Geometry based visualization with OpenCL

Dissertação para obtenção do Grau de Mestre em Engenharia InformáticaThis work targets the design and implementation of an isosurface extraction solution capable of handling large datasets. The Marching Cubes algorithm is the method used to extract the isosurfaces. These are graphical representations of points with a constant value (e.g. matter density) within volumetric datasets. A very useful approach to visualize particular regions of such data. One of the major goals of this work is to get a significant performance improvement, compared to the currently available CPU solutions. The OpenCL framework is used to accelerate the solution. This framework is an open standard for parallel programming of heterogeneous systems recently proposed. Unlike previous programming frameworks for GPUs such as CUDA, with OpenCL the workload can be distributed among CPUs, GPUs, DSPs, and other similar microprocessors

Multiple dataset visualization (MDV) framework for scalar volume data

Many applications require comparative analysis of multiple datasets representing different samples, conditions, time instants, or views in order to develop a better understanding of the scientific problem/system under consideration. One effective approach for such analysis is visualization of the data. In this PhD thesis, we propose an innovative multiple dataset visualization (MDV) approach in which two or more datasets of a given type are rendered concurrently in the same visualization. MDV is an important concept for the cases where it is not possible to make an inference based on one dataset, and comparisons between many datasets are required to reveal cross-correlations among them. The proposed MDV framework, which deals with some fundamental issues that arise when several datasets are visualized together, follows a multithreaded architecture consisting of three core components, data preparation/loading, visualization and rendering. The visualization module - the major focus of this study, currently deals with isosurface extraction and texture-based rendering techniques. For isosurface extraction, our all-in-memory approach keeps datasets under consideration and the corresponding geometric data in the memory. Alternatively, the only-polygons- or points-in-memory only keeps the geometric data in memory. To address the issues related to storage and computation, we develop adaptive data coherency and multiresolution schemes. The inter-dataset coherency scheme exploits the similarities among datasets to approximate the portions of isosurfaces of datasets using the isosurface of one or more reference datasets whereas the intra/inter-dataset multiresolution scheme processes the selected portions of each data volume at varying levels of resolution. The graphics hardware-accelerated approaches adopted for MDV include volume clipping, isosurface extraction and volume rendering, which use 3D textures and advanced per fragment operations. With appropriate user-defined threshold criteria, we find that various MDV techniques maintain a linear time-N relationship, improve the geometry generation and rendering time, and increase the maximum N that can be handled (N: number of datasets). Finally, we justify the effectiveness and usefulness of the proposed MDV by visualizing 3D scalar data (representing electron density distributions in magnesium oxide and magnesium silicate) from parallel quantum mechanical simulation

Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform

Macromolecular surfaces are fundamental representations of their three-dimensional geometric shape. Accurate calculation of protein surfaces is of critical importance in the protein structural and functional studies including ligand-protein docking and virtual screening. In contrast to analytical or parametric representation of macromolecular surfaces, triangulated mesh surfaces have been proved to be easy to describe, visualize and manipulate by computer programs. Here, we develop a new algorithm of EDTSurf for generating three major macromolecular surfaces of van der Waals surface, solvent-accessible surface and molecular surface, using the technique of fast Euclidean Distance Transform (EDT). The triangulated surfaces are constructed directly from volumetric solids by a Vertex-Connected Marching Cube algorithm that forms triangles from grid points. Compared to the analytical result, the relative error of the surface calculations by EDTSurf is <2–4% depending on the grid resolution, which is 1.5–4 times lower than the methods in the literature; and yet, the algorithm is faster and costs less computer memory than the comparative methods. The improvements in both accuracy and speed of the macromolecular surface determination should make EDTSurf a useful tool for the detailed study of protein docking and structure predictions. Both source code and the executable program of EDTSurf are freely available at http://zhang.bioinformatics.ku.edu/EDTSurf

Topology verification for isosurface extraction

Journal ArticleThe broad goals of verifiable visualization rely on correct algorithmic implementations. We extend a framework for verification of isosurfacing implementations to check topological properties. Specifically, we use stratified Morse theory and digital topology to design algorithms which verify topological invariants. Our extended framework reveals unexpected behavior and coding mistakes in popular publicly available isosurface codes

Doctor of Philosophy

dissertationIn this dissertation, we advance the theory and practice of verifying visualization algorithms. We present techniques to assess visualization correctness through testing of important mathematical properties. Where applicable, these techniques allow us to distinguish whether anomalies in visualization features can be attributed to the underlying physical process or to artifacts from the implementation under verification. Such scientific scrutiny is at the heart of verifiable visualization - subjecting visualization algorithms to the same verification process that is used in other components of the scientific pipeline. The contributions of this dissertation are manifold. We derive the mathematical framework for the expected behavior of several visualization algorithms, and compare them to experimentally observed results in the selected codes. In the Computational Science & Engineering community CS&E, this technique is know as the Method of Manufactured Solution (MMS). We apply MMS to the verification of geometrical and topological properties of isosurface extraction algorithms, and direct volume rendering. We derive the convergence of geometrical properties of isosurface extraction techniques, such as function value and normals. For the verification of topological properties, we use stratified Morse theory and digital topology to design algorithms that verify topological invariants. In the case of volume rendering algorithms, we provide the expected discretization errors for three different error sources. The results of applying the MMS is another important contribution of this dissertation. We report unexpected behavior for almost all implementations tested. In some cases, we were able to find and fix bugs that prevented the correctness of the visualization algorithm. In particular, we address an almost 2 0 -year-old bug with the core disambiguation procedure of Marching Cubes 33, one of the first algorithms intended to preserve the topology of the trilinear interpolant. Finally, an important by-product of this work is a range of responses practitioners can expect to encounter with the visualization technique under verification

PAVEL: Decorative Patterns with Packed Volumetric Elements

Many real-world hand-crafted objects are decorated with elements that are packed onto the object's surface and deformed to cover it as much as possible. Examples are artisanal ceramics and metal jewelry. Inspired by these objects, we present a method to enrich surfaces with packed volumetric decorations. Our algorithm works by first determining the locations in which to add the decorative elements and then removing the non-physical overlap between them while preserving the decoration volume. For the placement, we support several strategies depending on the desired overall motif. To remove the overlap, we use an approach based on implicit deformable models creating the qualitative effect of plastic warping while avoiding expensive and hard-to-control physical simulations. Our decorative elements can be used to enhance virtual surfaces, as well as 3D-printed pieces, by assembling the decorations onto real-surfaces to obtain tangible reproductions.Comment: 11 page

09251 Abstracts Collection -- Scientific Visualization

From 06-14-2009 to 06-19-2009, the Dagstuhl Seminar 09251 ``Scientific Visualization \u27\u27 was held in Schloss Dagstuhl~--~Leibniz Center for Informatics. During the seminar, over 50 international participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general

Animating physical phenomena with embedded surface meshes

Accurate computational representations of highly deformable surfaces are indispensable in the fields of computer animation, medical simulation, computer vision, digital modeling, and computational physics. The focus of this dissertation is on the animation of physics-based phenomena with highly detailed deformable surfaces represented by triangle meshes. We first present results from an algorithm that generates continuum mechanics animations with intricate surface features. This method combines a finite element method with a tetrahedral mesh generator and a high resolution surface mesh, and it is orders of magnitude more efficient than previous approaches. Next, we present an efficient solution for the challenging problem of computing topological changes in detailed dynamic surface meshes. We then introduce a new physics-inspired surface tracking algorithm that is capable of preserving arbitrarily thin features and reproducing realistic fine-scale topological changes like Rayleigh-Plateau instabilities. This physics-inspired surface tracking technique also opens the door for a unique coupling between surficial finite element methods and volumetric finite difference methods, in order to simulate liquid surface tension phenomena more efficiently than any previous method. Due to its dramatic increase in computational resolution and efficiency, this method yielded the first computer simulations of a fully developed crown splash with droplet pinch off.Ph.D.Committee Chair: Turk, Greg; Committee Member: Essa, Irfan; Committee Member: Liu, Karen; Committee Member: Mucha, Peter J.; Committee Member: Rossignac, Jare

What's the Situation with Intelligent Mesh Generation: A Survey and Perspectives

Intelligent Mesh Generation (IMG) represents a novel and promising field of research, utilizing machine learning techniques to generate meshes. Despite its relative infancy, IMG has significantly broadened the adaptability and practicality of mesh generation techniques, delivering numerous breakthroughs and unveiling potential future pathways. However, a noticeable void exists in the contemporary literature concerning comprehensive surveys of IMG methods. This paper endeavors to fill this gap by providing a systematic and thorough survey of the current IMG landscape. With a focus on 113 preliminary IMG methods, we undertake a meticulous analysis from various angles, encompassing core algorithm techniques and their application scope, agent learning objectives, data types, targeted challenges, as well as advantages and limitations. We have curated and categorized the literature, proposing three unique taxonomies based on key techniques, output mesh unit elements, and relevant input data types. This paper also underscores several promising future research directions and challenges in IMG. To augment reader accessibility, a dedicated IMG project page is available at \url{https://github.com/xzb030/IMG_Survey}