%Quickview of Exp Images one from each folder at selected timept
function QkVexps %QkviewImages
w=pwd;
[Selfile, pathname]=uigetfile({'*.bmp';'*.tif';'*.*'},'Select timepoint file','MultiSelect','off');
cd(pathname)
flist=dir
cd ..
ExpFdr=pwd
cd ..
EstudyDir=pwd
ExpList= dir;
cd(w)
day=[];
Dpos=[];
%Determine if Exps grouped into Day folders
    
    studyNum=1;
    dayIndx=0;
    studyIndx=0;
    
    for i=1:size(ExpList,1)
        if ~isequal(ExpList(i).name,'.DS_Store')   %|| ~strfind(ExpList(i),'DS') 
        Dpos=max(strfind(ExpList(i).name,'D'));
        
        
            if ~isempty(Dpos)
                tmpExpName=ExpList(i).name;
            if isempty(day)
              if isnumeric(str2double(tmpExpName((Dpos+1):end)))
                  dayIndx=dayIndx+1;
                day(dayIndx)= str2double(tmpExpName((Dpos+1):end));
                    daytx{dayIndx}= strcat('D',(tmpExpName((Dpos+1):end)));
                studyIndx=studyIndx+1;
                dayLst(dayIndx).study{studyIndx}= tmpExpName;
              end
            elseif sum(day==(str2double(tmpExpName((Dpos+1):end))))>0 %capture the experimentNames into studyLst sets  
                studyIndx=studyIndx+1;
                dayLst(dayIndx).study{studyIndx}= tmpExpName;
                
            elseif sum(day==(str2double(tmpExpName((Dpos+1):end))))==0 %capture the daynumber as a number 
                dayIndx=dayIndx+1;   
                day(dayIndx)= str2num(tmpExpName((Dpos+1):end));  %if the daynumber is unique store in day vector
                daytx{dayIndx}= strcat('D',(tmpExpName((Dpos+1):end)));
                studyIndx=1;
                dayLst(dayIndx).study{studyIndx}= tmpExpName;
           
                
            end  %if isempty(day)
            end  %if ~isempty(Dpos)
        end   %if ~isequal(ExpList(i),'.DS_Store')
    end    %for i=1:size(ExpList,1)
            nonstdDdirFlg=0
            if length(day)==1
                nonstdDirFlg=1;
            else
                nonstdDirFlg=0;
            end
if nonstdDirFlg==0
    cd(EstudyDir)
    %for i=1:size(ExpList,1)
     for i=1:length(dayLst)
       for j=1:length(dayLst(i).study)
             curDay= daytx(i)
             curExp= char(dayLst(i).study(j))
             curExpNumName= strcat('StudyExp',num2str(j));
             cd (fullfile(EstudyDir,curExp))
             curExpDir=pwd;
             
           plateDir=dir;  
           for k=1:length(plateDir)
             if ~isequal(plateDir(k).name,'.DS_Store') %if .DS_Store  Apple indiosyncratic fix  
               if isnumeric(str2double(plateDir(k).name)) && ~isnan(str2double(plateDir(k).name)),
                         curPlate= plateDir(k).name;
                        
                       cd (fullfile(curExpDir,curPlate))
                       curPlateDir=pwd;
                     %end
                    try
                         dotPos= strfind(Selfile,'.')
                         tptx= (Selfile(1:dotPos-1));
                        dstFileName= char(strcat('T',tptx,curDay,'_',curExp,'P',curPlate,'_',Selfile))
                         curPlateName=strcat('Plate',curPlate)
                         mkdir(fullfile(EstudyDir,'QkVstudySets',curExpNumName,curPlateName))
                        copyfile(fullfile(curPlateDir,Selfile),fullfile(EstudyDir,'QkVstudySets',curExpNumName,curPlateName,dstFileName))
 
                    catch
                    end 
                end  %if isnumeric(str2double(plateDirNonstd(k).name)),                   
                 
             end   %if .DS_Store  Apple indiosyncratic fix  
           end  %for k=1:length(plateDir)
       end   %j=1:length(dayLst(i).study)    for i=1:length(dayDirLst)        
    end   %i=1:length(dayLst)        for i=1:size(ExpList,1)
    
end  %if nonstdDirFlg==0

%****************************************************************************
%      Begin nonstandard Directory structure code
%****************************************************************************
if nonstdDirFlg==1
    cd(EstudyDir)
    cd ..
    studyDirNonstd=pwd;
    %mkdir(fullfile(studyDirNonstd,'QuikView'))
    dayDirLst=dir;
     for i=1:length(dayDirLst)  
        if ~isequal(dayDirLst(i).name,'.DS_Store') %if .DS_Store  Apple indiosyncratic fix
           if (strfind(dayDirLst(i).name,'Day')),
               curDay= dayDirLst(i).name;
               cd (fullfile(studyDirNonstd,curDay))  
               %curStudyDaynonStd=pwd
             expDirNonstd=dir
             expNum=0;
           for j=1:length(expDirNonstd)
             if ~isequal(expDirNonstd(j).name,'.DS_Store') %if .DS_Store  Apple indiosyncratic fix
                 if (strfind(expDirNonstd(j).name,'D')),
                     curExp= expDirNonstd(j).name;
                     expNum=expNum+1;
                     curExpNumName= strcat('StudyExp',num2str(expNum));
                     cd (fullfile(studyDirNonstd,curDay,curExp))
                     curExpDir=pwd;
                 %end
                  plateDirNonstd=dir;
                 for k=1:length(plateDirNonstd)
                   if ~isequal(plateDirNonstd(k).name,'.DS_Store') %if .DS_Store  Apple indiosyncratic fix
                     if isnumeric(str2double(plateDirNonstd(k).name)) && ~isnan(str2double(plateDirNonstd(k).name)),
                         curPlate= plateDirNonstd(k).name;
                        
                       cd (fullfile(curExpDir,curPlate))
                       curPlateDir=pwd;
                     
                    try
                         dotPos= strfind(Selfile,'.')
                         tptx= (Selfile(1:dotPos-1));
                        dstFileName= strcat('T',tptx,curDay,'_',curExp,'P',curPlate,'_',Selfile)
                         curPlateName=strcat('Plate',curPlate)
                         mkdir(fullfile(studyDirNonstd,'QkVstudySets',curExpNumName,curPlateName))
                        copyfile(fullfile(curPlateDir,Selfile),fullfile(studyDirNonstd,'QkVstudySets',curExpNumName,curPlateName,dstFileName))
                       
                    catch
                    end 
                    
                    end  %if isnumeric(str2double(plateDirNonstd(k).name)),
                    end %if (k) .DS_Store  Apple indiosyncratic fix
                 end  %for k=1:length(plateDirNonstd)
                end%if (strfind(expDirNonstd(j).name,'D'))
                end %if (j).DS_Store  Apple indiosyncratic fix
             end  %for j=1:length(expDirNonstd)
          end       %if (strfind(dayDirLst(i).name,'Day')),
          end %if (i).DS_Store  Apple indiosyncratic fix
       end  %for i=1:length(dayDirLst) 
    
end %if nonstdFlg



cd(w)

end



 %{     
 nonstdDdirFlg=0
            if length(day)==1
                nonstdDirFlg=1;
                %mkdir(fullfile(ExpFdr,'QkVstudySets'))
                %Experiments are grouped together in subfolders by the day
                %What if experiment are run on approximately the same day
                %but differ by say a day or two???
                
            else
                nonstdDirFlg=0;
                
                %Experiments are all together in the standard way
                %What if experiment are run on approximately the same day
                %but differ by say a day or two???
                %The user will have to label experiments the same which are
                %to be grouped together even if not on the same day. 
                
            end
    %+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
cd(w)
m=1;

for i=1:size(flist,1) 
    if isequal(Selfile,flist(i).name)
        fnum=m
        break
    end 
    m=m+1
end

%Select Image folders  ++++++++++++++++++++++++
d = dir(ExpFdr);
Scname={};
n=1;
for i=1:size(d,1)
if ~isempty(str2num(d(i).name))...
        ||~isempty(strfind(d(i).name,'Scan'))
    Scname{n}=d(i).name
    n=n+1
end
end
Srtnum=sort(str2double(Scname))
clear Srtname
for i=1:length(Srtnum)
    Srtname{i}=num2str(Srtnum(i));
end
    %str = {Scname};
[s,v] = listdlg('PromptString','Select a file:',...
                'SelectionMode','multiple',...
                'ListString',Srtname)
%*********************************************************************            
%+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


%++++++++++++++++++++++++++++++  
%Copy selected files to \QuikView Dir
mkdir(fullfile(ExpFdr,'QuikView'))
for j=1:size(s,2)
    srcDir= fullfile(ExpFdr,num2str(s(j)))
    %if Scan dir then must do something else to select '002' etc.
    try
    dstFileName= strcat(num2str(s(j)),'_',Selfile)
    copyfile(fullfile(srcDir,Selfile),fullfile(ExpFdr,'QuikView',dstFileName))
    
    catch
        sFileLst= dir(srcDir)
        selNumFile=sFileLst(fnum).name
        dstFileName= strcat(num2str(s(j)),'_',selNumFile)
        copyfile(fullfile(srcDir,selNumFile),fullfile(ExpFdr,'QuikView',dstFileName))
    end
  
end

cd(w)

end
%}