Mercurial > repos > imgteam > imagej2_find_maxima

comparison imagej2_find_maxima_jython_script.py @ 3:4409f9eb9433 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
author imgteam
date Wed, 25 Sep 2024 15:58:30 +0000
parents 6a07f71806bb
children
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2:6a07f71806bb 3:4409f9eb9433
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: