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from itertools import product
import os
import os.path as op
from pathlib import Path
import pytest
import numpy as np
from numpy.testing import assert_allclose, assert_array_equal
from numpy.testing import assert_array_less
from mne.bem import read_bem_surfaces, make_bem_solution
from mne.channels import make_standard_montage
from mne.datasets import testing
from mne.io import read_raw_fif, read_raw_kit, read_raw_bti, read_info
from mne.io.constants import FIFF
from mne import (read_forward_solution, write_forward_solution,
make_forward_solution, convert_forward_solution,
setup_volume_source_space, read_source_spaces, create_info,
make_sphere_model, pick_types_forward, pick_info, pick_types,
read_evokeds, read_cov, read_dipole,
get_volume_labels_from_aseg)
from mne.surface import _get_ico_surface
from mne.transforms import Transform
from mne.utils import (requires_mne, requires_nibabel, run_subprocess,
catch_logging, requires_mne_mark,
requires_openmeeg_mark)
from mne.forward._make_forward import _create_meg_coils, make_forward_dipole
from mne.forward._compute_forward import _magnetic_dipole_field_vec
from mne.forward import Forward, _do_forward_solution, use_coil_def
from mne.dipole import Dipole, fit_dipole
from mne.simulation import simulate_evoked
from mne.source_estimate import VolSourceEstimate
from mne.source_space import (write_source_spaces, _compare_source_spaces,
setup_source_space)
from mne.forward.tests.test_forward import assert_forward_allclose
data_path = testing.data_path(download=False)
fname_meeg = op.join(data_path, 'MEG', 'sample',
'sample_audvis_trunc-meg-eeg-oct-4-fwd.fif')
fname_raw = op.join(op.dirname(__file__), '..', '..', 'io', 'tests', 'data',
'test_raw.fif')
fname_evo = op.join(data_path, 'MEG', 'sample', 'sample_audvis_trunc-ave.fif')
fname_cov = op.join(data_path, 'MEG', 'sample', 'sample_audvis_trunc-cov.fif')
fname_dip = op.join(data_path, 'MEG', 'sample', 'sample_audvis_trunc_set1.dip')
fname_trans = op.join(data_path, 'MEG', 'sample',
'sample_audvis_trunc-trans.fif')
subjects_dir = os.path.join(data_path, 'subjects')
fname_src = op.join(subjects_dir, 'sample', 'bem', 'sample-oct-4-src.fif')
fname_bem = op.join(subjects_dir, 'sample', 'bem',
'sample-1280-1280-1280-bem-sol.fif')
fname_aseg = op.join(subjects_dir, 'sample', 'mri', 'aseg.mgz')
fname_bem_meg = op.join(subjects_dir, 'sample', 'bem',
'sample-1280-bem-sol.fif')
io_path = Path(__file__).parent.parent.parent / 'io'
bti_dir = io_path / 'bti' / 'tests' / 'data'
kit_dir = io_path / 'kit' / 'tests' / 'data'
trans_path = op.join(kit_dir, 'trans-sample.fif')
fname_ctf_raw = io_path / 'tests' / 'data' / 'test_ctf_comp_raw.fif'
def _col_corrs(a, b):
"""Compute correlation between paired columns, being careful about 0."""
a = a - a.mean(0)
b = b - b.mean(0)
num = (a * b).mean(0)
a_std = np.sqrt((a * a).mean(0))
b_std = np.sqrt((b * b).mean(0))
all_zero = (a_std == 0) & (b_std == 0)
num[all_zero] = 1.
a_std[all_zero] = 1.
b_std[all_zero] = 1.
return num / (a_std * b_std)
def _rdm(a, b):
"""Compute the ratio of norms, being careful about 0."""
a_norm = np.linalg.norm(a, axis=0)
b_norm = np.linalg.norm(b, axis=0)
all_zero = (a_norm == 0) & (b_norm == 0)
a_norm[all_zero] = 1.
b_norm[all_zero] = 1.
return a_norm / b_norm
def _compare_forwards(fwd, fwd_py, n_sensors, n_src,
meg_rtol=1e-4, meg_atol=1e-9,
meg_corr_tol=0.99, meg_rdm_tol=0.01,
eeg_rtol=1e-3, eeg_atol=1e-3,
eeg_corr_tol=0.99, eeg_rdm_tol=0.01):
"""Test forwards."""
# check source spaces
assert len(fwd['src']) == len(fwd_py['src'])
_compare_source_spaces(fwd['src'], fwd_py['src'], mode='approx')
for surf_ori, force_fixed in product([False, True], [False, True]):
# use copy here to leave our originals unmodified
fwd = convert_forward_solution(fwd, surf_ori, force_fixed, copy=True,
use_cps=True)
fwd_py = convert_forward_solution(fwd_py, surf_ori, force_fixed,
copy=True, use_cps=True)
check_src = n_src // 3 if force_fixed else n_src
for key in ('nchan', 'source_rr', 'source_ori',
'surf_ori', 'coord_frame', 'nsource'):
assert_allclose(fwd_py[key], fwd[key], rtol=1e-4, atol=1e-7,
err_msg=key)
# In surf_ori=True only Z matters for source_nn
if surf_ori and not force_fixed:
ori_sl = slice(2, None, 3)
else:
ori_sl = slice(None)
assert_allclose(fwd_py['source_nn'][ori_sl], fwd['source_nn'][ori_sl],
rtol=1e-4, atol=1e-6)
assert_allclose(fwd_py['mri_head_t']['trans'],
fwd['mri_head_t']['trans'], rtol=1e-5, atol=1e-8)
assert fwd_py['sol']['data'].shape == (n_sensors, check_src)
assert len(fwd['sol']['row_names']) == n_sensors
assert len(fwd_py['sol']['row_names']) == n_sensors
# check MEG
fwd_meg = fwd['sol']['data'][:306, ori_sl]
fwd_meg_py = fwd_py['sol']['data'][:306, ori_sl]
assert_allclose(fwd_meg, fwd_meg_py, rtol=meg_rtol, atol=meg_atol,
err_msg='MEG mismatch')
meg_corrs = _col_corrs(fwd_meg, fwd_meg_py)
assert_array_less(meg_corr_tol, meg_corrs, err_msg='MEG corr/MAG')
meg_rdm = _rdm(fwd_meg, fwd_meg_py)
assert_allclose(meg_rdm, 1, atol=meg_rdm_tol, err_msg='MEG RDM')
# check EEG
if fwd['sol']['data'].shape[0] > 306:
fwd_eeg = fwd['sol']['data'][306:, ori_sl]
fwd_eeg_py = fwd['sol']['data'][306:, ori_sl]
assert_allclose(fwd_eeg, fwd_eeg_py, rtol=eeg_rtol, atol=eeg_atol,
err_msg='EEG mismatch')
# To test so-called MAG we use correlation (related to cosine
# similarity) and also RDM to test the amplitude mismatch
eeg_corrs = _col_corrs(fwd_eeg, fwd_eeg_py)
assert_array_less(eeg_corr_tol, eeg_corrs, err_msg='EEG corr/MAG')
eeg_rdm = _rdm(fwd_eeg, fwd_eeg_py)
assert_allclose(eeg_rdm, 1, atol=eeg_rdm_tol, err_msg='EEG RDM')
def test_magnetic_dipole():
"""Test basic magnetic dipole forward calculation."""
info = read_info(fname_raw)
picks = pick_types(info, meg=True, eeg=False, exclude=[])
info = pick_info(info, picks[:12])
coils = _create_meg_coils(info['chs'], 'normal', None)
# magnetic dipole far (meters!) from device origin
r0 = np.array([0., 13., -6.])
for ch, coil in zip(info['chs'], coils):
rr = (ch['loc'][:3] + r0) / 2. # get halfway closer
far_fwd = _magnetic_dipole_field_vec(r0[np.newaxis, :], [coil])
near_fwd = _magnetic_dipole_field_vec(rr[np.newaxis, :], [coil])
ratio = 8. if ch['ch_name'][-1] == '1' else 16. # grad vs mag
assert_allclose(np.median(near_fwd / far_fwd), ratio, atol=1e-1)
# degenerate case
r0 = coils[0]['rmag'][[0]]
with pytest.raises(RuntimeError, match='Coil too close'):
_magnetic_dipole_field_vec(r0, coils[:1])
with pytest.warns(RuntimeWarning, match='Coil too close'):
fwd = _magnetic_dipole_field_vec(r0, coils[:1], too_close='warning')
assert not np.isfinite(fwd).any()
with np.errstate(invalid='ignore'):
fwd = _magnetic_dipole_field_vec(r0, coils[:1], too_close='info')
assert not np.isfinite(fwd).any()
@pytest.mark.slowtest # slow-ish on Travis OSX
@requires_mne
def test_make_forward_solution_kit(tmp_path, fname_src_small):
"""Test making fwd using KIT (compensated) files."""
sqd_path = op.join(kit_dir, 'test.sqd')
mrk_path = op.join(kit_dir, 'test_mrk.sqd')
elp_path = op.join(kit_dir, 'test_elp.txt')
hsp_path = op.join(kit_dir, 'test_hsp.txt')
fname_kit_raw = op.join(kit_dir, 'test_bin_raw.fif')
# first use mne-C: convert file, make forward solution
fwd = _do_forward_solution('sample', fname_kit_raw, src=fname_src_small,
bem=fname_bem_meg, mri=trans_path,
eeg=False, meg=True, subjects_dir=subjects_dir)
assert (isinstance(fwd, Forward))
# now let's use python with the same raw file
src = read_source_spaces(fname_src_small)
fwd_py = make_forward_solution(fname_kit_raw, trans_path, src,
fname_bem_meg, eeg=False, meg=True)
_compare_forwards(fwd, fwd_py, 157, n_src_small)
assert (isinstance(fwd_py, Forward))
# now let's use mne-python all the way
raw_py = read_raw_kit(sqd_path, mrk_path, elp_path, hsp_path)
# without ignore_ref=True, this should throw an error:
with pytest.raises(NotImplementedError, match='Cannot.*KIT reference'):
make_forward_solution(raw_py.info, src=src, eeg=False, meg=True,
bem=fname_bem_meg, trans=trans_path)
# check that asking for eeg channels (even if they don't exist) is handled
meg_only_info = pick_info(raw_py.info, pick_types(raw_py.info, meg=True,
eeg=False))
fwd_py = make_forward_solution(meg_only_info, src=src, meg=True, eeg=True,
bem=fname_bem_meg, trans=trans_path,
ignore_ref=True)
_compare_forwards(fwd, fwd_py, 157, n_src_small,
meg_rtol=1e-3, meg_atol=1e-7)
@requires_mne
def test_make_forward_solution_bti(fname_src_small):
"""Test BTI end-to-end versus C."""
bti_pdf = bti_dir / 'test_pdf_linux'
bti_config = bti_dir / 'test_config_linux'
bti_hs = bti_dir / 'test_hs_linux'
fname_bti_raw = bti_dir / 'exported4D_linux_raw.fif'
raw_py = read_raw_bti(bti_pdf, bti_config, bti_hs, preload=False)
src = read_source_spaces(fname_src_small)
fwd_py = make_forward_solution(raw_py.info, src=src, eeg=False, meg=True,
bem=fname_bem_meg, trans=trans_path)
fwd = _do_forward_solution('sample', fname_bti_raw, src=fname_src_small,
bem=fname_bem_meg, mri=trans_path,
eeg=False, meg=True, subjects_dir=subjects_dir)
_compare_forwards(fwd, fwd_py, 248, n_src_small)
@pytest.mark.parametrize('other', [
pytest.param('MNE-C', marks=requires_mne_mark()),
pytest.param('openmeeg', marks=requires_openmeeg_mark()),
])
def test_make_forward_solution_ctf(tmp_path, fname_src_small, other):
"""Test CTF w/compensation against MNE-C or OpenMEEG."""
src = read_source_spaces(fname_src_small)
raw = read_raw_fif(fname_ctf_raw)
assert raw.compensation_grade == 3
if other == 'openmeeg':
mindist = 20.
n_src_want = 51
else:
assert other == 'MNE-C'
mindist = 0.
n_src_want = n_src_small
assert n_src_want == 108
mindist = 20. if other == 'openmeeg' else 0.
fwd_py = make_forward_solution(
fname_ctf_raw, fname_trans, src, fname_bem_meg, eeg=False,
mindist=mindist, verbose=True)
if other == 'openmeeg':
# TODO: This should be a 1-layer, but it's broken
# (some correlations become negative!)...
bem_surfaces = read_bem_surfaces(fname_bem) # fname_bem_meg
bem = make_bem_solution(bem_surfaces, solver='openmeeg')
# TODO: These tolerances are bad
tol_kwargs = dict(meg_atol=1, meg_corr_tol=0.65, meg_rdm_tol=0.6)
fwd = make_forward_solution(
fname_ctf_raw, fname_trans, src, bem, eeg=False, mindist=mindist,
verbose=True)
else:
assert other == 'MNE-C'
bem = None
tol_kwargs = dict()
fwd = _do_forward_solution(
'sample', fname_ctf_raw, mri=fname_trans, src=fname_src_small,
bem=fname_bem_meg, eeg=False, meg=True, subjects_dir=subjects_dir,
mindist=mindist)
_compare_forwards(fwd, fwd_py, 274, n_src_want, **tol_kwargs)
# CTF with compensation changed in python
ctf_raw = read_raw_fif(fname_ctf_raw)
ctf_raw.info['bads'] = ['MRO24-2908'] # test that it works with some bads
ctf_raw.apply_gradient_compensation(2)
fwd_py = make_forward_solution(
ctf_raw.info, fname_trans, src, fname_bem_meg, eeg=False, meg=True,
mindist=mindist)
if other == 'openmeeg':
assert bem is not None
fwd = make_forward_solution(
ctf_raw.info, fname_trans, src, bem, eeg=False, mindist=mindist,
verbose=True)
else:
fwd = _do_forward_solution(
'sample', ctf_raw, mri=fname_trans, src=fname_src_small,
bem=fname_bem_meg, eeg=False, meg=True, subjects_dir=subjects_dir,
mindist=mindist)
_compare_forwards(fwd, fwd_py, 274, n_src_want, **tol_kwargs)
fname_temp = tmp_path / 'test-ctf-fwd.fif'
write_forward_solution(fname_temp, fwd_py)
fwd_py2 = read_forward_solution(fname_temp)
_compare_forwards(fwd_py, fwd_py2, 274, n_src_want, **tol_kwargs)
repr(fwd_py)
@testing.requires_testing_data
def test_make_forward_solution_basic():
"""Test making M-EEG forward solution from python."""
with catch_logging() as log:
# make sure everything can be path-like (gh #10872)
fwd_py = make_forward_solution(
Path(fname_raw), Path(fname_trans), Path(fname_src),
Path(fname_bem), mindist=5., verbose=True)
log = log.getvalue()
assert 'Total 258/258 points inside the surface' in log
assert (isinstance(fwd_py, Forward))
fwd = read_forward_solution(fname_meeg)
assert (isinstance(fwd, Forward))
_compare_forwards(fwd, fwd_py, 366, 1494, meg_rtol=1e-3)
# Homogeneous model
with pytest.raises(RuntimeError, match='homogeneous.*1-layer.*EEG'):
make_forward_solution(fname_raw, fname_trans, fname_src,
fname_bem_meg)
@requires_openmeeg_mark()
@pytest.mark.parametrize("n_layers", [
3,
pytest.param(1, marks=pytest.mark.xfail(raises=RuntimeError)),
])
@testing.requires_testing_data
def test_make_forward_solution_openmeeg(n_layers):
"""Test making M-EEG forward solution from OpenMEEG."""
solver = "openmeeg"
bem_surfaces = read_bem_surfaces(fname_bem)
raw = read_raw_fif(fname_raw)
n_sensors = 366
ch_types = ['eeg', 'meg']
if n_layers == 1:
ch_types = ['meg']
bem_surfaces = bem_surfaces[-1:]
assert bem_surfaces[0]['id'] == FIFF.FIFFV_BEM_SURF_ID_BRAIN
n_sensors = 306
raw.pick(ch_types)
n_sources_kept = 501 // 3
fwds = dict()
for solver in ["openmeeg", "mne"]:
bem = make_bem_solution(bem_surfaces, solver=solver)
assert bem['solver'] == solver
with catch_logging() as log:
# make sure everything can be path-like (gh #10872)
fwd = make_forward_solution(
raw.info, Path(fname_trans), Path(fname_src),
bem, mindist=20., verbose=True)
log = log.getvalue()
assert 'Total 258/258 points inside the surface' in log
assert (isinstance(fwd, Forward))
fwds[solver] = fwd
del fwd
_compare_forwards(fwds["openmeeg"],
fwds["mne"], n_sensors, n_sources_kept * 3,
meg_atol=1, eeg_atol=100,
meg_corr_tol=0.98, eeg_corr_tol=0.98,
meg_rdm_tol=0.1, eeg_rdm_tol=0.2)
def test_make_forward_solution_discrete(tmp_path, small_surf_src):
"""Test making and converting a forward solution with discrete src."""
# smoke test for depth weighting and discrete source spaces
src = small_surf_src
src = src + setup_volume_source_space(
pos=dict(rr=src[0]['rr'][src[0]['vertno'][:3]].copy(),
nn=src[0]['nn'][src[0]['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)
n_src_small = 108 # this is the resulting # of verts in fwd
@pytest.fixture(scope='module', params=[testing._pytest_param()])
def small_surf_src():
"""Create a small surface source space."""
src = setup_source_space('sample', 'oct2', subjects_dir=subjects_dir,
add_dist=False)
assert sum(s['nuse'] for s in src) * 3 == n_src_small
return src
@pytest.fixture()
def fname_src_small(tmp_path, small_surf_src):
"""Create a small source space."""
fname_src_small = tmp_path / 'sample-oct-2-src.fif'
write_source_spaces(fname_src_small, small_surf_src)
return fname_src_small
@requires_mne
@pytest.mark.timeout(90) # can take longer than 60 sec on Travis
def test_make_forward_solution_sphere(tmp_path, fname_src_small):
"""Test making a forward solution with a sphere model."""
out_name = tmp_path / '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)
src = read_source_spaces(fname_src_small)
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)
@pytest.mark.slowtest
@testing.requires_testing_data
@requires_nibabel()
def test_forward_mixed_source_space(tmp_path):
"""Test making the forward solution for a mixed source space."""
# get the surface source space
rng = np.random.RandomState(0)
surf = read_source_spaces(fname_src)
# setup two volume source spaces
label_names = get_volume_labels_from_aseg(fname_aseg)
vol_labels = rng.choice(label_names, 2)
with pytest.warns(RuntimeWarning, match='Found no usable.*CC_Mid_Ant.*'):
vol1 = setup_volume_source_space('sample', pos=20., mri=fname_aseg,
volume_label=vol_labels[0],
add_interpolator=False)
vol2 = setup_volume_source_space('sample', pos=20., mri=fname_aseg,
volume_label=vol_labels[1],
add_interpolator=False)
# merge surfaces and volume
src = surf + vol1 + vol2
# calculate forward solution
fwd = make_forward_solution(fname_raw, fname_trans, src, fname_bem)
assert (repr(fwd))
# extract source spaces
src_from_fwd = fwd['src']
# get the coordinate frame of each source space
coord_frames = np.array([s['coord_frame'] for s in src_from_fwd])
# assert that all source spaces are in head coordinates
assert ((coord_frames == FIFF.FIFFV_COORD_HEAD).all())
# run tests for SourceSpaces.export_volume
fname_img = tmp_path / 'temp-image.mgz'
# head coordinates and mri_resolution, but trans file
with pytest.raises(ValueError, match='trans containing mri to head'):
src_from_fwd.export_volume(fname_img, mri_resolution=True, trans=None)
# head coordinates and mri_resolution, but wrong trans file
vox_mri_t = vol1[0]['vox_mri_t']
with pytest.raises(ValueError, match='head<->mri, got mri_voxel->mri'):
src_from_fwd.export_volume(fname_img, mri_resolution=True,
trans=vox_mri_t)
@pytest.mark.slowtest
@testing.requires_testing_data
def test_make_forward_dipole(tmp_path):
"""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 = 400 # 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(tmp_path / '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))
# Test passing a list of Dipoles instead of a single Dipole object
fwd2, stc2 = make_forward_dipole([dip_even_samp[0], dip_even_samp[1:]],
sphere, info, trans=fname_trans)
assert_array_equal(fwd['sol']['data'], fwd2['sol']['data'])
assert_array_equal(stc.data, stc2.data)
@testing.requires_testing_data
def test_make_forward_no_meg(tmp_path):
"""Test that we can make and I/O forward solution with no MEG channels."""
pos = dict(rr=[[0.05, 0, 0]], nn=[[0, 0, 1.]])
src = setup_volume_source_space(pos=pos)
bem = make_sphere_model()
trans = None
montage = make_standard_montage('standard_1020')
info = create_info(['Cz'], 1000., 'eeg').set_montage(montage)
fwd = make_forward_solution(info, trans, src, bem)
fname = tmp_path / 'test-fwd.fif'
write_forward_solution(fname, fwd)
fwd_read = read_forward_solution(fname)
assert_allclose(fwd['sol']['data'], fwd_read['sol']['data'])
def test_use_coil_def(tmp_path):
"""Test use_coil_def."""
info = create_info(1, 1000., 'mag')
info['chs'][0]['coil_type'] = 9999
info['chs'][0]['loc'][:] = [0, 0, 0.02, 1, 0, 0, 0, 1, 0, 0, 0, 1]
sphere = make_sphere_model((0., 0., 0.), 0.01)
src = setup_volume_source_space(pos=5, sphere=sphere)
trans = Transform('head', 'mri', None)
with pytest.raises(RuntimeError, match='coil definition not found'):
make_forward_solution(info, trans, src, sphere)
coil_fname = tmp_path / 'coil_def.dat'
with open(coil_fname, 'w') as fid:
fid.write("""# custom cube coil def
1 9999 2 8 3e-03 0.000e+00 "Test"
0.1250 -0.750e-03 -0.750e-03 -0.750e-03 0.000 0.000""")
with pytest.raises(RuntimeError, match='Could not interpret'):
with use_coil_def(coil_fname):
make_forward_solution(info, trans, src, sphere)
with open(coil_fname, 'w') as fid:
fid.write("""# custom cube coil def
1 9999 2 8 3e-03 0.000e+00 "Test"
0.1250 -0.750e-03 -0.750e-03 -0.750e-03 0.000 0.000 1.000
0.1250 -0.750e-03 0.750e-03 -0.750e-03 0.000 0.000 1.000
0.1250 0.750e-03 -0.750e-03 -0.750e-03 0.000 0.000 1.000
0.1250 0.750e-03 0.750e-03 -0.750e-03 0.000 0.000 1.000
0.1250 -0.750e-03 -0.750e-03 0.750e-03 0.000 0.000 1.000
0.1250 -0.750e-03 0.750e-03 0.750e-03 0.000 0.000 1.000
0.1250 0.750e-03 -0.750e-03 0.750e-03 0.000 0.000 1.000
0.1250 0.750e-03 0.750e-03 0.750e-03 0.000 0.000 1.000""")
with use_coil_def(coil_fname):
make_forward_solution(info, trans, src, sphere)
@pytest.mark.slowtest
@testing.requires_testing_data
def test_sensors_inside_bem():
"""Test that sensors inside the BEM are problematic."""
rr = _get_ico_surface(1)['rr']
rr /= np.linalg.norm(rr, axis=1, keepdims=True)
rr *= 0.1
assert len(rr) == 42
info = create_info(len(rr), 1000., 'mag')
info['dev_head_t'] = Transform('meg', 'head', np.eye(4))
for ii, ch in enumerate(info['chs']):
ch['loc'][:] = np.concatenate((rr[ii], np.eye(3).ravel()))
trans = Transform('head', 'mri', np.eye(4))
trans['trans'][2, 3] = 0.03
sphere_noshell = make_sphere_model((0., 0., 0.), None)
sphere = make_sphere_model((0., 0., 0.), 1.01)
with pytest.raises(RuntimeError, match='.* 15 MEG.*inside the scalp.*'):
make_forward_solution(info, trans, fname_src, fname_bem)
make_forward_solution(info, trans, fname_src, fname_bem_meg) # okay
make_forward_solution(info, trans, fname_src, sphere_noshell) # okay
with pytest.raises(RuntimeError, match='.* 42 MEG.*outermost sphere sh.*'):
make_forward_solution(info, trans, fname_src, sphere)
sphere = make_sphere_model((0., 0., 2.0), 1.01) # weird, but okay
make_forward_solution(info, trans, fname_src, sphere)
for ch in info['chs']:
ch['loc'][:3] *= 0.1
with pytest.raises(RuntimeError, match='.* 42 MEG.*the inner skull.*'):
make_forward_solution(info, trans, fname_src, fname_bem_meg)
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