Mercurial > repos > iuc > imagej2_make_binary

annotate jython_script.py @ 2:c026d0eddc3e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
author iuc
date Sun, 11 Oct 2015 13:30:58 -0400
parents d26f11339f08
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
66d9e595dff2 planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
iuc
parents:
diff changeset
1 import jython_utils
66d9e595dff2 planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
iuc
parents:
diff changeset
2 import sys
66d9e595dff2 planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
iuc
parents:
diff changeset
3 from ij import IJ
66d9e595dff2 planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
iuc
parents:
diff changeset
4
66d9e595dff2 planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
iuc
parents:
diff changeset
5 # Fiji Jython interpreter implements Python 2.5 which does not
66d9e595dff2 planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
iuc
parents:
diff changeset
6 # provide support for argparse.
66d9e595dff2 planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
iuc
parents:
diff changeset
7 error_log = sys.argv[ -8 ]
66d9e595dff2 planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
iuc
parents:
diff changeset
8 input = sys.argv[ -7 ]
1
d26f11339f08 planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
iuc
parents: 0
diff changeset
9 iterations = int( sys.argv[ -6 ] )
d26f11339f08 planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
iuc
parents: 0
diff changeset
10 count = int( sys.argv[ -5 ] )
d26f11339f08 planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
iuc
parents: 0
diff changeset
11 black_background = jython_utils.asbool( sys.argv[ -4 ] )
d26f11339f08 planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
iuc
parents: 0
diff changeset
12 pad_edges_when_eroding = jython_utils.asbool( sys.argv[ -3 ] )
0
66d9e595dff2 planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
iuc
parents:
diff changeset
13 tmp_output_path = sys.argv[ -2 ]
66d9e595dff2 planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
iuc
parents:
diff changeset
14 output_datatype = sys.argv[ -1 ]
66d9e595dff2 planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
iuc
parents:
diff changeset
15
66d9e595dff2 planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
iuc
parents:
diff changeset
16 # Open the input image file.
66d9e595dff2 planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
iuc
parents:
diff changeset
17 input_image_plus = IJ.openImage( input )
66d9e595dff2 planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
iuc
parents:
diff changeset
18
66d9e595dff2 planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
iuc
parents:
diff changeset
19 # Create a copy of the image.
1
d26f11339f08 planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
iuc
parents: 0
diff changeset
20 input_image_plus_copy = input_image_plus.duplicate()
d26f11339f08 planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
iuc
parents: 0
diff changeset
21 image_processor_copy = input_image_plus_copy.getProcessor()
0
66d9e595dff2 planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
iuc
parents:
diff changeset
22
66d9e595dff2 planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
iuc
parents:
diff changeset
23 try:
1
d26f11339f08 planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
iuc
parents: 0
diff changeset
24 # Set binary options.
d26f11339f08 planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
iuc
parents: 0
diff changeset
25 options = jython_utils.get_binary_options( black_background=black_background,
d26f11339f08 planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
iuc
parents: 0
diff changeset
26 iterations=iterations,
d26f11339f08 planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
iuc
parents: 0
diff changeset
27 count=count,
d26f11339f08 planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
iuc
parents: 0
diff changeset
28 pad_edges_when_eroding=pad_edges_when_eroding )
d26f11339f08 planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
iuc
parents: 0
diff changeset
29 IJ.run( input_image_plus_copy, "Options...", options )
d26f11339f08 planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
iuc
parents: 0
diff changeset
30
0
66d9e595dff2 planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
iuc
parents:
diff changeset
31 # Run the command.
1
d26f11339f08 planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
iuc
parents: 0
diff changeset
32 IJ.run( input_image_plus_copy, "Make Binary", "" )
d26f11339f08 planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
iuc
parents: 0
diff changeset
33
0
66d9e595dff2 planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
iuc
parents:
diff changeset
34 # Save the ImagePlus object as a new image.
66d9e595dff2 planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
iuc
parents:
diff changeset
35 IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path )
66d9e595dff2 planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
iuc
parents:
diff changeset
36 except Exception, e:
66d9e595dff2 planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
iuc
parents:
diff changeset
37 jython_utils.handle_error( error_log, str( e ) )