Mercurial > repos > imgteam > imagej2_crop
comparison imagej2_sharpen_jython_script.py @ 0:db3066ae9b09 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
| author | imgteam |
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| date | Wed, 25 Sep 2024 16:28:45 +0000 |
| parents | |
| children |
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| -1:000000000000 | 0:db3066ae9b09 |
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| 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[-3] | |
| 8 tmp_output_path = sys.argv[-2] | |
| 9 output_datatype = sys.argv[-1] | |
| 10 | |
| 11 # Open the input image file. | |
| 12 input_image_plus = IJ.openImage(input_file) | |
| 13 | |
| 14 # Create a copy of the image. | |
| 15 input_image_plus_copy = input_image_plus.duplicate() | |
| 16 image_processor_copy = input_image_plus_copy.getProcessor() | |
| 17 | |
| 18 # Run the command. | |
| 19 IJ.run(input_image_plus_copy, "Sharpen", "") | |
| 20 # Save the ImagePlus object as a new image. | |
| 21 IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path) |