diff options
Diffstat (limited to 'src/Gudhi_stat/example')
| -rw-r--r-- | src/Gudhi_stat/example/CMakeLists.txt | 21 | ||||
| -rw-r--r-- | src/Gudhi_stat/example/persistence_heat_maps.cpp | 93 | ||||
| -rw-r--r-- | src/Gudhi_stat/example/persistence_intervals.cpp | 111 | ||||
| -rw-r--r-- | src/Gudhi_stat/example/persistence_landscape.cpp | 92 | ||||
| -rw-r--r-- | src/Gudhi_stat/example/persistence_landscape_on_grid.cpp | 88 | ||||
| -rw-r--r-- | src/Gudhi_stat/example/vector_representation.cpp | 80 |
6 files changed, 485 insertions, 0 deletions
diff --git a/src/Gudhi_stat/example/CMakeLists.txt b/src/Gudhi_stat/example/CMakeLists.txt new file mode 100644 index 00000000..5ae6cd6a --- /dev/null +++ b/src/Gudhi_stat/example/CMakeLists.txt @@ -0,0 +1,21 @@ +cmake_minimum_required(VERSION 2.6) +project(GUDHI_STAT) + +add_executable ( persistence_landscape_on_grid persistence_landscape_on_grid.cpp ) +target_link_libraries(persistence_landscape_on_grid ${Boost_SYSTEM_LIBRARY}) + +add_executable ( persistence_landscape persistence_landscape.cpp ) +target_link_libraries(persistence_landscape ${Boost_SYSTEM_LIBRARY}) + +add_executable ( persistence_intervals persistence_intervals.cpp ) +target_link_libraries(persistence_intervals ${Boost_SYSTEM_LIBRARY}) + +add_executable ( vector_representation vector_representation.cpp ) +target_link_libraries(vector_representation ${Boost_SYSTEM_LIBRARY}) + +add_executable ( persistence_heat_maps persistence_heat_maps.cpp ) +target_link_libraries(persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) + + + + diff --git a/src/Gudhi_stat/example/persistence_heat_maps.cpp b/src/Gudhi_stat/example/persistence_heat_maps.cpp new file mode 100644 index 00000000..0e5f7b79 --- /dev/null +++ b/src/Gudhi_stat/example/persistence_heat_maps.cpp @@ -0,0 +1,93 @@ +/* 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/reader_utils.h> +#include <gudhi/persistence_representations/Persistence_heat_maps.h> + +#include <iostream> +#include <vector> + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + + +double epsilon = 0.0000005; + + + +int main( int argc , char** argv ) +{ + //create two simple vectors with birth--death pairs: + + std::vector< std::pair< double , double > > persistence1; + std::vector< std::pair< double , double > > persistence2; + + persistence1.push_back( std::make_pair(1,2) ); + persistence1.push_back( std::make_pair(6,8) ); + persistence1.push_back( std::make_pair(0,4) ); + persistence1.push_back( std::make_pair(3,8) ); + + persistence2.push_back( std::make_pair(2,9) ); + persistence2.push_back( std::make_pair(1,6) ); + persistence2.push_back( std::make_pair(3,5) ); + persistence2.push_back( std::make_pair(6,10) ); + + //over here we define a function we sill put on a top on every birth--death pair in the persistence interval. It can be anything. Over here we will use standarg Gaussian + std::vector< std::vector<double> > filter = create_Gaussian_filter(5,1); + + //creating two heat maps. + Persistence_heat_maps<constant_scaling_function> hm1( persistence1 , filter , false , 20 , 0 , 11 ); + Persistence_heat_maps<constant_scaling_function> hm2( persistence2 , filter , false , 20 , 0 , 11 ); + + std::vector<Persistence_heat_maps<constant_scaling_function>*> vector_of_maps; + vector_of_maps.push_back( &hm1 ); + vector_of_maps.push_back( &hm2 ); + + //compute median/mean of a vector of heat maps: + Persistence_heat_maps<constant_scaling_function> mean; + mean.compute_mean( vector_of_maps ); + Persistence_heat_maps<constant_scaling_function> median; + median.compute_median( vector_of_maps ); + + //to compute L^1 disance between hm1 and hm2: + std::cout << "The L^1 distance is : " << hm1.distance( hm2 , 1 ) << std::endl; + + //to average of hm1 and hm2: + std::vector< Persistence_heat_maps<constant_scaling_function>* > to_average; + to_average.push_back( &hm1 ); + to_average.push_back( &hm2 ); + Persistence_heat_maps<constant_scaling_function> av; + av.compute_average( to_average ); + + //to compute scalar product of hm1 and hm2: + std::cout << "Scalar product is : " << hm1.compute_scalar_product( hm2 ) << std::endl; + + return 0; +} + + + + diff --git a/src/Gudhi_stat/example/persistence_intervals.cpp b/src/Gudhi_stat/example/persistence_intervals.cpp new file mode 100644 index 00000000..60d5a811 --- /dev/null +++ b/src/Gudhi_stat/example/persistence_intervals.cpp @@ -0,0 +1,111 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + + + +#include <gudhi/reader_utils.h> +#include <gudhi/persistence_representations/Persistence_intervals.h> + +#include <iostream> + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + + +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"; + return 1; + } + + Persistence_intervals p( argv[1] ); + std::pair<double,double> min_max_ = p.min_max(); + std::cout << "Birth-death range : " << min_max_.first << " " << min_max_.second << std::endl; + + + std::vector<double> dominant_ten_intervals_length = p.length_of_dominant_intervals(10); + std::cout << "Lendth of ten dominant intervals : " <<std::endl; + for ( size_t i = 0 ; i != dominant_ten_intervals_length.size() ; ++i ) + { + std::cout << dominant_ten_intervals_length[i] <<std::endl; + } + + std::vector< std::pair<double,double> > ten_dominant_intervals = p.dominant_intervals( 10 ); + std::cout << "Here are the dominant intervals : " <<std::endl; + for ( size_t i = 0 ; i != ten_dominant_intervals.size() ; ++i ) + { + std::cout << "( " << ten_dominant_intervals[i].first<< "," << ten_dominant_intervals[i].second <<std::endl; + } + + std::vector< size_t > histogram = p.histogram_of_lengths( 10 ); + std::cout << "Here is the histogram of barcode's length : " <<std::endl; + for ( size_t i = 0 ; i != histogram.size() ; ++i ) + { + std::cout << histogram[i] << " "; + } + std::cout <<std::endl; + + + std::vector< size_t > cumulative_histogram = p.cumulative_histogram_of_lengths( 10 ); + std::cout<< "Cumuative histogram : " <<std::endl; + for ( size_t i = 0 ; i != cumulative_histogram.size() ; ++i ) + { + std::cout << cumulative_histogram[i] << " "; + } + std::cout <<std::endl; + + std::vector< double > char_funct_diag = p.characteristic_function_of_diagram( min_max_.first , min_max_.second ); + std::cout << "Characteristic function of diagram : " <<std::endl; + for ( size_t i = 0 ; i != char_funct_diag.size() ; ++i ) + { + std::cout << char_funct_diag[i] << " "; + } + std::cout <<std::endl; + + std::vector< double > cumul_char_funct_diag = p.cumulative_characteristic_function_of_diagram( min_max_.first , min_max_.second ); + std::cout << "Cumulative characteristic function of diagram : " <<std::endl; + for ( size_t i = 0 ; i != cumul_char_funct_diag.size() ; ++i ) + { + std::cout << cumul_char_funct_diag[i] << " "; + } + std::cout <<std::endl; + + std::cout << "Persistence Betti numbers \n"; + std::vector< std::pair< double , size_t > > pbns = p.compute_persistent_betti_numbers(); + for ( size_t i = 0 ; i != pbns.size() ; ++i ) + { + std::cout << pbns[i].first << " " << pbns[i].second <<std::endl; + } + + return 0; +} + + + + + + + diff --git a/src/Gudhi_stat/example/persistence_landscape.cpp b/src/Gudhi_stat/example/persistence_landscape.cpp new file mode 100644 index 00000000..9385c408 --- /dev/null +++ b/src/Gudhi_stat/example/persistence_landscape.cpp @@ -0,0 +1,92 @@ +/* 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_landscape.h> + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +#include <iostream> + + +int main( int argc , char** argv ) +{ + //create two simple vectors with birth--death pairs: + + std::vector< std::pair< double , double > > persistence1; + std::vector< std::pair< double , double > > persistence2; + + persistence1.push_back( std::make_pair(1,2) ); + persistence1.push_back( std::make_pair(6,8) ); + persistence1.push_back( std::make_pair(0,4) ); + persistence1.push_back( std::make_pair(3,8) ); + + persistence2.push_back( std::make_pair(2,9) ); + persistence2.push_back( std::make_pair(1,6) ); + persistence2.push_back( std::make_pair(3,5) ); + persistence2.push_back( std::make_pair(6,10) ); + + //create two persistence landscapes based on persistence1 and persistence2: + Persistence_landscape l1( persistence1 ); + Persistence_landscape l2( persistence2 ); + + //This is how to compute integral of landscapes: + std::cout << "Integral of the first landscape : " << l1.compute_integral_of_landscape() << std::endl; + std::cout << "Integral of the second landscape : " << l2.compute_integral_of_landscape() << std::endl; + + //And here how to write landscapes to stream: + std::cout << "l1 : " << l1 << std::endl; + std::cout << "l2 : " << l2 << std::endl; + + //Arythmetic operations on landscapes: + Persistence_landscape sum = l1+l2; + std::cout << "sum : " << sum << std::endl; + + //here are the maxima of the functions: + std::cout << "Maximum of l1 : " << l1.compute_maximum() << std::endl; + std::cout << "Maximum of l2 : " << l2.compute_maximum() << std::endl; + + //here are the norms of landscapes: + std::cout << "L^1 Norm of l1 : " << l1.compute_norm_of_landscape( 1. ) << std::endl; + std::cout << "L^1 Norm of l2 : " << l2.compute_norm_of_landscape( 1. ) << std::endl; + + //here is the average of landscapes: + Persistence_landscape average; + average.compute_average( {&l1,&l2} ); + std::cout << "average : " << average << std::endl; + + //here is the distance of landscapes: + std::cout << "Distance : " << l1.distance( l2 ) << std::endl; + + //here is the scalar product of landscapes: + std::cout << "Scalar product : " << l1.compute_scalar_product( l2 ) << std::endl; + + //here is how to create a file which is suitable for vizualization via gnuplot: + average.plot( "average_landscape" ); + + return 0; +} + diff --git a/src/Gudhi_stat/example/persistence_landscape_on_grid.cpp b/src/Gudhi_stat/example/persistence_landscape_on_grid.cpp new file mode 100644 index 00000000..d432d757 --- /dev/null +++ b/src/Gudhi_stat/example/persistence_landscape_on_grid.cpp @@ -0,0 +1,88 @@ +/* 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_landscape_on_grid.h> + + + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + +#include <iostream> + + +int main( int argc , char** argv ) +{ + //create two simple vectors with birth--death pairs: + + std::vector< std::pair< double , double > > persistence1; + std::vector< std::pair< double , double > > persistence2; + + persistence1.push_back( std::make_pair(1,2) ); + persistence1.push_back( std::make_pair(6,8) ); + persistence1.push_back( std::make_pair(0,4) ); + persistence1.push_back( std::make_pair(3,8) ); + + persistence2.push_back( std::make_pair(2,9) ); + persistence2.push_back( std::make_pair(1,6) ); + persistence2.push_back( std::make_pair(3,5) ); + persistence2.push_back( std::make_pair(6,10) ); + + //create two persistence landscapes based on persistence1 and persistence2: + Persistence_landscape_on_grid l1( persistence1 , 0 , 11 , 20 ); + Persistence_landscape_on_grid l2( persistence2 , 0 , 11 , 20 ); + + //This is how to compute integral of landscapes: + std::cout << "Integral of the first landscape : " << l1.compute_integral_of_landscape() << std::endl; + std::cout << "Integral of the second landscape : " << l2.compute_integral_of_landscape() << std::endl; + + //And here how to write landscapes to stream: + std::cout << "l1 : " << l1 << std::endl; + std::cout << "l2 : " << l2 << std::endl; + + //here are the maxima of the functions: + std::cout << "Maximum of l1 : " << l1.compute_maximum() << std::endl; + std::cout << "Maximum of l2 : " << l2.compute_maximum() << std::endl; + + //here are the norms of landscapes: + std::cout << "L^1 Norm of l1 : " << l1.compute_norm_of_landscape( 1. ) << std::endl; + std::cout << "L^1 Norm of l2 : " << l2.compute_norm_of_landscape( 1. ) << std::endl; + + //here is the average of landscapes: + Persistence_landscape_on_grid average; + average.compute_average( {&l1,&l2} ); + std::cout << "average : " << average << std::endl; + + //here is the distance of landscapes: + std::cout << "Distance : " << l1.distance( l2 ) << std::endl; + + //here is the scalar product of landscapes: + std::cout << "Scalar product : " << l1.compute_scalar_product( l2 ) << std::endl; + + //here is how to create a file which is suitable for vizualization via gnuplot: + average.plot( "average_landscape" ); + + + return 0; +} diff --git a/src/Gudhi_stat/example/vector_representation.cpp b/src/Gudhi_stat/example/vector_representation.cpp new file mode 100644 index 00000000..476deeba --- /dev/null +++ b/src/Gudhi_stat/example/vector_representation.cpp @@ -0,0 +1,80 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2015 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + + + +#include <gudhi/persistence_representations/Vector_distances_in_diagram.h> +#include <iostream> + + +#include <gudhi/reader_utils.h> +#include <vector> +#include <cmath> +#include <iomanip> + +using namespace Gudhi; +using namespace Gudhi::Gudhi_stat; + + + + +int main( int argc , char** argv ) +{ + //create two simple vectors with birth--death pairs: + + std::vector< std::pair< double , double > > persistence1; + std::vector< std::pair< double , double > > persistence2; + + persistence1.push_back( std::make_pair(1,2) ); + persistence1.push_back( std::make_pair(6,8) ); + persistence1.push_back( std::make_pair(0,4) ); + persistence1.push_back( std::make_pair(3,8) ); + + persistence2.push_back( std::make_pair(2,9) ); + persistence2.push_back( std::make_pair(1,6) ); + persistence2.push_back( std::make_pair(3,5) ); + persistence2.push_back( std::make_pair(6,10) ); + + //create two persistence vectors based on persistence1 and persistence2: + Vector_distances_in_diagram<Euclidean_distance<double> > v1 = Vector_distances_in_diagram<Euclidean_distance<double> >( persistence1 , std::numeric_limits<size_t>::max() ); + Vector_distances_in_diagram<Euclidean_distance<double> > v2 = Vector_distances_in_diagram<Euclidean_distance<double> >( persistence2 , std::numeric_limits<size_t>::max() ); + + //writing to a stream: + std::cout << "v1 : " << v1 << std::endl; + std::cout << "v2 : " << v2 << std::endl; + + //averages: + Vector_distances_in_diagram<Euclidean_distance<double> > average; + average.compute_average( {&v1,&v2} ); + std::cout << "Average : " << average << std::endl; + + //computations of distances: + std::cout << "l^1 distance : " << v1.distance( v2 ) << std::endl; + + //computations of scalar product: + std::cout << "Scalar product of l1 and l2 : " << v1.compute_scalar_product( v2 ) << std::endl; + + //create a file with a gnuplot script: + v1.plot( "plot_of_vector_representation" ); + + return 0; +} |