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Added entire population to population data. #17

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2 changes: 1 addition & 1 deletion examples/pom.xml
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Expand Up @@ -22,7 +22,7 @@
<parent>
<groupId>org.uncommons.watchmaker</groupId>
<artifactId>watchmaker</artifactId>
<version>0.7.2</version>
<version>0.7.2-qumul</version>
</parent>
<artifactId>watchmaker-examples</artifactId>

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4 changes: 2 additions & 2 deletions framework/pom.xml
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Expand Up @@ -22,15 +22,15 @@
<parent>
<groupId>org.uncommons.watchmaker</groupId>
<artifactId>watchmaker</artifactId>
<version>0.7.2</version>
<version>0.7.2-qumul</version>
</parent>
<artifactId>watchmaker-framework</artifactId>

<dependencies>
<dependency>
<groupId>org.uncommons.maths</groupId>
<artifactId>uncommons-maths</artifactId>
<version>1.2.2</version>
<version>1.2.2a</version>
</dependency>
<dependency>
<groupId>com.google.collections</groupId>
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11 changes: 1 addition & 10 deletions framework/src/java/main/org/uncommons/watchmaker/framework/EvolutionUtils.java
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Expand Up @@ -111,17 +111,8 @@ public static <T> PopulationData<T> getPopulationData(List<EvaluatedCandidate<T>
int iterationNumber,
long startTime)
{
DataSet stats = new DataSet(evaluatedPopulation.size());
for (EvaluatedCandidate<T> candidate : evaluatedPopulation)
{
stats.addValue(candidate.getFitness());
}
return new PopulationData<T>(evaluatedPopulation.get(0).getCandidate(),
evaluatedPopulation.get(0).getFitness(),
stats.getArithmeticMean(),
stats.getStandardDeviation(),
return new PopulationData<T>(evaluatedPopulation,
naturalFitness,
stats.getSize(),
eliteCount,
iterationNumber,
System.currentTimeMillis() - startTime);
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70 changes: 60 additions & 10 deletions framework/src/java/main/org/uncommons/watchmaker/framework/PopulationData.java
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Expand Up @@ -15,6 +15,10 @@
//=============================================================================
package org.uncommons.watchmaker.framework;

import org.uncommons.maths.statistics.DataSet;

import java.util.List;

/**
* Immutable data object containing statistics about the state of
* an evolved population and a reference to the fittest candidate
Expand All @@ -26,6 +30,7 @@
*/
public final class PopulationData<T>
{
private final List<EvaluatedCandidate<T>> evaluatedPopulation;
private final T bestCandidate;
private final double bestCandidateFitness;
private final double meanFitness;
Expand All @@ -37,6 +42,8 @@ public final class PopulationData<T>
private final long elapsedTime;

/**
* Constructor only
* @param evaluatedPopulation List of all candidates
* @param bestCandidate The fittest candidate present in the population.
* @param bestCandidateFitness The fitness score for the fittest candidate
* in the population.
Expand All @@ -45,23 +52,25 @@ public final class PopulationData<T>
* @param fitnessStandardDeviation A measure of the variation in fitness
* scores.
* @param naturalFitness True if higher fitness scores are better, false
* otherwise.
* otherwise.
* @param populationSize The number of individuals in the population.
* @param eliteCount The number of candidates preserved via elitism.
* @param generationNumber The (zero-based) number of the last generation
* that was processed.
* @param elapsedTime The number of milliseconds since the start of the
*/
public PopulationData(T bestCandidate,
double bestCandidateFitness,
double meanFitness,
double fitnessStandardDeviation,
boolean naturalFitness,
int populationSize,
int eliteCount,
int generationNumber,
long elapsedTime)
public PopulationData(
List<EvaluatedCandidate<T>> evaluatedPopulation, T bestCandidate,
double bestCandidateFitness,
double meanFitness,
double fitnessStandardDeviation,
boolean naturalFitness,
int populationSize,
int eliteCount,
int generationNumber,
long elapsedTime)
{
this.evaluatedPopulation = evaluatedPopulation;
this.bestCandidate = bestCandidate;
this.bestCandidateFitness = bestCandidateFitness;
this.meanFitness = meanFitness;
Expand All @@ -72,7 +81,48 @@ public PopulationData(T bestCandidate,
this.generationNumber = generationNumber;
this.elapsedTime = elapsedTime;
}
/**
* @param evaluatedPopulation List of all candidates, the list should be
* ordered by fitness for the the best candidate to be meaningfull.
* Otherwise consider making your own statistics and use the other
* constructor
* @param naturalFitness True if higher fitness scores are better, false otherwise.
* @param eliteCount The number of candidates preserved via elitism.
* @param generationNumber The (zero-based) number of the last generation that was processed.
* @param elapsedTime The number of milliseconds since the start of the
*/
public PopulationData(List<EvaluatedCandidate<T>> evaluatedPopulation,
boolean naturalFitness,
int eliteCount,
int generationNumber,
long elapsedTime)
{
DataSet stats = new DataSet(evaluatedPopulation.size());
for (EvaluatedCandidate<T> candidate : evaluatedPopulation)
{
stats.addValue(candidate.getFitness());
}

this.bestCandidate = evaluatedPopulation.get(0).getCandidate();
this.bestCandidateFitness = evaluatedPopulation.get(0).getFitness();
this.meanFitness = stats.getArithmeticMean();
this.fitnessStandardDeviation = stats.getStandardDeviation();
this.naturalFitness = naturalFitness;
this.populationSize = stats.getSize();
this.eliteCount = eliteCount;
this.generationNumber = generationNumber;
this.elapsedTime = elapsedTime;
this.evaluatedPopulation = evaluatedPopulation;
}

/**
* @return The list of all candidates in the population at this stage,
* be carefull in the references you hold of this and don't assume this
* list to remain unchanged over generations.
*/
public List<EvaluatedCandidate<T>> getEvaluatedPopulation() {
return evaluatedPopulation;
}

/**
* @return The fittest candidate present in the population.
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6 changes: 4 additions & 2 deletions framework/src/java/test/org/uncommons/watchmaker/framework/termination/ElapsedTimeTest.java
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Expand Up @@ -19,6 +19,8 @@
import org.uncommons.watchmaker.framework.PopulationData;
import org.uncommons.watchmaker.framework.TerminationCondition;

import java.util.ArrayList;

/**
* Unit test for termination condition that checks the time taken so far by the
* evolutionary algorithm.
Expand All @@ -30,9 +32,9 @@ public class ElapsedTimeTest
public void testElapsedTimes()
{
TerminationCondition condition = new ElapsedTime(1000);
PopulationData<Object> data = new PopulationData<Object>(new Object(), 0, 0, 0, true, 2, 0, 0, 100);
PopulationData<Object> data = new PopulationData<Object>(new ArrayList(), new Object(), 0, 0, 0, true, 2, 0, 0, 100);
assert !condition.shouldTerminate(data) : "Should not terminate before timeout.";
data = new PopulationData<Object>(new Object(), 0, 0, 0, true, 2, 0, 0, 1000);
data = new PopulationData<Object>(new ArrayList(), new Object(), 0, 0, 0, true, 2, 0, 0, 1000);
assert condition.shouldTerminate(data) : "Should terminate after timeout.";
}

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6 changes: 4 additions & 2 deletions ...ork/src/java/test/org/uncommons/watchmaker/framework/termination/GenerationCountTest.java
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Expand Up @@ -19,6 +19,8 @@
import org.uncommons.watchmaker.framework.PopulationData;
import org.uncommons.watchmaker.framework.TerminationCondition;

import java.util.ArrayList;

/**
* Unit test for termination condition that checks the number of evolved generations.
* @author Daniel Dyer
Expand All @@ -29,10 +31,10 @@ public class GenerationCountTest
public void testGenerationCounts()
{
TerminationCondition condition = new GenerationCount(5);
PopulationData<Object> data = new PopulationData<Object>(new Object(), 0, 0, 0, true, 2, 0, 3, 100);
PopulationData<Object> data = new PopulationData<Object>(new ArrayList(), new Object(), 0, 0, 0, true, 2, 0, 3, 100);
// Generation number 3 is the 4th generation (generation numbers are zero-based).
assert !condition.shouldTerminate(data) : "Should not terminate after 4th generation.";
data = new PopulationData<Object>(new Object(), 0, 0, 0, true, 2, 0, 4, 100);
data = new PopulationData<Object>(new ArrayList(), new Object(), 0, 0, 0, true, 2, 0, 4, 100);
// Generation number 4 is the 5th generation (generation numbers are zero-based).
assert condition.shouldTerminate(data) : "Should terminate after 5th generation.";
}
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34 changes: 18 additions & 16 deletions framework/src/java/test/org/uncommons/watchmaker/framework/termination/StagnationTest.java
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Expand Up @@ -19,6 +19,8 @@
import org.uncommons.watchmaker.framework.PopulationData;
import org.uncommons.watchmaker.framework.TerminationCondition;

import java.util.ArrayList;

/**
* Unit test for the {@link Stagnation} termination condition.
* @author Daniel Dyer
Expand All @@ -29,27 +31,27 @@ public class StagnationTest
public void testFittestCandidateStagnation()
{
TerminationCondition stagnation = new Stagnation(2, true);
PopulationData<Object> data = new PopulationData<Object>(new Object(), 2, 1, 0.1, true, 10, 0, 0, 1);
PopulationData<Object> data = new PopulationData<Object>(new ArrayList(), new Object(), 2, 1, 0.1, true, 10, 0, 0, 1);
assert !stagnation.shouldTerminate(data) : "Stagnation should not be triggered for at least 2 more generations.";
// Best doesn't improve even though mean does.
data = new PopulationData<Object>(new Object(), 1.8, 1.2, 0.1, true, 10, 0, 1, 2);
data = new PopulationData<Object>(new ArrayList(), new Object(), 1.8, 1.2, 0.1, true, 10, 0, 1, 2);
assert !stagnation.shouldTerminate(data) : "Stagnation should not be triggered for at least 1 more generation.";
// Best doesn't improve even though mean does.
data = new PopulationData<Object>(new Object(), 2, 1.5, 0.1, true, 10, 0, 2, 3);
data = new PopulationData<Object>(new ArrayList(), new Object(), 2, 1.5, 0.1, true, 10, 0, 2, 3);
assert stagnation.shouldTerminate(data) : "Stagnation should be triggered after 2 generations without improvement.";
}

@Test
public void testFittestCandidateStagnationNonNatural()
{
TerminationCondition stagnation = new Stagnation(2, false);
PopulationData<Object> data = new PopulationData<Object>(new Object(), 2, 1.5, 0.1, true, 10, 0, 0, 1);
PopulationData<Object> data = new PopulationData<Object>(new ArrayList(), new Object(), 2, 1.5, 0.1, true, 10, 0, 0, 1);
assert !stagnation.shouldTerminate(data) : "Stagnation should not be triggered for at least 2 more generations.";
// Best doesn't improve even though mean does.
data = new PopulationData<Object>(new Object(), 2.2, 1.2, 0.1, true, 10, 0, 1, 2);
data = new PopulationData<Object>(new ArrayList(), new Object(), 2.2, 1.2, 0.1, true, 10, 0, 1, 2);
assert !stagnation.shouldTerminate(data) : "Stagnation should not be triggered for at least 1 more generation.";
// Best doesn't improve even though mean does.
data = new PopulationData<Object>(new Object(), 2, 1, 0.1, true, 10, 0, 2, 3);
data = new PopulationData<Object>(new ArrayList(), new Object(), 2, 1, 0.1, true, 10, 0, 2, 3);
assert stagnation.shouldTerminate(data) : "Stagnation should be triggered after 2 generations without improvement.";
}

Expand All @@ -58,19 +60,19 @@ public void testFittestCandidateStagnationNonNatural()
public void testPopulationMeanStagnation()
{
TerminationCondition stagnation = new Stagnation(2, true, true);
PopulationData<Object> data = new PopulationData<Object>(new Object(), 2, 1, 0.1, true, 10, 0, 0, 1);
PopulationData<Object> data = new PopulationData<Object>(new ArrayList(), new Object(), 2, 1, 0.1, true, 10, 0, 0, 1);
assert !stagnation.shouldTerminate(data) : "Stagnation should not be triggered for at least 2 more generations.";
// Best doesn't improve but mean does.
data = new PopulationData<Object>(new Object(), 2, 1.2, 0.1, true, 10, 0, 1, 2);
data = new PopulationData<Object>(new ArrayList(), new Object(), 2, 1.2, 0.1, true, 10, 0, 1, 2);
assert !stagnation.shouldTerminate(data) : "Stagnation should not be triggered for at least 2 more generations.";
// Best doesn't improve but mean does.
data = new PopulationData<Object>(new Object(), 2, 1.5, 0.1, true, 10, 0, 2, 3);
data = new PopulationData<Object>(new ArrayList(), new Object(), 2, 1.5, 0.1, true, 10, 0, 2, 3);
// Best has stagnated but mean hasn't so shouldn't terminate.
assert !stagnation.shouldTerminate(data) : "Stagnation should not be triggered for at least 2 more generations.";
// Now we let the mean stagnate...and let the best candidate get fitter...
data = new PopulationData<Object>(new Object(), 2.1, 1.5, 0.1, true, 10, 0, 3, 4);
data = new PopulationData<Object>(new ArrayList(), new Object(), 2.1, 1.5, 0.1, true, 10, 0, 3, 4);
assert !stagnation.shouldTerminate(data) : "Stagnation should not be triggered for at least 1 more generation.";
data = new PopulationData<Object>(new Object(), 2.2, 1.5, 0.1, true, 10, 0, 4, 4);
data = new PopulationData<Object>(new ArrayList(), new Object(), 2.2, 1.5, 0.1, true, 10, 0, 4, 4);
assert stagnation.shouldTerminate(data) : "Stagnation should be triggered after 2 generations without improvement.";
}

Expand All @@ -79,19 +81,19 @@ public void testPopulationMeanStagnation()
public void testPopulationMeanStagnationNonNatural()
{
TerminationCondition stagnation = new Stagnation(2, false, true);
PopulationData<Object> data = new PopulationData<Object>(new Object(), 2, 1.5, 0.1, true, 10, 0, 0, 1);
PopulationData<Object> data = new PopulationData<Object>(new ArrayList(), new Object(), 2, 1.5, 0.1, true, 10, 0, 0, 1);
assert !stagnation.shouldTerminate(data) : "Stagnation should not be triggered for at least 2 more generations.";
// Best doesn't improve but mean does.
data = new PopulationData<Object>(new Object(), 2, 1.2, 0.1, true, 10, 0, 1, 2);
data = new PopulationData<Object>(new ArrayList(), new Object(), 2, 1.2, 0.1, true, 10, 0, 1, 2);
assert !stagnation.shouldTerminate(data) : "Stagnation should not be triggered for at least 2 more generations.";
// Best doesn't improve but mean does.
data = new PopulationData<Object>(new Object(), 2, 1, 0.1, true, 10, 0, 2, 3);
data = new PopulationData<Object>(new ArrayList(), new Object(), 2, 1, 0.1, true, 10, 0, 2, 3);
// Best has stagnated but mean hasn't so shouldn't terminate.
assert !stagnation.shouldTerminate(data) : "Stagnation should not be triggered for at least 2 more generations.";
// Now we let the mean stagnate...and let the best candidate get fitter...
data = new PopulationData<Object>(new Object(), 2.1, 1.6, 0.1, true, 10, 0, 3, 4);
data = new PopulationData<Object>(new ArrayList(), new Object(), 2.1, 1.6, 0.1, true, 10, 0, 3, 4);
assert !stagnation.shouldTerminate(data) : "Stagnation should not be triggered for at least 1 more generation.";
data = new PopulationData<Object>(new Object(), 2.2, 1.5, 0.1, true, 10, 0, 4, 4);
data = new PopulationData<Object>(new ArrayList(), new Object(), 2.2, 1.5, 0.1, true, 10, 0, 4, 4);
assert stagnation.shouldTerminate(data) : "Stagnation should be triggered after 2 generations without improvement.";
}
}
10 changes: 6 additions & 4 deletions ...ework/src/java/test/org/uncommons/watchmaker/framework/termination/TargetFitnessTest.java
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Expand Up @@ -19,6 +19,8 @@
import org.uncommons.watchmaker.framework.PopulationData;
import org.uncommons.watchmaker.framework.TerminationCondition;

import java.util.ArrayList;

/**
* Unit test for termination condition that checks the best fitness attained so far
* against a pre-determined target.
Expand All @@ -30,9 +32,9 @@ public class TargetFitnessTest
public void testNaturalFitness()
{
TerminationCondition condition = new TargetFitness(10.0d, true);
PopulationData<Object> data = new PopulationData<Object>(new Object(), 5.0d, 4.0d, 0, true, 2, 0, 0, 100);
PopulationData<Object> data = new PopulationData<Object>(new ArrayList(), new Object(), 5.0d, 4.0d, 0, true, 2, 0, 0, 100);
assert !condition.shouldTerminate(data) : "Should not terminate before target fitness is reached.";
data = new PopulationData<Object>(new Object(), 10.0d, 8.0d, 0, true, 2, 0, 0, 100);
data = new PopulationData<Object>(new ArrayList(), new Object(), 10.0d, 8.0d, 0, true, 2, 0, 0, 100);
assert condition.shouldTerminate(data) : "Should terminate once target fitness is reached.";
}

Expand All @@ -41,9 +43,9 @@ public void testNaturalFitness()
public void testNonNaturalFitness()
{
TerminationCondition condition = new TargetFitness(1.0d, false);
PopulationData<Object> data = new PopulationData<Object>(new Object(), 5.0d, 4.0d, 0, true, 2, 0, 0, 100);
PopulationData<Object> data = new PopulationData<Object>(new ArrayList(), new Object(), 5.0d, 4.0d, 0, true, 2, 0, 0, 100);
assert !condition.shouldTerminate(data) : "Should not terminate before target fitness is reached.";
data = new PopulationData<Object>(new Object(), 1.0d, 3.1d, 0, true, 2, 0, 0, 100);
data = new PopulationData<Object>(new ArrayList(), new Object(), 1.0d, 3.1d, 0, true, 2, 0, 0, 100);
assert condition.shouldTerminate(data) : "Should terminate once target fitness is reached.";
}
}
4 changes: 3 additions & 1 deletion framework/src/java/test/org/uncommons/watchmaker/framework/termination/UserAbortTest.java
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Expand Up @@ -18,6 +18,8 @@
import org.testng.annotations.Test;
import org.uncommons.watchmaker.framework.PopulationData;

import java.util.ArrayList;

/**
* Unit test for termination condition that checks an abort flag set by the user.
* @author Daniel Dyer
Expand All @@ -29,7 +31,7 @@ public void testAbort()
{
UserAbort condition = new UserAbort();
// This population data should be irrelevant.
PopulationData<Object> data = new PopulationData<Object>(new Object(), 0, 0, 0, true, 2, 0, 0, 100);
PopulationData<Object> data = new PopulationData<Object>(new ArrayList(), new Object(), 0, 0, 0, true, 2, 0, 0, 100);
assert !condition.shouldTerminate(data) : "Should not terminate without user abort.";
assert !condition.isAborted() : "Should not be aborted without user intervention.";
condition.abort();
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2 changes: 1 addition & 1 deletion pom.xml
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Expand Up @@ -8,7 +8,7 @@
</parent>
<groupId>org.uncommons.watchmaker</groupId>
<artifactId>watchmaker</artifactId>
<version>0.7.2</version>
<version>0.7.2-qumul</version>
<packaging>pom</packaging>
<name>watchmaker</name>
<description>Watchmaker Framework - Root Project</description>
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2 changes: 1 addition & 1 deletion swing/pom.xml
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Expand Up @@ -22,7 +22,7 @@
<parent>
<groupId>org.uncommons.watchmaker</groupId>
<artifactId>watchmaker</artifactId>
<version>0.7.2</version>
<version>0.7.2-qumul</version>
</parent>
<artifactId>watchmaker-swing</artifactId>

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