function outputArg = dicominfoSCase(varargin)
%DICOMINFOSCASE Get info from dicom fields and save in csv, xls, mat, and SQL

% This function should be started from /shoulder/methods/matlab/database
% A logfile is written during execution in
% /shoulder/methods/matlab/database/log/dicominfoSCase.log
% If the function is called without arguments the csv file is overwritten,
% otherwise it is updated. The same applies for xls, mat and SQL.

% The fonction can be run from server (lbovenus) with
% cd /home/shoulder/methods/matlab/database; matlab -nojvm -nodisplay -nosplash -r "dicominfoSCase;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/dicominfoSCase.log

% This funtion replaces
% /home/shoulder/methods/matlab/database/CTinfoCT.m
% which only works matlab R2015a on a Windows system

% Syntax: outputArg = dicominfoSCase(varargin)
% 
% Input: 
%   varargin: can be nothing (all cases), 'N', 'P', or SCase(s)
%
% Output:
%   outputArg: 1 if ok and 0 otherwise
% 
% Example: CTdicomInfo, CTdicominfo('P'), CTdicominfo('P315')
% Other M-files required: listSCase
% Subfunctions: 
% See also: measureSCase
% 
% Author: Alexandre Terrier
% EPFL-LBO
% Creation date: 2018-07-01
% Revision date: 2018-12-30
% 
% TO DO:
% When list of SCases as arguments it doesn't work properly because it
% overwrites the CSV with only the listed SCased (by JSM 2019-02-13)
% Re-check for double slash in paths
% We should implement the ShoulderCase class
% We should save data in SCase/matlab directory
% We might add family name, given name (to check anonymity)
% We should first read csv and then update
% We should update MySQL
% Check 'Index exceeds matrix dimensions' when 'using dicomdisp'
% Structure SCaseDicom should match csv (and xlx aand sql) firld names
% rather than dicom

%% Open log file
% Check if log dir exists in working directory
logDir = 'log';
if ~exist('log', 'dir') % If not create dir log
       mkdir('log')
end
logFile = [logDir '/dicominfoSCase.log'];
logFileID = fopen(logFile, 'w');
fprintf(logFileID, 'dicominfoSCase log file');
fprintf(logFileID, '\nDate: ');
fprintf(logFileID, datestr(datetime));

%% Set the data directory from the configuration file config.txt
configFile = 'config.txt';
if ~exist(configFile, 'file')
    error([configFile, ' required']);
end
fileID = fopen(configFile,'r');
dataDir = fscanf(fileID, '%s'); % Read config file without spaces
fclose(fileID);
k = strfind(dataDir, 'dataDir='); % Find definition of dataDir
k = k + 8; % Remove 'dataDir='
dataDir = dataDir(k:end); % Assume that config file ends with dataDir content
% Check if dataDir exists
if ~exist(dataDir, 'dir')
    fprintf(logFileID, ['Data directory not found, check ' configFile]);
    %error(['Data directory not found, check ' configFile]);
    
    % Select the \data directory
    try
        dataDir = uigetdir(pwd,"Please select the directory 'data or dataDev'");
        if ~exist(dataDir, 'dir')
            errordlg(sprintf("%s",...
                "Run 'dicominfoSCase.m' manually and select the data directory"),...
                "Error: data directory not found.")
        end
    catch mistake
        errordlg(sprintf("%s\n%s",...
            "Run 'dicominfoSCase.m' manually and select the data directory",...
            mistake.message),"Error: data directory not found.")
    end
    
end
% Location of the XLS ShoulderDatabase
xlsDataDir = strcat(dataDir, '/Excel/xlsFromMatlab');

%% Get list of SCases
if nargin == 0 % dicominfoSCase called without argument
    SCaseList = listSCase(dataDir); % All SCases in data dir with valid dicom CT dir
    update = 0;
elseif nargin == 1
    update = 1;
    inputArg = varargin{1};
    SCaseList = listSCase(dataDir,inputArg); % SCase related to inputArg ('N', 'P', or list)
end

%% Read dicom info
tic; % Start stopwatch timer
fprintf(logFileID, '\n\nRead dicom meta data\n'); % log file message

% Struct below correponds to regular dicom field names, except SCase_ID
SCaseDicom = struct(...
    'SCase_id'               ,[],...
    'PatientID'              ,[],...
    'PatientSex'             ,[],...
    'PatientAge'             ,[],...
    'PatientBirthDate'       ,[],...
    'PatientSize'            ,[],...
    'PatientWeight'          ,[],...
    'PatientFamilyName'      ,[],...
    'PatientGivenName'       ,[],...
    'AcquisitionDate'        ,[],...
    'ConvolutionKernel'      ,[],...
    'PixelSpacing'           ,[],...
    'SpacingBetweenSlices'   ,[],...
    'SliceThickness'         ,[],...
    'KVP'                    ,[],...
    'XrayTubeCurrent'        ,[],...
    'InstitutionName'        ,[],...
    'StudyDescription'       ,[],...
    'SeriesDescription'      ,[],... % Might describe shoulder side
    'Manufacturer'           ,[],...
    'ManufacturerModelName'  ,[],...
    'ProtocolName'           ,[]...
    );

% Loop over all SCases collected above
for SCase_idx=1:1:numel(SCaseList)
    SCase_id = SCaseList(SCase_idx).id;
    dicomDir = [SCaseList(SCase_idx).dir '/dicom'];
    dicomFiles = dir([dicomDir, '/*.dcm']);
    
%     SCase_idx
    dicomFile1 = [dicomDir, '/', dicomFiles(10).name]; % seems better to check 10th than 1st !
    dicomInfoError = false;
    fprintf(logFileID, '\n');
    fprintf(logFileID, SCaseList(SCase_idx).id);
    fprintf(logFileID, ': ');
    % Try first with matlab function dicominfo
    try
        dicomInfo1 = dicominfo(dicomFile1, 'UseVRHeuristic', true);
        fprintf(logFileID, 'dicominfo ok');
        % If dicominfo didn't worked, try with matlab function dicomdisp
    catch ME
        dicomInfoError = true;
        fprintf(logFileID, '\n');
        fprintf(logFileID, 'dicominfo error --> using dicomdisp');
        fprintf(logFileID, ['\n' ME.message]);
        dicomdispStr = evalc('dicomdisp(dicomFile1)');
    end
    
    % If dicominfo didn't worked, continue with output of dicomdisp
    if dicomInfoError % get dicom info from dicomdisp()
        PatientID = extractAfter(dicomdispStr,'PatientID');
        PatientID = extractAfter(PatientID,'[');
        PatientID = extractBefore(PatientID,']');
        
        PatientSex = extractAfter(dicomdispStr,'PatientSex');
        PatientSex = extractAfter(PatientSex,'[');
        PatientSex = extractBefore(PatientSex,']');
        
        PatientAge = extractAfter(dicomdispStr,'PatientAge');
        PatientAge = extractAfter(PatientAge,'[');
        PatientAge = extractBefore(PatientAge,']');
        
        PatientBirthDate = extractAfter(dicomdispStr,'PatientBirthDate');
        PatientBirthDate = extractAfter(PatientBirthDate,'[');
        PatientBirthDate = extractBefore(PatientBirthDate,']');
        
        PatientSize = extractAfter(dicomdispStr,'PatientSize');
        PatientSize = extractAfter(PatientSize,'[');
        PatientSize = extractBefore(PatientSize,']');
        PatientSize = str2double(PatientSize);
        
        PatientWeight = extractAfter(dicomdispStr,'PatientWeight');
        PatientWeight = extractAfter(PatientWeight,'[');
        PatientWeight = extractBefore(PatientWeight,']');
        PatientWeight = str2double(PatientWeight);
        
        AcquisitionDate = extractAfter(dicomdispStr,'AcquisitionDate');
        AcquisitionDate = extractAfter(AcquisitionDate,'[');
        AcquisitionDate = extractBefore(AcquisitionDate,']');
        
        ConvolutionKernel = extractAfter(dicomdispStr,'ConvolutionKernel');
        ConvolutionKernel = extractAfter(ConvolutionKernel,'[');
        ConvolutionKernel = extractBefore(ConvolutionKernel,']');
        
        PixelSpacing = extractAfter(dicomdispStr,'PixelSpacing');
        PixelSpacing = extractAfter(PixelSpacing,'[');
        PixelSpacing = extractBefore(PixelSpacing,'\');
        
        SpacingBetweenSlices = extractAfter(dicomdispStr,'SpacingBetweenSlices');
        SpacingBetweenSlices = extractAfter(SpacingBetweenSlices,'[');
        SpacingBetweenSlices = extractBefore(SpacingBetweenSlices,']');
        SpacingBetweenSlices = str2double(SpacingBetweenSlices);
        
        SliceThickness = extractAfter(dicomdispStr,'SliceThickness');
        SliceThickness = extractAfter(SliceThickness,'[');
        SliceThickness = extractBefore(SliceThickness,']');
        SliceThickness = str2double(SliceThickness);
        
        KVP = extractAfter(dicomdispStr,'KVP');
        KVP = extractAfter(KVP,'[');
        KVP = extractBefore(KVP,']');
        KVP = str2double(KVP);
        
        XrayTubeCurrent = extractAfter(dicomdispStr,'XrayTubeCurrent');
        XrayTubeCurrent = extractAfter(XrayTubeCurrent,'[');
        XrayTubeCurrent = extractBefore(XrayTubeCurrent,']');
        XrayTubeCurrent = str2double(XrayTubeCurrent);
        
        InstitutionName = extractAfter(dicomdispStr,'InstitutionName');
        InstitutionName = extractAfter(InstitutionName,'[');
        InstitutionName = extractBefore(InstitutionName,']');
        
        Manufacturer = extractAfter(dicomdispStr,'Manufacturer');
        Manufacturer = extractAfter(Manufacturer,'[');
        Manufacturer = extractBefore(Manufacturer,']');
        
        ManufacturerModelName = extractAfter(dicomdispStr,'ManufacturerModelName');
        ManufacturerModelName = extractAfter(ManufacturerModelName,'[');
        ManufacturerModelName = extractBefore(ManufacturerModelName,']');
        
        ProtocolName = extractAfter(dicomdispStr,'ProtocolName');
        ProtocolName = extractAfter(ProtocolName,'[');
        ProtocolName = extractBefore(ProtocolName,']');
        
        SeriesDescription = extractAfter(dicomdispStr,'SeriesDescription');
        SeriesDescription = extractAfter(SeriesDescription,'[');
        SeriesDescription = extractBefore(SeriesDescription,']');
        
    else % dicomInfo exists
        if isfield(dicomInfo1,'PatientID')
            PatientID = dicomInfo1.PatientID;
        else
            PatientID = '';
        end
        if isfield(dicomInfo1,'PatientSex')
            PatientSex = dicomInfo1.PatientSex;
        else
            PatientSex = '';
        end
        if isfield(dicomInfo1,'PatientBirthDate')
            PatientBirthDate = dicomInfo1.PatientBirthDate;
        else
            PatientBirthDate = '';
        end
        if isfield(dicomInfo1,'PatientAge')
            PatientAge = dicomInfo1.PatientAge;
        else
            PatientAge = '';
        end
        if isfield(dicomInfo1,'PatientSize')
            PatientSize = dicomInfo1.PatientSize;
        else
            PatientSize = '';
        end
        if isfield(dicomInfo1,'PatientWeight')
            PatientWeight = dicomInfo1.PatientWeight;
        else
            PatientWeight='';
        end
        if isfield(dicomInfo1,'AcquisitionDate')
            AcquisitionDate = dicomInfo1.AcquisitionDate;
        else
            AcquisitionDate = '';
        end
        if isfield(dicomInfo1,'ConvolutionKernel')
            ConvolutionKernel = dicomInfo1.ConvolutionKernel;
        else
            ConvolutionKernel = '';
        end
        if isfield(dicomInfo1,'PixelSpacing')
            PixelSpacing = dicomInfo1.PixelSpacing(1);
            PixelSpacing = num2str(PixelSpacing);
%            PixelSpacing = [,PixelSpacing,]; % Commented because I (AT) don't
%            understand the effect
        else
            PixelSpacing='';
        end
        if isfield(dicomInfo1,'SpacingBetweenSlices')
            SpacingBetweenSlices = dicomInfo1.SpacingBetweenSlices;
        else % SpacingBetweenSlices estimated from 2 slices
            %            fprintf(logFileID, '\n');
            fprintf(logFileID, ', SpacingBetweenSlices estimated from 2 slices');
            dicomFile2 = [dicomDir, '/', dicomFiles(11).name];
            dicomInfo2 = dicominfo(dicomFile2, 'UseVRHeuristic', true);
            ImagePositionPatient1 = dicomInfo1.ImagePositionPatient(3);
            ImagePositionPatient2 = dicomInfo2.ImagePositionPatient(3);
            posdDiff = abs(ImagePositionPatient2 - ImagePositionPatient1);
            InstanceNumber1 = dicomInfo1.InstanceNumber;
            InstanceNumber2 = dicomInfo2.InstanceNumber;
            InstanceNumberDiff = abs(InstanceNumber2 - InstanceNumber1);
            if InstanceNumberDiff == 0
                InstanceNumberDiff=1;
            end
            SpacingBetweenSlices = posdDiff/InstanceNumberDiff;
        end
        if isfield(dicomInfo1,'SliceThickness')
            SliceThickness = dicomInfo1.SliceThickness;
        else
            SliceThickness='';
        end
        if isfield(dicomInfo1,'KVP')
            KVP = dicomInfo1.KVP;
        else
            KVP= '';
        end
        if isfield(dicomInfo1,'XrayTubeCurrent')
            XrayTubeCurrent = dicomInfo1.XrayTubeCurrent;
        else
            XrayTubeCurrent = '';
        end
        if isfield(dicomInfo1,'InstitutionName')
            InstitutionName = dicomInfo1.InstitutionName;
        else
            InstitutionName = '';
        end
        if isfield(dicomInfo1,'Manufacturer')
            Manufacturer = dicomInfo1.Manufacturer;
        else
            Manufacturer ='';
        end
        if isfield(dicomInfo1,'ManufacturerModelName')
            ManufacturerModelName = dicomInfo1.ManufacturerModelName;
        else
            ManufacturerModelName = '';
        end
        if isfield(dicomInfo1,'ProtocolName')
            ProtocolName = dicomInfo1.ProtocolName;
        else
            ProtocolName = '';
        end
        if isfield(dicomInfo1,'SeriesDescription')
            SeriesDescription = dicomInfo1.SeriesDescription;
        else
            SeriesDescription = '';
        end
        % End of reading dimcom info
    end
    
    %% Format data
    PatientBirthDate = datetime(PatientBirthDate,'InputFormat','yyyyMMdd');
    PatientBirthDate = datestr(PatientBirthDate, 'yyyy-mm-dd');
    PatientAge = str2double(strtok(PatientAge,'Y'));
    PatientSize = round(100 * PatientSize);
    if PatientSize == 0
        PatientSize = '';
    end
    PatientWeight = round(PatientWeight);
    if PatientWeight == 0
        PatientWeight = '';
    end
    AcquisitionDate = datetime(AcquisitionDate,'InputFormat','yyyyMMdd');
    AcquisitionDate = datestr(AcquisitionDate, 'yyyy-mm-dd');
    
    PixelSpacing = str2double(PixelSpacing);
    PixelSpacing = round(PixelSpacing, 3);
    SpacingBetweenSlices = round(SpacingBetweenSlices, 3);
    SliceThickness = round(SliceThickness, 3);
    KVP = round(KVP);
    XrayTubeCurrent = round(XrayTubeCurrent);
    % Replace any ',' by ' ' to avoid problem in csv
    InstitutionName = strrep(InstitutionName,',',' ');
    Manufacturer = strrep(Manufacturer,',',' ');
    ManufacturerModelName = strrep(ManufacturerModelName,',',' ');
    ProtocolName = strrep(ProtocolName,',',' ');
    SeriesDescription = strrep(SeriesDescription,',',' ');
    
    %% Add data in SCaseDicom structure
    % This could be directly in SCase.CT object
    SCaseDicom(SCase_idx).id = SCase_id;
    SCaseDicom(SCase_idx).PatientID = PatientID;
    SCaseDicom(SCase_idx).PatientSex = PatientSex;
    SCaseDicom(SCase_idx).PatientBirthDate = PatientBirthDate;
    SCaseDicom(SCase_idx).PatientAge = PatientAge;
    SCaseDicom(SCase_idx).PatientSize = PatientSize;
    SCaseDicom(SCase_idx).PatientWeight = PatientWeight;
    SCaseDicom(SCase_idx).AcquisitionDate = AcquisitionDate;
    SCaseDicom(SCase_idx).ConvolutionKernel = ConvolutionKernel;
    SCaseDicom(SCase_idx).PixelSpacing = PixelSpacing;
    SCaseDicom(SCase_idx).SpacingBetweenSlices = SpacingBetweenSlices;
    SCaseDicom(SCase_idx).SliceThickness = SliceThickness;
    SCaseDicom(SCase_idx).KVP = KVP;
    SCaseDicom(SCase_idx).XrayTubeCurrent = XrayTubeCurrent;
    SCaseDicom(SCase_idx).InstitutionName = InstitutionName;
    SCaseDicom(SCase_idx).Manufacturer = Manufacturer;
    SCaseDicom(SCase_idx).ManufacturerModelName = ManufacturerModelName;
    SCaseDicom(SCase_idx).ProtocolName = ProtocolName;
    SCaseDicom(SCase_idx).SeriesDescription = SeriesDescription;
end
fprintf(logFileID, '\n\nElapsed time (s): %s', num2str(toc)); % stopwatch timer

%% Write csv file
% This might be a function. The input would be a filename and a structure
% data

dataHeader = [...
    'SCase_ID,' ...
    'patient_IPP,' ...
    'patient_gender,' ...
    'patient_birthDate,' ...
    'patient_age,' ...
    'patient_height,' ...
    'patient_weight,' ...
    'CT_date,' ...
    'CT_kernel,' ...
    'CT_pixelSize,' ...
    'CT_sliceSpacing,' ...
    'CT_sliceThickness,' ...
    'CT_tension,' ...
    'CT_current,' ...
    'CT_institution,' ...
    'CT_manufacturer,' ...
    'CT_model,' ...
    'CT_protocol,' ...
    'CT_SeriesDescription' ...
    ];

csvFilename = strcat(xlsDataDir, '/CTdicomInfo.csv');

% If dicominfoSCase is called with argument, we have to update the csv.
if update
    % Read the csv and put data in a structure like SCaseDicom
    % We should chech that file exists
    csvTable = readtable(csvFilename,'DatetimeType', 'text');
    % If 'DatetimeType' is specified as 'text', then the type for imported
    % date and time data depends on the value specified in the 'TextType'
    % parameter: If 'TextType' is 'char', then readtable returns dates as a
    % cell array of character vectors. If 'TextType' is 'string', then
    % readtable returns dates as an array of strings.
    
    % Set csv data in temporary SCaseDicomTmp structure
    SCaseDicom_csv = table2struct(csvTable);
                                        
    % Update the SCaseDicomTmp structure with new data
    for iSCaseDicom = 1:length(SCaseDicom) % loop on new SCase(s)
        iSCaseDicomTmp = strcmp({SCaseDicom_csv.SCase_ID}, SCaseDicom(iSCaseDicom).id); % 0/1 array
        iSCaseDicomTmp = find(iSCaseDicomTmp); % index with non-zero, correponding to SCaseID
        % We should test iSCaseDicomTmp => is overwriting the whole array
        % Must be changed by last SCase position +1
        
        SCaseDicom_csv(iSCaseDicomTmp).patient_IPP = SCaseDicom(iSCaseDicom).PatientID;
        SCaseDicom_csv(iSCaseDicomTmp).patient_gender = SCaseDicom(iSCaseDicom).PatientSex;
        SCaseDicom_csv(iSCaseDicomTmp).patient_birthDate = SCaseDicom(iSCaseDicom).PatientBirthDate;
        SCaseDicom_csv(iSCaseDicomTmp).patient_age = SCaseDicom(iSCaseDicom).PatientAge;
        SCaseDicom_csv(iSCaseDicomTmp).patient_height = SCaseDicom(iSCaseDicom).PatientSize;
        SCaseDicom_csv(iSCaseDicomTmp).patient_weight = SCaseDicom(iSCaseDicom).PatientWeight;
        SCaseDicom_csv(iSCaseDicomTmp).CT_date = SCaseDicom(iSCaseDicom).AcquisitionDate;
        SCaseDicom_csv(iSCaseDicomTmp).CT_kernel = SCaseDicom(iSCaseDicom).ConvolutionKernel;
        SCaseDicom_csv(iSCaseDicomTmp).CT_pixelSize = SCaseDicom(iSCaseDicom).PixelSpacing;
        SCaseDicom_csv(iSCaseDicomTmp).CT_sliceSpacing = SCaseDicom(iSCaseDicom).SpacingBetweenSlices;
        SCaseDicom_csv(iSCaseDicomTmp).CT_sliceThickness = SCaseDicom(iSCaseDicom).SliceThickness;
        SCaseDicom_csv(iSCaseDicomTmp).CT_tension = SCaseDicom(iSCaseDicom).KVP;
        SCaseDicom_csv(iSCaseDicomTmp).CT_current = SCaseDicom(iSCaseDicom).XrayTubeCurrent;
        SCaseDicom_csv(iSCaseDicomTmp).CT_institution = SCaseDicom(iSCaseDicom).InstitutionName;
        SCaseDicom_csv(iSCaseDicomTmp).CT_manufacturer = SCaseDicom(iSCaseDicom).Manufacturer;
        SCaseDicom_csv(iSCaseDicomTmp).CT_model = SCaseDicom(iSCaseDicom).ManufacturerModelName;
        SCaseDicom_csv(iSCaseDicomTmp).CT_protocol = SCaseDicom(iSCaseDicom).ProtocolName;
        SCaseDicom_csv(iSCaseDicomTmp).CT_SeriesDescription = SCaseDicom(iSCaseDicom).SeriesDescription;
    end
    
    % SCaseDicom must now be updated 
    for iSCaseDicom = 1:length(SCaseDicom)
    SCaseDicom(iSCaseDicom).id = SCaseDicom_csv(iSCaseDicom).SCase_ID;
    SCaseDicom(iSCaseDicom).PatientID = SCaseDicom_csv(iSCaseDicom).patient_IPP;
    SCaseDicom(iSCaseDicom).PatientSex = SCaseDicom_csv(iSCaseDicom).patient_gender;
    SCaseDicom(iSCaseDicom).PatientBirthDate = SCaseDicom_csv(iSCaseDicom).patient_birthDate;
    SCaseDicom(iSCaseDicom).PatientAge = SCaseDicom_csv(iSCaseDicom).patient_age;
    SCaseDicom(iSCaseDicom).PatientSize = SCaseDicom_csv(iSCaseDicom).patient_height;
    SCaseDicom(iSCaseDicom).PatientWeight = SCaseDicom_csv(iSCaseDicom).patient_weight;
    SCaseDicom(iSCaseDicom).AcquisitionDate = SCaseDicom_csv(iSCaseDicom).CT_date;
    SCaseDicom(iSCaseDicom).ConvolutionKernel = SCaseDicom_csv(iSCaseDicom).CT_kernel;
    SCaseDicom(iSCaseDicom).PixelSpacing = SCaseDicom_csv(iSCaseDicom).CT_pixelSize;
    SCaseDicom(iSCaseDicom).SpacingBetweenSlices = SCaseDicom_csv(iSCaseDicom).CT_sliceSpacing;
    SCaseDicom(iSCaseDicom).SliceThickness = SCaseDicom_csv(iSCaseDicom).CT_sliceThickness;
    SCaseDicom(iSCaseDicom).KVP = SCaseDicom_csv(iSCaseDicom).CT_tension;
    SCaseDicom(iSCaseDicom).XrayTubeCurrent = SCaseDicom_csv(iSCaseDicom).CT_current;
    SCaseDicom(iSCaseDicom).InstitutionName = SCaseDicom_csv(iSCaseDicom).CT_institution;
    SCaseDicom(iSCaseDicom).Manufacturer = SCaseDicom_csv(iSCaseDicom).CT_manufacturer;
    SCaseDicom(iSCaseDicom).ManufacturerModelName = SCaseDicom_csv(iSCaseDicom).CT_model;
    SCaseDicom(iSCaseDicom).ProtocolName = SCaseDicom_csv(iSCaseDicom).CT_protocol;
    SCaseDicom(iSCaseDicom).SeriesDescription = SCaseDicom_csv(iSCaseDicom).CT_SeriesDescription;
    end

end

% Write csv file
csvFileId = fopen(csvFilename, 'w');
fprintf(csvFileId,dataHeader);
for SCase_idx=1:1:numel(SCaseDicom) % Loop on all SCase provided by listSCase()
    fprintf(csvFileId,'\n%s,%s,%s,%s,%f,%f,%f,%s,%s,%f,%f,%f,%f,%f,%s,%s,%s,%s,%s',...
        SCaseDicom(SCase_idx).id,...
        SCaseDicom(SCase_idx).PatientID,...
        SCaseDicom(SCase_idx).PatientSex,...
        SCaseDicom(SCase_idx).PatientBirthDate,...
        SCaseDicom(SCase_idx).PatientAge,...
        SCaseDicom(SCase_idx).PatientSize,...
        SCaseDicom(SCase_idx).PatientWeight,...
        SCaseDicom(SCase_idx).AcquisitionDate,...
        SCaseDicom(SCase_idx).ConvolutionKernel,...
        SCaseDicom(SCase_idx).PixelSpacing,...
        SCaseDicom(SCase_idx).SpacingBetweenSlices,...
        SCaseDicom(SCase_idx).SliceThickness,...
        SCaseDicom(SCase_idx).KVP,...
        SCaseDicom(SCase_idx).XrayTubeCurrent,...
        SCaseDicom(SCase_idx).InstitutionName,...
        SCaseDicom(SCase_idx).Manufacturer,...
        SCaseDicom(SCase_idx).ManufacturerModelName,...
        SCaseDicom(SCase_idx).ProtocolName,...
        SCaseDicom(SCase_idx).SeriesDescription...
        );
end
fclose(csvFileId);

fprintf(logFileID, sprintf('\n\n%s %s', 'Saved csv file: ', csvFilename));

%% Write xls file (Windows only)
[~,message] = csv2xlsSCase(csvFilename);
fprintf(logFileID, message);

%% Update MySQL
% To be done
%{
addpath('XLS_MySQL_DB');
MainExcel2SQL;
%}

%% Final log
fprintf(logFileID, '\n\nSCases treated: %s', num2str(numel(SCaseDicom))); % Number of SCases treated
fprintf(logFileID, '\nElapsed time (s): %s', num2str(toc)); % stopwatch timer
fclose(logFileID); % Close log file

outputArg = 1; % Might be extended
end