How to use the persim.bottleneck function in persim
To help you get started, we’ve selected a few persim examples, based on popular ways it is used in public projects.
Secure your code as it's written. Use Snyk Code to scan source code in minutes - no build needed - and fix issues immediately.
scikit-tda / persim / test / test_visuals.py View on Github 
def test_plot_labels(self):
dgm1 = np.array([
[0.1, 0.2],
[0.2, 0.4]
])
dgm2 = np.array([
[0.1, 0.2],
[0.3, 0.45]
])
d, (matching, D) = persim.bottleneck(dgm1, dgm2, matching=True)
persim.bottleneck_matching(
dgm1, dgm2, matching, D, labels=["X", "Y"])def test_matching(self):
dgm1 = np.array([
[0.5, 1],
[0.6, 1.1]
])
dgm2 = np.array([
[0.5, 1.1],
[0.6, 1.1],
[0.8, 1.1],
[1.0, 1.1],
])
d, (m, D) = bottleneck(
dgm1, dgm2,
matching=True
)
# These are very loose bounds
assert len(m) == len(dgm1) + len(dgm2)
assert D.shape == (len(dgm1) + len(dgm2), len(dgm1) + len(dgm2))def test_single(self):
d = bottleneck(
np.array([[0.5, 1]]),
np.array([[0.5, 1.1]])
)
# These are very loose bounds
assert d == pytest.approx(0.1, 0.001)def test_bottleneck_matching(self):
dgm1 = np.array([
[0.1, 0.2],
[0.2, 0.4]
])
dgm2 = np.array([
[0.1, 0.2],
[0.3, 0.45]
])
d, (matching, D) = persim.bottleneck(dgm1, dgm2, matching=True)
persim.bottleneck_matching(dgm1, dgm2, matching, D)def test_different_size(self):
d = bottleneck(
np.array([
[0.5, 1],
[0.6, 1.1]
]),
np.array([
[0.5, 1.1]
])
)
# These are very loose bounds
assert d == pytest.approx(0.1, 0.001)def test_some(self):
d = bottleneck(
np.array([
[0.5, 1],
[0.6, 1.1]
]),
np.array([
[0.5, 1.1],
[0.6, 1.3]
])
)
# These are very loose bounds
assert d == pytest.approx(0.2, 0.001)def test_diagonal(self):
d = bottleneck(
np.array([
[10.5, 10.5],
[10.6, 10.5],
[10.3, 10.3]
]),
np.array([
[0.5, 1.0],
[0.6, 1.2],
[0.3, 0.7]
])
)
# I expect this to be 0.6
assert d == pytest.approx(0.3, 0.001)persim
Distances and representations of persistence diagrams
