Sensory processing and world modeling for an active ranging device

In this project, we studied world modeling and sensory processing for laser range data. World Model data representation and operation were defined. Sensory processing algorithms for point processing and linear feature detection were designed and implemented. The interface between world modeling and sensory processing in the Servo and Primitive levels was investigated and implemented. In the primitive level, linear features detectors for edges were also implemented, analyzed and compared. The existing world model representations is surveyed. Also presented is the design and implementation of the Y-frame model, a hierarchical world model. The interfaces between the world model module and the sensory processing module are discussed as well as the linear feature detectors that were designed and implemented

Data Science, Data Visualization, and Digital Twins

Real-time, web-based, and interactive visualisations are proven to be outstanding methodologies and tools in numerous fields when knowledge in sophisticated data science and visualisation techniques is available. The rationale for this is because modern data science analytical approaches like machine/deep learning or artificial intelligence, as well as digital twinning, promise to give data insights, enable informed decision-making, and facilitate rich interactions among stakeholders.The benefits of data visualisation, data science, and digital twinning technologies motivate this book, which exhibits and presents numerous developed and advanced data science and visualisation approaches. Chapters cover such topics as deep learning techniques, web and dashboard-based visualisations during the COVID pandemic, 3D modelling of trees for mobile communications, digital twinning in the mining industry, data science libraries, and potential areas of future data science development

Human motion analysis

EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Improving the Tractography Pipeline: on Evaluation, Segmentation, and Visualization

Recent advances in tractography allow for connectomes to be constructed in vivo. These have applications for example in brain tumor surgery and understanding of brain development and diseases. The large size of the data produced by these methods lead to a variety problems, including how to evaluate tractography outputs, development of faster processing algorithms for tractography and clustering, and the development of advanced visualization methods for verification and exploration. This thesis presents several advances in these fields. First, an evaluation is presented for the robustness to noise of multiple commonly used tractography algorithms. It employs a Monte–Carlo simulation of measurement noise on a constructed ground truth dataset. As a result of this evaluation, evidence for obustness of global tractography is found, and algorithmic sources of uncertainty are identified. The second contribution is a fast clustering algorithm for tractography data based on k–means and vector fields for representing the flow of each cluster. It is demonstrated that this algorithm can handle large tractography datasets due to its linear time and memory complexity, and that it can effectively integrate interrupted fibers that would be rejected as outliers by other algorithms. Furthermore, a visualization for the exploration of structural connectomes is presented. It uses illustrative rendering techniques for efficient presentation of connecting fiber bundles in context in anatomical space. Visual hints are employed to improve the perception of spatial relations. Finally, a visualization method with application to exploration and verification of probabilistic tractography is presented, which improves on the previously presented Fiber Stippling technique. It is demonstrated that the method is able to show multiple overlapping tracts in context, and correctly present crossing fiber configurations

Frequency Domain Decomposition of Digital Video Containing Multiple Moving Objects

Motion estimation has been dominated by time domain methods such as block matching and optical flow. However, these methods have problems with multiple moving objects in the video scene, moving backgrounds, noise, and fractional pixel/frame motion. This dissertation proposes a frequency domain method (FDM) that solves these problems. The methodology introduced here addresses multiple moving objects, with or without a moving background, 3-D frequency domain decomposition of digital video as the sum of locally translational (or, in the case of background, a globally translational motion), with high noise rejection. Additionally, via a version of the chirp-Z, fractional pixel/frame motion detection and quantification is accomplished. Furthermore, images of particular moving objects can be extracted and reconstructed from the frequency domain. Finally, this method can be integrated into a larger system to support motion analysis. The method presented here has been tested with synthetic data, realistic, high fidelity simulations, and actual data from established video archives to verify the claims made for the method, all presented here. In addition, a convincing comparison with an up-and-coming spatial domain method, incremental principal component pursuit (iPCP), is presented, where the FDM performs markedly better than its competition

Shape-based invariant features extraction for object recognition

International audienceThe emergence of new technologies enables generating large quantity of digital information including images; this leads to an increasing number of generated digital images. Therefore it appears a necessity for automatic systems for image retrieval. These systems consist of techniques used for query specification and re-trieval of images from an image collection. The most frequent and the most com-mon means for image retrieval is the indexing using textual keywords. But for some special application domains and face to the huge quantity of images, key-words are no more sufficient or unpractical. Moreover, images are rich in content; so in order to overcome these mentioned difficulties, some approaches are pro-posed based on visual features derived directly from the content of the image: these are the content-based image retrieval (CBIR) approaches. They allow users to search the desired image by specifying image queries: a query can be an exam-ple, a sketch or visual features (e.g., colour, texture and shape). Once the features have been defined and extracted, the retrieval becomes a task of measuring simi-larity between image features. An important property of these features is to be in-variant under various deformations that the observed image could undergo. In this chapter, we will present a number of existing methods for CBIR applica-tions. We will also describe some measures that are usually used for similarity measurement. At the end, and as an application example, we present a specific ap-proach, that we are developing, to illustrate the topic by providing experimental results

Image Processing and Pattern Recognition Applied to Soil Structure

This thesis represents a collaborative research between the Department of Electronics & Electrical Engineering and the Department of Civil Engineering, University of Glasgow. The project was initially aimed at development of some theories and techniques of image processing and pattern recognition for the study of soil microstructures. More specifically, the aim was to study the shapes, orientations, and arrangements of soil particles and voids (i.e. pores): these three are very important properties, which are used both for description, recognition and classification of soils, and also for studying the relationships between the soil structures and physical, chemical, geological, geographical, and environmental changes. The work presented here was based principally on a need for analysing the structure of soil as recorded in two-dimensional images which might be conventional photographs, optical micrographs, or electron-micrographs. In this thesis, first a brief review of image processing and pattern recognition and their previous application in the study of soil microstructures is given. Then a convex hull based shape description and classification for soil particles is presented. A new algorithm, SPCH, is proposed for finding the convex hull of either a binary object or a cluster of points in a plane. This algorithm is efficient and reliable. Features of pattern vectors for shape description and classification are obtained from the convex hull and the object. These features are invariant with respect to coordinate rotation, translation, and scaling. The objects can then be classified by any standard feature-space method: here minimum-distance classification was used. Next the orientation analysis of soil particles is described. A new method, Directed Vein, is proposed for the analysis. Another three methods: Convex Hull, Principal Components, and Moments, are also presented. Comparison of the four methods shows that the Directed Vein method appears the fastest; but it also has the special property of estimating an 'internal preferred orientation' whereas the other methods estimate an 'elongation direction'. Fourth, the roundness/sharpness analysis of soil particles is presented. Three new algorithms, referred to as the Centre, Gradient Centre, and Radius methods, all based on the Circular Hough Transform, are proposed. Two traditional Circular Hough Transform algorithms are presented as well. The three new methods were successfully applied to the measurement of the roundness (sharpness of comers) of two-dimensional particles. The five methods were compared from the points of view of memory requirement, speed, and accuracy; and the Radius method appears to be the best for the special topic of sharpness/roundness analysis. Finally the analysis and classification of aggregates of objects is introduced. A new method. Extended Linear Hough Transform, is proposed. In this method, the orientations and locations of the objects are mapped into extended Hough space. The arrangements of the objects within an aggregate are then determined by analysing the data distributions in this space. The aggregates can then be classified using a tree classifier. Taken together, the methods developed or tested here provide a useful toolkit for analysing the shapes, orientation, and aggregation of particles such as those seen in two-dimensional images of soil structure at various scales

Parallel patch-based volumetric reconstruction from images.

M. Sc. Eng. University of KwaZulu-Natal, Durban 2014.Three Dimensional (3D) reconstruction relates to the creating of 3D computer models from sets of Two Dimensional (2D) images. 3D reconstruction algorithms tend to have long execution times, meaning they are ill suited to real time 3D reconstruction tasks. This is a significant limitation which this dissertation attempts to address. Modern Graphics Processing Units (GPUs) have become fully programmable and have spawned the field known as General Purpose GPU (GPGPU) processing. Using this technology it is possible to of- fload certain types of tasks from the Central Processing Unit (CPU) to the GPU. GPGPU processing is designed for problems that have data parallelism. This means that a particular task can be split into many smaller tasks that can run in parallel, the results of which and are not dependent upon the order in which the tasks are completed. Therefore to properly make use of both CPU parallelism and GPGPU processing a 3D reconstruction algorithm with data parallelism was required. The selected algorithm was the Patch-Based Multi-View Stereopsis (PMVS) method, proposed and implemented by Yasutaka Furukawa and Jean Ponce. This algorithm uses small oriented rectangular patches to model a surface and is broken into four major steps: Feature detection; feature matching, expansion and filtering. The reconstructed patches are independent and as such the algorithm is data parallel. Some segments of the PMVS algorithm were programmed for GPGPU and others for CPU parallelism. Results show that the feature detection stage runs 10 times faster on the GPU than the equivalent CPU implementation. The patch creation and expansion stages also benefited from GPU implementation. Which brought an improvement in the execution time of two times for large images, and equivalent execution times for small images, when compared to the CPU implementation. These results show that the use of GPGPU and CPU parallelism can indeed improve the performance of this 3D reconstruction algorithm

Geometric algorithms for cavity detection on protein surfaces

Macromolecular structures such as proteins heavily empower cellular processes or functions. These biological functions result from interactions between proteins and peptides, catalytic substrates, nucleotides or even human-made chemicals. Thus, several interactions can be distinguished: protein-ligand, protein-protein, protein-DNA, and so on. Furthermore, those interactions only happen under chemical- and shapecomplementarity conditions, and usually take place in regions known as binding sites. Typically, a protein consists of four structural levels. The primary structure of a protein is made up of its amino acid sequences (or chains). Its secondary structure essentially comprises -helices and -sheets, which are sub-sequences (or sub-domains) of amino acids of the primary structure. Its tertiary structure results from the composition of sub-domains into domains, which represent the geometric shape of the protein. Finally, the quaternary structure of a protein results from the aggregate of two or more tertiary structures, usually known as a protein complex. This thesis fits in the scope of structure-based drug design and protein docking. Specifically, one addresses the fundamental problem of detecting and identifying protein cavities, which are often seen as tentative binding sites for ligands in protein-ligand interactions. In general, cavity prediction algorithms split into three main categories: energy-based, geometry-based, and evolution-based. Evolutionary methods build upon evolutionary sequence conservation estimates; that is, these methods allow us to detect functional sites through the computation of the evolutionary conservation of the positions of amino acids in proteins. Energy-based methods build upon the computation of interaction energies between protein and ligand atoms. In turn, geometry-based algorithms build upon the analysis of the geometric shape of the protein (i.e., its tertiary structure) to identify cavities. This thesis focuses on geometric methods. We introduce here three new geometric-based algorithms for protein cavity detection. The main contribution of this thesis lies in the use of computer graphics techniques in the analysis and recognition of cavities in proteins, much in the spirit of molecular graphics and modeling. As seen further ahead, these techniques include field-of-view (FoV), voxel ray casting, back-face culling, shape diameter functions, Morse theory, and critical points. The leading idea is to come up with protein shape segmentation, much like we commonly do in mesh segmentation in computer graphics. In practice, protein cavity algorithms are nothing more than segmentation algorithms designed for proteins.Estruturas macromoleculares tais como as proteínas potencializam processos ou funções celulares. Estas funções resultam das interações entre proteínas e peptídeos, substratos catalíticos, nucleótideos, ou até mesmo substâncias químicas produzidas pelo homem. Assim, há vários tipos de interacções: proteína-ligante, proteína-proteína, proteína-DNA e assim por diante. Além disso, estas interações geralmente ocorrem em regiões conhecidas como locais de ligação (binding sites, do inglês) e só acontecem sob condições de complementaridade química e de forma. É também importante referir que uma proteína pode ser estruturada em quatro níveis. A estrutura primária que consiste em sequências de aminoácidos (ou cadeias), a estrutura secundária que compreende essencialmente por hélices e folhas , que são subsequências (ou subdomínios) dos aminoácidos da estrutura primária, a estrutura terciária que resulta da composição de subdomínios em domínios, que por sua vez representa a forma geométrica da proteína, e por fim a estrutura quaternária que é o resultado da agregação de duas ou mais estruturas terciárias. Este último nível estrutural é frequentemente conhecido por um complexo proteico. Esta tese enquadra-se no âmbito da conceção de fármacos baseados em estrutura e no acoplamento de proteínas. Mais especificamente, aborda-se o problema fundamental da deteção e identificação de cavidades que são frequentemente vistos como possíveis locais de ligação (putative binding sites, do inglês) para os seus ligantes (ligands, do inglês). De forma geral, os algoritmos de identificação de cavidades dividem-se em três categorias principais: baseados em energia, geometria ou evolução. Os métodos evolutivos baseiam-se em estimativas de conservação das sequências evolucionárias. Isto é, estes métodos permitem detectar locais funcionais através do cálculo da conservação evolutiva das posições dos aminoácidos das proteínas. Em relação aos métodos baseados em energia estes baseiam-se no cálculo das energias de interação entre átomos da proteína e do ligante. Por fim, os algoritmos geométricos baseiam-se na análise da forma geométrica da proteína para identificar cavidades. Esta tese foca-se nos métodos geométricos. Apresentamos nesta tese três novos algoritmos geométricos para detecção de cavidades em proteínas. A principal contribuição desta tese está no uso de técnicas de computação gráfica na análise e reconhecimento de cavidades em proteínas, muito no espírito da modelação e visualização molecular. Como pode ser visto mais à frente, estas técnicas incluem o field-of-view (FoV), voxel ray casting, back-face culling, funções de diâmetro de forma, a teoria de Morse, e os pontos críticos. A ideia principal é segmentar a proteína, à semelhança do que acontece na segmentação de malhas em computação gráfica. Na prática, os algoritmos de detecção de cavidades não são nada mais que algoritmos de segmentação de proteínas