From c88e3b93de22be92cc7027f4c14ea4294f8c366f Mon Sep 17 00:00:00 2001 From: skachano Date: Tue, 16 Jun 2015 09:36:00 +0000 Subject: Fixed the changing WL matrix bug in witness complex. Added is_witness_complex test git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/witness@615 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 60917e75766b53d08240b510c0508e7d781b56d6 --- .../example/relaxed_witness_complex_sphere.cpp | 1 + .../example/witness_complex_sphere.cpp | 10 +- .../include/gudhi/Relaxed_witness_complex.h | 886 +++++++++++++++++++++ .../include/gudhi/Witness_complex.h | 93 ++- 4 files changed, 962 insertions(+), 28 deletions(-) create mode 100644 src/Witness_complex/include/gudhi/Relaxed_witness_complex.h diff --git a/src/Witness_complex/example/relaxed_witness_complex_sphere.cpp b/src/Witness_complex/example/relaxed_witness_complex_sphere.cpp index 53380124..067321ce 100644 --- a/src/Witness_complex/example/relaxed_witness_complex_sphere.cpp +++ b/src/Witness_complex/example/relaxed_witness_complex_sphere.cpp @@ -36,6 +36,7 @@ //#include "gudhi/graph_simplicial_complex.h" #include "gudhi/Relaxed_witness_complex.h" #include "gudhi/reader_utils.h" +#include "gudhi/Collapse/Collapse.h" //#include //#include diff --git a/src/Witness_complex/example/witness_complex_sphere.cpp b/src/Witness_complex/example/witness_complex_sphere.cpp index f2bb9819..d08c763f 100644 --- a/src/Witness_complex/example/witness_complex_sphere.cpp +++ b/src/Witness_complex/example/witness_complex_sphere.cpp @@ -578,6 +578,10 @@ int landmark_perturbation(Point_Vector &W, Point_Vector& landmarks, std::vector< Witness_complex<> witnessComplex; witnessComplex.setNbL(nbL); witnessComplex.witness_complex(WL); + if (witnessComplex.is_witness_complex(WL)) + std::cout << "!!YES. IT IS A WITNESS COMPLEX!!\n"; + else + std::cout << "??NO. IT IS NOT A WITNESS COMPLEX??\n"; //******************** Making a set of bad link landmarks std::cout << "Entered bad links\n"; std::set< int > perturbL; @@ -614,7 +618,7 @@ int landmark_perturbation(Point_Vector &W, Point_Vector& landmarks, std::vector< for (auto u: perturbL) { - Random_point_iterator rp(D,sqrt(lambda)/8); + Random_point_iterator rp(D,sqrt(lambda)/8*nbL/count_badlinks); //std::cout << landmarks[u] << std::endl; std::vector point; @@ -721,8 +725,8 @@ int main (int argc, char * const argv[]) 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++) + //for (int i = 0; bl > 0; i++) + for (int i = 0; i < 1; i++) { std::cout << "========== Start iteration " << i << "== curr_min(" << curr_min << ")========\n"; bl=landmark_perturbation(point_vector, L, chosen_landmarks); diff --git a/src/Witness_complex/include/gudhi/Relaxed_witness_complex.h b/src/Witness_complex/include/gudhi/Relaxed_witness_complex.h new file mode 100644 index 00000000..c869628f --- /dev/null +++ b/src/Witness_complex/include/gudhi/Relaxed_witness_complex.h @@ -0,0 +1,886 @@ +/* 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 . + */ + +#ifndef GUDHI_RELAXED_WITNESS_COMPLEX_H_ +#define GUDHI_RELAXED_WITNESS_COMPLEX_H_ + +#include +#include +#include +#include +#include "gudhi/reader_utils.h" +#include "gudhi/distance_functions.h" +#include "gudhi/Simplex_tree.h" +#include +#include +#include +#include +#include +#include +#include +#include + +// Needed for nearest neighbours +#include +#include +#include +#include +#include +#include + +#include +#include +#include +#include + +// Needed for the adjacency graph in bad link search +#include +#include +#include + +namespace Gudhi { + + + /** \addtogroup simplex_tree + * Witness complex is a simplicial complex defined on two sets of points in \f$\mathbf{R}^D\f$: + * \f$W\f$ set of witnesses and \f$L \subseteq W\f$ set of landmarks. The simplices are based on points in \f$L\f$ + * and a simplex belongs to the witness complex if and only if it is witnessed (there exists a point \f$w \in W\f$ such that + * w is closer to the vertices of this simplex than others) and all of its faces are witnessed as well. + */ + template + class Witness_complex: public Simplex_tree<> { + + private: + + struct Active_witness { + int witness_id; + int landmark_id; + Simplex_handle simplex_handle; + + Active_witness(int witness_id_, int landmark_id_, Simplex_handle simplex_handle_) + : witness_id(witness_id_), + landmark_id(landmark_id_), + simplex_handle(simplex_handle_) + {} + }; + + + + + public: + + + /** \brief Type for the vertex handle. + * + * Must be a signed integer type. It admits a total order <. */ + typedef VertexHandle Vertex_handle; + + /* Type of node in the simplex tree. */ + typedef Simplex_tree_node_explicit_storage Node; + /* Type of dictionary Vertex_handle -> Node for traversing the simplex tree. */ + typedef typename boost::container::flat_map Dictionary; + typedef typename Dictionary::iterator Simplex_handle; + + typedef std::vector< double > Point_t; + typedef std::vector< Point_t > Point_Vector; + + typedef std::vector< Vertex_handle > typeVectorVertex; + typedef std::pair< typeVectorVertex, Filtration_value> typeSimplex; + typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool; + + typedef int Witness_id; + typedef int Landmark_id; + typedef std::list< Vertex_handle > ActiveWitnessList; + + private: + /** Number of landmarks + */ + int nbL; + /** Desired density + */ + double density; + + public: + + /** \brief Set number of landmarks to nbL_ + */ + void setNbL(int nbL_) + { + nbL = nbL_; + } + + /** \brief Set density to density_ + */ + void setDensity(double density_) + { + density = density_; + } + + /** + * /brief Iterative construction of the relaxed witness complex basing on a matrix of k nearest neighbours of the form {witnesses}x{landmarks} and (1+epsilon)-limit table {witnesses}*{landmarks} consisting of iterators of k nearest neighbor matrix. + * The line lengths can differ, however both matrices have the same corresponding line lengths. + */ + + template< typename KNearestNeighbours, typename OPELimits > + void relaxed_witness_complex(KNearestNeighbours & knn, OPELimits & rl) + //void witness_complex(std::vector< std::vector< Vertex_handle > > & knn) + { + std::cout << "**Start the procedure witness_complex" << std::endl; + //Construction of the active witness list + int nbW = knn.size(); + //int nbL = knn.at(0).size(); + typeVectorVertex vv; + //typeSimplex simplex; + //typePairSimplexBool returnValue; + //int counter = 0; + /* The list of still useful witnesses + * it will diminuish in the course of iterations + */ + ActiveWitnessList active_w;// = new ActiveWitnessList(); + for (int i=0; i != nbL; ++i) { + // initial fill of 0-dimensional simplices + // by doing it we don't assume that landmarks are necessarily witnesses themselves anymore + //counter++; + vv = {i}; + insert_simplex(vv, Filtration_value(0.0)); + /* TODO Error if not inserted : normally no need here though*/ + } + int k=1; /* current dimension in iterative construction */ + //std::cout << "Successfully added landmarks" << std::endl; + // PRINT2 + //print_sc(root()); std::cout << std::endl; + for (int i=0; i != nbW; ++i) + active_w.push_back(i); + /* + int u,v; // two extremities of an edge + if (nbL > 1) // if the supposed dimension of the complex is >0 + { + for (int i=0; i != nbW; ++i) + { + // initial fill of active witnesses list + u = knn[i][0]; + v = knn[i][1]; + vv = {u,v}; + this->insert_simplex(vv,Filtration_value(0.0)); + //print_sc(root()); std::cout << std::endl; + //std::cout << "Added edges" << std::endl; + } + //print_sc(root()); + + } + */ + std::cout << "k=0, active witnesses: " << active_w.size() << std::endl; + //std::cout << "Successfully added edges" << std::endl; + //count_good = {0,0}; + //count_bad = {0,0}; + while (!active_w.empty() && k < nbL ) + { + //count_good.push_back(0); + //count_bad.push_back(0); + //std::cout << "Started the step k=" << k << std::endl; + typename ActiveWitnessList::iterator aw_it = active_w.begin(); + while (aw_it != active_w.end()) + { + std::vector simplex; + bool ok = add_all_faces_of_dimension(k, knn[*aw_it].begin(), rl[*aw_it].begin(), simplex, knn[*aw_it].end(), knn[*aw_it].end()); + if (!ok) + active_w.erase(aw_it++); //First increase the iterator and then erase the previous element + else + aw_it++; + } + std::cout << "k=" << k << ", active witnesses: " << active_w.size() << std::endl; + k++; + } + //print_sc(root()); std::cout << std::endl; + } + + /* \brief Adds recursively all the faces of a certain dimension dim witnessed by the same witness + * Iterator is needed to know until how far we can take landmarks to form simplexes + * simplex is the prefix of the simplexes to insert + * The output value indicates if the witness rests active or not + */ + bool add_all_faces_of_dimension(int dim, std::vector::iterator curr_l, typename std::vector< std::vector::iterator >::iterator curr_until, std::vector& simplex, std::vector::iterator until, std::vector::iterator end) + { + /* + std::ofstream ofs ("stree_result.txt", std::ofstream::out); + st_to_file(ofs); + ofs.close(); + */ + //print_sc(root()); + bool will_be_active = false; + if (dim > 0) + for (std::vector::iterator it = curr_l; it != until && it != end; ++it, ++curr_until) + { + simplex.push_back(*it); + if (find(simplex) != null_simplex()) + will_be_active = will_be_active || add_all_faces_of_dimension(dim-1, it+1, curr_until+1, simplex, until, end); + simplex.pop_back(); + if (until == end) + until = *curr_until; + } + else if (dim == 0) + for (std::vector::iterator it = curr_l; it != until && it != end; ++it, ++curr_until) + { + simplex.push_back(*it); + if (all_faces_in(simplex)) + { + will_be_active = true; + insert_simplex(simplex, 0.0); + } + simplex.pop_back(); + if (until == end) + until = *curr_until; + } + return will_be_active; + } + + /** \brief Construction of witness complex from points given explicitly + * nbL must be set to the right value of landmarks for strategies + * FURTHEST_POINT_STRATEGY and RANDOM_POINT_STRATEGY and + * density must be set to the right value for DENSITY_STRATEGY + */ + // void witness_complex_from_points(Point_Vector point_vector) + // { + // std::vector > WL; + // landmark_choice_by_random_points(point_vector, point_vector.size(), WL); + // witness_complex(WL); + // } + +private: + + /** \brief Print functions + */ + void print_sc(Siblings * sibl) + { + if (sibl == NULL) + std::cout << "&"; + else + print_children(sibl->members_); + } + + void print_children(Dictionary map) + { + std::cout << "("; + if (!map.empty()) + { + std::cout << map.begin()->first; + if (has_children(map.begin())) + print_sc(map.begin()->second.children()); + typename Dictionary::iterator it; + for (it = map.begin()+1; it != map.end(); ++it) + { + std::cout << "," << it->first; + if (has_children(it)) + print_sc(it->second.children()); + } + } + std::cout << ")"; + } + + public: + /** \brief Print functions + */ + + void st_to_file(std::ofstream& out_file) + { + sc_to_file(out_file, root()); + } + + private: + void sc_to_file(std::ofstream& out_file, Siblings * sibl) + { + assert(sibl); + children_to_file(out_file, sibl->members_); + } + + void children_to_file(std::ofstream& out_file, Dictionary& map) + { + out_file << "(" << std::flush; + if (!map.empty()) + { + out_file << map.begin()->first << std::flush; + if (has_children(map.begin())) + sc_to_file(out_file, map.begin()->second.children()); + typename Dictionary::iterator it; + for (it = map.begin()+1; it != map.end(); ++it) + { + out_file << "," << it->first << std::flush; + if (has_children(it)) + sc_to_file(out_file, it->second.children()); + } + } + out_file << ")" << std::flush; + } + + + /** \brief Check if the facets of the k-dimensional simplex witnessed + * by witness witness_id are already in the complex. + * inserted_vertex is the handle of the (k+1)-th vertex witnessed by witness_id + */ + bool all_faces_in(std::vector& simplex) + { + //std::cout << "All face in with the landmark " << inserted_vertex << std::endl; + std::vector< VertexHandle > facet; + //VertexHandle curr_vh = curr_sh->first; + // CHECK ALL THE FACETS + for (std::vector::iterator not_it = simplex.begin(); not_it != simplex.end(); ++not_it) + { + facet.clear(); + //facet = {}; + for (std::vector::iterator it = simplex.begin(); it != simplex.end(); ++it) + if (it != not_it) + facet.push_back(*it); + if (find(facet) == null_simplex()) + return false; + } //endfor + return true; + } + + template + void print_vector(std::vector v) + { + std::cout << "["; + if (!v.empty()) + { + std::cout << *(v.begin()); + for (auto it = v.begin()+1; it != v.end(); ++it) + { + std::cout << ","; + std::cout << *it; + } + } + std::cout << "]"; + } + + template + void print_vvector(std::vector< std::vector > vv) + { + std::cout << "["; + if (!vv.empty()) + { + print_vector(*(vv.begin())); + for (auto it = vv.begin()+1; it != vv.end(); ++it) + { + std::cout << ","; + print_vector(*it); + } + } + std::cout << "]\n"; + } + + public: +/** + * \brief Landmark choice strategy by iteratively adding the landmark the furthest from the + * current landmark set + * \arg W is the vector of points which will be the witnesses + * \arg nbP is the number of witnesses + * \arg nbL is the number of landmarks + * \arg WL is the matrix of the nearest landmarks with respect to witnesses (output) + */ + + template + void landmark_choice_by_furthest_points(Point_Vector &W, int nbP, KNearestNeighbours &WL) + { + //std::cout << "Enter landmark_choice_by_furthest_points "<< std::endl; + //std::cout << "W="; print_vvector(W); + //double density = 5.; + Point_Vector wit_land_dist(nbP,std::vector()); // distance matrix witness x landmarks + typeVectorVertex chosen_landmarks; // landmark list + + WL = KNearestNeighbours(nbP,std::vector()); + int current_number_of_landmarks=0; // counter for landmarks + double curr_max_dist = 0; // used for defining the furhest point from L + double curr_dist; // used to stock the distance from the current point to L + double infty = std::numeric_limits::infinity(); // infinity (see next entry) + std::vector< double > dist_to_L(nbP,infty); // vector of current distances to L from points + // double mindist = infty; + int curr_max_w=0; // the point currently furthest from L + int j; + int temp_swap_int; + double temp_swap_double; + + //CHOICE OF THE FIRST LANDMARK + std::cout << "Enter the first landmark stage\n"; + srand(354698); + int rand_int = rand()% nbP; + curr_max_w = rand_int; //For testing purposes a pseudo-random number is used here + + for (current_number_of_landmarks = 0; current_number_of_landmarks != nbL; current_number_of_landmarks++) + { + //curr_max_w at this point is the next landmark + chosen_landmarks.push_back(curr_max_w); + //std::cout << "**********Entered loop with current number of landmarks = " << current_number_of_landmarks << std::endl; + //std::cout << "WL="; print_vvector(WL); + //std::cout << "WLD="; print_vvector(wit_land_dist); + //std::cout << "landmarks="; print_vector(chosen_landmarks); std::cout << std::endl; + for (auto v: WL) + v.push_back(current_number_of_landmarks); + for (int i = 0; i < nbP; ++i) + { + // iteration on points in W. update of distance vectors + + //std::cout << "In the loop with i=" << i << " and landmark=" << chosen_landmarks[current_number_of_landmarks] << std::endl; + //std::cout << "W[i]="; print_vector(W[i]); std::cout << " W[landmark]="; print_vector(W[chosen_landmarks[current_number_of_landmarks]]); std::cout << std::endl; + curr_dist = euclidean_distance(W[i],W[chosen_landmarks[current_number_of_landmarks]]); + //std::cout << "The problem is not in distance function\n"; + wit_land_dist[i].push_back(curr_dist); + WL[i].push_back(current_number_of_landmarks); + //std::cout << "Push't back\n"; + if (curr_dist < dist_to_L[i]) + dist_to_L[i] = curr_dist; + j = current_number_of_landmarks; + //std::cout << "First half complete\n"; + while (j > 0 && wit_land_dist[i][j-1] > wit_land_dist[i][j]) + { + // sort the closest landmark vector for every witness + temp_swap_int = WL[i][j]; + WL[i][j] = WL[i][j-1]; + WL[i][j-1] = temp_swap_int; + temp_swap_double = wit_land_dist[i][j]; + wit_land_dist[i][j] = wit_land_dist[i][j-1]; + wit_land_dist[i][j-1] = temp_swap_double; + --j; + } + //std::cout << "result WL="; print_vvector(WL); + //std::cout << "result WLD="; print_vvector(wit_land_dist); + //std::cout << "result distL="; print_vector(dist_to_L); std::cout << std::endl; + //std::cout << "End loop\n"; + } + //std::cout << "Distance to landmarks="; print_vector(dist_to_L); std::cout << std::endl; + curr_max_dist = 0; + for (int i = 0; i < nbP; ++i) { + if (dist_to_L[i] > curr_max_dist) + { + curr_max_dist = dist_to_L[i]; + curr_max_w = i; + } + } + //std::cout << "Chose " << curr_max_w << " as new landmark\n"; + } + //std::cout << endl; + } + + /** \brief Landmark choice strategy by taking random vertices for landmarks. + * + */ + + // template + // void landmark_choice_by_random_points(Point_Vector &W, int nbP, KNearestNeighbours &WL) + // { + // std::cout << "Enter landmark_choice_by_random_points "<< std::endl; + // //std::cout << "W="; print_vvector(W); + // std::unordered_set< int > chosen_landmarks; // landmark set + + // Point_Vector wit_land_dist(nbP,std::vector()); // distance matrix witness x landmarks + + // WL = KNearestNeighbours(nbP,std::vector()); + // int current_number_of_landmarks=0; // counter for landmarks + + // srand(24660); + // int chosen_landmark = rand()%nbP; + // double curr_dist; + + // //int j; + // //int temp_swap_int; + // //double temp_swap_double; + + + // for (current_number_of_landmarks = 0; current_number_of_landmarks != nbL; current_number_of_landmarks++) + // { + // while (chosen_landmarks.find(chosen_landmark) != chosen_landmarks.end()) + // { + // srand((int)clock()); + // chosen_landmark = rand()% nbP; + // //std::cout << chosen_landmark << "\n"; + // } + // chosen_landmarks.insert(chosen_landmark); + // //std::cout << "**********Entered loop with current number of landmarks = " << current_number_of_landmarks << std::endl; + // //std::cout << "WL="; print_vvector(WL); + // //std::cout << "WLD="; print_vvector(wit_land_dist); + // //std::cout << "landmarks="; print_vector(chosen_landmarks); std::cout << std::endl; + // for (auto v: WL) + // v.push_back(current_number_of_landmarks); + // for (int i = 0; i < nbP; ++i) + // { + // // iteration on points in W. update of distance vectors + + // //std::cout << "In the loop with i=" << i << " and landmark=" << chosen_landmarks[current_number_of_landmarks] << std::endl; + // //std::cout << "W[i]="; print_vector(W[i]); std::cout << " W[landmark]="; print_vector(W[chosen_landmarks[current_number_of_landmarks]]); std::cout << std::endl; + // curr_dist = euclidean_distance(W[i],W[chosen_landmark]); + // //std::cout << "The problem is not in distance function\n"; + // wit_land_dist[i].push_back(curr_dist); + // WL[i].push_back(current_number_of_landmarks); + // //std::cout << "Push't back\n"; + // //j = current_number_of_landmarks; + // //std::cout << "First half complete\n"; + // //std::cout << "result WL="; print_vvector(WL); + // //std::cout << "result WLD="; print_vvector(wit_land_dist); + // //std::cout << "End loop\n"; + // } + // } + // for (int i = 0; i < nbP; i++) + // { + // sort(WL[i].begin(), WL[i].end(), [&](int j1, int j2){return wit_land_dist[i][j1] < wit_land_dist[i][j2];}); + // } + // //std::cout << endl; + // } + + /** \brief Landmark choice strategy by taking random vertices for landmarks. + * + */ + + // template + void landmark_choice_by_random_points(Point_Vector &W, int nbP, std::set &L) + { + std::cout << "Enter landmark_choice_by_random_points "<< std::endl; + //std::cout << "W="; print_vvector(W); + //std::unordered_set< int > chosen_landmarks; // landmark set + + //Point_Vector wit_land_dist(nbP,std::vector()); // distance matrix witness x landmarks + + //WL = KNearestNeighbours(nbP,std::vector()); + int current_number_of_landmarks=0; // counter for landmarks + + srand(24660); + int chosen_landmark = rand()%nbP; + //double curr_dist; + //int j; + //int temp_swap_int; + //double temp_swap_double; + for (current_number_of_landmarks = 0; current_number_of_landmarks != nbL; current_number_of_landmarks++) + { + while (L.find(chosen_landmark) != L.end()) + { + srand((int)clock()); + chosen_landmark = rand()% nbP; + //std::cout << chosen_landmark << "\n"; + } + L.insert(chosen_landmark); + //std::cout << "**********Entered loop with current number of landmarks = " << current_number_of_landmarks << std::endl; + //std::cout << "WL="; print_vvector(WL); + //std::cout << "WLD="; print_vvector(wit_land_dist); + //std::cout << "landmarks="; print_vector(chosen_landmarks); std::cout << std::endl; + // for (auto v: WL) + // v.push_back(current_number_of_landmarks); + // for (int i = 0; i < nbP; ++i) + // { + // // iteration on points in W. update of distance vectors + + // //std::cout << "In the loop with i=" << i << " and landmark=" << chosen_landmarks[current_number_of_landmarks] << std::endl; + // //std::cout << "W[i]="; print_vector(W[i]); std::cout << " W[landmark]="; print_vector(W[chosen_landmarks[current_number_of_landmarks]]); std::cout << std::endl; + // curr_dist = euclidean_distance(W[i],W[chosen_landmark]); + // //std::cout << "The problem is not in distance function\n"; + // wit_land_dist[i].push_back(curr_dist); + // WL[i].push_back(current_number_of_landmarks); + // //std::cout << "Push't back\n"; + // //j = current_number_of_landmarks; + // //std::cout << "First half complete\n"; + // //std::cout << "result WL="; print_vvector(WL); + // //std::cout << "result WLD="; print_vvector(wit_land_dist); + // //std::cout << "End loop\n"; + // } + } + // for (int i = 0; i < nbP; i++) + // { + // sort(WL[i].begin(), WL[i].end(), [&](int j1, int j2){return wit_land_dist[i][j1] < wit_land_dist[i][j2];}); + // } + //std::cout << endl; + } + + + /** \brief Construct the matrix |W|x(D+1) of D+1 closest landmarks + * where W is the set of witnesses and D is the ambient dimension + */ + template + void nearest_landmarks(Point_Vector &W, std::set &L, KNearestNeighbours &WL) + { + int D = W[0].size(); + int nbP = W.size(); + WL = KNearestNeighbours(nbP,std::vector()); + typedef std::pair dist_i; + typedef bool (*comp)(dist_i,dist_i); + for (int W_i = 0; W_i < nbP; W_i++) + { + //std::cout << "<<<<<<<<<<<<<<" << W_i <<"\n"; + std::priority_queue, comp> l_heap([&](dist_i j1, dist_i j2){return j1.first > j2.first;}); + std::set::iterator L_it; + int L_i; + for (L_it = L.begin(), L_i=0; L_it != L.end(); L_it++, L_i++) + { + dist_i dist = std::make_pair(euclidean_distance(W[W_i],W[*L_it]), L_i); + l_heap.push(dist); + } + for (int i = 0; i < D+1; i++) + { + dist_i dist = l_heap.top(); + WL[W_i].push_back(dist.second); + //WL[W_i].insert(WL[W_i].begin(),dist.second); + //std::cout << dist.first << " " << dist.second << std::endl; + l_heap.pop(); + } + } + } + + /** \brief Search and output links around vertices that are not pseudomanifolds + * + */ + void write_bad_links(std::ofstream& out_file) + { + out_file << "Bad links list\n"; + std::cout << "Entered write_bad_links\n"; + //typeVectorVertex testv = {9,15,17}; + //int count = 0; + for (auto v: complex_vertex_range()) + { + //std::cout << "Vertex " << v << ":\n"; + std::vector< Vertex_handle > link_vertices; + // Fill link_vertices + for (auto u: complex_vertex_range()) + { + typeVectorVertex edge = {u,v}; + if (u != v && find(edge) != null_simplex()) + link_vertices.push_back(u); + } + /* + print_vector(link_vertices); + std::cout << "\n"; + */ + // Find the dimension + typeVectorVertex empty_simplex = {}; + int d = link_dim(link_vertices, link_vertices.begin(),-1, empty_simplex); + //std::cout << " dim " << d << "\n"; + //Siblings* curr_sibl = root(); + if (link_is_pseudomanifold(link_vertices,d)) + count_good[d]++; + //out_file << "Bad link at " << v << "\n"; + } + //out_file << "Number of bad links: " << count << "/" << root()->size(); + //std::cout << "Number of bad links: " << count << "/" << root()->size() << std::endl; + nc = nbL; + for (unsigned int i = 0; i != count_good.size(); i++) + { + out_file << "count_good[" << i << "] = " << count_good[i] << std::endl; + nc -= count_good[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++) + { + out_file << "count_bad[" << i << "] = " << count_bad[i] << std::endl; + nc -= count_bad[i]; + if (count_bad[i] != 0) + std::cout << "count_bad[" << i << "] = " << count_bad[i] << std::endl; + } + std::cout << "not_connected = " << nc << std::endl; + } + + private: + + std::vector count_good; + std::vector count_bad; + int nc; + + int link_dim(std::vector< Vertex_handle >& link_vertices, + typename std::vector< Vertex_handle >::iterator curr_v, + int curr_d, + typeVectorVertex& curr_simplex) + { + //std::cout << "Entered link_dim for " << *(curr_v-1) << "\n"; + Simplex_handle sh; + int final_d = curr_d; + typename std::vector< Vertex_handle >::iterator it; + for (it = curr_v; it != link_vertices.end(); ++it) + { + curr_simplex.push_back(*it); + /* + std::cout << "Searching for "; + print_vector(curr_simplex); + std::cout << " curr_dim " << curr_d << " final_dim " << final_d; + */ + sh = find(curr_simplex); + if (sh != null_simplex()) + { + //std::cout << " -> " << *it << "\n"; + int d = link_dim(link_vertices, it+1, curr_d+1, curr_simplex); + if (d > final_d) + final_d = d; + } + /* + else + std::cout << "\n"; + */ + curr_simplex.pop_back(); + } + return final_d; + } + + // color is false is a (d-1)-dim face, true is a d-dim face + //typedef bool Color; + // graph is an adjacency list + typedef typename boost::adjacency_list Adj_graph; + // map that gives to a certain simplex its node in graph and its dimension + //typedef std::pair Reference; + typedef boost::graph_traits::vertex_descriptor Vertex_t; + typedef boost::graph_traits::edge_descriptor Edge_t; + + typedef boost::container::flat_map Graph_map; + + /* \brief Verifies if the simplices formed by vertices given by link_vertices + * form a pseudomanifold. + * The idea is to make a bipartite graph, where vertices are the d- and (d-1)-dimensional + * faces and edges represent adjacency between them. + */ + bool link_is_pseudomanifold(std::vector< Vertex_handle >& link_vertices, + int dimension) + { + Adj_graph adj_graph; + Graph_map d_map, f_map; // d_map = map for d-dimensional simplices + // f_map = map for its facets + typeVectorVertex empty_vector = {}; + add_vertices(link_vertices, + link_vertices.begin(), + adj_graph, + d_map, + f_map, + empty_vector, + 0, dimension); + //std::cout << "DMAP_SIZE: " << d_map.size() << "\n"; + //std::cout << "FMAP_SIZE: " << f_map.size() << "\n"; + add_edges(adj_graph, d_map, f_map); + for (auto f_map_it : f_map) + { + //std::cout << "Degree of " << f_map_it.first->first << " is " << boost::out_degree(f_map_it.second, adj_graph) << "\n"; + if (boost::out_degree(f_map_it.second, adj_graph) != 2) + { + count_bad[dimension]++; + return false; + } + } + // At this point I know that all (d-1)-simplices are adjacent to exactly 2 d-simplices + // What is left is to check the connexity + std::vector components(boost::num_vertices(adj_graph)); + return (boost::connected_components(adj_graph, &components[0]) == 1); + } + + void add_vertices(typeVectorVertex& link_vertices, + typename typeVectorVertex::iterator curr_v, + Adj_graph& adj_graph, + Graph_map& d_map, + Graph_map& f_map, + typeVectorVertex& curr_simplex, + int curr_d, + int dimension) + { + Simplex_handle sh; + Vertex_t vert; + typename typeVectorVertex::iterator it; + std::pair resPair; + //typename Graph_map::iterator resPair; + //Add vertices + //std::cout << "Entered add vertices\n"; + for (it = curr_v; it != link_vertices.end(); ++it) + { + curr_simplex.push_back(*it); + /* + std::cout << "Searching for "; + print_vector(curr_simplex); + std::cout << " curr_dim " << curr_d << " d " << dimension << ""; + */ + sh = find(curr_simplex); + if (sh != null_simplex()) + { + //std::cout << " added\n"; + if (curr_d == dimension) + { + vert = boost::add_vertex(adj_graph); + resPair = d_map.emplace(sh,vert); + } + else + { + if (curr_d == dimension-1) + { + vert = boost::add_vertex(adj_graph); + resPair = f_map.emplace(sh,vert); + } + add_vertices(link_vertices, + it+1, + adj_graph, + d_map, + f_map, + curr_simplex, + curr_d+1, dimension); + } + } + /* + else + std::cout << "\n"; + */ + curr_simplex.pop_back(); + } + } + + void add_edges(Adj_graph& adj_graph, + Graph_map& d_map, + Graph_map& f_map) + { + Simplex_handle sh; + // Add edges + //std::cout << "Entered add edges:\n"; + typename Graph_map::iterator map_it; + for (auto d_map_pair : d_map) + { + //std::cout << "*"; + sh = d_map_pair.first; + Vertex_t d_vert = d_map_pair.second; + for (auto facet_sh : boundary_simplex_range(sh)) + //for (auto f_map_it : f_map) + { + //std::cout << "'"; + map_it = f_map.find(facet_sh); + //We must have all the facets in the graph at this point + assert(map_it != f_map.end()); + Vertex_t f_vert = map_it->second; + //std::cout << "Added edge " << sh->first << "-" << map_it->first->first << "\n"; + boost::add_edge(d_vert,f_vert,adj_graph); + } + } + } + + ////////////////////////////////////////////////////////////////////////////////////////////////// + //***********COLLAPSES**************************************************************************// + ////////////////////////////////////////////////////////////////////////////////////////////////// + + + + + + + +}; //class Witness_complex + + + +} // namespace Guhdi + +#endif diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h index 04fcc98f..201d6525 100644 --- a/src/Witness_complex/include/gudhi/Witness_complex.h +++ b/src/Witness_complex/include/gudhi/Witness_complex.h @@ -140,7 +140,6 @@ namespace Gudhi { //void witness_complex(std::vector< std::vector< Vertex_handle > > & knn) { std::cout << "**Start the procedure witness_complex" << std::endl; - int k=2; /* current dimension in iterative construction */ //Construction of the active witness list int nbW = knn.size(); //int nbL = knn.at(0).size(); @@ -157,13 +156,14 @@ namespace Gudhi { // by doing it we don't assume that landmarks are necessarily witnesses themselves anymore counter++; vv = {i}; - /* TODO Filtration */ returnValue = insert_simplex(vv, Filtration_value(0.0)); /* TODO Error if not inserted : normally no need here though*/ } + int k=1; /* current dimension in iterative construction */ //std::cout << "Successfully added landmarks" << std::endl; // PRINT2 //print_sc(root()); std::cout << std::endl; + /* int u,v; // two extremities of an edge int count = 0; if (nbL > 1) // if the supposed dimension of the complex is >0 @@ -202,39 +202,37 @@ namespace Gudhi { active_w.push_back(i); } } - std::cout << "k=1, active witnesses: " << active_w.size() << std::endl; + */ + for (int i=0; i != nbW; ++i) + active_w.push_back(i); + std::cout << "k=0, active witnesses: " << active_w.size() << std::endl; //std::cout << "Successfully added edges" << std::endl; - count_good = {0,0}; - count_bad = {0,0}; + count_good = {0}; + count_bad = {0}; int D = knn[0].size(); while (!active_w.empty() && k < D ) { count_good.push_back(0); count_bad.push_back(0); - count++; //std::cout << "Started the step k=" << k << std::endl; typename ActiveWitnessList::iterator it = active_w.begin(); while (it != active_w.end()) { typeVectorVertex simplex_vector; /* THE INSERTION: Checking if all the subfaces are in the simplex tree*/ - // First sort the first k landmarks - VertexHandle inserted_vertex = knn[*it][k]; - bool ok = all_faces_in(knn, *it, k, inserted_vertex); + bool ok = all_faces_in(knn, *it, k); if (ok) { for (int i = 0; i != k+1; ++i) simplex_vector.push_back(knn[*it][i]); returnValue = insert_simplex(simplex_vector,0.0); - if (returnValue.second) - count++; it++; } else active_w.erase(it++); //First increase the iterator and then erase the previous element } std::cout << "k=" << k << ", active witnesses: " << active_w.size() << std::endl; - std::cout << "** k=" << k << ", num_simplices: " < - bool all_faces_in(KNearestNeighbours &knn, int witness_id, int k, VertexHandle inserted_vertex) + bool all_faces_in(KNearestNeighbours &knn, int witness_id, int k) { //std::cout << "All face in with the landmark " << inserted_vertex << std::endl; std::vector< VertexHandle > facet; @@ -332,20 +330,17 @@ private: // CHECK ALL THE FACETS for (int i = 0; i != k+1; ++i) { - if (knn[witness_id][i] != inserted_vertex) + facet = {}; + for (int j = 0; j != k+1; ++j) { - facet = {}; - for (int j = 0; j != k+1; ++j) + if (j != i) { - if (j != i) - { - facet.push_back(knn[witness_id][j]); - } - }//endfor - if (find(facet) == null_simplex()) - return false; - //std::cout << "++++ finished loop safely\n"; - }//endif + facet.push_back(knn[witness_id][j]); + } + }//endfor + if (find(facet) == null_simplex()) + return false; + //std::cout << "++++ finished loop safely\n"; } //endfor return true; } @@ -1059,6 +1054,54 @@ bool complex_is_pseudomanifold(int dimension) } } + public: + /** \brief Verification if every simplex in the complex is witnessed + */ + template< class KNearestNeighbors > + bool is_witness_complex(KNearestNeighbors WL) + { + //bool final_result = true; + for (Simplex_handle sh: complex_simplex_range()) + { + bool is_witnessed = false; + typeVectorVertex simplex; + int nbV = 0; //number of verticed in the simplex + for (int v: simplex_vertex_range(sh)) + simplex.push_back(v); + nbV = simplex.size(); + for (typeVectorVertex w: WL) + { + bool has_vertices = true; + for (int v: simplex) + if (std::find(w.begin(), w.begin()+nbV, v) == w.begin()+nbV) + { + has_vertices = false; + //break; + } + if (has_vertices) + { + is_witnessed = true; + std::cout << "The simplex "; + print_vector(simplex); + std::cout << " is witnessed by the witness "; + print_vector(w); + std::cout << std::endl; + break; + } + } + if (!is_witnessed) + { + std::cout << "The following simplex is not witnessed "; + print_vector(simplex); + std::cout << std::endl; + assert(is_witnessed); + return false; + } + } + return true; // Arrive here if the not_witnessed check failed all the time + } + + }; //class Witness_complex -- cgit v1.2.3