def test_limits_to_control_points():
"""Test functionality for determing control points."""
sample_src = read_source_spaces(src_fname)
kwargs = dict(subjects_dir=subjects_dir, smoothing_steps=1)
vertices = [s['vertno'] for s in sample_src]
n_time = 5
n_verts = sum(len(v) for v in vertices)
stc_data = np.random.RandomState(0).rand((n_verts * n_time))
stc_data.shape = (n_verts, n_time)
stc = SourceEstimate(stc_data, vertices, 1, 1, 'sample')
# Test for simple use cases
mlab = _import_mlab()
stc.plot(**kwargs)
stc.plot(clim=dict(pos_lims=(10, 50, 90)), **kwargs)
stc.plot(colormap='hot', clim='auto', **kwargs)
stc.plot(colormap='mne', clim='auto', **kwargs)
figs = [mlab.figure(), mlab.figure()]
stc.plot(clim=dict(kind='value', lims=(10, 50, 90)), figure=99, **kwargs)
assert_raises(ValueError, stc.plot, clim='auto', figure=figs, **kwargs)
# Test both types of incorrect limits key (lims/pos_lims)
assert_raises(KeyError, plot_source_estimates, stc, colormap='mne',
clim=dict(kind='value', lims=(5, 10, 15)), **kwargs)
assert_raises(KeyError, plot_source_estimates, stc, colormap='hot',
clim=dict(kind='value', pos_lims=(5, 10, 15)), **kwargs)
# Test for correct clim values
assert_raises(ValueError, stc.plot,
clim=dict(kind='value', pos_lims=[0, 1, 0]), **kwargs)
assert_raises(ValueError, stc.plot, colormap='mne',
clim=dict(pos_lims=(5, 10, 15, 20)), **kwargs)
assert_raises(ValueError, stc.plot,
clim=dict(pos_lims=(5, 10, 15), kind='foo'), **kwargs)
assert_raises(ValueError, stc.plot, colormap='mne', clim='foo', **kwargs)
assert_raises(ValueError, stc.plot, clim=(5, 10, 15), **kwargs)
assert_raises(ValueError, plot_source_estimates, 'foo', clim='auto',
**kwargs)
assert_raises(ValueError, stc.plot, hemi='foo', clim='auto', **kwargs)
# Test handling of degenerate data
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
# thresholded maps
stc._data.fill(0.)
plot_source_estimates(stc, **kwargs)
assert any('All data were zero' in str(ww.message) for ww in w)
mlab.close(all=True)
def test_limits_to_control_points():
"""Test functionality for determing control points."""
sample_src = read_source_spaces(src_fname)
kwargs = dict(subjects_dir=subjects_dir, smoothing_steps=1)
vertices = [s['vertno'] for s in sample_src]
n_time = 5
n_verts = sum(len(v) for v in vertices)
stc_data = np.random.RandomState(0).rand((n_verts * n_time))
stc_data.shape = (n_verts, n_time)
stc = SourceEstimate(stc_data, vertices, 1, 1, 'sample')
# Test for simple use cases
mlab = _import_mlab()
stc.plot(**kwargs)
stc.plot(clim=dict(pos_lims=(10, 50, 90)), **kwargs)
stc.plot(colormap='hot', clim='auto', **kwargs)
stc.plot(colormap='mne', clim='auto', **kwargs)
figs = [mlab.figure(), mlab.figure()]
stc.plot(clim=dict(kind='value', lims=(10, 50, 90)), figure=99, **kwargs)
assert_raises(ValueError, stc.plot, clim='auto', figure=figs, **kwargs)
# Test both types of incorrect limits key (lims/pos_lims)
assert_raises(KeyError, plot_source_estimates, stc, colormap='mne',
clim=dict(kind='value', lims=(5, 10, 15)), **kwargs)
assert_raises(KeyError, plot_source_estimates, stc, colormap='hot',
clim=dict(kind='value', pos_lims=(5, 10, 15)), **kwargs)
# Test for correct clim values
assert_raises(ValueError, stc.plot,
clim=dict(kind='value', pos_lims=[0, 1, 0]), **kwargs)
assert_raises(ValueError, stc.plot, colormap='mne',
clim=dict(pos_lims=(5, 10, 15, 20)), **kwargs)
assert_raises(ValueError, stc.plot,
clim=dict(pos_lims=(5, 10, 15), kind='foo'), **kwargs)
assert_raises(ValueError, stc.plot, colormap='mne', clim='foo', **kwargs)
assert_raises(ValueError, stc.plot, clim=(5, 10, 15), **kwargs)
assert_raises(ValueError, plot_source_estimates, 'foo', clim='auto',
**kwargs)
assert_raises(ValueError, stc.plot, hemi='foo', clim='auto', **kwargs)
# Test handling of degenerate data
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
# thresholded maps
stc._data.fill(0.)
plot_source_estimates(stc, **kwargs)
assert_equal(len(w), 1)
mlab.close(all=True)
def test_limits_to_control_points():
"""Test functionality for determining control points."""
sample_src = read_source_spaces(src_fname)
kwargs = dict(subjects_dir=subjects_dir, smoothing_steps=1)
vertices = [s['vertno'] for s in sample_src]
n_time = 5
n_verts = sum(len(v) for v in vertices)
stc_data = np.random.RandomState(0).rand((n_verts * n_time))
stc_data.shape = (n_verts, n_time)
stc = SourceEstimate(stc_data, vertices, 1, 1, 'sample')
# Test for simple use cases
mlab = _import_mlab()
stc.plot(**kwargs)
stc.plot(clim=dict(pos_lims=(10, 50, 90)), **kwargs)
stc.plot(colormap='hot', clim='auto', **kwargs)
stc.plot(colormap='mne', clim='auto', **kwargs)
figs = [mlab.figure(), mlab.figure()]
stc.plot(clim=dict(kind='value', lims=(10, 50, 90)), figure=99, **kwargs)
pytest.raises(ValueError, stc.plot, clim='auto', figure=figs, **kwargs)
# Test for correct clim values
with pytest.raises(ValueError, match='monotonically'):
stc.plot(clim=dict(kind='value', pos_lims=[0, 1, 0]), **kwargs)
with pytest.raises(ValueError, match=r'.*must be \(3,\)'):
stc.plot(colormap='mne', clim=dict(pos_lims=(5, 10, 15, 20)), **kwargs)
with pytest.raises(ValueError, match="'value', 'values' and 'percent'"):
stc.plot(clim=dict(pos_lims=(5, 10, 15), kind='foo'), **kwargs)
with pytest.raises(ValueError, match='must be "auto" or dict'):
stc.plot(colormap='mne', clim='foo', **kwargs)
with pytest.raises(TypeError, match='must be an instance of'):
plot_source_estimates('foo', clim='auto', **kwargs)
with pytest.raises(ValueError, match='hemi'):
stc.plot(hemi='foo', clim='auto', **kwargs)
with pytest.raises(ValueError, match='Exactly one'):
stc.plot(clim=dict(lims=[0, 1, 2], pos_lims=[0, 1, 2], kind='value'),
**kwargs)
# Test handling of degenerate data: thresholded maps
stc._data.fill(0.)
with pytest.warns(RuntimeWarning, match='All data were zero'):
plot_source_estimates(stc, **kwargs)
mlab.close(all=True)
def test_limits_to_control_points():
"""Test functionality for determining control points."""
sample_src = read_source_spaces(src_fname)
kwargs = dict(subjects_dir=subjects_dir, smoothing_steps=1)
vertices = [s['vertno'] for s in sample_src]
n_time = 5
n_verts = sum(len(v) for v in vertices)
stc_data = np.random.RandomState(0).rand((n_verts * n_time))
stc_data.shape = (n_verts, n_time)
stc = SourceEstimate(stc_data, vertices, 1, 1, 'sample')
# Test for simple use cases
mlab = _import_mlab()
stc.plot(**kwargs)
stc.plot(clim=dict(pos_lims=(10, 50, 90)), **kwargs)
stc.plot(colormap='hot', clim='auto', **kwargs)
stc.plot(colormap='mne', clim='auto', **kwargs)
figs = [mlab.figure(), mlab.figure()]
stc.plot(clim=dict(kind='value', lims=(10, 50, 90)), figure=99, **kwargs)
pytest.raises(ValueError, stc.plot, clim='auto', figure=figs, **kwargs)
# Test for correct clim values
with pytest.raises(ValueError, match='monotonically'):
stc.plot(clim=dict(kind='value', pos_lims=[0, 1, 0]), **kwargs)
with pytest.raises(ValueError, match=r'.*must be \(3,\)'):
stc.plot(colormap='mne', clim=dict(pos_lims=(5, 10, 15, 20)), **kwargs)
with pytest.raises(ValueError, match='must be "value" or "percent"'):
stc.plot(clim=dict(pos_lims=(5, 10, 15), kind='foo'), **kwargs)
with pytest.raises(ValueError, match='must be "auto" or dict'):
stc.plot(colormap='mne', clim='foo', **kwargs)
with pytest.raises(TypeError, match='must be an instance of'):
plot_source_estimates('foo', clim='auto', **kwargs)
with pytest.raises(ValueError, match='hemi'):
stc.plot(hemi='foo', clim='auto', **kwargs)
with pytest.raises(ValueError, match='Exactly one'):
stc.plot(clim=dict(lims=[0, 1, 2], pos_lims=[0, 1, 2], kind='value'),
**kwargs)
# Test handling of degenerate data: thresholded maps
stc._data.fill(0.)
with pytest.warns(RuntimeWarning, match='All data were zero'):
plot_source_estimates(stc, **kwargs)
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)
def test_plot_trans():
"""Test plotting of -trans.fif files and MEG sensor layouts."""
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():
ref_meg = False if system == 'KIT' else True
plot_trans(info,
trans_fname,
subject='sample',
meg_sensors=True,
subjects_dir=subjects_dir,
ref_meg=ref_meg)
mlab.close(all=True)
# KIT ref sensor coil def is defined
plot_trans(infos['KIT'], None, meg_sensors=True, ref_meg=True)
mlab.close(all=True)
info = infos['Neuromag']
assert_raises(ValueError,
plot_trans,
info,
trans_fname,
subject='sample',
subjects_dir=subjects_dir,
ch_type='bad-chtype')
assert_raises(TypeError,
plot_trans,
'foo',
trans_fname,
subject='sample',
subjects_dir=subjects_dir)
assert_raises(TypeError,
plot_trans,
info,
trans_fname,
subject='sample',
subjects_dir=subjects_dir,
src='foo')
assert_raises(ValueError,
plot_trans,
info,
trans_fname,
subject='fsaverage',
subjects_dir=subjects_dir,
src=sample_src)
sample_src.plot(subjects_dir=subjects_dir)
mlab.close(all=True)
# no-head version
plot_trans(info, None, meg_sensors=True, dig=True, coord_frame='head')
mlab.close(all=True)
# all coord frames
for coord_frame in ('meg', 'head', 'mri'):
plot_trans(info,
meg_sensors=True,
dig=True,
coord_frame=coord_frame,
trans=trans_fname,
subject='sample',
subjects_dir=subjects_dir)
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_trans(evoked_eeg_ecog.info,
subject='sample',
trans=trans_fname,
source='outer_skin',
meg_sensors=True,
skull=True,
eeg_sensors=['original', 'projected'],
ecog_sensors=True,
brain='white',
head=True,
subjects_dir=subjects_dir)
mlab.close(all=True)
assert_true(['Cannot plot MEG' in str(ww.message) for ww in w])
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_trans():
"""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():
ref_meg = False if system == 'KIT' else True
plot_trans(info,
trans_fname,
subject='sample',
meg_sensors=True,
subjects_dir=subjects_dir,
ref_meg=ref_meg)
mlab.close(all=True)
# KIT ref sensor coil def is defined
plot_trans(infos['KIT'], None, meg_sensors=True, ref_meg=True)
mlab.close(all=True)
info = infos['Neuromag']
assert_raises(ValueError,
plot_trans,
info,
trans_fname,
subject='sample',
subjects_dir=subjects_dir,
ch_type='bad-chtype')
assert_raises(TypeError,
plot_trans,
'foo',
trans_fname,
subject='sample',
subjects_dir=subjects_dir)
assert_raises(TypeError,
plot_trans,
info,
trans_fname,
subject='sample',
subjects_dir=subjects_dir,
src='foo')
assert_raises(ValueError,
plot_trans,
info,
trans_fname,
subject='fsaverage',
subjects_dir=subjects_dir,
src=sample_src)
sample_src.plot(subjects_dir=subjects_dir)
mlab.close(all=True)
# no-head version
plot_trans(info, None, meg_sensors=True, dig=True, coord_frame='head')
mlab.close(all=True)
# all coord frames
for coord_frame in ('meg', 'head', 'mri'):
plot_trans(info,
meg_sensors=True,
dig=True,
coord_frame=coord_frame,
trans=trans_fname,
subject='sample',
mri_fiducials=fiducials_path,
subjects_dir=subjects_dir)
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_trans(evoked_eeg_ecog.info,
subject='sample',
trans=trans_fname,
source='outer_skin',
meg_sensors=True,
skull=True,
eeg_sensors=['original', 'projected'],
ecog_sensors=True,
brain='white',
head=True,
subjects_dir=subjects_dir)
mlab.close(all=True)
assert_true(['Cannot plot MEG' in str(ww.message) for ww in w])
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_trans():
"""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():
ref_meg = False if system == 'KIT' else True
plot_trans(info, trans_fname, subject='sample', meg_sensors=True,
subjects_dir=subjects_dir, ref_meg=ref_meg)
mlab.close(all=True)
# KIT ref sensor coil def is defined
plot_trans(infos['KIT'], None, meg_sensors=True, ref_meg=True)
mlab.close(all=True)
info = infos['Neuromag']
assert_raises(TypeError, plot_trans, 'foo', trans_fname,
subject='sample', subjects_dir=subjects_dir)
assert_raises(TypeError, plot_trans, info, trans_fname,
subject='sample', subjects_dir=subjects_dir, src='foo')
assert_raises(ValueError, plot_trans, info, trans_fname,
subject='fsaverage', subjects_dir=subjects_dir,
src=sample_src)
sample_src.plot(subjects_dir=subjects_dir)
mlab.close(all=True)
# no-head version
plot_trans(info, None, meg_sensors=True, dig=True, coord_frame='head')
mlab.close(all=True)
# all coord frames
for coord_frame in ('meg', 'head', 'mri'):
plot_trans(info, meg_sensors=True, dig=True, coord_frame=coord_frame,
trans=trans_fname, subject='sample',
mri_fiducials=fiducials_path, subjects_dir=subjects_dir)
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_trans(evoked_eeg_ecog.info, subject='sample', trans=trans_fname,
source='outer_skin', meg_sensors=True, skull=True,
eeg_sensors=['original', 'projected'], ecog_sensors=True,
brain='white', head=True, subjects_dir=subjects_dir)
mlab.close(all=True)
assert_true(['Cannot plot MEG' in str(ww.message) for ww in w])
