Implemented more tests, refactored chromosome more, added the beginnings of active node detection

1 files changed, 172 insertions, 44 deletions

diff --git a/src/jcgp/tests/ChromosomeTests.java b/src/jcgp/tests/ChromosomeTests.java
index 50d17b9..ece8203 100644
--- a/src/jcgp/tests/ChromosomeTests.java
+++ b/src/jcgp/tests/ChromosomeTests.java
@@ -1,15 +1,17 @@
 package jcgp.tests;
 
-import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.*;
 
 import java.util.Random;
 
 import jcgp.Parameters;
 import jcgp.Utilities;
+import jcgp.fitness.ParameterMismatchException;
 import jcgp.function.Addition;
 import jcgp.function.FunctionSet;
 import jcgp.function.Subtraction;
 import jcgp.population.Chromosome;
+import jcgp.population.Connection;
 import jcgp.population.Input;
 import jcgp.population.MutableElement;
 import jcgp.population.Node;
@@ -24,24 +26,24 @@ import org.junit.Test;
  * 
  *  - The chromosome should be able to return a specified node, input or output.
  *  - It should be able to return a random MutableElement.
- *  - It should be able to return a random Connection 
+ *  - It should be able to return a random allowed connection given a column
+ *  - It should be able to return any random connection
  *  - It should contain a freely modifiable fitness value.
- *  - It should be a good citizen - fully initialised upon instantiation.
+ *  - For truth table evaluations, it should be able to have its inputs set.
+ *  - For truth table evaluations, the output should return a value according to what
+ *    it is set to.
  *  - It should feature a clone constructor, which creates a deep copy of a 
  *    specified Chromosome object.
- *  - It should be able to return the number of active nodes.
- *  - For truth table evaluations, it should be able to have its inputs set.
+ *  - It should be able to return a list of active nodes.
+ *  
+ *  WARNING: changing parameters may cause the tests to incorrectly fail!
  * 
  * @author Eduardo Pedroni
  *
  */
 public class ChromosomeTests {
 
-	Chromosome chromosome;
-	int inputCount = 3, 
-			rows = 3, 
-			columns = 3, 
-			outputCount = 3;
+	private Chromosome chromosome;
 
 	@Before
 	public void setUp() throws Exception {
@@ -52,54 +54,180 @@ public class ChromosomeTests {
 		Utilities.setResources(new Random(1234), functionSet);
 
 		// initialise parameters
-		Parameters.setColumns(columns);
-		Parameters.setRows(rows);
-		Parameters.setInputs(inputCount);
-		Parameters.setOutputs(outputCount);
-		Parameters.setLevelsBack(1);
+		Parameters.setColumns(20);
+		Parameters.setRows(10);
+		Parameters.setInputs(2);
+		Parameters.setOutputs(4);
+		Parameters.setLevelsBack(20);
 		Parameters.setMutationRate(10);
 		Parameters.setTotalGenerations(100);
 		Parameters.setTotalRuns(5);
 		Parameters.setMaxArity(functionSet.getMaxArity());
 
-		chromosome = new Chromosome(inputCount, rows, columns, outputCount);
-		
+		chromosome = new Chromosome();
+
 	}
 
+	/**
+	 * 
+	 */
 	@Test
-	public void test() {
-		// pick arbitrary node, assume that if one node is right, all nodes are right
-		boolean nodeReturn = chromosome.getNode(1, 2).getColumn() == 2
-				&& chromosome.getNode(1, 2).getRow() == 1
-				&& chromosome.getNode(1, 2) instanceof Node;
-		assertTrue("Incorrect node returned.", nodeReturn);
-
-		// set input values, check that acquired values are correct
-		chromosome.setInputs(4, 5, 6);
-		boolean inputReturn = chromosome.getInput(0).getValue() ==  4 && chromosome.getInput(0) instanceof Input
-				&& chromosome.getInput(1).getValue() ==  5 && chromosome.getInput(0) instanceof Input
-				&& chromosome.getInput(2).getValue() ==  6 && chromosome.getInput(0) instanceof Input;
-		assertTrue("Incorrect inputs returned.", inputReturn);
-
-		// connect outputs to inputs, check that calculated outputs return input values
-		for (int i = 0; i < outputCount; i++) {
-			chromosome.getOutput(i).setConnection(chromosome.getInput(0));
-		}
-		boolean outputReturn = chromosome.getOutput(0).calculate() ==  4 && chromosome.getOutput(0) instanceof Output
-				&& chromosome.getOutput(1).calculate() ==  4 && chromosome.getOutput(0) instanceof Output
-				&& chromosome.getOutput(2).calculate() ==  4 && chromosome.getOutput(0) instanceof Output;
-		assertTrue("Incorrect output returned.", outputReturn);
-
-		// get a mutable element, check that it is a Mutable
-		boolean mutableReturn = chromosome.getRandomMutableElement() != chromosome.getRandomMutableElement() && chromosome.getRandomMutableElement() instanceof MutableElement;
-		assertTrue("Returned the same element.", mutableReturn);
+	public void cloneTest() {
+		int[] testInputs;
+		// create a clone, check to see if it really is a clone
+		Chromosome clone = new Chromosome(chromosome);
 		
+		// set input values
+		testInputs = new int[Parameters.getInputs()];
+		for (int i = 0; i < Parameters.getInputs(); i++) {
+			testInputs[i] = i * 2 - 3;
+		}
+		chromosome.setInputs(testInputs);
+		clone.setInputs(testInputs);
 		
+		// connect outputs to inputs, check that the outputs match
+		for (int i = 0; i < Parameters.getOutputs(); i++) {
+			chromosome.getOutput(i).setConnection(chromosome.getInput(i % Parameters.getInputs()));
+			clone.getOutput(i).setConnection(clone.getInput(i % Parameters.getInputs()));
+			assertTrue("Incorrect output returned.", chromosome.getOutput(i).calculate() == 
+													 clone.getOutput(i).calculate());
+		}
 		
+		// change clone inputs, outputs should no longer match
+		testInputs = new int[Parameters.getInputs()];
+		for (int i = 0; i < Parameters.getInputs(); i++) {
+			testInputs[i] = i * 2;
+		}
+		clone.setInputs(testInputs);
+		for (int i = 0; i < Parameters.getOutputs(); i++) {
+			assertTrue("Incorrect output returned.", chromosome.getOutput(i).calculate() != 
+													 clone.getOutput(i).calculate());
+		}
+	}
+
+	/**
+	 * 
+	 */
+	@Test
+	public void fitnessTest() {
 		// set a fitness value, check if returned value is the same
 		chromosome.setFitness(10);
 		assertTrue("Incorrect fitness returned.", chromosome.getFitness() == 10);
-		
 	}
 
+	/**
+	 * 
+	 */
+	@Test
+	public void randomConnectionTest() {
+		// get random connections with column 0, check that they are all inputs
+		for (int i = 0; i < 10000; i++) {
+			boolean connectionReturn = chromosome.getRandomConnection(0) instanceof Input;
+			assertTrue("Connection is not an input.", connectionReturn);
+		}
+
+		// get random connections with column 2
+		// they should all be nodes, and their columns should be within range
+		int connectionNodes = 0, connectionOutOfRange = 0, connectionInputs = 0, connectionPicks = 100000;
+		int chosenColumn = 2;
+		for (int i = 0; i < connectionPicks; i++) {
+			Connection c = chromosome.getRandomConnection(chosenColumn);
+			if (c instanceof Node) {
+				connectionNodes++;
+				if (((Node) c).getColumn() >= chosenColumn) {
+					connectionOutOfRange++;
+				}
+				assertTrue("Connection is not allowed : " + ((Node) c).getColumn(), ((Node) c).getColumn() < chosenColumn && ((Node) c).getColumn() < chosenColumn);
+			} else if (c instanceof Input) {
+				connectionInputs++;
+			} else {
+				fail("Return is neither Node nor Input.");
+
+			}	
+		}
+		System.out.println("Out of " + connectionPicks + " connections picked from " + ((chosenColumn >= Parameters.getLevelsBack()) ? Parameters.getLevelsBack() : chosenColumn) * Parameters.getRows() +
+				" nodes and " + Parameters.getInputs() + " allowed nodes, " + connectionNodes + " were nodes and " + connectionInputs + " were inputs.");
+
+		System.out.println("Node/input ratio: " + ((double) ((chosenColumn >= Parameters.getLevelsBack()) ? Parameters.getLevelsBack() : chosenColumn) * Parameters.getRows()) / (double) Parameters.getInputs() +
+				", picked ratio: " + (double) connectionNodes / (double) connectionInputs);
+
+		System.out.println(connectionOutOfRange + " nodes that disrespected levels back were picked.");
+	}
+
+	/**
+	 * 
+	 */
+	@Test
+	public void randomMutableTest() {
+		// get mutable elements, check Node to Output ratio
+		int mutablePicks = 100000;
+		int mutableNodes = 0, mutableOutputs = 0;
+		for (int i = 0; i < mutablePicks; i++) {
+			MutableElement m = chromosome.getRandomMutableElement();
+
+			if (m instanceof Node) {
+				mutableNodes++;
+			} else if (m instanceof Output) {
+				mutableOutputs++;
+			} else {
+				fail("Return is neither Node nor Output.");
+			}
+		}
+		System.out.println("Out of " + mutablePicks + " mutable elements picked from " + Parameters.getNodeCount() +
+				" nodes and " + Parameters.getOutputs() + " outputs, " + mutableNodes + " were nodes and " +
+				mutableOutputs + " were outputs.");
+		System.out.println("Node/output ratio: " + (double) Parameters.getNodeCount() / (double) Parameters.getOutputs() +
+				", picked ratio: " + (double) mutableNodes / (double) mutableOutputs + "\n");
+	}
+
+	/**
+	 * 
+	 */
+	@Test
+	public void getOutputsTest() {
+		// connect outputs to inputs, check that calculated outputs return input values
+		for (int i = 0; i < Parameters.getOutputs(); i++) {
+			chromosome.getOutput(i).setConnection(chromosome.getInput(i % Parameters.getInputs()));
+			assertTrue("Incorrect output returned.", chromosome.getOutput(i).calculate() == 
+					chromosome.getInput(i % Parameters.getInputs()).getValue());
+		}
+	}
+
+	/**
+	 * @throws ParameterMismatchException
+	 */
+	@Test
+	public void setInputTest() throws ParameterMismatchException {
+		// set input values, check that acquired values are correct
+		int[] testInputs = new int[Parameters.getInputs()];
+		for (int i = 0; i < Parameters.getInputs(); i++) {
+			testInputs[i] = i * 2 - 3;
+		}
+		chromosome.setInputs(testInputs);
+		for (int i = 0; i < Parameters.getInputs(); i++) {
+			assertTrue("Incorrect input returned.", chromosome.getInput(i).getValue() == i * 2 - 3);
+		}
+	}
+
+	/**
+	 * 
+	 */
+	@Test
+	public void getNodeTest() {
+		// get all nodes one by one, check that they are all correct
+		for (int r = 0; r < Parameters.getRows(); r++) {
+			for (int c = 0; c < Parameters.getColumns(); c++) {
+				assertTrue("Incorrect node returned.", chromosome.getNode(r, c).getColumn() == c &&
+						chromosome.getNode(r, c).getRow() == r);
+			}
+		}
+	}
+	
+	/**
+	 * 
+	 */
+	@Test
+	public void activeNodeTest() {
+		
+	}
 }