From 80c45e3f6a8a1f823840b3ae9e924362d7e376b7 Mon Sep 17 00:00:00 2001 From: skachano Date: Mon, 20 Jun 2016 21:49:38 +0000 Subject: Added the forgotten files git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/subsampling_and_spatialsearching@1317 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: f5fe0bce1c55e62c87bf0da9be915f081a90e9e7 --- .../gudhi/Landmark_choice_by_farthest_point.h | 158 --------------------- .../gudhi/Landmark_choice_by_random_point.h | 80 ----------- .../include/gudhi/choose_by_farthest_point.h | 96 +++++++++++++ src/Subsampling/include/gudhi/pick_random_points.h | 80 +++++++++++ 4 files changed, 176 insertions(+), 238 deletions(-) delete mode 100644 src/Subsampling/include/gudhi/Landmark_choice_by_farthest_point.h delete mode 100644 src/Subsampling/include/gudhi/Landmark_choice_by_random_point.h create mode 100644 src/Subsampling/include/gudhi/choose_by_farthest_point.h create mode 100644 src/Subsampling/include/gudhi/pick_random_points.h (limited to 'src/Subsampling/include/gudhi') diff --git a/src/Subsampling/include/gudhi/Landmark_choice_by_farthest_point.h b/src/Subsampling/include/gudhi/Landmark_choice_by_farthest_point.h deleted file mode 100644 index 198c9f9f..00000000 --- a/src/Subsampling/include/gudhi/Landmark_choice_by_farthest_point.h +++ /dev/null @@ -1,158 +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 . - */ - -#ifndef LANDMARK_CHOICE_BY_FARTHEST_POINT_H_ -#define LANDMARK_CHOICE_BY_FARTHEST_POINT_H_ - -#include - -#include -#include // for sort -#include -#include -#include - -namespace Gudhi { - - - template < typename Point_d, - typename Heap, - typename Tree, - typename Presence_table > - void update_heap( Point_d &l, - unsigned nbL, - Heap &heap, - Tree &tree, - Presence_table &table) - { - auto search = tree.query_incremental_ANN(l); - for (auto w: search) { - if (table[w.first].first) - if (w.second < table[w.first].second->second) { - heap.update(table[w.first].second, w); - } - } - } - - /** - * \ingroup witness_complex - * \brief Landmark choice strategy by iteratively adding the farthest witness from the - * current landmark set as the new landmark. - * \details It chooses nbL landmarks from a random access range `points` and - * writes {witness}*{closest landmarks} matrix in `knn`. - * - * The type KNearestNeighbors can be seen as - * Witness_range>, where - * Witness_range and Closest_landmark_range are random access ranges - * - */ - - template < typename Kernel, - typename Point_container, - typename OutputIterator> - void landmark_choice_by_farthest_point( Kernel& k, - Point_container const &points, - int nbL, - OutputIterator output_it) - { - - // typedef typename Kernel::FT FT; - // typedef std::pair Heap_node; - - // struct R_max_compare - // { - // bool operator()(const Heap_node &rmh1, const Heap_node &rmh2) const - // { - // return rmh1.second < rmh2.second; - // } - // }; - - // typedef boost::heap::fibonacci_heap> Heap; - // typedef Spatial_tree_data_structure Tree; - // typedef std::vector< std::pair > Presence_table; - - typename Kernel::Squared_distance_d sqdist = k.squared_distance_d_object(); - - // Tree tree(points); - // Heap heap; - // Presence_table table(points.size()); - // for (auto p: table) - // std::cout << p.first << "\n"; - // int number_landmarks = 0; // number of treated landmarks - - // double curr_max_dist = 0; // used for defining the furhest point from L - // const double infty = std::numeric_limits::infinity(); // infinity (see next entry) - // std::vector< double > dist_to_L(points.size(), infty); // vector of current distances to L from points - - // // Choose randomly the first landmark - // std::random_device rd; - // std::mt19937 gen(rd()); - // std::uniform_int_distribution<> dis(1, 6); - // int curr_landmark = dis(gen); - - // do { - // *output_landmarks++ = points[curr_landmark]; - // std::cout << curr_landmark << "\n"; - // number_landmarks++; - // } - // while (number_landmarks < nbL); - // } - - int nb_points = boost::size(points); - assert(nb_points >= nbL); - - int current_number_of_landmarks = 0; // counter for landmarks - double curr_max_dist = 0; // used for defining the furhest point from L - const double infty = std::numeric_limits::infinity(); // infinity (see next entry) - std::vector< double > dist_to_L(nb_points, infty); // vector of current distances to L from points - - // Choose randomly the first landmark - std::random_device rd; - std::mt19937 gen(rd()); - std::uniform_int_distribution<> dis(1, 6); - int curr_max_w = dis(gen); - - - 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 - *output_it++ = points[curr_max_w]; - std::cout << curr_max_w << "\n"; - unsigned i = 0; - for (auto& p : points) { - double curr_dist = sqdist(p, *(std::begin(points) + curr_max_w)); - if (curr_dist < dist_to_L[i]) - dist_to_L[i] = curr_dist; - ++i; - } - // choose the next curr_max_w - curr_max_dist = 0; - for (i = 0; i < dist_to_L.size(); i++) - if (dist_to_L[i] > curr_max_dist) { - curr_max_dist = dist_to_L[i]; - curr_max_w = i; - } - } - } - -} // namespace Gudhi - -#endif // LANDMARK_CHOICE_BY_FARTHEST_POINT_H_ diff --git a/src/Subsampling/include/gudhi/Landmark_choice_by_random_point.h b/src/Subsampling/include/gudhi/Landmark_choice_by_random_point.h deleted file mode 100644 index daa05d1a..00000000 --- a/src/Subsampling/include/gudhi/Landmark_choice_by_random_point.h +++ /dev/null @@ -1,80 +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) 2016 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 LANDMARK_CHOICE_BY_RANDOM_POINT_H_ -#define LANDMARK_CHOICE_BY_RANDOM_POINT_H_ - -#include - -#include // random_device, mt19937 -#include // shuffle -#include // iota -#include -#include - - -namespace Gudhi { - - /** - * \ingroup witness_complex - * \brief Landmark choice strategy by taking random vertices for landmarks. - * - * \details It chooses nbL distinct landmarks from a random access range `points` - * and outputs them to an output iterator. - * Point_container::iterator should be ValueSwappable and RandomAccessIterator. - */ - - template - void landmark_choice_by_random_point(Point_container const &points, - unsigned nbL, - OutputIterator output_it) { -#ifdef GUDHI_LM_PROFILING - Gudhi::Clock t; -#endif - - unsigned nbP = boost::size(points); - assert(nbP >= nbL); - std::vector landmarks(nbP); - std::iota(landmarks.begin(), landmarks.end(), 0); - - std::random_device rd; - std::mt19937 g(rd()); - - std::shuffle(landmarks.begin(), landmarks.end(), g); - landmarks.resize(nbL); - - for (int l: landmarks) - *output_it++ = points[l]; - -#ifdef GUDHI_LM_PROFILING - t.end(); - std::cerr << "Random landmark choice took " << t.num_seconds() - << " seconds." << std::endl; -#endif - - - } - -} // namespace Gudhi - -#endif // LANDMARK_CHOICE_BY_RANDOM_POINT_H_ diff --git a/src/Subsampling/include/gudhi/choose_by_farthest_point.h b/src/Subsampling/include/gudhi/choose_by_farthest_point.h new file mode 100644 index 00000000..61a21f44 --- /dev/null +++ b/src/Subsampling/include/gudhi/choose_by_farthest_point.h @@ -0,0 +1,96 @@ +/* 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 CHOOSE_BY_FARTHEST_POINT_H_ +#define CHOOSE_BY_FARTHEST_POINT_H_ + +#include + +#include +#include // for sort +#include +#include + +namespace Gudhi { + + /** + * \ingroup witness_complex + * \brief Landmark choice strategy by iteratively adding the farthest witness from the + * current landmark set as the new landmark. + * \details It chooses nbL landmarks from a random access range `points` and + * writes {witness}*{closest landmarks} matrix in `knn`. + * + * The type KNearestNeighbors can be seen as + * Witness_range>, where + * Witness_range and Closest_landmark_range are random access ranges + * + */ + + template < typename Kernel, + typename Point_container, + typename OutputIterator> + void choose_by_farthest_point( Kernel& k, + Point_container const &points, + int nbL, + OutputIterator output_it) + { + typename Kernel::Squared_distance_d sqdist = k.squared_distance_d_object(); + + int nb_points = boost::size(points); + assert(nb_points >= nbL); + + int current_number_of_landmarks = 0; // counter for landmarks + double curr_max_dist = 0; // used for defining the furhest point from L + const double infty = std::numeric_limits::infinity(); // infinity (see next entry) + std::vector< double > dist_to_L(nb_points, infty); // vector of current distances to L from points + + // Choose randomly the first landmark + std::random_device rd; + std::mt19937 gen(rd()); + std::uniform_int_distribution<> dis(1, 6); + int curr_max_w = dis(gen); + + + 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 + *output_it++ = points[curr_max_w]; + std::cout << curr_max_w << "\n"; + unsigned i = 0; + for (auto& p : points) { + double curr_dist = sqdist(p, *(std::begin(points) + curr_max_w)); + if (curr_dist < dist_to_L[i]) + dist_to_L[i] = curr_dist; + ++i; + } + // choose the next curr_max_w + curr_max_dist = 0; + for (i = 0; i < dist_to_L.size(); i++) + if (dist_to_L[i] > curr_max_dist) { + curr_max_dist = dist_to_L[i]; + curr_max_w = i; + } + } + } + +} // namespace Gudhi + +#endif // CHOOSE_BY_FARTHEST_POINT_H_ diff --git a/src/Subsampling/include/gudhi/pick_random_points.h b/src/Subsampling/include/gudhi/pick_random_points.h new file mode 100644 index 00000000..9a436ee3 --- /dev/null +++ b/src/Subsampling/include/gudhi/pick_random_points.h @@ -0,0 +1,80 @@ +/* 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) 2016 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 PICK_RANDOM_POINTS_H_ +#define PICK_RANDOM_POINTS_H_ + +#include + +#include // random_device, mt19937 +#include // shuffle +#include // iota +#include +#include + + +namespace Gudhi { + + /** + * \ingroup witness_complex + * \brief Landmark choice strategy by taking random vertices for landmarks. + * + * \details It chooses nbL distinct landmarks from a random access range `points` + * and outputs them to an output iterator. + * Point_container::iterator should be ValueSwappable and RandomAccessIterator. + */ + + template + void pick_random_points(Point_container const &points, + unsigned nbL, + OutputIterator output_it) { +#ifdef GUDHI_LM_PROFILING + Gudhi::Clock t; +#endif + + unsigned nbP = boost::size(points); + assert(nbP >= nbL); + std::vector landmarks(nbP); + std::iota(landmarks.begin(), landmarks.end(), 0); + + std::random_device rd; + std::mt19937 g(rd()); + + std::shuffle(landmarks.begin(), landmarks.end(), g); + landmarks.resize(nbL); + + for (int l: landmarks) + *output_it++ = points[l]; + +#ifdef GUDHI_LM_PROFILING + t.end(); + std::cerr << "Random landmark choice took " << t.num_seconds() + << " seconds." << std::endl; +#endif + + + } + +} // namespace Gudhi + +#endif // LANDMARK_CHOICE_BY_RANDOM_POINT_H_ -- cgit v1.2.3