Rips_complex/example_one_skeleton_rips_from_distance_matrix.cpp

#include <gudhi/Rips_complex.h>
#include <gudhi/Simplex_tree.h>
#include <gudhi/distance_functions.h>

#include <iostream>
#include <string>
#include <vector>
#include <limits>  // for std::numeric_limits

int main() {
  // Type definitions
  using Simplex_tree = Gudhi::Simplex_tree<>;
  using Filtration_value = Simplex_tree::Filtration_value;
  using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
  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;
}