PrincipalComponents

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## weka.attributeSelection
Class PrincipalComponents

    java.lang.Object
      weka.attributeSelection.ASEvaluation
          weka.attributeSelection.UnsupervisedAttributeEvaluator
              weka.attributeSelection.PrincipalComponents

All Implemented Interfaces:
  java.io.Serializable, AttributeEvaluator, AttributeTransformer, CapabilitiesHandler, OptionHandler, RevisionHandler

    public class PrincipalComponents

extends UnsupervisedAttributeEvaluator
implements AttributeTransformer, OptionHandler

Performs a principal components analysis and transformation of the data. Use in conjunction with a Ranker search. Dimensionality reduction is accomplished by choosing enough eigenvectors to account for some percentage of the variance in the original data---default 0.95 (95%). Attribute noise can be filtered by transforming to the PC space, eliminating some of the worst eigenvectors, and then transforming back to the original space.

Valid options are:

     -D
      Don't normalize input data.

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

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

     -A
      Maximum number of attributes to include in
      transformed attribute names. (-1 = include all)

Version:
  $Revision: 4615 $
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.
`Capabilities` | `getCapabilities()` Returns the capabilities of this evaluator.
`int` | `getMaximumAttributeNames()` Gets maximum number of attributes to include in transformed attribute names.
`boolean` | `getNormalize()` Gets whether or not input data is to be normalized
`java.lang.String[]` | `getOptions()` Gets the current settings of PrincipalComponents
`java.lang.String` | `getRevision()` Returns the revision string.
`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` | `maximumAttributeNamesTipText()` Returns the tip text for this property
`java.lang.String` | `normalizeTipText()` Returns the tip text for this property
`void` | `setMaximumAttributeNames(int m)` Sets maximum number of attributes to include in transformed attribute names.
`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(Instances data)` 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:

       -D
        Don't normalize input data.

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

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

       -A
        Maximum number of attributes to include in
        transformed attribute names. (-1 = include all)

  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

### 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 m)

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

  Parameters:
    `m` - 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

### 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()

### getCapabilities

    public Capabilities getCapabilities()

  Returns the capabilities of this evaluator.

  Specified by:
    `getCapabilities` in interface `CapabilitiesHandler`
  Overrides:
    `getCapabilities` in class `ASEvaluation`
  Returns:
    the capabilities of this evaluator
  See Also:
    `Capabilities`

### 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 transformedData().

  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(Instances data)
                              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 interface `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

### getRevision

    public java.lang.String getRevision()

  Returns the revision string.

  Specified by:
    `getRevision` in interface `RevisionHandler`
  Overrides:
    `getRevision` in class `ASEvaluation`
  Returns:
    the revision

### 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)

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