Format NCfitImCFparforFailGbl2.m
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@@ -2,8 +2,7 @@
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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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% 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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@@ -11,7 +10,6 @@ resMatStd= resMat;
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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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@@ -21,18 +19,14 @@ end
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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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% 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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@@ -48,9 +42,7 @@ for ii= 1:384 %startSpot:numCultures
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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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% 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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@@ -60,22 +52,16 @@ for ii= 1:384 %startSpot:numCultures
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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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% NCfilImCF.m
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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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hold off;
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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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@@ -84,11 +70,11 @@ dataMatrix=[];
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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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dataMatrix=[]; % arfor 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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% Basic filtering
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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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@@ -97,7 +83,8 @@ normIntens= currNormIntens;
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end
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dropThreshold=-0.0001* max(normIntens);
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%Initialize dataMatrix**********************************
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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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@@ -108,30 +95,27 @@ 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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if (loStimeN-2)>0
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dataMatrix(3,1:(n-2))=2; % add to lowIntensity cull flags, the pre S cull data
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else
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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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@@ -142,23 +126,31 @@ for n=1:meanIntIndPt
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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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if stdDev(n)>6
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flg1=1
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end % detect S curve rise->stop stdLoInt detection
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end
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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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% TODO repetitive code
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if (loStimeN-2)>0
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dataMatrix(3,1:(loStimeN-2))=2; % add to lowIntensity cull flags, the pre S cull data
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else
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dataMatrix(3,1:(loStimeN-2))=2
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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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if ~isempty(qind(3))
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qcutoff=qind(3)
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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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if (length(qind)>5)&&I>1
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dataMatrix(3,1:(I-1))=5
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end
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tGT2Flg=0;
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for n=1:length(normIntens)
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@@ -173,21 +165,18 @@ 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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% 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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% TODO 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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@@ -200,58 +189,34 @@ tmpIndx= 0;
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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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end
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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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end
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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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@@ -266,10 +231,4 @@ 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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end
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