Mercurial > repos > imgteam > imagej2_shadows

comparison imagej2_shadows_jython_script.py @ 1:c8bb47840c8d draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
author imgteam
date Mon, 28 Sep 2020 16:51:33 +0000
parents 7baf811ed973
children f7ae316b00e4
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0:7baf811ed973 1:c8bb47840c8d
1 import jython_utils
2 import sys 1 import sys
2
3 from ij import IJ 3 from ij import IJ
4 4
5 # Fiji Jython interpreter implements Python 2.5 which does not 5 # Fiji Jython interpreter implements Python 2.5 which does not
6 # provide support for argparse. 6 # provide support for argparse.
7 error_log = sys.argv[ -5 ] 7 error_log = sys.argv[-5]
8 input = sys.argv[ -4 ] 8 input_file = sys.argv[-4]
9 direction = sys.argv[ -3 ] 9 direction = sys.argv[-3]
10 tmp_output_path = sys.argv[ -2 ] 10 tmp_output_path = sys.argv[-2]
11 output_datatype = sys.argv[ -1 ] 11 output_datatype = sys.argv[-1]
12 12
13 # Open the input image file. 13 # Open the input image file.
14 input_image_plus = IJ.openImage( input ) 14 input_image_plus = IJ.openImage(input_file)
15 15
16 # Create a copy of the image. 16 # Create a copy of the image.
17 input_image_plus_copy = input_image_plus.duplicate() 17 input_image_plus_copy = input_image_plus.duplicate()
18 image_processor_copy = input_image_plus_copy.getProcessor() 18 image_processor_copy = input_image_plus_copy.getProcessor()
19 19
20 try: 20 # Run the command.
21 # Run the command. 21 IJ.run(input_image_plus_copy, direction, "")
22 IJ.run( input_image_plus_copy, direction, "" ) 22 # Save the ImagePlus object as a new image.
23 # Save the ImagePlus object as a new image. 23 IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path)
24 IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path )
25 except Exception, e:
26 jython_utils.handle_error( error_log, str( e ) )