Mercurial > repos > imgteam > imagej2_watershed_binary
diff imagej2_adjust_threshold_binary_jython_script.py @ 0:b143159845b4 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 17:02:55 -0400 |
parents | |
children | 5b154339fd90 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/imagej2_adjust_threshold_binary_jython_script.py Tue Sep 17 17:02:55 2019 -0400 @@ -0,0 +1,49 @@ +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[ -10 ] +input = sys.argv[ -9 ] +threshold_min = float( sys.argv[ -8 ] ) +threshold_max = float( sys.argv[ -7 ] ) +method = sys.argv[ -6 ] +display = sys.argv[ -5 ] +black_background = jython_utils.asbool( sys.argv[ -4 ] ) +# TODO: this is not being used. +stack_histogram = 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: + # 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","iterations=1 count=1 edm=Overwrite do=Nothing" ) + # Set the options. + if black_background: + method_str = "%s dark" % method + else: + method_str = method + IJ.setAutoThreshold( input_image_plus_copy, method_str ) + if display == "red": + display_mode = "Red" + elif display == "bw": + display_mode = "Black & White" + elif display == "over_under": + display_mode = "Over/Under" + IJ.setThreshold( input_image_plus_copy, threshold_min, threshold_max, display_mode ) + # Run the command. + IJ.run( input_image_plus_copy, "threshold", "" ) + # 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 ) )