Mike Vandenberg - 11 months ago 74

Python Question

I understand that

`transpose`

`ndarray`

`permute`

`C = @bsxfun(@times, permute(A,[4,2,5,1,3]), permute(B, [1,6,2,7,3,4,5])`

where A is a 3D tensor of shape NxNxM and B is a 5D tensor of shape NxNxMxPxP. The above function is meant to vectorize looped kronecker products. I'm assuming that Matlab is adding 2 singleton dimensions for both A and B which is why it's able to rearrange them. I'm looking to port this code over to Python

`bsxfun`

`ndarray`

`A = A[...,None,None]`

B = B[...,None,None]

C = transpose(A,[3,1,4,0,2])*transpose(B,[0,5,1,6,2,3,4])

`return transpose(axes)`

ValueError: axes don't match array

My first guess is to do a

`reshape`

I now get the following error:

`mults = transpose(rho_in,[3,1,4,0,2])*transpose(proj,[0,5,1,6,2,3,4])`

ValueError: operands could not be broadcast together with shapes (1,9,1,9,8) (9,1,9,1,8,40,40)

EDIT: Amended my question to be less about adding singleton dimensions but more about correctly broadcasting this matlab multiplication in python.

Answer Source

The huge difference between MATLAB and numpy is that the former uses column-major format for its arrays, while the latter row-major. The corollary is that implicit singleton dimensions are handled differently.

Specifically, MATLAB explicitly ignores trailing singleton dimensions: `rand(3,3,1,1,1,1,1)`

is actually a `3x3`

matrix. Along these lines, you can use `bsxfun`

to operate on two arrays if their *leading* dimensions match: `NxNxM`

is implicitly `NxNxMx1x1`

which is compatible with `NxNxMxPxP`

.

Numpy, on the other hand, allows implicit singletons *up front*. You need to `permute`

your arrays in a way that their *trailing* dimensions match up, for instance shape `(40,40,9,1,9,1,8)`

with shape `(1,9,1,9,8)`

, and the result should be of shape `(40,40,9,9,9,9,8)`

.

Dummy example:

```
>>> import numpy as np
>>> (np.random.rand(40,40,9,1,9,1,8)+np.random.rand(1,9,1,9,8)).shape
(40, 40, 9, 9, 9, 9, 8)
```

Note that what you're trying to do can probably be done using `numpy.einsum`

. I suggest taking a closer look at that. An example of what I mean: from your question I gathered that you want to perform this: take elements `A[1:N,1:N,1:M]`

and `B[1:N,1:N,1:M,1:P,1:P]`

and construct a new array `C[1:N,1:N,1:N,1:N,1:M,1:P,1:P]`

such that

```
C[i1,i2,i3,i4,i5,i6,i7] = A[i2,i4,i5]*B[i1,i3,i5,i6,i7]
```

If this is correct, you can indeed use `numpy.einsum()`

:

```
>>> a = np.random.rand(3,3,2)
>>> b = np.random.rand(3,3,2,4,4)
>>> np.einsum('ijk,lmkno->limjkno',a,b).shape
(3, 3, 3, 3, 2, 4, 4)
```

Two things should be noted, though. Firstly, the above operation will be very memory-intense, which should be expected for cases of vectorization (where you usually win CPU time at the expense of memory need). Secondly, you should seriously consider rearranging the data model when you port your code. The reason that broadcasting works differently in the two languages is intricately connected to the column-major/row-major difference. This also implies that in MATLAB you should work with *leading* indices first, since `A(:,i2,i3)`

corresponds to a contiguous block of memory, while `A(i1,i2,:)`

does not. Conversely, in numpy `A[i1,i2,:]`

is contiguous, while `A[:,i2,i3]`

is not.

These considerations suggest that you should set up the logistics of your data such that vectorized operations preferably work with leading indices in MATLAB and trailing indices in numpy. You could still use `numpy.einsum`

to perform the operation itself, however your dimensions should be in a different (possibly reverse) order compared to MATLAB, at least if we assume that both versions of the code use an optimal setup.