Mercurial > repos > imgteam > imagej2_create_image
comparison imagej2_find_edges_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 |
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date | Tue, 17 Sep 2019 16:57:52 -0400 |
parents | |
children | 1a7c29d5fc11 |
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-1:000000000000 | 0:dc3935a0165a |
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1 import jython_utils | |
2 import sys | |
3 from ij import IJ | |
4 | |
5 # Fiji Jython interpreter implements Python 2.5 which does not | |
6 # provide support for argparse. | |
7 error_log = sys.argv[ -4 ] | |
8 input = 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 ) | |
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 try: | |
20 # Run the command. | |
21 IJ.run( input_image_plus_copy, "Find Edges", "" ) | |
22 # Save the ImagePlus object as a new image. | |
23 IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path ) | |
24 except Exception, e: | |
25 jython_utils.handle_error( error_log, str( e ) ) |