Mercurial > repos > iuc > imagej2_analyze_skeleton

comparison jython_script.py @ 1:dd8e4e000d2f draft

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planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
author iuc
date Tue, 04 Aug 2015 13:19:34 -0400
parents a989ca433027
children 9631aab7da53
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0:a989ca433027 1:dd8e4e000d2f
123 input_image_plus_copy.setProcessor( "iCopy", image_processor_copy ) 123 input_image_plus_copy.setProcessor( "iCopy", image_processor_copy )
124 124
125 try: 125 try:
126 if image_type not in VALID_IMAGE_TYPES: 126 if image_type not in VALID_IMAGE_TYPES:
127 # Convert the image to binary grayscale. 127 # Convert the image to binary grayscale.
128 IJ.run( input_image_plus_copy, "Make Binary","" ) 128 IJ.run( input_image_plus_copy, "Make Binary","iterations=1 count=1 edm=Overwrite do=Nothing" )
129 # Run AnalyzeSkeleton 129 # Run AnalyzeSkeleton
130 analyze_skeleton = AnalyzeSkeleton_() 130 analyze_skeleton = AnalyzeSkeleton_()
131 analyze_skeleton.setup( "", input_image_plus_copy ) 131 analyze_skeleton.setup( "", input_image_plus_copy )
132 if prune_cycle_method == 'none': 132 if prune_cycle_method == 'none':
133 prune_index = analyze_skeleton.NONE 133 prune_index = analyze_skeleton.NONE