Mercurial > repos > iuc > imagej2_analyze_particles_binary
changeset 0:d065ec177dcd draft
planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
| author | iuc |
|---|---|
| date | Wed, 26 Aug 2015 14:36:17 -0400 |
| parents | |
| children | dd9041dc3c27 |
| files | imagej2_analyze_particles_binary.py imagej2_analyze_particles_binary.xml imagej2_base_utils.py imagej2_macros.xml jython_script.py jython_utils.py test-data/analyze_particles_masks.gif test-data/analyze_particles_nothing.tabular test-data/analyze_particles_outlines.gif test-data/blobs_watershed_binary.gif tool_dependencies.xml |
| diffstat | 11 files changed, 672 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/imagej2_analyze_particles_binary.py Wed Aug 26 14:36:17 2015 -0400 @@ -0,0 +1,81 @@ +#!/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( '--black_background', dest='black_background', help='Black background' ) +parser.add_argument( '--size', dest='size', help='Size (pixel^2)' ) +parser.add_argument( '--circularity_min', dest='circularity_min', type=float, help='Circularity minimum' ) +parser.add_argument( '--circularity_max', dest='circularity_max', type=float, help='Circularity maximum' ) +parser.add_argument( '--show', dest='show', help='Show' ) +parser.add_argument( '--display_results', dest='display_results', help='Display results' ) +parser.add_argument( '--all_results', dest='all_results', help='All results' ) +parser.add_argument( '--exclude_edges', dest='exclude_edges', help='Exclude edges' ) +parser.add_argument( '--include_holes', dest='include_holes', help='Include holes' ) +parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' ) +parser.add_argument( '--results', dest='results', default=None, help='Path to the output results file' ) +parser.add_argument( '--output', dest='output', default=None, help='Path to the output image file' ) +parser.add_argument( '--output_datatype', dest='output_datatype', default='data', 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 ) +if args.output is None: + tmp_output_path = None +else: + tmp_output_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.output_datatype ) + +# 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( None, 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 += ' %s' % args.black_background +cmd += ' %s' % args.size +cmd += ' %.3f' % args.circularity_min +cmd += ' %.3f' % args.circularity_max +cmd += ' %s' % args.show +cmd += ' %s' % args.display_results +cmd += '%s' % imagej2_base_utils.handle_none_type( args.all_results, val_type='str' ) +cmd += ' %s' % args.exclude_edges +cmd += ' %s' % args.include_holes +cmd += '%s' % imagej2_base_utils.handle_none_type( tmp_output_path, val_type='str' ) +cmd += ' %s' % args.output_datatype +cmd += '%s' % imagej2_base_utils.handle_none_type( args.results, val_type='str' ) + +# 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 ) + +if tmp_output_path is not None: + # 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_analyze_particles_binary.xml Wed Aug 26 14:36:17 2015 -0400 @@ -0,0 +1,132 @@ +<?xml version='1.0' encoding='UTF-8'?> +<tool id="imagej2_analyze_particles_binary" name="Analyze particles" version="@WRAPPER_VERSION@.0"> + <description>of binary image with ImageJ2</description> + <macros> + <import>imagej2_macros.xml</import> + </macros> + <expand macro="fiji_requirements" /> + <command> +<![CDATA[ + python $__tool_directory__/imagej2_analyze_particles_binary.py + --input "$input" + --input_datatype $input.ext + --black_background $black_background + --size "$size" + --circularity_min $circularity_min + --circularity_max $circularity_max + --show $show + --exclude_edges $exclude_edges + --include_holes $include_holes + --jython_script $__tool_directory__/jython_script.py + #if str($show) == 'Nothing': + --display_results "yes" + --all_results "yes" + #else: + --display_results $display_results_cond.display_results + --all_results $display_results_cond.all_results + --output_datatype $output.ext + --output "$output" + #end if + --results "$results" +]]> + </command> + <inputs> + <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/> + <expand macro="black_background_param" /> + <param name="size" type="text" value="0-Infinity" label="Size (pixel^2)" help="Enter a single value and particles smaller than that value will be ignored."/> + <param name="circularity_min" type="float" value="0.0" label="Circularity minimum" help="Values from 0.0 to 1.0, but less than maximum"> + <validator type="in_range" min="0" max="1"/> + </param> + <param name="circularity_max" type="float" value="1.0" label="Circularity maximum" help="Values from 0.0 to 1.0, but greater than minimum"> + <validator type="in_range" min="0" max="1"/> + </param> + <param name="show" type="select" label="Show" help="Selecting Nothing will display results, but no image."> + <option value="Outlines" selected="True">Outlines</option> + <option value="Bare_Outlines">Bare Outlines</option> + <option value="Ellipses">Ellipses</option> + <option value="Masks">Masks</option> + <option value="Count_Masks">Count Masks</option> + <option value="Nothing">Nothing</option> + </param> + <conditional name="display_results_cond"> + <param name="display_results" type="select" label="Display results"> + <option value="no" selected="True">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"> + <param name="all_results" type="hidden" value="no"/> + </when> + <when value="yes"> + <param name="all_results" type="select" label="All results?" help="If no, only summary displayed."> + <option value="yes" selected="True">Yes</option> + <option value="no">No</option> + </param> + </when> + </conditional> + <param name="exclude_edges" type="select" label="Exclude on edges?"> + <option value="no" selected="True">No</option> + <option value="yes">Yes</option> + </param> + <param name="include_holes" type="select" label="Include holes?"> + <option value="no" selected="True">No</option> + <option value="yes">Yes</option> + </param> + </inputs> + <outputs> + <data name="output" format_source="input" label="${tool.name} on ${on_string}"> + <filter>show != "Nothing"</filter> + </data> + <data format="tabular" name="results" label="${tool.name} on ${on_string}: Results"> + <filter>show == "Nothing" or display_results_cond['display_results'] == "yes"</filter> + </data> + </outputs> + <tests> + <test> + <param name="input" value="blobs_watershed_binary.gif" /> + <param name="show" value="Nothing" /> + <output name="output" file="analyze_particles_nothing.tabular" /> + </test> + <test> + <param name="input" value="blobs_watershed_binary.gif" /> + <param name="show" value="Outlines" /> + <output name="output" file="analyze_particles_outlines.gif" compare="sim_size" /> + </test> + <test> + <param name="input" value="blobs_watershed_binary.gif" /> + <param name="show" value="Masks" /> + <param name="exclude_edges" value="yes" /> + <param name="include_holes" value="yes" /> + <output name="output" file="analyze_particles_masks.gif" compare="sim_size" /> + </test> + </tests> + <help> +.. class:: warningmark + +@requires_binary_input@ + +**What it does** + +<![CDATA[ +Counts and measures objects in binary or thresholded images. It works by scanning the image until +it finds the edge of an object. It then outlines the object, measures it, fills it to make it +invisible, then resumes scanning until it reaches the end of the image. Features of thresholded +images can be extracted by specifying suitable **Size** and **Circularity** ranges and/or by choosing +if particles should be traced by their outer edge or by flood filling. + +- **Size** - Particles with size (area) outside the range specified in this field are ignored. Values may range between 0 and ‘Infinity’. Enter a single value and particles smaller than that value will be ignored. +- **Cicularity** - Particles with size circularity values outside the range specified in the min/max fields are also ignored. +- **Show: Nothing** - No image will be generated, but **Display Results** will be set to Yes. Note that the particle analyzer will display a blank image when the count of detected particles is zero and **Show** is not **Nothing**. +- **Show: Outlines** - Generates an 8-bit image containing numbered outlines of the measured particles (gray levels: Outlines: 0; Labels: 1; Background: 255). +- **Show: Bare Outlines** - Generates an 8-bit image containing simple outlines of the measured particles without labels (graylevels: Outlines: 0; Background: 255). +- **Show: Ellipses** - Generates an 8-bit image containing the best fit ellipse of each measured particle (gray levels: Ellipses: 0; Background: 255). +- **Show: Masks** - Generates an 8-bit image containing filled outlines of the measured particles (gray levels: Masks: 0; Background: 255). +- **Show: Count Masks** - Generates a 16-bit image containing filled outlines of the measured particles painted with a grayscale value corresponding to the particle number. +- **Display Results** - If Yes, the measurements for each particle will be generated. +- **All results** - If No, results will be restricted to the particle count, total particle area, average particle size, and area fraction. +- **Exclude on Edges** - If Yes, particles touching the edge of the image will be ignored. +- **Include Holes** - If Yes, interior holes will be included (set to No to exclude interior holes and to measure particles enclosed by other particles). +]]> + + </help> + <expand macro="fiji_headless_citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/imagej2_base_utils.py Wed Aug 26 14:36:17 2015 -0400 @@ -0,0 +1,164 @@ +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_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 + return ' %s' % 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 Wed Aug 26 14:36:17 2015 -0400 @@ -0,0 +1,121 @@ +<?xml version='1.0' encoding='UTF-8'?> +<macros> + <token name="@WRAPPER_VERSION@">1.0</token> + <xml name="fiji_requirements"> + <requirements> + <requirement type="package" version="20141125">fiji</requirement> + </requirements> + </xml> + <xml name="python_bioformats_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> + <xml name="black_background_param"> + <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> + </xml> + <token name="@make_binary_args@"> + --iterations $iterations + --count $count + --black_background $black_background + --pad_edges_when_eroding $pad_edges_when_eroding + </token> + <token name="@requires_binary_input@"> +.. class:: warningmark + +This tool works on binary images, so other image types will automatically be converted to binary +before they are analyzed. This step is performed using the ImageJ2 **Make Binary** command with +the following settings: **Iterations:** 1, **Count:** 1, **Pad edges when eroding:** No. The tool +allows you to choose the **Black background** setting. If these settings are not appropriate, +first manually convert the image to binary using the **Convert to binary (black and white) with ImageJ2** +tool, which allows you to change them. + </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/jython_script.py Wed Aug 26 14:36:17 2015 -0400 @@ -0,0 +1,72 @@ +import jython_utils +import sys +from ij import IJ +from ij.plugin.filter import Analyzer + +# Fiji Jython interpreter implements Python 2.5 which does not +# provide support for argparse. +error_log = sys.argv[ -14 ] +input = sys.argv[ -13 ] +black_background = jython_utils.asbool( sys.argv[ -12 ] ) +size = sys.argv[ -11 ] +circularity_min = float( sys.argv[ -10 ] ) +circularity_max = float( sys.argv[ -9 ] ) +show = sys.argv[ -8 ] +display_results = jython_utils.asbool( sys.argv[ -7 ] ) +all_results = jython_utils.asbool( sys.argv[ -6 ] ) +exclude_edges = jython_utils.asbool( sys.argv[ -5 ] ) +include_holes = jython_utils.asbool( sys.argv[ -4 ] ) +tmp_output_path = sys.argv[ -3 ] +output_datatype = sys.argv[ -2 ] +results_path = sys.argv[ -1 ] + +# Open the input image file. +input_image_plus = IJ.openImage( input ) + +# Create a copy of the image. +input_image_plus_copy = input_image_plus.duplicate() +image_processor_copy = input_image_plus_copy.getProcessor() +analyzer = Analyzer( input_image_plus_copy ) + +try: + # Set binary options. + options = jython_utils.get_binary_options( black_background=black_background ) + IJ.run( input_image_plus_copy, "Options...", options ) + + # Convert image to binary if necessary. + if not image_processor_copy.isBinary(): + # Convert the image to binary grayscale. + IJ.run( input_image_plus_copy, "Make Binary", "" ) + + # Set the options. + options = [ 'size=%s' % size ] + circularity_str = '%.3f-%.3f' % ( circularity_min, circularity_max ) + options.append( 'circularity=%s' % circularity_str ) + if show.find( '_' ) >= 0: + show_str = '[%s]' % show.replace( '_', ' ' ) + else: + show_str = show + options.append( 'show=%s' % show_str ) + if display_results: + options.append( 'display' ) + if not all_results: + options.append( 'summarize' ) + if exclude_edges: + options.append( 'exclude' ) + if include_holes: + options.append( 'include' ) + # Always run "in_situ". + options.append( 'in_situ' ) + + # Run the command. + IJ.run( input_image_plus_copy, "Analyze Particles...", " ".join( options ) ) + + # Save outputs. + if tmp_output_path not in [ None, 'None' ]: + # Save the ImagePlus object as a new image. + IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path ) + if display_results and results_path not in [ None, 'None' ]: + results_table = analyzer.getResultsTable() + results_table.saveAs( results_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 Wed Aug 26 14:36:17 2015 -0400 @@ -0,0 +1,48 @@ +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 asbool( val ): + return str( val ).lower() in [ 'yes', 'true' ] + +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_binary_options( black_background, iterations=1, count=1, pad_edges_when_eroding='no' ): + options = [ 'edm=Overwrite', 'iterations=%d' % iterations, 'count=%d' % count ] + if asbool( pad_edges_when_eroding ): + options.append( 'pad' ) + if asbool( black_background ): + options.append( "black" ) + return " ".join( options ) + +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/test-data/analyze_particles_nothing.tabular Wed Aug 26 14:36:17 2015 -0400 @@ -0,0 +1,48 @@ + Area Mean Min Max +1 86 0 0 0 +2 72 0 0 0 +3 25 0 0 0 +4 85 0 0 0 +5 157 0 0 0 +6 207 0 0 0 +7 29 0 0 0 +8 73 0 0 0 +9 143 0 0 0 +10 125 0 0 0 +11 159 0 0 0 +12 133 0 0 0 +13 85 0 0 0 +14 51 0 0 0 +15 133 0 0 0 +16 133 0 0 0 +17 81 0 0 0 +18 88 0 0 0 +19 212 0 0 0 +20 116 0 0 0 +21 172 0 0 0 +22 103 0 0 0 +23 4 0 0 0 +24 60 0 0 0 +25 198 0 0 0 +26 187 0 0 0 +27 80 0 0 0 +28 75 0 0 0 +29 103 0 0 0 +30 52 0 0 0 +31 122 0 0 0 +32 129 0 0 0 +33 77 0 0 0 +34 171 0 0 0 +35 117 0 0 0 +36 207 0 0 0 +37 119 0 0 0 +38 181 0 0 0 +39 49 0 0 0 +40 150 0 0 0 +41 191 0 0 0 +42 170 0 0 0 +43 174 0 0 0 +44 270 0 0 0 +45 87 0 0 0 +46 69 0 0 0 +47 1 0 0 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Aug 26 14:36:17 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>