diff options
Diffstat (limited to 'src/Persistence_representation/utilities/persistence_landscapes')
7 files changed, 423 insertions, 0 deletions
diff --git a/src/Persistence_representation/utilities/persistence_landscapes/CMakeLists.txt b/src/Persistence_representation/utilities/persistence_landscapes/CMakeLists.txt new file mode 100644 index 00000000..43533102 --- /dev/null +++ b/src/Persistence_representation/utilities/persistence_landscapes/CMakeLists.txt @@ -0,0 +1,26 @@ +cmake_minimum_required(VERSION 2.6) +project(GUDHI_STAT) + + + +#persitence landscapes +add_executable ( create_landscapes create_landscapes.cpp ) +target_link_libraries(create_landscapes ${Boost_SYSTEM_LIBRARY}) +add_test ( create_landscapes ${CMAKE_CURRENT_BINARY_DIR}/create_landscapes -1 "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" ) + +add_executable ( average_landscapes average_landscapes.cpp ) +target_link_libraries(average_landscapes ${Boost_SYSTEM_LIBRARY}) +add_test ( average_landscapes ${CMAKE_CURRENT_BINARY_DIR}/average_landscapes "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt.land" "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt.land" ) + +add_executable ( plot_landscapes plot_landscapes.cpp ) +target_link_libraries(plot_landscapes ${Boost_SYSTEM_LIBRARY}) +add_test ( plot_landscapes ${CMAKE_CURRENT_BINARY_DIR}/plot_landscapes "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt.land" ) + +add_executable ( compute_distance_of_landscapes compute_distance_of_landscapes.cpp ) +target_link_libraries(compute_distance_of_landscapes ${Boost_SYSTEM_LIBRARY}) +add_test ( compute_distance_of_landscapes ${CMAKE_CURRENT_BINARY_DIR}/compute_distance_of_landscapes 1 "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt.land" "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt.land" ) + +add_executable ( compute_scalar_product_of_landscapes compute_scalar_product_of_landscapes.cpp ) +target_link_libraries(compute_scalar_product_of_landscapes ${Boost_SYSTEM_LIBRARY}) +add_test ( compute_scalar_product_of_landscapes ${CMAKE_CURRENT_BINARY_DIR}/compute_scalar_product_of_landscapes "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt.land" "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt.land" ) + diff --git a/src/Persistence_representation/utilities/persistence_landscapes/average_landscapes.cpp b/src/Persistence_representation/utilities/persistence_landscapes/average_landscapes.cpp new file mode 100644 index 00000000..1e0caa30 --- /dev/null +++ b/src/Persistence_representation/utilities/persistence_landscapes/average_landscapes.cpp @@ -0,0 +1,74 @@ +/* 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) 2015 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + + + +#include <gudhi/Persistence_landscape.h> + + + +using namespace Gudhi; +using namespace Gudhi::Persistence_representations; + +#include <iostream> + + +int main( int argc , char** argv ) +{ + std::cout << "This program computes average persistence landscape of persistence landscapes created based on persistence diagrams provided as an input (you must create them first).\n"; + std::cout << "Please call this program with the names of files with persistence landscapes. The program will create a persistence landscape which will be their average \n"; + std::vector< const char* > filenames; + + if ( argc == 1 ) + { + std::cout << "No input files given, the program will now terminate \n"; + return 1; + } + + for ( int i = 1 ; i < argc ; ++i ) + { + filenames.push_back( argv[i] ); + } + + std::cout << "Creating persistence landscapes...\n"; + std::vector< Persistence_landscape* > lands; + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + Persistence_landscape* l = new Persistence_landscape; + l->load_landscape_from_file( filenames[i] ); + lands.push_back( l ); + } + + Persistence_landscape av; + av.compute_average( lands ); + + av.print_to_file( "average.land" ); + + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + delete lands[i]; + } + + std::cout << "Done \n"; + + return 0; +} diff --git a/src/Persistence_representation/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp b/src/Persistence_representation/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp new file mode 100644 index 00000000..85954cb2 --- /dev/null +++ b/src/Persistence_representation/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp @@ -0,0 +1,112 @@ +/* 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) 2015 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#include <gudhi/Persistence_landscape.h> + + + +using namespace Gudhi; +using namespace Gudhi::Persistence_representations; + +#include <iostream> +#include <sstream> + + +int main( int argc , char** argv ) +{ + std::cout << "This program compute distance of persistence landscapes stored in a file (the file needs to be created beforehand). \n"; + std::cout << "The first parameter of a program is an interger p. The program compute L^p distance of the given landscapes. For L^infty distance choose p = -1. \n"; + std::cout << "The remaining parameters of this programs are names of files with persistence landscapes."; + + if ( argc < 3 ) + { + std::cout << "Wrong number of parameters, the program will now terminate \n"; + return 1; + } + + int pp = atoi( argv[1] ); + double p = std::numeric_limits<double>::max(); + if ( pp != -1 ) + { + p = pp; + } + + + std::vector< const char* > filenames; + for ( int i = 2 ; i < argc ; ++i ) + { + filenames.push_back( argv[i] ); + } + std::vector< Persistence_landscape > landscaspes; + landscaspes.reserve( filenames.size() ); + for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no ) + { + std::cout << "Loading persistence landscape from a file : " << filenames[file_no] << std::endl; + Persistence_landscape l; + l.load_landscape_from_file( filenames[file_no] ); + landscaspes.push_back( l ); + } + + //and now we will compute the scalar product of landscapes. + + //first we prepare an array: + std::vector< std::vector< double > > distance( filenames.size() ); + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + std::vector< double > v( filenames.size() , 0 ); + distance[i] = v; + } + + //and now we can compute the distances: + for ( size_t i = 0 ; i != landscaspes.size() ; ++i ) + { + for ( size_t j = i ; j != landscaspes.size() ; ++j ) + { + distance[i][j] = distance[j][i] = compute_distance_of_landscapes( landscaspes[i], landscaspes[j] , p ) ; + + } + } + + //and now output the result to the screen and a file: + std::ofstream out; + out.open( "distance" ); + for ( size_t i = 0 ; i != distance.size() ; ++i ) + { + for ( size_t j = 0 ; j != distance.size() ; ++j ) + { + std::cout << distance[i][j] << " "; + out << distance[i][j] << " "; + } + std::cout << std::endl; + out << std::endl; + } + out.close(); + + return 0; +} + + + + + + + diff --git a/src/Persistence_representation/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp b/src/Persistence_representation/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp new file mode 100644 index 00000000..02b729b2 --- /dev/null +++ b/src/Persistence_representation/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp @@ -0,0 +1,89 @@ +/* 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) 2015 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#include <gudhi/Persistence_landscape.h> + + + +using namespace Gudhi; +using namespace Gudhi::Persistence_representations; + +#include <iostream> +#include <sstream> + + +int main( int argc , char** argv ) +{ + std::cout << "This program compute scalar product of persistence landscapes stored in a file (the file needs to be created beforehand). \n"; + std::cout << "The parameters of this programs are names of files with persistence landscapes.\n"; + + std::vector< const char* > filenames; + for ( int i = 1 ; i < argc ; ++i ) + { + filenames.push_back( argv[i] ); + } + std::vector< Persistence_landscape > landscaspes; + landscaspes.reserve( filenames.size() ); + for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no ) + { + std::cout << "Reading persistence landscape from a file : " << filenames[file_no] << std::endl; + Persistence_landscape l; + l.load_landscape_from_file( filenames[file_no] ); + landscaspes.push_back( l ); + } + + //and now we will compute the scalar product of landscapes. + + //first we prepare an array: + std::vector< std::vector< double > > scalar_product( filenames.size() ); + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + std::vector< double > v( filenames.size() , 0 ); + scalar_product[i] = v; + } + + //and now we can compute the scalar product: + for ( size_t i = 0 ; i != landscaspes.size() ; ++i ) + { + for ( size_t j = i ; j != landscaspes.size() ; ++j ) + { + scalar_product[i][j] = scalar_product[j][i] = compute_inner_product( landscaspes[i], landscaspes[j] ) ; + } + } + + //and now output the result to the screen and a file: + std::ofstream out; + out.open( "scalar_product" ); + for ( size_t i = 0 ; i != scalar_product.size() ; ++i ) + { + for ( size_t j = 0 ; j != scalar_product.size() ; ++j ) + { + std::cout << scalar_product[i][j] << " "; + out << scalar_product[i][j] << " "; + } + std::cout << std::endl; + out << std::endl; + } + out.close(); + + return 0; +} diff --git a/src/Persistence_representation/utilities/persistence_landscapes/create_landscapes.cpp b/src/Persistence_representation/utilities/persistence_landscapes/create_landscapes.cpp new file mode 100644 index 00000000..b85c8644 --- /dev/null +++ b/src/Persistence_representation/utilities/persistence_landscapes/create_landscapes.cpp @@ -0,0 +1,62 @@ +/* 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) 2015 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#include <gudhi/Persistence_landscape.h> + + +using namespace Gudhi; +using namespace Gudhi::Persistence_representations; + +#include <iostream> +#include <sstream> + + +int main( int argc , char** argv ) +{ + std::cout << "This program creates persistence landscapes of diagrams provided as an input. \n"; + std::cout << "The first parameter of the program is the dimension of persistence to be used to construct persistence landscapes. If your file contains "; + std::cout << "the information about dimension of persistence pairs, please provide here the dimension of persistence pairs you want to use. If your input files consist only "; + std::cout << "of birth-death pairs, please set this first parameter to -1 \n"; + std::cout << "The remaining parameters of the program are the names of files with persistence diagrams. \n"; + std::vector< const char* > filenames; + int dim = atoi(argv[1]); + unsigned dimension = std::numeric_limits<unsigned>::max(); + if ( dim >= 0 ) + { + dimension = (unsigned)dim; + } + for ( int i = 2 ; i < argc ; ++i ) + { + filenames.push_back( argv[i] ); + } + + std::cout << "Creating persistence landscapes...\n"; + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + Persistence_landscape l( filenames[i] , dimension ); + std::stringstream ss; + ss << filenames[i] << ".land"; + l.print_to_file( ss.str().c_str() ); + } + std::cout << "Done \n"; + return 0; +} diff --git a/src/Persistence_representation/utilities/persistence_landscapes/plot_landscapes.cpp b/src/Persistence_representation/utilities/persistence_landscapes/plot_landscapes.cpp new file mode 100644 index 00000000..b79a689d --- /dev/null +++ b/src/Persistence_representation/utilities/persistence_landscapes/plot_landscapes.cpp @@ -0,0 +1,47 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#include <gudhi/Persistence_landscape.h> + + + +using namespace Gudhi; +using namespace Gudhi::Persistence_representations; + +#include <iostream> +#include <sstream> + + +int main( int argc , char** argv ) +{ + std::cout << "This program plot persistence landscape stored in a file (the file needs to be created beforehand). Please call the code with the name of a landsape file \n"; + Persistence_landscape l; + l.load_landscape_from_file( argv[1] ); + + std::stringstream ss; + ss << argv[1] << "_gnuplot_script"; + l.plot( ss.str().c_str() ); + + std::cout << "Done \n"; + + return 0; +} diff --git a/src/Persistence_representation/utilities/persistence_landscapes/simple_diagram.txt.land b/src/Persistence_representation/utilities/persistence_landscapes/simple_diagram.txt.land new file mode 100644 index 00000000..b99d2f62 --- /dev/null +++ b/src/Persistence_representation/utilities/persistence_landscapes/simple_diagram.txt.land @@ -0,0 +1,13 @@ +#lambda_0 +1 0 +1.5 0.5 +2 0 +3 0 +3.5 0.5 +4 0 +5 0 +5.5 0.5 +6 0 +7 0 +7.5 0.5 +8 0 |