function [status,message] = measureSCase(varargin)
% MEASURESCASE Update the entire SCase DB with anatomical measurements.

% The function should be run from the server (lbovenus), from the user account containing the git repository,
% with the following shell command
% matlab -nodisplay -nosplash -r "measureSCase;quit"
% For long calculations, it can be run in the background using tmux, followed
% by Ctrl+b d to detach the session and keep the process running.

% Progress can be checked through log file with following shell command
% tail -f log/measureSCase.log

% It take ~30 min for 700 cases when run from server.
% After run from server, the output file
% /shoulder/data/Excel/xlsFromMatlab/anatomy.csv
% must be open from Excel and saved
% as xls at the same location. Excel file
% /shoulder/data/Excel/ShoulderDataBase.xlsx should also be open, updated, and saved.

% The script measureSCase was replacing 3 previous functions
% 1) rebuildDatabaseScapulaMeasurements.m --> list of all SCases --> execute scapula_measure.m
% 2) scapula_measure.m --> execute scapula_calculation and save results in Excel and SQL
% 3) scapula_calculation.m --> perform anatomical analysis --> results variable


% Input arguments can be one or several among:
%     {Empty,'glenoidDensity', 'update', 'musclesDegeneration' '[NP][1-999]', '[NP]'}
%
%     If there is no argument the function will measure every new case.
%     The 'N' or 'P' given as an argument will load all the Normal or Pathological cases.
%
%     The measurements are divided into three measurements: "morphology", "glenoidDensity",
%     and "musclesDegeneration". The default measurement is the "morphology" one, the
%     two others has to be given in arguments in order to be done.%
%
%     Examples:
%              measureSCase()
%                 is a valid instruction where on every new case is done the
%                 "morphology" measurement.
%              measureSCase('glenoidDensity','musclesDegeneration')
%                 is a valid instruction where on every cases are done the
%                 "morphology","glenoidDensity", and "musclesDegeneration" measurements
%                 if one of these measurements is missing.
%              measureSCase('P400','N520')
%                 is a valid instruction where on the cases 'P400' and 'N520' is
%                 done the "morphology" measurement  only if they have not already
%                 been measured yet (new cases).
%              measureSCase('P400','N520','update')
%                 is a valid instruction where on the cases 'P400' and 'N520' is
%                 done the "morphology" measurement whether they have already been
%                 measured yet or not.
%              measureSCase('glenoidDensity','P400','N520','update','P')
%                 is a valid instruction where on all the 'P' cases and the case N520 
%                 are done the "morphology" and "glenoidDensity" measurements whether 
%                 they have been  measured yet or not.

% Output
%    File /shoulder/data/Excel/xlsFromMatlab/anatomy.csv
%    File /shoulder/data/Excel/xlsFromMatlab/anatomy.xls (only windows)
%    File /home/shoulder/data/matlab/SCaseDB.mat
%    File {SCaseId}.mat in each {SCaseId}/{CT}/matlab directory
%    logs in /log/measureSCase.log

% Authors: Alexandre Terrier, EPFL-LBO
%          Matthieu Boubat, EPFL-LBO
% Creation date: 2018-07-01
% Revision date: 2020-06-09

% TO DO:
%  Read first last anatomy.csv and/or SCaseDB.mat
%  Fill with patient and clinical data, from excel or MySQL
%  use argument to redo or update
%  Save csv within the main loop (not sure it's a good idea)
%  Add more message in log
%  Add more test to assess validity of data
%  Update MySQL
%  Rename all objects with a capital
%  Make it faster by not loading scapula surface if already in SCaseDB.mat
%  Add argument 'load' to force reload files even if they are alerady in DB
%  Add argument 'measure' to force re-measuring event if measurement is already in DB
%  Add "scapula_addmeasure.m" --> should be coded in ShoulderCase class

startTime = datetime('now');

%% Add environment to path
addpath(genpath(pwd));

%% Open log file
logFileID = openLogFile('measureSCase.log');

%% Set the data directory from the configuration file config.txt
dataDir = ConfigFileExtractor.getVariable('dataDir');

%% Location of the XLS ShoulderDatabase
xlsDir    = [dataDir '/Excel/xlsFromMatlab'];
matlabDir = [dataDir '/matlab'];

%% Instanciate case loader
database = ShoulderCaseLoader();

%% Get list of all SCase
% Get list of SCases from varargin

% Delault value for varargin
calcGlenoidDensity = false;
calcMusclesDegeneration = false;
updateCalculations = false;
specificCases = true;

fprintf(logFileID, '\n\nList of SCase');

allCases = database.getAllCasesID();
assert(not(isempty(allCases)),'The database is empty, check that the provided data path is valid.');
requestedCases = {};

for argument = 1:nargin
  switch lower(varargin{argument})                                              % Test every argument in varargin.
    case 'glenoiddensity'
      calcGlenoidDensity = true;
    case 'musclesdegeneration'
      calcMusclesDegeneration = true;
    case 'update'
      updateCalculations = true;
    case regexp(lower(varargin{argument}),'[p]','match')                        % Detect if argument is 'P'.
      requestedCases = [requestedCases database.getAllPathologicalCasesIDs()];
    case regexp(lower(varargin{argument}),'[n]','match')                        % Detect if argument is 'N'.
      requestedCases = [requestedCases database.getAllNormalCasesIDs()];
    case regexp(lower(varargin{argument}),'[np][1-9][0-9]{0,2}','match')        % Test for a correct argument [NP][1-999]
      if database.containsCase(varargin{argument})
        requestedCases = [requestedCases varargin{argument}];
      end
    otherwise
      warning(['\n "%s" is not a valid argument and has not been added to the'...
               ' list of cases.\n measureSCase arguments format must be "[npNP]",'...
               ' "[npNP][1-999]", "GlenoidDensity", or "update"'],varargin{argument})
  end
end

SCaseList = allCases(find(ismember(allCases,requestedCases)));    % Remove cases that appears multiple times 
if isempty(SCaseList)
  disp('No valid ShoulderCase have been given in argument. All the cases found in the database will be measured.');
  SCaseList = allCases;
end

%% Load current xls database (for clinical data)
fprintf(logFileID, '\nLoad xls database\n\n');
addpath('XLS_MySQL_DB');
filename = [dataDir '/Excel/ShoulderDataBase.xlsx'];
excelRaw = rawFromExcel(filename); % cell array

excelSCaseID = excelRaw(2:end, 1);
excelDiagnosis = excelRaw(2:end, 4);
excelPatientHeight = excelRaw(2:end, 23);
excelGlenoidWalch = excelRaw(2:end, 55);


% Lines below adapted from XLS_MySQL_DB/MainExcel2XLS
% Excel.diagnosisList = diagnosisListFromExcel(Excel.Raw);
% Excel.treatmentList = treatmentListFromExcel(Excel.Raw);
% ExcelData.Patient = patientFromExcel(excelRaw); % Structure with patient data
% Excel.shoulder = shoulderFromExcel(Excel.patient, Excel.Raw);
% [Excel.SCase, Excel.diagnosis, Excel.treatment, Excel.outcome, Excel.study] = SCaseFromExcel(...
%     Excel.shoulder, Excel.patient, Excel.diagnosisList, Excel.treatmentList, Excel.Raw);
% fprintf(logFileID, ': OK');

%% Add path to ShoulderCase class
addpath('ShoulderCase');

%% Instance of a ShoulderCase object
if (exist('SCase','var') > 0)
    clear SCase; % Check for delete method
end
SCaseDB = {};
SCase = [];


% %%%% definition of analysis variables
% %
% %    % manual
% %
% ok = {};
% amira = {};
% scapulaLoad = {};
% scapulaCoord = {};
% degeneration = {};
% glenoidLoad = {};
% glenoidMorphology = {};
% glenoidDensity = {};
% humerusLoad = {};
% humerusSubluxation = {};
% acromionMorphology = {};
% %
% %    % auto
% %
% autoOk = {};
% autoScapulaLoad = {};
% autoScapulaCoord = {};
% %autoDegeneration = {};
% autoGlenoidLoad = {};
% autoGlenoidMorphology = {};
% autoGlenoidDensity = {};
% %autoHumerusLoad = {};
% %autoHumerusSubluxation = {};
% autoAcromionMorphology = {};
% %
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


%% Start loop over SCases in SCaseList
nSCase = length(SCaseList); % Number of SCases
for iSCaseID = 1:nSCase
  SCaseID = SCaseList{iSCaseID};

  if not(updateCalculations)
    try
      SCase = database.loadCase(SCaseID);
    catch ME
      SCase = database.createEmptyCase(SCaseID);
      warning(ME.message);
    end
  else
    SCase = database.createEmptyCase(SCaseID);
  end

  % newSCase = ShoulderCase(SCaseID);
  % SCase = newSCase;
  % SCase.dataPath = dataDir; % Set dataDir for SCase
  manualMeasurementAvailable = not(isempty(dir(SCase.dataAmiraPath))); % Set data path of this SCase
  autoMeasurementsAvailable = not(isempty(dir([SCase.dataMatlabPath '/scapulaLandmarksAuto*.mat'])));

  percentProgress = num2str(iSCaseID/nSCase*100, '%3.1f');
  fprintf(logFileID, ['\n___________________________________\n|\n| SCaseID: ' SCaseID ' (' percentProgress '%%)']);



  %% The following section is a temporary solution to the arguments handling.
  %% It splits the measurements process into six parts (shoulderMorphology,
  %% glenoidDensity, musclesDegeneration for both manual and auto cases).
  %% Each part are independently 'ordered' based on some conditions.

  orderMorphologyMeasurementManual = false;
  orderDensityMeasurementManual = false;
  orderDegenerationMeasurementManual = false;

  orderMorphologyMeasurementAuto = false;
  orderDensityMeasurementAuto = false;
  orderDegenerationMeasurementAuto = false;

  if or(not(exist([SCase.dataMatlabPath '/SCase.mat'],'file')), updateCalculations)
    orderMorphologyMeasurementManual = true;
    orderMorphologyMeasurementAuto = true;
    if (calcGlenoidDensity)
      orderDensityMeasurementManual = true;
      orderDensityMeasurementAuto = true;
    end
    if (calcMusclesDegeneration)
      orderDegenerationMeasurementManual = true;
      orderDegenerationMeasurementAuto = true;
    end
  else
    loadedSCase = database.loadCase(SCase.id);
    musclesManual = loadedSCase.shoulderManual.muscles;
    musclesAuto = loadedSCase.shoulderAuto.muscles;
    if and(calcGlenoidDensity, isempty(loadedSCase.shoulderManual.scapula.glenoid.density))
      orderMorphologyMeasurementManual = true;
      orderDensityMeasurementManual = true;
      SCase = loadedSCase;
    end
    if and(calcGlenoidDensity, isempty(loadedSCase.shoulderAuto.scapula.glenoid.density))
      orderMorphologyMeasurementAuto = true;
      orderDensityMeasurementAuto = true;
      SCase = loadedSCase;
    end
    if and(calcMusclesDegeneration, not(all(table2array(musclesManual.summary(:,{'PCSA'})))) )
      orderMorphologyMeasurementManual = true;
      orderDegenerationMeasurementManual = true;
      SCase = loadedSCase;
    end
    if and(calcMusclesDegeneration, not(all(table2array(musclesAuto.summary(:,{'PCSA'})))) )
      orderMorphologyMeasurementAuto = true;
      orderDegenerationMeasurementAuto = true;
      SCase = loadedSCase;
    end
  end

  %%
  %% The section above (and basically all the measureSCase function) will be removed
  %% in the upcoming implementation of ShoulderCase measurements.
  %% Matthieu Boubat, 06.03.2020
  %%



  % There are 3 parts within this SCase loop:
  % 1) Load & analyses manual data from amira
  % 2) Load & analyses auto   data from matlab (Statistical Shape Model)
  % 3) Load clinical data from Excel database, and set them to SCase
  % 4) Save SCase in file SCaseID/matlab/SCase.mat



  % 1) Load & analyses manual data from amira

  if manualMeasurementAvailable
    tic;
    fprintf(logFileID, '\n|  Segmentation manual ');

    try
      if orderMorphologyMeasurementManual
        measureShoulderMorphology(SCase.shoulderManual,logFileID);
      end
    catch ME
      fprintf(logFileID,ME.message);
    end

    try
      if orderDensityMeasurementManual
        measureGlenoidDensity(SCase.shoulderManual,logFileID);
      end
    catch ME
      fprintf(logFileID,ME.message);
    end

    try
      if orderDegenerationMeasurementManual
        measureMusclesDegeneration(SCase.shoulderManual,logFileID);
      end
    catch ME
      fprintf(logFileID,ME.message);
    end

    fprintf(logFileID, '\n|  Elapsed time (s): %s\n|', num2str(toc));
  end




  % 2) Load & analyses auto data from matlab

  if autoMeasurementsAvailable
    tic;
    fprintf(logFileID, '\n|  Segmentation auto ');

    try
      if orderMorphologyMeasurementAuto
        measureShoulderMorphology(SCase.shoulderAuto,logFileID);
      end
    catch ME
      fprintf(logFileID,ME.message);
    end

    try
      if orderDensityMeasurementAuto
        measureGlenoidDensity(SCase.shoulderAuto,logFileID);
      end
    catch ME
      fprintf(logFileID,ME.message);
    end

    try
      if orderDegenerationMeasurementAuto
        measureMusclesDegeneration(SCase.shoulderAuto,logFileID);
      end
    catch ME
      fprintf(logFileID,ME.message);
    end

    fprintf(logFileID, '\n|  Elapsed time (s): %s\n|', num2str(toc));
  end



  % 3) Set clinical data from Excel database to SCase
  fprintf(logFileID, '\n|\n|  Set clinical data from Excel');
  % Get idx of excelRaw for SCaseID
  % Use cell2struct when dots are removed from excel headers
  try
    idx = find(strcmp(excelRaw, SCaseID)); % Index of SCaseID in excelRaw
    SCase.diagnosis = excelRaw{idx,4};
    SCase.treatment = excelRaw{idx,9};
    SCase.patient.gender = excelRaw{idx,19};
    SCase.patient.age = excelRaw{idx,21};
    SCase.patient.height = excelRaw{idx,23};
    SCase.patient.weight = excelRaw{idx,24};
    SCase.patient.BMI = excelRaw{idx,25};
    SCase.shoulderAuto.scapula.glenoid.walch = excelRaw{idx,55};
    SCase.shoulderManual.scapula.glenoid.walch = excelRaw{idx,55};
    fprintf(logFileID, ': OK');
  catch
    fprintf(logFileID, ': ERROR');
  end

  % 4) Save SCase
  try
    fprintf(logFileID, '\n| Save SCase.mat');
    SCase.saveMatlab;
    fprintf(logFileID, ': OK');
  catch
    fprintf(logFileID, ': ERROR');
  end
  fprintf(logFileID, '\n|___________________________________\n\n');
  % 4) Load & analyses auto data from matlab (Statistical Shape Model)
  % Load scapula surface and landmarks
  % save('measureSCase_analysis.mat',...
  %      'ok','amira','scapulaLoad','scapulaCoord',...
  %      'degeneration','glenoidLoad','glenoidMorphology','glenoidDensity',...
  %      'humerusLoad','humerusSubluxation','acromionMorphology',...
  %      'autoOk','autoScapulaLoad','autoScapulaCoord','autoGlenoidLoad',...
  %      'autoGlenoidMorphology','autoGlenoidDensity','autoAcromionMorphology')

end % End of loop on SCaseList

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


% Replace header and data by structure. Currently not working
%{
txtFilename = [xlsDir, '/anatomy.txt']; % Name of the txt file

DataStruc = struc(...
    'SCase_id',              SCase.id, ...
    'shoulder_side',         SCase.shoulder.side,...
    'glenoid_radius',        SCase.shoulder.scapula.glenoid.radius,...
    'glenoid_sphereRMSE',    SCase.shoulder.scapula.glenoid.sphereRMSE,...
    'glenoid_depth',         SCase.shoulder.scapula.glenoid.depth,...
    'glenoid_width',         SCase.shoulder.scapula.glenoid.width,...
    'glenoid_height',        SCase.shoulder.scapula.glenoid.height,...
    'glenoid_centerPA',      SCase.shoulder.scapula.glenoid.centerLocal(1),...
    'glenoid_centerIS',      SCase.shoulder.scapula.glenoid.centerLocal(2),...
    'glenoid_centerML',      SCase.shoulder.scapula.glenoid.centerLocal(3),...
    'glenoid_versionAmpl',   SCase.shoulder.scapula.glenoid.versionAmpl,...
    'glenoid_versionOrient', SCase.shoulder.scapula.glenoid.versionOrient,...
    'glenoid_version',       SCase.shoulder.scapula.glenoid.version,...
    'glenoid_inclination',   SCase.shoulder.scapula.glenoid.inclination,...
    'humerus_jointRadius',   SCase.shoulder.humerus.jointRadius,...
    'humerus_headRadius',    SCase.shoulder.humerus.radius,...
    'humerus_GHSAmpl',       SCase.shoulder.humerus.GHSAmpl,...
    'humerus_GHSOrient',     SCase.shoulder.humerus.GHSOrient,...
    'humerus_SHSAmpl',       SCase.shoulder.humerus.SHSAmpl,...
    'humerus_SHSOrient',     SCase.shoulder.humerus.SHSOrient,...
    'humerus_SHSAngle',      SCase.shoulder.humerus.SHSAngle,...
    'humerus_SHSPA',         SCase.shoulder.humerus.SHSPA,...
    'humerus_SHSIS',         SCase.shoulder.humerus.SHSIS,...
    'acromion_AI',           SCase.shoulder.scapula.acromion.AI,...
    'acromion_CSA',          SCase.shoulder.scapula.acromion.CSA,...
    'acromion_PS',           SCase.shoulder.scapula.acromion.PS...
    );
DataTable = strct2table(Data);
writetable(DataTable,filename);
%}

% Header of the csv file

dataHeader = [...
    'SCase_id,' ...
    'shoulder_side,' ...
    'glenoid_radius,' ...
    'glenoid_sphereRMSE,' ...
    'glenoid_depth,' ...
    'glenoid_width,' ...
    'glenoid_height,' ...
    'glenoid_centerPA,' ...
    'glenoid_centerIS,' ...
    'glenoid_centerML,' ...
    'glenoid_versionAmpl,' ...
    'glenoid_versionOrient,' ...
    'glenoid_version,' ...
    'glenoid_inclination,' ...
    'humerus_jointRadius,' ...
    'humerus_headRadius,' ...
    'humerus_GHSAmpl,' ...
    'humerus_GHSOrient,' ...
    'humerus_SHSAmpl,' ...
    'humerus_SHSOrient,' ...
    'humerus_SHSAngle,' ...
    'humerus_SHSPA,' ...
    'humerus_SHSIS,' ...
    'acromion_AI,' ...
    'acromion_CSA,' ...
    'acromion_PSA,'...
    'acromion_AAA\n'...
    ];


fprintf(logFileID, '\n\nSave anatomy.csv file');
fid = fopen([xlsDir, '/anatomy.csv'],'w');      %Last csv is deleted and a new one, updated is being created
fprintf(fid,dataHeader);
fclose(fid);

% The following lines re-create the SCaseDB.mat and contruct the anatomy.csv file
SCaseDB = database.loadAllCases();
cellfun(@(SCase)SCase.appendToCSV('anatomy.csv'),SCaseDB);     % Call method appendToCSV() on all element of the SCaseDB cell array

fprintf(logFileID, ': OK');

%% Save the entire SCaseDB array as a matlab file
fprintf(logFileID, '\n\nSave SCase database');
filename = 'SCaseDB';
filename = [matlabDir '/' filename '.mat'];
try
  save(filename, 'SCaseDB');
  fprintf(logFileID, ': OK');
catch
  fprintf(logFileID, ': Error');
end

%fprintf(logFileID, [': ' csvFilename]);

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

% If run from non-windows system, only csv will be produced. The xls can be
% produced by opening the csv from Excel and save as xls.
% Could be a function with 1 input (cvsFilenames



%{
xlsFilename = strrep(csvFilename, '.csv', '.xls'); % Replace .csv by .xls
if ispc % Check if run from windows!
    % Read cvs file as table and write the table as xls
    cvsTable = readtable(csvFilename); % Get table from csv (only way to read non-numeric data)
    cvsCell = table2cell(cvsTable); % Tranform table cell array
    dataHeader = cvsTable.Properties.VariableNames; % Get header
    cvsCell = [dataHeader; cvsCell]; % Add header

    sheet = 'anatomy'; % Sheet name of the xls file

    [status,message] = xlswrite(xlsFilename, cvsCell, sheet); % Save xls
    if status
        fprintf(logFileId, ['\nSaved ' xlsFilename]);
    else
        fprintf(logFileId, ['\nCould not save ' xlsFilename]);
        fprintf(logFileId, ['\n' message.identifier]);
        fprintf(logFileId, ['\n' message.message]);
    end
else
    fprintf(logFileId, ['\n' xlsFilename ' not saved. Open and save as xls from Excel']);
end
%}


%% Close log file
fprintf(logFileID, '\n\nSCase measured: %s', num2str(length(SCaseList))); % Number of SCases measured

elapsedTime = char(datetime('now')-startTime);
elapsedTime = [elapsedTime(1:2) ' hours ' elapsedTime(4:5) ' minutes ' elapsedTime(7:8) ' seconds'];

fprintf(logFileID, ['\nTotal Elapsed time: ' elapsedTime ]);
fprintf(logFileID, '\n');
fclose(logFileID); % Close log file

%% Output of the SCase if required by argument
% SCase.output % inputArg = abaqus/density/references/

% update mySQL
% SCase.sqlSave


status  = 1;
message = 'OK';

end



function measureShoulderMorphology(shoulder,logFileID)

  fprintf(logFileID, '\n|   Load scapula surface and landmarks');
  output = shoulder.scapula.load;

        if ~output
          fprintf(logFileID, ': ERROR');
          % scapulaLoad{end+1} = SCaseID;
          return
        end

  fprintf(logFileID, ': OK');
  fprintf(logFileID, '\n|   Set coord. syst.');
  output = shoulder.scapula.coordSysSet;

        if ~output
          fprintf(logFileID, ': ERROR');
          % scapulaCoord{end+1} = SCaseID;
          return;
        end

  fprintf(logFileID, ': OK');
  fprintf(logFileID, '\n|   Load glenoid surface');
  output = shoulder.scapula.glenoid.load;

        if ~output
          fprintf(logFileID, '\n|   glenoid surface loading error');
          % glenoidLoad{end+1} = SCaseID;
          return;
        end

  fprintf(logFileID, ': OK');
  fprintf(logFileID, '\n|   Measure glenoid anatomy');
  output = shoulder.scapula.glenoid.morphology;

        if ~output
          fprintf(logFileID, ': ERROR');
          % glenoidMorphology{end+1} = SCaseID;
          return;
        end

  fprintf(logFileID, ': OK');
  fprintf(logFileID, '\n|   Load humerus data');
  output = shoulder.humerus.load;

        if ~output
          fprintf(logFileID, ': ERROR');
          % humerusLoad{end+1} = SCaseID;
          return;
        end

  fprintf(logFileID, ': OK');
  fprintf(logFileID, '\n|   Measure humerus subluxation');
  output = shoulder.humerus.subluxation(shoulder.scapula);

        if ~output
          fprintf(logFileID, ': ERROR');
          % humerusSubluxation{end+1} = SCaseID;
          return;
        end

  fprintf(logFileID, ': OK');
  fprintf(logFileID, '\n|   Measure acromion anatomy');
  % Should be run after SCase.shoulderManual.humerus (for AI)
  output = shoulder.scapula.acromion.morphology;

        if ~output
          fprintf(logFileID, ': ERROR');
          % acromionMorphology{end+1} = SCaseID;
          return;
        end

  fprintf(logFileID, ': OK');
end




function measureGlenoidDensity(shoulder,logFileID)
  fprintf(logFileID, '\n|   Measure glenoid density');
  output = shoulder.scapula.glenoid.calcDensity;

  if ~output
    fprintf(logFileID, ': Density calculus error. Could not read dicom');
    return;
  end

  fprintf(logFileID, ': OK');
end


function measureMusclesDegeneration(shoulder,logFileID)
  fprintf(logFileID, '\n|   Measure muscle''s degeneration');

  % auto segmentation with most recent slicing methods
  try
    shoulder.muscles.createRotatorCuffSlicesMatthieu('rotatorCuffMatthieu');
    shoulder.muscles.segmentRotatorCuffMuscles('rotatorCuffMatthieu','autoMatthieu');
  catch ME
    fprintf(logFileID,ME.message);
  end

  % auto segmentation with former slicing methods
  try
    shoulder.muscles.createRotatorCuffSlicesNathan('rotatorCuffNathan');
    shoulder.muscles.segmentRotatorCuffMuscles('rotatorCuffNathan','autoNathan');
  catch ME
    fprintf(logFileID,ME.message);
  end


  % muscles measurements
  try
    shoulder.muscles.measureAllMuscles('rotatorCuffMatthieu','autoMatthieu');
  catch ME
    fprintf(logFileID,ME.message);
  end
  
  fprintf(logFileID, ': OK');
end