def test_label_in_src():
"""Test label in src."""
src = read_source_spaces(src_fname)
label = read_label(v1_label_fname)
# construct label from source space vertices
vert_in_src = np.intersect1d(label.vertices, src[0]['vertno'], True)
where = np.in1d(label.vertices, vert_in_src)
pos_in_src = label.pos[where]
values_in_src = label.values[where]
label_src = Label(vert_in_src, pos_in_src, values_in_src,
hemi='lh').fill(src)
# check label vertices
vertices_status = np.in1d(src[0]['nearest'], label.vertices)
vertices_in = np.nonzero(vertices_status)[0]
vertices_out = np.nonzero(np.logical_not(vertices_status))[0]
assert_array_equal(label_src.vertices, vertices_in)
assert_array_equal(np.in1d(vertices_out, label_src.vertices), False)
# check values
value_idx = np.digitize(src[0]['nearest'][vertices_in], vert_in_src, True)
assert_array_equal(label_src.values, values_in_src[value_idx])
# test exception
vertices = np.append([-1], vert_in_src)
pytest.raises(ValueError, Label(vertices, hemi='lh').fill, src)
# test filling empty label
label = Label([], hemi='lh')
label.fill(src)
assert_array_equal(label.vertices, np.array([], int))
def test_label_addition():
"""Test label addition
"""
pos = np.random.rand(10, 3)
values = np.arange(10.) / 10
idx0 = list(range(7))
idx1 = list(range(7, 10)) # non-overlapping
idx2 = list(range(5, 10)) # overlapping
l0 = Label(idx0, pos[idx0], values[idx0], 'lh', color='red')
l1 = Label(idx1, pos[idx1], values[idx1], 'lh')
l2 = Label(idx2, pos[idx2], values[idx2], 'lh', color=(0, 1, 0, .5))
assert_equal(len(l0), len(idx0))
# adding non-overlapping labels
l01 = l0 + l1
assert_equal(len(l01), len(l0) + len(l1))
assert_array_equal(l01.values[:len(l0)], l0.values)
assert_equal(l01.color, l0.color)
# subtraction
assert_labels_equal(l01 - l0, l1, comment=False, color=False)
assert_labels_equal(l01 - l1, l0, comment=False, color=False)
# adding overlappig labels
l = l0 + l2
i0 = np.where(l0.vertices == 6)[0][0]
i2 = np.where(l2.vertices == 6)[0][0]
i = np.where(l.vertices == 6)[0][0]
assert_equal(l.values[i], l0.values[i0] + l2.values[i2])
assert_equal(l.values[0], l0.values[0])
assert_array_equal(np.unique(l.vertices), np.unique(idx0 + idx2))
assert_equal(l.color, _blend_colors(l0.color, l2.color))
# adding lh and rh
l2.hemi = 'rh'
# this now has deprecated behavior
bhl = l0 + l2
assert_equal(bhl.hemi, 'both')
assert_equal(len(bhl), len(l0) + len(l2))
assert_equal(bhl.color, l.color)
# subtraction
assert_labels_equal(bhl - l0, l2)
assert_labels_equal(bhl - l2, l0)
bhl2 = l1 + bhl
assert_labels_equal(bhl2.lh, l01)
assert_equal(bhl2.color, _blend_colors(l1.color, bhl.color))
# subtraction
bhl_ = bhl2 - l1
assert_labels_equal(bhl_.lh, bhl.lh, comment=False, color=False)
assert_labels_equal(bhl_.rh, bhl.rh)
assert_labels_equal(bhl2 - l2, l0 + l1)
assert_labels_equal(bhl2 - l1 - l0, l2)
def test_label_center_of_mass():
"""Test computing the center of mass of a label."""
stc = read_source_estimate(stc_fname)
stc.lh_data[:] = 0
vertex_stc = stc.center_of_mass('sample', subjects_dir=subjects_dir)[0]
assert_equal(vertex_stc, 124791)
label = Label(stc.vertices[1], pos=None, values=stc.rh_data.mean(axis=1),
hemi='rh', subject='sample')
vertex_label = label.center_of_mass(subjects_dir=subjects_dir)
assert_equal(vertex_label, vertex_stc)
labels = read_labels_from_annot('sample', parc='aparc.a2009s',
subjects_dir=subjects_dir)
src = read_source_spaces(src_fname)
# Try a couple of random ones, one from left and one from right
# Visually verified in about the right place using mne_analyze
for label, expected in zip([labels[2], labels[3], labels[-5]],
[141162, 145221, 55979]):
label.values[:] = -1
pytest.raises(ValueError, label.center_of_mass,
subjects_dir=subjects_dir)
label.values[:] = 0
pytest.raises(ValueError, label.center_of_mass,
subjects_dir=subjects_dir)
label.values[:] = 1
assert_equal(label.center_of_mass(subjects_dir=subjects_dir), expected)
assert_equal(label.center_of_mass(subjects_dir=subjects_dir,
restrict_vertices=label.vertices),
expected)
# restrict to source space
idx = 0 if label.hemi == 'lh' else 1
# this simple nearest version is not equivalent, but is probably
# close enough for many labels (including the test ones):
pos = label.pos[np.where(label.vertices == expected)[0][0]]
pos = (src[idx]['rr'][src[idx]['vertno']] - pos)
pos = np.argmin(np.sum(pos * pos, axis=1))
src_expected = src[idx]['vertno'][pos]
# see if we actually get the same one
src_restrict = np.intersect1d(label.vertices, src[idx]['vertno'])
assert_equal(label.center_of_mass(subjects_dir=subjects_dir,
restrict_vertices=src_restrict),
src_expected)
assert_equal(label.center_of_mass(subjects_dir=subjects_dir,
restrict_vertices=src),
src_expected)
# degenerate cases
pytest.raises(ValueError, label.center_of_mass, subjects_dir=subjects_dir,
restrict_vertices='foo')
pytest.raises(TypeError, label.center_of_mass, subjects_dir=subjects_dir,
surf=1)
pytest.raises(IOError, label.center_of_mass, subjects_dir=subjects_dir,
surf='foo')
def test_label_sign_flip():
src = read_source_spaces(src_fname)
label = Label(vertices=src[0]['vertno'][:5], hemi='lh')
src[0]['nn'][label.vertices] = np.array(
[[1., 0., 0.], [0., 1., 0.], [0, 0, 1.],
[1. / np.sqrt(2), 1. / np.sqrt(2), 0.],
[1. / np.sqrt(2), 1. / np.sqrt(2), 0.]])
known_flips = np.array([1, 1, np.nan, 1, 1])
idx = [0, 1, 3, 4] # indices that are usable (third row is orthognoal)
flip = label_sign_flip(label, src)
# Need the abs here because the direction is arbitrary
assert_array_almost_equal(np.abs(np.dot(flip[idx], known_flips[idx])),
len(idx))
def test_label_fill_restrict(fname):
"""Test label in fill and restrict."""
src = read_source_spaces(src_fname)
label = read_label(fname)
# construct label from source space vertices
label_src = label.restrict(src)
vert_in_src = label_src.vertices
values_in_src = label_src.values
if check_version('scipy', '1.3') and fname == real_label_fname:
# Check that we can auto-fill patch info quickly for one condition
for s in src:
s['nearest'] = None
with pytest.warns(None):
label_src = label_src.fill(src)
else:
label_src = label_src.fill(src)
assert src[0]['nearest'] is not None
# check label vertices
vertices_status = np.in1d(src[0]['nearest'], label.vertices)
vertices_in = np.nonzero(vertices_status)[0]
vertices_out = np.nonzero(np.logical_not(vertices_status))[0]
assert_array_equal(label_src.vertices, vertices_in)
assert_array_equal(np.in1d(vertices_out, label_src.vertices), False)
# check values
value_idx = np.digitize(src[0]['nearest'][vertices_in], vert_in_src, True)
assert_array_equal(label_src.values, values_in_src[value_idx])
# test exception
vertices = np.append([-1], vert_in_src)
with pytest.raises(ValueError, match='does not contain all of the label'):
Label(vertices, hemi='lh').fill(src)
# test filling empty label
label = Label([], hemi='lh')
label.fill(src)
assert_array_equal(label.vertices, np.array([], int))
def test_label_sign_flip():
"""Test label sign flip computation."""
src = read_source_spaces(src_fname)
label = Label(vertices=src[0]['vertno'][:5], hemi='lh')
src[0]['nn'][label.vertices] = np.array(
[[1., 0., 0.],
[0., 1., 0.],
[0, 0, 1.],
[1. / np.sqrt(2), 1. / np.sqrt(2), 0.],
[1. / np.sqrt(2), 1. / np.sqrt(2), 0.]])
known_flips = np.array([1, 1, np.nan, 1, 1])
idx = [0, 1, 3, 4] # indices that are usable (third row is orthognoal)
flip = label_sign_flip(label, src)
assert_array_almost_equal(np.dot(flip[idx], known_flips[idx]), len(idx))
bi_label = label + Label(vertices=src[1]['vertno'][:5], hemi='rh')
src[1]['nn'][src[1]['vertno'][:5]] = -src[0]['nn'][label.vertices]
flip = label_sign_flip(bi_label, src)
known_flips = np.array([1, 1, np.nan, 1, 1, 1, 1, np.nan, 1, 1])
idx = [0, 1, 3, 4, 5, 6, 8, 9]
assert_array_almost_equal(np.dot(flip[idx], known_flips[idx]), 0.)
src[1]['nn'][src[1]['vertno'][:5]] *= -1
flip = label_sign_flip(bi_label, src)
assert_array_almost_equal(np.dot(flip[idx], known_flips[idx]), len(idx))
def test_annot_io():
"""Test I/O from and to *.annot files."""
# copy necessary files from fsaverage to tempdir
tempdir = _TempDir()
subject = 'fsaverage'
label_src = os.path.join(subjects_dir, 'fsaverage', 'label')
surf_src = os.path.join(subjects_dir, 'fsaverage', 'surf')
label_dir = os.path.join(tempdir, subject, 'label')
surf_dir = os.path.join(tempdir, subject, 'surf')
os.makedirs(label_dir)
os.mkdir(surf_dir)
shutil.copy(os.path.join(label_src, 'lh.PALS_B12_Lobes.annot'), label_dir)
shutil.copy(os.path.join(label_src, 'rh.PALS_B12_Lobes.annot'), label_dir)
shutil.copy(os.path.join(surf_src, 'lh.white'), surf_dir)
shutil.copy(os.path.join(surf_src, 'rh.white'), surf_dir)
# read original labels
with pytest.raises(IOError, match='\nPALS_B12_Lobes$'):
read_labels_from_annot(subject, 'PALS_B12_Lobesey',
subjects_dir=tempdir)
labels = read_labels_from_annot(subject, 'PALS_B12_Lobes',
subjects_dir=tempdir)
# test saving parcellation only covering one hemisphere
parc = [label for label in labels if label.name == 'LOBE.TEMPORAL-lh']
write_labels_to_annot(parc, subject, 'myparc', subjects_dir=tempdir)
parc1 = read_labels_from_annot(subject, 'myparc', subjects_dir=tempdir)
parc1 = [label for label in parc1 if not label.name.startswith('unknown')]
assert_equal(len(parc1), len(parc))
for lt, rt in zip(parc1, parc):
assert_labels_equal(lt, rt)
# test saving only one hemisphere
parc = [label for label in labels if label.name.startswith('LOBE')]
write_labels_to_annot(parc, subject, 'myparc2', hemi='lh',
subjects_dir=tempdir)
annot_fname = os.path.join(tempdir, subject, 'label', '%sh.myparc2.annot')
assert os.path.isfile(annot_fname % 'l')
assert not os.path.isfile(annot_fname % 'r')
parc1 = read_labels_from_annot(subject, 'myparc2',
annot_fname=annot_fname % 'l',
subjects_dir=tempdir)
parc_lh = [label for label in parc if label.name.endswith('lh')]
for lt, rt in zip(parc1, parc_lh):
assert_labels_equal(lt, rt)
# test that the annotation is complete (test Label() support)
rr = read_surface(op.join(surf_dir, 'lh.white'))[0]
label = sum(labels, Label(hemi='lh', subject='fsaverage')).lh
assert_array_equal(label.vertices, np.arange(len(rr)))
def test_label_addition():
"""Test label addition
"""
pos = np.random.rand(10, 3)
values = np.arange(10.) / 10
idx0 = range(7)
idx1 = range(7, 10) # non-overlapping
idx2 = range(5, 10) # overlapping
l0 = Label(idx0, pos[idx0], values[idx0], 'lh')
l1 = Label(idx1, pos[idx1], values[idx1], 'lh')
l2 = Label(idx2, pos[idx2], values[idx2], 'lh')
assert len(l0) == len(idx0)
# adding non-overlapping labels
l01 = l0 + l1
assert len(l01) == len(l0) + len(l1)
assert_array_equal(l01.values[:len(l0)], l0.values)
# adding overlappig labels
l = l0 + l2
i0 = np.where(l0.vertices == 6)[0][0]
i2 = np.where(l2.vertices == 6)[0][0]
i = np.where(l.vertices == 6)[0][0]
assert l.values[i] == l0.values[i0] + l2.values[i2]
assert l.values[0] == l0.values[0]
assert_array_equal(np.unique(l.vertices), np.unique(idx0 + idx2))
# adding lh and rh
l2.hemi = 'rh'
# this now has deprecated behavior
bhl = l0 + l2
assert bhl.hemi == 'both'
assert len(bhl) == len(l0) + len(l2)
bhl = l1 + bhl
assert_labels_equal(bhl.lh, l01)
def test_label_addition():
"""Test label addition
"""
pos = np.random.rand(10, 3)
values = np.arange(10.) / 10
idx0 = range(7)
idx1 = range(7, 10) # non-overlapping
idx2 = range(5, 10) # overlapping
l0 = Label(idx0, pos[idx0], values[idx0], 'lh')
l1 = Label(idx1, pos[idx1], values[idx1], 'lh')
l2 = Label(idx2, pos[idx2], values[idx2], 'lh')
assert len(l0) == len(idx0)
# adding non-overlapping labels
l01 = l0 + l1
assert len(l01) == len(l0) + len(l1)
assert_array_equal(l01.values[:len(l0)], l0.values)
# adding overlappig labels
l = l0 + l2
i0 = np.where(l0.vertices == 6)[0][0]
i2 = np.where(l2.vertices == 6)[0][0]
i = np.where(l.vertices == 6)[0][0]
assert l.values[i] == l0.values[i0] + l2.values[i2]
assert l.values[0] == l0.values[0]
assert_array_equal(np.unique(l.vertices), np.unique(idx0 + idx2))
# adding lh and rh
l2.hemi = 'rh'
# this now has deprecated behavior
bhl = l0 + l2
assert bhl.hemi == 'both'
assert len(bhl) == len(l0) + len(l2)
bhl = l1 + bhl
assert_labels_equal(bhl.lh, l01)
def test_generate_stc_single_hemi(_get_fwd_labels):
"""Test generation of source estimate, single hemi."""
fwd, labels = _get_fwd_labels
labels_single_hemi = labels[1:] # keep only labels in one hemisphere
mylabels = []
for i, label in enumerate(labels_single_hemi):
new_label = Label(vertices=label.vertices,
pos=label.pos,
values=2 * i * np.ones(len(label.values)),
hemi=label.hemi,
comment=label.comment)
mylabels.append(new_label)
n_times = 10
tmin = 0
tstep = 1e-3
stc_data = np.ones((len(labels_single_hemi), n_times))
stc = simulate_stc(fwd['src'], mylabels, stc_data, tmin, tstep)
for label in labels_single_hemi:
idx = _get_idx_label_stc(label, stc)
assert (np.all(stc.data[idx] == 1.0))
assert (stc.data[idx].shape[1] == n_times)
# test with function
def fun(x):
return x**2
stc = simulate_stc(fwd['src'], mylabels, stc_data, tmin, tstep, fun)
# the first label has value 0, the second value 2, the third value 6
for i, label in enumerate(labels_single_hemi):
if label.hemi == 'lh':
hemi_idx = 0
else:
hemi_idx = 1
idx = np.intersect1d(stc.vertices[hemi_idx], label.vertices)
idx = np.searchsorted(stc.vertices[hemi_idx], idx)
if hemi_idx == 1:
idx += len(stc.vertices[0])
res = ((2. * i)**2.) * np.ones((len(idx), n_times))
assert_array_almost_equal(stc.data[idx], res)
def test_simulate_stc(_get_fwd_labels):
"""Test generation of source estimate."""
fwd, labels = _get_fwd_labels
mylabels = []
for i, label in enumerate(labels):
new_label = Label(vertices=label.vertices,
pos=label.pos,
values=2 * i * np.ones(len(label.values)),
hemi=label.hemi,
comment=label.comment)
mylabels.append(new_label)
n_times = 10
tmin = 0
tstep = 1e-3
stc_data = np.ones((len(labels), n_times))
stc = simulate_stc(fwd['src'], mylabels, stc_data, tmin, tstep)
assert_equal(stc.subject, 'sample')
for label in labels:
idx = _get_idx_label_stc(label, stc)
assert (np.all(stc.data[idx] == 1.0))
assert (stc.data[idx].shape[1] == n_times)
# test with function
def fun(x):
return x**2
stc = simulate_stc(fwd['src'], mylabels, stc_data, tmin, tstep, fun)
# the first label has value 0, the second value 2, the third value 6
for i, label in enumerate(labels):
idx = _get_idx_label_stc(label, stc)
res = ((2. * i)**2.) * np.ones((len(idx), n_times))
assert_array_almost_equal(stc.data[idx], res)
# degenerate conditions
label_subset = mylabels[:2]
data_subset = stc_data[:2]
stc = simulate_stc(fwd['src'], label_subset, data_subset, tmin, tstep, fun)
pytest.raises(ValueError, simulate_stc, fwd['src'], label_subset,
data_subset[:-1], tmin, tstep, fun)
pytest.raises(RuntimeError, simulate_stc, fwd['src'], label_subset * 2,
np.concatenate([data_subset] * 2, axis=0), tmin, tstep, fun)
def test_simulate_stc_labels_overlap():
"""Test generation of source estimate, overlapping labels."""
fwd = read_forward_solution_meg(fname_fwd, force_fixed=True, use_cps=True)
labels = [
read_label(
op.join(data_path, 'MEG', 'sample', 'labels', '%s.label' % label))
for label in label_names
]
mylabels = []
for i, label in enumerate(labels):
new_label = Label(vertices=label.vertices,
pos=label.pos,
values=2 * i * np.ones(len(label.values)),
hemi=label.hemi,
comment=label.comment)
mylabels.append(new_label)
# Adding the last label twice
mylabels.append(new_label)
n_times = 10
tmin = 0
tstep = 1e-3
stc_data = np.ones((len(mylabels), n_times))
# Test false
with pytest.raises(RuntimeError, match='must be non-overlapping'):
simulate_stc(fwd['src'],
mylabels,
stc_data,
tmin,
tstep,
allow_overlap=False)
# test True
stc = simulate_stc(fwd['src'],
mylabels,
stc_data,
tmin,
tstep,
allow_overlap=True)
assert_equal(stc.subject, 'sample')
assert (stc.data.shape[1] == n_times)
# Some of the elements should be equal to 2 since we have duplicate labels
assert (2 in stc.data)
def test_simulate_stc_labels_overlap(_get_fwd_labels):
"""Test generation of source estimate, overlapping labels."""
fwd, labels = _get_fwd_labels
mylabels = []
for i, label in enumerate(labels):
new_label = Label(vertices=label.vertices,
pos=label.pos,
values=2 * i * np.ones(len(label.values)),
hemi=label.hemi,
comment=label.comment)
mylabels.append(new_label)
# Adding the last label twice
mylabels.append(new_label)
n_times = 10
tmin = 0
tstep = 1e-3
stc_data = np.ones((len(mylabels), n_times))
# Test false
with pytest.raises(RuntimeError, match='must be non-overlapping'):
simulate_stc(fwd['src'],
mylabels,
stc_data,
tmin,
tstep,
allow_overlap=False)
# test True
stc = simulate_stc(fwd['src'],
mylabels,
stc_data,
tmin,
tstep,
allow_overlap=True)
assert_equal(stc.subject, 'sample')
assert (stc.data.shape[1] == n_times)
# Some of the elements should be equal to 2 since we have duplicate labels
assert (2 in stc.data)
def test_label_center_of_mass():
"""Test computing the center of mass of a label"""
stc = read_source_estimate(stc_fname)
stc.lh_data[:] = 0
vertex_stc = stc.center_of_mass('sample', subjects_dir=subjects_dir)[0]
assert_equal(vertex_stc, 124791)
label = Label(stc.vertices[1],
pos=None,
values=stc.rh_data.mean(axis=1),
hemi='rh',
subject='sample')
vertex_label = label.center_of_mass(subjects_dir=subjects_dir)
assert_equal(vertex_label, vertex_stc)
labels = read_labels_from_annot('sample',
parc='aparc.a2009s',
subjects_dir=subjects_dir)
src = read_source_spaces(src_fname)
# Try a couple of random ones, one from left and one from right
# Visually verified in about the right place using mne_analyze
for label, expected in zip([labels[2], labels[3], labels[-5]],
[141162, 145221, 55979]):
label.values[:] = -1
assert_raises(ValueError,
label.center_of_mass,
subjects_dir=subjects_dir)
label.values[:] = 0
assert_raises(ValueError,
label.center_of_mass,
subjects_dir=subjects_dir)
label.values[:] = 1
assert_equal(label.center_of_mass(subjects_dir=subjects_dir), expected)
assert_equal(
label.center_of_mass(subjects_dir=subjects_dir,
restrict_vertices=label.vertices), expected)
# restrict to source space
idx = 0 if label.hemi == 'lh' else 1
# this simple nearest version is not equivalent, but is probably
# close enough for many labels (including the test ones):
pos = label.pos[np.where(label.vertices == expected)[0][0]]
pos = (src[idx]['rr'][src[idx]['vertno']] - pos)
pos = np.argmin(np.sum(pos * pos, axis=1))
src_expected = src[idx]['vertno'][pos]
# see if we actually get the same one
src_restrict = np.intersect1d(label.vertices, src[idx]['vertno'])
assert_equal(
label.center_of_mass(subjects_dir=subjects_dir,
restrict_vertices=src_restrict), src_expected)
assert_equal(
label.center_of_mass(subjects_dir=subjects_dir,
restrict_vertices=src), src_expected)
# degenerate cases
assert_raises(ValueError,
label.center_of_mass,
subjects_dir=subjects_dir,
restrict_vertices='foo')
assert_raises(TypeError,
label.center_of_mass,
subjects_dir=subjects_dir,
surf=1)
assert_raises(IOError,
label.center_of_mass,
subjects_dir=subjects_dir,
surf='foo')
def _stc_to_label(stc, src, smooth, subjects_dir=None):
"""Compute a label from the non-zero sources in an stc object.
Parameters
----------
stc : SourceEstimate
The source estimates.
src : SourceSpaces | str | None
The source space over which the source estimates are defined.
If it's a string it should the subject name (e.g. fsaverage).
Can be None if stc.subject is not None.
smooth : int
Number of smoothing iterations.
subjects_dir : str | None
Path to SUBJECTS_DIR if it is not set in the environment.
Returns
-------
labels : list of Labels | list of list of Labels
The generated labels. If connected is False, it returns
a list of Labels (one per hemisphere). If no Label is available
in a hemisphere, None is returned. If connected is True,
it returns for each hemisphere a list of connected labels
ordered in decreasing order depending of the maximum value in the stc.
If no Label is available in an hemisphere, an empty list is returned.
"""
src = stc.subject if src is None else src
if isinstance(src, string_types):
subject = src
else:
subject = stc.subject
if isinstance(src, string_types):
subjects_dir = get_subjects_dir(subjects_dir)
surf_path_from = op.join(subjects_dir, src, 'surf')
rr_lh, tris_lh = read_surface(op.join(surf_path_from, 'lh.white'))
rr_rh, tris_rh = read_surface(op.join(surf_path_from, 'rh.white'))
rr = [rr_lh, rr_rh]
tris = [tris_lh, tris_rh]
else:
if not isinstance(src, SourceSpaces):
raise TypeError('src must be a string or a set of source spaces')
if len(src) != 2:
raise ValueError('source space should contain the 2 hemispheres')
rr = [1e3 * src[0]['rr'], 1e3 * src[1]['rr']]
tris = [src[0]['tris'], src[1]['tris']]
labels = []
cnt = 0
for hemi_idx, (hemi, this_vertno, this_tris, this_rr) in enumerate(
zip(['lh', 'rh'], stc.vertices, tris, rr)):
this_data = stc.data[cnt:cnt + len(this_vertno)]
e = mesh_edges(this_tris)
e.data[e.data == 2] = 1
n_vertices = e.shape[0]
e = e + sparse.eye(n_vertices, n_vertices)
clusters = [this_vertno[np.any(this_data, axis=1)]]
cnt += len(this_vertno)
clusters = [c for c in clusters if len(c) > 0]
if len(clusters) == 0:
this_labels = None
else:
this_labels = []
colors = _n_colors(len(clusters))
for c, color in zip(clusters, colors):
idx_use = c
for k in range(smooth):
e_use = e[:, idx_use]
data1 = e_use * np.ones(len(idx_use))
idx_use = np.where(data1)[0]
label = Label(idx_use,
this_rr[idx_use],
None,
hemi,
'Label from stc',
subject=subject,
color=color)
this_labels.append(label)
this_labels = this_labels[0]
labels.append(this_labels)
return labels
def test_label_addition():
"""Test label addition."""
pos = np.random.RandomState(0).rand(10, 3)
values = np.arange(10.) / 10
idx0 = list(range(7))
idx1 = list(range(7, 10)) # non-overlapping
idx2 = list(range(5, 10)) # overlapping
l0 = Label(idx0, pos[idx0], values[idx0], 'lh', color='red')
l1 = Label(idx1, pos[idx1], values[idx1], 'lh')
l2 = Label(idx2, pos[idx2], values[idx2], 'lh', color=(0, 1, 0, .5))
assert_equal(len(l0), len(idx0))
l_good = l0.copy()
l_good.subject = 'sample'
l_bad = l1.copy()
l_bad.subject = 'foo'
assert_raises(ValueError, l_good.__add__, l_bad)
assert_raises(TypeError, l_good.__add__, 'foo')
assert_raises(ValueError, l_good.__sub__, l_bad)
assert_raises(TypeError, l_good.__sub__, 'foo')
# adding non-overlapping labels
l01 = l0 + l1
assert_equal(len(l01), len(l0) + len(l1))
assert_array_equal(l01.values[:len(l0)], l0.values)
assert_equal(l01.color, l0.color)
# subtraction
assert_labels_equal(l01 - l0, l1, comment=False, color=False)
assert_labels_equal(l01 - l1, l0, comment=False, color=False)
# adding overlappig labels
l = l0 + l2
i0 = np.where(l0.vertices == 6)[0][0]
i2 = np.where(l2.vertices == 6)[0][0]
i = np.where(l.vertices == 6)[0][0]
assert_equal(l.values[i], l0.values[i0] + l2.values[i2])
assert_equal(l.values[0], l0.values[0])
assert_array_equal(np.unique(l.vertices), np.unique(idx0 + idx2))
assert_equal(l.color, _blend_colors(l0.color, l2.color))
# adding lh and rh
l2.hemi = 'rh'
bhl = l0 + l2
assert_equal(bhl.hemi, 'both')
assert_equal(len(bhl), len(l0) + len(l2))
assert_equal(bhl.color, l.color)
assert_true('BiHemiLabel' in repr(bhl))
# subtraction
assert_labels_equal(bhl - l0, l2)
assert_labels_equal(bhl - l2, l0)
bhl2 = l1 + bhl
assert_labels_equal(bhl2.lh, l01)
assert_equal(bhl2.color, _blend_colors(l1.color, bhl.color))
assert_array_equal((l2 + bhl).rh.vertices, bhl.rh.vertices) # rh label
assert_array_equal((bhl + bhl).lh.vertices, bhl.lh.vertices)
assert_raises(TypeError, bhl.__add__, 5)
# subtraction
bhl_ = bhl2 - l1
assert_labels_equal(bhl_.lh, bhl.lh, comment=False, color=False)
assert_labels_equal(bhl_.rh, bhl.rh)
assert_labels_equal(bhl2 - l2, l0 + l1)
assert_labels_equal(bhl2 - l1 - l0, l2)
bhl_ = bhl2 - bhl2
assert_array_equal(bhl_.vertices, [])
def test_source_simulator(_get_fwd_labels):
"""Test Source Simulator."""
fwd, _ = _get_fwd_labels
src = fwd['src']
hemi_to_ind = {'lh': 0, 'rh': 1}
tstep = 1. / 6.
label_vertices = [[], [], []]
label_vertices[0] = np.arange(1000)
label_vertices[1] = np.arange(500, 1500)
label_vertices[2] = np.arange(1000)
hemis = ['lh', 'lh', 'rh']
mylabels = []
src_vertices = []
for i, vert in enumerate(label_vertices):
new_label = Label(vertices=vert, hemi=hemis[i])
mylabels.append(new_label)
src_vertices.append(
np.intersect1d(src[hemi_to_ind[hemis[i]]]['vertno'],
new_label.vertices))
wfs = [[], [], []]
wfs[0] = np.array([0, 1., 0]) # 1d array
wfs[1] = [
np.array([0, 1., 0]), # list
np.array([0, 1.5, 0])
]
wfs[2] = np.array([[1, 1, 1.]]) # 2d array
events = [[], [], []]
events[0] = np.array([[0, 0, 1], [3, 0, 1]])
events[1] = np.array([[0, 0, 1], [3, 0, 1]])
events[2] = np.array([[0, 0, 1], [2, 0, 1]])
verts_lh = np.intersect1d(range(1500), src[0]['vertno'])
verts_rh = np.intersect1d(range(1000), src[1]['vertno'])
diff_01 = len(np.setdiff1d(src_vertices[0], src_vertices[1]))
diff_10 = len(np.setdiff1d(src_vertices[1], src_vertices[0]))
inter_10 = len(np.intersect1d(src_vertices[1], src_vertices[0]))
output_data_lh = np.zeros([len(verts_lh), 6])
tmp = np.array([0, 1., 0, 0, 1, 0])
output_data_lh[:diff_01, :] = np.tile(tmp, (diff_01, 1))
tmp = np.array([0, 2, 0, 0, 2.5, 0])
output_data_lh[diff_01:diff_01 + inter_10, :] = np.tile(tmp, (inter_10, 1))
tmp = np.array([0, 1, 0, 0, 1.5, 0])
output_data_lh[diff_01 + inter_10:, :] = np.tile(tmp, (diff_10, 1))
data_rh_wf = np.array([1., 1, 2, 1, 1, 0])
output_data_rh = np.tile(data_rh_wf, (len(src_vertices[2]), 1))
output_data = np.vstack([output_data_lh, output_data_rh])
ss = SourceSimulator(src, tstep)
for i in range(3):
ss.add_data(mylabels[i], wfs[i], events[i])
stc = ss.get_stc()
stim_channel = ss.get_stim_channel()
# Stim channel data must have the same size as stc time samples
assert len(stim_channel) == stc.data.shape[1]
stim_channel = ss.get_stim_channel(0, 0)
assert len(stim_channel) == 0
assert np.all(stc.vertices[0] == verts_lh)
assert np.all(stc.vertices[1] == verts_rh)
assert_array_almost_equal(stc.lh_data, output_data_lh)
assert_array_almost_equal(stc.rh_data, output_data_rh)
assert_array_almost_equal(stc.data, output_data)
counter = 0
for stc, stim in ss:
assert stc.data.shape[1] == 6
counter += 1
assert counter == 1
half_ss = SourceSimulator(src, tstep, duration=0.5)
for i in range(3):
half_ss.add_data(mylabels[i], wfs[i], events[i])
half_stc = half_ss.get_stc()
assert_array_almost_equal(stc.data[:, :3], half_stc.data)
ss = SourceSimulator(src)
with pytest.raises(ValueError, match='No simulation parameters'):
ss.get_stc()
with pytest.raises(ValueError, match='label must be a Label'):
ss.add_data(1, wfs, events)
with pytest.raises(ValueError,
match='Number of waveforms and events '
'should match'):
ss.add_data(mylabels[0], wfs[:2], events)
# Verify that the chunks have the correct length.
source_simulator = SourceSimulator(src, tstep=tstep, duration=10 * tstep)
source_simulator.add_data(mylabels[0], np.array([1, 1, 1]), [[0, 0, 0]])
source_simulator._chk_duration = 6 # Quick hack to get short chunks.
stcs = [stc for stc, _ in source_simulator]
assert len(stcs) == 2
assert stcs[0].data.shape[1] == 6
assert stcs[1].data.shape[1] == 4
def test_label_addition():
"""Test label addition
"""
pos = np.random.RandomState(0).rand(10, 3)
values = np.arange(10.) / 10
idx0 = list(range(7))
idx1 = list(range(7, 10)) # non-overlapping
idx2 = list(range(5, 10)) # overlapping
l0 = Label(idx0, pos[idx0], values[idx0], 'lh', color='red')
l1 = Label(idx1, pos[idx1], values[idx1], 'lh')
l2 = Label(idx2, pos[idx2], values[idx2], 'lh', color=(0, 1, 0, .5))
assert_equal(len(l0), len(idx0))
l_good = l0.copy()
l_good.subject = 'sample'
l_bad = l1.copy()
l_bad.subject = 'foo'
assert_raises(ValueError, l_good.__add__, l_bad)
assert_raises(TypeError, l_good.__add__, 'foo')
assert_raises(ValueError, l_good.__sub__, l_bad)
assert_raises(TypeError, l_good.__sub__, 'foo')
# adding non-overlapping labels
l01 = l0 + l1
assert_equal(len(l01), len(l0) + len(l1))
assert_array_equal(l01.values[:len(l0)], l0.values)
assert_equal(l01.color, l0.color)
# subtraction
assert_labels_equal(l01 - l0, l1, comment=False, color=False)
assert_labels_equal(l01 - l1, l0, comment=False, color=False)
# adding overlappig labels
l = l0 + l2
i0 = np.where(l0.vertices == 6)[0][0]
i2 = np.where(l2.vertices == 6)[0][0]
i = np.where(l.vertices == 6)[0][0]
assert_equal(l.values[i], l0.values[i0] + l2.values[i2])
assert_equal(l.values[0], l0.values[0])
assert_array_equal(np.unique(l.vertices), np.unique(idx0 + idx2))
assert_equal(l.color, _blend_colors(l0.color, l2.color))
# adding lh and rh
l2.hemi = 'rh'
# this now has deprecated behavior
bhl = l0 + l2
assert_equal(bhl.hemi, 'both')
assert_equal(len(bhl), len(l0) + len(l2))
assert_equal(bhl.color, l.color)
assert_true('BiHemiLabel' in repr(bhl))
# subtraction
assert_labels_equal(bhl - l0, l2)
assert_labels_equal(bhl - l2, l0)
bhl2 = l1 + bhl
assert_labels_equal(bhl2.lh, l01)
assert_equal(bhl2.color, _blend_colors(l1.color, bhl.color))
assert_array_equal((l2 + bhl).rh.vertices, bhl.rh.vertices) # rh label
assert_array_equal((bhl + bhl).lh.vertices, bhl.lh.vertices)
assert_raises(TypeError, bhl.__add__, 5)
# subtraction
bhl_ = bhl2 - l1
assert_labels_equal(bhl_.lh, bhl.lh, comment=False, color=False)
assert_labels_equal(bhl_.rh, bhl.rh)
assert_labels_equal(bhl2 - l2, l0 + l1)
assert_labels_equal(bhl2 - l1 - l0, l2)
bhl_ = bhl2 - bhl2
assert_array_equal(bhl_.vertices, [])
def labels_from_clusters(clusters, names=None):
"""Create Labels from source space clusters
Parameters
----------
clusters : NDVar
NDVar which is non-zero on the cluster. Can have a case dimension to
define multiple labels (one label per case).
names : None | list of str | str
Label names corresponding to clusters (default is "cluster%i").
Returns
-------
labels : list of mne.Label
One label for each cluster.
See Also
--------
NDVar.label_clusters : clusters from thresholding data
"""
from mne.label import _n_colors
if isinstance(names, str):
names = [names]
source = clusters.source
source_space = clusters.source.get_source_space()
subject = source.subject
collapse = tuple(dim for dim in clusters.dimnames
if dim not in ('case', 'source'))
if collapse:
clusters_index = clusters.any(collapse)
else:
clusters_index = clusters != 0
if clusters_index.has_case:
n_clusters = len(clusters)
else:
n_clusters = 1
clusters_index = (clusters_index, )
if names is None:
names = ("cluster%i" % i for i in range(n_clusters))
elif len(names) != n_clusters:
err = "Number of names difference from number of clusters."
raise ValueError(err)
colors = _n_colors(n_clusters)
labels = []
for cluster, color, name in zip(clusters_index, colors, names):
lh_vertices = source.lh_vertices[cluster.x[:source.lh_n]]
rh_vertices = source.rh_vertices[cluster.x[source.lh_n:]]
if len(lh_vertices) and len(rh_vertices):
lh = Label(lh_vertices,
hemi='lh',
name=name + '-lh',
subject=subject,
color=color).fill(source_space)
rh = Label(rh_vertices,
hemi='rh',
name=name + '-rh',
subject=subject,
color=color).fill(source_space)
label = BiHemiLabel(lh, rh, name, color)
elif len(lh_vertices):
label = Label(lh_vertices,
hemi='lh',
name=name + '-lh',
subject=subject,
color=color).fill(source_space)
elif len(rh_vertices):
label = Label(rh_vertices,
hemi='rh',
name=name + '-lh',
subject=subject,
color=color).fill(source_space)
else:
raise ValueError("Empty Cluster")
labels.append(label)
return labels
def test_generate_stc():
""" Test generation of source estimate """
fwd = read_forward_solution_meg(fname_fwd, force_fixed=True)
labels = [
read_label(
op.join(data_path, 'MEG', 'sample', 'labels', '%s.label' % label))
for label in label_names
]
mylabels = []
for i, label in enumerate(labels):
new_label = Label(vertices=label.vertices,
pos=label.pos,
values=2 * i * np.ones(len(label.values)),
hemi=label.hemi,
comment=label.comment)
mylabels.append(new_label)
n_times = 10
tmin = 0
tstep = 1e-3
stc_data = np.ones((len(labels), n_times))
stc = generate_stc(fwd['src'], mylabels, stc_data, tmin, tstep)
for label in labels:
if label.hemi == 'lh':
hemi_idx = 0
else:
hemi_idx = 1
idx = np.intersect1d(stc.vertices[hemi_idx], label.vertices)
idx = np.searchsorted(stc.vertices[hemi_idx], idx)
if hemi_idx == 1:
idx += len(stc.vertices[0])
assert_true(np.all(stc.data[idx] == 1.0))
assert_true(stc.data[idx].shape[1] == n_times)
# test with function
def fun(x):
return x**2
stc = generate_stc(fwd['src'], mylabels, stc_data, tmin, tstep, fun)
# the first label has value 0, the second value 2, the third value 6
for i, label in enumerate(labels):
if label.hemi == 'lh':
hemi_idx = 0
else:
hemi_idx = 1
idx = np.intersect1d(stc.vertices[hemi_idx], label.vertices)
idx = np.searchsorted(stc.vertices[hemi_idx], idx)
if hemi_idx == 1:
idx += len(stc.vertices[0])
res = ((2. * i)**2.) * np.ones((len(idx), n_times))
assert_array_almost_equal(stc.data[idx], res)
def test_simulate_stc():
"""Test generation of source estimate."""
fwd = read_forward_solution_meg(fname_fwd, force_fixed=True, use_cps=True)
labels = [read_label(op.join(data_path, 'MEG', 'sample', 'labels',
'%s.label' % label)) for label in label_names]
mylabels = []
for i, label in enumerate(labels):
new_label = Label(vertices=label.vertices,
pos=label.pos,
values=2 * i * np.ones(len(label.values)),
hemi=label.hemi,
comment=label.comment)
mylabels.append(new_label)
n_times = 10
tmin = 0
tstep = 1e-3
stc_data = np.ones((len(labels), n_times))
stc = simulate_stc(fwd['src'], mylabels, stc_data, tmin, tstep)
assert_equal(stc.subject, 'sample')
for label in labels:
if label.hemi == 'lh':
hemi_idx = 0
else:
hemi_idx = 1
idx = np.intersect1d(stc.vertices[hemi_idx], label.vertices)
idx = np.searchsorted(stc.vertices[hemi_idx], idx)
if hemi_idx == 1:
idx += len(stc.vertices[0])
assert (np.all(stc.data[idx] == 1.0))
assert (stc.data[idx].shape[1] == n_times)
# test with function
def fun(x):
return x ** 2
stc = simulate_stc(fwd['src'], mylabels, stc_data, tmin, tstep, fun)
# the first label has value 0, the second value 2, the third value 6
for i, label in enumerate(labels):
if label.hemi == 'lh':
hemi_idx = 0
else:
hemi_idx = 1
idx = np.intersect1d(stc.vertices[hemi_idx], label.vertices)
idx = np.searchsorted(stc.vertices[hemi_idx], idx)
if hemi_idx == 1:
idx += len(stc.vertices[0])
res = ((2. * i) ** 2.) * np.ones((len(idx), n_times))
assert_array_almost_equal(stc.data[idx], res)
# degenerate conditions
label_subset = mylabels[:2]
data_subset = stc_data[:2]
stc = simulate_stc(fwd['src'], label_subset, data_subset, tmin, tstep, fun)
pytest.raises(ValueError, simulate_stc, fwd['src'],
label_subset, data_subset[:-1], tmin, tstep, fun)
pytest.raises(RuntimeError, simulate_stc, fwd['src'], label_subset * 2,
np.concatenate([data_subset] * 2, axis=0), tmin, tstep, fun)
def test_source_simulator(_get_fwd_labels):
"""Test Source Simulator."""
fwd, _ = _get_fwd_labels
src = fwd['src']
hemi_to_ind = {'lh': 0, 'rh': 1}
tstep = 1. / 6.
label_vertices = [[], [], []]
label_vertices[0] = np.arange(1000)
label_vertices[1] = np.arange(500, 1500)
label_vertices[2] = np.arange(1000)
hemis = ['lh', 'lh', 'rh']
mylabels = []
src_vertices = []
for i, vert in enumerate(label_vertices):
new_label = Label(vertices=vert, hemi=hemis[i])
mylabels.append(new_label)
src_vertices.append(
np.intersect1d(src[hemi_to_ind[hemis[i]]]['vertno'],
new_label.vertices))
wfs = [[], [], []]
wfs[0] = np.array([0, 1., 0]) # 1d array
wfs[1] = [
np.array([0, 1., 0]), # list
np.array([0, 1.5, 0])
]
wfs[2] = np.array([[1, 1, 1.]]) # 2d array
events = [[], [], []]
events[0] = np.array([[0, 0, 1], [3, 0, 1]])
events[1] = np.array([[0, 0, 1], [3, 0, 1]])
events[2] = np.array([[0, 0, 1], [2, 0, 1]])
verts_lh = np.intersect1d(range(1500), src[0]['vertno'])
verts_rh = np.intersect1d(range(1000), src[1]['vertno'])
diff_01 = len(np.setdiff1d(src_vertices[0], src_vertices[1]))
diff_10 = len(np.setdiff1d(src_vertices[1], src_vertices[0]))
inter_10 = len(np.intersect1d(src_vertices[1], src_vertices[0]))
output_data_lh = np.zeros([len(verts_lh), 6])
tmp = np.array([0, 1., 0, 0, 1, 0])
output_data_lh[:diff_01, :] = np.tile(tmp, (diff_01, 1))
tmp = np.array([0, 2, 0, 0, 2.5, 0])
output_data_lh[diff_01:diff_01 + inter_10, :] = np.tile(tmp, (inter_10, 1))
tmp = np.array([0, 1, 0, 0, 1.5, 0])
output_data_lh[diff_01 + inter_10:, :] = np.tile(tmp, (diff_10, 1))
data_rh_wf = np.array([1., 1, 2, 1, 1, 0])
output_data_rh = np.tile(data_rh_wf, (len(src_vertices[2]), 1))
output_data = np.vstack([output_data_lh, output_data_rh])
ss = SourceSimulator(src, tstep)
for i in range(3):
ss.add_data(mylabels[i], wfs[i], events[i])
stc = ss.get_stc()
stim_channel = ss.get_stim_channel()
# Make some size checks.
assert ss.duration == 1.0
assert ss.n_times == 6
assert ss.last_samp == 5
assert len(stim_channel) == stc.data.shape[1]
assert np.all(stc.vertices[0] == verts_lh)
assert np.all(stc.vertices[1] == verts_rh)
assert_array_almost_equal(stc.lh_data, output_data_lh)
assert_array_almost_equal(stc.rh_data, output_data_rh)
assert_array_almost_equal(stc.data, output_data)
counter = 0
for stc, stim in ss:
assert stc.data.shape[1] == 6
counter += 1
assert counter == 1
# Check validity of setting duration and start/stop parameters.
half_ss = SourceSimulator(src, tstep, duration=0.5)
for i in range(3):
half_ss.add_data(mylabels[i], wfs[i], events[i])
half_stc = half_ss.get_stc()
assert_array_almost_equal(stc.data[:, :3], half_stc.data)
part_stc = ss.get_stc(start_sample=1, stop_sample=4)
assert part_stc.shape == (24, 4)
assert part_stc.times[0] == tstep
# Check validity of other arguments.
with pytest.raises(ValueError, match='start_sample must be'):
ss.get_stc(2, 0)
ss = SourceSimulator(src)
with pytest.raises(ValueError, match='No simulation parameters'):
ss.get_stc()
with pytest.raises(ValueError, match='label must be a Label'):
ss.add_data(1, wfs, events)
with pytest.raises(ValueError,
match='Number of waveforms and events '
'should match'):
ss.add_data(mylabels[0], wfs[:2], events)
with pytest.raises(ValueError, match='duration must be None or'):
ss = SourceSimulator(src, tstep, tstep / 2)
# Verify first_samp functionality.
ss = SourceSimulator(src, tstep)
offset = 50
for i in range(3): # events are offset, but first_samp = 0
events[i][:, 0] += offset
ss.add_data(mylabels[i], wfs[i], events[i])
offset_stc = ss.get_stc()
assert ss.n_times == 56
assert ss.first_samp == 0
assert offset_stc.data.shape == (stc.data.shape[0],
stc.data.shape[1] + offset)
ss = SourceSimulator(src, tstep, first_samp=offset)
for i in range(3): # events still offset, but first_samp > 0
ss.add_data(mylabels[i], wfs[i], events[i])
offset_stc = ss.get_stc()
assert ss.n_times == 6
assert ss.first_samp == offset
assert ss.last_samp == offset + 5
assert offset_stc.data.shape == stc.data.shape
# Verify that the chunks have the correct length.
source_simulator = SourceSimulator(src, tstep=tstep, duration=10 * tstep)
source_simulator.add_data(mylabels[0], np.array([1, 1, 1]), [[0, 0, 0]])
source_simulator._chk_duration = 6 # Quick hack to get short chunks.
stcs = [stc for stc, _ in source_simulator]
assert len(stcs) == 2
assert stcs[0].data.shape[1] == 6
assert stcs[1].data.shape[1] == 4
def test_simulate_raw_bem(raw_data):
"""Test simulation of raw data with BEM."""
raw, src_ss, stc, trans, sphere = raw_data
src = setup_source_space('sample', 'oct1', subjects_dir=subjects_dir)
for s in src:
s['nuse'] = 3
s['vertno'] = src[1]['vertno'][:3]
s['inuse'].fill(0)
s['inuse'][s['vertno']] = 1
# use different / more complete STC here
vertices = [s['vertno'] for s in src]
stc = SourceEstimate(np.eye(sum(len(v) for v in vertices)), vertices,
0, 1. / raw.info['sfreq'])
stcs = [stc] * 15
raw_sim_sph = simulate_raw(raw.info, stcs, trans, src, sphere)
raw_sim_bem = simulate_raw(raw.info, stcs, trans, src, bem_fname)
# some components (especially radial) might not match that well,
# so just make sure that most components have high correlation
assert_array_equal(raw_sim_sph.ch_names, raw_sim_bem.ch_names)
picks = pick_types(raw.info, meg=True, eeg=True)
n_ch = len(picks)
corr = np.corrcoef(raw_sim_sph[picks][0], raw_sim_bem[picks][0])
assert_array_equal(corr.shape, (2 * n_ch, 2 * n_ch))
med_corr = np.median(np.diag(corr[:n_ch, -n_ch:]))
assert med_corr > 0.65
# do some round-trip localization
for s in src:
transform_surface_to(s, 'head', trans)
locs = np.concatenate([s['rr'][s['vertno']] for s in src])
tmax = (len(locs) - 1) / raw.info['sfreq']
cov = make_ad_hoc_cov(raw.info)
# The tolerance for the BEM is surprisingly high (28) but I get the same
# result when using MNE-C and Xfit, even when using a proper 5120 BEM :(
for use_raw, bem, tol in ((raw_sim_sph, sphere, 2),
(raw_sim_bem, bem_fname, 31)):
events = find_events(use_raw, 'STI 014')
assert len(locs) == 6
evoked = Epochs(use_raw, events, 1, 0, tmax, baseline=None).average()
assert len(evoked.times) == len(locs)
fits = fit_dipole(evoked, cov, bem, trans, min_dist=1.)[0].pos
diffs = np.sqrt(np.sum((locs - fits) ** 2, axis=-1)) * 1000
med_diff = np.median(diffs)
assert med_diff < tol, '%s: %s' % (bem, med_diff)
# also test event timings with SourceSimulator
first_samp = raw.first_samp
events = find_events(raw, initial_event=True, verbose=False)
evt_times = events[:, 0]
assert len(events) == 3
labels_sim = [[], [], []] # random l+r hemisphere points
labels_sim[0] = Label([src_ss[0]['vertno'][1]], hemi='lh')
labels_sim[1] = Label([src_ss[0]['vertno'][4]], hemi='lh')
labels_sim[2] = Label([src_ss[1]['vertno'][2]], hemi='rh')
wf_sim = np.array([2, 1, 0])
for this_fs in (0, first_samp):
ss = SourceSimulator(src_ss, 1. / raw.info['sfreq'],
first_samp=this_fs)
for i in range(3):
ss.add_data(labels_sim[i], wf_sim, events[np.newaxis, i])
assert ss.n_times == evt_times[-1] + len(wf_sim) - this_fs
raw_sim = simulate_raw(raw.info, ss, src=src_ss, bem=bem_fname,
first_samp=first_samp)
data = raw_sim.get_data()
amp0 = data[:, evt_times - first_samp].max()
amp1 = data[:, evt_times + 1 - first_samp].max()
amp2 = data[:, evt_times + 2 - first_samp].max()
assert_allclose(amp0 / amp1, wf_sim[0] / wf_sim[1], rtol=1e-5)
assert amp2 == 0
assert raw_sim.n_times == ss.n_times
def test_source_simulator():
"""Test Source Simulator."""
fwd = read_forward_solution_meg(fname_fwd, force_fixed=True, use_cps=True)
src = fwd['src']
hemi_to_ind = {'lh': 0, 'rh': 1}
tmin = 0
tstep = 1. / 6.
label_vertices = [[], [], []]
label_vertices[0] = np.arange(1000)
label_vertices[1] = np.arange(500, 1500)
label_vertices[2] = np.arange(1000)
hemis = ['lh', 'lh', 'rh']
mylabels = []
src_vertices = []
for i, vert in enumerate(label_vertices):
new_label = Label(vertices=vert, hemi=hemis[i])
mylabels.append(new_label)
src_vertices.append(
np.intersect1d(src[hemi_to_ind[hemis[i]]]['vertno'],
new_label.vertices))
wfs = [[], [], []]
wfs[0] = np.array([0, 1., 0])
wfs[1] = [np.array([0, 1., 0]), np.array([0, 1.5, 0])]
wfs[2] = np.array([1, 1, 1.])
events = [[], [], []]
events[0] = np.array([[0, 0, 1], [3, 0, 1]])
events[1] = np.array([[0, 0, 1], [3, 0, 1]])
events[2] = np.array([[0, 0, 1], [2, 0, 1]])
verts_lh = np.intersect1d(range(1500), src[0]['vertno'])
verts_rh = np.intersect1d(range(1000), src[1]['vertno'])
diff_01 = len(np.setdiff1d(src_vertices[0], src_vertices[1]))
diff_10 = len(np.setdiff1d(src_vertices[1], src_vertices[0]))
inter_10 = len(np.intersect1d(src_vertices[1], src_vertices[0]))
output_data_lh = np.zeros([len(verts_lh), 6])
tmp = np.array([0, 1., 0, 0, 1, 0])
output_data_lh[:diff_01, :] = np.tile(tmp, (diff_01, 1))
tmp = np.array([0, 2, 0, 0, 2.5, 0])
output_data_lh[diff_01:diff_01 + inter_10, :] = np.tile(tmp, (inter_10, 1))
tmp = np.array([0, 1, 0, 0, 1.5, 0])
output_data_lh[diff_01 + inter_10:, :] = np.tile(tmp, (diff_10, 1))
data_rh_wf = np.array([1., 1, 2, 1, 1, 0])
output_data_rh = np.tile(data_rh_wf, (len(src_vertices[2]), 1))
output_data = np.vstack([output_data_lh, output_data_rh])
ss = SourceSimulator(src, tmin, tstep)
for i in range(3):
ss.add_data(mylabels[i], wfs[i], events[i])
stc = ss.get_stc()
stim_channel = ss.get_stim_channel()
# Stim channel data must have the same size as stc time samples
assert (len(stim_channel) == stc.data.shape[1])
stim_channel = ss.get_stim_channel(0., 0.)
assert (len(stim_channel) == 0)
assert (np.all(stc.vertices[0] == verts_lh))
assert (np.all(stc.vertices[1] == verts_rh))
assert_array_almost_equal(stc.lh_data, output_data_lh)
assert_array_almost_equal(stc.rh_data, output_data_rh)
assert_array_almost_equal(stc.data, output_data)
counter = 0
for stc, stim in ss:
counter += 1
assert counter == 1
half_ss = SourceSimulator(src, tmin, tstep, duration=0.5)
for i in range(3):
half_ss.add_data(mylabels[i], wfs[i], events[i])
half_stc = half_ss.get_stc()
assert_array_almost_equal(stc.data[:, :3], half_stc.data)
ss = SourceSimulator(src)
with pytest.raises(ValueError, match='No simulation parameters'):
ss.get_stc()
with pytest.raises(ValueError, match='label must be a Label'):
ss.add_data(1, wfs, events)
with pytest.raises(ValueError,
match='Number of waveforms and events '
'should match'):
ss.add_data(mylabels[0], wfs[:2], events)