Computer graphics is a branch of Computer Science that specializes in the virtual representation of real-life objects in a computer screen. While the past advancements in this field were commonly related to entertaining media industries such as video games and movies, these have found a use in others. For instance, they have provided a visual aid in medical exploration for healthcare and training simulation for military and defense.Ever since their first applications for data visualization, there has been a growth in the development of new technologies, methods and techniques to improve it. Today, among the most leading methods we can find the Volumetric or Volume Rendering techniques. These allow the display of 3-dimensional discretely sampled data in a 2dimensional projection on the screen.This thesis provides a study on volumetric rendering through the implementation of a real-time simulation. It presents the various steps, prior knowledge and research required to program it. By studying the necessary mathematical concepts including noise functions, flow maps and vector fields; an interactive effect can be applied to volumetric data. The result is a randomly behaved volumetric fog. The implementation issues, intricacies and paradigms are reflected upon and explained. The conclusion explores the results while these illustrate what can be accomplished using mathematical and programming notions in the manipulation of graphic data. / Datorgrafik är en filial inom datavetenskap som specialiserar sig på realistisk virtuell representation av verkliga objekt på en datorskärm. Medan de tidigare framstegen inom detta område vanligtvis var relaterade till underhållande medieindustrier som videospel och filmer, hade dessa hittat en annan användning i andra. De har tillhandahållit ett visuellt stöd inom bland annat sjukvård, arkitektur, militär och försvar och utbildning.Helt sedan deras första applikationer för visualisering av data har det skett en tillväxt av ny teknik, metoder och tekniker för att förbättra datarepresentationen. Idag, bland de mest ledande metoderna, kan vi hitta Volumetric eller Volume Renderingtekniker. Dessa möjliggör visning av 3-dimensionell diskret sampling av data i en tvådimensionell projektion på skärmen.Dennaavhandling ger en studie om volumetrisk rendering genom en realtidsimulering. Den presenterar de olika stegen, kunskapen och forskningen som krävs för att simulera den med hjälp av de matematiska grunderna som gör det mycket eftertraktat och även beräkningsproblematiskt. Implementeringsfrågor, komplikationer och paradigmer återspeglas och förklaras medan resultaten illustrerar vad som kan åstadkommas med matematiska och programmeringsmeddelanden när de tillämpas på manipulering av grafisk data.

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Detta examensarbete utfördes för att ta reda på hur viktig skuggning är som djupinformationsbärare i en multimodal simulator för operativ extraktion av visdomständer. Simulatorn har både haptik och stereografik som kan förmedla djupinformation. Frågeställningen för examensarbetet var därför att undersöka om det fanns något behov av att använda sig av en relativt beräkningstung rendering med skuggning, eller om det skulle duga med en enklare typ av rendering. Användartester har utförts med erfarna tandläkare som har fått prova på simulatorn med olika typer av renderingar av ett och samma patientfall. Metoden som användes kallas kooperativ utvärdering vilken tillåter diskussion mellan användaren och utvärderaren. Det visar sig att skuggningen spelar en mycket stor roll för användarens djupuppfattning. Skuggningen visar sig faktiskt vara betydligt viktigare än stereoinformationen, särskilt som tandläkarna fokuserar på ett mycket litet område där stereoeffekten verkar försumbar. Det är även viktigt att väga in det faktum att inte alla kan se djup i stereobilder. Då de tänkta användarna är relativt unga tandläkarstudenter är de vana vid nästan verklighetstrogen grafik från dataspel och datoranimerad film. Därför bör grafiken i simulatorn ligga så nära den standarden som möjligt. Användandet av haptik gör visserligen att användaren kan känna var denna befinner sig i djupled, men vid konflikt med synintrycken så verkar synen ta överhanden. Slutsatsen blir därmed att skuggning definitivt är värd att implementeras, trots de extra resurser som krävs. / The aim of this thesis was to investigate the importance shading has on the perception of depth in a multimodal simulator for operative extraction of wisdom teeth. The simulator uses both haptics and stereo graphics to convey information about depth. The problem formulated in the thesis was to investigate the necessity of using shading, which is quite demanding computationally, or if a simpler type of rendering would suffice. User tests have been performed with experienced dentists who have tried different graphical renderings of the same patient case in the simulator. The method used for the tests is called cooperative evaluation and allows for discussions between the user and the evaluator. Shading turns out to play an important role in the users’ perception of depth. It even seems to be more important than the stereo information since the area the dentists focus on is so small the stereo effect seems negligible. The fact that not all people can see depth in stereo images is also important to consider. As the intended users are relatively young dental students, they are accustomed to almost photorealistic graphics in computer games and computer animation. Therefore the graphics in the simulator needs to be as close to that standard as possible. The use of haptics does make it possible for the user to feel where s/he is located depthwise, but when a conflict with the visual feedback occurs, the visual information tends to dominate. The conclusion therefore is to recommend that shading definitely is worth implementing, even though it requires additional resources.

[pt] Este trabalho propõe uma técnica chamada de Opacidade 3D para visualização volumétrica de dados sísmicos. O grande desafio da visualização volumétrica é definir uma função de transferência multidimensional que melhor se adapte ao dado que se deseja visualizar. Será apresentada uma função de transferência que utiliza três tabelas de cores 1D para compor a uma tabela de cores 3D. O trabalho de Silva[30] sobre opacidade 2D serviu de motivação para o desenvolvimento da técnica de opacidade 3D e ao longo deste trabalho são feitas comparações entre ambos. São apresentados exemplos reproduzindo a opacidade 2D e outros mostrando como a técnica proposta pode auxiliar no estudo de determinados eventos sísmicos. / [en] This work proposes a 3D opacity technique for the volume rendering of seismic data. The greater challenge of volume rendering is to define a multidimensional transfer function better adapted to the data to be visualized. This work presents a transfer function that uses three 1D color tables to compose a 3D color table. The work from Silva[30] about 2D opacity has served as a motivation for the development of the 3D opacity technique and, hence, some comparisons are made between them. Some examples are presented in order to reproduce the 2D opacity technique and to show how the proposed technique can improve the visualization of specific seismic events.

Numerical simulations are often used in computer graphics to capture the effects of natural phenomena such as fire, water and smoke. However, simulating large-scale events in this way, with the details needed for feature film, poses serious problems. Grid-based simulations at resolutions sufficient to incorporate small-scale details would be costly and use large amounts of memory, and likewise for particle based techniques. To overcome these problems, a new framework for simulation and rendering of gaseous phenomena is presented in this thesis. It makes use of a combination of different existing concepts for such phenomena to resolve many of the issues in using them separately, and the result is a potent method for high-detailed simulation and rendering at low cost. The developed method utilizes a slice refinement technique, where a coarse particle input is transformed into a set of two-dimensional view-aligned slices, which are simulated at high resolution. These slices are subsequently used in a rendering framework accounting for light scattering behaviors in participating media to achieve a final highly detailed volume rendering outcome. However,the transformations from three to two dimensions and back easily introduces visible artifacts, so a number of techniques have been considered to overcome these problems, where e.g. a turbulence function is used in the final volume density function to break up possible interpolation artifacts.

Direct volume rendering techniques for scalar fields make use of transfer functions to map optical properties to the field; the field can subsequently be visualized through the drawing of isosurfaces in the volume spanned by the field. The utility of this approach is limited in the case of nested or clustered structures with the same isovalue and further does not easily allow for quantitative measurements of the visualized data. This report explores the use of topological structures (contour trees and Morse-Smale complexes) as an augmentation of traditional direct volume rendering and describes a fully functional implementation in the visualization software Inviwo. The implementation is evaluated through analysis of valency charge density fields in cubic MgO2 and FeO2. It is demonstrated that both contour trees and Morse-Smale complexes provide information and segmentation of initial volume data that allows for selective transfer function application (based on the segmentation), on-demand information on critical points and an overview of the scalar field through a topological representation embedded in the visualized volume. Analysis of the provided charge density fields show that contour trees generate physically irrelevant artefacts and thus are ill-suited for analysing highly symmetric data. On the other hand, the Morse-Smale complex approach is used to extract information of the bond strength of O-O contacts in MgO2 and FeO2 consistent with previous findings, as well as information on electronic charge configuration consistent with previous findings on MgO2. In the case of FeO2, the electronic configuration results are not consistent. This is speculated to be due to a combination of factors, most notably the lack of periodic boundary conditions in the implementation and the more complicated structure of FeO2.   In light of the partially accurate data analysis, as well as the added functionality and utility provided to visualization software, this approach to topology-guided visualization is considered promising and worthy of further study and/or development.

Les travaux de cette thèse s'inscrivent dans le cadre du projet PIA2 3DNeuroSecure. Ce dernier vise à proposer un système collaboratif de navigation multi-échelle interactive dans des données visuelles massives (Visual Big Data) ayant pour cadre applicatif l'imagerie biomédicale 3D ultra-haute résolution (ordre du micron) possiblement multi-modale. En outre, ce système devra être capable d'intégrer divers traitements et/ou annotations (tags) au travers de ressources HPC distantes. Toutes ces opérations doivent être envisagées sans possibilité de stockage complet en mémoire (techniques out-of-core : structures pyramidales, tuilées, … avec ou sans compression …). La volumétrie des données images envisagées (Visual Big Data) induit par ailleurs le découplage des lieux de capture/imagerie/génération (histologie, confocal, imageurs médicaux variés, simulation …), de ceux de stockage et calcul haute performance (data center) mais aussi de ceux de manipulation des données acquises (divers périphériques connectés, mobiles ou non, tablette, PC, mur d’images, salle de RV …). La visualisation restituée en streaming à l’usager sera adaptée à son périphérique, tant en termes de résolution (Full HD à GigaPixel) que de rendu 3D (« à plat » classique, en relief stéréoscopique à lunettes, en relief autostéréoscopique sans lunettes). L'ensemble de ces développements pris en charge par le CReSTIC avec l'appui de la MaSCA (Maison de la Simulation de Champagne-Ardenne) se résument donc par : - la définition et la mise en oeuvre des structures de données adaptées à la visualisation out-of-core des visual big data (VBD) ciblées - l’adaptation des traitements spécifiques des partenaires comme des rendus 3D interactifs à ces nouvelles structures de données - les choix techniques d’architecture pour le HPC et la virtualisation de l’application de navigation pour profiter au mieux des ressources du datacanter local ROMEO. Le rendu relief avec ou sans lunettes, avec ou sans compression du flux vidéo relief associé seront opérés au niveau du logiciel MINT de l’URCA qui servira de support de développement. / These thesis studies are part of the PIA2 project 3DNeuroSecure. This one aims to provide a collaborative system of interactive multi-scale navigation within visual big data (VDB) with ultra-high definition (tera-voxels), potentially multimodal, 3D biomedical imaging as application framework. In addition, this system will be able to integrate a variety of processing and/or annotations (tags) through remote HPC resources. All of these treatments must be possible in an out-of-core context. Because of the visual big data, we have to decoupled the location of acquisition from ones of storage and high performance computation and from ones for the manipulation of the data (various connected devices, mobile or not, smartphone, PC, large display wall, virtual reality room ...). The streaming visualization will be adapted to the user device in terms of both resolution (Full HD to GigaPixel) and 3D rendering (classic rendering on 2D screens, stereoscopic with glasses or autostereoscopic without glasses). All these developments supported by the CReSTIC with the support of MaSCA (Maison de la Simulation de Champagne-Ardenne) can therefore be summarized as: - the definition and implementation of the data structures adapted to the out-of-core visualization of the targeted visual big data. - the adaptation of the specific treatments partners, like interactive 3D rendering, to these new data structures. - the technical architecture choices for the HPC and the virtualization of the navigation software application, to take advantage of "ROMEO", the local datacenter. The auto-/stereoscopic rendering with or without glasses will be operated within the MINT software of the "université de Reims Champagne-Ardenne".

Algoritmos para rendering de superfícies são rápidos, mas não são compatíveis com situações em que é necessário investigar estruturas internas em volumes. Algoritmos de rendering volumétrico direto são adequados para a exploração de estruturas volumétricas, mas são lentos quando comparados a um rendering de superfícies. Várias soluções híbridas foram propostas na literatura, sendo que uma delas, conhecida como VoS (Volume on Surface), foi proposta recentemente com o objetivo de aumentar a capacidade de investigação do conteúdo de volumes por meio de superfícies. VoS é uma técnica híbrida que permite mapear o conteúdo de um volume em superfícies extraídas do mesmo. A técnica executa lançamento de raios para mapear as informações do volume na superfície, possibilitando a visualização das estruturas internas do volume utilizando rendering de superfícies convencional. No presente trabalho estudamos a técnica VoS e propomos diversas modificações com o intuito de generalizar a técnica e tratar algumas de suas limitações. As novas soluções apresentadas permitem a utilização da técnica com volumes de voxels regulares, e geram imagens de melhor qualidade. Assim como a VoS, as duas novas versões implementadas, VoSm e VoSm*, têm o objetivo de melhorar o poder de investigação do rendering de superfícies, permitindo a exploração do conteúdo de volumes. A técnica VoS e suas variações oferecem uma ferramenta alternativa para aplicações em que a utilização de superfícies é uma solução natural. / Surface rendering algorithms are fast, but are not suitable in situations where internal volume structures must be displayed for investigation. On the other hand, Direct Volume Rendering algorithms are effective to support exploration of internal volume structures, but software implementations are slow as compared to surface rendering solutions. Several hybrid solutions have been proposed in the literature. One of such hybrid solutions, named as VoS (Volume on Surface), has been recently introduced with the goal of using surfaces to enhance volume investigation capability. VoS is a hybrid technique that maps volume contents to surfaces extracted from this volume. The technique performs ray casting to map the volume information onto the surface, thus enabling the visualization of internal volume structures using standard surface rendering algorithms. In this work we study the VoS technique and propose several modifications in order to generalize the technique and treat some of its limitations. The new solutions presented here enable applying the technique to volumes described as a regular grid of voxels and produce images of superior quality as compared to the original. As with VoS, the two novel implementations, VoSm and VoSm*, have the goal of improving the investigative power of a surface rendering display, supporting exploration of volumetric contents. VoS and its variations are alternative tools for applications where surface rendering is a natural visualization solution.

The use of virtual reality (VR) for visualization can revolutionize medical training by simulating real world medical training procedures through intuitive and engaging user interface. Existing virtual reality based visualization systems for human anatomy are based on 3D surface and volumetric models and simulative systems based on model libraries. The visual impact as well as facilitation for learning are inadequate in such systems. This thesis research is aimed at eliminating such inadequacies by developing a non-immersive virtual reality system framework for storage, access and navigation of real human cadaveric data. Based on this framework, a real time software system called virtual cadaver navigation system (VCNS) is developed, that can be used as an aid for teaching human anatomy. The hardware components of the system include, a mannequin, an examination probe similar to a medical ultrasound probe, and a personal computer. The examination probe is moved over the mannequin to obtain the virtual tomographic slice from the real cadaveric3-D volume data. A 3-D binary space partitioning tree structure is defined to organize the entire volumetric data, by subdividing it into small blocks of predefined size, called as bricks that are assigned a unique address for identification. As the examination probe is moved over the mannequin, the set of bricks intersecting the corresponding tomographic slice are determined by traversing the tree structure, and only, the selected bricks are accessed from the main memory and brought into the texture memory on the graphics accelerator card for visualization. The texture memory in the graphics card and the main memory are divided into slots of size, that is a multiple of the brick size, and a tagging scheme that relates the brick addresses, texture memory slots, and the main memory blocks is developed. Based on spatial, temporal and sequential locality of reference, only the currently required bricks as well as some of the neighboring bricks are loaded from the main memory into the texture memory, in order to maintain the highest frame rates required forreal time visualization. The above framework consisting of the data organization and the access mechanism are critical in terms of achieving the interactive frame rates required for real-time visualization. The input data to the system consists of non-segmented voxel data, and the data segmented and labelled based on tissue classification. The software system includes a labeling tool, in order to display the specific tissue information at the the location of the mouse cursor. This facility is useful in both teaching anatomy and self learning. Thus, the proposed VCNS system supports efficient navigation through the human body for learning anatomy and provides the knowledge of spatial locations and the interrelationship among the various organs of the body. A prototype software system has been developed, which is capable of achieving a throughput of 30 frames per second and has been tested with a 18-Gigabyte human cadaveric data obtained from the National Library of Medicine, on a personal computer with 64 Megabytes of texture memory and 512 Megabytes of main memory.