Package adams.flow.transformer

Class SpectralAngleMapper

  • 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.TechnicalInformationHandler, adams.core.VariablesInspectionHandler, adams.event.VariableChangeListener, adams.flow.control.StorageUser, adams.flow.core.Actor, adams.flow.core.ErrorHandler, adams.flow.core.InputConsumer, adams.flow.core.OutputProducer, Serializable, Comparable
    public class SpectralAngleMapper
extends adams.flow.transformer.AbstractTransformer
implements adams.flow.control.StorageUser, adams.core.TechnicalInformationHandler
    Performs Spectral Angle Mapping on a set of spectra. Each spectrum is treated as a vector in band-space (where each spectral band is considered a basis), and the angle between the input and reference spectra is calculated to determine similarity. Emits an array of angles, one for each reference spectrum provided.

    For more information see:

    Kruse, Fred A, Lefkoff, AB, Boardman, JW, Heidebrecht, KB, Shapiro, AT, Barloon, PJ, Goetz, AFH (1993). The spectral image processing system (SIPS)—interactive visualization and analysis of imaging spectrometer data. Remote sensing of environment. 44(2-3):145--163.

    Oshigami, Shoko, Yamaguchi, Yasushi, Uezato, Tatsumi, Momose, Atsushi, Arvelyna, Yessy, Kawakami, Yuu, Yajima, Taro, Miyatake, Shuichi, Nguno, Anna (2013). Mineralogical mapping of southern Namibia by application of continuum-removal MSAM method to the HyMap data. International journal of remote sensing. 34(15):5282--5295. 

     @article{Kruse1993,
    author = {Kruse, Fred A and Lefkoff, AB and Boardman, JW and Heidebrecht, KB and Shapiro, AT and Barloon, PJ and Goetz, AFH},
    journal = {Remote sensing of environment},
    number = {2-3},
    pages = {145--163},
    publisher = {Elsevier},
    title = {The spectral image processing system (SIPS)—interactive visualization and analysis of imaging spectrometer data},
    volume = {44},
    year = {1993}
 }

 @article{Oshigami2013,
    author = {Oshigami, Shoko and Yamaguchi, Yasushi and Uezato, Tatsumi and Momose, Atsushi and Arvelyna, Yessy and Kawakami, Yuu and Yajima, Taro and Miyatake, Shuichi and Nguno, Anna},
    journal = {International journal of remote sensing},
    number = {15},
    pages = {5282--5295},
    publisher = {Taylor & Francis},
    title = {Mineralogical mapping of southern Namibia by application of continuum-removal MSAM method to the HyMap data},
    volume = {34},
    year = {2013}
 }
 


    -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: SpectralAngleMapper
 
    -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
 
    -references <adams.flow.control.StorageName> (property: references)
    The name of the storage location where the reference spectra are stored.
    default: storage
 
    -cache <adams.core.base.BaseString> (property: cache)
    The name of the LRU cache to get the reference storage from. An empty value
    specifies that regular storage should be used.
    default:
 
    -check-wave-number-alignment <boolean> (property: checkWaveNumberAlignment)
    Whether to check that all provided spectra have the same set of wave-numbers.
    default: true
 
    -modified <boolean> (property: modified)
    Whether to use the modified algorithm described in Oshigami et al.
    default: false
    Author:
    Corey Sterling (csterlin at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected adams.core.base.BaseString m_Cache
      The LRU cache to get the storage value from.
      protected boolean m_CheckWaveNumberAlignment
      Whether to check wave-numbers match between spectra.
      protected adams.flow.control.StorageName m_ReferencesStorage
      Storage of the reference spectra.
      protected boolean m_UseModifiedAlgorithm
      Whether to use the modified algorithm described in Oshigami et al.

      • 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.
      String cacheTipText()
      Gets the tip-text for the cache option.
      protected double[] calculateSpectralAngles​(Spectrum input, Spectrum[] references)
      Performs the calculation of spectral angles between the input spectrum and each reference spectrum.
      protected void checkInput​(Spectrum input)
      Checks the input spectrum for validity.
      protected void checkInputVersusReferences​(Spectrum input, Spectrum[] references)
      Checks that the input and the references are able to be angle-mapped.
      protected void checkReferences​(Spectrum[] references)
      Checks the reference spectra for validity.
      protected void checkWaveNumberAlignment​(Spectrum input, Spectrum[] references)
      Checks that the input and reference spectra have the same wave-number profile.
      String checkWaveNumberAlignmentTipText()
      Gets the tip-text for the checkWaveNumberAlignment option.
      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.
      adams.core.base.BaseString getCache()
      Gets the name of the LRU cache to use.
      boolean getCheckWaveNumberAlignment()
      Gets whether wave-number alignment should be checked.
      protected Spectrum getInput()
      Gets the input spectrum from the input token.
      boolean getModified()
      Gets whether to use the modified algorithm.
      String getQuickInfo()
      Returns a quick info about the actor, which will be displayed in the GUI.
      adams.flow.control.StorageName getReferences()
      Gets the name of the storage location for reference spectra.
      protected Spectrum[] getReferences​(adams.flow.control.StorageName name, String cache)
      Retrieves the reference spectra from storage.
      adams.core.TechnicalInformation getTechnicalInformation()
      Returns an instance of a TechnicalInformation object, containing detailed information about the technical background of this class, e.g., paper reference or book this class is based on.
      String globalInfo()
      Returns a string describing the object.
      boolean isUsingStorage()
      Returns whether storage items are being used.
      String modifiedTipText()
      Gets the tip-text for the modified option.
      String referencesTipText()
      Gets the tip-text for the references option.
      void setCache​(adams.core.base.BaseString value)
      Sets the name of the LRU cache to use.
      void setCheckWaveNumberAlignment​(boolean value)
      Sets whether wave-number alignment should be checked.
      void setModified​(boolean value)
      Sets whether to use the modified algorithm.
      protected void setOutput​(double[] angles)
      Sets the output token to the given array of angles.
      void setReferences​(adams.flow.control.StorageName value)
      Sets the name of the storage location for reference spectra.
      protected double[] toDoubleArray​(Spectrum spectrum)
      Converts a spectrum into a double array of its wave amplitudes.

      • 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_ReferencesStorage

        protected adams.flow.control.StorageName m_ReferencesStorage
        Storage of the reference spectra.

      • m_Cache

        protected adams.core.base.BaseString m_Cache
        The LRU cache to get the storage value from.

      • m_CheckWaveNumberAlignment

        protected boolean m_CheckWaveNumberAlignment
        Whether to check wave-numbers match between spectra.

      • m_UseModifiedAlgorithm

        protected boolean m_UseModifiedAlgorithm
        Whether to use the modified algorithm described in Oshigami et al.

    • Constructor Detail

      • SpectralAngleMapper

        public SpectralAngleMapper()

    • 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

      • getReferences

        public adams.flow.control.StorageName getReferences()
        Gets the name of the storage location for reference spectra.
        Returns:
        The storage name.

      • setReferences

        public void setReferences​(adams.flow.control.StorageName value)
        Sets the name of the storage location for reference spectra.
        Parameters:
        value - The storage name.

      • referencesTipText

        public String referencesTipText()
        Gets the tip-text for the references option.
        Returns:
        The tip-text as a string.

      • getCache

        public adams.core.base.BaseString getCache()
        Gets the name of the LRU cache to use.
        Returns:
        The name of the cache.

      • setCache

        public void setCache​(adams.core.base.BaseString value)
        Sets the name of the LRU cache to use.
        Parameters:
        value - The name of the cache.

      • cacheTipText

        public String cacheTipText()
        Gets the tip-text for the cache option.
        Returns:
        The tip-text as a string.

      • getCheckWaveNumberAlignment

        public boolean getCheckWaveNumberAlignment()
        Gets whether wave-number alignment should be checked.
        Returns:
        True if the check should be performed, false if not.

      • setCheckWaveNumberAlignment

        public void setCheckWaveNumberAlignment​(boolean value)
        Sets whether wave-number alignment should be checked.
        Parameters:
        value - True if the check should be performed, false if not.

      • checkWaveNumberAlignmentTipText

        public String checkWaveNumberAlignmentTipText()
        Gets the tip-text for the checkWaveNumberAlignment option.
        Returns:
        The tip-text as a string.

      • getModified

        public boolean getModified()
        Gets whether to use the modified algorithm.
        Returns:
        Whether to use the modified algorithm.

      • setModified

        public void setModified​(boolean value)
        Sets whether to use the modified algorithm.
        Parameters:
        value - Whether to use the modified algorithm.

      • modifiedTipText

        public String modifiedTipText()
        Gets the tip-text for the modified option.
        Returns:
        The tip-text as a string.

      • getQuickInfo

        public String getQuickInfo()
        Returns a quick info about the actor, which will be displayed in the GUI.

        Default implementation returns null.
        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

      • getTechnicalInformation

        public adams.core.TechnicalInformation getTechnicalInformation()
        Returns an instance of a TechnicalInformation object, containing detailed information about the technical background of this class, e.g., paper reference or book this class is based on.
        Specified by:
        getTechnicalInformation in interface adams.core.TechnicalInformationHandler
        Returns:
        the technical information about this class

      • getInput

        protected Spectrum getInput()
        Gets the input spectrum from the input token.
        Returns:
        The input spectrum.

      • checkInput

        protected void checkInput​(Spectrum input)
        Checks the input spectrum for validity.
        Parameters:
        input - The input spectrum to check;

      • getReferences

        protected Spectrum[] getReferences​(adams.flow.control.StorageName name,
                                   String cache)
        Retrieves the reference spectra from storage.
        Parameters:
        name - The name of the storage value to get from.
        cache - The name of the LRU cache to use.
        Returns:
        The array of reference spectra.

      • checkReferences

        protected void checkReferences​(Spectrum[] references)
        Checks the reference spectra for validity.
        Parameters:
        references - The reference spectra to check.

      • checkInputVersusReferences

        protected void checkInputVersusReferences​(Spectrum input,
                                          Spectrum[] references)
        Checks that the input and the references are able to be angle-mapped.
        Parameters:
        input - The input spectrum.
        references - The reference spectra.

      • checkWaveNumberAlignment

        protected void checkWaveNumberAlignment​(Spectrum input,
                                        Spectrum[] references)
        Checks that the input and reference spectra have the same wave-number profile.
        Parameters:
        input - The input spectrum.
        references - The reference spectra.

      • calculateSpectralAngles

        protected double[] calculateSpectralAngles​(Spectrum input,
                                           Spectrum[] references)
        Performs the calculation of spectral angles between the input spectrum and each reference spectrum.
        Parameters:
        input - The input spectrum.
        references - The reference spectra.
        Returns:
        An array of angles, one for each reference spectrum.

      • toDoubleArray

        protected double[] toDoubleArray​(Spectrum spectrum)
        Converts a spectrum into a double array of its wave amplitudes.
        Parameters:
        spectrum - The spectrum to convert.
        Returns:
        The array of amplitudes.

      • setOutput

        protected void setOutput​(double[] angles)
        Sets the output token to the given array of angles.
        Parameters:
        angles - The angles to output.

      • 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

      • accepts

        public Class[] accepts()
        Returns the class that the consumer accepts.
        Specified by:
        accepts in interface adams.flow.core.InputConsumer
        Returns:
        the Class of objects that can be processed

      • generates

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

      • isUsingStorage

        public boolean isUsingStorage()
        Returns whether storage items are being used.
        Specified by:
        isUsingStorage in interface adams.flow.control.StorageUser
        Returns:
        true if storage items are used