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R8218/listSCase.m
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listSCase.m
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function SCaseList = listSCase(varargin)
%LISTSCASE output list of sCases (id and path), accordind to inputList or
%filter arguments.
% Each sCase directory should at least contain at
% directory with a name staring with 'CT' and ending with either
% '-1' : preop/shoulder/sharp/noPhantom
% '-2' : preop/shoulder/smooth/noPhantom
% '-3' : preop/shoulder/sharp/phantom
% '-4' : preop/shoulder/smooth/phantom
% and containing a 'dicom' subdirectory. The priority is '1', '2', '3', '4',
% unless there is a amira folder already present in one of these diretories.
%
% The optional input argument inputList if an array of SCaseID, or 'N' or
% 'P'. If empty, listSCase will search for all SCaseID. The optional
% input argument filter can restrict le list.
% The fonction can be run from server (lbovenus) with
% cd /home/shoulder/methods/matlab/database; matlab -nojvm -nodisplay -nosplash -r "listSCase;quit"
% For 700 cases, it takes less than 60 seconds (when executed from server)
% Progress can be be checked throuhth log file with following shell command
% cd /home/shoulder/methods/matlab/database;tail -f log/listSCase.log
% Input:
% inputArg: can be nothing (=all), 'N', 'P', or SCase(s)
%
% Output:
% outputArg: 1 if ok and 0 otherwise
%
% Example: listSCase, listSCase('P'), listSCase('P001','P002')
% Other M-files required: None
% Subfunctions: None
% See also: Used by dicominfoSCase, measureSCase,
%
% Author: Alexandre Terrier
% EPFL-LBO
% Creation date: 2018-07-01
% Revision date: 2018-12-30
%
% TODO
% Two main looops might be merged in one, to avoid duplicagte post
% treatment
%% Open log file
logFileID = openLogFile('listSCase.log');
% %% Set the data directory from the configuration file config.txt
% dataDir = ConfigFileExtractor.getVariable('dataDir');
%% Struct contains id and associated directory
SCaseList = struct(...
'id' ,[],...
'dir' ,[],...
'comment' ,[]... % Might be used later
);
%% Check varargin
dirL0Array = '';
SCaseListIn = {};
nargin = length(varargin); % Strange MATLAB requirement here: nargin must be initialised before being evaluated if we want to re-assign a value to nargin later.
if nargin %
varargin = varargin{1}; % These lines are required because now measureSCase sends only one argument which is a structure.
end % It allows to keep the remaining listCase code unchanged.
nargin = length(varargin); %
switch nargin
case 0 % All SCase, default when no argument
dirL0Array = ['N';'P'];
fprintf(logFileID, '\nGet list of all SCase with a valid dicom folder');
% Set the data directory from the configuration file config.txt
dataDir = ConfigFileExtractor.getVariable('dataDir');
case 1
if exist(varargin{1},'dir') % Assumes the input is the data directory
dataDir = varargin{1};
% All SCase as default when no more arguments
dirL0Array = ['N';'P']; % All SCase, default when no argument
fprintf(logFileID, '\nGet list of all SCase with a valid dicom folder');
else % When the only argument is not a directory
% Set the data directory from the configuration file config.txt
dataDir = ConfigFileExtractor.getVariable('dataDir');
% Assumes the argument is 'N', 'P' or a list of SCases
switch varargin{1}
case 'N' % All normal SCase
dirL0Array = 'N';
fprintf(logFileID, '\nGet list of all normal SCase with a valid dicom folder');
case 'P' % All pathological SCase
dirL0Array = 'P';
fprintf(logFileID, '\nGet list of all pathological SCase with a valid dicom folder');
otherwise % A specific SCase
fprintf(logFileID, '\nGet list of a SCase with a valid dicom folder');
SCaseListIn = varargin;
end
end
otherwise
if exist(varargin{1},'dir') % Assumes the input is the data directory
dataDir = varargin{1};
switch varargin{2}
case 'N' % All normal SCase
dirL0Array = 'N';
fprintf(logFileID, '\nGet list of all normal SCase with a valid dicom folder');
case 'P' % All pathological SCase
dirL0Array = 'P';
fprintf(logFileID, '\nGet list of all pathological SCase with a valid dicom folder');
otherwise % Some specific SCase (wrong)
fprintf(logFileID, '\nGet list of a SCase with a valid dicom folder');
SCaseListIn = varargin;
SCaseListIn(1) = []; % removing the dataDir from the argument list
end
else % When the first argument is not a directory, assumes it is a list of SCases
% Set the data directory from the configuration file config.txt
dataDir = ConfigFileExtractor.getVariable('dataDir');
% list of multiple SCase given in varargin
fprintf(logFileID, '\nGet list of a SCase with a valid dicom folder');
SCaseListIn = varargin;
end
end
%% Only one of the two loops below are performed
SCaseListIdx = 0; % Used in one of two loops below
%% Loop over SCase (N, P, or both), if length(dirL0Array) > 1
for dirL0idx = 1:length(dirL0Array) % N or P
for dirL1idx = 0:9 % Hunderts dir
for dirL2idx = 0:9 % Tens dir
dirL0Str = dirL0Array(dirL0idx);
dirL1Str = num2str(dirL1idx);
dirL2Str = num2str(dirL2idx);
dirTens = [dataDir '/' dirL0Str '/' dirL1Str '/' dirL2Str];
dirTensList = dir(dirTens); % List all directories in tens dir
dirTensList = dirTensList(~ismember({dirTensList.name},{'.','..'})); % Remove . and ..
% We might add here a filter (only diretories, {N/P} followed
% by digits
for dirL3idx = 1:numel(dirTensList)
sCaseDirName = dirTensList(dirL3idx).name; % Root directory of this case
sCaseDirPath = dirTensList(dirL3idx).folder;
% Check if this SCaseID has a CT dir [CT?*-?] with a valid preoprative CT
SCaseID = strtok(sCaseDirName, '-'); % Get chars before '-'
CTdirList = dir([sCaseDirPath '/' sCaseDirName '/CT-*']); % List directories with CT
iCTdirAmira = 0;
iCTdir2use = 0;
for iCTdirList = length(CTdirList):-1:1 % Loop from last to first (4 to 1)
CTdir = CTdirList(iCTdirList);
% Check that dir name ends with -1,-2,-3,-4
dirName = CTdir.name;
if strcmp(dirName(end-1),'-') % Exclude postoperative 'p' CT
CTnum = str2num(dirName(end));
if CTnum <= 4 % Exlude non shoulder (elbow) CT
% Check that the dir contains a dicom dir
CTdir = [CTdir.folder '/' CTdir.name];
dicomDir = [CTdir '/dicom'];
if exist(dicomDir, 'dir')
% Chech if amira dir exist
amiraDir = [CTdir '/amira'];
if exist(amiraDir, 'dir')
% This is the CT folder to use
iCTdirAmira = iCTdirList;
end
iCTdir2use = iCTdirList;
end
end
end
end
if iCTdir2use == 0
fprintf(logFileID, ['\n', SCaseID, ' has no valid dicom directory']);
else
if iCTdirAmira % If amira dir exist, use it
iCTdir2use = iCTdirAmira;
end
CTdir = CTdirList(iCTdir2use);
SCaseListIdx = SCaseListIdx + 1;
SCaseList(SCaseListIdx).id = SCaseID;
CTdirPath = [CTdir.folder '/' CTdir.name];
SCaseList(SCaseListIdx).dir = CTdirPath;
if CTnum ~= 1
fprintf(logFileID, ['\n', SCaseID, ' dicom directory is CT-' num2str(CTnum)]);
end
end
end
end
end
end
%% Loop over input SCase list (given as input argument), if length(SCaseListIn) > 0
for iSCaseListIn = 1:length(SCaseListIn)
% Check if there is a valid dicom directory for this SCaseID
SCaseID = char(SCaseListIn{iSCaseListIn});
% Build directory from SCaseID (as in function ShoulderCase.path)
% The validity of the format should be either Pnnn or Nnnn.
if (numel(regexp(SCaseID,'^[PN]\d{1,3}$')) == 0)
error(['Invalid format of SCaseID: ' SCaseID{1} '. CaseID must start with "P" or "N" and be followed by 1 to 3 digits.']);
end
% Set the folder of the SCaseID
SCaseDirLevelPN = SCaseID(1); % Either 'P' or 'N'
strLengthSCaseID = strlength(SCaseID(2:end));
if (strLengthSCaseID < 2)
SCaseDirLevel2 = '0'; % Hunderets
SCaseDirLevel1 = '0'; % Dozent
elseif (strLengthSCaseID < 3)
SCaseDirLevel2 = '0'; % Hunderets
SCaseDirLevel1 = SCaseID(2); % Dozent
else
SCaseDirLevel2 = SCaseID(2); % Hunderets
SCaseDirLevel1 = SCaseID(3); % Dozent
end
% Set SCaseID with fixed 3 digits after P/N (needed when id <
% 10 inloading of data in amira directory.
SCaseID4C = [SCaseDirLevelPN SCaseDirLevel2 SCaseDirLevel1 SCaseID(end)];
% Check if a (!unique! to be done) directory exists for this SCaseID
FindSCaseIDFolder = dir([dataDir '/' SCaseDirLevelPN '/' SCaseDirLevel2 '/' SCaseDirLevel1 '/' SCaseID '*']);
if (isempty(FindSCaseIDFolder)) % No directory for this SCaseID
error(['Missing directory for SCaseID: ' SCaseID]);
end
SCaseDirLevel0 = FindSCaseIDFolder.name;
SCaseDir = [dataDir '/' SCaseDirLevelPN '/' SCaseDirLevel2 '/' SCaseDirLevel1 '/' SCaseDirLevel0];
% Check if this SCaseID has a CT directory with a valid preoprative CT
CTdirList=dir([SCaseDir '/CT-*']); % List directories with CT
iCTdirAmira = 0;
iCTdir2use = 0;
for iCTdirList = length(CTdirList):-1:1 % Loop from last to first (4 to 1)
CTdir = CTdirList(iCTdirList);
% Check that dir name ends with -1,-2,-3,-4
dirName = CTdir.name;
if strcmp(dirName(end-1),'-') % Exclude postoperative 'p' CT
CTnum = str2num(dirName(end));
if CTnum <= 4 % Exlude non shoulder (elbow) CT
% Check that the dir contains a dicom dir
CTdir = [CTdir.folder '/' CTdir.name];
dicomDir = [CTdir '/dicom'];
if exist(dicomDir, 'dir')
% Chech if amira dir exist
amiraDir = [CTdir '/amira'];
if exist(amiraDir, 'dir')
% This is the CT folder to use
iCTdirAmira = iCTdirList;
end
iCTdir2use = iCTdirList;
end
end
end
end
if iCTdir2use == 0
fprintf(logFileID, ['\n', SCaseID, ' has no valid dicom directory']);
else
if iCTdirAmira % If amira dir exist, use it
iCTdir2use = iCTdirAmira;
end
CTdir = CTdirList(iCTdir2use);
SCaseListIdx = SCaseListIdx + 1;
SCaseList(SCaseListIdx).id = SCaseID;
CTdirPath = [CTdir.folder '/' CTdir.name];
SCaseList(SCaseListIdx).dir = CTdirPath;
if CTnum ~= 1
fprintf(logFileID, ['\n', SCaseID, ' dicom directory is CT-' num2str(CTnum)]);
end
end
end
fprintf(logFileID, ['\nNumber of SCase: ' num2str(length(SCaseList))]);
fclose(logFileID); % Close log file
end
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