function output = measureScase(varargin)
  measureSCaseStart = tic;
  Logger.start("measureSCase");
  config = getConfig();
  
  % Initialise cases
  if nargin > 0
    casesToMeasure = [string(varargin)];
  else 
    casesToMeasure = config.casesToMeasure;
  end
  if config.overwriteMeasurements
    SCases = createEmptySCase(casesToMeasure);
  else
    SCases = loadSCase(casesToMeasure);
  end

  % Run measurements
  for i = 1:length(SCases)
    SCaseStart = tic;
    Logger.newDelimitedSection(SCases(i).id);

    if config.runMeasurements.loadData 
      Logger.logn("");
      SCases(i).patient.loadData();
    end
    if config.shouldersToMeasure.rightAuto
      Logger.newDelimitedSection("Shoulder Right Auto");
      runShoulderMeasurements(SCases(i).shoulders.right.auto);
      Logger.closeSection();
    end
    if config.shouldersToMeasure.rightManual
      Logger.newDelimitedSection("Shoulder Right Manual");
      runShoulderMeasurements(SCases(i).shoulders.right.manual);
      Logger.closeSection();
    end
    if config.shouldersToMeasure.leftAuto
      Logger.newDelimitedSection("Shoulder Left Auto");
      runShoulderMeasurements(SCases(i).shoulders.left.auto);
      Logger.closeSection();
    end
    if config.shouldersToMeasure.leftManual
      Logger.newDelimitedSection("Shoulder Left Manual");
      runShoulderMeasurements(SCases(i).shoulders.left.manual);
      Logger.closeSection();
    end

    Logger.newDelimitedSection(...
      sprintf("SCase measured in %.2fs", toc(SCaseStart)));
    Logger.closeBlock();
  end

  % Save results
  if config.saveMeasurements
    saveMeasurements(SCases);
  end
  if config.saveAllMeasurementsInOneFile
    saveAllMeasurementsInOneFile(SCases, casesToMeasure);
  end

  Logger.newDelimitedSection(...
    sprintf("Whole measureSCase() ran in %.2fs", toc(measureSCaseStart)));
  Logger.stop();
  output = SCases;
end


function runShoulderMeasurements(shoulder)
  shoulderStart = tic;
  config = getConfig();

  % Measurements
  if config.runMeasurements.loadData 
    shoulder.loadData();
  end
  if shoulder.isempty()
    Logger.logn("Not enough data loaded to perform further measurements.")
    return
  end
  if config.runMeasurements.sliceAndSegmentRotatorCuffMuscles 
    Logger.newDelimitedSection("Segment"); Logger.logn("");
    Logger.timeLogExecution("Slice and segment rotator cuff muscles: ",...
      @(shoulder) shoulder.rotatorCuff.sliceAndSegment(), shoulder);
    Logger.closeSection();
  end
  if config.runMeasurements.morphology 
    shoulder.morphology();
  end
  if config.runMeasurements.measureFirst 
    shoulder.measureFirst();
  end
  if config.runMeasurements.measureSecond 
    shoulder.measureSecond();
  end
  if config.runMeasurements.measureGlenoidDensity 
    Logger.newDelimitedSection("Glenoid density"); Logger.logn("");
    Logger.timeLogExecution("Glenoid density: ",...
      @(shoulder) shoulder.scapula.glenoid.measureDensity(), shoulder);
    Logger.closeSection();
  end

  Logger.newDelimitedSection(...
    sprintf("Shoulder measured in %.2fs", toc(shoulderStart)));
  Logger.closeSection();
end


function saveMeasurements(SCases)
  savingStart = tic;
  Logger.log("Saving new measurements: ")
  try 
    arrayfun(@(SCase) SCase.saveMatlab, SCases);
    Logger.logn("Done in %.2fs", toc(savingStart));
  catch ME 
    Logger.logn(ME.message);
  end
end
  

function saveAllMeasurementsInOneFile(SCases, casesToMeasure)
  savingStart = tic;
  Logger.log("Saving whole database in one file: ")
  try
    if not(isequal(casesToMeasure, "*"))
      SCaseDB = loadSCase("*");
    else
      SCaseDB = SCases;
    end
    save(fullfile(getConfig().dataDir, "matlab", "SCaseDB.mat"), "SCaseDB");
    Logger.logn("Done in %.2fs", toc(savingStart));
  catch ME
    Logger.logn(ME.message);
  end
end