Mercurial > repos > imgteam > imagej2_bunwarpj_adapt_transform
comparison imagej2_make_binary_jython_script.py @ 1:5d633d30316e draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
author | imgteam |
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date | Mon, 28 Sep 2020 16:57:45 +0000 |
parents | 706af1d7028a |
children | fa64e8aed5a5 |
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0:706af1d7028a | 1:5d633d30316e |
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1 import jython_utils | |
2 import sys | 1 import sys |
2 | |
3 from ij import IJ | 3 from ij import IJ |
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[ -8 ] | 7 error_log = sys.argv[-8] |
8 input = sys.argv[ -7 ] | 8 input = sys.argv[-7] |
9 iterations = int( sys.argv[ -6 ] ) | 9 iterations = int(sys.argv[-6]) |
10 count = int( sys.argv[ -5 ] ) | 10 count = int(sys.argv[-5]) |
11 black_background = jython_utils.asbool( sys.argv[ -4 ] ) | 11 black_background = sys.argv[-4] == 'yes' |
12 pad_edges_when_eroding = jython_utils.asbool( sys.argv[ -3 ] ) | 12 pad_edges_when_eroding = sys.argv[-3] == 'yes' |
13 tmp_output_path = sys.argv[ -2 ] | 13 tmp_output_path = sys.argv[-2] |
14 output_datatype = sys.argv[ -1 ] | 14 output_datatype = sys.argv[-1] |
15 | 15 |
16 # Open the input image file. | 16 # Open the input image file. |
17 input_image_plus = IJ.openImage( input ) | 17 input_image_plus = IJ.openImage(input) |
18 | 18 |
19 # Create a copy of the image. | 19 # Create a copy of the image. |
20 input_image_plus_copy = input_image_plus.duplicate() | 20 input_image_plus_copy = input_image_plus.duplicate() |
21 image_processor_copy = input_image_plus_copy.getProcessor() | 21 image_processor_copy = input_image_plus_copy.getProcessor() |
22 | 22 |
23 try: | 23 # Set binary options. |
24 # Set binary options. | 24 options = ['edm=Overwrite', 'iterations=%d' % iterations, 'count=%d' % count] |
25 options = jython_utils.get_binary_options( black_background=black_background, | 25 if pad_edges_when_eroding: |
26 iterations=iterations, | 26 options.append('pad') |
27 count=count, | 27 if black_background: |
28 pad_edges_when_eroding=pad_edges_when_eroding ) | 28 options.append('black') |
29 IJ.run( input_image_plus_copy, "Options...", options ) | 29 options = ' '.join(options) |
30 IJ.run(input_image_plus_copy, "Options...", options) | |
30 | 31 |
31 # Run the command. | 32 # Run the command. |
32 IJ.run( input_image_plus_copy, "Make Binary", "" ) | 33 IJ.run(input_image_plus_copy, "Make Binary", "") |
33 | 34 |
34 # Save the ImagePlus object as a new image. | 35 # Save the ImagePlus object as a new image. |
35 IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path ) | 36 IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path) |
36 except Exception, e: | |
37 jython_utils.handle_error( error_log, str( e ) ) |