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