CGAL 5.6.3 - 3D Skin Surface Meshing

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User Manual

Author
  Nico Kruithof

# Introduction

Skin surfaces, introduced by Edelsbrunner in [1], have a rich and simple combinatorial and geometric structure that makes them suitable for modeling large molecules in biological computing. Meshing such surfaces is often required for further processing of their geometry, like in numerical simulation and visualization.

A skin surface is defined by a set of weighted points (input balls) and a scalar called the shrink factor. If the shrink factor is equal to one, the surface is just the boundary of the union of the input balls. For a shrink factor smaller than one, the skin surface becomes tangent continuous, due to the appearance of patches of spheres and hyperboloids connecting the balls.

This package constructs a mesh isotopic to the skin surface defined by a set of balls and a shrink factor using the algorithm described in [2].

An optimized algorithm is implemented for meshing the union of a set of balls.

# Definition of a Skin Surface

Figure 57.1 Left: Convex combinations of two weighted points (the two dashed circles). Right: The skin curve of the weighted points. The smaller circles form a subset of the weighted points whose boundary is the skin curve.

This section first briefly reviews skin surfaces. For a more thorough introduction to skin surfaces, we refer to [1] where they were originally introduced.

A skin surface is defined in terms of a finite set of weighted points \( \ssWpoint{P}\) and a shrink factor \( s\), with \( 0\leq s\leq 1\). A weighted point \( \ssWpoint{p}=({p},\ssWeight{p})\in \mathbb{R}^3\times\mathbb{R}\) corresponds to a ball with center \( {p}\) and radius \( \sqrt{\ssWeight{p}}\). A weighted point with zero weight is called an unweighted point.

A pseudo distance between a weighted point \( \ssWpoint{p} = (p,\ssWeight{P})\) and an unweighted point \( x\) is defined as

\[ \pi(\ssWpoint{p},x) = \dabs{p-x}^2 - \ssWeight{p}, \]

where \( \dabs{p-x}\) is the Euclidean distance between \( p\) and \( x\). The ball corresponding to a weighted point \( \ssWpoint{p}\) is the zero set of \( \pi(\ssWpoint{p},\cdot)\). Note that if \( \ssWeight{p}<0\) the radius of the ball is imaginary and the zero-set is empty.

We can take convex combinations of weighted points by taking convex combinations of their distance functions. Figure 57.1 (left) shows weighted points that are obtained as convex combinations of the dashed circles. For further reading on the space of circles and spheres we refer to [3].

Starting from a weighted point \( \ssWpoint{p}=({p},\ssWeight{P})\), the shrunk weighted point \( \ssWpoint{p}^s\) is obtained by taking a convex combination with the unweighted point centered at \( p\), formally \( \ssWpoint{p}^s = s \ssWpoint{p} + (1-s) \ssWpoint{p}'\), with \( \ssWpoint{p}'=(p,0)\). A simple calculation shows that, \( \ssWpoint{p}^s = ({p},s\cdot \ssWeight{p})\). The set \( \ssWpoint{P}^s\) is the set obtained by shrinking every weighted point of \( \ssWpoint{P}\) by a factor \( s\): \( \ssWpoint{P}^s = \{\ssWpoint{p}^s \mid \ssWpoint{p}\in \ssWpoint{P}\}\). The shrunk weighted points of Figure 57.1 (left) are shown in Figure 57.1 (right).

We now define the skin surface \( \mbox{skn}^{s}(\ssWpoint{P})\) associated with a set of weighted points \( \ssWpoint{P}\). Consider the set of weighted points obtained by taking the convex hull of the input weighted points. A calculation shows that every weighted point lies within the union of the input balls. Next, we shrink each weighted point in the convex hull with the shrink factor \( s\). Hence, we multiply the radius of the corresponding (real) input circles with a factor \( \sqrt{s}\). The skin surface is the boundary of the union of this set of weighted points:

\begin{eqnarray} \mbox{skn}^{s}(\ssWpoint{P}) &=& \partial\;{\bigcup\{\ssWpoint{p}^s\mid \ssWpoint{p}\in \mbox{conv} (\ssWpoint{P})\}}. \end{eqnarray}

Here \( \mbox{conv}(\ssWpoint{P}) \subset \mathbb{R}^3\times\mathbb{R}\) is the convex hull of a set of weighted points \( \ssWpoint{P}\), whereas \( \partial\) denotes the boundary - in \( \mathbb{R}^3\) - of the union of the corresponding set of balls.

Recall that each weighted point in the convex hull of the input weighted points is contained in the union of the input weighted points. Hence, for a shrink factor equal to one, the skin surface is the boundary of the union of the input weighted points.

By definition of a skin surface, the weights of the input balls (their radius-squared) are shrunk with a factor of \( s\) and the skin surface wraps around the shrunk input balls. In order to make the skin surface wrap around the (unshrunk) input balls, we can first increase the weights of the input balls by multiplying them with a factor \( 1/s\) and then compute the skin surface.

# The Interface

The interface to the skin surface package consists of one main function, taking a set of weighted points and a shrink factor and outputting the meshed surface. Further, it defines classes and functions and classed used to perform the main steps of the algorithm. There are two global classes `Skin_surface_3` and `Union_of_balls_3` both of which are models of the concept `SkinSurface_3` and there are two functions to extract a mesh of the skin surface (union of balls) from the objects of the aforementioned classes. A final function takes a mesh and the `Skin_surface_3` (`Union_of_balls_3`) object it is constructed from and refines the mesh. This section describes these classes and functions in more detail.

The main function of the skin surface package takes an iterator range of weighted points, a shrink factor and the number of subdivision steps and outputs a mesh in a `Polyhedron_3`:

template <class WP_iterator, class Polyhedron_3>
void make_skin_surface_mesh_3(Polyhedron_3 &p,
WP_iterator begin, WP_iterator end,
FT shrink_factor=.5,
int nSubdiv=0,
bool grow_balls = true);
CGAL::make_skin_surface_mesh_3
void make_skin_surface_mesh_3(Polyhedron &p, WP_iterator begin, WP_iterator end, double shrink_factor=.5, int nSubdivisions=0, bool grow_balls=true)
constructs a mesh of the skin surface defined by the weighted points and the shrink factor.

Where, `FT` is the number type used by the `Weighted_points`.

To obtain more control over the algorithm, the different steps can also be performed separately. First, a `Skin_surface_3` object is created from an iterator range of weighted points and a shrink factor. Optional arguments are a boolean telling whether the input weighted points should be grown in such a way that the skin surface wraps around the input balls instead of the shrunk input balls.

template <class SkinSurfaceTraits_3>
Skin_surface_3(WP_iterator begin, WP_iterator end,
FT shrink_factor,
bool grow_balls = true);

The template parameter should implement the `SkinSurfaceTraits_3` concept. The type `WP_iterator`, is an iterator over weighted points as defined by `SkinSurfaceTraits_3` and `FT` is the number type used by the weighted points.

For a shrink factor equal to one the skin surface is the boundary of the union of the input balls. In this case the algorithm used for meshing the skin surface greatly simplifies. These optimizations are implemented in the class `Union_of_balls_3`. The constructor for the union of balls class is similar, except for the missing shrink factor:

template <class SkinSurfaceTraits_3>
Union_of_balls_3(WP_iterator begin, WP_iterator end,
bool grow_balls = true);

With a model of the concept `SkinSurface_3` it is possible to generate a coarse mesh isotopic to the skin surface. Using the function `mesh_skin_surface_3()` with signature:

template <class SkinSurface_3, class Polyhedron>
void mesh_skin_surface_3(const SkinSurface_3 &skin_surface, Polyhedron &p);
SkinSurface_3
The concept SkinSurface_3 defines a skin surface and provides an interface for the dedicated skin sur...
Definition: SkinSurface_3.h:17
CGAL::mesh_skin_surface_3
void mesh_skin_surface_3(const SkinSurface_3 &skin_surface, Polyhedron &p)
constructs a mesh of the skin_surface in p.

The last function takes the (coarse) mesh and subdivides it in-situ by applying a given number of 1-4 split operations (each triangle is split into four sub-triangles) and moving the new vertices towards the skin surface. If the number of iterations is not specified, one subdivision step is done. The object of the `SkinSurface_3` concept used to construct the coarse mesh is needed to move new points on the skin surface.

template <class SkinSurface_3, class Polyhedron >
void subdivide_skin_surface_mesh_3 (const SkinSurface_3 &skinsurface,
Polyhedron &p,
int iterations = 1);
CGAL::subdivide_skin_surface_mesh_3
void subdivide_skin_surface_mesh_3(const SkinSurface_3 &skin_surface, Polyhedron &p, int nSubdiv=1)
subdivides a skin surface mesh constructed by the function mesh_skin_surface_3() using nSubdiv 1-4 sp...

# Timings

The timings of the construction of the coarse mesh and the first subdivision are given in seconds and were done on a Pentium 4, 3.5 GHz, with 1 Gb of memory.

Data set | Number of weighted points | Coarse mesh | first subdivision step
Caffeine | 23 | 0.2 sec. | 0.05 sec.
Gramicidin A | 318 | 5 sec. | 2 sec.

# Example Programs

## Meshing a Skin Surface

The following example shows the construction of a coarse mesh of the skin surface using the function `make_skin_surface_mesh_3()`. The output is a `Polyhedron_3`.
File Skin_surface_3/skin_surface_simple.cpp

#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
#include <CGAL/make_skin_surface_mesh_3.h>
#include <list>
typedef CGAL::Exact_predicates_inexact_constructions_kernel K;
typedef K::Point_3 Bare_point;
typedef K::Weighted_point_3 Weighted_point;
typedef CGAL::Polyhedron_3<K> Polyhedron;
int main()
{
std::list<Weighted_point> l;
double shrinkfactor = 0.5;
l.push_front(Weighted_point(Bare_point( 1,-1,-1), 1.25));
l.push_front(Weighted_point(Bare_point( 1, 1, 1), 1.25));
l.push_front(Weighted_point(Bare_point(-1, 1,-1), 1.25));
l.push_front(Weighted_point(Bare_point(-1,-1, 1), 1.25));
Polyhedron p;
CGAL::make_skin_surface_mesh_3(p, l.begin(), l.end(), shrinkfactor);
return 0;
}
CGAL::Exact_predicates_inexact_constructions_kernel
CGAL::Polyhedron_3

## Meshing and Subdividing a Skin Surface

The following example shows the construction of mesh of the skin surface by explicitly performing different steps of the algorithm. It first constructs a `Skin_surface_3` object from an iterator range of weighted points and a shrink factor. From this object, the coarse mesh isotopic to the skin surface is extracted using the function `mesh_skin_surface_3()`

Next, the coarse mesh is refined to obtain a better approximation. The use of `Skin_surface_polyhedral_items_3<Skin_surface_3>` in the `Polyhedron_3` is not necessary, but gives the subdivision a significant speedup.
File Skin_surface_3/skin_surface_subdiv.cpp

#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
#include <CGAL/Skin_surface_3.h>
#include <CGAL/Polyhedron_3.h>
#include <CGAL/mesh_skin_surface_3.h>
#include <CGAL/subdivide_skin_surface_mesh_3.h>
#include "skin_surface_writer.h"
#include <list>
#include <fstream>
typedef CGAL::Exact_predicates_inexact_constructions_kernel K;
typedef CGAL::Skin_surface_traits_3<K> Traits;
typedef CGAL::Skin_surface_3<Traits> Skin_surface_3;
typedef Skin_surface_3::FT FT;
typedef Skin_surface_3::Bare_point Bare_point;
typedef Skin_surface_3::Weighted_point Weighted_point;
typedef CGAL::Polyhedron_3<K,
CGAL::Skin_surface_polyhedral_items_3<Skin_surface_3> > Polyhedron;
int main()
{
std::list<Weighted_point> l;
FT shrinkfactor = 0.5;
l.push_front(Weighted_point(Bare_point( 1,-1,-1), 1.25));
l.push_front(Weighted_point(Bare_point( 1, 1, 1), 1.25));
l.push_front(Weighted_point(Bare_point(-1, 1,-1), 1.25));
l.push_front(Weighted_point(Bare_point(-1,-1, 1), 1.25));
Polyhedron p;
Skin_surface_3 skin_surface(l.begin(), l.end(), shrinkfactor);
CGAL::mesh_skin_surface_3(skin_surface, p);
CGAL::subdivide_skin_surface_mesh_3(skin_surface, p);
std::ofstream out("mesh.off");
out << p;
return 0;
}
CGAL::Skin_surface_3
The Skin_surface_3 is the main class in this package.
Definition: Skin_surface_3.h:19
CGAL::Skin_surface_traits_3
The class Skin_surface_traits_3 is designed as a default traits class for the class Skin_surface_3<Sk...
Definition: Skin_surface_traits_3.h:17
CGAL::Skin_surface_polyhedral_items_3
An items class for the Polyhedron_3 that stores information in faces instead of an auxiliary data str...
Definition: Skin_surface_polyhedral_items_3.h:12