diff options
Diffstat (limited to 'src/Gudhi_stat/utilities')
17 files changed, 295 insertions, 60 deletions
diff --git a/src/Gudhi_stat/utilities/Multiplicative_bootstrap.cpp b/src/Gudhi_stat/utilities/Multiplicative_bootstrap.cpp index 42534752..7ee389f8 100644 --- a/src/Gudhi_stat/utilities/Multiplicative_bootstrap.cpp +++ b/src/Gudhi_stat/utilities/Multiplicative_bootstrap.cpp @@ -51,7 +51,7 @@ int main( int argc , char** argv ) std::vector< Persistence_landscape* > collection_of_landscapes( filenames.size() ); for ( size_t i = 0 ; i != filenames.size() ; ++i ) { - std::vector< std::pair< double , double > > diag = read_gudhi_persistence_file_in_one_dimension( filenames[i].c_str() , 1 );//read_standard_persistence_file( filenames[i].c_str() ); + std::vector< std::pair< double , double > > diag = read_persistence_intervals_in_one_dimension_from_file( filenames[i].c_str() ); collection_of_landscapes[i] = new Persistence_landscape( diag ); } diff --git a/src/Gudhi_stat/utilities/permutation_test.cpp b/src/Gudhi_stat/utilities/permutation_test.cpp index e431026f..62cd3f10 100644 --- a/src/Gudhi_stat/utilities/permutation_test.cpp +++ b/src/Gudhi_stat/utilities/permutation_test.cpp @@ -62,7 +62,7 @@ int main( int argc , char** argv ) std::vector< Persistence_landscape* > first_collection( first_group.size() ); for ( size_t i = 0 ; i != first_group.size() ; ++i ) { - std::vector< std::pair< double , double > > diag = read_standard_persistence_file( first_group[i].c_str() ); + std::vector< std::pair< double , double > > diag = read_persistence_intervals_in_one_dimension_from_file( first_group[i].c_str() ); Persistence_landscape* l = new Persistence_landscape( diag ); first_collection[i] = l; } diff --git a/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp b/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp index 5d2100aa..d9c7aded 100644 --- a/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp +++ b/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp @@ -40,26 +40,32 @@ int main( int argc , char** argv ) std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; std::cout << "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"; std::cerr << "The fourth parameter is an integer, the standard deviation of a gaussian kernel expressed in a number of pixels \n"; - std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; + std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the persistence heat maps."; + std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the procedure please provide the dimension of persistence you want to use."; + std::cout << "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"; if ( argc < 5 ) { std::cout << "Wrong parameter list, the program will now terminate \n"; return 1; - } - + } size_t size_of_grid = (size_t)atoi( argv[1] ); double min_ = atof( argv[2] ); double max_ = atof( argv[3] ); size_t stdiv = atof( argv[4] ); + unsigned dimension = std::numeric_limits<unsigned>::max(); + int dim = atoi( argv[5] ); + if ( (dim != -1) && (dim >= 0) ) + { + dimension = (unsigned)dim; + } std::vector< const char* > filenames; - for ( int i = 5 ; i < argc ; ++i ) + for ( int i = 6 ; i < argc ; ++i ) { filenames.push_back( argv[i] ); } - - std::cout << "Creating persistence heat maps...\n"; std::vector< std::vector<double> > filter = create_Gaussian_filter(stdiv,1); @@ -67,7 +73,7 @@ int main( int argc , char** argv ) 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<constant_scaling_function> l( filenames[i] , filter, false , size_of_grid , min_ , max_ ); + Persistence_heat_maps<constant_scaling_function> l( filenames[i] , filter, false , size_of_grid , min_ , max_ , dimension ); std::stringstream ss; ss << filenames[i] << ".mps"; diff --git a/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_arctan_of_their_persistence.cpp b/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_arctan_of_their_persistence.cpp index 8496e33e..7cb7eeb7 100644 --- a/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_arctan_of_their_persistence.cpp +++ b/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_arctan_of_their_persistence.cpp @@ -1,4 +1,4 @@ -/* This file is part of the Gudhi Library. The Gudhi library + /* This file is part of the Gudhi Library. The Gudhi library * (Geometric Understanding in Higher Dimensions) is a generic C++ * library for computational topology. * @@ -40,8 +40,11 @@ int main( int argc , char** argv ) std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; std::cout << "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"; std::cerr << "The fourth parameter is an integer, the standard deviation of a gaussian kernel expressed in a number of pixels \n"; + std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the persistence heat maps."; + std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the procedure please provide the dimension of persistence you want to use."; + std::cout << "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"; - + if ( argc < 5 ) { std::cout << "Wrong parameter list, the program will now terminate \n"; @@ -53,8 +56,15 @@ int main( int argc , char** argv ) double max_ = atof( argv[3] ); size_t stdiv = atof( argv[4] ); + unsigned dimension = std::numeric_limits<unsigned>::max(); + int dim = atoi( argv[5] ); + if ( (dim != -1) && (dim >= 0) ) + { + dimension = (unsigned)dim; + } + std::vector< const char* > filenames; - for ( int i = 5 ; i < argc ; ++i ) + for ( int i = 6 ; i < argc ; ++i ) { filenames.push_back( argv[i] ); } @@ -67,7 +77,7 @@ int main( int argc , char** argv ) 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<arc_tan_of_persistence_of_point> l( filenames[i] , filter, false , size_of_grid , min_ , max_ ); + Persistence_heat_maps<arc_tan_of_persistence_of_point> l( filenames[i] , filter, false , size_of_grid , min_ , max_ , dimension ); std::stringstream ss; ss << filenames[i] << ".mps"; diff --git a/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_distance_from_diagonal.cpp b/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_distance_from_diagonal.cpp index 83d4f3bc..3242e106 100644 --- a/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_distance_from_diagonal.cpp +++ b/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_distance_from_diagonal.cpp @@ -39,6 +39,9 @@ int main( int argc , char** argv ) std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; std::cout << "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"; std::cerr << "The fourth parameter is an integer, the standard deviation of a gaussian kernel expressed in a number of pixels \n"; + std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the persistence heat maps."; + std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the procedure please provide the dimension of persistence you want to use."; + std::cout << "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"; if ( argc < 5 ) @@ -52,8 +55,15 @@ int main( int argc , char** argv ) double max_ = atof( argv[3] ); size_t stdiv = atof( argv[4] ); + unsigned dimension = std::numeric_limits<unsigned>::max(); + int dim = atoi( argv[5] ); + if ( (dim != -1) && (dim >= 0) ) + { + dimension = (unsigned)dim; + } + std::vector< const char* > filenames; - for ( int i = 5 ; i < argc ; ++i ) + for ( int i = 6 ; i < argc ; ++i ) { filenames.push_back( argv[i] ); } @@ -66,7 +76,7 @@ int main( int argc , char** argv ) 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<distance_from_diagonal_scaling> l( filenames[i] , filter , size_of_grid , min_ , max_ ); + Persistence_heat_maps<distance_from_diagonal_scaling> l( filenames[i] , filter , size_of_grid , min_ , max_ , dimension ); std::stringstream ss; ss << filenames[i] << ".mps"; diff --git a/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal.cpp b/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal.cpp index f62615f5..27846a99 100644 --- a/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal.cpp +++ b/src/Gudhi_stat/utilities/persistence_heat_maps/create_persistence_heat_maps_weighted_by_squared_distance_from_diagonal.cpp @@ -39,8 +39,11 @@ int main( int argc , char** argv ) std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; std::cout << "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"; std::cerr << "The fourth parameter is an integer, the standard deviation of a gaussian kernel expressed in a number of pixels \n"; + std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the persistence heat maps."; + std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the procedure please provide the dimension of persistence you want to use."; + std::cout << "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"; - + if ( argc < 5 ) { std::cout << "Wrong parameter list, the program will now terminate \n"; @@ -51,14 +54,19 @@ int main( int argc , char** argv ) double min_ = atof( argv[2] ); double max_ = atof( argv[3] ); size_t stdiv = atof( argv[4] ); + + unsigned dimension = std::numeric_limits<unsigned>::max(); + int dim = atoi( argv[5] ); + if ( (dim != -1) && (dim >= 0) ) + { + dimension = (unsigned)dim; + } std::vector< const char* > filenames; - for ( int i = 5 ; i < argc ; ++i ) + for ( int i = 6 ; i < argc ; ++i ) { filenames.push_back( argv[i] ); } - - std::cout << "Creating persistence heat maps...\n"; std::vector< std::vector<double> > filter = create_Gaussian_filter(stdiv,1); @@ -66,7 +74,7 @@ int main( int argc , char** argv ) 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<squared_distance_from_diagonal_scaling> l( filenames[i] , filter, false , size_of_grid , min_ , max_ ); + Persistence_heat_maps<squared_distance_from_diagonal_scaling> l( filenames[i] , filter, false , size_of_grid , min_ , max_ , dimension ); std::stringstream ss; ss << filenames[i] << ".mps"; diff --git a/src/Gudhi_stat/utilities/persistence_heat_maps/create_pssk.cpp b/src/Gudhi_stat/utilities/persistence_heat_maps/create_pssk.cpp index d38bb8b9..404a4be3 100644 --- a/src/Gudhi_stat/utilities/persistence_heat_maps/create_pssk.cpp +++ b/src/Gudhi_stat/utilities/persistence_heat_maps/create_pssk.cpp @@ -38,8 +38,12 @@ int main( int argc , char** argv ) std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; std::cout << "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"; std::cerr << "The fourth parameter is an integer, the standard deviation of a gaussian kernel expressed in a number of pixels \n"; + std::cerr << "The fourth parameter is an integer, the standard deviation of a gaussian kernel expressed in a number of pixels \n"; + std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the persistence heat maps."; + std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the procedure please provide the dimension of persistence you want to use."; + std::cout << "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"; - + if ( argc < 5 ) { std::cout << "Wrong parameter list, the program will now terminate \n"; @@ -51,8 +55,15 @@ int main( int argc , char** argv ) double max_ = atof( argv[3] ); size_t stdiv = atof( argv[4] ); + unsigned dimension = std::numeric_limits<unsigned>::max(); + int dim = atoi( argv[5] ); + if ( (dim != -1) && (dim >= 0) ) + { + dimension = (unsigned)dim; + } + std::vector< const char* > filenames; - for ( int i = 5 ; i < argc ; ++i ) + for ( int i = 6 ; i < argc ; ++i ) { filenames.push_back( argv[i] ); } @@ -63,7 +74,7 @@ int main( int argc , char** argv ) for ( size_t i = 0 ; i != filenames.size() ; ++i ) { std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl; - PSSK l( filenames[i] , filter , size_of_grid , min_ , max_ ); + PSSK l( filenames[i] , filter , size_of_grid , min_ , max_ , dimension ); std::stringstream ss; ss << filenames[i] << ".pssk"; diff --git a/src/Gudhi_stat/utilities/persistence_intervals/CMakeLists.txt b/src/Gudhi_stat/utilities/persistence_intervals/CMakeLists.txt index 96cb1a5e..9420a8ea 100644 --- a/src/Gudhi_stat/utilities/persistence_intervals/CMakeLists.txt +++ b/src/Gudhi_stat/utilities/persistence_intervals/CMakeLists.txt @@ -1,8 +1,6 @@ cmake_minimum_required(VERSION 2.6) project(GUDHI_STAT) - - #persitence diagrams add_executable ( plot_persistence_intervals plot_persistence_intervals.cpp ) target_link_libraries( plot_persistence_intervals ${Boost_SYSTEM_LIBRARY}) @@ -16,7 +14,14 @@ target_link_libraries( compute_number_of_dominant_intervals ${Boost_SYSTEM_LIBRA add_executable ( plot_histogram_of_intervals_lengths plot_histogram_of_intervals_lengths.cpp ) target_link_libraries( plot_histogram_of_intervals_lengths ${Boost_SYSTEM_LIBRARY}) -add_executable ( plot_persistence_Betti_numebrs plot_persistence_Betti_numebrs.cpp ) -target_link_libraries( plot_persistence_Betti_numebrs ${Boost_SYSTEM_LIBRARY}) +add_executable ( plot_persistence_Betti_numbers plot_persistence_Betti_numbers.cpp ) +target_link_libraries( plot_persistence_Betti_numbers ${Boost_SYSTEM_LIBRARY}) + +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) +add_executable ( compute_bottleneck_distance compute_bottleneck_distance.cpp ) +target_link_libraries( compute_bottleneck_distance ${Boost_SYSTEM_LIBRARY}) +if (TBB_FOUND) +target_link_libraries(compute_bottleneck_distance ${TBB_LIBRARIES}) +endif(TBB_FOUND) -#when we have bottleneck and wasserstein distance computations, add suitable programs here. +endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Gudhi_stat/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp b/src/Gudhi_stat/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp index 145040fe..426a9b7b 100644 --- a/src/Gudhi_stat/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp +++ b/src/Gudhi_stat/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp @@ -37,18 +37,20 @@ using namespace Gudhi::Gudhi_stat; int main( int argc , char** argv ) { - //std::cout << "This program compute minimum birth and the maximum death time for a collection of persistence intervals \n"; - //if ( argc != 2 ) - //{ - // std::cout << "To run this program, please provide the name of a file with persistence diagram \n"; - // return 1; - //} - //Persistence_intervals p( argv[1] ); - //std::pair<double,double> min_max_ = p.min_max(); - //std::cout << "Birth-death range : min: " << min_max_.first << ", max: " << min_max_.second << endl; + std::cout << "This program compute the range of birth and death times of persistence pairs in diagrams provided as an input. \n"; + std::cout << "The first parameter of the program is the dimension of persistence to be used. 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"; + int dim = atoi( argv[1] ); + unsigned dimension = std::numeric_limits<unsigned>::max(); + if ( (dim != -1) && (dim >= 0) ) + { + dimension = (unsigned)dim; + } std::vector< const char* > filenames; - for ( int i = 1 ; i < argc ; ++i ) + for ( int i = 2 ; i < argc ; ++i ) { filenames.push_back( argv[i] ); } @@ -59,7 +61,7 @@ int main( int argc , char** argv ) 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] ); + Persistence_intervals p( filenames[file_no] , dimension ); std::pair<double,double> min_max_ = p.min_max(); if ( min_max_.first < min_ )min_ = min_max_.first; if ( min_max_.second > max_ )max_ = min_max_.second; diff --git a/src/Gudhi_stat/utilities/persistence_intervals/compute_bottleneck_distance.cpp b/src/Gudhi_stat/utilities/persistence_intervals/compute_bottleneck_distance.cpp new file mode 100644 index 00000000..6f0ba635 --- /dev/null +++ b/src/Gudhi_stat/utilities/persistence_intervals/compute_bottleneck_distance.cpp @@ -0,0 +1,115 @@ +/* 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/Persistence_intervals_with_distances.h> +#include <gudhi/read_persistence_from_file.h> + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +#include <iostream> +#include <sstream> + + +int main( int argc , char** argv ) +{ + std::cout << "This program compute the bottleneck distance of persistence diarams stored in a files. \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 this programs are names of files with persistence diagrams.\n"; + + if ( argc < 3 ) + { + std::cout << "Wrong number of parameters, the program will now terminate \n"; + return 1; + } + + int dim = atoi(argv[1]); + unsigned dimension = std::numeric_limits<unsigned>::max(); + if ( (dim != -1) && (dim >= 0) ) + { + dimension = (unsigned)dim; + } + + + std::vector< const char* > filenames; + for ( int i = 2 ; i < argc ; ++i ) + { + filenames.push_back( argv[i] ); + } + + //reading the persistence intervals: + std::vector< Persistence_intervals_with_distances > persistence_intervals; + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + Persistence_intervals_with_distances pers(filenames[i] , dimension ); + std::cerr << "perss : " << pers << std::endl; + getchar(); + persistence_intervals.push_back( pers ); + } + + //and now we will compute the scalar product of landscapes. + + //first we prepare an array: + std::vector< std::vector< double > > distance( filenames.size() ); + for ( size_t i = 0 ; i != filenames.size() ; ++i ) + { + std::vector< double > v( filenames.size() , 0 ); + distance[i] = v; + } + + //and now we can compute the distances: + for ( size_t i = 0 ; i != persistence_intervals.size() ; ++i ) + { + for ( size_t j = i+1 ; j != persistence_intervals.size() ; ++j ) + { + distance[i][j] = distance[j][i] = persistence_intervals[i].distance( persistence_intervals[j] ); + } + } + + //and now output the result to the screen and a file: + std::ofstream out; + out.open( "distance" ); + 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_intervals/compute_number_of_dominant_intervals.cpp b/src/Gudhi_stat/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp index eeda703a..0a7f7c2b 100644 --- a/src/Gudhi_stat/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp +++ b/src/Gudhi_stat/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp @@ -36,14 +36,19 @@ using namespace Gudhi::Gudhi_stat; 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 != 3 ) + if ( 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 \n"; + 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; } - - Persistence_intervals p( argv[1] ); - std::vector< std::pair<double,double> > dominant_intervals = p.dominant_intervals( atoi( argv[2] ) ); + int dim = atoi( argv[2] ); + unsigned dimension = std::numeric_limits<unsigned>::max(); + if ( (dim != -1) && (dim >= 0) ) + { + dimension = (unsigned)dim; + } + Persistence_intervals p( argv[1] , dimension ); + std::vector< std::pair<double,double> > dominant_intervals = p.dominant_intervals( atoi( argv[3] ) ); std::cout << "Here are the dominant intervals : " << std::endl; for ( size_t i = 0 ; i != dominant_intervals.size() ; ++i ) { diff --git a/src/Gudhi_stat/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp b/src/Gudhi_stat/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp index db9c3f98..11876a0d 100644 --- a/src/Gudhi_stat/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp +++ b/src/Gudhi_stat/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp @@ -39,10 +39,21 @@ int main( int argc , char** argv ) if ( argc != 3 ) { 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 \n"; + std::cout << "The second parameter of a program is the dimension of the persistence that is to be used. If your file contains only birth-death pairs, you can skip this parameter\n"; return 1; } + unsigned dimension = std::numeric_limits<unsigned>::max(); + int dim = -1; + if ( argc > 2 ) + { + dim = atoi( argv[2] ); + } + if ( (dim != -1) && (dim >= 0) ) + { + dimension = (unsigned)dim; + } - Persistence_intervals p( argv[1] ); + Persistence_intervals p( argv[1] , dimension ); std::vector< std::pair<double,double> > dominant_intervals = p.dominant_intervals( atoi( argv[2] ) ); std::vector< size_t > histogram = p.histogram_of_lengths( 10 ); diff --git a/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_Betti_numebrs.cpp b/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp index cb89f6b9..09c6cc22 100644 --- a/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_Betti_numebrs.cpp +++ b/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp @@ -36,12 +36,22 @@ using namespace Gudhi::Gudhi_stat; int main( int argc , char** argv ) { std::cout << "This program compute a plot of persistence Betti numbers. The input parameter is a file with persistence intervals. \n"; - if ( argc != 2 ) + std::cout << "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"; + if ( argc < 2 ) { 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 \n"; return 1; } - + unsigned dimension = std::numeric_limits<unsigned>::max(); + int dim = -1; + if ( argc > 2 ) + { + dim = atoi( argv[2] ); + } + if ( (dim != -1) && (dim >= 0) ) + { + dimension = (unsigned)dim; + } std::stringstream gnuplot_script; @@ -49,7 +59,7 @@ int main( int argc , char** argv ) std::ofstream out; out.open( gnuplot_script.str().c_str() ); - Persistence_intervals p( argv[1] ); + Persistence_intervals p( argv[1] , dimension ); std::vector< std::pair< double , size_t > > pbns = p.compute_persistent_betti_numbers(); //set up the ranges so that we see the image well. diff --git a/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_intervals.cpp b/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_intervals.cpp index bc466bd3..4315abb9 100644 --- a/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_intervals.cpp +++ b/src/Gudhi_stat/utilities/persistence_intervals/plot_persistence_intervals.cpp @@ -42,9 +42,23 @@ int main( int argc , char** argv ) if ( argc != 2 ) { std::cout << "To run this program, please provide the name of a file with persistence diagram \n"; + std::cout << "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; } - std::vector< std::pair< double , double > > intervals = read_gudhi_persistence_file_in_one_dimension( argv[1] , 2 ); + unsigned dimension = std::numeric_limits<unsigned>::max(); + int dim = -1; + if ( argc > 2 ) + { + dim = atoi( argv[2] ); + } + if ( (dim != -1) && (dim >= 0) ) + { + dimension = (unsigned)dim; + } + + + + std::vector< std::pair< double , double > > intervals = read_persistence_intervals_in_one_dimension_from_file( argv[1] , dimension ); Persistence_intervals b( intervals ); b.plot( argv[1] ); return 0; diff --git a/src/Gudhi_stat/utilities/persistence_landscapes/create_landscapes.cpp b/src/Gudhi_stat/utilities/persistence_landscapes/create_landscapes.cpp index 5485bf2a..f36e313a 100644 --- a/src/Gudhi_stat/utilities/persistence_landscapes/create_landscapes.cpp +++ b/src/Gudhi_stat/utilities/persistence_landscapes/create_landscapes.cpp @@ -32,9 +32,19 @@ using namespace Gudhi::Gudhi_stat; int main( int argc , char** argv ) { - std::cout << "This program creates persistence landscapes of diagrams provided as an input. Please call this program with the names of files with persistence diagrams \n"; + 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; - for ( int i = 1 ; i < argc ; ++i ) + int dim = atoi(argv[1]); + unsigned dimension = std::numeric_limits<unsigned>::max(); + if ( (dim != -1) && (dim >= 0) ) + { + dimension = (unsigned)dim; + } + for ( int i = 2 ; i < argc ; ++i ) { filenames.push_back( argv[i] ); } @@ -42,8 +52,7 @@ int main( int argc , char** argv ) std::cout << "Creating persistence landscapes...\n"; for ( size_t i = 0 ; i != filenames.size() ; ++i ) { - //std::vector< std::pair< double , double > > pers = read_standard_file( filename ); - Persistence_landscape l( filenames[i] , 1 ); + Persistence_landscape l( filenames[i] , dimension ); std::stringstream ss; ss << filenames[i] << ".land"; l.print_to_file( ss.str().c_str() ); diff --git a/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp b/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp index 4f36f02d..eb534bf1 100644 --- a/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp +++ b/src/Gudhi_stat/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp @@ -36,9 +36,12 @@ int main( int argc , char** argv ) std::cout << "This program creates persistence landscape on grid of diagrams provided as an input.\n"; std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; std::cout << "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"; + std::cout << "The fourth parameter of the program is the dimension of persistence to be used to construct persistence landscape on a grid. If your file contains "; + std::cout << "the information about dimension of birth-death pairs, please provide here the dimension of intervals you want to use. If your input files consist only "; + std::cout << "of birth-death pairs, please set the fourth parameter to -1 \n"; std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; - if ( argc < 4 ) + if ( argc < 5 ) { std::cout << "Wrong parameter list, the program will now terminate \n"; return 1; @@ -47,9 +50,15 @@ int main( int argc , char** argv ) size_t size_of_grid = (size_t)atoi( argv[1] ); double min_ = atof( argv[2] ); double max_ = atof( argv[3] ); + int dim = atoi( argv[4] ); + unsigned dimension = std::numeric_limits<unsigned>::max(); + if ( (dim != -1) && (dim >= 0) ) + { + dimension = (unsigned)dim; + } std::vector< const char* > filenames; - for ( int i = 4 ; i < argc ; ++i ) + for ( int i = 5 ; i < argc ; ++i ) { filenames.push_back( argv[i] ); } @@ -61,12 +70,12 @@ int main( int argc , char** argv ) Persistence_landscape_on_grid l; if ( (min_ != -1) || (max_ != -1) ) { - l = Persistence_landscape_on_grid( filenames[i] , min_ , max_ , size_of_grid ); + 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 ); + l = Persistence_landscape_on_grid( filenames[i] , size_of_grid , dimension ); } std::stringstream ss; ss << filenames[i] << ".g_land"; diff --git a/src/Gudhi_stat/utilities/persistence_vectors/create_persistence_vectors.cpp b/src/Gudhi_stat/utilities/persistence_vectors/create_persistence_vectors.cpp index fc434ba8..40f5e81f 100644 --- a/src/Gudhi_stat/utilities/persistence_vectors/create_persistence_vectors.cpp +++ b/src/Gudhi_stat/utilities/persistence_vectors/create_persistence_vectors.cpp @@ -33,9 +33,19 @@ using namespace Gudhi::Gudhi_stat; 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::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 != -1) && (dim >= 0) ) + { + dimension = (unsigned)dim; + } + std::vector< const char* > filenames; - for ( int i = 1 ; i < argc ; ++i ) + for ( int i = 2 ; i < argc ; ++i ) { filenames.push_back( argv[i] ); } @@ -44,7 +54,7 @@ int main( int argc , char** argv ) { 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] , -1 ); + 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() ); |