def test_rips_from_points():
point_list = [[0, 0], [1, 0], [0, 1], [1, 1]]
rips_complex = RipsComplex(points=point_list, max_edge_length=42)
simplex_tree = rips_complex.create_simplex_tree(max_dimension=1)
assert simplex_tree.__is_defined() == True
assert simplex_tree.__is_persistence_defined() == False
assert simplex_tree.num_simplices() == 10
assert simplex_tree.num_vertices() == 4
assert simplex_tree.get_filtration() == [
([0], 0.0),
([1], 0.0),
([2], 0.0),
([3], 0.0),
([0, 1], 1.0),
([0, 2], 1.0),
([1, 3], 1.0),
([2, 3], 1.0),
([1, 2], 1.4142135623730951),
([0, 3], 1.4142135623730951),
]
assert simplex_tree.get_star([0]) == [
([0], 0.0),
([0, 1], 1.0),
([0, 2], 1.0),
([0, 3], 1.4142135623730951),
]
assert simplex_tree.get_cofaces([0], 1) == [
([0, 1], 1.0),
([0, 2], 1.0),
([0, 3], 1.4142135623730951),
]
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 bettiNumbers(self, *args, **kwargs):
from gudhi import RipsComplex
import random as r
import numpy as np
nPoints = kwargs.get('nPoints', self.nPoints)
targetCluster = kwargs.get('targetCluster', [1])
maxEdge = kwargs.get('maxEdge', 10)
maxDim = kwargs.get('maxDim', self.dimension)
fromValue = kwargs.get('fromValue', 0.05)
toValue = kwargs.get('toValue', 0.05)
pointListTemp = []
for point in self.points:
if point.cluster in targetCluster:
pointListTemp.append(np.array(point.coordinates))
pointList = []
for point in pointListTemp:
random = r.random()
if random <= nPoints / len(pointListTemp):
pointList.append(point)
point_complex = RipsComplex(max_edge_length=maxEdge, points=pointList)
simplex_tree = point_complex.create_simplex_tree(max_dimension=maxDim)
persistence = simplex_tree.persistence()
return simplex_tree.persistent_betti_numbers(from_value=fromValue,
to_value=toValue)
def test_compatibility_with_rips():
distance_matrix = np.array([[0, 1, 1, sqrt(2)], [1, 0, sqrt(2), 1], [1, sqrt(2), 0, 1], [sqrt(2), 1, 1, 0]])
dtm_rips = DTMRipsComplex(distance_matrix=distance_matrix, max_filtration=42)
st = dtm_rips.create_simplex_tree(max_dimension=1)
rips_complex = RipsComplex(distance_matrix=distance_matrix, max_edge_length=42)
st_from_rips = rips_complex.create_simplex_tree(max_dimension=1)
assert list(st.get_filtration()) == list(st_from_rips.get_filtration())
def test_filtered_rips_from_points():
point_list = [[0, 0], [1, 0], [0, 1], [1, 1]]
filtered_rips = RipsComplex(points=point_list, max_edge_length=1.0)
simplex_tree = filtered_rips.create_simplex_tree(max_dimension=1)
assert simplex_tree.__is_defined() == True
assert simplex_tree.__is_persistence_defined() == False
assert simplex_tree.num_simplices() == 8
assert simplex_tree.num_vertices() == 4
def test_filtered_rips_from_distance_matrix():
distance_matrix = [[0], [1, 0], [1, sqrt(2), 0], [sqrt(2), 1, 1, 0]]
filtered_rips = RipsComplex(distance_matrix=distance_matrix,
max_edge_length=1.0)
simplex_tree = filtered_rips.create_simplex_tree(max_dimension=1)
assert simplex_tree.__is_defined() == True
assert simplex_tree.__is_persistence_defined() == False
assert simplex_tree.num_simplices() == 8
assert simplex_tree.num_vertices() == 4
def test_sparse_with_multiplicity():
points = [
[3, 4],
[0.1, 2],
[0.1, 2],
[0.1, 2],
[0.1, 2],
[0.1, 2],
[0.1, 2],
[0.1, 2],
[0.1, 2],
[0.1, 2],
[0.1, 2],
[3, 4.1],
]
rips = RipsComplex(points=points, sparse=0.01)
simplex_tree = rips.create_simplex_tree(max_dimension=2)
assert simplex_tree.num_simplices() == 7
diag = simplex_tree.persistence()
def test_rips_from_distance_matrix():
distance_matrix = [[0], [1, 0], [1, sqrt(2), 0], [sqrt(2), 1, 1, 0]]
rips_complex = RipsComplex(distance_matrix=distance_matrix,
max_edge_length=42)
simplex_tree = rips_complex.create_simplex_tree(max_dimension=1)
assert simplex_tree.__is_defined() == True
assert simplex_tree.__is_persistence_defined() == False
assert simplex_tree.num_simplices() == 10
assert simplex_tree.num_vertices() == 4
assert list(simplex_tree.get_filtration()) == [
([0], 0.0),
([1], 0.0),
([2], 0.0),
([3], 0.0),
([0, 1], 1.0),
([0, 2], 1.0),
([1, 3], 1.0),
([2, 3], 1.0),
([1, 2], 1.4142135623730951),
([0, 3], 1.4142135623730951),
]
assert simplex_tree.get_star([0]) == [
([0], 0.0),
([0, 1], 1.0),
([0, 2], 1.0),
([0, 3], 1.4142135623730951),
]
assert simplex_tree.get_cofaces([0], 1) == [
([0, 1], 1.0),
([0, 2], 1.0),
([0, 3], 1.4142135623730951),
]
from gudhi import RipsComplex, SimplexTree
import gudhi
from src.datasets import mnist
from pprint import pprint
import sys
print('Making Rips complex')
if len(sys.argv) > 1:
rc = RipsComplex(off_file=sys.argv[1])
else:
rc = RipsComplex(points=mnist(7))
print('And simplex tree')
simplex_tree = rc.create_simplex_tree(max_dimension=10)
diag = simplex_tree.persistence()
print("betti_numbers()=")
print(simplex_tree.betti_numbers())
pprint(diag)