creating Matlab cell arrays in python

Question

I'm trying to create a Matlab cell array in python and save it as a .mat file, but am running into problems when all the cells contain 2 values:

import scipy.io as sio

twoValues = {'a': array([[array([[2, 2]]), array([[3, 3]])]])}
sio.savemat('test.mat',twoValues)

In Matlab:

load('test.mat')
>>> a

a(:,:,1,1) =

           2           3


a(:,:,1,2) =

           2           3


>>> class(a)

ans =

int32

Back in python:

threeValues = {'a': array([[array([[2, 2, 2]]), array([[3, 3]])]])}
sio.savemat('test.mat',threeValues)

In Matlab:

>>> a

a = 

    [3x1 int32]    [2x1 int32]


>>> class(a)

ans =

cell

What's the reason for this?

array() is trying to pack your values in the most efficient way possible, because you're not specifying dtype, and it has to guess at how to store it. When your dimensions match, a plain matrix is evidently the preference. I am so far unsuccessful at coercing it into a cell array when the dimensions match up. — engineerC
– engineerC, Commented Nov 5, 2013 at 21:42
@CaptainMurphy As you can see in my answer, you have to make an array with dtype=object. — askewchan
– askewchan, Commented Nov 6, 2013 at 18:34

askewchan · Accepted Answer · 2013-11-05 21:11:55Z

When you do this:

a = np.array([[np.array([[2, 2]]), np.array([[3, 3]])]])

the final call to np.array actually concatenates the inner two, so you get one array at the end:

>>> a
array([[[[2, 2]],

        [[3, 3]]]])

>>> a.shape
(1, 2, 1, 2)

But to mimic a cell array you want to basically have an array of arrays. You can acheive this by setting dtype=object, but you must create the array and set the elements separately to avoid the automatic merging.

three = array([[array([[2, 2, 2]]), array([[3, 3]])]])
two = np.empty(three.shape, dtype=object)
two[0,0,0] = np.array([[2,2]])
two[0,1,0] = np.array([[3,3]])

Then:

sio.savemat('two.mat', {'two': two})

to see what they look like:

>>> two
array([[[array([[2, 2]])],
        [array([[3, 3]])]]], dtype=object)

>>> two.shape
(1, 2, 1)

Note that I may have gotten confused about your desired shape, since you have so many nested brackets, so you might have to reshape some of this, but the idea should hold regardless.

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