Mercurial > repos > imgteam > imagej2_skeletonize3d

diff imagej2_watershed_binary_jython_script.py @ 3:5f5b7185bc16 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 16:14:34 +0000
parents 49b5288dcd8c
children
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line diff
--- a/imagej2_watershed_binary_jython_script.py	Sun Nov 05 14:26:52 2023 +0000
+++ b/imagej2_watershed_binary_jython_script.py	Wed Sep 25 16:14:34 2024 +0000
@@ -4,7 +4,6 @@
 
 # Fiji Jython interpreter implements Python 2.5 which does not
 # provide support for argparse.
-error_log = sys.argv[-5]
 input = sys.argv[-4]
 black_background = sys.argv[-3] == "yes"
 tmp_output_path = sys.argv[-2]
@@ -30,7 +29,7 @@
     IJ.run(input_image_plus_copy, "Make Binary", "")
 
 # Run the command.
-IJ.run(input_image_plus_copy, "Watershed", "")
+IJ.run(input_image_plus_copy, "Watershed", "stack")
 
 # Save the ImagePlus object as a new image.
 IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path)