Mercurial > repos > iuc > imagej2_watershed_binary

annotate jython_script.py @ 0:e6c00b485c38 draft

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planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
author iuc
date Sun, 11 Oct 2015 14:06:05 -0400
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e6c00b485c38 planemo upload commit c48c14ca7bf77275a407157ed31b236f0a0bd794-dirty
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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
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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[ -5 ]
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8 input = sys.argv[ -4 ]
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9 black_background = jython_utils.asbool( sys.argv[ -3 ] )
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10 tmp_output_path = sys.argv[ -2 ]
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11 output_datatype = sys.argv[ -1 ]
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12
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13 # Open the input image file.
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14 input_image_plus = IJ.openImage( input )
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16 # Create a copy of the image.
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17 input_image_plus_copy = input_image_plus.duplicate()
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18 image_processor_copy = input_image_plus_copy.getProcessor()
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19
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20 try:
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21 # Set binary options.
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22 options = jython_utils.get_binary_options( black_background=black_background )
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23 IJ.run( input_image_plus_copy, "Options...", options )
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24
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25 # Convert image to binary if necessary.
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26 if not image_processor_copy.isBinary():
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27 # Convert the image to binary grayscale.
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28 IJ.run( input_image_plus_copy, "Make Binary", "" )
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30 # Run the command.
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31 IJ.run( input_image_plus_copy, "Watershed", "" )
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32
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33 # Save the ImagePlus object as a new image.
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34 IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path )
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35 except Exception, e:
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36 jython_utils.handle_error( error_log, str( e ) )