<p>A numerical simulation case involving space plasma and the evolution of instabilities that generates very fast electrons, i.e. approximately at half of the speed of light, is used as a test bed for scientific visualisation techniques. A visualisation system was developed to provide interactive real-time animation and visualisation of the simulation results. The work focuses on two themes and the integration of them. The first theme is the storage and management of the large data sets produced. The second theme deals with how the Visualisation System and Visual Objects are tailored to efficiently visualise the data at hand. </p><p>The integration of the themes has resulted in an interactive real-time animation and visualisation system which constitutes a very powerful tool for analysis and understanding of the plasma physics processes. The visualisations contained in this work have spawned many new possible research projects and provided insight into previously not fully understood plasma physics phenomena.</p>

<p>The technique of volume rendering can be a powerful tool when visualizing 3D medical data sets. Its characteristic of capturing 3D internal structures within a 2D rendered image makes it attractive in the analysis. However, the applications that implement this technique fail to reach out to most of the supposed end-users at the clinics and radiology departments of today. This is primarily due to problems centered on the design of the Transfer Function (TF), the tool that makes tissues visually appear in the rendered image. The interaction with the TF is too complex for a supposed end-user and its capability of separating tissues is often insufficient. This thesis presents methods for detecting the regions in the image volume where tissues are contained. The tissues that are of interest can furthermore be identified among these regions. This processing and classification is possible thanks to the use of a priori knowledge, i.e. what is known about the data set and its domain in advance. The identified regions can finally be visualized using tissue adapted TFs that can create cleaner renderings of tissues where a normal TF would fail to separate them. In addition an intuitive user control is presented that allows the user to easily interact with the detection and the visualization.</p>

Visualizing and manipulating volumetric data is a major component in many areas including anatomical registration in biomedical fields, seismic data analysis in the oil industry, machine part design in computer-aided geometric design, character animation in the movie industry, and fluid simulation. These industries have to meet the demands of the times and be able to make meaningful assertions about the data they generate. The shear size of this data presents many challenges to facilitating realtime interaction. In the recent decade, graphics hardware has become increasingly powerful and more sophisticated which has introduced a new realm of possibilities for processing volumetric data. This thesis focuses on a suite of techniques for viewing and editing volumetric data that efficiently use the processing power of central processing units (CPUs) as well as the large processing power of the graphics hardware (GPUs). This work begins with an algorithm to improve the efficiency of a texture-based volume rendering. We continue with a framework for performing realtime constructive solid geometry (CSG) with complex shapes and smoothing operations on watertight meshes based on a variation of Depth Peeling. We then move to an intuitive technique for deforming volumetric data using a collection of control points. Finally, we apply this technique to image registration of 3-dimensional computed tomography (CT) images used for lung cancel treatment, planning.

A modality device can today capture high resolution volumetric data sets and as the data resolutions increase so does the challenges of processing volumetric data through a visualization pipeline. Standard volume rendering pipelines often use a graphic processing unit (GPU) to accelerate rendering performance by taking beneficial use of the parallel architecture on such devices. Unfortunately, graphics cards have limited amounts of video memory (VRAM), causing a bottleneck in a standard pipeline. Multi-resolution techniques can be used to efficiently modify the rendering pipeline, allowing a sub-domain within the volume to be represented at different resolutions. The active resolution distribution is temporarily stored on the VRAM for rendering and the inactive parts are stored on secondary memory layers such as the system RAM or on disk. The active resolution set can be optimized to produce high quality renders while minimizing the amount of storage required. This is done by using a dynamic compression scheme which optimize the visual quality by evaluating user-input data. The optimized resolution of each sub-domain is then, on demand, streamed to the VRAM from secondary memory layers. Rendering a multi-resolution data set requires some extra care between boundaries of sub-domains. To avoid artifacts, an intrablock interpolation (II) sampling scheme capable of creating smooth transitions between sub-domains at arbitrary resolutions can be used. The result is a highly optimized rendering pipeline complemented with a preprocessing pipeline together capable of rendering large volumetric data sets in real-time.

The technique of volume rendering can be a powerful tool when visualizing 3D medical data sets. Its characteristic of capturing 3D internal structures within a 2D rendered image makes it attractive in the analysis. However, the applications that implement this technique fail to reach out to most of the supposed end-users at the clinics and radiology departments of today. This is primarily due to problems centered on the design of the Transfer Function (TF), the tool that makes tissues visually appear in the rendered image. The interaction with the TF is too complex for a supposed end-user and its capability of separating tissues is often insufficient. This thesis presents methods for detecting the regions in the image volume where tissues are contained. The tissues that are of interest can furthermore be identified among these regions. This processing and classification is possible thanks to the use of a priori knowledge, i.e. what is known about the data set and its domain in advance. The identified regions can finally be visualized using tissue adapted TFs that can create cleaner renderings of tissues where a normal TF would fail to separate them. In addition an intuitive user control is presented that allows the user to easily interact with the detection and the visualization.

Direct Volume Rendering (DVR) is a technique for creating images directly from a representation of a function defined over a three-dimensional domain. The technique has many application fields, such as scientific visualization and medical imaging. A striking property of the data sets produced within these fields is their ever increasing size and complexity. Despite the advancements of computing resources these data sets seem to grow at even faster rates causing severe bottlenecks in terms of data transfer bandwidths, memory capacity and processing requirements in the rendering pipeline. This thesis focuses on efficient methods for DVR of large data sets. At the core of the work lies a level-of-detail scheme that reduces the amount of data to process and handle, while optimizing the level-of-detail selection so that high visual quality is maintained. A set of techniques for domain knowledge encoding which significantly improves assessment and prediction of visual significance for blocks in a volume are introduced. A complete pipeline for DVR is presented that uses the data reduction achieved by the level-of-detail selection to minimize the data requirements in all stages. This leads to reduction of disk I/O as well as host and graphics memory. The data reduction is also exploited to improve the rendering performance in graphics hardware, employing adaptive sampling both within the volume and within the rendered image. The developed techniques have been applied in particular to medical visualization of large data sets on commodity desktop computers using consumer graphics processors. The specific application of virtual autopsies has received much interest, and several developed data classification schemes and rendering techniques have been motivated by this application. The results are, however, general and applicable in many fields and significant performance and quality improvements over previous techniques are shown. / On the defence date the status of article IX was Accepted.

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.

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.

Volume rendering (VRT) has been used with great success in studies of patients using computed tomography (CT), much because of the possibility of standardizing the rendering protocols. When using magnetic resonance imaging (MRI), this procedure is considerably more difficult, since the signal from a given tissue can vary dramatically, even for the same patient. This thesis work focuses on how to improve the presentation of MRI data by using VRT protocols including standardized transfer functions. The study is limited to exclusively examining data from patients with suspected renal artery stenosis. A total number of 11 patients are examined. A statistical approach is used to standardize the volume rendering protocols. The histogram of the image volume is modeled as the sum of two gamma distributions, corresponding to vessel and background voxels. Parameters describing the gamma distributions are estimated with a Maximum-likelihood technique, so that expectation (E1 and E2) and standard deviation of the two voxel distributions can be calculated from the histogram. These values are used to generate the transfer function. Different combinations of the values from the expectation and standard deviation were studied in a material of 11 MR angiography datasets, and the visual result was graded by a radiologist. By comparing the grades, it turned out that using only the expectation of the background distribution (E1) and vessel distribution (E2) gave the best result. The opacity is then defined with a value of 0 up to a signal threshold of E1, then increasing linearly up to 50 % at a second threshold E2, and after that a constant opacity of 50 %. The brightness curve follows the opacity curve to E2, after which it continues to increase linearly up to 100%. A graphical user interface was created to facilitate the user-control of the volumes and transfer functions. The result from the statistical calculations is displayed in the interface and is used to view and manipulate the transfer function directly in the volume histogram. A transfer function generated with the Maximum-likelihood VRT method (ML-VRT) gave a better visual result in 10 of the 11 cases than when using a transfer function not adapting to signal intensity variations.

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.