Mercurial > repos > bgruening > imagej2_crop
comparison imagej2_shadows_jython_script.py @ 0:018144807556 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
| author | bgruening |
|---|---|
| date | Tue, 24 Sep 2024 17:12:52 +0000 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:018144807556 |
|---|---|
| 1 import sys | |
| 2 | |
| 3 from ij import IJ | |
| 4 | |
| 5 # Fiji Jython interpreter implements Python 2.5 which does not | |
| 6 # provide support for argparse. | |
| 7 input_file = sys.argv[-4] | |
| 8 direction = sys.argv[-3] | |
| 9 tmp_output_path = sys.argv[-2] | |
| 10 output_datatype = sys.argv[-1] | |
| 11 | |
| 12 # Open the input image file. | |
| 13 input_image_plus = IJ.openImage(input_file) | |
| 14 | |
| 15 # Create a copy of the image. | |
| 16 input_image_plus_copy = input_image_plus.duplicate() | |
| 17 image_processor_copy = input_image_plus_copy.getProcessor() | |
| 18 | |
| 19 # Run the command. | |
| 20 IJ.run(input_image_plus_copy, direction, "") | |
| 21 # Save the ImagePlus object as a new image. | |
| 22 IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path) |