Changeset 721 for trunk/src/space.py

Timestamp:

03/03/10 10:41:30 (2 years ago)

Author:

pierre

Message:

Speed up the DistanceDependentProbabilityConnector? in parallel in the new implementation, by computing only distances that will be used by the nodes. Spot also a bug, not fixed yet, with the positions in parallel. They are not correctly assigned by defaults

Files:

• trunk/src/space.py (modified) (2 diffs)

trunk/src/space.py

@@ -53 +53 @@
         self.offset = offset
         
-    def distances(self, A, B):
+    def distances(self, A, B, post_mask=None):
         """
         Calculate the distance matrix between two sets of coordinates, given
@@ -66 +66 @@
         d = numpy.zeros((A.shape[1], B.shape[1]), dtype=A.dtype)
         for axis in self.axes:
-            diff2 = A[axis,:,None] - B[axis,:]
+            diff2 = A[axis,:,None] - B[axis, post_mask]
             if self.periodic_boundaries is not None:
                 boundaries = self.periodic_boundaries[axis]
                 if boundaries is not None:
                     range = boundaries[1]-boundaries[0]
-                    ad2 = abs(diff2)
+                    ad2   = abs(diff2)
                     diff2 = numpy.minimum(ad2, range-ad2)
             diff2 **= 2
-            d += diff2
-        numpy.sqrt(d, d)
+            d[:,post_mask] += diff2
+        numpy.sqrt(d[:,post_mask], d[:,post_mask])
         return d