Mercurial > repos > imgteam > imagej2_bunwarpj_compare_elastic_raw
comparison imagej2_skeletonize3d_jython_script.py @ 0:1bffabc15695 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 16:55:25 -0400 |
parents | |
children | 2be338fc671e |
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-1:000000000000 | 0:1bffabc15695 |
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1 import jython_utils | |
2 import sys | |
3 from ij import IJ | |
4 | |
5 # Fiji Jython interpreter implements Python 2.5 which does not | |
6 # provide support for argparse. | |
7 error_log = sys.argv[ -5 ] | |
8 input = sys.argv[ -4 ] | |
9 black_background = jython_utils.asbool( sys.argv[ -3 ] ) | |
10 tmp_output_path = sys.argv[ -2 ] | |
11 output_datatype = sys.argv[ -1 ] | |
12 | |
13 # Open the input image file. | |
14 input_image_plus = IJ.openImage( input ) | |
15 | |
16 # Create a copy of the image. | |
17 input_image_plus_copy = input_image_plus.duplicate() | |
18 image_processor_copy = input_image_plus_copy.getProcessor() | |
19 | |
20 try: | |
21 # Set binary options. | |
22 options = jython_utils.get_binary_options( black_background=black_background ) | |
23 IJ.run( input_image_plus_copy, "Options...", options ) | |
24 | |
25 # Convert image to binary if necessary. | |
26 if not image_processor_copy.isBinary(): | |
27 # Convert the image to binary grayscale. | |
28 IJ.run( input_image_plus_copy, "Make Binary", "" ) | |
29 | |
30 # Run the command. | |
31 IJ.run( input_image_plus_copy, "Skeletonize (2D/3D)", "" ) | |
32 | |
33 # Save the ImagePlus object as a new image. | |
34 IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path ) | |
35 except Exception, e: | |
36 jython_utils.handle_error( error_log, str( e ) ) |