Mercurial > repos > imgteam > imagej2_bunwarpj_compose_raw_elastic
view imagej2_skeletonize3d_jython_script.py @ 1:8d357579e407 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 16:56:53 +0000 |
parents | 1bf7e70e67f9 |
children | 4deffc9540a3 |
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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[-5] input_file = 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_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 = ['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", "") # Run the command. IJ.run(input_image_plus_copy, "Skeletonize (2D/3D)", "") # Save the ImagePlus object as a new image. IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path)