Mercurial > repos > iuc > imagej2_make_binary
view imagej2_bunwarpj_elastic_transform_jython_script.py @ 3:bb7bfa5bc1b0 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
| author | iuc |
|---|---|
| date | Fri, 22 Jul 2016 23:21:29 -0400 |
| parents | |
| children |
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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 )