comparison imagej2_smooth_jython_script.py @ 0:dd20ee3092e3 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 17:04:21 -0400
parents
children 53fb6f4afcc8
comparison
equal deleted inserted replaced
-1:000000000000 0:dd20ee3092e3
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[ -4 ]
8 input = sys.argv[ -3 ]
9 tmp_output_path = sys.argv[ -2 ]
10 output_datatype = sys.argv[ -1 ]
11
12 # Open the input image file.
13 input_image_plus = IJ.openImage( input )
14
15 # Create a copy of the image.
16 input_image_plus_copy = input_image_plus.duplicate()
17 image_processor_copy = input_image_plus_copy.getProcessor()
18
19 try:
20 # Run the command.
21 IJ.run( input_image_plus_copy, "Smooth", "" )
22 # Save the ImagePlus object as a new image.
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 ) )