making sure that all matrix allocations happen at compile time when possible

Optimal_bounding_box/benchmark/Optimal_bounding_box/bench_obb.cpp

@@ -1,7 +1,10 @@
 #include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
 #include <CGAL/Surface_mesh.h>
+#include <CGAL/convex_hull_3.h>
+#include <CGAL/Polyhedron_3.h>
 #include <CGAL/Optimal_bounding_box/population.h>
 #include <CGAL/Optimal_bounding_box/obb.h>
+#include <CGAL/Eigen_linear_algebra_traits.h>
 #include <iostream>
 #include <fstream>
 
@@ -41,6 +44,7 @@ void bench_finding_obb(std::string fname)
 {
   std::ifstream input(fname);
 
+  CGAL::Eigen_linear_algebra_traits la_traits;
   std::vector<K::Point_3> sm_points;
 
   // import a mesh
@@ -53,26 +57,29 @@ void bench_finding_obb(std::string fname)
   gather_mesh_points(mesh, sm_points);
 
   CGAL::Timer timer;
+
+  // 1) measure convex hull calculation
   timer.start();
-
+  CGAL::Polyhedron_3<K> poly;
-  CGAL::Eigen_linear_algebra_traits la_traits;
+  convex_hull_3(sm_points.begin(), sm_points.end(), poly);
-
+  std::vector<K::Point_3> ch_points(poly.points_begin(), poly.points_end());
-  // 1) using convex hull
-  std::vector<K::Point_3> obb_points1;
-  CGAL::Optimal_bounding_box::find_obb(sm_points, obb_points1, la_traits, true);
-
   timer.stop();
-  std::cout << "found obb with convex hull: " << timer.time() << " seconds\n";
+  std::cout << "takes : " << timer.time() << " seconds to find the convex hull\n";
 
+  // 2) using convex hull
   timer.reset();
   timer.start();
+  std::vector<K::Point_3> obb_points1;
+  CGAL::Optimal_bounding_box::find_obb(sm_points, obb_points1, la_traits, true);
+  timer.stop();
+  std::cout << "found obb using convex hull: " << timer.time() << " seconds\n";
 
-  // 2) without convex hull
+  // 3) without convex hull
+  timer.reset();
+  timer.start();
   std::vector<K::Point_3> obb_points2;
   CGAL::Optimal_bounding_box::find_obb(sm_points, obb_points2, la_traits, false);
-
   timer.stop();
-
   std::cout << "found obb without convex hull: " <<  timer.time() << " seconds\n";
   timer.reset();
 

Optimal_bounding_box/include/CGAL/Optimal_bounding_box/evolution.h

@@ -19,7 +19,6 @@
 //
 // Author(s)     : Konstantinos Katrioplas
 
-
 #ifndef CGAL_EVOLUTION_H
 #define CGAL_EVOLUTION_H
 
@@ -34,7 +33,7 @@ namespace Optimal_bounding_box {
 template <typename Linear_algebra_traits>
 class Evolution
 {
-  typedef typename Linear_algebra_traits::MatrixXd MatrixXd;
+  typedef typename Linear_algebra_traits::MatrixX3d MatrixXd;
   typedef typename Linear_algebra_traits::Matrix3d Matrix3d;
   typedef typename Linear_algebra_traits::Vector3d Vector3d;
 
@@ -280,14 +279,14 @@ public:
       //std::cout << "pop after nelder mead: " << std::endl;
       //pop.show_population();
       //std::cout << std::endl;
-      Fitness_map<Matrix3d, MatrixXd> fitness_map_debug(population, point_data);
+      Fitness_map<Linear_algebra_traits, Matrix3d, MatrixXd> fitness_map_debug(population, point_data);
       Matrix3d R_now = fitness_map_debug.get_best();
       std::cout << "det= " << Linear_algebra_traits::determinant(R_now) << std::endl;
   #endif
 
       // stopping criteria
-      Fitness_map<Matrix3d, MatrixXd> fitness_map(population, point_data);
+      Fitness_map<Linear_algebra_traits, Matrix3d, MatrixXd> fitness_map(population, point_data);
-      new_fit_value = fitness_map.get_best_fitness_value(point_data);
+      new_fit_value = fitness_map.get_best_fitness_value();
       double difference = new_fit_value - prev_fit_value;
       if(abs(difference) < tolerance * new_fit_value)
         stale++;
@@ -301,7 +300,7 @@ public:
 
   const Matrix3d get_best()
   {
-    Fitness_map<Matrix3d, MatrixXd> fitness_map(population, point_data);
+    Fitness_map<Linear_algebra_traits, Matrix3d, MatrixXd> fitness_map(population, point_data);
     return fitness_map.get_best();
   }
 

Optimal_bounding_box/include/CGAL/Optimal_bounding_box/fitness_function.h

@@ -27,14 +27,11 @@
 #include <CGAL/Optimal_bounding_box/population.h>
 #include <limits>
 
-#include <CGAL/Eigen_linear_algebra_traits.h>
-
 namespace CGAL {
 namespace Optimal_bounding_box {
 
-template <typename Linear_algebra_traits>
+template <typename Linear_algebra_traits, typename Vertex, typename Matrix>
-double compute_fitness(const typename Linear_algebra_traits::Matrix3d& R,
+double compute_fitness(const Vertex& R, const Matrix& data)
-                             typename Linear_algebra_traits::MatrixXd& data)
 {
   // R: rotation matrix
   CGAL_assertion(R.cols() == 3);
@@ -73,11 +70,9 @@ double compute_fitness(const typename Linear_algebra_traits::Matrix3d& R,
   return ((xmax - xmin) * (ymax - ymin) * (zmax - zmin));
 }
 
-template <typename Vertex, typename Matrix>
+template <typename Linear_algebra_traits, typename Vertex, typename Matrix>
 struct Fitness_map
 {
-  typedef CGAL::Eigen_linear_algebra_traits Linear_algebra_traits; // to be added as a parameter
-
   Fitness_map(Population<Vertex>& p, Matrix& points) : pop(p), points(points)
   {}
 
@@ -103,14 +98,14 @@ struct Fitness_map
     return pop[simplex_id][vertex_id];
   }
 
-  double get_best_fitness_value(Matrix& data)
+  double get_best_fitness_value()
   {
     const Vertex best_mat = get_best();
-    return compute_fitness<Linear_algebra_traits>(best_mat, data);
+    return compute_fitness<Linear_algebra_traits>(best_mat, points);
   }
 
   Population<Vertex>& pop;
-  Matrix& points;
+  const Matrix& points;
 };
 
 }} // end namespaces

Optimal_bounding_box/include/CGAL/Optimal_bounding_box/linear_algebra.h

@@ -38,26 +38,6 @@ namespace Optimal_bounding_box {
 typedef CGAL::Eigen_linear_algebra_traits Linear_algebra_traits;
 #endif
 
-/*
-template<typename Matrix>
-void qr_factorization(Matrix& A, Matrix& Q)
-{
-  Eigen::HouseholderQR<Matrix> qr(A);
-  Q = qr.householderQ();
-}
-
-template<typename Matrix>
-void qr_factorization(std::vector<Matrix>& Simplex)
-{
-  for(int i = 0; i < Simplex.size(); ++i)
-  {
-    Eigen::HouseholderQR<Matrix> qr(Simplex[i]);
-    Matrix Q = qr.householderQ();
-    Simplex[i] = Q;
-  }
-}
-*/
-
 template <typename Matrix>
 const Matrix reflection(const Matrix& S_centroid, const Matrix& S_worst)
 {
@@ -92,19 +72,15 @@ Matrix mean(const Matrix& m1, const Matrix& m2)
   CGAL_assertion(m2.cols() == 3);
 
   Matrix reduction = 0.5 * m1 + 0.5 * m2;
-  //Matrix Q;
-  //reduction.qr_factorization(Q);
   Matrix Q = Linear_algebra_traits::qr_factorization(reduction);
   double det = Linear_algebra_traits::determinant(Q);
   return Q / det;
 }
 
 template <typename Matrix>
-const Matrix centroid(Matrix& S1, Matrix& S2, Matrix& S3) // const?
+const Matrix centroid(const Matrix& S1, const Matrix& S2, const Matrix& S3)
 {
   Matrix mean = (S1 + S2 + S3) / 3.0;
-  //Matrix Q;
-  //mean.qr_factorization(Q);
   Matrix Q = Linear_algebra_traits::qr_factorization(mean);
   double det = Linear_algebra_traits::determinant(Q);
   return Q / det;

Optimal_bounding_box/include/CGAL/Optimal_bounding_box/obb.h

@@ -49,8 +49,8 @@ typedef CGAL::Eigen_linear_algebra_traits Linear_algebra_traits;
 
 
 // works on matrices only
-template <typename Vertex, typename Matrix_dynamic, typename Matrix_fixed>
+template <typename Vertex, typename Matrix>
-void post_processing(const Matrix_dynamic& points, Vertex& R, Matrix_fixed& obb)
+void post_processing(const Matrix& points, Vertex& R, Matrix& obb)
 {
   CGAL_assertion(points.cols() == 3);
   CGAL_assertion(R.rows() == 3);
@@ -59,7 +59,7 @@ void post_processing(const Matrix_dynamic& points, Vertex& R, Matrix_fixed& obb)
   CGAL_assertion(obb.cols() == 3);
 
   // 1) rotate points with R
-  Matrix_dynamic rotated_points(points.rows(), points.cols());
+  Matrix rotated_points(points.rows(), points.cols());
   rotated_points = points * Linear_algebra_traits::transpose(R);
 
   // 2) get AABB from rotated points
@@ -75,10 +75,8 @@ void post_processing(const Matrix_dynamic& points, Vertex& R, Matrix_fixed& obb)
   bbox = bbox_3(v_points.begin(), v_points.end());
   K::Iso_cuboid_3 ic(bbox);
 
-  Matrix_fixed aabb;
+  // Matrix is [dynamic, 3] at compile time, so it needs allocation of rows at run time.
-  // preallocate sanity: if Matrix is not preallocated in compile time
+  Matrix aabb(8, 3);
-  if(aabb.cols() != 3 && aabb.rows() != 8)
-    aabb.resize(8, 3);
 
   for(std::size_t i = 0; i < 8; ++i)
   {
@@ -104,7 +102,7 @@ void find_obb(std::vector<Point>& points,
   CGAL_assertion(obb_points.size() == 8);
 
   // eigen linear algebra traits
-  typedef typename LinearAlgebraTraits::MatrixXd MatrixXd;
+  typedef typename LinearAlgebraTraits::MatrixX3d MatrixXd;
   typedef typename LinearAlgebraTraits::Matrix3d Matrix3d;
 
   MatrixXd points_mat;

Optimal_bounding_box/test/Optimal_bounding_box/test_optimization_algorithms.cpp

@@ -20,7 +20,7 @@ void test_nelder_mead()
 {
   typedef CGAL::Eigen_linear_algebra_traits Linear_algebra_traits;
   typedef Linear_algebra_traits::Matrix3d Matrix3d;
-  typedef Linear_algebra_traits::MatrixXd MatrixXd;
+  typedef Linear_algebra_traits::MatrixX3d MatrixXd;
 
   MatrixXd data_points(4,3);
   data_points(0,0) = 0.866802;
@@ -143,7 +143,7 @@ void test_nelder_mead()
 
 void test_genetic_algorithm()
 {
-  CGAL::Eigen_dense_matrix<double> data_points(4, 3);
+  CGAL::Eigen_dense_matrix<double, -1, 3> data_points(4, 3); // -1 : dynamic size at run time
   data_points(0,0) = 0.866802;
   data_points(0,1) = 0.740808,
   data_points(0,2) = 0.895304,
@@ -170,7 +170,7 @@ void test_genetic_algorithm()
 void test_random_unit_tetra()
 {
   // this is dynamic at run times
-  CGAL::Eigen_dense_matrix<double> data_points(4, 3);
+  CGAL::Eigen_dense_matrix<double, -1, 3> data_points(4, 3);
 
   // points are on their convex hull
   data_points(0,0) = 0.866802;
@@ -244,7 +244,7 @@ void test_reference_tetrahedron(const char* fname)
   }
 
   typedef CGAL::Eigen_linear_algebra_traits Linear_algebra_traits;
-  typedef Linear_algebra_traits::MatrixXd MatrixXd;
+  typedef Linear_algebra_traits::MatrixX3d MatrixXd;
   typedef Linear_algebra_traits::Matrix3d Matrix3d;
 
   // points in a matrix
@@ -279,7 +279,7 @@ void test_long_tetrahedron(std::string fname)
   }
 
   typedef CGAL::Eigen_linear_algebra_traits Linear_algebra_traits;
-  typedef Linear_algebra_traits::MatrixXd MatrixXd;
+  typedef Linear_algebra_traits::MatrixX3d MatrixXd;
   typedef Linear_algebra_traits::Matrix3d Matrix3d;
 
   // points in a matrix

Solver_interface/include/CGAL/Eigen_linear_algebra_traits.h

@@ -38,7 +38,6 @@ class Eigen_dense_matrix
 {
 public:
   typedef Eigen::Matrix<T, D1, D2> EigenType;
-  typedef Eigen::Matrix<T, 3, 3> EigenType3;
 
   Eigen_dense_matrix(std::size_t nrows, std::size_t ncols)
     : m_matrix(static_cast<int>(nrows), static_cast<int>(ncols))
@@ -94,7 +93,6 @@ template <typename T, int D = Eigen::Dynamic>
 class Eigen_dense_vector
 {
 private:
-  //typedef Eigen::Vector3d EigenType;
   typedef Eigen::Matrix<T, D, 1> EigenType;
 
 public:
@@ -119,11 +117,14 @@ public:
   // dynamic size at run time
   typedef CGAL::Eigen_dense_matrix<NT> MatrixXd;
 
+  // dynamic rows in run time, fixed cols in compile time
+  typedef CGAL::Eigen_dense_matrix<NT, Eigen::Dynamic, 3> MatrixX3d;
+
   // fixed at compile time
   typedef CGAL::Eigen_dense_matrix<NT, 3, 3> Matrix3d;
 
   // fixed at compile time
-  typedef CGAL::Eigen_dense_vector<NT> Vector3d;
+  typedef CGAL::Eigen_dense_vector<NT, 3> Vector3d;
 
   template <class Matrix>
   static Matrix transpose(const Matrix& mat)
@@ -155,11 +156,11 @@ public:
   }
 
   template <class NT, int D1, int D2>
-  static CGAL::Eigen_dense_vector<NT, D1> row(CGAL::Eigen_dense_matrix<NT, D1, D2>& A, int i_)
+  static CGAL::Eigen_dense_vector<NT, 3> row(const CGAL::Eigen_dense_matrix<NT, D1, D2>& A,
+                                              int i)
   {
-    return CGAL::Eigen_dense_vector<NT, D1>(A.m_matrix.row(i_));
+    return CGAL::Eigen_dense_vector<NT, 3>(A.m_matrix.row(i));
   }
-
 };
 
 
@@ -214,7 +215,7 @@ const CGAL::Eigen_dense_matrix<NT, D1, D2> operator/ (const double& scalar,
   return CGAL::Eigen_dense_matrix<NT, D1, D2> (scalar / A.m_matrix);
 }
 
-// addition - subtraction
+// addition
 template <class NT, int D1, int D2>
 const CGAL::Eigen_dense_matrix<NT, D1, D2> operator+ (const CGAL::Eigen_dense_matrix<NT, D1, D2> & A,
                                                       const CGAL::Eigen_dense_matrix<NT, D1, D2> & B)
@@ -224,9 +225,10 @@ const CGAL::Eigen_dense_matrix<NT, D1, D2> operator+ (const CGAL::Eigen_dense_ma
 
 // vector - matrix multiplication
 template <class NT, int D1, int D2>
-const Eigen_dense_vector<NT> operator* (const CGAL::Eigen_dense_matrix<NT, D1, D2>& A, CGAL::Eigen_dense_vector<NT>& V)
+const Eigen_dense_vector<NT, D1> operator* (const CGAL::Eigen_dense_matrix<NT, D1, D2>& A,
+                                            const CGAL::Eigen_dense_vector<NT, D2>& V)
 {
-  return Eigen_dense_vector<NT>(A.m_matrix * V.m_vector);
+  return Eigen_dense_vector<NT, D1>(A.m_matrix * V.m_vector);
 }