diff options
author | mcarrier <mcarrier@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2018-06-23 04:59:39 +0000 |
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committer | mcarrier <mcarrier@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2018-06-23 04:59:39 +0000 |
commit | 0741c3eabbfece1c73ac76aa44adbe2904b6124d (patch) | |
tree | 83fc9edee2be2c5b1fc73d9d3cc1ddc4a66c828b /src/cython/include | |
parent | 10c6f6be72a2631cd1a1d28ed61343d55bd2b759 (diff) |
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/kernels@3628 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: 12f32a1c8ca31e7e0a40e1c3502e2a3d810d5bc5
Diffstat (limited to 'src/cython/include')
-rw-r--r-- | src/cython/include/Kernels_interface.h | 130 | ||||
-rw-r--r-- | src/cython/include/Vectors_interface.h | 59 |
2 files changed, 0 insertions, 189 deletions
diff --git a/src/cython/include/Kernels_interface.h b/src/cython/include/Kernels_interface.h deleted file mode 100644 index a07d7820..00000000 --- a/src/cython/include/Kernels_interface.h +++ /dev/null @@ -1,130 +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): Mathieu Carriere - * - * Copyright (C) 2018 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 - * 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 INCLUDE_KERNELS_INTERFACE_H_ -#define INCLUDE_KERNELS_INTERFACE_H_ - -#include <gudhi/common_persistence_representations.h> -#include <gudhi/Sliced_Wasserstein.h> -#include <gudhi/Persistence_weighted_gaussian.h> -#include <gudhi/Weight_functions.h> - -#include <iostream> -#include <vector> -#include <utility> // for std::pair - -namespace Gudhi { - -namespace persistence_diagram { - - - // ******************* - // Kernel evaluations. - // ******************* - - double sw(const std::vector<std::pair<double, double>>& diag1, const std::vector<std::pair<double, double>>& diag2, double sigma, int N) { - Gudhi::Persistence_representations::Sliced_Wasserstein sw1(diag1, sigma, N); - Gudhi::Persistence_representations::Sliced_Wasserstein sw2(diag2, sigma, N); - return sw1.compute_scalar_product(sw2); - } - - double pwg(const std::vector<std::pair<double, double>>& diag1, const std::vector<std::pair<double, double>>& diag2, int N, std::string weight, double sigma, double C, double p) { - Gudhi::Persistence_representations::Weight weight_fn; - if(weight.compare("linear") == 0) weight_fn = Gudhi::Persistence_representations::linear_weight; - if(weight.compare("arctan") == 0) weight_fn = Gudhi::Persistence_representations::arctan_weight(C,p); - if(weight.compare("const") == 0) weight_fn = Gudhi::Persistence_representations::const_weight; - Gudhi::Persistence_representations::Persistence_weighted_gaussian pwg1(diag1, sigma, N, weight_fn); - Gudhi::Persistence_representations::Persistence_weighted_gaussian pwg2(diag2, sigma, N, weight_fn); - return pwg1.compute_scalar_product(pwg2); - } - - double pss(const std::vector<std::pair<double, double>>& diag1, const std::vector<std::pair<double, double>>& diag2, double sigma, int N) { - std::vector<std::pair<double, double>> pd1 = diag1; int numpts = diag1.size(); for(int i = 0; i < numpts; i++) pd1.emplace_back(diag1[i].second,diag1[i].first); - std::vector<std::pair<double, double>> pd2 = diag2; numpts = diag2.size(); for(int i = 0; i < numpts; i++) pd2.emplace_back(diag2[i].second,diag2[i].first); - - Gudhi::Persistence_representations::Persistence_weighted_gaussian pwg1(pd1, 2*std::sqrt(sigma), N, Gudhi::Persistence_representations::pss_weight); - Gudhi::Persistence_representations::Persistence_weighted_gaussian pwg2(pd2, 2*std::sqrt(sigma), N, Gudhi::Persistence_representations::pss_weight); - - return pwg1.compute_scalar_product (pwg2) / (16*Gudhi::Persistence_representations::pi*sigma); - } - - double pss_sym(const std::vector<std::pair<double, double>>& diag1, const std::vector<std::pair<double, double>>& diag2, double sigma, int N) { - Gudhi::Persistence_representations::Persistence_weighted_gaussian pwg1(diag1, 2*std::sqrt(sigma), N, Gudhi::Persistence_representations::pss_weight); - Gudhi::Persistence_representations::Persistence_weighted_gaussian pwg2(diag2, 2*std::sqrt(sigma), N, Gudhi::Persistence_representations::pss_weight); - - return pwg1.compute_scalar_product (pwg2) / (16*Gudhi::Persistence_representations::pi*sigma); - } - - - // **************** - // Kernel matrices. - // **************** - - std::vector<std::vector<double> > sw_matrix(const std::vector<std::vector<std::pair<double, double> > >& s1, const std::vector<std::vector<std::pair<double, double> > >& s2, double sigma, int N){ - std::vector<std::vector<double> > matrix; - std::vector<Gudhi::Persistence_representations::Sliced_Wasserstein> ss1; - int num_diag_1 = s1.size(); for(int i = 0; i < num_diag_1; i++){Gudhi::Persistence_representations::Sliced_Wasserstein sw1(s1[i], sigma, N); ss1.push_back(sw1);} - std::vector<Gudhi::Persistence_representations::Sliced_Wasserstein> ss2; - int num_diag_2 = s2.size(); for(int i = 0; i < num_diag_2; i++){Gudhi::Persistence_representations::Sliced_Wasserstein sw2(s2[i], sigma, N); ss2.push_back(sw2);} - for(int i = 0; i < num_diag_1; i++){ - std::cout << 100.0*i/num_diag_1 << " %" << std::endl; - std::vector<double> ps; for(int j = 0; j < num_diag_2; j++) ps.push_back(ss1[i].compute_scalar_product(ss2[j])); matrix.push_back(ps); - } - return matrix; - } - - std::vector<std::vector<double> > pwg_matrix(const std::vector<std::vector<std::pair<double, double> > >& s1, const std::vector<std::vector<std::pair<double, double> > >& s2, int N, std::string weight, double sigma, double C, double p){ - std::vector<std::vector<double> > matrix; int num_diag_1 = s1.size(); int num_diag_2 = s2.size(); - for(int i = 0; i < num_diag_1; i++){ - std::cout << 100.0*i/num_diag_1 << " %" << std::endl; - std::vector<double> ps; for(int j = 0; j < num_diag_2; j++) ps.push_back(pwg(s1[i], s2[j], N, weight, sigma, C, p)); matrix.push_back(ps); - } - return matrix; - } - - std::vector<std::vector<double> > pss_matrix(const std::vector<std::vector<std::pair<double, double> > >& s1, const std::vector<std::vector<std::pair<double, double> > >& s2, double sigma, int N){ - std::vector<std::vector<std::pair<double, double> > > ss1, ss2; std::vector<std::vector<double> > matrix; int num_diag_1 = s1.size(); int num_diag_2 = s2.size(); - for(int i = 0; i < num_diag_1; i++){ - std::vector<std::pair<double, double>> pd1 = s1[i]; int numpts = s1[i].size(); - for(int j = 0; j < numpts; j++) pd1.emplace_back(s1[i][j].second,s1[i][j].first); - ss1.push_back(pd1); - } - - for(int i = 0; i < num_diag_2; i++){ - std::vector<std::pair<double, double>> pd2 = s2[i]; int numpts = s2[i].size(); - for(int j = 0; j < numpts; j++) pd2.emplace_back(s2[i][j].second,s2[i][j].first); - ss2.push_back(pd2); - } - - for(int i = 0; i < num_diag_1; i++){ - std::cout << 100.0*i/num_diag_1 << " %" << std::endl; - std::vector<double> ps; for(int j = 0; j < num_diag_2; j++) ps.push_back(pss_sym(ss1[i], ss2[j], sigma, N)); matrix.push_back(ps); - } - return matrix; - } - -} // namespace persistence_diagram - -} // namespace Gudhi - - -#endif // INCLUDE_KERNELS_INTERFACE_H_ diff --git a/src/cython/include/Vectors_interface.h b/src/cython/include/Vectors_interface.h deleted file mode 100644 index 902ccc10..00000000 --- a/src/cython/include/Vectors_interface.h +++ /dev/null @@ -1,59 +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): Mathieu Carriere - * - * Copyright (C) 2018 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 - * 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 INCLUDE_VECTORS_INTERFACE_H_ -#define INCLUDE_VECTORS_INTERFACE_H_ - -#include <gudhi/Persistence_landscape_on_grid_exact.h> -#include <gudhi/Persistence_heat_maps_exact.h> -#include <gudhi/Weight_functions.h> - -#include <iostream> -#include <vector> -#include <utility> // for std::pair - -using Weight = std::function<double (std::pair<double,double>) >; - -namespace Gudhi { - -namespace persistence_diagram { - - std::vector<std::vector<double> > compute_ls(const std::vector<std::pair<double, double> >& diag, int nb_ls, double min_x, double max_x, int res_x) { - Gudhi::Persistence_representations::Persistence_landscape_on_grid_exact L(diag, nb_ls, min_x, max_x, res_x); - return L.vectorize(); - } - - std::vector<std::vector<double> > compute_pim(const std::vector<std::pair<double, double> >& diag, double min_x, double max_x, int res_x, double min_y, double max_y, int res_y, std::string weight, double sigma, double C, double p) { - Weight weight_fn; - if(weight.compare("linear") == 0) weight_fn = Gudhi::Persistence_representations::linear_weight; - if(weight.compare("arctan") == 0) weight_fn = Gudhi::Persistence_representations::arctan_weight(C,p); - if(weight.compare("const") == 0) weight_fn = Gudhi::Persistence_representations::const_weight; - Gudhi::Persistence_representations::Persistence_heat_maps_exact P(diag, min_x, max_x, res_x, min_y, max_y, res_y, weight_fn, sigma); - return P.vectorize(); - } - -} // namespace persistence_diagram - -} // namespace Gudhi - - -#endif // INCLUDE_VECTORS_INTERFACE_H_ |