/* 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 .
*/
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
//#include
//#include "gudhi/graph_simplicial_complex.h"
#include "gudhi/Relaxed_witness_complex.h"
#include "gudhi/reader_utils.h"
#include "gudhi/Collapse/Collapse.h"
//#include
//#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
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#include
#include
#include
#include
using namespace Gudhi;
//using namespace boost::filesystem;
typedef CGAL::Epick_d K;
typedef K::FT FT;
typedef K::Point_d Point_d;
typedef CGAL::Search_traits<
FT, Point_d,
typename K::Cartesian_const_iterator_d,
typename K::Construct_cartesian_const_iterator_d> Traits_base;
typedef CGAL::Euclidean_distance Euclidean_distance;
typedef std::vector< Vertex_handle > typeVectorVertex;
//typedef std::pair typeSimplex;
//typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool;
typedef CGAL::Search_traits_adapter<
std::ptrdiff_t, Point_d*, Traits_base> STraits;
//typedef K TreeTraits;
//typedef CGAL::Distance_adapter Euclidean_adapter;
//typedef CGAL::Kd_tree Kd_tree;
typedef CGAL::Orthogonal_incremental_neighbor_search> Neighbor_search;
typedef Neighbor_search::Tree Tree;
typedef Neighbor_search::Distance Distance;
typedef Neighbor_search::iterator KNS_iterator;
typedef Neighbor_search::iterator KNS_range;
typedef boost::container::flat_map Point_etiquette_map;
typedef CGAL::Kd_tree Tree2;
typedef CGAL::Fuzzy_sphere Fuzzy_sphere;
typedef std::vector Point_Vector;
//typedef K::Equal_d Equal_d;
typedef CGAL::Random_points_in_cube_d Random_cube_iterator;
typedef CGAL::Random_points_in_ball_d Random_point_iterator;
bool toric=false;
/**
* \brief Customized version of read_points
* which takes into account a possible nbP first line
*
*/
inline void
read_points_cust ( std::string file_name , Point_Vector & points)
{
std::ifstream in_file (file_name.c_str(),std::ios::in);
if(!in_file.is_open())
{
std::cerr << "Unable to open file " << file_name << std::endl;
return;
}
std::string line;
double x;
while( getline ( in_file , line ) )
{
std::vector< double > point;
std::istringstream iss( line );
while(iss >> x) { point.push_back(x); }
Point_d p(point.begin(), point.end());
if (point.size() != 1)
points.push_back(p);
}
in_file.close();
}
void generate_points_sphere(Point_Vector& W, int nbP, int dim)
{
CGAL::Random_points_on_sphere_d rp(dim,1);
for (int i = 0; i < nbP; i++)
W.push_back(*rp++);
}
void write_wl( std::string file_name, std::vector< std::vector > & WL)
{
std::ofstream ofs (file_name, std::ofstream::out);
for (auto w : WL)
{
for (auto l: w)
ofs << l << " ";
ofs << "\n";
}
ofs.close();
}
void write_rl( std::string file_name, std::vector< std::vector ::iterator> > & rl)
{
std::ofstream ofs (file_name, std::ofstream::out);
for (auto w : rl)
{
for (auto l: w)
ofs << *l << " ";
ofs << "\n";
}
ofs.close();
}
std::vector convert_to_torus(std::vector< Point_d>& points)
{
std::vector< Point_d > points_torus;
for (auto p: points)
{
FT theta = M_PI*p[0];
FT phi = M_PI*p[1];
std::vector p_torus;
p_torus.push_back((1+0.2*cos(theta))*cos(phi));
p_torus.push_back((1+0.2*cos(theta))*sin(phi));
p_torus.push_back(0.2*sin(theta));
points_torus.push_back(Point_d(p_torus));
}
return points_torus;
}
void write_points_torus( std::string file_name, std::vector< Point_d > & points)
{
std::ofstream ofs (file_name, std::ofstream::out);
std::vector points_torus = convert_to_torus(points);
for (auto w : points_torus)
{
for (auto it = w.cartesian_begin(); it != w.cartesian_end(); ++it)
ofs << *it << " ";
ofs << "\n";
}
ofs.close();
}
void write_points( std::string file_name, std::vector< Point_d > & points)
{
if (toric) write_points_torus(file_name, points);
else
{
std::ofstream ofs (file_name, std::ofstream::out);
for (auto w : points)
{
for (auto it = w.cartesian_begin(); it != w.cartesian_end(); ++it)
ofs << *it << " ";
ofs << "\n";
}
ofs.close();
}
}
void write_edges_torus(std::string file_name, Witness_complex<>& witness_complex, Point_Vector& landmarks)
{
std::ofstream ofs (file_name, std::ofstream::out);
Point_Vector l_torus = convert_to_torus(landmarks);
for (auto u: witness_complex.complex_vertex_range())
for (auto v: witness_complex.complex_vertex_range())
{
typeVectorVertex edge = {u,v};
if (u < v && witness_complex.find(edge) != witness_complex.null_simplex())
{
for (auto it = l_torus[u].cartesian_begin(); it != l_torus[u].cartesian_end(); ++it)
ofs << *it << " ";
ofs << "\n";
for (auto it = l_torus[v].cartesian_begin(); it != l_torus[v].cartesian_end(); ++it)
ofs << *it << " ";
ofs << "\n\n\n";
}
}
ofs.close();
}
void write_edges(std::string file_name, Witness_complex<>& witness_complex, Point_Vector& landmarks)
{
std::ofstream ofs (file_name, std::ofstream::out);
if (toric) write_edges_torus(file_name, witness_complex, landmarks);
else
{
for (auto u: witness_complex.complex_vertex_range())
for (auto v: witness_complex.complex_vertex_range())
{
typeVectorVertex edge = {u,v};
if (u < v && witness_complex.find(edge) != witness_complex.null_simplex())
{
for (auto it = landmarks[u].cartesian_begin(); it != landmarks[u].cartesian_end(); ++it)
ofs << *it << " ";
ofs << "\n";
for (auto it = landmarks[v].cartesian_begin(); it != landmarks[v].cartesian_end(); ++it)
ofs << *it << " ";
ofs << "\n\n\n";
}
}
ofs.close();
}
}
/** Function that chooses landmarks from W and place it in the kd-tree L.
* Note: nbL hould be removed if the code moves to Witness_complex
*/
void landmark_choice(Point_Vector &W, int nbP, int nbL, Point_Vector& landmarks, std::vector& landmarks_ind)
{
std::cout << "Enter landmark choice to kd tree\n";
//std::vector landmarks;
int chosen_landmark;
//std::pair res = std::make_pair(L_i.begin(),false);
Point_d* p;
CGAL::Random rand;
for (int i = 0; i < nbL; i++)
{
// while (!res.second)
// {
do chosen_landmark = rand.get_int(0,nbP);
while (std::find(landmarks_ind.begin(), landmarks_ind.end(), chosen_landmark) != landmarks_ind.end());
//rand++;
//std::cout << "Chose " << chosen_landmark << std::endl;
p = &W[chosen_landmark];
//L_i.emplace(chosen_landmark,i);
// }
landmarks.push_back(*p);
landmarks_ind.push_back(chosen_landmark);
//std::cout << "Added landmark " << chosen_landmark << std::endl;
}
}
void landmarks_to_witness_complex(Point_Vector &W, Point_Vector& landmarks, std::vector& landmarks_ind, FT alpha)
{
//********************Preface: origin point
unsigned D = W[0].size();
std::vector orig_vector;
for (unsigned i = 0; i < D; i++)
orig_vector.push_back(0);
Point_d origin(orig_vector);
//Distance dist;
//dist.transformed_distance(0,1);
//******************** Constructing a WL matrix
int nbP = W.size();
int nbL = landmarks.size();
STraits traits(&(landmarks[0]));
Euclidean_distance ed;
std::vector< std::vector > WL(nbP);
std::vector< std::vector< typename std::vector::iterator > > ope_limits(nbP);
Tree L(boost::counting_iterator(0),
boost::counting_iterator(nbL),
typename Tree::Splitter(),
traits);
std::cout << "Enter (D+1) nearest landmarks\n";
//std::cout << "Size of the tree is " << L.size() << std::endl;
for (int i = 0; i < nbP; i++)
{
//std::cout << "Entered witness number " << i << std::endl;
Point_d& w = W[i];
std::queue< typename std::vector::iterator > ope_queue; // queue of points at (1+epsilon) distance to current landmark
Neighbor_search search(L, w, FT(0), true, CGAL::Distance_adapter(&(landmarks[0])));
Neighbor_search::iterator search_it = search.begin();
//Incremental search and filling WL
while (WL[i].size() < D)
WL[i].push_back((search_it++)->first);
FT dtow = ed.transformed_distance(w, landmarks[WL[i][D-1]]);
while (search_it->second < dtow + alpha)
WL[i].push_back((search_it++)->first);
//Filling the (1+epsilon)-limits table
for (std::vector::iterator wl_it = WL[i].begin(); wl_it != WL[i].end(); ++wl_it)
{
ope_queue.push(wl_it);
FT d_to_curr_l = ed.transformed_distance(w, landmarks[*wl_it]);
//std::cout << "d_to_curr_l=" << d_to_curr_l << std::endl;
//std::cout << "d_to_front+alpha=" << d_to_curr_l << std::endl;
while (d_to_curr_l > alpha + ed.transformed_distance(w, landmarks[*(ope_queue.front())]))
{
ope_limits[i].push_back(wl_it);
ope_queue.pop();
}
}
while (ope_queue.size() > 0)
{
ope_limits[i].push_back(WL[i].end());
ope_queue.pop();
}
//std::cout << "Safely constructed a point\n";
////Search D+1 nearest neighbours from the tree of landmarks L
/*
if (w[0]>0.95)
std::cout << i << std::endl;
*/
//K_neighbor_search search(L, w, D, FT(0), true,
// CGAL::Distance_adapter(&(landmarks[0])) );
//std::cout << "Safely found nearest landmarks\n";
/*
for(K_neighbor_search::iterator it = search.begin(); it != search.end(); ++it)
{
//std::cout << "Entered KNN_it with point at distance " << it->second << "\n";
//Point_etiquette_map::iterator itm = L_i.find(it->first);
//assert(itm != L_i.end());
//std::cout << "Entered KNN_it with point at distance " << it->second << "\n";
WL[i].push_back(it->first);
//std::cout << "ITFIRST " << it->first << std::endl;
//std::cout << i << " " << it->first << ": " << it->second << std::endl;
}
*/
}
//std::cout << "\n";
//std::string out_file = "wl_result";
write_wl("wl_result",WL);
write_rl("rl_result",ope_limits);
//******************** Constructng a witness complex
std::cout << "Entered witness complex construction\n";
Witness_complex<> witnessComplex;
witnessComplex.setNbL(nbL);
witnessComplex.relaxed_witness_complex(WL, ope_limits);
char buffer[100];
int i = sprintf(buffer,"stree_result.txt");
if (i >= 0)
{
std::string out_file = (std::string)buffer;
std::ofstream ofs (out_file, std::ofstream::out);
witnessComplex.st_to_file(ofs);
ofs.close();
}
write_edges("landmarks/edges", witnessComplex, landmarks);
std::cout << Distance().transformed_distance(Point_d(std::vector({0.1,0.1})), Point_d(std::vector({1.9,1.9}))) << std::endl;
}
int main (int argc, char * const argv[])
{
if (argc != 5)
{
std::cerr << "Usage: " << argv[0]
<< " nbP nbL dim alpha\n";
return 0;
}
/*
boost::filesystem::path p;
for (; argc > 2; --argc, ++argv)
p /= argv[1];
*/
int nbP = atoi(argv[1]);
int nbL = atoi(argv[2]);
int dim = atoi(argv[3]);
double alpha = atof(argv[4]);
//clock_t start, end;
//Construct the Simplex Tree
Witness_complex<> witnessComplex;
std::cout << "Let the carnage begin!\n";
Point_Vector point_vector;
//read_points_cust(file_name, point_vector);
generate_points_sphere(point_vector, nbP, dim);
/*
for (auto &p: point_vector)
{
assert(std::count(point_vector.begin(),point_vector.end(),p) == 1);
}
*/
//std::cout << "Successfully read the points\n";
//witnessComplex.setNbL(nbL);
Point_Vector L;
std::vector chosen_landmarks;
landmark_choice(point_vector, nbP, nbL, L, chosen_landmarks);
//start = clock();
write_points("landmarks/initial_pointset",point_vector);
write_points("landmarks/initial_landmarks",L);
landmarks_to_witness_complex(point_vector, L, chosen_landmarks, alpha);
//end = clock();
/*
std::cout << "Landmark choice took "
<< (double)(end-start)/CLOCKS_PER_SEC << " s. \n";
start = clock();
witnessComplex.witness_complex(WL);
//
end = clock();
std::cout << "Howdy world! The process took "
<< (double)(end-start)/CLOCKS_PER_SEC << " s. \n";
*/
/*
out_file = "output/"+file_name+"_"+argv[2]+".stree";
std::ofstream ofs (out_file, std::ofstream::out);
witnessComplex.st_to_file(ofs);
ofs.close();
out_file = "output/"+file_name+"_"+argv[2]+".badlinks";
std::ofstream ofs2(out_file, std::ofstream::out);
witnessComplex.write_bad_links(ofs2);
ofs2.close();
*/
}