Mercurial > repos > imgteam > imagej2_create_image

comparison imagej2_enhance_contrast_jython_script.py @ 1:1a7c29d5fc11 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
author imgteam
date Mon, 28 Sep 2020 16:43:06 +0000
parents dc3935a0165a
children 666af1279007
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0:dc3935a0165a 1:1a7c29d5fc11
1 import jython_utils
2 import sys 1 import sys
2
3 from ij import IJ 3 from ij import IJ
4 4
5 # Fiji Jython interpreter implements Python 2.5 which does not 5 # Fiji Jython interpreter implements Python 2.5 which does not
6 # provide support for argparse. 6 # provide support for argparse.
7 error_log = sys.argv[ -7 ] 7 error_log = sys.argv[-7]
8 input = sys.argv[ -6 ] 8 input = sys.argv[-6]
9 equalize_histogram = jython_utils.asbool( sys.argv[ -5 ] ) 9 equalize_histogram = sys.argv[-5] == "yes"
10 saturated_pixels = sys.argv[ -4 ] 10 saturated_pixels = sys.argv[-4]
11 normalize = jython_utils.asbool( sys.argv[ -3 ] ) 11 normalize = sys.argv[-3] == "yes"
12 tmp_output_path = sys.argv[ -2 ] 12 tmp_output_path = sys.argv[-2]
13 output_datatype = sys.argv[ -1 ] 13 output_datatype = sys.argv[-1]
14 14
15 # Open the input image file. 15 # Open the input image file.
16 input_image_plus = IJ.openImage( input ) 16 input_image_plus = IJ.openImage(input)
17 17
18 # Create a copy of the image. 18 # Create a copy of the image.
19 input_image_plus_copy = input_image_plus.duplicate() 19 input_image_plus_copy = input_image_plus.duplicate()
20 image_processor_copy = input_image_plus_copy.getProcessor() 20 image_processor_copy = input_image_plus_copy.getProcessor()
21 bit_depth = image_processor_copy.getBitDepth() 21 bit_depth = image_processor_copy.getBitDepth()
22 22
23 # Set the options 23 # Set the options
24 options = [] 24 options = []
25 # If equalize_histogram, saturated_pixels and normalize are ignored. 25 # If equalize_histogram, saturated_pixels and normalize are ignored.
26 if equalize_histogram: 26 if equalize_histogram:
27 options.append( 'equalize' ) 27 options.append('equalize')
28 else: 28 else:
29 if saturated_pixels not in [ None, 'None' ]: 29 if saturated_pixels not in [None, 'None']:
30 # Fiji allows only a single decimal place for this value. 30 # Fiji allows only a single decimal place for this value.
31 options.append( 'saturated=%.3f' % float( saturated_pixels ) ) 31 options.append('saturated=%.3f' % float(saturated_pixels))
32 # Normalization of RGB images is not supported. 32 # Normalization of RGB images is not supported.
33 if bit_depth != 24 and normalize: 33 if bit_depth != 24 and normalize:
34 options.append( 'normalize' ) 34 options.append('normalize')
35 try: 35 # Run the command.
36 # Run the command. 36 options = "%s" % ' '.join(options)
37 options = "%s" % ' '.join( options ) 37 IJ.run(input_image_plus_copy, "Enhance Contrast...", options)
38 IJ.run( input_image_plus_copy, "Enhance Contrast...", options ) 38 # Save the ImagePlus object as a new image.
39 # Save the ImagePlus object as a new image. 39 IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path)
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 ) )