Loon: Using Exemplars to Visualize Large Scale Microscopy Data
D. Lange, E. Polanco, R. Judson-Torres, T. Zangle, A. Lex. In OSF Preprints, 2021.
Which drug is most promising for a cancer patient? This is a question a new microscopy-based approach for measuring the mass of individual cancer cells treated with different drugs promises to answer in only a few hours. However, the analysis pipeline for extracting data from these images is still far from complete automation: human intervention is necessary for quality control for preprocessing steps such as segmentation, to adjust filters, and remove noise, and for the analysis of the result. To address this workflow, we developed Loon, a visualization tool for analyzing drug screening data based on quantitative phase microscopy imaging. Loon visualizes both, derived data such as growth rates, and imaging data. Since the images are collected automatically at a large scale, manual inspection of images and segmentations is infeasible. However, reviewing representative samples of cells is essential, both for quality control and for data analysis. We introduce a new approach of choosing and visualizing representative exemplar cells that retain a close connection to the low-level data. By tightly integrating the derived data visualization capabilities with the novel exemplar visualization and providing selection and filtering capabilities, Loon is well suited for making decisions about which drugs are suitable for a specific patient.
Adaptive Spatially Aware I/O for Multiresolution Particle Data Layouts
W. Usher, X. Huang, S. Petruzza, S. Kumar, S. R. Slattery, S. T. Reeve, F. Wang, C. R. Johnson,, V. Pascucci. In IPDPS, 2021.
Evaluation of GPU Volume Rendering in PyTorch Using Data-Parallel Primitives
N. Marshak, P. Grosset, A. Knoll, J. P. Ahrens, C. R. Johnson. In Eurographics Symposium on Parallel Graphics and Visualization (EGPGV), 2021.
Data-parallel programming (DPP) has attracted considerable interest from the visualization community, fostering major software initiatives such as VTK-m. However, there has been relatively little recent investigation of data-parallel APIs in higherlevel languages such as Python, which could help developers sidestep the need for low-level application programming in C++ and CUDA. Moreover, machine learning frameworks exposing data-parallel primitives, such as PyTorch and TensorFlow, have exploded in popularity, making them attractive platforms for parallel visualization and data analysis. In this work, we benchmark data-parallel primitives in PyTorch, and investigate its application to GPU volume rendering using two distinct DPP formulations: a parallel scan and reduce over the entire volume, and repeated application of data-parallel operators to an array of rays. We find that most relevant DPP primitives exhibit performance similar to a native CUDA library. However, our volume rendering implementation reveals that PyTorch is limited in expressiveness when compared to other DPP APIs. Furthermore, while render times are sufficient for an early ''proof of concept'', memory usage acutely limits scalability.
Visualization of Uncertain Multivariate Data via Feature Confidence Level-Sets
S. Sane, T. Athawale,, C.R. Johnson. In EuroVis 2021, 2021.
Recent advancements in multivariate data visualization have opened new research opportunities for the visualization community. In this paper, we propose an uncertain multivariate data visualization technique called feature confidence level-sets. Conceptually, feature level-sets refer to level-sets of multivariate data. Our proposed technique extends the existing idea of univariate confidence isosurfaces to multivariate feature level-sets. Feature confidence level-sets are computed by considering the trait for a specific feature, a confidence interval, and the distribution of data at each grid point in the domain. Using uncertain multivariate data sets, we demonstrate the utility of the technique to visualize regions with uncertainty in relation to the specific trait or feature, and the ability of the technique to provide secondary feature structure visualization based on uncertainty.
HyperLabels---Browsing of Dense and Hierarchical Molecular 3D Models
D Kouřil, T Isenberg, B Kozlíková, M Meyer, E Gröller, I Viola. In IEEE transactions on visualization and computer graphics, IEEE, 2021.
We present a method for the browsing of hierarchical 3D models in which we combine the typical navigation of hierarchical structures in a 2D environment---using clicks on nodes, links, or icons---with a 3D spatial data visualization. Our approach is motivated by large molecular models, for which the traditional single-scale navigational metaphors are not suitable. Multi-scale phenomena, e. g., in astronomy or geography, are complex to navigate due to their large data spaces and multi-level organization. Models from structural biology are in addition also densely crowded in space and scale. Cutaways are needed to show individual model subparts. The camera has to support exploration on the level of a whole virus, as well as on the level of a small molecule. We address these challenges by employing HyperLabels: active labels that---in addition to their annotational role---also support user interaction. Clicks on HyperLabels select the next structure to be explored. Then, we adjust the visualization to showcase the inner composition of the selected subpart and enable further exploration. Finally, we use a breadcrumbs panel for orientation and as a mechanism to traverse upwards in the model hierarchy. We demonstrate our concept of hierarchical 3D model browsing using two exemplary models from meso-scale biology.
reVISit: Looking Under the Hood of Interactive Visualization Studies
C. Nobre, D. Wootton, Z. T. Cutler, L. Harrison, H. Pfister, A. Lex. In SIGCHI Conference on Human Factors in Computing Systems (CHI), ACM, pp. 1--12. 2021.
Quantifying user performance with metrics such as time and accuracy does not show the whole picture when researchers evaluate complex, interactive visualization tools. In such systems, performance is often influenced by different analysis strategies that statistical analysis methods cannot account for. To remedy this lack of nuance, we propose a novel analysis methodology for evaluating complex interactive visualizations at scale. We implement our analysis methods in reVISit, which enables analysts to explore participant interaction performance metrics and responses in the context of users' analysis strategies. Replays of participant sessions can aid in identifying usability problems during pilot studies and make individual analysis processes salient. To demonstrate the applicability of reVISit to visualization studies, we analyze participant data from two published crowdsourced studies. Our findings show that reVISit can be used to reveal and describe novel interaction patterns, to analyze performance differences between different analysis strategies, and to validate or challenge design decisions.
Understanding a program's resiliency through error propagation
Z. Li, H. Menon, K. Mohror, P. T. Bremer, Y. Livant, V. Pascucci. In Proceedings of the 26th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, ACM, pp. 362-373. 2021.
Aggressive technology scaling trends have worsened the transient fault problem in high-performance computing (HPC) systems. Some faults are benign, but others can lead to silent data corruption (SDC), which represents a serious problem; a fault introducing an error that is not readily detected nto an HPC simulation. Due to the insidious nature of SDCs, researchers have worked to understand their impact on applications. Previous studies have relied on expensive fault injection campaigns with uniform sampling to provide overall SDC rates, but this solution does not provide any feedback on the code regions without samples.
Blueprint: Cyberinfrastructure Center of Excellence
Subtitled arXiv, E. Deelman, A. Mandal, A. P. Murillo, J. Nabrzyski, V. Pascucci, R. Ricci, I. Baldin, S. Sons, L. Christopherson, C. Vardeman, R. F. da Silva, J. Wyngaard, S. Petruzza, M. Rynge, K. Vahi, W. R. Whitcup, J. Drake, E. Scott. 2021.
In 2018, NSF funded an effort to pilot a Cyberinfrastructure Center of Excellence (CI CoE or Center) that would serve the cyberinfrastructure (CI) needs of the NSF Major Facilities (MFs) and large projects with advanced CI architectures. The goal of the CI CoE Pilot project (Pilot) effort was to develop a model and a blueprint for such a CoE by engaging with the MFs, understanding their CI needs, understanding the contributions the MFs are making to the CI community, and exploring opportunities for building a broader CI community. This document summarizes the results of community engagements conducted during the first two years of the project and describes the identified CI needs of the MFs. To better understand MFs' CI, the Pilot has developed and validated a model of the MF data lifecycle that follows the data generation and management within a facility and gained an understanding of how this model captures the fundamental stages that the facilities' data passes through from the scientific instruments to the principal investigators and their teams, to the broader collaborations and the public. The Pilot also aimed to understand what CI workforce development challenges the MFs face while designing, constructing, and operating their CI and what solutions they are exploring and adopting within their projects. Based on the needs of the MFs in the data lifecycle and workforce development areas, this document outlines a blueprint for a CI CoE that will learn about and share the CI solutions designed, developed, and/or adopted by the MFs, provide expertise to the largest NSF projects with advanced and complex CI architectures, and foster a …
Lessons learned towards the immediate delivery of massive aerial imagery to farmers and crop consultants
A. A. Gooch, S. Petruzza, A. Gyulassy, G. Scorzelli, V. Pascucci, L. Rantham, W. Adcock, C. Coopmans. In Autonomous Air and Ground Sensing Systems for Agricultural Optimization and Phenotyping VI, Vol. 11747, International Society for Optics and Photonics, pp. 22 -- 34. 2021.
In this paper, we document lessons learned from using ViSOAR Ag Explorer™ in the fields of Arkansas and Utah in the 2018-2020 growing seasons. Our insights come from creating software with fast reading and writing of 2D aerial image mosaics for platform-agnostic collaborative analytics and visualization. We currently enable stitching in the field on a laptop without the need for an internet connection. The full resolution result is then available for instant streaming visualization and analytics via Python scripting. While our software, ViSOAR Ag Explorer™ removes the time and labor software bottleneck in processing large aerial surveys, enabling a cost-effective process to deliver actionable information to farmers, we learned valuable lessons with regard to the acquisition, storage, viewing, analysis, and planning stages of aerial data surveys. Additionally, with the ultimate goal of stitching thousands of images in minutes on board a UAV at the time of data capture, we performed preliminary tests for on-board, real-time stitching and analysis on USU AggieAir sUAS using lightweight computational resources. This system is able to create a 2D map while flying and allow interactive exploration of the full resolution data as soon as the platform has landed or has access to a network. This capability further speeds up the assessment process on the field and opens opportunities for new real-time photogrammetry applications. Flying and imaging over 1500-2000 acres per week provides up-to-date maps that give crop consultants a much broader scope of the field in general as well as providing a better view into planting and field preparation than could be observed from field level. Ultimately, our software and hardware could provide a much better understanding of weed presence and intensity or lack thereof.
Data-Driven Space-Filling Curves
L. Zhou, C. R. Johnson, D. Weiskopf. In IEEE Transactions on Visualization and Computer Graphics, Vol. 27, No. 2, IEEE, pp. 1591-1600. 2021.
We propose a data-driven space-filling curve method for 2D and 3D visualization. Our flexible curve traverses the data elements in the spatial domain in a way that the resulting linearization better preserves features in space compared to existing methods. We achieve such data coherency by calculating a Hamiltonian path that approximately minimizes an objective function that describes the similarity of data values and location coherency in a neighborhood. Our extended variant even supports multiscale data via quadtrees and octrees. Our method is useful in many areas of visualization, including multivariate or comparative visualization,ensemble visualization of 2D and 3D data on regular grids, or multiscale visual analysis of particle simulations. The effectiveness of our method is evaluated with numerical comparisons to existing techniques and through examples of ensemble and multivariate datasets.
A virtual frame buffer abstraction for parallel rendering of large tiled display walls
M. Han, I. Wald, W. Usher, N. Morrical, A. Knoll, V. Pascucci, C.R. Johnson. In 2020 IEEE Visualization Conference (VIS), pp. 11--15. 2020.
We present dw2, a flexible and easy-to-use software infrastructure for interactive rendering of large tiled display walls. Our library represents the tiled display wall as a single virtual screen through a display "service", which renderers connect to and send image tiles to be displayed, either from an on-site or remote cluster. The display service can be easily configured to support a range of typical network and display hardware configurations; the client library provides a straightforward interface for easy integration into existing renderers. We evaluate the performance of our display wall service in different configurations using a CPU and GPU ray tracer, in both on-site and remote rendering scenarios using multiple display walls.
Uncertainty Visualization of 2D Morse Complex Ensembles using Statistical Summary Maps
T. M. Athawale, D. Maljovec, L. Yan, C. R. Johnson, V. Pascucci,, B. Wang. In IEEE Transactions on Visualization and Computer Graphics, 2020.
Morse complexes are gradient-based topological descriptors with close connections to Morse theory. They are widely applicable in scientific visualization as they serve as important abstractions for gaining insights into the topology of scalar fields. Noise inherent to scalar field data due to acquisitions and processing, however, limits our understanding of the Morse complexes as structural abstractions. We, therefore, explore uncertainty visualization of an ensemble of 2D Morse complexes that arise from scalar fields coupled with data uncertainty. We propose statistical summary maps as new entities for capturing structural variations and visualizing positional uncertainties of Morse complexes in ensembles. Specifically, we introduce two types of statistical summary maps -- the Probabilistic Map and the Survival Map -- to characterize the uncertain behaviors of local extrema and local gradient flows, respectively. We demonstrate the utility of our proposed approach using synthetic and real-world datasets.
High-Quality Rendering of Glyphs Using Hardware-Accelerated Ray Tracing
S. Zellmann, M. Aumüller, N. Marshak, I. Wald. In Eurographics Symposium on Parallel Graphics and Visualization (EGPGV), The Eurographics Association, 2020.
Glyph rendering is an important scientific visualization technique for 3D, time-varying simulation data and for higherdimensional data in general. Though conceptually simple, there are several different challenges when realizing glyph rendering on top of triangle rasterization APIs, such as possibly prohibitive polygon counts, limitations of what shapes can be used for the glyphs, issues with visual clutter, etc. In this paper, we investigate the use of hardware ray tracing for high-quality, highperformance glyph rendering, and show that this not only leads to a more flexible and often more elegant solution for dealing with number and shape of glyphs, but that this can also help address visual clutter, and even provide additional visual cues that can enhance understanding of the dataset.
A Terminology for In Situ Visualization and Analysis Systems
H. Childs, S. D. Ahern, J. Ahrens, A. C. Bauer, J. Bennett, E. W. Bethel, P. Bremer, E. Brugger, J. Cottam, M. Dorier, S. Dutta, J. M. Favre, T. Fogal, S. Frey, C. Garth, B. Geveci, W. F. Godoy, C. D. Hansen, C. Harrison, B. Hentschel, J. Insley, C. R. Johnson, S. Klasky, A. Knoll, J. Kress, M. Larsen, J. Lofstead, K. Ma, P. Malakar, J. Meredith, K. Moreland, P. Navratil, P. O’Leary, M. Parashar, V. Pascucci, J. Patchett, T. Peterka, S. Petruzza, N. Podhorszki, D. Pugmire, M. Rasquin, S. Rizzi, D. H. Rogers, S. Sane, F. Sauer, R. Sisneros, H. Shen, W. Usher, R. Vickery, V. Vishwanath, I. Wald, R. Wang, G. H. Weber, B. Whitlock, M. Wolf, H. Yu, S. B. Ziegeler. In International Journal of High Performance Computing Applications, Vol. 34, No. 6, pp. 676–691. 2020.
The term “in situ processing” has evolved over the last decade to mean both a specific strategy for visualizing and analyzing data and an umbrella term for a processing paradigm. The resulting confusion makes it difficult for visualization and analysis scientists to communicate with each other and with their stakeholders. To address this problem, a group of over fifty experts convened with the goal of standardizing terminology. This paper summarizes their findings and proposes a new terminology for describing in situ systems. An important finding from this group was that in situ systems are best described via multiple, distinct axes: integration type, proximity, access, division of execution, operation controls, and output type. This paper discusses these axes, evaluates existing systems within the axes, and explores how currently used terms relate to the axes.
Distributed Resources for the Earth System Grid Advanced Management (DREAM), Final Report
L. Cinquini, S. Petruzza, Jason J. Boutte, S. Ames, G. Abdulla, V. Balaji, R. Ferraro, A. Radhakrishnan, L. Carriere, T. Maxwell, G. Scorzelli, V. Pascucci. 2020.
The DREAM project was funded more than 3 years ago to design and implement a next-generation ESGF (Earth System Grid Federation ) architecture which would be suitable for managing and accessing data and services resources on a distributed and scalable environment. In particular, the project intended to focus on the computing and visualization capabilities of the stack, which at the time were rather primitive. At the beginning, the team had the general notion that a better ESGF architecture could be built by modularizing each component, and redefining its interaction with other components by defining and exposing a well defined API. Although this was still the high level principle that guided the work, the DREAM project was able to accomplish its goals by leveraging new practices in IT that started just about 3 or 4 years ago: the advent of containerization technologies (specifically, Docker), the development of frameworks to manage containers at scale (Docker Swarm and Kubernetes), and their application to the commercial Cloud. Thanks to these new technologies, DREAM was able to improve the ESGF architecture (including its computing and visualization services) to a level of deployability and scalability beyond the original expectations.
CPU Ray Tracing of Tree-Based Adaptive Mesh Refinement Data
F. Wang, N. Marshak, W. Usher, C. Burstedde, A. Knoll, T. Heister, C. R. Johnson. In Eurographics Conference on Visualization (EuroVis) 2020, Vol. 39, No. 3, 2020.
Adaptive mesh refinement (AMR) techniques allow for representing a simulation’s computation domain in an adaptive fashion. Although these techniques have found widespread adoption in high-performance computing simulations, visualizing their data output interactively and without cracks or artifacts remains challenging. In this paper, we present an efficient solution for direct volume rendering and hybrid implicit isosurface ray tracing of tree-based AMR (TB-AMR) data. We propose a novel reconstruction strategy, Generalized Trilinear Interpolation (GTI), to interpolate across AMR level boundaries without cracks or discontinuities in the surface normal. We employ a general sparse octree structure supporting a wide range of AMR data, and use it to accelerate volume rendering, hybrid implicit isosurface rendering and value queries. We demonstrate that our approach achieves artifact-free isosurface and volume rendering and provides higher quality output images compared to existing methods at interactive rendering rates.
Remembering Bill Lorensen: The Man, the Myth, and Marching Cubes
C. R. Johnson, T. Kapur, W. Schroeder,, T. Yoo. In IEEE Computer Graphics and Applications, Vol. 40, No. 2, pp. 112-118. March, 2020.
Photographic High-Dynamic-Range Scalar Visualization
L. Zhou, M. Rivinius, C. R. Johnson,, D. Weiskopf. In IEEE Transactions on Visualization and Computer Graphics, Vol. 26, No. 6, IEEE, pp. 2156-2167. 2020.
We propose a photographic method to show scalar values of high dynamic range (HDR) by color mapping for 2D visualization. We combine (1) tone-mapping operators that transform the data to the display range of the monitor while preserving perceptually important features based on a systematic evaluation and (2) simulated glares that highlight high-value regions. Simulated glares are effective for highlighting small areas (of a few pixels) that may not be visible with conventional visualizations; through a controlled perception study, we confirm that glare is preattentive. The usefulness of our overall photographic HDR visualization is validated through the feedback of expert users.
Interactive Rendering of Large-Scale Volumes on Multi-Core CPUs
F. Wang, I. Wald,, C.R. Johnson. In 2019 IEEE 9th Symposium on Large Data Analysis and Visualization (LDAV), pp. 27--36. 2019.
Recent advances in large-scale simulations have resulted in volume data of increasing size that stress the capabilities of off-the-shelf visualization tools. Users suffer from long data loading times, because large data must be read from disk into memory prior to rendering the first frame. In this work, we present a volume renderer that enables high-fidelity interactive visualization of large volumes on multi-core CPU architectures. Compared to existing CPU-based visualization frameworks, which take minutes or hours for data loading, our renderer allows users to get a data overview in seconds. Using a hierarchical representation of raw volumes and ray-guided streaming, we reduce the data loading time dramatically and improve the user's interactivity experience. We also examine system design choices with respect to performance and scalability. Specifically, we evaluate the hierarchy generation time, which has been ignored in most prior work, but which can become a significant bottleneck as data scales. Finally, we create a module on top of the OSPRay ray tracing framework that is ready to be integrated into general-purpose visualization frameworks such as Paraview.
In situ visualization of performance metrics in multiple domains
A. Sanderson, A. Humphrey, J. Schmidt, R. Sisneros,, M. Papka. In 2019 IEEE/ACM International Workshop on Programming and Performance Visualization Tools (ProTools), IEEE, Nov, 2019.
As application scientists develop and deploy simulation codes on to leadership-class computing resources, there is a need to instrument these codes to better understand performance to efficiently utilize these resources. This instrumentation may come from independent third-party tools that generate and store performance metrics or from custom instrumentation tools built directly into the application. The metrics collected are then available for visual analysis, typically in the domain in which there were collected. In this paper, we introduce an approach to visualize and analyze the performance metrics in situ in the context of the machine, application, and communication domains (MAC model) using a single visualization tool. This visualization model provides a holistic view of the application performance in the context of the resources where it is executing.