Mercurial > repos > imgteam > imagej2_skeletonize3d
diff imagej2_watershed_binary_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_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)