is&t scientific visualization tutorial – spring 2010 scientific visualization tutorial

IS&T Scientific Visualization Tutorial – Spring 2010

Scientific Visualization TutorialScientific Visualization Tutorial


Erik Brisson

Raymond Gasser

Robert Putnam

Aaron Fuegi

Visualization Tutorial Winter 2010Visualization Tutorial Winter 2010

[email protected]

[email protected]

[email protected]

[email protected]

TopicsTopics

Intro / overview (Erik) Matlab for Visualization (Ray) VTK and Paraview (Ray) Plotting (Robert) Image files for sci vis, and making animations

(Aaron) OpenGL, OpenSceneGraph, Maya, DAFFIE and

the display wall (Erik)


BU Scientific Computing & VisualizationBU Scientific Computing & Visualization


SCV ProvidesSCV Provides

High-performance, parallel computing systems and networks

Scientific code parallelization and optimization Scientific data visualization High-performance and high-resolution interactive

three-dimensional graphics Virtual environments/virtual reality Consulting and training Network-based video conferencing and

collaboration tools


What is sci-vis?What is sci-vis?

Could mean many things (e.g., plotting, illustration) Combination of 3-D graphics technology and human

perception of objects in space


Technique: CutplanesTechnique: Cutplanes


Technique: IsosurfacesTechnique: Isosurfaces


Technique: Vector glyphsTechnique: Vector glyphs


Technique: Vector field Technique: Vector field streaklinesstreaklines


The Visualization PipelineThe Visualization Pipeline


Math Proc Scientific visualization Computer Graphics

191 214 206 113 134 135 101 120 135 102 119 147 113 129 165117 131 170 125 138 170 158 168 195 219 227 246 244 251 255249 254 255 197 202 222 157 163 187 156 161 190 165 172 200218 224 246 250 255 255 252 255 251 251 255 252 245 249 250251 255 255 188 192 204 196 200 212 234 238 250 177 181 192111 114 133 122 121 155 154 151 194 182 176 220 243 240 255253 252 255 250 251 246 254 254 252 255 255 255 255 255 255254 254 254 255 255 255 255 255 255 254 254 254 255 255 255249 249 249 249 249 249 252 252 252 255 221 155 255 255 255255 255 255 255 255 255 255 255 255 255 255 255 255 255 255255 255 255 255 255 255 255 255 255 253 253 253 252 252 252252 252 252 253 253 253 255 255 255 255 255 255 255 255 255

The Visualization Pipeline - The Visualization Pipeline - HardwareHardware

Visualization with SCV – Dec 2008

Field instruments

Scientists/programmers

Supercomputers

Graphics machines

Publications, movies/DVDs, web Demos, educational software

The Visualization Pipeline - SoftwareThe Visualization Pipeline - Software


Data acquisition and preparation

Sci-vis tools

Geometric Representation

Rendering

Post-processing

Many possible workflowsMany possible workflows


Data Matlab VTK OpenGL Maya

IDL Paraview OSG Photoshop

Gnuplot DAFFIE Performer Premier

Xmgrace

Excel

Example using IDLExample using IDL


Your ProjectYour Project

Describe your work in visual / geometric way? What is goal, e.g., web, publication, presentation? What is the time line? How much learning time can you invest? How much do you expect to use?


Example workflow – molecular Example workflow – molecular dynamicsdynamics


Simulation creates data files Molecule x,y,z + type

colored spheres (C program) Electron density as volume data

isosurfaces (IDL) .obj files Rendered in Maya

Example workflow –Example workflow –pressure on turbinepressure on turbine


Simulation run on supercomputerProduced many Plot3d filesC code transforms data to .obj filesRendered in MayaProcessed using Imagemagick for

DVD Wall movies

Example workflow –Example workflow –showing entropyshowing entropy


Isosurfaces in IDLConvert output into .objRender in Maya, with transparencyView in 3D on Wall

Example workflow –Example workflow –stretched waterstretched water


Given positions of atoms in waterHow to show “holes”?Construct volume data of distanceUse volume visualization

Example workflow –Example workflow –CISMCISM


Researchers used OpenDXSCV staff modified OpenDX networksProduced wall movies and demos

Example workflow –Example workflow –Corporate ConnectionsCorporate Connections


Researchers provided dataSCV staff wrote custom viewing code

Artworld “family portrait”Artworld “family portrait”


……


Example - stereo protein visualization 1 Example - stereo protein visualization 1


Example - stereo protein Example - stereo protein visualization 2visualization 2


Example - magnetosphereExample - magnetosphere


Example - CFDExample - CFD


Example – medical illustrationExample – medical illustration


Example – medical Example – medical visualizationvisualization


Example – bat flightExample – bat flight


Example – GISExample – GIS


Examples – Tornado Examples – Tornado animationsanimations

http://access.ncsa.uiuc.edu/Stories/supertwister/page3.htm

http://access.ncsa.uiuc.edu/Stories/supertwister/index.htm


Image creditsImage credits

ArtWorld Family Portrait– Kat Curry / SCV

Stereo protein visualization 1 and 2– Dr Bernhard Rupp, Lawrence Livermore National

Laboratory and Dr Karl H Weisgraber, Gladstone Institute of Cardiovascular Disease http://www.answers.com/topic/scientific-visualization

Visualization Pipeline diagram– http://www.infovis-wiki.net/index.php/

Visualization_Pipeline

Magnetosphere


Image credits, continuedImage credits, continued

Magnetosphere– AICT Research Support Group, Univ. of Alberta

Medical illustration, standing male figure– www.posemaniacs.com

Medical illustration, synapse– Graham Johnson, Graham Johnson Medical Media,

Boulder, Colorado

Medical Visualization– Dr, Kai-hung Fung, Pamela Youde Nethersole Eastern

Hospital, Hong Kong


Image credits, continuedImage credits, continued

Bat flight– D J Willis (Brown, MIT)– M Kostandov, D K Riskin, D H Laidlaw, S M Swartz, K S

Breuer (Brown)– J Peraire (MIT)

Example – GIS of radio transmission– ESRI GIS and Mapping Software, www.esri.com


is&t scientific visualization tutorial – spring 2010 scientific visualization tutorial

Documents

idl visualization

visualization ray vtk

educational software

postprocessing slide

sci vis

d graphics technology

data acquisition

web demos