Issues in opening and reading .mat files in python

Question

I have some important data (structured array) in Matlab with .mat extension which I want to open in python, I tried almost every blog from stack-overflow to access my data but still unsuccessful I need not just to load the data in python but to work on them after making numpy arrays. I loaded them in Windows but unable to access sub-arrays.

I used the following command:

    import numpy as np, h5py, scipy.io
    scipy.io.loadmat('/media/sibte/DATA and SOFTWARE/DATA/recovery/GENERAL SOFTWARE/MATLAB/2_Programming Files/MATLAB Files/ASTRONOMICAL DATA and WORKING on it/NVSS.mat')

this result in the following error:

    Traceback (most recent call last):
    File "<pyshell#1>", line 1, in <module>
    scipy.io.loadmat('/media/sibte/DATA and SOFTWARE/DATA/recovery/GENERAL SOFTWARE/MATLAB/2_Programming Files/MATLAB Files/ASTRONOMICAL DATA and WORKING on it/NVSS.mat')
    File "/usr/lib/python2.7/dist-packages/scipy/io/matlab/mio.py", line 126, in loadmat
matfile_dict = MR.get_variables(variable_names)
    File "/usr/lib/python2.7/dist-packages/scipy/io/matlab/mio4.py", line 394, in get_variables
hdr, next_position = self.read_var_header()
    File "/usr/lib/python2.7/dist-packages/scipy/io/matlab/mio4.py", line 350, in read_var_header
hdr = self._matrix_reader.read_header()
    File "/usr/lib/python2.7/dist-packages/scipy/io/matlab/mio4.py", line 121, in read_header
    raise ValueError('O in MOPT integer should be 0, wrong format?')
    ValueError: O in MOPT integer should be 0, wrong format?

Then I used the h5py command to load:

    f = h5py.File('/media/sibte/DATA and SOFTWARE/DATA/recovery/GENERAL SOFTWARE/MATLAB/2_Programming Files/MATLAB Files/ASTRONOMICAL DATA and WORKING on it/NVSS.mat','r+')

this results in following error:

    Traceback (most recent call last):
    File "<pyshell#2>", line 1, in <module>
    f = h5py.File('/media/sibte/DATA and SOFTWARE/DATA/recovery/GENERAL SOFTWARE/MATLAB/2_Programming Files/MATLAB Files/ASTRONOMICAL DATA and WORKING on it/NVSS.mat','r+')
    File "/usr/lib/python2.7/dist-packages/h5py/_hl/files.py", line 207, in __init__
fid = make_fid(name, mode, userblock_size, fapl)
    File "/usr/lib/python2.7/dist-packages/h5py/_hl/files.py", line 81, in make_fid
fid = h5f.open(name, h5f.ACC_RDWR, fapl=fapl)
    File "h5f.pyx", line 71, in h5py.h5f.open (h5py/h5f.c:1806)
    IOError: unable to open file (File accessibilty: Unable to open file)

I have spent several days in loading this data, I have many other data in .mat format to access but fed up with this deadlock

NOTE: I am using IDLE-Python-2.7.6 shell on UBUNTU-14.04

I had worked on these file in Matlab-R2010a v7.1 on Windows-7

Any help regarding this issue?

I think your `.mat` files are crashed! It can read the entire files. Try to download it again or open it with `Matlab` to see whether it is correct or crashed!? Can you upload your `.mat` files? — Hadi, Aug 24 '14 at 08:44

score 0 · Answer 1 · answered Sep 16 '14 at 00:29

I suspect that you are trying to load V7.3+ hdf5 .mat files with a reader that expects to see old style 7.2 .mat files. I have not used h5py so I am not sure why that module is not working.

Try using the hdf5storage python module to load your .mat files:

import hdf5storage
hdf5storage.loadmat(...)

The hdf5storage module is modeled after scipy.io and has helped me avoid compatability problems. If hdf5storage doesn't work, your .mat files may be corrupt.

Issues in opening and reading .mat files in python

1 Answers1