comparison imagej2_shadows_jython_script.py @ 0:1bf7e70e67f9 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 16:56:02 -0400
parents
children 8d357579e407
comparison
equal deleted inserted replaced
-1:000000000000 0:1bf7e70e67f9
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 direction = 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 # Run the command.
22 IJ.run( input_image_plus_copy, direction, "" )
23 # Save the ImagePlus object as a new image.
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 ) )