Mercurial > repos > imgteam > imagej2_enhance_contrast
comparison imagej2_find_maxima_jython_script.py @ 3:1f92b1da556b draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
author | imgteam |
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date | Wed, 25 Sep 2024 16:04:54 +0000 |
parents | 056e74fbbf6c |
children |
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2:056e74fbbf6c | 3:1f92b1da556b |
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4 from ij.plugin.filter import Analyzer, MaximumFinder | 4 from ij.plugin.filter import Analyzer, MaximumFinder |
5 from ij.process import ImageProcessor | 5 from ij.process import ImageProcessor |
6 | 6 |
7 # Fiji Jython interpreter implements Python 2.5 which does not | 7 # Fiji Jython interpreter implements Python 2.5 which does not |
8 # provide support for argparse. | 8 # provide support for argparse. |
9 error_log = sys.argv[-10] | |
10 input_file = sys.argv[-9] | 9 input_file = sys.argv[-9] |
11 scale_when_converting = sys.argv[-8] == "yes" | 10 scale_when_converting = sys.argv[-8] == "yes" |
12 weighted_rgb_conversions = sys.argv[-7] == "yes" | 11 weighted_rgb_conversions = sys.argv[-7] == "yes" |
13 noise_tolerance = int(sys.argv[-6]) | 12 noise_tolerance = int(sys.argv[-6]) |
14 output_type = sys.argv[-5] | 13 output_type = sys.argv[-5] |
33 if scale_when_converting: | 32 if scale_when_converting: |
34 options.append("scale") | 33 options.append("scale") |
35 if weighted_rgb_conversions: | 34 if weighted_rgb_conversions: |
36 options.append("weighted") | 35 options.append("weighted") |
37 # Perform conversion - must happen even if no options are set. | 36 # Perform conversion - must happen even if no options are set. |
38 IJ.run(input_image_plus_copy, "Conversions...", "%s" % " ".join(options)) | 37 IJ.run(input_image_plus_copy, "Conversions...", " %s" % " ".join(options)) |
39 if output_type in ["List", "Count"]: | 38 if output_type in ["List", "Count"]: |
40 # W're generating a tabular file for the output. | 39 # W're generating a tabular file for the output. |
41 # Set the Find Maxima options. | 40 # Set the Find Maxima options. |
42 options = ["noise=%d" % noise_tolerance] | 41 options = ["noise=%d" % noise_tolerance] |
43 if output_type.find("_") > 0: | 42 if output_type.find("_") > 0: |