# Authors: The MNE-Python contributors. # License: BSD-3-Clause # Copyright the MNE-Python contributors. import os from collections.abc import Iterable from pathlib import Path import numpy as np from .._fiff.constants import FIFF from .._fiff.meas_info import Info from .._fiff.pick import pick_channels, pick_channels_forward, pick_info, pick_types from .._ola import _Interp2 from ..bem import fit_sphere_to_headshape, make_sphere_model, read_bem_solution from ..chpi import ( _get_hpi_initial_fit, get_chpi_info, head_pos_to_trans_rot_t, read_head_pos, ) from ..cov import Covariance, make_ad_hoc_cov, read_cov from ..event import _get_stim_channel from ..forward import ( _compute_forwards, _magnetic_dipole_field_vec, _merge_fwds, _prep_meg_channels, _prepare_for_forward, _stc_src_sel, _to_forward_dict, _transform_orig_meg_coils, convert_forward_solution, restrict_forward_to_stc, ) from ..io import BaseRaw, RawArray from ..source_estimate import _BaseSourceEstimate from ..source_space._source_space import ( _ensure_src, _set_source_space_vertices, setup_volume_source_space, ) from ..surface import _CheckInside from ..transforms import _get_trans, transform_surface_to from ..utils import ( _check_preload, _pl, _validate_type, check_random_state, logger, verbose, ) from .source import SourceSimulator def _check_cov(info, cov): """Check that the user provided a valid covariance matrix for the noise.""" _validate_type(cov, (Covariance, None, dict, str, "path-like"), "cov") if isinstance(cov, Covariance) or cov is None: pass elif isinstance(cov, dict): cov = make_ad_hoc_cov(info, cov, verbose=False) else: if cov == "simple": cov = make_ad_hoc_cov(info, None, verbose=False) else: cov = read_cov(cov, verbose=False) return cov def _check_stc_iterable(stc, info): # 1. Check that our STC is iterable (or convert it to one using cycle) # 2. Do first iter so we can get the vertex subselection # 3. Get the list of verts, which must stay the same across iterations if isinstance(stc, _BaseSourceEstimate): stc = [stc] _validate_type(stc, Iterable, "SourceEstimate, tuple, or iterable") stc_enum = enumerate(stc) del stc try: stc_counted = next(stc_enum) except StopIteration: raise RuntimeError("Iterable did not provide stc[0]") _, _, verts = _stc_data_event(stc_counted, 1, info["sfreq"]) return stc_enum, stc_counted, verts def _log_ch(start, info, ch): """Log channel information.""" if ch is not None: extra, just, ch = " stored on channel:", 50, info["ch_names"][ch] else: extra, just, ch = " not stored", 0, "" logger.info((start + extra).ljust(just) + ch) def _check_head_pos(head_pos, info, first_samp, times=None): if head_pos is None: # use pos from info['dev_head_t'] head_pos = dict() if isinstance(head_pos, (str, Path, os.PathLike)): head_pos = read_head_pos(head_pos) if isinstance(head_pos, np.ndarray): # can be head_pos quats head_pos = head_pos_to_trans_rot_t(head_pos) if isinstance(head_pos, tuple): # can be quats converted to trans, rot, t transs, rots, ts = head_pos first_time = first_samp / info["sfreq"] ts = ts - first_time # MF files need reref dev_head_ts = [ np.r_[np.c_[r, t[:, np.newaxis]], [[0, 0, 0, 1]]] for r, t in zip(rots, transs) ] del transs, rots elif isinstance(head_pos, dict): ts = np.array(list(head_pos.keys()), float) ts.sort() dev_head_ts = [head_pos[float(tt)] for tt in ts] else: raise TypeError(f"unknown head_pos type {type(head_pos)}") bad = ts < 0 if bad.any(): raise RuntimeError( f"All position times must be >= 0, found {bad.sum()}/{len(bad)}< 0" ) if times is not None: bad = ts > times[-1] if bad.any(): raise RuntimeError( f"All position times must be <= t_end ({times[-1]:0.1f} " f"s), found {bad.sum()}/{len(bad)} bad values (is this a split " "file?)" ) # If it starts close to zero, make it zero (else unique(offset) fails) if len(ts) > 0 and ts[0] < (0.5 / info["sfreq"]): ts[0] = 0.0 # If it doesn't start at zero, insert one at t=0 elif len(ts) == 0 or ts[0] > 0: ts = np.r_[[0.0], ts] dev_head_ts.insert(0, info["dev_head_t"]["trans"]) dev_head_ts = [ {"trans": d, "to": info["dev_head_t"]["to"], "from": info["dev_head_t"]["from"]} for d in dev_head_ts ] offsets = np.round(ts * info["sfreq"]).astype(int) assert np.array_equal(offsets, np.unique(offsets)) assert len(offsets) == len(dev_head_ts) offsets = list(offsets) return dev_head_ts, offsets @verbose def simulate_raw( info, stc=None, trans=None, src=None, bem=None, head_pos=None, mindist=1.0, interp="cos2", n_jobs=None, use_cps=True, forward=None, first_samp=0, max_iter=10000, verbose=None, ): """Simulate raw data. Head movements can optionally be simulated using the ``head_pos`` parameter. Parameters ---------- %(info_not_none)s Used for simulation. .. versionchanged:: 0.18 Support for :class:`mne.Info`. stc : iterable | SourceEstimate | SourceSimulator The source estimates to use to simulate data. Each must have the same sample rate as the raw data, and the vertices of all stcs in the iterable must match. Each entry in the iterable can also be a tuple of ``(SourceEstimate, ndarray)`` to allow specifying the stim channel (e.g., STI001) data accompany the source estimate. See Notes for details. .. versionchanged:: 0.18 Support for tuple, iterable of tuple or `~mne.SourceEstimate`, or `~mne.simulation.SourceSimulator`. trans : dict | str | None Either a transformation filename (usually made using mne_analyze) or an info dict (usually opened using read_trans()). If string, an ending of ``.fif`` or ``.fif.gz`` will be assumed to be in FIF format, any other ending will be assumed to be a text file with a 4x4 transformation matrix (like the ``--trans`` MNE-C option). If trans is None, an identity transform will be used. src : path-like | instance of SourceSpaces | None Source space corresponding to the stc. If string, should be a source space filename. Can also be an instance of loaded or generated SourceSpaces. Can be None if ``forward`` is provided. bem : path-like | dict | None BEM solution corresponding to the stc. If string, should be a BEM solution filename (e.g., "sample-5120-5120-5120-bem-sol.fif"). Can be None if ``forward`` is provided. %(head_pos)s See for example :footcite:`LarsonTaulu2017`. mindist : float Minimum distance between sources and the inner skull boundary to use during forward calculation. %(interp)s %(n_jobs)s %(use_cps)s forward : instance of Forward | None The forward operator to use. If None (default) it will be computed using ``bem``, ``trans``, and ``src``. If not None, ``bem``, ``trans``, and ``src`` are ignored. .. versionadded:: 0.17 first_samp : int The first_samp property in the output Raw instance. .. versionadded:: 0.18 max_iter : int The maximum number of STC iterations to allow. This is a sanity parameter to prevent accidental blowups. .. versionadded:: 0.18 %(verbose)s Returns ------- raw : instance of Raw The simulated raw file. See Also -------- mne.chpi.read_head_pos add_chpi add_noise add_ecg add_eog simulate_evoked simulate_stc simulate_sparse_stc Notes ----- **Stim channel encoding** By default, the stimulus channel will have the head position number (starting at 1) stored in the trigger channel (if available) at the t=0 point in each repetition of the ``stc``. If ``stc`` is a tuple of ``(SourceEstimate, ndarray)`` the array values will be placed in the stim channel aligned with the :class:`mne.SourceEstimate`. **Data simulation** In the most advanced case where ``stc`` is an iterable of tuples the output will be concatenated in time as: .. table:: Data alignment and stim channel encoding +---------+--------------------------+--------------------------+---------+ | Channel | Data | +=========+==========================+==========================+=========+ | M/EEG | ``fwd @ stc[0][0].data`` | ``fwd @ stc[1][0].data`` | ``...`` | +---------+--------------------------+--------------------------+---------+ | STIM | ``stc[0][1]`` | ``stc[1][1]`` | ``...`` | +---------+--------------------------+--------------------------+---------+ | | *time →* | +---------+--------------------------+--------------------------+---------+ .. versionadded:: 0.10.0 References ---------- .. footbibliography:: """ # noqa: E501 _validate_type(info, Info, "info") if len(pick_types(info, meg=False, stim=True)) == 0: event_ch = None else: event_ch = pick_channels(info["ch_names"], _get_stim_channel(None, info))[0] if forward is not None: if any(x is not None for x in (trans, src, bem, head_pos)): raise ValueError( "If forward is not None then trans, src, bem, " "and head_pos must all be None" ) if not np.allclose( forward["info"]["dev_head_t"]["trans"], info["dev_head_t"]["trans"], atol=1e-6, ): raise ValueError( "The forward meg<->head transform " 'forward["info"]["dev_head_t"] does not match ' 'the one in raw.info["dev_head_t"]' ) src = forward["src"] dev_head_ts, offsets = _check_head_pos(head_pos, info, first_samp, None) src = _ensure_src(src, verbose=False) if isinstance(bem, str): bem = read_bem_solution(bem, verbose=False) # Extract necessary info meeg_picks = pick_types(info, meg=True, eeg=True, exclude=[]) logger.info( f"Setting up raw simulation: {len(dev_head_ts)} " f'position{_pl(dev_head_ts)}, "{interp}" interpolation' ) if isinstance(stc, SourceSimulator) and stc.first_samp != first_samp: logger.info("SourceSimulator first_samp does not match argument.") stc_enum, stc_counted, verts = _check_stc_iterable(stc, info) if forward is not None: forward = restrict_forward_to_stc(forward, verts) src = forward["src"] else: _stc_src_sel(src, verts, on_missing="warn", extra="") src = _set_source_space_vertices(src.copy(), verts) # array used to store result raw_datas = list() _log_ch("Event information", info, event_ch) # don't process these any more if no MEG present n = 1 get_fwd = _SimForwards( dev_head_ts, offsets, info, trans, src, bem, mindist, n_jobs, meeg_picks, forward, use_cps, ) interper = _Interp2(offsets, get_fwd, interp) this_start = 0 for n in range(max_iter): if isinstance(stc_counted[1], (list, tuple)): this_n = stc_counted[1][0].data.shape[1] else: this_n = stc_counted[1].data.shape[1] this_stop = this_start + this_n logger.info( f" Interval {this_start / info['sfreq']:0.3f}–" f"{this_stop / info['sfreq']:0.3f} s" ) n_doing = this_stop - this_start assert n_doing > 0 this_data = np.zeros((len(info["ch_names"]), n_doing)) raw_datas.append(this_data) # Stim channel fwd, fi = interper.feed(this_stop - this_start) fi = fi[0] stc_data, stim_data, _ = _stc_data_event( stc_counted, fi, info["sfreq"], get_fwd.src, None if n == 0 else verts ) if event_ch is not None: this_data[event_ch, :] = stim_data[:n_doing] this_data[meeg_picks] = np.einsum("svt,vt->st", fwd, stc_data) try: stc_counted = next(stc_enum) except StopIteration: logger.info(f" {n + 1} STC iteration{_pl(n + 1)} provided") break del fwd else: raise RuntimeError(f"Maximum number of STC iterations ({n}) exceeded") raw_data = np.concatenate(raw_datas, axis=-1) raw = RawArray(raw_data, info, first_samp=first_samp, verbose=False) raw.set_annotations(raw.annotations) logger.info("[done]") return raw @verbose def add_eog( raw, head_pos=None, interp="cos2", n_jobs=None, random_state=None, verbose=None ): """Add blink noise to raw data. Parameters ---------- raw : instance of Raw The raw instance to modify. %(head_pos)s %(interp)s %(n_jobs)s %(random_state)s The random generator state used for blink, ECG, and sensor noise randomization. %(verbose)s Returns ------- raw : instance of Raw The instance, modified in place. See Also -------- add_chpi add_ecg add_noise simulate_raw Notes ----- The blink artifacts are generated by: 1. Random activation times are drawn from an inhomogeneous poisson process whose blink rate oscillates between 4.5 blinks/minute and 17 blinks/minute based on the low (reading) and high (resting) blink rates from :footcite:`BentivoglioEtAl1997`. 2. The activation kernel is a 250 ms Hanning window. 3. Two activated dipoles are located in the z=0 plane (in head coordinates) at ±30 degrees away from the y axis (nasion). 4. Activations affect MEG and EEG channels. The scale-factor of the activation function was chosen based on visual inspection to yield amplitudes generally consistent with those seen in experimental data. Noisy versions of the activation will be stored in the first EOG channel in the raw instance, if it exists. References ---------- .. footbibliography:: """ return _add_exg(raw, "blink", head_pos, interp, n_jobs, random_state) @verbose def add_ecg( raw, head_pos=None, interp="cos2", n_jobs=None, random_state=None, verbose=None ): """Add ECG noise to raw data. Parameters ---------- raw : instance of Raw The raw instance to modify. %(head_pos)s %(interp)s %(n_jobs)s %(random_state)s The random generator state used for blink, ECG, and sensor noise randomization. %(verbose)s Returns ------- raw : instance of Raw The instance, modified in place. See Also -------- add_chpi add_eog add_noise simulate_raw Notes ----- The ECG artifacts are generated by: 1. Random inter-beat intervals are drawn from a uniform distribution of times corresponding to 40 and 80 beats per minute. 2. The activation function is the sum of three Hanning windows with varying durations and scales to make a more complex waveform. 3. The activated dipole is located one (estimated) head radius to the left (-x) of head center and three head radii below (+z) head center; this dipole is oriented in the +x direction. 4. Activations only affect MEG channels. The scale-factor of the activation function was chosen based on visual inspection to yield amplitudes generally consistent with those seen in experimental data. Noisy versions of the activation will be stored in the first EOG channel in the raw instance, if it exists. .. versionadded:: 0.18 """ return _add_exg(raw, "ecg", head_pos, interp, n_jobs, random_state) def _add_exg(raw, kind, head_pos, interp, n_jobs, random_state): assert isinstance(kind, str) and kind in ("ecg", "blink") _validate_type(raw, BaseRaw, "raw") _check_preload(raw, f"Adding {kind} noise ") rng = check_random_state(random_state) info, times, first_samp = raw.info, raw.times, raw.first_samp data = raw._data meg_picks = pick_types(info, meg=True, eeg=False, exclude=()) meeg_picks = pick_types(info, meg=True, eeg=True, exclude=()) R, r0 = fit_sphere_to_headshape(info, units="m", verbose=False)[:2] bem = make_sphere_model( r0, head_radius=R, relative_radii=(0.97, 0.98, 0.99, 1.0), sigmas=(0.33, 1.0, 0.004, 0.33), verbose=False, ) trans = None dev_head_ts, offsets = _check_head_pos(head_pos, info, first_samp, times) if kind == "blink": # place dipoles at 45 degree angles in z=0 plane exg_rr = np.array( [ [np.cos(np.pi / 3.0), np.sin(np.pi / 3.0), 0.0], [-np.cos(np.pi / 3.0), np.sin(np.pi / 3), 0.0], ] ) exg_rr /= np.sqrt(np.sum(exg_rr * exg_rr, axis=1, keepdims=True)) exg_rr *= 0.96 * R exg_rr += r0 # oriented upward nn = np.array([[0.0, 0.0, 1.0], [0.0, 0.0, 1.0]]) # Blink times drawn from an inhomogeneous poisson process # by 1) creating the rate and 2) pulling random numbers blink_rate = (1 + np.cos(2 * np.pi * 1.0 / 60.0 * times)) / 2.0 blink_rate *= 12.5 / 60.0 blink_rate += 4.5 / 60.0 blink_data = rng.uniform(size=len(times)) < blink_rate / info["sfreq"] blink_data = blink_data * (rng.uniform(size=len(times)) + 0.5) # amps # Activation kernel is a simple hanning window blink_kernel = np.hanning(int(0.25 * info["sfreq"])) exg_data = np.convolve(blink_data, blink_kernel, "same")[np.newaxis, :] * 1e-7 # Add rescaled noisy data to EOG ch ch = pick_types(info, meg=False, eeg=False, eog=True) picks = meeg_picks del blink_kernel, blink_rate, blink_data else: if len(meg_picks) == 0: raise RuntimeError( "Can only add ECG artifacts if MEG data channels are present" ) exg_rr = np.array([[-R, 0, -3 * R]]) max_beats = int(np.ceil(times[-1] * 80.0 / 60.0)) # activation times with intervals drawn from a uniform distribution # based on activation rates between 40 and 80 beats per minute cardiac_idx = np.cumsum( rng.uniform(60.0 / 80.0, 60.0 / 40.0, max_beats) * info["sfreq"] ).astype(int) cardiac_idx = cardiac_idx[cardiac_idx < len(times)] cardiac_data = np.zeros(len(times)) cardiac_data[cardiac_idx] = 1 # kernel is the sum of three hanning windows cardiac_kernel = np.concatenate( [ 2 * np.hanning(int(0.04 * info["sfreq"])), -0.3 * np.hanning(int(0.05 * info["sfreq"])), 0.2 * np.hanning(int(0.26 * info["sfreq"])), ], axis=-1, ) exg_data = ( np.convolve(cardiac_data, cardiac_kernel, "same")[np.newaxis, :] * 15e-8 ) # Add rescaled noisy data to ECG ch ch = pick_types(info, meg=False, eeg=False, ecg=True) picks = meg_picks del cardiac_data, cardiac_kernel, max_beats, cardiac_idx nn = np.zeros_like(exg_rr) nn[:, 0] = 1 # arbitrarily rightward del meg_picks, meeg_picks noise = rng.standard_normal(exg_data.shape[1]) * 5e-6 if len(ch) >= 1: ch = ch[-1] data[ch, :] = exg_data * 1e3 + noise else: ch = None src = setup_volume_source_space(pos=dict(rr=exg_rr, nn=nn), sphere_units="mm") _log_ch(f"{kind} simulated and trace", info, ch) del ch, nn, noise used = np.zeros(len(raw.times), bool) get_fwd = _SimForwards( dev_head_ts, offsets, info, trans, src, bem, 0.005, n_jobs, picks ) interper = _Interp2(offsets, get_fwd, interp) proc_lims = np.concatenate([np.arange(0, len(used), 10000), [len(used)]]) for start, stop in zip(proc_lims[:-1], proc_lims[1:]): fwd, _ = interper.feed(stop - start) data[picks, start:stop] += np.einsum("svt,vt->st", fwd, exg_data[:, start:stop]) assert not used[start:stop].any() used[start:stop] = True assert used.all() @verbose def add_chpi(raw, head_pos=None, interp="cos2", n_jobs=None, verbose=None): """Add cHPI activations to raw data. Parameters ---------- raw : instance of Raw The raw instance to be modified. %(head_pos)s %(interp)s %(n_jobs)s %(verbose)s Returns ------- raw : instance of Raw The instance, modified in place. Notes ----- .. versionadded:: 0.18 """ _validate_type(raw, BaseRaw, "raw") _check_preload(raw, "Adding cHPI signals ") info, first_samp, times = raw.info, raw.first_samp, raw.times meg_picks = pick_types(info, meg=True, eeg=False, exclude=[]) # for CHPI if len(meg_picks) == 0: raise RuntimeError("Cannot add cHPI if no MEG picks are present") dev_head_ts, offsets = _check_head_pos(head_pos, info, first_samp, times) hpi_freqs, hpi_pick, hpi_ons = get_chpi_info(info, on_missing="raise") hpi_rrs = _get_hpi_initial_fit(info, verbose="error") hpi_nns = hpi_rrs / np.sqrt(np.sum(hpi_rrs * hpi_rrs, axis=1))[:, np.newaxis] # turn on cHPI in file data = raw._data data[hpi_pick, :] = hpi_ons.sum() _log_ch("cHPI status bits enabled and", info, hpi_pick) sinusoids = 70e-9 * np.sin( 2 * np.pi * hpi_freqs[:, np.newaxis] * (np.arange(len(times)) / info["sfreq"]) ) info = pick_info(info, meg_picks) with info._unlock(): info.update(projs=[], bads=[]) # Ensure no 'projs' or 'bads' megcoils = _prep_meg_channels(info, ignore_ref=True)["defs"] used = np.zeros(len(raw.times), bool) dev_head_ts.append(dev_head_ts[-1]) # ZOH after time ends get_fwd = _HPIForwards(offsets, dev_head_ts, megcoils, hpi_rrs, hpi_nns) interper = _Interp2(offsets, get_fwd, interp) lims = np.concatenate([offsets, [len(raw.times)]]) for start, stop in zip(lims[:-1], lims[1:]): (fwd,) = interper.feed(stop - start) data[meg_picks, start:stop] += np.einsum( "svt,vt->st", fwd, sinusoids[:, start:stop] ) assert not used[start:stop].any() used[start:stop] = True assert used.all() return raw class _HPIForwards: def __init__(self, offsets, dev_head_ts, megcoils, hpi_rrs, hpi_nns): self.offsets = offsets self.dev_head_ts = dev_head_ts self.hpi_rrs = hpi_rrs self.hpi_nns = hpi_nns self.megcoils = megcoils self.idx = 0 def __call__(self, offset): assert offset == self.offsets[self.idx] _transform_orig_meg_coils(self.megcoils, self.dev_head_ts[self.idx]) fwd = _magnetic_dipole_field_vec(self.hpi_rrs, self.megcoils).T # align cHPI magnetic dipoles in approx. radial direction fwd = np.array( [ np.dot(fwd[:, 3 * ii : 3 * (ii + 1)], self.hpi_nns[ii]) for ii in range(len(self.hpi_rrs)) ] ).T self.idx += 1 return (fwd,) def _stc_data_event(stc_counted, head_idx, sfreq, src=None, verts=None): stc_idx, stc = stc_counted if isinstance(stc, (list, tuple)): if len(stc) != 2: raise ValueError(f"stc, if tuple, must be length 2, got {len(stc)}") stc, stim_data = stc else: stim_data = None _validate_type( stc, _BaseSourceEstimate, "stc", "SourceEstimate or tuple with first entry SourceEstimate", ) # Convert event data if stim_data is None: stim_data = np.zeros(len(stc.times), int) stim_data[np.argmin(np.abs(stc.times))] = head_idx del head_idx _validate_type(stim_data, np.ndarray, "stim_data") if stim_data.dtype.kind != "i": raise ValueError( "stim_data in a stc tuple must be an integer ndarray," f" got dtype {stim_data.dtype}" ) if stim_data.shape != (len(stc.times),): raise ValueError( f"event data had shape {stim_data.shape} but needed to " f"be ({len(stc.times)},) tomatch stc" ) # Validate STC if not np.allclose(sfreq, 1.0 / stc.tstep): raise ValueError( f"stc and info must have same sample rate, " f"got {1.0 / stc.tstep} and {sfreq}" ) if len(stc.times) <= 2: # to ensure event encoding works raise ValueError( f"stc must have at least three time points, got {len(stc.times)}" ) verts_ = stc.vertices if verts is None: assert stc_idx == 0 else: if len(verts) != len(verts_) or not all( np.array_equal(a, b) for a, b in zip(verts, verts_) ): raise RuntimeError( f"Vertex mismatch for stc[{stc_idx}], all stc.vertices must match" ) stc_data = stc.data if src is None: assert stc_idx == 0 else: # on_missing depends on whether or not this is the first iteration on_missing = "warn" if verts is None else "ignore" _, stc_sel, _ = _stc_src_sel(src, stc, on_missing=on_missing) stc_data = stc_data[stc_sel] return stc_data, stim_data, verts_ class _SimForwards: def __init__( self, dev_head_ts, offsets, info, trans, src, bem, mindist, n_jobs, meeg_picks, forward=None, use_cps=True, ): self.idx = 0 self.offsets = offsets self.use_cps = use_cps self.iter = iter( _iter_forward_solutions( info, trans, src, bem, dev_head_ts, mindist, n_jobs, forward, meeg_picks ) ) def __call__(self, offset): assert self.offsets[self.idx] == offset self.idx += 1 fwd = next(self.iter) self.src = fwd["src"] # XXX eventually we could speed this up by allowing the forward # solution code to only compute the normal direction convert_forward_solution( fwd, surf_ori=True, force_fixed=True, use_cps=self.use_cps, copy=False, verbose=False, ) return fwd["sol"]["data"], np.array(self.idx, float) def _iter_forward_solutions( info, trans, src, bem, dev_head_ts, mindist, n_jobs, forward, picks ): """Calculate a forward solution for a subject.""" logger.info("Setting up forward solutions") info = pick_info(info, picks) with info._unlock(): info.update(projs=[], bads=[]) # Ensure no 'projs' or 'bads' mri_head_t, trans = _get_trans(trans) sensors, rr, info, update_kwargs, bem = _prepare_for_forward( src, mri_head_t, info, bem, mindist, n_jobs, allow_bem_none=True, verbose=False ) del (src, mindist) eegnames = sensors.get("eeg", dict()).get("ch_names", []) if not len(eegnames): eegfwd = None elif forward is not None: eegfwd = pick_channels_forward(forward, eegnames, verbose=False) else: eegels = sensors.get("eeg", dict()).get("defs", []) this_sensors = dict(eeg=dict(ch_names=eegnames, defs=eegels)) eegfwd = _compute_forwards( rr, bem=bem, sensors=this_sensors, n_jobs=n_jobs, verbose=False )["eeg"] eegfwd = _to_forward_dict(eegfwd, eegnames) del eegels del eegnames # short circuit here if there are no MEG channels (don't need to iterate) if "meg" not in sensors: eegfwd.update(**update_kwargs) for _ in dev_head_ts: yield eegfwd yield eegfwd return coord_frame = FIFF.FIFFV_COORD_HEAD if bem is not None and not bem["is_sphere"]: idx = np.where( np.array([s["id"] for s in bem["surfs"]]) == FIFF.FIFFV_BEM_SURF_ID_BRAIN )[0] assert len(idx) == 1 # make a copy so it isn't mangled in use bem_surf = transform_surface_to( bem["surfs"][idx[0]], coord_frame, mri_head_t, copy=True ) megcoils = sensors["meg"]["defs"] if "eeg" in sensors: del sensors["eeg"] megnames = sensors["meg"]["ch_names"] fwds = dict() if eegfwd is not None: fwds["eeg"] = eegfwd del eegfwd for ti, dev_head_t in enumerate(dev_head_ts): # Could be *slightly* more efficient not to do this N times, # but the cost here is tiny compared to actual fwd calculation logger.info(f"Computing gain matrix for transform #{ti + 1}/{len(dev_head_ts)}") _transform_orig_meg_coils(megcoils, dev_head_t) # Make sure our sensors are all outside our BEM coil_rr = np.array([coil["r0"] for coil in megcoils]) # Compute forward if forward is None: if not bem["is_sphere"]: outside = ~_CheckInside(bem_surf)(coil_rr, n_jobs, verbose=False) elif bem.radius is not None: d = coil_rr - bem["r0"] outside = np.sqrt(np.sum(d * d, axis=1)) > bem.radius else: # only r0 provided outside = np.ones(len(coil_rr), bool) if not outside.all(): raise RuntimeError( f"{np.sum(~outside)} MEG sensors collided with inner skull " f"surface for transform {ti}" ) megfwd = _compute_forwards( rr, sensors=sensors, bem=bem, n_jobs=n_jobs, verbose=False )["meg"] megfwd = _to_forward_dict(megfwd, megnames) else: megfwd = pick_channels_forward(forward, megnames, verbose=False) fwds["meg"] = megfwd fwd = _merge_fwds(fwds, verbose=False) fwd.update(**update_kwargs) yield fwd # need an extra one to fill last buffer yield fwd