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

Ariel Rokem arokem@berkeley....
Thu Jan 7 21:58:55 CST 2010


Hi Matthew,

further - if I set both squeeze_me and struct_as_record to True (does that
make sense?), I get into some rather nasty situations, where I can't use the
variables in the matfile:

For example:

In [40]: m =
sio.loadmat('C-RA_Adapt.mat',squeeze_me=True,struct_as_record=True)

In [41]: h = m['history']

In [42]: h1 = h[0]

In [43]: q = h1['q']

Yes - I know it's a bit convoluted, but that's how it is.

Now - I can't do anything with 'q':

In [44]: q[0]
---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)

/Users/arokem/Projects/SchizoSpread/OrientationTuningBehavior/DATA/<ipython
console> in <module>()

IndexError: 0-d arrays can't be indexed

In [45]: q.dtype
Out[45]: dtype('object')

There's supposed to be an array called 'x' in there:

In [46]: q['x']
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)

/Users/arokem/Projects/SchizoSpread/OrientationTuningBehavior/DATA/<ipython
console> in <module>()

ValueError: field named x not found.


Am I doing something unreasonable?

Cheers,

Ariel






On Thu, Jan 7, 2010 at 7:26 PM, Ariel Rokem <arokem@berkeley.edu> wrote:

> Hi Matthew,
>
> I updated my scipy from the repo and I am still getting the following
> behavior (also reported a couple of days ago on scipy-user), when dealing
> with the attached file:
>
> In [6]: m =
> sio.loadmat('/Users/arokem/Projects/SchizoSpread/OrientationTuningBehavior/DATA/C-RA_Adapt.mat')
>
> /Library/Frameworks/Python.framework/Versions/6.0.0/lib/python2.6/site-packages/scipy/io/matlab/mio.py:99:
> FutureWarning: Using struct_as_record default value (False) This will change
> to True in future versions
>   return MatFile5Reader(byte_stream, **kwargs)
>
> So far, so good - this is to be expected. But, for obvious reasons, I want
> to set the kwarg squeeze_me to True:
>
> In [7]: m =
> sio.loadmat('/Users/arokem/Projects/SchizoSpread/OrientationTuningBehavior/DATA/C-RA_Adapt.mat',squeeze_me=True)
> ---------------------------------------------------------------------------
> TypeError                                 Traceback (most recent call last)
>
> /Users/arokem/<ipython console> in <module>()
>
> /Library/Frameworks/Python.framework/Versions/6.0.0/lib/python2.6/site-packages/scipy/io/matlab/mio.pyc
> in loadmat(file_name, mdict, appendmat, **kwargs)
>     132     '''
>     133     MR = mat_reader_factory(file_name, appendmat, **kwargs)
> --> 134     matfile_dict = MR.get_variables()
>     135     if mdict is not None:
>     136         mdict.update(matfile_dict)
>
> /Library/Frameworks/Python.framework/Versions/6.0.0/lib/python2.6/site-packages/scipy/io/matlab/mio5.pyc
> in get_variables(self, variable_names)
>     411                 continue
>     412             try:
> --> 413                 res = self.read_var_array(hdr, process)
>     414             except MatReadError, err:
>     415                 warnings.warn(
>
> /Library/Frameworks/Python.framework/Versions/6.0.0/lib/python2.6/site-packages/scipy/io/matlab/mio5.pyc
> in read_var_array(self, header, process)
>     380            `process`.
>     381         '''
> --> 382         return self._matrix_reader.array_from_header(header,
> process)
>     383
>     384     def get_variables(self, variable_names=None):
>
> /Library/Frameworks/Python.framework/Versions/6.0.0/lib/python2.6/site-packages/scipy/io/matlab/mio5_utils.so
> in scipy.io.matlab.mio5_utils.VarReader5.array_from_header
> (scipy/io/matlab/mio5_utils.c:4718)()
>
> /Library/Frameworks/Python.framework/Versions/6.0.0/lib/python2.6/site-packages/scipy/io/matlab/mio5_utils.so
> in scipy.io.matlab.mio5_utils.VarReader5.array_from_header
> (scipy/io/matlab/mio5_utils.c:4367)()
>
> /Library/Frameworks/Python.framework/Versions/6.0.0/lib/python2.6/site-packages/scipy/io/matlab/mio5_utils.so
> in scipy.io.matlab.mio5_utils.VarReader5.read_struct
> (scipy/io/matlab/mio5_utils.c:6771)()
>
> /Library/Frameworks/Python.framework/Versions/6.0.0/lib/python2.6/site-packages/scipy/io/matlab/mio5_utils.so
> in scipy.io.matlab.mio5_utils.VarReader5.read_mi_matrix
> (scipy/io/matlab/mio5_utils.c:3995)()
>
> /Library/Frameworks/Python.framework/Versions/6.0.0/lib/python2.6/site-packages/scipy/io/matlab/mio5_utils.so
> in scipy.io.matlab.mio5_utils.VarReader5.array_from_header
> (scipy/io/matlab/mio5_utils.c:4610)()
>
> /Library/Frameworks/Python.framework/Versions/6.0.0/lib/python2.6/site-packages/scipy/io/matlab/mio_utils.so
> in scipy.io.matlab.mio_utils.process_element
> (scipy/io/matlab/mio_utils.c:1272)()
>
> /Library/Frameworks/Python.framework/Versions/6.0.0/lib/python2.6/site-packages/scipy/io/matlab/mio_utils.so
> in scipy.io.matlab.mio_utils.process_element
> (scipy/io/matlab/mio_utils.c:1149)()
>
> TypeError: Cannot convert mat_struct to numpy.ndarray
>
>
> This doesn't happen when I set struct_as_record to True as well, but then I
> need to deal with all these record arrays that I get. And yes - it does seem
> to work faster, when it works, though I haven't done any thorough testing of
> that.
>
> Any ideas?
>
> Cheers,
>
> Ariel
>
>
>
>
>


-- 
Ariel Rokem
Helen Wills Neuroscience Institute
University of California, Berkeley
http://argentum.ucbso.berkeley.edu/ariel
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