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R8218/ShoulderCase/@CasesFinder/CasesFinder.m
50e9b38f4d45aterrier-plotUpdate

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CasesFinder.m
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classdef (Abstract) CasesFinder < handle
% The CaseFinder class is looking for data related to a ShoulderCase in a folder tree.
% It has been designed to work with the datastructure found in lbovenus.epfl.ch/shoulder/.
%
% A concrete subclass of CasesFinder must implement the expression related to the
% 'branch' of the datastructure it is looking at.
% Then, the CasesFinder will list all the cases that can be found following a
% fullfile(dataRootPath,casesSpecificExpression) path.
% The found cases are then filtered according to the dicom files found following their
% path.
properties (Access = protected)
dataRootPath
casesSpecificExpression
casesDirectories
end
methods (Abstract)
setCasesSpecificExpression(obj);
end
methods
function obj = CasesFinder(dataRootPath)
obj.dataRootPath = dataRootPath;
obj.casesSpecificExpression = [];
obj.casesDirectories = containers.Map;
obj.setCasesSpecificExpression;
obj.mapCasesDirectories;
obj.removeCasesWithNoCTDirectory;
obj.reachBestCTDirectory;
end
end
methods (Access = protected)
function mapCasesDirectories(obj)
cases = dir(fullfile(obj.dataRootPath,obj.casesSpecificExpression));
cases = obj.addSCaseIDToDirOutput(cases);
obj.updateMapWithCases(cases);
end
function dirOutput = addSCaseIDToDirOutput(obj,dirOutput)
for i = 1:length(dirOutput)
dirOutput(i).SCaseID = regexp(dirOutput(i).name,'[NP]\d{1,3}','match','once');
end
end
function updateMapWithCases(obj,cases)
for i = 1:length(cases)
if not(isempty(cases(i).SCaseID))
obj.casesDirectories(cases(i).SCaseID) = fullfile(cases(i).folder,cases(i).name);
end
end
end
function removeCasesWithNoCTDirectory(obj)
SCases = obj.casesDirectories.keys;
for i = 1:length(SCases)
SCase = SCases{i};
if not(obj.containsCTDirectories(obj.casesDirectories(SCase)));
obj.casesDirectories.remove(SCase);
end
end
end
function output = containsCTDirectories(obj,directory)
if isempty(dir(fullfile(directory,'CT*')))
output = false;
else
output = true;
end
end
function reachBestCTDirectory(obj)
SCases = obj.casesDirectories.keys;
for i = 1:length(SCases)
SCase = SCases{i};
caseWithBestDirectory = obj.getBestCTDirectoryForSCase(SCase);
caseWithBestDirectory = obj.addSCaseIDToDirOutput(caseWithBestDirectory);
obj.updateMapWithCases(caseWithBestDirectory)
end
end
function output = getBestCTDirectoryForSCase(obj,SCase)
% Each SCase directory should at least contain a
% 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.
observedCTDirectories = dir(fullfile(obj.casesDirectories(SCase),'CT*'));
for i = 1:length(observedCTDirectories)
if obj.containsAmiraDirectory(observedCTDirectories(i))
output = observedCTDirectories(i);
return
end
end
output = observedCTDirectories(1);
end
function output = containsAmiraDirectory(obj,directory)
if isempty(dir(fullfile(directory.folder,directory.name,'amira')))
output = false;
else
output = true;
end
end
end
methods
function output = getPathTo(obj,SCase)
if obj.containsCase(SCase)
output = obj.casesDirectories(SCase);
else
output = [];
end
end
function output = getAllCasesIDs(obj)
output = obj.casesDirectories.keys;
end
function output = getNumberOfCases(obj)
output = obj.casesDirectories.Count;
end
function output = containsCase(obj,SCase)
output = obj.casesDirectories.isKey(SCase);
end
end
end
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