Rozprawy doktorskie na temat „Interactive volume visualization”

COORDENAÇÃO DE APERFEIÇOAMENTO DO PESSOAL DE ENSINO SUPERIOR
A visualização volumétrica é uma importante técnica para a exploração de dados tridimensionais complexos, como, por exemplo, o resultado de análises numéricas usando o método dos elementos finitos. A aplicação eficiente dessa técnica a malhas não-estruturadas tem sido uma importante área de pesquisa nos últimos anos. Há dois métodos básicos para a visualização dos dados volumétricos: extração de superfícies e renderização direta de volumes. Na primeira, iso-superfícies de um campo escalar são extraídas explicitamente. Na segunda, que é a utilizada neste trabalho, dados escalares são classificados a partir de uma função de transferência, que mapeia valores do campo escalar em cor e opacidade, para serem visualizados. Com a evolução das placas gráficas (GPU) dos computadores pessoais, foram desenvolvidas novas técnicas para visualização volumétrica interativa de malhas não-estruturadas. Os novos algoritmos tiram proveito da aceleração e da possibilidade de programação dessas placas, cujo poder de processamento cresce a um ritmo superior ao dos processadores convencionais (CPU). Este trabalho avalia e compara dois algoritmos para visualização volumétrica de malhas não-estruturadas, baseados em GPU: projeção de células independente do observador e traçado de raios. Adicionalmente, são propostas duas adaptações dos algoritmos estudados. Para o algoritmo de projeção de células, propõe-se uma estruturação dos dados na GPU para eliminar o alto custo de transferência de dados para a placa gráfica. Para o algoritmo de traçado de raios, propõe-se fazer a integração da função de transferência na GPU, melhorando a qualidade da imagem final obtida e permitindo a alteração da função de transferência de maneira interativa.
Volume visualization is an important technique for the exploration of threedimensional complex data sets, such as the results of numerical analysis using the finite elements method. The efficient application of this technique to unstructured meshes has been an important area of research in the past few years. There are two basic methods to visualize volumetric data: surface extraction and direct volume rendering. In the first, the iso-surfaces of the scalar field are explicitly extracted. In the second, which is the one used in this work, scalar data are classified by a transfer function, which maps the scalar values to color and opacity, to be visualized. With the evolution of personal computer graphics cards (GPU), new techniques for volume visualization have been developed. The new algorithms take advantage of modern programmable graphics cards, whose processing power increases at a faster rate than the one observed in conventional processors (CPU). This work evaluates and compares two GPU- based algorithms for volume visualization of unstructured meshes: view- independent cell projection (VICP) and ray-tracing. In addition, two adaptations of the studied algorithms are proposed. For the cell projection algorithm, we propose a GPU data structure in order to eliminate the high costs of the CPU to GPU data transfer. For the raytracing algorithm, we propose to integrate the transfer function in the GPU, which increases the quality of the generated image and allows to interactively change the transfer function.

Visualization of large scale time-varying volumetric datasets is an active topic of research. Technical limitations in terms of bandwidth and memory usage become a problem when visualizing these datasets on commodity computers at interactive frame rates. The overall objective is to overcome these limitations by adapting the methods of an existing Direct Volume Rendering pipeline. The objective is considered to be a proof of concept to assess the feasibility of visualizing large scale time-varying datasets using this pipeline. The pipeline consists of components from previous research, which make extensive use of graphics hardware to visualize large scale static data on commodity computers.

This report presents a diploma work, which adapts the pipeline to visualize flow features concealed inside the large scale Computational Fluid Dynamics dataset. The work provides a foundation to address the technical limitations of the commodity computer to visualize time-varying datasets. The report describes the components making up the Direct Volume Rendering pipeline together with the adaptations. It also briefly describes the Computational Fluid Dynamics simulation, the flow features and an earlier visualization approach to show the system’s limitations when exploring the dataset.

With current medical imaging improvements, specialists are being able to obtain correct information of anatomical structures of the human organism. By using different image visualization techniques, experts can obtain suitable images for bones, soft tissues, bloodstream among others. Present algorithms generate images with better and better resolution and information accuracy. Medical doctors are being more familiarized with three-dimensional structures reconstructed from bi-dimensional images. As a result, hospitals are becoming interested in tele-medicine and tele-diagnostic solutions. Client-server applications allow these functionalities. Sometimes the use of mobile devices is necessary due to their portability and easy maintenance. However, transmission time for the volumetric information and low performance hardware properties make quite complex the design of efficient visualization systems on these devices. The main objective of this thesis is to enrich user experience during the interactive visualization of volumetric medical models in low performance devices. To achieve this, a new transfer-function aware compression/decompression mechanism adapted to transmission, reconstruction and visualization has been studied. This work proposes several schemes to exploit the use of transfer functions (TFs) to enhance volume compression during data transmission to mobile devices. As far as we know, this possibility has not been considered by any of the described approaches in the previous work. The Wavelet-Based Volume Compression for Remote Visualization approach is a TF-aware compression scheme. It supports inspection of complex volume models with maximum level of detail in selected regions of interest (ROIs). It uses a GPU-based, ROI-aware ray-casting rendering algorithm in the client, with a limited amount of information being sent over the Network, decreasing storage size in the client side. Regarding the Remote Exploration of Volume Models using Gradient Octrees scheme, we have shown that this technique can efficiently encode volume datasets. It supports high-quality visualizations with Transfer Functions from a predefined TFs set. In the present implementation, Transfer Function sets can encode up to ten different volume materials. Gradient Octrees are multi-resolution, supporting progressive transmission and avoiding gradient computations in the client device. That is, Gradient Octrees encodes precomputed gradients to save costly computations in the client, and support illumination-based ray-casting without extra computations in the client GPU. The proposed scheme presents a minimum loss of visual quality as compared to state of the art ray-casting renderings. The octree structure is compacted into a small volume array and a set of texture-coded arrays, with only one bit per octree node. The proposed scheme supports planar volume sections which are visualized with high-resolution volume information, besides interactive extrusion of specific structures. As a final contribution, a Hybrid ROI-based Visualization Algorithm has been proposed. It inherits the advantages of the previously described contributions while keeping a good performance in terms of bandwidth requirements and storage needs in client devices. The scheme is flexible enough to represent several materials and volume structures in the ROI area at high resolution with a very limited information transmission cost. The Hybrid approach has been proved to be specially well suited in the case of large models. Experimental results show that this Hybrid approach is a scalable scheme, with compression rates that decrease when the size of the volume model increases.
Los adelantos actuales en imagenes médicas están permitiendo a los especialistas obtener información cada vez más precisa de las estructuras anatómicas del organismo humano. Mediante la utilización de diferentes técnicas de visualización, los expertos pueden obtener imágenes de calidad para los huesos, tejidos blandos y torrente sanguíneo, entre otros. Los actuales algoritmos de procesamiento de imágenes garantizan el equilibrio entre la resolución y la exactitud de la información. Paralelamente, los médicos están más familiarizados con las estructuras tridimensionales reconstruidas a partir de imágenes en dos dimensiones. Por otro lado, los hospitales están incorporando la tele-medicina y el tele-diagnóstico entre sus soluciones técnicas. Las aplicaciones cliente-servidor permiten estas funcionalidades. En ocasiones el uso de dispositivos móviles es necesario debido a su fácil mantenimiento y a su portabilidad. Sin embargo, el tiempo de transmisión de la información volumétrica así como el bajo rendimiento del hardware en estos dispositivos, hacen que el diseño de sistemas eficientes de visualización sea todavía una tarea compleja. El objetivo principal de esta tesis es enriquecer la experiencia del usuario en la visualización interactiva de modelos volumétricos de medicina en dispositivos de bajo rendimiento. Para conseguir esto, se ha puesto en práctica la implementación de un mecanismo de compresión/descompresión que depende de funciones de transferencia para optimizar la transmisión, reconstrucción y la visualización en estos dispositivos. Esta tesis, por lo tanto, propone varios esquemas para aprovechar el uso de las funciones de transferencia (TFs) e incrementar el ratio de compresión del volumen durante la transmisión a los dispositivos móviles. De acuerdo con nuestros conocimientos, ninguna de las técnicas descritas en los trabajos presentados anteriormente ha considerado esta posibilidad. El esquema de compresión de volumen basado en Wavelets para la visualización remota, es una propuesta para compresión que tiene en cuenta la función de transferencia. Permite la inspección de modelos de volumen complejos con máximos niveles de detalles en regiones de interés seleccionados. El rendering ejecuta un ray-casting adaptado a modelos con regiones de interés orientado a la GPU en el cliente con una cantidad de información muy limitada que se envía por la red. La otra contribución de esta tesis es la implementación de un esquema para la exploración remota de modelos volumétricos mediante Gradient Octrees. Esta técnica codifica de manera eficiente datos de volumen mientras garantiza visualizaciones de alta calidad con funciones de transferencias predefinidas en un determinado conjunto. La actual implementación permite codificiar hasta 10 materiales diferentes en los datos de Volumen. Gradient Octrees es una técnica multi-resolución, permite la transmisión progresiva y evita los cálculos del gradiente en el dispositivo cliente. En efecto, esta aproximación codifica gradientes previamente calculados para reducir el coste de los cálculos en la GPU del cliente y garantizar el ray-casting con iluminación en la GPU del dispositivo. En comparación con las propuestas estudiadas la pérdida de la calidad visual en los Gradient Octrees es mínima. La estructura del octree es compacta, compuesta de un pequeño vector de volumen y un conjunto de vectores de texturas codificadas, que utilizan solo 1 bit por nodo del octree. El esquema soporta además secciones planas de volumen que contienen información de alta resolución, además de la extrusión de estructuras en los modelos visualizados

This thesis details work carried out by two students working as contractors at the Community Coordinated Modelling Center at Goddard Space Flight Center of the National Aeronautics and Space Administration. The thesis is made possible by and aims to contribute to the OpenSpace project. The first track of the work implemented is the handling of and putting together new data for a visualization of coronal mass ejections in OpenSpace. The new data allows for observation of coronal mass ejections at their origin by the surface of the Sun, whereas previous data visualized them from 30 solar radii out from the Sun and outwards. Previously implemented visualization techniques are used together to visualize different volume data and fieldlines, which together with a synoptic magnetogram of the Sun gives a multi-layered visualization. The second track is an experimental implementation of a generalized and less user involved process for getting new data into OpenSpace, with a priority on volume data as that was a subject of experience. The results show a space weather model visualization, and how one such model can be adapted to fit within the parameters of the OpenSpace project. Additionally, the results show how a GUI connected to a series of background events can form a data pipeline to make complicated space weather models more easily available.

A visualização de conjuntos de dados volumétricos é comum em diversas áreas de aplicação e há já alguns anos os diversos aspectos envolvidos nessas técnicas vêm sendo pesquisados. No entanto, apesar dos avanços das técnicas de visualização de volumes, a interação com grandes volumes de dados ainda apresenta desafios devido a questões de percepção (ou isolamento) de estruturas internas e desempenho computacional. O suporte do hardware gráfico para visualização baseada em texturas permite o desenvolvimento de técnicas eficientes de rendering que podem ser combinadas com ferramentas de recorte interativas para possibilitar a inspeção de conjuntos de dados tridimensionais. Muitos estudos abordam a otimização do desempenho de ferramentas de recorte, mas muito poucos tratam das metáforas de interação utilizadas por essas ferramentas. O objetivo deste trabalho é desenvolver ferramentas interativas, intuitivas e fáceis de usar para o recorte de imagens volumétricas. Inicialmente, é apresentado um estudo sobre as principais técnicas de visualização direta de volumes e como é feita a exploração desses volumes utilizando-se recorte volumétrico. Nesse estudo é identificada a solução que melhor se enquadra no presente trabalho para garantir a interatividade necessária. Após, são apresentadas diversas técnicas de interação existentes, suas metáforas e taxonomias, para determinar as possíveis técnicas de interação mais fáceis de serem utilizadas por ferramentas de recorte. A partir desse embasamento, este trabalho apresenta o desenvolvimento de três ferramentas de recorte genéricas implementadas usando-se duas metáforas de interação distintas que são freqüentemente utilizadas por usuários de aplicativos 3D: apontador virtual e mão virtual. A taxa de interação dessas ferramentas é obtida através de programas de fragmentos especiais executados diretamente no hardware gráfico. Estes programas especificam regiões dentro do volume a serem descartadas durante o rendering, com base em predicados geométricos. Primeiramente, o desempenho, precisão e preferência (por parte dos usuários) das ferramentas de recorte volumétrico são avaliados para comparar as metáforas de interação empregadas. Após, é avaliada a interação utilizando-se diferentes dispositivos de entrada para a manipulação do volume e ferramentas. A utilização das duas mãos ao mesmo tempo para essa manipulação também é testada. Os resultados destes experimentos de avaliação são apresentados e discutidos.
Visualization of volumetric datasets is common in many fields and has been an active area of research in the past two decades. In spite of developments in volume visualization techniques, interacting with large datasets still demands research efforts due to perceptual and performance issues. The support of graphics hardware for texture-based visualization allows efficient implementation of rendering techniques that can be combined with interactive sculpting tools to enable interactive inspection of 3D datasets. Many studies regarding performance optimization of sculpting tools have been reported, but very few are concerned with the interaction techniques employed. The purpose of this work is the development of interactive, intuitive, and easy-to-use sculpting tools. Initially, a review of the main techniques for direct volume visualization and sculpting is presented. The best solution that guarantees the required interaction is highlighted. Afterwards, in order to identify the most user-friendly interaction technique for volume sculpting, several interaction techniques, metaphors and taxonomies are presented. Based on that, this work presents the development of three generic sculpting tools implemented using two different interaction metaphors, which are often used by users of 3D applications: virtual pointer and virtual hand. Interactive rates for these sculpting tools are obtained by running special fragment programs on the graphics hardware which specify regions within the volume to be discarded from rendering based on geometric predicates. After development, the performance, precision and user preference of the sculpting tools were evaluated to compare the interaction metaphors. Afterward, the tools were evaluated by comparing the use of a 3D mouse against a conventional wheel mouse for guiding volume and tools manipulation. Two-handed input was also tested with both types of mouse. The results from the evaluation experiments are presented and discussed.

Técnicas de visualização volumétrica direta são utilizadas para visualizar e explorar volumes de dados complexos. Dados volumétricos provêm de diversas fontes, tais como dispositivos de diagnóstico médico, radares de sensoriamento remoto ou ainda simulações científicas assistidas por computador. Um problema fundamental na visualização volumétrica é a especificação de Funções de Transferência (FTs) que atribuem cor e opacidade aos valores escalares que compõem o volume de dados. Essas funções são importantes para a exibição de características e objetos de interesse do volume, porém sua definição não é trivial ou intuitiva. Abordagens tradicionais permitem a edição manual de pontos de controle que representam a FT a ser utilizada no volume. No entanto, essas técnicas acabam conduzindo o usuário a um processo de “tentativa e erro” para serem obtidos os resultados desejados. Considera-se também que técnicas automáticas que excluem o usuário do processo não são consideradas as mais adequadas, visto que o mesmo deve possuir algum controle sobre o processo de visualização. Este trabalho apresenta uma ferramenta semi-automática e interativa destinada a auxiliar o usuário na geração de FTs de cor e opacidade. A ferramenta proposta possui dois níveis de interação com o usuário. No primeiro nível são apresentados várias FTs candidatas renderizadas como thumbnails 3D, seguindo o método conhecido como Design Galleries (MARKS et al., 1997). São aplicadas técnicas para reduzir o escopo das funções candidatas para um conjunto mais razoável, sendo possível ainda um refinamento das mesmas. No segundo nível é possível definir cores para a FT de opacidade escolhida, e ainda refinar essa função de modo a melhorála de acordo com as necessidades do usuário. Dessa forma, um dos objetivos desse trabalho é permitir ao usuário lidar com diferentes aspectos da especificação de FTs, que normalmente são dependentes da aplicação em questão e do volume de dados sendo visualizado. Para o rendering do volume, são exploradas as capacidades de mapeamento de textura e os recursos do hardware gráfico programável provenientes das plácas gráficas atuais visando a interação em tempo real. Os resultados obtidos utilizam volumes de dados médicos e sintéticos, além de volumes conhecidos, para a análise da ferramenta proposta. No entanto, é dada ênfase na especificação de FTs de propósito geral, sem a necessidade do usuário prover um mapeamento direto representando a função desejada.
Direct volume rendering techniques are used to visualize and explore large scalar volumes. Volume data can be acquired from many sources including medical diagnoses scanners, remote sensing radars or even computer-aided scientific simulations. A key issue in volume rendering is the specification of Transfer Functions (TFs) which assign color and opacity to the scalar values which comprise the volume. These functions are important to the exhibition of features and objects of interest from the volume, but their specification is not trivial or intuitive. Traditional approaches allow the manual editing of a graphic plot with control points representing the TF being applied to the volume. However, these techniques lead the user to an unintuitive trial and error task, which is time-consuming. It is also considered that automatic methods that exclude the user from the process should be avoided, since the user must have some control of the visualization process. This work presents a semi-automatic and interactive tool to assist the user in the specification of color and opacity TFs. The proposed tool has two levels of user interaction. The first level presents to the user several candidate TFs rendered as 3D thumbnails, following the method known as Design Galleries (MARKS et al., 1997). Techniques are applied to reduce the scope of the candidate functions to a more reasonable one. It is also possible to further refine these functions at this level. In the second level is permitted to define and edit colors in the chosen TF, and refine this function if desired. One of the objectives of this work is to allow users to deal with different aspects of TF specification, which is generally dependent of the application or the dataset being visualized. To render the volume, the programmability of the current generation of graphics hardware is explored, as well as the features of texture mapping in order to achieve real time interaction. The tool is applied to medical and synthetic datasets, but the main objective is to propose a general-purpose tool to specify TFs without the need for an explicit mapping from the user.

Live Surface allows users to segment and render complex surfaces from 3D image volumes at interactive (sub-second) rates using a novel, Cascading Graph Cut (CGC). Live Surface consists of two phases. (1) Preprocessing for generation of a complete 3D watershed hierarchy followed by tracking of all catchment basin surfaces. (2) User interaction in which, with each mouse movement, the 3D object is selected and rendered in real time. Real-time segmentation is ccomplished by cascading through the 3D watershed hierarchy from the top, applying graph cut successively at each level only to catchment basins bordering the segmented surface from the previous level. CGC allows the entire image volume to be segmented an order of magnitude faster than existing techniques that make use of graph cut. OpenGL rendering provides for display and update of the segmented surface at interactive rates. The user selects objects by tagging voxels with either (object) foreground or background seeds. Seeds can be placed on image cross-sections or directly on the 3D rendered surface. Interaction with the rendered surface improves the user's ability to steer the segmentation, augmenting or subtracting from the current selection. Segmentation and rendering, combined, is accomplished in about 0.5 seconds, allowing 3D surfaces to be displayed and updated dynamically as each additional seed is deposited. The immediate feedback of Live Surface allows for the segmentation of 3D image volumes with an interaction paradigm similar to the Live Wire (Intelligent Scissors) tool used in 2D images.

Aplikace pro vizualizaci a modelování molekul nejsou dosud příliš poznamenány současným hardware vyvinutým pro potřeby počítačových her. Cílem projektu je navrhnout intuitivní rozhraní s novými widgety specializovanými na atomové struktury a vizualizací využívající moderní hardware grafických karet. Důležitou částí je také dosažení vysoké přesnosti modelování, obvykle dostupné pouze u profesionálních CAD programů.

There is a growing need for custom visualization applications to deal with the rising amounts of volume data to be analyzed in fields like medicine, seismology, and meteorology. Visual programming techniques have been used in visualization and other fields to analyze and visualize data in an intuitive manner. However, this additional step of abstraction often results in a performance penalty during the actual rendering. In order to prevent this impact, a careful modularization of the required processing steps is necessary, which provides flexibility and good performance at the same time. In this paper, we will describe the technical foundations as well as the possible applications of such a modularization for GPU-based volume raycasting, which can be considered the state-of-the-art technique for interactive volume rendering. Based on the proposed modularization on a functional level, we will show how to integrate GPU-based volume ray-casting in a visual programming environment in such a way that a high degree of flexibility is achieved without any performance impact.

This dissertation provides empirical evidence for the effects of the fidelity of VR system components, and novel 3D interaction techniques for analyzing volume datasets. It provides domain-independent results based on an abstract task taxonomy for visual analysis of scientific datasets. Scientific data generated through various modalities e.g. computed tomography (CT), magnetic resonance imaging (MRI), etc. are in 3D spatial or volumetric format. Scientists from various domains e.g., geophysics, medical biology, etc. use visualizations to analyze data. This dissertation seeks to improve effectiveness of scientific visualizations. Traditional volume data analysis is performed on desktop computers with mouse and keyboard interfaces. Previous research and anecdotal experiences indicate improvements in volume data analysis in systems with very high fidelity of display and interaction (e.g., CAVE) over desktop environments. However, prior results are not generalizable beyond specific hardware platforms, or specific scientific domains and do not look into the effectiveness of 3D interaction techniques. We ran three controlled experiments to study the effects of a few components of VR system fidelity (field of regard, stereo and head tracking) on volume data analysis. We used volume data from paleontology, medical biology and biomechanics. Our results indicate that different components of system fidelity have different effects on the analysis of volume visualizations. One of our experiments provides evidence for validating the concept of Mixed Reality (MR) simulation. Our approach of controlled experimentation with MR simulation provides a methodology to generalize the effects of immersive virtual reality (VR) beyond individual systems. To generalize our (and other researchers') findings across disparate domains, we developed and evaluated a taxonomy of visual analysis tasks with volume visualizations. We report our empirical results tied to this taxonomy. We developed the Volume Cracker (VC) technique for improving the effectiveness of volume visualizations. This is a free-hand gesture-based novel 3D interaction (3DI) technique. We describe the design decisions in the development of the Volume Cracker (with a list of usability criteria), and provide the results from an evaluation study. Based on the results, we further demonstrate the design of a bare-hand version of the VC with the Leap Motion controller device. Our evaluations of the VC show the benefits of using 3DI over standard 2DI techniques. This body of work provides the building blocks for a three-way many-many-many mapping between the sets of VR system fidelity components, interaction techniques and visual analysis tasks with volume visualizations. Such a comprehensive mapping can inform the design of next-generation VR systems to improve the effectiveness of scientific data analysis.
Ph. D.

Examples of volume data include medical scanned data such as CT and MRI data, seismic survey data, and computational fluid dynamic (CFD) data, etc. To better understand volumetric datasets, people use computer hardware and software to manipulate the data and generate 2D projections for viewing; this process is called volume visualization. Much research on volume visualization has been focused on volume rendering (how to render larger sets of data faster with a higher level of realism) or transfer function generation (how to highlight the regions of interest). To help improve the efficiency and efficacy of volume visualization, this research proposed using two different approaches. The first approach is to integrate virtual reality environments (VEs) and human computer interaction (HCI) technologies in volume visualization applications. The second approach is to use various virtual tools that allow users to directly explore and manipulate the volume data in 3D space. A volume visualization system named VRVolVis (Virtual Reality Volumes Visualization System) has been designed and developed to implement these approaches. Many innovations have been integrated into this system, including a fast volume rendering engine, an intuitive HCI paradigm tailored for volume visualization in VEs, and 8 innovative geometric tools that can assist users to fully reveal the internal structure of volumetric datasets. The tools are the clipping plane widget, the data slab widget, the volume probing tool, the volume clipping tool, the regional enhancement tool, the virtual light, the volume eraser and restorer, and the shooting star tool. Two sets of experiments involving 33 participants were conducted, and the experimental results supported the assertion that volume visualization tasks would be performed significant better in VR viewing conditions than Stereo and Conventional conditions, and that using these geometric tools can significantly improve the efficiency and efficacy of the volume visualization process.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Information and Communication Technology
Science, Environment, Engineering and Technology
Full Text

Computed Tomography (CT) is a medical imaging modality which acquires anatomical data via the unique x-ray attenuation of materials. Yet, some clinically important materials remain difficult to distinguish with current CT technology. Spectral CT is an emerging technology which acquires multiple CT datasets for specific x-ray spectra. These spectra provide a fingerprint that allow materials to be distinguished that would otherwise look the same on conventional CT. The unique characteristics of spectral CT data motivates research into novel visualization techniques. In this thesis, we aim to provide the foundation for visualizing spectral CT data. Our initial investigation of similar multi-variate data types identified intermixing as a promising visualization technique. This promoted the development of a generic, modular and extensible intermixing framework. Therefore, the contribution of our work is a framework supporting the construction, analysis and storage of algorithms for visualizing spectral CT studies. To allow evaluation, we implemented the intermixing framework in an application called MARSCTExplorer along with a standard set of volume visualization tools. These tools provide user-interaction as well as supporting traditional visualization techniques for comparison. We evaluated our work with four spectral CT studies containing materials indistinguishable by conventional CT. Our results confirm that spectral CT can distinguish these materials, and reveal how these materials might be visualized with our intermixing framework.

Les études scientifiques et d'ingénierie actuelles font de plus en plus souvent appel à des techniques de simulation numérique pour étudier des phénomènes physiques complexes. La visualisation du résultat de ces simulations sur leur support spatial, souvent nécessaire à leur bonne compréhension, demande la mise en place d'outils adaptés, permettant une restitution fidèle et complète de l'information présente dans un jeu de données. Une telle visualisation doit donc prendre en compte les informations disponibles sur la qualité du jeu de données et l'incertitude présente. Cette thèse a pour but d'améliorer les méthodes de visualisation des champs de données scalaires de façon à intégrer une telle information d'incertitude. Les travaux présentés adoptent une approche perceptive, et utilisent les méthodes expérimentales et les connaissances préalables obtenues par la recherche sur la perception visuelle pour proposer, étudier et finalement mettre en oeuvre des nouvelles techniques de visualisation. Une revue de l'état de l'art sur la visualisation de données incertaines nous fait envisager l'utilisation d'un bruit procédural animé comme primitive pour la représentation de l'incertitude. Une expérience de psychophysique nous permet d'évaluer des seuils de sensibilité au contraste pour des stimuli de luminance générés par l'algorithme de bruit de Perlin, et de déterminer ainsi dans quelles conditions ces stimuli seront perçus. Ces résultats sont validés et étendus par l'utilisation d'un modèle computationnel de sensibilité au contraste, que nous avons réimplémenté et exécuté sur nos stimuli. Les informations obtenues nous permettent de proposer une technique de visualisation des données scalaires incertaines utilisant un bruit procédural animé et des échelles de couleur, intuitive et efficace même sur des géométries tridimensionnelles complexes. Cette technique est appliquée à deux jeux de données industriels, et présentée à des utilisateurs experts. Les commentaires de ces utilisateurs confirment l'efficacité et l'intérêt de notre technique et nous permettent de lui apporter quelques améliorations, ainsi que d'envisager des axes de recherche pour des travaux futurs.

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"

by Yu-Hang Siu.
Thesis (M.Phil.)--Chinese University of Hong Kong, 1998.
Includes bibliographical references (leaves 74-80).
Abstract also in Chinese.
Abstract --- p.iii
Acknowledgements --- p.v
Chapter 1 --- Introduction --- p.1
Chapter 1.1 --- Volume Visualization --- p.2
Chapter 1.2 --- Virtual Environment --- p.11
Chapter 1.3 --- Approach --- p.12
Chapter 1.4 --- Thesis Overview --- p.13
Chapter 2 --- Contour Extraction --- p.15
Chapter 2.1 --- Concept of Intelligent Scissors --- p.16
Chapter 2.2 --- Dijkstra's Algorithm --- p.18
Chapter 2.3 --- Cost Function --- p.20
Chapter 2.4 --- Summary --- p.23
Chapter 3 --- Volume Cutting --- p.24
Chapter 3.1 --- Basic idea of the algorithm --- p.25
Chapter 3.2 --- Intelligent Scissors on Surface Mesh --- p.27
Chapter 3.3 --- Internal Cutting Surface --- p.29
Chapter 3.4 --- Summary --- p.34
Chapter 4 --- Three-dimensional Intelligent Scissors --- p.35
Chapter 4.1 --- 3D Graph Construction --- p.36
Chapter 4.2 --- Cost Function --- p.40
Chapter 4.3 --- Applications --- p.42
Chapter 4.3.1 --- Surface Extraction --- p.42
Chapter 4.3.2 --- Vessel Tracking --- p.47
Chapter 4.4 --- Summary --- p.49
Chapter 5 --- Implementations in a Virtual Environment --- p.52
Chapter 5.1 --- Volume Cutting --- p.53
Chapter 5.2 --- Surface Extraction --- p.56
Chapter 5.3 --- Vessel Tracking --- p.59
Chapter 5.4 --- Summary --- p.64
Chapter 6 --- Conclusions --- p.68
Chapter 6.1 --- Summary of Results --- p.68
Chapter 6.2 --- Future Directions --- p.70
Chapter A --- Performance of Dijkstra's Shortest Path Algorithm --- p.72
Chapter B --- IsoRegion Construction --- p.73

Visual displays are a formidable means of conveying information to the human brain. They facilitate the formation of scientific knowledge about the physical world, based on underlying observations of diverse kinds, through representations that are understood by practitioners of the relevant discipline area. Such data visualizations are critical in the geosciences given the need to draw meaning from time-varying, spatial or volumetric data, and given the increasing size of the datasets available for analysis of the natural, physical world. The research described in this thesis aims to apply a novel set of technical resources to visualization in the geosciences. It draws on the immense potential of the human user for feature detection through connecting scientific data formats to computer graphics technologies. The software applications written in response to this opportunity therefore make strong use of interactivity in the reconnaissance exploration of example datasets. Throughout the research, a commitment to a well-posed visual display is developed, respecting underlying data values through the managed use of color and other graphic variables Following a review of the conceptual background, and the landscape of computer graphics technologies, the first original research chapter presents interactive software and workflows to visualize large geoscientific time-series datasets. It uses an animated interface and Human-Computer Interaction (HCI) to utilize the capacity of human expert observers to identify features via enhanced visual analytics. User-generated metadata allows subsets of the data to be tagged for subsequent closer investigation. The tool provides a rapid pre-pass process using fast GPU-based OpenGL graphics and data-handling. It makes use of interoperable data formats, and cloud-based (or local) data storage and computation. In a case study, the software was used to characterize a decade (2000–2009) of data recorded by the Cape Sorell Waverider Buoy, located approximately 10 km off the West coast of Tasmania, Australia. These data serve as a proxy for the understanding of Southern Ocean storminess, which has both local and global implications. Four different types of storm and non-storm events are characterized and compared with conventional analysis, noting the advantages and limitations of data analysis using animation and human interaction. The second original research chapter presents a suite of newly written computer applications for 2D data, which enable spatially varying data to be displayed and analyzed in a performant graphics environment. Color-mappings using illustrative color spaces (RGB, CIELAB) are compared with the aid of interactive displays of the applied gradient paths through the chosen color spaces. This facilitates the creation of color-maps that accommodate the non-uniformity of human color perception, producing an image where genuine features are seen, taking account of aspects of the data such as parameter uncertainty. For an illustrative case study using a seismic tomography result, interpolation in CIELAB color space is shown to enable the creation of perceptually uniform linear gradients that match the underlying data, along with a simply computable metric for color difference, ∆E. This color space assists the accuracy and reproducibility of visualization results. The well-posed use of color is further developed in the third original research chapter, for the exploratory interactive visualization of 3D volumes of global, deep Earth data. As an example, we address the challenge of reconnaissance visualization of a combined seismic tomography result, the primary means by which geoscientists infer structure and process in the deep Earth. A novel, interactive graphical application suite is presented that uses an intuitive 2.5D layer compositing approach. This allows the user to adjust the separation between data-slices, control graphics variables such as color mapping, opacity and compositing, and enables exploration and annotation of the architecture of the lithosphere. The methodology could find use in the visualization of multiple datasets representing aspects of the Earth’s deep interior, oceans and atmosphere, and in facilitating researcher interaction with the increasing number of rich datasets from missions to our neighboring planets. The three original research papers that form the core of this thesis all provide a means of amplifying analytical acuity through animated and/or interactive interfaces that enable both ‘overview’ and ‘detail’ visualization and navigation. Through all three studies, the ‘human in the loop’ aspects of the visualization process are drawn upon, e.g. in the use of perceptual color spaces for optimal display of data, or exploiting visual faculties such as stereopsis and depth perception. The dataflow software methodology employed is self-documenting, using a visual programming approach that can be replicated in alternative cross-platform software environments such as recent computer game engines. This flexible strategy assists the development of novel graphical user interfaces and interaction modalities for collaborative immersive screen technologies such as domes and future XR applications. In summary the research described herein bridges the gap between scientific data formats and the immense resources of the computer graphics and gaming industries. It exploits productive modes of HCI engagement with the data display to facilitate the search for new knowledge in the geosciences. It is anticipated that the newly written software applications will lead to wider usage of informed color-mapping in the geosciences and an awareness of the utility of emergent visualization platforms for enhancing scientific research. It is hoped that “visual literacy” and “visual numeracy” will substantially improve as a consequence of this work, and similar initiatives, as inference tasks are more routinely carried out using well-posed data visualization in the geosciences.

The most important resources to fulfill today’s energy demands are fossil fuels, such as oil and natural gas. When exploiting hydrocarbon reservoirs, a detailed and credible model of the subsurface structures to plan the path of the borehole, is crucial in order to minimize economic and ecological risks. Before that, the placement, as well as the operations of oil rigs need to be planned carefully, as off-shore oil exploration is vulnerable to hazards caused by strong currents. The oil and gas industry therefore relies on accurate ocean forecasting systems for planning their operations. This thesis presents visual workflows for creating subsurface models as well as planning the placement and operations of off-shore structures. Creating a credible subsurface model poses two major challenges: First, the structures in highly ambiguous seismic data are interpreted in the time domain. Second, a velocity model has to be built from this interpretation to match the model to depth measurements from wells. If it is not possible to obtain a match at all positions, the interpretation has to be updated, going back to the first step. This results in a lengthy back and forth between the different steps, or in an unphysical velocity model in many cases. We present a novel, integrated approach to interactively creating subsurface models from reflection seismics, by integrating the interpretation of the seismic data using an interactive horizon extraction technique based on piecewise global optimization with velocity modeling. Computing and visualizing the effects of changes to the interpretation and velocity model on the depth-converted model, on the fly enables an integrated feedback loop that enables a completely new connection of the seismic data in time domain, and well data in depth domain. For planning the operations of off-shore structures we present a novel integrated visualization system that enables interactive visual analysis of ensemble simulations used in ocean forecasting, i.e, simulations of sea surface elevation. Changes in sea surface elevation are a good indicator for the movement of loop current eddies. Our visualization approach enables their interactive exploration and analysis. We enable analysis of the spatial domain, for planning the placement of structures, as well as detailed exploration of the temporal evolution at any chosen position, for the prediction of critical ocean states that require the shutdown of rig operations. We illustrate this using a real-world simulation of the Gulf of Mexico.

Advances in the physical sciences have progressively delivered ever increasing, already extremely large data sets to be analyzed. High performance volume rendering has become critical to the scientists for a better understanding of the massive amounts of data to be visualized. Cluster based rendering systems have become the base line to achieve the power and flexibility required to perform such task. Furthermore, display arrays have become the most suitable solution to display these data sets at their natural size and resolution which can be critical for human perception and evaluation. The work in this thesis aims at improving the scalability and usability of volume rendering systems that target visualization on display arrays. The first part deals with improving the performance by introducing the implementations of two parallel compositing algorithms for volume rendering: direct send and binary swap. The High quality Volume Rendering (HVR) framework has been extended to accommodate parallel compositing where previously only serial compositing was possible. The preliminary results show improvements in the compositing times for direct send even for a small number of processors. Unfortunately, the results of binary swap exhibit a negative behavior. This is due to the naive use of the graphics hardware blending mechanism. The expensive transfers account for the lengthy compositing times. The second part targets the development of scalable and intuitive interaction mechanisms. It introduces the development of a new client application for multitouch tablet devices, like the Apple iPad. The main goal is to provide the HVR framework, that has been extended to use tiled displays, a more intuitive and portable interaction mechanism that can get advantage of the new environment. The previous client is a PC application for the typical desktop settings that use a mouse and keyboard as sources of interaction. The current implementation of the client lets the user steer and change the opacity transfer function of the visualization via simple multitouch gestures. Nonetheless, the user can freely move around, engage into discussion with other users and easily pass the tablet around for others to use. Before, this was not possible with the same ease of use. Ultimately, the collaborative possibilities are many and extremely interesting to explore.

Thesis (M.S.)--University of Wisconsin--Madison, 2003.
Typescript. eContent provider-neutral record in process. Description based on print version record. Includes bibliographical references (leaves 145-146).