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R8218/XLS_MySQL_DB/shoulderFromExcel.m
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shoulderFromExcel.m
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function [ shoulder ] = shoulderFromExcel(patient, rawExcel)
%SHOULDERFROMEXCEL build the shoulder structure array from Excel and from
%the patient structure
% The output is a shoulder strucure array that has the same form as the
% shoulder table of the mySQL database
fprintf('\nGet shoulder from Excel... ');
% define houlder structure array
shoulder = struct(...
'shoulder_id', [], ...
'patient_id', [], ...
'side', [], ...
'comment', [] ...
);
% get column of variables
header = rawExcel(1,:);
sCase_id_col = find(strcmp([header],'sCase.id'));
IPP_col = find(strcmp([header],'anonymity.IPP'));
side_col = find(strcmp([header],'shoulder.side'));
comment_col = find(strcmp([header],'shoulder.comment'));
% loop over rows of Excel table
[rowN, ~] = size(rawExcel);
shoulder_id = 0;
for row_idx = 2:rowN
row = rawExcel(row_idx, :); % get the entire row
sCaseE = row{sCase_id_col}; % sCase id from Excel
side = row{side_col};
% get shoulder comment
comment = row{comment_col};
if isnan(comment)
comment = '';
end
if ~isnan(sCaseE) & ~isnan(side) % check that sCase & side are defined
IPP = row{IPP_col};
patient_idx = find([patient.IPP] == IPP);
% get patient index of this sCase
if ~isempty(patient_idx)
% there is a patient with same IPP
% check that this shoulder patient_id & side is already in the shoulder array
patient_id = patient(patient_idx).patient_id; % patient_id of existing patient
% find this patient_id in shoulder array
shoulder_idx = find([shoulder.patient_id] == patient_id);
% might be 0, 1, or 2 (R/L)
shoulder_idxN = length(shoulder_idx) == 1; % number of matching patient_id in shoulder
addShoulder = 0; % 1 to add the shoulder in the shoulder array
switch shoulder_idxN
case 0
% this sCase patient is not in the shoulder array
% so the shoulder of this sCase is also not, so add it
addShoulder = 1;
case 1
% this sCase patient is in the shoulder array
% so we have to check the shoulder side
if side ~= shoulder(shoulder_idx).side
% this shoulder side in not yet in the shoulder array
% so add it
addShoulder = 1;
end
% fprintf('\nSecond shoulder in %s', sCase);
case 2
% both shoulder sides of this patient are in the
% shoulder array, meaning that this sCase is either
% a duplicate, or a multiple case of the same shoulder
% Nothing to add, but report for control
fprintf('\nDuplicate or multiple case in %s', sCaseE);
otherwise
% should not happend, so report in this case
fprintf('\nMore than 2 shoulders in %s', sCaseE);
end
if addShoulder
shoulder_id = shoulder_id + 1;
shoulder_idx = shoulder_id;
shoulder(shoulder_idx).shoulder_id = shoulder_id;
shoulder(shoulder_idx).patient_id = patient_id;
shoulder(shoulder_idx).side = side;
shoulder(shoulder_idx).comment = comment;
end
end
end
end
fprintf('Done\n');
end
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