Package adams.flow.transformer

Class WekaPrincipalComponents

  • All Implemented Interfaces:
    adams.core.AdditionalInformationHandler, adams.core.CleanUpHandler, adams.core.Destroyable, adams.core.GlobalInfoSupporter, adams.core.logging.LoggingLevelHandler, adams.core.logging.LoggingSupporter, adams.core.option.OptionHandler, adams.core.QuickInfoSupporter, adams.core.ShallowCopySupporter<adams.flow.core.Actor>, adams.core.SizeOfHandler, adams.core.Stoppable, adams.core.StoppableWithFeedback, adams.core.VariablesInspectionHandler, adams.event.VariableChangeListener, adams.flow.core.Actor, adams.flow.core.ErrorHandler, adams.flow.core.InputConsumer, adams.flow.core.OutputProducer, Serializable, Comparable
    public class WekaPrincipalComponents
extends adams.flow.transformer.AbstractTransformer
    Performs principal components analysis on the incoming data and outputs the loadings and the transformed data as spreadsheet array.
    Automatically filters out attributes that cannot be handled by PCA.

    Input/output:
    - accepts:
       weka.core.Instances
    - generates:
       adams.data.spreadsheet.SpreadSheet[]


    -logging-level <OFF|SEVERE|WARNING|INFO|CONFIG|FINE|FINER|FINEST> (property: loggingLevel)
    The logging level for outputting errors and debugging output.
    default: WARNING
 
    -name <java.lang.String> (property: name)
    The name of the actor.
    default: WekaPrincipalComponents
 
    -annotation <adams.core.base.BaseAnnotation> (property: annotations)
    The annotations to attach to this actor.
    default: 
 
    -skip <boolean> (property: skip)
    If set to true, transformation is skipped and the input token is just forwarded 
    as it is.
    default: false
 
    -stop-flow-on-error <boolean> (property: stopFlowOnError)
    If set to true, the flow execution at this level gets stopped in case this 
    actor encounters an error; the error gets propagated; useful for critical 
    actors.
    default: false
 
    -silent <boolean> (property: silent)
    If enabled, then no errors are output in the console; Note: the enclosing 
    actor handler must have this enabled as well.
    default: false
 
    -variance-covered <double> (property: varianceCovered)
    Retain enough PC attributes to account for this proportion of variance.
    default: 0.95
 
    -max-attributes <int> (property: maximumAttributes)
    The maximum number of PC attributes to retain.
    default: -1
    minimum: -1
 
    -max-attribute-names <int> (property: maximumAttributeNames)
    The maximum number of attribute names to use.
    default: 5
    minimum: -1
    Actor that takes in an instances object containing TGA-MS data and outputs the coefficients from a principal components analysis
    Version:
    $Revision$
    Author:
    michael.fowke, FracPete (fracpete at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected double m_CoverVariance
      the variance to cover.
      protected int m_MaxAttributeNames
      the maximum number of attribute names to use.
      protected int m_MaxAttributes
      the maximum number of attributes to keep.

      • Fields inherited from class adams.flow.transformer.AbstractTransformer

        BACKUP_INPUT, BACKUP_OUTPUT, m_InputToken, m_OutputToken

      • Fields inherited from class adams.flow.core.AbstractActor

        m_Annotations, m_BackupState, m_DetectedObjectVariables, m_DetectedVariables, m_ErrorHandler, m_Executed, m_Executing, m_ExecutionListeningSupporter, m_FullName, m_LoggingPrefix, m_Name, m_Parent, m_ScopeHandler, m_Self, m_Silent, m_Skip, m_StopFlowOnError, m_StopMessage, m_Stopped, m_StorageHandler, m_VariablesUpdated

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

        m_OptionManager

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

        m_Logger, m_LoggingIsEnabled, m_LoggingLevel

      • Fields inherited from interface adams.flow.core.Actor

        FILE_EXTENSION, FILE_EXTENSION_GZ

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      Class[] accepts()
      Returns the class that the consumer accepts.
      void defineOptions()
      Adds options to the internal list of options.
      protected String doExecute()
      Executes the flow item.
      Class[] generates()
      Returns the class of objects that it generates.
      int getMaximumAttributeNames()
      Gets maximum number of attribute names to use.
      int getMaximumAttributes()
      Gets maximum number of PC attributes to retain.
      String getQuickInfo()  
      double getVarianceCovered()
      Gets the proportion of total variance to account for when retaining principal components.
      String globalInfo()
      Returns a string describing the object.
      String maximumAttributeNamesTipText()
      Returns the tip text for this property.
      String maximumAttributesTipText()
      Returns the tip text for this property.
      void setMaximumAttributeNames​(int value)
      Sets maximum number of attribute names.
      void setMaximumAttributes​(int value)
      Sets maximum number of PC attributes to retain.
      void setVarianceCovered​(double value)
      Sets the amount of variance to account for when retaining principal components.
      String varianceCoveredTipText()
      Returns the tip text for this property.

      • Methods inherited from class adams.flow.transformer.AbstractTransformer

        backupState, currentInput, execute, hasInput, hasPendingOutput, input, output, postExecute, restoreState, wrapUp

      • Methods inherited from class adams.flow.core.AbstractActor

        annotationsTipText, canInspectOptions, canPerformSetUpCheck, cleanUp, compareTo, configureLogger, destroy, equals, finalUpdateVariables, findVariables, findVariables, forceVariables, forCommandLine, forName, forName, getAdditionalInformation, getAnnotations, getDefaultName, getDetectedVariables, getErrorHandler, getFlowActors, getFlowExecutionListeningSupporter, getFullName, getName, getNextSibling, getParent, getParentComponent, getPreviousSibling, getRoot, getScopeHandler, getSilent, getSkip, getStopFlowOnError, getStopMessage, getStorageHandler, getVariables, handleError, handleException, hasErrorHandler, hasStopMessage, index, initialize, isBackedUp, isExecuted, isExecuting, isFinished, isHeadless, isStopped, nameTipText, performSetUpChecks, performVariableChecks, preExecute, pruneBackup, pruneBackup, reset, setAnnotations, setErrorHandler, setName, setParent, setSilent, setSkip, setStopFlowOnError, setUp, setVariables, shallowCopy, shallowCopy, silentTipText, sizeOf, skipTipText, stopExecution, stopExecution, stopFlowOnErrorTipText, updateDetectedVariables, updatePrefix, updateVariables, variableChanged

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

        cleanUpOptions, finishInit, getDefaultLoggingLevel, getOptionManager, loggingLevelTipText, newOptionManager, setLoggingLevel, toCommandLine, toString

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

        getLogger, getLoggingLevel, initializeLogging, isLoggingEnabled

      • Methods inherited from interface adams.flow.core.Actor

        cleanUp, compareTo, destroy, equals, findVariables, getAnnotations, getDefaultName, getDetectedVariables, getErrorHandler, getFlowExecutionListeningSupporter, getFullName, getName, getNextSibling, getParent, getParentComponent, getPreviousSibling, getRoot, getScopeHandler, getSilent, getSkip, getStopFlowOnError, getStopMessage, getStorageHandler, getVariables, handleError, hasErrorHandler, hasStopMessage, index, isExecuted, isFinished, isHeadless, isStopped, setAnnotations, setErrorHandler, setName, setParent, setSilent, setSkip, setStopFlowOnError, setUp, setVariables, shallowCopy, shallowCopy, sizeOf, stopExecution, stopExecution, toCommandLine, variableChanged

      • Methods inherited from interface adams.core.AdditionalInformationHandler

        getAdditionalInformation

      • 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

      • Methods inherited from interface adams.core.VariablesInspectionHandler

        canInspectOptions

    • Field Detail

      • m_CoverVariance

        protected double m_CoverVariance
        the variance to cover.

      • m_MaxAttributes

        protected int m_MaxAttributes
        the maximum number of attributes to keep.

      • m_MaxAttributeNames

        protected int m_MaxAttributeNames
        the maximum number of attribute names to use.

    • Constructor Detail

      • WekaPrincipalComponents

        public WekaPrincipalComponents()

    • 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.flow.core.AbstractActor

      • setVarianceCovered

        public void setVarianceCovered​(double value)
        Sets the amount of variance to account for when retaining principal components.
        Parameters:
        value - the proportion of total variance to account for

      • getVarianceCovered

        public double getVarianceCovered()
        Gets the proportion of total variance to account for when retaining principal components.
        Returns:
        the proportion of variance to account for

      • varianceCoveredTipText

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

      • setMaximumAttributes

        public void setMaximumAttributes​(int value)
        Sets maximum number of PC attributes to retain.
        Parameters:
        value - the maximum number of attributes

      • getMaximumAttributes

        public int getMaximumAttributes()
        Gets maximum number of PC attributes to retain.
        Returns:
        the maximum number of attributes

      • maximumAttributesTipText

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

      • setMaximumAttributeNames

        public void setMaximumAttributeNames​(int value)
        Sets maximum number of attribute names.
        Parameters:
        value - the maximum number of attribute names

      • getMaximumAttributeNames

        public int getMaximumAttributeNames()
        Gets maximum number of attribute names to use.
        Returns:
        the maximum number of attribute names

      • maximumAttributeNamesTipText

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

      • getQuickInfo

        public String getQuickInfo()
        Specified by:
        getQuickInfo in interface adams.flow.core.Actor
        Specified by:
        getQuickInfo in interface adams.core.QuickInfoSupporter
        Overrides:
        getQuickInfo in class adams.flow.core.AbstractActor

      • accepts

        public Class[] accepts()
        Returns the class that the consumer accepts.
        Returns:
        the Class of objects that can be processed

      • generates

        public Class[] generates()
        Returns the class of objects that it generates.
        Returns:
        the Class of the generated tokens

      • doExecute

        protected String doExecute()
        Executes the flow item.
        Specified by:
        doExecute in class adams.flow.core.AbstractActor
        Returns:
        null if everything is fine, otherwise error message