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/* This file is part of the Gudhi Library. The Gudhi library
* (Geometric Understanding in Higher Dimensions) is a generic C++
* library for computational topology.
*
* Author(s): David Salinas
*
* Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France)
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef UTILS_PERSISTENCE_COMPUTE_H_
#define UTILS_PERSISTENCE_COMPUTE_H_
#include <gudhi/graph_simplicial_complex.h>
#include <gudhi/Simplex_tree.h>
#include <gudhi/distance_functions.h>
#include <gudhi/Persistent_cohomology.h>
#include <gudhi/Rips_complex.h>
#include <vector>
struct Persistence_params {
int p;
double threshold;
int max_dim;
double min_pers;
Persistence_params(int p_, double th_, int max_dim_ = 10, double min_pers_ = 0)
: p(p_), threshold(th_), max_dim(max_dim_), min_pers(min_pers_) { }
};
/**
* Show persistence into output stream
*/
template<typename SkBlComplex> class Persistence_compute {
public:
typedef typename SkBlComplex::Vertex_handle Vertex_handle;
typedef typename SkBlComplex::Edge_handle Edge_handle;
/**
* @brief Compute persistence
* parameters :
* unsigned dim_max
* double threshold
* int p for coefficient Z_p
*/
Persistence_compute(SkBlComplex& complex, std::ostream& stream, const Persistence_params& params) {
// for now everything is copied, todo boost adapt iterators to points of SkBlComplex instead of copying to an
// initial vector
typedef std::vector<double> Point_t;
std::vector< Point_t > points;
points.reserve(complex.num_vertices());
for (auto v : complex.vertex_range()) {
const auto & pt = complex.point(v);
Point_t pt_to_add(pt.cartesian_begin(), pt.cartesian_end());
points.emplace_back(std::move(pt_to_add));
}
using Simplex_tree = Gudhi::Simplex_tree<>;
using Filtration_value = Simplex_tree::Filtration_value;
using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp>;
Rips_complex rips_complex(points, params.threshold, Euclidean_distance());
Simplex_tree st;
rips_complex.create_complex(st, params.max_dim);
Persistent_cohomology pcoh(st);
// initializes the coefficient field for homology
pcoh.init_coefficients(params.p);
// put params.min_pers
pcoh.compute_persistent_cohomology(params.min_pers);
stream << "persistence: \n";
stream << "p dimension birth death: \n";
pcoh.output_diagram(stream);
}
};
#endif // UTILS_PERSISTENCE_COMPUTE_H_
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