%% CALLED By p4loop8c.m %%
function [p4L2, ...
          TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneRefs3,Tmpsbdg3]= ...
    par4GblFnc8c(parMat,tptLength,~,selScanNumLst,~,Fflg,PTmapPos,optCirMask,diaExt,doCircle,cirPixA,cirMask,~,...
    TmpexpScanIntens,TmpFexpScanSpots,TmpFexpScanBMtp,TmpanlZoneRefs,scCount,tifFileLstP4,~,ImParMat, ...
    numRows,numCols,scLst,resDir,expDir,~, Tmpsbdg)



selScan= selScanNumLst(scCount);

   tptLength0= length(tifFileLstP4{scCount});  
   %tptLength= numFiles;
   tifFileLst={tifFileLstP4(scCount)}; 
    
   % Extract the Imaging time stamps from selected tif files
   %clear('e','f'); %can't use clear inside a parfor loop. Preallocation
   %can be larger than useable .bmp files! Therefore must be small and
   %increased during for loop to maintain cell size integrity between e & f
   e= cell(1,2); f= cell(1,2);  %(tptLength,2); f= cell(tptLength,2);
   nndx=0;

       
   for tPt=1:tptLength0   %size(tifFileLst,1)  %length(tifFileLst) 
       tifFileLstP4{scCount}(tPt)
       scLst;
       scLst(scCount)
       char(scLst(scCount))
       char(fullfile(expDir,char(scLst(scCount))))
       expDir;
       swCatch=0;
       nndx=nndx+1;

tifFile=char(fullfile(expDir,char(scLst(scCount)), tifFileLstP4{scCount}(tPt)));
    try
    info = imfinfo(tifFile);  %('D:\jwrDevel\DevelCurveFittingJWR\ImageScans\Scan2\020hr002.tif')
   
    catch ME 
        %Note: During parallel operation Matlab will not open file (fid)
        %etc. Therefore error message text will not be written.The only way
        %to get it out would be to pass variable through called function to
        %the ..Main8c script outside the parfor loop and print to file from
        %there.  Consequently for now it only prints error to file when one
        %edits p4loop8c.m from 'parfor' to ordinary 'for' loop
      fFail=((fullfile(resDir,'PrintResults','ImageFileReadFailure.txt')));  
      fid = fopen(fFail,'a'); %create,open and append
      %fprintf(fid,'%s \n',char(tifFile))
      fclose(fid)
      nndx=nndx-1;
      swCatch=1;
       rep = getReport(ME, 'basic');
    rep=strcat('Read info failure for-',tifFile,' -', rep);
    %fprintf(fid,'%s \n',rep) %See Note:
         
    end
    tptLength= nndx;
   scTmNumeric= 1;  %initialize for parfor 
   if swCatch==0
           scTmNumeric(nndx)=datenum(info.FileModDate);
           e(nndx,:)= {tifFile, scTmNumeric(nndx)};
           %newtifFileLst(nndx)= tifFileLst(tPt);
   end
   end  % end for tPt=1:length(tifFileLst) loop 
   
   %clear tifFileLst; %Can't use clear inside a parfor loop
   tifFileLst= cell(nndx,1);
   f= {sortrows(e,2)};
   tifFileLst= f{1,1}(:,1);
  
    areaOfIntensAboveBG= zeros(24,16,length(tifFileLst));
% *******Calculate Time series for each Plate of Selected Scan ******** 
lastPlateOnScan=1;  %Ncode

    tSeriesv=[]; t0Seriesv=[];
    if tptLength>0  %added to jump over and fill data for invalid Sscan(plate runs    
    scTmNumv= cell2mat(f{1,1}(:,2));  %(:,2))   %120613 fix for variant length data
    prtTmNumv=min(scTmNumv)-.000001;
    tSeriesv=((scTmNumv-prtTmNumv)*24);
    t0Seriesv=((scTmNumv-scTmNumv(1))*24);
   
    end  

    %*********************

%-------------------------------------------------------

if tptLength>= 3  %added to jump over and fill data for invalid Sscan(plate runs
%*******Create Blank Scan*********************
    ImHeigth=2075;
    ImWidth=1400;
   Empsc=zeros(ImHeigth,ImWidth);  %Ncode
    

%**************************************************************************
%*********Start Scan Loop**************************************************
    lastPlateOnScan=1;  %Ncode
%**********************************************************************************************************************************    
disp('Before call to NIscanIntens.....')
resDir;  %debugging parfor
%>>>*******Execute Image conversion into Intensity Data******
[Tmpsbdg2, scanIntens, ~, ~, ~, TmpexpScanIntens2, TmpFexpScanSpots2, TmpFexpScanBMtp2, TmpanlZoneRefs2,areaOfIntensAboveBG]= ... 
    NIscanIntensBGpar4GblFnc(Fflg,tifFileLst, ImParMat, PTmapPos,optCirMask,diaExt,doCircle,cirPixA,numRows,numCols,ImHeigth,ImWidth,cirMask, ...
    tptLength,selScan,Empsc,TmpexpScanIntens,TmpFexpScanSpots,TmpFexpScanBMtp,TmpanlZoneRefs,resDir, Tmpsbdg);

%<<<<*******************************************************************************************************************************

TmpexpScanIntens3= TmpexpScanIntens2;
TmpFexpScanSpots3= TmpFexpScanSpots2;
TmpFexpScanBMtp3= TmpFexpScanBMtp2;
TmpanlZoneRefs3= TmpanlZoneRefs2;
Tmpsbdg3= Tmpsbdg2;


%***********************************************************************************

%Package Image data ->for Legacy Printing

%clear plate  %Can't use clear inside a parfor loop
CFscanIntens= zeros(384,1);%zeros(16,24);
plate= [];
plate= zeros(24,16,tptLength);

plate(:,:,:,1)= scanIntens(1:1:24,16:-1:1,:);  %TmpexpScanIntens2(1:1:24,16:-1:1,:);%Ncode Dev3Vertical Similar to below

%*******************************
%NIcheck   %Check for bad scans at time points (swapped plates etc.)
%*******************************
%set up cell arrays for storing each plate in each Scan ..(scan,plate)
SWprint=0;
if SWprint==1
wkDir=pwd;
cd (fullfile(resDir,'PrintResults'));
end

% Construct Legacy ...Intens.txt file
if SWprint==1
filename=(strcat('Plate',num2str(selScan),'_Intens.txt'));
fid = fopen(filename,'w');
end
        if length(size(plate))==2 %Only two dims if only one image
            numOfImages=1;
        else
            numOfImages= size(plate,3);
        end
CFscanIntens= zeros(384,numOfImages);        
locIndx=0; pl=1;
for n=1:numCols     %Ncode changed to 16 for Vert
    for m=1:numRows   %Ncode change to 24 for Vert
        locIndx=locIndx+1;
       
        for k=1:numOfImages
            if SWprint==1
            if k==1 && numOfImages==1, fprintf(fid,'%.2f\n',plate(m,n,k,pl));end
            if k==1 && numOfImages~=1, fprintf(fid,'%.2f',plate(m,n,k,pl));end
            if k>1  && k<numOfImages, fprintf(fid,'\t%.2f',plate(m,n,k,pl));end  %
            if k~=1 && k==numOfImages,fprintf(fid,'\t%.2f\n',plate(m,n,k,pl));end
            end
            
            
            CFscanIntens(locIndx,k)= plate(m,n,k,pl);
        end
        %MatLab Cell storage

    end
end %end row loop n

if SWprint==1
fclose(fid);
end

%++++++++++++++++++++++
%printGrwAreas

%Area as the max number of pixels with intensities greater than the Background 
%grArea(row,col,tPt,Plate) Note that images r and c are 90 degrees shifted
%and then mirror imaged.  Thus data must be inverted and rotated to get
%for the rows a-p and col 1-24 (and the EMS expected 1-384) orientation
%clear grArea
grArea= ones(24,16,tptLength);
grArea(:,:,:,1)= areaOfIntensAboveBG(1:1:24,16:-1:1,:);  %for Ncode dev3vert

  %for p=1:lastPlateOnScan
  if SWprint==1    
    if SWgrowthArea==1
      filename=(strcat('Plate',num2str(selScan),'_Areas.txt'));
    else
        filename=(strcat('ALTgrowthA_Scan',num2str(selScan),'_Plate',num2str(1),'_Areas.txt'));
        filename=(strcat('ALTgrowthA_Plate',num2str(selScan),'_Plate','_Areas.txt'));
    end
        fid = fopen(filename,'w');
  end
        locIndx=0;
        Ag= zeros(1,384);
        for m=1:16  %Ncode change from 16  %Vert back to 16
            for n=1:24     %Ncode change from  24 %Vert back to 24
                growthArea=max(grArea(n,m,:,1));
                if SWprint==1
                fprintf(fid,'%3.f\n',growthArea);
                end
                locIndx=locIndx+1;
                Ag(locIndx)= growthArea;
            end
        end
        if SWprint==1
        fclose(fid);
        end
  %end
%++++++++++++++++++++++++

if SWprint==1
cd(wkDir);
fclose('all');
end

%********AutoImCF curveFit kickoff setup***********************************************************
autoImCFlag=1;

if autoImCFlag==1, SWgrowthArea=1;end
   
   times= tSeriesv;
           
   scanAreas= Ag;  %growthArea;
      offsets=0; 
      suffix= strcat('Scan', num2str(selScan),'_Plate', num2str(1));    %char(QspLst(n));
      AUCfinalTime=96;
      arrayFormat=384;
      currDirResults= fullfile(resDir,'PrintResults');
      
%******Version compatability fixes*******assoc'd with diff and solve 
%{
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)';
%Fourth order derivative of logistic equation********************************
if isequal(v18a,version)||isequal(v18b,version)
    syms t K r l;
    fd4= diff(K / (1 +  exp(-r* (t - l ))),t,4);  
else
 fd4=diff(sym('K / (1 +  exp(-r* (t - l )))'),4);   
end
sols= solve(fd4);
if isequal(v11a,version) || isequal(v14a,version)
else
    tmpswap= sols(1);
    sols(1)= sols(3);
    sols(3)= tmpswap;
end
%}

if verLessThan('matlab','8.3') %original work 23_0227 updated 23_0525 (8.4 changed to 8.3)
    fd4=diff(sym('K / (1 +  exp(-r* (t - l )))'),4);
    sols= solve(fd4);
else  %accomodate new matlab changes after 2014a  fix 2nd update 23_0227
    syms t K r l;
    fd4= diff(K / (1 +  exp(-r* (t - l ))),t,4);
    sols= solve(fd4);
    tmpswap= sols(1);
    sols(1)= sols(3);
    sols(3)= tmpswap;
end
%********************************************************************************
%CFscanIntens
%adsd
%********************************************************************************

%>>>>>>>>>>>Call CurveFit routine >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>   
   %NCfitImCF(times, CFscanIntens, offsets, suffix, AUCfinalTime, arrayFormat, scanAreas, currDirResults, autoImCFlag, selScan,sols) %,scan)%, scPltList) outputDirectory;   
   %[scanTmp2]= NCfitImCFparforFailGbl(times, CFscanIntens, offsets, suffix, AUCfinalTime, arrayFormat, scanAreas, currDirResults, autoImCFlag, selScan, sols, scanTmp); %,scan)%, scPltList) outputDirectory;   
   
 [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanIntensELr,par4scanCFparameters,par4scanCFdate,outC2,outCstd2]= ...
      NCfitImCFparforFailGbl2(parMat,times, CFscanIntens, offsets, suffix, AUCfinalTime, arrayFormat, scanAreas, currDirResults, autoImCFlag, selScan, sols); %,scan)%, scPltList) outputDirectory;   
%<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
else  %fill with default values when an invalid plate scan occurs
      CFscanIntens= zeros(16,24);
      Ag= zeros(1,384); 
 %Preallocation for parfor loop**********************************
 
times= tSeriesv;
st(1,1:size(times,2))= 1111;
resMat(1,1:27)= 0; 
resMatStd= resMat;      
 outC2= zeros(384,27); 
 outCstd2= zeros(384,27);  
for m=1:384
    pa{m}= st;
    
    par4scanCFparameters{m}= parMat; 
    par4scanCFdate{m}= datestr((now),31); 
end
 par4scanselTimesStd= pa;   
 par4scanselIntensStd= pa;
 par4scanTimesELr= pa;
 par4scanIntensELr= pa;
 par4resMat= zeros(384,27);
 par4resMatStd= zeros(384,27);
%{ 
 TmpexpScanIntens00= cell(1);  %cell(1,scanMax);
TmpFexpScanSpots00= cell(1);  %cell(1,scanMax);
TmpFexpScanBMtp00= cell(1);  %cell(1,scanMax);
TmpanlZoneRefs00= cell(1);  %cell(1,scanMax);
Tmpsbdg00= cell(1); 
%}
 
TmpexpScanIntens3= cell(1);  %TmpexpScanIntens2;
TmpFexpScanSpots3= cell(1);  %TmpFexpScanSpots2;
TmpFexpScanBMtp3= cell(1);  %TmpFexpScanBMtp2;
TmpanlZoneRefs3= cell(1);  %TmpanlZoneRefs2;
Tmpsbdg3= cell(1);  %Tmpsbdg2;
%**************************************************************** 
       
       
end  %if tptLenth>=3  line19  20_0928 




tSeriesv;  %debuggin parfor
p4L1{1}= tSeriesv;  
p4L1{2}= t0Seriesv;  
p4L1{3}= datestr(prtTmNumv,31);  
p4L1{4}= CFscanIntens;


  locIndx=0;
  for n=1:numCols     %Ncode changed to 16 for Vert
    for m=1:numRows   %Ncode change to 24 for Vert
        locIndx=locIndx+1;
         rc=[n,m];
         p4rcTmp(locIndx)={rc};
         p4pIndxTmp(locIndx)=locIndx;
    end
  end
  
  p4L1{5}= p4rcTmp;
  p4L1{6}= p4pIndxTmp;
  p4L1{7}= Ag;
 
 p4L1{8}= par4scanselIntensStd; 
 p4L1{9}= par4scanselTimesStd; 
 p4L1{10}= par4scanTimesELr; 
 p4L1{11}= par4scanIntensELr; 
 
 p4L1{12}= par4scanCFparameters;
 p4L1{13}= par4scanCFdate;
   
 p4L1{14}= outC2; 
 p4L1{15}= outCstd2;
 p4L1{16}= selScan; 

p4L1{17}= cirPixA;
p4L1{18}= datestr((now),31);

p4L2= p4L1;
end