From 8428e315efa22a1b40eb996c98eff671f91a9b27 Mon Sep 17 00:00:00 2001 From: cjamin Date: Wed, 15 Nov 2017 14:20:30 +0000 Subject: Fixes according to Marc's review git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2881 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 84870193cb05cabd8c756a3bbc49083e4d739525 --- src/Bottleneck_distance/example/CMakeLists.txt | 12 +- src/Bottleneck_distance/example/README | 19 +++ .../alpha_rips_persistence_bottleneck_distance.cpp | 190 +++++++++++++++++++++ .../example/bottleneck_read_file_example.cpp | 50 ------ 4 files changed, 215 insertions(+), 56 deletions(-) create mode 100644 src/Bottleneck_distance/example/README create mode 100644 src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp delete mode 100644 src/Bottleneck_distance/example/bottleneck_read_file_example.cpp (limited to 'src/Bottleneck_distance/example') diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt index 6a602dbb..9677f5c5 100644 --- a/src/Bottleneck_distance/example/CMakeLists.txt +++ b/src/Bottleneck_distance/example/CMakeLists.txt @@ -3,15 +3,15 @@ project(Bottleneck_distance_examples) if (NOT CGAL_VERSION VERSION_LESS 4.8.1) add_executable (bottleneck_basic_example bottleneck_basic_example.cpp) - add_executable (bottleneck_read_file_example bottleneck_read_file_example.cpp) + add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp) + target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_PROGRAM_OPTIONS_LIBRARY}) add_test(NAME Bottleneck_distance_example_basic COMMAND $) + add_test(NAME Bottleneck_distance_example_alpha_rips_persistence_bottleneck + COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.15" "-m" "0.12" "-d" "3" "-p" "3") - add_test(NAME Bottleneck_read_file_example - COMMAND $ - "${CMAKE_SOURCE_DIR}/data/persistence_diagram/first.pers" "${CMAKE_SOURCE_DIR}/data/persistence_diagram/second.pers") - - install(TARGETS bottleneck_read_file_example DESTINATION bin) install(TARGETS bottleneck_basic_example DESTINATION bin) + install(TARGETS alpha_rips_persistence_bottleneck_distance DESTINATION bin) endif (NOT CGAL_VERSION VERSION_LESS 4.8.1) diff --git a/src/Bottleneck_distance/example/README b/src/Bottleneck_distance/example/README new file mode 100644 index 00000000..0e314608 --- /dev/null +++ b/src/Bottleneck_distance/example/README @@ -0,0 +1,19 @@ +# Bottleneck_distance # + +## `alpha_rips_persistence_bottleneck_distance` ## +This program computes the persistent homology with coefficient field Z/pZ of a Rips complex defined on a set of input points. The output diagram contains one bar per line, written with the convention: + +`p dim b d` + +where `dim` is the dimension of the homological feature, `b` and `d` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients. + +Usage: +`alpha_rips_persistence_bottleneck_distance [options] ` + +Allowed options: + +* `-h [ --help ]` Produce help message +* `-r [ --max-edge-length ]` (default = inf) Maximal length of an edge for the Rips complex construction.` +* `-d [ --cpx-dimension ]` (default = 1) Maximal dimension of the Rips complex we want to compute.` +* `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology. +* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals. diff --git a/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp b/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp new file mode 100644 index 00000000..fd164b22 --- /dev/null +++ b/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp @@ -0,0 +1,190 @@ +/* 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): Vincent Rouvreau + * + * Copyright (C) 2017 INRIA + * + * 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 +#include + +#include + +#include + +#include +#include +#include // infinity +#include // for pair +#include // for transform + + +// Types definition +using Simplex_tree = Gudhi::Simplex_tree; +using Filtration_value = Simplex_tree::Filtration_value; +using Rips_complex = Gudhi::rips_complex::Rips_complex; +using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; +using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology; +using Kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >; +using Point_d = Kernel::Point_d; +using Points_off_reader = Gudhi::Points_off_reader; + +void program_options(int argc, char * argv[] + , std::string & off_file_points + , Filtration_value & threshold + , int & dim_max + , int & p + , Filtration_value & min_persistence); + +static inline std::pair compute_root_square(std::pair input) { + return std::make_pair(std::sqrt(input.first), std::sqrt(input.second)); +} + +int main(int argc, char * argv[]) { + std::string off_file_points; + Filtration_value threshold; + int dim_max; + int p; + Filtration_value min_persistence; + + program_options(argc, argv, off_file_points, threshold, dim_max, p, min_persistence); + + Points_off_reader off_reader(off_file_points); + + // -------------------------------------------- + // Rips persistence + // -------------------------------------------- + Rips_complex rips_complex(off_reader.get_point_cloud(), threshold, Gudhi::Euclidean_distance()); + + // Construct the Rips complex in a Simplex Tree + Simplex_tree rips_stree; + + rips_complex.create_complex(rips_stree, dim_max); + std::cout << "The Rips complex contains " << rips_stree.num_simplices() << " simplices and has dimension " + << rips_stree.dimension() << " \n"; + + // Sort the simplices in the order of the filtration + rips_stree.initialize_filtration(); + + // Compute the persistence diagram of the complex + Persistent_cohomology rips_pcoh(rips_stree); + // initializes the coefficient field for homology + rips_pcoh.init_coefficients(p); + rips_pcoh.compute_persistent_cohomology(min_persistence); + + // rips_pcoh.output_diagram(); + + // -------------------------------------------- + // Alpha persistence + // -------------------------------------------- + Gudhi::alpha_complex::Alpha_complex alpha_complex(off_reader.get_point_cloud()); + + Simplex_tree alpha_stree; + alpha_complex.create_complex(alpha_stree, threshold * threshold); + std::cout << "The Alpha complex contains " << alpha_stree.num_simplices() << " simplices and has dimension " + << alpha_stree.dimension() << " \n"; + + // Sort the simplices in the order of the filtration + alpha_stree.initialize_filtration(); + + // Compute the persistence diagram of the complex + Persistent_cohomology alpha_pcoh(alpha_stree); + // initializes the coefficient field for homology + alpha_pcoh.init_coefficients(p); + alpha_pcoh.compute_persistent_cohomology(min_persistence * min_persistence); + + // alpha_pcoh.output_diagram(); + + // -------------------------------------------- + // Bottleneck distance between both persistence + // -------------------------------------------- + double max_b_distance {}; + for (int dim = 0; dim < dim_max; dim ++) { + std::vector< std::pair< Filtration_value , Filtration_value > > rips_intervals; + std::vector< std::pair< Filtration_value , Filtration_value > > alpha_intervals; + rips_intervals = rips_pcoh.intervals_in_dimension(dim); + alpha_intervals = alpha_pcoh.intervals_in_dimension(dim); + std::transform(alpha_intervals.begin(), alpha_intervals.end(), alpha_intervals.begin(), compute_root_square); + + double bottleneck_distance = Gudhi::persistence_diagram::bottleneck_distance(rips_intervals, alpha_intervals); + std::cout << "In dimension " << dim << ", bottleneck distance = " << bottleneck_distance << std::endl; + if (bottleneck_distance > max_b_distance) + max_b_distance = bottleneck_distance; + } + std::cout << "================================================================================" << std::endl; + std::cout << "Bottleneck distance is " << max_b_distance << std::endl; + + return 0; +} + +void program_options(int argc, char * argv[] + , std::string & off_file_points + , Filtration_value & threshold + , int & dim_max + , int & p + , Filtration_value & min_persistence) { + namespace po = boost::program_options; + po::options_description hidden("Hidden options"); + hidden.add_options() + ("input-file", po::value(&off_file_points), + "Name of an OFF file containing a point set.\n"); + + po::options_description visible("Allowed options", 100); + visible.add_options() + ("help,h", "produce help message") + ("max-edge-length,r", + po::value(&threshold)->default_value(std::numeric_limits::infinity()), + "Maximal length of an edge for the Rips complex construction.") + ("cpx-dimension,d", po::value(&dim_max)->default_value(1), + "Maximal dimension of the Rips complex we want to compute.") + ("field-charac,p", po::value(&p)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.") + ("min-persistence,m", po::value(&min_persistence), + "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals"); + + po::positional_options_description pos; + pos.add("input-file", 1); + + po::options_description all; + all.add(visible).add(hidden); + + po::variables_map vm; + po::store(po::command_line_parser(argc, argv). + options(all).positional(pos).run(), vm); + po::notify(vm); + + if (vm.count("help") || !vm.count("input-file")) { + std::cout << std::endl; + std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; + std::cout << "of a Rips complex defined on a set of input points.\n \n"; + std::cout << "The output diagram contains one bar per line, written with the convention: \n"; + std::cout << " p dim b d \n"; + std::cout << "where dim is the dimension of the homological feature,\n"; + std::cout << "b and d are respectively the birth and death of the feature and \n"; + std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; + + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); + } +} diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp deleted file mode 100644 index 24d73c57..00000000 --- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp +++ /dev/null @@ -1,50 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Authors: Francois Godi, small modifications by Pawel Dlotko - * - * Copyright (C) 2015 INRIA - * - * 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 // for pair -#include -#include // for numeric_limits - -int main(int argc, char** argv) { - if (argc < 3) { - std::cout << "To run this program please provide as an input two files with persistence diagrams. Each file" << - " should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck" << - " distance (set by default to the smallest positive double value). If you set the error bound to 0, be" << - " aware this version is exact but expensive. The program will now terminate \n"; - return -1; - } - std::vector> diag1 = Gudhi::read_persistence_intervals_in_dimension(argv[1]); - std::vector> diag2 = Gudhi::read_persistence_intervals_in_dimension(argv[2]); - - double tolerance = std::numeric_limits::min(); - if (argc == 4) { - tolerance = atof(argv[3]); - } - double b = Gudhi::persistence_diagram::bottleneck_distance(diag1, diag2, tolerance); - std::cout << "The distance between the diagrams is : " << b << ". The tolerance is : " << tolerance << std::endl; - - return 0; -} -- cgit v1.2.3