/*
 * 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-Méditerranée (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( INFINITY ); //put params.min_persistence
		stream_<<"persistence: \n";
		stream_<<"p dimension birth death: \n";

		pcoh.output_diagram(stream_);
	}

private:


};






#endif /* PERSISTENCE_COMPUTE_H_ */