Watertight and 2-Manifold Surface Meshes Using Dual Contouring With Tetrahedral Decomposition of Grid Cubes

The Dual Contouring algorithm (DC) is a grid-based process used to generate surface meshes from volumetric data. The advantage of DC is that it can reproduce sharp features by inserting vertices anywhere inside the grid cube, as opposed to the Marching Cubes (MC) algorithm that can insert vertices only on the grid edges. However, DC is unable to guarantee 2-manifold and watertight meshes due to the fact that it produces only one vertex for each grid cube. We present a modified Dual Contouring algorithm that is capable of overcoming this limitation. Our method decomposes an ambiguous grid cube into a maximum of twelve tetrahedral cells; we introduce novel polygon generation rules that produce 2-manifold and watertight surface meshes. We have applied our proposed method on realistic data, and a comparison of the results of our proposed method with results from traditional DC shows the effectiveness of our method

Variational approach to relaxed topological optimization: closed form solutions for structural problems in a sequential pseudo-time framework

The work explores a specific scenario for structural computational optimization based on the following elements: (a) a relaxed optimization setting considering the ersatz (bi-material) approximation, (b) a treatment based on a non-smoothed characteristic function field as a topological design variable, (c) the consistent derivation of a relaxed topological derivative whose determination is simple, general and efficient, (d) formulation of the overall increasing cost function topological sensitivity as a suitable optimality criterion, and (e) consideration of a pseudo-time framework for the problem solution, ruled by the problem constraint evolution. In this setting, it is shown that the optimization problem can be analytically solved in a variational framework, leading to, nonlinear, closed-form algebraic solutions for the characteristic function, which are then solved, in every time-step, via fixed point methods based on a pseudo-energy cutting algorithm combined with the exact fulfillment of the constraint, at every iteration of the non-linear algorithm, via a bisection method. The issue of the ill-posedness (mesh dependency) of the topological solution, is then easily solved via a Laplacian smoothing of that pseudo-energy. In the aforementioned context, a number of (3D) topological structural optimization benchmarks are solved, and the solutions obtained with the explored closed-form solution method, are analyzed, and compared, with their solution through an alternative level set method. Although the obtained results, in terms of the cost function and topology designs, are very similar in both methods, the associated computational cost is about five times smaller in the closed-form solution method this possibly being one of its advantages. Some comments, about the possible application of the method to other topological optimization problems, as well as envisaged modifications of the explored method to improve its performance close the workPeer ReviewedPostprint (author's final draft

The implementation of a disambiguation marching cubes algorithm

This thesis first systematically analyzes a classic surface generation algorithm, the marching cubes algorithm, in computer volume visualization, with emphasis on the mathematical background and the ambiguity problem of the algorithm. A simple and elegant disambiguation algorithm is then described and implemented. Finally, generated data from mathematical functions and real world data from scientific experiment are used to test the original marching cubes algorithm and the disambiguation algorithm

Doctor of Philosophy

dissertationThe medial axis of an object is a shape descriptor that intuitively presents the morphology or structure of the object as well as intrinsic geometric properties of the object’s shape. These properties have made the medial axis a vital ingredient for shape analysis applications, and therefore the computation of which is a fundamental problem in computational geometry. This dissertation presents new methods for accurately computing the 2D medial axis of planar objects bounded by B-spline curves, and the 3D medial axis of objects bounded by B-spline surfaces. The proposed methods for the 3D case are the first techniques that automatically compute the complete medial axis along with its topological structure directly from smooth boundary representations. Our approach is based on the eikonal (grassfire) flow where the boundary is offset along the inward normal direction. As the boundary deforms, different regions start intersecting with each other to create the medial axis. In the generic situation, the (self-) intersection set is born at certain creation-type transition points, then grows and undergoes intermediate transitions at special isolated points, and finally ends at annihilation-type transition points. The intersection set evolves smoothly in between transition points. Our approach first computes and classifies all types of transition points. The medial axis is then computed as a time trace of the evolving intersection set of the boundary using theoretically derived evolution vector fields. This dynamic approach enables accurate tracking of elements of the medial axis as they evolve and thus also enables computation of topological structure of the solution. Accurate computation of geometry and topology of 3D medial axes enables a new graph-theoretic method for shape analysis of objects represented with B-spline surfaces. Structural components are computed via the cycle basis of the graph representing the 1-complex of a 3D medial axis. This enables medial axis based surface segmentation, and structure based surface region selection and modification. We also present a new approach for structural analysis of 3D objects based on scalar functions defined on their surfaces. This approach is enabled by accurate computation of geometry and structure of 2D medial axes of level sets of the scalar functions. Edge curves of the 3D medial axis correspond to a subset of ridges on the bounding surfaces. Ridges are extremal curves of principal curvatures on a surface indicating salient intrinsic features of its shape, and hence are of particular interest as tools for shape analysis. This dissertation presents a new algorithm for accurately extracting all ridges directly from B-spline surfaces. The proposed technique is also extended to accurately extract ridges from isosurfaces of volumetric data using smooth implicit B-spline representations. Accurate ridge curves enable new higher-order methods for surface analysis. We present a new definition of salient regions in order to capture geometrically significant surface regions in the neighborhood of ridges as well as to identify salient segments of ridges

Multi-Material Mesh Representation of Anatomical Structures for Deep Brain Stimulation Planning

The Dual Contouring algorithm (DC) is a grid-based process used to generate surface meshes from volumetric data. However, DC is unable to guarantee 2-manifold and watertight meshes due to the fact that it produces only one vertex for each grid cube. We present a modified Dual Contouring algorithm that is capable of overcoming this limitation. The proposed method decomposes an ambiguous grid cube into a set of tetrahedral cells and uses novel polygon generation rules that produce 2-manifold and watertight surface meshes with good-quality triangles. These meshes, being watertight and 2-manifold, are geometrically correct, and therefore can be used to initialize tetrahedral meshes. The 2-manifold DC method has been extended into the multi-material domain. Due to its multi-material nature, multi-material surface meshes will contain non-manifold elements along material interfaces or shared boundaries. The proposed multi-material DC algorithm can (1) generate multi-material surface meshes where each material sub-mesh is a 2-manifold and watertight mesh, (2) preserve the non-manifold elements along the material interfaces, and (3) ensure that the material interface or shared boundary between materials is consistent. The proposed method is used to generate multi-material surface meshes of deep brain anatomical structures from a digital atlas of the basal ganglia and thalamus. Although deep brain anatomical structures can be labeled as functionally separate, they are in fact continuous tracts of soft tissue in close proximity to each other. The multi-material meshes generated by the proposed DC algorithm can accurately represent the closely-packed deep brain structures as a single mesh consisting of multiple material sub-meshes. Each sub-mesh represents a distinct functional structure of the brain. Printed and/or digital atlases are important tools for medical research and surgical intervention. While these atlases can provide guidance in identifying anatomical structures, they do not take into account the wide variations in the shape and size of anatomical structures that occur from patient to patient. Accurate, patient-specific representations are especially important for surgical interventions like deep brain stimulation, where even small inaccuracies can result in dangerous complications. The last part of this research effort extends the discrete deformable 2-simplex mesh into the multi-material domain where geometry-based internal forces and image-based external forces are used in the deformation process. This multi-material deformable framework is used to segment anatomical structures of the deep brain region from Magnetic Resonance (MR) data

Mesh generation using a correspondence distance field

The central tool of this work is a correspondence distance field to discrete surface points embedded within a quadtree data structure. The theory, development, and implementation of the distance field tool are described, and two main applications to two-dimensional mesh generation are presented with extension to three-dimensional capabilities in mind. First is a method for surface-oriented mesh generation from a sufficiently dense set of discrete surface points without connectivity information. Contour levels of distance from the body are specified and correspondences oriented normally to the contours are created. Regions of merging fronts inside and between objects are detected in the correspondence distance field and incorporated automatically. Second, the boundaries in a Voronoi diagram between specified coordinates are detected adaptively and used to make Delaunay tessellation. Tessellation of regions with holes is performed using ghost nodes. Images of meshed for each method are given for a sample set of test cases. Possible extensions, future work, and CFD applications are also discussed

Variational approach to relaxed topological optimization: closed form solutions for structural problems in a sequential pseudo-time framework (preprint)

The work explores a specific scenario for structural computational optimization based on the following elements: (a) a relaxed optimization setting considering the ersatz (bi-material) approximation, (b) a treatment based on a non-smoothed characteristic function field as a topological design variable, (c) the consistent derivation of a relaxed topological derivative whose determination is simple, general and efficient, (d) formulation of the overall increasing cost function topological sensitivity as a suitable optimality criterion, and (e) consideration of a pseudo-time framework for the problem solution, ruled by the problem constraint evolution. In this setting, it is shown that the optimization problem can be analytically solved in a variational framework, leading to, nonlinear, closed-form algebraic solutions for the characteristic function, which are then solved, in every time-step, via fixed point methods based on a pseudo-energy cutting algorithm combined with the exact fulfillment of the constraint, at every iteration of the non-linear algorithm, via a bisection method. The issue of the ill-posedness (mesh dependency) of the topological solution, is then easily solved via a Laplacian smoothing of that pseudo-energy. In the aforementioned context, a number of (3D) topological structural optimization benchmarks are solved, and the solutions obtained with the explored closed-form solution method, are analyzed, and compared, with their solution through an alternative level set method. Although the obtained results, in terms of the cost function and topology designs, are very similar in both methods, the associated computational cost is about five times smaller in the closed-form solution method this possibly being one of its advantages. Some comments, about the possible application of the method to other topological optimization problems, as well as envisaged modifications of the explored method to improve its performance close the wor

Doctor of Philosophy

dissertationVolumetric parameterization is an emerging field in computer graphics, where volumetric representations that have a semi-regular tensor-product structure are desired in applications such as three-dimensional (3D) texture mapping and physically-based simulation. At the same time, volumetric parameterization is also needed in the Isogeometric Analysis (IA) paradigm, which uses the same parametric space for representing geometry, simulation attributes and solutions. One of the main advantages of the IA framework is that the user gets feedback directly as attributes of the NURBS model representation, which can represent geometry exactly, avoiding both the need to generate a finite element mesh and the need to reverse engineer the simulation results from the finite element mesh back into the model. Research in this area has largely been concerned with issues of the quality of the analysis and simulation results assuming the existence of a high quality volumetric NURBS model that is appropriate for simulation. However, there are currently no generally applicable approaches to generating such a model or visualizing the higher order smooth isosurfaces of the simulation attributes, either as a part of current Computer Aided Design or Reverse Engineering systems and methodologies. Furthermore, even though the mesh generation pipeline is circumvented in the concept of IA, the quality of the model still significantly influences the analysis result. This work presents a pipeline to create, analyze and visualize NURBS geometries. Based on the concept of analysis-aware modeling, this work focusses in particular on methodologies to decompose a volumetric domain into simpler pieces based on appropriate midstructures by respecting other relevant interior material attributes. The domain is decomposed such that a tensor-product style parameterization can be established on the subvolumes, where the parameterization matches along subvolume boundaries. The volumetric parameterization is optimized using gradient-based nonlinear optimization algorithms and datafitting methods are introduced to fit trivariate B-splines to the parameterized subvolumes with guaranteed order of accuracy. Then, a visualization method is proposed allowing to directly inspect isosurfaces of attributes, such as the results of analysis, embedded in the NURBS geometry. Finally, the various methodologies proposed in this work are demonstrated on complex representations arising in practice and research