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""" 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): Yuichi Ike and Masatoshi Takenouchi
Copyright (C) 2020 Inria
Modification(s):
- YYYY/MM Author: Description of the modification
"""
from gudhi.weighted_rips_complex import WeightedRipsComplex
from gudhi.point_cloud.dtm import DistanceToMeasure
import numpy as np
from math import sqrt
from scipy.spatial.distance import cdist
import pytest
def test_non_dtm_rips_complex():
dist = [[], [1]]
weights = [1, 100]
w_rips = WeightedRipsComplex(distance_matrix=dist, weights=weights)
st = w_rips.create_simplex_tree(max_dimension=2)
assert st.filtration([0,1]) == pytest.approx(200.0)
def test_compatibility_with_rips():
distance_matrix = [[0], [1, 0], [1, sqrt(2), 0], [sqrt(2), 1, 1, 0]]
w_rips = WeightedRipsComplex(distance_matrix=distance_matrix,max_filtration=42)
st = w_rips.create_simplex_tree(max_dimension=1)
assert list(st.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),
]
def test_compatibility_with_filtered_rips():
distance_matrix = [[0], [1, 0], [1, sqrt(2), 0], [sqrt(2), 1, 1, 0]]
w_rips = WeightedRipsComplex(distance_matrix=distance_matrix,max_filtration=1.0)
st = w_rips.create_simplex_tree(max_dimension=1)
assert st.__is_defined() == True
assert st.__is_persistence_defined() == False
assert st.num_simplices() == 8
assert st.num_vertices() == 4
def test_dtm_rips_complex():
pts = np.array([[2.0, 2], [0, 1], [3, 4]])
dist = cdist(pts,pts)
dtm = DistanceToMeasure(2, q=2, metric="precomputed")
r = dtm.fit_transform(dist)
w_rips = WeightedRipsComplex(distance_matrix=dist, weights=r)
st = w_rips.create_simplex_tree(max_dimension=2)
st.persistence()
persistence_intervals0 = st.persistence_intervals_in_dimension(0)
assert persistence_intervals0 == pytest.approx(np.array([[3.16227766, 5.39834564],[3.16227766, 5.39834564], [3.16227766, float("inf")]]))
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