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R8218/degenerationAll.m
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degenerationAll.m
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function degenerationAll(caseID, musclesList)
%%DEGENERATIONALL 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. The measurements are stored in a XLS
% file.
%
% USE: degenerationAll(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.
%
% REMARKS The muscle values are saved in the muscles.xls file.
%
% created with MATLAB ver.: 9.2.0.556344 (R2017a) on Windows 7
% Author: EPFL-LBO-VMC
% Date: 12-Jun-2017
%
CTDatabaseLocation = 'Z://data'; % Location of the CT database
HUThresholdMuscle = -29; %#ok<NASGU>
HUThresholdOsteochondroma = 166.25; %#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
% 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']; %#ok<NASGU>
muscles_results = struct('CT_id', caseID{i});
for j=1:length(musclesList)
disp(caseID{i});
% Compute muscle degeneration values
eval([musclesList{j} '= muscleDegeneration(caseID{i}, musclesList{j},HUThresholdMuscle,HUThresholdOsteochondroma,muscleDirectory);']);
eval(['muscles_results = setfield(muscles_results, musclesList{j}, ' musclesList{j} ');']);
end
else
error(['"muscles" folder missing for CaseID: ' caseID{i}]);
end
end
end
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