From 5cb454f0100c3f5f0f6020ec61b84da9f463e5cb Mon Sep 17 00:00:00 2001
From: "Bernhard J. Berger" <bernhard.berger@uni-bremen.de>
Date: Tue, 27 Dec 2022 08:28:17 +0100
Subject: [PATCH] Re-implemented EvoAl core (except for constraint handling).
---
.../ea/chromosomes/BoundedOperations.java | 46 --
.../core/main/ea/gene/DynamicChromosome.java | 41 -
.../core/main/ea/gene/DynamicDoubleGene.java | 36 -
.../core/main/ea/gene/DynamicEnumGene.java | 35 -
.../evoal/core/main/ea/gene/DynamicGene.java | 57 --
.../core/main/ea/gene/DynamicIntegerGene.java | 32 -
.../core/main/ea/gene/StringUniverse.java | 46 --
src/core/de.evoal.core/pom.xml | 4 +
.../evoal/core/api/board/BlackboardEntry.java | 30 +-
.../de/evoal/core/api/cdi/BeanFactory.java | 28 +-
.../evoal/core/api/ea/codec/CustomCodec.java | 1 +
.../ea/fitness/comparator/FitnessValue.java | 4 +
.../api/ea/initial/InitialPopulation.java | 3 +-
.../evoal/core/api/properties/Properties.java | 44 +-
.../properties/PropertiesSpecification.java | 4 +
.../api/properties/io/PropertiesWriter.java | 12 +-
...opertiesBasedPropertiesStreamSupplier.java | 4 +
.../evoal/core/api/utils/LanguageHelper.java | 40 +-
.../de/evoal/core/api/utils/Requirements.java | 18 +
.../core/main/ea/alterer/AltererFactory.java | 62 +-
.../crossover/CorrelationCrossover.java | 4 +-
.../CorrelationCrossoverMemento.java | 2 +-
.../crossover/LineCorrelationCrossover.java | 2 +-
.../LineCorrelationCrossoverMemento.java | 2 +-
.../MultiPointCorrelationCrossover.java | 2 +-
...MultiPointCorrelationCrossoverMemento.java | 2 +-
.../PartiallyMatchedCorrelationCrossover.java | 2 +-
...llyMatchedCorrelationCrossoverMemento.java | 5 +-
.../SinglePointCorrelationCrossover.java | 2 +-
...inglePointCorrelationCrossoverMemento.java | 3 +-
.../UniformCorrelationCrossover.java | 2 +-
.../UniformCorrelationCrossoverMemento.java | 2 +-
.../internal/AbstractCorrelationAlterer.java | 0
.../internal/CorrelationCombineAlterer.java | 4 +-
.../internal/CorrelationRecombinator.java | 0
.../internal/MeanCorrelationAlterer.java | 2 +-
.../alterer/mutator/CorrelationMutator.java | 4 +-
.../mutator/CorrelationMutatorFactory.java | 2 +-
.../mutator/CorrelationMutatorMemento.java | 2 +-
.../mutator/GaussianCorrelationMutator.java | 2 +-
.../GaussianCorrelationMutatorMemento.java | 2 +-
.../SingleBitFlipCorrelationMutator.java | 2 +-
...ingleBitFlipCorrelationMutatorMemento.java | 2 +-
.../alterer/mutator/SingleBitFlipMutator.java | 2 -
.../mutator/SwapCorrelationMutator.java | 2 +-
.../SwapCorrelationMutatorMemento.java | 3 +-
.../core/main/ea/codec/DynamicCodec.java | 107 +++
.../main/ea/codec/DynamicCodecProducer.java | 21 +
.../chromosome/DynamicBitChromosome.java | 50 ++
.../chromosome/DynamicBoundedChromosome.java | 26 +
.../codec/chromosome/DynamicChromosome.java | 46 ++
.../chromosome/DynamicChromosomeFactory.java | 18 +
.../chromosome/DynamicDoubleChromosome.java | 58 ++
.../chromosome/DynamicGrayChromosome.java | 47 ++
.../chromosome/DynamicScaledChromosome.java | 34 +
.../ea/comparator/ParetoFitnessValue.java | 11 +
.../comparator/WeightedSumFitnessValue.java | 11 +
.../core/main/ea/fitness/DistanceFitness.java | 47 +-
.../ea/initial/InitialPopulationFactory.java | 15 +-
.../ea/initial/RandomInitialPopulation.java | 4 +-
.../core/main/ea/initial/RandomProducer.java | 30 +
.../evoal/core/main/ea/model/Correlation.java | 2 +-
.../core/main/ea/model/Correlations.java | 8 +-
.../de/evoal/core/main/ea/model/Range.java | 2 +-
.../core/main/ea/model/RangedCorrelation.java | 2 +-
.../main/ea/producer}/SelectorFactory.java | 2 +-
.../jenetics/AbstractBoundedChromosome.java | 93 +++
.../core/main/jenetics/BitChromosome.java | 700 ++++++++++++++++++
.../evoal/core/main/jenetics}/BitHelper.java | 2 +-
.../main/jenetics}/BoundedBitChromosome.java | 3 +-
.../jenetics/BoundedDoubleChromosome.java | 285 +++++++
.../core/main/jenetics/BoundedDoubleGene.java | 239 ++++++
.../core/main/jenetics/BoundedOperations.java | 25 +
.../core/main/jenetics}/DecimalFactory.java | 2 +-
.../jenetics}/GrayBoundedBitChromosome.java | 8 +-
.../evoal/core/main/jenetics}/GrayHelper.java | 2 +-
.../jenetics}/NaiveBoundedBitChromosome.java | 7 +-
.../main/jenetics/VariableChromosome.java | 100 +++
.../producer/ConfigurationValueProducer.java | 8 +
.../core/main/producer/MockupProducer.java | 15 +
.../main/producer/SpecificationProducer.java | 43 ++
.../core/main/search/HeuristicSearch.java | 47 +-
.../search/HeuristicSearchEvaluation.java | 22 +-
.../core/main/search/HeuristicSearchMain.java | 6 +-
.../statistics/fitness/FitnessStatistics.java | 23 +-
.../individuals/IndividualStatistics.java | 16 +-
.../main/statistics/nop/NopStatistics.java | 5 +-
.../statistics/writer/csv/CsvStrategy.java | 0
.../main/statistics/writer/csv/CsvWriter.java | 0
.../src/main/java/module-info.java | 20 +-
.../generator/main/benchmarks/Ackley.java | 3 +-
.../generator/main/benchmarks/Rastrigin.java | 2 +-
.../generator/main/benchmarks/Rosenbrock.java | 4 +-
.../main/benchmarks/WeightedSphere.java | 2 +-
.../main/functions/NormalNoiseFunction.java | 2 +-
.../api/SurrogateBlackboardEntry.java | 7 +-
.../surrogate/main/cdi/SurrogateProducer.java | 18 +-
.../surrogate/main/cdi/TargetPointLoader.java | 67 ++
.../main/ea/SurrogateFitnessFunction.java | 4 +-
.../main/ea/TrainingDataProducer.java | 29 +
.../main/ea/TrainingInitialPopulation.java | 12 +-
.../surrogate/main/ea/TrainingProducer.java | 31 +
.../gof/cross/CrossValidationCalculator.java | 2 +-
.../main/gof/rsquare/RSquareCalculator.java | 7 +-
.../GenerationStatisticsWriter.java | 8 +-
.../src/main/java/module-info.java | 2 +
src/core/de.evoal.surrogate.neural/pom.xml | 54 ++
.../neural/EvoalDataSetIterator.java | 21 +
.../neural/NeuralNetworkConfigurator.java | 154 ++++
.../neural/NeuralNetworkHelper.java | 37 +
.../neural/SimpleNeuralNetwork.java | 41 +
.../neural/SimpleNeuralNetworkFactory.java | 78 ++
.../src/main/java/module-info.java | 13 +
.../simple/identity/IdentityFunction.java | 2 +-
.../simple/linear/LinearFunction.java | 2 +-
.../simple/linear/LinearFunctionFactory.java | 2 +-
.../quadratic/SimpleQuadraticFunction.java | 2 +-
.../SimpleQuadraticFunctionFactory.java | 2 +-
.../src/main/java/module-info.java | 1 +
.../svr/GaussianKernelSVRFunctionFactory.java | 4 +-
.../surrogate/svr/KernelBasedSVRFunction.java | 6 +-
.../svr/KernelBasedSVRFunctionFactory.java | 13 +-
.../de/evoal/surrogate/svr/KernelHelper.java | 13 +-
123 files changed, 2874 insertions(+), 589 deletions(-)
delete mode 100644 src/core/attic/de/evoal/core/main/ea/chromosomes/BoundedOperations.java
delete mode 100644 src/core/attic/de/evoal/core/main/ea/gene/DynamicChromosome.java
delete mode 100644 src/core/attic/de/evoal/core/main/ea/gene/DynamicDoubleGene.java
delete mode 100644 src/core/attic/de/evoal/core/main/ea/gene/DynamicEnumGene.java
delete mode 100644 src/core/attic/de/evoal/core/main/ea/gene/DynamicGene.java
delete mode 100644 src/core/attic/de/evoal/core/main/ea/gene/DynamicIntegerGene.java
delete mode 100644 src/core/attic/de/evoal/core/main/ea/gene/StringUniverse.java
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/ea/alterer/AltererFactory.java (67%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/ea/alterer/crossover/CorrelationCrossover.java (96%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/ea/alterer/crossover/CorrelationCrossoverMemento.java (81%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/ea/alterer/crossover/LineCorrelationCrossover.java (97%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/ea/alterer/crossover/LineCorrelationCrossoverMemento.java (91%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/ea/alterer/crossover/MultiPointCorrelationCrossover.java (98%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/ea/alterer/crossover/MultiPointCorrelationCrossoverMemento.java (92%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/ea/alterer/crossover/PartiallyMatchedCorrelationCrossover.java (96%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/ea/alterer/crossover/PartiallyMatchedCorrelationCrossoverMemento.java (85%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/ea/alterer/crossover/SinglePointCorrelationCrossover.java (96%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/ea/alterer/crossover/SinglePointCorrelationCrossoverMemento.java (94%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/ea/alterer/crossover/UniformCorrelationCrossover.java (97%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/ea/alterer/crossover/UniformCorrelationCrossoverMemento.java (96%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/ea/alterer/internal/AbstractCorrelationAlterer.java (100%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/ea/alterer/internal/CorrelationCombineAlterer.java (97%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/ea/alterer/internal/CorrelationRecombinator.java (100%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/ea/alterer/internal/MeanCorrelationAlterer.java (92%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/ea/alterer/mutator/CorrelationMutator.java (98%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/ea/alterer/mutator/CorrelationMutatorFactory.java (91%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/ea/alterer/mutator/CorrelationMutatorMemento.java (80%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/ea/alterer/mutator/GaussianCorrelationMutator.java (96%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/ea/alterer/mutator/GaussianCorrelationMutatorMemento.java (94%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/ea/alterer/mutator/SingleBitFlipCorrelationMutator.java (98%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/ea/alterer/mutator/SingleBitFlipCorrelationMutatorMemento.java (97%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/ea/alterer/mutator/SingleBitFlipMutator.java (98%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/ea/alterer/mutator/SwapCorrelationMutator.java (96%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/ea/alterer/mutator/SwapCorrelationMutatorMemento.java (88%)
create mode 100644 src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/DynamicCodec.java
create mode 100644 src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/DynamicCodecProducer.java
create mode 100644 src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/chromosome/DynamicBitChromosome.java
create mode 100644 src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/chromosome/DynamicBoundedChromosome.java
create mode 100644 src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/chromosome/DynamicChromosome.java
create mode 100644 src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/chromosome/DynamicChromosomeFactory.java
create mode 100644 src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/chromosome/DynamicDoubleChromosome.java
create mode 100644 src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/chromosome/DynamicGrayChromosome.java
create mode 100644 src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/chromosome/DynamicScaledChromosome.java
create mode 100644 src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/initial/RandomProducer.java
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/ea/model/Correlation.java (93%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/ea/model/Correlations.java (87%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/ea/model/Range.java (85%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/ea/model/RangedCorrelation.java (93%)
rename src/core/{attic/de/evoal/core/main/ea => de.evoal.core/src/main/java/de/evoal/core/main/ea/producer}/SelectorFactory.java (99%)
create mode 100644 src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/AbstractBoundedChromosome.java
create mode 100644 src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/BitChromosome.java
rename src/core/{attic/de/evoal/core/main/ea/chromosomes => de.evoal.core/src/main/java/de/evoal/core/main/jenetics}/BitHelper.java (96%)
rename src/core/{attic/de/evoal/core/main/ea/chromosomes => de.evoal.core/src/main/java/de/evoal/core/main/jenetics}/BoundedBitChromosome.java (93%)
create mode 100644 src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/BoundedDoubleChromosome.java
create mode 100644 src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/BoundedDoubleGene.java
create mode 100644 src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/BoundedOperations.java
rename src/core/{attic/de/evoal/core/main/ea/chromosomes => de.evoal.core/src/main/java/de/evoal/core/main/jenetics}/DecimalFactory.java (91%)
rename src/core/{attic/de/evoal/core/main/ea/chromosomes => de.evoal.core/src/main/java/de/evoal/core/main/jenetics}/GrayBoundedBitChromosome.java (90%)
rename src/core/{attic/de/evoal/core/main/ea/chromosomes => de.evoal.core/src/main/java/de/evoal/core/main/jenetics}/GrayHelper.java (96%)
rename src/core/{attic/de/evoal/core/main/ea/chromosomes => de.evoal.core/src/main/java/de/evoal/core/main/jenetics}/NaiveBoundedBitChromosome.java (88%)
create mode 100644 src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/VariableChromosome.java
create mode 100644 src/core/de.evoal.core/src/main/java/de/evoal/core/main/producer/MockupProducer.java
create mode 100644 src/core/de.evoal.core/src/main/java/de/evoal/core/main/producer/SpecificationProducer.java
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/search/HeuristicSearchEvaluation.java (84%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/statistics/fitness/FitnessStatistics.java (74%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/statistics/individuals/IndividualStatistics.java (87%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/statistics/nop/NopStatistics.java (78%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/statistics/writer/csv/CsvStrategy.java (100%)
rename src/core/{attic => de.evoal.core/src/main/java}/de/evoal/core/main/statistics/writer/csv/CsvWriter.java (100%)
create mode 100644 src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/cdi/TargetPointLoader.java
create mode 100644 src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/ea/TrainingDataProducer.java
create mode 100644 src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/ea/TrainingProducer.java
create mode 100644 src/core/de.evoal.surrogate.neural/pom.xml
create mode 100644 src/core/de.evoal.surrogate.neural/src/main/java/de/evoal/surrogates/neural/EvoalDataSetIterator.java
create mode 100644 src/core/de.evoal.surrogate.neural/src/main/java/de/evoal/surrogates/neural/NeuralNetworkConfigurator.java
create mode 100644 src/core/de.evoal.surrogate.neural/src/main/java/de/evoal/surrogates/neural/NeuralNetworkHelper.java
create mode 100644 src/core/de.evoal.surrogate.neural/src/main/java/de/evoal/surrogates/neural/SimpleNeuralNetwork.java
create mode 100644 src/core/de.evoal.surrogate.neural/src/main/java/de/evoal/surrogates/neural/SimpleNeuralNetworkFactory.java
create mode 100644 src/core/de.evoal.surrogate.neural/src/main/java/module-info.java
diff --git a/src/core/attic/de/evoal/core/main/ea/chromosomes/BoundedOperations.java b/src/core/attic/de/evoal/core/main/ea/chromosomes/BoundedOperations.java
deleted file mode 100644
index cd8cca01..00000000
--- a/src/core/attic/de/evoal/core/main/ea/chromosomes/BoundedOperations.java
+++ /dev/null
@@ -1,46 +0,0 @@
-package de.evoal.core.main.ea.chromosomes;
-
-import io.jenetics.util.RandomRegistry;
-
-import java.util.random.RandomGenerator;
-
-public final class BoundedOperations {
- /**
- * Use bounded operations.
- */
- private static boolean useBoundedOperations = true;
-
- private BoundedOperations() {
- }
-
- public static void setUseBoundedOperations(final boolean useBoundedOperations) {
- BoundedOperations.useBoundedOperations = useBoundedOperations;
- }
-
- public static double boundValue(final double value, final double min, final double max) {
- if(useBoundedOperations) {
- return Math.min(max, Math.max(min, value));
- } else {
- return value;
- }
- }
-
- public static boolean isValid(final double value, final double min, final double max) {
- if(useBoundedOperations) {
- return Double.compare(value, min) >= 0 &&
- Double.compare(value, max) < 0;
-
- } else {
- return true;
- }
- }
-
- public static double random(final double min, final double max) {
- final RandomGenerator random = RandomRegistry.random();
- if(useBoundedOperations) {
- return random.nextDouble(min, max);
- } else {
- return random.nextDouble(-100_000_000 , 100_000_000);
- }
- }
-}
diff --git a/src/core/attic/de/evoal/core/main/ea/gene/DynamicChromosome.java b/src/core/attic/de/evoal/core/main/ea/gene/DynamicChromosome.java
deleted file mode 100644
index 6c506a4e..00000000
--- a/src/core/attic/de/evoal/core/main/ea/gene/DynamicChromosome.java
+++ /dev/null
@@ -1,41 +0,0 @@
-package de.evoal.core.main.ea.gene;
-
-import de.evoal.core.api.properties.PropertiesSpecification;
-import de.evoal.core.api.properties.PropertySpecification;
-import io.jenetics.AbstractChromosome;
-
-import io.jenetics.util.ISeq;
-
-public class DynamicChromosome<G extends DynamicGene<? extends Object>> extends AbstractChromosome<G> {
-
- protected DynamicChromosome(final ISeq<G> genes) {
- super(genes);
- }
-
- @Override
- public DynamicChromosome newInstance(final ISeq<G> iSeq) {
- return new DynamicChromosome(iSeq);
- }
-
- @Override
- public DynamicChromosome newInstance() {
- return new DynamicChromosome(random(_genes));
- }
-
- private static <G extends DynamicGene<? extends Object>> ISeq<G> random(final ISeq<G> template) {
- return template.stream()
- .map(DynamicGene::newInstance)
- .collect(ISeq.toISeq());
- }
-
- public static DynamicChromosome from(final PropertiesSpecification specification) {
- return new DynamicChromosome(specification.getProperties()
- .stream()
- .map(DynamicChromosome::toGene)
- .collect(ISeq.toISeq()));
- }
-
- private static DynamicGene<? extends Object> toGene(final PropertySpecification spec) {
-
- }
-}
diff --git a/src/core/attic/de/evoal/core/main/ea/gene/DynamicDoubleGene.java b/src/core/attic/de/evoal/core/main/ea/gene/DynamicDoubleGene.java
deleted file mode 100644
index ace1b582..00000000
--- a/src/core/attic/de/evoal/core/main/ea/gene/DynamicDoubleGene.java
+++ /dev/null
@@ -1,36 +0,0 @@
-package de.evoal.core.main.ea.gene;
-
-import io.jenetics.util.RandomRegistry;
-
-public class DynamicDoubleGene extends DynamicGene<Double> {
- protected DynamicDoubleGene(final Double data) {
- super(data);
- }
-
- /**
- * @param value The value to check.
- * @return
- */
- @Override
- protected boolean isValidValue(final Double value) {
- if(value == null) {
- return false;
- }
-
- return true; // TODO
- }
-
- /**
- * @return
- */
- @Override
- public DynamicGene newInstance() {
- double value = RandomRegistry.random().nextDouble();
-
- while(!isValidValue(value)) {
- value = RandomRegistry.random().nextDouble();
- }
-
- return new DynamicDoubleGene(value);
- }
-}
diff --git a/src/core/attic/de/evoal/core/main/ea/gene/DynamicEnumGene.java b/src/core/attic/de/evoal/core/main/ea/gene/DynamicEnumGene.java
deleted file mode 100644
index 4378bff9..00000000
--- a/src/core/attic/de/evoal/core/main/ea/gene/DynamicEnumGene.java
+++ /dev/null
@@ -1,35 +0,0 @@
-package de.evoal.core.main.ea.gene;
-
-import io.jenetics.util.RandomRegistry;
-
-public class DynamicEnumGene extends DynamicGene<Integer> {
- private StringUniverse literalManager;
-
- protected DynamicEnumGene(final String data, final StringUniverse manager) {
- super(manager.toID(data));
- this.literalManager = manager;
- }
-
- @Override
- protected boolean isValidValue(final Integer value) {
- if(value == null) {
- return false;
- }
-
- return literalManager.isInRange(value);
- }
-
- /**
- * @return
- */
- @Override
- public DynamicGene newInstance() {
- int value = RandomRegistry.random().nextInt(0, literalManager.lastId() + 1);
-
- while(!isValidValue(value)) {
- value = RandomRegistry.random().nextInt();
- }
-
- return new DynamicEnumGene(literalManager.fetch(value), literalManager);
- }
-}
diff --git a/src/core/attic/de/evoal/core/main/ea/gene/DynamicGene.java b/src/core/attic/de/evoal/core/main/ea/gene/DynamicGene.java
deleted file mode 100644
index 57db2a91..00000000
--- a/src/core/attic/de/evoal/core/main/ea/gene/DynamicGene.java
+++ /dev/null
@@ -1,57 +0,0 @@
-package de.evoal.core.main.ea.gene;
-
-import io.jenetics.Gene;
-import lombok.extern.slf4j.Slf4j;
-
-import java.lang.reflect.InvocationTargetException;
-
-@Slf4j
-public abstract class DynamicGene<T> implements Gene<Object, DynamicGene<T>> {
-
- private T data;
-
- protected DynamicGene(final T data) {
- this.data =(T) data;
- }
-
- /**
- * @return
- */
- @Override
- public Object allele() {
- return data;
- }
-
- /**
- * @param data
- * @return
- */
- @Override
- public DynamicGene<T> newInstance(final Object data) {
- try {
- return this.getClass()
- .getConstructor(Object.class)
- .newInstance(data);
- } catch (final Exception e) {
- log.error("Failed to create new instance of gene: {}.", this, e);
- throw new RuntimeException(e);
- }
- }
-
- /**
- * @return
- */
- @Override
- public boolean isValid() {
- return isValidValue(data);
- }
-
- /**
- * Checks if the given value is a valid one for this gene.
- *
- * @param value The value to check.
- * @return iff the value is valid.
- */
- protected abstract boolean isValidValue(final T value);
-}
-
diff --git a/src/core/attic/de/evoal/core/main/ea/gene/DynamicIntegerGene.java b/src/core/attic/de/evoal/core/main/ea/gene/DynamicIntegerGene.java
deleted file mode 100644
index c16e1458..00000000
--- a/src/core/attic/de/evoal/core/main/ea/gene/DynamicIntegerGene.java
+++ /dev/null
@@ -1,32 +0,0 @@
-package de.evoal.core.main.ea.gene;
-
-import io.jenetics.util.RandomRegistry;
-
-public class DynamicIntegerGene extends DynamicGene<Integer> {
- protected DynamicIntegerGene(final Integer data) {
- super(data);
- }
-
- @Override
- protected boolean isValidValue(final Integer value) {
- if(value == null) {
- return false;
- }
-
- return true;
- }
-
- /**
- * @return
- */
- @Override
- public DynamicGene newInstance() {
- int value = RandomRegistry.random().nextInt();
-
- while(!isValidValue(value)) {
- value = RandomRegistry.random().nextInt();
- }
-
- return new DynamicIntegerGene(value);
- }
-}
diff --git a/src/core/attic/de/evoal/core/main/ea/gene/StringUniverse.java b/src/core/attic/de/evoal/core/main/ea/gene/StringUniverse.java
deleted file mode 100644
index b2ba822f..00000000
--- a/src/core/attic/de/evoal/core/main/ea/gene/StringUniverse.java
+++ /dev/null
@@ -1,46 +0,0 @@
-package de.evoal.core.main.ea.gene;
-
-import lombok.Getter;
-import lombok.Setter;
-
-import java.util.HashMap;
-import java.util.Map;
-
-public class StringUniverse {
-
- private final Map<String, Integer> literals = new HashMap<>();
-
- @Getter
- @Setter
- private boolean sealed = false;
-
- public int toID(final String data) {
- Integer id = literals.get(data);
-
- if(id == null && isSealed()) {
- throw new IllegalStateException("The string '" + data + "' is an unknown literal.");
- } else if(id == null) {
- id = literals.size();
- literals.put(data, id);
- }
-
- return id;
- }
-
- public boolean isInRange(final int value) {
- return value >= 0 && value < literals.size();
- }
-
- public int lastId() {
- return literals.size() - 1;
- }
-
- public String fetch(final int value) {
- return literals.entrySet()
- .stream()
- .filter(e -> e.getValue().intValue() == value)
- .findFirst()
- .get()
- .getKey();
- }
-}
diff --git a/src/core/de.evoal.core/pom.xml b/src/core/de.evoal.core/pom.xml
index 4bc7b345..b2282d96 100644
--- a/src/core/de.evoal.core/pom.xml
+++ b/src/core/de.evoal.core/pom.xml
@@ -313,6 +313,10 @@
<compilerArgs>
<arg>--add-exports</arg>
<arg>io.jenetics.base/io.jenetics.internal.math=de.evoal.core</arg>
+ <arg>--add-exports</arg>
+ <arg>io.jenetics.base/io.jenetics.internal.util=de.evoal.core</arg>
+ <arg>--add-exports</arg>
+ <arg>io.jenetics.base/io.jenetics.internal.collection=de.evoal.core</arg>
</compilerArgs>
<forceJavacCompilerUse>true</forceJavacCompilerUse>
</configuration>
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/api/board/BlackboardEntry.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/api/board/BlackboardEntry.java
index 678b5fd9..b3e466e6 100644
--- a/src/core/de.evoal.core/src/main/java/de/evoal/core/api/board/BlackboardEntry.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/api/board/BlackboardEntry.java
@@ -5,7 +5,7 @@ public final class BlackboardEntry {
/**
* The target properties to search for.
*/
- public static final String TARGET_PROPERTIES = "TARGET_PROPERTIES";
+ public static final String TARGET_PROPERTIES = "core:target-properties";
// public static final String TARGET_PROPERTIES_SOURCE = "TARGET_PROPERTIES_SOURCE";
@@ -14,15 +14,10 @@ public final class BlackboardEntry {
*/
// public static final String CONSTRAINT_VALIDATION_FOLDER = "CONSTRAINT_VALIDATION_FOLDER";
- /**
- * Chooses the evaluation kind.
- */
-// public static final String EVALUATION = "EVALUATION";
-
/**
* Number of evaluation runs.
*/
-// public static final String EVALUATION_ITERATIONS = "EVALUATION_ITERATIONS";
+ public static final String EVALUATION_ITERATIONS = "core:evaluation-iterations";
/**
* The evaluation run number.
@@ -59,20 +54,6 @@ public final class BlackboardEntry {
*/
public static final String MAIN = "core:main";
- /**
- * The trained predictive function
- */
-// public static final String PREDICTIVE_FUNCTION = "PREDICTIVE_FUNCTION";
-
- /**
- * The predictive configuration to use
- */
-// public static final String PREDICTIVE_FUNCTION_CONFIGURATION = "PREDICTIVE_FUNCTION_CONFIGURATION";
-
- /**
- * File containing the predictive function file.
- */
-// public static final String PREDICTIVE_FUNCTION_FILE = "PREDICTIVE_FUNCTION_FILE";
/**
* Targets.
@@ -82,12 +63,7 @@ public final class BlackboardEntry {
/**
* File containing targets for evaluation.
*/
-// public static final String TARGETS_FILE = "TARGETS_FILE";
-
- /**
- * File containing the training points.
- */
-// public static final String TRAINING_POINT_FILE = "TRAINING_POINT_FILE";
+ public static final String TARGET_POINTS_FILE = "core:target-points-file";
private final String label;
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/api/cdi/BeanFactory.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/api/cdi/BeanFactory.java
index f7b90f12..61545d04 100644
--- a/src/core/de.evoal.core/src/main/java/de/evoal/core/api/cdi/BeanFactory.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/api/cdi/BeanFactory.java
@@ -1,5 +1,6 @@
package de.evoal.core.api.cdi;
+import de.evoal.core.api.ea.initial.InitialPopulation;
import de.evoal.core.api.utils.Requirements;
import lombok.extern.slf4j.Slf4j;
import org.apache.deltaspike.core.api.provider.BeanProvider;
@@ -22,17 +23,20 @@ public final class BeanFactory {
log.info("Creating bean of type {}.", type);
try {
return BeanProvider.getContextualReference(type);
- } catch(final IllegalStateException e) {
+ } catch(final IllegalStateException | IllegalArgumentException e) {
log.error("Failed to create contextual reference of type '{}'.", type);
- final Set<Bean<T>> beans = BeanProvider.getBeanDefinitions(type, true, true);
-
- final String existingBeans = beans.stream().map(Bean::getName).collect(Collectors.joining(", "));
- log.error(" existing beans are: {}", existingBeans);
-
+ logInstantiationError(type, e);
throw e;
}
}
+ private static <T> void logInstantiationError(Class<T> type, RuntimeException e) {
+ final Set<Bean<T>> beans = BeanProvider.getBeanDefinitions(type, true, true);
+
+ final String existingBeans = beans.stream().map(Bean::getName).collect(Collectors.joining(", "));
+ log.error(" existing beans are: {}", existingBeans);
+ }
+
/**
* Returns an instance of the given {@code type} and the given {@code name}.
* If necessary, the instance is created.
@@ -50,14 +54,14 @@ public final class BeanFactory {
try {
return BeanProvider.getContextualReference(name, false, type);
- } catch(final IllegalStateException e) {
+ } catch(final IllegalStateException | IllegalArgumentException e) {
log.error("Failed to create contextual reference of type '{}' with name '{}'.", type, name);
- final Set<Bean<T>> beans = BeanProvider.getBeanDefinitions(type, true, true);
-
- final String existingBeans = beans.stream().map(Bean::getName).collect(Collectors.joining(", "));
- log.error(" existing beans are: {}", existingBeans);
-
+ logInstantiationError(type, e);
throw e;
}
}
+
+ public static void injectFields(final Object instance) {
+ BeanProvider.injectFields(instance);
+ }
}
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/api/ea/codec/CustomCodec.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/api/ea/codec/CustomCodec.java
index fac1ddb7..683b2d94 100644
--- a/src/core/de.evoal.core/src/main/java/de/evoal/core/api/ea/codec/CustomCodec.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/api/ea/codec/CustomCodec.java
@@ -11,6 +11,7 @@ import io.jenetics.engine.Codec;
* @param <G> The gene type.
*/
public interface CustomCodec<G extends Gene<?, G>> extends Codec<Properties, G> {
+
/**
* Encodes an individual according to the codes into a genotype.
*
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/api/ea/fitness/comparator/FitnessValue.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/api/ea/fitness/comparator/FitnessValue.java
index fb8253ad..6b0e79e2 100644
--- a/src/core/de.evoal.core/src/main/java/de/evoal/core/api/ea/fitness/comparator/FitnessValue.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/api/ea/fitness/comparator/FitnessValue.java
@@ -4,4 +4,8 @@ package de.evoal.core.api.ea.fitness.comparator;
* The fitness value is an abstract type that allows comparing them.
*/
public interface FitnessValue extends Comparable<FitnessValue> {
+ /**
+ * @return A list of serializable information for fitness value statistics.
+ */
+ public Object [] toStatistics();
}
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/api/ea/initial/InitialPopulation.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/api/ea/initial/InitialPopulation.java
index 445e3335..1d419270 100644
--- a/src/core/de.evoal.core/src/main/java/de/evoal/core/api/ea/initial/InitialPopulation.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/api/ea/initial/InitialPopulation.java
@@ -8,8 +8,7 @@ import io.jenetics.engine.EvolutionStream;
import java.util.function.Function;
public interface InitialPopulation<G extends Gene<?, G>, C extends Comparable<C>> {
- InitialPopulation init(Instance initialization);
+ InitialPopulation init(final Instance initialization);
public EvolutionStream<G, C> create(final Engine<G, C> engine);
-
}
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/api/properties/Properties.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/api/properties/Properties.java
index ad55de2c..7b100609 100644
--- a/src/core/de.evoal.core/src/main/java/de/evoal/core/api/properties/Properties.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/api/properties/Properties.java
@@ -7,19 +7,27 @@ import java.util.Objects;
public class Properties {
private final PropertiesSpecification specification;
- private final double[] values;
+ private final Object[] values;
public Properties(final PropertiesSpecification specification) {
this.specification = specification;
- this.values = new double[specification.properties.size()];
+ this.values = new Object[specification.properties.size()];
}
- public Properties(final PropertiesSpecification specification, final double[] data) {
+ public Properties(final PropertiesSpecification specification, final Object[] data) {
this(specification);
System.arraycopy(data, 0, this.values, 0, data.length);
}
+ public Properties(final PropertiesSpecification specification, final double[] data) {
+ this(specification);
+
+ for(int i = 0; i < data.length; ++i) {
+ this.values[i] = data[i];
+ }
+ }
+
public Properties(final Properties other) {
this(other.specification, other.values);
}
@@ -34,23 +42,41 @@ public class Properties {
return result;
}
- public double get(int i) {
+ public Object get(int i) {
return values[i];
}
- public double get(final PropertySpecification spec) {
+ public Double getAsDouble(int i) {
+ return (Double)values[i];
+ }
+
+ public Object get(final PropertySpecification spec) {
return values[specification.indexOf(spec)];
}
+ public Double getAsDouble(final PropertySpecification spec) {
+ return (Double)values[specification.indexOf(spec)];
+ }
+
public PropertiesSpecification getSpecification() {
return specification;
}
- public double[] getValues() {
+ public Object[] getValues() {
+ return values;
+ }
+
+ public double[] getValuesAsDouble() {
+ final double [] values = new double[this.values.length];
+
+ for(int i = 0; i < values.length; ++i) {
+ values[i] = (Double)this.values[i];
+ }
+
return values;
}
- public final double put(final PropertySpecification property, double d) {
+ public final Object put(final PropertySpecification property, Object d) {
final Integer index = specification.indices.get(property);
if(index == null) {
@@ -60,11 +86,11 @@ public class Properties {
return put(index, d);
}
- public final double put(final int index, double d) {
+ public final Object put(final int index, Object d) {
return values[index] = d;
}
- public void set(final int index, final double value) {
+ public void set(final int index, final Object value) {
values[index] = value;
}
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/api/properties/PropertiesSpecification.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/api/properties/PropertiesSpecification.java
index 3cd82ef4..c5b02923 100644
--- a/src/core/de.evoal.core/src/main/java/de/evoal/core/api/properties/PropertiesSpecification.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/api/properties/PropertiesSpecification.java
@@ -81,6 +81,10 @@ public class PropertiesSpecification {
return this.indices.containsKey(spec);
}
+ public PropertySpecification get(final int i) {
+ return properties.get(i);
+ }
+
public List<PropertySpecification> getProperties() {
return Collections.unmodifiableList(properties);
}
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/api/properties/io/PropertiesWriter.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/api/properties/io/PropertiesWriter.java
index ce615e5b..21b887eb 100644
--- a/src/core/de.evoal.core/src/main/java/de/evoal/core/api/properties/io/PropertiesWriter.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/api/properties/io/PropertiesWriter.java
@@ -28,7 +28,17 @@ public class PropertiesWriter implements AutoCloseable {
for(final PropertySpecification spec : properties.getSpecification().getProperties()) {
jsonGenerator.writeStartObject();
jsonGenerator.writeStringField("name", spec.name());
- jsonGenerator.writeNumberField("value", properties.get(spec));
+
+ final Object value = properties.get(spec);
+ if(value instanceof Double || value instanceof Float) {
+ jsonGenerator.writeNumberField("value", ((Number)properties.get(spec)).doubleValue());
+ } else if(value instanceof Integer) {
+ jsonGenerator.writeNumberField("value", ((Number)properties.get(spec)).longValue());
+ } else if(value instanceof Boolean) {
+ jsonGenerator.writeBooleanField("value", (Boolean)properties.get(spec));
+ } else if(value instanceof String) {
+ jsonGenerator.writeStringField("value", (String)properties.get(spec));
+ }
jsonGenerator.writeEndObject();
}
jsonGenerator.writeEndArray();
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/api/properties/stream/PropertiesBasedPropertiesStreamSupplier.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/api/properties/stream/PropertiesBasedPropertiesStreamSupplier.java
index f69a76b9..2a037c5f 100644
--- a/src/core/de.evoal.core/src/main/java/de/evoal/core/api/properties/stream/PropertiesBasedPropertiesStreamSupplier.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/api/properties/stream/PropertiesBasedPropertiesStreamSupplier.java
@@ -31,4 +31,8 @@ public class PropertiesBasedPropertiesStreamSupplier implements PropertiesStream
public Stream<Properties> get() {
return properties.stream();
}
+
+ public int size() {
+ return properties.size();
+ }
}
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/api/utils/LanguageHelper.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/api/utils/LanguageHelper.java
index 513106d7..3bff0b7c 100644
--- a/src/core/de.evoal.core/src/main/java/de/evoal/core/api/utils/LanguageHelper.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/api/utils/LanguageHelper.java
@@ -30,32 +30,23 @@ public final class LanguageHelper {
for(final String part : parts) {
try {
if(!(current instanceof Instance)) {
- log.error("Failed to lookup part '{}' of path '{}'.", part, path);
+ log.error("Failed to lookup part '{}' of path '{}' in '{}'.", part, path, current);
throw new IllegalStateException("EA configuration is not valid.");
}
- boolean foundAttribute = false;
- for(final Attribute attr : ((Instance)current).getAttributes()) {
- final NameOrMisc nom = attr.getName();
+ final Attribute attribute = ((Instance)current).findAttribute(part);
- if(nom instanceof Misc && ((Misc)nom).getName().equals(part)) {
- current = attr.getValue();
- foundAttribute = true;
- break;
- } else if(nom instanceof Name && ((Name)nom).getName().getName().equals(part)) {
- current = attr.getValue();
- foundAttribute = true;
- break;
- }
- }
-
- if(!foundAttribute && "name".equals(part)) {
+ if(attribute != null) {
+ current = attribute.getValue();
+ } else if("name".equals(part)) {
current = ((Instance)current).getName().getName();
- foundAttribute = true;
- }
-
- if(!foundAttribute) {
- log.error("Failed to lookup part '{}' of path '{}'. Returning null.", part, path);
+ } else {
+ log.warn("Failed to lookup part '{}' of path '{}'. Returning null.", part, path);
+ log.warn("Current instance is: {}", ((Instance) current).getName().getName());
+ log.warn("Available attributes:");
+ for(final Attribute a : ((Instance) current).getAttributes()) {
+ log.warn(" {}", ((Name)a.getName()).getName().getName());
+ }
return null;
}
} catch(final NullPointerException e) {
@@ -78,8 +69,11 @@ public final class LanguageHelper {
}
}
- log.debug("Mapping " + path + " to " + current + " of type " + current.getClass());
-
+ if(current instanceof Instance) {
+ log.debug("Mapping '{}' to instance with name '{}'.", path, ((Instance)current).getName().getName());
+ } else {
+ log.debug("Mapping '{}' to '{}'.", path, current);
+ }
return (T) current;
}
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/api/utils/Requirements.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/api/utils/Requirements.java
index b608b1e5..597a496b 100644
--- a/src/core/de.evoal.core/src/main/java/de/evoal/core/api/utils/Requirements.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/api/utils/Requirements.java
@@ -41,6 +41,24 @@ public final class Requirements {
}
}
+ /**
+ * Requires the arrays to be present and of same size.
+ *
+ * @param a The first array.
+ * @param b The second array.
+ *
+ * @throws NullPointerException iff either {@code a} or {@code b} is {@code null}.
+ * @throws IllegalArgumentException iff the size of {@code a} and {@code b} differ.
+ */
+ public static <T>void requireSameSize(final double [] a, final T [] b) {
+ Objects.requireNonNull(a, "Array is not allowed to be null");
+ Objects.requireNonNull(b, "Array is not allowed to be null");
+
+ if(a.length != b.length) {
+ throw new IllegalArgumentException("Arrays are expected to have the same size: " + a.length + " -- " + b.length);
+ }
+ }
+
/**
* Requires the collections to be present and of same size.
*
diff --git a/src/core/attic/de/evoal/core/main/ea/alterer/AltererFactory.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/AltererFactory.java
similarity index 67%
rename from src/core/attic/de/evoal/core/main/ea/alterer/AltererFactory.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/AltererFactory.java
index 26927ebf..63fd72cc 100644
--- a/src/core/attic/de/evoal/core/main/ea/alterer/AltererFactory.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/AltererFactory.java
@@ -2,15 +2,15 @@ package de.evoal.core.main.ea.alterer;
import java.util.function.BiFunction;
-import de.evoal.core.main.ea.alterer.internal.MeanCorrelationAlterer;
+import de.evoal.core.api.ea.fitness.comparator.FitnessValue;
import de.evoal.core.main.ea.alterer.crossover.*;
-import de.evoal.core.main.ea.functions.correlation.model.Correlations;
-import de.evoal.languages.model.instance.Instance;
-import de.evoal.core.api.utils.LanguageHelper;
+import de.evoal.core.main.ea.alterer.internal.MeanCorrelationAlterer;
import de.evoal.core.main.ea.alterer.mutator.SingleBitFlipCorrelationMutator;
import de.evoal.core.main.ea.alterer.mutator.SingleBitFlipMutator;
import de.evoal.core.main.ea.alterer.mutator.SwapCorrelationMutator;
-import de.evoal.core.api.ea.fitness.type.FitnessType;
+import de.evoal.core.main.ea.model.Correlations;
+import de.evoal.languages.model.instance.Instance;
+import de.evoal.core.api.utils.LanguageHelper;
import io.jenetics.*;
import io.jenetics.util.Mean;
import javax.enterprise.context.ApplicationScoped;
@@ -36,7 +36,7 @@ public class AltererFactory {
* <li>None</li>
* </ul>
*/
- public <G extends Gene<?, G>> Alterer<G, FitnessType> create(final Instance config) {
+ public <G extends Gene<?, G>> Alterer<G, FitnessValue> create(final Instance config) {
final String name = LanguageHelper.lookup(config, "name");
log.info("Creating alterer with name '{}'.", name);
@@ -44,7 +44,7 @@ public class AltererFactory {
switch(name) {
//case "CompositeAlterer": return createCompositeAlterer(config);
case "mean_alterer": return createMeanAlterer(config);
- case "correlation_mean_alterer": return (Alterer<G, FitnessType>) createCorrelationMeanAlterer(config);
+ case "correlation_mean_alterer": return (Alterer<G, FitnessValue>) createCorrelationMeanAlterer(config);
case "partial_matched_alterer": return createPartiallyMatchedAlterer(config);
case "correlation_partial_matched_alterer": return createCorrelationPartiallyMatchedAlterer(config);
@@ -68,128 +68,128 @@ public class AltererFactory {
throw new IllegalStateException("Selector '" + name + "' is unknown.");
}
- private <G extends Gene<?, G>> Alterer<G, FitnessType> createUniformCrossover(final Instance config) {
+ private <G extends Gene<?, G>> Alterer<G, FitnessValue> createUniformCrossover(final Instance config) {
final Double crossoverProbability = LanguageHelper.lookup(config, "crossover_probability");
final Double swapProbability = LanguageHelper.lookup(config,"swap_probability");
return new UniformCrossover<>(crossoverProbability, swapProbability);
}
- private <G extends Gene<?, G>> Alterer<G, FitnessType> createCorrelationUniformCrossover(final Instance config) {
+ private <G extends Gene<?, G>> Alterer<G, FitnessValue> createCorrelationUniformCrossover(final Instance config) {
final Double crossoverProbability = LanguageHelper.lookup(config, "crossover_probability");
final Double swapProbability = LanguageHelper.lookup(config,"swap_probability");
return new UniformCorrelationCrossover(crossoverProbability, swapProbability, correlations);
}
- private <G extends Gene<?, G>> Alterer<G, FitnessType> createBitFlipMutator (final Instance config) {
+ private <G extends Gene<?, G>> Alterer<G, FitnessValue> createBitFlipMutator (final Instance config) {
final Double probability = LanguageHelper.lookup(config, "probability");
return new SingleBitFlipMutator(probability);
}
- private <G extends Gene<?, G>> Alterer<G, FitnessType> createCorrelationBitFlipMutator (final Instance config) {
+ private <G extends Gene<?, G>> Alterer<G, FitnessValue> createCorrelationBitFlipMutator (final Instance config) {
final Double probability = LanguageHelper.lookup(config, "probability");
final Double threshold = LanguageHelper.lookup(config, "threshold");
return new SingleBitFlipCorrelationMutator(probability, threshold, correlations);
}
- private <G extends Gene<?, G>> Alterer<G, FitnessType> createSwapMutator (final Instance config) {
+ private <G extends Gene<?, G>> Alterer<G, FitnessValue> createSwapMutator (final Instance config) {
final Double probability = LanguageHelper.lookup(config, "probability");
return new SwapMutator<>(probability);
}
- private <G extends Gene<?, G>> Alterer<G, FitnessType> createCorrelationSwapMutator (final Instance config) {
+ private <G extends Gene<?, G>> Alterer<G, FitnessValue> createCorrelationSwapMutator (final Instance config) {
final Double probability = LanguageHelper.lookup(config, "probability");
final Double threshold = LanguageHelper.lookup(config, "threshold");
return new SwapCorrelationMutator<>(probability, threshold, correlations);
}
- private <G extends Gene<?, G>> Alterer<G, FitnessType> createSinglePointCrossover(final Instance config) {
+ private <G extends Gene<?, G>> Alterer<G, FitnessValue> createSinglePointCrossover(final Instance config) {
final Double probability = LanguageHelper.lookup(config, "probability");
return new SinglePointCrossover<>(probability);
}
- private <G extends Gene<?, G>> Alterer<G, FitnessType> createCorrelationSinglePointCrossover(final Instance config) {
+ private <G extends Gene<?, G>> Alterer<G, FitnessValue> createCorrelationSinglePointCrossover(final Instance config) {
final Double probability = LanguageHelper.lookup(config, "probability");
return new SinglePointCorrelationCrossover(probability, correlations);
}
- private <G extends Gene<?, G>> Alterer<G, FitnessType> createPartiallyMatchedAlterer(final Instance config) {
+ private <G extends Gene<?, G>> Alterer<G, FitnessValue> createPartiallyMatchedAlterer(final Instance config) {
final Double probability = LanguageHelper.lookup(config, "probability");
- return (Alterer<G, FitnessType>) new PartiallyMatchedCrossover(probability);
+ return (Alterer<G, FitnessValue>) new PartiallyMatchedCrossover(probability);
}
- private <G extends Gene<?, G>> Alterer<G, FitnessType> createCorrelationPartiallyMatchedAlterer(final Instance config) {
+ private <G extends Gene<?, G>> Alterer<G, FitnessValue> createCorrelationPartiallyMatchedAlterer(final Instance config) {
final Double probability = LanguageHelper.lookup(config, "probability");
- return (Alterer<G, FitnessType>) new PartiallyMatchedCorrelationCrossover<G, FitnessType>(probability, correlations);
+ return (Alterer<G, FitnessValue>) new PartiallyMatchedCorrelationCrossover<G, FitnessValue>(probability, correlations);
}
- private <G extends Gene<?, G>> Alterer<G, FitnessType> createMultiPointCrossover(final Instance config) {
+ private <G extends Gene<?, G>> Alterer<G, FitnessValue> createMultiPointCrossover(final Instance config) {
final Double probability = LanguageHelper.lookup(config, "probability");
final Integer count = LanguageHelper.lookup(config, "count");
return new MultiPointCrossover<>(probability, count);
}
- private <G extends Gene<?, G>> Alterer<G, FitnessType> createCorrelationMultiPointCrossover(final Instance config) {
+ private <G extends Gene<?, G>> Alterer<G, FitnessValue> createCorrelationMultiPointCrossover(final Instance config) {
final Double probability = LanguageHelper.lookup(config, "probability");
final Integer count = LanguageHelper.lookup(config, "count");
return new MultiPointCorrelationCrossover<>(probability, count, correlations);
}
- private <G extends Gene<?, G>> Alterer<G, FitnessType> createMeanAlterer(final Instance config) {
+ private <G extends Gene<?, G>> Alterer<G, FitnessValue> createMeanAlterer(final Instance config) {
final Double probability = LanguageHelper.lookup(config, "probability");
- return (Alterer<G, FitnessType>) new MeanAlterer(probability);
+ return (Alterer<G, FitnessValue>) new MeanAlterer(probability);
}
- private <G extends NumericGene<?, G> & Mean<G>> Alterer<G, FitnessType> createCorrelationMeanAlterer(final Instance config) {
+ private <G extends NumericGene<?, G> & Mean<G>> Alterer<G, FitnessValue> createCorrelationMeanAlterer(final Instance config) {
final Double probability = LanguageHelper.lookup(config, "probability");
- return (Alterer<G, FitnessType>) new MeanCorrelationAlterer<G, FitnessType>(probability, correlations);
+ return (Alterer<G, FitnessValue>) new MeanCorrelationAlterer<G, FitnessValue>(probability, correlations);
}
- private <G extends Gene<?, G>> Alterer<G, FitnessType> createLineCrossover(final Instance config) {
+ private <G extends Gene<?, G>> Alterer<G, FitnessValue> createLineCrossover(final Instance config) {
final Double probability = LanguageHelper.lookup(config, "probability");
final Double position = LanguageHelper.lookup(config, "position");
return new LineCrossover(probability, position);
}
- private <G extends Gene<?, G>> Alterer<G, FitnessType> createCorrelationLineCrossover(final Instance config) {
+ private <G extends Gene<?, G>> Alterer<G, FitnessValue> createCorrelationLineCrossover(final Instance config) {
final Double probability = LanguageHelper.lookup(config, "probability");
final Double position = LanguageHelper.lookup(config, "position");
return new LineCorrelationCrossover(probability, position, correlations);
}
- private <G extends Gene<?, G>> Alterer<G, FitnessType> createIntermediateCrossover(final Instance config) {
+ private <G extends Gene<?, G>> Alterer<G, FitnessValue> createIntermediateCrossover(final Instance config) {
throw new IllegalStateException("Unsupported alterer.");
}
- private <G extends Gene<?,G>> Alterer<G, FitnessType> createGaussianMutator(final Instance config) {
+ private <G extends Gene<?,G>> Alterer<G, FitnessValue> createGaussianMutator(final Instance config) {
final Double probability = LanguageHelper.lookup(config, "probability");
return new GaussianMutator(probability);
}
- private <G extends Gene<?, G>> Alterer<G, FitnessType> createGaussianCorrelationMutator(final Instance config) {
+ private <G extends Gene<?, G>> Alterer<G, FitnessValue> createGaussianCorrelationMutator(final Instance config) {
final Double probability = LanguageHelper.lookup(config, "probability");
final Double threshold = LanguageHelper.lookup(config, "threshold");
return factory.apply(probability, threshold);
}
- private <G extends Gene<?, G>> Alterer<G, FitnessType> createCompositeAlterer(final Instance config) {
+ private <G extends Gene<?, G>> Alterer<G, FitnessValue> createCompositeAlterer(final Instance config) {
throw new IllegalStateException("Unsupported alterer.");
}
}
diff --git a/src/core/attic/de/evoal/core/main/ea/alterer/crossover/CorrelationCrossover.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/CorrelationCrossover.java
similarity index 96%
rename from src/core/attic/de/evoal/core/main/ea/alterer/crossover/CorrelationCrossover.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/CorrelationCrossover.java
index c5748e3c..437f41af 100644
--- a/src/core/attic/de/evoal/core/main/ea/alterer/crossover/CorrelationCrossover.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/CorrelationCrossover.java
@@ -1,7 +1,7 @@
package de.evoal.core.main.ea.alterer.crossover;
-import de.evoal.core.main.ea.functions.correlation.model.Correlation;
-import de.evoal.core.main.ea.functions.correlation.model.Correlations;
+import de.evoal.core.main.ea.model.Correlation;
+import de.evoal.core.main.ea.model.Correlations;
import io.jenetics.*;
import io.jenetics.util.MSeq;
import io.jenetics.util.RandomRegistry;
diff --git a/src/core/attic/de/evoal/core/main/ea/alterer/crossover/CorrelationCrossoverMemento.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/CorrelationCrossoverMemento.java
similarity index 81%
rename from src/core/attic/de/evoal/core/main/ea/alterer/crossover/CorrelationCrossoverMemento.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/CorrelationCrossoverMemento.java
index 929b2210..ef0cfe21 100644
--- a/src/core/attic/de/evoal/core/main/ea/alterer/crossover/CorrelationCrossoverMemento.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/CorrelationCrossoverMemento.java
@@ -1,6 +1,6 @@
package de.evoal.core.main.ea.alterer.crossover;
-import de.evoal.core.main.ea.functions.correlation.model.Correlation;
+import de.evoal.core.main.ea.model.Correlation;
public interface CorrelationCrossoverMemento<T extends CorrelationCrossoverMemento<T>> {
diff --git a/src/core/attic/de/evoal/core/main/ea/alterer/crossover/LineCorrelationCrossover.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/LineCorrelationCrossover.java
similarity index 97%
rename from src/core/attic/de/evoal/core/main/ea/alterer/crossover/LineCorrelationCrossover.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/LineCorrelationCrossover.java
index a044d677..f3ba1352 100644
--- a/src/core/attic/de/evoal/core/main/ea/alterer/crossover/LineCorrelationCrossover.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/LineCorrelationCrossover.java
@@ -1,7 +1,7 @@
package de.evoal.core.main.ea.alterer.crossover;
import de.evoal.core.api.utils.Requirements;
-import de.evoal.core.main.ea.functions.correlation.model.Correlations;
+import de.evoal.core.main.ea.model.Correlations;
import io.jenetics.NumericGene;
import io.jenetics.util.MSeq;
diff --git a/src/core/attic/de/evoal/core/main/ea/alterer/crossover/LineCorrelationCrossoverMemento.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/LineCorrelationCrossoverMemento.java
similarity index 91%
rename from src/core/attic/de/evoal/core/main/ea/alterer/crossover/LineCorrelationCrossoverMemento.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/LineCorrelationCrossoverMemento.java
index 3ddd0104..aa2a2082 100644
--- a/src/core/attic/de/evoal/core/main/ea/alterer/crossover/LineCorrelationCrossoverMemento.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/LineCorrelationCrossoverMemento.java
@@ -1,6 +1,6 @@
package de.evoal.core.main.ea.alterer.crossover;
-import de.evoal.core.main.ea.functions.correlation.model.Correlation;
+import de.evoal.core.main.ea.model.Correlation;
import io.jenetics.util.RandomRegistry;
import lombok.Data;
diff --git a/src/core/attic/de/evoal/core/main/ea/alterer/crossover/MultiPointCorrelationCrossover.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/MultiPointCorrelationCrossover.java
similarity index 98%
rename from src/core/attic/de/evoal/core/main/ea/alterer/crossover/MultiPointCorrelationCrossover.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/MultiPointCorrelationCrossover.java
index b829f6df..86edaa38 100644
--- a/src/core/attic/de/evoal/core/main/ea/alterer/crossover/MultiPointCorrelationCrossover.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/MultiPointCorrelationCrossover.java
@@ -1,6 +1,6 @@
package de.evoal.core.main.ea.alterer.crossover;
-import de.evoal.core.main.ea.functions.correlation.model.Correlations;
+import de.evoal.core.main.ea.model.Correlations;
import io.jenetics.Gene;
import io.jenetics.util.MSeq;
diff --git a/src/core/attic/de/evoal/core/main/ea/alterer/crossover/MultiPointCorrelationCrossoverMemento.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/MultiPointCorrelationCrossoverMemento.java
similarity index 92%
rename from src/core/attic/de/evoal/core/main/ea/alterer/crossover/MultiPointCorrelationCrossoverMemento.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/MultiPointCorrelationCrossoverMemento.java
index 1bdf0e05..3c755d6c 100644
--- a/src/core/attic/de/evoal/core/main/ea/alterer/crossover/MultiPointCorrelationCrossoverMemento.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/MultiPointCorrelationCrossoverMemento.java
@@ -1,6 +1,6 @@
package de.evoal.core.main.ea.alterer.crossover;
-import de.evoal.core.main.ea.functions.correlation.model.Correlation;
+import de.evoal.core.main.ea.model.Correlation;
import io.jenetics.internal.math.Subset;
import io.jenetics.util.RandomRegistry;
diff --git a/src/core/attic/de/evoal/core/main/ea/alterer/crossover/PartiallyMatchedCorrelationCrossover.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/PartiallyMatchedCorrelationCrossover.java
similarity index 96%
rename from src/core/attic/de/evoal/core/main/ea/alterer/crossover/PartiallyMatchedCorrelationCrossover.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/PartiallyMatchedCorrelationCrossover.java
index 66977b3b..dfeb518c 100644
--- a/src/core/attic/de/evoal/core/main/ea/alterer/crossover/PartiallyMatchedCorrelationCrossover.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/PartiallyMatchedCorrelationCrossover.java
@@ -1,6 +1,6 @@
package de.evoal.core.main.ea.alterer.crossover;
-import de.evoal.core.main.ea.functions.correlation.model.Correlations;
+import de.evoal.core.main.ea.model.Correlations;
import io.jenetics.EnumGene;
import io.jenetics.util.MSeq;
diff --git a/src/core/attic/de/evoal/core/main/ea/alterer/crossover/PartiallyMatchedCorrelationCrossoverMemento.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/PartiallyMatchedCorrelationCrossoverMemento.java
similarity index 85%
rename from src/core/attic/de/evoal/core/main/ea/alterer/crossover/PartiallyMatchedCorrelationCrossoverMemento.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/PartiallyMatchedCorrelationCrossoverMemento.java
index 84615c0a..12066ed2 100644
--- a/src/core/attic/de/evoal/core/main/ea/alterer/crossover/PartiallyMatchedCorrelationCrossoverMemento.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/PartiallyMatchedCorrelationCrossoverMemento.java
@@ -1,14 +1,11 @@
package de.evoal.core.main.ea.alterer.crossover;
-import de.evoal.core.main.ea.functions.correlation.model.Correlation;
+import de.evoal.core.main.ea.model.Correlation;
import io.jenetics.internal.math.Subset;
import io.jenetics.util.RandomRegistry;
-import java.util.Random;
import java.util.random.RandomGenerator;
-import static java.lang.Math.min;
-
public class PartiallyMatchedCorrelationCrossoverMemento implements CorrelationCrossoverMemento<PartiallyMatchedCorrelationCrossoverMemento> {
private int[] points = null;
diff --git a/src/core/attic/de/evoal/core/main/ea/alterer/crossover/SinglePointCorrelationCrossover.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/SinglePointCorrelationCrossover.java
similarity index 96%
rename from src/core/attic/de/evoal/core/main/ea/alterer/crossover/SinglePointCorrelationCrossover.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/SinglePointCorrelationCrossover.java
index 42957f14..42d2e08a 100644
--- a/src/core/attic/de/evoal/core/main/ea/alterer/crossover/SinglePointCorrelationCrossover.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/SinglePointCorrelationCrossover.java
@@ -1,6 +1,6 @@
package de.evoal.core.main.ea.alterer.crossover;
-import de.evoal.core.main.ea.functions.correlation.model.Correlations;
+import de.evoal.core.main.ea.model.Correlations;
import io.jenetics.Gene;
import io.jenetics.util.MSeq;
diff --git a/src/core/attic/de/evoal/core/main/ea/alterer/crossover/SinglePointCorrelationCrossoverMemento.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/SinglePointCorrelationCrossoverMemento.java
similarity index 94%
rename from src/core/attic/de/evoal/core/main/ea/alterer/crossover/SinglePointCorrelationCrossoverMemento.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/SinglePointCorrelationCrossoverMemento.java
index 53ee1d9a..df3bb82e 100644
--- a/src/core/attic/de/evoal/core/main/ea/alterer/crossover/SinglePointCorrelationCrossoverMemento.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/SinglePointCorrelationCrossoverMemento.java
@@ -1,11 +1,10 @@
package de.evoal.core.main.ea.alterer.crossover;
-import de.evoal.core.main.ea.functions.correlation.model.Correlation;
+import de.evoal.core.main.ea.model.Correlation;
import io.jenetics.util.RandomRegistry;
import lombok.Getter;
import lombok.Setter;
-import java.util.Random;
import java.util.random.RandomGenerator;
import static java.lang.Math.min;
diff --git a/src/core/attic/de/evoal/core/main/ea/alterer/crossover/UniformCorrelationCrossover.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/UniformCorrelationCrossover.java
similarity index 97%
rename from src/core/attic/de/evoal/core/main/ea/alterer/crossover/UniformCorrelationCrossover.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/UniformCorrelationCrossover.java
index 18a6ddd8..5f611d67 100644
--- a/src/core/attic/de/evoal/core/main/ea/alterer/crossover/UniformCorrelationCrossover.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/UniformCorrelationCrossover.java
@@ -1,7 +1,7 @@
package de.evoal.core.main.ea.alterer.crossover;
import de.evoal.core.api.utils.Requirements;
-import de.evoal.core.main.ea.functions.correlation.model.Correlations;
+import de.evoal.core.main.ea.model.Correlations;
import io.jenetics.Gene;
import io.jenetics.util.MSeq;
diff --git a/src/core/attic/de/evoal/core/main/ea/alterer/crossover/UniformCorrelationCrossoverMemento.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/UniformCorrelationCrossoverMemento.java
similarity index 96%
rename from src/core/attic/de/evoal/core/main/ea/alterer/crossover/UniformCorrelationCrossoverMemento.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/UniformCorrelationCrossoverMemento.java
index 4fe2316e..c87c0a30 100644
--- a/src/core/attic/de/evoal/core/main/ea/alterer/crossover/UniformCorrelationCrossoverMemento.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/crossover/UniformCorrelationCrossoverMemento.java
@@ -1,6 +1,6 @@
package de.evoal.core.main.ea.alterer.crossover;
-import de.evoal.core.main.ea.functions.correlation.model.Correlation;
+import de.evoal.core.main.ea.model.Correlation;
import io.jenetics.util.RandomRegistry;
import lombok.Getter;
import lombok.Setter;
diff --git a/src/core/attic/de/evoal/core/main/ea/alterer/internal/AbstractCorrelationAlterer.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/internal/AbstractCorrelationAlterer.java
similarity index 100%
rename from src/core/attic/de/evoal/core/main/ea/alterer/internal/AbstractCorrelationAlterer.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/internal/AbstractCorrelationAlterer.java
diff --git a/src/core/attic/de/evoal/core/main/ea/alterer/internal/CorrelationCombineAlterer.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/internal/CorrelationCombineAlterer.java
similarity index 97%
rename from src/core/attic/de/evoal/core/main/ea/alterer/internal/CorrelationCombineAlterer.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/internal/CorrelationCombineAlterer.java
index 0ce3b1c2..4e93aaf3 100644
--- a/src/core/attic/de/evoal/core/main/ea/alterer/internal/CorrelationCombineAlterer.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/internal/CorrelationCombineAlterer.java
@@ -1,7 +1,7 @@
package de.evoal.core.main.ea.alterer.internal;
-import de.evoal.core.main.ea.functions.correlation.model.Correlation;
-import de.evoal.core.main.ea.functions.correlation.model.Correlations;
+import de.evoal.core.main.ea.model.Correlation;
+import de.evoal.core.main.ea.model.Correlations;
import io.jenetics.*;
import io.jenetics.util.BaseSeq;
import io.jenetics.util.MSeq;
diff --git a/src/core/attic/de/evoal/core/main/ea/alterer/internal/CorrelationRecombinator.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/internal/CorrelationRecombinator.java
similarity index 100%
rename from src/core/attic/de/evoal/core/main/ea/alterer/internal/CorrelationRecombinator.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/internal/CorrelationRecombinator.java
diff --git a/src/core/attic/de/evoal/core/main/ea/alterer/internal/MeanCorrelationAlterer.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/internal/MeanCorrelationAlterer.java
similarity index 92%
rename from src/core/attic/de/evoal/core/main/ea/alterer/internal/MeanCorrelationAlterer.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/internal/MeanCorrelationAlterer.java
index d8f44559..d2b8604f 100644
--- a/src/core/attic/de/evoal/core/main/ea/alterer/internal/MeanCorrelationAlterer.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/internal/MeanCorrelationAlterer.java
@@ -1,6 +1,6 @@
package de.evoal.core.main.ea.alterer.internal;
-import de.evoal.core.main.ea.functions.correlation.model.Correlations;
+import de.evoal.core.main.ea.model.Correlations;
import io.jenetics.*;
import io.jenetics.util.Mean;
diff --git a/src/core/attic/de/evoal/core/main/ea/alterer/mutator/CorrelationMutator.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/mutator/CorrelationMutator.java
similarity index 98%
rename from src/core/attic/de/evoal/core/main/ea/alterer/mutator/CorrelationMutator.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/mutator/CorrelationMutator.java
index 186e7b94..b68141c8 100644
--- a/src/core/attic/de/evoal/core/main/ea/alterer/mutator/CorrelationMutator.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/mutator/CorrelationMutator.java
@@ -1,8 +1,8 @@
package de.evoal.core.main.ea.alterer.mutator;
import de.evoal.core.main.ea.alterer.internal.AbstractCorrelationAlterer;
-import de.evoal.core.main.ea.functions.correlation.model.Correlation;
-import de.evoal.core.main.ea.functions.correlation.model.Correlations;
+import de.evoal.core.main.ea.model.Correlation;
+import de.evoal.core.main.ea.model.Correlations;
import io.jenetics.*;
import io.jenetics.internal.math.Probabilities;
import io.jenetics.util.ISeq;
diff --git a/src/core/attic/de/evoal/core/main/ea/alterer/mutator/CorrelationMutatorFactory.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/mutator/CorrelationMutatorFactory.java
similarity index 91%
rename from src/core/attic/de/evoal/core/main/ea/alterer/mutator/CorrelationMutatorFactory.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/mutator/CorrelationMutatorFactory.java
index 25b3c926..2c38a4f8 100644
--- a/src/core/attic/de/evoal/core/main/ea/alterer/mutator/CorrelationMutatorFactory.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/mutator/CorrelationMutatorFactory.java
@@ -1,7 +1,7 @@
package de.evoal.core.main.ea.alterer.mutator;
import de.evoal.core.api.board.Blackboard;
-import de.evoal.core.main.ea.functions.correlation.model.Correlations;
+import de.evoal.core.main.ea.model.Correlations;
import io.jenetics.Alterer;
import javax.enterprise.context.ApplicationScoped;
import javax.enterprise.inject.Produces;
diff --git a/src/core/attic/de/evoal/core/main/ea/alterer/mutator/CorrelationMutatorMemento.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/mutator/CorrelationMutatorMemento.java
similarity index 80%
rename from src/core/attic/de/evoal/core/main/ea/alterer/mutator/CorrelationMutatorMemento.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/mutator/CorrelationMutatorMemento.java
index e7a7eee4..ad5e1b67 100644
--- a/src/core/attic/de/evoal/core/main/ea/alterer/mutator/CorrelationMutatorMemento.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/mutator/CorrelationMutatorMemento.java
@@ -1,7 +1,7 @@
package de.evoal.core.main.ea.alterer.mutator;
-import de.evoal.core.main.ea.functions.correlation.model.Correlation;
+import de.evoal.core.main.ea.model.Correlation;
/**
* Memento to preserve the state of correlation-aware mutator.
diff --git a/src/core/attic/de/evoal/core/main/ea/alterer/mutator/GaussianCorrelationMutator.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/mutator/GaussianCorrelationMutator.java
similarity index 96%
rename from src/core/attic/de/evoal/core/main/ea/alterer/mutator/GaussianCorrelationMutator.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/mutator/GaussianCorrelationMutator.java
index 66c1b305..e8165bed 100644
--- a/src/core/attic/de/evoal/core/main/ea/alterer/mutator/GaussianCorrelationMutator.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/mutator/GaussianCorrelationMutator.java
@@ -1,6 +1,6 @@
package de.evoal.core.main.ea.alterer.mutator;
-import de.evoal.core.main.ea.functions.correlation.model.Correlations;
+import de.evoal.core.main.ea.model.Correlations;
import io.jenetics.NumericGene;
import java.util.random.RandomGenerator;
diff --git a/src/core/attic/de/evoal/core/main/ea/alterer/mutator/GaussianCorrelationMutatorMemento.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/mutator/GaussianCorrelationMutatorMemento.java
similarity index 94%
rename from src/core/attic/de/evoal/core/main/ea/alterer/mutator/GaussianCorrelationMutatorMemento.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/mutator/GaussianCorrelationMutatorMemento.java
index 15a4c49c..07e625b3 100644
--- a/src/core/attic/de/evoal/core/main/ea/alterer/mutator/GaussianCorrelationMutatorMemento.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/mutator/GaussianCorrelationMutatorMemento.java
@@ -1,6 +1,6 @@
package de.evoal.core.main.ea.alterer.mutator;
-import de.evoal.core.main.ea.functions.correlation.model.Correlation;
+import de.evoal.core.main.ea.model.Correlation;
import lombok.Data;
import java.util.Random;
diff --git a/src/core/attic/de/evoal/core/main/ea/alterer/mutator/SingleBitFlipCorrelationMutator.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/mutator/SingleBitFlipCorrelationMutator.java
similarity index 98%
rename from src/core/attic/de/evoal/core/main/ea/alterer/mutator/SingleBitFlipCorrelationMutator.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/mutator/SingleBitFlipCorrelationMutator.java
index 5eddb9e0..efb3b762 100644
--- a/src/core/attic/de/evoal/core/main/ea/alterer/mutator/SingleBitFlipCorrelationMutator.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/mutator/SingleBitFlipCorrelationMutator.java
@@ -1,6 +1,6 @@
package de.evoal.core.main.ea.alterer.mutator;
-import de.evoal.core.main.ea.functions.correlation.model.Correlations;
+import de.evoal.core.main.ea.model.Correlations;
import io.jenetics.*;
import io.jenetics.util.MSeq;
diff --git a/src/core/attic/de/evoal/core/main/ea/alterer/mutator/SingleBitFlipCorrelationMutatorMemento.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/mutator/SingleBitFlipCorrelationMutatorMemento.java
similarity index 97%
rename from src/core/attic/de/evoal/core/main/ea/alterer/mutator/SingleBitFlipCorrelationMutatorMemento.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/mutator/SingleBitFlipCorrelationMutatorMemento.java
index a1fa9d38..c2ea8f05 100644
--- a/src/core/attic/de/evoal/core/main/ea/alterer/mutator/SingleBitFlipCorrelationMutatorMemento.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/mutator/SingleBitFlipCorrelationMutatorMemento.java
@@ -1,6 +1,6 @@
package de.evoal.core.main.ea.alterer.mutator;
-import de.evoal.core.main.ea.functions.correlation.model.Correlation;
+import de.evoal.core.main.ea.model.Correlation;
import lombok.Getter;
import lombok.Setter;
diff --git a/src/core/attic/de/evoal/core/main/ea/alterer/mutator/SingleBitFlipMutator.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/mutator/SingleBitFlipMutator.java
similarity index 98%
rename from src/core/attic/de/evoal/core/main/ea/alterer/mutator/SingleBitFlipMutator.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/mutator/SingleBitFlipMutator.java
index aa03b14f..2aab3ccf 100644
--- a/src/core/attic/de/evoal/core/main/ea/alterer/mutator/SingleBitFlipMutator.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/mutator/SingleBitFlipMutator.java
@@ -3,10 +3,8 @@ package de.evoal.core.main.ea.alterer.mutator;
import io.jenetics.*;
import io.jenetics.util.MSeq;
-import java.util.Random;
import java.util.random.RandomGenerator;
-
public class SingleBitFlipMutator<
C extends Comparable<? super C>
>
diff --git a/src/core/attic/de/evoal/core/main/ea/alterer/mutator/SwapCorrelationMutator.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/mutator/SwapCorrelationMutator.java
similarity index 96%
rename from src/core/attic/de/evoal/core/main/ea/alterer/mutator/SwapCorrelationMutator.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/mutator/SwapCorrelationMutator.java
index 7f3dfc11..beecd5fe 100644
--- a/src/core/attic/de/evoal/core/main/ea/alterer/mutator/SwapCorrelationMutator.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/mutator/SwapCorrelationMutator.java
@@ -1,6 +1,6 @@
package de.evoal.core.main.ea.alterer.mutator;
-import de.evoal.core.main.ea.functions.correlation.model.Correlations;
+import de.evoal.core.main.ea.model.Correlations;
import io.jenetics.Chromosome;
import io.jenetics.Gene;
import io.jenetics.MutatorResult;
diff --git a/src/core/attic/de/evoal/core/main/ea/alterer/mutator/SwapCorrelationMutatorMemento.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/mutator/SwapCorrelationMutatorMemento.java
similarity index 88%
rename from src/core/attic/de/evoal/core/main/ea/alterer/mutator/SwapCorrelationMutatorMemento.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/mutator/SwapCorrelationMutatorMemento.java
index b8e71b71..ca6a0543 100644
--- a/src/core/attic/de/evoal/core/main/ea/alterer/mutator/SwapCorrelationMutatorMemento.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/alterer/mutator/SwapCorrelationMutatorMemento.java
@@ -1,8 +1,7 @@
package de.evoal.core.main.ea.alterer.mutator;
-import de.evoal.core.main.ea.functions.correlation.model.Correlation;
+import de.evoal.core.main.ea.model.Correlation;
-import java.util.Random;
import java.util.random.RandomGenerator;
import static io.jenetics.internal.math.Randoms.indexes;
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/DynamicCodec.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/DynamicCodec.java
new file mode 100644
index 00000000..e986cd9a
--- /dev/null
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/DynamicCodec.java
@@ -0,0 +1,107 @@
+package de.evoal.core.main.ea.codec;
+
+import de.evoal.core.api.cdi.BeanFactory;
+import de.evoal.core.api.ea.codec.CustomCodec;
+import de.evoal.core.api.properties.Properties;
+import de.evoal.core.api.properties.PropertiesSpecification;
+import de.evoal.core.main.ea.codec.chromosome.DynamicChromosome;
+import de.evoal.core.main.ea.codec.chromosome.DynamicChromosomeFactory;
+import de.evoal.languages.model.ddl.DataDescription;
+import de.evoal.languages.model.instance.Array;
+import de.evoal.languages.model.instance.Attribute;
+import de.evoal.languages.model.instance.DataReference;
+import de.evoal.languages.model.instance.Instance;
+import io.jenetics.Chromosome;
+import io.jenetics.Gene;
+import io.jenetics.Genotype;
+import io.jenetics.util.Factory;
+import lombok.extern.slf4j.Slf4j;
+
+import java.util.List;
+import java.util.function.Function;
+import java.util.stream.Collectors;
+
+@Slf4j
+public class DynamicCodec<G extends Gene<?, G>> implements CustomCodec<G> {
+
+ private final List<DynamicChromosome> dynamicTemplates;
+
+ private final PropertiesSpecification specification;
+
+ public DynamicCodec(final PropertiesSpecification specification, final List<DynamicChromosome> dynamicTemplates, final List<Chromosome<G>> jeneticsTemplates) {
+ this.specification = specification;
+ this.dynamicTemplates = dynamicTemplates;
+ }
+
+ static DynamicCodec from(final Array config) {
+ final DynamicChromosomeFactory factory = BeanFactory.create(DynamicChromosomeFactory.class);
+ final List<DynamicChromosome> chromosomes = config.getValues()
+ .stream()
+ .map(Instance.class::cast)
+ .map(factory::create)
+ .collect(Collectors.toList());
+
+ final List<Chromosome> templates = chromosomes.stream()
+ .map(DynamicChromosome::toJenetics)
+ .collect(Collectors.toList());
+
+ final PropertiesSpecification specification = PropertiesSpecification.builder()
+ .add(config.getValues()
+ .stream()
+ .map(Instance.class::cast)
+ .map(i -> i.findAttribute("genes"))
+ .map(Attribute::getValue)
+ .map(Array.class::cast)
+ .map(Array::getValues)
+ .flatMap(vs -> vs.stream()
+ .map(Instance.class::cast)
+ .map(i -> i.findAttribute("content"))
+ .map(Attribute::getValue)
+ .map(DataReference.class::cast)
+ .map(DataReference::getDefinition)
+ .map(DataDescription::getName)
+ )
+ .distinct())
+ .build();
+
+ log.info("Created dynamic codec for properties specification {}.", specification);
+
+ return new DynamicCodec(specification, chromosomes, templates);
+ }
+
+ @Override
+ public Factory<Genotype<G>> encoding() {
+ final List<Chromosome<G>> chromosomes = dynamicTemplates.stream()
+ .map(c -> (Chromosome<G>)c.toJenetics())
+ .collect(Collectors.toList());
+
+ return Genotype.of(chromosomes);
+ }
+
+ @Override
+ public Function<Genotype<G>, Properties> decoder() {
+ return this::toProperties;
+ }
+
+ private Properties toProperties(final Genotype<G> genotype) {
+ Properties result = new Properties(specification);
+
+ for(int i = 0; i < dynamicTemplates.size(); ++i) {
+ final Chromosome<G> chromosome = genotype.get(i);
+ final DynamicChromosome dynamic = dynamicTemplates.get(i);
+
+ result = dynamic.toProperties(chromosome, result);
+ }
+
+ return result;
+ }
+
+ @Override
+ public Genotype<G> encode(final Properties p) {
+ final List<Chromosome<G>> chromosomes = dynamicTemplates.stream()
+ .map(c -> (Chromosome<G>)c.toJenetics(p))
+ .collect(Collectors.toList());
+
+ return Genotype.of(chromosomes);
+ }
+}
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/DynamicCodecProducer.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/DynamicCodecProducer.java
new file mode 100644
index 00000000..17376a08
--- /dev/null
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/DynamicCodecProducer.java
@@ -0,0 +1,21 @@
+package de.evoal.core.main.ea.codec;
+
+import de.evoal.core.api.board.BlackboardEntry;
+import de.evoal.core.api.cdi.ConfigurationValue;
+import de.evoal.languages.model.instance.Array;
+import lombok.extern.slf4j.Slf4j;
+
+import javax.enterprise.context.ApplicationScoped;
+import javax.enterprise.context.Dependent;
+import javax.enterprise.inject.Produces;
+
+@ApplicationScoped
+@Slf4j
+public class DynamicCodecProducer {
+ @Produces @Dependent
+ public DynamicCodec create(@ConfigurationValue(entry = BlackboardEntry.EA_CONFIGURATION, access = "algorithm.genotype") Array config) {
+ log.info("Creating encoding for EA problem.");
+
+ return DynamicCodec.from(config);
+ }
+}
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/chromosome/DynamicBitChromosome.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/chromosome/DynamicBitChromosome.java
new file mode 100644
index 00000000..c050bb51
--- /dev/null
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/chromosome/DynamicBitChromosome.java
@@ -0,0 +1,50 @@
+package de.evoal.core.main.ea.codec.chromosome;
+
+import de.evoal.core.api.properties.Properties;
+import de.evoal.core.api.properties.PropertySpecification;
+import de.evoal.core.api.utils.Requirements;
+import de.evoal.core.main.jenetics.BitHelper;
+import de.evoal.core.main.jenetics.GrayBoundedBitChromosome;
+import de.evoal.core.main.jenetics.NaiveBoundedBitChromosome;
+import de.evoal.languages.model.el.IntegerLiteral;
+import de.evoal.languages.model.instance.Instance;
+import de.evoal.languages.model.instance.LiteralValue;
+import io.jenetics.Chromosome;
+import io.jenetics.util.DoubleRange;
+
+import javax.enterprise.context.Dependent;
+import javax.inject.Named;
+
+@Dependent
+@Named("bit-chromosome")
+public class DynamicBitChromosome extends DynamicScaledChromosome {
+
+
+ @Override
+ public Chromosome toJenetics() {
+ final DoubleRange range = ranges.get(0);
+
+ return NaiveBoundedBitChromosome.of(range.min(), range.max(), scale);
+ }
+
+ @Override
+ public Chromosome toJenetics(final Properties values) {
+ final DoubleRange range = ranges.get(0);
+ final PropertySpecification spec = specification.get(0);
+
+ return NaiveBoundedBitChromosome.of(values.getAsDouble(spec), range.min(), range.max(), scale);
+ }
+
+ @Override
+ public Properties toProperties(final Chromosome chromosome, final Properties properties) {
+ final PropertySpecification spec = specification.get(0);
+ final NaiveBoundedBitChromosome actual = (NaiveBoundedBitChromosome)chromosome;
+
+ final byte [] bytes = actual.toByteArray();
+ final double value = BitHelper.toDouble(bytes, scale);
+
+ properties.put(spec, value);
+
+ return properties;
+ }
+}
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/chromosome/DynamicBoundedChromosome.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/chromosome/DynamicBoundedChromosome.java
new file mode 100644
index 00000000..def8f445
--- /dev/null
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/chromosome/DynamicBoundedChromosome.java
@@ -0,0 +1,26 @@
+package de.evoal.core.main.ea.codec.chromosome;
+
+import de.evoal.languages.model.ddl.DataDescription;
+import de.evoal.languages.model.instance.Instance;
+import io.jenetics.util.DoubleRange;
+
+import java.util.List;
+import java.util.stream.Collectors;
+
+public abstract class DynamicBoundedChromosome extends DynamicChromosome {
+ protected List<DoubleRange> ranges;
+
+ @Override
+ public void init(final Instance specification) {
+ super.init(specification);
+
+ ranges = dataRepresented.stream()
+ .map(this::toRange)
+ .collect(Collectors.toList());
+ }
+
+ protected DoubleRange toRange(final DataDescription dataDescription) {
+ // TODO Find actual ranges from DDL
+ return DoubleRange.of(-(Double.MAX_VALUE/2), (Double.MAX_VALUE/2));
+ }
+}
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/chromosome/DynamicChromosome.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/chromosome/DynamicChromosome.java
new file mode 100644
index 00000000..94b33169
--- /dev/null
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/chromosome/DynamicChromosome.java
@@ -0,0 +1,46 @@
+package de.evoal.core.main.ea.codec.chromosome;
+
+import de.evoal.core.api.properties.Properties;
+import de.evoal.core.api.properties.PropertiesSpecification;
+import de.evoal.core.api.properties.PropertySpecification;
+import de.evoal.languages.model.ddl.DataDescription;
+import de.evoal.languages.model.instance.Array;
+import de.evoal.languages.model.instance.Attribute;
+import de.evoal.languages.model.instance.DataReference;
+import de.evoal.languages.model.instance.Instance;
+import io.jenetics.Chromosome;
+
+import java.util.Collections;
+import java.util.List;
+import java.util.stream.Collectors;
+
+public abstract class DynamicChromosome {
+ protected List<DataDescription> dataRepresented;
+ protected PropertiesSpecification specification;
+
+ public void init(final Instance specification) {
+ final Array genes = (Array)specification.findAttribute("genes")
+ .getValue();
+
+ this.dataRepresented = genes.getValues()
+ .stream()
+ .map(Instance.class::cast)
+ .map(i -> i.findAttribute("content"))
+ .map(Attribute::getValue)
+ .map(DataReference.class::cast)
+ .map(DataReference::getDefinition)
+ .collect(Collectors.toList());
+
+ this.dataRepresented = Collections.unmodifiableList(dataRepresented);
+ this.specification = PropertiesSpecification.builder()
+ .add(dataRepresented.stream()
+ .map(DataDescription::getName)
+ )
+ .build();
+ }
+
+ public abstract Chromosome toJenetics();
+ public abstract Chromosome toJenetics(final Properties values);
+
+ public abstract Properties toProperties(final Chromosome chromosome, final Properties properties);
+}
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/chromosome/DynamicChromosomeFactory.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/chromosome/DynamicChromosomeFactory.java
new file mode 100644
index 00000000..721d9388
--- /dev/null
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/chromosome/DynamicChromosomeFactory.java
@@ -0,0 +1,18 @@
+package de.evoal.core.main.ea.codec.chromosome;
+
+import de.evoal.core.api.cdi.BeanFactory;
+import de.evoal.languages.model.instance.Instance;
+
+import javax.enterprise.context.ApplicationScoped;
+
+@ApplicationScoped
+public class DynamicChromosomeFactory {
+ public DynamicChromosome create(final Instance specification) {
+ final String chromosomeName = specification.getName().getName();
+
+ final DynamicChromosome chromosome = BeanFactory.create(chromosomeName, DynamicChromosome.class);
+ chromosome.init(specification);
+
+ return chromosome;
+ }
+}
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/chromosome/DynamicDoubleChromosome.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/chromosome/DynamicDoubleChromosome.java
new file mode 100644
index 00000000..7711394b
--- /dev/null
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/chromosome/DynamicDoubleChromosome.java
@@ -0,0 +1,58 @@
+package de.evoal.core.main.ea.codec.chromosome;
+
+import de.evoal.core.api.properties.Properties;
+import de.evoal.core.api.properties.PropertySpecification;
+import de.evoal.core.main.jenetics.BoundedDoubleChromosome;
+import de.evoal.core.main.jenetics.BoundedDoubleGene;
+import de.evoal.languages.model.ddl.DataDescription;
+import de.evoal.languages.model.instance.Instance;
+import io.jenetics.Chromosome;
+import io.jenetics.util.DoubleRange;
+
+import javax.enterprise.context.Dependent;
+import javax.inject.Named;
+import java.util.ArrayList;
+import java.util.List;
+
+import java.util.stream.Collectors;
+
+@Dependent
+@Named("double-chromosome")
+public class DynamicDoubleChromosome extends DynamicBoundedChromosome {
+ @Override
+ public Chromosome toJenetics() {
+ final List<BoundedDoubleGene> genes = ranges.stream()
+ .map(BoundedDoubleGene::of)
+ .collect(Collectors.toList());
+
+ return BoundedDoubleChromosome.of(genes);
+ }
+
+ @Override
+ public Chromosome toJenetics(final Properties values) {
+ final List<BoundedDoubleGene> genes = new ArrayList<>(ranges.size());
+
+ for(int i = 0; i < ranges.size(); ++i) {
+ final DoubleRange range = ranges.get(i);
+ final double value = values.getAsDouble(specification.get(i));
+
+ genes.add(BoundedDoubleGene.of(value, range));
+ }
+
+ return BoundedDoubleChromosome.of(genes);
+ }
+
+ @Override
+ public Properties toProperties(final Chromosome chromosome, final Properties properties) {
+ final BoundedDoubleChromosome doubleChromosome = (BoundedDoubleChromosome) chromosome;
+
+ for(int i = 0; i < specification.size(); ++i) {
+ final double value = doubleChromosome.get(i).doubleValue();
+ final PropertySpecification spec = specification.get(i);
+
+ properties.put(spec, value);
+ }
+
+ return properties;
+ }
+}
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/chromosome/DynamicGrayChromosome.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/chromosome/DynamicGrayChromosome.java
new file mode 100644
index 00000000..1c18683b
--- /dev/null
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/chromosome/DynamicGrayChromosome.java
@@ -0,0 +1,47 @@
+package de.evoal.core.main.ea.codec.chromosome;
+
+import de.evoal.core.api.properties.Properties;
+import de.evoal.core.api.properties.PropertySpecification;
+import de.evoal.core.api.utils.Requirements;
+import de.evoal.core.main.jenetics.GrayBoundedBitChromosome;
+import de.evoal.core.main.jenetics.GrayHelper;
+import de.evoal.languages.model.el.IntegerLiteral;
+import de.evoal.languages.model.instance.Instance;
+import de.evoal.languages.model.instance.LiteralValue;
+import io.jenetics.Chromosome;
+import io.jenetics.util.DoubleRange;
+
+import javax.enterprise.context.Dependent;
+import javax.inject.Named;
+import java.util.List;
+import java.util.stream.Collectors;
+
+@Dependent
+@Named("gray-chromosome")
+public class DynamicGrayChromosome extends DynamicScaledChromosome {
+ @Override
+ public Chromosome toJenetics() {
+ final DoubleRange range = ranges.get(0);
+
+ return GrayBoundedBitChromosome.of(range.min(), range.max(), scale);
+ }
+ @Override
+ public Chromosome toJenetics(final Properties values) {
+ final DoubleRange range = ranges.get(0);
+ final PropertySpecification spec = specification.get(0);
+
+ return GrayBoundedBitChromosome.of(values.getAsDouble(spec), range.min(), range.max(), scale);
+ }
+ @Override
+ public Properties toProperties(final Chromosome chromosome, final Properties properties) {
+ final PropertySpecification spec = specification.get(0);
+ final GrayBoundedBitChromosome actual = (GrayBoundedBitChromosome)chromosome;
+
+ final byte [] bytes = actual.toByteArray();
+ final double value = GrayHelper.fromGray(bytes, scale);
+
+ properties.put(spec, value);
+
+ return properties;
+ }
+}
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/chromosome/DynamicScaledChromosome.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/chromosome/DynamicScaledChromosome.java
new file mode 100644
index 00000000..0af13e48
--- /dev/null
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/codec/chromosome/DynamicScaledChromosome.java
@@ -0,0 +1,34 @@
+package de.evoal.core.main.ea.codec.chromosome;
+
+import de.evoal.core.api.utils.Requirements;
+import de.evoal.languages.model.ddl.DataDescription;
+import de.evoal.languages.model.el.IntegerLiteral;
+import de.evoal.languages.model.instance.Instance;
+import de.evoal.languages.model.instance.LiteralValue;
+import io.jenetics.util.DoubleRange;
+
+public abstract class DynamicScaledChromosome extends DynamicBoundedChromosome {
+ protected int scale;
+
+ @Override
+ public void init(final Instance specification) {
+ super.init(specification);
+ Requirements.requireSize(dataRepresented, 1);
+ Requirements.requireSize(ranges, 1);
+
+ scale = ((IntegerLiteral)((LiteralValue)specification.findAttribute("scale").getValue()).getLiteral()).getValue();
+ }
+
+ protected DoubleRange toRange(final DataDescription dataDescription) {
+ double min = -Double.MAX_VALUE / 2;
+ double max = Double.MAX_VALUE / 2;
+
+ final double scaleMax = Math.pow(2.0, scale);
+
+ max = Math.min(max, scaleMax);
+ min = Math.max(min, -scaleMax);
+
+ // TODO Find actual ranges from DDL
+ return DoubleRange.of(min, max);
+ }
+}
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/comparator/ParetoFitnessValue.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/comparator/ParetoFitnessValue.java
index e4bf15cd..4a975682 100644
--- a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/comparator/ParetoFitnessValue.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/comparator/ParetoFitnessValue.java
@@ -39,4 +39,15 @@ public class ParetoFitnessValue implements FitnessValue {
public String toString() {
return "ParetoComparatorType [values=" + fitnessValues + "]";
}
+
+ @Override
+ public Object[] toStatistics() {
+ final Object [] result = new Object[fitnessValues.length()];
+
+ for(int i = 0; i < result.length; ++i) {
+ result[i] = fitnessValues.data()[i];
+ }
+
+ return result;
+ }
}
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/comparator/WeightedSumFitnessValue.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/comparator/WeightedSumFitnessValue.java
index b8180614..6d77df73 100644
--- a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/comparator/WeightedSumFitnessValue.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/comparator/WeightedSumFitnessValue.java
@@ -52,4 +52,15 @@ public class WeightedSumFitnessValue implements FitnessValue {
public String toString() {
return "WeightedSum [fit=" + Arrays.toString(fitnessValues) + ", w" + Arrays.toString(normalizedWeights) + "]";
}
+
+ @Override
+ public Object[] toStatistics() {
+ final Object [] result = new Object[fitnessValues.length];
+
+ for(int i = 0; i < result.length; ++i) {
+ result[i] = fitnessValues[i];
+ }
+
+ return result;
+ }
}
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/fitness/DistanceFitness.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/fitness/DistanceFitness.java
index 7b971da3..39166471 100644
--- a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/fitness/DistanceFitness.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/fitness/DistanceFitness.java
@@ -4,10 +4,11 @@ import de.evoal.core.api.board.Blackboard;
import de.evoal.core.api.board.BlackboardEntry;
import de.evoal.core.api.ea.fitness.FitnessFunction;
import de.evoal.core.api.properties.Properties;
+import de.evoal.core.api.properties.PropertiesSpecification;
+import de.evoal.core.api.properties.PropertySpecification;
import de.evoal.core.api.utils.Requirements;
-import de.evoal.languages.model.instance.Array;
-import de.evoal.languages.model.instance.Attribute;
-import de.evoal.languages.model.instance.Instance;
+import de.evoal.languages.model.ddl.DataDescription;
+import de.evoal.languages.model.instance.*;
import org.apache.commons.math3.util.Pair;
import javax.enterprise.context.Dependent;
@@ -29,20 +30,23 @@ public class DistanceFitness extends FitnessDecorator {
@Override
public double[] evaluate(final Properties properties) {
- final double [] target = this.target.getValues();
+ final Object [] target = this.target.getValues();
final double [] current = decoratedFunction.evaluate(properties);
- Requirements.requireSameSize(current, target);
-
+ Requirements.<Object>requireSameSize(current, target);
final double result[] = new double[target.length];
for(int i = 0; i < target.length; ++i) {
- result[i] = target[i] - current[i];
+ result[i] = difference(target[i], current[i]);
}
return result;
}
+ private double difference(final Object o, final double v) {
+ return ((Number)o).doubleValue() - v;
+ }
+
@Override
public FitnessFunction init(final Instance config) {
super.init(config);
@@ -53,13 +57,36 @@ public class DistanceFitness extends FitnessDecorator {
this.target = board.get(BlackboardEntry.TARGET_PROPERTIES);
} else {
this.target = toProperties((Array)target.getValue());
+ board.bind(BlackboardEntry.TARGET_PROPERTIES, this.target);
}
return this;
}
- private static Properties toProperties(final Array value) {
-
- return null;
+ private static Properties toProperties(final Array array) {
+ PropertiesSpecification specification = PropertiesSpecification.builder()
+ .add(array.getValues()
+ .stream()
+ .map(Instance.class::cast)
+ .map(i -> i.findAttribute("name"))
+ .map(Attribute::getValue)
+ .map(DataReference.class::cast)
+ .map(DataReference::getDefinition)
+ .map(DataDescription::getName)
+ )
+ .build();
+
+ final Properties properties = new Properties(specification);
+ array.getValues()
+ .stream()
+ .map(Instance.class::cast)
+ .forEach(i -> {
+ final String name = ((DataReference)i.findAttribute("name").getValue()).getDefinition().getName();
+ final Object value = ((LiteralValue)i.findAttribute("val").getValue()).getLiteral().getValue();
+
+ properties.put(new PropertySpecification(name), value);
+ });
+
+ return properties;
}
}
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/initial/InitialPopulationFactory.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/initial/InitialPopulationFactory.java
index ac8f7f1d..2f69f838 100644
--- a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/initial/InitialPopulationFactory.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/initial/InitialPopulationFactory.java
@@ -8,19 +8,26 @@ import de.evoal.languages.model.instance.Instance;
import javax.enterprise.context.ApplicationScoped;
import javax.enterprise.context.Dependent;
import javax.enterprise.inject.Produces;
+import javax.inject.Inject;
+import javax.inject.Named;
-@ApplicationScoped
+@Dependent
public class InitialPopulationFactory {
+
+ @Inject
+ @ConfigurationValue(entry = BlackboardEntry.EA_CONFIGURATION, access = "algorithm.initialization")
+ private Instance initialization;
+
/**
- * Creates a initial generation based on the heuristic configuration.
+ * Creates an initial generation based on the heuristic configuration.
*
* Blackboard slots used:
* <ul>
* <li>{@link BlackboardEntry#EA_CONFIGURATION}.</li>
* </ul>
*/
- @Produces @Dependent
- public InitialPopulation create(@ConfigurationValue(entry = BlackboardEntry.EA_CONFIGURATION, access = "algorithm.initialization") final Instance initialization) {
+ @Produces @Dependent @Named("initial")
+ public InitialPopulation create() {
return BeanFactory.create(initialization.getName().getName(), InitialPopulation.class)
.init(initialization);
}
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/initial/RandomInitialPopulation.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/initial/RandomInitialPopulation.java
index 5f0c9482..9ea64a72 100644
--- a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/initial/RandomInitialPopulation.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/initial/RandomInitialPopulation.java
@@ -6,12 +6,12 @@ import io.jenetics.Gene;
import io.jenetics.engine.Engine;
import io.jenetics.engine.EvolutionStream;
+import javax.enterprise.context.Dependent;
import javax.inject.Named;
-@Named("random")
public class RandomInitialPopulation<G extends Gene<?, G>, C extends Comparable<C>> implements InitialPopulation<G, C> {
@Override
- public InitialPopulation init(Instance initialization) {
+ public InitialPopulation init(final Instance initialization) {
// this is not the function you are looking for.
return this;
}
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/initial/RandomProducer.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/initial/RandomProducer.java
new file mode 100644
index 00000000..113efb49
--- /dev/null
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/initial/RandomProducer.java
@@ -0,0 +1,30 @@
+package de.evoal.core.main.ea.initial;
+
+import de.evoal.core.api.board.BlackboardEntry;
+import de.evoal.core.api.cdi.BeanFactory;
+import de.evoal.core.api.cdi.ConfigurationValue;
+import de.evoal.core.api.ea.initial.InitialPopulation;
+import de.evoal.languages.model.instance.Instance;
+
+import javax.enterprise.context.ApplicationScoped;
+import javax.enterprise.context.Dependent;
+import javax.enterprise.inject.Produces;
+import javax.inject.Named;
+
+/**
+ * TODO For some reasons I am not able to create the training instance directly ...
+ */
+@ApplicationScoped
+public class RandomProducer {
+
+ @Produces
+ @Dependent
+ @Named("random")
+ public InitialPopulation create(@ConfigurationValue(entry = BlackboardEntry.EA_CONFIGURATION, access = "algorithm.initialization") Instance initialization) {
+ final InitialPopulation population = new RandomInitialPopulation();
+ BeanFactory.injectFields(population);
+ population.init(initialization);
+
+ return population;
+ }
+}
diff --git a/src/core/attic/de/evoal/core/main/ea/model/Correlation.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/model/Correlation.java
similarity index 93%
rename from src/core/attic/de/evoal/core/main/ea/model/Correlation.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/model/Correlation.java
index 450f8555..29df4674 100644
--- a/src/core/attic/de/evoal/core/main/ea/model/Correlation.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/model/Correlation.java
@@ -1,4 +1,4 @@
-package de.evoal.core.main.ea.functions.correlation.model;
+package de.evoal.core.main.ea.model;
import de.evoal.core.api.ea.codec.CustomCodec;
import lombok.Data;
diff --git a/src/core/attic/de/evoal/core/main/ea/model/Correlations.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/model/Correlations.java
similarity index 87%
rename from src/core/attic/de/evoal/core/main/ea/model/Correlations.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/model/Correlations.java
index bd199bba..949d0ab1 100644
--- a/src/core/attic/de/evoal/core/main/ea/model/Correlations.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/model/Correlations.java
@@ -1,4 +1,4 @@
-package de.evoal.core.main.ea.functions.correlation.model;
+package de.evoal.core.main.ea.model;
import de.evoal.core.api.ea.codec.CustomCodec;
import de.evoal.core.api.properties.Properties;
@@ -33,14 +33,14 @@ public class Correlations<G extends Gene<?, G>> {
final Properties properties = codec.decode(genotype);
return correlations.stream()
- .filter(c -> c.matchesSource(chromosomeIndex, properties.get(chromosomeIndex)))
+ .filter(c -> c.matchesSource(chromosomeIndex, properties.getAsDouble(chromosomeIndex)))
.collect(Collectors.toList());
}
public int findCorrelationRoot(final Genotype<G> genotype, final int chromosomeIndex) {
final Properties properties = codec.decode(genotype);
- final double chromosomeValue = properties.get(chromosomeIndex);
+ final double chromosomeValue = properties.getAsDouble(chromosomeIndex);
for(final Correlation correlation : correlations) {
if(!correlation.matchesTarget(chromosomeIndex, chromosomeValue)) {
@@ -48,7 +48,7 @@ public class Correlations<G extends Gene<?, G>> {
}
final int sourceIndex = correlation.getChromosomeOne();
- final double sourceValue = properties.get(sourceIndex);
+ final double sourceValue = properties.getAsDouble(sourceIndex);
if(!correlation.matchesSource(sourceIndex, sourceValue)) {
continue;
diff --git a/src/core/attic/de/evoal/core/main/ea/model/Range.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/model/Range.java
similarity index 85%
rename from src/core/attic/de/evoal/core/main/ea/model/Range.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/model/Range.java
index 6b71bad7..5110014b 100644
--- a/src/core/attic/de/evoal/core/main/ea/model/Range.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/model/Range.java
@@ -1,4 +1,4 @@
-package de.evoal.core.main.ea.functions.correlation.model;
+package de.evoal.core.main.ea.model;
import lombok.AllArgsConstructor;
import lombok.Data;
diff --git a/src/core/attic/de/evoal/core/main/ea/model/RangedCorrelation.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/model/RangedCorrelation.java
similarity index 93%
rename from src/core/attic/de/evoal/core/main/ea/model/RangedCorrelation.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/model/RangedCorrelation.java
index e4dc2468..cadbb0fc 100644
--- a/src/core/attic/de/evoal/core/main/ea/model/RangedCorrelation.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/model/RangedCorrelation.java
@@ -1,4 +1,4 @@
-package de.evoal.core.main.ea.functions.correlation.model;
+package de.evoal.core.main.ea.model;
import lombok.Data;
diff --git a/src/core/attic/de/evoal/core/main/ea/SelectorFactory.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/producer/SelectorFactory.java
similarity index 99%
rename from src/core/attic/de/evoal/core/main/ea/SelectorFactory.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/producer/SelectorFactory.java
index 856ae299..7df1ae1b 100644
--- a/src/core/attic/de/evoal/core/main/ea/SelectorFactory.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/ea/producer/SelectorFactory.java
@@ -1,4 +1,4 @@
-package de.evoal.core.main.ea;
+package de.evoal.core.main.ea.producer;
import de.evoal.core.api.board.BlackboardEntry;
import de.evoal.core.api.cdi.ConfigurationValue;
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/AbstractBoundedChromosome.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/AbstractBoundedChromosome.java
new file mode 100644
index 00000000..4b56a149
--- /dev/null
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/AbstractBoundedChromosome.java
@@ -0,0 +1,93 @@
+package de.evoal.core.main.jenetics;
+import static io.jenetics.internal.util.Hashes.hash;
+
+import java.util.Objects;
+import java.util.stream.Stream;
+
+import io.jenetics.BoundedChromosome;
+import io.jenetics.BoundedGene;
+import io.jenetics.util.ISeq;
+import io.jenetics.util.IntRange;
+
+/**
+ * Abstract chromosome for {@code BoundedGene}s.
+ *
+ * @author <a href="mailto:franz.wilhelmstoetter@gmail.com">Franz Wilhelmstötter</a>
+ * @version 5.2
+ * @since 1.6
+ */
+abstract class AbstractBoundedChromosome<
+ A extends Comparable<? super A>,
+ G extends BoundedGene<A, G>
+ >
+ extends VariableChromosome<G>
+ implements BoundedChromosome<A, G>
+{
+
+ /**
+ * The minimum value of this {@code BoundedChromosome}.
+ */
+ final A _min;
+
+ /**
+ * The maximum value of this {@code BoundedChromosome}.
+ */
+ final A _max;
+
+ /**
+ * Create a new chromosome from the given genes array.
+ *
+ * @param genes the genes of the new chromosome.
+ * @throws IllegalArgumentException if the length of the gene sequence is
+ * empty or doesn't match with the allowed length range.
+ * @throws IllegalArgumentException if the minimum or maximum of the range
+ * is smaller or equal zero
+ * @throws IllegalArgumentException if the given range size is zero
+ * @throws NullPointerException if the {@code genes} are {@code null}.
+ */
+ AbstractBoundedChromosome(
+ final ISeq<? extends G> genes,
+ final IntRange lengthRange
+ ) {
+ super(genes, lengthRange);
+ _min = genes.get(0).min();
+ _max = genes.get(0).max();
+ }
+
+ @Override
+ public A min() {
+ return _min;
+ }
+
+ @Override
+ public A max() {
+ return _max;
+ }
+
+ @Override
+ public int hashCode() {
+ return
+ hash(super.hashCode(),
+ hash(_min,
+ hash(_max)));
+ }
+
+ @Override
+ public boolean equals(final Object obj) {
+ return obj == this ||
+ obj != null &&
+ getClass() == obj.getClass() &&
+ Objects.equals(_min, ((AbstractBoundedChromosome<?, ?>)obj)._min) &&
+ Objects.equals(_max, ((AbstractBoundedChromosome<?, ?>)obj)._max) &&
+ super.equals(obj);
+ }
+
+ static void checkGeneRange(final Stream<?> ranges) {
+ if (ranges.distinct().count() > 1) {
+ throw new IllegalArgumentException(
+ "All genes must have the same range."
+ );
+ }
+ }
+
+}
\ No newline at end of file
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/BitChromosome.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/BitChromosome.java
new file mode 100644
index 00000000..f3d7eec0
--- /dev/null
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/BitChromosome.java
@@ -0,0 +1,700 @@
+package de.evoal.core.main.jenetics;
+
+import static java.lang.Math.min;
+import static java.util.Objects.requireNonNull;
+import static io.jenetics.internal.util.Requires.probability;
+import static io.jenetics.internal.util.SerialIO.readBytes;
+import static io.jenetics.internal.util.SerialIO.readInt;
+import static io.jenetics.internal.util.SerialIO.writeBytes;
+import static io.jenetics.internal.util.SerialIO.writeInt;
+
+import java.io.DataInput;
+import java.io.DataOutput;
+import java.io.IOException;
+import java.io.InvalidObjectException;
+import java.io.ObjectInputStream;
+import java.io.Serial;
+import java.io.Serializable;
+import java.math.BigInteger;
+import java.util.BitSet;
+import java.util.function.Function;
+import java.util.stream.IntStream;
+
+import io.jenetics.BitGene;
+import io.jenetics.Chromosome;
+import io.jenetics.internal.collection.BitArray;
+import io.jenetics.util.ISeq;
+
+/**
+ * Implementation of the <i>classical</i> BitChromosome.
+ *
+ * @see BitGene
+ *
+ * @implNote
+ * This class is immutable and thread-safe. The bits of the bit chromosome are
+ * backed by a {@code byte[]} array with the following layout:
+ * <pre> {@code
+ * Byte: 3 2 1 0
+ * | | | |
+ * Array: |11110011|10011101|01000000|00101010|
+ * | | | |
+ * Bit: 23 15 7 0
+ * }</pre>
+ *
+ * @author <a href="mailto:franz.wilhelmstoetter@gmail.com">Franz Wilhelmstötter</a>
+ * @since 1.0
+ * @version 7.0
+ */
+public class BitChromosome extends Number
+ implements
+ Chromosome<BitGene>,
+ Comparable<BitChromosome>,
+ Serializable
+{
+ @Serial
+ private static final long serialVersionUID = 2L;
+
+
+ private static final double DEFAULT_PROBABILITY = 0.5;
+
+ /**
+ * The boolean array which holds the {@link BitGene}s.
+ */
+ private final BitArray _genes;
+
+ /**
+ * The ones probability of the randomly generated Chromosome.
+ */
+ private final double _p;
+
+ // Private primary constructor.
+ private BitChromosome(final BitArray genes, final double p) {
+ _genes = requireNonNull(genes);
+ _p = probability(p);
+ }
+
+ /**
+ * Create a new bit chromosome from the given bit (byte) array.
+ *
+ * @since 7.0
+ *
+ * @param bits the bit values of the new chromosome gene.
+ * @param start the initial (bit) index of the range to be copied, inclusive
+ * @param end the final (bit) index of the range to be copied, exclusive.
+ * (This index may lie outside the array.)
+ * @param p the ones probability
+ * @throws java.lang.ArrayIndexOutOfBoundsException if {@code start < 0} or
+ * {@code start > bits.length*8}
+ * @throws java.lang.IllegalArgumentException if {@code start > end}
+ * @throws java.lang.NullPointerException if the {@code bits} array is
+ * {@code null}.
+ */
+ public BitChromosome(
+ final byte[] bits,
+ final int start,
+ final int end,
+ final double p
+ ) {
+ this(BitArray.of(bits, start, min(end, bits.length*Byte.SIZE)), p);
+ }
+
+ /**
+ * Create a new bit chromosome from the given bit (byte) array.
+ *
+ * @param bits the bit values of the new chromosome gene.
+ * @param start the initial (bit) index of the range to be copied, inclusive
+ * @param end the final (bit) index of the range to be copied, exclusive.
+ * (This index may lie outside the array.)
+ * @throws java.lang.ArrayIndexOutOfBoundsException if {@code start < 0} or
+ * {@code start > bits.length*8}
+ * @throws java.lang.IllegalArgumentException if {@code start > end}
+ * @throws java.lang.NullPointerException if the {@code bits} array is
+ * {@code null}.
+ */
+ public BitChromosome(final byte[] bits, final int start, final int end) {
+ this(bits, start, end, DEFAULT_PROBABILITY);
+ }
+
+ /**
+ * Create a new {@code BitChromosome} from the given {@code byte} array.
+ * This is a shortcut for {@code new BitChromosome(bits, 0, bits.length*8)}.
+ *
+ * @param bits the {@code byte} array.
+ */
+ public BitChromosome(final byte[] bits) {
+ this(bits, 0, bits.length*Byte.SIZE);
+ }
+
+ /**
+ * Return the one <em>nominal</em> probability of this chromosome. It's not
+ * the actual one-probability of {@code this} chromosome.
+ *
+ * @since 5.2
+ *
+ * @return the one probability of this chromosome.
+ */
+ public double oneProbability() {
+ return _p;
+ }
+
+ @Override
+ public BitGene gene() {
+ return BitGene.of(_genes.get(0));
+ }
+
+ /**
+ * Return the value of the first gene of this chromosome.
+ *
+ * @since 4.2
+ *
+ * @return the first value of this chromosome.
+ */
+ public boolean booleanValue() {
+ return _genes.get(0);
+ }
+
+ @Override
+ public BitGene get(final int index) {
+ return BitGene.of(_genes.get(index));
+ }
+
+ @Override
+ public int length() {
+ return _genes.length();
+ }
+
+ /**
+ * Return the value on the specified index.
+ *
+ * @since 4.2
+ *
+ * @param index the gene index
+ * @return the wanted gene value
+ * @throws IndexOutOfBoundsException if the index is out of range
+ * (index < 1 || index >= length()).
+ */
+ public boolean booleanValue(final int index) {
+ return _genes.get(index);
+ }
+
+ /**
+ * Returns the number of bits set to true in this {@code BitChromosome}.
+ *
+ * @return the number of bits set to true in this {@code BitChromosome}
+ */
+ public int bitCount() {
+ return _genes.bitCount();
+ }
+
+ /**
+ * Return the long value this BitChromosome represents.
+ *
+ * @return long value this BitChromosome represents.
+ */
+ @Override
+ public int intValue() {
+ return (int)longValue();
+ }
+
+ /**
+ * Return the long value this BitChromosome represents.
+ *
+ * @return long value this BitChromosome represents.
+ */
+ @Override
+ public long longValue() {
+ return toBigInteger().longValue();
+ }
+
+ /**
+ * Return the float value this BitChromosome represents.
+ *
+ * @return float value this BitChromosome represents.
+ */
+ @Override
+ public float floatValue() {
+ return (float)longValue();
+ }
+
+ /**
+ * Return the double value this BitChromosome represents.
+ *
+ * @return double value this BitChromosome represents.
+ */
+ @Override
+ public double doubleValue() {
+ return longValue();
+ }
+
+ /**
+ * Return always {@code true}.
+ *
+ * @return {@code true}, always
+ */
+ @Override
+ public boolean isValid() {
+ return true;
+ }
+
+ /**
+ * Return the {@code BigInteger} value this {@code BitChromosome} represents.
+ *
+ * @return {@code BigInteger} value this {@code BitChromosome} represents.
+ */
+ public BigInteger toBigInteger() {
+ return _genes.toBigInteger();
+ }
+
+ /**
+ * Returns the byte array, which represents the bit values of {@code this}
+ * chromosome.
+ *
+ * @return a byte array which represents this {@code BitChromosome}. The
+ * length of the array is {@code (int)Math.ceil(length()/8.0)}.
+ */
+ public byte[] toByteArray() {
+ return _genes.toByteArray();
+ }
+
+ /**
+ * Return the corresponding BitSet of this BitChromosome.
+ *
+ * @return The corresponding BitSet of this BitChromosome.
+ */
+ public BitSet toBitSet() {
+ final BitSet set = new BitSet(length());
+ for (int i = 0, n = length(); i < n; ++i) {
+ set.set(i, get(i).bit());
+ }
+ return set;
+ }
+
+ /**
+ * Return the indexes of the <i>ones</i> of this bit-chromosome as stream.
+ *
+ * @since 3.0
+ *
+ * @return the indexes of the <i>ones</i> of this bit-chromosome
+ */
+ public IntStream ones() {
+ return IntStream.range(0, length())
+ .filter(_genes::get);
+ }
+
+ /**
+ * Return the indexes of the <i>zeros</i> of this bit-chromosome as stream.
+ *
+ * @since 3.0
+ *
+ * @return the indexes of the <i>zeros</i> of this bit-chromosome
+ */
+ public IntStream zeros() {
+ return IntStream.range(0, length())
+ .filter(index -> !_genes.get(index));
+ }
+
+ @Override
+ public BitChromosome newInstance(final ISeq<BitGene> genes) {
+ if (genes.isEmpty()) {
+ throw new IllegalArgumentException(
+ "The genes sequence must contain at least one gene."
+ );
+ }
+
+ final var array = BitArray.ofLength(genes.length());
+ for (int i = 0; i < genes.length(); ++i) {
+ array.set(i, genes.get(i).booleanValue());
+ }
+
+ return new BitChromosome(array, _p);
+ }
+
+ @Override
+ public BitChromosome newInstance() {
+ return of(length(), _p);
+ }
+
+ /**
+ * Maps the gene alleles of this chromosome, given as {@link BitSet}, by
+ * applying the given mapper function {@code f}. The mapped gene values
+ * are then wrapped into a newly created chromosome.
+ *
+ * @since 6.1
+ *
+ * @param f the mapper function
+ * @return a newly created chromosome with the mapped gene values
+ * @throws NullPointerException if the mapper function is {@code null}.
+ */
+ public BitChromosome map(final Function<? super BitSet, ? extends BitSet> f) {
+ return of(f.apply(toBitSet()), length(), oneProbability());
+ }
+
+ /**
+ * Return the BitChromosome as String. A TRUE is represented by a 1 and
+ * a FALSE by a 0. The returned string can be used to create a new
+ * chromosome with the {@link #of(CharSequence)} constructor.
+ *
+ * @return String representation (containing only '1' and '0') of the
+ * BitChromosome.
+ */
+ public String toCanonicalString() {
+ return _genes.toString();
+ }
+
+ @Override
+ public int compareTo(final BitChromosome that) {
+ return toBigInteger().compareTo(that.toBigInteger());
+ }
+
+ /**
+ * Returns a {@code BitChromosome} whose value is ({@code this & other}).
+ *
+ * @since 7.1
+ *
+ * @param other value to be AND'ed with this {@code BitChromosome}.
+ * @return {@code this & other}
+ */
+ public BitChromosome and(final BitChromosome other) {
+ final var array = _genes.copy();
+ for (int i = 0; i < Math.min(length(), other.length()); ++i) {
+ array.set(i, array.get(i) && other._genes.get(i));
+ }
+
+ return new BitChromosome(array, _p);
+ }
+
+ /**
+ * Returns a {@code BitChromosome} whose value is ({@code this | other}).
+ *
+ * @since 7.1
+ *
+ * @param other value to be OR'ed with this {@code BitChromosome}.
+ * @return {@code this | other}
+ */
+ public BitChromosome or(final BitChromosome other) {
+ final var array = _genes.copy();
+ for (int i = 0; i < Math.min(length(), other.length()); ++i) {
+ array.set(i, array.get(i) || other._genes.get(i));
+ }
+
+ return new BitChromosome(array, _p);
+ }
+
+ /**
+ * Returns a {@code BitChromosome} whose value is ({@code this ^ other}).
+ *
+ * @since 7.1
+ *
+ * @param other value to be XOR'ed with this {@code BitChromosome}.
+ * @return {@code this ^ other}
+ */
+ public BitChromosome xor(final BitChromosome other) {
+ final var array = _genes.copy();
+ for (int i = 0; i < Math.min(length(), other.length()); ++i) {
+ array.set(i, array.get(i) ^ other._genes.get(i));
+ }
+
+ return new BitChromosome(array, _p);
+ }
+
+ /**
+ * Invert the ones and zeros of this bit chromosome.
+ *
+ * @return a new BitChromosome with inverted ones and zeros.
+ */
+ public BitChromosome invert() {
+ final var array = _genes.copy();
+ array.invert();
+ return new BitChromosome(array, 1.0 - _p);
+ }
+
+ /**
+ * Returns a new {@code BitChromosome} whose value is ({@code this << n}).
+ * The shift distance, n, may be negative, in which case this method performs
+ * a right shift.
+ *
+ * @param n shift distance, in bits
+ * @return {@code this << n}
+ */
+ public BitChromosome shiftLeft(final int n) {
+ final var genes = _genes.copy();
+ if (n >= 0) {
+ genes.shiftLeft(n);
+ } else {
+ genes.shiftRight(Math.abs(n));
+ }
+ return new BitChromosome(genes, _p);
+ }
+
+ /**
+ * Returns a new {@code BitChromosome} whose value is ({@code this >> n}). The shift
+ * distance, n, may be negative, in which case this method performs a left
+ * shift.
+ *
+ * @param n shift distance, in bits
+ * @return {@code this >> n}
+ */
+ public BitChromosome shiftRight(final int n) {
+ final var genes = _genes.copy();
+ if (n >= 0) {
+ genes.shiftRight(n);
+ } else {
+ genes.shiftLeft(Math.abs(n));
+ }
+ return new BitChromosome(genes, _p);
+ }
+
+ @Override
+ public int hashCode() {
+ return _genes.hashCode();
+ }
+
+ @Override
+ public boolean equals(final Object obj) {
+ return obj == this ||
+ obj instanceof BitChromosome other &&
+ _genes.equals(other._genes);
+ }
+
+ @Override
+ public String toString() {
+ return _genes.toByteString();
+ }
+
+
+ /* *************************************************************************
+ * Static factory methods.
+ **************************************************************************/
+
+ /**
+ * Constructing a new BitChromosome with the given {@code length} and
+ * randomly set bits. The TRUEs and FALSE in the {@code Chromosome} are
+ * equally distributed with one-probability of {@code p}.
+ *
+ * @param length Length of the BitChromosome, number of bits.
+ * @param p Probability of the TRUEs in the BitChromosome.
+ * @return a new {@code BitChromosome} with the given parameter
+ * @throws NegativeArraySizeException if the {@code length} is smaller
+ * than one.
+ * @throws IllegalArgumentException if {@code p} is not a valid probability.
+ */
+ public static BitChromosome of(final int length, final double p) {
+ return new BitChromosome(BitArray.ofLength(length, p), p);
+ }
+
+ /**
+ * Constructing a new BitChromosome with the given {@code length} and
+ * randomly set bits. The TRUEs and FALSE in the {@code Chromosome} are
+ * equally distributed with one-probability of 0.5.
+ *
+ * @param length Length of the BitChromosome.
+ * @return a new {@code BitChromosome} with the given parameter
+ * @throws NegativeArraySizeException if the {@code length} is smaller
+ * than one.
+ */
+ public static BitChromosome of(final int length) {
+ return of(length, DEFAULT_PROBABILITY);
+ }
+
+ /**
+ * Create a new {@code BitChromosome} with the given parameters.
+ *
+ * @param length length of the BitChromosome.
+ * @param bits the bit-set which initializes the chromosome
+ * @param p Probability of the TRUEs in the BitChromosome.
+ * @return a new {@code BitChromosome} with the given parameter
+ * @throws NegativeArraySizeException if the {@code length} is smaller than
+ * one.
+ * @throws NullPointerException if the {@code bitSet} is {@code null}.
+ * @throws IllegalArgumentException if {@code p} is not a valid probability.
+ */
+ public static BitChromosome of(
+ final BitSet bits,
+ final int length,
+ final double p
+ ) {
+ final var array = BitArray.ofLength(length);
+ for (int i = 0; i < length; ++i) {
+ if (bits.get(i)) {
+ array.set(i, true);
+ }
+ }
+
+ return new BitChromosome(array, probability(p));
+ }
+
+ /**
+ * Create a new {@code BitChromosome} with the given parameters. The
+ * {@link #oneProbability()} of the chromosome is set to {@code 0.5}.
+ *
+ * @param length length of the BitChromosome.
+ * @param bits the bit-set which initializes the chromosome
+ * @return a new {@code BitChromosome} with the given parameter
+ * @throws NegativeArraySizeException if the {@code length} is smaller
+ * than one.
+ * @throws NullPointerException if the {@code bitSet} is
+ * {@code null}.
+ */
+ public static BitChromosome of(final BitSet bits, final int length) {
+ return of(bits, length, DEFAULT_PROBABILITY);
+ }
+
+ /**
+ * Constructing a new BitChromosome from a given BitSet. The length of the
+ * constructed {@code BitChromosome} will be ({@link BitSet#length}).
+ *
+ * @see #of(BitSet, int, double)
+ * @see #of(BitSet, int)
+ *
+ * @param bits the bit-set which initializes the chromosome
+ * @return a new {@code BitChromosome} with the given parameter
+ * @throws NullPointerException if the {@code bitSet} is
+ * {@code null}.
+ */
+ public static BitChromosome of(final BitSet bits) {
+ return of(bits, bits.length());
+ }
+
+ /**
+ * Create a new {@code BitChromosome} from the given big integer value and
+ * ones probability.
+ *
+ * @param value the value of the created {@code BitChromosome}
+ * @param length length of the BitChromosome
+ * @param p Probability of the TRUEs in the BitChromosome.
+ * @return a new {@code BitChromosome} with the given parameter
+ * @throws NullPointerException if the given {@code value} is {@code null}.
+ * @throws IllegalArgumentException if {@code p} is not a valid probability.
+ */
+ public static BitChromosome of(
+ final BigInteger value,
+ final int length,
+ final double p
+ ) {
+ final var array = BitArray.of(value, length);
+ return new BitChromosome(array, probability(p));
+ }
+
+ /**
+ * Create a new {@code BitChromosome} from the given big integer value and
+ * ones probability. The {@link #oneProbability()} of the chromosome is set
+ * to {@code 0.5}.
+ *
+ * @since 7.0
+ *
+ * @param value the value of the created {@code BitChromosome}
+ * @param length length of the BitChromosome
+ * @return a new {@code BitChromosome} with the given parameter
+ * @throws NullPointerException if the given {@code value} is {@code null}.
+ * @throws IllegalArgumentException if {@code p} is not a valid probability.
+ */
+ public static BitChromosome of(
+ final BigInteger value,
+ final int length
+ ) {
+ return of(value, length, DEFAULT_PROBABILITY);
+ }
+
+
+ /**
+ * Create a new {@code BitChromosome} from the given big integer value. The
+ * {@link #oneProbability()} of the chromosome is set to {@code 0.5}.
+ *
+ * @param value the value of the created {@code BitChromosome}
+ * @return a new {@code BitChromosome} with the given parameter
+ * @throws NullPointerException if the given {@code value} is {@code null}.
+ */
+ public static BitChromosome of(final BigInteger value) {
+ final var array = BitArray.of(value);
+ return new BitChromosome(array, DEFAULT_PROBABILITY);
+ }
+
+ /**
+ * Create a new {@code BitChromosome} from the given character sequence
+ * containing '0' and '1'; as created with the {@link #toCanonicalString()}
+ * method.
+ *
+ * @param value the input string.
+ * @param length length of the BitChromosome
+ * @param p Probability of the TRUEs in the BitChromosome.
+ * @return a new {@code BitChromosome} with the given parameter
+ * @throws NullPointerException if the {@code value} is {@code null}.
+ * @throws IllegalArgumentException if the length of the character sequence
+ * is zero or contains other characters than '0' or '1'.
+ * @throws IllegalArgumentException if {@code p} is not a valid probability.
+ */
+ public static BitChromosome of(
+ final CharSequence value,
+ final int length,
+ final double p
+ ) {
+ final var array = BitArray.of(value, length);
+ return new BitChromosome(array, probability(p));
+ }
+
+ /**
+ * Create a new {@code BitChromosome} from the given character sequence
+ * containing '0' and '1'; as created with the {@link #toCanonicalString()}
+ * method.
+ *
+ * @param value the input string.
+ * @param p Probability of the TRUEs in the BitChromosome.
+ * @return a new {@code BitChromosome} with the given parameter
+ * @throws NullPointerException if the {@code value} is {@code null}.
+ * @throws IllegalArgumentException if the length of the character sequence
+ * is zero or contains other characters than '0' or '1'.
+ * @throws IllegalArgumentException if {@code p} is not a valid probability.
+ */
+ public static BitChromosome of(final CharSequence value, final double p) {
+ return of(value, value.length(), p);
+ }
+
+ /**
+ * Create a new {@code BitChromosome} from the given character sequence
+ * containing '0' and '1'; as created with the {@link #toCanonicalString()}
+ * method. The {@link #oneProbability()} of the chromosome is set to
+ * {@code 0.5}.
+ *
+ * @param value the input string.
+ * @return a new {@code BitChromosome} with the given parameter
+ * @throws NullPointerException if the {@code value} is {@code null}.
+ * @throws IllegalArgumentException if the length of the character sequence
+ * is zero or contains other characters than '0' or '1'.
+ */
+ public static BitChromosome of(final CharSequence value) {
+ return of(value, value.length(), DEFAULT_PROBABILITY);
+ }
+
+
+ /* *************************************************************************
+ * Java object serialization
+ * ************************************************************************/
+
+ @Serial
+ private Object writeReplace() {
+ throw new IllegalStateException();//new SerialProxy(SerialProxy.BIT_CHROMOSOME, this);
+ }
+
+ @Serial
+ private void readObject(final ObjectInputStream stream)
+ throws InvalidObjectException
+ {
+ throw new InvalidObjectException("Serialization proxy required.");
+ }
+
+ void write(final DataOutput out) throws IOException {
+ writeBytes(toByteArray(), out);
+ writeInt(length(), out);
+ out.writeDouble(oneProbability());
+ }
+
+ static BitChromosome read(final DataInput in) throws IOException {
+ final var bytes = readBytes(in);
+ final var length = readInt(in);
+ final var p = in.readDouble();
+ final var genes = BitArray.of(bytes,0, length);
+
+ return new BitChromosome(genes, p);
+ }
+}
+
diff --git a/src/core/attic/de/evoal/core/main/ea/chromosomes/BitHelper.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/BitHelper.java
similarity index 96%
rename from src/core/attic/de/evoal/core/main/ea/chromosomes/BitHelper.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/BitHelper.java
index 495cf619..5b476c49 100644
--- a/src/core/attic/de/evoal/core/main/ea/chromosomes/BitHelper.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/BitHelper.java
@@ -1,4 +1,4 @@
-package de.evoal.core.main.ea.chromosomes;
+package de.evoal.core.main.jenetics;
import org.decimal4j.api.ImmutableDecimal;
import org.decimal4j.factory.Factories;
diff --git a/src/core/attic/de/evoal/core/main/ea/chromosomes/BoundedBitChromosome.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/BoundedBitChromosome.java
similarity index 93%
rename from src/core/attic/de/evoal/core/main/ea/chromosomes/BoundedBitChromosome.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/BoundedBitChromosome.java
index 05edb2a5..b2ea8a64 100644
--- a/src/core/attic/de/evoal/core/main/ea/chromosomes/BoundedBitChromosome.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/BoundedBitChromosome.java
@@ -1,6 +1,5 @@
-package de.evoal.core.main.ea.chromosomes;
+package de.evoal.core.main.jenetics;
-import io.jenetics.BitChromosome;
import io.jenetics.BitGene;
import io.jenetics.util.ISeq;
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/BoundedDoubleChromosome.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/BoundedDoubleChromosome.java
new file mode 100644
index 00000000..d0999989
--- /dev/null
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/BoundedDoubleChromosome.java
@@ -0,0 +1,285 @@
+package de.evoal.core.main.jenetics;
+
+import io.jenetics.*;
+import io.jenetics.util.DoubleRange;
+import io.jenetics.util.ISeq;
+import io.jenetics.util.IntRange;
+
+import java.io.*;
+import java.util.function.Function;
+import java.util.stream.DoubleStream;
+import java.util.stream.IntStream;
+import java.util.stream.Stream;
+
+import static java.util.Objects.requireNonNull;
+
+public class BoundedDoubleChromosome
+ extends
+ AbstractBoundedChromosome<Double, BoundedDoubleGene>
+ implements
+ NumericChromosome<Double, BoundedDoubleGene>,
+ Serializable
+{
+ private static final long serialVersionUID = 3L;
+
+ /**
+ * Create a new chromosome from the given {@code genes} and the allowed
+ * length range of the chromosome.
+ *
+ * @since 4.0
+ *
+ * @param genes the genes that form the chromosome.
+ * @param lengthRange the allowed length range of the chromosome
+ * @throws NullPointerException if one of the arguments is {@code null}.
+ * @throws IllegalArgumentException if the length of the gene sequence is
+ * empty, doesn't match with the allowed length range, the minimum
+ * or maximum of the range is smaller or equal zero or the given
+ * range size is zero.
+ */
+ protected BoundedDoubleChromosome(
+ final ISeq<BoundedDoubleGene> genes,
+ final IntRange lengthRange
+ ) {
+ super(genes, lengthRange);
+ }
+
+ @Override
+ public BoundedDoubleChromosome newInstance(final ISeq<BoundedDoubleGene> genes) {
+ return new BoundedDoubleChromosome(genes, lengthRange());
+ }
+
+ @Override
+ public BoundedDoubleChromosome newInstance() {
+ return of(_min, _max, lengthRange());
+ }
+
+ /**
+ * Maps the gene alleles of this chromosome, given as {@code double[]} array,
+ * by applying the given mapper function {@code f}. The mapped gene values
+ * are then wrapped into a newly created chromosome.
+ *
+ * <pre>{@code
+ * final DoubleChromosome chromosome = ...;
+ * final DoubleChromosome normalized = chromosome.map(Main::normalize);
+ *
+ * static double[] normalize(final double[] values) {
+ * final double sum = sum(values);
+ * for (int i = 0; i < values.length; ++i) {
+ * values[i] /= sum;
+ * }
+ * return values;
+ * }
+ * }</pre>
+ *
+ * @since 6.1
+ *
+ * @param f the mapper function
+ * @return a newly created chromosome with the mapped gene values
+ * @throws NullPointerException if the mapper function is {@code null}.
+ * @throws IllegalArgumentException if the length of the mapped
+ * {@code double[]} array is empty or doesn't match with the allowed
+ * length range
+ */
+ public BoundedDoubleChromosome map(final Function<? super double[], double[]> f) {
+ requireNonNull(f);
+
+ final var range = DoubleRange.of(_min, _max);
+ final var genes = DoubleStream.of(f.apply(toArray()))
+ .mapToObj(v -> BoundedDoubleGene.of(v, range))
+ .collect(ISeq.toISeq());
+
+ return newInstance(genes);
+ }
+
+ /**
+ * Returns a sequential stream of the alleles with this chromosome as its
+ * source.
+ *
+ * @since 4.3
+ *
+ * @return a sequential stream of alleles
+ */
+ public DoubleStream doubleStream() {
+ return IntStream.range(0, length()).mapToDouble(this::doubleValue);
+ }
+
+ /**
+ * Returns an double array containing all of the elements in this chromosome
+ * in proper sequence. If the chromosome fits in the specified array, it is
+ * returned therein. Otherwise, a new array is allocated with the length of
+ * this chromosome.
+ *
+ * @since 3.0
+ *
+ * @param array the array into which the elements of this chromosomes are to
+ * be stored, if it is big enough; otherwise, a new array is
+ * allocated for this purpose.
+ * @return an array containing the elements of this chromosome
+ * @throws NullPointerException if the given {@code array} is {@code null}
+ */
+ public double[] toArray(final double[] array) {
+ final double[] a = array.length >= length()
+ ? array
+ : new double[length()];
+
+ for (int i = length(); --i >= 0;) {
+ a[i] = doubleValue(i);
+ }
+
+ return a;
+ }
+
+ /**
+ * Returns an double array containing all of the elements in this chromosome
+ * in proper sequence.
+ *
+ * @since 3.0
+ *
+ * @return an array containing the elements of this chromosome
+ */
+ public double[] toArray() {
+ return toArray(new double[length()]);
+ }
+
+
+ /* *************************************************************************
+ * Static factory methods.
+ * ************************************************************************/
+
+ /**
+ * Create a new {@code DoubleChromosome} with the given genes.
+ *
+ * @param genes the genes of the chromosome.
+ * @return a new chromosome with the given genes.
+ * @throws IllegalArgumentException if the length of the genes array is
+ * empty or the given {@code genes} doesn't have the same range.
+ * @throws NullPointerException if the given {@code genes} array is
+ * {@code null}
+ */
+ public static BoundedDoubleChromosome of(final BoundedDoubleGene... genes) {
+ checkGeneRange(Stream.of(genes).map(BoundedDoubleGene::range));
+ return new BoundedDoubleChromosome(ISeq.of(genes), IntRange.of(genes.length));
+ }
+
+ /**
+ * Create a new {@code DoubleChromosome} with the given genes.
+ *
+ * @since 4.3
+ *
+ * @param genes the genes of the chromosome.
+ * @return a new chromosome with the given genes.
+ * @throws NullPointerException if the given {@code genes} are {@code null}
+ * @throws IllegalArgumentException if the of the genes iterable is empty or
+ * the given {@code genes} doesn't have the same range.
+ */
+ public static BoundedDoubleChromosome of(final Iterable<BoundedDoubleGene> genes) {
+ final ISeq<BoundedDoubleGene> values = ISeq.of(genes);
+ checkGeneRange(values.stream().map(BoundedDoubleGene::range));
+ return new BoundedDoubleChromosome(values, IntRange.of(values.length()));
+ }
+
+ /**
+ * Create a new random chromosome.
+ *
+ * @since 4.0
+ *
+ * @param min the min value of the {@link DoubleGene}s (inclusively).
+ * @param max the max value of the {@link DoubleGene}s (exclusively).
+ * @param lengthRange the allowed length range of the chromosome.
+ * @return a new {@code DoubleChromosome} with the given parameter
+ * @throws IllegalArgumentException if the length of the gene sequence is
+ * empty, doesn't match with the allowed length range, the minimum
+ * or maximum of the range is smaller or equal zero or the given
+ * range size is zero.
+ * @throws NullPointerException if the given {@code lengthRange} is
+ * {@code null}
+ */
+ public static BoundedDoubleChromosome of(
+ final double min,
+ final double max,
+ final IntRange lengthRange
+ ) {
+ final ISeq<BoundedDoubleGene> genes = BoundedDoubleGene.seq(min, max, lengthRange);
+ return new BoundedDoubleChromosome(genes, lengthRange);
+ }
+
+ /**
+ * Create a new random {@code DoubleChromosome}.
+ *
+ * @param min the min value of the {@link DoubleGene}s (inclusively).
+ * @param max the max value of the {@link DoubleGene}s (exclusively).
+ * @param length the length of the chromosome.
+ * @return a new {@code DoubleChromosome} with the given parameter
+ * @throws IllegalArgumentException if the {@code length} is smaller than
+ * one.
+ */
+ public static BoundedDoubleChromosome of(
+ final double min,
+ final double max,
+ final int length
+ ) {
+ return of(min, max, IntRange.of(length));
+ }
+
+ /**
+ * Create a new random chromosome.
+ *
+ * @since 4.0
+ *
+ * @param range the integer range of the chromosome.
+ * @param lengthRange the allowed length range of the chromosome.
+ * @return a new {@code DoubleChromosome} with the given parameter
+ * @throws IllegalArgumentException if the length of the gene sequence is
+ * empty, doesn't match with the allowed length range, the minimum
+ * or maximum of the range is smaller or equal zero or the given
+ * range size is zero.
+ * @throws NullPointerException if the given {@code lengthRange} is
+ * {@code null}
+ */
+ public static BoundedDoubleChromosome of(
+ final DoubleRange range,
+ final IntRange lengthRange
+ ) {
+ return of(range.min(), range.max(), lengthRange);
+ }
+
+ /**
+ * Create a new random {@code DoubleChromosome}.
+ *
+ * @since 3.2
+ *
+ * @param range the integer range of the chromosome.
+ * @param length the length of the chromosome.
+ * @return a new random {@code DoubleChromosome}
+ * @throws NullPointerException if the given {@code range} is {@code null}
+ * @throws IllegalArgumentException if the {@code length} is smaller than
+ * one.
+ */
+ public static BoundedDoubleChromosome of(final DoubleRange range, final int length) {
+ return of(range.min(), range.max(), length);
+ }
+
+ /**
+ * Create a new random {@code DoubleChromosome} of length one.
+ *
+ * @param min the minimal value of this chromosome (inclusively).
+ * @param max the maximal value of this chromosome (exclusively).
+ * @return a new {@code DoubleChromosome} with the given parameter
+ */
+ public static BoundedDoubleChromosome of(final double min, final double max) {
+ return of(min, max, 1);
+ }
+
+ /**
+ * Create a new random {@code DoubleChromosome} of length one.
+ *
+ * @since 3.2
+ *
+ * @param range the double range of the chromosome.
+ * @return a new random {@code DoubleChromosome} of length one
+ * @throws NullPointerException if the given {@code range} is {@code null}
+ */
+ public static BoundedDoubleChromosome of(final DoubleRange range) {
+ return of(range.min(), range.max());
+ }
+}
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/BoundedDoubleGene.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/BoundedDoubleGene.java
new file mode 100644
index 00000000..e5bce3eb
--- /dev/null
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/BoundedDoubleGene.java
@@ -0,0 +1,239 @@
+package de.evoal.core.main.jenetics;
+
+import io.jenetics.DoubleGene;
+import io.jenetics.NumericGene;
+import io.jenetics.util.*;
+
+import java.io.*;
+import java.util.random.RandomGenerator;
+
+import static io.jenetics.internal.util.Hashes.hash;
+
+public class BoundedDoubleGene implements
+ NumericGene<Double, BoundedDoubleGene>,
+ Mean<BoundedDoubleGene>,
+ Comparable<BoundedDoubleGene>,
+ Serializable
+{
+
+ private static final long serialVersionUID = 2L;
+
+ private final double _allele;
+ private final double _min;
+ private final double _max;
+
+ /**
+ * Create a new random {@code DoubleGene} with the given value and the
+ * given range. If the {@code value} isn't within the interval [min, max),
+ * no exception is thrown. In this case the method
+ * {@link DoubleGene#isValid()} returns {@code false}.
+ *
+ * @param allele the value of the gene.
+ * @param min the minimal valid value of this gene (inclusively).
+ * @param max the maximal valid value of this gene (exclusively).
+ */
+ private BoundedDoubleGene(final double allele, final double min, final double max) {
+ _allele = BoundedOperations.boundValue(allele, min, max);
+ _min = min;
+ _max = max;
+ }
+
+ @Override
+ public Double allele() {
+ return _allele;
+ }
+
+ @Override
+ public Double min() {
+ return _min;
+ }
+
+ @Override
+ public Double max() {
+ return _max;
+ }
+
+ /**
+ * Return the range of {@code this} gene.
+ *
+ * @since 4.4
+ *
+ * @return the range of {@code this} gene
+ */
+ public DoubleRange range() {
+ return DoubleRange.of(_min, _max);
+ }
+
+ @Override
+ public byte byteValue() {
+ return (byte) _allele;
+ }
+
+ @Override
+ public short shortValue() {
+ return (short) _allele;
+ }
+
+ @Override
+ public int intValue() {
+ return (int) _allele;
+ }
+
+ @Override
+ public long longValue() {
+ return (long) _allele;
+ }
+
+ @Override
+ public float floatValue() {
+ return (float) _allele;
+ }
+
+ @Override
+ public double doubleValue() {
+ return _allele;
+ }
+
+ @Override
+ public boolean isValid() {
+ return
+ Double.isFinite(_allele) &&
+ Double.isFinite(_min) &&
+ Double.isFinite(_max) &&
+ BoundedOperations.isValid(_allele, _min, _max);
+ }
+
+ @Override
+ public int compareTo(final BoundedDoubleGene other) {
+ return Double.compare(_allele, other._allele);
+ }
+
+ @Override
+ public BoundedDoubleGene mean(final BoundedDoubleGene that) {
+ return of(_allele + (that._allele - _allele)/2.0, _min, _max);
+ }
+
+ /**
+ * Create a new gene from the given {@code value} and the gene context.
+ *
+ * @since 5.0
+ * @param allele the value of the new gene.
+ * @return a new gene with the given value.
+ */
+ public DoubleGene newInstance(final double allele) {
+ return DoubleGene.of(allele, _min, _max);
+ }
+
+ @Override
+ public BoundedDoubleGene newInstance(final Double allele) {
+ return of(allele, _min, _max);
+ }
+
+ @Override
+ public BoundedDoubleGene newInstance(final Number allele) {
+ return of(allele.doubleValue(), _min, _max);
+ }
+
+ @Override
+ public BoundedDoubleGene newInstance() {
+ return of(BoundedOperations.random(_min, _max), _min, _max);
+ }
+
+ @Override
+ public int hashCode() {
+ return hash(_allele, hash(_min, hash(_max)));
+ }
+
+ @Override
+ public boolean equals(final Object obj) {
+ return obj == this ||
+ obj instanceof BoundedDoubleGene &&
+ Double.compare(((BoundedDoubleGene)obj)._allele, _allele) == 0 &&
+ Double.compare(((BoundedDoubleGene)obj)._min, _min) == 0 &&
+ Double.compare(((BoundedDoubleGene)obj)._max, _max) == 0;
+ }
+
+ @Override
+ public String toString() {
+ return String.format("[%s]", _allele);
+ }
+
+
+ /* *************************************************************************
+ * Static factory methods.
+ * ************************************************************************/
+
+ /**
+ * Create a new random {@code DoubleGene} with the given value and the
+ * given range. If the {@code value} isn't within the interval [min, max),
+ * no exception is thrown. In this case the method
+ * {@link DoubleGene#isValid()} returns {@code false}.
+ *
+ * @param allele the value of the gene.
+ * @param min the minimal valid value of this gene (inclusively).
+ * @param max the maximal valid value of this gene (exclusively).
+ * @return a new {@code DoubleGene} with the given parameter
+ */
+ public static BoundedDoubleGene of(
+ final double allele,
+ final double min,
+ final double max
+ ) {
+ return new BoundedDoubleGene(allele, min, max);
+ }
+
+ /**
+ * Create a new random {@code DoubleGene} with the given value and the
+ * given range. If the {@code value} isn't within the interval [min, max),
+ * no exception is thrown. In this case the method
+ * {@link DoubleGene#isValid()} returns {@code false}.
+ *
+ * @since 3.2
+ *
+ * @param allele the value of the gene.
+ * @param range the double range to use
+ * @return a new random {@code DoubleGene}
+ * @throws NullPointerException if the given {@code range} is {@code null}.
+ */
+ public static BoundedDoubleGene of(final double allele, final DoubleRange range) {
+ return of(allele, range.min(), range.max());
+ }
+
+ /**
+ * Create a new random {@code DoubleGene}. It is guaranteed that the value
+ * of the {@code DoubleGene} lies in the interval [min, max).
+ *
+ * @param min the minimal valid value of this gene (inclusively).
+ * @param max the maximal valid value of this gene (exclusively).
+ * @return a new {@code DoubleGene} with the given parameter
+ */
+ public static BoundedDoubleGene of(final double min, final double max) {
+ return of(BoundedOperations.random(min, max), min, max);
+ }
+
+ /**
+ * Create a new random {@code DoubleGene}. It is guaranteed that the value
+ * of the {@code DoubleGene} lies in the interval [min, max).
+ *
+ * @since 3.2
+ *
+ * @param range the double range to use
+ * @return a new {@code DoubleGene} with the given parameter
+ * @throws NullPointerException if the given {@code range} is {@code null}.
+ */
+ public static BoundedDoubleGene of(final DoubleRange range) {
+ return of(BoundedOperations.random(range.min(), range.max()), range);
+ }
+ static ISeq<BoundedDoubleGene> seq(
+ final double min,
+ final double max,
+ final IntRange lengthRange
+ ) {
+ final RandomGenerator random = RandomRegistry.random();
+ final int length = random.nextInt(lengthRange.min(), lengthRange.max());
+
+ return MSeq.<BoundedDoubleGene>ofLength(length)
+ .fill(() -> new BoundedDoubleGene(BoundedOperations.random(min, max), min, max))
+ .toISeq();
+ }
+}
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/BoundedOperations.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/BoundedOperations.java
new file mode 100644
index 00000000..8d6ac70f
--- /dev/null
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/BoundedOperations.java
@@ -0,0 +1,25 @@
+package de.evoal.core.main.jenetics;
+
+import io.jenetics.util.RandomRegistry;
+
+import java.util.random.RandomGenerator;
+
+public final class BoundedOperations {
+
+ private BoundedOperations() {
+ }
+
+ public static double boundValue(final double value, final double min, final double max) {
+ return Math.min(max, Math.max(min, value));
+ }
+
+ public static boolean isValid(final double value, final double min, final double max) {
+ return Double.compare(value, min) >= 0 &&
+ Double.compare(value, max) < 0;
+ }
+
+ public static double random(final double min, final double max) {
+ return RandomRegistry.random()
+ .nextDouble(min, max);
+ }
+}
diff --git a/src/core/attic/de/evoal/core/main/ea/chromosomes/DecimalFactory.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/DecimalFactory.java
similarity index 91%
rename from src/core/attic/de/evoal/core/main/ea/chromosomes/DecimalFactory.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/DecimalFactory.java
index 24af5678..fd9e1160 100644
--- a/src/core/attic/de/evoal/core/main/ea/chromosomes/DecimalFactory.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/DecimalFactory.java
@@ -1,4 +1,4 @@
-package de.evoal.core.main.ea.chromosomes;
+package de.evoal.core.main.jenetics;
import org.decimal4j.api.ImmutableDecimal;
import org.decimal4j.factory.Factories;
diff --git a/src/core/attic/de/evoal/core/main/ea/chromosomes/GrayBoundedBitChromosome.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/GrayBoundedBitChromosome.java
similarity index 90%
rename from src/core/attic/de/evoal/core/main/ea/chromosomes/GrayBoundedBitChromosome.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/GrayBoundedBitChromosome.java
index 52f42efb..bf1398b8 100644
--- a/src/core/attic/de/evoal/core/main/ea/chromosomes/GrayBoundedBitChromosome.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/GrayBoundedBitChromosome.java
@@ -1,8 +1,6 @@
-package de.evoal.core.main.ea.chromosomes;
+package de.evoal.core.main.jenetics;
-import static io.jenetics.internal.math.Randoms.nextDouble;
-
-import java.util.Random;
+import io.jenetics.util.RandomRegistry;
public class GrayBoundedBitChromosome extends BoundedBitChromosome<GrayBoundedBitChromosome> {
/**
@@ -23,7 +21,7 @@ public class GrayBoundedBitChromosome extends BoundedBitChromosome<GrayBoundedBi
* Returns a random gray-encoded chromosome within the specified range.
*/
public static GrayBoundedBitChromosome of(final double min, final double max, final int scale) {
- final double value = nextDouble(min, max, new Random());
+ final double value = RandomRegistry.random().nextDouble(min, max);
return GrayBoundedBitChromosome.of(value, min, max, scale);
}
diff --git a/src/core/attic/de/evoal/core/main/ea/chromosomes/GrayHelper.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/GrayHelper.java
similarity index 96%
rename from src/core/attic/de/evoal/core/main/ea/chromosomes/GrayHelper.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/GrayHelper.java
index 5d30fbb6..65fe1161 100644
--- a/src/core/attic/de/evoal/core/main/ea/chromosomes/GrayHelper.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/GrayHelper.java
@@ -1,4 +1,4 @@
-package de.evoal.core.main.ea.chromosomes;
+package de.evoal.core.main.jenetics;
/**
* Helper class for the gray encoding
diff --git a/src/core/attic/de/evoal/core/main/ea/chromosomes/NaiveBoundedBitChromosome.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/NaiveBoundedBitChromosome.java
similarity index 88%
rename from src/core/attic/de/evoal/core/main/ea/chromosomes/NaiveBoundedBitChromosome.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/NaiveBoundedBitChromosome.java
index 1c478d81..20ae13a7 100644
--- a/src/core/attic/de/evoal/core/main/ea/chromosomes/NaiveBoundedBitChromosome.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/NaiveBoundedBitChromosome.java
@@ -1,8 +1,7 @@
-package de.evoal.core.main.ea.chromosomes;
+package de.evoal.core.main.jenetics;
-import static io.jenetics.internal.math.Randoms.nextDouble;
+import io.jenetics.util.RandomRegistry;
-import java.util.Random;
public class NaiveBoundedBitChromosome extends BoundedBitChromosome<NaiveBoundedBitChromosome> {
@@ -16,7 +15,7 @@ public class NaiveBoundedBitChromosome extends BoundedBitChromosome<NaiveBounded
}
public static NaiveBoundedBitChromosome of(final double min, final double max, final int scale) {
- double value = nextDouble(min, max, new Random());
+ double value = RandomRegistry.random().nextDouble(min, max);
return NaiveBoundedBitChromosome.of(value, min, max, scale);
}
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/VariableChromosome.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/VariableChromosome.java
new file mode 100644
index 00000000..f180cfb8
--- /dev/null
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/jenetics/VariableChromosome.java
@@ -0,0 +1,100 @@
+package de.evoal.core.main.jenetics;
+
+import static java.lang.String.format;
+import static java.util.Objects.requireNonNull;
+import static io.jenetics.internal.util.Hashes.hash;
+
+import java.util.Objects;
+
+import io.jenetics.AbstractChromosome;
+import io.jenetics.Gene;
+import io.jenetics.util.ISeq;
+import io.jenetics.util.IntRange;
+
+/**
+ * @author <a href="mailto:franz.wilhelmstoetter@gmail.com">Franz Wilhelmstötter</a>
+ * @version 4.0
+ * @since 4.0
+ */
+abstract class VariableChromosome<G extends Gene<?, G>>
+ extends AbstractChromosome<G>
+{
+
+ private final IntRange _lengthRange;
+
+ /**
+ * Create a new {@code VariableChromosome} from the given {@code genes}
+ * and the allowed length range of the chromosome.
+ *
+ * @param genes the genes that form the chromosome.
+ * @param lengthRange the allowed length range of the chromosome
+ * @throws NullPointerException if one of the arguments is {@code null}.
+ * @throws IllegalArgumentException if the length of the gene sequence is
+ * empty or doesn't match with the allowed length range.
+ * @throws IllegalArgumentException if the minimum or maximum of the range
+ * is smaller or equal zero
+ * @throws IllegalArgumentException if the given range size is zero
+ */
+ VariableChromosome(
+ final ISeq<? extends G> genes,
+ final IntRange lengthRange
+ ) {
+ super(genes);
+ _lengthRange = checkLengthRange(lengthRange, genes.size());
+ }
+
+ static IntRange checkLengthRange(final IntRange lengthRange, final int length) {
+ requireNonNull(lengthRange);
+ if (lengthRange.min() <= 0) {
+ throw new IllegalArgumentException(format(
+ "Minimum length must be positive: %d", lengthRange.min()
+ ));
+ }
+ if (lengthRange.max() <= 0) {
+ throw new IllegalArgumentException(format(
+ "Maximum length must be positive: %d", lengthRange.max()
+ ));
+ }
+ if (lengthRange.size() <= 0) {
+ throw new IllegalArgumentException(format(
+ "Maximal length must be positive: %d", lengthRange.size()
+ ));
+ }
+ if (length < lengthRange.min() ||
+ length >= lengthRange.max())
+ {
+ throw new IllegalArgumentException(format(
+ "Number of genes (%d) not within the allowed range: %s",
+ length,
+ lengthRange
+ ));
+ }
+
+ return lengthRange;
+ }
+
+ /**
+ * Return the allowed length range of the chromosome. The minimum value of
+ * the range is included and the maximum value is excluded.
+ *
+ * @return the allowed length range of the chromosome
+ */
+ public IntRange lengthRange() {
+ return _lengthRange;
+ }
+
+ @Override
+ public int hashCode() {
+ return hash(super.hashCode(), hash(_lengthRange));
+ }
+
+ @Override
+ public boolean equals(final Object obj) {
+ return obj == this ||
+ obj != null &&
+ getClass() == obj.getClass() &&
+ Objects.equals(_lengthRange, ((VariableChromosome<?>)obj)._lengthRange) &&
+ super.equals(obj);
+ }
+
+}
\ No newline at end of file
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/producer/ConfigurationValueProducer.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/producer/ConfigurationValueProducer.java
index 268f125f..4f341d3e 100644
--- a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/producer/ConfigurationValueProducer.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/producer/ConfigurationValueProducer.java
@@ -42,6 +42,14 @@ public class ConfigurationValueProducer {
return lookup(board.get(value.entry()), value.access());
}
+ @Produces
+ @ConfigurationValue(entry = BlackboardEntry.EA_CONFIGURATION, access = "")
+ public final Array injectArrayValue(final InjectionPoint ip, final Blackboard board) {
+ final ConfigurationValue value = ip.getAnnotated().getAnnotation(ConfigurationValue.class);
+
+ return lookup(board.get(value.entry()), value.access());
+ }
+
@Produces
@ConfigurationValue(entry = BlackboardEntry.EA_CONFIGURATION, access = "")
public final Instance injectInstanceValue(final InjectionPoint ip, final Blackboard board) {
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/producer/MockupProducer.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/producer/MockupProducer.java
new file mode 100644
index 00000000..362abce4
--- /dev/null
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/producer/MockupProducer.java
@@ -0,0 +1,15 @@
+package de.evoal.core.main.producer;
+
+import de.evoal.core.main.ea.model.Correlations;
+
+import javax.enterprise.context.ApplicationScoped;
+import javax.enterprise.context.Dependent;
+import javax.enterprise.inject.Produces;
+
+@ApplicationScoped
+public class MockupProducer {
+ @Produces @Dependent
+ Correlations create() {
+ return new Correlations(null);
+ }
+}
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/producer/SpecificationProducer.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/producer/SpecificationProducer.java
new file mode 100644
index 00000000..e7ef652d
--- /dev/null
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/producer/SpecificationProducer.java
@@ -0,0 +1,43 @@
+package de.evoal.core.main.producer;
+
+import de.evoal.core.api.board.BlackboardEntry;
+import de.evoal.core.api.cdi.ConfigurationValue;
+import de.evoal.core.api.properties.PropertiesSpecification;
+import de.evoal.languages.model.ddl.DataDescription;
+import de.evoal.languages.model.instance.Array;
+import de.evoal.languages.model.instance.Attribute;
+import de.evoal.languages.model.instance.DataReference;
+import de.evoal.languages.model.instance.Instance;
+
+import javax.enterprise.context.ApplicationScoped;
+import javax.enterprise.context.Dependent;
+import javax.enterprise.inject.Produces;
+import javax.inject.Inject;
+import javax.inject.Named;
+import java.util.List;
+import java.util.stream.Stream;
+
+@ApplicationScoped
+public class SpecificationProducer {
+ @Produces
+ @Dependent
+ @Named("genotype-specification")
+ public PropertiesSpecification createSourceSpecification(final @ConfigurationValue(entry = BlackboardEntry.EA_CONFIGURATION, access = "algorithm.genotype") Array genotype) {
+ final Stream<String> names = genotype.getValues()
+ .stream()
+ .map(Instance.class::cast)
+ .map(i -> i.findAttribute("genes"))
+ .map(Attribute::getValue)
+ .map(Array.class::cast)
+ .map(Array::getValues)
+ .flatMap(List::stream)
+ .map(Instance.class::cast)
+ .map(i -> i.findAttribute("content"))
+ .map(Attribute::getValue)
+ .map(DataReference.class::cast)
+ .map(DataReference::getDefinition)
+ .map(DataDescription::getName);
+
+ return PropertiesSpecification.builder().add(names).build();
+ }
+}
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/search/HeuristicSearch.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/search/HeuristicSearch.java
index 3ca2b025..75cfe96a 100644
--- a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/search/HeuristicSearch.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/search/HeuristicSearch.java
@@ -10,13 +10,16 @@ import de.evoal.core.api.board.BlackboardEntry;
import de.evoal.core.api.board.Blackboard;
import de.evoal.core.api.cdi.BlackboardValue;
import de.evoal.core.api.cdi.ConfigurationValue;
+import de.evoal.core.api.ea.initial.InitialPopulation;
import de.evoal.core.api.utils.LanguageHelper;
import de.evoal.core.api.ea.codec.CustomCodec;
import de.evoal.core.api.ea.fitness.comparator.FitnessValue;
import de.evoal.core.api.statistics.StatisticsWriter;
+import de.evoal.core.main.ea.alterer.AltererFactory;
+import de.evoal.core.main.ea.codec.DynamicCodec;
import de.evoal.core.main.ea.fitness.JeneticsFitnessFunction;
-import de.evoal.core.api.ea.initial.InitialPopulation;
+import de.evoal.core.main.ea.initial.InitialPopulationFactory;
import de.evoal.core.main.jenetics.ConstraintList;
import de.evoal.languages.model.eal.EAModel;
import de.evoal.languages.model.instance.Array;
@@ -28,11 +31,13 @@ import io.jenetics.engine.*;
import io.jenetics.stat.MinMax;
import io.jenetics.util.Factory;
import lombok.extern.slf4j.Slf4j;
+import org.apache.deltaspike.core.api.provider.BeanProvider;
import javax.enterprise.context.Dependent;
import javax.enterprise.inject.Instance;
import javax.inject.Inject;
+import javax.inject.Named;
@Slf4j
@Dependent
@@ -68,53 +73,53 @@ public class HeuristicSearch {
private final Map<String, List<Alterer<?, FitnessValue>>> alterers = new HashMap<>();
- // TODO @Inject
- private CustomCodec encoding;
+ @Inject
+ private DynamicCodec encoding;
private final ExecutorService executor = Executors.newFixedThreadPool(Runtime.getRuntime().availableProcessors());
@Inject
private JeneticsFitnessFunction fitnessFunction;
- // TODO @Inject @Named("offspring")
- // TODO private Selector offspringSelector;
+ @Inject @Named("offspring")
+ private Selector offspringSelector;
- // TODO @Inject @Named("statistics")
+ @Inject @Named("statistics")
private StatisticsWriter statistics;
-// TODO @Inject @Named("survivor")
-// TODO private Selector survivorSelector;
+ @Inject @Named("survivor")
+ private Selector survivorSelector;
-// TODO @Inject
-// TODO private AltererFactory factory;
+ @Inject
+ private AltererFactory factory;
// TODO @Inject
private Instance<List<Constraint>> constraints;
- // TODO @Inject
- private InitialPopulation initalStreamFactory;
+ @Inject @Named("initial")
+ private InitialPopulation initalStream;
public void run() {
setup();
final Factory<Genotype<?>> gtf = encoding.encoding();
- final Constraint<?, FitnessValue> constraint = new ConstraintList(constraints.get());
+ //final Constraint<?, FitnessValue> constraint = new ConstraintList(constraints.get());
final Engine<?, FitnessValue> engine= Engine.builder(this.fitnessFunction, encoding)
.alterers(flattenAltererMap())
- // TODO.offspringSelector(this.offspringSelector)
- // TODO.survivorsSelector(this.survivorSelector)
+ .offspringSelector(this.offspringSelector)
+ .survivorsSelector(this.survivorSelector)
.optimize(Optimize.MAXIMUM)
.populationSize(sizeOfPopulation)
- .constraint(constraint)
+// TODO .constraint(constraint)
.maximalPhenotypeAge(maximumAge)
.executor(executor)
.build();
EvolutionStatistics<FitnessValue, MinMax<FitnessValue>> statistics = EvolutionStatistics.ofComparable();
- EvolutionStream<?, FitnessValue> initialStream = initalStreamFactory.create(engine);
+ EvolutionStream<?, FitnessValue> initialStream = initalStream.create(engine);
final EvolutionResult<?, FitnessValue> result
= initialStream.limit(Limits.byFixedGeneration(numberOfGenerations))
@@ -142,13 +147,11 @@ public class HeuristicSearch {
final Array array = (Array) category.getValue();
for(final Value alterer : array.getValues()) {
-// TODO this.alterers
-// TODO .computeIfAbsent(name, k -> new ArrayList<>())
-// TODO .add(factory.create((de.evoal.languages.model.instance.Instance)alterer));
+ this.alterers
+ .computeIfAbsent(name, k -> new ArrayList<>())
+ .add(factory.create((de.evoal.languages.model.instance.Instance)alterer));
}
}
-
-
}
private <G extends Gene<?, G>> Alterer<?, FitnessValue> flattenAltererMap() {
diff --git a/src/core/attic/de/evoal/core/main/search/HeuristicSearchEvaluation.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/search/HeuristicSearchEvaluation.java
similarity index 84%
rename from src/core/attic/de/evoal/core/main/search/HeuristicSearchEvaluation.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/search/HeuristicSearchEvaluation.java
index ff621367..1aa0b95a 100644
--- a/src/core/attic/de/evoal/core/main/search/HeuristicSearchEvaluation.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/search/HeuristicSearchEvaluation.java
@@ -1,6 +1,7 @@
package de.evoal.core.main.search;
import de.evoal.core.api.board.BlackboardEntry;
+import de.evoal.core.api.cdi.BeanFactory;
import de.evoal.core.api.cdi.BlackboardValue;
import de.evoal.core.api.cdi.MainClass;
import de.evoal.core.api.properties.Properties;
@@ -13,7 +14,6 @@ import de.evoal.core.api.statistics.ColumnType;
import de.evoal.core.api.statistics.WriterContext;
import lombok.extern.slf4j.Slf4j;
import org.apache.commons.math3.util.Pair;
-import org.apache.deltaspike.core.api.provider.BeanProvider;
import javax.inject.Inject;
import javax.inject.Named;
@@ -42,18 +42,10 @@ public class HeuristicSearchEvaluation implements MainClass {
private File outputBaseDir;
- @Inject
- @BlackboardValue(BlackboardEntry.PREDICTIVE_FUNCTION_FILE)
- private String predictiveFile;
-
- @Inject
- @BlackboardValue(BlackboardEntry.TRAINING_POINT_FILE)
- private String pointsFile;
-
private List<Pair<Properties, Properties>> targets;
@Inject
- @BlackboardValue(BlackboardEntry.TARGETS_FILE)
+ @BlackboardValue(BlackboardEntry.TARGET_POINTS_FILE)
private String targetFile;
@Inject
@@ -65,8 +57,7 @@ public class HeuristicSearchEvaluation implements MainClass {
@Override
public void run() {
- log.info("Running heuristic search evaluation with the following configuartion:");
- log.info(" predictive function loaded from ({}/{})", predictiveFile, pointsFile);
+ log.info("Running heuristic search evaluation with the following configuration:");
log.info(" target points loaded from ({})", targetFile);
log.info(" heuristic configuration loaded from ({})", heuristicFile);
log.info(" running {} iterations.", iterations);
@@ -100,7 +91,7 @@ public class HeuristicSearchEvaluation implements MainClass {
context.bindColumn(targetColumn, targetIndex);
- board.bind(BlackboardEntry.TARGET_PROPERTIES_SOURCE, target.getFirst());
+// board.bind(BlackboardEntry.TARGET_PROPERTIES_SOURCE, target.getFirst());
board.bind(BlackboardEntry.TARGET_PROPERTIES, target.getSecond());
board.bind(BlackboardEntry.EVALUATION_OUTPUT_FOLDER, outputBaseDir);
@@ -112,9 +103,8 @@ public class HeuristicSearchEvaluation implements MainClass {
board.bind(BlackboardEntry.EVALUATION_RUN, run);
context.bindColumn(runColumn, i);
- final HeuristicSearch<?> search = new HeuristicSearch<>();
- BeanProvider.injectFields(search);
- search.run();
+ BeanFactory.create(HeuristicSearch.class)
+ .run();
}
}
diff --git a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/search/HeuristicSearchMain.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/search/HeuristicSearchMain.java
index ede13d74..cdedd099 100644
--- a/src/core/de.evoal.core/src/main/java/de/evoal/core/main/search/HeuristicSearchMain.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/search/HeuristicSearchMain.java
@@ -38,10 +38,7 @@ public class HeuristicSearchMain implements MainClass {
board.bind(BlackboardEntry.EVALUATION_OUTPUT_FOLDER, outputBaseDir);
board.bind(BlackboardEntry.EVALUATION_RUN, "0");
-/*
- final Stream<Pair<Properties, Properties>> targets = (Stream<Pair<Properties, Properties>>)BeanProvider.getContextualReference("target-stream");
- setTarget(targets, board);
-*/
+
BeanFactory.create(HeuristicSearch.class)
.run();
}
@@ -51,7 +48,6 @@ public class HeuristicSearchMain implements MainClass {
targets.findFirst()
.orElseThrow(() -> {throw new IllegalStateException("No target point found");});
-// TODO board.bind(BlackboardEntry.TARGET_PROPERTIES_SOURCE, targetProperties.getFirst());
board.bind(BlackboardEntry.TARGET_PROPERTIES, targetProperties.getSecond());
}
}
diff --git a/src/core/attic/de/evoal/core/main/statistics/fitness/FitnessStatistics.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/statistics/fitness/FitnessStatistics.java
similarity index 74%
rename from src/core/attic/de/evoal/core/main/statistics/fitness/FitnessStatistics.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/statistics/fitness/FitnessStatistics.java
index 1dd91a28..424be14f 100644
--- a/src/core/attic/de/evoal/core/main/statistics/fitness/FitnessStatistics.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/statistics/fitness/FitnessStatistics.java
@@ -1,9 +1,12 @@
package de.evoal.core.main.statistics.fitness;
+import de.evoal.core.api.board.Blackboard;
+import de.evoal.core.api.board.BlackboardEntry;
+import de.evoal.core.api.cdi.BlackboardValue;
+import de.evoal.core.api.ea.fitness.comparator.FitnessValue;
+import de.evoal.core.api.properties.Properties;
import de.evoal.core.api.statistics.*;
import de.evoal.languages.model.instance.Instance;
-import de.evoal.core.api.ea.fitness.type.FitnessType;
-import de.evoal.core.api.properties.PropertiesSpecification;
import io.jenetics.Phenotype;
import io.jenetics.engine.EvolutionResult;
import io.jenetics.util.ISeq;
@@ -24,8 +27,10 @@ import java.util.List;
@Named("fitness-per-individual")
@Dependent
public class FitnessStatistics implements StatisticsWriter {
- @Inject @Named("target-properties-specification")
- private PropertiesSpecification targetSpecification;
+
+ @Inject
+ @BlackboardValue(BlackboardEntry.TARGET_PROPERTIES)
+ private Properties targetSpecification;
@Inject
private WriterStrategy strategy;
@@ -50,19 +55,19 @@ public class FitnessStatistics implements StatisticsWriter {
columns.add(new Column("index", ColumnType.Integer));
for(int i = 0; i < targetSpecification.size(); ++i) {
- columns.add(new Column("fitness-value-" + targetSpecification.getProperties().get(i).name(), ColumnType.Double));
+ columns.add(new Column("fitness-value-" + targetSpecification.getSpecification().get(i).name(), ColumnType.Double));
}
writer = strategy.create("fitness-by-individual", columns);
}
- private Object[] dataOfPhenotype(final int index, final long generation, Phenotype<?, FitnessType> phenotype) {
+ private Object[] dataOfPhenotype(final int index, final long generation, Phenotype<?, FitnessValue> phenotype) {
final Object [] data = new Object[2 + targetSpecification.size()];
data[0] = generation;
data[1] = index;
- final double [] fitnessValues = phenotype.fitness().getFitnessValues();
+ final Object [] fitnessValues = phenotype.fitness().toStatistics();
for(int i = 0; i < fitnessValues.length; ++i) {
data[2 + i] = fitnessValues[i];
@@ -72,8 +77,8 @@ public class FitnessStatistics implements StatisticsWriter {
}
@SneakyThrows(WriterException.class)
- public void add(final EvolutionResult<?, FitnessType> evolutionResult) {
- final ISeq<Phenotype<?, FitnessType>> population = (ISeq<Phenotype<?, FitnessType>>)(Object)evolutionResult.population();
+ public void add(final EvolutionResult<?, FitnessValue> evolutionResult) {
+ final ISeq<Phenotype<?, FitnessValue>> population = (ISeq<Phenotype<?, FitnessValue>>)(Object)evolutionResult.population();
for(int i = 0; i < population.size(); ++i) {
writer.addRecord(dataOfPhenotype(i, evolutionResult.generation(), population.get(i)));
diff --git a/src/core/attic/de/evoal/core/main/statistics/individuals/IndividualStatistics.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/statistics/individuals/IndividualStatistics.java
similarity index 87%
rename from src/core/attic/de/evoal/core/main/statistics/individuals/IndividualStatistics.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/statistics/individuals/IndividualStatistics.java
index 6179819c..910cba1f 100644
--- a/src/core/attic/de/evoal/core/main/statistics/individuals/IndividualStatistics.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/statistics/individuals/IndividualStatistics.java
@@ -1,20 +1,22 @@
package de.evoal.core.main.statistics.individuals;
+import de.evoal.core.api.ea.fitness.comparator.FitnessValue;
import de.evoal.core.api.statistics.*;
import de.evoal.languages.model.instance.Instance;
import de.evoal.core.api.ea.codec.CustomCodec;
-import de.evoal.core.api.ea.fitness.type.FitnessType;
import de.evoal.core.api.properties.Properties;
import de.evoal.core.api.properties.PropertiesSpecification;
import io.jenetics.Genotype;
+import javax.annotation.PostConstruct;
+import javax.enterprise.context.Dependent;
+
import io.jenetics.Phenotype;
import io.jenetics.engine.EvolutionResult;
import io.jenetics.util.ISeq;
-import javax.annotation.PostConstruct;
-import javax.enterprise.context.Dependent;
import lombok.SneakyThrows;
import lombok.extern.slf4j.Slf4j;
+import javax.enterprise.inject.Produces;
import javax.inject.Inject;
import javax.inject.Named;
import java.util.ArrayList;
@@ -33,7 +35,7 @@ public class IndividualStatistics implements StatisticsWriter {
@Inject
private CustomCodec encoding;
- @Inject @Named("source-properties-specification")
+ @Inject @Named("surrogate-source-properties-specification")
private PropertiesSpecification sourceSpecification;
@Inject
@@ -67,7 +69,7 @@ public class IndividualStatistics implements StatisticsWriter {
writer = strategy.create("individuals", columns);
}
- private Object[] dataOfPhenotype(final int index, final long generation, Phenotype<?, FitnessType> phenotype) {
+ private Object[] dataOfPhenotype(final int index, final long generation, Phenotype<?, FitnessValue> phenotype) {
final Object [] data = new Object[4 + sourceSpecification.size()];
final Genotype<?> genotype = phenotype.genotype();
@@ -86,8 +88,8 @@ public class IndividualStatistics implements StatisticsWriter {
}
@SneakyThrows(WriterException.class)
- public void add(final EvolutionResult<?, FitnessType> evolutionResult) {
- final ISeq<Phenotype<?, FitnessType>> population = (ISeq<Phenotype<?, FitnessType>>)(Object)evolutionResult.population();
+ public void add(final EvolutionResult<?, FitnessValue> evolutionResult) {
+ final ISeq<Phenotype<?, FitnessValue>> population = (ISeq<Phenotype<?, FitnessValue>>)(Object)evolutionResult.population();
for(int i = 0; i < population.size(); ++i) {
writer.addRecord(dataOfPhenotype(i, evolutionResult.generation(), population.get(i)));
diff --git a/src/core/attic/de/evoal/core/main/statistics/nop/NopStatistics.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/statistics/nop/NopStatistics.java
similarity index 78%
rename from src/core/attic/de/evoal/core/main/statistics/nop/NopStatistics.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/statistics/nop/NopStatistics.java
index e0756ab8..195ae316 100644
--- a/src/core/attic/de/evoal/core/main/statistics/nop/NopStatistics.java
+++ b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/statistics/nop/NopStatistics.java
@@ -1,9 +1,10 @@
package de.evoal.core.main.statistics.nop;
+import de.evoal.core.api.ea.fitness.comparator.FitnessValue;
import de.evoal.languages.model.instance.Instance;
import de.evoal.core.api.statistics.StatisticsWriter;
-import de.evoal.core.api.ea.fitness.type.FitnessType;
import io.jenetics.engine.EvolutionResult;
+
import javax.enterprise.context.Dependent;
import javax.inject.Named;
@@ -12,7 +13,7 @@ import javax.inject.Named;
@Dependent
public class NopStatistics implements StatisticsWriter {
@Override
- public void add(final EvolutionResult<?, FitnessType> evolutionResult) {
+ public void add(final EvolutionResult<?, FitnessValue> evolutionResult) {
}
@Override
diff --git a/src/core/attic/de/evoal/core/main/statistics/writer/csv/CsvStrategy.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/statistics/writer/csv/CsvStrategy.java
similarity index 100%
rename from src/core/attic/de/evoal/core/main/statistics/writer/csv/CsvStrategy.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/statistics/writer/csv/CsvStrategy.java
diff --git a/src/core/attic/de/evoal/core/main/statistics/writer/csv/CsvWriter.java b/src/core/de.evoal.core/src/main/java/de/evoal/core/main/statistics/writer/csv/CsvWriter.java
similarity index 100%
rename from src/core/attic/de/evoal/core/main/statistics/writer/csv/CsvWriter.java
rename to src/core/de.evoal.core/src/main/java/de/evoal/core/main/statistics/writer/csv/CsvWriter.java
diff --git a/src/core/de.evoal.core/src/main/java/module-info.java b/src/core/de.evoal.core/src/main/java/module-info.java
index 73bb87b6..bd75d437 100644
--- a/src/core/de.evoal.core/src/main/java/module-info.java
+++ b/src/core/de.evoal.core/src/main/java/module-info.java
@@ -55,11 +55,10 @@ module de.evoal.core {
exports de.evoal.core.api.statistics;
exports de.evoal.core.api.utils;
-// opens de.evoal.core.api to weld.core.impl;
+
opens de.evoal.core.api.board to weld.core.impl;
opens de.evoal.core.api.cdi to weld.core.impl;
opens de.evoal.core.api.ea to weld.core.impl;
- opens de.evoal.core.api.ea.codec to weld.core.impl;
opens de.evoal.core.api.ea.constraints to weld.core.impl;
opens de.evoal.core.api.ea.fitness to weld.core.impl;
opens de.evoal.core.api.properties to weld.core.impl;
@@ -68,12 +67,21 @@ module de.evoal.core {
opens de.evoal.core.api.statistics to weld.core.impl;
opens de.evoal.core.api.utils to weld.core.impl;
- opens de.evoal.core.main.ea.fitness to weld.core.impl;
+ opens de.evoal.core.main.ea.alterer to weld.core.impl;
+ opens de.evoal.core.main.ea.alterer.mutator to weld.core.impl;
+ opens de.evoal.core.main.ea.codec to weld.core.impl;
+ opens de.evoal.core.main.ea.codec.chromosome to weld.core.impl;
opens de.evoal.core.main.ea.comparator to weld.core.impl;
+ opens de.evoal.core.main.ea.fitness to weld.core.impl;
opens de.evoal.core.main.ea.initial to weld.core.impl;
+ opens de.evoal.core.main.ea.producer to weld.core.impl;
opens de.evoal.core.main.producer to weld.core.impl;
opens de.evoal.core.main.search to weld.core.impl;
opens de.evoal.core.main.statistics to weld.core.impl;
+ opens de.evoal.core.main.statistics.fitness to weld.core.impl;
+ opens de.evoal.core.main.statistics.individuals to weld.core.impl;
+ opens de.evoal.core.main.statistics.nop to weld.core.impl;
+ opens de.evoal.core.main.statistics.writer.csv to weld.core.impl;
/*
opens de.evoal.core.main.ddl.correlation to weld.core.impl;
@@ -85,11 +93,5 @@ module de.evoal.core {
opens de.evoal.core.main.ddl.deviation to weld.core.impl;
opens de.evoal.core.main.ea.alterer to weld.core.impl;
opens de.evoal.core.main.ea.alterer.mutator to weld.core.impl;
- opens de.evoal.core.main.statistics to weld.core.impl;
- opens de.evoal.core.main.statistics.constraint to weld.core.impl;
- opens de.evoal.core.main.statistics.individuals to weld.core.impl;
- opens de.evoal.core.main.statistics.nop to weld.core.impl;
- opens de.evoal.core.main.statistics.rangeCorrelated to weld.core.impl;
- opens de.evoal.core.main.statistics.writer.csv to weld.core.impl;
*/
}
diff --git a/src/core/de.evoal.generator.main/src/main/java/de/evoal/generator/main/benchmarks/Ackley.java b/src/core/de.evoal.generator.main/src/main/java/de/evoal/generator/main/benchmarks/Ackley.java
index 6cca3ee9..7b518dd4 100644
--- a/src/core/de.evoal.generator.main/src/main/java/de/evoal/generator/main/benchmarks/Ackley.java
+++ b/src/core/de.evoal.generator.main/src/main/java/de/evoal/generator/main/benchmarks/Ackley.java
@@ -2,6 +2,7 @@ package de.evoal.generator.main.benchmarks;
import de.evoal.core.api.properties.Properties;
import de.evoal.core.api.properties.PropertySpecification;
+import de.evoal.core.api.utils.Requirements;
import de.evoal.generator.api.AbstractGeneratorFunction;
import de.evoal.generator.api.GeneratorFunction;
import de.evoal.generator.main.utils.ELHelper;
@@ -31,7 +32,7 @@ public class Ackley extends AbstractGeneratorFunction {
double sum2 = 0.0;
for(final PropertySpecification ps : readSpecification.getProperties()) {
- double read_i = in.get(ps);
+ double read_i = in.getAsDouble(ps);
sum1 += Math.pow(read_i, 2.0);
sum2 += Math.cos(c * read_i);
diff --git a/src/core/de.evoal.generator.main/src/main/java/de/evoal/generator/main/benchmarks/Rastrigin.java b/src/core/de.evoal.generator.main/src/main/java/de/evoal/generator/main/benchmarks/Rastrigin.java
index c5538d06..46e7bfee 100644
--- a/src/core/de.evoal.generator.main/src/main/java/de/evoal/generator/main/benchmarks/Rastrigin.java
+++ b/src/core/de.evoal.generator.main/src/main/java/de/evoal/generator/main/benchmarks/Rastrigin.java
@@ -24,7 +24,7 @@ public class Rastrigin extends AbstractGeneratorFunction {
double value = a * n;
for(final PropertySpecification ps : readSpecification.getProperties()) {
- double read_i = in.get(ps);
+ double read_i = in.getAsDouble(ps);
value += (Math.pow(read_i, 2.0) - a * Math.cos(2 * Math.PI * read_i));
}
diff --git a/src/core/de.evoal.generator.main/src/main/java/de/evoal/generator/main/benchmarks/Rosenbrock.java b/src/core/de.evoal.generator.main/src/main/java/de/evoal/generator/main/benchmarks/Rosenbrock.java
index 9e1b291f..1e3e6647 100644
--- a/src/core/de.evoal.generator.main/src/main/java/de/evoal/generator/main/benchmarks/Rosenbrock.java
+++ b/src/core/de.evoal.generator.main/src/main/java/de/evoal/generator/main/benchmarks/Rosenbrock.java
@@ -21,8 +21,8 @@ public class Rosenbrock extends AbstractGeneratorFunction {
final PropertySpecification ps_i = readSpecification.getProperties().get(i);
final PropertySpecification ps_n = readSpecification.getProperties().get(i+1);
- double read_i = in.get(ps_i);
- double read_n = in.get(ps_n);
+ double read_i = in.getAsDouble(ps_i);
+ double read_n = in.getAsDouble(ps_n);
value += 100 * Math.pow((Math.pow(read_i, 2.0) - read_n), 2.0) + Math.pow(1 - read_i, 2.0);
}
diff --git a/src/core/de.evoal.generator.main/src/main/java/de/evoal/generator/main/benchmarks/WeightedSphere.java b/src/core/de.evoal.generator.main/src/main/java/de/evoal/generator/main/benchmarks/WeightedSphere.java
index f59a1613..24cfc4d4 100644
--- a/src/core/de.evoal.generator.main/src/main/java/de/evoal/generator/main/benchmarks/WeightedSphere.java
+++ b/src/core/de.evoal.generator.main/src/main/java/de/evoal/generator/main/benchmarks/WeightedSphere.java
@@ -19,7 +19,7 @@ public class WeightedSphere extends AbstractGeneratorFunction {
int counter = 0;
for(final PropertySpecification ps : readSpecification.getProperties()) {
- double read_i = in.get(ps);
+ double read_i = in.getAsDouble(ps);
value += Math.pow(read_i, 2.0) * Math.pow(counter++, 2.0);
}
diff --git a/src/core/de.evoal.generator.main/src/main/java/de/evoal/generator/main/functions/NormalNoiseFunction.java b/src/core/de.evoal.generator.main/src/main/java/de/evoal/generator/main/functions/NormalNoiseFunction.java
index f6e176c6..e52bd620 100644
--- a/src/core/de.evoal.generator.main/src/main/java/de/evoal/generator/main/functions/NormalNoiseFunction.java
+++ b/src/core/de.evoal.generator.main/src/main/java/de/evoal/generator/main/functions/NormalNoiseFunction.java
@@ -43,7 +43,7 @@ public class NormalNoiseFunction extends AbstractGeneratorFunction {
for(int i = 0; i < dimension; ++i) {
final PropertySpecification ps = writeSpecification.getProperties().get(i);
- double value = result.get(ps) + distributions.get(i).sample();
+ double value = result.getAsDouble(ps) + distributions.get(i).sample();
result.put(ps, value);
}
diff --git a/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/api/SurrogateBlackboardEntry.java b/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/api/SurrogateBlackboardEntry.java
index 940cb15c..e3673242 100644
--- a/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/api/SurrogateBlackboardEntry.java
+++ b/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/api/SurrogateBlackboardEntry.java
@@ -14,7 +14,12 @@ public final class SurrogateBlackboardEntry {
/**
* File containing a pre-trained surrogate.
*/
- public static final String PRETRAINED_SURROGATE_FILE = "surrogate:pre-trained";
+ public static final String SURROGATE_PRETRAINED_FILE = "surrogate:pre-trained";
+
+ /**
+ * File containing the training data.
+ */
+ public static final String SURROGATE_TRAINING_DATA_FILE = "surrogate:training-data";
private SurrogateBlackboardEntry() {}
}
diff --git a/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/cdi/SurrogateProducer.java b/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/cdi/SurrogateProducer.java
index c833689d..53adc4e5 100644
--- a/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/cdi/SurrogateProducer.java
+++ b/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/cdi/SurrogateProducer.java
@@ -3,10 +3,11 @@ package de.evoal.surrogate.main.cdi;
import de.evoal.core.api.board.Blackboard;
import de.evoal.core.api.board.BlackboardEntry;
import de.evoal.core.api.properties.PropertiesSpecification;
+import de.evoal.core.api.utils.Requirements;
import de.evoal.surrogate.api.SurrogateBlackboardEntry;
import de.evoal.surrogate.api.configuration.SurrogateConfiguration;
import de.evoal.surrogate.api.function.SurrogateFunction;
-import lombok.Getter;
+import de.evoal.surrogate.main.internal.SurrogateFactory;
import lombok.NonNull;
import lombok.extern.slf4j.Slf4j;
@@ -14,7 +15,6 @@ import javax.enterprise.context.ApplicationScoped;
import javax.enterprise.context.Dependent;
import javax.enterprise.event.Observes;
import javax.enterprise.inject.Produces;
-import javax.inject.Inject;
import javax.inject.Named;
import java.io.File;
import java.util.function.Function;
@@ -26,13 +26,14 @@ public class SurrogateProducer {
private SurrogateConfiguration configuration;
public void setPreTrainedSurrogate(final @Observes BlackboardEntry event, final Blackboard board, final Function<@NonNull File, @NonNull SurrogateConfiguration> loader) {
- if(!event.isSame(SurrogateBlackboardEntry.PRETRAINED_SURROGATE_FILE)) {
+ if(!event.isSame(SurrogateBlackboardEntry.SURROGATE_PRETRAINED_FILE)) {
return;
}
- final String filename = board.get(SurrogateBlackboardEntry.PRETRAINED_SURROGATE_FILE);
+ final String filename = board.get(SurrogateBlackboardEntry.SURROGATE_PRETRAINED_FILE);
final File file = new File(filename);
+ log.info("Using pre-trained surrogate model {}.", filename);
if(!file.exists()) {
log.error("Cannot find pre-trained surrogate model: {}", file);
return;
@@ -70,4 +71,13 @@ public class SurrogateProducer {
.stream())
.build();
}
+
+ @Produces @Dependent
+ public SurrogateFunction createSurrogateFunction() {
+ final SurrogateConfiguration configuration = this.configuration;
+
+ Requirements.requireNotNull(configuration);
+
+ return SurrogateFactory.create(configuration, null);
+ }
}
diff --git a/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/cdi/TargetPointLoader.java b/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/cdi/TargetPointLoader.java
new file mode 100644
index 00000000..8b390572
--- /dev/null
+++ b/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/cdi/TargetPointLoader.java
@@ -0,0 +1,67 @@
+package de.evoal.surrogate.main.cdi;
+
+import de.evoal.core.api.board.Blackboard;
+import de.evoal.core.api.board.BlackboardEntry;
+import de.evoal.core.api.properties.PropertiesPair;
+import de.evoal.core.api.properties.PropertiesSpecification;
+import javax.enterprise.context.ApplicationScoped;
+import javax.enterprise.event.Observes;
+import javax.enterprise.inject.Produces;
+
+import de.evoal.core.api.properties.stream.FileBasedPropertiesStreamSupplier;
+import de.evoal.core.api.properties.stream.PropertiesBasedPropertiesPairStreamSupplier;
+import de.evoal.core.api.properties.stream.PropertiesBasedPropertiesStreamSupplier;
+import de.evoal.core.api.properties.stream.PropertiesStreamSupplier;
+import lombok.SneakyThrows;
+import lombok.extern.slf4j.Slf4j;
+
+import javax.inject.Inject;
+import javax.inject.Named;
+import java.io.File;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+@ApplicationScoped
+@Slf4j
+public class TargetPointLoader {
+
+ @Inject
+ private Blackboard board;
+
+ /**
+ * For loading points from file.
+ */
+ private PropertiesBasedPropertiesStreamSupplier loadedProperties;
+
+
+ private PropertiesStreamSupplier targetPoints;
+
+ @SneakyThrows
+ public void load(final @Observes BlackboardEntry entry) {
+ if (!BlackboardEntry.TARGET_POINTS_FILE.equals(entry)) {
+ return;
+ }
+
+ final String inputFileName = board.get(entry);
+
+ log.info("Loading target points from '{}'", inputFileName);
+ final File inputFile = new File(inputFileName);
+
+ if(!inputFile.exists() || ! inputFile.canRead()) {
+ log.error("Unable to read training points file '{}'", inputFile);
+ throw new IllegalArgumentException("Unable to read target points file: " + inputFile);
+ }
+
+ loadedProperties = new PropertiesBasedPropertiesStreamSupplier(new FileBasedPropertiesStreamSupplier(inputFile).get().collect(Collectors.toList()));
+ log.info("Loaded {} target points from '{}'", loadedProperties.size(), inputFile);
+ }
+
+ @Produces @Named("target-stream")
+ public Stream<PropertiesPair> getTargetStream(
+ @Named("surrogate-source-properties-specification") final PropertiesSpecification sourceSpecification,
+ @Named("surrogate-target-properties-specification") final PropertiesSpecification targetSpecification) {
+ log.info("Creating target stream using {} and {}.", sourceSpecification, targetSpecification);
+
+ return new PropertiesBasedPropertiesPairStreamSupplier(targetPoints, /*sourceSpecification*/ PropertiesSpecification.builder().build(), targetSpecification).get();
+ }
+}
diff --git a/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/ea/SurrogateFitnessFunction.java b/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/ea/SurrogateFitnessFunction.java
index 45d9a45c..fe102f28 100644
--- a/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/ea/SurrogateFitnessFunction.java
+++ b/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/ea/SurrogateFitnessFunction.java
@@ -6,17 +6,19 @@ import de.evoal.languages.model.instance.Instance;
import de.evoal.surrogate.api.function.SurrogateFunction;
import javax.enterprise.context.Dependent;
+import javax.inject.Inject;
import javax.inject.Named;
@Dependent
@Named("surrogate")
public class SurrogateFitnessFunction implements FitnessFunction {
+ @Inject
private SurrogateFunction function;
@Override
public double[] evaluate(final Properties properties) {
- return function.apply(properties).getValues();
+ return function.apply(properties).getValuesAsDouble();
}
@Override
diff --git a/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/ea/TrainingDataProducer.java b/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/ea/TrainingDataProducer.java
new file mode 100644
index 00000000..4b5dfce6
--- /dev/null
+++ b/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/ea/TrainingDataProducer.java
@@ -0,0 +1,29 @@
+package de.evoal.surrogate.main.ea;
+
+import de.evoal.core.api.board.Blackboard;
+import de.evoal.core.api.board.BlackboardEntry;
+import de.evoal.core.api.properties.stream.FileBasedPropertiesStreamSupplier;
+import de.evoal.surrogate.api.SurrogateBlackboardEntry;
+import de.evoal.surrogate.api.training.TrainingDataManager;
+import lombok.extern.slf4j.Slf4j;
+
+import javax.enterprise.context.ApplicationScoped;
+import javax.enterprise.event.Observes;
+import java.io.File;
+
+@ApplicationScoped
+@Slf4j
+public class TrainingDataProducer {
+ public void setTrainingData(final @Observes BlackboardEntry event, final Blackboard board, final TrainingDataManager manager) {
+ if (!event.isSame(SurrogateBlackboardEntry.SURROGATE_TRAINING_DATA_FILE)) {
+ return;
+ }
+
+ final String filename = board.get(SurrogateBlackboardEntry.SURROGATE_TRAINING_DATA_FILE);
+ final File trainingFile = new File(filename);
+
+ log.info("Using training data from {}.", filename);
+
+ manager.setTrainingStream(new FileBasedPropertiesStreamSupplier(trainingFile));
+ }
+}
diff --git a/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/ea/TrainingInitialPopulation.java b/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/ea/TrainingInitialPopulation.java
index 6e747777..f9a82e89 100644
--- a/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/ea/TrainingInitialPopulation.java
+++ b/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/ea/TrainingInitialPopulation.java
@@ -15,12 +15,9 @@ import io.jenetics.engine.EvolutionStream;
import io.jenetics.util.ISeq;
import javax.annotation.PostConstruct;
-import javax.enterprise.context.Dependent;
import javax.inject.Inject;
import javax.inject.Named;
-@Dependent
-@Named("training")
public class TrainingInitialPopulation<G extends Gene<?, G>, C extends Comparable<C>> implements InitialPopulation<G, C> {
@Inject
@@ -48,20 +45,19 @@ public class TrainingInitialPopulation<G extends Gene<?, G>, C extends Comparabl
.build();
}
- // TODO @Inject
- private CustomCodec<G> encoding;
+ @Inject
+ private CustomCodec encoding;
private EvolutionInit<G> createTargetBasedInitialPopulation() {
return EvolutionInit.of(createInitialPopulation(), 1l);
}
private ISeq<Genotype<G>> createInitialPopulation() {
- return
- manager.getTrainingStream()
+ return manager.getTrainingStream()
.apply(totalSpecification)
.unordered()
.limit(sizeOfPopulation)
- .map(encoding::encode)
+ .map(((CustomCodec<G>)encoding)::encode)
.collect(ISeq.toISeq());
}
diff --git a/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/ea/TrainingProducer.java b/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/ea/TrainingProducer.java
new file mode 100644
index 00000000..1e89c044
--- /dev/null
+++ b/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/ea/TrainingProducer.java
@@ -0,0 +1,31 @@
+package de.evoal.surrogate.main.ea;
+
+import de.evoal.core.api.board.BlackboardEntry;
+import de.evoal.core.api.cdi.BeanFactory;
+import de.evoal.core.api.cdi.ConfigurationValue;
+import de.evoal.core.api.ea.initial.InitialPopulation;
+import de.evoal.languages.model.instance.Instance;
+
+import javax.enterprise.context.ApplicationScoped;
+import javax.enterprise.context.Dependent;
+import javax.enterprise.inject.Produces;
+import javax.inject.Named;
+
+/**
+ * TODO For some reasons I am not able to create the training instance directly ...
+ */
+@ApplicationScoped
+public class TrainingProducer {
+
+ @Produces
+ @Dependent
+ @Named("training")
+ public InitialPopulation create(@ConfigurationValue(entry = BlackboardEntry.EA_CONFIGURATION, access = "algorithm.initialization") Instance initialization) {
+ final TrainingInitialPopulation population = new TrainingInitialPopulation();
+ BeanFactory.injectFields(population);
+ population.init();
+ population.init(initialization);
+
+ return population;
+ }
+}
diff --git a/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/gof/cross/CrossValidationCalculator.java b/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/gof/cross/CrossValidationCalculator.java
index 32d660a5..47592b13 100644
--- a/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/gof/cross/CrossValidationCalculator.java
+++ b/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/gof/cross/CrossValidationCalculator.java
@@ -120,7 +120,7 @@ public class CrossValidationCalculator implements SurrogateInformationCalculator
for (int cvi = 0; cvi < calculated.size(); ++cvi) {
//correctness[cvi] = correctness[cvi] + Math.abs((calculated.get(cvi) - predicted.get(cvi)) / calculated.get(cvi));
- correctness[cvi] = correctness[cvi] + Math.abs(calculated.get(cvi) - predicted.get(cvi));
+ correctness[cvi] = correctness[cvi] + Math.abs(calculated.getAsDouble(cvi) - predicted.getAsDouble(cvi));
}
});
diff --git a/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/gof/rsquare/RSquareCalculator.java b/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/gof/rsquare/RSquareCalculator.java
index deda8dce..ac43b3b0 100644
--- a/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/gof/rsquare/RSquareCalculator.java
+++ b/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/gof/rsquare/RSquareCalculator.java
@@ -50,7 +50,7 @@ public class RSquareCalculator implements SurrogateInformationCalculator {
final double [][] yValues = pairStream.get()
.map(Pair::getSecond)
- .map(Properties::getValues)
+ .map(Properties::getValuesAsDouble)
.toArray(size -> new double[size][]);
final double [] means = new double [yValues[0].length];
@@ -75,11 +75,10 @@ public class RSquareCalculator implements SurrogateInformationCalculator {
final Properties input = pair.getFirst();
final Properties calculated = function.apply(input);
- double [] values = new double[calculated.size()];
- System.arraycopy(calculated.getValues(), 0, values, 0, values.length);
+ double [] values = calculated.getValuesAsDouble();
for(int i = 0; i < values.length; ++i) {
- values[i] = Math.pow(pair.getSecond().get(i) - values[i], 2);
+ values[i] = Math.pow(pair.getSecond().getAsDouble(i) - values[i], 2);
}
return values;
diff --git a/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/statistics/correlated/GenerationStatisticsWriter.java b/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/statistics/correlated/GenerationStatisticsWriter.java
index 8bbd56a4..458e6f22 100644
--- a/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/statistics/correlated/GenerationStatisticsWriter.java
+++ b/src/core/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/statistics/correlated/GenerationStatisticsWriter.java
@@ -142,14 +142,14 @@ public class GenerationStatisticsWriter implements StatisticsWriter {
for(int d = 0; d < dimensions; ++d) {
final double value = sourceTrainingPoints
.get(t)
- .get(d);
+ .getAsDouble(d);
trainingsMatrix.set(d, t, value);
onTheFlyMatrix.set(d, t, value);
}
}
for(int d = 0; d < dimensions; ++d) {
- onTheFlyMatrix.set(d, onTheFlySize - 1, candidate.get(d));
+ onTheFlyMatrix.set(d, onTheFlySize - 1, candidate.getAsDouble(d));
}
final Matrix trainingsCovarianceMatrix = calculateCovarianceMatrix(trainingsMatrix);
@@ -178,10 +178,10 @@ public class GenerationStatisticsWriter implements StatisticsWriter {
final Genotype<?> genotype = genotypes.get(i);
final Properties individual = (Properties) encoding.decode(genotype);
- final double [] data = individual.getValues();
+ final Object [] data = individual.getValues();
for(int j = 0; j < data.length; ++j) {
- result.set(i, j, data[j]);
+ result.set(i, j, (Double)data[j]);
}
}
diff --git a/src/core/de.evoal.surrogate.api/src/main/java/module-info.java b/src/core/de.evoal.surrogate.api/src/main/java/module-info.java
index db812053..3dcaafd9 100644
--- a/src/core/de.evoal.surrogate.api/src/main/java/module-info.java
+++ b/src/core/de.evoal.surrogate.api/src/main/java/module-info.java
@@ -35,6 +35,8 @@ module de.evoal.surrogate.api {
// open packages for CDI
opens de.evoal.surrogate.api.training to weld.core.impl;
+ opens de.evoal.surrogate.api.configuration to com.fasterxml.jackson.databind;
+
opens de.evoal.surrogate.main to weld.core.impl;
opens de.evoal.surrogate.main.cdi to weld.core.impl;
opens de.evoal.surrogate.main.ea to weld.core.impl;
diff --git a/src/core/de.evoal.surrogate.neural/pom.xml b/src/core/de.evoal.surrogate.neural/pom.xml
new file mode 100644
index 00000000..7454dbb4
--- /dev/null
+++ b/src/core/de.evoal.surrogate.neural/pom.xml
@@ -0,0 +1,54 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+
+ <parent>
+ <groupId>de.evoal</groupId>
+ <artifactId>releng.parent</artifactId>
+ <version>0.9.0-SNAPSHOT</version>
+
+ <relativePath>../de.evoal.releng.parent</relativePath>
+ </parent>
+
+ <artifactId>surrogate.neural</artifactId>
+ <name>EvoAl - Surrogate - Neural Network</name>
+
+ <properties>
+ <deeplearning4j.version>1.0.0-M2.1</deeplearning4j.version>
+ </properties>
+
+ <dependencies>
+ <dependency>
+ <groupId>${project.groupId}</groupId>
+ <artifactId>core.plugin</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+
+ <!-- neural networks -->
+ <dependency>
+ <groupId>org.deeplearning4j</groupId>
+ <artifactId>deeplearning4j-nn</artifactId>
+ <version>${deeplearning4j.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.nd4j</groupId>
+ <artifactId>nd4j-native</artifactId>
+ <version>${deeplearning4j.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.nd4j</groupId>
+ <artifactId>nd4j-common</artifactId>
+ <version>${deeplearning4j.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>de.evoal</groupId>
+ <artifactId>surrogate.api</artifactId>
+ <version>0.9.0-SNAPSHOT</version>
+ <scope>provided</scope>
+ </dependency>
+ </dependencies>
+</project>
diff --git a/src/core/de.evoal.surrogate.neural/src/main/java/de/evoal/surrogates/neural/EvoalDataSetIterator.java b/src/core/de.evoal.surrogate.neural/src/main/java/de/evoal/surrogates/neural/EvoalDataSetIterator.java
new file mode 100644
index 00000000..7cbaf7d1
--- /dev/null
+++ b/src/core/de.evoal.surrogate.neural/src/main/java/de/evoal/surrogates/neural/EvoalDataSetIterator.java
@@ -0,0 +1,21 @@
+package de.evoal.surrogates.neural;
+
+import de.evoal.core.api.properties.stream.PropertiesPairStreamSupplier;
+import org.nd4j.common.primitives.Pair;
+
+import java.util.Iterator;
+
+public class EvoalDataSetIterator implements Iterable<Pair<double [], double []>> {
+ private final PropertiesPairStreamSupplier provider;
+
+ public EvoalDataSetIterator(final PropertiesPairStreamSupplier provider) {
+ this.provider = provider;
+ }
+
+ @Override
+ public Iterator<Pair<double[], double[]>> iterator() {
+ return provider.get()
+ .map(p -> new Pair<>(p.getFirst().getValues(), p.getSecond().getValues()))
+ .iterator();
+ }
+}
diff --git a/src/core/de.evoal.surrogate.neural/src/main/java/de/evoal/surrogates/neural/NeuralNetworkConfigurator.java b/src/core/de.evoal.surrogate.neural/src/main/java/de/evoal/surrogates/neural/NeuralNetworkConfigurator.java
new file mode 100644
index 00000000..d3da4e47
--- /dev/null
+++ b/src/core/de.evoal.surrogate.neural/src/main/java/de/evoal/surrogates/neural/NeuralNetworkConfigurator.java
@@ -0,0 +1,154 @@
+package de.evoal.surrogates.neural;
+
+import org.deeplearning4j.nn.api.OptimizationAlgorithm;
+import org.deeplearning4j.nn.conf.NeuralNetConfiguration;
+import org.deeplearning4j.nn.conf.inputs.InputType;
+import org.deeplearning4j.nn.conf.layers.DenseLayer;
+import org.deeplearning4j.nn.conf.layers.Layer;
+import org.deeplearning4j.nn.conf.layers.OutputLayer;
+import org.deeplearning4j.nn.multilayer.MultiLayerNetwork;
+import org.deeplearning4j.nn.weights.WeightInit;
+import org.nd4j.linalg.activations.Activation;
+import org.nd4j.linalg.learning.config.AdaGrad;
+import org.nd4j.linalg.learning.config.IUpdater;
+import org.nd4j.linalg.lossfunctions.LossFunctions;
+
+import java.security.SecureRandom;
+import java.util.List;
+import java.util.Map;
+
+public final class NeuralNetworkConfigurator {
+ private final Map<String, Object> parameters;
+
+ public NeuralNetworkConfigurator(final Map<String, Object> parameters) {
+ this.parameters = parameters;
+ }
+
+ public MultiLayerNetwork create() {
+ final NeuralNetConfiguration.ListBuilder builder =
+ new NeuralNetConfiguration.Builder()
+ .seed(seed())
+ .weightInit(weightInit())
+ .updater(updater())
+ .activation(activation())
+ .optimizationAlgo(optimizationAlgorithm())
+ .l2(regularizationCoefficient())
+ .list();
+
+ final List<Map<String, Object>> layers = parameter("layers");
+ for (int index = 0; index < layers.size(); ++index) {
+ final Map<String, Object> configuration = layers.get(index);
+
+ builder.layer(index, createLayer(index, configuration, index == layers.size() - 1));
+ }
+
+ builder.setInputType(InputType.feedForward((int)layers.get(0).get("in")));
+ final MultiLayerNetwork nn = new MultiLayerNetwork(builder.build());
+ nn.init();
+
+ return nn;
+ }
+
+ private Layer createLayer(final int index, final Map<String, Object> configuration, boolean isOutputLayer) {
+ if (isOutputLayer) {
+ final OutputLayer.Builder builder = new OutputLayer.Builder();
+ builder.nIn(value(configuration, "in"));
+ builder.nOut(value(configuration, "out"));
+
+ if (configuration.containsKey("weight-init")) {
+ builder.weightInit(weightInit(configuration));
+ }
+
+ if (configuration.containsKey("activation")) {
+ builder.activation(activation(configuration));
+ }
+
+ if (configuration.containsKey("loss-function")) {
+ builder.lossFunction(lossFunction(configuration));
+ }
+
+ return builder.build();
+ } else {
+ final DenseLayer.Builder builder = new DenseLayer.Builder();
+ builder.nIn(value(configuration, "in"));
+ builder.nOut(value(configuration, "out"));
+
+ if (configuration.containsKey("weight-init")) {
+ builder.weightInit(weightInit(configuration));
+ }
+
+ if (configuration.containsKey("activation")) {
+ builder.activation(activation(configuration));
+ }
+
+ return builder.build();
+ }
+ }
+
+ private LossFunctions.LossFunction lossFunction(final Map<String, Object> configuration) {
+ return LossFunctions.LossFunction.valueOf(value(configuration, "loss-function"));
+ }
+
+ private double regularizationCoefficient() {
+ return parameter("l2-regularization-coefficient");
+ }
+
+ private OptimizationAlgorithm optimizationAlgorithm() {
+ final String name = parameter("optimization-algorithm");
+
+ return OptimizationAlgorithm.valueOf(name);
+ }
+
+ private Activation activation() {
+ return activation(parameters);
+ }
+
+ private Activation activation(final Map<String, Object> configuration) {
+ final String name = value(configuration, "activation");
+
+ return Activation.valueOf(name);
+ }
+
+ private IUpdater updater() {
+ final Map<String, Object> updaterConfig = parameter("updater");
+
+ switch (this.<String>value(updaterConfig, "name")) {
+ case "ada-grad": {
+ final double learningRate = value(updaterConfig, "learning-rate");
+
+ return new AdaGrad(learningRate);
+ }
+
+ default:
+ throw new IllegalArgumentException("updater unknown: " + value(updaterConfig, "name"));
+ }
+ }
+
+ private WeightInit weightInit() {
+ return weightInit(parameters);
+ }
+
+ private WeightInit weightInit(final Map<String, Object> configuration) {
+ final String name = value(configuration, "weight-init");
+
+ return WeightInit.valueOf(name);
+ }
+
+ private long seed() {
+ final Object seed = parameter("seed");
+
+ if (seed instanceof Number) {
+ return ((Number) seed).longValue();
+ } else {
+ return new SecureRandom().nextLong();
+ }
+ }
+
+ private <T> T parameter(final String name) {
+ return value(parameters, name);
+ }
+
+ private static <T> T value(final Map<String, Object> map, final String name) {
+ return (T) map.get(name);
+ }
+}
\ No newline at end of file
diff --git a/src/core/de.evoal.surrogate.neural/src/main/java/de/evoal/surrogates/neural/NeuralNetworkHelper.java b/src/core/de.evoal.surrogate.neural/src/main/java/de/evoal/surrogates/neural/NeuralNetworkHelper.java
new file mode 100644
index 00000000..83fa65cb
--- /dev/null
+++ b/src/core/de.evoal.surrogate.neural/src/main/java/de/evoal/surrogates/neural/NeuralNetworkHelper.java
@@ -0,0 +1,37 @@
+package de.evoal.surrogates.neural;
+
+import de.evoal.surrogate.api.configuration.Parameter;
+import lombok.NonNull;
+import org.deeplearning4j.nn.multilayer.MultiLayerNetwork;
+import org.deeplearning4j.util.ModelSerializer;
+
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+public final class NeuralNetworkHelper {
+ private NeuralNetworkHelper() {
+ }
+
+ static List<Parameter> toParameters(final @NonNull MultiLayerNetwork nn) {
+ final List<Parameter> parameters = new ArrayList<>();
+ parameters.add(toNetworkConfig(nn));
+
+ return parameters;
+ }
+
+ private static Parameter toNetworkConfig(final MultiLayerNetwork nn) {
+ try (final ByteArrayOutputStream bos = new ByteArrayOutputStream()) {
+ ModelSerializer.writeModel(nn, bos, true);
+
+ return Parameter.builder()
+ .name("model")
+ .value(bos.toString("UTF8"))
+ .build();
+ } catch (final IOException e) {
+ e.printStackTrace();
+ throw new RuntimeException("Failed");
+ }
+ }
+}
diff --git a/src/core/de.evoal.surrogate.neural/src/main/java/de/evoal/surrogates/neural/SimpleNeuralNetwork.java b/src/core/de.evoal.surrogate.neural/src/main/java/de/evoal/surrogates/neural/SimpleNeuralNetwork.java
new file mode 100644
index 00000000..ecde75ad
--- /dev/null
+++ b/src/core/de.evoal.surrogate.neural/src/main/java/de/evoal/surrogates/neural/SimpleNeuralNetwork.java
@@ -0,0 +1,41 @@
+package de.evoal.surrogates.neural;
+
+
+import de.evoal.core.api.properties.Properties;
+import de.evoal.core.api.properties.PropertiesSpecification;
+import de.evoal.surrogate.api.configuration.PartialFunctionConfiguration;
+import de.evoal.surrogate.api.function.AbstractPartialSurrogateFunction;
+import org.deeplearning4j.nn.multilayer.MultiLayerNetwork;
+import org.nd4j.linalg.factory.Nd4j;
+
+public class SimpleNeuralNetwork extends AbstractPartialSurrogateFunction {
+
+ /**
+ * Indices of input data
+ */
+ private final int[] indices;
+
+ /**
+ * Actual SVR
+ */
+ private final MultiLayerNetwork nn;
+
+ public SimpleNeuralNetwork(final PartialFunctionConfiguration configuration, final MultiLayerNetwork nn, final PropertiesSpecification input, final PropertiesSpecification actualInput, final PropertiesSpecification output) {
+ super(configuration, NeuralNetworkHelper.toParameters(nn), input, output);
+
+ this.indices = input.getProperties().stream().mapToInt(p -> actualInput.indexOf(p)).toArray();
+
+ this.nn = nn;
+ }
+
+ @Override
+ public double [] apply(final Properties input) {
+ final double [] data = new double[indices.length];
+
+ for(int i = 0; i < data.length; ++i) {
+ data[i] = input.get(indices[i]);
+ }
+
+ return nn.output(Nd4j.create(new double[][]{data})).toDoubleVector();
+ }
+}
diff --git a/src/core/de.evoal.surrogate.neural/src/main/java/de/evoal/surrogates/neural/SimpleNeuralNetworkFactory.java b/src/core/de.evoal.surrogate.neural/src/main/java/de/evoal/surrogates/neural/SimpleNeuralNetworkFactory.java
new file mode 100644
index 00000000..b7752dc1
--- /dev/null
+++ b/src/core/de.evoal.surrogate.neural/src/main/java/de/evoal/surrogates/neural/SimpleNeuralNetworkFactory.java
@@ -0,0 +1,78 @@
+package de.evoal.surrogates.neural;
+
+import de.evoal.core.api.properties.PropertiesSpecification;
+import de.evoal.core.api.properties.stream.PropertiesPairStreamSupplier;
+import de.evoal.surrogate.api.configuration.Parameter;
+import de.evoal.surrogate.api.configuration.PartialFunctionConfiguration;
+import de.evoal.surrogate.api.function.AbstractPartialSurrogateFunctionFactory;
+import de.evoal.surrogate.api.function.PartialSurrogateFunction;
+import lombok.extern.slf4j.Slf4j;
+import org.deeplearning4j.datasets.iterator.DoublesDataSetIterator;
+import org.deeplearning4j.nn.multilayer.MultiLayerNetwork;
+import org.nd4j.evaluation.classification.Evaluation;
+import org.nd4j.evaluation.classification.ROCMultiClass;
+import org.nd4j.linalg.dataset.api.iterator.DataSetIterator;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import javax.enterprise.context.Dependent;
+import javax.inject.Named;
+import java.nio.channels.NotYetConnectedException;
+import java.util.List;
+import java.util.Map;
+import java.util.stream.Collectors;
+
+@Dependent
+@Named("neural-network")
+@Slf4j
+public class SimpleNeuralNetworkFactory extends AbstractPartialSurrogateFunctionFactory {
+ @Override
+ protected PartialSurrogateFunction calculateRegression(final PartialFunctionConfiguration configuration, final List<Parameter> parameters, final PropertiesSpecification actualInput, final PropertiesSpecification requiredInput, final PropertiesSpecification producedOutput, final PropertiesPairStreamSupplier provider) {
+ log.info("Calculate neural network from {} to {}.", requiredInput, producedOutput);
+
+ final Map<String, Object> params = parameters.stream()
+ .collect(Collectors.toMap(Parameter::getName, Parameter::getValue));
+
+ final MultiLayerNetwork nn = createNeuralNetwork(params);
+ final DataSetIterator iterator = new DoublesDataSetIterator(new EvoalDataSetIterator(provider), 5);
+
+ nn.fit(iterator, 1000);
+
+
+ Evaluation eval = nn.evaluate(iterator);
+ System.out.println("acc ->" + eval.accuracy());
+ System.out.println(eval.precision());
+ System.out.println(eval.recall());
+
+ // ROC for Area Under Curve on multi-class datasets (not binary classes)
+ ROCMultiClass [] roc = nn.doEvaluation(iterator, new ROCMultiClass());
+ for(int i = 0; i < roc.length; ++i) {
+ System.out.println("[i] -> " + roc[i].calculateAverageAUC());
+ System.out.println("[i] -> " + roc[i].calculateAverageAUCPR());
+ }
+
+ return new SimpleNeuralNetwork(configuration, nn, requiredInput, actualInput, producedOutput);
+ }
+
+ private MultiLayerNetwork createNeuralNetwork(final Map<String, Object> parameters) {
+ return new NeuralNetworkConfigurator(parameters).create();
+ }
+
+ @Override
+ protected PartialSurrogateFunction restoreRegression(final PartialFunctionConfiguration configuration, final PropertiesSpecification actualInput, final PropertiesSpecification requiredInput, final PropertiesSpecification producedOutput) {
+ throw new NotYetConnectedException();
+ /*
+ final KernelMachine<double []> regression = KernelHelper.fromParameters(configuration.getParameters(), configuration.getFunctionParameters());
+
+ final double margin = configuration.getParameters()
+ .stream()
+ .filter(p -> "soft-margin".equals(p.getName()))
+ .map(Parameter::getValue)
+ .map(Double.class::cast)
+ .findFirst()
+ .orElse(0.1);
+
+ return new KernelBasedSVRFunction(configuration, regression, requiredInput, actualInput, producedOutput, margin);
+ */
+ }
+}
diff --git a/src/core/de.evoal.surrogate.neural/src/main/java/module-info.java b/src/core/de.evoal.surrogate.neural/src/main/java/module-info.java
new file mode 100644
index 00000000..cdc97724
--- /dev/null
+++ b/src/core/de.evoal.surrogate.neural/src/main/java/module-info.java
@@ -0,0 +1,13 @@
+module de.evoal.surrogate.neural {
+ requires commons.math3;
+ requires jakarta.enterprise.cdi.api;
+ requires lombok;
+ requires org.slf4j;
+
+ requires de.evoal.core;
+ requires de.evoal.surrogate.api;
+ requires deeplearning4j.nn;
+ requires nd4j.api;
+ requires deeplearning4j.utility.iterators;
+ requires jakarta.inject.api;
+}
diff --git a/src/core/de.evoal.surrogate.simple/src/main/java/de/evoal/surrogate/simple/identity/IdentityFunction.java b/src/core/de.evoal.surrogate.simple/src/main/java/de/evoal/surrogate/simple/identity/IdentityFunction.java
index b04cccc2..b1051d69 100644
--- a/src/core/de.evoal.surrogate.simple/src/main/java/de/evoal/surrogate/simple/identity/IdentityFunction.java
+++ b/src/core/de.evoal.surrogate.simple/src/main/java/de/evoal/surrogate/simple/identity/IdentityFunction.java
@@ -24,6 +24,6 @@ public class IdentityFunction extends AbstractPartialSurrogateFunction {
}
public double [] apply(final Properties input) {
- return new double[] {input.get(propertyIndex)};
+ return new double[] {input.getAsDouble(propertyIndex)};
}
}
diff --git a/src/core/de.evoal.surrogate.simple/src/main/java/de/evoal/surrogate/simple/linear/LinearFunction.java b/src/core/de.evoal.surrogate.simple/src/main/java/de/evoal/surrogate/simple/linear/LinearFunction.java
index 0db00afc..8588235c 100644
--- a/src/core/de.evoal.surrogate.simple/src/main/java/de/evoal/surrogate/simple/linear/LinearFunction.java
+++ b/src/core/de.evoal.surrogate.simple/src/main/java/de/evoal/surrogate/simple/linear/LinearFunction.java
@@ -61,7 +61,7 @@ public class LinearFunction extends AbstractPartialSurrogateFunction {
final PropertySpecification inputProperty = input.getProperties().get(0);
final int propertyIndex = actualInput.indexOf(inputProperty);
- this.regression = vector -> intercept + slope * vector.get(propertyIndex);
+ this.regression = vector -> intercept + slope * vector.getAsDouble(propertyIndex);
}
public double [] apply(final Properties input) {
diff --git a/src/core/de.evoal.surrogate.simple/src/main/java/de/evoal/surrogate/simple/linear/LinearFunctionFactory.java b/src/core/de.evoal.surrogate.simple/src/main/java/de/evoal/surrogate/simple/linear/LinearFunctionFactory.java
index 8e961f5b..086826dc 100644
--- a/src/core/de.evoal.surrogate.simple/src/main/java/de/evoal/surrogate/simple/linear/LinearFunctionFactory.java
+++ b/src/core/de.evoal.surrogate.simple/src/main/java/de/evoal/surrogate/simple/linear/LinearFunctionFactory.java
@@ -32,7 +32,7 @@ public class LinearFunctionFactory extends AbstractPartialSurrogateFunctionFacto
provider.get()
.forEach(coordinate -> {
log.info("Mapping - ({}) to ({}).", coordinate.getFirst(), coordinate.getSecond());
- regression.addData(coordinate.getFirst().get(0), coordinate.getSecond().get(0));
+ regression.addData(coordinate.getFirst().getAsDouble(0), coordinate.getSecond().getAsDouble(0));
});
return new LinearFunction(configuration, LinearFunction.toParameters(regression), requiredInput, actualInput, producedOutput);
diff --git a/src/core/de.evoal.surrogate.simple/src/main/java/de/evoal/surrogate/simple/quadratic/SimpleQuadraticFunction.java b/src/core/de.evoal.surrogate.simple/src/main/java/de/evoal/surrogate/simple/quadratic/SimpleQuadraticFunction.java
index 455e4598..195ed63b 100644
--- a/src/core/de.evoal.surrogate.simple/src/main/java/de/evoal/surrogate/simple/quadratic/SimpleQuadraticFunction.java
+++ b/src/core/de.evoal.surrogate.simple/src/main/java/de/evoal/surrogate/simple/quadratic/SimpleQuadraticFunction.java
@@ -60,7 +60,7 @@ public class SimpleQuadraticFunction extends AbstractPartialSurrogateFunction {
final PropertySpecification inputProperty = input.getProperties().get(0);
final int propertyIndex = actualInput.indexOf(inputProperty);
- this.regression = vector -> intercept + slope * vector.get(propertyIndex);
+ this.regression = vector -> intercept + slope * vector.getAsDouble(propertyIndex);
}
public double [] apply(final Properties input) {
diff --git a/src/core/de.evoal.surrogate.simple/src/main/java/de/evoal/surrogate/simple/quadratic/SimpleQuadraticFunctionFactory.java b/src/core/de.evoal.surrogate.simple/src/main/java/de/evoal/surrogate/simple/quadratic/SimpleQuadraticFunctionFactory.java
index 63e673d0..acbdafff 100644
--- a/src/core/de.evoal.surrogate.simple/src/main/java/de/evoal/surrogate/simple/quadratic/SimpleQuadraticFunctionFactory.java
+++ b/src/core/de.evoal.surrogate.simple/src/main/java/de/evoal/surrogate/simple/quadratic/SimpleQuadraticFunctionFactory.java
@@ -33,7 +33,7 @@ public final class SimpleQuadraticFunctionFactory extends AbstractPartialSurroga
provider.get()
.forEach(coordinate -> {
log.info("Mapping - ({}) to ({}).", coordinate.getFirst(), coordinate.getSecond());
- regression.addData(Math.pow(coordinate.getFirst().get(0), 2), coordinate.getSecond().get(0));
+ regression.addData(Math.pow(coordinate.getFirst().getAsDouble(0), 2), coordinate.getSecond().getAsDouble(0));
});
return new SimpleQuadraticFunction(configuration, LinearFunction.toParameters(regression), requiredInput, actualInput, producedOutput);
diff --git a/src/core/de.evoal.surrogate.simple/src/main/java/module-info.java b/src/core/de.evoal.surrogate.simple/src/main/java/module-info.java
index 5d389895..8f69072b 100644
--- a/src/core/de.evoal.surrogate.simple/src/main/java/module-info.java
+++ b/src/core/de.evoal.surrogate.simple/src/main/java/module-info.java
@@ -6,4 +6,5 @@ module de.evoal.surrogate.simple {
requires de.evoal.core;
requires de.evoal.surrogate.api;
+ requires jakarta.inject.api;
}
diff --git a/src/core/de.evoal.surrogate.svr/src/main/java/de/evoal/surrogate/svr/GaussianKernelSVRFunctionFactory.java b/src/core/de.evoal.surrogate.svr/src/main/java/de/evoal/surrogate/svr/GaussianKernelSVRFunctionFactory.java
index b58d9b6e..5cc2dcdd 100644
--- a/src/core/de.evoal.surrogate.svr/src/main/java/de/evoal/surrogate/svr/GaussianKernelSVRFunctionFactory.java
+++ b/src/core/de.evoal.surrogate.svr/src/main/java/de/evoal/surrogate/svr/GaussianKernelSVRFunctionFactory.java
@@ -26,7 +26,7 @@ import java.util.stream.Collectors;
@Slf4j
public class GaussianKernelSVRFunctionFactory extends KernelBasedSVRFunctionFactory {
public GaussianKernelSVRFunctionFactory() {
- super(KernelHelper::toGaussianKernel);
+ super(KernelHelper::toGaussianKernel, "gaussian");
}
@Override
@@ -41,6 +41,6 @@ public class GaussianKernelSVRFunctionFactory extends KernelBasedSVRFunctionFact
.findFirst()
.orElse(0.1);
- return new KernelBasedSVRFunction(configuration, regression, requiredInput, actualInput, producedOutput, margin);
+ return new KernelBasedSVRFunction(configuration, regression, "gaussian", requiredInput, actualInput, producedOutput, margin);
}
}
diff --git a/src/core/de.evoal.surrogate.svr/src/main/java/de/evoal/surrogate/svr/KernelBasedSVRFunction.java b/src/core/de.evoal.surrogate.svr/src/main/java/de/evoal/surrogate/svr/KernelBasedSVRFunction.java
index 877a5391..4411b672 100644
--- a/src/core/de.evoal.surrogate.svr/src/main/java/de/evoal/surrogate/svr/KernelBasedSVRFunction.java
+++ b/src/core/de.evoal.surrogate.svr/src/main/java/de/evoal/surrogate/svr/KernelBasedSVRFunction.java
@@ -21,8 +21,8 @@ public class KernelBasedSVRFunction extends AbstractPartialSurrogateFunction {
private final double gamma;
- public KernelBasedSVRFunction(final PartialFunctionConfiguration configuration, final KernelMachine<double []> regression, final PropertiesSpecification input, final PropertiesSpecification actualInput, final PropertiesSpecification output, final double gamma) {
- super(configuration, KernelHelper.toParameters(regression), input, output);
+ public KernelBasedSVRFunction(final PartialFunctionConfiguration configuration, final KernelMachine<double []> regression, final String kernelName, final PropertiesSpecification input, final PropertiesSpecification actualInput, final PropertiesSpecification output, final double gamma) {
+ super(configuration, KernelHelper.toParameters(regression, kernelName), input, output);
this.indices = input.getProperties().stream().mapToInt(p -> actualInput.indexOf(p)).toArray();
@@ -35,7 +35,7 @@ public class KernelBasedSVRFunction extends AbstractPartialSurrogateFunction {
final double [] data = new double[indices.length];
for(int i = 0; i < data.length; ++i) {
- data[i] = input.get(indices[i]);
+ data[i] = input.getAsDouble(indices[i]);
}
return new double [] {regression.predict(data)};
diff --git a/src/core/de.evoal.surrogate.svr/src/main/java/de/evoal/surrogate/svr/KernelBasedSVRFunctionFactory.java b/src/core/de.evoal.surrogate.svr/src/main/java/de/evoal/surrogate/svr/KernelBasedSVRFunctionFactory.java
index c0914223..5555805f 100644
--- a/src/core/de.evoal.surrogate.svr/src/main/java/de/evoal/surrogate/svr/KernelBasedSVRFunctionFactory.java
+++ b/src/core/de.evoal.surrogate.svr/src/main/java/de/evoal/surrogate/svr/KernelBasedSVRFunctionFactory.java
@@ -25,12 +25,15 @@ public abstract class KernelBasedSVRFunctionFactory extends AbstractPartialSurro
*/
private final Function<Map<String, Object>, MercerKernel<double[]>> toKernel;
- public KernelBasedSVRFunctionFactory(final Function<Map<String, Object>, MercerKernel<double []>> toKernel) {
+ private final String nameOfKernel;
+
+ public KernelBasedSVRFunctionFactory(final Function<Map<String, Object>, MercerKernel<double []>> toKernel, final String nameOfKernel) {
this.toKernel = toKernel;
+ this.nameOfKernel = nameOfKernel;
}
@Override
- protected PartialSurrogateFunction calculateRegression(final PartialFunctionConfiguration configuration, List<Parameter> parameters, PropertiesSpecification actualInput, PropertiesSpecification requiredInput, PropertiesSpecification producedOutput, PropertiesPairStreamSupplier provider) {
+ protected PartialSurrogateFunction calculateRegression(final PartialFunctionConfiguration configuration, final List<Parameter> parameters, PropertiesSpecification actualInput, PropertiesSpecification requiredInput, PropertiesSpecification producedOutput, PropertiesPairStreamSupplier provider) {
log.info("Calculate SVR surrogate from {} to {}.", requiredInput, producedOutput);
Requirements.requireSizeGreaterThean(requiredInput.getProperties(), 0);
@@ -41,8 +44,8 @@ public abstract class KernelBasedSVRFunctionFactory extends AbstractPartialSurro
provider.get()
.forEach(p -> {
- sources.add(p.getFirst().getValues());
- targets.add(p.getSecond().get(0));
+ sources.add(p.getFirst().getValuesAsDouble());
+ targets.add(p.getSecond().getAsDouble(0));
});
log.info("Using {} points for regression.", sources.size());
@@ -59,6 +62,6 @@ public abstract class KernelBasedSVRFunctionFactory extends AbstractPartialSurro
final KernelMachine<double []> regression = SVR.fit(sourceArray, targetArray, toKernel.apply(params), epsilon, margin, tolerance);
- return new KernelBasedSVRFunction(configuration, regression, requiredInput, actualInput, producedOutput, margin);
+ return new KernelBasedSVRFunction(configuration, regression, nameOfKernel, requiredInput, actualInput, producedOutput, margin);
}
}
diff --git a/src/core/de.evoal.surrogate.svr/src/main/java/de/evoal/surrogate/svr/KernelHelper.java b/src/core/de.evoal.surrogate.svr/src/main/java/de/evoal/surrogate/svr/KernelHelper.java
index fc82572f..63e0007f 100644
--- a/src/core/de.evoal.surrogate.svr/src/main/java/de/evoal/surrogate/svr/KernelHelper.java
+++ b/src/core/de.evoal.surrogate.svr/src/main/java/de/evoal/surrogate/svr/KernelHelper.java
@@ -30,7 +30,7 @@ public final class KernelHelper {
public static final String TOLERANCE_PARAMETER = "tolerance";
- private static final String KERNEL_PARAMETER = "kernel";
+ public static final String KERNEL_PARAMETER = "kernel";
/**
* Logger instance
@@ -57,7 +57,7 @@ public final class KernelHelper {
public static KernelMachine<double []> fromParameters(final List<Parameter> parameters, final List<Parameter> kernelParameters) {
final Map<String, Object> kernelParameterMap = toMap(kernelParameters);
- final MercerKernel<double []> kernel = toKernel(toMap(parameters));
+ final MercerKernel<double []> kernel = toKernel(toMap(parameters), kernelParameterMap);
final double[][] instances =(double[][]) kernelParameterMap.get("instances");
final double[] weight = (double[]) kernelParameterMap.get("weights");
final double b = (double)kernelParameterMap.get("intercept");
@@ -73,10 +73,10 @@ public final class KernelHelper {
return new GaussianKernel(sigma);
}
- public static MercerKernel<double []> toKernel(final Map<String, Object> parameters) {
- log.info(" Using kernel '{}'", parameters.get(KERNEL_PARAMETER));
+ public static MercerKernel<double []> toKernel(final Map<String, Object> parameters, final Map<String, Object> state) {
+ log.info(" Using kernel '{}'", state.get(KERNEL_PARAMETER));
- switch((String)parameters.get(KERNEL_PARAMETER)) {
+ switch((String)state.get(KERNEL_PARAMETER)) {
case "gaussian": {
final double sigma = (double)parameters.get(SIGMA_PARAMETER);
@@ -142,13 +142,14 @@ public final class KernelHelper {
throw new IllegalArgumentException("The kernel " + parameters.get(KERNEL_PARAMETER) + " is not supported.");
}
- public static List<Parameter> toParameters(final Regression<double[]> regression) {
+ public static List<Parameter> toParameters(final Regression<double[]> regression, final String kernelName) {
final KernelMachine<double []> machine = (KernelMachine<double[]>)regression;
final List<Parameter> result = new LinkedList<>();
addParameter("weights", machine.weights(), result);
addParameter("intercept", machine.intercept(), result);
addParameter("instances", machine.instances(), result);
+ addParameter(KERNEL_PARAMETER, kernelName, result);
return result;
}
--
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