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Th iswo rkb y John Galeo tti and Damion Shel ton,©200 4-2 01 6,wasmadepo ssible inpartb yNIHNLMcontract#HHSN2 7 6 2 0 10 00 58 0P,and i sl i cen sed underaC reativeCommonsAttrib ution 3.0Unported Licen se.To viewacop yof thisl i cen se,vi si th ttp ://creativecommons.o rg/l icen ses/b y/3 .0 /or send a letter to CreativeCommons,1 712nd Street, Sui te300,San Fran cisco ,Cal i fo rn ia,94 10 5,USA. P ermissionsbeyond th escopeo fth is l i cen semayb eavai lab leb yemai l ing i tk@galeo tti .net.The most re ce n tve rsion of the sesl idesmaybe acce sse don lineviah ttp://itk.gale o tti .ne t/
Lecture 17ITKPipeline
MethodsinMedicalImageAnalysis- Spring201618-791(CMUECE):42-735(CMUBME):BioE 2630(Pitt)
Dr.JohnGaleotti
BasedinpartonShelton’s slides from2006
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ThePipeline
§ ITKisorganizedarounddataobjects andprocessobjects§ Youshouldnowbesomewhatfamiliarwiththeprimarydataobject,
§ Todaywe’lltalkabouthowtodocoolthingstoimages,usingprocessobjects
§Apipeline isaseriesofprocessobjectsthatoperateononeormoredataobjects
§Thedataobjects“flow” alongthepipeline
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Thepipelineidea
Thepipelineconsistsof:§Dataobjects§ Processobject(thingsthatcreatedataobjects)
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Source Image FilterA
ImageFilterBImage
Starthere
Endhere
Image sources
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itk::ImageSource<TOutputImage>Thebaseclassforallprocessobjectsthatproduceimageswithoutaninputimage
Source Image FilterA
ImageFilterBImage
Starthere
Endhere
Image toimagefilters
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itk::ImageToImageFilter<TInputImage, TOutputImage>
Thebaseclassforallprocessobjectsthatproduceimageswhenprovidedwithanimageasinput.
Source Image FilterA
ImageFilterBImage
Starthere
Endhere
Inputandoutput
§ ImageSource’s donotrequireinput,sotheyhaveonlya function
§ ImageToImageFilter’s havebothand functions
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Ignoringintermediate images
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Source Filter ImageFilterStarthere Endhere
=
Source Image FilterA
ImageFilterBImage
Starthere
Endhere
Howthis looksincode
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Whenexecutionoccurs
§Thepreviouspageofcodeonly setsupthepipeline- i.e.,whatconnectstowhat
§Thisdoesnot causethepipelinetoexecute§ Inorderto“run” thepipeline,youmustcall
onthelastfilterinthepipeline
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PropagationofUpdate()
§When iscalledonafilter,theupdatepropagatesback“up” thepipelineuntilitreachesaprocessobjectthatdoesnotneedtobeupdated,orthestartofthepipeline
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When are process objects updated?
§ Iftheinputtotheprocessobjecthaschanged§ Iftheprocessobjectitselfhasbeenmodified-e.g., IchangetheradiusofaGaussianblurfilter
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Howdoesitknow?
Detecting process objectmodification
§ Theeasyway(whenwritingyourownprocesobject) istouse
which produces thefunction
thatcalls foryouwhenanewvalueissetintheclass.
§ Forexample, thecompiler turns thislineof code:
intoamember function, ,thatsetsmember variable .
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Process objectmodification, cont.
§TheotherwayistocallModified()fromwithinaprocessobjectfunctionwhenyouknowsomethinghaschanged
§YoucancallModified()fromoutsidetheclassaswell, toforceanupdate
§Usingthemacrosisabetterideathough...
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Runningthepipeline– Step1
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Notsure ModifiedUpdated
Modified?Modified?
Source Filter ImageFilterStarthere Endhere
Runningthepipeline– Step2
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Source Filter ImageFilterStarthere Endhere
Notsure ModifiedUpdated
Runningthepipeline– Step3
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Source Filter ImageFilterStarthere Endhere
Notsure ModifiedUpdated
Runningthepipeline– Step4
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Source Filter ImageFilterStarthere Endhere
Notsure ModifiedUpdated
Modifyingthepipeline– Step1
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Source Filter ImageFilterStarthere Endhere
Changeafilterparameterhere
Thencall here
Notsure ModifiedUpdated
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Modifyingthepipeline– Step2
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Source Filter ImageFilterStarthere Endhere
Wedetectthattheinputismodified
Thisexecutes
Notsure ModifiedUpdated
Modifyingthepipeline– Step3
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Source Filter ImageFilterStarthere Endhere
Thisexecutes
Notsure ModifiedUpdated
Thoughts on pipelinemodification
§Notethatinthepreviousexamplethesourcenever re-executed;ithadnoinputanditwasnevermodified,sotheoutputcannothavechanged
§Thisisgood!Wecanchangethingsattheendofthepipelinewithoutwastingtimerecomputingthingsatthebeginning
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It’s easyinpractice
1. Buildapipeline2. Call onthelastfilter- gettheoutput3. Tweaksomeofthefilters4. Call onthelastfilter- gettheoutput5. ...adnauseam
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Reading&writing
§Youwilloftenbeginandendpipelineswithreadersandwriters
§Fortunately,ITKknowshowtoreadawidevarietyofimagetypes!
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Readingandwritingimages
§Readimageswith:
§Writeimageswith:
§Bothclasseshaveafunction
usedtooptionally specifyaparticulartypeofimage toreadorwrite
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Readinganimage(4.1.2)
§Createareader§ Ifyouknowthefileformat(optional):§ Createaninstanceofan derivedclass(e.g. )
§ PasstheIOobjecttothereader§Set thefilenameofthereader§Updatethereader
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Readernotes
§The templateparameteristhetypeofimageyouwanttoconvertthestoredimageto,notnecessarilythetypeofimagestoredinthefile
§ ITKassumesavalidconversionexistsbetweenthestoredpixeltypeandthetargetpixeltype
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Writinganimage
§Almostidenticaltothereadercase,butyouusean insteadofareader
§OutputformatcanbespecifiedwithanIOobject(optional)§ Ifyou’vealreadycreatedanIOobjectduringthereadstage,youcanrecycleitforusewiththewriter
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Moreread/writenotes
§ ITKactuallyhasseveraldifferentwaysofreadingfiles- whatI’vepresentedisthesimplestconceptually
§Remember, youcanreadfileswithoutknowingtheirformata-priori§ Justdon’tspecifyanyIOobjects.
§Manymoredetailsare inch. 7ofthesoftwareguide.
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SimpleITK Pipeline
Itdoesn’thaveone!
§SimpleITK’s interfacedoesNOTuseapipeline§Every timeyoucallafilterinSimpleITK, itre-executes.
§Youmanuallyexecuteeachfilterevery timeyouthinkitisnecessary
§Youalsomanuallypasstheupdatedoutputfromonefiltertotheinputofthenextfilter
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CombiningITKandSimpleITK
§YoucancombineITKwithSimpleITK!§Forexample:§UseSimpleITK toquicklyreadandpreprocessimages§Use“full”ITKtoperformacomplexregistration§UseSimpleITK tosavetheresults
§ThisisreallyeasyinC++§WejustneedtointegrateSimpleITK intoourITKpipeline
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Using SimpleITK inan ITK Pipeline
§ConvertaSimpleITK image intoa“full”ITKimage:
§Converta“full”ITKimageintoaSimpleITK image:
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Using SimpleITK inan ITK Pipeline
§Warning: Conversion from SimpleITK toITKrequiresmatching image types!§ “Full”ITKhard-codes(viatemplateparameters)eachoutputimage’spixeltypeanddimensionality
§ SimpleITK automaticallymakesdecisionsaboutanoutputimage’spixeltypeanddimensionality
§ ThedefinitivelistofSimpleITK pixeltypesisinitssourcecode,atthebottomofthisfile:
§ Solution:§ Verifythatdimensionsmatch,andthen…§ UseSimpleITK’s toconvertpixeltype§ See
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Example: ITKwithSimpleITK
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Example: ITKwithSimpleITK
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CMakeLists.txt: ITK+SimpleITK
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