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R8218/Excel2SQL/patientFromExcel.m
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patientFromExcel.m
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function [patient] = patientFromExcel(rawExcel)
%PATIENT builds the structure array patients from
% Detailed explanation goes here
fprintf('\nGet patient from Excel... ');
% define the patient structure array
patient = struct(...
'patient_id', [], ...
'IPP', [], ... % to be later move to another table for anonymous constrain
'initials', [], ... % to be later move to another table for anonymous constrain
'anonym_birth_date', [], ... % to be later move to another table for anonymous constrain
'gender', [], ...
'birth_date', [], ...
'height', [], ...
'weight', [],... % should we put weight here since it can vary?
'comment', []...
);
% get column of variables
header = rawExcel(1,:);
sCase_id_col = find(strcmp([header],'sCase.id'));
IPP_col = find(strcmp([header],'anonymity.IPP'));
initials_col = find(strcmp([header],'anonymity.initials'));
anonym_birth_date_col = find(strcmp([header],'anonymity.birth_date'));
gender_col = find(strcmp([header],'patient.gender'));
birth_date_col = find(strcmp([header],'patient.birth_date'));
height_col = find(strcmp([header],'patient.height'));
weight_col = find(strcmp([header],'patient.weight'));
comment_col = find(strcmp([header],'patient.comment'));
% loop over rows of Excel table to build patient structure
% patients are not included if caseExcel, IPP, initials, gender, birth_date are not
% defined
[rowN, ~] = size(rawExcel);
patient_id = 0;
for row_idx = 2:rowN
row = rawExcel(row_idx, :); % get the entire row
% check that there is a sCase for this row
sCase_id = row{sCase_id_col}; % sCase_id from Excel
if ~isempty(sCase_id)
% check validity of data
IPP = row{IPP_col};
initials = row{initials_col};
gender = row{gender_col};
anonym_birth_date = row{anonym_birth_date_col};
anonym_birth_date = datetime(anonym_birth_date,'InputFormat','dd.MM.yyyy','ConvertFrom','excel');
anonym_birth_date.Format = 'yyyy-MM-dd';
birth_date = row{birth_date_col};
birth_date = datetime(birth_date,'InputFormat','dd.MM.yyyy','ConvertFrom','excel');
birth_date.Format = 'yyyy-MM-dd';
% get muscle comment
comment = row{comment_col};
if isnan(comment)
comment = '';
end
if ~isnan(IPP) & ...
~isnan(initials) & ...
~isnan(gender) & ...
~isnat(birth_date)
% Check that patient in row sCase is not already in structure
% We asume here that IPP uniquely identifies a patient
sameIPP = find([patient.IPP] == IPP);
if ~isempty(sameIPP)
% IPP is allready in patient array, extra-checks to avoid false same patient
if birth_date ~= patient(sameIPP).birth_date % not same birthdate
fprintf('\nSame IPP (%i) but different birth date in case %s !', IPP, sCase_id);
end
if gender ~= patient(sameIPP).gender % not same gender
fprintf('\nSame IPP (%i) but different gender in case %s !', IPP, sCase_id);
end
if ~strcmp(initials, patient(sameIPP).initials) % not same initials
fprintf('\nSame IPP (%i) but different initials in case %s !', IPP, sCase_id);
end
else % patient is not in patient structure array, so add it
patient_id = patient_id + 1;
patient_idx = patient_id;
height = row{height_col};
if height == ' ' % to avoid strange behavior of the excel import
height = NaN;
end
weight = row{weight_col};
patient(patient_idx).patient_id = patient_id;
patient(patient_idx).IPP = IPP;
patient(patient_idx).initials = initials;
patient(patient_idx).gender = gender;
patient(patient_idx).birth_date = birth_date;
patient(patient_idx).height = height;
patient(patient_idx).weight = weight;
patient(patient_idx).anonym_birth_date = anonym_birth_date;
patient(patient_idx).comment = comment;
end
end
end
end
fprintf('Done\n');
end
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