def test_max_statistic_sequential():
data = Data()
data.generate_mute_data(104, 10)
settings = {
'cmi_estimator': 'JidtKraskovCMI',
'n_perm_max_stat': 21,
'n_perm_min_stat': 21,
'n_perm_omnibus': 21,
'n_perm_max_seq': 21,
'max_lag_sources': 5,
'min_lag_sources': 1,
'max_lag_target': 5
}
setup = MultivariateTE()
setup._initialise(settings, data, sources=[0, 1], target=2)
setup.current_value = (0, 4)
setup.selected_vars_sources = [(1, 1), (1, 2)]
setup.selected_vars_full = [(0, 1), (1, 1), (1, 2)]
setup._selected_vars_realisations = np.random.rand(
data.n_realisations(setup.current_value),
len(setup.selected_vars_full))
setup._current_value_realisations = np.random.rand(
data.n_realisations(setup.current_value),
1)
[sign, p, te] = stats.max_statistic_sequential(analysis_setup=setup,
data=data)
def test_get_permuted_replications():
"""Test if permutation of replications works."""
# Load previously generated example data
path = os.path.join(os.path.dirname(__file__), 'data/')
res_0 = pickle.load(open(path + 'mute_results_0.p', 'rb'))
res_1 = pickle.load(open(path + 'mute_results_1.p', 'rb'))
comp_settings = {
'cmi_estimator': 'JidtKraskovCMI',
'n_perm_max_stat': 50,
'n_perm_min_stat': 50,
'n_perm_omnibus': 200,
'n_perm_max_seq': 50,
'tail': 'two',
'n_perm_comp': 6,
'alpha_comp': 0.2,
'stats_type': 'dependent'
}
comp = NetworkComparison()
comp._initialise(comp_settings)
comp._create_union(res_0, res_1)
# Check permutation for dependent samples test: Replace realisations by
# zeros and ones, check if realisations get swapped correctly.
dat1 = Data()
dat1.normalise = False
dat1.set_data(np.zeros((5, 100, 5)), 'psr')
dat2 = Data()
dat2.normalise = False
dat2.set_data(np.ones((5, 100, 5)), 'psr')
[cond_a_perm, cv_a_perm, cond_b_perm,
cv_b_perm] = comp._get_permuted_replications(data_a=dat1,
data_b=dat2,
target=1)
n_vars = cond_a_perm.shape[1]
assert (np.sum(cond_a_perm + cond_b_perm, axis=1) == n_vars).all(), (
'Dependent samples permutation did not work correctly.')
assert np.logical_xor(cond_a_perm, cond_b_perm).all(), (
'Dependent samples permutation did not work correctly.')
# Check permutations for independent samples test: Check the sum over
# realisations.
comp_settings['stats_type'] = 'independent'
comp = NetworkComparison()
comp._initialise(comp_settings)
comp._create_union(res_0, res_1)
[cond_a_perm, cv_a_perm, cond_b_perm,
cv_b_perm] = comp._get_permuted_replications(data_a=dat1,
data_b=dat2,
target=1)
n_samples = n_vars * dat1.n_realisations((0, comp.union['max_lag']))
assert np.sum(cond_a_perm + cond_b_perm, axis=None) == n_samples, (
'Independent samples permutation did not work correctly.')
# test unequal number of replications
dat2.generate_mute_data(100, 7)
with pytest.raises(AssertionError):
comp._get_permuted_replications(data_a=dat1, data_b=dat2, target=1)
def test_permute_replications():
"""Test surrogate creation by permuting replications."""
n = 20
data = Data(np.vstack((np.zeros(n), np.ones(n) * 1, np.ones(n) * 2,
np.ones(n) * 3)).astype(int),
'rs',
normalise=False)
current_value = (0, n - 1)
l = [(0, 1), (0, 3), (0, 7)]
[perm, perm_idx] = data.permute_replications(current_value=current_value,
idx_list=l)
assert (np.all(perm[:, 0] == perm_idx)), 'Permutation did not work.'
# Assert that samples have been swapped within the permutation range for
# the first replication.
rng = 3
current_value = (0, 3)
l = [(0, 0), (0, 1), (0, 2)]
# data = Data(np.arange(n), 's', normalise=False)
data = Data(np.vstack((np.arange(n), np.arange(n))).astype(int),
'rs',
normalise=False)
perm_opts = {'perm_type': 'local', 'perm_range': rng}
[perm, perm_idx] = data.permute_samples(current_value=current_value,
idx_list=l,
perm_opts=perm_opts)
samples = np.arange(rng)
i = 0
n_per_repl = int(data.n_realisations(current_value) / data.n_replications)
for p in range(n_per_repl // rng):
assert (np.unique(perm[i:i + rng, 0]) == samples).all(), (
'The permutation range was not respected.')
samples += rng
i += rng
rem = n_per_repl % rng
if rem > 0:
assert (np.unique(perm[i:i + rem, 0]) == samples[0:rem]).all(), (
'The remainder did not contain the same realisations.')
# Test assertions that perm_range is not too low or too high.
perm_opts = {'perm_type': 'local', 'perm_range': 1}
with pytest.raises(AssertionError):
data.permute_samples(current_value=current_value,
idx_list=l,
perm_opts=perm_opts)
perm_opts['perm_range'] = np.inf
with pytest.raises(AssertionError):
data.permute_samples(current_value=current_value,
idx_list=l,
perm_opts=perm_opts)
# Test ValueError if a string other than 'max' is given for perm_range.
perm_opts['perm_range'] = 'foo'
with pytest.raises(ValueError):
data.permute_samples(current_value=current_value,
idx_list=l,
perm_opts=perm_opts)
def test_permute_replications():
"""Test surrogate creation by permuting replications."""
n = 20
data = Data(np.vstack((np.zeros(n),
np.ones(n) * 1,
np.ones(n) * 2,
np.ones(n) * 3)).astype(int),
'rs',
normalise=False)
current_value = (0, n)
l = [(0, 1), (0, 3), (0, 7)]
[perm, perm_idx] = data.permute_replications(current_value=current_value,
idx_list=l)
assert (np.all(perm[:, 0] == perm_idx)), 'Permutation did not work.'
# Assert that samples have been swapped within the permutation range for
# the first replication.
rng = 3
current_value = (0, 3)
l = [(0, 0), (0, 1), (0, 2)]
#data = Data(np.arange(n), 's', normalise=False)
data = Data(np.vstack((np.arange(n),
np.arange(n))).astype(int),
'rs',
normalise=False)
[perm, perm_idx] = data.permute_samples(current_value=current_value,
idx_list=l,
perm_range=rng)
samples = np.arange(rng)
i = 0
n_per_repl = int(data.n_realisations(current_value) / data.n_replications)
for p in range(n_per_repl // rng):
assert (np.unique(perm[i:i + rng, 0]) == samples).all(), ('The '
'permutation range was not respected.')
samples += rng
i += rng
rem = n_per_repl % rng
if rem > 0:
assert (np.unique(perm[i:i + rem, 0]) == samples[0:rem]).all(), ('The '
'remainder did not contain the same realisations.')
# Test assertions that perm_range is not too low or too high.
with pytest.raises(AssertionError):
data.permute_samples(current_value=current_value,
idx_list=l,
perm_range=1)
with pytest.raises(AssertionError):
data.permute_samples(current_value=current_value,
idx_list=l,
perm_range=np.inf)
# Test ValueError if a string other than 'max' is given for perm_range.
with pytest.raises(ValueError):
data.permute_samples(current_value=current_value,
idx_list=l,
perm_range='foo')
def test_max_statistic_sequential():
dat = Data()
dat.generate_mute_data(104, 10)
opts = {
'cmi_calc_name': 'jidt_kraskov',
'n_perm_max_stat': 21,
'n_perm_min_stat': 21,
'n_perm_omnibus': 21,
'n_perm_max_seq': 21,
}
setup = Multivariate_te(max_lag_sources=5, min_lag_sources=1,
max_lag_target=5, options=opts)
setup.current_value = (0, 4)
setup.selected_vars_sources = [(1, 1), (1, 2)]
setup.selected_vars_full = [(0, 1), (1, 1), (1, 2)]
setup._selected_vars_realisations = np.random.rand(dat.n_realisations(setup.current_value),
len(setup.selected_vars_full))
setup._current_value_realisations = np.random.rand(dat.n_realisations(setup.current_value),
1)
[sign, p, te] = stats.max_statistic_sequential(analysis_setup=setup,
data=dat, opts=opts)
def test_max_statistic_sequential():
dat = Data()
dat.generate_mute_data(104, 10)
opts = {
'cmi_calc_name': 'jidt_kraskov',
'n_perm_max_stat': 21,
'n_perm_min_stat': 21,
'n_perm_omnibus': 21,
'n_perm_max_seq': 21,
}
setup = Multivariate_te(max_lag_sources=5, min_lag_sources=1,
max_lag_target=5, options=opts)
setup.current_value = (0, 4)
setup.selected_vars_sources = [(1, 1), (1, 2)]
setup.selected_vars_full = [(0, 1), (1, 1), (1, 2)]
setup._selected_vars_realisations = np.random.rand(dat.n_realisations(setup.current_value),
len(setup.selected_vars_full))
setup._current_value_realisations = np.random.rand(dat.n_realisations(setup.current_value),
1)
[sign, p, te] = stats.max_statistic_sequential(analysis_setup=setup,
data=dat, opts=opts)
def test_permute_replications():
"""Test surrogate creation by permuting replications."""
n = 20
data = Data(np.vstack((np.zeros(n),
np.ones(n) * 1,
np.ones(n) * 2,
np.ones(n) * 3)).astype(int),
'rs',
normalise=False)
current_value = (0, n - 1)
l = [(0, 1), (0, 3), (0, 7)]
[perm, perm_idx] = data.permute_replications(current_value=current_value,
idx_list=l)
assert (np.all(perm[:, 0] == perm_idx)), 'Permutation did not work.'
# Assert that samples have been swapped within the permutation range for
# the first replication.
rng = 3
current_value = (0, 3)
l = [(0, 0), (0, 1), (0, 2)]
# data = Data(np.arange(n), 's', normalise=False)
data = Data(np.vstack((np.arange(n),
np.arange(n))).astype(int),
'rs',
normalise=False)
perm_settings = {
'perm_type': 'local',
'perm_range': rng
}
[perm, perm_idx] = data.permute_samples(current_value=current_value,
idx_list=l,
perm_settings=perm_settings)
samples = np.arange(rng)
i = 0
n_per_repl = int(data.n_realisations(current_value) / data.n_replications)
for p in range(n_per_repl // rng):
assert (np.unique(perm[i:i + rng, 0]) == samples).all(), (
'The permutation range was not respected.')
samples += rng
i += rng
rem = n_per_repl % rng
if rem > 0:
assert (np.unique(perm[i:i + rem, 0]) == samples[0:rem]).all(), (
'The remainder did not contain the same realisations.')
def test_get_permuted_replications():
"""Test if permutation of replications works."""
# Load previously generated example data
path = os.path.join(os.path.dirname(__file__), 'data/')
res_0 = pickle.load(open(path + 'mute_results_0.p', 'rb'))
res_1 = pickle.load(open(path + 'mute_results_1.p', 'rb'))
comp_settings = {
'cmi_estimator': 'JidtKraskovCMI',
'n_perm_max_stat': 50,
'n_perm_min_stat': 50,
'n_perm_omnibus': 200,
'n_perm_max_seq': 50,
'tail': 'two',
'n_perm_comp': 6,
'alpha_comp': 0.2,
'stats_type': 'dependent'
}
comp = NetworkComparison()
comp._initialise(comp_settings)
comp._create_union(res_0, res_1)
# Check permutation for dependent samples test: Replace realisations by
# zeros and ones, check if realisations get swapped correctly.
dat1 = Data()
dat1.normalise = False
dat1.set_data(np.zeros((5, 100, 5)), 'psr')
dat2 = Data()
dat2.normalise = False
dat2.set_data(np.ones((5, 100, 5)), 'psr')
[cond_a_perm,
cv_a_perm,
cond_b_perm,
cv_b_perm] = comp._get_permuted_replications(data_a=dat1,
data_b=dat2,
target=1)
n_vars = cond_a_perm.shape[1]
assert (np.sum(cond_a_perm + cond_b_perm, axis=1) == n_vars).all(), (
'Dependent samples permutation did not work correctly.')
assert np.logical_xor(cond_a_perm, cond_b_perm).all(), (
'Dependent samples permutation did not work correctly.')
# Check permutations for independent samples test: Check the sum over
# realisations.
comp_settings['stats_type'] = 'independent'
comp = NetworkComparison()
comp._initialise(comp_settings)
comp._create_union(res_0, res_1)
[cond_a_perm,
cv_a_perm,
cond_b_perm,
cv_b_perm] = comp._get_permuted_replications(data_a=dat1,
data_b=dat2,
target=1)
n_samples = n_vars * dat1.n_realisations((0, comp.union['max_lag']))
assert np.sum(cond_a_perm + cond_b_perm, axis=None) == n_samples, (
'Independent samples permutation did not work correctly.')
# test unequal number of replications
dat2.generate_mute_data(100, 7)
with pytest.raises(AssertionError):
comp._get_permuted_replications(data_a=dat1, data_b=dat2, target=1)
