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)
 
```
Version:

$Revision: 12660 $

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()

Constructors
Constructor and Description
`PrincipalComponents()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
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<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.
`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 java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface weka.core.OptionHandler
makeCopy

- 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
  - 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

Class PrincipalComponents

Constructor Summary

Method Summary

Methods inherited from class weka.filters.Filter

Methods inherited from class java.lang.Object

Methods inherited from interface weka.core.OptionHandler

Constructor Detail

PrincipalComponents

Method Detail

globalInfo

listOptions

setOptions

getOptions

centerDataTipText

setCenterData

getCenterData

varianceCoveredTipText

setVarianceCovered

getVarianceCovered

maximumAttributeNamesTipText

setMaximumAttributeNames

getMaximumAttributeNames

maximumAttributesTipText

setMaximumAttributes

getMaximumAttributes

getCapabilities

setInputFormat

input

batchFinished

getRevision

main