de.lmu.ifi.dbs.elki.algorithm.clustering
Class OPTICS<O extends DatabaseObject,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.OPTICS<O,D>

Type Parameters:

O - the type of DatabaseObjects handled by the algorithm

D - the type of Distance used to discern objects

All Implemented Interfaces:

Algorithm<O,ClusterOrderResult<D>>, Parameterizable

public class OPTICS<O extends DatabaseObject,D extends Distance<D>>
extends DistanceBasedAlgorithm<O,D,ClusterOrderResult<D>>

OPTICS provides the OPTICS algorithm.

Reference: M. Ankerst, M. Breunig, H.-P. Kriegel, and J. Sander: OPTICS: Ordering Points to Identify the Clustering Structure.
In: Proc. ACM SIGMOD Int. Conf. on Management of Data (SIGMOD '99).

Author:

Elke Achtert

Nested Class Summary

class

OPTICS.COEntry Encapsulates an entry in the cluster order.

Field Summary

private ClusterOrderResult<D>	clusterOrder Provides the result of the algorithm.
private String	epsilon Hold the value of EPSILON_PARAM.
static OptionID	EPSILON_ID OptionID for EPSILON_PARAM
private PatternParameter	EPSILON_PARAM Parameter to specify the maximum radius of the neighborhood to be considered, must be suitable to the distance function specified.
private Heap<D,OPTICS.COEntry>	heap The priority queue for the algorithm.
private int	minpts Holds the value of MINPTS_PARAM.
static OptionID	MINPTS_ID OptionID for MINPTS_PARAM
private IntParameter	MINPTS_PARAM Parameter to specify the threshold for minimum number of points in the epsilon-neighborhood of a point, must be an integer greater than 0.
private Set<Integer>	processedIDs Holds a set of processed ids.

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

OPTICS()
Provides the OPTICS algorithm, adding parameters EPSILON_PARAM and MINPTS_PARAM to the option handler additionally to parameters of super class.

Method Summary

protected void	expandClusterOrder(Database<O> database, Integer objectID, FiniteProgress progress) OPTICS-function expandClusterOrder.
Description	getDescription() Returns a description of the algorithm.
ClusterOrderResult<D>	getResult() Returns the result of the algorithm.
protected ClusterOrderResult<D>	runInTime(Database<O> database) Performs the OPTICS algorithm on the given database.
List<String>	setParameters(List<String> args) Calls the super method and sets additionally the values of the parameters EPSILON_PARAM and MINPTS_PARAM.
private void	updateHeap(D reachability, OPTICS.COEntry entry) 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

EPSILON_ID

public static final OptionID EPSILON_ID

OptionID for EPSILON_PARAM

EPSILON_PARAM

private final PatternParameter EPSILON_PARAM

Parameter to specify the maximum radius of the neighborhood to be considered, must be suitable to the distance function specified.

Key: -optics.epsilon

epsilon

private String epsilon

Hold the value of EPSILON_PARAM.

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 in the epsilon-neighborhood of a point, must be an integer greater than 0.

Key: -optics.minpts

minpts

private int minpts

Holds the value of MINPTS_PARAM.

clusterOrder

private ClusterOrderResult<D extends Distance<D>> clusterOrder

Provides the result of the algorithm.

processedIDs

private Set<Integer> processedIDs

Holds a set of processed ids.

heap

private Heap<D extends Distance<D>,OPTICS.COEntry> heap

The priority queue for the algorithm.

Constructor Detail

OPTICS

public OPTICS()

Provides the OPTICS algorithm, adding parameters EPSILON_PARAM and MINPTS_PARAM to the option handler additionally to parameters of super class.

Method Detail

runInTime

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

Performs the OPTICS algorithm on the given database.

Specified by:

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

Parameters:

database - the database to run the algorithm on

Returns:

the Result computed by this algorithm

expandClusterOrder

protected void expandClusterOrder(Database<O> database,
                                  Integer objectID,
                                  FiniteProgress progress)

OPTICS-function expandClusterOrder.

Parameters:

database - the database on which the algorithm is run

objectID - the currently processed object

progress - the progress object to actualize the current progress if the algorithm

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 and sets additionally the values of the parameters EPSILON_PARAM and MINPTS_PARAM.

Specified by:

setParameters in interface Parameterizable

Overrides:

setParameters in class DistanceBasedAlgorithm<O extends DatabaseObject,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

updateHeap

private void updateHeap(D reachability,
                        OPTICS.COEntry entry)

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

entry - the entry to be added