High school workshop: Scientific visualization

Universitat de Barcelona

January 2007

Introduction

Wearegoingtoexplorethedatafroma MagneticResonanceofaperson'shead. Program:ParaView,freesoftware, multiplatform(Linux,Mac,Windows...)

Loginthesystem ExecutetheprogramParaViewwith1clickoverthe iconplacedonthedesktop:

Openadatafile
1.Menu File OpenData 2.choose head.vtk andpress Open button.

Applicationareas
1.Display area (empty because wehave nopointed whatto render). 2. Modules list (wewill builda module pipelineto transfer datafrom moduleto module). 3.Module buttons(to accessthe common ones;we canfind morein MenuFilter)

4. Parameters area (wherewe canmodify themodule parameters)

Surfaceextraction
1.press surface extraction button. 3.press Addbutton (toaddthe valuetothe contour valueslist).

2.choose 1200as the surface value (itisahigh density value correspon dingto bones)

4.pressthe Accept button (toletthe module processthe data).

Cameramovements
1.press theLeft mouse buttonto change camera's pointof view. 3.pressthe Reset buttonto retrievethe default camera parameters.

2.press theRight mouse buttonto change camera's zoom.

4.pressthe Middle mouse buttonto dragthe camera.

Choosingadesiredcolor
1.press Display tab. 4.choose thedesird colorand pressOK button. 5.observe theresults. 6.before nextslide choose Colorby Point Normals. 7.press EditColor Map.

2.choose theColor by Property option. 3.pressthe ActorColor button

Choosingasetofcolors
1.choose Vector Compon. option. 3.press Backbutton toreturnto Displaytab.

2.selectX compon.

4.observe thecolors: whyare they different? 5.review previous slidesto leavea whitecolor again.

Representationstyles
1.check Pointsof surface optionsas Repres.

2.tryto change thePoint sizeto2 (finally, leavea1 again)

3.observe thatinstead ofthe surface,a setofpoints belongingto thesurface are rendered.

Interpolationstyles
1.choose Surfaces as Represen. 3.observe thatnow youcan distinguish every polygon usedto renderthe surface.

2.tagFlat interpolat. (=no interpol.)of thenormal vectors.

4.leave Gouraud interpolation again.

Show/Hideeachmodule
1.press theeye icon beforethe Contour0 module.

3.tryto show/hide theother modules.

2.observe thatthe boneisno longer displayed.

4.showall modules again.

Moduleinformation
1.press Informat. tab. 3.choose theinput datamodule (head.vtk) and observethat thedataare scalar values [0..4095]

2.observe thatthe module produces anarrayof vectors(3 floats)with arange [1..1]

4.observe each module Bounding dimensions.

Dataclipping
1.press Clipbutton todivide thedata. 2.ensure thatthe source data module (head.vtk) istheinput data. 3.choose theplane withnormal (1,0,0) 4.tagInside outtoget theouter division part.

5.press Accept buttonto viewthe results. 6.presseye iconsto viewonly thebone.

Skinsurfaceextraction
1.press theiso surfaces extraction button. 2.choose previous module Clip0as inputdata. 5.press Accept buttonto obtainthe results. 4.press Addbutton toaddthe density value.

3.choose 650as desired density.

Opacity
1.select Display tab. 3.entrya 0.6opacity.

2.choose anorange colorclose toskin color.

4.observe thattheskin surfaceis less opaque.

Datasections
1.press Cut button. 3.setthe plane normalto (1,0,0)

2.choose thesource data module (head.vtk) asinput.

4.press Accept buttonto observethe resulting section.

Thresholdfilter
1.press the Threshold button. 2.hidethe section module (Cut0). 4.choose therange [410..3500] (toavoidthe lower densities that represent theair). 5.pressthe Accept button. 6.changeto Displaytab andseta 0.8opacity.

3.choose thesection module (Cut0)as input.

Animation:initialstate
1.press Menu View Keyframe animation. 3.selectthe Xcompon. oftheinitial plane coordinates (Plane: Origin:0). 4.press Add KeyFrame button.

2.set60 frames.

2.choose thesection module (Cut0).

5.put1as initialvalue.

Animation:finalstate
1.press Add KeyFrame button. 3.place200 asthefinal valueofthe coordinate (pressenter keyboard keyto finish).

2.moveto the second frame.

4.press Playbutton topreview animation.

Animation:saving
1.press Save buttonto storethe animation. 2.change toyour user's directory. 4.choose thefile name (ani.mpg) 5.press Save button. 6.entry18 framesper second.

3.select MPEG2 moviefile type.

7.pressOK buttonto createthe animation movie.

Questions

Haveyouunderstoodwhatisscientific visualization? Howisthevolumedata? Citethreenormalsituationwherevolumedata isused. Saythreepossiblevisualizationtypestoobtain fromvolumedata. Whichotherinformationcouldbeextracted fromvolumedata?

Moreinformation...

Aboutthisworkshop:

http://truja.lsi.upc.edu/movibio/soft/paraview/Workshop

Interactivewebs:

Humanbody:http://www.madsci.org/~lynn/VH/ Mouse:http://mouseatlas.caltech.edu/ Lemur:http://atlasserv.caltech.edu/Lemur/Start_lemur.html

Wikipedia:http://en.wikipedia.org/wiki/Scientific_visualization Programs:

ParaView:http://www.paraview.org Mayavi:http://mayavi.sourceforge.net

Ifyouhavemoretime...

Createanewvisualization fromthedataset: lobster.dat.vtk Havealooktothe completevisualization: head.pvs

youhavetouseMenu FileLoadsession.