diff options
30 files changed, 506 insertions, 161 deletions
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 3779cb80..c94110a6 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -53,6 +53,7 @@ add_subdirectory(example/Subsampling) add_subdirectory(example/Tangential_complex) add_subdirectory(example/Bottleneck_distance) add_subdirectory(example/Gudhi_stat) +add_subdirectory(example/Gudhi_stat/utilities) # data points generator add_subdirectory(data/points/generator) diff --git a/src/Doxyfile b/src/Doxyfile index d2d0a447..f3782148 100644 --- a/src/Doxyfile +++ b/src/Doxyfile @@ -851,7 +851,8 @@ IMAGE_PATH = doc/Skeleton_blocker/ \ doc/Subsampling/ \ doc/Spatial_searching/ \ doc/Tangential_complex/ \ - doc/Bottleneck_distance/ + doc/Bottleneck_distance/ \ + doc/Gudhi_stat/ # The INPUT_FILTER tag can be used to specify a program that doxygen should # invoke to filter for each input file. Doxygen will invoke the filter program diff --git a/src/Gudhi_stat/doc/average_landscape.png b/src/Gudhi_stat/doc/average_landscape.png Binary files differnew file mode 100644 index 00000000..ea59926b --- /dev/null +++ b/src/Gudhi_stat/doc/average_landscape.png diff --git a/src/Gudhi_stat/include/gudhi/permutation_test.h b/src/Gudhi_stat/include/gudhi/permutation_test.h index b4c1a8ba..69b0790b 100644 --- a/src/Gudhi_stat/include/gudhi/permutation_test.h +++ b/src/Gudhi_stat/include/gudhi/permutation_test.h @@ -37,6 +37,8 @@ namespace Gudhi namespace Gudhi_stat { +//TODO change the reading procedures so that they accept the dimension value (by default std::nnumeric_limits<unsigned>::max(). + template <typename Representation_of_persistence> double permutation_test( const std::vector<Representation_of_persistence*>& data_1 , const std::vector<Representation_of_persistence*>& data_2 , size_t number_of_permutations , double exponent = 1 ) { diff --git a/src/Gudhi_stat/include/gudhi/persistence_representations/PSSK.h b/src/Gudhi_stat/include/gudhi/persistence_representations/PSSK.h index 7a299a86..d2fd3a86 100644 --- a/src/Gudhi_stat/include/gudhi/persistence_representations/PSSK.h +++ b/src/Gudhi_stat/include/gudhi/persistence_representations/PSSK.h @@ -53,10 +53,18 @@ public: } - PSSK( const char* filename , std::vector< std::vector<double> > filter = create_Gaussian_filter(5,1) , size_t number_of_pixels = 1000 , double min_ = -1 , double max_ = -1 ): + PSSK( const char* filename , std::vector< std::vector<double> > filter = create_Gaussian_filter(5,1) , size_t number_of_pixels = 1000 , double min_ = -1 , double max_ = -1 , unsigned dimension = std::numeric_limits<unsigned>::max() ): Persistence_heat_maps() { - std::vector< std::pair< double , double > > intervals_ = read_standard_persistence_file( filename ); + std::vector< std::pair< double , double > > intervals_; + if ( dimension == std::numeric_limits<unsigned>::max() ) + { + intervals_ = read_persistence_intervals_in_one_dimension_from_file( filename ); + } + else + { + intervals_ = read_persistence_intervals_in_one_dimension_from_file( filename , dimension ); + } this->construct( intervals_ , filter , number_of_pixels , min_ , max_ ); } diff --git a/src/Gudhi_stat/include/gudhi/persistence_representations/Persistence_heat_maps.h b/src/Gudhi_stat/include/gudhi/persistence_representations/Persistence_heat_maps.h index f82f3100..3cfd52f5 100644 --- a/src/Gudhi_stat/include/gudhi/persistence_representations/Persistence_heat_maps.h +++ b/src/Gudhi_stat/include/gudhi/persistence_representations/Persistence_heat_maps.h @@ -230,14 +230,14 @@ public: **/ /** * Construction that takes at the input the following parameters: - * (1) A a name of a file with persistence intervals. The file shold be readable by the function read_standard_persistence_file. All other parameters are optional. They are: + * (1) A a name of a file with persistence intervals. The file shold be readable by the function read_persistence_intervals_in_one_dimension_from_file. All other parameters are optional. They are: * (2) a Gausian filter generated by create_Gaussian_filter filter (the default value of this vaiable is a Gaussian filter of a radius 5), * (3) a boolean value which determines if the area of image below diagonal should, or should not be erased (it will be erased by default). * (4) a number of pixels in each direction (set to 1000 by default). * (5) a min x and y value of points that are to be taken into account. By default it is set to std::numeric_limits<double>::max(), in which case the program compute the values based on the data, * (6) a max x and y value of points that are to be taken into account. By default it is set to std::numeric_limits<double>::max(), in which case the program compute the values based on the data. **/ - Persistence_heat_maps( const char* filename , std::vector< std::vector<double> > filter = create_Gaussian_filter(5,1), bool erase_below_diagonal = false , size_t number_of_pixels = 1000 , double min_ = std::numeric_limits<double>::max() , double max_ = std::numeric_limits<double>::max() ); + Persistence_heat_maps( const char* filename , std::vector< std::vector<double> > filter = create_Gaussian_filter(5,1), bool erase_below_diagonal = false , size_t number_of_pixels = 1000 , double min_ = std::numeric_limits<double>::max() , double max_ = std::numeric_limits<double>::max() , unsigned dimension = std::numeric_limits<unsigned>::max() ); /** @@ -695,9 +695,17 @@ Persistence_heat_maps<Scalling_of_kernels>::Persistence_heat_maps( const std::ve template <typename Scalling_of_kernels> Persistence_heat_maps<Scalling_of_kernels>::Persistence_heat_maps( const char* filename , std::vector< std::vector<double> > filter, - bool erase_below_diagonal , size_t number_of_pixels , double min_ , double max_ ) + bool erase_below_diagonal , size_t number_of_pixels , double min_ , double max_ , unsigned dimension ) { - std::vector< std::pair< double , double > > intervals_ = read_standard_persistence_file( filename ); + std::vector< std::pair< double , double > > intervals_; + if ( dimension == std::numeric_limits<unsigned>::max() ) + { + intervals_ = read_persistence_intervals_in_one_dimension_from_file( filename ); + } + else + { + intervals_ = read_persistence_intervals_in_one_dimension_from_file( filename , dimension ); + } this->construct( intervals_ , filter, erase_below_diagonal , number_of_pixels , min_ , max_ ); this->set_up_parameters_for_basic_classes(); } diff --git a/src/Gudhi_stat/include/gudhi/persistence_representations/Persistence_intervals.h b/src/Gudhi_stat/include/gudhi/persistence_representations/Persistence_intervals.h index 2c3e4803..2ff4d7f7 100644 --- a/src/Gudhi_stat/include/gudhi/persistence_representations/Persistence_intervals.h +++ b/src/Gudhi_stat/include/gudhi/persistence_representations/Persistence_intervals.h @@ -25,8 +25,6 @@ //gudhi include #include <gudhi/read_persistence_from_file.h> -//Bottleneck distance: -//#include <gudhi/Bottleneck.h> //standard include #include <limits> @@ -51,8 +49,9 @@ public: /** * This is a constructor of a class Persistence_intervals from a text file. Each line of the input file is supposed to contain two numbers of a type doube (or convertable to double) * representing the birth and the death of the persistence interval. If the pairs are not sorted so that birth <= death, then the constructor will sort then that way. + * * The second parameter of a constructor is a dimension of intervals to be read from a file. If your file contains only birt-death pairs, use the default value. **/ - Persistence_intervals( const char* filename ); + Persistence_intervals( const char* filename , unsigned dimension = std::numeric_limits<unsigned>::max() ); /** * This is a constructor of a class Persistence_intervals from a vector of pairs. Each pair is assumed to represent a persistence interval. We assume that the first elemnets of pairs @@ -247,26 +246,6 @@ public: return this->number_of_functions_for_vectorization; } - /** - *Computations of distance from the current persistnce diagram to the persistence diagram given as a parameter of this function. - *The last but one parameter, power, is here in case we would like to compute p=th Wasserstein distance. At the moment, this method only implement Bottleneck distance, - * which is infinity Wasserstein distance. Therefore any power which is not the default std::numeric_limits< double >::max() will be ignored and an - * exception will be thrown. - * The last parameter, tolerance, it is an additiv error of the approimation, set by default to zero. - **/ - double distance( const Persistence_intervals& second , double power = std::numeric_limits< double >::max() , double tolerance = 0) const - { - if ( power >= std::numeric_limits< double >::max() ) - { - //return Gudhi::persistence_diagram::bottleneck_distance(this->intervals, second.intervals, tolerance); - return 1; - } - else - { - std::cerr << "At the moment Gudhi do not support Wasserstein distances. We only support Bottleneck distance." << std::endl; - throw "At the moment Gudhi do not support Wasserstein distances. We only support Bottleneck distance."; - } - } //end of implementation of functions needed for concepts. //end of implementation of functions needed for concepts. @@ -303,7 +282,7 @@ protected: }; -Persistence_intervals::Persistence_intervals( const char* filename ) +Persistence_intervals::Persistence_intervals( const char* filename , unsigned dimension ) { //bool dbg = false; //ifstream in; @@ -336,10 +315,14 @@ Persistence_intervals::Persistence_intervals( const char* filename ) // } //} //in.close(); - //standard file with barcode - this->intervals = read_standard_persistence_file( filename ); - //gudhi file with barcode - //this->intervals = read_gudhi_persistence_file_in_one_dimension( filename , dimension ); + if ( dimension == std::numeric_limits<unsigned>::max() ) + { + this->intervals = read_persistence_intervals_in_one_dimension_from_file( filename ); + } + else + { + this->intervals = read_persistence_intervals_in_one_dimension_from_file( filename , dimension ); + } this->set_up_numbers_of_functions_for_vectorization_and_projections_to_reals(); }//Persistence_intervals diff --git a/src/Gudhi_stat/include/gudhi/persistence_representations/Persistence_intervals_with_distances.h b/src/Gudhi_stat/include/gudhi/persistence_representations/Persistence_intervals_with_distances.h new file mode 100644 index 00000000..84a95e95 --- /dev/null +++ b/src/Gudhi_stat/include/gudhi/persistence_representations/Persistence_intervals_with_distances.h @@ -0,0 +1,76 @@ +/* This file is part of the Gudhi hiLibrary. 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/>. + */ + +#ifndef Persistence_intervals_WITH_DISTANCES_H_ +#define Persistence_intervals_WITH_DISTANCES_H_ + + +#include <gudhi/persistence_representations/Persistence_intervals.h> +#include <gudhi/Bottleneck.h> + +namespace Gudhi +{ +namespace Gudhi_stat +{ + +class Persistence_intervals_with_distances : public Persistence_intervals +{ +public: + /** + * This is a constructor of a class Persistence_intervals_with_distances from a text file. Each line of the input file is supposed to contain two numbers of a type doube (or convertable to double) + * representing the birth and the death of the persistence interval. If the pairs are not sorted so that birth <= death, then the constructor will sort then that way. + * The second parameter of a constructor is a dimension of intervals to be read from a file. If your file contains only birt-death pairs, use the default value. + **/ + Persistence_intervals_with_distances( const char* filename , unsigned dimension = std::numeric_limits<unsigned>::max() ):Persistence_intervals( filename , dimension ){} + + /** + * This is a constructor of a class Persistence_intervals_with_distances from a vector of pairs. Each pair is assumed to represent a persistence interval. We assume that the first elemnets of pairs + * are smaller or equal the second elements of pairs. + **/ + Persistence_intervals_with_distances( const std::vector< std::pair< double,double > >& intervals ):Persistence_intervals( intervals ){} + + /** + *Computations of distance from the current persistnce diagram to the persistence diagram given as a parameter of this function. + *The last but one parameter, power, is here in case we would like to compute p=th Wasserstein distance. At the moment, this method only implement Bottleneck distance, + * which is infinity Wasserstein distance. Therefore any power which is not the default std::numeric_limits< double >::max() will be ignored and an + * exception will be thrown. + * The last parameter, tolerance, it is an additiv error of the approimation, set by default to zero. + **/ + double distance( const Persistence_intervals_with_distances& second , double power = std::numeric_limits< double >::max() , double tolerance = 0) const + { + if ( power >= std::numeric_limits< double >::max() ) + { + return Gudhi::persistence_diagram::bottleneck_distance(this->intervals, second.intervals, tolerance); + } + else + { + std::cerr << "At the moment Gudhi do not support Wasserstein distances. We only support Bottleneck distance." << std::endl; + throw "At the moment Gudhi do not support Wasserstein distances. We only support Bottleneck distance."; + } + } +}; + + +}//namespace gudhi stat +}//namespace gudhi + +#endif diff --git a/src/Gudhi_stat/include/gudhi/persistence_representations/Persistence_landscape.h b/src/Gudhi_stat/include/gudhi/persistence_representations/Persistence_landscape.h index 0d8fe5fe..681f5d8d 100644 --- a/src/Gudhi_stat/include/gudhi/persistence_representations/Persistence_landscape.h +++ b/src/Gudhi_stat/include/gudhi/persistence_representations/Persistence_landscape.h @@ -80,7 +80,7 @@ public: * Constructor that reads persistence intervals from file and creates persistence landscape. The format of the input file is the following: in each line we put birth-death pair. Last line is assumed * to be empty. Even if the points within a line are not ordered, they will be ordered while the input is read. **/ - Persistence_landscape(const char* filename , size_t dimension = 0); + Persistence_landscape(const char* filename , size_t dimension = std::numeric_limits<unsigned>::max() ); @@ -548,13 +548,18 @@ Persistence_landscape::Persistence_landscape(const char* filename , size_t dimen if ( dbg ) { std::cerr << "Using constructor : Persistence_landscape(char* filename)" << std::endl; - } - //standard file with barcode - //std::vector< std::pair< double , double > > barcode = read_standard_persistence_file( filename ); - //gudhi file with barcode - std::vector< std::pair< double , double > > barcode = read_gudhi_persistence_file_in_one_dimension( filename , dimension ); - this->construct_persistence_landscape_from_barcode( barcode ); - this->set_up_numbers_of_functions_for_vectorization_and_projections_to_reals(); + } + std::vector< std::pair< double , double > > barcode; + if ( dimension == std::numeric_limits<unsigned>::max() ) + { + barcode = read_persistence_intervals_in_one_dimension_from_file( filename ); + } + else + { + barcode = read_persistence_intervals_in_one_dimension_from_file( filename , dimension ); + } + this->construct_persistence_landscape_from_barcode( barcode ); + this->set_up_numbers_of_functions_for_vectorization_and_projections_to_reals(); } diff --git a/src/Gudhi_stat/include/gudhi/persistence_representations/Persistence_landscape_on_grid.h b/src/Gudhi_stat/include/gudhi/persistence_representations/Persistence_landscape_on_grid.h index 02a80435..1f4cb3ff 100644 --- a/src/Gudhi_stat/include/gudhi/persistence_representations/Persistence_landscape_on_grid.h +++ b/src/Gudhi_stat/include/gudhi/persistence_representations/Persistence_landscape_on_grid.h @@ -33,6 +33,7 @@ #include <algorithm> #include <unistd.h> #include <cmath> +#include <limits> //gudhi include @@ -84,14 +85,14 @@ public: * to be empty. Even if the points within a line are not ordered, they will be ordered while the input is read. The additional parameters of this procedure are: ranges of grid, resoltion of a grid * number of landscape functions to be created and the dimension of intervals that are need to be read from a file (in case of Gudhi format files). **/ - Persistence_landscape_on_grid(const char* filename , double grid_min_, double grid_max_ , size_t number_of_points_ , unsigned number_of_levels_of_landscape , size_t dimension_ = 0 ); + Persistence_landscape_on_grid(const char* filename , double grid_min_, double grid_max_ , size_t number_of_points_ , unsigned number_of_levels_of_landscape , unsigned short dimension_ = std::numeric_limits<unsigned short>::max() ); /** * Constructor that reads persistence intervals from file and creates persistence landscape. The format of the input file is the following: in each line we put birth-death pair. Last line is assumed * to be empty. Even if the points within a line are not ordered, they will be ordered while the input is read. The additional parameters of this procedure are: ranges of grid, resoltion of a grid * and the dimension of intervals that are need to be read from a file (in case of Gudhi format files). **/ - Persistence_landscape_on_grid(const char* filename , double grid_min_, double grid_max_ , size_t number_of_points_ , size_t dimension_ = 0 ); + Persistence_landscape_on_grid(const char* filename , double grid_min_, double grid_max_ , size_t number_of_points_ , unsigned short dimension_ = std::numeric_limits<unsigned short>::max() ); /** @@ -99,14 +100,15 @@ public: * to be empty. Even if the points within a line are not ordered, they will be ordered while the input is read. The additional parameter is the resoution of a grid and the number of landscape * functions to be created. The remaning parameters are calculated based on data. **/ - Persistence_landscape_on_grid(const char* filename , size_t number_of_points , unsigned number_of_levels_of_landscape ); + Persistence_landscape_on_grid(const char* filename , size_t number_of_points , unsigned number_of_levels_of_landscape , unsigned short dimension = std::numeric_limits<unsigned short>::max() ); /** * Constructor that reads persistence intervals from file and creates persistence landscape. The format of the input file is the following: in each line we put birth-death pair. Last line is assumed - * to be empty. Even if the points within a line are not ordered, they will be ordered while the input is read. The additional parameter is the resoution of a grid. The remaning paraameters are - * calculated based on data. + * to be empty. Even if the points within a line are not ordered, they will be ordered while the input is read. The additional parameter is the resoution of a grid. The last parameter is the dimension + * of a persistence to read from the file. If your file contains only persistence pair in a single dimension, please set it up to std::numeric_limits<unsigned>::max(). + * The remaning parameters are calculated based on data. **/ - Persistence_landscape_on_grid(const char* filename , size_t number_of_points ); + Persistence_landscape_on_grid(const char* filename , size_t number_of_points , unsigned short dimension = std::numeric_limits<unsigned short>::max() ); /** @@ -1256,33 +1258,45 @@ Persistence_landscape_on_grid::Persistence_landscape_on_grid( const std::vector< } -Persistence_landscape_on_grid::Persistence_landscape_on_grid(const char* filename , double grid_min_, double grid_max_ , size_t number_of_points_ , size_t dimension ) +Persistence_landscape_on_grid::Persistence_landscape_on_grid(const char* filename , double grid_min_, double grid_max_ , size_t number_of_points_ , unsigned short dimension ) { - //standard file with barcode - std::vector< std::pair< double , double > > p = read_standard_persistence_file( filename ); - //gudhi file with barcode - //std::vector< std::pair< double , double > > p = read_gudhi_persistence_file_in_one_dimension( filename , dimension ); - - this->set_up_values_of_landscapes( p , grid_min_ , grid_max_ , number_of_points_ ); + std::vector< std::pair< double , double > > p; + if ( dimension == std::numeric_limits<unsigned short>::max() ) + { + p = read_persistence_intervals_in_one_dimension_from_file( filename ); + } + else + { + p = read_persistence_intervals_in_one_dimension_from_file( filename , dimension ); + } + this->set_up_values_of_landscapes( p , grid_min_ , grid_max_ , number_of_points_ ); } -Persistence_landscape_on_grid::Persistence_landscape_on_grid(const char* filename , double grid_min_, double grid_max_ , size_t number_of_points_, unsigned number_of_levels_of_landscape, size_t dimension ) +Persistence_landscape_on_grid::Persistence_landscape_on_grid(const char* filename , double grid_min_, double grid_max_ , size_t number_of_points_, unsigned number_of_levels_of_landscape, unsigned short dimension ) { - //standard file with barcode - std::vector< std::pair< double , double > > p = read_standard_persistence_file( filename ); - //gudhi file with barcode - //std::vector< std::pair< double , double > > p = read_gudhi_persistence_file_in_one_dimension( filename , dimension ); - - this->set_up_values_of_landscapes( p , grid_min_ , grid_max_ , number_of_points_ , number_of_levels_of_landscape ); + std::vector< std::pair< double , double > > p; + if ( dimension == std::numeric_limits<unsigned short>::max() ) + { + p = read_persistence_intervals_in_one_dimension_from_file( filename ); + } + else + { + p = read_persistence_intervals_in_one_dimension_from_file( filename , dimension ); + } + this->set_up_values_of_landscapes( p , grid_min_ , grid_max_ , number_of_points_ , number_of_levels_of_landscape ); } -Persistence_landscape_on_grid::Persistence_landscape_on_grid(const char* filename , size_t number_of_points_ ) +Persistence_landscape_on_grid::Persistence_landscape_on_grid(const char* filename , size_t number_of_points_ , unsigned short dimension ) { - //standard file with barcode - std::vector< std::pair< double , double > > p = read_standard_persistence_file( filename ); - //gudhi file with barcode - //std::vector< std::pair< double , double > > p = read_gudhi_persistence_file_in_one_dimension( filename , dimension ); - + std::vector< std::pair< double , double > > p; + if ( dimension == std::numeric_limits<unsigned short>::max() ) + { + p = read_persistence_intervals_in_one_dimension_from_file( filename ); + } + else + { + p = read_persistence_intervals_in_one_dimension_from_file( filename , dimension ); + } double grid_min_ = std::numeric_limits<double>::max(); double grid_max_ = -std::numeric_limits<double>::max(); for ( size_t i = 0 ; i != p.size() ; ++i ) @@ -1293,13 +1307,17 @@ Persistence_landscape_on_grid::Persistence_landscape_on_grid(const char* filenam this->set_up_values_of_landscapes( p , grid_min_ , grid_max_ , number_of_points_ ); } -Persistence_landscape_on_grid::Persistence_landscape_on_grid(const char* filename , size_t number_of_points_ , unsigned number_of_levels_of_landscape ) +Persistence_landscape_on_grid::Persistence_landscape_on_grid(const char* filename , size_t number_of_points_ , unsigned number_of_levels_of_landscape , unsigned short dimension ) { - //standard file with barcode - std::vector< std::pair< double , double > > p = read_standard_persistence_file( filename ); - //gudhi file with barcode - //std::vector< std::pair< double , double > > p = read_gudhi_persistence_file_in_one_dimension( filename , dimension ); - + std::vector< std::pair< double , double > > p; + if ( dimension == std::numeric_limits<unsigned short>::max() ) + { + p = read_persistence_intervals_in_one_dimension_from_file( filename ); + } + else + { + p = read_persistence_intervals_in_one_dimension_from_file( filename , dimension ); + } double grid_min_ = std::numeric_limits<double>::max(); double grid_max_ = -std::numeric_limits<double>::max(); for ( size_t i = 0 ; i != p.size() ; ++i ) diff --git a/src/Gudhi_stat/include/gudhi/persistence_representations/persistence_vectors.h b/src/Gudhi_stat/include/gudhi/persistence_representations/persistence_vectors.h index b1a3e4fd..aa1f23c2 100644 --- a/src/Gudhi_stat/include/gudhi/persistence_representations/persistence_vectors.h +++ b/src/Gudhi_stat/include/gudhi/persistence_representations/persistence_vectors.h @@ -105,7 +105,7 @@ public: /** * The constructor taking as an input a file with birth-death pairs. The second parameter is the desiered length of the output vectors. **/ - Vector_distances_in_diagram( const char* filename , size_t where_to_cut ); + Vector_distances_in_diagram( const char* filename , size_t where_to_cut , unsigned dimension = std::numeric_limits<unsigned>::max() ); /** @@ -432,13 +432,17 @@ Vector_distances_in_diagram<F>::Vector_distances_in_diagram( const std::vector< } template <typename F> -Vector_distances_in_diagram<F>::Vector_distances_in_diagram( const char* filename , size_t where_to_cut ):where_to_cut(where_to_cut) -{ - //standard file with barcode - std::vector< std::pair< double , double > > intervals = read_standard_persistence_file( filename ); - //gudhi file with barcode - //std::vector< std::pair< double , double > > intervals = read_gudhi_persistence_file( filename , dimension ); - +Vector_distances_in_diagram<F>::Vector_distances_in_diagram( const char* filename , size_t where_to_cut , unsigned dimension ):where_to_cut(where_to_cut) +{ + std::vector< std::pair< double , double > > intervals; + if ( dimension == std::numeric_limits<unsigned>::max() ) + { + intervals = read_persistence_intervals_in_one_dimension_from_file( filename ); + } + else + { + intervals = read_persistence_intervals_in_one_dimension_from_file( filename , dimension ); + } this->intervals = intervals; this->compute_sorted_vector_of_distances_via_heap( where_to_cut ); //this->compute_sorted_vector_of_distances_via_vector_sorting( where_to_cut ); diff --git a/src/Gudhi_stat/include/gudhi/topological_process.h b/src/Gudhi_stat/include/gudhi/topological_process.h index 17bea5ab..03edbb85 100644 --- a/src/Gudhi_stat/include/gudhi/topological_process.h +++ b/src/Gudhi_stat/include/gudhi/topological_process.h @@ -39,6 +39,9 @@ namespace Gudhi { namespace Gudhi_stat { + + +//TODO, change reading procedures so that they also accept the value of dimension. //over here we will need a few version of construct_representation_from_file procedure, since different representations may require different parameters. This is a procedure that in my //oppinion cannot be standarize, since construction of representation cannot. But, the remaining part of the code in my opinion is free from any details of representation. @@ -62,7 +65,7 @@ std::vector< std::vector< std::pair< double , double > > > read_persistence_pair for ( size_t i = 0 ; i != files.size() ; ++i ) { - std::vector< std::pair< double , double > > diag = read_standard_persistence_file( files[i].c_str() ); + std::vector< std::pair< double , double > > diag = read_persistence_intervals_in_one_dimension_from_file( files[i].c_str() ); result.push_back( diag ); if ( dbg ) { diff --git a/src/Gudhi_stat/test/persistence_lanscapes_on_grid_test.cpp b/src/Gudhi_stat/test/persistence_lanscapes_on_grid_test.cpp index ae771149..54fb2b84 100644 --- a/src/Gudhi_stat/test/persistence_lanscapes_on_grid_test.cpp +++ b/src/Gudhi_stat/test/persistence_lanscapes_on_grid_test.cpp @@ -44,7 +44,7 @@ double epsilon = 0.0000005; BOOST_AUTO_TEST_CASE(check_construction_of_landscape) { - Persistence_landscape_on_grid l( "data/file_with_diagram_1" , 100 ); + Persistence_landscape_on_grid l( "data/file_with_diagram_1" , 100 , std::numeric_limits<unsigned short>::max()); l.print_to_file( "landscape_from_file_with_diagram_1" ); Persistence_landscape_on_grid g; @@ -57,8 +57,8 @@ BOOST_AUTO_TEST_CASE(check_construction_of_landscape_using_only_ten_levels) { //TODO unsigned number = 10; - Persistence_landscape_on_grid l( "data/file_with_diagram_1" , 100 ,number ); - Persistence_landscape_on_grid g( "data/file_with_diagram_1" , 100 ); + Persistence_landscape_on_grid l( "data/file_with_diagram_1" , 100 , number ); + Persistence_landscape_on_grid g( "data/file_with_diagram_1" , 100 , std::numeric_limits<unsigned short>::max()); //cut all the elements of order > 10 in g. for ( size_t level = 0 ; level != number ; ++level ) @@ -77,7 +77,7 @@ BOOST_AUTO_TEST_CASE(check_construction_of_landscape_using_only_ten_levels) BOOST_AUTO_TEST_CASE(check_computations_of_integrals) { - Persistence_landscape_on_grid p( "data/file_with_diagram_1" , 100 ); + Persistence_landscape_on_grid p( "data/file_with_diagram_1" , 100 , std::numeric_limits<unsigned short>::max()); double integral = p.compute_integral_of_landscape(); //cerr << "integral : " << integral << endl;getchar(); BOOST_CHECK( fabs( integral - 27.343 ) <= 0.00005 ); @@ -86,7 +86,7 @@ BOOST_AUTO_TEST_CASE(check_computations_of_integrals) BOOST_AUTO_TEST_CASE(check_computations_of_integrals_for_each_level_separatelly) { - Persistence_landscape_on_grid p( "data/file_with_diagram_1" , 100 ); + Persistence_landscape_on_grid p( "data/file_with_diagram_1" , 100, std::numeric_limits<unsigned short>::max() ); std::vector< double > integrals_fir_different_levels; //integrals_fir_different_levels.push_back(); @@ -125,7 +125,7 @@ BOOST_AUTO_TEST_CASE(check_computations_of_integrals_for_each_level_separatelly) BOOST_AUTO_TEST_CASE(check_computations_of_integrals_of_powers_of_landscape) { - Persistence_landscape_on_grid p( "data/file_with_diagram_1" , 100 ); + Persistence_landscape_on_grid p( "data/file_with_diagram_1" , 100, std::numeric_limits<unsigned short>::max() ); std::vector<double> integrals_fir_different_powers; integrals_fir_different_powers.push_back( 0.241168); @@ -145,7 +145,7 @@ BOOST_AUTO_TEST_CASE(check_computations_of_integrals_of_powers_of_landscape) BOOST_AUTO_TEST_CASE(check_computations_of_values_on_different_points) { - Persistence_landscape_on_grid p( "data/file_with_diagram_1" , 100 ); + Persistence_landscape_on_grid p( "data/file_with_diagram_1" , 100, std::numeric_limits<unsigned short>::max() ); std::vector< double > results_level_0; results_level_0.push_back(0.00997867); @@ -184,8 +184,8 @@ BOOST_AUTO_TEST_CASE(check_computations_of_values_on_different_points) BOOST_AUTO_TEST_CASE(check_computations_sum_differences_and_multiplications) { - Persistence_landscape_on_grid p( "data/file_with_diagram_1" ,100 ); - Persistence_landscape_on_grid second("data/file_with_diagram_1" , 100 ); + Persistence_landscape_on_grid p( "data/file_with_diagram_1" ,100 , std::numeric_limits<unsigned short>::max()); + Persistence_landscape_on_grid second("data/file_with_diagram_1" , 100, std::numeric_limits<unsigned short>::max() ); Persistence_landscape_on_grid sum = p + second; Persistence_landscape_on_grid difference = p - second; @@ -210,8 +210,8 @@ BOOST_AUTO_TEST_CASE(check_computations_sum_differences_and_multiplications) BOOST_AUTO_TEST_CASE(check_computations_of_maxima_and_norms) { - Persistence_landscape_on_grid p( "data/file_with_diagram_1" , 0 , 1 , 100 ); - Persistence_landscape_on_grid second("data/file_with_diagram_2" , 0 , 1 , 100 ); + Persistence_landscape_on_grid p( "data/file_with_diagram_1" , 0. , 1. , 100 ); + Persistence_landscape_on_grid second("data/file_with_diagram_2" , 0. , 1. , 100 ); Persistence_landscape_on_grid sum = p + second; //cerr << p.compute_maximum() << endl; @@ -236,8 +236,8 @@ BOOST_AUTO_TEST_CASE(check_computations_of_maxima_and_norms) BOOST_AUTO_TEST_CASE(check_computations_of_averages) { - Persistence_landscape_on_grid p( "data/file_with_diagram", 0,1,100 ); - Persistence_landscape_on_grid q( "data/file_with_diagram_1", 0,1,100 ); + Persistence_landscape_on_grid p( "data/file_with_diagram", 0.,1.,100 ); + Persistence_landscape_on_grid q( "data/file_with_diagram_1", 0.,1.,100 ); Persistence_landscape_on_grid av; av.compute_average( {&p,&q} ); @@ -251,8 +251,8 @@ BOOST_AUTO_TEST_CASE(check_computations_of_averages) BOOST_AUTO_TEST_CASE(check_computations_of_distances) { - Persistence_landscape_on_grid p( "data/file_with_diagram", 0,1,10000 ); - Persistence_landscape_on_grid q( "data/file_with_diagram_1", 0,1,10000 ); + Persistence_landscape_on_grid p( "data/file_with_diagram", 0.,1.,10000 ); + Persistence_landscape_on_grid q( "data/file_with_diagram_1", 0.,1.,10000 ); BOOST_CHECK( fabs( p.distance( q )- 25.5779) <= 0.00005 ); BOOST_CHECK( fabs( p.distance( q , 2) - 2.04891) <= 0.00001 ); BOOST_CHECK( fabs( p.distance( q , std::numeric_limits<double>::max() )-0.359 ) <= 0.00001 ); @@ -261,8 +261,8 @@ BOOST_AUTO_TEST_CASE(check_computations_of_distances) BOOST_AUTO_TEST_CASE(check_computations_of_scalar_product) { - Persistence_landscape_on_grid p( "data/file_with_diagram" , 0,1,10000); - Persistence_landscape_on_grid q( "data/file_with_diagram_1", 0,1,10000 ); + Persistence_landscape_on_grid p( "data/file_with_diagram" , 0.,1.,10000); + Persistence_landscape_on_grid q( "data/file_with_diagram_1", 0.,1.,10000 ); //std::cerr << p.compute_scalar_product( q ) << std::endl; BOOST_CHECK( almost_equal( p.compute_scalar_product( q ) , 0.754367 ) ); } @@ -375,3 +375,4 @@ BOOST_AUTO_TEST_CASE(check_computations_of_scalar_product) //Persistence_landscape_on_grid q( aa, 0,1,10 ); cerr << p.compute_scalar_product( &q ) << endl; */ + 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() ); |
