Package adams.flow.transformer

Class MultiSpectrumOutlierDetector

  • 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.db.DatabaseConnectionUser, adams.event.VariableChangeListener, adams.flow.core.Actor, adams.flow.core.ErrorHandler, adams.flow.core.InputConsumer, adams.flow.core.OutputProducer, Serializable, Comparable
    public class MultiSpectrumOutlierDetector
extends adams.flow.transformer.AbstractTransformer
implements adams.db.DatabaseConnectionUser
    Uses the specified multi-spectrum filter to obtain a single spectrum from the multi-spectrum and applies the outlier detector to it.
    Any resulting detections get added to the multi-spectrum itself.

    Input/output:
    - accepts:
       knir.data.spectrum.MultiSpectrum
    - generates:
       knir.data.spectrum.MultiSpectrum


    -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: MultiSpectrumOutlierDetector
 
    -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 gets stopped in case this actor encounters an error;
     useful for critical actors.
    default: false
 
    -silent <boolean> (property: silent)
    If enabled, then no errors are output in the console.
    default: false
 
    -filter <knir.data.multifilter.AbstractMultiSpectrumFilter> (property: filter)
    The filter to use.
    default: knir.data.multifilter.PickByIndex
 
    -detector <adams.data.outlier.AbstractOutlierDetector> (property: detector)
    The outlier detector to use.
    default: adams.data.outlier.PassThrough
 
    -only-warning <boolean> (property: onlyWarning)
    If enabled, the detections get added merely as warnings instead of as errors.
    default: false
    Author:
    fracpete (fracpete at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected boolean m_DatabaseConnectionUpdated
      whether the database connection has been updated.
      protected adams.data.outlier.AbstractOutlierDetector m_Detector
      the outlier detector to apply.
      protected AbstractMultiSpectrumFilter m_Filter
      the filter to apply for extracting the spectrum to apply the outlier detector to.
      protected boolean m_OnlyWarning
      whether the detection is only added as warning instead of error.

      • 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.
      String detectorTipText()
      Returns the tip text for this property.
      protected String doExecute()
      Executes the flow item.
      String filterTipText()
      Returns the tip text for this property.
      Class[] generates()
      Returns the class of objects that it generates.
      protected adams.db.AbstractDatabaseConnection getDatabaseConnection()
      Determines the database connection in the flow.
      adams.data.outlier.AbstractOutlierDetector getDetector()
      Returns the outlier detector in use.
      AbstractMultiSpectrumFilter getFilter()
      Returns the filter in use.
      boolean getOnlyWarning()
      Returns whether the detections are added as error or warning.
      String getQuickInfo()
      Returns a quick info about the actor, which will be displayed in the GUI.
      String globalInfo()
      Returns a string describing the object.
      String onlyWarningTipText()
      Returns the tip text for this property.
      protected void reset()
      Resets the scheme.
      void setDetector​(adams.data.outlier.AbstractOutlierDetector value)
      Sets the outlier detector to use.
      void setFilter​(AbstractMultiSpectrumFilter value)
      Sets the filter to use.
      void setOnlyWarning​(boolean value)
      Sets whether the detections are added as error or warning.

      • 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, 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_Filter

        protected AbstractMultiSpectrumFilter m_Filter
        the filter to apply for extracting the spectrum to apply the outlier detector to.

      • m_Detector

        protected adams.data.outlier.AbstractOutlierDetector m_Detector
        the outlier detector to apply.

      • m_OnlyWarning

        protected boolean m_OnlyWarning
        whether the detection is only added as warning instead of error.

      • m_DatabaseConnectionUpdated

        protected boolean m_DatabaseConnectionUpdated
        whether the database connection has been updated.

    • Constructor Detail

      • MultiSpectrumOutlierDetector

        public MultiSpectrumOutlierDetector()

    • 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

      • reset

        protected void reset()
        Resets the scheme.
        Overrides:
        reset in class adams.flow.core.AbstractActor

      • filterTipText

        public String filterTipText()
        Returns the tip text for this property.
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • setDetector

        public void setDetector​(adams.data.outlier.AbstractOutlierDetector value)
        Sets the outlier detector to use.
        Parameters:
        value - the detector

      • getDetector

        public adams.data.outlier.AbstractOutlierDetector getDetector()
        Returns the outlier detector in use.
        Returns:
        the detector

      • detectorTipText

        public String detectorTipText()
        Returns the tip text for this property.
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • setOnlyWarning

        public void setOnlyWarning​(boolean value)
        Sets whether the detections are added as error or warning.
        Parameters:
        value - if true then the detections are added as warning instead of as error

      • getOnlyWarning

        public boolean getOnlyWarning()
        Returns whether the detections are added as error or warning.
        Returns:
        true if the detections get added as warning instead of as error

      • onlyWarningTipText

        public String onlyWarningTipText()
        Returns the tip text for this property.
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • getQuickInfo

        public String getQuickInfo()
        Returns a quick info about the actor, which will be displayed in the GUI.
        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
        Returns:
        null if no info available, otherwise short string

      • accepts

        public Class[] accepts()
        Returns the class that the consumer accepts.
        Specified by:
        accepts in interface adams.flow.core.InputConsumer
        Returns:
        the default DataContainer class for the project

      • generates

        public Class[] generates()
        Returns the class of objects that it generates.
        Specified by:
        generates in interface adams.flow.core.OutputProducer
        Returns:
        the default DataContainer class for the project

      • getDatabaseConnection

        protected adams.db.AbstractDatabaseConnection getDatabaseConnection()
        Determines the database connection in the flow.
        Returns:
        the database connection to use

      • 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