Package adams.data.spectrumfilter

Class PLS

  • 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.filter.Filter>, adams.core.SizeOfHandler, adams.data.filter.BatchFilter<Spectrum>, adams.data.filter.Filter<Spectrum>, Serializable, Comparable
    public class PLS
extends adams.data.filter.AbstractBatchFilter<Spectrum>
    Turns the spectra internally into instances and transforms them using the specified PLS algorithm. The generated output is then converted back into spectra.
    Only works as batch filter, not in single spectrum mode. 

    -logging-level <OFF|SEVERE|WARNING|INFO|CONFIG|FINE|FINER|FINEST> (property: loggingLevel)
    The logging level for outputting errors and debugging output.
    default: WARNING
 
    -no-id-update <boolean> (property: dontUpdateID)
    If enabled, suppresses updating the ID of adams.data.id.IDHandler data containers.
    default: false
 
    -generator <adams.data.instances.AbstractInstanceGenerator> (property: generator)
    The instance generator to use for turning the spectra into Weka Instance 
    objects.
    default: adams.data.instances.SimpleInstanceGenerator
 
    -algorithm <adams.data.instancesanalysis.pls.AbstractPLS> (property: algorithm)
    The PLS algorithm to use
    default: adams.data.instancesanalysis.pls.PLS1
    See Also:
    Serialized Form

    • Nested Class Summary

      • Nested classes/interfaces inherited from class adams.data.filter.AbstractFilter

        adams.data.filter.AbstractFilter.FilterJob<T extends adams.data.container.DataContainer>

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected adams.data.instancesanalysis.pls.AbstractPLS m_Algorithm
      the PLS algorithm.
      protected adams.data.instances.AbstractInstanceGenerator m_Generator
      the instance generator to use.

      • Fields inherited from class adams.data.filter.AbstractFilter

        m_DontUpdateID

      • 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
      PLS()  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      String algorithmTipText()
      Tip text for this property.
      void defineOptions()
      Adds options to the internal list of options.
      String generatorTipText()
      Tip text for this property.
      adams.data.instancesanalysis.pls.AbstractPLS getAlgorithm()
      Returns PLS algorithm in use.
      adams.data.instances.AbstractInstanceGenerator getGenerator()
      Returns the instance generator in use.
      String globalInfo()
      Returns a string describing the object.
      protected Spectrum[] processBatchData​(Spectrum[] data)
      Performs the actual batch filtering.
      protected Spectrum processData​(Spectrum data)
      Does nothing.
      void setAlgorithm​(adams.data.instancesanalysis.pls.AbstractPLS value)
      Sets PLS algorithm to use.
      void setGenerator​(adams.data.instances.AbstractInstanceGenerator value)
      Sets the instance generator to use.

      • Methods inherited from class adams.data.filter.AbstractBatchFilter

        batchFilter, checkBatchData

      • Methods inherited from class adams.data.filter.AbstractFilter

        checkData, cleanUp, compareTo, destroy, dontUpdateIDTipText, equals, filter, forCommandLine, getDontUpdateID, reset, setDontUpdateID, shallowCopy, shallowCopy

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

        cleanUpOptions, 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 interface adams.data.filter.Filter

        cleanUp, compareTo, destroy, dontUpdateIDTipText, equals, filter, getDontUpdateID, reset, setDontUpdateID, shallowCopy, shallowCopy

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

        getLoggingLevel, setLoggingLevel

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

        getLogger, isLoggingEnabled

      • Methods inherited from interface adams.core.option.OptionHandler

        cleanUpOptions, getOptionManager, toCommandLine

    • Field Detail

      • m_Generator

        protected adams.data.instances.AbstractInstanceGenerator m_Generator
        the instance generator to use.

      • m_Algorithm

        protected adams.data.instancesanalysis.pls.AbstractPLS m_Algorithm
        the PLS algorithm.

    • Constructor Detail

      • PLS

        public PLS()

    • Method Detail

      • globalInfo

        public String globalInfo()
        Returns a string describing the object.
        Specified by:
        globalInfo in interface adams.core.GlobalInfoSupporter
        Specified by:
        globalInfo in class adams.core.option.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 adams.core.option.OptionHandler
        Overrides:
        defineOptions in class adams.data.filter.AbstractFilter<Spectrum>

      • setGenerator

        public void setGenerator​(adams.data.instances.AbstractInstanceGenerator value)
        Sets the instance generator to use.
        Parameters:
        value - the generator

      • getGenerator

        public adams.data.instances.AbstractInstanceGenerator getGenerator()
        Returns the instance generator in use.
        Returns:
        the generator

      • generatorTipText

        public String generatorTipText()
        Tip text for this property.
        Returns:
        description for displaying in the GUI

      • setAlgorithm

        public void setAlgorithm​(adams.data.instancesanalysis.pls.AbstractPLS value)
        Sets PLS algorithm to use.
        Parameters:
        value - the algorithm

      • getAlgorithm

        public adams.data.instancesanalysis.pls.AbstractPLS getAlgorithm()
        Returns PLS algorithm in use.
        Returns:
        the algorithm

      • algorithmTipText

        public String algorithmTipText()
        Tip text for this property.
        Returns:
        description for displaying in the GUI

      • processBatchData

        protected Spectrum[] processBatchData​(Spectrum[] data)
        Performs the actual batch filtering.
        Specified by:
        processBatchData in class adams.data.filter.AbstractBatchFilter<Spectrum>
        Parameters:
        data - the data to filter
        Returns:
        the filtered data

      • processData

        protected Spectrum processData​(Spectrum data)
        Does nothing.
        Specified by:
        processData in class adams.data.filter.AbstractFilter<Spectrum>
        Parameters:
        data - the data to filter
        Returns:
        the filtered data