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from gudhi import SimplexTree
""" 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_insertion():
st = SimplexTree()
assert st.__is_defined() == True
assert st.__is_persistence_defined() == False
# insert test
assert st.insert([0, 1]) == True
assert st.dimension() == 1
assert st.insert([0, 1, 2], filtration=4.0) == True
assert st.dimension() == 2
assert st.num_simplices() == 7
assert st.num_vertices() == 3
# find test
assert st.find([0, 1, 2]) == True
assert st.find([0, 1]) == True
assert st.find([0, 2]) == True
assert st.find([0]) == True
assert st.find([1]) == True
assert st.find([2]) == True
assert st.find([3]) == False
assert st.find([0, 3]) == False
assert st.find([1, 3]) == False
assert st.find([2, 3]) == False
# filtration test
st.initialize_filtration()
assert st.filtration([0, 1, 2]) == 4.0
assert st.filtration([0, 2]) == 4.0
assert st.filtration([1, 2]) == 4.0
assert st.filtration([2]) == 4.0
assert st.filtration([0, 1]) == 0.0
assert st.filtration([0]) == 0.0
assert st.filtration([1]) == 0.0
# skeleton test
assert st.get_skeleton(2) == [
([0, 1, 2], 4.0),
([0, 1], 0.0),
([0, 2], 4.0),
([0], 0.0),
([1, 2], 4.0),
([1], 0.0),
([2], 4.0),
]
assert st.get_skeleton(1) == [
([0, 1], 0.0),
([0, 2], 4.0),
([0], 0.0),
([1, 2], 4.0),
([1], 0.0),
([2], 4.0),
]
assert st.get_skeleton(0) == [([0], 0.0), ([1], 0.0), ([2], 4.0)]
# remove_maximal_simplex test
assert st.get_cofaces([0, 1, 2], 1) == []
st.remove_maximal_simplex([0, 1, 2])
assert st.get_skeleton(2) == [
([0, 1], 0.0),
([0, 2], 4.0),
([0], 0.0),
([1, 2], 4.0),
([1], 0.0),
([2], 4.0),
]
assert st.find([0, 1, 2]) == False
assert st.find([0, 1]) == True
assert st.find([0, 2]) == True
assert st.find([0]) == True
assert st.find([1]) == True
assert st.find([2]) == True
st.initialize_filtration()
assert st.persistence(persistence_dim_max=True) == [
(1, (4.0, float("inf"))),
(0, (0.0, float("inf"))),
]
assert st.__is_persistence_defined() == True
assert st.betti_numbers() == [1, 1]
assert st.persistent_betti_numbers(-0.1, 10000.0) == [0, 0]
assert st.persistent_betti_numbers(0.0, 10000.0) == [1, 0]
assert st.persistent_betti_numbers(3.9, 10000.0) == [1, 0]
assert st.persistent_betti_numbers(4.0, 10000.0) == [1, 1]
assert st.persistent_betti_numbers(9999.0, 10000.0) == [1, 1]
def test_expansion():
st = SimplexTree()
assert st.__is_defined() == True
assert st.__is_persistence_defined() == False
# insert test
assert st.insert([3, 2], 0.1) == True
assert st.insert([2, 0], 0.2) == True
assert st.insert([1, 0], 0.3) == True
assert st.insert([3, 1], 0.4) == True
assert st.insert([2, 1], 0.5) == True
assert st.insert([6, 5], 0.6) == True
assert st.insert([4, 2], 0.7) == True
assert st.insert([3, 0], 0.8) == True
assert st.insert([6, 4], 0.9) == True
assert st.insert([6, 3], 1.0) == True
assert st.num_vertices() == 7
assert st.num_simplices() == 17
assert st.get_filtration() == [
([2], 0.1),
([3], 0.1),
([2, 3], 0.1),
([0], 0.2),
([0, 2], 0.2),
([1], 0.3),
([0, 1], 0.3),
([1, 3], 0.4),
([1, 2], 0.5),
([5], 0.6),
([6], 0.6),
([5, 6], 0.6),
([4], 0.7),
([2, 4], 0.7),
([0, 3], 0.8),
([4, 6], 0.9),
([3, 6], 1.0),
]
st.expansion(3)
assert st.num_vertices() == 7
assert st.num_simplices() == 22
st.initialize_filtration()
assert st.get_filtration() == [
([2], 0.1),
([3], 0.1),
([2, 3], 0.1),
([0], 0.2),
([0, 2], 0.2),
([1], 0.3),
([0, 1], 0.3),
([1, 3], 0.4),
([1, 2], 0.5),
([0, 1, 2], 0.5),
([1, 2, 3], 0.5),
([5], 0.6),
([6], 0.6),
([5, 6], 0.6),
([4], 0.7),
([2, 4], 0.7),
([0, 3], 0.8),
([0, 1, 3], 0.8),
([0, 2, 3], 0.8),
([0, 1, 2, 3], 0.8),
([4, 6], 0.9),
([3, 6], 1.0),
]
def test_automatic_dimension():
st = SimplexTree()
assert st.__is_defined() == True
assert st.__is_persistence_defined() == False
# insert test
assert st.insert([0, 1, 3], filtration=0.5) == True
assert st.insert([0, 1, 2], filtration=1.0) == True
assert st.num_vertices() == 4
assert st.num_simplices() == 11
assert st.dimension() == 2
assert st.upper_bound_dimension() == 2
assert st.prune_above_filtration(0.6) == True
assert st.dimension() == 2
assert st.upper_bound_dimension() == 2
st.assign_filtration([0, 1, 3], 0.7)
assert st.filtration([0, 1, 3]) == 0.7
st.remove_maximal_simplex([0, 1, 3])
assert st.upper_bound_dimension() == 2
assert st.dimension() == 1
assert st.upper_bound_dimension() == 1
def test_make_filtration_non_decreasing():
st = SimplexTree()
assert st.__is_defined() == True
assert st.__is_persistence_defined() == False
# Inserted simplex:
# 1
# o
# /X\
# o---o---o---o
# 2 0 3\X/4
# o
# 5
assert st.insert([2, 1, 0], filtration=2.0) == True
assert st.insert([3, 0], filtration=2.0) == True
assert st.insert([3, 4, 5], filtration=2.0) == True
assert st.make_filtration_non_decreasing() == False
# Because of non decreasing property of simplex tree, { 0 } , { 1 } and
# { 0, 1 } are going to be set from value 2.0 to 1.0
st.insert([0, 1, 6, 7], filtration=1.0)
assert st.make_filtration_non_decreasing() == False
# Modify specific values to test make_filtration_non_decreasing
st.assign_filtration([0, 1, 6, 7], 0.8)
st.assign_filtration([0, 1, 6], 0.9)
st.assign_filtration([0, 6], 0.6)
st.assign_filtration([3, 4, 5], 1.2)
st.assign_filtration([3, 4], 1.1)
st.assign_filtration([4, 5], 1.99)
assert st.make_filtration_non_decreasing() == True
assert st.filtration([0, 1, 6, 7]) == 1.0
assert st.filtration([0, 1, 6]) == 1.0
assert st.filtration([0, 1]) == 1.0
assert st.filtration([0]) == 1.0
assert st.filtration([1]) == 1.0
assert st.filtration([3, 4, 5]) == 2.0
assert st.filtration([3, 4]) == 2.0
assert st.filtration([4, 5]) == 2.0
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