Package weka.filters.supervised.attribute

Class PLSFilterExtended

  • All Implemented Interfaces:
    Serializable, weka.core.CapabilitiesHandler, weka.core.CapabilitiesIgnorer, weka.core.CommandlineRunnable, weka.core.OptionHandler, weka.core.RevisionHandler, weka.core.TechnicalInformationHandler, weka.filters.SupervisedFilter
    public class PLSFilterExtended
extends weka.filters.supervised.attribute.PLSFilter
    Class contains changes to the Weka's PLSFilter in order to have simpls work with multiple y attributes. * @author Cor Lieftink (c.lieftink at nki dot nl)
    See Also:
    Serialized Form

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected double[] m_Means  
      protected double[] m_StdDevs  

      • Fields inherited from class weka.filters.supervised.attribute.PLSFilter

        ALGORITHM_PLS1, ALGORITHM_SIMPLS, m_Algorithm, m_ClassMean, m_ClassStdDev, m_Filter, m_Missing, m_NumComponents, m_PerformPrediction, m_PLS1_b_hat, m_PLS1_P, m_PLS1_RegVector, m_PLS1_W, m_Preprocessing, m_ReplaceMissing, m_SIMPLS_B, m_SIMPLS_W, PREPROCESSING_CENTER, PREPROCESSING_NONE, PREPROCESSING_STANDARDIZE, TAGS_ALGORITHM, TAGS_PREPROCESSING

      • Fields inherited from class weka.filters.Filter

        m_Debug, m_DoNotCheckCapabilities, m_FirstBatchDone, m_InputRelAtts, m_InputStringAtts, m_NewBatch, m_OutputRelAtts, m_OutputStringAtts

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      protected weka.core.Instances determineOutputFormat​(weka.core.Instances inputFormat)
      Override original, in order to put more than one class attribute to the output format.
      weka.core.matrix.Matrix getbHat()  
      weka.core.matrix.Matrix getRegVector()  
      weka.core.matrix.Matrix getX​(weka.core.Instances instances)
      Override superclass method in order to deal with multiple y
      weka.core.matrix.Matrix getxWeights()  
      weka.core.matrix.Matrix getY​(weka.core.Instances instances)
      Override superclass method in order to deal with multiple y
      double[] means()
      the mean of all the attributes
      protected weka.core.Instances process​(weka.core.Instances instances)
      Override in order to have the destandardized predictions for multiple y added.
      protected weka.core.Instances processSIMPLS​(weka.core.Instances instances)
      Extended superclass method for increasing dimensions and/of changing handling of the Matrices C,W,P,Q to deal with multiple Y variables.
      double[] stdDevs()
      the standard deviation of the class
      protected weka.core.Instances toInstances​(weka.core.Instances header, weka.core.matrix.Matrix x, weka.core.matrix.Matrix y)
      Override superclass method, as this cannot deal with multiple y attributes Returns the X and Y matrix again as Instances object, based on the given header (must have a class attribute set).

      • Methods inherited from class weka.filters.supervised.attribute.PLSFilter

        algorithmTipText, columnAsVector, getAlgorithm, getCapabilities, getDominantEigenVector, getNumComponents, getOptions, getPerformPrediction, getPreprocessing, getReplaceMissing, getRevision, getTechnicalInformation, getVector, getX, getY, globalInfo, listOptions, main, normalizeVector, numComponentsTipText, performPredictionTipText, preprocessingTipText, processPLS1, replaceMissingTipText, setAlgorithm, setNumComponents, setOptions, setPerformPrediction, setPreprocessing, setReplaceMissing, setVector

      • Methods inherited from class weka.filters.SimpleBatchFilter

        allowAccessToFullInputFormat, batchFinished, hasImmediateOutputFormat, input, input

      • Methods inherited from class weka.filters.SimpleFilter

        reset, setInputFormat

      • Methods inherited from class weka.filters.Filter

        batchFilterFile, bufferInput, copyValues, copyValues, debugTipText, doNotCheckCapabilitiesTipText, filterFile, flushInput, getCapabilities, getCopyOfInputFormat, getDebug, getDoNotCheckCapabilities, getInputFormat, getOutputFormat, initInputLocators, initOutputLocators, inputFormatPeek, isFirstBatchDone, isNewBatch, isOutputFormatDefined, makeCopies, makeCopy, mayRemoveInstanceAfterFirstBatchDone, numPendingOutput, output, outputFormatPeek, outputPeek, postExecution, preExecution, push, push, resetQueue, run, runFilter, setDebug, setDoNotCheckCapabilities, setOutputFormat, testInputFormat, toString, useFilter, wekaStaticWrapper

    • Field Detail

      • m_Means

        protected double[] m_Means

      • m_StdDevs

        protected double[] m_StdDevs

    • Constructor Detail

      • PLSFilterExtended

        public PLSFilterExtended()

    • Method Detail

      • getxWeights

        public weka.core.matrix.Matrix getxWeights()

      • getX

        public weka.core.matrix.Matrix getX​(weka.core.Instances instances)
        Override superclass method in order to deal with multiple y
        Overrides:
        getX in class weka.filters.supervised.attribute.PLSFilter
        Parameters:
        instances - the data to work on
        Returns:
        the x attributes

      • getY

        public weka.core.matrix.Matrix getY​(weka.core.Instances instances)
        Override superclass method in order to deal with multiple y
        Overrides:
        getY in class weka.filters.supervised.attribute.PLSFilter
        Parameters:
        instances - the data to work on
        Returns:
        the y attributes

      • getbHat

        public weka.core.matrix.Matrix getbHat()

      • getRegVector

        public weka.core.matrix.Matrix getRegVector()

      • means

        public double[] means()
        the mean of all the attributes

      • stdDevs

        public double[] stdDevs()
        the standard deviation of the class

      • determineOutputFormat

        protected weka.core.Instances determineOutputFormat​(weka.core.Instances inputFormat)
                                             throws Exception
        Override original, in order to put more than one class attribute to the output format. Determines the output format based on the input format and returns this. In case the output format cannot be returned immediately, i.e., immediateOutputFormat() returns false, then this method will be called from batchFinished().
        Overrides:
        determineOutputFormat in class weka.filters.supervised.attribute.PLSFilter
        Parameters:
        inputFormat - the input format to base the output format on
        Returns:
        the output format
        Throws:
        Exception - in case the determination goes wrong
        See Also:
        SimpleBatchFilter.hasImmediateOutputFormat(), SimpleBatchFilter.batchFinished()

      • toInstances

        protected weka.core.Instances toInstances​(weka.core.Instances header,
                                          weka.core.matrix.Matrix x,
                                          weka.core.matrix.Matrix y)
        Override superclass method, as this cannot deal with multiple y attributes Returns the X and Y matrix again as Instances object, based on the given header (must have a class attribute set).
        Overrides:
        toInstances in class weka.filters.supervised.attribute.PLSFilter
        Parameters:
        header - the format of the instance object
        x - the X matrix (data)
        y - the Y matrix (class)
        Returns:
        the assembled data

      • process

        protected weka.core.Instances process​(weka.core.Instances instances)
                               throws Exception
        Override in order to have the destandardized predictions for multiple y added. Processes the given data (may change the provided dataset) and returns the modified version. This method is called in batchFinished().
        Overrides:
        process in class weka.filters.supervised.attribute.PLSFilter
        Parameters:
        instances - the data to process
        Returns:
        the modified data
        Throws:
        Exception - in case the processing goes wrong
        See Also:
        SimpleBatchFilter.batchFinished()

      • processSIMPLS

        protected weka.core.Instances processSIMPLS​(weka.core.Instances instances)
                                     throws Exception
        Extended superclass method for increasing dimensions and/of changing handling of the Matrices C,W,P,Q to deal with multiple Y variables. processes the instances using the SIMPLS algorithm
        Overrides:
        processSIMPLS in class weka.filters.supervised.attribute.PLSFilter
        Parameters:
        instances - the data to process
        Returns:
        the modified data
        Throws:
        Exception - in case the processing goes wrong