Pattern information extraction from crystal structures

Determining the crystal structure parameters of a material is an important issue in crystallography and material science. Knowing the crystal structure parameters helps in understanding the physical behavior of material. It can be difficult to obtain crystal parameters for complex structures, particularly those materials that show local symmetry as well as global symmetry. This work provides a tool that extracts crystal parameters such as primitive vectors, basis vectors and space groups from the atomic coordinates of crystal structures. A visualization tool for examining crystals is also provided. Accordingly, this work could help crystallographers, chemists and material scientists to analyze crystal structures efficiently.

Program summary

Title of program: BilKristalCatalogue identifier: ADYU_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYU_v1_0Program obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandLicensing provisions: NoneProgramming language used: C, C++, Microsoft .NET Framework 1.1 and OpenGL LibrariesComputer: Personal Computers with Windows operating systemOperating system: Windows XP ProfessionalRAM: 20-60 MBNo. of lines in distributed program, including test data, etc.:899 779No. of bytes in distributed program, including test date, etc.:9 271 521Distribution format:tar.gzExternal routines/libraries: Microsoft .NET Framework 1.1. For visualization tool, graphics card driver should also support OpenGLNature of problem: Determining crystal structure parameters of a material is a quite important issue in crystallography. Knowing the crystal structure parameters helps to understand physical behavior of material. For complex structures, particularly, for materials which also contain local symmetry as well as global symmetry, obtaining crystal parameters can be quite hard.Solution method: The tool extracts crystal parameters such as primitive vectors, basis vectors and identify the space group from atomic coordinates of crystal structures.Restrictions: Assumptions are explained in the paper. However, none of them can be considered as a restriction onto the complexity of the problem.Running time: All the examples presented in the paper take less than 30 seconds on a 2.4 GHz Pentium 4 computer.     

基于参数化设计的三维桥梁模型构建

参数化设计是几何体建模的重要手段,而桥梁的三维可视化是当今桥梁信 息化的发展趋势。论文针对桥梁外观参数化模型可视化的需要,对几何体参数化建模的原理 和方法进行了深入探讨。结合桥梁结构特点,分析了主要桥梁组件结构（如T 梁、盖梁柱 式墩、轻型桥台等）构件图的几何和拓扑关系,对组件进行了参数化设计,实现组件的三维 建模;并对组件中特殊图元（如圆弧倒角形墩柱、桥台近似锥面护坡）的绘制算法进行详细 研究;根据各组件间空间位置的拓扑关系,利用参数化变量驱动计算各组件空间位置坐标, 进行桥梁的快速拼接。完成的桥梁三维参数化建模以参数为驱动,用户可以对设计结果进行 可视化修改。所实现的三维参数桥梁可视化系统具有模型构建精致,参数化建模彻底、建模 速度快,参数分类清晰,可视化效果好的特点。     

A unified framework for web video topic discovery and visualization

Together with the explosive growth of web video in sharing sites like YouTube, automatic topic discovery and visualization have become increasingly important in helping to organize and navigate such large-scale videos. Previous work dealt with the topic discovery and visualization problem separately, and did not take fully into account of the distinctive characteristics of multi-modality and sparsity in web video features. This paper tries to solve web video topic discovery problem with visualization under a single framework, and proposes a Star-structured K-partite Graph based co-clustering and ranking framework, which consists of three stages: (1) firstly, represent the web videos and their multi-model features (e.g., keyword, near-duplicate keyframe, near-duplicate aural frame, etc.) as a Star-structured K-partite Graph; (2) secondly, group videos and their features simultaneously into clusters (topics) and organize the generated clusters as a linked cluster network; (3) finally, rank each type of nodes in the linked cluster network by “popularity” and visualize them as a novel interface to let user interactively browse topics in multi-level scales. Experiments on a YouTube benchmark dataset demonstrate the flexibility and effectiveness of our proposed framework.     

CTViz: A tool for the visualization of transport in nanocomposites

A visualization tool (CTViz) for charge transport processes in 3-D hybrid materials (nanocomposites) was developed, inspired by the need for a graphical application to assist in code debugging and data presentation of an existing in-house code. As the simulation code grew, troubleshooting problems grew increasingly difficult without an effective way to visualize 3-D samples and charge transport in those samples. CTViz is able to produce publication and presentation quality visuals of the simulation box, as well as static and animated visuals of the paths of individual carriers through the sample. CTViz was designed to provide a high degree of flexibility in the visualization of the data. A feature that characterizes this tool is the use of shade and transparency levels to highlight important details in the morphology or in the transport paths by hiding or dimming elements of little relevance to the current view. This is fundamental for the visualization of 3-D systems with complex structures. The code presented here provides these required capabilities, but has gone beyond the original design and could be used as is or easily adapted for the visualization of other particulate transport where transport occurs on discrete paths.     

A Survey on Multimodal Medical Data Visualization

Multi‐modal data of the complex human anatomy contain a wealth of information. To visualize and explore such data, techniques for emphasizing important structures and controlling visibility are essential. Such fused overview visualizations guide physicians to suspicious regions to be analysed in detail, e.g. with slice‐based viewing. We give an overview of state of the art in multi‐modal medical data visualization techniques. Multi‐modal medical data consist of multiple scans of the same subject using various acquisition methods, often combining multiple complimentary types of information. Three‐dimensional visualization techniques for multi‐modal medical data can be used in diagnosis, treatment planning, doctor–patient communication as well as interdisciplinary communication. Over the years, multiple techniques have been developed in order to cope with the various associated challenges and present the relevant information from multiple sources in an insightful way. We present an overview of these techniques and analyse the specific challenges that arise in multi‐modal data visualization and how recent works aimed to solve these, often using smart visibility techniques. We provide a taxonomy of these multi‐modal visualization applications based on the modalities used and the visualization techniques employed. Additionally, we identify unsolved problems as potential future research directions.     

Direct Visualization of Deformation in Volumes

Deformation is a topic of interest in many disciplines. In particular in medical research, deformations of surfaces and even entire volumetric structures are of interest. Clear visualization of such deformations can lead to important insight into growth processes and progression of disease.
We present new techniques for direct focus+context visualization of deformation fields representing transformations between pairs of volumetric datasets. Typically, such fields are computed by performing a non-rigid registration between two data volumes. Our visualization is based on direct volume rendering and uses the GPU to compute and interactively visualize features of these deformation fields in real-time. We integrate visualization of the deformation field with visualization of the scalar volume affected by the deformations. Furthermore, we present a novel use of texturing in volume rendered visualizations to show additional properties of the vector field on surfaces in the volume.     

Feature Model Visualization

Feature modelling is now the predominant way of modelling products. Feature visualization is an important aspect here that can still be considerably improved. In this paper, an integrated way of visualizing feature models is presented, using new techniques for both the geometry and the structure of models. For the geometry of feature models, techniques are presented to visualize a selected subset of form features in a way that clearly distinguishes them from the rest of the model, as well as functional information such as closure faces of subtractive form features. For the structure of features models, techniques are presented to visualize several types of graphs. The different visualization techniques are used in an integrated way. Implementation of some of the techniques requires a non‐manifold representation of the geometry of the feature model. This representation, and some other implementation aspects, are briefly described. Throughout the paper, numerous examples of images of feature models are given which show that the new visualization techniques can indeed improve the effectiveness of feature modelling. ACM CSS: I.3.7 Three‐Dimensional Graphics and Realism—visible line/surface algorithms, J.6 Computer‐AidedEngineering—feature modelling     

Quantitative and Qualitative Analysis of the Perception of Semi‐Transparent Structures in Direct Volume Rendering

Direct Volume Rendering (DVR) provides the possibility to visualize volumetric data sets as they occur in many scientific disciplines. With DVR semi‐transparency is facilitated to convey the complexity of the data. Unfortunately, semi‐transparency introduces challenges in spatial comprehension of the data, as the ambiguities inherent to semi‐transparent representations affect spatial comprehension. Accordingly, many techniques have been introduced to enhance the spatial comprehension of DVR images. In this paper, we present our findings obtained from two evaluations investigating the perception of semi‐transparent structures from volume rendered images. We have conducted a user evaluation in which we have compared standard DVR with five techniques previously proposed to enhance the spatial comprehension of DVR images. In this study, we investigated the perceptual performance of these techniques and have compared them against each other in a large‐scale quantitative user study with 300 participants. Each participant completed micro‐tasks designed such that the aggregated feedback gives insight on how well these techniques aid the user to perceive depth and shape of objects. To further clarify the findings, we conducted a qualitative evaluation in which we interviewed three experienced visualization researchers, in order to find out if we can identify the benefits and shortcomings of the individual techniques.     

On Visualizing Continuous Turbulence Scales

Turbulent flows are multi‐scale with vortices spanning a wide range of scales continuously. Due to such complexities, turbulence scales are particularly difficult to analyse and visualize. In this work, we present a novel and efficient optimization‐based method for continuous‐scale turbulence structure visualization with scale decomposition directly in the Kolmogorov energy spectrum. To achieve this, we first derive a new analytical objective function based on integration approximation. Using this new formulation, we can significantly improve the efficiency of the underlying optimization process and obtain the desired filter in the Kolmogorov energy spectrum for scale decomposition. More importantly, such a decomposition allows a ‘continuous‐scale visualization’ that enables us to efficiently explore the decomposed turbulence scales and further analyse the turbulence structures in a continuous manner. With our approach, we can present scale visualizations of direct numerical simulation data sets continuously over the scale domain for both isotropic and boundary layer turbulent flows. Compared with previous works on multi‐scale turbulence analysis and visualization, our method is highly flexible and efficient in generating scale decomposition and visualization results. The application of the proposed technique to both isotropic and boundary layer turbulence data sets verifies the capability of our technique to produce desirable scale visualization results.     

Hyperbolic Dependency Tree Visualization for Parser Evaluation

We present a novel tool to visualize dependency trees in a hyperbolic layout, and to provide visual support for comparative evaluation of parsing errors. Compared with traditional flat tree visualization, our hyperbolic tree visualization tool can be more convenient for showing long-range dependencies. Our tool integrates the hyperbolic view with a flat view, and support corpus-level error analysis. It offers several features, including statistical analysis of error distributions, visual analysis of individual dependency trees, and an integrated online interface.     

Visualization techniques for 3D vector fields: an application to electrostatic fields of molecules

In chemistry, computer graphics is now well established as a tool to interpret simulation results, since molecules are complicated in their structures and mutual interactions. As a probe to study such molecular interactions, electrostatic fields are considered to be useful. However, since they are given as 3D vector fields having cusps in the fields, conventional drawing techniques are not applicable. In this article, two new approaches are presented to visualize the electrostatic fields of molecules. One is an extension of topological skeletons, by which interactions between atoms having opposite charges are expressed, which is not shown with the conventional methods. The other is to define new functions called selective functions to select regions of interest only from the geometrical features of the fields. Furthermore, from the definition of the new functions, mathematical relations between the topological skeletons and selective functions are discussed. An example is presented in applications to chemical reactions to show how the scheme is used. Copyright © 2001 John Wiley & Sons, Ltd.     

Program graph visualization

Although there are many algorithms to draw hierarchical structures such as directed graphs and trees none specifically treat the problem of visualizing program graphs. This paper presents an algorithm and the underlying tool — ViewGraph — designed to visualize program graphs. The algorithm is divided in two parts: (1) determine node positions, and (2) assign routes to branches. The first part has three steps: level assignment, scope and position calculation. A modified algorithm used to assign levels to nodes in a tree is used to find Y coordinates; a concept called scope is used to define X coordinates. Scope is a prediction of the space required by a node and its descendants. A search on the available positions left by the placement of nodes is performed to route branches. A set of aesthetic aspects meant to help the development of program graph visualization algorithms is also proposed. The algorithm runs in an acceptable time making it useful even for interactive applications. © 1997 John Wiley & Sons, Ltd.     

Multicriteria decision making under uncertainty: a visual approach

Decision problems at the strategic level tend to have multiple criteria and outcomes that are uncertain. Many of the current decision‐making tools are too simplistic to incorporate the important features. This paper considers a multicriteria decision‐making scenario in which the outcomes of the decisions, evaluated on different criteria, are uncertain. The main contribution of this paper is the presentation of a tool that enables decision makers to visualize the expected payoff and likelihood that the payoff of a decision does not fall short of a preset target value. Furthermore, it presents decision makers with a tool that shows the tradeoff between expected payoff and downside risk. A variety of solution techniques are suggested that build upon this visualization.     

Model-driven visualizations of constraint-based local search

Visualization is often invaluable to understand the behavior of optimization algorithms, identify their bottlenecks or pathological behaviors, and suggest remedial techniques. Yet developing visualizations is often a tedious activity requiring significant time and expertise. This paper presents a framework for the visualization of constraint-based local search (CBLS) algorithms. Given a high-level model and a declarative visualization specification, the CBLS visualizer systematically produces animations to visualize constraints and objectives, violations, and conflicts, as well as the temporal behavior of these measures. The visualization specification is declarative and typically composed of a triple (what,where,how) indicating what to display, where, and with which graphical objects. The visualizer architecture is compositional and extensible. It provides building blocks which can be assembled freely by the user and focuses almost exclusively on static aspects, the dynamic aspects being automated by the use of invariants. The paper highlights various functionalities of the visualizer and describes a blueprint for its implementation.     

Recent Advances in Volume Visualization

In the past few years, there have been key advances in the three main approaches to the visualization of volumetric data: isosurfacing, slicing and volume rendering, which together make up the field of volume visualization.
In this survey paper we set the scene by describing the fundamental techniques for each of these approaches, using this to motivate the range of advances which have evolved over the past few years.
In isosurfacing, we see how the original marching cubes algorithm has matured, with improvements in robustness, topological consistency, accuracy and performance. In the performance area, we look in detail at pre-processing steps which help identify data which contributes to the particular isosurface required. In slicing too, there are performance gains from identifying active cells quickly.
In volume rendering, we describe the two main approaches of ray casting and projection. Both approaches have evolved technically over the past decade, and the holy grail of real-time volume rendering has arguably been reached.
The aim of this review paper is to pull these developments together in a coherent review of recent advances in volume visualization.     

拓扑分析在海洋特征提取中的应用

针对庞大复杂的海洋数据流场,利用三维标量场的拓扑分析方法,对海洋目标水团进行提取,达到特征可视化的目的。结合Morse理论对流形构造Morse—Smale复形,实现区域内水团的自动划分,并通过删除复形上的一系列临界点对对初始水团进行合并处理。实验结果验证了该方法的可行性和高效性。     

面向浏览器的医学影像可视化系统

目的 当前各大商业公司和开源社区所提供的医学影像可视化系统依赖于各类平台以及与平台相关的插件,难以实现跨平台访问.为此提出并实现了基于HTML5的面向现代浏览器的医学影像可视化系统.方法 基于B/S(browers/server)模式进行系统整体架构与设计,设计自定义的传输协议提供各种定制的图像可视化服务.对于2维影像,采用HTML的canvas技术和WebGL技术进行浏览器端硬件加速.对于3维医学影像,采用前后端异步操作的策略以提供渐进式可视化.算法构造原始数据的多分辨率采样,并在用户交互过程中实现自适应可视化.结果 在不同的浏览器、多组临床医学影像肝脏数据上测试了系统,表明系统支持跨浏览器的可视化.测试2维和3维可视化的结果表明,系统支持2维影像的实时可视化(25帧/s),支持3维影像的交互可视化.对于512×512×154的医学体数据,低精度绘制模式的可视化效率可以达到60帧/s,高精度绘制模式的可视化效率可达到 1帧/s 的绘制效率.结论 本文面向浏览器的医学影像可视化系统利用当下新兴的WEB技术实现了跨浏览器、跨平台地对用户提供服务,为远程及移动医疗影像可视化系统提供了机会.     

In vivo interactive visualization of four-dimensional blood flow patterns

In this paper we give an overview over a series of experiments to visualize and measure flow fields in the human vascular system with respect to their diagnostic capabilities. The experiments utilize a selection of GPU-based sparse and dense flow visualization algorithms to show the diagnostic opportunities for volumetric cardiovascular phase contrast magnetic resonance imaging data sets. Besides classical hardware accelerated particle and line-based approaches, an extensible tublet-based visualization, a four-dimensional volumetric line integral convolution and a new two-dimensional cutting plane tool for three-dimensional velocity data sets have been implemented. To evaluate the results, several hearts of human subjects have been investigated and a flow phantom was built to artificially simulate distinctive flow features. Our results demonstrate that we are able to provide an interactive tool for cardiovascular diagnostics with complementary hardware accelerated visualizations. Electronic Supplementary Material  The online version of this article () contains supplementary material, which is available to authorized users.

The communicative power of knowledge visualizations in mobilizing information and communication technology research

ABSTRACT

This editorial explores knowledge visualization, a field of study that investigates the power of visual formats to represent knowledge, as a strategy to enhance knowledge mobilization of results from ICT4D research. We highlight the fact that there are evidence-based guidelines for creating and crafting visualizations in academic writing. We also provide some visualization examples that highlight general knowledge visualization criteria such as anchor and extend, familiarity, clarity and consistency, include text, prudent simplicity and aesthetics. Although visualization is not the central theme of any of the papers in this issue, the papers offer a variety of visualization techniques as appropriate to the knowledge domain.