BUG: Utilize reference geometry in BatchStructureSetConversion

The reference geometry was not applied to the segmentation node when performing BatchStructureSetConversion.
Reference volume is now correctly passed by to ConvertStructureSetToLabelmap, and SetReferenceImageGeometryParameterFromVolumeNode is called on the segmentation to ensure that the ClosedSurface->Binary Labelmap conversion is performed using the reference geometry.

BatchProcessing/BatchStructureSetConversion.py

@@ -98,6 +98,10 @@ def ConvertStructureSetToLabelmap(self, use_ref_image, ref_image_node_id=None):
           logging.error('No reference volume found for segmentation ' + segmentationNode.GetName())
           continue
 
+        # Use reference image for closed surface to binary labelmap conversion
+        if use_ref_image:
+          segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(referenceVolume)
+
         # Perform conversion
         if not segmentationNode.CreateBinaryLabelmapRepresentation():
           logging.error('Failed to create binary labelmap representation for segmentation ' + segmentationNode.GetName())
@@ -310,7 +314,7 @@ def main(argv):
     def save_rtslices(output_dir, use_ref_image, ref_image_node_id=None):
       # package the saving code into a subfunction
       logging.info("Convert loaded structure set to labelmap volumes")
-      labelmaps = logic.ConvertStructureSetToLabelmap(use_ref_image, ref_image_node_id=None)
+      labelmaps = logic.ConvertStructureSetToLabelmap(use_ref_image, ref_image_node_id)
 
       logging.info("Save labelmaps to directory " + output_dir)
       logic.SaveLabelmaps(labelmaps, output_dir)