diff --git a/HDVF/doc/HDVF/PackageDescription.txt b/HDVF/doc/HDVF/PackageDescription.txt index 848779a8316..6f2366d96d6 100644 --- a/HDVF/doc/HDVF/PackageDescription.txt +++ b/HDVF/doc/HDVF/PackageDescription.txt @@ -10,8 +10,6 @@ /// \defgroup PkgHDVFTraitsClasses Traits Classes /// \ingroup PkgHDVFRef -/// \defgroup PkgHDVFMiscellaneous Miscellaneous -/// \ingroup PkgHDVFRef /*! \cgalPkgDescriptionBegin{HDVF,PkgHDVF} diff --git a/HDVF/doc/HDVF/dependencies b/HDVF/doc/HDVF/dependencies index 5b428db4aaa..6c33abe8990 100644 --- a/HDVF/doc/HDVF/dependencies +++ b/HDVF/doc/HDVF/dependencies @@ -3,6 +3,7 @@ Kernel_23 Kernel_d STL_Extension Algebraic_foundations +Number_types Circulator Stream_support Surface_mesh diff --git a/HDVF/include/CGAL/HDVF/Abstract_simplicial_chain_complex.h b/HDVF/include/CGAL/HDVF/Abstract_simplicial_chain_complex.h index 76951b599d2..5fab94c9764 100644 --- a/HDVF/include/CGAL/HDVF/Abstract_simplicial_chain_complex.h +++ b/HDVF/include/CGAL/HDVF/Abstract_simplicial_chain_complex.h @@ -25,7 +25,7 @@ namespace CGAL { namespace Homological_discrete_vector_field { /*! - \ingroup PkgHDVFAlgorithmClasses + \ingroup PkgHDVFRef The class `Abstract_simplicial_chain_complex` represents (topological) chain complexes associated to abstract simplicial complexes. diff --git a/HDVF/include/CGAL/HDVF/Cub_object_io.h b/HDVF/include/CGAL/HDVF/Cub_object_io.h index 155dba712c1..ae0ec57217a 100644 --- a/HDVF/include/CGAL/HDVF/Cub_object_io.h +++ b/HDVF/include/CGAL/HDVF/Cub_object_io.h @@ -32,8 +32,7 @@ typedef std::vector IOCubCellType ; typedef std::vector IOCubChainType ; /*! - \ingroup PkgHDVFAlgorithmClasses - + \ingroup PkgHDVFRef The class `Cub_object_io` is an intermediate IO class, used to load binary volumes and produce cubical complexes. */ @@ -132,7 +131,7 @@ public: std::cerr << "read_pgm error: dimension of Cubical_complex and Traits differ" << std::endl; throw "read_pgm error: dimension of Cubical_complex and Traits differ"; } - + N = std::vector(dim) ; for (size_t i=0; i Cell ; /*! - \ingroup PkgHDVFAlgorithmClasses + \ingroup PkgHDVFRef The class `Filtration_core` implements data structures and methods required by the `Filtration` concept. diff --git a/HDVF/include/CGAL/HDVF/Filtration_lower_star.h b/HDVF/include/CGAL/HDVF/Filtration_lower_star.h index 3ffd9778d95..9472408b7b9 100644 --- a/HDVF/include/CGAL/HDVF/Filtration_lower_star.h +++ b/HDVF/include/CGAL/HDVF/Filtration_lower_star.h @@ -70,7 +70,7 @@ std::function degree_function (const ChainComplex& complex, co } /*! - \ingroup PkgHDVFAlgorithmClasses + \ingroup PkgHDVFRef The class `Filtration_lower_star` implements the lower star filtration on a given complex implementing the concept `AbstractChainComplex`. diff --git a/HDVF/include/CGAL/HDVF/Geometric_chain_complex_tools.h b/HDVF/include/CGAL/HDVF/Geometric_chain_complex_tools.h index 4f47b3b02e5..135f0430da0 100644 --- a/HDVF/include/CGAL/HDVF/Geometric_chain_complex_tools.h +++ b/HDVF/include/CGAL/HDVF/Geometric_chain_complex_tools.h @@ -367,7 +367,7 @@ public: // Build K sub-chain complex of L (homeomorphic to B^n) /*! - \ingroup PkgHDVFAlgorithmClasses + \ingroup PkgHDVFRef The class `Duality_simplicial_complex_tools` is dedicated to Alexander duality for 3D surface meshes. Starting from a simplicial chain complex (encoding a 3D surface mesh), it provides methods to embed the complex into a larger icosphere and generate a 3D constrained Delaunay triangulation. @@ -609,7 +609,7 @@ public: // Adjust L size /*! - \ingroup PkgHDVFAlgorithmClasses + \ingroup PkgHDVFRef The class `Duality_cubical_complex_tools` is dedicated to Alexander duality for 3D binary volumes. diff --git a/HDVF/include/CGAL/HDVF/Hdvf.h b/HDVF/include/CGAL/HDVF/Hdvf.h index cbedb31fdc7..30dec27f84e 100644 --- a/HDVF/include/CGAL/HDVF/Hdvf.h +++ b/HDVF/include/CGAL/HDVF/Hdvf.h @@ -26,7 +26,7 @@ namespace CGAL { namespace Homological_discrete_vector_field { /*! - \ingroup PkgHDVFAlgorithmClasses + \ingroup PkgHDVFRef The class `Hdvf` implements homology and cohomology computation via homological discrete vector fields (%HDVF for short). It derives from `Hdvf_core` and shares all its data and methods. @@ -94,7 +94,7 @@ public: Type of parent Hdvf_core class. */ typedef Hdvf_core Base ; - + // Inherited types using Column_chain = Base::Column_chain; using Row_chain = Base::Row_chain; diff --git a/HDVF/include/CGAL/HDVF/Hdvf_core.h b/HDVF/include/CGAL/HDVF/Hdvf_core.h index 17bf3d53e8c..fa4722d0e7d 100644 --- a/HDVF/include/CGAL/HDVF/Hdvf_core.h +++ b/HDVF/include/CGAL/HDVF/Hdvf_core.h @@ -64,7 +64,7 @@ inline std::ostream& operator<<(std::ostream &out, const std::vector& } /*! - \ingroup PkgHDVFAlgorithmClasses + \ingroup PkgHDVFRef The class `Hdvf_core` is the core implementation of homological discrete vector fields (HDVF for short). The ring of coefficients for homology computation must be a model of `IntegralDomainWithoutDivision`. diff --git a/HDVF/include/CGAL/HDVF/Hdvf_duality.h b/HDVF/include/CGAL/HDVF/Hdvf_duality.h index 0245bb38099..13f4f092e83 100644 --- a/HDVF/include/CGAL/HDVF/Hdvf_duality.h +++ b/HDVF/include/CGAL/HDVF/Hdvf_duality.h @@ -76,16 +76,16 @@ public: /*! \brief Type of coefficients used to compute homology. */ typedef typename Chain_complex::Coefficient_ring Coefficient_ring; - + /*! Type of parent Hdvf_core class. */ typedef Hdvf_core Base ; - + // Inherited types using Column_chain = Base::Column_chain; using Row_chain = Base::Row_chain; - + private: // Complex L const ChainComplex& _L ; diff --git a/HDVF/include/CGAL/HDVF/Hdvf_persistence.h b/HDVF/include/CGAL/HDVF/Hdvf_persistence.h index fcca22ee0ea..85e64a289b2 100644 --- a/HDVF/include/CGAL/HDVF/Hdvf_persistence.h +++ b/HDVF/include/CGAL/HDVF/Hdvf_persistence.h @@ -32,7 +32,7 @@ namespace Homological_discrete_vector_field { /*! - \ingroup PkgHDVFAlgorithmClasses + \ingroup PkgHDVFRef The class `Hdvf_persistence` computes persistent homology using HDVFs (over a ring of coefficients which should actually be a **field**). Hence, unlike other persistence algorithms, beside standard persistent intervals informations (birth/death indices, degrees, associated cells), `Hdvf_persistence` also provides **homology and cohomology generators for persistent pairs**. Intuitively, holes die when they are "filled" by a cell: associated homology and cohomology generators provide a representation of the hole and of the cells filling the hole. diff --git a/HDVF/include/CGAL/HDVF/Hdvf_traits_2.h b/HDVF/include/CGAL/HDVF/Hdvf_traits_2.h index 9e7c508adff..8206d79f9c0 100644 --- a/HDVF/include/CGAL/HDVF/Hdvf_traits_2.h +++ b/HDVF/include/CGAL/HDVF/Hdvf_traits_2.h @@ -22,7 +22,7 @@ namespace CGAL { namespace Homological_discrete_vector_field { /*! - \ingroup PkgHDVFAlgorithmClasses + \ingroup PkgHDVFTraitsClasses The class `Hdvf_traits_2` implements the `HDVFTraits` concept for 2D data, using a geometric kernel `K`. diff --git a/HDVF/include/CGAL/HDVF/Hdvf_traits_3.h b/HDVF/include/CGAL/HDVF/Hdvf_traits_3.h index cec9b2c6647..4fab7ba82f1 100644 --- a/HDVF/include/CGAL/HDVF/Hdvf_traits_3.h +++ b/HDVF/include/CGAL/HDVF/Hdvf_traits_3.h @@ -22,7 +22,7 @@ namespace CGAL { namespace Homological_discrete_vector_field { /*! - \ingroup PkgHDVFAlgorithmClasses + \ingroup PkgHDVFTraitsClasses The class `Hdvf_traits_3` implements the `HDVFTraits` concept for 3D data, using a geometric kernel `K`. diff --git a/HDVF/include/CGAL/HDVF/Hdvf_traits_d.h b/HDVF/include/CGAL/HDVF/Hdvf_traits_d.h index e7d8abab10d..b0277c5eb81 100644 --- a/HDVF/include/CGAL/HDVF/Hdvf_traits_d.h +++ b/HDVF/include/CGAL/HDVF/Hdvf_traits_d.h @@ -25,7 +25,7 @@ namespace CGAL { namespace Homological_discrete_vector_field { /*! - \ingroup PkgHDVFAlgorithmClasses + \ingroup PkgHDVFTraitsClasses The class `Hdvf_traits_d` implements the `HDVFTraits` concept for dD data, using a geometric kernel `K`. @@ -96,7 +96,7 @@ struct Hdvf_traits_d { #else Eigen::JacobiSVD jacobiSvd(A.eigen_object(), ::Eigen::ComputeFullV); #endif - + std::vector> d(3); std::vector dirs(3); // Fill d[i] vector diff --git a/HDVF/include/CGAL/HDVF/Mesh_object_io.h b/HDVF/include/CGAL/HDVF/Mesh_object_io.h index 21a5b09f518..424584e3d45 100644 --- a/HDVF/include/CGAL/HDVF/Mesh_object_io.h +++ b/HDVF/include/CGAL/HDVF/Mesh_object_io.h @@ -159,7 +159,7 @@ inline size_t read_nodes(const std::string &filename, std::vector _io_cell_to_vertex_handle; std::map _vertex_handle_to_io_cell; - + std::map _io_cell_to_cell_handle; std::map _cell_handle_to_io_cell;