A Survey of GPU-Based Large-Scale Volume Visualization

This survey gives an overview of the current state of the art in GPU techniques for interactive large-scale volume visualization. Modern techniques in this field have brought about a sea change in how interactive visualization and analysis of giga-, tera-, and petabytes of volume data can be enabled on GPUs. In addition to combining the parallel processing power of GPUs with out-of-core methods and data streaming, a major enabler for interactivity is making both the computational and the visualization effort proportional to the amount and resolution of data that is actually visible on screen, i.e., “output-sensitive” algorithms and system designs. This leads to recent outputsensitive approaches that are “ray-guided,” “visualization-driven,” or “display-aware.” In this survey, we focus on these characteristics and propose a new categorization of GPU-based large-scale volume visualization techniques based on the notions of actual output-resolution visibility and the current working set of volume bricks—the current subset of data that is minimally required to produce an output image of the desired display resolution. For our purposes here, we view parallel (distributed) visualization using clusters as an orthogonal set of techniques that we do not discuss in detail but that can be used in conjunction with what we discuss in this survey.Engineering and Applied Science

A Review of Temporal Data Visualizations Based on Space-Time Cube Operations

International audienceWe review a range of temporal data visualization techniques through a new lens, by describing them as series of op- erations performed on a conceptual space-time cube. These operations include extracting subparts of a space-time cube, flattening it across space or time, or transforming the cube's geometry or content. We introduce a taxonomy of elementary space-time cube operations, and explain how they can be combined to turn a three-dimensional space-time cube into an easily-readable two-dimensional visualization. Our model captures most visualizations showing two or more data dimensions in addition to time, such as geotemporal visualizations, dynamic networks, time-evolving scatterplots, or videos. We finally review interactive systems that support a range of operations. By introducing this conceptual framework we hope to facilitate the description, criticism and comparison of existing temporal data visualizations, as well as encourage the exploration of new techniques and systems

Physics-based visual characterization of molecular interaction forces

Molecular simulations are used in many areas of biotechnology, such as drug design and enzyme engineering. Despite the development of automatic computational protocols, analysis of molecular interactions is still a major aspect where human comprehension and intuition are key to accelerate, analyze, and propose modifications to the molecule of interest. Most visualization algorithms help the users by providing an accurate depiction of the spatial arrangement: the atoms involved in inter-molecular contacts. There are few tools that provide visual information on the forces governing molecular docking. However, these tools, commonly restricted to close interaction between atoms, do not consider whole simulation paths, long-range distances and, importantly, do not provide visual cues for a quick and intuitive comprehension of the energy functions (modeling intermolecular interactions) involved. In this paper, we propose visualizations designed to enable the characterization of interaction forces by taking into account several relevant variables such as molecule-ligand distance and the energy function, which is essential to understand binding affinities. We put emphasis on mapping molecular docking paths obtained from Molecular Dynamics or Monte Carlo simulations, and provide time-dependent visualizations for different energy components and particle resolutions: atoms, groups or residues. The presented visualizations have the potential to support domain experts in a more efficient drug or enzyme design process.Peer ReviewedPostprint (author's final draft

Augmenting Public Deliberations through Stream Argument Analytics and Visualisations

Public deliberations are organised by governments and other large institutions to take the views of citizens around controversial issues. Increasing public demand and the associated burden on public funding make the quality of public deliberation events and their outcomes critical to modern democracies. This paper focuses on technology developed around streams of computational argument data intended to inform and improve deliberative communication in real time. Combining state-of-the-art speech recognition, argument mining, and analytics, we produce dynamic, interactive visualisations intended for non-experts, deployed incrementally in real time to deliberation participants via large screens, hand-held and personal computing devices. The goal is to bridge the gap between theoretical criteria on deliberation quality from the political sciences and objective analytics calculated automatically from computable argument data in actual public deliberations, presented as a set of visualisations which work on stream data and are simple, yet informative enough to make a positive impact on deliberative outcomes

Timages: Enhancing Time Graphs with Iconographic Information

Various time-based visualization techniques have been designed to support the temporal analysis of data collections. While quantities play a secondary role in traditional timelines that reserve space for each individual data item to be observed, time graphs rather display quantitative information and they provide interaction means to filter for a subset of the data. Timages is a hybrid approach that enhances quantitative time graphs with qualitative information in an infographic-style. By (1) scaling thumbnails of data items dependent on relevance to the observed topic and by (2) time-dependent positioning these thumbnails inside a temporally aligned area with a novel space-filling strategy, the most relevant items in the entire data collection as well as predominant data items of certain time ranges are instantly seizable without the need to interact with the time graph

Synergistic Visualization And Quantitative Analysis Of Volumetric Medical Images

The medical diagnosis process starts with an interview with the patient, and continues with the physical exam. In practice, the medical professional may require additional screenings to precisely diagnose. Medical imaging is one of the most frequently used non-invasive screening methods to acquire insight of human body. Medical imaging is not only essential for accurate diagnosis, but also it can enable early prevention. Medical data visualization refers to projecting the medical data into a human understandable format at mediums such as 2D or head-mounted displays without causing any interpretation which may lead to clinical intervention. In contrast to the medical visualization, quantification refers to extracting the information in the medical scan to enable the clinicians to make fast and accurate decisions. Despite the extraordinary process both in medical visualization and quantitative radiology, efforts to improve these two complementary fields are often performed independently and synergistic combination is under-studied. Existing image-based software platforms mostly fail to be used in routine clinics due to lack of a unified strategy that guides clinicians both visually and quan- titatively. Hence, there is an urgent need for a bridge connecting the medical visualization and automatic quantification algorithms in the same software platform. In this thesis, we aim to fill this research gap by visualizing medical images interactively from anywhere, and performing a fast, accurate and fully-automatic quantification of the medical imaging data. To end this, we propose several innovative and novel methods. Specifically, we solve the following sub-problems of the ul- timate goal: (1) direct web-based out-of-core volume rendering, (2) robust, accurate, and efficient learning based algorithms to segment highly pathological medical data, (3) automatic landmark- ing for aiding diagnosis and surgical planning and (4) novel artificial intelligence algorithms to determine the sufficient and necessary data to derive large-scale problems

In Situ Visualization of Performance Data in Parallel CFD Applications

This thesis summarizes the work of the author on visualization of performance data in parallel Computational Fluid Dynamics (CFD) simulations. Current performance analysis tools are unable to show their data on top of complex simulation geometries (e.g. an aircraft engine). But in CFD simulations, performance is expected to be affected by the computations being carried out, which in turn are tightly related to the underlying computational grid. Therefore it is imperative that performance data is visualized on top of the same computational geometry which they originate from. However, performance tools have no native knowledge of the underlying mesh of the simulation. This scientific gap can be filled by merging the branches of HPC performance analysis and in situ visualization of CFD simulations data, which shall be done by integrating existing, well established state-of-the-art tools from each field. In this threshold, an extension for the open-source performance tool Score-P was designed and developed, which intercepts an arbitrary number of manually selected code regions (mostly functions) and send their respective measurements – amount of executions and cumulative time spent – to the visualization software ParaView – through its in situ library, Catalyst –, as if they were any other flow-related variable. Subsequently the tool was extended with the capacity to also show communication data (messages sent between MPI ranks) on top of the CFD mesh. Testing and evaluation are done with two industry-grade codes: Rolls-Royce’s CFD code, Hydra, and Onera, DLR and Airbus’ CFD code, CODA. On the other hand, it has been also noticed that the current performance tools have limited capacity of displaying their data on top of three-dimensional, framed (i.e. time-stepped) representations of the cluster’s topology. Parallel to that, in order for the approach not to be limited to codes which already have the in situ adapter, it was extended to take the performance data and display it – also in codes without in situ – on a three-dimensional, framed representation of the hardware resources being used by the simulation. Testing is done with the Multi-Grid and Block Tri-diagonal NAS Parallel Benchmarks (NPB), as well as with Hydra and CODA again. The benchmarks are used to explain how the new visualizations work, while real performance analyses are done with the industry-grade CFD codes. The proposed solution is able to provide concrete performance insights, which would not have been reached with the current performance tools and which motivated beneficial changes in the respective source code in real life. Finally, its overhead is discussed and proven to be suitable for usage with CFD codes. The dissertation provides a valuable addition to the state of the art of highly parallel CFD performance analysis and serves as basis for further suggested research directions

Interactive Visual Alignment of Medieval Text Versions

Textual criticism consists of the identification and analysis of variant readings among different versions of a text. Being a relatively simple task for modern languages, the collation of medieval text traditions ranges from the complex to the virtually impossible depending on the degree of instability of textual transmission. We present a visual analytics environment that supports computationally aligning such complex textual differences typical of orally inflected medieval poetry. For the purpose of analyzing alignment, we provide interactive visualizations for different text hierarchy levels, specifically, a meso reading view to support investigating repetition and variance at the line level across text segments. In addition to outlining important aspects of our interdisciplinary collaboration, we emphasize the utility of the proposed system by various usage scenarios in medieval French literature