Mercurial > repos > imgteam > imagej2_bunwarpj_align
comparison imagej2_bunwarpj_elastic_transform_jython_script.py @ 0:ab54024c0a88 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 17:02:18 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:ab54024c0a88 |
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| 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 ) |