Mercurial > repos > imgteam > imagej2_skeletonize3d
view imagej2_smooth_jython_script.py @ 2:49b5288dcd8c draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author | imgteam |
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date | Sun, 05 Nov 2023 14:26:52 +0000 |
parents | 768825d9034a |
children | 5f5b7185bc16 |
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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[-4] input = sys.argv[-3] 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() # Run the command. IJ.run(input_image_plus_copy, "Smooth", "") # Save the ImagePlus object as a new image. IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path)