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

Class LevelPerObjectNeighbors

Object

AnchorBean<ChannelProvider>

InitializableBean<ChannelProvider,ImageInitialization>

ImageBean<ChannelProvider>

BeanProviderAsStackBase<ChannelProvider,Channel>

ChannelProvider

ChannelProviderUnary

LevelPerObjectBase

LevelPerObjectNeighbors

All Implemented Interfaces:

Provider<Channel>, ProviderAsStack

public class LevelPerObjectNeighbors
extends LevelPerObjectBase

Calculates a threshold-level for each object collectively based on other objects

A neighborhood-graph is compiled of objects that touch each other. The threshold for each objects is determined by the object itself and neigbors e.g. neighborhoodDistance==1 are all the immediate neighbors

Constructor Summary

Constructors

Constructor	Description
LevelPerObjectNeighbors()

Method Summary

Modifier and Type	Method	Description
int	getDistance()	How many neighbors to include by distance (distance==1 implies all directly touching neighbors, distance==2 implies those touching the directly touching etc.)
void	setDistance(int distance)	How many neighbors to include by distance (distance==1 implies all directly touching neighbors, distance==2 implies those touching the directly touching etc.)
protected void	writeLevelsForObjects(Channel channelIntensity, ObjectCollection objects, Channel output)	Creates a channel with the levels for a set of objects.

Methods inherited from class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase

createFromChannel, getCalculateLevel, getObjects, setCalculateLevel, setObjects

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

get, getChannel, setChannel

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

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

LevelPerObjectNeighbors

public LevelPerObjectNeighbors()

Method Details

writeLevelsForObjects

protected void writeLevelsForObjects(Channel channelIntensity,
 ObjectCollection objects,
 Channel output)
                              throws ProvisionFailedException

Description copied from class: LevelPerObjectBase

Creates a channel with the levels for a set of objects.

Specified by:

writeLevelsForObjects in class LevelPerObjectBase

Parameters:

channelIntensity - the channel whose intensity is passed to calculateLevel as a histogram variously for particular objects

objects - the ObjectCollection for which levels are calculated

output - the channel where the calculated-levels are written (for each object)

Throws:

ProvisionFailedException - if there's an error during the level calculation or writing process

getDistance

public int getDistance()

How many neighbors to include by distance (distance==1 implies all directly touching neighbors, distance==2 implies those touching the directly touching etc.)

setDistance

public void setDistance(int distance)

How many neighbors to include by distance (distance==1 implies all directly touching neighbors, distance==2 implies those touching the directly touching etc.)