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# Authors: Mark Wronkiewicz <wronk@uw.edu>
# Yousra Bekhti <yousra.bekhti@gmail.com>
# Eric Larson <larson.eric.d@gmail.com>
#
# License: BSD (3-clause)
import os.path as op
from copy import deepcopy
import numpy as np
from numpy.testing import assert_allclose, assert_array_equal
import pytest
from mne import (read_source_spaces, pick_types, read_trans, read_cov,
make_sphere_model, create_info, setup_volume_source_space,
find_events, Epochs, fit_dipole, transform_surface_to,
make_ad_hoc_cov, SourceEstimate, setup_source_space,
read_bem_solution, make_forward_solution,
convert_forward_solution, VolSourceEstimate,
make_bem_solution)
from mne.bem import _surfaces_to_bem
from mne.chpi import _calculate_chpi_positions, read_head_pos, _get_hpi_info
from mne.tests.test_chpi import _assert_quats
from mne.datasets import testing
from mne.simulation import simulate_sparse_stc, simulate_raw, add_eog, add_ecg
from mne.source_space import _compare_source_spaces
from mne.surface import _get_ico_surface
from mne.io import read_raw_fif, RawArray
from mne.io.constants import FIFF
from mne.time_frequency import psd_welch
from mne.utils import run_tests_if_main, catch_logging, check_version
base_path = op.join(op.dirname(__file__), '..', '..', 'io', 'tests', 'data')
raw_fname_short = op.join(base_path, 'test_raw.fif')
data_path = testing.data_path(download=False)
raw_fname = op.join(data_path, 'MEG', 'sample', 'sample_audvis_trunc_raw.fif')
cov_fname = op.join(data_path, 'MEG', 'sample',
'sample_audvis_trunc-cov.fif')
trans_fname = op.join(data_path, 'MEG', 'sample',
'sample_audvis_trunc-trans.fif')
subjects_dir = op.join(data_path, 'subjects')
bem_path = op.join(subjects_dir, 'sample', 'bem')
src_fname = op.join(bem_path, 'sample-oct-2-src.fif')
bem_fname = op.join(bem_path, 'sample-320-320-320-bem-sol.fif')
bem_1_fname = op.join(bem_path, 'sample-320-bem-sol.fif')
raw_chpi_fname = op.join(data_path, 'SSS', 'test_move_anon_raw.fif')
pos_fname = op.join(data_path, 'SSS', 'test_move_anon_raw_subsampled.pos')
def _assert_iter_sim(raw_sim, raw_new, new_event_id):
events = find_events(raw_sim, initial_event=True)
events_tuple = find_events(raw_new, initial_event=True)
assert_array_equal(events_tuple[:, :2], events[:, :2])
assert_array_equal(events_tuple[:, 2], new_event_id)
data_sim = raw_sim[:-1][0]
data_new = raw_new[:-1][0]
assert_array_equal(data_new, data_sim)
def test_iterable():
"""Test iterable support for simulate_raw."""
raw = read_raw_fif(raw_fname_short).load_data()
raw.pick_channels(raw.ch_names[:10] + ['STI 014'])
src = setup_volume_source_space(
pos=dict(rr=[[-0.05, 0, 0], [0.1, 0, 0]],
nn=[[0, 1., 0], [0, 1., 0]]))
assert src.kind == 'discrete'
trans = None
sphere = make_sphere_model(head_radius=None, info=raw.info)
tstep = 1. / raw.info['sfreq']
rng = np.random.RandomState(0)
vertices = np.array([1])
data = rng.randn(1, 2)
stc = VolSourceEstimate(data, vertices, 0, tstep)
assert isinstance(stc.vertices, np.ndarray)
with pytest.raises(ValueError, match='at least three time points'):
simulate_raw(raw.info, stc, trans, src, sphere, None)
data = rng.randn(1, 1000)
n_events = (len(raw.times) - 1) // 1000 + 1
stc = VolSourceEstimate(data, vertices, 0, tstep)
assert isinstance(stc.vertices, np.ndarray)
with catch_logging() as log:
with pytest.deprecated_call():
raw_sim = simulate_raw(raw, stc, trans, src, sphere, None,
verbose=True)
log = log.getvalue()
assert 'Making 15 copies of STC' in log
assert_allclose(raw.times, raw_sim.times)
events = find_events(raw_sim, initial_event=True)
assert len(events) == n_events
assert_array_equal(events[:, 2], 1)
# Degenerate STCs
with pytest.raises(RuntimeError,
match=r'Iterable did not provide stc\[0\]'):
simulate_raw(raw.info, [], trans, src, sphere, None)
with pytest.raises(RuntimeError,
match=r'Iterable did not provide stc\[2\].*duration'):
with pytest.deprecated_call():
simulate_raw(raw, [stc, stc], trans, src, sphere, None)
# tuple with ndarray
event_data = np.zeros(len(stc.times), int)
event_data[0] = 3
raw_new = simulate_raw(raw.info, [(stc, event_data)] * 15,
trans, src, sphere, None, first_samp=raw.first_samp)
assert raw_new.n_times == 15000
raw_new.crop(0, raw_sim.times[-1])
_assert_iter_sim(raw_sim, raw_new, 3)
with pytest.raises(ValueError, match='event data had shape .* but need'):
simulate_raw(raw.info, [(stc, event_data[:-1])], trans, src, sphere,
None)
with pytest.raises(ValueError, match='stim_data in a stc tuple .* int'):
simulate_raw(raw.info, [(stc, event_data * 1.)], trans, src, sphere,
None)
# iterable
def stc_iter():
stim_data = np.zeros(len(stc.times), int)
stim_data[0] = 4
ii = 0
while ii < 100:
ii += 1
yield (stc, stim_data)
with pytest.deprecated_call():
raw_new = simulate_raw(raw, stc_iter(), trans, src, sphere, None)
_assert_iter_sim(raw_sim, raw_new, 4)
def stc_iter_bad():
ii = 0
while ii < 100:
ii += 1
yield (stc, 4, 3)
with pytest.raises(ValueError, match='stc, if tuple, must be length'):
simulate_raw(raw.info, stc_iter_bad(), trans, src, sphere, None)
_assert_iter_sim(raw_sim, raw_new, 4)
def stc_iter_bad():
ii = 0
while ii < 100:
ii += 1
stc_new = stc.copy()
stc_new.vertices = np.array([ii % 2])
yield stc_new
with pytest.raises(RuntimeError, match=r'Vertex mismatch for stc\[1\]'):
simulate_raw(raw.info, stc_iter_bad(), trans, src, sphere, None)
# Forward omission
vertices = np.array([0, 1])
data = rng.randn(2, 1000)
stc = VolSourceEstimate(data, vertices, 0, tstep)
assert isinstance(stc.vertices, np.ndarray)
# XXX eventually we should support filtering based on sphere radius, too,
# by refactoring the code in source_space.py that does it!
surf = _get_ico_surface(3)
surf['rr'] *= 60 # mm
model = _surfaces_to_bem([surf], [FIFF.FIFFV_BEM_SURF_ID_BRAIN], [0.3])
bem = make_bem_solution(model)
with pytest.warns(RuntimeWarning,
match='1 of 2 SourceEstimate vertices'):
simulate_raw(raw, stc, trans, src, bem, None)
def _make_stc(raw, src):
"""Make a STC."""
seed = 42
sfreq = raw.info['sfreq'] # Hz
tstep = 1. / sfreq
n_samples = len(raw.times) // 10
times = np.arange(0, n_samples) * tstep
stc = simulate_sparse_stc(src, 10, times, random_state=seed)
return stc
@pytest.fixture(scope='function', params=[testing._pytest_param()])
def raw_data():
"""Get some starting data."""
# raw with ECG channel
raw = read_raw_fif(raw_fname).crop(0., 5.0).load_data()
data_picks = pick_types(raw.info, meg=True, eeg=True)
other_picks = pick_types(raw.info, meg=False, stim=True, eog=True)
picks = np.sort(np.concatenate((data_picks[::16], other_picks)))
raw = raw.pick_channels([raw.ch_names[p] for p in picks])
raw.info.normalize_proj()
ecg = RawArray(np.zeros((1, len(raw.times))),
create_info(['ECG 063'], raw.info['sfreq'], 'ecg'))
for key in ('dev_head_t', 'highpass', 'lowpass', 'dig'):
ecg.info[key] = raw.info[key]
raw.add_channels([ecg])
src = read_source_spaces(src_fname)
trans = read_trans(trans_fname)
sphere = make_sphere_model('auto', 'auto', raw.info)
stc = _make_stc(raw, src)
return raw, src, stc, trans, sphere
def _get_head_pos_sim(raw):
head_pos_sim = dict()
# these will be at 1., 2., ... sec
shifts = [[0.001, 0., -0.001], [-0.001, 0.001, 0.]]
for time_key, shift in enumerate(shifts):
# Create 4x4 matrix transform and normalize
temp_trans = deepcopy(raw.info['dev_head_t'])
temp_trans['trans'][:3, 3] += shift
head_pos_sim[time_key + 1.] = temp_trans['trans']
return head_pos_sim
def test_simulate_raw_sphere(raw_data, tmpdir):
"""Test simulation of raw data with sphere model."""
seed = 42
raw, src, stc, trans, sphere = raw_data
assert len(pick_types(raw.info, meg=False, ecg=True)) == 1
tempdir = str(tmpdir)
# head pos
head_pos_sim = _get_head_pos_sim(raw)
#
# Test raw simulation with basic parameters
#
raw.info.normalize_proj()
cov = read_cov(cov_fname)
cov['projs'] = raw.info['projs']
raw.info['bads'] = raw.ch_names[:1]
with pytest.deprecated_call(match='cov is deprecated'):
raw_sim = simulate_raw(raw, stc, trans, src, sphere, cov,
head_pos=head_pos_sim,
blink=True, ecg=True, random_state=seed,
verbose=True)
with pytest.warns(RuntimeWarning, match='applying projector with'):
raw_sim_2 = simulate_raw(raw, stc, trans_fname, src_fname, sphere,
cov_fname, head_pos=head_pos_sim,
blink=True, ecg=True, random_state=seed)
with pytest.raises(RuntimeError, match='Maximum number of STC iterations'):
simulate_raw(raw.info, [stc] * 5, trans_fname, src_fname, sphere,
cov=None, max_iter=1)
assert_array_equal(raw_sim_2[:][0], raw_sim[:][0])
std = dict(grad=2e-13, mag=10e-15, eeg=0.1e-6)
with pytest.deprecated_call():
raw_sim = simulate_raw(raw, stc, trans, src, sphere,
make_ad_hoc_cov(raw.info, std=std),
head_pos=head_pos_sim, blink=True, ecg=True,
random_state=seed)
with pytest.deprecated_call():
raw_sim_2 = simulate_raw(raw, stc, trans_fname, src_fname, sphere,
cov=std, head_pos=head_pos_sim, blink=True,
ecg=True, random_state=seed)
assert_array_equal(raw_sim_2[:][0], raw_sim[:][0])
sphere_norad = make_sphere_model('auto', None, raw.info)
raw_meg = raw.copy().pick_types()
with pytest.deprecated_call():
raw_sim = simulate_raw(raw_meg, stc, trans, src, sphere_norad,
cov=None,
head_pos=head_pos_sim, blink=True, ecg=True,
random_state=seed)
with pytest.deprecated_call():
raw_sim_2 = simulate_raw(raw_meg, stc, trans_fname, src_fname,
sphere_norad, cov=None, head_pos=head_pos_sim,
blink=True, ecg=True, random_state=seed)
assert_array_equal(raw_sim_2[:][0], raw_sim[:][0])
# Test IO on processed data
test_outname = op.join(tempdir, 'sim_test_raw.fif')
raw_sim.save(test_outname)
raw_sim_loaded = read_raw_fif(test_outname, preload=True)
assert_allclose(raw_sim_loaded[:][0], raw_sim[:][0], rtol=1e-6, atol=1e-20)
del raw_sim, raw_sim_2
# with no cov (no noise) but with artifacts, most time periods should match
# but the EOG/ECG channels should not
for ecg, eog in ((True, False), (False, True), (True, True)):
with pytest.deprecated_call():
raw_sim_3 = simulate_raw(raw, stc, trans, src, sphere,
cov=None, head_pos=head_pos_sim,
blink=eog, ecg=ecg, random_state=seed)
with pytest.deprecated_call():
raw_sim_4 = simulate_raw(raw, stc, trans, src, sphere,
cov=None, head_pos=head_pos_sim,
blink=False, ecg=False, random_state=seed)
picks = np.arange(len(raw.ch_names))
diff_picks = pick_types(raw.info, meg=False, ecg=ecg, eog=eog)
these_picks = np.setdiff1d(picks, diff_picks)
close = np.isclose(raw_sim_3[these_picks][0],
raw_sim_4[these_picks][0], atol=1e-20)
assert np.mean(close) > 0.7
far = ~np.isclose(raw_sim_3[diff_picks][0],
raw_sim_4[diff_picks][0], atol=1e-20)
assert np.mean(far) > 0.99
del raw_sim_3, raw_sim_4
# make sure it works with EEG-only and MEG-only
with pytest.deprecated_call():
raw_sim_meg = simulate_raw(raw.copy().pick_types(meg=True, eeg=False),
stc, trans, src, sphere, cov=None)
raw_sim_eeg = simulate_raw(raw.copy().pick_types(meg=False, eeg=True),
stc, trans, src, sphere, cov=None)
raw_sim_meeg = simulate_raw(raw.copy().pick_types(meg=True, eeg=True),
stc, trans, src, sphere, cov=None)
for this_raw in (raw_sim_meg, raw_sim_eeg, raw_sim_meeg):
add_eog(this_raw, random_state=seed)
for this_raw in (raw_sim_meg, raw_sim_meeg):
add_ecg(this_raw, random_state=seed)
with pytest.raises(RuntimeError, match='only add ECG artifacts if MEG'):
add_ecg(raw_sim_eeg)
assert_allclose(np.concatenate((raw_sim_meg[:][0], raw_sim_eeg[:][0])),
raw_sim_meeg[:][0], rtol=1e-7, atol=1e-20)
del raw_sim_meg, raw_sim_eeg, raw_sim_meeg
# check that raw-as-info is supported
n_samp = len(stc.times)
raw_crop = raw.copy().crop(0., (n_samp - 1.) / raw.info['sfreq'])
assert len(raw_crop.times) == len(stc.times)
with pytest.deprecated_call():
raw_sim = simulate_raw(raw_crop, stc, trans, src, sphere, cov=None)
with catch_logging() as log:
raw_sim_2 = simulate_raw(raw_crop.info, stc, trans, src, sphere,
cov=None, verbose=True)
log = log.getvalue()
assert '1 STC iteration provided' in log
assert len(raw_sim_2.times) == n_samp
assert_allclose(raw_sim[:, :n_samp][0],
raw_sim_2[:, :n_samp][0], rtol=1e-5, atol=1e-30)
del raw_sim, raw_sim_2
# check that different interpolations are similar given small movements
with pytest.deprecated_call():
raw_sim = simulate_raw(raw, stc, trans, src, sphere, cov=None,
head_pos=head_pos_sim, interp='linear')
with pytest.deprecated_call():
raw_sim_hann = simulate_raw(raw, stc, trans, src, sphere, cov=None,
head_pos=head_pos_sim, interp='hann')
assert_allclose(raw_sim[:][0], raw_sim_hann[:][0], rtol=1e-1, atol=1e-14)
del raw_sim_hann
# check that new Generator objects can be used
if check_version('numpy', '1.17'):
random_state = np.random.default_rng(seed)
add_ecg(raw_sim, random_state=random_state)
add_eog(raw_sim, random_state=random_state)
def test_degenerate(raw_data):
"""Test degenerate conditions."""
raw, src, stc, trans, sphere = raw_data
info = raw.info
# Make impossible transform (translate up into helmet) and ensure failure
hp_err = _get_head_pos_sim(raw)
hp_err[1.][2, 3] -= 0.1 # z trans upward 10cm
with pytest.raises(RuntimeError, match='collided with inner skull'):
simulate_raw(info, stc, trans, src, sphere, cov=None,
head_pos=hp_err)
# other degenerate conditions
with pytest.raises(TypeError, match='info must be an instance of'):
simulate_raw('foo', stc, trans, src, sphere)
with pytest.raises(TypeError, match='stc must be an instance of'):
simulate_raw(info, 'foo', trans, src, sphere)
with pytest.raises(ValueError, match='stc must have at least three time'):
simulate_raw(info, stc.copy().crop(0, 0), trans, src, sphere)
with pytest.raises(TypeError, match='must be an instance of Raw or Info'):
simulate_raw(0, stc, trans, src, sphere)
stc_bad = stc.copy()
stc_bad.tstep += 0.1
with pytest.raises(ValueError, match='same sample rate'):
simulate_raw(info, stc_bad, trans, src, sphere)
with pytest.raises(TypeError, match='Covariance matrix type'):
with pytest.deprecated_call():
simulate_raw(info, stc, trans, src, sphere, cov=0)
with pytest.raises(RuntimeError, match='cHPI information not found'):
with pytest.deprecated_call():
simulate_raw(info, stc, trans, src, sphere, chpi=True)
with pytest.raises(ValueError, match='interp must be one of'):
simulate_raw(info, stc, trans, src, sphere, interp='foo')
with pytest.raises(TypeError, match='unknown head_pos type'):
simulate_raw(info, stc, trans, src, sphere, head_pos=1.)
with pytest.raises(RuntimeError, match='All position times'):
with pytest.deprecated_call():
simulate_raw(raw, stc, trans, src, sphere, head_pos=pos_fname)
head_pos_sim_err = _get_head_pos_sim(raw)
head_pos_sim_err[-1.] = head_pos_sim_err[1.] # negative time
with pytest.raises(RuntimeError, match='All position times'):
simulate_raw(info, stc, trans, src, sphere,
head_pos=head_pos_sim_err)
raw_bad = raw.copy()
raw_bad.info['dig'] = None
with pytest.raises(RuntimeError, match='Cannot fit headshape'):
with pytest.deprecated_call():
simulate_raw(raw_bad, stc, trans, src, sphere, blink=True)
with pytest.raises(RuntimeError, match='Cannot fit headshape'):
add_eog(raw_bad)
@pytest.mark.slowtest
def test_simulate_raw_bem(raw_data):
"""Test simulation of raw data with BEM."""
raw, src, stc, trans, sphere = raw_data
src = setup_source_space('sample', 'oct1', subjects_dir=subjects_dir)
for s in src:
s['nuse'] = 3
s['vertno'] = src[1]['vertno'][:3]
s['inuse'].fill(0)
s['inuse'][s['vertno']] = 1
# use different / more complete STC here
vertices = [s['vertno'] for s in src]
stc = SourceEstimate(np.eye(sum(len(v) for v in vertices)), vertices,
0, 1. / raw.info['sfreq'])
with pytest.deprecated_call():
raw_sim_sph = simulate_raw(raw, stc, trans, src, sphere, cov=None,
verbose=True)
with pytest.deprecated_call():
raw_sim_bem = simulate_raw(raw, stc, trans, src, bem_fname, cov=None,
n_jobs=2)
# some components (especially radial) might not match that well,
# so just make sure that most components have high correlation
assert_array_equal(raw_sim_sph.ch_names, raw_sim_bem.ch_names)
picks = pick_types(raw.info, meg=True, eeg=True)
n_ch = len(picks)
corr = np.corrcoef(raw_sim_sph[picks][0], raw_sim_bem[picks][0])
assert_array_equal(corr.shape, (2 * n_ch, 2 * n_ch))
med_corr = np.median(np.diag(corr[:n_ch, -n_ch:]))
assert med_corr > 0.65
# do some round-trip localization
for s in src:
transform_surface_to(s, 'head', trans)
locs = np.concatenate([s['rr'][s['vertno']] for s in src])
tmax = (len(locs) - 1) / raw.info['sfreq']
cov = make_ad_hoc_cov(raw.info)
# The tolerance for the BEM is surprisingly high (28) but I get the same
# result when using MNE-C and Xfit, even when using a proper 5120 BEM :(
for use_raw, bem, tol in ((raw_sim_sph, sphere, 2),
(raw_sim_bem, bem_fname, 31)):
events = find_events(use_raw, 'STI 014')
assert len(locs) == 6
evoked = Epochs(use_raw, events, 1, 0, tmax, baseline=None).average()
assert len(evoked.times) == len(locs)
fits = fit_dipole(evoked, cov, bem, trans, min_dist=1.)[0].pos
diffs = np.sqrt(np.sum((locs - fits) ** 2, axis=-1)) * 1000
med_diff = np.median(diffs)
assert med_diff < tol, '%s: %s' % (bem, med_diff)
def test_simulate_round_trip(raw_data):
"""Test simulate_raw round trip calculations."""
# Check a diagonal round-trip
raw, src, stc, trans, sphere = raw_data
raw.pick_types(meg=True, stim=True)
bem = read_bem_solution(bem_1_fname)
old_bem = bem.copy()
old_src = src.copy()
old_trans = trans.copy()
fwd = make_forward_solution(raw.info, trans, src, bem)
# no omissions
assert (sum(len(s['vertno']) for s in src) ==
sum(len(s['vertno']) for s in fwd['src']) ==
36)
# make sure things were not modified
assert (old_bem['surfs'][0]['coord_frame'] ==
bem['surfs'][0]['coord_frame'])
assert trans == old_trans
_compare_source_spaces(src, old_src)
data = np.eye(fwd['nsource'])
raw.crop(0, len(data) / raw.info['sfreq'], include_tmax=False)
stc = SourceEstimate(data, [s['vertno'] for s in fwd['src']],
0, 1. / raw.info['sfreq'])
for use_fwd in (None, fwd):
if use_fwd is None:
use_trans, use_src, use_bem = trans, src, bem
else:
use_trans = use_src = use_bem = None
with pytest.deprecated_call():
this_raw = simulate_raw(raw, stc, use_trans, use_src, use_bem,
cov=None, forward=use_fwd)
this_raw.pick_types(meg=True, eeg=True)
assert (old_bem['surfs'][0]['coord_frame'] ==
bem['surfs'][0]['coord_frame'])
assert trans == old_trans
_compare_source_spaces(src, old_src)
this_fwd = convert_forward_solution(fwd, force_fixed=True)
assert_allclose(this_raw[:][0], this_fwd['sol']['data'],
atol=1e-12, rtol=1e-6)
with pytest.raises(ValueError, match='If forward is not None then'):
simulate_raw(raw.info, stc, trans, src, bem, forward=fwd)
# Not iterable
with pytest.raises(TypeError, match='SourceEstimate, tuple, or iterable'):
simulate_raw(raw.info, 0., trans, src, bem, None)
# STC with a source that `src` does not have
assert 0 not in src[0]['vertno']
vertices = [[0, fwd['src'][0]['vertno'][0]], []]
stc_bad = SourceEstimate(data[:2], vertices, 0, 1. / raw.info['sfreq'])
with pytest.warns(RuntimeWarning,
match='1 of 2 SourceEstimate vertices'):
simulate_raw(raw.info, stc_bad, trans, src, bem)
assert 0 not in fwd['src'][0]['vertno']
with pytest.warns(RuntimeWarning,
match='1 of 2 SourceEstimate vertices'):
simulate_raw(raw.info, stc_bad, None, None, None, forward=fwd)
# dev_head_t mismatch
fwd['info']['dev_head_t']['trans'][0, 0] = 1.
with pytest.raises(ValueError, match='dev_head_t.*does not match'):
simulate_raw(raw.info, stc, None, None, None, forward=fwd)
@pytest.mark.slowtest
@testing.requires_testing_data
def test_simulate_raw_chpi():
"""Test simulation of raw data with cHPI."""
raw = read_raw_fif(raw_chpi_fname, allow_maxshield='yes')
picks = np.arange(len(raw.ch_names))
picks = np.setdiff1d(picks, pick_types(raw.info, meg=True, eeg=True)[::4])
raw.load_data().pick_channels([raw.ch_names[pick] for pick in picks])
raw.info.normalize_proj()
sphere = make_sphere_model('auto', 'auto', raw.info)
# make sparse spherical source space
sphere_vol = tuple(sphere['r0'] * 1000.) + (sphere.radius * 1000.,)
src = setup_volume_source_space(sphere=sphere_vol, pos=70.)
stc = _make_stc(raw, src)
# simulate data with cHPI on
with pytest.deprecated_call():
raw_sim = simulate_raw(raw, stc, None, src, sphere, cov=None,
head_pos=pos_fname, interp='zero')
# need to trim extra samples off this one
with pytest.deprecated_call():
raw_chpi = simulate_raw(raw, stc, None, src, sphere, cov=None,
chpi=True, head_pos=pos_fname, interp='zero')
# test cHPI indication
hpi_freqs, hpi_pick, hpi_ons = _get_hpi_info(raw.info)
assert_allclose(raw_sim[hpi_pick][0], 0.)
assert_allclose(raw_chpi[hpi_pick][0], hpi_ons.sum())
# test that the cHPI signals make some reasonable values
picks_meg = pick_types(raw.info, meg=True, eeg=False)
picks_eeg = pick_types(raw.info, meg=False, eeg=True)
for picks in [picks_meg[:3], picks_eeg[:3]]:
psd_sim, freqs_sim = psd_welch(raw_sim, picks=picks)
psd_chpi, freqs_chpi = psd_welch(raw_chpi, picks=picks)
assert_array_equal(freqs_sim, freqs_chpi)
freq_idx = np.sort([np.argmin(np.abs(freqs_sim - f))
for f in hpi_freqs])
if picks is picks_meg:
assert (psd_chpi[:, freq_idx] >
100 * psd_sim[:, freq_idx]).all()
else:
assert_allclose(psd_sim, psd_chpi, atol=1e-20)
# test localization based on cHPI information
quats_sim = _calculate_chpi_positions(raw_chpi, t_step_min=10.)
quats = read_head_pos(pos_fname)
_assert_quats(quats, quats_sim, dist_tol=5e-3, angle_tol=3.5)
run_tests_if_main()
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