[Mne_analysis] Maxwell Filter and Projections

[Eric Larson]

That error is different from the SVD one, but I suspect it has the same
underlying cause (Anaconda using outdated build tools). To avoid derailing
the original topic too much, can you open an mne-python issue for this
specific error scipy.linalg error? We can tackle debugging steps there. If
you can anonymize the file, upload it somewhere, give the minimal steps to
reproduce it, and paste the output of `mne.sys_info()` (assuming you're on
`master`) that would help.

Eric


On Fri, Mar 25, 2016 at 2:18 PM, Sam Zorowitz <szorowi1 at gmail.com> wrote:

> @ Dan: We were trying to move away from the command line version for a
> number of reasons. As far as I know, there is no -skip option in the python
> implementation.
>
> @ Eric: We are using the Anaconda distribution, and I was not able to
> reproduce the error from the thread you linked. When we are getting an
> error, it looks like this:
>
> RuntimeWarning: invalid value encountered in greater
>>   num = np.sum(s > tol, dtype=int)
>>
>
>
> Traceback (most recent call last):
>>   File "motion_correction.py", line 32, in <module>
>>     raw = maxwell_filter(raw, st_duration=st_duration,
>> destination=trans.mean(axis=0), bad_condition='warning')
>>
>> File "<string>", line 2, in maxwell_filter
>>
>>  File "/homes/5/szoro/.local/lib/python2.7/site-packages/mne/utils.py",
>> line 551, in verbose
>>     return function(*args, **kwargs)
>>
>>  File
>> "/homes/5/szoro/.local/lib/python2.7/site-packages/mne/preprocessing/maxwell.py",
>> line 404, in maxwell_filter
>>     t_proj = _overlap_projector(orig_in_data, resid, st_correlation)
>>
>>  File
>> "/homes/5/szoro/.local/lib/python2.7/site-packages/mne/preprocessing/maxwell.py",
>> line 1237, in _overlap_projector
>>     overwrite_a=True, mode='economic', **check_disable)[0].T
>>
>>  File
>> "/homes/5/szoro/.local/lib/python2.7/site-packages/scipy/linalg/decomp_qr.py",
>> line 142, in qr
>>     overwrite_a=overwrite_a)
>>
>>  File
>> "/homes/5/szoro/.local/lib/python2.7/site-packages/scipy/linalg/decomp_qr.py",
>> line 20, in safecall
>>     ret = f(*args, **kwargs)
>>
>
>
> ValueError: failed to create intent(cache|hide)|optional array-- must
>> have defined dimensions but got (0,)
>
>
>  Unfortunately I can't quite parse what's going on here in the error
> message.
>
> On Fri, Mar 25, 2016 at 1:47 PM, Eric Larson <larson.eric.d at gmail.com>
> wrote:
>
>> The short of it is that we were running into some issues with the Maxwell
>>> filter function, such that the SVD will not converge for certain buffers if
>>> there is an abundance of noise.
>>>
>>
>> I have observed seen this "failure to converge" problem with SVD before.
>> Are you running Anaconda? If so, could you look here, see if you can
>> reproduce the error with the .npy file from the post, and also do the `cat
>> /proc/cpuinfo` step? It will help isolate the problem, and keep attention
>> on it:
>>
>> https://github.com/ContinuumIO/anaconda-issues/issues/695
>>
>> If you're not on Anaconda, I'm curious what Python setup you're using.
>>
>> Such "high noise" segments really shouldn't be a problem for SVD. If the
>> Anaconda folks don't fix the issue, we're going to try to put a workaround
>> solution in upstream scipy:
>>
>> https://github.com/scipy/scipy/pull/5994#issuecomment-200341678
>>
>> Eric
>>
>>
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