--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/jython_script.py	Tue Jun 09 12:22:23 2015 -0400
@@ -0,0 +1,52 @@
+import sys
+import imagej2_base_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 ]
+
+def convert_before_saving_as_tiff( registered_image ):
+    # The bUnwarpJ macro produces tiff image stacks consisting of 3
+    # slices which can be viewed in ImageJ.  The 3 slices are::
+    # 1) the registered image, 2) the target image and 3) the black/white
+    # warp image.  Galaxy supports only single-layered images, so we have
+    # to convert the image to something other than tiff so that slices are
+    # eliminated and we can then convert back to tiff for saving.  This is
+    # kind of a hack - there is probably a way to do this without converting
+    # twice.  I messed around with the the ImageJ getSlice() method, but
+    # couldn't get it to produce what is needed here.
+    tmp_dir = imagej2_base_utils.get_temp_dir()
+    tmp_out_png_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, 'png' )
+    IJ.saveAs( registered_image, 'png', tmp_out_png_path )
+    return IJ.openImage( tmp_out_png_path )
+
+# Save the Registered Source Image.
+registered_source_image = IJ.openImage( source_tiff_path )
+if source_datatype == 'tiff':
+    registered_source_image = 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 = convert_before_saving_as_tiff( registered_target_image )
+    IJ.saveAs( registered_target_image, target_datatype, target_path )