diff options
author | Eduardo Pedroni <ep625@york.ac.uk> | 2014-04-01 23:00:53 +0100 |
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committer | Eduardo Pedroni <ep625@york.ac.uk> | 2014-04-01 23:00:53 +0100 |
commit | 02fd2bc7059da416937beb1abe67e5ca60379030 (patch) | |
tree | 609341fe10aaa0f2dc45a1e72eba20bd24fb1281 /src/jcgp/backend/population/Chromosome.java | |
parent | a757deacded0d7357a9f68462d3f2051e16004ee (diff) |
Settings pane now actually controls the parameters, not much left to do.
Diffstat (limited to 'src/jcgp/backend/population/Chromosome.java')
-rw-r--r-- | src/jcgp/backend/population/Chromosome.java | 335 |
1 files changed, 335 insertions, 0 deletions
diff --git a/src/jcgp/backend/population/Chromosome.java b/src/jcgp/backend/population/Chromosome.java new file mode 100644 index 0000000..18ae9bb --- /dev/null +++ b/src/jcgp/backend/population/Chromosome.java @@ -0,0 +1,335 @@ +package jcgp.backend.population; + +import java.util.ArrayList; + +import jcgp.JCGP.Resources; +import jcgp.backend.exceptions.ParameterMismatchException; + +public class Chromosome { + + private Resources resources; + + private Input[] inputs; + private Node[][] nodes; + private Output[] outputs; + + private ArrayList<Node> activeNodes; + + private int fitness = 0; + private boolean recomputeActiveNodes = true; + + /** + * Initialise a chromosome with the specified parameters. Random valid connections + * are created. + * + * + */ + public Chromosome(Resources resources) { + // store a reference to the parameters + this.resources = resources; + + // allocate memory for all elements of the chromosome + instantiateElements(); + // set random connections so that the chromosome can be evaluated + initialiseConnections(); + } + + /** + * Copy constructor. + * + * Initialise a new chromosome with the exact same connections as a given instance of Chromosome. + * + * @param clone the chromosome to be copied + */ + public Chromosome(Chromosome clone) { + // store a reference to the parameters + this.resources = clone.getParameters(); + + // allocate memory for all elements of the chromosome + instantiateElements(); + // initialise all connections based on argument + copyConnections(clone); + } + + /** + * + */ + private void instantiateElements() { + inputs = new Input[(resources.getInt("inputs"))]; + for (int i = 0; i < (resources.getInt("inputs")); i++) { + inputs[i] = new Input(i); + } + + int arity = resources.getInt("arity"); + + // rows first + nodes = new Node[(resources.getInt("rows"))][(resources.getInt("columns"))]; + for (int r = 0; r < (resources.getInt("rows")); r++) { + for (int c = 0; c < (resources.getInt("columns")); c++) { + nodes[r][c] = new Node(this, r, c, arity); + } + } + outputs = new Output[(resources.getInt("outputs"))]; + for (int o = 0; o < (resources.getInt("outputs")); o++) { + outputs[o] = new Output(this, o); + } + } + + /** + * + */ + private void initialiseConnections() { + + int arity = resources.getInt("arity"); + + // initialise nodes - [rows][columns] + for (int r = 0; r < nodes.length; r++) { + for (int c = 0; c < nodes[r].length; c++) { + Connection[] connections = new Connection[arity]; + for (int i = 0; i < connections.length; i++) { + connections[i] = getRandomConnection(c); + } + nodes[r][c].initialise(resources.getRandomFunction(), connections); + } + } + + for (Output output : outputs) { + output.setConnection(0, getRandomConnection()); + } + + } + + /** + * @param clone + */ + public void copyConnections(Chromosome clone) { + int arity = resources.getInt("arity"); + + // copy nodes - [rows][columns] + for (int r = 0; r < nodes.length; r++) { + for (int c = 0; c < nodes[r].length; c++) { + // make array of connections to initialise with + Connection[] connections = new Connection[arity]; + // populate with connections equivalent to clone + Connection copyConnection; + for (int i = 0; i < connections.length; i++) { + copyConnection = clone.getNode(r, c).getConnection(i); + if (copyConnection instanceof Input) { + connections[i] = inputs[((Input) copyConnection).getIndex()]; + } else if (copyConnection instanceof Node) { + connections[i] = nodes[((Node) copyConnection).getRow()][((Node) copyConnection).getColumn()]; + } else { + System.out.println("Warning: Connection of subtype " + copyConnection.getClass().toString() + " is not explicitly handled by copy constructor."); + } + } + // initialise with copied arguments + nodes[r][c].initialise(clone.getNode(r, c).getFunction(), connections); + } + } + + // do the same to outputs + Connection copyOutput; + for (int o = 0; o < outputs.length; o++) { + copyOutput = clone.getOutput(o).getSource(); + if (copyOutput instanceof Input) { + outputs[o].setConnection(0, inputs[((Input) copyOutput).getIndex()]); + } else if (copyOutput instanceof Node) { + outputs[o].setConnection(0, nodes[((Node) copyOutput).getRow()][((Node) copyOutput).getColumn()]); + } else { + // something bad happened + System.out.println("Warning: Connection of subtype " + copyOutput.getClass().toString() + " is not explicitly handled by copy constructor."); + } + } + } + + public Node getNode(int row, int column) { + return nodes[row][column]; + } + + public Output getOutput(int index) { + return outputs[index]; + } + + public Input getInput(int index) { + return inputs[index]; + } + + public int getFitness() { + return fitness; + } + + public void setFitness(int newFitness) { + fitness = newFitness; + } + + /** + * + * @param values + * @throws ParameterMismatchException + */ + public void setInputs(Object ... values) throws ParameterMismatchException { + // if the values provided don't match the specified number of inputs, the user should be warned + if (values.length == inputs.length) { + // set inputs for evaluation + for (int i = 0; i < values.length; i++) { + inputs[i].setValue(values[i]); + } + } else { + throw new ParameterMismatchException(); + } + } + + /** + * This method is useful for mutating chromosomes. + * + * @return a random element that can be mutated - Node or Output + */ + public MutableElement getRandomMutableElement() { + // choose output or node + int index = resources.getRandomInt(outputs.length + (resources.getInt("rows")) * (resources.getInt("columns"))); + + if (index < outputs.length) { + // outputs + return outputs[index]; + } else { + // node + index -= outputs.length; + return nodes[index / (resources.getInt("columns"))][index % (resources.getInt("columns"))]; + } + } + + /** + * Returns a random allowed connection respecting levels back.</br> + * This method may always pick inputs, as they can be picked + * regardless of the column. + * + * @param column the column to use as reference + * @return a random connection + */ + public Connection getRandomConnection(int column) { + // work out the allowed range obeying levels back + int allowedColumns = ((column >= (resources.getInt("levelsBack"))) ? (resources.getInt("levelsBack")) : column); + int offset = ((column - allowedColumns) * nodes.length) - inputs.length; + + // choose input or allowed node + int index = resources.getRandomInt(inputs.length + (nodes.length * allowedColumns)); + if (index < inputs.length) { + // input + return inputs[index]; + } else { + // node + // offset it to address the right columns + index += offset; + return nodes[index % nodes.length][index / nodes.length]; + } + } + + /** + * This method will pick a completely random connection, independently + * of levels back, including inputs. + * + * Useful for setting outputs. + * + * + * @return a random connection + */ + public Connection getRandomConnection() { + // choose output or node + int index = resources.getRandomInt(inputs.length + (resources.getInt("columns")) * (resources.getInt("rows"))); + if (index < inputs.length) { + // outputs + return inputs[index]; + } else { + // node + index -= inputs.length; + return nodes[index / (resources.getInt("columns"))][index % (resources.getInt("columns"))]; + } + } + + /** + * This causes the list of active nodes to be recomputed lazily (once it is actually requested). + */ + public void recomputeActiveNodes() { + recomputeActiveNodes = true; + } + + /** + * This method computes a list of active connections (if necessary) and returns it. + * + * @return + */ + public ArrayList<Node> getActiveNodes() { + computeActiveNodes(); + return activeNodes; + } + + private void computeActiveNodes() { + // lazy recomputation has been triggered, do it + if (recomputeActiveNodes) { + recomputeActiveNodes = false; + activeNodes = new ArrayList<Node>(); + + for (Output output : outputs) { + output.getActiveNodes(activeNodes); + } + } + + } + + public boolean compareTo(Chromosome chromosome) { + for (int r = 0; r < (resources.getInt("rows")); r++) { + for (int c = 0; c < (resources.getInt("columns")); c++) { + if (!(nodes[r][c].copyOf(chromosome.getNode(r, c)))) { + return false; + } + } + } + + for (int o = 0; o < (resources.getInt("outputs")); o++) { + if (!(outputs[o].copyOf(chromosome.getOutput(o)))) { + return false; + } + } + + return true; + } + + public boolean compareActiveTo(Chromosome chromosome) { + // update list if it is out of date + computeActiveNodes(); + + if (activeNodes.size() == chromosome.getActiveNodes().size()) { + for (int i = 0; i < activeNodes.size(); i++) { + if (!(activeNodes.get(i).copyOf(chromosome.getActiveNodes().get(i)))){ + return false; + } + } + return true; + } + return false; + } + + public void printNodes() { + int arity = resources.getInt("arity"); + + for (int r = 0; r < (resources.getInt("rows")); r++) { + System.out.print("r: " + r + "\t"); + for (int c = 0; c < (resources.getInt("columns")); c++) { + System.out.print("N: (" + r + ", " + c + ") "); + for (int i = 0; i < arity; i++) { + System.out.print("C" + i + ": (" + nodes[r][c].getConnection(i).getDescription() + ") "); + } + System.out.print("F: " + nodes[r][c].getFunction().getName() + "\t"); + } + System.out.print("\n"); + } + + for (int o = 0; o < (resources.getInt("outputs")); o++) { + System.out.print("o: " + o + " (" + outputs[o].getSource().getDescription() + ")\t"); + } + } + + public Resources getParameters() { + return resources; + } +} |