Mercurial > repos > imgteam > imagej2_analyze_particles_binary
diff imagej2_make_binary_jython_script.py @ 1:1dd5396c734a draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
author | imgteam |
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date | Mon, 28 Sep 2020 16:59:30 +0000 |
parents | aeb9bb864b8c |
children | ae4ae9c5c56c |
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--- a/imagej2_make_binary_jython_script.py Tue Sep 17 16:56:37 2019 -0400 +++ b/imagej2_make_binary_jython_script.py Mon Sep 28 16:59:30 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)