Using high resolution displays for high resolution cardiac data

The ability to perform fast, accurate, high resolution visualization is fundamental to improving our understanding of anatomical data. As the volumes of data increase from improvements in scanning technology, the methods applied to rendering and visualization must evolve. In this paper we address the interactive display of data from high resolution MRI scanning of a rabbit heart and subsequent histological imaging. We describe a visualization environment involving a tiled LCD panel display wall and associated software which provide an interactive and intuitive user interface. The oView software is an OpenGL application which is written for the VRJuggler environment. This environment abstracts displays and devices away from the application itself, aiding portability between different systems, from desktop PCs to multi-tiled display walls. Portability between display walls has been demonstrated through its use on walls at both Leeds and Oxford Universities. We discuss important factors to be considered for interactive 2D display of large 3D datasets, including the use of intuitive input devices and level of detail aspects

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

Interactive ray tracing for volume visualization

Journal ArticleWe present a brute-force ray tracing system for interactive volume visualization, The system runs on a conventional (distributed) shared-memory multiprocessor machine. For each pixel we trace a ray through a volume to compute the color for that pixel. Although this method has high intrinsic computational cost, its simplicity and scalability make it ideal for large datasets on current high-end parallel systems

Molecular Surface Mesh Generation by Filtering Electron Density Map

Bioinformatics applied to macromolecules are now widely spread and in continuous expansion. In this context, representing external molecular surface such as the Van der Waals Surface or the Solvent Excluded Surface can be useful for several applications. We propose a fast and parameterizable algorithm giving good visual quality meshes representing molecular surfaces. It is obtained by isosurfacing a filtered electron density map. The density map is the result of the maximum of Gaussian functions placed around atom centers. This map is filtered by an ideal low-pass filter applied on the Fourier Transform of the density map. Applying the marching cubes algorithm on the inverse transform provides a mesh representation of the molecular surface

Fine-grained visualization pipelines and lazy functional languages

The pipeline model in visualization has evolved from a conceptual model of data processing into a widely used architecture for implementing visualization systems. In the process, a number of capabilities have been introduced, including streaming of data in chunks, distributed pipelines, and demand-driven processing. Visualization systems have invariably built on stateful programming technologies, and these capabilities have had to be implemented explicitly within the lower layers of a complex hierarchy of services. The good news for developers is that applications built on top of this hierarchy can access these capabilities without concern for how they are implemented. The bad news is that by freezing capabilities into low-level services expressive power and flexibility is lost. In this paper we express visualization systems in a programming language that more naturally supports this kind of processing model. Lazy functional languages support fine-grained demand-driven processing, a natural form of streaming, and pipeline-like function composition for assembling applications. The technology thus appears well suited to visualization applications. Using surface extraction algorithms as illustrative examples, and the lazy functional language Haskell, we argue the benefits of clear and concise expression combined with fine-grained, demand-driven computation. Just as visualization provides insight into data, functional abstraction provides new insight into visualization

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

Volume Ray casting with peak finding and differential sampling

Journal ArticleDirect volume rendering and isosurfacing are ubiquitous rendering techniques in scientific visualization, commonly employed in imaging 3D data from simulation and scan sources. Conventionally, these methods have been treated as separate modalities, necessitating different sampling strategies and rendering algorithms. In reality, an isosurface is a special case of a transfer function, namely a Dirac impulse at a given isovalue. However, artifact-free rendering of discrete isosurfaces in a volume rendering framework is an elusive goal, requiring either infinite sampling or smoothing of the transfer function. While preintegration approaches solve the most obvious deficiencies in handling sharp transfer functions, artifacts can still result, limiting classification. In this paper, we introduce a method for rendering such features by explicitly solving for isovalues within the volume rendering integral. In addition, we present a sampling strategy inspired by ray differentials that automatically matches the frequency of the image plane, resulting in fewer artifacts near the eye and better overall performance. These techniques exhibit clear advantages over standard uniform ray casting with and without preintegration, and allow for high-quality interactive volume rendering with sharp C0 transfer functions

Meshing Deforming Spacetime for Visualization and Analysis

We introduce a novel paradigm that simplifies the visualization and analysis of data that have a spatially/temporally varying frame of reference. The primary application driver is tokamak fusion plasma, where science variables (e.g., density and temperature) are interpolated in a complex magnetic field-line-following coordinate system. We also see a similar challenge in rotational fluid mechanics, cosmology, and Lagrangian ocean analysis; such physics implies a deforming spacetime and induces high complexity in volume rendering, isosurfacing, and feature tracking, among various visualization tasks. Without loss of generality, this paper proposes an algorithm to build a simplicial complex -- a tetrahedral mesh, for the deforming 3D spacetime derived from two 2D triangular meshes representing consecutive timesteps. Without introducing new nodes, the resulting mesh fills the gap between 2D meshes with tetrahedral cells while satisfying given constraints on how nodes connect between the two input meshes. In the algorithm we first divide the spacetime into smaller partitions to reduce complexity based on the input geometries and constraints. We then independently search for a feasible tessellation of each partition taking nonconvexity into consideration. We demonstrate multiple use cases for a simplified visualization analysis scheme with a synthetic case and fusion plasma applications

Interactive isosurface ray tracing of time-varying tetrahedral volumes

Journal ArticleAbstract- We describe a system for interactively rendering isosurfaces of tetrahedral finite-element scalar fields using coherent ray tracing techniques on the CPU. By employing state-of-the art methods in polygonal ray tracing, namely aggressive packet/frustum traversal of a bounding volume hierarchy, we can accomodate large and time-varying unstructured data. In conjunction with this efficiency structure, we introduce a novel technique for intersecting ray packets with tetrahedral primitives. Ray tracing is flexible, allowing for dynamic changes in isovalue and time step, visualization of multiple isosurfaces, shadows, and depth-peeling transparency effects. The resulting system offers the intuitive simplicity of isosurfacing, guaranteed-correct visual results, and ultimately a scalable, dynamic and consistently interactive solution for visualizing unstructured volumes