Mercurial > repos > iuc > imagej2_make_binary

comparison 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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-1:000000000000 0:66d9e595dff2
1 import jython_utils
2 import sys
3 from ij import IJ
4 from ij import ImagePlus
5
6 # Fiji Jython interpreter implements Python 2.5 which does not
7 # provide support for argparse.
8 error_log = sys.argv[ -8 ]
9 input = sys.argv[ -7 ]
10 iterations = sys.argv[ -6 ]
11 count = sys.argv[ -5 ]
12 black_background = sys.argv[ -4 ]
13 pad_edges_when_eroding = sys.argv[ -3 ]
14 tmp_output_path = sys.argv[ -2 ]
15 output_datatype = sys.argv[ -1 ]
16
17 # Open the input image file.
18 input_image_plus = IJ.openImage( input )
19 bit_depth = input_image_plus.getBitDepth()
20 image_type = input_image_plus.getType()
21
22 # Create a copy of the image.
23 input_image_plus_copy = input_image_plus.createImagePlus()
24 image_processor_copy = input_image_plus.getProcessor().duplicate()
25 input_image_plus_copy.setProcessor( "iCopy", image_processor_copy )
26
27 try:
28 options = [ "iterations=&iterations" "count=&count" ]
29 if black_background == "yes":
30 options.append( "black" )
31 if pad_edges_when_eroding == "yes":
32 options.append( "pad" )
33 # The following have no affect within this tool, but are necessary.
34 options.append( "edm=Overwrite" )
35 options.append( "do=Nothing" )
36 # Run the command.
37 IJ.run( input_image_plus_copy, "Make Binary", " ".join( options ) )
38 # Save the ImagePlus object as a new image.
39 IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path )
40 except Exception, e:
41 jython_utils.handle_error( error_log, str( e ) )