summaryrefslogtreecommitdiff
path: root/src/Cech_complex/test/test_cech_complex.cpp
blob: 6e00d7b57a6b975212914c59241387b051caf578 (plain)
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
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
/*    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) 2018 Inria
 *
 *    Modification(s):
 *      - YYYY/MM Author: Description of the modification
 */

#define BOOST_TEST_DYN_LINK
#define BOOST_TEST_MODULE "cech_complex"
#include <boost/test/unit_test.hpp>

#include <cmath>  // float comparison
#include <limits>
#include <string>
#include <vector>
#include <algorithm>  // std::max

#include <gudhi/Cech_complex.h>
// to construct Cech_complex from a OFF file of points
#include <gudhi/Points_off_io.h>
#include <gudhi/Simplex_tree.h>
#include <gudhi/distance_functions.h>
#include <gudhi/Unitary_tests_utils.h>
#include <gudhi/Miniball.hpp>

// Type definitions
using Simplex_tree = Gudhi::Simplex_tree<>;
using Filtration_value = Simplex_tree::Filtration_value;
using Point = std::vector<Filtration_value>;
using Point_cloud = std::vector<Point>;
using Points_off_reader = Gudhi::Points_off_reader<Point>;
using Cech_complex = Gudhi::cech_complex::Cech_complex<Simplex_tree, Point_cloud>;

using Point_iterator = Point_cloud::const_iterator;
using Coordinate_iterator = Point::const_iterator;
using Min_sphere = Gudhi::Miniball::Miniball<Gudhi::Miniball::CoordAccessor<Point_iterator, Coordinate_iterator>>;

BOOST_AUTO_TEST_CASE(Cech_complex_for_documentation) {
  // ----------------------------------------------------------------------------
  //
  // Init of a Cech complex from a point cloud
  //
  // ----------------------------------------------------------------------------
  Point_cloud points;
  points.push_back({1., 0.});                  // 0
  points.push_back({0., 1.});                  // 1
  points.push_back({2., 1.});                  // 2
  points.push_back({3., 2.});                  // 3
  points.push_back({0., 3.});                  // 4
  points.push_back({3. + std::sqrt(3.), 3.});  // 5
  points.push_back({1., 4.});                  // 6
  points.push_back({3., 4.});                  // 7
  points.push_back({2., 4. + std::sqrt(3.)});  // 8
  points.push_back({0., 4.});                  // 9
  points.push_back({-0.5, 2.});                // 10

  Filtration_value max_radius = 1.0;
  std::clog << "========== NUMBER OF POINTS = " << points.size() << " - Cech max_radius = " << max_radius
            << "==========" << std::endl;

  Cech_complex cech_complex_for_doc(points, max_radius);

  GUDHI_TEST_FLOAT_EQUALITY_CHECK(cech_complex_for_doc.max_radius(), max_radius);
  std::size_t i = 0;
  for (; i < points.size(); i++) {
    BOOST_CHECK(points[i] == cech_complex_for_doc.get_point(i));
  }

  const int DIMENSION_1 = 1;
  Simplex_tree st;
  cech_complex_for_doc.create_complex(st, DIMENSION_1);
  std::clog << "st.dimension()=" << st.dimension() << std::endl;
  BOOST_CHECK(st.dimension() == DIMENSION_1);

  const int NUMBER_OF_VERTICES = 11;
  std::clog << "st.num_vertices()=" << st.num_vertices() << std::endl;
  BOOST_CHECK(st.num_vertices() == NUMBER_OF_VERTICES);

  std::clog << "st.num_simplices()=" << st.num_simplices() << std::endl;
  BOOST_CHECK(st.num_simplices() == 27);

  // Check filtration values of vertices is 0.0
  for (auto f_simplex : st.skeleton_simplex_range(0)) {
    BOOST_CHECK(st.filtration(f_simplex) == 0.0);
  }

  // Check filtration values of edges
  for (auto f_simplex : st.skeleton_simplex_range(DIMENSION_1)) {
    if (DIMENSION_1 == st.dimension(f_simplex)) {
      std::vector<Point> vp;
      std::clog << "vertex = (";
      for (auto vertex : st.simplex_vertex_range(f_simplex)) {
        std::clog << vertex << ",";
        vp.push_back(points.at(vertex));
      }
      std::clog << ") - distance =" << Gudhi::Minimal_enclosing_ball_radius()(vp.at(0), vp.at(1))
                << " - filtration =" << st.filtration(f_simplex) << std::endl;
      BOOST_CHECK(vp.size() == 2);
      GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex),
                                      Gudhi::Minimal_enclosing_ball_radius()(vp.at(0), vp.at(1)));
    }
  }

  const int DIMENSION_2 = 2;

#ifdef GUDHI_DEBUG
  BOOST_CHECK_THROW(cech_complex_for_doc.create_complex(st, DIMENSION_2), std::invalid_argument);
#endif

  Simplex_tree st2;
  cech_complex_for_doc.create_complex(st2, DIMENSION_2);
  std::clog << "st2.dimension()=" << st2.dimension() << std::endl;
  BOOST_CHECK(st2.dimension() == DIMENSION_2);

  std::clog << "st2.num_vertices()=" << st2.num_vertices() << std::endl;
  BOOST_CHECK(st2.num_vertices() == NUMBER_OF_VERTICES);

  std::clog << "st2.num_simplices()=" << st2.num_simplices() << std::endl;
  BOOST_CHECK(st2.num_simplices() == 30);

  Point_cloud points012;
  for (std::size_t vertex = 0; vertex <= 2; vertex++) {
    points012.push_back(cech_complex_for_doc.get_point(vertex));
  }
  std::size_t dimension = points[0].end() - points[0].begin();
  Min_sphere ms012(dimension, points012.begin(), points012.end());

  Simplex_tree::Filtration_value f012 = st2.filtration(st2.find({0, 1, 2}));
  std::clog << "f012= " << f012 << " | ms012_radius= " << std::sqrt(ms012.squared_radius()) << std::endl;

  GUDHI_TEST_FLOAT_EQUALITY_CHECK(f012, std::sqrt(ms012.squared_radius()));

  Point_cloud points1410;
  points1410.push_back(cech_complex_for_doc.get_point(1));
  points1410.push_back(cech_complex_for_doc.get_point(4));
  points1410.push_back(cech_complex_for_doc.get_point(10));
  Min_sphere ms1410(dimension, points1410.begin(), points1410.end());

  Simplex_tree::Filtration_value f1410 = st2.filtration(st2.find({1, 4, 10}));
  std::clog << "f1410= " << f1410 << " | ms1410_radius= " << std::sqrt(ms1410.squared_radius()) << std::endl;

  GUDHI_TEST_FLOAT_EQUALITY_CHECK(f1410, std::sqrt(ms1410.squared_radius()));

  Point_cloud points469;
  points469.push_back(cech_complex_for_doc.get_point(4));
  points469.push_back(cech_complex_for_doc.get_point(6));
  points469.push_back(cech_complex_for_doc.get_point(9));
  Min_sphere ms469(dimension, points469.begin(), points469.end());

  Simplex_tree::Filtration_value f469 = st2.filtration(st2.find({4, 6, 9}));
  std::clog << "f469= " << f469 << " | ms469_radius= " << std::sqrt(ms469.squared_radius()) << std::endl;

  GUDHI_TEST_FLOAT_EQUALITY_CHECK(f469, std::sqrt(ms469.squared_radius()));

  BOOST_CHECK((st2.find({6, 7, 8}) == st2.null_simplex()));
  BOOST_CHECK((st2.find({3, 5, 7}) == st2.null_simplex()));
}

BOOST_AUTO_TEST_CASE(Cech_complex_from_points) {
  // ----------------------------------------------------------------------------
  // Init of a list of points
  // ----------------------------------------------------------------------------
  Point_cloud points;
  std::vector<double> coords = {0.0, 0.0, 0.0, 1.0};
  points.push_back(Point(coords.begin(), coords.end()));
  coords = {0.0, 0.0, 1.0, 0.0};
  points.push_back(Point(coords.begin(), coords.end()));
  coords = {0.0, 1.0, 0.0, 0.0};
  points.push_back(Point(coords.begin(), coords.end()));
  coords = {1.0, 0.0, 0.0, 0.0};
  points.push_back(Point(coords.begin(), coords.end()));

  // ----------------------------------------------------------------------------
  // Init of a Cech complex from the list of points
  // ----------------------------------------------------------------------------
  Cech_complex cech_complex_from_points(points, 2.0);

  std::clog << "========== cech_complex_from_points ==========" << std::endl;
  Simplex_tree st;
  const int DIMENSION = 3;
  cech_complex_from_points.create_complex(st, DIMENSION);

  // Another way to check num_simplices
  std::clog << "Iterator on Cech complex simplices in the filtration order, with [filtration value]:" << std::endl;
  int num_simplices = 0;
  for (auto f_simplex : st.filtration_simplex_range()) {
    num_simplices++;
    std::clog << "   ( ";
    for (auto vertex : st.simplex_vertex_range(f_simplex)) {
      std::clog << vertex << " ";
    }
    std::clog << ") -> "
              << "[" << st.filtration(f_simplex) << "] ";
    std::clog << std::endl;
  }
  BOOST_CHECK(num_simplices == 15);
  std::clog << "st.num_simplices()=" << st.num_simplices() << std::endl;
  BOOST_CHECK(st.num_simplices() == 15);

  std::clog << "st.dimension()=" << st.dimension() << std::endl;
  BOOST_CHECK(st.dimension() == DIMENSION);
  std::clog << "st.num_vertices()=" << st.num_vertices() << std::endl;
  BOOST_CHECK(st.num_vertices() == 4);

  for (auto f_simplex : st.filtration_simplex_range()) {
    std::clog << "dimension(" << st.dimension(f_simplex) << ") - f = " << st.filtration(f_simplex) << std::endl;
    switch (st.dimension(f_simplex)) {
      case 0:
        GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), 0.0);
        break;
      case 1:
        GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), 0.707107, .00001);
        break;
      case 2:
        GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), 0.816497, .00001);
        break;
      case 3:
        GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), 0.866025, .00001);
        break;
      default:
        BOOST_CHECK(false);  // Shall not happen
        break;
    }
  }
}

#ifdef GUDHI_DEBUG
BOOST_AUTO_TEST_CASE(Cech_create_complex_throw) {
  // ----------------------------------------------------------------------------
  //
  // Init of a Cech complex from a OFF file
  //
  // ----------------------------------------------------------------------------
  std::string off_file_name("alphacomplexdoc.off");
  double max_radius = 12.0;
  std::clog << "========== OFF FILE NAME = " << off_file_name << " - Cech max_radius=" << max_radius
            << "==========" << std::endl;

  Gudhi::Points_off_reader<Point> off_reader(off_file_name);
  Cech_complex cech_complex_from_file(off_reader.get_point_cloud(), max_radius);

  Simplex_tree stree;
  std::vector<int> simplex = {0, 1, 2};
  stree.insert_simplex_and_subfaces(simplex);
  std::clog << "Check exception throw in debug mode" << std::endl;
  // throw excpt because stree is not empty
  BOOST_CHECK_THROW(cech_complex_from_file.create_complex(stree, 1), std::invalid_argument);
}
#endif