Mercurial > repos > imgteam > imagej2_bunwarpj_compare_elastic_raw
diff imagej2_skeletonize3d_jython_script.py @ 0:1bffabc15695 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
author | imgteam |
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date | Tue, 17 Sep 2019 16:55:25 -0400 |
parents | |
children | 2be338fc671e |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/imagej2_skeletonize3d_jython_script.py Tue Sep 17 16:55:25 2019 -0400 @@ -0,0 +1,36 @@ +import jython_utils +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 = sys.argv[ -4 ] +black_background = jython_utils.asbool( 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() + +try: + # Set binary options. + options = jython_utils.get_binary_options( black_background=black_background ) + 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 ) +except Exception, e: + jython_utils.handle_error( error_log, str( e ) )