Uses of Class
org.anchoranalysis.core.exception.InitializeException

Packages that use InitializeException

Package	Description
org.anchoranalysis.bean	Defining, loading, initializing Anchor Beans.
org.anchoranalysis.bean.initializable	Initializing beans with particular parameters, including recursively.
org.anchoranalysis.bean.initializable.property	Initializating a bean with parameters.
org.anchoranalysis.bean.shared.dictionary	Setting, referencing and initializing key-value parameters.
org.anchoranalysis.core.exception	Very general exceptions and base classes for exceptions with wide applicability.
org.anchoranalysis.feature.bean	Beans pertaining to feature-calculation.
org.anchoranalysis.feature.bean.list	A feature-list (custom list type for features) and associated providers.
org.anchoranalysis.feature.calculate.bound	Interfaces like FeatureCalculator but bound to particular features.
org.anchoranalysis.feature.initialization	Initialization parameters used for beans in org.anchoranalysis.feature.bean.
org.anchoranalysis.feature.session	A defined context in which one or more features are provided inputs and produce results.
org.anchoranalysis.feature.shared	Features shared for referencing among calculations.
org.anchoranalysis.image.bean.segment.binary	Base classes to perform binary-segmentation.
org.anchoranalysis.image.feature.bean	Beans pertaining to feature definition and calculation.
org.anchoranalysis.image.feature.bean.physical	Features that convert to/from physical spatial units (e.g. meters) as opposed to pixels/voxels.
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.inference.bean.segment.instance	Instance-segmentation of a Stack.
org.anchoranalysis.mpp.bean.mark.factory	Beans related to creating Marks.
org.anchoranalysis.mpp.feature.addcriteria	Criteria for adding edges during optimization of marked-point-processes.
org.anchoranalysis.mpp.feature.energy.saved	Saved snapshots of energy-calculations.
org.anchoranalysis.mpp.mark	Non-bean classes related to Marks.
org.anchoranalysis.plugin.image.bean.channel.provider	Implementations of ChannelProvider that are generic base-classes or otherwise abstract or general.
org.anchoranalysis.plugin.image.bean.dimensions.provider	Implementations of DimensionsProvider.
org.anchoranalysis.plugin.image.bean.histogram.provider	Implementations of HistogramProvider.
org.anchoranalysis.plugin.image.bean.mask.provider.convert	Implementations of MaskProvider that convert providers of other types to ObjectMasks.
org.anchoranalysis.plugin.image.bean.object.provider	Implementations of ObjectCollectionProvider.
org.anchoranalysis.plugin.image.bean.stack.provider	Implementations of StackProvider.
org.anchoranalysis.plugin.image.feature.bean.list.permute	Implementations of FeatureListProvider that derive new features with permuted property-values.
org.anchoranalysis.plugin.image.feature.bean.object.combine	Features from combinations of ObjectMasks.
org.anchoranalysis.plugin.image.feature.bean.object.single.shared	Implementations of FeatureSingleObject that use SharedObjects for calculations.
org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting	Implementations of FeatureSingleObject that use SharedObjects for calculations, and measure the degree of intersection between objects.
org.anchoranalysis.plugin.image.feature.bean.score	Implementations of VoxelScore.
org.anchoranalysis.plugin.image.feature.bean.shared	Beans involving SharedObjects.
org.anchoranalysis.plugin.image.feature.bean.shared.object	Beans involving SharedObjects and ObjectCollection.
org.anchoranalysis.plugin.image.object.merge.condition	Conditions for merging ObjectMasks.
org.anchoranalysis.plugin.image.task.bean.labeller	Associating labels with images.
org.anchoranalysis.plugin.image.task.feature.calculator	Non-beans for calculating Features.
org.anchoranalysis.plugin.image.task.labeller	Non-bean classes about labelling images.
org.anchoranalysis.plugin.operator.feature.bean	Features that combine or convert other features in a generic way.
org.anchoranalysis.plugin.points.bean.fitter	Fitting geometric structures to points.

Uses of InitializeException in org.anchoranalysis.bean

Methods in org.anchoranalysis.bean that throw InitializeException

Modifier and Type	Method	Description
void	NullParametersBean.initializeRecursive(Logger logger)	Initialize this bean and any suitable child beans.
void	NullParametersBean.onInitialization()	As there's no parameters we expose a different method.
final void	NullParametersBean.onInitialization(NullInitialization so)

Uses of InitializeException in org.anchoranalysis.bean.initializable

Methods in org.anchoranalysis.bean.initializable that throw InitializeException

Modifier and Type	Method	Description
protected P	InitializableBean.getInitialization()	The parameters used for initialization.
void	InitializableBean.initialize(P parameters, Logger logger)	Initializes the bean with the necessary parameters.
void	InitializableBean.initializeRecursive(P parameters, Logger logger)	Initializes this object, and all children objects, so long as they have P once a Bean doesn't have P, the children are not evaluated.
void	InitializableBean.initRecursiveWithInitializer(BeanInitializer<?> initializer, Logger logger)	Initializes the bean and recursively all contained beans (who have compatible initialization requirements)
void	InitializableBean.onInitialization(P initialization)	Called after initialization.

Uses of InitializeException in org.anchoranalysis.bean.initializable.property

Methods in org.anchoranalysis.bean.initializable.property that throw InitializeException

Modifier and Type	Method	Description
boolean	BeanInitializer.applyInitializationIfPossibleTo(Object bean, Object parent, Logger logger)	Applies the initialization to a bean if possible.
void	AssignerMatchClass.assignInitializationToProperties(Object bean, Object initialization, Object parent, Logger logger)
void	InitializationParameterAssigner.assignInitializationToProperties(Object bean, Object initialization, Object parent, Logger logger)	Assigns the parameter to the bean.

Uses of InitializeException in org.anchoranalysis.bean.shared.dictionary

Methods in org.anchoranalysis.bean.shared.dictionary that throw InitializeException

Modifier and Type	Method	Description
void	DictionaryProviderReference.onInitialization(DictionaryInitialization initialization)

Uses of InitializeException in org.anchoranalysis.core.exception

Methods in org.anchoranalysis.core.exception that return InitializeException

Modifier and Type	Method	Description
static InitializeException	InitializeException.createOrReuse(Throwable exception)	Wraps exception in a InitializeException, unless it already its cause is a InitializeException.

Uses of InitializeException in org.anchoranalysis.feature.bean

Methods in org.anchoranalysis.feature.bean that throw InitializeException

Modifier and Type	Method	Description
protected void	Feature.beforeCalc(FeatureInitialization initialization)	Dummy method, that children can optionally override.
void	Feature.onInitialization(FeatureInitialization initialization)	Called after initialization.

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

Methods in org.anchoranalysis.feature.bean.list that throw InitializeException

Modifier and Type	Method	Description
void	FeatureList.initializeRecursive(FeatureInitialization initialization, Logger logger)	Initializes all features in the list, and recursively any features they contain.
void	ReferencingFeatureListProvider.onInitialization(FeatureRelatedInitialization soFeature)

Uses of InitializeException in org.anchoranalysis.feature.calculate.bound

Constructors in org.anchoranalysis.feature.calculate.bound that throw InitializeException

Modifier	Constructor	Description
	FeatureCalculatorSingleFromMulti(FeatureCalculatorMulti<T> multi)	Creates from a FeatureCalculatorMulti.

Uses of InitializeException in org.anchoranalysis.feature.initialization

Methods in org.anchoranalysis.feature.initialization that throw InitializeException

Modifier and Type	Method	Description
SharedObjects	FeatureInitialization.sharedObjectsRequired()	Retrieves the shared-objects associated with the initialization, or throws an an exception if they do not exist.

Uses of InitializeException in org.anchoranalysis.feature.session

Methods in org.anchoranalysis.feature.session that throw InitializeException

Modifier and Type	Method	Description
void	SequentialSession.start(FeatureInitialization initialization, SharedFeatures sharedFeatures, Logger logger)	Starts the session.
static <T extends FeatureInput> FeatureCalculatorSingle<T>	FeatureSession.with(Feature<T> feature, Logger logger)	Starts a feature-session for a single feature.
static <T extends FeatureInput> FeatureCalculatorSingle<T>	FeatureSession.with(Feature<T> feature, FeatureInitialization initialization, SharedFeatures sharedFeatures, Logger logger)	Starts a feature-session for a single feature, with specific initialization.
static <T extends FeatureInput> FeatureCalculatorSingle<T>	FeatureSession.with(Feature<T> feature, SharedFeatures sharedFeatures, Logger logger)	Starts a feature-session for a single feature, with default initialization.
static <T extends FeatureInput> FeatureCalculatorMulti<T>	FeatureSession.with(FeatureList<T> features, Logger logger)	Starts a feature-session for a list of features, with default initialization.
static <T extends FeatureInput> FeatureCalculatorMulti<T>	FeatureSession.with(FeatureList<T> features, FeatureInitialization initialization, Optional<SharedFeatures> sharedFeatures, Logger logger, BoundReplaceStrategy<T,? extends ReplaceStrategy<T>> replaceStrategy)	Starts a feature-session for a list of features, with particular initialization, and a replaceStrategy.
static <T extends FeatureInput> FeatureCalculatorMulti<T>	FeatureSession.with(FeatureList<T> features, FeatureInitialization initialization, SharedFeatures sharedFeatures, Logger logger)	Starts a feature-session for a list of features, with particular initialization.

Uses of InitializeException in org.anchoranalysis.feature.shared

Methods in org.anchoranalysis.feature.shared that throw InitializeException

Modifier and Type	Method	Description
void	SharedFeaturesSubset.initializeRecursive(FeatureInitialization initialization, Logger logger)	Initialize all features in this instance, recursively also initializating any child-features.

Uses of InitializeException in org.anchoranalysis.image.bean.segment.binary

Methods in org.anchoranalysis.image.bean.segment.binary that throw InitializeException

Modifier and Type	Method	Description
void	BinarySegmentationReference.onInitialization(ImageInitialization initialization)

Uses of InitializeException in org.anchoranalysis.image.feature.bean

Methods in org.anchoranalysis.image.feature.bean that throw InitializeException

Modifier and Type	Method	Description
void	VoxelScore.initialize(List<Histogram> histograms, Optional<Dictionary> dictionary)	Initializes the voxels-score.

Uses of InitializeException in org.anchoranalysis.image.feature.bean.physical

Methods in org.anchoranalysis.image.feature.bean.physical that throw InitializeException

Modifier and Type	Method	Description
protected void	ConvertToPhysicalDistance.beforeCalc(FeatureInitialization initialization)	Initializes the direction vector before calculation.

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

Methods in org.anchoranalysis.image.feature.calculator that throw InitializeException

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 InitializeException in org.anchoranalysis.image.feature.calculator.merged

Methods in org.anchoranalysis.image.feature.calculator.merged that throw InitializeException

Modifier and Type	Method	Description
FeatureCalculatorMulti<FeatureInputStack>	MergedPairsFeatures.createCalculator(CreateCalculatorHelper calculatorCreator, ImageInitialization initialization, BoundReplaceStrategy<FeatureInputStack,? extends ReplaceStrategy<FeatureInputStack>> cachingStrategy)	Creates a feature calculator for stack features.
FeatureCalculatorMulti<FeatureInputPairObjects>	MergedPairsFeatures.createPair(CreateCalculatorHelper calculatorCreator, ImageInitialization initialization, CacheTransferSourceCollection cacheTransferSource)	Creates a feature calculator for pair object features.
FeatureCalculatorMulti<FeatureInputSingleObject>	MergedPairsFeatures.createSingle(CreateCalculatorHelper calculatorCreator, ImageInitialization initialization, BoundReplaceStrategy<FeatureInputSingleObject,CacheAndReuseStrategy<FeatureInputSingleObject>> cachingStrategy)	Creates a feature calculator for single object features.
void	PairsTableCalculator.start(ImageInitialization initializtion, Optional<EnergyStack> energyStack, Logger logger)

Uses of InitializeException in org.anchoranalysis.image.inference.bean.segment.instance

Methods in org.anchoranalysis.image.inference.bean.segment.instance that throw InitializeException

Modifier and Type	Method	Description
protected Path	SegmentStackIntoObjectsPooled.resolve(String modelFilename)	Resolves a relative filename for a model into a path, relative to the model directory.

Uses of InitializeException in org.anchoranalysis.mpp.bean.mark.factory

Methods in org.anchoranalysis.mpp.bean.mark.factory that throw InitializeException

Modifier and Type	Method	Description
void	MarkWithIdentifierFactory.onInitialization()

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

Methods in org.anchoranalysis.mpp.feature.addcriteria that throw InitializeException

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

Constructors in org.anchoranalysis.mpp.feature.addcriteria that throw InitializeException

Modifier	Constructor	Description
	AddCriteriaEnergyPair(FeatureList<FeatureInputPairMemo> energyPairs, AddCriteriaPair pairAddCriteria)	Creates an AddCriteriaEnergyPair with specified energy pairs and add criteria.

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

Methods in org.anchoranalysis.mpp.feature.energy.saved that throw InitializeException

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

Uses of InitializeException in org.anchoranalysis.mpp.mark

Methods in org.anchoranalysis.mpp.mark that throw InitializeException

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 InitializeException in org.anchoranalysis.plugin.image.bean.channel.provider

Methods in org.anchoranalysis.plugin.image.bean.channel.provider that throw InitializeException

Modifier and Type	Method	Description
void	FromInput.onInitialization(ImageInitialization initialization)

Uses of InitializeException in org.anchoranalysis.plugin.image.bean.dimensions.provider

Methods in org.anchoranalysis.plugin.image.bean.dimensions.provider that throw InitializeException

Modifier and Type	Method	Description
void	FromChannel.onInitialization(ImageInitialization initialization)

Uses of InitializeException in org.anchoranalysis.plugin.image.bean.histogram.provider

Methods in org.anchoranalysis.plugin.image.bean.histogram.provider that throw InitializeException

Modifier and Type	Method	Description
void	Reference.onInitialization(ImageInitialization initialization)

Uses of InitializeException in org.anchoranalysis.plugin.image.bean.mask.provider.convert

Methods in org.anchoranalysis.plugin.image.bean.mask.provider.convert that throw InitializeException

Modifier and Type	Method	Description
void	FromStackChannel.onInitialization(ImageInitialization initialization)

Uses of InitializeException in org.anchoranalysis.plugin.image.bean.object.provider

Methods in org.anchoranalysis.plugin.image.bean.object.provider that throw InitializeException

Modifier and Type	Method	Description
void	ReferenceOrElse.onInitialization(ImageInitialization initialization)

Uses of InitializeException in org.anchoranalysis.plugin.image.bean.stack.provider

Methods in org.anchoranalysis.plugin.image.bean.stack.provider that throw InitializeException

Modifier and Type	Method	Description
void	FromInput.onInitialization(ImageInitialization initialization)

Uses of InitializeException in org.anchoranalysis.plugin.image.feature.bean.list.permute

Methods in org.anchoranalysis.plugin.image.feature.bean.list.permute that throw InitializeException

Modifier and Type	Method	Description
void	PermuteFeature.onInitialization(FeatureRelatedInitialization so)

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

Methods in org.anchoranalysis.plugin.image.feature.bean.object.combine that throw InitializeException

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.

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

Methods in org.anchoranalysis.plugin.image.feature.bean.object.single.shared that throw InitializeException

Modifier and Type	Method	Description
protected void	PairedWithMask.beforeCalc(FeatureInitialization initialization)

Uses of InitializeException in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting

Methods in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting that throw InitializeException

Modifier and Type	Method	Description
protected void	FeatureIntersectingObjects.beforeCalc(FeatureInitialization initialization)

Uses of InitializeException in org.anchoranalysis.plugin.image.feature.bean.score

Methods in org.anchoranalysis.plugin.image.feature.bean.score that throw InitializeException

Modifier and Type	Method	Description
protected static double	FromDictionaryBase.extractAsDouble(Dictionary dictionary, String key)	Extracts a double value from the dictionary for a given key.
void	CalculateLevelBase.initialize(List<Histogram> histograms, Optional<Dictionary> dictionary)
void	FromDictionaryBase.initialize(List<Histogram> histograms, Optional<Dictionary> dictionary)	Initializes the feature with histograms and a dictionary.
void	IdentityImposeValueRelationToHistogram.initialize(List<Histogram> histograms, Optional<Dictionary> dictionary)
void	NormalizeByMax.initialize(List<Histogram> histograms, Optional<Dictionary> dictionary)
protected abstract void	FromDictionaryBase.setupDictionary(Dictionary dictionary)	Sets up the feature using the provided dictionary.

Uses of InitializeException in org.anchoranalysis.plugin.image.feature.bean.shared

Methods in org.anchoranalysis.plugin.image.feature.bean.shared that throw InitializeException

Modifier and Type	Method	Description
protected void	ParamFromCollection.beforeCalc(FeatureInitialization initialization)

Uses of InitializeException in org.anchoranalysis.plugin.image.feature.bean.shared.object

Methods in org.anchoranalysis.plugin.image.feature.bean.shared.object that throw InitializeException

Modifier and Type	Method	Description
protected void	FeatureSingleObjectFromShared.beforeCalc(FeatureInitialization initialization)
protected abstract void	FeatureSingleObjectFromShared.beforeCalcWithInitialization(ImageInitialization initialization)	Performs initialization before calculation with image-specific initialization.
protected void	MaskAsSingleObject.beforeCalcWithInitialization(ImageInitialization initialization)
protected void	ObjectAggregationBase.beforeCalcWithInitialization(ImageInitialization initialization)

Uses of InitializeException in org.anchoranalysis.plugin.image.object.merge.condition

Methods in org.anchoranalysis.plugin.image.object.merge.condition that throw InitializeException

Modifier and Type	Method	Description
void	AfterCondition.initialize(Logger logger)	Initializes the condition with a logger.
void	IncreaseFeatureCondition.initialize(Logger logger)

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

Methods in org.anchoranalysis.plugin.image.task.bean.labeller that throw InitializeException

Modifier and Type	Method	Description
NoSharedState	BinaryOutcomeImageLabeller.initialize(Path pathForBinding)
ImageCSVLabellerInitialization	ImageCSVLabeller.initialize(Path pathForBinding)
abstract T	ImageLabeller.initialize(Path pathForBinding)	Initializes the labeller.
ImageLabellerStringMapInitialization<T>	ImageLabellerStringMap.initialize(Path pathForBinding)

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

Methods in org.anchoranalysis.plugin.image.task.feature.calculator that throw InitializeException

Modifier and Type	Method	Description
FeatureCalculatorMulti<T>	FeatureCalculatorFromProvider.calculatorForAll(FeatureList<T> features)	Calculates all image-features in the feature-store.

Uses of InitializeException in org.anchoranalysis.plugin.image.task.labeller

Methods in org.anchoranalysis.plugin.image.task.labeller that throw InitializeException

Modifier and Type	Method	Description
T	SharedStateFilteredImageOutput.getFilterInitialization(Path pathForBinding)	Gets the filter initialization, initializing it if necessary.

Uses of InitializeException in org.anchoranalysis.plugin.operator.feature.bean

Methods in org.anchoranalysis.plugin.operator.feature.bean that throw InitializeException

Modifier and Type	Method	Description
protected void	FromDictionary.beforeCalc(FeatureInitialization initialization)

Uses of InitializeException in org.anchoranalysis.plugin.points.bean.fitter

Methods in org.anchoranalysis.plugin.points.bean.fitter that throw InitializeException

Modifier and Type	Method	Description
void	Reference.onInitialization(PointsInitialization so)