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Diffstat (limited to 'src/Witness_complex/example/witness_complex_perturbations.cpp')
| -rw-r--r-- | src/Witness_complex/example/witness_complex_perturbations.cpp | 462 |
1 files changed, 0 insertions, 462 deletions
diff --git a/src/Witness_complex/example/witness_complex_perturbations.cpp b/src/Witness_complex/example/witness_complex_perturbations.cpp deleted file mode 100644 index f78bcdab..00000000 --- a/src/Witness_complex/example/witness_complex_perturbations.cpp +++ /dev/null @@ -1,462 +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 <set> -#include <iterator> - -#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 <boost/filesystem.hpp> - -//#include <CGAL/Delaunay_triangulation.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/Vector_d.h> -#include <CGAL/point_generators_d.h> -#include <CGAL/constructions_d.h> -#include <CGAL/Fuzzy_sphere.h> -#include <CGAL/Origin.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 std::vector< Vertex_handle > typeVectorVertex; - -//typedef std::pair<typeVectorVertex, Filtration_value> typeSimplex; -//typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool; - -typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> 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<STraits> 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 CGAL::Euclidean_distance<Traits_base> Euclidean_distance; -//typedef K::Equal_d Equal_d; -typedef CGAL::Random_points_in_ball_d<Point_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<double> 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 <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 > & 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<int>& landmarks_ind) -{ - std::cout << "Enter landmark choice to kd tree\n"; - //std::vector<Point_d> landmarks; - int chosen_landmark; - //std::pair<Point_etiquette_map::iterator,bool> 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<int>& landmarks_ind) -{ - std::cout << "Enter landmark choice to kd tree\n"; - //std::vector<Point_d> landmarks; - int chosen_landmark = 0; - //std::pair<Point_etiquette_map::iterator,bool> 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.uniform_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; - } - } - - -int landmark_perturbation(Point_Vector &W, Point_Vector& landmarks, std::vector<int>& 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 <int> > WL(nbP); - Tree L(boost::counting_iterator<std::ptrdiff_t>(0), - boost::counting_iterator<std::ptrdiff_t>(nbL), - typename Tree::Splitter(), - STraits(&(landmarks[0]))); - /*Tree2 L2(boost::counting_iterator<std::ptrdiff_t>(0), - boost::counting_iterator<std::ptrdiff_t>(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(); - clock_t start, end; - start = clock(); - 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<std::ptrdiff_t,Point_d*,CGAL::Euclidean_distance<Traits_base>>(&(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 << "\nBad links total: " << count_badlinks << " Points to perturb: " << perturbL.size() << std::endl; - } - //std::cout << "\n"; - end = clock(); - std::cout << "WL matrix construction on " << nbL << " landmarks took " << (double)(end-start)/CLOCKS_PER_SEC << "s.\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); - start = clock(); - witnessComplex.witness_complex(WL); - end = clock(); - std::cout << "Witness complex construction on " << nbL << " landmarks took " << (double)(end-start)/CLOCKS_PER_SEC << "s.\n"; - //******************** Making a set of bad link landmarks - std::cout << "Entered bad links\n"; - std::set< int > perturbL; - int count_badlinks = 0; - std::vector< int > count_bad(D); - std::vector< int > count_good(D); - //std::cout << "Bad links around "; - for (auto u: witnessComplex.complex_vertex_range()) - if (!witnessComplex.has_good_link(u, count_bad, count_good)) - { - //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<std::set<int>>(perturbL,perturbL.begin()),fs); - //L.search(std::inserter(perturbL,perturbL.begin()),fs); - //L.search(std::ostream_iterator<int>(std::cout,"\n"),fs); - //std::cout << "PerturbL size is " << perturbL.size() << std::endl; - } - 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 << "Bad 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<FT> 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<std::vector< int > > WL(nbP); - //std::set<int> L; - Point_Vector L; - std::vector<int> 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++) - for (int i = 0; i < 1; 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(); - */ -} |