From 9899ae167f281d10b1684dfcd02c6838c5bf28df Mon Sep 17 00:00:00 2001 From: Gard Spreemann Date: Fri, 2 Feb 2018 13:51:45 +0100 Subject: GUDHI 2.1.0 as released by upstream in a tarball. --- .../Persistence_representations/CMakeLists.txt | 53 ++++++++++++ .../persistence_heat_maps/CMakeLists.txt | 15 ++++ .../average_persistence_heat_maps.cpp | 63 ++++++++++++++ .../compute_distance_of_persistence_heat_maps.cpp | 94 +++++++++++++++++++++ ...ute_scalar_product_of_persistence_heat_maps.cpp | 85 +++++++++++++++++++ ...h_m_weighted_by_arctan_of_their_persistence.cpp | 81 ++++++++++++++++++ ...te_p_h_m_weighted_by_distance_from_diagonal.cpp | 81 ++++++++++++++++++ ...ate_p_h_m_weighted_by_squared_diag_distance.cpp | 83 +++++++++++++++++++ .../create_persistence_heat_maps.cpp | 78 ++++++++++++++++++ .../persistence_heat_maps/create_pssk.cpp | 79 ++++++++++++++++++ .../plot_persistence_heat_map.cpp | 42 ++++++++++ .../persistence_intervals/CMakeLists.txt | 32 ++++++++ ...te_birth_death_range_in_persistence_diagram.cpp | 68 ++++++++++++++++ .../compute_bottleneck_distance.cpp | 95 ++++++++++++++++++++++ .../compute_number_of_dominant_intervals.cpp | 54 ++++++++++++ .../plot_histogram_of_intervals_lengths.cpp | 77 ++++++++++++++++++ .../plot_persistence_Betti_numbers.cpp | 87 ++++++++++++++++++++ .../plot_persistence_intervals.cpp | 53 ++++++++++++ .../persistence_landscapes/CMakeLists.txt | 10 +++ .../persistence_landscapes/average_landscapes.cpp | 63 ++++++++++++++ .../compute_distance_of_landscapes.cpp | 93 +++++++++++++++++++++ .../compute_scalar_product_of_landscapes.cpp | 84 +++++++++++++++++++ .../persistence_landscapes/create_landscapes.cpp | 65 +++++++++++++++ .../persistence_landscapes/plot_landscapes.cpp | 43 ++++++++++ .../persistence_landscapes_on_grid/CMakeLists.txt | 11 +++ .../average_landscapes_on_grid.cpp | 63 ++++++++++++++ .../compute_distance_of_landscapes_on_grid.cpp | 93 +++++++++++++++++++++ ...ompute_scalar_product_of_landscapes_on_grid.cpp | 85 +++++++++++++++++++ .../create_landscapes_on_grid.cpp | 79 ++++++++++++++++++ .../plot_landscapes_on_grid.cpp | 44 ++++++++++ .../persistence_vectors/CMakeLists.txt | 10 +++ .../average_persistence_vectors.cpp | 65 +++++++++++++++ .../compute_distance_of_persistence_vectors.cpp | 94 +++++++++++++++++++++ ...mpute_scalar_product_of_persistence_vectors.cpp | 86 ++++++++++++++++++++ .../create_persistence_vectors.cpp | 69 ++++++++++++++++ .../plot_persistence_vectors.cpp | 43 ++++++++++ 36 files changed, 2320 insertions(+) create mode 100644 utilities/Persistence_representations/CMakeLists.txt create mode 100644 utilities/Persistence_representations/persistence_heat_maps/CMakeLists.txt create mode 100644 utilities/Persistence_representations/persistence_heat_maps/average_persistence_heat_maps.cpp create mode 100644 utilities/Persistence_representations/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp create mode 100644 utilities/Persistence_representations/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp create mode 100644 utilities/Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp create mode 100644 utilities/Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp create mode 100644 utilities/Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp create mode 100644 utilities/Persistence_representations/persistence_heat_maps/create_persistence_heat_maps.cpp create mode 100644 utilities/Persistence_representations/persistence_heat_maps/create_pssk.cpp create mode 100644 utilities/Persistence_representations/persistence_heat_maps/plot_persistence_heat_map.cpp create mode 100644 utilities/Persistence_representations/persistence_intervals/CMakeLists.txt create mode 100644 utilities/Persistence_representations/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp create mode 100644 utilities/Persistence_representations/persistence_intervals/compute_bottleneck_distance.cpp create mode 100644 utilities/Persistence_representations/persistence_intervals/compute_number_of_dominant_intervals.cpp create mode 100644 utilities/Persistence_representations/persistence_intervals/plot_histogram_of_intervals_lengths.cpp create mode 100644 utilities/Persistence_representations/persistence_intervals/plot_persistence_Betti_numbers.cpp create mode 100644 utilities/Persistence_representations/persistence_intervals/plot_persistence_intervals.cpp create mode 100644 utilities/Persistence_representations/persistence_landscapes/CMakeLists.txt create mode 100644 utilities/Persistence_representations/persistence_landscapes/average_landscapes.cpp create mode 100644 utilities/Persistence_representations/persistence_landscapes/compute_distance_of_landscapes.cpp create mode 100644 utilities/Persistence_representations/persistence_landscapes/compute_scalar_product_of_landscapes.cpp create mode 100644 utilities/Persistence_representations/persistence_landscapes/create_landscapes.cpp create mode 100644 utilities/Persistence_representations/persistence_landscapes/plot_landscapes.cpp create mode 100644 utilities/Persistence_representations/persistence_landscapes_on_grid/CMakeLists.txt create mode 100644 utilities/Persistence_representations/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp create mode 100644 utilities/Persistence_representations/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp create mode 100644 utilities/Persistence_representations/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp create mode 100644 utilities/Persistence_representations/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp create mode 100644 utilities/Persistence_representations/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp create mode 100644 utilities/Persistence_representations/persistence_vectors/CMakeLists.txt create mode 100644 utilities/Persistence_representations/persistence_vectors/average_persistence_vectors.cpp create mode 100644 utilities/Persistence_representations/persistence_vectors/compute_distance_of_persistence_vectors.cpp create mode 100644 utilities/Persistence_representations/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp create mode 100644 utilities/Persistence_representations/persistence_vectors/create_persistence_vectors.cpp create mode 100644 utilities/Persistence_representations/persistence_vectors/plot_persistence_vectors.cpp (limited to 'utilities/Persistence_representations') diff --git a/utilities/Persistence_representations/CMakeLists.txt b/utilities/Persistence_representations/CMakeLists.txt new file mode 100644 index 00000000..137eb0c1 --- /dev/null +++ b/utilities/Persistence_representations/CMakeLists.txt @@ -0,0 +1,53 @@ +# 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 $ + ${ARGN} "${CMAKE_CURRENT_BINARY_DIR}/../first.pers" + "${CMAKE_CURRENT_BINARY_DIR}/../second.pers") +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 $ + "${CMAKE_CURRENT_BINARY_DIR}/../first.pers${tool_extension}") + #add_test(NAME Persistence_representation_utilities_${plot_utility}_second COMMAND $ + # "${CMAKE_CURRENT_BINARY_DIR}/../second.pers${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() +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 $ + "${ARGV2}" + "${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 $ + "${CMAKE_CURRENT_BINARY_DIR}/../first.pers${tool_extension}" + "${CMAKE_CURRENT_BINARY_DIR}/../second.pers${tool_extension}") + endif() +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 new file mode 100644 index 00000000..386e9fa5 --- /dev/null +++ b/utilities/Persistence_representations/persistence_heat_maps/CMakeLists.txt @@ -0,0 +1,15 @@ +cmake_minimum_required(VERSION 2.6) +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 new file mode 100644 index 00000000..6739e0b6 --- /dev/null +++ b/utilities/Persistence_representations/persistence_heat_maps/average_persistence_heat_maps.cpp @@ -0,0 +1,63 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include + +#include +#include + +using constant_scaling_function = Gudhi::Persistence_representations::constant_scaling_function; +using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps; + +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 filenames; + for (int i = 1; i < argc; ++i) { + filenames.push_back(argv[i]); + } + + std::vector 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 new file mode 100644 index 00000000..ed8278a2 --- /dev/null +++ b/utilities/Persistence_representations/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp @@ -0,0 +1,94 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include + +#include +#include +#include +#include + +using constant_scaling_function = Gudhi::Persistence_representations::constant_scaling_function; +using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps; + +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::max(); + if (pp != -1) { + p = pp; + } + + std::vector filenames; + for (int i = 2; i < argc; ++i) { + filenames.push_back(argv[i]); + } + std::vector 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 > distance(filenames.size()); + for (size_t i = 0; i != filenames.size(); ++i) { + std::vector 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 new file mode 100644 index 00000000..63626853 --- /dev/null +++ b/utilities/Persistence_representations/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp @@ -0,0 +1,85 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include + +#include +#include +#include + +using constant_scaling_function = Gudhi::Persistence_representations::constant_scaling_function; +using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps; + +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 filenames; + for (int i = 1; i < argc; ++i) { + filenames.push_back(argv[i]); + } + std::vector 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 > scalar_product(filenames.size()); + for (size_t i = 0; i != filenames.size(); ++i) { + std::vector 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 new file mode 100644 index 00000000..b4a1daa5 --- /dev/null +++ b/utilities/Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp @@ -0,0 +1,81 @@ +/* This file is part of the Gudhi Library. The Gudhi library +* (Geometric Understanding in Higher Dimensions) is a generic C++ +* library for computational topology. +* +* Author(s): Pawel Dlotko +* +* Copyright (C) 2016 INRIA (France) +* +* This program is free software: you can redistribute it and/or modify +* it under the terms of the GNU General Public License as published by +* the Free Software Foundation, either version 3 of the License, or +* (at your option) any later version. +* +* This program is distributed in the hope that it will be useful, +* but WITHOUT ANY WARRANTY; without even the implied warranty of +* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +* GNU General Public License for more details. +* +* You should have received a copy of the GNU General Public License +* along with this program. If not, see . +*/ + +#include + +#include +#include +#include +#include + +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; + +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::max(); + int dim = atoi(argv[5]); + if (dim >= 0) { + dimension = (unsigned)dim; + } + + std::vector filenames; + for (int i = 6; i < argc; ++i) { + filenames.push_back(argv[i]); + } + + std::vector > 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 new file mode 100644 index 00000000..c50f9ddb --- /dev/null +++ b/utilities/Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp @@ -0,0 +1,81 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include + +#include +#include +#include +#include + +using distance_from_diagonal_scaling = Gudhi::Persistence_representations::distance_from_diagonal_scaling; +using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps; + +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::max(); + int dim = atoi(argv[5]); + if (dim >= 0) { + dimension = (unsigned)dim; + } + + std::vector filenames; + for (int i = 6; i != argc; ++i) { + filenames.push_back(argv[i]); + } + + std::vector > 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 new file mode 100644 index 00000000..59ff3c24 --- /dev/null +++ b/utilities/Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp @@ -0,0 +1,83 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include + +#include +#include +#include +#include + +using squared_distance_from_diagonal_scaling = + Gudhi::Persistence_representations::squared_distance_from_diagonal_scaling; +using Persistence_heat_maps = + Gudhi::Persistence_representations::Persistence_heat_maps; + +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::max(); + int dim = atoi(argv[5]); + if (dim >= 0) { + dimension = (unsigned)dim; + } + + std::vector filenames; + for (int i = 6; i < argc; ++i) { + filenames.push_back(argv[i]); + } + + std::vector > 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 new file mode 100644 index 00000000..25cd1067 --- /dev/null +++ b/utilities/Persistence_representations/persistence_heat_maps/create_persistence_heat_maps.cpp @@ -0,0 +1,78 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include + +#include +#include +#include +#include + +using constant_scaling_function = Gudhi::Persistence_representations::constant_scaling_function; +using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps; + +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::max(); + int dim = atoi(argv[5]); + if (dim >= 0) { + dimension = (unsigned)dim; + } + std::vector filenames; + for (int i = 6; i < argc; ++i) { + filenames.push_back(argv[i]); + } + + std::vector > 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 new file mode 100644 index 00000000..97ddb8f0 --- /dev/null +++ b/utilities/Persistence_representations/persistence_heat_maps/create_pssk.cpp @@ -0,0 +1,79 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include + +#include +#include +#include +#include + +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::max(); + int dim = atoi(argv[5]); + if (dim >= 0) { + dimension = (unsigned)dim; + } + + std::vector filenames; + for (int i = 6; i < argc; ++i) { + filenames.push_back(argv[i]); + } + + std::vector > 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 new file mode 100644 index 00000000..63711d83 --- /dev/null +++ b/utilities/Persistence_representations/persistence_heat_maps/plot_persistence_heat_map.cpp @@ -0,0 +1,42 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include + +#include +#include + +using constant_scaling_function = Gudhi::Persistence_representations::constant_scaling_function; +using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps; + +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 new file mode 100644 index 00000000..897e12a3 --- /dev/null +++ b/utilities/Persistence_representations/persistence_intervals/CMakeLists.txt @@ -0,0 +1,32 @@ +cmake_minimum_required(VERSION 2.6) +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 $ + "${CMAKE_CURRENT_BINARY_DIR}/../first.pers" "-1") + +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 $ + "${CMAKE_CURRENT_BINARY_DIR}/../first.pers" "-1" "2") + + +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 $ + "-1" + "${CMAKE_CURRENT_BINARY_DIR}/../first.pers" + "${CMAKE_CURRENT_BINARY_DIR}/../second.pers") +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 new file mode 100644 index 00000000..9102da79 --- /dev/null +++ b/utilities/Persistence_representations/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp @@ -0,0 +1,68 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include + +#include +#include +#include +#include + +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::max(); + int dim = atoi(argv[1]); + if (dim >= 0) { + dimension = (unsigned)dim; + } + std::vector filenames; + for (int i = 2; i < argc; ++i) { + filenames.push_back(argv[i]); + } + + double min_ = std::numeric_limits::max(); + double max_ = -std::numeric_limits::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 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 new file mode 100644 index 00000000..c8290845 --- /dev/null +++ b/utilities/Persistence_representations/persistence_intervals/compute_bottleneck_distance.cpp @@ -0,0 +1,95 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include + +#include +#include +#include +#include + +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::max(); + int dim = atoi(argv[1]); + if (dim >= 0) { + dimension = (unsigned)dim; + } + + std::vector filenames; + for (int i = 2; i < argc; ++i) { + filenames.push_back(argv[i]); + } + + // reading the persistence intervals: + std::vector 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 > distance(filenames.size()); + for (size_t i = 0; i != filenames.size(); ++i) { + std::vector 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 new file mode 100644 index 00000000..b3d126f0 --- /dev/null +++ b/utilities/Persistence_representations/persistence_intervals/compute_number_of_dominant_intervals.cpp @@ -0,0 +1,54 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include + +#include +#include +#include +#include + +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::max(); + if (dim >= 0) { + dimension = (unsigned)dim; + } + Persistence_intervals p(argv[1], dimension); + std::vector > 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 new file mode 100644 index 00000000..ccb5b645 --- /dev/null +++ b/utilities/Persistence_representations/persistence_intervals/plot_histogram_of_intervals_lengths.cpp @@ -0,0 +1,77 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include + +#include +#include +#include +#include + +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::max(); + int nbr = atoi(argv[2]); + if (nbr >= 0) { + dominant_interval_number = static_cast(nbr); + } + + int persistence_dimension = -1; + if (argc == 4) { + persistence_dimension = atoi(argv[3]); + } + + Persistence_intervals p(argv[1], dominant_interval_number); + std::vector > dominant_intervals = p.dominant_intervals(persistence_dimension); + std::vector 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 new file mode 100644 index 00000000..b433c2b3 --- /dev/null +++ b/utilities/Persistence_representations/persistence_intervals/plot_persistence_Betti_numbers.cpp @@ -0,0 +1,87 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include + +#include +#include +#include +#include + +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::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 > 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 new file mode 100644 index 00000000..33387802 --- /dev/null +++ b/utilities/Persistence_representations/persistence_intervals/plot_persistence_intervals.cpp @@ -0,0 +1,53 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include + +#include +#include +#include +#include + +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::max(); + int dim = -1; + if (argc == 3) { + dim = atoi(argv[2]); + } + if (dim >= 0) { + dimension = (unsigned)dim; + } + std::vector > 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 new file mode 100644 index 00000000..d7087ed8 --- /dev/null +++ b/utilities/Persistence_representations/persistence_landscapes/CMakeLists.txt @@ -0,0 +1,10 @@ +cmake_minimum_required(VERSION 2.6) +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 new file mode 100644 index 00000000..1a59be8c --- /dev/null +++ b/utilities/Persistence_representations/persistence_landscapes/average_landscapes.cpp @@ -0,0 +1,63 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include + +#include +#include + +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 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 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 new file mode 100644 index 00000000..5062f521 --- /dev/null +++ b/utilities/Persistence_representations/persistence_landscapes/compute_distance_of_landscapes.cpp @@ -0,0 +1,93 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include + +#include +#include +#include +#include + +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::max(); + if (pp != -1) { + p = pp; + } + + std::vector filenames; + for (int i = 2; i < argc; ++i) { + filenames.push_back(argv[i]); + } + std::vector 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 > distance(filenames.size()); + for (size_t i = 0; i != filenames.size(); ++i) { + std::vector 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 new file mode 100644 index 00000000..5b5e9fa3 --- /dev/null +++ b/utilities/Persistence_representations/persistence_landscapes/compute_scalar_product_of_landscapes.cpp @@ -0,0 +1,84 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include + +#include +#include +#include + +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 filenames; + for (int i = 1; i < argc; ++i) { + filenames.push_back(argv[i]); + } + std::vector 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 > scalar_product(filenames.size()); + for (size_t i = 0; i != filenames.size(); ++i) { + std::vector 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 new file mode 100644 index 00000000..6030e994 --- /dev/null +++ b/utilities/Persistence_representations/persistence_landscapes/create_landscapes.cpp @@ -0,0 +1,65 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include + +#include +#include +#include +#include + +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 filenames; + int dim = atoi(argv[1]); + unsigned dimension = std::numeric_limits::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 new file mode 100644 index 00000000..c797a7a8 --- /dev/null +++ b/utilities/Persistence_representations/persistence_landscapes/plot_landscapes.cpp @@ -0,0 +1,43 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include + +#include +#include + +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 new file mode 100644 index 00000000..c5ea4bbf --- /dev/null +++ b/utilities/Persistence_representations/persistence_landscapes_on_grid/CMakeLists.txt @@ -0,0 +1,11 @@ +cmake_minimum_required(VERSION 2.6) +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 new file mode 100644 index 00000000..0b098d1a --- /dev/null +++ b/utilities/Persistence_representations/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp @@ -0,0 +1,63 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include + +#include +#include + +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 filenames; + for (int i = 1; i < argc; ++i) { + filenames.push_back(argv[i]); + } + + std::vector 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 new file mode 100644 index 00000000..fd0fcd15 --- /dev/null +++ b/utilities/Persistence_representations/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp @@ -0,0 +1,93 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include + +#include +#include +#include +#include + +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::max(); + if (pp != -1) { + p = pp; + } + + std::vector filenames; + for (int i = 2; i < argc; ++i) { + filenames.push_back(argv[i]); + } + std::vector 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 > distance(filenames.size()); + for (size_t i = 0; i != filenames.size(); ++i) { + std::vector 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 new file mode 100644 index 00000000..01de3dee --- /dev/null +++ b/utilities/Persistence_representations/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp @@ -0,0 +1,85 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include + +#include +#include +#include + +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 filenames; + for (int i = 1; i < argc; ++i) { + filenames.push_back(argv[i]); + } + std::vector 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 > scalar_product(filenames.size()); + for (size_t i = 0; i != filenames.size(); ++i) { + std::vector 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 new file mode 100644 index 00000000..78e8ef57 --- /dev/null +++ b/utilities/Persistence_representations/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp @@ -0,0 +1,79 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include + +#include +#include +#include +#include + +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::max(); + if (dim >= 0) { + dimension = (unsigned)dim; + } + + std::vector 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 new file mode 100644 index 00000000..dddb3615 --- /dev/null +++ b/utilities/Persistence_representations/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp @@ -0,0 +1,44 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include + +#include +#include + +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 new file mode 100644 index 00000000..a401c955 --- /dev/null +++ b/utilities/Persistence_representations/persistence_vectors/CMakeLists.txt @@ -0,0 +1,10 @@ +cmake_minimum_required(VERSION 2.6) +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 new file mode 100644 index 00000000..0144e76f --- /dev/null +++ b/utilities/Persistence_representations/persistence_vectors/average_persistence_vectors.cpp @@ -0,0 +1,65 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include + +#include +#include + +using Euclidean_distance = Gudhi::Euclidean_distance; +using Vector_distances_in_diagram = Gudhi::Persistence_representations::Vector_distances_in_diagram; + +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 filenames; + for (int i = 1; i < argc; ++i) { + filenames.push_back(argv[i]); + } + + std::vector 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 new file mode 100644 index 00000000..7e66d25e --- /dev/null +++ b/utilities/Persistence_representations/persistence_vectors/compute_distance_of_persistence_vectors.cpp @@ -0,0 +1,94 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include + +#include +#include +#include +#include + +using Euclidean_distance = Gudhi::Euclidean_distance; +using Vector_distances_in_diagram = Gudhi::Persistence_representations::Vector_distances_in_diagram; + +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::max(); + if (pp != -1) { + p = pp; + } + + std::vector filenames; + for (int i = 2; i < argc; ++i) { + filenames.push_back(argv[i]); + } + std::vector 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 > distance(filenames.size()); + for (size_t i = 0; i != filenames.size(); ++i) { + std::vector 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 new file mode 100644 index 00000000..303c6e3e --- /dev/null +++ b/utilities/Persistence_representations/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp @@ -0,0 +1,86 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include + +#include +#include +#include +#include + +using Euclidean_distance = Gudhi::Euclidean_distance; +using Vector_distances_in_diagram = Gudhi::Persistence_representations::Vector_distances_in_diagram; + +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 filenames; + for (int i = 1; i < argc; ++i) { + filenames.push_back(argv[i]); + } + std::vector 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 > scalar_product(filenames.size()); + for (size_t i = 0; i != filenames.size(); ++i) { + std::vector 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 new file mode 100644 index 00000000..cc5e5393 --- /dev/null +++ b/utilities/Persistence_representations/persistence_vectors/create_persistence_vectors.cpp @@ -0,0 +1,69 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include + +#include +#include +#include +#include + +using Euclidean_distance = Gudhi::Euclidean_distance; +using Vector_distances_in_diagram = Gudhi::Persistence_representations::Vector_distances_in_diagram; + +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::max(); + if (dim >= 0) { + dimension = (unsigned)dim; + } + + std::vector 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 new file mode 100644 index 00000000..aa33107d --- /dev/null +++ b/utilities/Persistence_representations/persistence_vectors/plot_persistence_vectors.cpp @@ -0,0 +1,43 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include + +#include +#include + +using Euclidean_distance = Gudhi::Euclidean_distance; +using Vector_distances_in_diagram = Gudhi::Persistence_representations::Vector_distances_in_diagram; + +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; +} -- cgit v1.2.3