Context Preserving Focal Probes for Exploration of Volumetric Medical Datasets

During real-time medical data exploration using volume rendering, it is often difficult to enhance a particular region of interest without losing context information. In this paper, we present a new illustrative technique for focusing on a user-driven region of interest while preserving context information. Our focal probes define a region of interest using a distance function which controls the opacity of the voxels within the probe, exploit silhouette enhancement and use non-photorealistic shading techniques to improve shape depiction.187-19

Interactive High Performance Volume Rendering

This thesis is about Direct Volume Rendering on high performance computing systems. As direct rendering methods do not create a lower-dimensional geometric representation, the whole scientific dataset must be kept in memory. Thus, this family of algorithms has a tremendous resource demand. Direct Volume Rendering algorithms in general are well suited to be implemented for dedicated graphics hardware. Nevertheless, high performance computing systems often do not provide resources for hardware accelerated rendering, so that the visualization algorithm must be implemented for the available general-purpose hardware. Ever growing datasets that imply copying large amounts of data from the compute system to the workstation of the scientist, and the need to review intermediate simulation results, make porting Direct Volume Rendering to high performance computing systems highly relevant. The contribution of this thesis is twofold. As part of the first contribution, after devising a software architecture for general implementations of Direct Volume Rendering on highly parallel platforms, parallelization issues and implementation details for various modern architectures are discussed. The contribution results in a highly parallel implementation that tackles several platforms. The second contribution is concerned with the display phase of the “Distributed Volume Rendering Pipeline”. Rendering on a high performance computing system typically implies displaying the rendered result at a remote location. This thesis presents a remote rendering technique that is capable of hiding latency and can thus be used in an interactive environment

Doctor of Philosophy in Computing

dissertationThe aim of direct volume rendering is to facilitate exploration and understanding of three-dimensional scalar fields referred to as volume datasets. Improving understanding is done by improving depth perception, whereas facilitating exploration is done by speeding up volume rendering. In this dissertation, improving both depth perception and rendering speed is considered. The impact of depth of field (DoF) on depth perception in direct volume rendering is evaluated by conducting a user study in which the test subjects had to choose which of two features, located at different depths, appeared to be in front in a volume-rendered image. Whereas DoF was expected to improve perception in all cases, the user study revealed that if used on the back feature, DoF reduced depth perception, whereas it produced a marked improvement when used on the front feature. We then worked on improving the speed of volume rendering on distributed memory machines. Distributed volume rendering has three stages: loading, rendering, and compositing. In this dissertation, the focus is on image compositing, more specifically, trying to optimize communication in image compositing algorithms. For that, we have developed the Task Overlapped Direct Send Tree image compositing algorithm, which works on both CPU- and GPU-accelerated supercomputers, which focuses on communication avoidance and overlapping communication with computation; the Dynamically Scheduled Region-Based image compositing algorithm that uses spatial and temporal awareness to efficiently schedule communication among compositing nodes, and a rendering and compositing pipeline that allows both image compositing and rendering to be done on GPUs of GPU-accelerated supercomputers. We tested these on CPU- and GPU-accelerated supercomputers and explain how these improvements allow us to obtain better performance than image compositing algorithms that focus on load-balancing and algorithms that have no spatial and temporal awareness of the rendering and compositing stages

Visualisation of Ultrasound Computer Tomography Breast Dataset

Medical visualisation plays a vital role in diagnosing and detecting early symptoms. In particular, visualising the anatomy of breast model allows doctors or practitioners to identify first signs of the breast cancer. However, despite the advancement in visualisation techniques, most standard visualisation approaches in the medical field still rely on analysing 2D images which lack spatial information. In this paper, we present an interactive web-based 3D visualisation tool for ultrasound computer tomography (USCT) breast dataset. We base our implementation on the Web-based Graphics Language (WebGL) technology that utilises the GPU parallel architecture. The tool serves as a common platform among research collaborators to analyse and share findings on their dataset. We render the data using state-of-the-art algorithms of interactive computer graphics and produce results with quality comparable to the desktop application. Aside from that, our tool enables researchers to perform arbitrary view slicing, modality thresholding and multiple rendering modes. In the evaluation, our tool maintains an interactive frame rate above 30 fps on a standard desktop

Real-time quality visualization of medical models on commodity and mobile devices

This thesis concerns the specific field of visualization of medical models using commodity and mobile devices. Mechanisms for medical imaging acquisition such as MRI, CT, and micro-CT scanners are continuously evolving, up to the point of obtaining volume datasets of large resolutions (> 512^3). As these datasets grow in resolution, its treatment and visualization become more and more expensive due to their computational requirements. For this reason, special techniques such as data pre-processing (filtering, construction of multi-resolution structures, etc.) and sophisticated algorithms have to be introduced in different points of the visualization pipeline to achieve the best visual quality without compromising performance times. The problem of managing big datasets comes from the fact that we have limited computational resources. Not long ago, the only physicians that were rendering volumes were radiologists. Nowadays, the outcome of diagnosis is the data itself, and medical doctors need to render them in commodity PCs (even patients may want to render the data, and the DVDs are commonly accompanied with a DICOM viewer software). Furthermore, with the increasing use of technology in daily clinical tasks, small devices such as mobile phones and tablets can fit the needs of medical doctors in some specific areas. Visualizing diagnosis images of patients becomes more challenging when it comes to using these devices instead of desktop computers, as they generally have more restrictive hardware specifications. The goal of this Ph.D. thesis is the real-time, quality visualization of medium to large medical volume datasets (resolutions >= 512^3 voxels) on mobile phones and commodity devices. To address this problem, we use multiresolution techniques that apply downsampling techniques on the full resolution datasets to produce coarser representations which are easier to handle. We have focused our efforts on the application of Volume Visualization in the clinical practice, so we have a particular interest in creating solutions that require short pre-processing times that quickly provide the specialists with the data outcome, maximize the preservation of features and the visual quality of the final images, achieve high frame rates that allow interactive visualizations, and make efficient use of the computational resources. The contributions achieved during this thesis comprise improvements in several stages of the visualization pipeline. The techniques we propose are located in the stages of multi-resolution generation, transfer function design and the GPU ray casting algorithm itself.Esta tesis se centra en la visualización de modelos médicos de volumen en dispositivos móviles y de bajas prestaciones. Los sistemas médicos de captación tales como escáners MRI, CT y micro-CT, están en constante evolución, hasta el punto de obtener modelos de volumen de gran resolución (> 512^3). A medida que estos datos crecen en resolución, su manejo y visualización se vuelve más y más costoso debido a sus requisitos computacionales. Por este motivo, técnicas especiales como el pre-proceso de datos (filtrado, construcción de estructuras multiresolución, etc.) y algoritmos específicos se tienen que introducir en diferentes puntos de la pipeline de visualización para conseguir la mejor calidad visual posible sin comprometer el rendimiento. El problema que supone manejar grandes volumenes de datos es debido a que tenemos recursos computacionales limitados. Hace no mucho, las únicas personas en el ámbito médico que visualizaban datos de volumen eran los radiólogos. Hoy en día, el resultado de la diagnosis son los datos en sí, y los médicos necesitan renderizar estos datos en PCs de características modestas (incluso los pacientes pueden querer visualizar estos datos, pues los DVDs con los resultados suelen venir acompañados de un visor de imágenes DICOM). Además, con el reciente aumento del uso de las tecnologías en la clínica práctica habitual, dispositivos pequeños como teléfonos móviles o tablets son los más convenientes en algunos casos. La visualización de volumen es más difícil en este tipo de dispositivos que en equipos de sobremesa, pues las limitaciones de su hardware son superiores. El objetivo de esta tesis doctoral es la visualización de calidad en tiempo real de modelos grandes de volumen (resoluciones >= 512^3 voxels) en teléfonos móviles y dispositivos de bajas prestaciones. Para enfrentarnos a este problema, utilizamos técnicas multiresolución que aplican técnicas de reducción de datos a los modelos en resolución original, para así obtener modelos de menor resolución. Hemos centrado nuestros esfuerzos en la aplicación de la visualización de volumen en la práctica clínica, así que tenemos especial interés en diseñar soluciones que requieran cortos tiempos de pre-proceso para que los especialistas tengan rápidamente los resultados a su disposición. También, queremos maximizar la conservación de detalles de interés y la calidad de las imágenes finales, conseguir frame rates altos que faciliten visualizaciones interactivas y que hagan un uso eficiente de los recursos computacionales. Las contribuciones aportadas por esta tesis són mejoras en varias etapas de la pipeline de visualización. Las técnicas que proponemos se situan en las etapas de generación de la estructura multiresolución, el diseño de la función de transferencia y el algoritmo de ray casting en la GPU

Real-time quality visualization of medical models on commodity and mobile devices

This thesis concerns the specific field of visualization of medical models using commodity and mobile devices. Mechanisms for medical imaging acquisition such as MRI, CT, and micro-CT scanners are continuously evolving, up to the point of obtaining volume datasets of large resolutions (> 512^3). As these datasets grow in resolution, its treatment and visualization become more and more expensive due to their computational requirements. For this reason, special techniques such as data pre-processing (filtering, construction of multi-resolution structures, etc.) and sophisticated algorithms have to be introduced in different points of the visualization pipeline to achieve the best visual quality without compromising performance times. The problem of managing big datasets comes from the fact that we have limited computational resources. Not long ago, the only physicians that were rendering volumes were radiologists. Nowadays, the outcome of diagnosis is the data itself, and medical doctors need to render them in commodity PCs (even patients may want to render the data, and the DVDs are commonly accompanied with a DICOM viewer software). Furthermore, with the increasing use of technology in daily clinical tasks, small devices such as mobile phones and tablets can fit the needs of medical doctors in some specific areas. Visualizing diagnosis images of patients becomes more challenging when it comes to using these devices instead of desktop computers, as they generally have more restrictive hardware specifications. The goal of this Ph.D. thesis is the real-time, quality visualization of medium to large medical volume datasets (resolutions >= 512^3 voxels) on mobile phones and commodity devices. To address this problem, we use multiresolution techniques that apply downsampling techniques on the full resolution datasets to produce coarser representations which are easier to handle. We have focused our efforts on the application of Volume Visualization in the clinical practice, so we have a particular interest in creating solutions that require short pre-processing times that quickly provide the specialists with the data outcome, maximize the preservation of features and the visual quality of the final images, achieve high frame rates that allow interactive visualizations, and make efficient use of the computational resources. The contributions achieved during this thesis comprise improvements in several stages of the visualization pipeline. The techniques we propose are located in the stages of multi-resolution generation, transfer function design and the GPU ray casting algorithm itself.Esta tesis se centra en la visualización de modelos médicos de volumen en dispositivos móviles y de bajas prestaciones. Los sistemas médicos de captación tales como escáners MRI, CT y micro-CT, están en constante evolución, hasta el punto de obtener modelos de volumen de gran resolución (> 512^3). A medida que estos datos crecen en resolución, su manejo y visualización se vuelve más y más costoso debido a sus requisitos computacionales. Por este motivo, técnicas especiales como el pre-proceso de datos (filtrado, construcción de estructuras multiresolución, etc.) y algoritmos específicos se tienen que introducir en diferentes puntos de la pipeline de visualización para conseguir la mejor calidad visual posible sin comprometer el rendimiento. El problema que supone manejar grandes volumenes de datos es debido a que tenemos recursos computacionales limitados. Hace no mucho, las únicas personas en el ámbito médico que visualizaban datos de volumen eran los radiólogos. Hoy en día, el resultado de la diagnosis son los datos en sí, y los médicos necesitan renderizar estos datos en PCs de características modestas (incluso los pacientes pueden querer visualizar estos datos, pues los DVDs con los resultados suelen venir acompañados de un visor de imágenes DICOM). Además, con el reciente aumento del uso de las tecnologías en la clínica práctica habitual, dispositivos pequeños como teléfonos móviles o tablets son los más convenientes en algunos casos. La visualización de volumen es más difícil en este tipo de dispositivos que en equipos de sobremesa, pues las limitaciones de su hardware son superiores. El objetivo de esta tesis doctoral es la visualización de calidad en tiempo real de modelos grandes de volumen (resoluciones >= 512^3 voxels) en teléfonos móviles y dispositivos de bajas prestaciones. Para enfrentarnos a este problema, utilizamos técnicas multiresolución que aplican técnicas de reducción de datos a los modelos en resolución original, para así obtener modelos de menor resolución. Hemos centrado nuestros esfuerzos en la aplicación de la visualización de volumen en la práctica clínica, así que tenemos especial interés en diseñar soluciones que requieran cortos tiempos de pre-proceso para que los especialistas tengan rápidamente los resultados a su disposición. También, queremos maximizar la conservación de detalles de interés y la calidad de las imágenes finales, conseguir frame rates altos que faciliten visualizaciones interactivas y que hagan un uso eficiente de los recursos computacionales. Las contribuciones aportadas por esta tesis són mejoras en varias etapas de la pipeline de visualización. Las técnicas que proponemos se situan en las etapas de generación de la estructura multiresolución, el diseño de la función de transferencia y el algoritmo de ray casting en la GPU.Postprint (published version

General Purpose Computation on Graphics Processing Units Using OpenCL

Computational Science has emerged as a third pillar of science along with theory and experiment, where the parallelization for scientific computing is promised by different shared and distributed memory architectures such as, super-computer systems, grid and cluster based systems, multi-core and multiprocessor systems etc. In the recent years the use of GPUs (Graphic Processing Units) for General purpose computing commonly known as GPGPU made it an exciting addition to high performance computing systems (HPC) with respect to price and performance ratio. Current GPUs consist of several hundred computing cores arranged in streaming multi-processors so the degree of parallelism is promising. Moreover with the development of new and easy to use interfacing tools and programming languages such as OpenCL and CUDA made the GPUs suitable for different computation demanding applications such as micromagnetic simulations. In micromagnetic simulations, the study of magnetic behavior at very small time and space scale demands a huge computation time, where the calculation of magnetostatic field with complexity of O(Nlog(N)) using FFT algorithm for discrete convolution is the main contribution towards the whole simulation time, and it is computed many times at each time step interval. This study and observation of magnetization behavior at sub-nanosecond time-scales is crucial to a number of areas such as magnetic sensors, non volatile storage devices and magnetic nanowires etc. Since micromagnetic codes in general are suitable for parallel programming as it can be easily divided into independent parts which can run in parallel, therefore current trend for micromagnetic code concerns shifting the computationally intensive parts to GPUs. My PhD work mainly focuses on the development of highly parallel magnetostatic field solver for micromagnetic simulators on GPUs. I am using OpenCL for GPU implementation, with consideration that it is an open standard for parallel programming of heterogeneous systems for cross platform. The magnetostatic field calculation is dominated by the multidimensional FFTs (Fast Fourier Transform) computation. Therefore i have developed the specialized OpenCL based 3D-FFT library for magnetostatic field calculation which made it possible to fully exploit the zero padded input data with out transposition and symmetries inherent in the field calculation. Moreover it also provides a common interface for different vendors' GPUs. In order to fully utilize the GPUs parallel architecture the code needs to handle many hardware specific technicalities such as coalesced memory access, data transfer overhead between GPU and CPU, GPU global memory utilization, arithmetic computation, batch execution etc. In the second step to further increase the level of parallelism and performance, I have developed a parallel magnetostatic field solver on multiple GPUs. Utilizing multiple GPUs avoids dealing with many of the limitations of GPUs (e.g., on-chip memory resources) by exploiting the combined resources of multiple on board GPUs. The GPU implementation have shown an impressive speedup against equivalent OpenMp based parallel implementation on CPU, which means the micromagnetic simulations which require weeks of computation on CPU now can be performed very fast in hours or even in minutes on GPUs. In parallel I also worked on ordered queue management on GPUs. Ordered queue management is used in many applications including real-time systems, operating systems, and discrete event simulations. In most cases, the efficiency of an application itself depends on usage of a sorting algorithm for priority queues. Lately, the usage of graphic cards for general purpose computing has again revisited sorting algorithms. In this work i have presented the analysis of different sorting algorithms with respect to sorting time, sorting rate and speedup on different GPU and CPU architectures and provided a new sorting technique on GPU

Real-time GPU-accelerated Out-of-Core Rendering and Light-field Display Visualization for Improved Massive Volume Understanding

Nowadays huge digital models are becoming increasingly available for a number of different applications ranging from CAD, industrial design to medicine and natural sciences. Particularly, in the field of medicine, data acquisition devices such as MRI or CT scanners routinely produce huge volumetric datasets. Currently, these datasets can easily reach dimensions of 1024^3 voxels and datasets larger than that are not uncommon. This thesis focuses on efficient methods for the interactive exploration of such large volumes using direct volume visualization techniques on commodity platforms. To reach this goal specialized multi-resolution structures and algorithms, which are able to directly render volumes of potentially unlimited size are introduced. The developed techniques are output sensitive and their rendering costs depend only on the complexity of the generated images and not on the complexity of the input datasets. The advanced characteristics of modern GPGPU architectures are exploited and combined with an out-of-core framework in order to provide a more flexible, scalable and efficient implementation of these algorithms and data structures on single GPUs and GPU clusters. To improve visual perception and understanding, the use of novel 3D display technology based on a light-field approach is introduced. This kind of device allows multiple naked-eye users to perceive virtual objects floating inside the display workspace, exploiting the stereo and horizontal parallax. A set of specialized and interactive illustrative techniques capable of providing different contextual information in different areas of the display, as well as an out-of-core CUDA based ray-casting engine with a number of improvements over current GPU volume ray-casters are both reported. The possibilities of the system are demonstrated by the multi-user interactive exploration of 64-GVoxel datasets on a 35-MPixel light-field display driven by a cluster of PCs. ------------------------------------------------------------------------------------------------------ Negli ultimi anni si sta verificando una proliferazione sempre più consistente di modelli digitali di notevoli dimensioni in campi applicativi che variano dal CAD e la progettazione industriale alla medicina e le scienze naturali. In modo particolare, nel settore della medicina, le apparecchiature di acquisizione dei dati come RM o TAC producono comunemente dei dataset volumetrici di grosse dimensioni. Questi dataset possono facilmente raggiungere taglie dell’ordine di 10243 voxels e dataset di dimensioni maggiori possono essere frequenti. Questa tesi si focalizza su metodi efficienti per l’esplorazione di tali grossi volumi utilizzando tecniche di visualizzazione diretta su piattaforme HW di diffusione di massa. Per raggiungere tale obiettivo si introducono strutture specializzate multi-risoluzione e algoritmi in grado di visualizzare volumi di dimensioni potenzialmente infinite. Le tecniche sviluppate sono “ouput sensitive” e la loro complessità di rendering dipende soltanto dalle dimensioni delle immagini generate e non dalle dimensioni dei dataset di input. Le caratteristiche avanzate delle architetture moderne GPGPU vengono inoltre sfruttate e combinate con un framework “out-of-core” in modo da offrire una implementazione di questi algoritmi e strutture dati più flessibile, scalabile ed efficiente su singole GPU o cluster di GPU. Per migliorare la percezione visiva e la comprensione dei dati, viene introdotto inoltre l’uso di tecnologie di display 3D di nuova generazione basate su un approccio di tipo light-field. Questi tipi di dispositivi consentono a diversi utenti di percepire ad occhio nudo oggetti che galleggiano all’interno dello spazio di lavoro del display, sfruttando lo stereo e la parallasse orizzontale. Si descrivono infine un insieme di tecniche illustrative interattive in grado di fornire diverse informazioni contestuali in diverse zone del display, così come un motore di “ray-casting out-of-core” basato su CUDA e contenente una serie di miglioramenti rispetto agli attuali metodi GPU di “ray-casting” di volumi. Le possibilità del sistema sono dimostrate attraverso l’esplorazione interattiva di dataset di 64-GVoxel su un display di tipo light-field da 35-MPixel pilotato da un cluster di PC

Exploiting spatial and temporal coherence in GPU-based volume rendering

Effizienz spielt eine wichtige Rolle bei der Darstellung von Volumendaten, selbst wenn leistungsstarke Grafikhardware zur Verfügung steht, da steigende Datensatzgrößen und höhere Anforderungen an Visualisierungstechniken Fortschritte bei Grafikprozessoren ausgleichen. In dieser Dissertation wird untersucht, wie räumliche und zeitliche Kohärenz in Volumendaten zur Optimierung von Volumenrendering genutzt werden kann. Es werden mehrere neue Ansätze für statische und zeitvariante Daten eingeführt, die verschieden Arten von Kohärenz in verschiedenen Stufen der Volumenrendering-Pipeline ausnutzen. Zu den vorgestellten Beschleunigungstechniken gehört Empty Space Skipping mittels Occlusion Frustums, eine auf Slabs basierende Cachestruktur für Raycasting und ein verlustfreies Kompressionsscheme für zeitvariante Daten. Die Algorithmen wurden zur Verwendung mit GPU-basiertem Volumen-Raycasting entworfen und nutzen die Fähigkeiten moderner Grafikprozessoren, insbesondere Stream Processing. Efficiency is a key aspect in volume rendering, even if powerful graphics hardware is employed, since increasing data set sizes and growing demands on visualization techniques outweigh improvements in graphics processor performance. This dissertation examines how spatial and temporal coherence in volume data can be used to optimize volume rendering. Several new approaches for static as well as for time-varying data sets are introduced, which exploit different types of coherence in different stages of the volume rendering pipeline. The presented acceleration algorithms include empty space skipping using occlusion frustums, a slab-based cache structure for raycasting, and a lossless compression scheme for time-varying data. The algorithms were designed for use with GPU-based volume raycasting and to efficiently exploit the features of modern graphics processors, especially stream processing