Apply function to every matrix of numpy array

Question

I would like to apply a function to each of the 3x3 matrices in my (6890,6890,3,3) numpy array. Until now, I have tried using vectorization on a smaller example and with a simpler function which didn't work out.

def myfunc(x):
    return np.linalg.norm(x)

m = np.arange(45).reshape(5,3,3)
t = m.shape[0]
r = np.zeros((t, t))

q = m[:,None,...] @ m.swapaxes(1,2) # m[i] @ m[j].T
f = np.vectorize(q, otypes=[np.float])
res = myfunc(f)

Is vectorization even the right approach to solve this problem efficiently or should I try something else? I've also looked into numpy.apply_along_axis but this only applies to 1D-subarrays.

Is the listed myfunc the actual function that you are working with? — Divakar
– Divakar, Commented Jun 3, 2019 at 11:58
No, it isn't. This is the actual one: pyquaternion.Quaternion.log(pyquaternion.Quaternion(matrix=m)).norm — Rani
– Rani, Commented Jun 3, 2019 at 12:29
If your function can only work with the 3x3 array, there's no way around calling it 6890*6890 times. — hpaulj
– hpaulj, Commented Jun 3, 2019 at 13:16
np.vectorize will be hard to apply, annd is slower. `apply_along isn't any easier. — hpaulj
– hpaulj, Commented Jun 3, 2019 at 13:17
np.vectorize has a note saying it doesn't promise any speedup. Also it normally passes scalar elements to your function, where as you want to pass 2d elements. It has a signature mode that can do that, but that's even slower. — hpaulj
– hpaulj, Commented Jun 3, 2019 at 16:48

Zaraki Kenpachi · Accepted Answer · 2019-06-03 12:16:44Z

1

You need loop over each element and apply function:

import numpy as np

# setup function
def myfunc(x):
    return np.linalg.norm(x*2)

# setup data array
data = np.arange(45).reshape(5, 3, 3)

# loop over elements and update
for item in np.nditer(data, op_flags = ['readwrite']):
    item[...] = myfunc(item)

If you need apply function for entire 3x3 array then use:

out_data = []
for item in data:
    out_data.append(myfunc(item))

Output:

[14.2828568570857, 39.761790704142086, 66.4529909033446, 93.32202312423365, 120.24974012445931]

edited Jun 3, 2019 at 12:16

answered Jun 3, 2019 at 12:09

Zaraki Kenpachi

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1 Comment

Rani Over a year ago

If I wanted to apply the function to all the 6890*6890 3x3 matrices in my actual (6890,6890,3,3) array would I have to introduce a nested for-loop (with 6890*6890 iterations)? Because this is exactly what I want to avoid as it's way too slow.

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