Mercurial > repos > imgteam > imagej2_bunwarpj_compose_raw_elastic
view imagej2_watershed_binary_jython_script.py @ 0:1bf7e70e67f9 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 16:56:02 -0400 |
parents | |
children | 8d357579e407 |
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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, "Watershed", "" ) # 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 ) )