weka.filters.unsupervised.attribute

Class PrincipalComponents

java.lang.Object

weka.filters.Filter

weka.filters.unsupervised.attribute.PrincipalComponents

All Implemented Interfaces:

java.io.Serializable, CapabilitiesHandler, OptionHandler, RevisionHandler, UnsupervisedFilter

public class PrincipalComponents
extends Filter
implements OptionHandler, UnsupervisedFilter

Performs a principal components analysis and transformation of the data.
Dimensionality reduction is accomplished by choosing enough eigenvectors to account for some percentage of the variance in the original data -- default 0.95 (95%).
Based on code of the attribute selection scheme 'PrincipalComponents' by Mark Hall and Gabi Schmidberger.

Valid options are:

 -D
  Don't normalize input data.

 -R <num>
  Retain enough PC attributes to account
  for this proportion of variance in the original data.
  (default: 0.95)

 -A <num>
  Maximum number of attributes to include in 
  transformed attribute names.
  (-1 = include all, default: 5)

 -M <num>
  Maximum number of PC attributes to retain.
  (-1 = include all, default: -1)

Version:

$Revision: 11449 $

Author:

Mark Hall (mhall@cs.waikato.ac.nz) -- attribute selection code, Gabi Schmidberger (gabi@cs.waikato.ac.nz) -- attribute selection code, fracpete (fracpete at waikato dot ac dot nz) -- filter code

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
PrincipalComponents()

Method Summary

Modifier and Type	Method and Description
boolean	batchFinished() Signify that this batch of input to the filter is finished.
java.lang.String	centerDataTipText() Returns the tip text for this property
Capabilities	getCapabilities() Returns the capabilities of this evaluator.
boolean	getCenterData() Get whether to center (rather than standardize) the data.
int	getMaximumAttributeNames() Gets maximum number of attributes to include in transformed attribute names.
int	getMaximumAttributes() Gets maximum number of PC attributes to retain.
java.lang.String[]	getOptions() Gets the current settings of the filter.
java.lang.String	getRevision() Returns the revision string.
double	getVarianceCovered() Gets the proportion of total variance to account for when retaining principal components.
java.lang.String	globalInfo() Returns a string describing this filter.
boolean	input(Instance instance) Input an instance for filtering.
java.util.Enumeration	listOptions() Returns an enumeration describing the available options.
static void	main(java.lang.String[] args) Main method for running this filter.
java.lang.String	maximumAttributeNamesTipText() Returns the tip text for this property.
java.lang.String	maximumAttributesTipText() Returns the tip text for this property.
void	setCenterData(boolean center) Set whether to center (rather than standardize) the data.
boolean	setInputFormat(Instances instanceInfo) Sets the format of the input instances.
void	setMaximumAttributeNames(int value) Sets maximum number of attributes to include in transformed attribute names.
void	setMaximumAttributes(int value) Sets maximum number of PC attributes to retain.
void	setOptions(java.lang.String[] options) Parses a list of options for this object.
void	setVarianceCovered(double value) Sets the amount of variance to account for when retaining principal components.
java.lang.String	varianceCoveredTipText() Returns the tip text for this property.

Methods inherited from class weka.filters.Filter

batchFilterFile, filterFile, getCapabilities, getOutputFormat, isFirstBatchDone, isNewBatch, isOutputFormatDefined, makeCopies, makeCopy, numPendingOutput, output, outputPeek, toString, useFilter, wekaStaticWrapper

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

PrincipalComponents

public PrincipalComponents()

Method Detail

globalInfo

public java.lang.String globalInfo()

Returns a string describing this filter.

Returns:

a description of the filter suitable for displaying in the explorer/experimenter gui

listOptions

public java.util.Enumeration listOptions()

Returns an enumeration describing the available options.

Specified by:

listOptions in interface OptionHandler

Returns:

an enumeration of all the available options.

setOptions

public void setOptions(java.lang.String[] options)
                throws java.lang.Exception

Parses a list of options for this object.

Valid options are:

 -D
  Don't normalize input data.

 -R <num>
  Retain enough PC attributes to account
  for this proportion of variance in the original data.
  (default: 0.95)

 -A <num>
  Maximum number of attributes to include in 
  transformed attribute names.
  (-1 = include all, default: 5)

 -M <num>
  Maximum number of PC attributes to retain.
  (-1 = include all, default: -1)

Specified by:

setOptions in interface OptionHandler

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 settings of the filter.

Specified by:

getOptions in interface OptionHandler

Returns:

an array of strings suitable for passing to setOptions

centerDataTipText

public java.lang.String centerDataTipText()

Returns the tip text for this property

Returns:

tip text for this property suitable for displaying in the explorer/experimenter gui

setCenterData

public void setCenterData(boolean center)

Set whether to center (rather than standardize) the data. If set to true then PCA is computed from the covariance rather than correlation matrix.

Parameters:

center - true if the data is to be centered rather than standardized

getCenterData

public boolean getCenterData()

Get whether to center (rather than standardize) the data. If true then PCA is computed from the covariance rather than correlation matrix.

Returns:

true if the data is to be centered rather than standardized.

varianceCoveredTipText

public java.lang.String varianceCoveredTipText()

Returns the tip text for this property.

Returns:

tip text for this property suitable for displaying in the explorer/experimenter gui

setVarianceCovered

public void setVarianceCovered(double value)

Sets the amount of variance to account for when retaining principal components.

Parameters:

value - the proportion of total variance to account for

getVarianceCovered

public double getVarianceCovered()

Gets the proportion of total variance to account for when retaining principal components.

Returns:

the proportion of variance to account for

maximumAttributeNamesTipText

public java.lang.String maximumAttributeNamesTipText()

Returns the tip text for this property.

Returns:

tip text for this property suitable for displaying in the explorer/experimenter gui

setMaximumAttributeNames

public void setMaximumAttributeNames(int value)

Sets maximum number of attributes to include in transformed attribute names.

Parameters:

value - the maximum number of attributes

getMaximumAttributeNames

public int getMaximumAttributeNames()

Gets maximum number of attributes to include in transformed attribute names.

Returns:

the maximum number of attributes

maximumAttributesTipText

public java.lang.String maximumAttributesTipText()

Returns the tip text for this property.

Returns:

tip text for this property suitable for displaying in the explorer/experimenter gui

setMaximumAttributes

public void setMaximumAttributes(int value)

Sets maximum number of PC attributes to retain.

Parameters:

value - the maximum number of attributes

getMaximumAttributes

public int getMaximumAttributes()

Gets maximum number of PC attributes to retain.

Returns:

the maximum number of attributes

getCapabilities

public Capabilities getCapabilities()

Returns the capabilities of this evaluator.

Specified by:

getCapabilities in interface CapabilitiesHandler

Overrides:

getCapabilities in class Filter

Returns:

the capabilities of this evaluator

See Also:

Capabilities

setInputFormat

public boolean setInputFormat(Instances instanceInfo)
                       throws java.lang.Exception

Sets the format of the input instances.

Overrides:

setInputFormat in class Filter

Parameters:

instanceInfo - an Instances object containing the input instance structure (any instances contained in the object are ignored - only the structure is required).

Returns:

true if the outputFormat may be collected immediately

Throws:

java.lang.Exception - if the input format can't be set successfully

input

public boolean input(Instance instance)
              throws java.lang.Exception

Input an instance for filtering. Filter requires all training instances be read before producing output.

Overrides:

input in class Filter

Parameters:

instance - the input instance

Returns:

true if the filtered instance may now be collected with output().

Throws:

java.lang.IllegalStateException - if no input format has been set

java.lang.Exception - if conversion fails

batchFinished

public boolean batchFinished()
                      throws java.lang.Exception

Signify that this batch of input to the filter is finished.

Overrides:

batchFinished in class Filter

Returns:

true if there are instances pending output

Throws:

java.lang.NullPointerException - if no input structure has been defined,

java.lang.Exception - if there was a problem finishing the batch.

getRevision

public java.lang.String getRevision()

Returns the revision string.

Specified by:

getRevision in interface RevisionHandler

Overrides:

getRevision in class Filter

Returns:

the revision

main

public static void main(java.lang.String[] args)

Main method for running this filter.

Parameters:

args - should contain arguments to the filter: use -h for help