def test_spatio_temporal_src_connectivity():
"""Test spatio-temporal connectivity from source spaces"""
tris = np.array([[0, 1, 2], [3, 4, 5]])
src = [dict(), dict()]
connectivity = spatio_temporal_tris_connectivity(tris, 2)
src[0]['use_tris'] = np.array([[0, 1, 2]])
src[1]['use_tris'] = np.array([[0, 1, 2]])
src[0]['vertno'] = np.array([0, 1, 2])
src[1]['vertno'] = np.array([0, 1, 2])
connectivity2 = spatio_temporal_src_connectivity(src, 2)
assert_array_equal(connectivity.todense(), connectivity2.todense())
# add test for dist connectivity
src[0]['dist'] = np.ones((3, 3)) - np.eye(3)
src[1]['dist'] = np.ones((3, 3)) - np.eye(3)
src[0]['vertno'] = [0, 1, 2]
src[1]['vertno'] = [0, 1, 2]
connectivity3 = spatio_temporal_src_connectivity(src, 2, dist=2)
assert_array_equal(connectivity.todense(), connectivity3.todense())
# add test for source space connectivity with omitted vertices
inverse_operator = read_inverse_operator(fname_inv)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
src_ = inverse_operator['src']
connectivity = spatio_temporal_src_connectivity(src_, n_times=2)
assert len(w) == 1
a = connectivity.shape[0] / 2
b = sum([s['nuse'] for s in inverse_operator['src']])
assert_true(a == b)
assert_equal(grade_to_tris(5).shape, [40960, 3])
def test_spatio_temporal_src_connectivity():
"""Test spatio-temporal connectivity from source spaces."""
tris = np.array([[0, 1, 2], [3, 4, 5]])
src = [dict(), dict()]
connectivity = spatio_temporal_tris_connectivity(tris, 2)
src[0]['use_tris'] = np.array([[0, 1, 2]])
src[1]['use_tris'] = np.array([[0, 1, 2]])
src[0]['vertno'] = np.array([0, 1, 2])
src[1]['vertno'] = np.array([0, 1, 2])
src[0]['type'] = 'surf'
src[1]['type'] = 'surf'
connectivity2 = spatio_temporal_src_connectivity(src, 2)
assert_array_equal(connectivity.todense(), connectivity2.todense())
# add test for dist connectivity
src[0]['dist'] = np.ones((3, 3)) - np.eye(3)
src[1]['dist'] = np.ones((3, 3)) - np.eye(3)
src[0]['vertno'] = [0, 1, 2]
src[1]['vertno'] = [0, 1, 2]
src[0]['type'] = 'surf'
src[1]['type'] = 'surf'
connectivity3 = spatio_temporal_src_connectivity(src, 2, dist=2)
assert_array_equal(connectivity.todense(), connectivity3.todense())
# add test for source space connectivity with omitted vertices
inverse_operator = read_inverse_operator(fname_inv)
src_ = inverse_operator['src']
with pytest.warns(RuntimeWarning, match='will have holes'):
connectivity = spatio_temporal_src_connectivity(src_, n_times=2)
a = connectivity.shape[0] / 2
b = sum([s['nuse'] for s in inverse_operator['src']])
assert (a == b)
assert_equal(grade_to_tris(5).shape, [40960, 3])
def test_spatio_temporal_src_connectivity():
"""Test spatio-temporal connectivity from source spaces"""
tris = np.array([[0, 1, 2], [3, 4, 5]])
src = [dict(), dict()]
connectivity = spatio_temporal_tris_connectivity(tris, 2)
src[0]['use_tris'] = np.array([[0, 1, 2]])
src[1]['use_tris'] = np.array([[0, 1, 2]])
src[0]['vertno'] = np.array([0, 1, 2])
src[1]['vertno'] = np.array([0, 1, 2])
connectivity2 = spatio_temporal_src_connectivity(src, 2)
assert_array_equal(connectivity.todense(), connectivity2.todense())
# add test for dist connectivity
src[0]['dist'] = np.ones((3, 3)) - np.eye(3)
src[1]['dist'] = np.ones((3, 3)) - np.eye(3)
src[0]['vertno'] = [0, 1, 2]
src[1]['vertno'] = [0, 1, 2]
connectivity3 = spatio_temporal_src_connectivity(src, 2, dist=2)
assert_array_equal(connectivity.todense(), connectivity3.todense())
# add test for source space connectivity with omitted vertices
inverse_operator = read_inverse_operator(fname_inv)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
src_ = inverse_operator['src']
connectivity = spatio_temporal_src_connectivity(src_, n_times=2)
assert len(w) == 1
a = connectivity.shape[0] / 2
b = sum([s['nuse'] for s in inverse_operator['src']])
assert_true(a == b)
assert_equal(grade_to_tris(5).shape, [40960, 3])
def test_spatio_temporal_src_connectivity():
"""Test spatio-temporal connectivity from source spaces."""
tris = np.array([[0, 1, 2], [3, 4, 5]])
src = [dict(), dict()]
connectivity = spatio_temporal_tris_connectivity(tris, 2)
src[0]['use_tris'] = np.array([[0, 1, 2]])
src[1]['use_tris'] = np.array([[0, 1, 2]])
src[0]['vertno'] = np.array([0, 1, 2])
src[1]['vertno'] = np.array([0, 1, 2])
src[0]['type'] = 'surf'
src[1]['type'] = 'surf'
connectivity2 = spatio_temporal_src_connectivity(src, 2)
assert_array_equal(connectivity.todense(), connectivity2.todense())
# add test for dist connectivity
src[0]['dist'] = np.ones((3, 3)) - np.eye(3)
src[1]['dist'] = np.ones((3, 3)) - np.eye(3)
src[0]['vertno'] = [0, 1, 2]
src[1]['vertno'] = [0, 1, 2]
src[0]['type'] = 'surf'
src[1]['type'] = 'surf'
connectivity3 = spatio_temporal_src_connectivity(src, 2, dist=2)
assert_array_equal(connectivity.todense(), connectivity3.todense())
# add test for source space connectivity with omitted vertices
inverse_operator = read_inverse_operator(fname_inv)
src_ = inverse_operator['src']
with pytest.warns(RuntimeWarning, match='will have holes'):
connectivity = spatio_temporal_src_connectivity(src_, n_times=2)
a = connectivity.shape[0] / 2
b = sum([s['nuse'] for s in inverse_operator['src']])
assert (a == b)
assert_equal(grade_to_tris(5).shape, [40960, 3])
def test_spatio_temporal_tris_connectivity():
"""Test spatio-temporal connectivity from triangles"""
tris = np.array([[0, 1, 2], [3, 4, 5]])
connectivity = spatio_temporal_tris_connectivity(tris, 2)
x = [1, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1]
components = stats.cluster_level._get_components(np.array(x), connectivity)
# _get_components works differently now...
old_fmt = [0, 0, -2, -2, -2, -2, 0, -2, -2, -2, -2, 1]
new_fmt = np.array(old_fmt)
new_fmt = [np.nonzero(new_fmt == v)[0]
for v in np.unique(new_fmt[new_fmt >= 0])]
assert_true(len(new_fmt), len(components))
for c, n in zip(components, new_fmt):
assert_array_equal(c, n)
def perform_statistics_2(morphed_data, parameter_cache, vector, p_value=None):
"""Performs the statistical analysis using spatial_tris_connectivity.
:param morphed_data: Morphed data obtained from morph_data function
:param parameter_cache: Morphed parameter cache obtained from morph_data function.
:param vector: Method to perform modelling ('sLORETA' etc.)
:param p_value: Statistical p-value
:return: clu, good_cluster_inds
"""
# Unpack parameter cache dictionary
n_subjects = parameter_cache['n_subjects']
n_times = parameter_cache['n_times']
# Take on the absolute
X = np.abs(morphed_data)
# Obtain the paired contrast
if vector is False:
X = X[:, :, :, 0] - X[:, :, :,
1] # Dimension is (space, time, subjects)
else:
X = X[:, :, :, :,
0] - X[:, :, :, :,
1] # Dimension is (space, vector, time, subjects)
print('Computing connectivity... ')
connectivity_2 = mne.spatio_temporal_tris_connectivity(
grade_to_tris(5), n_times)
# Note that X needs to be a multi-dimensional array of shape [samples (subjects) x time x space]
if vector is False:
X = np.transpose(X, [2, 1, 0])
else:
X = np.transpose(X, [3, 2, 1, 0]) ##### TO DOUBLE CHECK #####
# Perform the clustering
p_threshold = p_value # 0.001
t_threshold = -stats.distributions.t.ppf(p_threshold / 2., n_subjects - 1)
print('Clustering... ')
T_obs, clusters, cluster_p_values, H0 = spatio_temporal_cluster_1samp_test(
X, connectivity=connectivity_2, n_jobs=1, threshold=t_threshold)
# Pack the outputs into tuple
clu = (T_obs, clusters, cluster_p_values, H0)
# Select the clusters that are sig. at p < p_value (Note this value is multiple-comparisons corrected)
good_cluster_inds = np.where(cluster_p_values < p_value)[0]
return clu, good_cluster_inds
