1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
|
from gudhi import SimplexTree
"""This file is part of the Gudhi Library. The Gudhi library
(Geometric Understanding in Higher Dimensions) is a generic C++
library for computational topology.
Author(s): Vincent Rouvreau
Copyright (C) 2016 INRIA
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
__author__ = "Vincent Rouvreau"
__copyright__ = "Copyright (C) 2016 INRIA"
__license__ = "GPL v3"
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.) == 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
|
