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a few cosmetics

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This commit is contained in:
Marcel Kronfeld 2008-01-15 13:14:19 +00:00
parent 6ecc695886
commit e3f2768a29
7 changed files with 127 additions and 46 deletions
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2
src/javaeva/server/go/individuals/GAIndividualIntegerData.java
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@ -196,6 +196,7 @@ public class GAIndividualIntegerData extends AbstractEAIndividual implements Int
*/
public void SetIntegerDataLamarkian(int[] doubleData) {
this.SetIntegerData(doubleData);
if (doubleData != null) {
int[] locus = new int[2];
locus[0] = 0;
locus[1] = 0;
@ -205,6 +206,7 @@ public class GAIndividualIntegerData extends AbstractEAIndividual implements Int
this.m_IntegerCoding.codeValue(doubleData[i], this.m_Range[i], this.m_Genotype, locus);
}
}
}
/************************************************************************************
* AbstractEAIndividual methods

19
src/javaeva/server/go/operators/mutation/MutateESGlobal.java
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@ -25,11 +25,12 @@ public class MutateESGlobal implements InterfaceMutation, java.io.Serializable {
protected SelectedTag m_CrossoverType;
public MutateESGlobal() {
Tag[] tag = new Tag[3];
tag[0] = new Tag(0, "None");
tag[1] = new Tag(1, "Intermediate");
tag[2] = new Tag(2, "Discrete");
this.m_CrossoverType = new SelectedTag(0, tag);
initTags();
}
public MutateESGlobal(double mutationStepSize) {
initTags();
setMutationStepSize(mutationStepSize);
}
public MutateESGlobal(MutateESGlobal mutator) {
@ -39,6 +40,14 @@ public class MutateESGlobal implements InterfaceMutation, java.io.Serializable {
this.m_CrossoverType = (SelectedTag)mutator.m_CrossoverType.clone();
}
protected void initTags() {
Tag[] tag = new Tag[3];
tag[0] = new Tag(0, "None");
tag[1] = new Tag(1, "Intermediate");
tag[2] = new Tag(2, "Discrete");
this.m_CrossoverType = new SelectedTag(0, tag);
}
/** This method will enable you to clone a given mutation operator
* @return The clone
*/

48
src/javaeva/server/go/problems/FM0Problem.java
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@ -21,8 +21,7 @@ public class FM0Problem extends F1Problem implements Interface2DBorderProblem, I
protected InterfaceDistanceMetric m_Metric = new PhenotypeMetricDoubleData();
protected double m_GlobalOpt = 0;
protected Population m_Optima;
protected double m_XEpsilon = 0.05;
protected double m_YEpsilon = 0.05;
protected double m_Epsilon = 0.05;
protected boolean m_UseXCrit = true;
protected boolean m_UseYCrit = true;
protected double[][] m_Range;
@ -64,12 +63,9 @@ public class FM0Problem extends F1Problem implements Interface2DBorderProblem, I
this.m_UseTestConstraint = b.m_UseTestConstraint;
//FM0Problem
this.m_GlobalOpt = b.m_GlobalOpt;
this.m_XEpsilon = b.m_XEpsilon;
this.m_YEpsilon = b.m_YEpsilon;
this.m_Epsilon = b.m_Epsilon;
this.m_UseXCrit = b.m_UseXCrit;
this.m_UseYCrit = b.m_UseYCrit;
this.m_XEpsilon = b.m_XEpsilon;
this.m_YEpsilon = b.m_YEpsilon;
this.m_UseXCrit = b.m_UseXCrit;
if (b.m_Metric != null)
this.m_Metric = (InterfaceDistanceMetric)((InterfaceDistanceMetric)b.m_Metric).clone();
@ -187,15 +183,21 @@ public class FM0Problem extends F1Problem implements Interface2DBorderProblem, I
* @param y
*/
protected void add2DOptimum(double x, double y) {
InterfaceDataTypeDouble tmpIndy;
double[] point;
tmpIndy = (InterfaceDataTypeDouble)((AbstractEAIndividual)this.m_Template).clone();
point = new double[2];
double[] point = new double[2];
point[0] = x;
point[1] = y;
addOptimum(point);
}
/** This method allows you to add a 2d optima to the list of optima
* @param x
* @param y
*/
protected void addOptimum(double[] point) {
InterfaceDataTypeDouble tmpIndy;
tmpIndy = (InterfaceDataTypeDouble)((AbstractEAIndividual)this.m_Template).clone();
tmpIndy.SetDoubleDataLamarkian(point);
((AbstractEAIndividual)tmpIndy).SetFitness(0, this.doEvaluationUnNormalized(point)[0]);
((AbstractEAIndividual)tmpIndy).SetFitness(this.doEvaluationUnNormalized(point));
this.m_GlobalOpt = Math.max(this.m_GlobalOpt, ((AbstractEAIndividual)tmpIndy).getFitness(0));
this.m_Optima.add(tmpIndy);
}
@ -244,7 +246,7 @@ public class FM0Problem extends F1Problem implements Interface2DBorderProblem, I
for (int j = 0; j < this.m_Optima.size(); j++) {
opt = (AbstractEAIndividual) this.m_Optima.get(j);
if (!found[j]) {
if (this.m_Metric.distance(posOpt, opt) < this.m_XEpsilon) found[j] = true;
if (this.m_Metric.distance(posOpt, opt) < this.m_Epsilon) found[j] = true;
}
}
}
@ -271,7 +273,7 @@ public class FM0Problem extends F1Problem implements Interface2DBorderProblem, I
for (int j = 0; j < this.m_Optima.size(); j++) {
if (!found[j]) {
opt = (AbstractEAIndividual) this.m_Optima.get(j);
if (this.m_Metric.distance(posOpt, opt) < this.m_XEpsilon) {
if (this.m_Metric.distance(posOpt, opt) < this.m_Epsilon) {
found[j] = true;
result += this.m_GlobalOpt - posOpt.getFitness(0);
//System.out.println("Found Optimum " + j + ".: " + (this.m_GlobalOpt - posOpt.getFitness(0)));
@ -324,4 +326,22 @@ public class FM0Problem extends F1Problem implements Interface2DBorderProblem, I
range[1] = 5;
return range;
}
/**
* @return the m_Epsilon
*/
public double getEpsilon() {
return m_Epsilon;
}
/**
* @param epsilon the m_Epsilon to set
*/
public void setEpsilon(double epsilon) {
m_Epsilon = epsilon;
}
public String epsilonTipText() {
return "Epsilon criterion indicating whether an optimum was found";
}
}

65
src/javaeva/server/go/strategies/ClusterBasedNichingEA.java
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@ -58,9 +58,10 @@ public class ClusterBasedNichingEA implements InterfacePopulationChangedEventLis
private int m_PopulationSize = 50;
private boolean m_Debug = true;
private int m_ShowCycle = 2;
private TopoPlot m_Topology;
private int m_ShowCycle = 10;
transient private TopoPlot m_Topology;
private int haltingWindow = 15;
private double muLambdaRatio = 0.5;
public ClusterBasedNichingEA() {
@ -284,6 +285,23 @@ public class ClusterBasedNichingEA implements InterfacePopulationChangedEventLis
return true;
}
private Population optimizeSpecies(Population species) {
m_Optimizer.setPopulation(species);
if (m_Optimizer instanceof EvolutionStrategies) {
EvolutionStrategies es = (EvolutionStrategies)m_Optimizer;
int mu = (int)(muLambdaRatio*species.size());
if (mu < 1) mu = 1;
else if (mu >= species.size()) {
if (m_Debug) System.err.println("warning, muLambdaRatio produced mu >= lambda.. reducing to mu=lambda-1");
mu = species.size() - 1;
}
es.setMyu(mu);
es.setLambda(species.size());
}
this.m_Optimizer.optimize();
return m_Optimizer.getPopulation();
}
public void optimize() {
// plot the populations
if (this.m_ShowCycle > 0) {
@ -304,9 +322,7 @@ public class ClusterBasedNichingEA implements InterfacePopulationChangedEventLis
this.m_Undifferentiated.setPopulationSize(this.m_Undifferentiated.size());
if (isActive(m_Undifferentiated)) {
this.capMutationRate(this.m_Undifferentiated, 0); // MK TODO this sets mutation rate to 0! why?
this.m_Optimizer.setPopulation(this.m_Undifferentiated);
this.m_Optimizer.optimize();
this.m_Undifferentiated = this.m_Optimizer.getPopulation();
m_Undifferentiated = optimizeSpecies(m_Undifferentiated);
} else {
this.m_Undifferentiated.incrGeneration();
}
@ -352,13 +368,15 @@ public class ClusterBasedNichingEA implements InterfacePopulationChangedEventLis
} else {
// actually optimize D_i
this.capMutationRate(curSpecies, 0.05);
this.m_Optimizer.setPopulation(curSpecies);
this.m_Optimizer.optimize();
this.m_Species.set(i, this.m_Optimizer.getPopulation());
//this.m_Optimizer.setPopulation(curSpecies);
//this.m_Optimizer.optimize();
//this.m_Species.set(i, this.m_Optimizer.getPopulation());
this.m_Species.set(i, optimizeSpecies(curSpecies));
curSpecies = ((Population)this.m_Species.get(i)); // reset to expected population, just to be sure
}
} else {
// a single individual species, this element is inactive
if (m_Debug) System.out.println("inactive species not optimized");
}
// This is necessary to keep track to the function calls needed
this.m_Undifferentiated.SetFunctionCalls(this.m_Undifferentiated.getFunctionCalls() + curSpecies.getFunctionCalls());
@ -492,9 +510,8 @@ public class ClusterBasedNichingEA implements InterfacePopulationChangedEventLis
}
// output the result
if (this.m_Debug) System.out.println("-Number of species: " + this.m_Species.size());
this.m_Population = new Population();
m_Population.setUseHistory(true);
this.m_Population = (Population)this.m_Undifferentiated.clone();
m_Population.setUseHistory(true);
if (this.m_Debug) System.out.println("initing with " + this.m_Undifferentiated.size());
for (int i = 0; i < this.m_Species.size(); i++) {
if (this.m_Debug) System.out.println("Adding deme " + i + " with size " + ((Population)this.m_Species.get(i)).size());
@ -596,7 +613,8 @@ public class ClusterBasedNichingEA implements InterfacePopulationChangedEventLis
* @return The population of current solutions to a given problem.
*/
public Population getPopulation() {
this.m_Population = (Population)this.m_Undifferentiated.clone();
this.m_Population = (Population)m_Undifferentiated.clone();
// m_Population.addPopulation(this.m_Undifferentiated);
for (int i = 0; i < this.m_Species.size(); i++) this.m_Population.addPopulation((Population)this.m_Species.get(i));
return this.m_Population;
}
@ -669,12 +687,16 @@ public class ClusterBasedNichingEA implements InterfacePopulationChangedEventLis
}
public void setOptimizer(InterfaceOptimizer b){
this.m_Optimizer = b;
if (b instanceof EvolutionStrategies) {
EvolutionStrategies es = (EvolutionStrategies)b;
setMuLambdaRatio(es.getMyu()/(double)es.getLambda());
}
}
public String optimizerTipText() {
return "Choose a population based optimizing technique to use.";
}
/** The cluster algorithm on which the species differentation is based
/** The cluster algorithm on which the species differentiation is based
* @return The current clustering method
*/
public InterfaceClustering getDifferentationCA() {
@ -737,4 +759,23 @@ public class ClusterBasedNichingEA implements InterfacePopulationChangedEventLis
public String populationSizeTipText() {
return "Determines the size of the initial population.";
}
// /**
// * @return the muLambdaRatio
// */
// public double getMuLambdaRatio() {
// return muLambdaRatio;
// }
/**
* This is now set if an ES is set as optimizer.
* @param muLambdaRatio the muLambdaRatio to set
*/
public void setMuLambdaRatio(double muLambdaRatio) {
this.muLambdaRatio = muLambdaRatio;
}
// public String muLambdaRatioTipText() {
// return "ratio between mu and lambda for a CBN-ES";
// }
}

2
src/javaeva/server/go/strategies/HillClimbing.java
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@ -83,7 +83,7 @@ public class HillClimbing implements InterfaceOptimizer, java.io.Serializable {
if (((AbstractEAIndividual)original.get(i)).isDominatingDebConstraints(((AbstractEAIndividual)this.m_Population.get(i)))) {
this.m_Population.remove(i);
this.m_Population.add(i, original.get(i));
}
} // else: mutation improved the individual
}
this.m_Population.incrGeneration();
// for (int i = 0; i < this.m_Population.size(); i++) {

7
src/javaeva/server/modules/Processor.java
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@ -16,6 +16,7 @@ import javaeva.server.go.PopulationInterface;
import javaeva.server.go.individuals.AbstractEAIndividual;
import javaeva.server.go.operators.terminators.EvaluationTerminator;
import javaeva.server.go.populations.Population;
import javaeva.server.go.problems.InterfaceMultimodalProblem;
import javaeva.server.go.strategies.InterfaceOptimizer;
import javaeva.server.go.tools.RandomNumberGenerator;
import javaeva.server.stat.Statistics;
@ -208,7 +209,11 @@ public class Processor extends Thread implements InterfaceProcessor, InterfacePo
// m_Statistics.createNextGenerationPerformed((PopulationInterface)this.m_ModulParameter.getOptimizer().getPopulation());
// m_ListenerModule.updateProgress(getStatusPercent(m_ModulParameter.getOptimizer().getPopulation(), runCounter, m_Statistics.getStatisticsParameter().getMultiRuns()));
// } // end of while (m_doOpt==true)
if (m_ModulParameter.getProblem() instanceof InterfaceMultimodalProblem) {
// TODO improve this?
InterfaceMultimodalProblem mmProb = (InterfaceMultimodalProblem)m_ModulParameter.getProblem();
System.out.println("no optima found: " + mmProb.getNumberOfFoundOptima(m_ModulParameter.getOptimizer().getPopulation()));
}
m_Statistics.stopOptPerformed(isOptRunning()); // stop is "normal" if opt wasnt set false by the user
}
setOptRunning(false); // normal finish

14
src/javaeva/tools/ReflectPackage.java
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@ -16,7 +16,7 @@ import java.util.jar.JarInputStream;
/**
* Allow for java to list Classes that exist in one package and can be instantiated from
* the classpath, either directly or through a jar on the classpath.
* So far, jars which are located <i>whithin</i> another jar will not be searched.
* So far, jars which are located <i>within</i> another jar will not be searched.
*
* @author mkron
*
@ -44,26 +44,30 @@ public class ReflectPackage {
try {
// Get a File object for the package
File directory = null;
String dir = null;
try {
ClassLoader cld = ClassLoader.getSystemClassLoader();
if (cld == null) {
throw new ClassNotFoundException("Can't get class loader.");
}
String dir = path + "/" + pckgname.replace(".","/");
dir = path + "/" + pckgname.replace(".","/");
if (TRACE) System.out.println(path);
if (TRACE) System.out.println(".. opening " + path);
directory = new File(dir);
} catch (NullPointerException x) {
if (TRACE) System.err.println(directory.getPath()+ " not found in " + path);
if (TRACE) {
System.err.println(directory.getPath()+ " not found in " + path);
System.err.println("directory " + (directory.exists() ? "exists" : "doesnt exist"));
}
return set;
}
if (directory.exists()) {
// Get the list of the files contained in the package
getClassesFromDirFltr(set, directory, pckgname, includeSubs, reqSuperCls);
} else {
if (TRACE) System.err.println(directory.getPath()+ " not found in " + path);
if (TRACE) System.err.println(directory.getPath() + " doesnt exist in " + path + ", dir was " + dir);
}
} catch(ClassNotFoundException e) {
System.err.println(e.getMessage());