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from gudhi import RipsComplex
from math import sqrt
""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
Author(s): Vincent Rouvreau
Copyright (C) 2016 Inria
Modification(s):
- YYYY/MM Author: Description of the modification
"""
__author__ = "Vincent Rouvreau"
__copyright__ = "Copyright (C) 2016 Inria"
__license__ = "MIT"
def test_empty_rips():
rips_complex = RipsComplex()
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 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_sparse_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, sparse=0.001)
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_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 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 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
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