java.lang.Object
- adams.core.logging.LoggingObject
- - adams.core.logging.CustomLoggingLevelObject
  - - adams.core.option.AbstractOptionHandler
    - - adams.data.analysis.AbstractAnalysis<weka.core.Instances>
      - adams.data.instancesanalysis.AbstractInstancesAnalysis
        
        adams.data.instancesanalysis.PCA

All Implemented Interfaces:

Destroyable, GlobalInfoSupporter, LoggingLevelHandler, LoggingSupporter, OptionHandler, SizeOfHandler, Serializable
```
public class PCA
extends AbstractInstancesAnalysis
```
Performs principal components analysis and allows access to loadings and scores.

Version:

$Revision$

Author:

FracPete (fracpete at waikato dot ac dot nz)

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type	Field	Description
`protected WekaAttributeRange`	`m_AttributeRange`	the range of attributes to work.
`protected ArrayList<Integer>`	`m_Kept`	the indices of the kept attributes.
`protected SpreadSheet`	`m_Loadings`	the loadings.
`protected int`	`m_MaxAttributeNames`	the maximum number of attribute names.
`protected int`	`m_MaxAttributes`	the maximum number of attributes.
`protected int`	`m_NumAttributes`	the number of attributes in the data (excl class).
`protected SpreadSheet`	`m_Scores`	the scores.
`protected boolean`	`m_SkipNominal`	whether to skip nominal attributes (and not apply NominalToBinary).
`protected gnu.trove.list.TIntList`	`m_Supported`	the supported attributes.
`protected gnu.trove.list.TIntList`	`m_Unsupported`	the unsupported attributes.
`protected double`	`m_Variance`	the variance to cover.

Fields inherited from class adams.core.option.AbstractOptionHandler
m_OptionManager

Fields inherited from class adams.core.logging.LoggingObject
m_Logger, m_LoggingIsEnabled, m_LoggingLevel

Constructor Summary

Constructors
Constructor Description

PCA()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`String`	`attributeRangeTipText()`	Returns the tip text for this property.
`protected void`	`check(weka.core.Instances data)`	Hook method for checks.
`void`	`defineOptions()`	Adds options to the internal list of options.
`protected String`	`doAnalyze(weka.core.Instances data)`	Performs the actual analysis.
`protected SpreadSheet`	`extractLoadings(weka.core.Instances data, ArrayList<ArrayList<Double>> coeff)`	Create a spreadsheet to output from the coefficients 2D array
`WekaAttributeRange`	`getAttributeRange()`	Returns the attribute range parameter.
`SpreadSheet`	`getLoadings()`	Returns the loadings.
`int`	`getMaxAttributeNames()`	Returns the maximum number of attribute names.
`int`	`getMaxAttributes()`	Returns the maximum attributes.
`SpreadSheet`	`getScores()`	Returns the scores.
`boolean`	`getSkipNominal()`	Returns whether to skip NOMINAL attributes from the PCA process by turning them into STRING attributes.
`double`	`getVariance()`	Returns the variance.
`String`	`globalInfo()`	Returns a string describing the object.
`String`	`maxAttributeNamesTipText()`	Returns the tip text for this property.
`String`	`maxAttributesTipText()`	Returns the tip text for this property.
`protected void`	`reset()`	Resets the scheme.
`void`	`setAttributeRange(WekaAttributeRange value)`	Sets the attribute range parameter.
`void`	`setMaxAttributeNames(int value)`	Sets the maximum number of attribute names.
`void`	`setMaxAttributes(int value)`	Sets the maximum attributes.
`void`	`setSkipNominal(boolean value)`	Sets whether to skip NOMINAL attributes from the PCA process by turning them into STRING attributes.
`void`	`setVariance(double value)`	Sets the variance.
`String`	`skipNominalTipText()`	Returns the tip text for this property.
`String`	`varianceTipText()`	Returns the tip text for this property.

Methods inherited from class adams.data.analysis.AbstractAnalysis
analyze

Methods inherited from class adams.core.option.AbstractOptionHandler
cleanUpOptions, destroy, finishInit, getDefaultLoggingLevel, getOptionManager, initialize, loggingLevelTipText, newOptionManager, setLoggingLevel, toCommandLine, toString

Methods inherited from class adams.core.logging.LoggingObject
configureLogger, getLogger, getLoggingLevel, initializeLogging, isLoggingEnabled, sizeOf

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface adams.core.logging.LoggingLevelHandler
getLoggingLevel

- Field Detail
  - m_AttributeRange
```
protected WekaAttributeRange m_AttributeRange
```
    the range of attributes to work.
  - m_Variance
```
protected double m_Variance
```
    the variance to cover.
  - m_MaxAttributes
```
protected int m_MaxAttributes
```
    the maximum number of attributes.
  - m_MaxAttributeNames
```
protected int m_MaxAttributeNames
```
    the maximum number of attribute names.
  - m_SkipNominal
```
protected boolean m_SkipNominal
```
    whether to skip nominal attributes (and not apply NominalToBinary).
  - m_Loadings
```
protected SpreadSheet m_Loadings
```
    the loadings.
  - m_Scores
```
protected SpreadSheet m_Scores
```
    the scores.
  - m_Supported
```
protected gnu.trove.list.TIntList m_Supported
```
    the supported attributes.
  - m_Unsupported
```
protected gnu.trove.list.TIntList m_Unsupported
```
    the unsupported attributes.
  - m_Kept
```
protected ArrayList<Integer> m_Kept
```
    the indices of the kept attributes.
  - m_NumAttributes
```
protected int m_NumAttributes
```
    the number of attributes in the data (excl class).
- Constructor Detail
  - PCA
```
public PCA()
```
- Method Detail
  - globalInfo
```
public String globalInfo()
```
    Returns a string describing the object.
    
    Specified by:
    
    globalInfo in interface GlobalInfoSupporter
    
    Specified by:
    
    globalInfo in class AbstractOptionHandler
    
    Returns:
    
    a description suitable for displaying in the gui
  - defineOptions
```
public void defineOptions()
```
    Adds options to the internal list of options.
    
    Specified by:
    
    defineOptions in interface OptionHandler
    
    Overrides:
    
    defineOptions in class AbstractOptionHandler
  - reset
```
protected void reset()
```
    Resets the scheme.
    
    Overrides:
    
    reset in class AbstractOptionHandler
  - setAttributeRange
```
public void setAttributeRange(WekaAttributeRange value)
```
    Sets the attribute range parameter.
    
    Parameters:
    
    value - the range
  - getAttributeRange
```
public WekaAttributeRange getAttributeRange()
```
    Returns the attribute range parameter.
    
    Returns:
    
    the range
  - attributeRangeTipText
```
public String attributeRangeTipText()
```
    Returns the tip text for this property.
    
    Returns:
    
    tip text for this property suitable for displaying in the GUI or for listing the options.
  - setVariance
```
public void setVariance(double value)
```
    Sets the variance.
    
    Parameters:
    
    value - the variance
  - getVariance
```
public double getVariance()
```
    Returns the variance.
    
    Returns:
    
    the variance
  - varianceTipText
```
public String varianceTipText()
```
    Returns the tip text for this property.
    
    Returns:
    
    tip text for this property suitable for displaying in the GUI or for listing the options.
  - setMaxAttributes
```
public void setMaxAttributes(int value)
```
    Sets the maximum attributes.
    
    Parameters:
    
    value - the maximum
  - getMaxAttributes
```
public int getMaxAttributes()
```
    Returns the maximum attributes.
    
    Returns:
    
    the maximum
  - maxAttributesTipText
```
public String maxAttributesTipText()
```
    Returns the tip text for this property.
    
    Returns:
    
    tip text for this property suitable for displaying in the GUI or for listing the options.
  - setMaxAttributeNames
```
public void setMaxAttributeNames(int value)
```
    Sets the maximum number of attribute names.
    
    Parameters:
    
    value - the maximum
  - getMaxAttributeNames
```
public int getMaxAttributeNames()
```
    Returns the maximum number of attribute names.
    
    Returns:
    
    the maximum
  - maxAttributeNamesTipText
```
public String maxAttributeNamesTipText()
```
    Returns the tip text for this property.
    
    Returns:
    
    tip text for this property suitable for displaying in the GUI or for listing the options.
  - setSkipNominal
```
public void setSkipNominal(boolean value)
```
    Sets whether to skip NOMINAL attributes from the PCA process by turning them into STRING attributes.
    
    Parameters:
    
    value - true if to skip
  - getSkipNominal
```
public boolean getSkipNominal()
```
    Returns whether to skip NOMINAL attributes from the PCA process by turning them into STRING attributes.
    
    Returns:
    
    true if to skip
  - skipNominalTipText
```
public String skipNominalTipText()
```
    Returns the tip text for this property.
    
    Returns:
    
    tip text for this property suitable for displaying in the GUI or for listing the options.
  - check
```
protected void check(weka.core.Instances data)
```
    Hook method for checks.
    
    Overrides:
    
    check in class AbstractAnalysis<weka.core.Instances>
    
    Parameters:
    
    data - the data to check
  - extractLoadings
```
protected SpreadSheet extractLoadings(weka.core.Instances data,
                                      ArrayList<ArrayList<Double>> coeff)
```
    Create a spreadsheet to output from the coefficients 2D array
    
    Parameters:
    
    data - the underlying dataset
    
    coeff - The coefficients from the principal components analysis
    
    Returns:
    
    A spreadsheet containing the components
  - doAnalyze
```
protected String doAnalyze(weka.core.Instances data)
                    throws Exception
```
    Performs the actual analysis.
    
    Specified by:
    
    doAnalyze in class AbstractAnalysis<weka.core.Instances>
    
    Parameters:
    
    data - the data to analyze
    
    Returns:
    
    null if successful, otherwise error message
    
    Throws:
    
    Exception - if analysis fails
  - getLoadings
```
public SpreadSheet getLoadings()
```
    Returns the loadings.
    
    Returns:
    
    the loadings, null if not available
  - getScores
```
public SpreadSheet getScores()
```
    Returns the scores.
    
    Returns:
    
    the scores, null if not available

Class PCA

Field Summary

Fields inherited from class adams.core.option.AbstractOptionHandler

Fields inherited from class adams.core.logging.LoggingObject

Constructor Summary

Method Summary

Methods inherited from class adams.data.analysis.AbstractAnalysis

Methods inherited from class adams.core.option.AbstractOptionHandler

Methods inherited from class adams.core.logging.LoggingObject

Methods inherited from class java.lang.Object

Methods inherited from interface adams.core.logging.LoggingLevelHandler

Field Detail

m_AttributeRange

m_Variance

m_MaxAttributes

m_MaxAttributeNames

m_SkipNominal

m_Loadings

m_Scores

m_Supported

m_Unsupported

m_Kept

m_NumAttributes

Constructor Detail

PCA

Method Detail

globalInfo

defineOptions

reset

setAttributeRange

getAttributeRange

attributeRangeTipText

setVariance

getVariance

varianceTipText

setMaxAttributes

getMaxAttributes

maxAttributesTipText

setMaxAttributeNames

getMaxAttributeNames

maxAttributeNamesTipText

setSkipNominal

getSkipNominal

skipNominalTipText

check

extractLoadings

doAnalyze

getLoadings

getScores