diff options
Diffstat (limited to 'src/Witness_complex/include/gudhi/Witness_complex.h')
| -rw-r--r-- | src/Witness_complex/include/gudhi/Witness_complex.h | 241 |
1 files changed, 163 insertions, 78 deletions
diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h index 5c6d087f..4c489e7a 100644 --- a/src/Witness_complex/include/gudhi/Witness_complex.h +++ b/src/Witness_complex/include/gudhi/Witness_complex.h @@ -31,6 +31,7 @@ #include <boost/range/size.hpp> #include <gudhi/distance_functions.h> +#include <gudhi/Kd_tree_search.h> #include <algorithm> #include <utility> @@ -42,8 +43,10 @@ #include <ctime> #include <iostream> -namespace Gudhi { +namespace gss = Gudhi::spatial_searching; +namespace Gudhi { + namespace witness_complex { // /* @@ -55,9 +58,15 @@ namespace witness_complex { template< class SimplicialComplex, class Kernel_ > class Witness_complex { - typedef Kernel_ K; - typedef K::Point_d Point_d; - + typedef Kernel_ K; + typedef typename K::Point_d Point_d; + typedef typename K::FT FT; + typedef std::vector<Point_d> Point_range; + typedef gss::Kd_tree_search<Kernel_, Point_range> Kd_tree; + typedef typename Kd_tree::INS_range Nearest_landmark_range; + typedef typename std::vector<Nearest_landmark_range> Nearest_landmark_table; + typedef typename Nearest_landmark_table::const_iterator Nearest_landmark_table_iterator; + //typedef std::vector<std::pair<unsigned,FT>> Nearest_landmarks; private: struct Active_witness { @@ -86,9 +95,10 @@ class Witness_complex { private: int nbL_; // Number of landmarks - SimplicialComplex& sc_; // Simplicial complex - std::vector<Point_d> witnesses_, landmarks_; - + SimplicialComplex& sc_; // Simplicial complex + Point_range witnesses_, landmarks_; + Kd_tree landmark_tree_; + std::vector<Nearest_landmark_range> nearest_landmarks_; public: ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////// @@ -118,52 +128,53 @@ class Witness_complex { Witness_complex(InputIteratorLandmarks landmarks_first, InputIteratorLandmarks landmarks_last, InputIteratorWitnesses witnesses_first, - InputIteratorWitnesses witnesses_last) - : witnesses_(witnesses_first, witnesses_last), landmarks_(landmarks_first, landmarks_last) + InputIteratorWitnesses witnesses_last, + SimplicialComplex& sc) + : witnesses_(witnesses_first, witnesses_last), landmarks_(landmarks_first, landmarks_last), landmark_tree_(landmarks_), sc_(sc) { + for (Point_d w : witnesses_) + nearest_landmarks_.push_back(landmark_tree_.query_incremental_nearest_neighbors(w)); } + Point_d get_point( std::size_t vertex ) const + { + return landmarks_[vertex]; + } - - template< typename KNearestNeighbors > - Witness_complex(KNearestNeighbors const & knn, - int nbL, - int dim, - SimplicialComplex & sc) : nbL_(nbL), sc_(sc) { - // Construction of the active witness list - int nbW = boost::size(knn); + template < typename SimplicialComplexForWitness > + bool create_complex(SimplicialComplexForWitness& complex, + FT max_alpha_square) const + { + unsigned nbW = witnesses_.size(), + nbL = landmarks_.size(); typeVectorVertex vv; - int counter = 0; - /* The list of still useful witnesses - * it will diminuish in the course of iterations - */ - ActiveWitnessList active_w; // = new ActiveWitnessList(); - for (Vertex_handle i = 0; i != nbL_; ++i) { + 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++; + //counter++; vv = {i}; - sc_.insert_simplex(vv); - // TODO(SK) Error if not inserted : normally no need here though + complex.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 */ - for (int i = 0; i != nbW; ++i) + unsigned k = 1; /* current dimension in iterative construction */ + for (int i=0; i != nbW; ++i) active_w.push_back(i); - while (!active_w.empty() && k < dim) { - 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*/ - 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]); - sc_.insert_simplex(simplex_vector); - // TODO(SK) Error if not inserted : normally no need here though - ++it; - } else { - active_w.erase(it++); // First increase the iterator and then erase the previous element - } + while (!active_w.empty() && k < nbL ) { + typename ActiveWitnessList::iterator aw_it = active_w.begin(); + while (aw_it != active_w.end()) { + std::vector<int> simplex; + bool ok = add_all_faces_of_dimension(k, + max_alpha_square, + std::numeric_limits<double>::infinity(), + nearest_landmarks_[*aw_it].begin(), + simplex, + complex, + nearest_landmarks_[*aw_it].end()); + if (!ok) + active_w.erase(aw_it++); //First increase the iterator and then erase the previous element + else + aw_it++; } k++; } @@ -172,40 +183,114 @@ class Witness_complex { //@} private: - /* \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 + + /* \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 */ - template <typename KNearestNeighbors> - bool all_faces_in(KNearestNeighbors const &knn, int witness_id, int k) { - std::vector< Vertex_handle > facet; - // CHECK ALL THE FACETS - for (int i = 0; i != k + 1; ++i) { - facet = {}; - for (int j = 0; j != k + 1; ++j) { - if (j != i) { - facet.push_back(knn[witness_id][j]); + template < typename SimplicialComplexForWitness > + bool add_all_faces_of_dimension(int dim, + double alpha2, + double norelax_dist2, + Nearest_landmark_table_iterator curr_l, + std::vector<int>& simplex, + SimplicialComplexForWitness& sc, + Nearest_landmark_table_iterator end) + { + if (curr_l == end) + return false; + bool will_be_active = false; + Nearest_landmark_table_iterator l_it = curr_l; + if (dim > 0) + for (; l_it->second - alpha2 <= norelax_dist2 && l_it != end; ++l_it) { + simplex.push_back(l_it->first); + if (sc.find(simplex) != sc.null_simplex()) + will_be_active = add_all_faces_of_dimension(dim-1, + alpha2, + norelax_dist2, + l_it+1, + simplex, + sc, + end) || will_be_active; + simplex.pop_back(); + // If norelax_dist is infinity, change to first omitted distance + if (l_it->second <= norelax_dist2) + norelax_dist2 = l_it->second; + will_be_active = add_all_faces_of_dimension(dim-1, + alpha2, + norelax_dist2, + l_it+1, + simplex, + sc, + end) || will_be_active; + } + else if (dim == 0) + for (; l_it->second - alpha2 <= norelax_dist2 && l_it != end; ++l_it) { + simplex.push_back(l_it->second); + double filtration_value = 0; + // if norelax_dist is infinite, relaxation is 0. + if (l_it->second > norelax_dist2) + filtration_value = l_it->second - norelax_dist2; + if (all_faces_in(simplex, &filtration_value, sc)) { + will_be_active = true; + sc.insert_simplex(simplex, filtration_value); } - } // endfor - if (sc_.find(facet) == sc_.null_simplex()) - return false; - } // endfor - return true; + simplex.pop_back(); + // If norelax_dist is infinity, change to first omitted distance + if (l_it->second < norelax_dist2) + norelax_dist2 = l_it->second; + } + return will_be_active; } - - template <typename T> - static void print_vector(const std::vector<T>& 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; + + /** \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 + */ + template < typename SimplicialComplexForWitness > + bool all_faces_in(std::vector<int>& simplex, + double* filtration_value, + SimplicialComplexForWitness& sc) + { + std::vector< int > facet; + for (std::vector<int>::iterator not_it = simplex.begin(); not_it != simplex.end(); ++not_it) + { + facet.clear(); + for (std::vector<int>::iterator it = simplex.begin(); it != simplex.end(); ++it) + if (it != not_it) + facet.push_back(*it); + Simplex_handle facet_sh = sc.find(facet); + if (facet_sh == sc.null_simplex()) + return false; + else if (sc.filtration(facet_sh) > *filtration_value) + *filtration_value = sc.filtration(facet_sh); } - } - std::cout << "]"; + return true; } + // bool is_face(Simplex_handle face, Simplex_handle coface) + // { + // // vertex range is sorted in decreasing order + // auto fvr = sc.simplex_vertex_range(face); + // auto cfvr = sc.simplex_vertex_range(coface); + // auto fv_it = fvr.begin(); + // auto cfv_it = cfvr.begin(); + // while (fv_it != fvr.end() && cfv_it != cfvr.end()) { + // if (*fv_it < *cfv_it) + // ++cfv_it; + // else if (*fv_it == *cfv_it) { + // ++cfv_it; + // ++fv_it; + // } + // else + // return false; + + // } + // return (fv_it == fvr.end()); + // } + + public: // /* // * \brief Verification if every simplex in the complex is witnessed by witnesses in knn. @@ -269,13 +354,13 @@ class Witness_complex { * * Landmarks are supposed to be in [0,nbL_-1] */ - template <class KNearestNeighbors, class SimplicialComplexForWitness> - void witness_complex(KNearestNeighbors const & knn, - int nbL, - int dim, - SimplicialComplexForWitness & sc) { - Witness_complex<SimplicialComplexForWitness>(knn, nbL, dim, sc); - } + // template <class KNearestNeighbors, class SimplicialComplexForWitness> + // void witness_complex(KNearestNeighbors const & knn, + // int nbL, + // int dim, + // SimplicialComplexForWitness & sc) { + // Witness_complex<SimplicialComplexForWitness>(knn, nbL, dim, sc); + // } } // namespace witness_complex |