classdef ShoulderCase < handle % Properties and methods associated to the SoulderCase object. % Author: Alexandre Terrier, EPFL-LBO % Matthieu Boubat, EPFL-LBO % Creation date: 2018-07-01 % Revision date: 2020-07-23 % TODO: % Need method to load properties (from amira, matlab, excel, SQL) % Need method to save properties (in matlab, excel, SQL) % Remove datapath from constants % properties id = []; % id of the shoulder case, as it appears in the database (Pnnn) id4C = []; % SCaseId with P/N followed by 3 digits --> 4 char diagnosis = []; treatment = []; outcome = []; patient = []; shoulderManual = []; shoulderAuto = []; study = []; comment = []; dataCTPath = []; end methods (Access = ?ShoulderCaseLoader) function obj = ShoulderCase(SCaseID,dataCTPath) % SCaseID validation rawSCaseID = SCaseIDParser(SCaseID); assert(rawSCaseID.isValidID,'The input argument is not a valid SCaseID.') obj.id = SCaseID; obj.id4C = rawSCaseID.getIDWithNumberOfDigits(3); % path attribution obj.dataCTPath = dataCTPath; % Folder creation if not(isfolder(obj.dataMatlabPath)) mkdir(obj.dataMatlabPath); end % Initialsation obj.patient = Patient(obj); obj.shoulderManual = ShoulderManual(obj); obj.shoulderAuto = ShoulderAuto(obj); end end methods function output = dataPath(obj) output = fileparts(obj.dataCTPath); end function output = dataAmiraPath(obj) output = fullfile(obj.dataCTPath, "amira"); end function output = dataMatlabPath(obj) output = fullfile(obj.dataCTPath, "matlab"); end function output = dataDicomPath(obj) output = fullfile(obj.dataCTPath, "dicom"); end function output = dataSlicerPath(obj) output = fullfile(obj.dataCTPath, "slicer"); end function outputArg = output(obj, varargin) % Below is copy/past from previous version % This function is used to output the variable Results, used % by scapula_measurePKG the modified funcion scapula_measure. % inputArg could be as in scapula_calculation % 'density', 'References', 'obliqueSlice', 'display' Result.SCase_id = obj.id; % 1 Result.glenoid_Radius = obj.shoulderManual.scapula.glenoid.radius; % 2 Result.glenoid_radiusRMSE = obj.shoulderManual.scapula.glenoid.fittedSphere.RMSE; % 3 % 3 %Result.glenoidSphericity = ' '; %Result.glenoid_biconcave = ' '; Result.glenoid_depth = obj.shoulderManual.scapula.glenoid.depth; % 4 Result.glenoid_width = obj.shoulderManual.scapula.glenoid.width; % 5 Result.glenoid_height = obj.shoulderManual.scapula.glenoid.height; % 6 Result.glenoid_center_PA = obj.shoulderManual.scapula.glenoid.centerLocal(1); % 7 Result.glenoid_center_IS = obj.shoulderManual.scapula.glenoid.centerLocal(2); % 8 Result.glenoid_center_ML = obj.shoulderManual.scapula.glenoid.centerLocal(3); % 9 Result.glenoid_version_ampl = obj.shoulderManual.scapula.glenoid.versionAmplitude; % 10 Result.glenoid_version_orient = obj.shoulderManual.scapula.glenoid.versionOrientation; % 11 Result.glenoid_Version = obj.shoulderManual.scapula.glenoid.version; % 12 Result.glenoid_Inclination = obj.shoulderManual.scapula.glenoid.inclination; % 13 Result.humerus_joint_radius = ' '; % 14 Result.humeral_head_radius = obj.shoulderManual.humerus.radius; % 15 % Result.humerus_GHsublux_2D = ' '; % Result.humerus_SHsublux_2D = ' '; Result.humerus_GHsubluxation_ampl = obj.shoulderManual.humerus.GHSAmpl; % 16 Result.humerus_GHsubluxation_orient = obj.shoulderManual.humerus.GHSOrient; % 17 Result.humerus_SHsubluxation_ampl = obj.shoulderManual.humerus.SHSAmpl; % 18 Result.humerus_SHsubluxation_orient = obj.shoulderManual.humerus.SHSOrient; % 19 Result.scapula_CSA = obj.shoulderManual.scapula.acromion.criticalShoulderAngle; % radCSA; % 5 Lines below should be updated Result.scapula_CTangle = 0; %CTorientation; %20 Result.scapula_CTangleVersion = 0; % WearPlaneAngle; %21 Result.scapula_CTangleSHS = 0; % SHSPlaneAngle; % 22 Result.scapula_CTangleGHS = 0; % GHSPlaneAngle; % 23 Result.scapula_PlaneRMSE = 0; %PlaneRMSE;%24 Result.scapula_AI = obj.shoulderManual.scapula.acromion.acromionIndex; outputArg = Result; end function outputArg = saveMatlab(obj) % Save SCase to matlab file dir = obj.dataMatlabPath; % Create dir if not exist try if ~exist(dir, 'dir') % create directory if it does not exist mkdir(dir); end catch fprintf('Error creating the matlab directory \n'); % Should be in log end % Save SCase in matlab directoty, in a file named SCaseCNNN.m filename = 'SCase'; filename = fullfile(obj.dataMatlabPath, filename + ".mat"); dataCTPath = obj.dataCTPath; try SCase = obj; % Delete CT path wich must be set when loading/creating the % SCase to avoid messing with paths on different systems. SCase.dataCTPath = []; save(filename, 'SCase'); outputArg = 1; catch fprintf('Error creating SCase matlab file \n'); % Should be in log outputArg = -1; end obj.dataCTPath = dataCTPath; end function outputArg = appendToCSV(obj,filename) % Save SCase to csv file logFid = fopen('log/measureSCase.log', 'a'); dataDir = getConfig().dataDir; xlsDir = [dataDir '/Excel/xlsFromMatlab']; fid = fopen([xlsDir '/' filename],'a'); fprintf(fid,[... obj.id ','... % SCase_id obj.shoulderManual.side ','... % shoulder_side num2str(obj.shoulderManual.scapula.glenoid.radius) ','... % glenoid_radius num2str(obj.shoulderManual.scapula.glenoid.fittedSphere.RMSE) ','... % glenoid_sphereRMSE num2str(obj.shoulderManual.scapula.glenoid.depth) ','... % glenoid_depth num2str(obj.shoulderManual.scapula.glenoid.width) ','... % glenoid_width num2str(obj.shoulderManual.scapula.glenoid.height) ','... % glenoid_height num2str(obj.shoulderManual.scapula.glenoid.centerLocal.x) ','... % glenoid_centerPA num2str(obj.shoulderManual.scapula.glenoid.centerLocal.y) ','... % glenoid_centerIS num2str(obj.shoulderManual.scapula.glenoid.centerLocal.z) ','... % glenoid_centerML num2str(obj.shoulderManual.scapula.glenoid.versionAmplitude) ','... % glenoid_versionAmpl num2str(obj.shoulderManual.scapula.glenoid.versionOrientation) ','... % glenoid_versionOrientation num2str(obj.shoulderManual.scapula.glenoid.version) ','... % glenoid_version num2str(obj.shoulderManual.scapula.glenoid.inclination) ','... % glenoid_inclination num2str(obj.shoulderManual.humerus.jointRadius) ','... % humerus_jointRadius num2str(obj.shoulderManual.humerus.radius) ','... % humerus_headRadius num2str(obj.shoulderManual.humerus.GHSAmpl) ','... % humerus_GHSAmpl num2str(obj.shoulderManual.humerus.GHSOrient) ','... % humerus_GHSOrient num2str(obj.shoulderManual.humerus.SHSAmpl) ','... % humerus_SHSAmpl num2str(obj.shoulderManual.humerus.SHSOrient) ','... % humerus_SHSOrient num2str(obj.shoulderManual.humerus.SHSAngle) ','... % humerus_SHSAgle num2str(obj.shoulderManual.humerus.SHSPA) ','... % humerus_SHSPA num2str(obj.shoulderManual.humerus.SHSIS) ','... % humerus_SHSIS num2str(obj.shoulderManual.scapula.acromion.AI) ','... % acromion_AI num2str(obj.shoulderManual.scapula.acromion.CSA) ','... % acromion_CSA num2str(obj.shoulderManual.scapula.acromion.PSA) ','... % acromion_PSA num2str(obj.shoulderManual.scapula.acromion.AAA) '\n'... % acromion_AAA ]); fclose(fid); fclose(logFid); outputArg = 1; end function outputArg = saveExcel(~) % Save SCase to Excel file outputArg = 1; end function outputArg = saveSQL(~) % Save SCase to MySQL database outputArg = 1; end function output = getTableOfData(obj, varargin) % This method export all of the measurements and data of a % SCase to a table, which then can be used to export all of the % measurements as csv or excel file (see exportSCaseData function) metadataSCase = getTabulatedProperties(obj); metadataPatient = getTabulatedProperties(obj.patient,... "prefix", "patient"); % Auto shoulder landmarksAcquisition = table("auto",... 'VariableName', "landmarks_acquisition"); autoData = getTabulatedProperties(obj.shoulderAuto,... "recursive", true,... "parentObjects", {obj}); autoTable = [metadataSCase landmarksAcquisition metadataPatient,... autoData]; % Manual shoulder landmarksAcquisition = table("manual",... 'VariableName', "landmarks_acquisition"); manualData = getTabulatedProperties(obj.shoulderManual,... "recursive", true,... "parentObjects", {obj}); manualTable = [metadataSCase landmarksAcquisition metadataPatient,... manualData]; output = outerjoin(autoTable, manualTable, "MergeKeys", true); end end end