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R8218/measureSCase.m
54ddcc3bd331Bashardoust_SystCoord

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measureSCase.m
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function [status,message] = measureSCase(varargin)
% MEASURESCASE Update the entire SCase DB with anatimical measurements.
% The script measureSCase will replace 3 prevvious 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
% Currently, the script should be run for the entire DB
% Run from lbovenus
% The script can be run from (lbovenus) server as follows
% cd /home/shoulder/methods/matlab/database
% matlab -nojvm -nodisplay -nosplash -r "measureSCase;quit"
% The log file can be checked with 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.
% Input
% No output yet
% 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: 2018-08-15
% 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
% Remove xls before writing csv
tic; % Start stopwatch timer
%% Initialisation of paths
% Should be replaced by a function
dataDir = '../../../data'; % location of data
logDir = 'log'; % log file in xls folder
xlsDir = [dataDir '/Excel/xlsFromMatlab'];
matlabDir = [dataDir '/matlab'];
%% Add path to ShoulderCase class
addpath('ShoulderCase');
%% Open log file
filename = 'measureSCase.log';
filename = [logDir '/' filename];
logFileId = fopen(filename, 'w');
fprintf(logFileId, 'measureSCase log file');
fprintf(logFileId, ['\nDate: ' datestr(datetime)]);
%% Instance of a ShoulderCase object
if (exist('sCase','var') > 0)
clear sCase; % Check for delete method
end
sCase = ShoulderCase; % Instanciate a ShoulderCase object
%% Get list of all SCase
sCaseList = listSCase(); % get list of sCases ('N', 'P', no arg for all)
% For debuging, sCaseList is reduced to the first 5 cases
% sCaseList = sCaseList(1:5);
% For debuging, sCaseList is reduced to 1 element
% sCaseList(1) = struct('id', 'P313', 'dir', 'toto');
% sCaseList(2) = struct('id', 'P315', 'dir', 'toto');
%% Start loop over sCases in sCaseList
sCaseN = length(sCaseList); % Number of sCases
for sCaseIdx = 1:sCaseN
sCaseId = sCaseList(sCaseIdx).id; %
fprintf(logFileId, ['\n' num2str(sCaseIdx) '/' num2str(sCaseN) '. ' sCaseId ': ']);
sCase(sCaseIdx).id = sCaseId;
output = sCase(sCaseIdx).path; % Set data path of this sCase
if output % Continue if sCase amira path exist
% Load scapula data from amira folder and set scapular coordinate system
output = sCase(sCaseIdx).shoulder.scapula.load; % Load data from amira directory
if output
sCase(sCaseIdx).shoulder.scapula.coordSysSet; % Set scapular coordinate system
% Load glenoid data from amira folder and set glenoid morphology
output = sCase(sCaseIdx).shoulder.scapula.glenoid.load; % Load data from amira directory
if output
sCase(sCaseIdx).shoulder.scapula.glenoid.morphology; % Perform morphological measurements
% Load humerus data from amira folder and set subluxation
output = sCase(sCaseIdx).shoulder.humerus.load; % load data from amira directory
if output
sCase(sCaseIdx).shoulder.humerus.subluxation; % Calcul subluxation
% Acromion morphology
sCase(sCaseIdx).shoulder.scapula.acromion.morphology; % Should be run after sCase.shoulder.humerus
% Save sCase object in file sCase.id/matlab/sCase_CNNN.m
sCase(sCaseIdx).matlabSave;
% We might add here the cvs save
fprintf(logFileId, 'OK');
else
fprintf(logFileId, 'humerus.load problem');
end
else
fprintf(logFileId, 'glenoid.load problem');
end
else
fprintf(logFileId, 'scapula.load problem');
end
else
fprintf(logFileId, 'No amira folder');
end
end
%% Save the entire SCase array as a matlab file
filename = 'SCaseDB';
filename = [matlabDir '/' filename '.mat'];
try
SCaseDB = sCase;
save(filename, 'SCaseDB');
fprintf(logFileId, ['\nSaved dat file: ' filename]);
outputArg = 1;
catch
fprintf(logFileId, '\nError saving SCaseDB matlab file \n');
outputArg = -1;
end
%% 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_PS,'...
'acromion_IE'...
];
csvFilename = [xlsDir, '/anatomy.csv']; % Name of the csv file
csvFileId = fopen(csvFilename, 'w');
fprintf(csvFileId,dataHeader); % Write header
for sCaseIdx = 1:length(sCaseList) % Loop on sCaseList to write data in csv
fprintf(csvFileId,['\n'...
sCase(sCaseIdx).id ','... % sCase_id
sCase(sCaseIdx).shoulder.side ','... % shoulder_side
num2str(sCase(sCaseIdx).shoulder.scapula.glenoid.radius) ','... % glenoid_radius
num2str(sCase(sCaseIdx).shoulder.scapula.glenoid.sphereRMSE) ','... % glenoid_sphereRMSE
num2str(sCase(sCaseIdx).shoulder.scapula.glenoid.depth) ','... % glenoid_depth
num2str(sCase(sCaseIdx).shoulder.scapula.glenoid.width) ','... % glenoid_width
num2str(sCase(sCaseIdx).shoulder.scapula.glenoid.height) ','... % glenoid_height
num2str(sCase(sCaseIdx).shoulder.scapula.glenoid.centerLocal(1)) ','... % glenoid_centerPA
num2str(sCase(sCaseIdx).shoulder.scapula.glenoid.centerLocal(2)) ','... % glenoid_centerIS
num2str(sCase(sCaseIdx).shoulder.scapula.glenoid.centerLocal(3)) ','... % glenoid_centerML
num2str(sCase(sCaseIdx).shoulder.scapula.glenoid.versionAmpl) ','... % glenoid_versionAmpl
num2str(sCase(sCaseIdx).shoulder.scapula.glenoid.versionOrient) ','... % glenoid_versionOrient
num2str(sCase(sCaseIdx).shoulder.scapula.glenoid.version) ','... % glenoid_version
num2str(sCase(sCaseIdx).shoulder.scapula.glenoid.inclination) ','... % glenoid_inclination
num2str(sCase(sCaseIdx).shoulder.humerus.jointRadius) ','... % humerus_jointRadius
num2str(sCase(sCaseIdx).shoulder.humerus.radius) ','... % humerus_headRadius
num2str(sCase(sCaseIdx).shoulder.humerus.GHSAmpl) ','... % humerus_GHSAmpl
num2str(sCase(sCaseIdx).shoulder.humerus.GHSOrient) ','... % humerus_GHSOrient
num2str(sCase(sCaseIdx).shoulder.humerus.SHSAmpl) ','... % humerus_SHSAmpl
num2str(sCase(sCaseIdx).shoulder.humerus.SHSOrient) ','... % humerus_SHSOrient
num2str(sCase(sCaseIdx).shoulder.humerus.SHSAngle) ','... % humerus_SHSAgle
num2str(sCase(sCaseIdx).shoulder.humerus.SHSPA) ','... % humerus_SHSPA
num2str(sCase(sCaseIdx).shoulder.humerus.SHSIS) ','... % humerus_SHSIS
num2str(sCase(sCaseIdx).shoulder.scapula.acromion.AI) ','... % acromion_AI
num2str(sCase(sCaseIdx).shoulder.scapula.acromion.CSA) ','... % acromion_CSA
num2str(sCase(sCaseIdx).shoulder.scapula.acromion.PS) ','... % acromion_PS
num2str(sCase(sCaseIdx).shoulder.scapula.acromion.IE)... % acromion_IE
]);
end
fclose(csvFileId);
fprintf(logFileId, ['\nSaved csv file: ' 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\nsCases measured: %s', num2str(length(sCaseList))); % Number of sCases measured
fprintf(logFileId, '\nElapsed time (s): %s', num2str(toc)); % stopwatch timer
fprintf(logFileId, '\n\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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