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/*
* Persistence_compute.h
* Created on: Jan 26, 2015
* 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-M�diterran�e (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 PERSISTENCE_COMPUTE_H_
#define PERSISTENCE_COMPUTE_H_
#include "gudhi/graph_simplicial_complex.h"
#include "gudhi/Simplex_tree.h"
#include "gudhi/distance_functions.h"
#include "gudhi/Persistent_cohomology.h"
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{
private:
SkBlComplex& complex_;
std::ostream& stream_;
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):
//
// double threshold = 0.5,unsigned dim_max = 8):
complex_(complex),stream_(stream){
//for now everything is copied, todo boost adapt iterators to points of SkBlComplex instead of copying to an intial 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));
}
Graph_t prox_graph = compute_proximity_graph( points, params.threshold, euclidean_distance<Point_t> );
Gudhi::Simplex_tree<> st;
st.insert_graph(prox_graph);
st.expansion( params.max_dim );
Gudhi::persistent_cohomology::Persistent_cohomology< Gudhi::Simplex_tree<>,Gudhi::persistent_cohomology::Field_Zp > pcoh (st);
pcoh.init_coefficients( params.p ); //initilizes the coefficient field for homology
pcoh.compute_persistent_cohomology( params.min_pers ); //put params.min_pers
stream_<<"persistence: \n";
stream_<<"p dimension birth death: \n";
pcoh.output_diagram(stream_);
}
private:
};
#endif /* PERSISTENCE_COMPUTE_H_ */
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