Mercurial > repos > imgteam > imagej2_create_image
comparison imagej2_create_image_jython_script.py @ 1:1a7c29d5fc11 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
author | imgteam |
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date | Mon, 28 Sep 2020 16:43:06 +0000 |
parents | dc3935a0165a |
children | 666af1279007 |
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0:dc3935a0165a | 1:1a7c29d5fc11 |
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1 import sys | 1 import sys |
2 | |
2 from ij import IJ | 3 from ij import IJ |
3 | 4 |
4 # Fiji Jython interpreter implements Python 2.5 which does not | 5 # Fiji Jython interpreter implements Python 2.5 which does not |
5 # provide support for argparse. | 6 # provide support for argparse. |
6 title = sys.argv[ -6 ] | 7 title = sys.argv[-6] |
7 width = int( sys.argv[ -5 ] ) | 8 width = int(sys.argv[-5]) |
8 height = int( sys.argv[ -4 ] ) | 9 height = int(sys.argv[-4]) |
9 depth = int( sys.argv[ -3 ] ) | 10 depth = int(sys.argv[-3]) |
10 type = sys.argv[ -2 ].replace( '_', ' ' ) | 11 type = sys.argv[-2].replace('_', ' ') |
11 tmp_image_path = sys.argv[ -1 ] | 12 tmp_image_path = sys.argv[-1] |
12 | 13 |
13 imp = IJ.newImage( title, type, width, height, depth ) | 14 imp = IJ.newImage(title, type, width, height, depth) |
14 IJ.save( imp, "%s" % tmp_image_path ) | 15 IJ.save(imp, "%s" % tmp_image_path) |