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R8218/ShoulderCase/@Muscles/segmentRotatorCuffMuscles.m
fd75f40ff87daterrier-plotUpdate

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segmentRotatorCuffMuscles.m
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function segmentRotatorCuffMuscles(obj)
cleanRotatorCuffSegmentationWorkspace(obj);
sendImageToRotatorCuffSegmentationWorkspace(obj);
callRotatorCuffSegmentation(obj);
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)
SCase = obj.shoulder.SCase;
rotatorCuffSegmentationPath = ConfigFileExtractor.getVariable('pythonDir');
imageForSegmentationPath = fullfile(SCase.dataCTPath,'muscles','imageForSegmentation.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)
SCase = obj.shoulder.SCase;
muscles = {'IS' 'SS' 'SC' 'TM'};
rotatorCuffSegmentationPath = ConfigFileExtractor.getVariable('pythonDir');
autoSegmentationPath = fullfile(SCase.dataCTPath,'muscles','segmentations','auto');
if not(isfolder(autoSegmentationPath))
mkdir(autoSegmentationPath);
end
for i = 1:length(muscles)
copyfile(fullfile(rotatorCuffSegmentationPath,muscles{i},[SCase.id '.png']),...
fullfile(autoSegmentationPath,[muscles{i} '.png']) );
end
end
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