Tetrahedral Meshes in Biomedical Applications: Generation, Boundary Recovery and Quality Enhancements

Mesh generation is a fundamental precursor to finite element implementations for solution of partial differential equations in engineering and science. This dissertation advances the field in three distinct but coupled areas. A robust and fast three dimensional mesh generator for arbitrarily shaped geometries was developed. It deploys nodes throughout the domain based upon user-specified mesh density requirements. The system is integer and pixel based which eliminates round off errors, substantial memory requirements and cpu intensive calculations. Linked, but fully detachable, to the mesh generation system is a physical boundary recovery routine. Frequently, the original boundary topology is required for specific boundary condition applications or multiple material constraints. Historically, this boundary preservation was not available. An algorithm was developed, refined and optimized that recovers the original boundaries, internal and external, with fidelity. Finally, a node repositioning algorithm was developed that maximizes the minimum solid angle of tetrahedral meshes. The highly coveted 2D Delaunay property that maximizes the minimum interior angle of a triangle mesh does not extend to its 3D counterpart, to maximize the minimum solid angle of a tetrahedron mesh. As a consequence, 3D Delaunay created meshes have unacceptable sliver tetrahedral elements albeit composed of 4 high quality triangle sides. These compromised elements are virtually unavoidable and can foil an otherwise intact mesh. The numerical optimization routine developed takes any preexisting tetrahedral mesh and repositions the nodes without changing the mesh topology so that the minimum solid angle of the tetrahedrons is maximized. The overall quality enhancement of the volume mesh might be small, depending upon the initial mesh. However, highly distorted elements that create ill-conditioned global matrices and foil a finite element solver are enhanced significantly

VoroCrust: Voronoi Meshing Without Clipping

Polyhedral meshes are increasingly becoming an attractive option with particular advantages over traditional meshes for certain applications. What has been missing is a robust polyhedral meshing algorithm that can handle broad classes of domains exhibiting arbitrarily curved boundaries and sharp features. In addition, the power of primal-dual mesh pairs, exemplified by Voronoi-Delaunay meshes, has been recognized as an important ingredient in numerous formulations. The VoroCrust algorithm is the first provably-correct algorithm for conforming polyhedral Voronoi meshing for non-convex and non-manifold domains with guarantees on the quality of both surface and volume elements. A robust refinement process estimates a suitable sizing field that enables the careful placement of Voronoi seeds across the surface circumventing the need for clipping and avoiding its many drawbacks. The algorithm has the flexibility of filling the interior by either structured or random samples, while preserving all sharp features in the output mesh. We demonstrate the capabilities of the algorithm on a variety of models and compare against state-of-the-art polyhedral meshing methods based on clipped Voronoi cells establishing the clear advantage of VoroCrust output.Comment: 18 pages (including appendix), 18 figures. Version without compressed images available on https://www.dropbox.com/s/qc6sot1gaujundy/VoroCrust.pdf. Supplemental materials available on https://www.dropbox.com/s/6p72h1e2ivw6kj3/VoroCrust_supplemental_materials.pd

Constrained Delaunay tetrahedral mesh generation and refinement

A {\it constrained Delaunay tetrahedralization} of a domain in $\mathbb{R}^3$ is a tetrahedralization such that it respects the boundaries of this domain, and it has properties similar to those of a Delaunay tetrahedralization. Such objects have various applications such as finite element analysis, computer graphics rendering, geometric modeling, and shape analysis. This article is devoted to presenting recent developments on constrained Delaunay tetrahedralizations of piecewise linear domains. The focus is for the application of numerically solving partial differential equations using finite element or finite volume methods. We survey various related results and detail two core algorithms that have provable guarantees and are amenable to practical implementation. We end this article by listing a set of open questions

TetGen, towards a quality tetrahedral mesh generator

TetGen is a C++ program for generating quality tetrahedral meshes aimed to support numerical methods and scientific computing. It is also a research project for studying the underlying mathematical problems and evaluating algorithms. This paper presents the essential meshing components developed in TetGen for robust and efficient software implementation. And it highlights the state-of-the-art algorithms and technologies currently implemented and developed in TetGen for automatic quality tetrahedral mesh generation

3D boundary recovery by constrained Delaunay tetrahedralization

Three-dimensional boundary recovery is a fundamental problem in mesh generation. In this paper, we propose a practical algorithm for solving this problem. Our algorithm is based on the construction of a {\it constrained Delaunay tetrahedralization} (CDT) for a set of constraints (segments and facets). The algorithm adds additional points (so-called Steiner points) on segments only. The Steiner points are chosen in such a way that the resulting subsegments are Delaunay and their lengths are not unnecessarily short. It is theoretically guaranteed that the facets can be recovered without using Steiner points. The complexity of this algorithm is analyzed. The proposed algorithm has been implemented. Its performance is reported through various application examples

Doctor of Philosophy

dissertationOne of the fundamental building blocks of many computational sciences is the construction and use of a discretized, geometric representation of a problem domain, often referred to as a mesh. Such a discretization enables an otherwise complex domain to be represented simply, and computation to be performed over that domain with a finite number of basis elements. As mesh generation techniques have become more sophisticated over the years, focus has largely shifted to quality mesh generation techniques that guarantee or empirically generate numerically well-behaved elements. In this dissertation, the two complementary meshing subproblems of vertex placement and element creation are analyzed, both separately and together. First, a dynamic particle system achieves adaptivity over domains by inferring feature size through a new information passing algorithm. Second, a new tetrahedral algorithm is constructed that carefully combines lattice-based stenciling and mesh warping to produce guaranteed quality meshes on multimaterial volumetric domains. Finally, the ideas of lattice cleaving and dynamic particle systems are merged into a unified framework for producing guaranteed quality, unstructured and adaptive meshing of multimaterial volumetric domains

Toward mixed-element meshing based on restricted Voronoi diagrams

In this paper we propose a method to generate mixed-element meshes (tetrahedra, triangular prisms, square pyramids) for B-Rep models. The vertices, edges, facets, and cells of the final volumetric mesh are determined from the combinatorial analysis of the intersections between the model components and the Voronoi diagram of sites distributed to sample the model. Inside the volumetric regions, Delaunay tetrahedra dual of the Voronoi diagram are built. Where the intersections of the Voronoi cells with the model surfaces have a unique connected component, tetrahedra are modified to fit the input triangulated surfaces. Where these intersections are more complicated, a correspondence between the elements of the Voronoi diagram and the elements of the mixedelement mesh is used to build the final volumetric mesh. The method which was motivated by meshing challenges encountered in geological modeling is demonstrated on several 3D synthetic models of subsurface rock volumes

Higher-quality tetrahedral mesh generation for domains with small angles by constrained Delaunay refinement

Algorithms for generating Delaunay tetrahedral meshes have difficulty with domains whose boundary polygons meet at small angles. The requirement that all tetrahedra be Delaunay often forces mesh generators to overrefine near small domain angles---that is, to produce too many tetrahedra, making them too small. We describe a provably good algorithm that generates meshes that are constrained Delaunay triangulations, rather than purely Delaunay. Given a piecewise linear domain free of small angles, our algorithm is guaranteed to construct a mesh in which every tetrahedron has a radius-edge ratio of $2 \sqrt{2 / 3} \doteq 1.63$ or better. This is a substantial improvement over the usual bound of $2$; it is obtained by relaxing the conditions in which boundary triangles are subdivided. Given a domain with small angles, our algorithm produces a mesh in which the quality guarantee is compromised only in specific places near small domain angles. We prove that most mesh edges have lengths proportional to the domain's minimum local feature size; the exceptions span small domain angles. Our algorithm tends to generate meshes with fewer tetrahedra than purely Delaunay methods because it uses the constrained Delaunay property, rather than vertex insertions, to enforce the conformity of the mesh to the domain boundaries. An implementation demonstrates that our algorithm does not overrefine near small domain angles

Deformable Simplicial Complexes

In this dissertation we present a novel method for deformable interface tracking in 2D and 3D|deformable simplicial complexes (DSC). Deformable interfaces are used in several applications, such as fluid simulation, image analysis, reconstruction or structural optimization. In the DSC method, the interface (curve in 2D; surface in 3D) is represented explicitly as a piecewise linear curve or surface. However, the domain is also subject to discretization: triangulation in 2D; tetrahedralization in 3D. This way, the interface can be alternatively represented as a set of edges/triangles separating triangles/tetrahedra marked as outside from those marked as inside. Such an approach allows for robust topological adaptivity. Among other advantages of the deformable simplicial complexes there are: space adaptivity, ability to handle and preserve sharp features, possibility for topology control. We demonstrate those strengths in several applications. In particular, a novel, DSC-based fluid dynamics solver has been developed during the PhD project. A special feature of this solver is that due to the fact that DSC maintains an explicit interface representation, surface tension is more easily dealt with. One particular advantage of DSC is the fact that as an alternative to topology adaptivity, topology control is also possible. This is exploited in the construction of cut loci on tori where a front expands from a single point on a torus and stops when it self-intersects