Mercurial > repos > imgteam > imagej2_math
view imagej2_binary_to_edm_jython_script.py @ 3:d426c25946d4 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
author | imgteam |
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date | Wed, 25 Sep 2024 16:11:17 +0000 |
parents | d7fbe9662213 |
children |
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import sys from ij import IJ # Fiji Jython interpreter implements Python 2.5 which does not # provide support for argparse. 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_file) # Create a copy of the image. input_image_plus_copy = input_image_plus.duplicate() image_processor_copy = input_image_plus_copy.getProcessor() # 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", "") # 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)