Mercurial > repos > imgteam > imagej2_bunwarpj_compose_elastic
comparison imagej2_binary_to_edm_jython_script.py @ 0:6840ce593a91 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 17:08:47 -0400 |
| parents | |
| children | 423400b3c47f |
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| -1:000000000000 | 0:6840ce593a91 |
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| 1 import jython_utils | |
| 2 import sys | |
| 3 from ij import IJ | |
| 4 from ij import ImagePlus | |
| 5 from ij.plugin.filter import Analyzer | |
| 6 from ij.plugin.filter import EDM | |
| 7 | |
| 8 # Fiji Jython interpreter implements Python 2.5 which does not | |
| 9 # provide support for argparse. | |
| 10 error_log = sys.argv[ -8 ] | |
| 11 input = sys.argv[ -7 ] | |
| 12 iterations = int( sys.argv[ -6 ] ) | |
| 13 count = int( sys.argv[ -5 ] ) | |
| 14 black_background = jython_utils.asbool( sys.argv[ -4 ] ) | |
| 15 pad_edges_when_eroding = jython_utils.asbool( sys.argv[ -3 ] ) | |
| 16 tmp_output_path = sys.argv[ -2 ] | |
| 17 output_datatype = sys.argv[ -1 ] | |
| 18 | |
| 19 # Open the input image file. | |
| 20 input_image_plus = IJ.openImage( input ) | |
| 21 | |
| 22 # Create a copy of the image. | |
| 23 input_image_plus_copy = input_image_plus.duplicate() | |
| 24 image_processor_copy = input_image_plus_copy.getProcessor() | |
| 25 | |
| 26 try: | |
| 27 # Set binary options. | |
| 28 options = jython_utils.get_binary_options( black_background=black_background, | |
| 29 iterations=iterations, | |
| 30 count=count, | |
| 31 pad_edges_when_eroding=pad_edges_when_eroding ) | |
| 32 IJ.run( input_image_plus_copy, "Options...", options ) | |
| 33 | |
| 34 # Convert image to binary if necessary. | |
| 35 if not image_processor_copy.isBinary(): | |
| 36 # Convert the image to binary grayscale. | |
| 37 IJ.run( input_image_plus_copy, "Make Binary", "" ) | |
| 38 | |
| 39 # Run the command. | |
| 40 IJ.run( input_image_plus_copy, "Distance Map", "" ) | |
| 41 # Save the ImagePlus object as a new image. | |
| 42 IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path ) | |
| 43 except Exception, e: | |
| 44 jython_utils.handle_error( error_log, str( e ) ) |