cross products with einsums

问题

I'm trying to compute the cross-products of many 3x1 vector pairs as fast as possible. This

n = 10000
a = np.random.rand(n, 3)
b = np.random.rand(n, 3)
numpy.cross(a, b)

gives the correct answer, but motivated by this answer to a similar question, I thought that einsum would get me somewhere. I found that both

eijk = np.zeros((3, 3, 3))
eijk[0, 1, 2] = eijk[1, 2, 0] = eijk[2, 0, 1] = 1
eijk[0, 2, 1] = eijk[2, 1, 0] = eijk[1, 0, 2] = -1

np.einsum('ijk,aj,ak->ai', eijk, a, b)
np.einsum('iak,ak->ai', np.einsum('ijk,aj->iak', eijk, a), b)

compute the cross product, but their performance is disappointing: Both methods perform much worse than np.cross:

%timeit np.cross(a, b)
1000 loops, best of 3: 628 µs per loop

%timeit np.einsum('ijk,aj,ak->ai', eijk, a, b)
100 loops, best of 3: 9.02 ms per loop

%timeit np.einsum('iak,ak->ai', np.einsum('ijk,aj->iak', eijk, a), b)
100 loops, best of 3: 10.6 ms per loop

Any ideas of how to improve the einsums?

回答1:

The count of multiply operation of einsum() is more then cross(), and in the newest NumPy version, cross() doesn't create many temporary arrays. So einsum() can't be faster than cross().

Here is the old code of cross:

x = a[1]*b[2] - a[2]*b[1]
y = a[2]*b[0] - a[0]*b[2]
z = a[0]*b[1] - a[1]*b[0]

Here is the new code of cross:

multiply(a1, b2, out=cp0)
tmp = array(a2 * b1)
cp0 -= tmp
multiply(a2, b0, out=cp1)
multiply(a0, b2, out=tmp)
cp1 -= tmp
multiply(a0, b1, out=cp2)
multiply(a1, b0, out=tmp)
cp2 -= tmp

To speedup it, you need cython or numba.

回答2:

You can bring in matrix-multiplication using np.tensordot to lose one of the dimensions at the first level and then use np.einsum to lose the other dimension, like so -

np.einsum('aik,ak->ai',np.tensordot(a,eijk,axes=([1],[1])),b)

Alternatively, we can perform broadcasted elementwise multiplications between a and b using np.einsum and then lose the two dimensions in one go with np.tensordot, like so -

np.tensordot(np.einsum('aj,ak->ajk', a, b),eijk,axes=([1,2],[1,2]))

We could have performed the elementwise multiplications by introducing new axes too with something like a[...,None]*b[:,None], but it seems to slow it down.

Though, these show good improvement over the proposed np.einsum only based approaches, but fail to beat np.cross.

Runtime test -

In [26]: # Setup input arrays
    ...: n = 10000
    ...: a = np.random.rand(n, 3)
    ...: b = np.random.rand(n, 3)
    ...: 

In [27]: # Time already posted approaches
    ...: %timeit np.cross(a, b)
    ...: %timeit np.einsum('ijk,aj,ak->ai', eijk, a, b)
    ...: %timeit np.einsum('iak,ak->ai', np.einsum('ijk,aj->iak', eijk, a), b)
    ...: 
1000 loops, best of 3: 298 µs per loop
100 loops, best of 3: 5.29 ms per loop
100 loops, best of 3: 9 ms per loop

In [28]: %timeit np.einsum('aik,ak->ai',np.tensordot(a,eijk,axes=([1],[1])),b)
1000 loops, best of 3: 838 µs per loop

In [30]: %timeit np.tensordot(np.einsum('aj,ak->ajk',a,b),eijk,axes=([1,2],[1,2]))
1000 loops, best of 3: 882 µs per loop

来源：https://stackoverflow.com/questions/39662540/cross-products-with-einsums

标签

python

performance

numpy

cross-product

numpy-einsum