def test_min_distance_fit_dipole():
"""Test dipole min_dist to inner_skull."""
subject = 'sample'
raw = read_raw_fif(fname_raw, preload=True)
# select eeg data
picks = pick_types(raw.info, meg=False, eeg=True, exclude='bads')
info = pick_info(raw.info, picks)
# Let's use cov = Identity
cov = read_cov(fname_cov)
cov['data'] = np.eye(cov['data'].shape[0])
# Simulated scal map
simulated_scalp_map = np.zeros(picks.shape[0])
simulated_scalp_map[27:34] = 1
simulated_scalp_map = simulated_scalp_map[:, None]
evoked = EvokedArray(simulated_scalp_map, info, tmin=0)
min_dist = 5. # distance in mm
bem = read_bem_solution(fname_bem)
dip, residual = fit_dipole(evoked, cov, bem, fname_trans,
min_dist=min_dist)
assert isinstance(residual, Evoked)
dist = _compute_depth(dip, fname_bem, fname_trans, subject, subjects_dir)
# Constraints are not exact, so bump the minimum slightly
assert (min_dist - 0.1 < (dist[0] * 1000.) < (min_dist + 1.))
pytest.raises(ValueError, fit_dipole, evoked, cov, fname_bem, fname_trans,
-1.)
def test_min_distance_fit_dipole():
"""Test dipole min_dist to inner_skull."""
subject = 'sample'
raw = read_raw_fif(fname_raw, preload=True)
# select eeg data
picks = pick_types(raw.info, meg=False, eeg=True, exclude='bads')
info = pick_info(raw.info, picks)
# Let's use cov = Identity
cov = read_cov(fname_cov)
cov['data'] = np.eye(cov['data'].shape[0])
# Simulated scal map
simulated_scalp_map = np.zeros(picks.shape[0])
simulated_scalp_map[27:34] = 1
simulated_scalp_map = simulated_scalp_map[:, None]
evoked = EvokedArray(simulated_scalp_map, info, tmin=0)
min_dist = 5. # distance in mm
bem = read_bem_solution(fname_bem)
dip, residual = fit_dipole(evoked, cov, bem, fname_trans,
min_dist=min_dist)
dist = _compute_depth(dip, fname_bem, fname_trans, subject, subjects_dir)
# Constraints are not exact, so bump the minimum slightly
assert_true(min_dist - 0.1 < (dist[0] * 1000.) < (min_dist + 1.))
assert_raises(ValueError, fit_dipole, evoked, cov, fname_bem, fname_trans,
-1.)
def _setup_bem(bem, bem_extra, neeg, mri_head_t, verbose=None):
"""Set up a BEM for forward computation, making a copy and modifying."""
logger.info('')
if isinstance(bem, string_types):
logger.info('Setting up the BEM model using %s...\n' % bem_extra)
bem = read_bem_solution(bem)
else:
if not isinstance(bem, ConductorModel):
raise TypeError('bem must be a string or ConductorModel')
bem = bem.copy()
if bem['is_sphere']:
logger.info('Using the sphere model.\n')
if len(bem['layers']) == 0 and neeg > 0:
raise RuntimeError('Spherical model has zero shells, cannot use '
'with EEG data')
if bem['coord_frame'] != FIFF.FIFFV_COORD_HEAD:
raise RuntimeError('Spherical model is not in head coordinates')
else:
if bem['surfs'][0]['coord_frame'] != FIFF.FIFFV_COORD_MRI:
raise RuntimeError(
'BEM is in %s coordinates, should be in MRI' %
(_coord_frame_name(bem['surfs'][0]['coord_frame']), ))
if neeg > 0 and len(bem['surfs']) == 1:
raise RuntimeError('Cannot use a homogeneous model in EEG '
'calculations')
logger.info('Employing the head->MRI coordinate transform with the '
'BEM model.')
# fwd_bem_set_head_mri_t: Set the coordinate transformation
bem['head_mri_t'] = _ensure_trans(mri_head_t, 'head', 'mri')
logger.info('BEM model %s is now set up' % op.split(bem_extra)[1])
logger.info('')
return bem
def _compute_depth(dip, fname_bem, fname_trans, subject, subjects_dir):
"""Compute dipole depth."""
trans = _get_trans(fname_trans)[0]
bem = read_bem_solution(fname_bem)
surf = _bem_find_surface(bem, 'inner_skull')
points = surf['rr']
points = apply_trans(trans['trans'], points)
depth = _compute_nearest(points, dip.pos, return_dists=True)[1][0]
return np.ravel(depth)
def _compute_depth(dip, fname_bem, fname_trans, subject, subjects_dir):
"""Compute dipole depth."""
trans = _get_trans(fname_trans)[0]
bem = read_bem_solution(fname_bem)
surf = _bem_find_surface(bem, 'inner_skull')
points = surf['rr']
points = apply_trans(trans['trans'], points)
depth = _compute_nearest(points, dip.pos, return_dists=True)[1][0]
return np.ravel(depth)
def test_plot_alignment_basic(tmpdir, renderer, mixed_fwd_cov_evoked):
"""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)
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'
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)
renderer.backend._close_all()
# no-head version
renderer.backend._close_all()
# trans required
with pytest.raises(ValueError, match='transformation matrix is required'):
plot_alignment(info, trans=None, src=src_fname)
with pytest.raises(ValueError, match='transformation matrix is required'):
plot_alignment(info, trans=None, mri_fiducials=True)
with pytest.raises(ValueError, match='transformation matrix is required'):
plot_alignment(info, trans=None, surfaces=['brain'])
# 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 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,
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'):
fig = 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
fig = 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()
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, np.arange(6))
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 is required'):
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():
"""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
assert_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 = 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, 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)
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', '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)
# 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'])
mlab.close(all=True)
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._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,
trans_fname,
subject='sample',
subjects_dir=subjects_dir,
meg=meg)
rend = renderer._Renderer(fig=fig)
rend.close()
# KIT ref sensor coil def is defined
renderer._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._close_all()
# no-head version
renderer._close_all()
# all coord frames
pytest.raises(ValueError, plot_alignment, info)
plot_alignment(info, surfaces=[])
for coord_frame in ('meg', 'head', 'mri'):
fig = 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=src_fname)
renderer._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._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._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='eeg must only contain'):
plot_alignment(info=info,
trans=trans_fname,
subject='sample',
subjects_dir=subjects_dir,
eeg='foo')
# wrong meg value:
with pytest.raises(ValueError, match='meg must only contain'):
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')
renderer._close_all()
def test_plot_alignment(tmpdir, backends_3d):
"""Test plotting of -trans.fif files and MEG sensor layouts."""
backend_name = get_3d_backend()
# 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)
if backend_name == 'mayavi':
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)
if backend_name == 'mayavi':
mlab.close(all=True)
# KIT ref sensor coil def is defined
if backend_name == 'mayavi':
mlab.close(all=True)
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')
if backend_name == 'mayavi':
mlab.close(all=True)
# no-head version
if backend_name == 'mayavi':
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=src_fname)
if backend_name == 'mayavi':
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)
if backend_name == 'mayavi':
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
# 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)
if backend_name == '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:
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'])
if backend_name == 'mayavi':
mlab.close(all=True)
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)
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
assert_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 = 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, 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)
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', '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)
# 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'])
mlab.close(all=True)
