Re: [Numpy-discussion] Distance Matrix speed

[Alan G I. <ai...@am...>]

I think the distance matrix version below is about as good=20
as it gets with these basic strategies.

fwiw,
Alan Isaac

def dist(A,B):
    rowsA, rowsB =3D A.shape[0], B.shape[0]
    distanceAB =3D empty( [rowsA,rowsB] , dtype=3Dfloat)
    if rowsA <=3D rowsB:
        temp =3D empty_like(B)
        for i in range(rowsA):
            #store A[i]-B in temp
            subtract( A[i], B, temp )
            temp *=3D temp
            sqrt( temp.sum(axis=3D1), distanceAB[i,:])
    else:
        temp =3D empty_like(A)
        for j in range(rowsB):
            #store A-B[j] in temp
            temp =3D subtract( A, B[j], temp )
            temp *=3D temp
            sqrt( temp.sum(axis=3D1), distanceAB[:,j])
    return distanceAB