Uses of Class
org.anchoranalysis.bean.NamedBean

Packages that use NamedBean

Package	Description
org.anchoranalysis.annotation.io.bean.comparer	What to compare an annotation (ground truth) against?
org.anchoranalysis.bean.define	Define and related-classes.
org.anchoranalysis.feature.bean.list	A feature-list (custom list type for features) and associated providers.
org.anchoranalysis.feature.initialization	Initialization parameters used for beans in org.anchoranalysis.feature.bean.
org.anchoranalysis.feature.store	A collection of named-Features.
org.anchoranalysis.io.output.bean	Beans for the framework around writing files to the file-system.
org.anchoranalysis.io.output.bean.rules	Rules for determining if a particular output is enabled or not in a context of a hierarchy.
org.anchoranalysis.mpp.feature.bean.energy.scheme	Creating EnergySchemes.
org.anchoranalysis.mpp.feature.energy.scheme	Factorized form of storing the energy during an energy-minimization optimization scheme.
org.anchoranalysis.mpp.io.bean.input	Beans for reading data structures related to marked point processes from the file system.
org.anchoranalysis.plugin.annotation.bean.strategy	Strategies for how to annotate an image, such label per image etc.
org.anchoranalysis.plugin.image.feature.bean.object.combine	Features from combinations of ObjectMasks.
org.anchoranalysis.plugin.image.task.bean.feature	Tasks pertaining to Features.
org.anchoranalysis.plugin.image.task.bean.feature.source	Source of rows in feature-tables with FeatureSource and derived classes.
org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels	Selecting a subset of a set of channels.
org.anchoranalysis.plugin.image.task.bean.labeller	Associating labels with images.
org.anchoranalysis.plugin.image.task.bean.segment	Tasks to segment an image.
org.anchoranalysis.plugin.image.task.feature	Non-bean classes pertaining to Features as used in tasks.
org.anchoranalysis.plugin.io.bean.input.channel	InputManagers that accept a set of named-channels.
org.anchoranalysis.test.feature.plugins	Testing utilities and fixtures with no greater downstream dependency than anchor-image-feature or anchor-mpp.

Uses of NamedBean in org.anchoranalysis.annotation.io.bean.comparer

Methods in org.anchoranalysis.annotation.io.bean.comparer that return types with arguments of type NamedBean

Modifier and Type	Method	Description
List<NamedBean<ComparableSource>>	MultipleComparer.getSources()	The other entities to compare with the annotation.

Method parameters in org.anchoranalysis.annotation.io.bean.comparer with type arguments of type NamedBean

Modifier and Type	Method	Description
void	MultipleComparer.setSources(List<NamedBean<ComparableSource>> sources)	The other entities to compare with the annotation.

Uses of NamedBean in org.anchoranalysis.bean.define

Methods in org.anchoranalysis.bean.define that return types with arguments of type NamedBean

Modifier and Type	Method	Description
<T extends AnchorBean<?>> List<NamedBean<T>>	Define.listFor(Class<?> groupingRoot)	Retrieves the list of elements associated with a grouping-root.

Methods in org.anchoranalysis.bean.define with parameters of type NamedBean

Modifier and Type	Method	Description
void	Define.add(NamedBean<?> bean)	Adds a named-bean to our definitions, using the {#link GroupingRoot} annotation to determine a group where definitions are stored.

Method parameters in org.anchoranalysis.bean.define with type arguments of type NamedBean

Modifier and Type	Method	Description
<T extends AnchorBean<?>> void	Define.addAll(List<NamedBean<T>> list)	Adds all the named-beans from source to the current map.

Uses of NamedBean in org.anchoranalysis.feature.bean.list

Methods in org.anchoranalysis.feature.bean.list that return types with arguments of type NamedBean

Modifier and Type	Method	Description
List<NamedBean<FeatureListProvider<T>>>	DefinedNamed.getList()	A list of FeatureListProviders with an associated name.

Method parameters in org.anchoranalysis.feature.bean.list with type arguments of type NamedBean

Modifier and Type	Method	Description
void	DefinedNamed.setList(List<NamedBean<FeatureListProvider<T>>> list)	A list of FeatureListProviders with an associated name.

Uses of NamedBean in org.anchoranalysis.feature.initialization

Method parameters in org.anchoranalysis.feature.initialization with type arguments of type NamedBean

Modifier and Type	Method	Description
void	FeatureRelatedInitialization.populate(List<NamedBean<FeatureListProvider<FeatureInput>>> namedProviders, Logger logger)	Adds features into the shared-feature storage from a list of named-beans.

Uses of NamedBean in org.anchoranalysis.feature.store

Methods in org.anchoranalysis.feature.store that return NamedBean

Modifier and Type	Method	Description
NamedBean<Feature<T>>	NamedFeatureStore.get(int index)	Gets a feature at a particular position.
NamedBean<Feature<T>>	NamedFeatureStore.get(String name)	Gets a feature corresponding to a particular name.

Methods in org.anchoranalysis.feature.store that return types with arguments of type NamedBean

Modifier and Type	Method	Description
Iterator<NamedBean<Feature<T>>>	NamedFeatureStore.iterator()

Method parameters in org.anchoranalysis.feature.store with type arguments of type NamedBean

Modifier and Type	Method	Description
<T extends FeatureInput> NamedFeatureStore<T>	NamedFeatureStoreFactory.createNamedFeatureList(List<NamedBean<FeatureListProvider<T>>> namedFeatures)	Create a NamedFeatureStore from a list of beans.

Uses of NamedBean in org.anchoranalysis.io.output.bean

Methods in org.anchoranalysis.io.output.bean that return types with arguments of type NamedBean

Modifier and Type	Method	Description
List<NamedBean<?>>	OutputWriteSettings.getWriters()	Specifies a writer bean instance for a particular type of writer (identified by the writer bean class)

Method parameters in org.anchoranalysis.io.output.bean with type arguments of type NamedBean

Modifier and Type	Method	Description
void	OutputWriteSettings.setWriters(List<NamedBean<?>> writers)	Specifies a writer bean instance for a particular type of writer (identified by the writer bean class)

Uses of NamedBean in org.anchoranalysis.io.output.bean.rules

Methods in org.anchoranalysis.io.output.bean.rules that return types with arguments of type NamedBean

Modifier and Type	Method	Description
List<NamedBean<StringSet>>	OutputEnableRulesSpecify.getSecond()	Output-names in the second-level (for all first level output-names).

Method parameters in org.anchoranalysis.io.output.bean.rules with type arguments of type NamedBean

Modifier and Type	Method	Description
void	OutputEnableRulesSpecify.setSecond(List<NamedBean<StringSet>> second)	Output-names in the second-level (for all first level output-names).

Uses of NamedBean in org.anchoranalysis.mpp.feature.bean.energy.scheme

Methods in org.anchoranalysis.mpp.feature.bean.energy.scheme that return types with arguments of type NamedBean

Modifier and Type	Method	Description
List<NamedBean<FeatureListProvider<FeatureInputStack>>>	EnergySchemeCreatorByElement.getListImageFeatures()	List of named feature providers for image-based features.

Method parameters in org.anchoranalysis.mpp.feature.bean.energy.scheme with type arguments of type NamedBean

Modifier and Type	Method	Description
void	EnergySchemeCreatorByElement.setListImageFeatures(List<NamedBean<FeatureListProvider<FeatureInputStack>>> listImageFeatures)	List of named feature providers for image-based features.

Uses of NamedBean in org.anchoranalysis.mpp.feature.energy.scheme

Methods in org.anchoranalysis.mpp.feature.energy.scheme that return types with arguments of type NamedBean

Modifier and Type	Method	Description
List<NamedBean<Feature<FeatureInputStack>>>	EnergyScheme.getListImageFeatures()	A list of features of the image that are calculated first, and exposed to the other features as parameters.

Constructor parameters in org.anchoranalysis.mpp.feature.energy.scheme with type arguments of type NamedBean

Modifier	Constructor	Description
	EnergyScheme(FeatureList<FeatureInputSingleMemo> individual, FeatureList<FeatureInputPairMemo> pair, FeatureList<FeatureInputAllMemo> all, RegionMap regionMap, AddCriteriaPair pairAddCriteria, Optional<DictionaryProvider> dictionary, List<NamedBean<Feature<FeatureInputStack>>> listImageFeatures)	Creates an energy scheme with the specified features, region map, and additional options.

Uses of NamedBean in org.anchoranalysis.mpp.io.bean.input

Methods in org.anchoranalysis.mpp.io.bean.input that return types with arguments of type NamedBean

Modifier and Type	Method	Description
List<NamedBean<DerivePath>>	MultiInputManager.getAppendDictionary()	List of dictionaries to append.
List<NamedBean<DerivePath>>	MultiInputManager.getAppendFilePath()	List of file paths to append.
List<NamedBean<DerivePath>>	MultiInputManager.getAppendHistogram()	List of histograms to append.
List<NamedBean<DerivePath>>	MultiInputManager.getAppendMarks()	List of marks to append.
List<NamedBean<DerivePath>>	MultiInputManager.getAppendMarksFromAnnotation()	List of marks from annotations (both accepted and rejected) to append.
List<NamedBean<DerivePath>>	MultiInputManager.getAppendMarksFromAnnotationAcceptedOnly()	List of marks from annotations (accepted only) to append.
List<NamedBean<DerivePath>>	MultiInputManager.getAppendMarksFromAnnotationRejectedOnly()	List of marks from annotations (rejected only) to append.
List<NamedBean<DerivePath>>	MultiInputManager.getAppendObjects()	List of object-collections to append to the MultiInput.
List<NamedBean<DerivePath>>	MultiInputManager.getAppendStack()	List of additional stacks to append.

Method parameters in org.anchoranalysis.mpp.io.bean.input with type arguments of type NamedBean

Modifier and Type	Method	Description
void	MultiInputManager.setAppendDictionary(List<NamedBean<DerivePath>> appendDictionary)	List of dictionaries to append.
void	MultiInputManager.setAppendFilePath(List<NamedBean<DerivePath>> appendFilePath)	List of file paths to append.
void	MultiInputManager.setAppendHistogram(List<NamedBean<DerivePath>> appendHistogram)	List of histograms to append.
void	MultiInputManager.setAppendMarks(List<NamedBean<DerivePath>> appendMarks)	List of marks to append.
void	MultiInputManager.setAppendMarksFromAnnotation(List<NamedBean<DerivePath>> appendMarksFromAnnotation)	List of marks from annotations (both accepted and rejected) to append.
void	MultiInputManager.setAppendMarksFromAnnotationAcceptedOnly(List<NamedBean<DerivePath>> appendMarksFromAnnotationAcceptedOnly)	List of marks from annotations (accepted only) to append.
void	MultiInputManager.setAppendMarksFromAnnotationRejectedOnly(List<NamedBean<DerivePath>> appendMarksFromAnnotationRejectedOnly)	List of marks from annotations (rejected only) to append.
void	MultiInputManager.setAppendObjects(List<NamedBean<DerivePath>> appendObjects)	List of object-collections to append to the MultiInput.
void	MultiInputManager.setAppendStack(List<NamedBean<DerivePath>> appendStack)	List of additional stacks to append.

Uses of NamedBean in org.anchoranalysis.plugin.annotation.bean.strategy

Methods in org.anchoranalysis.plugin.annotation.bean.strategy that return NamedBean

Modifier and Type	Method	Description
NamedBean<MarkEvaluator>	MarkProposerStrategy.getMarkEvaluator()	A mark-evaluator that is added to the GUI to support this annotation

Methods in org.anchoranalysis.plugin.annotation.bean.strategy with parameters of type NamedBean

Modifier and Type	Method	Description
void	MarkProposerStrategy.setMarkEvaluator(NamedBean<MarkEvaluator> markEvaluator)	A mark-evaluator that is added to the GUI to support this annotation

Uses of NamedBean in org.anchoranalysis.plugin.image.feature.bean.object.combine

Methods in org.anchoranalysis.plugin.image.feature.bean.object.combine that return types with arguments of type NamedBean

Modifier and Type	Method	Description
List<NamedBean<FeatureListProvider<FeatureInputStack>>>	PairNeighbors.getFeaturesImage()	Additional features that only depend on the image, so do not need to be replicated for every object.
List<NamedBean<FeatureListProvider<FeatureInputPairObjects>>>	PairNeighbors.getFeaturesPair()	Additional features that are processed on the pair of images (i.e.

Method parameters in org.anchoranalysis.plugin.image.feature.bean.object.combine with type arguments of type NamedBean

Modifier and Type	Method	Description
abstract FeatureTableCalculator<T>	CombineObjectsForFeatures.createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>> featuresSingleObject, NamedFeatureStoreFactory storeFactory, boolean suppressErrors)	Creates features that will be applied on the objects.
FeatureTableCalculator<FeatureInputSingleObject>	EachObjectIndependently.createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>> list, NamedFeatureStoreFactory storeFactory, boolean suppressErrors)
FeatureTableCalculator<FeatureInputPairObjects>	PairNeighbors.createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>> list, NamedFeatureStoreFactory storeFactory, boolean suppressErrors)
void	PairNeighbors.setFeaturesImage(List<NamedBean<FeatureListProvider<FeatureInputStack>>> featuresImage)	Additional features that only depend on the image, so do not need to be replicated for every object.
void	PairNeighbors.setFeaturesPair(List<NamedBean<FeatureListProvider<FeatureInputPairObjects>>> featuresPair)	Additional features that are processed on the pair of images (i.e.

Uses of NamedBean in org.anchoranalysis.plugin.image.task.bean.feature

Methods in org.anchoranalysis.plugin.image.task.bean.feature that return types with arguments of type NamedBean

Modifier and Type	Method	Description
List<NamedBean<FeatureListProvider<U>>>	ExportFeatures.getFeatures()	The features to be exported (after possibly some manipulation or augmentation).
List<NamedBean<FeatureListProvider<FeatureInputResults>>>	ExportFeatures.getFeaturesAggregate()	Features applied to each group to aggregate values (accepting FeatureInputResults).

Method parameters in org.anchoranalysis.plugin.image.task.bean.feature with type arguments of type NamedBean

Modifier and Type	Method	Description
void	ExportFeatures.setFeatures(List<NamedBean<FeatureListProvider<U>>> features)	The features to be exported (after possibly some manipulation or augmentation).
void	ExportFeatures.setFeaturesAggregate(List<NamedBean<FeatureListProvider<FeatureInputResults>>> featuresAggregate)	Features applied to each group to aggregate values (accepting FeatureInputResults).

Uses of NamedBean in org.anchoranalysis.plugin.image.task.bean.feature.source

Method parameters in org.anchoranalysis.plugin.image.task.bean.feature.source with type arguments of type NamedBean

Modifier and Type	Method	Description
abstract FeatureExporter<S>	FeatureSource.createExporter(LabelHeaders metadataHeaders, List<NamedBean<FeatureListProvider<U>>> features, FeatureOutputNames outputNames, Optional<InputGrouper> grouper, FeatureExporterContext context)	Creates the FeatureExporter to be used for calculating and exporting feature-results.
FeatureExporter<FeatureList<S>>	SingleRowPerInput.createExporter(LabelHeaders metadataHeaders, List<NamedBean<FeatureListProvider<S>>> features, FeatureOutputNames outputNames, Optional<InputGrouper> grouper, FeatureExporterContext context)

Uses of NamedBean in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels

Methods in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels that return types with arguments of type NamedBean

Modifier and Type	Method	Description
List<NamedBean<FromStack>>	SpecificAndRename.getList()

Method parameters in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels with type arguments of type NamedBean

Modifier and Type	Method	Description
void	SpecificAndRename.setList(List<NamedBean<FromStack>> list)

Uses of NamedBean in org.anchoranalysis.plugin.image.task.bean.labeller

Methods in org.anchoranalysis.plugin.image.task.bean.labeller that return types with arguments of type NamedBean

Modifier and Type	Method	Description
List<NamedBean<FeatureListProvider<FeatureInputStack>>>	BinaryClassifierImageLabeller.getListFeatures()	List of named feature list providers for additional features.

Method parameters in org.anchoranalysis.plugin.image.task.bean.labeller with type arguments of type NamedBean

Modifier and Type	Method	Description
void	BinaryClassifierImageLabeller.setListFeatures(List<NamedBean<FeatureListProvider<FeatureInputStack>>> listFeatures)	List of named feature list providers for additional features.

Uses of NamedBean in org.anchoranalysis.plugin.image.task.bean.segment

Methods in org.anchoranalysis.plugin.image.task.bean.segment that return types with arguments of type NamedBean

Modifier and Type	Method	Description
List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>	SegmentInstanceWithModel.getFeatures()	Features to calculate for objects in the features output.

Method parameters in org.anchoranalysis.plugin.image.task.bean.segment with type arguments of type NamedBean

Modifier and Type	Method	Description
void	SegmentInstanceWithModel.setFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>> features)	Features to calculate for objects in the features output.

Uses of NamedBean in org.anchoranalysis.plugin.image.task.feature

Method parameters in org.anchoranalysis.plugin.image.task.feature with type arguments of type NamedBean

Modifier and Type	Method	Description
static <T extends FeatureInput> FeatureExporter<FeatureList<T>>	FeatureExporter.create(List<NamedBean<FeatureListProvider<T>>> features, LabelHeaders metadataHeaders, FeatureOutputNames outputNames, Optional<InputGrouper> grouper, FeatureExporterContext context)	Alternative static constructor that creates a shared-state from a list of named FeatureListProviders.

Uses of NamedBean in org.anchoranalysis.plugin.io.bean.input.channel

Methods in org.anchoranalysis.plugin.io.bean.input.channel that return types with arguments of type NamedBean

Modifier and Type	Method	Description
List<NamedBean<DerivePath>>	NamedChannelsAppend.getListAppend()

Method parameters in org.anchoranalysis.plugin.io.bean.input.channel with type arguments of type NamedBean

Modifier and Type	Method	Description
void	NamedChannelsAppend.setListAppend(List<NamedBean<DerivePath>> listAppend)

Uses of NamedBean in org.anchoranalysis.test.feature.plugins

Methods in org.anchoranalysis.test.feature.plugins that return types with arguments of type NamedBean

Modifier and Type	Method	Description
static <T extends FeatureInput> List<NamedBean<FeatureListProvider<T>>>	FeaturesFromXMLFixture.createNamedFeatureProviders(String xmlPath, TestLoader loader)	Creates a list of named feature list providers from an XML file.