Mercurial > repos > imgteam > imagej2_analyze_skeleton
diff imagej2_bunwarpj_elastic_transform_jython_script.py @ 0:bb84f130a4e1 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
author | imgteam |
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date | Tue, 17 Sep 2019 17:04:59 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/imagej2_bunwarpj_elastic_transform_jython_script.py Tue Sep 17 17:04:59 2019 -0400 @@ -0,0 +1,16 @@ +import sys +import jython_utils +from ij import IJ + +# Fiji Jython interpreter implements Python 2.5 which does not +# provide support for argparse. + +source_tiff_path = sys.argv[ -3 ] +source_datatype = sys.argv[ -2 ] +source_path = sys.argv[ -1 ] + +# Save the Registered Source Image. +registered_source_image = IJ.openImage( source_tiff_path ) +if source_datatype == 'tiff': + registered_source_image = jython_utils.convert_before_saving_as_tiff( registered_source_image ) +IJ.saveAs( registered_source_image, source_datatype, source_path )