Rips_complex.h
1/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
2 * See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
3 * Author(s): Clément Maria, Pawel Dlotko, Vincent Rouvreau
4 *
5 * Copyright (C) 2016 Inria
6 *
7 * Modification(s):
8 * - YYYY/MM Author: Description of the modification
9 */
10
11#ifndef RIPS_COMPLEX_H_
12#define RIPS_COMPLEX_H_
13
14#include <gudhi/Debug_utils.h>
16
17#include <boost/graph/adjacency_list.hpp>
18
19#include <iostream>
20#include <vector>
21#include <map>
22#include <string>
23#include <limits> // for numeric_limits
24#include <utility> // for pair<>
25
26
27namespace Gudhi {
28
29namespace rips_complex {
30
44template<typename Filtration_value>
46 public:
50 typedef typename boost::adjacency_list < boost::vecS, boost::vecS, boost::directedS
51 , boost::property < vertex_filtration_t, Filtration_value >
52 , boost::property < edge_filtration_t, Filtration_value >> OneSkeletonGraph;
53
54 private:
55 typedef int Vertex_handle;
56
57 public:
70 template<typename ForwardPointRange, typename Distance >
71 Rips_complex(const ForwardPointRange& points, Filtration_value threshold, Distance distance) {
72 compute_proximity_graph(points, threshold, distance);
73 }
74
84 template<typename DistanceMatrix>
85 Rips_complex(const DistanceMatrix& distance_matrix, Filtration_value threshold) {
86 compute_proximity_graph(boost::irange((size_t)0, distance_matrix.size()), threshold,
87 [&](size_t i, size_t j){return distance_matrix[j][i];});
88 }
89
100 template <typename SimplicialComplexForRips>
101 void create_complex(SimplicialComplexForRips& complex, int dim_max) {
102 GUDHI_CHECK(complex.num_vertices() == 0,
103 std::invalid_argument("Rips_complex::create_complex - simplicial complex is not empty"));
104
105 // insert the proximity graph in the simplicial complex
106 complex.insert_graph(rips_skeleton_graph_);
107 // expand the graph until dimension dim_max
108 complex.expansion(dim_max);
109 }
110
111 private:
123 template< typename ForwardPointRange, typename Distance >
124 void compute_proximity_graph(const ForwardPointRange& points, Filtration_value threshold,
125 Distance distance) {
126 std::vector< std::pair< Vertex_handle, Vertex_handle > > edges;
127 std::vector< Filtration_value > edges_fil;
128
129 // Compute the proximity graph of the points.
130 // If points contains n elements, the proximity graph is the graph with n vertices, and an edge [u,v] iff the
131 // distance function between points u and v is smaller than threshold.
132 // --------------------------------------------------------------------------------------------
133 // Creates the vector of edges and its filtration values (returned by distance function)
134 Vertex_handle idx_u = 0;
135 for (auto it_u = std::begin(points); it_u != std::end(points); ++it_u, ++idx_u) {
136 Vertex_handle idx_v = idx_u + 1;
137 for (auto it_v = it_u + 1; it_v != std::end(points); ++it_v, ++idx_v) {
138 Filtration_value fil = distance(*it_u, *it_v);
139 if (fil <= threshold) {
140 edges.emplace_back(idx_u, idx_v);
141 edges_fil.push_back(fil);
142 }
143 }
144 }
145
146 // --------------------------------------------------------------------------------------------
147 // Creates the proximity graph from edges and sets the property with the filtration value.
148 // Number of points is labeled from 0 to idx_u-1
149 // --------------------------------------------------------------------------------------------
150 // Do not use : rips_skeleton_graph_ = OneSkeletonGraph(...) -> deep copy of the graph (boost graph is not
151 // move-enabled)
152 rips_skeleton_graph_.~OneSkeletonGraph();
153 new(&rips_skeleton_graph_)OneSkeletonGraph(edges.begin(), edges.end(), edges_fil.begin(), idx_u);
154
155 auto vertex_prop = boost::get(vertex_filtration_t(), rips_skeleton_graph_);
156
157 using vertex_iterator = typename boost::graph_traits<OneSkeletonGraph>::vertex_iterator;
158 vertex_iterator vi, vi_end;
159 for (std::tie(vi, vi_end) = boost::vertices(rips_skeleton_graph_);
160 vi != vi_end; ++vi) {
161 boost::put(vertex_prop, *vi, 0.);
162 }
163 }
164
165 private:
166 OneSkeletonGraph rips_skeleton_graph_;
167};
168
169} // namespace rips_complex
170
171} // namespace Gudhi
172
173#endif // RIPS_COMPLEX_H_
Rips complex data structure.
Definition: Rips_complex.h:45
Rips_complex(const ForwardPointRange &points, Filtration_value threshold, Distance distance)
Rips_complex constructor from a list of points.
Definition: Rips_complex.h:71
boost::adjacency_list< boost::vecS, boost::vecS, boost::directedS, boost::property< vertex_filtration_t, Filtration_value >, boost::property< edge_filtration_t, Filtration_value > > OneSkeletonGraph
Type of the one skeleton graph stored inside the Rips complex structure.
Definition: Rips_complex.h:52
void create_complex(SimplicialComplexForRips &complex, int dim_max)
Initializes the simplicial complex from the Rips graph and expands it until a given maximal dimension...
Definition: Rips_complex.h:101
Rips_complex(const DistanceMatrix &distance_matrix, Filtration_value threshold)
Rips_complex constructor from a distance matrix.
Definition: Rips_complex.h:85
Graph simplicial complex methods.
Value type for a filtration function on a cell complex.
Definition: FiltrationValue.h:20
The concept SimplicialComplexForRips describes the requirements for a type to implement a simplicial ...
Definition: SimplicialComplexForRips.h:21
std::size_t num_vertices()
Returns the number of vertices in the simplicial complex.
void expansion(int max_dim)
Expands the simplicial complex containing only its one skeleton until a given maximal dimension as ex...
void insert_graph(const OneSkeletonGraph &skel_graph)
Inserts a given Gudhi::rips_complex::Rips_complex::OneSkeletonGraph in the simplicial complex.
Handle type for the vertices of a cell complex.
Definition: VertexHandle.h:15