changeset 1:768825d9034a draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
author imgteam
date Mon, 28 Sep 2020 17:01:19 +0000
parents f6df6830d5ec
children
files imagej2_adjust_threshold_binary.py imagej2_adjust_threshold_binary_jython_script.py imagej2_analyze_particles_binary.py imagej2_analyze_particles_binary_jython_script.py imagej2_analyze_skeleton.py imagej2_analyze_skeleton_jython_script.py imagej2_base_utils.py imagej2_binary_to_edm.py imagej2_binary_to_edm_jython_script.py imagej2_bunwarpj_adapt_transform.py imagej2_bunwarpj_align.py imagej2_bunwarpj_align_jython_script.py imagej2_bunwarpj_compare_elastic.py imagej2_bunwarpj_compare_elastic_raw.py imagej2_bunwarpj_compare_raw.py imagej2_bunwarpj_compose_elastic.py imagej2_bunwarpj_compose_raw.py imagej2_bunwarpj_compose_raw_elastic.py imagej2_bunwarpj_convert_to_raw.py imagej2_bunwarpj_elastic_transform.py imagej2_bunwarpj_elastic_transform_jython_script.py imagej2_bunwarpj_raw_transform.py imagej2_bunwarpj_raw_transform_jython_script.py imagej2_create_image.py imagej2_create_image_jython_script.py imagej2_enhance_contrast.py imagej2_enhance_contrast_jython_script.py imagej2_find_edges.py imagej2_find_edges_jython_script.py imagej2_find_maxima.py imagej2_find_maxima_jython_script.py imagej2_macros.xml imagej2_make_binary.py imagej2_make_binary_jython_script.py imagej2_math.py imagej2_math_jython_script.py imagej2_noise.py imagej2_noise_jython_script.py imagej2_shadows.py imagej2_shadows_jython_script.py imagej2_sharpen.py imagej2_sharpen_jython_script.py imagej2_skeletonize3d.py imagej2_skeletonize3d.xml imagej2_skeletonize3d_jython_script.py imagej2_smooth.py imagej2_smooth_jython_script.py imagej2_watershed_binary.py imagej2_watershed_binary_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/basic.tabular test-data/blobs_black_edm.gif test-data/blobs_edm.gif test-data/blobs_equalize.gif test-data/blobs_find_edges.gif test-data/blobs_log.gif test-data/blobs_min.gif test-data/blobs_multiply.gif test-data/blobs_normalize.gif test-data/blobs_northwest.gif test-data/blobs_saturate.gif test-data/blobs_segmented.gif test-data/blobs_single_points.gif test-data/blobs_square.gif test-data/blobs_tolerance.gif test-data/blobs_watershed_binary.gif test-data/elastic_trans_registered_source1.png test-data/largest_shortest_path_basic.tabular test-data/raw_trans_registered_source1.png test-data/registered_source1.png test-data/registered_source2.png test-data/registered_target1.png test-data/registered_target2.png test-data/skeletonized_blobs.gif test-data/source_elastic_transformation_out.txt test-data/target_elastic_transformation_out.txt
diffstat 79 files changed, 746 insertions(+), 2671 deletions(-) [+]
line wrap: on
line diff
--- a/imagej2_adjust_threshold_binary.py	Tue Sep 17 16:57:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,63 +0,0 @@
-#!/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( '--threshold_min', dest='threshold_min', type=float, help='Minimum threshold value' )
-parser.add_argument( '--threshold_max', dest='threshold_max', type=float, help='Maximum threshold value' )
-parser.add_argument( '--method', dest='method', help='Threshold method' )
-parser.add_argument( '--display', dest='display', help='Display mode' )
-parser.add_argument( '--black_background', dest='black_background', help='Black background' )
-parser.add_argument( '--stack_histogram', dest='stack_histogram', help='Stack histogram' )
-parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' )
-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 )
-# 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 += ' %.3f' % args.threshold_min
-cmd += ' %.3f' % args.threshold_max
-cmd += ' %s' % args.method
-cmd += ' %s' % args.display
-cmd += ' %s' % args.black_background
-cmd += ' %s' % args.stack_histogram
-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 )
--- a/imagej2_adjust_threshold_binary_jython_script.py	Tue Sep 17 16:57:15 2019 -0400
+++ b/imagej2_adjust_threshold_binary_jython_script.py	Mon Sep 28 17:01:19 2020 +0000
@@ -1,49 +1,46 @@
-import jython_utils
 import sys
+
 from ij import IJ
 
 # Fiji Jython interpreter implements Python 2.5 which does not
 # provide support for argparse.
-error_log = sys.argv[ -10 ]
-input = sys.argv[ -9 ]
-threshold_min = float( sys.argv[ -8 ] )
-threshold_max = float( sys.argv[ -7 ] )
-method = sys.argv[ -6 ]
-display = sys.argv[ -5 ]
-black_background = jython_utils.asbool( sys.argv[ -4 ] )
+error_log = sys.argv[-10]
+input_file = sys.argv[-9]
+threshold_min = float(sys.argv[-8])
+threshold_max = float(sys.argv[-7])
+method = sys.argv[-6]
+display = sys.argv[-5]
+black_background = sys.argv[-4] == "yes"
 # TODO: this is not being used.
-stack_histogram = jython_utils.asbool( sys.argv[ -3 ] )
-tmp_output_path = sys.argv[ -2 ]
-output_datatype = sys.argv[ -1 ]
+stack_histogram = sys.argv[-3] == "yes"
+output_filename = sys.argv[-2]
+output_datatype = sys.argv[-1]
 
 # Open the input image file.
-input_image_plus = IJ.openImage( input )
+input_image_plus = IJ.openImage(input_file)
 
 # Create a copy of the image.
 input_image_plus_copy = input_image_plus.duplicate()
 image_processor_copy = input_image_plus_copy.getProcessor()
 
-try:
-    # 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","iterations=1 count=1 edm=Overwrite do=Nothing" )
-    # Set the options.
-    if black_background:
-        method_str = "%s dark" % method
-    else:
-        method_str = method
-    IJ.setAutoThreshold( input_image_plus_copy, method_str )
-    if display == "red":
-        display_mode = "Red"
-    elif display == "bw":
-        display_mode = "Black & White"
-    elif display == "over_under":
-        display_mode = "Over/Under"
-    IJ.setThreshold( input_image_plus_copy, threshold_min, threshold_max, display_mode )
-    # Run the command.
-    IJ.run( input_image_plus_copy, "threshold", "" )
-    # 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 ) )
+# 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", "iterations=1 count=1 edm=Overwrite do=Nothing")
+# Set the options.
+if black_background:
+    method_str = "%s dark" % method
+else:
+    method_str = method
+IJ.setAutoThreshold(input_image_plus_copy, method_str)
+if display == "red":
+    display_mode = "Red"
+elif display == "bw":
+    display_mode = "Black & White"
+elif display == "over_under":
+    display_mode = "Over/Under"
+IJ.setThreshold(input_image_plus_copy, threshold_min, threshold_max, display_mode)
+# Run the command.
+IJ.run(input_image_plus_copy, "threshold", "")
+# Save the ImagePlus object as a new image.
+IJ.saveAs(input_image_plus_copy, output_datatype, output_filename)
--- a/imagej2_analyze_particles_binary.py	Tue Sep 17 16:57:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,81 +0,0 @@
-#!/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 )
--- a/imagej2_analyze_particles_binary_jython_script.py	Tue Sep 17 16:57:15 2019 -0400
+++ b/imagej2_analyze_particles_binary_jython_script.py	Mon Sep 28 17:01:19 2020 +0000
@@ -1,72 +1,74 @@
-import jython_utils
 import sys
+
 from ij import IJ
 from ij.plugin.filter import Analyzer
 
+
+OPTIONS = ['edm=Overwrite', 'iterations=1', 'count=1']
+
 # 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 ]
+error_log = sys.argv[-14]
+input_file = sys.argv[-13]
+black_background = sys.argv[-12] == "yes"
+size = sys.argv[-11]
+circularity_min = float(sys.argv[-10])
+circularity_max = float(sys.argv[-9])
+show = sys.argv[-8]
+display_results = sys.argv[-7] == "yes"
+all_results = sys.argv[-6] == "yes"
+exclude_edges = sys.argv[-5] == "yes"
+include_holes = sys.argv[-4] == "yes"
+output_filename = sys.argv[-3]
+output_datatype = sys.argv[-2]
+results_path = sys.argv[-1]
 
 # Open the input image file.
-input_image_plus = IJ.openImage( input )
+input_image_plus = IJ.openImage(input_file)
 
 # 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 )
+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 )
+# Set binary options.
+options_list = OPTIONS
+if black_background:
+    options_list.append("black")
+options = " ".join(options_list)
+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", "" )
+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' )
+# 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 ) )
+# 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 ) )
+# Save outputs.
+if len(output_filename) > 0:
+    # Save the ImagePlus object as a new image.
+    IJ.saveAs(input_image_plus_copy, output_datatype, output_filename)
+if display_results and len(results_path) > 0:
+    results_table = analyzer.getResultsTable()
+    results_table.saveAs(results_path)
--- a/imagej2_analyze_skeleton.py	Tue Sep 17 16:57:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,61 +0,0 @@
-#!/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( '--prune_cycle_method', dest='prune_cycle_method', default='none', help='Prune cycle method' )
-parser.add_argument( '--prune_ends', dest='prune_ends', default='no', help='Prune ends' )
-parser.add_argument( '--calculate_largest_shortest_path', dest='calculate_largest_shortest_path', default='no', help='Calculate largest shortest path' )
-parser.add_argument( '--show_detailed_info', dest='show_detailed_info', default='no', help='Show detailed info' )
-parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' )
-parser.add_argument( '--output', dest='output', help='Path to the output file' )
-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 )
-
-# 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.prune_cycle_method
-cmd += ' %s' % args.prune_ends
-cmd += ' %s' % args.calculate_largest_shortest_path
-cmd += ' %s' % args.show_detailed_info
-cmd += ' %s' % args.output
-
-# 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 )
-
-imagej2_base_utils.cleanup_before_exit( tmp_dir )
--- a/imagej2_analyze_skeleton_jython_script.py	Tue Sep 17 16:57:15 2019 -0400
+++ b/imagej2_analyze_skeleton_jython_script.py	Mon Sep 28 17:01:19 2020 +0000
@@ -1,147 +1,148 @@
-import jython_utils
 import math
 import sys
+
 from ij import IJ
 from sc.fiji.analyzeSkeleton import AnalyzeSkeleton_
 
-BASIC_NAMES = [ 'Branches', 'Junctions', 'End-point Voxels',
-                'Junction Voxels', 'Slab Voxels', 'Average branch length',
-                'Triple Points', 'Quadruple Points', 'Maximum Branch Length' ]
-DETAIL_NAMES = [ 'Skeleton ID', 'Branch length', 'V1 x', 'V1 y', 'V1 z', 'V2 x',
-                 'V2 y', 'V2 z', 'Euclidean distance' ]
+BASIC_NAMES = ['Branches', 'Junctions', 'End-point Voxels',
+               'Junction Voxels', 'Slab Voxels', 'Average branch length',
+               'Triple Points', 'Quadruple Points', 'Maximum Branch Length']
+DETAIL_NAMES = ['Skeleton ID', 'Branch length', 'V1 x', 'V1 y', 'V1 z', 'V2 x',
+                'V2 y', 'V2 z', 'Euclidean distance']
+OPTIONS = ['edm=Overwrite', 'iterations=1', 'count=1']
+
 
-def get_euclidean_distance( vertex1, vertex2 ):
-    x1, y1, z1 = get_points( vertex1 )
-    x2, y2, z2 = get_points( vertex2 )
-    return math.sqrt( math.pow( ( x2 - x1 ), 2 ) +
-                      math.pow( ( y2 - y1 ), 2 ) +
-                      math.pow( ( z2 - z1 ), 2 ) )
+def get_euclidean_distance(vertex1, vertex2):
+    x1, y1, z1 = get_points(vertex1)
+    x2, y2, z2 = get_points(vertex2)
+    return math.sqrt(math.pow((x2 - x1), 2) + math.pow((y2 - y1), 2) + math.pow((z2 - z1), 2))
 
-def get_graph_length( graph ):
+
+def get_graph_length(graph):
     length = 0
     for edge in graph.getEdges():
         length = length + edge.getLength()
     return length
 
-def get_points( vertex ):
+
+def get_points(vertex):
     # An array of Point, which has attributes x,y,z.
-    point = vertex.getPoints()[ 0 ]
+    point = vertex.getPoints()[0]
     return point.x, point.y, point.z
-    
-def get_sorted_edge_lengths( graph ):
+
+
+def get_sorted_edge_lengths(graph):
     # Return graph edges sorted from longest to shortest.
     edges = graph.getEdges()
-    edges = sorted( edges, key=lambda edge: edge.getLength(), reverse=True )
+    edges = sorted(edges, key=lambda edge: edge.getLength(), reverse=True)
     return edges
 
-def get_sorted_graph_lengths( result ):
+
+def get_sorted_graph_lengths(result):
     # Get the separate graphs (skeletons).
     graphs = result.getGraph()
     # Sort graphs from longest to shortest.
-    graphs = sorted( graphs, key=lambda g: get_graph_length( g ), reverse=True )
+    graphs = sorted(graphs, key=lambda g: get_graph_length(g), reverse=True)
     return graphs
 
-def save( result, output, show_detailed_info, calculate_largest_shortest_path, sep='\t' ):
-    num_trees = int( result.getNumOfTrees() )
-    outf = open( output, 'wb' )
-    outf.write( '# %s\n' % sep.join( BASIC_NAMES ) )
-    for index in range( num_trees ):
-        outf.write( '%d%s' % ( result.getBranches()[ index ], sep ) )
-        outf.write( '%d%s' % ( result.getJunctions()[ index ], sep ) )
-        outf.write( '%d%s' % ( result.getEndPoints()[ index ], sep ) )
-        outf.write( '%d%s' % ( result.getJunctionVoxels()[ index ], sep ) )
-        outf.write( '%d%s' % ( result.getSlabs()[ index ], sep ) )
-        outf.write( '%.3f%s' % ( result.getAverageBranchLength()[ index ], sep ) )
-        outf.write( '%d%s' % ( result.getTriples()[ index ], sep ) )
-        outf.write( '%d%s' % ( result.getQuadruples()[ index ], sep ) )
-        outf.write( '%.3f' % result.getMaximumBranchLength()[ index ] )
+
+def save(result, output, show_detailed_info, calculate_largest_shortest_path, sep='\t'):
+    num_trees = int(result.getNumOfTrees())
+    outf = open(output, 'wb')
+    outf.write('# %s\n' % sep.join(BASIC_NAMES))
+    for index in range(num_trees):
+        outf.write('%d%s' % (result.getBranches()[index], sep))
+        outf.write('%d%s' % (result.getJunctions()[index], sep))
+        outf.write('%d%s' % (result.getEndPoints()[index], sep))
+        outf.write('%d%s' % (result.getJunctionVoxels()[index], sep))
+        outf.write('%d%s' % (result.getSlabs()[index], sep))
+        outf.write('%.3f%s' % (result.getAverageBranchLength()[index], sep))
+        outf.write('%d%s' % (result.getTriples()[index], sep))
+        outf.write('%d%s' % (result.getQuadruples()[index], sep))
+        outf.write('%.3f' % result.getMaximumBranchLength()[index])
         if calculate_largest_shortest_path:
-            outf.write( '%s%.3f%s' % ( sep, result.shortestPathList.get( index ), sep ) )
-            outf.write( '%d%s' % ( result.spStartPosition[ index ][ 0 ], sep ) )
-            outf.write( '%d%s' % ( result.spStartPosition[ index ][ 1 ], sep ) )
-            outf.write( '%d\n' % result.spStartPosition[ index ][ 2 ] )
+            outf.write('%s%.3f%s' % (sep, result.shortestPathList.get(index), sep))
+            outf.write('%d%s' % (result.spStartPosition[index][0], sep))
+            outf.write('%d%s' % (result.spStartPosition[index][1], sep))
+            outf.write('%d\n' % result.spStartPosition[index][2])
         else:
-            outf.write( '\n' )
+            outf.write('\n')
     if show_detailed_info:
-        outf.write( '# %s\n' % sep.join( DETAIL_NAMES ) )
+        outf.write('# %s\n' % sep.join(DETAIL_NAMES))
         # The following index is a placeholder for the skeleton ID.
         # The terms "graph" and "skeleton" refer to the same thing.
         # Also, the SkeletonResult.java code states that the
         # private Graph[] graph object is an array of graphs (one
         # per tree).
-        for index, graph in enumerate( get_sorted_graph_lengths( result ) ):
-            for edge in get_sorted_edge_lengths( graph ):
+        for index, graph in enumerate(get_sorted_graph_lengths(result)):
+            for edge in get_sorted_edge_lengths(graph):
                 vertex1 = edge.getV1()
-                x1, y1, z1 = get_points( vertex1 )
+                x1, y1, z1 = get_points(vertex1)
                 vertex2 = edge.getV2()
-                x2, y2, z2 = get_points( vertex2 )
-                outf.write( '%d%s' % ( index+1, sep ) )
-                outf.write( '%.3f%s' % ( edge.getLength(), sep ) )
-                outf.write( '%d%s' % ( x1, sep ) )
-                outf.write( '%d%s' % ( y1, sep ) )
-                outf.write( '%d%s' % ( z1, sep ) )
-                outf.write( '%d%s' % ( x2, sep ) )
-                outf.write( '%d%s' % ( y2, sep ) )
-                outf.write( '%d%s' % ( z2, sep ) )
-                outf.write( '%.3f' % get_euclidean_distance( vertex1, vertex2 ) )
+                x2, y2, z2 = get_points(vertex2)
+                outf.write('%d%s' % (index + 1, sep))
+                outf.write('%.3f%s' % (edge.getLength(), sep))
+                outf.write('%d%s' % (x1, sep))
+                outf.write('%d%s' % (y1, sep))
+                outf.write('%d%s' % (z1, sep))
+                outf.write('%d%s' % (x2, sep))
+                outf.write('%d%s' % (y2, sep))
+                outf.write('%d%s' % (z2, sep))
+                outf.write('%.3f' % get_euclidean_distance(vertex1, vertex2))
                 if calculate_largest_shortest_path:
                     # Keep number of separated items the same for each line.
-                    outf.write( '%s %s' % ( sep, sep ) )
-                    outf.write( ' %s' % sep )
-                    outf.write( ' %s' % sep )
-                    outf.write( ' \n' )
+                    outf.write('%s %s' % (sep, sep))
+                    outf.write(' %s' % sep)
+                    outf.write(' %s' % sep)
+                    outf.write(' \n')
                 else:
-                    outf.write( '\n' )
+                    outf.write('\n')
     outf.close()
 
+
 # Fiji Jython interpreter implements Python 2.5 which does not
 # provide support for argparse.
-error_log = sys.argv[ -8 ]
-input = sys.argv[ -7 ]
-black_background = jython_utils.asbool( sys.argv[ -6 ] )
-prune_cycle_method = sys.argv[ -5 ]
-prune_ends = jython_utils.asbool( sys.argv[ -4 ] )
-calculate_largest_shortest_path = jython_utils.asbool( sys.argv[ -3 ] )
+error_log = sys.argv[-8]
+input = sys.argv[-7]
+black_background = sys.argv[-6] == "yes"
+prune_cycle_method = sys.argv[-5]
+prune_ends = sys.argv[-4] == "yes"
+calculate_largest_shortest_path = sys.argv[-3] == "yes"
 if calculate_largest_shortest_path:
-    BASIC_NAMES.extend( [ 'Longest Shortest Path', 'spx', 'spy', 'spz' ] )
-    DETAIL_NAMES.extend( [ ' ', ' ', ' ', ' ' ] )
-show_detailed_info = jython_utils.asbool( sys.argv[ -2 ] )
-output = sys.argv[ -1 ]
+    BASIC_NAMES.extend(['Longest Shortest Path', 'spx', 'spy', 'spz'])
+    DETAIL_NAMES.extend([' ', ' ', ' ', ' '])
+show_detailed_info = sys.argv[-2] == "yes"
+output = sys.argv[-1]
 
 # Open the input image file.
-input_image_plus = IJ.openImage( input )
+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()
 
-try:
-    # Set binary options.
-    options = jython_utils.get_binary_options( black_background=black_background )
-    IJ.run( input_image_plus_copy, "Options...", options )
+# Set binary options.
+options_list = OPTIONS
+if black_background:
+    options_list.append("black")
+options = " ".join(options_list)
+IJ.run(input_image_plus_copy, "Options...", options)
 
-    # Convert image to binary if necessary.
-    if not image_processor_copy.isBinary():
-        IJ.run( input_image_plus_copy, "Make Binary", "" )
+# Convert image to binary if necessary.
+if not image_processor_copy.isBinary():
+    IJ.run(input_image_plus_copy, "Make Binary", "")
 
-    # Run AnalyzeSkeleton
-    analyze_skeleton = AnalyzeSkeleton_()
-    analyze_skeleton.setup( "", input_image_plus_copy )
-    if prune_cycle_method == 'none':
-        prune_index  = analyze_skeleton.NONE
-    elif prune_cycle_method == 'shortest_branch':
-        prune_index  = analyze_skeleton.SHORTEST_BRANCH
-    elif prune_cycle_method == 'lowest_intensity_voxel':
-        prune_index  = analyze_skeleton.LOWEST_INTENSITY_VOXEL
-    elif prune_cycle_method == 'lowest_intensity_branch':
-        prune_index  = analyze_skeleton.LOWEST_INTENSITY_BRANCH
-    result = analyze_skeleton.run( prune_index,
-                                   prune_ends,
-                                   calculate_largest_shortest_path,
-                                   input_image_plus_copy,
-                                   True,
-                                   True )
-    # Save the results.
-    save( result, output, show_detailed_info, calculate_largest_shortest_path )
-except Exception, e:
-    jython_utils.handle_error( error_log, str( e ) )
+# Run AnalyzeSkeleton
+analyze_skeleton = AnalyzeSkeleton_()
+analyze_skeleton.setup("", input_image_plus_copy)
+if prune_cycle_method == 'none':
+    prune_index = analyze_skeleton.NONE
+elif prune_cycle_method == 'shortest_branch':
+    prune_index = analyze_skeleton.SHORTEST_BRANCH
+elif prune_cycle_method == 'lowest_intensity_voxel':
+    prune_index = analyze_skeleton.LOWEST_INTENSITY_VOXEL
+elif prune_cycle_method == 'lowest_intensity_branch':
+    prune_index = analyze_skeleton.LOWEST_INTENSITY_BRANCH
+result = analyze_skeleton.run(prune_index, prune_ends, calculate_largest_shortest_path, input_image_plus_copy, True, True)
+# Save the results.
+save(result, output, show_detailed_info, calculate_largest_shortest_path)
--- a/imagej2_base_utils.py	Tue Sep 17 16:57:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,169 +0,0 @@
-import os
-import shutil
-import sys
-import tempfile
-
-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 jvm_memory in [None, 'None']:
-        jvm_memory_str = ''
-    else:
-        jvm_memory_str = '-Xmx%s' % jvm_memory
-    # The following bunwarpj_base_cmd string will look something like this:
-    # "java %s -cp $JAR_DIR/ij-1.49k.jar:$PLUGINS_DIR/bUnwarpJ_-2.6.1.jar \
-    # bunwarpj.bUnwarpJ_" % (jvm_memory_str)
-    # See the bunwarpj.sh script for the fiji 20151222
-    # bioconda recipe in github.
-    bunwarpj_base_cmd = "bunwarpj %s" % jvm_memory_str
-    return bunwarpj_base_cmd
-
-
-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, but our bioconda recipe allows us to do this.
-    """
-    return 'ImageJ'
-
-
-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 ' %.3f' % val
-        elif val_type == 'int':
-            return ' %d' % val
-    return ' %s' % val
-
-
-def stop_err(msg):
-    sys.stderr.write(msg)
-    sys.exit(1)
--- a/imagej2_binary_to_edm.py	Tue Sep 17 16:57:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,65 +0,0 @@
-#!/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( '--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 )
-
-# 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 += ' %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 )
--- a/imagej2_binary_to_edm_jython_script.py	Tue Sep 17 16:57:15 2019 -0400
+++ b/imagej2_binary_to_edm_jython_script.py	Mon Sep 28 17:01:19 2020 +0000
@@ -1,44 +1,40 @@
-import jython_utils
 import sys
+
 from ij import IJ
-from ij import ImagePlus
-from ij.plugin.filter import Analyzer
-from ij.plugin.filter import EDM
 
 # Fiji Jython interpreter implements Python 2.5 which does not
 # provide support for argparse.
-error_log = sys.argv[ -8 ]
-input = sys.argv[ -7 ]
-iterations = int( sys.argv[ -6 ] )
-count = int( sys.argv[ -5 ] )
-black_background = jython_utils.asbool( sys.argv[ -4 ] )
-pad_edges_when_eroding = jython_utils.asbool( sys.argv[ -3 ] )
-tmp_output_path = sys.argv[ -2 ]
-output_datatype = sys.argv[ -1 ]
+error_log = sys.argv[-8]
+input_file = sys.argv[-7]
+iterations = int(sys.argv[-6])
+count = int(sys.argv[-5])
+black_background = sys.argv[-4] == "yes"
+pad_edges_when_eroding = sys.argv[-3] == "yes"
+output_filename = sys.argv[-2]
+output_datatype = sys.argv[-1]
 
 # Open the input image file.
-input_image_plus = IJ.openImage( input )
+input_image_plus = IJ.openImage(input_file)
 
 # Create a copy of the image.
 input_image_plus_copy = input_image_plus.duplicate()
 image_processor_copy = input_image_plus_copy.getProcessor()
 
-try:
-    # Set binary options.
-    options = jython_utils.get_binary_options( black_background=black_background,
-                                               iterations=iterations,
-                                               count=count,
-                                               pad_edges_when_eroding=pad_edges_when_eroding )
-    IJ.run( input_image_plus_copy, "Options...", options )
+# Set binary options.
+options_list = ['edm=Overwrite', 'iterations=%d' % iterations, 'count=%d' % count]
+if black_background:
+    options_list.append("black")
+if pad_edges_when_eroding:
+    options_list.append("pad")
+options = " ".join(options_list)
+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", "" )
+# 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", "")
 
-    # Run the command.
-    IJ.run( input_image_plus_copy, "Distance Map", "" )
-    # 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 ) )
+# Run the command.
+IJ.run(input_image_plus_copy, "Distance Map", "")
+# Save the ImagePlus object as a new image.
+IJ.saveAs(input_image_plus_copy, output_datatype, output_filename)
--- a/imagej2_bunwarpj_adapt_transform.py	Tue Sep 17 16:57:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,65 +0,0 @@
-#!/usr/bin/env python
-import argparse
-import subprocess
-import tempfile
-import imagej2_base_utils
-
-# Parse Command Line.
-parser = argparse.ArgumentParser()
-parser.add_argument( '--source_image', dest='source_image', help='Source image' )
-parser.add_argument( '--source_image_format', dest='source_image_format', help='Source image format' )
-parser.add_argument( '--target_image', dest='target_image', help='Target image' )
-parser.add_argument( '--target_image_format', dest='target_image_format', help='Target image format' )
-parser.add_argument( '--input_elastic_transformation', dest='input_elastic_transformation', help='Input elastic transformation matrix' )
-parser.add_argument( '--image_size_factor', dest='image_size_factor', type=float, help='Image size factor' )
-parser.add_argument( '--output', dest='output', help='Warping index' )
-
-args = parser.parse_args()
-
-tmp_dir = imagej2_base_utils.get_temp_dir()
-source_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_image, args.source_image_format )
-target_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_image, args.target_image_format )
-input_elastic_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.input_elastic_transformation, 'txt' )
-
-# 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' )
-
-def is_power2( val ):
-    if val < 0:
-        return False
-    if val < 1:
-        val = 1.0 / val
-    val = int( val )
-    return ( ( val & ( val - 1 ) ) == 0 )
-
-# Build the command line to adapt the transformation.
-cmd = imagej2_base_utils.get_base_cmd_bunwarpj( None )
-if cmd is None:
-    imagej2_base_utils.stop_err( "bUnwarpJ not found!" )
-cmd += ' -adapt_transform'
-
-# Make sure the value of image_size_factor is a power of 2 (positive or negative).
-if is_power2( args.image_size_factor ):
-    image_size_factor = args.image_size_factor
-else:
-    msg = "Image size factor must be a positive or negative power of 2 (0.25, 0.5, 2, 4, 8, etc)."
-    imagej2_base_utils.stop_err( msg )
-
-# Target is sent before source.
-cmd += ' %s' % target_image_path
-cmd += ' %s' % source_image_path
-cmd += ' %s' % input_elastic_transformation_path
-cmd += ' %s' % args.output
-cmd += ' %2.f' % image_size_factor
-
-# Adapt the transformation based on the image size factor using bUnwarpJ.
-proc = subprocess.Popen( args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True )
-rc = proc.wait()
-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 )
-
-imagej2_base_utils.cleanup_before_exit( tmp_dir )
--- a/imagej2_bunwarpj_align.py	Tue Sep 17 16:57:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,178 +0,0 @@
-#!/usr/bin/env python
-import argparse
-import os
-import shutil
-import subprocess
-import tempfile
-import imagej2_base_utils
-
-# Parse Command Line.
-parser = argparse.ArgumentParser()
-parser.add_argument( '--source_image', dest='source_image', help='Source image' )
-parser.add_argument( '--source_image_format', dest='source_image_format', help='Source image format' )
-parser.add_argument( '--source_mask', dest='source_mask', default=None, help='Source mask' )
-parser.add_argument( '--source_mask_format', dest='source_mask_format', default=None, help='Source mask image format' )
-parser.add_argument( '--target_image', dest='target_image', help='Target image' )
-parser.add_argument( '--target_image_format', dest='target_image_format', help='Target image format' )
-parser.add_argument( '--target_mask', dest='target_mask', default=None, help='Target mask' )
-parser.add_argument( '--target_mask_format', dest='target_mask_format', default=None, help='Target mask image format' )
-parser.add_argument( '--min_scale_def', dest='min_scale_def', type=int, help='Initial deformation' )
-parser.add_argument( '--max_scale_def', dest='max_scale_def', type=int, help='Final deformation' )
-parser.add_argument( '--max_subsamp_fact', dest='max_subsamp_fact', type=int, help='Image sub-sample factor' )
-parser.add_argument( '--divergence_weight', dest='divergence_weight', type=float, help='Divergence weight' )
-parser.add_argument( '--curl_weight', dest='curl_weight', type=float, help='Curl weight' )
-parser.add_argument( '--image_weight', dest='image_weight', type=float, help='Image weight' )
-parser.add_argument( '--consistency_weight', dest='consistency_weight', type=float, help='Consistency weight' )
-parser.add_argument( '--landmarks_weight', dest='landmarks_weight', type=float, help='Landmarks weight' )
-parser.add_argument( '--landmarks_file', dest='landmarks_file', default=None, help='Landmarks file' )
-parser.add_argument( '--source_affine_file', dest='source_affine_file', default=None, help='Initial source affine matrix transformation' )
-parser.add_argument( '--target_affine_file', dest='target_affine_file', default=None, help='Initial target affine matrix transformation' )
-parser.add_argument( '--mono', dest='mono', default=False, help='Unidirectional registration (source to target)' )
-parser.add_argument( '--source_trans_out', dest='source_trans_out', default=None, help='Direct source transformation matrix' )
-parser.add_argument( '--target_trans_out', dest='target_trans_out', default=None, help='Inverse target transformation matrix' )
-parser.add_argument( '--source_out', help='Output source image' )
-parser.add_argument( '--source_out_datatype', help='Output registered source image format' )
-parser.add_argument( '--target_out', default=None, help='Output target image' )
-parser.add_argument( '--target_out_datatype', default=None, help='Output registered target image format' )
-parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' )
-
-args = parser.parse_args()
-
-if args.source_trans_out is not None and args.target_trans_out is not None:
-    save_transformation = True
-else:
-    save_transformation = False
-
-tmp_dir = imagej2_base_utils.get_temp_dir()
-source_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_image, args.source_image_format )
-tmp_source_out_tiff_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, 'tiff' )
-tmp_source_out_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.source_out_datatype )
-target_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_image, args.target_image_format )
-if not args.mono:
-    tmp_target_out_tiff_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, 'tiff' )
-    tmp_target_out_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.target_out_datatype )
-if args.source_mask is not None and args.target_mask is not None:
-    tmp_source_mask_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_mask, args.source_mask_format )
-    tmp_target_mask_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_mask, args.target_mask_format )
-if save_transformation:
-    # bUnwarpJ automatically names the transformation files based on the names
-    # of the source and target image file names.  We've defined symlinks to 
-    # temporary files with valid image extensions since ImageJ does not handle
-    # the Galaxy "dataset.dat" file extensions.
-    source_file_name = imagej2_base_utils.get_file_name_without_extension( tmp_source_out_tiff_path )
-    tmp_source_out_transf_path = os.path.join( tmp_dir, '%s_transf.txt' % source_file_name )
-    target_file_name = imagej2_base_utils.get_file_name_without_extension( tmp_target_out_tiff_path )
-    tmp_target_out_transf_path = os.path.join( tmp_dir, '%s_transf.txt' % target_file_name )
-
-# 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' )
-
-# Build the command line to align the two images.
-cmd = imagej2_base_utils.get_base_cmd_bunwarpj( None )
-if cmd is None:
-    imagej2_base_utils.stop_err( "bUnwarpJ not found!" )
-cmd += ' -align'
-# Target is sent before source.
-cmd += ' %s' % target_image_path
-if args.target_mask is None:
-    target_mask_str = ' NULL'
-else:
-    target_mask_str = ' %s' % tmp_target_mask_path
-cmd += target_mask_str
-cmd += ' %s' % source_image_path
-if args.source_mask is None:
-    source_mask_str = ' NULL'
-else:
-    source_mask_str = ' %s' % tmp_source_mask_path
-cmd += source_mask_str
-cmd += ' %d' % args.min_scale_def
-cmd += ' %d' % args.max_scale_def
-cmd += ' %d' % args.max_subsamp_fact
-cmd += ' %.1f' % args.divergence_weight
-cmd += ' %.1f' % args.curl_weight
-cmd += ' %.1f' % args.image_weight
-cmd += ' %.1f' % args.consistency_weight
-# Source is produced before target.
-cmd += ' %s' % tmp_source_out_tiff_path
-if not args.mono:
-    cmd += ' %s' % tmp_target_out_tiff_path
-if args.landmarks_file is not None:
-    # We have to create a temporary file with a .txt extension here so that
-    # bUnwarpJ will not ignore the Galaxy "dataset.dat" file.
-    tmp_landmarks_file_path = imagej2_base_utils.get_input_image_path( tmp_dir,
-                                                                       args.landmarks_file,
-                                                                       'txt' )
-    cmd += ' -landmarks'
-    cmd += ' %.1f' % args.landmarks_weight
-    cmd += ' %s' % tmp_landmarks_file_path
-if args.source_affine_file is not None and args.target_affine_file is not None:
-    # Target is sent before source.
-    cmd += ' -affine'
-    cmd += ' %s' % args.target_affine_file
-    cmd += ' %s' % args.source_affine_file
-if args.mono:
-    cmd += ' -mono'
-if save_transformation:
-    cmd += ' -save_transformation'
-
-# Align the two images using bUnwarpJ.
-proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True )
-rc = proc.wait()
-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 )
-
-# bUnwarpJ 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.  Galaxy supports only single-layered images, so we'll convert the images so they
-# can be viewed in Galaxy.
-
-# 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' )
-
-# Build the command line to handle the multi-slice tiff images.
-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!" )
-if args.mono:
-    # bUnwarpJ will produce only a registered source image.
-    cmd += ' %s %s %s %s' % ( tmp_source_out_tiff_path,
-                              args.source_out_datatype,
-                              tmp_source_out_path,
-                              args.mono )
-else:
-    # bUnwarpJ will produce registered source and target images.
-    cmd += ' %s %s %s %s %s %s %s' % ( tmp_source_out_tiff_path,
-                                       args.source_out_datatype,
-                                       tmp_source_out_path,
-                                       tmp_target_out_tiff_path,
-                                       args.target_out_datatype,
-                                       tmp_target_out_path,
-                                       args.mono )
-
-# Merge the multi-slice tiff layers into an image that can be viewed in Galaxy.
-proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True )
-rc = proc.wait()
-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 )
-
-# Save the Registered Source Image to the output dataset.
-shutil.move( tmp_source_out_path, args.source_out )
-if not args.mono:
-    # Move the Registered Target Image to the output dataset.
-    shutil.move( tmp_target_out_path, args.target_out )
-
-# If requested, save matrix transformations as additional datasets.
-if save_transformation:
-    shutil.move( tmp_source_out_transf_path, args.source_trans_out )
-    if not args.mono:
-        shutil.move( tmp_target_out_transf_path, args.target_trans_out )
-
-imagej2_base_utils.cleanup_before_exit( tmp_dir )
--- a/imagej2_bunwarpj_align_jython_script.py	Tue Sep 17 16:57:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,37 +0,0 @@
-import sys
-import jython_utils
-from ij import IJ
-
-# Fiji Jython interpreter implements Python 2.5 which does not
-# provide support for argparse.
-
-if sys.argv[ -1 ].lower() in [ 'true' ]:
-    mono = True
-else:
-    mono = False
-
-if mono:
-    # bUnwarpJ has been called with the -mono param.
-    source_tiff_path = sys.argv[ -4 ]
-    source_datatype = sys.argv[ -3 ]
-    source_path = sys.argv[ -2 ]
-else:
-    source_tiff_path = sys.argv[ -7 ]
-    source_datatype = sys.argv[ -6 ]
-    source_path = sys.argv[ -5 ]
-    target_tiff_path = sys.argv[ -4 ]
-    target_datatype = sys.argv[ -3 ]
-    target_path = sys.argv[ -2 ]
-
-# Save the Registered Source Image.
-registered_source_image = IJ.openImage( source_tiff_path )
-if source_datatype == 'tiff':
-    registered_source_image = jython_utils.convert_before_saving_as_tiff( registered_source_image )
-IJ.saveAs( registered_source_image, source_datatype, source_path )
-
-if not mono:
-    # Save the Registered Target Image.
-    registered_target_image = IJ.openImage( target_tiff_path )
-    if target_datatype == 'tiff':
-        registered_target_image = jython_utils.convert_before_saving_as_tiff( registered_target_image )
-    IJ.saveAs( registered_target_image, target_datatype, target_path )
--- a/imagej2_bunwarpj_compare_elastic.py	Tue Sep 17 16:57:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,65 +0,0 @@
-#!/usr/bin/env python
-import argparse
-import subprocess
-import tempfile
-import imagej2_base_utils
-
-# Parse Command Line.
-parser = argparse.ArgumentParser()
-parser.add_argument( '--source_image', dest='source_image', help='Source image' )
-parser.add_argument( '--source_image_format', dest='source_image_format', help='Source image format' )
-parser.add_argument( '--target_image', dest='target_image', help='Target image' )
-parser.add_argument( '--target_image_format', dest='target_image_format', help='Target image format' )
-parser.add_argument( '--source_transformation', dest='source_transformation', help='Direct source transformation matrix' )
-parser.add_argument( '--target_transformation', dest='target_transformation', help='Inverse target transformation matrix' )
-parser.add_argument( '--output', dest='output', help='Warping index' )
-
-args = parser.parse_args()
-
-tmp_dir = imagej2_base_utils.get_temp_dir()
-source_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_image, args.source_image_format )
-target_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_image, args.target_image_format )
-source_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_transformation, 'txt' )
-target_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_transformation, 'txt' )
-# bUnwarpJ produces several lines of output that we need to discard, so
-# we'll use a temporary output file from which we'll read only the last line.
-tmp_output_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.output, 'txt' )
-
-# 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' )
-
-# Build the command line to calculate the warping index.
-cmd = imagej2_base_utils.get_base_cmd_bunwarpj( None )
-if cmd is None:
-    imagej2_base_utils.stop_err( "bUnwarpJ not found!" )
-cmd += ' -compare_elastic'
-# Target is sent before source.
-cmd += ' %s' % target_image_path
-cmd += ' %s' % source_image_path
-cmd += ' %s' % target_transformation_path
-cmd += ' %s' % source_transformation_path
-cmd += ' > %s' % tmp_output_path
-
-# Calculate the warping index of two elastic transformations using bUnwarpJ.
-proc = subprocess.Popen( args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True )
-rc = proc.wait()
-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 )
-
-# Example contents of tmp_output_path:
-# ['Target image : ~/tmpKAYF1P.jpg\n',
-#  'Source image : ~/tmpgQX0dy.gif\n',
-#  'Target Transformation file : ~/tmpZJC_4B.txt\n',
-#  'Source Transformation file : ~/tmphsSojl.txt\n',
-#  ' Warping index = 14.87777347388348\n']
-results = open( tmp_output_path, 'r' ).readlines()
-warp_index = results[ -1 ].split( ' ' )[ -1 ]
-outf = open( args.output, 'wb' )
-outf.write( '%s' % warp_index )
-outf.close()
-
-imagej2_base_utils.cleanup_before_exit( tmp_dir )
--- a/imagej2_bunwarpj_compare_elastic_raw.py	Tue Sep 17 16:57:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,64 +0,0 @@
-#!/usr/bin/env python
-import argparse
-import subprocess
-import tempfile
-import imagej2_base_utils
-
-# Parse Command Line.
-parser = argparse.ArgumentParser()
-parser.add_argument( '--source_image', dest='source_image', help='Source image' )
-parser.add_argument( '--source_image_format', dest='source_image_format', help='Source image format' )
-parser.add_argument( '--target_image', dest='target_image', help='Target image' )
-parser.add_argument( '--target_image_format', dest='target_image_format', help='Target image format' )
-parser.add_argument( '--target_elastic_transformation', dest='target_elastic_transformation', help='Target elastic transformation matrix' )
-parser.add_argument( '--source_raw_transformation', dest='source_raw_transformation', help='Source raw transformation matrix' )
-parser.add_argument( '--output', dest='output', help='Warping index' )
-
-args = parser.parse_args()
-
-tmp_dir = imagej2_base_utils.get_temp_dir()
-source_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_image, args.source_image_format )
-target_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_image, args.target_image_format )
-target_elastic_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_elastic_transformation, 'txt' )
-source_raw_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_raw_transformation, 'txt' )
-# bUnwarpJ produces several lines of output that we need to discard, so
-# we'll use a temporary output file from which we'll read only the last line.
-tmp_output_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.output, 'txt' )
-
-# 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' )
-
-# Build the command line to calculate the warping index.
-cmd = imagej2_base_utils.get_base_cmd_bunwarpj( None )
-if cmd is None:
-    imagej2_base_utils.stop_err( "bUnwarpJ not found!" )
-cmd += ' -compare_elastic_raw'
-cmd += ' %s' % target_image_path
-cmd += ' %s' % source_image_path
-cmd += ' %s' % target_elastic_transformation_path
-cmd += ' %s' % source_raw_transformation_path
-cmd += ' > %s' % tmp_output_path
-
-# Calculate the warping index of elastic and raw transformations using bUnwarpJ.
-proc = subprocess.Popen( args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True )
-rc = proc.wait()
-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 )
-
-# Example contents of tmp_output_path:
-# ['Target image : ~/tmpHdt9Cs.jpg\n',
-#  'Source image : ~/tmpu6kyfc.gif\n',
-#  'Elastic Transformation file   : ~/tmp4vZurG.txt\n',
-#  'Raw Transformation file : ~/tmp2PNQcT.txt\n',
-#  ' Warping index = 25.007467512204983\n']
-results = open( tmp_output_path, 'r' ).readlines()
-warp_index = results[ -1 ].split( ' ' )[ -1 ]
-outf = open( args.output, 'wb' )
-outf.write( '%s' % warp_index )
-outf.close()
-
-imagej2_base_utils.cleanup_before_exit( tmp_dir )
--- a/imagej2_bunwarpj_compare_raw.py	Tue Sep 17 16:57:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,64 +0,0 @@
-#!/usr/bin/env python
-import argparse
-import subprocess
-import tempfile
-import imagej2_base_utils
-
-# Parse Command Line.
-parser = argparse.ArgumentParser()
-parser.add_argument( '--source_image', dest='source_image', help='Source image' )
-parser.add_argument( '--source_image_format', dest='source_image_format', help='Source image format' )
-parser.add_argument( '--target_image', dest='target_image', help='Target image' )
-parser.add_argument( '--target_image_format', dest='target_image_format', help='Target image format' )
-parser.add_argument( '--target_raw_transformation', dest='target_raw_transformation', help='First raw transformation matrix' )
-parser.add_argument( '--source_raw_transformation', dest='source_raw_transformation', help='Second raw transformation matrix' )
-parser.add_argument( '--output', dest='output', help='Warping index' )
-
-args = parser.parse_args()
-
-tmp_dir = imagej2_base_utils.get_temp_dir()
-source_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_image, args.source_image_format )
-target_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_image, args.target_image_format )
-target_raw_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_raw_transformation, 'txt' )
-source_raw_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_raw_transformation, 'txt' )
-# bUnwarpJ produces several lines of output that we need to discard, so
-# we'll use a temporary output file from which we'll read only the last line.
-tmp_output_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.output, 'txt' )
-
-# 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' )
-
-# Build the command line to calculate the warping index.
-cmd = imagej2_base_utils.get_base_cmd_bunwarpj( None )
-if cmd is None:
-    imagej2_base_utils.stop_err( "bUnwarpJ not found!" )
-cmd += ' -compare_raw'
-cmd += ' %s' % target_image_path
-cmd += ' %s' % source_image_path
-cmd += ' %s' % target_raw_transformation_path
-cmd += ' %s' % source_raw_transformation_path
-cmd += ' > %s' % tmp_output_path
-
-# Calculate the warping index of two raw transformations using bUnwarpJ.
-proc = subprocess.Popen( args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True )
-rc = proc.wait()
-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 )
-
-# Example contents of tmp_output_path:
-# ['Target image : ~/tmp5WmDku.jpg\n',
-#  'Source image : ~/tmps74U40.gif\n',
-#  'Target Transformation file : ~/tmpXofC1x.txt\n',
-#  'Source Transformation file : ~/tmpFqNYe4.txt\n',
-#  ' Warping index = 24.111209027033937\n']
-results = open( tmp_output_path, 'r' ).readlines()
-warp_index = results[ -1 ].split( ' ' )[ -1 ]
-outf = open( args.output, 'wb' )
-outf.write( '%s' % warp_index )
-outf.close()
-
-imagej2_base_utils.cleanup_before_exit( tmp_dir )
--- a/imagej2_bunwarpj_compose_elastic.py	Tue Sep 17 16:57:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,50 +0,0 @@
-#!/usr/bin/env python
-import argparse
-import subprocess
-import tempfile
-import imagej2_base_utils
-
-# Parse Command Line.
-parser = argparse.ArgumentParser()
-parser.add_argument( '--source_image', dest='source_image', help='Source image' )
-parser.add_argument( '--source_image_format', dest='source_image_format', help='Source image format' )
-parser.add_argument( '--target_image', dest='target_image', help='Target image' )
-parser.add_argument( '--target_image_format', dest='target_image_format', help='Target image format' )
-parser.add_argument( '--source_elastic_transformation', dest='source_elastic_transformation', help='Direct source transformation matrix' )
-parser.add_argument( '--target_elastic_transformation', dest='target_elastic_transformation', help='Inverse target transformation matrix' )
-parser.add_argument( '--output', dest='output', help='Warping index' )
-
-args = parser.parse_args()
-
-tmp_dir = imagej2_base_utils.get_temp_dir()
-source_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_image, args.source_image_format )
-target_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_image, args.target_image_format )
-source_elastic_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_elastic_transformation, 'txt' )
-target_elastic_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_elastic_transformation, 'txt' )
-
-# 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' )
-
-# Build the command line to compose the transformations.
-cmd = imagej2_base_utils.get_base_cmd_bunwarpj( None )
-if cmd is None:
-    imagej2_base_utils.stop_err( "bUnwarpJ not found!" )
-cmd += ' -compose_elastic'
-# Target is sent before source.
-cmd += ' %s' % target_image_path
-cmd += ' %s' % source_image_path
-cmd += ' %s' % target_elastic_transformation_path
-cmd += ' %s' % source_elastic_transformation_path
-cmd += ' %s' % args.output
-
-# Compose the two elastic transformations into a raw transformation using bUnwarpJ.
-proc = subprocess.Popen( args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True )
-rc = proc.wait()
-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 )
-
-imagej2_base_utils.cleanup_before_exit( tmp_dir )
--- a/imagej2_bunwarpj_compose_raw.py	Tue Sep 17 16:57:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,50 +0,0 @@
-#!/usr/bin/env python
-import argparse
-import subprocess
-import tempfile
-import imagej2_base_utils
-
-# Parse Command Line.
-parser = argparse.ArgumentParser()
-parser.add_argument( '--source_image', dest='source_image', help='Source image' )
-parser.add_argument( '--source_image_format', dest='source_image_format', help='Source image format' )
-parser.add_argument( '--target_image', dest='target_image', help='Target image' )
-parser.add_argument( '--target_image_format', dest='target_image_format', help='Target image format' )
-parser.add_argument( '--source_raw_transformation', dest='source_raw_transformation', help='Direct source transformation matrix' )
-parser.add_argument( '--target_raw_transformation', dest='target_raw_transformation', help='Inverse target transformation matrix' )
-parser.add_argument( '--output', dest='output', help='Warping index' )
-
-args = parser.parse_args()
-
-tmp_dir = imagej2_base_utils.get_temp_dir()
-source_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_image, args.source_image_format )
-target_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_image, args.target_image_format )
-source_raw_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_raw_transformation, 'txt' )
-target_raw_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_raw_transformation, 'txt' )
-
-# 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' )
-
-# Build the command line to compose the two raw transformations.
-cmd = imagej2_base_utils.get_base_cmd_bunwarpj( None )
-if cmd is None:
-    imagej2_base_utils.stop_err( "bUnwarpJ not found!" )
-cmd += ' -compose_raw'
-# Target is sent before source.
-cmd += ' %s' % target_image_path
-cmd += ' %s' % source_image_path
-cmd += ' %s' % target_raw_transformation_path
-cmd += ' %s' % source_raw_transformation_path
-cmd += ' %s' % args.output
-
-# Compose the two raw transformations into another raw transformation using bUnwarpJ.
-proc = subprocess.Popen( args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True )
-rc = proc.wait()
-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 )
-
-imagej2_base_utils.cleanup_before_exit( tmp_dir )
--- a/imagej2_bunwarpj_compose_raw_elastic.py	Tue Sep 17 16:57:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,50 +0,0 @@
-#!/usr/bin/env python
-import argparse
-import subprocess
-import tempfile
-import imagej2_base_utils
-
-# Parse Command Line.
-parser = argparse.ArgumentParser()
-parser.add_argument( '--source_image', dest='source_image', help='Source image' )
-parser.add_argument( '--source_image_format', dest='source_image_format', help='Source image format' )
-parser.add_argument( '--target_image', dest='target_image', help='Target image' )
-parser.add_argument( '--target_image_format', dest='target_image_format', help='Target image format' )
-parser.add_argument( '--source_elastic_transformation', dest='source_elastic_transformation', help='Direct source transformation matrix' )
-parser.add_argument( '--target_raw_transformation', dest='target_raw_transformation', help='Inverse target transformation matrix' )
-parser.add_argument( '--output', dest='output', help='Warping index' )
-
-args = parser.parse_args()
-
-tmp_dir = imagej2_base_utils.get_temp_dir()
-source_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_image, args.source_image_format )
-target_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_image, args.target_image_format )
-source_elastic_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_elastic_transformation, 'txt' )
-target_raw_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_raw_transformation, 'txt' )
-
-# 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' )
-
-# Build the command line to compose the raw and elastic transformations.
-cmd = imagej2_base_utils.get_base_cmd_bunwarpj( None )
-if cmd is None:
-    imagej2_base_utils.stop_err( "bUnwarpJ not found!" )
-cmd += ' -compose_raw_elastic'
-# Target is sent before source.
-cmd += ' %s' % target_image_path
-cmd += ' %s' % source_image_path
-cmd += ' %s' % target_raw_transformation_path
-cmd += ' %s' % source_elastic_transformation_path
-cmd += ' %s' % args.output
-
-# Compose the raw and elastic transformations into another raw transformation using bUnwarpJ.
-proc = subprocess.Popen( args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True )
-rc = proc.wait()
-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 )
-
-imagej2_base_utils.cleanup_before_exit( tmp_dir )
--- a/imagej2_bunwarpj_convert_to_raw.py	Tue Sep 17 16:57:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,47 +0,0 @@
-#!/usr/bin/env python
-import argparse
-import subprocess
-import tempfile
-import imagej2_base_utils
-
-# Parse Command Line.
-parser = argparse.ArgumentParser()
-parser.add_argument( '--source_image', dest='source_image', help='Source image' )
-parser.add_argument( '--source_image_format', dest='source_image_format', help='Source image format' )
-parser.add_argument( '--target_image', dest='target_image', help='Target image' )
-parser.add_argument( '--target_image_format', dest='target_image_format', help='Target image format' )
-parser.add_argument( '--elastic_transformation', dest='elastic_transformation', help='Elastic transformation as saved by bUnwarpJ in elastic format' )
-parser.add_argument( '--raw_transformation', dest='raw_transformation', help='Raw transformation' )
-
-args = parser.parse_args()
-
-tmp_dir = imagej2_base_utils.get_temp_dir()
-source_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_image, args.source_image_format )
-target_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_image, args.target_image_format )
-elastic_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.elastic_transformation, 'txt' )
-
-# 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' )
-
-# Build the command line to convert the B-spline (i.e., elastic) transformation to raw.
-cmd = imagej2_base_utils.get_base_cmd_bunwarpj( None )
-if cmd is None:
-    imagej2_base_utils.stop_err( "bUnwarpJ not found!" )
-cmd += ' -convert_to_raw'
-# Target is sent before source.
-cmd += ' %s' % target_image_path
-cmd += ' %s' % source_image_path
-cmd += ' %s' % elastic_transformation_path
-cmd += ' %s' % args.raw_transformation
-
-# Convert the elastic transformation to raw using bUnwarpJ.
-proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True )
-rc = proc.wait()
-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 )
-
-imagej2_base_utils.cleanup_before_exit( tmp_dir )
--- a/imagej2_bunwarpj_elastic_transform.py	Tue Sep 17 16:57:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,73 +0,0 @@
-#!/usr/bin/env python
-import argparse
-import shutil
-import subprocess
-import tempfile
-import imagej2_base_utils
-
-# Parse Command Line.
-parser = argparse.ArgumentParser()
-parser.add_argument( '--source_image', dest='source_image', help='Source image' )
-parser.add_argument( '--source_image_format', dest='source_image_format', help='Source image format' )
-parser.add_argument( '--target_image', dest='target_image', help='Target image' )
-parser.add_argument( '--target_image_format', dest='target_image_format', help='Target image format' )
-parser.add_argument( '--elastic_transformation', dest='elastic_transformation', help='Elastic transformation as saved by bUnwarpJ in elastic format' )
-parser.add_argument( '--source_out', help='Output source image' )
-parser.add_argument( '--source_out_datatype', help='Output registered source image format' )
-parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' )
-
-args = parser.parse_args()
-
-tmp_dir = imagej2_base_utils.get_temp_dir()
-source_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_image, args.source_image_format )
-tmp_source_out_tiff_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, 'tiff' )
-tmp_source_out_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.source_out_datatype )
-target_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_image, args.target_image_format )
-elastic_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.elastic_transformation, 'txt' )
-
-# 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' )
-
-# Build the command line to apply the transformation.
-cmd = imagej2_base_utils.get_base_cmd_bunwarpj( None )
-if cmd is None:
-    imagej2_base_utils.stop_err( "bUnwarpJ not found!" )
-cmd += ' -elastic_transform'
-# Target is sent before source.
-cmd += ' %s' % target_image_path
-cmd += ' %s' % source_image_path
-cmd += ' %s' % elastic_transformation_path
-cmd += ' %s' % tmp_source_out_tiff_path
-
-# Apply the elastic transformation using bUnwarpJ.
-proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True )
-rc = proc.wait()
-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 )
-
-# Convert the registered image to the specified output format.
-tmp_out = tempfile.NamedTemporaryFile().name
-tmp_stdout = open( tmp_out, 'wb' )
-tmp_err = tempfile.NamedTemporaryFile().name
-tmp_stderr = open( tmp_err, 'wb' )
-
-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 %s %s' % ( tmp_source_out_tiff_path,
-                       args.source_out_datatype,
-                       tmp_source_out_path )
-
-proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True )
-rc = proc.wait()
-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 )
-
-# Save the Registered Source Image to the defined output.
-shutil.move( tmp_source_out_path, args.source_out )
-imagej2_base_utils.cleanup_before_exit( tmp_dir )
--- a/imagej2_bunwarpj_elastic_transform_jython_script.py	Tue Sep 17 16:57:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +0,0 @@
-import sys
-import jython_utils
-from ij import IJ
-
-# Fiji Jython interpreter implements Python 2.5 which does not
-# provide support for argparse.
-
-source_tiff_path = sys.argv[ -3 ]
-source_datatype = sys.argv[ -2 ]
-source_path = sys.argv[ -1 ]
-
-# Save the Registered Source Image.
-registered_source_image = IJ.openImage( source_tiff_path )
-if source_datatype == 'tiff':
-    registered_source_image = jython_utils.convert_before_saving_as_tiff( registered_source_image )
-IJ.saveAs( registered_source_image, source_datatype, source_path )
--- a/imagej2_bunwarpj_raw_transform.py	Tue Sep 17 16:57:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,73 +0,0 @@
-#!/usr/bin/env python
-import argparse
-import shutil
-import subprocess
-import tempfile
-import imagej2_base_utils
-
-# Parse Command Line.
-parser = argparse.ArgumentParser()
-parser.add_argument( '--source_image', dest='source_image', help='Source image' )
-parser.add_argument( '--source_image_format', dest='source_image_format', help='Source image format' )
-parser.add_argument( '--target_image', dest='target_image', help='Target image' )
-parser.add_argument( '--target_image_format', dest='target_image_format', help='Target image format' )
-parser.add_argument( '--raw_transformation', dest='raw_transformation', help='Raw transformation as saved by bUnwarpJ' )
-parser.add_argument( '--source_out', help='Output source image' )
-parser.add_argument( '--source_out_datatype', help='Output registered source image format' )
-parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' )
-
-args = parser.parse_args()
-
-tmp_dir = imagej2_base_utils.get_temp_dir()
-source_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_image, args.source_image_format )
-tmp_source_out_tiff_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, 'tiff' )
-tmp_source_out_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.source_out_datatype )
-target_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_image, args.target_image_format )
-raw_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.raw_transformation, 'txt' )
-
-# 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' )
-
-# Build the command line to apply the raw transformation.
-cmd = imagej2_base_utils.get_base_cmd_bunwarpj( None )
-if cmd is None:
-    imagej2_base_utils.stop_err( "bUnwarpJ not found!" )
-cmd += ' -raw_transform'
-# Target is sent before source.
-cmd += ' %s' % target_image_path
-cmd += ' %s' % source_image_path
-cmd += ' %s' % raw_transformation_path
-cmd += ' %s' % tmp_source_out_tiff_path
-
-# Apply the raw transformation using bUnwarpJ.
-proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True )
-rc = proc.wait()
-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 )
-
-# Convert the registered image to the specified output format.
-tmp_out = tempfile.NamedTemporaryFile().name
-tmp_stdout = open( tmp_out, 'wb' )
-tmp_err = tempfile.NamedTemporaryFile().name
-tmp_stderr = open( tmp_err, 'wb' )
-
-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 %s %s' % ( tmp_source_out_tiff_path,
-                       args.source_out_datatype,
-                       tmp_source_out_path )
-
-proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True )
-rc = proc.wait()
-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 )
-
-# Save the Registered Source Image to the defined output.
-shutil.move( tmp_source_out_path, args.source_out )
-imagej2_base_utils.cleanup_before_exit( tmp_dir )
--- a/imagej2_bunwarpj_raw_transform_jython_script.py	Tue Sep 17 16:57:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +0,0 @@
-import sys
-import jython_utils
-from ij import IJ
-
-# Fiji Jython interpreter implements Python 2.5 which does not
-# provide support for argparse.
-
-source_tiff_path = sys.argv[ -3 ]
-source_datatype = sys.argv[ -2 ]
-source_path = sys.argv[ -1 ]
-
-# Save the Registered Source Image.
-registered_source_image = IJ.openImage( source_tiff_path )
-if source_datatype == 'tiff':
-    registered_source_image = jython_utils.convert_before_saving_as_tiff( registered_source_image )
-IJ.saveAs( registered_source_image, source_datatype, source_path )
--- a/imagej2_create_image.py	Tue Sep 17 16:57:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,40 +0,0 @@
-#!/usr/bin/env python
-import argparse
-import shutil
-import subprocess
-import tempfile
-import imagej2_base_utils
-
-if __name__=="__main__":
-    # Parse Command Line.
-    parser = argparse.ArgumentParser()
-    parser.add_argument( '--width', dest='width', type=int, help='Image width in pixels' )
-    parser.add_argument( '--height', dest='height', type=int, help='Image height in pixels' )
-    parser.add_argument( '--depth', dest='depth', type=int, help='Image depth (specifies the number of stack slices)' )
-    parser.add_argument( '--image_type', dest='image_type', help='Image type' )
-    parser.add_argument( '--image_title', dest='image_title', default='', help='Image title' )
-    parser.add_argument( '--output_datatype', dest='output_datatype', help='Output image format' )
-    parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' )
-    parser.add_argument( '--out_fname', help='Path to the output file' )
-    args = parser.parse_args()
-
-    tmp_dir = imagej2_base_utils.get_temp_dir()
-    tmp_image_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' )
-    # 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 %d %d %d %s %s' % ( args.image_title, args.width, args.height, args.depth, args.image_type, tmp_image_path )
-    proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True )
-    rc = proc.wait()
-    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 )
-    shutil.move( tmp_image_path, args.out_fname )
-    imagej2_base_utils.cleanup_before_exit( tmp_dir )
--- a/imagej2_create_image_jython_script.py	Tue Sep 17 16:57:15 2019 -0400
+++ b/imagej2_create_image_jython_script.py	Mon Sep 28 17:01:19 2020 +0000
@@ -1,14 +1,15 @@
 import sys
+
 from ij import IJ
 
 # Fiji Jython interpreter implements Python 2.5 which does not
 # provide support for argparse.
-title = sys.argv[ -6 ]
-width = int( sys.argv[ -5 ] )
-height = int( sys.argv[ -4 ] )
-depth = int( sys.argv[ -3 ] )
-type = sys.argv[ -2 ].replace( '_', ' ' )
-tmp_image_path = sys.argv[ -1 ]
+title = sys.argv[-6]
+width = int(sys.argv[-5])
+height = int(sys.argv[-4])
+depth = int(sys.argv[-3])
+type = sys.argv[-2].replace('_', ' ')
+tmp_image_path = sys.argv[-1]
 
-imp = IJ.newImage( title, type, width, height, depth )
-IJ.save( imp, "%s" % tmp_image_path )
+imp = IJ.newImage(title, type, width, height, depth)
+IJ.save(imp, "%s" % tmp_image_path)
--- a/imagej2_enhance_contrast.py	Tue Sep 17 16:57:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,63 +0,0 @@
-#!/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( '--equalize_histogram', dest='equalize_histogram', help='Equalize_histogram' )
-parser.add_argument( '--saturated_pixels', dest='saturated_pixels', type=float, default=None, help='Saturated pixel pct' )
-parser.add_argument( '--normalize', dest='normalize', help='Normalize' )
-parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' )
-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 )
-
-# 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.equalize_histogram
-cmd += imagej2_base_utils.handle_none_type( args.saturated_pixels )
-cmd += ' %s' % args.normalize
-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 )
--- a/imagej2_enhance_contrast_jython_script.py	Tue Sep 17 16:57:15 2019 -0400
+++ b/imagej2_enhance_contrast_jython_script.py	Mon Sep 28 17:01:19 2020 +0000
@@ -1,19 +1,19 @@
-import jython_utils
 import sys
+
 from ij import IJ
 
 # Fiji Jython interpreter implements Python 2.5 which does not
 # provide support for argparse.
-error_log = sys.argv[ -7 ]
-input = sys.argv[ -6 ]
-equalize_histogram = jython_utils.asbool( sys.argv[ -5 ] )
-saturated_pixels = sys.argv[ -4 ]
-normalize = jython_utils.asbool( sys.argv[ -3 ] )
-tmp_output_path = sys.argv[ -2 ]
-output_datatype = sys.argv[ -1 ]
+error_log = sys.argv[-7]
+input = sys.argv[-6]
+equalize_histogram = sys.argv[-5] == "yes"
+saturated_pixels = sys.argv[-4]
+normalize = sys.argv[-3] == "yes"
+tmp_output_path = sys.argv[-2]
+output_datatype = sys.argv[-1]
 
 # Open the input image file.
-input_image_plus = IJ.openImage( input )
+input_image_plus = IJ.openImage(input)
 
 # Create a copy of the image.
 input_image_plus_copy = input_image_plus.duplicate()
@@ -24,19 +24,16 @@
 options = []
 # If equalize_histogram, saturated_pixels and normalize are ignored.
 if equalize_histogram:
-    options.append( 'equalize' )
+    options.append('equalize')
 else:
-    if saturated_pixels not in [ None, 'None' ]:
+    if saturated_pixels not in [None, 'None']:
         # Fiji allows only a single decimal place for this value.
-        options.append( 'saturated=%.3f' % float( saturated_pixels ) )
+        options.append('saturated=%.3f' % float(saturated_pixels))
     # Normalization of RGB images is not supported.
     if bit_depth != 24 and normalize:
-        options.append( 'normalize' )
-try:
-    # Run the command.
-    options = "%s" % ' '.join( options )
-    IJ.run( input_image_plus_copy, "Enhance Contrast...", 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 ) )
+        options.append('normalize')
+# Run the command.
+options = "%s" % ' '.join(options)
+IJ.run(input_image_plus_copy, "Enhance Contrast...", options)
+# Save the ImagePlus object as a new image.
+IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path)
--- a/imagej2_find_edges.py	Tue Sep 17 16:57:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,57 +0,0 @@
-#!/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( '--jython_script', dest='jython_script', help='Path to the Jython script' )
-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 )
-
-# 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' % 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 )
--- a/imagej2_find_edges_jython_script.py	Tue Sep 17 16:57:15 2019 -0400
+++ b/imagej2_find_edges_jython_script.py	Mon Sep 28 17:01:19 2020 +0000
@@ -1,25 +1,22 @@
-import jython_utils
 import sys
+
 from ij import IJ
 
 # Fiji Jython interpreter implements Python 2.5 which does not
 # provide support for argparse.
-error_log = sys.argv[ -4 ]
-input = sys.argv[ -3 ]
-tmp_output_path = sys.argv[ -2 ]
-output_datatype = sys.argv[ -1 ]
+error_log = sys.argv[-4]
+input = 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 )
+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()
 
-try:
-    # Run the command.
-    IJ.run( input_image_plus_copy, "Find Edges", "" )
-    # 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 ) )
+# Run the command.
+IJ.run(input_image_plus_copy, "Find Edges", "")
+# Save the ImagePlus object as a new image.
+IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path)
--- a/imagej2_find_maxima.py	Tue Sep 17 16:57:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,69 +0,0 @@
-#!/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( '--scale_when_converting', dest='scale_when_converting', help='Scale when converting RGB image' )
-parser.add_argument( '--weighted_rgb_conversions', dest='weighted_rgb_conversions', help='Weighted RGB conversions for RGB image' )
-parser.add_argument( '--noise_tolerance', dest='noise_tolerance', type=int, help='Noise tolerance' )
-parser.add_argument( '--output_type', dest='output_type', help='Output type' )
-parser.add_argument( '--exclude_edge_maxima', dest='exclude_edge_maxima', help='Exclude edge maxima' )
-parser.add_argument( '--light_background', dest='light_background', help='Light background' )
-parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' )
-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 )
-
-# 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.scale_when_converting
-cmd += ' %s' % args.weighted_rgb_conversions
-cmd += ' %d' % args.noise_tolerance
-cmd += ' %s' % args.output_type
-cmd += ' %s' % args.exclude_edge_maxima
-cmd += ' %s' % args.light_background
-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 )
--- a/imagej2_find_maxima_jython_script.py	Tue Sep 17 16:57:15 2019 -0400
+++ b/imagej2_find_maxima_jython_script.py	Mon Sep 28 17:01:19 2020 +0000
@@ -1,94 +1,90 @@
 import sys
-import jython_utils
-from ij import ImagePlus, IJ
+
+from ij import IJ, ImagePlus
 from ij.plugin.filter import Analyzer, MaximumFinder
 from ij.process import ImageProcessor
-from jarray import array
 
 # Fiji Jython interpreter implements Python 2.5 which does not
 # provide support for argparse.
-error_log = sys.argv[ -10 ]
-input = sys.argv[ -9 ]
-scale_when_converting = jython_utils.asbool( sys.argv[ -8 ] )
-weighted_rgb_conversions = jython_utils.asbool( sys.argv[ -7 ] )
-noise_tolerance = int( sys.argv[ -6 ] )
-output_type = sys.argv[ -5 ]
-exclude_edge_maxima = jython_utils.asbool( sys.argv[ -4 ] )
-light_background = jython_utils.asbool( sys.argv[ -3 ] )
-tmp_output_path = sys.argv[ -2 ]
-output_datatype = sys.argv[ -1 ]
+error_log = sys.argv[-10]
+input_file = sys.argv[-9]
+scale_when_converting = sys.argv[-8] == 'yes'
+weighted_rgb_conversions = sys.argv[-7] == 'yes'
+noise_tolerance = int(sys.argv[-6])
+output_type = sys.argv[-5]
+exclude_edge_maxima = sys.argv[-4] == 'yes'
+light_background = 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 )
+input_image_plus = IJ.openImage(input_file)
 
 # Create a copy of the image.
 input_image_plus_copy = input_image_plus.duplicate()
 image_processor_copy = input_image_plus_copy.getProcessor()
 bit_depth = image_processor_copy.getBitDepth()
-analyzer = Analyzer( input_image_plus_copy )
+analyzer = Analyzer(input_image_plus_copy)
 
-try:
-    # Set the conversion options.
-    options = []
-    # The following 2 options are applicable only to RGB images.
-    if bit_depth == 24:
-        if scale_when_converting:
-            option.append( "scale" )
-        if weighted_rgb_conversions:
-            options.append( "weighted" )
-    # Perform conversion - must happen even if no options are set.
-    IJ.run( input_image_plus_copy, "Conversions...", "%s" % " ".join( options ) )
-    if output_type in [ 'List', 'Count' ]:
-        # W're  generating a tabular file for the output.
-        # Set the Find Maxima options.
-        options = [ 'noise=%d' % noise_tolerance ]
-        if output_type.find( '_' ) > 0:
-            output_type_str = 'output=[%s]' % output_type.replace( '_', ' ' )
-        else:
-            output_type_str = 'output=%s' % output_type
-        options.append( output_type_str )
-        if exclude_edge_maxima:
-            options.append( 'exclude' )
-        if light_background:
-            options.append( 'light' )
-        # Run the command.
-        IJ.run( input_image_plus_copy, "Find Maxima...", "%s" % " ".join( options ) )
-        results_table = analyzer.getResultsTable()
-        results_table.saveAs( tmp_output_path )
+# Set the conversion options.
+options = []
+# The following 2 options are applicable only to RGB images.
+if bit_depth == 24:
+    if scale_when_converting:
+        options.append("scale")
+    if weighted_rgb_conversions:
+        options.append("weighted")
+# Perform conversion - must happen even if no options are set.
+IJ.run(input_image_plus_copy, "Conversions...", "%s" % " ".join(options))
+if output_type in ['List', 'Count']:
+    # W're  generating a tabular file for the output.
+    # Set the Find Maxima options.
+    options = ['noise=%d' % noise_tolerance]
+    if output_type.find('_') > 0:
+        output_type_str = 'output=[%s]' % output_type.replace('_', ' ')
     else:
-        # Find the maxima of an image (does not find minima).
-        # LIMITATIONS: With output_type=Segmented_Particles
-        # (watershed segmentation), some segmentation lines
-        # may be improperly placed if local maxima are suppressed
-        # by the tolerance.
-        mf = MaximumFinder()
-        if output_type == 'Single_Points':
-            output_type_param = mf.SINGLE_POINTS
-        elif output_type == 'Maxima_Within_Tolerance':
-            output_type_param = mf.IN_TOLERANCE
-        elif output_type == 'Segmented_Particles':
-            output_type_param = mf.SEGMENTED
-        elif output_type == 'List':
-            output_type_param = mf.LIST
-        elif output_type == 'Count':
-            output_type_param = mf.COUNT
-        # Get a new byteProcessor with a normal (uninverted) LUT where
-        # the marked points are set to 255 (Background 0). Pixels outside
-        # of the roi of the input image_processor_copy are not set. No
-        # output image is created for output types POINT_SELECTION, LIST
-        # and COUNT.  In these cases findMaxima returns null.
-        byte_processor = mf.findMaxima( image_processor_copy,
-                                        noise_tolerance,
-                                        ImageProcessor.NO_THRESHOLD,
-                                        output_type_param,
-                                        exclude_edge_maxima,
-                                        False )
-        # Invert the image or ROI.
-        byte_processor.invert()
-        if output_type == 'Segmented_Particles' and not light_background:
-            # Invert the values in this image's LUT (indexed color model).
-            byte_processor.invertLut()
-        image_plus = ImagePlus( "output", byte_processor )
-        IJ.saveAs( image_plus, output_datatype, tmp_output_path )
-except Exception, e:
-    jython_utils.handle_error( error_log, str( e ) )
+        output_type_str = 'output=%s' % output_type
+    options.append(output_type_str)
+    if exclude_edge_maxima:
+        options.append('exclude')
+    if light_background:
+        options.append('light')
+    # Run the command.
+    IJ.run(input_image_plus_copy, "Find Maxima...", "%s" % " ".join(options))
+    results_table = analyzer.getResultsTable()
+    results_table.saveAs(tmp_output_path)
+else:
+    # Find the maxima of an image (does not find minima).
+    # LIMITATIONS: With output_type=Segmented_Particles
+    # (watershed segmentation), some segmentation lines
+    # may be improperly placed if local maxima are suppressed
+    # by the tolerance.
+    mf = MaximumFinder()
+    if output_type == 'Single_Points':
+        output_type_param = mf.SINGLE_POINTS
+    elif output_type == 'Maxima_Within_Tolerance':
+        output_type_param = mf.IN_TOLERANCE
+    elif output_type == 'Segmented_Particles':
+        output_type_param = mf.SEGMENTED
+    elif output_type == 'List':
+        output_type_param = mf.LIST
+    elif output_type == 'Count':
+        output_type_param = mf.COUNT
+    # Get a new byteProcessor with a normal (uninverted) LUT where
+    # the marked points are set to 255 (Background 0). Pixels outside
+    # of the roi of the input image_processor_copy are not set. No
+    # output image is created for output types POINT_SELECTION, LIST
+    # and COUNT.  In these cases findMaxima returns null.
+    byte_processor = mf.findMaxima(image_processor_copy,
+                                   noise_tolerance,
+                                   ImageProcessor.NO_THRESHOLD,
+                                   output_type_param,
+                                   exclude_edge_maxima,
+                                   False)
+    # Invert the image or ROI.
+    byte_processor.invert()
+    if output_type == 'Segmented_Particles' and not light_background:
+        # Invert the values in this image's LUT (indexed color model).
+        byte_processor.invertLut()
+    image_plus = ImagePlus("output", byte_processor)
+    IJ.saveAs(image_plus, output_datatype, tmp_output_path)
--- a/imagej2_macros.xml	Tue Sep 17 16:57:15 2019 -0400
+++ b/imagej2_macros.xml	Mon Sep 28 17:01:19 2020 +0000
@@ -1,9 +1,9 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <macros>
     <token name="@WRAPPER_VERSION@">3.0</token>
     <xml name="fiji_requirements">
         <requirements>
             <requirement type="package" version="20170530">fiji</requirement>
+            <requirement type="package" version="3.4">grep</requirement>
         </requirements>
     </xml>
     <xml name="stdio">
@@ -16,7 +16,7 @@
     </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_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>
@@ -38,20 +38,45 @@
         <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="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="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="no" selected="true">No</option>
             <option value="yes">Yes</option>
         </param>
     </xml>
+    <xml name="param_input">
+        <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/>
+    </xml>
+    <xml name="param_source_image">
+        <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="source_image" type="data" label="Source image"/>
+    </xml>
+    <xml name="param_source_mask">
+        <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="source_mask" type="data" label="Source mask"/>
+    </xml>
+    <xml name="param_target_image">
+        <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="target_image" type="data" label="Target image"/>
+    </xml>
+    <xml name="param_target_mask">
+        <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="target_mask" type="data" label="Target mask"/>
+    </xml>
+    <xml name="test_bunwarpj_raw_transform">
+        <param name="target_image" value="dotblot.jpg"/>
+        <param name="source_image" value="blobs.gif"/>
+        <param name="target_raw_transformation" value="target_raw_transformation.txt"/>
+        <param name="source_raw_transformation" value="source_raw_transformation.txt"/>
+    </xml>
+    <xml name="test_target_source_images">
+        <param name="target_image" value="dotblot.jpg"/>
+        <param name="source_image" value="blobs.gif"/>
+    </xml>
     <token name="@make_binary_args@">
         --iterations $iterations
         --count $count
--- a/imagej2_make_binary.py	Tue Sep 17 16:57:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,59 +0,0 @@
-#!/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( '--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 )
-# 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 += ' %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 )
--- a/imagej2_make_binary_jython_script.py	Tue Sep 17 16:57:15 2019 -0400
+++ b/imagej2_make_binary_jython_script.py	Mon Sep 28 17:01:19 2020 +0000
@@ -1,37 +1,36 @@
-import jython_utils
 import sys
+
 from ij import IJ
 
 # Fiji Jython interpreter implements Python 2.5 which does not
 # provide support for argparse.
-error_log = sys.argv[ -8 ]
-input = sys.argv[ -7 ]
-iterations = int( sys.argv[ -6 ] )
-count = int( sys.argv[ -5 ] )
-black_background = jython_utils.asbool( sys.argv[ -4 ] )
-pad_edges_when_eroding = jython_utils.asbool( sys.argv[ -3 ] )
-tmp_output_path = sys.argv[ -2 ]
-output_datatype = sys.argv[ -1 ]
+error_log = sys.argv[-8]
+input = sys.argv[-7]
+iterations = int(sys.argv[-6])
+count = int(sys.argv[-5])
+black_background = sys.argv[-4] == 'yes'
+pad_edges_when_eroding = sys.argv[-3] == 'yes'
+tmp_output_path = sys.argv[-2]
+output_datatype = sys.argv[-1]
 
 # Open the input image file.
-input_image_plus = IJ.openImage( input )
+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()
 
-try:
-    # Set binary options.
-    options = jython_utils.get_binary_options( black_background=black_background,
-                                               iterations=iterations,
-                                               count=count,
-                                               pad_edges_when_eroding=pad_edges_when_eroding )
-    IJ.run( input_image_plus_copy, "Options...", options )
+# Set binary options.
+options = ['edm=Overwrite', 'iterations=%d' % iterations, 'count=%d' % count]
+if pad_edges_when_eroding:
+    options.append('pad')
+if black_background:
+    options.append('black')
+options = ' '.join(options)
+IJ.run(input_image_plus_copy, "Options...", options)
 
-    # Run the command.
-    IJ.run( input_image_plus_copy, "Make Binary", "" )
+# Run the command.
+IJ.run(input_image_plus_copy, "Make Binary", "")
 
-    # 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 ) )
+# Save the ImagePlus object as a new image.
+IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path)
--- a/imagej2_math.py	Tue Sep 17 16:57:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,69 +0,0 @@
-#!/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( '--operation', dest='operation', help='Operation' )
-parser.add_argument( '--expression', dest='expression', default=None, help='Expression' )
-parser.add_argument( '--bin_constant', dest='bin_constant', type=int, default=None, help='Constant of type binary integer' )
-parser.add_argument( '--float_constant', dest='float_constant', type=float, default=None, help='Constant of type float' )
-parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' )
-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 )
-
-# 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.operation
-# Handle the expression, which must be enclosed in " if not None.
-if args.expression in [ None, 'None' ]:
-    cmd += ' None'
-else:
-    cmd += ' "%s"' % args.expression
-cmd += imagej2_base_utils.handle_none_type( args.bin_constant, val_type='int' )
-cmd += imagej2_base_utils.handle_none_type( args.float_constant )
-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 )
--- a/imagej2_math_jython_script.py	Tue Sep 17 16:57:15 2019 -0400
+++ b/imagej2_math_jython_script.py	Mon Sep 28 17:01:19 2020 +0000
@@ -1,78 +1,84 @@
-import jython_utils
 import sys
+
 from ij import IJ
 
 # Fiji Jython interpreter implements Python 2.5 which does not
 # provide support for argparse.
-error_log = sys.argv[ -8 ]
-input = sys.argv[ -7 ]
-operation = sys.argv[ -6 ]
-expression = sys.argv[ -5 ]
-if sys.argv[ -4 ] in [ None, 'None' ]:
+error_log = sys.argv[-8]
+input_file = sys.argv[-7]
+operation = sys.argv[-6]
+expression = sys.argv[-5]
+if sys.argv[-4] in [None, 'None']:
     bin_constant = None
 else:
-    bin_constant = int( sys.argv[ -4 ] )
-if sys.argv[ -3 ] in [ None, 'None' ]:
+    bin_constant = int(sys.argv[-4])
+if sys.argv[-3] in [None, 'None']:
     float_constant = None
 else:
-    float_constant = float( sys.argv[ -3 ] )
-tmp_output_path = sys.argv[ -2 ]
-output_datatype = sys.argv[ -1 ]
+    float_constant = float(sys.argv[-3])
+tmp_output_path = sys.argv[-2]
+output_datatype = sys.argv[-1]
+
+print("\nerror_log: %s\n" % str(error_log))
+print("\ninput_file: %s\n" % str(input_file))
+print("\noperation: %s\n" % str(operation))
+print("\nexpression: %s\n" % str(expression))
+print("\nbin_constant: %s\n" % str(bin_constant))
+print("\nfloat_constant: %s\n" % str(float_constant))
+print("\ntmp_output_path: %s\n" % str(tmp_output_path))
+print("\noutput_datatype: %s\n" % str(output_datatype))
 
 # Open the input image file.
-input_image_plus = IJ.openImage( input )
+input_image_plus = IJ.openImage(input_file)
 
 # Create a copy of the image.
 input_image_plus_copy = input_image_plus.duplicate()
 image_processor_copy = input_image_plus_copy.getProcessor()
 bit_depth = image_processor_copy.getBitDepth()
 
-try:
-    if operation.find( '_' ) > 0:
-        # Square_Root.
-        new_operation = operation.replace( '_', ' ' )
-    elif operation in [ 'Square', 'Log', 'Exp', 'Abs', 'Reciprocal' ]:
-        # Unfortunately some ImageJ commands require a "..." ending
-        # while others do not.  There seems to be no pattern.
-        new_operation = '%s' % operation
-    else:
-        new_operation = '%s...' % operation
+if operation.find('_') > 0:
+    # Square_Root.
+    new_operation = operation.replace('_', ' ')
+elif operation in ['Square', 'Log', 'Exp', 'Abs', 'Reciprocal']:
+    # Unfortunately some ImageJ commands require a "..." ending
+    # while others do not.  There seems to be no pattern.
+    new_operation = '%s' % operation
+else:
+    new_operation = '%s...' % operation
 
-    if operation == 'Macro':
-        # Apply the macro code to the image via a call to it's
-        # ImageProcessor since this option does not work using
-        # the IJ.run() method.
-        new_expression = expression.lstrip( '"' ).rstrip( '"' )
-        options = 'code=%s' % new_expression
-        image_processor_copy.applyMacro( new_expression )
-    elif operation == 'Min':
-        # Min does not work without using the ImageProcessor.
-        image_processor_copy.min( float_constant )
-    elif operation == 'Max':
-        # Max does not work without using the ImageProcessor.
-        image_processor_copy.max( float_constant )
-    elif operation == 'Abs':
-        if bit_depth not in [ 16, 32 ]:
-            # Convert the image to 32-bit.
-            IJ.run( input_image_plus_copy, "32-bit", "" )
-            IJ.run( input_image_plus_copy, new_operation, "" )
-    elif operation == 'Reciprocal':
-        if bit_depth != 32:
-            # Convert the image to 32 bit.
-            IJ.run( input_image_plus_copy, "32-bit", "" )
-            IJ.run( input_image_plus_copy, new_operation, "" )
+if operation == 'Macro':
+    # Apply the macro code to the image via a call to it's
+    # ImageProcessor since this option does not work using
+    # the IJ.run() method.
+    new_expression = expression.lstrip('"').rstrip('"')
+    options = 'code=%s' % new_expression
+    image_processor_copy.applyMacro(new_expression)
+elif operation == 'Min':
+    # Min does not work without using the ImageProcessor.
+    image_processor_copy.min(float_constant)
+elif operation == 'Max':
+    # Max does not work without using the ImageProcessor.
+    image_processor_copy.max(float_constant)
+elif operation == 'Abs':
+    if bit_depth not in [16, 32]:
+        # Convert the image to 32-bit.
+        IJ.run(input_image_plus_copy, "32-bit", "")
+        IJ.run(input_image_plus_copy, new_operation, "")
+elif operation == 'Reciprocal':
+    if bit_depth != 32:
+        # Convert the image to 32 bit.
+        IJ.run(input_image_plus_copy, "32-bit", "")
+        IJ.run(input_image_plus_copy, new_operation, "")
+else:
+    if operation in ['AND', 'OR', 'XOR']:
+        # Value is a binary number.
+        options = 'value=%d' % bin_constant
+    elif operation in ['Log', 'Exp', 'Square', 'Square_Root']:
+        # No constant value.
+        options = ''
     else:
-        if operation in [ 'AND', 'OR', 'XOR' ]:
-            # Value is a binary number.
-            options = 'value=%d' % bin_constant
-        elif operation in [ 'Log', 'Exp', 'Square', 'Square_Root' ]:
-            # No constant value.
-            options = ''
-        else:
-            # Value is a floating point number.
-            options = 'value=%.3f' % float_constant
-        IJ.run( input_image_plus_copy, "%s" % new_operation, "%s" % 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 ) )
+        # Value is a floating point number.
+        options = 'value=%.3f' % float_constant
+    IJ.run(input_image_plus_copy, "%s" % new_operation, "%s" % options)
+# Save the ImagePlus object as a new image.
+IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path)
--- a/imagej2_noise.py	Tue Sep 17 16:57:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,84 +0,0 @@
-#!/usr/bin/env python
-import argparse
-import os
-import shutil
-import subprocess
-import tempfile
-import imagej2_base_utils
-
-if __name__=="__main__":
-    # Parse Command Line.
-    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( '--noise', dest='noise', help='Specified noise to add to or remove from the image' )
-    parser.add_argument( '--standard_deviation', dest='standard_deviation', type=float, default=None, help='Standard deviation' )
-    parser.add_argument( '--radius', dest='radius', type=float, default=None, help='Radius' )
-    parser.add_argument( '--threshold', dest='threshold', type=float, default=None, help='Threshold' )
-    parser.add_argument( '--which_outliers', dest='which_outliers', default=None, help='Which outliers' )
-    parser.add_argument( '--randomj', dest='randomj', default=None, help='RandomJ' )
-    parser.add_argument( '--trials', dest='trials', type=float, default=None, help='Trials' )
-    parser.add_argument( '--probability', dest='probability', type=float, default=None, help='Probability' )
-    parser.add_argument( '--lammbda', dest='lammbda', type=float, default=None, help='Lambda' )
-    parser.add_argument( '--order', dest='order', type=int, default=None, help='Order' )
-    parser.add_argument( '--mean', dest='mean', type=float, default=None, help='Mean' )
-    parser.add_argument( '--sigma', dest='sigma', type=float, default=None, help='Sigma' )
-    parser.add_argument( '--min', dest='min', type=float, default=None, help='Min' )
-    parser.add_argument( '--max', dest='max', type=float, default=None, help='Max' )
-    parser.add_argument( '--insertion', dest='insertion', default=None, help='Insertion' )
-    parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' )
-    parser.add_argument( '--output', dest='output', help='Path to the output file' )
-    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.input_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.input_datatype
-    cmd += ' %s ' % args.noise
-    cmd += imagej2_base_utils.handle_none_type( args.standard_deviation )
-    cmd += imagej2_base_utils.handle_none_type( args.radius )
-    cmd += imagej2_base_utils.handle_none_type( args.threshold )
-    cmd += ' %s' % args.which_outliers
-    cmd += ' %s' % args.randomj
-    cmd += imagej2_base_utils.handle_none_type( args.trials )
-    cmd += imagej2_base_utils.handle_none_type( args.probability )
-    cmd += imagej2_base_utils.handle_none_type( args.lammbda )
-    cmd += imagej2_base_utils.handle_none_type( args.order, val_type='int' )
-    cmd += imagej2_base_utils.handle_none_type( args.mean )
-    cmd += imagej2_base_utils.handle_none_type( args.sigma )
-    cmd += imagej2_base_utils.handle_none_type( args.min )
-    cmd += imagej2_base_utils.handle_none_type( args.max )
-    cmd += ' %s' % args.insertion
-    cmd += ' %s' % tmp_output_path
-
-    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 )
--- a/imagej2_noise_jython_script.py	Tue Sep 17 16:57:15 2019 -0400
+++ b/imagej2_noise_jython_script.py	Mon Sep 28 17:01:19 2020 +0000
@@ -1,35 +1,32 @@
 import sys
+
 from ij import IJ
-from ij import ImagePlus
-import jython_utils
 
 # Fiji Jython interpreter implements Python 2.5 which does not
 # provide support for argparse.
-error_log = sys.argv[ -19 ]
-input = sys.argv[ -18 ]
-image_datatype = sys.argv[ -17 ]
-noise = sys.argv[ -16 ]
-standard_deviation = sys.argv[ -15 ]
-radius = sys.argv[ -14 ]
-threshold = sys.argv[ -13 ]
-which_outliers = sys.argv[ -12 ]
-randomj = sys.argv[ -11 ]
-trials = sys.argv[ -10 ]
-probability = sys.argv[ -9 ]
+error_log = sys.argv[-19]
+input_file = sys.argv[-18]
+image_datatype = sys.argv[-17]
+noise = sys.argv[-16]
+standard_deviation = sys.argv[-15]
+radius = sys.argv[-14]
+threshold = sys.argv[-13]
+which_outliers = sys.argv[-12]
+randomj = sys.argv[-11]
+trials = sys.argv[-10]
+probability = sys.argv[-9]
 # Note the spelling - so things don't get confused due to Python lambda function.
-lammbda = sys.argv[ -8 ]
-order = sys.argv[ -7 ]
-mean = sys.argv[ -6 ]
-sigma = sys.argv[ -5 ]
-min = sys.argv[ -4 ]
-max = sys.argv[ -3 ]
-insertion = sys.argv[ -2 ]
-tmp_output_path = sys.argv[ -1 ]
-
-error = False
+lammbda = sys.argv[-8]
+order = sys.argv[-7]
+mean = sys.argv[-6]
+sigma = sys.argv[-5]
+min = sys.argv[-4]
+max = sys.argv[-3]
+insertion = sys.argv[-2]
+tmp_output_path = sys.argv[-1]
 
 # Open the input image file.
-image_plus = IJ.openImage( input )
+image_plus = IJ.openImage(input_file)
 bit_depth = image_plus.getBitDepth()
 image_type = image_plus.getType()
 # Create an ImagePlus object for the image.
@@ -39,46 +36,32 @@
 
 # Perform the analysis on the ImagePlus object.
 if noise == 'add_noise':
-    IJ.run( image_plus_copy, "Add Noise", "" )
+    IJ.run(image_plus_copy, "Add Noise", "")
 elif noise == 'add_specified_noise':
-    IJ.run( image_plus_copy, "Add Specified Noise", "standard=&standard_deviation" )
+    IJ.run(image_plus_copy, "Add Specified Noise", "standard=&standard_deviation")
 elif noise == 'salt_and_pepper':
-    IJ.run( image_plus_copy, "Salt and Pepper", "" )
+    IJ.run(image_plus_copy, "Salt and Pepper", "")
 elif noise == 'despeckle':
-    IJ.run( image_plus_copy, "Despeckle", "" )
+    IJ.run(image_plus_copy, "Despeckle", "")
 elif noise == 'remove_outliers':
-    IJ.run( image_plus_copy, "Remove Outliers", "radius=&radius threshold=&threshold which=&which_outliers" )
+    IJ.run(image_plus_copy, "Remove Outliers", "radius=&radius threshold=&threshold which=&which_outliers")
 elif noise == 'remove_nans':
-    if bit_depth == 32:
-        IJ.run( image_plus_copy, "Remove NaNs", "" )
-    else:
-        # When Galaxy metadata for images is enhanced to include information like this,
-        # we'll be able to write tool validators rather than having to stop the job in
-        # an error state.
-        msg = "Remove NaNs requires a 32-bit image, the selected image is %d-bit" % bit_depth
-        jython_utils.handle_error( error_log, msg )
-        error = True
+    IJ.run(image_plus_copy, "Remove NaNs", "")
 elif noise == 'rof_denoise':
-    if image_type == ImagePlus.GRAY32:
-        IJ.run( image_plus_copy, "ROF Denoise", "" )
-    else:
-        msg = "ROF Denoise requires an image of type 32-bit grayscale, the selected image is %d-bit" % ( bit_depth )
-        jython_utils.handle_error( error_log, msg )
-        error = True
+    IJ.run(image_plus_copy, "ROF Denoise", "")
 elif noise == 'randomj':
     if randomj == 'randomj_binomial':
-        IJ.run( image_plus_copy, "RandomJ Binomial", "trials=&trials probability=&probability insertion=&insertion" )
+        IJ.run(image_plus_copy, "RandomJ Binomial", "trials=&trials probability=&probability insertion=&insertion")
     elif randomj == 'randomj_exponential':
-        IJ.run( image_plus_copy, "RandomJ Exponential", "lambda=&lammbda insertion=&insertion" )
+        IJ.run(image_plus_copy, "RandomJ Exponential", "lambda=&lammbda insertion=&insertion")
     elif randomj == 'randomj_gamma':
-        IJ.run( image_plus_copy, "RandomJ Gamma", "order=&order insertion=&insertion" )
+        IJ.run(image_plus_copy, "RandomJ Gamma", "order=&order insertion=&insertion")
     elif randomj == 'randomj_gaussian':
-        IJ.run( image_plus_copy, "RandomJ Gaussian", "mean=&mean sigma=&sigma insertion=&insertion" )
+        IJ.run(image_plus_copy, "RandomJ Gaussian", "mean=&mean sigma=&sigma insertion=&insertion")
     elif randomj == 'randomj_poisson':
-        IJ.run( image_plus_copy, "RandomJ Poisson", "mean=&mean insertion=&insertion" )
+        IJ.run(image_plus_copy, "RandomJ Poisson", "mean=&mean insertion=&insertion")
     elif randomj == 'randomj_uniform':
-        IJ.run( image_plus_copy, "RandomJ Uniform", "min=&min max=&max insertion=&insertion" )
+        IJ.run(image_plus_copy, "RandomJ Uniform", "min=&min max=&max insertion=&insertion")
 
-if not error:
-    # Save the ImagePlus object as a new image.
-    IJ.saveAs( image_plus_copy, image_datatype, tmp_output_path )
+# Save the ImagePlus object as a new image.
+IJ.saveAs(image_plus_copy, image_datatype, tmp_output_path)
--- a/imagej2_shadows.py	Tue Sep 17 16:57:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,59 +0,0 @@
-#!/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( '--direction', dest='direction', help='Direction' )
-parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' )
-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 )
-
-# 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.direction
-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 )
--- a/imagej2_shadows_jython_script.py	Tue Sep 17 16:57:15 2019 -0400
+++ b/imagej2_shadows_jython_script.py	Mon Sep 28 17:01:19 2020 +0000
@@ -1,26 +1,23 @@
-import jython_utils
 import sys
+
 from ij import IJ
 
 # Fiji Jython interpreter implements Python 2.5 which does not
 # provide support for argparse.
-error_log = sys.argv[ -5 ]
-input = sys.argv[ -4 ]
-direction = sys.argv[ -3 ]
-tmp_output_path = sys.argv[ -2 ]
-output_datatype = sys.argv[ -1 ]
+error_log = sys.argv[-5]
+input_file = sys.argv[-4]
+direction = 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 )
+input_image_plus = IJ.openImage(input_file)
 
 # Create a copy of the image.
 input_image_plus_copy = input_image_plus.duplicate()
 image_processor_copy = input_image_plus_copy.getProcessor()
 
-try:
-    # Run the command.
-    IJ.run( input_image_plus_copy, direction, "" )
-    # 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 ) )
+# Run the command.
+IJ.run(input_image_plus_copy, direction, "")
+# Save the ImagePlus object as a new image.
+IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path)
--- a/imagej2_sharpen.py	Tue Sep 17 16:57:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,57 +0,0 @@
-#!/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( '--jython_script', dest='jython_script', help='Path to the Jython script' )
-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 )
-
-# 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' % 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 )
--- a/imagej2_sharpen_jython_script.py	Tue Sep 17 16:57:15 2019 -0400
+++ b/imagej2_sharpen_jython_script.py	Mon Sep 28 17:01:19 2020 +0000
@@ -1,25 +1,22 @@
-import jython_utils
 import sys
+
 from ij import IJ
 
 # Fiji Jython interpreter implements Python 2.5 which does not
 # provide support for argparse.
-error_log = sys.argv[ -4 ]
-input = sys.argv[ -3 ]
-tmp_output_path = sys.argv[ -2 ]
-output_datatype = sys.argv[ -1 ]
+error_log = sys.argv[-4]
+input_file = 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 )
+input_image_plus = IJ.openImage(input_file)
 
 # Create a copy of the image.
 input_image_plus_copy = input_image_plus.duplicate()
 image_processor_copy = input_image_plus_copy.getProcessor()
 
-try:
-    # Run the command.
-    IJ.run( input_image_plus_copy, "Sharpen", "" )
-    # 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 ) )
+# Run the command.
+IJ.run(input_image_plus_copy, "Sharpen", "")
+# Save the ImagePlus object as a new image.
+IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path)
--- a/imagej2_skeletonize3d.py	Tue Sep 17 16:57:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,53 +0,0 @@
-#!/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( '--jython_script', dest='jython_script', help='Path to the Jython script' )
-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 )
-# 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' % 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 )
--- a/imagej2_skeletonize3d.xml	Tue Sep 17 16:57:15 2019 -0400
+++ b/imagej2_skeletonize3d.xml	Mon Sep 28 17:01:19 2020 +0000
@@ -1,40 +1,47 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="imagej2_skeletonize3d" name="Skeletonize" version="@WRAPPER_VERSION@.0">
+<tool id="imagej2_skeletonize3d" name="Skeletonize" version="@WRAPPER_VERSION@.1">
     <description></description>
     <macros>
         <import>imagej2_macros.xml</import>
     </macros>
-    <expand macro="fiji_requirements" />
-    <command>
-<![CDATA[
-    python $__tool_directory__/imagej2_skeletonize3d.py
-    --input "$input"
-    --input_datatype $input.ext
-    --black_background $black_background
-    --jython_script $__tool_directory__/imagej2_skeletonize3d_jython_script.py
-    --output "$output"
-    --output_datatype $output.ext
-]]>
-    </command>
+    <expand macro="fiji_requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+#import os
+#set error_log = 'output_log.txt'
+touch '$error_log' &&
+#set input_sans_ext = $os.path.splitext($os.path.basename($input.file_name))[0]
+#set input_with_ext = '.'.join([input_sans_ext, $input.ext])
+ln -s '$input.file_name' '$input_with_ext' &&
+#set output_filename = '.'.join(['output', $input.ext])
+touch '$output_filename' &&
+ImageJ --ij2 --headless --debug
+--jython '$__tool_directory__/imagej2_skeletonize3d_jython_script.py'
+'$error_log'
+'$input_with_ext'
+'$black_background'
+'$output_filename'
+'$input.ext'
+&>'$error_log';
+if [[ $? -ne 0 ]]; then
+    cat '$error_log' >&2;
+else
+    mv '$output_filename' '$output';
+fi
+]]></command>
     <inputs>
-        <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select grayscale image"/>
-        <expand macro="black_background_param" />
+        <expand macro="param_input"/>
+        <expand macro="black_background_param"/>
     </inputs>
     <outputs>
         <data name="output" format_source="input" label="${tool.name} on ${on_string}"/>
     </outputs>
     <tests>
         <test>
-            <param name="input" value="blobs.gif" />
-            <param name="input_datatype" value="gif" />
-            <param name="output_datatype" value="gif" />
-            <output name="output" file="skeletonized_blobs.gif" compare="sim_size" />
+            <param name="input" value="blobs.gif"/>
+            <output name="output" file="skeletonized_blobs.gif" compare="sim_size"/>
         </test>
         <test>
-            <param name="input" value="clown.jpg" />
-            <param name="input_datatype" value="jpg" />
-            <param name="output_datatype" value="jpg" />
-            <output name="output" file="skeletonized_clown.jpg" compare="sim_size" />
+            <param name="input" value="clown.jpg"/>
+            <output name="output" file="skeletonized_clown.jpg" compare="sim_size"/>
         </test>
     </tests>
     <help>
--- a/imagej2_skeletonize3d_jython_script.py	Tue Sep 17 16:57:15 2019 -0400
+++ b/imagej2_skeletonize3d_jython_script.py	Mon Sep 28 17:01:19 2020 +0000
@@ -1,36 +1,36 @@
-import jython_utils
 import sys
+
 from ij import IJ
 
 # Fiji Jython interpreter implements Python 2.5 which does not
 # provide support for argparse.
-error_log = sys.argv[ -5 ]
-input = sys.argv[ -4 ]
-black_background = jython_utils.asbool( sys.argv[ -3 ] )
-tmp_output_path = sys.argv[ -2 ]
-output_datatype = sys.argv[ -1 ]
+error_log = sys.argv[-5]
+input_file = sys.argv[-4]
+black_background = sys.argv[-3] == 'yes'
+tmp_output_path = sys.argv[-2]
+output_datatype = sys.argv[-1]
 
 # Open the input image file.
-input_image_plus = IJ.openImage( input )
+input_image_plus = IJ.openImage(input_file)
 
 # Create a copy of the image.
 input_image_plus_copy = input_image_plus.duplicate()
 image_processor_copy = input_image_plus_copy.getProcessor()
 
-try:
-    # Set binary options.
-    options = jython_utils.get_binary_options( black_background=black_background )
-    IJ.run( input_image_plus_copy, "Options...", options )
+# Set binary options.
+options = ['edm=Overwrite', 'iterations=1', 'count=1']
+if (black_background):
+    options.append('black')
+options = " ".join(options)
+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", "" )
+# 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", "")
 
-    # Run the command.
-    IJ.run( input_image_plus_copy, "Skeletonize (2D/3D)", "" )
+# Run the command.
+IJ.run(input_image_plus_copy, "Skeletonize (2D/3D)", "")
 
-    # 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 ) )
+# Save the ImagePlus object as a new image.
+IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path)
--- a/imagej2_smooth.py	Tue Sep 17 16:57:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,57 +0,0 @@
-#!/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( '--jython_script', dest='jython_script', help='Path to the Jython script' )
-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 )
-
-# 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' % 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 )
--- a/imagej2_smooth_jython_script.py	Tue Sep 17 16:57:15 2019 -0400
+++ b/imagej2_smooth_jython_script.py	Mon Sep 28 17:01:19 2020 +0000
@@ -1,25 +1,22 @@
-import jython_utils
 import sys
+
 from ij import IJ
 
 # Fiji Jython interpreter implements Python 2.5 which does not
 # provide support for argparse.
-error_log = sys.argv[ -4 ]
-input = sys.argv[ -3 ]
-tmp_output_path = sys.argv[ -2 ]
-output_datatype = sys.argv[ -1 ]
+error_log = sys.argv[-4]
+input = 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 )
+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()
 
-try:
-    # Run the command.
-    IJ.run( input_image_plus_copy, "Smooth", "" )
-    # 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 ) )
+# Run the command.
+IJ.run(input_image_plus_copy, "Smooth", "")
+# Save the ImagePlus object as a new image.
+IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path)
--- a/imagej2_watershed_binary.py	Tue Sep 17 16:57:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,53 +0,0 @@
-#!/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( '--jython_script', dest='jython_script', help='Path to the Jython script' )
-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 )
-# 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' % 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 )
--- a/imagej2_watershed_binary_jython_script.py	Tue Sep 17 16:57:15 2019 -0400
+++ b/imagej2_watershed_binary_jython_script.py	Mon Sep 28 17:01:19 2020 +0000
@@ -1,36 +1,36 @@
-import jython_utils
 import sys
+
 from ij import IJ
 
 # Fiji Jython interpreter implements Python 2.5 which does not
 # provide support for argparse.
-error_log = sys.argv[ -5 ]
-input = sys.argv[ -4 ]
-black_background = jython_utils.asbool( sys.argv[ -3 ] )
-tmp_output_path = sys.argv[ -2 ]
-output_datatype = sys.argv[ -1 ]
+error_log = sys.argv[-5]
+input = sys.argv[-4]
+black_background = sys.argv[-3] == 'yes'
+tmp_output_path = sys.argv[-2]
+output_datatype = sys.argv[-1]
 
 # Open the input image file.
-input_image_plus = IJ.openImage( input )
+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()
 
-try:
-    # Set binary options.
-    options = jython_utils.get_binary_options( black_background=black_background )
-    IJ.run( input_image_plus_copy, "Options...", options )
+# Set binary options.
+options = ['edm=Overwrite', 'iterations=1', 'count=1']
+if (black_background):
+    options.append('black')
+options = " ".join(options)
+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", "" )
+# 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", "")
 
-    # Run the command.
-    IJ.run( input_image_plus_copy, "Watershed", "" )
+# Run the command.
+IJ.run(input_image_plus_copy, "Watershed", "")
 
-    # 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 ) )
+# Save the ImagePlus object as a new image.
+IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path)
--- a/jython_utils.py	Tue Sep 17 16:57:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,48 +0,0 @@
-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()
Binary file test-data/analyze_particles_masks.gif has changed
--- a/test-data/analyze_particles_nothing.tabular	Tue Sep 17 16:57:15 2019 -0400
+++ b/test-data/analyze_particles_nothing.tabular	Mon Sep 28 17:01:19 2020 +0000
@@ -29,38 +29,36 @@
 28	55	255	255	255
 29	116	255	255	255
 30	172	255	255	255
-31	103	255	255	255
+31	191	255	255	255
 32	4	255	255	255
 33	60	255	255	255
 34	198	255	255	255
 35	187	255	255	255
 36	7	255	255	255
 37	85	255	255	255
-38	80	255	255	255
-39	75	255	255	255
-40	103	255	255	255
-41	151	255	255	255
-42	52	255	255	255
-43	122	255	255	255
-44	129	255	255	255
-45	77	255	255	255
-46	171	255	255	255
-47	117	255	255	255
-48	207	255	255	255
-49	119	255	255	255
-50	181	255	255	255
-51	22	255	255	255
-52	49	255	255	255
-53	150	255	255	255
-54	191	255	255	255
-55	170	255	255	255
-56	64	255	255	255
-57	174	255	255	255
-58	270	255	255	255
-59	87	255	255	255
-60	69	255	255	255
-61	1	255	255	255
-62	29	255	255	255
-63	25	255	255	255
-64	16	255	255	255
-65	15	255	255	255
+38	75	255	255	255
+39	283	255	255	255
+40	151	255	255	255
+41	52	255	255	255
+42	122	255	255	255
+43	129	255	255	255
+44	77	255	255	255
+45	117	255	255	255
+46	207	255	255	255
+47	119	255	255	255
+48	181	255	255	255
+49	22	255	255	255
+50	49	255	255	255
+51	150	255	255	255
+52	191	255	255	255
+53	170	255	255	255
+54	64	255	255	255
+55	174	255	255	255
+56	270	255	255	255
+57	87	255	255	255
+58	69	255	255	255
+59	1	255	255	255
+60	29	255	255	255
+61	25	255	255	255
+62	16	255	255	255
+63	15	255	255	255
Binary file test-data/analyze_particles_outlines.gif has changed
--- a/test-data/basic.tabular	Tue Sep 17 16:57:15 2019 -0400
+++ b/test-data/basic.tabular	Mon Sep 28 17:01:19 2020 +0000
@@ -1,2 +1,64 @@
 # Branches	Junctions	End-point Voxels	Junction Voxels	Slab Voxels	Average branch length	Triple Points	Quadruple Points	Maximum Branch Length
-96	60	7	120	1246	17.344	56	3	70.882
+1	0	2	0	5	6.000	0	0	6.000
+1	0	2	0	3	4.000	0	0	4.000
+0	0	1	0	0	0.000	0	0	0.000
+1	0	2	0	2	3.000	0	0	3.000
+0	0	1	0	0	0.000	0	0	0.000
+1	0	2	0	1	2.414	0	0	2.414
+1	0	2	0	6	8.243	0	0	8.243
+1	0	2	0	7	9.243	0	0	9.243
+1	0	2	0	0	1.414	0	0	1.414
+0	0	1	0	0	0.000	0	0	0.000
+0	0	1	0	0	0.000	0	0	0.000
+1	0	2	0	1	2.000	0	0	2.000
+0	0	1	0	0	0.000	0	0	0.000
+1	0	2	0	0	1.000	0	0	1.000
+1	0	2	0	3	4.414	0	0	4.414
+0	0	1	0	0	0.000	0	0	0.000
+1	0	2	0	3	4.414	0	0	4.414
+1	0	2	0	0	1.000	0	0	1.000
+0	0	1	0	0	0.000	0	0	0.000
+1	0	2	0	8	9.000	0	0	9.000
+1	0	2	0	1	2.828	0	0	2.828
+0	0	1	0	0	0.000	0	0	0.000
+1	0	2	0	0	1.000	0	0	1.000
+1	0	2	0	15	17.243	0	0	17.243
+1	0	2	0	2	3.828	0	0	3.828
+1	0	2	0	2	3.828	0	0	3.828
+1	0	2	0	0	1.000	0	0	1.000
+0	0	1	0	0	0.000	0	0	0.000
+1	0	2	0	11	14.485	0	0	14.485
+1	0	2	0	9	10.828	0	0	10.828
+1	0	2	0	8	9.828	0	0	9.828
+1	0	2	0	0	1.000	0	0	1.000
+1	0	2	0	2	4.243	0	0	4.243
+0	0	1	0	0	0.000	0	0	0.000
+1	0	2	0	0	1.414	0	0	1.414
+1	0	2	0	1	2.000	0	0	2.000
+1	0	2	0	0	1.000	0	0	1.000
+1	0	2	0	7	10.071	0	0	10.071
+1	0	2	0	7	8.414	0	0	8.414
+0	0	1	0	0	0.000	0	0	0.000
+1	0	2	0	6	7.414	0	0	7.414
+0	0	1	0	0	0.000	0	0	0.000
+1	0	2	0	4	5.414	0	0	5.414
+1	0	2	0	0	1.000	0	0	1.000
+0	0	1	0	0	0.000	0	0	0.000
+1	0	2	0	8	11.071	0	0	11.071
+0	0	1	0	0	0.000	0	0	0.000
+1	0	2	0	0	1.414	0	0	1.414
+1	0	2	0	0	1.414	0	0	1.414
+1	0	2	0	0	1.000	0	0	1.000
+1	0	2	0	3	4.828	0	0	4.828
+0	0	1	0	0	0.000	0	0	0.000
+1	0	2	0	0	1.000	0	0	1.000
+1	0	2	0	4	5.828	0	0	5.828
+1	0	2	0	0	1.414	0	0	1.414
+0	0	1	0	0	0.000	0	0	0.000
+1	0	2	0	0	1.000	0	0	1.000
+1	0	2	0	5	7.243	0	0	7.243
+1	0	2	0	0	1.414	0	0	1.414
+1	0	2	0	4	5.000	0	0	5.000
+1	0	2	0	2	3.000	0	0	3.000
+1	0	2	0	1	2.000	0	0	2.000
+1	0	2	0	3	4.000	0	0	4.000
Binary file test-data/blobs_black_edm.gif has changed
Binary file test-data/blobs_edm.gif has changed
Binary file test-data/blobs_equalize.gif has changed
Binary file test-data/blobs_find_edges.gif has changed
Binary file test-data/blobs_log.gif has changed
Binary file test-data/blobs_min.gif has changed
Binary file test-data/blobs_multiply.gif has changed
Binary file test-data/blobs_normalize.gif has changed
Binary file test-data/blobs_northwest.gif has changed
Binary file test-data/blobs_saturate.gif has changed
Binary file test-data/blobs_segmented.gif has changed
Binary file test-data/blobs_single_points.gif has changed
Binary file test-data/blobs_square.gif has changed
Binary file test-data/blobs_tolerance.gif has changed
Binary file test-data/blobs_watershed_binary.gif has changed
Binary file test-data/elastic_trans_registered_source1.png has changed
--- a/test-data/largest_shortest_path_basic.tabular	Tue Sep 17 16:57:15 2019 -0400
+++ b/test-data/largest_shortest_path_basic.tabular	Mon Sep 28 17:01:19 2020 +0000
@@ -1,2 +1,64 @@
 # Branches	Junctions	End-point Voxels	Junction Voxels	Slab Voxels	Average branch length	Triple Points	Quadruple Points	Maximum Branch Length	Longest Shortest Path	spx	spy	spz
-96	60	7	120	1246	17.344	56	3	70.882	207.380	135	137	0
+1	0	2	0	5	6.000	0	0	6.000	6.000	0	18	0
+1	0	2	0	3	4.000	0	0	4.000	4.000	2	130	0
+0	0	1	0	0	0.000	0	0	0.000	0.000	4	25	0
+1	0	2	0	2	3.000	0	0	3.000	3.000	4	56	0
+0	0	1	0	0	0.000	0	0	0.000	0.000	4	79	0
+1	0	2	0	1	2.414	0	0	2.414	2.414	9	94	0
+1	0	2	0	6	8.243	0	0	8.243	8.243	12	4	0
+1	0	2	0	7	9.243	0	0	9.243	9.243	16	126	0
+1	0	2	0	0	1.414	0	0	1.414	1.414	16	32	0
+0	0	1	0	0	0.000	0	0	0.000	0.000	19	49	0
+0	0	1	0	0	0.000	0	0	0.000	0.000	20	69	0
+1	0	2	0	1	2.000	0	0	2.000	2.000	24	98	0
+0	0	1	0	0	0.000	0	0	0.000	0.000	25	14	0
+1	0	2	0	0	1.000	0	0	1.000	1.000	25	137	0
+1	0	2	0	3	4.414	0	0	4.414	4.414	38	2	0
+0	0	1	0	0	0.000	0	0	0.000	0.000	34	69	0
+1	0	2	0	3	4.414	0	0	4.414	4.414	35	126	0
+1	0	2	0	0	1.000	0	0	1.000	1.000	36	47	0
+0	0	1	0	0	0.000	0	0	0.000	0.000	37	83	0
+1	0	2	0	8	9.000	0	0	9.000	9.000	46	143	0
+1	0	2	0	1	2.828	0	0	2.828	2.828	42	22	0
+0	0	1	0	0	0.000	0	0	0.000	0.000	43	137	0
+1	0	2	0	0	1.000	0	0	1.000	1.000	47	65	0
+1	0	2	0	15	17.243	0	0	17.243	17.243	51	83	0
+1	0	2	0	2	3.828	0	0	3.828	3.828	56	40	0
+1	0	2	0	2	3.828	0	0	3.828	3.828	59	122	0
+1	0	2	0	0	1.000	0	0	1.000	1.000	58	63	0
+0	0	1	0	0	0.000	0	0	0.000	0.000	60	6	0
+1	0	2	0	11	14.485	0	0	14.485	14.485	73	68	0
+1	0	2	0	9	10.828	0	0	10.828	10.828	77	143	0
+1	0	2	0	8	9.828	0	0	9.828	9.828	79	46	0
+1	0	2	0	0	1.000	0	0	1.000	1.000	73	112	0
+1	0	2	0	2	4.243	0	0	4.243	4.243	78	91	0
+0	0	1	0	0	0.000	0	0	0.000	0.000	77	12	0
+1	0	2	0	0	1.414	0	0	1.414	1.414	78	32	0
+1	0	2	0	1	2.000	0	0	2.000	2.000	77	134	0
+1	0	2	0	0	1.000	0	0	1.000	1.000	87	5	0
+1	0	2	0	7	10.071	0	0	10.071	10.071	95	78	0
+1	0	2	0	7	8.414	0	0	8.414	8.414	101	56	0
+0	0	1	0	0	0.000	0	0	0.000	0.000	94	41	0
+1	0	2	0	6	7.414	0	0	7.414	7.414	103	142	0
+0	0	1	0	0	0.000	0	0	0.000	0.000	98	18	0
+1	0	2	0	4	5.414	0	0	5.414	5.414	104	131	0
+1	0	2	0	0	1.000	0	0	1.000	1.000	101	103	0
+0	0	1	0	0	0.000	0	0	0.000	0.000	106	88	0
+1	0	2	0	8	11.071	0	0	11.071	11.071	112	28	0
+0	0	1	0	0	0.000	0	0	0.000	0.000	111	9	0
+1	0	2	0	0	1.414	0	0	1.414	1.414	116	115	0
+1	0	2	0	0	1.414	0	0	1.414	1.414	121	39	0
+1	0	2	0	0	1.000	0	0	1.000	1.000	120	95	0
+1	0	2	0	3	4.828	0	0	4.828	4.828	123	16	0
+0	0	1	0	0	0.000	0	0	0.000	0.000	125	54	0
+1	0	2	0	0	1.000	0	0	1.000	1.000	126	72	0
+1	0	2	0	4	5.828	0	0	5.828	5.828	134	143	0
+1	0	2	0	0	1.414	0	0	1.414	1.414	131	104	0
+0	0	1	0	0	0.000	0	0	0.000	0.000	131	26	0
+1	0	2	0	0	1.000	0	0	1.000	1.000	131	129	0
+1	0	2	0	5	7.243	0	0	7.243	7.243	140	84	0
+1	0	2	0	0	1.414	0	0	1.414	1.414	138	41	0
+1	0	2	0	4	5.000	0	0	5.000	5.000	139	10	0
+1	0	2	0	2	3.000	0	0	3.000	3.000	141	61	0
+1	0	2	0	1	2.000	0	0	2.000	2.000	143	71	0
+1	0	2	0	3	4.000	0	0	4.000	4.000	142	115	0
Binary file test-data/raw_trans_registered_source1.png has changed
Binary file test-data/registered_source1.png has changed
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Binary file test-data/registered_target1.png has changed
Binary file test-data/registered_target2.png has changed
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/source_elastic_transformation_out.txt	Mon Sep 28 17:01:19 2020 +0000
@@ -0,0 +1,5 @@
+Intervals=4
+
+X Coeffs -----------------------------------
+
+Y Coeffs -----------------------------------
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/target_elastic_transformation_out.txt	Mon Sep 28 17:01:19 2020 +0000
@@ -0,0 +1,5 @@
+Intervals=4
+
+X Coeffs -----------------------------------
+
+Y Coeffs -----------------------------------