Mercurial > repos > imgteam > imagej2_make_binary
comparison imagej2_shadows_jython_script.py @ 0:baa308e2533a 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 17:07:31 -0400 |
parents | |
children | 6e8be21a505c |
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-1:000000000000 | 0:baa308e2533a |
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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 direction = 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 # Run the command. | |
22 IJ.run( input_image_plus_copy, direction, "" ) | |
23 # Save the ImagePlus object as a new image. | |
24 IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path ) | |
25 except Exception, e: | |
26 jython_utils.handle_error( error_log, str( e ) ) |