Mercurial > repos > iuc > imagej2_make_binary

annotate jython_script.py @ 0:66d9e595dff2 draft

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planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
author iuc
date Tue, 04 Aug 2015 13:20:29 -0400
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children d26f11339f08
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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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6 # Fiji Jython interpreter implements Python 2.5 which does not
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7 # provide support for argparse.
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8 error_log = sys.argv[ -8 ]
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9 input = sys.argv[ -7 ]
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10 iterations = sys.argv[ -6 ]
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11 count = sys.argv[ -5 ]
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12 black_background = sys.argv[ -4 ]
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13 pad_edges_when_eroding = sys.argv[ -3 ]
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14 tmp_output_path = sys.argv[ -2 ]
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15 output_datatype = sys.argv[ -1 ]
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17 # Open the input image file.
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18 input_image_plus = IJ.openImage( input )
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19 bit_depth = input_image_plus.getBitDepth()
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20 image_type = input_image_plus.getType()
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22 # Create a copy of the image.
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23 input_image_plus_copy = input_image_plus.createImagePlus()
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24 image_processor_copy = input_image_plus.getProcessor().duplicate()
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25 input_image_plus_copy.setProcessor( "iCopy", image_processor_copy )
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26
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27 try:
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28 options = [ "iterations=&iterations" "count=&count" ]
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29 if black_background == "yes":
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30 options.append( "black" )
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31 if pad_edges_when_eroding == "yes":
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32 options.append( "pad" )
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33 # The following have no affect within this tool, but are necessary.
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34 options.append( "edm=Overwrite" )
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35 options.append( "do=Nothing" )
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36 # Run the command.
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37 IJ.run( input_image_plus_copy, "Make Binary", " ".join( options ) )
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38 # Save the ImagePlus object as a new image.
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39 IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path )
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40 except Exception, e:
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41 jython_utils.handle_error( error_log, str( e ) )