[Mne_analysis] Maxwell Filter and Projections

[dgw]

What does the data look like where you need to "fix it"? It still
isn't clear what problems the data are causing.

Alternatively, you could just set the raw to 0s there (the same
equivalent as skip in maxfilter).

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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