R8218/setup.m
8566b2f9bc32glenoidCap

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.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