def sample_pers(self):
"""
Subsample from the point cloud and build the Vietoris-Rips complex"""
sample_pts = gd.pick_n_random_points(self.points,
nb_points=self.sample_size)
rips = gd.RipsComplex(points=sample_pts,
max_edge_length=self.max_edge_length)
simplex_tree = rips.create_simplex_tree(max_dimension=2)
pers = simplex_tree.persistence()
return pers
def test_simple_pick_n_random_points():
point_set = [[0, 1], [0, 0], [1, 0], [1, 1]]
# Test the limits
assert gudhi.pick_n_random_points(points=[], nb_points=0) == []
assert gudhi.pick_n_random_points(points=[], nb_points=1) == []
assert gudhi.pick_n_random_points(points=point_set, nb_points=0) == []
# Go furter than point set on purpose
for iter in range(1, 10):
sub_set = gudhi.pick_n_random_points(points=point_set, nb_points=iter)
for sub in sub_set:
found = False
for point in point_set:
if point == sub:
found = True
# Check each sub set point is existing in the point set
assert found == True
# From off file test
for i in range(0, 7):
assert (len(
gudhi.pick_n_random_points(off_file="subsample.off",
nb_points=i)) == i)
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
help="Flag for not to display the diagrams",
)
args = parser.parse_args()
with open(args.file, "r") as f:
first_line = f.readline()
if (first_line == "OFF\n") or (first_line == "nOFF\n"):
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)
