weka.attributeSelection
Class PrincipalComponents

java.lang.Object
  |
  +--weka.attributeSelection.ASEvaluation
        |
        +--weka.attributeSelection.AttributeEvaluator
              |
              +--weka.attributeSelection.UnsupervisedAttributeEvaluator
                    |
                    +--weka.attributeSelection.PrincipalComponents

All Implemented Interfaces:

AttributeTransformer, OptionHandler, java.io.Serializable

public class PrincipalComponents

extends UnsupervisedAttributeEvaluator

implements AttributeTransformer, OptionHandler

Class for performing principal components analysis/transformation.

Valid options are:

-N
Don't normalize the input data.

-R
Retain enough pcs to account for this proportion of the variance.

-T
Transform through the PC space and back to the original space.

Version:

$Revision: 1.25 $

Author:

Mark Hall (mhall@cs.waikato.ac.nz), Gabi Schmidberger (gabi@cs.waikato.ac.nz)

See Also:

Serialized Form

Constructor Summary

PrincipalComponents()

Method Summary

void	buildEvaluator(Instances data) Initializes principal components and performs the analysis
Instance	convertInstance(Instance instance) Transform an instance in original (unormalized) format.
double	evaluateAttribute(int att) Evaluates the merit of a transformed attribute.
boolean	getNormalize() Gets whether or not input data is to be normalized
java.lang.String[]	getOptions() Gets the current settings of PrincipalComponents
boolean	getTransformBackToOriginal() Gets whether the data is to be transformed back to the original space.
double	getVarianceCovered() Gets the proportion of total variance to account for when retaining principal components
java.lang.String	globalInfo() Returns a string describing this attribute transformer
java.util.Enumeration	listOptions() Returns an enumeration describing the available options.
static void	main(java.lang.String[] argv) Main method for testing this class
java.lang.String	normalizeTipText() Returns the tip text for this property
void	setNormalize(boolean n) Set whether input data will be normalized.
void	setOptions(java.lang.String[] options) Parses a given list of options.
void	setTransformBackToOriginal(boolean b) Sets whether the data should be transformed back to the original space
void	setVarianceCovered(double vc) Sets the amount of variance to account for when retaining principal components
java.lang.String	toString() Returns a description of this attribute transformer
java.lang.String	transformBackToOriginalTipText() Returns the tip text for this property
Instances	transformedData() Gets the transformed training data.
Instances	transformedHeader() Returns just the header for the transformed data (ie.
java.lang.String	varianceCoveredTipText() Returns the tip text for this property

Methods inherited from class weka.attributeSelection.ASEvaluation

forName, makeCopies, postProcess

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 attribute transformer

Returns:

a description of the evaluator 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 given list of options. Valid options are:

-N
Don't normalize the input data.

-R
Retain enough pcs to account for this proportion of the variance.

-T
Transform through the PC space and back to the original space.

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

normalizeTipText

public java.lang.String normalizeTipText()

Returns the tip text for this property

Returns:

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

setNormalize

public void setNormalize(boolean n)

Set whether input data will be normalized.

Parameters:

n - true if input data is to be normalized

getNormalize

public boolean getNormalize()

Gets whether or not input data is to be normalized

Returns:

true if input data is to be normalized

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 vc)

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

Parameters:

vc - 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

transformBackToOriginalTipText

public java.lang.String transformBackToOriginalTipText()

Returns the tip text for this property

Returns:

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

setTransformBackToOriginal

public void setTransformBackToOriginal(boolean b)

Sets whether the data should be transformed back to the original space

Parameters:

b - true if the data should be transformed back to the original space

getTransformBackToOriginal

public boolean getTransformBackToOriginal()

Gets whether the data is to be transformed back to the original space.

Returns:

true if the data is to be transformed back to the original space

getOptions

public java.lang.String[] getOptions()

Gets the current settings of PrincipalComponents

Specified by:

getOptions in interface OptionHandler

Returns:

an array of strings suitable for passing to setOptions()

buildEvaluator

public void buildEvaluator(Instances data)
                    throws java.lang.Exception

Initializes principal components and performs the analysis

Specified by:

buildEvaluator in class ASEvaluation

Parameters:

data - the instances to analyse/transform

Throws:

java.lang.Exception - if analysis fails

transformedHeader

public Instances transformedHeader()
                            throws java.lang.Exception

Returns just the header for the transformed data (ie. an empty set of instances. This is so that AttributeSelection can determine the structure of the transformed data without actually having to get all the transformed data through getTransformedData().

Specified by:

transformedHeader in interface AttributeTransformer

Returns:

the header of the transformed data.

Throws:

java.lang.Exception - if the header of the transformed data can't be determined.

transformedData

public Instances transformedData()
                          throws java.lang.Exception

Gets the transformed training data.

Specified by:

transformedData in interface AttributeTransformer

Returns:

the transformed training data

Throws:

java.lang.Exception - if transformed data can't be returned

evaluateAttribute

public double evaluateAttribute(int att)
                         throws java.lang.Exception

Evaluates the merit of a transformed attribute. This is defined to be 1 minus the cumulative variance explained. Merit can't be meaningfully evaluated if the data is to be transformed back to the original space.

Specified by:

evaluateAttribute in class AttributeEvaluator

Parameters:

att - the attribute to be evaluated

Returns:

the merit of a transformed attribute

Throws:

java.lang.Exception - if attribute can't be evaluated

toString

public java.lang.String toString()

Returns a description of this attribute transformer

Overrides:

toString in class java.lang.Object

Returns:

a String describing this attribute transformer

convertInstance

public Instance convertInstance(Instance instance)
                         throws java.lang.Exception

Transform an instance in original (unormalized) format. Convert back to the original space if requested.

Specified by:

convertInstance in interface AttributeTransformer

Parameters:

instance - an instance in the original (unormalized) format

Returns:

a transformed instance

Throws:

java.lang.Exception - if instance cant be transformed

main

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

Main method for testing this class

Parameters:

argv - should contain the command line arguments to the evaluator/transformer (see AttributeSelection)