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()