Package adams.data.baseline

Class AbstractLinearRegressionBased<T extends DataContainer>

java.lang.Object

adams.core.logging.LoggingObject

adams.core.logging.CustomLoggingLevelObject

adams.core.option.AbstractOptionHandler

adams.data.baseline.AbstractBaselineCorrection<T>

adams.data.baseline.AbstractLinearRegressionBased<T>

Type Parameters:

T - the type of data to process

All Implemented Interfaces:

CleanUpHandler, Destroyable, GlobalInfoSupporter, LoggingLevelHandler, LoggingSupporter, OptionHandler, ShallowCopySupporter<AbstractBaselineCorrection>, SizeOfHandler, Serializable, Comparable

public abstract class AbstractLinearRegressionBased<T extends DataContainer>
extends AbstractBaselineCorrection<T>

Abstract ancestor for linear regression based baseline correction schemes.

Version:

$Revision$

Author:

dale (dale at cs dot waikato dot ac dot nz)

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class adams.data.baseline.AbstractBaselineCorrection

AbstractBaselineCorrection.BaselineCorrectionJob<T extends DataContainer>

Field Summary

Fields

Modifier and Type	Field	Description
protected boolean	m_GenerateLine	whether to return the line as fake data or the corrected data.
protected double	m_Ridge	the ridge.

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
AbstractLinearRegressionBased()

Method Summary

Modifier and Type	Method	Description
protected abstract T	correctData(T data, double[] coeff)	Corrects the data with the given coefficients.
void	defineOptions()	Adds options to the internal list of options.
protected abstract T	generateLine(T data, double[] coeff)	Generates fake data for the plotting the line.
String	generateLineTipText()	Returns the tip text for this property.
boolean	getGenerateLine()	Returns whether to return the line as fake data or the corrected data.
protected abstract weka.core.Instances	getInstances(T data)	Returns a dataset containing the x and y values.
double	getRidge()	Returns the ridge parameter.
String	globalInfo()	Returns a string describing the object.
protected T	processData(T data)	Performs the actual correcting.
String	ridgeTipText()	Returns the tip text for this property.
void	setGenerateLine(boolean value)	Sets whether to return the line as fake data or the corrected data.
void	setRidge(double value)	Sets the ridge parameter.

Methods inherited from class adams.data.baseline.AbstractBaselineCorrection

checkData, cleanUp, compareTo, correct, doCorrect, equals, forCommandLine, reset, shallowCopy, shallowCopy

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, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface adams.core.logging.LoggingLevelHandler

getLoggingLevel

Field Detail

m_Ridge

protected double m_Ridge

the ridge.

m_GenerateLine

protected boolean m_GenerateLine

whether to return the line as fake data or the corrected data.

Constructor Detail

AbstractLinearRegressionBased

public AbstractLinearRegressionBased()

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

setRidge

public void setRidge(double value)

Sets the ridge parameter.

Parameters:

value - the ridge

getRidge

public double getRidge()

Returns the ridge parameter.

Returns:

the ridge

ridgeTipText

public String ridgeTipText()

Returns the tip text for this property.

Returns:

tip text for this property suitable for displaying in the GUI or for listing the options.

setGenerateLine

public void setGenerateLine(boolean value)

Sets whether to return the line as fake data or the corrected data.

Parameters:

value - true if debug output should be printed

getGenerateLine

public boolean getGenerateLine()

Returns whether to return the line as fake data or the corrected data.

Returns:

true if debugging output is on

generateLineTipText

public String generateLineTipText()

Returns the tip text for this property.

Returns:

tip text for this property suitable for displaying in the GUI or for listing the options.

getInstances

protected abstract weka.core.Instances getInstances(T data)

Returns a dataset containing the x and y values.

Parameters:

data - the original data

Returns:

the dataset for LinearRegression

correctData

protected abstract T correctData(T data,
                                 double[] coeff)

Corrects the data with the given coefficients.

Parameters:

data - the original data

coeff - the coefficients to use for correcting the data, the last element is the offset

Returns:

the baseline corrected data

generateLine

protected abstract T generateLine(T data,
                                  double[] coeff)

Generates fake data for the plotting the line.

Parameters:

data - the original data

coeff - the coefficients to use for generating the line data, the last element is the offset

Returns:

the fake data for the line

processData

protected T processData(T data)

Performs the actual correcting.

Specified by:

processData in class AbstractBaselineCorrection<T extends DataContainer>

Parameters:

data - the data to correct

Returns:

the corrected data