Package org.anchoranalysis.plugin.image.feature.bean.object.single.intensity

Class Intensity

Object
org.anchoranalysis.bean.AnchorBean<B>
org.anchoranalysis.bean.initializable.InitializableBean<org.anchoranalysis.feature.bean.Feature<T>,​org.anchoranalysis.feature.initialization.FeatureInitialization>
org.anchoranalysis.feature.bean.Feature<org.anchoranalysis.image.feature.input.FeatureInputSingleObject>
org.anchoranalysis.image.feature.bean.object.single.FeatureSingleObject
org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.FeatureEnergyChannel
org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.Intensity
public class Intensity
extends FeatureEnergyChannel
Calculates a statistic from the intensity values covered by a single object-mask in a channel.

Specifically, a histogram of intensity-values is constructed for the region covered by the object in one specific channnel in the energy-stack (specified by energyIndex).

Then a customizable FeatureHistogram (specified by item) extracts a statistic from the histogram. By default, the mean is calculated.

Author:
Owen Feehan

  • Constructor Summary

    Constructors 
    Constructor Description
    Intensity()  

  • Method Summary

    Modifier and Type Method Description
    protected double calculateForChannel​(org.anchoranalysis.feature.calculate.FeatureCalculationInput<org.anchoranalysis.image.feature.input.FeatureInputSingleObject> input, org.anchoranalysis.image.core.channel.Channel channel)
    Calculates the feature value for a specific channel in the energy stack.
    org.anchoranalysis.feature.bean.Feature<org.anchoranalysis.image.feature.input.FeatureInputHistogram> getItem()
    Feature to apply to the histogram
    boolean isExcludeZero()
    Iff true, zero-valued voxels are excluded from the histogram
    void setExcludeZero​(boolean excludeZero)
    Iff true, zero-valued voxels are excluded from the histogram
    void setItem​(org.anchoranalysis.feature.bean.Feature<org.anchoranalysis.image.feature.input.FeatureInputHistogram> item)
    Feature to apply to the histogram

    Methods inherited from class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.FeatureEnergyChannel

    calculate, getEnergyIndex, setEnergyIndex

    Methods inherited from class org.anchoranalysis.image.feature.bean.object.single.FeatureSingleObject

    inputType

    Methods inherited from class org.anchoranalysis.feature.bean.Feature

    assignTo, beforeCalc, calculateCheckInitialized, castAs, createListChildFeatures, describeBean, describeParameters, descriptionLong, duplicateChangeName, getCustomName, getFriendlyName, onInitialization, setCustomName, toString

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

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

    Methods inherited from class org.anchoranalysis.bean.AnchorBean

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

    Methods inherited from class java.lang.Object

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

  • Constructor Details

  • Method Details

    • calculateForChannel

      protected double calculateForChannel​(org.anchoranalysis.feature.calculate.FeatureCalculationInput<org.anchoranalysis.image.feature.input.FeatureInputSingleObject> input, org.anchoranalysis.image.core.channel.Channel channel) throws org.anchoranalysis.feature.calculate.FeatureCalculationException
      Description copied from class: FeatureEnergyChannel
      Calculates the feature value for a specific channel in the energy stack.
      Specified by:
      calculateForChannel in class FeatureEnergyChannel
      Parameters:
      input - the FeatureCalculationInput containing the FeatureInputSingleObject
      channel - the Channel from the energy stack to calculate the feature on
      Returns:
      the calculated feature value
      Throws:
      org.anchoranalysis.feature.calculate.FeatureCalculationException - if the calculation fails

    • getItem

      public org.anchoranalysis.feature.bean.Feature<org.anchoranalysis.image.feature.input.FeatureInputHistogram> getItem()
      Feature to apply to the histogram

    • setItem

      public void setItem​(org.anchoranalysis.feature.bean.Feature<org.anchoranalysis.image.feature.input.FeatureInputHistogram> item)
      Feature to apply to the histogram

    • isExcludeZero

      public boolean isExcludeZero()
      Iff true, zero-valued voxels are excluded from the histogram

    • setExcludeZero

      public void setExcludeZero​(boolean excludeZero)
      Iff true, zero-valued voxels are excluded from the histogram