SetCoLa: High‐Level Constraints for Graph Layout

Constraints enable flexible graph layout by combining the ease of automatic layout with customizations for a particular domain. However, constraint‐based layout often requires many individual constraints defined over specific nodes and node pairs. In addition to the effort of writing and maintaining a large number of similar constraints, such constraints are specific to the particular graph and thus cannot generalize to other graphs in the same domain. To facilitate the specification of customized and generalizable constraint layouts, we contribute SetCoLa: a domain‐specific language for specifying high‐level constraints relative to properties of the backing data. Users identify node sets based on data or graph properties and apply high‐level constraints within each set. Applying constraints to node sets rather than individual nodes reduces specification effort and facilitates reapplication of customized layouts across distinct graphs. We demonstrate the conciseness, generalizability, and expressiveness of SetCoLa on a series of real‐world examples from ecological networks, biological systems, and social networks.     

A Random Sampling O(n) Force‐calculation Algorithm for Graph Layouts

This paper proposes a linear‐time repulsive‐force‐calculation algorithm with sub‐linear auxiliary space requirements, achieving an asymptotic improvement over the Barnes‐Hut and Fast Multipole Method force‐calculation algorithms. The algorithm, named random vertex sampling (RVS), achieves its speed by updating a random sample of vertices at each iteration, each with a random sample of repulsive forces. This paper also proposes a combination algorithm that uses RVS to derive an initial layout and then applies Barnes‐Hut to refine the layout. An evaluation of RVS and the combination algorithm compares their speed and quality on 109 graphs against a Barnes‐Hut layout algorithm. The RVS algorithm performs up to 6.1 times faster on the tested graphs while maintaining comparable layout quality. The combination algorithm also performs faster than Barnes‐Hut, but produces layouts that are more symmetric than using RVS alone. Data and code: https://osf.io/nb7m8/     

Parallel Globally Consistent Normal Orientation of Raw Unorganized Point Clouds

A mandatory component for many point set algorithms is the availability of consistently oriented vertex‐normals (e.g. for surface reconstruction, feature detection, visualization). Previous orientation methods on meshes or raw point clouds do not consider a global context, are often based on unrealistic assumptions, or have extremely long computation times, making them unusable on real‐world data. We present a novel massively parallelized method to compute globally consistent oriented point normals for raw and unsorted point clouds. Built on the idea of graph‐based energy optimization, we create a complete kNN‐graph over the entire point cloud. A new weighted similarity criterion encodes the graph‐energy. To orient normals in a globally consistent way we perform a highly parallel greedy edge collapse, which merges similar parts of the graph and orients them consistently. We compare our method to current state‐of‐the‐art approaches and achieve speedups of up to two orders of magnitude. The achieved quality of normal orientation is on par or better than existing solutions, especially for real‐world noisy 3D scanned data.     

Dynamic Visibility‐Driven Molecular Surfaces

Molecular surface representations are an important tool for the visual analysis of molecular structure and function. In this paper, we present a novel method for the visualization of dynamic molecular surfaces based on the Gaussian model. In contrast to previous approaches, our technique does not rely on the construction of intermediate representations such as grids or triangulated surfaces. Instead, it operates entirely in image space, which enables us to exploit visibility information to efficiently skip unnecessary computations. With this visibility‐driven approach, we can visualize dynamic high‐quality surfaces for molecules consisting of millions of atoms. Our approach requires no preprocessing, allows for the interactive adjustment of all properties and parameters, and is significantly faster than previous approaches, while providing superior quality.     

Rendering and Extracting Extremal Features in 3D Fields

Visualizing and extracting three‐dimensional features is important for many computational science applications, each with their own feature definitions and data types. While some are simple to state and implement (e.g. isosurfaces), others require more complicated mathematics (e.g. multiple derivatives, curvature, eigenvectors, etc.). Correctly implementing mathematical definitions is difficult, so experimenting with new features requires substantial investments. Furthermore, traditional interpolants rarely support the necessary derivatives, and approximations can reduce numerical stability. Our new approach directly translates mathematical notation into practical visualization and feature extraction, with minimal mental and implementation overhead. Using a mathematically expressive domain‐specific language, Diderot, we compute direct volume renderings and particle‐based feature samplings for a range of mathematical features. Non‐expert users can experiment with feature definitions without any exposure to meshes, interpolants, derivative computation, etc. We demonstrate high‐quality results on notoriously difficult features, such as ridges and vortex cores, using working code simple enough to be presented in its entirety.     

DimSUM: Dimension and Scale Unifying Map for Visual Abstraction of DNA Origami Structures

We present a novel visualization concept for DNA origami structures that integrates a multitude of representations into a Dimension and Scale Unifying Map (DimSUM). This novel abstraction map provides means to analyze, smoothly transition between, and interact with many visual representations of the DNA origami structures in an effective way that was not possible before. DNA origami structures are nanoscale objects, which are challenging to model in silico. In our holistic approach we seamlessly combine three‐dimensional realistic shape models, two‐dimensional diagrammatic representations, and ordered alignments in one‐dimensional arrangements, with semantic transitions across many scales. To navigate through this large, two‐dimensional abstraction map we highlight locations that users frequently visit for certain tasks and datasets. Particularly interesting viewpoints can be explicitly saved to optimize the workflow. We have developed DimSUM together with domain scientists specialized in DNA nanotechnology. In the paper we discuss our design decisions for both the visualization and the interaction techniques. We demonstrate two practical use cases in which our approach increases the specialists’ understanding and improves their effectiveness in the analysis. Finally, we discuss the implications of our concept for the use of controlled abstraction in visualization in general.     

Ray Tracing Generalized Tube Primitives: Method and Applications

We present a general high‐performance technique for ray tracing generalized tube primitives. Our technique efficiently supports tube primitives with fixed and varying radii, general acyclic graph structures with bifurcations, and correct transparency with interior surface removal. Such tube primitives are widely used in scientific visualization to represent diffusion tensor imaging tractographies, neuron morphologies, and scalar or vector fields of 3D flow. We implement our approach within the OSPRay ray tracing framework, and evaluate it on a range of interactive visualization use cases of fixed‐ and varying‐radius streamlines, pathlines, complex neuron morphologies, and brain tractographies. Our proposed approach provides interactive, high‐quality rendering, with low memory overhead.     

Scalable Ray Tracing Using the Distributed FrameBuffer

Image‐ and data‐parallel rendering across multiple nodes on high‐performance computing systems is widely used in visualization to provide higher frame rates, support large data sets, and render data in situ. Specifically for in situ visualization, reducing bottlenecks incurred by the visualization and compositing is of key concern to reduce the overall simulation runtime. Moreover, prior algorithms have been designed to support either image‐ or data‐parallel rendering and impose restrictions on the data distribution, requiring different implementations for each configuration. In this paper, we introduce the Distributed FrameBuffer, an asynchronous image‐processing framework for multi‐node rendering. We demonstrate that our approach achieves performance superior to the state of the art for common use cases, while providing the flexibility to support a wide range of parallel rendering algorithms and data distributions. By building on this framework, we extend the open‐source ray tracing library OSPRay with a data‐distributed API, enabling its use in data‐distributed and in situ visualization applications.     

An Interactive Visualization System for Large Sets of Phase Space Trajectories

We introduce a visual analysis system with GPU acceleration techniques for large sets of trajectories from complex dynamical systems. The approach is based on an interactive Boolean combination of subsets into a Focus+Context phase‐space visualization. We achieve high performance through efficient bitwise algorithms utilizing runtime generated GPU shaders and kernels. This enables a higher level of interactivity for visualizing the large multivariate trajectory data. We explain how our design meets a set of carefully considered analysis requirements, provide performance results, and demonstrate utility through case studies with many‐particle simulation data from two application areas.     

Spatio‐Temporal Contours from Deep Volume Raycasting

We visualize contours for spatio‐temporal processes to indicate where and when non‐continuous changes occur or spatial bounds are encountered. All time steps are comprised densely in one visualization, with contours allowing to efficiently analyze processes in the data even in case of spatial or temporal overlap. Contours are determined on the basis of deep raycasting that collects samples across time and depth along each ray. For each sample along a ray, its closest neighbors from adjacent rays are identified, considering time, depth, and value in the process. Large distances are represented as contours in image space, using color to indicate temporal occurrence. This contour representation can easily be combined with volume rendering‐based techniques, providing both full spatial detail for individual time steps and an outline of the whole time series in one view. Our view‐dependent technique supports efficient progressive computation, and requires no prior assumptions regarding the shape or nature of processes in the data. We discuss and demonstrate the performance and utility of our approach via a variety of data sets, comparison and combination with an alternative technique, and feedback by a domain scientist.     

Multi-level graph layout on the GPU

This paper presents a new algorithm for force directed graph layout on the GPU. The algorithm, whose goal is to compute layouts accurately and quickly, has two contributions. The first contribution is proposing a general multi-level scheme, which is based on spectral partitioning. The second contribution is computing the layout on the GPU. Since the GPU requires a data parallel programming model, the challenge is devising a mapping of a naturally unstructured graph into a well-partitioned structured one. This is done by computing a balanced partitioning of a general graph. This algorithm provides a general multi-level scheme, which has the potential to be used not only for computation on the GPU, but also on emerging multi-core architectures. The algorithm manages to compute high quality layouts of large graphs in a fraction of the time required by existing algorithms of similar quality. An application for visualization of the topologies of ISP (Internet Service Provider) networks is presented.     

Automatic modeling of cluttered multi‐room floor plans from panoramic images

We present a novel and light‐weight approach to capture and reconstruct structured 3D models of multi‐room floor plans. Starting from a small set of registered panoramic images, we automatically generate a 3D layout of the rooms and of all the main objects inside. Such a 3D layout is directly suitable for use in a number of real‐world applications, such as guidance, location, routing, or content creation for security and energy management. Our novel pipeline introduces several contributions to indoor reconstruction from purely visual data. In particular, we automatically partition panoramic images in a connectivity graph, according to the visual layout of the rooms, and exploit this graph to support object recovery and rooms boundaries extraction. Moreover, we introduce a plane‐sweeping approach to jointly reason about the content of multiple images and solve the problem of object inference in a top‐down 2D domain. Finally, we combine these methods in a fully automated pipeline for creating a structured 3D model of a multi‐room floor plan and of the location and extent of clutter objects. These contribution make our pipeline able to handle cluttered scenes with complex geometry that are challenging to existing techniques. The effectiveness and performance of our approach is evaluated on both real‐world and synthetic models.     

Towards Glyphs for Uncertain Symmetric Second‐Order Tensors

Measured data often incorporates some amount of uncertainty, which is generally modeled as a distribution of possible samples. In this paper, we consider second‐order symmetric tensors with uncertainty. In the 3D case, this means the tensor data consists of 6 coefficients – uncertainty, however, is encoded by 21 coefficients assuming a multivariate Gaussian distribution as model. The high dimension makes the direct visualization of tensor data with uncertainty a difficult problem, which was until now unsolved. The contribution of this paper consists in the design of glyphs for uncertain second‐order symmetric tensors in 2D and 3D. The construction consists of a standard glyph for the mean tensor that is augmented by a scalar field that represents uncertainty. We show that this scalar field and therefore the displayed glyph encode the uncertainty comprehensively, i.e., there exists a bijective map between the glyph and the parameters of the distribution. Our approach can extend several classes of existing glyphs for symmetric tensors to additionally encode uncertainty and therefore provides a possible foundation for further uncertain tensor glyph design. For demonstration, we choose the well‐known superquadric glyphs, and we show that the uncertainty visualization satisfies all their design constraints.     

A framework for GPU‐accelerated exploration of massive time‐varying rectilinear scalar volumes

We introduce a novel flexible approach to spatiotemporal exploration of rectilinear scalar volumes. Our out‐of‐core representation, based on per‐frame levels of hierarchically tiled non‐redundant 3D grids, efficiently supports spatiotemporal random access and streaming to the GPU in compressed formats. A novel low‐bitrate codec able to store into fixed‐size pages a variable‐rate approximation based on sparse coding with learned dictionaries is exploited to meet stringent bandwidth constraint during time‐critical operations, while a near‐lossless representation is employed to support high‐quality static frame rendering. A flexible high‐speed GPU decoder and raycasting framework mixes and matches GPU kernels performing parallel object‐space and image‐space operations for seamless support, on fat and thin clients, of different exploration use cases, including animation and temporal browsing, dynamic exploration of single frames, and high‐quality snapshots generated from near‐lossless data. The quality and performance of our approach are demonstrated on large data sets with thousands of multi‐billion‐voxel frames.     

Analyzing Residue Surface Proximity to Interpret Molecular Dynamics

The surface of a molecule holds important information about the interaction behavior with other molecules. In dynamic folding or docking processes, residues of amino acids with different properties change their position within the molecule over time. The atoms of the residues that are accessible to the solvent can directly contribute to binding interactions, while residues buried within the molecular structure contribute to the stability of the molecule. Understanding patterns and causality of structural changes is important for experts in the pharmaceutical domain, e.g., in the process of drug design. We apply an iterative computation of the Solvent Accessible Surface in order to extract virtual layers of a molecule. The extraction allows to track the movement of residues in the body of the molecule, with respect to the distance of the residue to the surface or the core during dynamics simulations. We visualize the obtained layer information for the complete time span of the molecular dynamics simulation as a 2D‐map and for individual time‐steps as a 3D‐representation of the molecule. The data acquisition has been implemented alongside with further analysis functionality in a prototypical application, which is available to the public domain. We underline the feasibility of our approach with a study from the pharmaceutical domain, where our approach has been used for novel insights into the folding behavior of μ‐conotoxins.     

Visualizing Multidimensional Data with Order Statistics

Multidimensional data sets are common in many domains, and dimensionality reduction methods that determine a lower dimensional embedding are widely used for visualizing such data sets. This paper presents a novel method to project data onto a lower dimensional space by taking into account the order statistics of the individual data points, which are quantified by their depth or centrality in the overall set. Thus, in addition to conveying relative distances in the data, the proposed method also preserves the order statistics, which are often lost or misrepresented by existing visualization methods. The proposed method entails a modification of the optimization objective of conventional multidimensional scaling (MDS) by introducing a term that penalizes discrepancies between centrality structures in the original space and the embedding. We also introduce two strategies for visualizing lower dimensional embeddings of multidimensional data that takes advantage of the coherent representation of centrality provided by the proposed projection method. We demonstrate the effectiveness of our visualization with comparisons on different kinds of multidimensional data, including categorical and multimodal, from a variety of domains such as botany and health care.     

Visual Analysis of Charge Flow Networks for Complex Morphologies

In the field of organic electronics, understanding complex material morphologies and their role in efficient charge transport in solar cells is extremely important. Related processes are studied using the Ising model and Kinetic Monte Carlo simulations resulting in large ensembles of stochastic trajectories. Naive visualization of these trajectories, individually or as a whole, does not lead to new knowledge discovery through exploration. In this paper, we present novel visualization and exploration methods to analyze this complex dynamic data, which provide succinct and meaningful abstractions leading to scientific insights. We propose a morphology abstraction yielding a network composed of material pockets and the interfaces, which serves as backbone for the visualization of the charge diffusion. The trajectory network is created using a novel way of implicitly attracting the trajectories to the skeleton of the morphology relying on a relaxation process. Each individual trajectory is then represented as a connected sequence of nodes in the skeleton. The final network summarizes all of these sequences in a single aggregated network. We apply our method to three different morphologies and demonstrate its suitability for exploring this kind of data.     

Runtime Shader Simplification via Instant Search in Reduced Optimization Space

Traditional automatic shader simplification simplifies shaders in an offline process, which is typically carried out in a context‐oblivious manner or with the use of some example contexts, e.g., certain hardware platforms, scenes, and uniform parameters, etc. As a result, these pre‐simplified shaders may fail at adapting to runtime changes of the rendering context that were not considered in the simplification process. In this paper, we propose a new automatic shader simplification technique, which explores two key aspects of a runtime simplification framework: the optimization space and the instant search for optimal simplified shaders with runtime context. The proposed technique still requires a preprocess stage to process the original shader. However, instead of directly computing optimal simplified shaders, the proposed preprocess generates a reduced shader optimization space. In particular, two heuristic estimates of the quality and performance of simplified shaders are presented to group similar variants into representative ones, which serve as basic graph nodes of the simplification dependency graph (SDG), a new representation of the optimization space. At the runtime simplification stage, a parallel discrete optimization algorithm is employed to instantly search in the SDG for optimal simplified shaders. New data‐driven cost models are proposed to predict the runtime quality and performance of simplified shaders on the basis of data collected during runtime. Results show that the selected simplifications of complex shaders achieve 1.6 to 2.5 times speedup and still retain high rendering quality.     

Visual‐Interactive Preprocessing of Multivariate Time Series Data

Pre‐processing is a prerequisite to conduct effective and efficient downstream data analysis. Pre‐processing pipelines often require multiple routines to address data quality challenges and to bring the data into a usable form. For both the construction and the refinement of pre‐processing pipelines, human‐in‐the‐loop approaches are highly beneficial. This particularly applies to multivariate time series, a complex data type with multiple values developing over time. Due to the high specificity of this domain, it has not been subject to in‐depth research in visual analytics. We present a visual‐interactive approach for preprocessing multivariate time series data with the following aspects. Our approach supports analysts to carry out six core analysis tasks related to pre‐processing of multivariate time series. To support these tasks, we identify requirements to baseline toolkits that may help practitioners in their choice. We characterize the space of visualization designs for uncertainty‐aware pre‐processing and justify our decisions. Two usage scenarios demonstrate applicability of our approach, design choices, and uncertainty visualizations for the six analysis tasks. This work is one step towards strengthening the visual analytics support for data pre‐processing in general and for uncertainty‐aware pre‐processing of multivariate time series in particular.     

IGM‐Vis: Analyzing Intergalactic and Circumgalactic Medium Absorption Using Quasar Sightlines in a Cosmic Web Context

We introduce IGM‐Vis, a novel astrophysics visualization and data analysis application for investigating galaxies and the gas that surrounds them in context with their larger scale environment, the Cosmic Web. Environment is an important factor in the evolution of galaxies from actively forming stars to quiescent states with little, if any, discernible star formation activity. The gaseous halos of galaxies (the circumgalactic medium, or CGM) play a critical role in their evolution, because the gas necessary to fuel star formation and any gas expelled from widely observed galactic winds must encounter this interface region between galaxies and the intergalactic medium (IGM). We present a taxonomy of tasks typically employed in IGM/CGM studies informed by a survey of astrophysicists at various career levels, and demonstrate how these tasks are facilitated via the use of our visualization software. Finally, we evaluate the effectiveness of IGM‐Vis through two in‐depth use cases that depict real‐world analysis sessions that use IGM/CGM data.