cmu_mocap() example mostly working except some fiddling with axes for visualization. Also changes to naming of scaling and offset parameters in GP.py and deal with the case where the scale parameter is zero.

GPy/util/mocap.py

@@ -157,6 +157,13 @@ class skeleton(tree):
     def __init__(self):
         tree.__init__(self)
 
+    def connection_matrix(self):
+        connection = np.zeros((len(self.vertices), len(self.vertices)), dtype=bool)
+        for i in range(len(self.vertices)):
+            for j in range(len(self.vertices[i].children)):
+                connection[i, self.vertices[i].children[j]] = True
+        return connection
+
     def to_xyz(self, channels):
         raise NotImplementedError, "this needs to be implemented to use the skeleton class"
 
@@ -557,6 +564,7 @@ class acclaim_skeleton(skeleton):
                     lin = self.read_line(fid)
             else:
                 raise Error, 'Unrecognised file format'
+            self.finalize()
             
     def read_units(self, fid):
         """Read units from an acclaim skeleton file stream."""