diff options
Diffstat (limited to 'src/Persistence_representations/utilities')
40 files changed, 2523 insertions, 0 deletions
diff --git a/src/Persistence_representations/utilities/CMakeLists.txt b/src/Persistence_representations/utilities/CMakeLists.txt new file mode 100644 index 00000000..66524666 --- /dev/null +++ b/src/Persistence_representations/utilities/CMakeLists.txt @@ -0,0 +1,6 @@ +add_subdirectory(persistence_heat_maps) +add_subdirectory(persistence_intervals) +add_subdirectory(persistence_landscapes) +add_subdirectory(persistence_landscapes_on_grid) +add_subdirectory(persistence_vectors) + diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt new file mode 100644 index 00000000..0dd63852 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt @@ -0,0 +1,63 @@ +cmake_minimum_required(VERSION 2.6) +project(Persistence_representations_heat_maps_utilities) + +file(COPY "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/") + +add_executable ( create_persistence_heat_maps create_persistence_heat_maps.cpp ) +target_link_libraries(create_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME create_persistence_heat_maps COMMAND $<TARGET_FILE:create_persistence_heat_maps> + "10" "-1" "-1" "4" "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") + + +add_executable ( create_pssk create_pssk.cpp ) +target_link_libraries(create_pssk ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME create_pssk COMMAND $<TARGET_FILE:create_pssk> + "10" "-1" "-1" "4" "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") + +add_executable ( create_p_h_m_weighted_by_distance_from_diagonal create_p_h_m_weighted_by_distance_from_diagonal.cpp ) +target_link_libraries(create_p_h_m_weighted_by_distance_from_diagonal ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME create_p_h_m_weighted_by_distance_from_diagonal COMMAND $<TARGET_FILE:create_p_h_m_weighted_by_distance_from_diagonal> + "10" "-1" "-1" "4" "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") + +add_executable ( create_p_h_m_weighted_by_squared_diag_distance create_p_h_m_weighted_by_squared_diag_distance.cpp ) +target_link_libraries(create_p_h_m_weighted_by_squared_diag_distance ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME create_p_h_m_weighted_by_squared_diag_distance COMMAND $<TARGET_FILE:create_p_h_m_weighted_by_squared_diag_distance> + "10" "-1" "-1" "4" "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") + +add_executable ( create_p_h_m_weighted_by_arctan_of_their_persistence create_p_h_m_weighted_by_arctan_of_their_persistence.cpp ) +target_link_libraries(create_p_h_m_weighted_by_arctan_of_their_persistence ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME create_p_h_m_weighted_by_arctan_of_their_persistence COMMAND $<TARGET_FILE:create_p_h_m_weighted_by_arctan_of_their_persistence> + "10" "-1" "-1" "4" "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") + +add_executable ( average_persistence_heat_maps average_persistence_heat_maps.cpp ) +target_link_libraries(average_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME average_persistence_heat_maps COMMAND $<TARGET_FILE:average_persistence_heat_maps> + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt" + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") + +add_executable ( plot_persistence_heat_map plot_persistence_heat_map.cpp ) +target_link_libraries(plot_persistence_heat_map ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME plot_persistence_heat_map COMMAND $<TARGET_FILE:plot_persistence_heat_map> + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") + +add_executable ( compute_distance_of_persistence_heat_maps compute_distance_of_persistence_heat_maps.cpp ) +target_link_libraries(compute_distance_of_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME compute_distance_of_persistence_heat_maps COMMAND $<TARGET_FILE:compute_distance_of_persistence_heat_maps> + "1" + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt" + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") + +add_executable ( compute_scalar_product_of_persistence_heat_maps compute_scalar_product_of_persistence_heat_maps.cpp ) +target_link_libraries(compute_scalar_product_of_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME compute_scalar_product_of_persistence_heat_maps COMMAND $<TARGET_FILE:compute_scalar_product_of_persistence_heat_maps> + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt" + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp new file mode 100644 index 00000000..4e81375a --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_heat_maps/average_persistence_heat_maps.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_heat_maps.h> + +#include <iostream> +#include <vector> + +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) { + std::cout << "This program computes average persistence landscape of persistence landscapes 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_heat_maps*> maps; + for (size_t i = 0; i != filenames.size(); ++i) { + Persistence_heat_maps* l = new Persistence_heat_maps; + l->load_from_file(filenames[i]); + maps.push_back(l); + } + + Persistence_heat_maps av; + av.compute_average(maps); + + av.print_to_file("average.mps"); + + for (size_t i = 0; i != filenames.size(); ++i) { + delete maps[i]; + } + + std::cout << "Done \n"; + return 0; +} diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp new file mode 100644 index 00000000..befb0837 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.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_heat_maps.h> + +#include <iostream> +#include <sstream> +#include <limits> +#include <vector> + +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) { + std::cout << "This program computes distance of persistence heat maps 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 two heat " + "maps. For L^infty distance choose p = -1. \n"; + std::cout << "The remaining parameters of this program are names of files with persistence heat maps.\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_heat_maps> maps; + maps.reserve(filenames.size()); + for (size_t file_no = 0; file_no != filenames.size(); ++file_no) { + Persistence_heat_maps l; + l.load_from_file(filenames[file_no]); + maps.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 != filenames.size(); ++i) { + for (size_t j = i; j != filenames.size(); ++j) { + distance[i][j] = distance[j][i] = maps[i].distance(maps[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_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp new file mode 100644 index 00000000..c684a336 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.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_heat_maps.h> + +#include <iostream> +#include <sstream> +#include <vector> + +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) { + std::cout << "This program computes 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_heat_maps> maps; + maps.reserve(filenames.size()); + for (size_t file_no = 0; file_no != filenames.size(); ++file_no) { + Persistence_heat_maps l; + l.load_from_file(filenames[file_no]); + maps.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 != maps.size(); ++i) { + for (size_t j = i; j != maps.size(); ++j) { + scalar_product[i][j] = scalar_product[j][i] = maps[i].compute_scalar_product(maps[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_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp new file mode 100644 index 00000000..2bf185a3 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp @@ -0,0 +1,84 @@ +/* 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_heat_maps.h> + +#include <iostream> +#include <sstream> +#include <limits> +#include <vector> + +using arc_tan_of_persistence_of_point = Gudhi::Persistence_representations::arc_tan_of_persistence_of_point; +using Persistence_heat_maps = + Gudhi::Persistence_representations::Persistence_heat_maps<arc_tan_of_persistence_of_point>; + +int main(int argc, char** argv) { + std::cout << "This program creates persistence heat map of diagrams provided as an input. The Gaussian kernels are " + "weighted by the arc tangential of their persistence.\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::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " + "of pixels \n"; + std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the " + "persistence heat maps."; + std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the " + "procedure please provide the dimension of persistence you want to use."; + std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1." + << std::endl; + 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]); + size_t stdiv = atof(argv[4]); + + unsigned dimension = std::numeric_limits<unsigned>::max(); + int dim = atoi(argv[5]); + if (dim >= 0) { + dimension = (unsigned)dim; + } + + std::vector<const char*> filenames; + for (int i = 6; i < argc; ++i) { + filenames.push_back(argv[i]); + } + + std::cout << "Creating persistence heat maps...\n"; + std::vector<std::vector<double> > filter = Gudhi::Persistence_representations::create_Gaussian_filter(stdiv, 1); + + for (size_t i = 0; i != filenames.size(); ++i) { + std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl; + Persistence_heat_maps l(filenames[i], filter, false, size_of_grid, min_, max_, dimension); + + std::stringstream ss; + ss << filenames[i] << ".mps"; + l.print_to_file(ss.str().c_str()); + } + std::cout << "Done \n"; + return 0; +} diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp new file mode 100644 index 00000000..ec9477f1 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp @@ -0,0 +1,84 @@ +/* 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_heat_maps.h> + +#include <iostream> +#include <sstream> +#include <limits> +#include <vector> + +using distance_from_diagonal_scaling = Gudhi::Persistence_representations::distance_from_diagonal_scaling; +using Persistence_heat_maps = + Gudhi::Persistence_representations::Persistence_heat_maps<distance_from_diagonal_scaling>; + +int main(int argc, char** argv) { + std::cout << "This program creates persistence heat map of diagrams provided as an input. The Gaussian kernels are " + "weighted by the distance of a center from the diagonal.\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::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " + "of pixels \n"; + std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the " + "persistence heat maps."; + std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the " + "procedure please provide the dimension of persistence you want to use."; + std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1." + << std::endl; + 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]); + size_t stdiv = atof(argv[4]); + + unsigned dimension = std::numeric_limits<unsigned>::max(); + int dim = atoi(argv[5]); + if (dim >= 0) { + dimension = (unsigned)dim; + } + + std::vector<const char*> filenames; + for (int i = 6; i != argc; ++i) { + filenames.push_back(argv[i]); + } + + std::cout << "Creating persistence heat maps...\n"; + std::vector<std::vector<double> > filter = Gudhi::Persistence_representations::create_Gaussian_filter(stdiv, 1); + + for (size_t i = 0; i != filenames.size(); ++i) { + std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl; + Persistence_heat_maps l(filenames[i], filter, false, size_of_grid, min_, max_, dimension); + + std::stringstream ss; + ss << filenames[i] << ".mps"; + l.print_to_file(ss.str().c_str()); + } + std::cout << "Done \n"; + return 0; +} diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp new file mode 100644 index 00000000..ffec8b3d --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp @@ -0,0 +1,85 @@ +/* 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_heat_maps.h> + +#include <iostream> +#include <sstream> +#include <limits> +#include <vector> + +using squared_distance_from_diagonal_scaling = + Gudhi::Persistence_representations::squared_distance_from_diagonal_scaling; +using Persistence_heat_maps = + Gudhi::Persistence_representations::Persistence_heat_maps<squared_distance_from_diagonal_scaling>; + +int main(int argc, char** argv) { + std::cout << "This program creates persistence heat map of diagrams provided as an input. The Gaussian kernels are " + "weighted by the square of distance of a center from the diagonal.\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::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " + "of pixels \n"; + std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the " + "persistence heat maps."; + std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the " + "procedure please provide the dimension of persistence you want to use."; + std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1." + << std::endl; + 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]); + size_t stdiv = atof(argv[4]); + + unsigned dimension = std::numeric_limits<unsigned>::max(); + int dim = atoi(argv[5]); + if (dim >= 0) { + dimension = (unsigned)dim; + } + + std::vector<const char*> filenames; + for (int i = 6; i < argc; ++i) { + filenames.push_back(argv[i]); + } + + std::cout << "Creating persistence heat maps...\n"; + std::vector<std::vector<double> > filter = Gudhi::Persistence_representations::create_Gaussian_filter(stdiv, 1); + + for (size_t i = 0; i != filenames.size(); ++i) { + std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl; + Persistence_heat_maps l(filenames[i], filter, false, size_of_grid, min_, max_, dimension); + + std::stringstream ss; + ss << filenames[i] << ".mps"; + l.print_to_file(ss.str().c_str()); + } + std::cout << "Done \n"; + return 0; +} diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp new file mode 100644 index 00000000..db2f0008 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp @@ -0,0 +1,80 @@ +/* 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_heat_maps.h> + +#include <iostream> +#include <sstream> +#include <limits> +#include <vector> + +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) { + std::cout << "This program creates persistence heat map 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::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " + "of pixels \n"; + + std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the " + "persistence heat maps."; + std::cout << "If your input file contains persistence pairs of various dimension, as a fifth parameter of the " + "procedure please provide the dimension of persistence you want to use."; + std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1." + << std::endl; + 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]); + size_t stdiv = atof(argv[4]); + + unsigned dimension = std::numeric_limits<unsigned>::max(); + int dim = atoi(argv[5]); + if (dim >= 0) { + dimension = (unsigned)dim; + } + std::vector<const char*> filenames; + for (int i = 6; i < argc; ++i) { + filenames.push_back(argv[i]); + } + + std::cout << "Creating persistence heat maps...\n"; + std::vector<std::vector<double> > filter = Gudhi::Persistence_representations::create_Gaussian_filter(stdiv, 1); + + for (size_t i = 0; i != filenames.size(); ++i) { + std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl; + Persistence_heat_maps l(filenames[i], filter, false, size_of_grid, min_, max_, dimension); + + std::stringstream ss; + ss << filenames[i] << ".mps"; + l.print_to_file(ss.str().c_str()); + } + std::cout << "Done \n"; + return 0; +} diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp new file mode 100644 index 00000000..6aefbb00 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp @@ -0,0 +1,81 @@ +/* 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/PSSK.h> + +#include <iostream> +#include <sstream> +#include <limits> +#include <vector> + +using PSSK = Gudhi::Persistence_representations::PSSK; + +int main(int argc, char** argv) { + std::cout << "This program creates PSSK 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::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " + "of pixels \n"; + std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the " + "persistence heat maps."; + std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the " + "procedure please provide the dimension of persistence you want to use."; + std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1." + << std::endl; + 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]); + size_t stdiv = atof(argv[4]); + + unsigned dimension = std::numeric_limits<unsigned>::max(); + int dim = atoi(argv[5]); + if (dim >= 0) { + dimension = (unsigned)dim; + } + + std::vector<const char*> filenames; + for (int i = 6; i < argc; ++i) { + filenames.push_back(argv[i]); + } + + std::cout << "Creating persistence heat maps...\n"; + std::vector<std::vector<double> > filter = Gudhi::Persistence_representations::create_Gaussian_filter(stdiv, 1); + + for (size_t i = 0; i != filenames.size(); ++i) { + std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl; + PSSK l(filenames[i], filter, size_of_grid, min_, max_, dimension); + + std::stringstream ss; + ss << filenames[i] << ".pssk"; + l.print_to_file(ss.str().c_str()); + } + std::cout << "Done \n"; + return 0; +} diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp new file mode 100644 index 00000000..a7c9f2d8 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp @@ -0,0 +1,38 @@ +/* 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_heat_maps.h> + +#include <iostream> +#include <sstream> + +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) { + 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_heat_maps l; + l.load_from_file(argv[1]); + l.plot(argv[1]); + return 0; +} diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/simple_diagram.txt.mps b/src/Persistence_representations/utilities/persistence_heat_maps/simple_diagram.txt.mps new file mode 100644 index 00000000..b7643887 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_heat_maps/simple_diagram.txt.mps @@ -0,0 +1,11 @@ +0.93 8.0707 +0.0492104 0.03889 0.0190956 0.00603584 0.00131569 0.000120934 2.10152e-05 0 0 0 +0.0650745 0.0539306 0.0296488 0.011745 0.00357642 0.000695928 0.000120934 0 0 0 +0.0572665 0.0559446 0.0409942 0.0230905 0.00937173 0.00242903 0.000422102 0 0 0 +0.0409942 0.0559656 0.0573874 0.0408475 0.0192639 0.00628964 0.00178718 0.000422102 0.000120934 2.10152e-05 +0.0296488 0.0540515 0.0657704 0.0519133 0.0283092 0.0132056 0.00628964 0.00242903 0.000695928 0.000120934 +0.0190956 0.0393121 0.0516395 0.0465955 0.0359385 0.0283092 0.0192639 0.00937173 0.00357642 0.00131569 +0.00847814 0.0188418 0.0281882 0.0358964 0.0465955 0.0519133 0.0408475 0.0230905 0.011745 0.00603584 +0.00242903 0.00628964 0.0132056 0.0281882 0.0516395 0.0657704 0.0573874 0.0409942 0.0296488 0.0190956 +0.000422102 0.00178718 0.00628964 0.0188418 0.0393121 0.0540515 0.0559656 0.0559446 0.0539306 0.03889 +0 0.000422102 0.00242903 0.00847814 0.0190956 0.0296488 0.0409942 0.0572665 0.0650745 0.0492104 diff --git a/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt new file mode 100644 index 00000000..105b7efb --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt @@ -0,0 +1,46 @@ +cmake_minimum_required(VERSION 2.6) +project(Persistence_representations_intervals_utilities) + +file(COPY "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/") + +add_executable ( plot_persistence_intervals plot_persistence_intervals.cpp ) +target_link_libraries( plot_persistence_intervals ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME plot_persistence_intervals COMMAND $<TARGET_FILE:plot_persistence_intervals> + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") + +add_executable ( compute_birth_death_range_in_persistence_diagram compute_birth_death_range_in_persistence_diagram.cpp ) +target_link_libraries( compute_birth_death_range_in_persistence_diagram ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME compute_birth_death_range_in_persistence_diagram COMMAND $<TARGET_FILE:compute_birth_death_range_in_persistence_diagram> + "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") + +add_executable ( compute_number_of_dominant_intervals compute_number_of_dominant_intervals.cpp ) +target_link_libraries( compute_number_of_dominant_intervals ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME compute_number_of_dominant_intervals COMMAND $<TARGET_FILE:compute_number_of_dominant_intervals> + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt" "-1" "2") + +add_executable ( plot_histogram_of_intervals_lengths plot_histogram_of_intervals_lengths.cpp ) +target_link_libraries( plot_histogram_of_intervals_lengths ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME plot_histogram_of_intervals_lengths COMMAND $<TARGET_FILE:plot_histogram_of_intervals_lengths> + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt" "2") + +add_executable ( plot_persistence_Betti_numbers plot_persistence_Betti_numbers.cpp ) +target_link_libraries( plot_persistence_Betti_numbers ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME plot_persistence_Betti_numbers COMMAND $<TARGET_FILE:plot_persistence_Betti_numbers> + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") + +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + add_executable ( compute_bottleneck_distance compute_bottleneck_distance.cpp ) + target_link_libraries( compute_bottleneck_distance ${Boost_SYSTEM_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(compute_bottleneck_distance ${TBB_LIBRARIES}) + endif(TBB_FOUND) + + add_test(NAME compute_bottleneck_distance COMMAND $<TARGET_FILE:compute_bottleneck_distance> + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt" + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") +endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Persistence_representations/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp b/src/Persistence_representations/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp new file mode 100644 index 00000000..66fa31ca --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp @@ -0,0 +1,64 @@ +/* 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/reader_utils.h> +#include <gudhi/Persistence_intervals.h> + +#include <iostream> +#include <vector> +#include <limits> +#include <utility> + +using Persistence_intervals = Gudhi::Persistence_representations::Persistence_intervals; + +int main(int argc, char** argv) { + std::cout << "This program compute the range of birth and death times of persistence pairs in diagrams provided as " + "an input. \n"; + std::cout << "The first parameter of the program is the dimension of persistence to be used. 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"; + + 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]); + } + + double min_ = std::numeric_limits<double>::max(); + double max_ = -std::numeric_limits<double>::max(); + + for (size_t file_no = 0; file_no != filenames.size(); ++file_no) { + std::cout << "Creating diagram based on a file : " << filenames[file_no] << std::endl; + Persistence_intervals p(filenames[file_no], dimension); + std::pair<double, double> min_max_ = p.get_x_range(); + if (min_max_.first < min_) min_ = min_max_.first; + if (min_max_.second > max_) max_ = min_max_.second; + } + std::cout << "Birth-death range : min: " << min_ << ", max: " << max_ << std::endl; + return 0; +} diff --git a/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp b/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp new file mode 100644 index 00000000..0b1b526d --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp @@ -0,0 +1,95 @@ +/* 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_intervals_with_distances.h> +#include <gudhi/read_persistence_from_file.h> + +#include <iostream> +#include <sstream> +#include <limits> +#include <vector> + +using Persistence_intervals_with_distances = Gudhi::Persistence_representations::Persistence_intervals_with_distances; + +int main(int argc, char** argv) { + std::cout << "This program compute the bottleneck distance of persistence diagrams stored in a files. \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 this programs are names of files with persistence diagrams.\n"; + + if (argc < 3) { + std::cout << "Wrong number of parameters, the program will now terminate \n"; + return 1; + } + + 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]); + } + + // reading the persistence intervals: + std::vector<Persistence_intervals_with_distances> persistence_intervals; + for (size_t i = 0; i != filenames.size(); ++i) { + Persistence_intervals_with_distances pers(filenames[i], dimension); + persistence_intervals.push_back(pers); + } + + // 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 != persistence_intervals.size(); ++i) { + for (size_t j = i + 1; j != persistence_intervals.size(); ++j) { + distance[i][j] = distance[j][i] = persistence_intervals[i].distance(persistence_intervals[j]); + } + } + + // 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_intervals/compute_number_of_dominant_intervals.cpp b/src/Persistence_representations/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp new file mode 100644 index 00000000..1286ca57 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp @@ -0,0 +1,55 @@ +/* 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/reader_utils.h> +#include <gudhi/Persistence_intervals.h> + +#include <iostream> +#include <limits> +#include <vector> +#include <utility> + +using Persistence_intervals = Gudhi::Persistence_representations::Persistence_intervals; + +int main(int argc, char** argv) { + std::cout << "This program compute the dominant intervals. A number of intervals to be displayed is a parameter of " + "this program. \n"; + if (argc != 4) { + std::cout << "To run this program, please provide the name of a file with persistence diagram, dimension of " + "intervals that should be taken into account (if your file contains only persistence pairs in a " + "single dimension, set it up to -1) and number of dominant intervals you would like to get \n"; + return 1; + } + int dim = atoi(argv[2]); + unsigned dimension = std::numeric_limits<unsigned>::max(); + if (dim >= 0) { + dimension = (unsigned)dim; + } + Persistence_intervals p(argv[1], dimension); + std::vector<std::pair<double, double> > dominant_intervals = p.dominant_intervals(atoi(argv[3])); + std::cout << "Here are the dominant intervals : " << std::endl; + for (size_t i = 0; i != dominant_intervals.size(); ++i) { + std::cout << " " << dominant_intervals[i].first << "," << dominant_intervals[i].second << " " << std::endl; + } + + return 0; +} diff --git a/src/Persistence_representations/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp b/src/Persistence_representations/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp new file mode 100644 index 00000000..d68f4584 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp @@ -0,0 +1,72 @@ +/* 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/reader_utils.h> +#include <gudhi/Persistence_intervals.h> + +#include <iostream> +#include <vector> +#include <limits> +#include <utility> + +using Persistence_intervals = Gudhi::Persistence_representations::Persistence_intervals; + +int main(int argc, char** argv) { + std::cout << "This program compute a histogram of barcode's length. A number of bins in the histogram is a parameter " + "of this program. \n"; + if (argc != 3) { + std::cout << "To run this program, please provide the name of a file with persistence diagram and number of " + "dominant intervals you would like to get \n"; + std::cout << "The third parameter of a program is the dimension of the persistence that is to be used. If your " + "file contains only birth-death pairs, you can skip this parameter\n"; + return 1; + } + unsigned dimension = std::numeric_limits<unsigned>::max(); + int dim = -1; + if (argc > 2) { + dim = atoi(argv[2]); + } + if (dim >= 0) { + dimension = (unsigned)dim; + } + + Persistence_intervals p(argv[1], dimension); + std::vector<std::pair<double, double> > dominant_intervals = p.dominant_intervals(atoi(argv[2])); + std::vector<size_t> histogram = p.histogram_of_lengths(10); + + std::stringstream gnuplot_script; + gnuplot_script << argv[1] << "_Gnuplot_script"; + std::ofstream out; + out.open(gnuplot_script.str().c_str()); + + out << "set style data histogram" << std::endl; + out << "set style histogram cluster gap 1" << std::endl; + out << "set style fill solid border -1" << std::endl; + out << "plot '-' notitle" << std::endl; + for (size_t i = 0; i != histogram.size(); ++i) { + out << histogram[i] << std::endl; + } + out << std::endl; + std::cout << "To visualize, open gnuplot and type: load \'" << gnuplot_script.str().c_str() << "\'" << std::endl; + out.close(); + return 0; +} diff --git a/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp b/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp new file mode 100644 index 00000000..da2b9319 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp @@ -0,0 +1,87 @@ +/* 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/reader_utils.h> +#include <gudhi/Persistence_intervals.h> + +#include <iostream> +#include <vector> +#include <limits> +#include <utility> + +using Persistence_intervals = Gudhi::Persistence_representations::Persistence_intervals; + +int main(int argc, char** argv) { + std::cout << "This program compute a plot of persistence Betti numbers. The input parameter is a file with " + "persistence intervals. \n"; + std::cout << "The second optional parameter of a program is the dimension of the persistence that is to be used. If " + "your file contains only birth-death pairs, you can skip this parameter\n"; + if (argc < 2) { + std::cout << "To run this program, please provide the name of a file with persistence diagram and number of " + "dominant intervals you would like to get \n"; + return 1; + } + unsigned dimension = std::numeric_limits<unsigned>::max(); + int dim = -1; + if (argc > 2) { + dim = atoi(argv[2]); + } + if (dim >= 0) { + dimension = (unsigned)dim; + } + + std::stringstream gnuplot_script; + gnuplot_script << argv[1] << "_Gnuplot_script"; + std::ofstream out; + out.open(gnuplot_script.str().c_str()); + + Persistence_intervals p(argv[1], dimension); + std::vector<std::pair<double, size_t> > pbns = p.compute_persistent_betti_numbers(); + + // set up the ranges so that we see the image well. + double xRangeBegin = pbns[0].first; + double xRangeEnd = pbns[pbns.size() - 1].first; + double yRangeBegin = 0; + double yRangeEnd = 0; + for (size_t i = 0; i != pbns.size(); ++i) { + if (pbns[i].second > yRangeEnd) yRangeEnd = pbns[i].second; + } + xRangeBegin -= (xRangeEnd - xRangeBegin) / 100.0; + xRangeEnd += (xRangeEnd - xRangeBegin) / 100.0; + yRangeEnd += yRangeEnd / 100; + + out << "set xrange [" << xRangeBegin << " : " << xRangeEnd << "]" << std::endl; + out << "set yrange [" << yRangeBegin << " : " << yRangeEnd << "]" << std::endl; + out << "plot '-' using 1:2 notitle with lp " << std::endl; + double previous_y = 0; + for (size_t i = 0; i != pbns.size(); ++i) { + out << pbns[i].first << " " << previous_y << std::endl; + out << pbns[i].first << " " << pbns[i].second << std::endl; + previous_y = pbns[i].second; + } + out << std::endl; + out.close(); + + std::cout << "To visualize, open gnuplot and type: load \'" << gnuplot_script.str().c_str() << "\'" << std::endl; + + return 0; +} diff --git a/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_intervals.cpp b/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_intervals.cpp new file mode 100644 index 00000000..e7d29e84 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_intervals.cpp @@ -0,0 +1,54 @@ +/* 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/reader_utils.h> +#include <gudhi/Persistence_intervals.h> +#include <gudhi/read_persistence_from_file.h> + +#include <iostream> +#include <limits> +#include <vector> +#include <utility> + +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"; + std::cout << "The second optional parameter of a program is the dimension of the persistence that is to be used. " + "If your file contains only birth-death pairs, you can skip this parameter\n"; + return 1; + } + unsigned dimension = std::numeric_limits<unsigned>::max(); + int dim = -1; + if (argc > 2) { + dim = atoi(argv[2]); + } + if (dim >= 0) { + dimension = (unsigned)dim; + } + std::vector<std::pair<double, double> > intervals = + Gudhi::Persistence_representations::read_persistence_intervals_in_one_dimension_from_file(argv[1], dimension); + Persistence_intervals b(intervals); + b.plot(argv[1]); + return 0; +} 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 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 + + 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..e3d1013b --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt @@ -0,0 +1,38 @@ +cmake_minimum_required(VERSION 2.6) +project(Persistence_vectors_utilities) + +file(COPY "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/") + +add_executable ( create_persistence_vectors create_persistence_vectors.cpp ) +target_link_libraries(create_persistence_vectors ${Boost_SYSTEM_LIBRARY}) + +# Will create simple_diagram.txt.vect +add_test(NAME create_persistence_vectors COMMAND $<TARGET_FILE:create_persistence_vectors> + "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") + +add_executable ( average_persistence_vectors average_persistence_vectors.cpp ) +target_link_libraries(average_persistence_vectors ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME average_persistence_vectors COMMAND $<TARGET_FILE:average_persistence_vectors> + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.vect" + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.vect") + +add_executable ( compute_distance_of_persistence_vectors compute_distance_of_persistence_vectors.cpp ) +target_link_libraries(compute_distance_of_persistence_vectors ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME compute_distance_of_persistence_vectors COMMAND $<TARGET_FILE:compute_distance_of_persistence_vectors> + "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.vect" + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.vect") + +add_executable ( compute_scalar_product_of_persistence_vectors compute_scalar_product_of_persistence_vectors.cpp ) +target_link_libraries(compute_scalar_product_of_persistence_vectors ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME compute_scalar_product_of_persistence_vectors COMMAND $<TARGET_FILE:compute_scalar_product_of_persistence_vectors> + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.vect" + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.vect") + +add_executable ( plot_persistence_vectors plot_persistence_vectors.cpp ) +target_link_libraries(plot_persistence_vectors ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME plot_persistence_vectors COMMAND $<TARGET_FILE:plot_persistence_vectors> + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.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..366ee2bc --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_vectors/average_persistence_vectors.cpp @@ -0,0 +1,67 @@ +/* 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_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 persistence vector of persistence vectors created based on persistence " + "diagrams provided as an input. \n"; + std::cout << "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 << "Reading persistence vectors...\n"; + 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..3aed297e --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp @@ -0,0 +1,94 @@ +/* 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_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"); + 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_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..d9ad4360 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp @@ -0,0 +1,80 @@ +/* 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_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 scalar product of persistence vectors 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 vectors.\n"; + + 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"); + 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_vectors/create_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp new file mode 100644 index 00000000..b618ca67 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp @@ -0,0 +1,63 @@ +/* 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_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 of diagrams provided as an input. The first parameter of this " + "program is a dimension of persistence "; + std::cout << " that will be used in creation of the persistence vectors. If our input files contain persistence " + "pairs of various dimension, as a second parameter of the "; + std::cout << " procedure please provide the dimension of persistence you want to use. If in your file there are only " + "birth-death pairs of the same dimension, set the first parameter to -1." + << std::endl; + 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()); + } + std::cout << "Done \n"; + 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..e52b8f7d --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_vectors/plot_persistence_vectors.cpp @@ -0,0 +1,44 @@ +/* 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_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; +} diff --git a/src/Persistence_representations/utilities/persistence_vectors/simple_diagram.txt.vect b/src/Persistence_representations/utilities/persistence_vectors/simple_diagram.txt.vect new file mode 100644 index 00000000..1d4eeaaf --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_vectors/simple_diagram.txt.vect @@ -0,0 +1 @@ +0.707107 0.707107 0.707107 0.707107 0.707107 0.707107 0.707107 0.707107 0.707107 0.707107
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