def get_persistence_images(persistence_diagram):
pi = PersistenceImage(sigma=0.001,
n_bins=N_BINS,
weight_function=None,
n_jobs=N_JOBS)
print("Computed persistence images")
return pi.fit_transform(persistence_diagram)
def test_pi_positive(pts):
pi = PersistenceImage(sigma=1)
diagrams = np.expand_dims(np.concatenate(
[np.sort(pts, axis=1),
np.zeros((pts.shape[0], 1))], axis=1),
axis=0)
assert np.all(pi.fit_transform(diagrams) >= 0.)
def test_pi_positive(pts):
diagrams = np.expand_dims(np.concatenate(
[np.sort(pts, axis=1),
np.zeros((pts.shape[0], 1))], axis=1),
axis=0)
sigma = (np.max(diagrams[:, :, 1] - np.min(diagrams[:, :, 0]))) / 2
pi = PersistenceImage(sigma=sigma)
assert np.all(pi.fit_transform(diagrams) >= 0.)
def persistence_image(persistence_diagram, sigma, title):
pi = PersistenceImage(sigma=sigma,
n_bins=100,
weight_function=None,
n_jobs=N_JOBS)
persistence_image = pi.fit_transform(persistence_diagram)
fig = pi.plot(persistence_image)
fig.update_layout(title=title).show()
return persistence_image
def test_large_pi_null_parallel():
"""Test that pi is computed correctly when the input array is at least 1MB
and more than 1 process is used, triggering joblib's use of memmaps"""
X = np.linspace(0, 100, 300000)
pi = PersistenceImage(sigma=1, n_bins=10, n_jobs=2)
diagrams = np.expand_dims(np.stack([X, X, np.zeros(len(X))]).transpose(),
axis=0)
diagrams = np.repeat(diagrams, 2, axis=0)
diagrams[1, :, 1] += 1
assert_almost_equal(pi.fit_transform(diagrams)[0], 0)
def test_pi_null(X):
"""Test that, if one trivial diagram (all pts on the diagonal) is provided,
(along with a non-trivial one), then its pi is null"""
pi = PersistenceImage(sigma=1, n_bins=10)
X = np.append(X, 1 + X[-1])
diagrams = np.expand_dims(np.stack(
[X, X, np.zeros((X.shape[0], ), dtype=int)]).transpose(),
axis=0)
diagrams = np.repeat(diagrams, 2, axis=0)
diagrams[1, :, 1] += 1
assert_almost_equal(pi.fit_transform(diagrams)[0], 0)
def test_pi_null(X):
"""Test that, if one trivial diagram (all pts on the diagonal) is provided,
along with a non-trivial one, then its persistence image is null"""
n_bins = 10
X = np.append(X, 1 + X[-1])
diagrams = np.expand_dims(np.stack([X, X, np.zeros(len(X))]).transpose(),
axis=0)
diagrams = np.repeat(diagrams, 2, axis=0)
diagrams[1, :, 1] += 1
sigma = (np.max(diagrams[:, :, 1] - np.min(diagrams[:, :, 0]))) / 2
pi = PersistenceImage(sigma=sigma, n_bins=n_bins)
assert_almost_equal(pi.fit_transform(diagrams)[0], 0)
def test_pi_zero_weight_function(n_jobs):
pi = PersistenceImage(weight_function=lambda x: x * 0., n_jobs=n_jobs)
X_res = pi.fit_transform(X)
assert np.array_equal(X_res, np.zeros_like(X_res))
