Visualization Facilities Research Articles

An X-ray system for visualizing fluid flows

A unique flow visualization facility, based on X-ray imaging, has been developed to study, characterize, and measure various flow characteristics in large vertical systems that have internal diameters of up to 32 cm and are as tall as 4 m. This facility provides digital X-ray radiography and stereography imaging to visualize and time-resolve 3D flow structures in multiphase and opaque fluid flows at up to 60 frames/s. In addition, X-ray computed tomography (CT) imaging records local time-averaged phase distributions in multiphase flows with a spatial resolution of less than 0.5 mm (∼0.15% of a 32-cm-diameter object). The X-ray hardware and image processing software for this facility are described. Selected imaging results are then presented for various single and multiphase fluid flows.

DSMDiff: a differentiation tool for domain-specific models

Model differentiation techniques, which provide the capability to identify mappings and differences between models, are essential to many model development and management practices. There has been initial research toward model differentiation applied to Unified Modeling Language (UML) diagrams, but differentiation of domain-specific models has not been explored deeply in the modeling community. Traditional modeling practice using the UML relies on a single fixed general-purpose language (i.e., all UML diagrams conform to a single metamodel). In contrast, Domain-Specific Modeling (DSM) is an emerging model-driven paradigm in which multiple metamodels are used to define various modeling languages that represent the key concepts and abstractions for particular domains. Therefore, domain-specific models may conform to various metamodels, which requires model differentiation algorithms be metamodel-independent and able to apply to multiple domain-specific modeling languages. This paper presents metamodel-independent algorithms and associated tools for detecting mappings and differences between domain-specific models, with facilities for graphical visualization of the detected differences.

BioWeka—extending the Weka framework for bioinformatics

Given the growing amount of biological data, data mining methods have become an integral part of bioinformatics research. Unfortunately, standard data mining tools are often not sufficiently equipped for handling raw data such as e.g. amino acid sequences. One popular and freely available framework that contains many well-known data mining algorithms is the Waikato Environment for Knowledge Analysis (Weka). In the BioWeka project, we introduce various input formats for bioinformatics data and bioinformatics methods like alignments to Weka. This allows users to easily combine them with Weka's classification, clustering, validation and visualization facilities on a single platform and therefore reduces the overhead of converting data between different data formats as well as the need to write custom evaluation procedures that can deal with many different programs. We encourage users to participate in this project by adding their own components and data formats to BioWeka. The software, documentation and tutorial are available at http://www.bioweka.org.

VALIDATION OF PREDICTIVE AXIS CONTROL STRUCTURE WITHIN A VIRTUAL OPEN ARCHITECTURE MACHINE TOOL

This paper first presents the elaboration of a virtual machine tool within an open architecture framework, including CAM (Computer Aided Manufacturing) modules such as trajectory generation and visualization facilities. The proposed advanced controller is then introduced within this simulator. Based on predictive strategies, it appears as an excellent control alternative coupled to a simple design procedure and implementation facilities. Moreover, the resulting controller, structured under the polynomial RST form, considered as a generic formalism for any SISO (Single Input Single Output) numerical controller, fulfills the requirements towards an open architecture framework. Validation tests are achieved within this virtual environment and compared to those obtained on a real machining center under its current control structure.

Characterization of the Content of the Cavity Behind a High-Speed Supercavitating Body

A high speed/high flow test facility was designed and implemented to study experimentally the supercavitating flow behind a projectile nose in a controlled laboratory setting. The simulated projectile nose was held in position in the flow and the cavity interior was made visible by having the walls of the visualization facility “cut through” the supercavity. Direct visualization of the cavity interior and measurements of the properties of the cavity contents were made. Transducers were positioned in the test section within the supercavitation volume to enable measurement of the sound speed and attenuation as a function of the flow and geometry parameters. These characterized indirectly the content of the cavity. Photography, high speed videos, and acoustic measurements were used to investigate the contents of the cavity. A side sampling cell was also used to sample in real time the contents of the cavity and measure the properties. Calibration tests conducted in parallel in a vapor cell enabled confirmation that, in absence of air injection, the properties of the supercavity medium match those of a mixture of water vapor and water droplets. Such a mixture has a very high sound speed with strong sound attenuation. Injection of air was also found to significantly decrease sound speed and to increase transmission.

The global lambda visualization facility: An international ultra-high-definition wide-area visualization collaboratory

The research outlined in this paper marks an initial global cooperative effort between visualization and collaboration researchers to build a persistent virtual visualization facility linked by ultra-high-speed optical networks. The goal is to enable the comprehensive and synergistic research and development of the necessary hardware, software and interaction techniques to realize the next generation of end-user tools for scientists to collaborate on the global Lambda Grid. This paper outlines some of the visualization research projects that were demonstrated at the iGrid 2005 workshop in San Diego, California.

The Agent Visualization System: A Graphical and Textual Representation for Multi-Agent Systems

As scientists from various domains increasingly resort to agent-based simulation for a more thorough understanding of real-world phenomena, the need for a simulation environment that facilitates rapid development of multi-agent systems is growing. Such a platform should provide means of visualizing the simulated scenario. In this paper we present the agent visualization system, the first system of its kind to specifically focus on catering to the visualization needs of agent-based simulation. The proposed system is a generic add-on that equips a simulation environment with a rich set of visualization facilities offering a variety of textual and graphical browsers that allow the modeler to detect trends and relationships in the simulation scenario. Some techniques from the field of information visualization were adapted and added to the system, while others were devised especially to be used in it. Regardless of their origin, all visualization techniques were thoroughly revised to make them generic enough to fit in our generic system. Agent visualization is more challenging than traditional information visualization in more than one respect. One of them is that the data to be visualized is not static; the simulation system is constantly producing data with every time step. Moreover, the sheer amount of data, together with its diversity, call for special adaptations to ensure that the system remains responsive and generic. To illustrate the various features of the proposed agent visualization system, we present a visualization of MicroTerra; a simulation scenario involving a group of beings trying to maximize their food intake.

The Design and Implementation of a Framework for Automatic Modularization of Software Systems

It is a difficult task to manually cluster a large software system into loosely coupled modules with a large number of highly cohesive classes. On the other hand clustering is a NP-Hard problem. In this paper the design and implementation of a flexible software environment, called DAGC, to assemble and experiment with genetic clustering algorithms, for software (re)modularization, is described. The main idea behind the design of the DAGC is to define a general genetic clustering algorithm which may invoke different implementations for the parts from an extendable list of components. The DAGC provides visualization facilities to compare and evaluate different genetic clustering algorithms, regarding the two parameters of running time and the quality of clusters generated by the algorithms.

Biological workflow with BlastQuest

Besides domain-specific biological problems, biologists are confronted with many computational problems. The large amount of varying, heterogeneous, and semi-structured biological data, the increasing complexity of biological applications, methods, and tools afflicted with uncertainty and missing knowledge, as well as the lacking interoperability of available tools necessitate integrative measures to enable biology workflow. In this paper we address these problems in the context of the processing and evaluation of BLAST query results. We present a new tool, called BlastQuest, which relies on database technology and provides sophisticated interactive and Web-enabled query, analysis, and visualization facilities for genomics data. The interface with the Gene Ontology and the KEGG pathway databases decisively foster the biological workflow. Finally, based on our experience with BlastQuest, we briefly sketch a new concept, called Genomics Algebra, for solving genomic data management problems from a broader perspective.

Biological workflow with BlastQuest

Besides domain-specific biological problems, biologists are confronted with many computational problems. The large amount of varying, heterogeneous, and semi-structured biological data, the increasing complexity of biological applications, methods, and tools afflicted with uncertainty and missing knowledge, as well as the lacking interoperability of available tools necessitate integrative measures to enable biology workflow. In this paper we address these problems in the context of the processing and evaluation of BLAST query results. We present a new tool, called BlastQuest, which relies on database technology and provides sophisticated interactive and Web-enabled query, analysis, and visualization facilities for genomics data. The interface with the Gene Ontology and the KEGG pathway databases decisively foster the biological workflow. Finally, based on our experience with BlastQuest, we briefly sketch a new concept, called Genomics Algebra, for solving genomic data management problems from a broader perspective.

Recent advances in the marker and cell method

In this article recent advances in the MAC method will be reviewed. The MAC technique dates back to the early sixties at the Los Alamos Laboratories and this paper starts with a historical review, and then a summary of related techniques. Improvements since the early days of MAC (and the Simplified MAC-SMAC) include automatic time-stepping, the use of the conjugate gradient method to solve the Poisson equation for the corrected velocity potential, greater efficiency through stripping out all particles (markers) other than those near the free surface, more accurate approximations of the free surface boundary conditions, the addition of a bounded high accuracy upwinding for the convected terms (thereby being able to solve higher Reynolds number flows), and a (dynamic) flow visualization facility. This article will concentrate, in the main, on a three-dimensional version of the SMAC method. It will show how to approximate curved boundaries by considering one configurational example in detail; the same will also be done for the free surface. The article will avoid validation, but rather focus on many of the examples and applications that the MAC method can solve from turbulent flows to rheology. It will conclude with some speculative comments on the future direction of the methodology.

CIF applications. XV.enCIFer: a program for viewing, editing and visualizing CIFs

TheenCIFerprogram permits the location, reporting and correction of syntax and format violations in single- or multi-block crystallographic information files (CIFs). The program also permits the editing of existing individual or looped data items and the addition of new data in these categories, and provides data-entry wizards for the addition of two types of standard information for small-molecule structural studies, namely publication data and chemical and physical property information. Facilities for the graphical visualization and manipulation of structure(s) in a CIF are also provided.

Explorative and dynamic visualization of data in virtual reality

A software system has been developed for the study of dynamic glyph visualizations in the context of Visual Data Mining in Virtual Reality. The system uses parallel processing to calculate data visualizations in real-time, with real-time interaction and dynamic changes to the view. The system allows morphing between different visualizations, the use of dynamic features like “vibrations” and “rotations” of thousands of objects individually, and dynamic visualization, where the influence of any variable of a dataset with a “reasonable” distribution, can be shown as a dynamic development. It appears that these facilities for dynamic data visualization have a very promising potential, but their optimal use will depend on further developments in the context of their individual practical application.

Reconstructing urban contexts online for interactive urban designs

The Sheffield Urban Contextual Databank (SUCoD) system was developed as a Web-based urban information system to host the urban data gathered by the Sheffield Urban Study programme. Our development of the SUCoD system provides user-centred dynamic retrieval and visualisation facilities for accessing multidimensional city datasets. The paper reports on a study of applying the SUCoD resources in an educational setting to explore its usability in two accounts: presenting urban site investigations as online urban narratives and the development of 3D schematic urban proposals. The current experiment suggests that SUCoD could be further developed into an online Urban Design Collaboratory.

Informed Spatial Decisions Through Coordinated Views

According to a commonly accepted view, the process of decision making comprises three major phases: intelligence (situation analysis and problem recognition), design (finding possible variants of problem solution), and choice (evaluation of the options and selection of the most appropriate ones). It is widely recognised that exploratory data visualisation is very helpful during the first phase of the decision-making process, while the other phases require different software tools. In particular, the choice phase is typically supported by various computational methods that find appropriate trade-offs among multiple conflicting criteria taking into account user-specified priorities. Visualisation plays a limited role: in the best case, it is used to represent the final results of the computations. We argue that conscious, well-substantiated choice requires a more extensive use of exploratory visualisation facilities, which need to be properly coordinated with the computational multi-criteria decision support methods. Extremely important is a high degree of user interactivity, which allows the user to probe the robustness and quality of computationally derived solutions. We suggest several mechanisms for linking and coordinating visual exploratory tools with two types of computational methods differing in the sort of output they produce. We demonstrate the use of this dynamic link with an example of a real spatially related decision problem.

QMTool: an xmi-based management platform for QoS-aware IP networks

Technological and human factors have contributed to the increasing complexity of the network management problem. Heterogeneity and globalization of network resources have, on one hand, increased user expectations for flexible and easy-to-use environments and, on the other, propounded entirely novel ways to face the management problem. Several research efforts recognize the need for integrated solutions to manage both network resources and services in open and global environments. Undoubtedly, these solutions should permit the coexistence of different management models and should interoperate with legacy systems. The presented management system, QoS management tool (QMTool), aspires to address the heterogeneity, complexity, and dynamic behavior of QoS-enabled IP networks by taking advantage of the optimum fit of a number of novel technologies. A layered framework architecture, including element, network management, and visualization service, is provided, and a high level of information abstraction in network configuration and monitoring is introduced mainly based on the capabilities of the Extensible Markup Language (XML). Moreover, the functional components for providing (re-)configuration, fault management monitoring, and network visualization facilities are also presented, followed by notes of implementation issues.

NERSC “Visualization Greenbook” Future Visualization Needs of the Doe Computational Science Community Hosted at NERSC

In this paper we present the findings and recommendations that emerged from a one-day workshop held at Lawrence Berkeley National Laboratory (LBNL) on June 5, 2002, in conjunction with the National Energy Research Scientific Computing (NERSC) User Group (NUG) Meeting. The motivation for this workshop was to solicit direct input from the application science community on the subject of visualization. The workshop speakers and participants included computational scientists from a cross-section of disciplines that use the NERSC facility, as well as visualization researchers from across the country. We asked the workshop contributors how they currently visualize their results, and how they would like to do visualization in the future. We were especially interested in each individual's view of how visualization tools and services could be improved in order to better meet the needs of future computational science projects. The outcome of this workshop is a set of findings and recommendations that are presented in more detail later in this paper, and are briefly summarized here. Scientific visualization is a crucial technological capability that plays an important role in understanding data created by computational science projects as well as experiments. In order to be effective, visualization technology should be easy to use for a non-expert. The term “easy to use” encompasses a number of different categories, including a short learning curve, tight integration with computational frameworks, availability on the desktop as well as the fixed visualization facility, tools that are tailored for each specific application domain, and low cost. Current visualization tools fall short in several key areas of capability. Few visualization tools are capable of processing large datasets, such as those commonly generated at NERSC. Better support for parallel visualization tools may prove useful in leveraging large parallel machines as visualization resources. Multivariate visualization - multiple grids, many species, and many dimensions - is needed in order to quickly gain insight into large datasets. Related “drill-down” capabilities, such as the ability to quickly move from macro to micro views (used in “data mining”), would be extremely helpful in understanding data but are missing from most visualization tools. Many application scientists perceive a conundrum when it comes to visualization support. Support for visualization within each individual program level is often inadequate or nonexistent due to funding constraints, yet support for visualization at the institutional level is also often inadequate or nonexistent. Better solutions are needed for remote visualization. Current approaches are further constrained by network bandwidth and access to resources. The proliferation of visualization tools and data formats poses challenges. Researchers must often master many different tools in order to achieve the desired results. Data format conversion is often required when moving between tools. Common data formats and frameworks for visualization tools are needed to reduce duplication of effort and better promote sharing of resources and results. Better communication is needed between the visualization and computational science communities. The computational scientists are often unaware of current trends and practices in the visualization community. By being more aware of the needs of the computational science community, the visualization research programs can be crafted so as to be more responsive to their needs. As a result of the workshop, we have developed a set of recommendations that can be summarized as follows: • Establish a coherent program that focuses on remote visualization. A remote visualization program should provide tools and infrastructure that can be used by multiple “virtual teams”. • Establish mechanisms whereby generally-applicable visualization technology is developed and deployed in a centralized fashion. • Develop a research program in interactive visualization with running codes that stresses the integrated design and development of coupled simulation-visualization methods. • Establish a research program in the areas of multi-field visualization and multi-dimensional data visualization. • Establish a research program in the area of automated data exploration for next generation petascale datasets.

Nuclear magnetic resonance data processing. MestRe‐C: A software package for desktop computers

AbstractMagnetic Resonance Companion (MestRe‐C) is a software package that offers state‐of‐the‐art facilities for data processing, visualization, and analysis of high‐resolution nuclear magnetic resonance (NMR) data, combined with a robust, user‐friendly graphical interface that fully exploits the power and flexibility of the Windows platform. The program provides a variety of conversion facilities for most NMR spectrometer formats and includes all the conventional processing, displaying, and plotting capabilities of an NMR program, as well as more advanced processing techniques. A brief review of the basic concepts of NMR data processing is included also. © 2003 Wiley Periodicals, Inc. Concepts Magn Reson Part A 19A: 80–96, 2003.

Shock waves in aviation security and safety

Accident investigations such as of Pan Am 103 and TWA 800 reveal the key role of shock-wave propagation in destroying the aircraft when an on-board explosion occurs. This paper surveys shock wave propagation inside an aircraft fuselage, caused either by a terrorist device or by accident, and provides some new experimental results. While aircraft-hardening research has been under way for more than a decade, no such experiments to date have used the crucial tool of high-speed optical imaging to visualize shock motion. Here, Penn State's Full-Scale Schlieren flow visualization facility yields the first shock-motion images in aviation security scenarios: 1) Explosions beneath full-size aircraft seats occupied by mannequins, 2) Explosions inside partially-filled luggage containers, and 3) Luggage-container explosions resulting in hull-holing. Both single-frame images and drum-camera movies are obtained. The implications of these results are discussed, though the overall topic must still be considered in its infancy.

Barcelona, Spain, October 7-8, 2002: Graph-Based Tools (GraBaTs 2002)

Barcelona, Spain, October 7-8, 2002: Graph-Based Tools (GraBaTs 2002)