Package org.anchoranalysis.plugin.image.bean.mask.provider.segment

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