Package adams.flow.transformer

Class MultiSpectrumFilter

  • All Implemented Interfaces:
    adams.core.AdditionalInformationHandler, adams.core.ClassCrossReference, adams.core.CleanUpHandler, adams.core.CrossReference, 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 MultiSpectrumFilter
extends adams.flow.transformer.AbstractTransformer
implements adams.db.DatabaseConnectionUser, adams.core.ClassCrossReference
    Generates a single spectrum from a multi-spectrum using the specified filter.
    For some filters that use several spectra, the order of the spectra is important. The internal order of the MultiSpectrum is used to pick the spectra, which can be influenced via custom spectrum comparators.

    See also:
    adams.data.conversion.SpectraToMultiSpectrum
    adams.flow.transformer.SpectrumFileReader

    Input/output:
    - accepts:
       adams.data.spectrum.MultiSpectrum
    - generates:
       adams.data.spectrum.Spectrum


    -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: MultiSpectrumFilter
 
    -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
 
    -filter <adams.data.multifilter.AbstractMultiSpectrumFilter> (property: filter)
    The filter to use.
    default: adams.data.multifilter.PickByIndex
 
    -transfer-report <boolean> (property: transferReport)
    If enabled, the report values from the multi-spectrum get transferred into
    the sub-spectra.
    default: false
 
    -transfer-prefix <java.lang.String> (property: transferPrefix)
    The (optional) prefix for report fields that get transferred.
    default:
 
    -transfer-regexp <adams.core.base.BaseRegExp> (property: transferRegExp)
    The regular expression that the field names must match in order to get transferred.
    default: .*
    more: https://docs.oracle.com/javase/tutorial/essential/regex/
    https://docs.oracle.com/javase/8/docs/api/java/util/regex/Pattern.html
    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 AbstractMultiSpectrumFilter m_Filter
      the filter to apply.
      protected String m_TransferPrefix
      the (optional) prefix for fields from the multi-spectrum.
      protected adams.core.base.BaseRegExp m_TransferRegExp
      the regular expression for field names to transfer.
      protected boolean m_TransferReport
      whether to transfer the multi-spectrum's report into the sub-spectra.

      • 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.
      String filterTipText()
      Returns the tip text for this property.
      Class[] generates()
      Returns the class of objects that it generates.
      Class[] getClassCrossReferences()
      Returns the cross-referenced classes.
      protected adams.db.AbstractDatabaseConnection getDatabaseConnection()
      Determines the database connection in the flow.
      AbstractMultiSpectrumFilter getFilter()
      Returns the filter in use.
      String getQuickInfo()
      Returns a quick info about the actor, which will be displayed in the GUI.
      String getTransferPrefix()
      Returns the (optional) prefix for report fields that get transferred.
      adams.core.base.BaseRegExp getTransferRegExp()
      Returns the regular expression that the field names must match in order to get transferred.
      boolean getTransferReport()
      Returns whether to transfer the report values from the multi-spectrum into the sub-spectra.
      String globalInfo()
      Returns a string describing the object.
      protected void reset()
      Resets the scheme.
      void setFilter​(AbstractMultiSpectrumFilter value)
      Sets the filter to use.
      void setTransferPrefix​(String value)
      Sets the (optional) prefix for report fields that get transferred.
      void setTransferRegExp​(adams.core.base.BaseRegExp value)
      Sets the regular expression that the field names must match in order to get transferred.
      void setTransferReport​(boolean value)
      Sets whether to transfer the report values from the multi-spectrum into the sub-spectra.
      String transferPrefixTipText()
      Returns the tip text for this property.
      String transferRegExpTipText()
      Returns the tip text for this property.
      String transferReportTipText()
      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, 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_TransferReport

        protected boolean m_TransferReport
        whether to transfer the multi-spectrum's report into the sub-spectra.

      • m_TransferPrefix

        protected String m_TransferPrefix
        the (optional) prefix for fields from the multi-spectrum.

      • m_TransferRegExp

        protected adams.core.base.BaseRegExp m_TransferRegExp
        the regular expression for field names to transfer.

      • m_DatabaseConnectionUpdated

        protected boolean m_DatabaseConnectionUpdated
        whether the database connection has been updated.

    • Constructor Detail

      • MultiSpectrumFilter

        public MultiSpectrumFilter()

    • 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

      • getClassCrossReferences

        public Class[] getClassCrossReferences()
        Returns the cross-referenced classes.
        Specified by:
        getClassCrossReferences in interface adams.core.ClassCrossReference
        Returns:
        the classes

      • 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.

      • setTransferReport

        public void setTransferReport​(boolean value)
        Sets whether to transfer the report values from the multi-spectrum into the sub-spectra.
        Parameters:
        value - true if to transfer

      • getTransferReport

        public boolean getTransferReport()
        Returns whether to transfer the report values from the multi-spectrum into the sub-spectra.
        Returns:
        true if to transfer

      • transferReportTipText

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

      • setTransferPrefix

        public void setTransferPrefix​(String value)
        Sets the (optional) prefix for report fields that get transferred.
        Parameters:
        value - the prefix

      • getTransferPrefix

        public String getTransferPrefix()
        Returns the (optional) prefix for report fields that get transferred.
        Returns:
        the prefix

      • transferPrefixTipText

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

      • setTransferRegExp

        public void setTransferRegExp​(adams.core.base.BaseRegExp value)
        Sets the regular expression that the field names must match in order to get transferred.
        Parameters:
        value - the regular expression

      • getTransferRegExp

        public adams.core.base.BaseRegExp getTransferRegExp()
        Returns the regular expression that the field names must match in order to get transferred.
        Returns:
        the regular expression

      • transferRegExpTipText

        public String transferRegExpTipText()
        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