Package adams.data.spectrumfilter

Class PCA

  • 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 PCA
extends adams.data.filter.AbstractBatchFilter<Spectrum>
    Turns the spectra internally into instances and transforms them using principal component analysis (PCA).
    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 <knir.data.instances.AbstractInstanceGenerator> (property: generator)
    The instance generator to use for turning the spectra into Weka Instance 
    objects.
    default: knir.data.instances.SimpleInstanceGenerator
 
    -variance <double> (property: variance)
    The variance to cover.
    default: 0.95
    minimum: 0.0
 
    -max-attributes <int> (property: maxAttributes)
    The maximum attributes.
    default: -1
    minimum: -1
 
    -max-attribute-names <int> (property: maxAttributeNames)
    The maximum number of attribute names.
    default: 5
    minimum: -1
    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.instances.AbstractInstanceGenerator m_Generator
      the instance generator to use.
      protected int m_MaxAttributeNames
      the maximum number of attribute names.
      protected int m_MaxAttributes
      the maximum number of attributes.
      protected double m_Variance
      the variance to cover.

      • 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
      PCA()  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void defineOptions()
      Adds options to the internal list of options.
      String generatorTipText()
      Tip text for this property.
      adams.data.instances.AbstractInstanceGenerator getGenerator()
      Returns the instance generator in use.
      int getMaxAttributeNames()
      Returns the maximum number of attribute names.
      int getMaxAttributes()
      Returns the maximum 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 Spectrum[] processBatchData​(Spectrum[] data)
      Performs the actual batch filtering.
      protected Spectrum processData​(Spectrum data)
      Does nothing.
      void setGenerator​(adams.data.instances.AbstractInstanceGenerator value)
      Sets the instance generator to use.
      void setMaxAttributeNames​(int value)
      Sets the maximum number of attribute names.
      void setMaxAttributes​(int value)
      Sets the maximum attributes.
      void setVariance​(double value)
      Sets the variance.
      String varianceTipText()
      Returns the tip text for this property.

      • 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_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.

    • Constructor Detail

      • PCA

        public PCA()

    • 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

      • 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.

      • 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