Search code examples
pythonmatlabscikit-learndata-import

Import matlab cell array into python for scikit-learn

I have a 1x81 cell array in matlab.

Each cell is a 30x30 matrix of doubles.

I want to store this in python (for use in scikit-learn) with the shape (81,30,30).

I've read a few questions here and worked through their code but I'm not having any success.

Solution

  • You can do this just using scipy.io.loadmat. But you have to be careful because of some of the differences in the formats. 

    from scipy import io
import numpy as np

C = io.loadmat('test.mat')
print type(C)
print C.keys()

    Outputs:

    <type 'dict'>
['C', '__version__', '__header__', '__globals__']

    So you can see that scipy is inlcuding a bunch more information that we don't really need, but we can see your cell C.

    C = C['C']
print type(C)

    Ouputs:

    <type 'numpy.ndarray'>

    Okay so that's got use the Cell from Matlab.

    print C.shape

    Ouputs:

    (1, 81)

    Which isn't quite right, but with a bit of processing we can get it the way you want. 

    C = np.squeeze(C)
X = np.empty((C.shape[0], C[0].shape[0], C[0].shape[1]))
for i in xrange(X.shape[0]):
    X[i] = C[i]
print X.shape

    Outputs:

    (81, 30, 30)

    Voila, we have your cell in a numpy array. Just as a forward warning, in general scikit-learn takes a 2D array as an input, not a 3D array.