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

Combinatorial Gradient Fields for 2D Images with Empirically Convergent Separatrices

This paper proposes an efficient probabilistic method that computes combinatorial gradient fields for two dimensional image data. In contrast to existing algorithms, this approach yields a geometric Morse-Smale complex that converges almost surely to its continuous counterpart when the image resolution is increased. This approach is motivated using basic ideas from probability theory and builds upon an algorithm from discrete Morse theory with a strong mathematical foundation. While a formal proof is only hinted at, we do provide a thorough numerical evaluation of our method and compare it to established algorithms.Comment: 17 pages, 7 figure

Density-equalizing maps for simply-connected open surfaces

In this paper, we are concerned with the problem of creating flattening maps of simply-connected open surfaces in $\mathbb{R}^3$. Using a natural principle of density diffusion in physics, we propose an effective algorithm for computing density-equalizing flattening maps with any prescribed density distribution. By varying the initial density distribution, a large variety of mappings with different properties can be achieved. For instance, area-preserving parameterizations of simply-connected open surfaces can be easily computed. Experimental results are presented to demonstrate the effectiveness of our proposed method. Applications to data visualization and surface remeshing are explored

A Phase Field Model for Continuous Clustering on Vector Fields

A new method for the simplification of flow fields is presented. It is based on continuous clustering. A well-known physical clustering model, the Cahn Hilliard model, which describes phase separation, is modified to reflect the properties of the data to be visualized. Clusters are defined implicitly as connected components of the positivity set of a density function. An evolution equation for this function is obtained as a suitable gradient flow of an underlying anisotropic energy functional. Here, time serves as the scale parameter. The evolution is characterized by a successive coarsening of patterns-the actual clustering-during which the underlying simulation data specifies preferable pattern boundaries. We introduce specific physical quantities in the simulation to control the shape, orientation and distribution of the clusters as a function of the underlying flow field. In addition, the model is expanded, involving elastic effects. In the early stages of the evolution shear layer type representation of the flow field can thereby be generated, whereas, for later stages, the distribution of clusters can be influenced. Furthermore, we incorporate upwind ideas to give the clusters an oriented drop-shaped appearance. Here, we discuss the applicability of this new type of approach mainly for flow fields, where the cluster energy penalizes cross streamline boundaries. However, the method also carries provisions for other fields as well. The clusters can be displayed directly as a flow texture. Alternatively, the clusters can be visualized by iconic representations, which are positioned by using a skeletonization algorithm.

Anisotropic Radial Layout for Visualizing Centrality and Structure in Graphs

This paper presents a novel method for layout of undirected graphs, where nodes (vertices) are constrained to lie on a set of nested, simple, closed curves. Such a layout is useful to simultaneously display the structural centrality and vertex distance information for graphs in many domains, including social networks. Closed curves are a more general constraint than the previously proposed circles, and afford our method more flexibility to preserve vertex relationships compared to existing radial layout methods. The proposed approach modifies the multidimensional scaling (MDS) stress to include the estimation of a vertex depth or centrality field as well as a term that penalizes discord between structural centrality of vertices and their alignment with this carefully estimated field. We also propose a visualization strategy for the proposed layout and demonstrate its effectiveness using three social network datasets.Comment: Appears in the Proceedings of the 25th International Symposium on Graph Drawing and Network Visualization (GD 2017

Multilevel Solvers for Unstructured Surface Meshes

Parameterization of unstructured surface meshes is of fundamental importance in many applications of digital geometry processing. Such parameterization approaches give rise to large and exceedingly ill-conditioned systems which are difficult or impossible to solve without the use of sophisticated multilevel preconditioning strategies. Since the underlying meshes are very fine to begin with, such multilevel preconditioners require mesh coarsening to build an appropriate hierarchy. In this paper we consider several strategies for the construction of hierarchies using ideas from mesh simplification algorithms used in the computer graphics literature. We introduce two novel hierarchy construction schemes and demonstrate their superior performance when used in conjunction with a multigrid preconditioner

Frequency Analysis of Gradient Estimators in Volume Rendering

Gradient information is used in volume rendering to classify and color samples along a ray. In this paper, we present an analysis of the theoretically ideal gradient estimator and compare it to some commonly used gradient estimators. A new method is presented to calculate the gradient at arbitrary sample positions, using the derivative of the interpolation filter as the basis for the new gradient filter. As an example, we will discuss the use of the derivative of the cubic spline. Comparisons with several other methods are demonstrated. Computational efficiency can be realized since parts of the interpolation computation can be leveraged in the gradient estimatio