Mercurial > repos > imgteam > imagej2_bunwarpj_compose_raw_elastic
view imagej2_make_binary_jython_script.py @ 3:bdc70b34153a 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 16:15:22 +0000 |
parents | 4deffc9540a3 |
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 = 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) # 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 = ["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", "") # Save the ImagePlus object as a new image. IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path)