def test_cov_scaling():
"""Test rescaling covs."""
evoked = read_evokeds(ave_fname,
condition=0,
baseline=(None, 0),
proj=True)
cov = read_cov(cov_fname)['data']
cov2 = read_cov(cov_fname)['data']
assert_array_equal(cov, cov2)
evoked.pick_channels([
evoked.ch_names[k] for k in pick_types(evoked.info, meg=True, eeg=True)
])
picks_list = _picks_by_type(evoked.info)
scalings = dict(mag=1e15, grad=1e13, eeg=1e6)
_apply_scaling_cov(cov2, picks_list, scalings=scalings)
_apply_scaling_cov(cov, picks_list, scalings=scalings)
assert_array_equal(cov, cov2)
assert cov.max() > 1
_undo_scaling_cov(cov2, picks_list, scalings=scalings)
_undo_scaling_cov(cov, picks_list, scalings=scalings)
assert_array_equal(cov, cov2)
assert cov.max() < 1
data = evoked.data.copy()
_apply_scaling_array(data, picks_list, scalings=scalings)
_undo_scaling_array(data, picks_list, scalings=scalings)
assert_allclose(data, evoked.data, atol=1e-20)
def test_cov_scaling():
"""Test rescaling covs."""
evoked = read_evokeds(ave_fname, condition=0, baseline=(None, 0),
proj=True)
cov = read_cov(cov_fname)['data']
cov2 = read_cov(cov_fname)['data']
assert_array_equal(cov, cov2)
evoked.pick_channels([evoked.ch_names[k] for k in pick_types(
evoked.info, meg=True, eeg=True
)])
picks_list = _picks_by_type(evoked.info)
scalings = dict(mag=1e15, grad=1e13, eeg=1e6)
_apply_scaling_cov(cov2, picks_list, scalings=scalings)
_apply_scaling_cov(cov, picks_list, scalings=scalings)
assert_array_equal(cov, cov2)
assert cov.max() > 1
_undo_scaling_cov(cov2, picks_list, scalings=scalings)
_undo_scaling_cov(cov, picks_list, scalings=scalings)
assert_array_equal(cov, cov2)
assert cov.max() < 1
data = evoked.data.copy()
_apply_scaling_array(data, picks_list, scalings=scalings)
_undo_scaling_array(data, picks_list, scalings=scalings)
assert_allclose(data, evoked.data, atol=1e-20)
def _estimate_rank_meeg_cov(data,
info,
scalings,
tol='auto',
return_singular=False):
"""Estimate rank of M/EEG covariance data, given the covariance.
Parameters
----------
data : np.ndarray of float, shape (n_channels, n_channels)
The M/EEG covariance.
info : Info
The measurement info.
scalings : dict | 'norm' | np.ndarray | None
The rescaling method to be applied. If dict, it will override the
following default dict:
dict(mag=1e12, grad=1e11, eeg=1e5)
If 'norm' data will be scaled by channel-wise norms. If array,
pre-specified norms will be used. If None, no scaling will be applied.
tol : float | str
Tolerance. See ``estimate_rank``.
return_singular : bool
If True, also return the singular values that were used
to determine the rank.
Returns
-------
rank : int
Estimated rank of the data.
s : array
If return_singular is True, the singular values that were
thresholded to determine the rank are also returned.
"""
picks_list = _picks_by_type(info)
scalings = _handle_default('scalings_cov_rank', scalings)
_apply_scaling_cov(data, picks_list, scalings)
if data.shape[1] < data.shape[0]:
ValueError("You've got fewer samples than channels, your "
"rank estimate might be inaccurate.")
out = estimate_rank(data,
tol=tol,
norm=False,
return_singular=return_singular)
rank = out[0] if isinstance(out, tuple) else out
ch_type = ' + '.join(list(zip(*picks_list))[0])
logger.info('estimated rank (%s): %d' % (ch_type, rank))
_undo_scaling_cov(data, picks_list, scalings)
return out
def _estimate_rank_meeg_cov(data, info, scalings, tol='auto',
return_singular=False):
"""Estimate rank of M/EEG covariance data, given the covariance.
Parameters
----------
data : np.ndarray of float, shape (n_channels, n_channels)
The M/EEG covariance.
info : Info
The measurement info.
scalings : dict | 'norm' | np.ndarray | None
The rescaling method to be applied. If dict, it will override the
following default dict:
dict(mag=1e12, grad=1e11, eeg=1e5)
If 'norm' data will be scaled by channel-wise norms. If array,
pre-specified norms will be used. If None, no scaling will be applied.
tol : float | str
Tolerance. See ``estimate_rank``.
return_singular : bool
If True, also return the singular values that were used
to determine the rank.
Returns
-------
rank : int
Estimated rank of the data.
s : array
If return_singular is True, the singular values that were
thresholded to determine the rank are also returned.
"""
picks_list = _picks_by_type(info)
scalings = _handle_default('scalings_cov_rank', scalings)
_apply_scaling_cov(data, picks_list, scalings)
if data.shape[1] < data.shape[0]:
ValueError("You've got fewer samples than channels, your "
"rank estimate might be inaccurate.")
out = estimate_rank(data, tol=tol, norm=False,
return_singular=return_singular)
rank = out[0] if isinstance(out, tuple) else out
ch_type = ' + '.join(list(zip(*picks_list))[0])
logger.info('estimated rank (%s): %d' % (ch_type, rank))
_undo_scaling_cov(data, picks_list, scalings)
return out
def fit(self, raw, verbose=None):
"""Fit the SNS operator
Parameters
----------
raw : Instance of Raw
The raw data to fit.
verbose : bool, str, int, or None
If not None, override default verbose level (see mne.verbose).
Returns
-------
sns : Instance of SensorNoiseSuppression
The modified instance.
Notes
-----
In the resulting operator, bad channels will be reconstructed by
using the good channels.
"""
logger.info('Processing data with sensor noise suppression algorithm')
logger.info(' Loading raw data')
if not isinstance(raw, BaseRaw):
raise TypeError('raw must be an instance of Raw, got %s' %
type(raw))
good_picks = _pick_data_channels(raw.info, exclude='bads')
if self._n_neighbors > len(good_picks) - 1:
raise ValueError('n_neighbors must be at most len(good_picks) '
'- 1 (%s)' % (len(good_picks) - 1, ))
logger.info(' Loading data')
picks = _pick_data_channels(raw.info, exclude=())
# The following lines are equivalent to this, but require less mem use:
# data_cov = np.cov(orig_data)
# data_corrs = np.corrcoef(orig_data) ** 2
logger.info(' Computing covariance for %s good channels' %
len(good_picks))
data_cov = compute_raw_covariance(
raw,
picks=picks,
reject=self._reject,
flat=self._flat,
verbose=False if verbose is None else verbose)['data']
good_subpicks = np.searchsorted(picks, good_picks)
del good_picks
# scale the norms so everything is close enough to unity for our checks
picks_list = _picks_by_type(pick_info(raw.info, picks), exclude=())
_apply_scaling_cov(data_cov, picks_list, self._scalings)
data_norm = np.diag(data_cov).copy()
eps = np.finfo(np.float32).eps
pos_mask = data_norm >= eps
data_norm[pos_mask] = 1. / data_norm[pos_mask]
data_norm[~pos_mask] = 0
# normalize
data_corrs = data_cov * data_cov
data_corrs *= data_norm
data_corrs *= data_norm[:, np.newaxis]
del data_norm
operator = np.zeros((len(picks), len(picks)))
logger.info(' Assembling spatial operator')
for ii in range(len(picks)):
# For each channel, the set of other signals is orthogonalized by
# applying PCA to obtain an orthogonal basis of the subspace
# spanned by the other channels.
idx = np.argsort(data_corrs[ii][good_subpicks])[::-1]
if ii in good_subpicks:
idx = good_subpicks[idx[:self._n_neighbors + 1]].tolist()
idx.pop(idx.index(ii)) # should be in there iff it is good
else:
idx = good_subpicks[idx[:self._n_neighbors]].tolist()
# We have already effectively thresholded by zeroing out components
eigval, eigvec = _pca(data_cov[np.ix_(idx, idx)], thresh=None)
# Some of the eigenvalues could be zero, don't let it blow up
norm = np.zeros(len(eigval))
use_mask = eigval > eps
norm[use_mask] = 1. / np.sqrt(eigval[use_mask])
eigvec *= norm
del eigval
# The channel is projected on this basis and replaced by its
# projection
operator[ii, idx] = np.dot(eigvec, np.dot(data_cov[ii][idx],
eigvec))
# Equivalently (and less efficiently):
# eigvec = linalg.block_diag([1.], eigvec)
# idx = np.concatenate(([ii], idx))
# corr = np.dot(np.dot(eigvec.T, data_cov[np.ix_(idx, idx)]),
# eigvec)
# operator[ii, idx[1:]] = np.dot(corr[0, 1:], eigvec[1:, 1:].T)
if operator[ii, ii] != 0:
raise RuntimeError
# scale our results back (the ratio of channel scales is what matters)
_apply_scaling_array(operator.T, picks_list, self._scalings)
_undo_scaling_array(operator, picks_list, self._scalings)
logger.info('Done')
self._operator = operator
self._used_chs = [raw.ch_names[pick] for pick in picks]
return self