comparison imagej2_watershed_binary_jython_script.py @ 3:2b007b1e6c1b draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56

2:da29019170f1

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]
black_background = sys.argv[-3] == "yes"
tmp_output_path = sys.argv[-2]
output_datatype = sys.argv[-1]

if not image_processor_copy.isBinary():
    # Convert the image to binary grayscale.
    IJ.run(input_image_plus_copy, "Make Binary", "")

# Run the command.
IJ.run(input_image_plus_copy, "Watershed", "")

# Save the ImagePlus object as a new image.
IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path)

3:2b007b1e6c1b

from ij import IJ

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

if not image_processor_copy.isBinary():
    # Convert the image to binary grayscale.
    IJ.run(input_image_plus_copy, "Make Binary", "")

# Run the command.
IJ.run(input_image_plus_copy, "Watershed", "stack")

# Save the ImagePlus object as a new image.
IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path)