From 5096889af20a04d25439ffbe5c37e663c11087bc Mon Sep 17 00:00:00 2001 From: cjamin Date: Wed, 31 May 2017 16:20:12 +0000 Subject: Move 1 example from Bottleneck_distance to utilities git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2493 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 9ca00220e5c3c4e2d2ad9c3aa3b3a54ed320f223 --- src/Bottleneck_distance/example/CMakeLists.txt | 13 -- .../alpha_rips_persistence_bottleneck_distance.cpp | 190 --------------------- 2 files changed, 203 deletions(-) delete mode 100644 src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp (limited to 'src/Bottleneck_distance/example') diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt index 0534a2c4..93eb7b2f 100644 --- a/src/Bottleneck_distance/example/CMakeLists.txt +++ b/src/Bottleneck_distance/example/CMakeLists.txt @@ -5,22 +5,9 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) add_executable (bottleneck_read_file_example bottleneck_read_file_example.cpp) add_executable (bottleneck_basic_example bottleneck_basic_example.cpp) - add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp) - target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) - if (TBB_FOUND) - target_link_libraries(bottleneck_read_file_example ${TBB_LIBRARIES}) - target_link_libraries(bottleneck_basic_example ${TBB_LIBRARIES}) - target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES}) - endif(TBB_FOUND) - 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") - 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_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp b/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp deleted file mode 100644 index fd164b22..00000000 --- a/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp +++ /dev/null @@ -1,190 +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. - * - * 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(); - } -} -- cgit v1.2.3