])[:-3] + '_' + dstgrd.name + '.nc' if os.path.exists(dstfile) is False: - print 'Creating destination file', dstfile + print('Creating destination file', dstfile) pyroms_toolbox.nc_create_roms_file(dstfile, dstgrd, ocean_time) # open destination file @@ -86,10 +86,10 @@ def remapping_tensor(varname, srcfile, wts_files, srcgrd, dstgrd, \ # loop over variable for nv in range(nvar): - print ' ' - print 'remapping', varname[nv], 'from', srcgrd.name, \ - 'to', dstgrd.name - print 'time =', ocean_time[nt] + print(' ') + print('remapping', varname[nv], 'from', srcgrd.name, \ + 'to', dstgrd.name) + print('time =', ocean_time[nt]) # get source data src_var = pyroms.utility.get_nc_var(varname[nv], srcfile[nf]) @@ -98,7 +98,7 @@ def remapping_tensor(varname, srcfile, wts_files, srcgrd, dstgrd, \ try: spval = src_var._FillValue except: - raise Warning, 'Did not find a _FillValue attribute.' + raise Warning('Did not find a _FillValue attribute.') # irange if irange is None: @@ -116,19 +116,19 @@ def remapping_tensor(varname, srcfile, wts_files, srcgrd, dstgrd, \ if src_var.dimensions[2].find('_rho') != -1: Cpos='rho' else: - print "Sigma should be on rho points" + print("Sigma should be on rho points") - print 'Arakawa C-grid position is', Cpos + print('Arakawa C-grid position is', Cpos) # create variable in _destination file if nt == trange[0]: - print 'Creating variable', varname[nv] + print('Creating variable', varname[nv]) nc.createVariable(varname[nv], 'f8', src_var.dimensions, fill_value=spval) nc.variables[varname[nv]].long_name = src_var.long_name try: nc.variables[varname[nv]].units = src_var.units except: - print varname[nv]+' has no units' + print(varname[nv]+' has no units') nc.variables[varname[nv]].time = src_var.time nc.variables[varname[nv]].coordinates = \ src_var.coordinates @@ -142,7 +142,7 @@ def remapping_tensor(varname, srcfile, wts_files, srcgrd, dstgrd, \ break else: if s == len(wts_files) - 1: - raise ValueError, 'Did not find the appropriate remap weights file' + raise ValueError('Did not find the appropriate remap weights file') # write data in destination file @@ -151,9 +151,9 @@ def remapping_tensor(varname, srcfile, wts_files, srcgrd, dstgrd, \ # rotate the velocity field if requested # print datetime.datetime.now() - print ' ' - print 'remapping and rotating sigma from', srcgrd.name, \ - 'to', dstgrd.name + print(' ') + print('remapping and rotating sigma from', srcgrd.name, \ + 'to', dstgrd.name) # get source data src_11 = pyroms.utility.get_nc_var(varname[0], srcfile[nf]) @@ -161,7 +161,7 @@ def remapping_tensor(varname, srcfile, wts_files, srcgrd, dstgrd, \ try: spval = src_11._FillValue except: - raise Warning, 'Did not find a _FillValue attribute.' + raise Warning('Did not find a _FillValue attribute.') src_11 = src_11[nt,jjrange[0]:jjrange[1],iirange[0]:iirange[1]] @@ -171,22 +171,22 @@ def remapping_tensor(varname, srcfile, wts_files, srcgrd, dstgrd, \ src_12 = pyroms.utility.get_nc_var(varname[2], srcfile[nf]) src_12 = src_12[nt,jjrange[0]:jjrange[1],iirange[0]:iirange[1]] - print "before", src_11[-1,30], src_12[-1,30], src_22[-1,30] + print("before", src_11[-1,30], src_12[-1,30], src_22[-1,30]) if shapiro: src_11 = pyroms_toolbox.shapiro_filter.shapiro2(src_11,2) src_22 = pyroms_toolbox.shapiro_filter.shapiro2(src_22,2) src_12 = pyroms_toolbox.shapiro_filter.shapiro2(src_12,2) - print "after", src_11[-1,30], src_12[-1,30], src_22[-1,30] + print("after", src_11[-1,30], src_12[-1,30], src_22[-1,30]) # horizontal interpolation using scrip weights - print 'horizontal interpolation using scrip weights' + print('horizontal interpolation using scrip weights') dst_11 = pyroms.remapping.remap(src_11, wts_file, \ spval=spval) dst_22 = pyroms.remapping.remap(src_22, wts_file, \ spval=spval) dst_12 = pyroms.remapping.remap(src_12, wts_file, \ spval=spval) - print "after remapping", dst_11[-1,30], dst_12[-1,30], dst_22[-1,30] + print("after remapping", dst_11[-1,30], dst_12[-1,30], dst_22[-1,30]) if rotate_sig is True: # rotate stress tensor @@ -198,7 +198,7 @@ def remapping_tensor(varname, srcfile, wts_files, srcgrd, dstgrd, \ sin_ang = np.sin(angle) Lp = cos_ang.shape[-1] Mp = cos_ang.shape[-2] - print "Lp, Mp", Lp, Mp + print("Lp, Mp", Lp, Mp) for j in range(Mp): for i in range(Lp): @@ -216,7 +216,7 @@ def remapping_tensor(varname, srcfile, wts_files, srcgrd, dstgrd, \ dst_11[j,i] = sig_rot[0,0] dst_12[j,i] = sig_rot[0,1] dst_22[j,i] = sig_rot[1,1] - print "after rotating", dst_11[-1,30], dst_12[-1,30], dst_22[-1,30] + print("after rotating", dst_11[-1,30], dst_12[-1,30], dst_22[-1,30]) # spval @@ -226,7 +226,7 @@ def remapping_tensor(varname, srcfile, wts_files, srcgrd, dstgrd, \ dst_22[idx[0], idx[1]] = spval # write data in destination file - print 'write data in destination file' + print('write data in destination file') nc.variables['sig11'][nctidx] = dst_11 nc.variables['sig12'][nctidx] = dst_12 nc.variables['sig22'][nctidx] = dst_22 diff --git a/pyroms_toolbox/pyroms_toolbox/rvalue.py b/pyroms_toolbox/pyroms_toolbox/rvalue.py index 9f7e92d..036bd6f 100644 --- a/pyroms_toolbox/pyroms_toolbox/rvalue.py +++ b/pyroms_toolbox/pyroms_toolbox/rvalue.py @@ -15,10 +15,10 @@ def rvalue(h): """ #check that h is 2D if (len(h.squeeze().shape)!=2): - raise ValueError, 'h must be two dimensions' + raise ValueError('h must be two dimensions') #check whether h contains any NaNs - if np.isnan(h).any(): raise Warning, 'the height array contains NaNs' + if np.isnan(h).any(): raise Warning('the height array contains NaNs') #compute diff(h)/2*mean(h) at each velocity grid point dhdx_u = np.diff(h, axis=1) diff --git a/pyroms_toolbox/pyroms_toolbox/rx0.py b/pyroms_toolbox/pyroms_toolbox/rx0.py index 530205e..d0846b7 100644 --- a/pyroms_toolbox/pyroms_toolbox/rx0.py +++ b/pyroms_toolbox/pyroms_toolbox/rx0.py @@ -50,10 +50,10 @@ def rx0(h,rmask): ravg = rx0.mean() rmed = np.median(rx0) - print ' ' - print 'Minimum r-value = ', rmin - print 'Maximum r-value = ', rmax - print 'Mean r-value = ', ravg - print 'Median r-value = ', rmed + print(' ') + print('Minimum r-value = ', rmin) + print('Maximum r-value = ', rmax) + print('Mean r-value = ', ravg) + print('Median r-value = ', rmed) return rx0 diff --git a/pyroms_toolbox/pyroms_toolbox/rx1.py b/pyroms_toolbox/pyroms_toolbox/rx1.py index 84e28fa..db8a221 100644 --- a/pyroms_toolbox/pyroms_toolbox/rx1.py +++ b/pyroms_toolbox/pyroms_toolbox/rx1.py @@ -55,10 +55,10 @@ def rx1(z_w,rmask): ravg = rx1.mean() rmed = np.median(rx1) - print ' ' - print 'Minimum r-value = ', rmin - print 'Maximum r-value = ', rmax - print 'Mean r-value = ', ravg - print 'Median r-value = ', rmed + print(' ') + print('Minimum r-value = ', rmin) + print('Maximum r-value = ', rmax) + print('Mean r-value = ', ravg) + print('Median r-value = ', rmed) return rx1 diff --git a/pyroms_toolbox/pyroms_toolbox/sandbox/roms_movie.py b/pyroms_toolbox/pyroms_toolbox/sandbox/roms_movie.py index 18ad0c2..c4284ce 100644 --- a/pyroms_toolbox/pyroms_toolbox/sandbox/roms_movie.py +++ b/pyroms_toolbox/pyroms_toolbox/sandbox/roms_movie.py @@ -66,7 +66,7 @@ def make_movie(filelst, varname, cmin, cmax, view, lev=0, istart=None, iend=None cmax = float(cmax) if imode is 'off': - print 'Turn interactive mode off' + print('Turn interactive mode off') plt.ioff() for tindex in range(istart, iend, 1): @@ -83,7 +83,7 @@ def make_movie(filelst, varname, cmin, cmax, view, lev=0, istart=None, iend=None title=title, outfile='plot.png') else: - print 'Option not available. view must be set to sview, zview or view2D' + print('Option not available. view must be set to sview, zview or view2D') outfile = str('%05d' % tindex) + '.png' @@ -103,13 +103,13 @@ def make_movie(filelst, varname, cmin, cmax, view, lev=0, istart=None, iend=None '-o', 'output.avi') - print "\n\nabout to execute:\n%s\n\n" % ' '.join(command) + print("\n\nabout to execute:\n%s\n\n" % ' '.join(command)) subprocess.check_call(command) - print "\n\n The movie was written to 'output.avi'" + print("\n\n The movie was written to 'output.avi'") if imode is 'off': - print 'Turn interactive mode on again' + print('Turn interactive mode on again') plt.ion() if clean is True: @@ -146,7 +146,7 @@ def make_big_movie(filelst, varname, cmin, cmax, Cpos, view, lev=0, grd=None, \ nfile = len(filelst) if imode is 'off': - print 'Turn interactive mode off' + print('Turn interactive mode off') plt.ioff() counter = 0 @@ -174,7 +174,7 @@ def make_big_movie(filelst, varname, cmin, cmax, Cpos, view, lev=0, grd=None, \ title=title, outfile='plot.png') else: - print 'Option not available. view must be set to sview, zview or view2D' + print('Option not available. view must be set to sview, zview or view2D') Tindex = counter + tindex @@ -199,13 +199,13 @@ def make_big_movie(filelst, varname, cmin, cmax, Cpos, view, lev=0, grd=None, \ 'output.avi') if imode is 'off': - print 'Turn interactive mode on again' + print('Turn interactive mode on again') plt.ion() - print "\n\nabout to execute:\n%s\n\n" % ' '.join(command) + print("\n\nabout to execute:\n%s\n\n" % ' '.join(command)) subprocess.check_call(command) - print "\n\n The movie was written to 'output.avi'" + print("\n\n The movie was written to 'output.avi'") if clean is True: for tindex in range(counter): diff --git a/pyroms_toolbox/pyroms_toolbox/seawater/__init__.py b/pyroms_toolbox/pyroms_toolbox/seawater/__init__.py index 194bf94..98e61a0 100644 --- a/pyroms_toolbox/pyroms_toolbox/seawater/__init__.py +++ b/pyroms_toolbox/pyroms_toolbox/seawater/__init__.py @@ -56,9 +56,9 @@ # --- Exceptions --- class OutOfRangeError(Exception): pass -from density import dens, svan, sigma, drhodt, alpha, drhods, beta -from salinity import salt, cond -from heat import heatcap, adtgrad, temppot, temppot0 -from misc import freezept, soundvel, depth +from .density import dens, svan, sigma, drhodt, alpha, drhods, beta +from .salinity import salt, cond +from .heat import heatcap, adtgrad, temppot, temppot0 +from .misc import freezept, soundvel, depth diff --git a/pyroms_toolbox/pyroms_toolbox/seawater/heat.py b/pyroms_toolbox/pyroms_toolbox/seawater/heat.py index 596d9ae..26c3fd3 100644 --- a/pyroms_toolbox/pyroms_toolbox/seawater/heat.py +++ b/pyroms_toolbox/pyroms_toolbox/seawater/heat.py @@ -101,9 +101,9 @@ def heatcap(S, T, P=0): CP2 = ((d0 + d1*T + d2*T**2 + d3*T**3 + d4*T**4)*S \ + (e0 + e1*T + e2*T**2)*S3_2)*P \ - + ((f0 + f1*T + f2*T**2 + f3*T**3)*S \ - + g0*S3_2)*P**2 \ - + ((h0 + h1*T + h2*T**2)*S + j1*T*S3_2)*P**3 + + ((f0 + f1*T + f2*T**2 + f3*T**3)*S \ + + g0*S3_2)*P**2 \ + + ((h0 + h1*T + h2*T**2)*S + j1*T*S3_2)*P**3 return CP0 + CP1 + CP2 @@ -150,7 +150,7 @@ def adtgrad(S, T, P=0): return a0 + (a1 + (a2 + a3*T)*T)*T \ + (b0 + b1*T)*(S-35) \ - + ( (c0 + (c1 + (c2 + c3*T)*T)*T) \ + + ( (c0 + (c1 + (c2 + c3*T)*T)*T) \ + (d0 + d1*T)*(S-35) )*P \ + (e0 + (e1 + e2*T)*T )*P*P diff --git a/pyroms_toolbox/pyroms_toolbox/seawater/salinity.py b/pyroms_toolbox/pyroms_toolbox/seawater/salinity.py index 6db6bb6..06070fa 100644 --- a/pyroms_toolbox/pyroms_toolbox/seawater/salinity.py +++ b/pyroms_toolbox/pyroms_toolbox/seawater/salinity.py @@ -149,7 +149,7 @@ def cond(S, T, P): RT = (S/35.0)**0.5 SI = _sal(RT,DT) # Iteration - for n in xrange(100): + for n in range(100): RT = RT + (S-SI)/_dsal(RT,DT) SI = _sal(RT,DT) try: diff --git a/pyroms_toolbox/pyroms_toolbox/seawater/test.py b/pyroms_toolbox/pyroms_toolbox/seawater/test.py index b91cc20..9ef3235 100644 --- a/pyroms_toolbox/pyroms_toolbox/seawater/test.py +++ b/pyroms_toolbox/pyroms_toolbox/seawater/test.py @@ -1,95 +1,95 @@ - + ### TEST-CODE ##################################### if __name__ == '__main__': format1 = "Computed: %25s = " format2 = "Check value = " - - print + + print() # Check value from UNESCO 1983, p. 20 - print "Checking svan" - print - print "S = 40, T = 40 °C, P = 10000 dbar" - print format1 % "svan(40, 40, 10000)", svan(40, 40, 10000) - print format2, "981.30210E-8" + print("Checking svan") + print() + print("S = 40, T = 40 C, P = 10000 dbar") + print(format1 % "svan(40, 40, 10000)", svan(40, 40, 10000)) + print(format2, "981.30210E-8") - print + print() # Check value from UNESCO 1983, p. 20 - print "Checking sigma" - print - print "S = 40, T = 40 °C, P = 10000 dbar" - print format1 % "sigma(40, 40, 10000)", sigma(40, 40, 10000) - print format2, 59.82037 + print("Checking sigma") + print() + print("S = 40, T = 40 C, P = 10000 dbar") + print(format1 % "sigma(40, 40, 10000)", sigma(40, 40, 10000)) + print(format2, 59.82037) - print + print() # Check value from UNESCO 1983, p. 11 - print "Checking salt" - print - print "Salinity = 40.0000" - print "cond = 1.888091, T = 40 °C, P = 10000 dbar" - print format1 % "salt(1.888091, 40, 10000)", salt(1.888091, 40, 10000) - print format2, 40.0000 - - print + print("Checking salt") + print() + print("Salinity = 40.0000") + print("cond = 1.888091, T = 40 C, P = 10000 dbar") + print(format1 % "salt(1.888091, 40, 10000)", salt(1.888091, 40, 10000)) + print(format2, 40.0000) + + print() # Check value from UNESCO 1983, p. 11 - print "Checking cond" - print - print "S = 40, T = 40 °C, P = 10000 dbar" - print format1 % "cond(40, 40, 10000)", cond(40, 40, 10000) - print format2, 1.888091 + print("Checking cond") + print() + print("S = 40, T = 40 C, P = 10000 dbar") + print(format1 % "cond(40, 40, 10000)", cond(40, 40, 10000)) + print(format2, 1.888091) - print + print() # Check value from UNESCO 1983, p. 35 - print "Checking heatcap" - print - print "S = 40, T = 40 °C, P = 10000 dbar" - print format1 % "heatcap(40, 40, 10000)", heatcap(40, 40, 10000) - print format2, "3849.500" + print("Checking heatcap") + print() + print("S = 40, T = 40 C, P = 10000 dbar") + print(format1 % "heatcap(40, 40, 10000)", heatcap(40, 40, 10000)) + print(format2, "3849.500") - print + print() # Check value from UNESCO 1983, p. 36 - print "Checking adtgrad" - print - print "S = 40, T = 40 °C, P = 10000 dbar" - print format1 % "adtgrad(40, 40, 10000)", adtgrad(40, 40, 10000) - print format2, "3.255976E-4" + print("Checking adtgrad") + print() + print("S = 40, T = 40 C, P = 10000 dbar") + print(format1 % "adtgrad(40, 40, 10000)", adtgrad(40, 40, 10000)) + print(format2, "3.255976E-4") - print + print() # Check value from UNESCO 1983, p. 44 - print "Checking temppot" - print - print "S = 40, T = 40 °C, P = 10000 dbar, Pref = 0" - print format1 % "temppot(40, 40, 10000)", temppot(40, 40, 10000) - print format2, 36.89073 + print("Checking temppot") + print() + print("S = 40, T = 40 C, P = 10000 dbar, Pref = 0") + print(format1 % "temppot(40, 40, 10000)", temppot(40, 40, 10000)) + print(format2, 36.89073) - print + print() # Check value from UNESCO 1983, p. 30 - print "Checking freezept" - print - print "S = 40, p = 500 dbar" - print format1 % "freezept(40, 500)", freezept(40, 500) - print format2, -2.588567 + print("Checking freezept") + print() + print("S = 40, p = 500 dbar") + print(format1 % "freezept(40, 500)", freezept(40, 500)) + print(format2, -2.588567) - print + print() # Check value from UNESCO 1983, p. 49 - print "Checking soundvel" - print - print "S = 40, T = 40 °C, P = 10000 dbar" - print format1 % "soundvel(40, 40, 10000)", soundvel(40, 40, 10000) - print format2, 1731.995 + print("Checking soundvel") + print() + print("S = 40, T = 40 C, P = 10000 dbar") + print(format1 % "soundvel(40, 40, 10000)", soundvel(40, 40, 10000)) + print(format2, 1731.995) - print + print() # Check value from UNESCO 1983, p. 28 - print "Checking depth" - print - print "P = 10000 dbar, latitude = 30 degrees" - print format1 % "depth(10000, 30)", depth(10000, 30) - print format2, 9712.653 + print("Checking depth") + print() + print("P = 10000 dbar, latitude = 30 degrees") + print(format1 % "depth(10000, 30)", depth(10000, 30)) + print(format2, 9712.653) # ---------------------------------------------------------------- - + diff --git a/pyroms_toolbox/pyroms_toolbox/setup.py b/pyroms_toolbox/pyroms_toolbox/setup.py index c4a7256..f4f42be 100644 --- a/pyroms_toolbox/pyroms_toolbox/setup.py +++ b/pyroms_toolbox/pyroms_toolbox/setup.py @@ -6,6 +6,7 @@ def configuration(parent_package='',top_path=None): config.add_subpackage('BGrid_GFDL') config.add_subpackage('BGrid_POP') config.add_subpackage('BGrid_SODA') + config.add_subpackage('CGrid_GLORYS') config.add_subpackage('seawater') config.add_subpackage('Grid_HYCOM') config.add_library('_average', sources=['src/average.f90']), diff --git a/pyroms_toolbox/pyroms_toolbox/smooth_1D.py b/pyroms_toolbox/pyroms_toolbox/smooth_1D.py index c0d208c..5f4d67b 100644 --- a/pyroms_toolbox/pyroms_toolbox/smooth_1D.py +++ b/pyroms_toolbox/pyroms_toolbox/smooth_1D.py @@ -34,16 +34,16 @@ def smooth_1D(x, window_len=10, window='hanning'): """ if x.ndim != 1: - raise ValueError, "smooth only accepts 1 dimension arrays." + raise ValueError("smooth only accepts 1 dimension arrays.") if x.size < window_len: - raise ValueError, "Input vector needs to be bigger than window size." + raise ValueError("Input vector needs to be bigger than window size.") if window_len < 3: return x if not window in ['flat', 'hanning', 'hamming', 'bartlett', 'blackman']: - raise ValueError, "Window is on of 'flat', 'hanning', 'hamming', 'bartlett', 'blackman'" + raise ValueError("Window is on of 'flat', 'hanning', 'hamming', 'bartlett', 'blackman'") s=np.r_[2*x[0]-x[window_len:1:-1], x, 2*x[-1]-x[-1:-window_len:-1]] #print(len(s)) diff --git a/pyroms_toolbox/pyroms_toolbox/sview.py b/pyroms_toolbox/pyroms_toolbox/sview.py index 1395d75..9c06ee9 100644 --- a/pyroms_toolbox/pyroms_toolbox/sview.py +++ b/pyroms_toolbox/pyroms_toolbox/sview.py @@ -146,7 +146,7 @@ def sview(var, tindex, sindex, grid, filename=None, \ urcrnrlon=lon_max, urcrnrlat=lat_max, lat_0=lat_0, lon_0=lon_0, \ resolution='h', area_thresh=5.) #map = pyroms.utility.get_grid_proj(grd, type=proj) - x, y = map(lon,lat) + x, y = list(map(lon,lat)) if fill_land is True and proj is not None: # fill land and draw coastlines @@ -174,9 +174,9 @@ def sview(var, tindex, sindex, grid, filename=None, \ cf = plt.pcolor(lon, lat, sslice, cmap = pal, norm = pal_norm) if clb is True: - clb = plt.colorbar(cf, fraction=0.075,format='%.2f') - for t in clb.ax.get_yticklabels(): - t.set_fontsize(fts) + clb = plt.colorbar(cf, fraction=0.075,format='%.2f') + for t in clb.ax.get_yticklabels(): + t.set_fontsize(fts) if contour is True: if fill is not True: @@ -208,11 +208,11 @@ def sview(var, tindex, sindex, grid, filename=None, \ if outfile is not None: if outfile.find('.png') != -1 or outfile.find('.svg') != -1 or \ outfile.find('.eps') != -1: - print 'Write figure to file', outfile + print('Write figure to file', outfile) plt.savefig(outfile, dpi=200, facecolor='w', edgecolor='w', \ orientation='portrait') else: - print 'Unrecognized file extension. Please use .png, .svg or .eps file extension.' + print('Unrecognized file extension. Please use .png, .svg or .eps file extension.') if proj is None: diff --git a/pyroms_toolbox/pyroms_toolbox/transectview.py b/pyroms_toolbox/pyroms_toolbox/transectview.py index edf85f2..49b5dc0 100644 --- a/pyroms_toolbox/pyroms_toolbox/transectview.py +++ b/pyroms_toolbox/pyroms_toolbox/transectview.py @@ -11,7 +11,7 @@ def transectview(var, tindex, istart, iend, jstart, jend, gridid, \ fts=None, title=None, map=False, \ pal=None, clb=True, xaxis='lon', outfile=None): """ - transectview(var, tindex, istart, iend, jstart, jend, gridid, + transectview(var, tindex, istart, iend, jstart, jend, gridid, {optional switch}) optional switch: @@ -22,7 +22,7 @@ def transectview(var, tindex, istart, iend, jstart, jend, gridid, \ - clev set the number of color step - fill use contourf instead of pcolor - contour overlay contour - - c desired contour level. If not specified, + - c desired contour level. If not specified, plot every 4 contour level. - jrange j range - hrange h range @@ -134,21 +134,21 @@ def transectview(var, tindex, istart, iend, jstart, jend, gridid, \ #pal.set_bad('w', 1.0) pal_norm = colors.BoundaryNorm(vc,ncolors=256, clip = False) - + # clear figure #plt.clf() if map is True: - # set axes for the main plot in order to keep space for the map - if fts < 12: - ax=None - else: - ax = plt.axes([0.15, 0.08, 0.8, 0.65]) - else: - if fts < 12: - ax=None - else: - ax=plt.axes([0.15, 0.1, 0.8, 0.8]) + # set axes for the main plot in order to keep space for the map + if fts < 12: + ax=None + else: + ax = plt.axes([0.15, 0.08, 0.8, 0.65]) + else: + if fts < 12: + ax=None + else: + ax=plt.axes([0.15, 0.1, 0.8, 0.8]) if fill is True: @@ -157,20 +157,20 @@ def transectview(var, tindex, istart, iend, jstart, jend, gridid, \ cf = plt.pcolor(xt, zt, transect, cmap = pal, norm = pal_norm, axes=ax) if clb is True: - clb = plt.colorbar(cf, fraction=0.075,format='%.2f') - for t in clb.ax.get_yticklabels(): - t.set_fontsize(fts) + clb = plt.colorbar(cf, fraction=0.075,format='%.2f') + for t in clb.ax.get_yticklabels(): + t.set_fontsize(fts) if contour is True: if c is None: - c = vc[::10] + c = vc[::10] if fill is True: plt.contour(xt, zt, transect, c, colors='k', linewidths=0.5, linestyles='solid', axes=ax) else: xc = 0.5*(xt[1:,:]+xt[:-1,:]) xc = 0.5*(xc[:,1:]+xc[:,:-1]) zc = 0.5*(zt[1:,:]+zt[:-1,:]) - zc = 0.5*(zc[:,1:]+zc[:,:-1]) + zc = 0.5*(zc[:,1:]+zc[:,:-1]) plt.contour(xc, zc, transect, c, colors='k', linewidths=0.5, linestyles='solid', axes=ax) if jrange is not None: @@ -196,18 +196,18 @@ def transectview(var, tindex, istart, iend, jstart, jend, gridid, \ if map is True: # draw a map with constant-i slice location ax_map = plt.axes([0.4, 0.76, 0.2, 0.23]) - varm = np.ma.masked_where(mask[:,:] == 0, var[var.shape[0]-1,:,:]) + varm = np.ma.masked_where(mask[:,:] == 0, var[var.shape[0]-1,:,:]) lon_min = lon.min() lon_max = lon.max() lon_0 = (lon_min + lon_max) / 2. lat_min = lat.min() - lat_max = lat.max() + lat_max = lat.max() lat_0 = (lat_min + lat_max) / 2. map = Basemap(projection='merc', llcrnrlon=lon_min, llcrnrlat=lat_min, \ urcrnrlon=lon_max, urcrnrlat=lat_max, lat_0=lat_0, lon_0=lon_0, \ resolution='i', area_thresh=10.) - x, y = map(lon,lat) - xt, yt = map(lont[0,:],latt[0,:]) + x, y = list(map(lon,lat)) + xt, yt = list(map(lont[0,:],latt[0,:])) # fill land and draw coastlines map.drawcoastlines() map.fillcontinents(color='grey') @@ -218,10 +218,10 @@ def transectview(var, tindex, istart, iend, jstart, jend, gridid, \ if outfile is not None: if outfile.find('.png') != -1 or outfile.find('.svg') != -1 or outfile.find('.eps') != -1: - print 'Write figure to file', outfile + print('Write figure to file', outfile) plt.savefig(outfile, dpi=200, facecolor='w', edgecolor='w', orientation='portrait') else: - print 'Unrecognized file extension. Please use .png, .svg or .eps file extension.' + print('Unrecognized file extension. Please use .png, .svg or .eps file extension.') return diff --git a/pyroms_toolbox/pyroms_toolbox/twoDview.py b/pyroms_toolbox/pyroms_toolbox/twoDview.py index 575f63e..6bc6039 100644 --- a/pyroms_toolbox/pyroms_toolbox/twoDview.py +++ b/pyroms_toolbox/pyroms_toolbox/twoDview.py @@ -16,12 +16,12 @@ def twoDview(var, tindex, grid, filename=None, \ optional switch: - filename if defined, load the variable from file - - cmin set color minimum limit - - cmax set color maximum limit - - clev set the number of color step + - cmin set color minimum limit + - cmax set color maximum limit + - clev set the number of color step - fill use contourf instead of pcolor - contour overlay contour (request fill=True) - - d contour density (default d=4) + - d contour density (default d=4) - range set axis limit - fts set font size (default: 12) - title add title to the plot @@ -35,8 +35,8 @@ def twoDview(var, tindex, grid, filename=None, \ var must be a string and the variable will be load from the file. grid can be a grid object or a gridid. In the later case, the grid object correponding to the provided gridid will be loaded. - If proj is not None, return a Basemap object to be used with quiver - for example. + If proj is not None, return a Basemap object to be used with quiver + for example. """ # get grid @@ -153,7 +153,7 @@ def twoDview(var, tindex, grid, filename=None, \ lon_max = lon.max() lon_0 = (lon_min + lon_max) / 2. lat_min = lat.min() - lat_max = lat.max() + lat_max = lat.max() lat_0 = (lat_min + lat_max) / 2. else: lon_min = range[0] @@ -171,49 +171,49 @@ def twoDview(var, tindex, grid, filename=None, \ urcrnrlon=lon_max, urcrnrlat=lat_max, lat_0=lat_0, lon_0=lon_0, \ resolution='h', area_thresh=5.) #map = pyroms.utility.get_grid_proj(grd, type=proj) - x, y = map(lon,lat) - + x, y = list(map(lon,lat)) + if fill_land is True and proj is not None: # fill land and draw coastlines map.drawcoastlines() map.fillcontinents(color='grey') else: - if proj is not None: + if proj is not None: Basemap.pcolor(map, x, y, mask, vmin=-2, cmap=cm.gray, edgecolors='face') pyroms_toolbox.plot_coast_line(grd, map) - else: + else: plt.pcolor(lon, lat, mask, vmin=-2, cmap=cm.gray, edgecolors='face') pyroms_toolbox.plot_coast_line(grd) - + if fill is True: - if proj is not None: + if proj is not None: cf = Basemap.contourf(map, x, y, var, vc, cmap = pal, \ norm = pal_norm) - else: + else: cf = plt.contourf(lon, lat, var, vc, cmap = pal, \ norm = pal_norm) else: - if proj is not None: + if proj is not None: cf = Basemap.pcolor(map, x, y, var, cmap = pal, norm = pal_norm, edgecolors='face') - else: + else: cf = plt.pcolor(lon, lat, var, cmap = pal, norm = pal_norm, edgecolors='face') if clb is True: - clb = plt.colorbar(cf, fraction=0.075,format='%.2f') - for t in clb.ax.get_yticklabels(): - t.set_fontsize(fts) + clb = plt.colorbar(cf, fraction=0.075,format='%.2f') + for t in clb.ax.get_yticklabels(): + t.set_fontsize(fts) if contour is True: if fill is not True: - raise Warning, 'Please run again with fill=True to overlay contour.' + raise Warning('Please run again with fill=True to overlay contour.') else: if proj is not None: Basemap.contour(map, x, y, var, vc[::d], colors='k', linewidths=0.5, linestyles='solid') - else: + else: plt.contour(lon, lat, var, vc[::d], colors='k', linewidths=0.5, linestyles='solid') if proj is None and range is not None: - plt.axis(range) + plt.axis(range) if title is not None: @@ -228,11 +228,11 @@ def twoDview(var, tindex, grid, filename=None, \ if outfile is not None: if outfile.find('.png') != -1 or outfile.find('.svg') != -1 or \ outfile.find('.eps') != -1: - print 'Write figure to file', outfile + print('Write figure to file', outfile) plt.savefig(outfile, dpi=200, facecolor='w', edgecolor='w', \ orientation='portrait') else: - print 'Unrecognized file extension. Please use .png, .svg or .eps file extension.' + print('Unrecognized file extension. Please use .png, .svg or .eps file extension.') if proj is None: diff --git a/pyroms_toolbox/pyroms_toolbox/zview.py b/pyroms_toolbox/pyroms_toolbox/zview.py index f331365..de0809a 100644 --- a/pyroms_toolbox/pyroms_toolbox/zview.py +++ b/pyroms_toolbox/pyroms_toolbox/zview.py @@ -16,9 +16,9 @@ def zview(var, tindex, depth, grid, filename=None, \ optional switch: - filename if defined, load the variable from file - - cmin set color minimum limit - - cmax set color maximum limit - - clev set the number of color step + - cmin set color minimum limit + - cmax set color maximum limit + - clev set the number of color step - fill use contourf instead of pcolor - contour overlay contour (request fill=True) - range set axis limit @@ -34,8 +34,8 @@ def zview(var, tindex, depth, grid, filename=None, \ var must be a string and the variable will be load from the file. grid can be a grid object or a gridid. In the later case, the grid object correponding to the provided gridid will be loaded. - If proj is not None, return a Basemap object to be used with quiver - for example. + If proj is not None, return a Basemap object to be used with quiver + for example. """ # get grid @@ -128,7 +128,7 @@ def zview(var, tindex, depth, grid, filename=None, \ lon_max = lon.max() lon_0 = (lon_min + lon_max) / 2. lat_min = lat.min() - lat_max = lat.max() + lat_max = lat.max() lat_0 = (lat_min + lat_max) / 2. else: lon_min = range[0] @@ -146,49 +146,49 @@ def zview(var, tindex, depth, grid, filename=None, \ urcrnrlon=lon_max, urcrnrlat=lat_max, lat_0=lat_0, lon_0=lon_0, \ resolution='h', area_thresh=5.) #map = pyroms.utility.get_grid_proj(grd, type=proj) - x, y = map(lon,lat) - + x, y = list(map(lon,lat)) + if fill_land is True and proj is not None: # fill land and draw coastlines map.drawcoastlines() map.fillcontinents(color='grey') else: - if proj is not None: + if proj is not None: Basemap.pcolor(map, x, y, mask, vmin=-2, cmap=cm.gray) pyroms_toolbox.plot_coast_line(grd, map) - else: + else: plt.pcolor(lon, lat, mask, vmin=-2, cmap=cm.gray) pyroms_toolbox.plot_coast_line(grd) - + if fill is True: - if proj is not None: + if proj is not None: cf = Basemap.contourf(map, x, y, zslice, vc, cmap = pal, \ norm = pal_norm) - else: + else: cf = plt.contourf(lon, lat, zslice, vc, cmap = pal, \ norm = pal_norm) else: - if proj is not None: + if proj is not None: cf = Basemap.pcolor(map, x, y, zslice, cmap = pal, norm = pal_norm) - else: + else: cf = plt.pcolor(lon, lat, zslice, cmap = pal, norm = pal_norm) if clb is True: - clb = plt.colorbar(cf, fraction=0.075,format=clb_format) - for t in clb.ax.get_yticklabels(): - t.set_fontsize(fts) + clb = plt.colorbar(cf, fraction=0.075,format=clb_format) + for t in clb.ax.get_yticklabels(): + t.set_fontsize(fts) if contour is True: if fill is not True: - raise Warning, 'Please run again with fill=True to overlay contour.' + raise Warning('Please run again with fill=True to overlay contour.') else: if proj is not None: Basemap.contour(map, x, y, zslice, vc[::d], colors='k', linewidths=0.5, linestyles='solid') - else: + else: plt.contour(lon, lat, zslice, vc[::d], colors='k', linewidths=0.5, linestyles='solid') if proj is None and range is not None: - plt.axis(range) + plt.axis(range) if title is not None: @@ -203,11 +203,11 @@ def zview(var, tindex, depth, grid, filename=None, \ if outfile is not None: if outfile.find('.png') != -1 or outfile.find('.svg') != -1 or \ outfile.find('.eps') != -1: - print 'Write figure to file', outfile + print('Write figure to file', outfile) plt.savefig(outfile, dpi=200, facecolor='w', edgecolor='w', \ orientation='portrait') else: - print 'Unrecognized file extension. Please use .png, .svg or .eps file extension.' + print('Unrecognized file extension. Please use .png, .svg or .eps file extension.') if proj is None: diff --git a/pyroms_toolbox/setup.py b/pyroms_toolbox/setup.py index b8e42d0..77df91b 100644 --- a/pyroms_toolbox/setup.py +++ b/pyroms_toolbox/setup.py @@ -4,13 +4,28 @@ pyroms_toolbox is a suite of tools for working with ROMS. Requires: - pyroms (https://github.com/kshedstrom/pyroms) + pyroms (https://github.com/ESMG/pyroms) Contains: many things... """ +from numpy.distutils.core import Extension + +average = Extension(name = '_average', + sources = ['pyroms_toolbox/src/average.f90']) + +creep = Extension(name = 'creep', + sources = ['pyroms_toolbox/src/creeping_sea.f90']) + +move_river = Extension(name = '_move_river_t', + sources = ['pyroms_toolbox/src/move_river_t.f90']) + +move_runoff = Extension(name = '_move_runoff', + sources = ['pyroms_toolbox/src/move_runoff.f90']) + + doclines = __doc__.split("\n") def configuration(parent_package='',top_path=None): @@ -29,10 +44,10 @@ def configuration(parent_package='',top_path=None): version = '0.1', description = doclines[0], long_description = "\n".join(doclines[2:]), - author = "Pyroms Group", - author_email = "kshedstrom@alaska.edu", - url = 'https://github.com/kshedstrom/pyroms', + author = "ESMG", + url = 'https://github.com/ESMG/pyroms', license = 'BSD', platforms = ["any"], + ext_modules=[average, creep, move_river, move_runoff], configuration=configuration, )