Mercurial > repos > imgteam > imagej2_bunwarpj_compose_elastic
diff imagej2_make_binary_jython_script.py @ 0:6840ce593a91 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
author | imgteam |
---|---|
date | Tue, 17 Sep 2019 17:08:47 -0400 |
parents | |
children | 423400b3c47f |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/imagej2_make_binary_jython_script.py Tue Sep 17 17:08:47 2019 -0400 @@ -0,0 +1,37 @@ +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[ -8 ] +input = sys.argv[ -7 ] +iterations = int( sys.argv[ -6 ] ) +count = int( sys.argv[ -5 ] ) +black_background = jython_utils.asbool( sys.argv[ -4 ] ) +pad_edges_when_eroding = 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, + iterations=iterations, + count=count, + pad_edges_when_eroding=pad_edges_when_eroding ) + IJ.run( input_image_plus_copy, "Options...", options ) + + # Run the command. + IJ.run( input_image_plus_copy, "Make Binary", "" ) + + # 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 ) )