Mercurial > repos > iuc > imagej2_binary_to_edm
comparison imagej2_skeletonize3d_jython_script.py @ 2:c58b939c862a draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
| author | iuc |
|---|---|
| date | Fri, 22 Jul 2016 23:15:40 -0400 |
| parents | |
| children |
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| 1:51188f1b546e | 2:c58b939c862a |
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| 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 ) ) |