From 377b59e5e7fa6a92bd21b0cb9b9b86e33632e4ed Mon Sep 17 00:00:00 2001 From: skachano Date: Fri, 15 Jan 2016 08:57:23 +0000 Subject: Removed relaxed_witness_complex_sphere from repository git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/witness@971 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 886ea9c52839e6cb21872da5097a55037b027ca7 --- .../example/relaxed_witness_complex_sphere.cpp | 461 --------------------- 1 file changed, 461 deletions(-) delete mode 100644 src/Witness_complex/example/relaxed_witness_complex_sphere.cpp (limited to 'src/Witness_complex/example') diff --git a/src/Witness_complex/example/relaxed_witness_complex_sphere.cpp b/src/Witness_complex/example/relaxed_witness_complex_sphere.cpp deleted file mode 100644 index 067321ce..00000000 --- a/src/Witness_complex/example/relaxed_witness_complex_sphere.cpp +++ /dev/null @@ -1,461 +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 . - */ - -#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 -#include -#include -#include -#include - - -#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(); - */ -} -- cgit v1.2.3