Doctor of Philosophy

dissertationRay tracing presents an efficient rendering algorithm for scientific visualization using common visualization tools and scales with increasingly large geometry counts while allowing for accurate physically-based visualization and analysis, which enables enhanced rendering and new visualization techniques. Interactivity is of great importance for data exploration and analysis in order to gain insight into large-scale data. Increasingly large data sizes are pushing the limits of brute-force rasterization algorithms present in the most widely-used visualization software. Interactive ray tracing presents an alternative rendering solution which scales well on multicore shared memory machines and multinode distributed systems while scaling with increasing geometry counts through logarithmic acceleration structure traversals. Ray tracing within existing tools also provides enhanced rendering options over current implementations, giving users additional insight from better depth cues while also enabling publication-quality rendering and new models of visualization such as replicating photographic visualization techniques

Novel high performance techniques for high definition computer aided tomography

Mención Internacional en el título de doctorMedical image processing is an interdisciplinary field in which multiple research areas are involved: image acquisition, scanner design, image reconstruction algorithms, visualization, etc. X-Ray Computed Tomography (CT) is a medical imaging modality based on the attenuation suffered by the X-rays as they pass through the body. Intrinsic differences in attenuation properties of bone, air, and soft tissue result in high-contrast images of anatomical structures. The main objective of CT is to obtain tomographic images from radiographs acquired using X-Ray scanners. The process of building a 3D image or volume from the 2D radiographs is known as reconstruction. One of the latest trends in CT is the reduction of the radiation dose delivered to patients through the decrease of the amount of acquired data. This reduction results in artefacts in the final images if conventional reconstruction methods are used, making it advisable to employ iterative reconstruction algorithms. There are numerous reconstruction algorithms available, from which we can highlight two specific types: traditional algorithms, which are fast but do not enable the obtaining of high quality images in situations of limited data; and iterative algorithms, slower but more reliable when traditional methods do not reach the quality standard requirements. One of the priorities of reconstruction is the obtaining of the final images in near real time, in order to reduce the time spent in diagnosis. To accomplish this objective, new high performance techniques and methods for accelerating these types of algorithms are needed. This thesis addresses the challenges of both traditional and iterative reconstruction algorithms, regarding acceleration and image quality. One common approach for accelerating these algorithms is the usage of shared-memory and heterogeneous architectures. In this thesis, we propose a novel simulation/reconstruction framework, namely FUX-Sim. This framework follows the hypothesis that the development of new flexible X-ray systems can benefit from computer simulations, which may also enable performance to be checked before expensive real systems are implemented. Its modular design abstracts the complexities of programming for accelerated devices to facilitate the development and evaluation of the different configurations and geometries available. In order to obtain near real execution times, low-level optimizations for the main components of the framework are provided for Graphics Processing Unit (GPU) architectures. Other alternative tackled in this thesis is the acceleration of iterative reconstruction algorithms by using distributed memory architectures. We present a novel architecture that unifies the two most important computing paradigms for scientific computing nowadays: High Performance Computing (HPC). The proposed architecture combines Big Data frameworks with the advantages of accelerated computing. The proposed methods presented in this thesis provide more flexible scanner configurations as they offer an accelerated solution. Regarding performance, our approach is as competitive as the solutions found in the literature. Additionally, we demonstrate that our solution scales with the size of the problem, enabling the reconstruction of high resolution images.El procesamiento de imágenes médicas es un campo interdisciplinario en el que participan múltiples áreas de investigación como la adquisición de imágenes, diseño de escáneres, algoritmos de reconstrucción de imágenes, visualización, etc. La tomografía computarizada (TC) de rayos X es una modalidad de imágen médica basada en el cálculo de la atenuación sufrida por los rayos X a medida que pasan por el cuerpo a escanear. Las diferencias intrínsecas en la atenuación de hueso, aire y tejido blando dan como resultado imágenes de alto contraste de estas estructuras anatómicas. El objetivo principal de la TC es obtener imágenes tomográficas a partir estas radiografías obtenidas mediante escáneres de rayos X. El proceso de construir una imagen o volumen en 3D a partir de las radiografías 2D se conoce como reconstrucción. Una de las últimas tendencias en la tomografía computarizada es la reducción de la dosis de radiación administrada a los pacientes a través de la reducción de la cantidad de datos adquiridos. Esta reducción da como resultado artefactos en las imágenes finales si se utilizan métodos de reconstrucción convencionales, por lo que es aconsejable emplear algoritmos de reconstrucción iterativos. Existen numerosos algoritmos de reconstrucción disponibles a partir de los cuales podemos destacar dos categorías: algoritmos tradicionales, rápidos pero no permiten obtener imágenes de alta calidad en situaciones en las que los datos son limitados; y algoritmos iterativos, más lentos pero más estables en situaciones donde los métodos tradicionales no alcanzan los requisitos en cuanto a la calidad de la imagen. Una de las prioridades de la reconstrucción es la obtención de las imágenes finales en tiempo casi real, con el fin de reducir el tiempo de diagnóstico. Para lograr este objetivo, se necesitan nuevas técnicas y métodos de alto rendimiento para acelerar estos algoritmos. Esta tesis aborda los desafíos de los algoritmos de reconstrucción tradicionales e iterativos, con respecto a la aceleración y la calidad de imagen. Un enfoque común para acelerar estos algoritmos es el uso de arquitecturas de memoria compartida y heterogéneas. En esta tesis, proponemos un nuevo sistema de simulación/reconstrucción, llamado FUX-Sim. Este sistema se construye alrededor de la hipótesis de que el desarrollo de nuevos sistemas de rayos X flexibles puede beneficiarse de las simulaciones por computador, en los que también se puede realizar un control del rendimiento de los nuevos sistemas a desarrollar antes de su implementación física. Su diseño modular abstrae las complejidades de la programación para aceleradores con el objetivo de facilitar el desarrollo y la evaluación de las diferentes configuraciones y geometrías disponibles. Para obtener ejecuciones en casi tiempo real, se proporcionan optimizaciones de bajo nivel para los componentes principales del sistema en las arquitecturas GPU. Otra alternativa abordada en esta tesis es la aceleración de los algoritmos de reconstrucción iterativa mediante el uso de arquitecturas de memoria distribuidas. Presentamos una arquitectura novedosa que unifica los dos paradigmas informáticos más importantes en la actualidad: computación de alto rendimiento (HPC) y Big Data. La arquitectura propuesta combina sistemas Big Data con las ventajas de los dispositivos aceleradores. Los métodos propuestos presentados en esta tesis proporcionan configuraciones de escáner más flexibles y ofrecen una solución acelerada. En cuanto al rendimiento, nuestro enfoque es tan competitivo como las soluciones encontradas en la literatura. Además, demostramos que nuestra solución escala con el tamaño del problema, lo que permite la reconstrucción de imágenes de alta resolución.This work has been mainly funded thanks to a FPU fellowship (FPU14/03875) from the Spanish Ministry of Education. It has also been partially supported by other grants: • DPI2016-79075-R. “Nuevos escenarios de tomografía por rayos X”, from the Spanish Ministry of Economy and Competitiveness. • TIN2016-79637-P Towards unification of HPC and Big Data Paradigms from the Spanish Ministry of Economy and Competitiveness. • Short-term scientific missions (STSM) grant from NESUS COST Action IC1305. • TIN2013-41350-P, Scalable Data Management Techniques for High-End Computing Systems from the Spanish Ministry of Economy and Competitiveness. • RTC-2014-3028-1 NECRA Nuevos escenarios clinicos con radiología avanzada from the Spanish Ministry of Economy and Competitiveness.Programa Oficial de Doctorado en Ciencia y Tecnología InformáticaPresidente: José Daniel García Sánchez.- Secretario: Katzlin Olcoz Herrero.- Vocal: Domenico Tali

Fast feature matching for detailed point cloud generation

Structure from motion is a very popular technique for obtaining three-dimensional point cloud-based reconstructions of objects from un-organised sets of images by analysing the correspondences between feature points detected in those images. However, the point clouds stemming from usual feature point extractors such as SIFT are frequently too sparse for reliable surface recovery. In this paper we show that alternate feature descriptors such as A-KAZE, which provide denser coverage of images, yield better results and more detailed point clouds. Unfortunately, the use of a dramatically increased number of points per image poses a computational challenge. We propose a technique based on epipolar geometry restrictions to significantly cut down on processing time and an efficient implementation thereof on a GPU

SELF-ADAPTING PARALLEL FRAMEWORK FOR LONG-TERM OBJECT TRACKING

Object tracking is a crucial field in computer vision that has many uses in human-computer interaction, security and surveillance, video communication and compression, augmented reality, traffic control, etc. Many implementations are introduced in practice, and yet recent methods emphasize on tracking objects adaptively by learning the object’s perspectives and rediscovering it when it becomes untraceable, so that object’s absence problem (in case of occlusion, cluttering or blurring) is resolved. Most of these algorithms have high computational burden on the computational units and need powerful CPUs to attain real-time tracking and high bitrate video processing. These computational units may handle no more than a single video source, making it unsuitable for large-scale implementations like multiple sources or higher resolution videos. In this thesis, we choose one popular algorithm called TLD, Tracking-Learning-Detection, study the core components of the algorithm that impede its performance, and implement these components in a parallel computational environment such as multi-core CPUs, GPUs, etc., also known as heterogeneous computing. OpenCL is used as a development platform to produce parallel kernels for the algorithm. The goals are to create an acceptable heterogeneous computing environment through utilizing current computer technologies, to imbue real-time applications with an alternative implementation methodology, and to circumvent the upcoming limitations of hardware in terms of cost, power, and speedup. We are able to bring true parallel speedup to the existing implementations, which greatly improves the frame rate for long-term object tracking and with some algorithm parameter modification, it provides more accurate object tracking. According to the experiments, developed kernels have achieved a range of performance improvement. As for reduction based kernels, a maximum of 78X speedup is achieved. While for window based kernels, a range of couple hundreds to 2000X speedup is achieved. And for the optical flow tracking kernel, a maximum of 5.7X speedup is recorded. Global speedup is highly dependent on the hardware specifications, especially for memory transfers. With the use of a medium sized input, the self-adapting parallel framework has successfully obtained a fast learning curve and converged to an average of 1.6X speedup compared to the original implementation. Lastly, for future programming convenience, an OpenCL based library is built to facilitate the use of OpenCL programming on parallel hardware devices, hide the complexity of building and compiling OpenCL kernels, and provide a C-based latency measurement tool that is compatible with several operating systems

Applied Visualization in the Neurosciences and the Enhancement of Visualization through Computer Graphics

The complexity and size of measured and simulated data in many fields of science is increasing constantly. The technical evolution allows for capturing smaller features and more complex structures in the data. To make this data accessible by the scientists, efficient and specialized visualization techniques are required. Maximum efficiency and value for the user can only be achieved by adapting visualization to the specific application area and the specific requirements of the scientific field. Part I: In the first part of my work, I address the visualization in the neurosciences. The neuroscience tries to understand the human brain; beginning at its smallest parts, up to its global infrastructure. To achieve this ambitious goal, the neuroscience uses a combination of three-dimensional data from a myriad of sources, like MRI, CT, or functional MRI. To handle this diversity of different data types and sources, the neuroscience need specialized and well evaluated visualization techniques. As a start, I will introduce an extensive software called \"OpenWalnut\". It forms the common base for developing and using visualization techniques with our neuroscientific collaborators. Using OpenWalnut, standard and novel visualization approaches are available to the neuroscientific researchers too. Afterwards, I am introducing a very specialized method to illustrate the causal relation of brain areas, which was, prior to that, only representable via abstract graph models. I will finalize the first part of my work with an evaluation of several standard visualization techniques in the context of simulated electrical fields in the brain. The goal of this evaluation was clarify the advantages and disadvantages of the used visualization techniques to the neuroscientific community. We exemplified these, using clinically relevant scenarios. Part II: Besides the data preprocessing, which plays a tremendous role in visualization, the final graphical representation of the data is essential to understand structure and features in the data. The graphical representation of data can be seen as the interface between the data and the human mind. The second part of my work is focused on the improvement of structural and spatial perception of visualization -- the improvement of the interface. Unfortunately, visual improvements using computer graphics methods of the computer game industry is often seen sceptically. In the second part, I will show that such methods can be applied to existing visualization techniques to improve spatiality and to emphasize structural details in the data. I will use a computer graphics paradigm called \"screen space rendering\". Its advantage, amongst others, is its seamless applicability to nearly every visualization technique. I will start with two methods that improve the perception of mesh-like structures on arbitrary surfaces. Those mesh structures represent second-order tensors and are generated by a method named \"TensorMesh\". Afterwards I show a novel approach to optimally shade line and point data renderings. With this technique it is possible for the first time to emphasize local details and global, spatial relations in dense line and point data.In vielen Bereichen der Wissenschaft nimmt die Größe und Komplexität von gemessenen und simulierten Daten zu. Die technische Entwicklung erlaubt das Erfassen immer kleinerer Strukturen und komplexerer Sachverhalte. Um solche Daten dem Menschen zugänglich zu machen, benötigt man effiziente und spezialisierte Visualisierungswerkzeuge. Nur die Anpassung der Visualisierung auf ein Anwendungsgebiet und dessen Anforderungen erlaubt maximale Effizienz und Nutzen für den Anwender. Teil I: Im ersten Teil meiner Arbeit befasse ich mich mit der Visualisierung im Bereich der Neurowissenschaften. Ihr Ziel ist es, das menschliche Gehirn zu begreifen; von seinen kleinsten Teilen bis hin zu seiner Gesamtstruktur. Um dieses ehrgeizige Ziel zu erreichen nutzt die Neurowissenschaft vor allem kombinierte, dreidimensionale Daten aus vielzähligen Quellen, wie MRT, CT oder funktionalem MRT. Um mit dieser Vielfalt umgehen zu können, benötigt man in der Neurowissenschaft vor allem spezialisierte und evaluierte Visualisierungsmethoden. Zunächst stelle ich ein umfangreiches Softwareprojekt namens \"OpenWalnut\" vor. Es bildet die gemeinsame Basis für die Entwicklung und Nutzung von Visualisierungstechniken mit unseren neurowissenschaftlichen Kollaborationspartnern. Auf dieser Basis sind klassische und neu entwickelte Visualisierungen auch für Neurowissenschaftler zugänglich. Anschließend stelle ich ein spezialisiertes Visualisierungsverfahren vor, welches es ermöglicht, den kausalen Zusammenhang zwischen Gehirnarealen zu illustrieren. Das war vorher nur durch abstrakte Graphenmodelle möglich. Den ersten Teil der Arbeit schließe ich mit einer Evaluation verschiedener Standardmethoden unter dem Blickwinkel simulierter elektrischer Felder im Gehirn ab. Das Ziel dieser Evaluation war es, der neurowissenschaftlichen Gemeinde die Vor- und Nachteile bestimmter Techniken zu verdeutlichen und anhand klinisch relevanter Fälle zu erläutern. Teil II: Neben der eigentlichen Datenvorverarbeitung, welche in der Visualisierung eine enorme Rolle spielt, ist die grafische Darstellung essenziell für das Verständnis der Strukturen und Bestandteile in den Daten. Die grafische Repräsentation von Daten bildet die Schnittstelle zum Gehirn des Menschen. Der zweite Teile meiner Arbeit befasst sich mit der Verbesserung der strukturellen und räumlichen Wahrnehmung in Visualisierungsverfahren -- mit der Verbesserung der Schnittstelle. Leider werden viele visuelle Verbesserungen durch Computergrafikmethoden der Spieleindustrie mit Argwohn beäugt. Im zweiten Teil meiner Arbeit werde ich zeigen, dass solche Methoden in der Visualisierung angewendet werden können um den räumlichen Eindruck zu verbessern und Strukturen in den Daten hervorzuheben. Dazu nutze ich ein in der Computergrafik bekanntes Paradigma: das \"Screen Space Rendering\". Dieses Paradigma hat den Vorteil, dass es auf nahezu jede existierende Visualiserungsmethode als Nachbearbeitunsgschritt angewendet werden kann. Zunächst führe ich zwei Methoden ein, die die Wahrnehmung von gitterartigen Strukturen auf beliebigen Oberflächen verbessern. Diese Gitter repräsentieren die Struktur von Tensoren zweiter Ordnung und wurden durch eine Methode namens \"TensorMesh\" erzeugt. Anschließend zeige ich eine neuartige Technik für die optimale Schattierung von Linien und Punktdaten. Mit dieser Technik ist es erstmals möglich sowohl lokale Details als auch globale räumliche Zusammenhänge in dichten Linien- und Punktdaten zu erfassen

G-PUF : asoftware-only PUF for GPUs

Physical Unclonable Functions (PUFs) are security primitives which allow the generation of unique IDs and security keys. Their security stems from the inherent process variations of silicon chips manufacturing, and the minute random effects introduced in integrated circuits. PUFs usually are manufactured speciffically for this purpose, but in the last few years several proposals have developed PUFs from off-the-shelf components. These Intrinsic PUFs avoid modifications in the hardware and explore the low cost of adapting existing technologies. Graphical Processing Units (GPUs) present themselves as promising candidates for an Intrinsic PUF. GPUs are massively multi-processed systems originally built for graphical computing and more recently re-designed for general computing. These devices are distributed across a variety of systems and application environments, from computer vision platforms, to server clusters and home computers. Building PUFs with software-only strategies is a challenging problem, since a PUF must evaluate process variations without rendering system performance, characteristics which are easily done in hardware. In this work we present G-PUF, an intrinsic PUF technology running entirely on CUDA. The proposed solution maps the distribution of soft-errors in matrix multiplications when the GPU is running on adversarial conditions of overclock and undervoltage. The resulting error map will be unique to each GPU, and using a novel Challenge-Response Pair extraction algorithm, G-PUF is able to retrieve secure-keys or an device ID without disclosing information about the PUF randomness. The system was tested in real setups and requires no modifications whatsoever to an already operational GPU. G-PUF was capable of achieving upwards of 94.73% of reliability without any error correction code and can provide up to 253 unique Challenge-Response Pairs.Physically Unclonable Functions (PUFs) são primitivas de segurança que permitem a criação de identidades únicas e de chaves seguras. Sua segurança deriva das variações de processo intrínsecas à fabricação de chips de silício, e os diminutos efeitos aleatórios introduzidos em circuitos integrados. PUFs normalmente são fabricados especificamente para esse propósito, mas nos últimos anos várias propostas desenvolveram PUFs com componentes comuns. Esses PUFs Intrínsecos evitam modificações de hardware e exploram o baixo custo de adaptar tecnologias já existentes. Unidades de Processamento Gráfico (GPUs) se apresentam como candidatos promissores para um PUF Intrínseco. GPUs são sistemas massivamente multi-processados, desenvolvidos originalmente para computação gráfica e mais recentemente reprojetadas para computação genérica. Esses dispositivos estão distribuidos através de uma variedade de sistemas e aplicações, desde plataformas de visão computacional até clusters de servidores e computadores pessoais. Construir PUFs com estratégias puramente em software é um processo desafiador, já que um PUF deve avaliar variações de processo sem afetar a performance do sistema, características que são mais facilmente alcançáceis em hardware. Nesse trabalho, apresentamos o G-PUF, uma tecnologia de PUF Intrínseco rodando puramente em CUDA. A solução proposta mapeia a distribuição de soft-errors em multiplicações de matrizes, enquanto a GPU opera em condições adversas como overclock e subalimentação. O mapa de erros resultante será único para cada GPU, e utilizando um novo algorítmo para a extração de pares de desafio-resposta, o G-PUF consegue extrair chaves seguras e a identidade do dispositivo sem revelar informações sobre a sua aleatoriedade. O sistema foi testado em condições reais e não requer nenhuma modificação para um sistema de GPU já em operação. G-PUF foi capaz de alcançar uma reliability de até 94.73% sem utilizar nenhum código de correção de erros e pode prover até 253 pares de desafio-resposta únicos