Updated set_spline routine to include more detail

mrdna/segmentmodel.py

@@ -503,11 +503,11 @@ class Segment(ConnectableElement, Group):
 
         if about is None:
             ## TODO: do this more efficiently
-            r[ids,:] = np.array([rotation_matrix.dot(r[i,:]) for i in range(r.shape[0])])
+            r[ids,:] = np.array([rotation_matrix.dot(r[i,:]) for i in ids])
         else:
             dr = np.array(about)
             ## TODO: do this more efficiently
-            r[ids,:] = np.array([rotation_matrix.dot(r[i,:]-dr) + dr for  i in range(r.shape[0])])
+            r[ids,:] = np.array([rotation_matrix.dot(r[i,:]-dr) + dr for i in ids])
 
         self.set_splines(u,r)
 
@@ -520,10 +520,14 @@ class Segment(ConnectableElement, Group):
             quats = [quaternion_from_matrix(o) for o in orientations]
             self.set_orientation_splines(u, quats)
 
-    def _set_splines_from_ends(self):
+    def _set_splines_from_ends(self, resolution=4):
         self.quaternion_spline_params = None
-        coords = np.array([self.start_position, self.end_position])
-        self.set_splines([0,1], coords)
+        r0 = np.array(self.start_position)[np.newaxis,:]
+        r1 = np.array(self.end_position)[np.newaxis,:]
+        u = np.linspace(0,1, max(3,self.num_nt//int(resolution)))
+        s = u[:,np.newaxis]
+        coords = (1-s)*r0 + s*r1
+        self.set_splines(u, coords)
 
     def clear_all(self):
         Group.clear_all(self)  # TODO: use super?
@@ -1002,11 +1006,6 @@ class DoubleStrandedSegment(Segment):
         # for l in (self.start5,self.start3,self.end3,self.end5):
         #     self.locations.append(l)
 
-        ## Set up interpolation for azimuthal angles 
-        a = np.array([self.start_position,self.end_position]).T
-        tck, u = interpolate.splprep( a, u=[0,1], s=0, k=1)
-        self.position_spline_params = (tck,u)
-        
         ## TODO: initialize sensible spline for orientation
 
     ## Convenience methods