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#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 correlation matrix is:
// |1 0.06 0.23 0.01 0.89|
// |0.06 1 0.74 0.01 0.61|
// |0.23 0.74 1 0.72 0.03|
// |0.01 0.01 0.72 1 0.7 |
// |0.89 0.61 0.03 0.7 1 |
Distance_matrix correlations;
correlations.push_back({});
correlations.push_back({0.06});
correlations.push_back({0.23, 0.74});
correlations.push_back({0.01, 0.01, 0.72});
correlations.push_back({0.89, 0.61, 0.03, 0.7});
// ----------------------------------------------------------------------------
// Convert correlation matrix to a distance matrix:
// ----------------------------------------------------------------------------
for ( size_t i = 0 ; i != correlations.size() ; ++i )
{
for ( size_t j = 0 ; j != correlations[i].size() ; ++j )
{
correlations[i][j] = 1-correlations[i][j];
if ( correlations[i][j] < 0 )
{
std::cerr << "The input matrix is not a correlation matrix. \n";
throw "The input matrix is not a correlation matrix. \n";
}
}
}
//-----------------------------------------------------------------------------
// Now the correlation matrix is really the distance matrix and can be processed further.
//-----------------------------------------------------------------------------
Distance_matrix distances = correlations;
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::cout << "Rips complex is of dimension " << stree.dimension() <<
" - " << stree.num_simplices() << " simplices - " <<
stree.num_vertices() << " vertices." << std::endl;
std::cout << "Iterator on Rips complex simplices in the filtration order, with [filtration value]:" <<
std::endl;
for (auto f_simplex : stree.filtration_simplex_range()) {
std::cout << " ( ";
for (auto vertex : stree.simplex_vertex_range(f_simplex)) {
std::cout << vertex << " ";
}
std::cout << ") -> " << "[" << stree.filtration(f_simplex) << "] ";
std::cout << std::endl;
}
return 0;
}
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