[Mne_analysis] Strange errors with calculating source estimates in a frequency band
Mainak Jas
mainakjas at gmail.com
Thu Jul 31 18:20:35 EDT 2014
Also, can you try something like this?
for ii, ep in enumerate(epochs):
stc = compute_source_psd_epochs(epochs=ep ...)
which would not require EpochsArray.
Mainak
On Thu, Jul 31, 2014 at 11:31 PM, Eric Larson <larson.eric.d at gmail.com>
wrote:
> What are you using for `events`? It should have the same number of entries
> as the number of epochs (1), I suspect it might not. (We should probably
> add a check in mne-python that this is the case...)
>
> Eric
>
>
> On Thu, Jul 31, 2014 at 3:37 AM, Silfverberg Sebastian <
> sebastian.silfverberg at aalto.fi> wrote:
>
>> This next snippet is from the offline version I've been testing:
>>
>>
>> for ii, data in enumerate(epochs.get_data()):
>>
>> # make the 2D epoch to 3D
>>
>> data = data[newaxis, ...]
>>
>> ep = EpochsArray(data=data, info=raw.info, events=events,
>> tmin=0,event_id=event_id, reject=reject)
>>
>> stc = compute_source_psd_epochs(epochs=ep,
>> inverse_operator=inverse_operator, lambda2=lambda2,method=method,
>> fmin=15.0, fmax=25.0, pick_ori=None, pca=True,
>>
>> bandwidth=bandwidth, n_jobs=10,
>> return_generator=False)
>>
>> and the error comes in the last command.
>>
>> What is the best way to iterate over rt_epochs? rt.epochs.next()? I'm now
>> doing just
>>
>> for ii, data in enumerate(rt_epochs):
>>
>>
>> Sebastian
>>
>> ------------------------------
>> *Lähettäjä:* mne_analysis-bounces at nmr.mgh.harvard.edu [
>> mne_analysis-bounces at nmr.mgh.harvard.edu] käyttäjän Mainak Jas [
>> mainakjas at gmail.com] puolesta
>> *Lähetetty:* 31. heinäkuuta 2014 12:22
>> *Vastaanottaja:* Discussion and support forum for the users of MNE
>> Software
>> *Aihe:* Re: [Mne_analysis] Strange errors with calculating source
>> estimates in a frequency band
>>
>> Hi Sebastian,
>>
>> It seems to me that you are somehow iterating over the epochs and stc
>> objects incorrectly. You do not need to use EpochsArray because you can
>> iterate over the Epochs object directly (same with RtEpochs I think). For
>> stc, if you have a single epoch, can you check if your iterations are
>> correct?
>>
>> A small code snippet / gist that reproduces this issue would be great.
>>
>> Mainak
>>
>>
>> On Thu, Jul 31, 2014 at 9:14 AM, Silfverberg Sebastian <
>> sebastian.silfverberg at aalto.fi> wrote:
>>
>>> Hi everyone!
>>>
>>> I have been trying to code a program that would enable to plot user
>>> selectable time windows of averaged source estimates in a certain frequency
>>> band in real time with FieldTrip Buffer. I'm now trying to simulate that in
>>> offline mode with looping through the epochs.get_data() and then building
>>> an Epoch from a single epoch with EpochsArray (because that's the way the
>>> real time sytem works). I end up with a couple of odd errors using
>>> *compute_source_psd_epochs* depending on how long my time window is. If
>>> my time window is shorter than 10 seconds, my error is this:
>>>
>>> /usr/lib/python2.7/dist-packages/IPython/utils/py3compat.pyc in
>>> execfile(fname, *where)
>>> 173 else:
>>> 174 filename = fname
>>> --> 175 __builtin__.execfile(filename, *where)
>>>
>>> /home/silfves1/mne-python/examples/omatfunktiot/jatk_off.py in <module>()
>>> 380
>>> 381
>>> --> 382 stc = compute_source_psd_epochs(epochs=ep,
>>> inverse_operator=inverse_operator, lambda2=lambda2, method=method,
>>> fmin=15.0, fmax=25.0, pick_ori=None, pca=True, bandwidth=bandwidth,
>>> n_jobs=10, return_generator=False)
>>> 383
>>> 384
>>>
>>> /home/silfves1/.local/lib/python2.7/site-packages/mne-0.8.git-py2.7.egg/mne/minimum_norm/time_frequency.pyc
>>> in compute_source_psd_epochs(epochs, inverse_operator, lambda2, method,
>>> fmin, fmax, pick_ori, label, nave, pca, inv_split, bandwidth, adaptive,
>>> low_bias, return_generator, n_jobs, verbose, pick_normal)
>>>
>>> /home/silfves1/.local/lib/python2.7/site-packages/mne-0.8.git-py2.7.egg/mne/utils.pyc
>>> in verbose(function, *args, **kwargs)
>>> 549 return ret
>>> 550 else:
>>> --> 551 ret = function(*args, **kwargs)
>>> 552 return ret
>>> 553
>>>
>>> /home/silfves1/.local/lib/python2.7/site-packages/mne-0.8.git-py2.7.egg/mne/minimum_norm/time_frequency.pyc
>>> in compute_source_psd_epochs(epochs, inverse_operator, lambda2, method,
>>> fmin, fmax, pick_ori, label, nave, pca, inv_split, bandwidth, adaptive,
>>> low_bias, return_generator, n_jobs, verbose, pick_normal)
>>> 669 # return a list
>>>
>>> 670 stcs = list()
>>> --> 671 for stc in stcs_gen:
>>> 672 stcs.append(stc)
>>> 673
>>>
>>> /home/silfves1/.local/lib/python2.7/site-packages/mne-0.8.git-py2.7.egg/mne/minimum_norm/time_frequency.pyc
>>> in _compute_source_psd_epochs(epochs, inverse_operator, lambda2, method,
>>> fmin, fmax, pick_ori, label, nave, pca, inv_split, bandwidth, adaptive,
>>> low_bias, n_jobs, verbose)
>>> 519
>>> 520 dpss, eigvals = dpss_windows(n_times, half_nbw, n_tapers_max,
>>> --> 521 low_bias=low_bias)
>>> 522 n_tapers = len(dpss)
>>> 523
>>>
>>> /home/silfves1/.local/lib/python2.7/site-packages/mne-0.8.git-py2.7.egg/mne/time_frequency/multitaper.pyc
>>> in dpss_windows(N, half_nbw, Kmax, low_bias, interp_from, interp_kind)
>>> 202 # only calculate the highest Kmax eigenvalues
>>>
>>> 203 w = linalg.eigvals_banded(ab, select='i',
>>> --> 204 select_range=(N - Kmax, N - 1))
>>> 205 w = w[::-1]
>>> 206
>>>
>>> /usr/lib/python2.7/dist-packages/scipy/linalg/decomp.pyc in
>>> eigvals_banded(a_band, lower, overwrite_a_band, select, select_range)
>>> 698 return eig_banded(a_band, lower=lower, eigvals_only=1,
>>> 699 overwrite_a_band=overwrite_a_band,
>>> select=select,
>>> --> 700 select_range=select_range)
>>> 701
>>> 702 _double_precision = ['i','l','d']
>>>
>>> /usr/lib/python2.7/dist-packages/scipy/linalg/decomp.pyc in
>>> eig_banded(a_band, lower, eigvals_only, overwrite_a_band, select,
>>> select_range, max_ev)
>>> 490 vl, vu, il, iu = 0.0, 0.0, min(select_range),
>>> max(select_range)
>>> 491 if min(il, iu) < 0 or max(il, iu) >= a1.shape[1]:
>>> --> 492 raise ValueError('select_range out of bounds')
>>> 493 max_ev = iu - il + 1
>>> 494 else: # 1, 'v', 'value'
>>>
>>> ValueError: select_range out of bounds
>>>
>>>
>>> However, if my time window is 10 seconds, here's the error then:
>>>
>>> error Traceback (most recent call
>>> last)
>>> /usr/lib/python2.7/dist-packages/IPython/utils/py3compat.pyc in
>>> execfile(fname, *where)
>>> 173 else:
>>> 174 filename = fname
>>> --> 175 __builtin__.execfile(filename, *where)
>>>
>>> /home/silfves1/mne-python/examples/omatfunktiot/jatk_off.py in <module>()
>>> 380
>>> 381
>>> --> 382 stc = compute_source_psd_epochs(epochs=ep,
>>> inverse_operator=inverse_operator, lambda2=lambda2, method=method,
>>> fmin=15.0, fmax=25.0, pick_ori=None, pca=True, bandwidth=bandwidth,
>>> n_jobs=10, return_generator=False)
>>> 383
>>> 384
>>>
>>> /home/silfves1/.local/lib/python2.7/site-packages/mne-0.8.git-py2.7.egg/mne/minimum_norm/time_frequency.pyc
>>> in compute_source_psd_epochs(epochs, inverse_operator, lambda2, method,
>>> fmin, fmax, pick_ori, label, nave, pca, inv_split, bandwidth, adaptive,
>>> low_bias, return_generator, n_jobs, verbose, pick_normal)
>>>
>>> /home/silfves1/.local/lib/python2.7/site-packages/mne-0.8.git-py2.7.egg/mne/utils.pyc
>>> in verbose(function, *args, **kwargs)
>>> 549 return ret
>>> 550 else:
>>> --> 551 ret = function(*args, **kwargs)
>>> 552 return ret
>>> 553
>>>
>>> /home/silfves1/.local/lib/python2.7/site-packages/mne-0.8.git-py2.7.egg/mne/minimum_norm/time_frequency.pyc
>>> in compute_source_psd_epochs(epochs, inverse_operator, lambda2, method,
>>> fmin, fmax, pick_ori, label, nave, pca, inv_split, bandwidth, adaptive,
>>> low_bias, return_generator, n_jobs, verbose, pick_normal)
>>> 669 # return a list
>>>
>>> 670 stcs = list()
>>> --> 671 for stc in stcs_gen:
>>> 672 stcs.append(stc)
>>> 673
>>>
>>> /home/silfves1/.local/lib/python2.7/site-packages/mne-0.8.git-py2.7.egg/mne/minimum_norm/time_frequency.pyc
>>> in _compute_source_psd_epochs(epochs, inverse_operator, lambda2, method,
>>> fmin, fmax, pick_ori, label, nave, pca, inv_split, bandwidth, adaptive,
>>> low_bias, n_jobs, verbose)
>>> 545
>>> 546 # compute tapered spectra in sensor space
>>>
>>> --> 547 x_mt, freqs = _mt_spectra(data, dpss, sfreq)
>>> 548
>>> 549 if k == 0:
>>>
>>> /home/silfves1/.local/lib/python2.7/site-packages/mne-0.8.git-py2.7.egg/mne/time_frequency/multitaper.pyc
>>> in _mt_spectra(x, dpss, sfreq, n_fft)
>>> 439 # remove mean (do not use in-place subtraction as it may
>>> modify input x)
>>>
>>> 440 x = x - np.mean(x, axis=-1)[:, np.newaxis]
>>> --> 441 x_mt = fftpack.fft(x[:, np.newaxis, :] * dpss, n=n_fft)
>>> 442
>>> 443 # only keep positive frequencies
>>>
>>>
>>> /usr/lib/python2.7/dist-packages/scipy/fftpack/basic.pyc in fft(x, n,
>>> axis, overwrite_x)
>>> 213
>>> 214 if axis == -1 or axis == len(tmp.shape) - 1:
>>> --> 215 return work_function(tmp,n,1,0,overwrite_x)
>>> 216
>>> 217 tmp = swapaxes(tmp, axis, -1)
>>>
>>> error: failed in converting 1st argument `x' of _fftpack.zrfft to
>>> C/Fortran array
>>>
>>> I don't know, why these error come up. Do some of you have any ideas to
>>> help? Thank you so much!
>>>
>>> Best regards
>>>
>>> Sebastian
>>>
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