diff options
Diffstat (limited to 'src/Persistence_representations/utilities/persistence_landscapes')
7 files changed, 391 insertions, 0 deletions
diff --git a/src/Persistence_representations/utilities/persistence_landscapes/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_landscapes/CMakeLists.txt new file mode 100644 index 00000000..baf8de3c --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_landscapes/CMakeLists.txt @@ -0,0 +1,38 @@ +cmake_minimum_required(VERSION 2.6) +project(Persistence_representations_lanscapes_utilities) + +file(COPY "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/") + +add_executable ( create_landscapes create_landscapes.cpp ) +target_link_libraries(create_landscapes ${Boost_SYSTEM_LIBRARY}) + +# Will create simple_diagram.txt.land +add_test(NAME create_landscapes COMMAND $<TARGET_FILE:create_landscapes> + "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") + +add_executable ( average_landscapes average_landscapes.cpp ) +target_link_libraries(average_landscapes ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME average_landscapes COMMAND $<TARGET_FILE:average_landscapes> + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt" + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") + +add_executable ( plot_landscapes plot_landscapes.cpp ) +target_link_libraries(plot_landscapes ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME plot_landscapes COMMAND $<TARGET_FILE:plot_landscapes> + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") + +add_executable ( compute_distance_of_landscapes compute_distance_of_landscapes.cpp ) +target_link_libraries(compute_distance_of_landscapes ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME compute_distance_of_landscapes COMMAND $<TARGET_FILE:compute_distance_of_landscapes> + "1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.land" + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.land") + +add_executable ( compute_scalar_product_of_landscapes compute_scalar_product_of_landscapes.cpp ) +target_link_libraries(compute_scalar_product_of_landscapes ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME compute_scalar_product_of_landscapes COMMAND $<TARGET_FILE:compute_scalar_product_of_landscapes> + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.land" + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.land") diff --git a/src/Persistence_representations/utilities/persistence_landscapes/average_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/average_landscapes.cpp new file mode 100644 index 00000000..526130e9 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_landscapes/average_landscapes.cpp @@ -0,0 +1,66 @@ +/* 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 (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.h> + +#include <iostream> +#include <vector> + +using Persistence_landscape = Gudhi::Persistence_representations::Persistence_landscape; + +int main(int argc, char** argv) { + std::cout << "This program computes average persistence landscape of persistence landscapes created based on " + "persistence diagrams provided as an input (you must create them first).\n"; + std::cout << "Please call this program with the names of files with persistence landscapes. The program will create " + "a persistence landscape which will be their average \n"; + std::vector<const char*> filenames; + + if (argc == 1) { + std::cout << "No input files given, the program will now terminate \n"; + return 1; + } + + for (int i = 1; i < argc; ++i) { + filenames.push_back(argv[i]); + } + + std::cout << "Creating persistence landscapes...\n"; + std::vector<Persistence_landscape*> lands; + for (size_t i = 0; i != filenames.size(); ++i) { + Persistence_landscape* l = new Persistence_landscape; + l->load_landscape_from_file(filenames[i]); + lands.push_back(l); + } + + Persistence_landscape av; + av.compute_average(lands); + + av.print_to_file("average.land"); + + 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_landscapes/compute_distance_of_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp new file mode 100644 index 00000000..b3881d6a --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp @@ -0,0 +1,93 @@ +/* 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 (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.h> + +#include <iostream> +#include <sstream> +#include <limits> +#include <vector> + +using Persistence_landscape = Gudhi::Persistence_representations::Persistence_landscape; + +int main(int argc, char** argv) { + std::cout << "This program compute distance of persistence landscapes 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 given " + "landscapes. For L^infty distance choose p = -1. \n"; + std::cout << "The remaining parameters of this programs are names of files with persistence landscapes."; + + 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<Persistence_landscape> landscaspes; + landscaspes.reserve(filenames.size()); + for (size_t file_no = 0; file_no != filenames.size(); ++file_no) { + std::cout << "Loading persistence landscape from a file : " << filenames[file_no] << std::endl; + Persistence_landscape l; + l.load_landscape_from_file(filenames[file_no]); + landscaspes.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 != landscaspes.size(); ++i) { + for (size_t j = i; j != landscaspes.size(); ++j) { + distance[i][j] = distance[j][i] = compute_distance_of_landscapes(landscaspes[i], landscaspes[j], p); + } + } + + // and now output the result to the screen and a file: + std::ofstream out; + out.open("distance"); + 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(); + + return 0; +} diff --git a/src/Persistence_representations/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp new file mode 100644 index 00000000..8dad7b4d --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp @@ -0,0 +1,79 @@ +/* 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 (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.h> + +#include <iostream> +#include <sstream> +#include <vector> + +using Persistence_landscape = Gudhi::Persistence_representations::Persistence_landscape; + +int main(int argc, char** argv) { + std::cout << "This program compute scalar product of persistence landscapes stored in a file (the file needs to be " + "created beforehand). \n"; + std::cout << "The parameters of this programs are names of files with persistence landscapes.\n"; + + std::vector<const char*> filenames; + for (int i = 1; i < argc; ++i) { + filenames.push_back(argv[i]); + } + std::vector<Persistence_landscape> landscaspes; + landscaspes.reserve(filenames.size()); + for (size_t file_no = 0; file_no != filenames.size(); ++file_no) { + std::cout << "Reading persistence landscape from a file : " << filenames[file_no] << std::endl; + Persistence_landscape l; + l.load_landscape_from_file(filenames[file_no]); + landscaspes.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 != landscaspes.size(); ++i) { + for (size_t j = i; j != landscaspes.size(); ++j) { + scalar_product[i][j] = scalar_product[j][i] = compute_inner_product(landscaspes[i], landscaspes[j]); + } + } + + // and now output the result to the screen and a file: + std::ofstream out; + out.open("scalar_product"); + 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(); + + return 0; +} diff --git a/src/Persistence_representations/utilities/persistence_landscapes/create_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/create_landscapes.cpp new file mode 100644 index 00000000..325081d1 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_landscapes/create_landscapes.cpp @@ -0,0 +1,59 @@ +/* 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 (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.h> + +#include <iostream> +#include <sstream> +#include <vector> +#include <limits> + +using Persistence_landscape = Gudhi::Persistence_representations::Persistence_landscape; + +int main(int argc, char** argv) { + std::cout << "This program creates persistence landscapes of diagrams provided as an input. \n"; + std::cout << "The first parameter of the program is the dimension of persistence to be used to construct persistence " + "landscapes. If your file contains "; + std::cout << "the information about dimension of persistence pairs, please provide here the dimension of persistence " + "pairs you want to use. If your input files consist only "; + std::cout << "of birth-death pairs, please set this first parameter to -1 \n"; + std::cout << "The remaining parameters of the program are the names of files with persistence diagrams. \n"; + std::vector<const char*> filenames; + int dim = atoi(argv[1]); + unsigned dimension = std::numeric_limits<unsigned>::max(); + if (dim >= 0) { + dimension = (unsigned)dim; + } + for (int i = 2; i < argc; ++i) { + filenames.push_back(argv[i]); + } + + std::cout << "Creating persistence landscapes...\n"; + for (size_t i = 0; i != filenames.size(); ++i) { + Persistence_landscape l(filenames[i], dimension); + std::stringstream ss; + ss << filenames[i] << ".land"; + l.print_to_file(ss.str().c_str()); + } + std::cout << "Done \n"; + return 0; +} diff --git a/src/Persistence_representations/utilities/persistence_landscapes/plot_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/plot_landscapes.cpp new file mode 100644 index 00000000..ebdb20a1 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_landscapes/plot_landscapes.cpp @@ -0,0 +1,43 @@ +/* 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 (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.h> + +#include <iostream> +#include <sstream> + +using Persistence_landscape = Gudhi::Persistence_representations::Persistence_landscape; + +int main(int argc, char** argv) { + std::cout << "This program plot persistence landscape stored in a file (the file needs to be created beforehand). " + "Please call the code with the name of a landscape file \n"; + Persistence_landscape l; + l.load_landscape_from_file(argv[1]); + + std::stringstream ss; + ss << argv[1] << "_gnuplot_script"; + l.plot(ss.str().c_str()); + + std::cout << "Done \n"; + + return 0; +} diff --git a/src/Persistence_representations/utilities/persistence_landscapes/simple_diagram.txt.land b/src/Persistence_representations/utilities/persistence_landscapes/simple_diagram.txt.land new file mode 100644 index 00000000..b99d2f62 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_landscapes/simple_diagram.txt.land @@ -0,0 +1,13 @@ +#lambda_0 +1 0 +1.5 0.5 +2 0 +3 0 +3.5 0.5 +4 0 +5 0 +5.5 0.5 +6 0 +7 0 +7.5 0.5 +8 0 |