A framework for hull form reverse engineering and geometry integration into numerical simulations

The thesis presents a ship hull form specific reverse engineering and CAD integration framework. The reverse engineering part proposes three alternative suitable reconstruction approaches namely curves network, direct surface fitting, and triangulated surface reconstruction. The CAD integration part includes surface healing, region identification, and domain preparation strategies which used to adapt the CAD model to downstream application requirements. In general, the developed framework bridges a point cloud and a CAD model obtained from IGES and STL file into downstream applications

Geometric modeling, simulation, and visualization methods for plasmid DNA molecules

Plasmid DNA molecules are a special type of DNA molecules that are used, among other applications, in DNA vaccination and gene therapy. These molecules are characterized by, when in their natural state, presenting a closed-circular conformation and by being supercoiled. The production of plasmid DNA using bacteria as hosts implies a purification step where the plasmid DNA molecules are separated from the DNA of the host and other contaminants. This purification process, and all the physical and chemical variations involved, such as temperature changes, may affect the plasmid DNA molecules conformation by uncoiling or even by open them, which makes them useless for therapeutic applications. Because of that, researchers are always searching for new purification techniques that maximize the amount of supercoiled plasmid DNA that is produced. Computer simulations and 3D visualization of plasmid DNA can bring many advantages because they allow researchers to actually see what can happen to the molecules under certain conditions. In this sense, it was necessary to develop reliable and accurate geometric models specific for plasmid DNA simulations. This dissertation presents a new assembling algorithm for B-DNA specifically developed for plasmid DNA assembling. This new assembling algorithm is completely adaptive in the sense that it allows researchers to assemble any plasmid DNA base-pair sequence along any arbitrary conformation that fits the length of the plasmid DNA molecule. This is specially suitable for plasmid DNA simulations, where conformations are generated by simulation procedures and there is the need to assemble the given base-pair sequence over that conformation, what can not be done by conventional predictive DNA assembling methods. Unlike traditional molecular visualization methods that are based on the atomic structure, this new assembling algorithm uses color coded 3D molecular surfaces of the nucleotides as the building blocks for DNA assembling. This new approach, not only reduces the amount of graphical objects and, consequently, makes the rendering faster, but also makes it easier to visually identify the nucleotides in the DNA strands. The algorithm used to triangulate the molecular surfaces of the nucleotides building blocks is also a novelty presented as part of this dissertation. This new triangulation algorithm for Gaussian molecular surfaces introduces a new mechanism that divides the atomic structure of molecules into boxes and spheres. This new space division method is faster because it confines the local calculation of the molecular surface to a specific region of influence of the atomic structure, not taking into account atoms that do not influence the triangulation of the molecular surface in that region. This new method also guarantees the continuity of the molecular surface. Having in mind that the aim of this dissertation is to present a complete set of methods for plasmid DNA visualization and simulation, it is also proposed a new deformation algorithm to be used for plasmid DNA Monte Carlo simulations. This new deformation algorithm uses a 3D polyline to represent the plasmid DNA conformation and performs small deformations on that polyline, keeping the segments length and connectivity. Experiments have been performed in order to compare this new deformation method with deformation methods traditionally used by Monte Carlo plasmid DNA simulations These experiments shown that the new method is more efficient in the sense that its trial acceptance ratio is higher and it converges sooner and faster to the elastic energy equilibrium state of the plasmid DNA molecule. In sum, this dissertation successfully presents an end-to-end set of models and algorithms for plasmid DNA geometric modelling, visualization and simulation

Sparse Volumetric Deformation

Volume rendering is becoming increasingly popular as applications require realistic solid shape representations with seamless texture mapping and accurate filtering. However rendering sparse volumetric data is difficult because of the limited memory and processing capabilities of current hardware. To address these limitations, the volumetric information can be stored at progressive resolutions in the hierarchical branches of a tree structure, and sampled according to the region of interest. This means that only a partial region of the full dataset is processed, and therefore massive volumetric scenes can be rendered efficiently. The problem with this approach is that it currently only supports static scenes. This is because it is difficult to accurately deform massive amounts of volume elements and reconstruct the scene hierarchy in real-time. Another problem is that deformation operations distort the shape where more than one volume element tries to occupy the same location, and similarly gaps occur where deformation stretches the elements further than one discrete location. It is also challenging to efficiently support sophisticated deformations at hierarchical resolutions, such as character skinning or physically based animation. These types of deformation are expensive and require a control structure (for example a cage or skeleton) that maps to a set of features to accelerate the deformation process. The problems with this technique are that the varying volume hierarchy reflects different feature sizes, and manipulating the features at the original resolution is too expensive; therefore the control structure must also hierarchically capture features according to the varying volumetric resolution. This thesis investigates the area of deforming and rendering massive amounts of dynamic volumetric content. The proposed approach efficiently deforms hierarchical volume elements without introducing artifacts and supports both ray casting and rasterization renderers. This enables light transport to be modeled both accurately and efficiently with applications in the fields of real-time rendering and computer animation. Sophisticated volumetric deformation, including character animation, is also supported in real-time. This is achieved by automatically generating a control skeleton which is mapped to the varying feature resolution of the volume hierarchy. The output deformations are demonstrated in massive dynamic volumetric scenes

Hierarchical processing, editing and rendering of acquired geometry

La représentation des surfaces du monde réel dans la mémoire d’une machine peut désormais être obtenue automatiquement via divers périphériques de capture tels que les scanners 3D. Ces nouvelles sources de données, précises et rapides, amplifient de plusieurs ordres de grandeur la résolution des surfaces 3D, apportant un niveau de précision élevé pour les applications nécessitant des modèles numériques de surfaces telles que la conception assistée par ordinateur, la simulation physique, la réalité virtuelle, l’imagerie médicale, l’architecture, l’étude archéologique, les effets spéciaux, l’animation ou bien encore les jeux video. Malheureusement, la richesse de la géométrie produite par ces méthodes induit une grande, voire gigantesque masse de données à traiter, nécessitant de nouvelles structures de données et de nouveaux algorithmes capables de passer à l’échelle d’objets pouvant atteindre le milliard d’échantillons. Dans cette thèse, je propose des solutions performantes en temps et en espace aux problèmes de la modélisation, du traitement géométrique, de l’édition intéractive et de la visualisation de ces surfaces 3D complexes. La méthodologie adoptée pendant l’élaboration transverse de ces nouveaux algorithmes est articulée autour de 4 éléments clés : une approche hiérarchique systématique, une réduction locale de la dimension des problèmes, un principe d’échantillonage-reconstruction et une indépendance à l’énumération explicite des relations topologiques aussi appelée approche basée-points. En pratique, ce manuscrit propose un certain nombre de contributions, parmi lesquelles : une nouvelle structure hiérarchique hybride de partitionnement, l’Arbre Volume-Surface (VS-Tree) ainsi que de nouveaux algorithmes de simplification et de reconstruction ; un système d’édition intéractive de grands objets ; un noyau temps-réel de synthèse géométrique par raffinement et une structure multi-résolution offrant un rendu efficace de grands objets. Ces structures, algorithmes et systèmes forment une chaîne capable de traiter les objets en provenance du pipeline d’acquisition, qu’ils soient représentés par des nuages de points ou des maillages, possiblement non 2-variétés. Les solutions obtenues ont été appliquées avec succès aux données issues des divers domaines d’application précités.Digital representations of real-world surfaces can now be obtained automatically using various acquisition devices such as 3D scanners and stereo camera systems. These new fast and accurate data sources increase 3D surface resolution by several orders of magnitude, borrowing higher precision to applications which require digital surfaces. All major computer graphics applications can take benefit of this automatic modeling process, including: computer-aided design, physical simulation, virtual reality, medical imaging, architecture, archaeological study, special effects, computer animation and video games. Unfortunately, the richness of the geometry produced by these media comes at the price of a large, possibility gigantic, amount of data which requires new efficient data structures and algorithms offering scalability for processing such objects. This thesis proposes time and space efficient solutions for modeling, editing and rendering such complex surfaces, solving these problems with new algorithms sharing 4 fundamental elements: a systematic hierarchical approach, a local dimension reduction, a sampling-reconstruction paradigm and a pointbased basis. Basically, this manuscript proposes several contributions, including: a new hierarchical space subdivision structure, the Volume-Surface Tree, for geometry processing such as simplification and reconstruction; a streaming system featuring new algorithms for interactive editing of large objects, an appearancepreserving multiresolution structure for efficient rendering of large point-based surfaces, and a generic kernel for real-time geometry synthesis by refinement. These elements form a pipeline able to process acquired geometry, either represented by point clouds or non-manifold meshes. Effective results have been successfully obtained with data coming from the various applications mentioned

Methods for 3D Geometry Processing in the Cultural Heritage Domain

This thesis presents methods for 3D geometry processing under the aspects of cultural heritage applications. After a short overview over the relevant basics in 3D geometry processing, the present thesis investigates the digital acquisition of 3D models. A particular challenge in this context are on the one hand difficult surface or material properties of the model to be captured. On the other hand, the fully automatic reconstruction of models even with suitable surface properties that can be captured with Laser range scanners is not yet completely solved. This thesis presents two approaches to tackle these challenges. One exploits a thorough capture of the object’s appearance and a coarse reconstruction for a concise and realistic object representation even for objects with problematic surface properties like reflectivity and transparency. The other method concentrates on digitisation via Laser-range scanners and exploits 2D colour images that are typically recorded with the range images for a fully automatic registration technique. After reconstruction, the captured models are often still incomplete, exhibit holes and/or regions of insufficient sampling. In addition to that, holes are often deliberately introduced into a registered model to remove some undesired or defective surface part. In order to produce a visually appealing model, for instance for visualisation purposes, for prototype or replica production, these holes have to be detected and filled. Although completion is a well-established research field in 2D image processing and many approaches do exist for image completion, surface completion in 3D is a fairly new field of research. This thesis presents a hierarchical completion approach that employs and extends successful exemplar-based 2D image processing approaches to 3D and fills in detail-equipped surface patches into missing surface regions. In order to identify and construct suitable surface patches, selfsimilarity and coherence properties of the surface context of the hole are exploited. In addition to the reconstruction and repair, the present thesis also investigates methods for a modification of captured models via interactive modelling. In this context, modelling is regarded as a creative process, for instance for animation purposes. On the other hand, it is also demonstrated how this creative process can be used to introduce human expertise into the otherwise automatic completion process. This way, reconstructions are feasible even of objects where already the data source, the object itself, is incomplete due to corrosion, demolition, or decay.Methoden zur 3D-Geometrieverarbeitung im Kulturerbesektor In dieser Arbeit werden Methoden zur Bearbeitung von digitaler 3D-Geometrie unter besonderer Berücksichtigung des Anwendungsbereichs im Kulturerbesektor vorgestellt. Nach einem kurzen Überblick über die relevanten Grundlagen der dreidimensionalen Geometriebehandlung wird zunächst die digitale Akquise von dreidimensionalen Objekten untersucht. Eine besondere Herausforderung stellen bei der Erfassung einerseits ungünstige Oberflächen- oder Materialeigenschaften der Objekte dar (wie z.B. Reflexivität oder Transparenz), andererseits ist auch die vollautomatische Rekonstruktion von solchen Modellen, die sich verhältnismäßig problemlos mit Laser-Range Scannern erfassen lassen, immer noch nicht vollständig gelöst. Daher bilden zwei neuartige Verfahren, die diesen Herausforderungen begegnen, den Anfang. Auch nach der Registrierung sind die erfassten Datensätze in vielen Fällen unvollständig, weisen Löcher oder nicht ausreichend abgetastete Regionen auf. Darüber hinaus werden in vielen Anwendungen auch, z.B. durch Entfernen unerwünschter Oberflächenregionen, Löcher gewollt hinzugefügt. Für eine optisch ansprechende Rekonstruktion, vor allem zu Visualisierungszwecken, im Bildungs- oder Unterhaltungssektor oder zur Prototyp- und Replik-Erzeugung müssen diese Löcher zunächst automatisch detektiert und anschließend geschlossen werden. Obwohl dies im zweidimensionalen Fall der Bildbearbeitung bereits ein gut untersuchtes Forschungsfeld darstellt und vielfältige Ansätze zur automatischen Bildvervollständigung existieren, ist die Lage im dreidimensionalen Fall anders, und die Übertragung von zweidimensionalen Ansätzen in den 3D stellt vielfach eine große Herausforderung dar, die bislang keine zufriedenstellenden Lösungen erlaubt hat. Nichtsdestoweniger wird in dieser Arbeit ein hierarchisches Verfahren vorgestellt, das beispielbasierte Konzepte aus dem 2D aufgreift und Löcher in Oberflächen im 3D unter Ausnutzung von Selbstähnlichkeiten und Kohärenzeigenschaften des Oberflächenkontextes schließt. Um plausible Oberflächen zu erzeugen werden die Löcher dabei nicht nur glatt gefüllt, sondern auch feinere Details aus dem Kontext rekonstruiert. Abschließend untersucht die vorliegende Arbeit noch die Modifikation der vervollständigten Objekte durch Freiformmodellierung. Dies wird dabei zum einen als kreativer Prozess z.B. zu Animationszwecken betrachtet. Zum anderen wird aber auch untersucht, wie dieser kreative Prozess benutzt werden kann, um etwaig vorhandenes Expertenwissen in die ansonsten automatische Vervollständigung mit einfließen zu lassen. Auf diese Weise werden auch Rekonstruktionen ermöglicht von Objekten, bei denen schon die Datenquelle, also das Objekt selbst z.B. durch Korrosion oder mutwillige Zerstörung unvollständig ist

Interactions gestuelles multi-point et géométrie déformable pour l’édition 3D sur écran tactile

Despite the advances made in the fields of existing objects capture and of procedural generation, creation of content for virtual worlds can not be perform without human interaction. This thesis suggests to exploit new touch devices ("multi-touch" screens) to obtain an easy, intuitive 2D interaction in order to navigate inside a virtual environment, to manipulate, position and deform 3D objects.First, we study the possibilities and limitations of the hand and finger gestures while interacting on a touch screen in order to discover which gestures are the most adapted to edit 3D scene and environment. In particular, we evaluate the effective number of degrees of freedom of the human hand when constrained on a planar surface. Meanwhile, we develop a new gesture analysis method using phases to identify key motion of the hand and fingers in real time. These results, combined to several specific user-studies, lead to a gestural design pattern which handle not only navigation (camera positioning), but also object positioning, rotation and global scaling. Then, this pattern is extended to complex deformation (such as adding and deleting material, bending or twisting part of objects, using local control). Using these results, we are able to propose and evaluate a 3D world editing interface that handle a naturaltouch interaction, in which mode selection (i.e. navigation, object positioning or object deformation) and task selections is automatically processed by the system, relying on the gesture and the interaction context (without any menu or button). Finally, we extend this interface to integrate more complex deformations, adapting the garment transfer from a character to any other in order to process interactive deformation of the garment while the wearing character is deformed.Malgré les progrès en capture d’objets réels et en génération procédurale, la création de contenus pour les mondes virtuels ne peut se faire sans interaction humaine. Cette thèse propose d’exploiter les nouvelles technologies tactiles (écrans "multi-touch") pour offrir une interaction 2D simple et intuitive afin de naviguer dans un environnement virtuel, et d’y manipuler, positionner et déformer des objets 3D.En premier lieu, nous étudions les possibilité et les limitations gestuelles de la main et des doigts lors d’une interaction sur écran tactile afin de découvrir quels gestes semblent les plus adaptés à l’édition des environnements et des objets 3D. En particulier, nous évaluons le nombre de degré de liberté efficaces d’une main humaine lorsque son geste est contraint à une surface plane. Nous proposons également une nouvelle méthode d’analyse gestuelle par phases permettant d’identifier en temps réel les mouvements clés de la main et des doigts. Ces résultats, combinés à plusieurs études utilisateur spécifiques, débouchent sur l’identification d’un patron pour les interactions gestuelles de base incluant non seulement navigation (placement de caméra), mais aussi placement, rotation et mise à l’échelle des objets. Ce patron est étendudans un second temps aux déformations complexes (ajout et suppression de matière ainsi que courbure ou torsion des objets, avec contrôle de la localité). Tout ceci nous permet de proposer et d’évaluer une interface d’édition des mondes 3D permettant une interaction tactile naturelle, pour laquelle le choix du mode (navigation, positionnement ou déformation) et des tâches correspondantes est automatiquement géré par le système en fonction du geste et de son contexte (sans menu ni boutons). Enfin, nous étendons cette interface pour y intégrer des déformations plus complexe à travers le transfert de vêtements d’un personnage à un autre, qui est étendu pour permettre la déformation interactive du vêtement lorsque le personnage qui le porte est déformé par interaction tactile

Incremental polygonization of deforming NURBS surfaces.

Nonuniform rational B-splines (NURBS) are a powerful tool to model deformable objects. Their shapes can be easily modified by moving the control points. A common method used to render these objects is polygonization. However, the polygonization process is computationally very expensive. If the object deforms, we need to execute this process in every frame to reflect the geometric change of the object. This limitation makes real-time rendering of deforming objects very difficult. In this paper, we present an incremental method for polygonizing deforming objects modeled by NURBS surfaces. Some incremental techniques are introduced here to further improve the performance of the method. They include an efficient mechanism for determining the deformation region when the surface deforms, an incremental crack prevention technique, and an updating method for multiple control point movement

Large bichromatic point sets admit empty monochromatic 4-gons

We consider a variation of a problem stated by Erd˝os and Szekeres in 1935 about the existence of a number fES(k) such that any set S of at least fES(k) points in general position in the plane has a subset of k points that are the vertices of a convex k-gon. In our setting the points of S are colored, and we say that a (not necessarily convex) spanned polygon is monochromatic if all its vertices have the same color. Moreover, a polygon is called empty if it does not contain any points of S in its interior. We show that any bichromatic set of n ≥ 5044 points in R2 in general position determines at least one empty, monochromatic quadrilateral (and thus linearly many).Postprint (published version