def test_bad_proj():
"""Test dealing with bad projection application."""
raw = read_raw_fif(raw_fname, preload=True)
events = read_events(event_fname)
picks = pick_types(raw.info,
meg=True,
stim=False,
ecg=False,
eog=False,
exclude='bads')
picks = picks[2:18:3]
_check_warnings(raw, events, picks)
# still bad
raw.pick_channels([raw.ch_names[ii] for ii in picks])
_check_warnings(raw, events)
# "fixed"
raw.info.normalize_proj() # avoid projection warnings
_check_warnings(raw, events, count=0)
# eeg avg ref is okay
raw = read_raw_fif(raw_fname, preload=True).pick_types(meg=False, eeg=True)
raw.set_eeg_reference(projection=True)
_check_warnings(raw, events, count=0)
raw.info['bads'] = raw.ch_names[:10]
_check_warnings(raw, events, count=0)
raw = read_raw_fif(raw_fname)
pytest.raises(ValueError, raw.del_proj, 'foo')
n_proj = len(raw.info['projs'])
raw.del_proj(0)
assert_equal(len(raw.info['projs']), n_proj - 1)
raw.del_proj()
assert_equal(len(raw.info['projs']), 0)
# Ensure we deal with newer-style Neuromag projs properly, were getting:
#
# Projection vector "PCA-v2" has magnitude 1.00 (should be unity),
# applying projector with 101/306 of the original channels available
# may be dangerous.
raw = read_raw_fif(raw_fname).crop(0, 1)
raw.set_eeg_reference(projection=True)
raw.info['bads'] = ['MEG 0111']
meg_picks = pick_types(raw.info, meg=True, exclude=())
ch_names = [raw.ch_names[pick] for pick in meg_picks]
for p in raw.info['projs'][:-1]:
data = np.zeros((1, len(ch_names)))
idx = [ch_names.index(ch_name) for ch_name in p['data']['col_names']]
data[:, idx] = p['data']['data']
p['data'].update(ncol=len(meg_picks), col_names=ch_names, data=data)
# smoke test for no warnings during reg
regularize(compute_raw_covariance(raw, verbose='error'), raw.info)
def test_evoked_whiten():
"""Test whitening of evoked data"""
evoked = Evoked(ave_fname, setno=0, baseline=(None, 0), proj=True)
cov = read_cov(cov_fname)
###########################################################################
# Show result
picks = pick_types(evoked.info,
meg=True,
eeg=True,
ref_meg=False,
exclude='bads')
noise_cov = regularize(cov,
evoked.info,
grad=0.1,
mag=0.1,
eeg=0.1,
exclude='bads')
evoked_white = whiten_evoked(evoked, noise_cov, picks, diag=True)
whiten_baseline_data = evoked_white.data[picks][:, evoked.times < 0]
mean_baseline = np.mean(np.abs(whiten_baseline_data), axis=1)
assert_true(np.all(mean_baseline < 1.))
assert_true(np.all(mean_baseline > 0.2))
def test_gamma_map():
"""Test Gamma MAP inverse"""
forward = read_forward_solution(fname_fwd)
forward = convert_forward_solution(forward, surf_ori=True)
forward = pick_types_forward(forward, meg=False, eeg=True)
evoked = read_evokeds(fname_evoked, condition=0, baseline=(None, 0),
proj=False)
evoked.resample(50, npad=100)
evoked.crop(tmin=0.1, tmax=0.16) # crop to window around peak
cov = read_cov(fname_cov)
cov = regularize(cov, evoked.info)
alpha = 0.5
stc = gamma_map(evoked, forward, cov, alpha, tol=1e-4,
xyz_same_gamma=True, update_mode=1)
_check_stc(stc, evoked, 68477)
stc = gamma_map(evoked, forward, cov, alpha, tol=1e-4,
xyz_same_gamma=False, update_mode=1)
_check_stc(stc, evoked, 82010)
dips = gamma_map(evoked, forward, cov, alpha, tol=1e-4,
xyz_same_gamma=False, update_mode=1,
return_as_dipoles=True)
assert_true(isinstance(dips[0], Dipole))
stc_dip = make_stc_from_dipoles(dips, forward['src'])
_check_stcs(stc, stc_dip)
# force fixed orientation
stc = gamma_map(evoked, forward, cov, alpha, tol=1e-4,
xyz_same_gamma=False, update_mode=2,
loose=0, return_residual=False)
_check_stc(stc, evoked, 85739, 20)
def test_gamma_map_vol_sphere():
"""Gamma MAP with a sphere forward and volumic source space"""
evoked = read_evokeds(fname_evoked, condition=0, baseline=(None, 0),
proj=False)
evoked.resample(50, npad=100)
evoked.crop(tmin=0.1, tmax=0.16) # crop to window around peak
cov = read_cov(fname_cov)
cov = regularize(cov, evoked.info)
info = evoked.info
sphere = mne.make_sphere_model(r0=(0., 0., 0.), head_radius=0.080)
src = mne.setup_volume_source_space(subject=None, pos=15., mri=None,
sphere=(0.0, 0.0, 0.0, 80.0),
bem=None, mindist=5.0,
exclude=2.0)
fwd = mne.make_forward_solution(info, trans=None, src=src, bem=sphere,
eeg=False, meg=True)
alpha = 0.5
assert_raises(ValueError, gamma_map, evoked, fwd, cov, alpha,
loose=0, return_residual=False)
assert_raises(ValueError, gamma_map, evoked, fwd, cov, alpha,
loose=0.2, return_residual=False)
stc = gamma_map(evoked, fwd, cov, alpha, tol=1e-4,
xyz_same_gamma=False, update_mode=2,
return_residual=False)
assert_array_almost_equal(stc.times, evoked.times, 5)
def test_gamma_map():
"""Test Gamma MAP inverse"""
forward = read_forward_solution(fname_fwd, force_fixed=False,
surf_ori=True)
forward = pick_types_forward(forward, meg=False, eeg=True)
evoked = read_evokeds(fname_evoked, condition=0, baseline=(None, 0),
proj=False)
evoked.resample(50, npad=100)
evoked.crop(tmin=0.1, tmax=0.16) # crop to nice window near samp border
cov = read_cov(fname_cov)
cov = regularize(cov, evoked.info)
alpha = 0.5
stc = gamma_map(evoked, forward, cov, alpha, tol=1e-4,
xyz_same_gamma=True, update_mode=1)
_check_stc(stc, evoked, 68477)
stc = gamma_map(evoked, forward, cov, alpha, tol=1e-4,
xyz_same_gamma=False, update_mode=1)
_check_stc(stc, evoked, 82010)
# force fixed orientation
stc = gamma_map(evoked, forward, cov, alpha, tol=1e-4,
xyz_same_gamma=False, update_mode=2,
loose=None, return_residual=False)
_check_stc(stc, evoked, 85739, 20)
def test_gamma_map():
"""Test Gamma MAP inverse."""
forward = read_forward_solution(fname_fwd)
forward = convert_forward_solution(forward, surf_ori=True)
forward = pick_types_forward(forward, meg=False, eeg=True)
evoked = read_evokeds(fname_evoked, condition=0, baseline=(None, 0),
proj=False)
evoked.resample(50, npad=100)
evoked.crop(tmin=0.1, tmax=0.14) # crop to window around peak
cov = read_cov(fname_cov)
cov = regularize(cov, evoked.info, rank=None)
alpha = 0.5
stc = gamma_map(evoked, forward, cov, alpha, tol=1e-4,
xyz_same_gamma=True, update_mode=1)
_check_stc(stc, evoked, 68477, 'lh', fwd=forward)
stc = gamma_map(evoked, forward, cov, alpha, tol=1e-4,
xyz_same_gamma=False, update_mode=1)
_check_stc(stc, evoked, 82010, 'lh', fwd=forward)
dips = gamma_map(evoked, forward, cov, alpha, tol=1e-4,
xyz_same_gamma=False, update_mode=1,
return_as_dipoles=True)
assert (isinstance(dips[0], Dipole))
stc_dip = make_stc_from_dipoles(dips, forward['src'])
_check_stcs(stc, stc_dip)
# force fixed orientation
stc = gamma_map(evoked, forward, cov, alpha, tol=1e-4,
xyz_same_gamma=False, update_mode=2,
loose=0, return_residual=False)
_check_stc(stc, evoked, 85739, 'lh', fwd=forward, ratio=20.)
def test_gamma_map():
"""Test Gamma MAP inverse"""
forward = read_forward_solution(fname_fwd, force_fixed=False,
surf_ori=True)
forward = pick_types_forward(forward, meg=False, eeg=True)
evoked = read_evokeds(fname_evoked, condition=0, baseline=(None, 0))
evoked.resample(50)
evoked.crop(tmin=0, tmax=0.3)
cov = read_cov(fname_cov)
cov = regularize(cov, evoked.info)
alpha = 0.2
stc = gamma_map(evoked, forward, cov, alpha, tol=1e-5,
xyz_same_gamma=True, update_mode=1, verbose=False)
idx = np.argmax(np.sum(stc.data ** 2, axis=1))
assert_true(np.concatenate(stc.vertices)[idx] == 96397)
stc = gamma_map(evoked, forward, cov, alpha, tol=1e-5,
xyz_same_gamma=False, update_mode=1, verbose=False)
idx = np.argmax(np.sum(stc.data ** 2, axis=1))
assert_true(np.concatenate(stc.vertices)[idx] == 82010)
# force fixed orientation
stc, res = gamma_map(evoked, forward, cov, alpha, tol=1e-5,
xyz_same_gamma=False, update_mode=2,
loose=None, return_residual=True, verbose=False)
idx = np.argmax(np.sum(stc.data ** 2, axis=1))
# assert_true(np.concatenate(stc.vertices)[idx] == 83398) # XXX FIX
assert_array_almost_equal(evoked.times, res.times)
def test_whiten_evoked():
"""Test whitening of evoked data."""
evoked = read_evokeds(ave_fname,
condition=0,
baseline=(None, 0),
proj=True)
cov = read_cov(cov_fname)
###########################################################################
# Show result
picks = pick_types(evoked.info,
meg=True,
eeg=True,
ref_meg=False,
exclude='bads')
noise_cov = regularize(cov,
evoked.info,
grad=0.1,
mag=0.1,
eeg=0.1,
exclude='bads')
evoked_white = whiten_evoked(evoked, noise_cov, picks, diag=True)
whiten_baseline_data = evoked_white.data[picks][:, evoked.times < 0]
mean_baseline = np.mean(np.abs(whiten_baseline_data), axis=1)
assert_true(np.all(mean_baseline < 1.))
assert_true(np.all(mean_baseline > 0.2))
# degenerate
cov_bad = pick_channels_cov(cov, include=evoked.ch_names[:10])
assert_raises(RuntimeError, whiten_evoked, evoked, cov_bad, picks)
def test_gamma_map():
"""Test Gamma MAP inverse"""
forward = read_forward_solution(fname_fwd, force_fixed=False,
surf_ori=True)
forward = pick_types_forward(forward, meg=False, eeg=True)
evoked = read_evokeds(fname_evoked, condition=0, baseline=(None, 0))
evoked.resample(50)
evoked.crop(tmin=0, tmax=0.3)
cov = read_cov(fname_cov)
cov = regularize(cov, evoked.info)
alpha = 0.2
stc = gamma_map(evoked, forward, cov, alpha, tol=1e-5,
xyz_same_gamma=True, update_mode=1, verbose=False)
idx = np.argmax(np.sum(stc.data ** 2, axis=1))
assert_true(np.concatenate(stc.vertno)[idx] == 96397)
stc = gamma_map(evoked, forward, cov, alpha, tol=1e-5,
xyz_same_gamma=False, update_mode=1, verbose=False)
idx = np.argmax(np.sum(stc.data ** 2, axis=1))
assert_true(np.concatenate(stc.vertno)[idx] == 82010)
# force fixed orientation
stc, res = gamma_map(evoked, forward, cov, alpha, tol=1e-5,
xyz_same_gamma=False, update_mode=2,
loose=None, return_residual=True, verbose=False)
idx = np.argmax(np.sum(stc.data ** 2, axis=1))
# assert_true(np.concatenate(stc.vertno)[idx] == 83398) # XXX FIX
assert_array_almost_equal(evoked.times, res.times)
def test_cov_order():
"""Test covariance ordering."""
raw = read_raw_fif(raw_fname)
raw.set_eeg_reference(projection=True)
info = raw.info
# add MEG channel with low enough index number to affect EEG if
# order is incorrect
info['bads'] += ['MEG 0113']
ch_names = [info['ch_names'][pick]
for pick in pick_types(info, meg=False, eeg=True)]
cov = read_cov(cov_fname)
# no avg ref present warning
prepare_noise_cov(cov, info, ch_names, verbose='error')
# big reordering
cov_reorder = cov.copy()
order = np.random.RandomState(0).permutation(np.arange(len(cov.ch_names)))
cov_reorder['names'] = [cov['names'][ii] for ii in order]
cov_reorder['data'] = cov['data'][order][:, order]
# Make sure we did this properly
_assert_reorder(cov_reorder, cov, order)
# Now check some functions that should get the same result for both
# regularize
with pytest.raises(ValueError, match='rank, if str'):
regularize(cov, info, rank='foo')
with pytest.raises(TypeError, match='rank must be'):
regularize(cov, info, rank=False)
with pytest.raises(TypeError, match='rank must be'):
regularize(cov, info, rank=1.)
cov_reg = regularize(cov, info, rank='full')
cov_reg_reorder = regularize(cov_reorder, info, rank='full')
_assert_reorder(cov_reg_reorder, cov_reg, order)
# prepare_noise_cov
cov_prep = prepare_noise_cov(cov, info, ch_names)
cov_prep_reorder = prepare_noise_cov(cov, info, ch_names)
_assert_reorder(cov_prep, cov_prep_reorder,
order=np.arange(len(cov_prep['names'])))
# compute_whitener
whitener, w_ch_names, n_nzero = compute_whitener(
cov, info, return_rank=True)
assert whitener.shape[0] == whitener.shape[1]
whitener_2, w_ch_names_2, n_nzero_2 = compute_whitener(
cov_reorder, info, return_rank=True)
assert_array_equal(w_ch_names_2, w_ch_names)
assert_allclose(whitener_2, whitener, rtol=1e-6)
assert n_nzero == n_nzero_2
# with pca
assert n_nzero < whitener.shape[0]
whitener_pca, w_ch_names_pca, n_nzero_pca = compute_whitener(
cov, info, pca=True, return_rank=True)
assert_array_equal(w_ch_names_pca, w_ch_names)
assert n_nzero_pca == n_nzero
assert whitener_pca.shape == (n_nzero_pca, len(w_ch_names))
# whiten_evoked
evoked = read_evokeds(ave_fname)[0]
evoked_white = whiten_evoked(evoked, cov)
evoked_white_2 = whiten_evoked(evoked, cov_reorder)
assert_allclose(evoked_white_2.data, evoked_white.data, atol=1e-7)
def test_cov_order():
"""Test covariance ordering."""
raw = read_raw_fif(raw_fname)
raw.set_eeg_reference(projection=True)
info = raw.info
# add MEG channel with low enough index number to affect EEG if
# order is incorrect
info['bads'] += ['MEG 0113']
ch_names = [info['ch_names'][pick]
for pick in pick_types(info, meg=False, eeg=True)]
cov = read_cov(cov_fname)
# no avg ref present warning
prepare_noise_cov(cov, info, ch_names, verbose='error')
# big reordering
cov_reorder = cov.copy()
order = np.random.RandomState(0).permutation(np.arange(len(cov.ch_names)))
cov_reorder['names'] = [cov['names'][ii] for ii in order]
cov_reorder['data'] = cov['data'][order][:, order]
# Make sure we did this properly
_assert_reorder(cov_reorder, cov, order)
# Now check some functions that should get the same result for both
# regularize
with pytest.raises(ValueError, match='rank, if str'):
regularize(cov, info, rank='foo')
with pytest.raises(TypeError, match='rank must be'):
regularize(cov, info, rank=False)
with pytest.raises(TypeError, match='rank must be'):
regularize(cov, info, rank=1.)
cov_reg = regularize(cov, info, rank='full')
cov_reg_reorder = regularize(cov_reorder, info, rank='full')
_assert_reorder(cov_reg_reorder, cov_reg, order)
# prepare_noise_cov
cov_prep = prepare_noise_cov(cov, info, ch_names)
cov_prep_reorder = prepare_noise_cov(cov, info, ch_names)
_assert_reorder(cov_prep, cov_prep_reorder,
order=np.arange(len(cov_prep['names'])))
# compute_whitener
whitener, w_ch_names, n_nzero = compute_whitener(
cov, info, return_rank=True)
assert whitener.shape[0] == whitener.shape[1]
whitener_2, w_ch_names_2, n_nzero_2 = compute_whitener(
cov_reorder, info, return_rank=True)
assert_array_equal(w_ch_names_2, w_ch_names)
assert_allclose(whitener_2, whitener)
assert n_nzero == n_nzero_2
# with pca
assert n_nzero < whitener.shape[0]
whitener_pca, w_ch_names_pca, n_nzero_pca = compute_whitener(
cov, info, pca=True, return_rank=True)
assert_array_equal(w_ch_names_pca, w_ch_names)
assert n_nzero_pca == n_nzero
assert whitener_pca.shape == (n_nzero_pca, len(w_ch_names))
# whiten_evoked
evoked = read_evokeds(ave_fname)[0]
evoked_white = whiten_evoked(evoked, cov)
evoked_white_2 = whiten_evoked(evoked, cov_reorder)
assert_allclose(evoked_white_2.data, evoked_white.data)
def test_bad_proj():
"""Test dealing with bad projection application."""
raw = read_raw_fif(raw_fname, preload=True)
events = read_events(event_fname)
picks = pick_types(raw.info, meg=True, stim=False, ecg=False,
eog=False, exclude='bads')
picks = picks[2:18:3]
_check_warnings(raw, events, picks)
# still bad
raw.pick_channels([raw.ch_names[ii] for ii in picks])
_check_warnings(raw, events)
# "fixed"
raw.info.normalize_proj() # avoid projection warnings
_check_warnings(raw, events, count=0)
# eeg avg ref is okay
raw = read_raw_fif(raw_fname, preload=True).pick_types(meg=False, eeg=True)
raw.set_eeg_reference(projection=True)
_check_warnings(raw, events, count=0)
raw.info['bads'] = raw.ch_names[:10]
_check_warnings(raw, events, count=0)
raw = read_raw_fif(raw_fname)
pytest.raises(ValueError, raw.del_proj, 'foo')
n_proj = len(raw.info['projs'])
raw.del_proj(0)
assert_equal(len(raw.info['projs']), n_proj - 1)
raw.del_proj()
assert_equal(len(raw.info['projs']), 0)
# Ensure we deal with newer-style Neuromag projs properly, were getting:
#
# Projection vector "PCA-v2" has magnitude 1.00 (should be unity),
# applying projector with 101/306 of the original channels available
# may be dangerous.
raw = read_raw_fif(raw_fname).crop(0, 1)
raw.set_eeg_reference(projection=True)
raw.info['bads'] = ['MEG 0111']
meg_picks = pick_types(raw.info, meg=True, exclude=())
ch_names = [raw.ch_names[pick] for pick in meg_picks]
for p in raw.info['projs'][:-1]:
data = np.zeros((1, len(ch_names)))
idx = [ch_names.index(ch_name) for ch_name in p['data']['col_names']]
data[:, idx] = p['data']['data']
p['data'].update(ncol=len(meg_picks), col_names=ch_names, data=data)
# smoke test for no warnings during reg
regularize(compute_raw_covariance(raw, verbose='error'), raw.info)
def test_gamma_map_vol_sphere():
"""Gamma MAP with a sphere forward and volumic source space"""
evoked = read_evokeds(fname_evoked,
condition=0,
baseline=(None, 0),
proj=False)
evoked.resample(50, npad=100)
evoked.crop(tmin=0.1, tmax=0.16) # crop to window around peak
cov = read_cov(fname_cov)
cov = regularize(cov, evoked.info)
info = evoked.info
sphere = mne.make_sphere_model(r0=(0., 0., 0.), head_radius=0.080)
src = mne.setup_volume_source_space(subject=None,
pos=15.,
mri=None,
sphere=(0.0, 0.0, 0.0, 80.0),
bem=None,
mindist=5.0,
exclude=2.0)
fwd = mne.make_forward_solution(info,
trans=None,
src=src,
bem=sphere,
eeg=False,
meg=True)
alpha = 0.5
assert_raises(ValueError,
gamma_map,
evoked,
fwd,
cov,
alpha,
loose=None,
return_residual=False)
assert_raises(ValueError,
gamma_map,
evoked,
fwd,
cov,
alpha,
loose=0.2,
return_residual=False)
stc = gamma_map(evoked,
fwd,
cov,
alpha,
tol=1e-4,
xyz_same_gamma=False,
update_mode=2,
return_residual=False)
assert_array_almost_equal(stc.times, evoked.times, 5)
def test_simulate_evoked():
"""Test simulation of evoked data."""
raw = read_raw_fif(raw_fname)
fwd = read_forward_solution(fwd_fname)
fwd = convert_forward_solution(fwd, force_fixed=True, use_cps=False)
fwd = pick_types_forward(fwd, meg=True, eeg=True, exclude=raw.info['bads'])
cov = read_cov(cov_fname)
evoked_template = read_evokeds(ave_fname, condition=0, baseline=None)
evoked_template.pick_types(meg=True, eeg=True, exclude=raw.info['bads'])
cov = regularize(cov, evoked_template.info)
nave = evoked_template.nave
tmin = -0.1
sfreq = 1000. # Hz
tstep = 1. / sfreq
n_samples = 600
times = np.linspace(tmin, tmin + n_samples * tstep, n_samples)
# Generate times series for 2 dipoles
stc = simulate_sparse_stc(fwd['src'], n_dipoles=2, times=times,
random_state=42)
# Generate noisy evoked data
iir_filter = [1, -0.9]
evoked = simulate_evoked(fwd, stc, evoked_template.info, cov,
iir_filter=iir_filter, nave=nave)
assert_array_almost_equal(evoked.times, stc.times)
assert_true(len(evoked.data) == len(fwd['sol']['data']))
assert_equal(evoked.nave, nave)
# make a vertex that doesn't exist in fwd, should throw error
stc_bad = stc.copy()
mv = np.max(fwd['src'][0]['vertno'][fwd['src'][0]['inuse']])
stc_bad.vertices[0][0] = mv + 1
assert_raises(RuntimeError, simulate_evoked, fwd, stc_bad,
evoked_template.info, cov)
evoked_1 = simulate_evoked(fwd, stc, evoked_template.info, cov,
nave=np.inf)
evoked_2 = simulate_evoked(fwd, stc, evoked_template.info, cov,
nave=np.inf)
assert_array_equal(evoked_1.data, evoked_2.data)
# Test the equivalence snr to nave
with warnings.catch_warnings(record=True): # deprecation
evoked = simulate_evoked(fwd, stc, evoked_template.info, cov,
snr=6, random_state=42)
assert_allclose(np.linalg.norm(evoked.data, ord='fro'),
0.00078346820226502716)
cov['names'] = cov.ch_names[:-2] # Error channels are different.
assert_raises(ValueError, simulate_evoked, fwd, stc, evoked_template.info,
cov, nave=nave, iir_filter=None)
def test_regularize_cov():
"""Test cov regularization."""
raw = read_raw_fif(raw_fname, preload=False, add_eeg_ref=False)
raw.info["bads"].append(raw.ch_names[0]) # test with bad channels
noise_cov = read_cov(cov_fname)
# Regularize noise cov
reg_noise_cov = regularize(noise_cov, raw.info, mag=0.1, grad=0.1, eeg=0.1, proj=True, exclude="bads")
assert_true(noise_cov["dim"] == reg_noise_cov["dim"])
assert_true(noise_cov["data"].shape == reg_noise_cov["data"].shape)
assert_true(np.mean(noise_cov["data"] < reg_noise_cov["data"]) < 0.08)
def test_regularize_cov():
"""Test cov regularization
"""
noise_cov = read_cov(cov_fname)
# Regularize noise cov
reg_noise_cov = regularize(noise_cov, raw.info,
mag=0.1, grad=0.1, eeg=0.1, proj=True)
assert_true(noise_cov['dim'] == reg_noise_cov['dim'])
assert_true(noise_cov['data'].shape == reg_noise_cov['data'].shape)
assert_true(np.mean(noise_cov['data'] < reg_noise_cov['data']) < 0.08)
def test_cov_order():
"""Test covariance ordering."""
info = read_info(raw_fname)
# add MEG channel with low enough index number to affect EEG if
# order is incorrect
info['bads'] += ['MEG 0113']
ch_names = [
info['ch_names'][pick]
for pick in pick_types(info, meg=False, eeg=True)
]
cov = read_cov(cov_fname)
# no avg ref present warning
prepare_noise_cov(cov, info, ch_names, verbose='error')
# big reordering
cov_reorder = cov.copy()
order = np.random.RandomState(0).permutation(np.arange(len(cov.ch_names)))
cov_reorder['names'] = [cov['names'][ii] for ii in order]
cov_reorder['data'] = cov['data'][order][:, order]
# Make sure we did this properly
_assert_reorder(cov_reorder, cov, order)
# Now check some functions that should get the same result for both
# regularize
cov_reg = regularize(cov, info)
cov_reg_reorder = regularize(cov_reorder, info)
_assert_reorder(cov_reg_reorder, cov_reg, order)
# prepare_noise_cov
cov_prep = prepare_noise_cov(cov, info, ch_names)
cov_prep_reorder = prepare_noise_cov(cov, info, ch_names)
_assert_reorder(cov_prep,
cov_prep_reorder,
order=np.arange(len(cov_prep['names'])))
# compute_whitener
whitener, w_ch_names = compute_whitener(cov, info)
whitener_2, w_ch_names_2 = compute_whitener(cov_reorder, info)
assert_array_equal(w_ch_names_2, w_ch_names)
assert_allclose(whitener_2, whitener)
# whiten_evoked
evoked = read_evokeds(ave_fname)[0]
evoked_white = whiten_evoked(evoked, cov)
evoked_white_2 = whiten_evoked(evoked, cov_reorder)
assert_allclose(evoked_white_2.data, evoked_white.data)
def test_regularize_cov():
"""Test cov regularization."""
raw = read_raw_fif(raw_fname)
raw.info['bads'].append(raw.ch_names[0]) # test with bad channels
noise_cov = read_cov(cov_fname)
# Regularize noise cov
reg_noise_cov = regularize(noise_cov, raw.info,
mag=0.1, grad=0.1, eeg=0.1, proj=True,
exclude='bads')
assert_true(noise_cov['dim'] == reg_noise_cov['dim'])
assert_true(noise_cov['data'].shape == reg_noise_cov['data'].shape)
assert_true(np.mean(noise_cov['data'] < reg_noise_cov['data']) < 0.08)
def test_regularize_cov():
"""Test cov regularization."""
raw = read_raw_fif(raw_fname)
raw.info['bads'].append(raw.ch_names[0]) # test with bad channels
noise_cov = read_cov(cov_fname)
# Regularize noise cov
reg_noise_cov = regularize(noise_cov, raw.info,
mag=0.1, grad=0.1, eeg=0.1, proj=True,
exclude='bads')
assert_true(noise_cov['dim'] == reg_noise_cov['dim'])
assert_true(noise_cov['data'].shape == reg_noise_cov['data'].shape)
assert_true(np.mean(noise_cov['data'] < reg_noise_cov['data']) < 0.08)
def test_simulate_evoked():
"""Test simulation of evoked data."""
raw = read_raw_fif(raw_fname)
fwd = read_forward_solution(fwd_fname)
fwd = convert_forward_solution(fwd, force_fixed=True, use_cps=False)
fwd = pick_types_forward(fwd, meg=True, eeg=True, exclude=raw.info['bads'])
cov = read_cov(cov_fname)
evoked_template = read_evokeds(ave_fname, condition=0, baseline=None)
evoked_template.pick_types(meg=True, eeg=True, exclude=raw.info['bads'])
cov = regularize(cov, evoked_template.info)
nave = evoked_template.nave
tmin = -0.1
sfreq = 1000. # Hz
tstep = 1. / sfreq
n_samples = 600
times = np.linspace(tmin, tmin + n_samples * tstep, n_samples)
# Generate times series for 2 dipoles
stc = simulate_sparse_stc(fwd['src'], n_dipoles=2, times=times,
random_state=42)
# Generate noisy evoked data
iir_filter = [1, -0.9]
evoked = simulate_evoked(fwd, stc, evoked_template.info, cov,
iir_filter=iir_filter, nave=nave)
assert_array_almost_equal(evoked.times, stc.times)
assert len(evoked.data) == len(fwd['sol']['data'])
assert_equal(evoked.nave, nave)
assert len(evoked.info['projs']) == len(cov['projs'])
evoked_white = whiten_evoked(evoked, cov)
assert abs(evoked_white.data[:, 0].std() - 1.) < 0.1
# make a vertex that doesn't exist in fwd, should throw error
stc_bad = stc.copy()
mv = np.max(fwd['src'][0]['vertno'][fwd['src'][0]['inuse']])
stc_bad.vertices[0][0] = mv + 1
pytest.raises(ValueError, simulate_evoked, fwd, stc_bad,
evoked_template.info, cov)
evoked_1 = simulate_evoked(fwd, stc, evoked_template.info, cov,
nave=np.inf)
evoked_2 = simulate_evoked(fwd, stc, evoked_template.info, cov,
nave=np.inf)
assert_array_equal(evoked_1.data, evoked_2.data)
cov['names'] = cov.ch_names[:-2] # Error channels are different.
with pytest.raises(RuntimeError, match='Not all channels present'):
simulate_evoked(fwd, stc, evoked_template.info, cov)
def test_simulate_evoked():
"""Test simulation of evoked data."""
raw = read_raw_fif(raw_fname)
fwd = read_forward_solution(fwd_fname)
fwd = convert_forward_solution(fwd, force_fixed=True, use_cps=False)
fwd = pick_types_forward(fwd, meg=True, eeg=True, exclude=raw.info['bads'])
cov = read_cov(cov_fname)
evoked_template = read_evokeds(ave_fname, condition=0, baseline=None)
evoked_template.pick_types(meg=True, eeg=True, exclude=raw.info['bads'])
cov = regularize(cov, evoked_template.info)
nave = evoked_template.nave
tmin = -0.1
sfreq = 1000. # Hz
tstep = 1. / sfreq
n_samples = 600
times = np.linspace(tmin, tmin + n_samples * tstep, n_samples)
# Generate times series for 2 dipoles
stc = simulate_sparse_stc(fwd['src'], n_dipoles=2, times=times,
random_state=42)
# Generate noisy evoked data
iir_filter = [1, -0.9]
evoked = simulate_evoked(fwd, stc, evoked_template.info, cov,
iir_filter=iir_filter, nave=nave)
assert_array_almost_equal(evoked.times, stc.times)
assert len(evoked.data) == len(fwd['sol']['data'])
assert_equal(evoked.nave, nave)
assert len(evoked.info['projs']) == len(cov['projs'])
evoked_white = whiten_evoked(evoked, cov)
assert abs(evoked_white.data[:, 0].std() - 1.) < 0.1
# make a vertex that doesn't exist in fwd, should throw error
stc_bad = stc.copy()
mv = np.max(fwd['src'][0]['vertno'][fwd['src'][0]['inuse']])
stc_bad.vertices[0][0] = mv + 1
pytest.raises(RuntimeError, simulate_evoked, fwd, stc_bad,
evoked_template.info, cov)
evoked_1 = simulate_evoked(fwd, stc, evoked_template.info, cov,
nave=np.inf)
evoked_2 = simulate_evoked(fwd, stc, evoked_template.info, cov,
nave=np.inf)
assert_array_equal(evoked_1.data, evoked_2.data)
cov['names'] = cov.ch_names[:-2] # Error channels are different.
with pytest.raises(RuntimeError, match='Not all channels present'):
simulate_evoked(fwd, stc, evoked_template.info, cov)
def test_cov_order():
"""Test covariance ordering."""
info = read_info(raw_fname)
# add MEG channel with low enough index number to affect EEG if
# order is incorrect
info['bads'] += ['MEG 0113']
ch_names = [info['ch_names'][pick]
for pick in pick_types(info, meg=False, eeg=True)]
cov = read_cov(cov_fname)
# no avg ref present warning
prepare_noise_cov(cov, info, ch_names, verbose='error')
# big reordering
cov_reorder = cov.copy()
order = np.random.RandomState(0).permutation(np.arange(len(cov.ch_names)))
cov_reorder['names'] = [cov['names'][ii] for ii in order]
cov_reorder['data'] = cov['data'][order][:, order]
# Make sure we did this properly
_assert_reorder(cov_reorder, cov, order)
# Now check some functions that should get the same result for both
# regularize
cov_reg = regularize(cov, info)
cov_reg_reorder = regularize(cov_reorder, info)
_assert_reorder(cov_reg_reorder, cov_reg, order)
# prepare_noise_cov
cov_prep = prepare_noise_cov(cov, info, ch_names)
cov_prep_reorder = prepare_noise_cov(cov, info, ch_names)
_assert_reorder(cov_prep, cov_prep_reorder,
order=np.arange(len(cov_prep['names'])))
# compute_whitener
whitener, w_ch_names = compute_whitener(cov, info)
whitener_2, w_ch_names_2 = compute_whitener(cov_reorder, info)
assert_array_equal(w_ch_names_2, w_ch_names)
assert_allclose(whitener_2, whitener)
# whiten_evoked
evoked = read_evokeds(ave_fname)[0]
evoked_white = whiten_evoked(evoked, cov)
evoked_white_2 = whiten_evoked(evoked, cov_reorder)
assert_allclose(evoked_white_2.data, evoked_white.data)
def test_regularize_cov():
"""Test cov regularization
"""
noise_cov = read_cov(cov_fname)
# Regularize noise cov
reg_noise_cov = regularize(noise_cov,
raw.info,
mag=0.1,
grad=0.1,
eeg=0.1,
proj=True)
assert_true(noise_cov['dim'] == reg_noise_cov['dim'])
assert_true(noise_cov['data'].shape == reg_noise_cov['data'].shape)
assert_true(np.mean(noise_cov['data'] < reg_noise_cov['data']) < 0.08)
def test_regularize_cov():
"""Test cov regularization."""
raw = read_raw_fif(raw_fname)
raw.info['bads'].append(raw.ch_names[0]) # test with bad channels
noise_cov = read_cov(cov_fname)
# Regularize noise cov
reg_noise_cov = regularize(noise_cov, raw.info,
mag=0.1, grad=0.1, eeg=0.1, proj=True,
exclude='bads')
assert noise_cov['dim'] == reg_noise_cov['dim']
assert noise_cov['data'].shape == reg_noise_cov['data'].shape
assert np.mean(noise_cov['data'] < reg_noise_cov['data']) < 0.08
# make sure all args are represented
assert set(_DATA_CH_TYPES_SPLIT) - set(_get_args(regularize)) == set()
def test_regularize_cov():
"""Test cov regularization."""
raw = read_raw_fif(raw_fname)
raw.info['bads'].append(raw.ch_names[0]) # test with bad channels
noise_cov = read_cov(cov_fname)
# Regularize noise cov
reg_noise_cov = regularize(noise_cov, raw.info,
mag=0.1, grad=0.1, eeg=0.1, proj=True,
exclude='bads', rank='full')
assert noise_cov['dim'] == reg_noise_cov['dim']
assert noise_cov['data'].shape == reg_noise_cov['data'].shape
assert np.mean(noise_cov['data'] < reg_noise_cov['data']) < 0.08
# make sure all args are represented
assert set(_DATA_CH_TYPES_SPLIT) - set(_get_args(regularize)) == set()
def test_gamma_map_vol_sphere():
"""Gamma MAP with a sphere forward and volumic source space."""
evoked = read_evokeds(fname_evoked, condition=0, baseline=(None, 0),
proj=False)
evoked.resample(50, npad=100)
evoked.crop(tmin=0.1, tmax=0.16) # crop to window around peak
cov = read_cov(fname_cov)
cov = regularize(cov, evoked.info, rank=None)
info = evoked.info
sphere = mne.make_sphere_model(r0=(0., 0., 0.), head_radius=0.080)
src = mne.setup_volume_source_space(subject=None, pos=30., mri=None,
sphere=(0.0, 0.0, 0.0, 80.0),
bem=None, mindist=5.0,
exclude=2.0)
fwd = mne.make_forward_solution(info, trans=None, src=src, bem=sphere,
eeg=False, meg=True)
alpha = 0.5
pytest.raises(ValueError, gamma_map, evoked, fwd, cov, alpha,
loose=0, return_residual=False)
pytest.raises(ValueError, gamma_map, evoked, fwd, cov, alpha,
loose=0.2, return_residual=False)
stc = gamma_map(evoked, fwd, cov, alpha, tol=1e-4,
xyz_same_gamma=False, update_mode=2,
return_residual=False)
assert_array_almost_equal(stc.times, evoked.times, 5)
# Compare orientation obtained using fit_dipole and gamma_map
# for a simulated evoked containing a single dipole
stc = mne.VolSourceEstimate(50e-9 * np.random.RandomState(42).randn(1, 4),
vertices=stc.vertices[:1],
tmin=stc.tmin,
tstep=stc.tstep)
evoked_dip = mne.simulation.simulate_evoked(fwd, stc, info, cov, nave=1e9,
use_cps=True)
dip_gmap = gamma_map(evoked_dip, fwd, cov, 0.1, return_as_dipoles=True)
amp_max = [np.max(d.amplitude) for d in dip_gmap]
dip_gmap = dip_gmap[np.argmax(amp_max)]
assert (dip_gmap[0].pos[0] in src[0]['rr'][stc.vertices])
dip_fit = mne.fit_dipole(evoked_dip, cov, sphere)[0]
assert (np.abs(np.dot(dip_fit.ori[0], dip_gmap.ori[0])) > 0.99)
def test_gamma_map_vol_sphere():
"""Gamma MAP with a sphere forward and volumic source space."""
evoked = read_evokeds(fname_evoked, condition=0, baseline=(None, 0),
proj=False)
evoked.resample(50, npad=100)
evoked.crop(tmin=0.1, tmax=0.16) # crop to window around peak
cov = read_cov(fname_cov)
cov = regularize(cov, evoked.info, rank=None)
info = evoked.info
sphere = mne.make_sphere_model(r0=(0., 0., 0.), head_radius=0.080)
src = mne.setup_volume_source_space(subject=None, pos=30., mri=None,
sphere=(0.0, 0.0, 0.0, 80.0),
bem=None, mindist=5.0,
exclude=2.0)
fwd = mne.make_forward_solution(info, trans=None, src=src, bem=sphere,
eeg=False, meg=True)
alpha = 0.5
pytest.raises(ValueError, gamma_map, evoked, fwd, cov, alpha,
loose=0, return_residual=False)
pytest.raises(ValueError, gamma_map, evoked, fwd, cov, alpha,
loose=0.2, return_residual=False)
stc = gamma_map(evoked, fwd, cov, alpha, tol=1e-4,
xyz_same_gamma=False, update_mode=2,
return_residual=False)
assert_array_almost_equal(stc.times, evoked.times, 5)
# Compare orientation obtained using fit_dipole and gamma_map
# for a simulated evoked containing a single dipole
stc = mne.VolSourceEstimate(50e-9 * np.random.RandomState(42).randn(1, 4),
vertices=stc.vertices[:1],
tmin=stc.tmin,
tstep=stc.tstep)
evoked_dip = mne.simulation.simulate_evoked(fwd, stc, info, cov, nave=1e9,
use_cps=True)
dip_gmap = gamma_map(evoked_dip, fwd, cov, 0.1, return_as_dipoles=True)
amp_max = [np.max(d.amplitude) for d in dip_gmap]
dip_gmap = dip_gmap[np.argmax(amp_max)]
assert (dip_gmap[0].pos[0] in src[0]['rr'][stc.vertices])
dip_fit = mne.fit_dipole(evoked_dip, cov, sphere)[0]
assert (np.abs(np.dot(dip_fit.ori[0], dip_gmap.ori[0])) > 0.99)
def test_evoked_whiten():
"""Test whitening of evoked data"""
evoked = Evoked(ave_fname, setno=0, baseline=(None, 0), proj=True)
cov = read_cov(cov_fname)
###########################################################################
# Show result
picks = pick_types(evoked.info, meg=True, eeg=True, exclude='bads')
noise_cov = regularize(cov, evoked.info, grad=0.1, mag=0.1, eeg=0.1)
evoked_white = whiten_evoked(evoked, noise_cov, picks, diag=True)
whiten_baseline_data = evoked_white.data[picks][:, evoked.times < 0]
mean_baseline = np.mean(np.abs(whiten_baseline_data), axis=1)
assert_true(np.all(mean_baseline < 1.))
assert_true(np.all(mean_baseline > 0.2))
def _get_data(ch_decim=1):
"""Read in data used in tests."""
# Read evoked
evoked = mne.read_evokeds(fname_ave, 0, baseline=(None, 0))
evoked.info['bads'] = ['MEG 2443']
evoked.info['lowpass'] = 20 # fake for decim
evoked.decimate(12)
evoked.crop(0.0, 0.3)
picks = mne.pick_types(evoked.info, meg=True, eeg=False)
picks = picks[::ch_decim]
evoked.pick_channels([evoked.ch_names[pick] for pick in picks])
evoked.info.normalize_proj()
noise_cov = mne.read_cov(fname_cov)
noise_cov['projs'] = []
noise_cov = regularize(noise_cov, evoked.info, rank='full', proj=False)
return evoked, noise_cov
def test_gamma_map():
"""Test Gamma MAP inverse"""
forward = read_forward_solution(fname_fwd,
force_fixed=False,
surf_ori=True)
forward = pick_types_forward(forward, meg=False, eeg=True)
evoked = read_evokeds(fname_evoked,
condition=0,
baseline=(None, 0),
proj=False)
evoked.resample(50, npad=100)
evoked.crop(tmin=0.1, tmax=0.16) # crop to nice window near samp border
cov = read_cov(fname_cov)
cov = regularize(cov, evoked.info)
alpha = 0.5
stc = gamma_map(evoked,
forward,
cov,
alpha,
tol=1e-4,
xyz_same_gamma=True,
update_mode=1)
_check_stc(stc, evoked, 68477)
stc = gamma_map(evoked,
forward,
cov,
alpha,
tol=1e-4,
xyz_same_gamma=False,
update_mode=1)
_check_stc(stc, evoked, 82010)
# force fixed orientation
stc = gamma_map(evoked,
forward,
cov,
alpha,
tol=1e-4,
xyz_same_gamma=False,
update_mode=2,
loose=None,
return_residual=False)
_check_stc(stc, evoked, 85739, 20)
def _get_data(ch_decim=1):
"""Read in data used in tests."""
# Read evoked
evoked = mne.read_evokeds(fname_ave, 0, baseline=(None, 0))
evoked.info['bads'] = ['MEG 2443']
evoked.info['lowpass'] = 20 # fake for decim
evoked.decimate(12)
evoked.crop(0.0, 0.3)
picks = mne.pick_types(evoked.info, meg=True, eeg=False)
picks = picks[::ch_decim]
evoked.pick_channels([evoked.ch_names[pick] for pick in picks])
evoked.info.normalize_proj()
noise_cov = mne.read_cov(fname_cov)
noise_cov['projs'] = []
noise_cov = regularize(noise_cov, evoked.info)
return evoked, noise_cov
def test_whiten_evoked():
"""Test whitening of evoked data."""
evoked = read_evokeds(ave_fname, condition=0, baseline=(None, 0), proj=True)
cov = read_cov(cov_fname)
###########################################################################
# Show result
picks = pick_types(evoked.info, meg=True, eeg=True, ref_meg=False, exclude="bads")
noise_cov = regularize(cov, evoked.info, grad=0.1, mag=0.1, eeg=0.1, exclude="bads")
evoked_white = whiten_evoked(evoked, noise_cov, picks, diag=True)
whiten_baseline_data = evoked_white.data[picks][:, evoked.times < 0]
mean_baseline = np.mean(np.abs(whiten_baseline_data), axis=1)
assert_true(np.all(mean_baseline < 1.0))
assert_true(np.all(mean_baseline > 0.2))
# degenerate
cov_bad = pick_channels_cov(cov, include=evoked.ch_names[:10])
assert_raises(RuntimeError, whiten_evoked, evoked, cov_bad, picks)
def test_rank_deficiency():
"""Test adding noise from M/EEG float32 (I/O) cov with projectors."""
# See gh-5940
evoked = read_evokeds(ave_fname, 0, baseline=(None, 0))
evoked.info['bads'] = ['MEG 2443']
evoked.info['lowpass'] = 20 # fake for decim
picks = pick_types(evoked.info, meg=True, eeg=False)
picks = picks[::16]
evoked.pick_channels([evoked.ch_names[pick] for pick in picks])
evoked.info.normalize_proj()
cov = read_cov(cov_fname)
cov['projs'] = []
cov = regularize(cov, evoked.info, rank=None)
cov = pick_channels_cov(cov, evoked.ch_names)
evoked.data[:] = 0
add_noise(evoked, cov)
cov_new = compute_covariance(
EpochsArray(evoked.data[np.newaxis], evoked.info), verbose='error')
assert cov['names'] == cov_new['names']
r = np.corrcoef(cov['data'].ravel(), cov_new['data'].ravel())[0, 1]
assert r > 0.98
def test_rank_deficiency():
"""Test adding noise from M/EEG float32 (I/O) cov with projectors."""
# See gh-5940
evoked = read_evokeds(ave_fname, 0, baseline=(None, 0))
evoked.info['bads'] = ['MEG 2443']
evoked.info['lowpass'] = 20 # fake for decim
picks = pick_types(evoked.info, meg=True, eeg=False)
picks = picks[::16]
evoked.pick_channels([evoked.ch_names[pick] for pick in picks])
evoked.info.normalize_proj()
cov = read_cov(cov_fname)
cov['projs'] = []
cov = regularize(cov, evoked.info, rank=None)
cov = pick_channels_cov(cov, evoked.ch_names)
evoked.data[:] = 0
add_noise(evoked, cov)
cov_new = compute_covariance(
EpochsArray(evoked.data[np.newaxis], evoked.info), verbose='error')
assert cov['names'] == cov_new['names']
r = np.corrcoef(cov['data'].ravel(), cov_new['data'].ravel())[0, 1]
assert r > 0.98
)
# epochs.plot_psd()
roi_nms = np.setdiff1d(np.arange(len(events)), epochs.selection)
# raw = raw.copy().filter(lf, hf, fir_window='blackman',
# method='iir', n_jobs=config.N_JOBS)
iir_params = dict(order=4, ftype="butter", output="sos")
epochs_ = epochs.copy().filter(
hp, lp, method="iir", iir_params=iir_params, n_jobs=config.N_JOBS
)
# epochs_.plot_psd(average=True, spatial_colors=False)
mne.Info.normalize_proj(epochs_.info)
# epochs_.plot_projs_topomap()
# regularize covariance
# rank = compute_rank(cov, rank='full', info=epochs_.info)
cov = regularize(cov, raw.info)
inv = make_inverse_operator(epochs_.info, fwd, cov)
# Compute ROI time series and do envelope correlation
stcs = apply_inverse_epochs(
epochs_, inv, lambda2=1.0 / 9.0, pick_ori="normal", return_generator=True
)
label_ts = mne.extract_label_time_course(
stcs, rois, fwd["src"], return_generator=True, verbose=True
)
# compute ROI level envelop power
aec = envelope_correlation(label_ts)
assert aec.shape == (len(rois), len(rois))
# compute ROI laplacian as per Ginset
# TODO cite paper
def test_low_rank():
"""Test low-rank covariance matrix estimation."""
raw = read_raw_fif(raw_fname).set_eeg_reference(projection=True).crop(0, 3)
raw = maxwell_filter(raw, regularize=None) # heavily reduce the rank
sss_proj_rank = 139 # 80 MEG + 60 EEG - 1 proj
n_ch = 366
proj_rank = 365 # one EEG proj
events = make_fixed_length_events(raw)
methods = ('empirical', 'diagonal_fixed', 'oas')
epochs = Epochs(raw, events, tmin=-0.2, tmax=0, preload=True)
bounds = {
'None':
dict(empirical=(-6000, -5000),
diagonal_fixed=(-1500, -500),
oas=(-700, -600)),
'full':
dict(empirical=(-9000, -8000),
diagonal_fixed=(-2000, -1600),
oas=(-1600, -1000)),
}
for rank in ('full', None):
covs = compute_covariance(epochs,
method=methods,
return_estimators=True,
verbose='error',
rank=rank)
for cov in covs:
method = cov['method']
these_bounds = bounds[str(rank)][method]
this_rank = _cov_rank(cov, epochs.info)
if rank is None or method == 'empirical':
assert this_rank == sss_proj_rank
else:
assert this_rank == proj_rank
assert these_bounds[0] < cov['loglik'] < these_bounds[1], \
(rank, method)
if method == 'empirical':
emp_cov = cov # save for later, rank param does not matter
# Test equivalence with mne.cov.regularize subspace
with pytest.raises(ValueError, match='are dependent.*must equal'):
regularize(emp_cov, epochs.info, rank=None, mag=0.1, grad=0.2)
assert _cov_rank(emp_cov, epochs.info) == sss_proj_rank
reg_cov = regularize(emp_cov, epochs.info, proj=True, rank='full')
assert _cov_rank(reg_cov, epochs.info) == proj_rank
del reg_cov
with catch_logging() as log:
reg_r_cov = regularize(emp_cov,
epochs.info,
proj=True,
rank=None,
verbose=True)
log = log.getvalue()
assert 'jointly' in log
assert _cov_rank(reg_r_cov, epochs.info) == sss_proj_rank
reg_r_only_cov = regularize(emp_cov, epochs.info, proj=False, rank=None)
assert _cov_rank(reg_r_only_cov, epochs.info) == sss_proj_rank
assert_allclose(reg_r_only_cov['data'], reg_r_cov['data'])
del reg_r_only_cov, reg_r_cov
# test that rank=306 is same as rank='full'
epochs_meg = epochs.copy().pick_types()
assert len(epochs_meg.ch_names) == 306
epochs_meg.info.update(bads=[], projs=[])
cov_full = compute_covariance(epochs_meg,
method='oas',
rank='full',
verbose='error')
assert _cov_rank(cov_full, epochs_meg.info) == 306
cov_dict = compute_covariance(epochs_meg,
method='oas',
rank=306,
verbose='error')
assert _cov_rank(cov_dict, epochs_meg.info) == 306
assert_allclose(cov_full['data'], cov_dict['data'])
# Work with just EEG data to simplify projection / rank reduction
raw.pick_types(meg=False, eeg=True)
n_proj = 2
raw.add_proj(compute_proj_raw(raw, n_eeg=n_proj))
n_ch = len(raw.ch_names)
rank = n_ch - n_proj - 1 # plus avg proj
assert len(raw.info['projs']) == 3
epochs = Epochs(raw, events, tmin=-0.2, tmax=0, preload=True)
assert len(raw.ch_names) == n_ch
emp_cov = compute_covariance(epochs, rank='full', verbose='error')
assert _cov_rank(emp_cov, epochs.info) == rank
reg_cov = regularize(emp_cov, epochs.info, proj=True, rank='full')
assert _cov_rank(reg_cov, epochs.info) == rank
reg_r_cov = regularize(emp_cov, epochs.info, proj=False, rank=None)
assert _cov_rank(reg_r_cov, epochs.info) == rank
dia_cov = compute_covariance(epochs,
rank=None,
method='diagonal_fixed',
verbose='error')
assert _cov_rank(dia_cov, epochs.info) == rank
assert_allclose(dia_cov['data'], reg_cov['data'])
# test our deprecation: can simply remove later
epochs.pick_channels(epochs.ch_names[:103])
# degenerate
with pytest.raises(ValueError, match='can.*only be used with rank="full"'):
compute_covariance(epochs, rank=None, method='pca')
with pytest.raises(ValueError, match='can.*only be used with rank="full"'):
compute_covariance(epochs, rank=None, method='factor_analysis')
def test_low_rank():
"""Test low-rank covariance matrix estimation."""
raw = read_raw_fif(raw_fname).set_eeg_reference(projection=True).crop(0, 3)
raw = maxwell_filter(raw, regularize=None) # heavily reduce the rank
sss_proj_rank = 139 # 80 MEG + 60 EEG - 1 proj
n_ch = 366
proj_rank = 365 # one EEG proj
events = make_fixed_length_events(raw)
methods = ('empirical', 'diagonal_fixed', 'oas')
epochs = Epochs(raw, events, tmin=-0.2, tmax=0, preload=True)
bounds = {
'None': dict(empirical=(-6000, -5000),
diagonal_fixed=(-1500, -500),
oas=(-700, -600)),
'full': dict(empirical=(-9000, -8000),
diagonal_fixed=(-2000, -1600),
oas=(-1600, -1000)),
}
for rank in ('full', None):
covs = compute_covariance(
epochs, method=methods, return_estimators=True,
verbose='error', rank=rank)
for cov in covs:
method = cov['method']
these_bounds = bounds[str(rank)][method]
this_rank = _cov_rank(cov, epochs.info)
if rank is None or method == 'empirical':
assert this_rank == sss_proj_rank
else:
assert this_rank == proj_rank
assert these_bounds[0] < cov['loglik'] < these_bounds[1], \
(rank, method)
if method == 'empirical':
emp_cov = cov # save for later, rank param does not matter
# Test equivalence with mne.cov.regularize subspace
with pytest.raises(ValueError, match='are dependent.*must equal'):
regularize(emp_cov, epochs.info, rank=None, mag=0.1, grad=0.2)
assert _cov_rank(emp_cov, epochs.info) == sss_proj_rank
reg_cov = regularize(emp_cov, epochs.info, proj=True, rank='full')
assert _cov_rank(reg_cov, epochs.info) == proj_rank
del reg_cov
with catch_logging() as log:
reg_r_cov = regularize(emp_cov, epochs.info, proj=True, rank=None,
verbose=True)
log = log.getvalue()
assert 'jointly' in log
assert _cov_rank(reg_r_cov, epochs.info) == sss_proj_rank
reg_r_only_cov = regularize(emp_cov, epochs.info, proj=False, rank=None)
assert _cov_rank(reg_r_only_cov, epochs.info) == sss_proj_rank
assert_allclose(reg_r_only_cov['data'], reg_r_cov['data'])
del reg_r_only_cov, reg_r_cov
# test that rank=306 is same as rank='full'
epochs_meg = epochs.copy().pick_types()
assert len(epochs_meg.ch_names) == 306
epochs_meg.info.update(bads=[], projs=[])
cov_full = compute_covariance(epochs_meg, method='oas',
rank='full', verbose='error')
assert _cov_rank(cov_full, epochs_meg.info) == 306
cov_dict = compute_covariance(epochs_meg, method='oas',
rank=306, verbose='error')
assert _cov_rank(cov_dict, epochs_meg.info) == 306
assert_allclose(cov_full['data'], cov_dict['data'])
# Work with just EEG data to simplify projection / rank reduction
raw.pick_types(meg=False, eeg=True)
n_proj = 2
raw.add_proj(compute_proj_raw(raw, n_eeg=n_proj))
n_ch = len(raw.ch_names)
rank = n_ch - n_proj - 1 # plus avg proj
assert len(raw.info['projs']) == 3
epochs = Epochs(raw, events, tmin=-0.2, tmax=0, preload=True)
assert len(raw.ch_names) == n_ch
emp_cov = compute_covariance(epochs, rank='full', verbose='error')
assert _cov_rank(emp_cov, epochs.info) == rank
reg_cov = regularize(emp_cov, epochs.info, proj=True, rank='full')
assert _cov_rank(reg_cov, epochs.info) == rank
reg_r_cov = regularize(emp_cov, epochs.info, proj=False, rank=None)
assert _cov_rank(reg_r_cov, epochs.info) == rank
dia_cov = compute_covariance(epochs, rank=None, method='diagonal_fixed',
verbose='error')
assert _cov_rank(dia_cov, epochs.info) == rank
assert_allclose(dia_cov['data'], reg_cov['data'])
# test our deprecation: can simply remove later
epochs.pick_channels(epochs.ch_names[:103])
# degenerate
with pytest.raises(ValueError, match='can.*only be used with rank="full"'):
compute_covariance(epochs, rank=None, method='pca')
with pytest.raises(ValueError, match='can.*only be used with rank="full"'):
compute_covariance(epochs, rank=None, method='factor_analysis')
def gen_inverses(p, subjects, run_indices):
"""Generate inverses.
Can only complete successfully following forward solution
calculation and covariance estimation.
Parameters
----------
p : instance of Parameters
Analysis parameters.
subjects : list of str
Subject names to analyze (e.g., ['Eric_SoP_001', ...]).
run_indices : array-like | None
Run indices to include.
"""
for si, subj in enumerate(subjects):
out_flags, meg_bools, eeg_bools = [], [], []
if p.disp_files:
print(' Subject %s' % subj, end='')
inv_dir = op.join(p.work_dir, subj, p.inverse_dir)
cov_dir = op.join(p.work_dir, subj, p.cov_dir)
if not op.isdir(inv_dir):
os.mkdir(inv_dir)
make_erm_inv = len(p.runs_empty) > 0
epochs_fnames, _ = get_epochs_evokeds_fnames(p, subj, p.analyses)
_, fif_file = epochs_fnames
epochs = read_epochs(fif_file, preload=False)
del epochs_fnames, fif_file
meg, eeg = 'meg' in epochs, 'eeg' in epochs
if meg:
out_flags += ['-meg']
meg_bools += [True]
eeg_bools += [False]
if eeg:
out_flags += ['-eeg']
meg_bools += [False]
eeg_bools += [True]
if meg and eeg:
out_flags += ['-meg-eeg']
meg_bools += [True]
eeg_bools += [True]
if p.cov_rank == 'full' and p.compute_rank:
rank = _compute_rank(p, subj, run_indices[si])
else:
rank = None # should be safe from our gen_covariances step
if make_erm_inv:
# We now process the empty room with "movement
# compensation" so it should get the same rank!
erm_name = op.join(cov_dir, safe_inserter(p.runs_empty[0], subj) +
p.pca_extra + p.inv_tag + '-cov.fif')
empty_cov = read_cov(erm_name)
if p.force_erm_cov_rank_full and p.cov_method == 'empirical':
empty_cov = regularize(
empty_cov, epochs.info, rank='full')
fwd_name = get_cov_fwd_inv_fnames(p, subj, run_indices[si])[1][0]
fwd = read_forward_solution(fwd_name)
fwd = convert_forward_solution(fwd, surf_ori=True)
looses = [1]
tags = [p.inv_free_tag]
fixeds = [False]
depths = [0.8]
if fwd['src'].kind == 'surface':
looses += [0, 0.2]
tags += [p.inv_fixed_tag, p.inv_loose_tag]
fixeds += [True, False]
depths += [0.8, 0.8]
else:
assert fwd['src'].kind == 'volume'
for name in p.inv_names + ([make_erm_inv] if make_erm_inv else []):
if name is True: # meaning: make empty-room one
temp_name = subj
cov = empty_cov
tag = p.inv_erm_tag
else:
s_name = safe_inserter(name, subj)
temp_name = s_name + ('-%d' % p.lp_cut) + p.inv_tag
cov_name = op.join(cov_dir, safe_inserter(name, subj) +
('-%d' % p.lp_cut) + p.inv_tag + '-cov.fif')
cov = read_cov(cov_name)
if cov.get('method', 'empirical') == 'empirical':
cov = regularize(cov, epochs.info, rank=rank)
tag = ''
del s_name
for f, m, e in zip(out_flags, meg_bools, eeg_bools):
fwd_restricted = pick_types_forward(fwd, meg=m, eeg=e)
for l_, s, x, d in zip(looses, tags, fixeds, depths):
inv_name = op.join(
inv_dir, temp_name + f + tag + s + '-inv.fif')
kwargs = dict(loose=l_, depth=d, fixed=x, use_cps=True,
verbose='error')
if name is not True or not e:
inv = make_inverse_operator(
epochs.info, fwd_restricted, cov, rank=rank,
**kwargs)
write_inverse_operator(inv_name, inv)
if p.disp_files:
print()
def test_low_rank_cov(raw_epochs_events):
"""Test additional properties of low rank computations."""
raw, epochs, events = raw_epochs_events
sss_proj_rank = 139 # 80 MEG + 60 EEG - 1 proj
n_ch = 366
proj_rank = 365 # one EEG proj
with pytest.warns(RuntimeWarning, match='Too few samples'):
emp_cov = compute_covariance(epochs)
# Test equivalence with mne.cov.regularize subspace
with pytest.raises(ValueError, match='are dependent.*must equal'):
regularize(emp_cov, epochs.info, rank=None, mag=0.1, grad=0.2)
assert _cov_rank(emp_cov, epochs.info) == sss_proj_rank
reg_cov = regularize(emp_cov, epochs.info, proj=True, rank='full')
assert _cov_rank(reg_cov, epochs.info) == proj_rank
with pytest.warns(RuntimeWarning, match='exceeds the theoretical'):
_compute_rank_int(reg_cov, info=epochs.info)
del reg_cov
with catch_logging() as log:
reg_r_cov = regularize(emp_cov,
epochs.info,
proj=True,
rank=None,
verbose=True)
log = log.getvalue()
assert 'jointly' in log
assert _cov_rank(reg_r_cov, epochs.info) == sss_proj_rank
reg_r_only_cov = regularize(emp_cov, epochs.info, proj=False, rank=None)
assert _cov_rank(reg_r_only_cov, epochs.info) == sss_proj_rank
assert_allclose(reg_r_only_cov['data'], reg_r_cov['data'])
del reg_r_only_cov, reg_r_cov
# test that rank=306 is same as rank='full'
epochs_meg = epochs.copy().pick_types(meg=True)
assert len(epochs_meg.ch_names) == 306
epochs_meg.info.update(bads=[], projs=[])
cov_full = compute_covariance(epochs_meg,
method='oas',
rank='full',
verbose='error')
assert _cov_rank(cov_full, epochs_meg.info) == 306
with pytest.warns(RuntimeWarning, match='few samples'):
cov_dict = compute_covariance(epochs_meg,
method='oas',
rank=dict(meg=306))
assert _cov_rank(cov_dict, epochs_meg.info) == 306
assert_allclose(cov_full['data'], cov_dict['data'])
cov_dict = compute_covariance(epochs_meg,
method='oas',
rank=dict(meg=306),
verbose='error')
assert _cov_rank(cov_dict, epochs_meg.info) == 306
assert_allclose(cov_full['data'], cov_dict['data'])
# Work with just EEG data to simplify projection / rank reduction
raw = raw.copy().pick_types(meg=False, eeg=True)
n_proj = 2
raw.add_proj(compute_proj_raw(raw, n_eeg=n_proj))
n_ch = len(raw.ch_names)
rank = n_ch - n_proj - 1 # plus avg proj
assert len(raw.info['projs']) == 3
epochs = Epochs(raw, events, tmin=-0.2, tmax=0, preload=True)
assert len(raw.ch_names) == n_ch
emp_cov = compute_covariance(epochs, rank='full', verbose='error')
assert _cov_rank(emp_cov, epochs.info) == rank
reg_cov = regularize(emp_cov, epochs.info, proj=True, rank='full')
assert _cov_rank(reg_cov, epochs.info) == rank
reg_r_cov = regularize(emp_cov, epochs.info, proj=False, rank=None)
assert _cov_rank(reg_r_cov, epochs.info) == rank
dia_cov = compute_covariance(epochs,
rank=None,
method='diagonal_fixed',
verbose='error')
assert _cov_rank(dia_cov, epochs.info) == rank
assert_allclose(dia_cov['data'], reg_cov['data'])
epochs.pick_channels(epochs.ch_names[:103])
# degenerate
with pytest.raises(ValueError, match='can.*only be used with rank="full"'):
compute_covariance(epochs, rank=None, method='pca')
with pytest.raises(ValueError, match='can.*only be used with rank="full"'):
compute_covariance(epochs, rank=None, method='factor_analysis')
print(__doc__) from mne import read_cov, whiten_evoked, pick_types, read_evokeds from mne.cov import regularize from mne.datasets import sample data_path = sample.data_path() fname = data_path + '/MEG/sample/sample_audvis-ave.fif' cov_fname = data_path + '/MEG/sample/sample_audvis-cov.fif' # Reading evoked = read_evokeds(fname, condition=0, baseline=(None, 0), proj=True) noise_cov = read_cov(cov_fname) ############################################################################### # Show result # Pick channels to view picks = pick_types(evoked.info, meg=True, eeg=True, exclude='bads') evoked.plot(picks=picks) noise_cov = regularize(noise_cov, evoked.info, grad=0.1, mag=0.1, eeg=0.1) evoked_white = whiten_evoked(evoked, noise_cov, picks, diag=True) # plot the whitened evoked data to see if baseline signals match the # assumption of Gaussian whiten noise from which we expect values around # and less than 2 standard deviations. evoked_white.plot(picks=picks, unit=False, hline=[-2, 2])
def test_gamma_map_standard():
"""Test Gamma MAP inverse."""
forward = read_forward_solution(fname_fwd)
forward = convert_forward_solution(forward, surf_ori=True)
forward = pick_types_forward(forward, meg=False, eeg=True)
evoked = read_evokeds(fname_evoked,
condition=0,
baseline=(None, 0),
proj=False)
evoked.resample(50, npad=100)
evoked.crop(tmin=0.1, tmax=0.14) # crop to window around peak
cov = read_cov(fname_cov)
cov = regularize(cov, evoked.info, rank=None)
alpha = 0.5
with catch_logging() as log:
stc = gamma_map(evoked,
forward,
cov,
alpha,
tol=1e-4,
xyz_same_gamma=True,
update_mode=1,
verbose=True)
_check_stc(stc, evoked, 68477, 'lh', fwd=forward)
assert_var_exp_log(log.getvalue(), 20, 22)
with catch_logging() as log:
stc_vec, res = gamma_map(evoked,
forward,
cov,
alpha,
tol=1e-4,
xyz_same_gamma=True,
update_mode=1,
pick_ori='vector',
return_residual=True,
verbose=True)
assert_var_exp_log(log.getvalue(), 20, 22)
assert_stcs_equal(stc_vec.magnitude(), stc)
_check_stc(stc_vec, evoked, 68477, 'lh', fwd=forward, res=res)
stc, res = gamma_map(evoked,
forward,
cov,
alpha,
tol=1e-4,
xyz_same_gamma=False,
update_mode=1,
pick_ori='vector',
return_residual=True)
_check_stc(stc,
evoked,
82010,
'lh',
fwd=forward,
dist_limit=6.,
ratio=2.,
res=res)
with catch_logging() as log:
dips = gamma_map(evoked,
forward,
cov,
alpha,
tol=1e-4,
xyz_same_gamma=False,
update_mode=1,
return_as_dipoles=True,
verbose=True)
exp_var = assert_var_exp_log(log.getvalue(), 58, 60)
dip_exp_var = np.mean(sum(dip.gof for dip in dips))
assert_allclose(exp_var, dip_exp_var, atol=10) # not really equiv, close
assert (isinstance(dips[0], Dipole))
stc_dip = make_stc_from_dipoles(dips, forward['src'])
assert_stcs_equal(stc.magnitude(), stc_dip)
# force fixed orientation
stc, res = gamma_map(evoked,
forward,
cov,
alpha,
tol=1e-4,
xyz_same_gamma=False,
update_mode=2,
loose=0,
return_residual=True)
_check_stc(stc, evoked, 85739, 'lh', fwd=forward, ratio=20., res=res)
def test_low_rank_cov(raw_epochs_events):
"""Test additional properties of low rank computations."""
raw, epochs, events = raw_epochs_events
sss_proj_rank = 139 # 80 MEG + 60 EEG - 1 proj
n_ch = 366
proj_rank = 365 # one EEG proj
with pytest.warns(RuntimeWarning, match='Too few samples'):
emp_cov = compute_covariance(epochs)
# Test equivalence with mne.cov.regularize subspace
with pytest.raises(ValueError, match='are dependent.*must equal'):
regularize(emp_cov, epochs.info, rank=None, mag=0.1, grad=0.2)
assert _cov_rank(emp_cov, epochs.info) == sss_proj_rank
reg_cov = regularize(emp_cov, epochs.info, proj=True, rank='full')
assert _cov_rank(reg_cov, epochs.info) == proj_rank
with pytest.warns(RuntimeWarning, match='exceeds the theoretical'):
_compute_rank_int(reg_cov, info=epochs.info)
del reg_cov
with catch_logging() as log:
reg_r_cov = regularize(emp_cov, epochs.info, proj=True, rank=None,
verbose=True)
log = log.getvalue()
assert 'jointly' in log
assert _cov_rank(reg_r_cov, epochs.info) == sss_proj_rank
reg_r_only_cov = regularize(emp_cov, epochs.info, proj=False, rank=None)
assert _cov_rank(reg_r_only_cov, epochs.info) == sss_proj_rank
assert_allclose(reg_r_only_cov['data'], reg_r_cov['data'])
del reg_r_only_cov, reg_r_cov
# test that rank=306 is same as rank='full'
epochs_meg = epochs.copy().pick_types()
assert len(epochs_meg.ch_names) == 306
epochs_meg.info.update(bads=[], projs=[])
cov_full = compute_covariance(epochs_meg, method='oas',
rank='full', verbose='error')
assert _cov_rank(cov_full, epochs_meg.info) == 306
with pytest.deprecated_call(match='int is deprecated'):
cov_dict = compute_covariance(epochs_meg, method='oas', rank=306)
assert _cov_rank(cov_dict, epochs_meg.info) == 306
assert_allclose(cov_full['data'], cov_dict['data'])
cov_dict = compute_covariance(epochs_meg, method='oas',
rank=dict(meg=306), verbose='error')
assert _cov_rank(cov_dict, epochs_meg.info) == 306
assert_allclose(cov_full['data'], cov_dict['data'])
# Work with just EEG data to simplify projection / rank reduction
raw = raw.copy().pick_types(meg=False, eeg=True)
n_proj = 2
raw.add_proj(compute_proj_raw(raw, n_eeg=n_proj))
n_ch = len(raw.ch_names)
rank = n_ch - n_proj - 1 # plus avg proj
assert len(raw.info['projs']) == 3
epochs = Epochs(raw, events, tmin=-0.2, tmax=0, preload=True)
assert len(raw.ch_names) == n_ch
emp_cov = compute_covariance(epochs, rank='full', verbose='error')
assert _cov_rank(emp_cov, epochs.info) == rank
reg_cov = regularize(emp_cov, epochs.info, proj=True, rank='full')
assert _cov_rank(reg_cov, epochs.info) == rank
reg_r_cov = regularize(emp_cov, epochs.info, proj=False, rank=None)
assert _cov_rank(reg_r_cov, epochs.info) == rank
dia_cov = compute_covariance(epochs, rank=None, method='diagonal_fixed',
verbose='error')
assert _cov_rank(dia_cov, epochs.info) == rank
assert_allclose(dia_cov['data'], reg_cov['data'])
# test our deprecation: can simply remove later
epochs.pick_channels(epochs.ch_names[:103])
# degenerate
with pytest.raises(ValueError, match='can.*only be used with rank="full"'):
compute_covariance(epochs, rank=None, method='pca')
with pytest.raises(ValueError, match='can.*only be used with rank="full"'):
compute_covariance(epochs, rank=None, method='factor_analysis')
from mne import read_cov, whiten_evoked, pick_types from mne.cov import regularize from mne.io import read_evokeds from mne.datasets import sample data_path = sample.data_path() fname = data_path + '/MEG/sample/sample_audvis-ave.fif' cov_fname = data_path + '/MEG/sample/sample_audvis-cov.fif' # Reading evoked = read_evokeds(fname, condition=0, baseline=(None, 0), proj=True) noise_cov = read_cov(cov_fname) ############################################################################### # Show result # Pick channels to view picks = pick_types(evoked.info, meg=True, eeg=True, exclude='bads') evoked.plot(picks=picks) noise_cov = regularize(noise_cov, evoked.info, grad=0.1, mag=0.1, eeg=0.1) evoked_white = whiten_evoked(evoked, noise_cov, picks, diag=True) # plot the whitened evoked data to see if baseline signals match the # assumption of Gaussian whiten noise from which we expect values around # and less than 2 standard deviations. evoked_white.plot(picks=picks, unit=False, hline=[-2, 2])