%EZvInitLoad
global Exp
global Expaa
global Expbb
global userPars
global usrExpJobsDir
global zonePB

% Initialize some variables from matlab
ezPath=which(mfilename);
[ezDir,ezFileName]=fileparts(ezPath);
ezDir=fullfile(easyDir);
[parentDir, ~]=fileparts(ezDir);
parentDir=fullfile(parentDir); % ../easy/apps

debug=1;
if debug
  disp('Running in debug mode');
  disp('Initialized variables:');
  whos;
end

% Set scansDir (project scans directory) intelligently
if exist('PROJECT', 'var') && ~isempty(getenv('PROJECT'))
  scansDir=getenv('PROJECT');
  fprintf('Using project path: %s from environment variable PROJECT\n', scansDir);
  disp('This usually indicates that we are in standalone mode');
elseif exist('PROJECT_SCANS_DIR', 'var') && ~isempty(getenv('PROJECT_SCANS_DIR'))
  scansDir=getenv('PROJECT_SCANS_DIR');
  fprintf('Using scans directory: %s from environment variable PROJECT_SCANS_DIR\n', scansDir);
  disp('This usually indicates that we are in module mode');
else
  % TODO Lots of this is hardcoded logic, this TODO is just a reminder to change this block
  % when changing EZ_DIR and other variables in the parent script
  fprintf('Beginning parent scans directory search\n');
  fprintf('This usually indicates that we are in stand-alone mode without PROJECT or PROJECT_SCANS_DIR environment variables\n');
  dirsToScan={
    fullfile(parentDir,'..', '..', 'scans'),
    fullfile(parentDir, '..', '..', 'ExpJobs'),
    fullfile('/mnt/data/scans'),
    fullfile('/mnt/data/ExpJobs'),
    fullfile(parentDir, '..', '..', 'templates', 'scans-demo')
  };
  for d=dirsToScan
    if exist(d, 'dir')
      subDirs=dir(d);
      if ~isempty(subDirs)
        fprintf('Found a non-empty parent scans directory in our list: %s\n', d);
        fprintf('Scanning inside for a project scan directory\n');
        [~, sortedIndices]=sort(datenum({dirs.date}), 'descend'); % sort by newest first
        sortedDirs=dirs{sortedIndices};
        scansDir=sortedDirs{1};
        fprintf('Selected newest project scans directory: %s\n', scansDir);
      end
    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

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));








% 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 
  [openExpfile,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.DM=;
    Exp(i).cTraceIndx(1)=1;
  end

  
  Exp(1).Dexp(1).DM=DM;
  Exp(2).Dexp(1).DM=DM;
  Exp(3).Dexp(1).DM=DM;
  Exp(1).Dexp(1).MP=MP;
  Exp(2).Dexp(1).MP=MP;
  Exp(3).Dexp(1).MP=MP;
  Exp(1).Dexp(1).scan=scan;
  Exp(2).Dexp(1).scan=scan;
  Exp(3).Dexp(1).scan=scan;

  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'))
  Exp(1).Dexp(1).FexpScanSpots=FexpScanSpots;
  Exp(2).Dexp(1).FexpScanSpots=FexpScanSpots;
  Exp(3).Dexp(1).FexpScanSpots=FexpScanSpots;
  Exp(1).Dexp(1).FexpScanBMtp=FexpScanBMtp;
  Exp(2).Dexp(1).FexpScanBMtp=FexpScanBMtp;
  Exp(3).Dexp(1).FexpScanBMtp=FexpScanBMtp;
  Exp(1).Dexp(1).anlZoneRefs=anlZoneRefs;
  Exp(2).Dexp(1).anlZoneRefs=anlZoneRefs;
  Exp(3).Dexp(1).anlZoneRefs=anlZoneRefs;
  catch
  end

  Exp(1).traceN=0; Exp(2).traceN=0; Exp(3).traceN=0;  %ZoneRelated

  Exp(1).hOL =[]; Exp(1).hOLb=[];
  Exp(1).hOLname = {}; Exp(1).hOLexpNm={}; Exp(1).hOLresDir={}
  Exp(1).hOLplateNum=[];
  Exp(1).hOLresDir= {};
  Exp(1).RFmd1indx=[];
  Exp(1).RFmd1pltN=[];
  Exp(1).RFmd2indx=[];
  Exp(1).RFmd2pltN=[];

  Exp(2).hOL =[]; Exp(2).hOLb=[];
  Exp(2).hOLname = {}; Exp(2).hOLexpNm={}; Exp(2).hOLresDir={};
  Exp(2).hOLplateNum=[];
  Exp(2).hOLresDir= {};
  Exp(2).RFmd1indx=[];
  Exp(2).RFmd1pltN=[];
  Exp(2).RFmd2indx=[];
  Exp(2).RFmd2pltN=[];

  Exp(3).hOL =[]; Exp(3).hOLb=[];
  Exp(3).hOLname = {}; Exp(3).hOLexpNm={}; Exp(3).hOLresDir={};
  Exp(3).hOLplateNum=[];
  Exp(3).hOLresDir= {};
  Exp(3).RFmd1indx=[];
  Exp(3).RFmd1pltN=[];
  Exp(3).RFmd2indx=[];
  Exp(3).RFmd2pltN=[];

  %sefaults 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  %nested try-catch-end from ->ExpOutmat= fullfile(scansDir,openExpfile);

  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 %end associated with for ind384=1:384
      mp 
  end  %end associated with for mp=1:length(Exp(expN).Dexp(1).MP)
  %*****************************************************
    %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   %try ~ln219
    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
          catchissue='Ln328'
        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
      error='EZvInit after Ln278'
  end %try ~ln219

  end   %for d=0:DMnum
  end  % if exist('RF1scanN','var')
  %*************************************************************************************
      
  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
        catchissue='Ln402'
        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
          catchissue='Ln408'
          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);
      
      %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   %for d=0:DMnum
  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  %if exist('RF2scanN','var')

  %*************************************************************************************************
  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  %*************************************************************************************************
  %***********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  %~isempty(NZrefIndxP) && length(medianIndxDisp) > 3   ln584
  catch   %try ln565
    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 %try ~ln565

    end   %for d=0:DMnum 
    end    %for mm=1:length(dMPs)

  %****************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  %if ~isempty(NZrfIndxG(:,d)) && length(medianIndxD) > (.15*size(drf,1))
  end  %for d=1:DMnum

  end  % if exist('drf','var')
  %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'}; {' '}]);
          
          %[openExpfile,scansDir]
          if isempty(strfind(openExpfile,'.mat'))
              
              cd(scansDir)
              cd ..
              ExpPath=pwd;
              cd(w)
              ExpOutImFile= fullfile(scansDir,openExpfile);
              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

  %************************************************************************
  %Added 17-1023 For User Addition of Gene Composites to ListBox
  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 
  %------Adapt for AppDesigner 230821-----------
              global ghandles
              ghandles= handles;
              %global Exp(4)
              ghandles.guiFig= gcf;
              Exp(4).guiFig=gcf;