diff options
Diffstat (limited to 'src/jcgp/population')
| -rw-r--r-- | src/jcgp/population/Chromosome.java | 335 | ||||
| -rw-r--r-- | src/jcgp/population/Connection.java | 9 | ||||
| -rw-r--r-- | src/jcgp/population/Gene.java | 5 | ||||
| -rw-r--r-- | src/jcgp/population/Input.java | 29 | ||||
| -rw-r--r-- | src/jcgp/population/MutableElement.java | 34 | ||||
| -rw-r--r-- | src/jcgp/population/Node.java | 114 | ||||
| -rw-r--r-- | src/jcgp/population/Output.java | 69 | ||||
| -rw-r--r-- | src/jcgp/population/Population.java | 45 |
8 files changed, 0 insertions, 640 deletions
diff --git a/src/jcgp/population/Chromosome.java b/src/jcgp/population/Chromosome.java deleted file mode 100644 index 297d298..0000000 --- a/src/jcgp/population/Chromosome.java +++ /dev/null @@ -1,335 +0,0 @@ -package jcgp.population; - -import java.util.ArrayList; - -import jcgp.JCGP.Resources; -import jcgp.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; - } -} diff --git a/src/jcgp/population/Connection.java b/src/jcgp/population/Connection.java deleted file mode 100644 index 63a171e..0000000 --- a/src/jcgp/population/Connection.java +++ /dev/null @@ -1,9 +0,0 @@ -package jcgp.population; - -public interface Connection { - - public Object getValue(); - - public String getDescription(); - -} diff --git a/src/jcgp/population/Gene.java b/src/jcgp/population/Gene.java deleted file mode 100644 index 8865a01..0000000 --- a/src/jcgp/population/Gene.java +++ /dev/null @@ -1,5 +0,0 @@ -package jcgp.population; - -public abstract class Gene { - -} diff --git a/src/jcgp/population/Input.java b/src/jcgp/population/Input.java deleted file mode 100644 index cfcb3ce..0000000 --- a/src/jcgp/population/Input.java +++ /dev/null @@ -1,29 +0,0 @@ -package jcgp.population; - -public class Input extends Gene implements Connection { - - private Object value = 0; - private int index; - - public Input(int index) { - this.index = index; - } - - public void setValue(Object newValue) { - value = newValue; - } - - @Override - public Object getValue() { - return value; - } - - public int getIndex() { - return index; - } - - @Override - public String getDescription() { - return "i: " + index; - } -} diff --git a/src/jcgp/population/MutableElement.java b/src/jcgp/population/MutableElement.java deleted file mode 100644 index 12f6bd1..0000000 --- a/src/jcgp/population/MutableElement.java +++ /dev/null @@ -1,34 +0,0 @@ -package jcgp.population; - -public interface MutableElement { - - /** - * This method sets the indexed connection to the specified new connection. - * Implementing classes may choose to ignore the given index (such as in the - * case of outputs, which only have one connection). - * - * @param index - * @param newConnection - */ - public void setConnection(int index, Connection newConnection); - - /** - * This method returns true if and only if:</br> - * - the elements being compared are not the same instance;</br> - * - the connections of the compared elements are not the same instance;</br> - * - the elements have the same function (in the case of Node);</br> - * - the grid position of the elements themselves are the same;</br> - * - the grid position of all equivalent connections are the same;</br></br> - * - * The relationship computed by this method is:</br> - * - symmetric: a.copyOf(b) == b.copyOf(a);</br> - * - not reflexive: a.copyOf(a) returns false;</br> - * - not transitive: if a.copyOf(b) is true and b.copyOf(c) is true, a.copyOf(c) is - * not necessarily true since it is possible that a == c.</br> - * - * @param m - * @return - */ - boolean copyOf(MutableElement m); - -} diff --git a/src/jcgp/population/Node.java b/src/jcgp/population/Node.java deleted file mode 100644 index 141a32a..0000000 --- a/src/jcgp/population/Node.java +++ /dev/null @@ -1,114 +0,0 @@ -package jcgp.population; - -import java.util.ArrayList; -import java.util.Arrays; - -import jcgp.exceptions.InsufficientConnectionsException; -import jcgp.function.Function; - - -public class Node extends Gene implements MutableElement, Connection { - - private Function function; - private Connection[] connections; - private int column, row; - private Chromosome chromosome; - - public Node(Chromosome chromosome, int row, int column, int arity) { - this.chromosome = chromosome; - this.column = column; - this.row = row; - } - - @Override - public Object getValue() { - //System.out.print("Calculating node: (" + row + ", " + column + ") > "); - return function.run(Arrays.copyOfRange(connections, 0, function.getArity())); - } - - public void setFunction(Function newFunction) { - function = newFunction; - chromosome.recomputeActiveNodes(); - } - - @Override - public void setConnection(int index, Connection newConnection) { - connections[index] = newConnection; - chromosome.recomputeActiveNodes(); - } - - public void initialise(Function newFunction, Connection ... newConnections) throws InsufficientConnectionsException { - function = newFunction; - if (newConnections.length == function.getArity()) { - connections = newConnections; - } else { - throw new InsufficientConnectionsException(); - } - } - - public int getColumn() { - return column; - } - - public int getRow() { - return row; - } - - public Function getFunction() { - return function; - } - - public Connection getConnection(int index) { - return connections[index]; - } - - public void getActive(ArrayList<Node> activeNodes) { - if (!activeNodes.contains(this)) { - activeNodes.add(this); - } - for (int i = 0; i < function.getArity(); i++) { - if (connections[i] instanceof Node) { - ((Node) connections[i]).getActive(activeNodes); - } - - } - } - - @Override - public boolean copyOf(MutableElement m) { - if (this != m) { - if (m instanceof Node) { - Node n = (Node) m; - if (function == n.getFunction()) { - if (column == n.getColumn() && row == n.getRow()) { - for (int i = 0; i < connections.length; i++) { - if (connections[i] != n.getConnection(i)) { - if (connections[i] instanceof Input && n.getConnection(i) instanceof Input) { - if (((Input) connections[i]).getIndex() != ((Input) n.getConnection(i)).getIndex()) { - return false; - } - } else if (connections[i] instanceof Node && n.getConnection(i) instanceof Node) { - if (((Node) connections[i]).getRow() != ((Node) n.getConnection(i)).getRow() && - ((Node) connections[i]).getColumn() != ((Node) n.getConnection(i)).getColumn()) { - return false; - } - } else { - return false; - } - } else { - return false; - } - } - return true; - } - } - } - } - return false; - } - - @Override - public String getDescription() { - return "n: " + row + ", " + column; - } -} diff --git a/src/jcgp/population/Output.java b/src/jcgp/population/Output.java deleted file mode 100644 index 5cc6dcf..0000000 --- a/src/jcgp/population/Output.java +++ /dev/null @@ -1,69 +0,0 @@ -package jcgp.population; - -import java.util.ArrayList; - -public class Output extends Gene implements MutableElement { - - private Connection source; - private Chromosome chromosome; - private int index; - - public Output(Chromosome chromosome, int index) { - this.chromosome = chromosome; - this.index = index; - //this.source = new SimpleObjectProperty<Connection>(); - } - - public Object calculate() { - Object result = source.getValue(); - return result; - } - - @Override - public void setConnection(int index, Connection newConnection) { - source = newConnection; - chromosome.recomputeActiveNodes(); - } - - public int getIndex() { - return index; - } - - public Connection getSource() { - return source; - } - -// public SimpleObjectProperty<Connection> sourceProperty() { -// return source; -// } - - public void getActiveNodes(ArrayList<Node> activeNodes) { - if (source instanceof Node) { - ((Node) source).getActive(activeNodes); - } - } - - @Override - public boolean copyOf(MutableElement m) { - if (this != m) { - if (m instanceof Output) { - Output o = (Output) m; - if (index == o.getIndex()) { - if (source != o.getSource()) { - if (source instanceof Input && o.getSource() instanceof Input) { - if (((Input) source).getIndex() == ((Input) o.getSource()).getIndex()) { - return true; - } - } else if (source instanceof Node && o.getSource() instanceof Node) { - if (((Node) source).getRow() == ((Node) o.getSource()).getRow() && - ((Node) source).getColumn() == ((Node) o.getSource()).getColumn()) { - return true; - } - } - } - } - } - } - return false; - } -} diff --git a/src/jcgp/population/Population.java b/src/jcgp/population/Population.java deleted file mode 100644 index f5e0517..0000000 --- a/src/jcgp/population/Population.java +++ /dev/null @@ -1,45 +0,0 @@ -package jcgp.population; - -import jcgp.JCGP.Resources; - - -public class Population { - - private Chromosome[] chromosomes; - private int fittest; - - public Population(Resources resources) { - chromosomes = new Chromosome[(resources.getInt("popSize"))]; - for (int c = 0; c < chromosomes.length; c++) { - chromosomes[c] = new Chromosome(resources); - } - } - - public Population(Chromosome parent, Resources resources) { - chromosomes = new Chromosome[(resources.getInt("popSize"))]; - // make a clone for safety - this.chromosomes[0] = new Chromosome(parent); - // generate the rest of the individuals - for (int c = 1; c < chromosomes.length; c++) { - chromosomes[c] = new Chromosome(chromosomes[0]); - } - } - - /** - * Returns all chromosomes, parents first, then offspring. - * - * @param index - * @return - */ - public Chromosome getChromosome(int index) { - return chromosomes[index]; - } - - public void setBestIndividual(int index) { - fittest = index; - } - - public Chromosome getBestIndividual() { - return chromosomes[fittest]; - } -} |