From f9b84f79232ec2fa5935327e38e2862d9c33ab2c Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 30 May 2017 11:13:27 +0000 Subject: Rename Gudhi_stat in Persistence representation git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_representation_integration@2471 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 5307a48496d758110274ef021834394b0a60bf95 --- .../example/CMakeLists.txt | 31 ++++++ .../example/persistence_heat_maps.cpp | 93 +++++++++++++++++ .../example/persistence_intervals.cpp | 111 +++++++++++++++++++++ .../example/persistence_landscape.cpp | 92 +++++++++++++++++ .../example/persistence_landscape_on_grid.cpp | 88 ++++++++++++++++ .../example/persistence_vectors.cpp | 80 +++++++++++++++ .../example/simple_diagram.txt | 4 + 7 files changed, 499 insertions(+) create mode 100644 src/Persistence_representation/example/CMakeLists.txt create mode 100644 src/Persistence_representation/example/persistence_heat_maps.cpp create mode 100644 src/Persistence_representation/example/persistence_intervals.cpp create mode 100644 src/Persistence_representation/example/persistence_landscape.cpp create mode 100644 src/Persistence_representation/example/persistence_landscape_on_grid.cpp create mode 100644 src/Persistence_representation/example/persistence_vectors.cpp create mode 100644 src/Persistence_representation/example/simple_diagram.txt (limited to 'src/Persistence_representation/example') diff --git a/src/Persistence_representation/example/CMakeLists.txt b/src/Persistence_representation/example/CMakeLists.txt new file mode 100644 index 00000000..3c783d36 --- /dev/null +++ b/src/Persistence_representation/example/CMakeLists.txt @@ -0,0 +1,31 @@ +cmake_minimum_required(VERSION 2.6) +project(GUDHI_STAT) + +file(COPY "simple_diagram.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) +add_executable ( persistence_landscape_on_grid persistence_landscape_on_grid.cpp ) +target_link_libraries(persistence_landscape_on_grid ${Boost_SYSTEM_LIBRARY}) +add_test ( persistence_landscape_on_grid ${CMAKE_CURRENT_BINARY_DIR}/persistence_landscape_on_grid ) + +file(COPY "simple_diagram.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) +add_executable ( persistence_landscape persistence_landscape.cpp ) +target_link_libraries(persistence_landscape ${Boost_SYSTEM_LIBRARY}) +add_test ( persistence_landscape ${CMAKE_CURRENT_BINARY_DIR}/persistence_landscape ) + +file(COPY "simple_diagram.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) +add_executable ( persistence_intervals persistence_intervals.cpp ) +target_link_libraries(persistence_intervals ${Boost_SYSTEM_LIBRARY}) +add_test ( persistence_intervals ${CMAKE_CURRENT_BINARY_DIR}/persistence_intervals simple_diagram.txt ) + +file(COPY "simple_diagram.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) +add_executable ( persistence_vectors persistence_vectors.cpp ) +target_link_libraries(persistence_vectors ${Boost_SYSTEM_LIBRARY}) +add_test ( persistence_vectors ${CMAKE_CURRENT_BINARY_DIR}/persistence_vectors ) + +file(COPY "simple_diagram.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) +add_executable ( persistence_heat_maps persistence_heat_maps.cpp ) +target_link_libraries(persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) +add_test ( persistence_heat_maps ${CMAKE_CURRENT_BINARY_DIR}/persistence_heat_maps ) + + + + diff --git a/src/Persistence_representation/example/persistence_heat_maps.cpp b/src/Persistence_representation/example/persistence_heat_maps.cpp new file mode 100644 index 00000000..da87486d --- /dev/null +++ b/src/Persistence_representation/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 . + */ + + + +#include +#include + +#include +#include + + + +using namespace Gudhi; +using namespace Gudhi::Persistence_representations; + + +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 > filter = create_Gaussian_filter(5,1); + + //creating two heat maps. + Persistence_heat_maps hm1( persistence1 , filter , false , 20 , 0 , 11 ); + Persistence_heat_maps hm2( persistence2 , filter , false , 20 , 0 , 11 ); + + std::vector*> 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 mean; + mean.compute_mean( vector_of_maps ); + Persistence_heat_maps 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* > to_average; + to_average.push_back( &hm1 ); + to_average.push_back( &hm2 ); + Persistence_heat_maps 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/Persistence_representation/example/persistence_intervals.cpp b/src/Persistence_representation/example/persistence_intervals.cpp new file mode 100644 index 00000000..ed5b4e34 --- /dev/null +++ b/src/Persistence_representation/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 . + */ + + + +#include +#include + +#include + + + +using namespace Gudhi; +using namespace Gudhi::Persistence_representations; + + +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 min_max_ = p.get_x_range(); + std::cout << "Birth-death range : " << min_max_.first << " " << min_max_.second << std::endl; + + + std::vector dominant_ten_intervals_length = p.length_of_dominant_intervals(10); + std::cout << "Lendth of ten dominant intervals : " < > ten_dominant_intervals = p.dominant_intervals( 10 ); + std::cout << "Here are the dominant intervals : " < histogram = p.histogram_of_lengths( 10 ); + std::cout << "Here is the histogram of barcode's length : " < cumulative_histogram = p.cumulative_histogram_of_lengths( 10 ); + std::cout<< "Cumuative histogram : " < char_funct_diag = p.characteristic_function_of_diagram( min_max_.first , min_max_.second ); + std::cout << "Characteristic function of diagram : " < cumul_char_funct_diag = p.cumulative_characteristic_function_of_diagram( min_max_.first , min_max_.second ); + std::cout << "Cumulative characteristic function of diagram : " < > pbns = p.compute_persistent_betti_numbers(); + for ( size_t i = 0 ; i != pbns.size() ; ++i ) + { + std::cout << pbns[i].first << " " << pbns[i].second <. + */ + + + +#include + + + +using namespace Gudhi; +using namespace Gudhi::Persistence_representations; + +#include + + +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/Persistence_representation/example/persistence_landscape_on_grid.cpp b/src/Persistence_representation/example/persistence_landscape_on_grid.cpp new file mode 100644 index 00000000..b38ac3d9 --- /dev/null +++ b/src/Persistence_representation/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 . + */ + + + +#include + + + +using namespace Gudhi; +using namespace Gudhi::Persistence_representations; + +#include + + +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/Persistence_representation/example/persistence_vectors.cpp b/src/Persistence_representation/example/persistence_vectors.cpp new file mode 100644 index 00000000..028d95eb --- /dev/null +++ b/src/Persistence_representation/example/persistence_vectors.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 . + */ + + + +#include +#include + + +#include +#include +#include +#include + +using namespace Gudhi; +using namespace Gudhi::Persistence_representations; + + + + +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 v1 = Vector_distances_in_diagram( persistence1 , std::numeric_limits::max() ); + Vector_distances_in_diagram v2 = Vector_distances_in_diagram( persistence2 , std::numeric_limits::max() ); + + //writing to a stream: + std::cout << "v1 : " << v1 << std::endl; + std::cout << "v2 : " << v2 << std::endl; + + //averages: + Vector_distances_in_diagram 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; +} diff --git a/src/Persistence_representation/example/simple_diagram.txt b/src/Persistence_representation/example/simple_diagram.txt new file mode 100644 index 00000000..2f199fd4 --- /dev/null +++ b/src/Persistence_representation/example/simple_diagram.txt @@ -0,0 +1,4 @@ +1 2 +3 4 +5 6 +7 8 \ No newline at end of file -- cgit v1.2.3