Mercurial > repos > imgteam > imagej2_analyze_skeleton
view imagej2_smooth_jython_script.py @ 1:3272e0439968 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 16:52:29 +0000 |
parents | bb84f130a4e1 |
children | 50f2b961b192 |
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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)