rst readme and fixed python2 download file bug

Author: Chen Xie

README.md

@@ -0,0 +1,191 @@
+wfdb-python
+===========
+
+|Build Status|
+
+.. figure:: https://raw.githubusercontent.com/MIT-LCP/wfdb-python/master/demoimg1.png
+   :alt: wfdb signals
+
+Introduction
+------------
+
+Native python scripts for reading and writing WFDB signals and
+annotations.
+
+Usage
+-----
+
+Distribution hosted on pypi. No need to manualy download or clone this
+repository. To install the package, run from your terminal:
+``pip install wfdb``
+
+See the **wfdbdemo.ipynb** file for example scripts on how to call the
+functions.
+
+Reading Signals
+~~~~~~~~~~~~~~~
+
+**rdsamp** - Read a WFDB file and return the signal as a numpy array and
+the metadata as a dictionary.
+
+::
+
+    sig, fields = rdsamp(recordname, sampfrom=0, sampto=[], channels=[], physical=1, stacksegments=1, pbdl=0, dldir=os.cwd(), keepfiles=0)
+
+Example Usage:
+
+::
+
+    import wfdb
+    sig, fields = wfdb.rdsamp('mitdb/100', sampto=2000, pbdl=1)
+
+Input Arguments:
+
+-  ``recordname`` (mandatory) - The name of the WFDB record to be read
+   (without any file extensions).
+-  ``sampfrom`` (default=0) - The starting sample number to read for
+   each channel.
+-  ``sampto`` (default=length of entire signal)- The final sample number
+   to read for each channel.
+-  ``channels`` (default=all channels) - Indices specifying the channel
+   to be returned.
+-  ``physical`` (default=1) - Flag that specifies whether to return
+   signals in physical (1) or digital (0) units.
+-  ``stacksegments`` (default=1) - Flag used only for multi-segment
+   files. Specifies whether to return the signal as a single
+   stacked/concatenated numpy array (1) or as a list of one numpy array
+   for each segment (0).
+-  ``pbdl`` (default=0): If this argument is set, the function will
+   assume that the user is trying to download a physiobank file.
+   Therefore the ‘recordname’ argument will be interpreted as a
+   physiobank record name including the database subdirectory, rather
+   than a local directory.
+-  ``dldir`` (default=os.getcwd()): The directory to download physiobank
+   files to.
+-  ``keepfiles`` (default=0): Flag specifying whether to keep physiobank
+   files newly downloaded through the function call.
+
+Output Arguments:
+
+-  ``sig`` - An nxm numpy array where n is the signal length and m is
+   the number of channels. If the input record is a multi-segment
+   record, depending on the input stacksegments flag, sig will either be
+   a single stacked/concatenated numpy array (1) or a list of one numpy
+   array for each segment (0). For empty segments, stacked format will
+   contain Nan values, and non-stacked format will contain a single
+   integer specifying the length of the empty segment.
+-  ``fields`` - A dictionary of metadata about the record extracted or
+   deduced from the header/signal file. If the input record is a
+   multi-segment record, the output argument will be a list of
+   dictionaries:
+
+   -  The first list element will be a dictionary of metadata about the
+      master header.
+   -  If the record is in variable layout format, the next list element
+      will be a dictionary of metadata about the layout specification
+      header.
+   -  The last list element will be a list of dictionaries of metadata
+      for each segment. For empty segments, the dictionary will be
+      replaced by a single string: ‘Empty Segment’
+
+Reading Annotations
+~~~~~~~~~~~~~~~~~~~
+
+**rdann** - Read a WFDB annotation file ``recordname.annot`` and return
+the fields as lists or arrays.
+
+::
+
+    annsamp, anntype, subtype, chan, num, aux, annfs = wfdb.rdann(recordname, annot, sampfrom=0, sampto=[], anndisp=1)
+
+Example Usage:
+
+::
+
+    import wfdb
+    annsamp, anntype, subtype, chan, num, aux, annfs = wfdb.rdann('100', 'atr')
+
+Input Arguments:
+
+-  ``recordname`` (required) - The record name of the WFDB annotation
+   file. ie. for file ``100.atr`` recordname=‘100’.
+-  ``annot`` (required) - The annotator extension of the annotation
+   file. ie. for file ``100.atr`` annot=‘atr’.
+-  ``sampfrom`` (default=0)- The minimum sample number for annotations
+   to be returned.
+-  ``sampto`` (default=the final annotation sample) - The maximum sample
+   number for annotations to be returned.
+-  ``anndisp`` (default=1) - The annotation display flag that controls
+   the data type of the ``anntype`` output parameter. ``anntype`` will
+   either be an integer key(0), a shorthand display symbol(1), or a
+   longer annotation code(2).
+
+Output arguments:
+
+-  ``annsamp`` - The annotation location in samples relative to the
+   beginning of the record.
+-  ``anntype`` - The annotation type according the the standard WFDB
+   keys.
+-  ``subtype`` - The marked class/category of the annotation.
+-  ``chan`` - The signal channel associated with the annotations.
+-  ``num`` - The marked annotation number. This is not equal to the
+   index of the current annotation.
+-  ``aux`` - The auxiliary information string for the annotation.
+-  ``annfs`` - The sampling frequency written in the beginning of the
+   annotation file if present.
+
+\*\ **NOTE**: Every annotation contains the ‘annsamp’ and ‘anntype’
+field. All other fields default to 0 or empty if not present.
+
+
+Plotting Data
+~~~~~~~~~~~~~
+
+**plotwfdb** - Subplot and label each channel of an nxm signal on a
+graph. Also subplot annotation locations on selected channels if
+present.
+
+::
+
+    plotwfdb(sig, fields, annsamp=[], annch=[0], title=[], plottime=1)
+
+Example Usage:
+
+::
+
+    import wfdb
+    sig, fields = wfdb.rdsamp('100')
+    annsamp=wfdb.rdann('100', 'atr')[0]
+    wfdb.plotwfdb(sig, fields, annsamp, 'mitdb record 100'): 
+     
+
+Input Arguments:
+
+-  ``sig`` (required)- An nxm numpy array containing the signal to be
+   plotted - the first output argument of ``wfdb.rdsamp``.
+-  ``fields`` (required) - A dictionary of metadata about the record -
+   the second output argument of ``wfdb.rdsamp``.
+-  ``annsamp`` (optional) - A 1d numpy array of annotation locations to
+   be plotted on top of selected channels - first output argument of
+   ``rdann``.
+-  ``annch`` (default=[0]) - A list of channels on which to plot the
+   annotations.
+-  ``title`` (optional)- A string containing the title of the graph.
+-  ``plottime`` (default=1) - Flag that specifies whether to plot the x
+   axis as time (1) or samples (0). Defaults to samples if the input
+   ``fields`` dictionary does not contain a value for ``fs``.
+
+Based on the original WFDB software package specifications
+----------------------------------------------------------
+
+| `WFDB Software Package`_
+| `WFDB Applications Guide`_
+| `WFDB Header File Specifications`_
+
+.. _WFDB Software Package: http://physionet.org/physiotools/wfdb.shtml
+.. _WFDB Applications Guide: http://physionet.org/physiotools/wag/
+.. _WFDB Header File Specifications: https://physionet.org/physiotools/wag/header-5.htm
+
+
+.. |Build Status| image:: https://travis-ci.org/MIT-LCP/wfdb-python.svg?branch=master
+   :target: https://travis-ci.org/MIT-LCP/wfdb-python

README.rst

@@ -11,7 +11,7 @@
 here = path.abspath(path.dirname(__file__))
 
 # Get the long description from the README file
-with open(path.join(here, 'README.md'), encoding='utf-8') as f:
+with open(path.join(here, 'README.rst'), encoding='utf-8') as f:
     long_description = f.read()
 
 setup(

setup.py

@@ -93,8 +93,8 @@ def dlorexit(url, filename, displaydlmsg=0, targetdir=[]):
         print('Downloading missing file(s) into directory: {}'.format(targetdir))
     try:
         r = requests.get(url)
-        with open(filename, "w") as text_file:
-            text_file.write(r.text)
+        with open(filename, "wb") as writefile:
+            writefile.write(r.content)
         return filename
     except requests.HTTPError:
         sys.exit("Attempted to download invalid target file: " + url)