Mercurial > repos > imgteam > imagej2_bunwarpj_convert_to_raw
comparison imagej2_analyze_particles_binary_jython_script.py @ 2:0cdd96322600 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author | imgteam |
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date | Sun, 05 Nov 2023 11:00:42 +0000 |
parents | 7f9840d3b7e7 |
children |
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1:7f9840d3b7e7 | 2:0cdd96322600 |
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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. |