comparison imagej2_bunwarpj_raw_transform_jython_script.py @ 0:dc3935a0165a 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 16:57:52 -0400
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-1:000000000000 0:dc3935a0165a
1 import sys
2 import jython_utils
3 from ij import IJ
4
5 # Fiji Jython interpreter implements Python 2.5 which does not
6 # provide support for argparse.
7
8 source_tiff_path = sys.argv[ -3 ]
9 source_datatype = sys.argv[ -2 ]
10 source_path = sys.argv[ -1 ]
11
12 # Save the Registered Source Image.
13 registered_source_image = IJ.openImage( source_tiff_path )
14 if source_datatype == 'tiff':
15 registered_source_image = jython_utils.convert_before_saving_as_tiff( registered_source_image )
16 IJ.saveAs( registered_source_image, source_datatype, source_path )