Uses of Class
org.anchoranalysis.feature.energy.EnergyStack

Packages that use EnergyStack

Package	Description
org.anchoranalysis.feature.energy	A particular stack used in feature-calculations called a EnergyStack together with related classes.
org.anchoranalysis.feature.initialization	Initialization parameters used for beans in org.anchoranalysis.feature.bean.
org.anchoranalysis.feature.input	Base classes providing inputs to feature calculations.
org.anchoranalysis.image.feature.bean.evaluator	Beans that define context (which feature, which energy-stack) for evaluating feature-inputs.
org.anchoranalysis.image.feature.calculator	Implementations of FeatureCalculatorMulti related to images, especially to create tables of feature-calculations.
org.anchoranalysis.image.feature.calculator.merged	A particular implementation of FeatureCalculatorMulti for feature-calculations based upon pairs of image-objects.
org.anchoranalysis.image.feature.input	Image-related implementations of FeatureInput.
org.anchoranalysis.mpp.feature.addcriteria	Criteria for adding edges during optimization of marked-point-processes.
org.anchoranalysis.mpp.feature.energy.marks	Non-bean classes pertaining to calculating energy of {org.anchoranalysis.mpp.mark.Mark}s.
org.anchoranalysis.mpp.feature.energy.saved	Saved snapshots of energy-calculations.
org.anchoranalysis.mpp.feature.input	Inputs to mark-point-processes related Features.
org.anchoranalysis.mpp.io.output	Non-beans for writing data structures related to marked point processes from the file system.
org.anchoranalysis.mpp.mark	Non-bean classes related to Marks.
org.anchoranalysis.mpp.proposer	Non-bean classes for proposing Marks or other data-structures with particular attributes.
org.anchoranalysis.plugin.image.feature.bean.object.combine	Features from combinations of ObjectMasks.
org.anchoranalysis.plugin.image.feature.bean.object.single	Implementations of FeatureSingleObject.
org.anchoranalysis.plugin.image.feature.bean.object.single.border	Implementations of FeatureSingleObject that determine if an object lies at the border of an image.
org.anchoranalysis.plugin.image.feature.bean.object.single.energy	Implementations of FeatureSingleObject that reference a particular Channel in the associated EnergyStack.
org.anchoranalysis.plugin.image.task.feature	Non-bean classes pertaining to Features as used in tasks.
org.anchoranalysis.plugin.image.task.feature.calculator	Non-beans for calculating Features.
org.anchoranalysis.plugin.mpp.bean.define	Beans related to Define involving Mark or related classes.
org.anchoranalysis.test.feature.plugins.objects	Fixtures for creating object-masks and related feature-inputs.
org.anchoranalysis.test.image	Testing utilities and fixtures with no greater downstream dependency than anchor-image-io or anchor-io-bioformats or anchor-imagej.

Uses of EnergyStack in org.anchoranalysis.feature.energy

Methods in org.anchoranalysis.feature.energy that return EnergyStack

Modifier and Type	Method	Description
EnergyStack	EnergyStack.copyChangeDictionary(Dictionary dictionaryToAssign)	Makes a copy of the EnergyStack but assigns a new Dictionary.
EnergyStack	EnergyStack.extractSlice(int z)	Extract a particular z-slice from the EnergyStack as a new stack.

Uses of EnergyStack in org.anchoranalysis.feature.initialization

Constructors in org.anchoranalysis.feature.initialization with parameters of type EnergyStack

Modifier	Constructor	Description
	FeatureInitialization(EnergyStack energyStack)	Create only with an energy-stack.

Uses of EnergyStack in org.anchoranalysis.feature.input

Methods in org.anchoranalysis.feature.input that return EnergyStack

Modifier and Type	Method	Description
EnergyStack	FeatureInputEnergy.getEnergyStackRequired()	The associated energy-stack or throws an exception if it isn't present.

Methods in org.anchoranalysis.feature.input that return types with arguments of type EnergyStack

Modifier and Type	Method	Description
Optional<EnergyStack>	FeatureInputEnergy.getEnergyStackOptional()	The associated energy-stack.

Methods in org.anchoranalysis.feature.input with parameters of type EnergyStack

Modifier and Type	Method	Description
void	FeatureInputEnergy.setEnergyStack(EnergyStack energyStack)	Assigns an EnergyStack to be associated with the input.

Method parameters in org.anchoranalysis.feature.input with type arguments of type EnergyStack

Modifier and Type	Method	Description
void	FeatureInputEnergy.setEnergyStack(Optional<EnergyStack> energyStack)	Assigns an optional EnergyStack to be associated with the input.

Constructor parameters in org.anchoranalysis.feature.input with type arguments of type EnergyStack

Modifier	Constructor	Description
	FeatureInputEnergy(Optional<EnergyStack> energyStack)

Uses of EnergyStack in org.anchoranalysis.image.feature.bean.evaluator

Methods in org.anchoranalysis.image.feature.bean.evaluator that return types with arguments of type EnergyStack

Modifier and Type	Method	Description
Optional<EnergyStack>	FeatureEvaluator.energyStack()	The specified energy stack.

Uses of EnergyStack in org.anchoranalysis.image.feature.calculator

Method parameters in org.anchoranalysis.image.feature.calculator with type arguments of type EnergyStack

Modifier and Type	Method	Description
void	FeatureTableCalculator.start(ImageInitialization initialization, Optional<EnergyStack> energyStack, Logger logger)	Initializes a feature store that has the same structure as that previously created by createFeatures() from the same object.
void	SingleTableCalculator.start(ImageInitialization initialization, Optional<EnergyStack> energyStack, Logger logger)

Uses of EnergyStack in org.anchoranalysis.image.feature.calculator.merged

Method parameters in org.anchoranalysis.image.feature.calculator.merged with type arguments of type EnergyStack

Modifier and Type	Method	Description
void	PairsTableCalculator.start(ImageInitialization initializtion, Optional<EnergyStack> energyStack, Logger logger)

Uses of EnergyStack in org.anchoranalysis.image.feature.input

Constructors in org.anchoranalysis.image.feature.input with parameters of type EnergyStack

Modifier	Constructor	Description
	FeatureInputPairObjects(ObjectMask first, ObjectMask second, EnergyStack energyStack)	Constructs a FeatureInputPairObjects with two ObjectMasks and an EnergyStack.
	FeatureInputSingleObject(ObjectMask object, EnergyStack energyStack)	Constructs a FeatureInputSingleObject with an ObjectMask and an EnergyStack.

Constructor parameters in org.anchoranalysis.image.feature.input with type arguments of type EnergyStack

Modifier	Constructor	Description
	FeatureInputObjectCollection(ObjectCollection objects, Optional<EnergyStack> energyStack)	Constructs a FeatureInputObjectCollection with a collection of objects and an optional energy stack.
	FeatureInputPairObjects(ObjectMask first, ObjectMask second, Optional<EnergyStack> energyStack)	Constructs a FeatureInputPairObjects with two ObjectMasks and an optional EnergyStack.
	FeatureInputPairObjects(ObjectMask first, ObjectMask second, Optional<EnergyStack> energyStack, Optional<ObjectMask> merged)	Constructs a FeatureInputPairObjects with two ObjectMasks, an optional EnergyStack, and an optional merged ObjectMask.
	FeatureInputSingleObject(ObjectMask object, Optional<EnergyStack> energyStack)	Constructs a FeatureInputSingleObject with an ObjectMask and an optional EnergyStack.

Uses of EnergyStack in org.anchoranalysis.mpp.feature.addcriteria

Methods in org.anchoranalysis.mpp.feature.addcriteria with parameters of type EnergyStack

Modifier and Type	Method	Description
Optional<T>	AddCriteria.generateEdge(VoxelizedMarkMemo mark1, VoxelizedMarkMemo mark2, EnergyStack energyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>> session, boolean do3D)	Generates an edge between two marks based on the defined criteria.
Optional<EnergyPair>	AddCriteriaEnergyPair.generateEdge(VoxelizedMarkMemo mark1, VoxelizedMarkMemo mark2, EnergyStack energyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>> session, boolean do3D)
Optional<T>	AddCriteriaNever.generateEdge(VoxelizedMarkMemo mark1, VoxelizedMarkMemo mark2, EnergyStack energyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>> session, boolean do3D)
Optional<MarkPair<Mark>>	AddCriteriaPair.generateEdge(VoxelizedMarkMemo mark1, VoxelizedMarkMemo mark2, EnergyStack energyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>> session, boolean do3D)
void	RandomCollectionWithAddCriteria.initUpdatableMarks(MemoForIndex marks, EnergyStack stack, Logger logger, SharedFeatures sharedFeatures)

Uses of EnergyStack in org.anchoranalysis.mpp.feature.energy.marks

Methods in org.anchoranalysis.mpp.feature.energy.marks with parameters of type EnergyStack

Modifier and Type	Method	Description
void	MarksWithEnergyBreakdown.exchange(EnergyMemoList wrapperInd, int index, VoxelizedMarkMemo newMark, EnergyStack energyStack)	Exchanges a mark at a specific index with a new mark and updates energies.

Uses of EnergyStack in org.anchoranalysis.mpp.feature.energy.saved

Methods in org.anchoranalysis.mpp.feature.energy.saved with parameters of type EnergyStack

Modifier and Type	Method	Description
void	EnergySavedPairs.initUpdatableMarks(MemoForIndex pxlMarkMemoList, EnergyStack stack, Logger logger, SharedFeatures sharedFeatures)

Uses of EnergyStack in org.anchoranalysis.mpp.feature.input

Constructors in org.anchoranalysis.mpp.feature.input with parameters of type EnergyStack

Modifier	Constructor	Description
	FeatureInputAllMemo(EnergyMemoList pxlMarkMemoList, EnergyStack raster)	Creates a new instance with a list of memoized energy calculations and an energy stack.
	FeatureInputPairMemo(VoxelizedMarkMemo object1, VoxelizedMarkMemo object2, EnergyStack energyStack)	Creates a new instance with two memoized voxelized marks and an energy stack.
	FeatureInputSingleMemo(VoxelizedMarkMemo pxlPartMemo, EnergyStack energyStack)	Creates a new instance with a memoized voxelized mark and a non-optional energy stack.

Constructor parameters in org.anchoranalysis.mpp.feature.input with type arguments of type EnergyStack

Modifier	Constructor	Description
	FeatureInputSingleMemo(VoxelizedMarkMemo pxlPartMemo, Optional<EnergyStack> energyStack)	Creates a new instance with a memoized voxelized mark and an optional energy stack.

Uses of EnergyStack in org.anchoranalysis.mpp.io.output

Constructors in org.anchoranalysis.mpp.io.output with parameters of type EnergyStack

Modifier	Constructor	Description
	EnergyStackWriter(EnergyStack energyStack, Outputter outputter)	Creates a new EnergyStackWriter instance.

Uses of EnergyStack in org.anchoranalysis.mpp.mark

Methods in org.anchoranalysis.mpp.mark with parameters of type EnergyStack

Modifier and Type	Method	Description
void	UpdatableMarks.initUpdatableMarks(MemoForIndex memo, EnergyStack energyStack, Logger logger, SharedFeatures sharedFeatures)	Initializes the updatable marks with necessary context.

Uses of EnergyStack in org.anchoranalysis.mpp.proposer

Methods in org.anchoranalysis.mpp.proposer that return EnergyStack

Modifier and Type	Method	Description
EnergyStack	ProposerContext.getEnergyStack()	Energy stack for the current context.

Constructors in org.anchoranalysis.mpp.proposer with parameters of type EnergyStack

Modifier	Constructor	Description
	ProposerContext(RandomNumberGenerator randomNumberGenerator, EnergyStack energyStack, RegionMap regionMap, OperationContext operationContext, ErrorNode errorNode)	Creates a new ProposerContext instance.

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

Methods in org.anchoranalysis.plugin.image.feature.bean.object.combine with parameters of type EnergyStack

Modifier and Type	Method	Description
ListWithThumbnails<T,ObjectCollection>	CombineObjectsForFeatures.deriveInputsStartBatch(ObjectCollection objects, EnergyStack energyStack, boolean thumbnailsEnabled, OperationContext context)	Derives a list of inputs (i.e. rows in a feature table) and starts a batch of related thumbnail generation.
protected abstract List<T>	CombineObjectsForFeatures.startBatchDeriveInputs(ObjectCollection objects, EnergyStack energyStack, Logger logger)	Derives a list of inputs from an object-collection.
List<FeatureInputSingleObject>	EachObjectIndependently.startBatchDeriveInputs(ObjectCollection objects, EnergyStack energyStack, Logger logger)
List<FeatureInputPairObjects>	PairNeighbors.startBatchDeriveInputs(ObjectCollection objects, EnergyStack energyStack, Logger logger)

Uses of EnergyStack in org.anchoranalysis.plugin.image.feature.bean.object.single

Method parameters in org.anchoranalysis.plugin.image.feature.bean.object.single with type arguments of type EnergyStack

Modifier and Type	Method	Description
protected abstract double	OutlineKernelBase.calculateWithParameters(ObjectMask object, KernelApplicationParameters parameters, CheckedSupplier<EnergyStack,FeatureCalculationException> energyStack)	Calculates the feature value using the specified parameters.

Uses of EnergyStack in org.anchoranalysis.plugin.image.feature.bean.object.single.border

Method parameters in org.anchoranalysis.plugin.image.feature.bean.object.single.border with type arguments of type EnergyStack

Modifier and Type	Method	Description
protected double	NumberVoxelsAtBorder.calculateWithParameters(ObjectMask object, KernelApplicationParameters parameters, CheckedSupplier<EnergyStack,FeatureCalculationException> energyStack)

Uses of EnergyStack in org.anchoranalysis.plugin.image.feature.bean.object.single.energy

Method parameters in org.anchoranalysis.plugin.image.feature.bean.object.single.energy with type arguments of type EnergyStack

Modifier and Type	Method	Description
protected double	NumberNeighboringVoxels.calculateWithParameters(ObjectMask object, KernelApplicationParameters parameters, CheckedSupplier<EnergyStack,FeatureCalculationException> energyStack)

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

Methods in org.anchoranalysis.plugin.image.task.feature that return EnergyStack

Modifier and Type	Method	Description
EnergyStack	InitializationWithEnergyStack.getEnergyStack()	The energy stack.

Constructors in org.anchoranalysis.plugin.image.task.feature with parameters of type EnergyStack

Modifier	Constructor	Description
	InitializationWithEnergyStack(EnergyStack energyStack, InitializationContext context)	Creates a new instance with a given energy stack and initialization context.
	InitializationWithEnergyStack(ImageInitialization image, EnergyStack energyStack)	Creates a new InitializationWithEnergyStack instance.

Uses of EnergyStack in org.anchoranalysis.plugin.image.task.feature.calculator

Methods in org.anchoranalysis.plugin.image.task.feature.calculator that return EnergyStack

Modifier and Type	Method	Description
static EnergyStack	FeatureCalculatorRepeated.extractStack(ProvidesStackInput input, StackProvider stackEnergy, InputOutputContext context)	Extracts an EnergyStack from the given input and stack provider.
EnergyStack	FeatureCalculatorFromProvider.getEnergyStack()	The energy stack used for feature calculations.

Methods in org.anchoranalysis.plugin.image.task.feature.calculator with parameters of type EnergyStack

Modifier and Type	Method	Description
void	CalculateFeaturesForObjects.calculateForObjects(ObjectCollection objects, EnergyStack energyStack, LabelsForInput labelsForInput)	Calculates the feature-results for objects, and stores the results.

Uses of EnergyStack in org.anchoranalysis.plugin.mpp.bean.define

Methods in org.anchoranalysis.plugin.mpp.bean.define with parameters of type EnergyStack

Modifier and Type	Method	Description
S	DefineOutputterWithEnergy.ProcessWithEnergyStack.process(T initialization, EnergyStack energyStack)	Processes the initialization with an energy stack.

Method parameters in org.anchoranalysis.plugin.mpp.bean.define with type arguments of type EnergyStack

Modifier and Type	Method	Description
protected void	DefineOutputter.outputSharedObjects(SharedObjects sharedObjects, Optional<EnergyStack> energyStack, Outputter outputter)	Outputs shared objects and optionally an energy stack.

Uses of EnergyStack in org.anchoranalysis.test.feature.plugins.objects

Methods in org.anchoranalysis.test.feature.plugins.objects that return EnergyStack

Modifier and Type	Method	Description
static EnergyStack	CircleObjectFixture.energyStack()	Creates an EnergyStack with the fixture's dimensions.

Uses of EnergyStack in org.anchoranalysis.test.image

Methods in org.anchoranalysis.test.image that return EnergyStack

Modifier and Type	Method	Description
static EnergyStack	EnergyStackFixture.create(boolean big, boolean do3D)	Creates an energy-stack with default settings.
static EnergyStack	EnergyStackFixture.create(boolean big, boolean do3D, boolean singleChannel, boolean includeResolution)	Creates the energy-stack to use.