276 lines
9.2 KiB
Matlab
Executable File
276 lines
9.2 KiB
Matlab
Executable File
%% CALLED BY par4GblFnc8c.m %%
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function [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanIntensELr,par4scanCFparameters,par4scanCFdate,outC,outCstd]= ...
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NCfitImCFparforFailGbl2(parMat,times, values, timeOffsets, fileSuffix, AUCfinalTime, ~, spotAreas, outputDirectory, ~,~, sols, ~) %,scan)
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%Preallocation for parfor loop**********************************
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st(1,1:size(times,2))= 1111;
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resMat(1,1:27)= 0;
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resMatStd= resMat;
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outC= zeros(384,27);
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outCstd= zeros(384,27);
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for m=1:384
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pa{m}= st;
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par4scanCFparameters{m}= parMat;
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par4scanCFdate{m}= datestr((now),31);
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end
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par4scanselTimesStd= pa;
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par4scanselIntensStd= pa;
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par4scanTimesELr= pa;
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par4scanIntensELr= pa;
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par4resMat= zeros(384,27);
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par4resMatStd= zeros(384,27);
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%****************************************************************
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%*****************Begin the Spot(cultures) loop****************************
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for ii= 1:384 %startSpot:numCultures
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%parfor ii= 1:384 %startSpot:numCultures
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ii; %%%db print out the culture number
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timepts= [];
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currValues=[];
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currSpotAreas=[];
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currSpotArea=[];
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dataMatrix=[];
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selTimesStd=[]; %191024 parfor
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selIntensStd=[]; %191024 parfor
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FiltTimesELr=[]; %191024 parfor
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NormIntensELr=[]; %191024 parfor
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% add offset...1 offset PER PLATE
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timepts = times + timeOffsets; %(floor((ii-1)/arrayFormat) + 1);
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currValues = values(ii,:); %change values(spotNum,:);
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% get spot areas for this culture
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currSpotArea = spotAreas(:,ii);
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% just use the area at the last time point
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%currSpotArea = currSpotAreas(1);
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%--------------------------------------------------------------
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%Preallocate to accomodate parfor loop **************************
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resMatStd= zeros(1,27);
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resMat= zeros(1,27);
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currNormIntens = currValues/currSpotArea;
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tmpx=find(currNormIntens>5); %15jh % 2.3);
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validSpot=true;
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if(isempty(tmpx) || (length(tmpx)<3))
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validSpot= false;
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normIntens= currNormIntens;
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filterTimes= timepts; %filterTimes; %currTimes;
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selTimesStd= timepts;
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selIntensStd= currNormIntens;
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FiltTimesELr= timepts;
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NormIntensELr= currNormIntens;
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else
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%*******************************************************
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%NCfilImCF
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%NCfilImCF.m called from NCfitImCF.m line 119*******************
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%Preallocate incase something bails in NCscurImCFparfor
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resMatStd= zeros(1,27);
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resMat= zeros(1,27);
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hold off %09_0704
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dataMatrix=[];
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K=0;r=0;l=0;Klow=0;Kup=0;rlow=0;rup=0;llow=0;lup=0;AUC=0;MSR=0; rsquare=0;
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bl=0;
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Tpt1=0; numFitTpts =0;thresGT2=0;minTime=0;fitbl=0; %diagnostic outputs only
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timepts= timepts; %timepts= currTimes; parfor
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normIntens= currNormIntens;
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dataMatrix= []; %parfor move clear from NCfitImCF...m
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loIntensThres=parMat(4);
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stdLoIntLim=parMat(5);
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%******Begin basic filter**********
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%[loInten Thres,stdbased Trim before Scurve start, and dropout detection]
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if(max(normIntens) > 2.29)
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threshold = loIntensThres; %1.9; %Increase this value to reduce low data point (flag=2)
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else
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threshold = 0;
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end
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dropThreshold= -0.0001* max(normIntens);
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%Initialize dataMatrix**********************************
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dataMatrix(1,:)=timepts;
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dataMatrix(2,:)=normIntens;
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dataMatrix(3,:)= ones;
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dataMatrix(4,:)=normIntens;
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%Determine a mean Intensity Index point and assoc'd TimePt
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a= min(normIntens(normIntens>=0)); %(find(normIntens>=0)));
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b= max(normIntens(normIntens>=0)); %(find(normIntens>=0)));
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c= 0.5*(b-a);
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d= b-c;
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meanIntIndPt= find(normIntens>d,1);
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meanInt= normIntens(meanIntIndPt);
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meanTime= times(meanIntIndPt);
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%**********************************************************
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%**************************************************************************
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% NCLoIntstdTrim
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%NCLoSstdTrim.m called by NCfilImCF and NCfil.m
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flg1=0;
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loScurvLim=stdLoIntLim; %
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loStimeN=1;
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last2n=1;
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stdDev= [];
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nrmIntens0= normIntens;
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for n=1:meanIntIndPt
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if nrmIntens0(n)<=0
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nrmIntens0(n)=0;
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end
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if(nrmIntens0(n)<threshold)
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if (loStimeN-2)>0,dataMatrix(3,1:(n-2))= 2; %add to lowIntensity cull flags, the pre S cull data
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else dataMatrix(3,1:n)= 2;end
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dataMatrix(3,1:(n-2))= 2;
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last2n=n;
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end
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if n<(length(nrmIntens0)-3)
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x=nrmIntens0(n:(n+3));
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stdDev(n)=std(x);
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if (stdDev(n)<loScurvLim && flg1~=1)
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loStime=timepts(n);
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loStimeN=n;
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end
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if stdDev(n)>6 ,flg1=1;end %detect S curve rise->stop stdLoInt detection
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end
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end %end for
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if (loStimeN-2)>0,dataMatrix(3,1:(loStimeN-2))= 2; %add to lowIntensity cull flags, the pre S cull data
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else dataMatrix(3,1:(loStimeN-2))= 2;end
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qcutoff=2;
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qind=find(normIntens>2); %,:,'first');
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if ~isempty(qind(3)), qcutoff=qind(3);end
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[minInt,I]= min(normIntens(2:qcutoff));
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bl=minInt;
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minTime=dataMatrix(1,I); %diagnostic output only
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if (length(qind)>5)&&I>1,dataMatrix(3,1:(I-1))=5; end
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tGT2Flg=0;
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for n=1:length(normIntens)
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dataMatrix(4,n)=normIntens(n)-bl;
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if n>I && dataMatrix(4,n)>=2 && tGT2Flg==0
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thresGT2=n;thresGT2Tm=dataMatrix(1,n);tGT2Flg=1;
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end %diagnostic output only
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end
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resMat(18)= bl;
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resMatStd(18)= bl;
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resMatStd(20)= minTime;
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resMat(20)= minTime;
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%&&&&&&&&&&&&&&&&&&&&&&& &&&&&&&&&&&&&&&&&&&&&&&&
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%*********************************************************
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%DropOut cull section(single drop points)*******************
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DropOutStartPt=length(normIntens);
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for n=1:length(normIntens)
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if(n>1)
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if(((normIntens(n)- normIntens(n-1))< dropThreshold))&& ...
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(n > max(meanIntIndPt,thresGT2) )
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dataMatrix(3,n)= 6;
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end
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end
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end
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%??????should/could this be removed as recreated in%NCscurImCF_3parfor.m????????????????????
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%Post Stdtest cull for low intensities inclusion of additional low value points
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%selTimes= [--,--] %don't know size before as it is a filtered output
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tmpIndx= 0;
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for n=1:length(normIntens)
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if (dataMatrix(3,n)==1)
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tmpIndx= tmpIndx+1;
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selTimes(tmpIndx)= dataMatrix(1,n); %selTimes(nn)= dataMatrix(1,n);
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selIntens(tmpIndx)= dataMatrix(4,n); %selIntens(nn)= dataMatrix(4,n);
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end
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end
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selTimes=selTimes';
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selIntens=selIntens';
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%???????????????????????????????????????????????????
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%**********End Basic filter******************
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%******************************************************
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filtNormIntens=normIntens;
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dataMatrix0= dataMatrix;
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filterTimes= timepts; %parfor
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%_____________________________________________________________
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%*******************************************
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%NCscurImCF
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%NCscurImCF_1
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%NCscurImCF_2
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%NCscurImCF_3
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%NCscurImCF_3parfor
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%NCscurImCF_3parfor(dataMatrix, AUCfinalTime)
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%dataMatrix %debugging parfor gbl ok 85.7145; 126.4579,6, 124.5264 37tPt
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%adsfj %debugging parfor gbl
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[resMatStd, resMat, selTimesStd, selIntensStd, FiltTimesELr, NormIntensELr] =...
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NCscurImCF_3parfor(dataMatrix0, AUCfinalTime, currSpotArea, sols, bl, minTime);
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end % end JUMP OVER associated with if(find(intensities>1000)<5)
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%resMatStd
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%asdf
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%To accommodate parfor can't use global 'scan' variable 191002================
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% {
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par4scanselTimesStd{ii}= selTimesStd; %timepts'; %filterTimes';
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par4scanselIntensStd{ii}= selIntensStd; %normIntens';
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par4scanTimesELr{ii}= FiltTimesELr; %19_1021 preserve for CurveDisplay and EZview
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par4scanIntensELr{ii}= NormIntensELr; %19_1021 preserve for CurveDisplay and EZview
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%}
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%$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
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%************* striped down OutCell code was put back into NCfitImCF
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outC(ii,:)= resMat; %{ii, par4resMat};
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outCstd(ii,:)= resMatStd; %{ii, par4resMatStd};
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end %Multispot parfor ii loop end PARFOR LOOP END##############################################################################
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%###############################################################################################################################
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%###############################################################################################################################
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%outC
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%*********************************19_1001***********************************
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%To accomodate parfor copy par4scan thru global p4 functions inside of
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%parfor loop --then outside to par4Gbl_Main8b.m
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%**************************************************************************
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fileExt = '.txt';
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filePrefix = 'FitResultsComplete_';
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fileNamePlate = [filePrefix fileSuffix fileExt];
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fileName= fullfile(outputDirectory, fileNamePlate); %[outputDirectory fileNamePlate];
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fid = fopen(fileName,'w');
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fprintf(fid, 'Fit Results Complete\n');
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%fprintf(fid, 'Num.\tAUC\tMSR\tK\tr\tl\tR-squared\tK-lower\tK-upper\tr-lower\tr-upper\tl-upper\tl-lower\tArea\tLastInten\tSpineMaxRateTimePt\tLastFitTimePt\n');
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fclose(fid);
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end %function end
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%&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&
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%##########################################################################
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