HexBox: Interactive Box Modeling of Hexahedral Meshes

We introduce HexBox, an intuitive modeling method and interactive tool for creating and editing hexahedral meshes. Hexbox brings the major and widely validated surface modeling paradigm of surface box modeling into the world of hex meshing. The main idea is to allow the user to box-model a volumetric mesh by primarily modifying its surface through a set of topological and geometric operations. We support, in particular, local and global subdivision, various instantiations of extrusion, removal, and cloning of elements, the creation of non-conformal or conformal grids, as well as shape modifications through vertex positioning, including manual editing, automatic smoothing, or, eventually, projection on an externally-provided target surface. At the core of the efficient implementation of the method is the coherent maintenance, at all steps, of two parallel data structures: a hexahedral mesh representing the topology and geometry of the currently modeled shape, and a directed acyclic graph that connects operation nodes to the affected mesh hexahedra. Operations are realized by exploiting recent advancements in grid- based meshing, such as mixing of 3-refinement, 2-refinement, and face-refinement, and using templated topological bridges to enforce on-the-fly mesh conformity across pairs of adjacent elements. A direct manipulation user interface lets users control all operations. The effectiveness of our tool, released as open source to the community, is demonstrated by modeling several complex shapes hard to realize with competing tools and techniques

Higher-order block-structured hex meshing of tubular structures

Numerical simulations of the cardiovascular system are growing in popularity due to the increasing availability of computational power, and their proven contribution to the understanding of pathodynamics and validation of medical devices with in-silico trials as a potential future breakthrough. Such simulations are performed on volumetric meshes reconstructed from patient-specific imaging data. These meshes are most often unstructured, and result in a brutally large amount of elements, significantly increasing the computational complexity of the simulations, whilst potentially adversely affecting their accuracy. To reduce such complexity, we introduce a new approach for fully automatic generation of higher-order, structured hexahedral meshes of tubular structures, with a focus on healthy blood vessels. The structures are modeled as skeleton-based convolution surfaces. From the same skeleton, the topology is captured by a block-structure, and the geometry by a higher-order surface mesh. Grading may be induced to obtain tailored refinement, thus resolving, e.g., boundary layers. The volumetric meshing is then performed via transfinite mappings. The resulting meshes are of arbitrary order, their elements are of good quality, while the spatial resolution may be as coarse as needed, greatly reducing computing time. Their suitability for practical applications is showcased by a simulation of physiological blood flow modelled by a generalised Newtonian fluid in the human aorta

Solid NURBS Conforming Scaffolding for Isogeometric Analysis

This work introduces a scaffolding framework to compactly parametrise solid structures with conforming NURBS elements for isogeometric analysis. A novel formulation introduces a topological, geometrical and parametric subdivision of the space in a minimal plurality of conforming vectorial elements. These determine a multi-compartmental scaffolding for arbitrary branching patterns. A solid smoothing paradigm is devised for the conforming scaffolding achieving higher than positional geometrical and parametric continuity. Results are shown for synthetic shapes of varying complexity, for modular CAD geometries, for branching structures from tessellated meshes and for organic biological structures from imaging data. Representative simulations demonstrate the validity of the introduced scaffolding framework with scalable performance and groundbreaking applications for isogeometric analysis

Loopy Cuts: Surface-Field Aware Block Decomposition for Hex-Meshing.

We present a new fully automatic block-decomposition hexahedral meshing algorithm capable of producing high quality meshes that strictly preserve feature curve networks on the input surface and align with an input surface cross-field. We produce all-hex meshes on the vast majority of inputs, and introduce localized non-hex elements only when the surface feature network necessitates those. The input to our framework is a closed surface with a collection of geometric or user-demarcated feature curves and a feature-aligned surface cross-field. Its output is a compact set of blocks whose edges interpolate these features and are loosely aligned with this cross-field. We obtain this block decomposition by cutting the input model using a collection of simple cutting surfaces bounded by closed surface loops. The set of cutting loops spans the input feature curves, ensuring feature preservation, and is obtained using a field-space sampling process. The computed loops are uniformly distributed across the surface, cross orthogonally, and are loosely aligned with the cross-field directions, inducing the desired block decomposition. We validate our method by applying it to a large range of complex inputs and comparing our results to those produced by state-of-the-art alternatives. Contrary to prior approaches, our framework consistently produces high-quality field aligned meshes while strictly preserving geometric or user-specified surface features

Frame Fields for Hexahedral Mesh Generation

As a discretized representation of the volumetric domain, hexahedral meshes have been a popular choice in computational engineering science and serve as one of the main mesh types in leading industrial software of relevance. The generation of high quality hexahedral meshes is extremely challenging because it is essentially an optimization problem involving multiple (conflicting) objectives, such as fidelity, element quality, and structural regularity. Various hexahedral meshing methods have been proposed in past decades, attempting to solve the problem from different perspectives. Unfortunately, algorithmic hexahedral meshing with guarantees of robustness and quality remains unsolved. The frame field based hexahedral meshing method is the most promising approach that is capable of automatically generating hexahedral meshes of high quality, but unfortunately, it suffers from several robustness issues. Field based hexahedral meshing follows the idea of integer-grid maps, which pull back the Cartesian hexahedral grid formed by integer isoplanes from a parametric domain to a surface-conforming hexahedral mesh of the input object. Since directly optimizing for a high quality integer-grid map is mathematically challenging, the construction is usually split into two steps: (1) generation of a feature-aligned frame field and (2) generation of an integer-grid map that best aligns with the frame field. The main robustness issue stems from the fact that smooth frame fields frequently exhibit singularity graphs that are inappropriate for hexahedral meshing and induce heavily degenerate integer-grid maps. The thesis aims at analyzing the gap between the topologies of frame fields and hexahedral meshes and developing algorithms to realize a more robust field based hexahedral mesh generation. The first contribution of this work is an enumeration of all local configurations that exist in hexahedral meshes with bounded edge valence and a generalization of the Hopf-Poincaré formula to octahedral (orthonormal frame) fields, leading to necessary local and global conditions for the hex-meshability of an octahedral field in terms of its singularity graph. The second contribution is a novel algorithm to generate octahedral fields with prescribed hex-meshable singularity graphs, which requires the solution of a large non-linear mixed-integer algebraic system. This algorithm is an important step toward robust automatic hexahedral meshing since it enables the generation of a hex-meshable octahedral field. In the collaboration work with colleagues [BRK+22], the dataset HexMe consisting of practically relevant models with feature tags is set up, allowing a fair evaluation for practical hexahedral mesh generation algorithms. The extendable and mutable dataset remains valuable as hexahedral meshing algorithms develop. The results of the standard field based hexahedral meshing algorithms on the HexMesh dataset expose the fragility of the automatic pipeline. The major contribution of this thesis improves the robustness of the automatic field based hexahedral meshing by guaranteeing local meshability of general feature aligned smooth frame fields. We derive conditions on the meshability of frame fields when feature constraints are considered, and describe an algorithm to automatically turn a given non-meshable frame field into a similar but locally meshable one. Despite the fact that local meshability is only a necessary but not sufficient condition for the stronger requirement of meshability, our algorithm increases the 2% success rate of generating valid integer-grid maps with state-of-the-art methods to 57%, when compared on the challenging HexMe dataset

Optimal Dual Schemes for Adaptive Grid Based Hexmeshing

Hexahedral meshes are an ubiquitous domain for the numerical resolution of partial differential equations. Computing a pure hexahedral mesh from an adaptively refined grid is a prominent approach to automatic hexmeshing, and requires the ability to restore the all hex property around the hanging nodes that arise at the interface between cells having different size. The most advanced tools to accomplish this task are based on mesh dualization. These approaches use topological schemes to regularize the valence of inner vertices and edges, such that dualizing the grid yields a pure hexahedral mesh. In this paper we study in detail the dual approach, and propose four main contributions to it: (i) we enumerate all the possible transitions that dual methods must be able to handle, showing that prior schemes do not natively cover all of them; (ii) we show that schemes are internally asymmetric, therefore not only their implementation is ambiguous, but different implementation choices lead to hexahedral meshes with different singular structure; (iii) we explore the combinatorial space of dual schemes, selecting the minimum set that covers all the possible configurations and also yields the simplest singular structure in the output hexmesh; (iv) we enlarge the class of adaptive grids that can be transformed into pure hexahedral meshes, relaxing one of the tight requirements imposed by previous approaches, and ultimately permitting to obtain much coarser meshes for same geometric accuracy. Last but not least, for the first time we make grid-based hexmeshing truly reproducible, releasing our code and also revealing a conspicuous amount of technical details that were always overlooked in previous literature, creating an entry barrier that was hard to overcome for practitioners in the field

CAD-Based Porous Scaffold Design of Intervertebral Discs in Tissue Engineering

With the development and maturity of three-dimensional (3D) printing technology over the past decade, 3D printing has been widely investigated and applied in the field of tissue engineering to repair damaged tissues or organs, such as muscles, skin, and bones, Although a number of automated fabrication methods have been developed to create superior bio-scaffolds with specific surface properties and porosity, the major challenges still focus on how to fabricate 3D natural biodegradable scaffolds that have tailor properties such as intricate architecture, porosity, and interconnectivity in order to provide the needed structural integrity, strength, transport, and ideal microenvironment for cell- and tissue-growth. In this dissertation, a robust pipeline of fabricating bio-functional porous scaffolds of intervertebral discs based on different innovative porous design methodologies is illustrated. Firstly, a triply periodic minimal surface (TPMS) based parameterization method, which has overcome the integrity problem of traditional TPMS method, is presented in Chapter 3. Then, an implicit surface modeling (ISM) approach using tetrahedral implicit surface (TIS) is demonstrated and compared with the TPMS method in Chapter 4. In Chapter 5, we present an advanced porous design method with higher flexibility using anisotropic radial basis function (ARBF) and volumetric meshes. Based on all these advanced porous design methods, the 3D model of a bio-functional porous intervertebral disc scaffold can be easily designed and its physical model can also be manufactured through 3D printing. However, due to the unique shape of each intervertebral disc and the intricate topological relationship between the intervertebral discs and the spine, the accurate localization and segmentation of dysfunctional discs are regarded as another obstacle to fabricating porous 3D disc models. To that end, we discuss in Chapter 6 a segmentation technique of intervertebral discs from CT-scanned medical images by using deep convolutional neural networks. Additionally, some examples of applying different porous designs on the segmented intervertebral disc models are demonstrated in Chapter 6

Theory and applications of bijective barycentric mappings

Barycentric coordinates provide a convenient way to represent a point inside a triangle as a convex combination of the triangle's vertices, and to linearly interpolate data given at these vertices. Due to their favourable properties, they are commonly applied in geometric modelling, finite element methods, computer graphics, and many other fields. In some of these applications it is desirable to extend the concept of barycentric coordinates from triangles to polygons. Several variants of such generalized barycentric coordinates have been proposed in recent years. An important application of barycentric coordinates consists of barycentric mappings, which allow to naturally warp a source polygon to a corresponding target polygon, or more generally, to create mappings between closed curves or polyhedra. The principal practical application is image warping, which takes as input a control polygon drawn around an image and smoothly warps the image by moving the polygon vertices. A required property of image warping is to avoid fold-overs in the resulting image. The problem of fold-overs is a manifestation of a larger problem related to the lack of bijectivity of the barycentric mapping. Unfortunately, bijectivity of such barycentric mappings can only be guaranteed for the special case of warping between convex polygons or by triangulating the domain and hence renouncing smoothness. In fact, for any barycentric coordinates, it is always possible to construct a pair of polygons such that the barycentric mapping is not bijective. In the first part of this thesis we illustrate three methods to achieve bijective mappings. The first method is based on the intuition that, if two polygons are sufficiently close, then the mapping is close to the identity and hence bijective. This suggests to ``split'' the mapping into several intermediate mappings and to create a composite barycentric mapping which is guaranteed to be bijective between arbitrary polygons, polyhedra, or closed planar curves. We provide theoretical bounds on the bijectivity of the composite mapping related to the norm of the gradient of the coordinates. The fact that the bound depends on the gradient implies that these bounds exist only if the gradient of the coordinates is bounded. We focus on mean value coordinates and analyse the behaviour of their directional derivatives and gradient at the vertices of a polygon. The composition of barycentric mappings for closed planar curves leads to the problem of blending between two planar curves. We suggest to solve it by linearly interpolating the signed curvature and then reconstructing the intermediate curve from the interpolated curvature values. However, when both input curves are closed, this strategy can lead to open intermediate curves. We present a new algorithm for solving this problem, which finds the closed curve whose curvature is closest to the interpolated values. Our method relies on the definition of a suitable metric for measuring the distance between two planar curves and an appropriate discretization of the signed curvature functions. The second method to construct smooth bijective mappings with prescribed behaviour along the domain boundary exploits the properties of harmonic maps. These maps can be approximated in different ways, and we discuss their respective advantages and disadvantages. We further present a simple procedure for reducing their distortion and demonstrate the effectiveness of our approach by providing examples. The last method relies on a reformulation of complex barycentric mappings, which allows us to modify the ``speed'' along the edges to create complex bijective mappings. We provide some initial results and an optimization procedure which creates complex bijective maps. In the second part we provide two main applications of bijective mapping. The first one is in the context of finite elements simulations, where the discretization of the computational domain plays a central role. In the standard discretization, the domain is triangulated with a mesh and its boundary is approximated by a polygon. We present an approach which combines parametric finite elements with smooth bijective mappings, leaving the choice of approximation spaces free. This approach allows to represent arbitrarily complex geometries on coarse meshes with curved edges, regardless of the domain boundary complexity. The main idea is to use a bijective mapping for automatically warping the volume of a simple parametrization domain to the complex computational domain, thus creating a curved mesh of the latter. The second application addresses the meshing problem and the possibility to solve finite element simulations on polygonal meshes. In this context we present several methods to discretize the bijective mapping to create polygonal and piece-wise polynomial meshes