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R8218/muscles/degenerationAll3D.m
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degenerationAll3D.m
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function muscles_results = degenerationAll3D(caseID, musclesList)
%%DEGENERATIONALL3D returns a structure array containing muscle
% measurements for each case ID entered as input and fills the Shoulder
% database with muscle degeneration measurements
%
% This function fills the Shoulder database with the muscle degeneration
% values of the case given as input, for all CT slices available.
% The measurements are stored in a XLS file and in the MySQL database.
%
% USE: degenerationAll3D(caseID, musclesList)
%
% INPUT caseID: Case IDs for which you want to compute muscle degeneration.
% 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).
%
% musclesList: List of muscles which you want to compute muscle
% degeneration. Cell array that stores each msucle name as a char.
%
% OUTPUT muscles_results: structure array containing fields 'Case_ID',
% and structure array field "muscle name" with muscle
% measurements for each slice for the current patient: 'Stot',
% 'Satrophy', 'Sinfiltration', 'Sosteochondroma' and
% 'Sdegeneration', 'atrophy', 'infiltration', 'osteochondroma'
% and 'degeneration'
%
% REMARKS The muscle values (ratios) for all available CT slices are
% saved in the muscles.xls file and in the shoulder MySQL
% database.
%
% created with MATLAB ver.: 9.2.0.556344 (R2017a) on Windows 7
% Author: EPFL-LBO-VMC
% Date: 29-kun-2017
%
CTDatabaseLocation = '../../../data'; % Location of the CT database
% XLSShoulderDatabaseLocation = 'C:/Users/vmalfroy/Dropbox/shoulderDatabase/'; % Location of the XLS ShoulderDatabase
XLSShoulderDatabaseLocation = '../../../data/Excel/'; % Location of the XLS ShoulderDatabase
HUThresholdMuscle = 0; %#ok<NASGU>
HUThresholdFat = 30; %#ok<NASGU>
HUThresholdOsteochondroma = 166; %#ok<NASGU>
% 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
conn = openSQL();
% Get the list of exisiting cases in XLS database
[~,~,currDatabase] = xlsread([XLSShoulderDatabaseLocation 'xlsFromMatlab/muscles.xls']);
currDatabaseCaseIDlist = currDatabase(2:end,1);
%Initialize structure array for results
muscles_results = [];
muscles_results = setfield(muscles_results,{length(caseID),1},'Case_ID',[]);
% Compute muscle degeneration values 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
% Find CT folder for the given Case ID
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
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 musle degeneration values and store in the XLS database
if exist([CaseCTFolder '/CT-' CaseID_IPP '-1/muscles'],'dir') == 7 %if a folder "muscles" exist, the patient name is added to the "measured" column
muscleDirectory = [CaseCTFolder '/CT-' CaseID_IPP '-1/muscles'];
slicesList = dir(muscleDirectory);
slicesList = slicesList(3:end);
muscles_results(i).Case_ID = caseID{i};
field2sort = 'SliceNumber'; %#ok<NASGU>
for j=1:length(slicesList)
for k=1:length(musclesList)
disp(caseID{i});
% Compute muscle degeneration values
eval([musclesList{k} '= muscleDegeneration3D(caseID{i}, musclesList{k},HUThresholdMuscle,HUThresholdFat,HUThresholdOsteochondroma,muscleDirectory);']);
eval(['muscles_results = setfield(muscles_results,{i,1}, musclesList{k}, ' musclesList{k} ');']);
% Sort muscle field by slice number
eval(['[~,I] = sort(arrayfun (@(x) x.(field2sort), muscles_results(i,1).' musclesList{k} '));']);
eval(['muscles_results(i,1).' musclesList{k} ' = muscles_results(i,1).' musclesList{k} '(I);']);
end
end
muscles = cellstr(muscles_results(i).CT_id)';
for k = 1:length(musclesList)
eval(['muscles = horzcat(muscles, transpose(struct2cell(muscles_results.' musclesList{k} ')));']);
end
% Write to XLS file
% Replace line if already existing or append
if(any(strcmp(currDatabaseCaseIDlist, caseID{i})))
xlswrite([XLSShoulderDatabaseLocation 'xlsFromMatlab/muscles.xls'],muscles,'Feuil1',['A' int2str(find(strcmp(currDatabaseCaseIDlist, caseID{i}))+1)]);
else
xlswrite([XLSShoulderDatabaseLocation 'xlsFromMatlab/muscles.xls'],muscles,'Feuil1',['A' int2str(length(currDatabaseCaseIDlist)+1+i)]);
end
% Write to MySQL database
% Replace line if already existing or issue warning message
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})
SS_atrophy = sum([muscles_results(i).SS(:).Satrophy])/sum([muscles_results(i).SS(:).Stot]);
SS_infiltration = sum([muscles_results(i).SS(:).Sinfiltration])/sum([muscles_results(i).SS(:).Stot]);
SS_osteochondroma = sum([muscles_results(i).SS(:).Sosteochondroma])/sum([muscles_results(i).SS(:).Stot]);
SS_degeneration = (sum([muscles_results(i).SS(:).Stot]) - sum([muscles_results(i).SS(:).Sdegeneration]))/sum([muscles_results(i).SS(:).Stot]);
IS_atrophy = sum([muscles_results(i).IS(:).Satrophy])/sum([muscles_results(i).IS(:).Stot]);
IS_infiltration = sum([muscles_results(i).IS(:).Sinfiltration])/sum([muscles_results(i).IS(:).Stot]);
IS_osteochondroma = sum([muscles_results(i).IS(:).Sosteochondroma])/sum([muscles_results(i).IS(:).Stot]);
IS_degeneration = (sum([muscles_results(i).IS(:).Stot]) - sum([muscles_results(i).IS(:).Sdegeneration]))/sum([muscles_results(i).IS(:).Stot]);
SC_atrophy = sum([muscles_results(i).SC(:).Satrophy])/sum([muscles_results(i).SC(:).Stot]);
SC_infiltration = sum([muscles_results(i).SC(:).Sinfiltration])/sum([muscles_results(i).SC(:).Stot]);
SC_osteochondroma = sum([muscles_results(i).SC(:).Sosteochondroma])/sum([muscles_results(i).SC(:).Stot]);
SC_degeneration = (sum([muscles_results(i).SC(:).Stot]) - sum([muscles_results(i).SC(:).Sdegeneration]))/sum([muscles_results(i).SC(:).Stot]);
TM_atrophy = sum([muscles_results(i).TM(:).Satrophy])/sum([muscles_results(i).TM(:).Stot]);
TM_infiltration = sum([muscles_results(i).TM(:).Sinfiltration])/sum([muscles_results(i).TM(:).Stot]);
TM_osteochondroma = sum([muscles_results(i).TM(:).Sosteochondroma])/sum([muscles_results(i).TM(:).Stot]);
TM_degeneration = (sum([muscles_results(i).TM(:).Stot]) - sum([muscles_results(i).TM(:).Sdegeneration]))/sum([muscles_results(i).TM(:).Stot]);
% Update data in table 'muscle'
data = {sqlresult{1} SS_atrophy SS_infiltration SS_osteochondroma SS_degeneration IS_atrophy IS_infiltration IS_osteochondroma IS_degeneration SC_atrophy SC_infiltration SC_osteochondroma SC_degeneration TM_atrophy TM_infiltration TM_osteochondroma TM_degeneration};
fieldNames = {'CT_id','SSA','SSI','SSO','SSD','ISA','ISI','ISO','ISD','SCA','SCI','SCO','SCD', 'TMA', 'TMI', 'TMO', 'TMD'};
upsert(conn, 'muscle', fieldNames, [1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0], data);
else
error(['No entry for caseID ' caseID{i} ' was found in the ' conn.Instance ' MySQL database.']);
end
else
error(['"muscles" folder missing for CaseID: ' caseID{i}]);
end
end
end
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