diff options
author | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2016-11-17 09:52:03 +0000 |
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committer | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2016-11-17 09:52:03 +0000 |
commit | ede6f875e8340fb72d114ad9db3b54862566594f (patch) | |
tree | d096337589d4ff217c31d12f558a150e19c47e39 /src/Witness_complex | |
parent | 668e76bbe8f350ab0fdf6f6105e8c7818a5ad38f (diff) |
Modify examples
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_module@1757 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: 4b6f26947ad16f440ea4d4b7cb5e145a58f28dcb
Diffstat (limited to 'src/Witness_complex')
8 files changed, 7 insertions, 209 deletions
diff --git a/src/Witness_complex/example/witness_complex_from_file.cpp b/src/Witness_complex/example/witness_complex_from_file.cpp index 59dd28e0..5dd18d0a 100644 --- a/src/Witness_complex/example/witness_complex_from_file.cpp +++ b/src/Witness_complex/example/witness_complex_from_file.cpp @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2015 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2015 INRIA * * 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 @@ -36,9 +36,9 @@ #include <string> #include <vector> -typedef std::vector< int > typeVectorVertex; -typedef std::vector< std::vector <double> > Point_Vector; typedef Gudhi::Simplex_tree<> Simplex_tree; +typedef std::vector< Simplex_tree::Vertex_handle > typeVectorVertex; +typedef std::vector< std::vector <double> > Point_Vector; int main(int argc, char * const argv[]) { if (argc != 3) { diff --git a/src/Witness_complex/example/witness_complex_sphere.cpp b/src/Witness_complex/example/witness_complex_sphere.cpp index 7ab86cc0..60e02225 100644 --- a/src/Witness_complex/example/witness_complex_sphere.cpp +++ b/src/Witness_complex/example/witness_complex_sphere.cpp @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2015 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2015 INRIA * * 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 diff --git a/src/Witness_complex/include/gudhi/Construct_closest_landmark_table.h b/src/Witness_complex/include/gudhi/Construct_closest_landmark_table.h index ec93ae71..1ae2e393 100644 --- a/src/Witness_complex/include/gudhi/Construct_closest_landmark_table.h +++ b/src/Witness_complex/include/gudhi/Construct_closest_landmark_table.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2015 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2015 INRIA * * 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 diff --git a/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h b/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h deleted file mode 100644 index bcb89e00..00000000 --- a/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h +++ /dev/null @@ -1,105 +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 LANDMARK_CHOICE_BY_FURTHEST_POINT_H_ -#define LANDMARK_CHOICE_BY_FURTHEST_POINT_H_ - -#include <boost/range/size.hpp> - -#include <limits> // for numeric_limits<> -#include <iterator> -#include <algorithm> // for sort -#include <vector> - -namespace Gudhi { - -namespace witness_complex { - - typedef std::vector<int> typeVectorVertex; - - /** - * \ingroup witness_complex - * \brief Landmark choice strategy by iteratively adding the furthest 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<Closest_landmark_range<Vertex_handle>>, where - * Witness_range and Closest_landmark_range are random access ranges - * - */ - - template <typename KNearestNeighbours, - typename Point_random_access_range> - void landmark_choice_by_furthest_point(Point_random_access_range const &points, - int nbL, - KNearestNeighbours &knn) { - int nb_points = boost::size(points); - assert(nb_points >= nbL); - // distance matrix witness x landmarks - std::vector<std::vector<double>> wit_land_dist(nb_points, std::vector<double>()); - // landmark list - typeVectorVertex chosen_landmarks; - - knn = KNearestNeighbours(nb_points, std::vector<int>()); - 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<double>::infinity(); // infinity (see next entry) - std::vector< double > dist_to_L(nb_points, infty); // vector of current distances to L from points - - // TODO(SK) Consider using rand_r(...) instead of rand(...) for improved thread safety - // or better yet std::uniform_int_distribution - int rand_int = rand() % nb_points; - int curr_max_w = rand_int; // For testing purposes a pseudo-random number is used here - - 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 - chosen_landmarks.push_back(curr_max_w); - unsigned i = 0; - for (auto& p : points) { - double curr_dist = euclidean_distance<double>(p, *(std::begin(points) + chosen_landmarks[current_number_of_landmarks])); - wit_land_dist[i].push_back(curr_dist); - knn[i].push_back(current_number_of_landmarks); - if (curr_dist < dist_to_L[i]) - dist_to_L[i] = curr_dist; - ++i; - } - 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; - } - } - for (int i = 0; i < nb_points; ++i) - std::sort(std::begin(knn[i]), - std::end(knn[i]), - [&wit_land_dist, i](int a, int b) { - return wit_land_dist[i][a] < wit_land_dist[i][b]; }); - } - -} // namespace witness_complex - -} // namespace Gudhi - -#endif // LANDMARK_CHOICE_BY_FURTHEST_POINT_H_ diff --git a/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h b/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h deleted file mode 100644 index b5aab9d5..00000000 --- a/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h +++ /dev/null @@ -1,96 +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 LANDMARK_CHOICE_BY_RANDOM_POINT_H_ -#define LANDMARK_CHOICE_BY_RANDOM_POINT_H_ - -#include <boost/range/size.hpp> - -#include <queue> // for priority_queue<> -#include <utility> // for pair<> -#include <iterator> -#include <vector> -#include <set> - -namespace Gudhi { - -namespace witness_complex { - - /** - * \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 a matrix {witness}*{closest landmarks} in knn. - * - * 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 and - * Vertex_handle is the label type of a vertex in a simplicial complex. - * Closest_landmark_range needs to have push_back operation. - */ - - template <typename KNearestNeighbours, - typename Point_random_access_range> - void landmark_choice_by_random_point(Point_random_access_range const &points, - int nbL, - KNearestNeighbours &knn) { - int nbP = boost::size(points); - assert(nbP >= nbL); - std::set<int> landmarks; - int current_number_of_landmarks = 0; // counter for landmarks - - // TODO(SK) Consider using rand_r(...) instead of rand(...) for improved thread safety - int chosen_landmark = rand() % nbP; - for (current_number_of_landmarks = 0; current_number_of_landmarks != nbL; current_number_of_landmarks++) { - while (landmarks.find(chosen_landmark) != landmarks.end()) - chosen_landmark = rand() % nbP; - landmarks.insert(chosen_landmark); - } - - int dim = boost::size(*std::begin(points)); - typedef std::pair<double, int> dist_i; - typedef bool (*comp)(dist_i, dist_i); - knn = KNearestNeighbours(nbP); - for (int points_i = 0; points_i < nbP; points_i++) { - std::priority_queue<dist_i, std::vector<dist_i>, comp> l_heap([](dist_i j1, dist_i j2) { - return j1.first > j2.first; - }); - std::set<int>::iterator landmarks_it; - int landmarks_i = 0; - for (landmarks_it = landmarks.begin(), landmarks_i = 0; landmarks_it != landmarks.end(); - ++landmarks_it, landmarks_i++) { - dist_i dist = std::make_pair(euclidean_distance<double>(points[points_i], points[*landmarks_it]), landmarks_i); - l_heap.push(dist); - } - for (int i = 0; i < dim + 1; i++) { - dist_i dist = l_heap.top(); - knn[points_i].push_back(dist.second); - l_heap.pop(); - } - } - } - -} // namespace witness_complex - -} // namespace Gudhi - -#endif // LANDMARK_CHOICE_BY_RANDOM_POINT_H_ diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h index 2cec921a..1eb126f1 100644 --- a/src/Witness_complex/include/gudhi/Witness_complex.h +++ b/src/Witness_complex/include/gudhi/Witness_complex.h @@ -72,7 +72,6 @@ class Witness_complex { typedef std::vector< Point_t > Point_Vector; typedef std::vector< Vertex_handle > typeVectorVertex; - //typedef std::pair< typeVectorVertex, Filtration_value> typeSimplex; typedef std::pair< Simplex_handle, bool > typePairSimplexBool; typedef int Witness_id; diff --git a/src/Witness_complex/test/simple_witness_complex.cpp b/src/Witness_complex/test/simple_witness_complex.cpp index adaadfb0..6be39f58 100644 --- a/src/Witness_complex/test/simple_witness_complex.cpp +++ b/src/Witness_complex/test/simple_witness_complex.cpp @@ -33,7 +33,7 @@ #include <vector> typedef Gudhi::Simplex_tree<> Simplex_tree; -typedef std::vector< int > typeVectorVertex; +typedef std::vector< Simplex_tree::Vertex_handle > typeVectorVertex; typedef Gudhi::witness_complex::Witness_complex<Simplex_tree> WitnessComplex; BOOST_AUTO_TEST_CASE(simple_witness_complex) { diff --git a/src/Witness_complex/test/witness_complex_points.cpp b/src/Witness_complex/test/witness_complex_points.cpp index b7067f87..92f53417 100644 --- a/src/Witness_complex/test/witness_complex_points.cpp +++ b/src/Witness_complex/test/witness_complex_points.cpp @@ -34,8 +34,8 @@ #include <vector> typedef std::vector<double> Point; -typedef std::vector< int > typeVectorVertex; typedef Gudhi::Simplex_tree<> Simplex_tree; +typedef std::vector< Simplex_tree::Vertex_handle > typeVectorVertex; typedef Gudhi::witness_complex::Witness_complex<Simplex_tree> WitnessComplex; BOOST_AUTO_TEST_CASE(witness_complex_points) { |