annotate imagej2_adjust_threshold_binary_jython_script.py @ 3:f72f8e6787cd draft default tip

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

import sys

from ij import IJ, Prefs

# Fiji Jython interpreter implements Python 2.5 which does not
# provide support for argparse.
input_file = sys.argv[-8]
threshold_min = float(sys.argv[-7])
threshold_max = float(sys.argv[-6])
method = sys.argv[-5]
display = sys.argv[-4]
black_background = sys.argv[-3] == "yes"
output_filename = 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()

bit_depth = input_image_plus_copy.getBitDepth()

if black_background:
    Prefs.blackBackground = True
else:
    Prefs.blackBackground = False

if method != "Manual":
    # Set the options.
    if black_background:
        method_str = "%s dark" % method
        suffix = "black"
    else:
        method_str = method
        suffix = ""
    threshold_min = 1
    # Set threshold_max based on image bit-depth
    # For 8-bit images, use 255; for 16-bit images, use 65535
    if bit_depth == 8:
        threshold_max = 255  # Default for 8-bit images
    elif bit_depth == 16:
        threshold_max = 65535  # Default for 16-bit images
    else:
        threshold_max = float('inf')  # General fallback if bit depth is unknown

    IJ.setAutoThreshold(input_image_plus_copy, method_str)
    IJ.run(input_image_plus_copy, "Convert to Mask", "calculate %s" % suffix)
if display == "red":
    display_mode = "Red"
elif display == "bw":
    display_mode = "Black & White"
elif display == "over_under":
    display_mode = "Over/Under"
IJ.setThreshold(input_image_plus_copy, threshold_min, threshold_max, display_mode)
# Save the ImagePlus object as a new image.
IJ.saveAs(input_image_plus_copy, output_datatype, output_filename)