Package adams.data.instances

Class AbstractSpectrumBasedInstanceGenerator

  • All Implemented Interfaces:
    adams.core.CleanUpHandler, adams.core.Destroyable, adams.core.GlobalInfoSupporter, adams.core.logging.LoggingLevelHandler, adams.core.logging.LoggingSupporter, adams.core.option.OptionHandler, adams.core.ShallowCopySupporter<adams.data.instances.AbstractInstanceGenerator>, adams.core.SizeOfHandler, InstanceGeneratorWithSampleID, adams.db.DatabaseConnectionHandler, adams.db.DatabaseConnectionProvider, adams.db.DatabaseConnectionUser, adams.db.OptionalDatabaseConnectionUser, Serializable, Comparable
    Direct Known Subclasses:
    AbstractFieldInstanceGenerator, AbstractSpectrumInstanceGenerator
    public abstract class AbstractSpectrumBasedInstanceGenerator
extends adams.data.instances.AbstractInstanceGenerator<Spectrum>
implements InstanceGeneratorWithSampleID
    Abstract base class for schemes that turn spectra/sample data into weka.core.Instance objects.
    Author:
    fracpete (fracpete at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected boolean m_AddSampleID
      whether to add the sample ID.
      protected boolean m_LoadSampleData
      whether to load the sample data if only dummy.
      protected adams.core.base.BaseString[] m_Notes
      the notes to add as attributes.

      • Fields inherited from class adams.data.instances.AbstractInstanceGenerator

        LABEL_FALSE, LABEL_TRUE, m_AddDatabaseID, m_DatabaseConnection, m_Offline, m_OutputHeader, m_TolerateHeaderChanges

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

        m_OptionManager

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

        m_Logger, m_LoggingIsEnabled, m_LoggingLevel

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      String addSampleIDTipText()
      Returns the tip text for this property.
      protected void checkInput​(Spectrum data)
      Checks the input spectrum.
      void defineOptions()
      Adds options to the internal list of options.
      boolean getAddSampleID()
      Returns whether the sample ID is added.
      protected adams.db.AbstractDatabaseConnection getDefaultDatabaseConnection()
      Returns the default database connection.
      boolean getLoadSampleData()
      Returns whether to load the sample data via the sample ID if only dummy report available.
      adams.core.base.BaseString[] getNotes()
      Returns the current notes to add as attributes.
      String loadSampleDataTipText()
      Returns the tip text for this property.
      String notesTipText()
      Returns the tip text for this property.
      protected void postProcessHeader​(Spectrum data)
      Adds IDs, notes, additional fields to header.
      protected weka.core.Instance postProcessOutput​(Spectrum data, weka.core.Instance inst)
      Adds the IDs, notes, additional fields to the data.
      void setAddSampleID​(boolean value)
      Sets whether the sample ID is added to the data or not.
      void setLoadSampleData​(boolean value)
      Sets whether to load the sample data via the sample ID if only dummy report available.
      void setNotes​(adams.core.base.BaseString[] value)
      Sets the notes to add as attributes.

      • Methods inherited from class adams.data.instances.AbstractInstanceGenerator

        addDatabaseIDTipText, checkHeader, checkSetup, cleanUp, compareTo, destroy, equals, forCommandLine, forName, generate, generateHeader, generateOutput, getAddDatabaseID, getDatabaseConnection, getGenerators, getOffline, getOutputHeader, getTolerateHeaderChanges, initialize, interpretePosition, offlineTipText, reset, setAddDatabaseID, setDatabaseConnection, setOffline, setTolerateHeaderChanges, shallowCopy, shallowCopy, tolerateHeaderChangesTipText

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

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

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

        configureLogger, getLogger, getLoggingLevel, initializeLogging, isLoggingEnabled, sizeOf

      • Methods inherited from interface adams.core.logging.LoggingLevelHandler

        getLoggingLevel

    • Field Detail

      • m_AddSampleID

        protected boolean m_AddSampleID
        whether to add the sample ID.

      • m_Notes

        protected adams.core.base.BaseString[] m_Notes
        the notes to add as attributes.

      • m_LoadSampleData

        protected boolean m_LoadSampleData
        whether to load the sample data if only dummy.

    • Constructor Detail

      • AbstractSpectrumBasedInstanceGenerator

        public AbstractSpectrumBasedInstanceGenerator()

    • Method Detail

      • 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.data.instances.AbstractInstanceGenerator<Spectrum>

      • getDefaultDatabaseConnection

        protected adams.db.AbstractDatabaseConnection getDefaultDatabaseConnection()
        Returns the default database connection.
        Specified by:
        getDefaultDatabaseConnection in class adams.data.instances.AbstractInstanceGenerator<Spectrum>
        Returns:
        the default database connection

      • setAddSampleID

        public void setAddSampleID​(boolean value)
        Sets whether the sample ID is added to the data or not.
        Specified by:
        setAddSampleID in interface InstanceGeneratorWithSampleID
        Parameters:
        value - true if sample ID should be added

      • addSampleIDTipText

        public String addSampleIDTipText()
        Returns the tip text for this property.
        Specified by:
        addSampleIDTipText in interface InstanceGeneratorWithSampleID
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • setNotes

        public void setNotes​(adams.core.base.BaseString[] value)
        Sets the notes to add as attributes.
        Parameters:
        value - the notes prefixes, e.g., "PROCESS INFORMATION"

      • getNotes

        public adams.core.base.BaseString[] getNotes()
        Returns the current notes to add as attributes.
        Returns:
        the notes prefixes, e.g., "PROCESS INFORMATION"

      • notesTipText

        public String notesTipText()
        Returns the tip text for this property.
        Returns:
        tip text for this property suitable for displaying in the gui

      • setLoadSampleData

        public void setLoadSampleData​(boolean value)
        Sets whether to load the sample data via the sample ID if only dummy report available.
        Parameters:
        value - true if the sample data should be retrieved if only dummy report available

      • getLoadSampleData

        public boolean getLoadSampleData()
        Returns whether to load the sample data via the sample ID if only dummy report available.
        Returns:
        true if the sample data should be retrieved if only dummy report available

      • loadSampleDataTipText

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

      • checkInput

        protected void checkInput​(Spectrum data)
        Checks the input spectrum.

        The default implementation only checks whether there is any data set and loads missing sample data via the sample ID if requested.
        Overrides:
        checkInput in class adams.data.instances.AbstractInstanceGenerator<Spectrum>
        Parameters:
        data - the data to process

      • postProcessHeader

        protected void postProcessHeader​(Spectrum data)
        Adds IDs, notes, additional fields to header.
        Overrides:
        postProcessHeader in class adams.data.instances.AbstractInstanceGenerator<Spectrum>
        Parameters:
        data - the input data

      • postProcessOutput

        protected weka.core.Instance postProcessOutput​(Spectrum data,
                                               weka.core.Instance inst)
        Adds the IDs, notes, additional fields to the data.
        Overrides:
        postProcessOutput in class adams.data.instances.AbstractInstanceGenerator<Spectrum>
        Parameters:
        data - the input data
        inst - the generated instance
        Returns:
        the processed instance