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Diffstat (limited to 'src/Gudhi_stat/utilities/persistence_vectors')
6 files changed, 394 insertions, 0 deletions
diff --git a/src/Gudhi_stat/utilities/persistence_vectors/CMakeLists.txt b/src/Gudhi_stat/utilities/persistence_vectors/CMakeLists.txt new file mode 100644 index 00000000..ebf4898e --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_vectors/CMakeLists.txt @@ -0,0 +1,20 @@ +cmake_minimum_required(VERSION 2.6) +project(GUDHI_STAT) + +#persitence vectors +add_executable ( average_persistence_vectors average_persistence_vectors.cpp ) +target_link_libraries(average_persistence_vectors ${Boost_SYSTEM_LIBRARY}) + +add_executable ( create_persistence_vectors create_persistence_vectors.cpp ) +target_link_libraries(create_persistence_vectors ${Boost_SYSTEM_LIBRARY}) + +add_executable ( compute_distance_of_persistence_vectors compute_distance_of_persistence_vectors.cpp ) +target_link_libraries(compute_distance_of_persistence_vectors ${Boost_SYSTEM_LIBRARY}) + +add_executable ( compute_scalar_product_of_persistence_vectors compute_scalar_product_of_persistence_vectors.cpp ) +target_link_libraries(compute_scalar_product_of_persistence_vectors ${Boost_SYSTEM_LIBRARY}) + +add_executable ( plot_persistence_vectors plot_persistence_vectors.cpp ) +target_link_libraries(plot_persistence_vectors ${Boost_SYSTEM_LIBRARY}) + + diff --git a/src/Gudhi_stat/utilities/persistence_vectors/average_persistence_vectors.cpp b/src/Gudhi_stat/utilities/persistence_vectors/average_persistence_vectors.cpp new file mode 100644 index 00000000..822d0e2a --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_vectors/average_persistence_vectors.cpp @@ -0,0 +1,73 @@ +/* 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_representations/Vector_distances_in_diagram.h> + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +#include <iostream> + + +int main( int argc , char** argv ) +{ + std::cout << "This program computes average persistence vector of persistence vectors created based on persistence diagrams provided as an input. \n"; + std::cout << "Please call this program with the names of files with persistence diagrams \n"; + std::vector< const char* > filenames; + + if ( argc == 1 ) + { + std::cout << "No input files given, the program will now terminate \n"; + return 1; + } + + for ( int i = 1 ; i < argc ; ++i ) + { + filenames.push_back( argv[i] ); + } + + std::cout << "Reading persistence vectors...\n"; + std::vector< Vector_distances_in_diagram< Euclidean_distance<double> >* > lands; + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + Vector_distances_in_diagram< Euclidean_distance<double> >* l = new Vector_distances_in_diagram< Euclidean_distance<double> >; + l->load_from_file( filenames[i] ); + lands.push_back(l ); + } + + Vector_distances_in_diagram< Euclidean_distance<double> > av; + av.compute_average( lands ); + + av.print_to_file( "average.vect" ); + + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + delete lands[i]; + } + + std::cout << "Done \n"; + + return 0; +} diff --git a/src/Gudhi_stat/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp b/src/Gudhi_stat/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp new file mode 100644 index 00000000..6d242cd1 --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp @@ -0,0 +1,111 @@ +/* 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_representations/Vector_distances_in_diagram.h> + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +#include <iostream> +#include <sstream> + + +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 interger p. The program compute l^p distance of the vectors. For l^infty distance choose p = -1. \n"; + std::cout << "The remaining parameters of this programs are names of files with persistence vectors.\n"; + + if ( argc < 3 ) + { + std::cout << "Wrong number of parameters, the program will now terminate \n"; + return 1; + } + + int pp = atoi( argv[1] ); + double p = std::numeric_limits<double>::max(); + if ( pp != -1 ) + { + p = pp; + } + + + std::vector< const char* > filenames; + for ( int i = 2 ; i < argc ; ++i ) + { + filenames.push_back( argv[i] ); + } + std::vector< Vector_distances_in_diagram< Euclidean_distance<double> > > vectors; + vectors.reserve( filenames.size() ); + for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no ) + { + //cerr << filenames[file_no] << endl; + Vector_distances_in_diagram< Euclidean_distance<double> > l; + l.load_from_file( filenames[file_no] ); + vectors.push_back( l ); + } + + //and now we will compute the scalar product of landscapes. + + //first we prepare an array: + std::vector< std::vector< double > > distance( filenames.size() ); + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + std::vector< double > v( filenames.size() , 0 ); + distance[i] = v; + } + + //and now we can compute the distances: + for ( size_t i = 0 ; i != vectors.size() ; ++i ) + { + for ( size_t j = i+1 ; j != vectors.size() ; ++j ) + { + distance[i][j] = distance[j][i] = vectors[i].distance( vectors[j] , p ) ; + } + } + + //and now output the result to the screen and a file: + std::ofstream out; + out.open( "distance" ); + for ( size_t i = 0 ; i != distance.size() ; ++i ) + { + for ( size_t j = 0 ; j != distance.size() ; ++j ) + { + std::cout << distance[i][j] << " "; + out << distance[i][j] << " "; + } + std::cout << std::endl; + out << std::endl; + } + out.close(); + + return 0; +} + + + + + + + diff --git a/src/Gudhi_stat/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp b/src/Gudhi_stat/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp new file mode 100644 index 00000000..e4c62194 --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.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) 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_representations/Vector_distances_in_diagram.h> + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +#include <iostream> +#include <sstream> + + +int main( int argc , char** argv ) +{ + std::cout << "This program compute scalar product of persistence vectors stored in a file (the file needs to be created beforehand). \n"; + std::cout << "The parameters of this programs are names of files with persistence vectors.\n"; + + std::vector< const char* > filenames; + for ( int i = 1 ; i < argc ; ++i ) + { + filenames.push_back( argv[i] ); + } + std::vector< Vector_distances_in_diagram< Euclidean_distance<double> > > vectors; + vectors.reserve( filenames.size() ); + for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no ) + { + Vector_distances_in_diagram< Euclidean_distance<double> > l; + l.load_from_file( filenames[file_no] ); + vectors.push_back( l ); + } + + //and now we will compute the scalar product of landscapes. + + //first we prepare an array: + std::vector< std::vector< double > > scalar_product( filenames.size() ); + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + std::vector< double > v( filenames.size() , 0 ); + scalar_product[i] = v; + } + + //and now we can compute the scalar product: + for ( size_t i = 0 ; i != vectors.size() ; ++i ) + { + for ( size_t j = i ; j != vectors.size() ; ++j ) + { + scalar_product[i][j] = scalar_product[j][i] = vectors[i].compute_scalar_product( vectors[j] ) ; + } + } + + //and now output the result to the screen and a file: + std::ofstream out; + out.open( "scalar_product" ); + for ( size_t i = 0 ; i != scalar_product.size() ; ++i ) + { + for ( size_t j = 0 ; j != scalar_product.size() ; ++j ) + { + std::cout << scalar_product[i][j] << " "; + out << scalar_product[i][j] << " "; + } + std::cout << std::endl; + out << std::endl; + } + out.close(); + return 0; +} diff --git a/src/Gudhi_stat/utilities/persistence_vectors/create_persistence_vectors.cpp b/src/Gudhi_stat/utilities/persistence_vectors/create_persistence_vectors.cpp new file mode 100644 index 00000000..926e46fd --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_vectors/create_persistence_vectors.cpp @@ -0,0 +1,55 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 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_representations/Vector_distances_in_diagram.h> + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +#include <iostream> +#include <sstream> + + +int main( int argc , char** argv ) +{ + std::cout << "This program creates persistence vectors of diagrams provided as an input. Please call this program with the names of files with persistence diagrams \n"; + std::vector< const char* > filenames; + for ( int i = 1 ; i < argc ; ++i ) + { + filenames.push_back( argv[i] ); + } + + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + std::cerr << "Creatign persistence vectors based on a file : " << filenames[i] << std::endl; + //std::vector< std::pair< double , double > > persistence_pairs = read_gudhi_file( filenames[i] , size_t dimension = 0 ) + Vector_distances_in_diagram< Euclidean_distance<double> > l( filenames[i] , -1 ); + std::stringstream ss; + ss << filenames[i] << ".vect"; + l.print_to_file( ss.str().c_str() ); + } + std::cout << "Done \n"; + return 0; +} + diff --git a/src/Gudhi_stat/utilities/persistence_vectors/plot_persistence_vectors.cpp b/src/Gudhi_stat/utilities/persistence_vectors/plot_persistence_vectors.cpp new file mode 100644 index 00000000..0ef30be8 --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_vectors/plot_persistence_vectors.cpp @@ -0,0 +1,48 @@ +/* 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_representations/Vector_distances_in_diagram.h> + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +#include <iostream> +#include <sstream> + + +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< Euclidean_distance<double> > l; + l.load_from_file( argv[1] ); + l.plot( argv[1] ); + + return 0; +} + |