Mercurial > repos > imgteam > imagej2_analyze_particles_binary

comparison imagej2_make_binary_jython_script.py @ 1:1dd5396c734a draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
author imgteam
date Mon, 28 Sep 2020 16:59:30 +0000
parents aeb9bb864b8c
children ae4ae9c5c56c
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0:aeb9bb864b8c 1:1dd5396c734a
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 ) )