Class SegmentChannel

Object
AnchorBean<MaskProvider>
InitializableBean<MaskProvider, ImageInitialization>
ImageBean<MaskProvider>
BeanProviderAsStackBase<MaskProvider, Mask>
MaskProvider
FromChannelBase
SegmentChannel
All Implemented Interfaces:
Provider<Mask>, ProviderAsStack
public class SegmentChannel extends FromChannelBase
Applies a BinarySegmentation algorithm to derive a mask from a channel

Optionally, a mask restricts which part of the channel the algorithm is applied to. In this case, the remainder of the channel is unaltered in the output-mask, and no check occurs to ensure it containlys only the valid binary-values for off and on.

Optionally a histogram of voxel intensity values is passed to the segmentation algorithm.

Author:
Owen Feehan

  • Constructor Summary

    Constructors
    Constructor
    Description
    SegmentChannel()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    protected Mask
    createFromSource(Channel source)
    Creates a Mask from the source Channel.
    HistogramProvider
    getHistogram()
    An optional histogram of voxel intensity values which can be used by segment
    MaskProvider
    getMask()
    An optional mask which restricts the algorithm to only parts of the channel where the mask has an on voxel
    BinarySegmentation
    getSegment()
    Segmentation algorithm
    void
    setHistogram(HistogramProvider histogram)
    An optional histogram of voxel intensity values which can be used by segment
    void
    setMask(MaskProvider mask)
    An optional mask which restricts the algorithm to only parts of the channel where the mask has an on voxel
    void
    setSegment(BinarySegmentation segment)
    Segmentation algorithm

    Methods inherited from class org.anchoranalysis.plugin.image.bean.mask.provider.FromChannelBase

    get, getChannel, setChannel

    Methods inherited from class org.anchoranalysis.image.bean.provider.MaskProvider

    getAsStack

    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

    • SegmentChannel

      public SegmentChannel()

  • Method Details

    • createFromSource

      protected Mask createFromSource(Channel source) throws CreateException
      Description copied from class: FromChannelBase
      Creates a Mask from the source Channel.
      Specified by:
      createFromSource in class FromChannelBase
      Parameters:
      source - the source channel
      Returns:
      the created mask
      Throws:
      CreateException - if the mask creation fails

    • getSegment

      public BinarySegmentation getSegment()
      Segmentation algorithm

    • setSegment

      public void setSegment(BinarySegmentation segment)
      Segmentation algorithm

    • getHistogram

      public HistogramProvider getHistogram()
      An optional histogram of voxel intensity values which can be used by segment

    • setHistogram

      public void setHistogram(HistogramProvider histogram)
      An optional histogram of voxel intensity values which can be used by segment

    • getMask

      public MaskProvider getMask()
      An optional mask which restricts the algorithm to only parts of the channel where the mask has an on voxel

    • setMask

      public void setMask(MaskProvider mask)
      An optional mask which restricts the algorithm to only parts of the channel where the mask has an on voxel