def cubical_persistence(images,
title,
plot_diagrams=False,
betti_curves=False,
scaled=False):
homology_dimensions = (0, 1, 2)
cp = CubicalPersistence(
homology_dimensions=homology_dimensions,
coeff=2,
periodic_dimensions=None,
infinity_values=None,
reduced_homology=True,
n_jobs=N_JOBS,
)
diagrams_cubical_persistence = cp.fit_transform(images)
if scaled:
sc = Scaler(metric="bottleneck")
diagrams_cubical_persistence = sc.fit_transform(
diagrams_cubical_persistence)
else:
scaled_diagrams_cubical_persistence = diagrams_cubical_persistence
if plot_diagrams:
fig = cp.plot(diagrams_cubical_persistence)
fig.update_layout(title=title)
fig.show()
if betti_curves:
BC = BettiCurve()
X_betti_curves = BC.fit_transform(diagrams_cubical_persistence)
fig = BC.plot(X_betti_curves)
fig.update_layout(title=title)
fig.show()
if title is not None:
print(f"Computed CP for {title}")
return diagrams_cubical_persistence
def vr_persistent_homology(patch_pc):
homology_dimensions = (0, 1, 2)
VR = VietorisRipsPersistence(
metric="euclidean",
max_edge_length=5,
homology_dimensions=homology_dimensions,
n_jobs=N_JOBS,
)
diagrams_VietorisRips = VR.fit_transform(np.asarray(patch_pc))
VR.plot(diagrams_VietorisRips).show()
BC = BettiCurve()
X_betti_curves = BC.fit_transform(diagrams_VietorisRips)
BC.plot(X_betti_curves).show()
return diagrams_VietorisRips
def test_bc_transform_shape(n_bins):
bc = BettiCurve(n_bins=n_bins)
X_res = bc.fit_transform(X)
assert X_res.shape == (1, bc._n_dimensions, n_bins)