From e061bc2e16e8fdb7368479f101642ae239ffc7dc Mon Sep 17 00:00:00 2001 From: skachano Date: Wed, 5 Oct 2016 08:57:58 +0000 Subject: Added the forgotten strong witness complex git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/relaxed-witness@1640 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 19e4a60b7b6a71db6148bb99f11dbf10ff8cc248 --- .../include/gudhi/Strong_witness_complex.h | 198 +++++++++++++++++++++ 1 file changed, 198 insertions(+) create mode 100644 src/Witness_complex/include/gudhi/Strong_witness_complex.h 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 . + */ + +#ifndef STRONG_WITNESS_COMPLEX_H_ +#define STRONG_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 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_range; + typedef gss::Kd_tree_search Kd_tree; + typedef typename Kd_tree::INS_range Nearest_landmark_range; + typedef typename std::vector Nearest_landmark_table; + typedef typename Nearest_landmark_range::iterator Nearest_landmark_row_iterator; + //typedef std::vector> 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 Id_distance_pair; + typedef Active_witness 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> + + /* + * \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>, 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 -- cgit v1.2.3