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Scientific Visualization

Scientific visualization, sometimes referred to as visual data analysis, uses the graphical representation of data as a means of gaining understanding and insight into the data. Scientific visualization research at SCI has focused on applications spanning computational fluid dynamics, medical imaging and analysis, and fire simulations. Research involves novel algorithm development to building tools and systems that assist in the comprehension of massive amounts of scientific data. In helping researchers to comprehend spatial and temporal relationships between data, interactive techniques provide better cues than noninteractive techniques; therefore, much of scientific visualization research focuses on better methods for visualization and rendering at interactive rates.


chuck

Charles Hansen

Volume Rendering
Ray Tracing
Graphics
pascucci

Valerio Pascucci

Topological Methods
Data Streaming
Big Data
chris

Chris Johnson

Volume Rendering
Uncertainty Visualization
mike

Mike Kirby

Uncertainty Visualization
ross

Ross Whitaker

Topological Methods
Uncertainty Visualization
 

Scientific Visualization Project Sites:


Publications in Visualization:




TOD-Tree: Task-Overlapped Direct send Tree Image Compositing for Hybrid MPI Parallelism
A. V. P. Grosset, M. Prasad, C. Christensen, A. Knoll, C. Hansen. In Eurographics Symposium on Parallel Graphics and Visualization (2015), Edited by C. Dachsbacher, P. Navrátil, 2015.

Modern supercomputers have very powerful multi-core CPUs. The programming model on these supercomputer is switching from pure MPI to MPI for inter-node communication, and shared memory and threads for intra-node communication. Consequently the bottleneck in most systems is no longer computation but communication between nodes. In this paper, we present a new compositing algorithm for hybrid MPI parallelism that focuses on communication avoidance and overlapping communication with computation at the expense of evenly balancing the workload. The algorithm has three stages: a direct send stage where nodes are arranged in groups and exchange regions of an image, followed by a tree compositing stage and a gather stage. We compare our algorithm with radix-k and binary-swap from the IceT library in a hybrid OpenMP/MPI setting, show strong scaling results and explain how we generally achieve better performance than these two algorithms.



GPU Surface Extraction with the Closest Point Embedding
M. Kim, C.D. Hansen. In Proceedings of IS&T/SPIE Visualization and Data Analysis, 2015, February, 2015.

Isosurface extraction is a fundamental technique used for both surface reconstruction and mesh generation. One method to extract well-formed isosurfaces is a particle system; unfortunately, particle systems can be slow. In this paper, we introduce an enhanced parallel particle system that uses the closest point embedding as the surface representation to speedup the particle system for isosurface extraction. The closest point embedding is used in the Closest Point Method (CPM), a technique that uses a standard three dimensional numerical PDE solver on two dimensional embedded surfaces. To fully take advantage of the closest point embedding, it is coupled with a Barnes-Hut tree code on the GPU. This new technique produces well-formed, conformal unstructured triangular and tetrahedral meshes from labeled multi-material volume datasets. Further, this new parallel implementation of the particle system is faster than any known methods for conformal multi-material mesh extraction. The resulting speed-ups gained in this implementation can reduce the time from labeled data to mesh from hours to minutes and benefits users, such as bioengineers, who employ triangular and tetrahedral meshes.

Keywords: scalar field methods, GPGPU, curvature based, scientific visualization



Surface Flow Visualization using the Closest Point Embedding
M. Kim, C.D. Hansen. In 2015 IEEE Pacific Visualization Symposium, April, 2015.

In this paper, we introduce a novel flow visualization technique for arbitrary surfaces. This new technique utilizes the closest point embedding to represent the surface, which allows for accurate particle advection on the surface as well as supports the unsteady flow line integral convolution (UFLIC) technique on the surface. This global approach is faster than previous parameterization techniques and prevents the visual artifacts associated with image-based approaches.

Keywords: vector field, flow visualization



Topological and Statistical Methods for Complex Data,
Subtitled “Tackling Large-Scale, High-Dimensional, and Multivariate Data Spaces,” J. Bennett, F. Vivodtzev, V. Pascucci (Eds.). Mathematics and Visualization, 2015.
ISBN: 978-3-662-44899-1

This book contains papers presented at the Workshop on the Analysis of Large-scale,
High-Dimensional, and Multi-Variate Data Using Topology and Statistics, held in Le Barp,
France, June 2013. It features the work of some of the most prominent and recognized
leaders in the field who examine challenges as well as detail solutions to the analysis of
extreme scale data.
The book presents new methods that leverage the mutual strengths of both topological
and statistical techniques to support the management, analysis, and visualization
of complex data. It covers both theory and application and provides readers with an
overview of important key concepts and the latest research trends.
Coverage in the book includes multi-variate and/or high-dimensional analysis techniques,
feature-based statistical methods, combinatorial algorithms, scalable statistics algorithms,
scalar and vector field topology, and multi-scale representations. In addition, the book
details algorithms that are broadly applicable and can be used by application scientists to
glean insight from a wide range of complex data sets.



Overview and State-of-the-Art of Uncertainty Visualization
G.P. Bonneau, H.C. Hege, C.R. Johnson, M.M. Oliveira, K. Potter, P. Rheingans, T. Schultz. In Scientific Visualization: Uncertainty, Multifield, Biomedical, and Scalable Visualization, Mathematics and Visualization, Ch. 1, Edited by M. Chen and H. Hagen and C.D. Hansen and C.R. Johnson and A. Kauffman, Springer-Verlag, pp. 3--27. 2014.
ISBN: 978-1-4471-6496-8
ISSN: 1612-3786
DOI: 10.1007/978-1-4471-6497-5_1

The goal of visualization is to effectively and accurately communicate data. Visualization research has often overlooked the errors and uncertainty which accompany the scientific process and describe key characteristics used to fully understand the data. The lack of these representations can be attributed, in part, to the inherent difficulty in defining, characterizing, and controlling this uncertainty, and in part, to the difficulty in including additional visual metaphors in a well designed, potent display. However, the exclusion of this information cripples the use of visualization as a decision making tool due to the fact that the display is no longer a true representation of the data. This systematic omission of uncertainty commands fundamental research within the visualization community to address, integrate, and expect uncertainty information. In this chapter, we outline sources and models of uncertainty, give an overview of the state-of-the-art, provide general guidelines, outline small exemplary applications, and finally, discuss open problems in uncertainty visualization.



Data-Parallel Halo Finding with Variable Linking Lengths
W. Widanagamaachchi, P.-T. Bremer, C. Sewell, L.-T. Lo; J. Ahrens, V. Pascucci. In Proceedings of the 2014 IEEE 4th Symposium on Large Data Analysis and Visualization (LDAV), pp. 27--34. November, 2014.

State-of-the-art cosmological simulations regularly contain billions of particles, providing scientists the opportunity to study the evolution of the Universe in great detail. However, the rate at which these simulations generate data severely taxes existing analysis techniques. Therefore, developing new scalable alternatives is essential for continued scientific progress. Here, we present a dataparallel, friends-of-friends halo finding algorithm that provides unprecedented flexibility in the analysis by extracting multiple linking lengths. Even for a single linking length, it is as fast as the existing techniques, and is portable to multi-threaded many-core systems as well as co-processing resources. Our system is implemented using PISTON and is coupled to an interactive analysis environment used to study halos at different linking lengths and track their evolution over time.



Towards Paint and Click: Unified Interactions for Image Boundaries
SCI Technical Report, B. Summa, A.A. Gooch, G. Scorzelli, V. Pascucci. No. UUSCI-2014-004, SCI Institute, University of Utah, December, 2014.

Image boundaries are a fundamental component of many interactive digital photography techniques, enabling applications such as segmentation, panoramas, and seamless image composition. Interactions for image boundaries often rely on two complimentary but separate approaches: editing via painting or clicking constraints. In this work, we provide a novel, unified approach for interactive editing of pairwise image boundaries that combines the ease of painting with the direct control of constraints. Rather than a sequential coupling, this new formulation allows full use of both interactions simultaneously, giving users unprecedented flexibility for fast boundary editing. To enable this new approach, we provide technical advancements. In particular, we detail a reformulation of image boundaries as a problem of finding cycles, expanding and correcting limitations of the previous work. Our new formulation provides boundary solutions for painted regions with performance on par with state-of-the-art specialized, paint-only techniques. In addition, we provide instantaneous exploration of the boundary solution space with user constraints. Furthermore, we show how to increase performance and decrease memory consumption through novel strategies and/or optional approximations. Finally, we provide examples of common graphics applications impacted by our new approach.



In-situ feature extraction of large scale combustion simulations using segmented merge trees
A.G. Landge, V. Pascucci, A. Gyulassy, J.C. Bennett, H. Kolla, J. Chen, P.-T. Bremer. In Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC 2014), New Orleans, Louisana, IEEE Press, Piscataway, NJ, USA pp. 1020--1031. 2014.
ISBN: 978-1-4799-5500-8
DOI: 10.1109/SC.2014.88

The ever increasing amount of data generated by scientific simulations coupled with system I/O constraints are fueling a need for in-situ analysis techniques. Of particular interest are approaches that produce reduced data representations while maintaining the ability to redefine, extract, and study features in a post-process to obtain scientific insights.

This paper presents two variants of in-situ feature extraction techniques using segmented merge trees, which encode a wide range of threshold based features. The first approach is a fast, low communication cost technique that generates an exact solution but has limited scalability. The second is a scalable, local approximation that nevertheless is guaranteed to correctly extract all features up to a predefined size. We demonstrate both variants using some of the largest combustion simulations available on leadership class supercomputers. Our approach allows state-of-the-art, feature-based analysis to be performed in-situ at significantly higher frequency than currently possible and with negligible impact on the overall simulation runtime.



Efficient I/O and storage of adaptive-resolution data
S. Kumar, J. Edwards, P.-T. Bremer, A. Knoll, C. Christensen, V. Vishwanath, P. Carns, J.A. Schmidt, V. Pascucci. In Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, IEEE Press, pp. 413--423. 2014.
DOI: 10.1109/SC.2014.39

We present an efficient, flexible, adaptive-resolution I/O framework that is suitable for both uniform and Adaptive Mesh Refinement (AMR) simulations. In an AMR setting, current solutions typically represent each resolution level as an independent grid which often results in inefficient storage and performance. Our technique coalesces domain data into a unified, multiresolution representation with fast, spatially aggregated I/O. Furthermore, our framework easily extends to importance-driven storage of uniform grids, for example, by storing regions of interest at full resolution and nonessential regions at lower resolution for visualization or analysis. Our framework, which is an extension of the PIDX framework, achieves state of the art disk usage and I/O performance regardless of resolution of the data, regions of interest, and the number of processes that generated the data. We demonstrate the scalability and efficiency of our framework using the Uintah and S3D large-scale combustion codes on the Mira and Edison supercomputers.



Robust Detection of Singularities in Vector Fields
H. Bhatia, A. Gyulassy, H. Wang, P.-T. Bremer, V. Pascucci . In Topological Methods in Data Analysis and Visualization III, Mathematics and Visualization, Springer International Publishing, pp. 3--18. March, 2014.
DOI: 10.1007/978-3-319-04099-8_1

Recent advances in computational science enable the creation of massive datasets of ever increasing resolution and complexity. Dealing effectively with such data requires new analysis techniques that are provably robust and that generate reproducible results on any machine. In this context, combinatorial methods become particularly attractive, as they are not sensitive to numerical instabilities or the details of a particular implementation. We introduce a robust method for detecting singularities in vector fields. We establish, in combinatorial terms, necessary and sufficient conditions for the existence of a critical point in a cell of a simplicial mesh for a large class of interpolation functions. These conditions are entirely local and lead to a provably consistent and practical algorithm to identify cells containing singularities.



Scientific Visualization: Uncertainty, Multifield, Biomedical, and Scalable Visualization,
C.D. Hansen, M. Chen, C.R. Johnson, A.E. Kaufman, H. Hagen (Eds.). Mathematics and Visualization, Springer, 2014.
ISBN: 978-1-4471-6496-8



Surface boxplots
M.G. Genton, C.R. Johnson, K. Potter, G. Stenchikov, Y. Sun. In Stat Journal, Vol. 3, No. 1, pp. 1--11. 2014.

In this paper, we introduce a surface boxplot as a tool for visualization and exploratory analysis of samples of images. First, we use the notion of volume depth to order the images viewed as surfaces. In particular, we define the median image. We use an exact and fast algorithm for the ranking of the images. This allows us to detect potential outlying images that often contain interesting features not present in most of the images. Second, we build a graphical tool to visualize the surface boxplot and its various characteristics. A graph and histogram of the volume depth values allow us to identify images of interest. The code is available in the supporting information of this paper. We apply our surface boxplot to a sample of brain images and to a sample of climate model outputs.



Multivariate Volume Visualization through Dynamic Projections
Shusen Liu, Bei Wang, J.J. Thiagarajan, P.-T. Bremer, V. Pascucci. In Proceedings of the IEEE Symposium on Large Data Analysis and Visualization (LDAV), 2014.

We propose a multivariate volume visualization framework that tightly couples dynamic projections with a high-dimensional transfer function design for interactive volume visualization. We assume that the complex, high-dimensional data in the attribute space can be well-represented through a collection of low-dimensional linear subspaces, and embed the data points in a variety of 2D views created as projections onto these subspaces. Through dynamic projections, we present animated transitions between different views to help the user navigate and explore the attribute space for effective transfer function design. Our framework not only provides a more intuitive understanding of the attribute space but also allows the design of the transfer function under multiple dynamic views, which is more flexible than being restricted to a single static view of the data. For large volumetric datasets, we maintain interactivity during the transfer function design via intelligent sampling and scalable clustering. Using examples in combustion and climate simulations, we demonstrate how our framework can be used to visualize interesting structures in the volumetric space.



Visual Exploration of High-Dimensional Data: Subspace Analysis through Dynamic Projections
SCI Technical Report, Shusen Liu, Bei Wang, J.J. Thiagarajan, P.-T. Bremer, V. Pascucci. No. UUSCI-2014-003, SCI Institute, University of Utah, 2014.

Understanding high-dimensional data is rapidly becoming a central challenge in many areas of science and engineering. Most current techniques either rely on manifold learning based techniques which typically create a single embedding of the data or on subspace selection to find subsets of the original attributes that highlight the structure. However, the former creates a single, difficult-to-interpret view and assumes the data to be drawn from a single manifold, while the latter is limited to axis-aligned projections with restrictive viewing angles. Instead, we introduce ideas based on subspace clustering that can faithfully represent more complex data than the axis-aligned projections, yet do not assume the data to lie on a single manifold. In particular, subspace clustering assumes that the data can be represented by a union of low-dimensional subspaces, which can subsequently be used for analysis and visualization. In this paper, we introduce new techniques to reliably estimate both the intrinsic dimension and the linear basis of a mixture of subspaces extracted through subspace clustering. We show that the resulting bases represent the high-dimensional structures more reliably than traditional approaches. Subsequently, we use the bases to define different “viewpoints”, i.e., different projections onto pairs of basis vectors, from which to visualize the data. While more intuitive than non-linear projections, interpreting linear subspaces in terms of the original dimensions can still be challenging. To address this problem, we present new, animated transitions between different views to help the user navigate and explore the high-dimensional space. More specifically, we introduce the view transition graph which contains nodes for each subspace viewpoint and edges for potential transition between views. The transition graph enables users to explore both the structure within a subspace and the relations between different subspaces, for better understanding of the data. Using a number of case studies on well-know reference datasets, we demonstrate that the interactive exploration through such dynamic projections provides additional insights not readily available from existing tools.

Keywords: High-dimensional data, Subspace, Dynamic projection



Distortion-Guided Structure-Driven Interactive Exploration of High-Dimensional Data
S. Liu, Bei Wang, P.-T. Bremer, V. Pascucci. In Computer Graphics Forum (CGF) (Proceedings of EuroVis), Vol. 33, No. 3, pp. 101--110. 2014.

Dimension reduction techniques are essential for feature selection and feature extraction of complex high-dimensional data. These techniques, which construct low-dimensional representations of data, are typically geometrically motivated, computationally efficient and approximately preserve certain structural properties of the data. However, they are often used as black box solutions in data exploration and their results can be difficult to interpret. To assess the quality of these results, quality measures, such as co-ranking [ LV09 ], have been proposed to quantify structural distortions that occur between high-dimensional and low-dimensional data representations. Such measures could be evaluated and visualized point-wise to further highlight erroneous regions [ MLGH13 ]. In this work, we provide an interactive visualization framework for exploring high-dimensional data via its two-dimensional embeddings obtained from dimension reduction, using a rich set of user interactions. We ask the following question: what new insights do we obtain regarding the structure of the data, with interactive manipulations of its embeddings in the visual space? We augment the two-dimensional embeddings with structural abstrac- tions obtained from hierarchical clusterings, to help users navigate and manipulate subsets of the data. We use point-wise distortion measures to highlight interesting regions in the domain, and further to guide our selection of the appropriate level of clusterings that are aligned with the regions of interest. Under the static setting, point-wise distortions indicate the level of structural uncertainty within the embeddings. Under the dynamic setting, on-the-fly updates of point-wise distortions due to data movement and data deletion reflect structural relations among different parts of the data, which may lead to new and valuable insights.



Overview of New Tools to Perform Safety Analysis: BWR Station Black Out Test Case
D. Mandelli, C. Smith, T. Riley, J. Nielsen, J. Schroeder, C. Rabiti, A. Alfonsi, J. Cogliati, R. Kinoshita, V. Pascucci, Bei Wang, D. Maljovec. In Proceedings of the Probabilistic Safety Assessment & Management conference (PSAM), 2014.

The existing fleet of nuclear power plants is in the process of extending its lifetime and increasing the power generated from these plants via power uprates. In order to evaluate the impacts of these two factors on the safety of the plant, the Risk Informed Safety Margin Characterization project aims to provide insights to decision makers through a series of simulations of the plant dynamics for different initial conditions (e.g., probabilistic analysis and uncertainty quantification). This paper focuses on the impacts of power uprate on the safety margin of a boiling water reactor for a station black-out event. Analysis is performed by using a combination of thermal-hydraulic codes and a stochastic analysis tool currently under development at the Idaho National Laboratory, i.e. RAVEN. We employed both classical statistical tools, i.e. Monte-Carlo, and more advanced machine learning based algorithms to perform uncertainty quantification in order to quantify changes in system performance and limitations as a consequence of power uprate. We also employed advanced data analysis and visualization tools that helped us to correlate simulation outcomes such as maximum core temperature with a set of input uncertain parameters. Results obtained give a detailed investigation of the issues associated with a plant power uprate including the effects of station black-out accident scenarios. We were able to quantify how the timing of specific events was impacted by a higher nominal reactor core power. Such safety insights can provide useful information to the decision makers to perform risk-informed margins management.



Analyzing Simulation-Based PRA Data Through Clustering: a BWR Station Blackout Case Study
D. Maljovec, S. Liu, Bei Wang, V. Pascucci, P.-T. Bremer, D. Mandelli, C. Smith. In Proceedings of the Probabilistic Safety Assessment & Management conference (PSAM), 2014.

Dynamic probabilistic risk assessment (DPRA) methodologies couple system simulator codes (e.g., RELAP, MELCOR) with simulation controller codes (e.g., RAVEN, ADAPT). Whereas system simulator codes accurately model system dynamics deterministically, simulation controller codes introduce both deterministic (e.g., system control logic, operating procedures) and stochastic (e.g., component failures, parameter uncertainties) elements into the simulation. Typically, a DPRA is performed by 1) sampling values of a set of parameters from the uncertainty space of interest (using the simulation controller codes), and 2) simulating the system behavior for that specific set of parameter values (using the system simulator codes). For complex systems, one of the major challenges in using DPRA methodologies is to analyze the large amount of information (i.e., large number of scenarios ) generated, where clustering techniques are typically employed to allow users to better organize and interpret the data. In this paper, we focus on the analysis of a nuclear simulation dataset that is part of the risk-informed safety margin characterization (RISMC) boiling water reactor (BWR) station blackout (SBO) case study. We apply a software tool that provides the domain experts with an interactive analysis and visualization environment for understanding the structures of such high-dimensional nuclear simulation datasets. Our tool encodes traditional and topology-based clustering techniques, where the latter partitions the data points into clusters based on their uniform gradient flow behavior. We demonstrate through our case study that both types of clustering techniques complement each other in bringing enhanced structural understanding of the data.

Keywords: PRA, computational topology, clustering, high-dimensional analysis



Topological Methods in Data Analysis and Visualization III
P.-T. Bremer, I. Hotz, V. Pascucci, R. Peikert. Mathematics and Visualization, 2014.
ISBN: 978-3-319-04099-8



The Natural Helmholtz-Hodge Decomposition For Open-Boundary Flow Analysis
H. Bhatia, V. Pascucci, P.-T. Bremer. In IEEE Transactions on Visualization and Computer Graphics (TVCG), Vol. 99, pp. 1566--1578. 2014.
DOI: 10.1109/TVCG.2014.2312012

The Helmholtz-Hodge decomposition (HHD) describes a flow as the sum of an incompressible, an irrotational, and a harmonic flow, and is a fundamental tool for simulation and analysis. Unfortunately, for bounded domains, the HHD is not uniquely defined, and traditionally, boundary conditions are imposed to obtain a unique solution. However, in general, the boundary conditions used during the simulation may not be known and many simulations use open boundary conditions. In these cases, the flow imposed by traditional boundary conditions may not be compatible with the given data, which leads to sometimes drastic artifacts and distortions in all three components, hence producing unphysical results. Instead, this paper proposes the natural HHD, which is defined by separating the flow into internal and external components. Using a completely data-driven approach, the proposed technique obtains uniqueness without assuming boundary conditions a priori. As a result, it enables a reliable and artifact-free analysis for flows with open boundaries or unknown boundary conditions. Furthermore, our approach computes the HHD on a point-wise basis in contrast to the existing global techniques, and thus supports computing inexpensive local approximations for any subset of the domain. Finally, the technique is easy to implement for a variety of spatial discretizations and interpolated fields in both two and three dimensions.



Extracting Features from Time-Dependent Vector Fields Using Internal Reference Frames
H. Bhatia, V. Pascucci, R.M. Kirby, P.-T. Bremer. In Computer Graphics Forum, Vol. 33, No. 3, pp. 21--30. June, 2014.
DOI: 10.1111/cgf.12358

Extracting features from complex, time-dependent flow fields remains a significant challenge despite substantial research efforts, especially because most flow features of interest are defined with respect to a given reference frame. Pathline-based techniques, such as the FTLE field, are complex to implement and resource intensive, whereas scalar transforms, such as λ2, often produce artifacts and require somewhat arbitrary thresholds. Both approaches aim to analyze the flow in a more suitable frame, yet neither technique explicitly constructs one.

This paper introduces a new data-driven technique to compute internal reference frames for large-scale complex flows. More general than uniformly moving frames, these frames can transform unsteady fields, which otherwise require substantial processing of resources, into a sequence of individual snapshots that can be analyzed using the large body of steady-flow analysis techniques. Our approach is simple, theoretically well-founded, and uses an embarrassingly parallel algorithm for structured as well as unstructured data. Using several case studies from fluid flow and turbulent combustion, we demonstrate that internal frames are distinguished, result in temporally coherent structures, and can extract well-known as well as notoriously elusive features one snapshot at a time.