MatlabPARAFAC运行办法.pdf

1、Appendix 1:TutorialCharacterizing DOM fluorescence using theDOMFluor Toolbox for MATLABIn this section a brief tutorial in applying PARAFAC toDOM fluorescence EEMs will be given with recommendationson a suitable series of stages to follow in order to facilitate theprocess based on the authors own ex

2、perience.The tutorial isbased on MATLAB software and requires that this is installedon your computer.The DOMFluor toolbox for MATLAB pro-vided is in the compressed file“DOMFluorv1_4.zip”(Appen-dix 1)and works independent of your computers operatingsystem.This is also freely downloadable from the Che

3、momet-rics site at University of Copenhagen(www.models.life.ku.dk).The toolbox contains within it the N-Way toolbox v.3.1(Anderson and Bro,2000)and additional functions whichfacilitate running PARAFAC on DOM fluorescence data.TheDOMFluor toolbox is written and tested in MATLAB release2007b(v7.5)and

4、is free software that can be used and modi-fied under the terms of the GNU General Public License.Within the toolbox a test dataset is provided for the tutorial,consisting of 65 EEMs which have been spectrally corrected forinstrument biases,corrected for inner filter effects and Ramancalibrated.As a

5、 result,all of the Rayleigh scatter and most ofthe Raman scatter has been removed.The remaining scatterwill be removed in the pre-processing phase.The data consistsof samples collected from a cruise on RV Gunnar Thorson inthe Kattegat and Belt Sea region(at the entrance to the BalticSea)in August 20

6、01.Three“outlier”samples were created andare present in the data for the benefit of the tutorial.The tutorial is composed of phases;i)data pre-processing,ii)initial explorative data analysis,iii)modeling and modelvalidation,iv)interpreting results.The more thoroughly thefirst two phases are carried

7、out,the easier the latter two willbe.Part of the pre-processing on the example data set hasalready been carried out(importing the data to MATLAB,spec-tral corrections,calibrations,etc.).This is very instrument spe-cific and therefore not appropriate for this tutorial,whichfocus on the modeling of th

8、e data.During this tutorial any statements to be written in MAT-LAB will be written in green with Courier New font.When writing in the Command Window,note that MATLABis case sensitive.A.Setting up MATLAB to run with N-way toolbox and DOMFluortoolbox.1.Decide on a sensible place to locate the DOMFluo

9、rtoolbox on your computer.(This could,for example,be C:Program FilesMATLABR2007btoolbox butcan also be elsewhere).Create a folder and name itDOMFluor.Extract the contents of the zip file“DOM-Fluor.zip”into the DOMFluor folder.2.Start MATLAB.Select File menu then click Set path.Click Add with sub fol

10、ders and locate the DOMFluorfolder you created in Step 1 above.If the N-Way tool-box is currently installed,remove it from the Path listto avoid conflicts.The N-Way toolbox is included aspart of the DOMFluor toolbox.Click Save thenClose.You have now associated the DOMFluor tool-box with MATLAB and t

11、his means that the functionsin these folders can be recognized.3.To check that the toolboxes are correctly associatedyou can typeDOMFluorand press enter in the Command Window in MATLAB.If“Yes”is printed to the Command Window,the tool-box is installed.If red text appears the toolbox has notbeen corre

12、ctly installed.Redo Step 2.Note that if youhave other toolboxes with similarly named functions,only the function upmost in the folder-list will workproperly.4.Section A will have to be repeated if a new version ofMATLAB is installed.B.Loading the tutorial data and plotting the EEMs.1.Typeload PARAFA

13、Cexample.matin the Command Window.This will load the tutorialdata into the MATLAB Workspace.This consists of adata structure called OriginalData.Try typingOriginalDataCharacterizing dissolved organic matter fluorescence with paral-lel factor analysis:a tutorialColin A.Stedmon1*and Rasmus Bro21Depart

14、ment of Marine Ecology,National Environmental Research Institute,Aarhus University,Frederiksborgvej 399,Roskilde,Denmark2Dept.Food Science,Faculty of Life Sciences,University Copenhagen,Rolighedsvej 30,DK-1958,Frederiksberg,Denmark*Corresponding author e-mail:cstdmu.dk,Tel:+45 46301805.Limnol.Oceano

15、gr.:Methods 6,2008 2008,by the American Society of Limnology and Oceanography,Inc.in the command window.This will output the following:This details the data that is contained within the datastructure.i.Ex-is a list of the excitation wavelengths mea-sured(in nm).In this case 240 to 450 every 5nm.ii.E

16、m-is a list of the emission wavelengths mea-sured(in nm).In this case 300 to 600 every 2nm.iii.X-is the fluorescence data as a three dimen-sional array(65 samples x 151 emission wave-lengths x 43 excitation wavelengths).iv.nSample,nEx and nEm:state the number ofsamples,excitation and emission wavelengths.v.XBackup-is a backup copy of the data and notused in the tutorial.2.Now we will plot the EEMs to check that the data iscorrectly loaded.In the toolbox there are several func-tions that can be u