diff --git a/HDVF/doc/HDVF/PackageDescription.txt b/HDVF/doc/HDVF/PackageDescription.txt index 6f2366d96d6..4379c79e4e2 100644 --- a/HDVF/doc/HDVF/PackageDescription.txt +++ b/HDVF/doc/HDVF/PackageDescription.txt @@ -4,7 +4,7 @@ /// \defgroup PkgHDVFConcepts Concepts /// \ingroup PkgHDVFRef -/// \defgroup PkgHDVFAlgorithmClasses Algorithm Classes +/// \defgroup PkgHDVFAlgorithmClasses Sparse Matrices and Vectors /// \ingroup PkgHDVFRef /// \defgroup PkgHDVFTraitsClasses Traits Classes diff --git a/HDVF/include/CGAL/HDVF/Abstract_simplicial_chain_complex.h b/HDVF/include/CGAL/HDVF/Abstract_simplicial_chain_complex.h index 5fab94c9764..d29b5658519 100644 --- a/HDVF/include/CGAL/HDVF/Abstract_simplicial_chain_complex.h +++ b/HDVF/include/CGAL/HDVF/Abstract_simplicial_chain_complex.h @@ -294,7 +294,7 @@ protected: * * \param q Dimension considered for computation. */ - void calculate_d(int q) const; + void compute_d(int q) const; /* * \brief Method inserting a simplex (and its faces if necessary) into the abstract simplicial complex. @@ -350,7 +350,7 @@ Abstract_simplicial_chain_complex::Abstract_simplicial_chain_co _d.resize(_dim+1); for (int dim = 0; dim <= _dim; ++dim) { - calculate_d(dim); + compute_d(dim); } } @@ -373,9 +373,9 @@ void Abstract_simplicial_chain_complex::insert_simplex(const Si } } -// calculate _d boundary matrix +// compute _d boundary matrix template -void Abstract_simplicial_chain_complex::calculate_d(int dim) const { +void Abstract_simplicial_chain_complex::compute_d(int dim) const { size_t nb_lignes = (dim == 0) ? 0 : _nb_cells[dim - 1]; _d[dim] = Column_matrix(nb_lignes, _nb_cells[dim]); @@ -398,7 +398,7 @@ void Abstract_simplicial_chain_complex::calculate_d(int dim) co chain.set_coefficient(ind_j, (j % 2 == 0) ? 1 : -1); } else - throw "calculate_d boundary simplex not found!"; + throw "compute_d boundary simplex not found!"; } // Insert the chain into the corresponding column of the delta matrix diff --git a/HDVF/include/CGAL/HDVF/Cub_object_io.h b/HDVF/include/CGAL/HDVF/Cub_object_io.h index ae0ec57217a..57740928e3b 100644 --- a/HDVF/include/CGAL/HDVF/Cub_object_io.h +++ b/HDVF/include/CGAL/HDVF/Cub_object_io.h @@ -33,7 +33,7 @@ typedef std::vector IOCubChainType ; /*! \ingroup PkgHDVFRef - The class `Cub_object_io` is an intermediate IO class, used to load binary volumes and produce cubical complexes. + The class `Cub_object_io` is an intermediate %IO class, used to load binary volumes and produce cubical complexes. */ diff --git a/HDVF/include/CGAL/HDVF/Cubical_chain_complex.h b/HDVF/include/CGAL/HDVF/Cubical_chain_complex.h index e105105b330..d96b67a6c16 100644 --- a/HDVF/include/CGAL/HDVF/Cubical_chain_complex.h +++ b/HDVF/include/CGAL/HDVF/Cubical_chain_complex.h @@ -385,7 +385,7 @@ protected: std::ostream& print_complex(std::ostream& out = std::cout) const { for (int q = 0; q <= _dim; ++q) { out << "-------- dimension " << q << std::endl; - out << "cellules de dimension " << q << " : " << _base2bool.at(q).size() << std::endl; + out << "cells of dimension " << q << " : " << _base2bool.at(q).size() << std::endl; for (size_t id_base = 0; id_base < _base2bool.at(q).size(); ++id_base) { size_t id_bool = _base2bool.at(q).at(id_base); std::vector khal = bindex_to_cell(id_bool); @@ -395,7 +395,7 @@ protected: } if (_base2bool[q].size() > 0 && q <= _dim) { - out << "matrice de bord de dimension " << q << std::endl; + out << "border matrix of dimension " << q << std::endl; out << _d[q] << std::endl; } } @@ -636,7 +636,7 @@ protected: CoefficientRing sign = 1; for (size_t i = 0; i < _dim; ++i) { if (c[i] % 2 == 1) { - // Calculate the coefficient based on the number of odd entries in c from 0 to i-1 + // compute the coefficient based on the number of odd entries in c from 0 to i-1 sign *= -1; size_t cell1 = index_bool + _P[i]; @@ -752,7 +752,7 @@ protected: /* Initialize _cells, _base2bool and _bool2base */ void initialize_cells(const Cub_object_io& cub,Cubical_complex_primal_dual type); - /* \brief Calculate the dimension of a cell (given by its Boolean index) */ + /* \brief compute the dimension of a cell (given by its Boolean index) */ int dimension(size_t cell_index) const { return dimension(bindex_to_cell(cell_index)) ; @@ -801,13 +801,13 @@ protected: /* \brief Computes the boundary matrix of dimension q */ - void calculate_d(int q) ; + void compute_d(int q) ; /* \brief Insert a cell into the complex (and its faces if necessary) */ void insert_cell(size_t cell); /* \brief Compute (the Boolean indices of) cells belonging to the boundary of `cell` (given by its Boolean index) */ - std::vector calculate_boundaries(size_t cell) const; + std::vector compute_boundaries(size_t cell) const; }; @@ -848,7 +848,7 @@ Cubical_chain_complex::Cubical_chain_complex(const Cub_ // Initialize _d _d.resize(_dim+1); for (int q = 0; q <= _dim; ++q) { - calculate_d(q); + compute_d(q); } // Initialize _points @@ -877,7 +877,7 @@ void Cubical_chain_complex::initialize_cells(const Cub_ for (size_t i=0; i coords(cub.cubs.at(i)) ; - // Calculate the coordinates of the voxel in the dual complex + // compute the coordinates of the voxel in the dual complex for (size_t i=0; i<_dim; ++i) coords.at(i)*=2 ; const size_t cell_index(cell_to_bindex(coords)) ; @@ -896,7 +896,7 @@ void Cubical_chain_complex::initialize_cells(const Cub_ for (size_t i = 0; i < _P[_dim]; ++i) { if (dimension(bindex_to_cell(i)) == q) { - std::vector boundaries = calculate_boundaries(i); + std::vector boundaries = compute_boundaries(i); bool all_boundaries_present = true; for (const auto& boundary_cell : boundaries) { if (!_cells[boundary_cell]) { @@ -963,7 +963,7 @@ void Cubical_chain_complex::insert_cell(size_t cell) { _base2bool[dim].push_back(cell); _bool2base[dim][cell] = cell_base_index; - std::vector boundaries(calculate_boundaries(cell)); + std::vector boundaries(compute_boundaries(cell)); for (const auto& boundary : boundaries) { if (!_cells[boundary]) { insert_cell(boundary); @@ -975,9 +975,9 @@ void Cubical_chain_complex::insert_cell(size_t cell) { } -// calculate_d implementation +// compute_d implementation template -void Cubical_chain_complex::calculate_d(int dim) { +void Cubical_chain_complex::compute_d(int dim) { size_t nb_lignes = (dim == 0) ? 0 : number_of_cells(dim - 1); _d[dim] = Column_matrix(nb_lignes, number_of_cells(dim)); @@ -1004,16 +1004,16 @@ int Cubical_chain_complex::dimension(const std::vector -std::vector Cubical_chain_complex::calculate_boundaries(size_t idcell) const { +std::vector Cubical_chain_complex::compute_boundaries(size_t idcell) const { std::vector boundaries; std::vector c = bindex_to_cell(idcell); for (size_t i = 0; i < _dim; ++i) { if (c[i] % 2 == 1) { - // Calculate the coefficient based on the number of odd entries in c from 0 to i-1 + // compute the coefficient based on the number of odd entries in c from 0 to i-1 size_t cell1 = idcell + _P[i]; if (is_valid_cell(cell1)) boundaries.push_back(cell1) ; diff --git a/HDVF/include/CGAL/HDVF/Simplex.h b/HDVF/include/CGAL/HDVF/Simplex.h index 6eab409b8ed..2bab2e2ff9d 100644 --- a/HDVF/include/CGAL/HDVF/Simplex.h +++ b/HDVF/include/CGAL/HDVF/Simplex.h @@ -28,7 +28,7 @@ namespace Homological_discrete_vector_field { /*! \ingroup PkgHDVFRef - The class `Simplex` is used by the class `Abstract_simplicial_chain_complex` to implement the structure de simplex (i.e.\ cells of a simplicial complex). + The class `Simplex` is used by the class `Abstract_simplicial_chain_complex` to represent a simplex (i.e.\ cells of a simplicial complex). Simplices are described by the *ordered vector* of the indices of their vertices (see the documentation of `Abstract_simplicial_chain_complex` for examples). diff --git a/HDVF/include/CGAL/HDVF/Surface_mesh_io.h b/HDVF/include/CGAL/HDVF/Surface_mesh_io.h index ccf809f6a06..1675f34e455 100644 --- a/HDVF/include/CGAL/HDVF/Surface_mesh_io.h +++ b/HDVF/include/CGAL/HDVF/Surface_mesh_io.h @@ -29,7 +29,7 @@ namespace Homological_discrete_vector_field { /*! \ingroup PkgHDVFRef - The class `Surface_mesh_io` is an intermediate IO class, used to load a triangle mesh and produce simplicial complexes. + The class `Surface_mesh_io` is an intermediate %IO class, used to load a triangle mesh and produce simplicial complexes. \tparam TriangleMesh a model of `FaceGraph` and `HalfedgeGraph` concepts, e.g., a `CGAL::Surface_mesh`. \tparam Traits a geometric traits class model of the `HDVFTraits` concept. */ diff --git a/HDVF/include/CGAL/HDVF/Triangulation_3_io.h b/HDVF/include/CGAL/HDVF/Triangulation_3_io.h index 37f4e6f3b9b..bea2fe1699a 100644 --- a/HDVF/include/CGAL/HDVF/Triangulation_3_io.h +++ b/HDVF/include/CGAL/HDVF/Triangulation_3_io.h @@ -29,7 +29,7 @@ namespace Homological_discrete_vector_field { /*! \ingroup PkgHDVFRef - The class `Triangulation_3_io` is an intermediate IO class, used to load a `Triangulation_3` and produce simplicial complexes. The class loads the vertices and the cells (ie. tetrahedra) of the `Triangulation_3` into a `Mesh_object_io`. + The class `Triangulation_3_io` is an intermediate %IO class, used to load a `Triangulation_3` and produce simplicial complexes. The class loads the vertices and the cells (ie. tetrahedra) of the `Triangulation_3` into a `Mesh_object_io`. \tparam Triangulation3 a model of `CGAL::Triangulation_3`. \tparam Traits a geometric traits class model of the `HDVFTraits` concept. */