Package elki.clustering.hierarchical

Class AbstractHDBSCAN<O>

java.lang.Object

elki.clustering.hierarchical.AbstractHDBSCAN<O>

Type Parameters:

O - Input object type

All Implemented Interfaces:

Algorithm

Direct Known Subclasses:

HDBSCANLinearMemory, SLINKHDBSCANLinearMemory

@Reference(authors="R. J. G. B. Campello, D. Moulavi, J. Sander",
           title="Density-Based Clustering Based on Hierarchical Density Estimates",
           booktitle="Pacific-Asia Conf. Advances in Knowledge Discovery and Data Mining (PAKDD)",
           url="https://doi.org/10.1007/978-3-642-37456-2_14",
           bibkey="DBLP:conf/pakdd/CampelloMS13")
public abstract class AbstractHDBSCAN<O>
extends java.lang.Object
implements Algorithm

Abstract base class for HDBSCAN variations.

Reference:

R. J. G. B. Campello, D. Moulavi, J. Sander
Density-Based Clustering Based on Hierarchical Density Estimates
Pacific-Asia Conf. Advances in Knowledge Discovery and Data Mining (PAKDD)

Since:

0.7.0

Author:

Erich Schubert

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
protected static class	AbstractHDBSCAN.HDBSCANAdapter	Class for processing the HDBSCAN G_mpts graph.
static class	AbstractHDBSCAN.HeapMSTCollector	Class for collecting the minimum spanning tree edges into a heap.

Nested classes/interfaces inherited from interface elki.Algorithm

Algorithm.Utils

Field Summary

Fields

Modifier and Type	Field	Description
protected Distance<? super O>	distance	Distance function used.
protected int	minPts	MinPts parameter.

Constructor Summary

Constructors

Constructor	Description
AbstractHDBSCAN(Distance<? super O> distance, int minPts)	Constructor.

Method Summary

Modifier and Type	Method	Description
protected WritableDoubleDataStore	computeCoreDists(DBIDs ids, KNNSearcher<DBIDRef> knnQ, int minPts)	Compute the core distances for all objects.
protected ClusterMergeHistoryBuilder	convertToMergeList(ArrayDBIDs ids, DoubleLongHeap heap, ClusterMergeHistoryBuilder builder)	Convert spanning tree to a pointer representation.
TypeInformation[]	getInputTypeRestriction()	Get the input type restriction used for negotiating the data query.
protected abstract Logging	getLogger()	Get the (STATIC) logger for this class.

Methods inherited from class java.lang.Object

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

Methods inherited from interface elki.Algorithm

autorun

Field Detail

minPts

protected final int minPts

MinPts parameter.

distance

protected Distance<? super O> distance

Distance function used.

Constructor Detail

AbstractHDBSCAN

public AbstractHDBSCAN(Distance<? super O> distance,
                       int minPts)

Constructor.

Parameters:

distance - Distance function

minPts - Minimum number of points for coredists

Method Detail

computeCoreDists

protected WritableDoubleDataStore computeCoreDists(DBIDs ids,
                                                   KNNSearcher<DBIDRef> knnQ,
                                                   int minPts)

Compute the core distances for all objects.

Parameters:

ids - Objects

knnQ - kNN query

minPts - Minimum neighborhood size

Returns:

Data store with core distances

convertToMergeList

protected ClusterMergeHistoryBuilder convertToMergeList(ArrayDBIDs ids,
                                                        DoubleLongHeap heap,
                                                        ClusterMergeHistoryBuilder builder)

Convert spanning tree to a pointer representation.

Note: the heap must use the correct encoding of indexes.

Parameters:

ids - IDs indexed

heap - Heap

builder - Hierarchy builder

Returns:

builder, for method chaining

getInputTypeRestriction

public TypeInformation[] getInputTypeRestriction()

Description copied from interface: Algorithm

Get the input type restriction used for negotiating the data query.

Specified by:

getInputTypeRestriction in interface Algorithm

Returns:

Type restriction

getLogger

protected abstract Logging getLogger()

Get the (STATIC) logger for this class.

Returns:

the static logger