diff options
Diffstat (limited to 'src/Persistence_representations/utilities/persistence_landscapes_on_grid')
7 files changed, 503 insertions, 0 deletions
diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt new file mode 100644 index 00000000..55a4fd50 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt @@ -0,0 +1,38 @@ +cmake_minimum_required(VERSION 2.6) +project(Persistence_representations_lanscapes_on_grid_utilities) + +file(COPY "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/") + +add_executable ( create_landscapes_on_grid create_landscapes_on_grid.cpp ) +target_link_libraries(create_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) + +# Will create simple_diagram.txt.land +add_test(NAME create_landscapes_on_grid COMMAND $<TARGET_FILE:create_landscapes_on_grid> + "100" "-1" "-1" "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") + +add_executable ( average_landscapes_on_grid average_landscapes_on_grid.cpp ) +target_link_libraries(average_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME average_landscapes_on_grid COMMAND $<TARGET_FILE:average_landscapes_on_grid> + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.g_land" + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.g_land") + +add_executable ( plot_landscapes_on_grid plot_landscapes_on_grid.cpp ) +target_link_libraries(plot_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME plot_landscapes_on_grid COMMAND $<TARGET_FILE:plot_landscapes_on_grid> + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.g_land") + +add_executable ( compute_distance_of_landscapes_on_grid compute_distance_of_landscapes_on_grid.cpp ) +target_link_libraries(compute_distance_of_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME compute_distance_of_landscapes_on_grid COMMAND $<TARGET_FILE:compute_distance_of_landscapes_on_grid> + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.g_land" + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.g_land") + +add_executable ( compute_scalar_product_of_landscapes_on_grid compute_scalar_product_of_landscapes_on_grid.cpp ) +target_link_libraries(compute_scalar_product_of_landscapes_on_grid ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME compute_scalar_product_of_landscapes_on_grid COMMAND $<TARGET_FILE:compute_scalar_product_of_landscapes_on_grid> + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.g_land" + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.g_land") diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp new file mode 100644 index 00000000..d50118a0 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp @@ -0,0 +1,65 @@ +/* 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_on_grid.h> + +#include <iostream> +#include <vector> + +using Persistence_landscape_on_grid = Gudhi::Persistence_representations::Persistence_landscape_on_grid; + +int main(int argc, char** argv) { + std::cout << "This program computes average persistence landscape on grid of persistence landscapes on grid created " + "based on persistence diagrams provided as an input. Please call this program with the names of files " + "with persistence diagrams \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_on_grid*> lands; + for (size_t i = 0; i != filenames.size(); ++i) { + Persistence_landscape_on_grid* l = new Persistence_landscape_on_grid; + l->load_landscape_from_file(filenames[i]); + lands.push_back(l); + } + + Persistence_landscape_on_grid av; + av.compute_average(lands); + + av.print_to_file("average.g_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_on_grid/compute_distance_of_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp new file mode 100644 index 00000000..859c6991 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp @@ -0,0 +1,92 @@ +/* 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_on_grid.h> + +#include <iostream> +#include <sstream> +#include <limits> +#include <vector> + +using Persistence_landscape_on_grid = Gudhi::Persistence_representations::Persistence_landscape_on_grid; + +int main(int argc, char** argv) { + std::cout << "This program compute distance of persistence landscapes on grid 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 landscapes " + "on grid. For L^infty distance choose p = -1. \n"; + std::cout << "The remaining parameters of this programs are names of files with persistence landscapes on grid.\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<Persistence_landscape_on_grid> landscaspes; + landscaspes.reserve(filenames.size()); + for (size_t file_no = 0; file_no != filenames.size(); ++file_no) { + Persistence_landscape_on_grid 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 scalar product: + 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_on_grid(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_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp new file mode 100644 index 00000000..e95bf8ad --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp @@ -0,0 +1,78 @@ +/* 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_on_grid.h> + +#include <iostream> +#include <sstream> +#include <vector> + +using Persistence_landscape_on_grid = Gudhi::Persistence_representations::Persistence_landscape_on_grid; + +int main(int argc, char** argv) { + std::cout << "This program compute scalar product of persistence landscapes on grid 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 on grid.\n"; + + std::vector<const char*> filenames; + for (int i = 1; i < argc; ++i) { + filenames.push_back(argv[i]); + } + std::vector<Persistence_landscape_on_grid> landscaspes; + landscaspes.reserve(filenames.size()); + for (size_t file_no = 0; file_no != filenames.size(); ++file_no) { + Persistence_landscape_on_grid 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_on_grid/create_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp new file mode 100644 index 00000000..8d747c14 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.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_on_grid.h> + +#include <iostream> +#include <sstream> +#include <limits> +#include <vector> + +using Persistence_landscape_on_grid = Gudhi::Persistence_representations::Persistence_landscape_on_grid; + +int main(int argc, char** argv) { + std::cout << "This program creates persistence landscape on grid of diagrams provided as an input.\n"; + std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; + std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed " + "based on the data, set them both to -1 \n"; + std::cout << "The fourth parameter of the program is the dimension of persistence to be used to construct " + "persistence landscape on a grid. If your file contains "; + std::cout << "the information about dimension of birth-death pairs, please provide here the dimension of intervals " + "you want to use. If your input files consist only "; + std::cout << "of birth-death pairs, please set the fourth parameter to -1 \n"; + std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; + + if (argc < 5) { + std::cout << "Wrong parameter list, the program will now terminate \n"; + return 1; + } + + size_t size_of_grid = (size_t)atoi(argv[1]); + double min_ = atof(argv[2]); + double max_ = atof(argv[3]); + int dim = atoi(argv[4]); + unsigned dimension = std::numeric_limits<unsigned>::max(); + if (dim >= 0) { + dimension = (unsigned)dim; + } + + std::vector<const char*> filenames; + for (int i = 5; i < argc; ++i) { + filenames.push_back(argv[i]); + } + + std::cout << "Creating persistence landscapes...\n"; + for (size_t i = 0; i != filenames.size(); ++i) { + std::cout << "Creating persistence landscape on a grid based on a file : " << filenames[i] << std::endl; + Persistence_landscape_on_grid l; + if ((min_ != -1) || (max_ != -1)) { + l = Persistence_landscape_on_grid(filenames[i], min_, max_, size_of_grid, dimension); + } else { + // (min_ == -1) && (max_ == -1), in this case the program will find min_ and max_ based on the data. + l = Persistence_landscape_on_grid(filenames[i], size_of_grid, dimension); + } + std::stringstream ss; + ss << filenames[i] << ".g_land"; + l.print_to_file(ss.str().c_str()); + } + std::cout << "Done \n"; + return 0; +} diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp new file mode 100644 index 00000000..42822a01 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp @@ -0,0 +1,47 @@ +/* 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_on_grid.h> + +#include <iostream> +#include <sstream> + +using Persistence_landscape_on_grid = Gudhi::Persistence_representations::Persistence_landscape_on_grid; + +int main(int argc, char** argv) { + std::cout << "This program plot persistence landscape on grid stored in a file (the file needs to be created " + "beforehand). Please call the code with the name of a landscape on grid file \n"; + if (argc == 1) { + std::cout << "Wrong parameters of a program call, the program will now terminate \n"; + return 1; + } + Persistence_landscape_on_grid 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_on_grid/simple_diagram.txt.g_land b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/simple_diagram.txt.g_land new file mode 100644 index 00000000..dc53b932 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/simple_diagram.txt.g_land @@ -0,0 +1,104 @@ +1 +8 +101 + +0.07 +0.14 +0.21 +0.28 +0.35 +0.42 +0.49 +0.42 +0.35 +0.28 +0.21 +0.14 +0.07 + + + + + + + + + + + + + + + +0.07 +0.14 +0.21 +0.28 +0.35 +0.42 +0.49 +0.42 +0.35 +0.28 +0.21 +0.14 +0.07 + + + + + + + + + + + + + + + + +0.07 +0.14 +0.21 +0.28 +0.35 +0.42 +0.49 +0.42 +0.35 +0.28 +0.21 +0.14 +0.07 + + + + + + + + + + + + + + + +0.07 +0.14 +0.21 +0.28 +0.35 +0.42 +0.49 +0.42 +0.35 +0.28 +0.21 +0.14 +0.07 + + |