def _calculate_chpi_positions(raw,
t_step_min=0.01,
t_step_max=1.,
t_window='auto',
too_close='raise',
dist_limit=0.005,
gof_limit=0.98,
ext_order=1,
verbose=None):
chpi_amplitudes = compute_chpi_amplitudes(raw,
t_step_min=t_step_min,
t_window=t_window,
ext_order=ext_order,
verbose=verbose)
chpi_locs = compute_chpi_locs(raw.info,
chpi_amplitudes,
t_step_max=t_step_max,
too_close=too_close,
verbose=verbose)
head_pos = compute_head_pos(raw.info,
chpi_locs,
dist_limit=dist_limit,
gof_limit=gof_limit,
verbose=verbose)
return head_pos
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']) + (sphere.radius, )
src = setup_volume_source_space(sphere=sphere_vol,
pos=70.,
sphere_units='m')
stcs = [_make_stc(raw, src)] * 15
# simulate data with cHPI on
raw_sim = simulate_raw(raw.info,
stcs,
None,
src,
sphere,
head_pos=pos_fname,
interp='zero',
first_samp=raw.first_samp)
# need to trim extra samples off this one
raw_chpi = add_chpi(raw_sim.copy(), 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
chpi_amplitudes = compute_chpi_amplitudes(raw, t_step_min=10.)
coil_locs = compute_chpi_locs(raw.info, chpi_amplitudes)
quats_sim = compute_head_pos(raw_chpi.info, coil_locs)
quats = read_head_pos(pos_fname)
_assert_quats(quats,
quats_sim,
dist_tol=5e-3,
angle_tol=3.5,
vel_atol=0.03) # velicity huge because of t_step_min above
def test_calculate_head_pos_kit():
"""Test calculation of head position using KIT data."""
raw = read_raw_kit(con_fname, mrk_fname, elp_fname, hsp_fname)
assert len(raw.info['hpi_results']) == 1
chpi_locs = extract_chpi_locs_kit(raw)
assert chpi_locs['rrs'].shape == (2, 5, 3)
assert_array_less(chpi_locs['gofs'], 1.)
assert_array_less(0.98, chpi_locs['gofs'])
quats = compute_head_pos(raw.info, chpi_locs)
assert quats.shape == (2, 10)
# plotting works
plot_head_positions(quats, info=raw.info)
raw_berlin = read_raw_kit(berlin_fname)
assert_allclose(raw_berlin.info['dev_head_t']['trans'], np.eye(4))
assert len(raw_berlin.info['hpi_results']) == 0
with pytest.raises(ValueError, match='Invalid value'):
extract_chpi_locs_kit(raw_berlin)
with pytest.raises(RuntimeError, match='not find appropriate'):
extract_chpi_locs_kit(raw_berlin, 'STI 014')
with pytest.raises(RuntimeError, match='no initial cHPI'):
compute_head_pos(raw_berlin.info, chpi_locs)
def test_calculate_head_pos_ctf():
"""Test extracting of cHPI positions from CTF data."""
raw = read_raw_ctf(ctf_chpi_fname)
chpi_locs = extract_chpi_locs_ctf(raw)
quats = compute_head_pos(raw.info, chpi_locs)
mc_quats = read_head_pos(ctf_chpi_pos_fname)
mc_quats[:, 9] /= 10000 # had old factor in there twice somehow...
_assert_quats(quats, mc_quats, dist_tol=0.004, angle_tol=2.5, err_rtol=1.,
vel_atol=7e-3) # 7 mm/s
plot_head_positions(quats, info=raw.info)
raw = read_raw_fif(ctf_fname)
with pytest.raises(RuntimeError, match='Could not find'):
extract_chpi_locs_ctf(raw)
def test_calculate_chpi_coil_locs_artemis():
"""Test computing just cHPI locations."""
raw = read_raw_fif(chpi_fif_fname, allow_maxshield='yes', preload=True)
# This is a little hack (aliasing while decimating) to make it much faster
# for testing purposes only. We can relax this later if we find it breaks
# something.
raw_dec = _decimate_chpi(raw, 15)
times, cHPI_digs = _calculate_chpi_coil_locs(raw_dec, verbose='debug')
# spot check
assert_allclose(times[0], 9., atol=1e-2)
assert_allclose(cHPI_digs[0][2]['r'],
[-0.01937833, 0.00346804, 0.06331209], atol=1e-3)
assert_allclose(cHPI_digs[0][2]['gof'], 0.9957, atol=1e-3)
assert_allclose(cHPI_digs[0][4]['r'],
[-0.0655, 0.0755, 0.0004], atol=3e-3)
assert_allclose(cHPI_digs[0][4]['gof'], 0.9323, atol=1e-3)
_check_dists(raw.info, cHPI_digs[0], n_bad=1)
# test on 5k artemis data
raw = read_raw_artemis123(art_fname, preload=True)
times, cHPI_digs = _calculate_chpi_coil_locs(raw, verbose='debug')
assert len(np.setdiff1d(times, raw.times + raw.first_time)) == 0
# Should be somewhere around 1.5 sec, depending on coil GOF values
# around 0.98 it can change
assert_allclose(times[5], 1.5, atol=2e-1)
assert_allclose(cHPI_digs[5][0]['gof'], 0.995, atol=5e-3)
assert_allclose(cHPI_digs[5][0]['r'],
[-0.0157, 0.0655, 0.0018], atol=1e-3)
_check_dists(raw.info, cHPI_digs[5])
coil_amplitudes = compute_chpi_amplitudes(raw)
with pytest.raises(ValueError, match='too_close'):
compute_chpi_locs(raw.info, coil_amplitudes, too_close='foo')
# ensure values are in a reasonable range
amps = np.linalg.norm(coil_amplitudes['slopes'], axis=-1)
amps /= coil_amplitudes['slopes'].shape[-1]
assert amps.shape == (len(coil_amplitudes['times']), 3)
assert_array_less(amps, 1e-11)
assert_array_less(1e-13, amps)
# with nan amplitudes (i.e., cHPI off) it should return an empty array,
# but still one that is 3D
coil_amplitudes['slopes'].fill(np.nan)
chpi_locs = compute_chpi_locs(raw.info, coil_amplitudes)
assert chpi_locs['rrs'].shape == (0, 3, 3)
pos = compute_head_pos(raw.info, chpi_locs)
assert pos.shape == (0, 10)
def test_initial_fit_redo():
"""Test that initial fits can be redone based on moments."""
raw = read_raw_fif(chpi_fif_fname, allow_maxshield='yes')
slopes = np.array(
[[c['slopes'] for c in raw.info['hpi_meas'][0]['hpi_coils']]])
amps = np.linalg.norm(slopes, axis=-1)
amps /= slopes.shape[-1]
assert_array_less(amps, 5e-11)
assert_array_less(1e-12, amps)
proj, _, _ = _setup_ext_proj(raw.info, ext_order=1)
chpi_amplitudes = dict(times=np.zeros(1), slopes=slopes, proj=proj)
chpi_locs = compute_chpi_locs(raw.info, chpi_amplitudes)
# check GOF
coil_gof = raw.info['hpi_results'][0]['goodness']
assert_allclose(chpi_locs['gofs'][0], coil_gof, atol=0.3) # XXX not good
# check moment
# XXX our forward and theirs differ by an extra mult by _MAG_FACTOR
coil_moment = raw.info['hpi_results'][0]['moments'] / _MAG_FACTOR
py_moment = chpi_locs['moments'][0]
coil_amp = np.linalg.norm(coil_moment, axis=-1, keepdims=True)
py_amp = np.linalg.norm(py_moment, axis=-1, keepdims=True)
assert_allclose(coil_amp, py_amp, rtol=0.2)
coil_ori = coil_moment / coil_amp
py_ori = py_moment / py_amp
angles = np.rad2deg(np.arccos(np.abs(np.sum(coil_ori * py_ori, axis=1))))
assert_array_less(angles, 20)
# check resulting dev_head_t
head_pos = compute_head_pos(raw.info, chpi_locs)
assert head_pos.shape == (1, 10)
nm_pos = raw.info['dev_head_t']['trans']
dist = 1000 * np.linalg.norm(nm_pos[:3, 3] - head_pos[0, 4:7])
assert 0.1 < dist < 2
angle = np.rad2deg(
_angle_between_quats(rot_to_quat(nm_pos[:3, :3]), head_pos[0, 1:4]))
assert 0.1 < angle < 2
gof = head_pos[0, 7]
assert_allclose(gof, 0.9999, atol=1e-4)
def calculate_head_pos_ctf(raw):
"""Wrap to facilitate API change."""
chpi_locs = extract_chpi_locs_ctf(raw)
return compute_head_pos(raw.info, chpi_locs)
def compute_head_position(src: Path) -> np.ndarray:
raw = read_raw_fif(src)
chpi_ampl = compute_chpi_amplitudes(raw)
chpi_locs = compute_chpi_locs(raw.info, chpi_ampl)
return compute_head_pos(raw.info, chpi_locs)