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Diffstat (limited to 'src/Witness_complex/example/witness_complex_protected_delaunay.cpp')
| -rw-r--r-- | src/Witness_complex/example/witness_complex_protected_delaunay.cpp | 604 |
1 files changed, 0 insertions, 604 deletions
diff --git a/src/Witness_complex/example/witness_complex_protected_delaunay.cpp b/src/Witness_complex/example/witness_complex_protected_delaunay.cpp deleted file mode 100644 index 77a167a5..00000000 --- a/src/Witness_complex/example/witness_complex_protected_delaunay.cpp +++ /dev/null @@ -1,604 +0,0 @@ -/* 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/>. - */ - -#include <iostream> -#include <fstream> -#include <ctime> -#include <utility> -#include <algorithm> -#include <set> -#include <iterator> -#include <chrono> - -#include <sys/types.h> -#include <sys/stat.h> -//#include <stdlib.h> - -//#include "gudhi/graph_simplicial_complex.h" -#include "gudhi/Witness_complex.h" -#include "gudhi/reader_utils.h" -#include "Torus_distance.h" - -#include <CGAL/Cartesian_d.h> -#include <CGAL/Search_traits.h> -#include <CGAL/Search_traits_adapter.h> -#include <CGAL/property_map.h> -#include <CGAL/Epick_d.h> -#include <CGAL/Orthogonal_k_neighbor_search.h> -#include <CGAL/Kd_tree.h> -#include <CGAL/Euclidean_distance.h> -#include <CGAL/Kernel_d/Sphere_d.h> - -#include <CGAL/Kernel_d/Vector_d.h> -#include <CGAL/point_generators_d.h> -#include <CGAL/constructions_d.h> -#include <CGAL/Fuzzy_sphere.h> -#include <CGAL/Random.h> -#include <CGAL/Delaunay_triangulation.h> - - -#include <boost/tuple/tuple.hpp> -#include <boost/iterator/zip_iterator.hpp> -#include <boost/iterator/counting_iterator.hpp> -#include <boost/range/iterator_range.hpp> - -using namespace Gudhi; -//using namespace boost::filesystem; - -typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K; -typedef K::Point_d Point_d; -//typedef CGAL::Cartesian_d<double> K; -//typedef CGAL::Point_d<K> 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<Traits_base> Euclidean_distance; - - -typedef std::vector< Vertex_handle > typeVectorVertex; - -//typedef std::pair<typeVectorVertex, Filtration_value> 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<std::ptrdiff_t,Point_d*,Euclidean_distance > Euclidean_adapter; -//typedef CGAL::Kd_tree<STraits> Kd_tree; -typedef CGAL::Orthogonal_k_neighbor_search<STraits, CGAL::Distance_adapter<std::ptrdiff_t,Point_d*,Euclidean_distance>> 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<int, int> Point_etiquette_map; -typedef CGAL::Kd_tree<STraits> Tree2; - -typedef CGAL::Fuzzy_sphere<STraits> Fuzzy_sphere; - -typedef std::vector<Point_d> Point_Vector; - -//typedef K::Equal_d Equal_d; -//typedef CGAL::Random_points_in_cube_d<CGAL::Point_d<CGAL::Cartesian_d<FT> > > Random_cube_iterator; -typedef CGAL::Random_points_in_cube_d<Point_d> Random_cube_iterator; -typedef CGAL::Random_points_in_ball_d<Point_d> Random_point_iterator; - -typedef CGAL::Delaunay_triangulation<K> Delaunay_triangulation; -typedef Delaunay_triangulation::Facet Facet; -typedef CGAL::Sphere_d<K> 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_grid(Point_Vector& W, int width, int D) -{ - int nb_points = 1; - for (int i = 0; i < D; ++i) - nb_points *= width; - for (int i = 0; i < nb_points; ++i) - { - std::vector<double> point; - int cell_i = i; - for (int l = 0; l < D; ++l) - { - point.push_back(0.01*(cell_i%width)); - cell_i /= width; - } - W.push_back(point); - } -} - -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<double> 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 <int> > & 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<int>& 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 insert_delaunay_landmark_with_copies(Point_Vector& W, int chosen_landmark, std::vector<int>& landmarks_ind, Delaunay_triangulation& delaunay, int& landmark_count) -{ - int D = W[0].size(); - int nb_cells = pow(3, D); - for (int i = 0; i < nb_cells; ++i) - { - std::vector<FT> point; - int cell_i = i; - for (int l = 0; l < D; ++l) - { - point.push_back(W[chosen_landmark][l] + 2.0*(cell_i%3-1)); - cell_i /= 3; - } - delaunay.insert(point); - } - landmarks_ind.push_back(chosen_landmark); - landmark_count++; -} - - - - -//////////////////////////////////////////////////////////////////////// -// OLD CODE VVVVVVVV -//////////////////////////////////////////////////////////////////////// - - -/* -bool is_violating_protection(Point_d& p, Delaunay_triangulation& t, int D, FT delta) -{ - Euclidean_distance ed; - Delaunay_triangulation::Vertex_handle v; - Delaunay_triangulation::Face f(t.current_dimension()); - Delaunay_triangulation::Facet ft; - Delaunay_triangulation::Full_cell_handle c; - Delaunay_triangulation::Locate_type lt; - c = t.locate(p, lt, f, ft, v); - for (auto fc_it = t.full_cells_begin(); fc_it != t.full_cells_end(); ++fc_it) - if (!t.is_infinite(fc_it)) - { - std::vector<Point_d> vertices; - for (auto v_it = fc_it->vertices_begin(); v_it != fc_it->vertices_end(); ++v_it) - vertices.push_back((*v_it)->point()); - Sphere_d cs(D, vertices.begin(), vertices.end()); - Point_d center_cs = cs.center(); - FT r = sqrt(ed.transformed_distance(center_cs, fc_it->vertex(1)->point())); - FT dist2 = ed.transformed_distance(center_cs, p); - //if the new point is inside the protection ball of a non conflicting simplex - if (dist2 >= r*r && dist2 <= (r+delta)*(r+delta)) - return true; - } - return false; -} - -bool triangulation_is_protected(Delaunay_triangulation& t, FT delta) -{ - Euclidean_distance ed; - int D = t.current_dimension(); - for (auto fc_it = t.full_cells_begin(); fc_it != t.full_cells_end(); ++fc_it) - if (!t.is_infinite(fc_it)) - for (auto v_it = t.vertices_begin(); v_it != t.vertices_end(); ++v_it) - { - //check if vertex belongs to the face - bool belongs = false; - for (auto fc_v_it = fc_it->vertices_begin(); fc_v_it != fc_it->vertices_end(); ++fc_v_it) - if (v_it == *fc_v_it) - { - belongs = true; - break; - } - if (!belongs) - { - std::vector<Point_d> vertices; - for (auto fc_v_it = fc_it->vertices_begin(); fc_v_it != fc_it->vertices_end(); ++fc_v_it) - vertices.push_back((*fc_v_it)->point()); - Sphere_d cs(D, vertices.begin(), vertices.end()); - Point_d center_cs = cs.center(); - FT r = sqrt(ed.transformed_distance(center_cs, fc_it->vertex(1)->point())); - FT dist2 = ed.transformed_distance(center_cs, v_it->point()); - //if the new point is inside the protection ball of a non conflicting simplex - if (dist2 <= (r+delta)*(r+delta)) - return false; - } - } - return true; -} - -void fill_landmark_copies(Point_Vector& W, Point_Vector& landmarks, std::vector<int>& landmarks_ind) -{ - int D = W[0].size(); - int nb_cells = pow(3, D); - int nbL = landmarks_ind.size(); - // Fill landmarks - for (int i = 0; i < nb_cells-1; ++i) - for (int j = 0; j < nbL; ++j) - { - int cell_i = i; - Point_d point; - for (int l = 0; l < D; ++l) - { - point.push_back(W[landmarks_ind[j]][l] + 2.0*(cell_i-1)); - cell_i /= 3; - } - landmarks.push_back(point); - } -} - -void landmark_choice_by_delaunay(Point_Vector& W, int nbP, int nbL, Point_Vector& landmarks, std::vector<int>& landmarks_ind, FT delta) -{ - int D = W[0].size(); - Delaunay_triangulation t(D); - CGAL::Random rand; - int chosen_landmark; - int landmark_count = 0; - for (int i = 0; i <= D+1; ++i) - { - do chosen_landmark = rand.get_int(0,nbP); - while (std::count(landmarks_ind.begin(),landmarks_ind.end(),chosen_landmark)!=0); - insert_delaunay_landmark_with_copies(W, chosen_landmark, landmarks_ind, t, landmark_count); - } - while (landmark_count < nbL) - { - do chosen_landmark = rand.get_int(0,nbP); - while (std::count(landmarks_ind.begin(),landmarks_ind.end(),chosen_landmark)!=0); - // If no conflicts then insert in every copy of T^3 - if (!is_violating_protection(W[chosen_landmark], t, D, delta)) - insert_delaunay_landmark_with_copies(W, chosen_landmark, landmarks_ind, t, landmark_count); - } - fill_landmark_copies(W, landmarks, landmarks_ind); -} - - -void landmark_choice_protected_delaunay(Point_Vector& W, int nbP, Point_Vector& landmarks, std::vector<int>& landmarks_ind, FT delta) -{ - int D = W[0].size(); - Torus_distance td; - Euclidean_distance ed; - Delaunay_triangulation t(D); - CGAL::Random rand; - int landmark_count = 0; - std::list<int> index_list; - // shuffle the list of indexes (via a vector) - { - std::vector<int> temp_vector; - for (int i = 0; i < nbP; ++i) - temp_vector.push_back(i); - unsigned seed = std::chrono::system_clock::now().time_since_epoch().count(); - std::shuffle(temp_vector.begin(), temp_vector.end(), std::default_random_engine(seed)); - for (std::vector<int>::iterator it = temp_vector.begin(); it != temp_vector.end(); ++it) - index_list.push_front(*it); - } - // add the first D+1 vertices to form one non-empty cell - for (int i = 0; i <= D+1; ++i) - { - insert_delaunay_landmark_with_copies(W, index_list.front(), landmarks_ind, t, landmark_count); - index_list.pop_front(); - } - // add other vertices if they don't violate protection - std::list<int>::iterator list_it = index_list.begin(); - while (list_it != index_list.end()) - if (!is_violating_protection(W[*list_it], t, D, delta)) - { - // If no conflicts then insert in every copy of T^3 - insert_delaunay_landmark_with_copies(W, *list_it, landmarks_ind, t, landmark_count); - index_list.erase(list_it); - list_it = index_list.begin(); - } - else - list_it++; - fill_landmark_copies(W, landmarks, landmarks_ind); -} - - -int landmark_perturbation(Point_Vector &W, int nbL, Point_Vector& landmarks, std::vector<int>& landmarks_ind) -{ - //******************** Preface: origin point - int D = W[0].size(); - std::vector<FT> orig_vector; - for (int i=0; i<D; i++) - orig_vector.push_back(0); - Point_d origin(orig_vector); - - //******************** Constructing a WL matrix - int nbP = W.size(); - Euclidean_distance ed; - FT lambda = ed.transformed_distance(landmarks[0],landmarks[1]); - std::vector<Point_d> 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<double> 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 <int> > WL(nbP); - - //********************** Neighbor search in a Kd tree - Tree L(boost::counting_iterator<std::ptrdiff_t>(0), - boost::counting_iterator<std::ptrdiff_t>(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<std::ptrdiff_t,Point_d*,Euclidean_distance>(&(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)) - { - count_badlinks++; - Point_d& l = landmarks[u]; - Fuzzy_sphere fs(l, sqrt(lambda)*3, 0, traits); - std::vector<int> curr_perturb; - L.search(std::insert_iterator<std::vector<int>>(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<FT> 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; -} - - -int main (int argc, char * const argv[]) -{ - if (argc != 5) - { - std::cerr << "Usage: " << argv[0] - << " nbP nbL dim delta\n"; - return 0; - } - int nbP = atoi(argv[1]); - int nbL = atoi(argv[2]); - int dim = atoi(argv[3]); - FT delta = atof(argv[4]); - - std::cout << "Let the carnage begin!\n"; - Point_Vector point_vector; - generate_points_random_box(point_vector, nbP, dim); - Point_Vector L; - std::vector<int> chosen_landmarks; - bool ok=false; - while (!ok) - { - ok = true; - L = {}; - chosen_landmarks = {}; - //landmark_choice_by_delaunay(point_vector, nbP, nbL, L, chosen_landmarks, delta); - landmark_choice_protected_delaunay(point_vector, nbP, L, chosen_landmarks, delta); - nbL = chosen_landmarks.size(); - std::cout << "Number of landmarks is " << nbL << std::endl; - //int width = (int)pow(nbL, 1.0/dim); landmark_choice_bcc(point_vector, nbP, width, L, chosen_landmarks); - for (auto i: chosen_landmarks) - { - ok = ok && (std::count(chosen_landmarks.begin(),chosen_landmarks.end(),i) == 1); - if (!ok) break; - } - - } - 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, nbL, L, chosen_landmarks); - if (bl < curr_min) - curr_min=bl; - write_points("landmarks/landmarks0",L); - } - -} -*/ |