annotate imagej2_adjust_threshold_binary_jython_script.py @ 0:bb84f130a4e1 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[ -10 ]
input = sys.argv[ -9 ]
threshold_min = float( sys.argv[ -8 ] )
threshold_max = float( sys.argv[ -7 ] )
method = sys.argv[ -6 ]
display = sys.argv[ -5 ]
black_background = jython_utils.asbool( sys.argv[ -4 ] )
# TODO: this is not being used.
stack_histogram = 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:
    # 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","iterations=1 count=1 edm=Overwrite do=Nothing" )
    # Set the options.
    if black_background:
        method_str = "%s dark" % method
    else:
        method_str = method
    IJ.setAutoThreshold( input_image_plus_copy, method_str )
    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 )
    # Run the command.
    IJ.run( input_image_plus_copy, "threshold", "" )
    # 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 ) )