cech_complex_step_by_step.cpp
/* 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/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_handle = Simplex_tree::Simplex_handle;
using Point = std::vector<double>;
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
}
#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,
// Construct the Rips complex in a Simplex Tree
// 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
#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);
}
}
Compute the radius of the minimal enclosing ball between Points given by a range of coordinates....
Definition: distance_functions.h:64
OFF file reader implementation in order to read points from an OFF file.
Definition: Points_off_io.h:122
Options::Filtration_value Filtration_value
Type for the value of the filtration function.
Definition: Simplex_tree.h:82
Dictionary::iterator Simplex_handle
Handle type to a simplex contained in the simplicial complex represented by the simplex tree.
Definition: Simplex_tree.h:149
Filtration_simplex_range const & filtration_simplex_range(Indexing_tag=Indexing_tag())
Returns a range over the simplices of the simplicial complex, in the order of the filtration.
Definition: Simplex_tree.h:262
Simplex_vertex_range simplex_vertex_range(Simplex_handle sh) const
Returns a range over the vertices of a simplex.
Definition: Simplex_tree.h:273
static Filtration_value filtration(Simplex_handle sh)
Returns the filtration value of a simplex.
Definition: Simplex_tree.h:509
void expansion_with_blockers(int max_dim, Blocker block_simplex)
Expands a simplex tree containing only a graph. Simplices corresponding to cliques in the graph are a...
Definition: Simplex_tree.h:1241
void initialize_filtration()
Initializes the filtration cache, i.e. sorts the simplices according to their order in the filtration...
Definition: Simplex_tree.h:886
int dimension(Simplex_handle sh)
Returns the dimension of a simplex.
Definition: Simplex_tree.h:574
size_t num_simplices()
returns the number of simplices in the simplex_tree.
Definition: Simplex_tree.h:552
void insert_graph(const OneSkeletonGraph &skel_graph)
Inserts a 1-skeleton in an empty Simplex_tree.
Definition: Simplex_tree.h:1080
Global distance functions.
Graph simplicial complex methods.
typename boost::adjacency_list< boost::vecS, boost::vecS, boost::directedS, boost::property< vertex_filtration_t, typename SimplicialComplexForProximityGraph::Filtration_value >, boost::property< edge_filtration_t, typename SimplicialComplexForProximityGraph::Filtration_value > > Proximity_graph
Proximity_graph contains the vertices and edges with their filtration values in order to store the re...
Definition: graph_simplicial_complex.h:45
Value type for a filtration function on a cell complex.
Definition: FiltrationValue.h:20
GUDHI  Version 3.5.0  - C++ library for Topological Data Analysis (TDA) and Higher Dimensional Geometry Understanding.  - Copyright : MIT Generated on Thu Jan 13 2022 08:34:27 for GUDHI by Doxygen 1.9.2