%%% extract a series of image folders from RDvision
% to run on the cluster, edit the file extract.sh in the folder TOP_view or SCANSIDE, 
% Then oarsub -l "walltime=20:00:00" /fsnet/project/coriolis/2018/18ADDUCE/TOP_View/extract.sh
function batch_extract_rdvision(RootDir,FirstFolder)
%%%%%%%%%%%%%%  CHOOSE THE ROOT FOLDER %%%%%%%%%%
%RootDir='TOP_View'
%RootDir='SCANSIDE';%
%%%%%%%%%%%%%%%%%%%%%%%
RootFolder=fullfile('/fsnet/project/coriolis/2018/18ADDUCE',RootDir);
ParamFile=fullfile(RootFolder,'extract_param.xml');
%XmlFile='/fsnet/project/coriolis/2018/18ADDUCE/TOP_View/im.xml';
Param=xml2struct(ParamFile);
switch RootDir
    case 'TOP_View'
        XmlFile='';
        Param.OutputRootFile='Falcon';
    case 'SCANSIDE'
        XmlFile='im.xml';
        Param.OutputRootFile='im';
end
ListStruct=dir(RootFolder); % get structure of the Root directory
ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray
ListNames=ListCells(1,:);%list of file names
index_dir=find(strcmp('isdir',fieldnames(ListStruct)));%detect folders
check_dir=cell2mat(ListCells(index_dir,:));% =1 for directories, =0 for files
ListDir=ListNames(check_dir);
FirstFolder
first=find(strcmp(FirstFolder,ListDir))
NbFolders=1%5; %totql number of folders to process
% first=9;% #3 is the first folder in the list (#1='.', #2='..')
% disp('first folder')
% dd(first).name
% last=15;%19;
% disp('last folder')
% dd(last).name

for ilist=first:first+NbFolders-1
    Param.InputTable{1}=fullfile(RootFolder,ListDir{ilist});%folder exp
    ddd=dir(Param.InputTable{1});
    Param.InputTable{2}=ddd(3).name;
    DataFolder=fullfile(Param.InputTable{1},Param.InputTable{2});
    ExtractFolder=fullfile(Param.InputTable{1},[Param.InputTable{2} '.extract']);
    mkdir(ExtractFolder)
    if ~isempty(XmlFile)
    copyfile(fullfile(RootFolder,XmlFile),fullfile(DataFolder,[Param.OutputRootFile '.xml']));
    end
    seqname=fullfile(DataFolder,[Param.InputTable{3} Param.InputTable{5}]);
    [A,FileInfo,timestamps,errormsg]=read_rdvision(seqname,[]);
    Param.IndexRange.last_i=str2num(FileInfo.numberoffiles);   
    Param.OutputSubDir=Param.InputTable{2};
    Param.ActionInput.LogPath= DataFolder;
    extract_rdvision(Param)% apply the function used in series
end
%%%%% COMMAND CLUSTER
%oarsub -l "walltime=10:00:00" /fsnet/project/coriolis/2018/18ADDUCE/SCANSIDE/extract.sh -E /fsnet/project/coriolis/2018/18ADDUCE/SCANSIDE/error -O /fsnet/project/coriolis/2018/18ADDUCE/SCANSIDE/stdout