Class ThresholderSimpleFillHoles2D

Object
AnchorBean<VoxelsThresholder>
InitializableBean<VoxelsThresholder, NullInitialization>
NullParametersBean<VoxelsThresholder>
Thresholder
ThresholderSimpleFillHoles2D
public class ThresholderSimpleFillHoles2D extends Thresholder
A thresholder that applies a simple intensity threshold and then fills holes in 2D.

This thresholder first applies an intensity threshold to create a binary image, and then uses ImageJ's "fill" morphological operation to fill holes in each 2D slice.

  • Constructor Summary

    Constructors
    Constructor
    Description
    ThresholderSimpleFillHoles2D()
     
    ThresholderSimpleFillHoles2D(int minIntensity)
    Creates a new ThresholderSimpleFillHoles2D instance.

  • Method Summary

    Modifier and Type
    Method
    Description
    int
    getMinIntensity()
    The minimum intensity value for thresholding.
    void
    setMinIntensity(int minIntensity)
    The minimum intensity value for thresholding.
    BinaryVoxels<UnsignedByteBuffer>
    threshold(VoxelsUntyped inputBuffer, BinaryValuesByte binaryValues, Optional<Histogram> histogram, Optional<ObjectMask> objectMask)
     

    Methods inherited from class org.anchoranalysis.image.bean.threshold.Thresholder

    threshold, threshold

    Methods inherited from class org.anchoranalysis.bean.NullParametersBean

    initializeRecursive, onInitialization, onInitialization

    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, 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

    • ThresholderSimpleFillHoles2D

      public ThresholderSimpleFillHoles2D()

    • ThresholderSimpleFillHoles2D

      public ThresholderSimpleFillHoles2D(int minIntensity)
      Creates a new ThresholderSimpleFillHoles2D instance.
      Parameters:
      minIntensity - The minimum intensity value for thresholding.

      Voxels with intensity greater than or equal to this value are considered foreground.

  • Method Details

    • threshold

      public BinaryVoxels<UnsignedByteBuffer> threshold(VoxelsUntyped inputBuffer, BinaryValuesByte binaryValues, Optional<Histogram> histogram, Optional<ObjectMask> objectMask) throws OperationFailedException
      Specified by:
      threshold in class Thresholder
      Throws:
      OperationFailedException

    • getMinIntensity

      public int getMinIntensity()
      The minimum intensity value for thresholding.

      Voxels with intensity greater than or equal to this value are considered foreground.

    • setMinIntensity

      public void setMinIntensity(int minIntensity)
      The minimum intensity value for thresholding.

      Voxels with intensity greater than or equal to this value are considered foreground.