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R8218/anatomy/scapula_measure.m
abcd19405ed2Bashardoust_SystCoord

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scapula_measure.m
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function scapula_measure(caseID)
%%SCAPULA_MEASURE fills the Shoulder database with scapula anatomical data
%
% This function fills the Shoulder database with the scapula anatomical
% data of the case given as input. The anatomical measurements are stored
% simultaneously in a XLS file and in the MySQL database.
%
% USE: scapula_measure(caseID)
%
% INPUT caseID: Case IDs for which you want to compute scapula anatomical
% data. Cell array that stores the case IDs as a char in the form 'P###' or
% 'N###' (starts with "P" or "N" followed by 1 to 3 digits).
%
% REMARKS The anatomical data are saved in the ScapulaAnatomicalData.xls
% file.
%
% created with MATLAB ver.: 8.6.0.267246 (R2015b) on Windows 7
% Author: EPFL-LBO-VMC
% Date: 20-Apr-2017
%
DBaccess=0; % Variable for database access deactivation due to driver problems
CTDatabaseLocation = '../../../data'; % Location of the CT database
XLSShoulderDatabaseLocation = '../../../data/Excel/'; % Location of the XLS ShoulderDatabase
% Check validity of input argument (cell array)
validateattributes(caseID,{'cell'},{'nonempty'});
% Check that imput case IDs are unique
[caseIDNames,~,uniqueCaseID] = unique(caseID);
countOfCaseID = hist(uniqueCaseID,unique(uniqueCaseID))';
freqCaseIDs = struct('name',caseIDNames,'freq',num2cell(countOfCaseID));
repeatedValues = find([freqCaseIDs.freq] > 1);
if(~isempty(repeatedValues))
warning('Input contains repeated Case ID: %s. Repeated occurences of that Case ID will be omitted. \n', freqCaseIDs(repeatedValues).name)
caseID = caseIDNames;
end
% open mySQL connection
if DBaccess
conn = openSQL();
end
% Get the list of exisiting cases in XLS database
exist([XLSShoulderDatabaseLocation 'xlsFromMatlab/anatomy.xls']) % add by JSM for debbuging
[~,~,currDatabase] = xlsread([XLSShoulderDatabaseLocation 'xlsFromMatlab/anatomy.xls']);
currDatabaseCaseIDlist = currDatabase(2:end,1);
% --Get CT directory adress from CT database location and case ID--
% Compute scapula anatomical data and fill database
for i = 1:length(caseID)
% Check validity of input arguments (char and format 'P###' or 'N###')
validateattributes(caseID{i},{'char'},{'nonempty'});
if (numel(regexp(caseID{i},'^[PN]\d{1,3}$')) == 0)
error(['Invalid format of CaseID: ' caseID{i} '. CaseID must start with "P" or "N" and be followed by 1 to 3 digits.']);
end
levelDir1 = caseID{i}(1);
if (length(caseID{i}(2:end)) < 2)
levelDir2 = '0';
levelDir3 = '0';
elseif (length(caseID{i}(2:end)) < 3)
levelDir2 = '0';
levelDir3 = caseID{i}(2);
else
levelDir2 = caseID{i}(2);
levelDir3 = caseID{i}(3);
end
% [CTDatabaseLocation '/' levelDir1 '/' levelDir2 '/' levelDir3 '/' caseID{i} '*']
FindCaseCTFolder = dir([CTDatabaseLocation '/' levelDir1 '/' levelDir2 '/' levelDir3 '/' caseID{i} '*'])
if (isempty(FindCaseCTFolder))
error(['Missing CT directory for CaseID: ' caseID{i}]);
end
CaseID_IPP = FindCaseCTFolder.name;
CaseCTFolder = [CTDatabaseLocation '/' levelDir1 '/' levelDir2 '/' levelDir3 '/' CaseID_IPP];
% Compute scapula measurements and store in the XLS database
if exist([CaseCTFolder '/CT-' CaseID_IPP '-1/amira'],'dir') == 7 %if a folder "amira" exist, the patient name is added to the "measured" column
finalDirectory = [CTDatabaseLocation '/' levelDir1 '/' levelDir2 '/' levelDir3] ;
anatomy = scapula_calculation(CaseID_IPP, finalDirectory, levelDir1); % Function that calculates the anatomical data
% Write to XLS file
% Replace line if already existing or append
if(any(strcmp(currDatabaseCaseIDlist, caseID{i})))
xlswrite([XLSShoulderDatabaseLocation 'xlsFromMatlab/anatomy.xls'],struct2cell(anatomy)','Feuil1',['A' int2str(find(strcmp(currDatabaseCaseIDlist, caseID{i}))+1)]);
else
xlswrite([XLSShoulderDatabaseLocation 'xlsFromMatlab/anatomy.xls'],struct2cell(anatomy)','Feuil1',['A' int2str(length(currDatabaseCaseIDlist)+1+i)]);
end
struct2cell(anatomy)'
% Write to MySQL database
% Replace line if already existing or issue warning message
if DBaccess
sqlquery = ['SELECT CT_id FROM CT WHERE shoulder_id IN (SELECT shoulder_id FROM sCase WHERE folder_name = "' caseID{i} '")'];
curs = exec(conn,sqlquery);
if ~isempty(curs.Message)
fprintf('\nMessage: %s\n', curs.Message);
end
curs=fetch(curs);
sqlresult = curs.Data;
if isnumeric(sqlresult{1})
% Update data in table 'glenoid'
data = {sqlresult{1} anatomy.glenoid_Radius anatomy.glenoid_Radius/anatomy.glenoid_radiusRMSE '' anatomy.glenoid_depth anatomy.glenoid_width anatomy.glenoid_height anatomy.glenoid_version_ampl anatomy.glenoid_version_orient anatomy.glenoid_center_PA anatomy.glenoid_center_IS anatomy.glenoid_center_ML anatomy.glenoid_Version anatomy.glenoid_Inclination 1 ''};
fieldNames = {'CT_id','radius','sphericity','biconcave','depth','width','height','version_ampl','version_orient','center_PA','center_IS','center_ML','version', 'inclination', 'version_2D', 'walch_class'};
upsert(conn, 'glenoid', fieldNames, [1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0], data);
% Update data in table 'humerus'
data = {sqlresult{1} 0.0 anatomy.humeral_head_radius anatomy.humerus_SHsubluxation_ampl anatomy.humerus_SHsubluxation_orient anatomy.humerus_GHsubluxation_ampl anatomy.humerus_GHsubluxation_orient 0.0 0.0};
fieldNames = {'CT_id','joint_radius','head_radius','SHsublux_ampl','SHsublux_orient','GHsublux_ampl','GHsublux_orient','SHsublux_2D','GHsublux_2D'};
upsert(conn, 'humerus', fieldNames, [1 0 0 0 0 0 0 0 0], data);
% Update data in table 'scapula'
data = {sqlresult{1} anatomy.scapula_CTangle anatomy.scapula_AI};
fieldNames = {'CT_id','CT_angle','AI'};
upsert(conn, 'scapula', fieldNames, [1 0 0], data);
else
error(['No entry for caseID ' caseID{i} ' was found in the ' conn.Instance ' MySQL database.']);
end
end
else
error(['Amira files missing for CaseID: ' caseID{i}]);
end
end
% Close mySQL database
if DBaccess
closeSQL(conn);
end
end
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