Package elki.clustering.kmeans

Class AbstractKMeans.Instance

java.lang.Object

elki.clustering.kmeans.AbstractKMeans.Instance

Direct Known Subclasses:

CompareMeans.Instance, HamerlyKMeans.Instance, HartiganWongKMeans.Instance, KDTreePruningKMeans.Instance, KMeansMinusMinus.Instance, KMediansLloyd.Instance, LloydKMeans.Instance, MacQueenKMeans.Instance, SimplifiedElkanKMeans.Instance, SingleAssignmentKMeans.Instance, SphericalKMeans.Instance, YinYangKMeans.Instance

Enclosing class:

AbstractKMeans<V extends elki.data.NumberVector,M extends Model>

public abstract static class AbstractKMeans.Instance
extends java.lang.Object

Inner instance for a run, for better encapsulation, that encapsulates the standard flow of most (but not all) k-means variations.

Author:

Erich Schubert

Field Summary

Fields

Modifier and Type	Field	Description
protected elki.database.datastore.WritableIntegerDataStore	assignment	A mapping of elements to cluster ids.
protected java.util.List<elki.database.ids.ModifiableDBIDs>	clusters	Store the elements per cluster.
private elki.distance.NumberVectorDistance<?>	df	Distance function.
protected long	diststat	Number of distance computations
protected boolean	isSquared	Indicates whether the distance function is squared.
protected int	k	Number of clusters.
protected java.lang.String	key	Key for statistics logging.
protected double[][]	means	Cluster means.
protected elki.database.relation.Relation<? extends elki.data.NumberVector>	relation	Data relation.
protected double[]	varsum	Sum of squared deviations in each cluster.

Constructor Summary

Constructors

Constructor	Description
Instance(elki.database.relation.Relation<? extends elki.data.NumberVector> relation, elki.distance.NumberVectorDistance<?> df, double[][] means)	Constructor.

Method Summary

Modifier and Type	Method	Description
protected int	assignToNearestCluster()	Assign each object to the nearest cluster.
Clustering<KMeansModel>	buildResult()	Build a standard k-means result, with known cluster variance sums.
Clustering<KMeansModel>	buildResult(boolean varstat, elki.database.relation.Relation<? extends elki.data.NumberVector> relation)	Build the result, recomputing the cluster variance if varstat is set to true.
protected void	computeSquaredSeparation(double[][] cost)	Initial separation of means.
protected void	copyMeans(double[][] src, double[][] dst)	Copy means
protected double	distance(double[] x, double[] y)	Compute the squared distance (and count the distance computations).
protected double	distance(elki.data.NumberVector x, double[] y)	Compute the squared distance (and count the distance computations).
protected double	distance(elki.data.NumberVector x, elki.data.NumberVector y)	Compute the squared distance (and count the distance computations).
protected abstract elki.logging.Logging	getLogger()	Get the class logger.
protected void	initialSeperation(double[][] cdist)	Initial separation of means.
protected abstract int	iterate(int iteration)	Main loop function.
protected void	meansFromSums(double[][] dst, double[][] sums, double[][] prev)	Compute means from cluster sums by averaging.
protected void	movedDistance(double[][] means, double[][] newmeans, double[] dists)	Maximum distance moved.
protected void	recomputeSeperation(double[] sep, double[][] cdist)	Recompute the separation of cluster means.
protected void	recomputeVariance(elki.database.relation.Relation<? extends elki.data.NumberVector> relation)	Recompute the cluster variances.
void	run(int maxiter)	Run the clustering.
protected double	sqrtdistance(double[] x, double[] y)	Compute the distance (and count the distance computations).
protected double	sqrtdistance(elki.data.NumberVector x, double[] y)	Compute the distance (and count the distance computations).
protected double	sqrtdistance(elki.data.NumberVector x, elki.data.NumberVector y)	Compute the distance (and count the distance computations).

Methods inherited from class java.lang.Object

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

Field Detail

means

protected double[][] means

Cluster means.

clusters

protected java.util.List<elki.database.ids.ModifiableDBIDs> clusters

Store the elements per cluster.

assignment

protected elki.database.datastore.WritableIntegerDataStore assignment

A mapping of elements to cluster ids.

varsum

protected double[] varsum

Sum of squared deviations in each cluster.

relation

protected elki.database.relation.Relation<? extends elki.data.NumberVector> relation

Data relation.

diststat

protected long diststat

Number of distance computations

df

private final elki.distance.NumberVectorDistance<?> df

Distance function.

k

protected final int k

Number of clusters.

isSquared

protected final boolean isSquared

Indicates whether the distance function is squared.

key

protected java.lang.String key

Key for statistics logging.

Constructor Detail

Instance

public Instance(elki.database.relation.Relation<? extends elki.data.NumberVector> relation,
                elki.distance.NumberVectorDistance<?> df,
                double[][] means)

Constructor.

Parameters:

relation - Relation to process

means - Initial mean

Method Detail

distance

protected double distance(elki.data.NumberVector x,
                          elki.data.NumberVector y)

Compute the squared distance (and count the distance computations).

Parameters:

x - First object

y - Second object

Returns:

Distance

distance

protected double distance(elki.data.NumberVector x,
                          double[] y)

Compute the squared distance (and count the distance computations).

Parameters:

x - First object

y - Second object

Returns:

Distance

distance

protected double distance(double[] x,
                          double[] y)

Compute the squared distance (and count the distance computations).

Parameters:

x - First object

y - Second object

Returns:

Distance

sqrtdistance

protected double sqrtdistance(elki.data.NumberVector x,
                              elki.data.NumberVector y)

Compute the distance (and count the distance computations). If the distance is squared, also compute the square root.

Parameters:

x - First object

y - Second object

Returns:

Distance

sqrtdistance

protected double sqrtdistance(elki.data.NumberVector x,
                              double[] y)

Compute the distance (and count the distance computations). If the distance is squared, also compute the square root.

Parameters:

x - First object

y - Second object

Returns:

Distance

sqrtdistance

protected double sqrtdistance(double[] x,
                              double[] y)

Compute the distance (and count the distance computations). If the distance is squared, also compute the square root.

Parameters:

x - First object

y - Second object

Returns:

Distance

run

public void run(int maxiter)

Run the clustering.

Parameters:

maxiter - Maximum number of iterations

iterate

protected abstract int iterate(int iteration)

Main loop function.

Parameters:

iteration - Iteration number (beginning at 1)

Returns:

Number of reassigned points

meansFromSums

protected void meansFromSums(double[][] dst,
                             double[][] sums,
                             double[][] prev)

Compute means from cluster sums by averaging.

Parameters:

dst - Output means

sums - Input sums

prev - Previous means, to handle empty clusters

copyMeans

protected void copyMeans(double[][] src,
                         double[][] dst)

Copy means

Parameters:

src - Source values

dst - Destination values

assignToNearestCluster

protected int assignToNearestCluster()

Assign each object to the nearest cluster.

Returns:

number of objects reassigned

recomputeSeperation

protected void recomputeSeperation(double[] sep,
                                   double[][] cdist)

Recompute the separation of cluster means.

Used by Elkan's variant and Exponion.

Parameters:

sep - Output array of separation

cdist - Center-to-Center distances (half-sqrt scaled)

initialSeperation

protected void initialSeperation(double[][] cdist)

Initial separation of means. Used by Elkan, SimplifiedElkan.

Parameters:

cdist - Pairwise separation output (as sqrt/2)

computeSquaredSeparation

protected void computeSquaredSeparation(double[][] cost)

Initial separation of means. Used by Hamerly, Exponion, and Annulus.

Parameters:

cost - Pairwise separation output (as squared/4)

movedDistance

protected void movedDistance(double[][] means,
                             double[][] newmeans,
                             double[] dists)

Maximum distance moved.

Used by Hamerly, Elkan, and derived classes.

Parameters:

means - Old means

newmeans - New means

dists - Distances moved (output)

buildResult

public Clustering<KMeansModel> buildResult()

Build a standard k-means result, with known cluster variance sums.

Note: this expects the varsum field to be correct!

Returns:

Clustering result

buildResult

public Clustering<KMeansModel> buildResult(boolean varstat,
                                           elki.database.relation.Relation<? extends elki.data.NumberVector> relation)

Build the result, recomputing the cluster variance if varstat is set to true.

Parameters:

varstat - Recompute cluster variance

relation - Data relation (only needed if varstat is set)

Returns:

Clustering result

recomputeVariance

protected void recomputeVariance(elki.database.relation.Relation<? extends elki.data.NumberVector> relation)

Recompute the cluster variances.

Parameters:

relation - Data relation

getLogger

protected abstract elki.logging.Logging getLogger()

Get the class logger.

Returns:

Logger