annotate imagej2_skeletonize3d_jython_script.py @ 2:6a07f71806bb draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5

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]
black_background = sys.argv[-3] == "yes"
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()

# Set binary options.
options = ["edm=Overwrite", "iterations=1", "count=1"]
if black_background:
    options.append("black")
options = " ".join(options)
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)