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.shouldersToMeasure.rightAuto = true;
    defaultConfig.shouldersToMeasure.rightManual = true;
    defaultConfig.shouldersToMeasure.leftAuto = true;
    defaultConfig.shouldersToMeasure.leftManual = true;
    
    defaultConfig.standardMeasurementsToRun.loadData = true;
    defaultConfig.standardMeasurementsToRun.morphology = true;
    defaultConfig.standardMeasurementsToRun.measureFirst = true;
    defaultConfig.standardMeasurementsToRun.measureSecond = true;
    defaultConfig.standardMeasurementsToRun.measureThird = true;

    defaultConfig.specialMeasurementsToRun.sliceAndSegment = false;
    defaultConfig.specialMeasurementsToRun.calcDensity = false;

    defaultConfig.specialMeasurementsArguments.sliceAndSegment = [];
    defaultConfig.specialMeasurementsArguments.calcDensity = [];

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

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