MatlabPARAFAC运行办法.pdf

MatlabPARAFAC运行办法.pdf

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Appendix1:

TutorialCharacterizingDOMfluorescenceusingtheDOMFluorToolboxforMATLABInthissectionabrieftutorialinapplyingPARAFACtoDOMfluorescenceEEMswillbegivenwithrecommendationsonasuitableseriesofstagestofollowinordertofacilitatetheprocessbasedontheauthorsownexperience.ThetutorialisbasedonMATLABsoftwareandrequiresthatthisisinstalledonyourcomputer.TheDOMFluortoolboxforMATLABpro-videdisinthecompressedfile“DOMFluorv1_4.zip”（Appen-dix1）andworksindependentofyourcomputersoperatingsystem.ThisisalsofreelydownloadablefromtheChemomet-ricssiteatUniversityofCopenhagen（www.models.life.ku.dk）.ThetoolboxcontainswithinittheN-Waytoolboxv.3.1（AndersonandBro,2000）andadditionalfunctionswhichfacilitaterunningPARAFAConDOMfluorescencedata.TheDOMFluortoolboxiswrittenandtestedinMATLABrelease2007b（v7.5）andisfreesoftwarethatcanbeusedandmodi-fiedunderthetermsoftheGNUGeneralPublicLicense.Withinthetoolboxatestdatasetisprovidedforthetutorial,consistingof65EEMswhichhavebeenspectrallycorrectedforinstrumentbiases,correctedforinnerfiltereffectsandRamancalibrated.Asaresult,alloftheRayleighscatterandmostoftheRamanscatterhasbeenremoved.Theremainingscatterwillberemovedinthepre-processingphase.ThedataconsistsofsamplescollectedfromacruiseonRVGunnarThorsonintheKattegatandBeltSearegion（attheentrancetotheBalticSea）inAugust2001.Three“outlier”sampleswerecreatedandarepresentinthedataforthebenefitofthetutorial.Thetutorialiscomposedofphases;i）datapre-processing,ii）initialexplorativedataanalysis,iii）modelingandmodelvalidation,iv）interpretingresults.Themorethoroughlythefirsttwophasesarecarriedout,theeasierthelattertwowillbe.Partofthepre-processingontheexampledatasethasalreadybeencarriedout（importingthedatatoMATLAB,spec-tralcorrections,calibrations,etc.）.Thisisveryinstrumentspe-cificandthereforenotappropriateforthistutorial,whichfocusonthemodelingofthedata.DuringthistutorialanystatementstobewritteninMAT-LABwillbewritteningreenwithCourierNewfont.WhenwritingintheCommandWindow,notethatMATLABiscasesensitive.A.SettingupMATLABtorunwithN-waytoolboxandDOMFluortoolbox.1.DecideonasensibleplacetolocatetheDOMFluortoolboxonyourcomputer.（Thiscould,forexample,beC:

ProgramFilesMATLABR2007btoolboxbutcanalsobeelsewhere）.CreateafolderandnameitDOMFluor.Extractthecontentsofthezipfile“DOM-Fluor.zip”intotheDOMFluorfolder.2.StartMATLAB.SelectFilemenuthenclickSetpath.ClickAddwithsubfoldersandlocatetheDOMFluorfolderyoucreatedinStep1above.IftheN-Waytool-boxiscurrentlyinstalled,removeitfromthePathlisttoavoidconflicts.TheN-WaytoolboxisincludedaspartoftheDOMFluortoolbox.ClickSavethenClose.YouhavenowassociatedtheDOMFluortool-boxwithMATLABandthismeansthatthefunctionsinthesefolderscanberecognized.3.TocheckthatthetoolboxesarecorrectlyassociatedyoucantypeDOMFluorandpressenterintheCommandWindowinMATLAB.If“Yes”isprintedtotheCommandWindow,thetool-boxisinstalled.Ifredtextappearsthetoolboxhasnotbeencorrectlyinstalled.RedoStep2.Notethatifyouhaveothertoolboxeswithsimilarlynamedfunctions,onlythefunctionupmostinthefolder-listwillworkproperly.4.SectionAwillhavetoberepeatedifanewversionofMATLABisinstalled.B.LoadingthetutorialdataandplottingtheEEMs.1.TypeloadPARAFACexample.matintheCommandWindow.ThiswillloadthetutorialdataintotheMATLABWorkspace.ThisconsistsofadatastructurecalledOriginalData.TrytypingOriginalDataCharacterizingdissolvedorganicmatterfluorescencewithparal-lelfactoranalysis:

atutorialColinA.Stedmon1*andRasmusBro21DepartmentofMarineEcology,NationalEnvironmentalResearchInstitute,AarhusUniversity,Frederiksborgvej399,Roskilde,Denmark2Dept.FoodScience,FacultyofLifeSciences,UniversityCopenhagen,Rolighedsvej30,DK-1958,Frederiksberg,Denmark*Correspondingauthore-mail:

cstdmu.dk,Tel:

+4546301805.Limnol.Oceanogr.:

Methods6,20082008,bytheAmericanSocietyofLimnologyandOceanography,Inc.inthecommandwindow.Thiswilloutputthefollowing:

Thisdetailsthedatathatiscontainedwithinthedatastructure.i.Ex-isalistoftheexcitationwavelengthsmea-sured（innm）.Inthiscase240to450every5nm.ii.Em-isalistoftheemissionwavelengthsmea-sured（innm）.Inthiscase300to600every2nm.iii.X-isthefluorescencedataasathreedimen-sionalarray（65samplesx151emissionwave-lengthsx43excitationwavelengths）.iv.nSample,nExandnEm:

statethenumberofsamples,excitationandemissionwavelengths.v.XBackup-isabackupcopyofthedataandnotusedinthetutorial.2.NowwewillplottheEEMstocheckthatthedataiscorrectlyloaded.Inthetoolboxthereareseveralfunc-tionsthatcanbeu