def test_schur_b_neg(self):
mu0 = mu(0)
P, sd = get_known_input(mu0)
with pytest.raises(
ValueError,
match=
"The number of clusters/states is not supposed to be negative",
):
_do_schur(P, eta=sd, m=-3)
def _generate_ground_truth_rot_matrices(self):
# this function generates the data for "test_init_final_rotation_matrix"
P, sd = get_known_input(mu(0))
g_ks = GPCCA(csr_matrix(P), method="krylov").optimize(3)
g_kd = GPCCA(P, method="krylov").optimize(3)
for g in [g_ks, g_kd]:
g.schur_vectors
_initialize_rot_matrix(sd)
g.rotation_matrix
def test_initialize_A(self):
mu0 = mu(0)
P, sd = get_known_input(mu0)
X, _, _ = _do_schur(P, sd, m=4)
evs = X[:, :4]
A = _initialize_rot_matrix(evs)
index = _indexsearch(evs)
A_exp = pinv(X[index, :4])
assert_allclose(A, A_exp)
def test_schur_b_pos(self):
N = 9
mu0 = mu(0)
P, sd = get_known_input(mu0)
X, RR, _ = _do_schur(P, eta=sd, m=3)
np.testing.assert_array_equal(P.shape, [N, N])
np.testing.assert_array_equal(X.shape, [9, 3])
np.testing.assert_array_equal(RR.shape, [3, 3])
_assert_schur(P, X, RR, N=None)
def test_use_minChi(self):
kmin, kmax = 2, 9
kopt = []
for mu_ in [10, 50, 100, 200, 500, 1000]:
P, sd = get_known_input(mu(mu_))
g = GPCCA(P, eta=sd)
minChi = g.minChi(kmin, kmax)
kopt.append(kmax - 1 - np.argmax(np.flipud(minChi[1:-1])))
np.testing.assert_array_equal(kopt, [3] * 5 + [7])
def test_cluster_by_isa(self, chi_isa_mu0_n3: np.ndarray,
chi_isa_mu100_n3: np.ndarray):
# chi_sa_mu0_n3 has permuted 2nd and 3d columns when compared to the matlab version
for mu_, chi_exp in zip([0, 100], [chi_isa_mu0_n3, chi_isa_mu100_n3]):
P, sd = get_known_input(mu(mu_))
X, _, _ = _do_schur(P, sd, m=3)
chi, _ = _cluster_by_isa(X[:, :3])
chi = chi[:, _find_permutation(chi_exp, chi)]
assert_allclose(chi.T @ chi, chi_exp.T @ chi_exp)
assert_allclose(chi, chi_exp)
def test_objective_1st_col(self, mocker):
# check_in_matlab: _objective
P, _ = get_known_input(mu(0))
N, M = P.shape[0], 4
_, L, _ = lu(P[:, :M])
mocker.patch(
"pygpcca._sorted_schur",
return_value=(np.eye(M), L, np.array([np.nan] * M)),
)
mocker.patch("pygpcca._gpcca._gram_schmidt_mod", return_value=L)
with pytest.raises(
ValueError,
match=r"The first column X\[:, 0\] of the Schur "
r"vector matrix isn't constantly equal 1.",
):
_do_schur(P,
eta=np.true_divide(np.ones((N, ), dtype=np.float64), N),
m=M)
def test_opt_soft_nelder_mead_more(self):
kmin, kmax = 2, 8
kopt = []
ks = np.arange(kmin, kmax)
for mu_ in [10, 50, 100, 200, 500, 1000]:
mu_ = mu(mu_)
P, sd = get_known_input(mu_)
X, _, _ = _do_schur(P, eta=sd, m=kmax)
crisp = [-np.inf] * (kmax - kmin)
for j, k in enumerate(range(kmin, kmax)):
svecs = X[:, :k]
A = _initialize_rot_matrix(svecs)
_, _, fopt = _opt_soft(svecs, A)
crisp[j] = (k - fopt) / k
kopt.append(ks[np.argmax(crisp)])
np.testing.assert_array_equal(kopt, [3, 3, 3, 2, 2, 7])