Read Matlab matrix into Python

Question

When I'm trying to read a Matlab matrix into python, I get the following error

>>> scipy.io.loadmat("Dynamical.mat")
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/python2.7/dist-packages/scipy/io/matlab/mio.py", line 151, in loadmat
    MR = mat_reader_factory(file_name, appendmat, **kwargs)
  File "/usr/lib/python2.7/dist-packages/scipy/io/matlab/mio.py", line 105, in mat_reader_factory
    mjv, mnv = get_matfile_version(byte_stream)
  File "/usr/lib/python2.7/dist-packages/scipy/io/matlab/miobase.py", line 221, in get_matfile_version
    % ret)
ValueError: Unknown mat file type, version 46, 48

The Dynamical.mat is a file containing the matrix

% Size = 30 30 
% Nonzeros = 252 
zzz = zeros(252,3);
zzz = [
1 1  1.4019896354966477e+01
1 2  0.0000000000000000e+00
1 3  0.0000000000000000e+00
...

It is output from a Petsc package and has not been generated by Matlab — Roy
– Roy, Commented Feb 7, 2013 at 4:52
If Matlab can indeed read these files, a convenience script to start Matlab, and open and re-save the .mat files sounds like it's in order. — Thomas
– Thomas, Commented Feb 7, 2013 at 8:28
also look into h5py. *.mat files are really just hdf files with a very particular layout. — tacaswell
– tacaswell, Commented Feb 7, 2013 at 14:45

Saullo G. P. Castro · Accepted Answer · 2013-06-09 14:14:45Z

2

This question seems to be inactive for a while, but it is good to let one alternative in case you still need to read this .mat file, assuming it is always in the format you specified:

def read_mat( file_path ):
    import numpy as np
    mat = open(file_path, 'r')
    mat.next() # % Size = 30 30
    length = int(mat.next().split()[-1])
    mat.next() # zzz = zeros(18,3)
    mat.next() # zzz = [
    ans = np.array([ map(float, mat.next().split()) for i in xrange(length) ])
    mat.close()
    return ans

answered Jun 9, 2013 at 14:14

Saullo G. P. Castro

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3 Comments

ChuNan Over a year ago

This won't work because .mat file is not ascii. You will receive the error: could not convert string to float

Saullo G. P. Castro Over a year ago

@ChuNan the answer assumes the format specified by the OP and in this case it works. Do you have an example of a binary .mat file?

ChuNan Over a year ago

I generated a simple 3X3 matrix with all double numbers. When I tried to print mat.next().split(), it shows me :"MATLAB 5.0 MAT-file Platform PCWIN created on......" and then something like x00\x01IM\x0f\x00....

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