diff --git a/SCase.mat b/SCase.mat deleted file mode 100755 index 8d81480..0000000 Binary files a/SCase.mat and /dev/null differ diff --git a/measureSCase.m b/measureSCase.m index 08e1c9a..0a7dc42 100755 --- a/measureSCase.m +++ b/measureSCase.m @@ -1,474 +1,475 @@ 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][000-999]', '[NP]'} % % If there is no argument the function will measure every new case. % The first '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][000-999]' given before and will % not take the next arguments into account. % % 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','P','Update') % is a valid instruction where all the 'P' cases are measured % including their glenoid density only if they have not been % measured yet (new P cases). % 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 tic; % Start stopwatch timer %% 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 inputArg calcGlenoidDensity = false; updateCalculations = false; fprintf(logFileID, '\n\nList of SCase'); cases = {}; for argument = 1:nargin switch varargin{argument} % Test every argument in varargin. case 'GlenoidDensity' calcGlenoidDensity = true; case 'Update' updateCalculations = true; case regexp(varargin{argument},'[NP]','match') % Detect if argument is 'N' or 'P'. cases = {}; % If it's the case the for loop cases{end+1} = varargin{argument}; % ends here. break % case regexp(varargin{argument},'[NP]\d{3}','match') % Test for a correct argument [NP]+[000-999] cases{end+1} = varargin{argument}; 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 "[NP]",'... ' "[NP][000-999]", "GlenoidDensity", or "Update"'],varargin{argument}) end end SCaseList = listSCase(cases); %% Load current xls database (for clinical data) fprintf(logFileID, '\nLoad xls database'); 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; % Instanciate a ShoulderCase object SCase.dataPath = dataDir; % Set dataDir for SCase %% 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 percentProgress = num2str(iSCaseID/nSCase*100, '%3.1f'); fprintf(logFileID, ['\n\nSCaseID: ' SCaseID ' (' percentProgress '%%)']); % 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 (~exist([SCase(iSCaseID).dataMatlabPath '\SCase.mat'],'file') || updateCalculations) % New calculation of SCase.mat or update the current calculation fprintf(logFileID, '\n Segmentation manual '); output = SCase(iSCaseID).path; % Set data path of this SCase if output % Continue if amira dir exists in SCase fprintf(logFileID, '\n Load scapula surface and landmarks'); output = SCase(iSCaseID).shoulder.scapula.load; if output fprintf(logFileID, ': OK'); fprintf(logFileID, '\n Set coord. syst.'); output = SCase(iSCaseID).shoulder.scapula.coordSysSet; if output fprintf(logFileID, ': OK'); fprintf(logFileID, '\n Load glenoid surface'); output = SCase(iSCaseID).shoulder.scapula.glenoid.load; if output fprintf(logFileID, ': OK'); fprintf(logFileID, '\n Measure glenoid anatomy'); output = SCase(iSCaseID).shoulder.scapula.glenoid.morphology; if output fprintf(logFileID, ': OK'); if calcGlenoidDensity fprintf(logFileID, '\n Measure glenoid density'); output = SCase(iSCaseID).shoulder.scapula.glenoid.calcDensity; if output fprintf(logFileID, ': OK'); else fprintf(logFileID, ': Could no read dicom'); end end fprintf(logFileID, '\n Load humerus data'); output = SCase(iSCaseID).shoulder.humerus.load; if output fprintf(logFileID, ': OK'); fprintf(logFileID, '\n Measure humerus subluxation'); output = SCase(iSCaseID).shoulder.humerus.subluxation; if output fprintf(logFileID, ': OK'); fprintf(logFileID, '\n Measure acromion anatomy'); % Should be run after SCase.shoulder.humerus (for AI) output = SCase(iSCaseID).shoulder.scapula.acromion.morphology; if output fprintf(logFileID, ': OK'); else fprintf(logFileID, '\n: Measure acromion anatomy error'); end % Acromion anatomy else fprintf(logFileID, '\n: Measure humerus subluxation error'); end % Subluxation humerus else fprintf(logFileID, '\n: Load humerus data error'); end % Load humerus else fprintf(logFileID, '\n: Measure glenoid anatomy error'); end % Anatomy glenoid else fprintf(logFileID, '\n: Density calculus error'); end % Load glenoid else fprintf(logFileID, '\n Scapula coord syst error '); end % Set coord. syst. else fprintf(logFileID, '\n Scapula loading error'); end % Load scapula else fprintf(logFileID, '\n No amira folder'); end % Amira path exist end % 2) Load & analyses auto data from matlab (Statistical Shape Model) fprintf(logFileID, '\n Segmentation auto '); % Load scapula surface and landmarks fprintf(logFileID, '\n Load scapula surface and landmarks'); output = SCase(iSCaseID).shoulder.scapulaAuto.loadAuto; % Load auto data from matlab directory if output fprintf(logFileID, ': OK'); fprintf(logFileID, '\n Set coord. syst.'); output = SCase(iSCaseID).shoulder.scapulaAuto.coordSysSet; if output fprintf(logFileID, ': OK'); fprintf(logFileID, '\n Load glenoid surface'); output = SCase(iSCaseID).shoulder.scapulaAuto.glenoid.loadAuto; if output fprintf(logFileID, ': OK'); fprintf(logFileID, '\n Measure glenoid anatomy'); output = SCase(iSCaseID).shoulder.scapulaAuto.glenoid.morphology; if output fprintf(logFileID, ': OK'); else fprintf(logFileID, '\n: Error in measuring glenoid anatomy'); end else fprintf(logFileID, '\n: Error in loading glenoid surface'); end else fprintf(logFileID, '\n: Error in setting the coordonnate System'); end else fprintf(logFileID, '\n: Error in loading scapula surface and landmarks'); end % 3) Set clinical data from Excel database to SCase fprintf(logFileID, '\n Set clinical data from Excel'); % Get idx of excelRaw for SCaseID % Use cell2struct when dots are removed from excel headers 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).shoulder.scapula.glenoid.walch = excelRaw{idx,55}; % Patient data --> TO DO % find patient id (in SQL) corresponding to iSCaseID % % % idxSCase = find(contains(ExcelData, SCaseID)); % SCase(iSCaseID).patient.id = ExcelData(idxSCase).patient.patient_id; % SQL patient id % SCase(iSCaseID).patient.idMed = ExcelData(idxSCase).patient.IPP; % IPP to be replace by coded (anonymized) IPP from SecuTrial % SCase(iSCaseID).patient.gender = ExcelData(idxSCase).patient.gender; % SCase(iSCaseID).patient.age = []; % Age (years) at treatment, or preop CT (we might also add birthdate wi day et at 15 of the month) % SCase(iSCaseID).patient.ethnicity = ExcelData(idxSCase).patient.IPP; % SCase(iSCaseID).patient.weight = ExcelData(idxSCase).patient.weight; % SCase(iSCaseID).patient.height = ExcelData(idxSCase).patient.height; % SCase(iSCaseID).patient.BMI = ExcelData(idxSCase).pateint.BMI; % SCase(iSCaseID).patient.comment = ExcelData(idxSCase).patient.comment; % 4) Save SCase in file SCaseID/matlab/SCase.mat fprintf(logFileID, '\n Save SCase'); output = SCase(iSCaseID).saveMatlab; if output fprintf(logFileID, ': OK'); else fprintf(logFileID, ': Error'); end end % End of loop on SCaseList %% Save the entire SCase array as a matlab file -fprintf(logFileID, '\n\n Save SCase database'); +fprintf(logFileID, '\n\nSave SCase database'); filename = 'SCaseDB'; filename = [matlabDir '/' filename '.mat']; try SCaseDB = SCase; save(filename, 'SCaseDB'); fprintf(logFileID, ': OK'); catch fprintf(logFileID, ': Error'); end %% Write csv file % This might be a function (SCase.csvSave()). The input would be a filename and a structure % data -fprintf(logFileID, '\n Save csv database'); % 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 + +fprintf(logFileID, '\n\nSave csv database'); + 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\n\nUpdating CSV\n'); - updateSCase = listSCase; fid = fopen([xlsDir, '/anatomy.csv'],'w'); %Last csv is deleted and a new one, updated is being created fprintf(fid,dataHeader); fclose(fid); for iSCaseID=1:length(updateSCase) SCaseID = updateSCase(iSCaseID).id; SCase(iSCaseID).id = SCaseID; SCase(iSCaseID).dataPath = dataDir; SCase(iSCaseID).path; loadingVariable = load([SCase(iSCaseID).dataMatlabPath '/SCase.mat']); %Loading current SCase.mat content in loadingVariable loadingVariable(1,1).SCase.appendToCSV('anatomy.csv'); end +fprintf(logFileID, ': OK'); %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 fprintf(logFileID, '\nElapsed time (s): %s', num2str(toc)); % stopwatch timer 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