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

%EZusrSelRef

% User Select Reference Diaglog Box
try
  if n==1 && ~exist('RF1scanN','var') && ~exist('RF2scanN','var')  %change || &&
   %{
   prompt={'Enter Masterplate Number(s) of Your Reference GeneName spots:',...
              'Enter GeneName of Your Reference:'};
    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);
    %}
    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={'None','Specifics Term'};
    answer=inputdlg(prompt,dlg_title,num_lines,def);
    rfGenestr=cell2mat(answer(1));
    rfSpec=cell2mat(answer(2));
  end

  %try
  for mp=1:length(Exp(expN).Dexp(DexpN).MP)  
    for ind384=1:384   
      spN=spN+1;
    end
  %catch
  %end  %try   for user selected Reference routine
  end

  % Disperse Reference Plates
  Exp(expN).Dexp(DexpN).RFmdPindx=[];
  Exp(expN).Dexp(DexpN).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:MPnum
        nonZrfIndx.mp{mm,:}=drfPindx((find(drfPindx(:,mm))),mm);
    end
    
    %}
    % nzValsG=zeros(DMnum,size(drf,1));
    % nzValsAcc=zeros(DMnum,384);
    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(DexpN).scan(rf1scNdisp).plate(1).CFout(drf(chgIndx(cI):chgIndx(cI+1)),5));
          % vv=Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
          vv(chgIndx(mm):(chgIndx(mm+1)-1),d)=Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
          nonZeroValsP=nonzeros(Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5));
          std1Disp=std(nonZeroValsP);
          mean1Disp=mean(nonZeroValsP);
          minDisp=min(nonZeroValsP);
          maxDisp=max(nonZeroValsP);
          drfVals=Exp(expN).Dexp(DexpN).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
          %nzValsAcc(mm).DM(d,:)=nonZeroValsP;
          %MEDIAN Determination for PLATES with Dispersed RFs
          %NZrefIndxP=NZrefIndxP %find(Exp(expN).Dexp(DexpN).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(DexpN).scan(rf1scNdisp).plate(1).CFout(medianIndxDisp,5);
            %medValList1Disp{d}=medValLstDisp;
            mval1Disp=median(medValLstDisp);  %mval1=median(Exp(expN).Dexp(DexpN).scan(RF1mps).plate(1).CFout(1:384,5));  %CFout(1:383,5));
            nonZeroMedPosIndx=find(mval1Disp==nonZeroValsP);  %(Exp(expN).Dexp(DexpN).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(DexpN).RFmdPLB(d,dMPs(mm))=strcat(aa(lstindx,1),aa(lstindx,2));
            Exp(expN).Dexp(DexpN).RFmdPindx(d,dMPs(mm))=RFmd1posD;
            Exp(expN).Dexp(DexpN).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(DexpN).RFmdPscanN(d,dMPs(mm))=rf1scNdisp;
            Exp(expN).Dexp(DexpN).RFmedianP(d,dMPs(mm))=mval1Disp;
            Exp(expN).Dexp(DexpN).stdP(d,dMPs(mm))=std1Disp;
            Exp(expN).Dexp(DexpN).meanP(d,dMPs(mm))=mean1Disp; 
            Exp(expN).Dexp(DexpN).minP(d,dMPs(mm))=minDisp;
            Exp(expN).Dexp(DexpN).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(DexpN).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5))==0),1,'first');
            firstZeroD=drfPindx((firstZeroDindx),dMPs(mm));
            Exp(expN).Dexp(DexpN).RFmdPindx(d,dMPs(mm))=firstZeroD; 
            Exp(expN).Dexp(DexpN).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(DexpN).RFmdPpltN(d,dMPs(mm))=dMPs(mm);
            Exp(expN).Dexp(DexpN).RFmdPindx(d,dMPs(mm))=firstZeroPindx;
          catch
            Exp(expN).Dexp(DexpN).RFmdPpltN(d,dMPs(mm))=dMPs(mm);
            Exp(expN).Dexp(DexpN).RFmdPindx(d,dMPs(mm))=384; %if crapout,Then use spot384 as default to keep going  
          end
          try
            Exp(expN).Dexp(DexpN).RFmdPpltN=dMPs(mm);  
          catch
            Exp(expN).Dexp(DexpN).RFmdPpltN=1;  %This might keep from breaking BUT ??? 
          end
        end 
      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
      medianIndxG=[];
      NZrfIndxG=[];
      minG=min(nonzeros(vv(:,d)));
      maxG=max(nonzeros(vv(:,d)));
      RFmeanG=mean(nonzeros(vv(:,d)));
      RFstdG=std(nonzeros(vv(:,d)));
      NZrfIndxG=find(nonzeros(vv(:,d)));

      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))};

        Exp(expN).Dexp(DexpN).RFmdGLB(d)=strcat(aa(lstindx,1),aa(lstindx,2));
        Exp(expN).Dexp(DexpN).RFmdGindx(d)=nzPosIndxDG;
        Exp(expN).Dexp(DexpN).RFmdGpltN(d)=RFmdDGloc(d,1);  
        Exp(expN).Dexp(DexpN).RFmdGscanN(d)=uu(nzPosIndxDG,4);
        Exp(expN).Dexp(DexpN).RFmedianG(d)=mvalsDG;
        Exp(expN).Dexp(DexpN).RFminG(d)=minG;
        Exp(expN).Dexp(DexpN).RFmaxG(d)=maxG;
        Exp(expN).Dexp(DexpN).RFstdG(d)=RFstdG;
        Exp(expN).Dexp(DexpN).RFmeanG(d)=RFmeanG; 
      end
    end  
  end
catch
  msg='Failed attempt to apply User Selected Reference'
end