Mercurial > repos > imgteam > imagej2_skeletonize3d
diff imagej2_binary_to_edm_jython_script.py @ 1:768825d9034a draft
"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 | 49b5288dcd8c |
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--- 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)