comparison imagej2_enhance_contrast_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
date Tue, 17 Sep 2019 16:57:52 -0400
parents
children 1a7c29d5fc11
comparison
equal deleted inserted replaced
-1:000000000000 0:dc3935a0165a
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[ -7 ]
8 input = sys.argv[ -6 ]
9 equalize_histogram = jython_utils.asbool( sys.argv[ -5 ] )
10 saturated_pixels = sys.argv[ -4 ]
11 normalize = jython_utils.asbool( sys.argv[ -3 ] )
12 tmp_output_path = sys.argv[ -2 ]
13 output_datatype = sys.argv[ -1 ]
14
15 # Open the input image file.
16 input_image_plus = IJ.openImage( input )
17
18 # Create a copy of the image.
19 input_image_plus_copy = input_image_plus.duplicate()
20 image_processor_copy = input_image_plus_copy.getProcessor()
21 bit_depth = image_processor_copy.getBitDepth()
22
23 # Set the options
24 options = []
25 # If equalize_histogram, saturated_pixels and normalize are ignored.
26 if equalize_histogram:
27 options.append( 'equalize' )
28 else:
29 if saturated_pixels not in [ None, 'None' ]:
30 # Fiji allows only a single decimal place for this value.
31 options.append( 'saturated=%.3f' % float( saturated_pixels ) )
32 # Normalization of RGB images is not supported.
33 if bit_depth != 24 and normalize:
34 options.append( 'normalize' )
35 try:
36 # Run the command.
37 options = "%s" % ' '.join( options )
38 IJ.run( input_image_plus_copy, "Enhance Contrast...", options )
39 # Save the ImagePlus object as a new image.
40 IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path )
41 except Exception, e:
42 jython_utils.handle_error( error_log, str( e ) )