removing trash

bftools/bf.bat

@@ -0,0 +1,69 @@
+@echo off
+
+rem bf.bat: the batch file that actually launches a command line tool
+
+setlocal enabledelayedexpansion
+set BF_DIR=%~dp0
+if "%BF_DIR:~-1%" == "\" set BF_DIR=%BF_DIR:~0,-1%
+
+rem Include the master configuration file.
+call "%BF_DIR%\config.bat"
+
+rem Check that a command to run was specified.
+if "%BF_PROG%" == "" (
+  echo The command to launch must be set in the BF_PROG environment variable.
+  goto end
+)
+
+rem Set the max heap size.
+if "%BF_MAX_MEM%" == "" (
+  rem Set a reasonable default max heap size.
+  set BF_MAX_MEM=512m
+)
+set BF_FLAGS=%BF_FLAGS% -Xmx%BF_MAX_MEM%
+
+rem Skip the update check if the NO_UPDATE_CHECK flag is set.
+if not "%NO_UPDATE_CHECK%" == "" (
+  set BF_FLAGS=%BF_FLAGS% -Dbioformats_can_do_upgrade_check=false
+)
+
+rem Run profiling if the BF_PROFILE flag is set.
+if not "%BF_PROFILE%" == "" (
+  if "%BF_PROFILE_DEPTH%" == "" (
+    rem Set default profiling depth
+    set BF_PROFILE_DEPTH=30
+  )
+  set BF_FLAGS=%BF_FLAGS% -agentlib:hprof=cpu=samples,depth=!BF_PROFILE_DEPTH!,file=%BF_PROG%.hprof
+)
+
+
+rem Use any available proxy settings.
+set BF_FLAGS=%BF_FLAGS% -Dhttp.proxyHost=%PROXY_HOST% -Dhttp.proxyPort=%PROXY_PORT%
+
+rem Run the command!
+if not "%BF_DEVEL%" == "" (
+  rem Developer environment variable set; launch with existing classpath.
+  java %BF_FLAGS% %BF_PROG% %*
+  goto end
+)
+
+rem Developer environment variable unset; add JAR libraries to classpath.
+if exist "%BF_JAR_DIR%\bioformats_package.jar" (
+    set BF_CP=%BF_CP%;"%BF_JAR_DIR%\bioformats_package.jar"
+) else if exist "%BF_JAR_DIR%\loci_tools.jar" (
+    set BF_CP=%BF_CP%;"%BF_JAR_DIR%\loci_tools.jar"
+) else if exist "%BF_JAR_DIR%\formats-gpl.jar" (
+    set BF_CP=%BF_CP%;"%BF_JAR_DIR%\formats-gpl.jar";"%BF_JAR_DIR%\bio-formats-tools.jar"
+) else (
+  rem Libraries not found; issue an error.
+  echo Required JAR libraries not found. Please download:
+  echo   bioformats_package.jar
+  echo from:
+  echo   http://downloads.openmicroscopy.org/latest/bio-formats5.1
+  echo and place in the same directory as the command line tools.
+  goto end
+)
+
+java %BF_FLAGS% -cp "%BF_DIR%";%BF_CP% %BF_PROG% %*
+
+:end

bftools/bf.sh

@@ -0,0 +1,77 @@
+#!/usr/bin/env bash
+
+# bf.sh: the script that actually launches a command line tool
+
+BF_DIR=`dirname "$0"`
+
+# Include the master configuration file.
+source "$BF_DIR/config.sh"
+
+# Check that a command to run was specified.
+if [ -z "$BF_PROG" ]
+then
+  echo The command to launch must be set in the BF_PROG environment variable.
+  exit 1
+fi
+
+# Prepare the flags.
+if [ -z "$BF_FLAGS" ]
+then
+   BF_FLAGS=""
+fi
+
+# Set the max heap size.
+if [ -z "$BF_MAX_MEM" ]
+then
+  # Set a reasonable default max heap size.
+  BF_MAX_MEM="512m"
+fi
+BF_FLAGS="$BF_FLAGS -Xmx$BF_MAX_MEM"
+
+# Skip the update check if the NO_UPDATE_CHECK flag is set.
+if [ -n "$NO_UPDATE_CHECK" ]
+then
+  BF_FLAGS="$BF_FLAGS -Dbioformats_can_do_upgrade_check=false"
+fi
+
+# Run profiling if the BF_PROFILE flag is set.
+if [ -n "$BF_PROFILE" ]
+then
+  # Set default profiling depth
+  if [ -z "$BF_PROFILE_DEPTH" ]
+  then
+    BF_PROFILE_DEPTH="30"
+  fi
+  BF_FLAGS="$BF_FLAGS -agentlib:hprof=cpu=samples,depth=$BF_PROFILE_DEPTH,file=$BF_PROG.hprof"
+fi
+
+# Use any available proxy settings.
+BF_FLAGS="$BF_FLAGS -Dhttp.proxyHost=$PROXY_HOST -Dhttp.proxyPort=$PROXY_PORT"
+
+# Run the command!
+if [ -n "$BF_DEVEL" ]
+then
+  # Developer environment variable set; launch with existing classpath.
+  java $BF_FLAGS $BF_PROG "$@"
+else
+  # Developer environment variable unset; add JAR libraries to classpath.
+  if [ -e "$BF_JAR_DIR/bioformats_package.jar" ]
+  then
+    BF_CP="$BF_JAR_DIR/bioformats_package.jar:$BF_CP"
+  elif [ -e "$BF_JAR_DIR/loci_tools.jar" ]
+  then
+    BF_CP="$BF_JAR_DIR/loci_tools.jar:$BF_CP"
+  elif [ -e "$BF_JAR_DIR/formats-gpl.jar" ]
+  then
+    BF_CP="$BF_JAR_DIR/formats-gpl.jar:$BF_JAR_DIR/bio-formats-tools.jar:$BF_CP"
+  else
+    # Libraries not found; issue an error.
+    echo "Required JAR libraries not found. Please download:"
+    echo "  bioformats_package.jar"
+    echo "from:"
+    echo "  http://downloads.openmicroscopy.org/latest/bio-formats5.1"
+    echo "and place in the same directory as the command line tools."
+    exit 2
+  fi
+  java $BF_FLAGS -cp "$BF_DIR:$BF_CP" $BF_PROG "$@"
+fi

bftools/bfconvert

@@ -0,0 +1,12 @@
+#!/usr/bin/env bash
+
+# bfconvert: a script for converting image files between formats
+
+# Required JARs: loci_tools.jar or bioformats_package.jar
+
+RESOLVED_PATH=$(readlink -f "$0" 2>/dev/null \
+  || perl -MCwd -le 'print Cwd::abs_path(shift)' "$0" 2>/dev/null \
+  || echo "$0")
+BF_DIR=$(dirname $RESOLVED_PATH)
+
+BF_PROG=loci.formats.tools.ImageConverter "$BF_DIR/bf.sh" "$@"

bftools/bfconvert.bat

@@ -0,0 +1,12 @@
+@echo off
+
+rem bfconvert.bat: a batch file for converting image files between formats
+
+rem Required JARs: loci_tools.jar or bioformats_package.jar
+
+setlocal
+set BF_DIR=%~dp0
+if "%BF_DIR:~-1%" == "\" set BF_DIR=%BF_DIR:~0,-1%
+
+set BF_PROG=loci.formats.tools.ImageConverter
+call "%BF_DIR%\bf.bat" %*

bftools/config.bat

@@ -0,0 +1,35 @@
+@echo off
+
+rem config.bat: master configuration file for the batch files
+
+rem Running this command directly has no effect,
+rem but you can tweak the settings to your liking.
+
+rem Set the amount of RAM available to the command line tools.
+rem Use "m" suffix for megabytes, "g" for gigabytes; e.g., 2g = 2GB.
+rem set BF_MAX_MEM=1g
+
+rem Set the NO_UPDATE_CHECK flag to skip the update check.
+rem set NO_UPDATE_CHECK=1
+
+rem If you are behind a proxy server, the host name and port must be set.
+rem set PROXY_HOST=
+rem set PROXY_PORT=
+
+rem If your CLASSPATH already includes the needed classes,
+rem you can set the BF_DEVEL environment variable to
+rem disable the required JAR library checks.
+rem set BF_DEVEL=1
+
+rem Set the directory containing the JAR libraries.
+if "%BF_JAR_DIR%" == "" (
+  if exist "%BF_DIR%\..\artifacts" (
+    rem Batch files reside in a git working copy.
+    rem Look for JARs in the artifacts directory.
+    set BF_JAR_DIR=%BF_DIR%\..\artifacts
+  ) else (
+    rem Batch files reside in a standalone distribution.
+    rem Look for JARs in the same directory as the batch files.
+    set BF_JAR_DIR=%BF_DIR%
+  )
+)

bftools/config.sh

@@ -0,0 +1,37 @@
+#!/usr/bin/env bash
+
+# config.sh: master configuration file for the scripts
+
+# Running this command directly has no effect,
+# but you can tweak the settings to your liking.
+
+# Set the amount of RAM available to the command line tools.
+# Use "m" suffix for megabytes, "g" for gigabytes; e.g., 2g = 2 GB.
+#BF_MAX_MEM=1g
+
+# Set the NO_UPDATE_CHECK flag to skip the update check.
+#NO_UPDATE_CHECK=1
+
+# If you are behind a proxy server, the host name and port must be set.
+#PROXY_HOST=
+#PROXY_PORT=
+
+# If your CLASSPATH already includes the needed classes,
+# you can set the BF_DEVEL environment variable to
+# disable the required JAR library checks.
+#BF_DEVEL=1
+
+# Set the directory containing the JAR libraries.
+if [ -z "$BF_JAR_DIR" ]
+then
+  if [ -d "$BF_DIR/../artifacts" ]
+  then
+    # Scripts reside in a git working copy.
+    # Look for JARs in the artifacts directory.
+    BF_JAR_DIR="$BF_DIR/../artifacts"
+  else
+    # Scripts reside in a standalone distribution.
+    # Look for JARs in the same directory as the scripts.
+    BF_JAR_DIR="$BF_DIR"
+  fi
+fi

bftools/domainlist

@@ -0,0 +1,12 @@
+#!/usr/bin/env bash
+
+# domainlist: a script for listing supported domains in Bio-Formats
+
+# Required JARs: loci_tools.jar or bioformats_package.jar
+
+RESOLVED_PATH=$(readlink -f "$0" 2>/dev/null \
+  || perl -MCwd -le 'print Cwd::abs_path(shift)' "$0" 2>/dev/null \
+  || echo "$0")
+BF_DIR=$(dirname $RESOLVED_PATH)
+
+BF_PROG=loci.formats.tools.PrintDomains "$BF_DIR/bf.sh" "$@"

bftools/domainlist.bat

@@ -0,0 +1,12 @@
+@echo off
+
+rem domainlist.bat: a batch file for listing supported domains in Bio-Formats
+
+rem Required JARs: loci_tools.jar or bioformats_package.jar
+
+setlocal
+set BF_DIR=%~dp0
+if "%BF_DIR:~-1%" == "\" set BF_DIR=%BF_DIR:~0,-1%
+
+set BF_PROG=loci.formats.tools.PrintDomains
+call "%BF_DIR%\bf.bat" %*

bftools/formatlist

@@ -0,0 +1,12 @@
+#!/usr/bin/env bash
+
+# formatlist: a script for listing supported formats in Bio-Formats
+
+# Required JARs: loci_tools.jar or bioformats_package.jar
+
+RESOLVED_PATH=$(readlink -f "$0" 2>/dev/null \
+  || perl -MCwd -le 'print Cwd::abs_path(shift)' "$0" 2>/dev/null \
+  || echo "$0")
+BF_DIR=$(dirname $RESOLVED_PATH)
+
+BF_PROG=loci.formats.tools.PrintFormatTable "$BF_DIR/bf.sh" "$@"

bftools/formatlist.bat

@@ -0,0 +1,12 @@
+@echo off
+
+rem formatlist.bat: a batch file for listing supported formats in Bio-Formats
+
+rem Required JARs: loci_tools.jar or bioformats_package.jar
+
+setlocal
+set BF_DIR=%~dp0
+if "%BF_DIR:~-1%" == "\" set BF_DIR=%BF_DIR:~0,-1%
+
+set BF_PROG=loci.formats.tools.PrintFormatTable
+call "%BF_DIR%\bf.bat" %*

bftools/ijview

@@ -0,0 +1,49 @@
+#!/usr/bin/env bash
+
+# ijview: a script for displaying an image file in ImageJ
+#         using the Bio-Formats Importer plugin
+
+# Required JARs: loci_tools.jar or bioformats_package.jar, ij.jar
+
+
+RESOLVED_PATH=$(readlink -f "$0" 2>/dev/null \
+  || perl -MCwd -le 'print Cwd::abs_path(shift)' "$0" 2>/dev/null \
+  || echo "$0")
+BF_DIR=$(dirname $RESOLVED_PATH)
+
+source "$BF_DIR/config.sh"
+
+if [ -z "$BF_DEVEL" ]
+then
+  # Developer environment variable unset; add JAR libraries to classpath.
+  if [ -e "$BF_JAR_DIR/ij.jar" ]
+  then
+    BF_CP="$BF_JAR_DIR/ij.jar"
+  else
+    # Libraries not found; issue an error
+    echo "Required JAR libraries not found. Please download:"
+    echo "  ij.jar"
+    echo "from:"
+    echo "  http://imagej.nih.gov/ij/upgrade/"
+    echo "and place in the same directory as the command line tools."
+    echo ""
+    exit 3
+  fi
+  if [ -e "$BF_JAR_DIR/bio-formats_plugins.jar" ]
+  then
+    BF_CP="$BF_CP:$BF_JAR_DIR/bio-formats_plugins.jar"
+  elif [ ! -e "$BF_JAR_DIR/loci_tools.jar" -a ! -e "$BF_JAR_DIR/bioformats_package.jar" ]
+  then
+    # Libraries not found; issue an error
+    echo "Required JAR libraries not found. Please download:"
+    echo "  bioformats_package.jar"
+    echo "from:"
+    echo "  http://www.openmicroscopy.org/site/products/bio-formats/downloads"
+    echo "and place in the same directory as the command line tools."
+    echo ""
+    exit 4
+  fi
+fi
+
+BF_PROG=loci.plugins.in.Importer \
+  BF_CP="$BF_CP" "$BF_DIR/bf.sh" "$@"

bftools/ijview.bat

@@ -0,0 +1,43 @@
+@echo off
+
+rem ijview.bat: a batch file for displaying an image file in ImageJ
+rem             using the Bio-Formats Importer plugin
+
+rem Required JARs: loci_tools.jar or bioformats_package.jar, ij.jar
+
+setlocal
+set BF_DIR=%~dp0
+if "%BF_DIR:~-1%" == "\" set BF_DIR=%BF_DIR:~0,-1%
+
+call "%BF_DIR%\config.bat"
+
+if "%BF_DEVEL%" == "" (
+  rem Developer environment variable unset; add JAR libraries to classpath.
+  if exist "%BF_JAR_DIR%\ij.jar" (
+    set BF_CP="%BF_JAR_DIR%\ij.jar"
+  ) else (
+    rem Libraries not found; issue an error.
+    echo Required JAR libraries not found. Please download:
+    echo   ij.jar
+    echo from:
+    echo   http://imagej.nih.gov/ij/upgrade/
+    echo and place in the same directory as the command line tools.
+    goto end
+  )
+  if exist "%BF_JAR_DIR%\bio-formats_plugins.jar" (
+    set BF_CP=%BF_CP%;"%BF_JAR_DIR%\bio-formats_plugins.jar"
+  ) else if not exist "%BF_JAR_DIR%\bioformats_package.jar" (
+    rem Libraries not found; issue an error.
+    echo Required JAR libraries not found. Please download:
+    echo   bioformats_package.jar
+    echo from:
+    echo   http://www.openmicroscopy.org/site/products/bio-formats/downloads
+    echo and place in the same directory as the command line tools.
+    goto end
+  )
+)
+
+set BF_PROG=loci.plugins.in.Importer
+call "%BF_DIR%\bf.bat" %*
+
+:end