Mercurial > repos > iuc > imagej2_binary_to_edm

annotate jython_script.py @ 1:51188f1b546e draft

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author iuc
date Sun, 11 Oct 2015 13:30:11 -0400
parents c43f184786a0
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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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4 from ij import ImagePlus
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5 from ij.plugin.filter import Analyzer
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6 from ij.plugin.filter import EDM
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8 # Fiji Jython interpreter implements Python 2.5 which does not
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9 # provide support for argparse.
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10 error_log = sys.argv[ -8 ]
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11 input = sys.argv[ -7 ]
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12 iterations = int( sys.argv[ -6 ] )
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13 count = int( sys.argv[ -5 ] )
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14 black_background = jython_utils.asbool( sys.argv[ -4 ] )
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15 pad_edges_when_eroding = jython_utils.asbool( sys.argv[ -3 ] )
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16 tmp_output_path = sys.argv[ -2 ]
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17 output_datatype = sys.argv[ -1 ]
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18
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19 # Open the input image file.
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20 input_image_plus = IJ.openImage( input )
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22 # Create a copy of the image.
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23 input_image_plus_copy = input_image_plus.duplicate()
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24 image_processor_copy = input_image_plus_copy.getProcessor()
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26 try:
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27 # Set binary options.
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28 options = jython_utils.get_binary_options( black_background=black_background,
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29 iterations=iterations,
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30 count=count,
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31 pad_edges_when_eroding=pad_edges_when_eroding )
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32 IJ.run( input_image_plus_copy, "Options...", options )
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33
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34 # Convert image to binary if necessary.
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35 if not image_processor_copy.isBinary():
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36 # Convert the image to binary grayscale.
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37 IJ.run( input_image_plus_copy, "Make Binary", "" )
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38
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39 # Run the command.
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40 IJ.run( input_image_plus_copy, "Distance Map", "" )
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41 # Save the ImagePlus object as a new image.
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42 IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path )
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43 except Exception, e:
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44 jython_utils.handle_error( error_log, str( e ) )