def bettiNumbers(self, *args, **kwargs):
from gudhi import RipsComplex, plot_persistence_diagram, plot_persistence_barcode, sparsify_point_set
import random as r
import numpy as np
import matplotlib.pyplot as plt
targetCluster = kwargs.get('targetCluster', [1])
threshold = kwargs.get('threshold', 0.05)
sparsifyThreshold = kwargs.get('sparsifyThreshold', threshold/8)
plot = kwargs.get('plot', False)
pointList = []
for point in self.points:
if point.cluster in targetCluster:
pointList.append(np.array(point.coordinates))
pointList = sparsify_point_set(
points=pointList, min_squared_dist=sparsifyThreshold**2)
point_complex = RipsComplex(
max_edge_length=threshold/2, points=pointList)
simplex_tree = point_complex.create_simplex_tree(
max_dimension=self.dimension)
persistence = simplex_tree.persistence()
if plot:
plot_persistence_barcode(persistence)
plt.plot()
plot_persistence_diagram(persistence)
plt.plot()
return simplex_tree.betti_numbers()
def test_simple_sparsify_points():
point_set = [[0, 1], [0, 0], [1, 0], [1, 1]]
# Test the limits
# assert gudhi.sparsify_point_set(points = [], min_squared_dist = 0.0) == []
# assert gudhi.sparsify_point_set(points = [], min_squared_dist = 10.0) == []
assert gudhi.sparsify_point_set(points=point_set,
min_squared_dist=0.0) == point_set
assert gudhi.sparsify_point_set(points=point_set,
min_squared_dist=0.999) == point_set
assert gudhi.sparsify_point_set(points=point_set,
min_squared_dist=1.001) == [
[0, 1],
[1, 0],
]
assert gudhi.sparsify_point_set(points=point_set,
min_squared_dist=1.999) == [
[0, 1],
[1, 0],
]
assert gudhi.sparsify_point_set(points=point_set,
min_squared_dist=2.001) == [[0, 1]]
assert (len(
gudhi.sparsify_point_set(off_file="subsample.off",
min_squared_dist=0.0)) == 7)
assert (len(
gudhi.sparsify_point_set(off_file="subsample.off",
min_squared_dist=30.0)) == 5)
assert (len(
gudhi.sparsify_point_set(off_file="subsample.off",
min_squared_dist=40.1)) == 4)
assert (len(
gudhi.sparsify_point_set(off_file="subsample.off",
min_squared_dist=89.9)) == 3)
assert (len(
gudhi.sparsify_point_set(off_file="subsample.off",
min_squared_dist=100.0)) == 2)
assert (len(
gudhi.sparsify_point_set(off_file="subsample.off",
min_squared_dist=324.9)) == 2)
assert (len(
gudhi.sparsify_point_set(off_file="subsample.off",
min_squared_dist=325.01)) == 1)