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/* 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/Points_off_io.h>
#include <gudhi/distance_functions.h>
#include <gudhi/Clock.h>
#include <gudhi/Rips_complex.h>
#include <gudhi/Cech_complex.h>
#include <gudhi/Simplex_tree.h>
#include <CGAL/Epick_d.h>
#include <CGAL/Epeck_d.h>
#include "boost/filesystem.hpp" // includes all needed Boost.Filesystem declarations
#include <string>
#include <vector>
// Types definition
using Simplex_tree = Gudhi::Simplex_tree<>;
using Filtration_value = Simplex_tree::Filtration_value;
using Point = std::vector<Filtration_value>;
using Points_off_reader = Gudhi::Points_off_reader<Point>;
using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
template<typename Kernel>
Simplex_tree benchmark_cech(const std::string& off_file_points, const Filtration_value& radius, const int& dim_max, const bool exact) {
using Point_cgal = typename Kernel::Point_d;
using Points_off_reader_cgal = Gudhi::Points_off_reader<Point_cgal>;
using Cech_complex = Gudhi::cech_complex::Cech_complex<Kernel, Simplex_tree>;
// Extract the points from the file filepoints
Points_off_reader_cgal off_reader_cgal(off_file_points);
Gudhi::Clock cech_clock("Cech computation");
Cech_complex cech_complex_from_points(off_reader_cgal.get_point_cloud(), radius, exact);
Simplex_tree cech_stree;
cech_complex_from_points.create_complex(cech_stree, dim_max);
// ------------------------------------------
// Display information about the Cech complex
// ------------------------------------------
double cech_sec = cech_clock.num_seconds();
std::clog << cech_sec << " ; ";
return cech_stree;
}
int main(int argc, char* argv[]) {
boost::filesystem::path full_path(boost::filesystem::current_path());
std::clog << "Current path is : " << full_path << std::endl;
std::clog << "File name ; Radius ; Rips time ; Dim-3 Fast Cech time ; Dynamic_dim Fast Cech time ; "
"Dim-3 Safe Cech time ; Dynamic_dim Safe Cech time ; Dim-3 Exact Cech time ; Dynamic_dim Exact Cech time ; "
"Cech nb simplices ; Rips nb simplices;"
<< std::endl;
boost::filesystem::directory_iterator end_itr; // default construction yields past-the-end
// For every ".off" file in the current directory, and for 3 predefined thresholds, compare Rips and various Cech constructions
for (boost::filesystem::directory_iterator itr(boost::filesystem::current_path()); itr != end_itr; ++itr) {
if (!boost::filesystem::is_directory(itr->status())) {
if (itr->path().extension() == ".off") {
Points_off_reader off_reader(itr->path().string());
Point p0 = off_reader.get_point_cloud()[0];
// Loop over the different thresholds
for (Filtration_value radius = 0.1; radius < 0.35; radius += 0.1) {
std::clog << itr->path().stem() << " ; ";
std::clog << radius << " ; ";
Gudhi::Clock rips_clock("Rips computation");
Rips_complex rips_complex_from_points(off_reader.get_point_cloud(), radius, Gudhi::Euclidean_distance());
Simplex_tree rips_stree;
int dim_max = p0.size() - 1;
rips_complex_from_points.create_complex(rips_stree, dim_max);
// ------------------------------------------
// Display information about the Rips complex
// ------------------------------------------
double rips_sec = rips_clock.num_seconds();
std::clog << rips_sec << " ; ";
// --------------
// Cech complex
// --------------
// Fast
benchmark_cech<CGAL::Epick_d<CGAL::Dimension_tag<3>>>(itr->path().string(), radius, dim_max, false);
benchmark_cech<CGAL::Epick_d<CGAL::Dynamic_dimension_tag>>(itr->path().string(), radius, dim_max, false);
// Safe
benchmark_cech<CGAL::Epeck_d<CGAL::Dimension_tag<3>>>(itr->path().string(), radius, dim_max, false);
benchmark_cech<CGAL::Epeck_d<CGAL::Dynamic_dimension_tag>>(itr->path().string(), radius, dim_max, false);
// Exact
benchmark_cech<CGAL::Epeck_d<CGAL::Dimension_tag<3>>>(itr->path().string(), radius, dim_max, true);
auto cech_stree = benchmark_cech<CGAL::Epeck_d<CGAL::Dynamic_dimension_tag>>(itr->path().string(), radius, dim_max, true);
std::clog << cech_stree.num_simplices() << " ; ";
std::clog << rips_stree.num_simplices() << ";" << std::endl;
}
}
}
}
return 0;
}
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