Tuning of the Serializer - should load faster now.

src/eva2/gui/GOEPanel.java

@@ -75,7 +75,13 @@ public class GOEPanel extends JPanel implements ItemListener {
 		m_goe  = goe;
 		
 		//System.out.println("GOEPanel.Constructor !!");
+		try {
 		if (!(Proxy.isProxyClass(m_Object.getClass()))) m_Backup = copyObject(m_Object);
+		} catch(OutOfMemoryError err) {
+			m_Backup=null;
+			System.gc();
+			System.err.println("Could not create backup object: not enough memory (GOEPanel backup of " + m_Object + ")");
+		}
 		m_ObjectNames = new DefaultComboBoxModel(new String [0]);
 		m_ObjectChooser = new JComboBox(m_ObjectNames);
 		m_ObjectChooser.setEditable(false);
@@ -211,6 +217,7 @@ public class GOEPanel extends JPanel implements ItemListener {
 	protected Object copyObject(Object source) {
 		Object result = null;
 		try {
+//			System.out.println("Copying " + BeanInspector.toString(source));
 			SerializedObject so = new SerializedObject(source);
 			result = so.getObject();
 		} catch (Exception ex) {

src/eva2/gui/SerializedObject.java

@@ -12,8 +12,21 @@ package eva2.gui;
 /*==========================================================================*
  * IMPORTS
  *==========================================================================*/
-import java.io.*;
+import java.io.BufferedInputStream;
-import java.util.zip.*;
+import java.io.BufferedOutputStream;
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+import java.io.OutputStream;
+import java.io.Serializable;
+import java.util.zip.GZIPInputStream;
+import java.util.zip.GZIPOutputStream;
+
+import eva2.server.modules.GOParameters;
+import eva2.tools.Serializer;
 /**
  * This class stores an object serialized in memory. It allows compression,
  * to be used to conserve memory (for example, when storing large strings
@@ -29,9 +42,10 @@ public class SerializedObject implements Serializable {
    * Serializes the supplied object into a byte array without compression.
    *
    * @param obj the Object to serialize.
+ * @throws IOException 
    * @exception Exception if the object is not Serializable.
    */
-  public SerializedObject(Object obj) throws Exception {
+  public SerializedObject(Object obj) throws IOException {
     this(obj, false);
   }
   /**
@@ -39,9 +53,10 @@ public class SerializedObject implements Serializable {
    *
    * @param obj the Object to serialize.
    * @param compress true if the object should be stored compressed.
+ * @throws IOException 
    * @exception Exception if the object is not Serializable.
    */
-  public SerializedObject(Object obj, boolean compress) throws Exception {
+  public SerializedObject(Object obj, boolean compress) throws IOException {
     //System.err.print("."); System.err.flush();
     m_Compressed = compress;
     m_Serialized = toByteArray(obj, m_Compressed);
@@ -52,9 +67,10 @@ public class SerializedObject implements Serializable {
    * @param obj the Object to serialize
    * @param compress true if the object should be compressed.
    * @return the byte array containing the serialized object.
+   * @throws IOException 
    * @exception Exception if the object is not Serializable.
    */
-  protected static byte [] toByteArray(Object obj, boolean compress) throws Exception {
+  protected static byte [] toByteArray(Object obj, boolean compress) throws IOException {
     ByteArrayOutputStream bo = new ByteArrayOutputStream();
     OutputStream os = bo;
     if (compress)

src/eva2/server/go/operators/selection/SelectXProbRouletteWheel.java

@@ -59,7 +59,7 @@ class treeElement implements java.io.Serializable {
  */
 public class SelectXProbRouletteWheel implements InterfaceSelection, java.io.Serializable {
 
-    private treeElement[]                   m_TreeRoot;
+    private transient treeElement[]         m_TreeRoot = null;
     private InterfaceSelectionProbability   m_SelProbCalculator = new SelProbStandard();
     private boolean                         m_ObeyDebsConstViolationPrinciple = true;
 
@@ -86,8 +86,9 @@ public class SelectXProbRouletteWheel implements InterfaceSelection, java.io.Ser
         this.m_TreeRoot = this.buildSelectionTree(population);
     }
 
-    /** This method will select a pool of individuals from the given
+    /** 
-     * Population in respect to the selection propability of the
+     * This method will select a pool of individuals from the given
+     * Population in respect to the selection probability of the
      * individuals.
      * @param population    The source population where to select from
      * @param size          The number of Individuals to select
@@ -97,21 +98,15 @@ public class SelectXProbRouletteWheel implements InterfaceSelection, java.io.Ser
         Population result = new Population();
         result.setTargetSize(size);
 
-        if (true) {
+        for (int i = 0; i < size; i++) {
-            //this.m_TreeRoot = this.buildSelectionTree(population);
+        	result.add(this.selectTree(population));
-            for (int i = 0; i < size; i++) {
-                result.add(this.selectTree(population));
-            }
-        } else {
-            for (int i = 0; i < size; i++) {
-                result.add(this.selectStandard(population));
-            }
         }
 
         return result;
     }
 
-    /** This method will build a selection tree
+    /** 
+     * This method will build a selection tree.
      * @param p     The population
      */
     private treeElement[] buildSelectionTree(Population p) {
@@ -155,6 +150,7 @@ public class SelectXProbRouletteWheel implements InterfaceSelection, java.io.Ser
     }
 
     private AbstractEAIndividual selectStandard(Population population) {
+    	// old version
         double                  sum = 1, random, tmpD;
         int                     currentCriteria = 0, critSize;
 

src/eva2/server/go/populations/Population.java

@@ -1677,8 +1677,8 @@ public class Population extends ArrayList implements PopulationInterface, Clonea
 			return new double[]{1.,1.,1.,1.};
 		}
 		if (!(pop.getEAIndividual(0) instanceof InterfaceDataTypeDouble)) {
-			EVAERROR.errorMsgOnce("Warning: population correlations can only be calculated for double valued data!");
+			// EVAERROR.errorMsgOnce("Warning: population correlations can only be calculated for double valued data!");
-			return new double[]{1.,1.,1.,1.};
+			return new double[]{Double.NaN,Double.NaN,Double.NaN,Double.NaN};
 		}
 		int index=0;
 		double corsSum=0, minCor = 10., maxCor=-10.;

src/eva2/server/go/strategies/GeneticAlgorithm.java

@@ -68,6 +68,7 @@ public class GeneticAlgorithm implements InterfaceOptimizer, java.io.Serializabl
         public void initByPopulation(Population pop, boolean reset) {
             this.m_Population = (Population)pop.clone();
             if (reset) {
+            	this.m_Problem.initPopulation(m_Population);
             	this.m_Population.init();
                 this.evaluatePopulation(this.m_Population);
                 this.firePropertyChangedEvent(Population.nextGenerationPerformed);

src/eva2/server/modules/GOParameters.java

@@ -3,7 +3,6 @@ package eva2.server.modules;
 import java.io.Serializable;
 
 import eva2.server.go.InterfaceGOParameters;
-import eva2.server.go.individuals.GAIndividualDoubleData;
 import eva2.server.go.operators.terminators.EvaluationTerminator;
 import eva2.server.go.problems.F1Problem;
 import eva2.server.go.strategies.GeneticAlgorithm;

src/eva2/tools/Serializer.java

@@ -21,9 +21,11 @@ import java.io.IOException;
 import java.io.InvalidClassException;
 import java.io.ObjectInputStream;
 import java.io.ObjectOutputStream;
-import java.io.PipedInputStream;
-import java.io.PipedOutputStream;
 import java.io.Serializable;
+
+import eva2.gui.SerializedObject;
+import eva2.server.go.problems.PSymbolicRegression;
+import eva2.server.modules.GOParameters;
 /*==========================================================================*
  * CLASS DECLARATION
  *==========================================================================*/
@@ -33,13 +35,23 @@ import java.io.Serializable;
 public class Serializer {
   /**
   * Serialize the object o (and any Serializable objects it refers to) and
-  * store its serialized state in File f.
+  * store its serialized state in File f. If serializeInMem is true, the object
+  * is wrapped in a SerializedObject first, which seems to be more efficient than
+  * writing a nested object directly to a file.
+  * 
+  * @param o the object to write
+  * @param f the file to write to
+  * @param serializeInMem flag whether to wrap the object in a SerializedObject
+  * @throws IOException
   **/
-  static public void store(Serializable o, File f) throws IOException {
+  static public void store(Serializable o, File f, boolean serializeInMem) throws IOException {
     FileOutputStream file = new FileOutputStream(f);
     ObjectOutputStream out = new ObjectOutputStream(file);
     try {
-    	out.writeObject(o);
+    	Object objToStore = o;
+    	if (serializeInMem) objToStore = new SerializedObject((Object)o);
+//    	System.out.println("Writing " + o.getClass());
+    	out.writeObject(objToStore);
     } catch (java.io.NotSerializableException e) {
     	System.err.println("Error: Object " + o.getClass() + " is not serializable - run settings cannot be stored.");
     	e.printStackTrace();
@@ -59,12 +71,14 @@ public class Serializer {
 //    }
 
   /**
-  * Deserialize the contents of File f and return the resulting object
+  * Deserialize the contents of File f and return the resulting object.
+  * A SerializedObject is unwrapped once.
   **/
   static public Object load(File f) throws IOException, ClassNotFoundException {
     FileInputStream file = new FileInputStream(f);
     ObjectInputStream in = new ObjectInputStream(file);
     Object ret = in.readObject();
+    if (ret instanceof SerializedObject) ret = ((SerializedObject)ret).getObject();
     in.close();
     file.close();
     return ret;
@@ -167,7 +181,7 @@ public class Serializer {
       // Output it to a file
       File f = new File("datastructure.ser");
       System.out.println("Storing to a file...");
-      Serializer.store(ds, f);
+      Serializer.store(ds, f, true);
       // Read it back from the file, and display it again
       ds = (DataStructure) Serializer.load(f);
       System.out.println("Read from the file: " + ds);
@@ -184,7 +198,7 @@ public class Serializer {
   **/
   public static void storeString (String Filename,String s) {
     try {
-      store(s, new File(Filename));
+      store(s, new File(Filename), false);
     } catch (Exception e) {
       System.out.println("ERROR writing string File "+Filename+ " String "+s);
     }
@@ -209,7 +223,7 @@ public class Serializer {
   public static File storeObject (String Filename,Serializable s) {
     File ret = new File(Filename);
     try {
-      store(s, ret);
+      store(s, ret, true);
     } catch (Exception e) {
       System.err.println("ERROR writing Object File "+Filename+ " String "+s);
       System.err.println(e.getMessage());