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Diffstat (limited to 'src/Cech_complex/example/cech_complex_step_by_step.cpp')
-rw-r--r-- | src/Cech_complex/example/cech_complex_step_by_step.cpp | 154 |
1 files changed, 0 insertions, 154 deletions
diff --git a/src/Cech_complex/example/cech_complex_step_by_step.cpp b/src/Cech_complex/example/cech_complex_step_by_step.cpp deleted file mode 100644 index f59f0293..00000000 --- a/src/Cech_complex/example/cech_complex_step_by_step.cpp +++ /dev/null @@ -1,154 +0,0 @@ -/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. - * See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. - * Author(s): Vincent Rouvreau - * - * Copyright (C) 2018 Inria - * - * Modification(s): - * - YYYY/MM Author: Description of the modification - */ - -#include <gudhi/graph_simplicial_complex.h> -#include <gudhi/distance_functions.h> -#include <gudhi/Simplex_tree.h> -#include <gudhi/Points_off_io.h> - -#include <gudhi/Miniball.hpp> - -#include <boost/program_options.hpp> - -#include <string> -#include <vector> -#include <limits> // infinity -#include <utility> // for pair -#include <map> - -// ---------------------------------------------------------------------------- -// rips_persistence_step_by_step is an example of each step that is required to -// build a Rips over a Simplex_tree. Please refer to rips_persistence to see -// how to do the same thing with the Rips_complex wrapper for less detailed -// steps. -// ---------------------------------------------------------------------------- - -// Types definition -using Simplex_tree = Gudhi::Simplex_tree<>; -using Simplex_handle = Simplex_tree::Simplex_handle; -using Filtration_value = Simplex_tree::Filtration_value; -using Point = std::vector<double>; -using Points_off_reader = Gudhi::Points_off_reader<Point>; -using Proximity_graph = Gudhi::Proximity_graph<Simplex_tree>; - -class Cech_blocker { - private: - using Point_cloud = std::vector<Point>; - using Point_iterator = Point_cloud::const_iterator; - using Coordinate_iterator = Point::const_iterator; - using Min_sphere = Gudhi::Miniball::Miniball<Gudhi::Miniball::CoordAccessor<Point_iterator, Coordinate_iterator>>; - - public: - bool operator()(Simplex_handle sh) { - std::vector<Point> points; - for (auto vertex : simplex_tree_.simplex_vertex_range(sh)) { - points.push_back(point_cloud_[vertex]); -#ifdef DEBUG_TRACES - std::clog << "#(" << vertex << ")#"; -#endif // DEBUG_TRACES - } - Filtration_value radius = Gudhi::Minimal_enclosing_ball_radius()(points); -#ifdef DEBUG_TRACES - std::clog << "radius = " << radius << " - " << (radius > max_radius_) << std::endl; -#endif // DEBUG_TRACES - simplex_tree_.assign_filtration(sh, radius); - return (radius > max_radius_); - } - Cech_blocker(Simplex_tree& simplex_tree, Filtration_value max_radius, const std::vector<Point>& point_cloud) - : simplex_tree_(simplex_tree), max_radius_(max_radius), point_cloud_(point_cloud) { - dimension_ = point_cloud_[0].size(); - } - - private: - Simplex_tree simplex_tree_; - Filtration_value max_radius_; - std::vector<Point> point_cloud_; - int dimension_; -}; - -void program_options(int argc, char* argv[], std::string& off_file_points, Filtration_value& max_radius, int& dim_max); - -int main(int argc, char* argv[]) { - std::string off_file_points; - Filtration_value max_radius; - int dim_max; - - program_options(argc, argv, off_file_points, max_radius, dim_max); - - // Extract the points from the file filepoints - Points_off_reader off_reader(off_file_points); - - // Compute the proximity graph of the points - Proximity_graph prox_graph = Gudhi::compute_proximity_graph<Simplex_tree>(off_reader.get_point_cloud(), max_radius, - Gudhi::Minimal_enclosing_ball_radius()); - - // Construct the Rips complex in a Simplex Tree - Simplex_tree st; - // insert the proximity graph in the simplex tree - st.insert_graph(prox_graph); - // expand the graph until dimension dim_max - st.expansion_with_blockers(dim_max, Cech_blocker(st, max_radius, off_reader.get_point_cloud())); - - std::clog << "The complex contains " << st.num_simplices() << " simplices \n"; - std::clog << " and has dimension " << st.dimension() << " \n"; - - // Sort the simplices in the order of the filtration - st.initialize_filtration(); - -#if DEBUG_TRACES - std::clog << "********************************************************************\n"; - std::clog << "* The complex contains " << st.num_simplices() << " simplices - dimension=" << st.dimension() << "\n"; - std::clog << "* Iterator on Simplices in the filtration, with [filtration value]:\n"; - for (auto f_simplex : st.filtration_simplex_range()) { - std::clog << " " - << "[" << st.filtration(f_simplex) << "] "; - for (auto vertex : st.simplex_vertex_range(f_simplex)) { - std::clog << static_cast<int>(vertex) << " "; - } - std::clog << std::endl; - } -#endif // DEBUG_TRACES - - return 0; -} - -void program_options(int argc, char* argv[], std::string& off_file_points, Filtration_value& max_radius, int& dim_max) { - namespace po = boost::program_options; - po::options_description hidden("Hidden options"); - hidden.add_options()("input-file", po::value<std::string>(&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-radius,r", - po::value<Filtration_value>(&max_radius)->default_value(std::numeric_limits<Filtration_value>::infinity()), - "Maximal length of an edge for the Rips complex construction.")( - "cpx-dimension,d", po::value<int>(&dim_max)->default_value(1), - "Maximal dimension of the Rips complex we want to compute."); - - 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::clog << std::endl; - std::clog << "Construct a Cech complex defined on a set of input points.\n \n"; - - std::clog << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; - std::clog << visible << std::endl; - exit(-1); - } -} |