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R8218/measureSCase.m
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measureSCase.m
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			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(contains(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.createRotatorCuffSlices('rotatorCuff');
			shoulder.muscles.segmentRotatorCuffMuscles('rotatorCuff','auto');
			catch ME
			fprintf(logFileID,ME.message);
			end

			% auto segmentation with former slicing methods
			try
			shoulder.muscles.createRotatorCuffSlicesOld('rotatorCuffOld');
			shoulder.muscles.segmentRotatorCuffMuscles('rotatorCuffOld','autoOld');
			catch ME
			fprintf(logFileID,ME.message);
			end


			% muscles measurements
			try
			shoulder.muscles.measureAllMuscles('rotatorCuff','auto_Mask');
			catch ME
			fprintf(logFileID,ME.message);
			end

			fprintf(logFileID, ': OK');
			end

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