[Numpy-discussion] Distance Matrix speed
Alan G Isaac
aisaac at american.edu
Tue Jun 20 02:15:31 CDT 2006
I think the distance matrix version below is about as good
as it gets with these basic strategies.
fwiw,
Alan Isaac
def dist(A,B):
rowsA, rowsB = A.shape[0], B.shape[0]
distanceAB = empty( [rowsA,rowsB] , dtype=float)
if rowsA <= rowsB:
temp = empty_like(B)
for i in range(rowsA):
#store A[i]-B in temp
subtract( A[i], B, temp )
temp *= temp
sqrt( temp.sum(axis=1), distanceAB[i,:])
else:
temp = empty_like(A)
for j in range(rowsB):
#store A-B[j] in temp
temp = subtract( A, B[j], temp )
temp *= temp
sqrt( temp.sum(axis=1), distanceAB[:,j])
return distanceAB
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