def test_make_sphere_model():
"""Test making a sphere model."""
info = read_info(fname_raw)
pytest.raises(ValueError, make_sphere_model, 'foo', 'auto', info)
pytest.raises(ValueError, make_sphere_model, 'auto', 'auto', None)
pytest.raises(ValueError, make_sphere_model, 'auto', 'auto', info,
relative_radii=(), sigmas=())
pytest.raises(ValueError, make_sphere_model, 'auto', 'auto', info,
relative_radii=(1,)) # wrong number of radii
# here we just make sure it works -- the functionality is actually
# tested more extensively e.g. in the forward and dipole code
with catch_logging() as log:
bem = make_sphere_model('auto', 'auto', info, verbose=True)
log = log.getvalue()
assert ' RV = ' in log
for line in log.split('\n'):
if ' RV = ' in line:
val = float(line.split()[-2])
assert val < 0.01 # actually decent fitting
break
assert '3 layers' in repr(bem)
assert 'Sphere ' in repr(bem)
assert ' mm' in repr(bem)
bem = make_sphere_model('auto', None, info)
assert 'no layers' in repr(bem)
assert 'Sphere ' in repr(bem)
pytest.raises(ValueError, make_sphere_model, sigmas=(0.33,),
relative_radii=(1.0,))
def test_volume_source_space():
"""Test setting up volume source spaces."""
tempdir = _TempDir()
src = read_source_spaces(fname_vol)
temp_name = op.join(tempdir, 'temp-src.fif')
surf = read_bem_surfaces(fname_bem, s_id=FIFF.FIFFV_BEM_SURF_ID_BRAIN)
surf['rr'] *= 1e3 # convert to mm
# The one in the testing dataset (uses bem as bounds)
for bem, surf in zip((fname_bem, None), (None, surf)):
src_new = setup_volume_source_space(
'sample', pos=7.0, bem=bem, surface=surf, mri='T1.mgz',
subjects_dir=subjects_dir)
write_source_spaces(temp_name, src_new, overwrite=True)
src[0]['subject_his_id'] = 'sample' # XXX: to make comparison pass
_compare_source_spaces(src, src_new, mode='approx')
del src_new
src_new = read_source_spaces(temp_name)
_compare_source_spaces(src, src_new, mode='approx')
pytest.raises(IOError, setup_volume_source_space, 'sample',
pos=7.0, bem=None, surface='foo', # bad surf
mri=fname_mri, subjects_dir=subjects_dir)
assert repr(src) == repr(src_new)
assert src.kind == 'volume'
# Spheres
sphere = make_sphere_model(r0=(0., 0., 0.), head_radius=0.1,
relative_radii=(0.9, 1.0), sigmas=(0.33, 1.0))
src = setup_volume_source_space(pos=10)
src_new = setup_volume_source_space(pos=10, sphere=sphere)
_compare_source_spaces(src, src_new, mode='exact')
pytest.raises(ValueError, setup_volume_source_space, sphere='foo')
# Need a radius
sphere = make_sphere_model(head_radius=None)
pytest.raises(ValueError, setup_volume_source_space, sphere=sphere)
def test_make_sphere_model():
"""Test making a sphere model"""
info = read_info(fname_raw)
assert_raises(ValueError, make_sphere_model, 'foo', 'auto', info)
assert_raises(ValueError, make_sphere_model, 'auto', 'auto', None)
# here we just make sure it works -- the functionality is actually
# tested more extensively e.g. in the forward and dipole code
make_sphere_model('auto', 'auto', info)
def test_make_sphere_model():
"""Test making a sphere model"""
info = read_info(fname_raw)
assert_raises(ValueError, make_sphere_model, "foo", "auto", info)
assert_raises(ValueError, make_sphere_model, "auto", "auto", None)
# here we just make sure it works -- the functionality is actually
# tested more extensively e.g. in the forward and dipole code
bem = make_sphere_model("auto", "auto", info)
assert_true("3 layers" in repr(bem))
assert_true("Sphere " in repr(bem))
assert_true(" mm" in repr(bem))
bem = make_sphere_model("auto", None, info)
assert_true("no layers" in repr(bem))
assert_true("Sphere " in repr(bem))
def test_make_forward_solution_sphere():
"""Test making a forward solution with a sphere model"""
temp_dir = _TempDir()
fname_src_small = op.join(temp_dir, "sample-oct-2-src.fif")
src = setup_source_space("sample", fname_src_small, "oct2", subjects_dir=subjects_dir, add_dist=False)
out_name = op.join(temp_dir, "tmp-fwd.fif")
run_subprocess(
[
"mne_forward_solution",
"--meg",
"--eeg",
"--meas",
fname_raw,
"--src",
fname_src_small,
"--mri",
fname_trans,
"--fwd",
out_name,
]
)
fwd = read_forward_solution(out_name)
sphere = make_sphere_model(verbose=True)
fwd_py = make_forward_solution(fname_raw, fname_trans, src, sphere, meg=True, eeg=True, verbose=True)
_compare_forwards(fwd, fwd_py, 366, 108, meg_rtol=5e-1, meg_atol=1e-6, eeg_rtol=5e-1, eeg_atol=5e-1)
# Since the above is pretty lax, let's check a different way
for meg, eeg in zip([True, False], [False, True]):
fwd_ = pick_types_forward(fwd, meg=meg, eeg=eeg)
fwd_py_ = pick_types_forward(fwd, meg=meg, eeg=eeg)
assert_allclose(np.corrcoef(fwd_["sol"]["data"].ravel(), fwd_py_["sol"]["data"].ravel())[0, 1], 1.0, rtol=1e-3)
def make_montage(info, kind, check=False):
from . import _reorder
assert kind in ('mgh60', 'mgh70', 'uw_70', 'uw_60')
picks = mne.pick_types(info, meg=False, eeg=True, exclude=())
if kind in ('mgh60', 'mgh70'):
ch_names = mne.utils._clean_names(
[info['ch_names'][pick] for pick in picks], remove_whitespace=True)
if kind == 'mgh60':
assert len(ch_names) in (59, 60)
else:
assert len(ch_names) in (70,)
montage = mne.channels.read_montage(kind, ch_names=ch_names)
else:
ch_names = getattr(_reorder, 'ch_names_' + kind)
ch_names = ch_names
montage = mne.channels.read_montage('standard_1020', ch_names=ch_names)
assert len(montage.ch_names) == len(ch_names)
montage.ch_names = ['EEG%03d' % ii for ii in range(1, 61)]
sphere = mne.make_sphere_model('auto', 'auto', info)
montage.pos /= np.linalg.norm(montage.pos, axis=-1, keepdims=True)
montage.pos *= sphere.radius
montage.pos += sphere['r0']
info = mne.pick_info(info, picks)
eeg_pos = np.array([ch['loc'][:3] for ch in info['chs']])
assert len(eeg_pos) == len(montage.pos), (len(eeg_pos), len(montage.pos))
if check:
from mayavi import mlab
mlab.figure(size=(800, 800))
mlab.points3d(*sphere['r0'], scale_factor=2 * sphere.radius,
color=(0., 0., 1.), opacity=0.1, mode='sphere')
mlab.points3d(*montage.pos.T, scale_factor=0.01,
color=(1, 0, 0), mode='sphere', opacity=0.5)
mlab.points3d(*eeg_pos.T, scale_factor=0.005, color=(1, 1, 1),
mode='sphere', opacity=1)
return montage, sphere
def test_apply_inverse_sphere():
"""Test applying an inverse with a sphere model (rank-deficient)."""
evoked = _get_evoked()
evoked.pick_channels(evoked.ch_names[:306:8])
evoked.info['projs'] = []
cov = make_ad_hoc_cov(evoked.info)
sphere = make_sphere_model('auto', 'auto', evoked.info)
fwd = read_forward_solution(fname_fwd)
vertices = [fwd['src'][0]['vertno'][::5],
fwd['src'][1]['vertno'][::5]]
stc = SourceEstimate(np.zeros((sum(len(v) for v in vertices), 1)),
vertices, 0., 1.)
fwd = restrict_forward_to_stc(fwd, stc)
fwd = make_forward_solution(evoked.info, fwd['mri_head_t'], fwd['src'],
sphere, mindist=5.)
evoked = EvokedArray(fwd['sol']['data'].copy(), evoked.info)
assert fwd['sol']['nrow'] == 39
assert fwd['nsource'] == 101
assert fwd['sol']['ncol'] == 303
tempdir = _TempDir()
temp_fname = op.join(tempdir, 'temp-inv.fif')
inv = make_inverse_operator(evoked.info, fwd, cov, loose=1.)
# This forces everything to be float32
write_inverse_operator(temp_fname, inv)
inv = read_inverse_operator(temp_fname)
stc = apply_inverse(evoked, inv, method='eLORETA',
method_params=dict(eps=1e-2))
# assert zero localization bias
assert_array_equal(np.argmax(stc.data, axis=0),
np.repeat(np.arange(101), 3))
def test_simulate_raw_chpi():
"""Test simulation of raw data with cHPI"""
with warnings.catch_warnings(record=True): # MaxShield
raw = Raw(raw_chpi_fname, allow_maxshield=True)
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('sample', sphere=sphere_vol, pos=70.)
stc = _make_stc(raw, src)
# simulate data with cHPI on
raw_sim = simulate_raw(raw, stc, None, src, sphere, cov=None, chpi=False)
raw_chpi = simulate_raw(raw, stc, None, src, sphere, cov=None, chpi=True)
# XXX we need to test that the cHPI signals are actually in the correct
# place, but that should be a subsequent enhancement (not trivial to do so)
psd_sim, freqs_sim = compute_raw_psd(raw_sim)
psd_chpi, freqs_chpi = compute_raw_psd(raw_chpi)
assert_array_equal(freqs_sim, freqs_chpi)
hpi_freqs = np.array([x['custom_ref'][0]
for x in raw.info['hpi_meas'][0]['hpi_coils']])
freq_idx = np.sort([np.argmin(np.abs(freqs_sim - f)) for f in hpi_freqs])
picks_meg = pick_types(raw.info, meg=True, eeg=False)
picks_eeg = pick_types(raw.info, meg=False, eeg=True)
assert_allclose(psd_sim[picks_eeg], psd_chpi[picks_eeg])
assert_true((psd_chpi[picks_meg][:, freq_idx] >
100 * psd_sim[picks_meg][:, freq_idx]).all())
def test_make_forward_solution_sphere():
"""Test making a forward solution with a sphere model."""
temp_dir = _TempDir()
fname_src_small = op.join(temp_dir, 'sample-oct-2-src.fif')
src = setup_source_space('sample', 'oct2', subjects_dir=subjects_dir,
add_dist=False)
write_source_spaces(fname_src_small, src) # to enable working with MNE-C
out_name = op.join(temp_dir, 'tmp-fwd.fif')
run_subprocess(['mne_forward_solution', '--meg', '--eeg',
'--meas', fname_raw, '--src', fname_src_small,
'--mri', fname_trans, '--fwd', out_name])
fwd = read_forward_solution(out_name)
sphere = make_sphere_model(verbose=True)
fwd_py = make_forward_solution(fname_raw, fname_trans, src, sphere,
meg=True, eeg=True, verbose=True)
_compare_forwards(fwd, fwd_py, 366, 108,
meg_rtol=5e-1, meg_atol=1e-6,
eeg_rtol=5e-1, eeg_atol=5e-1)
# Since the above is pretty lax, let's check a different way
for meg, eeg in zip([True, False], [False, True]):
fwd_ = pick_types_forward(fwd, meg=meg, eeg=eeg)
fwd_py_ = pick_types_forward(fwd, meg=meg, eeg=eeg)
assert_allclose(np.corrcoef(fwd_['sol']['data'].ravel(),
fwd_py_['sol']['data'].ravel())[0, 1],
1.0, rtol=1e-3)
def test_simulate_raw_chpi():
"""Test simulation of raw data with cHPI"""
with warnings.catch_warnings(record=True): # MaxShield
raw = Raw(raw_chpi_fname, allow_maxshield=True)
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('sample', sphere=sphere_vol, pos=70.)
stc = _make_stc(raw, src)
# simulate data with cHPI on
raw_sim = simulate_raw(raw, stc, None, src, sphere, cov=None, chpi=False)
# need to trim extra samples off this one
raw_chpi = simulate_raw(raw, stc, None, src, sphere, cov=None, chpi=True,
head_pos=pos_fname)
# test that the cHPI signals make some reasonable values
psd_sim, freqs_sim = compute_raw_psd(raw_sim)
psd_chpi, freqs_chpi = compute_raw_psd(raw_chpi)
assert_array_equal(freqs_sim, freqs_chpi)
hpi_freqs = _get_hpi_info(raw.info)[0]
freq_idx = np.sort([np.argmin(np.abs(freqs_sim - f)) for f in hpi_freqs])
picks_meg = pick_types(raw.info, meg=True, eeg=False)
picks_eeg = pick_types(raw.info, meg=False, eeg=True)
assert_allclose(psd_sim[picks_eeg], psd_chpi[picks_eeg], atol=1e-20)
assert_true((psd_chpi[picks_meg][:, freq_idx] >
100 * psd_sim[picks_meg][:, freq_idx]).all())
# test localization based on cHPI information
trans_sim, rot_sim, t_sim = _calculate_chpi_positions(raw_chpi)
trans, rot, t = get_chpi_positions(pos_fname)
t -= raw.first_samp / raw.info['sfreq']
_compare_positions((trans, rot, t), (trans_sim, rot_sim, t_sim),
max_dist=0.005)
def test_volume_labels_morph(tmpdir):
"""Test generating a source space from volume label."""
# see gh-5224
evoked = mne.read_evokeds(fname_evoked)[0].crop(0, 0)
evoked.pick_channels(evoked.ch_names[:306:8])
evoked.info.normalize_proj()
n_ch = len(evoked.ch_names)
aseg_fname = op.join(subjects_dir, 'sample', 'mri', 'aseg.mgz')
label_names = get_volume_labels_from_aseg(aseg_fname)
src = setup_volume_source_space(
'sample', subjects_dir=subjects_dir, volume_label=label_names[:2],
mri=aseg_fname)
assert len(src) == 2
assert src.kind == 'volume'
n_src = sum(s['nuse'] for s in src)
sphere = make_sphere_model('auto', 'auto', evoked.info)
fwd = make_forward_solution(evoked.info, fname_trans, src, sphere)
assert fwd['sol']['data'].shape == (n_ch, n_src * 3)
inv = make_inverse_operator(evoked.info, fwd, make_ad_hoc_cov(evoked.info),
loose=1.)
stc = apply_inverse(evoked, inv)
assert stc.data.shape == (n_src, 1)
img = stc.as_volume(src, mri_resolution=True)
n_on = np.array(img.dataobj).astype(bool).sum()
assert n_on == 291 # was 291 on `master` before gh-5590
img = stc.as_volume(src, mri_resolution=False)
n_on = np.array(img.dataobj).astype(bool).sum()
assert n_on == 44 # was 20 on `master` before gh-5590
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_make_sphere_model():
"""Test making a sphere model"""
info = read_info(fname_raw)
assert_raises(ValueError, make_sphere_model, 'foo', 'auto', info)
assert_raises(ValueError, make_sphere_model, 'auto', 'auto', None)
assert_raises(ValueError, make_sphere_model, 'auto', 'auto', info,
relative_radii=(), sigmas=())
assert_raises(ValueError, make_sphere_model, 'auto', 'auto', info,
relative_radii=(1,)) # wrong number of radii
# here we just make sure it works -- the functionality is actually
# tested more extensively e.g. in the forward and dipole code
bem = make_sphere_model('auto', 'auto', info)
assert_true('3 layers' in repr(bem))
assert_true('Sphere ' in repr(bem))
assert_true(' mm' in repr(bem))
bem = make_sphere_model('auto', None, info)
assert_true('no layers' in repr(bem))
assert_true('Sphere ' in repr(bem))
def test_dipole_fitting_fixed():
"""Test dipole fitting with a fixed position."""
import matplotlib.pyplot as plt
tpeak = 0.073
sphere = make_sphere_model(head_radius=0.1)
evoked = read_evokeds(fname_evo, baseline=(None, 0))[0]
evoked.pick_types(meg=True)
t_idx = np.argmin(np.abs(tpeak - evoked.times))
evoked_crop = evoked.copy().crop(tpeak, tpeak)
assert_equal(len(evoked_crop.times), 1)
cov = read_cov(fname_cov)
dip_seq, resid = fit_dipole(evoked_crop, cov, sphere)
assert isinstance(dip_seq, Dipole)
assert isinstance(resid, Evoked)
assert_equal(len(dip_seq.times), 1)
pos, ori, gof = dip_seq.pos[0], dip_seq.ori[0], dip_seq.gof[0]
amp = dip_seq.amplitude[0]
# Fix position, allow orientation to change
dip_free, resid_free = fit_dipole(evoked, cov, sphere, pos=pos)
assert isinstance(dip_free, Dipole)
assert isinstance(resid_free, Evoked)
assert_allclose(dip_free.times, evoked.times)
assert_allclose(np.tile(pos[np.newaxis], (len(evoked.times), 1)),
dip_free.pos)
assert_allclose(ori, dip_free.ori[t_idx]) # should find same ori
assert (np.dot(dip_free.ori, ori).mean() < 0.9) # but few the same
assert_allclose(gof, dip_free.gof[t_idx]) # ... same gof
assert_allclose(amp, dip_free.amplitude[t_idx]) # and same amp
assert_allclose(resid.data, resid_free.data[:, [t_idx]])
# Fix position and orientation
dip_fixed, resid_fixed = fit_dipole(evoked, cov, sphere, pos=pos, ori=ori)
assert (isinstance(dip_fixed, DipoleFixed))
assert_allclose(dip_fixed.times, evoked.times)
assert_allclose(dip_fixed.info['chs'][0]['loc'][:3], pos)
assert_allclose(dip_fixed.info['chs'][0]['loc'][3:6], ori)
assert_allclose(dip_fixed.data[1, t_idx], gof)
assert_allclose(resid.data, resid_fixed.data[:, [t_idx]])
_check_roundtrip_fixed(dip_fixed)
# bad resetting
evoked.info['bads'] = [evoked.ch_names[3]]
dip_fixed, resid_fixed = fit_dipole(evoked, cov, sphere, pos=pos, ori=ori)
# Degenerate conditions
evoked_nan = evoked.copy().crop(0, 0)
evoked_nan.data[0, 0] = None
pytest.raises(ValueError, fit_dipole, evoked_nan, cov, sphere)
pytest.raises(ValueError, fit_dipole, evoked, cov, sphere, ori=[1, 0, 0])
pytest.raises(ValueError, fit_dipole, evoked, cov, sphere, pos=[0, 0, 0],
ori=[2, 0, 0])
pytest.raises(ValueError, fit_dipole, evoked, cov, sphere, pos=[0.1, 0, 0])
# copying
dip_fixed_2 = dip_fixed.copy()
dip_fixed_2.data[:] = 0.
assert not np.isclose(dip_fixed.data, 0., atol=1e-20).any()
# plotting
plt.close('all')
dip_fixed.plot()
plt.close('all')
def test_make_forward_solution_discrete():
"""Test making and converting a forward solution with discrete src."""
# smoke test for depth weighting and discrete source spaces
src = read_source_spaces(fname_src)[0]
src = SourceSpaces([src] + setup_volume_source_space(
pos=dict(rr=src['rr'][src['vertno'][:3]].copy(),
nn=src['nn'][src['vertno'][:3]].copy())))
sphere = make_sphere_model()
fwd = make_forward_solution(fname_raw, fname_trans, src, sphere,
meg=True, eeg=False)
convert_forward_solution(fwd, surf_ori=True)
def test_dipole_fitting_ctf():
"""Test dipole fitting with CTF data."""
raw_ctf = read_raw_ctf(fname_ctf).set_eeg_reference()
events = make_fixed_length_events(raw_ctf, 1)
evoked = Epochs(raw_ctf, events, 1, 0, 0, baseline=None).average()
cov = make_ad_hoc_cov(evoked.info)
sphere = make_sphere_model((0., 0., 0.))
# XXX Eventually we should do some better checks about accuracy, but
# for now our CTF phantom fitting tutorials will have to do
# (otherwise we need to add that to the testing dataset, which is
# a bit too big)
fit_dipole(evoked, cov, sphere)
def test_make_forward_solution_sphere():
"""Test making a forward solution with a sphere model."""
temp_dir = _TempDir()
fname_src_small = op.join(temp_dir, 'sample-oct-2-src.fif')
src = setup_source_space('sample', 'oct2', subjects_dir=subjects_dir,
add_dist=False)
write_source_spaces(fname_src_small, src) # to enable working with MNE-C
out_name = op.join(temp_dir, 'tmp-fwd.fif')
run_subprocess(['mne_forward_solution', '--meg', '--eeg',
'--meas', fname_raw, '--src', fname_src_small,
'--mri', fname_trans, '--fwd', out_name])
fwd = read_forward_solution(out_name)
sphere = make_sphere_model(verbose=True)
fwd_py = make_forward_solution(fname_raw, fname_trans, src, sphere,
meg=True, eeg=True, verbose=True)
_compare_forwards(fwd, fwd_py, 366, 108,
meg_rtol=5e-1, meg_atol=1e-6,
eeg_rtol=5e-1, eeg_atol=5e-1)
# Since the above is pretty lax, let's check a different way
for meg, eeg in zip([True, False], [False, True]):
fwd_ = pick_types_forward(fwd, meg=meg, eeg=eeg)
fwd_py_ = pick_types_forward(fwd, meg=meg, eeg=eeg)
assert_allclose(np.corrcoef(fwd_['sol']['data'].ravel(),
fwd_py_['sol']['data'].ravel())[0, 1],
1.0, rtol=1e-3)
# Number of layers in the sphere model doesn't matter for MEG
# (as long as no sources are omitted due to distance)
assert len(sphere['layers']) == 4
fwd = make_forward_solution(fname_raw, fname_trans, src, sphere,
meg=True, eeg=False)
sphere_1 = make_sphere_model(head_radius=None)
assert len(sphere_1['layers']) == 0
assert_array_equal(sphere['r0'], sphere_1['r0'])
fwd_1 = make_forward_solution(fname_raw, fname_trans, src, sphere,
meg=True, eeg=False)
_compare_forwards(fwd, fwd_1, 306, 108, meg_rtol=1e-12, meg_atol=1e-12)
# Homogeneous model
sphere = make_sphere_model(head_radius=None)
with pytest.raises(RuntimeError, match='zero shells.*EEG'):
make_forward_solution(fname_raw, fname_trans, src, sphere)
def test_inverse_ctf_comp():
"""Test interpolation with compensated CTF data."""
ctf_dir = op.join(testing.data_path(download=False), 'CTF')
raw_fname = op.join(ctf_dir, 'somMDYO-18av.ds')
raw = mne.io.read_raw_ctf(raw_fname)
raw.apply_gradient_compensation(1)
sphere = make_sphere_model()
cov = make_ad_hoc_cov(raw.info)
src = mne.setup_volume_source_space(
pos=dict(rr=[[0., 0., 0.01]], nn=[[0., 1., 0.]]))
fwd = make_forward_solution(raw.info, None, src, sphere, eeg=False)
inv = make_inverse_operator(raw.info, fwd, cov, loose=1.)
apply_inverse_raw(raw, inv, 1. / 9.)
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 compute_bias(raw):
events = find_events(raw, 'STI201', verbose=False)
events = events[1:] # first one has an artifact
tmin, tmax = -0.2, 0.1
epochs = mne.Epochs(raw, events, dipole_number, tmin, tmax,
baseline=(None, -0.01), preload=True, verbose=False)
sphere = mne.make_sphere_model(r0=(0., 0., 0.), head_radius=None,
verbose=False)
cov = mne.compute_covariance(epochs, tmax=0, method='oas',
rank=None, verbose=False)
idx = epochs.time_as_index(0.036)[0]
data = epochs.get_data()[:, :, idx].T
evoked = mne.EvokedArray(data, epochs.info, tmin=0.)
dip = fit_dipole(evoked, cov, sphere, n_jobs=1, verbose=False)[0]
actual_pos = mne.dipole.get_phantom_dipoles()[0][dipole_number - 1]
misses = 1000 * np.linalg.norm(dip.pos - actual_pos, axis=-1)
return misses
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)
def _get_data():
"""Helper to get some starting data"""
# raw with ECG channel
raw = Raw(raw_fname).crop(0.0, 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])
ecg = RawArray(np.zeros((1, len(raw.times))), create_info(["ECG 063"], raw.info["sfreq"], "ecg"))
for key in ("dev_head_t", "buffer_size_sec", "highpass", "lowpass", "filename", "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 test_lcmv_ctf_comp():
"""Test interpolation with compensated CTF data."""
ctf_dir = op.join(testing.data_path(download=False), 'CTF')
raw_fname = op.join(ctf_dir, 'somMDYO-18av.ds')
raw = mne.io.read_raw_ctf(raw_fname, preload=True)
events = mne.make_fixed_length_events(raw, duration=0.2)[:2]
epochs = mne.Epochs(raw, events, tmin=0., tmax=0.2)
evoked = epochs.average()
with pytest.warns(RuntimeWarning,
match='Too few samples .* estimate may be unreliable'):
data_cov = mne.compute_covariance(epochs)
fwd = mne.make_forward_solution(evoked.info, None,
mne.setup_volume_source_space(pos=15.0),
mne.make_sphere_model())
filters = mne.beamformer.make_lcmv(evoked.info, fwd, data_cov)
assert 'weights' in filters
def test_inverse_ctf_comp():
"""Test interpolation with compensated CTF data."""
raw = mne.io.read_raw_ctf(fname_raw_ctf).crop(0, 0)
raw.apply_gradient_compensation(1)
sphere = make_sphere_model()
cov = make_ad_hoc_cov(raw.info)
src = mne.setup_volume_source_space(
pos=dict(rr=[[0., 0., 0.01]], nn=[[0., 1., 0.]]))
fwd = make_forward_solution(raw.info, None, src, sphere, eeg=False)
raw.apply_gradient_compensation(0)
with pytest.raises(RuntimeError, match='compensation grade mismatch'):
make_inverse_operator(raw.info, fwd, cov, loose=1.)
raw.apply_gradient_compensation(1)
inv = make_inverse_operator(raw.info, fwd, cov, loose=1.)
apply_inverse_raw(raw, inv, 1. / 9.) # smoke test
raw.apply_gradient_compensation(0)
with pytest.raises(RuntimeError, match='compensation grade mismatch'):
apply_inverse_raw(raw, inv, 1. / 9.)
def test_rap_music_sphere():
"""Test RAP-MUSIC with real data, sphere model, MEG only."""
evoked, noise_cov = _get_data(ch_decim=8)
sphere = mne.make_sphere_model(r0=(0., 0., 0.04))
src = mne.setup_volume_source_space(subject=None, pos=10.,
sphere=(0.0, 0.0, 40, 65.0),
mindist=5.0, exclude=0.0)
forward = mne.make_forward_solution(evoked.info, trans=None, src=src,
bem=sphere)
dipoles = rap_music(evoked, forward, noise_cov, n_dipoles=2)
# Test that there is one dipole on each hemisphere
pos = np.array([dip.pos[0] for dip in dipoles])
assert_equal(pos.shape, (2, 3))
assert_equal((pos[:, 0] < 0).sum(), 1)
assert_equal((pos[:, 0] > 0).sum(), 1)
# Check the amplitude scale
assert_true(1e-10 < dipoles[0].amplitude[0] < 1e-7)
def test_mxne_vol_sphere():
"""(TF-)MxNE with a sphere forward and volumic source space"""
evoked = read_evokeds(fname_data, condition=0, baseline=(None, 0))
evoked.crop(tmin=-0.05, tmax=0.2)
cov = read_cov(fname_cov)
evoked_l21 = evoked.copy()
evoked_l21.crop(tmin=0.081, tmax=0.1)
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 = 80.
assert_raises(ValueError, mixed_norm, evoked, fwd, cov, alpha,
loose=0.0, return_residual=False,
maxit=3, tol=1e-8, active_set_size=10)
assert_raises(ValueError, mixed_norm, evoked, fwd, cov, alpha,
loose=0.2, return_residual=False,
maxit=3, tol=1e-8, active_set_size=10)
# irMxNE tests
stc = mixed_norm(evoked_l21, fwd, cov, alpha,
n_mxne_iter=1, maxit=30, tol=1e-8,
active_set_size=10)
assert_true(isinstance(stc, VolSourceEstimate))
assert_array_almost_equal(stc.times, evoked_l21.times, 5)
# Do with TF-MxNE for test memory savings
alpha_space = 60. # spatial regularization parameter
alpha_time = 1. # temporal regularization parameter
stc, _ = tf_mixed_norm(evoked, fwd, cov, alpha_space, alpha_time,
maxit=3, tol=1e-4,
tstep=16, wsize=32, window=0.1,
return_residual=True)
assert_true(isinstance(stc, VolSourceEstimate))
assert_array_almost_equal(stc.times, evoked.times, 5)
def test_simulate_raw_chpi():
"""Test simulation of raw data with cHPI."""
raw = read_raw_fif(raw_chpi_fname, allow_maxshield='yes',
add_eeg_ref=False)
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('sample', sphere=sphere_vol, pos=70.)
stc = _make_stc(raw, src)
# simulate data with cHPI on
raw_sim = simulate_raw(raw, stc, None, src, sphere, cov=None, chpi=False)
# need to trim extra samples off this one
raw_chpi = simulate_raw(raw, stc, None, src, sphere, cov=None, chpi=True,
head_pos=pos_fname)
# test cHPI indication
hpi_freqs, _, hpi_pick, hpi_ons = _get_hpi_info(raw.info)[:4]
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, picks_eeg]:
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_true((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)
trans_sim, rot_sim, t_sim = head_pos_to_trans_rot_t(quats_sim)
trans, rot, t = head_pos_to_trans_rot_t(read_head_pos(pos_fname))
t -= raw.first_samp / raw.info['sfreq']
_compare_positions((trans, rot, t), (trans_sim, rot_sim, t_sim),
max_dist=0.005)
def _get_data():
"""Helper to 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', 'buffer_size_sec', '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 test_dipole_fitting_fixed():
"""Test dipole fitting with a fixed position"""
tpeak = 0.073
sphere = make_sphere_model(head_radius=0.1)
evoked = read_evokeds(fname_evo, baseline=(None, 0))[0]
evoked.pick_types(meg=True)
t_idx = np.argmin(np.abs(tpeak - evoked.times))
evoked_crop = evoked.copy().crop(tpeak, tpeak)
assert_equal(len(evoked_crop.times), 1)
cov = read_cov(fname_cov)
dip_seq, resid = fit_dipole(evoked_crop, cov, sphere)
assert_true(isinstance(dip_seq, Dipole))
assert_equal(len(dip_seq.times), 1)
pos, ori, gof = dip_seq.pos[0], dip_seq.ori[0], dip_seq.gof[0]
amp = dip_seq.amplitude[0]
# Fix position, allow orientation to change
dip_free, resid_free = fit_dipole(evoked, cov, sphere, pos=pos)
assert_true(isinstance(dip_free, Dipole))
assert_allclose(dip_free.times, evoked.times)
assert_allclose(np.tile(pos[np.newaxis], (len(evoked.times), 1)),
dip_free.pos)
assert_allclose(ori, dip_free.ori[t_idx]) # should find same ori
assert_true(np.dot(dip_free.ori, ori).mean() < 0.9) # but few the same
assert_allclose(gof, dip_free.gof[t_idx]) # ... same gof
assert_allclose(amp, dip_free.amplitude[t_idx]) # and same amp
assert_allclose(resid, resid_free[:, [t_idx]])
# Fix position and orientation
dip_fixed, resid_fixed = fit_dipole(evoked, cov, sphere, pos=pos, ori=ori)
assert_true(isinstance(dip_fixed, DipoleFixed))
assert_allclose(dip_fixed.times, evoked.times)
assert_allclose(dip_fixed.info['chs'][0]['loc'][:3], pos)
assert_allclose(dip_fixed.info['chs'][0]['loc'][3:6], ori)
assert_allclose(dip_fixed.data[1, t_idx], gof)
assert_allclose(resid, resid_fixed[:, [t_idx]])
_check_roundtrip_fixed(dip_fixed)
# Degenerate conditions
assert_raises(ValueError, fit_dipole, evoked, cov, sphere, pos=[0])
assert_raises(ValueError, fit_dipole, evoked, cov, sphere, ori=[1, 0, 0])
assert_raises(ValueError, fit_dipole, evoked, cov, sphere, pos=[0, 0, 0],
ori=[2, 0, 0])
assert_raises(ValueError, fit_dipole, evoked, cov, sphere, pos=[0.1, 0, 0])
def test_accuracy():
"""Test dipole fitting to sub-mm accuracy."""
evoked = read_evokeds(fname_evo)[0].crop(0., 0.,)
evoked.pick_types(meg=True, eeg=False)
evoked.pick_channels([c for c in evoked.ch_names[::4]])
for rad, perc_90 in zip((0.09, None), (0.002, 0.004)):
bem = make_sphere_model('auto', rad, evoked.info,
relative_radii=(0.999, 0.998, 0.997, 0.995))
src = read_source_spaces(fname_src)
fwd = make_forward_solution(evoked.info, None, src, bem)
fwd = convert_forward_solution(fwd, force_fixed=True, use_cps=True)
vertices = [src[0]['vertno'], src[1]['vertno']]
n_vertices = sum(len(v) for v in vertices)
amp = 10e-9
data = np.eye(n_vertices + 1)[:n_vertices]
data[-1, -1] = 1.
data *= amp
stc = SourceEstimate(data, vertices, 0., 1e-3, 'sample')
evoked.info.normalize_proj()
sim = simulate_evoked(fwd, stc, evoked.info, cov=None, nave=np.inf)
cov = make_ad_hoc_cov(evoked.info)
dip = fit_dipole(sim, cov, bem, min_dist=0.001)[0]
ds = []
for vi in range(n_vertices):
if vi < len(vertices[0]):
hi = 0
vertno = vi
else:
hi = 1
vertno = vi - len(vertices[0])
vertno = src[hi]['vertno'][vertno]
rr = src[hi]['rr'][vertno]
d = np.sqrt(np.sum((rr - dip.pos[vi]) ** 2))
ds.append(d)
# make sure that our median is sub-mm and the large majority are very
# close (we expect some to be off by a bit e.g. because they are
# radial)
assert_true((np.percentile(ds, [50, 90]) < [0.0005, perc_90]).all())
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)
raw_sim = simulate_raw(raw.info, [stc] * 15, trans, src, sphere, None,
first_samp=raw.first_samp)
raw_sim.crop(0, raw.times[-1])
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)
# 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.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 < 15:
ii += 1
yield (stc, stim_data)
raw_new = simulate_raw(raw.info, stc_iter(), trans, src, sphere, None,
first_samp=raw.first_samp)
raw_new.crop(0, raw.times[-1])
_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.info, stc, trans, src, bem, None)
def test_plot_alignment():
"""Test plotting of -trans.fif files and MEG sensor layouts."""
# generate fiducials file for testing
tempdir = _TempDir()
fiducials_path = op.join(tempdir, 'fiducials.fif')
fid = [{'coord_frame': 5, 'ident': 1, 'kind': 1,
'r': [-0.08061612, -0.02908875, -0.04131077]},
{'coord_frame': 5, 'ident': 2, 'kind': 1,
'r': [0.00146763, 0.08506715, -0.03483611]},
{'coord_frame': 5, 'ident': 3, 'kind': 1,
'r': [0.08436285, -0.02850276, -0.04127743]}]
write_dig(fiducials_path, fid, 5)
mlab = _import_mlab()
evoked = read_evokeds(evoked_fname)[0]
sample_src = read_source_spaces(src_fname)
with warnings.catch_warnings(record=True): # 4D weight tables
bti = read_raw_bti(pdf_fname, config_fname, hs_fname, convert=True,
preload=False).info
infos = dict(
Neuromag=evoked.info,
CTF=read_raw_ctf(ctf_fname).info,
BTi=bti,
KIT=read_raw_kit(sqd_fname).info,
)
for system, info in infos.items():
meg = ['helmet', 'sensors']
if system == 'KIT':
meg.append('ref')
plot_alignment(info, trans_fname, subject='sample',
subjects_dir=subjects_dir, meg=meg)
mlab.close(all=True)
# KIT ref sensor coil def is defined
mlab.close(all=True)
info = infos['Neuromag']
assert_raises(TypeError, plot_alignment, 'foo', trans_fname,
subject='sample', subjects_dir=subjects_dir)
assert_raises(TypeError, plot_alignment, info, trans_fname,
subject='sample', subjects_dir=subjects_dir, src='foo')
assert_raises(ValueError, plot_alignment, info, trans_fname,
subject='fsaverage', subjects_dir=subjects_dir,
src=sample_src)
sample_src.plot(subjects_dir=subjects_dir, head=True, skull=True,
brain='white')
mlab.close(all=True)
# no-head version
mlab.close(all=True)
# all coord frames
for coord_frame in ('meg', 'head', 'mri'):
plot_alignment(info, meg=['helmet', 'sensors'], dig=True,
coord_frame=coord_frame, trans=trans_fname,
subject='sample', mri_fiducials=fiducials_path,
subjects_dir=subjects_dir, src=sample_src)
mlab.close(all=True)
# EEG only with strange options
evoked_eeg_ecog = evoked.copy().pick_types(meg=False, eeg=True)
evoked_eeg_ecog.info['projs'] = [] # "remove" avg proj
evoked_eeg_ecog.set_channel_types({'EEG 001': 'ecog'})
with warnings.catch_warnings(record=True) as w:
plot_alignment(evoked_eeg_ecog.info, subject='sample',
trans=trans_fname, subjects_dir=subjects_dir,
surfaces=['white', 'outer_skin', 'outer_skull'],
meg=['helmet', 'sensors'],
eeg=['original', 'projected'], ecog=True)
mlab.close(all=True)
assert_true(['Cannot plot MEG' in str(ww.message) for ww in w])
sphere = make_sphere_model(info=evoked.info, r0='auto', head_radius='auto')
bem_sol = read_bem_solution(op.join(subjects_dir, 'sample', 'bem',
'sample-1280-1280-1280-bem-sol.fif'))
bem_surfs = read_bem_surfaces(op.join(subjects_dir, 'sample', 'bem',
'sample-1280-1280-1280-bem.fif'))
sample_src[0]['coord_frame'] = 4 # hack for coverage
plot_alignment(info, trans_fname, subject='sample', meg='helmet',
subjects_dir=subjects_dir, eeg='projected', bem=sphere,
surfaces=['head', 'brain'], src=sample_src)
plot_alignment(info, trans_fname, subject='sample', meg=[],
subjects_dir=subjects_dir, bem=bem_sol, eeg=True,
surfaces=['head', 'inflated', 'outer_skull', 'inner_skull'])
plot_alignment(info, trans_fname, subject='sample',
meg=True, subjects_dir=subjects_dir,
surfaces=['head', 'inner_skull'], bem=bem_surfs)
sphere = make_sphere_model('auto', None, evoked.info) # one layer
plot_alignment(info, trans_fname, subject='sample', meg=False,
coord_frame='mri', subjects_dir=subjects_dir,
surfaces=['brain'], bem=sphere)
# one layer bem with skull surfaces:
assert_raises(ValueError, plot_alignment, info=info, trans=trans_fname,
subject='sample', subjects_dir=subjects_dir,
surfaces=['brain', 'head', 'inner_skull'], bem=sphere)
# wrong eeg value:
assert_raises(ValueError, plot_alignment, info=info, trans=trans_fname,
subject='sample', subjects_dir=subjects_dir, eeg='foo')
# wrong meg value:
assert_raises(ValueError, plot_alignment, info=info, trans=trans_fname,
subject='sample', subjects_dir=subjects_dir, meg='bar')
# multiple brain surfaces:
assert_raises(ValueError, plot_alignment, info=info, trans=trans_fname,
subject='sample', subjects_dir=subjects_dir,
surfaces=['white', 'pial'])
assert_raises(TypeError, plot_alignment, info=info, trans=trans_fname,
subject='sample', subjects_dir=subjects_dir,
surfaces=[1])
assert_raises(ValueError, plot_alignment, info=info, trans=trans_fname,
subject='sample', subjects_dir=subjects_dir,
surfaces=['foo'])
import mne
from mne.datasets import sample
import numpy as np
from sim_funcs import fit_dips
sphere = mne.make_sphere_model(r0=(0., 0., 0.),
head_radius=None) # Use this for all testing
perts = dict(max_percent_imb=10,
variance_imb=0,
preferred_side_imb=1,
max_error_nn=0,
variance_nn=0,
preferred_direction_nn=0,
max_translation=4)
sign = perts['preferred_side_imb']
max_imbalance = perts['max_percent_imb']
max_shift = perts['max_translation']
local_data_path = 'C:\Pert_Inv\Local_mne_data\side%s' % (sign, )
min_rad, max_rad = 0, 90
big_data = np.zeros(
(max_shift + 1, max_imbalance + 1, max_rad - min_rad + 1, 22))
nn = [0, 1, 1]
sourcenorm = [0, 1, 0] / np.linalg.norm([0, 1, 0])
for l in range(0, max_shift + 1):
perts['max_translation'] = l
for k in range(0, max_imbalance + 1):
perts['max_percent_imb'] = k
dip_fit_long, dip_fit_pert, testsources = fit_dips(
min_rad, max_rad, nn, sphere, perts, sourcenorm)
def test_simulate_raw_sphere():
"""Test simulation of raw data with sphere model."""
seed = 42
raw, src, stc, trans, sphere = _get_data()
assert len(pick_types(raw.info, meg=False, ecg=True)) == 1
# head pos
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']
#
# Test raw simulation with basic parameters
#
raw_sim = simulate_raw(raw,
stc,
trans,
src,
sphere,
read_cov(cov_fname),
head_pos=head_pos_sim,
blink=True,
ecg=True,
random_state=seed,
use_cps=True)
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,
use_cps=True)
assert_array_equal(raw_sim_2[:][0], raw_sim[:][0])
std = dict(grad=2e-13, mag=10e-15, eeg=0.1e-6)
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,
use_cps=True)
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,
use_cps=True)
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()
raw_sim = simulate_raw(raw_meg,
stc,
trans,
src,
sphere_norad,
make_ad_hoc_cov(raw.info, std=None),
head_pos=head_pos_sim,
blink=True,
ecg=True,
random_state=seed,
use_cps=True)
raw_sim_2 = simulate_raw(raw_meg,
stc,
trans_fname,
src_fname,
sphere_norad,
cov='simple',
head_pos=head_pos_sim,
blink=True,
ecg=True,
random_state=seed,
use_cps=True)
assert_array_equal(raw_sim_2[:][0], raw_sim[:][0])
# Test IO on processed data
tempdir = _TempDir()
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)):
raw_sim_3 = simulate_raw(raw,
stc,
trans,
src,
sphere,
cov=None,
head_pos=head_pos_sim,
blink=eog,
ecg=ecg,
random_state=seed,
use_cps=True)
raw_sim_4 = simulate_raw(raw,
stc,
trans,
src,
sphere,
cov=None,
head_pos=head_pos_sim,
blink=False,
ecg=False,
random_state=seed,
use_cps=True)
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
raw_sim_meg = simulate_raw(raw.copy().pick_types(meg=True, eeg=False),
stc,
trans,
src,
sphere,
cov=None,
ecg=True,
blink=True,
random_state=seed,
use_cps=True)
raw_sim_eeg = simulate_raw(raw.copy().pick_types(meg=False, eeg=True),
stc,
trans,
src,
sphere,
cov=None,
ecg=True,
blink=True,
random_state=seed,
use_cps=True)
raw_sim_meeg = simulate_raw(raw.copy().pick_types(meg=True, eeg=True),
stc,
trans,
src,
sphere,
cov=None,
ecg=True,
blink=True,
random_state=seed,
use_cps=True)
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 different interpolations are similar given small movements
raw_sim = simulate_raw(raw,
stc,
trans,
src,
sphere,
cov=None,
head_pos=head_pos_sim,
interp='linear',
use_cps=True)
raw_sim_hann = simulate_raw(raw,
stc,
trans,
src,
sphere,
cov=None,
head_pos=head_pos_sim,
interp='hann',
use_cps=True)
assert_allclose(raw_sim[:][0], raw_sim_hann[:][0], rtol=1e-1, atol=1e-14)
del raw_sim, raw_sim_hann
# Make impossible transform (translate up into helmet) and ensure failure
head_pos_sim_err = deepcopy(head_pos_sim)
head_pos_sim_err[1.][2, 3] -= 0.1 # z trans upward 10cm
pytest.raises(RuntimeError,
simulate_raw,
raw,
stc,
trans,
src,
sphere,
ecg=False,
blink=False,
head_pos=head_pos_sim_err,
use_cps=True)
pytest.raises(RuntimeError,
simulate_raw,
raw,
stc,
trans,
src,
bem_fname,
ecg=False,
blink=False,
head_pos=head_pos_sim_err,
use_cps=True)
# other degenerate conditions
pytest.raises(TypeError,
simulate_raw,
'foo',
stc,
trans,
src,
sphere,
use_cps=True)
pytest.raises(TypeError,
simulate_raw,
raw,
'foo',
trans,
src,
sphere,
use_cps=True)
pytest.raises(ValueError,
simulate_raw,
raw,
stc.copy().crop(0, 0),
trans,
src,
sphere,
use_cps=True)
stc_bad = stc.copy()
stc_bad.tstep += 0.1
pytest.raises(ValueError,
simulate_raw,
raw,
stc_bad,
trans,
src,
sphere,
use_cps=True)
pytest.raises(TypeError,
simulate_raw,
raw,
stc,
trans,
src,
sphere,
cov=0,
use_cps=True) # wrong covariance type
pytest.raises(RuntimeError,
simulate_raw,
raw,
stc,
trans,
src,
sphere,
chpi=True,
use_cps=True) # no cHPI info
pytest.raises(ValueError,
simulate_raw,
raw,
stc,
trans,
src,
sphere,
interp='foo',
use_cps=True)
pytest.raises(TypeError,
simulate_raw,
raw,
stc,
trans,
src,
sphere,
head_pos=1.,
use_cps=True)
pytest.raises(RuntimeError,
simulate_raw,
raw,
stc,
trans,
src,
sphere,
head_pos=pos_fname,
use_cps=True) # ends up with t>t_end
head_pos_sim_err = deepcopy(head_pos_sim)
head_pos_sim_err[-1.] = head_pos_sim_err[1.] # negative time
pytest.raises(RuntimeError,
simulate_raw,
raw,
stc,
trans,
src,
sphere,
head_pos=head_pos_sim_err,
use_cps=True)
raw_bad = raw.copy()
raw_bad.info['dig'] = None
pytest.raises(RuntimeError,
simulate_raw,
raw_bad,
stc,
trans,
src,
sphere,
blink=True,
use_cps=True)
def test_dipole_fitting(tmpdir):
"""Test dipole fitting."""
amp = 100e-9
tempdir = str(tmpdir)
rng = np.random.RandomState(0)
fname_dtemp = op.join(tempdir, 'test.dip')
fname_sim = op.join(tempdir, 'test-ave.fif')
fwd = convert_forward_solution(read_forward_solution(fname_fwd),
surf_ori=False,
force_fixed=True,
use_cps=True)
evoked = read_evokeds(fname_evo)[0]
cov = read_cov(fname_cov)
n_per_hemi = 5
vertices = [
np.sort(rng.permutation(s['vertno'])[:n_per_hemi]) for s in fwd['src']
]
nv = sum(len(v) for v in vertices)
stc = SourceEstimate(amp * np.eye(nv), vertices, 0, 0.001)
evoked = simulate_evoked(fwd,
stc,
evoked.info,
cov,
nave=evoked.nave,
random_state=rng)
# For speed, let's use a subset of channels (strange but works)
picks = np.sort(
np.concatenate([
pick_types(evoked.info, meg=True, eeg=False)[::2],
pick_types(evoked.info, meg=False, eeg=True)[::2]
]))
evoked.pick_channels([evoked.ch_names[p] for p in picks])
evoked.add_proj(make_eeg_average_ref_proj(evoked.info))
write_evokeds(fname_sim, evoked)
# Run MNE-C version
run_subprocess([
'mne_dipole_fit',
'--meas',
fname_sim,
'--meg',
'--eeg',
'--noise',
fname_cov,
'--dip',
fname_dtemp,
'--mri',
fname_fwd,
'--reg',
'0',
'--tmin',
'0',
])
dip_c = read_dipole(fname_dtemp)
# Run mne-python version
sphere = make_sphere_model(head_radius=0.1)
with pytest.warns(RuntimeWarning, match='projection'):
dip, residual = fit_dipole(evoked, cov, sphere, fname_fwd)
assert isinstance(residual, Evoked)
# Sanity check: do our residuals have less power than orig data?
data_rms = np.sqrt(np.sum(evoked.data**2, axis=0))
resi_rms = np.sqrt(np.sum(residual.data**2, axis=0))
assert (data_rms > resi_rms * 0.95).all(), \
'%s (factor: %s)' % ((data_rms / resi_rms).min(), 0.95)
# Compare to original points
transform_surface_to(fwd['src'][0], 'head', fwd['mri_head_t'])
transform_surface_to(fwd['src'][1], 'head', fwd['mri_head_t'])
assert fwd['src'][0]['coord_frame'] == FIFF.FIFFV_COORD_HEAD
src_rr = np.concatenate([s['rr'][v] for s, v in zip(fwd['src'], vertices)],
axis=0)
src_nn = np.concatenate([s['nn'][v] for s, v in zip(fwd['src'], vertices)],
axis=0)
# MNE-C skips the last "time" point :(
out = dip.crop(dip_c.times[0], dip_c.times[-1])
assert (dip is out)
src_rr, src_nn = src_rr[:-1], src_nn[:-1]
# check that we did about as well
corrs, dists, gc_dists, amp_errs, gofs = [], [], [], [], []
for d in (dip_c, dip):
new = d.pos
diffs = new - src_rr
corrs += [np.corrcoef(src_rr.ravel(), new.ravel())[0, 1]]
dists += [np.sqrt(np.mean(np.sum(diffs * diffs, axis=1)))]
gc_dists += [
180 / np.pi * np.mean(np.arccos(np.sum(src_nn * d.ori, axis=1)))
]
amp_errs += [np.sqrt(np.mean((amp - d.amplitude)**2))]
gofs += [np.mean(d.gof)]
# XXX possibly some OpenBLAS numerical differences make
# things slightly worse for us
factor = 0.7
assert dists[0] / factor >= dists[1], 'dists: %s' % dists
assert corrs[0] * factor <= corrs[1], 'corrs: %s' % corrs
assert gc_dists[0] / factor >= gc_dists[1] * 0.8, \
'gc-dists (ori): %s' % gc_dists
assert amp_errs[0] / factor >= amp_errs[1],\
'amplitude errors: %s' % amp_errs
# This one is weird because our cov/sim/picking is weird
assert gofs[0] * factor <= gofs[1] * 2, 'gof: %s' % gofs
def test_plot_alignment_basic(tmp_path, renderer, mixed_fwd_cov_evoked):
"""Test plotting of -trans.fif files and MEG sensor layouts."""
# generate fiducials file for testing
tempdir = str(tmp_path)
fiducials_path = op.join(tempdir, 'fiducials.fif')
fid = [{
'coord_frame': 5,
'ident': 1,
'kind': 1,
'r': [-0.08061612, -0.02908875, -0.04131077]
}, {
'coord_frame': 5,
'ident': 2,
'kind': 1,
'r': [0.00146763, 0.08506715, -0.03483611]
}, {
'coord_frame': 5,
'ident': 3,
'kind': 1,
'r': [0.08436285, -0.02850276, -0.04127743]
}]
write_dig(fiducials_path, fid, 5)
evoked = read_evokeds(evoked_fname)[0]
info = evoked.info
sample_src = read_source_spaces(src_fname)
pytest.raises(TypeError,
plot_alignment,
'foo',
trans_fname,
subject='sample',
subjects_dir=subjects_dir)
pytest.raises(OSError,
plot_alignment,
info,
trans_fname,
subject='sample',
subjects_dir=subjects_dir,
src='foo')
pytest.raises(ValueError,
plot_alignment,
info,
trans_fname,
subject='fsaverage',
subjects_dir=subjects_dir,
src=sample_src)
sample_src.plot(subjects_dir=subjects_dir,
head=True,
skull=True,
brain='white')
# mixed source space
mixed_src = mixed_fwd_cov_evoked[0]['src']
assert mixed_src.kind == 'mixed'
fig = plot_alignment(info,
meg=['helmet', 'sensors'],
dig=True,
coord_frame='head',
trans=Path(trans_fname),
subject='sample',
mri_fiducials=fiducials_path,
subjects_dir=subjects_dir,
src=mixed_src)
assert isinstance(fig, Figure3D)
renderer.backend._close_all()
# no-head version
renderer.backend._close_all()
# trans required
with pytest.raises(ValueError, match='transformation matrix.*in head'):
plot_alignment(info, trans=None, src=src_fname)
with pytest.raises(ValueError, match='transformation matrix.*in head'):
plot_alignment(info, trans=None, mri_fiducials=True)
with pytest.raises(ValueError, match='transformation matrix.*in head'):
plot_alignment(info, trans=None, surfaces=['brain'])
assert mixed_src[0]['coord_frame'] == FIFF.FIFFV_COORD_HEAD
with pytest.raises(ValueError, match='head-coordinate source space in mr'):
plot_alignment(trans=None, src=mixed_src, coord_frame='mri')
# all coord frames
plot_alignment(info) # works: surfaces='auto' default
for coord_frame in ('meg', 'head', 'mri'):
plot_alignment(info,
meg=['helmet', 'sensors'],
dig=True,
coord_frame=coord_frame,
trans=Path(trans_fname),
subject='sample',
src=src_fname,
mri_fiducials=fiducials_path,
subjects_dir=subjects_dir)
renderer.backend._close_all()
# EEG only with strange options
evoked_eeg_ecog_seeg = evoked.copy().pick_types(meg=False, eeg=True)
with evoked_eeg_ecog_seeg.info._unlock():
evoked_eeg_ecog_seeg.info['projs'] = [] # "remove" avg proj
evoked_eeg_ecog_seeg.set_channel_types({
'EEG 001': 'ecog',
'EEG 002': 'seeg'
})
with catch_logging() as log:
plot_alignment(evoked_eeg_ecog_seeg.info,
subject='sample',
trans=trans_fname,
subjects_dir=subjects_dir,
surfaces=['white', 'outer_skin', 'outer_skull'],
meg=['helmet', 'sensors'],
eeg=['original', 'projected'],
ecog=True,
seeg=True,
verbose=True)
log = log.getvalue()
assert 'ecog: 1' in log
assert 'seeg: 1' in log
renderer.backend._close_all()
sphere = make_sphere_model(info=info, r0='auto', head_radius='auto')
bem_sol = read_bem_solution(
op.join(subjects_dir, 'sample', 'bem',
'sample-1280-1280-1280-bem-sol.fif'))
bem_surfs = read_bem_surfaces(
op.join(subjects_dir, 'sample', 'bem',
'sample-1280-1280-1280-bem.fif'))
sample_src[0]['coord_frame'] = 4 # hack for coverage
plot_alignment(
info,
trans_fname,
subject='sample',
eeg='projected',
meg='helmet',
bem=sphere,
dig=True,
surfaces=['brain', 'inner_skull', 'outer_skull', 'outer_skin'])
plot_alignment(info,
trans_fname,
subject='sample',
meg='helmet',
subjects_dir=subjects_dir,
eeg='projected',
bem=sphere,
surfaces=['head', 'brain'],
src=sample_src)
# no trans okay, no mri surfaces
plot_alignment(info, bem=sphere, surfaces=['brain'])
with pytest.raises(ValueError, match='A head surface is required'):
plot_alignment(info,
trans=trans_fname,
subject='sample',
subjects_dir=subjects_dir,
eeg='projected',
surfaces=[])
with pytest.raises(RuntimeError, match='No brain surface found'):
plot_alignment(info,
trans=trans_fname,
subject='foo',
subjects_dir=subjects_dir,
surfaces=['brain'])
assert all(surf['coord_frame'] == FIFF.FIFFV_COORD_MRI
for surf in bem_sol['surfs'])
plot_alignment(info,
trans_fname,
subject='sample',
meg=[],
subjects_dir=subjects_dir,
bem=bem_sol,
eeg=True,
surfaces=['head', 'inflated', 'outer_skull', 'inner_skull'])
assert all(surf['coord_frame'] == FIFF.FIFFV_COORD_MRI
for surf in bem_sol['surfs'])
plot_alignment(info,
trans_fname,
subject='sample',
meg=True,
subjects_dir=subjects_dir,
surfaces=['head', 'inner_skull'],
bem=bem_surfs)
# single-layer BEM can still plot head surface
assert bem_surfs[-1]['id'] == FIFF.FIFFV_BEM_SURF_ID_BRAIN
bem_sol_homog = read_bem_solution(
op.join(subjects_dir, 'sample', 'bem', 'sample-1280-bem-sol.fif'))
for use_bem in (bem_surfs[-1:], bem_sol_homog):
with catch_logging() as log:
plot_alignment(info,
trans_fname,
subject='sample',
meg=True,
subjects_dir=subjects_dir,
surfaces=['head', 'inner_skull'],
bem=use_bem,
verbose=True)
log = log.getvalue()
assert 'not find the surface for head in the provided BEM model' in log
# sphere model
sphere = make_sphere_model('auto', 'auto', info)
src = setup_volume_source_space(sphere=sphere)
plot_alignment(
info,
trans=Transform('head', 'mri'),
eeg='projected',
meg='helmet',
bem=sphere,
src=src,
dig=True,
surfaces=['brain', 'inner_skull', 'outer_skull', 'outer_skin'])
sphere = make_sphere_model('auto', None, info) # one layer
# if you ask for a brain surface with a 1-layer sphere model it's an error
with pytest.raises(RuntimeError, match='Sphere model does not have'):
plot_alignment(trans=trans_fname,
subject='sample',
subjects_dir=subjects_dir,
surfaces=['brain'],
bem=sphere)
# but you can ask for a specific brain surface, and
# no info is permitted
plot_alignment(trans=trans_fname,
subject='sample',
meg=False,
coord_frame='mri',
subjects_dir=subjects_dir,
surfaces=['white'],
bem=sphere,
show_axes=True)
renderer.backend._close_all()
# TODO: We need to make this class public and document it properly
# assert isinstance(fig, some_public_class)
# 3D coil with no defined draw (ConvexHull)
info_cube = pick_info(info, np.arange(6))
with info._unlock():
info['dig'] = None
info_cube['chs'][0]['coil_type'] = 9999
info_cube['chs'][1]['coil_type'] = 9998
with pytest.raises(RuntimeError, match='coil definition not found'):
plot_alignment(info_cube, meg='sensors', surfaces=())
coil_def_fname = op.join(tempdir, 'temp')
with open(coil_def_fname, 'w') as fid:
fid.write(coil_3d)
# make sure our other OPMs can be plotted, too
for ii, kind in enumerate(
('QUSPIN_ZFOPM_MAG', 'QUSPIN_ZFOPM_MAG2', 'FIELDLINE_OPM_MAG_GEN1',
'KERNEL_OPM_MAG_GEN1'), 2):
info_cube['chs'][ii]['coil_type'] = getattr(FIFF, f'FIFFV_COIL_{kind}')
with use_coil_def(coil_def_fname):
with catch_logging() as log:
plot_alignment(info_cube,
meg='sensors',
surfaces=(),
dig=True,
verbose='debug')
log = log.getvalue()
assert 'planar geometry' in log
# one layer bem with skull surfaces:
with pytest.raises(RuntimeError, match='Sphere model does not.*boundary'):
plot_alignment(info=info,
trans=trans_fname,
subject='sample',
subjects_dir=subjects_dir,
surfaces=['brain', 'head', 'inner_skull'],
bem=sphere)
# wrong eeg value:
with pytest.raises(ValueError, match='Invalid value for the .eeg'):
plot_alignment(info=info,
trans=trans_fname,
subject='sample',
subjects_dir=subjects_dir,
eeg='foo')
# wrong meg value:
with pytest.raises(ValueError, match='Invalid value for the .meg'):
plot_alignment(info=info,
trans=trans_fname,
subject='sample',
subjects_dir=subjects_dir,
meg='bar')
# multiple brain surfaces:
with pytest.raises(ValueError, match='Only one brain surface can be plot'):
plot_alignment(info=info,
trans=trans_fname,
subject='sample',
subjects_dir=subjects_dir,
surfaces=['white', 'pial'])
with pytest.raises(TypeError, match='surfaces.*must be'):
plot_alignment(info=info,
trans=trans_fname,
subject='sample',
subjects_dir=subjects_dir,
surfaces=[1])
with pytest.raises(ValueError, match='Unknown surface type'):
plot_alignment(info=info,
trans=trans_fname,
subject='sample',
subjects_dir=subjects_dir,
surfaces=['foo'])
with pytest.raises(TypeError, match="must be an instance of "):
plot_alignment(info=info,
trans=trans_fname,
subject='sample',
subjects_dir=subjects_dir,
surfaces=dict(brain='super clear'))
with pytest.raises(ValueError, match="must be between 0 and 1"):
plot_alignment(info=info,
trans=trans_fname,
subject='sample',
subjects_dir=subjects_dir,
surfaces=dict(brain=42))
fwd_fname = op.join(data_dir, 'MEG', 'sample',
'sample_audvis_trunc-meg-eeg-oct-4-fwd.fif')
fwd = read_forward_solution(fwd_fname)
plot_alignment(subject='sample',
subjects_dir=subjects_dir,
trans=trans_fname,
fwd=fwd,
surfaces='white',
coord_frame='head')
fwd = convert_forward_solution(fwd, force_fixed=True)
plot_alignment(subject='sample',
subjects_dir=subjects_dir,
trans=trans_fname,
fwd=fwd,
surfaces='white',
coord_frame='head')
fwd['coord_frame'] = FIFF.FIFFV_COORD_MRI # check required to get to MRI
with pytest.raises(ValueError, match='transformation matrix.*in head coo'):
plot_alignment(info, trans=None, fwd=fwd)
# surfaces as dict
plot_alignment(subject='sample',
coord_frame='head',
trans=trans_fname,
subjects_dir=subjects_dir,
surfaces={
'white': 0.4,
'outer_skull': 0.6,
'head': None
})
def test_plot_alignment(tmpdir, renderer):
"""Test plotting of -trans.fif files and MEG sensor layouts."""
# generate fiducials file for testing
tempdir = str(tmpdir)
fiducials_path = op.join(tempdir, 'fiducials.fif')
fid = [{
'coord_frame': 5,
'ident': 1,
'kind': 1,
'r': [-0.08061612, -0.02908875, -0.04131077]
}, {
'coord_frame': 5,
'ident': 2,
'kind': 1,
'r': [0.00146763, 0.08506715, -0.03483611]
}, {
'coord_frame': 5,
'ident': 3,
'kind': 1,
'r': [0.08436285, -0.02850276, -0.04127743]
}]
write_dig(fiducials_path, fid, 5)
renderer.backend._close_all()
evoked = read_evokeds(evoked_fname)[0]
sample_src = read_source_spaces(src_fname)
bti = read_raw_bti(pdf_fname,
config_fname,
hs_fname,
convert=True,
preload=False).info
infos = dict(
Neuromag=evoked.info,
CTF=read_raw_ctf(ctf_fname).info,
BTi=bti,
KIT=read_raw_kit(sqd_fname).info,
)
for system, info in infos.items():
meg = ['helmet', 'sensors']
if system == 'KIT':
meg.append('ref')
fig = plot_alignment(info,
read_trans(trans_fname),
subject='sample',
subjects_dir=subjects_dir,
meg=meg)
rend = renderer.backend._Renderer(fig=fig)
rend.close()
# KIT ref sensor coil def is defined
renderer.backend._close_all()
info = infos['Neuromag']
pytest.raises(TypeError,
plot_alignment,
'foo',
trans_fname,
subject='sample',
subjects_dir=subjects_dir)
pytest.raises(OSError,
plot_alignment,
info,
trans_fname,
subject='sample',
subjects_dir=subjects_dir,
src='foo')
pytest.raises(ValueError,
plot_alignment,
info,
trans_fname,
subject='fsaverage',
subjects_dir=subjects_dir,
src=sample_src)
sample_src.plot(subjects_dir=subjects_dir,
head=True,
skull=True,
brain='white')
renderer.backend._close_all()
# no-head version
renderer.backend._close_all()
# all coord frames
plot_alignment(info) # works: surfaces='auto' default
for coord_frame in ('meg', 'head', 'mri'):
fig = plot_alignment(info,
meg=['helmet', 'sensors'],
dig=True,
coord_frame=coord_frame,
trans=Path(trans_fname),
subject='sample',
mri_fiducials=fiducials_path,
subjects_dir=subjects_dir,
src=src_fname)
renderer.backend._close_all()
# EEG only with strange options
evoked_eeg_ecog_seeg = evoked.copy().pick_types(meg=False, eeg=True)
evoked_eeg_ecog_seeg.info['projs'] = [] # "remove" avg proj
evoked_eeg_ecog_seeg.set_channel_types({
'EEG 001': 'ecog',
'EEG 002': 'seeg'
})
with pytest.warns(RuntimeWarning, match='Cannot plot MEG'):
plot_alignment(evoked_eeg_ecog_seeg.info,
subject='sample',
trans=trans_fname,
subjects_dir=subjects_dir,
surfaces=['white', 'outer_skin', 'outer_skull'],
meg=['helmet', 'sensors'],
eeg=['original', 'projected'],
ecog=True,
seeg=True)
renderer.backend._close_all()
sphere = make_sphere_model(info=evoked.info, r0='auto', head_radius='auto')
bem_sol = read_bem_solution(
op.join(subjects_dir, 'sample', 'bem',
'sample-1280-1280-1280-bem-sol.fif'))
bem_surfs = read_bem_surfaces(
op.join(subjects_dir, 'sample', 'bem',
'sample-1280-1280-1280-bem.fif'))
sample_src[0]['coord_frame'] = 4 # hack for coverage
plot_alignment(
info,
subject='sample',
eeg='projected',
meg='helmet',
bem=sphere,
dig=True,
surfaces=['brain', 'inner_skull', 'outer_skull', 'outer_skin'])
plot_alignment(info,
trans_fname,
subject='sample',
meg='helmet',
subjects_dir=subjects_dir,
eeg='projected',
bem=sphere,
surfaces=['head', 'brain'],
src=sample_src)
assert all(surf['coord_frame'] == FIFF.FIFFV_COORD_MRI
for surf in bem_sol['surfs'])
plot_alignment(info,
trans_fname,
subject='sample',
meg=[],
subjects_dir=subjects_dir,
bem=bem_sol,
eeg=True,
surfaces=['head', 'inflated', 'outer_skull', 'inner_skull'])
assert all(surf['coord_frame'] == FIFF.FIFFV_COORD_MRI
for surf in bem_sol['surfs'])
plot_alignment(info,
trans_fname,
subject='sample',
meg=True,
subjects_dir=subjects_dir,
surfaces=['head', 'inner_skull'],
bem=bem_surfs)
# single-layer BEM can still plot head surface
assert bem_surfs[-1]['id'] == FIFF.FIFFV_BEM_SURF_ID_BRAIN
bem_sol_homog = read_bem_solution(
op.join(subjects_dir, 'sample', 'bem', 'sample-1280-bem-sol.fif'))
for use_bem in (bem_surfs[-1:], bem_sol_homog):
with catch_logging() as log:
plot_alignment(info,
trans_fname,
subject='sample',
meg=True,
subjects_dir=subjects_dir,
surfaces=['head', 'inner_skull'],
bem=use_bem,
verbose=True)
log = log.getvalue()
assert 'not find the surface for head in the provided BEM model' in log
# sphere model
sphere = make_sphere_model('auto', 'auto', evoked.info)
src = setup_volume_source_space(sphere=sphere)
plot_alignment(
info,
eeg='projected',
meg='helmet',
bem=sphere,
src=src,
dig=True,
surfaces=['brain', 'inner_skull', 'outer_skull', 'outer_skin'])
sphere = make_sphere_model('auto', None, evoked.info) # one layer
# no info is permitted
fig = plot_alignment(trans=trans_fname,
subject='sample',
meg=False,
coord_frame='mri',
subjects_dir=subjects_dir,
surfaces=['brain'],
bem=sphere,
show_axes=True)
renderer.backend._close_all()
if renderer._get_3d_backend() == 'mayavi':
import mayavi # noqa: F401 analysis:ignore
assert isinstance(fig, mayavi.core.scene.Scene)
# 3D coil with no defined draw (ConvexHull)
info_cube = pick_info(info, [0])
info['dig'] = None
info_cube['chs'][0]['coil_type'] = 9999
with pytest.raises(RuntimeError, match='coil definition not found'):
plot_alignment(info_cube, meg='sensors', surfaces=())
coil_def_fname = op.join(tempdir, 'temp')
with open(coil_def_fname, 'w') as fid:
fid.write(coil_3d)
with use_coil_def(coil_def_fname):
plot_alignment(info_cube, meg='sensors', surfaces=(), dig=True)
# one layer bem with skull surfaces:
with pytest.raises(ValueError, match='sphere conductor model must have'):
plot_alignment(info=info,
trans=trans_fname,
subject='sample',
subjects_dir=subjects_dir,
surfaces=['brain', 'head', 'inner_skull'],
bem=sphere)
# wrong eeg value:
with pytest.raises(ValueError, match='Invalid value for the .eeg'):
plot_alignment(info=info,
trans=trans_fname,
subject='sample',
subjects_dir=subjects_dir,
eeg='foo')
# wrong meg value:
with pytest.raises(ValueError, match='Invalid value for the .meg'):
plot_alignment(info=info,
trans=trans_fname,
subject='sample',
subjects_dir=subjects_dir,
meg='bar')
# multiple brain surfaces:
with pytest.raises(ValueError, match='Only one brain surface can be plot'):
plot_alignment(info=info,
trans=trans_fname,
subject='sample',
subjects_dir=subjects_dir,
surfaces=['white', 'pial'])
with pytest.raises(TypeError, match='all entries in surfaces must be'):
plot_alignment(info=info,
trans=trans_fname,
subject='sample',
subjects_dir=subjects_dir,
surfaces=[1])
with pytest.raises(ValueError, match='Unknown surface type'):
plot_alignment(info=info,
trans=trans_fname,
subject='sample',
subjects_dir=subjects_dir,
surfaces=['foo'])
fwd_fname = op.join(data_dir, 'MEG', 'sample',
'sample_audvis_trunc-meg-eeg-oct-4-fwd.fif')
fwd = read_forward_solution(fwd_fname)
plot_alignment(subject='sample',
subjects_dir=subjects_dir,
trans=trans_fname,
fwd=fwd,
surfaces='white',
coord_frame='head')
fwd = convert_forward_solution(fwd, force_fixed=True)
plot_alignment(subject='sample',
subjects_dir=subjects_dir,
trans=trans_fname,
fwd=fwd,
surfaces='white',
coord_frame='head')
# fNIRS
info = read_raw_nirx(nirx_fname).info
with catch_logging() as log:
plot_alignment(info, subject='fsaverage', surfaces=(), verbose=True)
log = log.getvalue()
assert '26 fnirs pairs' in log
with catch_logging() as log:
plot_alignment(info,
subject='fsaverage',
surfaces=(),
verbose=True,
fnirs='channels')
log = log.getvalue()
assert '26 fnirs locations' in log
with catch_logging() as log:
plot_alignment(info,
subject='fsaverage',
surfaces=(),
verbose=True,
fnirs='pairs')
log = log.getvalue()
assert '26 fnirs pairs' in log
with catch_logging() as log:
plot_alignment(info,
subject='fsaverage',
surfaces=(),
verbose=True,
fnirs='sources')
log = log.getvalue()
assert '26 fnirs sources' in log
with catch_logging() as log:
plot_alignment(info,
subject='fsaverage',
surfaces=(),
verbose=True,
fnirs='detectors')
log = log.getvalue()
assert '26 fnirs detectors' in log
with catch_logging() as log:
plot_alignment(info,
subject='fsaverage',
surfaces=(),
verbose=True,
fnirs=['channels', 'pairs'])
log = log.getvalue()
assert '26 fnirs pairs' in log
assert '26 fnirs locations' in log
with catch_logging() as log:
plot_alignment(info,
subject='fsaverage',
surfaces=(),
verbose=True,
fnirs=['pairs', 'sources', 'detectors'])
log = log.getvalue()
assert '26 fnirs pairs' in log
assert '26 fnirs sources' in log
assert '26 fnirs detectors' in log
with catch_logging() as log:
plot_alignment(info,
subject='fsaverage',
surfaces=(),
verbose=True,
fnirs=['channels', 'pairs', 'sources', 'detectors'])
log = log.getvalue()
assert '26 fnirs pairs' in log
assert '26 fnirs locations' in log
assert '26 fnirs sources' in log
assert '26 fnirs detectors' in log
renderer.backend._close_all()
def test_make_forward_solution_sphere(tmpdir):
"""Test making a forward solution with a sphere model."""
fname_src_small = tmpdir.join('sample-oct-2-src.fif')
src = setup_source_space('sample',
'oct2',
subjects_dir=subjects_dir,
add_dist=False)
write_source_spaces(fname_src_small, src) # to enable working with MNE-C
out_name = tmpdir.join('tmp-fwd.fif')
run_subprocess([
'mne_forward_solution', '--meg', '--eeg', '--meas', fname_raw, '--src',
fname_src_small, '--mri', fname_trans, '--fwd', out_name
])
fwd = read_forward_solution(out_name)
sphere = make_sphere_model(verbose=True)
fwd_py = make_forward_solution(fname_raw,
fname_trans,
src,
sphere,
meg=True,
eeg=True,
verbose=True)
_compare_forwards(fwd,
fwd_py,
366,
108,
meg_rtol=5e-1,
meg_atol=1e-6,
eeg_rtol=5e-1,
eeg_atol=5e-1)
# Since the above is pretty lax, let's check a different way
for meg, eeg in zip([True, False], [False, True]):
fwd_ = pick_types_forward(fwd, meg=meg, eeg=eeg)
fwd_py_ = pick_types_forward(fwd, meg=meg, eeg=eeg)
assert_allclose(np.corrcoef(fwd_['sol']['data'].ravel(),
fwd_py_['sol']['data'].ravel())[0, 1],
1.0,
rtol=1e-3)
# Number of layers in the sphere model doesn't matter for MEG
# (as long as no sources are omitted due to distance)
assert len(sphere['layers']) == 4
fwd = make_forward_solution(fname_raw,
fname_trans,
src,
sphere,
meg=True,
eeg=False)
sphere_1 = make_sphere_model(head_radius=None)
assert len(sphere_1['layers']) == 0
assert_array_equal(sphere['r0'], sphere_1['r0'])
fwd_1 = make_forward_solution(fname_raw,
fname_trans,
src,
sphere,
meg=True,
eeg=False)
_compare_forwards(fwd, fwd_1, 306, 108, meg_rtol=1e-12, meg_atol=1e-12)
# Homogeneous model
sphere = make_sphere_model(head_radius=None)
with pytest.raises(RuntimeError, match='zero shells.*EEG'):
make_forward_solution(fname_raw, fname_trans, src, sphere)
def get_data(base_path,
dipole_idx,
dipole_amplitude,
use_maxwell_filter,
bads=[],
show=False):
if "phantom_aston" in base_path:
if use_maxwell_filter is True:
data_path = base_path + '/tSSS Data'
# data_path += '/Amp%d_IASoff_movement/' % dipole_amplitude
data_path = data_path + '/Amp%d_IASoff_tSSS/' % dipole_amplitude
fname = 'Amp%d_Dip%d_IASoff_tsss.fif' % (dipole_amplitude,
dipole_idx)
else:
data_path = base_path + '/Raw Data'
data_path = data_path + '/Amp%d_IASoff/' % dipole_amplitude
fname = 'Amp%d_Dip%d_IASoff.fif' % (dipole_amplitude, dipole_idx)
stim_channel = 'SYS201'
else:
data_path = base_path + '/%dnAm/' % dipole_amplitude
if use_maxwell_filter is True:
fname = 'dip%02d_%dnAm_sss.fif' % (dipole_idx, dipole_amplitude)
else:
fname = 'dip%02d_%dnAm.fif' % (dipole_idx, dipole_amplitude)
stim_channel = 'STI201'
raw_fname = op.join(data_path, fname)
raw = mne.io.read_raw_fif(raw_fname, preload=True, verbose='error')
if use_maxwell_filter is not True: # ie 'mne' or False
raw.info['bads'] = bads
if "phantom_aston" in base_path:
raw.crop(20, None)
events = mne.find_events(raw, stim_channel=stim_channel)
if show:
raw.plot(events=events)
if show:
raw.plot_psd(tmax=np.inf, fmax=60, average=False)
raw.fix_mag_coil_types()
if use_maxwell_filter == 'mne':
# Use Maxwell filtering from MNE
raw = mne.preprocessing.maxwell_filter(raw, origin=(0., 0., 0.))
if show:
raw.plot(events=events)
#######################################################################
# We know our phantom produces sinusoidal bursts below 25 Hz, so let's
# filter.
raw.filter(None,
40.,
h_trans_bandwidth='auto',
filter_length='auto',
phase='zero')
if show:
raw.plot(events=events)
#######################################################################
# Now we epoch our data, average it
tmin, tmax = -0.5, 0.5
event_id = events[0, 2]
# reject = dict(grad=4000e-13, mag=4e-12)
reject = None
epochs = mne.Epochs(raw,
events,
event_id,
tmin,
tmax,
baseline=(None, -0.05),
preload=True,
reject=reject)
evoked = epochs.average()
if show:
evoked.plot(spatial_colors=True)
if show:
evoked.plot_joint()
evoked.crop(0, None)
sphere = mne.make_sphere_model(r0=(0., 0., 0.), head_radius=0.08)
cov = mne.compute_covariance(epochs, tmax=-0.05)
print(fname + " nave=%d" % evoked.nave, end='')
return epochs, evoked, cov, sphere
def test_simulate_calculate_chpi_positions():
"""Test calculation of cHPI positions with simulated data."""
# Read info dict from raw FIF file
info = read_info(raw_fname)
# Tune the info structure
chpi_channel = u'STI201'
ncoil = len(info['hpi_results'][0]['order'])
coil_freq = 10 + np.arange(ncoil) * 5
hpi_subsystem = {
'event_channel':
chpi_channel,
'hpi_coils': [{
'event_bits':
np.array([256, 0, 256, 256], dtype=np.int32)
}, {
'event_bits':
np.array([512, 0, 512, 512], dtype=np.int32)
}, {
'event_bits':
np.array([1024, 0, 1024, 1024], dtype=np.int32)
}, {
'event_bits':
np.array([2048, 0, 2048, 2048], dtype=np.int32)
}],
'ncoil':
ncoil
}
info['hpi_subsystem'] = hpi_subsystem
for l, freq in enumerate(coil_freq):
info['hpi_meas'][0]['hpi_coils'][l]['coil_freq'] = freq
picks = pick_types(info, meg=True, stim=True, eeg=False, exclude=[])
info['sfreq'] = 100. # this will speed it up a lot
info = pick_info(info, picks)
info['chs'][info['ch_names'].index('STI 001')]['ch_name'] = 'STI201'
info._update_redundant()
info['projs'] = []
info_trans = info['dev_head_t']['trans'].copy()
dev_head_pos_ini = np.concatenate(
[rot_to_quat(info_trans[:3, :3]), info_trans[:3, 3]])
ez = np.array([0, 0, 1]) # Unit vector in z-direction of head coordinates
# Define some constants
duration = 30 # Time / s
# Quotient of head position sampling frequency
# and raw sampling frequency
head_pos_sfreq_quotient = 0.1
# Round number of head positions to the next integer
S = int(duration / (info['sfreq'] * head_pos_sfreq_quotient))
dz = 0.001 # Shift in z-direction is 0.1mm for each step
dev_head_pos = np.zeros((S, 10))
dev_head_pos[:, 0] = np.arange(S) * info['sfreq'] * head_pos_sfreq_quotient
dev_head_pos[:, 1:4] = dev_head_pos_ini[:3]
dev_head_pos[:, 4:7] = dev_head_pos_ini[3:] + \
np.outer(np.arange(S) * dz, ez)
dev_head_pos[:, 7] = 1.0
# cm/s
dev_head_pos[:, 9] = 100 * dz / (info['sfreq'] * head_pos_sfreq_quotient)
# Round number of samples to the next integer
raw_data = np.zeros((len(picks), int(duration * info['sfreq'] + 0.5)))
raw = RawArray(raw_data, info)
dip = Dipole(np.array([0.0, 0.1, 0.2]),
np.array([[0.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 0.0, 0.0]]),
np.array([1e-9, 1e-9, 1e-9]),
np.array([[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]]),
np.array([1.0, 1.0, 1.0]), 'dip')
sphere = make_sphere_model('auto',
'auto',
info=info,
relative_radii=(1.0, 0.9),
sigmas=(0.33, 0.3))
fwd, stc = make_forward_dipole(dip, sphere, info)
stc.resample(info['sfreq'])
raw = simulate_raw(raw,
stc,
None,
fwd['src'],
sphere,
cov=None,
blink=False,
ecg=False,
chpi=True,
head_pos=dev_head_pos,
mindist=1.0,
interp='zero',
verbose=None,
use_cps=True)
quats = _calculate_chpi_positions(
raw,
t_step_min=raw.info['sfreq'] * head_pos_sfreq_quotient,
t_step_max=raw.info['sfreq'] * head_pos_sfreq_quotient,
t_window=1.0)
_assert_quats(quats, dev_head_pos, dist_tol=0.001, angle_tol=1.)
# make room for title
fig.subplots_adjust(top=0.9)
fig.suptitle('{} reference'.format(title), size='xx-large', weight='bold')
###############################################################################
# Using an infinite reference (REST)
# ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
#
# To use the "point at infinity" reference technique described in
# :footcite:`Yao2001` requires a forward model, which we can create in a few
# steps. Here we use a fairly large spacing of vertices (``pos`` = 15 mm) to
# reduce computation time; a 5 mm spacing is more typical for real data
# analysis:
raw.del_proj() # remove our average reference projector first
sphere = mne.make_sphere_model('auto', 'auto', raw.info)
src = mne.setup_volume_source_space(sphere=sphere, exclude=30., pos=15.)
forward = mne.make_forward_solution(raw.info, trans=None, src=src, bem=sphere)
raw_rest = raw.copy().set_eeg_reference('REST', forward=forward)
for title, _raw in zip(['Original', 'REST (∞)'], [raw, raw_rest]):
fig = _raw.plot(n_channels=len(raw), scalings=dict(eeg=5e-5))
# make room for title
fig.subplots_adjust(top=0.9)
fig.suptitle('{} reference'.format(title), size='xx-large', weight='bold')
###############################################################################
# EEG reference and source modeling
# ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
#
# If you plan to perform source modeling (either with EEG or combined EEG/MEG
def test_mxne_vol_sphere():
"""Test (TF-)MxNE with a sphere forward and volumic source space."""
evoked = read_evokeds(fname_data, condition=0, baseline=(None, 0))
evoked.crop(tmin=-0.05, tmax=0.2)
cov = read_cov(fname_cov)
evoked_l21 = evoked.copy()
evoked_l21.crop(tmin=0.081, tmax=0.1)
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, 0.08),
bem=None, mindist=5.0,
exclude=2.0, sphere_units='m')
fwd = mne.make_forward_solution(info, trans=None, src=src,
bem=sphere, eeg=False, meg=True)
alpha = 80.
pytest.raises(ValueError, mixed_norm, evoked, fwd, cov, alpha,
loose=0.0, return_residual=False,
maxit=3, tol=1e-8, active_set_size=10)
pytest.raises(ValueError, mixed_norm, evoked, fwd, cov, alpha,
loose=0.2, return_residual=False,
maxit=3, tol=1e-8, active_set_size=10)
# irMxNE tests
with catch_logging() as log:
stc = mixed_norm(evoked_l21, fwd, cov, alpha,
n_mxne_iter=1, maxit=30, tol=1e-8,
active_set_size=10, verbose=True)
assert isinstance(stc, VolSourceEstimate)
assert_array_almost_equal(stc.times, evoked_l21.times, 5)
assert_var_exp_log(log.getvalue(), 9, 11) # 10.2
# 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[0][:1]],
tmin=stc.tmin,
tstep=stc.tstep)
evoked_dip = mne.simulation.simulate_evoked(fwd, stc, info, cov, nave=1e9,
use_cps=True)
dip_mxne = mixed_norm(evoked_dip, fwd, cov, alpha=80,
n_mxne_iter=1, maxit=30, tol=1e-8,
active_set_size=10, return_as_dipoles=True)
amp_max = [np.max(d.amplitude) for d in dip_mxne]
dip_mxne = dip_mxne[np.argmax(amp_max)]
assert dip_mxne.pos[0] in src[0]['rr'][stc.vertices[0]]
dip_fit = mne.fit_dipole(evoked_dip, cov, sphere)[0]
assert np.abs(np.dot(dip_fit.ori[0], dip_mxne.ori[0])) > 0.99
dist = 1000 * np.linalg.norm(dip_fit.pos[0] - dip_mxne.pos[0])
assert dist < 4. # within 4 mm
# Do with TF-MxNE for test memory savings
alpha = 60. # overall regularization parameter
l1_ratio = 0.01 # temporal regularization proportion
stc, _ = tf_mixed_norm(evoked, fwd, cov, maxit=3, tol=1e-4,
tstep=16, wsize=32, window=0.1, alpha=alpha,
l1_ratio=l1_ratio, return_residual=True)
assert isinstance(stc, VolSourceEstimate)
assert_array_almost_equal(stc.times, evoked.times, 5)
def test_make_lcmv(tmpdir, reg, proj):
"""Test LCMV with evoked data and single trials."""
raw, epochs, evoked, data_cov, noise_cov, label, forward,\
forward_surf_ori, forward_fixed, forward_vol = _get_data(proj=proj)
for fwd in [forward, forward_vol]:
filters = make_lcmv(evoked.info, fwd, data_cov, reg=reg,
noise_cov=noise_cov)
stc = apply_lcmv(evoked, filters, max_ori_out='signed')
stc.crop(0.02, None)
stc_pow = np.sum(np.abs(stc.data), axis=1)
idx = np.argmax(stc_pow)
max_stc = stc.data[idx]
tmax = stc.times[np.argmax(max_stc)]
assert 0.09 < tmax < 0.12, tmax
assert 0.9 < np.max(max_stc) < 3., np.max(max_stc)
if fwd is forward:
# Test picking normal orientation (surface source space only).
filters = make_lcmv(evoked.info, forward_surf_ori, data_cov,
reg=reg, noise_cov=noise_cov,
pick_ori='normal', weight_norm=None)
stc_normal = apply_lcmv(evoked, filters, max_ori_out='signed')
stc_normal.crop(0.02, None)
stc_pow = np.sum(np.abs(stc_normal.data), axis=1)
idx = np.argmax(stc_pow)
max_stc = stc_normal.data[idx]
tmax = stc_normal.times[np.argmax(max_stc)]
lower = 0.04 if proj else 0.025
assert lower < tmax < 0.13, tmax
lower = 3e-7 if proj else 2e-7
assert lower < np.max(max_stc) < 5e-7, np.max(max_stc)
# No weight normalization was applied, so the amplitude of normal
# orientation results should always be smaller than free
# orientation results.
assert (np.abs(stc_normal.data) <= stc.data).all()
# Test picking source orientation maximizing output source power
filters = make_lcmv(evoked.info, fwd, data_cov, reg=reg,
noise_cov=noise_cov, pick_ori='max-power')
stc_max_power = apply_lcmv(evoked, filters, max_ori_out='signed')
stc_max_power.crop(0.02, None)
stc_pow = np.sum(np.abs(stc_max_power.data), axis=1)
idx = np.argmax(stc_pow)
max_stc = np.abs(stc_max_power.data[idx])
tmax = stc.times[np.argmax(max_stc)]
lower = 0.08 if proj else 0.04
assert lower < tmax < 0.12, tmax
assert 0.8 < np.max(max_stc) < 3., np.max(max_stc)
stc_max_power.data[:, :] = np.abs(stc_max_power.data)
if fwd is forward:
# Maximum output source power orientation results should be
# similar to free orientation results in areas with channel
# coverage
label = mne.read_label(fname_label)
mean_stc = stc.extract_label_time_course(label, fwd['src'],
mode='mean')
mean_stc_max_pow = \
stc_max_power.extract_label_time_course(label, fwd['src'],
mode='mean')
assert_array_less(np.abs(mean_stc - mean_stc_max_pow), 0.6)
# Test NAI weight normalization:
filters = make_lcmv(evoked.info, fwd, data_cov, reg=reg,
noise_cov=noise_cov, pick_ori='max-power',
weight_norm='nai')
stc_nai = apply_lcmv(evoked, filters, max_ori_out='signed')
stc_nai.crop(0.02, None)
# Test whether unit-noise-gain solution is a scaled version of NAI
pearsoncorr = np.corrcoef(np.concatenate(np.abs(stc_nai.data)),
np.concatenate(stc_max_power.data))
assert_almost_equal(pearsoncorr[0, 1], 1.)
# Test sphere head model with unit-noise gain beamformer and orientation
# selection and rank reduction of the leadfield
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_sphere = mne.make_forward_solution(evoked.info, trans=None, src=src,
bem=sphere, eeg=False, meg=True)
# Test that we get an error if not reducing rank
with pytest.raises(ValueError): # Singular matrix or complex spectrum
make_lcmv(
evoked.info, fwd_sphere, data_cov, reg=0.1,
noise_cov=noise_cov, weight_norm='unit-noise-gain',
pick_ori='max-power', reduce_rank=False, rank='full')
# Now let's reduce it
filters = make_lcmv(evoked.info, fwd_sphere, data_cov, reg=0.1,
noise_cov=noise_cov, weight_norm='unit-noise-gain',
pick_ori='max-power', reduce_rank=True)
stc_sphere = apply_lcmv(evoked, filters, max_ori_out='signed')
stc_sphere = np.abs(stc_sphere)
stc_sphere.crop(0.02, None)
stc_pow = np.sum(stc_sphere.data, axis=1)
idx = np.argmax(stc_pow)
max_stc = stc_sphere.data[idx]
tmax = stc_sphere.times[np.argmax(max_stc)]
lower = 0.08 if proj else 0.04
assert lower < tmax < 0.15, tmax
assert 0.4 < np.max(max_stc) < 2., np.max(max_stc)
# Test if spatial filter contains src_type
assert 'src_type' in filters
# __repr__
assert len(evoked.ch_names) == 22
assert len(evoked.info['projs']) == (4 if proj else 0)
assert len(evoked.info['bads']) == 2
rank = 17 if proj else 20
assert 'LCMV' in repr(filters)
assert 'unknown subject' not in repr(filters)
assert '484' in repr(filters)
assert '20' in repr(filters)
assert 'rank %s' % rank in repr(filters)
# I/O
fname = op.join(str(tmpdir), 'filters.h5')
with pytest.warns(RuntimeWarning, match='-lcmv.h5'):
filters.save(fname)
filters_read = read_beamformer(fname)
assert isinstance(filters, Beamformer)
assert isinstance(filters_read, Beamformer)
# deal with object_diff strictness
filters_read['rank'] = int(filters_read['rank'])
filters['rank'] = int(filters['rank'])
assert object_diff(filters, filters_read) == ''
# Test if fixed forward operator is detected when picking normal or
# max-power orientation
pytest.raises(ValueError, make_lcmv, evoked.info, forward_fixed, data_cov,
reg=0.01, noise_cov=noise_cov, pick_ori='normal')
pytest.raises(ValueError, make_lcmv, evoked.info, forward_fixed, data_cov,
reg=0.01, noise_cov=noise_cov, pick_ori='max-power')
# Test if non-surface oriented forward operator is detected when picking
# normal orientation
pytest.raises(ValueError, make_lcmv, evoked.info, forward, data_cov,
reg=0.01, noise_cov=noise_cov, pick_ori='normal')
# Test if volume forward operator is detected when picking normal
# orientation
pytest.raises(ValueError, make_lcmv, evoked.info, forward_vol, data_cov,
reg=0.01, noise_cov=noise_cov, pick_ori='normal')
# Test if missing of noise covariance matrix is detected when more than
# one channel type is present in the data
pytest.raises(ValueError, make_lcmv, evoked.info, forward_vol,
data_cov=data_cov, reg=0.01, noise_cov=None,
pick_ori='max-power')
# Test if wrong channel selection is detected in application of filter
evoked_ch = deepcopy(evoked)
evoked_ch.pick_channels(evoked_ch.ch_names[1:])
filters = make_lcmv(evoked.info, forward_vol, data_cov, reg=0.01,
noise_cov=noise_cov)
pytest.raises(ValueError, apply_lcmv, evoked_ch, filters,
max_ori_out='signed')
# Test if discrepancies in channel selection of data and fwd model are
# handled correctly in apply_lcmv
# make filter with data where first channel was removed
filters = make_lcmv(evoked_ch.info, forward_vol, data_cov, reg=0.01,
noise_cov=noise_cov)
# applying that filter to the full data set should automatically exclude
# this channel from the data
# also test here that no warnings are thrown - implemented to check whether
# src should not be None warning occurs
with pytest.warns(None) as w:
stc = apply_lcmv(evoked, filters, max_ori_out='signed')
assert len(w) == 0
# the result should be equal to applying this filter to a dataset without
# this channel:
stc_ch = apply_lcmv(evoked_ch, filters, max_ori_out='signed')
assert_array_almost_equal(stc.data, stc_ch.data)
# Test if non-matching SSP projection is detected in application of filter
if proj:
raw_proj = deepcopy(raw)
raw_proj.del_proj()
with pytest.raises(ValueError, match='do not match the projections'):
apply_lcmv_raw(raw_proj, filters, max_ori_out='signed')
# Test if setting reduce_rank to True returns a NotImplementedError
# when no orientation selection is done or pick_ori='normal'
pytest.raises(NotImplementedError, make_lcmv, evoked.info, forward_vol,
data_cov, noise_cov=noise_cov, pick_ori=None,
weight_norm='nai', reduce_rank=True)
pytest.raises(NotImplementedError, make_lcmv, evoked.info,
forward_surf_ori, data_cov, noise_cov=noise_cov,
pick_ori='normal', weight_norm='nai', reduce_rank=True)
# Test if spatial filter contains src_type
assert 'src_type' in filters
# check whether a filters object without src_type throws expected warning
del filters['src_type'] # emulate 0.16 behaviour to cause warning
with pytest.warns(RuntimeWarning, match='spatial filter does not contain '
'src_type'):
apply_lcmv(evoked, filters, max_ori_out='signed')
# Now test single trial using fixed orientation forward solution
# so we can compare it to the evoked solution
filters = make_lcmv(epochs.info, forward_fixed, data_cov, reg=0.01,
noise_cov=noise_cov)
stcs = apply_lcmv_epochs(epochs, filters, max_ori_out='signed')
stcs_ = apply_lcmv_epochs(epochs, filters, return_generator=True,
max_ori_out='signed')
assert_array_equal(stcs[0].data, next(stcs_).data)
epochs.drop_bad()
assert (len(epochs.events) == len(stcs))
# average the single trial estimates
stc_avg = np.zeros_like(stcs[0].data)
for this_stc in stcs:
stc_avg += this_stc.data
stc_avg /= len(stcs)
# compare it to the solution using evoked with fixed orientation
filters = make_lcmv(evoked.info, forward_fixed, data_cov, reg=0.01,
noise_cov=noise_cov)
stc_fixed = apply_lcmv(evoked, filters, max_ori_out='signed')
assert_array_almost_equal(stc_avg, stc_fixed.data)
# use a label so we have few source vertices and delayed computation is
# not used
filters = make_lcmv(epochs.info, forward_fixed, data_cov, reg=0.01,
noise_cov=noise_cov, label=label)
stcs_label = apply_lcmv_epochs(epochs, filters, max_ori_out='signed')
assert_array_almost_equal(stcs_label[0].data, stcs[0].in_label(label).data)
# Test condition where the filters weights are zero. There should not be
# any divide-by-zero errors
zero_cov = data_cov.copy()
zero_cov['data'][:] = 0
filters = make_lcmv(epochs.info, forward_fixed, zero_cov, reg=0.01,
noise_cov=noise_cov)
assert_array_equal(filters['weights'], 0)
def test_lcmv():
"""Test LCMV with evoked data and single trials."""
raw, epochs, evoked, data_cov, noise_cov, label, forward,\
forward_surf_ori, forward_fixed, forward_vol = _get_data()
for fwd in [forward, forward_vol]:
filters = make_lcmv(evoked.info,
fwd,
data_cov,
reg=0.01,
noise_cov=noise_cov)
stc = apply_lcmv(evoked, filters, max_ori_out='signed')
stc.crop(0.02, None)
stc_pow = np.sum(np.abs(stc.data), axis=1)
idx = np.argmax(stc_pow)
max_stc = stc.data[idx]
tmax = stc.times[np.argmax(max_stc)]
assert_true(0.09 < tmax < 0.105, tmax)
assert_true(0.9 < np.max(max_stc) < 3., np.max(max_stc))
if fwd is forward:
# Test picking normal orientation (surface source space only)
filters = make_lcmv(evoked.info,
forward_surf_ori,
data_cov,
reg=0.01,
noise_cov=noise_cov,
pick_ori='normal')
stc_normal = apply_lcmv(evoked, filters, max_ori_out='signed')
stc_normal.crop(0.02, None)
stc_pow = np.sum(np.abs(stc_normal.data), axis=1)
idx = np.argmax(stc_pow)
max_stc = stc_normal.data[idx]
tmax = stc_normal.times[np.argmax(max_stc)]
assert_true(0.04 < tmax < 0.11, tmax)
assert_true(0.4 < np.max(max_stc) < 2., np.max(max_stc))
# The amplitude of normal orientation results should always be
# smaller than free orientation results
assert_true((np.abs(stc_normal.data) <= stc.data).all())
# Test picking source orientation maximizing output source power
filters = make_lcmv(evoked.info,
fwd,
data_cov,
reg=0.01,
noise_cov=noise_cov,
pick_ori='max-power')
stc_max_power = apply_lcmv(evoked, filters, max_ori_out='signed')
stc_max_power.crop(0.02, None)
stc_pow = np.sum(np.abs(stc_max_power.data), axis=1)
idx = np.argmax(stc_pow)
max_stc = np.abs(stc_max_power.data[idx])
tmax = stc.times[np.argmax(max_stc)]
assert_true(0.08 < tmax < 0.11, tmax)
assert_true(0.8 < np.max(max_stc) < 3., np.max(max_stc))
stc_max_power.data[:, :] = np.abs(stc_max_power.data)
if fwd is forward:
# Maximum output source power orientation results should be
# similar to free orientation results in areas with channel
# coverage
label = mne.read_label(fname_label)
mean_stc = stc.extract_label_time_course(label,
fwd['src'],
mode='mean')
mean_stc_max_pow = \
stc_max_power.extract_label_time_course(label, fwd['src'],
mode='mean')
assert_true((np.abs(mean_stc - mean_stc_max_pow) < 0.5).all())
# Test NAI weight normalization:
filters = make_lcmv(evoked.info,
fwd,
data_cov,
reg=0.01,
noise_cov=noise_cov,
pick_ori='max-power',
weight_norm='nai')
stc_nai = apply_lcmv(evoked, filters, max_ori_out='signed')
stc_nai.crop(0.02, None)
# Test whether unit-noise-gain solution is a scaled version of NAI
pearsoncorr = np.corrcoef(np.concatenate(np.abs(stc_nai.data)),
np.concatenate(stc_max_power.data))
assert_almost_equal(pearsoncorr[0, 1], 1.)
# Test sphere head model with unit-noise gain beamformer and orientation
# selection and rank reduction of the leadfield
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_sphere = mne.make_forward_solution(evoked.info,
trans=None,
src=src,
bem=sphere,
eeg=False,
meg=True)
# Test that we get an error if not reducing rank
assert_raises(ValueError,
make_lcmv,
evoked.info,
fwd_sphere,
data_cov,
reg=0.1,
noise_cov=noise_cov,
weight_norm='unit-noise-gain',
pick_ori='max-power',
reduce_rank=False)
# Now let's reduce it
filters = make_lcmv(evoked.info,
fwd_sphere,
data_cov,
reg=0.1,
noise_cov=noise_cov,
weight_norm='unit-noise-gain',
pick_ori='max-power',
reduce_rank=True)
stc_sphere = apply_lcmv(evoked, filters, max_ori_out='signed')
stc_sphere = np.abs(stc_sphere)
stc_sphere.crop(0.02, None)
stc_pow = np.sum(stc_sphere.data, axis=1)
idx = np.argmax(stc_pow)
max_stc = stc_sphere.data[idx]
tmax = stc_sphere.times[np.argmax(max_stc)]
assert_true(0.08 < tmax < 0.11, tmax)
assert_true(0.4 < np.max(max_stc) < 2., np.max(max_stc))
# Test if fixed forward operator is detected when picking normal or
# max-power orientation
assert_raises(ValueError,
make_lcmv,
evoked.info,
forward_fixed,
data_cov,
reg=0.01,
noise_cov=noise_cov,
pick_ori='normal')
assert_raises(ValueError,
make_lcmv,
evoked.info,
forward_fixed,
data_cov,
reg=0.01,
noise_cov=noise_cov,
pick_ori='max-power')
# Test if non-surface oriented forward operator is detected when picking
# normal orientation
assert_raises(ValueError,
make_lcmv,
evoked.info,
forward,
data_cov,
reg=0.01,
noise_cov=noise_cov,
pick_ori='normal')
# Test if volume forward operator is detected when picking normal
# orientation
assert_raises(ValueError,
make_lcmv,
evoked.info,
forward_vol,
data_cov,
reg=0.01,
noise_cov=noise_cov,
pick_ori='normal')
# Test if missing of noise covariance matrix is detected when more than
# one channel type is present in the data
assert_raises(ValueError,
make_lcmv,
evoked.info,
forward_vol,
data_cov=data_cov,
reg=0.01,
noise_cov=None,
pick_ori='max-power')
# Test if not-yet-implemented orientation selections raise error with
# neural activity index
assert_raises(NotImplementedError,
make_lcmv,
evoked.info,
forward_surf_ori,
data_cov,
reg=0.01,
noise_cov=noise_cov,
pick_ori='normal',
weight_norm='nai')
assert_raises(NotImplementedError,
make_lcmv,
evoked.info,
forward_vol,
data_cov,
reg=0.01,
noise_cov=noise_cov,
pick_ori=None,
weight_norm='nai')
# Test if no weight-normalization and max-power source orientation throws
# an error
assert_raises(NotImplementedError,
make_lcmv,
evoked.info,
forward_vol,
data_cov,
reg=0.01,
noise_cov=noise_cov,
pick_ori='max-power',
weight_norm=None)
# Test if wrong channel selection is detected in application of filter
evoked_ch = deepcopy(evoked)
evoked_ch.pick_channels(evoked_ch.ch_names[1:])
filters = make_lcmv(evoked.info,
forward_vol,
data_cov,
reg=0.01,
noise_cov=noise_cov)
assert_raises(ValueError,
apply_lcmv,
evoked_ch,
filters,
max_ori_out='signed')
# Test if discrepancies in channel selection of data and fwd model are
# handled correctly in apply_lcmv
# make filter with data where first channel was removed
filters = make_lcmv(evoked_ch.info,
forward_vol,
data_cov,
reg=0.01,
noise_cov=noise_cov)
# applying that filter to the full data set should automatically exclude
# this channel from the data
stc = apply_lcmv(evoked, filters, max_ori_out='signed')
# the result should be equal to applying this filter to a dataset without
# this channel:
stc_ch = apply_lcmv(evoked_ch, filters, max_ori_out='signed')
assert_array_almost_equal(stc.data, stc_ch.data)
# Test if non-matching SSP projection is detected in application of filter
raw_proj = deepcopy(raw)
raw_proj.del_proj()
assert_raises(ValueError,
apply_lcmv_raw,
raw_proj,
filters,
max_ori_out='signed')
# Test if setting reduce_rank to True returns a NotImplementedError
# when no orientation selection is done or pick_ori='normal'
assert_raises(NotImplementedError,
make_lcmv,
evoked.info,
forward_vol,
data_cov,
noise_cov=noise_cov,
pick_ori=None,
weight_norm='nai',
reduce_rank=True)
assert_raises(NotImplementedError,
make_lcmv,
evoked.info,
forward_surf_ori,
data_cov,
noise_cov=noise_cov,
pick_ori='normal',
weight_norm='nai',
reduce_rank=True)
# Now test single trial using fixed orientation forward solution
# so we can compare it to the evoked solution
filters = make_lcmv(epochs.info,
forward_fixed,
data_cov,
reg=0.01,
noise_cov=noise_cov)
stcs = apply_lcmv_epochs(epochs, filters, max_ori_out='signed')
stcs_ = apply_lcmv_epochs(epochs,
filters,
return_generator=True,
max_ori_out='signed')
assert_array_equal(stcs[0].data, advance_iterator(stcs_).data)
epochs.drop_bad()
assert_true(len(epochs.events) == len(stcs))
# average the single trial estimates
stc_avg = np.zeros_like(stcs[0].data)
for this_stc in stcs:
stc_avg += this_stc.data
stc_avg /= len(stcs)
# compare it to the solution using evoked with fixed orientation
filters = make_lcmv(evoked.info,
forward_fixed,
data_cov,
reg=0.01,
noise_cov=noise_cov)
stc_fixed = apply_lcmv(evoked, filters, max_ori_out='signed')
assert_array_almost_equal(stc_avg, stc_fixed.data)
# use a label so we have few source vertices and delayed computation is
# not used
filters = make_lcmv(epochs.info,
forward_fixed,
data_cov,
reg=0.01,
noise_cov=noise_cov,
label=label)
stcs_label = apply_lcmv_epochs(epochs, filters, max_ori_out='signed')
assert_array_almost_equal(stcs_label[0].data, stcs[0].in_label(label).data)
def test_dipole_fitting():
"""Test dipole fitting"""
amp = 10e-9
tempdir = _TempDir()
rng = np.random.RandomState(0)
fname_dtemp = op.join(tempdir, 'test.dip')
fname_sim = op.join(tempdir, 'test-ave.fif')
fwd = convert_forward_solution(read_forward_solution(fname_fwd),
surf_ori=False,
force_fixed=True)
evoked = read_evokeds(fname_evo)[0]
cov = read_cov(fname_cov)
n_per_hemi = 5
vertices = [
np.sort(rng.permutation(s['vertno'])[:n_per_hemi]) for s in fwd['src']
]
nv = sum(len(v) for v in vertices)
stc = SourceEstimate(amp * np.eye(nv), vertices, 0, 0.001)
evoked = simulate_evoked(fwd,
stc,
evoked.info,
cov,
snr=20,
random_state=rng)
# For speed, let's use a subset of channels (strange but works)
picks = np.sort(
np.concatenate([
pick_types(evoked.info, meg=True, eeg=False)[::2],
pick_types(evoked.info, meg=False, eeg=True)[::2]
]))
evoked.pick_channels([evoked.ch_names[p] for p in picks])
evoked.add_proj(make_eeg_average_ref_proj(evoked.info))
write_evokeds(fname_sim, evoked)
# Run MNE-C version
run_subprocess([
'mne_dipole_fit',
'--meas',
fname_sim,
'--meg',
'--eeg',
'--noise',
fname_cov,
'--dip',
fname_dtemp,
'--mri',
fname_fwd,
'--reg',
'0',
'--tmin',
'0',
])
dip_c = read_dipole(fname_dtemp)
# Run mne-python version
sphere = make_sphere_model(head_radius=0.1)
dip, residuals = fit_dipole(evoked, fname_cov, sphere, fname_fwd)
# Sanity check: do our residuals have less power than orig data?
data_rms = np.sqrt(np.sum(evoked.data**2, axis=0))
resi_rms = np.sqrt(np.sum(residuals**2, axis=0))
factor = 1.
# XXX weird, inexplicable differenc for 3.5 build we'll assume is due to
# Anaconda bug for now...
if os.getenv('TRAVIS', 'false') == 'true' and \
sys.version[:3] in ('3.5', '2.7'):
factor = 0.8
assert_true((data_rms > factor * resi_rms).all(),
msg='%s (factor: %s)' % ((data_rms / resi_rms).min(), factor))
# Compare to original points
transform_surface_to(fwd['src'][0], 'head', fwd['mri_head_t'])
transform_surface_to(fwd['src'][1], 'head', fwd['mri_head_t'])
src_rr = np.concatenate([s['rr'][v] for s, v in zip(fwd['src'], vertices)],
axis=0)
src_nn = np.concatenate([s['nn'][v] for s, v in zip(fwd['src'], vertices)],
axis=0)
# MNE-C skips the last "time" point :(
dip.crop(dip_c.times[0], dip_c.times[-1])
src_rr, src_nn = src_rr[:-1], src_nn[:-1]
# check that we did at least as well
corrs, dists, gc_dists, amp_errs, gofs = [], [], [], [], []
for d in (dip_c, dip):
new = d.pos
diffs = new - src_rr
corrs += [np.corrcoef(src_rr.ravel(), new.ravel())[0, 1]]
dists += [np.sqrt(np.mean(np.sum(diffs * diffs, axis=1)))]
gc_dists += [
180 / np.pi * np.mean(np.arccos(np.sum(src_nn * d.ori, axis=1)))
]
amp_errs += [np.sqrt(np.mean((amp - d.amplitude)**2))]
gofs += [np.mean(d.gof)]
assert_true(dists[0] >= dists[1] * factor, 'dists: %s' % dists)
assert_true(corrs[0] <= corrs[1] / factor, 'corrs: %s' % corrs)
assert_true(gc_dists[0] >= gc_dists[1] * factor,
'gc-dists (ori): %s' % gc_dists)
assert_true(amp_errs[0] >= amp_errs[1] * factor,
'amplitude errors: %s' % amp_errs)
assert_true(gofs[0] <= gofs[1] / factor, 'gof: %s' % gofs)
reject = dict(mag=5000e-15, grad=300000e-15)
eventID = dipnum
epochs = mne.Epochs(raw, events, eventID, -0.5, 0.5, baseline=(None,0), picks=None, #reject=reject,
preload=True, flat=None, proj=False, decim=1,reject_tmin=None, reject_tmax=None,
detrend= None, on_missing='error', reject_by_annotation=True, verbose=True)
epochs.drop(badtrial, badreason)
#%% Find trial variance > index outliers> remove beyond plow and phigh percentile
plow, phigh = 2.0, 98.0
bad_trials=my_var_cut_fn(epochs, plow, phigh, to_plot=True)
print('\n%d trial to remove from total %d trials...\nNo. of remaining trials = %d\n'%(len(bad_trials),
len(epochs),
len(epochs)-len(bad_trials)))
epochs.drop(bad_trials, reason='eye_blink and high variance', verbose=True)
#%% Compute forward solution/leadfield
bem=mne.make_sphere_model(r0=(0.0, 0.0, 0.0), head_radius=None, info=None, verbose=True)
if not 'src_vol' in locals():
src_vol = mne.setup_volume_source_space(subject=subject, pos=5.0, mri=mrifile, bem=None, surface=surffile,
mindist=5.0, exclude=10.0, subjects_dir=subjects_dir,
volume_label=None, add_interpolator=True, verbose=True)
if more_plots:
mne.viz.plot_bem(subject=subject, subjects_dir=subjects_dir, orientation='coronal', slices=range(73,193,5),
brain_surfaces=None, src=src_vol, show=True)
mne.viz.plot_alignment(epochs.info, trans=transfile, subject=subject, subjects_dir=subjects_dir, fig=None,
surfaces=['head-dense', 'inner_skull'], coord_frame='head', show_axes=True,
meg=False, eeg='original', dig=True, ecog=True, bem=None, seeg=True,
src=src_vol, mri_fiducials=False, verbose=True)
if not 'fwd' in locals():
fwd = mne.make_forward_solution(epochs.info, trans=transfile, src=src_vol, bem=bem,
raw_filt = raw_sss_pca.copy().filter(h_freq=4., l_freq=None,
filter_length='30s', n_jobs=n_jobs,
fir_design='firwin2', phase='zero-double')
# Pick the channels of interest
raw_filt.pick_types(meg='grad')
# Re-normalize projectors after subselection
raw_filt.info.normalize_proj()
# regularized data covariance
data_cov = mne.compute_raw_covariance(raw_filt, n_jobs=n_jobs)
# beamformer requirements
bem = op.join(subjects_dir, subject, 'bem', 'genz501_17a-5120-bem-sol.fif')
sphere = mne.make_sphere_model(r0='auto', head_radius='auto',
info=raw_filt.info)
src = mne.setup_volume_source_space(subject='fsaverage', bem=bem,
mri=op.join(subjects_dir, 'fsaverage',
'mri', 'T1.mgz')
subjects_dir=subjects_dir)
fwd = mne.make_forward_solution(raw_filt.info, trans=None, src=src,
bem=bem, n_jobs=n_jobs)
filters = make_lcmv(raw_filt.info, fwd, data_cov, reg=0.05,
pick_ori='max-power', weight_norm='nai',
reduce_rank=True)
t0 = time.time()
stc = apply_lcmv_raw(raw_filt, filters)
print(' Time: %s mns' % round((time.time() - t0) / 60, 2))
# Save result in stc files
stc.save(op.join(datapath, subject, 'lcmv-vol'))
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_make_forward_dipole(tmpdir):
"""Test forward-projecting dipoles."""
rng = np.random.RandomState(0)
evoked = read_evokeds(fname_evo)[0]
cov = read_cov(fname_cov)
cov['projs'] = [] # avoid proj warning
dip_c = read_dipole(fname_dip)
# Only use magnetometers for speed!
picks = pick_types(evoked.info, meg='mag', eeg=False)[::8]
evoked.pick_channels([evoked.ch_names[p] for p in picks])
evoked.info.normalize_proj()
info = evoked.info
# Make new Dipole object with n_test_dipoles picked from the dipoles
# in the test dataset.
n_test_dipoles = 3 # minimum 3 needed to get uneven sampling in time
dipsel = np.sort(rng.permutation(np.arange(len(dip_c)))[:n_test_dipoles])
dip_test = Dipole(times=dip_c.times[dipsel],
pos=dip_c.pos[dipsel],
amplitude=dip_c.amplitude[dipsel],
ori=dip_c.ori[dipsel],
gof=dip_c.gof[dipsel])
sphere = make_sphere_model(head_radius=0.1)
# Warning emitted due to uneven sampling in time
with pytest.warns(RuntimeWarning, match='unevenly spaced'):
fwd, stc = make_forward_dipole(dip_test, sphere, info,
trans=fname_trans)
# stc is list of VolSourceEstimate's
assert isinstance(stc, list)
for n_dip in range(n_test_dipoles):
assert isinstance(stc[n_dip], VolSourceEstimate)
# Now simulate evoked responses for each of the test dipoles,
# and fit dipoles to them (sphere model, MEG and EEG)
times, pos, amplitude, ori, gof = [], [], [], [], []
nave = 200 # add a tiny amount of noise to the simulated evokeds
for s in stc:
evo_test = simulate_evoked(fwd, s, info, cov,
nave=nave, random_state=rng)
# evo_test.add_proj(make_eeg_average_ref_proj(evo_test.info))
dfit, resid = fit_dipole(evo_test, cov, sphere, None)
times += dfit.times.tolist()
pos += dfit.pos.tolist()
amplitude += dfit.amplitude.tolist()
ori += dfit.ori.tolist()
gof += dfit.gof.tolist()
# Create a new Dipole object with the dipole fits
dip_fit = Dipole(times, pos, amplitude, ori, gof)
# check that true (test) dipoles and fits are "close"
# cf. mne/tests/test_dipole.py
diff = dip_test.pos - dip_fit.pos
corr = np.corrcoef(dip_test.pos.ravel(), dip_fit.pos.ravel())[0, 1]
dist = np.sqrt(np.mean(np.sum(diff * diff, axis=1)))
gc_dist = 180 / np.pi * \
np.mean(np.arccos(np.sum(dip_test.ori * dip_fit.ori, axis=1)))
amp_err = np.sqrt(np.mean((dip_test.amplitude - dip_fit.amplitude) ** 2))
# Make sure each coordinate is close to reference
# NB tolerance should be set relative to snr of simulated evoked!
assert_allclose(dip_fit.pos, dip_test.pos, rtol=0, atol=1e-2,
err_msg='position mismatch')
assert dist < 1e-2 # within 1 cm
assert corr > 0.985
assert gc_dist < 20 # less than 20 degrees
assert amp_err < 10e-9 # within 10 nAm
# Make sure rejection works with BEM: one dipole at z=1m
# NB _make_forward.py:_prepare_for_forward will raise a RuntimeError
# if no points are left after min_dist exclusions, hence 2 dips here!
dip_outside = Dipole(times=[0., 0.001],
pos=[[0., 0., 1.0], [0., 0., 0.040]],
amplitude=[100e-9, 100e-9],
ori=[[1., 0., 0.], [1., 0., 0.]], gof=1)
with pytest.raises(ValueError, match='outside the inner skull'):
make_forward_dipole(dip_outside, fname_bem, info, fname_trans)
# if we get this far, can safely assume the code works with BEMs too
# -> use sphere again below for speed
# Now make an evenly sampled set of dipoles, some simultaneous,
# should return a VolSourceEstimate regardless
times = [0., 0., 0., 0.001, 0.001, 0.002]
pos = np.random.rand(6, 3) * 0.020 + \
np.array([0., 0., 0.040])[np.newaxis, :]
amplitude = np.random.rand(6) * 100e-9
ori = np.eye(6, 3) + np.eye(6, 3, -3)
gof = np.arange(len(times)) / len(times) # arbitrary
dip_even_samp = Dipole(times, pos, amplitude, ori, gof)
# I/O round-trip
fname = str(tmpdir.join('test-fwd.fif'))
with pytest.warns(RuntimeWarning, match='free orientation'):
write_forward_solution(fname, fwd)
fwd_read = convert_forward_solution(
read_forward_solution(fname), force_fixed=True)
assert_forward_allclose(fwd, fwd_read, rtol=1e-6)
fwd, stc = make_forward_dipole(dip_even_samp, sphere, info,
trans=fname_trans)
assert isinstance(stc, VolSourceEstimate)
assert_allclose(stc.times, np.arange(0., 0.003, 0.001))
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, 0.08),
bem=None,
mindist=5.0,
exclude=2.0,
sphere_units='m')
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[0][: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[0]])
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)
#
# License: BSD (3-clause)
import os.path as op
import numpy as np
from mne.datasets import phantom_4dbti
import mne
###############################################################################
# Read data and compute a dipole fit at the peak of the evoked response
data_path = phantom_4dbti.data_path()
raw_fname = op.join(data_path, '%d/e,rfhp1.0Hz')
dipoles = list()
sphere = mne.make_sphere_model(r0=(0., 0., 0.), head_radius=0.080)
t0 = 0.07 # peak of the response
pos = np.empty((4, 3))
ori = np.empty((4, 3))
for ii in range(4):
raw = mne.io.read_raw_bti(raw_fname % (ii + 1,),
rename_channels=False, preload=True)
raw.info['bads'] = ['A173', 'A213', 'A232']
events = mne.find_events(raw, 'TRIGGER', mask=4350, mask_type='not_and')
epochs = mne.Epochs(raw, events=events, event_id=8192, tmin=-0.2, tmax=0.4,
preload=True)
evoked = epochs.average()
evoked.plot(time_unit='s')
def test_channel_name_limit(tmpdir, monkeypatch, fname):
"""Test that our remapping works properly."""
#
# raw
#
if fname.endswith('fif'):
raw = read_raw_fif(fname)
raw.pick_channels(raw.ch_names[:3])
ref_names = []
data_names = raw.ch_names
else:
assert fname.endswith('.ds')
raw = read_raw_ctf(fname)
ref_names = [
raw.ch_names[pick]
for pick in pick_types(raw.info, meg=False, ref_meg=True)
]
data_names = raw.ch_names[32:35]
proj = dict(data=np.ones((1, len(data_names))),
col_names=data_names[:2].copy(),
row_names=None,
nrow=1)
proj = Projection(data=proj,
active=False,
desc='test',
kind=0,
explained_var=0.)
raw.add_proj(proj, remove_existing=True)
raw.info.normalize_proj()
raw.pick_channels(data_names + ref_names).crop(0, 2)
long_names = ['123456789abcdefg' + name for name in raw.ch_names]
fname = tmpdir.join('test-raw.fif')
with catch_logging() as log:
raw.save(fname)
log = log.getvalue()
assert 'truncated' not in log
rename = dict(zip(raw.ch_names, long_names))
long_data_names = [rename[name] for name in data_names]
long_proj_names = long_data_names[:2]
raw.rename_channels(rename)
for comp in raw.info['comps']:
for key in ('row_names', 'col_names'):
for name in comp['data'][key]:
assert name in raw.ch_names
if raw.info['comps']:
assert raw.compensation_grade == 0
raw.apply_gradient_compensation(3)
assert raw.compensation_grade == 3
assert len(raw.info['projs']) == 1
assert raw.info['projs'][0]['data']['col_names'] == long_proj_names
raw.info['bads'] = bads = long_data_names[2:3]
good_long_data_names = [
name for name in long_data_names if name not in bads
]
with catch_logging() as log:
raw.save(fname, overwrite=True, verbose=True)
log = log.getvalue()
assert 'truncated to 15' in log
for name in raw.ch_names:
assert len(name) > 15
# first read the full way
with catch_logging() as log:
raw_read = read_raw_fif(fname, verbose=True)
log = log.getvalue()
assert 'Reading extended channel information' in log
for ra in (raw, raw_read):
assert ra.ch_names == long_names
assert raw_read.info['projs'][0]['data']['col_names'] == long_proj_names
del raw_read
# next read as if no longer names could be read
monkeypatch.setattr(meas_info, '_read_extended_ch_info',
lambda x, y, z: None)
with catch_logging() as log:
raw_read = read_raw_fif(fname, verbose=True)
log = log.getvalue()
assert 'extended' not in log
if raw.info['comps']:
assert raw_read.compensation_grade == 3
raw_read.apply_gradient_compensation(0)
assert raw_read.compensation_grade == 0
monkeypatch.setattr( # restore
meas_info, '_read_extended_ch_info', _read_extended_ch_info)
short_proj_names = [
f'{name[:13 - bool(len(ref_names))]}-{len(ref_names) + ni}'
for ni, name in enumerate(long_data_names[:2])
]
assert raw_read.info['projs'][0]['data']['col_names'] == short_proj_names
#
# epochs
#
epochs = Epochs(raw, make_fixed_length_events(raw))
fname = tmpdir.join('test-epo.fif')
epochs.save(fname)
epochs_read = read_epochs(fname)
for ep in (epochs, epochs_read):
assert ep.info['ch_names'] == long_names
assert ep.ch_names == long_names
del raw, epochs_read
# cov
epochs.info['bads'] = []
cov = compute_covariance(epochs, verbose='error')
fname = tmpdir.join('test-cov.fif')
write_cov(fname, cov)
cov_read = read_cov(fname)
for co in (cov, cov_read):
assert co['names'] == long_data_names
assert co['bads'] == []
del cov_read
#
# evoked
#
evoked = epochs.average()
evoked.info['bads'] = bads
assert evoked.nave == 1
fname = tmpdir.join('test-ave.fif')
evoked.save(fname)
evoked_read = read_evokeds(fname)[0]
for ev in (evoked, evoked_read):
assert ev.ch_names == long_names
assert ev.info['bads'] == bads
del evoked_read, epochs
#
# forward
#
with pytest.warns(None): # not enough points for CTF
sphere = make_sphere_model('auto', 'auto', evoked.info)
src = setup_volume_source_space(
pos=dict(rr=[[0, 0, 0.04]], nn=[[0, 1., 0.]]))
fwd = make_forward_solution(evoked.info, None, src, sphere)
fname = tmpdir.join('temp-fwd.fif')
write_forward_solution(fname, fwd)
fwd_read = read_forward_solution(fname)
for fw in (fwd, fwd_read):
assert fw['sol']['row_names'] == long_data_names
assert fw['info']['ch_names'] == long_data_names
assert fw['info']['bads'] == bads
del fwd_read
#
# inv
#
inv = make_inverse_operator(evoked.info, fwd, cov)
fname = tmpdir.join('test-inv.fif')
write_inverse_operator(fname, inv)
inv_read = read_inverse_operator(fname)
for iv in (inv, inv_read):
assert iv['info']['ch_names'] == good_long_data_names
apply_inverse(evoked, inv) # smoke test
def dipolarity(mixing,
inst,
picks,
fname_bem=None,
fname_trans=None,
min_dist=5,
n_jobs=1,
verbose=None):
n_channels = inst.info['nchan']
ch_names = inst.info['ch_names']
cov = mne.Covariance(np.eye(n_channels),
ch_names,
bads=[],
projs=[],
nfree=1)
if fname_bem is None:
head_radius = 0.085
pos = np.array([c['loc'][:3] for c in inst.info['chs']])
pos /= np.sqrt(np.sum(pos**2, axis=1))[:, None]
pos *= head_radius
kind = "eeglab"
selection = np.arange(n_channels)
montage = mne.channels.Montage(pos, ch_names, kind, selection)
inst.set_montage(montage)
inst.set_channel_types({'LEYE': 'eog', 'REYE': 'eog'})
fname_bem =\
mne.make_sphere_model(r0=(0.0, 0.0, 0.0),
head_radius=head_radius,
relative_radii=[0.8353, 0.847, 0.93, 1],
sigmas=(0.33, 1.0, 0.0042, 0.33))
picks = mne.pick_types(inst.info, eeg=True, eog=False)
info = mne.pick_info(inst.info, sel=picks)
evoked = mne.EvokedArray(mixing, info, tmin=0, comment='ICA components')
info['projs'] = [] # get rid of SSP projections
if 'eeg' in evoked:
evoked = evoked.copy()
avg_proj = mne.io.make_eeg_average_ref_proj(evoked.info)
evoked.add_proj([avg_proj])
evoked.apply_proj()
dip, residual = mne.fit_dipole(evoked,
cov,
fname_bem,
fname_trans,
min_dist=min_dist,
verbose=verbose,
n_jobs=n_jobs)
gof = (1. -
np.sum(residual.data**2, axis=0) / np.sum(evoked.data**2, axis=0))
gof = 100. * gof # Scale the gof between 0 and 100
# if some gof is NaN, raise an Error
if np.sum(np.isnan(gof)) > 0:
raise ValueError('ERROR!, some gof are NaN. This usually happens '
'because some dipoles position resulting to be too '
'close to the inner sphere. To solve this issue, '
'consider using a different value for the min_dist '
'parameter.')
# Do not sort the columns of A, neither the gof, this way is easier to
# mantain the one-to-one correspondence between the columns of A and the
# the measures associated to them (gof, depth, radiality, etc)
# idx_sort_desc = np.argsort(gof)[::-1]
# evoked.data = evoked.data[:, idx_sort_desc]
# gof = gof[idx_sort_desc]
return gof, dip, evoked
# Uncomment the following line to align the data yourself.
# mne.gui.coregistration(subject='sample', subjects_dir=subjects_dir)
###############################################################################
# .. _plot_source_alignment_without_mri:
#
# Alignment without MRI
# ---------------------
# The surface alignments above are possible if you have the surfaces available
# from Freesurfer. :func:`mne.viz.plot_alignment` automatically searches for
# the correct surfaces from the provided ``subjects_dir``. Another option is
# to use a :ref:`spherical conductor model <ch_forward_spherical_model>`. It is
# passed through ``bem`` parameter.
sphere = mne.make_sphere_model(info=raw.info, r0='auto', head_radius='auto')
src = mne.setup_volume_source_space(sphere=sphere, pos=10.)
mne.viz.plot_alignment(raw.info,
eeg='projected',
bem=sphere,
src=src,
dig=True,
surfaces=['brain', 'outer_skin'],
coord_frame='meg',
show_axes=True)
###############################################################################
# It is also possible to use :func:`mne.gui.coregistration`
# to warp a subject (usually ``fsaverage``) to subject digitization data, see
# `these slides
# <https://www.slideshare.net/mne-python/mnepython-scale-mri>`_.
'{}_ann_MEGartif_flt.txt'.format(fname_noext)))
if len(anns_MEG_artif_flt) > 0:
print('Artif found in filtered {}, maxlen {:.3f} totlen {:.3f}'.
format(anns_MEG_artif_flt,
np.max(anns_MEG_artif_flt.duration),
np.sum(anns_MEG_artif_flt.duration)))
else:
print('Artif found in filtered {} is NONE'.format(
anns_MEG_artif_flt))
if not do_removeMEG and not do_ICA_only:
mod_info, infos = upre.readInfo(fname_noext, f)
radius, origin, _ = mne.bem.fit_sphere_to_headshape(
mod_info, dig_kinds=('cardinal', 'hpi'))
sphere = mne.make_sphere_model(info=mod_info,
r0=origin,
head_radius=radius)
src = mne.setup_volume_source_space(sphere=sphere, pos=10.)
if do_plot_helmet:
import mayavi
mne.viz.plot_alignment(mod_info,
eeg='projected',
bem=sphere,
src=src,
dig=True,
surfaces=['brain', 'outer_skin'],
coord_frame='meg',
show_axes=True)
mayavi.mlab.savefig(
os.path.join(dir_fig,
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]
sphere_norad = make_sphere_model('auto', None, raw.info)
raw_meg = raw.copy().pick_types()
raw_sim = simulate_raw(raw_meg.info, stc, trans, src, sphere_norad,
head_pos=head_pos_sim)
# 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
# make sure it works with EEG-only and MEG-only
raw_sim_meg = simulate_raw(
raw.copy().pick_types(meg=True, eeg=False).info,
stc, trans, src, sphere)
raw_sim_eeg = simulate_raw(
raw.copy().pick_types(meg=False, eeg=True).info,
stc, trans, src, sphere)
raw_sim_meeg = simulate_raw(
raw.copy().pick_types(meg=True, eeg=True).info,
stc, trans, src, sphere)
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)
raw_sim = simulate_raw(raw_crop.info, stc, trans, src, sphere)
with catch_logging() as log:
raw_sim_2 = simulate_raw(raw_crop.info, stc, trans, src, sphere,
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
raw_sim = simulate_raw(raw.info, stc, trans, src, sphere,
head_pos=head_pos_sim, interp='linear')
raw_sim_hann = simulate_raw(raw.info, stc, trans, src, sphere,
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_dipole_fitting_fixed(tmpdir):
"""Test dipole fitting with a fixed position."""
tpeak = 0.073
sphere = make_sphere_model(head_radius=0.1)
evoked = read_evokeds(fname_evo, baseline=(None, 0))[0]
evoked.pick_types(meg=True)
t_idx = np.argmin(np.abs(tpeak - evoked.times))
evoked_crop = evoked.copy().crop(tpeak, tpeak)
assert len(evoked_crop.times) == 1
cov = read_cov(fname_cov)
dip_seq, resid = fit_dipole(evoked_crop, cov, sphere)
assert isinstance(dip_seq, Dipole)
assert isinstance(resid, Evoked)
assert len(dip_seq.times) == 1
pos, ori, gof = dip_seq.pos[0], dip_seq.ori[0], dip_seq.gof[0]
amp = dip_seq.amplitude[0]
# Fix position, allow orientation to change
dip_free, resid_free = fit_dipole(evoked, cov, sphere, pos=pos)
assert isinstance(dip_free, Dipole)
assert isinstance(resid_free, Evoked)
assert_allclose(dip_free.times, evoked.times)
assert_allclose(np.tile(pos[np.newaxis], (len(evoked.times), 1)),
dip_free.pos)
assert_allclose(ori, dip_free.ori[t_idx]) # should find same ori
assert (np.dot(dip_free.ori, ori).mean() < 0.9) # but few the same
assert_allclose(gof, dip_free.gof[t_idx]) # ... same gof
assert_allclose(amp, dip_free.amplitude[t_idx]) # and same amp
assert_allclose(resid.data, resid_free.data[:, [t_idx]])
# Fix position and orientation
dip_fixed, resid_fixed = fit_dipole(evoked, cov, sphere, pos=pos, ori=ori)
assert (isinstance(dip_fixed, DipoleFixed))
assert_allclose(dip_fixed.times, evoked.times)
assert_allclose(dip_fixed.info['chs'][0]['loc'][:3], pos)
assert_allclose(dip_fixed.info['chs'][0]['loc'][3:6], ori)
assert_allclose(dip_fixed.data[1, t_idx], gof)
assert_allclose(resid.data, resid_fixed.data[:, [t_idx]])
_check_roundtrip_fixed(dip_fixed, tmpdir)
# bad resetting
evoked.info['bads'] = [evoked.ch_names[3]]
dip_fixed, resid_fixed = fit_dipole(evoked, cov, sphere, pos=pos, ori=ori)
# Degenerate conditions
evoked_nan = evoked.copy().crop(0, 0)
evoked_nan.data[0, 0] = None
pytest.raises(ValueError, fit_dipole, evoked_nan, cov, sphere)
pytest.raises(ValueError, fit_dipole, evoked, cov, sphere, ori=[1, 0, 0])
pytest.raises(ValueError,
fit_dipole,
evoked,
cov,
sphere,
pos=[0, 0, 0],
ori=[2, 0, 0])
pytest.raises(ValueError, fit_dipole, evoked, cov, sphere, pos=[0.1, 0, 0])
# copying
dip_fixed_2 = dip_fixed.copy()
dip_fixed_2.data[:] = 0.
assert not np.isclose(dip_fixed.data, 0., atol=1e-20).any()
# plotting
plt.close('all')
dip_fixed.plot()
plt.close('all')
orig_times = np.array(dip_fixed.times)
shift_times = dip_fixed.shift_time(1.).times
assert_allclose(shift_times, orig_times + 1)
def test_plot_alignment(tmpdir):
"""Test plotting of -trans.fif files and MEG sensor layouts."""
# generate fiducials file for testing
tempdir = str(tmpdir)
fiducials_path = op.join(tempdir, 'fiducials.fif')
fid = [{'coord_frame': 5, 'ident': 1, 'kind': 1,
'r': [-0.08061612, -0.02908875, -0.04131077]},
{'coord_frame': 5, 'ident': 2, 'kind': 1,
'r': [0.00146763, 0.08506715, -0.03483611]},
{'coord_frame': 5, 'ident': 3, 'kind': 1,
'r': [0.08436285, -0.02850276, -0.04127743]}]
write_dig(fiducials_path, fid, 5)
mlab = _import_mlab()
evoked = read_evokeds(evoked_fname)[0]
sample_src = read_source_spaces(src_fname)
bti = read_raw_bti(pdf_fname, config_fname, hs_fname, convert=True,
preload=False).info
infos = dict(
Neuromag=evoked.info,
CTF=read_raw_ctf(ctf_fname).info,
BTi=bti,
KIT=read_raw_kit(sqd_fname).info,
)
for system, info in infos.items():
meg = ['helmet', 'sensors']
if system == 'KIT':
meg.append('ref')
plot_alignment(info, trans_fname, subject='sample',
subjects_dir=subjects_dir, meg=meg)
mlab.close(all=True)
# KIT ref sensor coil def is defined
mlab.close(all=True)
info = infos['Neuromag']
pytest.raises(TypeError, plot_alignment, 'foo', trans_fname,
subject='sample', subjects_dir=subjects_dir)
pytest.raises(TypeError, plot_alignment, info, trans_fname,
subject='sample', subjects_dir=subjects_dir, src='foo')
pytest.raises(ValueError, plot_alignment, info, trans_fname,
subject='fsaverage', subjects_dir=subjects_dir,
src=sample_src)
sample_src.plot(subjects_dir=subjects_dir, head=True, skull=True,
brain='white')
mlab.close(all=True)
# no-head version
mlab.close(all=True)
# all coord frames
pytest.raises(ValueError, plot_alignment, info)
plot_alignment(info, surfaces=[])
for coord_frame in ('meg', 'head', 'mri'):
plot_alignment(info, meg=['helmet', 'sensors'], dig=True,
coord_frame=coord_frame, trans=trans_fname,
subject='sample', mri_fiducials=fiducials_path,
subjects_dir=subjects_dir, src=sample_src)
mlab.close(all=True)
# EEG only with strange options
evoked_eeg_ecog_seeg = evoked.copy().pick_types(meg=False, eeg=True)
evoked_eeg_ecog_seeg.info['projs'] = [] # "remove" avg proj
evoked_eeg_ecog_seeg.set_channel_types({'EEG 001': 'ecog',
'EEG 002': 'seeg'})
with pytest.warns(RuntimeWarning, match='Cannot plot MEG'):
plot_alignment(evoked_eeg_ecog_seeg.info, subject='sample',
trans=trans_fname, subjects_dir=subjects_dir,
surfaces=['white', 'outer_skin', 'outer_skull'],
meg=['helmet', 'sensors'],
eeg=['original', 'projected'], ecog=True, seeg=True)
mlab.close(all=True)
sphere = make_sphere_model(info=evoked.info, r0='auto', head_radius='auto')
bem_sol = read_bem_solution(op.join(subjects_dir, 'sample', 'bem',
'sample-1280-1280-1280-bem-sol.fif'))
bem_surfs = read_bem_surfaces(op.join(subjects_dir, 'sample', 'bem',
'sample-1280-1280-1280-bem.fif'))
sample_src[0]['coord_frame'] = 4 # hack for coverage
plot_alignment(info, subject='sample', eeg='projected',
meg='helmet', bem=sphere, dig=True,
surfaces=['brain', 'inner_skull', 'outer_skull',
'outer_skin'])
plot_alignment(info, trans_fname, subject='sample', meg='helmet',
subjects_dir=subjects_dir, eeg='projected', bem=sphere,
surfaces=['head', 'brain'], src=sample_src)
assert all(surf['coord_frame'] == FIFF.FIFFV_COORD_MRI
for surf in bem_sol['surfs'])
plot_alignment(info, trans_fname, subject='sample', meg=[],
subjects_dir=subjects_dir, bem=bem_sol, eeg=True,
surfaces=['head', 'inflated', 'outer_skull', 'inner_skull'])
assert all(surf['coord_frame'] == FIFF.FIFFV_COORD_MRI
for surf in bem_sol['surfs'])
plot_alignment(info, trans_fname, subject='sample',
meg=True, subjects_dir=subjects_dir,
surfaces=['head', 'inner_skull'], bem=bem_surfs)
sphere = make_sphere_model('auto', 'auto', evoked.info)
src = setup_volume_source_space(sphere=sphere)
plot_alignment(info, eeg='projected', meg='helmet', bem=sphere,
src=src, dig=True, surfaces=['brain', 'inner_skull',
'outer_skull', 'outer_skin'])
sphere = make_sphere_model('auto', None, evoked.info) # one layer
plot_alignment(info, trans_fname, subject='sample', meg=False,
coord_frame='mri', subjects_dir=subjects_dir,
surfaces=['brain'], bem=sphere, show_axes=True)
# 3D coil with no defined draw (ConvexHull)
info_cube = pick_info(info, [0])
info['dig'] = None
info_cube['chs'][0]['coil_type'] = 9999
with pytest.raises(RuntimeError, match='coil definition not found'):
plot_alignment(info_cube, meg='sensors', surfaces=())
coil_def_fname = op.join(tempdir, 'temp')
with open(coil_def_fname, 'w') as fid:
fid.write(coil_3d)
with use_coil_def(coil_def_fname):
plot_alignment(info_cube, meg='sensors', surfaces=(), dig=True)
# one layer bem with skull surfaces:
pytest.raises(ValueError, plot_alignment, info=info, trans=trans_fname,
subject='sample', subjects_dir=subjects_dir,
surfaces=['brain', 'head', 'inner_skull'], bem=sphere)
# wrong eeg value:
pytest.raises(ValueError, plot_alignment, info=info, trans=trans_fname,
subject='sample', subjects_dir=subjects_dir, eeg='foo')
# wrong meg value:
pytest.raises(ValueError, plot_alignment, info=info, trans=trans_fname,
subject='sample', subjects_dir=subjects_dir, meg='bar')
# multiple brain surfaces:
pytest.raises(ValueError, plot_alignment, info=info, trans=trans_fname,
subject='sample', subjects_dir=subjects_dir,
surfaces=['white', 'pial'])
pytest.raises(TypeError, plot_alignment, info=info, trans=trans_fname,
subject='sample', subjects_dir=subjects_dir,
surfaces=[1])
pytest.raises(ValueError, plot_alignment, info=info, trans=trans_fname,
subject='sample', subjects_dir=subjects_dir,
surfaces=['foo'])
mlab.close(all=True)