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R8218/ShoulderCase/@MusclesContainer/segmentRotatorCuffMuscles.m
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segmentRotatorCuffMuscles.m
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function segmentRotatorCuffMuscles(obj,sliceName)
% sliceName is the part before the '_ForSegmentation.png' part of the name of
% the file that is sent to rcseg.
cleanRotatorCuffSegmentationWorkspace(obj);
sendImageToRotatorCuffSegmentationWorkspace(obj,sliceName);
callRotatorCuffSegmentation(obj);
% (Re)initialize the muscle objects to refer to the new segmentation results
obj.addMuscle('IS',sliceName);
obj.addMuscle('SS',sliceName);
obj.addMuscle('SC',sliceName);
obj.addMuscle('TM',sliceName);
saveSegmentationResults(obj);
cleanRotatorCuffSegmentationWorkspace(obj);
end
function cleanRotatorCuffSegmentationWorkspace(obj)
rotatorCuffSegmentationPath = ConfigFileExtractor.getVariable('pythonDir');
delete(fullfile(rotatorCuffSegmentationPath,'input','*'));
delete(fullfile(rotatorCuffSegmentationPath,'IS','*'));
delete(fullfile(rotatorCuffSegmentationPath,'SC','*'));
delete(fullfile(rotatorCuffSegmentationPath,'SS','*'));
delete(fullfile(rotatorCuffSegmentationPath,'TM','*'));
end
function sendImageToRotatorCuffSegmentationWorkspace(obj,sliceName)
SCase = obj.shoulder.SCase;
rotatorCuffSegmentationPath = ConfigFileExtractor.getVariable('pythonDir');
imageForSegmentationPath = fullfile(obj.slicesDataPath,[sliceName '_ForSegmentation.png']);
copyfile(imageForSegmentationPath,fullfile(rotatorCuffSegmentationPath,'input',[SCase.id '.png']));
end
function callRotatorCuffSegmentation(obj)
%% Apply UNIBE method to automatically segment normal muscle
pythonDir = ConfigFileExtractor.getVariable('pythonDir');
pythonCommandActivateEnvironment= ['source ' fullfile(pythonDir,'venv','bin','activate') ';'];
pythonCommandMoveToSegmentationWorkspace = ['cd ' pythonDir ';'];
pythonCommandExecuteSegmentation = [fullfile(pythonDir,'rcseg.py') ' segment input' ';'];
[~, pythonCommandOutput] = system([pythonCommandActivateEnvironment,...
pythonCommandMoveToSegmentationWorkspace,...
pythonCommandExecuteSegmentation]);
disp(pythonCommandOutput);
end
function saveSegmentationResults(obj)
SCaseID = obj.shoulder.SCase.id;
muscleNames = fields(obj.list);
rotatorCuffSegmentationPath = ConfigFileExtractor.getVariable('pythonDir');
for i = 1:length(muscleNames)
try
copyfile(fullfile(rotatorCuffSegmentationPath,muscleNames{i},[SCaseID '.png']),...
fullfile(obj.list.(muscleNames{i}).maskDataPath,'auto_Mask.png') );
catch ME
warning(ME.message)
end
end
end
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