Mercurial > repos > imgteam > imagej2_skeletonize3d

comparison imagej2_analyze_particles_binary_jython_script.py @ 1:768825d9034a 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 17:01:19 +0000
parents f6df6830d5ec
children 49b5288dcd8c
comparison
equal deleted inserted replaced
0:f6df6830d5ec 1:768825d9034a
1 import jython_utils
2 import sys 1 import sys
2
3 from ij import IJ 3 from ij import IJ
4 from ij.plugin.filter import Analyzer 4 from ij.plugin.filter import Analyzer
5 5
6
7 OPTIONS = ['edm=Overwrite', 'iterations=1', 'count=1']
8
6 # Fiji Jython interpreter implements Python 2.5 which does not 9 # Fiji Jython interpreter implements Python 2.5 which does not
7 # provide support for argparse. 10 # provide support for argparse.
8 error_log = sys.argv[ -14 ] 11 error_log = sys.argv[-14]
9 input = sys.argv[ -13 ] 12 input_file = sys.argv[-13]
10 black_background = jython_utils.asbool( sys.argv[ -12 ] ) 13 black_background = sys.argv[-12] == "yes"
11 size = sys.argv[ -11 ] 14 size = sys.argv[-11]
12 circularity_min = float( sys.argv[ -10 ] ) 15 circularity_min = float(sys.argv[-10])
13 circularity_max = float( sys.argv[ -9 ] ) 16 circularity_max = float(sys.argv[-9])
14 show = sys.argv[ -8 ] 17 show = sys.argv[-8]
15 display_results = jython_utils.asbool( sys.argv[ -7 ] ) 18 display_results = sys.argv[-7] == "yes"
16 all_results = jython_utils.asbool( sys.argv[ -6 ] ) 19 all_results = sys.argv[-6] == "yes"
17 exclude_edges = jython_utils.asbool( sys.argv[ -5 ] ) 20 exclude_edges = sys.argv[-5] == "yes"
18 include_holes = jython_utils.asbool( sys.argv[ -4 ] ) 21 include_holes = sys.argv[-4] == "yes"
19 tmp_output_path = sys.argv[ -3 ] 22 output_filename = sys.argv[-3]
20 output_datatype = sys.argv[ -2 ] 23 output_datatype = sys.argv[-2]
21 results_path = sys.argv[ -1 ] 24 results_path = sys.argv[-1]
22 25
23 # Open the input image file. 26 # Open the input image file.
24 input_image_plus = IJ.openImage( input ) 27 input_image_plus = IJ.openImage(input_file)
25 28
26 # Create a copy of the image. 29 # Create a copy of the image.
27 input_image_plus_copy = input_image_plus.duplicate() 30 input_image_plus_copy = input_image_plus.duplicate()
28 image_processor_copy = input_image_plus_copy.getProcessor() 31 image_processor_copy = input_image_plus_copy.getProcessor()
29 analyzer = Analyzer( input_image_plus_copy ) 32 analyzer = Analyzer(input_image_plus_copy)
30 33
31 try: 34 # Set binary options.
32 # Set binary options. 35 options_list = OPTIONS
33 options = jython_utils.get_binary_options( black_background=black_background ) 36 if black_background:
34 IJ.run( input_image_plus_copy, "Options...", options ) 37 options_list.append("black")
38 options = " ".join(options_list)
39 IJ.run(input_image_plus_copy, "Options...", options)
35 40
36 # Convert image to binary if necessary. 41 if not image_processor_copy.isBinary():
37 if not image_processor_copy.isBinary(): 42 # Convert the image to binary grayscale.
38 # Convert the image to binary grayscale. 43 IJ.run(input_image_plus_copy, "Make Binary", "")
39 IJ.run( input_image_plus_copy, "Make Binary", "" )
40 44
41 # Set the options. 45 # Set the options.
42 options = [ 'size=%s' % size ] 46 options = ['size=%s' % size]
43 circularity_str = '%.3f-%.3f' % ( circularity_min, circularity_max ) 47 circularity_str = '%.3f-%.3f' % (circularity_min, circularity_max)
44 options.append( 'circularity=%s' % circularity_str ) 48 options.append('circularity=%s' % circularity_str)
45 if show.find( '_' ) >= 0: 49 if show.find('_') >= 0:
46 show_str = '[%s]' % show.replace( '_', ' ' ) 50 show_str = '[%s]' % show.replace('_', ' ')
47 else: 51 else:
48 show_str = show 52 show_str = show
49 options.append( 'show=%s' % show_str ) 53 options.append('show=%s' % show_str)
50 if display_results: 54 if display_results:
51 options.append( 'display' ) 55 options.append('display')
52 if not all_results: 56 if not all_results:
53 options.append( 'summarize' ) 57 options.append('summarize')
54 if exclude_edges: 58 if exclude_edges:
55 options.append( 'exclude' ) 59 options.append('exclude')
56 if include_holes: 60 if include_holes:
57 options.append( 'include' ) 61 options.append('include')
58 # Always run "in_situ". 62 # Always run "in_situ".
59 options.append( 'in_situ' ) 63 options.append('in_situ')
60 64
61 # Run the command. 65 # Run the command.
62 IJ.run( input_image_plus_copy, "Analyze Particles...", " ".join( options ) ) 66 IJ.run(input_image_plus_copy, "Analyze Particles...", " ".join(options))
63 67
64 # Save outputs. 68 # Save outputs.
65 if tmp_output_path not in [ None, 'None' ]: 69 if len(output_filename) > 0:
66 # Save the ImagePlus object as a new image. 70 # Save the ImagePlus object as a new image.
67 IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path ) 71 IJ.saveAs(input_image_plus_copy, output_datatype, output_filename)
68 if display_results and results_path not in [ None, 'None' ]: 72 if display_results and len(results_path) > 0:
69 results_table = analyzer.getResultsTable() 73 results_table = analyzer.getResultsTable()
70 results_table.saveAs( results_path ) 74 results_table.saveAs(results_path)
71 except Exception, e:
72 jython_utils.handle_error( error_log, str( e ) )