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Diffstat (limited to 'src/Witness_complex/include/gudhi/Strong_witness_complex.h')
-rw-r--r-- | src/Witness_complex/include/gudhi/Strong_witness_complex.h | 198 |
1 files changed, 198 insertions, 0 deletions
diff --git a/src/Witness_complex/include/gudhi/Strong_witness_complex.h b/src/Witness_complex/include/gudhi/Strong_witness_complex.h new file mode 100644 index 00000000..539c872d --- /dev/null +++ b/src/Witness_complex/include/gudhi/Strong_witness_complex.h @@ -0,0 +1,198 @@ +/* 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_WITNESS_COMPLEX_H_ +#define STRONG_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 gss = Gudhi::spatial_searching; + +namespace Gudhi { + +namespace witness_complex { + +// /* +// * \private +// \class Witness_complex +// \brief Constructs the witness complex for the given set of witnesses and landmarks. +// \ingroup witness_complex +// */ +template< class Kernel_ > +class Strong_witness_complex { +private: + 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_range::iterator Nearest_landmark_row_iterator; + //typedef std::vector<std::pair<unsigned,FT>> Nearest_landmarks; + + // 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_) { } + // }; + + typedef std::vector< double > Point_t; + typedef std::vector< Point_t > Point_Vector; + + typedef FT Filtration_value; + + + typedef std::ptrdiff_t Witness_id; + typedef std::ptrdiff_t Landmark_id; + typedef std::pair<Landmark_id, FT> Id_distance_pair; + typedef Active_witness<Id_distance_pair, Nearest_landmark_range> ActiveWitness; + typedef std::list< ActiveWitness > ActiveWitnessList; + typedef std::vector< Landmark_id > typeVectorVertex; + typedef std::pair< typeVectorVertex, Filtration_value> typeSimplex; + + private: + Point_range witnesses_, landmarks_; + Kd_tree landmark_tree_; + + public: + ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////// + /* @name Constructor + */ + + //@{ + + // Witness_range<Closest_landmark_range<Vertex_handle>> + + /* + * \brief Iterative construction of the (weak) witness complex. + * \details The witness complex is written in sc_ basing on a matrix knn of + * nearest neighbours of the form {witnesses}x{landmarks}. + * + * 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 InputIteratorLandmarks, + typename InputIteratorWitnesses > + Strong_witness_complex(InputIteratorLandmarks landmarks_first, + InputIteratorLandmarks landmarks_last, + InputIteratorWitnesses witnesses_first, + InputIteratorWitnesses witnesses_last) + : witnesses_(witnesses_first, witnesses_last), landmarks_(landmarks_first, landmarks_last), landmark_tree_(landmarks_) + { + } + + /** \brief Returns the point corresponding to the given vertex. + */ + Point_d get_point( std::size_t vertex ) const + { + return landmarks_[vertex]; + } + + /** \brief Outputs the (weak) witness complex with + * squared relaxation parameter 'max_alpha_square' + * to simplicial complex 'complex'. + */ + template < typename SimplicialComplexForWitness > + bool create_complex(SimplicialComplexForWitness& complex, + FT max_alpha_square) + { + unsigned nbL = landmarks_.size(); + if (complex.num_vertices() > 0) { + std::cerr << "Witness complex cannot create complex - complex is not empty.\n"; + return false; + } + if (max_alpha_square < 0) { + std::cerr << "Witness complex cannot create complex - squared relaxation parameter must be non-negative.\n"; + return false; + } + typeVectorVertex vv; + //ActiveWitnessList active_witnesses;// = new ActiveWitnessList(); + for (unsigned i = 0; i != nbL; ++i) { + // initial fill of 0-dimensional simplices + vv = {i}; + complex.insert_simplex(vv, Filtration_value(0.0)); + /* TODO Error if not inserted : normally no need here though*/ + } + for (auto w: witnesses_) { + ActiveWitness aw(landmark_tree_.query_incremental_nearest_neighbors(w)); + typeVectorVertex simplex; + typename ActiveWitness::iterator aw_it = aw.begin(); + float lim_d2 = aw.begin()->second + max_alpha_square; + while (aw_it != aw.end() && aw_it->second < lim_d2) { + simplex.push_back(aw_it->first); + complex.insert_simplex_and_subfaces(simplex, aw_it->second - aw.begin()->second); + aw_it++; + } + } + return true; + } + + //@} +}; + +} // namespace witness_complex + +} // namespace Gudhi + +#endif |