Bimodal Visualization of Industrial X-Ray and Neutron Computed Tomography Data.

Advanced manufacturing creates increasingly complex objects with material compositions that are often difficult to characterize by a single modality. Our collaborating domain scientists are going beyond traditional methods by employing both X-ray and neutron computed tomography to obtain complementary representations expected to better resolve material boundaries. However, the use of two modalities creates its own challenges for visualization, requiring either complex adjustments of bimodal transfer functions or the need for multiple views. Together with experts in nondestructive evaluation, we designed a novel interactive bimodal visualization approach to create a combined view of the co-registered X-ray and neutron acquisitions of industrial objects. Using an automatic topological segmentation of the bivariate histogram of X-ray and neutron values as a starting point, the system provides a simple yet effective interface to easily create, explore, and adjust a bimodal visualization. We propose a widget with simple brushing interactions that enables the user to quickly correct the segmented histogram results. Our semiautomated system enables domain experts to intuitively explore large bimodal datasets without the need for either advanced segmentation algorithms or knowledge of visualization techniques. We demonstrate our approach using synthetic examples, industrial phantom objects created to stress bimodal scanning techniques, and real-world objects, and we discuss expert feedback.

Attribute-Aware RBFs: Interactive Visualization of Time Series Particle Volumes Using RT Core Range Queries.

Smoothed-particle hydrodynamics (SPH) is a mesh-free method used to simulate volumetric media in fluids, astrophysics, and solid mechanics. Visualizing these simulations is problematic because these datasets often contain millions, if not billions of particles carrying physical attributes and moving over time. Radial basis functions (RBFs) are used to model particles, and overlapping particles are interpolated to reconstruct a high-quality volumetric field; however, this interpolation process is expensive and makes interactive visualization difficult. Existing RBF interpolation schemes do not account for color-mapped attributes and are instead constrained to visualizing just the density field. To address these challenges, we exploit ray tracing cores in modern GPU architectures to accelerate scalar field reconstruction. We use a novel RBF interpolation scheme to integrate per-particle colors and densities, and leverage GPU-parallel tree construction and refitting to quickly update the tree as the simulation animates over time or when the user manipulates particle radii. We also propose a Hilbert reordering scheme to cluster particles together at the leaves of the tree to reduce tree memory consumption. Finally, we reduce the noise of volumetric shadows by adopting a spatially temporal blue noise sampling scheme. Our method can provide a more detailed and interactive view of these large, volumetric, time-series particle datasets than traditional methods, leading to new insights into these physics simulations.

Exploring Classification of Topological Priors with Machine Learning for Feature Extraction.

In many scientific endeavors, increasingly abstract representations of data allow for new interpretive methodologies and conceptualization of phenomena. For example, moving from raw imaged pixels to segmented and reconstructed objects allows researchers new insights and means to direct their studies toward relevant areas. Thus, the development of new and improved methods for segmentation remains an active area of research. With advances in machine learning and neural networks, scientists have been focused on employing deep neural networks such as U-Net to obtain pixel-level segmentations, namely, defining associations between pixels and corresponding/referent objects and gathering those objects afterward. Topological analysis, such as the use of the Morse-Smale complex to encode regions of uniform gradient flow behavior, offers an alternative approach: first, create geometric priors, and then apply machine learning to classify. This approach is empirically motivated since phenomena of interest often appear as subsets of topological priors in many applications. Using topological elements not only reduces the learning space but also introduces the ability to use learnable geometries and connectivity to aid the classification of the segmentation target. In this paper, we describe an approach to creating learnable topological elements, explore the application of ML techniques to classification tasks in a number of areas, and demonstrate this approach as a viable alternative to pixel-level classification, with similar accuracy, improved execution time, and requiring marginal training data.

Progressive Tree-Based Compression of Large-Scale Particle Data.

Scientific simulations and observations using particles have been creating large datasets that require effective and efficient data reduction to store, transfer, and analyze. However, current approaches either compress only small data well while being inefficient for large data, or handle large data but with insufficient compression. Toward effective and scalable compression/decompression of particle positions, we introduce new kinds of particle hierarchies and corresponding traversal orders that quickly reduce reconstruction error while being fast and low in memory footprint. Our solution to compression of large-scale particle data is a flexible block-based hierarchy that supports progressive, random-access, and error-driven decoding, where error estimation heuristics can be supplied by the user. For low-level node encoding, we introduce new schemes that effectively compress both uniform and densely structured particle distributions.

Quick Clusters: A GPU-Parallel Partitioning for Efficient Path Tracing of Unstructured Volumetric Grids.

We propose a simple yet effective method for clustering finite elements to improve preprocessing times and rendering performance of unstructured volumetric grids without requiring auxiliary connectivity data. Rather than building bounding volume hierarchies (BVHs) over individual elements, we sort elements along with a Hilbert curve and aggregate neighboring elements together, improving BVH memory consumption by over an order of magnitude. Then to further reduce memory consumption, we cluster the mesh on the fly into sub-meshes with smaller indices using a series of efficient parallel mesh re-indexing operations. These clusters are then passed to a highly optimized ray tracing API for point containment queries and ray-cluster intersection testing. Each cluster is assigned a maximum extinction value for adaptive sampling, which we rasterize into non-overlapping view-aligned bins allocated along the ray. These maximum extinction bins are then used to guide the placement of samples along the ray during visualization, reducing the number of samples required by multiple orders of magnitude (depending on the dataset), thereby improving overall visualization interactivity. Using our approach, we improve rendering performance over a competitive baseline on the NASA Mars Lander dataset from 6× (1 frame per second (fps) and 1.0 M rays per second (rps) up to now 6 fps and 12.4 M rps, now including volumetric shadows) while simultaneously reducing memory consumption by 3×(33 GB down to 11 GB) and avoiding any offline preprocessing steps, enabling high-quality interactive visualization on consumer graphics cards. Then by utilizing the full 48 GB of an RTX 8000, we improve the performance of Lander by 17 × (1 fps up to 17 fps, 1.0 M rps up to 35.6 M rps).

AMM: Adaptive Multilinear Meshes.

Adaptive representations are increasingly indispensable for reducing the in-memory and on-disk footprints of large-scale data. Usual solutions are designed broadly along two themes: reducing data precision, e.g., through compression, or adapting data resolution, e.g., using spatial hierarchies. Recent research suggests that combining the two approaches, i.e., adapting both resolution and precision simultaneously, can offer significant gains over using them individually. However, there currently exist no practical solutions to creating and evaluating such representations at scale. In this work, we present a new resolution-precision-adaptive representation to support hybrid data reduction schemes and offer an interface to existing tools and algorithms. Through novelties in spatial hierarchy, our representation, Adaptive Multilinear Meshes (AMM), provides considerable reduction in the mesh size. AMM creates a piecewise multilinear representation of uniformly sampled scalar data and can selectively relax or enforce constraints on conformity, continuity, and coverage, delivering a flexible adaptive representation. AMM also supports representing the function using mixed-precision values to further the achievable gains in data reduction. We describe a practical approach to creating AMM incrementally using arbitrary orderings of data and demonstrate AMM on six types of resolution and precision datastreams. By interfacing with state-of-the-art rendering tools through VTK, we demonstrate the practical and computational advantages of our representation for visualization techniques. With an open-source release of our tool to create AMM, we make such evaluation of data reduction accessible to the community, which we hope will foster new opportunities and future data reduction schemes.

Towards replacing physical testing of granular materials with a Topology-based Model.

In the study of packed granular materials, the performance of a sample (e.g., the detonation of a high-energy explosive) often correlates to measurements of a fluid flowing through it. The "effective surface area," the surface area accessible to the airflow, is typically measured using a permeametry apparatus that relates the flow conductance to the permeable surface area via the Carman-Kozeny equation. This equation allows calculating the flow rate of a fluid flowing through the granules packed in the sample for a given pressure drop. However, Carman-Kozeny makes inherent assumptions about tunnel shapes and flow paths that may not accurately hold in situations where the particles possess a wide distribution in shapes, sizes, and aspect ratios, as is true with many powdered systems of technological and commercial interest. To address this challenge, we replicate these measurements virtually on micro-CT images of the powdered material, introducing a new Pore Network Model based on the skeleton of the Morse-Smale complex. Pores are identified as basins of the complex, their incidence encodes adjacency, and the conductivity of the capillary between them is computed from the cross-section at their interface. We build and solve a resistive network to compute an approximate laminar fluid flow through the pore structure. We provide two means of estimating flow-permeable surface area: (i) by direct computation of conductivity, and (ii) by identifying dead-ends in the flow coupled with isosurface extraction and the application of the Carman-Kozeny equation, with the aim of establishing consistency over a range of particle shapes, sizes, porosity levels, and void distribution patterns.

A Visual Comparison of Silent Error Propagation.

High-performance computing (HPC) systems play a critical role in facilitating scientific discoveries. Their scale and complexity (e.g., the number of computational units and software stack) continue to grow as new systems are expected to process increasingly more data and reduce computing time. However, with more processing elements, the probability that these systems will experience a random bit-flip error that corrupts a program's output also increases, which is often recognized as silent data corruption. Analyzing the resiliency of HPC applications in extreme-scale computing to silent data corruption is crucial but difficult. An HPC application often contains a large number of computation units that need to be tested, and error propagation caused by error corruption is complex and difficult to interpret. To accommodate this challenge, we propose an interactive visualization system that helps HPC researchers understand the resiliency of HPC applications and compare their error propagation. Our system models an application's error propagation to study a program's resiliency by constructing and visualizing its fault tolerance boundary. Coordinating with multiple interactive designs, our system enables domain experts to efficiently explore the complicated spatial and temporal correlation between error propagations. At the end, the system integrated a nonmonotonic error propagation analysis with an adjustable graph propagation visualization to help domain experts examine the details of error propagation and answer such questions as why an error is mitigated or amplified by program execution.

Uncertainty Visualization of 2D Morse Complex Ensembles Using Statistical Summary Maps.

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. Data uncertainty inherent to scalar fields due to randomness in their acquisition and processing, however, limits our understanding of Morse complexes as structural abstractions. We, therefore, explore uncertainty visualization of an ensemble of 2D Morse complexes that arises from scalar fields coupled with data uncertainty. We propose several statistical summary maps as new entities for quantifying structural variations and visualizing positional uncertainties of Morse complexes in ensembles. Specifically, we introduce three types of statistical summary maps - the probabilistic map, the significance map, and the survival map - to characterize the uncertain behaviors of gradient flows. We demonstrate the utility of our proposed approach using wind, flow, and ocean eddy simulation datasets.

Accelerating Unstructured Mesh Point Location With RT Cores.

We present a technique that leverages ray tracing hardware available in recent Nvidia RTX GPUs to solve a problem other than classical ray tracing. Specifically, we demonstrate how to use these units to accelerate the point location of general unstructured elements consisting of both planar and bilinear faces. This unstructured mesh point location problem has previously been challenging to accelerate on GPU architectures; yet, the performance of these queries is crucial to many unstructured volume rendering and compute applications. Starting with a CUDA reference method, we describe and evaluate three approaches that reformulate these point queries to incrementally map algorithmic complexity to these new hardware ray tracing units. Each variant replaces the simpler problem of point queries with a more complex one of ray queries. Initial variants exploit ray tracing cores for accelerated BVH traversal, and subsequent variants use ray-triangle intersections and per-face metadata to detect point-in-element intersections. Although these later variants are more algorithmically complex, they are significantly faster than the reference method thanks to hardware acceleration. Using our approach, we improve the performance of an unstructured volume renderer by up to 4× for tetrahedral meshes and up to 15× for general bilinear element meshes, matching, or out-performing state-of-the-art solutions while simultaneously improving on robustness and ease-of-implementation.

Vector Field Decompositions Using Multiscale Poisson Kernel.

Extraction of multiscale features using scale-space is one of the fundamental approaches to analyze scalar fields. However, similar techniques for vector fields are much less common, even though it is well known that, for example, turbulent flows contain cascades of nested vortices at different scales. The challenge is that the ideas related to scale-space are based upon iteratively smoothing the data to extract features at progressively larger scale, making it difficult to extract overlapping features. Instead, we consider spatial regions of influence in vector fields as scale, and introduce a new approach for the multiscale analysis of vector fields. Rather than smoothing the flow, we use the natural Helmholtz-Hodge decomposition to split it into small-scale and large-scale components using progressively larger neighborhoods. Our approach creates a natural separation of features by extracting local flow behavior, for example, a small vortex, from large-scale effects, for example, a background flow. We demonstrate our technique on large-scale, turbulent flows, and show multiscale features that cannot be extracted using state-of-the-art techniques.

Efficient and Flexible Hierarchical Data Layouts for a Unified Encoding of Scalar Field Precision and Resolution.

To address the problem of ever-growing scientific data sizes making data movement a major hindrance to analysis, we introduce a novel encoding for scalar fields: a unified tree of resolution and precision, specifically constructed so that valid cuts correspond to sensible approximations of the original field in the precision-resolution space. Furthermore, we introduce a highly flexible encoding of such trees that forms a parameterized family of data hierarchies. We discuss how different parameter choices lead to different trade-offs in practice, and show how specific choices result in known data representation schemes such as zfp [52], idx [58], and jpeg2000 [76]. Finally, we provide system-level details and empirical evidence on how such hierarchies facilitate common approximate queries with minimal data movement and time, using real-world data sets ranging from a few gigabytes to nearly a terabyte in size. Experiments suggest that our new strategy of combining reductions in resolution and precision is competitive with state-of-the-art compression techniques with respect to data quality, while being significantly more flexible and orders of magnitude faster, and requiring significantly reduced resources.

Ray Tracing Structured AMR Data Using ExaBricks.

Structured Adaptive Mesh Refinement (Structured AMR) enables simulations to adapt the domain resolution to save computation and storage, and has become one of the dominant data representations used by scientific simulations; however, efficiently rendering such data remains a challenge. We present an efficient approach for volume- and iso-surface ray tracing of Structured AMR data on GPU-equipped workstations, using a combination of two different data structures. Together, these data structures allow a ray tracing based renderer to quickly determine which segments along the ray need to be integrated and at what frequency, while also providing quick access to all data values required for a smooth sample reconstruction kernel. Our method makes use of the RTX ray tracing hardware for surface rendering, ray marching, space skipping, and adaptive sampling; and allows for interactive changes to the transfer function and implicit iso-surfacing thresholds. We demonstrate that our method achieves high performance with little memory overhead, enabling interactive high quality rendering of complex AMR data sets on individual GPU workstations.

Improving the Usability of Virtual Reality Neuron Tracing with Topological Elements.

Researchers in the field of connectomics are working to reconstruct a map of neural connections in the brain in order to understand at a fundamental level how the brain processes information. Constructing this wiring diagram is done by tracing neurons through high-resolution image stacks acquired with fluorescence microscopy imaging techniques. While a large number of automatic tracing algorithms have been proposed, these frequently rely on local features in the data and fail on noisy data or ambiguous cases, requiring time-consuming manual correction. As a result, manual and semi-automatic tracing methods remain the state-of-the-art for creating accurate neuron reconstructions. We propose a new semi-automatic method that uses topological features to guide users in tracing neurons and integrate this method within a virtual reality (VR) framework previously used for manual tracing. Our approach augments both visualization and interaction with topological elements, allowing rapid understanding and tracing of complex morphologies. In our pilot study, neuroscientists demonstrated a strong preference for using our tool over prior approaches, reported less fatigue during tracing, and commended the ability to better understand possible paths and alternatives. Quantitative evaluation of the traces reveals that users' tracing speed increased, while retaining similar accuracy compared to a fully manual approach.

SpotSDC: Revealing the Silent Data Corruption Propagation in High-Performance Computing Systems.

The trend of rapid technology scaling is expected to make the hardware of high-performance computing (HPC) systems more susceptible to computational errors due to random bit flips. Some bit flips may cause a program to crash or have a minimal effect on the output, but others may lead to silent data corruption (SDC), i.e., undetected yet significant output errors. Classical fault injection analysis methods employ uniform sampling of random bit flips during program execution to derive a statistical resiliency profile. However, summarizing such fault injection result with sufficient detail is difficult, and understanding the behavior of the fault-corrupted program is still a challenge. In this article, we introduce SpotSDC, a visualization system to facilitate the analysis of a program's resilience to SDC. SpotSDC provides multiple perspectives at various levels of detail of the impact on the output relative to where in the source code the flipped bit occurs, which bit is flipped, and when during the execution it happens. SpotSDC also enables users to study the code protection and provide new insights to understand the behavior of a fault-injected program. Based on lessons learned, we demonstrate how what we found can improve the fault injection campaign method.

Improving Augmented Human Intelligence to Distinguish Burkitt Lymphoma From Diffuse Large B-Cell Lymphoma Cases.

OBJECTIVES: To assess and improve the assistive role of a deep, densely connected convolutional neural network (CNN) to hematopathologists in differentiating histologic images of Burkitt lymphoma (BL) from diffuse large B-cell lymphoma (DLBCL). METHODS: A total of 10,818 images from BL (n = 34) and DLBCL (n = 36) cases were used to either train or apply different CNNs. Networks differed by number of training images and pixels of images, absence of color, pixel and staining augmentation, and depth of the network, among other parameters. RESULTS: Cases classified correctly were 17 of 18 (94%), nine with 100% of images correct by the best performing network showing a receiver operating characteristic curve analysis area under the curve 0.92 for both DLBCL and BL. The best performing CNN used all available training images, two random subcrops per image of 448 × 448 pixels, random H&E staining image augmentation, random horizontal flipping of images, random alteration of contrast, reduction on validation error plateau of 15 epochs, block size of six, batch size of 32, and depth of 22. Other networks and decreasing training images had poorer performance. CONCLUSIONS: CNNs are promising augmented human intelligence tools for differentiating a subset of BL and DLBCL cases.

High-throughput feature extraction for measuring attributes of deforming open-cell foams.

Metallic open-cell foams are promising structural materials with applications in multifunctional systems such as biomedical implants, energy absorbers in impact, noise mitigation, and batteries. There is a high demand for means to understand and correlate the design space of material performance metrics to the material structure in terms of attributes such as density, ligament and node properties, void sizes, and alignments. Currently, X-ray Computed Tomography (CT) scans of these materials are segmented either manually or with skeletonization approaches that may not accurately model the variety of shapes present in nodes and ligaments, especially irregularities that arise from manufacturing, image artifacts, or deterioration due to compression. In this paper, we present a new workflow for analysis of open-cell foams that combines a new density measurement to identify nodal structures, and topological approaches to identify ligament structures between them. Additionally, we provide automated measurement of foam properties. We demonstrate stable extraction of features and time-tracking in an image sequence of a foam being compressed. Our approach allows researchers to study larger and more complex foams than could previously be segmented only manually, and enables the high-throughput analysis needed to predict future foam performance.

Scalable Topological Data Analysis and Visualization for Evaluating Data-Driven Models in Scientific Applications.

With the rapid adoption of machine learning techniques for large-scale applications in science and engineering comes the convergence of two grand challenges in visualization. First, the utilization of black box models (e.g., deep neural networks) calls for advanced techniques in exploring and interpreting model behaviors. Second, the rapid growth in computing has produced enormous datasets that require techniques that can handle millions or more samples. Although some solutions to these interpretability challenges have been proposed, they typically do not scale beyond thousands of samples, nor do they provide the high-level intuition scientists are looking for. Here, we present the first scalable solution to explore and analyze high-dimensional functions often encountered in the scientific data analysis pipeline. By combining a new streaming neighborhood graph construction, the corresponding topology computation, and a novel data aggregation scheme, namely topology aware datacubes, we enable interactive exploration of both the topological and the geometric aspect of high-dimensional data. Following two use cases from high-energy-density (HED) physics and computational biology, we demonstrate how these capabilities have led to crucial new insights in both applications.

Toward Localized Topological Data Structures: Querying the Forest for the Tree.

Topological approaches to data analysis can answer complex questions about the number, connectivity, and scale of intrinsic features in scalar data. However, the global nature of many topological structures makes their computation challenging at scale, and thus often limits the size of data that can be processed. One key quality to achieving scalability and performance on modern architectures is data locality, i.e., a process operates on data that resides in a nearby memory system, avoiding frequent jumps in data access patterns. From this perspective, topological computations are particularly challenging because the implied data structures represent features that can span the entire data set, often requiring a global traversal phase that limits their scalability. Traditionally, expensive preprocessing is considered an acceptable trade-off as it accelerates all subsequent queries. Most published use cases, however, explore only a fraction of all possible queries, most often those returning small, local features. In these cases, much of the global information is not utilized, yet computing it dominates the overall response time. We address this challenge for merge trees, one of the most commonly used topological structures. In particular, we propose an alternative representation, the merge forest, a collection of local trees corresponding to regions in a domain decomposition. Local trees are connected by a bridge set that allows us to recover any necessary global information at query time. The resulting system couples (i) a preprocessing that scales linearly in practice with (ii) fast runtime queries that provide the same functionality as traditional queries of a global merge tree. We test the scalability of our approach on a shared-memory parallel computer and demonstrate how data structure locality enables the analysis of large data with an order of magnitude performance improvement over the status quo. Furthermore, a merge forest reduces the memory overhead compared to a global merge tree and enables the processing of data sets that are an order of magnitude larger than possible with previous algorithms.

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.