Mercurial > repos > imgteam > imagej2_watershed_binary

comparison imagej2_skeletonize3d_jython_script.py @ 2:aeae7e29d525 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author imgteam
date Sun, 05 Nov 2023 10:47:25 +0000
parents 5b154339fd90
children 29aca8eebdaa
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1:5b154339fd90 2:aeae7e29d525
4 4
5 # Fiji Jython interpreter implements Python 2.5 which does not 5 # Fiji Jython interpreter implements Python 2.5 which does not
6 # provide support for argparse. 6 # provide support for argparse.
7 error_log = sys.argv[-5] 7 error_log = sys.argv[-5]
8 input_file = sys.argv[-4] 8 input_file = sys.argv[-4]
9 black_background = sys.argv[-3] == 'yes' 9 black_background = sys.argv[-3] == "yes"
10 tmp_output_path = sys.argv[-2] 10 tmp_output_path = sys.argv[-2]
11 output_datatype = sys.argv[-1] 11 output_datatype = sys.argv[-1]
12 12
13 # Open the input image file. 13 # Open the input image file.
14 input_image_plus = IJ.openImage(input_file) 14 input_image_plus = IJ.openImage(input_file)
16 # Create a copy of the image. 16 # Create a copy of the image.
17 input_image_plus_copy = input_image_plus.duplicate() 17 input_image_plus_copy = input_image_plus.duplicate()
18 image_processor_copy = input_image_plus_copy.getProcessor() 18 image_processor_copy = input_image_plus_copy.getProcessor()
19 19
20 # Set binary options. 20 # Set binary options.
21 options = ['edm=Overwrite', 'iterations=1', 'count=1'] 21 options = ["edm=Overwrite", "iterations=1", "count=1"]
22 if (black_background): 22 if black_background:
23 options.append('black') 23 options.append("black")
24 options = " ".join(options) 24 options = " ".join(options)
25 IJ.run(input_image_plus_copy, "Options...", options) 25 IJ.run(input_image_plus_copy, "Options...", options)
26 26
27 # Convert image to binary if necessary. 27 # Convert image to binary if necessary.
28 if not image_processor_copy.isBinary(): 28 if not image_processor_copy.isBinary():