Copyrightnotice TopNext

DeVIDEiscopyright(c)2002-2008CharlP.Botha,TUDelft

Allrightsreserved.

Redistributionanduseinsourceandbinaryforms,withorwithoutmodification,arepermittedprovidedthatthefollowingconditionsaremet:

·Redistributionsofsourcecodemustretaintheabovecopyrightnotice,thislistofconditionsandthefollowingdisclaimer.

·Redistributionsinbinaryformmustreproducetheabovecopyrightnotice,thislistofconditionsandthefollowingdisclaimerinthedocumentationand/orothermaterialsprovidedwiththedistribution.

·NeitherthenameoftheTUDelftnorthenamesofitscontributorsmaybeusedtoendorseorpromoteproductsderivedfromthissoftwarewithoutspecificpriorwrittenpermission.

THISSOFTWAREISPROVIDEDBYTHECOPYRIGHTHOLDERSANDCONTRIBUTORS"ASIS"ANDANYEXPRESSORIMPLIEDWARRANTIES,INCLUDING,BUTNOTLIMITEDTO,THEIMPLIEDWARRANTIESOFMERCHANTABILITYANDFITNESSFORAPARTICULARPURPOSEAREDISCLAIMED.INNOEVENTSHALLTHECOPYRIGHTOWNERORCONTRIBUTORSBELIABLEFORANYDIRECT,INDIRECT,INCIDENTAL,SPECIAL,EXEMPLARY,ORCONSEQUENTIALDAMAGES(INCLUDING,BUTNOTLIMITEDTO,PROCUREMENTOFSUBSTITUTEGOODSORSERVICES;LOSSOFUSE,DATA,ORPROFITS;ORBUSINESSINTERRUPTION)HOWEVERCAUSEDANDONANYTHEORYOFLIABILITY,WHETHERINCONTRACT,STRICTLIABILITY,ORTORT(INCLUDINGNEGLIGENCEOROTHERWISE)ARISINGINANYWAYOUTOFTHEUSEOFTHISSOFTWARE,EVENIFADVISEDOFTHEPOSSIBILITYOFSUCHDAMAGE.

Sponsors PreviousTopNext

Thedevelopmentofthissoftwarewassupportedbythefollowinginstitutions:

TheDelftUniversityofTechnology(TUDelft),myfabulousemployerandpermanentresearchhome.WeDoReallyCoolStuff(tm).

TheVirtualLaboratoryfore-Science(VL-e)projecthaspartlyfundedrecentdevelopmentofthesoftware.

DevelopmentofImprovedendo-ProsthesesfortheupperEXtremity,orDIPEX,istheresearchprogrammewhereitallbegan.DSCAS1,DSCAS3andfinallyDeVIDE.

Introduction PreviousTopNext

ThisistheusermanualandhelpfilefortheDeVIDEsoftwarepackage.DeVIDEistheopensourceDelftVisualisationandImageprocessingDevelopmentEnvironment.

Thesoftwarewasdesignedfortherapidprototypingandtestingofvisualisationandimageprocessingtechniques.Allfunctionalityispackagedintheformofmodules.Oneofthewaysinwhichthesemodulescanbeused,istomakeuseoftheDeVIDEGraphEditor,whereglyphs,representingmodules,canbeconnecteduptoformfunctionaldata-processingnetworks.Akeyfeatureisthatanycodeobjectcanbeaccessedandinteractedwithinreal-time.ThisenablesbothmodulewritersandusersoftheGraphEditortoexperimentwithforexampleallparametersandeventhelogicbehindarunningpieceoffunctionality.

DeVIDEisavailableasopensourceunderthetermsofthenewBSDlicense.BinariesareusuallymadeavailablefortheWindowsandLinuxplatforms.

Themainwebsiteofthissoftwareisathttp://visualisation.tudelft.nl/Projects/DeVIDE.Pleasegothereforlinkstomoredocumentation,theGoogleCodeprojectsite,themailinglistandthenewsblog.

Thismanualisinaperpetualstateofbeingunderheavyconstruction.TheGraphEditorandUsefulPatternssectionsareespeciallyusefulandshouldbereadbeforeyoustartworkingwiththesoftware.

Introduction PreviousTopNext

TheDeVIDEGraphEditorisavisualprogramminginterfacewhereglyphsrepresentingtheunderlyingDeVIDEmodulescanbeconnectedtogethertoformnewprograms.

It'sthemostflexiblewayofworkingwithDeVIDE,shortofdirectlyinterfacingwiththeunderlyingcode.

Thischapterwillgiveabriefoverviewofgrapheditorusage.

Asmallsamplenetwork PreviousTopNext

TheGraphEditorisintroducedbyputtingtogetherasimplenetworkforrenderingthe3D0-surfaceofaSuperQuadric.It'sfarsimplerthanitsounds.

ConstructingthenetworkStartbybuildingthenetworkshowninthefigurebelow.Firstselectthe"Sources''categoryonthetopleftoftheGraphEditor.Draganddropthe"superQuadric''modulefromthemoduleslistonthebottomlefttothecanvas.Youshouldseethe"superQuadric''glyphbeingcreated.

Nowdothesameforthe"slice3dVWR''moduleinthe"Viewers''category.NotethatyoucanselectmultiplecategoriesbyholdingtheShiftkeyandclickingacategory(thiswillselectallcategoriesbetweenthepreviousselectedcategory

andyourcurrentclick)orholdingthecontrolkeyandclicking(thiswillselectthecurrentlyclickedmodulealongwithanypreviouslyselectedmodules).Themodulelistwillcontainallmodulesinallselectedcategories.Themodulesarealwaysalphabeticallysorted.

Connectthesecondoutputofthe"superQuadric''glyphtoanyinputofthe"slice3dVWR''glyphbydraggingthemouse,withtheleftbuttondepressed,fromtheoutputporttotheinputport.NotethathoveringthemousepointeroveranyportshowsmoreinformationaboutthatportinthestatusbaroftheGraphEditor.

AdmiringyourresultsNowpressF5orselectNetwork|Executefromthemainmenubartoexecutethenetwork.

Right-clickontheslice3dVWRmoduleandselect"View-Configure''toseethe3Dsurfacerepresentingthe0-surfaceofthegeneratedSuperQuadric.Notethatthisishowoneactivatesthegraphicalinterfaceofanyglyphonthecanvas.Youcanrotateyourviewpointaroundthegenerated3Dobjectbydraggingwithyourleftmousebutton.Draggingwiththerightbuttonwillzoom.Draggingwiththemiddlebuttonwillpantheviewpoint.

Thenetworkcanbesavedbyselecting"Save''fromthe"File''menu.ThedefaultextensionforaDeVIDEnetworkis.dvn.

WarpingtheSuperQuadricTheslice3dVWRisaveryspecialDeVIDEmodule.Becauseofthis,itsView/Configinterfaceisnon-standard.Rightclickonthe"superQuadric''glyphandselect"View-Config''toseeamorestandarduserinterface(youcanalsojustdouble-clickontheglyph,manyusersfindthistobequicker).Thisinterfaceisshowninthefigurebelow:

MostmoduleView/Configwindowshavethesetofbuttonsatthebottom.Ifyoumakeanychangestoanyofthemoduleparameters,youhavetoclickonthe"Apply''button(inwhichcasetheparameterswillbetransferredtotheunderlyinglogic)orthe"Execute''button,(inwhichcasethenewparameterswillbetransferredtotheunderlyinglogicandthemodulewillbeaskedtore-performitsexecutionwiththemodifiedparameters).Clickingonthe"Cancel''buttonwillundoanychangesyou'vemadewithoutapplyingandclosethewindow.Clickingon"OK"willapplyallchangesandclosethewindow.

Changethe"PhiRoundness''parameterto3.0andclickon"Execute''orsimplypressF5orAlt-X.Pressingoneofthesekey-combinationsiseffectivelythesameasclickingon"Execute''.Seetheresultsofyourchangesintheslice3dVWRwindow.

Afewimportanttips PreviousTopNext

Beforewestart,afewproductivity-enhancingsecretsoftheGraphEditorarerevealedhere.

PlacingmodulesYoucanplacemodulesonthecanvasinmorethanoneway.·Draganddropthemodulenamefromthemodulelistonthebottom-left

ontothecanvas.Youcannarrowdownthelistofmodulesbyselectingoneormorecategories.The"ALL''categoryincludesallmodulesavailable.

·Doubleclickingonamodulenamewillplacethatmoduleonthecanvas.·Typinginthemodulesearchboxontheupperleftandthenpressingthe

ENTER-keywillplacethefirstautomaticallyselectedmoduleinthesearchresultsonthecanvas.Seethenextsectionformoredetailsonthis.

PlacingmodulesquicklyAsmentionedabove,modulescanbeplacedbytypinginsearchphrasesinthemodulesearchboxintheupperleftofthemainDeVIDEwindow.Onlymodulesinthecurrentlyselectedcategorieswillbefound,thereforeitisrecommendedthatyouselectthe"ALL''categorywhenmakinguseofthisfunctionality.

YoucanquicklygotothesearchboxbyusingtheCtrl-Fhotkeys.Typinganysearchtermswillshowsearchresultsinreal-timeinthemodulelistbox.Modulesaresearchedbyexaminingtheirnames,keywordsandthemodule-specificdocumentation.Atalltimes,amodulewillbeautomaticallyselectedinthesearchresults.Youcanchangetheselectionbyusingtheupanddowncursors.PressingtheENTERkeyatanytimewillplacethatmoduleonthecanvas.

Gettingmodule-specifichelpManymoduleshavemodule-specifichelp-textbuiltin.Toseethishelp,justselectthismodulefromthemodulelistatthebottomleftofthemainDeVIDEwindow.Themodulehelpwillappearinthemoduledocumentationwindowbelowthemodulelist.

Alsorememberthatselected(special)modulesaredocumentedinthechapterSpecialModules.

Readingdata,quicklyDragginganddroppingcertaindata-filesontheGraphEditorcanvaswillcausethesystemtoautomaticallycreateandconfiguretheapplicablemodule.Forexample:selecting,dragginganddroppingacollectionofDICOM.dcmfilesonthecanvaswillresultinadicomRDRglyphtobecreatedandpre-configuredwiththelistoffilesthathasbeendropped.

Followingthesametheme,dragginganddroppingafilename(oracollectionoffilenames)onamodulethathasafilenameattribute(suchasmostfilereaders)willsetthatfiletobereadonthenextnetworkexecute.Thisisusefulwhenyouhaveasinglenetworkthatyouwanttoapplyonanumberofdifferentdatasets:justdragthenewfilenameontothereaderinquestionandexecute!

Re-usingnetworks,quicklyDragginganddroppinga.dvn(DeVIDENetwork)fileonthecanvaswillinstantlyloadthenetworkandbuilditatthemouseposition.Thiswillnotdestroyanyofyourcurrentnetworksonthecanvas.

Introduction PreviousTopNext

ThischapterhasmoredocumentationonsomeofthemorecomplexmodulesinDeVIDE.Rememberthatallmoduleshavemodule-specificdocumentation,availablebyrightclickingonthemoduleglyphandselecting"HelponModule''orbyqueryingthedoc-stringofthemainmoduleclass.

slice3dVWR PreviousTopNext

IntroductionThisisprobablythemoduleyou'llusemostoften.It'salsothefirstthingyoushouldtrywheneveryouhaveanydatayou'dliketovisualise.Simplyconnecttheoutputofanydata-generatingorfilteringmoduletoanyinputoftheslice3dVWRandexecutethenetwork.Theslice3dVWRpicksasuitabledefaultvisualisationbasedontheinputdatayousupply.

SlicesWhenavolumehasbeenconnectedtoaninputoftheslice3dVWR,thevolumecanbeexaminedby"slicing''throughit.Bydefault,anaxialsliceiscreatedautomatically,butanynumberofadditionalslicescanbeactivated.

OverlaymodesTheslice3dVWRhasseveraloverlaymodes.Thesemodesmakeitpossibletovisualisethecorrespondencebetweenmultipleinputs,fore.g.originalCTdataandasegmentation.Ifasecondvolumeinputisconnected,theslice3dVWRchecksifthedimensionsofthealreadyconnectedvolume.Ifthisisthecase,theconnectionisallowedandthesecondvolumeisoverlayed(superimposed)onthefirst.

Thereareseveralwaystoperformthisoverlay.Thissettingisuser-configurableanditsuserinterfacecanbefoundonthe"Main''taboftheslice3dVWR"Controls''window,inthe"Slices''section.TheuserinterfaceconsistsofanOverlayModechoiceboxandanAlphaslider.Thealphasliderdeterminesthealphaparameterusedforthefusion-basedoverlaymodes.·GreenFusion:Theoverlayiscompositedwiththeuser-definedalpha

parameter.Thevalue(i.e.brightness)isdirectlyrelatedtotheimageintensityoftheoverlay,soweseeshadesofgreen(reflectingtheoverlayintensity)alphablendedwiththeprimaryinput.

·RedFusion:Sameasabove,exceptwithshadesofred.·BlueFusion:Sameasabove,exceptwithshadesofblue.·HueFusion:Thevalueiskeptconstant,butthehueisdirectlyrelatedtothe

overlayimageintensity.Theoverlayisalphablendedwiththeuser-suppliedalphaparameter.

·Hue/ValueFusion:Hueandbrightnessaredirectlyrelatedtotheoverlay

imageintensity.Theoverlayisalpha-blendedwiththeuser-suppliedalphaparameter.

·GreenOpacityRange:Theopacityoftheoverlayisdirectlyrelatedtoitsimageintensity.Thehueisconstantgreenandthebrightnessisconstantunity.

·BlueOpacityRange:Thesameasabove,exceptthehueisconstantred.·BlueOpacityRange:Thesameasabove,exceptthehueisconstantblue.·HueOpacityRange:Thehueandtheopacityoftheoverlayaredirectly

relatedtotheoverlayimageintensity.

Adjustingthealphasliderwhilstoneofthe"fusion''overlaymodesisactivewillresultinreal-timechanges.Theideaistoadjustitupanddownitscompleterangeinordertogetabetterideaoftheamountoftheimagecorrespondence.

CodeRunner PreviousTopNext

IntroductionWiththeCodeRunner,arbitrarysnippetsofPythoncode,usinganyofthelibrariesshippingwithDeVIDE,canbeinsertedintoafunctionalnetwork.Thisisaprettypowerfulconceptthatenables*very*rapidprototypingofnewideasorquickimplementationofprocessingsolutions.

AnexampleWe'llillustratewithanexample.Firstbuildupthissmallnetwork:

DoubleclickontheCodeRunner,causingitsViewtoappear.TheView'stop-halfconsistsofaneditorcomponentwiththreetabs:Scratch,SetupandExecute.PastetheblockofcodebelowintotheSetuptab:

#thisblockgoesintothe"Setup"taboftheCodeRunnerimportvtkfe=vtk.vtkFeatureEdges()tf=vtk.vtkTubeFilter()tf.SetRadius(0.01)tf.SetNumberOfSides(16)tf.SetInputConnection(fe.GetOutputPort())

...andthefollowingblockintothe"Execute"tab:

#thisblockgoesintothe"Execute"taboftheCodeRunnerfe.SetInput(obj.inputs[0])tf.Update()

obj.outputs[0]=tf.GetOutput()

Nowclickonthe"Execute"buttonatthebottomoftheCodeRunnerView.Inyourslice3dVWR,youshouldseesomethinglookingmoreorlesslikethefigurebelow:

Prettyslickeh?

WorkingwithScratch,SetupandExecutetabsUsingCodeRunnermodules,youcaninsertarbitrarycodesegmentsintoyourDeVIDEnetworks.The"Scratch"tabisforexperimentation,the"Setup"tabcoderunsONCEforanychangesthatyoumake(youshouldusethisforbuildingpipelinesforexample),andthe"Execute"tabrunseverytimethenetworkisexecutedandtheCodeRunner'sinputshavechangedoranyoftheCodeRunnertabshavebeenmodified.

Whilsteditinganyofthetabs,pressControl-Entertoexecutejustthattabatthatmoment.Clickingonthe"Execute"buttonatthebottomoftheViewrequeststhewholenetworktoberun.LiberaluseofControl-EnterwhilsteditingwillmakesurethatallPythonobjectsthatyouhavecreatedwillbeinstantiated.Besidesthefactthatcode-completionandinlinedocumentationcanthendoitsthing,you

caneasilyexperimentatrun-time.

DICOMBrowser PreviousTopNext

IntroductionWiththeDeVIDEDICOMBrowser,releasedwith8.5,youcaneasilyexplorecollectionsofDICOMdata.ItisintendedtobeusedasavisualinterfacewithwhichDICOMseriescanbeeasilyselectedandloaded,usingthecompanionDICOMReadermodule,intoDeVIDEforfurtherprocessing.

BelowascreenshotoftheDICOMBrowserGUIisshown:

Alsoseeourintroductoryscreencastonyoutube:http://www.youtube.com/watch?v=iLfu6JXkWP4

StartingtheexplorationEnteranynumberofdirectoriesandorfilenamesintothe"FilesandDirectoriestoScan"textinputbox,separatedbysemicolons.Youcaneithertypetheseinyourself,cutandpastethemfromsomeotherapplication,ormakeuseofthe"AddDirs"and"AddFiles"dialogbuttons.

Afterhavingenteredallpathsthatyouwishtoscan,clickonthe"Scan"button.Post8.5versionsoftheDICOMBrowserwillshowaprogressbarwhilstscanning.

Whenscanninghasbeencompleted,allotherpanelsintheinterfacewillbefilledoutwithinformation.

ExploringyourdataDICOMdataisdividedupintostudies,whereeachstudyisassociatedwithapatient,anumberofseriesperstudy,andanumberofimagesperseries.TheDICOMBrowserallowsyoutoselectanyoftheseelementsbyclickingintherelevantpanel.Onceyou'veselectedaspecificseries,whichcanusuallybeseenasasingledatavolume,youcanbrowsethroughtheimagesinthatseriesbyclickingontherelevantfileinthe"ImageFiles"panel,orbymakinguseoftheCtrl-NCtrl-Photkeysfornextimageandpreviousimage,orbyclickingontheimageandthenusingthemousewheeltomove,1imageatatime,throughtheseries.Control-Mousewheelwillskip10imagesatatimeandallowsrapidscrollingthroughaseries.

LoadingdataforfurtherprocessingOnceyouhaveidentifiedaninterestingseries,youcancreateaDICOMReadermoduleontheDeVIDEcanvas,andthendragdirectlyfromtheseriesitemorfromaselectionoffilenamesontotheDICOMReader.TheDICOMReaderwillnowbeconfiguredwiththecorrectfilenamesandcanbeexecutedtoloadthedataforfurtherprocessingbyDeVIDEnetworks.

Youcanalsodragaseriesorselectionoffilesontomostfilemanagerwindows(exploreronWindows,nautilusonGnome)tocopythosefilesintothedestinationdirectory.

ShortcutsCtrl-N,mousewheeldownonimage Nextimageinseries

Ctrl-P,mousewheeluponimage PreviousimageinseriesCtrl-mousewheelonimage Skip10images

Ctrl-0,Ctrl-1 Changeviewlayouts(default,maximage)

Introduction PreviousTopNext

Thischaptercontainsaselectionofhowtos,i.e.veryshortdescriptionsofhowtoperformsomeactionwiththeDeVIDEsoftware.

LoadingandviewingDICOMdata PreviousTopNext

TheeasiestwaytoloadaDICOMdatasetistoselecttherelevantDICOMfiles(oftenwitha.dcmextension)inyourfilebrowser(e.g.ExplorerinWindowsandKonquerorinKDE)andtodraganddroptheselectedfilesontheGraphEditorCanvas.ADICOMReadermodulewillbeautomaticallycreatedwiththeselectedfilenamesadded.

Alternatively,youcancreateaDICOMReadermoduleinthenormalway,i.e.bydragginganddroppingthemodulefromtheModulePaletteontothecanvas.DoubleclickonthemoduletoopenitsView/Configwindow.ClickontheAddFilesbuttontoaddanynumberofDICOMfilenames.RemembertoclickonApplyafterhavingaddedtherelevantfilenames.AlternativelydraganddropanumberofDICOMfilesontothelistbox,ordirectlyontotheglyphonthecanvas.Thisisoftenfareasier.

Tostartvisualisingthevolumethatyouhavejustloaded,createaslice3dVWRmoduleandthenconnecttheoutputoftheDICOMReadermoduletoanyinputoftheslice3dVWRmodule.Themoduleinterfacewillautomaticallyappearwiththedefaultaxialslice.Toreadmoreaboutinteractingwiththisslice,seetheslicessectionoftheslice3dVWRdocumentation.

ForafarmorepleasantDICOMbrowsingexperience,trytheDICOMBrowser.Ascreencastdemonstratingthisfunctionalityisavailableathttp://www.youtube.com/watch?v=iLfu6JXkWP4.

Smoothingdata PreviousTopNext

ThereareanumberoffiltersinDeVIDEthatcanbeusedforsmoothingvolumedata.

Filters.imageGaussianSmoothperformsastraight-forwardGaussiansmoothing(alsoknownas"blurring''insomeimageprocessingpackages).Thestandarddeviation(inpixels)canbesetforallthreedimensions.Atruncation,orcut-off,canalsobesetforallthreedimensions.Takeintoaccounttheresolutionofyourimagewhenselectingtheseparameters.

curvatureFlowDenoising,curvatureAnisotropicDiffusionandgradientAnisotropicDiffusion,allinthe"Insight''modulecategory,aremoreadvancedsmoothingalgorithmsthatattempttosmoothhomogeneousregionswhilstretainingedgeinformation.Theseareallcompute-intensiveITK-basedfilters.Pleasereadthetooltipsavailableintheconfigurationwindows:i.e.doubleclickonthemoduleandthenletyourmousehoveroveranyoftheinputboxestogetmoreinformationaboutthevariablerequiredforthatinputbox.Thedefaultsarenaturallygoodvaluestostartwith.

WhenyouusethesewithVTKdata,forexampletheoutputofavtiRDR,youhavetouseaVTKtoITKF3conversionmodule.Tovisualisationtheoutput,youneedtoconvertbacktoVTKdatabymakinguseofanITKF3toVTKmodule.However,ifyou'replanningtousetheoutputinanITKfilter,forexamplethedemonsRegistration,youdon'tneedanITKF3toVTKconversionmoduleattheoutput.Thefigurebelowshowsanexampleofthis.

Performinglandmarkregistrationontwovolumes PreviousTopNext

IntheMRIretrobulbarfatmobilitystudy,multipleMRIdatasetsaremadeofasubjectduringdifferentdirectionsofgaze.Althoughgreatcareistakentopreventrigidheadmotion,thisdoesstilloccur.Sobeforethedeformationofthefatiscalculated,rigidheadmotionhastobeeliminatedbymeansofalandmark-basedrigidregistration.

Oneofthedirectionsofgazeischosenasthecentralorreferencedirection:allotherdatasetshavetoberegisteredontothisdataset.Inthisway,alldatasetswillshareacommonframeofreference.

Inthenextsubsections,wewillexplainhowtoperformonesuchregistration.Thisobviouslyhastobeperformedforalldatasetsthatyouhavetoregisterontothereferencedataset.ThefigurebelowshowsanexampleDeVIDEnetworkforperformingthislandmark-basedrigidregistration.Refertoitduringthefollowingexplanation.

SelectsourceandtargetpointsSelectatleast3,preferablymorerigidlandmarksthatcanbeaccuratelylocalisedinalldatasets.

Selectthesepointsinthereferencedatasetsbyusingthemousecursorina3Dslice3dVWR.Youhavetonamethesepoints(intheslicedVWRcontrolpanel,

enterthenameintothe"name''inputboxbeforeclickingonthe"Storethispoint''button.Thenamesofthesepointshavetostartwith"Target'',forexample"TargetZygoma1''.

Saveyournetworkregularly!

Nowloadinthefirstdatasetthatyouwanttoregisterontothereferencedataset.Selectandstoreallcorrespondingpointsinthisdataset.Useaseparateslice3dVWR.Thenamesofthesepointsallhavetostartwith"Source'',forexample"SourceZygoma1''.

Itisveryimportantthatyouselectthesepointsinthesameorderasthetargetpoints.

DerivethetransformInstantiatea"landmarkTransform''modulefromtheFilterscategory.Readitshelpbyright-clickingonthemoduleandselecting"HelponModule''.

Brieflyconnectanddisconnectthefirstoutputofthereferencedataset"slice3dVWR''toanyinputofthesecond"slice3dVWR''.Thiswillcopythe"Target''pointstothesecond"slice3dVWR''.

Nowconnectthefirstoutputofthesecond"slice3dVWR''totheinputofthe"landmarkTransform''module.Thismodulewillnowhaveaccesstothesourceandtargetpointsofthetwodatasetsthatyouaretryingtoregister.Asmentionedearlier,theorderofthesourcepointsshouldbeidenticaltothatofthetargetpoints.

TransformthedatasetConnecttheoutputofthe"landmarkTransform''tothesecondinputofa"transformVolumeData''module(category"Filters'').Connectthedatasetthatyouareregisteringontothereferencedatasettothefirstinputofthe"transformVolumeData''module.Theoutputofthismodulewillbethetransformedvolumedataset.Youcanaddittooneofthereferencedataset'sslice3dVWR'sinputsforanoverlay.Selectthe"PrimaryLUTfusion''overlaymodeintheslice3dVWRcontrolpanel.TheAlpha-parametercanbeadjustedto"fade''fromthereferencedatasettotheregistereddatasetandback.

Don'tforgettosaveyourtransformeddataset:Connecttheoutputofthe"transformVolume''moduletotheinputofa"vtiWRT''moduleforexample.Doubleclickonthe"vtkWRT''moduleandthenclickonthebrowsebuttontoselectafilename.Forallwritermodules,youHAVEtoclickonthe"Execute''buttonforittosavethefile.

Determiningopticalflowbetweentwovolumes PreviousTopNext

Inordertodeterminetheopticalflowbetweentworigidlyregistereddatasets,wemakeuseofthedemonsRegistrationnon-rigidregistrationmodule.Dothisaftertherpgidlandmark-basedpre-registrationandafterhavingextractedacommonsub-volumefromalldatasets.

ThisisanITKmodule,soyouhavetousetheITK-enabledversionofDeVIDE.Foreachpairofsuccessivevolumes,determinetheopticalflowbymakinguseofanetworkliketheoneshowninthefigurebelow:

Texttobecompleted...

Flowvisualisationwithglyphsonlyonslice3dVWRslices PreviousTopNext

Ifavectordatasetisavailable,suchastheonegeneratedbytheopticalflowproceduredescribedabove,thedeformationvectorfieldcanbevisualisedbymakinguseoftheFilters|glyphsmodule.However,thismodulevisualisesthecompletevectorfield.

Onecanalsovisualiseonlythevectorsonthecurrentslicesintheslice3dVWR.Todothis,buildanetworkasshownbelow:

Theslice3dVWRoutputsapolydatarepresentingthegeometryofallcurrentplanes.Inthiscase,weuseitasaprobeinputsothatwecanvisualisearrowglyphslocatedontheplane.

Rememberthattheopacityofslicescanbeadjusted(Slicesmenu:"SetOpacity'')sothatvisualisingabackgroundslicealongwiththedeformationvectorsonitiseasier.

Probingandwarping(interactiveadvection) PreviousTopNext

Thefigurebelowshowshowtoperforminteractiveprobingandwarping(advection)withDeVIDE:

ThevolumedatahasbeenloadedwithvtkRDRdvm11andservesascontextintheslice3dVWR.Inthiscase,weareusingtwovectorfields,loadedwithrespectivelymetaImageRDRdvm7anddvm11fyi11.Pointsthathavebeenselectedandstoredwiththeslice3dVWR(thesecanbechangedatanytime,thenetworkupdatesinteractively)arechangedintosphericalshellsofpointsbythepointsToSpheresmoduledvm6ldz6.Theoutputofthismodulecanbeconnectedtotheslice3dVWRtoviewtheinitialsphere.

ThefirstprobeFilterdvm7fxg7mapsandinterpolatesthevectorsfromthefirstvectorfieldontothepointsofthesphericalcloud.ConnecttheoutputoftheprobeFiltertothewarpPointsmodule.AfterconnectingthewarpPointsinput,makesureto"Execute''and"Apply''thewarpPointsmoduleonce.Thecorrect"Vectorsselection''canthenbemadefromitsView/Configwindow."Default

ActiveVectors''isveryoftenNOTwhatyouwant.Experimentwiththis.(ThijsenRonald,injulliegevalmoetdit"ImageFile''zijn!).Afterhavingmadethisselection,"Apply''or"Execute''themoduleagain.Nowyoucanconnectitsoutputtotheslice3dVWR.Thepointsareadvectedbythevectorsthatyouhaveassociatedtothem.

Thisoutputisalsousedinthenextadvectionstep,usingthenextvectorfield.Onceagain,makesuretoselectthecorrectvectorsinthewarpPointsmoduleView/Configwindow.YoucouldalsosimplycopyandpastethefirstprobeFilterandwarpPointsmodule(AFTERyou'veperformedthevectorselectionstep),inwhichcasetheselectionwillalreadybecorrect.

Addasmanyofthesestepsasarenecessarytocompletethefulladvectionwithallyouravailablevectorfields.Ateachstep,checkthatyoursphereisbeingcorrectlyadvectedbeforeyoucontinue.

Introduction PreviousTop

ThischapterwillexplainthevariouswaysinwhichyoucanextendDeVIDE'sfunctionality.ThismostlyhappensviathecreationofnewDeVIDEmodules.Therearevarioustypesofmodulesthatonecancreate,thischapterdocumentsmostof'em.

OtherpossibilitiesforextendingDeVIDEincludewritingSnippets(akindofpoorman'splugins)orsimplymakinguseoftheCodeRunnermodule.Thelatterisrecommendedifyouwanttotestyourideaasquicklyaspossibleandcan'tbebotheredwithreadingmanuals.Makinganewmodule,althoughtakingslightlymoretime,hasitsadvantages,suchasmoreflexibility,easierdistribution,andcreatingDeVIDEMiniApps!