Package org.anchoranalysis.plugin.image.feature.bean.score

Class CalculateLevelBase

Object
org.anchoranalysis.bean.AnchorBean<B>
org.anchoranalysis.bean.initializable.InitializableBean<T,​org.anchoranalysis.image.bean.nonbean.init.ImageInitialization>
org.anchoranalysis.image.bean.ImageBean<org.anchoranalysis.image.feature.bean.VoxelScore>
org.anchoranalysis.image.feature.bean.VoxelScore
org.anchoranalysis.plugin.image.feature.bean.score.SingleChannel
org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
Direct Known Subclasses:
CalculateLevel, DifferenceCalculateLevelStandardDeviation
public abstract class CalculateLevelBase
extends SingleChannel
Base class for calculating a score based on a threshold level derived from a histogram.

  • Constructor Summary

    Constructors 
    Constructor Description
    CalculateLevelBase()  

  • Method Summary

    Modifier and Type Method Description
    protected abstract void beforeCalcSetup​(org.anchoranalysis.math.histogram.Histogram histogram, int level)
    Performs setup operations before calculation.
    protected abstract double calculateForVoxel​(int voxelIntensity, int level)
    Calculates a score for a single voxel based on its intensity and the threshold level.
    protected double deriveScoreFromVoxel​(int voxelIntensity)
    Derives a score from a single voxel intensity.
    org.anchoranalysis.image.bean.threshold.CalculateLevel getCalculateLevel()
    The method to calculate the threshold level.
    int getHistogramChannelIndex()
    The index of the histogram channel to use for calculations.
    void initialize​(List<org.anchoranalysis.math.histogram.Histogram> histograms, Optional<org.anchoranalysis.core.value.Dictionary> dictionary)  
    void setCalculateLevel​(org.anchoranalysis.image.bean.threshold.CalculateLevel calculateLevel)
    The method to calculate the threshold level.
    void setHistogramChannelIndex​(int histogramChannelIndex)
    The index of the histogram channel to use for calculations.

    Methods inherited from class org.anchoranalysis.plugin.image.feature.bean.score.SingleChannel

    calculate, getEnergyChannelIndex, setEnergyChannelIndex

    Methods inherited from class org.anchoranalysis.bean.initializable.InitializableBean

    getInitialization, getLogger, getPropertyInitializer, initialize, initializeRecursive, initRecursiveWithInitializer, isInitialized, onInitialization

    Methods inherited from class org.anchoranalysis.bean.AnchorBean

    checkMisconfigured, describeBean, describeChildren, duplicateBean, fields, findFieldsOfClass, getBeanName, getLocalPath, localise, toString

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

  • Constructor Details

  • Method Details

    • initialize

      public void initialize​(List<org.anchoranalysis.math.histogram.Histogram> histograms, Optional<org.anchoranalysis.core.value.Dictionary> dictionary) throws org.anchoranalysis.core.exception.InitializeException
      Overrides:
      initialize in class org.anchoranalysis.image.feature.bean.VoxelScore
      Throws:
      org.anchoranalysis.core.exception.InitializeException

    • deriveScoreFromVoxel

      protected double deriveScoreFromVoxel​(int voxelIntensity)
      Description copied from class: SingleChannel
      Derives a score from a single voxel intensity.
      Specified by:
      deriveScoreFromVoxel in class SingleChannel
      Parameters:
      voxelIntensity - the intensity of the voxel in the specified energy channel
      Returns:
      the calculated score for the voxel

    • beforeCalcSetup

      protected abstract void beforeCalcSetup​(org.anchoranalysis.math.histogram.Histogram histogram, int level) throws org.anchoranalysis.core.exception.OperationFailedException
      Performs setup operations before calculation.
      Parameters:
      histogram - the Histogram to use for setup
      level - the calculated threshold level
      Throws:
      org.anchoranalysis.core.exception.OperationFailedException - if the setup operation fails

    • calculateForVoxel

      protected abstract double calculateForVoxel​(int voxelIntensity, int level)
      Calculates a score for a single voxel based on its intensity and the threshold level.
      Parameters:
      voxelIntensity - the intensity of the voxel
      level - the threshold level
      Returns:
      a score for the voxel

    • getCalculateLevel

      public org.anchoranalysis.image.bean.threshold.CalculateLevel getCalculateLevel()
      The method to calculate the threshold level.

    • setCalculateLevel

      public void setCalculateLevel​(org.anchoranalysis.image.bean.threshold.CalculateLevel calculateLevel)
      The method to calculate the threshold level.

    • getHistogramChannelIndex

      public int getHistogramChannelIndex()
      The index of the histogram channel to use for calculations.

    • setHistogramChannelIndex

      public void setHistogramChannelIndex​(int histogramChannelIndex)
      The index of the histogram channel to use for calculations.