Package adams.data.multispectrumoperation.outlierremoval

Class MeanSpectrumCosineSimilarityBasedThreshold

  • All Implemented Interfaces:
    adams.core.Destroyable, adams.core.GlobalInfoSupporter, adams.core.logging.LoggingLevelHandler, adams.core.logging.LoggingSupporter, adams.core.option.OptionHandler, adams.core.QuickInfoSupporter, adams.core.SizeOfHandler, Serializable
    public class MeanSpectrumCosineSimilarityBasedThreshold
extends AbstractOutlierRemoval
    Calculates the mean spectrum from the incoming spectra and then calculates the cosine similarity between the mean spectrum and the spectra. Spectra with a similarity score that falls below threshold get removed.
    Author:
    fracpete (fracpete at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected adams.data.filter.Filter m_PreFilter
      the prefilter to apply before computing the cosine similarity.
      protected double m_Threshold
      the threshold.

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

        m_OptionManager

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

        m_Logger, m_LoggingIsEnabled, m_LoggingLevel

    • Field Detail

      • m_PreFilter

        protected adams.data.filter.Filter m_PreFilter
        the prefilter to apply before computing the cosine similarity.

      • m_Threshold

        protected double m_Threshold
        the threshold.

    • Constructor Detail

      • MeanSpectrumCosineSimilarityBasedThreshold

        public MeanSpectrumCosineSimilarityBasedThreshold()

    • 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.core.option.AbstractOptionHandler

      • setPreFilter

        public void setPreFilter​(adams.data.filter.Filter value)
        Sets the pre-filter to use.
        Parameters:
        value - the filter

      • getPreFilter

        public adams.data.filter.Filter getPreFilter()
        Returns the pre-filter to use.
        Returns:
        the filter

      • preFilterTipText

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

      • setThreshold

        public void setThreshold​(double value)
        Sets the threshold to use.
        Parameters:
        value - the threshold

      • getThreshold

        public double getThreshold()
        Returns the threshold to use.
        Returns:
        the threshold

      • thresholdTipText

        public String thresholdTipText()
        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 object, which can be displayed in the GUI.
        Specified by:
        getQuickInfo in interface adams.core.QuickInfoSupporter
        Overrides:
        getQuickInfo in class AbstractOutlierRemoval
        Returns:
        null if no info available, otherwise short string

      • doRemoveOutliers

        protected MultiSpectrum doRemoveOutliers​(MultiSpectrum multi,
                                         adams.core.MessageCollection errors)
        Performs the actual outlier removal.
        Specified by:
        doRemoveOutliers in class AbstractOutlierRemoval
        Parameters:
        multi - the data to process
        errors - for collecting errors
        Returns:
        the clean data, null if failed to process