Package org.anchoranalysis.plugin.annotation.bean.comparison.assigner

Class FeatureCostAssigner

Object

org.anchoranalysis.bean.AnchorBean<AnnotationComparisonAssigner<T>>

org.anchoranalysis.plugin.annotation.bean.comparison.assigner.AnnotationComparisonAssigner<org.anchoranalysis.annotation.io.assignment.OverlappingObjects>

org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner

public class FeatureCostAssigner
extends AnnotationComparisonAssigner<org.anchoranalysis.annotation.io.assignment.OverlappingObjects>

Assigns an objects from one set of objects to another based upon a cost (degree of overlap).

This is a form of bipartite matching.

The following outputs are produced:

Output Name	Default?	Description
"costMatrix"	no	a CSV file showing a matrix of costs calculated for the objects.

Author:

Owen Feehan

Constructor Summary

Constructors

Constructor	Description
FeatureCostAssigner()

Method Summary

Modifier and Type	Method	Description
void	addDefaultOutputs(org.anchoranalysis.io.output.enabled.OutputEnabledMutable outputs)	Adds any default outputs that should occur from the assigner.
org.anchoranalysis.annotation.io.assignment.OverlappingObjects	createAssignment(ObjectsToCompare objectsToCompare, org.anchoranalysis.image.core.dimensions.Dimensions dimensions, boolean useMIP, org.anchoranalysis.io.output.outputter.InputOutputContext context)	Creates an assignment based on the objects to compare.
org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator<org.anchoranalysis.image.feature.input.FeatureInputPairObjects>	getFeatureEvaluator()
double	getMaxCost()
int	getNumberDecimalPlaces()
ImageCounterWithStatistics<org.anchoranalysis.annotation.io.assignment.OverlappingObjects>	groupForKey(String key)	Gets the ImageCounterWithStatistics for a specific key.
boolean	isRemoveTouchingBorderXY()
boolean	moreThanOneObject()	Checks if more than one object can exist in the assignment.
void	setFeatureEvaluator(org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator<org.anchoranalysis.image.feature.input.FeatureInputPairObjects> featureEvaluator)
void	setMaxCost(double maxCost)
void	setNumberDecimalPlaces(int numberDecimalPlaces)
void	setRemoveTouchingBorderXY(boolean removeTouchingBorderXY)

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

FeatureCostAssigner

public FeatureCostAssigner()

Method Details

createAssignment

public org.anchoranalysis.annotation.io.assignment.OverlappingObjects createAssignment(ObjectsToCompare objectsToCompare, org.anchoranalysis.image.core.dimensions.Dimensions dimensions, boolean useMIP, org.anchoranalysis.io.output.outputter.InputOutputContext context) throws org.anchoranalysis.core.exception.CreateException

Description copied from class: AnnotationComparisonAssigner

Creates an assignment based on the objects to compare.

Specified by:

createAssignment in class AnnotationComparisonAssigner<org.anchoranalysis.annotation.io.assignment.OverlappingObjects>

Parameters:

objectsToCompare - the objects to compare.

dimensions - the dimensions of the image.

useMIP - whether to use Maximum Intensity Projection.

context - the input-output context.

Returns:

the created assignment.

Throws:

org.anchoranalysis.core.exception.CreateException - if the assignment cannot be created.

groupForKey

public ImageCounterWithStatistics<org.anchoranalysis.annotation.io.assignment.OverlappingObjects> groupForKey(String key)

Description copied from class: AnnotationComparisonAssigner

Gets the ImageCounterWithStatistics for a specific key.

Specified by:

groupForKey in class AnnotationComparisonAssigner<org.anchoranalysis.annotation.io.assignment.OverlappingObjects>

Parameters:

key - the key to get the group for.

Returns:

the ImageCounterWithStatistics for the given key.

moreThanOneObject

public boolean moreThanOneObject()

Description copied from class: AnnotationComparisonAssigner

Checks if more than one object can exist in the assignment.

Specified by:

moreThanOneObject in class AnnotationComparisonAssigner<org.anchoranalysis.annotation.io.assignment.OverlappingObjects>

Returns:

true if more than one object can exist, false otherwise.

addDefaultOutputs

public void addDefaultOutputs(org.anchoranalysis.io.output.enabled.OutputEnabledMutable outputs)

Description copied from class: AnnotationComparisonAssigner

Adds any default outputs that should occur from the assigner.

Specified by:

addDefaultOutputs in class AnnotationComparisonAssigner<org.anchoranalysis.annotation.io.assignment.OverlappingObjects>

Parameters:

outputs - the OutputEnabledMutable to add the default outputs to.

getFeatureEvaluator

public org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator<org.anchoranalysis.image.feature.input.FeatureInputPairObjects> getFeatureEvaluator()

setFeatureEvaluator

public void setFeatureEvaluator(org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator<org.anchoranalysis.image.feature.input.FeatureInputPairObjects> featureEvaluator)

getMaxCost

public double getMaxCost()

setMaxCost

public void setMaxCost(double maxCost)

getNumberDecimalPlaces

public int getNumberDecimalPlaces()

setNumberDecimalPlaces

public void setNumberDecimalPlaces(int numberDecimalPlaces)

isRemoveTouchingBorderXY

public boolean isRemoveTouchingBorderXY()

setRemoveTouchingBorderXY

public void setRemoveTouchingBorderXY(boolean removeTouchingBorderXY)