
namespace CGAL {
/*!

\mainpage User Manual 
\anchor Chapter_3D_Alpha_Shapes
\cgalAutoToc
\authors Tran Kai Frank Da, S&eacute;bastien Loriot, and Mariette Yvinec

\image html alphashape.png 
\image latex alphashape.png 

Assume we are given a set \f$ S\f$ of points in 2D or 3D and we would like to
have something like "the shape formed by these points". This is
quite a vague notion and there are probably many possible
interpretations, the alpha shape being one of them. Alpha shapes
can be used for shape reconstruction from a dense unorganized set of
data points. Indeed, an alpha shape is demarcated by a frontier,
which is a linear approximation of the original shape \cgalCite{bb-srmua-97t}.

As mentioned in Edelsbrunner's and M&uuml;cke's paper \cgalCite{em-tdas-94},
one can intuitively think of an alpha shape as the
following. Imagine a huge mass of ice-cream making up the space \f$ \mathbb{R}^3\f$
and containing the points as "hard" chocolate pieces. Using one of
those sphere-formed ice-cream spoons, we carve out all parts of the
ice-cream block we can reach without bumping into chocolate pieces,
thereby even carving out holes in the inside (e.g. parts not reachable
by simply moving the spoon from the outside). We will eventually end
up with a (not necessarily convex) object bounded by caps, arcs and
points. If we now straighten all "round" faces to triangles and line
segments, we have an intuitive description of what is called the
alpha shape of \f$ S\f$. The drawing above provides an example
of this process in 2D (where our ice-cream spoon is simply a circle).

Alpha shapes depend on a parameter \f$ \alpha\f$ after which they are named.
In the ice-cream analogy above, \f$ \alpha\f$ is the squared radius of the
carving spoon. A very small value will allow us to eat up all of the
ice-cream except the chocolate points themselves. Thus we already see
that the alpha shape degenerates to the point-set \f$ S\f$ for
\f$ \alpha \rightarrow 0\f$. On the other hand, a huge value of \f$ \alpha\f$
will prevent us even from moving the spoon between two points since
it is too large and we will never spoon up the ice-cream lying in the
inside of the convex hull of \f$ S\f$. Hence, the alpha shape becomes
the convex hull of \f$ S\f$ as \f$ \alpha \rightarrow \infty\f$.

\cgal offers 2D and 3D alpha shapes. The GUDHI library offers a
<a href="http://gudhi.gforge.inria.fr/doc/latest/group__alpha__complex.html"> dD Alpha complex</a>.


\section Alpha_shapes_3Definitions Definitions

We distinguish two versions of alpha shapes. <I>Basic alpha shapes</I>
are based on the Delaunay triangulation. <I>Weighted alpha shapes</I>
are based on its generalization, the regular triangulation
(cf. Section \ref Triangulation3secclassRegulartriangulation "Regular Triangulations"),
replacing the euclidean distance by the power to weighted points.

Let us consider the basic case with a Delaunay triangulation.
We first define the alpha complex of the set of points \f$ S\f$. 
The alpha complex is a subcomplex 
of the Delaunay triangulation.
For a given value of \f$ \alpha\f$, the alpha complex includes
all the simplices in the Delaunay triangulation which have
an empty circumscribing sphere with squared radius equal or smaller than \f$ \alpha\f$.
Here "empty" means that the open sphere does not include any points of \f$ S\f$.
The alpha shape is then simply the domain covered by the simplices
of the alpha complex (see \cgalCite{em-tdas-94}).

In general, an alpha complex is a disconnected and non-pure complex,
meaning in particular that the alpha complex may have
singular faces. For \f$ 0 \leq k \leq d-1\f$,
a \f$ k\f$-simplex of the alpha complex is said to be
singular if it is not a facet of a \f$ (k+1)\f$-simplex of the complex.
%CGAL provides two versions of alpha shapes. In the general mode,
the alpha shapes correspond strictly to the above definition.
The regularized mode provides a regularized version of the alpha shapes.
It corresponds to the domain covered by a regularized version
of the alpha complex where singular faces are removed 
(See \cgalFigureRef{figgenregex} for an example).

\cgalFigureBegin{figgenregex,gen-reg-ex.png} 
Comparison of general and regularized alpha-shape. <B>Left:</B> Some points are taken on the surface of a torus, three points being taken relatively far from the surface of the torus; <B>Middle:</B> The general alpha-shape (for a large enough alpha value) contains the singular triangle facet of the three isolated points; <B>Right:</B> The regularized version (for the same value of alpha) does not contains any singular facet.
\cgalFigureEnd

The alpha shapes of a set of points 
\f$ S\f$ form a discrete family, even though they
are defined for all real numbers \f$ \alpha\f$.
The entire family of alpha shapes can be represented 
through the underlying triangulation of \f$ S\f$. In this representation
each \f$ k\f$-simplex of the underlying triangulation is associated with an
interval that specifies for which values of \f$ \alpha\f$ the \f$ k\f$-simplex
belongs to the alpha complex. Relying on this fact, the family of
alpha shapes can be computed efficiently and relatively
easily. Furthermore, we can select the optimal value
of \f$ \alpha\f$ to get an alpha shape including all data points
and having less than a given number of connected components.
Also, the alpha-values allows to define a filtration on the
faces of the triangulation of a set of points. 
In this filtration, the faces of the triangulation are output
in increasing order of the alpha value 
for which they appear 
in the alpha complex. In case of equal alpha values,
lower dimensional faces are output first.

The definition is analog in the case of weighted alpha shapes.
The input set is now a set of weighted points (which can be regarded
as spheres) and the underlying triangulation 
is the regular triangulation of this set.
Two spheres, or two weighted points, with centers \f$ C_1, C_2\f$
and radii \f$ r_1, r_2 \f$ are said to be orthogonal iff 
\f$ C_1C_2 ^2 = r_1^2 + r_2^2\f$ and suborthogonal
iff \f$ C_1C_2 ^2 < r_1^2 + r_2^2\f$.
For a given value of \f$ \alpha\f$,
the weighted alpha complex is formed with the simplices of the 
regular triangulation triangulation
such that there is a sphere orthogonal to the weighted points associated
with the vertices of the simplex and suborthogonal to all the other
input weighted points. Once again the alpha shape is then defined as
the domain covered by a the alpha complex and comes in general and
regularized versions.

\section Alpha_Shape_3Functionality Functionality

\subsection AlphaShape_3DFamilyOfAlphaShapes Family of Alpha Shapes

The class `Alpha_shape_3<Dt,ExactAlphaComparisonTag>` represents the whole
family of alpha shapes for a given set of points.
The class includes the underlying triangulation `Dt`
of the set, and associates to each \f$ k\f$-face of this triangulation
an interval specifying 
for which values of \f$ \alpha\f$ the face belongs to the
alpha complex.
The second template parameter, `ExactAlphaComparisonTag`, is a tag that,
when set to CGAL::Tag_true, triggers exact comparisons between alpha values.

The class provides functions to set and
get the current \f$ \alpha\f$-value, as well as an iterator that enumerates
the \f$ \alpha\f$ values where the alpha shape changes.

Additionally, the class has a filtration member function that, given
an output iterator with `Object`
as value type, outputs the faces of the triangulation 
according to the 
order of apparition in the alpha complex when alpha increases.

Finally, it provides a function to determine 
the smallest value \f$ \alpha\f$
such that the alpha shape satisfies the following two properties: <br>
<ol>
<li> All data points are either on the boundary or in the interior
of the regularized version of the alpha shape (no singular faces).
<li> The number of components is equal or less than a given number.
</ol>

The current implementation is static, that is after its construction
points cannot be inserted or removed.

\subsection AlphaShape_3DAlphaShapeForAFixedAlpha Alpha Shape for a Fixed Alpha

Given a value of alpha, the class `Fixed_alpha_shape_3<Dt>` represents one 
alpha shape for a given set of points.
The class includes the underlying triangulation `Dt`
of the set, and associates to each \f$ k\f$-face of this triangulation
a classification type. This class is dynamic, that is after its construction
points can be inserted or removed.

\subsection AlphaShape_3DClassificationAndIterators Classification and Iterators

Both classes provide member functions to classify for a (given) value
of \f$ \alpha\f$ the different faces of the triangulation as
`EXTERIOR`, `SINGULAR`, `REGULAR` or 
`INTERIOR` with respect
to the alpha shape. A \f$ k\f$-face on the boundary of the alpha complex
is said to be: `REGULAR` if it is a subface of the alpha-complex which
is a subface of a \f$ (k+1)\f$-face of the alpha complex, and `SINGULAR` otherwise.
A \f$ k\f$-face of the alpha complex which is not on the boundary of the alpha complex
is said to be `INTERIOR`. See \cgalFigureRef{figclassif} for a 2D illustration.

\cgalFigureBegin{figclassif,classif.png} Classification of simplices, a 2D example. <B>Left:</B> The 2D
Delaunay triangulation of a set of points; <B>Right:</B>
Classification of simplices for a given alpha (the squared radius of
the red circle). `INTERIOR`, `REGULAR` and `SINGULAR` simplices are
depicted in black, green and blue respectively. `EXTERIOR` simplices
are not depicted. The vertex `s` and the edge `tu` are `SINGULAR`
since all higher dimension simplices they are incident to are
`EXTERIOR`. The facet `pqr` is `EXTERIOR` because the squared radius
of its circumscribed circle is larger than alpha.
\cgalFigureEnd

The classes provide also output iterators to get for a given `alpha` value
the vertices, edges, facets and cells of the different types
(`EXTERIOR`, `SINGULAR`, `REGULAR` or 
`INTERIOR`).

\section AlphaShape3D_ConceptAndModels Concepts and Models

We currently do not specify concepts for the underlying triangulation
type. Models that work for a family of alpha-shapes are the instantiations
of the classes `Delaunay_triangulation_3` and
`Periodic_3_Delaunay_triangulation_3` (see
example \ref AlphaShape_3DExampleForPeriodicAlphaShapes).
A model that works for a fixed alpha-shape are the instantiations
of the class `Delaunay_triangulation_3`.
Models that work for a weighted alpha-shape are the instantiations
of the classes `Regular_triangulation_3` and
`Periodic_3_regular_triangulation_3`.
The triangulation needs a geometric traits class
and a triangulation data structure as template parameters.

\subsection AlphaShape3D_ConceptAndModelsAlphaShapes Alpha Shapes

For the class `Alpha_shape_3<Dt,ExactAlphaComparisonTag>`, the requirements of
the traits class are described in the concepts `AlphaShapeTraits_3`
in the non-weighted case and `WeightedAlphaShapeTraits_3` in the weighted case.
All \cgal kernels are models of both concepts.

The triangulation data structure of the triangulation
has to be a model of the concept `TriangulationDataStructure_3`,
and it must be parameterized with vertex and cell classes, which are model of the concepts
`AlphaShapeVertex_3` and `AlphaShapeCell_3`.
The classes `Alpha_shape_vertex_base_3<Gt>` and `Alpha_shape_cell_base_3<Gt>`
are models of these concepts and can be used for all type of alpha shapes,
provided that the template parameters `Vb` and `Fb` are appropriately chosen,
as we shall see in the following section.

\subsection AlphaShape3D_ConceptAndModelsFixedAlphaShapes Fixed Alpha Shapes

For the class `Fixed_alpha_shape_3<Dt>`, the requirements of
the traits class are described in the concepts `FixedAlphaShapeTraits_3`
in the non-weighted case and `FixedWeightedAlphaShapeTraits_3` in the weighted case.
All \cgal kernels are models of both concepts.
The triangulation data structure of the triangulation
has to be a model of the concept `TriangulationDataStructure_3`,
and it must be parameterized with vertex and cell classes, which are model of the concepts
`FixedAlphaShapeVertex_3` and `FixedAlphaShapeCell_3`.
The package provides models `Fixed_alpha_shape_vertex_base_3<Gt>` 
and `Fixed_alpha_shape_cell_base_3<Gt>`, respectively.

\subsection AlphaShape3D_ConceptAndModelsTDS Triangulation data structure

Additional requirements are put when using weighted or
periodic triangulations as underlying triangulation:
<ul>
<li> When using a weighted triangulation (`Regular_triangulation_3` or
`Periodic_3_regular_triangulation_3`), the vertex
and cell classes must respectively be models to both `AlphaShapeVertex_3` and
`RegularTriangulationVertexBase_3`, and to both
`AlphaShapeCell_3` and `RegularTriangulationCellBase_3`
(see example: \ref AlphaShape_3DExampleforWeightedAlphaShapes).
<li> When using a periodic triangulation (`Periodic_3_Delaunay_triangulation_3`
or `Periodic_3_regular_triangulation_3`), the vertex and cell classes must
respectively be models to both `AlphaShapeVertex_3` and `Periodic_3TriangulationDSVertexBase_3`,
and to both `AlphaShapeCell_3` and `Periodic_3TriangulationDSCellBase_3`
(see example: \ref  AlphaShape_3DExampleForPeriodicAlphaShapes).
</ul>

\section Alpha_shapes_3AlphaShape3OrFixedAlphaShape3 Alpha_shape_3 vs. Fixed_alpha_shape_3

The class `Alpha_shape_3<Dt,ExactAlphaComparisonTag>` represents the whole family
of alpha shapes for a given set of points while the class `Fixed_alpha_shape_3<Dt>`
represents only one alpha shape (for a fixed alpha). When using the same kernel,
`Fixed_alpha_shape_3<Dt>` is a lighter version. It is thus naturally much more efficient
when the alpha-shape is needed for a single given value of alpha.
In addition, note that the class `Alpha_shape_3<Dt,ExactAlphaComparisonTag>`
requires constructions (squared radius of simplices) while the 
class `Fixed_alpha_shape_3<Dt>` uses only predicates.
This implies that a certified construction of one (several)
alpha-shape, using the `Alpha_shape_3<Dt,ExactAlphaComparisonTag>` requires a kernel
with exact predicates and exact constructions (or setting `ExactAlphaComparisonTag` to `Tag_true`)
while using a kernel with exact predicates is sufficient for the class `Fixed_alpha_shape_3<Dt>`.
This makes the class `Fixed_alpha_shape_3<Dt>` even more efficient in this setting.
In addition, note that the `Fixed` version is the only of the
two that supports incremental insertion and removal of points.

We give the time spent while computing the alpha shape of a protein (considered
as a set of weighted points) featuring 4251 atoms (using `gcc 4.3` under Linux with `-O3`
and `-DNDEBUG` flags, on a 2.27GHz Intel(R) Xeon(R) E5520 CPU): 
Using `Exact_predicates_inexact_constructions_kernel`, building
the regular triangulation requires 0.09s, then the class `Fixed_alpha_shape_3<Dt>`
required 0.05s while the class `Alpha_shape_3<Dt,ExactAlphaComparisonTag>` requires 0.35s
if `ExactAlphaComparisonTag` is `Tag_false` (and 0.70s with `Tag_true`).
Using `Exact_predicates_exact_constructions_kernel`, building
the regular triangulation requires 0.19s and then the class `Alpha_shape_3<Dt,ExactAlphaComparisonTag>` 
requires 0.90s.

\section Alpha_shapes_3Examples Examples

\subsection AlphaShape_3DExampleForBasicAlphaShapes Example for Basic Alpha-Shapes

This example builds a basic alpha shape using a Delaunay triangulation
as underlying triangulation.

\cgalExample{Alpha_shapes_3/ex_alpha_shapes_3.cpp}

\subsection AlphaShape_3DBuildingBasicAlphaShapesForManyPoints Building Basic Alpha Shapes for Many Points

When many points are input in the alpha shape, say more than 10 000,
it may pay off to use a Delaunay triangulation with the `Fast_location`
policy as underlying triangulation in order to speed up point location
queries (cf. Section \ref Triangulation3seclocpol "The Location Policy Parameter").

\cgalExample{Alpha_shapes_3/ex_alpha_shapes_with_fast_location_3.cpp}

\subsection AlphaShape_3DExampleforWeightedAlphaShapes Example for Weighted Alpha-Shapes

The following examples build a weighted alpha shape requiring a
regular triangulation as underlying triangulation.
The alpha shape is built in `GENERAL` mode.

\cgalExample{Alpha_shapes_3/ex_weighted_alpha_shapes_3.cpp}

\subsection AlphaShape_3DExampleForFixedWeightedAlphaShapes Example for Fixed Weighted Alpha-Shapes

Same example as previous but using a fixed value of alpha.

\cgalExample{Alpha_shapes_3/ex_fixed_weighted_alpha_shapes_3.cpp}

\subsection AlphaShape_3DBuildingAnAlphaShapesWithExactComparisonsOfAlphaValues Building an Alpha Shapes with Exact Comparisons of Alpha Values

On some platforms, the alpha shapes of the set of points of this example
cannot be computed when using a traits with inexact constructions. To be able to compute
them with a traits with inexact constructions, the tag
`ExactAlphaComparisonTag` is set to `Tag_true`.
\cgalExample{Alpha_shapes_3/ex_alpha_shapes_exact_alpha.cpp}

\subsection AlphaShape_3DExampleForPeriodicAlphaShapes Example for Periodic Alpha Shapes

The following example shows how to use a periodic Delaunay
triangulation (Chapter \ref Chapter_3D_Periodic_Triangulations "3D Periodic Triangulations") as underlying
triangulation for the alpha shape computation. Usage of a weighted Delaunay periodic
triangulation is presented in the example: \ref Alpha_shapes_3/ex_weighted_periodic_alpha_shapes_3.cpp "ex_weighted_periodic_alpha_shapes_3.cpp".

In order to define the original domain and to benefit from the
built-in heuristic optimizations of the periodic triangulation computation,
it is recommended to first construct the triangulation and
then construct the alpha shape from it. The alpha
shape constructor that takes a point range can be used as well but in
this case the original domain cannot be specified and the default unit
cube will be chosen and no optimizations will be used.

It is also recommended to switch the triangulation to 1-sheeted
covering if possible. Note that a periodic triangulation in 27-sheeted
covering space is degenerate. In this case, an exact constructions
kernel needs to be used to compute the alpha shapes. Otherwise the
results will suffer from round-off problems.

\cgalExample{Alpha_shapes_3/ex_periodic_alpha_shapes_3.cpp}

*/ 
} /* namespace CGAL */

