#include <gudhi/Simplex_tree.h>
#include <gudhi/Points_off_io.h>
#include <CGAL/Epick_d.h>
#include <CGAL/Min_sphere_of_spheres_d.h>
#include <CGAL/Min_sphere_of_points_d_traits_d.h>
#include <boost/program_options.hpp>
#include <string>
#include <vector>
#include <limits>
#include <utility>
#include <map>
using Graph_t = boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS,
boost::property<Gudhi::vertex_filtration_t, Filtration_value>,
boost::property<Gudhi::edge_filtration_t, Filtration_value> >;
using Edge_t = std::pair<Vertex_handle, Vertex_handle>;
using Kernel = CGAL::Epick_d<CGAL::Dimension_tag<3> >;
using Point = Kernel::Point_d;
using Traits = CGAL::Min_sphere_of_points_d_traits_d<Kernel, Filtration_value, 3>;
using Min_sphere = CGAL::Min_sphere_of_spheres_d<Traits>;
class Cech_blocker {
public:
bool operator()(Simplex_handle sh) {
std::vector<Point> points;
#if DEBUG_TRACES
std::clog << "Cech_blocker on [";
#endif
for (auto vertex : simplex_tree_.simplex_vertex_range(sh)) {
points.push_back(point_cloud_[vertex]);
#if DEBUG_TRACES
std::clog << vertex << ", ";
#endif
}
Min_sphere ms(points.begin(), points.end());
#if DEBUG_TRACES
std::clog << "] - radius = " << radius << " - returns " << (radius > threshold_) << std::endl;
#endif
simplex_tree_.assign_filtration(sh, radius);
return (radius > threshold_);
}
: simplex_tree_(simplex_tree), threshold_(threshold), point_cloud_(point_cloud) {}
private:
std::vector<Point> point_cloud_;
};
template <typename InputPointRange>
void program_options(
int argc,
char* argv[], std::string& off_file_points,
Filtration_value& threshold,
int& dim_max);
int main(int argc, char* argv[]) {
std::string off_file_points;
int dim_max;
program_options(argc, argv, off_file_points, threshold, dim_max);
std::clog <<
"The complex contains " << st.
num_simplices() <<
" simplices \n";
std::clog <<
" and has dimension " << st.
dimension() <<
" \n";
#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";
std::clog << " "
std::clog << static_cast<int>(vertex) << " ";
}
std::clog << std::endl;
}
#endif
return 0;
}
void program_options(
int argc,
char* argv[], std::string& off_file_points,
Filtration_value& threshold,
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 3d point set.\n");
po::options_description visible("Allowed options", 100);
visible.add_options()("help,h", "produce help message")(
"max-edge-length,r",
po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()),
"Maximal length of an edge for the Cech complex construction.")(
"cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
"Maximal dimension of the Cech 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);
}
}
template <typename InputPointRange>
std::vector<Edge_t> edges;
std::vector<Filtration_value> edges_fil;
Kernel k;
idx_u = 0;
for (auto it_u = points.begin(); it_u != points.end(); ++it_u) {
idx_v = idx_u + 1;
for (auto it_v = it_u + 1; it_v != points.end(); ++it_v, ++idx_v) {
fil = k.squared_distance_d_object()(*it_u, *it_v);
fil = std::sqrt(fil) / 2.;
if (fil <= threshold) {
edges.emplace_back(idx_u, idx_v);
edges_fil.push_back(fil);
}
}
++idx_u;
}
Graph_t skel_graph(edges.begin(), edges.end(), edges_fil.begin(),
idx_u);
auto vertex_prop = boost::get(Gudhi::vertex_filtration_t(), skel_graph);
boost::graph_traits<Graph_t>::vertex_iterator vi, vi_end;
for (std::tie(vi, vi_end) = boost::vertices(skel_graph); vi != vi_end; ++vi) {
boost::put(vertex_prop, *vi, 0.);
}
return skel_graph;
}
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:102
Dictionary::iterator Simplex_handle
Handle type to a simplex contained in the simplicial complex represented by the simplex tree.
Definition: Simplex_tree.h:175
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:338
Simplex_vertex_range simplex_vertex_range(Simplex_handle sh) const
Returns a range over the vertices of a simplex.
Definition: Simplex_tree.h:349
static Filtration_value filtration(Simplex_handle sh)
Returns the filtration value of a simplex.
Definition: Simplex_tree.h:614
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:1732
void initialize_filtration(bool ignore_infinite_values=false)
Initializes the filtration cache, i.e. sorts the simplices according to their order in the filtration...
Definition: Simplex_tree.h:1055
Simplex_tree_siblings< Simplex_tree, Dictionary > Siblings
Set of nodes sharing a same parent in the simplex tree.
Definition: Simplex_tree.h:127
Options::Vertex_handle Vertex_handle
Type for the vertex handle.
Definition: Simplex_tree.h:110
size_t num_simplices()
Returns the number of simplices in the simplex_tree.
Definition: Simplex_tree.h:664
void insert_graph(const OneSkeletonGraph &skel_graph)
Inserts a 1-skeleton in an empty Simplex_tree.
Definition: Simplex_tree.h:1272
Global distance functions.
Graph simplicial complex methods.
Proximity_graph< SimplicialComplexForProximityGraph > compute_proximity_graph(const ForwardPointRange &points, typename SimplicialComplexForProximityGraph::Filtration_value threshold, Distance distance)
Computes the proximity graph of the points.
Definition: graph_simplicial_complex.h:62
Value type for a filtration function on a cell complex.
Definition: FiltrationValue.h:20
Handle type for the vertices of a cell complex.
Definition: VertexHandle.h:15