def test_witness_complex():
point_cloud = [
[1.0, 1.0],
[7.0, 0.0],
[4.0, 6.0],
[9.0, 6.0],
[0.0, 14.0],
[2.0, 19.0],
[9.0, 17.0],
]
landmarks = [[1.0, 1.0], [7.0, 0.0], [4.0, 6.0]]
euclidean_witness_complex = gudhi.EuclideanWitnessComplex(
landmarks=landmarks, witnesses=point_cloud)
simplex_tree = euclidean_witness_complex.create_simplex_tree(
max_alpha_square=4.1)
assert landmarks[0] == euclidean_witness_complex.get_point(0)
assert landmarks[1] == euclidean_witness_complex.get_point(1)
assert landmarks[2] == euclidean_witness_complex.get_point(2)
assert list(simplex_tree.get_filtration()) == [
([0], 0.0),
([1], 0.0),
([0, 1], 0.0),
([2], 0.0),
([0, 2], 0.0),
([1, 2], 0.0),
([0, 1, 2], 0.0),
]
def witness_complex_persistence(points, numb_landmarks, alpha, dim, field):
start_time = time.time()
landmarks = g.pick_n_random_points(points=points, nb_points=numb_landmarks)
witness_complex = g.EuclideanWitnessComplex(witnesses=points,
landmarks=landmarks)
simplex_tree = witness_complex.create_simplex_tree(
max_alpha_square=alpha**2, limit_dimension=dim)
logger.info("Build complex in {} sec".format(time.time() - start_time))
logger.info("{} vertices, {} simplices".format(
simplex_tree.num_vertices(), simplex_tree.num_simplices()))
start_time = time.time()
simplex_tree.initialize_filtration()
simplex_tree.persistence(homology_coeff_field=field)
logger.info("Build persistence in {} sec".format(time.time() - start_time))
return simplex_tree
print(
"#####################################################################"
)
print(
"EuclideanWitnessComplex creation from points read in a OFF file")
witnesses = gudhi.read_points_from_off_file(off_file=args.file)
landmarks = gudhi.pick_n_random_points(
points=witnesses, nb_points=args.number_of_landmarks)
message = ("EuclideanWitnessComplex with max_edge_length=" +
repr(args.max_alpha_square) + " - Number of landmarks=" +
repr(args.number_of_landmarks))
print(message)
witness_complex = gudhi.EuclideanWitnessComplex(witnesses=witnesses,
landmarks=landmarks)
simplex_tree = witness_complex.create_simplex_tree(
max_alpha_square=args.max_alpha_square,
limit_dimension=args.limit_dimension)
message = "Number of simplices=" + repr(simplex_tree.num_simplices())
print(message)
diag = simplex_tree.persistence()
print("betti_numbers()=")
print(simplex_tree.betti_numbers())
if args.no_diagram == False:
import matplotlib.pyplot as plot
gudhi.plot_persistence_diagram(diag, band=args.band)
def test_empty_euclidean_witness_complex():
euclidean_witness = gudhi.EuclideanWitnessComplex()
assert euclidean_witness.__is_defined() == False
