# -*- coding: utf-8 -*- # Authors: Mark Wronkiewicz # Yousra Bekhti # Eric Larson # # License: BSD (3-clause) from copy import deepcopy import numpy as np from .evoked import _generate_noise from ..event import _get_stim_channel from ..filter import _Interp2 from ..io.pick import (pick_types, pick_info, pick_channels, pick_channels_forward) from ..source_estimate import VolSourceEstimate from ..cov import make_ad_hoc_cov, read_cov, Covariance from ..bem import fit_sphere_to_headshape, make_sphere_model, read_bem_solution from ..io import RawArray, BaseRaw from ..chpi import (read_head_pos, head_pos_to_trans_rot_t, _get_hpi_info, _get_hpi_initial_fit) from ..io.constants import FIFF from ..forward import (_magnetic_dipole_field_vec, _merge_meg_eeg_fwds, _stc_src_sel, convert_forward_solution, _prepare_for_forward, _transform_orig_meg_coils, _compute_forwards, _to_forward_dict, restrict_forward_to_stc) from ..transforms import _get_trans, transform_surface_to from ..source_space import (_ensure_src, _points_outside_surface, _adjust_patch_info) from ..source_estimate import _BaseSourceEstimate from ..utils import logger, verbose, check_random_state, warn, _pl from ..parallel import check_n_jobs from ..externals.six import string_types def _check_cov(info, cov): """Check that the user provided a valid covariance matrix for the noise.""" if isinstance(cov, Covariance) or cov is None: pass elif isinstance(cov, dict): cov = make_ad_hoc_cov(info, cov, verbose=False) elif isinstance(cov, string_types): if cov == 'simple': cov = make_ad_hoc_cov(info, None, verbose=False) else: cov = read_cov(cov, verbose=False) else: raise TypeError('Covariance matrix type not recognized. Valid input ' 'types are: instance of Covariance, dict, str, None. ' ', got %s' % (cov,)) return cov 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) @verbose def simulate_raw(raw, stc, trans, src, bem, cov='simple', blink=False, ecg=False, chpi=False, head_pos=None, mindist=1.0, interp='cos2', iir_filter=None, n_jobs=1, random_state=None, use_cps=True, forward=None, verbose=None): u"""Simulate raw data. Head movements can optionally be simulated using the ``head_pos`` parameter. Parameters ---------- raw : instance of Raw The raw template to use for simulation. The ``info``, ``times``, and potentially ``first_samp`` properties will be used. stc : instance of SourceEstimate The source estimate to use to simulate data. Must have the same sample rate as the raw data. 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 : str | instance of SourceSpaces Source space corresponding to the stc. If string, should be a source space filename. Can also be an instance of loaded or generated SourceSpaces. bem : str | dict BEM solution corresponding to the stc. If string, should be a BEM solution filename (e.g., "sample-5120-5120-5120-bem-sol.fif"). cov : instance of Covariance | str | dict of float | None The sensor covariance matrix used to generate noise. If string, should be a filename or 'simple'. If 'simple', an ad hoc covariance matrix will be generated with default values. If dict, an ad hoc covariance matrix will be generated with the values specified by the dict entries. If None, no noise will be added. blink : bool If true, add simulated blink artifacts. See Notes for details. ecg : bool If true, add simulated ECG artifacts. See Notes for details. chpi : bool If true, simulate continuous head position indicator information. Valid cHPI information must encoded in ``raw.info['hpi_meas']`` to use this option. head_pos : None | str | dict | tuple | array Name of the position estimates file. Should be in the format of the files produced by maxfilter. If dict, keys should be the time points and entries should be 4x4 ``dev_head_t`` matrices. If None, the original head position (from ``info['dev_head_t']``) will be used. If tuple, should have the same format as data returned by `head_pos_to_trans_rot_t`. If array, should be of the form returned by :func:`mne.chpi.read_head_pos`. mindist : float Minimum distance between sources and the inner skull boundary to use during forward calculation. interp : str Either 'hann', 'cos2', 'linear', or 'zero', the type of forward-solution interpolation to use between forward solutions at different head positions. iir_filter : None | array IIR filter coefficients (denominator) e.g. [1, -1, 0.2]. n_jobs : int Number of jobs to use. random_state : None | int | np.random.RandomState The random generator state used for blink, ECG, and sensor noise randomization. use_cps : None | bool (default True) Whether to use cortical patch statistics to define normal orientations. Only used when surf_ori and/or force_fixed are True. forward : instance of Forward | None The forward operator to use. If None (default) it will be computed using `bem`, `trans`, and `src`. verbose : bool, str, int, or None If not None, override default verbose level (see :func:`mne.verbose` and :ref:`Logging documentation ` for more). Returns ------- raw : instance of Raw The simulated raw file. See Also -------- mne.chpi.read_head_pos simulate_evoked simulate_stc simulate_sparse_stc Notes ----- Events coded with the position number (starting at 1) will be stored in the trigger channel (if available) at times corresponding to t=0 in the ``stc``. The resulting SNR will be determined by the structure of the noise covariance, the amplitudes of ``stc``, and the head position(s) provided. The blink and ECG artifacts are generated by 1) placing impulses at random times of activation, and 2) convolving with activation kernel functions. In both cases, the scale-factors of the activation functions (and for the resulting EOG and ECG channel traces) were chosen based on visual inspection to yield amplitudes generally consistent with those seen in experimental data. Noisy versions of the blink and ECG activations will be stored in the first EOG and ECG channel in the raw file, respectively, if they exist. For blink artifacts: 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 [1]_. 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. For ECG artifacts: 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. If you have a :class:`mne.Info` that you want to use with no associated :class:`mne.io.Raw` instance, consider creating a dummy one using :class:`mne.io.RawArray`. .. versionadded:: 0.10.0 References ---------- .. [1] Bentivoglio et al. "Analysis of blink rate patterns in normal subjects" Movement Disorders, 1997 Nov;12(6):1028-34. """ if not isinstance(raw, BaseRaw): raise TypeError('raw should be an instance of Raw') times, info, first_samp = raw.times, raw.info, raw.first_samp raw_verbose = raw.verbose # Check for common flag errors and try to override if not isinstance(stc, _BaseSourceEstimate): raise TypeError('stc must be a SourceEstimate') if not np.allclose(info['sfreq'], 1. / stc.tstep): raise ValueError('stc and info must have same sample rate') if len(stc.times) <= 2: # to ensure event encoding works raise ValueError('stc must have at least three time points') stim = False if len(pick_types(info, meg=False, stim=True)) == 0 else True n_jobs = check_n_jobs(n_jobs) rng = check_random_state(random_state) interper = _Interp2(interp) 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'], raw.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'] if head_pos is None: # use pos from info['dev_head_t'] head_pos = dict() if isinstance(head_pos, string_types): # can be a head pos file 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 ts -= raw._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('unknown head_pos type %s' % type(head_pos)) bad = ts < 0 if bad.any(): raise RuntimeError('All position times must be >= 0, found %s/%s' '< 0' % (bad.sum(), len(bad))) bad = ts > times[-1] if bad.any(): raise RuntimeError('All position times must be <= t_end (%0.1f ' 'sec), found %s/%s bad values (is this a split ' 'file?)' % (times[-1], bad.sum(), len(bad))) # If it doesn't start at zero, insert one at t=0 if len(ts) == 0 or ts[0] > 0: ts = np.r_[[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 = raw.time_as_index(ts) offsets = np.concatenate([offsets, [len(times)]]) assert offsets[-2] != offsets[-1] assert np.array_equal(offsets, np.unique(offsets)) assert len(offsets) == len(dev_head_ts) + 1 del ts src = _ensure_src(src, verbose=False) if isinstance(bem, string_types): bem = read_bem_solution(bem, verbose=False) cov = _check_cov(info, cov) approx_events = int((len(times) / info['sfreq']) / (stc.times[-1] - stc.times[0])) logger.info('Provided parameters will provide approximately %s event%s' % (approx_events, _pl(approx_events))) # Extract necessary info meeg_picks = pick_types(info, meg=True, eeg=True, exclude=[]) # for sim meg_picks = pick_types(info, meg=True, eeg=False, exclude=[]) # for CHPI fwd_info = pick_info(info, meeg_picks) fwd_info['projs'] = [] # Ensure no 'projs' applied logger.info('Setting up raw simulation: %s position%s, "%s" interpolation' % (len(dev_head_ts), _pl(dev_head_ts), interp)) del interp verts = stc.vertices verts = [verts] if isinstance(stc, VolSourceEstimate) else verts src = _restrict_source_space_to(src, verts) if forward is not None: forward = restrict_forward_to_stc(forward, stc) # array used to store result raw_data = np.zeros((len(info['ch_names']), len(times))) # figure out our cHPI, ECG, and blink dipoles ecg_rr = blink_rrs = exg_bem = hpi_rrs = None ecg = ecg and len(meg_picks) > 0 chpi = chpi and len(meg_picks) > 0 if chpi: hpi_freqs, hpi_pick, hpi_ons = _get_hpi_info(info) 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 raw_data[hpi_pick, :] = hpi_ons.sum() _log_ch('cHPI status bits enbled and', info, hpi_pick) if blink or ecg: R, r0 = fit_sphere_to_headshape(info, units='m', verbose=False)[:2] exg_bem = make_sphere_model(r0, head_radius=R, relative_radii=(0.97, 0.98, 0.99, 1.), sigmas=(0.33, 1.0, 0.004, 0.33), verbose=False) if blink: # place dipoles at 45 degree angles in z=0 plane blink_rrs = np.array([[np.cos(np.pi / 3.), np.sin(np.pi / 3.), 0.], [-np.cos(np.pi / 3.), np.sin(np.pi / 3), 0.]]) blink_rrs /= np.sqrt(np.sum(blink_rrs * blink_rrs, axis=1))[:, np.newaxis] blink_rrs *= 0.96 * R blink_rrs += r0 # oriented upward blink_nns = np.array([[0., 0., 1.], [0., 0., 1.]]) # 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. / 60. * times)) / 2. blink_rate *= 12.5 / 60. blink_rate += 4.5 / 60. blink_data = rng.rand(len(times)) < blink_rate / info['sfreq'] blink_data = blink_data * (rng.rand(len(times)) + 0.5) # varying amps # Activation kernel is a simple hanning window blink_kernel = np.hanning(int(0.25 * info['sfreq'])) blink_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) noise = rng.randn(blink_data.shape[1]) * 5e-6 if len(ch) >= 1: ch = ch[-1] raw_data[ch, :] = blink_data * 1e3 + noise else: ch = None _log_ch('Blinks simulated and trace', info, ch) del blink_kernel, blink_rate, noise if ecg: ecg_rr = np.array([[-R, 0, -3 * R]]) max_beats = int(np.ceil(times[-1] * 80. / 60.)) # 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. / 80., 60. / 40., 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) ecg_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) noise = rng.randn(ecg_data.shape[1]) * 1.5e-5 if len(ch) >= 1: ch = ch[-1] raw_data[ch, :] = ecg_data * 2e3 + noise else: ch = None _log_ch('ECG simulated and trace', info, ch) del cardiac_data, cardiac_kernel, max_beats, cardiac_idx stc_event_idx = np.argmin(np.abs(stc.times)) if stim: event_ch = pick_channels(info['ch_names'], _get_stim_channel(None, info))[0] raw_data[event_ch, :] = 0. else: event_ch = None _log_ch('Event information', info, event_ch) used = np.zeros(len(times), bool) stc_indices = np.arange(len(times)) % len(stc.times) raw_data[meeg_picks, :] = 0. if chpi: sinusoids = 70e-9 * np.sin(2 * np.pi * hpi_freqs[:, np.newaxis] * (np.arange(len(times)) / info['sfreq'])) zf = None # final filter conditions for the noise # don't process these any more if no MEG present for fi, (fwd, fwd_blink, fwd_ecg, fwd_chpi) in \ enumerate(_iter_forward_solutions( fwd_info, trans, src, bem, exg_bem, dev_head_ts, mindist, hpi_rrs, blink_rrs, ecg_rr, n_jobs, forward)): # must be fixed orientation # XXX eventually we could speed this up by allowing the forward # solution code to only compute the normal direction fwd = convert_forward_solution(fwd, surf_ori=True, force_fixed=True, use_cps=use_cps, verbose=False) if blink: fwd_blink = fwd_blink['sol']['data'] for ii in range(len(blink_rrs)): fwd_blink[:, ii] = np.dot(fwd_blink[:, 3 * ii:3 * (ii + 1)], blink_nns[ii]) fwd_blink = fwd_blink[:, :len(blink_rrs)] fwd_blink = fwd_blink.sum(axis=1)[:, np.newaxis] # just use one arbitrary direction if ecg: fwd_ecg = fwd_ecg['sol']['data'][:, [0]] # align cHPI magnetic dipoles in approx. radial direction if chpi: for ii in range(len(hpi_rrs)): fwd_chpi[:, ii] = np.dot(fwd_chpi[:, 3 * ii:3 * (ii + 1)], hpi_nns[ii]) fwd_chpi = fwd_chpi[:, :len(hpi_rrs)].copy() assert fwd['sol']['data'].shape[0] == len(meeg_picks) interper['fwd'] = fwd['sol']['data'] interper['fwd_blink'] = fwd_blink interper['fwd_ecg'] = fwd_ecg interper['fwd_chpi'] = fwd_chpi if fi == 0: src_sel = _stc_src_sel(fwd['src'], stc) verts = stc.vertices verts = [verts] if isinstance(stc, VolSourceEstimate) else verts diff_ = sum([len(v) for v in verts]) - len(src_sel) if diff_ != 0: warn('%s STC vertices omitted due to fwd calculation' % diff_) stc_data = stc.data[src_sel] del stc, src_sel, diff_, verts continue del fwd, fwd_blink, fwd_ecg, fwd_chpi start, stop = offsets[fi - 1:fi + 1] assert not used[start:stop].any() event_idxs = np.where(stc_indices[start:stop] == stc_event_idx)[0] + start if stim: raw_data[event_ch, event_idxs] = fi logger.info(' Simulating data for %0.3f-%0.3f sec with %s event%s' % (start / info['sfreq'], stop / info['sfreq'], len(event_idxs), _pl(event_idxs))) used[start:stop] = True time_sl = slice(start, stop) stc_idxs = stc_indices[time_sl] # simulate brain data this_data = raw_data[:, time_sl] this_data[meeg_picks] = 0. interper.n_samp = stop - start interper.interpolate('fwd', stc_data, this_data, meeg_picks, stc_idxs) if blink: interper.interpolate('fwd_blink', blink_data[:, time_sl], this_data, meeg_picks) if ecg: interper.interpolate('fwd_ecg', ecg_data[:, time_sl], this_data, meg_picks) if chpi: interper.interpolate('fwd_chpi', sinusoids[:, time_sl], this_data, meg_picks) # add sensor noise, ECG, blink, cHPI if cov is not None: noise, zf = _generate_noise(fwd_info, cov, iir_filter, rng, len(stc_idxs), zi=zf) raw_data[meeg_picks, time_sl] += noise this_data[meeg_picks] += noise assert used[start:stop].all() assert used.all() raw = RawArray(raw_data, info, first_samp=first_samp, verbose=False) raw.verbose = raw_verbose logger.info('Done') return raw def _iter_forward_solutions(info, trans, src, bem, exg_bem, dev_head_ts, mindist, hpi_rrs, blink_rrs, ecg_rrs, n_jobs, forward): """Calculate a forward solution for a subject.""" logger.info('Setting up forward solutions') mri_head_t, trans = _get_trans(trans) megcoils, meg_info, compcoils, megnames, eegels, eegnames, 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) if forward is None: eegfwd = _compute_forwards(rr, bem, [eegels], [None], [None], ['eeg'], n_jobs, verbose=False)[0] eegfwd = _to_forward_dict(eegfwd, eegnames) else: if len(eegnames) > 0: eegfwd = pick_channels_forward(forward, eegnames, verbose=False) else: eegfwd = None if blink_rrs is not None: eegblink = _compute_forwards(blink_rrs, exg_bem, [eegels], [None], [None], ['eeg'], n_jobs, verbose=False)[0] eegblink = _to_forward_dict(eegblink, eegnames) else: eegblink = None # short circuit here if there are no MEG channels (don't need to iterate) if len(pick_types(info, meg=True)) == 0: eegfwd.update(**update_kwargs) for _ in dev_head_ts: yield eegfwd, eegblink, None, None # extra one to fill last buffer yield eegfwd, eegblink, None, None 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) 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('Computing gain matrix for transform #%s/%s' % (ti + 1, len(dev_head_ts))) _transform_orig_meg_coils(megcoils, dev_head_t) _transform_orig_meg_coils(compcoils, dev_head_t) # Make sure our sensors are all outside our BEM coil_rr = [coil['r0'] for coil in megcoils] # Compute forward if forward is None: if not bem['is_sphere']: outside = _points_outside_surface(coil_rr, bem_surf, 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('%s MEG sensors collided with inner skull ' 'surface for transform %s' % (np.sum(~outside), ti)) megfwd = _compute_forwards(rr, bem, [megcoils], [compcoils], [meg_info], ['meg'], n_jobs, verbose=False)[0] megfwd = _to_forward_dict(megfwd, megnames) else: megfwd = pick_channels_forward(forward, megnames, verbose=False) fwd = _merge_meg_eeg_fwds(megfwd, eegfwd, verbose=False) fwd.update(**update_kwargs) fwd_blink = fwd_ecg = fwd_chpi = None if blink_rrs is not None: megblink = _compute_forwards(blink_rrs, exg_bem, [megcoils], [compcoils], [meg_info], ['meg'], n_jobs, verbose=False)[0] megblink = _to_forward_dict(megblink, megnames) fwd_blink = _merge_meg_eeg_fwds(megblink, eegblink, verbose=False) if ecg_rrs is not None: megecg = _compute_forwards(ecg_rrs, exg_bem, [megcoils], [compcoils], [meg_info], ['meg'], n_jobs, verbose=False)[0] fwd_ecg = _to_forward_dict(megecg, megnames) if hpi_rrs is not None: fwd_chpi = _magnetic_dipole_field_vec(hpi_rrs, megcoils).T yield fwd, fwd_blink, fwd_ecg, fwd_chpi # need an extra one to fill last buffer yield fwd, fwd_blink, fwd_ecg, fwd_chpi def _restrict_source_space_to(src, vertices): """Trim down a source space.""" assert len(src) == len(vertices) src = deepcopy(src) for s, v in zip(src, vertices): s['inuse'].fill(0) s['nuse'] = len(v) s['vertno'] = v s['inuse'][s['vertno']] = 1 for key in ('nuse_tri', 'use_tris'): if key in s: del s[key] # This will fix 'patch_info' and 'pinfo' _adjust_patch_info(s, verbose=False) return src