OPTICS

java.lang.Object
- weka.clusterers.AbstractClusterer
- - weka.clusterers.OPTICS

All Implemented Interfaces:: java.io.Serializable, java.lang.Cloneable, weka.clusterers.Clusterer, weka.core.CapabilitiesHandler, weka.core.CapabilitiesIgnorer, weka.core.CommandlineRunnable, weka.core.OptionHandler, weka.core.RevisionHandler, weka.core.TechnicalInformationHandler

public class OPTICS
extends weka.clusterers.AbstractClusterer
implements weka.core.OptionHandler, weka.core.TechnicalInformationHandler

Basic implementation of OPTICS clustering algorithm that should *not* be used as a reference for runtime benchmarks: more sophisticated implementations exist! Clustering of new instances is not supported. More info:

Mihael Ankerst, Markus M. Breunig, Hans-Peter Kriegel, Joerg Sander: OPTICS: Ordering Points To Identify the Clustering Structure. In: ACM SIGMOD International Conference on Management of Data, 49-60, 1999.

BibTeX:

 @inproceedings{Ankerst1999,
    author = {Mihael Ankerst and Markus M. Breunig and Hans-Peter Kriegel and Joerg Sander},
    booktitle = {ACM SIGMOD International Conference on Management of Data},
    pages = {49-60},
    publisher = {ACM Press},
    title = {OPTICS: Ordering Points To Identify the Clustering Structure},
    year = {1999}
 }

Valid options are:

 -E <double>
  epsilon (default = 0.9)

 -M <int>
  minPoints (default = 6)

 -I <String>
  index (database) used for OPTICS (default = weka.clusterers.forOPTICSAndDBScan.Databases.SequentialDatabase)

 -D <String>
  distance-type (default = weka.clusterers.forOPTICSAndDBScan.DataObjects.EuclideanDataObject)

 -F
  write results to OPTICS_#TimeStamp#.TXT - File

 -no-gui
  suppress the display of the GUI after building the clusterer

 -db-output <file>
  The file to save the generated database to. If a directory
  is provided, the database doesn't get saved.
  The generated file can be viewed with the OPTICS Visualizer:
    java weka.clusterers.forOPTICSAndDBScan.OPTICS_GUI.OPTICS_Visualizer [file.ser]
  (default: .)

Version:: $Revision: 10838 $
Author:: Matthias Schubert (schubert@dbs.ifi.lmu.de), Zhanna Melnikova-Albrecht (melnikov@cip.ifi.lmu.de), Rainer Holzmann (holzmann@cip.ifi.lmu.de)
See Also:: Serialized Form

Constructor Summary

Constructors
Constructor and Description

OPTICS()

Constructors
Constructor and Description
`OPTICS()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`buildClusterer(weka.core.Instances instances)` Generate Clustering via OPTICS
`int`	`clusterInstance(weka.core.Instance instance)` Classifies a given instance.
`java.lang.String`	`databaseOutputTipText()` Returns the tip text for this property.
`java.lang.String`	`distanceFunctionTipText()` Returns the tip text for this property.
`java.lang.String`	`epsilonTipText()` Returns the tip text for this property
`weka.core.Capabilities`	`getCapabilities()` Returns default capabilities of the clusterer.
`java.io.File`	`getDatabaseOutput()` Returns the file to save the database to - if directory, database is not saved.
`weka.core.DistanceFunction`	`getDistanceFunction()` returns the distance function currently in use.
`double`	`getEpsilon()` Returns the value of epsilon
`int`	`getMinPoints()` Returns the value of minPoints
`java.lang.String[]`	`getOptions()` Gets the current option settings for the OptionHandler.
`java.util.ArrayList`	`getResultVector()` Returns the resultVector
`java.lang.String`	`getRevision()` Returns the revision string.
`SERObject`	`getSERObject()` Returns the internal database
`boolean`	`getShowGUI()` Returns the flag for showing the OPTICS visualizer GUI.
`weka.core.TechnicalInformation`	`getTechnicalInformation()` Returns an instance of a TechnicalInformation object, containing detailed information about the technical background of this class, e.g., paper reference or book this class is based on.
`boolean`	`getWriteOPTICSresults()` Returns the flag for writing actions
`java.lang.String`	`globalInfo()` Returns a string describing this DataMining-Algorithm
`java.util.Enumeration`	`listOptions()` Returns an enumeration of all the available options.
`static void`	`main(java.lang.String[] args)` Main Method for testing OPTICS
`java.lang.String`	`minPointsTipText()` Returns the tip text for this property
`int`	`numberOfClusters()` Returns the number of clusters.
`void`	`setDatabaseOutput(java.io.File value)` Sets the the file to save the generated database to.
`void`	`setDistanceFunction(weka.core.DistanceFunction df)` sets the distance function to use for nearest neighbour search.
`void`	`setEpsilon(double epsilon)` Sets a new value for epsilon
`void`	`setMinPoints(int minPoints)` Sets a new value for minPoints
`void`	`setOptions(java.lang.String[] options)` Sets the OptionHandler's options using the given list.
`void`	`setShowGUI(boolean value)` Sets the flag for displaying the GUI.
`void`	`setWriteOPTICSresults(boolean writeOPTICSresults)` Sets the flag for writing actions
`java.lang.String`	`showGUITipText()` Returns the tip text for this property.
`java.lang.String`	`toString()` Returns a description of the clusterer
`java.lang.String`	`writeOPTICSresultsTipText()` Returns the tip text for this property

Methods inherited from class weka.clusterers.AbstractClusterer
debugTipText, distributionForInstance, doNotCheckCapabilitiesTipText, forName, getDebug, getDoNotCheckCapabilities, makeCopies, makeCopy, postExecution, preExecution, run, runClusterer, setDebug, setDoNotCheckCapabilities

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface weka.core.OptionHandler
makeCopy

- Constructor Detail
  - OPTICS
```
public OPTICS()
```
- Method Detail
  - getCapabilities
```
public weka.core.Capabilities getCapabilities()
```
    Returns default capabilities of the clusterer.
    
    Specified by:
    
    getCapabilities in interface weka.clusterers.Clusterer
    
    Specified by:
    
    getCapabilities in interface weka.core.CapabilitiesHandler
    
    Overrides:
    
    getCapabilities in class weka.clusterers.AbstractClusterer
    
    Returns:
    
    the capabilities of this clusterer
  - buildClusterer
```
public void buildClusterer(weka.core.Instances instances)
                    throws java.lang.Exception
```
    Generate Clustering via OPTICS
    
    Specified by:
    
    buildClusterer in interface weka.clusterers.Clusterer
    
    Specified by:
    
    buildClusterer in class weka.clusterers.AbstractClusterer
    
    Parameters:
    
    instances - The instances that need to be clustered
    
    Throws:
    
    java.lang.Exception - If clustering was not successful
  - clusterInstance
```
public int clusterInstance(weka.core.Instance instance)
                    throws java.lang.Exception
```
    Classifies a given instance.
    
    Specified by:
    
    clusterInstance in interface weka.clusterers.Clusterer
    
    Overrides:
    
    clusterInstance in class weka.clusterers.AbstractClusterer
    
    Parameters:
    
    instance - The instance to be assigned to a cluster
    
    Returns:
    
    int The number of the assigned cluster as an integer
    
    Throws:
    
    java.lang.Exception - If instance could not be clustered successfully
  - numberOfClusters
```
public int numberOfClusters()
                     throws java.lang.Exception
```
    Returns the number of clusters.
    
    Specified by:
    
    numberOfClusters in interface weka.clusterers.Clusterer
    
    Specified by:
    
    numberOfClusters in class weka.clusterers.AbstractClusterer
    
    Returns:
    
    int The number of clusters generated for a training dataset.
    
    Throws:
    
    java.lang.Exception - If number of clusters could not be returned successfully
  - listOptions
```
public java.util.Enumeration listOptions()
```
    Returns an enumeration of all the available options.
    
    Specified by:
    
    listOptions in interface weka.core.OptionHandler
    
    Overrides:
    
    listOptions in class weka.clusterers.AbstractClusterer
    
    Returns:
    
    Enumeration An enumeration of all available options.
  - setOptions
```
public void setOptions(java.lang.String[] options)
                throws java.lang.Exception
```
    Sets the OptionHandler's options using the given list. All options will be set (or reset) during this call (i.e. incremental setting of options is not possible).
    Valid options are:
```
 -E <double>
  epsilon (default = 0.9)
```
```
 -M <int>
  minPoints (default = 6)
```
```
 -I <String>
  index (database) used for OPTICS (default = weka.clusterers.forOPTICSAndDBScan.Databases.SequentialDatabase)
```
```
 -D <String>
  distance-type (default = weka.clusterers.forOPTICSAndDBScan.DataObjects.EuclideanDataObject)
```
```
 -F
  write results to OPTICS_#TimeStamp#.TXT - File
```
```
 -no-gui
  suppress the display of the GUI after building the clusterer
```
```
 -db-output <file>
  The file to save the generated database to. If a directory
  is provided, the database doesn't get saved.
  The generated file can be viewed with the OPTICS Visualizer:
    java weka.clusterers.forOPTICSAndDBScan.OPTICS_GUI.OPTICS_Visualizer [file.ser]
  (default: .)
```
    Specified by:
    
    setOptions in interface weka.core.OptionHandler
    
    Overrides:
    
    setOptions in class weka.clusterers.AbstractClusterer
    
    Parameters:
    
    options - The list of options as an array of strings
    
    Throws:
    
    java.lang.Exception - If an option is not supported
  - getOptions
```
public java.lang.String[] getOptions()
```
    Gets the current option settings for the OptionHandler.
    
    Specified by:
    
    getOptions in interface weka.core.OptionHandler
    
    Overrides:
    
    getOptions in class weka.clusterers.AbstractClusterer
    
    Returns:
    
    String[] The list of current option settings as an array of strings
  - setMinPoints
```
public void setMinPoints(int minPoints)
```
    Sets a new value for minPoints
    
    Parameters:
    
    minPoints - MinPoints
  - setEpsilon
```
public void setEpsilon(double epsilon)
```
    Sets a new value for epsilon
    
    Parameters:
    
    epsilon - Epsilon
  - getEpsilon
```
public double getEpsilon()
```
    Returns the value of epsilon
    
    Returns:
    
    double Epsilon
  - getMinPoints
```
public int getMinPoints()
```
    Returns the value of minPoints
    
    Returns:
    
    int MinPoints
  - distanceFunctionTipText
```
public java.lang.String distanceFunctionTipText()
```
    Returns the tip text for this property.
    
    Returns:
    
    tip text for this property suitable for displaying in the explorer/experimenter gui
  - getDistanceFunction
```
public weka.core.DistanceFunction getDistanceFunction()
```
    returns the distance function currently in use.
    
    Returns:
    
    the distance function
  - setDistanceFunction
```
public void setDistanceFunction(weka.core.DistanceFunction df)
                         throws java.lang.Exception
```
    sets the distance function to use for nearest neighbour search.
    
    Parameters:
    
    df - the new distance function to use
    
    Throws:
    
    java.lang.Exception - if instances cannot be processed
  - getWriteOPTICSresults
```
public boolean getWriteOPTICSresults()
```
    Returns the flag for writing actions
    
    Returns:
    
    writeOPTICSresults (flag)
  - setWriteOPTICSresults
```
public void setWriteOPTICSresults(boolean writeOPTICSresults)
```
    Sets the flag for writing actions
    
    Parameters:
    
    writeOPTICSresults - Results are written to a file if the flag is set
  - getShowGUI
```
public boolean getShowGUI()
```
    Returns the flag for showing the OPTICS visualizer GUI.
    
    Returns:
    
    true if the GUI is displayed
  - setShowGUI
```
public void setShowGUI(boolean value)
```
    Sets the flag for displaying the GUI.
    
    Parameters:
    
    value - if true, then the OPTICS visualizer GUI will be displayed after building the clusterer
  - getDatabaseOutput
```
public java.io.File getDatabaseOutput()
```
    Returns the file to save the database to - if directory, database is not saved.
    
    Returns:
    
    the file to save the database to a directory if saving is ignored
  - setDatabaseOutput
```
public void setDatabaseOutput(java.io.File value)
```
    Sets the the file to save the generated database to. If a directory is provided, the datbase doesn't get saved.
    
    Parameters:
    
    value - the file to save the database to or a directory if saving is to be ignored
  - getResultVector
```
public java.util.ArrayList getResultVector()
```
    Returns the resultVector
    
    Returns:
    
    resultVector
  - epsilonTipText
```
public java.lang.String epsilonTipText()
```
    Returns the tip text for this property
    
    Returns:
    
    tip text for this property suitable for displaying in the explorer/experimenter gui
  - minPointsTipText
```
public java.lang.String minPointsTipText()
```
    Returns the tip text for this property
    
    Returns:
    
    tip text for this property suitable for displaying in the explorer/experimenter gui
  - writeOPTICSresultsTipText
```
public java.lang.String writeOPTICSresultsTipText()
```
    Returns the tip text for this property
    
    Returns:
    
    tip text for this property suitable for displaying in the explorer/experimenter gui
  - showGUITipText
```
public java.lang.String showGUITipText()
```
    Returns the tip text for this property.
    
    Returns:
    
    tip text for this property suitable for displaying in the explorer/experimenter gui
  - databaseOutputTipText
```
public java.lang.String databaseOutputTipText()
```
    Returns the tip text for this property.
    
    Returns:
    
    tip text for this property suitable for displaying in the explorer/experimenter gui
  - globalInfo
```
public java.lang.String globalInfo()
```
    Returns a string describing this DataMining-Algorithm
    
    Returns:
    
    String Information for the gui-explorer
  - getTechnicalInformation
```
public weka.core.TechnicalInformation getTechnicalInformation()
```
    Returns an instance of a TechnicalInformation object, containing detailed information about the technical background of this class, e.g., paper reference or book this class is based on.
    
    Specified by:
    
    getTechnicalInformation in interface weka.core.TechnicalInformationHandler
    
    Returns:
    
    the technical information about this class
  - getSERObject
```
public SERObject getSERObject()
```
    Returns the internal database
    
    Returns:
    
    the internal database
  - toString
```
public java.lang.String toString()
```
    Returns a description of the clusterer
    
    Overrides:
    
    toString in class java.lang.Object
    
    Returns:
    
    the clusterer as string
  - getRevision
```
public java.lang.String getRevision()
```
    Returns the revision string.
    
    Specified by:
    
    getRevision in interface weka.core.RevisionHandler
    
    Overrides:
    
    getRevision in class weka.clusterers.AbstractClusterer
    
    Returns:
    
    the revision
  - main
```
public static void main(java.lang.String[] args)
```
    Main Method for testing OPTICS
    
    Parameters:
    
    args - Valid parameters are: 'E' epsilon (default = 0.9); 'M' minPoints (default = 6); 'I' index-type (default = weka.clusterers.forOPTICSAndDBScan.Databases.SequentialDatabase); 'D' distance-type (default = weka.clusterers.forOPTICSAndDBScan.DataObjects.EuclideanDataObject); 'F' write results to OPTICS_#TimeStamp#.TXT - File

Class OPTICS

Constructor Summary

Method Summary

Methods inherited from class weka.clusterers.AbstractClusterer

Methods inherited from class java.lang.Object

Methods inherited from interface weka.core.OptionHandler

Constructor Detail

OPTICS

Method Detail

getCapabilities

buildClusterer

clusterInstance

numberOfClusters

listOptions

setOptions

getOptions

setMinPoints

setEpsilon

getEpsilon

getMinPoints

distanceFunctionTipText

getDistanceFunction

setDistanceFunction

getWriteOPTICSresults

setWriteOPTICSresults

getShowGUI

setShowGUI

getDatabaseOutput

setDatabaseOutput

getResultVector

epsilonTipText

minPointsTipText

writeOPTICSresultsTipText

showGUITipText

databaseOutputTipText

globalInfo

getTechnicalInformation

getSERObject

toString

getRevision

main