comparison imagej2_shadows_jython_script.py @ 1:e9243cad1d67 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"

0:ab54024c0a88

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 ) )

1:e9243cad1d67

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_file = 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_file)

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

# 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)