The Topology ToolKit

This system paper presents the Topology ToolKit (TTK), a software platform designed for topological data analysis in scientific visualization. TTK provides a unified, generic, efficient, and robust implementation of key algorithms for the topological analysis of scalar data, including: critical points, integral lines, persistence diagrams, persistence curves, merge trees, contour trees, Morse-Smale complexes, fiber surfaces, continuous scatterplots, Jacobi sets, Reeb spaces, and more. TTK is easily accessible to end users due to a tight integration with ParaView. It is also easily accessible to developers through a variety of bindings (Python, VTK/C++) for fast prototyping or through direct, dependence-free, C++, to ease integration into pre-existing complex systems. While developing TTK, we faced several algorithmic and software engineering challenges, which we document in this paper. In particular, we present an algorithm for the construction of a discrete gradient that complies to the critical points extracted in the piecewise-linear setting. This algorithm guarantees a combinatorial consistency across the topological abstractions supported by TTK, and importantly, a unified implementation of topological data simplification for multi-scale exploration and analysis. We also present a cached triangulation data structure, that supports time efficient and generic traversals, which self-adjusts its memory usage on demand for input simplicial meshes and which implicitly emulates a triangulation for regular grids with no memory overhead. Finally, we describe an original software architecture, which guarantees memory efficient and direct accesses to TTK features, while still allowing for researchers powerful and easy bindings and extensions. TTK is open source (BSD license) and its code, online documentation and video tutorials are available on TTK's website

Scalable Realtime Rendering and Interaction with Digital Surface Models of Landscapes and Cities

Interactive, realistic rendering of landscapes and cities differs substantially from classical terrain rendering. Due to the sheer size and detail of the data which need to be processed, realtime rendering (i.e. more than 25 images per second) is only feasible with level of detail (LOD) models. Even the design and implementation of efficient, automatic LOD generation is ambitious for such out-of-core datasets considering the large number of scales that are covered in a single view and the necessity to maintain screen-space accuracy for realistic representation. Moreover, users want to interact with the model based on semantic information which needs to be linked to the LOD model. In this thesis I present LOD schemes for the efficient rendering of 2.5d digital surface models (DSMs) and 3d point-clouds, a method for the automatic derivation of city models from raw DSMs, and an approach allowing semantic interaction with complex LOD models. The hierarchical LOD model for digital surface models is based on a quadtree of precomputed, simplified triangle mesh approximations. The rendering of the proposed model is proved to allow real-time rendering of very large and complex models with pixel-accurate details. Moreover, the necessary preprocessing is scalable and fast. For 3d point clouds, I introduce an LOD scheme based on an octree of hybrid plane-polygon representations. For each LOD, the algorithm detects planar regions in an adequately subsampled point cloud and models them as textured rectangles. The rendering of the resulting hybrid model is an order of magnitude faster than comparable point-based LOD schemes. To automatically derive a city model from a DSM, I propose a constrained mesh simplification. Apart from the geometric distance between simplified and original model, it evaluates constraints based on detected planar structures and their mutual topological relations. The resulting models are much less complex than the original DSM but still represent the characteristic building structures faithfully. Finally, I present a method to combine semantic information with complex geometric models. My approach links the semantic entities to the geometric entities on-the-fly via coarser proxy geometries which carry the semantic information. Thus, semantic information can be layered on top of complex LOD models without an explicit attribution step. All findings are supported by experimental results which demonstrate the practical applicability and efficiency of the methods

Evaluation of an efficient etack-RLE clustering concept for dynamically adaptive grids

This is the author accepted manuscript. The final version is available from the Society for Industrial and Applied Mathematics via the DOI in this record.Abstract. One approach to tackle the challenge of efficient implementations for parallel PDE simulations on dynamically changing grids is the usage of space-filling curves (SFC). While SFC algorithms possess advantageous properties such as low memory requirements and close-to-optimal partitioning approaches with linear complexity, they require efficient communication strategies for keeping and utilizing the connectivity information, in particular for dynamically changing grids. Our approach is to use a sparse communication graph to store the connectivity information and to transfer data block-wise. This permits efficient generation of multiple partitions per memory context (denoted by clustering) which - in combination with a run-length encoding (RLE) - directly leads to elegant solutions for shared, distributed and hybrid parallelization and allows cluster-based optimizations. While previous work focused on specific aspects, we present in this paper an overall compact summary of the stack-RLE clustering approach completed by aspects on the vertex-based communication that ease up understanding the approach. The central contribution of this work is the proof of suitability of the stack-RLE clustering approach for an efficient realization of different, relevant building blocks of Scientific Computing methodology and real-life CSE applications: We show 95% strong scalability for small-scale scalability benchmarks on 512 cores and weak scalability of over 90% on 8192 cores for finite-volume solvers and changing grid structure in every time step; optimizations of simulation data backends by writer tasks; comparisons of analytical benchmarks to analyze the adaptivity criteria; and a Tsunami simulation as a representative real-world showcase of a wave propagation for our approach which reduces the overall workload by 95% for parallel fully-adaptive mesh refinement and, based on a comparison with SFC-ordered regular grid cells, reduces the computation time by a factor of 7.6 with improved results and a factor of 62.2 with results of similar accuracy of buoy station dataThis work was partly supported by the German Research Foundation (DFG) as part of the Transregional Collaborative Research Centre “Invasive Computing” (SFB/TR 89)

Subdivision surface fitting to a dense mesh using ridges and umbilics

Fitting a sparse surface to approximate vast dense data is of interest for many applications: reverse engineering, recognition and compression, etc. The present work provides an approach to fit a Loop subdivision surface to a dense triangular mesh of arbitrary topology, whilst preserving and aligning the original features. The natural ridge-joined connectivity of umbilics and ridge-crossings is used as the connectivity of the control mesh for subdivision, so that the edges follow salient features on the surface. Furthermore, the chosen features and connectivity characterise the overall shape of the original mesh, since ridges capture extreme principal curvatures and ridges start and end at umbilics. A metric of Hausdorff distance including curvature vectors is proposed and implemented in a distance transform algorithm to construct the connectivity. Ridge-colour matching is introduced as a criterion for edge flipping to improve feature alignment. Several examples are provided to demonstrate the feature-preserving capability of the proposed approach

Diamond-based models for scientific visualization

Hierarchical spatial decompositions are a basic modeling tool in a variety of application domains including scientific visualization, finite element analysis and shape modeling and analysis. A popular class of such approaches is based on the regular simplex bisection operator, which bisects simplices (e.g. line segments, triangles, tetrahedra) along the midpoint of a predetermined edge. Regular simplex bisection produces adaptive simplicial meshes of high geometric quality, while simplifying the extraction of crack-free, or conforming, approximations to the original dataset. Efficient multiresolution representations for such models have been achieved in 2D and 3D by clustering sets of simplices sharing the same bisection edge into structures called diamonds. In this thesis, we introduce several diamond-based approaches for scientific visualization. We first formalize the notion of diamonds in arbitrary dimensions in terms of two related simplicial decompositions of hypercubes. This enables us to enumerate the vertices, simplices, parents and children of a diamond. In particular, we identify the number of simplices involved in conforming updates to be factorial in the dimension and group these into a linear number of subclusters of simplices that are generated simultaneously. The latter form the basis for a compact pointerless representation for conforming meshes generated by regular simplex bisection and for efficiently navigating the topological connectivity of these meshes. Secondly, we introduce the supercube as a high-level primitive on such nested meshes based on the atomic units within the underlying triangulation grid. We propose the use of supercubes to associate information with coherent subsets of the full hierarchy and demonstrate the effectiveness of such a representation for modeling multiresolution terrain and volumetric datasets. Next, we introduce Isodiamond Hierarchies, a general framework for spatial access structures on a hierarchy of diamonds that exploits the implicit hierarchical and geometric relationships of the diamond model. We use an isodiamond hierarchy to encode irregular updates to a multiresolution isosurface or interval volume in terms of regular updates to diamonds. Finally, we consider nested hypercubic meshes, such as quadtrees, octrees and their higher dimensional analogues, through the lens of diamond hierarchies. This allows us to determine the relationships involved in generating balanced hypercubic meshes and to propose a compact pointerless representation of such meshes. We also provide a local diamond-based triangulation algorithm to generate high-quality conforming simplicial meshes

New Models for High-Quality Surface Reconstruction and Rendering

The efficient reconstruction and artifact-free visualization of surfaces from measured real-world data is an important issue in various applications, such as medical and scientific visualization, quality control, and the media-related industry. The main contribution of this thesis is the development of the first efficient GPU-based reconstruction and visualization methods using trivariate splines, i.e., splines defined on tetrahedral partitions. Our methods show that these models are very well-suited for real-time reconstruction and high-quality visualizations of surfaces from volume data. We create a new quasi-interpolating operator which for the first time solves the problem of finding a globally C1-smooth quadratic spline approximating data and where no tetrahedra need to be further subdivided. In addition, we devise a new projection method for point sets arising from a sufficiently dense sampling of objects. Compared with existing approaches, high-quality surface triangulations can be generated with guaranteed numerical stability. Keywords. Piecewise polynomials; trivariate splines; quasi-interpolation; volume data; GPU ray casting; surface reconstruction; point set surface

New Models for High-Quality Surface Reconstruction and Rendering

The efficient reconstruction and artifact-free visualization of surfaces from measured real-world data is an important issue in various applications, such as medical and scientific visualization, quality control, and the media-related industry. The main contribution of this thesis is the development of the first efficient GPU-based reconstruction and visualization methods using trivariate splines, i.e., splines defined on tetrahedral partitions. Our methods show that these models are very well-suited for real-time reconstruction and high-quality visualizations of surfaces from volume data. We create a new quasi-interpolating operator which for the first time solves the problem of finding a globally C1-smooth quadratic spline approximating data and where no tetrahedra need to be further subdivided. In addition, we devise a new projection method for point sets arising from a sufficiently dense sampling of objects. Compared with existing approaches, high-quality surface triangulations can be generated with guaranteed numerical stability. Keywords. Piecewise polynomials; trivariate splines; quasi-interpolation; volume data; GPU ray casting; surface reconstruction; point set surface