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

global Expaa
global Expbb
global expType
global scansDir
global zonePB

w=pwd;

% Single Exp or Chronological Study
% Construct a questdlg with three options
Exp(expN).expLoadCnt=0;
% Initiation for composite plotting cPlots
Exp(expN).cTraceN=1;
Exp(expN).cTraceIndx=1;
Exp(expN).CompositPlot=0;

choice='Cancel';
expType=0;
choice=questdlg('Choose Single Exp, Chronological Study OR Multi Exp', ...
  'Experiment Type Menu', ...
  'Single Exp','Chronological Study','Multi Exp','Single Exp');

% Handle response
switch choice
  case 'Single Exp'
    disp([choice 'Single Exp Selected'])
    expType=1;
  case 'Chronological Study'
    disp([choice 'Chronological Study Selected'])
    expType=2;
  case 'Multi Exp'
    disp([choice 'Multi Exp Selected'])
    expType=3;
  case 'Cancel'
    disp('Cancel Load Exp')
    expType=0
end

fprintf('expType=%d\n',expType);
if expType==0, return; end
zonePB=expN;

% Pre Load setup incase failure to Load occurs
% updated 230818 to migrate to AppDesigner
if expN==1
  set(handles.zonePB1,'value',1);
  set(handles.zonePB2,'value',0);
  set(handles.zonePB3,'value',0);
  set(handles.zonePB1,'BackgroundColor',[1.0 0.6 0.6]);
  set(handles.zonePB2,'BackgroundColor',[1.0 1.0 1.0]);
  set(handles.zonePB3,'BackgroundColor',[1.0 1.0 1.0]);
end

if expN==2
  set(handles.zonePB2,'value',1);
  set(handles.zonePB1,'value',0);
  set(handles.zonePB3,'value',0);
  set(handles.zonePB2,'BackgroundColor',[1.0 0.6 0.6]);
  set(handles.zonePB1,'BackgroundColor',[1.0 1.0 1.0]);
  set(handles.zonePB3,'BackgroundColor',[1.0 1.0 1.0]);
end

if expN==3
  set(handles.zonePB3,'value',1);
  set(handles.zonePB1,'value',0);
  set(handles.zonePB2,'value',0);
  set(handles.zonePB3,'BackgroundColor',[1.0 0.6 0.6]);
  set(handles.zonePB1,'BackgroundColor',[1.0 1.0 1.0]);
  set(handles.zonePB2,'BackgroundColor',[1.0 1.0 1.0]);
end

Exp(expN).htmapRFanswer={'G','L'};  %ZoneData

if expType==1
  Exp(expN).DexpType='single';

  % 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(expN).Dexp(1).MP(mx).genename{1}(384)))      
      MPnum=mx;
    catch
      break
    end
  end

  datacursormode off;
  
  % Return without execution if user cancels or doesn't select a .mat file
  try 
    if matFile==0 || scansDir==0
      return
    end
  catch
  end

  if expN==1 || expN==2 || expN==3
    orfLstSel=get(handles.GeneOrfTog,'value')
  end

  Exp(expN).Dexp(1).srtGnLst={('CheckMP/MPDMfile')};
  Exp(expN).Dexp(1).srtOrfLst={('CheckMP/MPDMfile')};
  set(handles.listboxGnOrf,'value',1)  %Fix accomodation for bug in App Designer .. .wlapp converter 230906
  set(handles.listboxGnOrf,'string',cellstr([{'Failed To Load'}; {' '}]));
  load(matFile);
  cd(scansDir)
  cd ..;
  resDir=pwd;
  Exp(expN).Dexp(1).resDir=resDir;
  cd ..;
  try   % this try-catch is to go up one more dir if the images aren't found (from /OtherResults)
    test4imageDir=imread(fullfile(pwd,'1','1.bmp'));
    ExpPath=pwd;
    Exp(expN).Dexp(1).ExpFoldr=ExpPath;
  catch
    try
      cd ..
      test4imageDir=imread(fullfile(pwd,'1','1.bmp'));
      ExpPath=pwd;
      Exp(expN).Dexp(1).ExpFoldr=ExpPath;
    catch
      cd(w)
    end
  end
  cd(w)

  % Experiment Loads
  % load (fullfile(ExpFoldr,'MasterPlateFiles','MPDMmat.mat')) 
  load(fullfile(Exp(expN).Dexp(1).ExpFoldr,'MasterPlateFiles','MPDMmat.mat')) 
  load(fullfile(resDir,'Fotos','Coordinates')) 
  load(fullfile(resDir,'Fotos','anlZones'))
  load(fullfile(resDir,'Fotos','BGatTpts'))
  load(fullfile(resDir,'PTmats','NImParameters'))
  %Backup for cond. sothat failure to load is recovered back prev. ExpJob data 

  Exp(expN).Dexp(1).temp.DM=DM;
  Exp(expN).Dexp(1).temp.MP=MP;
  Exp(expN).Dexp(1).temp.scan=scan;
  Exp(expN).Dexp(1).temp.FexpScanSpots=FexpScanSpots;
  Exp(expN).Dexp(1).temp.FexpScanBMtp=FexpScanBMtp;
  Exp(expN).Dexp(1).temp.anlZoneRefs=anlZoneRefs;
  Exp(expN).Dexp(1).temp.ImParMat=ImParMat;

  Exp(expN).Dexp(1).DM=Exp(expN).Dexp(1).temp.DM;
  Exp(expN).Dexp(1).MP=Exp(expN).Dexp(1).temp.MP;
  Exp(expN).Dexp(1).scan=Exp(expN).Dexp(1).temp.scan;
  Exp(expN).Dexp(1).FexpScanSpots=Exp(expN).Dexp(1).temp.FexpScanSpots;
  Exp(expN).Dexp(1).FexpScanBMtp=Exp(expN).Dexp(1).temp.FexpScanBMtp;
  Exp(expN).Dexp(1).anlZoneRefs=Exp(expN).Dexp(1).temp.anlZoneRefs;
  Exp(expN).Dexp(1).ImParMat=Exp(expN).Dexp(1).temp.ImParMat;

  Exp(expN).DexpLength=1;
  Exp(expN).Dexp((Exp(expN).DexpLength+1):end)=[];

  % Load new ExpJob
  if expN==1,
    % Exp(1).traceN=0;
    tPtsSize=size(FexpScanBMtp{1,1},3);
    set(handles.MPsldr1,'max',length(MP));
    set(handles.DMsldr1,'max',length(DM.drug));
    set(handles.Tptsldr1,'max',tPtsSize);

    % MPnum=length(Exp(expN).Dexp(1).MP);
    set(handles.MPsldr1,'min',1)  %,'max',MPnum+.1)
    DMnum=length(Exp(expN).Dexp(1).DM.drug);
    set(handles.DMsldr1,'min',1,'max',DMnum)  
    tPtsSize=size(Exp(expN).Dexp(1).FexpScanBMtp{1,1},(3));
    set(handles.Tptsldr1,'min',1,'max',tPtsSize)

    set(handles.MPsldr1,'value',1)
    set(handles.DMsldr1,'value',1)
    set(handles.Tptsldr1,'value',1)
    set(handles.MPed1,'string','1')
    set(handles.DMed1,'string','1')
    set(handles.Tpted1,'string','1')
    set(handles.MPsldr1,'SliderStep',[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.DN1,'value',1)
    set(handles.DN1,'string',1)
    end
    if expN==2,
    %Exp(2).traceN=0;
    tPtsSize=size(FexpScanBMtp{1,1},3);
    set(handles.MPsldr2,'max',length(MP));
    set(handles.DMsldr2,'max',length(DM.drug));
    set(handles.Tptsldr2,'max',tPtsSize);
    %MPnum=length(Exp(expN).Dexp(1).MP);
    set(handles.MPsldr2,'min',1)  %,'max',MPnum)
    DMnum=length(Exp(expN).Dexp(1).DM.drug);
    set(handles.DMsldr2,'min',1,'max',DMnum)  
    tPtsSize=size(Exp(expN).Dexp(1).FexpScanBMtp{1,1},(3));
    set(handles.Tptsldr2,'min',1,'max',tPtsSize)

    set(handles.MPsldr2,'value',1)
    set(handles.DMsldr2,'value',1)
    set(handles.Tptsldr2,'value',1)
    set(handles.MPed2,'string','1')
    set(handles.DMed2,'string','1')
    set(handles.Tpted2,'string','1')
    set(handles.MPsldr2,'SliderStep',[1/length(MP) 1/length(MP)]);
    set(handles.DMsldr2,'SliderStep',[1/length(DM.drug) 1/length(DM.drug)]);
    set(handles.Tptsldr2,'SliderStep',[1/tPtsSize 1/tPtsSize]);

    set(handles.DN2,'value',1)
    set(handles.DN2,'string',1)
  end

  if expN==3,
    % Exp(3).traceN=0;
    tPtsSize=size(FexpScanBMtp{1,1},3);
    set(handles.MPsldr3,'max',length(MP));
    set(handles.DMsldr3,'max',length(DM.drug));
    set(handles.Tptsldr3,'max',tPtsSize);
    % MPnum=length(Exp(expN).Dexp(1).MP);
    set(handles.MPsldr3,'min',1)  %,'max',MPnum)
    DMnum=length(Exp(expN).Dexp(1).DM.drug);
    set(handles.DMsldr3,'min',1,'max',DMnum)  
    tPtsSize=size(Exp(expN).Dexp(1).FexpScanBMtp{1,1},(3));
    set(handles.Tptsldr3,'min',1,'max',tPtsSize)
    set(handles.MPsldr3,'value',1)
    set(handles.DMsldr3,'value',1)
    set(handles.Tptsldr3,'value',1)
    set(handles.MPed3,'string','1')
    set(handles.DMed3,'string','1')
    set(handles.Tpted3,'string','1')
    set(handles.MPsldr3,'SliderStep',[1/length(MP) 1/length(MP)]);
    set(handles.DMsldr3,'SliderStep',[1/length(DM.drug) 1/length(DM.drug)]);
    set(handles.Tptsldr3,'SliderStep',[1/tPtsSize 1/tPtsSize]);

    set(handles.DN3,'value',1)
    set(handles.DN3,'string',1)
  end

  if expN==1,
    set(handles.GeneOrfLoc1,'string',{''});
    set(handles.graphStrLoc1,'string',{''});
    cla(handles.Paxes1);
  end 
  if expN==2
    set(handles.GeneOrfLoc2,'string',{''});
    set(handles.graphStrLoc2,'string',{''});
    cla(handles.Paxes2)
  end
  if expN==3
    set(handles.GeneOrfLoc3,'string',{''});
    set(handles.graphStrLoc3,'string',{''})
    cla(handles.Paxes3)
  end
  Exp(expN).Dexp(1).srtGnLst={('CheckMP/MPDMfile')};
  Exp(expN).Dexp(1).srtOrfLst={('CheckMP/MPDMfile')};
  set(handles.listboxGnOrf,'string',Exp(expN).Dexp(1).srtGnLst)
  set(handles.listboxGnOrf,'string',Exp(expN).Dexp(1).srtOrfLst)

  EZVimDisplay

  % Capture Exp Name
  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)-2) +1;
    endPos=(slashPos(length(slashPos)) -1);
    expStrn=xp(startPos:end);
    if expN==1,set(handles.expName1,'string',expStrn);end
    if expN==2,set(handles.expName2,'string',expStrn);end
    if expN==3,set(handles.expName3,'string',expStrn);end
  catch
    catchissue='Ln198'
  end % nested try-catch-end

  % Compile GeneList and OrfList
  % Sort and add the medians of Ref Plates if RF1,RF2 exist
  % Added 17-1023 For User Addition of Gene Composites to ListBox 
  Expaa{expN,1}=[];
  Expbb{expN,1}=[];
  lstindx=0;
  lstindxOrf=0;
  spN=0;
  rfcnt=0;
  dRF1indx=0;
  RF1mp=[];
  RF2mp=[];
  for mp=1:MPnum % length(Exp(expN).Dexp(1).MP) 
   
    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_'}; 
        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).genename{1}(ind384)),'RF1'))... %&& mp==1)...
        && (~strcmpi((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)),'RF2'))... %||~strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),'RF2'))... %&& mp==length(Exp(expN).Dexp(1).MP))...
        && iscellstr((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)))     
          lstindxOrf=lstindxOrf+1;
          Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)=strrep((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)),':',' ');
          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
          %Exp(expN).Dexp(1).mutSpotIndx(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'))...  %&& ~RF1fullPlate)...
        && (~strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),'RF2'))...  %&& ~RF2fullPlate)...
        && iscellstr((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)))          
          lstindx=lstindx+1;
          Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)=strrep((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),':',' ');
          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;
        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')))
          rfcnt=rfcnt+1;
          RFs(spN:spN+383)=spN:spN+383;
          RF1mp=mp
          RF1scanN=(mp*DMnum)-(DMnum-1)     
        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;
          RF2mp=mp              
          RF2scanN=(mp*DMnum)-(DMnum-1)    
        % Dispersed Reference capture and find Medians                
        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    
      catch
        error='EZexpSel lineAfter 236 EZexpSel.m'   
        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(expN).Dexp(1).mutSpotIndx.wRFs=union(RFs, mutorfs);
    catch
      msg='No RFs Found in Exp! wRFs'
      Exp(expN).Dexp(1).mutSpotIndx.wRFs=mutorfs;
  end
  try
    Exp(expN).Dexp(1).mutSpotIndx.woRFs=setdiff(mutorfs,RFs);
  catch
    Exp(expN).Dexp(1).mutSpotIndx.woRFs=mutorfs;
    msg='No RFs Found in Exp! woRFs'
  end

  Exp(expN).Dexp(1).RFmd1indx=[];
  Exp(expN).Dexp(1).RFmd1LB={[]};
  Exp(expN).Dexp(1).RFmd1pltN={}; 
  Exp(expN).Dexp(1).RFmd1val=[];
  Exp(expN).Dexp(1).mean1=[]; 
  Exp(expN).Dexp(1).std1=[];
  Exp(expN).Dexp(1).min1=[];
  Exp(expN).Dexp(1).max1=[];
  Exp(expN).Dexp(1).RFcmpK=[]; %For Ref Composite 17_1009 
  Exp(expN).Dexp(1).RFcmpr=[]; %For Ref Composite 17_1009 
  Exp(expN).Dexp(1).RFcmpL=[]; %For Ref Composite 17_1009 

  Exp(expN).Dexp(1).RFmd2indx=[];
  Exp(expN).Dexp(1).RFmd2LB={[]};
  Exp(expN).Dexp(1).RFmd2pltN={};
  Exp(expN).Dexp(1).RFmd2val=[];
  Exp(expN).Dexp(1).mean2=[]; 
  Exp(expN).Dexp(1).std2=[]; 
  Exp(expN).Dexp(1).min2=[]; 
  Exp(expN).Dexp(1).max2=[];

  Exp(expN).Dexp(1).RFmean=[];
  Exp(expN).Dexp(1).RFstd=[];
  Exp(expN).Dexp(1).RFmin=[];
  Exp(expN).Dexp(1).RFmax=[];

  Exp(expN).Dexp(1).RFmdPLvals=[];  %17_1201 TrendOL
  Exp(expN).Dexp(1).RFmdPLB={[]};
  Exp(expN).Dexp(1).RFmdPindx=[];
  Exp(expN).Dexp(1).RFmdPpltN=[];
  Exp(expN).Dexp(1).RFmdPscanN=[];
  Exp(expN).Dexp(1).RFmedianP=[];
  Exp(expN).Dexp(1).stdP=[];
  Exp(expN).Dexp(1).meanP=[];
  Exp(expN).Dexp(1).minP=[];
  Exp(expN).Dexp(1).maxP=[];
  Exp(expN).Dexp(1).RFcmpPK=[]; %For Ref Composite 17_1009 
  Exp(expN).Dexp(1).RFcmpPr=[]; %For Ref Composite 17_1009 
  Exp(expN).Dexp(1).RFcmpPL=[]; %For Ref Composite 17_1009 

  Exp(expN).Dexp(1).RFmdGLB={[]};
  Exp(expN).Dexp(1).RFmdGindx=[];
  Exp(expN).Dexp(1).RFmdGpltN=[];
  Exp(expN).Dexp(1).RFmdGscanN=[];
  Exp(expN).Dexp(1).RFmedianG=[];
  Exp(expN).Dexp(1).RFmeanG=[];
  Exp(expN).Dexp(1).RFstdG=[];
  Exp(expN).Dexp(1).RFminG=[];
  Exp(expN).Dexp(1).RFmaxG=[];
  Exp(expN).Dexp(1).RFcmpGK=[]; %For Ref Composite 17_1009 
  Exp(expN).Dexp(1).RFcmpGr=[]; %For Ref Composite 17_1009 
  Exp(expN).Dexp(1).RFcmpGL=[]; %For Ref Composite 17_1009 

  %{
  Exp(expN).Dexp(1).RFmeanGK=[]; %For Ref Composite 17_1009
  Exp(expN).Dexp(1).RFstdGK=[]; %For Ref Composite 17_1009
  Exp(expN).Dexp(1).RFminGK=[]; %For Ref Composite 17_1009
  Exp(expN).Dexp(1).RFmaxGK=[]; %For Ref Composite 17_1009
  Exp(expN).Dexp(1).RFmeanGr=[]; %For Ref Composite 17_1009
  Exp(expN).Dexp(1).RFstdGr=[]; %For Ref Composite 17_1009
  Exp(expN).Dexp(1).RFminGr=[]; %For Ref Composite 17_1009
  Exp(expN).Dexp(1).RFmaxGr=[]; %For Ref Composite 17_1009
  %}



  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);  %mval1=median(Exp(expN).Dexp(1).scan(RF1mps).plate(1).CFout(1:384,5));  %CFout(1:383,5));
          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),')')};  %{'RF1md'};
          aa(lstindx,2)={strcat(':',num2str(RF1mp),':',num2str(RFmd1loc(1)),':',num2str(RFmd1loc(2)))};  %,'std_',num2str(std1))};
          bb(lstindxOrf,1)={strcat('RF1md(',num2str(d+1),')')};  %{'RF1md'};
          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(expN).Dexp(1).RFmd1LB(d+1)=strcat(aa(lstindx,1),aa(lstindx,2));
          Exp(expN).Dexp(1).RFmd1indx(d+1)=RFmd1pos;
          Exp(expN).Dexp(1).RFmd1pltN=RF1mp;
          Exp(expN).Dexp(1).RFmd1val(d+1)=mval1;
          Exp(expN).Dexp(1).RFmd1Lvals=medValLst;  %17_1201 TrendOL
          Exp(expN).Dexp(1).mean1(d+1)=mean1; 
          Exp(expN).Dexp(1).std1(d+1)=std1;
          Exp(expN).Dexp(1).min1(d+1)=min1;
          Exp(expN).Dexp(1).max1(d+1)=max1;
          Exp(expN).Dexp(1).RFcmpL(1).dm(d+1).Lvals=medValLst;  %17_1201 TrendOL
          Exp(expN).Dexp(1).RFcmpL(1).dm(d+1).med=median(medValLst); %For Ref Composite 17_1009
          Exp(expN).Dexp(1).RFcmpL(1).dm(d+1).mean=mean(medValLst); %For Ref Composite 17_1009 
          Exp(expN).Dexp(1).RFcmpL(1).dm(d+1).std=std(medValLst); %For Ref Composite 17_1009 
          Exp(expN).Dexp(1).RFcmpL(1).dm(d+1).min=min(medValLst); %For Ref Composite 17_1009 
          Exp(expN).Dexp(1).RFcmpL(1).dm(d+1).max=max(medValLst); %For Ref Composite 17_1009
          Exp(expN).Dexp(1).RFcmpK(1).dm(d+1).Kvals=kValLst;  %17_1201 TrendOL
          Exp(expN).Dexp(1).RFcmpK(1).dm(d+1).med=median(kValLst); %For Ref Composite 17_1009
          Exp(expN).Dexp(1).RFcmpK(1).dm(d+1).mean=mean(kValLst); %For Ref Composite 17_1009 
          Exp(expN).Dexp(1).RFcmpK(1).dm(d+1).std=std(kValLst); %For Ref Composite 17_1009 
          Exp(expN).Dexp(1).RFcmpK(1).dm(d+1).min=min(kValLst); %For Ref Composite 17_1009 
          Exp(expN).Dexp(1).RFcmpK(1).dm(d+1).max=max(kValLst); %For Ref Composite 17_1009
          Exp(expN).Dexp(1).RFcmpr(1).dm(d+1).rvals=rValLst;  %17_1201 TrendOL
          Exp(expN).Dexp(1).RFcmpr(1).dm(d+1).med=median(rValLst); %For Ref Composite 17_1009
          Exp(expN).Dexp(1).RFcmpr(1).dm(d+1).mean=mean(rValLst); %For Ref Composite 17_1009 
          Exp(expN).Dexp(1).RFcmpr(1).dm(d+1).std=std(rValLst); %For Ref Composite 17_1009 
          Exp(expN).Dexp(1).RFcmpr(1).dm(d+1).min=min(rValLst); %For Ref Composite 17_1009 
          Exp(expN).Dexp(1).RFcmpr(1).dm(d+1).max=max(rValLst); %For Ref Composite 17_1009 
        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
          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(expN).Dexp(1).RFmd1indx(d+1)=firstZero; 
          Exp(expN).Dexp(1).RFmd1pltN=RF1mp;  
          try 
            medValList1{d+1}=Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(medianIndx,5); nonZeroCnt; 
          catch
            catcherror='Ln356'
          end
        end  % ~isempty(nonZeroIndx) && length(medianIndx) > (.15*384)
      catch
        medianCalcTryFailed1='Failed! Failed! Ln362 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(expN).Dexp(1).RFmd1indx(d+1)=firstZero;
        catch
          catchissue='Ln366'
          Exp(expN).Dexp(1).RFmd1indx(d+1)=384; % if crapout,Then use spot384 as default to keep going  
        end
        try
          Exp(expN).Dexp(1).RFmd1pltN=RF1mp;  
        catch
          catchissue='Ln372'
          Exp(expN).Dexp(1).RFmd1pltN=1; 
        end
      end
    end
  end

  % Calc RF2 median if a full plate of RF2s exist
  Exp(expN).Dexp(1).RFmd2indx=[];
  Exp(expN).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);  %mval2=median(Exp(expN).Dexp(1).scan(RF2mps).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(expN).Dexp(1).RFmd2LB(d+1)=strcat(aa(lstindx,1),aa(lstindx,2));
          Exp(expN).Dexp(1).RFmd2indx(d+1)=RFmd2pos;
          Exp(expN).Dexp(1).RFmd2pltN=RF2mp;
          Exp(expN).Dexp(1).RFmd2val(d+1)=mval2;
          Exp(expN).Dexp(1).RFmd1Lvals=medValLst2;  %17_1201 TrendOL
          Exp(expN).Dexp(1).mean2(d+1)=mean2;
          Exp(expN).Dexp(1).std2(d+1)=std2;
          Exp(expN).Dexp(1).min2(d+1)=min2;
          Exp(expN).Dexp(1).max2(d+1)=max2;
          Exp(expN).Dexp(1).RFcmpL(2).dm(d+1).Lvals=medValLst2;  %17_1201 TrendOL
          Exp(expN).Dexp(1).RFcmpL(2).dm(d+1).med=median(medValLst2); %For Ref Composite 17_1009 
          Exp(expN).Dexp(1).RFcmpL(2).dm(d+1).mean=mean(medValLst2); %For Ref Composite 17_1009 
          Exp(expN).Dexp(1).RFcmpL(2).dm(d+1).std=std(medValLst2); %For Ref Composite 17_1009 
          Exp(expN).Dexp(1).RFcmpL(2).dm(d+1).min=min(medValLst2); %For Ref Composite 17_1009 
          Exp(expN).Dexp(1).RFcmpL(2).dm(d+1).max=max(medValLst2); %For Ref Composite 17_1009
          Exp(expN).Dexp(1).RFcmpK(2).dm(d+1).Kvals=kValLst2;  %17_1201 TrendOL
          Exp(expN).Dexp(1).RFcmpK(2).dm(d+1).med=median(kValLst2); %For Ref Composite 17_1009 
          Exp(expN).Dexp(1).RFcmpK(2).dm(d+1).mean=mean(kValLst2); %For Ref Composite 17_1009 
          Exp(expN).Dexp(1).RFcmpK(2).dm(d+1).std=std(kValLst2); %For Ref Composite 17_1009 
          Exp(expN).Dexp(1).RFcmpK(2).dm(d+1).min=min(kValLst2); %For Ref Composite 17_1009 
          Exp(expN).Dexp(1).RFcmpK(2).dm(d+1).max=max(kValLst2); %For Ref Composite 17_1009
          Exp(expN).Dexp(1).RFcmpr(2).dm(d+1).rvals=rValLst2;  %17_1201 TrendOL
          Exp(expN).Dexp(1).RFcmpr(2).dm(d+1).med=median(rValLst2); %For Ref Composite 17_1009 
          Exp(expN).Dexp(1).RFcmpr(2).dm(d+1).mean=mean(rValLst2); %For Ref Composite 17_1009 
          Exp(expN).Dexp(1).RFcmpr(2).dm(d+1).std=std(rValLst2); %For Ref Composite 17_1009 
          Exp(expN).Dexp(1).RFcmpr(2).dm(d+1).min=min(rValLst2); %For Ref Composite 17_1009 
          Exp(expN).Dexp(1).RFcmpr(2).dm(d+1).max=max(rValLst); %For Ref Composite 17_1009 
        else
          % Pick the first spot with zeros
          % Use that position to satisfy and keep process OK
          medianCalcFailed2='Too 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(expN).Dexp(1).RFmd2indx(d+1)=firstZero2; 
          Exp(expN).Dexp(1).RFmd2pltN=RF2mp; 
          try medValList2{d+1}=Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(medianIndx2,5);  nonZeroCnt2; catch, catchissue='Ln431', end
        end
      catch
          medianCalcTryFailed2='Failed! Failed! Ln436 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(expN).Dexp(1).RFmd2indx(d+1)=firstZero2;
        catch
          Exp(expN).Dexp(1).RFmd2indx(d+1)=384;  %if crapout,Then use spot384 as default to keep going  
        end
        try
          Exp(expN).Dexp(1).RFmd2pltN=RF2mp; 
        catch
          catchissue='Ln448'
          Exp(expN).Dexp(1).RFmd2pltN=1;
        end
      end
      clear RFcombValList
      RFcombValList=cat(1,medValList1{d+1},medValList2{d+1});
      Exp(expN).Dexp(1).RFmean(d+1)=mean(RFcombValList);
      Exp(expN).Dexp(1).RFstd(d+1)=std(RFcombValList);
      try, Exp(expN).Dexp(1).RFmin(d+1)=min(RFcombValList);
      catch, Exp(expN).Dexp(1).RFmin(d+1)=0; end
      try, Exp(expN).Dexp(1).RFmax(d+1)=max(RFcombValList);
      catch, Exp(expN).Dexp(1).RFmax(d+1)=0; end
    end
  elseif exist('RF1scanN','var')  
    Exp(expN).Dexp(1).RFmean=Exp(expN).Dexp(1).mean1;
    Exp(expN).Dexp(1).RFstd=Exp(expN).Dexp(1).std1;
    Exp(expN).Dexp(1).RFmin=Exp(expN).Dexp(1).min1;
    Exp(expN).Dexp(1).RFmax=Exp(expN).Dexp(1).max1;
  end

  % Disperse Reference Plates
  Exp(expN).Dexp(1).RFmdPindx=[];
  Exp(expN).Dexp(1).RFmdPpltN=[];
  if exist('drf','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) % length(chgIndx)
      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));   %find(Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(drf(chgIndx(cI):chgIndx(cI+1)),5));
          %vv=Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
          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));
          std1Disp=std(nonZeroValsP);
          mean1Disp=mean(nonZeroValsP);
          minDisp=min(nonZeroValsP);
          maxDisp=max(nonZeroValsP);
          drfVals=Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);

          % MEDIAN Determination for PLATES with Dispersed RFs
          % NZrefIndxP=NZrefIndxP %find(Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5));
          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);
            % medValList1Disp{d}=medValLstDisp;
            mval1Disp=median(medValLstDisp);  % mval1=median(Exp(expN).Dexp(1).scan(RF1mps).plate(1).CFout(1:384,5));  %CFout(1:383,5));
            nonZeroMedPosIndx=find(mval1Disp==nonZeroValsP);  % (Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5)));  %(nonZeroIndxDisp,5)));   %((nonZrfIndx.mp{dMPs(mm),:}),5)));
            RFmd1posD=NZrefIndxP(nonZeroMedPosIndx);  % drfPindx((RFmd1posIndx),dMPs(mm));
            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),')')};
            aa(lstindx,2)={strcat(':',num2str(dMPs(mm)),':',num2str(RFmd1locD(1)),':',num2str(RFmd1locD(2)))};  
            bb(lstindxOrf,1)={strcat('RF1mdP(',num2str(d),')')};
            bb(lstindxOrf,2)={strcat(':',num2str(dMPs(mm)),':',num2str(RFmd1locD(1)),':',num2str(RFmd1locD(2)))};

            Exp(expN).Dexp(1).RFmdPLvals(d,dMPs(mm))=mval1Disp;  %17_1201 TrendOL
            Exp(expN).Dexp(1).RFmdPLB(d,dMPs(mm))=strcat(aa(lstindx,1),aa(lstindx,2));
            Exp(expN).Dexp(1).RFmdPindx(d,dMPs(mm))=RFmd1posD;
            Exp(expN).Dexp(1).RFmdPpltN(d,dMPs(mm))=dMPs(mm);   %This is a storage of the MasterPlate used NOT the ScanPlate?  WeMight wish to store the ScanPlateNumber also???
            Exp(expN).Dexp(1).RFmdPscanN(d,dMPs(mm))=rf1scNdisp;
            Exp(expN).Dexp(1).RFmedianP(d,dMPs(mm))=mval1Disp;
            Exp(expN).Dexp(1).stdP(d,dMPs(mm))=std1Disp;
            Exp(expN).Dexp(1).meanP(d,dMPs(mm))=mean1Disp; 
            Exp(expN).Dexp(1).minP(d,dMPs(mm))=minDisp;
            Exp(expN).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='Ln619'
            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
      medianIndxG=[];
      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! 
      if isempty(RFmeanG)
        nonZeroCntD=0; % medianIndxDisp=RFmeanG(d); 
      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(expN).Dexp(1).RFmdGLvals=vv(medianIndxD,d); %17_1201 TrendOL
        Exp(expN).Dexp(1).RFmdGLB(d)=strcat(aa(lstindx,1),aa(lstindx,2));
        Exp(expN).Dexp(1).RFmdGindx(d)=nzPosIndxDG;
        Exp(expN).Dexp(1).RFmdGpltN(d)=RFmdDGloc(d,1);  
        Exp(expN).Dexp(1).RFmdGscanN(d)=uu(nzPosIndxDG,4);
        Exp(expN).Dexp(1).RFmedianG(d)=mvalsDG;
        Exp(expN).Dexp(1).RFminG(d)=minG;
        Exp(expN).Dexp(1).RFmaxG(d)=maxG;
        Exp(expN).Dexp(1).RFstdG(d)=RFstdG;
        Exp(expN).Dexp(1).RFmeanG(d)=RFmeanG; 
        Exp(expN).Dexp(1).RFcmpGL.dm(d).Lvals=vv(medianIndxD,d); %17_1201 TrendOL
        Exp(expN).Dexp(1).RFcmpGL.dm(d).med=median(vv(medianIndxD,d)); %For Ref Composite 17_1009 
        Exp(expN).Dexp(1).RFcmpGL.dm(d).mean=mean(vv(medianIndxD,d)); %For Ref Composite 17_1009 
        Exp(expN).Dexp(1).RFcmpGL.dm(d).std=std(vv(medianIndxD,d)); %For Ref Composite 17_1009 
        Exp(expN).Dexp(1).RFcmpGL.dm(d).min=min(vv(medianIndxD,d)); %For Ref Composite 17_1009 
        Exp(expN).Dexp(1).RFcmpGL.dm(d).max=max(vv(medianIndxD,d)); %For Ref Composite 17_1009
        Exp(expN).Dexp(1).RFcmpGK.dm(d).Kvals=vvK(medianIndxD,d); %17_1201 TrendOL
        Exp(expN).Dexp(1).RFcmpGK.dm(d).med=median(vvK(medianIndxD,d)); %For Ref Composite 17_1009 
        Exp(expN).Dexp(1).RFcmpGK.dm(d).mean=mean(vvK(medianIndxD,d)); %For Ref Composite 17_1009 
        Exp(expN).Dexp(1).RFcmpGK.dm(d).std=std(vvK(medianIndxD,d)); %For Ref Composite 17_1009 
        Exp(expN).Dexp(1).RFcmpGK.dm(d).min=min(vvK(medianIndxD,d)); %For Ref Composite 17_1009 
        Exp(expN).Dexp(1).RFcmpGK.dm(d).max=max(vvK(medianIndxD,d)); %For Ref Composite 17_1009
        Exp(expN).Dexp(1).RFcmpGr.dm(d).rvals=vvr(medianIndxD,d); %17_1201 TrendOL
        Exp(expN).Dexp(1).RFcmpGr.dm(d).med=median(vvr(medianIndxD,d)); %For Ref Composite 17_1009 
        Exp(expN).Dexp(1).RFcmpGr.dm(d).mean=mean(vvr(medianIndxD,d)); %For Ref Composite 17_1009 
        Exp(expN).Dexp(1).RFcmpGr.dm(d).std=std(vvr(medianIndxD,d)); %For Ref Composite 17_1009 
        Exp(expN).Dexp(1).RFcmpGr.dm(d).min=min(vvr(medianIndxD,d)); %For Ref Composite 17_1009 
        Exp(expN).Dexp(1).RFcmpGr.dm(d).max=max(vvr(medianIndxD,d)); %For Ref Composite 17_1009 
      end
    end  
  end

  for mp=1:MPnum  % length(Exp(expN).Dexp(1).MP)
    for ind384=1:384   
      spN=spN+1;
    end
  end

  gnLstRaw=strcat(aa(:,1),aa(:,2));
  Exp(expN).Dexp(1).srtGnLst=sort(gnLstRaw);
  orfLstRaw=strcat(bb(:,1),bb(:,2));
  Exp(expN).Dexp(1).srtOrfLst=sort(orfLstRaw);

  % Auto select Zone and load listboxGnOrf data
  zeroCLn=zeros(1,DMnum);
  Exp(expN).expLoadCnt=Exp(expN).expLoadCnt+1; expLdCnt=Exp(expN).expLoadCnt;
  zonePB=expN;
  if expN==1
    set(handles.zonePB1,'value',1)
    set(handles.zonePB2,'value',0)
    set(handles.zonePB3,'value',0)
    set(handles.zonePB1,'BackgroundColor',[1.0 0.6 0.6])
    set(handles.zonePB2,'BackgroundColor',[1.0 1.0 1.0])
    set(handles.zonePB3,'BackgroundColor',[1.0 1.0 1.0]) 
    orfLstSel=get(handles.GeneOrfTog,'value')
    if orfLstSel==1
      set(handles.listboxGnOrf,'string',Exp(1).Dexp(1).srtOrfLst)   
    else
      set(handles.listboxGnOrf,'string',Exp(1).Dexp(1).srtGnLst)
    end
    DNLaxes1=handles.DNLaxes1; % ZoneRelated
    Exp(1).hzeroCLn(expLdCnt)=plot(DNLaxes1,zeroCLn,1:DMnum,'y');
  end

  if expN==2
    set(handles.zonePB1,'value',0)
    set(handles.zonePB3,'value',0)
    set(handles.zonePB2,'value',1)
    set(handles.zonePB2,'BackgroundColor',[1.0 0.6 0.6])
    set(handles.zonePB1,'BackgroundColor',[1.0 1.0 1.0])
    set(handles.zonePB3,'BackgroundColor',[1.0 1.0 1.0])
    orfLstSel=get(handles.GeneOrfTog,'value');
    if orfLstSel==1
      set(handles.listboxGnOrf,'string',Exp(2).Dexp(1).srtOrfLst)   
    else
      set(handles.listboxGnOrf,'string',Exp(2).Dexp(1).srtGnLst)
    end
    DNLaxes2=handles.DNLaxes2;  % ZoneRelated
    Exp(2).hzeroCLn(expLdCnt)=plot(DNLaxes2,zeroCLn,1:DMnum,'y');
  end

  if expN==3
    set(handles.zonePB1,'value',0)
    set(handles.zonePB2,'value',0)
    set(handles.zonePB3,'value',1)
    set(handles.zonePB3,'BackgroundColor',[1.0 0.6 0.6]);
    set(handles.zonePB1,'BackgroundColor',[1.0 1.0 1.0]);
    set(handles.zonePB2,'BackgroundColor',[1.0 1.0 1.0]);
    orfLstSel=get(handles.GeneOrfTog,'value');
    if orfLstSel==1
      set(handles.listboxGnOrf,'string',Exp(3).Dexp(1).srtOrfLst)   
    else
      set(handles.listboxGnOrf,'string',Exp(3).Dexp(1).srtGnLst)
    end
    DNLaxes3=handles.DNLaxes3; % ZoneRelated
    Exp(3).hzeroCLn(expLdCnt)=plot(DNLaxes3,zeroCLn,1:DMnum,'y');
  end

  if Exp(4).interacPBsel==0  % if interaction "raw" don't show a center line
    for i=1:Exp(expN).expLoadCnt
      try 
        set(Exp(expN).hzeroCLn(i),'visible','off'); 
      catch
      end
    end
  end

  EZdiagRFsSheet

  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(expN).RFconfig=RFconfig;  % ZoneRelated

  if RFconfig~=0
    Exp(expN).Dexp(1).RFrnames=rnames;
    Exp(expN).Dexp(1).RFdata=data;
    Exp(expN).Dexp(1).resetHtmpTg=5;  % ZoneRelated    
    % HtMapTog 'string', 'Current user L/N' selection'
    Exp(expN).Dexp(1).spotIndx=[];
    if expN==1
      Exp(1).htmapPBsel=0;
      set(handles.HtMapTog1,'string','L')
      EZhtMap
    end
    if expN==2
      Exp(2).htmapPBsel=0;
      set(handles.HtMapTog2,'string','L')
      EZhtMap
    end
    if expN==3,
      Exp(3).htmapPBsel=0;
      set(handles.HtMapTog3,'string','L')
      EZhtMap
    end
    htMapTogPBfg=0;
  elseif RFconfig==0
    RFconfigMsg='No RF1 references in this Experiment Job'
    try
      EZsingleExUserRF
      % EZmultiDayGui
      % cd(w)
      % EZmultiDay
      % EZmultiExLoad
    catch
      RFconfigMsg='No RF1 or User selected references in this Experiment Job'
      Exp(expN).Dexp(1).resetHtmpTg=3; % ZoneRelated
    end       
    % Exp(expN).Dexp(1).resetHtmpTg=3;  %ZoneRelated
  end

  %{
  try msgBadGeneName, catch, end
  try
    if RFconfig==0,
      RFconfigMsg='No RF1 references in this Experiment Job'
      Exp(expN).Dexp(1).resetHtmpTg=3;  %ZoneRelated
    end
  catch
  end
  %}
elseif expType==2  %Multiple Experiment from in one Folder extraction
  Exp(expN).DexpType='chrono'; 
  % 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(expN).Dexp(1).MP(mx).genename{1}(384)))      
      MPnum=mx;
    catch
      break
    end
  end

  ww=pwd;
  try EZmultiDayGui; catch ME
  msg=ME.message, cd(ww); end
  try EZmultiDay; catch ME
  msg=ME.message, cd(ww); end
  try EZmultiExLoad; catch ME
  msg=ME.message, cd(ww); end
elseif expType==3
  Exp(expN).DexpType='multi';
  % 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(expN).Dexp(1).MP(mx).genename{1}(384)))      
      MPnum=mx;
    catch
      break
    end
  end

  ww=pwd;
  try EZmultiDayGui; catch ME
  msg=ME.message,cd(ww); end
  try EZmultiDay; catch ME
  msg=ME.message, cd(ww); end
  try EZmultiExLoad;  catch ME
  msg=ME.message, cd(ww); end
else
  disp('Cancel Load Exp')
end
        
% Deprecated Functions
%{
%Exp(expN).Dexp(1).RF1cmpK.[]; %For Ref Composite 17_1009 
%Exp(expN).Dexp(1).std1K=[]; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).min1K=[]; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).max1K=[]; %For Ref Composite 17_1009
%Exp(expN).Dexp(1)RF1cmpr=[];  %For Ref Composite 17_1009
%Exp(expN).Dexp(1).std1r=[]; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).min1r=[]; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).max1r=[]; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).RF=[]; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).std2K=[]; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).min2K=[]; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).max2K=[]; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).RF2cmpr=[]; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).std2r=[]; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).min2r=[]; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).max2r=[]; %For Ref Composite 17_1009

%kValList1{d+1}=kValLst; %For Ref Composite 17_1009
%kmin1=min(kValLst); %For Ref Composite 17_1009
%kmax1=max(kValLst); %For Ref Composite 17_1009
%kstd1=std(kValLst); %For Ref Composite 17_1009
%kmean1=mean(kValLst); %For Ref Composite 17_1009
%rValList1{d+1}=rValLst; %For Ref Composite 17_1009
%rmin1=min(rValLst); %For Ref Composite 17_1009
%rmax1=max(rValLst); %For Ref Composite 17_1009
%rstd1=std(rValLst); %For Ref Composite 17_1009
%rmean1=mean(rValLst); %For Ref Composite 17_1009
%kValList2{d+1}=kValLst2; %For Ref Composite 17_1009
%kmin2=min(kValLst2); %For Ref Composite 17_1009
%kmax2=max(kValLst2); %For Ref Composite 17_1009
%kstd2=std(kValLst2); %For Ref Composite 17_1009
%kmean2=mean(kValLst2); %For Ref Composite 17_1009  
%rValList2{d+1}=rValLst2; %For Ref Composite 17_1009
% rmin2=min(rValLst2); %For Ref Composite 17_1009
%rmax2=max(rValLst2); %For Ref Composite 17_1009
%rstd2=std(rValLst2); %For Ref Composite 17_1009
%rmean2=mean(rValLst2); %For Ref Composite 17_1009    

%User Reference Input Dialog Box used in the multiExperiment Chrono setup

prompt={'Enter GeneName to use as Reference:',...
'Enter Specifics Term if used to futher specify Reference '}       
dlg_title='User Reference Input';
num_lines=1;
def={'RF1','None'};
answer=inputdlg(prompt,dlg_title,num_lines,def);
rfGene=cell2mat(answer(1));
if ~strcmpi(rfGene,'RF1')|| ~strcmpi(rfGene,'RF2'), usrRefFg=1; end
rfSpec=answer(2); %if strcmpi(answer(2),'None'), rfSpec=''; end
rfGnSp=strcat(rfGene,rfSpec);

%First user input prototype code
if ~exist('RF1scanN','var') && ~exist('RF2scanN','var')  %change || &&
  prompt={'Enter Masterplate Number(s) of Your Reference GeneName spots:',...
            'Enter GeneName of Your Reference:'};
  dlg_title='User Reference Input';
  num_lines=1;
  def={'Ref MP(s)','USRrefGeneName'};
  answer=inputdlg(prompt,dlg_title,num_lines,def);
  rfMPstr=cell2mat(answer(1));
  rfMPcomas=strfind((cell2mat(answer(1))),',');
  n=0;
  if isempty(rfMPcomas)|| max(rfMPcomas)==length(rfMPstr)
      usrMPs=rfMPstr
  else
  for i=rfMPcomas,
      n=n+1
      usrMPs(n)=str2double(rfMPstr(i-1:i))
  if i==max(rfMPcomas)
      usrMPs(n+1)=str2double(rfMPstr(i:end))
  end 
  end
  end
  usrMPs=answer(1); 
  refGene=answer(2);

end
%}