Package net.bmahe.genetics4j.samples.clustering

Class Clustering

java.lang.Object

net.bmahe.genetics4j.samples.clustering.Clustering

public class Clustering
extends Object

Field Summary

Fields

Modifier and Type	Field	Description
static final int	DEFAULT_COMBINATION_ARITHMETIC
static final int	DEFAULT_COMBINATION_CROSSOVER_ARITHMETIC
static final double	DEFAULT_CREEP_MUTATION_MEAN
static final double	DEFAULT_CREEP_MUTATION_RATE
static final double	DEFAULT_CREEP_MUTATION_STDDEV
static final int	DEFAULT_NUM_CLUSTERS
static final int	DEFAULT_NUMBER_TOURNAMENTS
static final int	DEFAULT_POPULATION_SIZE
static final double	DEFAULT_RANDOM_MUTATION_RATE
static final org.apache.logging.log4j.Logger	logger
static final String	LONG_PARAM_BASE_DIR_OUTPUT
static final String	LONG_PARAM_COMBINATION_ARITHMETIC
static final String	LONG_PARAM_COMBINATION_CROSSOVER
static final String	LONG_PARAM_CREEP_MUTATION_MEAN
static final String	LONG_PARAM_CREEP_MUTATION_RATE
static final String	LONG_PARAM_CREEP_MUTATION_STD_DEV
static final String	LONG_PARAM_FIXED_TERMINATION
static final String	LONG_PARAM_NUM_CLUSTERS
static final String	LONG_PARAM_NUMBER_TOURNAMENTS
static final String	LONG_PARAM_OUTPUT_CSV
static final String	LONG_PARAM_OUTPUT_WITH_SSE_CSV
static final String	LONG_PARAM_POPULATION_SIZE
static final String	LONG_PARAM_RANDOM_MUTATION_RATE
static final String	LONG_PARAM_SOURCE_CUSTERS_CSV
static final String	LONG_PARAM_SOURCE_DATA_CSV
static final String	PARAM_BASE_DIR_OUTPUT
static final String	PARAM_COMBINATION_ARITHMETIC
static final String	PARAM_COMBINATION_CROSSOVER
static final String	PARAM_CREEP_MUTATION_MEAN
static final String	PARAM_CREEP_MUTATION_RATE
static final String	PARAM_CREEP_MUTATION_STD_DEV
static final String	PARAM_FIXED_TERMINATION
static final String	PARAM_NUM_CLUSTERS
static final String	PARAM_NUMBER_TOURNAMENTS
static final String	PARAM_OUTPUT_CSV
static final String	PARAM_OUTPUT_WITH_SSE_CSV
static final String	PARAM_POPULATION_SIZE
static final String	PARAM_RANDOM_MUTATION_RATE
static final String	PARAM_SOURCE_CLUSTERS_CSV
static final String	PARAM_SOURCE_DATA_CSV

Constructor Summary

Constructors

Constructor	Description
Clustering()

Method Summary

Modifier and Type	Method	Description
static List<org.apache.commons.math3.ml.clustering.CentroidCluster<LocationWrapper>>	apacheCommonsMathCluster(double[][] clusters, double[][] data)
static void	cliError(org.apache.commons.cli.Options options, String errorMessage)
private static final double[][]	computeAllDistances(double[][] array)
private static final double	computeDistance(double[][] array, int i, int j)
static void	doGA(int k, double min, double max, int numberTournaments, int combinationArithmetic, int combinationCrossover, double randomMutationRate, double creepMutationRate, double creepMutationMean, double creepMutationStdDev, Fitness<Double> fitnessFunction, Termination<Double> terminations, int populationSize, String outputCSV, double[][] data, double[][] distances, String baseDir, String filenameSuffix)
static double[][]	generateClusters(Random random, int numClusters, double minX, double maxX, double minY, double maxY)
static double[][]	generateDataPoints(Random random, double[][] clusters, int numDataPoints, double radius)
static void	main(String[] args)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

logger

public static final org.apache.logging.log4j.Logger logger

DEFAULT_NUM_CLUSTERS

public static final int DEFAULT_NUM_CLUSTERS

See Also:

• Constant Field Values

DEFAULT_NUMBER_TOURNAMENTS

public static final int DEFAULT_NUMBER_TOURNAMENTS

See Also:

• Constant Field Values

DEFAULT_POPULATION_SIZE

public static final int DEFAULT_POPULATION_SIZE

See Also:

• Constant Field Values

DEFAULT_RANDOM_MUTATION_RATE

public static final double DEFAULT_RANDOM_MUTATION_RATE

See Also:

• Constant Field Values

DEFAULT_CREEP_MUTATION_RATE

public static final double DEFAULT_CREEP_MUTATION_RATE

See Also:

• Constant Field Values

DEFAULT_CREEP_MUTATION_MEAN

public static final double DEFAULT_CREEP_MUTATION_MEAN

See Also:

• Constant Field Values

DEFAULT_CREEP_MUTATION_STDDEV

public static final double DEFAULT_CREEP_MUTATION_STDDEV

See Also:

• Constant Field Values

DEFAULT_COMBINATION_ARITHMETIC

public static final int DEFAULT_COMBINATION_ARITHMETIC

See Also:

• Constant Field Values

DEFAULT_COMBINATION_CROSSOVER_ARITHMETIC

public static final int DEFAULT_COMBINATION_CROSSOVER_ARITHMETIC

See Also:

• Constant Field Values

PARAM_NUM_CLUSTERS

public static final String PARAM_NUM_CLUSTERS

See Also:

• Constant Field Values

LONG_PARAM_NUM_CLUSTERS

public static final String LONG_PARAM_NUM_CLUSTERS

See Also:

• Constant Field Values

PARAM_NUMBER_TOURNAMENTS

public static final String PARAM_NUMBER_TOURNAMENTS

See Also:

• Constant Field Values

LONG_PARAM_NUMBER_TOURNAMENTS

public static final String LONG_PARAM_NUMBER_TOURNAMENTS

See Also:

• Constant Field Values

PARAM_POPULATION_SIZE

public static final String PARAM_POPULATION_SIZE

See Also:

• Constant Field Values

LONG_PARAM_POPULATION_SIZE

public static final String LONG_PARAM_POPULATION_SIZE

See Also:

• Constant Field Values

PARAM_SOURCE_CLUSTERS_CSV

public static final String PARAM_SOURCE_CLUSTERS_CSV

See Also:

• Constant Field Values

LONG_PARAM_SOURCE_CUSTERS_CSV

public static final String LONG_PARAM_SOURCE_CUSTERS_CSV

See Also:

• Constant Field Values

PARAM_SOURCE_DATA_CSV

public static final String PARAM_SOURCE_DATA_CSV

See Also:

• Constant Field Values

LONG_PARAM_SOURCE_DATA_CSV

public static final String LONG_PARAM_SOURCE_DATA_CSV

See Also:

• Constant Field Values

PARAM_FIXED_TERMINATION

public static final String PARAM_FIXED_TERMINATION

See Also:

• Constant Field Values

LONG_PARAM_FIXED_TERMINATION

public static final String LONG_PARAM_FIXED_TERMINATION

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• Constant Field Values

PARAM_RANDOM_MUTATION_RATE

public static final String PARAM_RANDOM_MUTATION_RATE

See Also:

• Constant Field Values

LONG_PARAM_RANDOM_MUTATION_RATE

public static final String LONG_PARAM_RANDOM_MUTATION_RATE

See Also:

• Constant Field Values

PARAM_CREEP_MUTATION_RATE

public static final String PARAM_CREEP_MUTATION_RATE

See Also:

• Constant Field Values

LONG_PARAM_CREEP_MUTATION_RATE

public static final String LONG_PARAM_CREEP_MUTATION_RATE

See Also:

• Constant Field Values

PARAM_CREEP_MUTATION_MEAN

public static final String PARAM_CREEP_MUTATION_MEAN

See Also:

• Constant Field Values

LONG_PARAM_CREEP_MUTATION_MEAN

public static final String LONG_PARAM_CREEP_MUTATION_MEAN

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• Constant Field Values

PARAM_CREEP_MUTATION_STD_DEV

public static final String PARAM_CREEP_MUTATION_STD_DEV

See Also:

• Constant Field Values

LONG_PARAM_CREEP_MUTATION_STD_DEV

public static final String LONG_PARAM_CREEP_MUTATION_STD_DEV

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• Constant Field Values

PARAM_COMBINATION_ARITHMETIC

public static final String PARAM_COMBINATION_ARITHMETIC

See Also:

• Constant Field Values

LONG_PARAM_COMBINATION_ARITHMETIC

public static final String LONG_PARAM_COMBINATION_ARITHMETIC

See Also:

• Constant Field Values

PARAM_COMBINATION_CROSSOVER

public static final String PARAM_COMBINATION_CROSSOVER

See Also:

• Constant Field Values

LONG_PARAM_COMBINATION_CROSSOVER

public static final String LONG_PARAM_COMBINATION_CROSSOVER

See Also:

• Constant Field Values

PARAM_OUTPUT_CSV

public static final String PARAM_OUTPUT_CSV

See Also:

• Constant Field Values

LONG_PARAM_OUTPUT_CSV

public static final String LONG_PARAM_OUTPUT_CSV

See Also:

• Constant Field Values

PARAM_OUTPUT_WITH_SSE_CSV

public static final String PARAM_OUTPUT_WITH_SSE_CSV

See Also:

• Constant Field Values

LONG_PARAM_OUTPUT_WITH_SSE_CSV

public static final String LONG_PARAM_OUTPUT_WITH_SSE_CSV

See Also:

• Constant Field Values

PARAM_BASE_DIR_OUTPUT

public static final String PARAM_BASE_DIR_OUTPUT

See Also:

• Constant Field Values

LONG_PARAM_BASE_DIR_OUTPUT

public static final String LONG_PARAM_BASE_DIR_OUTPUT

See Also:

• Constant Field Values

Constructor Details

Clustering

public Clustering()

Method Details

cliError

public static void cliError(org.apache.commons.cli.Options options,
 String errorMessage)

computeDistance

private static final double computeDistance(double[][] array,
 int i,
 int j)

computeAllDistances

private static final double[][] computeAllDistances(double[][] array)

generateClusters

public static double[][] generateClusters(Random random,
 int numClusters,
 double minX,
 double maxX,
 double minY,
 double maxY)

generateDataPoints

public static double[][] generateDataPoints(Random random,
 double[][] clusters,
 int numDataPoints,
 double radius)

doGA

public static void doGA(int k,
 double min,
 double max,
 int numberTournaments,
 int combinationArithmetic,
 int combinationCrossover,
 double randomMutationRate,
 double creepMutationRate,
 double creepMutationMean,
 double creepMutationStdDev,
 Fitness<Double> fitnessFunction,
 Termination<Double> terminations,
 int populationSize,
 String outputCSV,
 double[][] data,
 double[][] distances,
 String baseDir,
 String filenameSuffix)
                 throws IOException

Throws:

IOException

apacheCommonsMathCluster

public static List<org.apache.commons.math3.ml.clustering.CentroidCluster<LocationWrapper>> apacheCommonsMathCluster(double[][] clusters,
 double[][] data)

main

public static void main(String[] args)
                 throws IOException

Throws:

IOException