diff options
Diffstat (limited to 'utilities/Persistence_representations')
36 files changed, 0 insertions, 2327 deletions
diff --git a/utilities/Persistence_representations/CMakeLists.txt b/utilities/Persistence_representations/CMakeLists.txt deleted file mode 100644 index fc51b1d6..00000000 --- a/utilities/Persistence_representations/CMakeLists.txt +++ /dev/null @@ -1,59 +0,0 @@ -# Copy files, otherwise result files are created in sources -file(COPY "${CMAKE_SOURCE_DIR}/data/persistence_diagram/first.pers" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/") -file(COPY "${CMAKE_SOURCE_DIR}/data/persistence_diagram/second.pers" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/") - -function(add_persistence_representation_creation_utility creation_utility) - add_executable ( ${creation_utility} ${creation_utility}.cpp ) - - # as the function is called in a subdirectory level, need to '../' to find persistence files - # ARGN will add all the other arguments (except creation_utility) sent to the CMake functions - add_test(NAME Persistence_representation_utilities_${creation_utility} COMMAND $<TARGET_FILE:${creation_utility}> - ${ARGN} "${CMAKE_CURRENT_BINARY_DIR}/../first.pers" - "${CMAKE_CURRENT_BINARY_DIR}/../second.pers") - - install(TARGETS ${creation_utility} DESTINATION bin) -endfunction(add_persistence_representation_creation_utility) - -function(add_persistence_representation_plot_utility plot_utility tool_extension) - add_executable ( ${plot_utility} ${plot_utility}.cpp ) - - # as the function is called in a subdirectory level, need to '../' to find persistence heat maps files - add_test(NAME Persistence_representation_utilities_${plot_utility}_first COMMAND $<TARGET_FILE:${plot_utility}> - "${CMAKE_CURRENT_BINARY_DIR}/../first.pers${tool_extension}") - #add_test(NAME Persistence_representation_utilities_${plot_utility}_second COMMAND $<TARGET_FILE:${plot_utility}> - # "${CMAKE_CURRENT_BINARY_DIR}/../second.pers${tool_extension}") - if(GNUPLOT_PATH) - add_test(NAME Persistence_representation_utilities_${plot_utility}_first_gnuplot COMMAND ${GNUPLOT_PATH} - "-e" "load '${CMAKE_CURRENT_BINARY_DIR}/../first.pers${tool_extension}_GnuplotScript'") - #add_test(NAME Persistence_representation_utilities_${plot_utility}_second_gnuplot COMMAND ${GNUPLOT_PATH} - # "-e" "load '${CMAKE_CURRENT_BINARY_DIR}/../second.pers${tool_extension}_GnuplotScript'") - endif() - - install(TARGETS ${plot_utility} DESTINATION bin) -endfunction(add_persistence_representation_plot_utility) - -function(add_persistence_representation_function_utility function_utility tool_extension) - add_executable ( ${function_utility} ${function_utility}.cpp ) - - # ARGV2 is an optional argument - if (${ARGV2}) - # as the function is called in a subdirectory level, need to '../' to find persistence heat maps files - add_test(NAME Persistence_representation_utilities_${function_utility} COMMAND $<TARGET_FILE:${function_utility}> - "${ARGV2}" - "${CMAKE_CURRENT_BINARY_DIR}/../first.pers${tool_extension}" - "${CMAKE_CURRENT_BINARY_DIR}/../second.pers${tool_extension}") - else() - # as the function is called in a subdirectory level, need to '../' to find persistence heat maps files - add_test(NAME Persistence_representation_utilities_${function_utility} COMMAND $<TARGET_FILE:${function_utility}> - "${CMAKE_CURRENT_BINARY_DIR}/../first.pers${tool_extension}" - "${CMAKE_CURRENT_BINARY_DIR}/../second.pers${tool_extension}") - endif() - - install(TARGETS ${function_utility} DESTINATION bin) -endfunction(add_persistence_representation_function_utility) - -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/utilities/Persistence_representations/persistence_heat_maps/CMakeLists.txt b/utilities/Persistence_representations/persistence_heat_maps/CMakeLists.txt deleted file mode 100644 index 89ef232f..00000000 --- a/utilities/Persistence_representations/persistence_heat_maps/CMakeLists.txt +++ /dev/null @@ -1,14 +0,0 @@ -project(Persistence_representations_heat_maps_utilities) - -add_persistence_representation_creation_utility(create_pssk "10" "-1" "-1" "4" "-1") -add_persistence_representation_creation_utility(create_p_h_m_weighted_by_arctan_of_their_persistence "10" "-1" "-1" "4" "-1") -add_persistence_representation_creation_utility(create_p_h_m_weighted_by_distance_from_diagonal "10" "-1" "-1" "4" "-1") -add_persistence_representation_creation_utility(create_p_h_m_weighted_by_squared_diag_distance "10" "-1" "-1" "4" "-1") -# Need to set grid min and max for further average, distance and scalar_product -add_persistence_representation_creation_utility(create_persistence_heat_maps "10" "0" "35" "10" "-1") - -add_persistence_representation_plot_utility(plot_persistence_heat_map ".mps") - -add_persistence_representation_function_utility(average_persistence_heat_maps ".mps") -add_persistence_representation_function_utility(compute_distance_of_persistence_heat_maps ".mps" "1") -add_persistence_representation_function_utility(compute_scalar_product_of_persistence_heat_maps ".mps") diff --git a/utilities/Persistence_representations/persistence_heat_maps/average_persistence_heat_maps.cpp b/utilities/Persistence_representations/persistence_heat_maps/average_persistence_heat_maps.cpp deleted file mode 100644 index 2cbd812b..00000000 --- a/utilities/Persistence_representations/persistence_heat_maps/average_persistence_heat_maps.cpp +++ /dev/null @@ -1,63 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Pawel Dlotko - * - * Copyright (C) 2016 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/Persistence_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 of persistence heat maps stored in files (the files needs to be " - << "created beforehand).\n" - << "The parameters of this programs 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; - } - - std::vector<const char*> filenames; - for (int i = 1; i < argc; ++i) { - filenames.push_back(argv[i]); - } - - 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 << "Average can be found in 'average.mps' file\n"; - return 0; -} diff --git a/utilities/Persistence_representations/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp b/utilities/Persistence_representations/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp deleted file mode 100644 index 14d0db8f..00000000 --- a/utilities/Persistence_representations/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp +++ /dev/null @@ -1,94 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Pawel Dlotko - * - * Copyright (C) 2016 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/Persistence_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 files (the files needs to be " - << "created beforehand).\n" - << "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" - << "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.mps"); - for (size_t i = 0; i != distance.size(); ++i) { - for (size_t j = 0; j != distance.size(); ++j) { - std::cout << distance[i][j] << " "; - out << distance[i][j] << " "; - } - std::cout << std::endl; - out << std::endl; - } - out.close(); - - std::cout << "Distance can be found in 'distance.mps' file\n"; - return 0; -} diff --git a/utilities/Persistence_representations/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp b/utilities/Persistence_representations/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp deleted file mode 100644 index 12fceedc..00000000 --- a/utilities/Persistence_representations/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp +++ /dev/null @@ -1,85 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Pawel Dlotko - * - * Copyright (C) 2016 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/Persistence_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 heat maps stored in a file (the file needs to be " - << "created beforehand). \n" - << "The parameters of this programs 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; - } - - 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.mps"); - for (size_t i = 0; i != scalar_product.size(); ++i) { - for (size_t j = 0; j != scalar_product.size(); ++j) { - std::cout << scalar_product[i][j] << " "; - out << scalar_product[i][j] << " "; - } - std::cout << std::endl; - out << std::endl; - } - out.close(); - - std::cout << "Distance can be found in 'scalar_product.mps' file\n"; - return 0; -} diff --git a/utilities/Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp b/utilities/Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp deleted file mode 100644 index 21c553b9..00000000 --- a/utilities/Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp +++ /dev/null @@ -1,81 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library -* (Geometric Understanding in Higher Dimensions) is a generic C++ -* library for computational topology. -* -* Author(s): Pawel Dlotko -* -* Copyright (C) 2016 Inria -* -* This program is free software: you can redistribute it and/or modify -* it under the terms of the GNU General Public License as published by -* the Free Software Foundation, either version 3 of the License, or -* (at your option) any later version. -* -* This program is distributed in the hope that it will be useful, -* but WITHOUT ANY WARRANTY; without even the implied warranty of -* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -* GNU General Public License for more details. -* -* You should have received a copy of the GNU General Public License -* along with this program. If not, see <http://www.gnu.org/licenses/>. -*/ - -#include <gudhi/Persistence_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 files (*.mps) of persistence diagrams files (*.pers) " - << "provided as an input.The Gaussian kernels are weighted by the arc tangential of their persistence.\n" - << "The first parameter of a program is an integer, a size of a grid.\n" - << "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" - << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " - << "of pixels.\n" - << "The fifth parameter of this program is a dimension of persistence that will be used in creation of " - << "the persistence heat maps." - << "If your input files contains persistence pairs of various dimension, as a fifth parameter of the " - << "procedure please provide the dimension of persistence you want to use." - << "If in your files there are only birth-death pairs of the same dimension, set the fifth parameter to " - << "-1.\n" - << "The remaining parameters are the names of files with persistence diagrams. \n"; - - if (argc < 7) { - 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::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()); - } - return 0; -} diff --git a/utilities/Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp b/utilities/Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp deleted file mode 100644 index 99b0bd17..00000000 --- a/utilities/Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp +++ /dev/null @@ -1,81 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Pawel Dlotko - * - * Copyright (C) 2016 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/Persistence_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 files (*.mps) of persistence diagrams files (*.pers) " - << "provided as an input.The Gaussian kernels are weighted by the distance of a center from the " - << "diagonal.\n" - << "The first parameter of a program is an integer, a size of a grid.\n" - << "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" - << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " - << "of pixels.\n" - << "The fifth parameter of this program is a dimension of persistence that will be used in creation of " - << "the persistence heat maps." - << "If your input files contains persistence pairs of various dimension, as a fifth parameter of the " - << "procedure please provide the dimension of persistence you want to use." - << "If in your files there are only birth-death pairs of the same dimension, set the fifth parameter to " - << "-1.\n" - << "The remaining parameters are the names of files with persistence diagrams. \n"; - - if (argc < 7) { - 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::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()); - } - return 0; -} diff --git a/utilities/Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp b/utilities/Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp deleted file mode 100644 index a4b6e458..00000000 --- a/utilities/Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp +++ /dev/null @@ -1,83 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Pawel Dlotko - * - * Copyright (C) 2016 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/Persistence_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 files (*.mps) of persistence diagrams files (*.pers) " - << "provided as an input.The Gaussian kernels are weighted by the square of distance of a center from the " - << "diagonal.\n" - << "The first parameter of a program is an integer, a size of a grid.\n" - << "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" - << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " - << "of pixels.\n" - << "The fifth parameter of this program is a dimension of persistence that will be used in creation of " - << "the persistence heat maps." - << "If your input files contains persistence pairs of various dimension, as a fifth parameter of the " - << "procedure please provide the dimension of persistence you want to use." - << "If in your files there are only birth-death pairs of the same dimension, set the fifth parameter to " - << "-1.\n" - << "The remaining parameters are the names of files with persistence diagrams. \n"; - - if (argc < 7) { - 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::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()); - } - return 0; -} diff --git a/utilities/Persistence_representations/persistence_heat_maps/create_persistence_heat_maps.cpp b/utilities/Persistence_representations/persistence_heat_maps/create_persistence_heat_maps.cpp deleted file mode 100644 index 5960a89f..00000000 --- a/utilities/Persistence_representations/persistence_heat_maps/create_persistence_heat_maps.cpp +++ /dev/null @@ -1,78 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Pawel Dlotko - * - * Copyright (C) 2016 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/Persistence_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 files (*.mps) of persistence diagrams files (*.pers) " - << "provided as an input.\n" - << "The first parameter of a program is an integer, a size of a grid.\n" - << "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" - << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " - << "of pixels.\n" - << "The fifth parameter of this program is a dimension of persistence that will be used in creation of " - << "the persistence heat maps." - << "If your input files contains persistence pairs of various dimension, as a fifth parameter of the " - << "procedure please provide the dimension of persistence you want to use." - << "If in your files there are only birth-death pairs of the same dimension, set the fifth parameter to " - << "-1.\n" - << "The remaining parameters are the names of files with persistence diagrams. \n"; - - if (argc < 7) { - 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::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 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()); - } - return 0; -} diff --git a/utilities/Persistence_representations/persistence_heat_maps/create_pssk.cpp b/utilities/Persistence_representations/persistence_heat_maps/create_pssk.cpp deleted file mode 100644 index 04f33915..00000000 --- a/utilities/Persistence_representations/persistence_heat_maps/create_pssk.cpp +++ /dev/null @@ -1,79 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Pawel Dlotko - * - * Copyright (C) 2016 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/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 files (*.pssk) of persistence diagrams files (*.pers) " - << "provided as an input.\n" - << "The first parameter of a program is an integer, a size of a grid.\n" - << "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" - << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " - << "of pixels.\n" - << "The fifth parameter of this program is a dimension of persistence that will be used in creation of " - << "the PSSK." - << "If your input files contains persistence pairs of various dimension, as a fifth parameter of the " - << "procedure please provide the dimension of persistence you want to use." - << "If in your files there are only birth-death pairs of the same dimension, set the first parameter to " - << "-1.\n" - << "The remaining parameters are the names of files with persistence diagrams. \n"; - - if (argc < 7) { - 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::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 PSSK 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()); - } - return 0; -} diff --git a/utilities/Persistence_representations/persistence_heat_maps/plot_persistence_heat_map.cpp b/utilities/Persistence_representations/persistence_heat_maps/plot_persistence_heat_map.cpp deleted file mode 100644 index e4402589..00000000 --- a/utilities/Persistence_representations/persistence_heat_maps/plot_persistence_heat_map.cpp +++ /dev/null @@ -1,42 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Pawel Dlotko - * - * Copyright (C) 2016 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/Persistence_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 creates a gnuplot script from a persistence heat maps stored in a file (the file needs " - << "to be created beforehand). Please call the code with the name of a single heat maps file \n"; - if (argc != 2) { - std::cout << "Wrong parameter list, the program will now terminate \n"; - return 1; - } - Persistence_heat_maps l; - l.load_from_file(argv[1]); - l.plot(argv[1]); - return 0; -} diff --git a/utilities/Persistence_representations/persistence_intervals/CMakeLists.txt b/utilities/Persistence_representations/persistence_intervals/CMakeLists.txt deleted file mode 100644 index 649b72cb..00000000 --- a/utilities/Persistence_representations/persistence_intervals/CMakeLists.txt +++ /dev/null @@ -1,37 +0,0 @@ -project(Persistence_representations_intervals_utilities) - - -add_executable ( plot_histogram_of_intervals_lengths plot_histogram_of_intervals_lengths.cpp ) - -add_test(NAME plot_histogram_of_intervals_lengths COMMAND $<TARGET_FILE:plot_histogram_of_intervals_lengths> - "${CMAKE_CURRENT_BINARY_DIR}/../first.pers" "-1") - -install(TARGETS plot_histogram_of_intervals_lengths DESTINATION bin) - -add_persistence_representation_plot_utility(plot_persistence_intervals "") -add_persistence_representation_plot_utility(plot_persistence_Betti_numbers "") - -add_persistence_representation_creation_utility(compute_birth_death_range_in_persistence_diagram "-1") - - -add_executable ( compute_number_of_dominant_intervals compute_number_of_dominant_intervals.cpp ) -add_test(NAME Persistence_representation_utilities_compute_number_of_dominant_intervals - COMMAND $<TARGET_FILE:compute_number_of_dominant_intervals> - "${CMAKE_CURRENT_BINARY_DIR}/../first.pers" "-1" "2") - -install(TARGETS compute_number_of_dominant_intervals DESTINATION bin) - - -if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) - add_executable ( compute_bottleneck_distance compute_bottleneck_distance.cpp ) - if (TBB_FOUND) - target_link_libraries(compute_bottleneck_distance ${TBB_LIBRARIES}) - endif(TBB_FOUND) - add_test(NAME Persistence_representation_utilities_compute_bottleneck_distance - COMMAND $<TARGET_FILE:compute_bottleneck_distance> - "-1" - "${CMAKE_CURRENT_BINARY_DIR}/../first.pers" - "${CMAKE_CURRENT_BINARY_DIR}/../second.pers") - - install(TARGETS compute_bottleneck_distance DESTINATION bin) -endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/utilities/Persistence_representations/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp b/utilities/Persistence_representations/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp deleted file mode 100644 index 3be3de8f..00000000 --- a/utilities/Persistence_representations/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp +++ /dev/null @@ -1,68 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Pawel Dlotko - * - * Copyright (C) 2016 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/Persistence_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 computes the range of birth and death times of persistence pairs in diagrams provided as " - << "an input.\n" - << "The first parameter is the dimension of persistence to be used to create persistence intervals. " - << "If your file contains 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 of birth-death pairs, please set this first parameter to -1.\n" - << "The remaining parameters of the program are the names of files with persistence diagrams.\n"; - - if (argc < 3) { - std::cout << "Wrong parameter list, the program will now terminate \n"; - return 1; - } - - unsigned dimension = std::numeric_limits<unsigned>::max(); - int dim = atoi(argv[1]); - 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/utilities/Persistence_representations/persistence_intervals/compute_bottleneck_distance.cpp b/utilities/Persistence_representations/persistence_intervals/compute_bottleneck_distance.cpp deleted file mode 100644 index a6953b98..00000000 --- a/utilities/Persistence_representations/persistence_intervals/compute_bottleneck_distance.cpp +++ /dev/null @@ -1,95 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Pawel Dlotko - * - * Copyright (C) 2016 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/Persistence_intervals_with_distances.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 computes the bottleneck distance of persistence pairs in diagrams provided as " - << "an input.\n" - << "The first parameter is the dimension of persistence to be used to create persistence intervals. " - << "If your file contains 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 of birth-death pairs, please set this first parameter to -1.\n" - << "The remaining parameters of the program are the names of files with persistence diagrams.\n"; - - if (argc < 3) { - std::cout << "Wrong number of parameters, the program will now terminate \n"; - return 1; - } - - unsigned dimension = std::numeric_limits<unsigned>::max(); - int dim = atoi(argv[1]); - 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.itv"); - for (size_t i = 0; i != distance.size(); ++i) { - for (size_t j = 0; j != distance.size(); ++j) { - std::cout << distance[i][j] << " "; - out << distance[i][j] << " "; - } - std::cout << std::endl; - out << std::endl; - } - out.close(); - - std::cout << "Distance can be found in 'distance.itv' file\n"; - return 0; -} diff --git a/utilities/Persistence_representations/persistence_intervals/compute_number_of_dominant_intervals.cpp b/utilities/Persistence_representations/persistence_intervals/compute_number_of_dominant_intervals.cpp deleted file mode 100644 index 4f052f42..00000000 --- a/utilities/Persistence_representations/persistence_intervals/compute_number_of_dominant_intervals.cpp +++ /dev/null @@ -1,54 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Pawel Dlotko - * - * Copyright (C) 2016 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/Persistence_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/utilities/Persistence_representations/persistence_intervals/plot_histogram_of_intervals_lengths.cpp b/utilities/Persistence_representations/persistence_intervals/plot_histogram_of_intervals_lengths.cpp deleted file mode 100644 index f283971b..00000000 --- a/utilities/Persistence_representations/persistence_intervals/plot_histogram_of_intervals_lengths.cpp +++ /dev/null @@ -1,77 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Pawel Dlotko - * - * Copyright (C) 2016 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/Persistence_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 computes a histogram of barcode's length. A number of bins in the histogram is a " - << "parameter of this program. \n"; - if ((argc != 3) && (argc != 4)) { - 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. Set a negative number dominant intervals value " - << "If your file contains only birth-death pairs.\n" - << "The third parameter 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 dominant_interval_number = std::numeric_limits<unsigned>::max(); - int nbr = atoi(argv[2]); - if (nbr >= 0) { - dominant_interval_number = static_cast<unsigned>(nbr); - } - - int persistence_dimension = -1; - if (argc == 4) { - persistence_dimension = atoi(argv[3]); - } - - Persistence_intervals p(argv[1], dominant_interval_number); - std::vector<std::pair<double, double> > dominant_intervals = p.dominant_intervals(persistence_dimension); - std::vector<size_t> histogram = p.histogram_of_lengths(10); - - std::stringstream gnuplot_script; - gnuplot_script << argv[1] << "_GnuplotScript"; - 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; - out.close(); - - std::cout << "To visualize, install gnuplot and type the command: gnuplot -persist -e \"load \'" - << gnuplot_script.str().c_str() << "\'\"" << std::endl; - return 0; -} diff --git a/utilities/Persistence_representations/persistence_intervals/plot_persistence_Betti_numbers.cpp b/utilities/Persistence_representations/persistence_intervals/plot_persistence_Betti_numbers.cpp deleted file mode 100644 index 1cacbcd0..00000000 --- a/utilities/Persistence_representations/persistence_intervals/plot_persistence_Betti_numbers.cpp +++ /dev/null @@ -1,87 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Pawel Dlotko - * - * Copyright (C) 2016 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/Persistence_intervals.h> - -#include <iostream> -#include <vector> -#include <limits> -#include <utility> - -using Persistence_intervals = Gudhi::Persistence_representations::Persistence_intervals; - -int main(int argc, char** argv) { - if ((argc != 3) && (argc != 2)) { - std::cout << "This program creates a gnuplot script of Betti numbers from a single persistence diagram file" - << "(*.pers).\n" - << "To run this program, please provide the name of a file with persistence diagram.\n" - << "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 == 3) { - dim = atoi(argv[2]); - } - if (dim >= 0) { - dimension = (unsigned)dim; - } - - 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; - - std::stringstream gnuplot_script; - gnuplot_script << argv[1] << "_GnuplotScript"; - std::ofstream out; - out.open(gnuplot_script.str().c_str()); - - 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, install gnuplot and type the command: gnuplot -persist -e \"load \'" - << gnuplot_script.str().c_str() << "\'\"" << std::endl; - - return 0; -} diff --git a/utilities/Persistence_representations/persistence_intervals/plot_persistence_intervals.cpp b/utilities/Persistence_representations/persistence_intervals/plot_persistence_intervals.cpp deleted file mode 100644 index f92d5782..00000000 --- a/utilities/Persistence_representations/persistence_intervals/plot_persistence_intervals.cpp +++ /dev/null @@ -1,53 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Pawel Dlotko - * - * Copyright (C) 2016 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/Persistence_intervals.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 != 3) && (argc != 2)) { - std::cout << "This program creates a gnuplot script from a single persistence diagram file (*.pers).\n" - << "To run this program, please provide the name of a file with persistence diagram.\n" - << "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 == 3) { - 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/utilities/Persistence_representations/persistence_landscapes/CMakeLists.txt b/utilities/Persistence_representations/persistence_landscapes/CMakeLists.txt deleted file mode 100644 index 6b24d032..00000000 --- a/utilities/Persistence_representations/persistence_landscapes/CMakeLists.txt +++ /dev/null @@ -1,9 +0,0 @@ -project(Persistence_representations_landscapes_utilities) - -add_persistence_representation_creation_utility(create_landscapes "-1") - -add_persistence_representation_plot_utility(plot_landscapes ".land") - -add_persistence_representation_function_utility(average_landscapes ".land") -add_persistence_representation_function_utility(compute_distance_of_landscapes ".land" "1") -add_persistence_representation_function_utility(compute_scalar_product_of_landscapes ".land") diff --git a/utilities/Persistence_representations/persistence_landscapes/average_landscapes.cpp b/utilities/Persistence_representations/persistence_landscapes/average_landscapes.cpp deleted file mode 100644 index 4048f508..00000000 --- a/utilities/Persistence_representations/persistence_landscapes/average_landscapes.cpp +++ /dev/null @@ -1,63 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Pawel Dlotko - * - * Copyright (C) 2016 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/Persistence_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 of persistence landscapes stored in files (the files needs to be " - << "created beforehand).\n" - << "The parameters of this programs are names of files with persistence landscapes.\n"; - std::vector<const char*> filenames; - - if (argc < 3) { - std::cout << "Wrong number of parameters, the program will now terminate \n"; - return 1; - } - - for (int i = 1; i < argc; ++i) { - filenames.push_back(argv[i]); - } - - 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 << "Average can be found in 'average.land' file\n"; - return 0; -} diff --git a/utilities/Persistence_representations/persistence_landscapes/compute_distance_of_landscapes.cpp b/utilities/Persistence_representations/persistence_landscapes/compute_distance_of_landscapes.cpp deleted file mode 100644 index 253fa273..00000000 --- a/utilities/Persistence_representations/persistence_landscapes/compute_distance_of_landscapes.cpp +++ /dev/null @@ -1,93 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Pawel Dlotko - * - * Copyright (C) 2016 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/Persistence_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 computes distance of persistence landscapes stored in files (the files needs to be " - << "created beforehand).\n" - << "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" - << "The remaining parameters of this program are names of files with persistence landscapes.\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> landscaspes; - landscaspes.reserve(filenames.size()); - for (size_t file_no = 0; file_no != filenames.size(); ++file_no) { - 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.land"); - for (size_t i = 0; i != distance.size(); ++i) { - for (size_t j = 0; j != distance.size(); ++j) { - std::cout << distance[i][j] << " "; - out << distance[i][j] << " "; - } - std::cout << std::endl; - out << std::endl; - } - out.close(); - - std::cout << "Distance can be found in 'distance.land' file\n"; - return 0; -} diff --git a/utilities/Persistence_representations/persistence_landscapes/compute_scalar_product_of_landscapes.cpp b/utilities/Persistence_representations/persistence_landscapes/compute_scalar_product_of_landscapes.cpp deleted file mode 100644 index 11fe2886..00000000 --- a/utilities/Persistence_representations/persistence_landscapes/compute_scalar_product_of_landscapes.cpp +++ /dev/null @@ -1,84 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Pawel Dlotko - * - * Copyright (C) 2016 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/Persistence_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 computes scalar product of persistence landscapes stored in a file (the file needs to be " - << "created beforehand). \n" - << "The parameters of this programs are names of files with persistence landscapes.\n"; - - if (argc < 3) { - std::cout << "Wrong number of parameters, the program will now terminate \n"; - return 1; - } - - std::vector<const char*> filenames; - for (int i = 1; i < argc; ++i) { - filenames.push_back(argv[i]); - } - std::vector<Persistence_landscape> landscaspes; - landscaspes.reserve(filenames.size()); - for (size_t file_no = 0; file_no != filenames.size(); ++file_no) { - 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.land"); - for (size_t i = 0; i != scalar_product.size(); ++i) { - for (size_t j = 0; j != scalar_product.size(); ++j) { - std::cout << scalar_product[i][j] << " "; - out << scalar_product[i][j] << " "; - } - std::cout << std::endl; - out << std::endl; - } - out.close(); - - std::cout << "Distance can be found in 'scalar_product.land' file\n"; - return 0; -} diff --git a/utilities/Persistence_representations/persistence_landscapes/create_landscapes.cpp b/utilities/Persistence_representations/persistence_landscapes/create_landscapes.cpp deleted file mode 100644 index 59aad2f3..00000000 --- a/utilities/Persistence_representations/persistence_landscapes/create_landscapes.cpp +++ /dev/null @@ -1,65 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Pawel Dlotko - * - * Copyright (C) 2016 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/Persistence_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 files (*.land) of persistence diagrams files (*.pers) " - << "provided as an input.\n" - << "The first parameter of this program is a dimension of persistence that will be used in creation of " - << "the persistence heat maps." - << "If your input files contains persistence pairs of various dimension, as a first parameter of the " - << "procedure please provide the dimension of persistence you want to use." - << "If in your files there are only birth-death pairs of the same dimension, set the first parameter to " - << "-1.\n" - << "The remaining parameters are the names of files with persistence diagrams. \n"; - - if (argc < 3) { - std::cout << "Wrong parameter list, the program will now terminate \n"; - return 1; - } - std::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]); - } - - for (size_t i = 0; i != filenames.size(); ++i) { - std::cout << "Creating a landscape based on file : " << filenames[i] << std::endl; - Persistence_landscape l(filenames[i], dimension); - std::stringstream ss; - ss << filenames[i] << ".land"; - l.print_to_file(ss.str().c_str()); - } - return 0; -} diff --git a/utilities/Persistence_representations/persistence_landscapes/plot_landscapes.cpp b/utilities/Persistence_representations/persistence_landscapes/plot_landscapes.cpp deleted file mode 100644 index f32a92a1..00000000 --- a/utilities/Persistence_representations/persistence_landscapes/plot_landscapes.cpp +++ /dev/null @@ -1,43 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Pawel Dlotko - * - * Copyright (C) 2016 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/Persistence_landscape.h> - -#include <iostream> -#include <sstream> - -using Persistence_landscape = Gudhi::Persistence_representations::Persistence_landscape; - -int main(int argc, char** argv) { - std::cout << "This program creates a gnuplot script from a persistence landscape stored in a file (the file needs " - << "to be created beforehand). Please call the code with the name of a single landscape file.\n"; - if (argc != 2) { - std::cout << "Wrong parameter list, the program will now terminate \n"; - return 1; - } - - Persistence_landscape l; - l.load_landscape_from_file(argv[1]); - l.plot(argv[1]); - - return 0; -} diff --git a/utilities/Persistence_representations/persistence_landscapes_on_grid/CMakeLists.txt b/utilities/Persistence_representations/persistence_landscapes_on_grid/CMakeLists.txt deleted file mode 100644 index 36f3196b..00000000 --- a/utilities/Persistence_representations/persistence_landscapes_on_grid/CMakeLists.txt +++ /dev/null @@ -1,10 +0,0 @@ -project(Persistence_representations_lanscapes_on_grid_utilities) - -# Need to set grid min and max for further average, distance and scalar_product -add_persistence_representation_creation_utility(create_landscapes_on_grid "100" "0" "35" "-1") - -add_persistence_representation_plot_utility(plot_landscapes_on_grid ".g_land") - -add_persistence_representation_function_utility(average_landscapes_on_grid ".g_land") -add_persistence_representation_function_utility(compute_distance_of_landscapes_on_grid ".g_land" "1") -add_persistence_representation_function_utility(compute_scalar_product_of_landscapes_on_grid ".g_land") diff --git a/utilities/Persistence_representations/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp b/utilities/Persistence_representations/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp deleted file mode 100644 index 47102087..00000000 --- a/utilities/Persistence_representations/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp +++ /dev/null @@ -1,63 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Pawel Dlotko - * - * Copyright (C) 2016 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/Persistence_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 of persistence landscapes on grid stored in files (the files needs to " - << "be created beforehand).\n" - << "The 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; - } - - std::vector<const char*> filenames; - for (int i = 1; i < argc; ++i) { - filenames.push_back(argv[i]); - } - - 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 << "Average can be found in 'average.g_land' file\n"; - return 0; -} diff --git a/utilities/Persistence_representations/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp b/utilities/Persistence_representations/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp deleted file mode 100644 index 6cf2739d..00000000 --- a/utilities/Persistence_representations/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp +++ /dev/null @@ -1,93 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Pawel Dlotko - * - * Copyright (C) 2016 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/Persistence_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 computes distance of persistence landscapes on grid stored in files (the files needs to " - << "be created beforehand).\n" - << "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" - << "The remaining parameters of this program 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.g_land"); - for (size_t i = 0; i != distance.size(); ++i) { - for (size_t j = 0; j != distance.size(); ++j) { - std::cout << distance[i][j] << " "; - out << distance[i][j] << " "; - } - std::cout << std::endl; - out << std::endl; - } - out.close(); - - std::cout << "Distance can be found in 'distance.g_land' file\n"; - return 0; -} diff --git a/utilities/Persistence_representations/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp b/utilities/Persistence_representations/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp deleted file mode 100644 index 9417be6b..00000000 --- a/utilities/Persistence_representations/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp +++ /dev/null @@ -1,85 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Pawel Dlotko - * - * Copyright (C) 2016 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/Persistence_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 computes scalar product of persistence landscapes on grid stored in a file (the file needs to " - << "be created beforehand). \n" - << "The 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; - } - - 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.g_land"); - for (size_t i = 0; i != scalar_product.size(); ++i) { - for (size_t j = 0; j != scalar_product.size(); ++j) { - std::cout << scalar_product[i][j] << " "; - out << scalar_product[i][j] << " "; - } - std::cout << std::endl; - out << std::endl; - } - out.close(); - - std::cout << "Distance can be found in 'scalar_product.g_land' file\n"; - return 0; -} diff --git a/utilities/Persistence_representations/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp b/utilities/Persistence_representations/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp deleted file mode 100644 index 46e229bc..00000000 --- a/utilities/Persistence_representations/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp +++ /dev/null @@ -1,79 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Pawel Dlotko - * - * Copyright (C) 2016 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/Persistence_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 landscapes on grid files (*.g_land) of persistence diagrams files " - << "(*.pers) provided as an input.\n" - << "The first parameter of a program is an integer, a size of a grid.\n" - << "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" - << "The fourth parameter of this program is a dimension of persistence that will be used in creation of " - << "the persistence heat maps." - << "If your input files contains persistence pairs of various dimension, as a fourth parameter of the " - << "procedure please provide the dimension of persistence you want to use." - << "If in your files there are only birth-death pairs of the same dimension, set the fourth parameter to " - << "-1.\n" - << "The remaining parameters are the names of files with persistence diagrams. \n"; - - if (argc < 6) { - 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]); - } - - 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()); - } - return 0; -} diff --git a/utilities/Persistence_representations/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp b/utilities/Persistence_representations/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp deleted file mode 100644 index 39e438d2..00000000 --- a/utilities/Persistence_representations/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp +++ /dev/null @@ -1,44 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Pawel Dlotko - * - * Copyright (C) 2016 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/Persistence_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 creates a gnuplot script from a persistence landscape on grid stored in a file (the file " - << "needs to be created beforehand). Please call the code with the name of a single landscape on grid file" - << ".\n"; - if (argc != 2) { - std::cout << "Wrong parameter list, the program will now terminate \n"; - return 1; - } - - Persistence_landscape_on_grid l; - l.load_landscape_from_file(argv[1]); - l.plot(argv[1]); - - return 0; -} diff --git a/utilities/Persistence_representations/persistence_vectors/CMakeLists.txt b/utilities/Persistence_representations/persistence_vectors/CMakeLists.txt deleted file mode 100644 index bc982094..00000000 --- a/utilities/Persistence_representations/persistence_vectors/CMakeLists.txt +++ /dev/null @@ -1,9 +0,0 @@ -project(Persistence_vectors_utilities) - -add_persistence_representation_creation_utility(create_persistence_vectors "-1") - -add_persistence_representation_plot_utility(plot_persistence_vectors ".vect") - -add_persistence_representation_function_utility(average_persistence_vectors ".vect") -add_persistence_representation_function_utility(compute_distance_of_persistence_vectors ".vect" "1") -add_persistence_representation_function_utility(compute_scalar_product_of_persistence_vectors ".vect") diff --git a/utilities/Persistence_representations/persistence_vectors/average_persistence_vectors.cpp b/utilities/Persistence_representations/persistence_vectors/average_persistence_vectors.cpp deleted file mode 100644 index 45199838..00000000 --- a/utilities/Persistence_representations/persistence_vectors/average_persistence_vectors.cpp +++ /dev/null @@ -1,65 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Pawel Dlotko - * - * Copyright (C) 2016 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/Persistence_vectors.h> - -#include <iostream> -#include <vector> - -using Euclidean_distance = Gudhi::Euclidean_distance; -using Vector_distances_in_diagram = Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>; - -int main(int argc, char** argv) { - std::cout << "This program computes average of persistence vectors stored in files (the files needs to " - << "be created beforehand).\n" - << "The parameters of this programs are names of files with persistence vectors.\n"; - - if (argc < 3) { - std::cout << "Wrong number of parameters, the program will now terminate \n"; - return 1; - } - - std::vector<const char*> filenames; - for (int i = 1; i < argc; ++i) { - filenames.push_back(argv[i]); - } - - std::vector<Vector_distances_in_diagram*> lands; - for (size_t i = 0; i != filenames.size(); ++i) { - Vector_distances_in_diagram* l = new Vector_distances_in_diagram; - l->load_from_file(filenames[i]); - lands.push_back(l); - } - - Vector_distances_in_diagram av; - av.compute_average(lands); - - av.print_to_file("average.vect"); - - for (size_t i = 0; i != filenames.size(); ++i) { - delete lands[i]; - } - - std::cout << "Done \n"; - - return 0; -} diff --git a/utilities/Persistence_representations/persistence_vectors/compute_distance_of_persistence_vectors.cpp b/utilities/Persistence_representations/persistence_vectors/compute_distance_of_persistence_vectors.cpp deleted file mode 100644 index 0db7dbec..00000000 --- a/utilities/Persistence_representations/persistence_vectors/compute_distance_of_persistence_vectors.cpp +++ /dev/null @@ -1,94 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Pawel Dlotko - * - * Copyright (C) 2016 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/Persistence_vectors.h> - -#include <iostream> -#include <sstream> -#include <limits> -#include <vector> - -using Euclidean_distance = Gudhi::Euclidean_distance; -using Vector_distances_in_diagram = Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>; - -int main(int argc, char** argv) { - std::cout << "This program compute distance of persistence vectors stored in a file (the file needs to be created " - "beforehand). \n"; - std::cout << "The first parameter of a program is an integer p. The program compute l^p distance of the vectors. For " - "l^infty distance choose p = -1. \n"; - std::cout << "The remaining parameters of this programs are names of files with persistence vectors.\n"; - - if (argc < 3) { - std::cout << "Wrong number of parameters, the program will now terminate \n"; - return 1; - } - - int pp = atoi(argv[1]); - double p = std::numeric_limits<double>::max(); - if (pp != -1) { - p = pp; - } - - std::vector<const char*> filenames; - for (int i = 2; i < argc; ++i) { - filenames.push_back(argv[i]); - } - std::vector<Vector_distances_in_diagram> vectors; - vectors.reserve(filenames.size()); - for (size_t file_no = 0; file_no != filenames.size(); ++file_no) { - Vector_distances_in_diagram l; - l.load_from_file(filenames[file_no]); - vectors.push_back(l); - } - - // and now we will compute the scalar product of landscapes. - - // first we prepare an array: - std::vector<std::vector<double> > distance(filenames.size()); - for (size_t i = 0; i != filenames.size(); ++i) { - std::vector<double> v(filenames.size(), 0); - distance[i] = v; - } - - // and now we can compute the distances: - for (size_t i = 0; i != vectors.size(); ++i) { - for (size_t j = i + 1; j != vectors.size(); ++j) { - distance[i][j] = distance[j][i] = vectors[i].distance(vectors[j], p); - } - } - - // and now output the result to the screen and a file: - std::ofstream out; - out.open("distance.vect"); - for (size_t i = 0; i != distance.size(); ++i) { - for (size_t j = 0; j != distance.size(); ++j) { - std::cout << distance[i][j] << " "; - out << distance[i][j] << " "; - } - std::cout << std::endl; - out << std::endl; - } - out.close(); - - std::cout << "Distance can be found in 'distance.vect' file\n"; - return 0; -} diff --git a/utilities/Persistence_representations/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp b/utilities/Persistence_representations/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp deleted file mode 100644 index 8e99251b..00000000 --- a/utilities/Persistence_representations/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp +++ /dev/null @@ -1,86 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Pawel Dlotko - * - * Copyright (C) 2016 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/Persistence_vectors.h> - -#include <iostream> -#include <sstream> -#include <limits> -#include <vector> - -using Euclidean_distance = Gudhi::Euclidean_distance; -using Vector_distances_in_diagram = Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>; - -int main(int argc, char** argv) { - std::cout << "This program computes scalar product of persistence vectors stored in a file (the file needs to " - << "be created beforehand). \n" - << "The parameters of this programs are names of files with persistence vectors.\n"; - - if (argc < 3) { - std::cout << "Wrong number of parameters, the program will now terminate \n"; - return 1; - } - - std::vector<const char*> filenames; - for (int i = 1; i < argc; ++i) { - filenames.push_back(argv[i]); - } - std::vector<Vector_distances_in_diagram> vectors; - vectors.reserve(filenames.size()); - for (size_t file_no = 0; file_no != filenames.size(); ++file_no) { - Vector_distances_in_diagram l; - l.load_from_file(filenames[file_no]); - vectors.push_back(l); - } - - // and now we will compute the scalar product of landscapes. - - // first we prepare an array: - std::vector<std::vector<double> > scalar_product(filenames.size()); - for (size_t i = 0; i != filenames.size(); ++i) { - std::vector<double> v(filenames.size(), 0); - scalar_product[i] = v; - } - - // and now we can compute the scalar product: - for (size_t i = 0; i != vectors.size(); ++i) { - for (size_t j = i; j != vectors.size(); ++j) { - scalar_product[i][j] = scalar_product[j][i] = vectors[i].compute_scalar_product(vectors[j]); - } - } - - // and now output the result to the screen and a file: - std::ofstream out; - out.open("scalar_product.vect"); - for (size_t i = 0; i != scalar_product.size(); ++i) { - for (size_t j = 0; j != scalar_product.size(); ++j) { - std::cout << scalar_product[i][j] << " "; - out << scalar_product[i][j] << " "; - } - std::cout << std::endl; - out << std::endl; - } - out.close(); - - std::cout << "Distance can be found in 'scalar_product.vect' file\n"; - return 0; -} diff --git a/utilities/Persistence_representations/persistence_vectors/create_persistence_vectors.cpp b/utilities/Persistence_representations/persistence_vectors/create_persistence_vectors.cpp deleted file mode 100644 index 364284e5..00000000 --- a/utilities/Persistence_representations/persistence_vectors/create_persistence_vectors.cpp +++ /dev/null @@ -1,69 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Pawel Dlotko - * - * Copyright (C) 2016 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/Persistence_vectors.h> - -#include <iostream> -#include <sstream> -#include <limits> -#include <vector> - -using Euclidean_distance = Gudhi::Euclidean_distance; -using Vector_distances_in_diagram = Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>; - -int main(int argc, char** argv) { - std::cout << "This program creates persistence vectors files (*.vect) of persistence diagrams files (*.pers) " - << "provided as an input.\n" - << "The first parameter of this program is a dimension of persistence that will be used in creation of " - << "the persistence heat maps." - << "If your input files contains persistence pairs of various dimension, as a first parameter of the " - << "procedure please provide the dimension of persistence you want to use." - << "If in your files there are only birth-death pairs of the same dimension, set the first parameter to " - << "-1.\n" - << "The remaining parameters are the names of files with persistence diagrams. \n"; - - if (argc < 3) { - std::cout << "Wrong parameter list, the program will now terminate \n"; - return 1; - } - - std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; - int dim = atoi(argv[1]); - unsigned dimension = std::numeric_limits<unsigned>::max(); - if (dim >= 0) { - dimension = (unsigned)dim; - } - - std::vector<const char*> filenames; - for (int i = 2; i < argc; ++i) { - filenames.push_back(argv[i]); - } - - for (size_t i = 0; i != filenames.size(); ++i) { - std::cerr << "Creating persistence vectors based on a file : " << filenames[i] << std::endl; - Vector_distances_in_diagram l(filenames[i], dimension); - std::stringstream ss; - ss << filenames[i] << ".vect"; - l.print_to_file(ss.str().c_str()); - } - return 0; -} diff --git a/utilities/Persistence_representations/persistence_vectors/plot_persistence_vectors.cpp b/utilities/Persistence_representations/persistence_vectors/plot_persistence_vectors.cpp deleted file mode 100644 index 550e47c5..00000000 --- a/utilities/Persistence_representations/persistence_vectors/plot_persistence_vectors.cpp +++ /dev/null @@ -1,43 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Pawel Dlotko - * - * Copyright (C) 2016 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/Persistence_vectors.h> - -#include <iostream> -#include <sstream> - -using Euclidean_distance = Gudhi::Euclidean_distance; -using Vector_distances_in_diagram = Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>; - -int main(int argc, char** argv) { - std::cout << "This program create a Gnuplot script to plot persistence vector. Please call this program with the " - "name of file with persistence vector. \n"; - if (argc != 2) { - std::cout << "Wrong number of parameters, the program will now terminate. \n"; - return 1; - } - Vector_distances_in_diagram l; - l.load_from_file(argv[1]); - l.plot(argv[1]); - - return 0; -} |