example_one_skeleton_rips_from_distance_matrix.cpp
#include <gudhi/Rips_complex.h>
#include <gudhi/Simplex_tree.h>
#include <iostream>
#include <string>
#include <vector>
#include <limits> // for std::numeric_limits
int main() {
// Type definitions
using Distance_matrix = std::vector<std::vector<Filtration_value>>;
// User defined distance matrix is:
// | 0 0.94 0.77 0.99 0.11 |
// | 0.94 0 0.26 0.99 0.39 |
// | 0.77 0.26 0 0.28 0.97 |
// | 0.99 0.99 0.28 0 0.30 |
// | 0.11 0.39 0.97 0.30 0 |
Distance_matrix distances;
distances.push_back({});
distances.push_back({0.94});
distances.push_back({0.77, 0.26});
distances.push_back({0.99, 0.99, 0.28});
distances.push_back({0.11, 0.39, 0.97, 0.30});
// ----------------------------------------------------------------------------
// Init of a Rips complex from points
// ----------------------------------------------------------------------------
double threshold = 1.0;
Rips_complex rips_complex_from_points(distances, threshold);
Simplex_tree stree;
rips_complex_from_points.create_complex(stree, 1);
// ----------------------------------------------------------------------------
// Display information about the one skeleton Rips complex
// ----------------------------------------------------------------------------
std::clog << "Rips complex is of dimension " << stree.dimension() <<
" - " << stree.num_simplices() << " simplices - " <<
stree.num_vertices() << " vertices." << std::endl;
std::clog << "Iterator on Rips complex simplices in the filtration order, with [filtration value]:" <<
std::endl;
for (auto f_simplex : stree.filtration_simplex_range()) {
std::clog << " ( ";
for (auto vertex : stree.simplex_vertex_range(f_simplex)) {
std::clog << vertex << " ";
}
std::clog << ") -> " << "[" << stree.filtration(f_simplex) << "] ";
std::clog << std::endl;
}
return 0;
}
Options::Filtration_value Filtration_value
Type for the value of the filtration function.
Definition: Simplex_tree.h:86
Filtration_simplex_range const & filtration_simplex_range(Indexing_tag=Indexing_tag())
Returns a range over the simplices of the simplicial complex, in the order of the filtration.
Definition: Simplex_tree.h:271
Simplex_vertex_range simplex_vertex_range(Simplex_handle sh) const
Returns a range over the vertices of a simplex.
Definition: Simplex_tree.h:282
static Filtration_value filtration(Simplex_handle sh)
Returns the filtration value of a simplex.
Definition: Simplex_tree.h:535
size_t num_vertices() const
Returns the number of vertices in the complex.
Definition: Simplex_tree.h:572
int dimension(Simplex_handle sh)
Returns the dimension of a simplex.
Definition: Simplex_tree.h:600
size_t num_simplices()
returns the number of simplices in the simplex_tree.
Definition: Simplex_tree.h:578
Rips complex data structure.
Definition: Rips_complex.h:45
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
Global distance functions.
Value type for a filtration function on a cell complex.
Definition: FiltrationValue.h:20