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)
def test_empty_rips():
rips_complex = RipsComplex()