ScientificScientific VisualizationVisualization

SpringSpring 20112011

2011-1-5 1 InstructorInstructor

XiaoqiangXiaoqiang WangWang Office:Office: DSLDSL 495495 Webpage:Webpage: –– http://people.sc.fsu.edu/~xwang/http://people.sc.fsu.edu/~xwang/ Email:Email: [email protected]@.fsu.edu CourseCourse Time:Time: MWFMWF 10:10am10:10am –– 11:0011:00 amam OfficeOffice Hour:Hour: MWFMWF 11:00am11:00am –– 12:0012:00 amam –– AppointmentAppointment

2011-1-5 2 PrerequisitesPrerequisites

YouYou willwill bebe writingwriting programsprograms Eg. CGS 3406 – OO PROGRAM IN C++ AnAn abilityability toto learnlearn aa programmingprogramming librarylibrary onon youryour ownown OpenGL ComfortableComfortable withwith matrixmatrix algebraalgebra andand calculuscalculus Basic linear algebra used

2011-1-5 3 CourseCourse materialsmaterials

No textbook required – Graphics by Hearn and Baker – Handbook

Lecture notes

Research papers – Distributed/referred in class

Web sources

2011-1-5 4 WorkWork

HomeworkHomework – Programming assignments (60%) – A paper and presentation (15%) ProjectsProjects (25%)(25%) – Final project LateLate submissionsubmission willwill bebe punished.punished. AcademicAcademic dishonestydishonesty willwill bebe treatedtreated seriouslyseriously – Do not share code with another student or debug together

2011-1-5 5 OutlineOutline

CourseCourse ContentContent WhatWhat’’ss Visualization?Visualization? WhyWhy wewe needneed Visualization?Visualization? TypesTypes ofof Visualization?Visualization? ApplicationsApplications ofof Visualization?Visualization? HistoryHistory ofof VisualizationVisualization -- TheThe fourfour phasesphases ofof visualization.visualization. TheThe challengeschallenges ofof visualization.visualization.

2011-1-5 6 ComputerComputer GraphicsGraphics forfor VisualizationVisualization OpenGLOpenGL DrawingDrawing geometricgeometric objectsobjects ViewingViewing InterceptionInterception andand CullingCulling LightingLighting andand ShadingShading SpecialSpecial topicstopics

2011-1-5 7 ScientificScientific VisualizationVisualization IsosurfaceIsosurface renderingrendering VolumeVolume renderingrendering –– SplattingSplatting –– RaycastingRaycasting VectorVector andand tensortensor visualizationvisualization SelectedSelected topicstopics

2011-1-5 8 WhatWhat isis Visualization?Visualization?

““AA picturepicture sayssays moremore thanthan aa thousandthousand wordswords”” (Chinese(Chinese proverb)proverb) ““AA picturepicture sayssays moremore thanthan aa thousandthousand numbersnumbers”” (Slight(Slight variationvariation ofof thethe ChineseChinese proverb)proverb)

2011-1-5 9 WhatWhat isis Visualization?Visualization? ProcessProcess ofof makingmaking aa computercomputer imageimage oror graphgraph forfor givinggiving anan insightinsight onon data/informationdata/information –– TransformingTransforming abstract,abstract, physicalphysical data/informationdata/information toto aa formform thatthat cancan bebe seenseen –– InterpretingInterpreting inin visualvisual termsterms oror puttingputting intointo visualvisual formsforms (i.e.,(i.e., intointo pictures)pictures) CognitiveCognitive processprocess –– FormForm aa mentalmental imageimage ofof somethingsomething –– InternalizeInternalize anan understandingunderstanding

2011-1-5 10 VisualizationVisualization ProcessProcess Measured/Scanned Data: Computation: -CT, MRI, ultrasound Financial data: -/modeling -transactions per day

Data

Transform Display 2011-1-5 11 VizViz vs.vs. GraphicsGraphics vs..vs.. ImagingImaging

ImagingImaging -- Enhance,Enhance, analyze,analyze, manipulatemanipulate imagesimages GraphicsGraphics -- MakeMake pictures!pictures! geometricgeometric datadata isis storedstored inin thethe computercomputer forfor thethe purposespurposes ofof performingperforming calculationscalculations andand renderingrendering 2D2D imagesimages VisualizationVisualization -- Exploration,Exploration, transformation,transformation, viewingviewing datadata asas imagesimages

2011-1-5 12 RelationRelation ToTo OtherOther FieldsFields

Illumination Signal/ Engineering Processing Optics Vision Computational Geometry Visualization Applied Psychology Mathematics Cognition Hardware User Interfaces

2011-1-5 13 Why?Why? ExtendsExtends ourour visionvision –– RemovesRemoves limitslimits ofof humanhuman visionvision inin space,space, time,time, frequencyfrequency andand complexitycomplexity –– CreatesCreates imagesimages oror picturespictures ofof thingsthings thatthat otherwiseotherwise cancan notnot bebe seenseen See an object’s internal structure (visible man) See things that are far away or slow in evolution (stars and nebulas) See microscopic world (crystal structure) See things that move very fast (molecular dynamics)

2011-1-5 14 HumanHuman InnerInner OrgansOrgans VisibleVisible ()(voxel) manman –– ReconstructionReconstruction ofof humanhuman bodybody fromfrom tomographictomographic datasetsdatasets ofof dissecteddissected realreal bodybody

2011-1-5 www.uke.uni-hamburg.de 15 StarsStars andand EmissionEmission NebulasNebulas

VisualizingVisualizing OrionOrion Nebula:Nebula:

Nadeau et al., Computer Graphs Forum, 20: 27 (2001)

2011-1-5 16 CrystalCrystal StructureStructure

MgSiO3MgSiO3 perovskiteperovskite

AnAn orthorhombicorthorhombic unitunit cellcell

AtomicAtomic coordinationcoordination

2011-1-5 17 TypesTypes ofof VisualizationVisualization ScientificScientific VisualizationVisualization – Scientific data InformationInformation VisualizationVisualization – abstract data has no inherent spatial structure thus it does not allow for a straightforward mapping to any geometry with arbitrary relationship DataData VisualizationVisualization – A more general term – data sources beyond science such as financial, marketing, or business data – Broad enough to encompass both scientific and information visualization 2011-1-5 18 VisualizationVisualization ScientificScientific InformationInformation VisualizationVisualization VisualizationVisualization – Visualization of – Visualization of physical data abstract data

Automobile web site Ozone layer around earth - visualizing links

2011-1-5 19 ScientificScientific VisualizationVisualization RelatesRelates toto andand representsrepresents somethingsomething physicalphysical oror geometricgeometric –– ImagesImages ofof humanhuman brainbrain –– AirAir flowflow overover aa wingwing

DataData comecome fromfrom scientificscientific computingcomputing andand measurementsmeasurements

2011-1-5 20 ScientificScientific ComputingComputing

RealReal materialsmaterials simulation/modelingsimulation/modeling –– ElectronicElectronic calculationscalculations –– AtomisticAtomistic MDMD (molecular(molecular dynamics)dynamics) modelingmodeling –– FiniteFinite elementelement (continuum)(continuum) modelingmodeling SolvingSolving differentialdifferential equationsequations –– ComputationalComputational fluidfluid dynamicsdynamics –– TemperatureTemperature distributiondistribution –– ElectromagneticElectromagnetic fieldfield

2011-1-5 21 ApplicationsApplications -- MeteorologyMeteorology

Pressure at levels in atmosphere - illustrated by contour lines in a slice plane

Generated by the Vis5D system from University of Wisconsin (now Vis5d+) Vis5d: http://www.ssec.wisc.edu/~billh/vis5d.html Vis5d+ : http://vis5d.sourceforge.net

2011-1-5 22 ApplicationsApplications -- MedicineMedicine

From scanner data, we can visualize 3D pictures of human anatomy, using

Generated by Anatomy.TV used by medical students to learn anatomy

Look under Anatomy.TV in Library electronic resources 2011-1-5 23 ApplicationsApplications –– ClimateClimate PredictionPrediction

Simulation of 21st century climate evolution Real-time display of results – temperature, cloud, precipitation, etc Massive ensemble of runs : distributed public-resource computing project – see www.climateprediction.net to participate!

2011-1-5 24 ApplicationsApplications –– ComputationalComputational FluidFluid DynamicsDynamics Interface between immiscible fluids – e.g. oil / water Loops and fingers arise when mixing starts – Rayleigh-Taylor instability Simulated on ASCII Blue Pacific (Cook & Dimotakis, 2001) Interface visualized using a density

2011-1-5 25 ApplicationsApplications –– ComputationalComputational FluidFluid DynamicsDynamics

Flow of air around a car – Vectors and particle paths illustrate flow – Coloured slice indicates pressure

2011-1-5 26 ApplicationsApplications –– IntegrativeIntegrative BiologyBiology A large e-science project on Integrative Biology

This involves modelling behaviour of human heart, and of cancer tumours

Visualization is of electrical activity in heart, showing the spiral wave pattern that is a precursor to fibrillation

2011-1-5 27 ApplicationsApplications -- AstronomyAstronomy The Astrogrid project is building a virtual observatory http://www.astrogrid.org http://www.eurovotech.org

Visualization is a fundamental tool in presenting star and in understanding relationships between observations 2011-1-5 28 VisualizationVisualization BCBC

Imagination or visualization, and in particular the use of , has a crucial part to play in scientific investigation. – Who said this? When? There are many examples of the use of visualization Before (BC) – graph plots in 10th century – business graphics in 18th century (Playfair) – contour plots in 18th century (Halley)

Answer: Rene Descartes, 1637

2011-1-5 29 TheThe FirstFirst VisualizationVisualization

This and following two pictures are taken from Brian Collins ‘ - Has it all been seen before?’ in ‘Animation and Scientific Visualization’, Academic Press

2011-1-5 30 TheThe FirstFirst BusinessBusiness GraphicsGraphics

2011-1-5 31 TheThe FirstFirst ContourContour MapMap

2011-1-5 32 EarlyEarly ComputerComputer VisualizationVisualization

FromFrom earlyearly daysdays ofof computing,computing, scientistsscientists havehave carriedcarried outout numericalnumerical simulationsimulation -- andand lookedlooked toto visualizationvisualization toto helphelp understandunderstand thethe results.results. VisualizationVisualization systemssystems havehave evolvedevolved inin fourfour differentdifferent stylesstyles -- allall stillstill inin useuse todaytoday (so(so notnot reallyreally history!)history!)

2011-1-5 33 SubprogramSubprogram LibrariesLibraries

1960 onwards Libraries of subprograms to draw graphs, contour plots … Scientists include calls to library routines from within their own code Leading examples from 1970- 1985 era were: – GHOST (UKAEA Culham) – NAG Graphics Library

2011-1-5 34 SubprogramSubprogram LibrariesLibraries

ThisThis stylestyle continuescontinues todaytoday – NAG Graphics Library still available – C++ classes provide modern version of this style GreatGreat flexibilityflexibility –– butbut needneed toto programprogram ApplicationApplication ProgrammingProgramming InterfaceInterface vtk : www.visualizationtoolkit.org

2011-1-5 35 InteractiveInteractive PackagesPackages

From late 1970 onwards Specialist packages gnuplot allowing data to be visualized using special purpose scripting language Example: – gnuplot www.gnuplot.info Less flexible, but simpler (provided commands are easy to learn!)

2011-1-5 36 InteractiveInteractive PackagesPackages

Matlab is a powerful system for computation and visualization – Has its own C-like language www.mathworks.com

2011-1-5 37 InteractiveInteractive PackagesPackages

ThisThis stylestyle continuescontinues todaytoday…… RR isis aa powerfulpowerful interactiveinteractive environmentenvironment forfor statisticalstatistical computationcomputation andand visualizationvisualization FreelyFreely availableavailable –– forfor bothboth linuxlinux andand WindowsWindows

2011-1-5 38 InteractiveInteractive PackagesPackages

The popularity of spreadsheets has brought a requirement to provide visualization … Excel has a wizard to guide construction of a variety of chart types…

2011-1-5 39 ScientificScientific VisualizationVisualization Recent surge of interest in scientific visualization was sparked by an NSF report: Visualization in Scientific Computing – McCormick, de Fanti and Brown - 1987

Argued that investment in high performance computing in US was wasted unless there was corresponding investment in visualization

This motivated a third style of visualization system...

2011-1-5 40 VisualVisual ProgrammingProgramming SystemsSystems

From late 1980s onwards Scientific visualization seen as a sequence of simple processing steps: eg contouring – read in data – create contour lines – draw contour lines Systems provide modules implementingimplementing simplesimple stepssteps in a visualization pipeline Scientist uses ‘visual programming’ to connect modules together

2011-1-5 41 VisualVisual ProgrammingProgramming -- IRISIRIS ExplorerExplorer

2011-1-5 42 VisualVisual ProgrammingProgramming SystemsSystems

Visual programming allows easy experimentation which is what one needs in visualization Examples are: – www.amira.com – IRIS Explorer www.nag.co.uk – AVS www.avs.com – OpenDX (grown from IBM Visualization Data Explorer) www.opendx.org

2011-1-5 43 ServiceService--basedbased VisualizationVisualization

TheThe InternetInternet eraera hashas introducedintroduced aa fourthfourth stylestyle ofof systemsystem –– wherewhere aa visualizationvisualization ‘‘serviceservice’’ isis delivereddelivered overover thethe internetinternet usingusing WebWeb technologiestechnologies www.sdsc.edu/vizwiz ClientClient--sideside withwith JavaJava appletsapplets……..

2011-1-5 44 ServiceService--basedbased VisualizationVisualization

… or server side Here a form on a web page is used to make a visualization ‘request’ Processed by a visualization system on server and returned to client as VRML – the Web standard for 3D graphics

2011-1-5 45 ServiceService BasedBased VisualizationVisualization

KartooKartoo allowsallows youyou toto visualizevisualize resultsresults ofof webweb searches..searches.. See:See: www.kartoo.com

Search for ‘Scientific Visualization’

2011-1-5 46 TheThe FourFour PhasesPhases ofof VisualizationVisualization SystemsSystems

These four phases correlate with four phases in computing generally Subprogram libraries – begun in era of batch computing Interactive packages – begun in era of interactive computing, with terminals connected to host Visual programming systems – begun in era of workstation computing, with graphical user interfaces Service-based visualization – begun in era of computing

2011-1-5 47 Challenges?Challenges?

ScaleScale DimensionalityDimensionality DataData typestypes PresentationPresentation InteractivityInteractivity

2011-1-5 48 DataData ExplosionExplosion HowHow toto makemake sensesense outout ofof thethe datasetsdatasets whenwhen theythey becomebecome veryvery largelarge

ScientificScientific datadata –– AA millionmillion--atomatom simulation:simulation: 77 GB/stepGB/step –– SatelliteSatellite oror spacespace station:station: TB/dayTB/day –– MRIMRI dataset:dataset: 25632563 == 1616 MB/sliceMB/slice –– LaserLaser scanning:scanning: 22 millionmillion points/minutepoints/minute

2011-1-5 49 DimensionalityDimensionality ThreeThree dimensiondimension (trivariate(trivariate data)data) –– WeWe areare inin 3D3D worldworld –– VolumeVolume visualizationvisualization (mapping(mapping 3D3D datadata toto 2D2D screen)screen) MultidimensionMultidimension (hypervariate(hypervariate data)data) –– CarCar attributes:attributes: Make,Make, model,model, year,year, milesmiles perper gallon,gallon, cost,cost, no.no. ofof cylinders,cylinders, size,size, weightweight –– HowHow toto displaydisplay relationshipsrelationships betweenbetween manymany variablesvariables

2011-1-5 50 DataData TypesTypes StructuredStructured versusversus unstructuredunstructured datadata – Unstructured (irregular) data are less compact and efficient – Preprocessing of data Scalar,Scalar, vectorvector andand tensortensor datadata – Density, temperature – Data from flow dynamics – Stress-strain data NonNon--numericalnumerical datadata – Ordinal: days of the week – Categorical data: names of animals

2011-1-5 51 PresentationPresentation ProblemProblem DisplayDisplay withoutwithout ambiguityambiguity –– Colors,Colors, lighting,lighting, translucent,translucent, animation,animation, texturetexture mappingmapping TooToo muchmuch datadata forfor tootoo littlelittle displaydisplay areaarea (screen)(screen) –– TooToo manymany casescases –– TooToo manymany variablesvariables NeedNeed toto highlighthighlight particularparticular casescases oror variablesvariables

2011-1-5 52 InteractivityInteractivity

VisualizationVisualization isis naturallynaturally interactiveinteractive –– RealReal--timetime interactions,interactions, i.ei.e,, virtualvirtual environmentsenvironments –– ShowShow multiplemultiple differentdifferent perspectivesperspectives onon thethe datadata

2011-1-5 53 ReviewReview

WhatWhat’’ss Visualization?Visualization? WhyWhy wewe needneed Visualization?Visualization? TypesTypes ofof Visualization?Visualization? ApplicationsApplications ofof Visualization?Visualization? HistoryHistory ofof VisualizationVisualization -- TheThe fourfour phasesphases ofof visualization.visualization. TheThe challengeschallenges ofof visualization.visualization.

2011-1-5 54