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-rw-r--r--src/Alpha_complex/benchmark/Alpha_complex_3d_benchmark.cpp278
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diff --git a/src/Alpha_complex/benchmark/Alpha_complex_3d_benchmark.cpp b/src/Alpha_complex/benchmark/Alpha_complex_3d_benchmark.cpp
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+++ b/src/Alpha_complex/benchmark/Alpha_complex_3d_benchmark.cpp
@@ -0,0 +1,278 @@
+#include <gudhi/Alpha_complex_3d.h>
+#include <gudhi/Alpha_complex.h>
+// to construct a simplex_tree from alpha complex
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/random_point_generators.h>
+#include <gudhi/Clock.h>
+
+#include <iostream>
+#include <string>
+#include <vector>
+#include <limits> // for numeric limits
+#include <fstream>
+
+#include <CGAL/Epick_d.h>
+#include <CGAL/Epeck_d.h>
+#include <CGAL/Random.h>
+
+std::ofstream results_csv("results.csv");
+
+template <typename Kernel>
+void benchmark_points_on_torus_dD(const std::string& msg) {
+ std::cout << "+ " << msg << std::endl;
+
+ results_csv << "\"" << msg << "\";" << std::endl;
+ results_csv << "\"nb_points\";"
+ << "\"nb_simplices\";"
+ << "\"alpha_creation_time(sec.)\";"
+ << "\"complex_creation_time(sec.)\";" << std::endl;
+
+ using K = CGAL::Epick_d<CGAL::Dimension_tag<3>>;
+ for (int nb_points = 1000; nb_points <= 125000; nb_points *= 5) {
+ std::cout << " Alpha complex dD on torus with " << nb_points << " points." << std::endl;
+ std::vector<K::Point_d> points_on_torus = Gudhi::generate_points_on_torus_3D<K>(nb_points, 1.0, 0.5);
+ std::vector<typename Kernel::Point_d> points;
+
+ for (auto p : points_on_torus) {
+ points.push_back(typename Kernel::Point_d(p.begin(), p.end()));
+ }
+
+ Gudhi::Clock ac_create_clock(" benchmark_points_on_torus_dD - Alpha complex 3d creation");
+ ac_create_clock.begin();
+ Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_points(points);
+ ac_create_clock.end();
+ std::cout << ac_create_clock;
+
+ Gudhi::Simplex_tree<> complex;
+ Gudhi::Clock st_create_clock(" benchmark_points_on_torus_dD - complex creation");
+ st_create_clock.begin();
+ alpha_complex_from_points.create_complex(complex);
+ st_create_clock.end();
+ std::cout << st_create_clock;
+
+ results_csv << nb_points << ";" << complex.num_simplices() << ";" << ac_create_clock.num_seconds() << ";"
+ << st_create_clock.num_seconds() << ";" << std::endl;
+
+ std::cout << " benchmark_points_on_torus_dD - nb simplices = " << complex.num_simplices() << std::endl;
+ }
+}
+
+template <typename Alpha_complex_3d>
+void benchmark_points_on_torus_3D(const std::string& msg) {
+ using K = CGAL::Epick_d<CGAL::Dimension_tag<3>>;
+ std::cout << "+ " << msg << std::endl;
+
+ results_csv << "\"" << msg << "\";" << std::endl;
+ results_csv << "\"nb_points\";"
+ << "\"nb_simplices\";"
+ << "\"alpha_creation_time(sec.)\";"
+ << "\"complex_creation_time(sec.)\";" << std::endl;
+
+ for (int nb_points = 1000; nb_points <= 125000; nb_points *= 5) {
+ std::cout << " Alpha complex 3d on torus with " << nb_points << " points." << std::endl;
+ std::vector<K::Point_d> points_on_torus = Gudhi::generate_points_on_torus_3D<K>(nb_points, 1.0, 0.5);
+ std::vector<typename Alpha_complex_3d::Point_3> points;
+
+ for (auto p : points_on_torus) {
+ points.push_back(typename Alpha_complex_3d::Point_3(p[0], p[1], p[2]));
+ }
+
+ Gudhi::Clock ac_create_clock(" benchmark_points_on_torus_3D - Alpha complex 3d creation");
+ ac_create_clock.begin();
+ Alpha_complex_3d alpha_complex_from_points(points);
+ ac_create_clock.end();
+ std::cout << ac_create_clock;
+
+ Gudhi::Simplex_tree<> complex;
+ Gudhi::Clock st_create_clock(" benchmark_points_on_torus_3D - complex creation");
+ st_create_clock.begin();
+ alpha_complex_from_points.create_complex(complex);
+ st_create_clock.end();
+ std::cout << st_create_clock;
+
+ results_csv << nb_points << ";" << complex.num_simplices() << ";" << ac_create_clock.num_seconds() << ";"
+ << st_create_clock.num_seconds() << ";" << std::endl;
+
+ std::cout << " benchmark_points_on_torus_3D - nb simplices = " << complex.num_simplices() << std::endl;
+ }
+}
+
+template <typename Weighted_alpha_complex_3d>
+void benchmark_weighted_points_on_torus_3D(const std::string& msg) {
+ using K = CGAL::Epick_d<CGAL::Dimension_tag<3>>;
+
+ std::cout << "+ " << msg << std::endl;
+
+ results_csv << "\"" << msg << "\";" << std::endl;
+ results_csv << "\"nb_points\";"
+ << "\"nb_simplices\";"
+ << "\"alpha_creation_time(sec.)\";"
+ << "\"complex_creation_time(sec.)\";" << std::endl;
+
+ CGAL::Random random(8);
+
+ for (int nb_points = 1000; nb_points <= 125000; nb_points *= 5) {
+ std::cout << " Alpha complex 3d on torus with " << nb_points << " points." << std::endl;
+ std::vector<K::Point_d> points_on_torus = Gudhi::generate_points_on_torus_3D<K>(nb_points, 1.0, 0.5);
+
+ using Point = typename Weighted_alpha_complex_3d::Point_3;
+ using Weighted_point = typename Weighted_alpha_complex_3d::Weighted_point_3;
+
+ std::vector<Weighted_point> points;
+
+ for (auto p : points_on_torus) {
+ points.push_back(Weighted_point(Point(p[0], p[1], p[2]), 0.9 + random.get_double(0., 0.01)));
+ }
+
+ Gudhi::Clock ac_create_clock(" benchmark_weighted_points_on_torus_3D - Alpha complex 3d creation");
+ ac_create_clock.begin();
+ Weighted_alpha_complex_3d alpha_complex_from_points(points);
+ ac_create_clock.end();
+ std::cout << ac_create_clock;
+
+ Gudhi::Simplex_tree<> complex;
+ Gudhi::Clock st_create_clock(" benchmark_weighted_points_on_torus_3D - complex creation");
+ st_create_clock.begin();
+ alpha_complex_from_points.create_complex(complex);
+ st_create_clock.end();
+ std::cout << st_create_clock;
+
+ results_csv << nb_points << ";" << complex.num_simplices() << ";" << ac_create_clock.num_seconds() << ";"
+ << st_create_clock.num_seconds() << ";" << std::endl;
+
+ std::cout << " benchmark_weighted_points_on_torus_3D - nb simplices = " << complex.num_simplices() << std::endl;
+ }
+}
+
+template <typename Periodic_alpha_complex_3d>
+void benchmark_periodic_points(const std::string& msg) {
+ std::cout << "+ " << msg << std::endl;
+
+ results_csv << "\"" << msg << "\";" << std::endl;
+ results_csv << "\"nb_points\";"
+ << "\"nb_simplices\";"
+ << "\"alpha_creation_time(sec.)\";"
+ << "\"complex_creation_time(sec.)\";" << std::endl;
+
+ CGAL::Random random(8);
+
+ for (double nb_points = 10.; nb_points <= 40.; nb_points += 10.) {
+ std::cout << " Periodic alpha complex 3d with " << nb_points * nb_points * nb_points << " points." << std::endl;
+ using Point = typename Periodic_alpha_complex_3d::Point_3;
+ std::vector<Point> points;
+
+ for (double i = 0; i < nb_points; i++) {
+ for (double j = 0; j < nb_points; j++) {
+ for (double k = 0; k < nb_points; k++) {
+ points.push_back(
+ Point(i + random.get_double(0., 0.1), j + random.get_double(0., 0.1), k + random.get_double(0., 0.1)));
+ }
+ }
+ }
+
+ Gudhi::Clock ac_create_clock(" benchmark_periodic_points - Alpha complex 3d creation");
+ ac_create_clock.begin();
+ Periodic_alpha_complex_3d alpha_complex_from_points(points, 0., 0., 0., nb_points, nb_points, nb_points);
+ ac_create_clock.end();
+ std::cout << ac_create_clock;
+
+ Gudhi::Simplex_tree<> complex;
+ Gudhi::Clock st_create_clock(" benchmark_periodic_points - complex creation");
+ st_create_clock.begin();
+ alpha_complex_from_points.create_complex(complex);
+ st_create_clock.end();
+ std::cout << st_create_clock;
+
+ results_csv << nb_points * nb_points * nb_points << ";" << complex.num_simplices() << ";"
+ << ac_create_clock.num_seconds() << ";" << st_create_clock.num_seconds() << ";" << std::endl;
+
+ std::cout << " benchmark_periodic_points - nb simplices = " << complex.num_simplices() << std::endl;
+ }
+}
+
+template <typename Weighted_periodic_alpha_complex_3d>
+void benchmark_weighted_periodic_points(const std::string& msg) {
+ std::cout << "+ " << msg << std::endl;
+
+ results_csv << "\"" << msg << "\";" << std::endl;
+ results_csv << "\"nb_points\";"
+ << "\"nb_simplices\";"
+ << "\"alpha_creation_time(sec.)\";"
+ << "\"complex_creation_time(sec.)\";" << std::endl;
+
+ CGAL::Random random(8);
+
+ for (double nb_points = 10.; nb_points <= 40.; nb_points += 10.) {
+ std::cout << " Weighted periodic alpha complex 3d with " << nb_points * nb_points * nb_points << " points."
+ << std::endl;
+
+ using Point = typename Weighted_periodic_alpha_complex_3d::Point_3;
+ using Weighted_point = typename Weighted_periodic_alpha_complex_3d::Weighted_point_3;
+ std::vector<Weighted_point> points;
+
+ for (double i = 0; i < nb_points; i++) {
+ for (double j = 0; j < nb_points; j++) {
+ for (double k = 0; k < nb_points; k++) {
+ points.push_back(Weighted_point(
+ Point(i + random.get_double(0., 0.1), j + random.get_double(0., 0.1), k + random.get_double(0., 0.1)),
+ random.get_double(0., (nb_points * nb_points) / 64.)));
+ }
+ }
+ }
+
+ Gudhi::Clock ac_create_clock(" benchmark_weighted_periodic_points - Alpha complex 3d creation");
+ ac_create_clock.begin();
+ Weighted_periodic_alpha_complex_3d alpha_complex_from_points(points, 0., 0., 0., nb_points, nb_points, nb_points);
+ ac_create_clock.end();
+ std::cout << ac_create_clock;
+
+ Gudhi::Simplex_tree<> complex;
+ Gudhi::Clock st_create_clock(" benchmark_weighted_periodic_points - complex creation");
+ st_create_clock.begin();
+ alpha_complex_from_points.create_complex(complex);
+ st_create_clock.end();
+ std::cout << st_create_clock;
+
+ results_csv << nb_points * nb_points * nb_points << ";" << complex.num_simplices() << ";"
+ << ac_create_clock.num_seconds() << ";" << st_create_clock.num_seconds() << ";" << std::endl;
+
+ std::cout << " benchmark_weighted_periodic_points - nb simplices = " << complex.num_simplices() << std::endl;
+ }
+}
+
+int main(int argc, char** argv) {
+ benchmark_points_on_torus_dD<CGAL::Epick_d<CGAL::Dimension_tag<3>>>("Fast static dimension version");
+ benchmark_points_on_torus_dD<CGAL::Epick_d<CGAL::Dynamic_dimension_tag>>("Fast dynamic dimension version");
+ benchmark_points_on_torus_dD<CGAL::Epeck_d<CGAL::Dimension_tag<3>>>("Exact static dimension version");
+ benchmark_points_on_torus_dD<CGAL::Epeck_d<CGAL::Dynamic_dimension_tag>>("Exact dynamic dimension version");
+
+ benchmark_points_on_torus_3D<
+ Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::FAST, false, false>>("Fast version");
+ benchmark_points_on_torus_3D<
+ Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::SAFE, false, false>>("Safe version");
+ benchmark_points_on_torus_3D<
+ Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::EXACT, false, false>>("Exact version");
+
+ benchmark_weighted_points_on_torus_3D<
+ Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::FAST, true, false>>("Fast version");
+ benchmark_weighted_points_on_torus_3D<
+ Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::SAFE, true, false>>("Safe version");
+ benchmark_weighted_points_on_torus_3D<
+ Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::EXACT, true, false>>("Exact version");
+
+ benchmark_periodic_points<
+ Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::FAST, false, true>>("Fast version");
+ benchmark_periodic_points<
+ Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::SAFE, false, true>>("Safe version");
+ benchmark_periodic_points<
+ Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::EXACT, false, true>>("Exact version");
+
+ benchmark_weighted_periodic_points<
+ Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::FAST, true, true>>("Fast version");
+ benchmark_weighted_periodic_points<
+ Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::SAFE, true, true>>("Safe version");
+ benchmark_weighted_periodic_points<
+ Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::EXACT, true, true>>("Exact version");
+
+ return 0;
+}
generated by cgit v1.2.3 (git 2.39.1) at 2024-05-02 20:26:44 +0000