diff options
author | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2017-05-30 11:14:43 +0000 |
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committer | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2017-05-30 11:14:43 +0000 |
commit | 5de02a8e89ce7905281a0ef6d40f82ef04d426d6 (patch) | |
tree | 71fe2871fc6b73fb67c3fae0156ff4d470e0c8eb /src/Persistence_representations/utilities/persistence_vectors | |
parent | f9b84f79232ec2fa5935327e38e2862d9c33ab2c (diff) |
Typo
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_representation_integration@2472 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: 457b970258b8a99519db664358c19d0dee80d879
Diffstat (limited to 'src/Persistence_representations/utilities/persistence_vectors')
7 files changed, 410 insertions, 0 deletions
diff --git a/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt new file mode 100644 index 00000000..8033e27a --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt @@ -0,0 +1,25 @@ +cmake_minimum_required(VERSION 2.6) +project(GUDHI_STAT) + +#persitence vectors +add_executable ( create_persistence_vectors create_persistence_vectors.cpp ) +target_link_libraries(create_persistence_vectors ${Boost_SYSTEM_LIBRARY}) +add_test ( create_persistence_vectors ${CMAKE_CURRENT_BINARY_DIR}/create_persistence_vectors -1 "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" ) + +add_executable ( average_persistence_vectors average_persistence_vectors.cpp ) +target_link_libraries(average_persistence_vectors ${Boost_SYSTEM_LIBRARY}) +add_test ( average_persistence_vectors ${CMAKE_CURRENT_BINARY_DIR}/average_persistence_vectors "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt.vect" "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt.vect" ) + +add_executable ( compute_distance_of_persistence_vectors compute_distance_of_persistence_vectors.cpp ) +target_link_libraries(compute_distance_of_persistence_vectors ${Boost_SYSTEM_LIBRARY}) +add_test ( compute_distance_of_persistence_vectors ${CMAKE_CURRENT_BINARY_DIR}/compute_distance_of_persistence_vectors -1 "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt.vect" "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt.vect" ) + +add_executable ( compute_scalar_product_of_persistence_vectors compute_scalar_product_of_persistence_vectors.cpp ) +target_link_libraries(compute_scalar_product_of_persistence_vectors ${Boost_SYSTEM_LIBRARY}) +add_test ( compute_scalar_product_of_persistence_vectors ${CMAKE_CURRENT_BINARY_DIR}/compute_scalar_product_of_persistence_vectors "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt.vect" "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt.vect" ) + +add_executable ( plot_persistence_vectors plot_persistence_vectors.cpp ) +target_link_libraries(plot_persistence_vectors ${Boost_SYSTEM_LIBRARY}) +add_test ( plot_persistence_vectors ${CMAKE_CURRENT_BINARY_DIR}/plot_persistence_vectors "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt.vect" ) + + diff --git a/src/Persistence_representations/utilities/persistence_vectors/average_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/average_persistence_vectors.cpp new file mode 100644 index 00000000..320d1f63 --- /dev/null +++ b/src/Persistence_representations/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_vectors.h> + + + +using namespace Gudhi; +using namespace Gudhi::Persistence_representations; + +#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 >* > lands; + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + Vector_distances_in_diagram< Euclidean_distance >* l = new Vector_distances_in_diagram< Euclidean_distance >; + l->load_from_file( filenames[i] ); + lands.push_back(l ); + } + + Vector_distances_in_diagram< Euclidean_distance > av; + av.compute_average( lands ); + + av.print_to_file( "average.vect" ); + + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + delete lands[i]; + } + + std::cout << "Done \n"; + + return 0; +} diff --git a/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp new file mode 100644 index 00000000..39e24cd7 --- /dev/null +++ b/src/Persistence_representations/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_vectors.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 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 > > 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 > l; + l.load_from_file( filenames[file_no] ); + vectors.push_back( l ); + } + + //and now we will compute the scalar product of landscapes. + + //first we prepare an array: + std::vector< std::vector< double > > distance( filenames.size() ); + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + std::vector< double > v( filenames.size() , 0 ); + distance[i] = v; + } + + //and now we can compute the distances: + for ( size_t i = 0 ; i != vectors.size() ; ++i ) + { + for ( size_t j = i+1 ; j != vectors.size() ; ++j ) + { + distance[i][j] = distance[j][i] = vectors[i].distance( vectors[j] , p ) ; + } + } + + //and now output the result to the screen and a file: + std::ofstream out; + out.open( "distance" ); + for ( size_t i = 0 ; i != distance.size() ; ++i ) + { + for ( size_t j = 0 ; j != distance.size() ; ++j ) + { + std::cout << distance[i][j] << " "; + out << distance[i][j] << " "; + } + std::cout << std::endl; + out << std::endl; + } + out.close(); + + return 0; +} + + + + + + + diff --git a/src/Persistence_representations/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp new file mode 100644 index 00000000..7a1bbaf0 --- /dev/null +++ b/src/Persistence_representations/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_vectors.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 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 > > vectors; + vectors.reserve( filenames.size() ); + for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no ) + { + Vector_distances_in_diagram< Euclidean_distance > l; + l.load_from_file( filenames[file_no] ); + vectors.push_back( l ); + } + + //and now we will compute the scalar product of landscapes. + + //first we prepare an array: + std::vector< std::vector< double > > scalar_product( filenames.size() ); + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + std::vector< double > v( filenames.size() , 0 ); + scalar_product[i] = v; + } + + //and now we can compute the scalar product: + for ( size_t i = 0 ; i != vectors.size() ; ++i ) + { + for ( size_t j = i ; j != vectors.size() ; ++j ) + { + scalar_product[i][j] = scalar_product[j][i] = vectors[i].compute_scalar_product( vectors[j] ) ; + } + } + + //and now output the result to the screen and a file: + std::ofstream out; + out.open( "scalar_product" ); + for ( size_t i = 0 ; i != scalar_product.size() ; ++i ) + { + for ( size_t j = 0 ; j != scalar_product.size() ; ++j ) + { + std::cout << scalar_product[i][j] << " "; + out << scalar_product[i][j] << " "; + } + std::cout << std::endl; + out << std::endl; + } + out.close(); + return 0; +} diff --git a/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp new file mode 100644 index 00000000..634bcb13 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_vectors/create_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) 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_vectors.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 vectors of diagrams provided as an input. The first parameter of this program is a dimension of persistence "; + std::cout << " that will be used in creation of the persistence vectors. If our input files contain persistence pairs of various dimension, as a second parameter of the "; + std::cout << " procedure please provide the dimension of persistence you want to use. If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1." << std::endl; + std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; + int dim = atoi( argv[1] ); + unsigned dimension = std::numeric_limits<unsigned>::max(); + if ( dim >= 0 ) + { + dimension = (unsigned)dim; + } + + std::vector< const char* > filenames; + for ( int i = 2 ; i < argc ; ++i ) + { + filenames.push_back( argv[i] ); + } + + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + std::cerr << "Creatign persistence vectors based on a file : " << filenames[i] << std::endl; + //std::vector< std::pair< double , double > > persistence_pairs = read_gudhi_persistence_file_in_one_dimension( filenames[i] , size_t dimension = 0 ) + Vector_distances_in_diagram< Euclidean_distance > l( filenames[i] , dimension ); + std::stringstream ss; + ss << filenames[i] << ".vect"; + l.print_to_file( ss.str().c_str() ); + } + std::cout << "Done \n"; + return 0; +} + diff --git a/src/Persistence_representations/utilities/persistence_vectors/plot_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/plot_persistence_vectors.cpp new file mode 100644 index 00000000..c72fc1ee --- /dev/null +++ b/src/Persistence_representations/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_vectors.h> + + + +using namespace Gudhi; +using namespace Gudhi::Persistence_representations; + +#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 > l; + l.load_from_file( argv[1] ); + l.plot( argv[1] ); + + return 0; +} + diff --git a/src/Persistence_representations/utilities/persistence_vectors/simple_diagram.txt.vect b/src/Persistence_representations/utilities/persistence_vectors/simple_diagram.txt.vect new file mode 100644 index 00000000..1d4eeaaf --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_vectors/simple_diagram.txt.vect @@ -0,0 +1 @@ +0.707107 0.707107 0.707107 0.707107 0.707107 0.707107 0.707107 0.707107 0.707107 0.707107
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