--- a/imagej2_analyze_skeleton.py	Tue Aug 04 13:19:34 2015 -0400
+++ b/imagej2_analyze_skeleton.py	Wed Aug 26 14:36:10 2015 -0400
@@ -9,13 +9,12 @@
 parser = argparse.ArgumentParser()
 parser.add_argument( '--input', dest='input', help='Path to the input file' )
 parser.add_argument( '--input_datatype', dest='input_datatype', help='Datatype of the input image' )
+parser.add_argument( '--black_background', dest='black_background', help='Black background' )
 parser.add_argument( '--prune_cycle_method', dest='prune_cycle_method', default='none', help='Prune cycle method' )
 parser.add_argument( '--prune_ends', dest='prune_ends', default='no', help='Prune ends' )
 parser.add_argument( '--calculate_largest_shortest_path', dest='calculate_largest_shortest_path', default='no', help='Calculate largest shortest path' )
 parser.add_argument( '--show_detailed_info', dest='show_detailed_info', default='no', help='Show detailed info' )
 parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' )
-parser.add_argument( '--max_heap_size_type', dest='max_heap_size_type', help='Type (default or megabytes) of max_heap_size value' )
-parser.add_argument( '--max_heap_size', dest='max_heap_size', help='Maximum size of the memory allocation pool used by the JVM.' )
 parser.add_argument( '--output', dest='output', help='Path to the output file' )
 args = parser.parse_args()
 
@@ -24,8 +23,6 @@
 # work for some features.  The following creates a symlink with an appropriate file
 # extension that points to the Galaxy dataset.  This symlink is used by ImageJ.
 tmp_input_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.input, args.input_datatype )
-# Set the size of the memory allocation pool used by the JVM.
-memory_size = imagej2_base_utils.get_max_heap_size_value( args.max_heap_size_type, args.max_heap_size )
 
 # Define command response buffers.
 tmp_out = tempfile.NamedTemporaryFile().name
@@ -36,11 +33,12 @@
 error_log = tempfile.NamedTemporaryFile( delete=False ).name
 
 # Build the command line.
-cmd = imagej2_base_utils.get_base_command_imagej2( memory_size, jython_script=args.jython_script )
+cmd = imagej2_base_utils.get_base_command_imagej2( None, jython_script=args.jython_script )
 if cmd is None:
     imagej2_base_utils.stop_err( "ImageJ not found!" )
 cmd += ' %s' % error_log
 cmd += ' %s' % tmp_input_path
+cmd += ' %s' % args.black_background
 cmd += ' %s' % args.prune_cycle_method
 cmd += ' %s' % args.prune_ends
 cmd += ' %s' % args.calculate_largest_shortest_path