diff options
Diffstat (limited to 'src/Persistence_representations/utilities/persistence_vectors')
6 files changed, 306 insertions, 0 deletions
diff --git a/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt new file mode 100644 index 00000000..bc982094 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt @@ -0,0 +1,9 @@ +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/src/Persistence_representations/utilities/persistence_vectors/average_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/average_persistence_vectors.cpp new file mode 100644 index 00000000..89e42f0f --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_vectors/average_persistence_vectors.cpp @@ -0,0 +1,53 @@ +/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + * See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 Inria + * + * Modification(s): + * - YYYY/MM Author: Description of the modification + */ + +#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/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp new file mode 100644 index 00000000..541dd25f --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp @@ -0,0 +1,82 @@ +/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + * See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 Inria + * + * Modification(s): + * - YYYY/MM Author: Description of the modification + */ + +#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/src/Persistence_representations/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp new file mode 100644 index 00000000..bbc50c98 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp @@ -0,0 +1,74 @@ +/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + * See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 Inria + * + * Modification(s): + * - YYYY/MM Author: Description of the modification + */ + +#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/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp new file mode 100644 index 00000000..f974c3d3 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp @@ -0,0 +1,57 @@ +/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + * See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 Inria + * + * Modification(s): + * - YYYY/MM Author: Description of the modification + */ + +#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/src/Persistence_representations/utilities/persistence_vectors/plot_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/plot_persistence_vectors.cpp new file mode 100644 index 00000000..de08fcfe --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_vectors/plot_persistence_vectors.cpp @@ -0,0 +1,31 @@ +/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + * See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 Inria + * + * Modification(s): + * - YYYY/MM Author: Description of the modification + */ + +#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; +} |