Mercurial > repos > imgteam > imagej2_analyze_particles_binary
diff imagej2_analyze_particles_binary_jython_script.py @ 2:ae4ae9c5c56c draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author | imgteam |
---|---|
date | Sun, 05 Nov 2023 14:25:37 +0000 |
parents | 1dd5396c734a |
children | 862af85a50ec |
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--- a/imagej2_analyze_particles_binary_jython_script.py Mon Sep 28 16:59:30 2020 +0000 +++ b/imagej2_analyze_particles_binary_jython_script.py Sun Nov 05 14:25:37 2023 +0000 @@ -3,8 +3,7 @@ from ij import IJ from ij.plugin.filter import Analyzer - -OPTIONS = ['edm=Overwrite', 'iterations=1', 'count=1'] +OPTIONS = ["edm=Overwrite", "iterations=1", "count=1"] # Fiji Jython interpreter implements Python 2.5 which does not # provide support for argparse. @@ -43,24 +42,24 @@ IJ.run(input_image_plus_copy, "Make Binary", "") # Set the options. -options = ['size=%s' % size] -circularity_str = '%.3f-%.3f' % (circularity_min, circularity_max) -options.append('circularity=%s' % circularity_str) -if show.find('_') >= 0: - show_str = '[%s]' % show.replace('_', ' ') +options = ["size=%s" % size] +circularity_str = "%.3f-%.3f" % (circularity_min, circularity_max) +options.append("circularity=%s" % circularity_str) +if show.find("_") >= 0: + show_str = "[%s]" % show.replace("_", " ") else: show_str = show -options.append('show=%s' % show_str) +options.append("show=%s" % show_str) if display_results: - options.append('display') + options.append("display") if not all_results: - options.append('summarize') + options.append("summarize") if exclude_edges: - options.append('exclude') + options.append("exclude") if include_holes: - options.append('include') + options.append("include") # Always run "in_situ". -options.append('in_situ') +options.append("in_situ") # Run the command. IJ.run(input_image_plus_copy, "Analyze Particles...", " ".join(options))