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
|
""" 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
"""
from gudhi import CubicalComplex, PeriodicCubicalComplex
import numpy as np
__author__ = "Vincent Rouvreau"
__copyright__ = "Copyright (C) 2016 Inria"
__license__ = "MIT"
def test_empty_constructor():
# Try to create an empty CubicalComplex
cub = CubicalComplex()
assert cub.__is_defined() == False
assert cub.__is_persistence_defined() == False
def test_non_existing_perseus_file_constructor():
# Try to open a non existing file
cub = CubicalComplex(perseus_file="pouetpouettralala.toubiloubabdou")
assert cub.__is_defined() == False
assert cub.__is_persistence_defined() == False
def test_dimension_or_perseus_file_constructor():
# Create test file
test_file = open("CubicalOneSphere.txt", "w")
test_file.write("2\n3\n3\n0\n0\n0\n0\n100\n0\n0\n0\n0\n")
test_file.close()
# CubicalComplex can be constructed from dimensions and
# top_dimensional_cells OR from a Perseus-style file name.
cub = CubicalComplex(
dimensions=[3, 3],
top_dimensional_cells=[1, 2, 3, 4, 5, 6, 7, 8, 9],
perseus_file="CubicalOneSphere.txt",
)
assert cub.__is_defined() == False
assert cub.__is_persistence_defined() == False
cub = CubicalComplex(
top_dimensional_cells=[1, 2, 3, 4, 5, 6, 7, 8, 9],
perseus_file="CubicalOneSphere.txt",
)
assert cub.__is_defined() == False
assert cub.__is_persistence_defined() == False
cub = CubicalComplex(dimensions=[3, 3], perseus_file="CubicalOneSphere.txt")
assert cub.__is_defined() == False
assert cub.__is_persistence_defined() == False
def simple_constructor(cub):
cub = CubicalComplex(
dimensions=[3, 3], top_dimensional_cells=[1, 2, 3, 4, 5, 6, 7, 8, 9]
)
assert cub.__is_defined() == True
assert cub.__is_persistence_defined() == False
assert cub.persistence() == [(0, (1.0, float("inf")))]
assert cub.__is_persistence_defined() == True
assert cub.betti_numbers() == [1, 0, 0]
assert cub.persistent_betti_numbers(0, 1000) == [0, 0, 0]
def test_simple_constructor_from_top_cells():
cub = CubicalComplex(
dimensions=[3, 3],
top_dimensional_cells=[1, 2, 3, 4, 5, 6, 7, 8, 9],
)
simple_constructor(cub)
def test_simple_constructor_from_numpy_array():
cub = CubicalComplex(
top_dimensional_cells=np.array([[1, 2, 3],
[4, 5, 6],
[7, 8, 9]])
)
simple_constructor(cub)
def user_case_simple_constructor(cub):
assert cub.__is_defined() == True
assert cub.__is_persistence_defined() == False
assert cub.persistence() == [(1, (0.0, 1.0)), (0, (0.0, float("inf")))]
assert cub.__is_persistence_defined() == True
other_cub = CubicalComplex(
dimensions=[3, 3],
top_dimensional_cells=[1000.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0],
)
assert other_cub.persistence() == [(1, (0.0, 1.0)), (0, (0.0, float("inf")))]
def test_user_case_simple_constructor_from_top_cells():
cub = CubicalComplex(
dimensions=[3, 3],
top_dimensional_cells=[float("inf"), 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0],
)
user_case_simple_constructor(cub)
def test_user_case_simple_constructor_from_numpy_array():
cub = CubicalComplex(
top_dimensional_cells=np.array([[float("inf"), 0.0, 0.0],
[0.0, 1.0, 0.0],
[0.0, 0.0, 0.0]])
)
user_case_simple_constructor(cub)
def test_dimension_file_constructor():
# Create test file
test_file = open("CubicalOneSphere.txt", "w")
test_file.write("2\n3\n3\n0\n0\n0\n0\n100\n0\n0\n0\n0\n")
test_file.close()
cub = CubicalComplex(perseus_file="CubicalOneSphere.txt")
assert cub.__is_defined() == True
assert cub.__is_persistence_defined() == False
assert cub.persistence() == [(1, (0.0, 100.0)), (0, (0.0, float("inf")))]
assert cub.__is_persistence_defined() == True
assert cub.betti_numbers() == [1, 0, 0]
assert cub.persistent_betti_numbers(0, 1000) == [1, 0, 0]
def test_connected_sublevel_sets():
array_cells = np.array([[3, 3], [2, 2], [4, 4]])
linear_cells = [3, 3, 2, 2, 4, 4]
dimensions = [2, 3]
periodic_dimensions = [False, False]
# with a numpy array version
cub = CubicalComplex(top_dimensional_cells = array_cells)
assert cub.persistence() == [(0, (2.0, float("inf")))]
assert cub.betti_numbers() == [1, 0, 0]
# with vector of dimensions
cub = CubicalComplex(dimensions = dimensions,
top_dimensional_cells = linear_cells)
assert cub.persistence() == [(0, (2.0, float("inf")))]
assert cub.betti_numbers() == [1, 0, 0]
# periodic with a numpy array version
cub = PeriodicCubicalComplex(top_dimensional_cells = array_cells,
periodic_dimensions = periodic_dimensions)
assert cub.persistence() == [(0, (2.0, float("inf")))]
assert cub.betti_numbers() == [1, 0, 0]
# periodic with vector of dimensions
cub = PeriodicCubicalComplex(dimensions = dimensions,
top_dimensional_cells = linear_cells,
periodic_dimensions = periodic_dimensions)
assert cub.persistence() == [(0, (2.0, float("inf")))]
assert cub.betti_numbers() == [1, 0, 0]
def test_cubical_generators():
cub = CubicalComplex(top_dimensional_cells = [[0, 0, 0], [0, 1, 0], [0, 0, 0]])
cub.persistence()
assert np.array_equal(cub.cofaces_of_persistence_pairs(), np.array([[1, 7, 4], [0, 8, -1]]))
|