Package org.anchoranalysis.annotation.io.bean.comparer

Class MultipleComparer

Object

AnchorBean<MultipleComparer>

MultipleComparer

public class MultipleComparer
extends AnchorBean<MultipleComparer>

Allows comparison of an annotation with multiple other entities.

Author:

Owen Feehan

Constructor Summary

Constructors

Constructor	Description
MultipleComparer()

Method Summary

Modifier and Type	Method	Description
List<NameValue<Stack>>	createComparisonStacks(AnnotationWithMarks annotation, DisplayStack background, Path annotationPath, ColorScheme colorScheme, Path modelDirectory, OperationContext context, boolean debugMode)	Creates a Stack illustrating the comparison between annotation and each source in sources.
FeatureEvaluator<FeatureInputPairObjects>	getFeatureEvaluator()	Calculates the cost used when making assignments.
double	getMaxCost()	The maximum cost (as calculated by featureEvaluator) to accept when creating an assignment between objects.
List<NamedBean<ComparableSource>>	getSources()	The other entities to compare with the annotation.
boolean	isFlatten()	If true, a maximum-intensity-projection is first applied to any 3D objects into a 2D plane, before comparison.
void	setFeatureEvaluator(FeatureEvaluator<FeatureInputPairObjects> featureEvaluator)	Calculates the cost used when making assignments.
void	setFlatten(boolean flatten)	If true, a maximum-intensity-projection is first applied to any 3D objects into a 2D plane, before comparison.
void	setMaxCost(double maxCost)	The maximum cost (as calculated by featureEvaluator) to accept when creating an assignment between objects.
void	setSources(List<NamedBean<ComparableSource>> sources)	The other entities to compare with the annotation.

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

MultipleComparer

public MultipleComparer()

Method Details

createComparisonStacks

public List<NameValue<Stack>> createComparisonStacks(AnnotationWithMarks annotation,
 DisplayStack background,
 Path annotationPath,
 ColorScheme colorScheme,
 Path modelDirectory,
 OperationContext context,
 boolean debugMode)
                                              throws CreateException

Creates a Stack illustrating the comparison between annotation and each source in sources.

Parameters:

annotation - the annotation to compare.

background - the background to use when comparing.

annotationPath - the path on the file-system to annotation to use as a reference.

colorScheme - the color-scheme to use for unpaired objects.

modelDirectory - a directory in which models reside.

context - context for reading a stack from the file-system.

debugMode - whether in debug-mode or not.

Returns:

a list of stacks showing the comparisons, with with a corresponding name.

Throws:

CreateException - if any one of the stacks cannot be created.

getFeatureEvaluator

public FeatureEvaluator<FeatureInputPairObjects> getFeatureEvaluator()

Calculates the cost used when making assignments.

setFeatureEvaluator

public void setFeatureEvaluator(FeatureEvaluator<FeatureInputPairObjects> featureEvaluator)

Calculates the cost used when making assignments.

getMaxCost

public double getMaxCost()

The maximum cost (as calculated by featureEvaluator) to accept when creating an assignment between objects.

setMaxCost

public void setMaxCost(double maxCost)

The maximum cost (as calculated by featureEvaluator) to accept when creating an assignment between objects.

getSources

public List<NamedBean<ComparableSource>> getSources()

The other entities to compare with the annotation.

setSources

public void setSources(List<NamedBean<ComparableSource>> sources)

The other entities to compare with the annotation.

isFlatten

public boolean isFlatten()

If true, a maximum-intensity-projection is first applied to any 3D objects into a 2D plane, before comparison.

setFlatten

public void setFlatten(boolean flatten)

If true, a maximum-intensity-projection is first applied to any 3D objects into a 2D plane, before comparison.