Package org.anchoranalysis.image.bean.segment.object

Class SegmentChannelIntoObjects

Object

org.anchoranalysis.bean.AnchorBean<B>

org.anchoranalysis.bean.initializable.InitializableBean<T,ImageInitialization>

org.anchoranalysis.image.bean.ImageBean<T>

org.anchoranalysis.image.bean.segment.SegmentationBean<SegmentChannelIntoObjects>

org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjects

Direct Known Subclasses:

SegmentChannelIntoObjectsUnary

public abstract class SegmentChannelIntoObjects
extends SegmentationBean<SegmentChannelIntoObjects>

A base class for algorithms to segment a channel into one or more objects.

Some algorithms can be restricted by an object-mask on the channel.

Some algorithms can be influenced by passing a set of seeds.

Author:

Owen Feehan

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	SegmentChannelIntoObjects()

Method Summary

Modifier and Type	Method	Description
protected static void	checkUnsupported3D(Channel channel)	Throws an exception if the channel has more than one z-slice, as 3D is unsupported by the implementation.
protected static void	checkUnsupportedObjectMask(Optional<org.anchoranalysis.image.voxel.object.ObjectMask> objectMask)	Throws an exception if object is present, as it is unsupported by the implementation.
protected static void	checkUnsupportedSeeds(Optional<org.anchoranalysis.image.voxel.object.ObjectCollection> seeds)	Throws an exception if seeds is present, as it is unsupported by the implementation.
abstract org.anchoranalysis.image.voxel.object.ObjectCollection	segment(Channel channel, Optional<org.anchoranalysis.image.voxel.object.ObjectMask> objectMask, Optional<org.anchoranalysis.image.voxel.object.ObjectCollection> seeds)	Segments a channel to produce an object-collection.

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

SegmentChannelIntoObjects

protected SegmentChannelIntoObjects()

Method Details

segment

public abstract org.anchoranalysis.image.voxel.object.ObjectCollection segment(Channel channel, Optional<org.anchoranalysis.image.voxel.object.ObjectMask> objectMask, Optional<org.anchoranalysis.image.voxel.object.ObjectCollection> seeds) throws SegmentationFailedException

Segments a channel to produce an object-collection.

Parameters:

channel - the channel to segment

objectMask - an object-mask that can restrict which areas of the channel are considered.

seeds - seeds that can be used to determine starting-points for segmentation regions.

Returns:

a newly created collection of objects for each segment. The created objects will always exist inside the channel's extent.

Throws:

SegmentationFailedException - if anything goes wrong during the segmentation.

checkUnsupportedObjectMask

protected static void checkUnsupportedObjectMask(Optional<org.anchoranalysis.image.voxel.object.ObjectMask> objectMask) throws SegmentationFailedException

Throws an exception if object is present, as it is unsupported by the implementation.

Parameters:

objectMask - an optional ObjectMask.

Throws:

SegmentationFailedException - if objectMask is present.

checkUnsupportedSeeds

protected static void checkUnsupportedSeeds(Optional<org.anchoranalysis.image.voxel.object.ObjectCollection> seeds) throws SegmentationFailedException

Throws an exception if seeds is present, as it is unsupported by the implementation.

Parameters:

seeds - an optional ObjectMask.

Throws:

SegmentationFailedException - if seeds is present.

checkUnsupported3D

protected static void checkUnsupported3D(Channel channel) throws SegmentationFailedException

Throws an exception if the channel has more than one z-slice, as 3D is unsupported by the implementation.

Parameters:

channel - the channel that have multiple z-slices (i.e. is 3D) or a single z-slice (i.e. is 2D).

Throws:

SegmentationFailedException - if channel is 3D.