Mercurial > repos > imgteam > imagej2_bunwarpj_align

comparison imagej2_analyze_particles_binary_jython_script.py @ 2:0a0d2dfd17e0 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author imgteam
date Sun, 05 Nov 2023 10:51:33 +0000
parents e9243cad1d67
children 711adedc5bb8
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1:e9243cad1d67 2:0a0d2dfd17e0
1 import sys 1 import sys
2 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 6 OPTIONS = ["edm=Overwrite", "iterations=1", "count=1"]
7 OPTIONS = ['edm=Overwrite', 'iterations=1', 'count=1']
8 7
9 # Fiji Jython interpreter implements Python 2.5 which does not 8 # Fiji Jython interpreter implements Python 2.5 which does not
10 # provide support for argparse. 9 # provide support for argparse.
11 error_log = sys.argv[-14] 10 error_log = sys.argv[-14]
12 input_file = sys.argv[-13] 11 input_file = sys.argv[-13]
41 if not image_processor_copy.isBinary(): 40 if not image_processor_copy.isBinary():
42 # Convert the image to binary grayscale. 41 # Convert the image to binary grayscale.
43 IJ.run(input_image_plus_copy, "Make Binary", "") 42 IJ.run(input_image_plus_copy, "Make Binary", "")
44 43
45 # Set the options. 44 # Set the options.
46 options = ['size=%s' % size] 45 options = ["size=%s" % size]
47 circularity_str = '%.3f-%.3f' % (circularity_min, circularity_max) 46 circularity_str = "%.3f-%.3f" % (circularity_min, circularity_max)
48 options.append('circularity=%s' % circularity_str) 47 options.append("circularity=%s" % circularity_str)
49 if show.find('_') >= 0: 48 if show.find("_") >= 0:
50 show_str = '[%s]' % show.replace('_', ' ') 49 show_str = "[%s]" % show.replace("_", " ")
51 else: 50 else:
52 show_str = show 51 show_str = show
53 options.append('show=%s' % show_str) 52 options.append("show=%s" % show_str)
54 if display_results: 53 if display_results:
55 options.append('display') 54 options.append("display")
56 if not all_results: 55 if not all_results:
57 options.append('summarize') 56 options.append("summarize")
58 if exclude_edges: 57 if exclude_edges:
59 options.append('exclude') 58 options.append("exclude")
60 if include_holes: 59 if include_holes:
61 options.append('include') 60 options.append("include")
62 # Always run "in_situ". 61 # Always run "in_situ".
63 options.append('in_situ') 62 options.append("in_situ")
64 63
65 # Run the command. 64 # Run the command.
66 IJ.run(input_image_plus_copy, "Analyze Particles...", " ".join(options)) 65 IJ.run(input_image_plus_copy, "Analyze Particles...", " ".join(options))
67 66
68 # Save outputs. 67 # Save outputs.