Mercurial > repos > iuc > imagej2_adjust_threshold_binary

annotate jython_script.py @ 1:8f7beef4f1f3 draft

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planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
author iuc
date Sun, 11 Oct 2015 13:30:44 -0400
parents 91d82f24657a
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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[ -10 ]
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8 input = sys.argv[ -9 ]
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9 threshold_min = float( sys.argv[ -8 ] )
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10 threshold_max = float( sys.argv[ -7 ] )
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11 method = sys.argv[ -6 ]
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12 display = sys.argv[ -5 ]
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13 black_background = jython_utils.asbool( sys.argv[ -4 ] )
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14 # TODO: this is not being used.
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15 stack_histogram = 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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21
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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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25
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26 try:
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27 # Convert image to binary if necessary.
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28 if not image_processor_copy.isBinary():
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29 # Convert the image to binary grayscale.
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30 IJ.run( input_image_plus_copy, "Make Binary","iterations=1 count=1 edm=Overwrite do=Nothing" )
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31 # Set the options.
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32 if black_background:
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33 method_str = "%s dark" % method
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34 else:
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35 method_str = method
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36 IJ.setAutoThreshold( input_image_plus_copy, method_str )
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37 if display == "red":
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38 display_mode = "Red"
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39 elif display == "bw":
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40 display_mode = "Black & White"
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41 elif display == "over_under":
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42 display_mode = "Over/Under"
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43 IJ.setThreshold( input_image_plus_copy, threshold_min, threshold_max, display_mode )
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44 # Run the command.
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45 IJ.run( input_image_plus_copy, "threshold", "" )
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46 # Save the ImagePlus object as a new image.
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47 IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path )
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48 except Exception, e:
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49 jython_utils.handle_error( error_log, str( e ) )