R8218/setup.m
fd16f3bb1f63feat_muscle_subdivisions

setup.m
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			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.measureDegeneration = false;
			defaultConfig.specialMeasurementsToRun.calcDensity = false;

			defaultConfig.specialMeasurementsArguments.sliceAndSegment = [];
			defaultConfig.specialMeasurementsArguments.measureDegeneration =...
			["rotatorCuffMatthieu", "autoMatthieu"];
			defaultConfig.specialMeasurementsArguments.calcDensity = [];

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

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