Mercurial > repos > imgteam > imagej2_analyze_skeleton
diff imagej2_shadows_jython_script.py @ 1:3272e0439968 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
author | imgteam |
---|---|
date | Mon, 28 Sep 2020 16:52:29 +0000 |
parents | bb84f130a4e1 |
children |
line wrap: on
line diff
--- a/imagej2_shadows_jython_script.py Tue Sep 17 17:04:59 2019 -0400 +++ b/imagej2_shadows_jython_script.py Mon Sep 28 16:52:29 2020 +0000 @@ -1,26 +1,23 @@ -import jython_utils import sys + from ij import IJ # Fiji Jython interpreter implements Python 2.5 which does not # provide support for argparse. -error_log = sys.argv[ -5 ] -input = sys.argv[ -4 ] -direction = sys.argv[ -3 ] -tmp_output_path = sys.argv[ -2 ] -output_datatype = sys.argv[ -1 ] +error_log = sys.argv[-5] +input_file = sys.argv[-4] +direction = sys.argv[-3] +tmp_output_path = sys.argv[-2] +output_datatype = sys.argv[-1] # Open the input image file. -input_image_plus = IJ.openImage( input ) +input_image_plus = IJ.openImage(input_file) # Create a copy of the image. input_image_plus_copy = input_image_plus.duplicate() image_processor_copy = input_image_plus_copy.getProcessor() -try: - # Run the command. - IJ.run( input_image_plus_copy, direction, "" ) - # Save the ImagePlus object as a new image. - IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path ) -except Exception, e: - jython_utils.handle_error( error_log, str( e ) ) +# Run the command. +IJ.run(input_image_plus_copy, direction, "") +# Save the ImagePlus object as a new image. +IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path)