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Diffstat (limited to 'example/Persistence_representations')
6 files changed, 0 insertions, 439 deletions
diff --git a/example/Persistence_representations/CMakeLists.txt b/example/Persistence_representations/CMakeLists.txt deleted file mode 100644 index 33558df3..00000000 --- a/example/Persistence_representations/CMakeLists.txt +++ /dev/null @@ -1,28 +0,0 @@ -project(Persistence_representations_example) - -add_executable ( Persistence_representations_example_landscape_on_grid persistence_landscape_on_grid.cpp ) -add_test(NAME Persistence_representations_example_landscape_on_grid - COMMAND $<TARGET_FILE:Persistence_representations_example_landscape_on_grid>) -install(TARGETS Persistence_representations_example_landscape_on_grid DESTINATION bin) - -add_executable ( Persistence_representations_example_landscape persistence_landscape.cpp ) -add_test(NAME Persistence_representations_example_landscape - COMMAND $<TARGET_FILE:Persistence_representations_example_landscape>) -install(TARGETS Persistence_representations_example_landscape DESTINATION bin) - -add_executable ( Persistence_representations_example_intervals persistence_intervals.cpp ) -add_test(NAME Persistence_representations_example_intervals - COMMAND $<TARGET_FILE:Persistence_representations_example_intervals> - "${CMAKE_SOURCE_DIR}/data/persistence_diagram/first.pers") -install(TARGETS Persistence_representations_example_intervals DESTINATION bin) - -add_executable ( Persistence_representations_example_vectors persistence_vectors.cpp ) -add_test(NAME Persistence_representations_example_vectors - COMMAND $<TARGET_FILE:Persistence_representations_example_vectors>) -install(TARGETS Persistence_representations_example_vectors DESTINATION bin) - -add_executable ( Persistence_representations_example_heat_maps persistence_heat_maps.cpp ) -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) - diff --git a/example/Persistence_representations/persistence_heat_maps.cpp b/example/Persistence_representations/persistence_heat_maps.cpp deleted file mode 100644 index 323b57e9..00000000 --- a/example/Persistence_representations/persistence_heat_maps.cpp +++ /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): Pawel Dlotko - * - * Copyright (C) 2016 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/>. - */ - -#include <gudhi/Persistence_heat_maps.h> - -#include <iostream> -#include <vector> -#include <utility> - -using constant_scaling_function = Gudhi::Persistence_representations::constant_scaling_function; -using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps<constant_scaling_function>; - -int main(int argc, char** argv) { - // create two simple vectors with birth--death pairs: - - std::vector<std::pair<double, double> > persistence1; - std::vector<std::pair<double, double> > 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)); - - // over here we define a function we sill put on a top on every birth--death pair in the persistence interval. It can - // be anything. Over here we will use standard Gaussian - std::vector<std::vector<double> > filter = Gudhi::Persistence_representations::create_Gaussian_filter(5, 1); - - // creating two heat maps. - Persistence_heat_maps hm1(persistence1, filter, false, 20, 0, 11); - Persistence_heat_maps hm2(persistence2, filter, false, 20, 0, 11); - - std::vector<Persistence_heat_maps*> vector_of_maps; - vector_of_maps.push_back(&hm1); - vector_of_maps.push_back(&hm2); - - // compute median/mean of a vector of heat maps: - Persistence_heat_maps mean; - mean.compute_mean(vector_of_maps); - Persistence_heat_maps median; - median.compute_median(vector_of_maps); - - // to compute L^1 distance between hm1 and hm2: - std::cout << "The L^1 distance is : " << hm1.distance(hm2, 1) << std::endl; - - // to average of hm1 and hm2: - std::vector<Persistence_heat_maps*> to_average; - to_average.push_back(&hm1); - to_average.push_back(&hm2); - Persistence_heat_maps av; - av.compute_average(to_average); - - // to compute scalar product of hm1 and hm2: - std::cout << "Scalar product is : " << hm1.compute_scalar_product(hm2) << std::endl; - - return 0; -} diff --git a/example/Persistence_representations/persistence_intervals.cpp b/example/Persistence_representations/persistence_intervals.cpp deleted file mode 100644 index b5dcf25c..00000000 --- a/example/Persistence_representations/persistence_intervals.cpp +++ /dev/null @@ -1,89 +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): Pawel Dlotko - * - * Copyright (C) 2016 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/>. - */ - -#include <gudhi/Persistence_intervals.h> - -#include <iostream> -#include <utility> -#include <vector> - -using Persistence_intervals = Gudhi::Persistence_representations::Persistence_intervals; - -int main(int argc, char** argv) { - if (argc != 2) { - std::cout << "To run this program, please provide the name of a file with persistence diagram \n"; - return 1; - } - - Persistence_intervals p(argv[1]); - std::pair<double, double> min_max_ = p.get_x_range(); - std::cout << "Birth-death range : " << min_max_.first << " " << min_max_.second << std::endl; - - std::vector<double> dominant_ten_intervals_length = p.length_of_dominant_intervals(10); - std::cout << "Length of ten dominant intervals : " << std::endl; - for (size_t i = 0; i != dominant_ten_intervals_length.size(); ++i) { - std::cout << dominant_ten_intervals_length[i] << std::endl; - } - - std::vector<std::pair<double, double> > ten_dominant_intervals = p.dominant_intervals(10); - std::cout << "Here are the dominant intervals : " << std::endl; - for (size_t i = 0; i != ten_dominant_intervals.size(); ++i) { - std::cout << "( " << ten_dominant_intervals[i].first << "," << ten_dominant_intervals[i].second << std::endl; - } - - std::vector<size_t> histogram = p.histogram_of_lengths(10); - std::cout << "Here is the histogram of barcode's length : " << std::endl; - for (size_t i = 0; i != histogram.size(); ++i) { - std::cout << histogram[i] << " "; - } - std::cout << std::endl; - - std::vector<size_t> cumulative_histogram = p.cumulative_histogram_of_lengths(10); - std::cout << "Cumulative histogram : " << std::endl; - for (size_t i = 0; i != cumulative_histogram.size(); ++i) { - std::cout << cumulative_histogram[i] << " "; - } - std::cout << std::endl; - - std::vector<double> char_funct_diag = p.characteristic_function_of_diagram(min_max_.first, min_max_.second); - std::cout << "Characteristic function of diagram : " << std::endl; - for (size_t i = 0; i != char_funct_diag.size(); ++i) { - std::cout << char_funct_diag[i] << " "; - } - std::cout << std::endl; - - std::vector<double> cumul_char_funct_diag = - p.cumulative_characteristic_function_of_diagram(min_max_.first, min_max_.second); - std::cout << "Cumulative characteristic function of diagram : " << std::endl; - for (size_t i = 0; i != cumul_char_funct_diag.size(); ++i) { - std::cout << cumul_char_funct_diag[i] << " "; - } - std::cout << std::endl; - - std::cout << "Persistence Betti numbers \n"; - std::vector<std::pair<double, size_t> > pbns = p.compute_persistent_betti_numbers(); - for (size_t i = 0; i != pbns.size(); ++i) { - std::cout << pbns[i].first << " " << pbns[i].second << std::endl; - } - - return 0; -} diff --git a/example/Persistence_representations/persistence_landscape.cpp b/example/Persistence_representations/persistence_landscape.cpp deleted file mode 100644 index 27542cf7..00000000 --- a/example/Persistence_representations/persistence_landscape.cpp +++ /dev/null @@ -1,86 +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): Pawel Dlotko - * - * Copyright (C) 2016 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/>. - */ - -#include <gudhi/Persistence_landscape.h> - -#include <iostream> -#include <vector> -#include <utility> - -using Persistence_landscape = Gudhi::Persistence_representations::Persistence_landscape; - -int main(int argc, char** argv) { - // create two simple vectors with birth--death pairs: - - std::vector<std::pair<double, double> > persistence1; - std::vector<std::pair<double, double> > 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)); - - // create two persistence landscapes based on persistence1 and persistence2: - Persistence_landscape l1(persistence1); - Persistence_landscape l2(persistence2); - - // This is how to compute integral of landscapes: - std::cout << "Integral of the first landscape : " << l1.compute_integral_of_landscape() << std::endl; - std::cout << "Integral of the second landscape : " << l2.compute_integral_of_landscape() << std::endl; - - // And here how to write landscapes to stream: - std::cout << "l1 : " << l1 << std::endl; - std::cout << "l2 : " << l2 << std::endl; - - // Arithmetic operations on landscapes: - Persistence_landscape sum = l1 + l2; - std::cout << "sum : " << sum << std::endl; - - // here are the maxima of the functions: - std::cout << "Maximum of l1 : " << l1.compute_maximum() << std::endl; - std::cout << "Maximum of l2 : " << l2.compute_maximum() << std::endl; - - // here are the norms of landscapes: - std::cout << "L^1 Norm of l1 : " << l1.compute_norm_of_landscape(1.) << std::endl; - std::cout << "L^1 Norm of l2 : " << l2.compute_norm_of_landscape(1.) << std::endl; - - // here is the average of landscapes: - Persistence_landscape average; - average.compute_average({&l1, &l2}); - std::cout << "average : " << average << std::endl; - - // here is the distance of landscapes: - std::cout << "Distance : " << l1.distance(l2) << std::endl; - - // here is the scalar product of landscapes: - std::cout << "Scalar product : " << l1.compute_scalar_product(l2) << std::endl; - - // here is how to create a file which is suitable for visualization via gnuplot: - average.plot("average_landscape"); - - return 0; -} diff --git a/example/Persistence_representations/persistence_landscape_on_grid.cpp b/example/Persistence_representations/persistence_landscape_on_grid.cpp deleted file mode 100644 index 0f471a67..00000000 --- a/example/Persistence_representations/persistence_landscape_on_grid.cpp +++ /dev/null @@ -1,82 +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): Pawel Dlotko - * - * Copyright (C) 2016 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/>. - */ - -#include <gudhi/Persistence_landscape_on_grid.h> - -#include <iostream> -#include <utility> -#include <vector> - -using Persistence_landscape_on_grid = Gudhi::Persistence_representations::Persistence_landscape_on_grid; - -int main(int argc, char** argv) { - // create two simple vectors with birth--death pairs: - - std::vector<std::pair<double, double> > persistence1; - std::vector<std::pair<double, double> > 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)); - - // create two persistence landscapes based on persistence1 and persistence2: - Persistence_landscape_on_grid l1(persistence1, 0, 11, 20); - Persistence_landscape_on_grid l2(persistence2, 0, 11, 20); - - // This is how to compute integral of landscapes: - std::cout << "Integral of the first landscape : " << l1.compute_integral_of_landscape() << std::endl; - std::cout << "Integral of the second landscape : " << l2.compute_integral_of_landscape() << std::endl; - - // And here how to write landscapes to stream: - std::cout << "l1 : " << l1 << std::endl; - std::cout << "l2 : " << l2 << std::endl; - - // here are the maxima of the functions: - std::cout << "Maximum of l1 : " << l1.compute_maximum() << std::endl; - std::cout << "Maximum of l2 : " << l2.compute_maximum() << std::endl; - - // here are the norms of landscapes: - std::cout << "L^1 Norm of l1 : " << l1.compute_norm_of_landscape(1.) << std::endl; - std::cout << "L^1 Norm of l2 : " << l2.compute_norm_of_landscape(1.) << std::endl; - - // here is the average of landscapes: - Persistence_landscape_on_grid average; - average.compute_average({&l1, &l2}); - std::cout << "average : " << average << std::endl; - - // here is the distance of landscapes: - std::cout << "Distance : " << l1.distance(l2) << std::endl; - - // here is the scalar product of landscapes: - std::cout << "Scalar product : " << l1.compute_scalar_product(l2) << std::endl; - - // here is how to create a file which is suitable for visualization via gnuplot: - average.plot("average_landscape"); - - return 0; -} diff --git a/example/Persistence_representations/persistence_vectors.cpp b/example/Persistence_representations/persistence_vectors.cpp deleted file mode 100644 index 072e530d..00000000 --- a/example/Persistence_representations/persistence_vectors.cpp +++ /dev/null @@ -1,74 +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): Pawel Dlotko - * - * Copyright (C) 2016 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/>. - */ - -#include <gudhi/Persistence_vectors.h> - -#include <iostream> -#include <vector> -#include <cmath> -#include <iomanip> -#include <limits> -#include <utility> - -using Vector_distances_in_diagram = - Gudhi::Persistence_representations::Vector_distances_in_diagram<Gudhi::Euclidean_distance>; - -int main(int argc, char** argv) { - // create two simple vectors with birth--death pairs: - - std::vector<std::pair<double, double> > persistence1; - std::vector<std::pair<double, double> > 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)); - - // create two persistence vectors based on persistence1 and persistence2: - Vector_distances_in_diagram v1(persistence1, std::numeric_limits<size_t>::max()); - Vector_distances_in_diagram v2(persistence2, std::numeric_limits<size_t>::max()); - - // writing to a stream: - std::cout << "v1 : " << v1 << std::endl; - std::cout << "v2 : " << v2 << std::endl; - - // averages: - Vector_distances_in_diagram average; - average.compute_average({&v1, &v2}); - std::cout << "Average : " << average << std::endl; - - // computations of distances: - std::cout << "l^1 distance : " << v1.distance(v2) << std::endl; - - // computations of scalar product: - std::cout << "Scalar product of l1 and l2 : " << v1.compute_scalar_product(v2) << std::endl; - - // create a file with a gnuplot script: - v1.plot("plot_of_vector_representation"); - - return 0; -} |