Mercurial > repos > imgteam > imagej2_binary_to_edm

comparison imagej2_smooth_jython_script.py @ 1:33f6b1f921e7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
author imgteam
date Mon, 28 Sep 2020 16:55:57 +0000
parents f62303e87275
children 91b8f4730a93
comparison
equal deleted inserted replaced
0:f62303e87275 1:33f6b1f921e7
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[ -4 ] 7 error_log = sys.argv[-4]
8 input = sys.argv[ -3 ] 8 input = sys.argv[-3]
9 tmp_output_path = sys.argv[ -2 ] 9 tmp_output_path = sys.argv[-2]
10 output_datatype = sys.argv[ -1 ] 10 output_datatype = sys.argv[-1]
11 11
12 # Open the input image file. 12 # Open the input image file.
13 input_image_plus = IJ.openImage( input ) 13 input_image_plus = IJ.openImage(input)
14 14
15 # Create a copy of the image. 15 # Create a copy of the image.
16 input_image_plus_copy = input_image_plus.duplicate() 16 input_image_plus_copy = input_image_plus.duplicate()
17 image_processor_copy = input_image_plus_copy.getProcessor() 17 image_processor_copy = input_image_plus_copy.getProcessor()
18 18
19 try: 19 # Run the command.
20 # Run the command. 20 IJ.run(input_image_plus_copy, "Smooth", "")
21 IJ.run( input_image_plus_copy, "Smooth", "" ) 21 # Save the ImagePlus object as a new image.
22 # Save the ImagePlus object as a new image. 22 IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path)
23 IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path )
24 except Exception, e:
25 jython_utils.handle_error( error_log, str( e ) )