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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"
% 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;
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 '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; % Instanciate a ShoulderCase object
SCaseDB = ShoulderCase;
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
output = SCase(iSCaseID).path; % Set data path of this SCase
percentProgress = num2str(iSCaseID/nSCase*100, '%3.1f');
fprintf(logFileID, ['\n___________________________________\n|\n| SCaseID: ' 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
continue
end
while true
tic;
fprintf(logFileID, '\n| Segmentation manual ');
if ~output % Continue if amira dir exists in SCase
fprintf(logFileID, '\n| No amira folder');
amira{end+1} = SCaseID;
break
end
fprintf(logFileID, '\n| Load scapula surface and landmarks');
output = SCase(iSCaseID).shoulder.scapula.load;
if ~output
fprintf(logFileID, ': ERROR');
scapulaLoad{end+1} = SCaseID;
break
end
fprintf(logFileID, ': OK');
fprintf(logFileID, '\n| Set coord. syst.');
output = SCase(iSCaseID).shoulder.scapula.coordSysSet;
if ~output
fprintf(logFileID, ': ERROR');
scapulaCoord{end+1} = SCaseID;
break;
end
fprintf(logFileID, ': OK');
fprintf(logFileID, '\n| Load glenoid surface');
output = SCase(iSCaseID).shoulder.scapula.glenoid.load;
if ~output
fprintf(logFileID, '\n| glenoid surface loading error');
glenoidLoad{end+1} = SCaseID;
break;
end
fprintf(logFileID, ': OK');
fprintf(logFileID, '\n| Measure glenoid anatomy');
output = SCase(iSCaseID).shoulder.scapula.glenoid.morphology;
if ~output
fprintf(logFileID, ': ERROR');
glenoidMorphology{end+1} = SCaseID;
break;
end
fprintf(logFileID, ': OK');
if calcGlenoidDensity
fprintf(logFileID, '\n| Measure glenoid density');
output = SCase(iSCaseID).shoulder.scapula.glenoid.calcDensity;
if ~output
fprintf(logFileID, ': Density calculus error. Could not read dicom');
glenoidDensity{end+1} = SCaseID;
break;
end
fprintf(logFileID, ': OK');
end
fprintf(logFileID, '\n| Load humerus data');
output = SCase(iSCaseID).shoulder.humerus.load;
if ~output
fprintf(logFileID, ': ERROR');
humerusLoad{end+1} = SCaseID;
break;
end
fprintf(logFileID, ': OK');
fprintf(logFileID, '\n| Measure humerus subluxation');
output = SCase(iSCaseID).shoulder.humerus.subluxation(SCase(iSCaseID).shoulder.scapula);
if ~output
fprintf(logFileID, ': ERROR');
humerusSubluxation{end+1} = SCaseID;
break;
end
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, ': ERROR');
acromionMorphology{end+1} = SCaseID;
break;
end
fprintf(logFileID, ': OK');
fprintf(logFileID, '\n| Measure muscle''s degeneration');
output = SCase(iSCaseID).shoulder.muscles.degeneration(logFileID);
switch output % output is reversed here to differenciate different types of degeneration errors
case 1
degeneration{1,end+1} = SCaseID;
degeneration{2,end} = output;
degeneration{3,end} = 'dicomRead() error';
break;
case 2
degeneration{1,end+1} = SCaseID;
degeneration{2,end} = output;
degeneration{3,end} = 'slice() error';
break;
case 3
degeneration{1,end+1} = SCaseID;
degeneration{2,end} = output;
degeneration{3,end} = 'slice is to small';
break;
case 4
degeneration{1,end+1} = SCaseID;
degeneration{2,end} = output;
degeneration{3,end} = 'crop error';
break;
case 5
degeneration{1,end+1} = SCaseID;
degeneration{2,end} = output;
degeneration{3,end} = 'imwrite() gave black image';
break;
case 6
degeneration{1,end+1} = SCaseID;
degeneration{2,end} = output;
degeneration{3,end} = 'automatic segmentation error';
break;
end
fprintf(logFileID, ': OK');
ok{end+1} = SCaseID;
break;
end
fprintf(logFileID, '\n| Elapsed time (s): %s\n|', num2str(toc));
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 2) Load & analyses auto data from matlab
if (exist([SCase(iSCaseID).dataMatlabPath '/scapulaLandmarksAutoR.mat'],'file') && ~updateCalculations)
continue
end
while true
tic;
fprintf(logFileID, '\n| Segmentation auto ');
fprintf(logFileID, '\n| Load scapula surface and landmarks');
output = SCase(iSCaseID).shoulder.scapulaAuto.loadAuto; % Load auto data from matlab directory
if ~output
fprintf(logFileID, ': ERROR');
autoScapulaLoad{end+1} = SCaseID;
break;
end
fprintf(logFileID, ': OK');
fprintf(logFileID, '\n| Set coord. syst.');
output = SCase(iSCaseID).shoulder.scapulaAuto.coordSysSet;
if ~output
fprintf(logFileID, ': ERROR');
autoScapulaCoord{end+1} = SCaseID;
break;
end
fprintf(logFileID, ': OK');
fprintf(logFileID, '\n| Load glenoid surface');
output = SCase(iSCaseID).shoulder.scapulaAuto.glenoid.loadAuto;
if ~output
fprintf(logFileID, ': ERROR');
autoGlenoidLoad{end+1} = SCaseID;
break;
end
fprintf(logFileID, ': OK');
fprintf(logFileID, '\n| Measure glenoid anatomy');
output = SCase(iSCaseID).shoulder.scapulaAuto.glenoid.morphology;
if ~output
fprintf(logFileID, ': ERROR');
autoGlenoidMorphology{end+1} = SCaseID;
break;
end
fprintf(logFileID, ': OK');
if calcGlenoidDensity
fprintf(logFileID, '\n| Measure glenoid density');
output = SCase(iSCaseID).shoulder.scapulaAuto.glenoid.calcDensity;
if ~output
fprintf(logFileID, ': Density calculus error. Could not read dicom');
autoGlenoidDensity{end+1} = SCaseID;
break;
end
fprintf(logFileID, ': OK');
end
fprintf(logFileID, '\n| Load humerus data');
output = SCase(iSCaseID).shoulder.humerus.load;
if ~output
fprintf(logFileID, ': ERROR');
if ~isempty(humerusLoad)
if humerusLoad{end} ~= SCaseID;
humerusLoad{end+1} = SCaseID;
end
end
else
fprintf(logFileID, ': OK');
fprintf(logFileID, '\n| Measure humerus subluxation');
output = SCase(iSCaseID).shoulder.humerus.subluxation(SCase(iSCaseID).shoulder.scapulaAuto);
if ~output
fprintf(logFileID, ': ERROR');
humerusSubluxation{end+1} = SCaseID;
break;
else
fprintf(logFileID, ': OK');
end
end
fprintf(logFileID, '\n| Measure acromion anatomy');
% Should be run after SCase.shoulder.humerus (for AI)
output = SCase(iSCaseID).shoulder.scapulaAuto.acromion.morphology;
if ~output
fprintf(logFileID, ': ERROR');
autoAcromionMorphology{end+1} = SCaseID;
break;
end
fprintf(logFileID, ': OK');
autoOk{end+1} = SCaseID;
break;
end
fprintf(logFileID, '\n| Elapsed time (s): %s', num2str(toc));
% 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).shoulder.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 = ShoulderCase;
for Case=1:length(updateList)
S(Case).id = 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
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