Mercurial > repos > imgteam > imagej2_watershed_binary

comparison imagej2_binary_to_edm_jython_script.py @ 1:5b154339fd90 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 16:36:30 +0000
parents b143159845b4
children aeae7e29d525
comparison
equal deleted inserted replaced
0:b143159845b4 1:5b154339fd90
1 import jython_utils
2 import sys 1 import sys
2
3 from ij import IJ 3 from ij import IJ
4 from ij import ImagePlus
5 from ij.plugin.filter import Analyzer
6 from ij.plugin.filter import EDM
7 4
8 # Fiji Jython interpreter implements Python 2.5 which does not 5 # Fiji Jython interpreter implements Python 2.5 which does not
9 # provide support for argparse. 6 # provide support for argparse.
10 error_log = sys.argv[ -8 ] 7 error_log = sys.argv[-8]
11 input = sys.argv[ -7 ] 8 input_file = sys.argv[-7]
12 iterations = int( sys.argv[ -6 ] ) 9 iterations = int(sys.argv[-6])
13 count = int( sys.argv[ -5 ] ) 10 count = int(sys.argv[-5])
14 black_background = jython_utils.asbool( sys.argv[ -4 ] ) 11 black_background = sys.argv[-4] == "yes"
15 pad_edges_when_eroding = jython_utils.asbool( sys.argv[ -3 ] ) 12 pad_edges_when_eroding = sys.argv[-3] == "yes"
16 tmp_output_path = sys.argv[ -2 ] 13 output_filename = sys.argv[-2]
17 output_datatype = sys.argv[ -1 ] 14 output_datatype = sys.argv[-1]
18 15
19 # Open the input image file. 16 # Open the input image file.
20 input_image_plus = IJ.openImage( input ) 17 input_image_plus = IJ.openImage(input_file)
21 18
22 # Create a copy of the image. 19 # Create a copy of the image.
23 input_image_plus_copy = input_image_plus.duplicate() 20 input_image_plus_copy = input_image_plus.duplicate()
24 image_processor_copy = input_image_plus_copy.getProcessor() 21 image_processor_copy = input_image_plus_copy.getProcessor()
25 22
26 try: 23 # Set binary options.
27 # Set binary options. 24 options_list = ['edm=Overwrite', 'iterations=%d' % iterations, 'count=%d' % count]
28 options = jython_utils.get_binary_options( black_background=black_background, 25 if black_background:
29 iterations=iterations, 26 options_list.append("black")
30 count=count, 27 if pad_edges_when_eroding:
31 pad_edges_when_eroding=pad_edges_when_eroding ) 28 options_list.append("pad")
32 IJ.run( input_image_plus_copy, "Options...", options ) 29 options = " ".join(options_list)
30 IJ.run(input_image_plus_copy, "Options...", options)
33 31
34 # Convert image to binary if necessary. 32 # Convert image to binary if necessary.
35 if not image_processor_copy.isBinary(): 33 if not image_processor_copy.isBinary():
36 # Convert the image to binary grayscale. 34 # Convert the image to binary grayscale.
37 IJ.run( input_image_plus_copy, "Make Binary", "" ) 35 IJ.run(input_image_plus_copy, "Make Binary", "")
38 36
39 # Run the command. 37 # Run the command.
40 IJ.run( input_image_plus_copy, "Distance Map", "" ) 38 IJ.run(input_image_plus_copy, "Distance Map", "")
41 # Save the ImagePlus object as a new image. 39 # Save the ImagePlus object as a new image.
42 IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path ) 40 IJ.saveAs(input_image_plus_copy, output_datatype, output_filename)
43 except Exception, e:
44 jython_utils.handle_error( error_log, str( e ) )