Package elki.clustering.hierarchical

Class MedoidLinkage.Instance

java.lang.Object

elki.clustering.hierarchical.AGNES.Instance

elki.clustering.hierarchical.MedoidLinkage.Instance

Enclosing class:

MedoidLinkage<O>

public static class MedoidLinkage.Instance
extends AGNES.Instance

Main worker instance of AGNES.

Author:

Erich Schubert

Field Summary

Fields

Modifier and Type	Field	Description
protected it.unimi.dsi.fastutil.ints.Int2ObjectOpenHashMap<elki.database.ids.ModifiableDBIDs>	clusters	Cluster to members map
protected elki.database.query.distance.DistanceQuery<?>	dq	Distance query
protected elki.database.ids.DBIDArrayIter	ix	Iterators into the object ids.
protected elki.database.ids.DBIDArrayIter	iy	Iterators into the object ids.
protected elki.database.ids.DBIDArrayMIter	mi	Iterators into medoid array.
protected elki.database.ids.DBIDArrayMIter	mj	Iterators into medoid array.

Fields inherited from class elki.clustering.hierarchical.AGNES.Instance

builder, end, linkage, mat

Constructor Summary

Constructors

Constructor	Description
Instance()	Constructor.

Method Summary

Modifier and Type	Method	Description
private static double	findMedoid(elki.database.query.distance.DistanceQuery<?> dq, elki.database.ids.DBIDs c, elki.database.ids.DBIDArrayMIter prototype)	Find the prototypes.
protected int	findMerge()	Perform the next merge step in AGNES.
protected void	merge(int x, int y)	Execute the cluster merge.
ClusterMergeHistory	run(ClusterDistanceMatrix mat, ClusterMergeHistoryBuilder builder)	Run the main algorithm.
ClusterPrototypeMergeHistory	run(elki.database.ids.ArrayDBIDs ids, ClusterDistanceMatrix mat, ClusterMergeHistoryBuilder builder, elki.database.query.distance.DistanceQuery<?> dq)	Run medoid linkage
protected void	updateMatrix(int x, int y)	Update the scratch distance matrix.

Methods inherited from class elki.clustering.hierarchical.AGNES.Instance

merge, shrinkActiveSet, updateMatrix

Methods inherited from class java.lang.Object

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

Field Detail

clusters

protected it.unimi.dsi.fastutil.ints.Int2ObjectOpenHashMap<elki.database.ids.ModifiableDBIDs> clusters

Cluster to members map

dq

protected elki.database.query.distance.DistanceQuery<?> dq

Distance query

mi

protected elki.database.ids.DBIDArrayMIter mi

Iterators into medoid array.

mj

protected elki.database.ids.DBIDArrayMIter mj

Iterators into medoid array.

ix

protected elki.database.ids.DBIDArrayIter ix

Iterators into the object ids.

iy

protected elki.database.ids.DBIDArrayIter iy

Iterators into the object ids.

Constructor Detail

Instance

public Instance()

Constructor.

Method Detail

run

public ClusterMergeHistory run(ClusterDistanceMatrix mat,
                               ClusterMergeHistoryBuilder builder)

Description copied from class: AGNES.Instance

Run the main algorithm.

Overrides:

run in class AGNES.Instance

Parameters:

mat - Distance matrix

builder - Result builder

Returns:

Cluster history

run

public ClusterPrototypeMergeHistory run(elki.database.ids.ArrayDBIDs ids,
                                        ClusterDistanceMatrix mat,
                                        ClusterMergeHistoryBuilder builder,
                                        elki.database.query.distance.DistanceQuery<?> dq)

Run medoid linkage

Parameters:

ids - Object ids

mat - Distance matrix

builder - Result builder

dq - Distance query

Returns:

Cluster merge history

findMerge

protected int findMerge()

Description copied from class: AGNES.Instance

Perform the next merge step in AGNES.

Overrides:

findMerge in class AGNES.Instance

Returns:

the index that has disappeared, for shrinking the working set

merge

protected void merge(int x,
                     int y)

Execute the cluster merge.

Parameters:

x - first cluster to merge, with x > y

y - second cluster to merge, with y < x

findMedoid

private static double findMedoid(elki.database.query.distance.DistanceQuery<?> dq,
                                 elki.database.ids.DBIDs c,
                                 elki.database.ids.DBIDArrayMIter prototype)

Find the prototypes.

Parameters:

dq - Distance query

c - Cluster

prototype - Prototype output

Returns:

New best distance

updateMatrix

protected void updateMatrix(int x,
                            int y)

Update the scratch distance matrix.

Parameters:

x - First matrix position

y - Second matrix position