Created parameters for rat and human

src/scaffoldmaker/annotation/brainstem_terms.py

@@ -3,15 +3,39 @@
 """
 
 # convention: preferred name, preferred id, followed by any other ids and alternative names
-brainstem_terms = [
-                    ("medulla oblongata", "UBERON:0001896"),
-                    ("pons", "UBERON:0000988"),
-                    ("midbrain", "UBERON:0001891"),
-                    ("diencephalon", "UBERON:0001894"),
-                    ("brainstem", "UBERON:0002298")
-                ]
+brainstem_terms = [ # Landmarks and groups
+                    ("brainstem", "UBERON:0002298", "ILX:0101444"),
+                    ("central canal of spinal cord", "UBERON:0002291", "ILX:0724457"),
+                    ("cerebral aqueduct", "UBERON:0002289", "ILX:0101977"),
+                    ("diencephalon", "UBERON:0001894", "ILX:0103217"),
+                    ("foramen caecum of medulla oblongata", "ILX:0746371"),
+                    ("medulla oblongata", "UBERON:0001896", "ILX:0106736"),
+                    ("midbrain", "UBERON:0001891", "ILX:0106935"),
+                    ("middle cerebellar peduncle", "UBERON:0002152", "ILX:0106956"),
+                    ("obex", "ILX:0107862"),
+                    ("pons", "UBERON:0000988", "ILX:0109019"),
 
-def get_brainstem_annotation_term(name : str):
+                    # Geometric markers
+                    ("brainstem dorsal midline caudal point", "ILX:0778144"),
+                    ("brainstem ventral midline caudal point", "ILX:0778145"),
+                    ("brainstem dorsal midline cranial point", "ILX:0778146 "),
+                    ("brainstem ventral midline cranial point", "ILX:0778147"),
+                    ("brainstem dorsal midline pons-medulla junction", "ILX:0778148"),
+                    ("brainstem ventral midline pons-medulla junction", "ILX:0778149"),
+                    ("brainstem dorsal midline midbrain-pons junction", "ILX:0778150"),
+                    ("brainstem ventral midline midbrain-pons junction", "ILX:0778151"),
+
+                    # Surface
+                    ("brainstem exterior", "ILX:0778157"),
+                    ("midbrain exterior", "ILX:0778158"),
+                    ("medulla oblongata exterior", "ILX:0778159"),
+                    ("pons exterior", "ILX:0778160"),
+                    ("brainstem-spinal cord interface", "ILX:0778162"),
+                    ("thalamus-brainstem interface", "ILX:0778163")
+
+]
+
+def get_brainstem_term(name : str):
     """
     Find term by matching name to any identifier held for a term.
     Raise exception if name not found.

src/scaffoldmaker/meshtypes/meshtype_1d_path1.py

@@ -155,6 +155,7 @@ def makeSideDerivativesNormal(cls, region, options, functionOptions, editGroupNa
         if makeD3Normal:
             d3 = parameters[-1]
             if options['D2 derivatives']:
+                d2 = parameters[1]
                 for c in range(len(d1)):
                     d3[c] = vector.setMagnitude(vector.crossproduct3(d1[c], d2[c]), vector.magnitude(d3[c]))
             else: