Mercurial > repos > bgruening > imagej2_enhance_contrast

annotate imagej2_shadows_jython_script.py @ 0:5c1467b54342 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
author bgruening
date Sat, 18 Mar 2017 09:42:41 -0400
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5c1467b54342 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
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diff changeset
1 import jython_utils
5c1467b54342 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
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2 import sys
5c1467b54342 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
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3 from ij import IJ
5c1467b54342 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
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5c1467b54342 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
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5 # Fiji Jython interpreter implements Python 2.5 which does not
5c1467b54342 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
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6 # provide support for argparse.
5c1467b54342 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
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7 error_log = sys.argv[ -5 ]
5c1467b54342 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
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8 input = sys.argv[ -4 ]
5c1467b54342 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
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9 direction = sys.argv[ -3 ]
5c1467b54342 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
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10 tmp_output_path = sys.argv[ -2 ]
5c1467b54342 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
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11 output_datatype = sys.argv[ -1 ]
5c1467b54342 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
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5c1467b54342 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
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13 # Open the input image file.
5c1467b54342 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
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14 input_image_plus = IJ.openImage( input )
5c1467b54342 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
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5c1467b54342 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
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16 # Create a copy of the image.
5c1467b54342 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
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17 input_image_plus_copy = input_image_plus.duplicate()
5c1467b54342 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
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18 image_processor_copy = input_image_plus_copy.getProcessor()
5c1467b54342 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
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5c1467b54342 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
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20 try:
5c1467b54342 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
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21 # Run the command.
5c1467b54342 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
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22 IJ.run( input_image_plus_copy, direction, "" )
5c1467b54342 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
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23 # Save the ImagePlus object as a new image.
5c1467b54342 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
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24 IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path )
5c1467b54342 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
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25 except Exception, e:
5c1467b54342 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
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26 jython_utils.handle_error( error_log, str( e ) )