/* 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 "gudhi/graph_simplicial_complex.h"
#include "gudhi/Witness_complex.h"
#include "gudhi/reader_utils.h"
//#include
//#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
using namespace Gudhi;
//using namespace boost::filesystem;
typedef std::vector< Vertex_handle > typeVectorVertex;
//typedef std::pair typeSimplex;
//typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool;
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::Search_traits_adapter<
std::ptrdiff_t, Point_d*, Traits_base> STraits;
//typedef K TreeTraits;
typedef CGAL::Orthogonal_k_neighbor_search K_neighbor_search;
typedef K_neighbor_search::Tree Tree;
typedef K_neighbor_search::Distance Distance;
typedef K_neighbor_search::iterator KNS_iterator;
typedef K_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 CGAL::Euclidean_distance Euclidean_distance;
//typedef K::Equal_d Equal_d;
typedef CGAL::Random_points_in_ball_d Random_point_iterator;
/**
* \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 read_points_to_tree (std::string file_name, Tree& tree)
{
//I assume here that tree is empty
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 coords;
std::istringstream iss( line );
while(iss >> x) { coords.push_back(x); }
if (coords.size() != 1)
{
Point_d point(coords.begin(), coords.end());
tree.insert(point);
}
}
in_file.close();
}
*/
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_points( std::string file_name, std::vector< Point_d > & WL)
{
std::ofstream ofs (file_name, std::ofstream::out);
for (auto w : WL)
{
for (auto it = w.cartesian_begin(); it != w.cartesian_end(); ++it)
ofs << *it << " ";
ofs << "\n";
}
ofs.close();
}
void write_edges_gnuplot(std::string file_name, Witness_complex<>& witness_complex, Point_Vector& landmarks)
{
std::ofstream ofs (file_name, std::ofstream::out);
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;
srand(24660);
for (int i = 0; i < nbL; i++)
{
// while (!res.second)
// {
chosen_landmark = rand()%nbP;
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 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)
// {
while (std::count(landmarks_ind.begin(),landmarks_ind.end(),chosen_landmark)!=0)
chosen_landmark = rand.get_int(0,nbP);
//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;
}
}
*/
int landmark_perturbation(Point_Vector &W, Point_Vector& landmarks, std::vector& landmarks_ind)
{
//******************** Constructing a WL matrix
int nbP = W.size();
int nbL = landmarks.size();
//Point_Vector landmarks_ = landmarks;
Euclidean_distance ed;
//Equal_d ed;
FT lambda = ed.transformed_distance(landmarks[0],landmarks[1]);
//FT lambda = 0.1;//Euclidean_distance();
std::vector< std::vector > WL(nbP);
Tree L(boost::counting_iterator(0),
boost::counting_iterator(nbL),
typename Tree::Splitter(),
STraits(&(landmarks[0])));
/*Tree2 L2(boost::counting_iterator(0),
boost::counting_iterator(nbL),
typename Tree::Splitter(),
STraits(&(landmarks[0])));
*/
std::cout << "Enter (D+1) nearest landmarks\n";
//std::cout << "Size of the tree is " << L.size() << std::endl;
int D = W[0].size();
for (int i = 0; i < nbP; i++)
{
//std::cout << "Entered witness number " << i << std::endl;
Point_d& w = W[i];
//std::cout << "Safely constructed a point\n";
////Search D+1 nearest neighbours from the tree of landmarks L
K_neighbor_search search(L, w, D+1, 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;
}
if (i == landmarks_ind[WL[i][0]])
{
//std::cout << "'";
FT dist = ed.transformed_distance(W[i], landmarks[WL[i][1]]);
if (dist < lambda)
lambda = dist;
}
}
//std::cout << "\n";
std::string out_file = "wl_result";
write_wl(out_file,WL);
//******************** Constructng a witness complex
std::cout << "Entered witness complex construction\n";
Witness_complex<> witnessComplex;
witnessComplex.setNbL(nbL);
witnessComplex.witness_complex(WL);
//******************** Making a set of bad link landmarks
std::cout << "Entered bad links\n";
std::set< int > perturbL;
int count_badlinks = 0;
std::cout << "Bad links around ";
for (auto u: witnessComplex.complex_vertex_range())
if (!witnessComplex.has_good_link(u))
{
//std::cout << "Landmark " << u << " start!" << std::endl;
//perturbL.insert(u);
count_badlinks++;
std::cout << u << " ";
Point_d& l = landmarks[u];
Fuzzy_sphere fs(l, sqrt(lambda)*2, 0, STraits(&(landmarks[0])));
L.search(std::insert_iterator>(perturbL,perturbL.begin()),fs);
//L.search(std::inserter(perturbL,perturbL.begin()),fs);
//L.search(std::ostream_iterator(std::cout,"\n"),fs);
//std::cout << "PerturbL size is " << perturbL.size() << std::endl;
}
std::cout << "\nBad links total: " << count_badlinks << " Points to perturb: " << perturbL.size() << std::endl;
//std::cout << "landmark[0][0] before" << landmarks[0][0] << std::endl;
//*********************** Perturb bad link landmarks
for (auto u: perturbL)
{
Random_point_iterator rp(D,sqrt(lambda)/4);
//std::cout << landmarks[u] << std::endl;
std::vector point;
for (int i = 0; i < D; i++)
{
point.push_back(W[landmarks_ind[u]][i] + (*rp)[i]);
}
landmarks[u] = Point_d(point);
//std::cout << landmarks[u] << std::endl;
}
//std::cout << "landmark[0][0] after" << landmarks[0][0] << std::endl;
std::cout << "lambda=" << lambda << std::endl;
// Write the WL matrix in a file
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();
}
//witnessComplex.write_badlinks("badlinks");
write_edges_gnuplot("landmarks/edges", witnessComplex, landmarks);
return count_badlinks;
}
int main (int argc, char * const argv[])
{
if (argc != 3)
{
std::cerr << "Usage: " << argv[0]
<< " path_to_point_file nbL \n";
return 0;
}
/*
boost::filesystem::path p;
for (; argc > 2; --argc, ++argv)
p /= argv[1];
*/
std::string file_name = argv[1];
int nbL = atoi(argv[2]);
//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);
//std::cout << "Successfully read the points\n";
//witnessComplex.setNbL(nbL);
// witnessComplex.witness_complex_from_points(point_vector);
int nbP = point_vector.size();
//std::vector > WL(nbP);
//std::set L;
Point_Vector L;
std::vector chosen_landmarks;
//Point_etiquette_map L_i;
//start = clock();
//witnessComplex.landmark_choice_by_furthest_points(point_vector, point_vector.size(), WL);
landmark_choice(point_vector, nbP, nbL, L, chosen_landmarks);
int bl = 1;
mkdir("landmarks", S_IRWXU);
const size_t last_slash_idx = file_name.find_last_of("/");
if (std::string::npos != last_slash_idx)
{
file_name.erase(0, last_slash_idx + 1);
}
write_points("landmarks/initial_pointset",point_vector);
write_points("landmarks/initial_landmarks",L);
for (int i = 0; bl != 0; i++)
{
std::cout << "========== Start iteration " << i << " ========\n";
bl = landmark_perturbation(point_vector, L, chosen_landmarks);
std::ostringstream os(std::ostringstream::ate);;
os << "landmarks/landmarks0";
write_points(os.str(),L);
}
//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();
*/
}