Real-Time Dense Stereo Matching With ELAS on FPGA Accelerated Embedded Devices

For many applications in low-power real-time robotics, stereo cameras are the sensors of choice for depth perception as they are typically cheaper and more versatile than their active counterparts. Their biggest drawback, however, is that they do not directly sense depth maps; instead, these must be estimated through data-intensive processes. Therefore, appropriate algorithm selection plays an important role in achieving the desired performance characteristics. Motivated by applications in space and mobile robotics, we implement and evaluate a FPGA-accelerated adaptation of the ELAS algorithm. Despite offering one of the best trade-offs between efficiency and accuracy, ELAS has only been shown to run at 1.5-3 fps on a high-end CPU. Our system preserves all intriguing properties of the original algorithm, such as the slanted plane priors, but can achieve a frame rate of 47fps whilst consuming under 4W of power. Unlike previous FPGA based designs, we take advantage of both components on the CPU/FPGA System-on-Chip to showcase the strategy necessary to accelerate more complex and computationally diverse algorithms for such low power, real-time systems.Comment: 8 pages, 7 figures, 2 table

Polylidar3D -- Fast Polygon Extraction from 3D Data

Flat surfaces captured by 3D point clouds are often used for localization, mapping, and modeling. Dense point cloud processing has high computation and memory costs making low-dimensional representations of flat surfaces such as polygons desirable. We present Polylidar3D, a non-convex polygon extraction algorithm which takes as input unorganized 3D point clouds (e.g., LiDAR data), organized point clouds (e.g., range images), or user-provided meshes. Non-convex polygons represent flat surfaces in an environment with interior cutouts representing obstacles or holes. The Polylidar3D front-end transforms input data into a half-edge triangular mesh. This representation provides a common level of input data abstraction for subsequent back-end processing. The Polylidar3D back-end is composed of four core algorithms: mesh smoothing, dominant plane normal estimation, planar segment extraction, and finally polygon extraction. Polylidar3D is shown to be quite fast, making use of CPU multi-threading and GPU acceleration when available. We demonstrate Polylidar3D's versatility and speed with real-world datasets including aerial LiDAR point clouds for rooftop mapping, autonomous driving LiDAR point clouds for road surface detection, and RGBD cameras for indoor floor/wall detection. We also evaluate Polylidar3D on a challenging planar segmentation benchmark dataset. Results consistently show excellent speed and accuracy.Comment: 40 page

Haptic Interaction with 3D oriented point clouds on the GPU

Real-time point-based rendering and interaction with virtual objects is gaining popularity and importance as di�erent haptic devices and technologies increasingly provide the basis for realistic interaction. Haptic Interaction is being used for a wide range of applications such as medical training, remote robot operators, tactile displays and video games. Virtual object visualization and interaction using haptic devices is the main focus; this process involves several steps such as: Data Acquisition, Graphic Rendering, Haptic Interaction and Data Modi�cation. This work presents a framework for Haptic Interaction using the GPU as a hardware accelerator, and includes an approach for enabling the modi�cation of data during interaction. The results demonstrate the limits and capabilities of these techniques in the context of volume rendering for haptic applications. Also, the use of dynamic parallelism as a technique to scale the number of threads needed from the accelerator according to the interaction requirements is studied allowing the editing of data sets of up to one million points at interactive haptic frame rates

Primary arm array during directional solidification of a single-crystal binary alloy: Large-scale phase-field study

AbstractPrimary arm arrays formed during the directional solidification of a single-crystal binary alloy were investigated by performing large-scale phase-field simulations using the GPU supercomputer TSUBAME2.5 at Tokyo Institute of Technology. The primary arm array and spacing were investigated by Voronoi decomposition and Delaunay triangulation, respectively. It was concluded that a hexagonal array was dominant for both the dendrite and cell structures and that penta–hepta defects, which are typical defects in hexagonal patterns, were formed. The primary arms continuously moved such that the number of hexagons increased, and the distribution of primary arm spacing became uniform over time even after the number of primary arms was constant. The order of array was highest in the growth condition of the dendrite close to the cell-to-dendrite transition region. In addition, we proposed a realistic and accurate evaluation method of primary arm array by removing small sides from the Voronoi polygons

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

Real-time stress analysis of three-dimensional boundary element problems with continuously updating geometry

Computational design of mechanical components is an iterative process that involves multiple stress analysis runs; this can be time consuming and expensive. Significant improvements in the efficiency of this process can be made by increasing the level of interactivity. One approach is through real-time re-analysis of models with continuously updating geometry. In this work the boundary element method is used to realise this vision. Three primary areas need to be considered to accelerate the re-solution of boundary element problems. These are re-meshing the model, updating the boundary element system of equations and re-solution of the system. Once the initial model has been constructed and solved, the user may apply geometric perturbations to parts of the model. A new re-meshing algorithm accommodates these changes in geometry whilst retaining as much of the existing mesh as possible. This allows the majority of the previous boundary element system of equations to be re-used for the new analysis. Efficiency is achieved during re-integration by applying a reusable intrinsic sample point (RISP) integration scheme with a 64-bit single precision code. Parts of the boundary element system that have not been updated are retained by the re-analysis and integrals that multiply zero boundary conditions are suppressed. For models with fewer than 10,000 degrees of freedom, the re-integration algorithm performs up to five times faster than a standard integration scheme with less than 0.15% reduction in the L_2-norm accuracy of the solution vector. The method parallelises easily and an additional six times speed-up can be achieved on eight processors over the serial implementation. The performance of a range of direct, iterative and reduction based linear solvers have been compared for solving the boundary element system with the iterative generalised minimal residual (GMRES) solver providing the fastest convergence rate and the most accurate result. Further time savings are made by preconditioning the updated system with the LU decomposition of the original system. Using these techniques, near real-time analysis can be achieved for three-dimensional simulations; for two-dimensional models such real-time performance has already been demonstrated