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Diffstat (limited to 'src/Witness_complex/include/gudhi/Strong_relaxed_witness_complex.h')
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1 files changed, 0 insertions, 337 deletions
diff --git a/src/Witness_complex/include/gudhi/Strong_relaxed_witness_complex.h b/src/Witness_complex/include/gudhi/Strong_relaxed_witness_complex.h deleted file mode 100644 index ee863a42..00000000 --- a/src/Witness_complex/include/gudhi/Strong_relaxed_witness_complex.h +++ /dev/null @@ -1,337 +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/>. - */ - -#ifndef STRONG_RELAXED_WITNESS_COMPLEX_H_ -#define STRONG_RELAXED_WITNESS_COMPLEX_H_ - -#include <boost/container/flat_map.hpp> -#include <boost/iterator/transform_iterator.hpp> -#include <algorithm> -#include <utility> -#include "gudhi/reader_utils.h" -#include "gudhi/distance_functions.h" -#include "gudhi/Simplex_tree.h" -#include <vector> -#include <list> -#include <set> -#include <queue> -#include <limits> -#include <math.h> -#include <ctime> -#include <iostream> - -// Needed for nearest neighbours -#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 <boost/tuple/tuple.hpp> -#include <boost/iterator/zip_iterator.hpp> -#include <boost/iterator/counting_iterator.hpp> -#include <boost/range/iterator_range.hpp> - -// Needed for the adjacency graph in bad link search -#include <boost/graph/graph_traits.hpp> -#include <boost/graph/adjacency_list.hpp> -#include <boost/graph/connected_components.hpp> - -namespace Gudhi { - -namespace witness_complex { - - /** \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 Simplicial_complex > -class Strong_relaxed_witness_complex { - -private: - struct Active_witness { - int witness_id; - int landmark_id; - - Active_witness(int witness_id_, int landmark_id_) - : witness_id(witness_id_), - landmark_id(landmark_id_) { } - }; - -private: - typedef typename Simplicial_complex::Simplex_handle Simplex_handle; - typedef typename Simplicial_complex::Vertex_handle Vertex_handle; - typedef typename Simplicial_complex::Filtration_value FT; - - typedef std::vector< double > Point_t; - typedef std::vector< Point_t > Point_Vector; - - // typedef typename Simplicial_complex::Filtration_value Filtration_value; - typedef std::vector< Vertex_handle > typeVectorVertex; - typedef std::pair< typeVectorVertex, Filtration_value> typeSimplex; - typedef std::pair< Simplex_handle, bool > typePairSimplexBool; - - typedef int Witness_id; - typedef int Landmark_id; - typedef std::list< Vertex_handle > ActiveWitnessList; - - private: - int nbL; // Number of landmarks - Simplicial_complex& sc; // Simplicial complex - - public: - /** @name Constructor - */ - - //@{ - - /** - * \brief Iterative construction of the relaxed witness complex. - * \details The witness complex is written in sc_ basing on a matrix knn - * of k nearest neighbours of the form {witnesses}x{landmarks} and - * and a matrix distances of distances to these landmarks from witnesses. - * The parameter alpha defines relaxation and - * limD defines the - * - * The line lengths in one given matrix can differ, - * however both matrices have the same corresponding line lengths. - * - * The type KNearestNeighbors can be seen as - * Witness_range<Closest_landmark_range<Vertex_handle>>, where - * Witness_range and Closest_landmark_range are random access ranges. - * - * Constructor takes into account at most (dim+1) - * first landmarks from each landmark range to construct simplices. - * - * Landmarks are supposed to be in [0,nbL_-1] - */ - - template< typename KNearestNeighbours > - Strong_relaxed_witness_complex(std::vector< std::vector<double> > const & distances, - KNearestNeighbours const & knn, - Simplicial_complex & sc_, - int nbL_, - double alpha2, - unsigned limD) : nbL(nbL_), sc(sc_) { - int nbW = knn.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 (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}; - sc.insert_simplex(vv, Filtration_value(0.0)); - /* TODO Error if not inserted : normally no need here though*/ - } - for (int i=0; i != nbW; ++i) { - // int i_end = limD+1; - // if (knn[i].size() < limD+1) - // i_end = knn[i].size(); - // double dist_wL = *(distances[i].begin()); - // while (distances[i][i_end] > dist_wL + alpha2) - // i_end--; - // add_all_witnessed_faces(distances[i].begin(), - // knn[i].begin(), - // knn[i].begin() + i_end + 1); - unsigned j_end = 0; - while (j_end < distances[i].size() && j_end <= limD && distances[i][j_end] <= distances[i][0] + alpha2) { - std::vector<int> simplex; - for (unsigned j = 0; j <= j_end; ++j) - simplex.push_back(knn[i][j]); - assert(distances[i][j_end] - distances[i][0] >= 0); - sc.insert_simplex_and_subfaces(simplex, distances[i][j_end] - distances[i][0]); - j_end++; - } - } - sc.set_dimension(limD); - } - - //@} - -private: - /* \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 - */ - void add_all_witnessed_faces(std::vector<double>::const_iterator curr_d, - std::vector<int>::const_iterator curr_l, - std::vector<int>::const_iterator end) - { - std::vector<int> simplex; - std::vector<int>::const_iterator l_end = curr_l; - for (; l_end != end; ++l_end) { - std::vector<int>::const_iterator l_it = curr_l; - std::vector<double>::const_iterator d_it = curr_d; - simplex = {}; - for (; l_it != l_end; ++l_it, ++d_it) - simplex.push_back(*l_it); - sc.insert_simplex_and_subfaces(simplex, *(d_it--) - *curr_d); - } - } - - /** \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<int>& simplex, double* filtration_value) - { - 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); - } - 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()); - } - - // void erase_simplex(Simplex_handle sh) - // { - // auto siblings = sc.self_siblings(sh); - // auto oncles = siblings->oncles(); - // int prev_vertex = siblings->parent(); - // siblings->members().erase(sh->first); - // if (siblings->members().empty()) { - // typename typedef Simplicial_complex::Siblings Siblings; - // oncles->members().find(prev_vertex)->second.assign_children(new Siblings(oncles, prev_vertex)); - // assert(!sc.has_children(oncles->members().find(prev_vertex))); - // //delete siblings; - // } - - // } - - void elementary_collapse(Simplex_handle face_sh, Simplex_handle coface_sh) - { - erase_simplex(coface_sh); - erase_simplex(face_sh); - } - -public: - // void collapse(std::vector<Simplex_handle>& simplices) - // { - // // Get a vector of simplex handles ordered by filtration value - // std::cout << sc << std::endl; - // //std::vector<Simplex_handle> simplices; - // for (Simplex_handle sh: sc.filtration_simplex_range()) - // simplices.push_back(sh); - // // std::sort(simplices.begin(), - // // simplices.end(), - // // [&](Simplex_handle sh1, Simplex_handle sh2) - // // { double f1 = sc.filtration(sh1), f2 = sc.filtration(sh2); - // // return (f1 > f2) || (f1 >= f2 && sc.dimension(sh1) > sc.dimension(sh2)); }); - // // Double iteration - // auto face_it = simplices.rbegin(); - // while (face_it != simplices.rend() && sc.filtration(*face_it) != 0) { - // int coface_count = 0; - // auto reduced_coface = simplices.rbegin(); - // for (auto coface_it = simplices.rbegin(); coface_it != simplices.rend() && sc.filtration(*coface_it) != 0; ++coface_it) - // if (face_it != coface_it && is_face(*face_it, *coface_it)) { - // coface_count++; - // if (coface_count == 1) - // reduced_coface = coface_it; - // else - // break; - // } - // if (coface_count == 1) { - // std::cout << "Erase ( "; - // for (auto v: sc.simplex_vertex_range(*(--reduced_coface.base()))) - // std::cout << v << " "; - - // simplices.erase(--(reduced_coface.base())); - // //elementary_collapse(*face_it, *reduced_coface); - // std::cout << ") and then ( "; - // for (auto v: sc.simplex_vertex_range(*(--face_it.base()))) - // std::cout << v << " "; - // std::cout << ")\n"; - // simplices.erase(--((face_it++).base())); - // //face_it = simplices.rbegin(); - // //std::cout << "Size of vector: " << simplices.size() << "\n"; - // } - // else - // face_it++; - // } - // sc.initialize_filtration(); - // //std::cout << sc << std::endl; - // } - - template <class Dim_lists> - void collapse(Dim_lists& dim_lists) - { - dim_lists.collapse(); - } - -private: - - /** Collapse recursively boundary faces of the given simplex - * if its filtration is bigger than alpha_lim. - */ - void rec_boundary_collapse(Simplex_handle sh, FT alpha_lim) - { - for (Simplex_handle face_it : sc.boundary_simplex_range()) { - - } - - } - -}; //class Strong_relaxed_witness_complex - -} // namespace witness_complex - -} // namespace Gudhi - -#endif |