function SCaseList = listSCase(varargin)
%LISTSCASE output list of sCases (id and path), accordind to inputList and
%filter arguments.

%  Each sCase directory should at least contain at
%  directory with a name staring with 'CT' and ending with either
%  '-1' : preop/shoulder/sharp/noPhantom
%  '-2' : preop/shoulder/smooth/noPhantom
%  '-3' : preop/shoulder/sharp/phantom
%  '-4' : preop/shoulder/smooth/phantom
%  and containing a 'dicom' subdirectory. The priority is '1', '2', '3', '4',
%  unless there is a amira folder already present in one of these diretories.
%
%   The optional input argument inputList if an array of SCaseID. If empty,
%   listSCase will search for all SCaseID. The optional input argument
%   filter can restrict le list.

% The fonction can be run from server (lbovenus) with
% cd /home/shoulder/methods/matlab/database; matlab -nojvm -nodisplay -nosplash -r "listSCase;quit"
% For 700 cases, it takes less than 60 seconds (when executed from server)

% Progress can be be checked throuhth log file with following shell command
% cd /home/shoulder/methods/matlab/database;tail -f log/listSCase.log



% Input: 
%   inputArg: can be nothing (=all), 'N', 'P', or SCase(s) 
%
% Output:
%   outputArg: 1 if ok and 0 otherwise
% 
% Example: listSCase, listSCase('P'), listSCase('P001','P002')
% Other M-files required:
% Subfunctions:
% See also:
% 
% Author: Alexandre Terrier
% EPFL-LBO
% Creation date: 2018-07-01
% Revision date: 2018-08-09
% 
% TO DO:
% If no dir CT*-1, check for other, wit the priority with one having amira
% directory
 
%% Initialisation of paths
% Should be replaced by a function
currentDir = pwd;
rootDir = strfind(currentDir, 'methods/matlab'); % Check it for windows
rootDir = currentDir(1:rootDir-2);
% We should check here that currentDir contains 'Dev' to associate dataDev 
dataDir = [rootDir '/data']; % location of data
%dataDir = '../../../data'; % location of data --> remove if above ok
logDir = 'log'; % log file in xls folder

%% Open log file
logFile = [logDir '/listSCase.log'];
logFileId = fopen(logFile, 'w');
fprintf(logFileId, 'listSCase log file');
fprintf(logFileId, '\nDate: ');
fprintf(logFileId, datestr(datetime));

%% Struct contains id and associated directory
SCaseList = struct(...
    'id'       ,[],...
    'dir'      ,[],...
    'comment'  ,[]...   % Might be used later
    );

%% Check varargin

dirL0Array = '';
SCaseListIn = {};

if nargin == 0
    dirL0Array = ['N';'P']; % All SCase, default when no argument
    fprintf(logFileId, '\nGet list of all SCase with a valid dicom folder');
elseif nargin == 1
    if strcmp(varargin,'N') % All normal SCase
        dirL0Array = 'N';
        fprintf(logFileId, '\nGet list of all normal SCase with a valid dicom folder');
    elseif strcmp(varargin,'P')  % All pathological SCase
        dirL0Array = 'P';
        fprintf(logFileId, '\nGet list of all pathological SCase with a valid dicom folder');
    else % A specific SCase
        fprintf(logFileId, '\nGet list of a SCase with a valid dicom folder');
        SCaseListIn = varargin;
    end
else % list of multiple SCase given in varargin
        fprintf(logFileId, '\nGet list of a SCase with a valid dicom folder');
        SCaseListIn = varargin;
end

%% Only one of the two loops below are performed
SCaseListIdx = 0; % Used in one of two loops below

%% Loop over SCase (N, P, or both), if length(dirL0Array) > 1
for dirL0idx = 1:length(dirL0Array) % N or P
    for dirL1idx = 0:9 % Hunderts
        for dirL2idx = 0:9 % Tens
            dirL0Str = dirL0Array(dirL0idx);
            dirL1Str = num2str(dirL1idx);
            dirL2Str = num2str(dirL2idx);
            dirTens  = [dataDir '/' dirL0Str '/' dirL1Str '/' dirL2Str];
            dirTensList  = dir(dirTens); % List all directories in tens directory
            dirTensList  = dirTensList(~ismember({dirTensList.name},{'.','..'})); % Remove . and ..
            % We might add here a filter (only diretories, {N/P} followed
            % by digits
            for dirL3idx = 1:numel(dirTensList)
                sCaseDirName = dirTensList(dirL3idx).name; % Root directory of this case
                sCaseDirPath = dirTensList(dirL3idx).folder;
                % Check that this sCase directory contains a directory with the
                % name [CT?*-1] and with a dicom directory in it.
                SCaseID = strtok(sCaseDirName, '-'); % Get chars before '-'
                
                % Check if this SCaseID has a CT directory with a valid preoprative CT
                CTdirList = dir([sCaseDirPath '/' sCaseDirName '/CT-*']); % List directories with CT
                iCTdirAmira = 0;
                iCTdir2use  = 0;
                for iCTdirList = length(CTdirList):-1:1 % Loop from last to first (4 to 1)
                    CTdir = CTdirList(iCTdirList);
                    % Check that dir name ends with -1,-2,-3,-4
                    dirName = CTdir.name;
                    if strcmp(dirName(end-1),'-') % Exclude postoperative 'p' CT
                        CTnum = str2num(dirName(end));
                        if CTnum <= 4 % Exlude non shoulder (elbow) CT
                            % Check that the dir contains a dicom dir
                            CTdir = [CTdir.folder '/' CTdir.name];
                            dicomDir = [CTdir '/dicom'];
                            if exist(dicomDir, 'dir')
                                % Chech if amira dir exist
                                amiraDir = [CTdir '/amira'];
                                if exist(amiraDir, 'dir')
                                    % This is the CT folder to use
                                    iCTdirAmira = iCTdirList;
                                end
                                iCTdir2use = iCTdirList;
                            end
                        end
                    end
                end
                if iCTdir2use == 0
                    fprintf(logFileId, ['\n', SCaseID, ' has no valid dicom directory']);
                else
                    if iCTdirAmira % If amira dir exist, use it
                        iCTdir2use = iCTdirAmira;
                    end
                    CTdir = CTdirList(iCTdir2use);
                    SCaseListIdx = SCaseListIdx + 1;
                    SCaseList(SCaseListIdx).id = SCaseID;
                    CTdirPath = [CTdir.folder '/' CTdir.name];
                    SCaseList(SCaseListIdx).dir = CTdirPath;
                    if CTnum ~= 1
                        fprintf(logFileId, ['\n', SCaseID, ' dicom directory is CT-' num2str(CTnum)]);
                    end
                    
                end
                
                
                
                
%                 % Listing of (CT) folders in sCaseDirPath staring with CT
%                 % and ending with '-1'
%                 CTdir = dir([sCaseDirPath '/' sCaseDirName '/CT*-1']);
%                 if ~isempty(CTdir)
%                     CTdirPath = [CTdir.folder '/' CTdir.name];
%                     dicomDirName = [CTdirPath '/dicom'];
%                     if exist(dicomDirName, 'dir')
%                         SCaseListIdx = SCaseListIdx + 1;
%                         SCaseList(SCaseListIdx).id = SCaseID;
%                         SCaseList(SCaseListIdx).dir = CTdirPath;
%                         % We might get here the readme.txt if present
%                     else
%                         fprintf(logFileId, ['\n', SCaseID, ' has no valid dicom directory']);
%                     end
%                 else
%                     fprintf(logFileId, ['\n', SCaseID, ' has no CT*-1 directory']);
%                 end
            end
        end
    end
end

%% Loop over input SCase list (given as input argument), if length(SCaseListIn) > 0
for iSCaseListIn = 1:length(SCaseListIn)
    % Check if there is a valid dicom directory for this SCaseID
    
     SCaseID = char(SCaseListIn{iSCaseListIn});
    % Build directory from SCaseID (as in function ShoulderCase.path)
    
    % The validity of the format should be either Pnnn or Nnnn.
    if (numel(regexp(SCaseID,'^[PN]\d{1,3}$')) == 0)
        error(['Invalid format of SCaseID: ' SCaseID{1} '. CaseID must start with "P" or "N" and be followed by 1 to 3 digits.']);
    end
    
    % Set the folder of the SCaseID
    SCaseDirLevelPN = SCaseID(1); % Either 'P' or 'N'
    strLengthSCaseID = strlength(SCaseID(2:end));
    if (strLengthSCaseID < 2)
        SCaseDirLevel2 = '0';        % Hunderets
        SCaseDirLevel1 = '0';        % Dozent
    elseif (strLengthSCaseID < 3)
        SCaseDirLevel2 = '0';        % Hunderets
        SCaseDirLevel1 = SCaseID(2); % Dozent
    else
        SCaseDirLevel2 = SCaseID(2); % Hunderets
        SCaseDirLevel1 = SCaseID(3); % Dozent
    end
    % Set SCaseID with fixed 3 digits after P/N (needed when id <
    % 10 inloading of data in amira directory.
    SCaseID4C = [SCaseDirLevelPN SCaseDirLevel2 SCaseDirLevel1 SCaseID(end)];
    
    % Check if a (!unique! to be done) directory exists for this SCaseID
    FindSCaseIDFolder = dir([dataDir '/' SCaseDirLevelPN '/' SCaseDirLevel2 '/' SCaseDirLevel1 '/' SCaseID '*']);
    if (isempty(FindSCaseIDFolder)) % No directory for this SCaseID
        error(['Missing directory for SCaseID: ' SCaseID]);
    end
    SCaseDirLevel0 = FindSCaseIDFolder.name;
    SCaseDir = [dataDir '/' SCaseDirLevelPN '/' SCaseDirLevel2 '/' SCaseDirLevel1 '/' SCaseDirLevel0];
    
    % Check if this SCaseID has a CT directory with a valid preoprative CT 
    CTdirList=dir([SCaseDir '/CT-*']); % List directories with CT
    iCTdirAmira = 0;
    iCTdir2use  = 0;
    for iCTdirList = length(CTdirList):-1:1 % Loop from last to first (4 to 1)
        CTdir = CTdirList(iCTdirList);
        % Check that dir name ends with -1,-2,-3,-4
        dirName = CTdir.name;
        if strcmp(dirName(end-1),'-') % Exclude postoperative 'p' CT
            CTnum = str2num(dirName(end));
            if CTnum <= 4 % Exlude non shoulder (elbow) CT
                % Check that the dir contains a dicom dir
                CTdir = [CTdir.folder '/' CTdir.name];
                dicomDir = [CTdir '/dicom'];
                if exist(dicomDir, 'dir')
                    % Chech if amira dir exist
                    amiraDir = [CTdir '/amira'];
                    if exist(amiraDir, 'dir')
                        % This is the CT folder to use
                        iCTdirAmira = iCTdirList;
                    end
                    iCTdir2use = iCTdirList;
                end
            end
        end
    end
    if iCTdir2use == 0
        fprintf(logFileId, ['\n', SCaseID, ' has no valid dicom directory']);
    else
        if iCTdirAmira % If amira dir exist, use it
            iCTdir2use = iCTdirAmira;
        end
        CTdir = CTdirList(iCTdir2use);
        SCaseListIdx = SCaseListIdx + 1;
        SCaseList(SCaseListIdx).id = SCaseID;
        CTdirPath = [CTdir.folder '/' CTdir.name];
        SCaseList(SCaseListIdx).dir = CTdirPath;
    end
end

fprintf(logFileId, ['\nNumber of SCase: ' num2str(length(SCaseList))]);
end