function setup()
    % to execute once after cloning the repo.
    createDefaultConfigFile();

    addpath(genpath(pwd));
end



function createDefaultConfigFile()
    defaultConfig.maxSCaseIDDigits = 3;
    defaultConfig.SCaseIDValidTypes = ["N", "P"];
    defaultConfig.pythonDir = "/shoulder/methods/python/rcseg";
    defaultConfig.dataDir = "/shoulder/dataDev";
    defaultConfig.casesToMeasure = ["*"];
    
    defaultConfig.shouldersToMeasure.rightAuto = true;
    defaultConfig.shouldersToMeasure.rightManual = true;
    defaultConfig.shouldersToMeasure.leftAuto = true;
    defaultConfig.shouldersToMeasure.leftManual = true;
    
    defaultConfig.runMeasurements.loadData = true;
    defaultConfig.runMeasurements.sliceAndSegmentRotatorCuffMuscles = true;
    defaultConfig.runMeasurements.morphology = true;
    defaultConfig.runMeasurements.measureFirst = true;
    defaultConfig.runMeasurements.measureSecond = true;
    defaultConfig.runMeasurements.measureGlenoidDensity = true;

    defaultConfig.rotatorCuffSliceName = "rotatorCuffMatthieu";
    defaultConfig.rotatorCuffSegmentationName = "autoMatthieu";
    defaultConfig.muscleSubdivisionsResolutionInMm.x = 5;
    defaultConfig.muscleSubdivisionsResolutionInMm.y = 5;

    defaultConfig.overwriteMeasurements = false;
    defaultConfig.saveMeasurements = false;
    defaultConfig.saveAllMeasurementsInOneFile = false;

    fid = fopen('config.json','w');
    fprintf(fid, replace(jsonencode(defaultConfig), ",", ",\n"));
    fclose(fid);
end