Mercurial > repos > imgteam > imagej2_enhance_contrast
view imagej2_binary_to_edm_jython_script.py @ 1:ef3de3e84817 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 16:58:37 +0000 |
parents | edfc597fb180 |
children | 056e74fbbf6c |
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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_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)