Identification and classification of off-vertex critical points for contour tree construction on unstructured meshes of hexahedra

The topology of isosurfaces changes at isovalues of critical points, making such points an important feature when building contour trees or Morse-Smale complexes. Hexahedral elements with linear interpolants can contain additional off-vertex critical points in element bodies and on element faces. Moreover, a point on the face of a hexahedron which is critical in the element-local context is not necessarily critical in the global context. In ‘`Exploring Scalar Fields Using Critical Isovalues’' Weber et al. introduce a method to determine whether critical points on faces are also critical in the global context, based on the gradient of the asymptotic decider in each element that shares the face. However, as defined, the method of Weber et al. contains an error, and can lead to incorrect results. In this work we correct the error

Flexible isosurfaces: Simplifying and displaying scalar topology using the contour tree

The contour tree is an abstraction of a scalar field that encodes the nesting relationships of isosurfaces. We show how to use the contour tree to represent individual contours of a scalar field, how to simplify both the contour tree and the topology of the scalar field, how to compute and store geometric properties for all possible contours in the contour tree, and how to use the simplified contour tree as an interface for exploratory visualization

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

Subdomain Aware Contour Trees and Contour Evolution in Time-Dependent Scalar Fields

For time-dependent scalar fields, one is often interested in topology changes of contours in time. In this paper, we focus on describing how contours split and merge over a certain time interval. Rather than attempting to describe all individual contour splitting and merging events, we focus on the simpler and therefore more tractable in practice problem: describing and querying the cumulative effect of the splitting and merging events over a user-specified time interval. Using our system one can, for example, find all contours at time tº that continue to two contours at time t¹ without hitting the boundary of the domain. For any such contour, there has to be a bifurcation happening to it somewhere between the two times, but, in addition to that, many other events may possibly happen without changing the cumulative outcome (e.g. merging with several contours born after tº or splitting off several contours that disappear before t¹). Our approach is flexible enough to enable other types of queries, if they can be cast as counting queries for numbers of connected components of intersections of contours with certain simply connected domains. Examples of such queries include finding contours with large life spans, contours avoiding certain subset of the domain over a given time interval or contours that continue to two at a later time and then merge back to one some time later. Experimental results show that our method can handle large 3D (2 space dimensions plus time) and 4D (3D+time) datasets. Both preprocessing and query algorithms can easily be parallelized

Contours in Visualization

This thesis studies the visualization of set collections either via or defines as the relations among contours. In the first part, dynamic Euler diagrams are used to communicate and improve semimanually the result of clustering methods which allow clusters to overlap arbitrarily. The contours of the Euler diagram are rendered as implicit surfaces called blobs in computer graphics. The interaction metaphor is the moving of items into or out of these blobs. The utility of the method is demonstrated on data arising from the analysis of gene expressions. The method works well for small datasets of up to one hundred items and few clusters. In the second part, these limitations are mitigated employing a GPU-based rendering of Euler diagrams and mixing textures and colors to resolve overlapping regions better. The GPU-based approach subdivides the screen into triangles on which it performs a contour interpolation, i.e. a fragment shader determines for each pixel which zones of an Euler diagram it belongs to. The rendering speed is thus increased to allow multiple hundred items. The method is applied to an example comparing different document clustering results. The contour tree compactly describes scalar field topology. From the viewpoint of graph drawing, it is a tree with attributes at vertices and optionally on edges. Standard tree drawing algorithms emphasize structural properties of the tree and neglect the attributes. Adapting popular graph drawing approaches to the problem of contour tree drawing it is found that they are unable to convey this information. Five aesthetic criteria for drawing contour trees are proposed and a novel algorithm for drawing contour trees in the plane that satisfies four of these criteria is presented. The implementation is fast and effective for contour tree sizes usually used in interactive systems and also produces readable pictures for larger trees. Dynamical models that explain the formation of spatial structures of RNA molecules have reached a complexity that requires novel visualization methods to analyze these model\''s validity. The fourth part of the thesis focuses on the visualization of so-called folding landscapes of a growing RNA molecule. Folding landscapes describe the energy of a molecule as a function of its spatial configuration; they are huge and high dimensional. Their most salient features are described by their so-called barrier tree -- a contour tree for discrete observation spaces. The changing folding landscapes of a growing RNA chain are visualized as an animation of the corresponding barrier tree sequence. The animation is created as an adaption of the foresight layout with tolerance algorithm for dynamic graph layout. The adaptation requires changes to the concept of supergraph and it layout. The thesis finishes with some thoughts on how these approaches can be combined and how the task the application should support can help inform the choice of visualization modality

The edge as a Lagrangian Coherent Structure in a high-dimensional state space

Dissipative dynamical systems characterised by two basins of attraction are found in many physical systems, notably in hydrodynamics where laminar and turbulent regimes can coexist. The state space of such systems is structured around a dividing manifold called the edge, which separates trajectories attracted by the laminar state from those reaching the turbulent state. We apply here concepts and tools from Lagrangian data analysis to investigate this edge manifold. This approach is carried out in the state space of automous arbitrarily high-dimensional dissipative systems, in which the edge manifold is re-interpreted as a Lagrangian Coherent Structure (LCS). Two different diagnostics, finite-time Lyapunov exponents and Lagrangian Descriptors, are used and compared with respect to their ability to identify the edge and to their scalability. Their properties are illustrated on several low-order models of subcritical transition of increasing dimension and complexity, as well on well-resolved simulations of the Navier-Stokes equations in the case of plane Couette flow. They allow for a mapping of the global structure of both the state space and the edge manifold based on quantitative information. Both diagnostics can also be used to generate efficient bisection algorithms to approach asymptotic edge states, which outperform classical edge tracking.Comment: 16 pages, 10 figures, Accepted in Phys. Rev. Researc

Comparative Uncertainty Visualization for High-Level Analysis of Scalar- and Vector-Valued Ensembles

With this thesis, I contribute to the research field of uncertainty visualization, considering parameter dependencies in multi valued fields and the uncertainty of automated data analysis. Like uncertainty visualization in general, both of these fields are becoming more and more important due to increasing computational power, growing importance and availability of complex models and collected data, and progress in artificial intelligence. I contribute in the following application areas: Uncertain Topology of Scalar Field Ensembles. The generalization of topology-based visualizations to multi valued data involves many challenges. An example is the comparative visualization of multiple contour trees, complicated by the random nature of prevalent contour tree layout algorithms. I present a novel approach for the comparative visualization of contour trees - the Fuzzy Contour Tree. Uncertain Topological Features in Time-Dependent Scalar Fields. Tracking features in time-dependent scalar fields is an active field of research, where most approaches rely on the comparison of consecutive time steps. I created a more holistic visualization for time-varying scalar field topology by adapting Fuzzy Contour Trees to the time-dependent setting. Uncertain Trajectories in Vector Field Ensembles. Visitation maps are an intuitive and well-known visualization of uncertain trajectories in vector field ensembles. For large ensembles, visitation maps are not applicable, or only with extensive time requirements. I developed Visitation Graphs, a new representation and data reduction method for vector field ensembles that can be calculated in situ and is an optimal basis for the efficient generation of visitation maps. This is accomplished by bringing forward calculation times to the pre-processing. Visually Supported Anomaly Detection in Cyber Security. Numerous cyber attacks and the increasing complexity of networks and their protection necessitate the application of automated data analysis in cyber security. Due to uncertainty in automated anomaly detection, the results need to be communicated to analysts to ensure appropriate reactions. I introduce a visualization system combining device readings and anomaly detection results: the Security in Process System. To further support analysts I developed an application agnostic framework that supports the integration of knowledge assistance and applied it to the Security in Process System. I present this Knowledge Rocks Framework, its application and the results of evaluations for both, the original and the knowledge assisted Security in Process System. For all presented systems, I provide implementation details, illustrations and applications

Evolution of galaxies due to self-excitation

These lectures will cover methods for studying the evolution of galaxies since their formation. Because the properties of a galaxy depend on its history, an understanding of galaxy evolution requires that we understand the dynamical interplay between all components. The first part will emphasize n-body simulation methods which minimize sampling noise. These techniques are based on harmonic expansions and scale linearly with the number of bodies, similar to Fourier transform solutions used in cosmological simulations. Although fast, until recently they were only efficiently used for small number of geometries and background profiles. These same techniques may be used to study the modes and response of a galaxy to an arbitrary perturbation. In particular, I will describe the modal spectra of stellar systems and role of damped modes which are generic to stellar systems in interactions and appear to play a significant role in determining the common structures that we see. The general development leads indirectly to guidelines for the number of particles necessary to adequately represent the gravitational field such that the modal spectrum is resolvable. I will then apply these same excitation to understanding the importance of noise to galaxy evolution.Comment: 24 pages, 7 figures, using Sussp.sty (included). Lectures presented at the NATO Advanced Study Institute, "The Restless Universe: Applications of Gravitational N-Body Dynamics to Planetary, Stellar and Galactic Systems," Blair Atholl, July 200