Package org.anchoranalysis.plugin.imagej.bean.object.segment

Class FloodFillEachIntensityLevel

Object

AnchorBean<SegmentChannelIntoObjects>

InitializableBean<SegmentChannelIntoObjects,ImageInitialization>

ImageBean<SegmentChannelIntoObjects>

SegmentationBean<SegmentChannelIntoObjects>

SegmentChannelIntoObjects

FloodFillEachIntensityLevel

public class FloodFillEachIntensityLevel
extends SegmentChannelIntoObjects

Creates an object for each separate intensity-value (beginning at startingColor) by flood-filling.

This algorithm only works with 2D images.

Author:

Owen Feehan

Constructor Summary

Constructors

Constructor	Description
FloodFillEachIntensityLevel()

Method Summary

Modifier and Type	Method	Description
int	getMinimumBoundingBoxVolume()	Only objects whose bounding-box volume is greater or equal to this threshold are included.
int	getStartingIntensity()	The first intensity-value to consider as a valid object (e.g. usually 0 is ignored as background).
ObjectCollection	segment(Channel channel, Optional<ObjectMask> objectMask, Optional<ObjectCollection> seeds)	Segments a channel to produce an object-collection.
void	setMinimumBoundingBoxVolume(int minimumBoundingBoxVolume)	Only objects whose bounding-box volume is greater or equal to this threshold are included.
void	setStartingIntensity(int startingIntensity)	The first intensity-value to consider as a valid object (e.g. usually 0 is ignored as background).

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

FloodFillEachIntensityLevel

public FloodFillEachIntensityLevel()

Method Details

segment

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

Description copied from class: SegmentChannelIntoObjects

Segments a channel to produce an object-collection.

Specified by:

segment in class SegmentChannelIntoObjects

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.

getMinimumBoundingBoxVolume

public int getMinimumBoundingBoxVolume()

Only objects whose bounding-box volume is greater or equal to this threshold are included. By default, all objects are included.

setMinimumBoundingBoxVolume

public void setMinimumBoundingBoxVolume(int minimumBoundingBoxVolume)

Only objects whose bounding-box volume is greater or equal to this threshold are included. By default, all objects are included.

getStartingIntensity

public int getStartingIntensity()

The first intensity-value to consider as a valid object (e.g. usually 0 is ignored as background).

setStartingIntensity

public void setStartingIntensity(int startingIntensity)

The first intensity-value to consider as a valid object (e.g. usually 0 is ignored as background).