[Mne_analysis] Strange errors with calculating source estimates in a frequency band
Silfverberg Sebastian
sebastian.silfverberg at aalto.fi
Thu Jul 31 06:37:39 EDT 2014
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<mailto: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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