Updated initial placement of orientation beads

segmentmodel.py

@@ -394,15 +394,23 @@ class Segment(ConnectableElement, Group):
     def contour_to_orientation(self,s):
         assert( isinstance(s,float) or isinstance(s,int) or len(s) == 1 )   # TODO make vectorized version
         orientation = None
-        if self.start_orientation is not None:
-            # axis = self.start_orientation.dot( np.array((0,0,1)) )
-            if self.quaternion_spline_params is None:
-                axis = self.contour_to_tangent(s)
-                orientation = rotationAboutAxis( axis, self.twist_per_nt*self.contour_to_nt_pos(s), normalizeAxis=True )
+        if self.quaternion_spline_params is None:
+            axis = self.contour_to_tangent(s)
+            axis = axis / np.linalg.norm(axis)
+            rotAxis = np.cross(axis,np.array((0,0,1)))
+            rotAxisL = np.linalg.norm(rotAxis)
+            theta = np.arcsin(rotAxisL)
+
+            if rotAxisL > 0.001:
+                orientation0 = rotationAboutAxis( rotAxis/rotAxisL, theta*180/np.pi, normalizeAxis=False )
             else:
-                q = interpolate.splev( s, self.quaternion_spline_params )
-                if len(q) > 1: q = np.array(q).T # TODO: is this needed?
-                orientation = quaternion_to_matrix(q)
+                orientation0 = np.eye(3)
+            orientation = rotationAboutAxis( axis, self.twist_per_nt*self.contour_to_nt_pos(s), normalizeAxis=False )
+            orientation = orientation.dot(orientation0)
+        else:
+            q = interpolate.splev( s, self.quaternion_spline_params )
+            if len(q) > 1: q = np.array(q).T # TODO: is this needed?
+            orientation = quaternion_to_matrix(q)
         return orientation
 
     def get_contour_sorted_connections_and_locations(self,type_):