view @ 2:da29019170f1 draft default tip

planemo upload for repository commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author imgteam
date Sun, 05 Nov 2023 10:52:33 +0000
parents 29a4d422f32a
line wrap: on
line source

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 = 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)

# 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 = " ".join(options), "Options...", options)

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

# Run the command., "Watershed", "")

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