Mercurial > repos > imgteam > imagej2_bunwarpj_convert_to_raw
diff imagej2_smooth_jython_script.py @ 0:95fb6fa70c2f draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
| author | imgteam |
|---|---|
| date | Tue, 17 Sep 2019 17:06:56 -0400 |
| parents | |
| children | 7f9840d3b7e7 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/imagej2_smooth_jython_script.py Tue Sep 17 17:06:56 2019 -0400 @@ -0,0 +1,25 @@ +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 ] + +# Open the input image file. +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 ) )