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-rw-r--r--src/Cech_complex/benchmark/cech_complex_benchmark.cpp169
1 files changed, 72 insertions, 97 deletions
diff --git a/src/Cech_complex/benchmark/cech_complex_benchmark.cpp b/src/Cech_complex/benchmark/cech_complex_benchmark.cpp
index e489e8a4..a0e727be 100644
--- a/src/Cech_complex/benchmark/cech_complex_benchmark.cpp
+++ b/src/Cech_complex/benchmark/cech_complex_benchmark.cpp
@@ -10,12 +10,13 @@
#include <gudhi/Points_off_io.h>
#include <gudhi/distance_functions.h>
-#include <gudhi/graph_simplicial_complex.h>
#include <gudhi/Clock.h>
#include <gudhi/Rips_complex.h>
#include <gudhi/Cech_complex.h>
#include <gudhi/Simplex_tree.h>
-#include <gudhi/Miniball.hpp>
+
+#include <CGAL/Epick_d.h>
+#include <CGAL/Epeck_d.h>
#include "boost/filesystem.hpp" // includes all needed Boost.Filesystem declarations
@@ -26,107 +27,81 @@
using Simplex_tree = Gudhi::Simplex_tree<>;
using Filtration_value = Simplex_tree::Filtration_value;
using Point = std::vector<Filtration_value>;
-using Point_cloud = std::vector<Point>;
using Points_off_reader = Gudhi::Points_off_reader<Point>;
-using Proximity_graph = Gudhi::Proximity_graph<Simplex_tree>;
using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
-using Cech_complex = Gudhi::cech_complex::Cech_complex<Simplex_tree, Point_cloud>;
-
-class Minimal_enclosing_ball_radius {
- public:
- // boost::range_value is not SFINAE-friendly so we cannot use it in the return type
- template <typename Point>
- typename std::iterator_traits<typename boost::range_iterator<Point>::type>::value_type operator()(
- const Point& p1, const Point& p2) const {
- // Type def
- using Point_cloud = std::vector<Point>;
- using Point_iterator = typename Point_cloud::const_iterator;
- using Coordinate_iterator = typename Point::const_iterator;
- using Min_sphere =
- typename Gudhi::Miniball::Miniball<Gudhi::Miniball::CoordAccessor<Point_iterator, Coordinate_iterator>>;
-
- Point_cloud point_cloud;
- point_cloud.push_back(p1);
- point_cloud.push_back(p2);
-
- GUDHI_CHECK((p1.end() - p1.begin()) != (p2.end() - p2.begin()), "inconsistent point dimensions");
- Min_sphere min_sphere(p1.end() - p1.begin(), point_cloud.begin(), point_cloud.end());
- return std::sqrt(min_sphere.squared_radius());
- }
-};
+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[]) {
- std::string off_file_points = "tore3D_1307.off";
- Filtration_value threshold = 1e20;
-
- // Extract the points from the file filepoints
- Points_off_reader off_reader(off_file_points);
-
- Gudhi::Clock euclidean_clock("Gudhi::Euclidean_distance");
- // Compute the proximity graph of the points
- Proximity_graph euclidean_prox_graph = Gudhi::compute_proximity_graph<Simplex_tree>(
- off_reader.get_point_cloud(), threshold, Gudhi::Euclidean_distance());
-
- std::clog << euclidean_clock << std::endl;
-
- Gudhi::Clock miniball_clock("Minimal_enclosing_ball_radius");
- // Compute the proximity graph of the points
- Proximity_graph miniball_prox_graph = Gudhi::compute_proximity_graph<Simplex_tree>(
- off_reader.get_point_cloud(), threshold, Minimal_enclosing_ball_radius());
- std::clog << miniball_clock << std::endl;
-
- Gudhi::Clock common_miniball_clock("Gudhi::Minimal_enclosing_ball_radius()");
- // Compute the proximity graph of the points
- Proximity_graph common_miniball_prox_graph = Gudhi::compute_proximity_graph<Simplex_tree>(
- off_reader.get_point_cloud(), threshold, Gudhi::Minimal_enclosing_ball_radius());
- std::clog << common_miniball_clock << std::endl;
-
- 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;Cech time; Ratio Rips/Cech time;Rips nb simplices;Cech nb simplices;"
- << std::endl;
- boost::filesystem::directory_iterator end_itr; // default construction yields past-the-end
- 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") // see below
- {
- Points_off_reader off_reader(itr->path().string());
- Point p0 = off_reader.get_point_cloud()[0];
-
- for (Filtration_value radius = 0.1; radius < 0.4; 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::Minimal_enclosing_ball_radius());
- Simplex_tree rips_stree;
- rips_complex_from_points.create_complex(rips_stree, p0.size() - 1);
- // ------------------------------------------
- // Display information about the Rips complex
- // ------------------------------------------
- double rips_sec = rips_clock.num_seconds();
- std::clog << rips_sec << ";";
-
- Gudhi::Clock cech_clock("Cech computation");
- Cech_complex cech_complex_from_points(off_reader.get_point_cloud(), radius);
- Simplex_tree cech_stree;
- cech_complex_from_points.create_complex(cech_stree, p0.size() - 1);
- // ------------------------------------------
- // Display information about the Cech complex
- // ------------------------------------------
- double cech_sec = cech_clock.num_seconds();
- std::clog << cech_sec << ";";
- std::clog << cech_sec / rips_sec << ";";
-
- assert(rips_stree.num_simplices() >= cech_stree.num_simplices());
- std::clog << rips_stree.num_simplices() << ";";
- std::clog << cech_stree.num_simplices() << ";" << std::endl;
+ 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;
+ return 0;
}
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