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comparison jython_script.py @ 2:c8fc3f34cbff draft

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planemo upload commit 8f8692e83217a072a3ed928469621f1f606ab28a-dirty
author iuc
date Tue, 04 Aug 2015 11:15:16 -0400
parents da9a450c85b7
children d99cf938ad41
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1:1af4f60294c3 2:c8fc3f34cbff
1 import sys 1 import sys
2 from ij import IJ 2 from ij import IJ
3 from ij import ImagePlus 3 from ij import ImagePlus
4 4 import jython_utils
5 def handle_error( error_log, msg ):
6 elh = open( error_log, 'wb' )
7 elh.write( msg )
8 elh.close()
9 5
10 # Fiji Jython interpreter implements Python 2.5 which does not 6 # Fiji Jython interpreter implements Python 2.5 which does not
11 # provide support for argparse. 7 # provide support for argparse.
12 error_log = sys.argv[ -19 ] 8 error_log = sys.argv[ -19 ]
13 input = sys.argv[ -18 ] 9 input = sys.argv[ -18 ]
60 else: 56 else:
61 # When Galaxy metadata for images is enhanced to include information like this, 57 # When Galaxy metadata for images is enhanced to include information like this,
62 # we'll be able to write tool validators rather than having to stop the job in 58 # we'll be able to write tool validators rather than having to stop the job in
63 # an error state. 59 # an error state.
64 msg = "Remove NaNs requires a 32-bit image, the selected image is %d-bit" % bit_depth 60 msg = "Remove NaNs requires a 32-bit image, the selected image is %d-bit" % bit_depth
65 handle_error( error_log, msg ) 61 jython_utils.handle_error( error_log, msg )
66 error = True 62 error = True
67 elif noise == 'rof_denoise': 63 elif noise == 'rof_denoise':
68 if image_type == ImagePlus.GRAY32: 64 if image_type == ImagePlus.GRAY32:
69 IJ.run( image_plus_copy, "ROF Denoise", "" ) 65 IJ.run( image_plus_copy, "ROF Denoise", "" )
70 else: 66 else:
71 msg = "ROF Denoise requires an image of type 32-bit grayscale, the selected image is %d-bit" % ( bit_depth ) 67 msg = "ROF Denoise requires an image of type 32-bit grayscale, the selected image is %d-bit" % ( bit_depth )
72 handle_error( error_log, msg ) 68 jython_utils.handle_error( error_log, msg )
73 error = True 69 error = True
74 elif noise == 'randomj': 70 elif noise == 'randomj':
75 if randomj == 'randomj_binomial': 71 if randomj == 'randomj_binomial':
76 IJ.run( image_plus_copy, "RandomJ Binomial", "trials=&trials probability=&probability insertion=&insertion" ) 72 IJ.run( image_plus_copy, "RandomJ Binomial", "trials=&trials probability=&probability insertion=&insertion" )
77 elif randomj == 'randomj_exponential': 73 elif randomj == 'randomj_exponential':