From 6769419bea279935c4a3a84616d45ee7d4a6345c Mon Sep 17 00:00:00 2001
From: Eduardo Pedroni <ep625@york.ac.uk>
Date: Tue, 22 Apr 2014 08:48:11 +0100
Subject: Chromosome parser is buggy, need to fix that.
---
src/jcgp/JCGP.java | 6 +--
src/jcgp/backend/parser/ChromosomeParser.java | 60 +++++++++++++++++++---
src/jcgp/backend/population/Node.java | 8 ++-
src/jcgp/backend/population/Population.java | 2 +-
src/jcgp/backend/resources/Resources.java | 10 ++++
src/jcgp/gui/settings/SettingsPane.java | 13 +++--
.../settings/parameters/GUIDoubleParameter.java | 1 -
src/jcgp/gui/settings/parameters/GUIParameter.java | 1 -
8 files changed, 83 insertions(+), 18 deletions(-)
(limited to 'src')
diff --git a/src/jcgp/JCGP.java b/src/jcgp/JCGP.java
index f949944..2a6552c 100644
--- a/src/jcgp/JCGP.java
+++ b/src/jcgp/JCGP.java
@@ -267,12 +267,12 @@ public class JCGP {
}
}
- public void loadChromosome(File file) {
- ChromosomeParser.parse(file, population.getChromosome(0), resources);
+ public void loadChromosome(File file, int chromosomeIndex) {
+ ChromosomeParser.parse(file, population.getChromosome(chromosomeIndex), resources);
}
public void saveChromosome(File file, int chromosomeIndex) {
- ChromosomeParser.save(file, population.getChromosome(chromosomeIndex));
+ ChromosomeParser.save(file, population.getChromosome(chromosomeIndex), resources);
}
public boolean isFinished() {
diff --git a/src/jcgp/backend/parser/ChromosomeParser.java b/src/jcgp/backend/parser/ChromosomeParser.java
index d5af1bd..fd03b7d 100644
--- a/src/jcgp/backend/parser/ChromosomeParser.java
+++ b/src/jcgp/backend/parser/ChromosomeParser.java
@@ -3,10 +3,12 @@ package jcgp.backend.parser;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
+import java.io.PrintWriter;
import java.util.Scanner;
import jcgp.backend.population.Chromosome;
import jcgp.backend.population.Connection;
+import jcgp.backend.population.Input;
import jcgp.backend.population.Node;
import jcgp.backend.resources.Resources;
@@ -73,15 +75,16 @@ public abstract class ChromosomeParser {
Connection newConnection;
Node changingNode;
// for all nodes, columns first
- for (int c = 0; c < resources.columns(); c ++) {
- for (int r = 0; r < resources.rows(); r ++) {
+ for (int c = 0; c < resources.columns(); c++) {
+ for (int r = 0; r < resources.rows(); r++) {
// store the changing node
changingNode = chromosome.getNode(r, c);
// for every connection
- for (int i = 0; i < resources.arity(); i ++) {
+ for (int i = 0; i < resources.arity(); i++) {
// get connection number from the .chr file
gene = in.nextInt();
+ System.out.println("r: " + r + " c: " + c + " i: " + i + " gene: " + gene);
if (gene < resources.inputs()) {
// connection was an input
newConnection = chromosome.getInput(gene);
@@ -113,6 +116,8 @@ public abstract class ChromosomeParser {
chromosome.getOutput(o).setConnection(0, newConnection);
}
in.close();
+ } else {
+ throw new IllegalArgumentException("The topology of the chromosome in " + file.getName() + " does not match that of the experiment.");
}
}
@@ -120,12 +125,53 @@ public abstract class ChromosomeParser {
* Writes a chromosome into the specified .chr file.
*
*
- *
- * @param file
- * @param chromosome
+ * @param file the file to write to
+ * @param chromosome the chromosome to save
*/
- public static void save(File file, Chromosome chromosome) {
+ public static void save(File file, Chromosome chromosome, Resources resources) {
+ PrintWriter writer;
+ try {
+ writer = new PrintWriter(file);
+ } catch (FileNotFoundException e) {
+ // something bad happened
+ return;
+ }
+
+ // for all nodes, columns first
+ for (int c = 0; c < resources.columns(); c++) {
+ for (int r = 0; r < resources.rows(); r++) {
+ for (int i = 0; i < resources.arity(); i++) {
+ // print the connections, separated by spaces
+ Connection conn = chromosome.getNode(r, c).getConnection(i);
+ if (conn instanceof Input) {
+ writer.print(" " + ((Input) conn).getIndex());
+ } else if (conn instanceof Node) {
+ writer.print(" " + (((((Node) conn).getColumn() + 1) * resources.inputs()) + ((Node) conn).getRow()));
+ } else {
+ throw new ClassCastException("Could not handle " + conn.getClass() + " as a subclass of Connection");
+ }
+ }
+ // print the function numbers
+ writer.print(" " + resources.getFunctionIndex(chromosome.getNode(r, c).getFunction()));
+ // node is done, print tab
+ writer.print("\t");
+ }
+ }
+ // nodes are done, print two tabs to separate from output
+ writer.print("\t\t");
+ for (int o = 0; o < resources.outputs(); o ++) {
+ Connection source = chromosome.getOutput(o).getSource();
+ if (source instanceof Input) {
+ writer.print(" " + ((Input) source).getIndex());
+ } else if (source instanceof Node) {
+ writer.print(" " + (((((Node) source).getColumn() + 1) * resources.inputs()) + ((Node) source).getRow()));
+ } else {
+ throw new ClassCastException("Could not handle " + source.getClass() + " as a subclass of Connection");
+ }
+ }
+ writer.close();
+ System.out.println("writer is closed");
}
}
diff --git a/src/jcgp/backend/population/Node.java b/src/jcgp/backend/population/Node.java
index 6a558a4..b716ff8 100644
--- a/src/jcgp/backend/population/Node.java
+++ b/src/jcgp/backend/population/Node.java
@@ -31,8 +31,12 @@ public class Node extends Gene implements MutableElement, Connection {
@Override
public void setConnection(int index, Connection newConnection) {
- connections[index] = newConnection;
- chromosome.recomputeActiveNodes();
+ if (newConnection instanceof Node) {
+ if (((Node) newConnection).getColumn() < column) {
+ connections[index] = newConnection;
+ chromosome.recomputeActiveNodes();
+ }
+ }
}
public void initialise(Function newFunction, Connection ... newConnections) throws InsufficientConnectionsException {
diff --git a/src/jcgp/backend/population/Population.java b/src/jcgp/backend/population/Population.java
index 1bbdc54..b6dd055 100644
--- a/src/jcgp/backend/population/Population.java
+++ b/src/jcgp/backend/population/Population.java
@@ -4,7 +4,7 @@ import jcgp.backend.resources.Resources;
public class Population {
- private Chromosome[] chromosomes;
+ private final Chromosome[] chromosomes;
private final Resources resources;
private int fittest = 0;
diff --git a/src/jcgp/backend/resources/Resources.java b/src/jcgp/backend/resources/Resources.java
index 151d536..6eb75cd 100644
--- a/src/jcgp/backend/resources/Resources.java
+++ b/src/jcgp/backend/resources/Resources.java
@@ -320,6 +320,16 @@ public class Resources {
return functionSet;
}
+ public int getFunctionIndex(Function function) {
+ for (int i = 0; i < functionSet.getTotalFunctionCount(); i++) {
+ if (function == functionSet.getFunction(i)) {
+ return i;
+ }
+ }
+ // not found, default to 0
+ return 0;
+ }
+
/*
* Console functionality
* These are affected by parameter report
diff --git a/src/jcgp/gui/settings/SettingsPane.java b/src/jcgp/gui/settings/SettingsPane.java
index 4050a89..302e96d 100644
--- a/src/jcgp/gui/settings/SettingsPane.java
+++ b/src/jcgp/gui/settings/SettingsPane.java
@@ -326,12 +326,12 @@ public class SettingsPane extends AnchorPane {
@Override
public void handle(ActionEvent event) {
FileChooser fc = new FileChooser();
- fc.setTitle("Open .chr file...");
+ fc.setTitle("Load .chr file...");
fc.getExtensionFilters().add(new ExtensionFilter("CGP chromosome files", "*.chr"));
fc.getExtensionFilters().add(new ExtensionFilter("All files", "*.*"));
File chrFile = fc.showOpenDialog(gui.getStage());
if (chrFile != null) {
- gui.getExperiment().loadChromosome(chrFile);
+ gui.getExperiment().loadChromosome(chrFile, 0);
gui.reDraw();
}
}
@@ -339,7 +339,14 @@ public class SettingsPane extends AnchorPane {
saveChromosome.setOnAction(new EventHandler<ActionEvent>() {
@Override
public void handle(ActionEvent event) {
-
+ FileChooser fc = new FileChooser();
+ fc.setTitle("Save .chr file...");
+ fc.getExtensionFilters().add(new ExtensionFilter("CGP chromosome files", "*.chr"));
+ fc.getExtensionFilters().add(new ExtensionFilter("All files", "*.*"));
+ File chrFile = fc.showSaveDialog(gui.getStage());
+ if (chrFile != null) {
+ gui.getExperiment().saveChromosome(chrFile, 0);
+ }
}
});
diff --git a/src/jcgp/gui/settings/parameters/GUIDoubleParameter.java b/src/jcgp/gui/settings/parameters/GUIDoubleParameter.java
index 9a6ec4a..5331364 100644
--- a/src/jcgp/gui/settings/parameters/GUIDoubleParameter.java
+++ b/src/jcgp/gui/settings/parameters/GUIDoubleParameter.java
@@ -100,7 +100,6 @@ public class GUIDoubleParameter extends GUIParameter<Number> {
@Override
public void refreshValue() {
- System.out.println("setting text to: " + parameter.get().doubleValue());
textField.setText(decimalFormat.format(parameter.get().doubleValue()));
}
}
diff --git a/src/jcgp/gui/settings/parameters/GUIParameter.java b/src/jcgp/gui/settings/parameters/GUIParameter.java
index 7dd7231..c6ac2e6 100644
--- a/src/jcgp/gui/settings/parameters/GUIParameter.java
+++ b/src/jcgp/gui/settings/parameters/GUIParameter.java
@@ -85,7 +85,6 @@ public abstract class GUIParameter<T> extends HBox {
// the tooltip is the hover-over label containing status information, when appropriate
tooltip = new Tooltip();
- tooltip.setStyle("-fx-background-color: white; -fx-border-color: black;");
tooltip.setSkin(null);
valueControl = makeControl();
--
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