--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/imagej2_bunwarpj_align_jython_script.py	Tue Sep 17 16:57:15 2019 -0400
@@ -0,0 +1,37 @@
+import sys
+import jython_utils
+from ij import IJ
+
+# Fiji Jython interpreter implements Python 2.5 which does not
+# provide support for argparse.
+
+if sys.argv[ -1 ].lower() in [ 'true' ]:
+    mono = True
+else:
+    mono = False
+
+if mono:
+    # bUnwarpJ has been called with the -mono param.
+    source_tiff_path = sys.argv[ -4 ]
+    source_datatype = sys.argv[ -3 ]
+    source_path = sys.argv[ -2 ]
+else:
+    source_tiff_path = sys.argv[ -7 ]
+    source_datatype = sys.argv[ -6 ]
+    source_path = sys.argv[ -5 ]
+    target_tiff_path = sys.argv[ -4 ]
+    target_datatype = sys.argv[ -3 ]
+    target_path = sys.argv[ -2 ]
+
+# Save the Registered Source Image.
+registered_source_image = IJ.openImage( source_tiff_path )
+if source_datatype == 'tiff':
+    registered_source_image = jython_utils.convert_before_saving_as_tiff( registered_source_image )
+IJ.saveAs( registered_source_image, source_datatype, source_path )
+
+if not mono:
+    # Save the Registered Target Image.
+    registered_target_image = IJ.openImage( target_tiff_path )
+    if target_datatype == 'tiff':
+        registered_target_image = jython_utils.convert_before_saving_as_tiff( registered_target_image )
+    IJ.saveAs( registered_target_image, target_datatype, target_path )