How to use persim - 10 common examples
To help you get started, we’ve selected a few persim examples, based on popular ways it is used in public projects.
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scikit-tda / persim / test / test_visuals.py View on Github 
def test_set_title(self):
diagrams = [
np.array([[0, 1], [1, 1], [2, 4], [3, 5]]),
np.array([[0.5, 3], [2, 4], [4, 5], [10, 15]])
]
f, ax = plt.subplots()
plot_diagrams(diagrams, title='my title', show=False)
assert ax.get_title() == 'my title'
f, ax = plt.subplots()
plot_diagrams(diagrams, show=False)
assert ax.get_title() == ''def test_legend_true(self):
diagrams = [
np.array([[0, 1], [1, 1], [2, 4], [3, 5]]),
np.array([[0.5, 3], [2, 4], [4, 5], [10, 15]])
]
f, ax = plt.subplots()
plot_diagrams(diagrams, legend=True, show=False)
legend = [child for child in ax.get_children()
if child.__class__.__name__ == "Legend"]
assert len(legend) == 1def test_single(self):
""" Most just test this doesn't crash
"""
diagram = np.array([[0, 1], [1, 1], [2, 4], [3, 5]])
f, ax = plt.subplots()
plot_diagrams(diagram, show=False)
x_plot, y_plot = ax.lines[0].get_xydata().T
assert x_plot[0] <= np.min(diagram)
assert x_plot[1] >= np.max(diagram)
# get PathCollection
pathcols = [child for child in ax.get_children()
if child.__class__.__name__ == "PathCollection"]
assert len(pathcols) == 1def test_plot_only(self):
diagrams = [
np.array([[0, 1], [1, 1], [2, 4], [3, 5]]),
np.array([[0.5, 3], [2, 4], [4, 5], [10, 15]])
]
f, ax = plt.subplots()
plot_diagrams(diagrams, legend=False, show=False, plot_only=[1])def test_default_square(self):
diagrams = [
np.array([[0, 1], [1, 1], [2, 4], [3, 5]]),
np.array([[0.5, 3], [2, 4], [4, 5], [10, 15]])
]
f, ax = plt.subplots()
plot_diagrams(diagrams, show=False)
diagonal = ax.lines[0].get_xydata()
assert diagonal[0, 0] == diagonal[0, 1]
assert diagonal[1, 0] == diagonal[1, 1]def test_multiple(self):
diagrams = [
np.array([[0, 1], [1, 1], [2, 4], [3, 5]]),
np.array([[0.5, 3], [2, 4], [4, 5], [10, 15]])
]
f, ax = plt.subplots()
plot_diagrams(diagrams, show=False)
pathcols = [child for child in ax.get_children()
if child.__class__.__name__ == "PathCollection"]
assert len(pathcols) == 2
np.testing.assert_array_equal(pathcols[0].get_offsets(), diagrams[0])
np.testing.assert_array_equal(pathcols[1].get_offsets(), diagrams[1])def test_lifetime_removes_birth(self):
diagrams = [
np.array([[0, 1], [1, 1], [2, 4], [3, 5]]),
np.array([[0.5, 3], [2, 4], [4, 5], [10, 15]])
]
f, ax = plt.subplots()
plot_diagrams(diagrams, lifetime=True, show=False)
pathcols = [child for child in ax.get_children()
if child.__class__.__name__ == "PathCollection"]
modded1 = diagrams[0]
modded1[:, 1] = diagrams[0][:, 1] - diagrams[0][:, 0]
modded2 = diagrams[1]
modded2[:, 1] = diagrams[1][:, 1] - diagrams[1][:, 0]
assert len(pathcols) == 2
np.testing.assert_array_equal(pathcols[0].get_offsets(), modded1)
np.testing.assert_array_equal(pathcols[1].get_offsets(), modded2)def test_legend_false(self):
diagrams = [
np.array([[0, 1], [1, 1], [2, 4], [3, 5]]),
np.array([[0.5, 3], [2, 4], [4, 5], [10, 15]])
]
f, ax = plt.subplots()
plot_diagrams(diagrams, legend=False, show=False)
legend = [child for child in ax.get_children()
if child.__class__.__name__ == "Legend"]
assert len(legend) == 0def test_infty(self):
diagrams = [
np.array([[0, np.inf], [1, 1], [2, 4], [3, 5]]),
np.array([[0.5, 3], [2, 4], [4, 5], [10, 15]])
]
f, ax = plt.subplots()
plot_diagrams(diagrams, legend=True, show=False)def test_kernel_mean(self):
pim = PersImage()
kf = pim.kernel(2)
data = np.array([[0, 0]])
assert kf(np.array([[0, 0]]), [0, 0]) >= kf(
np.array([[1, 1]]), [0, 0]
), "decreasing away"
assert kf(np.array([[0, 0]]), [1, 1]) == kf(
np.array([[1, 1]]), [0, 0]
), "symmetric"persim
Distances and representations of persistence diagrams
