A scripting interface for doubly linked face list based polygonal meshes

This thesis presents a scripting language interface for modeling manifold meshes represented by a Doubly Linked Face List (DLFL).With a scripting language users can create procedurally generated meshes that would otherwise be tedious or impractical to create with a graphical user interface. I have implemented a scripting language interface for the user to create stand-alone scripts as well as script interactively within a graphical environment

3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries

Recent advances in electron microscopy have enabled the imaging of single cells in 3D at nanometer length scale resolutions. An uncharted frontier for in silico biology is the ability to simulate cellular processes using these observed geometries. Enabling such simulations requires watertight meshing of electron micrograph images into 3D volume meshes, which can then form the basis of computer simulations of such processes using numerical techniques such as the Finite Element Method. In this paper, we describe the use of our recently rewritten mesh processing software, GAMer 2, to bridge the gap between poorly conditioned meshes generated from segmented micrographs and boundary marked tetrahedral meshes which are compatible with simulation. We demonstrate the application of a workflow using GAMer 2 to a series of electron micrographs of neuronal dendrite morphology explored at three different length scales and show that the resulting meshes are suitable for finite element simulations. This work is an important step towards making physical simulations of biological processes in realistic geometries routine. Innovations in algorithms to reconstruct and simulate cellular length scale phenomena based on emerging structural data will enable realistic physical models and advance discovery at the interface of geometry and cellular processes. We posit that a new frontier at the intersection of computational technologies and single cell biology is now open.Comment: 39 pages, 14 figures. High resolution figures and supplemental movies available upon reques

Analyse de modèles géométriques d'assemblages pour les structures et les enrichir avec des informations fonctionnelles

The digital mock-up (DMU) of a product has taken a central position in the product development process (PDP). It provides the geometric reference of the product assembly, as it defines the shape of each individual component, as well as the way components are put together. However, observations show that this geometric model is no more than a conventional representation of what the real product is. Additionally, and because of its pivotal role, the DMU is more and more required to provide information beyond mere geometry to be used in different stages of the PDP. An increasingly urging demand is functional information at different levels of the geometric representation of the assembly. This information is shown to be essential in phases such as geometric pre-processing for finite element analysis (FEA) purposes. In this work, an automated method is put forward that enriches a geometric model, which is the product DMU, with function information needed for FEA preparations. To this end, the initial geometry is restructured at different levels according to functional annotation needs. Prevailing industrial practices and representation conventions are taken into account in order to functionally interpret the pure geometric model that provides a start point to the proposed method.La maquette numérique d'un produit occupe une position centrale dans le processus de développement de produit. Elle est utilisée comme représentation de référence des produits, en définissant la forme géométrique de chaque composant, ainsi que les représentations simplifiées des liaisons entre composants. Toutefois, les observations montrent que ce modèle géométrique n'est qu'une représentation simplifiée du produit réel. De plus, et grâce à son rôle clé, la maquette numérique est de plus en plus utilisée pour structurer les informations non-géométriques qui sont ensuite utilisées dans diverses étapes du processus de développement de produits. Une demande importante est d'accéder aux informations fonctionnelles à différents niveaux de la représentation géométrique d'un assemblage. Ces informations fonctionnelles s'avèrent essentielles pour préparer des analyses éléments finis. Dans ce travail, nous proposons une méthode automatisée afin d'enrichir le modèle géométrique extrait d'une maquette numérique avec les informations fonctionnelles nécessaires pour la préparation d'un modèle de simulation par éléments finis. Les pratiques industrielles et les représentations géométriques simplifiées sont prises en compte lors de l'interprétation d'un modèle purement géométrique qui constitue le point de départ de la méthode proposée

The design and analysis of boundary data structures

The thesis is concerned with the efficient interrogation of CAD data. CAD data finds use in diverse range of applications which necessitates extension and integration of the CAD data base. By an exhaustive categorization of such application requirements and analysis of various CAD techniques, it is shown that boundary data structures are the most suitable in CAD, CAM and advanced robotic applications. Several boundary data structures have been proposed since the classic Winged edge data structure, these aimed at reducing the storage requirement and increasing information retrieval speeds. In this thesis methodologies are developed which enable us to discover compact and fast access time schemes and analyze and fine tune for individual applications. We demonstrate how the application of the optimality concepts can lead us to the discovery of more efficient data structures than popular data structures. All the boundary data structures proposed to date have been based on the underlying assumption that all the data resides in main memory. We show that in an integrated CAD environment (characterized by virtual a memory environment or a data base environment), these data structures are inefficient in both storage and time. We propose a new data structure shaped like A which is the most compact as well as more efficient in access time, under certain conditions of real memory and virtual memory. Experiments reveal a paradoxical phenomenon: access time increases with storage, violating the classic law of storage vs. time. Recently non-manifold boundary geometric modeling has become popular to meet the growing needs such as uniform treatment of wire frame, surface and solid modeling and design by features. We introduce a uniform terminology and notation to distinguish and critically analyze several non-manifold boundary data structures. It is hoped to fulfill the need for a ready reference for the design of efficient boundary data structures. The other aspects dealt with are the validity and conversion of Boundary data structures. To verify the concepts developed, in practice, a whole suite of fast algorithms have been implemented for model manipulation, visualization and data conversion

Boolean operations on 3D selective Nef complexes : data structure, algorithms, optimized implementation, experiments and applications

Nef polyhedra in d-dimensional space are the closure of half-spaces under boolean set operations. Consequently, they can represent non-manifold situations, open and closed sets, mixed-dimensional complexes, and they are closed under all boolean and topological operations, such as complement and boundary. The generality of Nef complexes is essential for some applications. In this thesis, we present a new data structure for the boundary representation of three-dimensional Nef polyhedra and efficient algorithms for boolean operations. We use exact arithmetic to avoid well known problems with floating-point arithmetic and handle all degeneracies. Furthermore, we present important optimizations for the algorithms, and evaluate this optimized implementation with extensive experiments. The experiments supplement the theoretical runtime analysisNef-Polyeder sind d-dimensionale Punktmengen, die durch eine endliche Anzahl boolescher Operationen über Halbräumen generiert werden. Sie sind abgeschlossen hinsichtlich boolescher und topologischer Operationen. Als Konsequenz daraus können sie nicht-mannigfaltige Situationen, offene und geschlossene Mengen und gemischt-dimensionale Komplexe darstellen. Die Allgemeinheit von Nef-Komplexen ist unentbehrlich für einige Anwendungen. In dieser Doktorarbeit stellen wir eine neue Datenstruktur vor, die eine Randdarstellung von dreidimensionalen Nef-polyedern und Algorithmen für boolesche Operationen realisiert. Wir benutzen exakte Arithmetik um die bekannten Probleme mit Gleitkommaarithmetik und Degeneriertheiten zu vermeiden. Außerdem präsentieren wir wichtige Optimierungen der Algorithmen und bewerten die optimierte Implementierung an Hand umfassender Experimente. Weitere Experimente belegen die theoretische Laufzeitanalyse und vergleichen unsere Implementation mit dem kommerziellen CAD kernel ACIS. ACIS is meistens bis zu sechs mal schneller, aber es gibt auch Beispiele bei denen ACIS scheitert. Nef-Polyeder können bei einer Vielzahl von Anwendungen eingesetzt werden. Wir präsentieren einfache Implementationen zweier Anwendungen - von der visuellen Hülle und von der Minkowski-Summe zwei abgeschlossener Nef-Polyeder