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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 and filter
%arguments. Each sCase directory should at least contain at directory with a
%name staring with 'CT' and ending with '1', containing a 'dicom'
%subdirectory.
%
% The optional input argument inputList if an array of sCases. If empty, sCaseList
% will search for all sCases. The optional input argument filter can restrict le list.
% Syntax: sCaseList = listsCase(varargin)
%
% Input:
% inputArg: can be nothing (=all), 'N', 'P', or a sCaseId
%
% Output:
% outputArg: 1 if ok and 0 otherwise
%
% Example: listSCase, listSCase('P315')
% Other M-files required:
% Subfunctions:
% See also:
%
% Author: Alexandre Terrier
% EPFL-LBO
% Creation date: 2018-07-01
% Revision date: 2018-08-09
%
% TO DO:
% When varargin = a sCaseId
%% Initialisation of paths
% Should be replaced by a function
dataDir = '../../../data'; % location of data
logDir = 'log'; % log file in xls folder
%% Open log file
logFile = [logDir '/listSCase.log'];
logFileId = fopen(logFile, 'w');
fprintf(logFileId, 'listSCase log file');
fprintf(logFileId, '\nDate: ');
fprintf(logFileId, datestr(datetime));
fprintf(logFileId, '\nGet list of all SCase with a valid dicom folder');
%%
% Struct contains id and associated directory
SCaseList = struct(...
'id' ,[],...
'dir' ,[],...
'comment' ,[]... % Might be used later
);
sCaseListIdx = 0;
%% Loop over all cases
% At the root of dataDir, two directories should be considered:
% N (normal) and P (pathological).
dirL0Array = ['N';'P'];
if strcmp(varargin,'N')
dirL0Array = 'N';
elseif strcmp(varargin,'P')
dirL0Array = 'P';
end
for dirL0idx = 1:length(dirL0Array) % N or P
for dirL1idx = 0:9 % Hunderts
for dirL2idx = 0:9 % Tens
dirL0Str = dirL0Array(dirL0idx);
dirL1Str = num2str(dirL1idx);
dirL2Str = num2str(dirL2idx);
dirTens = [dataDir '/' dirL0Str '/' dirL1Str '/' dirL2Str];
dirTensList = dir(dirTens); % List all directories in tens directory
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 that this sCase directory contains a directory with the
% name [CT?*-1] and with a dicom directory in it.
sCaseID = strtok(sCaseDirName, '-'); % Get chars before '-'
% Listing of (CT) folders in sCaseDirPath staring with CT
% and ending with '-1'
CTdir = dir([sCaseDirPath '/' sCaseDirName '/CT*-1']);
if ~isempty(CTdir)
CTdirPath = [CTdir.folder '/' CTdir.name];
dicomDirName = [CTdirPath '/dicom'];
if exist(dicomDirName, 'dir')
sCaseListIdx = sCaseListIdx + 1;
SCaseList(sCaseListIdx).id = sCaseID;
SCaseList(sCaseListIdx).dir = CTdirPath;
% We might get here the readme.txt if present
else
fprintf(logFileId, ['\n', sCaseID, ' has no valid dicom directory']);
end
else
fprintf(logFileId, ['\n', sCaseID, ' has no CT*-1 directory']);
end
end
end
end
end
fprintf(logFileId, ['\nNumber of SCase: ' num2str(length(SCaseList))]);
end
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