Mercurial > repos > iuc > imagej2_make_binary
changeset 0:66d9e595dff2 draft
planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
| author | iuc |
|---|---|
| date | Tue, 04 Aug 2015 13:20:29 -0400 |
| parents | |
| children | d26f11339f08 |
| files | imagej2_base_utils.py imagej2_macros.xml imagej2_make_binary.py imagej2_make_binary.xml jython_script.py jython_utils.py test-data/clown.jpg test-data/clown_binary.jpg tool_dependencies.xml |
| diffstat | 9 files changed, 516 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/imagej2_base_utils.py Tue Aug 04 13:20:29 2015 -0400 @@ -0,0 +1,178 @@ +import os +import shutil +import sys +import tempfile + +FIJI_JAR_DIR = os.environ.get( 'FIJI_JAR_DIR', None ) +FIJI_OSX_JAVA3D_DIR = os.environ.get( 'FIJI_OSX_JAVA3D_DIR', None ) +FIJI_PLUGIN_DIR = os.environ.get( 'FIJI_PLUGIN_DIR', None ) +FIJI_ROOT_DIR = os.environ.get( 'FIJI_ROOT_DIR', None ) + +BUFF_SIZE = 1048576 + +def cleanup_before_exit( tmp_dir ): + """ + Remove temporary files and directories prior to tool exit. + """ + if tmp_dir and os.path.exists( tmp_dir ): + shutil.rmtree( tmp_dir ) + +def get_base_cmd_bunwarpj( jvm_memory ): + if FIJI_JAR_DIR is not None and FIJI_PLUGIN_DIR is not None: + if jvm_memory in [ None, 'None' ]: + jvm_memory_str = '' + else: + jvm_memory_str = '-Xmx%s' % jvm_memory + bunwarpj_base_cmd = "java %s -cp %s/ij-1.49k.jar:%s/bUnwarpJ_-2.6.1.jar bunwarpj.bUnwarpJ_" % \ + ( jvm_memory_str, FIJI_JAR_DIR, FIJI_PLUGIN_DIR ) + return bunwarpj_base_cmd + return None + +def get_base_command_imagej2( memory_size=None, macro=None, jython_script=None ): + imagej2_executable = get_imagej2_executable() + if imagej2_executable is None: + return None + cmd = '%s --ij2 --headless --debug' % imagej2_executable + if memory_size is not None: + memory_size_cmd = ' -DXms=%s -DXmx=%s' % ( memory_size, memory_size ) + cmd += memory_size_cmd + if macro is not None: + cmd += ' --macro %s' % os.path.abspath( macro ) + if jython_script is not None: + cmd += ' --jython %s' % os.path.abspath( jython_script ) + return cmd + +def get_file_extension( image_format ): + """ + Return a valid bioformats file extension based on the received + value of image_format( e.g., "gif" is returned as ".gif". + """ + return '.%s' % image_format + +def get_file_name_without_extension( file_path ): + """ + Eliminate the .ext from the received file name, assuming that + the file name consists of only a single '.'. + """ + if os.path.exists( file_path ): + path, name = os.path.split( file_path ) + name_items = name.split( '.' ) + return name_items[ 0 ] + return None + +def get_imagej2_executable(): + """ + Fiji names the ImageJ executable different names for different + architectures, so figure out which name we need. + """ + platform_dict = get_platform_info_dict() + if platform_dict.get( 'architecture', None ) in [ 'x86_64' ]: + if platform_dict.get( 'os', None ) in [ 'darwin' ]: + return 'ImageJ-macosx' + if platform_dict.get( 'os', None ) in [ 'linux' ]: + return 'ImageJ-linux64' + return None + +def get_input_image_path( tmp_dir, input_file, image_format ): + """ + Bioformats uses file extensions (e.g., .job, .gif, etc) + when reading and writing image files, so the Galaxy dataset + naming convention of setting all file extensions as .dat + must be handled. + """ + image_path = get_temporary_image_path( tmp_dir, image_format ) + # Remove the file so we can create a symlink. + os.remove( image_path ) + os.symlink( input_file, image_path ) + return image_path + +def get_max_heap_size_value( max_heap_size_type, max_heap_size ): + """ + Return a string that can be used by the javabridge to set the size + of the memory allocation pool used by the JVM. The value must be + determined to be a multiple of 1024 or it will be ignored. + """ + if max_heap_size_type == 'default': + return None + if max_heap_size_type == 'megabytes': + if int( max_heap_size ) % 1024 not in [ 0, 256, 512 ]: + return None + return '%sm' % str( max_heap_size ) + if max_heap_size_type == 'gigabytes': + return '%sg' % str( max_heap_size ) + +def get_platform_info_dict(): + '''Return a dict with information about the current platform.''' + platform_dict = {} + sysname, nodename, release, version, machine = os.uname() + platform_dict[ 'os' ] = sysname.lower() + platform_dict[ 'architecture' ] = machine.lower() + return platform_dict + +def get_stderr_exception( tmp_err, tmp_stderr, tmp_out, tmp_stdout, include_stdout=False ): + tmp_stderr.close() + """ + Return a stderr string of reasonable size. + """ + # Get stderr, allowing for case where it's very large. + tmp_stderr = open( tmp_err, 'rb' ) + stderr_str = '' + buffsize = BUFF_SIZE + try: + while True: + stderr_str += tmp_stderr.read( buffsize ) + if not stderr_str or len( stderr_str ) % buffsize != 0: + break + except OverflowError: + pass + tmp_stderr.close() + if include_stdout: + tmp_stdout = open( tmp_out, 'rb' ) + stdout_str = '' + buffsize = BUFF_SIZE + try: + while True: + stdout_str += tmp_stdout.read( buffsize ) + if not stdout_str or len( stdout_str ) % buffsize != 0: + break + except OverflowError: + pass + tmp_stdout.close() + if include_stdout: + return 'STDOUT\n%s\n\nSTDERR\n%s\n' % ( stdout_str, stderr_str ) + return stderr_str + +def get_temp_dir( prefix='tmp-imagej-', dir=None ): + """ + Return a temporary directory. + """ + return tempfile.mkdtemp( prefix=prefix, dir=dir ) + +def get_tempfilename( dir=None, suffix=None ): + """ + Return a temporary file name. + """ + fd, name = tempfile.mkstemp( suffix=suffix, dir=dir ) + os.close( fd ) + return name + +def get_temporary_image_path( tmp_dir, image_format ): + """ + Return the path to a temporary file with a valid image format + file extension that can be used with bioformats. + """ + file_extension = get_file_extension( image_format ) + return get_tempfilename( tmp_dir, file_extension ) + +def handle_none_type( val, val_type='float' ): + if val is None: + return ' None' + else: + if val_type == 'float': + return ' %.1f' % val + elif val_type == 'int': + return ' %d' % val + +def stop_err( msg ): + sys.stderr.write( msg ) + sys.exit( 1 )
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/imagej2_macros.xml Tue Aug 04 13:20:29 2015 -0400 @@ -0,0 +1,126 @@ +<?xml version='1.0' encoding='UTF-8'?> +<macros> + <xml name="fiji_20141125_requirements"> + <requirements> + <requirement type="package" version="20141125">fiji</requirement> + </requirements> + </xml> + <xml name="python_bioformats_104_requirements"> + <requirements> + <requirement type="package" version="20141125">fiji</requirement> + <requirement type="package" version="1.0.11">javabridge</requirement> + <requirement type="package" version="1.9">numpy</requirement> + <requirement type="package" version="1.0.4">python_bioformats</requirement> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:"/> + <exit_code range=":-1"/> + <regex match="Error:"/> + <regex match="Exception:"/> + </stdio> + </xml> + <xml name="image_type"> + <param name="image_type" type="select" label="Image type"> + <option value="8-bit_white" selected="True">8-bit white</option> + <option value="8-bit_black">8-bit black</option> + <option value="8-bit_random">8-bit random</option> + <option value="8-bit_ramp">8-bit ramp</option> + <option value="16-bit_white">16-bit white</option> + <option value="16-bit_black">16-bit black</option> + <option value="16-bit_random">16-bit random</option> + <option value="16-bit_ramp">16-bit ramp</option> + <option value="32-bit_white">32-bit white</option> + <option value="32-bit_black">32-bit black</option> + <option value="32-bit_random">32-bit random</option> + <option value="32-bit_ramp">32-bit ramp</option> + <option value="RGB_white">RGB white</option> + <option value="RGB_black">RGB black</option> + <option value="RGB_random">RGB random</option> + <option value="RGB_ramp">RGB ramp</option> + </param> + </xml> + <xml name="make_binary_params"> + <param name="iterations" type="integer" value="1" min="1" max="100" label="Iterations" help="The number of times (1-100) erosion, dilation, opening, and closing are performed."/> + <param name="count" type="integer" value="1" min="1" max="8" label="Count" help="The number of adjacent background pixels necessary (1-8) for erosion or dilation."/> + <param name="black_background" type="select" label="Black background" help="If Yes, the background is black and the foreground is white (no implies the opposite)."> + <option value="no" selected="True">No</option> + <option value="yes">Yes</option> + </param> + <param name="pad_edges_when_eroding" type="select" label="Pad edges when eroding" help="If Yes, eroding does not erode from the edges of the image."> + <option value="no" selected="True">No</option> + <option value="yes">Yes</option> + </param> + </xml> + <token name="@make_binary_args@"> + --iterations $iterations + --count $count + --black_background $black_background + --pad_edges_when_eroding $pad_edges_when_eroding + </token> + <xml name="max_heap_size_type_conditional"> + <conditional name="set_max_heap_size"> + <param name="max_heap_size_type" type="select" label="Maximum size of the memory allocation pool used by the JVM" help="This value must be a multiple of 1024 or it will be ignored and the system default will be used."> + <option value="default" selected="True">Do not set</option> + <option value="megabytes">Set in megabytes</option> + <option value="gigabytes">Set in gigabytes</option> + </param> + <when value="default" > + <param name="max_heap_size" type="integer" value="0" hidden="true" label="Do not set" help="Use system default"/> + </when> + <when value="megabytes"> + <param name="max_heap_size" type="integer" value="512" min="256" label="Maximum size, in megabytes, of the memory allocation pool" help="Examples: 256, 512, etc."/> + </when> + <when value="gigabytes"> + <param name="max_heap_size" type="integer" value="1" min="1" label="Maximum size, in gigabytes, of the memory allocation pool" help="Examples: 1, 2, etc."/> + </when> + </conditional> + </xml> + <token name="@max_heap_size_args@"> + --max_heap_size_type $set_max_heap_size.max_heap_size_type + --max_heap_size $set_max_heap_size.max_heap_size + </token> + <xml name="image_datatypes"> + <option value="bmp">bmp</option> + <option value="gif">gif</option> + <option value="jpg">jpg</option> + <option value="png" selected="true">png</option> + <option value="tiff">tiff</option> + </xml> + <xml name="bunwarpj_citations"> + <citations> + <citation type="bibtex"> + @InProceedings(Arganda-Carreras2006, + author = "Ignacio Arganda-Carreras and + Carlos Oscar S{\'a}nchez Sorzano and + Roberto Marabini and + Jos{\'e} Mar\'{\i}a Carazo and + Carlos Ortiz-de-Solorzano and + Jan Kybic", + title = "Consistent and Elastic Registration of Histological Sections Using Vector-Spline Regularization", + publisher = "Springer Berlin / Heidelberg", + booktitle = "Computer Vision Approaches to Medical Image Analysis", + series = "Lecture Notes in Computer Science", + year = "2006", + volume = "4241", + pages = "85-95", + month = "May", + city = "Graz, Austria") + </citation> + <citation type="doi">10.1038/nmeth.2019</citation> + </citations> + </xml> + <xml name="fiji_headless_citations"> + <citations> + <citation type="doi">10.1038/nmeth.2102</citation> + </citations> + </xml> + <xml name="bioformats_fiji_javabridge_citations"> + <citations> + <citation type="doi">10.1038/nmeth.2102</citation> + <citation type="doi">10.1038/nmeth.2019</citation> + <citation type="doi">10.1083/jcb.201004104</citation> + </citations> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/imagej2_make_binary.py Tue Aug 04 13:20:29 2015 -0400 @@ -0,0 +1,63 @@ +#!/usr/bin/env python +import argparse +import os +import shutil +import subprocess +import tempfile +import imagej2_base_utils + +parser = argparse.ArgumentParser() +parser.add_argument( '--input', dest='input', help='Path to the input file' ) +parser.add_argument( '--input_datatype', dest='input_datatype', help='Datatype of the input image' ) +parser.add_argument( '--iterations', dest='iterations', type=int, help='Iterations' ) +parser.add_argument( '--count', dest='count', type=int, help='Count' ) +parser.add_argument( '--black_background', dest='black_background', help='Black background' ) +parser.add_argument( '--pad_edges_when_eroding', dest='pad_edges_when_eroding', help='Pad edges when eroding' ) +parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' ) +parser.add_argument( '--max_heap_size_type', dest='max_heap_size_type', help='Type (default or megabytes) of max_heap_size value' ) +parser.add_argument( '--max_heap_size', dest='max_heap_size', help='Maximum size of the memory allocation pool used by the JVM.' ) +parser.add_argument( '--output', dest='output', help='Path to the output file' ) +parser.add_argument( '--output_datatype', dest='output_datatype', help='Datatype of the output image' ) +args = parser.parse_args() + +tmp_dir = imagej2_base_utils.get_temp_dir() +# ImageJ expects valid image file extensions, so the Galaxy .dat extension does not +# work for some features. The following creates a symlink with an appropriate file +# extension that points to the Galaxy dataset. This symlink is used by ImageJ. +tmp_input_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.input, args.input_datatype ) +tmp_output_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.output_datatype ) +# Set the size of the memory allocation pool used by the JVM. +memory_size = imagej2_base_utils.get_max_heap_size_value( args.max_heap_size_type, args.max_heap_size ) +# Define command response buffers. +tmp_out = tempfile.NamedTemporaryFile().name +tmp_stdout = open( tmp_out, 'wb' ) +tmp_err = tempfile.NamedTemporaryFile().name +tmp_stderr = open( tmp_err, 'wb' ) +# Java writes a lot of stuff to stderr, so we'll specify a file for handling actual errors. +error_log = tempfile.NamedTemporaryFile( delete=False ).name +# Build the command line. +cmd = imagej2_base_utils.get_base_command_imagej2( memory_size, jython_script=args.jython_script ) +if cmd is None: + imagej2_base_utils.stop_err( "ImageJ not found!" ) +cmd += ' %s' % error_log +cmd += ' %s' % tmp_input_path +cmd += ' %d' % args.iterations +cmd += ' %d' % args.count +cmd += ' %s' % args.black_background +cmd += ' %s' % args.pad_edges_when_eroding +cmd += ' %s' % tmp_output_path +cmd += ' %s' % args.output_datatype +# Run the command. +proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True ) +rc = proc.wait() +# Handle execution errors. +if rc != 0: + error_message = imagej2_base_utils.get_stderr_exception( tmp_err, tmp_stderr, tmp_out, tmp_stdout ) + imagej2_base_utils.stop_err( error_message ) +# Handle processing errors. +if os.path.getsize( error_log ) > 0: + error_message = open( error_log, 'r' ).read() + imagej2_base_utils.stop_err( error_message ) +# Save the output image. +shutil.move( tmp_output_path, args.output ) +imagej2_base_utils.cleanup_before_exit( tmp_dir )
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/imagej2_make_binary.xml Tue Aug 04 13:20:29 2015 -0400 @@ -0,0 +1,65 @@ +<?xml version='1.0' encoding='UTF-8'?> +<tool id="imagej2_make_binary" name="Convert to binary" version="1.0.0"> + <description>(black and white) with ImageJ2</description> + <macros> + <import>imagej2_macros.xml</import> + </macros> + <expand macro="fiji_20141125_requirements" /> + <command> +<![CDATA[ + python $__tool_directory__/imagej2_make_binary.py + --input "$input" + --input_datatype $input.ext + @make_binary_args@ + @max_heap_size_args@ + --jython_script $__tool_directory__/jython_script.py + --output_datatype $output_datatype + --output "$output" +]]> + </command> + <inputs> + <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/> + <expand macro="make_binary_params" /> + <param name="output_datatype" type="select" label="Save as format"> + <expand macro="image_datatypes" /> + </param> + <expand macro="max_heap_size_type_conditional" /> + </inputs> + <outputs> + <data name="output" format_source="input" label="${tool.name} on ${on_string}"> + <actions> + <action type="format"> + <option type="from_param" name="output_datatype" /> + </action> + </actions> + </data> + </outputs> + <tests> + <test> + <param name="input" value="clown.jpg" /> + <param name="input_datatype" value="jpg" /> + <param name="iterations" value="1" /> + <param name="count" value="1" /> + <param name="black_background" value="no" /> + <param name="pad_edges_when_eroding" value="no" /> + <param name="output_datatype" value="jpg" /> + <output name="output" file="clown_binary.jpg" compare="sim_size" /> + </test> + </tests> + <help> +**What it does** + +<![CDATA[ +Converts an image into a binary (black and white) image by analyzing the histogram of +the entire image and setting an automatic threshold level to create the binary image. + +- **Iterations** - Specifies the number of times erosion, dilation, opening, and closing are performed. +- **Count** - Specifies the number of adjacent background pixels necessary before a pixel is removed from the edge of an object during erosion and the number of adjacent foreground pixels necessary before a pixel is added to the edge of an object during dilation. +- **Black background** - If **Yes**, binary images will be created without using an inverted LUT and an assumption that the input image contains white objects on a black background will be made. +- **Pad edges when eroding** - If **Yes**, eroding does not erode from the edges of the image. + +]]> + + </help> + <expand macro="fiji_headless_citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/jython_script.py Tue Aug 04 13:20:29 2015 -0400 @@ -0,0 +1,41 @@ +import jython_utils +import sys +from ij import IJ +from ij import ImagePlus + +# Fiji Jython interpreter implements Python 2.5 which does not +# provide support for argparse. +error_log = sys.argv[ -8 ] +input = sys.argv[ -7 ] +iterations = sys.argv[ -6 ] +count = sys.argv[ -5 ] +black_background = sys.argv[ -4 ] +pad_edges_when_eroding = sys.argv[ -3 ] +tmp_output_path = sys.argv[ -2 ] +output_datatype = sys.argv[ -1 ] + +# Open the input image file. +input_image_plus = IJ.openImage( input ) +bit_depth = input_image_plus.getBitDepth() +image_type = input_image_plus.getType() + +# Create a copy of the image. +input_image_plus_copy = input_image_plus.createImagePlus() +image_processor_copy = input_image_plus.getProcessor().duplicate() +input_image_plus_copy.setProcessor( "iCopy", image_processor_copy ) + +try: + options = [ "iterations=&iterations" "count=&count" ] + if black_background == "yes": + options.append( "black" ) + if pad_edges_when_eroding == "yes": + options.append( "pad" ) + # The following have no affect within this tool, but are necessary. + options.append( "edm=Overwrite" ) + options.append( "do=Nothing" ) + # Run the command. + IJ.run( input_image_plus_copy, "Make Binary", " ".join( options ) ) + # Save the ImagePlus object as a new image. + IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path ) +except Exception, e: + jython_utils.handle_error( error_log, str( e ) )
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/jython_utils.py Tue Aug 04 13:20:29 2015 -0400 @@ -0,0 +1,37 @@ +import imagej2_base_utils +from ij import IJ + +IMAGE_PLUS_IMAGE_TYPE_FIELD_VALUES = { '0':'GRAY8', '1':'GRAY16', '2':'GRAY32', + '3':'COLOR_256', '4':'COLOR_RGB' } + +def convert_before_saving_as_tiff( image_plus ): + # The bUnwarpJ plug-in produces TIFF image stacks consisting of 3 + # slices which can be viewed in ImageJ. The 3 slices are: 1) the + # registered image, 2) the target image and 3) the black/white warp + # image. When running bUnwarpJ from the command line (as these + # Galaxy wrappers do) the initial call to IJ.openImage() (to open the + # registered source and target images produced by bUnwarpJ) in the + # tool's jython_script.py returns an ImagePlus object with a single + # slice which is the "generally undesired" slice 3 discussed above. + # However, a call to IJ.saveAs() will convert the single-slice TIFF + # into a 3-slice TIFF image stack (as described above) if the selected + # format for saving is TIFF. Galaxy supports only single-layered + # images, so to work around this behavior, we have to convert the + # image to something other than TIFF so that slices are eliminated. + # We can then convert back to TIFF for saving. There might be a way + # to do this without converting twice, but I spent a lot of time looking + # and I have yet to discover it. + tmp_dir = imagej2_base_utils.get_temp_dir() + tmp_out_png_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, 'png' ) + IJ.saveAs( image_plus, 'png', tmp_out_png_path ) + return IJ.openImage( tmp_out_png_path ) + +def get_display_image_type( image_type ): + return IMAGE_PLUS_IMAGE_TYPE_FIELD_VALUES.get( str( image_type ), None ) + +def handle_error( error_log, msg ): + # Java writes a lot of stuff to stderr, so the received error_log + # will log actual errors. + elh = open( error_log, 'wb' ) + elh.write( msg ) + elh.close()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Aug 04 13:20:29 2015 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="fiji" version="20141125"> + <repository changeset_revision="9dbe89105a25" name="package_fiji_20141125" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>