server-scripts/qhtcp-workflow/apps/matlab/ezview/EZvInitLoad.m

% EZvInitLoad
global Exp
global Expaa
global Expbb
global userPars
global scansDir
global matFile
global zonePB
global mpdmFile
global ghandles

% Initialize some variables from matlab
ezPath=which(mfilename);
[ezDir,ezFileName]=fileparts(ezPath);
ezDir=fullfile(easyDir);
[parentDir, ~]=fileparts(ezDir);
parentDir=fullfile(parentDir);
debug=1;
if debug
  disp('Running in debug mode');
  disp('Initialized variables:');
  whos;
end

fprintf('This script name: %s\n', ezFileName);

  % Set scansDir (project scans directory) intelligently
  if exist('PROJECT_SCANS_DIR', 'var') && ~isempty(getenv('PROJECT_SCANS_DIR'))
    scansDir=fullfile(getenv('PROJECT_SCANS_DIR'));
    if exist(scansDir, 'dir')
      fprintf('Using scans directory: %s from environment variable PROJECT_SCANS_DIR\n', scansDir);
      disp('This usually indicates that we are in module mode');
      if ~exist('PROJECT', 'var') || isempty(getenv('PROJECT'))
        dirInfo=fileparts(scansDir);
        project=dirInfo.name;
      end
    else
      disp('WARNING: PROJECT_SCANS_DIR does not exist');
    end
  elseif exist('PROJECT', 'var') && ~isempty(getenv('PROJECT')) % for standalone mode
    % scansDir=fullfile(parentDir, '..', '..', 'scans', getenv('PROJECT') 'out', 'easy', getenv('PROJECT'));
    scansDir=fullfile(parentDir, '..', '..', 'scans', getenv('PROJECT'));
    project=getenv('PROJECT');
    fprintf('Using project path: %s from environment variable PROJECT\n', scansDir);
    disp('This usually indicates that we are in standalone mode');
  else
    % TODO Lots of this is hardcoded logic, this TODO is just a reminder to change this block
    % when changing EASY/EZdir and other variables in the parent script
    fprintf('WARNING: Running in standalone mode without PROJECT or PROJECT_SCANS_DIR environment variables (not recommended)\n');
    fprintf('Beginning parent scans directory search\n');
    dirsToScan={
      fullfile(parentDir, '..', '..', 'scans')
      fullfile(parentDir, '..', '..', 'ExpJobs')
      fullfile('mnt','data','scans')
      fullfile('mnt','data', 'ExpJobs')
      fullfile(parentDir, '..', '..', 'templates', 'scans-demo')
    };
    for i=1:length(dirsToScan)
      d=dirsToScan(i);
      d=char(d);
      if exist(d, 'dir')
        subDirs=dir(d);
        pattern='^\d{6}_.*_.*';
        matchedDirs={dirs(regexp(subDirs.name, pattern)).name};
        if ~isempty(matchedDirs)
          fprintf('Found a non-empty scans directory in our list: %s\n', char(d));
          fprintf('Setting scansDir to %s\n', char(d));
          scansDir=fullfile(d);
        end
        fprintf('Scanning inside %s for a project directory\n', char(d));
        sortedMatchedDirs=sortrows(matchedDirs);
        project=sortedMatchedDirs{1}; % select the latest dir (by date prefix)
        fprintf('Selected latest project directory %s\n', char(project));
      end
    end
  end

% User sanity check and warning
if exist('PROJECT_USER', 'var') && ~isempty(getenv('PROJECT_USER'))
  if ~equal(getenv('PROJECT_USER'), userName)
    disp("WARNING: PROJECT_USER does not match the current namespace");
  end
end

% Allow module to override hardcoded default EZview directory
if exist('EZVIEW_DIR','var') && ~isempty(getenv('EZVIEW_DIR'))
  EZVIEW_DIR=fullfile(getenv('EZVIEW_DIR'));
  if ~strcmp(ezDir, EZVIEW_DIR) % sanity check
    disp("WARNING: EZVIEW_DIR does not match this script's hardcoded EZview location");
    disp("This is probably OK but if strange beahvior arises, we'll need to fix it in code");
    ezDir=EZVIEW_DIR;
  end
  fprintf('Using EZview script directory: %s from environment variable EZVIEW_DIR\n', ezDir);
else
  fprintf('Using EZview script directory: %s from hardcoded default\n', ezDir);
end

% Allow module to override hardcoded default EASY directory
if exist('EASY_DIR','var') && ~isempty(getenv('EASY_DIR'))
  EASY_DIR=fullfile(getenv('EASY_DIR'));
  if ~strcmp(easyDir, EASY_DIR) % sanity check
    disp("WARNING: EASY_DIR does not match this script's hardcoded EASY location");
    disp("This is probably OK but if strange beahvior arises, we'll need to fix it in code");
    easyDir=EASY_DIR;
  end
  fprintf('Using EASY script directory: %s from environment variable EASY_DIR\n', easyDir);
else
  fprintf('Using EASY script directory: %s from hardcoded default\n', easyDir);
end

userPars.BPdefault={'on','on','0.3','8','45','1000'};
userPars.boxplotFlg=1;
userPars.BPoutliers='On';
userPars.BPnotch='On';
userPars.BPlblShft=0.3;
userPars.BPfontSz=8;
userPars.BProt=45;
userPars.Trenddefault={'1000'};
userPars.kfiltLim=str2double(userPars.BPdefault(6));

try
  % Generate the Exp arrays
  numExps=3;
  for i=1:numExps
    Exp(i).cTraceN=0;
    Exp(i).cTraceIndx(1)=1;
  end
  Exp(1).CompositPlot=0;Exp(2).CompositPlot=0;Exp(3).CompositPlot=0;
  for i=1:numExps
    Exp(i).DexpType='single';
    Exp(i).DexpN=1;
    Exp(i).DexpLength=1;
    eval(['set(handles.DN' num2str(i) ', ''value'', 1);']); % MATLAB level unlocked
  end
  set(handles.GeneOrfTog,'value',0)
  try 
    load('EZsgdInfo'); 
  catch
    disp('Fail to load EZsgdInfo file from code directory'); 
  end

  Exp(numExps+1).SGDnum=SGDnum;
  Exp(numExps+1).SGDtext=SGDtext;
  Exp(numExps+1).SGDraw=SGDraw;
  Exp(numExps+1).interacPBsel=0;

  % Big outer loop try catch to ln844 end ln868
  % try to use user selected 'ExpJobs' folder otherwise use a default
  % directory in the uigetfile to load the experiment .mat file.

  try 
    [matFile,scansDir]=uigetfile('.mat','Open Experiment folder and data storage .mat file name','MultiSelect','off')
    load (fullfile(Exp(1).Dexp(1).ExpFoldr,'MasterPlateFiles','MPDMmat.mat'))
    for i=1:numExps
      Exp(i).Dexp(1).DM=DM;
      Exp(i).Dexp(1).MP=MP;
      Exp(i).Dexp(1).scan=scan;
      Exp(i).cTraceIndx(1)=1;
    end
    
    load(fullfile(resDir,'PTmats','NImParameters'))
    Exp(1).Dexp(1).ImParMat=ImParMat;
    Exp(2).Dexp(1).ImParMat=ImParMat;
    Exp(3).Dexp(1).ImParMat=ImParMat;

    try
      load(fullfile(resDir,'Fotos','Coordinates')) 
      load(fullfile(resDir,'Fotos','anlZones'))
      load(fullfile(resDir,'Fotos','BGatTpts'))
      for i=1:numExps
        Exp(i).Dexp(1).FexpScanSpots=FexpScanSpots;
        Exp(i).Dexp(1).FexpScanBMtp=FexpScanBMtp;
        Exp(i).Dexp(1).anlZoneRefs=anlZoneRefs;
        Exp(i).cTraceIndx(1)=1;
      end
    catch
    end

    for i=1:numExps
      Exp(i).traceN=0; % ZoneRelated
      Exp(i).traceN=0;
      Exp(i).hOL=[];
      Exp(i).hOLb=[];
      Exp(i).hOLname={};
      Exp(i).hOLexpNm={};
      Exp(i).hOLresDir={}
      Exp(i).hOLplateNum=[];
      Exp(i).hOLresDir={};
      Exp(i).RFmd1indx=[];
      Exp(i).RFmd1pltN=[];
      Exp(i).RFmd2indx=[];
      Exp(i).RFmd2pltN=[];
    end

    % default values for EZvFigPrint that meet JLH preferences
    Exp(4).plotPars={'4','36','10','5'};
    expN=1;
    
    % Test for Bad MP cell array (usually 384 [NaN}'s)
    % replaced length(Exp(expN).Dexp(1).MP) with MPnum 
    for mx=1:length(Exp(expN).Dexp(1).MP)
      try
        char((Exp(1).Dexp(1).MP(mx).genename{1}(384)))      
        MPnum=mx;
      catch
        break
      end
    end

    % MPnum=length(Exp(expN).Dexp(1).MP);
    set(handles.MPsldr1,'min',1,'max',MPnum)
    set(handles.MPsldr2,'min',1,'max',MPnum)
    set(handles.MPsldr3,'min',1,'max',MPnum)
    DMnum=length(Exp(expN).Dexp(1).DM.drug);
    set(handles.DMsldr1,'min',1,'max',DMnum)  %DMnum,'value',1.01)  %100,'value',1.01)
    set(handles.DMsldr2,'min',1,'max',DMnum)
    set(handles.DMsldr3,'min',1,'max',DMnum)
    tPtsSize=size(Exp(expN).Dexp(1).FexpScanBMtp{1,1},(3));
    set(handles.Tptsldr1,'min',1,'max',tPtsSize)
    set(handles.Tptsldr2,'min',1,'max',tPtsSize)
    set(handles.Tptsldr3,'min',1,'max',tPtsSize)
    set(handles.MPsldr1,'SliderStep',[1/MPnum 1/MPnum]);  %[1/length(MP) 1/length(MP)])
    set(handles.DMsldr1,'SliderStep',[1/length(DM.drug) 1/length(DM.drug)]);
    set(handles.Tptsldr1,'SliderStep',[1/tPtsSize 1/tPtsSize]);
    set(handles.MPsldr2,'SliderStep',[1/MPnum 1/MPnum]);
    set(handles.DMsldr2,'SliderStep',[1/length(DM.drug) 1/length(DM.drug)]);
    set(handles.Tptsldr2,'SliderStep',[1/tPtsSize 1/tPtsSize]);
    set(handles.MPsldr3,'SliderStep',[1/MPnum 1/MPnum]);
    set(handles.DMsldr3,'SliderStep',[1/length(DM.drug) 1/length(DM.drug)]);
    set(handles.Tptsldr3,'SliderStep',[1/tPtsSize 1/tPtsSize]);

    try
      xp=char(Exp(expN).Dexp(1).resDir);
      if ispc
        slashPos=strfind(char(Exp(expN).Dexp(1).resDir),'\');
      else
        slashPos=strfind(char(Exp(expN).Dexp(1).resDir),'/');
      end 
      startPos=slashPos(length(slashPos)-1) +1;
      endPos=slashPos(length(slashPos)) -1;
      expStr=xp(startPos:endPos);
      set(handles.expName1,'string',expStr);
      set(handles.expName2,'string',expStr); 
      set(handles.expName3,'string',expStr);
    catch
      cd(w)
    end %internal try xp=char(Exp(expN).Dexp(1).resDir); if ispc,...
  catch  
    cd(w)
    msg='LOADing or Setup issue'
    % if no load, then Message try SelExp PB to reload or try and different experiment
  end

  try 
    DNLaxes1=handles.DNLaxes1; DNLaxes2=handles.DNLaxes2; DNLaxes3=handles.DNLaxes3;
    zeroCLn=zeros(1,DMnum);
    %Exp(expN).expLoadCnt(1)=1;  %ZoneRelated
    Exp(1).hzeroCLn(1)=plot(DNLaxes1,zeroCLn,1:DMnum,'y'); try set(Exp(1).hzeroCLn,'visible','off'); catch ME, end
    Exp(2).hzeroCLn(1)=plot(DNLaxes2,zeroCLn,1:DMnum,'y'); try set(Exp(2).hzeroCLn,'visible','off'); catch ME, end
    Exp(3).hzeroCLn(1)=plot(DNLaxes3,zeroCLn,1:DMnum,'y'); try set(Exp(3).hzeroCLn,'visible','off'); catch ME, end
    Exp(1).expLoadCnt=1;
    Exp(2).expLoadCnt=1;
    Exp(3).expLoadCnt=1;
  catch ME
    ME.message,
  end

  % Compile GeneList and OrfList
  % Sort and add the medians of Ref Plates if RF1,RF2 exist
  set(handles.listboxGnOrf,'string',{('Loading')})
  lstindx=0;
  lstindxOrf=0;
  spN=0;
  rfcnt=0;
  dRF1indx=0;
  RF1mp=[];
  RF2mp=[];
  for mp=1:MPnum    %length(Exp(expN).Dexp(1).MP)
    RF1fullPlate=0;
    try RF1fullPlate=sum(ismember((Exp(expN).Dexp(1).MP(mp).genename{1}),'RF1'))==384; catch, mp, msg=strcat(num2str(mp),' genename ERROR'), end
    RF2fullPlate=0;
    try RF2fullPlate=sum(ismember((Exp(expN).Dexp(1).MP(mp).genename{1}),'RF2'))==384; catch, mp, msg=strcat(num2str(mp),' genename ERROR'), end
    for ind384=1:384
      spN=spN+1; 
      try % temp find data error
        r=ceil(ind384/24); 
        if rem(ind384,24)==0, c=24; else c=rem(ind384,24); end
        % Insert test for numeric in genename and orf if isnumeric
        % Correct common EXCEL problem of converting OCT1 into a date numeric
        if cell2mat(Exp(expN).Dexp(1).MP(mp).genename{1}(ind384))==38991,
          Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)={'OCT1_'}; 
          % genename{1}(ind384) replace numeric with a space ' ' or something   
        elseif isnumeric(cell2mat(Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)))
          Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)={' '}; 
        end
        % Check for full(384spot) Reference Plates (RF1 or/and RF2)        
        RF1fullPlate=0;
        try RF1fullPlate=sum(ismember((Exp(expN).Dexp(1).MP(mp).genename{1}),'RF1'))==384; catch, mp, msg=strcat(num2str(mp),' genename ERROR'), end
        RF2fullPlate=0;
        try RF2fullPlate=sum(ismember((Exp(expN).Dexp(1).MP(mp).genename{1}),'RF2'))==384; catch, mp, msg=strcat(num2str(mp),' genename ERROR'), end

        if isempty(regexpi(char((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384))),'blank'))...    %,'\<blank\>'
        && ~isnumeric(Exp(expN).Dexp(1).MP(mp).orf{1}(ind384))...
        && ~strcmpi((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)),' ')...
        && ~strcmpi((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)),'  ')...
        && ~strcmpi((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)),'')...
        && ~isempty((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)))...
        && ~strcmpi((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)),'RF1')...
        && ~strcmpi((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)),'RF2')... 
        && iscellstr((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)))  %  .genename{1}(ind384)))
          lstindxOrf=lstindxOrf+1;
          bb(lstindxOrf,1)=(Exp(expN).Dexp(1).MP(mp).orf{1}(ind384));
          bb(lstindxOrf,2)={strcat(':',num2str(mp),':',num2str(r),':',num2str(c))};
          bb(lstindxOrf,3)={mp};
          bb(lstindxOrf,4)={r};
          bb(lstindxOrf,5)={c};
          mutorfs(lstindxOrf)=spN;  %16_0318 added for Interaction EZinteract
        end    
        if isempty(regexpi(char((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384))),'blank'))...   %,'\<blank\>'
        && ~isnumeric(Exp(expN).Dexp(1).MP(mp).genename{1}(ind384))...
        && ~strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),' ')...
        && ~strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),'  ')...
        && ~strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),'')...
        && ~isempty((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)))...
        && ~strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),'RF1')...
        && ~strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),'RF2')...
        && iscellstr((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)))
          lstindx=lstindx+1;
          aa(lstindx,1)=(Exp(expN).Dexp(1).MP(mp).genename{1}(ind384));
          aa(lstindx,2)={strcat(':',num2str(mp),':',num2str(r),':',num2str(c))};
          aa(lstindx,3)={mp};
          aa(lstindx,4)={r};
          aa(lstindx,5)={c};
          mutgenes(lstindx)=spN;
          % Exp(expN).Dexp(1).mutSpotIndx.woRFs(lstindx)=spN;
        elseif (RF1fullPlate==1 ...   % sum(ismember((Exp(expN).Dexp(1).MP(mp).genename{1}),'RF1'))==384 || ...
        || (length(unique(Exp(expN).Dexp(1).MP(mp).genename{1}(1:384))))==1 && mp==1 ) ...   %(isequal((Exp(expN).Dexp(1).MP(mp).genename{1}(1:384)), (Exp(expN).Dexp(1).MP(mp).genename{1}(384:-1:1)))&& mp==1 )) && ...
        && ~exist('RF1scanN','var') 
          RF1mp=mp
          RF1scanN=(mp*DMnum)-(DMnum-1);     %mp;
          rfcnt=rfcnt+1;
          RFs(spN:spN+383)=spN:spN+383;
        elseif (RF2fullPlate==1 ...          %sum(ismember((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),'RF2'))==384 ||... 
        || (length(unique(Exp(expN).Dexp(1).MP(mp).genename{1}(1:384))))==1 && mp==MPnum ) && ~exist('RF2scanN','var')
          rfcnt=rfcnt+1;
          RFs(spN:spN+383)=spN:spN+383;
          asdf=sparse(RFs);
          asd=find(asdf);
          RFs=asd;
          RF2mp=mp              
          RF2scanN=(mp*DMnum)-(DMnum-1);   %mp;
        elseif strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),'RF1') && (RF1fullPlate~=1)
          dRF1indx=dRF1indx+1;
          Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)=strrep((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),':',' ');
          drf(dRF1indx,1)=(Exp(expN).Dexp(1).MP(mp).genename{1}(ind384));
          drf(dRF1indx,2)={strcat(':',num2str(mp),':',num2str(r),':',num2str(c))};
          drf(dRF1indx,3)={mp}; drfMP(dRF1indx,mp)=mp;
          drf(dRF1indx,4)={r};  drfr(dRF1indx,mp)=r;
          drf(dRF1indx,5)={c};  drfc(dRF1indx,mp)=c;
          drf(dRF1indx,6)={ind384}; drfPindx(dRF1indx,mp)=ind384;
        end % if isempty(regexpi(char((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384))),'blank'))...  
      catch
        mp
        ind384
        msgBadGeneName=strcat('check genename at mp=',num2str(mp),' indx=',num2str(ind384))
      end
    end
    mp 
  end

  % Cover case if mutorfs RFs are labeled RF1 or RF2
  try
    Exp(1).Dexp(1).mutSpotIndx.wRFs=union(RFs, mutorfs);
  catch
    msg='No RFs Found in Exp! wRFs'
    Exp(1).Dexp(1).mutSpotIndx.wRFs=mutorfs;
  end
  try
    Exp(1).Dexp(1).mutSpotIndx.woRFs=setdiff(mutorfs,RFs);
  catch
    Exp(expN).Dexp(1).mutSpotIndx.woRFs=mutorfs;
    msg='No RFs Found in Exp! woRFs'
  end

  Exp(2).Dexp(1).mutSpotIndx.wRFs=Exp(1).Dexp(1).mutSpotIndx.wRFs;
  Exp(2).Dexp(1).mutSpotIndx.woRFs=Exp(1).Dexp(1).mutSpotIndx.woRFs;
  Exp(3).Dexp(1).mutSpotIndx.wRFs=Exp(1).Dexp(1).mutSpotIndx.wRFs;
  Exp(3).Dexp(1).mutSpotIndx.woRFs=Exp(1).Dexp(1).mutSpotIndx.woRFs;
  Exp(1).Dexp(1).RFmd1indx=[]; Exp(2).Dexp(1).RFmd1indx=[]; Exp(3).Dexp(1).RFmd1indx=[];
  Exp(1).Dexp(1).RFmd1pltN=[]; Exp(2).Dexp(1).RFmd1pltN=[]; Exp(3).Dexp(1).RFmd1pltN=[];
  Exp(1).Dexp(1).RFmean=[]; Exp(2).Dexp(1).RFmean=[]; Exp(3).Dexp(1).RFmean=[];
  Exp(1).Dexp(1).RFmeanG=[]; Exp(2).Dexp(1).RFmeanG=[]; Exp(3).Dexp(1).RFmeanG=[];

  if exist('RF1scanN','var')     
    for d=0:(DMnum-1)
      medianIndx=[];
      nonZeroIndx=[];
      medValList=[];
      rf1scN=RF1scanN+d;

      try  %if RF1scanN doesn't exist this addition to list will be skipped
        nonZeroIndx=find(Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(1:384,5));
        if isempty(nonZeroIndx)
          nonZeroCnt=0
          medianIndx=nonZeroIndx; 
        else
          nonZeroCnt=length(nonZeroIndx); 
        end                          
        if ~isempty(nonZeroIndx) && mod(nonZeroCnt,2)==0, medianIndx=nonZeroIndx(1:nonZeroCnt-1); end
        if ~isempty(nonZeroIndx) && mod(nonZeroCnt,2)~=0, medianIndx=nonZeroIndx; end 
        clear medValLst
        clear kValLst
        clear rValLst           
        if ~isempty(nonZeroIndx) && length(medianIndx) > (.15*384) % To calc. a median, more than 15% of spots must be nonZero
          medValLst=Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(medianIndx,5);
          medValList1{d+1}=medValLst;
          min1=min(medValLst);
          max1=max(medValLst);
          std1=std(medValLst); 
          mean1=mean(medValLst)
          kValLst=Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(medianIndx,3); % For Ref Composite 17_1009
          rValLst=Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(medianIndx,4); % For Ref Composite 17_1009
          mval1=median(medValLst);  % (Exp(expN).Dexp(1).scan(RF1scanN).plate(1).CFout(383,5));
          RFmd1pos=find(mval1==(Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(1:384,5)))
          RFmd1loc(1)=ceil(RFmd1pos/24); %calc r value
          RFmd1loc(2)=RFmd1pos - ((RFmd1loc(1)-1)*24);  %calc c value
          lstindx=lstindx+1;
          lstindxOrf=lstindxOrf+1;
          aa(lstindx,1)={strcat('RF1md(',num2str(d+1),')')};
          aa(lstindx,2)={strcat(':',num2str(RF1mp),':',num2str(RFmd1loc(1)),':',num2str(RFmd1loc(2)))};  %,' std',num2str(std1))};
          bb(lstindxOrf,1)={strcat('RF1md(',num2str(d+1),')')};
          bb(lstindxOrf,2)={strcat(':',num2str(RF1mp),':',num2str(RFmd1loc(1)),':',num2str(RFmd1loc(2)))};  %,' std',num2str(std1))};
          % Composite Reference Amalgum Plot
          lstindx=lstindx+1;
          lstindxOrf=lstindxOrf+1;
          aa(lstindx,1)={strcat('RF1cmp(',num2str(d+1),')')}; 
          aa(lstindx,2)={''};
          bb(lstindxOrf,1)={strcat('RF1cmp(',num2str(d+1),')')};
          bb(lstindxOrf,2)={''};

          Exp(1).Dexp(1).RFmd1LB(d+1)=strcat(aa(lstindx,1),aa(lstindx,2)); Exp(2).Dexp(1).RFmd1LB(d+1)=strcat(aa(lstindx,1),aa(lstindx,2)); Exp(3).Dexp(1).RFmd1LB(d+1)=strcat(aa(lstindx,1),aa(lstindx,2));
          Exp(1).Dexp(1).RFmd1indx(d+1)=RFmd1pos; Exp(2).Dexp(1).RFmd1indx(d+1)=RFmd1pos; Exp(3).Dexp(1).RFmd1indx(d+1)=RFmd1pos;
          Exp(1).Dexp(1).RFmd1pltN=RF1mp; Exp(2).Dexp(1).RFmd1pltN=RF1mp; Exp(3).Dexp(1).RFmd1pltN=RF1mp;
          Exp(1).Dexp(1).RFmd1val(d+1)=mval1; Exp(2).Dexp(1).RFmd1val(d+1)=mval1; Exp(3).Dexp(1).RFmd1val(d+1)=mval1;
          Exp(1).Dexp(1).mean1(d+1)=mean1; Exp(2).Dexp(1).mean1(d+1)=mean1; Exp(3).Dexp(1).mean1(d+1)=mean1;
          Exp(1).Dexp(1).std1(d+1)=std1;  Exp(2).Dexp(1).std1(d+1)=std1; Exp(3).Dexp(1).std1(d+1)=std1;
          Exp(1).Dexp(1).min1(d+1)=min1;  Exp(2).Dexp(1).min1(d+1)=min1; Exp(3).Dexp(1).min1(d+1)=min1;
          Exp(1).Dexp(1).max1(d+1)=max1;  Exp(2).Dexp(1).max1(d+1)=max1; Exp(3).Dexp(1).max1(d+1)=max1;

          for ic=1:3
            Exp(ic).Dexp(1).RFcmpL(1).dm(d+1).Lvals=medValLst;  %17_1201 TrendOL    
            Exp(ic).Dexp(1).RFcmpL(1).dm(d+1).med=median(medValLst); %For Ref Composite 17_1009    
            Exp(ic).Dexp(1).RFcmpL(1).dm(d+1).mean=mean(medValLst); %For Ref Composite 17_1009 
            Exp(ic).Dexp(1).RFcmpL(1).dm(d+1).std=std(medValLst); %For Ref Composite 17_1009 
            Exp(ic).Dexp(1).RFcmpL(1).dm(d+1).min=min(medValLst); %For Ref Composite 17_1009 
            Exp(ic).Dexp(1).RFcmpL(1).dm(d+1).max=max(medValLst); %For Ref Composite 17_1009 

            Exp(ic).Dexp(1).RFcmpK(1).dm(d+1).Kvals=kValLst;  %17_1201 TrendOL 
            Exp(ic).Dexp(1).RFcmpK(1).dm(d+1).mean=mean(kValLst); %For Ref Composite 17_1009 
            Exp(ic).Dexp(1).RFcmpK(1).dm(d+1).med=median(kValLst); %For Ref Composite 17_1009
            Exp(ic).Dexp(1).RFcmpK(1).dm(d+1).std=std(kValLst); %For Ref Composite 17_1009 
            Exp(ic).Dexp(1).RFcmpK(1).dm(d+1).min=min(kValLst); %For Ref Composite 17_1009 
            Exp(ic).Dexp(1).RFcmpK(1).dm(d+1).max=max(kValLst); %For Ref Composite 17_1009

            Exp(ic).Dexp(1).RFcmpr(1).dm(d+1).rvals=rValLst;  %17_1201 TrendOL 
            Exp(ic).Dexp(1).RFcmpr(1).dm(d+1).med=median(rValLst); %For Ref Composite 17_1009
            Exp(ic).Dexp(1).RFcmpr(1).dm(d+1).mean=mean(rValLst); %For Ref Composite 17_1009 
            Exp(ic).Dexp(1).RFcmpr(1).dm(d+1).std=std(rValLst); %For Ref Composite 17_1009 
            Exp(ic).Dexp(1).RFcmpr(1).dm(d+1).min=min(rValLst); %For Ref Composite 17_1009 
            Exp(ic).Dexp(1).RFcmpr(1).dm(d+1).mean=max(rValLst); %For Ref Composite 17_1009 
          end
        else
          % Pick the first spot with zeros
          medianCalcFailed='To Few nonZero spots for valid median RF1 selection' 
          firstZero=find(((Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(1:384,5))==0),1,'first') 
          Exp(1).Dexp(1).RFmd1indx(d+1)=firstZero; Exp(2).Dexp(1).RFmd1indx(d+1)=firstZero; Exp(3).Dexp(1).RFmd1indx(d+1)=firstZero;  
          Exp(1).Dexp(1).RFmd1pltN=RF1mp; Exp(2).Dexp(1).RFmd1pltN=RF1mp; Exp(3).Dexp(1).RFmd1pltN=RF1mp;   %EZdestComp uses the masterplate number to get all the destPlates scanNumbers
          try, medValList1{d+1}=Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(medianIndx,5); nonZeroCnt; catch end
        end
      catch
        medianCalcTryFailed1='Failed! Failed! But process continued with bogus P1ind384 spot value!'
        try
          firstZero=find(((Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(1:384,5))==0),1,'first')  
          Exp(1).Dexp(1).RFmd1indx(d+1)=firstZero; Exp(2).Dexp(1).RFmd1indx(d+1)=firstZero; Exp(3).Dexp(1).RFmd1indx(d+1)=firstZero;  
        catch
          Exp(1).Dexp(1).RFmd1indx(d+1)=384; Exp(2).Dexp(1).RFmd1indx(d+1)=384; Exp(3).Dexp(1).RFmd1indx(d+1)=384; %if crapout,Then use spot384 as default to keep going  
        end
        try
          Exp(1).Dexp(1).RFmd1pltN=RF1mp; Exp(2).Dexp(1).RFmd1pltN=RF1mp; Exp(3).Dexp(1).RFmd1pltN=RF1mp; 
        catch
          catchissue='Ln334'
          Exp(1).Dexp(1).RFmd1pltN=1; Exp(2).Dexp(1).RFmd1pltN=1; Exp(3).Dexp(1).RFmd1pltN=1;
        end
      end 
    end
  end

  Exp(1).Dexp(1).RFmd2indx=[]; Exp(2).Dexp(1).RFmd2indx=[]; Exp(3).Dexp(1).RFmd2indx=[];
  Exp(1).Dexp(1).RFmd2pltN=[]; Exp(2).Dexp(1).RFmd2pltN=[]; Exp(3).Dexp(1).RFmd2pltN=[];

  if exist('RF2scanN','var')  
    for d=0:(DMnum-1);
      medianIndx2=[];
      nonZeroIndx2=[];
      medValList2=[];
      rf2scN=RF2scanN+d;
      try % if RF2scanN doesn't exist this addition to list will be skipped
        nonZeroIndx2=find(Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(1:384,5));
        if isempty(nonZeroIndx2)
          nonZeroCnt2=0
          medianIndx2=nonZeroIndx2; 
        else 
          nonZeroCnt2=length(nonZeroIndx2); 
        end
        if ~isempty(nonZeroIndx2) && mod(nonZeroCnt2,2)==0, medianIndx2=nonZeroIndx2(1:nonZeroCnt2-1); end
        if ~isempty(nonZeroIndx2) && mod(nonZeroCnt2,2)~=0, medianIndx2=nonZeroIndx2; end    
        clear medValLst2
        clear kValLst2
        clear rValLst2
        if ~isempty(nonZeroIndx2) && length(medianIndx2) > (.15*384) % to calc. a median, more than 15% of spots must be nonZero
          medValLst2=Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(medianIndx2,5);
          medValList2{d+1}=medValLst2;
          min2=min(medValLst2);
          max2=max(medValLst2);
          std2=std(medValLst2)    
          mean2=mean(medValLst2);
          kValLst2=Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(medianIndx2,3); %For Ref Composite 17_1009
          rValLst2=Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(medianIndx2,4); %For Ref Composite 17_1009
          mval2=median(medValLst2);   %(Exp(expN).Dexp(1).scan(RF2scanN).plate(1).CFout(1:383,5));
          RFmd2pos=find(mval2==(Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(1:384,5)));
          RFmd2loc(1)=ceil(RFmd2pos/24); %calc r value
          RFmd2loc(2)=RFmd2pos - ((RFmd2loc(1)-1)*24);  %calc c value
          lstindx=lstindx+1;
          lstindxOrf=lstindxOrf+1;
          aa(lstindx,1)={strcat('RF2md(',num2str(d+1),')')};  %{'RF2md'};
          aa(lstindx,2)={strcat(':',num2str(RF2mp),':',num2str(RFmd2loc(1)),':',num2str(RFmd2loc(2)))};  %,' std~',num2str(std2))};
          bb(lstindxOrf,1)={strcat('RF2md(',num2str(d+1),')')};  %{'RF2md'};
          bb(lstindxOrf,2)={strcat(':',num2str(RF2mp),':',num2str(RFmd2loc(1)),':',num2str(RFmd2loc(2)))};  %,' std~',num2str(std2))};
          %Composite Reference Amalgum Plot   (CRAP)
          lstindx=lstindx+1;
          lstindxOrf=lstindxOrf+1;
          aa(lstindx,1)={strcat('RF2cmp(',num2str(d+1),')')}; 
          aa(lstindx,2)={''};
          bb(lstindxOrf,1)={strcat('RF2cmp(',num2str(d+1),')')}; 
          bb(lstindxOrf,2)={''};
          Exp(1).Dexp(1).RFmd2LB(d+1)=strcat(aa(lstindx,1),aa(lstindx,2)); Exp(2).Dexp(1).RFmd2LB(d+1)=strcat(aa(lstindx,1),aa(lstindx,2)); Exp(3).Dexp(1).RFmd2LB(d+1)=strcat(aa(lstindx,1),aa(lstindx,2));
          Exp(1).Dexp(1).RFmd2indx(d+1)=RFmd2pos; Exp(2).Dexp(1).RFmd2indx(d+1)=RFmd2pos; Exp(3).Dexp(1).RFmd2indx(d+1)=RFmd2pos;
          Exp(1).Dexp(1).RFmd2pltN=RF2mp; Exp(2).Dexp(1).RFmd2pltN=RF2mp; Exp(3).Dexp(1).RFmd2pltN=RF2mp;
          Exp(1).Dexp(1).RFmd2val(d+1)=mval2; Exp(2).Dexp(1).RFmd2val(d+1)=mval2; Exp(3).Dexp(1).RFmd2val(d+1)=mval2;
          Exp(1).Dexp(1).mean2(d+1)=mean2; Exp(2).Dexp(1).mean2(d+1)=mean2; Exp(3).Dexp(1).mean2(d+1)=mean2;
          Exp(1).Dexp(1).std2(d+1)=std2;  Exp(2).Dexp(1).std2(d+1)=std2; Exp(3).Dexp(1).std2(d+1)=std2;
          Exp(1).Dexp(1).min2(d+1)=min2;  Exp(2).Dexp(1).min2(d+1)=min2; Exp(3).Dexp(1).min2(d+1)=min2;
          Exp(1).Dexp(1).max2(d+1)=max2;  Exp(2).Dexp(1).max2(d+1)=max2; Exp(3).Dexp(1).max2(d+1)=max2;

          for ic=1:3
            Exp(ic).Dexp(1).RFcmpL(2).dm(d+1).Lvals=medValLst2;  %17_1201 TrendOL     
            Exp(ic).Dexp(1).RFcmpL(2).dm(d+1).med=median(medValLst2); %For Ref Composite 17_1009     
            Exp(ic).Dexp(1).RFcmpL(2).dm(d+1).mean=mean(medValLst2); %For Ref Composite 17_1009 
            Exp(ic).Dexp(1).RFcmpL(2).dm(d+1).std=std(medValLst2); %For Ref Composite 17_1009 
            Exp(ic).Dexp(1).RFcmpL(2).dm(d+1).min=min(medValLst2); %For Ref Composite 17_1009 
            Exp(ic).Dexp(1).RFcmpL(2).dm(d+1).max=max(medValLst2); %For Ref Composite 17_1009 

            Exp(ic).Dexp(1).RFcmpK(2).dm(d+1).Kvals=kValLst2;  %17_1201 TrendOL   
            Exp(ic).Dexp(1).RFcmpK(2).dm(d+1).med=median(kValLst2); %For Ref Composite 17_1009 
            Exp(ic).Dexp(1).RFcmpK(2).dm(d+1).mean=mean(kValLst2); %For Ref Composite 17_1009 
            Exp(ic).Dexp(1).RFcmpK(2).dm(d+1).std=std(kValLst2); %For Ref Composite 17_1009 
            Exp(ic).Dexp(1).RFcmpK(2).dm(d+1).min=min(kValLst2); %For Ref Composite 17_1009 
            Exp(ic).Dexp(1).RFcmpK(2).dm(d+1).max=max(kValLst2); %For Ref Composite 17_1009 

            Exp(ic).Dexp(1).RFcmpr(2).dm(d+1).rvals=rValLst2;  %17_1201 TrendOL   
            Exp(ic).Dexp(1).RFcmpr(2).dm(d+1).med=median(rValLst2); %For Ref Composite 17_1009 
            Exp(ic).Dexp(1).RFcmpr(2).dm(d+1).mean=mean(rValLst2); %For Ref Composite 17_1009 
            Exp(ic).Dexp(1).RFcmpr(2).dm(d+1).std=std(rValLst2); %For Ref Composite 17_1009 
            Exp(ic).Dexp(1).RFcmpr(2).dm(d+1).min=min(rValLst2); %For Ref Composite 17_1009 
            Exp(ic).Dexp(1).RFcmpr(2).dm(d+1).max=max(rValLst); %For Ref Composite 17_1009 
          end
        else
          % Pick the first spot with zeros
          % Use that position to satisfy and keep process OK
          medianCalcFailed2='To Few nonZero spots for valid median RF2 selection'
          firstZero2=find(((Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(1:384,5))==0),1,'first')   
          Exp(1).Dexp(1).RFmd2indx(d+1)=firstZero2; Exp(2).Dexp(1).RFmd2indx(d+1)=firstZero2; Exp(3).Dexp(1).RFmd2indx(d+1)=firstZero2;  
          Exp(1).Dexp(1).RFmd2pltN=RF2mp; Exp(2).Dexp(1).RFmd2pltN=RF2mp; Exp(3).Dexp(1).RFmd2pltN=RF2mp;  
          try
            medValList2{d+1}=Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(medianIndx2,5);
            nonZeroCnt2;
          catch 
          end
        end
      catch
        medianCalcTryFailed2='Failed! Failed! No RF1median But process continued with bogus P1ind384 spot value!'
        try
          firstZero2=find(((Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(1:384,5))==0),1,'first')   
          Exp(1).Dexp(1).RFmd2indx(d+1)=firstZero2; Exp(2).Dexp(1).RFmd2indx(d+1)=firstZero2; Exp(3).Dexp(1).RFmd2indx(d+1)=firstZero2;  
        catch
          Exp(1).Dexp(1).RFmd2indx(d+1)=384; Exp(2).Dexp(1).RFmd2indx(d+1)=384; Exp(3).Dexp(1).RFmd2indx(d+1)=384; %if crapout,Then use spot384 as default to keep going  
        end
        try
          Exp(1).Dexp(1).RFmd2pltN=RF2mp; Exp(2).Dexp(1).RFmd2pltN=RF2mp; Exp(3).Dexp(1).RFmd2pltN=RF2mp; 
        catch
          Exp(1).Dexp(1).RFmd2pltN=1; Exp(2).Dexp(1).RFmd2pltN=1; Exp(3).Dexp(1).RFmd2pltN=1;
        end
      end  % if RF2scanN doesn't exist this addition to list will be skipped  
      RFcombValList=cat(1,medValList1{d+1},medValList2{d+1});
      Exp(1).Dexp(1).RFmean(d+1)=mean(RFcombValList);Exp(2).Dexp(1).RFmean(d+1)=mean(RFcombValList);Exp(3).Dexp(1).RFmean(d+1)=mean(RFcombValList);
      Exp(1).Dexp(1).RFstd(d+1)=std(RFcombValList);Exp(2).Dexp(1).RFstd(d+1)=std(RFcombValList);Exp(3).Dexp(1).RFstd(d+1)=std(RFcombValList);
      Exp(1).Dexp(1).RFmin(d+1)=min(RFcombValList);Exp(2).Dexp(1).RFmin(d+1)=min(RFcombValList);Exp(3).Dexp(1).RFmin(d+1)=min(RFcombValList);
      Exp(1).Dexp(1).RFmax(d+1)=max(RFcombValList);Exp(2).Dexp(1).RFmax(d+1)=max(RFcombValList);Exp(3).Dexp(1).RFmax(d+1)=max(RFcombValList);
      % TODO can delete the following redundant line of code
      Exp(2).Dexp(1).RFmean(d+1)=Exp(1).Dexp(1).RFmean(d+1); Exp(3).Dexp(1).RFmean(d+1)=Exp(1).Dexp(1).RFmean(d+1);
    end
  elseif exist('RF1scanN','var')
    Exp(1).Dexp(1).RFmean=Exp(1).Dexp(1).mean1; Exp(2).Dexp(1).RFmean=Exp(2).Dexp(1).mean1; Exp(3).Dexp(1).RFmean=Exp(3).Dexp(1).mean1;
    Exp(1).Dexp(1).RFstd=Exp(1).Dexp(1).std1; Exp(2).Dexp(1).RFstd=Exp(2).Dexp(1).std1; Exp(3).Dexp(1).RFstd=Exp(3).Dexp(1).std1; 
    Exp(1).Dexp(1).RFmin=Exp(1).Dexp(1).min1; Exp(2).Dexp(1).RFmin=Exp(2).Dexp(1).min1; Exp(3).Dexp(1).RFmin=Exp(3).Dexp(1).min1;
    Exp(1).Dexp(1).RFmax=Exp(1).Dexp(1).max1; Exp(2).Dexp(1).RFmax=Exp(2).Dexp(1).max1; Exp(3).Dexp(1).RFmax=Exp(3).Dexp(1).max1;
  end

  % DISPERSE REFERENCE PLATES
  Exp(expN).Dexp(1).RFmdPindx=[];
  Exp(expN).Dexp(1).RFmdPpltN=[];
  if exist('drf','var') % ('RF1scanN','var') 
    % Det. index of change from one MP to the next 
    i=2;
    chgIndx(1)=1;
    for j=1:length(drf(:,3))
      if j>1
        if cell2mat(drf(j,3))~=cell2mat(drf((j-1),3)), chgIndx(i)=j; i=i+1; end
      end
    end
    chgIndx(length(chgIndx)+1)=length(drf)+1;
    uu=zeros(size(drf,1),4);
    uu(:,1:4)=cell2mat(drf(:,3:6));
    vv=zeros(length(drf),DMnum);
    dMPs=unique(cell2mat(drf(:,3))); 
    for mm=1:length(dMPs)    
      for d=1:(DMnum)
        medianIndxDisp=[];
        NZrefIndxP=[];
        nonZeroValsP=[];
        medValLstDisp=[];
        rf1scNdisp=((dMPs(mm)-1)*DMnum)+(d);
        try  % Determine the dispersed RFs median mean and std if such exist
          NZrefIndxP=drfPindx((find(drfPindx(:,dMPs(mm)))),dMPs(mm));   
          vv(chgIndx(mm):(chgIndx(mm+1)-1),d)=Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
          % For Global Ref Composite 17_1009
          vvK(chgIndx(mm):(chgIndx(mm+1)-1),d)=Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,3);
          vvr(chgIndx(mm):(chgIndx(mm+1)-1),d)=Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,4);
          nonZeroValsP=nonzeros(Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5));
          minDisp=min(nonZeroValsP);
          maxDisp=max(nonZeroValsP);
          std1Disp=std(nonZeroValsP);
          mean1Disp=mean(nonZeroValsP);
          drfVals=Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
          %MEDIAN Determination for PLATES with Dispersed RFs
          if isempty(NZrefIndxP)
            nonZeroCntDisp=0
            medianIndxDisp=NZrefIndxP; 
          else 
            nonZeroCntDisp=length(NZrefIndxP); 
          end
          if ~isempty(NZrefIndxP) && mod(nonZeroCntDisp,2)==0, medianIndxDisp=NZrefIndxP(1:nonZeroCntDisp-1); end
          if ~isempty(NZrefIndxP) && mod(nonZeroCntDisp,2)~=0, medianIndxDisp=NZrefIndxP; end 
          if ~isempty(NZrefIndxP) && length(medianIndxDisp) > 3 %(.15*384) %To calc. a median, more than 15% of spots must be nonZero
            medValLstDisp=Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(medianIndxDisp,5);
            mval1Disp=median(medValLstDisp);  
            nonZeroMedPosIndx=find(mval1Disp==nonZeroValsP);  
            RFmd1posD=NZrefIndxP(nonZeroMedPosIndx);  
            RFmd1locD(1)=ceil(RFmd1posD/24); %calc r value
            RFmd1locD(2)=RFmd1posD - ((RFmd1locD(1)-1)*24);  %calc c value
            lstindx=lstindx+1;
            lstindxOrf=lstindxOrf+1;
            aa(lstindx,1)={strcat('RF1mdP(',num2str(d),')')};  %{'RF1md'};
            aa(lstindx,2)={strcat(':',num2str(dMPs(mm)),':',num2str(RFmd1locD(1)),':',num2str(RFmd1locD(2)))};  %,'std_',num2str(std1))};
            bb(lstindxOrf,1)={strcat('RF1mdP(',num2str(d),')')};  %{'RF1md'};
            bb(lstindxOrf,2)={strcat(':',num2str(dMPs(mm)),':',num2str(RFmd1locD(1)),':',num2str(RFmd1locD(2)))};  %,'std_',num2str(std1))};
            Exp(1).Dexp(1).RFmdPLB(d,dMPs(mm))=strcat(aa(lstindx,1),aa(lstindx,2)); Exp(2).Dexp(1).RFmdPLB(d,dMPs(mm))=strcat(aa(lstindx,1),aa(lstindx,2)); Exp(3).Dexp(1).RFmdPLB(d,dMPs(mm))=strcat(aa(lstindx,1),aa(lstindx,2));
            Exp(1).Dexp(1).RFmdPindx(d,dMPs(mm))=RFmd1posD; Exp(2).Dexp(1).RFmdPindx(d,dMPs(mm))=RFmd1posD; Exp(3).Dexp(1).RFmdPindx(d,dMPs(mm))=RFmd1posD;
            Exp(1).Dexp(1).RFmdPpltN(d,dMPs(mm))=dMPs(mm); Exp(2).Dexp(1).RFmdPpltN(d,dMPs(mm))=dMPs(mm); Exp(3).Dexp(1).RFmdPpltN(d,dMPs(mm))=dMPs(mm);   
            Exp(1).Dexp(1).RFmedianP(d,dMPs(mm))=mval1Disp; Exp(2).Dexp(1).RFmedianP(d,dMPs(mm))=mval1Disp; Exp(3).Dexp(1).RFmedianP(d,dMPs(mm))=mval1Disp;
            Exp(1).Dexp(1).meanP(d,dMPs(mm))=mean1Disp; Exp(2).Dexp(1).meanP(d,dMPs(mm))=mean1Disp; Exp(3).Dexp(1).meanP(d,dMPs(mm))=mean1Disp; 
            Exp(1).Dexp(1).stdP(d,dMPs(mm))=std1Disp; Exp(2).Dexp(1).stdP(d,dMPs(mm))=std1Disp; Exp(3).Dexp(1).stdP(d,dMPs(mm))=std1Disp;
            Exp(1).Dexp(1).minP(d,dMPs(mm))=minDisp; Exp(2).Dexp(1).minP(d,dMPs(mm))=minDisp; Exp(3).Dexp(1).minP(d,dMPs(mm))=minDisp;
            Exp(1).Dexp(1).maxP(d,dMPs(mm))=maxDisp; Exp(2).Dexp(1).maxP(d,dMPs(mm))=maxDisp; Exp(3).Dexp(1).maxP(d,dMPs(mm))=maxDisp;
          else
            % Need to set L r K values to zeros or pick the first spot with zeros
            % Spot 1 could be other than zero as the median isn't calculated if fewer than some percent are nonzero
            medianCalcFailedD='To Few nonZero spots for valid median RF1 selection' 
            firstZeroDindx=find(((Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5))==0),1,'first');
            firstZeroD=drfPindx((firstZeroDindx),dMPs(mm));
            Exp(expN).Dexp(1).RFmdPindx(d,dMPs(mm))=firstZeroD; 
            Exp(expN).Dexp(1).RFmdPpltN(d,dMPs(mm))=dMPs(mm);   %RF1mp;   %Is this supposed to be the MP number or the ScanPlate number???
          end 
        catch 
          medianCalcTryFailed1D='Failed! Failed! Ln565 {Dispersed RF1s} "try" But process continued with bogus Plate spot value!'
          try
            firstZeroindxD=find(vv((chgIndx(d):chgIndx(d+1)-1),5)==0,1,'first') 
            firstZeroPindx=uu(firstZeroindxD,4);
            Exp(expN).Dexp(1).RFmdPpltN(d,dMPs(mm))=dMPs(mm);
            Exp(expN).Dexp(1).RFmdPindx(d,dMPs(mm))=firstZeroPindx;
          catch
            catchissue='try at Ln565'
            Exp(expN).Dexp(1).RFmdPpltN(d,dMPs(mm))=dMPs(mm);
            Exp(expN).Dexp(1).RFmdPindx(d,dMPs(mm))=384; % if crapout,Then use spot384 as default to keep going  
          end
          try
            Exp(expN).Dexp(1).RFmdPpltN=dMPs(mm);  
          catch
            catchissue='Ln'
            Exp(expN).Dexp(1).RFmdPpltN=1;  %This might keep from breaking BUT ??? 
          end
        end
      end
    end

    % Calc. Global Mean, Std, And Median For Distributed References
    uu=horzcat(uu,vv);
    for d=1:DMnum
      medianIndxD=[];
      NZrfIndxG=[];
      minG=min(nonzeros(vv(:,d)));
      maxG=max(nonzeros(vv(:,d)));
      RFmeanG=mean(nonzeros(vv(:,d)));
      RFstdG=std(nonzeros(vv(:,d)));
      NZrfIndxG=find(vv(:,d));  % find(nonzeros(vv(:,d)));  WWRONG FOR A WHILE! find(nonzeros(vv(:,d)));
      if isempty(RFmeanG)
        nonZeroCntD=0;    
      else 
        nonZeroCntD=length(nonzeros(vv(:,d))); 
      end
      % Calc. of median requires an odd number of indx items
      if ~isempty(NZrfIndxG) && mod(nonZeroCntD,2)==0, medianIndxD=NZrfIndxG(1:(size(NZrfIndxG,1)-1)); end
      if ~isempty(NZrfIndxG) && mod(nonZeroCntD,2)~=0, medianIndxD=NZrfIndxG(:); end 
      if ~isempty(NZrfIndxG) && length(medianIndxD) > (.15*size(drf,1)) % To calc. a median, more than 15% of spots must be nonZero
        mvalsDG=median(vv(medianIndxD,d)); % (nonzeros(vv(:,d))); 
        nzPosIndxDG=find(mvalsDG==vv(:,d)); 
        RFmdDGloc(d,1)=uu(nzPosIndxDG,1);  % MP of distributedGlobal Median value
        RFmdDGloc(d,2)=uu(nzPosIndxDG,2);   % calc r value
        RFmdDGloc(d,3)=uu(nzPosIndxDG,3);  % calc c value
        lstindx=lstindx+1;
        lstindxOrf=lstindxOrf+1;
        aa(lstindx,1)={strcat('RF1mdG(',num2str(d),')')};
        aa(lstindx,2)={strcat(':',num2str(RFmdDGloc(d,1)),':',num2str(RFmdDGloc(d,2)),':',num2str(RFmdDGloc(d,3)))};  %,'std_',num2str(std2))};
        bb(lstindxOrf,1)={strcat('RF1mdG(',num2str(d),')')};
        bb(lstindxOrf,2)={strcat(':',num2str(RFmdDGloc(d,1)),':',num2str(RFmdDGloc(d,2)),':',num2str(RFmdDGloc(d,3)))};  %,'std_',num2str(std2))};
        % Composite Reference Amalgum Plot
        lstindx=lstindx+1;
        lstindxOrf=lstindxOrf+1;
        aa(lstindx,1)={strcat('RFcmpG(',num2str(d),')')}; 
        aa(lstindx,2)={''};
        bb(lstindxOrf,1)={strcat('RFcmpG(',num2str(d),')')}; 
        bb(lstindxOrf,2)={''};
        Exp(1).Dexp(1).RFmdGLB(d)=strcat(aa(lstindx,1),aa(lstindx,2)); Exp(2).Dexp(1).RFmdGLB(d)=strcat(aa(lstindx,1),aa(lstindx,2)); Exp(3).Dexp(1).RFmdGLB(d)=strcat(aa(lstindx,1),aa(lstindx,2));
        Exp(1).Dexp(1).RFmdGindx(d)=nzPosIndxDG; Exp(2).Dexp(1).RFmdGindx(d)=nzPosIndxDG; Exp(3).Dexp(1).RFmdGindx(d)=nzPosIndxDG;   
        Exp(1).Dexp(1).RFmdGpltN(d)=RFmdDGloc(d,1); Exp(2).Dexp(1).RFmdGpltN(d)=RFmdDGloc(d,1); Exp(3).Dexp(1).RFmdGpltN(d)=RFmdDGloc(d,1);   
        Exp(1).Dexp(1).RFmdGscanN(d)=uu(nzPosIndxDG,4); Exp(2).Dexp(1).RFmdGscanN(d)=uu(nzPosIndxDG,4); Exp(3).Dexp(1).RFmdGscanN(d)=uu(nzPosIndxDG,4);
        Exp(1).Dexp(1).RFmedianG(d)=mvalsDG; Exp(2).Dexp(1).RFmedianG(d)=mvalsDG; Exp(3).Dexp(1).RFmedianG(d)=mvalsDG;
        Exp(1).Dexp(1).RFmeanG(d)=RFmeanG; Exp(2).Dexp(1).RFmeanG(d)=RFmeanG; Exp(3).Dexp(1).RFmeanG(d)=RFmeanG;  
        Exp(1).Dexp(1).RFstdG(d)=RFstdG; Exp(2).Dexp(1).RFstdG(d)=RFstdG; Exp(3).Dexp(1).RFstdG(d)=RFstdG; 
        Exp(1).Dexp(1).RFminG(d)=minG; Exp(2).Dexp(1).RFminG(d)=minG; Exp(3).Dexp(1).RFminG(d)=minG; 
        Exp(1).Dexp(1).RFmaxG(d)=maxG; Exp(2).Dexp(1).RFmaxG(d)=maxG; Exp(3).Dexp(1).RFmaxG(d)=maxG; 
        for ic=1:3
          Exp(ic).Dexp(1).RFcmpGL.dm(d).Lvals=vv(medianIndxD,d); %17_1201 TrendOL
          Exp(ic).Dexp(1).RFcmpGL.dm(d).med=median(vv(medianIndxD,d)); %For Ref Composite 17_1009 
          Exp(ic).Dexp(1).RFcmpGL.dm(d).mean=mean(vv(medianIndxD,d)); %For Ref Composite 17_1009 
          Exp(ic).Dexp(1).RFcmpGL.dm(d).std=std(vv(medianIndxD,d)); %For Ref Composite 17_1009 
          Exp(ic).Dexp(1).RFcmpGL.dm(d).min=min(vv(medianIndxD,d)); %For Ref Composite 17_1009 
          Exp(ic).Dexp(1).RFcmpGL.dm(d).max=max(vv(medianIndxD,d)); %For Ref Composite 17_1009
          Exp(ic).Dexp(1).RFcmpGK.dm(d).Kvals=vvK(medianIndxD,d); %17_1201 TrendOL
          Exp(ic).Dexp(1).RFcmpGK.dm(d).med=median(vvK(medianIndxD,d)); %For Ref Composite 17_1009 
          Exp(ic).Dexp(1).RFcmpGK.dm(d).mean=mean(vvK(medianIndxD,d)); %For Ref Composite 17_1009 
          Exp(ic).Dexp(1).RFcmpGK.dm(d).std=std(vvK(medianIndxD,d)); %For Ref Composite 17_1009 
          Exp(ic).Dexp(1).RFcmpGK.dm(d).min=min(vvK(medianIndxD,d)); %For Ref Composite 17_1009 
          Exp(ic).Dexp(1).RFcmpGK.dm(d).max=max(vvK(medianIndxD,d)); %For Ref Composite 17_1009 
          Exp(ic).Dexp(1).RFcmpGr.dm(d).rvals=vvr(medianIndxD,d); %17_1201 TrendOL
          Exp(ic).Dexp(1).RFcmpGr.dm(d).med=median(vvr(medianIndxD,d)); %For Ref Composite 17_1009 
          Exp(ic).Dexp(1).RFcmpGr.dm(d).mean=mean(vvr(medianIndxD,d)); %For Ref Composite 17_1009 
          Exp(ic).Dexp(1).RFcmpGr.dm(d).std=std(vvr(medianIndxD,d)); %For Ref Composite 17_1009 
          Exp(ic).Dexp(1).RFcmpGr.dm(d).min=min(vvr(medianIndxD,d)); %For Ref Composite 17_1009 
          Exp(ic).Dexp(1).RFcmpGr.dm(d).max=max(vvr(medianIndxD,d)); %For Ref Composite 17_1009 
        end
      end
    end
  end

  % End Of Disperse Reference Plataes Calculations And List Additions
  % Sort And Build Genelist
  Exp(1).Dexp(1).srtGnLst={('CheckMP/MPDMfile')};
  gnLstRaw=strcat(aa(:,1),aa(:,2));
  Exp(1).Dexp(1).srtGnLst=sort(gnLstRaw);
  Exp(2).Dexp(1).srtGnLst=Exp(1).Dexp(1).srtGnLst;
  Exp(3).Dexp(1).srtGnLst=Exp(1).Dexp(1).srtGnLst;
  orfLstRaw=strcat(bb(:,1),bb(:,2));
  Exp(1).Dexp(1).srtOrfLst=sort(orfLstRaw);
  Exp(2).Dexp(1).srtOrfLst=Exp(1).Dexp(1).srtOrfLst;
  Exp(3).Dexp(1).srtOrfLst=Exp(1).Dexp(1).srtOrfLst;
  set(handles.listboxGnOrf,'string',Exp(1).Dexp(1).srtGnLst)
catch ME  %Outer loop try around entire code subroutine
  cd(w)
  set(handles.listboxGnOrf,'string',cellstr([{'Failed To Load'}; {'Check MPDMmat file'};{'Check .xls files'};{'Check \Fotos .mat files'};{'Check \matResults file'}]))
  %Exp(expN).Dexp(1).srtGnLst={('Failed To Load')};
  Exp(1).Dexp(1).srtGnLst=cellstr([{'Failed To Load'}; {' '}]);
  Exp(2).Dexp(1).srtGnLst=cellstr([{'Failed To Load'}; {' '}]);
  Exp(3).Dexp(1).srtGnLst=cellstr([{'Failed To Load'}; {' '}]);
  %Exp(expN).srtOrfLst={('Failed To Load')};
  Exp(1).Dexp(1).srtOrfLst=cellstr([{'Failed To Load'}; {' '}]);
  Exp(2).Dexp(1).srtOrfLst=cellstr([{'Failed To Load'}; {' '}]);
  Exp(3).Dexp(1).srtOrfLst=cellstr([{'Failed To Load'}; {' '}]);

  if ~contains(matFile,'.mat')
    ExpOutImFile=fullfile(matFile);
    EZvImagesOnly
  end
end
expN=1; % Fix 170424
DexpN=1;
EZdiagRFsSheet
Exp(1).Dexp(1).RFrnames=rnames; Exp(2).Dexp(1).RFrnames=rnames; Exp(3).Dexp(1).RFrnames=rnames;
Exp(1).Dexp(1).RFdata=data; Exp(2).Dexp(1).RFdata=data; Exp(3).Dexp(1).RFdata=data;
RFconfig=0;
if sum(ismember(fieldnames(Exp(expN).Dexp(1)),'RFmean')) ...
&& ~isempty(Exp(expN).Dexp(1).RFmean) ...
&& sum(ismember(fieldnames(Exp(expN).Dexp(1)),'RFmeanG')) ...
&& isempty(Exp(expN).Dexp(1).RFmeanG)
  RFconfig=1;
end
if sum(ismember(fieldnames(Exp(expN).Dexp(1)),'RFmean'))==0 ...
|| isempty(Exp(expN).Dexp(1).RFmean) ...
&& sum(ismember(fieldnames(Exp(expN).Dexp(1)),'RFmeanG')) ...
&& ~isempty(Exp(expN).Dexp(1).RFmeanG)
  RFconfig=2;
end
if sum(ismember(fieldnames(Exp(expN).Dexp(1)),'RFmean')) ...
&& ~isempty(Exp(expN).Dexp(1).RFmean) ...
&& sum(ismember(fieldnames(Exp(expN).Dexp(1)),'RFmeanG')) ...
&& ~isempty(Exp(expN).Dexp(1).RFmeanG)
  RFconfig=3;
end
Exp(1).RFconfig=RFconfig; Exp(2).RFconfig=RFconfig; Exp(3).RFconfig=RFconfig;  % ZoneRelated
try 
  msgBadGeneName  
catch
end
try
  Exp(1).Dexp(1).resetHtmpTg=3; Exp(2).Dexp(1).resetHtmpTg=3; Exp(3).Dexp(1).resetHtmpTg=3; % ZoneRelated
  if RFconfig==0
    RFconfigMsg='No RF1 references in this Experiment Job'
    Exp(1).resetHtmpTg=3; Exp(2).resetHtmpTg=3; Exp(3).resetHtmpTg=3;  % ZoneRelated
  end
catch
end
prntHt=0;
% HtMapTog 'string', 'Current user HL/HN' selection'
try
  Exp(1).htmapPBsel=0;
  set(handles.HtMapTog1,'string','L')
  Exp(2).htmapPBsel=0;  %ZoneRelated
  set(handles.HtMapTog2,'string','L')
  Exp(3).htmapPBsel=0;
  set(handles.HtMapTog3,'string','L')
catch
  % expN=1;
end

for ic=1:3
  Expaa{ic,1}=aa;
  Expbb{ic,1}=bb;
end
htMapTogPBfg=0;
Exp(1).htmapRFanswer={'G','L'}; % ZoneRelated
Exp(2).htmapRFanswer={'G','L'};
Exp(3).htmapRFanswer={'G','L'};
zonePB=expN; % added 230828 to fix migration 
ghandles=handles;
ghandles.guiFig=gcf;
Exp(4).guiFig=gcf;