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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): Siargey Kachanovich
*
* Copyright (C) 2015 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 GUDHI_WITNESS_COMPLEX_H_
#define GUDHI_WITNESS_COMPLEX_H_
#include <boost/iterator/transform_iterator.hpp>
#include <algorithm>
#include <utility>
#include "gudhi/reader_utils.h"
#include "gudhi/distance_functions.h"
#include "gudhi/Simplex_tree.h"
#include <vector>
#include <forward_list>
#include <math.h>
namespace Gudhi {
/*
template<typename FiltrationValue = double,
typename SimplexKey = int,
typename VertexHandle = int>
class Simplex_tree;
*/
template<typename FiltrationValue = double,
typename SimplexKey = int,
typename VertexHandle = int>
class Witness_complex: public Simplex_tree<> {
//class Witness_complex: public Simplex_tree<FiltrationValue, SimplexKey, VertexHandle> {
//class Witness_complex {
public:
//Simplex_tree<> st;
// typedef int Simplex_handle; //index in vector complex_
// typedef typename std::vector< Simplex_handle >::iterator Boundary_simplex_iterator;
// typedef boost::iterator_range<Boundary_simplex_iterator> Boundary_simplex_range;
// typedef typename std::vector< Simplex_handle >::iterator Skeleton_simplex_iterator;
// typedef boost::iterator_range< Skeleton_simplex_iterator > Skeleton_simplex_range;
// typedef IndexingTag Indexing_tag;
/** \brief Type for the value of the filtration function.
*
* Must be comparable with <. */
// typedef FiltrationValue Filtration_value;
/** \brief Key associated to each simplex.
*
* Must be a signed integer type. */
// typedef SimplexKey Simplex_key;
/** \brief Type for the vertex handle.
*
* Must be a signed integer type. It admits a total order <. */
// typedef VertexHandle Vertex_handle;
/* Type of node in the simplex tree. */
// typedef Simplex_tree_node_explicit_storage<Simplex_tree> Node;
/* Type of dictionary Vertex_handle -> Node for traversing the simplex tree. */
// typedef typename boost::container::flat_map<Vertex_handle, Node> Dictionary;
/*
friend class Simplex_tree_node_explicit_storage< Simplex_tree<FiltrationValue, SimplexKey, VertexHandle> >;
friend class Simplex_tree_siblings< Simplex_tree<FiltrationValue, SimplexKey, VertexHandle>, Dictionary>;
friend class Simplex_tree_simplex_vertex_iterator< Simplex_tree<FiltrationValue, SimplexKey, VertexHandle> >;
friend class Simplex_tree_boundary_simplex_iterator< Simplex_tree<FiltrationValue, SimplexKey, VertexHandle> >;
friend class Simplex_tree_complex_simplex_iterator< Simplex_tree<FiltrationValue, SimplexKey, VertexHandle> >;
friend class Simplex_tree_skeleton_simplex_iterator< Simplex_tree<FiltrationValue, SimplexKey, VertexHandle> >;
*/
/* \brief Set of nodes sharing a same parent in the simplex tree. */
/* \brief Set of nodes sharing a same parent in the simplex tree. */
// typedef Simplex_tree_siblings<Simplex_tree, Dictionary> Siblings;
typedef std::vector< double > Point_t;
typedef std::vector< Point_t > Point_Vector;
typedef std::vector< Vertex_handle > typeVectorVertex;
typedef std::pair<typeVectorVertex, Filtration_value> typeSimplex;
typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool;
/*
Witness_complex(int number_of_landmarks, std::string file_name)
{
}
*/
/**
* /brief Iterative construction of the witness complex basing on a matrix of k nearest neighbours of the form {witnesses}x{landmarks}.
* Landmarks are supposed to be in [0,nbL-1]
*/
template< typename KNearestNeighbours >
void witness_complex(KNearestNeighbours & knn)
{
int k=1; /* current dimension in iterative construction */
//Construction of the active witness list
int nbW = knn.size();
int nbL = knn.at(0).size();
VertexHandle vh;
typeVectorVertex vv;
typeSimplex simplex;
typePairSimplexBool returnValue;
/* The list of still useful witnesses
* it will diminuish in the course of iterations
*/
std::forward_list<int> active_w = new std::forward_list<int>();
for (int i=0; i != nbW; ++i) {
// initial fill of active witnesses list
active_w.push_front(i);
}
for (int i=0; i != nbL; ++i) {
// initial fill of 0-dimensional simplices
// by doing it we don't assume that landmarks are necessarily witnesses themselves anymore
vh = (Vertex_handle)i;
vv = {i};
/* TODO Filtration */
simplex = std::make_pair(vv,Filtration_value(0.0));
returnValue = this.insert_simplex(simplex.first, simplex.second);
/* TODO Error if not inserted : normally no need here though*/
}
while (!active_w.empty() && k+1 < nbL ) {
std::forward_list<int>::iterator it = active_w.begin();
while (it != active_w.end()) {
typeVectorVertex simplex_vector;
for (int i=0; i != k+1; ++i) {
// create a (k+1) element array for the given active landmark
/*
typeVectorVertex::iterator itSV = simplex_vector.begin();
while (itSV != simplex_vector.end() && *itSV < knn[*it][i]) {
itSV++;
}
simplex_vector.insert(itSV,knn[*it][i]);
*/
simplex_vector.push_back(knn[*it][i]);
}
/* THE INSERTION: Checking if all the subfaces are in the simplex tree is mandatory */
bool ok = all_faces_in(simplex_vecter);
returnValue = this.insert_simplex(simplex_vector,0.0);
}
}
}
private:
bool all_faces_in(typeVectorVertex v)
{
return true;
}
/**
* \brief Permutes the vector in such a way that the landmarks appear first
*/
void furthestPoints(Point_Vector &W, int nbP, std::string file_land, int dim, int nbL, Point_Vector &L) {
//std::cout << "Enter furthestPoints "<< endl;
//Point_Vector *L = new Point_Vector();
double density = 5.;
int current_number_of_landmarks=0;
double curr_max_dist;
double curr_dist;
double mindist = 10005.;
int curr_max_w=0;
int curr_w=0;
srand(354698);
int rand_int = rand()% nbP;
//std::cout << rand_int << endl;
L.push_back(W[rand_int]);// first landmark is random
current_number_of_landmarks++;
while (1) {
curr_w = 0;
curr_max_dist = -1;
for(Point_Vector::iterator itW = W.begin(); itW != W.end(); itW++) {
//compute distance from w and L
mindist = 100000.;
for(Point_Vector::iterator itL = L.begin(); itL != L.end(); itL++) {
//curr_dist = distPoints(*itW,*itL);
curr_dist = euclidean_distance(*itW,*itL);
if(curr_dist < mindist) {
mindist = curr_dist;
}
}
if(mindist > curr_max_dist) {
curr_max_w = curr_w; //???
curr_max_dist = mindist;
}
curr_w++;
}
L.push_back(W[curr_max_w]);
current_number_of_landmarks++;
density = sqrt(curr_max_dist);
//std::cout << "[" << current_number_of_landmarks << ":" << density <<"] ";
if(L.size() == nbL) break;
}
//std::cout << endl;
return L;
}
}; //class Witness_complex
} // namespace Guhdi
#endif
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