Exploration of cyber-physical systems for GPGPU computer vision-based detection of biological viruses

This work presents a method for a computer vision-based detection of biological viruses in PAMONO sensor images and, related to this, methods to explore cyber-physical systems such as those consisting of the PAMONO sensor, the detection software, and processing hardware. The focus is especially on an exploration of Graphics Processing Units (GPU) hardware for “General-Purpose computing on Graphics Processing Units” (GPGPU) software and the targeted systems are high performance servers, desktop systems, mobile systems, and hand-held systems. The first problem that is addressed and solved in this work is to automatically detect biological viruses in PAMONO sensor images. PAMONO is short for “Plasmon Assisted Microscopy Of Nano-sized Objects”. The images from the PAMONO sensor are very challenging to process. The signal magnitude and spatial extension from attaching viruses is small, and it is not visible to the human eye on raw sensor images. Compared to the signal, the noise magnitude in the images is large, resulting in a small Signal-to-Noise Ratio (SNR). With the VirusDetectionCL method for a computer vision-based detection of viruses, presented in this work, an automatic detection and counting of individual viruses in PAMONO sensor images has been made possible. A data set of 4000 images can be evaluated in less than three minutes, whereas a manual evaluation by an expert can take up to two days. As the most important result, sensor signals with a median SNR of two can be handled. This enables the detection of particles down to 100 nm. The VirusDetectionCL method has been realized as a GPGPU software. The PAMONO sensor, the detection software, and the processing hardware form a so called cyber-physical system. For different PAMONO scenarios, e.g., using the PAMONO sensor in laboratories, hospitals, airports, and in mobile scenarios, one or more cyber-physical systems need to be explored. Depending on the particular use case, the demands toward the cyber-physical system differ. This leads to the second problem for which a solution is presented in this work: how can existing software with several degrees of freedom be automatically mapped to a selection of hardware architectures with several hardware configurations to fulfill the demands to the system? Answering this question is a difficult task. Especially, when several possibly conflicting objectives, e.g., quality of the results, energy consumption, and execution time have to be optimized. An extensive exploration of different software and hardware configurations is expensive and time-consuming. Sometimes it is not even possible, e.g., if the desired architecture is not yet available on the market or the design space is too big to be explored manually in reasonable time. A Pareto optimal selection of software parameters, hardware architectures, and hardware configurations has to be found. To achieve this, three parameter and design space exploration methods have been developed. These are named SOG-PSE, SOG-DSE, and MOGEA-DSE. MOGEA-DSE is the most advanced method of these three. It enables a multi-objective, energy-aware, measurement-based or simulation-based exploration of cyber-physical systems. This can be done in a hardware/software codesign manner. In addition, offloading of tasks to a server and approximate computing can be taken into account. With the simulation-based exploration, systems that do not exist can be explored. This is useful if a system should be equipped, e.g., with the next generation of GPUs. Such an exploration can reveal bottlenecks of the existing software before new GPUs are bought. With MOGEA-DSE the overall goal—to develop a method to automatically explore suitable cyber-physical systems for different PAMONO scenarios—could be achieved. As a result, a rapid, reliable detection and counting of viruses in PAMONO sensor data using high-performance, desktop, laptop, down to hand-held systems has been made possible. The fact that this could be achieved even for a small, hand-held device is the most important result of MOGEA-DSE. With the automatic parameter and design space exploration 84% energy could be saved on the hand-held device compared to a baseline measurement. At the same time, a speedup of four and an F-1 quality score of 0.995 could be obtained. The speedup enables live processing of the sensor data on the embedded system with a very high detection quality. With this result, viruses can be detected and counted on a mobile, hand-held device in less than three minutes and with real-time visualization of results. This opens up completely new possibilities for biological virus detection that were not possible before

Nova combinação de hardware e de software para veículos de desporto automóvel baseada no processamento directo de funções gráficas

Doutoramento em Engenharia EletrónicaThe main motivation for the work presented here began with previously conducted experiments with a programming concept at the time named "Macro". These experiments led to the conviction that it would be possible to build a system of engine control from scratch, which could eliminate many of the current problems of engine management systems in a direct and intrinsic way. It was also hoped that it would minimize the full range of software and hardware needed to make a final and fully functional system. Initially, this paper proposes to make a comprehensive survey of the state of the art in the specific area of software and corresponding hardware of automotive tools and automotive ECUs. Problems arising from such software will be identified, and it will be clear that practically all of these problems stem directly or indirectly from the fact that we continue to make comprehensive use of extremely long and complex "tool chains". Similarly, in the hardware, it will be argued that the problems stem from the extreme complexity and inter-dependency inside processor architectures. The conclusions are presented through an extensive list of "pitfalls" which will be thoroughly enumerated, identified and characterized. Solutions will also be proposed for the various current issues and for the implementation of these same solutions. All this final work will be part of a "proof-of-concept" system called "ECU2010". The central element of this system is the before mentioned "Macro" concept, which is an graphical block representing one of many operations required in a automotive system having arithmetic, logic, filtering, integration, multiplexing functions among others. The end result of the proposed work is a single tool, fully integrated, enabling the development and management of the entire system in one simple visual interface. Part of the presented result relies on a hardware platform fully adapted to the software, as well as enabling high flexibility and scalability in addition to using exactly the same technology for ECU, data logger and peripherals alike. Current systems rely on a mostly evolutionary path, only allowing online calibration of parameters, but never the online alteration of their own automotive functionality algorithms. By contrast, the system developed and described in this thesis had the advantage of following a "clean-slate" approach, whereby everything could be rethought globally. In the end, out of all the system characteristics, "LIVE-Prototyping" is the most relevant feature, allowing the adjustment of automotive algorithms (eg. Injection, ignition, lambda control, etc.) 100% online, keeping the engine constantly working, without ever having to stop or reboot to make such changes. This consequently eliminates any "turnaround delay" typically present in current automotive systems, thereby enhancing the efficiency and handling of such systems.A principal motivação para o trabalho que conduziu a esta tese residiu na constatação de que os actuais métodos de modelação de centralinas automóveis conduzem a significativos problemas de desenvolvimento e manutenção. Como resultado dessa constatação, o objectivo deste trabalho centrou-se no desenvolvimento de um conceito de arquitectura que rompe radicalmente com os modelos state-of-the-art e que assenta num conjunto de conceitos que vieram a ser designados de "Macro" e "Celular ECU". Com este modelo pretendeu-se simultaneamente minimizar a panóplia de software e de hardware necessários à obtenção de uma sistema funcional final. Inicialmente, esta tese propõem-se fazer um levantamento exaustivo do estado da arte na área específica do software e correspondente hardware das ferramentas e centralinas automóveis. Os problemas decorrentes de tal software serão identificados e, dessa identificação deverá ficar claro, que praticamente todos esses problemas têm origem directa ou indirecta no facto de se continuar a fazer um uso exaustivo de "tool chains" extremamente compridas e complexas. De forma semelhante, no hardware, os problemas têm origem na extrema complexidade e inter-dependência das arquitecturas dos processadores. As consequências distribuem-se por uma extensa lista de "pitfalls" que também serão exaustivamente enumeradas, identificadas e caracterizadas. São ainda propostas soluções para os diversos problemas actuais e correspondentes implementações dessas mesmas soluções. Todo este trabalho final faz parte de um sistema "proof-of-concept" designado "ECU2010". O elemento central deste sistema é o já referido conceito de “Macro”, que consiste num bloco gráfico que representa uma de muitas operações necessárias num sistema automóvel, como sejam funções aritméticas, lógicas, de filtragem, de integração, de multiplexagem, entre outras. O resultado final do trabalho proposto assenta numa única ferramenta, totalmente integrada que permite o desenvolvimento e gestão de todo o sistema de forma simples numa única interface visual. Parte do resultado apresentado assenta numa plataforma hardware totalmente adaptada ao software, bem como na elevada flexibilidade e escalabilidade, para além de permitir a utilização de exactamente a mesma tecnologia quer para a centralina, como para o datalogger e para os periféricos. Os sistemas actuais assentam num percurso maioritariamente evolutivo, apenas permitindo a calibração online de parâmetros, mas nunca a alteração online dos próprios algoritmos das funcionalidades automóveis. Pelo contrário, o sistema desenvolvido e descrito nesta tese apresenta a vantagem de seguir um "clean-slate approach", pelo que tudo pode ser globalmente repensado. No final e para além de todas as restantes características, o “LIVE-PROTOTYPING” é a funcionalidade mais relevante, ao permitir alterar algoritmos automóveis (ex: injecção, ignição, controlo lambda, etc.) de forma 100% online, mantendo o motor constantemente a trabalhar e sem nunca ter de o parar ou re-arrancar para efectuar tais alterações. Isto elimina consequentemente qualquer "turnaround delay" tipicamente presente em qualquer sistema automóvel actual, aumentando de forma significativa a eficiência global do sistema e da sua utilização