function [status,message] = measureSCase(varargin) % MEASURESCASE Update the entire SCase DB with anatomical measurements. % The function can be run from (lbovenus) server with the following shell command % cd /home/shoulder/methods/matlab/database; matlab -nodisplay -nosplash -r "measureSCase;quit" % Progress can be checked through log file with following shell command % cd /home/shoulder/methods/matlab/database;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 varaiable % Input arguments can be one or several among: % {Empty,'GlenoidDensity', 'update', '[NP][1-999]', '[NP]'} % % If there is no argument the function will measure every new case. % The last 'N' or 'P' given as an argument will force the function to be % executed on all the corresponding 'N' or 'P' cases. This will overwrite % every other ShoulderCase argument '[NP][1-999]' given before. % % Examples: % measureSCase('GlenoidDensity') % is a valid instruction where every new case is measured % including its glenoid density. % measureSCase('P400','N520') % is a valid instruction where the cases 'P400' and 'N520' are % measured only if they have not already been measured yet (new % cases). % measureSCase('P400','N520','update') % is a valid instruction where the cases 'P400' and 'N520' are % measured whether they have already been measured or not. % measureSCase('GlenoidDensity','P400','N520','update','P') % is a valid instruction where all the 'P' cases are measured % including their glenoid density whether they have been % measured or not. % measureSCase('Z1590','trollingArgumentLol') % is a valid instruction which raises a warning about the % arguments and will result in the same as executing % measureSCase() i.e. every new case is calculated. % 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 % Example: measureSCase % Author: Alexandre Terrier, EPFL-LBO % Creation date: 2018-07-01 % Revision date: 2019-06-29 % 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'); %% Open log file logFileID = openLogFile('measureSCase.log'); %% Set the data directory from the configuration file config.txt dataDir = openConfigFile('config.txt', logFileID); %% Location of the XLS ShoulderDatabase xlsDir = [dataDir '/Excel/xlsFromMatlab']; matlabDir = [dataDir '/matlab']; %% 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'); cases = {}; 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}),'[np]','match') specificCases = false; % Detect if argument is 'N' or 'P'. cases = {varargin{argument}}; % ends here. case regexp(lower(varargin{argument}),'[np][1-9][0-9]{0,2}','match') % Test for a correct argument [NP][1-999] if specificCases cases{end+1} = upper(varargin{argument}); % for element = 1:length(cases)-1 % Check if the case has already been added to the case list before if strfind(upper(varargin{argument}),cases{element}) cases = cases(1:end-1); % Delete the last element added to cases if it is already in the list end end 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 = listSCase(cases); %% 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 SCase = ShoulderCase('N000'); % Instanciate a ShoulderCase object SCaseDB = {}; SCase.dataPath = dataDir; % Set dataDir for 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).id; SCase(iSCaseID).id = SCaseID; SCase(iSCaseID).dataPath = dataDir; % Set dataDir for SCase manualMeasurementAvailable = SCase(iSCaseID).path; % Set data path of this SCase autoMeasurementsAvailable = exist([SCase(iSCaseID).dataMatlabPath '/scapulaLandmarksAutoR.mat'],'file'); 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(iSCaseID).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 = load([SCase(iSCaseID).dataMatlabPath '/SCase.mat']); loadedSCase = loadedSCase.SCase; loadedSCase.dataPath = dataDir; loadedSCase.path; musclesManual = loadedSCase.shoulderManual.muscles; musclesAuto = loadedSCase.shoulderAuto.muscles; if and(calcGlenoidDensity, isempty(loadedSCase.shoulderManual.scapula.glenoid.density)) orderMorphologyMeasurementManual = true; orderDensityMeasurementManual = true; SCase(iSCaseID) = loadedSCase; end if and(calcGlenoidDensity, isempty(loadedSCase.shoulderAuto.scapula.glenoid.density)) orderMorphologyMeasurementAuto = true; orderDensityMeasurementAuto = true; SCase(iSCaseID) = loadedSCase; end if and(calcMusclesDegeneration, isempty([musclesManual.SS_man, musclesManual.SC_man, musclesManual.IS_man, musclesManual.TM_man])) orderMorphologyMeasurementManual = true; orderDegenerationMeasurementManual = true; SCase(iSCaseID) = loadedSCase; end if and(calcMusclesDegeneration, isempty([musclesAuto.SS_auto, musclesAuto.SC_auto, musclesAuto.IS_auto, musclesAuto.TM_auto])) orderMorphologyMeasurementAuto = true; orderDegenerationMeasurementAuto = true; SCase(iSCaseID) = 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 '); if orderMorphologyMeasurementManual measureShoulderMorphology(SCase(iSCaseID).shoulderManual,logFileID); end if orderDensityMeasurementManual measureGlenoidDensity(SCase(iSCaseID).shoulderManual,logFileID); end if orderDegenerationMeasurementManual measureMusclesDegeneration(SCase(iSCaseID).shoulderManual,logFileID); 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 '); if orderMorphologyMeasurementAuto measureShoulderMorphology(SCase(iSCaseID).shoulderAuto,logFileID); end if orderDensityMeasurementAuto measureGlenoidDensity(SCase(iSCaseID).shoulderAuto,logFileID); end if orderDegenerationMeasurementAuto measureMusclesDegeneration(SCase(iSCaseID).shoulderAuto,logFileID); 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(iSCaseID).diagnosis = excelRaw{idx,4}; SCase(iSCaseID).treatment = excelRaw{idx,9}; SCase(iSCaseID).patient.gender = excelRaw{idx,19}; SCase(iSCaseID).patient.age = excelRaw{idx,21}; SCase(iSCaseID).patient.height = excelRaw{idx,23}; SCase(iSCaseID).patient.weight = excelRaw{idx,24}; SCase(iSCaseID).patient.BMI = excelRaw{idx,25}; SCase(iSCaseID).shoulderAuto.scapula.glenoid.walch = excelRaw{idx,55}; SCase(iSCaseID).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(iSCaseID).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'... ]; updateList = listSCase; % The list of SCase to use to construct anatomy.csv and SCaseDB.mat 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 S = {}; for Case=1:length(updateList) S{Case} = ShoulderCase(updateList(Case).id); % S{Case}.dataPath = dataDir; % S{Case}.path; % Compute the SCase.dataMatlabPath loaded = load([S{Case}.dataMatlabPath '/SCase.mat']); % Load SCase.mat SCaseDB{Case} = loaded.SCase; %SCaseDB{Case}.appendToCSV('anatomy.csv'); end 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'); output = shoulder.muscles.degeneration(logFileID); if output return end fprintf(logFileID, ': OK'); end