--- a/jython_script.py	Sun Oct 11 13:30:44 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,49 +0,0 @@
-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 ) )