function segmentMuscles(obj, sliceName, maskName)
  % sliceName is the part before the '_ForSegmentation.png' part of the name of
  % the file that is sent to rcseg.
  % maskName is the part before the '_Mask.png' part of the name of
  % the file that is saved in the SCase folder.
  cleanRotatorCuffSegmentationWorkspace(obj);
  sendImageToRotatorCuffSegmentationWorkspace(obj,sliceName);
  callRotatorCuffSegmentation(obj);
  saveSegmentationResults(obj,maskName);
  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.dataSlicesPath,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,maskName)
  SCaseID = obj.shoulder.SCase.id;
  rotatorCuffSegmentationPath = ConfigFileExtractor.getVariable('pythonDir');
  
  for muscleName = ["SC", "SS", "IS", "TM"]
    try
      copyfile(fullfile(rotatorCuffSegmentationPath,muscleName,SCaseID + ".png"),...
        fullfile(obj.(muscleName).dataMaskPath,maskName + "_Mask.png") );
    catch ME
      warning(ME.message)
    end
  end
end