--- a/jython_script.py	Sun Oct 11 13:29:46 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,72 +0,0 @@
-import jython_utils
-import sys
-from ij import IJ
-from ij.plugin.filter import Analyzer
-
-# Fiji Jython interpreter implements Python 2.5 which does not
-# provide support for argparse.
-error_log = sys.argv[ -14 ]
-input = sys.argv[ -13 ]
-black_background = jython_utils.asbool( sys.argv[ -12 ] )
-size = sys.argv[ -11 ]
-circularity_min = float( sys.argv[ -10 ] )
-circularity_max = float( sys.argv[ -9 ] )
-show = sys.argv[ -8 ]
-display_results = jython_utils.asbool( sys.argv[ -7 ] )
-all_results = jython_utils.asbool( sys.argv[ -6 ] )
-exclude_edges = jython_utils.asbool( sys.argv[ -5 ] )
-include_holes = jython_utils.asbool( sys.argv[ -4 ] )
-tmp_output_path = sys.argv[ -3 ]
-output_datatype = sys.argv[ -2 ]
-results_path = 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()
-analyzer = Analyzer( input_image_plus_copy )
-
-try:
-    # Set binary options.
-    options = jython_utils.get_binary_options( black_background=black_background )
-    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", "" )
-
-    # Set the options.
-    options = [ 'size=%s' % size ]
-    circularity_str = '%.3f-%.3f' % ( circularity_min, circularity_max )
-    options.append( 'circularity=%s' % circularity_str )
-    if show.find( '_' ) >= 0:
-        show_str = '[%s]' % show.replace( '_', ' ' )
-    else:
-        show_str = show
-    options.append( 'show=%s' % show_str )
-    if display_results:
-        options.append( 'display' )
-        if not all_results:
-            options.append( 'summarize' )
-    if exclude_edges:
-        options.append( 'exclude' )
-    if include_holes:
-        options.append( 'include' )
-    # Always run "in_situ".
-    options.append( 'in_situ' )
-
-    # Run the command.
-    IJ.run( input_image_plus_copy, "Analyze Particles...", " ".join( options ) )
-
-    # Save outputs.
-    if tmp_output_path not in [ None, 'None' ]:
-        # Save the ImagePlus object as a new image.
-        IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path )
-    if display_results and results_path not in [ None, 'None' ]:
-        results_table = analyzer.getResultsTable()
-        results_table.saveAs( results_path )
-except Exception, e:
-    jython_utils.handle_error( error_log, str( e ) )