Package adams.data.spectrumbaseline

Class SavitzkyGolayBased

  • All Implemented Interfaces:
    adams.core.CleanUpHandler, adams.core.Destroyable, adams.core.GlobalInfoSupporter, adams.core.logging.LoggingLevelHandler, adams.core.logging.LoggingSupporter, adams.core.option.OptionHandler, adams.core.ShallowCopySupporter<adams.data.baseline.AbstractBaselineCorrection>, adams.core.SizeOfHandler, Serializable, Comparable
    public class SavitzkyGolayBased
extends adams.data.baseline.AbstractSavitzkyGolayBased<Spectrum>
    A baseline correction scheme that uses SavitzkyGolay smoothing to determine the baseline.

    For more information see:

    A. Savitzky, Marcel J.E. Golay (1964). Smoothing and Differentiation of Data by Simplified Least Squares Procedures. Analytical Chemistry. 36:1627-1639.

    William H. Press, Saul A. Teukolsky, William T. Vetterling, Brian P. Flannery (1992). Savitzky-Golay Smoothing Filters. 

    -logging-level <OFF|SEVERE|WARNING|INFO|CONFIG|FINE|FINER|FINEST> (property: loggingLevel)
    The logging level for outputting errors and debugging output.
    default: WARNING
 
    -polynomial <int> (property: polynomialOrder)
    The polynomial order to use, must be at least 2.
    default: 2
    minimum: 2
 
    -left <int> (property: numPointsLeft)
    The number of points left of a data point, >= 0.
    default: 3
    minimum: 0
 
    -right <int> (property: numPointsRight)
    The number of points right of a data point, >= 0.
    default: 3
    minimum: 0
    Version:
    $Revision: 2242 $
    Author:
    fracpete (fracpete at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Nested Class Summary

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

        adams.data.baseline.AbstractBaselineCorrection.BaselineCorrectionJob<T extends adams.data.container.DataContainer>

    • Field Summary

      • Fields inherited from class adams.data.baseline.AbstractSavitzkyGolayBased

        m_Filter

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

        m_OptionManager

      • Fields inherited from class adams.core.logging.LoggingObject

        m_Logger, m_LoggingIsEnabled, m_LoggingLevel

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      protected adams.data.filter.AbstractSavitzkyGolay getFilter()
      Returns a new instance of a SavitzkyGolay filter.
      protected adams.data.container.DataPoint getOriginalPoint​(adams.data.container.DataPoint newPoint, Spectrum original)
      Retrieves the data point from the original signal that corresponds to the provided new one.
      protected adams.data.container.DataPoint subtract​(adams.data.container.DataPoint old, adams.data.container.DataPoint baseline)
      Subtracts the baseline from the old data point and creates a new data point.

      • Methods inherited from class adams.data.baseline.AbstractSavitzkyGolayBased

        defineOptions, getNumPointsLeft, getNumPointsRight, getPolynomialOrder, getTechnicalInformation, globalInfo, initialize, numPointsLeftTipText, numPointsRightTipText, polynomialOrderTipText, processData, setNumPointsLeft, setNumPointsRight, setPolynomialOrder

      • 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, loggingLevelTipText, newOptionManager, setLoggingLevel, toCommandLine, toString

      • Methods inherited from class adams.core.logging.LoggingObject

        configureLogger, getLogger, getLoggingLevel, initializeLogging, isLoggingEnabled, sizeOf

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

        getLoggingLevel

    • Constructor Detail

      • SavitzkyGolayBased

        public SavitzkyGolayBased()

    • Method Detail

      • getFilter

        protected adams.data.filter.AbstractSavitzkyGolay getFilter()
        Returns a new instance of a SavitzkyGolay filter.
        Specified by:
        getFilter in class adams.data.baseline.AbstractSavitzkyGolayBased<Spectrum>
        Returns:
        the filter

      • getOriginalPoint

        protected adams.data.container.DataPoint getOriginalPoint​(adams.data.container.DataPoint newPoint,
                                                          Spectrum original)
        Retrieves the data point from the original signal that corresponds to the provided new one.
        Specified by:
        getOriginalPoint in class adams.data.baseline.AbstractSavitzkyGolayBased<Spectrum>
        Parameters:
        newPoint - the point to obtain the corresponding one for
        original - the original signal
        Returns:
        the corresponding data point, null if not found

      • subtract

        protected adams.data.container.DataPoint subtract​(adams.data.container.DataPoint old,
                                                  adams.data.container.DataPoint baseline)
        Subtracts the baseline from the old data point and creates a new data point.
        Specified by:
        subtract in class adams.data.baseline.AbstractSavitzkyGolayBased<Spectrum>
        Parameters:
        old - the old data point to subtract the baseline from
        baseline - the baseline value to subtract
        Returns:
        the new corrected data point