annotate imagej2_skeletonize3d_jython_script.py @ 0:7baf811ed973 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"

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 ]
black_background = jython_utils.asbool( 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:
    # Set binary options.
    options = jython_utils.get_binary_options( black_background=black_background )
    IJ.run( input_image_plus_copy, "Options...", options )

    # Convert image to binary if necessary.
    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, "Skeletonize (2D/3D)", "" )

    # 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 ) )