Mercurial > repos > imgteam > imagej2_bunwarpj_compose_raw
comparison imagej2_enhance_contrast_jython_script.py @ 0:93b416f8e9e3 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 17:00:19 -0400 |
| parents | |
| children | 8c0ace7ae77c |
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| -1:000000000000 | 0:93b416f8e9e3 |
|---|---|
| 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 ) ) |