Re: [Numpy-discussion] distance matrix speed

[Johannes L. <a.u...@gm...>]

Hi,

def dtest():
=A0 =A0 A =3D random( [4,2])
=A0 =A0 B =3D random( [1000,2])

    # drawback: memory usage temporarily doubled
    # solution see below
    d =3D A[:, newaxis, :] - B[newaxis, :, :]
    # written as 3 expressions for more clarity
    d =3D sqrt((d**2).sum(axis=3D2))
    return d


def dtest_lowmem():
    A =3D random( [4,2])
    B =3D random( [1000,2])

    d =3D zeros([4, 1000], dtype=3D'f')  # stores result
    for i in range(len(A)):
        # the loop should not impose much loss in speed
        dtemp =3D A[i, newaxis, :] - B[:, :]
        dtemp =3D sqrt((dtemp**2).sum(axis=3D1))
        d[i] =3D dtemp
    return d

(both functions untested....)

HTH, Johannes