def test_dist_mat_to_vec_func_out_of_bounds(self, N, i, j):
"""Test that ValueError is raised when i or j or both are
out of bounds of N"""
# Check if i is out of bounds of N
with pytest.raises(ValueError):
PSA.dist_mat_to_vec(N, i, j)
def test_dist_mat_to_vec_func_i_equals_j(self):
"""Test that ValueError is raised when i == j or i,j == N"""
with self.assertRaises(ValueError):
PSA.dist_mat_to_vec(5, 4, 4)
with self.assertRaises(ValueError):
PSA.dist_mat_to_vec(4, 6, 4)
def test_dist_mat_to_vec_func_i_equals_j(self):
"""Test that ValueError is raised when i == j or i,j == N"""
with self.assertRaises(ValueError):
PSA.dist_mat_to_vec(5, 4, 4)
with self.assertRaises(ValueError):
PSA.dist_mat_to_vec(4, 6, 4)
def test_dist_mat_to_vec_func_bad_integers(self):
"""Test that ValueError is raised when i or j are
not Integers"""
with self.assertRaises(ValueError):
PSA.dist_mat_to_vec(5, '6', '7')
with self.assertRaises(ValueError):
PSA.dist_mat_to_vec(5, float(6), 7)
def test_dist_mat_to_vec_func_bad_integers(self):
"""Test that ValueError is raised when i or j are
not Integers"""
with self.assertRaises(ValueError):
PSA.dist_mat_to_vec(5, '6', '7')
with self.assertRaises(ValueError):
PSA.dist_mat_to_vec(5, float(6), 7)
def test_dist_mat_to_vec_func_bad_integers(self):
"""Test that ValueError is raised when i or j are
not Integers"""
with pytest.raises(ValueError) as err:
PSA.dist_mat_to_vec(5, '6', '7')
assert 'all must be of type int' in str(err.value)
with pytest.raises(ValueError):
PSA.dist_mat_to_vec(5, float(6), 7)
def test_distances_from_hausdorff_pairs_frames(self, psa):
"""Test whether actual distances between frames of Hausdorff
pairs of a path give the expected Hausdorff distance"""
psa.run_pairs_analysis(neighbors=True, hausdorff_pairs=True)
hausd_pairs = psa.hausdorff_pairs
npairs = int(psa.npaths * (psa.npaths - 1) / 2)
hausd_pairs_dists2 = np.array([hausd_pairs[i]['distance']
for i in range(npairs)])
err_msg = ("A Hausdorff pair analysis distance when accessed "
"by frame varies from expected Hausdorff distance")
dists = np.zeros((psa.npaths, psa.npaths))
for i in range(0, psa.npaths-1):
for j in range(i+1, psa.npaths):
pairidx = PSA.dist_mat_to_vec(psa.npaths, i, j)
p, q = hausd_pairs[pairidx]['frames']
dists[i,j] = (PSA.sqnorm(psa.paths[i][p,:,:] -
psa.paths[j][q,:,:]) /
psa.natoms)**0.5
assert_almost_equal(hausd_pairs_dists2,
dists[self.iu1],
decimal=6, err_msg=err_msg)
def test_dist_mat_to_vec_func_i_equals_j(self, N, i, j):
"""Test that ValueError is raised when i == j or i,j == N"""
with pytest.raises(ValueError):
PSA.dist_mat_to_vec(N, i, j)
def test_dist_mat_to_vec_input_numpy_integer_16(self):
"""Test whether inputs are supported as numpy integers rather than normal Integers"""
err_msg = "dist_mat_to_vec function returning wrong values"
assert_equal(
PSA.dist_mat_to_vec(np.int16(5), np.int16(3), np.int16(4)), np.int16(9),
err_msg)
def test_dist_mat_to_vec_i_greater_j(self):
"""Test the index of corresponding distance vector is correct if i > j"""
err_msg = "dist_mat_to_vec function returning wrong values"
assert_equal(PSA.dist_mat_to_vec(5, 4, 3), 9, err_msg)
def test_dist_mat_to_vec_func_out_of_bounds(self):
"""Test that ValueError is raised when i or j or both are
out of bounds of N"""
# Check if i is out of bounds of N
with self.assertRaises(ValueError):
PSA.dist_mat_to_vec(5, 6, 4)
# Check if j is out of bounds of N
with self.assertRaises(ValueError):
PSA.dist_mat_to_vec(5, 4, 6)
# Check if both i and j are out of bounds of N
with self.assertRaises(ValueError):
PSA.dist_mat_to_vec(5, 6, 7)
# Check if i is negative
with self.assertRaises(ValueError):
PSA.dist_mat_to_vec(5, -1, 2)
# Check if j is negative
with self.assertRaises(ValueError):
PSA.dist_mat_to_vec(5, 1, -2)
# Check if N is less than 2
with self.assertRaises(ValueError):
PSA.dist_mat_to_vec(1, 0, 0)
def test_dist_mat_to_vec_i_less_j(self):
"""Test the index of corresponding distance vector is correct if i < j"""
err_msg = "dist_mat_to_vec function returning wrong values"
assert_equal(PSA.dist_mat_to_vec(5, 3, 4), 9, err_msg)
def test_dist_mat_to_vec_func_out_of_bounds(self):
"""Test that ValueError is raised when i or j or both are
out of bounds of N"""
# Check if i is out of bounds of N
with self.assertRaises(ValueError):
PSA.dist_mat_to_vec(5, 6, 4)
# Check if j is out of bounds of N
with self.assertRaises(ValueError):
PSA.dist_mat_to_vec(5, 4, 6)
# Check if both i and j are out of bounds of N
with self.assertRaises(ValueError):
PSA.dist_mat_to_vec(5, 6, 7)
# Check if i is negative
with self.assertRaises(ValueError):
PSA.dist_mat_to_vec(5, -1, 2)
# Check if j is negative
with self.assertRaises(ValueError):
PSA.dist_mat_to_vec(5, 1, -2)
# Check if N is less than 2
with self.assertRaises(ValueError):
PSA.dist_mat_to_vec(1, 0, 0)
def test_dist_mat_to_vec_input_numpy_integer_16(self):
"""Test whether inputs are supported as numpy integers rather than normal Integers"""
err_msg = "dist_mat_to_vec function returning wrong values"
assert_equal(PSA.dist_mat_to_vec(np.int16(5), np.int16(3), np.int16(4)), np.int16(9), err_msg)
