301 lines
11 KiB
Matlab
Executable File
301 lines
11 KiB
Matlab
Executable File
%% CALLED By p4loop8c.m %%
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function [p4L2, TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneRefs3,Tmpsbdg3]= ...
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par4GblFnc8c(parMat,tptLength,~,selScanNumLst,~,Fflg,PTmapPos,optCirMask,diaExt,doCircle,cirPixA,cirMask,~,...
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TmpexpScanIntens,TmpFexpScanSpots,TmpFexpScanBMtp,TmpanlZoneRefs,scCount,tifFileLstP4,~,ImParMat, ...
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numRows,numCols,scLst,easyResultsDir,projectScansDir,~, Tmpsbdg)
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global printResultsDir
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selScan=selScanNumLst(scCount);
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tptLength0=length(tifFileLstP4{scCount});
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% tptLength=numFiles;
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tifFileLst={tifFileLstP4(scCount)};
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% Extract the Imaging time stamps from selected tif files
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% clear('e','f'); %can't use clear inside a parfor loop. Preallocation
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% can be larger than useable .bmp files! Therefore must be small and
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% increased during for loop to maintain cell size integrity between e & f
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e=cell(1,2); f=cell(1,2); %(tptLength,2); f=cell(tptLength,2);
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nndx=0;
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for tPt=1:tptLength0 %size(tifFileLst,1) %length(tifFileLst)
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tifFileLstP4{scCount}(tPt)
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scLst;
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scLst(scCount)
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char(scLst(scCount))
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char(fullfile(projectScansDir,char(scLst(scCount))))
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projectScansDir;
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swCatch=0;
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nndx=nndx+1;
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tifFile=char(fullfile(projectScansDir,char(scLst(scCount)), tifFileLstP4{scCount}(tPt)));
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try
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info=imfinfo(tifFile); % D:\jwrDevel\DevelCurveFittingJWR\ImageScans\Scan2\020hr002.tif
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catch ME
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% Note: During parallel operation Matlab will not open file (fid)
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% etc. Therefore error message text will not be written.The only way
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% to get it out would be to pass variable through called function to
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% the ..Main8c script outside the parfor loop and print to file from
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% there. Consequently for now it only prints error to file when one
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% edits p4loop8c.m from 'parfor' to ordinary 'for' loop
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fFail=((fullfile(printResultsDir,'ImageFileReadFailure.txt')));
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fid=fopen(fFail,'a'); %create,open and append
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% fprintf(fid,'%s \n',char(tifFile))
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fclose(fid);
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nndx=nndx-1;
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swCatch=1;
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rep=getReport(ME, 'basic');
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rep=strcat('Read info failure for-',tifFile,' -', rep);
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% fprintf(fid,'%s \n',rep) %See Note:
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end
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tptLength=nndx;
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scTmNumeric=1; %initialize for parfor
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if swCatch==0
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scTmNumeric(nndx)=datenum(info.FileModDate);
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e(nndx,:)={tifFile, scTmNumeric(nndx)};
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% newtifFileLst(nndx)=tifFileLst(tPt);
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end
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end
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% Clear tifFileLst;
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tifFileLst=cell(nndx,1);
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f={sortrows(e,2)};
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tifFileLst=f{1,1}(:,1);
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areaOfIntensAboveBG=zeros(24,16,length(tifFileLst));
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% Calculate Time series for each Plate of Selected Scan
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lastPlateOnScan=1; %Ncode
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tSeriesv=[]; t0Seriesv=[];
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if tptLength>0 % added to jump over and fill data for invalid Sscan(plate runs
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scTmNumv=cell2mat(f{1,1}(:,2)); % (:,2))120613 fix for variant length data
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prtTmNumv=min(scTmNumv)-.000001;
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tSeriesv=((scTmNumv-prtTmNumv)*24);
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t0Seriesv=((scTmNumv-scTmNumv(1))*24);
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end
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% Added to jump over and fill data for invalid Sscan(plate runs
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if tptLength>=3
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% Create blank scan
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ImHeigth=2075;
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ImWidth=1400;
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Empsc=zeros(ImHeigth,ImWidth); %Ncode
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% Start scan loop
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lastPlateOnScan=1; %Ncode
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disp('Before call to NIscanIntens.....')
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% Execute Image conversion into Intensity Data
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[Tmpsbdg2, scanIntens, ~, ~, ~, TmpexpScanIntens2, TmpFexpScanSpots2, TmpFexpScanBMtp2, TmpanlZoneRefs2,areaOfIntensAboveBG]= ...
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NIscanIntensBGpar4GblFnc(Fflg,tifFileLst, ImParMat, PTmapPos,optCirMask,diaExt,doCircle,cirPixA,numRows,numCols,ImHeigth,ImWidth,cirMask, ...
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tptLength,selScan,Empsc,TmpexpScanIntens,TmpFexpScanSpots,TmpFexpScanBMtp,TmpanlZoneRefs,easyResultsDir, Tmpsbdg);
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TmpexpScanIntens3=TmpexpScanIntens2;
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TmpFexpScanSpots3=TmpFexpScanSpots2;
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TmpFexpScanBMtp3=TmpFexpScanBMtp2;
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TmpanlZoneRefs3=TmpanlZoneRefs2;
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Tmpsbdg3=Tmpsbdg2;
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% clear plate
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CFscanIntens=zeros(384,1); % zeros(16,24);
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plate=[];
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plate=zeros(24,16,tptLength);
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plate(:,:,:,1)=scanIntens(1:1:24,16:-1:1,:); % TmpexpScanIntens2(1:1:24,16:-1:1,:);%Ncode Dev3Vertical Similar to below
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% NIcheck: Check for bad scans at time points (swapped plates etc.)
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% Set up cell arrays for storing each plate in each Scan ..(scan,plate)
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SWprint=0;
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% Construct Legacy ...Intens.txt file
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if SWprint==1
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filename=fullfile(easyResultsDir,'PrintResults',(strcat('Plate',num2str(selScan),'_Intens.txt')));
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fid=fopen(filename,'w');
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end
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if length(size(plate))==2 % only two dims if only one image
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numOfImages=1;
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else
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numOfImages=size(plate,3);
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end
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CFscanIntens=zeros(384,numOfImages);
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locIndx=0; pl=1;
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for n=1:numCols % Ncode changed to 16 for Vert
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for m=1:numRows % Ncode change to 24 for Vert
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locIndx=locIndx+1;
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for k=1:numOfImages
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if SWprint==1
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if k==1 && numOfImages==1, fprintf(fid,'%.2f\n',plate(m,n,k,pl));end
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if k==1 && numOfImages~=1, fprintf(fid,'%.2f',plate(m,n,k,pl));end
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if k>1 && k<numOfImages, fprintf(fid,'\t%.2f',plate(m,n,k,pl));end %
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if k~=1 && k==numOfImages,fprintf(fid,'\t%.2f\n',plate(m,n,k,pl));end
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end
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CFscanIntens(locIndx,k)=plate(m,n,k,pl);
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end
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end
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end
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if SWprint==1
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fclose(fid);
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end
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% printGrwAreas
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% Area as the max number of pixels with intensities greater than the Background
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% grArea(row,col,tPt,Plate) Note that images r and c are 90 degrees shifted
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% and then mirror imaged. Thus data must be inverted and rotated to get
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% for the rows a-p and col 1-24 (and the EMS expected 1-384) orientation
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% clear grArea
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grArea=ones(24,16,tptLength);
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grArea(:,:,:,1)=areaOfIntensAboveBG(1:1:24,16:-1:1,:); %for Ncode dev3vert
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% for p=1:lastPlateOnScan
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if SWprint==1
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if SWgrowthArea==1
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filename=fullfile(printResultsDir,(strcat('Plate',num2str(selScan),'_Areas.txt')));
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else
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filename=fullfile(printResultsDir,(strcat('ALTgrowthA_Scan',num2str(selScan),'_Plate',num2str(1),'_Areas.txt')));
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filename=fullfile(printResultsDir,(strcat('ALTgrowthA_Plate',num2str(selScan),'_Plate','_Areas.txt')));
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end
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fid=fopen(filename,'w');
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end
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locIndx=0;
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Ag=zeros(1,384);
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for m=1:16 % Ncode change from 16 %Vert back to 16
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for n=1:24 % Ncode change from 24 %Vert back to 24
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growthArea=max(grArea(n,m,:,1));
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if SWprint==1
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fprintf(fid,'%3.f\n',growthArea);
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end
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locIndx=locIndx+1;
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Ag(locIndx)=growthArea;
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end
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end
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if SWprint==1
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fclose(fid);
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% fclose('all'); % TODO do we need this?
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end
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% AutoImCF curveFit kickoff setup
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autoImCFlag=1;
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if autoImCFlag==1, SWgrowthArea=1;end
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times=tSeriesv;
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scanAreas=Ag; % growthArea;
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offsets=0;
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suffix=strcat('Scan', num2str(selScan),'_Plate', num2str(1)); % char(QspLst(n));
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AUCfinalTime=96;
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arrayFormat=384;
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% Version compatability fixes
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%{
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v11a='7.12.0.635 (R2011a)';
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v14a='8.3.0.532 (R2014a)';
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%v14b='8.4.0.150421 (R2014b)';
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v18a='9.4.0.813654 (R2018a)';
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v18b='9.5.0.944444 (R2018b)';
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% Fourth order derivative of logistic equation
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if isequal(v18a,version)||isequal(v18b,version)
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syms t K r l;
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fd4=diff(K / (1 + exp(-r* (t - l ))),t,4);
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else
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fd4=diff(sym('K / (1 + exp(-r* (t - l )))'),4);
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end
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sols=solve(fd4);
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if isequal(v11a,version) || isequal(v14a,version)
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else
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tmpswap=sols(1);
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sols(1)=sols(3);
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sols(3)=tmpswap;
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end
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%}
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if verLessThan('matlab','8.3') % original work 23_0227 updated 23_0525 (8.4 changed to 8.3)
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fd4=diff(sym('K / (1 + exp(-r* (t - l )))'),4);
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sols=solve(fd4);
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else % accomodate new matlab changes after 2014a fix 2nd update 23_0227
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syms t K r l;
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fd4=diff(K / (1 + exp(-r* (t - l ))),t,4);
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sols=solve(fd4);
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tmpswap=sols(1);
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sols(1)=sols(3);
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sols(3)=tmpswap;
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end
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% CFscanIntens
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% Call CurveFit routine
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% NCfitImCF(times, CFscanIntens, offsets, suffix, AUCfinalTime, arrayFormat, scanAreas, printResultsDir, autoImCFlag, selScan,sols) %,scan)%, scPltList) outputDirectory;
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% [scanTmp2]=NCfitImCFparforFailGbl(times, CFscanIntens, offsets, suffix, AUCfinalTime, arrayFormat, scanAreas, printResultsDir, autoImCFlag, selScan, sols, scanTmp); %,scan)%, scPltList) outputDirectory;
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[par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanIntensELr,par4scanCFparameters,par4scanCFdate,outC2,outCstd2]= ...
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NCfitImCFparforFailGbl2(parMat,times, CFscanIntens, offsets, suffix, AUCfinalTime, arrayFormat, scanAreas, printResultsDir, autoImCFlag, selScan, sols); %,scan)%, scPltList) outputDirectory;
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else %fill with default values when an invalid plate scan occurs
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CFscanIntens=zeros(16,24);
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Ag=zeros(1,384);
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% Preallocation for parfor loop
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times=tSeriesv;
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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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outC2=zeros(384,27);
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outCstd2=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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TmpexpScanIntens00=cell(1); %cell(1,scanMax);
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TmpFexpScanSpots00=cell(1); %cell(1,scanMax);
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TmpFexpScanBMtp00=cell(1); %cell(1,scanMax);
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TmpanlZoneRefs00=cell(1); %cell(1,scanMax);
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Tmpsbdg00=cell(1);
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%}
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TmpexpScanIntens3=cell(1); %TmpexpScanIntens2;
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TmpFexpScanSpots3=cell(1); %TmpFexpScanSpots2;
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TmpFexpScanBMtp3=cell(1); %TmpFexpScanBMtp2;
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TmpanlZoneRefs3=cell(1); %TmpanlZoneRefs2;
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Tmpsbdg3=cell(1); %Tmpsbdg2;
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end %if tptLenth>=3 line19 20_0928
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tSeriesv; %debuggin parfor
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p4L1{1}=tSeriesv;
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p4L1{2}=t0Seriesv;
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p4L1{3}=datestr(prtTmNumv,31);
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p4L1{4}=CFscanIntens;
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locIndx=0;
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for n=1:numCols % Ncode changed to 16 for Vert
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for m=1:numRows % Ncode change to 24 for Vert
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locIndx=locIndx+1;
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rc=[n,m];
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p4rcTmp(locIndx)={rc};
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p4pIndxTmp(locIndx)=locIndx;
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end
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end
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p4L1{5}=p4rcTmp;
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p4L1{6}=p4pIndxTmp;
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p4L1{7}=Ag;
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p4L1{8}=par4scanselIntensStd;
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p4L1{9}=par4scanselTimesStd;
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p4L1{10}=par4scanTimesELr;
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p4L1{11}=par4scanIntensELr;
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p4L1{12}=par4scanCFparameters;
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p4L1{13}=par4scanCFdate;
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p4L1{14}=outC2;
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p4L1{15}=outCstd2;
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p4L1{16}=selScan;
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p4L1{17}=cirPixA;
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p4L1{18}=datestr((now),31); % TODO this seems bad
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p4L2=p4L1;
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end
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