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_fit_transform_plot_one_hom_dim(hom_dim_ix):
HeatKernel().fit_transform_plot(X,
sample=0,
homology_dimension_ix=hom_dim_ix)
PersistenceImage().fit_transform_plot(X,
sample=0,
homology_dimension_ix=hom_dim_ix)
def test_not_fitted():
with pytest.raises(NotFittedError):
PersistenceEntropy().transform(X)
with pytest.raises(NotFittedError):
BettiCurve().transform(X)
with pytest.raises(NotFittedError):
PersistenceLandscape().transform(X)
with pytest.raises(NotFittedError):
HeatKernel().transform(X)
with pytest.raises(NotFittedError):
PersistenceImage().transform(X)
with pytest.raises(NotFittedError):
Silhouette().transform(X)
def generate_sample_representations(paths_to_patches, labels):
sample_rep_dir = DOTENV_KEY2VAL["GEN_FIGURES_DIR"] + "/sample_rep/"
try:
os.mkdir(sample_rep_dir)
except OSError:
print("Creation of the directory %s failed" % sample_rep_dir)
else:
print("Successfully created the directory %s " % sample_rep_dir)
for i, path in enumerate(paths_to_patches):
patch = np.load(path)
cp = CubicalPersistence(
homology_dimensions=(0, 1, 2),
coeff=2,
periodic_dimensions=None,
infinity_values=None,
reduced_homology=True,
n_jobs=N_JOBS,
)
diagrams_cubical_persistence = cp.fit_transform(
patch.reshape(1, 30, 36, 30)
)
for h_dim in HOMOLOGY_DIMENSIONS:
cp.plot(
diagrams_cubical_persistence,
homology_dimensions=[h_dim],
).update_traces(
marker=dict(size=10, color=HOMOLOGY_CMAP[h_dim]),
).write_image(
sample_rep_dir
+ f"persistence_diagram_{labels[i]}_H_{h_dim}.png",
scale=SCALE,
)
representation_names = [
"Persistence landscape",
"Betti curve",
"Persistence image",
"Heat kernel",
"Silhouette",
]
for j, rep in enumerate(representation_names):
# Have not found a better way of doing this yet.
if rep == "Persistence landscape":
rep = PersistenceLandscape(
n_layers=N_LAYERS, n_bins=VEC_SIZE, n_jobs=N_JOBS
)
elif rep == "Betti curve":
rep = BettiCurve()
elif rep == "Persistence image":
rep = PersistenceImage(
sigma=0.001, n_bins=VEC_SIZE, n_jobs=N_JOBS
)
elif rep == "Heat kernel":
rep = HeatKernel(sigma=0.001, n_bins=VEC_SIZE, n_jobs=N_JOBS)
elif rep == "Silhouette":
rep = Silhouette(power=1.0, n_bins=VEC_SIZE, n_jobs=N_JOBS)
vectorial_representation = rep.fit_transform(
diagrams_cubical_persistence
)
if representation_names[j] in ["Persistence image", "Heat kernel"]:
for h_dim in range(vectorial_representation.shape[1]):
plt.imshow(
vectorial_representation[0:, h_dim, :, :].reshape(
VEC_SIZE, VEC_SIZE
),
cmap=(HOMOLOGY_CMAP[h_dim] + "s").capitalize(),
)
# plt.title(
# f"{representation_names[j]} representation of a "
# f"{labels[i]} patient in h_{image}"
# )
plt.savefig(
sample_rep_dir
+ f"{representation_names[j].replace(' ', '_')}"
f"_{labels[i]}_h_{h_dim}.png",
bbox_inches="tight",
)
else:
rep.plot(vectorial_representation).update_layout(
title=None,
margin=dict(l=0, r=0, b=0, t=0, pad=4),
).write_image(
sample_rep_dir
+ f"{representation_names[j].replace(' ', '_')}"
f"_{labels[i]}.png",
scale=SCALE,
)
print(f"Done plotting {labels[i]} sample")
def test_pi_not_fitted():
pi = PersistenceImage(sigma=1)
with pytest.raises(NotFittedError):
pi.transform(diagram)
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))
pio.renderers.default = 'plotly_mimetype'
X = np.array([[[0., 0., 0.], [0., 1., 0.], [2., 3., 0.],
[4., 6., 1.], [2., 6., 1.]]])
line_plots_traces_params = {"mode": "lines+markers"}
heatmap_trace_params = {"colorscale": "viridis"}
layout_params = {"title": "New title"}
@pytest.mark.parametrize('transformer',
[PersistenceEntropy(), NumberOfPoints(),
ComplexPolynomial(), BettiCurve(),
PersistenceLandscape(), HeatKernel(),
PersistenceImage(), Silhouette()])
def test_not_fitted(transformer):
with pytest.raises(NotFittedError):
transformer.transform(X)
@pytest.mark.parametrize('transformer',
[HeatKernel(), PersistenceImage()])
@pytest.mark.parametrize('hom_dim_idx', [0, 1])
def test_fit_transform_plot_one_hom_dim(transformer, hom_dim_idx):
plotly_params = \
{"trace": heatmap_trace_params, "layout": layout_params}
transformer.fit_transform_plot(
X, sample=0, homology_dimension_idx=hom_dim_idx,
plotly_params=plotly_params
)
X = np.array([[[0., 0., 0.], [0., 1., 0.], [2., 3., 0.], [4., 6., 1.],
[2., 6., 1.]]])
line_plots_traces_params = {"mode": "lines+markers"}
heatmap_trace_params = {"colorscale": "viridis"}
layout_params = {"title": "New title"}
@pytest.mark.parametrize('transformer', [
PersistenceEntropy(),
NumberOfPoints(),
ComplexPolynomial(),
BettiCurve(),
PersistenceLandscape(),
HeatKernel(),
PersistenceImage(),
Silhouette()
])
def test_not_fitted(transformer):
with pytest.raises(NotFittedError):
transformer.transform(X)
@pytest.mark.parametrize('transformer', [HeatKernel(), PersistenceImage()])
@pytest.mark.parametrize('hom_dim_idx', [0, 1])
def test_fit_transform_plot_one_hom_dim(transformer, hom_dim_idx):
plotly_params = \
{"trace": heatmap_trace_params, "layout": layout_params}
transformer.fit_transform_plot(X,
sample=0,
homology_dimension_idx=hom_dim_idx,
