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move files in another doxygen group

This commit is contained in:
Andreas Fabri 2025-12-02 12:58:07 +00:00
parent 806f74e9d7
commit 228b9e07b8
20 changed files with 27 additions and 29 deletions
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2
HDVF/doc/HDVF/PackageDescription.txt
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@ -10,8 +10,6 @@
/// \defgroup PkgHDVFTraitsClasses Traits Classes
/// \ingroup PkgHDVFRef
/// \defgroup PkgHDVFMiscellaneous Miscellaneous
/// \ingroup PkgHDVFRef
/*!
\cgalPkgDescriptionBegin{HDVF,PkgHDVF}

1
HDVF/doc/HDVF/dependencies
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@ -3,6 +3,7 @@ Kernel_23
Kernel_d
STL_Extension
Algebraic_foundations
Number_types
Circulator
Stream_support
Surface_mesh

2
HDVF/include/CGAL/HDVF/Abstract_simplicial_chain_complex.h
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@ -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.

5
HDVF/include/CGAL/HDVF/Cub_object_io.h
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@ -32,8 +32,7 @@ typedef std::vector<size_t> IOCubCellType ;
typedef std::vector<IOCubCellType> 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<size_t>(dim) ;
for (size_t i=0; i<dim; ++i)
N.at(i) = sizes.at(i) ;

2
HDVF/include/CGAL/HDVF/Cubical_chain_complex.h
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@ -26,7 +26,7 @@ namespace CGAL {
namespace Homological_discrete_vector_field {
/*!
\ingroup PkgHDVFAlgorithmClasses
\ingroup PkgHDVFRef
The class `Cubical_chain_complex` represents (topological) chain complexes associated to cubical complexes.

2
HDVF/include/CGAL/HDVF/Filtration_core.h
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@ -37,7 +37,7 @@ typedef std::pair<std::size_t, int> Cell ;
/*!
\ingroup PkgHDVFAlgorithmClasses
\ingroup PkgHDVFRef
The class `Filtration_core` implements data structures and methods required by the `Filtration` concept.

2
HDVF/include/CGAL/HDVF/Filtration_lower_star.h
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@ -70,7 +70,7 @@ std::function<double(size_t)> 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`.

4
HDVF/include/CGAL/HDVF/Geometric_chain_complex_tools.h
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@ -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.

4
HDVF/include/CGAL/HDVF/Hdvf.h
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@ -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<Chain_complex, OSM::Sparse_chain, OSM::Sparse_matrix> Base ;
// Inherited types
using Column_chain = Base::Column_chain;
using Row_chain = Base::Row_chain;

2
HDVF/include/CGAL/HDVF/Hdvf_core.h
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@ -64,7 +64,7 @@ inline std::ostream& operator<<(std::ostream &out, const std::vector<Cell_pair>&
}
/*!
\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`.

6
HDVF/include/CGAL/HDVF/Hdvf_duality.h
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@ -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<ChainComplex, CGAL::OSM::Sparse_chain, CGAL::OSM::Sub_sparse_matrix> Base ;
// Inherited types
using Column_chain = Base::Column_chain;
using Row_chain = Base::Row_chain;
private:
// Complex L
const ChainComplex& _L ;

2
HDVF/include/CGAL/HDVF/Hdvf_persistence.h
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@ -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.

2
HDVF/include/CGAL/HDVF/Hdvf_traits_2.h
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@ -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`.

2
HDVF/include/CGAL/HDVF/Hdvf_traits_3.h
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@ -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`.

4
HDVF/include/CGAL/HDVF/Hdvf_traits_d.h
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@ -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<Matrix::EigenType> jacobiSvd(A.eigen_object(), ::Eigen::ComputeFullV);
#endif
std::vector<std::vector<double>> d(3);
std::vector<Vector_d> dirs(3);
// Fill d[i] vector

2
HDVF/include/CGAL/HDVF/Mesh_object_io.h
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@ -159,7 +159,7 @@ inline size_t read_nodes(const std::string &filename, std::vector<typename Trait
}
/*!
\ingroup PkgHDVFAlgorithmClasses
\ingroup PkgHDVFRef
The class `Mesh_object_io` is an intermediate IO class, used to load triangular/tetraedral meshes and produce simplicial complexes.

2
HDVF/include/CGAL/HDVF/Simplex.h
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@ -26,7 +26,7 @@ namespace CGAL {
namespace Homological_discrete_vector_field {
/*!
\ingroup PkgHDVFAlgorithmClasses
\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).

2
HDVF/include/CGAL/HDVF/Sub_chain_complex_mask.h
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@ -26,7 +26,7 @@ namespace CGAL {
namespace Homological_discrete_vector_field {
/*!
\ingroup PkgHDVFAlgorithmClasses
\ingroup PkgHDVFRef
The class `Sub_chain_complex_mask` is a technical class implementing a sub chain complex. A sub chain complex \f$A\f$ of a chain complex \f$K\f$ is a subset \f$A\subseteq K\f$ such that the restricted boundary operator \f$\partial_A = \partial_K|_A\f$ still satisfies \f$\partial_A^2 = 0\f$.

2
HDVF/include/CGAL/HDVF/Surface_mesh_io.h
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@ -27,7 +27,7 @@ namespace Homological_discrete_vector_field {
/*!
\ingroup PkgHDVFAlgorithmClasses
\ingroup PkgHDVFRef
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`.

6
HDVF/include/CGAL/HDVF/Triangulation_3_io.h
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@ -27,9 +27,9 @@ namespace Homological_discrete_vector_field {
/*!
\ingroup PkgHDVFAlgorithmClasses
\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.
*/
@ -57,7 +57,7 @@ private:
*/
std::map<size_t, vertex_descriptor> _io_cell_to_vertex_handle;
std::map<vertex_descriptor, size_t> _vertex_handle_to_io_cell;
std::map<Io_cell_type, cell_descriptor> _io_cell_to_cell_handle;
std::map<cell_descriptor, Io_cell_type> _cell_handle_to_io_cell;