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

Class SegmentOnMaximumIntensityAndExpandInZ

Object

AnchorBean<SegmentChannelIntoObjects>

InitializableBean<SegmentChannelIntoObjects,ImageInitialization>

ImageBean<SegmentChannelIntoObjects>

SegmentationBean<SegmentChannelIntoObjects>

SegmentChannelIntoObjects

SegmentChannelIntoObjectsUnary

SegmentOnMaximumIntensityAndExpandInZ

public class SegmentOnMaximumIntensityAndExpandInZ
extends SegmentChannelIntoObjectsUnary

Perform a segmentation in a MIP instead of z-stacks, and fits the result back into a 3D segmentation.

The upstream segmentation should return 2D objects as it is executed on the maximum-intensity projection.

A 3D binary-segmentation is applied to the z-stack with segmentStack to produce a mask over the z-stack. The the 2D objects are then expanded in the z-dimension to fit this mask.

Author:

Owen Feehan

Constructor Summary

Constructors

Constructor	Description
SegmentOnMaximumIntensityAndExpandInZ()

Method Summary

Modifier and Type	Method	Description
BinarySegmentation	getSegmentStack()
ObjectCollection	segment(Channel channel, Optional<ObjectMask> objectMask, Optional<ObjectCollection> seeds, SegmentChannelIntoObjects upstreamSegmenter)	Creates an ObjectCollection given the segmentation-results provided by the delegate.
void	setSegmentStack(BinarySegmentation segmentStack)

Methods inherited from class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjectsUnary

getSegment, segment, setSegment

Methods inherited from class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjects

checkUnsupported3D, checkUnsupportedObjectMask, checkUnsupportedSeeds

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

SegmentOnMaximumIntensityAndExpandInZ

public SegmentOnMaximumIntensityAndExpandInZ()

Method Details

segment

public ObjectCollection segment(Channel channel,
 Optional<ObjectMask> objectMask,
 Optional<ObjectCollection> seeds,
 SegmentChannelIntoObjects upstreamSegmenter)
                         throws SegmentationFailedException

Description copied from class: SegmentChannelIntoObjectsUnary

Creates an ObjectCollection given the segmentation-results provided by the delegate.

Specified by:

segment in class SegmentChannelIntoObjectsUnary

Parameters:

channel - the channel as passed to SegmentChannelIntoObjectsUnary.segment(Channel, Optional, Optional).

objectMask - the object-mask as passed to SegmentChannelIntoObjectsUnary.segment(Channel, Optional, Optional).

seeds - the seeds as passed to SegmentChannelIntoObjectsUnary.segment(Channel, Optional, Optional).

upstreamSegmenter - the delegate segmenter.

Returns:

the created ObjectCollection that is returned by the segmentation.

Throws:

SegmentationFailedException - if segmentation cannot complete successfully.

getSegmentStack

public BinarySegmentation getSegmentStack()

setSegmentStack

public void setSegmentStack(BinarySegmentation segmentStack)