[SciPy-dev] Please stress-test SVN version pf matlab reader

David Cournapeau cournape@gmail....
Tue Jan 5 21:07:39 CST 2010


Hi Matthew,

On Wed, Jan 6, 2010 at 11:00 AM, Matthew Brett <matthew.brett@gmail.com> wrote:
> Hi,
>
> For those of you interested in the matlab reader in scipy - a bout of
> 'flu left me with only enough energy to try and work out the last
> undocumented bits of the matlab file format.  I _believe_ that the
> current  SVN version of the reader:
>
> import scipy.io as sio
> a = sio.loadmat('your_matfile_here.mat')
>
> should successfully read any non-HDF matlab-written matfile - and this
> is just to ask if those of you, with mat files lying around, could try
> out the latest SVN version, and let me know that I am wrong, most
> usefully with some way of me being able to reproduce the problem.

That's great news. I have just added the numscons scripts for the new files.

Funnily enough, I was just toying with sparse matrices, and needed to
load some sparse matrices. Here is the problem I got with some sparse
files:

from scipy.io import loadmat
loadmat("odepa400.mat")

This raises an exception:

Traceback (most recent call last):
  File "read.py", line 3, in <module>
    loadmat("odepa400.mat")
  File "/home/david/local/lib/python2.6/site-packages/scipy/io/matlab/mio.py",
line 134, in loadmat
    matfile_dict = MR.get_variables()
  File "/home/david/local/lib/python2.6/site-packages/scipy/io/matlab/mio5.py",
line 347, in get_variables
    res = self.read_var_array(hdr)
  File "/home/david/local/lib/python2.6/site-packages/scipy/io/matlab/mio5.py",
line 321, in read_var_array
    return self._matrix_reader.array_from_header(header, process)
  File "mio5_utils.pyx", line 584, in
scipy.io.matlab.mio5_utils.VarReader5.array_from_header
(scipy/io/matlab/mio5_utils.c:4721)
  File "mio5_utils.pyx", line 629, in
scipy.io.matlab.mio5_utils.VarReader5.array_from_header
(scipy/io/matlab/mio5_utils.c:4370)
  File "mio5_utils.pyx", line 835, in
scipy.io.matlab.mio5_utils.VarReader5.read_struct
(scipy/io/matlab/mio5_utils.c:6774)
  File "mio5_utils.pyx", line 582, in
scipy.io.matlab.mio5_utils.VarReader5.read_mi_matrix
(scipy/io/matlab/mio5_utils.c:3999)
TypeError: Cannot convert csc_matrix to numpy.ndarray

(I needed to fix a missing import first)

The matrix may be found here:

http://www.cise.ufl.edu/research/sparse/mat/Bai/odepa400.mat (small file)

David


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