org.eclipse.stem.tests.diseasemodels/src/org/eclipse/stem/diseasemodels/standard/tests/StochasticSEIRDiseaseModelTest.java - stem/org.eclipse.stem - Git at Google

 package org.eclipse.stem.diseasemodels.standard.tests;

 /*******************************************************************************
  * Copyright (c) 2006, 2008 IBM Corporation and others.
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
  * which accompanies this distribution, and is available at
  * http://www.eclipse.org/legal/epl-v10.html
  *
  * Contributors:
  *     IBM Corporation - initial API and implementation
  *******************************************************************************/

 import java.util.Random;

 import junit.textui.TestRunner;

 //import org.eclipse.stem.diseasemodels.standard.StandardFactory;
 import org.eclipse.emf.ecore.util.EcoreUtil;
 import org.eclipse.stem.diseasemodels.standard.DiseaseModelState;
 import org.eclipse.stem.diseasemodels.standard.SEIRLabelValue;
 import org.eclipse.stem.diseasemodels.standard.SIRLabelValue;
 import org.eclipse.stem.diseasemodels.standard.StandardDiseaseModelLabel;
 import org.eclipse.stem.diseasemodels.standard.StandardDiseaseModelLabelValue;
 import org.eclipse.stem.diseasemodels.standard.StochasticSEIRDiseaseModel;
 import org.eclipse.stem.diseasemodels.standard.impl.SEIRLabelValueImpl;
 import org.eclipse.stem.diseasemodels.standard.impl.StandardStochasticDiseaseModelImpl;
 import org.eclipse.stem.diseasemodels.standard.impl.StochasticSEIRDiseaseModelImpl;

 /**
  * <!-- begin-user-doc --> A test case for the model object '<em><b>Stochastic SEIR Disease Model</b></em>'.
  * <!-- end-user-doc -->
  * <p>
  * The following operations are tested:
  * <ul>
  *   <li>{@link org.eclipse.stem.diseasemodels.standard.StandardStochasticDiseaseModel#computeNoise() <em>Compute Noise</em>}</li>
  * </ul>
  * </p>
  * @generated
  */
 @SuppressWarnings("all")
 public class StochasticSEIRDiseaseModelTest extends SEIRTest {

 	public static final long RANDOM_SEED = 1l;
 	public static final double TEST_GAIN = 0.01d;

 	/**
 	 * The name of the test disease (an instance of a disease model)
 	 */
 	public static final String TEST_SEIR_DISEASE_NAME = "Test Stocastic SEIR Disease";


 	/**
 	 * <!-- begin-user-doc -->
 	 *
 	 * @param args
 	 *
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	public static void main(String[] args) {
 		TestRunner.run(StochasticSEIRDiseaseModelTest.class);
 	}

 	/**
 	 * Constructs a new Stochastic SEIR Disease Model test case with the given name.
 	 * <!-- begin-user-doc -->
 	 *
 	 * @param name
 	 *
 	 * <!-- end-user-doc -->
 	 * @generated
 	 */
 	public StochasticSEIRDiseaseModelTest(String name) {
 		super(name);
 	}

 	/**
 	 * Returns the fixture for this Stochastic SEIR Disease Model test case.
 	 * <!-- begin-user-doc --> <!-- end-user-doc -->
 	 * @generated
 	 */
 	@Override
 	protected StochasticSEIRDiseaseModel getFixture() {
 		return (StochasticSEIRDiseaseModel)fixture;
 	}

 	/**
 	 * <!-- begin-user-doc --> <!-- end-user-doc -->
 	 *
 	 * @see junit.framework.TestCase#setUp()
 	 * @generated NOT
 	 */
 	protected void setUp() throws Exception {
 		setFixture(createFixture());
 		StandardDiseaseModelLabel dml = createLabelFixture();
 		DiseaseModelState dms = getFixture().createDiseaseModelState();
 		dml.setDiseaseModelState(dms);
 		setLabelFixture(dml);
 		fixture.initializeDiseaseState(dms, dml);
 	} // setUp

 	/**
 	 * <!-- begin-user-doc --> <!-- end-user-doc -->
 	 *
 	 * @see junit.framework.TestCase#tearDown()
 	 * @generated NOT
 	 */
 	protected void tearDown() throws Exception {
 		super.tearDown();
 	} // tearDown

 	/**
 	 * Tests the '{@link org.eclipse.stem.diseasemodels.standard.StandardStochasticDiseaseModel#computeNoise() <em>Compute Noise</em>}' operation.
 	 * <!-- begin-user-doc -->
 	 * <!-- end-user-doc -->
 	 * @see org.eclipse.stem.diseasemodels.standard.StandardStochasticDiseaseModel#computeNoise()
 	 * @generated NOT
 	 */
 	public void testComputeNoise() {
 		StandardStochasticDiseaseModelTest.staticComputeNoiseTest();
 	}

 	/**
 	 * Create disease model instance
 	 *
 	 * @return a disease model instance for test purposes
 	 */
 	public static StochasticSEIRDiseaseModel createFixture() {
 		return createFixture(StandardStochasticDiseaseModelImpl.GAIN_EDEFAULT);
 	} // createFixture

 	/**
 	 * Create disease model instance
 	 *
 	 * @return a disease model instance for test purposes
 	 */
 	public static StochasticSEIRDiseaseModel createFixture(double newGain) {
 		return StochasticSEIRDiseaseModelImpl.createStochasticSEIRDiseaseModel(
 				TEST_SEIR_DISEASE_NAME, MORTALITY_RATE,
 				INFECTIOUS_MORTALITY_RATE, TRANSMISSION_RATE, RECOVERY_RATE,
 				IMMUNITY_LOSS_RATE, INCUBATION_RATE, NON_LINEARITY_COEFFICIENT,
 				TEST_TIME_PERIOD, TEST_POPULATION_IDENTIFIER, newGain);


 	} // createFixture


 	/**
 	 * Tests the '{@link org.eclipse.stem.diseasemodels.standard.impl.StochasticDiseaseModelImpl#doModelSpecificAdjustments() <em>doModelSpecificAdjustments</em>}' operation.
 	 * @see org.eclipse.stem.diseasemodels.standard.impl.StochasticDiseaseModelImpl#doModelSpecificAdjustments()
 	 * @generated NOT
 	 */
 	@SuppressWarnings("synthetic-access")
 	public void testModelSpecificAdjustments(){
 		StochasticSEIRDiseaseModelTesterImpl stochasticSEIRDiseaseModel = new StochasticSEIRDiseaseModelTesterImpl();
 		SEIRLabelValueImpl currentSEIR = new SEIRLabelValueImpl(1000d, 50d, 40d, 30d, 20d, 10d);
 		doTest(stochasticSEIRDiseaseModel, currentSEIR);
 	}

 //	private void doTestWithPermutations() {
 //		StochasticSEIRDiseaseModelTesterImpl stochasticSEIRDiseaseModel = new StochasticSEIRDiseaseModelTesterImpl();
 //		List<SEIRLabelValueImpl> modelLableValues = SEIRLabelValueTestUtil.createRandomSEIRLabelValueImpl();
 //
 //		int count1 = 0;
 //		int count2 = 0;
 //		System.out.println();
 //		for(SEIRLabelValueImpl currentSEIR: modelLableValues){
 //			System.out.println(count1++);
 //			for(SEIRLabelValueImpl seirAdditions: modelLableValues){
 //				System.out.println("	" + count2++);
 //				for(SEIRLabelValueImpl seirDeaths: modelLableValues){
 //					//seirDeaths and seirAdditions will be modified my the test method, so we better clone them
 //					doTest(stochasticSEIRDiseaseModel, currentSEIR,
 //							seirAdditions, seirDeaths);
 //			 	}
 //			}
 //		}
 //	}

 	private void doTest(StochasticSEIRDiseaseModelTesterImpl stochasticSEIRDiseaseModel,
 			SEIRLabelValueImpl currentSEIR) {

 		SEIRLabelValueImpl oldSEIR = (SEIRLabelValueImpl)EcoreUtil.copy(currentSEIR);
 		stochasticSEIRDiseaseModel.doModelSpecificAdjustments(currentSEIR, RANDOM_SEED, TEST_GAIN);

 		doCalculateModelSpecificAdjustments(currentSEIR, RANDOM_SEED, TEST_GAIN);

 		String state = getState(currentSEIR, oldSEIR);

 		validateModelSpecificAdjustments(currentSEIR,
 				oldSEIR,
 				state);
 	}

 	/**
 	 * This method returns a double precision random noise variable
 	 * r between (1.0+x) and (1.0-x)
 	 * where x is a product G* Math.rand(), and G is a gain factor 0<G<max noise
 	 *
 	 * @param gain
 	 * @param rand
 	 * @return noise
 	 */
 	public static double computeNoise(final double gain, final Random rand) {

 		double x = (2.0*rand.nextDouble())-1.0; // +/- 1
 		x *= gain;
 		x += 1.0;
 		assert ((x>0.0)&&(x<2.0)) : "random noise should be a small perturbation Gain factor, g,  must 0.0 < g << 1.0 ";
 		return x;

 	} // getNoise


 	private void doCalculateModelSpecificAdjustments(
 			SEIRLabelValueImpl pCurrentSEIR, long pRandomSeed, double pTestGain) {


 		final SEIRLabelValue currentSEIR = (SEIRLabelValue) pCurrentSEIR;
 		Random random = new Random(pRandomSeed);
 		double Inoisy = currentSEIR.getI()* computeNoise(pTestGain, random);
 		currentSEIR.setI(Inoisy);
 		return;


 	}

 	private void validateModelSpecificAdjustments(SEIRLabelValueImpl currentSEIR,
 			SEIRLabelValueImpl oldSEIR,
 			String state) {


 		try{
 			currentSEIR.sane();
 		}
 		catch(Throwable t){
 			throw new IllegalStateException("currentSEIR is insane, state is: " + state, t);
 		}
 		try{
 			oldSEIR.sane();
 		}
 		catch(Throwable t){
 			throw new IllegalStateException("oldSEIR is insane, state is: " + state, t);
 		}


 		assertTrue(String.format("currentSEIR has insane values %s", state), mySanityCheck(currentSEIR));
 		assertTrue(String.format("oldSEIR has insane values %s", state), mySanityCheck(oldSEIR));

 	}

 	private boolean checkEqual(SEIRLabelValueImpl pCalculatedSeirAdditions,
 			SEIRLabelValueImpl pNewSeirAdditions) {
 		if((pCalculatedSeirAdditions.getDiseaseDeaths() != pNewSeirAdditions.getDiseaseDeaths()) ||
 				(pCalculatedSeirAdditions.getE() != pNewSeirAdditions.getE()) ||
 				(pCalculatedSeirAdditions.getI() != pNewSeirAdditions.getI()) ||
 				(pCalculatedSeirAdditions.getPopulationCount() != pNewSeirAdditions.getPopulationCount()) ||
 				(pCalculatedSeirAdditions.getR() != pNewSeirAdditions.getR()) ||
 				(pCalculatedSeirAdditions.getS() != pNewSeirAdditions.getS())){
 					return false;
 				}
 		return true;
 	}

 	private boolean mySanityCheck(SEIRLabelValueImpl pSeir) {
 		return assertValidDouble(pSeir.getE()) &&
 			assertValidDouble(pSeir.getI()) &&
 			assertValidDouble(pSeir.getR()) &&
 			assertValidDouble(pSeir.getS());

 	}

 	private boolean assertValidDouble(double pDouble) {
 		return !(Double.isNaN(pDouble) || Double.isInfinite(pDouble));
 	}

 	private String getState(SEIRLabelValueImpl pCurrentSEIR,
 			SEIRLabelValueImpl oldSEIR) {
 		return String.format("\npresent state is: \ncurrentSEIR[%s]\n oldSEIR[%s]",
 				pCurrentSEIR, oldSEIR);
 	}


 	/**
 	 * created just for testings since '{@link org.eclipse.stem.diseasemodels.standard.impl.StochasticDiseaseModelImpl#doModelSpecificAdjustments() <em>doModelSpecificAdjustments</em>}' is protected.
 	 * @author eishay
 	 *
 	 */
 	private class StochasticSEIRDiseaseModelTesterImpl extends StochasticSEIRDiseaseModelImpl{

 		public void doModelSpecificAdjustments(
 				StandardDiseaseModelLabelValue pCurrentState,
 				long pRandomSeed, double pTestGain) {
 			setSeed(pRandomSeed);
 			setGain(pTestGain);

 			SEIRLabelValueImpl oldCurrentState = SEIRLabelValueTestUtil.cloneSEIRLabelValueImpl((SEIRLabelValueImpl)pCurrentState);
 			super.doModelSpecificAdjustments(pCurrentState);
 		}

 	}

 } // StochasticSEIRDiseaseModelTest
	package org.eclipse.stem.diseasemodels.standard.tests;

	/*******************************************************************************
	* Copyright (c) 2006, 2008 IBM Corporation and others.
	* All rights reserved. This program and the accompanying materials
	* are made available under the terms of the Eclipse Public License v1.0
	* which accompanies this distribution, and is available at
	* http://www.eclipse.org/legal/epl-v10.html
	*
	* Contributors:
	* IBM Corporation - initial API and implementation
	*******************************************************************************/

	import java.util.Random;

	import junit.textui.TestRunner;

	//import org.eclipse.stem.diseasemodels.standard.StandardFactory;
	import org.eclipse.emf.ecore.util.EcoreUtil;
	import org.eclipse.stem.diseasemodels.standard.DiseaseModelState;
	import org.eclipse.stem.diseasemodels.standard.SEIRLabelValue;
	import org.eclipse.stem.diseasemodels.standard.SIRLabelValue;
	import org.eclipse.stem.diseasemodels.standard.StandardDiseaseModelLabel;
	import org.eclipse.stem.diseasemodels.standard.StandardDiseaseModelLabelValue;
	import org.eclipse.stem.diseasemodels.standard.StochasticSEIRDiseaseModel;
	import org.eclipse.stem.diseasemodels.standard.impl.SEIRLabelValueImpl;
	import org.eclipse.stem.diseasemodels.standard.impl.StandardStochasticDiseaseModelImpl;
	import org.eclipse.stem.diseasemodels.standard.impl.StochasticSEIRDiseaseModelImpl;

	/**
	* <!-- begin-user-doc --> A test case for the model object '<em><b>Stochastic SEIR Disease Model</b></em>'.
	* <!-- end-user-doc -->
	* <p>
	* The following operations are tested:
	* <ul>
	* <li>{@link org.eclipse.stem.diseasemodels.standard.StandardStochasticDiseaseModel#computeNoise() <em>Compute Noise</em>}</li>
	* </ul>
	* </p>
	* @generated
	*/
	@SuppressWarnings("all")
	public class StochasticSEIRDiseaseModelTest extends SEIRTest {

	public static final long RANDOM_SEED = 1l;
	public static final double TEST_GAIN = 0.01d;

	/**
	* The name of the test disease (an instance of a disease model)
	*/
	public static final String TEST_SEIR_DISEASE_NAME = "Test Stocastic SEIR Disease";


	/**
	* <!-- begin-user-doc -->
	*
	* @param args
	*
	* <!-- end-user-doc -->
	* @generated
	*/
	public static void main(String[] args) {
	TestRunner.run(StochasticSEIRDiseaseModelTest.class);
	}

	/**
	* Constructs a new Stochastic SEIR Disease Model test case with the given name.
	* <!-- begin-user-doc -->
	*
	* @param name
	*
	* <!-- end-user-doc -->
	* @generated
	*/
	public StochasticSEIRDiseaseModelTest(String name) {
	super(name);
	}

	/**
	* Returns the fixture for this Stochastic SEIR Disease Model test case.
	* <!-- begin-user-doc --> <!-- end-user-doc -->
	* @generated
	*/
	@Override
	protected StochasticSEIRDiseaseModel getFixture() {
	return (StochasticSEIRDiseaseModel)fixture;
	}

	/**
	* <!-- begin-user-doc --> <!-- end-user-doc -->
	*
	* @see junit.framework.TestCase#setUp()
	* @generated NOT
	*/
	protected void setUp() throws Exception {
	setFixture(createFixture());
	StandardDiseaseModelLabel dml = createLabelFixture();
	DiseaseModelState dms = getFixture().createDiseaseModelState();
	dml.setDiseaseModelState(dms);
	setLabelFixture(dml);
	fixture.initializeDiseaseState(dms, dml);
	} // setUp

	/**
	* <!-- begin-user-doc --> <!-- end-user-doc -->
	*
	* @see junit.framework.TestCase#tearDown()
	* @generated NOT
	*/
	protected void tearDown() throws Exception {
	super.tearDown();
	} // tearDown

	/**
	* Tests the '{@link org.eclipse.stem.diseasemodels.standard.StandardStochasticDiseaseModel#computeNoise() <em>Compute Noise</em>}' operation.
	* <!-- begin-user-doc -->
	* <!-- end-user-doc -->
	* @see org.eclipse.stem.diseasemodels.standard.StandardStochasticDiseaseModel#computeNoise()
	* @generated NOT
	*/
	public void testComputeNoise() {
	StandardStochasticDiseaseModelTest.staticComputeNoiseTest();
	}

	/**
	* Create disease model instance
	*
	* @return a disease model instance for test purposes
	*/
	public static StochasticSEIRDiseaseModel createFixture() {
	return createFixture(StandardStochasticDiseaseModelImpl.GAIN_EDEFAULT);
	} // createFixture

	/**
	* Create disease model instance
	*
	* @return a disease model instance for test purposes
	*/
	public static StochasticSEIRDiseaseModel createFixture(double newGain) {
	return StochasticSEIRDiseaseModelImpl.createStochasticSEIRDiseaseModel(
	TEST_SEIR_DISEASE_NAME, MORTALITY_RATE,
	INFECTIOUS_MORTALITY_RATE, TRANSMISSION_RATE, RECOVERY_RATE,
	IMMUNITY_LOSS_RATE, INCUBATION_RATE, NON_LINEARITY_COEFFICIENT,
	TEST_TIME_PERIOD, TEST_POPULATION_IDENTIFIER, newGain);


	} // createFixture


	/**
	* Tests the '{@link org.eclipse.stem.diseasemodels.standard.impl.StochasticDiseaseModelImpl#doModelSpecificAdjustments() <em>doModelSpecificAdjustments</em>}' operation.
	* @see org.eclipse.stem.diseasemodels.standard.impl.StochasticDiseaseModelImpl#doModelSpecificAdjustments()
	* @generated NOT
	*/
	@SuppressWarnings("synthetic-access")
	public void testModelSpecificAdjustments(){
	StochasticSEIRDiseaseModelTesterImpl stochasticSEIRDiseaseModel = new StochasticSEIRDiseaseModelTesterImpl();
	SEIRLabelValueImpl currentSEIR = new SEIRLabelValueImpl(1000d, 50d, 40d, 30d, 20d, 10d);
	doTest(stochasticSEIRDiseaseModel, currentSEIR);
	}

	// private void doTestWithPermutations() {
	// StochasticSEIRDiseaseModelTesterImpl stochasticSEIRDiseaseModel = new StochasticSEIRDiseaseModelTesterImpl();
	// List<SEIRLabelValueImpl> modelLableValues = SEIRLabelValueTestUtil.createRandomSEIRLabelValueImpl();
	//
	// int count1 = 0;
	// int count2 = 0;
	// System.out.println();
	// for(SEIRLabelValueImpl currentSEIR: modelLableValues){
	// System.out.println(count1++);
	// for(SEIRLabelValueImpl seirAdditions: modelLableValues){
	// System.out.println(" " + count2++);
	// for(SEIRLabelValueImpl seirDeaths: modelLableValues){
	// //seirDeaths and seirAdditions will be modified my the test method, so we better clone them
	// doTest(stochasticSEIRDiseaseModel, currentSEIR,
	// seirAdditions, seirDeaths);
	// }
	// }
	// }
	// }

	private void doTest(StochasticSEIRDiseaseModelTesterImpl stochasticSEIRDiseaseModel,
	SEIRLabelValueImpl currentSEIR) {

	SEIRLabelValueImpl oldSEIR = (SEIRLabelValueImpl)EcoreUtil.copy(currentSEIR);
	stochasticSEIRDiseaseModel.doModelSpecificAdjustments(currentSEIR, RANDOM_SEED, TEST_GAIN);

	doCalculateModelSpecificAdjustments(currentSEIR, RANDOM_SEED, TEST_GAIN);

	String state = getState(currentSEIR, oldSEIR);

	validateModelSpecificAdjustments(currentSEIR,
	oldSEIR,
	state);
	}

	/**
	* This method returns a double precision random noise variable
	* r between (1.0+x) and (1.0-x)
	* where x is a product G* Math.rand(), and G is a gain factor 0<G<max noise
	*
	* @param gain
	* @param rand
	* @return noise
	*/
	public static double computeNoise(final double gain, final Random rand) {

	double x = (2.0*rand.nextDouble())-1.0; // +/- 1
	x *= gain;
	x += 1.0;
	assert ((x>0.0)&&(x<2.0)) : "random noise should be a small perturbation Gain factor, g, must 0.0 < g << 1.0 ";
	return x;

	} // getNoise


	private void doCalculateModelSpecificAdjustments(
	SEIRLabelValueImpl pCurrentSEIR, long pRandomSeed, double pTestGain) {


	final SEIRLabelValue currentSEIR = (SEIRLabelValue) pCurrentSEIR;
	Random random = new Random(pRandomSeed);
	double Inoisy = currentSEIR.getI()* computeNoise(pTestGain, random);
	currentSEIR.setI(Inoisy);
	return;


	}

	private void validateModelSpecificAdjustments(SEIRLabelValueImpl currentSEIR,
	SEIRLabelValueImpl oldSEIR,
	String state) {


	try{
	currentSEIR.sane();
	}
	catch(Throwable t){
	throw new IllegalStateException("currentSEIR is insane, state is: " + state, t);
	}
	try{
	oldSEIR.sane();
	}
	catch(Throwable t){
	throw new IllegalStateException("oldSEIR is insane, state is: " + state, t);
	}



	assertTrue(String.format("currentSEIR has insane values %s", state), mySanityCheck(currentSEIR));
	assertTrue(String.format("oldSEIR has insane values %s", state), mySanityCheck(oldSEIR));

	}

	private boolean checkEqual(SEIRLabelValueImpl pCalculatedSeirAdditions,
	SEIRLabelValueImpl pNewSeirAdditions) {
	if((pCalculatedSeirAdditions.getDiseaseDeaths() != pNewSeirAdditions.getDiseaseDeaths()) \|\|
	(pCalculatedSeirAdditions.getE() != pNewSeirAdditions.getE()) \|\|
	(pCalculatedSeirAdditions.getI() != pNewSeirAdditions.getI()) \|\|
	(pCalculatedSeirAdditions.getPopulationCount() != pNewSeirAdditions.getPopulationCount()) \|\|
	(pCalculatedSeirAdditions.getR() != pNewSeirAdditions.getR()) \|\|
	(pCalculatedSeirAdditions.getS() != pNewSeirAdditions.getS())){
	return false;
	}
	return true;
	}

	private boolean mySanityCheck(SEIRLabelValueImpl pSeir) {
	return assertValidDouble(pSeir.getE()) &&
	assertValidDouble(pSeir.getI()) &&
	assertValidDouble(pSeir.getR()) &&
	assertValidDouble(pSeir.getS());

	}

	private boolean assertValidDouble(double pDouble) {
	return !(Double.isNaN(pDouble) \|\| Double.isInfinite(pDouble));
	}

	private String getState(SEIRLabelValueImpl pCurrentSEIR,
	SEIRLabelValueImpl oldSEIR) {
	return String.format("\npresent state is: \ncurrentSEIR[%s]\n oldSEIR[%s]",
	pCurrentSEIR, oldSEIR);
	}


	/**
	* created just for testings since '{@link org.eclipse.stem.diseasemodels.standard.impl.StochasticDiseaseModelImpl#doModelSpecificAdjustments() <em>doModelSpecificAdjustments</em>}' is protected.
	* @author eishay
	*
	*/
	private class StochasticSEIRDiseaseModelTesterImpl extends StochasticSEIRDiseaseModelImpl{

	public void doModelSpecificAdjustments(
	StandardDiseaseModelLabelValue pCurrentState,
	long pRandomSeed, double pTestGain) {
	setSeed(pRandomSeed);
	setGain(pTestGain);

	SEIRLabelValueImpl oldCurrentState = SEIRLabelValueTestUtil.cloneSEIRLabelValueImpl((SEIRLabelValueImpl)pCurrentState);
	super.doModelSpecificAdjustments(pCurrentState);
	}

	}

	} // StochasticSEIRDiseaseModelTest