Mercurial > repos > iuc > imagej2_make_binary

annotate jython_script.py @ 1:d26f11339f08 draft

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author iuc
date Wed, 26 Aug 2015 14:37:41 -0400
parents 66d9e595dff2
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1 import jython_utils
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2 import sys
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3 from ij import IJ
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5 # Fiji Jython interpreter implements Python 2.5 which does not
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6 # provide support for argparse.
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7 error_log = sys.argv[ -8 ]
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8 input = sys.argv[ -7 ]
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9 iterations = int( sys.argv[ -6 ] )
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10 count = int( sys.argv[ -5 ] )
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11 black_background = jython_utils.asbool( sys.argv[ -4 ] )
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12 pad_edges_when_eroding = jython_utils.asbool( sys.argv[ -3 ] )
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13 tmp_output_path = sys.argv[ -2 ]
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14 output_datatype = sys.argv[ -1 ]
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16 # Open the input image file.
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17 input_image_plus = IJ.openImage( input )
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19 # Create a copy of the image.
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20 input_image_plus_copy = input_image_plus.duplicate()
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21 image_processor_copy = input_image_plus_copy.getProcessor()
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23 try:
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24 # Set binary options.
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25 options = jython_utils.get_binary_options( black_background=black_background,
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26 iterations=iterations,
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27 count=count,
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28 pad_edges_when_eroding=pad_edges_when_eroding )
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29 IJ.run( input_image_plus_copy, "Options...", options )
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31 # Run the command.
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32 IJ.run( input_image_plus_copy, "Make Binary", "" )
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34 # Save the ImagePlus object as a new image.
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35 IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path )
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36 except Exception, e:
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37 jython_utils.handle_error( error_log, str( e ) )