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 --- .../utilities/persistence_intervals/CMakeLists.txt | 32 ++++++ ...te_birth_death_range_in_persistence_diagram.cpp | 71 +++++++++++++ .../compute_bottleneck_distance.cpp | 113 +++++++++++++++++++++ .../compute_number_of_dominant_intervals.cpp | 59 +++++++++++ .../plot_histogram_of_intervals_lengths.cpp | 77 ++++++++++++++ .../plot_persistence_Betti_numbers.cpp | 100 ++++++++++++++++++ .../plot_persistence_intervals.cpp | 69 +++++++++++++ 7 files changed, 521 insertions(+) create mode 100644 src/Persistence_representation/utilities/persistence_intervals/CMakeLists.txt create mode 100644 src/Persistence_representation/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp create mode 100644 src/Persistence_representation/utilities/persistence_intervals/compute_bottleneck_distance.cpp create mode 100644 src/Persistence_representation/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp create mode 100644 src/Persistence_representation/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp create mode 100644 src/Persistence_representation/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp create mode 100644 src/Persistence_representation/utilities/persistence_intervals/plot_persistence_intervals.cpp (limited to 'src/Persistence_representation/utilities/persistence_intervals') diff --git a/src/Persistence_representation/utilities/persistence_intervals/CMakeLists.txt b/src/Persistence_representation/utilities/persistence_intervals/CMakeLists.txt new file mode 100644 index 00000000..b5c5928d --- /dev/null +++ b/src/Persistence_representation/utilities/persistence_intervals/CMakeLists.txt @@ -0,0 +1,32 @@ +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}) +add_test ( plot_persistence_intervals ${CMAKE_CURRENT_BINARY_DIR}/plot_persistence_intervals "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" ) + +add_executable ( compute_birth_death_range_in_persistence_diagram compute_birth_death_range_in_persistence_diagram.cpp ) +target_link_libraries( compute_birth_death_range_in_persistence_diagram ${Boost_SYSTEM_LIBRARY}) +add_test ( compute_birth_death_range_in_persistence_diagram ${CMAKE_CURRENT_BINARY_DIR}/compute_birth_death_range_in_persistence_diagram -1 "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" ) + +add_executable ( compute_number_of_dominant_intervals compute_number_of_dominant_intervals.cpp ) +target_link_libraries( compute_number_of_dominant_intervals ${Boost_SYSTEM_LIBRARY}) +add_test ( compute_number_of_dominant_intervals ${CMAKE_CURRENT_BINARY_DIR}/compute_number_of_dominant_intervals "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" -1 2 ) + +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_test ( plot_histogram_of_intervals_lengths ${CMAKE_CURRENT_BINARY_DIR}/plot_histogram_of_intervals_lengths "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" 2 ) + +add_executable ( plot_persistence_Betti_numbers plot_persistence_Betti_numbers.cpp ) +target_link_libraries( plot_persistence_Betti_numbers ${Boost_SYSTEM_LIBRARY}) +add_test ( plot_persistence_Betti_numbers ${CMAKE_CURRENT_BINARY_DIR}/plot_persistence_Betti_numbers "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" ) + +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) +add_test ( compute_bottleneck_distance ${CMAKE_CURRENT_BINARY_DIR}/compute_bottleneck_distance "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" ) +endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Persistence_representation/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp b/src/Persistence_representation/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp new file mode 100644 index 00000000..2e0d680f --- /dev/null +++ b/src/Persistence_representation/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp @@ -0,0 +1,71 @@ +/* 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 + + + +using namespace Gudhi; +using namespace Gudhi::Persistence_representations; + + +int main( int argc , char** argv ) +{ + 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::max(); + if ( dim >= 0 ) + { + dimension = (unsigned)dim; + } + std::vector< const char* > filenames; + for ( int i = 2 ; i < argc ; ++i ) + { + filenames.push_back( argv[i] ); + } + + double min_ = std::numeric_limits::max(); + double max_ = -std::numeric_limits::max(); + + 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] , dimension ); + std::pair min_max_ = p.get_x_range(); + if ( min_max_.first < min_ )min_ = min_max_.first; + if ( min_max_.second > max_ )max_ = min_max_.second; + } + std::cout << "Birth-death range : min: " << min_ << ", max: " << max_ << std::endl; + return 0; +} diff --git a/src/Persistence_representation/utilities/persistence_intervals/compute_bottleneck_distance.cpp b/src/Persistence_representation/utilities/persistence_intervals/compute_bottleneck_distance.cpp new file mode 100644 index 00000000..19e49bbb --- /dev/null +++ b/src/Persistence_representation/utilities/persistence_intervals/compute_bottleneck_distance.cpp @@ -0,0 +1,113 @@ +/* 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 + + + +using namespace Gudhi; +using namespace Gudhi::Persistence_representations; + +#include +#include + + +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::max(); + if ( 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 ); + 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/Persistence_representation/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp b/src/Persistence_representation/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp new file mode 100644 index 00000000..c099befc --- /dev/null +++ b/src/Persistence_representation/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp @@ -0,0 +1,59 @@ +/* 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 ) +{ + std::cout << "This program compute the dominant intervals. A number of intervals to be displayed is a parameter of this program. \n"; + if ( argc != 4 ) + { + 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; + } + int dim = atoi( argv[2] ); + unsigned dimension = std::numeric_limits::max(); + if ( dim >= 0 ) + { + dimension = (unsigned)dim; + } + Persistence_intervals p( argv[1] , dimension ); + std::vector< std::pair > 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 ) + { + std::cout << " " << dominant_intervals[i].first<< "," << dominant_intervals[i].second << " "<< std::endl; + } + + return 0; +} diff --git a/src/Persistence_representation/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp b/src/Persistence_representation/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp new file mode 100644 index 00000000..b2cbac70 --- /dev/null +++ b/src/Persistence_representation/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp @@ -0,0 +1,77 @@ +/* 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 ) +{ + std::cout << "This program compute a histogram of barcode's length. A number of bins in the histogram is a parameter of this program. \n"; + 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 third 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::max(); + int dim = -1; + if ( argc > 2 ) + { + dim = atoi( argv[2] ); + } + if ( dim >= 0 ) + { + dimension = (unsigned)dim; + } + + Persistence_intervals p( argv[1] , dimension ); + std::vector< std::pair > dominant_intervals = p.dominant_intervals( atoi( argv[2] ) ); + std::vector< size_t > histogram = p.histogram_of_lengths( 10 ); + + std::stringstream gnuplot_script; + gnuplot_script << argv[1] << "_Gnuplot_script"; + std::ofstream out; + out.open( gnuplot_script.str().c_str() ); + + out << "set style data histogram" << std::endl; + out << "set style histogram cluster gap 1" << std::endl; + out << "set style fill solid border -1" << std::endl; + out << "plot '-' notitle" << std::endl; + for ( size_t i = 0 ; i != histogram.size() ; ++i ) + { + out << histogram[i] << std::endl; + } + out << std::endl; + std::cout << "To vizualize, open gnuplot and type: load \'" << gnuplot_script.str().c_str() << "\'" << std::endl; + out.close(); + return 0; +} diff --git a/src/Persistence_representation/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp b/src/Persistence_representation/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp new file mode 100644 index 00000000..e20f85c0 --- /dev/null +++ b/src/Persistence_representation/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp @@ -0,0 +1,100 @@ +/* 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 ) +{ + std::cout << "This program compute a plot of persistence Betti numbers. The input parameter is a file with persistence intervals. \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"; + 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::max(); + int dim = -1; + if ( argc > 2 ) + { + dim = atoi( argv[2] ); + } + if ( dim >= 0 ) + { + dimension = (unsigned)dim; + } + + + std::stringstream gnuplot_script; + gnuplot_script << argv[1] << "_Gnuplot_script"; + std::ofstream out; + out.open( gnuplot_script.str().c_str() ); + + 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. + double xRangeBegin = pbns[0].first; + double xRangeEnd = pbns[ pbns.size()-1 ].first; + double yRangeBegin = 0; + double yRangeEnd = 0; + for ( size_t i = 0 ; i != pbns.size() ; ++i ) + { + if ( pbns[i].second > yRangeEnd )yRangeEnd = pbns[i].second; + } + xRangeBegin -= (xRangeEnd -xRangeBegin)/100.0; + xRangeEnd += (xRangeEnd -xRangeBegin)/100.0; + yRangeEnd += yRangeEnd/100; + + + out << "set xrange [" << xRangeBegin << " : " << xRangeEnd << "]" << std::endl; + out << "set yrange [" << yRangeBegin << " : " << yRangeEnd << "]" << std::endl; + out << "plot '-' using 1:2 notitle with lp " << std::endl; + double previous_y = 0; + for ( size_t i = 0 ; i != pbns.size() ; ++i ) + { + out << pbns[i].first << " " << previous_y << std::endl; + out << pbns[i].first << " " << pbns[i].second << std::endl; + previous_y = pbns[i].second; + } + out << std::endl; + out.close(); + + //for ( size_t i = 0 ; i != pbns.size() ; ++i ) + //{ + // std::cout << pbns[i].first << " " << pbns[i].second << std::endl; + //} + + std::cout << "To vizualize, open gnuplot and type: load \'" << gnuplot_script.str().c_str() << "\'" << std::endl; + + return 0; +} diff --git a/src/Persistence_representation/utilities/persistence_intervals/plot_persistence_intervals.cpp b/src/Persistence_representation/utilities/persistence_intervals/plot_persistence_intervals.cpp new file mode 100644 index 00000000..ed03459b --- /dev/null +++ b/src/Persistence_representation/utilities/persistence_intervals/plot_persistence_intervals.cpp @@ -0,0 +1,69 @@ +/* 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 ) +{ + 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; + } + unsigned dimension = std::numeric_limits::max(); + int dim = -1; + if ( argc > 2 ) + { + dim = atoi( argv[2] ); + } + if ( 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; +} + + + + + + + -- cgit v1.2.3