Package weka.filters.supervised.attribute

Class MultiPLS

  • All Implemented Interfaces:
    Serializable, weka.core.CapabilitiesHandler, weka.core.CapabilitiesIgnorer, weka.core.CommandlineRunnable, GenericPLSMatrixAccess, weka.core.OptionHandler, weka.core.RevisionHandler, weka.filters.SupervisedFilter
    public class MultiPLS
extends weka.filters.SimpleBatchFilter
implements weka.filters.SupervisedFilter, GenericPLSMatrixAccess
    For each Y that gets identified by the regular expression for Y attributes, the specified PLS (partial least squares) algorithm gets applied to the X attributes identified by the corresponding regular expression.

    Valid options are: 

     -x-regexp <value>
  The regular expression to identify the X attributes for PLS.
  (default: amplitude-.*)
     -y-regexp <value>
  The regular expression to identify the Y attributes for PLS.
  (default: A_.*)
     -algorithm <value>
  The PLS algorithm to apply.
  (default: adams.data.instancesanalysis.pls.PLS1)
     -drop-non-class-ys <value>
  If enabled, Y attributes that aren't the class attribute are removed from the output.
  (default: off)
     -output-debug-info
  If set, filter is run in debug mode and
  may output additional info to the console
     -do-not-check-capabilities
  If set, filter capabilities are not checked before filter is built
  (use with caution).
    Version:
    $Revision$
    Author:
    FracPete (fracpete at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected AbstractPLS m_Algorithm
      the PLS algorithm.
      protected boolean m_DropNonClassYs
      whether to keep Ys that are not the class or not.
      protected String[] m_MatrixNames
      the matrix names.
      protected gnu.trove.list.TIntList m_OtherIndices
      the indices of the other attributes.
      protected Map<String,​AbstractPLS> m_PLS
      the PLS algorithms corresponding to the Y attributes.
      protected gnu.trove.list.TIntList m_XIndices
      the indices of the X attributes.
      protected BaseRegExp m_XRegExp
      the regular expression for the X columns.
      protected gnu.trove.list.TIntList m_YIndices
      the indices of the Y attributes.
      protected BaseRegExp m_YRegExp
      the regular expression for the Y columns.

      • Fields inherited from class weka.filters.Filter

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

    • Constructor Summary

      Constructors 
      Constructor Description
      MultiPLS()  

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      String algorithmTipText()
      Returns the tip text for this property
      protected weka.core.Instances determineOutputFormat​(weka.core.Instances inputFormat)
      Determines the output format based on the input format and returns this.
      String dropNonClassYsTipText()
      Returns the tip text for this property
      protected String extractPLSKey​(String matrixName)
      Extracts key in the PLS map from the combined matrix name.
      AbstractPLS getAlgorithm()
      Returns the PLS algorithm to use.
      protected AbstractPLS getDefaultAlgorithm()
      Returns the default algorithm.
      protected BaseRegExp getDefaultXRegExp()
      Returns the default X regexp.
      protected BaseRegExp getDefaultYRegExp()
      Returns the default Y regexp.
      boolean getDropNonClassYs()
      Returns whether to remove Y attributes from the output that are not the class attribute.
      weka.core.matrix.Matrix getLoadings()
      Returns the loadings, if available.
      weka.core.matrix.Matrix getMatrix​(String name)
      Returns the matrix with the specified name.
      String[] getMatrixNames()
      Returns the all the available matrices.
      String[] getOptions()
      returns the options of the current setup
      String getRevision()
      Returns the revision string.
      BaseRegExp getXRegExp()
      Returns the regular expression to identify the X attributes.
      BaseRegExp getYRegExp()
      Returns the regular expression to identify the Y attributes.
      String globalInfo()
      Returns a string describing this classifier.
      boolean hasLoadings()
      Whether the algorithm supports return of loadings.
      Enumeration<weka.core.Option> listOptions()
      Gets an enumeration describing the available options.
      static void main​(String[] args)
      runs the filter with the given arguments.
      protected weka.core.Instances process​(weka.core.Instances instances)
      Processes the given data (may change the provided dataset) and returns the modified version.
      void setAlgorithm​(AbstractPLS value)
      Sets the PLS algorithm to use.
      void setDropNonClassYs​(boolean value)
      Sets whether to remove Y attributes from the output that are not the class attribute.
      void setOptions​(String[] options)
      Parses the options for this object.
      void setXRegExp​(BaseRegExp value)
      Sets the regular expression to identify the X attributes.
      void setYRegExp​(BaseRegExp value)
      Sets the regular expression to identify the Y attributes.
      String XRegExpTipText()
      Returns the tip text for this property
      String YRegExpTipText()
      Returns the tip text for this property

      • 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, 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_XRegExp

        protected BaseRegExp m_XRegExp
        the regular expression for the X columns.

      • m_YRegExp

        protected BaseRegExp m_YRegExp
        the regular expression for the Y columns.

      • m_Algorithm

        protected AbstractPLS m_Algorithm
        the PLS algorithm.

      • m_DropNonClassYs

        protected boolean m_DropNonClassYs
        whether to keep Ys that are not the class or not.

      • m_XIndices

        protected gnu.trove.list.TIntList m_XIndices
        the indices of the X attributes.

      • m_YIndices

        protected gnu.trove.list.TIntList m_YIndices
        the indices of the Y attributes.

      • m_OtherIndices

        protected gnu.trove.list.TIntList m_OtherIndices
        the indices of the other attributes.

      • m_PLS

        protected Map<String,​AbstractPLS> m_PLS
        the PLS algorithms corresponding to the Y attributes.

      • m_MatrixNames

        protected String[] m_MatrixNames
        the matrix names.

    • Constructor Detail

      • MultiPLS

        public MultiPLS()

    • Method Detail

      • globalInfo

        public String globalInfo()
        Returns a string describing this classifier.
        Specified by:
        globalInfo in class weka.filters.SimpleFilter
        Returns:
        a description of the classifier suitable for displaying in the explorer/experimenter gui

      • listOptions

        public Enumeration<weka.core.Option> listOptions()
        Gets an enumeration describing the available options.
        Specified by:
        listOptions in interface weka.core.OptionHandler
        Overrides:
        listOptions in class weka.filters.Filter
        Returns:
        an enumeration of all the available options.

      • getOptions

        public String[] getOptions()
        returns the options of the current setup
        Specified by:
        getOptions in interface weka.core.OptionHandler
        Overrides:
        getOptions in class weka.filters.Filter
        Returns:
        the current options

      • setOptions

        public void setOptions​(String[] options)
                throws Exception
        Parses the options for this object.
        Specified by:
        setOptions in interface weka.core.OptionHandler
        Overrides:
        setOptions in class weka.filters.Filter
        Parameters:
        options - the options to use
        Throws:
        Exception - if the option setting fails

      • getDefaultXRegExp

        protected BaseRegExp getDefaultXRegExp()
        Returns the default X regexp.
        Returns:
        the default

      • setXRegExp

        public void setXRegExp​(BaseRegExp value)
        Sets the regular expression to identify the X attributes.
        Parameters:
        value - the expression

      • getXRegExp

        public BaseRegExp getXRegExp()
        Returns the regular expression to identify the X attributes.
        Returns:
        the expression

      • XRegExpTipText

        public String XRegExpTipText()
        Returns the tip text for this property
        Returns:
        tip text for this property suitable for displaying in the explorer/experimenter gui

      • getDefaultYRegExp

        protected BaseRegExp getDefaultYRegExp()
        Returns the default Y regexp.
        Returns:
        the default

      • setYRegExp

        public void setYRegExp​(BaseRegExp value)
        Sets the regular expression to identify the Y attributes.
        Parameters:
        value - the expression

      • getYRegExp

        public BaseRegExp getYRegExp()
        Returns the regular expression to identify the Y attributes.
        Returns:
        the expression

      • YRegExpTipText

        public String YRegExpTipText()
        Returns the tip text for this property
        Returns:
        tip text for this property suitable for displaying in the explorer/experimenter gui

      • getDefaultAlgorithm

        protected AbstractPLS getDefaultAlgorithm()
        Returns the default algorithm.
        Returns:
        the default

      • setAlgorithm

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

      • getAlgorithm

        public AbstractPLS getAlgorithm()
        Returns the PLS algorithm to use.
        Returns:
        the algorithm

      • algorithmTipText

        public String algorithmTipText()
        Returns the tip text for this property
        Returns:
        tip text for this property suitable for displaying in the explorer/experimenter gui

      • setDropNonClassYs

        public void setDropNonClassYs​(boolean value)
        Sets whether to remove Y attributes from the output that are not the class attribute.
        Parameters:
        value - true if to drop

      • getDropNonClassYs

        public boolean getDropNonClassYs()
        Returns whether to remove Y attributes from the output that are not the class attribute.
        Returns:
        true if to to drop

      • dropNonClassYsTipText

        public String dropNonClassYsTipText()
        Returns the tip text for this property
        Returns:
        tip text for this property suitable for displaying in the explorer/experimenter gui

      • determineOutputFormat

        protected weka.core.Instances determineOutputFormat​(weka.core.Instances inputFormat)
                                             throws Exception
        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().
        Specified by:
        determineOutputFormat in class weka.filters.SimpleFilter
        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()

      • process

        protected weka.core.Instances process​(weka.core.Instances instances)
                               throws Exception
        Processes the given data (may change the provided dataset) and returns the modified version. This method is called in batchFinished().
        Specified by:
        process in class weka.filters.SimpleFilter
        Parameters:
        instances - the data to process
        Returns:
        the modified data
        Throws:
        Exception - in case the processing goes wrong
        See Also:
        SimpleBatchFilter.batchFinished()

      • extractPLSKey

        protected String extractPLSKey​(String matrixName)
        Extracts key in the PLS map from the combined matrix name.
        Parameters:
        matrixName - the matrix name to process
        Returns:
        the key, input if failed to extract

      • getMatrix

        public weka.core.matrix.Matrix getMatrix​(String name)
        Returns the matrix with the specified name.
        Specified by:
        getMatrix in interface GenericPLSMatrixAccess
        Parameters:
        name - the name of the matrix
        Returns:
        the matrix, null if not available

      • getLoadings

        public weka.core.matrix.Matrix getLoadings()
        Returns the loadings, if available.
        Specified by:
        getLoadings in interface GenericPLSMatrixAccess
        Returns:
        always null

      • getRevision

        public String getRevision()
        Returns the revision string.
        Specified by:
        getRevision in interface weka.core.RevisionHandler
        Overrides:
        getRevision in class weka.filters.Filter
        Returns:
        the revision

      • main

        public static void main​(String[] args)
        runs the filter with the given arguments.
        Parameters:
        args - the commandline arguments