server-scripts/qhtcp-workflow/apps/matlab/easy/par4GblFnc8c.m

%% 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,easyResultsDir,projectScansDir,~, Tmpsbdg)

  global printResultsDir

  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(projectScansDir,char(scLst(scCount))))
    projectScansDir;
    swCatch=0;
    nndx=nndx+1;
    tifFile=char(fullfile(projectScansDir,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(printResultsDir,'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

  % Clear tifFileLst;
  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  

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

    % Start scan loop
    lastPlateOnScan=1;  %Ncode
    disp('Before call to NIscanIntens.....')

    % 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,easyResultsDir, Tmpsbdg);

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

    % clear plate
    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;

    % Construct Legacy ...Intens.txt file
    if SWprint==1
      filename=fullfile(easyResultsDir,'PrintResults',(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
      end
    end

    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=fullfile(printResultsDir,(strcat('Plate',num2str(selScan),'_Areas.txt')));
      else
        filename=fullfile(printResultsDir,(strcat('ALTgrowthA_Scan',num2str(selScan),'_Plate',num2str(1),'_Areas.txt')));
        filename=fullfile(printResultsDir,(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);
      % fclose('all'); % TODO do we need this? 
    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;
        
    % 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)';
    % 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
    % Call CurveFit routine
    % NCfitImCF(times, CFscanIntens, offsets, suffix, AUCfinalTime, arrayFormat, scanAreas, printResultsDir, autoImCFlag, selScan,sols) %,scan)%, scPltList) outputDirectory;   
    % [scanTmp2]=NCfitImCFparforFailGbl(times, CFscanIntens, offsets, suffix, AUCfinalTime, arrayFormat, scanAreas, printResultsDir, autoImCFlag, selScan, sols, scanTmp); %,scan)%, scPltList) outputDirectory;
    [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanIntensELr,par4scanCFparameters,par4scanCFdate,outC2,outCstd2]= ...
        NCfitImCFparforFailGbl2(parMat,times, CFscanIntens, offsets, suffix, AUCfinalTime, arrayFormat, scanAreas, printResultsDir, 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); % TODO this seems bad

  p4L2=p4L1;
end