diff options
Diffstat (limited to 'src/Persistence_representations/example')
5 files changed, 286 insertions, 0 deletions
diff --git a/src/Persistence_representations/example/CMakeLists.txt b/src/Persistence_representations/example/CMakeLists.txt index 54d719ac..3142f19b 100644 --- a/src/Persistence_representations/example/CMakeLists.txt +++ b/src/Persistence_representations/example/CMakeLists.txt @@ -27,3 +27,22 @@ add_test(NAME Persistence_representations_example_heat_maps COMMAND $<TARGET_FILE:Persistence_representations_example_heat_maps>) install(TARGETS Persistence_representations_example_heat_maps DESTINATION bin) +add_executable ( Sliced_Wasserstein sliced_wasserstein.cpp ) +add_test(NAME Sliced_Wasserstein + COMMAND $<TARGET_FILE:Sliced_Wasserstein>) +install(TARGETS Sliced_Wasserstein DESTINATION bin) + +add_executable ( Persistence_weighted_gaussian persistence_weighted_gaussian.cpp ) +add_test(NAME Persistence_weighted_gaussian + COMMAND $<TARGET_FILE:Persistence_weighted_gaussian>) +install(TARGETS Persistence_weighted_gaussian DESTINATION bin) + +add_executable ( Persistence_heat_maps_exact persistence_heat_maps_exact.cpp ) +add_test(NAME Persistence_heat_maps_exact + COMMAND $<TARGET_FILE:Persistence_heat_maps_exact>) +install(TARGETS Persistence_heat_maps_exact DESTINATION bin) + +add_executable ( Persistence_landscape_on_grid_exact persistence_landscape_on_grid_exact.cpp ) +add_test(NAME Persistence_landscape_on_grid_exact + COMMAND $<TARGET_FILE:Persistence_landscape_on_grid_exact>) +install(TARGETS Persistence_landscape_on_grid_exact DESTINATION bin) diff --git a/src/Persistence_representations/example/persistence_heat_maps_exact.cpp b/src/Persistence_representations/example/persistence_heat_maps_exact.cpp new file mode 100644 index 00000000..f15b710d --- /dev/null +++ b/src/Persistence_representations/example/persistence_heat_maps_exact.cpp @@ -0,0 +1,55 @@ +/* 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 (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/>. + */ + +#include <gudhi/Persistence_heat_maps_exact.h> +#include <gudhi/Weight_functions.h> + +#include <iostream> +#include <vector> +#include <utility> +#include <string> + +using Persistence_diagram = Gudhi::Persistence_representations::Persistence_diagram; +using PI = Gudhi::Persistence_representations::Persistence_heat_maps_exact; +using Weight = std::function<double (std::pair<double,double>) >; + +int main(int argc, char** argv) { + + Persistence_diagram persistence; + + persistence.push_back(std::make_pair(1, 2)); + persistence.push_back(std::make_pair(6, 8)); + persistence.push_back(std::make_pair(0, 4)); + persistence.push_back(std::make_pair(3, 8)); + + double min_x = 0.0; double max_x = 10.0; int res_x = 100; double min_y = 0.0; double max_y = 10.0; int res_y = 100; double sigma = 1.0; Weight weight = Gudhi::Persistence_representations::linear_weight; + + PI pim(persistence, min_x, max_x, res_x, min_y, max_y, res_y, weight, sigma); + std::vector<std::vector<double> > P = pim.vectorize(); + + for(int i = 0; i < res_y; i++){ + for(int j = 0; j < res_x; j++) std::cout << P[i][j] << " "; + std::cout << std::endl; + } + + return 0; +} diff --git a/src/Persistence_representations/example/persistence_landscape_on_grid_exact.cpp b/src/Persistence_representations/example/persistence_landscape_on_grid_exact.cpp new file mode 100644 index 00000000..da27bc5a --- /dev/null +++ b/src/Persistence_representations/example/persistence_landscape_on_grid_exact.cpp @@ -0,0 +1,52 @@ +/* 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 (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/>. + */ + +#include <gudhi/Persistence_landscape_on_grid_exact.h> + +#include <iostream> +#include <vector> +#include <utility> + +using Persistence_diagram = Gudhi::Persistence_representations::Persistence_diagram; +using LS = Gudhi::Persistence_representations::Persistence_landscape_on_grid_exact; + +int main(int argc, char** argv) { + + Persistence_diagram persistence; + + persistence.push_back(std::make_pair(1, 2)); + persistence.push_back(std::make_pair(6, 8)); + persistence.push_back(std::make_pair(0, 4)); + persistence.push_back(std::make_pair(3, 8)); + + int nb_ls = 3; double min_x = 0.0; double max_x = 10.0; int res_x = 100; + + LS ls(persistence, nb_ls, min_x, max_x, res_x); + std::vector<std::vector<double> > L = ls.vectorize(); + + for(int i = 0; i < nb_ls; i++){ + for(int j = 0; j < res_x; j++) std::cout << L[i][j] << " "; + std::cout << std::endl; + } + + return 0; +} diff --git a/src/Persistence_representations/example/persistence_weighted_gaussian.cpp b/src/Persistence_representations/example/persistence_weighted_gaussian.cpp new file mode 100644 index 00000000..7945e4f1 --- /dev/null +++ b/src/Persistence_representations/example/persistence_weighted_gaussian.cpp @@ -0,0 +1,99 @@ +/* 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 (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/>. + */ + +#include <gudhi/Persistence_weighted_gaussian.h> + +#include <iostream> +#include <vector> +#include <utility> + +using Persistence_diagram = Gudhi::Persistence_representations::Persistence_diagram; +using PWG = Gudhi::Persistence_representations::Persistence_weighted_gaussian; + +int main(int argc, char** argv) { + + Persistence_diagram persistence1, persistence2; + + persistence1.push_back(std::make_pair(1, 2)); + persistence1.push_back(std::make_pair(6, 8)); + persistence1.push_back(std::make_pair(0, 4)); + persistence1.push_back(std::make_pair(3, 8)); + + persistence2.push_back(std::make_pair(2, 9)); + persistence2.push_back(std::make_pair(1, 6)); + persistence2.push_back(std::make_pair(3, 5)); + persistence2.push_back(std::make_pair(6, 10)); + + double sigma = 1; + double tau = 1; + int m = 10000; + + PWG PWG1(persistence1, sigma, m, Gudhi::Persistence_representations::arctan_weight(1,1)); + PWG PWG2(persistence2, sigma, m, Gudhi::Persistence_representations::arctan_weight(1,1)); + + PWG PWGex1(persistence1, sigma, -1, Gudhi::Persistence_representations::arctan_weight(1,1)); + PWG PWGex2(persistence2, sigma, -1, Gudhi::Persistence_representations::arctan_weight(1,1)); + + + // Linear PWG + + std::cout << "Approx PWG kernel: " << PWG1.compute_scalar_product (PWG2) << std::endl; + std::cout << "Exact PWG kernel: " << PWGex1.compute_scalar_product (PWGex2) << std::endl; + + std::cout << "Distance induced by approx PWG kernel: " << PWG1.distance (PWG2) << std::endl; + std::cout << "Distance induced by exact PWG kernel: " << PWGex1.distance (PWGex2) << std::endl; + + + + + + + + // Gaussian PWG + + std::cout << "Approx Gaussian PWG kernel: " << std::exp( -PWG1.distance (PWG2) ) / (2*tau*tau) << std::endl; + std::cout << "Exact Gaussian PWG kernel: " << std::exp( -PWGex1.distance (PWGex2) ) / (2*tau*tau) << std::endl; + + + + + + + + // PSS + + Persistence_diagram pd1 = persistence1; int numpts = persistence1.size(); for(int i = 0; i < numpts; i++) pd1.emplace_back(persistence1[i].second,persistence1[i].first); + Persistence_diagram pd2 = persistence2; numpts = persistence2.size(); for(int i = 0; i < numpts; i++) pd2.emplace_back(persistence2[i].second,persistence2[i].first); + + PWG pwg1(pd1, 2*std::sqrt(sigma), m, Gudhi::Persistence_representations::pss_weight); + PWG pwg2(pd2, 2*std::sqrt(sigma), m, Gudhi::Persistence_representations::pss_weight); + + PWG pwgex1(pd1, 2*std::sqrt(sigma), -1, Gudhi::Persistence_representations::pss_weight); + PWG pwgex2(pd2, 2*std::sqrt(sigma), -1, Gudhi::Persistence_representations::pss_weight); + + std::cout << "Approx PSS kernel: " << pwg1.compute_scalar_product (pwg2) / (16*Gudhi::Persistence_representations::pi*sigma) << std::endl; + std::cout << "Exact PSS kernel: " << pwgex1.compute_scalar_product (pwgex2) / (16*Gudhi::Persistence_representations::pi*sigma) << std::endl; + + + + return 0; +} diff --git a/src/Persistence_representations/example/sliced_wasserstein.cpp b/src/Persistence_representations/example/sliced_wasserstein.cpp new file mode 100644 index 00000000..2104e2b2 --- /dev/null +++ b/src/Persistence_representations/example/sliced_wasserstein.cpp @@ -0,0 +1,61 @@ +/* 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 (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/>. + */ + +#include <gudhi/Sliced_Wasserstein.h> + +#include <iostream> +#include <vector> +#include <utility> + +using Persistence_diagram = Gudhi::Persistence_representations::Persistence_diagram; +using SW = Gudhi::Persistence_representations::Sliced_Wasserstein; + +int main(int argc, char** argv) { + + Persistence_diagram persistence1, persistence2; + + persistence1.push_back(std::make_pair(1, 2)); + persistence1.push_back(std::make_pair(6, 8)); + persistence1.push_back(std::make_pair(0, 4)); + persistence1.push_back(std::make_pair(3, 8)); + + persistence2.push_back(std::make_pair(2, 9)); + persistence2.push_back(std::make_pair(1, 6)); + persistence2.push_back(std::make_pair(3, 5)); + persistence2.push_back(std::make_pair(6, 10)); + + + SW sw1(persistence1, 1, 100); + SW sw2(persistence2, 1, 100); + + SW swex1(persistence1, 1, -1); + SW swex2(persistence2, 1, -1); + + std::cout << "Approx SW distance: " << sw1.compute_sliced_wasserstein_distance(sw2) << std::endl; + std::cout << "Exact SW distance: " << swex1.compute_sliced_wasserstein_distance(swex2) << std::endl; + std::cout << "Approx SW kernel: " << sw1.compute_scalar_product(sw2) << std::endl; + std::cout << "Exact SW kernel: " << swex1.compute_scalar_product(swex2) << std::endl; + std::cout << "Distance induced by approx SW kernel: " << sw1.distance(sw2) << std::endl; + std::cout << "Distance induced by exact SW kernel: " << swex1.distance(swex2) << std::endl; + + return 0; +} |