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R8218/Excel2SQL/sCaseFromExcel.m
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sCaseFromExcel.m
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function [ sCase, diagnosis, treatment, outcome, study ] = sCaseFromExcel(shoulder, patient, diagnosisList, treatmentList, rawExcel)
% PCASEFROMEXCEL build the sCase (shoulder case) structure array from Excel and from
% patient and shoulder structure. A sCase is associated to a shoulder. The
% same shoulder can be associated to more than one sCase.
% pCase stand for patient case. The variable case could not be used since
% alrewad usd by Matlab
fprintf('\nGet sCase from Excel... ');
% define sCase structure array
sCase = struct(...
'sCase_id' ,[],...
'shoulder_id' ,[],...
'folder_name' ,[],...
'comment' ,[] ...
);
% defne diagnosis structure
diagnosis = struct(...
'diagnosis_id' ,[],...
'sCase_id' ,[],...
'diagnosisList_id',[],...
'date' ,[],...
'comment' ,[]...
);
% defne treatment structure
treatment = struct(...
'treatment_id' ,[],...
'sCase_id' ,[],...
'treatmentList_id',[],...
'date' ,[],...
'comment' ,[]...
);
% defne outcome structure
outcome = struct(...
'outcome_id' ,[],...
'sCase_id' ,[],...
'date' ,[],...
'comment' ,[],...
'loosening' ,[]...
);
% define study structure
study = struct(...
'study_id' ,[],...
'sCase_id' ,[],...
'name' ,[],...
'comment' ,[]...
);
% get column of variables
header = rawExcel(1,:);
sCase_id_col = find(strcmp([header],'sCase.id'));
sCaseComm_col = find(strcmp([header],'sCase.comment'));
diagnosisName_col = find(strcmp([header],'diagnosis.name'));
diagnosisDate_col = find(strcmp([header],'diagnosis.date'));
diagnosisComm_col = find(strcmp([header],'diagnosis.comment'));
treatmentName_col = find(strcmp([header],'treatment.name'));
treatmentDate_col = find(strcmp([header],'treatment.date'));
treatmentComm_col = find(strcmp([header],'treatment.comment'));
outcomeDate_col = find(strcmp([header],'outcome.date'));
outcomeComm_col = find(strcmp([header],'outcome.comment'));
outcomeLoos_col = find(strcmp([header],'outcome.loosening'));
IPP_col = find(strcmp([header],'anonymity.IPP'));
side_col = find(strcmp([header],'shoulder.side'));
% loop over rows of Excel table
[rowN, ~] = size(rawExcel);
sCase_id = 0;
diagnosis_id = 0;
treatment_id = 0;
outcome_id = 0;
for row_idx = 2:rowN
row = rawExcel(row_idx, :); % get the entire row
sCaseE = row{sCase_id_col}; % sCase id from Excel -> folder_name
side = row{side_col};
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 caseExcel
if ~isempty(patient_idx)
% there is a patient with same IPP
patient_idx = patient(patient_idx).patient_id; % get patient_id
shoulder_idx = find([shoulder.patient_id] == patient_idx); % get shoulder_id
% should be 1 or 2 (R/L), but not 0 (test it however)
shoulder_idxN = length(shoulder_idx);
switch shoulder_idxN
case 0
% this sCase patient is not in the shoulder array
% report an error
fprintf('\nsCase %s not in shoulder array', sCaseE);
addCase = 0;
case 1
% this sCase patient has 1 match in the shoulder array
% so we have to check side
if side == shoulder(shoulder_idx).side
shoulder_id = shoulder(shoulder_idx).shoulder_id;
addCase = 1;
else
% not same side so report a problem
fprintf('\nsCase in soulder array but not same side');
end
case 2
% both shoulder sides of this patient are in the
% shoulder array, so we have to check side
if side == shoulder(shoulder_idx(1)).side
shoulder_id = shoulder(shoulder_idx(1)).shoulder_id;
addCase = 1;
else
if side == shoulder(shoulder_idx(2)).side
shoulder_id = shoulder(shoulder_idx(2)).shoulder_id;
addCase = 1;
end
end
end
if addCase
% add sCase
sCase_id = sCase_id + 1;
sCase_idx = sCase_id;
folder_name = sCaseE;
% get sCase comment
sCase_comment = row{sCaseComm_col};
if isnan(sCase_comment)
sCase_comment = '';
end
sCase(sCase_idx).sCase_id = sCase_id;
sCase(sCase_idx).shoulder_id = shoulder_id;
sCase(sCase_idx).folder_name = folder_name;
sCase(sCase_idx).comment = sCase_comment;
% check & add diagnosis
diagnosisName = row{diagnosisName_col};
diagnosisList_idx = find(strcmp({diagnosisList.name}, diagnosisName) == 1);
if isempty(diagnosisList_idx)
fprintf('\nsCase %s has not associated diagnosisList_id', sCaseE);
else
diagnosis_id = diagnosis_id + 1;
diagnosis_idx = diagnosis_id;
% get diagnosis date
diagnosis_date = row{diagnosisDate_col};
diagnosis_date = datetime(diagnosis_date,'ConvertFrom','excel');
diagnosis_date.Format = 'yyyy-MM-dd';
% get diagnosis comment
diagnosis_comment = row{diagnosisComm_col};
if isnan(diagnosis_comment)
diagnosis_comment = '';
end
diagnosis(diagnosis_idx).diagnosis_id = diagnosis_id;
diagnosis(diagnosis_idx).sCase_id = sCase_id;
diagnosis(diagnosis_idx).diagnosisList_id = diagnosisList(diagnosisList_idx).diagnosisList_id;
diagnosis(diagnosis_idx).date = diagnosis_date;
diagnosis(diagnosis_idx).comment = diagnosis_comment;
end
% check & add treatment
treatmentName = row{treatmentName_col};
treatmentList_idx = find(strcmp({treatmentList.name}, treatmentName) == 1);
if isempty(treatmentList_idx)
fprintf('\nsCase %s has not associated treatmentList_id', sCaseE);
else
treatment_id = treatment_id + 1;
treatment_idx = treatment_id;
% get treatment date
treatment_date = row{treatmentDate_col};
treatment_date = datetime(treatment_date,'InputFormat','dd.MM.yyyy','ConvertFrom','excel');
treatment_date.Format = 'yyyy-MM-dd';
% get treatment comment
treatment_comment = row{treatmentComm_col};
treatment(treatment_idx).treatment_id = treatment_id;
treatment(treatment_idx).sCase_id = sCase_id;
treatment(treatment_idx).treatmentList_id = treatmentList(treatmentList_idx).treatmentList_id;
treatment(treatment_idx).date = treatment_date;
treatment(treatment_idx).comment = treatment_comment;
end
% check & add outcome
% get outcome date
outcome_date = row{outcomeDate_col};
if ~isempty(outcome_date)
outcome_date = datetime(outcome_date,'InputFormat','dd.MM.yyyy','ConvertFrom','excel');
outcome_date.Format = 'yyyy-MM-dd';
end
% get outcome comment
outcome_comment = row{outcomeComm_col};
% get outcome loosening
outcome_loosening = row{outcomeLoos_col};
if isempty(outcome_comment) || isempty(outcome_loosening)
fprintf('\nsCase %s has not associated outcome', sCaseE);
else
outcome_id = outcome_id + 1;
outcome_idx = outcome_id;
outcome(outcome_idx).outcome_id = outcome_id;
outcome(outcome_idx).sCase_id = sCase_id;
outcome(outcome_idx).date = outcome_date;
outcome(outcome_idx).comment = outcome_comment;
outcome(outcome_idx).loosening = outcome_loosening;
end
% check & add study
% to be done
study(1).study_id = 1;
study(1).sCase_id = 1;
study(1).name = 'studyTest';
study(1).comment = 'studyComment';
end
end
end
end
fprintf(' Done\n');
end
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