de.lmu.ifi.dbs.elki.algorithm.clustering
Class DeLiClu<O extends NumberVector<O,?>,D extends Distance<D>>

java.lang.Object
  de.lmu.ifi.dbs.elki.logging.AbstractLoggable
      de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizable
          de.lmu.ifi.dbs.elki.algorithm.AbstractAlgorithm<O,R>
              de.lmu.ifi.dbs.elki.algorithm.DistanceBasedAlgorithm<O,D,ClusterOrderResult<D>>
                  de.lmu.ifi.dbs.elki.algorithm.clustering.DeLiClu<O,D>

Type Parameters:

O - the type of NumberVector handled by this Algorithm

D - the type of Distance used

All Implemented Interfaces:

Algorithm<O,ClusterOrderResult<D>>, Parameterizable

public class DeLiClu<O extends NumberVector<O,?>,D extends Distance<D>>
extends DistanceBasedAlgorithm<O,D,ClusterOrderResult<D>>

DeLiClu provides the DeLiClu algorithm, a hierarchical algorithm to find density-connected sets in a database.

Reference:
E. Achtert, C. Böhm, P. Kröger: DeLiClu: Boosting Robustness, Completeness, Usability, and Efficiency of Hierarchical Clustering by a Closest Pair Ranking.
In Proc. 10th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD 2006), Singapore, 2006.

Author:

Elke Achtert

Nested Class Summary

class

DeLiClu.SpatialObjectPair Encapsulates an entry in the cluster order.

Field Summary

private ClusterOrderResult<D>	clusterOrder Provides the result of the algorithm.
private Heap<D,DeLiClu.SpatialObjectPair>	heap The priority queue for the algorithm.
private KNNJoin<O,D,DeLiCluNode,DeLiCluEntry>	knnJoin Holds the knnJoin algorithm.
static OptionID	MINPTS_ID OptionID for MINPTS_PARAM
private IntParameter	MINPTS_PARAM Parameter to specify the threshold for minimum number of points within a cluster, must be an integer greater than 0.
protected int	numNodes The number of nodes of the DeLiCluTree.

Fields inherited from class de.lmu.ifi.dbs.elki.algorithm.DistanceBasedAlgorithm

DISTANCE_FUNCTION_ID, DISTANCE_FUNCTION_PARAM

Fields inherited from class de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizable

optionHandler

Fields inherited from class de.lmu.ifi.dbs.elki.logging.AbstractLoggable

debug, logger

Constructor Summary

DeLiClu()
Provides the DeLiClu algorithm, adding parameter MINPTS_PARAM to the option handler additionally to parameters of super class.

Method Summary

private void	expandDirNodes(SpatialDistanceFunction<O,D> distFunction, DeLiCluNode node1, DeLiCluNode node2) Expands the specified directory nodes.
private void	expandLeafNodes(SpatialDistanceFunction<O,D> distFunction, DeLiCluNode node1, DeLiCluNode node2, AnnotationResult<KNNList<D>> knns) Expands the specified directory nodes.
private void	expandNodes(DeLiCluTree<O> index, SpatialDistanceFunction<O,D> distFunction, DeLiClu.SpatialObjectPair nodePair, AnnotationResult<KNNList<D>> knns) Expands the spatial nodes of the specified pair.
Description	getDescription() Returns a description of the algorithm.
ClusterOrderResult<D>	getResult() Returns the result of the algorithm.
private Integer	getStartObject(SpatialIndexDatabase<O,DeLiCluNode,DeLiCluEntry> database) Returns the id of the start object for the run method.
private void	reinsertExpanded(SpatialDistanceFunction<O,D> distFunction, DeLiCluTree<O> index, List<TreeIndexPathComponent<DeLiCluEntry>> path, AnnotationResult<KNNList<D>> knns) Reinserts the objects of the already expanded nodes.
private void	reinsertExpanded(SpatialDistanceFunction<O,D> distFunction, DeLiCluTree<O> index, List<TreeIndexPathComponent<DeLiCluEntry>> path, int pos, SpatialEntry parentEntry, AnnotationResult<KNNList<D>> knns)
protected ClusterOrderResult<D>	runInTime(Database<O> database) Performs the DeLiClu algorithm on the given database.
List<String>	setParameters(List<String> args) Calls the super method.
private void	updateHeap(D reachability, DeLiClu.SpatialObjectPair pair) Adds the specified entry with the specified key tp the heap.

Methods inherited from class de.lmu.ifi.dbs.elki.algorithm.DistanceBasedAlgorithm

getDistanceFunction

Methods inherited from class de.lmu.ifi.dbs.elki.algorithm.AbstractAlgorithm

isTime, isVerbose, run, setTime, setVerbose

Methods inherited from class de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizable

addOption, addParameterizable, addParameterizable, checkGlobalParameterConstraints, collectOptions, getAttributeSettings, getParameters, rememberParametersExcept, removeOption, removeParameterizable, shortDescription

Methods inherited from class de.lmu.ifi.dbs.elki.logging.AbstractLoggable

debugFine, debugFiner, debugFinest, exception, progress, verbose, warning

Methods inherited from class java.lang.Object

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

Methods inherited from interface de.lmu.ifi.dbs.elki.utilities.optionhandling.Parameterizable

checkGlobalParameterConstraints, collectOptions, getParameters, shortDescription

Field Detail

MINPTS_ID

public static final OptionID MINPTS_ID

OptionID for MINPTS_PARAM

MINPTS_PARAM

private final IntParameter MINPTS_PARAM

Parameter to specify the threshold for minimum number of points within a cluster, must be an integer greater than 0.

Key: -deliclu.minpts

clusterOrder

private ClusterOrderResult<D extends Distance<D>> clusterOrder

Provides the result of the algorithm.

heap

private Heap<D extends Distance<D>,DeLiClu.SpatialObjectPair> heap

The priority queue for the algorithm.

knnJoin

private KNNJoin<O extends NumberVector<O,?>,D extends Distance<D>,DeLiCluNode,DeLiCluEntry> knnJoin

Holds the knnJoin algorithm.

numNodes

protected int numNodes

The number of nodes of the DeLiCluTree.

Constructor Detail

DeLiClu

public DeLiClu()

Provides the DeLiClu algorithm, adding parameter MINPTS_PARAM to the option handler additionally to parameters of super class.

Method Detail

runInTime

protected ClusterOrderResult<D> runInTime(Database<O> database)
                                                       throws IllegalStateException

Performs the DeLiClu algorithm on the given database.

Specified by:

runInTime in class AbstractAlgorithm<O extends NumberVector<O,?>,ClusterOrderResult<D extends Distance<D>>>

Parameters:

database - the database to run the algorithm on

Returns:

the Result computed by this algorithm

Throws:

IllegalStateException - if the algorithm has not been initialized properly (e.g. the setParameters(String[]) method has been failed to be called).

getDescription

public Description getDescription()

Description copied from interface: Algorithm

Returns a description of the algorithm.

Returns:

a description of the algorithm

setParameters

public List<String> setParameters(List<String> args)
                           throws ParameterException

Calls the super method. The remaining parameters and the value of parameter MINPTS_PARAM are passed to the knnJoin.

Specified by:

setParameters in interface Parameterizable

Overrides:

setParameters in class DistanceBasedAlgorithm<O extends NumberVector<O,?>,D extends Distance<D>,ClusterOrderResult<D extends Distance<D>>>

Parameters:

args - parameters to set the attributes accordingly to

Returns:

a list containing the unused parameters

Throws:

ParameterException - in case of wrong parameter-setting

getResult

public ClusterOrderResult<D> getResult()

Description copied from interface: Algorithm

Returns the result of the algorithm.

Returns:

the result of the algorithm

getStartObject

private Integer getStartObject(SpatialIndexDatabase<O,DeLiCluNode,DeLiCluEntry> database)

Returns the id of the start object for the run method.

Parameters:

database - the database storing the objects

Returns:

the id of the start object for the run method

updateHeap

private void updateHeap(D reachability,
                        DeLiClu.SpatialObjectPair pair)

Adds the specified entry with the specified key tp the heap. If the entry's object is already in the heap, it will only be updated.

Parameters:

reachability - the reachability of the entry's object

pair - the entry to be added

expandNodes

private void expandNodes(DeLiCluTree<O> index,
                         SpatialDistanceFunction<O,D> distFunction,
                         DeLiClu.SpatialObjectPair nodePair,
                         AnnotationResult<KNNList<D>> knns)

Expands the spatial nodes of the specified pair.

Parameters:

index - the index storing the objects

distFunction - the spatial distance function of this algorithm

nodePair - the pair of nodes to be expanded

knns - the knn list

expandDirNodes

private void expandDirNodes(SpatialDistanceFunction<O,D> distFunction,
                            DeLiCluNode node1,
                            DeLiCluNode node2)

Expands the specified directory nodes.

Parameters:

distFunction - the spatial distance function of this algorithm

node1 - the first node

node2 - the second node

expandLeafNodes

private void expandLeafNodes(SpatialDistanceFunction<O,D> distFunction,
                             DeLiCluNode node1,
                             DeLiCluNode node2,
                             AnnotationResult<KNNList<D>> knns)

Expands the specified directory nodes.

Parameters:

distFunction - the spatial distance function of this algorithm

node1 - the first node

node2 - the second node

knns - the knn list

reinsertExpanded

private void reinsertExpanded(SpatialDistanceFunction<O,D> distFunction,
                              DeLiCluTree<O> index,
                              List<TreeIndexPathComponent<DeLiCluEntry>> path,
                              AnnotationResult<KNNList<D>> knns)

Reinserts the objects of the already expanded nodes.

Parameters:

distFunction - the spatial distance function of this algorithm

index - the index storing the objects

path - the path of the object inserted last

knns - the knn list

reinsertExpanded

private void reinsertExpanded(SpatialDistanceFunction<O,D> distFunction,
                              DeLiCluTree<O> index,
                              List<TreeIndexPathComponent<DeLiCluEntry>> path,
                              int pos,
                              SpatialEntry parentEntry,
                              AnnotationResult<KNNList<D>> knns)