weka.filters.unsupervised.attribute

Class PrincipalComponents

java.lang.Object

weka.filters.Filter

weka.filters.unsupervised.attribute.PrincipalComponents

All Implemented Interfaces:

java.io.Serializable, CapabilitiesHandler, CapabilitiesIgnorer, CommandlineRunnable, 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:

 -C
  Center (rather than standardize) the
  data and compute PCA using the covariance (rather
   than the correlation) matrix.
 

 -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)
 

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected Remove	m_AttributeFilter Filter for removing class attribute, nominal attributes with 0 or 1 value.
protected Center	m_centerFilter Filter for centering the data
protected int	m_ClassIndex Class index.
protected no.uib.cipr.matrix.UpperSymmDenseMatrix	m_Correlation Correlation matrix for the original data.
protected double	m_CoverVariance the amount of varaince to cover in the original data when retaining the best n PC's.
protected double[]	m_Eigenvalues Eigenvalues for the corresponding eigenvectors.
protected double[][]	m_Eigenvectors Will hold the unordered linear transformations of the (normalized) original data.
protected boolean	m_HasClass Data has a class set.
protected int	m_MaxAttributes maximum number of attributes in the transformed data (-1 for all).
protected int	m_MaxAttrsInName maximum number of attributes in the transformed attribute name.
protected NominalToBinary	m_NominalToBinaryFilter Filter for turning nominal values into numeric ones.
protected int	m_NumAttribs Number of attributes.
protected int	m_NumInstances Number of instances.
protected int	m_OutputNumAtts The number of attributes in the pc transformed data.
protected ReplaceMissingValues	m_ReplaceMissingFilter Filters for replacing missing values.
protected int[]	m_SortedEigens Sorted eigenvalues.
protected Standardize	m_standardizeFilter Filter for standardizing the data
protected double	m_SumOfEigenValues sum of the eigenvalues.
protected Instances	m_TrainCopy Keep a copy for the class attribute (if set).
protected Instances	m_TrainInstances The data to transform analyse/transform.
protected Instances	m_TransformedFormat The header for the transformed data format.

Fields inherited from class weka.filters.Filter

m_Debug, m_DoNotCheckCapabilities, m_FirstBatchDone, m_InputRelAtts, m_InputStringAtts, m_NewBatch, m_OutputRelAtts, m_OutputStringAtts

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
protected Instance	convertInstance(Instance instance) Transform an instance in original (unormalized) format.
protected Instances	determineOutputFormat(Instances inputFormat) Determines the output format based on the input format and returns this.
protected void	fillCovariance()
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<Option>	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.
protected void	setup(Instances instances) Initializes the filter with the given input data.
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, bufferInput, copyValues, copyValues, debugTipText, doNotCheckCapabilitiesTipText, filterFile, flushInput, getCapabilities, getCopyOfInputFormat, getDebug, getDoNotCheckCapabilities, getInputFormat, getOutputFormat, initInputLocators, initOutputLocators, inputFormatPeek, isFirstBatchDone, isNewBatch, isOutputFormatDefined, makeCopies, makeCopy, mayRemoveInstanceAfterFirstBatchDone, numPendingOutput, output, outputFormatPeek, outputPeek, postExecution, preExecution, push, push, resetQueue, run, runFilter, setDebug, setDoNotCheckCapabilities, setOutputFormat, testInputFormat, toString, useFilter, wekaStaticWrapper

Methods inherited from class java.lang.Object

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

Field Detail

m_TrainInstances

protected Instances m_TrainInstances

The data to transform analyse/transform.

m_TrainCopy

protected Instances m_TrainCopy

Keep a copy for the class attribute (if set).

m_TransformedFormat

protected Instances m_TransformedFormat

The header for the transformed data format.

m_HasClass

protected boolean m_HasClass

Data has a class set.

m_ClassIndex

protected int m_ClassIndex

Class index.

m_NumAttribs

protected int m_NumAttribs

Number of attributes.

m_NumInstances

protected int m_NumInstances

Number of instances.

m_Correlation

protected no.uib.cipr.matrix.UpperSymmDenseMatrix m_Correlation

Correlation matrix for the original data.

m_Eigenvectors

protected double[][] m_Eigenvectors

Will hold the unordered linear transformations of the (normalized) original data.

m_Eigenvalues

protected double[] m_Eigenvalues

Eigenvalues for the corresponding eigenvectors.

m_SortedEigens

protected int[] m_SortedEigens

Sorted eigenvalues.

m_SumOfEigenValues

protected double m_SumOfEigenValues

sum of the eigenvalues.

m_ReplaceMissingFilter

protected ReplaceMissingValues m_ReplaceMissingFilter

Filters for replacing missing values.

m_NominalToBinaryFilter

protected NominalToBinary m_NominalToBinaryFilter

Filter for turning nominal values into numeric ones.

m_AttributeFilter

protected Remove m_AttributeFilter

Filter for removing class attribute, nominal attributes with 0 or 1 value.

m_standardizeFilter

protected Standardize m_standardizeFilter

Filter for standardizing the data

m_centerFilter

protected Center m_centerFilter

Filter for centering the data

m_OutputNumAtts

protected int m_OutputNumAtts

The number of attributes in the pc transformed data.

m_CoverVariance

protected double m_CoverVariance

the amount of varaince to cover in the original data when retaining the best n PC's.

m_MaxAttrsInName

protected int m_MaxAttrsInName

maximum number of attributes in the transformed attribute name.

m_MaxAttributes

protected int m_MaxAttributes

maximum number of attributes in the transformed data (-1 for all).

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<Option> listOptions()

Returns an enumeration describing the available options.

Specified by:

listOptions in interface OptionHandler

Overrides:

listOptions in class Filter

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:

 -C
  Center (rather than standardize) the
  data and compute PCA using the covariance (rather
   than the correlation) matrix.
 

 -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

Overrides:

setOptions in class Filter

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

Overrides:

getOptions in class Filter

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

determineOutputFormat

protected Instances determineOutputFormat(Instances inputFormat)
                                   throws java.lang.Exception

Determines the output format based on the input format and returns this. In case the output format cannot be returned immediately, i.e., immediateOutputFormat() returns false, then this method will be called from batchFinished().

Parameters:

inputFormat - the input format to base the output format on

Returns:

the output format

Throws:

java.lang.Exception - in case the determination goes wrong

See Also:

batchFinished()

fillCovariance

protected void fillCovariance()
                       throws java.lang.Exception

Throws:

java.lang.Exception

convertInstance

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

Transform an instance in original (unormalized) format.

Parameters:

instance - an instance in the original (unormalized) format

Returns:

a transformed instance

Throws:

java.lang.Exception - if instance can't be transformed

setup

protected void setup(Instances instances)
              throws java.lang.Exception

Initializes the filter with the given input data.

Parameters:

instances - the data to process

Throws:

java.lang.Exception - in case the processing goes wrong

See Also:

batchFinished()

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