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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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2

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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