# -*- coding: utf-8 -*- # Authors: Alexandre Gramfort # Matti Hamalainen # Teon Brooks # # License: BSD (3-clause) from copy import deepcopy from math import sqrt import numpy as np from scipy import linalg from ._eloreta import _compute_eloreta from ..fixes import _safe_svd from ..io.compensator import get_current_comp from ..io.constants import FIFF from ..io.open import fiff_open from ..io.tag import find_tag from ..io.matrix import (_read_named_matrix, _transpose_named_matrix, write_named_matrix) from ..io.proj import (_read_proj, make_projector, _write_proj, _needs_eeg_average_ref_proj) from ..io.tree import dir_tree_find from ..io.write import (write_int, write_float_matrix, start_file, start_block, end_block, end_file, write_float, write_coord_trans, write_string) from ..io.pick import channel_type, pick_info, pick_types from ..cov import _get_whitener, _read_cov, _write_cov, Covariance from ..forward import (compute_depth_prior, _read_forward_meas_info, write_forward_meas_info, is_fixed_orient, compute_orient_prior, convert_forward_solution) from ..source_space import (_read_source_spaces_from_tree, find_source_space_hemi, _get_vertno, _write_source_spaces_to_fid, label_src_vertno_sel) from ..transforms import _ensure_trans, transform_surface_to from ..source_estimate import _make_stc, _get_src_type from ..utils import check_fname, logger, verbose, warn class InverseOperator(dict): """InverseOperator class to represent info from inverse operator.""" def copy(self): """Return a copy of the InverseOperator.""" return InverseOperator(deepcopy(self)) def __repr__(self): # noqa: D105 """Summarize inverse info instead of printing all.""" entr = '` for more). Returns ------- inv : instance of InverseOperator The inverse operator. See Also -------- write_inverse_operator, make_inverse_operator """ check_fname(fname, 'inverse operator', ('-inv.fif', '-inv.fif.gz', '_inv.fif', '_inv.fif.gz')) # # Open the file, create directory # logger.info('Reading inverse operator decomposition from %s...' % fname) f, tree, _ = fiff_open(fname, preload=True) with f as fid: # # Find all inverse operators # invs = dir_tree_find(tree, FIFF.FIFFB_MNE_INVERSE_SOLUTION) if invs is None or len(invs) < 1: raise Exception('No inverse solutions in %s' % fname) invs = invs[0] # # Parent MRI data # parent_mri = dir_tree_find(tree, FIFF.FIFFB_MNE_PARENT_MRI_FILE) if len(parent_mri) == 0: raise Exception('No parent MRI information in %s' % fname) parent_mri = parent_mri[0] # take only first one logger.info(' Reading inverse operator info...') # # Methods and source orientations # tag = find_tag(fid, invs, FIFF.FIFF_MNE_INCLUDED_METHODS) if tag is None: raise Exception('Modalities not found') inv = dict() inv['methods'] = int(tag.data) tag = find_tag(fid, invs, FIFF.FIFF_MNE_SOURCE_ORIENTATION) if tag is None: raise Exception('Source orientation constraints not found') inv['source_ori'] = int(tag.data) tag = find_tag(fid, invs, FIFF.FIFF_MNE_SOURCE_SPACE_NPOINTS) if tag is None: raise Exception('Number of sources not found') inv['nsource'] = int(tag.data) inv['nchan'] = 0 # # Coordinate frame # tag = find_tag(fid, invs, FIFF.FIFF_MNE_COORD_FRAME) if tag is None: raise Exception('Coordinate frame tag not found') inv['coord_frame'] = tag.data # # Units # tag = find_tag(fid, invs, FIFF.FIFF_MNE_INVERSE_SOURCE_UNIT) unit_dict = {FIFF.FIFF_UNIT_AM: 'Am', FIFF.FIFF_UNIT_AM_M2: 'Am/m^2', FIFF.FIFF_UNIT_AM_M3: 'Am/m^3'} inv['units'] = unit_dict.get(int(getattr(tag, 'data', -1)), None) # # The actual source orientation vectors # tag = find_tag(fid, invs, FIFF.FIFF_MNE_INVERSE_SOURCE_ORIENTATIONS) if tag is None: raise Exception('Source orientation information not found') inv['source_nn'] = tag.data logger.info(' [done]') # # The SVD decomposition... # logger.info(' Reading inverse operator decomposition...') tag = find_tag(fid, invs, FIFF.FIFF_MNE_INVERSE_SING) if tag is None: raise Exception('Singular values not found') inv['sing'] = tag.data inv['nchan'] = len(inv['sing']) # # The eigenleads and eigenfields # inv['eigen_leads_weighted'] = False inv['eigen_leads'] = _read_named_matrix( fid, invs, FIFF.FIFF_MNE_INVERSE_LEADS, transpose=True) if inv['eigen_leads'] is None: inv['eigen_leads_weighted'] = True inv['eigen_leads'] = _read_named_matrix( fid, invs, FIFF.FIFF_MNE_INVERSE_LEADS_WEIGHTED, transpose=True) if inv['eigen_leads'] is None: raise ValueError('Eigen leads not found in inverse operator.') # # Having the eigenleads as cols is better for the inverse calcs # inv['eigen_fields'] = _read_named_matrix(fid, invs, FIFF.FIFF_MNE_INVERSE_FIELDS) logger.info(' [done]') # # Read the covariance matrices # inv['noise_cov'] = Covariance( **_read_cov(fid, invs, FIFF.FIFFV_MNE_NOISE_COV, limited=True)) logger.info(' Noise covariance matrix read.') inv['source_cov'] = _read_cov(fid, invs, FIFF.FIFFV_MNE_SOURCE_COV) logger.info(' Source covariance matrix read.') # # Read the various priors # inv['orient_prior'] = _read_cov(fid, invs, FIFF.FIFFV_MNE_ORIENT_PRIOR_COV) if inv['orient_prior'] is not None: logger.info(' Orientation priors read.') inv['depth_prior'] = _read_cov(fid, invs, FIFF.FIFFV_MNE_DEPTH_PRIOR_COV) if inv['depth_prior'] is not None: logger.info(' Depth priors read.') inv['fmri_prior'] = _read_cov(fid, invs, FIFF.FIFFV_MNE_FMRI_PRIOR_COV) if inv['fmri_prior'] is not None: logger.info(' fMRI priors read.') # # Read the source spaces # inv['src'] = _read_source_spaces_from_tree(fid, tree, patch_stats=False) for s in inv['src']: s['id'] = find_source_space_hemi(s) # # Get the MRI <-> head coordinate transformation # tag = find_tag(fid, parent_mri, FIFF.FIFF_COORD_TRANS) if tag is None: raise Exception('MRI/head coordinate transformation not found') mri_head_t = _ensure_trans(tag.data, 'mri', 'head') inv['mri_head_t'] = mri_head_t # # get parent MEG info # inv['info'] = _read_forward_meas_info(tree, fid) # # Transform the source spaces to the correct coordinate frame # if necessary # if inv['coord_frame'] not in (FIFF.FIFFV_COORD_MRI, FIFF.FIFFV_COORD_HEAD): raise Exception('Only inverse solutions computed in MRI or ' 'head coordinates are acceptable') # # Number of averages is initially one # inv['nave'] = 1 # # We also need the SSP operator # inv['projs'] = _read_proj(fid, tree) # # Some empty fields to be filled in later # inv['proj'] = [] # This is the projector to apply to the data inv['whitener'] = [] # This whitens the data # This the diagonal matrix implementing regularization and the inverse inv['reginv'] = [] inv['noisenorm'] = [] # These are the noise-normalization factors # nuse = 0 for k in range(len(inv['src'])): try: inv['src'][k] = transform_surface_to(inv['src'][k], inv['coord_frame'], mri_head_t) except Exception as inst: raise Exception('Could not transform source space (%s)' % inst) nuse += inv['src'][k]['nuse'] logger.info(' Source spaces transformed to the inverse solution ' 'coordinate frame') # # Done! # return InverseOperator(inv) @verbose def write_inverse_operator(fname, inv, verbose=None): """Write an inverse operator to a FIF file. Parameters ---------- fname : string The name of the FIF file, which ends with -inv.fif or -inv.fif.gz. inv : dict The inverse operator. verbose : bool, str, int, or None If not None, override default verbose level (see :func:`mne.verbose` and :ref:`Logging documentation ` for more). See Also -------- read_inverse_operator """ check_fname(fname, 'inverse operator', ('-inv.fif', '-inv.fif.gz', '_inv.fif', '_inv.fif.gz')) # # Open the file, create directory # logger.info('Write inverse operator decomposition in %s...' % fname) # Create the file and save the essentials fid = start_file(fname) start_block(fid, FIFF.FIFFB_MNE) # # Parent MEG measurement info # write_forward_meas_info(fid, inv['info']) # # Parent MRI data # start_block(fid, FIFF.FIFFB_MNE_PARENT_MRI_FILE) write_string(fid, FIFF.FIFF_MNE_FILE_NAME, inv['info']['mri_file']) write_coord_trans(fid, inv['mri_head_t']) end_block(fid, FIFF.FIFFB_MNE_PARENT_MRI_FILE) # # Write SSP operator # _write_proj(fid, inv['projs']) # # Write the source spaces # if 'src' in inv: _write_source_spaces_to_fid(fid, inv['src']) start_block(fid, FIFF.FIFFB_MNE_INVERSE_SOLUTION) logger.info(' Writing inverse operator info...') write_int(fid, FIFF.FIFF_MNE_INCLUDED_METHODS, inv['methods']) write_int(fid, FIFF.FIFF_MNE_COORD_FRAME, inv['coord_frame']) udict = {'Am': FIFF.FIFF_UNIT_AM, 'Am/m^2': FIFF.FIFF_UNIT_AM_M2, 'Am/m^3': FIFF.FIFF_UNIT_AM_M3} if 'units' in inv and inv['units'] is not None: write_int(fid, FIFF.FIFF_MNE_INVERSE_SOURCE_UNIT, udict[inv['units']]) write_int(fid, FIFF.FIFF_MNE_SOURCE_ORIENTATION, inv['source_ori']) write_int(fid, FIFF.FIFF_MNE_SOURCE_SPACE_NPOINTS, inv['nsource']) if 'nchan' in inv: write_int(fid, FIFF.FIFF_NCHAN, inv['nchan']) elif 'nchan' in inv['info']: write_int(fid, FIFF.FIFF_NCHAN, inv['info']['nchan']) write_float_matrix(fid, FIFF.FIFF_MNE_INVERSE_SOURCE_ORIENTATIONS, inv['source_nn']) write_float(fid, FIFF.FIFF_MNE_INVERSE_SING, inv['sing']) # # write the covariance matrices # logger.info(' Writing noise covariance matrix.') _write_cov(fid, inv['noise_cov']) logger.info(' Writing source covariance matrix.') _write_cov(fid, inv['source_cov']) # # write the various priors # logger.info(' Writing orientation priors.') if inv['depth_prior'] is not None: _write_cov(fid, inv['depth_prior']) if inv['orient_prior'] is not None: _write_cov(fid, inv['orient_prior']) if inv['fmri_prior'] is not None: _write_cov(fid, inv['fmri_prior']) write_named_matrix(fid, FIFF.FIFF_MNE_INVERSE_FIELDS, inv['eigen_fields']) # # The eigenleads and eigenfields # if inv['eigen_leads_weighted']: kind = FIFF.FIFF_MNE_INVERSE_LEADS_WEIGHTED else: kind = FIFF.FIFF_MNE_INVERSE_LEADS _transpose_named_matrix(inv['eigen_leads']) write_named_matrix(fid, kind, inv['eigen_leads']) _transpose_named_matrix(inv['eigen_leads']) # # Done! # logger.info(' [done]') end_block(fid, FIFF.FIFFB_MNE_INVERSE_SOLUTION) end_block(fid, FIFF.FIFFB_MNE) end_file(fid) fid.close() ############################################################################### # Compute inverse solution def combine_xyz(vec, square=False): """Compute the three Cartesian components of a vector or matrix together. Parameters ---------- vec : 2d array of shape [3 n x p] Input [ x1 y1 z1 ... x_n y_n z_n ] where x1 ... z_n can be vectors Returns ------- comb : array Output vector [sqrt(x1^2+y1^2+z1^2), ..., sqrt(x_n^2+y_n^2+z_n^2)] """ if vec.ndim != 2: raise ValueError('Input must be 2D') if (vec.shape[0] % 3) != 0: raise ValueError('Input must have 3N rows') n, p = vec.shape if np.iscomplexobj(vec): vec = np.abs(vec) comb = vec[0::3] ** 2 comb += vec[1::3] ** 2 comb += vec[2::3] ** 2 if not square: comb = np.sqrt(comb) return comb def _check_ch_names(inv, info): """Check that channels in inverse operator are measurements.""" inv_ch_names = inv['eigen_fields']['col_names'] if inv['noise_cov'].ch_names != inv_ch_names: raise ValueError('Channels in inverse operator eigen fields do not ' 'match noise covariance channels.') data_ch_names = info['ch_names'] missing_ch_names = sorted(set(inv_ch_names) - set(data_ch_names)) n_missing = len(missing_ch_names) if n_missing > 0: raise ValueError('%d channels in inverse operator ' % n_missing + 'are not present in the data (%s)' % missing_ch_names) _check_comps(inv['info'], info, 'inverse') def _check_or_prepare(inv, nave, lambda2, method, method_params, prepared): """Check if inverse was prepared, or prepare it.""" if not prepared: inv = prepare_inverse_operator( inv, nave, lambda2, method, method_params) elif 'colorer' not in inv: raise ValueError('inverse operator has not been prepared, but got ' 'argument prepared=True. Either pass prepared=False ' 'or use prepare_inverse_operator.') return inv @verbose def prepare_inverse_operator(orig, nave, lambda2, method='dSPM', method_params=None, verbose=None): """Prepare an inverse operator for actually computing the inverse. Parameters ---------- orig : dict The inverse operator structure read from a file. nave : int Number of averages (scales the noise covariance). lambda2 : float The regularization factor. Recommended to be 1 / SNR**2. method : "MNE" | "dSPM" | "sLORETA" | "eLORETA" Use minimum norm, dSPM (default), sLORETA, or eLORETA. method_params : dict | None Additional options for eLORETA. See Notes of :func:`apply_inverse`. .. versionadded:: 0.16 verbose : bool, str, int, or None If not None, override default verbose level (see :func:`mne.verbose` and :ref:`Logging documentation ` for more). Returns ------- inv : instance of InverseOperator Prepared inverse operator. """ if nave <= 0: raise ValueError('The number of averages should be positive') logger.info('Preparing the inverse operator for use...') inv = orig.copy() # # Scale some of the stuff # scale = float(inv['nave']) / nave inv['noise_cov']['data'] = scale * inv['noise_cov']['data'] # deal with diagonal case if inv['noise_cov']['data'].ndim == 1: logger.info(' Diagonal noise covariance found') inv['noise_cov']['eig'] = inv['noise_cov']['data'] inv['noise_cov']['eigvec'] = np.eye(len(inv['noise_cov']['data'])) inv['noise_cov']['eig'] = scale * inv['noise_cov']['eig'] inv['source_cov']['data'] = scale * inv['source_cov']['data'] # if inv['eigen_leads_weighted']: inv['eigen_leads']['data'] = sqrt(scale) * inv['eigen_leads']['data'] logger.info(' Scaled noise and source covariance from nave = %d to' ' nave = %d' % (inv['nave'], nave)) inv['nave'] = nave # # Create the diagonal matrix for computing the regularized inverse # sing = np.array(inv['sing'], dtype=np.float64) with np.errstate(invalid='ignore'): # if lambda2==0 inv['reginv'] = np.where(sing > 0, sing / (sing ** 2 + lambda2), 0) logger.info(' Created the regularized inverter') # # Create the projection operator # inv['proj'], ncomp, _ = make_projector(inv['projs'], inv['noise_cov']['names']) if ncomp > 0: logger.info(' Created an SSP operator (subspace dimension = %d)' % ncomp) else: logger.info(' The projection vectors do not apply to these ' 'channels.') # # Create the whitener # inv['whitener'], inv['colorer'], _, _ = _get_whitener( inv['noise_cov'], pca=False, prepared=True) # # Finally, compute the noise-normalization factors # inv['noisenorm'] = [] if method != 'MNE': logger.info(' Computing noise-normalization factors (%s)...' % method) if method == 'eLORETA': _compute_eloreta(inv, lambda2, method_params) elif method != 'MNE': # Here we have:: # # inv['reginv'] = sing / (sing ** 2 + lambda2) # # where ``sing`` are the singular values of the whitened gain matrix. if method == "dSPM": # dSPM normalization noise_weight = inv['reginv'] elif method == 'sLORETA': # sLORETA normalization is given by the square root of the # diagonal entries of the resolution matrix R, which is # the product of the inverse and forward operators as: # # w = diag(diag(R)) ** 0.5 # noise_weight = (inv['reginv'] * np.sqrt((1. + inv['sing'] ** 2 / lambda2))) noise_norm = np.zeros(inv['eigen_leads']['nrow']) nrm2, = linalg.get_blas_funcs(('nrm2',), (noise_norm,)) if inv['eigen_leads_weighted']: for k in range(inv['eigen_leads']['nrow']): one = inv['eigen_leads']['data'][k, :] * noise_weight noise_norm[k] = nrm2(one) else: for k in range(inv['eigen_leads']['nrow']): one = (sqrt(inv['source_cov']['data'][k]) * inv['eigen_leads']['data'][k, :] * noise_weight) noise_norm[k] = nrm2(one) # # Compute the final result # if inv['source_ori'] == FIFF.FIFFV_MNE_FREE_ORI: # # The three-component case is a little bit more involved # The variances at three consecutive entries must be squared and # added together # # Even in this case return only one noise-normalization factor # per source location # noise_norm = combine_xyz(noise_norm[:, None]).ravel() inv['noisenorm'] = 1.0 / np.abs(noise_norm) logger.info('[done]') else: inv['noisenorm'] = [] return InverseOperator(inv) @verbose def _assemble_kernel(inv, label, method, pick_ori, verbose=None): """Assemble the kernel. Simple matrix multiplication followed by combination of the current components. This does all the data transformations to compute the weights for the eigenleads. Parameters ---------- inv : instance of InverseOperator The inverse operator to use. This object contains the matrices that will be multiplied to assemble the kernel. label : Label | None Restricts the source estimates to a given label. If None, source estimates will be computed for the entire source space. method : "MNE" | "dSPM" | "sLORETA" | "eLORETA" Use minimum norm, dSPM, sLORETA, or eLORETA. pick_ori : None | "normal" | "vector" Which orientation to pick (only matters in the case of 'normal'). Returns ------- K : array, shape (n_vertices, n_channels) | (3 * n_vertices, n_channels) The kernel matrix. Multiply this with the data to obtain the source estimate. noise_norm : array, shape (n_vertices, n_samples) | (3 * n_vertices, n_samples) Normalization to apply to the source estimate in order to obtain dSPM or sLORETA solutions. vertices : list of length 2 Vertex numbers for lh and rh hemispheres that correspond to the vertices in the source estimate. When the label parameter has been set, these correspond to the vertices in the label. Otherwise, all vertex numbers are returned. source_nn : array, shape (3 * n_vertices, 3) The direction in carthesian coordicates of the direction of the source dipoles. """ # noqa: E501 eigen_leads = inv['eigen_leads']['data'] source_cov = inv['source_cov']['data'][:, None] if method in ('dSPM', 'sLORETA'): noise_norm = inv['noisenorm'][:, None] else: noise_norm = None src = inv['src'] vertno = _get_vertno(src) source_nn = inv['source_nn'] if label is not None: vertno, src_sel = label_src_vertno_sel(label, inv['src']) if method != "MNE": noise_norm = noise_norm[src_sel] if inv['source_ori'] == FIFF.FIFFV_MNE_FREE_ORI: src_sel = 3 * src_sel src_sel = np.c_[src_sel, src_sel + 1, src_sel + 2] src_sel = src_sel.ravel() eigen_leads = eigen_leads[src_sel] source_cov = source_cov[src_sel] source_nn = source_nn[src_sel] if pick_ori == "normal": if not inv['source_ori'] == FIFF.FIFFV_MNE_FREE_ORI: raise ValueError('Picking normal orientation can only be done ' 'with a free orientation inverse operator.') is_loose = 0 < inv['orient_prior']['data'][0] <= 1 if not is_loose: raise ValueError('Picking normal orientation can only be done ' 'when working with loose orientations.') # keep only the normal components eigen_leads = eigen_leads[2::3] source_cov = source_cov[2::3] trans = np.dot(inv['eigen_fields']['data'], np.dot(inv['whitener'], inv['proj'])) trans *= inv['reginv'][:, None] # # Transformation into current distributions by weighting the eigenleads # with the weights computed above # if inv['eigen_leads_weighted']: # # R^0.5 has been already factored in # logger.info(' Eigenleads already weighted ... ') K = np.dot(eigen_leads, trans) else: # # R^0.5 has to be factored in # logger.info(' Eigenleads need to be weighted ...') K = np.sqrt(source_cov) * np.dot(eigen_leads, trans) return K, noise_norm, vertno, source_nn def _check_comps(info, data_info, kind): """Check for compatibility between compensation grades.""" comp = get_current_comp(info) data_comp = get_current_comp(data_info) if comp != data_comp and \ any(c not in (None, 0) for c in (comp, data_comp)): raise RuntimeError('compensation grade mismatch between %s (%s) ' 'and data (%s), consider recomputing the %s.' % (kind, comp, data_comp, kind)) def _check_method(method): """Check the method.""" if method not in ['MNE', 'dSPM', 'sLORETA', 'eLORETA']: raise ValueError('method parameter should be "MNE", "dSPM", ' '"sLORETA" or "eLORETA", got %s.' % (method,)) def _check_ori(pick_ori, source_ori): """Check pick_ori.""" if pick_ori not in [None, 'normal', 'vector']: raise RuntimeError('pick_ori must be None, "normal" or "vector", not ' '%s' % pick_ori) if pick_ori == 'vector' and source_ori != FIFF.FIFFV_MNE_FREE_ORI: raise RuntimeError('pick_ori="vector" cannot be combined with an ' 'inverse operator with fixed orientations.') def _check_loose_forward(loose, forward): """Check the compatibility between loose and forward.""" src_kind = forward['src'].kind if src_kind != 'surface': if loose == 'auto': loose = 1. if loose != 1: raise ValueError('loose parameter has to be 1 or "auto" for ' 'non-surface source space (Got loose=%s for %s ' 'source space).' % (loose, src_kind)) else: # surface if loose == 'auto': loose = 0.2 # put the forward solution in fixed orientation if it's not already if loose == 0. and not is_fixed_orient(forward): logger.info('Converting forward solution to fixed orietnation') forward = convert_forward_solution(forward, force_fixed=True, use_cps=True) elif loose < 1. and not forward['surf_ori']: logger.info('Converting forward solution to surface orientation') forward = convert_forward_solution(forward, surf_ori=True, use_cps=True) assert loose is not None loose = float(loose) if loose < 0 or loose > 1: raise ValueError('loose must be between 0 and 1, got %s' % loose) if loose == 0. and not is_fixed_orient(forward): forward = convert_forward_solution(forward, force_fixed=True, use_cps=True) return loose, forward def _check_reference(inst, ch_names=None): """Check for EEG ref.""" info = inst.info if ch_names is not None: picks = [ci for ci, ch_name in enumerate(info['ch_names']) if ch_name in ch_names] info = pick_info(info, sel=picks) if _needs_eeg_average_ref_proj(info): raise ValueError('EEG average reference is mandatory for inverse ' 'modeling, use set_eeg_reference method.') if info['custom_ref_applied']: raise ValueError('Custom EEG reference is not allowed for inverse ' 'modeling.') def _subject_from_inverse(inverse_operator): """Get subject id from inverse operator.""" return inverse_operator['src'][0].get('subject_his_id', None) @verbose def apply_inverse(evoked, inverse_operator, lambda2=1. / 9., method="dSPM", pick_ori=None, prepared=False, label=None, method_params=None, return_residual=False, verbose=None): """Apply inverse operator to evoked data. Parameters ---------- evoked : Evoked object Evoked data. inverse_operator: instance of InverseOperator Inverse operator. lambda2 : float The regularization parameter. method : "MNE" | "dSPM" | "sLORETA" | "eLORETA" Use minimum norm [1]_, dSPM (default) [2]_, sLORETA [3]_, or eLORETA [4]_. pick_ori : None | "normal" | "vector" If "normal", rather than pooling the orientations by taking the norm, only the radial component is kept. This is only implemented when working with loose orientations. If "vector", no pooling of the orientations is done and the vector result will be returned in the form of a :class:`mne.VectorSourceEstimate` object. This is only implemented when working with loose orientations. prepared : bool If True, do not call :func:`prepare_inverse_operator`. label : Label | None Restricts the source estimates to a given label. If None, source estimates will be computed for the entire source space. method_params : dict | None Additional options for eLORETA. See Notes for details. .. versionadded:: 0.16 return_residual : bool If True (default False), return the residual evoked data. Cannot be used with ``method=='eLORETA'``. .. versionadded:: 0.17 verbose : bool, str, int, or None If not None, override default verbose level (see :func:`mne.verbose` and :ref:`Logging documentation ` for more). Returns ------- stc : SourceEstimate | VectorSourceEstimate | VolSourceEstimate The source estimates. residual : instance of Evoked The residual evoked data, only returned if return_residual is True. See Also -------- apply_inverse_raw : Apply inverse operator to raw object apply_inverse_epochs : Apply inverse operator to epochs object Notes ----- Currently only the ``method='eLORETA'`` has additional options. It performs an iterative fit with a convergence criterion, so you can pass a ``method_params`` :class:`dict` with string keys mapping to values for: 'eps' : float The convergence epsilon (default 1e-6). 'max_iter' : int The maximum number of iterations (default 20). If less regularization is applied, more iterations may be necessary. 'force_equal' : bool Force all eLORETA weights for each direction for a given location equal. The default is None, which means ``True`` for loose-orientation inverses and ``False`` for free- and fixed-orientation inverses. See below. The eLORETA paper [4]_ defines how to compute inverses for fixed- and free-orientation inverses. In the free orientation case, the X/Y/Z orientation triplet for each location is effectively multiplied by a 3x3 weight matrix. This is the behavior obtained with ``force_equal=False`` parameter. However, other noise normalization methods (dSPM, sLORETA) multiply all orientations for a given location by a single value. Using ``force_equal=True`` mimics this behavior by modifying the iterative algorithm to choose uniform weights (equivalent to a 3x3 diagonal matrix with equal entries). It is necessary to use ``force_equal=True`` with loose orientation inverses (e.g., ``loose=0.2``), otherwise the solution resembles a free-orientation inverse (``loose=1.0``). It is thus recommended to use ``force_equal=True`` for loose orientation and ``force_equal=False`` for free orientation inverses. This is the behavior used when the parameter ``force_equal=None`` (default behavior). References ---------- .. [1] Hamalainen M S and Ilmoniemi R. Interpreting magnetic fields of the brain: minimum norm estimates. Medical & Biological Engineering & Computing, 32(1):35-42, 1994. .. [2] Dale A, Liu A, Fischl B, Buckner R. (2000) Dynamic statistical parametric mapping: combining fMRI and MEG for high-resolution imaging of cortical activity. Neuron, 26:55-67. .. [3] Pascual-Marqui RD (2002), Standardized low resolution brain electromagnetic tomography (sLORETA): technical details. Methods Find. Exp. Clin. Pharmacology, 24(D):5-12. .. [4] Pascual-Marqui RD (2007). Discrete, 3D distributed, linear imaging methods of electric neuronal activity. Part 1: exact, zero error localization. arXiv:0710.3341 """ _check_reference(evoked, inverse_operator['info']['ch_names']) _check_method(method) if method == 'eLORETA' and return_residual: raise ValueError('eLORETA does not currently support return_residual') _check_ori(pick_ori, inverse_operator['source_ori']) # # Set up the inverse according to the parameters # nave = evoked.nave _check_ch_names(inverse_operator, evoked.info) inv = _check_or_prepare(inverse_operator, nave, lambda2, method, method_params, prepared) # # Pick the correct channels from the data # sel = _pick_channels_inverse_operator(evoked.ch_names, inv) logger.info('Applying inverse operator to "%s"...' % (evoked.comment,)) logger.info(' Picked %d channels from the data' % len(sel)) logger.info(' Computing inverse...') K, noise_norm, vertno, source_nn = _assemble_kernel(inv, label, method, pick_ori) sol = np.dot(K, evoked.data[sel]) # apply imaging kernel logger.info(' Computing residual...') # x̂(t) = G ĵ(t) = C ** 1/2 U Π w(t) # where the diagonal matrix Π has elements πk = λk γk Pi = inv['sing'] * inv['reginv'] data_w = np.dot(inv['whitener'], # C ** -0.5 np.dot(inv['proj'], evoked.data[sel])) w_t = np.dot(inv['eigen_fields']['data'], data_w) # U.T @ data data_est = np.dot(inv['colorer'], # C ** 0.5 np.dot(inv['eigen_fields']['data'].T, # U Pi[:, np.newaxis] * w_t)) data_est_w = np.dot(inv['whitener'], np.dot(inv['proj'], data_est)) var_exp = 1 - ((data_est_w - data_w) ** 2).sum() / (data_w ** 2).sum() logger.info(' Explained %5.1f%% variance' % (100 * var_exp,)) if return_residual: residual = evoked.copy() residual.data[sel] -= data_est is_free_ori = (inverse_operator['source_ori'] == FIFF.FIFFV_MNE_FREE_ORI and pick_ori != 'normal') if is_free_ori and pick_ori != 'vector': logger.info(' Combining the current components...') sol = combine_xyz(sol) if noise_norm is not None: logger.info(' %s...' % (method,)) if is_free_ori and pick_ori == 'vector': noise_norm = noise_norm.repeat(3, axis=0) sol *= noise_norm tstep = 1.0 / evoked.info['sfreq'] tmin = float(evoked.times[0]) subject = _subject_from_inverse(inverse_operator) src_type = _get_src_type(inverse_operator['src'], vertno) stc = _make_stc(sol, vertno, tmin=tmin, tstep=tstep, subject=subject, vector=(pick_ori == 'vector'), source_nn=source_nn, src_type=src_type) logger.info('[done]') return (stc, residual) if return_residual else stc @verbose def apply_inverse_raw(raw, inverse_operator, lambda2, method="dSPM", label=None, start=None, stop=None, nave=1, time_func=None, pick_ori=None, buffer_size=None, prepared=False, method_params=None, verbose=None): """Apply inverse operator to Raw data. Parameters ---------- raw : Raw object Raw data. inverse_operator : dict Inverse operator. lambda2 : float The regularization parameter. method : "MNE" | "dSPM" | "sLORETA" | "eLORETA" Use minimum norm, dSPM (default), sLORETA, or eLORETA. label : Label | None Restricts the source estimates to a given label. If None, source estimates will be computed for the entire source space. start : int Index of first time sample (index not time is seconds). stop : int Index of first time sample not to include (index not time is seconds). nave : int Number of averages used to regularize the solution. Set to 1 on raw data. time_func : callable Linear function applied to sensor space time series. pick_ori : None | "normal" | "vector" If "normal", rather than pooling the orientations by taking the norm, only the radial component is kept. This is only implemented when working with loose orientations. If "vector", no pooling of the orientations is done and the vector result will be returned in the form of a :class:`mne.VectorSourceEstimate` object. This does not work when using an inverse operator with fixed orientations. buffer_size : int (or None) If not None, the computation of the inverse and the combination of the current components is performed in segments of length buffer_size samples. While slightly slower, this is useful for long datasets as it reduces the memory requirements by approx. a factor of 3 (assuming buffer_size << data length). Note that this setting has no effect for fixed-orientation inverse operators. prepared : bool If True, do not call :func:`prepare_inverse_operator`. method_params : dict | None Additional options for eLORETA. See Notes of :func:`apply_inverse`. .. versionadded:: 0.16 verbose : bool, str, int, or None If not None, override default verbose level (see :func:`mne.verbose` and :ref:`Logging documentation ` for more). Returns ------- stc : SourceEstimate | VectorSourceEstimate | VolSourceEstimate The source estimates. See Also -------- apply_inverse_epochs : Apply inverse operator to epochs object apply_inverse : Apply inverse operator to evoked object """ _check_reference(raw, inverse_operator['info']['ch_names']) _check_method(method) _check_ori(pick_ori, inverse_operator['source_ori']) _check_ch_names(inverse_operator, raw.info) # # Set up the inverse according to the parameters # inv = _check_or_prepare(inverse_operator, nave, lambda2, method, method_params, prepared) # # Pick the correct channels from the data # sel = _pick_channels_inverse_operator(raw.ch_names, inv) logger.info('Applying inverse to raw...') logger.info(' Picked %d channels from the data' % len(sel)) logger.info(' Computing inverse...') data, times = raw[sel, start:stop] if time_func is not None: data = time_func(data) K, noise_norm, vertno, source_nn = _assemble_kernel(inv, label, method, pick_ori) is_free_ori = (inverse_operator['source_ori'] == FIFF.FIFFV_MNE_FREE_ORI and pick_ori != 'normal') if buffer_size is not None and is_free_ori: # Process the data in segments to conserve memory n_seg = int(np.ceil(data.shape[1] / float(buffer_size))) logger.info(' computing inverse and combining the current ' 'components (using %d segments)...' % (n_seg)) # Allocate space for inverse solution n_times = data.shape[1] n_dipoles = K.shape[0] if pick_ori == 'vector' else K.shape[0] // 3 sol = np.empty((n_dipoles, n_times), dtype=np.result_type(K, data)) for pos in range(0, n_times, buffer_size): sol_chunk = np.dot(K, data[:, pos:pos + buffer_size]) if pick_ori != 'vector': sol_chunk = combine_xyz(sol_chunk) sol[:, pos:pos + buffer_size] = sol_chunk logger.info(' segment %d / %d done..' % (pos / buffer_size + 1, n_seg)) else: sol = np.dot(K, data) if is_free_ori and pick_ori != 'vector': logger.info(' combining the current components...') sol = combine_xyz(sol) if noise_norm is not None: if pick_ori == 'vector' and is_free_ori: noise_norm = noise_norm.repeat(3, axis=0) sol *= noise_norm tmin = float(times[0]) tstep = 1.0 / raw.info['sfreq'] subject = _subject_from_inverse(inverse_operator) src_type = _get_src_type(inverse_operator['src'], vertno) stc = _make_stc(sol, vertno, tmin=tmin, tstep=tstep, subject=subject, vector=(pick_ori == 'vector'), source_nn=source_nn, src_type=src_type) logger.info('[done]') return stc def _apply_inverse_epochs_gen(epochs, inverse_operator, lambda2, method='dSPM', label=None, nave=1, pick_ori=None, prepared=False, method_params=None, verbose=None): """Generate inverse solutions for epochs. Used in apply_inverse_epochs.""" _check_method(method) _check_ori(pick_ori, inverse_operator['source_ori']) _check_ch_names(inverse_operator, epochs.info) # # Set up the inverse according to the parameters # inv = _check_or_prepare(inverse_operator, nave, lambda2, method, method_params, prepared) # # Pick the correct channels from the data # sel = _pick_channels_inverse_operator(epochs.ch_names, inv) logger.info('Picked %d channels from the data' % len(sel)) logger.info('Computing inverse...') K, noise_norm, vertno, source_nn = _assemble_kernel(inv, label, method, pick_ori) tstep = 1.0 / epochs.info['sfreq'] tmin = epochs.times[0] is_free_ori = (inverse_operator['source_ori'] == FIFF.FIFFV_MNE_FREE_ORI and pick_ori != 'normal') if pick_ori == 'vector' and noise_norm is not None: noise_norm = noise_norm.repeat(3, axis=0) if not is_free_ori and noise_norm is not None: # premultiply kernel with noise normalization K *= noise_norm subject = _subject_from_inverse(inverse_operator) for k, e in enumerate(epochs): logger.info('Processing epoch : %d' % (k + 1)) if is_free_ori: # Compute solution and combine current components (non-linear) sol = np.dot(K, e[sel]) # apply imaging kernel logger.info('combining the current components...') if pick_ori != 'vector': sol = combine_xyz(sol) if noise_norm is not None: sol *= noise_norm else: # Linear inverse: do computation here or delayed if len(sel) < K.shape[1]: sol = (K, e[sel]) else: sol = np.dot(K, e[sel]) src_type = _get_src_type(inverse_operator['src'], vertno) stc = _make_stc(sol, vertno, tmin=tmin, tstep=tstep, subject=subject, vector=(pick_ori == 'vector'), source_nn=source_nn, src_type=src_type) yield stc logger.info('[done]') @verbose def apply_inverse_epochs(epochs, inverse_operator, lambda2, method="dSPM", label=None, nave=1, pick_ori=None, return_generator=False, prepared=False, method_params=None, verbose=None): """Apply inverse operator to Epochs. Parameters ---------- epochs : Epochs object Single trial epochs. inverse_operator : dict Inverse operator. lambda2 : float The regularization parameter. method : "MNE" | "dSPM" | "sLORETA" | "eLORETA" Use minimum norm, dSPM (default), sLORETA, or eLORETA. label : Label | None Restricts the source estimates to a given label. If None, source estimates will be computed for the entire source space. nave : int Number of averages used to regularize the solution. Set to 1 on single Epoch by default. pick_ori : None | "normal" | "vector" If "normal", rather than pooling the orientations by taking the norm, only the radial component is kept. This is only implemented when working with loose orientations. If "vector", no pooling of the orientations is done and the vector result will be returned in the form of a :class:`mne.VectorSourceEstimate` object. This does not work when using an inverse operator with fixed orientations. return_generator : bool Return a generator object instead of a list. This allows iterating over the stcs without having to keep them all in memory. prepared : bool If True, do not call :func:`prepare_inverse_operator`. method_params : dict | None Additional options for eLORETA. See Notes of :func:`apply_inverse`. .. versionadded:: 0.16 verbose : bool, str, int, or None If not None, override default verbose level (see :func:`mne.verbose` and :ref:`Logging documentation ` for more). Returns ------- stc : list of (SourceEstimate | VectorSourceEstimate | VolSourceEstimate) The source estimates for all epochs. See Also -------- apply_inverse_raw : Apply inverse operator to raw object apply_inverse : Apply inverse operator to evoked object """ stcs = _apply_inverse_epochs_gen( epochs, inverse_operator, lambda2, method=method, label=label, nave=nave, pick_ori=pick_ori, verbose=verbose, prepared=prepared, method_params=method_params) if not return_generator: # return a list stcs = [stc for stc in stcs] return stcs # XXX what is this??? ''' def _xyz2lf(Lf_xyz, normals): """Reorient leadfield to one component matching the normal to the cortex This program takes a leadfield matrix computed for dipole components pointing in the x, y, and z directions, and outputs a new lead field matrix for dipole components pointing in the normal direction of the cortical surfaces and in the two tangential directions to the cortex (that is on the tangent cortical space). These two tangential dipole components are uniquely determined by the SVD (reduction of variance). Parameters ---------- Lf_xyz: array of shape [n_sensors, n_positions x 3] Leadfield normals : array of shape [n_positions, 3] Normals to the cortex Returns ------- Lf_cortex : array of shape [n_sensors, n_positions x 3] Lf_cortex is a leadfield matrix for dipoles in rotated orientations, so that the first column is the gain vector for the cortical normal dipole and the following two column vectors are the gain vectors for the tangential orientations (tangent space of cortical surface). """ n_sensors, n_dipoles = Lf_xyz.shape n_positions = n_dipoles // 3 Lf_xyz = Lf_xyz.reshape(n_sensors, n_positions, 3) n_sensors, n_positions, _ = Lf_xyz.shape Lf_cortex = np.zeros_like(Lf_xyz) for k in range(n_positions): lf_normal = np.dot(Lf_xyz[:, k, :], normals[k]) lf_normal_n = lf_normal[:, None] / linalg.norm(lf_normal) P = np.eye(n_sensors, n_sensors) - np.dot(lf_normal_n, lf_normal_n.T) lf_p = np.dot(P, Lf_xyz[:, k, :]) U, s, Vh = linalg.svd(lf_p) Lf_cortex[:, k, 0] = lf_normal Lf_cortex[:, k, 1:] = np.c_[U[:, 0] * s[0], U[:, 1] * s[1]] Lf_cortex = Lf_cortex.reshape(n_sensors, n_dipoles) return Lf_cortex ''' ############################################################################### # Assemble the inverse operator @verbose def _prepare_forward(forward, info, noise_cov, pca=False, rank=None, verbose=None): """Prepare forward solution for inverse solvers.""" # fwd['sol']['row_names'] may be different order from fwd['info']['chs'] fwd_sol_ch_names = forward['sol']['row_names'] ch_names = [c['ch_name'] for c in info['chs'] if ((c['ch_name'] not in info['bads'] and c['ch_name'] not in noise_cov['bads']) and (c['ch_name'] in fwd_sol_ch_names and c['ch_name'] in noise_cov.ch_names))] if not len(info['bads']) == len(noise_cov['bads']) or \ not all(b in noise_cov['bads'] for b in info['bads']): logger.info('info["bads"] and noise_cov["bads"] do not match, ' 'excluding bad channels from both') # check the compensation grade _check_comps(forward['info'], info, 'forward') n_chan = len(ch_names) logger.info("Computing inverse operator with %d channels." % n_chan) whitener, _, noise_cov, n_nzero = _get_whitener( noise_cov, info, ch_names, rank, pca) gain = forward['sol']['data'] # This actually reorders the gain matrix to conform to the info ch order fwd_idx = [fwd_sol_ch_names.index(name) for name in ch_names] gain = gain[fwd_idx] # Any function calling this helper will be using the returned fwd_info # dict, so fwd['sol']['row_names'] becomes obsolete and is NOT re-ordered info_idx = [info['ch_names'].index(name) for name in ch_names] fwd_info = pick_info(info, info_idx) return fwd_info, gain, noise_cov, whitener, n_nzero @verbose def make_inverse_operator(info, forward, noise_cov, loose='auto', depth=0.8, fixed='auto', limit_depth_chs=True, rank=None, use_cps=True, verbose=None): """Assemble inverse operator. Parameters ---------- info : dict The measurement info to specify the channels to include. Bad channels in info['bads'] are not used. forward : dict Forward operator. noise_cov : instance of Covariance The noise covariance matrix. loose : float in [0, 1] | 'auto' Value that weights the source variances of the dipole components that are parallel (tangential) to the cortical surface. If loose is 0 then the solution is computed with fixed orientation, and fixed must be True or "auto". If loose is 1, it corresponds to free orientations. The default value ('auto') is set to 0.2 for surface-oriented source space and set to 1.0 for volumetric, discrete, or mixed source spaces, unless ``fixed is True`` in which case the value 0. is used. depth : None | float in [0, 1] Depth weighting coefficients. If None, no depth weighting is performed. fixed : bool | 'auto' Use fixed source orientations normal to the cortical mantle. If True, the loose parameter must be "auto" or 0. If 'auto', the loose value is used. limit_depth_chs : bool If True, use only grad channels in depth weighting (equivalent to MNE C code). If grad channels aren't present, only mag channels will be used (if no mag, then eeg). If False, use all channels. rank : None | int | dict Specified rank of the noise covariance matrix. If None, the rank is detected automatically. If int, the rank is specified for the MEG channels. A dictionary with entries 'eeg' and/or 'meg' can be used to specify the rank for each modality. use_cps : None | bool (default True) Whether to use cortical patch statistics to define normal orientations. Only used when converting to surface orientation (i.e., for surface source spaces and ``loose < 1``). verbose : bool, str, int, or None If not None, override default verbose level (see :func:`mne.verbose`). Returns ------- inv : instance of InverseOperator Inverse operator. Notes ----- For different sets of options (**loose**, **depth**, **fixed**) to work, the forward operator must have been loaded using a certain configuration (i.e., with **force_fixed** and **surf_ori** set appropriately). For example, given the desired inverse type (with representative choices of **loose** = 0.2 and **depth** = 0.8 shown in the table in various places, as these are the defaults for those parameters): +---------------------+-----------+-----------+-----------+-----------------+--------------+ | Inverse desired | Forward parameters allowed | +=====================+===========+===========+===========+=================+==============+ | | **loose** | **depth** | **fixed** | **force_fixed** | **surf_ori** | +---------------------+-----------+-----------+-----------+-----------------+--------------+ | | Loose constraint, | 0.2 | 0.8 | False | False | True | | | Depth weighted | | | | | | +---------------------+-----------+-----------+-----------+-----------------+--------------+ | | Loose constraint | 0.2 | None | False | False | True | +---------------------+-----------+-----------+-----------+-----------------+--------------+ | | Free orientation, | 1.0 | 0.8 | False | False | True | | | Depth weighted | | | | | | +---------------------+-----------+-----------+-----------+-----------------+--------------+ | | Free orientation | 1.0 | None | False | False | True | False | +---------------------+-----------+-----------+-----------+-----------------+--------------+ | | Fixed constraint, | 0.0 | 0.8 | True | False | True | | | Depth weighted | | | | | | +---------------------+-----------+-----------+-----------+-----------------+--------------+ | | Fixed constraint | 0.0 | None | True | True | True | +---------------------+-----------+-----------+-----------+-----------------+--------------+ Also note that, if the source space (as stored in the forward solution) has patch statistics computed, these are used to improve the depth weighting. Thus slightly different results are to be expected with and without this information. """ # noqa: E501 is_fixed_ori = is_fixed_orient(forward) # These gymnastics are necessary due to the redundancy between # "fixed" and "loose" if fixed == 'auto': if loose == 'auto': fixed, loose = False, 0.2 else: fixed = True if float(loose) == 0 else False if fixed: if loose not in ['auto', 0.]: raise ValueError('When invoking make_inverse_operator with ' 'fixed=True, loose must be 0. or "auto", ' 'got %s' % (loose,)) loose = 0. if loose == 0.: if fixed not in (True, 'auto'): raise ValueError('If loose==0., then fixed must be True or "auto",' 'got %s' % (fixed,)) fixed = True if fixed and not is_fixed_ori: # Here we use loose=1. because computation of depth priors is improved # by operating on the free orientation forward; see code at the # comment below "Deal with fixed orientation forward / inverse" loose = 1. if is_fixed_ori: if not fixed: raise ValueError( 'Forward operator has fixed orientation and can only ' 'be used to make a fixed-orientation inverse ' 'operator.') if fixed and depth is not None: raise ValueError( 'For a fixed orientation inverse solution with depth ' 'weighting, the forward solution must be free-orientation and ' 'in surface orientation') # depth=None can use fixed fwd, depth=0 0) else: ncomp = make_projector(inv['projs'], inv['noise_cov']['names'])[1] rank = inv['noise_cov']['dim'] - ncomp return rank # ############################################################################# # SNR Estimation @verbose def estimate_snr(evoked, inv, verbose=None): r"""Estimate the SNR as a function of time for evoked data. Parameters ---------- evoked : instance of Evoked Evoked instance. inv : instance of InverseOperator The inverse operator. verbose : bool, str, int, or None If not None, override default verbose level (see :func:`mne.verbose`). Returns ------- snr : ndarray, shape (n_times,) The SNR estimated from the whitened data. snr_est : ndarray, shape (n_times,) The SNR estimated using the mismatch between the unregularized solution and the regularized solution. Notes ----- ``snr_est`` is estimated by using different amounts of inverse regularization and checking the mismatch between predicted and measured whitened data. In more detail, given our whitened inverse obtained from SVD: .. math:: \tilde{M} = R^\frac{1}{2}V\Gamma U^T The values in the diagonal matrix :math:`\Gamma` are expressed in terms of the chosen regularization :math:`\lambda\approx\frac{1}{\rm{SNR}^2}` and singular values :math:`\lambda_k` as: .. math:: \gamma_k = \frac{1}{\lambda_k}\frac{\lambda_k^2}{\lambda_k^2 + \lambda^2} We also know that our predicted data is given by: .. math:: \hat{x}(t) = G\hat{j}(t)=C^\frac{1}{2}U\Pi w(t) And thus our predicted whitened data is just: .. math:: \hat{w}(t) = U\Pi w(t) Where :math:`\Pi` is diagonal with entries entries: .. math:: \lambda_k\gamma_k = \frac{\lambda_k^2}{\lambda_k^2 + \lambda^2} If we use no regularization, note that :math:`\Pi` is just the identity matrix. Here we test the squared magnitude of the difference between unregularized solution and regularized solutions, choosing the biggest regularization that achieves a :math:`\chi^2`-test significance of 0.001. .. versionadded:: 0.9.0 """ # noqa: E501 from scipy.stats import chi2 _check_reference(evoked, inv['info']['ch_names']) _check_ch_names(inv, evoked.info) inv = prepare_inverse_operator(inv, evoked.nave, 1. / 9., 'MNE') sel = _pick_channels_inverse_operator(evoked.ch_names, inv) logger.info('Picked %d channels from the data' % len(sel)) data_white = np.dot(inv['whitener'], np.dot(inv['proj'], evoked.data[sel])) data_white_ef = np.dot(inv['eigen_fields']['data'], data_white) n_ch, n_times = data_white.shape # Adapted from mne_analyze/regularization.c, compute_regularization n_zero = (inv['noise_cov']['eig'] <= 0).sum() n_ch_eff = n_ch - n_zero logger.info('Effective nchan = %d - %d = %d' % (n_ch, n_zero, n_ch_eff)) del n_ch signal = np.sum(data_white ** 2, axis=0) # sum of squares across channels snr = signal / n_ch_eff # Adapted from noise_regularization lambda2_est = np.empty(n_times) lambda2_est.fill(10.) remaining = np.ones(n_times, bool) # deal with low SNRs bad = (snr <= 1) lambda2_est[bad] = np.inf remaining[bad] = False # parameters lambda_mult = 0.99 sing2 = (inv['sing'] * inv['sing'])[:, np.newaxis] val = chi2.isf(1e-3, n_ch_eff) for n_iter in range(1000): # get_mne_weights (ew=error_weights) # (split newaxis creation here for old numpy) f = sing2 / (sing2 + lambda2_est[np.newaxis][:, remaining]) f[inv['sing'] == 0] = 0 ew = data_white_ef[:, remaining] * (1.0 - f) # check condition err = np.sum(ew * ew, axis=0) remaining[np.where(remaining)[0][err < val]] = False if not remaining.any(): break lambda2_est[remaining] *= lambda_mult else: warn('SNR estimation did not converge') snr_est = 1.0 / np.sqrt(lambda2_est) snr = np.sqrt(snr) return snr, snr_est