Mercurial > repos > imgteam > imagej2_enhance_contrast
diff imagej2_smooth_jython_script.py @ 1:ef3de3e84817 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 16:58:37 +0000 |
parents | edfc597fb180 |
children | 1f92b1da556b |
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--- a/imagej2_smooth_jython_script.py Tue Sep 17 17:01:04 2019 -0400 +++ b/imagej2_smooth_jython_script.py Mon Sep 28 16:58:37 2020 +0000 @@ -1,25 +1,22 @@ -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[ -4 ] -input = sys.argv[ -3 ] -tmp_output_path = sys.argv[ -2 ] -output_datatype = sys.argv[ -1 ] +error_log = sys.argv[-4] +input = 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) # 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, "Smooth", "" ) - # 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, "Smooth", "") +# Save the ImagePlus object as a new image. +IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path)