How to use the persim.plot_diagrams function in persim
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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)Essentially, visualize (x, y-x).
legend: bool, default is True
If true, show the legend.
show: bool, default is True
Call plt.show() after plotting.
If you are using self.plot() as part of a subplot,
set show=False and call plt.show() only once at the end.
"""
if diagrams is None:
# Allow using transformed diagrams as default
diagrams = self.dgms_
persim.plot_diagrams(
diagrams,
*args,
**kwargs
)persim
Distances and representations of persistence diagrams
