server-scripts/qhtcp-workflow/apps/matlab/easy/NIscanIntensBGpar4GblFnc.m

%% CALLED BY par4GblFnc8c.m %%
function [Tmpsbdg2, scanIntens, F_spots, bmtp, optomizedPos, TmpexpScanIntens2, TmpFexpScanSpots2, TmpFexpScanBMtp2, TmpanlZoneRefs2,areaOfIntensAboveBG]= ...
  NIscanIntensBGpar4GblFnc(Fflg, tifFileLst, ImParMat,PTmapPos,optCirMask,diaExt,doCircle,cirPixA,numRows,numCols,ImHeigth,ImWidth,cirMask, ...
  tptLength,selScan,Empsc,~, ~, ~, ~,easyResultsDir, Tmpsbdg1)    

  global matFile
  global CSrchRng
  global figsResultsDir
  global fotosResultsDir

  searchIntens=[];intensMax=[];detMaxPos=[];scIntens=[];areaOfIntensAboveBG=[];BkgrdMat=[];

  % TODO needs explanation
  if Fflg==1
    % Preallocation
    tPtLength=length(tifFileLst);
    optomizedPos=cell(24,16,tPtLength);
    F_spots=cell(24,16,tPtLength);  % Foto spot coordinates Preallocation
    bmtp=zeros(24,16,tPtLength);  % Added/used for FOTOS Preallocation
    MPnum=ImParMat(1);
    destPerMP=ImParMat(2);
    spotThres=ImParMat(4)/100;
    % width=ImParMat(5);
    CSrchRng=ImParMat(12);
    width=24; % absolute fixed after Sept 2014
    ditherF=ImParMat(6);
    ditherF=1; % absolute fixed after Sept 2014
    % Get PTmap data (detPos) and create PTimage with cirMask 2019_0904
    PTmapOnesDbl=zeros(2075,1400);
    for r=1:24
      for c=1:16
        [PTrefPt]=PTmapPos{r,c};
        PTrefPtR=PTrefPt(1);
        PTrefPtC=PTrefPt(2);
        % doCircle
        PTmapOnesDbl(PTrefPtR:(PTrefPtR+(diaExt-1)),PTrefPtC:(PTrefPtC+(diaExt-1)))=optCirMask; 
      end
    end
  end

  % Zeroth Initial Search Parameters
  rRangeUpper=-12; 
  rRangeLower=12;
  cRangeLower=-12;
  cRangeUpper=12;
  ditherI=width/3;
  searchRange=floor(width*0.75); %generally -/+18
  %searchRange=CSrchRng
  rCRangeUpper=-searchRange; % -12 % -8;    %Ranges should be multiples of dither 
  rCRangeLower=searchRange; %12;  %Ranges should be multiples of dither
  cCRangeLower=-searchRange; %-12  %-8; %-12;  %Ranges should be multiples of dither 
  cCRangeUpper=searchRange; %12;  %8;    %Ranges should be multiples of dither 
  ditherC=floor((2*searchRange)/9); %gnerally /6 0r /9 -> dither=6 or 4 pixels 
  if ditherC==0,ditherC=1;end
  rFRangeUpper=-floor(1/2*width); %(searchRange*2/3) %-12 % -8;    %Ranges should be multiples of dither 
  rFRangeLower=floor(1/2*width); %(searchRange*2/3); %12;  %Ranges should be multiples of dither
  cFRangeLower=-floor(1/2*width); %(searchRange*2/3); %-12  %-8; %-12;  %Ranges should be multiples of dither 
  cFRangeUpper=floor(1/2*width); %(searchRange*2/3)  %12;  %8;    %Ranges should be multiples of dither
  ditherF=1;
  % The purpose is to reduce incidence of 'chasing' scratches and abrasions to
  % the edge of a frame and also to limit late timept finds of overgrown
  % spot(that are yet small). The idea is to make the threshold high enough to
  % prevent the tracking of scratches and small contaminants(overgrowth) while
  % not limiting detection of small slow grow cultures. Recommend value
  % slightly above the expected background level. 
  noSpotThres=60; % If PixelIntensity for area < area*this, use the Orig.search Refpt 
  if doCircle==1
    noSpot=cirPixA*noSpotThres;     
  else  
    noSpot=(width^2)*noSpotThres;  %Area * (a selected background pixel level i.e., 70)
  end

  % Begin Time series loop
  % Preallocation
  stopSearch=zeros(numRows,numCols); %set all spots 'stopSearch' to false
  intens=zeros(24,16);
  intensPrev=zeros(24,16);
  cent=cell(24,16);
  BGTav=zeros(numRows,numCols);
  % 7 0;before incr.to95 to accommodate dark media %50forEpson;%Initialize for first tPt run
  BGthres(1:numRows,1:numCols)=95;
  if length(tifFileLst)>2
    % Determine a good Plate Image from all the timepoints to use for Registration
    % Plate Intensity curve over time points
    % clear plateImage
    plateImage={};
    %{
    % Version compatability fixes
    v11a='7.12.0.635 (R2011a)';
    v14a='8.3.0.532 (R2014a)';
    %v14b='8.4.0.150421 (R2014b)';
    v18a='9.4.0.813654 (R2018a)';
    v18b='9.5.0.944444 (R2018b)';
    pool=2;
    if isequal(v11a,version)|| isequal(v14a,version)
      if matlabpool('size')==0
        matlabpool(pool)
      end
    else
      if parpool('local')==0
        parpool('local', pool)
      end
    end
    %}
    % parfor iii=1:length(tifFileLst)
    for iii=1:length(tifFileLst)
      tifFile=char(tifFileLst(iii));
      fullplt=imread(tifFile); % Ncode actually reading a .bmp file for Ncode
      fullpl=255 - fullplt(:,:,1);
      %fullpl=(fullplt(1:ImHeigth,1:ImWidth));
      pltInts(iii)=sum(sum(fullpl(:,:)))/(ImHeigth*ImWidth);
      plateImage{iii}=fullpl;   % 190919 to use instead of re-reading in NIscanIntensBG.m
    end
    guessOffsetAdj=0.5; %Half(0.5) is the midpoint intensity
    guessOffset=(max(pltInts)- min(pltInts)) * guessOffsetAdj; %Could plug-in a curvefit routine to determine an 'L' value
    guessVal=max(pltInts)- guessOffset;
    guesTpt=find(pltInts > guessVal,1,'first');
    if isempty(guesTpt)
      guesTpt=1;
    end
    PtptIm=tifFileLst(guesTpt);
    PtptImg=char(tifFileLst(guesTpt));
    ImageRd=imread(PtptImg); %Ncode actually reading a .bmp file for Ncode
    PltImg=(ImageRd(1:ImHeigth,1:ImWidth));
    PltImg=255 - PltImg;
    % Convert to image to BW then AND with PTmapOnesDbl   
    GraythrShift=1;
    BWimage=im2bw(PltImg, GraythrShift*graythresh(PltImg));
    matchAnded=BWimage & PTmapOnesDbl;
    initPTANDed=matchAnded;
    ANDValInitPT=sum(sum(initPTANDed(:,:)));  

    % Begin Image Registration for Pintool
    MaxANDVal=0; % sum(sum(BWimage(:,:)));  %seed MaxANDVal from the BWimage 
    regDith=4;
    TestmapOnesDbl=zeros(2075,1400);

    % Create a Search Range centered on C==1 and R==1 of the PinTool map
    RtopBndry=96; RbotBndry=176;
    ClfBndry=96; CrtBndry=154;
    [PTrefPt]=PTmapPos{1,1};
    PTrefPtR=PTrefPt(1);
    PTrefPtC=PTrefPt(2);
    rngUpper=RtopBndry - PTrefPtR;
    quotT=round(abs(rngUpper)/regDith); 
    topRang=regDith * quotT;
    if rngUpper<0, topRang=-1*topRang; end
    rngLower=RbotBndry - PTrefPtR;
    quotB=round(abs(rngLower)/regDith);
    botRang=regDith * quotB;
    if rngLower<0, botRang=-1*botRang; end  
    rngLeft=ClfBndry - PTrefPtC;
    quotLf=round(abs(rngLeft)/regDith);
    leftRang=regDith * quotLf;
    if rngLeft<0, leftRang=-1*leftRang; end
    rngRight=CrtBndry - PTrefPtC;
    quotRt=round(abs(rngRight)/regDith);
    rightRang=regDith * quotRt;
    if rngRight<0, rightRang=-1*rightRang; end

    % Orthagonal Registration
    testPos=cell(24,16);
    for shiftPosR=topRang:regDith:botRang
      for shiftPosC=leftRang:regDith:rightRang 
        TestmapOnesDbl=zeros(2075,1400);
        for r=1:24
          for c=1:16
            [PTrefPt]=PTmapPos{r,c};
            testPosR=PTrefPt(1) + shiftPosR;  
            testPosC=PTrefPt(2) + shiftPosC;         
            a=[testPosR,testPosC];   %testPos(r,c)={testPosR,testPosC};
            testPos(r,c)={a};
            doCircle;
            TestmapOnesDbl(testPosR:(testPosR+(diaExt-1)),testPosC:(testPosC+(diaExt-1)))=cirMask;  %optCirMask;
          end
        end
        GraythrShift=1.0;
        BWtestimage=im2bw(TestmapOnesDbl, GraythrShift*graythresh(TestmapOnesDbl));
        matchAnded=BWimage & BWtestimage;
        ANDVal=sum(sum(matchAnded(:,:)));
        if ANDVal> MaxANDVal
          MaxANDVal=ANDVal;
          MaxPos=testPos;
          MaxPosDbl=TestmapOnesDbl;
        end
      end
    end
    if MaxANDVal>ANDValInitPT 
      MaxPosDbl=MaxPosDbl; 
      MaxPos=MaxPos;
    else
      MaxPosDbl=PTmapOnesDbl;
      MaxPos=PTmapPos;
    end

    % SKEW Registration
    testSkPos=MaxPos;
    MaxANDValSk=0; %MaxANDVal;
    skQty=0.05;
    regDith=4;
    for shiftPos=-regDith/2:regDith/2 
      for k=-5:5
        sk=k* skQty;
        TestmapSkDbl=zeros(2075,1400);
        for r=1:24
          for c=1:16
            [skrefPt]=testSkPos{r,c};
            testSkPosR=round(skrefPt(1) + (c*sk + shiftPos));  
            testSkPosC=round(skrefPt(2) + (-r*sk + shiftPos));            
            a=[testSkPosR,testSkPosC]; % testPos(r,c)={testPosR,testPosC};
            testSkPos(r,c)={a}; 
            % doCircle
            TestmapSkDbl(testSkPosR:(testSkPosR+(diaExt-1)),testSkPosC:(testSkPosC+(diaExt-1)))=cirMask; % optCirMask;          
          end
        end
        GraythrShift=1;
        BWtestSkimage=im2bw(TestmapSkDbl, GraythrShift*graythresh(TestmapSkDbl));
        matchAndedSk=BWimage & BWtestSkimage;
        ANDValSk=sum(sum(matchAndedSk(:,:)));
        if ANDValSk> MaxANDValSk
          MaxANDValSk=ANDValSk;
          MaxPosSk=testSkPos;
          MaxPosSkDbl=TestmapSkDbl;
        end
      end
    end

    if MaxANDValSk> MaxANDVal 
      MaxANDVal=MaxANDValSk;
      MaxPosDbl=MaxPosSkDbl; 
      MaxPos=MaxPosSk;
    end

    % Center of Area for Final Registration
    % Note GraythrShift in NImapPT can be used to a lower or higher 'decider'
    % and thus effect the centroid(center of area) that this module determines.
    % GraythrShift=1.0 normally allowing the Matlab graythresh to calc. the BW decider
    range=0;   
    lastDetMaxCentDbl=zeros(2075,1400);
    lastDetMaxPos=cell(24,16);
    % CIRCLE related
    for r=1:24
      for c=1:16
        [refPt]=MaxPos{r,c};
        refPtR=refPt(1);
        refPtC=refPt(2);
        % Calc. Centroid Position of spot
        detPrLo=(MaxPos{r,c}(1)) -(range); detPrHi=(MaxPos{r,c}(1)) + (diaExt+range);
        detPcLo=(MaxPos{r,c}(2)) -(range); detPcHi=(MaxPos{r,c}(2)) + (diaExt+range);
        rsum=(sum(BWimage(detPrLo:detPrHi,detPcLo:detPcHi),2));
        csum=(sum(BWimage(detPrLo:detPrHi,detPcLo:detPcHi),1));
        if sum(rsum)>1 && sum(csum)>1
          Rvec=detPrLo:detPrHi;
          Cvec=detPcLo:detPcHi;
          centR=round((sum(Rvec .*rsum')) /sum(rsum));
          centC=round((sum(Cvec .*csum)) /sum(csum));
          aa=[(centR-diaExt/2) (centC-diaExt/2)];
        else
          rsum=(sum(MaxPosDbl(detPrLo:detPrHi,detPcLo:detPcHi),2));
          csum=(sum(MaxPosDbl(detPrLo:detPrHi,detPcLo:detPcHi),1));
          Rvec=detPrLo:detPrHi;
          Cvec=detPcLo:detPcHi;
          centR=round((sum(Rvec .*rsum')) /sum(rsum));
          centC=round((sum(Cvec .*csum)) /sum(csum));
        end
        aa=[(centR-diaExt/2) (centC-diaExt/2)];
        lastDetMaxPos(r,c)={aa};
        % 2nd Recenter Based on Previous
        detPrLo=lastDetMaxPos{r,c}(1) -(range); detPrHi=lastDetMaxPos{r,c}(1) + (diaExt+range);
        detPcLo=lastDetMaxPos{r,c}(2) -(range); detPcHi=lastDetMaxPos{r,c}(2) + (diaExt+range);             
        rsum=(sum(BWimage(detPrLo:detPrHi,detPcLo:detPcHi),2));
        csum=(sum(BWimage(detPrLo:detPrHi,detPcLo:detPcHi),1));
        if sum(rsum)>1 && sum(csum)>1
          Rvec=detPrLo:detPrHi;
          Cvec=detPcLo:detPcHi;
          centR=round((sum(Rvec .*rsum')) /sum(rsum));
          centC=round((sum(Cvec .*csum)) /sum(csum));
          aa=[(centR-diaExt/2) (centC-diaExt/2)];
        else
          rsum=(sum(MaxPosDbl(detPrLo:detPrHi,detPcLo:detPcHi),2));
          csum=(sum(MaxPosDbl(detPrLo:detPrHi,detPcLo:detPcHi),1));
          Rvec=detPrLo:detPrHi;
          Cvec=detPcLo:detPcHi;
          centR=round((sum(Rvec .*rsum')) /sum(rsum));
          centC=round((sum(Cvec .*csum)) /sum(csum));
        end
        aa=[(centR-diaExt/2) (centC-diaExt/2)];
        lastDetMaxPos(r,c)={aa};            
        [CentPt]=lastDetMaxPos{r,c};
        CentPtR=CentPt(1);
        CentPtC=CentPt(2);
        % doCircle
        lastDetMaxCentDbl(CentPtR:(CentPtR+(diaExt-1)),CentPtC:(CentPtC+(diaExt-1)))=cirMask; % optCirMask;
      end
    end

    BWtestCentimage=im2bw(lastDetMaxCentDbl, GraythrShift*graythresh(lastDetMaxCentDbl));
    matchAndedCent=BWimage & BWtestCentimage;
    ANDValCent=sum(sum(matchAndedCent(:,:))); 
    if ANDValCent>=MaxANDVal 
      MaxPosDbl=lastDetMaxCentDbl; 
      MaxPos=lastDetMaxPos;
      % detPos=lastDetMaxPos;
    end
    % detPos=lastDetMaxPos;
    detPos=MaxPos;
  end

  % Preallocation for speed on 2019_1121 ***
  scIntens=zeros(24,16,length(tifFileLst));
  BkgrdMat=zeros(24,16,length(tifFileLst));
  % areaOfIntensAboveBG=zeros(24,16,length(tifFileLst));
  lastDetMaxPos=cell(numRows, numCols);

  for tPt=1:length(tifFileLst)
    tPt;
    tifFile=char(tifFileLst(tPt));
    fullsc=plateImage{tPt};
    fIntsc=fullsc;
    % Bad Image Filter Zone
    % NORMALLY turned off; This is Hand HARD CODE SPECIFIC to particular ExpJOB
    specificHardFilterCode=0;
    if specificHardFilterCode==1 && tPt==1
      % Plate scratch filter prototype could be added here 
      fIntsc(:,1105:1190)=uint8(67);   %Specific blocking area set to background level here
      % fIntsc(:,:)=uint8(67);  % set entire image to background level if 1.bmp is
      % bad. This allows acquisiton of the initial "Print Time" from .bmp time stamp.
    end
    tp=90; bt=1935; lf=90; rt=1318; blkVal=10;  %tp=90;  
    fIntsc(1:tp,:)=uint8(blkVal);  %top of blocking frame
    fIntsc(bt:ImHeigth,:)=uint8(blkVal);  %bottom of blocking frame
    fIntsc(:,1:lf)=uint8(blkVal);   %left side of blocking frame
    fIntsc(:,rt:ImWidth)=uint8(blkVal);   %right side of blocking frame
    bwIntsc=im2bw(fIntsc,80/255);

    % Collect Intensities (Absorbances)
    % end for search for maximum intensity spot detection alignment
    if doCircle==1
      earlySrc1Thres=.31*cirPixA*255; % Initial search spot det. threshold
      earlySrc2Thres=spotThres*cirPixA*255; % Course search spot det. threshold
      definedSpot=(spotThres+.03)*cirPixA*255; % typically .34 ; 20000; %Intensity at which a spot is well defined for a width=24 {formerly20} % 0.5*((width^2 * (255- backgrdPixel))
    else
      earlySrc1Thres=.31*(width^2)*255; % Initial search spot det. threshold
      earlySrc2Thres=spotThres*(width^2)*255; % Course search spot det. threshold
      definedSpot=(spotThres+.03)*(width^2)*255;  % typically .34 ; 20000; %Intensity at which a spot is well defined for a width=24 {formerly20} % 0.5*((width^2 * (255- backgrdPixel))
    end
    detMaxPos=cell(numRows, numCols);
    bcent=cell(numRows, numCols);
    for r=1:numRows
      for c=1:numCols
        [refPt]=detPos{r,c};
        refPtR=refPt(1); InitR=refPt(1);
        refPtC=refPt(2); InitC=refPt(2);
        % ZeroSearchIntens  
        % clear ('searchIntens')
        searchIntens=[];
        if doCircle==1
          % cutout=fIntsc(refPtR+1:(refPtR+(diaExt)),(refPtC+1:(refPtC+diaExt)));
          cutout=fIntsc(refPtR:(refPtR+(diaExt-1)),refPtC:(refPtC+(diaExt-1)));
          Imcir=cutout .* uint8(cirMask);
          zeroSearchIntens=sum(sum(Imcir(1:(diaExt-1),1:(diaExt-1))));  
        else % standard square analysis area
          refPtRExt=refPtR+widthEx;
          if (refPtRExt)> size(fIntsc,1), refPtRExt=size(fIntsc,1); end
          refPtCExt=refPtC+widthEx;
          if (refPtCExt)> size(fIntsc,2), refPtCExt=size(fIntsc,2); end
          zeroSearchIntens=sum(sum(fIntsc(refPtR:(refPtRExt),refPtC:(refPtCExt))));
        end
        % clear ('searchIntens')
        searchIntens=[];
        intensMax=-1;
        src1cnt=0;  % zero count for oneshot calc of centroid after initial location of spot during Src1
        if stopSearch(r,c)==false      
          % Set Range and Dither********          
          if intensPrev(r,c)< earlySrc1Thres  %First Search parameters insert
            rRangeUpper=rCRangeUpper; 
            rRangeLower=rCRangeLower;
            cRangeLower=cCRangeLower;
            cRangeUpper=cCRangeUpper;
            dither=ditherI;                    
            [searchStartRef]=detPos{r,c};    
          elseif intensPrev(r,c)> earlySrc1Thres &&intensPrev(r,c)<= earlySrc2Thres  %Second Search parameters insert
            rRangeUpper=-CSrchRng; % rCRangeUpper; 
            rRangeLower=CSrchRng; % rCRangeLower;
            cRangeLower=-CSrchRng; % cCRangeLower;
            cRangeUpper=CSrchRng; % cCRangeUpper;
            dither=ditherC;
            % src1cnt=src1cnt+1;
            % After spot defined above selected threshold, start search from
            % center of the calc'd spot area
            % Calc. Center of Area (black and white (1's and 0's)
            % detPrLo=(detPos{r,c}(1)) -18; detPrHi=(detPos{r,c}(1)) +width+18;
            % detPcLo=(detPos{r,c}(2)) -18; detPcHi=(detPos{r,c}(2)) +width+18;
            detPrLo=(detPos{r,c}(1)) -CSrchRng; detPrHi=(detPos{r,c}(1)) +width+CSrchRng;
            detPcLo=(detPos{r,c}(2)) -CSrchRng; detPcHi=(detPos{r,c}(2)) +width+CSrchRng;         
            brsum=(sum(bwIntsc(detPrLo:detPrHi,detPcLo:detPcHi),2));
            bcsum=(sum(bwIntsc(detPrLo:detPrHi,detPcLo:detPcHi),1));
            bRvec=detPrLo:detPrHi;
            bCvec=detPcLo:detPcHi;
            bcentR=round((sum(bRvec .*brsum')) /sum(brsum));
            bcentC=round((sum(bCvec .*bcsum)) /sum(bcsum));
            bcent{r,c}=[bcentR, bcentC];
            cornerOfset=ceil((0.5*width)+CSrchRng); %ceil(0.5*(width+(2*CSrchRng)));
            refCorner{r,c}=[(bcentR-cornerOfset),(bcentC-cornerOfset)];
            %NAN blowup preventive
            if sum(brsum)>5 && sum(bcsum)>5
              % [searchStartRef]=cell2mat(bcent(r,c));
              [searchStartRef]=cell2mat(refCorner(r,c));
            else
              [searchStartRef]=detPos{r,c};
            end  
          elseif intensPrev(r,c) >earlySrc2Thres &&  intensPrev(r,c)<= definedSpot
            rRangeUpper=rFRangeUpper; %Fine Search parameters insert
            rRangeLower=rFRangeLower;
            cRangeLower=cFRangeLower;
            cRangeUpper=cFRangeUpper;
            dither=ditherF;
            zz=lastDetMaxPos(r,c);
            [searchStartRef]=zz{1,1};
          end    
          % Fixed to Roam Switch
          %{
          if intensPrev(r,c)<=earlySrc1Thres
            % [searchRef]=detPos{r,c}+ [rOff,cOff];
            [searchStartRef]=detPos{r,c};
          end
          if intensPrev(r,c)> earlySrc1Thres && intensMax<earlySrc2Thres
            % [searchRef]=detPos{r,c}+ [rOff,cOff];
            [searchStartRef]=cell2mat(cent(r,c));
          end
          if intensPrev(r,c) >=earlySrc2Thres,  %Let Roam
            zz=lastDetMaxPos(r,c);
            [searchStartRef]=zz{1,1};        
          end
          %}             
          extent=CSrchRng;
          Rmin=InitR-extent; Rmax=InitR+extent;
          Cmin=InitC-extent; Cmax=InitC+extent;

          % clear cutout  %just found 20_0327
          cutout=[];
          for rOff=rRangeUpper:dither:rRangeLower 
            for cOff=cRangeLower:dither:cRangeUpper          
              [searchRef]=searchStartRef + [rOff,cOff];
              refPtR=searchRef(1);
              refPtC=searchRef(2);
              if refPtR<Rmin,refPtR=Rmin;end
              if refPtR>Rmax,refPtR=Rmax;end
              if refPtC<Cmin,refPtC=Cmin;end
              if refPtC>Cmax,refPtC=Cmax;end
              % Do Circle analysis
              if doCircle==1
                % cutout=fIntsc(refPtR+1:(refPtR+(diaExt)),(refPtC+1:(refPtC+diaExt)));
                try
                  cutout=fIntsc(refPtR:(refPtR+(diaExt-1)),refPtC:(refPtC+(diaExt-1)));
                catch
                  tPt;
                  r;
                  c;
                end
                Imcir=cutout .* uint8(cirMask);
                searchIntens=sum(sum(Imcir(1:(diaExt-1),1:(diaExt-1))));              
              else  %standard square analysis area
                refPtRExt=refPtR+widthEx;
                if (refPtRExt)> size(fIntsc,1), refPtRExt=size(fIntsc,1); end
                refPtCExt=refPtC+widthEx;
                if (refPtCExt)> size(fIntsc,2), refPtCExt=size(fIntsc,2); end
                searchIntens=sum(sum(fIntsc(refPtR:(refPtRExt),refPtC:(refPtCExt))));
              end
              if searchIntens > intensMax 
                intensMax=searchIntens;
                intens(r,c)=searchIntens;
                intensPrev(r,c)=searchIntens;
                a=[refPtR,refPtC];
                detMaxPos(r,c)={a};
                lastDetMaxPos(r,c)=detMaxPos(r,c);
              end  
              if intensMax>definedSpot || intensMax<2
                stopSearch(r,c)=true;
              end
            end
          end  
          if intensMax< noSpot 
            intensMax=zeroSearchIntens;
            lastDetMaxPos(r,c)={refPt};
          end  
        else  % elseif Spot is well defined  STOPSearch strong 
          [refPt]=lastDetMaxPos{r,c};
          refPtR=refPt(1);
          refPtC=refPt(2);
          if doCircle==1
            cutout=fIntsc(refPtR:(refPtR+(diaExt-1)),refPtC:(refPtC+(diaExt-1)));
            Imcir=cutout .* uint8(cirMask);
            intens(r,c)=sum(sum(Imcir(1:(diaExt-1),1:(diaExt-1))));
          else %standard square analysis area
            intens(r,c)=sum(sum(fIntsc(refPtR:(refPtR+widthEx),refPtC:(refPtC+widthEx))));
          end
        end
        %{   
        if intensMax> earlySrc1Thres && intensMax< earlySrc2Thres && src1cnt==0,         
          %{          
          src1cnt=src1cnt+1;
          detPrLo=(detPos{r,c}(1)) -12; detPrHi=(detPos{r,c}(1)) +width+12;
          detPcLo=(detPos{r,c}(2)) -12; detPcHi=(detPos{r,c}(2)) +width+12;
          rsum=(sum(fIntsc(detPrLo:detPrHi,detPcLo:detPcHi),2));
          csum=(sum(fIntsc(detPrLo:detPrHi,detPcLo:detPcHi),1));
          Rvec=detPrLo:detPrHi;
          Cvec=detPcLo:detPcHi;
          centR=round((sum(Rvec .*rsum')) /sum(rsum));
          centC=round((sum(Cvec .*csum)) /sum(csum));
          cent{r,c}=[centR, centC];
            %}
        end
        %}
      end
    end

    % [F_spots,bmtp, BGthres,bmm,rwm,lstTpt,BGsc,totBkgrd]=... 
    % NIgenBkGrdDataPar4Fnc(ImParMat, tifFileLst, lastDetMaxPos, numRows, numCols, fullsc, tPt,BGthres, doCircle, cirPixA,diaExt, cirMask, BGTav);
    % NIgenBkGrdDataPar4Fnc
    % function [F_spots,bmtp, BGthres,bmm,rwm,lstTpt,BGsc,totBkgrd ]=... 
    % NIgenBkGrdDataPar4Fnc(ImParMat, tifFileLst, lastDetMaxPos, numRows, numCols, fullsc, tPt, BGthres, doCircle, cirPixA, diaExt, cirMask, BGTav)
    % Called by NIscanIntensBG.m
    
    MPnum=ImParMat(1);
    destPerMP=ImParMat(2);
    spotThres=ImParMat(4)/100;  %selScan=ImParMat(4);
    width=ImParMat(5);
    dither=ImParMat(6);
    BGthresInput=ImParMat(3); % a value of percent to be added (20=>1.20*BGTav)
    lstTpt=length(tifFileLst);
    LfOffset=65;   %lf;   %Ncode
    TopOffset=65;  %tp;
    rtLim=1350;  %1400;  %1350;
    rtNotchOffset=10;
    cushion=20;
    % close2edgeTol=90;
    botLim=2003;
    botNotchOffset=60;

    % Initialize
    % clear('totBkgrd')
    % clear('pixsAboveBG')
    % clear('lineV','pixCnt','lineSum,meanBkgrd')
    % clear('rw','rwm')
    totBkgrd=0;
    pixsAboveBG=0;
    lineV=0; pixCnt=0; lineSum=0; meanBkgrd=85;
    rw=0; rwm=0;
    % Start Generation of BackGround data after the 2nd Row (&& 2nd Col)
    % Optimized spot positions determined
    %if r>=2 && c>=2,
    BGsc=zeros(2075,1400);  %Empsc;
    widthEx=width-1;  %width extention from reference point
    for r=1:numRows      
      for c=1:numCols
        refP=lastDetMaxPos{r,c};
        if r<numRows,refNxR=lastDetMaxPos{r+1,c}; end
        if c<numCols,refNxC=lastDetMaxPos{r,c+1}; end
        if r>1, refPrR=lastDetMaxPos{r-1,c}; end    
        if c>1, refPrC=lastDetMaxPos{r,c-1}; end

        % At least NINE conditions which must be treated differently
        % Condition 0: most spots fall in this central category
        if r>1 && r<numRows && c>1 && c<numCols 
          if rem(r,numRows)==1
            refBG(1)=refP(1)-floor(0.5*(plateBotSpace));    
          else    
            refBG(1)=refP(1)-floor(0.5*(refP(1)-(refPrR(1)+widthEx))); 
          end
          if rem(c,numCols)==1
            refBG(2)=refP(2)-floor(0.5*(plateEdgeSpace));
          else
            refBG(2)=refP(2)-floor(0.5*(refP(2)-(refPrC(2)+widthEx)));
          end
          if rem(r,numRows)==0
            refBG(3)=refP(1)+widthEx+ floor(0.5*(plateBotSpace));    
          else
            refBG(3)=refP(1)+widthEx+ floor(0.5*(refNxR(1)-(refP(1)+widthEx)));
          end
          if rem(c,numCols)==0
            refBG(4)=refP(2)+widthEx+ floor(0.5*(plateEdgeSpace));
          else
            refBG(4)=refP(2)+widthEx+ floor(0.5*(refNxC(2)-(refP(2)+widthEx)));
          end
          %refBG(4)=refP(2)+widthEx+ floor(0.5*(refNxC(2)-refP(2)+widthEx));
          detBG(r,c)={uint8(refBG)};  %Store Background Reference pt data in a Cell
          % clear('lineV','pixCnt','lineSum')          
          lineV=fullsc(refBG(1),refBG(2):refBG(4)-1); % across top rt
          if tPt==1 || tPt==lstTpt,rw=lineV';end
          pixCnt(1)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
          lineSum(1)=sum(lineV .* uint8(lineV<BGthres(r,c)));
          % clear('lineV')
          lineV=fullsc(refBG(1):refBG(3)-1,refBG(2)); % mean down lf
          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
          pixCnt(2)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
          lineSum(2)=sum(lineV .* uint8(lineV<BGthres(r,c)));
          % clear('lineV')
          lineV=fullsc(refBG(1):refBG(3)-1,refBG(4)); % mean down rt
          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
          pixCnt(3)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
          lineSum(3)=sum(lineV .* uint8(lineV<BGthres(r,c)));
          % clear('lineV')
          lineV=fullsc(refBG(3),refBG(2):refBG(4)-1); % mean across bot rt
          if tPt==1 || tPt==lstTpt,rw=[rw;lineV'];end
          pixCnt(4)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
          lineSum(4)=sum(lineV .* uint8(lineV<BGthres(r,c)));
          if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end
          meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
          if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
          if doCircle==1
            totBkgrd(r,c)=meanBkgrd* cirPixA;
          else 
            totBkgrd(r,c)=meanBkgrd* width^2;
          end
          %{
          lineSum(1)=sum((fullsc(refBG(1),refBG(2):refBG(4)-1))); %mean across top rt
          lineSum(2)=sum((fullsc(refBG(1):refBG(3)-1,refBG(2)))); %mean down lf
          lineSum(3)=sum((fullsc(refBG(1):refBG(3)-1,refBG(4)))); %mean down rt
          lineSum(4)=sum((fullsc(refBG(3),refBG(2):refBG(4)-1))); %mean across bot rt
          meanBkgrd=(sum(lineSum(1:4)))./ (2*((refBG(4)-refBG(2))+(refBG(3)-refBG(1))));
          totBkgrd(r,c)=meanBkgrd* width^2;
          %}             
        end
    
        % Condition 1
        if r==1 && c==1
          % if (size(refP(1)-4)>0    
          refBG(1)=refP(1)- floor(0.5*(refP(1) - TopOffset));             
          refBG(2)=refP(2)- floor(0.5*(refP(2) - LfOffset)); % Icode -0
          refBG(3)=refP(1)+widthEx+ floor(0.5*((refNxR(1)-(refP(1)+widthEx))));
          refBG(4)=refP(2)+widthEx+ floor(0.5*((refNxC(2)-(refP(2)+widthEx))));
          detBG(r,c)={uint8(refBG)}; % Store Background Reference pt data in a Cell
          % clear('lineV','pixCnt','lineSum')          
          lineV=fullsc(refBG(1),refBG(2):refBG(4)-1); %mean across top rt
          if tPt==1 || tPt==lstTpt,rw=lineV';end
          pixCnt(1)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
          lineSum(1)=sum(lineV .* uint8(lineV<BGthres(r,c)));
          % clear('lineV')
          lineV=fullsc(refBG(1):refBG(3)-1,refBG(2)); %mean down lf
          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
          pixCnt(2)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
          lineSum(2)=sum(lineV .* uint8(lineV<BGthres(r,c)));
          % clear('lineV')
          lineV=fullsc(refBG(1):refBG(3)-1,refBG(4)); %mean down rt
          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
          pixCnt(3)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
          lineSum(3)=sum(lineV .* uint8(lineV<BGthres(r,c)));
          % clear('lineV')
          lineV=fullsc(refBG(3),refBG(2):refBG(4)-1); %mean across bot rt
          if tPt==1 || tPt==lstTpt,rw=[rw;lineV'];end
          pixCnt(4)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
          lineSum(4)=sum(lineV .* uint8(lineV<BGthres(r,c)));          
          meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
          if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end
          if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
          % meanBkgrd=(sum(lineSum(1:4)))./ (2*((refBG(4)-refBG(2))+(refBG(3)-refBG(1))));
          if doCircle==1
            totBkgrd(r,c)=meanBkgrd* cirPixA;
          else
            totBkgrd(r,c)=meanBkgrd* width^2;
          end
          %{
          lineSum(1)=sum((fullsc(refBG(1),refBG(2):refBG(4)-1))); %mean across top rt
          lineSum(2)=sum((fullsc(refBG(1):refBG(3)-1,refBG(2)))); %mean down lf
          lineSum(3)=sum((fullsc(refBG(1):refBG(3)-1,refBG(4)))); %mean down rt
          lineSum(4)=sum((fullsc(refBG(3),refBG(2):refBG(4)-1))); %mean across bot rt
          meanBkgrd=(sum(lineSum(1:4)))./ (2*((refBG(4)-refBG(2))+(refBG(3)-refBG(1))));
          totBkgrd(r,c)=round(meanBkgrd* width^2);
          %}
        end

        % Condition 1a
        if r==1 && c>1 && c<numCols
          refBG=zeros(1,4); 
          refBG(1)=refP(1)-floor(0.5*(refP(1)-TopOffset));
          if rem(c,numCols)==1
            refBG(2)=refP(2)-floor(0.5*(plateEdgeSpace));
          else
            refBG(2)=refP(2)-floor(0.5*(refP(2)-(refPrC(2)+widthEx)));
          end
          refBG(3)=refP(1)+widthEx+ floor(0.5*(refNxR(1)-(refP(1)+widthEx)));
          if rem(c,numCols)==0
            refBG(4)=refP(2)+widthEx+ floor(0.5*(plateEdgeSpace));
          else
            refBG(4)=refP(2)+widthEx+ floor(0.5*(refNxC(2)-(refP(2)+widthEx)));
          end
          detBG(r,c)={uint8(refBG)};  %Store Background Reference pt data in a Cell
          % clear('lineV','pixCnt','lineSum')          
          lineV=fullsc(refBG(1),refBG(2):refBG(4)-1); % across top rt 
          if tPt==1 || tPt==lstTpt,rw=lineV';end
          pixCnt(1)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
          lineSum(1)=sum(lineV .* uint8(lineV<BGthres(r,c)));
          % clear('lineV')
          lineV=fullsc(refBG(1):refBG(3)-1,refBG(2)); %mean down lf
          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
          pixCnt(2)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
          lineSum(2)=sum(lineV .* uint8(lineV<BGthres(r,c)));
          % clear('lineV')
          lineV=fullsc(refBG(1):refBG(3)-1,refBG(4)); %mean down rt
          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
          pixCnt(3)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
          lineSum(3)=sum(lineV .* uint8(lineV<BGthres(r,c)));
          % clear('lineV')
          lineV=fullsc(refBG(3),refBG(2):refBG(4)-1); %mean across bot rt
          if tPt==1 || tPt==lstTpt,rw=[rw;lineV'];end
          pixCnt(4)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
          lineSum(4)=sum(lineV .* uint8(lineV<BGthres(r,c)));
          meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
          if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end
          if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
          if doCircle==1
            totBkgrd(r,c)=meanBkgrd* cirPixA;
          else 
            totBkgrd(r,c)=meanBkgrd* width^2;
          end    
          %{          
          lineSum(1)=sum((fullsc(refBG(1),refBG(2):refBG(4)-1))); %mean across top rt
          lineSum(2)=sum((fullsc(refBG(1):refBG(3)-1,refBG(2)))); %mean down lf
          lineSum(3)=sum((fullsc(refBG(1):refBG(3)-1,refBG(4)))); %mean down rt
          lineSum(4)=sum((fullsc(refBG(3),refBG(2):refBG(4)-1))); %mean across bot rt
          meanBkgrd=(sum(lineSum(1:4)))./ (2*((refBG(4)-refBG(2))+(refBG(3)-refBG(1))));
          totBkgrd(r,c)=meanBkgrd* width^2;
          %}
        end

        % Condition 2
        if r==1 && c==numCols
          % close2edgeTol=14;
          refBGcExt=refP(2)+ widthEx;
          refBG(1)=refP(1)-floor(0.5*(refP(1)-TopOffset));  %vertical (row)          
          refBG(2)=refP(2)-floor(0.5*(refP(2)-(refPrC(2)+widthEx)));  %horizontal(col)
          refBG(3)=refP(1)+widthEx+ floor(0.5*((refNxR(1)-(refP(1)+widthEx))));
          % if refBGcExt>(size(fullsc,2)-close2edgeTol)%if intens area too close to edge
          if refBGcExt>(rtLim-cushion)%if intens area too close to edge
            refBG(4)=rtLim-rtNotchOffset;
          else
            refBG(4)=refP(2)+widthEx+ floor(0.5*(rtLim-refBGcExt));    
          end
          detBG(r,c)={uint8(refBG)};  %Store Background Reference pt data in a Cell             
          % clear('lineV','pixCnt','lineSum')          
          lineV=fullsc(refBG(1),refBG(2):refBG(4)-1); % across top rt 
          if tPt==1 || tPt==lstTpt,rw=lineV';end
          pixCnt(1)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
          lineSum(1)=sum(lineV .* uint8(lineV<BGthres(r,c)));
          % clear('lineV')
          lineV=fullsc(refBG(1):refBG(3)-1,refBG(2)); %mean down lf
          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
          pixCnt(2)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
          lineSum(2)=sum(lineV .* uint8(lineV<BGthres(r,c)));
          % clear('lineV')
          lineV=fullsc(refBG(3),refBG(2):refBG(4)-1); %mean across bot rt
          if tPt==1 || tPt==lstTpt,rw=[rw;lineV'];end
          pixCnt(4)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
          lineSum(4)=sum(lineV .* uint8(lineV<BGthres(r,c)));
          % if refBGcExt>(size(fullsc,2)-close2edgeTol) %if intens area too close to edge
          if refBGcExt>(rtLim-cushion) %if intens area too close to edge
            meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
            if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
            % meanBkgrd=(lineSum(1)+lineSum(2)+lineSum(4))./ ...
            % ((2*(refBG(4)-refBG(2))+(refBG(3)-refBG(1))));  %divby 2*across+1*down
            if doCircle==1
              totBkgrd(r,c)=meanBkgrd* cirPixA;
            else
              totBkgrd(r,c)=meanBkgrd* width^2;
            end   
          else
            % clear('lineV')  %3
            lineV=fullsc(refBG(1):refBG(3)-1,refBG(4)); %mean down rt
            if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
            pixCnt(3)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
            lineSum(3)=sum(lineV .* uint8(lineV<BGthres(r,c)));
            meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
            if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
            % meanBkgrd=(sum(lineSum(1:4)))./ (2*((refBG(4)-refBG(2))+(refBG(3)-refBG(1))));
            if doCircle==1
              totBkgrd(r,c)=meanBkgrd* cirPixA;
            else 
              totBkgrd(r,c)=meanBkgrd* width^2;
            end   
          end
          if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end
        end
            
        % Condition 2a: down rows 2->47  farRight col edge
        if r>1 && r<numRows && c==numCols
          % close2edgeTol=14;  %Icode=4
          refBGcExt=refP(2)+widthEx;
          if rem(r,numRows)==1
            refBG(1)=refP(1)-floor(0.5*(plateBotSpace));                 
          else
            refBG(1)=refP(1)-floor(0.5*(refP(1)-(refPrR(1)+widthEx)));             
          end
          refBG(2)=refP(2)-floor(0.5*(refP(2)-(refPrC(2)+widthEx)));
          if rem(r,numRows)==0
            refBG(3)=refP(1)+widthEx+ floor(0.5*(plateBotSpace));          
          else
            refBG(3)=refP(1)+widthEx+ floor(0.5*(refNxR(1)-(refP(1)+widthEx)));      
          end
          if refBGcExt<(rtLim-cushion) %if intens area too close to edge
            refBG(4)=refP(2)+widthEx+ floor(0.5*(rtLim-refBGcExt));
          else
            refBG(4)=rtLim-cushion;
          end
          detBG(r,c)={uint8(refBG)};  % store Background Reference pt data in a Cell          
          % clear('lineV','pixCnt','lineSum')  %1        
          lineV=fullsc(refBG(1),refBG(2):refBG(4)-1); % across top rt 
          if tPt==1 || tPt==lstTpt,rw=lineV';end
          pixCnt(1)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
          lineSum(1)=sum(lineV .* uint8(lineV<BGthres(r,c)));
          % clear('lineV')  %2
          lineV=fullsc(refBG(1):refBG(3)-1,refBG(2)); %mean down lf
          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
          pixCnt(2)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
          lineSum(2)=sum(lineV .* uint8(lineV<BGthres(r,c)));
          % clear('lineV')  %4
          lineV=fullsc(refBG(3),refBG(2):refBG(4)-1); % mean across bot rt
          if tPt==1 || tPt==lstTpt,rw=[rw;lineV'];end
          pixCnt(4)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
          lineSum(4)=sum(lineV .* uint8(lineV<BGthres(r,c)));
          %if refBGcExt<(size(fullsc,2)-close2edgeTol) % if intens area too close to edge
          if refBGcExt<(rtLim-cushion) % if intens area too close to edge
            % clear('lineV')  %3
            lineV=fullsc(refBG(1):refBG(3)-1,refBG(4)); % mean down rt
            if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
            pixCnt(3)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
            lineSum(3)=sum(lineV .* uint8(lineV<BGthres(r,c)));
            meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
            if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
            % meanBkgrd=(sum(lineSum(1:4)))./ (2*((refBG(4)-refBG(2))+(refBG(3)-refBG(1))));
            if doCircle==1
              totBkgrd(r,c)=meanBkgrd* cirPixA;
            else 
              totBkgrd(r,c)=meanBkgrd* width^2;
            end
          else
            meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
            if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end   
            % meanBkgrd=(lineSum(1)+lineSum(2)+lineSum(4))./ ...
            % ((2*(refBG(4)-refBG(2))+(refBG(3)-refBG(1))));  %divby 2*across+1*down
            if doCircle==1
              totBkgrd(r,c)=meanBkgrd* cirPixA
            else 
              totBkgrd(r,c)=meanBkgrd* width^2
            end  
          end 
          if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end
        end
      
        % Condition 3: Lower right corner
        if r==numRows && c==numCols
          %close2edgeTol=14;
          refBGrExt=refP(1)+ widthEx;
          refBGcExt=refP(2)+ widthEx;
          refBG(1)=refP(1)-floor(0.5*(refP(1)-(refPrR(1)+widthEx)));  %vertical (row)          
          refBG(2)=refP(2)-floor(0.5*(refP(2)-(refPrC(2)+widthEx)));  %horizontal(col)
          if refBGrExt>(botLim-botNotchOffset)%if intens area not too close to bot edge else
            refBG(3)=botLim + cushion;
          else
            refBG(3)=refP(1)+widthEx+ floor(0.5*(botLim-refBGrExt));
          end
          if refBGcExt>(rtLim- cushion)%if intens area not too close to edge else
            refBG(4)=rtLim -cushion;
          else
            refBG(4)=refP(2)+widthEx+ floor(0.5*(rtLim-refBGcExt));    
          end
          detBG(r,c)={uint8(refBG)};  %Store Background Reference pt data in a Cell
                        
          % clear('lineV','pixCnt','lineSum')  %1        
          lineV=fullsc(refBG(1),refBG(2):refBG(4)-1); % across top rt 
          if tPt==1 || tPt==lstTpt,rw=lineV';end
          pixCnt(1)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
          lineSum(1)=sum(lineV .* uint8(lineV<BGthres(r,c)));
          % clear('lineV')  %2
          lineV=fullsc(refBG(1):refBG(3)-1,refBG(2)); % mean down lf
          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
          pixCnt(2)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
          lineSum(2)=sum(lineV .* uint8(lineV<BGthres(r,c)));

          % if refBGcExt>(size(fullsc,2)-close2edgeTol)&&...
          if refBGcExt>(rtLim-cushion)&&...
            refBGrExt<(botLim-botNotchOffset) % if intens area too close to right edge only
            % clear('lineV')  %4
            lineV=fullsc(refBG(3),refBG(2):refBG(4)-1); % mean across bot rt
            if tPt==1 || tPt==lstTpt,rw=[rw;lineV'];end
            pixCnt(4)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
            lineSum(4)=sum(lineV .* uint8(lineV<BGthres(r,c)));
            meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
            if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
            % meanBkgrd=(lineSum(1)+lineSum(2)+lineSum(4))./ ...
            % ((2*(refBG(4)-refBG(2))+(refBG(3)-refBG(1))));  % divby 2*across+1*down
            if doCircle==1
              totBkgrd(r,c)=meanBkgrd* cirPixA;
            else 
              totBkgrd(r,c)=meanBkgrd* width^2;
            end   
          elseif refBGrExt>(botLim-botNotchOffset) && ...
            refBGcExt>(rtLim-cushion)%if intens area too close to bottom edge only
            % clear('lineV')  %3
            lineV=fullsc(refBG(1):refBG(3)-1,refBG(4)); % mean down rt
            if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
            pixCnt(3)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
            lineSum(3)=sum(lineV .* uint8(lineV<BGthres(r,c)));
            meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
            if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end % meanBkgrd=(lineSum(1)+lineSum(2)+lineSum(3))./ ...
            %((refBG(4)-refBG(2)+(2*(refBG(3)-refBG(1)))));  % divby 1*across+2*down
            if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end  
          % elseif refBGcExt>(size(fullsc,2)-close2edgeTol)&& ...    
          elseif refBGcExt>(rtLim-cushion)&& ...
            refBGrExt>(botLim-botNotchOffset) % if intens area too close to both right edge and bottom edge
            meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
            if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
            % meanBkgrd=(lineSum(1)+lineSum(2))./ ...
            % ((refBG(4)-refBG(2)+(refBG(3)-refBG(1))));  %divby 1across+1*down
            if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end  
          else
            % clear('lineV')  %3
            lineV=fullsc(refBG(1):refBG(3)-1,refBG(4)); %mean down rt
            if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
            pixCnt(3)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
            lineSum(3)=sum(lineV .* uint8(lineV<BGthres(r,c)));
            % clear('lineV')  %4
            lineV=fullsc(refBG(3),refBG(2):refBG(4)-1); %mean across bot rt
            if tPt==1 || tPt==lstTpt,rw=[rw;lineV'];end
            pixCnt(4)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
            lineSum(4)=sum(lineV .* uint8(lineV<BGthres(r,c)));
            meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
            if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
              % meanBkgrd=(sum(lineSum(1:4)))./ (2*((refBG(4)-refBG(2))+(refBG(3)-refBG(1))));
            if doCircle==1
              totBkgrd(r,c)=meanBkgrd* cirPixA;
            else 
              totBkgrd(r,c)=meanBkgrd* width^2;
            end   
          end
          if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end
        end
                
        % Condition 3a: Bottom across row48 col2-79
        if r==numRows && c>1 && c<numCols
          refBG=zeros(1,4);
          % close2edgeTol=14; % Icode=4
          refBGrExt=refP(1)+ widthEx;  
          refBG(1)=refP(1)-floor(0.5*(refP(1)-(refPrR(1)+widthEx)));  % vertical (row)          
          if rem(c,numCols)==1
            refBG(2)=refP(2)-floor(0.5*(plateEdgeSpace));  % horizontal(col)    
          else
            refBG(2)=refP(2)-floor(0.5*(refP(2)-(refPrC(2)+widthEx)));  % horizontal(col)
          end             
          if refBGrExt>(botLim-botNotchOffset) % if intens area not too close to bot edge else
            refBG(3)=botLim + cushion;
          else
            refBG(3)=refP(1)+widthEx+ floor(0.5*(botLim-refBGrExt)); 
          end
          if rem(c,numCols)==0
            refBG(4)=refP(2)+widthEx+ floor(0.5*(plateEdgeSpace));   
          else
            refBG(4)=refP(2)+widthEx+ floor(0.5*(refNxC(2)-(refP(2)+widthEx)));    
            %refBG(4)=refP(2)+widthEx+ floor(0.5*(size(fullsc,2)-refBGcExt));
          end
          detBG(r,c)={uint8(refBG)};  % Store Background Reference pt data in a Cell       
          % clear('lineV','pixCnt','lineSum')  %1        
          lineV=fullsc(refBG(1),refBG(2):refBG(4)-1); % across top rt 
          if tPt==1 || tPt==lstTpt,rw=lineV';end
          pixCnt(1)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
          lineSum(1)=sum(lineV .* uint8(lineV<BGthres(r,c)));
          % clear('lineV')  %2
          lineV=fullsc(refBG(1):refBG(3)-1,refBG(2)); % mean down lf
          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
          pixCnt(2)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
          lineSum(2)=sum(lineV .* uint8(lineV<BGthres(r,c)));
          % clear('lineV')  %3
          lineV=fullsc(refBG(1):refBG(3)-1,refBG(4)); % mean down rt
          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
          pixCnt(3)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
          lineSum(3)=sum(lineV .* uint8(lineV<BGthres(r,c)));
          if refBGrExt>(botLim-botNotchOffset) % if intens area too close to bottom edge
            meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
            if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
            % meanBkgrd=(lineSum(1)+lineSum(2)+lineSum(4))./ ...
            % ((refBG(4)-refBG(2)+(2*(refBG(3)-refBG(1)))));  %divby 1*across+2*down
            if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end 
          else
            % clear('lineV')  %4
            lineV=fullsc(refBG(3),refBG(2):refBG(4)-1); % mean across bot rt
            if tPt==1 || tPt==lstTpt,rw=[rw;lineV'];end
            pixCnt(4)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
            lineSum(4)=sum(lineV .* uint8(lineV<BGthres(r,c)));
            meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
            if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
            % meanBkgrd=(sum(lineSum(1:4)))./ ((2*(refBG(4)-refBG(2))+ 2*(refBG(3)-refBG(1))));
            if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end 
          end
          if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end          
        end

        % Condition 4: Bottom Left Corner row48 col1
        if r==numRows && c==1
          %close2edgeTol=14;   %Icode=4
          refBGrExt=refP(1)+ widthEx;              
          refBG(1)=refP(1)-floor(0.5*(refP(1)-(refPrR(1)+widthEx))); % vertical (row)          
          refBG(2)=refP(2)- floor(0.5*(refP(2) - LfOffset)); % horizontal(col)  Icode -0 instead of LfOffset
          if refBGrExt>(botLim-botNotchOffset) % if intens area not too close to bot edge else
            refBG(3)=botLim + cushion; 
          else
            refBG(3)=refP(1)+widthEx+ floor(0.5*(botLim-refBGrExt));
          end
          refBG(4)=refP(2)+widthEx+ floor(0.5*(refNxC(2)-(refP(2)+widthEx)));
          detBG(r,c)={uint8(refBG)};  % Store Background Reference pt data in a Cell
          % clear('lineV','pixCnt','lineSum')  %1        
          lineV=fullsc(refBG(1),refBG(2):refBG(4)-1); % across top rt
          if tPt==1 || tPt==lstTpt,rw=lineV';end
          pixCnt(1)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
          lineSum(1)=sum(lineV .* uint8(lineV<BGthres(r,c)));
          % clear('lineV')  %2
          lineV=fullsc(refBG(1):refBG(3)-1,refBG(2)); % mean down lf
          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
          pixCnt(2)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
          lineSum(2)=sum(lineV .* uint8(lineV<BGthres(r,c)));
          % clear('lineV')  %3
          lineV=fullsc(refBG(1):refBG(3)-1,refBG(4)); % mean down rt
          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
          pixCnt(3)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
          lineSum(3)=sum(lineV .* uint8(lineV<BGthres(r,c)));
          if refBGrExt>(botLim-botNotchOffset) % if intens area too close to bottom edge
            meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
            if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
            % meanBkgrd=(lineSum(1)+lineSum(2)+lineSum(3))./ ...
            % ((refBG(4)-refBG(2)+(2*(refBG(3)-refBG(1)))));  % divby 1*across+2*down
            if doCircle==1, totBkgrd(r,c)=meanBkgrd* cirPixA; else totBkgrd(r,c)=meanBkgrd* width^2; end 
          else
            % clear('lineV')  %4
            lineV=fullsc(refBG(3),refBG(2):refBG(4)-1); %mean across bot rt
            if tPt==1 || tPt==lstTpt,rw=[rw;lineV'];end
            pixCnt(4)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
            lineSum(4)=sum(lineV .* uint8(lineV<BGthres(r,c)));    
            meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
            if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
            % meanBkgrd=(sum(lineSum(1:4)))./ ((2*(refBG(4)-refBG(2))+ 2*(refBG(3)-refBG(1))));
            if doCircle==1
              totBkgrd(r,c)=meanBkgrd* cirPixA;
            else 
              totBkgrd(r,c)=meanBkgrd* width^2;
            end 
          end 
          if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end
        end

        % Condition 4a:  Left edge center area  rows2-47 col1
        if r>1  && r<numRows && c==1
          % close2edgeTol=14; %Icode=4
          refBGrExt=refP(1)+ widthEx;
          if rem(r,numRows)==1
            refBG(1)=refP(1)-floor(0.5*(plateBotSpace));  % vertical (row)          
          else    
            refBG(1)=refP(1)-floor(0.5*(refP(1)-(refPrR(1)+widthEx)));  % vertical (row)          
          end
          refBG(2)=refP(2)- floor(0.5*(refP(2) - LfOffset));  % horizontal(col) %Icode=0
          if rem(r,numRows)==0
            refBG(3)=refP(1)+widthEx+ floor(0.5*(plateBotSpace));
          else
            refBG(3)=refP(1)+widthEx+ floor(0.5*(refNxR(1)-(refP(1)+widthEx)));
          end
          refBG(4)=refP(2)+widthEx+ floor(0.5*(refNxC(2)-(refP(2)+widthEx)));
          detBG(r,c)={uint8(refBG)};  % Store Background Reference pt data in a Cell              
          % clear('lineV','pixCnt','lineSum')  %1        
          lineV=fullsc(refBG(1),refBG(2):refBG(4)-1); % across top rt
          if tPt==1 || tPt==lstTpt,rw=lineV';end
          pixCnt(1)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
          lineSum(1)=sum(lineV .* uint8(lineV<BGthres(r,c)));
          % clear('lineV')  %2
          lineV=fullsc(refBG(1):refBG(3)-1,refBG(2)); %mean down lf
          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
          pixCnt(2)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
          lineSum(2)=sum(lineV .* uint8(lineV<BGthres(r,c)));
          % clear('lineV')  %3
          lineV=fullsc(refBG(1):refBG(3)-1,refBG(4)); %mean down rt
          if tPt==1 || tPt==lstTpt,rw=[rw;lineV];end
          pixCnt(3)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
          lineSum(3)=sum(lineV .* uint8(lineV<BGthres(r,c)));
          % clear('lineV')  %4
          lineV=fullsc(refBG(3),refBG(2):refBG(4)-1); %mean across bot rt
          if tPt==1 || tPt==lstTpt,rw=[rw;lineV'];end
          pixCnt(4)=nnz(lineV .* uint8(lineV<BGthres(r,c)));
          lineSum(4)=sum(lineV .* uint8(lineV<BGthres(r,c)));
          meanBkgrd=(sum(lineSum(1:4)))./ (sum(pixCnt(1:4)));
          if tPt==1 || tPt==lstTpt,rwm(r,c)=floor(mean(rw));end
          if sum(pixCnt(1:4))==0, meanBkgrd=double(BGthres(r,c));end
          if doCircle==1
            totBkgrd(r,c)=meanBkgrd* cirPixA;
          else 
            totBkgrd(r,c)=meanBkgrd* width^2;
          end
        end
      
        % Determine the actual number of pixels(area) of growth above the  background
        % Intensity
        BG=meanBkgrd;
        [refPtPxAbove]=lastDetMaxPos{r,c};
        refPtRx=refPtPxAbove(1);
        refPtCx=refPtPxAbove(2);
        if doCircle==1
          cutout=(fullsc(refPtRx:(refPtRx+ (diaExt-1)),refPtCx:(refPtCx+ (diaExt-1)))); 
          Imcir=cutout .* uint8(cirMask);
          pixsAboveBG(r,c)=nnz(Imcir>BG);  %calc non-background within circular analysis area  
          % pixsAboveBG(r,c)=nnz(fullsc(refPtRx:(refPtRx+ (diaExt-1)),refPtCx:(refPtCx+ (diaExt-1)))>BG);  %BG);
        else % standard square analysis area
          pixsAboveBG(r,c)=nnz(fullsc(refPtRx:(refPtRx+widthEx),refPtCx:(refPtCx+widthEx))>BG); % calc non-background within square analysis area 
        end
          
        % TimePT average
        % meanBGTsum(r,c)=meanBGTsum(r,c)+meanBkgrd;
        % meanBGTav(r,c)=meanBGTsum(r,c) /tPt;
        bmm(r,c)=uint8(floor(meanBkgrd));

        % For FOTOS only
        F_spots(r,c,tPt)={refBG}; % Foto spot coordinates
        bmtp(r,c,tPt)=bmm(r,c); % Added/used for FOTOS 11_0830

        % TimePT Average BG intensity calc method
        BGTav(r,c)=uint8(round((BGTav(r,c)*(tPt-1))+meanBkgrd)/tPt);
        % BGTav(r,c)=((BGTav(r,c)*(tPt-1))+meanBkgrd)/tPt;

        % sliding BG average
        % if r==1 && c==1, slavg(1:5)=BG;end % slavg(1:5)=50; %120620 Epsonvalue is 33; end
        % slavg(5)=slavg(4);
        % slavg(4)=slavg(3);
        % slavg(3)=slavg(2);
        % slavg(2)=slavg(1);
        % slavg(1)=BG;
        % slidingAvg=mean(slavg);
      
        % For Visualization Purposes only
        %1->2  across rt 1, 2-4
        BGsc(refBG(1),refBG(2):refBG(4))=1;
        %1->4 down lf 1-3, 2
        BGsc(refBG(1):refBG(3),refBG(2))=1;
        %2->3 down rt 1-3, 4
        BGsc(refBG(1):refBG(3),refBG(4))=1;
        %4->3 Bot Across rt 1, 2-4
        BGsc(refBG(3),refBG(2):refBG(4))=1;
        % BGsc(refBG(1):refBG(3),refBG(2):refBG(4)) %just displays matrices
      end
    end

    BGthres=uint8(double(BGTav) * (1+(BGthresInput/100)));
    optomizedPos(:,:,tPt)=lastDetMaxPos;
    % if(isequal(SWsingleSc,1))|| ((~isequal(SWsingleSc,1))&&tPt==tptLength)   %190731 change to capture last timePt PTmap if(isequal(SWsingleSc,1))
    % if(isequal(SWsingleSc,1))&& (tPt==1 || tPt==guesTpt || tPt==tptLength)|| ((~isequal(SWsingleSc,1))&&tPt==tptLength)   %190919 Option for observation
    % if (tPt==1 || tPt==guesTpt || tPt==tptLength)  %190919 Option for observation
    if (tPt==tptLength) % 190919 change to capture ONLY last timePt PTmap
      % clear OptmapOnes;
      OptmapOnes=[];
      % OptmapOnes=Empsc+ 1.4;
      OptmapOnesDbl=double(Empsc)+ .8;
      for r=1:numRows
        for c=1:numCols
          [refPt]=lastDetMaxPos{r,c};
          refPtR=refPt(1);
          refPtC=refPt(2);
          if doCircle==1
            % OptmapOnesDbl(refPtR:(refPtR+diaExt),refPtC:(refPtC+diaExt))=cirMask;
            OptmapOnesDbl(refPtR:(refPtR+(diaExt-1)),refPtC:(refPtC+(diaExt-1)))=optCirMask;   
          else
            refPtRExt=refPtR+widthEx; 
            if (refPtRExt)> size(fullsc,1), refPtRExt=size(fullsc,1); end
            refPtCExt=refPtC+widthEx;
            if (refPtCExt)> size(fullsc,2), refPtCExt=size(fullsc,2); end
            OptmapOnesDbl(refPtR:(refPtRExt),refPtC:(refPtCExt))=1;%255;
          end
        end
      end

      % Cross-optimized Map Matrix onto tifFile Matrix
      % For visualization purposes only
      if tPt==1,figure;end  
      resIm=uint8((double(BGsc) + OptmapOnesDbl) .* double(fullsc));
      % clear('OptmapOnesDbl')
      OptmapOnesDbl=[];
      % hres=imagesc(resIm);
      hfscanIm=imagesc(resIm);
      hfIm=gcf;
      haxis=gca;
      title(strcat('Scan',num2str(selScan),'timePt-',num2str(tPt)));
      clf(hfscanIm,'reset');
      set(hfIm,'NumberTitle','off')
      set(hfIm,'Name', char(matFile))
      if Fflg==1
        fullfile(fotosResultsDir,strcat('Scan',num2str(selScan),'_timePt-',num2str(tPt)))  
        hgsave(fullfile(fotosResultsDir,strcat('Scan',num2str(selScan),'_timePt-',num2str(tPt)))); %F 14_0626 
      else
        hgsave(fullfile(figsResultsDir,strcat('Scan',num2str(selScan),'_timePt-',num2str(tPt))));
      end
    else
      selScan;
      % tifFile
    end

    BkgrdMat=totBkgrd; % BkgrdMat(:,:,tPt)=totBkgrd;  %debug parfor effort
    areaOfIntensAboveBG(:,:,tPt)=pixsAboveBG; % actual area of growth for each timepoint  (used for printout of grArea ?not used in previous analysis)
    scanIntens(:,:,tPt)=intens-BkgrdMat;

    % Capture first and last background values
    if tPt==1
      bdg(:,:,1)=bmm;  
      bdg(:,:,3)=rwm;
      Tmpsbdg1={bdg};
    end
    if tPt==lstTpt
      bdg(:,:,2)=bmm;
      bdg(:,:,4)=rwm;
      Tmpsbdg1={bdg};
    end

    TmpexpScanIntens1={scanIntens}; % par4Gbl 20_0122
    TmpFexpScanSpots1={F_spots};
    TmpFexpScanBMtp1={bmtp};
    TmpanlZoneRefs1={optomizedPos}; % added to store tPt by tPt positions
    TmpexpScanIntens2=TmpexpScanIntens1;
    TmpFexpScanSpots2=TmpFexpScanSpots1;
    TmpFexpScanBMtp2=TmpFexpScanBMtp1;
    TmpanlZoneRefs2=TmpanlZoneRefs1;
    Tmpsbdg2=Tmpsbdg1;
  end
end