Visualization of scientific data - Domain-specific applications

1
Visualization of scientific data -
Domain-specific applications

• Mike Walterman,
• Manager of Graphics Programming,
• Scientific Computing and Visualization Group,
• Boston University

2
Introduction

• Objective of the presentation
• - Present methods for finding and/or creating
  domain specific visualization applications for
  LINUX
• Main topics
• - What is a domain specific application
• - Types of software
• - Sources for applications
• - Applications supported at BU
• - Web resources for finding applications
• - Conclusions

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What is a domain specific application?

• One persons domain is anothers supporting
  technology
• My criteria
• - Interface speaks the language for a specific
  group (e.g. astronomy, MRI, ...)
• - Operation of tool fits into domain
  work-flow
• - Has desired functionality, or is adaptable
  by means understood by target community

4
Types of software

• Toolkits
• - Programming oriented
• - Provide greatest flexibility
• - Provide basis for other software types
• Authoring and Modeling
• - Build applications via simple models (e.g.
  flow graph)
• - Create visual objects via intuitive
  interfaces
• - Domain specific applications can be obtained
  as shareware/freeware
• Domain Specific
• - Works out of the box
• - Targeted at specific community

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Sources for Visualization Software

• Universities
• - University of Illinois
• - University of Minnesota
• - University of Utah
• Government Labs
• - Argonne
• - Los Alamos
• - National Center for Atmospheric Research
  (NCAR)
• Commercial
• - Kitware
• - AVS
• - Flometrics
• Military
• - Naval Research Laboratory
• - U.S. Army Construction Engineering Research
  Laboratories

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What we support/have on LINUX at BU

• Toolkits
• - OpenGL
• - Inventor
• - OpenGL Performer
• - VTK
• - IDL
• - MatLab
• Authoring Systems
• - Maya
• - AVS
• - OpenDX
• Domain Specific
• - Gaussian 98
• - Quanta

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Toolkits - OpenGL, OpenInventor, Performer

• OpenGL
• - Low level de facto standard graphics API.
  Basic rendering technology for other packages.
• - Vendor Many (esp. if you want HW
  acceleration) - www.opengl.org
• OpenInventor
• - An object-oriented, cross-platform 3D
  graphics API for C and Java developers.
• - Heavily scene graph based.
• - Vendor Template Graphics - www.tgs.com
• Performer
• - A programming interface for creating
  real-time visual simulation and other
  performance-oriented 3D graphics applications.
• - Vendor Silicon Graphics - www.sgi.com

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VTK, IDL - Toolkits

• VTK (Visualization ToolKit)
• - Set of C classes
• - Interfaces to tcl, Java, and Python
• - Extensible through Object oriented means
• - Data flow model
• - Programers Environment
• - Vendor Kitware - www.kitware.com
• IDL (Interactive Data Language)
• - interpretative, allows interactive use
• - command-line driven, language with
  Fortran-like feel
• - extensible via user defined functions
• - Scientists Tool
• - Vendor Research Systems/Kodak -
  www.rsinc.com

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Authoring Systems - Maya, AVS, OpenDX

• Maya
• - General modeling tool for digital content
• - BU artists are primary users
• - Vendor Alias wavefront - www.aliaswavefront.
  com
• AVS
• - Data flow graph modeling system for
  building SciVis Applications
• - Applied in traditional and non-traditional
  scientific areas
• - Vendor Advanced Visual Systems -
  www.avs.com
• OpenDX
• - Data flow graph modeling system for building
  SciVis Applications
• - Free
• - Experimenting with this tool internally
• - Vendor IBMs Data Visualization Explorer -
  www.opendx.org

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Domain Specific ApplicationsQuanta, Gaussian 98,
Ideas

• Quanta
• - A molecular graphics analysis program.
  Modeling, Simulation, Visualization.
• - Used by BU Biomedical Engineering
• - Vendor Accelrys - www.accelrys.com/quanta
• Gaussian98
• - Molecular modeling system, performs
  computation based on laws of quantum mechanics.
• - Used by BU Chemistry
• - Vendor Gaussian, Inc. - www.gaussian.com
• Ideas
• - CAD/CAM/CAE - product design.
• - Used by BU Biomedical Engineering
• - Vendor Electronic Data Systems -
  www.eds.com/products/plm/ideas

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Sources on the Web

• NASA Ames Data Analysis Group
• - Good page listing sources of SciVis apps and
  examples
• - www.nas.nasa.gov/Groups/VisTech
• Student Page at Silesian University of Technology
  in Poland
• - A fair number of LINUX based Chemistry
  Packages
• - http//zeus.polsl.gliwice.pl/nikodem//linux4
  chemistry.html
• University of Minnesota Super Computing Institute
• - Good catalog of the more popular packages.
• - http//www.msi.umn.edu/user_support/scivis/s
  civis-list.html

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Sources on the Web continued

• OpenGL based visualization tools
• www.opengl.org/users/apps_hardware/applica
  tions/linux_apps.html
• SourceForges Scientific Plotting and
  Visualization packages for Linux.
• scilinux.sourceforge.net/graphvis.html
• Debians list of SciVIs Tools
• packages.debian.org/unstable/science

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Conclusion - Development Options

• Develop from scratch using programming toolkits
• Author a system
• Buy/Obtain an end user solution

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IDL Example

• Creates a 3D Plot of a surface stored in a data
  file
• File xsurface.pro
• Author Erik Brisson
• c fltarr(60,60)
• openr, 3, 'dat/ex_surf_60x60.dat'
• readf, 3, c
• xsurface, c
• end

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Conclusions