comparison imagej2_skeletonize3d_jython_script.py @ 0:f6df6830d5ec draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
author imgteam
date Tue, 17 Sep 2019 16:57:15 -0400
parents
children 768825d9034a
comparison
equal deleted inserted replaced
-1:000000000000 0:f6df6830d5ec
1 import jython_utils
2 import sys
3 from ij import IJ
4
5 # Fiji Jython interpreter implements Python 2.5 which does not
6 # provide support for argparse.
7 error_log = sys.argv[ -5 ]
8 input = sys.argv[ -4 ]
9 black_background = jython_utils.asbool( sys.argv[ -3 ] )
10 tmp_output_path = sys.argv[ -2 ]
11 output_datatype = sys.argv[ -1 ]
12
13 # Open the input image file.
14 input_image_plus = IJ.openImage( input )
15
16 # Create a copy of the image.
17 input_image_plus_copy = input_image_plus.duplicate()
18 image_processor_copy = input_image_plus_copy.getProcessor()
19
20 try:
21 # Set binary options.
22 options = jython_utils.get_binary_options( black_background=black_background )
23 IJ.run( input_image_plus_copy, "Options...", options )
24
25 # Convert image to binary if necessary.
26 if not image_processor_copy.isBinary():
27 # Convert the image to binary grayscale.
28 IJ.run( input_image_plus_copy, "Make Binary", "" )
29
30 # Run the command.
31 IJ.run( input_image_plus_copy, "Skeletonize (2D/3D)", "" )
32
33 # Save the ImagePlus object as a new image.
34 IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path )
35 except Exception, e:
36 jython_utils.handle_error( error_log, str( e ) )