comparison jython_script.py @ 0:42e645a20a6e draft

planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty

0:42e645a20a6e

import jython_utils
import sys
from ij import IJ

# Fiji Jython interpreter implements Python 2.5 which does not
# provide support for argparse.
error_log = sys.argv[ -5 ]
input = sys.argv[ -4 ]
direction = sys.argv[ -3 ]
tmp_output_path = sys.argv[ -2 ]
output_datatype = sys.argv[ -1 ]

# Open the input image file.
input_image_plus = IJ.openImage( input )

# Create a copy of the image.
input_image_plus_copy = input_image_plus.duplicate()
image_processor_copy = input_image_plus_copy.getProcessor()

try:
    # Run the command.
    IJ.run( input_image_plus_copy, direction, "" )
    # Save the ImagePlus object as a new image.
    IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path )
except Exception, e:
    jython_utils.handle_error( error_log, str( e ) )