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Fix all errors in javadoc generation.

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This commit is contained in:
Fabian Becker
2015-12-20 17:35:17 +01:00
parent 65b1f7df74
commit f4dc718b33
69 changed files with 246 additions and 476 deletions
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15
src/main/java/eva2/OptimizerFactory.java
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@@ -47,11 +47,11 @@ import java.util.List;
* optimization procedures in EvA2. The arguments passed to the methods
* initialize the respective optimization procedure. To perform an optimization
* one has to do the following:
* <code>
* {@code
* InterfaceOptimizer optimizer = OptimizerFactory.createCertainOptimizer(arguments);
* EvaluationTerminator terminator = new EvaluationTerminator(numOfFitnessCalls);
* while (!terminator.isTerminated(optimizer.getPopulation())) optimizer.optimize();
* </code>
* }
*/
public class OptimizerFactory {
@@ -323,7 +323,7 @@ public class OptimizerFactory {
* This method creates a Hill Climber algorithm with a default fixed-size
* mutation.
*
* @param pop The size of the population
* @param popSize The size of the population
* @param problem The problem to be optimized
* @param listener
* @return An optimization procedure that performs hill climbing.
@@ -715,8 +715,8 @@ public class OptimizerFactory {
* Use default random seed and the population size of the optimizer.
*
* @param opt
* @param popSize
* @param problem
* @param term
* @return
* @see #makeParams(InterfaceOptimizer, int, AbstractOptimizationProblem,
* long, InterfaceTerminator)
@@ -1117,7 +1117,7 @@ public class OptimizerFactory {
/**
* Add a new InterfaceTerminator to the current user-defined optimizer in a
* boolean combination. The old and the given terminator will be combined as
* in (TOld && TNew) if bAnd is true, and as in (TOld || TNew) if bAnd is
* in (TOld &amp;&amp; TNew) if bAnd is true, and as in (TOld || TNew) if bAnd is
* false. If there was no user-defined terminator (or it was set to null)
* the new one is used without conjunction.
*
@@ -1327,7 +1327,6 @@ public class OptimizerFactory {
* @param evalCycle
* @param popSize
* @param minImprovement
* @param method
* @param sigmaClust
* @return
*/
@@ -1500,7 +1499,7 @@ public class OptimizerFactory {
* A standard niching ES which employs predefined values and standard ES
* variation operators.
*
* @param problem
* @param prob
* @return
*/
public static OptimizationParameters standardNichingEs(AbstractOptimizationProblem prob) {
@@ -1513,7 +1512,7 @@ public class OptimizerFactory {
/**
* A niching ES.
*
* @param problem
* @param prob
* @return
*/
public static OptimizationParameters createNichingEs(AbstractOptimizationProblem prob, double nicheRadius, int muPerPeak, int lambdaPerPeak, int expectedPeaks, int rndImmigrants, int explorerPeaks, int resetExplInterval, int etaPresel) {

2
src/main/java/eva2/gui/SplashScreen.java
View File

@@ -32,7 +32,7 @@ class SplashScreen extends JWindow {
* Once this method returns, the splash screen is realized, which means
* that almost all work on the splash screen should proceed through the
* event dispatch thread. In particular, any call to
* <code>dispose</code> for the splash screen must be performed in the event
* {@code dispose} for the splash screen must be performed in the event
* dispatch thread.
*/
public void splash() {

10
src/main/java/eva2/gui/SwingWorker.java
View File

@@ -59,23 +59,23 @@ public abstract class SwingWorker {
}
/**
* Compute the value to be returned by the <code>get</code> method.
* Compute the value to be returned by the {@code get} method.
*/
public abstract Object construct();
/**
* Called on the event dispatching thread (not on the worker thread)
* after the <code>construct</code> method has returned.
* after the {@code construct} method has returned.
*/
public void finished() {
}
/**
* Return the value created by the <code>construct</code> method.
* Return the value created by the {@code construct} method.
* Returns null if either the constructing thread or the current
* thread was interrupted before a value was produced.
*
* @return the value created by the <code>construct</code> method
* @return the value created by the {@code construct} method
*/
public Object get() {
while (true) {
@@ -93,7 +93,7 @@ public abstract class SwingWorker {
}
/**
* Start a thread that will call the <code>construct</code> method
* Start a thread that will call the {@code construct} method
* and then exit.
*/
public SwingWorker() {

8
src/main/java/eva2/gui/plot/DPointSetMultiIcon.java
View File

@@ -150,9 +150,9 @@ public class DPointSetMultiIcon extends DComponent {
}
/**
* method returns the nearest <code>DPoint</code> in this <code>DPointSet</code>.
* method returns the nearest {@code DPoint} in this {@code DPointSet}.
*
* @return the nearest <code>DPoint</code>
* @return the nearest {@code DPoint}
*/
public DPoint getNearestDPoint(DPoint point) {
int minIndex = getNearestDPointIndex(point);
@@ -169,9 +169,9 @@ public class DPointSetMultiIcon extends DComponent {
}
/**
* method returns the index to the nearest <code>DPoint</code> in this <code>DPointSet</code>.
* method returns the index to the nearest {@code DPoint} in this {@code DPointSet}.
*
* @return the index to the nearest <code>DPoint</code>. -1 if no nearest <code>DPoint</code> was found.
* @return the index to the nearest {@code DPoint}. -1 if no nearest {@code DPoint} was found.
*/
public int getNearestDPointIndex(DPoint point) {
double minValue = Double.MAX_VALUE;

2
src/main/java/eva2/optimization/individuals/AbstractEAIndividual.java
View File

@@ -497,8 +497,6 @@ public abstract class AbstractEAIndividual implements IndividualInterface, java.
/**
* Allows marking an individual as infeasible if fitness penalty is used.
*
* @return
*/
public void setMarkPenalized(boolean p) {
isPenalized = p;

4
src/main/java/eva2/optimization/individuals/EAIndividualComparator.java
View File

@@ -49,7 +49,7 @@ public class EAIndividualComparator implements Comparator<Object>, Serializable
/**
* Constructor for a specific fitness criterion in the multi-objective case.
* For comparison, only the given fitness criterion is used if it is >= 0.
* For comparison, only the given fitness criterion is used if it is &gt;= 0.
*
* @param fitnessCriterion
*/
@@ -59,7 +59,7 @@ public class EAIndividualComparator implements Comparator<Object>, Serializable
/**
* Constructor for a specific fitness criterion in the multi-objective case.
* For comparison, only the given fitness criterion is used if it is >= 0.
* For comparison, only the given fitness criterion is used if it is &gt;= 0.
* If preferFeasible is true, feasible individuals will always be prefered.
*
* @param fitIndex

7
src/main/java/eva2/optimization/individuals/GAESIndividualBinaryDoubleData.java
View File

@@ -274,7 +274,6 @@ public class GAESIndividualBinaryDoubleData extends AbstractEAIndividual impleme
* This method allows you to set the double data.
*
* @param doubleData The new double data.
* @see InterfaceDataTypeDouble.SetDoubleData()
*/
@Override
public void setDoublePhenotype(double[] doubleData) {
@@ -286,7 +285,6 @@ public class GAESIndividualBinaryDoubleData extends AbstractEAIndividual impleme
* memetic algorithms.
*
* @param doubleData The new double data.
* @see InterfaceDataTypeDouble.SetDoubleDataLamarckian()
*/
@Override
public void setDoubleGenotype(double[] doubleData) {
@@ -341,7 +339,6 @@ public class GAESIndividualBinaryDoubleData extends AbstractEAIndividual impleme
* This method allows you to set the binary data.
*
* @param binaryData The new binary data.
* @see InterfaceDataTypeBinary.SetBinaryData()
*/
@Override
public void setBinaryPhenotype(BitSet binaryData) {
@@ -353,16 +350,12 @@ public class GAESIndividualBinaryDoubleData extends AbstractEAIndividual impleme
* memetic algorithms.
*
* @param binaryData The new binary data.
* @see InterfaceBinaryData.setBinaryDataLamarckian()
*/
@Override
public void setBinaryGenotype(BitSet binaryData) {
this.binaryIndividual.setBinaryGenotype(binaryData);
}
/**********************************************************************************************************************
* These are for GUI
*/
/**
* This method allows the CommonJavaObjectEditorPanel to read the
* name to the current object.

2
src/main/java/eva2/optimization/operator/cluster/ClusteringDynPeakIdent.java
View File

@@ -169,7 +169,7 @@ public class ClusteringDynPeakIdent implements InterfaceClustering, java.io.Seri
* which are not dominated by other individuals within distance rho.
* Note that the returned set may be smaller than q.
*
* @param pop
* @param metric Distance Metric
* @param q the number of peaks to be identified
* @param rho the niche radius
* @return the dynamic peak set

2
src/main/java/eva2/optimization/operator/crossover/CrossoverESUNDX.java
View File

@@ -17,7 +17,7 @@ import java.util.ArrayList;
/**
* This is the Unimodal Normal Distribution Crossover by Ono and Kobayashi, 1997. Cf.:
*
* @INPROCEEDINGS{Ono1997, author = {Ono, Isao and Kobayashi, Shigenobu},
* INPROCEEDINGS{Ono1997, author = {Ono, Isao and Kobayashi, Shigenobu},
* title = {{A Real Coded Genetic Algorithm for Function Optimization Using Unimodal Normal Distributed Crossover}},
* booktitle = {ICGA},
* year = {1997},

2
src/main/java/eva2/optimization/operator/initialization/GAGIInitializeSegmentwise.java
View File

@@ -21,7 +21,7 @@ import java.util.BitSet;
* elements to a certain type and all to a subset of the range).
* <p>
* The initialization may be parameterized in two ways, where each takes a fixed
* segment length s. Firstly, a fixed number of bits (k<=s) is set per segment,
* segment length s. Firstly, a fixed number of bits (k&lt;=s) is set per segment,
* so each segment has equal cardinality.
* Secondly, an int-array can be specified which defines possibly varying k_i for
* each segment i, so different segments may have different cardinality. The array

2
src/main/java/eva2/optimization/operator/mutation/MutateESPathLengthAdaption.java
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@@ -12,7 +12,7 @@ import eva2.util.annotation.Description;
* ES mutation with path length control. The step size (single sigma) is
* adapted using the evolution path length by adapting the real path length
* to the expected path length in for uncorrelated single steps.
* See Hansen&Ostermeier 2001, Eqs. 16,17.
* See Hansen&amp;Ostermeier 2001, Eqs. 16,17.
*/
@Description("The single step size is controlled using the evolution path.")
public class MutateESPathLengthAdaption implements InterfaceMutation, java.io.Serializable {

18
src/main/java/eva2/optimization/operator/mutation/MutateESRankMuCMA.java
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@@ -21,9 +21,9 @@ import java.io.Serializable;
/**
* Implementing CMA ES with rank-mu-update and weighted recombination. More information can be found here:
* - http://www.bionik.tu-berlin.de/user/niko/cmaesintro.html
* - N.Hansen & S.Kern 2004: Evaluating the CMA Evolution Strategy on Multimodal Test Functions.
* - N.Hansen &amp; S.Kern 2004: Evaluating the CMA Evolution Strategy on Multimodal Test Functions.
* Parallel Problem Solving from Nature 2004.
* - For the stopping criteria: Auger&Hansen, CEC '05, A Restart CMA ES with increasing population size.
* - For the stopping criteria: Auger&amp;Hansen, CEC '05, A Restart CMA ES with increasing population size.
* <p>
* The implementation uses a structure for keeping all adaptive parameters, CMAParamSet, which is stored
* in the populations, so that in principle, multi-modal optimization with several populations becomes possible.
@@ -105,7 +105,7 @@ public class MutateESRankMuCMA implements InterfaceAdaptOperatorGenerational, In
* Perform the main adaption of sigma and C using evolution paths.
* The evolution path is deduced from the center of the selected population compared to the old
* mean value.
* See Hansen&Kern 04 for further information.
* See Hansen&amp;Kern 04 for further information.
*
* @param oldGen
* @param selectedP
@@ -702,7 +702,7 @@ public class MutateESRankMuCMA implements InterfaceAdaptOperatorGenerational, In
}
/**
* From Auger&Hansen, CEC '05, stopping criterion TolX.
* From Auger&amp;Hansen, CEC '05, stopping criterion TolX.
*
* @param tolX
* @return
@@ -720,7 +720,7 @@ public class MutateESRankMuCMA implements InterfaceAdaptOperatorGenerational, In
}
/**
* From Auger&Hansen, CEC '05, stopping criterion noeffectaxis.
* From Auger&amp;Hansen, CEC '05, stopping criterion noeffectaxis.
*
* @param d
* @param gen
@@ -743,7 +743,7 @@ public class MutateESRankMuCMA implements InterfaceAdaptOperatorGenerational, In
}
/**
* From Auger&Hansen, CEC '05, stopping criterion noeffectcoord.
* From Auger&amp;Hansen, CEC '05, stopping criterion noeffectcoord.
*
* @param d
* @return
@@ -760,11 +760,11 @@ public class MutateESRankMuCMA implements InterfaceAdaptOperatorGenerational, In
}
/**
* Test condition of C (Auger&Hansen, CEC '05, stopping criterion conditioncov).
* Return true, if a diagonal entry is <= 0 or >= d.
* Test condition of C (Auger&amp;Hansen, CEC '05, stopping criterion conditioncov).
* Return true, if a diagonal entry is &lt;= 0 or &gt;= d.
*
* @param d
* @return true, if a diagonal entry is <= 0 or >= d, else false
* @return true, if a diagonal entry is &lt;= 0 or &gt;= d, else false
*/
public boolean testCCondition(Population pop, double d) {
CMAParamSet params = (CMAParamSet) pop.getData(cmaParamsKey);

9
src/main/java/eva2/optimization/operator/mutation/MutateGAGISwapBits.java
View File

@@ -161,12 +161,12 @@ public class MutateGAGISwapBits implements InterfaceMutation, java.io.Serializab
/**
* Select a random index within the given genotype lying in [iMin,iMax]. If applicable, the given
* value is avoided with certain probility, namely by trying to find a different value for maxTries
* value is avoided with certain probality, namely by trying to find a different value for maxTries
* times.
*
* @param maxTries
* @param genotype
* @param maybePreferedValue
* @param avoidValue
* @param iMin
* @param iMax
* @return
@@ -182,11 +182,6 @@ public class MutateGAGISwapBits implements InterfaceMutation, java.io.Serializab
return k;
}
// private int getRandomSecondIndex(int firstIndex, AbstractEAIndividual individual) {
// int genoLen = ((InterfaceGAIndividual)individual).getGenotypeLength();
// return RNG.randomInt(0, genoLen);
// }
protected Object valueAt(Object genotype, int k) {
if (genotype instanceof BitSet) {
return ((BitSet) genotype).get(k);

2
src/main/java/eva2/optimization/operator/mutation/MutateGASwapBitsSegmentwise.java
View File

@@ -14,7 +14,7 @@ import java.util.BitSet;
/**
* Swap two random bits of a GA individual within subsequences (segments) of fixed length.
* If preferPairs is true, unequal pairs
* are picked with some preference (by trying for >= s/2 times, where s is the binary
* are picked with some preference (by trying for &gt;= s/2 times, where s is the binary
* segment length).
* Multiple mutations per segment can occur if the boolean switch is activated, meaning
* that further mutations are performed recursively with p_mut. Thus, the probability

6
src/main/java/eva2/optimization/operator/mutation/MutateOBGAInversion.java
View File

@@ -15,7 +15,7 @@ import eva2.util.annotation.Description;
* <br><br>
* <b>Example: </b>
* <pre>
* 1 2 | 3 4 5 | 6 7 8 9 ->
* 1 2 | 3 4 5 | 6 7 8 9 -&gt;
* 1 2 | 5 4 3 | 6 7 8 9
* </pre>
*/
@@ -30,8 +30,10 @@ public class MutateOBGAInversion implements java.io.Serializable, InterfaceMutat
return this;
}
/** This method allows you to evaluate wether two mutation operators
/**
* This method allows you to evaluate whether two mutation operators
* are actually the same.
*
* @param mutator The other mutation operator
*/
@Override

16
src/main/java/eva2/optimization/operator/nichepso/absorption/EuclideanDiversityAbsorptionStrategy.java
View File

@@ -35,15 +35,11 @@ public class EuclideanDiversityAbsorptionStrategy extends StandardAbsorptionStra
epsilon = eps;
}
/**********************************************************************************************************************
* shouldAbsorbParticleIntoSubswarm
*/
/**
* @tested true if
* the subswarm is active and
* the particle lies in the radius of the subswarm and
* the diversity (mean distance from the gbest) of the subswarm < epsilon
* (non-Javadoc) @see javaeva.server.oa.go.Operators.NichePSO.StandardAbsorptionStrategy#shouldAbsorbParticleIntoSubswarm(javaeva.server.oa.go.EAIndividuals.AbstractEAIndividual, javaeva.server.oa.go.Strategies.ParticleSubSwarmOptimization)
* true if
* the sub-swarm is active and
* the particle lies in the radius of the sub-swarm and
* the diversity (mean distance from the gbest) of the sub-swarm &lt; epsilon
*/
@Override
public boolean shouldAbsorbParticleIntoSubswarm(AbstractEAIndividual indy, ParticleSubSwarmOptimization subswarm, ParticleSubSwarmOptimization mainswarm) {
@@ -58,10 +54,6 @@ public class EuclideanDiversityAbsorptionStrategy extends StandardAbsorptionStra
return meanDistanceFromGBestPos < getEpsilon();
}
/**
* *******************************************************************************************************************
* setter, getter
*/
public void setEpsilon(double epsilon) {
this.epsilon = epsilon;
}

10
src/main/java/eva2/optimization/operator/nichepso/absorption/InterfaceAbsorptionStrategy.java
View File

@@ -9,12 +9,11 @@ import eva2.optimization.strategies.ParticleSubSwarmOptimization;
public interface InterfaceAbsorptionStrategy {
/**
* @param indy
* @param indy Individual
* @param subswarm the swarm indy will be absorbed from
* @param mainswarm the swarm indy currently belongs to
* (population statistics from that swarm may be used to decide whether indy should be absorbed)
* @return
* @tested decides whether indy should be absorbed into the subswarm according to the absorption strategie
* @return Decides whether indy should be absorbed into the sub-swarm according to the absorption strategy
*/
boolean shouldAbsorbParticleIntoSubswarm(
AbstractEAIndividual indy,
@@ -22,10 +21,11 @@ public interface InterfaceAbsorptionStrategy {
ParticleSubSwarmOptimization mainswarm);
/**
* @param indy
* Absorbs indy according to the absorption strategy
*
* @param indy Individual
* @param subswarm the swarm indy will be absorbed from
* @param mainswarm the swarm indy currently belongs to
* @tested absorbs indy according to the absorbtion strategy
*/
void absorbParticle(
AbstractEAIndividual indy,

14
src/main/java/eva2/optimization/operator/nichepso/absorption/StandardAbsorptionStrategy.java
View File

@@ -22,10 +22,9 @@ public class StandardAbsorptionStrategy implements InterfaceAbsorptionStrategy,
}
/**
* @tested true if
* tested true if
* the subswarm is active and
* the particle lies in the radius of the subswarm
* (non-Javadoc) @see javaeva.server.oa.go.Operators.NichePSO.InterfaceAbsorptionStrategy#shouldAbsorbParticleIntoSubswarm(javaeva.server.oa.go.EAIndividuals.AbstractEAIndividual, javaeva.server.oa.go.Strategies.ParticleSubSwarmOptimization)
*/
@Override
public boolean shouldAbsorbParticleIntoSubswarm(AbstractEAIndividual indy, ParticleSubSwarmOptimization subswarm, ParticleSubSwarmOptimization mainswarm) {
@@ -43,20 +42,13 @@ public class StandardAbsorptionStrategy implements InterfaceAbsorptionStrategy,
return dist <= R;
}
/**********************************************************************************************************************
* absorbParticle
*/
/**
* @tested junit
* adds indy to an active subswarm, then removes indy from the mainswarm.
* (non-Javadoc) @see javaeva.server.oa.go.Operators.NichePSO.InterfaceAbsorptionStrategy#absorbParticle(javaeva.server.oa.go.EAIndividuals.AbstractEAIndividual, javaeva.server.oa.go.Strategies.ParticleSubSwarmOptimization, javaeva.server.oa.go.Strategies.ParticleSubSwarmOptimization)
* Adds indy to an active sub-swarm, then removes indy from the main-swarm.
*/
@Override
public void absorbParticle(AbstractEAIndividual indy, ParticleSubSwarmOptimization subswarm, ParticleSubSwarmOptimization mainswarm) {
if (!subswarm.isActive()) {
System.out.println("absorbParticle: trying to absorb a particle into an inactive subswarm.");
System.out.println("absorbParticle: trying to absorb a particle into an inactive sub-swarm.");
return;
}
subswarm.add(indy);

17
src/main/java/eva2/optimization/operator/nichepso/deactivation/ImprovementDeactivationStrategy.java
View File

@@ -83,9 +83,8 @@ public class ImprovementDeactivationStrategy implements InterfaceDeactivationStr
}
/**
* @tested true if the subswarm is active and all particles are completely converged
* (i.e. the stddev over the past 3 iterations is < epsilson)
* (non-Javadoc) @see javaeva.server.oa.go.Operators.NichePSO.InterfaceDeactivationStrategy#shouldDeactivateSubswarm(javaeva.server.oa.go.Strategies.ParticleSubSwarmOptimization)
* True if the subswarm is active and all particles are completely converged
* (i.e. the stddev over the past 3 iterations is &lt; epsilson)
*/
@Override
public boolean shouldDeactivateSubswarm(ParticleSubSwarmOptimization subswarm) {
@@ -98,14 +97,9 @@ public class ImprovementDeactivationStrategy implements InterfaceDeactivationStr
return (isConverged(subswarm.getPopulation()));
}
/**********************************************************************************************************************
* deactivateSubswarm
*/
/**
* @tested the subswarm is deactivated and the particles indices are returned. They are
* The subswarm is deactivated and the particles indices are returned. They are
* to be reinitialized into the mainswarm.
* (non-Javadoc) @see javaeva.server.oa.go.Operators.NichePSO.InterfaceDeactivationStrategy#deactivateSubswarm(javaeva.server.oa.go.Strategies.ParticleSubSwarmOptimization, javaeva.server.oa.go.Strategies.ParticleSubSwarmOptimization)
*/
@Override
public int[] deactivateSubswarm(ParticleSubSwarmOptimization subswarm, ParticleSubSwarmOptimization mainswarm) {
@@ -126,11 +120,6 @@ public class ImprovementDeactivationStrategy implements InterfaceDeactivationStr
return particleIndices;
}
/**
* *******************************************************************************************************************
* getter, setter
*/
public void setEpsilon(double epsilon) {
this.epsilon = epsilon;
}

10
src/main/java/eva2/optimization/operator/nichepso/deactivation/InterfaceDeactivationStrategy.java
View File

@@ -8,18 +8,20 @@ import eva2.optimization.strategies.ParticleSubSwarmOptimization;
public interface InterfaceDeactivationStrategy {
/**
* Decides whether a subswarm should be deactivated according to the deactivation strategy
*
* @param subswarm
* @return
* @tested decides whether a subswarm should be deacitvated according to the deactivation strategy
*/
boolean shouldDeactivateSubswarm(ParticleSubSwarmOptimization subswarm);
/**
* Deactivates a given subswarm.
* What happens to the particles in this subswarm depends on the concrete strategy.
*
* @param subswarm
* @param mainswarm
* @tested deactivates a given subswarm.
* What happens to the particles in this subswarm depends on the concrete strategy.
* Return the list of indices to be reinitialized or null.
* @return the list of indices to be reinitialized or null.
*/
int[] deactivateSubswarm(ParticleSubSwarmOptimization subswarm, ParticleSubSwarmOptimization mainswarm);

21
src/main/java/eva2/optimization/operator/nichepso/deactivation/StandardDeactivationStrategy.java
View File

@@ -21,10 +21,6 @@ public class StandardDeactivationStrategy implements InterfaceDeactivationStrate
private double epsilon = 0.0001;
private int stdDevHorizon = 3;
/**
* *******************************************************************************************************************
* ctors
*/
public StandardDeactivationStrategy() {
}
@@ -51,7 +47,6 @@ public class StandardDeactivationStrategy implements InterfaceDeactivationStrate
/**
* @param pop
* @return
* @tested
*/
public boolean areAllConverged(Population pop) {
for (int i = 0; i < pop.size(); ++i) {
@@ -72,9 +67,8 @@ public class StandardDeactivationStrategy implements InterfaceDeactivationStrate
}
/**
* @tested true if the subswarm is active and all particles are completely converged
* (i.e. the stddev over the past 3 iterations is < epsilson)
* (non-Javadoc) @see javaeva.server.oa.go.Operators.NichePSO.InterfaceDeactivationStrategy#shouldDeactivateSubswarm(javaeva.server.oa.go.Strategies.ParticleSubSwarmOptimization)
* True if the subswarm is active and all particles are completely converged
* (i.e. the stddev over the past 3 iterations is &lt; epsilson)
*/
@Override
public boolean shouldDeactivateSubswarm(ParticleSubSwarmOptimization subswarm) {
@@ -87,14 +81,10 @@ public class StandardDeactivationStrategy implements InterfaceDeactivationStrate
return (areAllConverged(subswarm.getPopulation()));
}
/**********************************************************************************************************************
* deactivateSubswarm
*/
/**
* @tested the subswarm is deactivated and the particles indices are returned. They are
* The subswarm is deactivated and the particles indices are returned. They are
* to be reinitialized into the mainswarm.
* (non-Javadoc) @see javaeva.server.oa.go.Operators.NichePSO.InterfaceDeactivationStrategy#deactivateSubswarm(javaeva.server.oa.go.Strategies.ParticleSubSwarmOptimization, javaeva.server.oa.go.Strategies.ParticleSubSwarmOptimization)
*/
@Override
public int[] deactivateSubswarm(ParticleSubSwarmOptimization subswarm, ParticleSubSwarmOptimization mainswarm) {
@@ -115,11 +105,6 @@ public class StandardDeactivationStrategy implements InterfaceDeactivationStrate
return particleIndices;
}
/**
* *******************************************************************************************************************
* getter, setter
*/
public void setEpsilon(double epsilon) {
this.epsilon = epsilon;
}

2
src/main/java/eva2/optimization/operator/nichepso/merging/ScatterMergingStrategy.java
View File

@@ -31,7 +31,7 @@ public class ScatterMergingStrategy extends StandardMergingStrategy {
/**
* @param i
* @param j
* @tested if both active: reinitializes subswarm j back into the main swarm and deletes it from the subswarms.
* if both active: reinitializes subswarm j back into the main swarm and deletes it from the subswarms.
* if both inactive: adds population of subswarm j to population of subswarm i, then deletes subswarm j.
*/
@Override

4
src/main/java/eva2/optimization/operator/nichepso/merging/StandardMergingStrategy.java
View File

@@ -41,8 +41,7 @@ public class StandardMergingStrategy implements InterfaceMergingStrategy, java.i
}
/**
* @tested the subswarms are merged, if they overlap (or are very close) and if they are of equal state
* (non-Javadoc) @see javaeva.server.oa.go.Operators.NichePSO.InterfaceMergingStrategie#shouldMergeSubswarms(javaeva.server.oa.go.Strategies.ParticleSubSwarmOptimization, javaeva.server.oa.go.Strategies.ParticleSubSwarmOptimization)
* the subswarms are merged, if they overlap (or are very close) and if they are of equal state
*/
@Override
public boolean shouldMergeSubswarms(ParticleSubSwarmOptimization subswarm1, ParticleSubSwarmOptimization subswarm2) {
@@ -108,7 +107,6 @@ public class StandardMergingStrategy implements InterfaceMergingStrategy, java.i
/**
* @param i
* @param j
* @tested junit
* adds population of subswarm j to population of subswarm i, then deletes subswarm j.
*/
@Override

2
src/main/java/eva2/optimization/operator/nichepso/subswarmcreation/GenerateNeighborSubswarmCreationStrategy.java
View File

@@ -20,7 +20,7 @@ public class GenerateNeighborSubswarmCreationStrategy extends
private double mu = 0.1;
/**
* @tested creates a subswarm from the given particle and its neighbor in the mainswarm.
* Creates a subswarm from the given particle and its neighbor in the mainswarm.
* If the neighbors pbest is better than the particles pbest, a new neighbor is generated.
*/
@Override

11
src/main/java/eva2/optimization/operator/nichepso/subswarmcreation/InterfaceSubswarmCreationStrategy.java
View File

@@ -9,22 +9,25 @@ import eva2.optimization.strategies.ParticleSubSwarmOptimization;
public interface InterfaceSubswarmCreationStrategy {
/**
* Decides whether a subswarm should be created for the given indy and mainswarm according to the creation strategy
*
* @param indy
* @param mainswarm
* @return
* @tested decides whether a subswarm should be created for the given indy and mainswarm according to the creation strategie
*/
boolean shouldCreateSubswarm(
AbstractEAIndividual indy,
ParticleSubSwarmOptimization mainswarm);
/**
* @param preparedSubswarm a subswarm which is appropriatly prepared
* Creates a subswarm from indy, the details depend on the concrete strategy.
*
* @param preparedSubswarm a subswarm which is appropriately prepared
* (ie its problem, optimization strategy etc. are set correctly from the "meta-optimizer")
* Afterwards the subswarm containes the generated particles
* Afterwards the subswarm contains the generated particles
* @param indy a particle from which a subswarm should be created
* @param mainSwarm the main swarm which contains indy
* @tested creates a subswarm from indy, the details depend on the concrete strategy.
* Creates a subswarm from indy, the details depend on the concrete strategy.
*/
void createSubswarm(
ParticleSubSwarmOptimization preparedSubswarm,

15
src/main/java/eva2/optimization/operator/nichepso/subswarmcreation/StandardSubswarmCreationStrategy.java
View File

@@ -36,9 +36,7 @@ public class StandardSubswarmCreationStrategy implements InterfaceSubswarmCreati
/**
* @param indy main swarm particle
* @return
* @tested junit
* true if the stddev of the particles fitness < delta and no constraints are violated
* @return true if the stddev of the particles fitness &lt; delta and no constraints are violated
*/
@Override
public boolean shouldCreateSubswarm(AbstractEAIndividual indy, ParticleSubSwarmOptimization mainswarm) {
@@ -54,9 +52,8 @@ public class StandardSubswarmCreationStrategy implements InterfaceSubswarmCreati
/**
* @param indy main swarm particle
* @return
* @tested junit
* true, if reasons exist why no subswarm should be created from indy.
* @return true, if reasons exist why no subswarm should be created from indy.
*
* Reasons like:
* poor fitness (not implemented),
* convergence on plateau (not implemented),
@@ -74,14 +71,10 @@ public class StandardSubswarmCreationStrategy implements InterfaceSubswarmCreati
return result;
}
/**********************************************************************************************************************
* createSubswarm
*/
/**
* @tested creates a subswarm from the given particle and its neighbor in the mainswarm,
* Creates a subswarm from the given particle and its neighbor in the mainswarm,
* then deletes the two particles from the mainswarm.
* (non-Javadoc) @see javaeva.server.oa.go.Operators.NichePSO.InterfaceSubswarmCreationStrategy#createSubswarm(javaeva.server.oa.go.Strategies.ParticleSubSwarmOptimization, javaeva.server.oa.go.EAIndividuals.AbstractEAIndividual, javaeva.server.oa.go.Strategies.ParticleSubSwarmOptimization)
*/
@Override
public void createSubswarm(ParticleSubSwarmOptimization preparedSubswarm, AbstractEAIndividual indy, ParticleSubSwarmOptimization mainSwarm) {

27
src/main/java/eva2/optimization/operator/postprocess/PostProcess.java
View File

@@ -156,8 +156,8 @@ public class PostProcess {
* or a random subset of the cluster or the best and a random subset. Returns shallow copies!
* returnQuota should be in [0,1] and defines, which percentage of individuals of each cluster is kept, however
* at least one is kept per cluster.
* lonerMode defines whether loners are discarded, kept, or treated as clusters, meaning they are kept if returnQuota > 0.
* takeOverMode defines whether, of a cluster with size > 1, which n individuals are kept. Either the n best only,
* lonerMode defines whether loners are discarded, kept, or treated as clusters, meaning they are kept if returnQuota &gt; 0.
* takeOverMode defines whether, of a cluster with size &gt; 1, which n individuals are kept. Either the n best only,
* or the single best and random n-1, or all n random.
*
* @param pop
@@ -238,9 +238,9 @@ public class PostProcess {
* Filter the individuals of a population which have a fitness norm below a given value.
* Returns shallow copies!
*
* @param pop
* @param fitNorm
* @param bSmaller if true, return individuals with lower or equal, else with higher fitness norm only
* @param pop Population
* @param fitNorm The fitness threshold
* @param bSmallerEq if true, return individuals with lower or equal, else with higher fitness norm only
* @return
*/
public static Population filterFitnessNormed(Population pop, double fitNorm, boolean bSmallerEq) {
@@ -436,7 +436,7 @@ public class PostProcess {
* Returns the number of function calls really performed by the method and a flag indicating whether the
* processing was aborted by the user. Sets the number of function calls
* in the population back to the original count.
* If the baseEvals parameter (which should be >= 0) is > 0, then the number of evaluations is set as
* If the baseEvals parameter (which should be &gt;= 0) is &gt; 0, then the number of evaluations is set as
* number of evaluations before the optimization using the given terminator.
*
* @param pop
@@ -471,7 +471,7 @@ public class PostProcess {
* meaning that typically only one best is returned.
* Returns the number of function calls really performed by the method and a flag indicating whether the
* processing was aborted by the user. Sets the number of function calls
* in the population back to the original count. If the baseEvals parameter (which should be >= 0) is > 0,
* in the population back to the original count. If the baseEvals parameter (which should be &gt;= 0) is &gt; 0,
* then the number of evaluations is set as
* number of evaluations before the optimization using the given terminator.
*
@@ -525,7 +525,7 @@ public class PostProcess {
* @param initPerturbation
* @param prob
* @return
* @see NelderMeadSimplex#createNMSPopulation(candidate, perturbRatio, range, includeCand)
* @see NelderMeadSimplex#createNMSPopulation
*/
public static Pair<AbstractEAIndividual, Integer> localSolverNMS(AbstractEAIndividual cand, int hcSteps,
double initPerturbation, AbstractOptimizationProblem prob) {
@@ -548,7 +548,7 @@ public class PostProcess {
* @param index index of the individual for which to produce the sub population
* @param maxRelativePerturbation
* @param includeCand
* @see #createPopInSubRange(double, AbstractOptimizationProblem, AbstractEAIndividual)
* @see #createPopInSubRange
* @see NelderMeadSimplex#createNMSPopulation(AbstractEAIndividual, double, double[][], boolean)
*/
public static Population createLSSupPopulation(PostProcessMethod method, AbstractOptimizationProblem problem, Population candidates, int index, double maxRelativePerturbation, boolean includeCand) {
@@ -763,7 +763,6 @@ public class PostProcess {
*
* @param searchBoxLen
* @param indy
* @return
*/
public static void createPopInSubRange(Population destPop, double searchBoxLen,
int targetSize, AbstractEAIndividual indy) {
@@ -1133,8 +1132,8 @@ public class PostProcess {
* @param treatAsUnknown
* @param listener
* @return
* @see {@link AbstractOptimizationProblem#extractPotentialOptima}
* @see AbstractOptimizationProblem#isPotentialOptimumNMS(AbstractEAIndividual, double, double, int)
* @see AbstractOptimizationProblem#extractPotentialOptima
* @see AbstractOptimizationProblem#isPotentialOptimumNMS
*/
public static int[] checkAccuracy(AbstractOptimizationProblem prob, Population sols, double[] epsilonPhenoSpace,
double extrOptEpsFitConf, double extrOptClustSig, int maxEvals, SolutionHistogram[] solHists, boolean treatAsUnknown,
@@ -1225,7 +1224,7 @@ public class PostProcess {
/**
* Select a local search range for a given method based on the clustering parameter.
* If clustering was deactivated (sigma <= 0), then the default mutation step size is used.
* If clustering was deactivated (sigma &lt;= 0), then the default mutation step size is used.
* The specific search method may interpret the search range differently.
*
* @param method
@@ -1254,7 +1253,7 @@ public class PostProcess {
/**
* Select a perturbation for individual i fitting to the population - avoiding overlap.
* In this case, return the third of the minimum distance to the next neighbor in the population.
* The maxPerturb can be given as upper bound of the perturbation if it is > 0.
* The maxPerturb can be given as upper bound of the perturbation if it is &gt; 0.
*
* @param candidates population of solutions to look at
* @param i index of the individual in the population to look at

1
src/main/java/eva2/optimization/operator/postprocess/SolutionHistogram.java
View File

@@ -168,7 +168,6 @@ public class SolutionHistogram {
* @param upperBound upper bound of the fitness interval
* @param nBins number of bins
* @return an integer array with the number of individuals in each bin
* @see filterFitnessIn()
*/
public static SolutionHistogram createFitNormHistogram(Population pop, double lowerBound, double upperBound, int nBins, int crit) {
SolutionHistogram res = new SolutionHistogram(lowerBound, upperBound, nBins);

4
src/main/java/eva2/optimization/operator/selection/InterfaceSelection.java
View File

@@ -34,7 +34,7 @@ public interface InterfaceSelection {
void prepareSelection(Population population);
/**
* This method will select >size< individuals from the given
* This method will select *size* individuals from the given
* Population.
*
* @param population The source population where to select from
@@ -44,7 +44,7 @@ public interface InterfaceSelection {
Population selectFrom(Population population, int size);
/**
* This method allows you to select >size< partners for a given Individual
* This method allows you to select *size* partners for a given Individual
*
* @param dad The already seleceted parent
* @param availablePartners The mating pool.

4
src/main/java/eva2/optimization/operator/selection/SelectBestSingle.java
View File

@@ -48,7 +48,7 @@ public class SelectBestSingle implements InterfaceSelection, java.io.Serializabl
}
/**
* This method will select >size< individuals from the given
* This method will select *size* individuals from the given
* Population.
*
* @param population The source population where to select from
@@ -107,7 +107,7 @@ public class SelectBestSingle implements InterfaceSelection, java.io.Serializabl
}
/**
* This method allows you to select >size< partners for a given Individual
* This method allows you to select *size* partners for a given Individual
*
* @param dad The already selected parent
* @param availablePartners The mating pool.

4
src/main/java/eva2/optimization/operator/selection/SelectParticleWheel.java
View File

@@ -20,7 +20,7 @@ public class SelectParticleWheel implements InterfaceSelection, java.io.Serializ
private boolean obeyDebsConstViolationPrinciple = true;
/**
* Comment for <code>serialVersionUID</code>
* Comment for {@code serialVersionUID}
*/
private static final long serialVersionUID = 1L;
private InterfaceSelectionProbability selProbCalculator = new SelProbStandard();
@@ -55,7 +55,7 @@ public class SelectParticleWheel implements InterfaceSelection, java.io.Serializ
/**
* This method will select individuals from the given Population with respect to their
* selection propability. This implements a fixed segment roulette wheel selection which ensures
* that every individual which has a selection probability p >= (k/size) is selected k or k+1 times.
* that every individual which has a selection probability p &gt;= (k/size) is selected k or k+1 times.
*
* @param population The source population where to select from
* @param size The number of Individuals to select

2
src/main/java/eva2/optimization/operator/selection/probability/SelProbFitnessSharing.java
View File

@@ -38,7 +38,7 @@ public class SelProbFitnessSharing extends AbstractSelProb implements java.io.Se
* This method computes the selection probability for each individual
* in the population. Note: Summed over the complete population the selection
* probability sums up to one. Keep in mind that fitness is always to be
* minimizied! Small values for data => big values for selectionprob.
* minimizied! Small values for data =&gt; big values for selectionprob.
*
* @param population The population to compute.
* @param data The input data as double[][].

2
src/main/java/eva2/optimization/operator/selection/probability/SelProbStandard.java
View File

@@ -26,7 +26,7 @@ public class SelProbStandard extends AbstractSelProb implements java.io.Serializ
* This method computes the selection probability for each individual
* in the population. Note: Summed over the complete population the selection
* probability sums up to one. Keep in mind that fitness is always to be
* minimizied! Small values for data => big values for selectionprob.
* minimizied! Small values for data =&gt; big values for selectionprob.
*
* @param population The population to compute.
* @param data The input data as double[][].

23
src/main/java/eva2/optimization/population/Population.java
View File

@@ -100,7 +100,7 @@ public class Population extends ArrayList<AbstractEAIndividual> implements Popul
public static final String NEXT_GENERATION_PERFORMED = "NextGenerationPerformed";
/**
* With <code>autoAging = true</code> #incrGeneration automatically
* With {@code autoAging = true} #incrGeneration automatically
* ages individuals.
*/
private boolean autoAging = true;
@@ -485,8 +485,6 @@ public class Population extends ArrayList<AbstractEAIndividual> implements Popul
/**
* Create a population instance which distributes the individuals according
* to a random latin hypercube sampling.
*
* @return
*/
public static void createRLHSampling(Population pop, boolean fillPop) {
if (pop.size() <= 0) {
@@ -523,7 +521,6 @@ public class Population extends ArrayList<AbstractEAIndividual> implements Popul
* @param cardinality an integer giving the number of (random) bits to set
* @param stdDev standard deviation of the cardinality variation (can be
* zero to fix the cardinality)
* @return
*/
public static void createBinCardinality(Population pop, boolean fillPop, int cardinality, int stdDev) {
if (pop.size() <= 0) {
@@ -630,7 +627,7 @@ public class Population extends ArrayList<AbstractEAIndividual> implements Popul
/**
* This method will allow you to increment the current number of function
* calls by a number > 1. Notice that it might slightly disturb notification
* calls by a number &gt; 1. Notice that it might slightly disturb notification
* if a notifyEvalInterval is set.
*
* @param d The number of function calls to increment by.
@@ -991,7 +988,7 @@ public class Population extends ArrayList<AbstractEAIndividual> implements Popul
/**
* This method will return the index of the current best individual from the
* population in the given fitness component (or using dominance when
* fitIndex < 0). If the population is empty, -1 is returned.
* fitIndex &lt; 0). If the population is empty, -1 is returned.
*
* @return The index of the best individual.
* @see #getIndexOfBestOrWorstIndividual(boolean, java.util.Comparator)
@@ -1006,7 +1003,7 @@ public class Population extends ArrayList<AbstractEAIndividual> implements Popul
/**
* This method will return the index of the current best individual from the
* population in the given fitness component (or using dominance when
* fitIndex < 0).
* fitIndex &lt; 0).
*
* @return The index of the best individual.
* @see #getIndexOfBestOrWorstIndividual(boolean, java.util.Comparator)
@@ -1163,12 +1160,12 @@ public class Population extends ArrayList<AbstractEAIndividual> implements Popul
* This method returns the n current best individuals from the population,
* where the sorting criterion is delivered by an
* AbstractEAIndividualComparator. There are less than n individuals
* returned if the population is smaller than n. If n is <= 0, then all
* returned if the population is smaller than n. If n is &lt;= 0, then all
* individuals are returned and effectively just sorted by fitness. This
* does not check constraints!
*
* @param n number of individuals to look out for
* @return The m best individuals, where m <= n
* @return The m best individuals, where m &lt;= n
*/
public Population getBestNIndividuals(int n, int fitIndex) {
if (n <= 0 || (n > super.size())) {
@@ -1183,12 +1180,12 @@ public class Population extends ArrayList<AbstractEAIndividual> implements Popul
* This method returns the n current worst individuals from the population,
* where the sorting criterion is delivered by an
* AbstractEAIndividualComparator. There are less than n individuals
* returned if the population is smaller than n. If n is <= 0, then all
* returned if the population is smaller than n. If n is &lt;= 0, then all
* individuals are returned and effectively just sorted by fitness. This
* does not check constraints!
*
* @param n number of individuals to look out for
* @return The m worst individuals, where m <= n
* @return The m worst individuals, where m &lt;= n
*/
public Population getWorstNIndividuals(int n, int fitIndex) {
Population pop = new Population(n);
@@ -1222,7 +1219,7 @@ public class Population extends ArrayList<AbstractEAIndividual> implements Popul
* individuals
* @param res sorted result population, will be cleared
* @param comp the Comparator to use with individuals
* @return The m sorted best or worst individuals, where m <= n
* @param res The m sorted best or worst individuals, where m &lt;= n (will be added to res)
*/
public void getSortedNIndividuals(int n, boolean bBestOrWorst, Population res, Comparator<Object> comp) {
if ((n < 0) || (n > super.size())) {
@@ -2082,7 +2079,7 @@ public class Population extends ArrayList<AbstractEAIndividual> implements Popul
* @param indy
* @param d
* @param metric
* @return true if d(indy,pop)<=d, else false
* @return true if d(indy,pop)&lt;=d, else false
*/
public boolean isWithinPopDist(AbstractEAIndividual indy, double d, InterfaceDistanceMetric metric) {
Pair<Integer, Double> closest = Population.getClosestFarthestIndy(indy, this, metric, true);

1
src/main/java/eva2/optimization/strategies/ClusterBasedNichingEA.java
View File

@@ -1184,7 +1184,6 @@ public class ClusterBasedNichingEA extends AbstractOptimizer implements Interfac
* the upper limit if the clustering parameter is controlled.
*
* @param prob
* @param q
*/
public void setUpperBoundClustDiff(InterfaceProblemDouble prob) {
if (caForSpeciesDifferentation instanceof ClusteringDensityBased) {

6
src/main/java/eva2/optimization/strategies/EsDpiNiching.java
View File

@@ -33,7 +33,7 @@ import java.util.Formatter;
* predefined, and lambda new samples are drawn for every peak in every
* iteration. Thus, in relation to the standard ES, some new parameters are due.
* On the other hand, the selection schemes are predefined. This is done
* according to Shir&Bäck, Niching in Evolution Strategies, Tec.Report 2005.
* according to Shir&amp;Bäck, Niching in Evolution Strategies, Tec.Report 2005.
* <p>
* Unfortunately the algorithm was not described in every detail. It remained
* unclear how exactly the peak population where filled and esp. what happens if
@@ -54,7 +54,7 @@ import java.util.Formatter;
* framework which is still used to optimize the single peak populations.
* <p>
* This class should also cover "Dynamic niching in evolution strategies with
* covariance matrix adaptation" by Shir & Bäck, CEC 2005, when employing
* covariance matrix adaptation" by Shir &amp; Bäck, CEC 2005, when employing
* SelectBest as parent selection and muPerPeak=1.
* <p>
* Some notes:
@@ -267,7 +267,7 @@ public class EsDpiNiching extends AbstractOptimizer implements Serializable, Int
/**
* Use the deactivation of converged species, storing them to an archive,
* with the given parameters. If windowLen <= 0, the deactivation mechanism
* with the given parameters. If windowLen &lt;= 0, the deactivation mechanism
* is disabled. This provides for semi-sequential niching with DPI-ES
*
* @param threshold

2
src/main/java/eva2/optimization/strategies/EvolutionStrategies.java
View File

@@ -259,7 +259,7 @@ public class EvolutionStrategies extends AbstractOptimizer implements java.io.Se
}
/**
* This method will check the population constraints myu <= lambda and will
* This method will check the population constraints myu &lt;= lambda and will
* calculate the population size accordingly.
*/
protected void checkPopulationConstraints() {

7
src/main/java/eva2/optimization/strategies/EvolutionStrategyIPOP.java
View File

@@ -30,9 +30,9 @@ import java.util.LinkedList;
* Lambda is increased multiplicatively for every restart, and typical initial values are
* mu=5, lambda=10, incFact=2.
* The IPOP-CMA-ES won the CEC 2005 benchmark challenge.
* Refer to Auger&Hansen 05 for more details.
* Refer to Auger&amp;Hansen 05 for more details.
* <p>
* A.Auger & N.Hansen. A Restart CMA Evolution Strategy With Increasing Population Size. CEC 2005.
* A.Auger &amp; N.Hansen. A Restart CMA Evolution Strategy With Increasing Population Size. CEC 2005.
*/
@Description("An ES with increasing population size.")
public class EvolutionStrategyIPOP extends EvolutionStrategies implements InterfacePopulationChangedEventListener, InterfaceAdditionalPopulationInformer {
@@ -186,7 +186,8 @@ public class EvolutionStrategyIPOP extends EvolutionStrategies implements Interf
/**
* Test for the IPOP stopping criteria.
*
* @param population
* @param term
* @param pop
* @return
*/
public static boolean testIPOPStopCrit(InterfaceTerminator term, Population pop) {

3
src/main/java/eva2/optimization/strategies/IslandModelEA.java
View File

@@ -445,9 +445,8 @@ public class IslandModelEA implements InterfacePopulationChangedEventListener, I
* This method allows you to toggle between a truly parallel and a serial
* implementation.
*
* @return The current optimization mode
*/
// TODO Deactivated from GUI because the current implementation does not really parallelize on a multicore.
// TODO Deactivated from GUI because the current implementation does not really paralelize on a multicore.
// Instead, the new direct problem parallelization can be used.
// public boolean isLocalOnly() {
// return this.numLocalOnly;

136
src/main/java/eva2/optimization/strategies/NichePSO.java
View File

@@ -66,7 +66,7 @@ import java.util.Vector;
* subswarm can formally have, but it does not affect the actual radius. This
* adjustment is proposed in [2] in order to improve the performance of the
* NichePSO. Experiments showed a good performance for relatively small values
* of maxAllowedSwarmRadius <= 0.0001 on lower dimensional problems. For higher
* of maxAllowedSwarmRadius &lt;= 0.0001 on lower dimensional problems. For higher
* dimensional problems, larger values may be preferable.
* <p>
* [1] R. Brits, A. P. Engelbrecht and B. Bergh. A Niching Particle Swarm
@@ -147,13 +147,6 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
// by default, calculate the individuals fitness std dev using this number of past fitness values
public static final int defaultFitStdDevHorizon = 3;
/**
* ********************************************************************************************************************
* ctors, clone
*/
/**
* @tested
*/
public NichePSO() {
if (log) {
initLogFile();
@@ -177,9 +170,6 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
GenericObjectEditor.setHideProperty(getClass(), "maxAllowedSwarmRadius", false);
}
/**
* @tested @param a
*/
public NichePSO(NichePSO a) {
this.mainSwarmSize = a.mainSwarmSize;
this.maxAllowedSwarmRadius = a.maxAllowedSwarmRadius;
@@ -213,17 +203,13 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
this.optimizationProblem = (InterfaceOptimizationProblem) a.optimizationProblem.clone();
}
/**
* @tested (non-Javadoc)
* @see java.lang.Object#clone()
*/
@Override
public Object clone() {
return new NichePSO(this);
}
/**
* @tested ps sets the mainswarm according to the NichePSO Parameters,
* ps sets the mainswarm according to the NichePSO Parameters,
* called via initialize()
*/
protected void initMainSwarm() {
@@ -252,7 +238,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
}
/**
* @tested inits the template used for creating subswarms this is only
* inits the template used for creating subswarms this is only
* called in the ctor not via initialize() (would overwrite changes set from
* outside for the next run)
*/
@@ -279,7 +265,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
/**
* @return an optimizer with parameters set according to the nichePSO
* @tested returns the optimizer that should be used to create a new
* returns the optimizer that should be used to create a new
* subswarm
*/
public ParticleSubSwarmOptimization getNewSubSwarmOptimizer() {
@@ -290,7 +276,6 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
}
/**
* @tested junit, junit&, emp, ... (non-Javadoc)
* @see eva2.optimization.strategies.InterfaceOptimizer#initialize()
*/
@Override
@@ -319,7 +304,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
}
/**
* @tested (non-Javadoc) uses the given population and basically sets rnd
* uses the given population and basically sets rnd
* velocity vectors (if reset == false)
*/
@Override
@@ -335,11 +320,6 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
}
/**
* ********************************************************************************************************************
* Optimization
*/
/**
* @tested (non-Javadoc)
* @see eva2.optimization.strategies.InterfaceOptimizer#optimize()
*/
@Override
@@ -498,7 +478,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
}
/**
* @tested junit deactivates the subswarms according to the decativation
* deactivates the subswarms according to the decativation
* strategy
*/
protected void deactivateSubSwarmsIfPossible() {
@@ -546,10 +526,6 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
return actCnt;
}
/**
* ********************************************************************************************************************
* Merging
*/
protected void mergingEventFor(int i, int j) {
if (isVerbose()) {
System.out.print("merge condition \n");
@@ -564,7 +540,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
}
/**
* @tested junit merges the subswarms according to the merging strategy
* merges the subswarms according to the merging strategy
*/
protected void mergeSubswarmsIfPossible() {
boolean runagain = false;
@@ -608,7 +584,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
}
/**
* junit absorbs the mainswarm particles into the subswarm according
* absorbs the mainswarm particles into the subswarm according
* to the absorbtion strategy
*/
protected void absorbParticlesIfPossible() {
@@ -636,10 +612,6 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
}
}
/**
* ********************************************************************************************************************
* Subswarm Creation
*/
protected void subswarmCreationEventFor(AbstractEAIndividual currentindy, ParticleSubSwarmOptimization subswarm) {
if (isVerbose()) {
System.out.print("creating subswarm\n");
@@ -655,7 +627,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
}
/**
* @tested junit creates a subswarm from every particle in the mainswarm
* creates a subswarm from every particle in the mainswarm
* that meets the convergence-criteria of the creation strategy
*/
protected void createSubswarmIfPossible() {
@@ -679,13 +651,6 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
}
}
/**
* ********************************************************************************************************************
* setter, getter: population and solutions
*/
/**
* @tested nn (non-Javadoc)
*/
@Override
public void setPopulation(Population pop) {
//pass on to mainswarm optimizer
@@ -695,7 +660,6 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
/**
* @return a population consisting of copies from the mainswarm and all
* active subswarms
* @tested junit, junit&
*/
public Population getActivePopulation() {
// construct a metapop with clones from the mainswarm and all active subswarms
@@ -727,7 +691,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
/**
* @return a population consisting of copies from the mainswarm and all
* subswarms.
* @tested junit returns a population consisting of copies from the
* returns a population consisting of copies from the
* mainswarm and all subswarms (active and inactive, so the size of this
* Population is not necessarily constant). (Especially important for the
* call back regarding the output file... ) Beware:
@@ -788,7 +752,6 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
/**
* @return a population consisting of the personal best solutions of every
* particle in the mainswarm and all subswarms
* @tested junit (non-Javadoc)
* @see eva2.optimization.strategies.InterfaceOptimizer#getAllSolutions()
*/
@Override
@@ -819,7 +782,6 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
/**
* @return the best solution found by any particle in any swarm
* @tested junit
*/
public AbstractEAIndividual getGlobalBestSolution() {
Population metapop = getPopulation();
@@ -839,7 +801,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
/**
* @return array with copies of the gbest individuals
* @tested junit returns the cloned global best individuals (ie best of all
* returns the cloned global best individuals (ie best of all
* time) from every subswarm and the main swarm
*/
public Population getSubswarmRepresentatives(boolean onlyInactive) {
@@ -859,7 +821,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
/**
* @param size
* @tested ps sets the !initial! size of the mainswarm population use this
* ps sets the !initial! size of the mainswarm population use this
* instead of getPopulation.setPopulationSize()
*/
public void setMainSwarmSize(int size) {
@@ -871,7 +833,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
/**
* @return the !initial! size of the mainswarm population
* @tested nn returns the !initial! size of the mainswarm population
* returns the !initial! size of the mainswarm population
*/
public int getMainSwarmSize() {
return this.mainSwarmSize;
@@ -883,7 +845,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
/**
* @param val
* @tested ps defines the maximal allowed subswarm radius for absorption and
* defines the maximal allowed subswarm radius for absorption and
* merging
*/
public void setMaxAllowedSwarmRadius(double val) {
@@ -899,7 +861,6 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
/**
* @return
* @tested nn
*/
public double getMaxAllowedSwarmRadius() {
return this.maxAllowedSwarmRadius;
@@ -1002,7 +963,6 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
/**
* @param val
* @tested nn
*/
public void SetPartlyInactive(boolean val) {
this.partlyInactive = val;
@@ -1010,7 +970,6 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
/**
* @return
* @tested nn
*/
public boolean isPartlyInactive() {
return partlyInactive;
@@ -1186,7 +1145,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
}
/**
* @param problem
* @tested ps This method will set the problem that is to be optimized
* This method will set the problem that is to be optimized
*/
@Override
@Hidden
@@ -1221,7 +1180,6 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
/**
* @param vals
* @return
* @tested junit
*/
public double getMedian(double[] vals) {
java.util.Arrays.sort(vals);
@@ -1299,13 +1257,9 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
return meanDiv;
}
/**
* ********************************************************************************************************************
* setter, getter: infostrings
*/
/**
* @return The name of the algorithm
* @tested nn This method will return a naming String
* This method will return a naming String
*/
@Override
public String getName() {
@@ -1314,7 +1268,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
/**
* @return A descriptive string
* @tested nn This method will return a string describing all properties of
* This method will return a string describing all properties of
* the optimizer and the applied methods.
*/
@Override
@@ -1327,7 +1281,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
/**
* @return descriptive string of the elite
* @tested emp returns a string that lists the global best individuals (ie
* emp returns a string that lists the global best individuals (ie
* best of all time) from every subswarm
*/
public String getSubswarmRepresentativesAsString(boolean onlyInactive) {
@@ -1342,7 +1296,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
/**
* @return
* @tested emp
* emp
*/
public String getPerformanceAsString() {
if (!(optimizationProblem instanceof InterfaceMultimodalProblem)) {
@@ -1390,7 +1344,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
* for the logfile
*/
/**
* @tested emp generates the NichePSO_date file
* emp generates the NichePSO_date file
*/
protected void initLogFile() {
// opening output file...
@@ -1426,7 +1380,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
/**
* @param line string to be written
* @tested emp writes something to the LogFile
* emp writes something to the LogFile
*/
protected void writeToLogFile(String line) {
String write = line + "\n";
@@ -1441,16 +1395,10 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
}
}
/**
* ************************************************- plotting analysing
* debugging -************************************
* /**********************************************************************************************************************
* getter for debugging and analysing
*/
/**
* @param index
* @return particle with given index
* @tested @param pop
* @param pop
*/
public AbstractEAIndividual getIndyByParticleIndexAndPopulation(Population pop, Integer index) {
for (int i = 0; i < pop.size(); ++i) {
@@ -1466,7 +1414,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
/**
* @return main swarm particle with given index
* @tested @param index
* @param index
*/
public AbstractEAIndividual getIndyByParticleIndex(Integer index) {
AbstractEAIndividual indy = null;
@@ -1486,7 +1434,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
}
/**
* @tested @return particle with minimal stddev in fitness over the last 3
* @return particle with minimal stddev in fitness over the last 3
* iterations
*/
protected AbstractEAIndividual getIndyWithMinStdDev() {
@@ -1510,11 +1458,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
}
/**
* ********************************************************************************************************************
* plotting
*/
/**
* @tested inits a new Topoplot
* Inits a new Topoplot
*/
protected void initPlotSwarm() {
double[] a = new double[2];
@@ -1528,7 +1472,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
}
/**
* @tested clean everything except topology colors
* Clean everything except topology colors
*/
protected void cleanPlotSwarm() {
// delete all previous points
@@ -1544,7 +1488,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
}
/**
* @tested plots the std dev of all particles in the main swarm
* Plots the std dev of all particles in the main swarm
*/
protected void plotAllStdDevsInMainSwarm() {
//add further information to MainSwarm-Plot point by point
@@ -1569,7 +1513,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
}
/**
* @tested plots only the minimal std dev for the respective particle
* Plots only the minimal std dev for the respective particle
*/
protected void plotMinStdDevInMainSwarm() {
//add further information to MainSwarm-Plot (minimal stddev)
@@ -1588,7 +1532,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
/**
* @param boundary
* @tested plots all std devs < boundary for the respective particles
* Plots all std devs &lt; boundary for the respective particles
*/
protected void plotBoundStdDevInMainSwarm(double boundary) {
InterfaceDataTypeDouble tmpIndy1;
@@ -1616,7 +1560,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
/**
* @param index index of the particle
* @param text information to be added
* @tested plots a circle around the individual and adds some information
* Plots a circle around the individual and adds some information
*/
protected void plotCircleForIndy(int index, String text) {
AbstractEAIndividual indy = getIndyByParticleIndex(index);
@@ -1631,7 +1575,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
/**
* @param indy invidual
* @param text information to be added
* @tested plots a circle around the individual and adds some information
* Plots a circle around the individual and adds some information
*/
protected void plotCircleForIndy(AbstractEAIndividual indy, String text) {
InterfaceDataTypeDouble tmpIndy1 = (InterfaceDataTypeDouble) indy;
@@ -1643,7 +1587,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
}
/**
* @tested cleans the previous plot and plots the mainswarm as points
* Cleans the previous plot and plots the mainswarm as points
*/
protected void plotMainSwarm(boolean withIDs) {
if (this.optimizationProblem instanceof Interface2DBorderProblem) {
@@ -1750,7 +1694,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
}
/**
* @tested plots all subswarms as connected lines to their respective best
* Plots all subswarms as connected lines to their respective best
* individual
*/
protected void plotSubSwarms() {
@@ -1823,7 +1767,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
}
/**
* @tested plots information about merging, absorbtion and subswarm-creation
* Plots information about merging, absorption and subswarm-creation
*/
protected void plotAdditionalInfo() {
// from merging
@@ -1872,7 +1816,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
}
/**
* @tested @param particleIndex
* @param particleIndex
*/
protected void plotTraceIndy(int particleIndex) {
AbstractEAIndividual indy = getIndyByParticleIndex(particleIndex);
@@ -1890,7 +1834,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
/**
* @param indy
* @tested plots the old position, new position, personal best position and
* Plots the old position, new position, personal best position and
* neighborhood best position for a given individual
*/
protected void plotStatusForIndy(AbstractEAIndividual indy) {
@@ -1991,7 +1935,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
}
/**
* Create a Niche PSO with parameters as to Brits, Engelbrecht & Bergh: A
* Create a Niche PSO with parameters as to Brits, Engelbrecht &amp; Bergh: A
* Niching Particle Swarm Optimizer. SEAL 2002. Exeption: the swarm size is
* 200 by default, because 30 (of the orig. paper) seems way too low.
* <p>
@@ -2015,7 +1959,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
}
/**
* Set parameters as to Brits, Engelbrecht & Bergh: A Niching Particle Swarm
* Set parameters as to Brits, Engelbrecht &amp; Bergh: A Niching Particle Swarm
* Optimizer. SEAL 2002. Exception: the swarm size is 100 by default, because
* 30 (of the orig. paper) seems way too low.
*
@@ -2065,8 +2009,8 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
}
/**
* Set parameters as to Brits, Engelbrecht & Bergh: A Niching Particle Swarm
* Optimizer. SEAL 2002. Exeption: the swarm size is 200 by default, because
* Set parameters as to Brits, Engelbrecht &amp; Bergh: A Niching Particle Swarm
* Optimizer. SEAL 2002. Exception: the swarm size is 200 by default, because
* 30 (of the orig. paper) seems way too low.
*
* @param npso an already existing NichePSO instance or null to create a new one

80
src/main/java/eva2/optimization/strategies/ParticleSubSwarmOptimization.java
View File

@@ -31,10 +31,6 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
private int particleIndexCounter; // used to give each particle a unique index (for debbugging and plotting)
private int fitnessArchiveSize = 15; // maximal number of fitnessvalues remembered from former iterations
/**
* @tested ps
* ctor
*/
public ParticleSubSwarmOptimization() {
updateMaxPosDist();
this.maxAllowedSwarmRadiusNormal = 0.1; // set similar to "particle swarms for multimodal optimization" by Oezcan and Yilmaz
@@ -43,9 +39,6 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
// setInitialVelocity(1.);
}
/**
* @tested cpyctor
*/
public ParticleSubSwarmOptimization(ParticleSubSwarmOptimization a) {
super(a);
if (a.bestIndividual != null) {
@@ -60,22 +53,12 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
fitnessArchiveSize = a.fitnessArchiveSize;
}
/**
* @tested (non-Javadoc) @see javaeva.server.oa.go.Strategies.ParticleSwarmOptimization#clone()
*/
@Override
public Object clone() {
return new ParticleSubSwarmOptimization(this);
}
/**********************************************************************************************************************
* inits
*/
/**
* @tested ps
* (non-Javadoc) @see javaeva.server.oa.go.Strategies.ParticleSwarmOptimization#initialize()
*/
@Override
public void initialize() {
super.initialize();
@@ -88,10 +71,6 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
// setInertnessOrChi(inertnessAging.getStartValue());
}
/**
* @tested ps
* (non-Javadoc) @see javaeva.server.oa.go.Strategies.ParticleSwarmOptimization#initializeByPopulation(javaeva.server.oa.go.Populations.Population, boolean)
*/
@Override
public void initializeByPopulation(Population pop, boolean reset) {
super.initializeByPopulation(pop, reset);
@@ -103,7 +82,6 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
}
/**
* @tested junit&
* adds a vector for fitnessvalues to all individuals in the swarm
* and sets the current fitness as the first value
*/
@@ -129,7 +107,6 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
}
/**
* @tested emp
* adds a std deviation value to an individual
* and initially sets this value to infinity.
*/
@@ -143,7 +120,6 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
}
/**
* @tested junit
* adds a representation of the personal best to an individual
* and initially sets the current individual as its personal best.
*/
@@ -153,13 +129,6 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
indy.putData("PersonalBestKey", newpbest);
}
/**********************************************************************************************************************
* Optimization
*/
/**
* @tested ps
* (non-Javadoc) @see javaeva.server.oa.go.Strategies.ParticleSwarmOptimization#optimize()
*/
@Override
public void optimize() {
super.optimize();
@@ -230,11 +199,7 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
}
}
/**********************************************************************************************************************
* updates
*/
/**
* @tested ps
* when particles enter or leave the population,
* call this method to update the status of the population
*/
@@ -243,7 +208,6 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
}
/**
* @tested junit&
* updates the bestIndividual member which represents the gbest individual
* (i.e. the best position and fitness encountered by any particle of the swarm)
* Beware: if a particle enters the swarm its knowledge about its pbest enters the swarm,
@@ -271,7 +235,6 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
}
/**
* @tested junit, dbg
* adds the current fitnessvalue to the fitnessarchive for every individual in the swarm.
* Keeps the fitnessarchive at a limited size (lim+1).
*/
@@ -299,7 +262,6 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
}
/**
* @tested junit
* sets the std dev value of all individuals in the swarm
* to the std deviation over the last 3 fitness values
*/
@@ -315,7 +277,6 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
}
/**
* @tested junit&, junit
* update the personal best representation if the current individual is better than the pbest
*/
public void updatePersonalBest() {
@@ -336,7 +297,6 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
}
/**
* @tested junit ..
* updates the member representing the maximal possible distance in the current searchspace
*/
public void updateMaxPosDist() {
@@ -385,7 +345,6 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
* @param indy1
* @param indy2
* @return
* @tested junit
* returns the euclidean distance in the search space between indy1 and indy2.
*/
public double distance(AbstractEAIndividual indy1, AbstractEAIndividual indy2) {
@@ -397,9 +356,8 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
* @param vec
* @param range number of values (beginning at the end of vec!) considered to compute the mean
* @return
* @tested junit
* returns the mean value for the provided data vec but only for a given number of values.
* If range > vec.size() the mean is computed only for the available data.
* If range &gt; vec.size() the mean is computed only for the available data.
*/
protected static double mean(Vector<Double> vec, int range) {
if (vec.size() < range) {
@@ -416,7 +374,6 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
* @param vec data
* @param range number of values (beginning at the end of vec!) considered to compute the std deviation
* @return
* @tested junit
* returns the std deviation for the provided data vec but only for a given number of values
*/
public static double stdDev(Vector<Double> vec, int range) {
@@ -443,11 +400,10 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
/**
* @param normalisedRadius
* @return
* @tested ps
* Interpretes the given maximal radius as normalised according to the current search space.
* Values from [0,1], 1 means the radius can be as large as the maximal possible distance
* (between any two points) in the search space.
* Because the swarmradius and distances (e.g. in merging and absortion) are given in a standard euclidean metric,
* Because the swarmradius and distances (e.g. in merging and absorption) are given in a standard euclidean metric,
* this function converts the normalised distance into the standard euclidean distance.
*/
public double interpreteAsNormalisedSwarmRadius(double normalisedRadius) {
@@ -458,13 +414,8 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
return normalisedRadius * maxPosDist;
}
/**********************************************************************************************************************
* addNewParticlesToPopulation ...
*/
/**
* @param particleIndices set of indices that should be used for the added particles, if null new indices are created
* @tested junit ...
* adds new particles to this swarm, rndly inited over the search space by the problem
*/
private void addNewParticlesToPopulation(int[] particleIndices) {
@@ -510,7 +461,6 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
*/
/**
* @param pop
* @tested nn
* adds a population and its function calls to this.population
*/
public void addPopulation(ParticleSubSwarmOptimization pop) {
@@ -519,7 +469,6 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
/**
* @param pop
* @tested junit& ..
* adds a population and its function calls to this.population
*/
public void addPopulation(Population pop) {
@@ -532,7 +481,6 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
/**
* @param ind
* @return
* @tested nn
* adss an inidividual
*/
public boolean addIndividual(IndividualInterface ind) {
@@ -544,7 +492,6 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
/**
* @param o
* @return
* @tested nn
*/
public boolean add(Object o) {
return addIndividual((IndividualInterface) o);
@@ -552,7 +499,6 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
/**
* @param indy
* @tested nn
* adds indy to the swarm
*/
public void add(AbstractEAIndividual indy) {
@@ -561,7 +507,6 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
/**
* @param ind
* @tested nn
* removes an individual
*/
public boolean removeSubIndividual(IndividualInterface ind) {
@@ -579,22 +524,8 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
}
}
/*
public void removeNIndividuals(int n) {
}
public void removeDoubleInstances() {
}
public void removeDoubleInstancesUsingFitness() {
}
public void removeIndexSwitched(int index) {
}*/
/**********************************************************************************************************************
* getter, setter
*/
/**
* @param problem
* @tested ps
* This method will set the problem that is to be optimized
*/
@Override
@@ -605,7 +536,6 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
/**
* @return the maximal euclidean distance between the swarms gbest and any other particle in the swarm.
* @tested junit
*/
public double getSwarmRadius() {
if (getPopulation().size() == 0 || getPopulation().size() == 1) {
@@ -631,7 +561,6 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
/**
* @return
* @tested ps
* returns the maximal distance between the gbest position and any individual in the swarm
* this distance is not allowed to exceed a given threshold
*/
@@ -680,7 +609,6 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
/**
* @param maxAllowedSwarmRadius value from the intervall [0,1]
* @tested nn
* binds the swarmradius to the given normalised value
* (f.e. 1 means, that the swarmradius is allowed to take the maximal possible range in the search space)
*/
@@ -690,7 +618,6 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
/**
* @return
* @tested nn
*/
public double getMaxAllowedSwarmRadius() {
return this.maxAllowedSwarmRadiusNormal;
@@ -698,7 +625,6 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
/**
* @param active
* @tested nn
* marks the swarm as active or inactive
*/
public void SetActive(boolean active) {
@@ -707,7 +633,6 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
/**
* @return
* @tested nn
*/
public boolean isActive() {
return active;
@@ -728,7 +653,6 @@ public class ParticleSubSwarmOptimization extends ParticleSwarmOptimizationGCPSO
/**
* @param indy particle should be from this swarm
* @return null if there is no neighbor else neighbor
* @tested junit
* returns the particle with the minimal distance to indy
*/
public AbstractEAIndividual getMemberNeighbor(AbstractEAIndividual indy) {

7
src/main/java/eva2/optimization/strategies/ParticleSwarmOptimization.java
View File

@@ -585,8 +585,8 @@ public class ParticleSwarmOptimization extends AbstractOptimizer implements java
* This method will update a given individual according to the PSO method
*
* @param index The individual to update.
* @param indy An individual
* @param pop The current population.
* @param best The best individual found so far.
*/
protected void updateIndividual(int index, AbstractEAIndividual indy, Population pop) {
if (indy instanceof InterfaceDataTypeDouble) {
@@ -845,7 +845,6 @@ public class ParticleSwarmOptimization extends AbstractOptimizer implements java
*
* @param index index of the individual for which to check
* @param pop the current swarm
* @param best the currently best individual
* @return a copy of the position of the best remembered individual in the
* neigbourhood
*/
@@ -1558,7 +1557,7 @@ public class ParticleSwarmOptimization extends AbstractOptimizer implements java
* usually set to 2.05. The sum tau1 and tau2 must be greater than 4. The
* Chi parameter (constriction) is set as in 2 Chi =
* ------------------------ |2-tau-sqrt(tau^2-4 tau)| where tau = tau1 +
* tau2 See Clerc&Kennedy: The Particle Swarm: Explosion, stability and
* tau2 See Clerc&amp;Kennedy: The Particle Swarm: Explosion, stability and
* convergence, 2002.
*
* @param tau1
@@ -1744,7 +1743,7 @@ public class ParticleSwarmOptimization extends AbstractOptimizer implements java
}
/**
* @param set swarm visualization (2D)
* @param show
*/
public void setShow(boolean show) {
this.show = show;

21
src/main/java/eva2/optimization/strategies/ParticleSwarmOptimizationGCPSO.java
View File

@@ -28,13 +28,9 @@ public class ParticleSwarmOptimizationGCPSO extends ParticleSwarmOptimization {
protected int getAccelerationForGlobalBestParticleCounter = 0; // only for testing
/**********************************************************************************************************************
* ctors, inits
*/
/**
* @tested ps
* ctor - sets default values according to
* "An Analyis of Paricle Swarm Optimizers" by Franz van den Bergh
* Sets default values according to
* "An Analysis of Particle Swarm Optimizers" by Franz van den Bergh
*/
public ParticleSwarmOptimizationGCPSO() {
setGcpso(true);
@@ -52,7 +48,6 @@ public class ParticleSwarmOptimizationGCPSO extends ParticleSwarmOptimization {
/**
* @param a
* @tested ps
*/
public ParticleSwarmOptimizationGCPSO(ParticleSwarmOptimizationGCPSO a) {
super(a);
@@ -73,12 +68,6 @@ public class ParticleSwarmOptimizationGCPSO extends ParticleSwarmOptimization {
this.SetRhoDecreaseFactor(a.getRhoDecreaseFactor());
}
/**********************************************************************************************************************
* overwritten
*/
/**
* @tested (non-Javadoc) @see javaeva.server.go.strategies.ParticleSwarmOptimization#optimize()
*/
@Override
public void optimize() {
super.optimize(); //updatePopulation->updateIndividual->updateVelocity (s.u.)
@@ -86,7 +75,6 @@ public class ParticleSwarmOptimizationGCPSO extends ParticleSwarmOptimization {
}
/**
* @tested junit&
* (non-Javadoc) @see javaeva.server.go.strategies.ParticleSwarmOptimization#updateVelocity(int, double[], double[], double[], double[], double[][])
* uses a special velocity update strategy for the gobal best particle.
*/
@@ -138,7 +126,6 @@ public class ParticleSwarmOptimizationGCPSO extends ParticleSwarmOptimization {
/**
* @return the index of the particle with the best personal best position
* (i.e. the index of the global best particle)
* @tested junit
*/
protected int getIndexOfGlobalBestParticle() {
if (getPopulation().size() == 0) {
@@ -158,11 +145,7 @@ public class ParticleSwarmOptimizationGCPSO extends ParticleSwarmOptimization {
return index;
}
/**********************************************************************************************************************
* updateGCPSOMember
*/
/**
* @tested junit
* updates: gbestParticleIndex,gbestParticleHasChanged,numOfSuccesses,numOfFailures,gbestParticle,rho
*/
protected void updateGCPSOMember() {

15
src/main/java/eva2/optimization/strategies/Tribes.java
View File

@@ -39,10 +39,7 @@ import java.util.List;
* though.
*
* @author Maurice Clerc, Marcel Kronfeld
* @author Maurice.Clerc@WriteMe.com {@link http://mauriceclerc.net}
* {@link http://clerc.maurice.free.fr/pso/}
* @version 2006-02 21
* @date 2007-09-13
* @author Maurice.Clerc@WriteMe.com
* <p>
* Original notes:
*/
@@ -461,21 +458,21 @@ public class Tribes implements InterfaceOptimizer, java.io.Serializable {
* save("\n" + iter + " " + evalF + " " + swarm.Best.position.totalError + "
* " + swarm.size, runSave);
*
* // Evaluate the stop criterion stop = evalF >= pb.maxEval || pb.accuracy
* // Evaluate the stop criterion stop = evalF &gt;= pb.maxEval || pb.accuracy
* > swarm.Best.position.totalError;
*
* if (Tribes.adaptOption == 0) { continue iterations; }
*
* if (Tribes.adaptOption == 1) { // Just reinitialize the swarm
* adaptThreshold = iter - adapt; // adaptMax=swarmSize; adaptMax =
* swarm.linkNb(swarm); if (adaptThreshold >= adaptMax) { if
* (swarm.Best.positionPrev.totalError <= swarm.Best.position.totalError) {
* swarm.linkNb(swarm); if (adaptThreshold &gt;= adaptMax) { if
* (swarm.Best.positionPrev.totalError &lt;= swarm.Best.position.totalError) {
* adapt = iter; // Memorize at which iteration adaptation occurs
*
* for (n = 0; n < swarm.tribeNb; n++) {
* evalF=swarm.tribes[n].reinitTribe(pb,evalF); } } } continue iterations; }
*
* // if(swarm.Best.positionPrev.totalError<=swarm.Best.position.totalError)
* // if(swarm.Best.positionPrev.totalError&lt;=swarm.Best.position.totalError)
* { // Structural adaptations
*
* //swarmSize = swarm.swarmSize(swarm);
@@ -490,7 +487,7 @@ public class Tribes implements InterfaceOptimizer, java.io.Serializable {
* adaptThreshold = iter - adapt; // adaptMax=swarmSize; adaptMax =
* swarm.linkNb(swarm);
*
* if (adaptThreshold >= adaptMax) { adapt = iter; // Memorize at which
* if (adaptThreshold &gt;= adaptMax) { adapt = iter; // Memorize at which
* iteration adaptation occurs evalF=swarm.adaptSwarm(pb,
* Tribes.adaptOption, swarm, displayPb,evalF); // Réalise l'adaptation
*

2
src/main/java/eva2/optimization/tools/DoubleArrayComparator.java
View File

@@ -8,7 +8,7 @@ import java.util.Comparator;
* Comparator implementation which compares two double arrays.
* It assigns -1 if first is pareto dominant (smaller), 1 if second is pareto dominant (larger), 0 if the two ind.s
* are not comparable.
* If a criterion>=0 is specified, only the thereby indexed entry of any array
* If a criterion&gt;=0 is specified, only the thereby indexed entry of any array
* will be used for comparison (single criterion case).
*/
public class DoubleArrayComparator implements Comparator<Object> {

2
src/main/java/eva2/problems/AbstractDynamicOptimizationProblem.java
View File

@@ -251,7 +251,7 @@ public abstract class AbstractDynamicOptimizationProblem extends AbstractOptimiz
/**
* Implement an indicator for when changes in the problem environment are necessary. If it returns
* <code>true</code>, the <code>changeProblemAt(double problemTime)</code> will be called.
* {@code true}, the {@code changeProblemAt(double problemTime)} will be called.
*
* @param problemTime the current simulation time of the problem
* @return true, if the problem is to change at the given time, else false

2
src/main/java/eva2/problems/AbstractMultiModalProblemKnown.java
View File

@@ -308,7 +308,7 @@ public abstract class AbstractMultiModalProblemKnown extends AbstractProblemDoub
/**
* Calculates the maximum peak ratio based on the given fitness values.
* This is the standard formulation of MPR which assumes that all fitness
* values are positive (and for a corresponding pair, foundFits[i]<realFits[i]).
* values are positive (and for a corresponding pair, foundFits[i] &lt; realFits[i]).
* If these assumptions hold, the MPR lies in [0,1].
*
* @param realFits

6
src/main/java/eva2/problems/AbstractOptimizationProblem.java
View File

@@ -337,7 +337,7 @@ public abstract class AbstractOptimizationProblem implements InterfaceOptimizati
/**
* This method allows you to request a graphical representation for a given individual.
* The additional informations generation and funCalls are shown if they are >= 0.
* The additional informations generation and funCalls are shown if they are &gt;= 0.
* individual.
*
* @param generation generation of the individual or -1
@@ -446,9 +446,9 @@ public abstract class AbstractOptimizationProblem implements InterfaceOptimizati
* @param orig individual that is to be tested
* @param epsilon maximal allowed improvement before considered premature (given as distance in the search space)
* @param mutationStepSize step size used to mutate the individual in one step
* (if < 0 a default value of 0.0001 is used)
* (if &lt; 0 a default value of 0.0001 is used)
* @param numOfFailures number of unsuccessful improvement steps in a row before an individual is considered to be locally unimproveable
* (if < 0 a default value of 100*problem dimensions is used )
* (if &lt; 0 a default value of 100*problem dimensions is used )
* @return estimation if the given individual is within epsilon of an optimum (local or global)
*/
public boolean isPotentialOptimum(AbstractEAIndividual orig, double epsilon, double mutationStepSize, int numOfFailures) {

4
src/main/java/eva2/problems/ERPStarter.java
View File

@@ -28,7 +28,7 @@ public class ERPStarter {
/**
* Start an external runtime problem with some basic configs. The
* default variant uses equally weighs all objectives through an equally weighted sum.
* Arguments: --csv <path-to-csv-config-file> --cmd <command-with-full-path> --maxEvals <maxEvals> [--multiObjective] [--gui]
* Arguments: {@code --csv path-to-csv-config-file> --cmd <command-with-full-path> --maxEvals <maxEvals> [--multiObjective] [--gui]}
*
* @param args
*/
@@ -40,7 +40,7 @@ public class ERPStarter {
// prefix for data output file - set null to deactivate
String outputFilePrefix = "erpTest";
/** Argument handling ****************/
// Argument handling
String[] keys = new String[]{"--gui", "--multiObjective", "--csv", "--cmd", "--maxEvals"};
int[] arities = new int[]{0, 0, 1, 1, 1};
Object[] values = new Object[6];

2
src/main/java/eva2/problems/F17Problem.java
View File

@@ -5,7 +5,7 @@ import eva2.util.annotation.Description;
/**
* Bohachevsky function, numerous optima on an oval hyperparabola with similar attractor sizes
* but decreasing fitness towards the bounds. Described e.g. in Shir&Bäck, PPSN 2006,
* but decreasing fitness towards the bounds. Described e.g. in Shir&amp;Bäck, PPSN 2006,
* "Niche radius adaption in the CMA-ES Niching Algorithm".
* f_B(\vec{x})=\sum_{i=1}^{n-1} x_i^2+2(x_{i+1}^2)+0.7-0.3 cos (3 \pi x_i)-0.4 cos (4 \pi x_{i+1})
*/

2
src/main/java/eva2/problems/F18Problem.java
View File

@@ -3,7 +3,7 @@ package eva2.problems;
import eva2.util.annotation.Description;
/**
* N-Function from Shir&Baeck, PPSN 2006.
* N-Function from Shir&amp;Baeck, PPSN 2006.
*/
@Description("N-Function from Shir&Baeck, PPSN 2006")
public class F18Problem extends AbstractProblemDouble implements

2
src/main/java/eva2/problems/F19Problem.java
View File

@@ -8,7 +8,7 @@ import java.util.Arrays;
import java.util.Random;
/**
* Fletcher-Powell function with up to 2^n optima from Shir&Baeck, PPSN 2006,
* Fletcher-Powell function with up to 2^n optima from Shir&amp;Baeck, PPSN 2006,
* after Bäck 1996. Alphas and Matrices A and B are randomly created with a fixed seed.
*
*/

4
src/main/java/eva2/problems/F1Problem.java
View File

@@ -7,7 +7,7 @@ import eva2.util.annotation.Description;
/**
* Sphere Problem
*/
@Description(value ="Sphere Problem")
@Description(value = "Sphere Problem")
public class F1Problem extends AbstractProblemDoubleOffset implements Interface2DBorderProblem, InterfaceHasInitRange, java.io.Serializable, InterfaceFirstOrderDerivableProblem {
private double initialRangeRatio = 1.; // reduce to initialize in a smaller subrange of the original range (in the corner box)
@@ -103,7 +103,7 @@ public class F1Problem extends AbstractProblemDoubleOffset implements Interface2
}
/**
* If initialRangeRatio<1, produce a reduced initial range in the negative corner of the range.
* If initialRangeRatio &lt; 1, produce a reduced initial range in the negative corner of the range.
*/
@Override
public Object getInitializationRange() {

2
src/main/java/eva2/problems/F22Problem.java
View File

@@ -89,7 +89,7 @@ public class F22Problem extends AbstractProblemDoubleOffset implements Interface
}
/**
* If initialRangeRatio<1, produce a reduced initial range in the negative corner of the range.
* If initialRangeRatio &lt; 1, produce a reduced initial range in the negative corner of the range.
*/
@Override
public Object getInitializationRange() {

2
src/main/java/eva2/problems/F23Problem.java
View File

@@ -90,7 +90,7 @@ public class F23Problem extends AbstractProblemDoubleOffset implements Interface
}
/**
* If initialRangeRatio<1, produce a reduced initial range in the negative corner of the range.
* If initialRangeRatio &lt; 1, produce a reduced initial range in the negative corner of the range.
*/
@Override
public Object getInitializationRange() {

2
src/main/java/eva2/problems/GPFunctionProblem.java
View File

@@ -10,7 +10,7 @@ import eva2.tools.EVAERROR;
* A helper problem class which takes a GP program as argument and serves as target function
* for evaluating the GP function in optimization. A scaling option is implemented to flatten the
* function by scaling it logarithmically. This avoids ugly functions in GP. To activate scaling,
* set the scStart and scLimit parameters to positive values. Function values y with |y|>scStart
* set the scStart and scLimit parameters to positive values. Function values y with |y| &gt; scStart
* will be rescaled to values below scLimit.
*/
public class GPFunctionProblem extends AbstractProblemDouble implements InterfaceProgramProblem {

1
src/main/java/eva2/tools/BasicResourceLoader.java
View File

@@ -48,7 +48,6 @@ import java.util.zip.ZipInputStream;
* @author wegnerj
* @author Robin Friedman, rfriedman@TriadTherapeutics.com
* @author Gerd Mueller
* @license GPL
*/
public class BasicResourceLoader implements ResourceLoader {
/**

20
src/main/java/eva2/tools/chart2d/DArea.java
View File

@@ -21,9 +21,9 @@ import java.awt.print.PageFormat;
import java.awt.print.Printable;
/**
* DArea is the crossing of the <code>JComponent</code>s and the
* <code>DComponent</code>s. It's the <code>DParent</code> which can be added to
* <code>JComponent</code>s
* DArea is the crossing of the {@code JComponent}s and the
* {@code DComponent}s. It's the {@code DParent} which can be added to
* {@code JComponent}s
*/
public class DArea extends JComponent implements DParent, Printable {
/**
@@ -282,8 +282,8 @@ public class DArea extends JComponent implements DParent, Printable {
}
/**
* returns if the grid is visible <code>true</code> if the grid is visible
* or <code>false</code> if not
* returns if the grid is visible {@code true} if the grid is visible
* or {@code false} if not
*
* @return true or false
*/
@@ -294,7 +294,7 @@ public class DArea extends JComponent implements DParent, Printable {
/**
* returns whether the DArea's auto focus is on or not
*
* @return <code>true</code> or <code>false</code>
* @return {@code true} or {@code false}
*/
public boolean isOnAutoFocus() {
return autoFocus;
@@ -347,7 +347,7 @@ public class DArea extends JComponent implements DParent, Printable {
/**
* method paints the grid how the method paints the grid depends on whether
* the area is wrapped in a <code>ScaledBorder</code> or not and on the
* the area is wrapped in a {@code ScaledBorder} or not and on the
* autoGrid option
*/
private void paintGrid(DMeasures m) {
@@ -586,7 +586,7 @@ public class DArea extends JComponent implements DParent, Printable {
/**
* sets the grid to the front that means that the grid is painted as last
* element default value is <code>false</code>
* element default value is {@code false}
*
* @param aFlag grid t front or not
*/
@@ -669,7 +669,7 @@ public class DArea extends JComponent implements DParent, Printable {
/**
* sets the minimal rectangle
*
* @param rect the visible <code>DRectangle</code> in DArea coordinates
* @param rect the visible {@code DRectangle} in DArea coordinates
*/
public void setMinRectangle(DRectangle rect) {
if (rect.isEmpty()) {
@@ -724,7 +724,7 @@ public class DArea extends JComponent implements DParent, Printable {
/**
* sets the visible rectangle
*
* @param rect the visible <code>DRectangle</code> in DArea coordinates
* @param rect the visible {@code DRectangle} in DArea coordinates
*/
public void setVisibleRectangle(DRectangle rect) {
if (rect.isEmpty()) {

8
src/main/java/eva2/tools/chart2d/DArray.java
View File

@@ -97,9 +97,9 @@ public class DArray implements DIntDoubleMap {
* the given image value becomes the image of (highest source value + 1)
*
* @param image the new image value
* @return <code>true</code> when the minimal or the maximal image value
* @return {@code true} when the minimal or the maximal image value
* has been changed by this method call, else it returns
* <code>false</code> @see #getMinImageValue(), #getMaxImageValue()
* {@code false} @see #getMinImageValue(), #getMaxImageValue()
*/
@Override
public boolean addImage(double image) {
@@ -150,7 +150,7 @@ public class DArray implements DIntDoubleMap {
/**
* this method checks if the minimal and the maximal image value has changed
*
* @return <code>true</code> if one of them changed
* @return {@code true} if one of them changed
*/
@Override
public boolean restore() {
@@ -230,7 +230,7 @@ public class DArray implements DIntDoubleMap {
* It looks for differences in the stored image values
*
* @param o the object to compare with
* @return <code>true</code> when the object is an DArray object, containing
* @return {@code true} when the object is an DArray object, containing
* the same values
*/
@Override

6
src/main/java/eva2/tools/chart2d/DComponent.java
View File

@@ -3,9 +3,9 @@ package eva2.tools.chart2d;
import java.awt.*;
/**
* <code>DComponent</code> is the mother of all objects which can be displayed
* by a <code>DArea</code> object, even when it would be also enough to
* implement the <code>DElement</code> interface to an class
* {@code DComponent} is the mother of all objects which can be displayed
* by a {@code DArea} object, even when it would be also enough to
* implement the {@code DElement} interface to an class
* <p>
* DComponent is abstract because the paint method has to be overridden
*/

2
src/main/java/eva2/tools/chart2d/DGrid.java
View File

@@ -65,7 +65,7 @@ public class DGrid extends DComponent {
/**
* paints the grid...
*
* @param m the <code>DMeasures</code> object to paint the grid
* @param m the {@code DMeasures} object to paint the grid
*/
@Override
public void paint(DMeasures m) {

12
src/main/java/eva2/tools/chart2d/DIntDoubleMap.java
View File

@@ -16,9 +16,9 @@ public interface DIntDoubleMap {
*
* @param source the preimage of the image
* @param image the new image of the source value
* @return <code>true</code> when the minimal or the maximal image value
* @return {@code true} when the minimal or the maximal image value
* has been changed by this method call, else it returns
* <code>false</code> @see #getMinImageValue(), #getMaxImageValue()
* {@code false} @see #getMinImageValue(), #getMaxImageValue()
*/
boolean setImage(int source, double image);
@@ -34,9 +34,9 @@ public interface DIntDoubleMap {
* the image of the highest source value + 1 should be the given image value
*
* @param image the new image value
* @return <code>true</code> when the minimal or the maximal image value
* @return {@code true} when the minimal or the maximal image value
* has been changed by this method call, else it returns
* <code>false</code> @see #getMinImageValue(), #getMaxImageValue()
* {@code false} @see #getMinImageValue(), #getMaxImageValue()
*/
boolean addImage(double image);
@@ -72,10 +72,10 @@ public interface DIntDoubleMap {
double getMinPositiveImageValue();
/**
* checks the minimal and the maximal image values and returns <code>true</code>
* checks the minimal and the maximal image values and returns {@code true}
* when at least one of them has changed
*
* @return <code>true</code> when either the maximal image value or the
* @return {@code true} when either the maximal image value or the
* minimal image value has changed
*/
boolean restore();

8
src/main/java/eva2/tools/chart2d/DMeasures.java
View File

@@ -41,7 +41,7 @@ public class DMeasures implements Serializable {
/**
* method returns the pixel-point which belongs to the given D-coordinates
* it says where to paint a certain DPoint
* returns <code>null</code> if the double coordinates do not belong to the
* returns {@code null} if the double coordinates do not belong to the
* image of the scale functions
*
* @param x the double x D-coordinate
@@ -74,7 +74,7 @@ public class DMeasures implements Serializable {
/**
* method returns the point in D-coordinates which corresponds to the
* given pixel-coordinates
* returns <code>null</code> if the given coordinates can not be calculated to
* returns {@code null} if the given coordinates can not be calculated to
* the double coordinates, when they represent a point outside of the definition
* area of the scale functions
*
@@ -168,7 +168,7 @@ public class DMeasures implements Serializable {
* method returns the image rectangle of the given rectangle
* they differ if there are scale functions selected which are not the identity
* if the given rectangle does not belong to the definition area of the scale
* functions, the method returns <code>null</code>
* functions, the method returns {@code null}
*
* @return the source of it
*/
@@ -201,7 +201,7 @@ public class DMeasures implements Serializable {
* method returns the source rectangle of the given rectangle
* they differ if there are scale functions selected which are not the identity
* if the given rectangle does not belong to the image area of the scale
* functions, the method returns <code>null</code>
* functions, the method returns {@code null}
* <p>
* Tuning: rect must not be empty
*

14
src/main/java/eva2/tools/chart2d/DPointSet.java
View File

@@ -238,12 +238,12 @@ public class DPointSet extends DComponent {
/**
* method returns the index to the nearest
* <code>DPoint</code> in this
* <code>DPointSet</code>.
* {@code DPoint} in this
* {@code DPointSet}.
*
* @return the index to the nearest
* <code>DPoint</code>. -1 if no nearest
* <code>DPoint</code> was found.
* {@code DPoint}. -1 if no nearest
* {@code DPoint} was found.
*/
public int getNearestDPointIndex(DPoint point) {
double minValue = Double.MAX_VALUE;
@@ -262,11 +262,11 @@ public class DPointSet extends DComponent {
/**
* method returns the nearest
* <code>DPoint</code> in this
* <code>DPointSet</code>.
* {@code DPoint} in this
* {@code DPointSet}.
*
* @return the nearest
* <code>DPoint</code>
* {@code DPoint}
*/
public DPoint getNearestDPoint(DPoint point) {
int minIndex = getNearestDPointIndex(point);

4
src/main/java/eva2/tools/chart2d/ScaledBorder.java
View File

@@ -145,8 +145,8 @@ public class ScaledBorder implements Border {
}
/**
* constructor creates a new <code>ScaledBorder</code>
* surrounded by the specified <code>Border</code>
* constructor creates a new {@code ScaledBorder}
* surrounded by the specified {@code Border}
*/
public ScaledBorder(Border outer) {
outerBorder = outer;

8
src/main/java/eva2/tools/diagram/ColorBarCalculator.java
View File

@@ -39,6 +39,8 @@ public class ColorBarCalculator {
/**
* Returns color for the given float-value, which must be in the range from 0 to 1.
* Warning: Creates new color object, better use the method 'getRGB' if possible.
*
* @param value Value to be converted into RGB color.
*/
public Color getColor(float value) {
return new Color(getRGB(value));
@@ -46,6 +48,8 @@ public class ColorBarCalculator {
/**
* Returns color RGB-value for the given float-value, which must be in the range from 0 to 1.
*
* @param value Value to be converted into RGB color.
*/
public int getRGB(float value) {
int rgbValue = 0;
@@ -82,7 +86,7 @@ public class ColorBarCalculator {
/**
* Reverts color scale (e.g. black will be white and vice versa).
*
* @param isInverse Color scale is inverted, if <code>isInverse</code> is set to true.
* @param isInverse Color scale is inverted, if {@code isInverse} is set to true.
*/
public void setInverseScale(boolean isInverse) {
inverseScale = isInverse;
@@ -91,7 +95,7 @@ public class ColorBarCalculator {
/**
* Returns current scale mode.
*
* @return <code>true</code> if scale is inverted, else <code>false</code>.
* @return {@code true} if scale is inverted, else {@code false}.
*/
public boolean isInverseScale() {
return inverseScale;

31
src/main/java/eva2/tools/math/Mathematics.java
View File

@@ -90,15 +90,15 @@ public final class Mathematics {
* @param y another vector
* @param root what kind of distance function
* @return the distance of x and y
* @throws Exception if x and y have different dimensions an exception is thrown.
* @throws IllegalArgumentException if x and y have different dimensions an exception is thrown.
*/
public static double dist(double[] x, double[] y, int root) {
if (x.length != y.length) {
throw new RuntimeException(
throw new IllegalArgumentException(
"The vectors x and y must have the same dimension");
}
if (root == 0) {
throw new RuntimeException("There is no 0-root!");
throw new IllegalArgumentException("There is no 0-root!");
}
double d = 0;
for (int i = 0; i < x.length; i++) {
@@ -108,12 +108,12 @@ public final class Mathematics {
}
/**
* Computes the euclidian distance function.
* Computes the euclidean distance function.
*
* @param x a vector
* @param y another vector
* @return the distance of x and y
* @throws Exception if x and y have different dimensions an exception is thrown.
* @throws IllegalArgumentException if x and y have different dimensions an exception is thrown.
*/
public static double euclideanDist(double[] x, double[] y) {
if (x.length != y.length) {
@@ -787,7 +787,6 @@ public final class Mathematics {
* Normalize the given vector to a euclidean length of 1.
*
* @param v
* @return
*/
public static void normVect(double[] v, double[] res) {
svDiv(norm(v), v, res);
@@ -910,8 +909,8 @@ public final class Mathematics {
/**
* Simple version of reflection of a value moving by a step and bouncing of
* min and max values like a pool ball. Precondition is min <= val <= max,
* post condition is min <= retVal <= max.
* min and max values like a pool ball. Precondition is min &lt;= val &lt;= max,
* post condition is min &lt;= retVal &lt;= max.
*
* @param val
* @param step
@@ -1051,7 +1050,7 @@ public final class Mathematics {
/**
* Scale a range by the given factor, meaning that the interval in each
* dimension is extended (fact>1) or reduced (fact < 1) by the defined ratio
* dimension is extended (fact &gt; 1) or reduced (fact &lt; 1) by the defined ratio
* around the center.
*
* @param rangeScaleFact
@@ -1075,7 +1074,6 @@ public final class Mathematics {
*
* @param range
* @param dist
* @return
*/
public static void shiftRange(double[][] range, double dist) {
for (int i = 0; i < range.length; i++) {
@@ -1088,7 +1086,6 @@ public final class Mathematics {
* dimensions as the range.
*
* @param range
* @return
*/
public static void shiftRange(double[][] range, double[] dists) {
for (int i = 0; i < range.length; i++) {
@@ -1174,7 +1171,6 @@ public final class Mathematics {
*
* @param s Scalar
* @param v Vector
* @return
*/
public static void svAdd(double s, double[] v, double[] res) {
for (int i = 0; i < v.length; i++) {
@@ -1200,7 +1196,6 @@ public final class Mathematics {
*
* @param s
* @param v
* @return
*/
public static void svDiv(double s, double[] v, double[] res) {
for (int i = 0; i < v.length; i++) {
@@ -1240,7 +1235,6 @@ public final class Mathematics {
* @param s Scaling factor
* @param v
* @param w
* @return
*/
public static void svvAddScaled(double s, double[] v, double[] w,
double[] res) {
@@ -1255,7 +1249,6 @@ public final class Mathematics {
* @param s
* @param v
* @param w
* @return
*/
public static void svvAddAndScale(double s, double[] v, double[] w,
double[] res) {
@@ -1284,7 +1277,6 @@ public final class Mathematics {
*
* @param v1
* @param v2
* @return vector addition
*/
public static void vvAdd(double[] v1, double[] v2, double[] res) {
vvAddOffs(v1, 0, v2, 0, res, 0, v1.length);
@@ -1311,7 +1303,6 @@ public final class Mathematics {
*
* @param v1
* @param v2
* @return vector addition
*/
public static void vvAddOffs(double[] v1, int v1Offs, double[] v2,
int v2Offs, double[] res, int resOffs, int len) {
@@ -1338,9 +1329,9 @@ public final class Mathematics {
/**
* Component wise multiplication of vectors: res[i]=u[i]*v[i]
*
* @param s
* @param u
* @param v
* @return
* @param res The result vector
*/
public static void vvMultCw(double[] u, double[] v, double[] res) {
for (int i = 0; i < res.length; i++) {
@@ -1366,7 +1357,7 @@ public final class Mathematics {
*
* @param a
* @param b
* @return a new vector c = a - b
* @param res Result vector c = a - b
*/
public static void vvSub(double[] a, double[] b, double[] res) {
for (int i = 0; i < a.length; i++) {

4
src/main/java/eva2/tools/math/RNG.java
View File

@@ -393,8 +393,8 @@ public final class RNG {
/**
* Returns a vector denoting a random point around the center - inside a
* hypersphere of uniform distribution if nonUnif=0, - inside a hypersphere
* of non-uniform distribution if nonUnif > 0, - inside a D-Gaussian if
* nonUnif < 0. For case 2, the nonUnif parameter is used as standard
* of non-uniform distribution if nonUnif &gt; 0, - inside a D-Gaussian if
* nonUnif &lt; 0. For case 2, the nonUnif parameter is used as standard
* deviation (instead of 1/D), the parameter is not further used in the
* other two cases. Original code by Maurice Clerc, from the TRIBES package
*

14
src/main/java/eva2/tools/math/SpecialFunction.java
View File

@@ -236,7 +236,7 @@ public final class SpecialFunction {
}
/**
* @param x a double value
* @param xx a double value
* @return the hyperbolic arc sine of the argument
*/
static public double asinh(double xx) throws ArithmeticException {
@@ -504,7 +504,7 @@ public final class SpecialFunction {
}
/**
* @param x an integer value
* @param j an integer value
* @return the factorial of the argument
*/
static public int fac(int j) throws ArithmeticException {
@@ -528,7 +528,6 @@ public final class SpecialFunction {
* @param x a double value
* @return the Gamma function of the value.
* <p>
* <FONT size=2>
* Converted to Java from<BR>
* Cephes Math Library Release 2.2: July, 1992<BR>
* Copyright 1984, 1987, 1989, 1992 by Stephen L. Moshier<BR>
@@ -626,7 +625,7 @@ public final class SpecialFunction {
}
/* Gamma function computed by Stirling's formula.
* The polynomial STIR is valid for 33 <= x <= 172.
* The polynomial STIR is valid for 33 &lt;= x &lt;= 172.
Cephes Math Library Release 2.2: July, 1992
Copyright 1984, 1987, 1989, 1992 by Stephen L. Moshier
@@ -663,7 +662,6 @@ public final class SpecialFunction {
* @param x double value
* @return the Complemented Incomplete Gamma function.
* <p>
* <FONT size=2>
* Converted to Java from<BR>
* Cephes Math Library Release 2.2: July, 1992<BR>
* Copyright 1984, 1987, 1989, 1992 by Stephen L. Moshier<BR>
@@ -738,7 +736,6 @@ public final class SpecialFunction {
* @param x double value
* @return the Incomplete Gamma function.
* <p>
* <FONT size=2>
* Converted to Java from<BR>
* Cephes Math Library Release 2.2: July, 1992<BR>
* Copyright 1984, 1987, 1989, 1992 by Stephen L. Moshier<BR>
@@ -894,7 +891,6 @@ public final class SpecialFunction {
* @param a double value
* @return The complementary Error function
* <p>
* <FONT size=2>
* Converted to Java from<BR>
* Cephes Math Library Release 2.2: July, 1992<BR>
* Copyright 1984, 1987, 1989, 1992 by Stephen L. Moshier<BR>
@@ -995,10 +991,9 @@ public final class SpecialFunction {
}
/**
* @param a double value
* @param x double value
* @return The Error function
* <p>
* <FONT size=2>
* Converted to Java from<BR>
* Cephes Math Library Release 2.2: July, 1992<BR>
* Copyright 1984, 1987, 1989, 1992 by Stephen L. Moshier<BR>
@@ -1175,7 +1170,6 @@ Direct inquiries to 30 Frost Street, Cambridge, MA 02140
* @param xx double value
* @return The Incomplete Beta Function evaluated from zero to xx.
* <p>
* <FONT size=2>
* Converted to Java from<BR>
* Cephes Math Library Release 2.3: July, 1995<BR>
* Copyright 1984, 1995 by Stephen L. Moshier<BR>