diff options
Diffstat (limited to 'utilities/Persistence_representations/persistence_vectors')
6 files changed, 0 insertions, 366 deletions
diff --git a/utilities/Persistence_representations/persistence_vectors/CMakeLists.txt b/utilities/Persistence_representations/persistence_vectors/CMakeLists.txt deleted file mode 100644 index bc982094..00000000 --- a/utilities/Persistence_representations/persistence_vectors/CMakeLists.txt +++ /dev/null @@ -1,9 +0,0 @@ -project(Persistence_vectors_utilities) - -add_persistence_representation_creation_utility(create_persistence_vectors "-1") - -add_persistence_representation_plot_utility(plot_persistence_vectors ".vect") - -add_persistence_representation_function_utility(average_persistence_vectors ".vect") -add_persistence_representation_function_utility(compute_distance_of_persistence_vectors ".vect" "1") -add_persistence_representation_function_utility(compute_scalar_product_of_persistence_vectors ".vect") diff --git a/utilities/Persistence_representations/persistence_vectors/average_persistence_vectors.cpp b/utilities/Persistence_representations/persistence_vectors/average_persistence_vectors.cpp deleted file mode 100644 index 45199838..00000000 --- a/utilities/Persistence_representations/persistence_vectors/average_persistence_vectors.cpp +++ /dev/null @@ -1,65 +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> - -using Euclidean_distance = Gudhi::Euclidean_distance; -using Vector_distances_in_diagram = Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>; - -int main(int argc, char** argv) { - std::cout << "This program computes average of persistence vectors stored in files (the files needs to " - << "be created beforehand).\n" - << "The parameters of this programs are names of files with persistence vectors.\n"; - - if (argc < 3) { - std::cout << "Wrong number of parameters, the program will now terminate \n"; - return 1; - } - - std::vector<const char*> filenames; - for (int i = 1; i < argc; ++i) { - filenames.push_back(argv[i]); - } - - std::vector<Vector_distances_in_diagram*> lands; - for (size_t i = 0; i != filenames.size(); ++i) { - Vector_distances_in_diagram* l = new Vector_distances_in_diagram; - l->load_from_file(filenames[i]); - lands.push_back(l); - } - - Vector_distances_in_diagram av; - av.compute_average(lands); - - av.print_to_file("average.vect"); - - for (size_t i = 0; i != filenames.size(); ++i) { - delete lands[i]; - } - - std::cout << "Done \n"; - - return 0; -} diff --git a/utilities/Persistence_representations/persistence_vectors/compute_distance_of_persistence_vectors.cpp b/utilities/Persistence_representations/persistence_vectors/compute_distance_of_persistence_vectors.cpp deleted file mode 100644 index 0db7dbec..00000000 --- a/utilities/Persistence_representations/persistence_vectors/compute_distance_of_persistence_vectors.cpp +++ /dev/null @@ -1,94 +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 <sstream> -#include <limits> -#include <vector> - -using Euclidean_distance = Gudhi::Euclidean_distance; -using Vector_distances_in_diagram = Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>; - -int main(int argc, char** argv) { - std::cout << "This program compute distance of persistence vectors stored in a file (the file needs to be created " - "beforehand). \n"; - std::cout << "The first parameter of a program is an integer p. The program compute l^p distance of the vectors. For " - "l^infty distance choose p = -1. \n"; - std::cout << "The remaining parameters of this programs are names of files with persistence vectors.\n"; - - if (argc < 3) { - std::cout << "Wrong number of parameters, the program will now terminate \n"; - return 1; - } - - int pp = atoi(argv[1]); - double p = std::numeric_limits<double>::max(); - if (pp != -1) { - p = pp; - } - - std::vector<const char*> filenames; - for (int i = 2; i < argc; ++i) { - filenames.push_back(argv[i]); - } - std::vector<Vector_distances_in_diagram> vectors; - vectors.reserve(filenames.size()); - for (size_t file_no = 0; file_no != filenames.size(); ++file_no) { - Vector_distances_in_diagram l; - l.load_from_file(filenames[file_no]); - vectors.push_back(l); - } - - // and now we will compute the scalar product of landscapes. - - // first we prepare an array: - std::vector<std::vector<double> > distance(filenames.size()); - for (size_t i = 0; i != filenames.size(); ++i) { - std::vector<double> v(filenames.size(), 0); - distance[i] = v; - } - - // and now we can compute the distances: - for (size_t i = 0; i != vectors.size(); ++i) { - for (size_t j = i + 1; j != vectors.size(); ++j) { - distance[i][j] = distance[j][i] = vectors[i].distance(vectors[j], p); - } - } - - // and now output the result to the screen and a file: - std::ofstream out; - out.open("distance.vect"); - for (size_t i = 0; i != distance.size(); ++i) { - for (size_t j = 0; j != distance.size(); ++j) { - std::cout << distance[i][j] << " "; - out << distance[i][j] << " "; - } - std::cout << std::endl; - out << std::endl; - } - out.close(); - - std::cout << "Distance can be found in 'distance.vect' file\n"; - return 0; -} diff --git a/utilities/Persistence_representations/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp b/utilities/Persistence_representations/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp deleted file mode 100644 index 8e99251b..00000000 --- a/utilities/Persistence_representations/persistence_vectors/compute_scalar_product_of_persistence_vectors.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_vectors.h> - -#include <iostream> -#include <sstream> -#include <limits> -#include <vector> - -using Euclidean_distance = Gudhi::Euclidean_distance; -using Vector_distances_in_diagram = Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>; - -int main(int argc, char** argv) { - std::cout << "This program computes scalar product of persistence vectors stored in a file (the file needs to " - << "be created beforehand). \n" - << "The parameters of this programs are names of files with persistence vectors.\n"; - - if (argc < 3) { - std::cout << "Wrong number of parameters, the program will now terminate \n"; - return 1; - } - - std::vector<const char*> filenames; - for (int i = 1; i < argc; ++i) { - filenames.push_back(argv[i]); - } - std::vector<Vector_distances_in_diagram> vectors; - vectors.reserve(filenames.size()); - for (size_t file_no = 0; file_no != filenames.size(); ++file_no) { - Vector_distances_in_diagram l; - l.load_from_file(filenames[file_no]); - vectors.push_back(l); - } - - // and now we will compute the scalar product of landscapes. - - // first we prepare an array: - std::vector<std::vector<double> > scalar_product(filenames.size()); - for (size_t i = 0; i != filenames.size(); ++i) { - std::vector<double> v(filenames.size(), 0); - scalar_product[i] = v; - } - - // and now we can compute the scalar product: - for (size_t i = 0; i != vectors.size(); ++i) { - for (size_t j = i; j != vectors.size(); ++j) { - scalar_product[i][j] = scalar_product[j][i] = vectors[i].compute_scalar_product(vectors[j]); - } - } - - // and now output the result to the screen and a file: - std::ofstream out; - out.open("scalar_product.vect"); - for (size_t i = 0; i != scalar_product.size(); ++i) { - for (size_t j = 0; j != scalar_product.size(); ++j) { - std::cout << scalar_product[i][j] << " "; - out << scalar_product[i][j] << " "; - } - std::cout << std::endl; - out << std::endl; - } - out.close(); - - std::cout << "Distance can be found in 'scalar_product.vect' file\n"; - return 0; -} diff --git a/utilities/Persistence_representations/persistence_vectors/create_persistence_vectors.cpp b/utilities/Persistence_representations/persistence_vectors/create_persistence_vectors.cpp deleted file mode 100644 index 364284e5..00000000 --- a/utilities/Persistence_representations/persistence_vectors/create_persistence_vectors.cpp +++ /dev/null @@ -1,69 +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 <sstream> -#include <limits> -#include <vector> - -using Euclidean_distance = Gudhi::Euclidean_distance; -using Vector_distances_in_diagram = Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>; - -int main(int argc, char** argv) { - std::cout << "This program creates persistence vectors files (*.vect) of persistence diagrams files (*.pers) " - << "provided as an input.\n" - << "The first parameter of this program is a dimension of persistence that will be used in creation of " - << "the persistence heat maps." - << "If your input files contains persistence pairs of various dimension, as a first parameter of the " - << "procedure please provide the dimension of persistence you want to use." - << "If in your files there are only birth-death pairs of the same dimension, set the first parameter to " - << "-1.\n" - << "The remaining parameters are the names of files with persistence diagrams. \n"; - - if (argc < 3) { - std::cout << "Wrong parameter list, the program will now terminate \n"; - return 1; - } - - std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; - int dim = atoi(argv[1]); - unsigned dimension = std::numeric_limits<unsigned>::max(); - if (dim >= 0) { - dimension = (unsigned)dim; - } - - std::vector<const char*> filenames; - for (int i = 2; i < argc; ++i) { - filenames.push_back(argv[i]); - } - - for (size_t i = 0; i != filenames.size(); ++i) { - std::cerr << "Creating persistence vectors based on a file : " << filenames[i] << std::endl; - Vector_distances_in_diagram l(filenames[i], dimension); - std::stringstream ss; - ss << filenames[i] << ".vect"; - l.print_to_file(ss.str().c_str()); - } - return 0; -} diff --git a/utilities/Persistence_representations/persistence_vectors/plot_persistence_vectors.cpp b/utilities/Persistence_representations/persistence_vectors/plot_persistence_vectors.cpp deleted file mode 100644 index 550e47c5..00000000 --- a/utilities/Persistence_representations/persistence_vectors/plot_persistence_vectors.cpp +++ /dev/null @@ -1,43 +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 <sstream> - -using Euclidean_distance = Gudhi::Euclidean_distance; -using Vector_distances_in_diagram = Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>; - -int main(int argc, char** argv) { - std::cout << "This program create a Gnuplot script to plot persistence vector. Please call this program with the " - "name of file with persistence vector. \n"; - if (argc != 2) { - std::cout << "Wrong number of parameters, the program will now terminate. \n"; - return 1; - } - Vector_distances_in_diagram l; - l.load_from_file(argv[1]); - l.plot(argv[1]); - - return 0; -} |