/* 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 "gudhi/graph_simplicial_complex.h"
#include "gudhi/Witness_complex.h"
#include "gudhi/reader_utils.h"
#include "Torus_distance.h"
#include
#include
#include
#include
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#include
#include
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using namespace Gudhi;
//using namespace boost::filesystem;
typedef CGAL::Epick_d K;
typedef K::Point_d Point_d;
//typedef CGAL::Cartesian_d K;
//typedef CGAL::Point_d Point_d;
typedef K::FT FT;
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_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 K::Equal_d Equal_d;
//typedef CGAL::Random_points_in_cube_d > > Random_cube_iterator;
typedef CGAL::Random_points_in_cube_d Random_cube_iterator;
typedef CGAL::Random_points_in_ball_d Random_point_iterator;
typedef CGAL::Delaunay_triangulation Delaunay_triangulation;
typedef Delaunay_triangulation::Facet Facet;
typedef CGAL::Sphere_d Sphere_d;
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_random_box(Point_Vector& W, int nbP, int dim)
{
/*
Random_cube_iterator rp(dim, 1);
for (int i = 0; i < nbP; i++)
{
std::vector point;
for (auto it = rp->cartesian_begin(); it != rp->cartesian_end(); ++it)
point.push_back(*it);
W.push_back(Point_d(point));
rp++;
}
*/
Random_cube_iterator rp(dim, 1.0);
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_points( std::string file_name, std::vector< Point_d > & points)
{
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(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";
int chosen_landmark;
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::count(landmarks_ind.begin(),landmarks_ind.end(),chosen_landmark)!=0);
//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 aux_fill_grid(Point_Vector& W, int& width, Point_Vector& landmarks, std::vector& landmarks_ind, std::vector & curr_pattern)
{
int D = W[0].size();
int nb_points = 1;
for (int i = 0; i < D; ++i)
nb_points *= width;
for (int i = 0; i < nb_points; ++i)
{
std::vector point;
int cell_i = i;
for (int l = 0; l < D; ++l)
{
if (curr_pattern[l])
point.push_back(-1.0+(2.0/width)*(cell_i%width)+(1.0/width));
else
point.push_back(-1.0+(2.0/width)*(cell_i%width));
cell_i /= width;
}
landmarks.push_back(Point_d(point));
landmarks_ind.push_back(0);//landmarks_ind.push_back(W.size());
//std::cout << "Added point " << W.size() << std::endl;;
//W.push_back(Point_d(point));
}
}
void aux_put_halves(Point_Vector& W, int& width, Point_Vector& landmarks, std::vector& landmarks_ind, std::vector& curr_pattern, std::vector::iterator curr_pattern_it, std::vector::iterator bool_it, std::vector::iterator bool_end)
{
if (curr_pattern_it != curr_pattern.end())
{
if (bool_it != bool_end)
{
*curr_pattern_it = false;
aux_put_halves(W, width, landmarks, landmarks_ind, curr_pattern, curr_pattern_it+1, bool_it, bool_end);
*curr_pattern_it = true;
aux_put_halves(W, width, landmarks, landmarks_ind, curr_pattern, curr_pattern_it+1, bool_it+1, bool_end);
}
}
else
if (*bool_it)
{
std::cout << "Filling the pattern ";
for (bool b: curr_pattern)
if (b) std::cout << '1';
else std::cout << '0';
std::cout << "\n";
aux_fill_grid(W, width, landmarks, landmarks_ind, curr_pattern);
}
}
void landmark_choice_cs(Point_Vector& W, int width, Point_Vector& landmarks, std::vector& landmarks_ind, std::vector& face_centers)
{
std::cout << "Enter landmark choice to kd tree\n";
//int chosen_landmark;
CGAL::Random rand;
//To speed things up check the last true in the code and put it as the finishing condition
unsigned last_true = face_centers.size()-1;
while (!face_centers[last_true] && last_true != 0)
last_true--;
//Recursive procedure to understand where we put +1/2 in centers' coordinates
std::vector curr_pattern(W[0].size(), false);
aux_put_halves(W, width, landmarks, landmarks_ind, curr_pattern, curr_pattern.begin(), face_centers.begin(), face_centers.begin()+(last_true+1));
std::cout << "The number of landmarks is: " << landmarks.size() << std::endl;
}
int landmark_perturbation(Point_Vector &W, Point_Vector& landmarks, std::vector& landmarks_ind)
{
//******************** Preface: origin point
int D = W[0].size();
std::vector orig_vector;
for (int i=0; i landmarks_ext;
int nb_cells = 1;
for (int i = 0; i < D; ++i)
nb_cells *= 3;
for (int i = 0; i < nb_cells; ++i)
for (int k = 0; k < nbL; ++k)
{
std::vector point;
int cell_i = i;
for (int l = 0; l < D; ++l)
{
point.push_back(landmarks[k][l] + 2.0*((cell_i%3)-1.0));
cell_i /= 3;
}
landmarks_ext.push_back(point);
}
write_points("landmarks/initial_landmarks",landmarks_ext);
STraits traits(&(landmarks_ext[0]));
std::vector< std::vector > WL(nbP);
//********************** Neighbor search in a Kd tree
Tree L(boost::counting_iterator(0),
boost::counting_iterator(nb_cells*nbL),
typename Tree::Splitter(),
traits);
std::cout << "Enter (D+1) nearest landmarks\n";
for (int i = 0; i < nbP; i++)
{
Point_d& w = W[i];
////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_ext[0])) );
for(K_neighbor_search::iterator it = search.begin(); it != search.end(); ++it)
{
if (std::find(WL[i].begin(), WL[i].end(), (it->first)%nbL) == WL[i].end())
WL[i].push_back((it->first)%nbL);
}
if (i == landmarks_ind[WL[i][0]])
{
FT dist = ed.transformed_distance(W[i], landmarks[WL[i][1]]);
if (dist < lambda)
lambda = dist;
}
}
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 ";
std::vector< int > count_bad(D);
std::vector< int > count_good(D);
for (auto u: witnessComplex.complex_vertex_range())
{
if (!witnessComplex.has_good_link(u, count_bad, count_good, D))
{
count_badlinks++;
Point_d& l = landmarks[u];
Fuzzy_sphere fs(l, sqrt(lambda)*3, 0, traits);
std::vector curr_perturb;
L.search(std::insert_iterator>(curr_perturb,curr_perturb.begin()),fs);
for (int i: curr_perturb)
perturbL.insert(i%nbL);
}
}
for (unsigned int i = 0; i != count_good.size(); i++)
if (count_good[i] != 0)
std::cout << "count_good[" << i << "] = " << count_good[i] << std::endl;
for (unsigned int i = 0; i != count_bad.size(); i++)
if (count_bad[i] != 0)
std::cout << "count_bad[" << i << "] = " << count_bad[i] << std::endl;
std::cout << "\nBad links total: " << count_badlinks << " Points to perturb: " << perturbL.size() << std::endl;
//*********************** Perturb bad link landmarks
for (auto u: perturbL)
{
Random_point_iterator rp(D,sqrt(lambda)/8);
std::vector point;
for (int i = 0; i < D; i++)
{
while (K().squared_distance_d_object()(*rp,origin) < lambda/256)
rp++;
FT coord = landmarks[u][i] + (*rp)[i];
if (coord > 1)
point.push_back(coord-1);
else if (coord < -1)
point.push_back(coord+1);
else
point.push_back(coord);
}
landmarks[u] = Point_d(point);
}
std::cout << "lambda=" << lambda << std::endl;
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);
return count_badlinks;
}
void exaustive_search(Point_Vector& W, int width)
{
int D = W[0].size()+1;
int nb_points = pow(2,D);
std::vector face_centers(D, false);
int bl = 0; //Bad links
std::vector> good_patterns;
for (int i = 0; i < nb_points; ++i)
{
int cell_i = i;
for (int l = 0; l < D; ++l)
{
if (cell_i%2 == 0)
face_centers[l] = false;
else
face_centers[l] = true;
cell_i /= 2;
}
std::cout << "**Current pattern ";
for (bool b: face_centers)
if (b) std::cout << '1';
else std::cout << '0';
std::cout << "\n";
Point_Vector landmarks;
std::vector landmarks_ind;
Point_Vector W_copy(W);
landmark_choice_cs(W_copy, width, landmarks, landmarks_ind, face_centers);
if (landmarks.size() != 0)
{
bl = landmark_perturbation(W_copy, landmarks, landmarks_ind);
if ((1.0*bl)/landmarks.size() < 0.5)
good_patterns.push_back(face_centers);
}
}
std::cout << "The following patterns worked: ";
for (std::vector pattern : good_patterns)
{
std::cout << "[";
for (bool b: pattern)
if (b) std::cout << '1';
else std::cout << '0';
std::cout << "] ";
}
std::cout << "\n";
}
int main (int argc, char * const argv[])
{
unsigned nbP = atoi(argv[1]);
unsigned width = atoi(argv[2]);
unsigned dim = atoi(argv[3]);
std::string code = (std::string) argv[4];
bool e_option = false;
int c;
if (argc != 5)
{
std::cerr << "Usage: " << argv[0]
<< "witness_complex_cubic_systems nbP width dim code || witness_complex_systems -e nbP width dim\n"
<< "where nbP stands for the number of witnesses, width for the width of the grid, dim for dimension "
<< "and code is a sequence of (dim+1) symbols 0 and 1 representing if we take the centers of k-dimensional faces of the cubic system depending if it is 0 or 1."
<< "-e stands for the 'exaustive' option";
return 0;
}
while ((c = getopt (argc, argv, "e::")) != -1)
switch(c)
{
case 'e' :
e_option = true;
nbP = atoi(argv[2]);
width = atoi(argv[3]);
dim = atoi(argv[4]);
break;
default :
nbP = atoi(argv[1]);
width = atoi(argv[2]);
dim = atoi(argv[3]);
code = (std::string) argv[4];
}
Point_Vector point_vector;
generate_points_random_box(point_vector, nbP, dim);
// Exaustive search
if (e_option)
{
std::cout << "Start exaustive search!\n";
exaustive_search(point_vector, width);
return 0;
}
// Search with a specific cubic system
std::vector face_centers;
if (code.size() != dim+1)
{
std::cerr << "The code should contain (dim+1) symbols";
return 1;
}
for (char c: code)
if (c == '0')
face_centers.push_back(false);
else
face_centers.push_back(true);
std::cout << "Let the carnage begin!\n";
Point_Vector L;
std::vector chosen_landmarks;
landmark_choice_cs(point_vector, width, L, chosen_landmarks, face_centers);
int nbL = width; //!!!!!!!!!!!!!
int bl = nbL, curr_min = bl;
write_points("landmarks/initial_pointset",point_vector);
//write_points("landmarks/initial_landmarks",L);
//for (int i = 0; i < 1; i++)
for (int i = 0; bl > 0; i++)
{
std::cout << "========== Start iteration " << i << "== curr_min(" << curr_min << ")========\n";
bl=landmark_perturbation(point_vector, L, chosen_landmarks);
if (bl < curr_min)
curr_min=bl;
write_points("landmarks/landmarks0",L);
}
}