3D Alpha Shapes

Assume we are given a set $$*S* of points in 2D or 3D and we'd 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 [BB97].

As mentionned in Edelsbrunner's and Mücke's paper [EM94],
one can intuitively think of an alpha shape as the
following. Imagine a huge mass of ice-cream making up the space $$* ^{3}*
and containing the points as ``hard'' chocolate pieces. Using one of
those sphere-formed ice-cream spoons we carve out all parts of the
ice-cream block we can reach without bumping into chocolate pieces,
thereby even carving out holes in the inside (eg. parts not reachable
by simply moving the spoon from the outside). We will eventually end
up with a (not necessarily convex) object bounded by caps, arcs and
points. If we now straighten all ``round'' faces to triangles and line
segments, we have an intuitive description of what is called the
alpha shape of $$

Alpha shapes depend on a parameter $$ from which they
are named.
What is $$ in the ice-cream game? $$ is the squared radius of the
carving spoon. A very small value will allow us to eat up all of the
ice-cream except the chocolate points themselves. Thus we already see
that the alpha shape degenerates to the point-set $$*S* for
$$* 0*. On the other hand, a huge value of $$
will prevent us even from moving the spoon between two points since
it's way too large. So we will never spoon up ice-cream lying in the
inside of the convex hull of $$*S*, and hence the alpha shape for
$$* * is the convex hull of $$*S*.^{1}

More precisely, the definition of alpha shapes is based on an underlying triangulation that may be a Delaunay triangulation in case of basic alpha shapes or a regular triangulation (cf. ) in case of weighted alpha shapes.

Let us consider the basic case with a Delaunay triangulation.
We first define the alpha complex of the set of points $$*S*.
The alpha complex is a subcomplex
of the Delaunay triangulation.
For a given value of $$, the alpha complex includes
all the simplices in the Delaunay triangulation which have
an empty circumsphere with squared radius equal or smaller than $$.
Here ``empty'' means that the open sphere
do not include any points of $$*S*.
The alpha shape is then simply the domain covered by the simplices
of the alpha complex (see [EM94]).

In general, an alpha complex is a non-connected and non-pure complex.
This means in particular that the alpha complex may have
singular faces. For $$*0 k d-1*,
a $$*k*-simplex of the alpha complex is said to be
singular if it is not a facet of a $$*(k+1)*-simplex of the complex
CGAL provides two versions of the 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
corresponding to the domain covered by a regularized version
of the alpha complex where singular faces are removed.

The alpha shapes of a set of points
$$*S* form a discrete family, even though they
are defined for all real numbers $$.
The entire family of alpha shapes can be represented
through the underlying triangulation of $$*S*. In this representation
each $$*k*-simplex of the underlying triangulation is associated with an
interval that specifies for which values of $$ the $$*k*-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 $$ to get an alpha shape including all data points
and having less than a given number of connected components.

The definition is analog in the case of weigthed 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 $$*C _{1}, C_{2}*
and radii $$

The class *CGAL::Alpha_shape_3<Dt>* 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 $$*k*-face of this triangulation
an interval specifying
for which values of $$ the face belongs to the
alpha complex.

The class *CGAL::Alpha_shape_3<Dt>* provides functions to set and
get the current $$-value, as well as an iterator that enumerates
the $$ values where the alpha shape changes.

The class provides member functions to classify for a given value
of $$*alpha* the different faces of the triangulation as
*EXTERIOR*, *SINGULAR*, *REGULAR* or
*INTERIOR* with respect
to the alpha shape. A $$*k* 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 some $$*k+1* face of the alpha complex
and *SINGULAR* otherwise.

The class provides 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*).

Finally, it provides a function to determine
the smallest value $$
such that the alpha shape satisfies the following two properties

(ii) all data points are either on the boundary or in the interior
of the regularized version of the alpha shape (no singular faces).

(i) The number of components is equal or less than a given number .

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

We currently do not specify concepts for the underlying triangulation
type. Models that work for a basic alpha-shape are the classes
*CGAL::Delaunay_triangulation_3* and
*CGAL::Triangulation_hierarchy_3* templatized with a Delaunay
triangulation. A model that works for a weighted alpha-shape is
the class *CGAL::Regular_triangulation_3*.

The triangulation needs a geometric traits class as argument.
The requirements of this class are described in the
concept *CGAL::AlphaShapeTraits_3* for which
the CGAL kernels are models in the non-weighted case, and for which
the class *CGAL::Weighted_alpha_shape_euclidean_traits_3* is model
in the weighted case.

The triangulation data structure of the triangulation with any
has to be a model of the concept *CGAL::TriangulationDataStructure_3*.
However it must be parameterized with
vertex and cell classes, which are model of the concepts
*AlphaShapeVertex_3* and *AlphaShapeCell_3*.
The package provides
by default the classes *CGAL::Alpha_shape_vertex_base_3<Gt>*
and *CGAL::Alpha_shape_cell_base_3<Gt>*.

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

// examples/Alpha_shapes_3/example_alpha.C #include <CGAL/Exact_predicates_inexact_constructions_kernel.h> #include <CGAL/Delaunay_triangulation_3.h> #include <CGAL/Alpha_shape_3.h> #include <fstream> #include <list> struct K : CGAL::Exact_predicates_inexact_constructions_kernel {}; typedef CGAL::Alpha_shape_vertex_base_3<K> Vb; typedef CGAL::Alpha_shape_cell_base_3<K> Fb; typedef CGAL::Triangulation_data_structure_3<Vb,Fb> Tds; typedef CGAL::Delaunay_triangulation_3<K,Tds> Triangulation_3; typedef CGAL::Alpha_shape_3<Triangulation_3> Alpha_shape_3; typedef K::Point_3 Point; typedef Alpha_shape_3::Alpha_iterator Alpha_iterator; int main() { std::list<Point> lp; //read input std::ifstream is("./data/bunny_1000"); int n; is >> n; std::cout << "Reading " << n << " points " << std::endl; Point p; for( ; n>0 ; n--) { is >> p; lp.push_back(p); } // compute alpha shape Alpha_shape_3 as(lp.begin(),lp.end()); std::cout << "Alpha shape computed in REGULARIZED mode by defaut" << std::endl; // find optimal alpha value Alpha_iterator opt = as.find_optimal_alpha(1); std::cout << "Optimal alpha value to get one connected component is " << *opt << std::endl; as.set_alpha(*opt); assert(as.number_of_solid_components() == 1); return 0; }

// examples/Alpha_shapes_3/example_big_alpha.C #include <CGAL/Exact_predicates_inexact_constructions_kernel.h> #include <CGAL/Delaunay_triangulation_3.h> #include <CGAL/Triangulation_hierarchy_3.h> #include <CGAL/Alpha_shape_3.h> #include <fstream> #include <list> struct K : CGAL::Exact_predicates_inexact_constructions_kernel {}; typedef CGAL::Alpha_shape_vertex_base_3<K> Vb; typedef CGAL::Triangulation_hierarchy_vertex_base_3<Vb> Vbh; typedef CGAL::Alpha_shape_cell_base_3<K> Fb; typedef CGAL::Triangulation_data_structure_3<Vbh,Fb> Tds; typedef CGAL::Delaunay_triangulation_3<K,Tds> Delaunay; typedef CGAL::Triangulation_hierarchy_3<Delaunay> Delaunay_hierarchy; typedef CGAL::Alpha_shape_3<Delaunay_hierarchy> Alpha_shape_3; typedef K::Point_3 Point; typedef Alpha_shape_3::Alpha_iterator Alpha_iterator; typedef Alpha_shape_3::NT NT; int main() { Delaunay_hierarchy dt; std::ifstream is("./data/bunny_1000"); int n; is >> n; Point p; std::cout << n << " points read" << std::endl; for( ; n>0 ; n--) { is >> p; dt.insert(p); } std::cout << "Delaunay computed." << std::endl; // compute alpha shape Alpha_shape_3 as(dt); std::cout << "Alpha shape computed in REGULARIZED mode by defaut." << std::endl; // find optimal alpha values Alpha_shape_3::NT alpha_solid = as.find_alpha_solid(); Alpha_iterator opt = as.find_optimal_alpha(1); std::cout << "Smallest alpha value to get a solid through data points is " << alpha_solid << std::endl; std::cout << "Optimal alpha value to get one connected component is " << *opt << std::endl; as.set_alpha(*opt); assert(as.number_of_solid_components() == 1); return 0; }

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

// examples/Alpha_shapes_3/example_weight.C #include <CGAL/Simple_cartesian.h> #include <CGAL/MP_Float.h> #include <CGAL/Filtered_exact.h> #include <list> #include <CGAL/Weighted_alpha_shape_euclidean_traits_3.h> #include <CGAL/Regular_triangulation_3.h> #include <CGAL/Alpha_shape_3.h> typedef CGAL::Filtered_exact<double, CGAL::MP_Float> NT; struct K : public CGAL::Simple_cartesian<NT> {}; typedef CGAL::Weighted_alpha_shape_euclidean_traits_3<K> Gt; typedef CGAL::Alpha_shape_vertex_base_3<Gt> Vb; typedef CGAL::Alpha_shape_cell_base_3<Gt> Fb; typedef CGAL::Triangulation_data_structure_3<Vb,Fb> Tds; typedef CGAL::Regular_triangulation_3<Gt,Tds> Triangulation_3; typedef CGAL::Alpha_shape_3<Triangulation_3> Alpha_shape_3; typedef Alpha_shape_3::Cell_handle Cell_handle; typedef Alpha_shape_3::Vertex_handle Vertex_handle; typedef Alpha_shape_3::Facet Facet; typedef Alpha_shape_3::Edge Edge; typedef Gt::Weighted_point Weighted_point; typedef Gt::Bare_point Bare_point; int main() { std::list<Weighted_point> lwp; //input : a small molecule lwp.push_back(Weighted_point(Bare_point( 1, -1, -1), 4)); lwp.push_back(Weighted_point(Bare_point(-1, 1, -1), 4)); lwp.push_back(Weighted_point(Bare_point(-1, -1, 1), 4)); lwp.push_back(Weighted_point(Bare_point( 1, 1, 1), 4)); lwp.push_back(Weighted_point(Bare_point( 2, 2, 2), 1)); //build alpha_shape in GENERAL mode and set alpha=0 Alpha_shape_3 as(lwp.begin(), lwp.end(), 0, Alpha_shape_3::GENERAL); //explore the 0-shape - It is dual to the boundary of the union. std::list<Cell_handle> cells; std::list<Facet> facets; std::list<Edge> edges; as.get_alpha_shape_cells(std::back_inserter(cells), Alpha_shape_3::INTERIOR); as.get_alpha_shape_facets(std::back_inserter(facets), Alpha_shape_3::REGULAR); as.get_alpha_shape_facets(std::back_inserter(facets), Alpha_shape_3::SINGULAR); as.get_alpha_shape_edges(std::back_inserter(edges), Alpha_shape_3::SINGULAR); std::cout << " The 0-shape has : " << std::endl; std::cout << cells.size() << " interior tetrahedra" << std::endl; std::cout << facets.size() << " boundary facets" << std::endl; std::cout << edges.size() << " singular edges" << std::endl; return 0; }

^{1} | ice cream, ice cream!!! The wording of this introductory paragraphs is borrowed from Kaspar Fischer's `` Introduction to Alpha Shapes'' which can be found at http://n.ethz.ch/student/fischerk/alphashapes/as/index.html. The picture has been taken from Walter Luh's homepage at http://www.stanford.edu/&wtilde;luh/cs448b/alphashapes.html. |

Next chapter: 3D Alpha Shapes

The CGAL Project .
Tue, December 21, 2004 .