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

Packages that use OperationFailedException

Package	Description
org.anchoranalysis.annotation.io	Reading and writing annotations to the filesystem.
org.anchoranalysis.annotation.io.assignment.generator	Generates output images to illustrate a Assignment between annotations.
org.anchoranalysis.annotation.io.bean	Beans related to reading / writing / specifying annotations.
org.anchoranalysis.bean.shared.color.scheme	Beans that create lists or indices of colors according to particular schemes.
org.anchoranalysis.core.collection	Collection-related classes with general applicability that don't belong elsewhere.
org.anchoranalysis.core.format	File formats and associated extensions.
org.anchoranalysis.core.graph	Data-structures for directed and undirected graphs, with or without an edge payload.
org.anchoranalysis.core.identifier.provider	A collection of named-elements, a NamedProvider and related operations.
org.anchoranalysis.core.identifier.provider.store	Data structures like NamedProvider with supporting for adding new elements.
org.anchoranalysis.core.index	Classes to support getting / setting / specifying unique-integers (indices) for elements.
org.anchoranalysis.core.index.range	A range of indices from minimum to maximum.
org.anchoranalysis.core.value	Encapsulating values or sets of named-values.
org.anchoranalysis.experiment.bean.io	Generic experiments that handle input and output in structured ways.
org.anchoranalysis.experiment.bean.processor	How a task is executed on multiple inputs.
org.anchoranalysis.experiment.io	Interfaces for replacing attributes of an experiment: input, output, task etc.
org.anchoranalysis.experiment.log	Helpful classes for logging.
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.session.cache.finder	Strategies to determine which child-cache (among hierarchy) to employ for a particular feature calculation.
org.anchoranalysis.feature.session.replace	Strategies on whether to reuse or invalidate a feature-input's cache.
org.anchoranalysis.image.bean.channel	Base classes for performing operations on Channels.
org.anchoranalysis.image.bean.nonbean	Classes that are used elsewhere in this package but which aren't themselves AnchorBeans.
org.anchoranalysis.image.bean.nonbean.init	Classes that aren't AnchorBeans that pertain to the initialization of image-related beans.
org.anchoranalysis.image.bean.object	Beans pertaining to ObjectMask and their collections.
org.anchoranalysis.image.bean.spatial	Beans to define entities or operate that consider Euclidian space.
org.anchoranalysis.image.bean.spatial.arrange.align	Aligning a BoundingBox to fit inside another BoundingBox.
org.anchoranalysis.image.bean.threshold	Base classes for thresholding and calculating levels for thresholding.
org.anchoranalysis.image.bean.unitvalue.distance	Converting quantities of distance between units.
org.anchoranalysis.image.core.bufferedimage	Conversions and operations involving Java AWT's BufferedImage.
org.anchoranalysis.image.core.channel.convert.attached	Converts a channel to another data-type based upon another object to which it is attached.
org.anchoranalysis.image.core.channel.convert.attached.histogram	Converts a channel to another data-type based upon a Histogram to which it is attached.
org.anchoranalysis.image.core.dimensions.size.suggestion	Suggestions on a size for an image.
org.anchoranalysis.image.core.merge	Merges two or more entities.
org.anchoranalysis.image.core.object.scale	Scaling object-collections, or lists of elements with object-representations.
org.anchoranalysis.image.core.object.scale.method	Scaling elements with an associated ObjectMask either collectively or independently.
org.anchoranalysis.image.core.points	Operations that extract points from image data entities or vice versa.
org.anchoranalysis.image.core.stack	Defines the key data object, Stack, and related classes.
org.anchoranalysis.image.core.stack.named	A collection of Stacks, each with a unique identifier as a name.
org.anchoranalysis.image.feature.bean.evaluator	Beans that define context (which feature, which energy-stack) for evaluating feature-inputs.
org.anchoranalysis.image.inference	Inference of machine learning models on images.
org.anchoranalysis.image.inference.bean.reduce	Beans to reduce the number of results that are returned from inference, by removing overlaping entities etc.
org.anchoranalysis.image.inference.bean.segment.instance	Instance-segmentation of a Stack.
org.anchoranalysis.image.inference.bean.segment.reduce	Non-bean classes to reduce the number of results that are returned from inference, by removing overlapping entities etc.
org.anchoranalysis.image.inference.segment	Non-beans pertaining to segmentation of images via model inference.
org.anchoranalysis.image.io.bean.object.draw	How to represent an object-mask in a raster that is being drawn.
org.anchoranalysis.image.io.channel.input	Non-bean classes for reading a Channel from the filesystem.
org.anchoranalysis.image.io.channel.map	Non-bean classes for a mapping of names to Channels.
org.anchoranalysis.image.io.stack.input	Non-bean classes for reading a Stack from the filesystem.
org.anchoranalysis.image.io.stack.output.box	Base classes for generators that ultimately write only a bounding-box portion of a Stack to the filesystem.
org.anchoranalysis.image.io.stack.output.generator	Base classes for generators that ultimately write a Stack to the filesystem.
org.anchoranalysis.image.io.stack.time	A time-sequence of Stacks.
org.anchoranalysis.image.voxel	Data-structures to store and manipulate image raster-data or voxels.
org.anchoranalysis.image.voxel.convert	Converting Voxels to different data-types.
org.anchoranalysis.image.voxel.iterator.neighbor.kernel	Routines for moving a KernelPointCursor around the neighboring voxels of the point.
org.anchoranalysis.image.voxel.kernel	Applying a kernel via convolution to voxels.
org.anchoranalysis.image.voxel.object	The fundamental data class that is an ObjectMask and related structures.
org.anchoranalysis.image.voxel.object.morphological.predicate	Predicates to match certain voxels as used in org.anchoranalysis.image.voxel.object.morphological.
org.anchoranalysis.image.voxel.projection	Classes for calculating differnet kind of projections of voxel values across multiple buffers.
org.anchoranalysis.image.voxel.statistics	Statistics about aggregated voxel intensities.
org.anchoranalysis.image.voxel.thresholder	Thresholding operations on voxels.
org.anchoranalysis.inference	High-level classes for performing machine learning model inference.
org.anchoranalysis.io.generator	Base-classes and utilities for generators, which write different types of objects to the file system.
org.anchoranalysis.io.input	Classes relating to creating inputs for an experiment / task.
org.anchoranalysis.io.input.csv	Classes for reading comma-separated-values (CSV) files.
org.anchoranalysis.math.equation	Solving or manipulating equations.
org.anchoranalysis.math.histogram	The Histogram data class and related operations.
org.anchoranalysis.mpp.bean.points	Operations based on sets of points.
org.anchoranalysis.mpp.bean.proposer	Proposing Marks or other data-structures with particular attributes.
org.anchoranalysis.mpp.init	Parameters used to initialize certain types of beans.
org.anchoranalysis.mpp.io.input	Non-beans for reading data structures related to marked point processes from the file system.
org.anchoranalysis.overlay.bean	Beans relating to drawing an Overlay on an image.
org.anchoranalysis.overlay.writer	Drawing an overlay on an image.
org.anchoranalysis.plugin.annotation.bean.strategy	Strategies for how to annotate an image, such label per image etc.
org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction	Morphological grayscale-reconstruction algorithm.
org.anchoranalysis.plugin.fiji.bean.threshold	Implementations of Thresholder that use FIJI.
org.anchoranalysis.plugin.image.bean.blur	Filters that perform blurring.
org.anchoranalysis.plugin.image.bean.channel.aggregator	Implementations of ConvertChannelTo and ConvertChannelToWithHistogram.
org.anchoranalysis.plugin.image.bean.histogram.threshold	Thresholding of intensity values represented in at Histogram.
org.anchoranalysis.plugin.image.bean.object.filter	Implementations of ObjectFilter.
org.anchoranalysis.plugin.image.bean.object.filter.collective	Implementations of ObjectFilter that assess each element in a collection collectively.
org.anchoranalysis.plugin.image.bean.object.filter.combine	Implementations of ObjectFilter that combine two or more other ObjectFilters.
org.anchoranalysis.plugin.image.bean.object.filter.independent	Implementations of ObjectFilter that independently assess each element in a collection.
org.anchoranalysis.plugin.image.bean.object.match	Implementations of ObjectMatcher.
org.anchoranalysis.plugin.image.bean.object.provider.merge	Implementations of ObjectCollectionProvider involving merging objects together.
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima	Minima imposition for a Watershed transformation.
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction	Grayscale reconstruction to support the Watershed transformation.
org.anchoranalysis.plugin.image.bean.object.segment.reduce	Strategies for reducing the number of elements with a list by merging/removing lower-confidence elements that overlap.
org.anchoranalysis.plugin.image.bean.scale	Implementations of ScaleCalculator for calculating a scaling-factor from dimensions.
org.anchoranalysis.plugin.image.bean.thumbnail.object	Implementations of ThumbnailFromObjects.
org.anchoranalysis.plugin.image.feature.bean.score	Implementations of VoxelScore.
org.anchoranalysis.plugin.image.feature.object.calculation.single	Implementations of CalculationPart that that process a single ObjectMask.
org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological	Implementations of CalculationPart that that process a single ObjectMask - with morphological operations.
org.anchoranalysis.plugin.image.intensity	Non-bean for operations or calculations relating to intensity.
org.anchoranalysis.plugin.image.object	Non-beans pertaining to ObjectMasks.
org.anchoranalysis.plugin.image.object.merge	Merging ObjectMasks.
org.anchoranalysis.plugin.image.object.merge.condition	Conditions for merging ObjectMasks.
org.anchoranalysis.plugin.image.object.merge.priority	Assigning priority when merging ObjectMasks.
org.anchoranalysis.plugin.image.task.bean.combine	Combining multiple images together into a single image.
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.format.convertstyle	Different approaches for converting sets of channels (RGB, independently etc.) to another image format.
org.anchoranalysis.plugin.image.task.bean.grouped	Tasks that involved stacks (usually each channel from an image) that are somehow grouped-together.
org.anchoranalysis.plugin.image.task.bean.grouped.histogram	Task(s) to export histograms of intensity values.
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.scale	Tasks to scale an image.
org.anchoranalysis.plugin.image.task.channel.aggregator	Combines multiple Channels voxel-wise to form a single aggregated Channel.
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.image.task.grouped	Non-bean classes about grouping channels or other inputs.
org.anchoranalysis.plugin.image.task.labeller	Non-bean classes about labelling images.
org.anchoranalysis.plugin.image.task.slice	Non-bean classes pertaining to combining stacks into a single stack.
org.anchoranalysis.plugin.image.task.stack	Non-bean classes pertaining to stacks and channels as used in tasks.
org.anchoranalysis.plugin.imagej.bean.threshold	Implementations of Thresholder that call ImageJ.
org.anchoranalysis.plugin.imagej.channel.provider	Implementations of ChannelProvider that call ImageJ.
org.anchoranalysis.plugin.imagej.mask	Non-bean classes involving ObjectMask that call ImageJ.
org.anchoranalysis.plugin.io.bean.file.copy.naming	Rules for preserving or changing the naming of files when copying on the file-system.
org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster	Implementations of CopyFilesNaming that perform clustering of files.
org.anchoranalysis.plugin.io.bean.input.stack	Implementations of InputManager that process Stacks.
org.anchoranalysis.plugin.io.bean.summarizer	Summarizing a set of elements into a descriptive-string.
org.anchoranalysis.plugin.io.bean.summarizer.image	Implementations of Summarizer that summarize images.
org.anchoranalysis.plugin.io.bean.summarizer.input	Implementations of Summarizer that summarize generically InputFromManagers.
org.anchoranalysis.plugin.io.bean.summarizer.path	Implementations of Summarizer that summarize generically Paths.
org.anchoranalysis.plugin.io.file.copy	Non-bean classes to help tasks in org.anchoranalysis.plugin.io.bean.file.copy.
org.anchoranalysis.plugin.io.input.path	Non-bean classes to help in processing paths.
org.anchoranalysis.plugin.io.shared	Objects used in shared-state in Tasks in this plugin.
org.anchoranalysis.plugin.mpp.bean.convert	Converting from NamedChannelsInput to the input-type expected by a Task.
org.anchoranalysis.plugin.mpp.bean.define	Beans related to Define involving Mark or related classes.
org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.maskrcnn	Decodes the outputted tensors from a Mask R-CNN implementation.
org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.text	Decodes the outputted tensors from text-segmentation models.
org.anchoranalysis.plugin.onnx.bean.object.segment.stack	Segmenting a Stack using the ONNX Runtime to produce an ObjectCollection.
org.anchoranalysis.plugin.onnx.model	Non-bean classes for running an inference model with the ONNX Runtime.
org.anchoranalysis.plugin.opencv	Plugins that call OpenCV.
org.anchoranalysis.plugin.opencv.bean.object.segment.stack	Segmentation of a Stack using OpenCV.
org.anchoranalysis.plugin.opencv.convert	Conversion to/from OpenCV data-structures.
org.anchoranalysis.plugin.opencv.segment	Non-bean classes pertaining to segmentation.
org.anchoranalysis.plugin.points.bean.fitter	Fitting geometric structures to points.
org.anchoranalysis.plugin.points.convexhull	Non-bean convex hull operations.
org.anchoranalysis.spatial.box	Axis-aligned bounding-boxes and related operations.
org.anchoranalysis.spatial.orientation	Various methods to specify the orientation (general direction) of an entity.
org.anchoranalysis.test.experiment.task	Helper classes to execute Tasks in tests.
org.anchoranalysis.test.feature.plugins.mockfeature	A mocked feature internally using a feature-calculation.

Uses of OperationFailedException in org.anchoranalysis.annotation.io

Methods in org.anchoranalysis.annotation.io that throw OperationFailedException

Modifier and Type	Method	Description
Optional<String>	AnnotationWithStrategy.label(OperationContext context)	A human-friendly textual description of the annotation, or Optional.empty() if no label is available.

Constructors in org.anchoranalysis.annotation.io that throw OperationFailedException

Modifier	Constructor	Description
	AnnotationWithStrategy(ProvidesStackInput input, T strategy)	Creates for a particular input and associated annotation strategy.

Uses of OperationFailedException in org.anchoranalysis.annotation.io.assignment.generator

Methods in org.anchoranalysis.annotation.io.assignment.generator that throw OperationFailedException

Modifier and Type	Method	Description
ColorList	AssignmentColorPool.createColors(int numberUnpaired)	Creates a list of colors to describe the assignment.

Uses of OperationFailedException in org.anchoranalysis.annotation.io.bean

Methods in org.anchoranalysis.annotation.io.bean that throw OperationFailedException

Modifier and Type	Method	Description
abstract Optional<String>	AnnotatorStrategy.annotationLabelFor(ProvidesStackInput input, OperationContext context)	A human-friendly textual description of the annotation, or Optional.empty() if no label is available.
abstract Path	AnnotatorStrategy.pathFor(ProvidesStackInput input)	The path to where an annotation file for a particular input would be located.

Uses of OperationFailedException in org.anchoranalysis.bean.shared.color.scheme

Methods in org.anchoranalysis.bean.shared.color.scheme that throw OperationFailedException

Modifier and Type	Method	Description
ColorIndex	ColorScheme.colorForEachIndex(int numberColors)	Assigns a color to each index value from a list of size numberColors.
abstract ColorList	ColorScheme.createList(int size)	Creates a sequence of related colors.
ColorList	ColorSchemeUnary.createList(int size)
ColorList	FromList.createList(int size)
ColorList	FromSingle.createList(int size)

Uses of OperationFailedException in org.anchoranalysis.core.collection

Method parameters in org.anchoranalysis.core.collection with type arguments of type OperationFailedException

Modifier and Type	Method	Description
void	MapCreateCountdown.processElement(K key, CheckedConsumer<V,OperationFailedException> operation)	Runs an operation on the element, creating if necessary, without decrementing the count.
void	MapCreateCountdown.processElementDecrement(K key, CheckedConsumer<V,OperationFailedException> operation)	Runs an operation on the element, creating if necessary, and decrementing the count.

Methods in org.anchoranalysis.core.collection that throw OperationFailedException

Modifier and Type	Method	Description
void	MapCreateCountdown.cleanUpRemaining()	Applies the clean-up function on any keys remaining in the map.
void	MapCreateCountdown.processElement(K key, CheckedConsumer<V,OperationFailedException> operation)	Runs an operation on the element, creating if necessary, without decrementing the count.
void	MapCreateCountdown.processElementDecrement(K key, CheckedConsumer<V,OperationFailedException> operation)	Runs an operation on the element, creating if necessary, and decrementing the count.

Constructor parameters in org.anchoranalysis.core.collection with type arguments of type OperationFailedException

Modifier	Constructor	Description
	MapCreateCountdown(Supplier<V> createNewElement, CheckedBiConsumer<K,V,OperationFailedException> cleanUpElement)	Creates without a comparator, using a HashMap internally.

Uses of OperationFailedException in org.anchoranalysis.core.format

Methods in org.anchoranalysis.core.format that throw OperationFailedException

Modifier and Type	Method	Description
static Path	FormatExtensions.changeExtension(Path path, NonImageFileFormat formatToChangeFrom, FileFormat formatToAssign)	Change the extension in a path.

Uses of OperationFailedException in org.anchoranalysis.core.graph

Methods in org.anchoranalysis.core.graph that throw OperationFailedException

Modifier and Type	Method	Description
void	GraphWithoutPayload.removeVertex(V vertex)	Removes a vertex and any edges connected to it.
void	GraphWithPayload.removeVertex(V vertex)	Removes a vertex and any edges connected to it.

Uses of OperationFailedException in org.anchoranalysis.core.identifier.provider

Methods in org.anchoranalysis.core.identifier.provider that throw OperationFailedException

Modifier and Type	Method	Description
default T	NamedProvider.getArbitraryElement()	Gets one element of the provider (arbitrarily).

Uses of OperationFailedException in org.anchoranalysis.core.identifier.provider.store

Methods in org.anchoranalysis.core.identifier.provider.store that return types with arguments of type OperationFailedException

Modifier and Type	Method	Description
static <T> CachedSupplier<T,OperationFailedException>	StoreSupplier.cacheResettable(StoreSupplier<T> supplier)	Memoizes (caches) the supplied object, and returning it with a CachedSupplier interface

Methods in org.anchoranalysis.core.identifier.provider.store that throw OperationFailedException

Modifier and Type	Method	Description
void	EagerEvaluationStore.add(String identifier, StoreSupplier<T> supplier)
void	LazyEvaluationStore.add(String identifier, StoreSupplier<T> supplier)
void	NamedProviderStore.add(String identifier, StoreSupplier<T> supplier)	Adds an element to the store.
T	StoreSupplier.get()	Gets the object being supplied to the store.

Uses of OperationFailedException in org.anchoranalysis.core.index

Methods in org.anchoranalysis.core.index that return OperationFailedException

Modifier and Type	Method	Description
OperationFailedException	GetOperationFailedException.asOperationFailedException()	Converts to a OperationFailedException using an identical message.

Uses of OperationFailedException in org.anchoranalysis.core.index.range

Methods in org.anchoranalysis.core.index.range that throw OperationFailedException

Modifier and Type	Method	Description
int	IndexRangeNegative.correctedEndIndex(int size)	The end-index, maybe corrected so that it is no longer negative.
int	IndexRangeNegative.correctedStartIndex(int size)	The start-index, maybe corrected so that it is no longer negative.
<T> List<T>	IndexRangeNegative.extract(int numberElements, IntFunction<T> extractIndex)	Extracts a subset of elements from a collection according to the specified index/range.
<T> List<T>	IndexRangeNegative.extract(List<T> list)	Extracts a subset of elements from a list according to the specified index/range.
static IndexRangeNegative	IndexRangeNegativeFactory.parse(String str)	Parses a string to convert it into an IndexRangeNegative.

Constructors in org.anchoranalysis.core.index.range that throw OperationFailedException

Modifier	Constructor	Description
	IndexRangeNegative(int startIndex, int endIndex)	Create with a start and end index.

Uses of OperationFailedException in org.anchoranalysis.core.value

Methods in org.anchoranalysis.core.value that throw OperationFailedException

Modifier and Type	Method	Description
void	Dictionary.putCheck(String key, double value)	Inserts a key/value pair, checking that the key doesn't already exist.
void	Dictionary.putCheck(String key, String value)	Inserts a key/value pair, checking that the key doesn't already exist.
void	Dictionary.putCheck(Dictionary dictionary)	Inserts all key/value pairs from another dictionary, checking that no key already exists.

Uses of OperationFailedException in org.anchoranalysis.experiment.bean.io

Methods in org.anchoranalysis.experiment.bean.io that throw OperationFailedException

Modifier and Type	Method	Description
void	InputOutputExperiment.replaceInputManager(InputManager<T> inputManager)
void	InputOutputExperiment.replaceOutputManager(OutputManager output)
void	InputOutputExperiment.replaceTask(Task<T,S> taskToReplace)

Uses of OperationFailedException in org.anchoranalysis.experiment.bean.processor

Methods in org.anchoranalysis.experiment.bean.processor that throw OperationFailedException

Modifier and Type	Method	Description
void	JobProcessor.replaceTask(Task<T,S> taskToReplace)

Uses of OperationFailedException in org.anchoranalysis.experiment.io

Methods in org.anchoranalysis.experiment.io that throw OperationFailedException

Modifier and Type	Method	Description
void	ReplaceInputManager.replaceInputManager(InputManager<T> inputManager)	Replace the existing @{link InputManager} associated with this class.
void	ReplaceOutputManager.replaceOutputManager(OutputManager output)	Replace the currently-assigned OutputManager with another.
void	ReplaceTask.replaceTask(Task<T,S> taskToReplace)	Replace the currently-assigned Task with another.

Uses of OperationFailedException in org.anchoranalysis.experiment.log

Methods in org.anchoranalysis.experiment.log that throw OperationFailedException

Modifier and Type	Method	Description
void	MultipleLoggers.start()
void	StatefulMessageLogger.start()	Starts logging.
void	TextFileMessageLogger.start()

Uses of OperationFailedException in org.anchoranalysis.feature.energy

Methods in org.anchoranalysis.feature.energy that throw OperationFailedException

Modifier and Type	Method	Description
EnergyStack	EnergyStack.extractSlice(int z)	Extract a particular z-slice from the EnergyStack as a new stack.
EnergyStackWithoutParameters	EnergyStackWithoutParameters.extractSlice(int z)	Extract a particular z-slice from the EnergyStackWithoutParameters as a new stack.

Uses of OperationFailedException in org.anchoranalysis.feature.initialization

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

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 OperationFailedException in org.anchoranalysis.feature.session.cache.finder

Methods in org.anchoranalysis.feature.session.cache.finder that throw OperationFailedException

Modifier and Type	Method	Description
Optional<FeatureCalculationInput<T>>	CacheTransferSource.getInputIfPresent(T input)	Gets corresponding FeatureCalculationInput for an input, if present, but doesn't create any new entry if it's absent.

Constructor parameters in org.anchoranalysis.feature.session.cache.finder with type arguments of type OperationFailedException

Modifier	Constructor	Description
	CacheTransferSource(CacheSupplier<T,OperationFailedException> cacheToSearch, Set<ChildCacheName> specificChildren)	Creates a new CacheTransferSource instance.

Uses of OperationFailedException in org.anchoranalysis.feature.session.replace

Methods in org.anchoranalysis.feature.session.replace that throw OperationFailedException

Modifier and Type	Method	Description
FeatureCalculationInput<T>	CacheAndReuseStrategy.createOrReuse(T input)
FeatureCalculationInput<T>	ReplaceStrategy.createOrReuse(T input)	Find or create a FeatureCalculationInput to associate with input.
FeatureCalculationInput<T>	ReuseSingletonStrategy.createOrReuse(T input)

Uses of OperationFailedException in org.anchoranalysis.image.bean.channel

Methods in org.anchoranalysis.image.bean.channel that throw OperationFailedException

Modifier and Type	Method	Description
void	ChannelAggregator.addChannel(Channel channel, Logger logger)	Adds a Channel to the aggregation.
protected abstract void	ChannelAggregator.addChannelAfterCheck(Channel channel)	Adds a Channel to the aggregation - after checking channel has acceptable dimensions.
Channel	ChannelAggregator.aggregatedChannel()	Retrieve or create a Channel with containing the aggregated values.

Uses of OperationFailedException in org.anchoranalysis.image.bean.nonbean

Methods in org.anchoranalysis.image.bean.nonbean that throw OperationFailedException

Modifier and Type	Method	Description
void	ConsistentChannelChecker.checkChannelType(Channel channel)	Checks that a channel has the same type (max value) as the others.

Uses of OperationFailedException in org.anchoranalysis.image.bean.nonbean.init

Methods in org.anchoranalysis.image.bean.nonbean.init that throw OperationFailedException

Modifier and Type	Method	Description
void	ImageInitialization.addDictionary(String identifier, Dictionary toAdd)	Adds a Dictionary to the corresponding named-collection of dictionaries.
void	ImageInitialization.addObjectsFrom(NamedProvider<ObjectCollection> source)	Adds all the ObjectCollections available in a NamedProvider using the corresponding identifiers.
void	ImageInitialization.addSharedObjectsDictionary(Optional<SharedObjects> sharedObjects, Optional<Dictionary> dictionary)	Adds stacks and object-collections from a SharedObjects using the respective identifiers, and also adds a Dictionary.
void	ImageInitialization.addStack(String identifier, Stack toAdd)	Adds a Stack to the corresponding named-collection of stacks.
void	ImageInitialization.addStacksFrom(NamedProvider<Stack> source)	Adds all the Stacks available in a NamedProvider using the corresponding identifiers.
<S extends InitializableBean<S, V>> void	PopulateStoreFromDefine.copyInitialize(Class<?> defineClass, NamedProviderStore<S> destination)	Copies objects of a particular class from the define and initializes.
<S extends InitializableBean<?, V> & Provider<T>, T> void	PopulateStoreFromDefine.copyProviderInitialize(Class<?> defineClass, NamedProviderStore<T> destination)	Copies objects of a particular class (which must be a Provider) from define and initializes each.
<S extends AnchorBean<S>> void	PopulateStoreFromDefine.copyWithoutInitialize(Class<?> defineClass, NamedProviderStore<S> destination)	Copies objects of a particular class from the define without performing any initialization.
void	ImageInitialization.populate(BeanInitializer<?> propertyInitializer, Define define, Logger logger)	Adds diverse entities from a Define into the corresponding name-collections.

Uses of OperationFailedException in org.anchoranalysis.image.bean.object

Methods in org.anchoranalysis.image.bean.object that throw OperationFailedException

Modifier and Type	Method	Description
abstract ObjectCollection	ObjectFilter.filter(ObjectCollection objectsToFilter, Optional<Dimensions> dimensions)	Filters an ObjectCollection to remove objects.
abstract List<MatchedObject>	ObjectMatcher.findMatch(ObjectCollection sourceObjects)	Finds matches for objects.

Uses of OperationFailedException in org.anchoranalysis.image.bean.spatial

Methods in org.anchoranalysis.image.bean.spatial that throw OperationFailedException

Modifier and Type	Method	Description
abstract ScaleFactor	ScaleCalculator.calculate(Optional<Dimensions> dimensionsToBeScaled, Optional<ImageSizeSuggestion> suggestedSize)	Calculates a scaling-factor for a source image/entity of particular dimensions.

Uses of OperationFailedException in org.anchoranalysis.image.bean.spatial.arrange.align

Methods in org.anchoranalysis.image.bean.spatial.arrange.align that throw OperationFailedException

Modifier and Type	Method	Description
BoundingBox	BoxAligner.align(BoundingBox smaller, BoundingBox larger)	Determines a BoundingBox to use for smaller BoundingBox so that it fits inside larger BoundingBox.
BoundingBox	BoxAligner.align(Extent smaller, BoundingBox larger)	Determines a BoundingBox to use for a smaller Extent so that it fits inside larger BoundingBox.
BoundingBox	BoxAligner.align(Extent smaller, Extent larger)	Determines a BoundingBox to use for a smaller Extent so that it fits inside larger Extent.
protected BoundingBox	Align.alignAfterCheck(Extent smaller, BoundingBox larger)
protected BoundingBox	Align.alignAfterCheck(Extent smaller, Extent larger)
protected abstract BoundingBox	BoxAligner.alignAfterCheck(BoundingBox smaller, BoundingBox larger)	Determines a BoundingBox to use for smaller BoundingBox so that it fits inside larger BoundingBox.
protected abstract BoundingBox	BoxAligner.alignAfterCheck(Extent smaller, BoundingBox larger)	Determines a BoundingBox to use for smaller Extent so that it fits inside larger BoundingBox.
protected abstract BoundingBox	BoxAligner.alignAfterCheck(Extent smaller, Extent larger)	Determines a BoundingBox to use for smaller Extent so that it fits inside larger Extent.
protected BoundingBox	Grow.alignAfterCheck(BoundingBox smaller, BoundingBox larger)
protected BoundingBox	Grow.alignAfterCheck(Extent smaller, BoundingBox larger)
protected BoundingBox	Grow.alignAfterCheck(Extent smaller, Extent larger)

Uses of OperationFailedException in org.anchoranalysis.image.bean.threshold

Methods in org.anchoranalysis.image.bean.threshold that throw OperationFailedException

Modifier and Type	Method	Description
abstract int	CalculateLevel.calculateLevel(Histogram histogram)	Determines a voxel intensity that can be used for thresholding.
protected int	CalculateLevelUnary.calculateLevelFromDelegate(Histogram histogram)	Determines a voxel intensity that can be used for thresholding from the delegate calculateLevel.
BinaryVoxels<UnsignedByteBuffer>	Thresholder.threshold(VoxelsUntyped voxels)	Like Thresholder.threshold(VoxelsUntyped) but using default binary-values.
BinaryVoxels<UnsignedByteBuffer>	Thresholder.threshold(VoxelsUntyped voxels, BinaryValuesByte binaryValues)	Like Thresholder.threshold(VoxelsUntyped, BinaryValuesByte, Optional, Optional) applying the thresholding to the entire set of voxels.
abstract BinaryVoxels<UnsignedByteBuffer>	Thresholder.threshold(VoxelsUntyped voxels, BinaryValuesByte binaryValues, Optional<Histogram> histogram, Optional<ObjectMask> objectMask)	Thresholds voxels (across a range of values) so that they have only binary range (i.e. two voxel values representing on and off).
BinaryVoxels<UnsignedByteBuffer>	ThresholderGlobal.threshold(VoxelsUntyped inputBuffer, BinaryValuesByte bvOut, Optional<Histogram> histogram, Optional<ObjectMask> objectMask)

Uses of OperationFailedException in org.anchoranalysis.image.bean.unitvalue.distance

Methods in org.anchoranalysis.image.bean.unitvalue.distance that throw OperationFailedException

Modifier and Type	Method	Description
double	DistancePhysical.resolve(Optional<UnitConverter> unitConverter, DirectionVector direction)
abstract double	UnitValueDistance.resolve(Optional<UnitConverter> unitConverter, DirectionVector direction)	Resolves the distance using a DirectionVector.
double	UnitValueDistance.resolve(Optional<UnitConverter> unitConverter, Point3d point1, Point3d point2)	Resolves the distance using the direction between two points of type Point3d.
double	UnitValueDistance.resolve(Optional<UnitConverter> unitConverter, Point3i point1, Point3i point2)	Resolves the distance using the direction between two points of type Point3i.
double	UnitValueDistance.resolveForAxis(Optional<UnitConverter> unitConverter, Axis axis)	Resolves the distance in a direction aligned to a particular axis.

Uses of OperationFailedException in org.anchoranalysis.image.core.bufferedimage

Methods in org.anchoranalysis.image.core.bufferedimage that throw OperationFailedException

Modifier and Type	Method	Description
static Stack	CreateStackFromBufferedImage.createFrom(BufferedImage bufferedImage)	Create a Stack by converting a BufferedImage.

Uses of OperationFailedException in org.anchoranalysis.image.core.channel.convert.attached

Methods in org.anchoranalysis.image.core.channel.convert.attached that throw OperationFailedException

Modifier and Type	Method	Description
void	ChannelConverterAttached.attachObject(S object)	Associate the convert with a particular object.

Uses of OperationFailedException in org.anchoranalysis.image.core.channel.convert.attached.histogram

Methods in org.anchoranalysis.image.core.channel.convert.attached.histogram that throw OperationFailedException

Modifier and Type	Method	Description
void	MaxIntensityFromHistogram.attachObject(Histogram histogram)
void	QuantileIntensityFromHistogram.attachObject(Histogram object)
void	UpperLowerQuantileIntensityFromHistogram.attachObject(Histogram histogram)

Uses of OperationFailedException in org.anchoranalysis.image.core.dimensions.size.suggestion

Methods in org.anchoranalysis.image.core.dimensions.size.suggestion that throw OperationFailedException

Modifier and Type	Method	Description
ScaleFactor	ImageSizeSuggestion.calculateScaleFactor(Optional<Extent> extentToBeScaled)	Calculates the scaling factor.

Uses of OperationFailedException in org.anchoranalysis.image.core.merge

Methods in org.anchoranalysis.image.core.merge that throw OperationFailedException

Modifier and Type	Method	Description
static ObjectMask	ObjectMaskMerger.merge(ObjectCollection objects)	Merges all the objects together that are found in a collection.
static BoundingBox	ObjectMaskMerger.mergeBoundingBoxes(ObjectCollection objects)	Merges all the bounding boxes of a collection of objects.

Uses of OperationFailedException in org.anchoranalysis.image.core.object.scale

Methods in org.anchoranalysis.image.core.object.scale that throw OperationFailedException

Modifier and Type	Method	Description
static <T> ScaledElements<T>	Scaler.scaleElements(List<T> elements, ScaleFactor factor, boolean overlappingObjects, Extent clipTo, AccessObjectMask<T> access)	Scales every element in a list collectively, ensuring the results remain inside a particular region.
static ScaledElements<ObjectMask>	Scaler.scaleObjects(ObjectCollection objects, ScaleFactor factor)	Scales every object-mask in a collection collectively.
static ScaledElements<ObjectMask>	Scaler.scaleObjects(ObjectCollection objects, ScaleFactor factor, boolean overlappingObjects, Optional<UnaryOperator<ObjectMask>> preOperation, Optional<UnaryOperator<ObjectMask>> postOperation)	Scales every object-mask in a collection collectively (if not overlappjng), allowing for additional manipulation before and after scaling.
static ScaledElements<ObjectMask>	Scaler.scaleObjects(ObjectCollection objects, ScaleFactor factor, boolean overlappingObjects, Extent clipTo)	Scales every object-mask in a collection collectively, ensuring the results remain inside a particular region.

Uses of OperationFailedException in org.anchoranalysis.image.core.object.scale.method

Methods in org.anchoranalysis.image.core.object.scale.method that throw OperationFailedException

Modifier and Type	Method	Description
<T> Map<T,T>	ObjectScalingMethod.scaleElements(List<T> elements, ScaleFactor scaleFactor, Optional<UnaryOperator<T>> preOperation, Optional<UnaryOperator<T>> postOperation, AccessObjectMask<T> access)	Applies a scaling factor to elements, where each element is associated with a unique ObjectMask.
default <T> Map<T,T>	ObjectScalingMethod.scaleElements(List<T> elements, ScaleFactor scaleFactor, AccessObjectMask<T> access)	Applies a scaling factor to elements, where each element is associated with a unique ObjectMask.

Uses of OperationFailedException in org.anchoranalysis.image.core.points

Methods in org.anchoranalysis.image.core.points that throw OperationFailedException

Modifier and Type	Method	Description
static BoundingBox	BoundingBoxFromPoints.fromStream(Stream<Point3i> points)	Create from a stream of Point3is.

Uses of OperationFailedException in org.anchoranalysis.image.core.stack

Method parameters in org.anchoranalysis.image.core.stack with type arguments of type OperationFailedException

Modifier and Type	Method	Description
RGBStack	RGBStack.mapChannel(CheckedUnaryOperator<Channel,OperationFailedException> mapping)	Produces a new stack with a particular mapping applied to each channel.
Stack	Stack.mapChannel(CheckedUnaryOperator<Channel,OperationFailedException> mapping)	Produces a new stack with a particular mapping applied to each channel.
Stack	Stack.mapChannelWithIndex(CheckedBiFunction<Channel,Integer,Channel,OperationFailedException> mapping)	Produces a new stack with a particular mapping applied to each channel (with an index of the channel also available).

Methods in org.anchoranalysis.image.core.stack that throw OperationFailedException

Modifier and Type	Method	Description
void	Stack.addBlankChannel()	Adds a new empty Channel in the final-most position in the list.
RGBStack	RGBStack.mapChannel(CheckedUnaryOperator<Channel,OperationFailedException> mapping)	Produces a new stack with a particular mapping applied to each channel.
Stack	Stack.mapChannel(CheckedUnaryOperator<Channel,OperationFailedException> mapping)	Produces a new stack with a particular mapping applied to each channel.
Stack	Stack.mapChannelWithIndex(CheckedBiFunction<Channel,Integer,Channel,OperationFailedException> mapping)	Produces a new stack with a particular mapping applied to each channel (with an index of the channel also available).
Optional<ObjectMask>	RGBStack.objectWithColor(RGBColor color)	Extracts an ObjectMask from a Channel of all voxels that have a particular color.

Uses of OperationFailedException in org.anchoranalysis.image.core.stack.named

Methods in org.anchoranalysis.image.core.stack.named that throw OperationFailedException

Modifier and Type	Method	Description
void	NamedStacksUniformSize.add(String identifier, Stack stack)	Adds an element to the store.
NamedStacks	NamedStacks.applyOperation(UnaryOperator<Stack> operation, Optional<Dimensions> dimensions)	Applies an operation on each Stack in the collection and returns a new derived collection.
NamedProvider<Stack>	NamedStacksSupplier.get()	Gets the NamedProvider of Stacks.

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

Methods in org.anchoranalysis.image.feature.bean.evaluator that throw OperationFailedException

Modifier and Type	Method	Description
FeatureCalculatorSingle<T>	FeatureEvaluator.createFeatureSession()	Creates session for evaluating feature optionally adding an energy-stack.
NamedFeatureCalculatorMulti<T>	FeatureListEvaluator.createFeatureSession(UnaryOperator<FeatureList<T>> addFeatures, SharedObjects sharedObjects)	Creates session for evaluating features.
Optional<EnergyStack>	FeatureEvaluator.energyStack()	The specified energy stack.

Uses of OperationFailedException in org.anchoranalysis.image.inference

Method parameters in org.anchoranalysis.image.inference with type arguments of type OperationFailedException

Modifier and Type	Method	Description
<S> S	ImageInferenceModel.performInference(T input, String inputName, List<String> outputIdentifiers, CheckedFunction<List<T>,S,OperationFailedException> convertOutput)	Performs inference on a single-input, to create an output.

Methods in org.anchoranalysis.image.inference that throw OperationFailedException

Modifier and Type	Method	Description
<S> S	ImageInferenceModel.performInference(T input, String inputName, List<String> outputIdentifiers, CheckedFunction<List<T>,S,OperationFailedException> convertOutput)	Performs inference on a single-input, to create an output.

Uses of OperationFailedException in org.anchoranalysis.image.inference.bean.reduce

Methods in org.anchoranalysis.image.inference.bean.reduce that throw OperationFailedException

Modifier and Type	Method	Description
void	ReduceObjectsGraph.removeVertex(ObjectForReduction vertex)	Removes a vertex and any edges connected to it.

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

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

Modifier and Type	Method	Description
abstract List<LabelledWithConfidence<MultiScaleObject>>	DecodeInstanceSegmentation.decode(List<T> inferenceOutput, ImageInferenceContext context)	Decodes the output tensors from inference into ObjectMasks with confidence and labels.
protected abstract T	SegmentStackIntoObjectsScaleDecode.deriveInput(Stack stack, Optional<double[]> subtractMeans)	Derives the input tensor from an image.

Uses of OperationFailedException in org.anchoranalysis.image.inference.bean.segment.reduce

Methods in org.anchoranalysis.image.inference.bean.segment.reduce that throw OperationFailedException

Modifier and Type	Method	Description
abstract ReductionOutcome<LabelledWithConfidence<T>>	ReduceElements.reduce(List<LabelledWithConfidence<T>> elements, Extent extent, ExecutionTimeRecorder executionTimeRecorder)	Reduce a list of elements (each with a confidence score and a label) to a smaller-list.

Uses of OperationFailedException in org.anchoranalysis.image.inference.segment

Methods in org.anchoranalysis.image.inference.segment that throw OperationFailedException

Modifier and Type	Method	Description
SegmentedObjects	SegmentedObjects.reduce(ReduceElements<ObjectMask> reduce, boolean separateEachLabel, ExecutionTimeRecorder executionTimeRecorder)	Reduces the segmented-objects, applying a reduction algorithm separately to each object-class.

Uses of OperationFailedException in org.anchoranalysis.image.io.bean.object.draw

Methods in org.anchoranalysis.image.io.bean.object.draw that throw OperationFailedException

Modifier and Type	Method	Description
void	Filled.drawSingle(ObjectWithProperties object, RGBStack stack, ObjectDrawAttributes attributes, int iteration, BoundingBox restrictTo)
void	Flatten.drawSingle(ObjectWithProperties object, RGBStack stack, ObjectDrawAttributes attributes, int iteration, BoundingBox restrictTo)
void	IfElse.drawSingle(ObjectWithProperties object, RGBStack stack, ObjectDrawAttributes attributes, int iteration, BoundingBox restrictTo)
void	Outline.drawSingle(ObjectWithProperties object, RGBStack stack, ObjectDrawAttributes attributes, int iteration, BoundingBox restrictTo)

Uses of OperationFailedException in org.anchoranalysis.image.io.channel.input

Methods in org.anchoranalysis.image.io.channel.input that throw OperationFailedException

Modifier and Type	Method	Description
void	NamedChannelsInput.addToStoreInferNames(NamedProviderStore<TimeSeries> stacks, int seriesIndex, Logger logger)
void	NamedChannelsInput.addToStoreWithName(String name, NamedProviderStore<TimeSeries> stacks, int seriesIndex, Logger logger)

Uses of OperationFailedException in org.anchoranalysis.image.io.channel.map

Methods in org.anchoranalysis.image.io.channel.map that throw OperationFailedException

Modifier and Type	Method	Description
void	NamedChannelsConcatenate.addAsSeparateChannels(NamedProviderStore<TimeSeries> stackCollection, int timeIndex, Logger logger)
void	NamedChannelsConcatenate.addAsSeparateChannels(NamedStacks stackCollection, int t, Logger logger)
void	NamedChannelsMap.addAsSeparateChannels(NamedProviderStore<TimeSeries> destination, int timeIndex, Logger logger)	Adds each Channel as a separate TimeSeries in a NamedProviderStore.
void	NamedChannelsMap.addAsSeparateChannels(NamedStacks destination, int timeIndex, Logger logger)	Adds each Channel as a separate Stack in a NamedStacks.
void	OpenedNamedChannels.addAsSeparateChannels(NamedProviderStore<TimeSeries> destination, int timeIndex, Logger logger)
void	OpenedNamedChannels.addAsSeparateChannels(NamedStacks destination, int timeIndex, Logger logger)

Uses of OperationFailedException in org.anchoranalysis.image.io.stack.input

Methods in org.anchoranalysis.image.io.stack.input that throw OperationFailedException

Modifier and Type	Method	Description
default void	ProvidesStackInput.addToStoreInferNames(NamedProviderStore<Stack> store, Logger logger)	Adds the current object to a named-store of stacks (using the default series).
void	ProvidesStackInput.addToStoreInferNames(NamedProviderStore<TimeSeries> stacks, int seriesIndex, Logger logger)	Adds any stacks exposed by the current element to a named-store of stacks - inferring the names of the Stacks.
void	ProvidesStackInput.addToStoreWithName(String name, NamedProviderStore<TimeSeries> stacks, int seriesIndex, Logger logger)	Adds any stacks exposed by the current element to a named-store of stacks - with a particular name.
default NamedStacks	ProvidesStackInput.asSet(Logger logger)	Exposes the input as a set of named stacks (inferring the names).
default Stack	ProvidesStackInput.asStack(Logger logger)	Exposes the input as a single Stack throw an error if more than one exists.
int	ProvidesStackInput.numberFrames()	The number of time-frames in the underlying input image.

Uses of OperationFailedException in org.anchoranalysis.image.io.stack.output.box

Methods in org.anchoranalysis.image.io.stack.output.box that throw OperationFailedException

Modifier and Type	Method	Description
Stack	ScaleableBackground.extractRegionFromStack(BoundingBox box)	Extracts a portion of a stack (flattened and maybe scaled) corresponding to a bounding-box

Uses of OperationFailedException in org.anchoranalysis.image.io.stack.output.generator

Methods in org.anchoranalysis.image.io.stack.output.generator that throw OperationFailedException

Modifier and Type	Method	Description
protected Stack	DisplayStackGenerator.convertBeforeAssign(DisplayStack element)
protected Stack	FlattenStackGenerator.convertBeforeAssign(Stack element)
protected V	RasterGeneratorBridge.convertBeforeAssign(T element)
protected abstract S	RasterGeneratorDelegateToRaster.convertBeforeAssign(T element)	Converts an element before setting it on the delegate.
protected abstract String	RasterGenerator.selectFileExtension(Stack stack, StackWriteOptions options, OutputWriteSettings settings, Optional<Logger> logger)	Selects the file-extension to use for a particular stack.
protected String	RasterGeneratorSelectFormat.selectFileExtension(Stack stack, StackWriteOptions options, OutputWriteSettings settings, Optional<Logger> logger)	Combines stack-write-options derived for a particular stack with the general write-options associated with the RasterGenerator.

Uses of OperationFailedException in org.anchoranalysis.image.io.stack.time

Methods in org.anchoranalysis.image.io.stack.time that throw OperationFailedException

Modifier and Type	Method	Description
void	ExtractFrameStore.add(String identifier, StoreSupplier<TimeSeries> supplier)

Uses of OperationFailedException in org.anchoranalysis.image.voxel

Methods in org.anchoranalysis.image.voxel that throw OperationFailedException

Modifier and Type	Method	Description
BoundedVoxels<T>	BoundedVoxels.growBuffer(Point3i growthNegative, Point3i growthPositive, Optional<Extent> clipRegion, VoxelsFactoryTypeBound<T> factory)	Grows the voxel buffer in the positive and negative directions by a certain amount.
BoundedVoxels<T>	BoundedVoxels.growToZ(int sizeZ, VoxelsFactoryTypeBound<T> factory)	Grows a single z-sliced BoundedVoxels by duplicating the slice across the z-dimension sizeZ number of times.

Uses of OperationFailedException in org.anchoranalysis.image.voxel.convert

Methods in org.anchoranalysis.image.voxel.convert that throw OperationFailedException

Modifier and Type	Method	Description
void	VoxelsConverter.copyFrom(VoxelsUntyped from, Voxels<T> to)	Copies voxels from a source (of any type) to voxels of type T.
void	VoxelsConverter.copyFromFloat(Voxels<FloatBuffer> from, Voxels<T> to)	Copies voxels from a source of type @{link FloatBuffer} to voxels of type T.
void	VoxelsConverter.copyFromUnsignedByte(Voxels<UnsignedByteBuffer> from, Voxels<T> to)	Copies voxels from a source of type @{link UnsignedByteBuffer} to voxels of type T.
void	VoxelsConverter.copyFromUnsignedInt(Voxels<UnsignedIntBuffer> from, Voxels<T> to)	Copies voxels from a source of type @{link UnsignedIntBuffer} to voxels of type T.
void	VoxelsConverter.copyFromUnsignedShort(Voxels<UnsignedShortBuffer> from, Voxels<T> to)	Copies voxels from a source of type @{link UnsignedShortBuffer} to voxels of type T.

Uses of OperationFailedException in org.anchoranalysis.image.voxel.iterator.neighbor.kernel

Methods in org.anchoranalysis.image.voxel.iterator.neighbor.kernel that throw OperationFailedException

Modifier and Type	Method	Description
static void	IterateKernelHelper.overBox(Kernel kernel, BinaryVoxels<UnsignedByteBuffer> voxels, BoundingBox box, KernelApplicationParameters parameters, ProcessKernelPointCursor processor)	Iterates over only voxels contained within a bounding-box.
static boolean	IterateKernelHelper.overBoxUntil(Kernel kernel, BinaryVoxels<UnsignedByteBuffer> voxels, BoundingBox box, KernelApplicationParameters parameters, PredicateKernelPointCursor predicate)	Iterates over only voxels contained within a bounding-box until a predicate is matched on a voxel.

Uses of OperationFailedException in org.anchoranalysis.image.voxel.kernel

Methods in org.anchoranalysis.image.voxel.kernel that throw OperationFailedException

Modifier and Type	Method	Description
static int	ApplyKernel.applyForCount(CountKernel kernel, BinaryVoxels<UnsignedByteBuffer> voxels, BoundingBox box, KernelApplicationParameters parameters)	Applies the kernel to voxels and sums the returned value.
static boolean	ApplyKernel.applyUntilPositive(CountKernel kernel, BinaryVoxels<UnsignedByteBuffer> voxels, BoundingBox box, KernelApplicationParameters parameters)	Applies the kernel to voxels until a positive value is returned, then exits with true.

Uses of OperationFailedException in org.anchoranalysis.image.voxel.object

Methods in org.anchoranalysis.image.voxel.object that throw OperationFailedException

Modifier and Type	Method	Description
ObjectMask	ObjectMask.growBuffer(Point3i growthNegative, Point3i growthPositive, Optional<Extent> clipRegion)	Grows the object-mask's voxel buffers in the positive and negative directions by a certain amount.
ObjectMask	ObjectMask.growToZ(int sizeZ)	Grows a single z-sliced ObjectMask by duplicating the slice across the z-dimension sizeZ number of times.

Uses of OperationFailedException in org.anchoranalysis.image.voxel.object.morphological.predicate

Methods in org.anchoranalysis.image.voxel.object.morphological.predicate that throw OperationFailedException

Modifier and Type	Method	Description
boolean	AcceptIterationList.accept(BinaryVoxels<UnsignedByteBuffer> voxels)
boolean	AcceptIterationPredicate.accept(BinaryVoxels<UnsignedByteBuffer> voxels)	Whether a particular voxels fulfills the condition or not.

Uses of OperationFailedException in org.anchoranalysis.image.voxel.projection

Methods in org.anchoranalysis.image.voxel.projection that throw OperationFailedException

Modifier and Type	Method	Description
<T> ProjectableBuffer<T>	Projection.create(VoxelDataType dataType, Extent extent)	Creates a buffer for the projection for a particular voxel-type and size (extent).

Uses of OperationFailedException in org.anchoranalysis.image.voxel.statistics

Methods in org.anchoranalysis.image.voxel.statistics that throw OperationFailedException

Modifier and Type	Method	Description
Histogram	VoxelStatistics.histogram()	A Histogram of all voxel values.
Histogram	VoxelStatisticsCombined.histogram()
double	VoxelStatistics.quantile(double quantile)	The voxel value corresponding to a particular quantile.
double	VoxelStatisticsFromHistogram.quantile(double quantile)

Uses of OperationFailedException in org.anchoranalysis.image.voxel.thresholder

Methods in org.anchoranalysis.image.voxel.thresholder that throw OperationFailedException

Modifier and Type	Method	Description
static BinaryVoxels<UnsignedByteBuffer>	VoxelsThresholder.threshold(VoxelsUntyped voxels, float level, BinaryValuesByte binaryValues, Optional<ObjectMask> objectMask, boolean alwaysDuplicate)	Applies thresholding to VoxelsUntyped.

Uses of OperationFailedException in org.anchoranalysis.inference

Methods in org.anchoranalysis.inference that throw OperationFailedException

Modifier and Type	Method	Description
void	InferenceModel.close()	Indicates that the model will no longer be used, and does appropriate tidying up and freeing of resources.

Uses of OperationFailedException in org.anchoranalysis.io.generator

Methods in org.anchoranalysis.io.generator that throw OperationFailedException

Modifier and Type	Method	Description
abstract String	SingleFileTypeGenerator.selectFileExtension(OutputWriteSettings settings, Optional<Logger> logger)	Selects the file/extension to be used for outputting the file.
String	SingleFileTypeGeneratorBridge.selectFileExtension(OutputWriteSettings settings, Optional<Logger> logger)

Uses of OperationFailedException in org.anchoranalysis.io.input

Methods in org.anchoranalysis.io.input that throw OperationFailedException

Modifier and Type	Method	Description
Collection<NamedFile>	InputsWithDirectory.findAllNonInputFiles()	Find all files in the input directory are not used as inputs.

Uses of OperationFailedException in org.anchoranalysis.io.input.csv

Methods in org.anchoranalysis.io.input.csv that throw OperationFailedException

Modifier and Type	Method	Description
void	ProcessCSVLine.processLine(String[] line, boolean firstLine)	Called when a single line is read by a CSV-reader to determine how the entry is further processed.

Uses of OperationFailedException in org.anchoranalysis.math.equation

Methods in org.anchoranalysis.math.equation that throw OperationFailedException

Modifier and Type	Method	Description
static QuadraticEquationSolver.QuadraticRoots	QuadraticEquationSolver.solveQuadraticEquation(double a, double b, double c)	Solves a quadratic equation in form x^2 + b^x + c = 0.

Uses of OperationFailedException in org.anchoranalysis.math.histogram

Methods in org.anchoranalysis.math.histogram that throw OperationFailedException

Modifier and Type	Method	Description
void	Histogram.addHistogram(Histogram other)	Adds the counts from another histogram to the current object.
int	Histogram.calculateMaximum()	Calculates the maximum value with non zero-count among the histogram values.
int	Histogram.calculateMinimum()	Calculates the minimum value with non zero-count among the histogram values.
int	Histogram.calculateMode()	Calculates the mode of the histogram values.
static double	HistogramStatistics.coefficientOfVariation(Histogram histogram)	Calculates the coefficient-of-variation of a distribution of values, represented by their histogram.
static double	HistogramStatistics.kurtosis(Histogram histogram)	Calculates the kurtosis of a distribution of values, represented by their histogram.
double	Histogram.mean()	Calculates the mean of the histogram values, considering their frequency.
double	Histogram.mean(double power)	Calculates the mean of the values in the distribution, if each value is raised to a power.
double	Histogram.mean(double power, double subtractValue)	Like Histogram.mean(double) but a value may be subtracted before raising to a power.
int	Histogram.quantile(double quantile)	Calculates the corresponding value for a particular quantile in the distribution of values in the histogram.
static double	HistogramStatistics.skewness(Histogram histogram)	Calculates the skewness of a distribution of values, represented by their histogram.
double	Histogram.standardDeviation()	Calculates the standard-deviation of the distribution represented by the histogram.
double	Histogram.variance()	Calculates the variance of the distribution represented by the histogram.

Uses of OperationFailedException in org.anchoranalysis.mpp.bean.points

Methods in org.anchoranalysis.mpp.bean.points that throw OperationFailedException

Modifier and Type	Method	Description
Optional<Mark>	CreateMarkFromPoints.fitMarkToPointsFromMarks(MarkCollection marks, Dimensions dimensions)	Extracts points from marks, creates a new mark, and fits this mark to the extracted points.

Uses of OperationFailedException in org.anchoranalysis.mpp.bean.proposer

Methods in org.anchoranalysis.mpp.bean.proposer that throw OperationFailedException

Modifier and Type	Method	Description
abstract double	ScalarProposer.propose(RandomNumberGenerator randomNumberGenerator, Optional<Resolution> resolution)	Proposes a scalar value based on the given parameters.

Uses of OperationFailedException in org.anchoranalysis.mpp.init

Methods in org.anchoranalysis.mpp.init that throw OperationFailedException

Modifier and Type	Method	Description
void	MarksInitialization.populate(BeanInitializer<?> initializer, Define define, Logger logger)	Populates the stores with beans from the given Define.
void	PointsInitialization.populate(BeanInitializer<?> initializer, Define define, Logger logger)	Populates the stores with beans from the given Define.

Uses of OperationFailedException in org.anchoranalysis.mpp.io.input

Methods in org.anchoranalysis.mpp.io.input that throw OperationFailedException

Modifier and Type	Method	Description
void	MultiInputSubMap.addToStore(NamedProviderStore<T> namedStore, Logger logger)	Copies all the existing entries into a NamedProviderStore.
void	OperationMap.addToStore(NamedProviderStore<T> namedStore, Logger logger)
void	StackWithMap.addToStore(NamedProviderStore<TimeSeries> stackCollection, int seriesNum, Logger logger)	Adds the main stack and other stacks to the store.
void	StackWithMap.addToStore(NamedProviderStore<TimeSeries> stackCollection, Logger logger)
void	MultiInput.addToStoreInferNames(NamedProviderStore<TimeSeries> stacks, int seriesIndex, Logger logger)
void	MultiInput.addToStoreWithName(String name, NamedProviderStore<TimeSeries> stacks, int seriesIndex, Logger logger)
void	ExportSharedObjects.copyTo(SharedObjects target, Logger logger)	Adds any exported shared objects to the target container.
void	MultiInput.copyTo(SharedObjects target, Logger logger)
StoreSupplier<T>	MultiInputSubMap.get(String name)	Retrieves an entry from the map.
StoreSupplier<T>	OperationMap.get(String name)
StoreSupplier<TimeSeries>	StackWithMap.get(String name)
int	MultiInput.numberFrames()
int	StackWithMap.numFrames()	Gets the number of frames.

Uses of OperationFailedException in org.anchoranalysis.overlay.bean

Methods in org.anchoranalysis.overlay.bean that throw OperationFailedException

Modifier and Type	Method	Description
void	DrawObject.drawCollection(ObjectCollectionWithProperties objects, RGBStack stack, ObjectDrawAttributes attributes)	Writes object-masks onto of a RGBStack - across all of the stack.
void	DrawObject.drawCollection(ObjectCollectionWithProperties objects, RGBStack stack, ObjectDrawAttributes attributes, BoundingBox boxContainer)	Writes object-masks onto of a RGBStack - within a bounding box only.
abstract void	DrawObject.drawSingle(ObjectWithProperties object, RGBStack stack, ObjectDrawAttributes attributes, int iteration, BoundingBox restrictTo)	Draws a single-object on top of a RGB-stack.

Uses of OperationFailedException in org.anchoranalysis.overlay.writer

Methods in org.anchoranalysis.overlay.writer that throw OperationFailedException

Modifier and Type	Method	Description
void	DrawOverlay.drawOverlays(ColoredOverlayCollection overlays, RGBStack stack, IdentifierGetter<Overlay> idGetter)	Draw a collection of colored-overlays on top of a RGBStack.

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

Methods in org.anchoranalysis.plugin.annotation.bean.strategy that throw OperationFailedException

Modifier and Type	Method	Description
Optional<String>	ImageLabelStrategy.annotationLabelFor(ProvidesStackInput item, OperationContext context)
Path	SinglePathStrategy.pathFor(ProvidesStackInput input)

Uses of OperationFailedException in org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction

Methods in org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction that throw OperationFailedException

Modifier and Type	Method	Description
VoxelsUntyped	GrayscaleReconstruction2DIJ.reconstruction(VoxelsUntyped mask, VoxelsUntyped marker, Optional<ObjectMask> containingMask)

Uses of OperationFailedException in org.anchoranalysis.plugin.fiji.bean.threshold

Methods in org.anchoranalysis.plugin.fiji.bean.threshold that throw OperationFailedException

Modifier and Type	Method	Description
BinaryVoxels<UnsignedByteBuffer>	ThresholderAutoIJ.threshold(VoxelsUntyped inputBuffer, BinaryValuesByte binaryValues, Optional<Histogram> histogram, Optional<ObjectMask> objectMask)

Uses of OperationFailedException in org.anchoranalysis.plugin.image.bean.blur

Methods in org.anchoranalysis.plugin.image.bean.blur that throw OperationFailedException

Modifier and Type	Method	Description
void	BlurGaussian3D.blur(VoxelsUntyped voxels, Dimensions dimensions, MessageLogger logger)
void	BlurGaussianEachSlice2D.blur(VoxelsUntyped voxels, Dimensions dimensions, MessageLogger logger)
abstract void	BlurStrategy.blur(VoxelsUntyped voxels, Dimensions dimensions, MessageLogger logger)	Applies the blur operation to the given voxels.
protected double	BlurStrategy.calculateSigma(Dimensions dimensions, MessageLogger logger)	Calculates the sigma value to use for blurring, considering the dimensions and whether sigma is in meters.

Uses of OperationFailedException in org.anchoranalysis.plugin.image.bean.channel.aggregator

Methods in org.anchoranalysis.plugin.image.bean.channel.aggregator that throw OperationFailedException

Modifier and Type	Method	Description
protected void	ProjectableBufferAggregator.addChannelAfterCheck(Channel channel)
protected ProjectableBuffer<T>	MaxProjection.create(VoxelDataType dataType, Extent extent)
protected ProjectableBuffer<T>	MeanProjection.create(VoxelDataType dataType, Extent extent)
protected ProjectableBuffer<T>	MinProjection.create(VoxelDataType dataType, Extent extent)
protected abstract ProjectableBuffer<T>	ProjectableBufferAggregator.create(VoxelDataType dataType, Extent extent)	Creates the ProjectableBuffer used for aggregation.
protected ProjectableBuffer<T>	StandardDeviationProjection.create(VoxelDataType dataType, Extent extent)

Uses of OperationFailedException in org.anchoranalysis.plugin.image.bean.histogram.threshold

Methods in org.anchoranalysis.plugin.image.bean.histogram.threshold that throw OperationFailedException

Modifier and Type	Method	Description
int	CalculateLevelRelativeToThreshold.calculateLevel(Histogram histogram)
int	ClampHistogramMax.calculateLevel(Histogram histogram)
int	EmptyHistogramConstant.calculateLevel(Histogram histogram)
int	Maximum.calculateLevel(Histogram h)
int	Minimum.calculateLevel(Histogram h)
int	Otsu.calculateLevel(Histogram histogram)
int	OtsuWeighted.calculateLevel(Histogram histogram)
int	Quantile.calculateLevel(Histogram histogram)

Uses of OperationFailedException in org.anchoranalysis.plugin.image.bean.object.filter

Methods in org.anchoranalysis.plugin.image.bean.object.filter that throw OperationFailedException

Modifier and Type	Method	Description
protected abstract void	ObjectFilterPredicate.end()	Performs any necessary cleanup after filtering is complete.
protected void	ObjectFilterRelation.end()
ObjectCollection	ObjectFilterPredicate.filter(ObjectCollection objectsToFilter, Optional<Dimensions> dimensions)
protected abstract boolean	ObjectFilterPredicate.match(ObjectMask object, Optional<Dimensions> dimensions)	A predicate condition for an object to be kept in the collection.
protected boolean	ObjectFilterRelation.match(ObjectMask object, Optional<Dimensions> dimensions)
protected abstract boolean	ObjectFilterRelation.match(ObjectMask object, Optional<Dimensions> dim, DoubleBiPredicate relation)	Performs the matching operation using the resolved relation.
protected void	ObjectFilterPredicate.start(Optional<Dimensions> dimensions, ObjectCollection objectsToFilter)	Performs any necessary initialization before filtering begins.
protected void	ObjectFilterRelation.start(Optional<Dimensions> dimensions, ObjectCollection objectsToFilter)

Uses of OperationFailedException in org.anchoranalysis.plugin.image.bean.object.filter.collective

Methods in org.anchoranalysis.plugin.image.bean.object.filter.collective that throw OperationFailedException

Modifier and Type	Method	Description
protected void	DiscardOutliers.end()
protected void	RelationWithMatches.end()
protected boolean	DiscardOutliers.match(ObjectMask object, Optional<Dimensions> dimensions)
protected boolean	RelationWithMatches.match(ObjectMask object, Optional<Dimensions> dim, DoubleBiPredicate relation)
protected void	DiscardOutliers.start(Optional<Dimensions> dimensions, ObjectCollection objectsToFilter)
protected void	RelationWithMatches.start(Optional<Dimensions> dimensions, ObjectCollection objectsToFilter)

Uses of OperationFailedException in org.anchoranalysis.plugin.image.bean.object.filter.combine

Methods in org.anchoranalysis.plugin.image.bean.object.filter.combine that throw OperationFailedException

Modifier and Type	Method	Description
ObjectCollection	And.filter(ObjectCollection objects, Optional<Dimensions> dim)
ObjectCollection	Or.filter(ObjectCollection objectsToFilter, Optional<Dimensions> dim)

Uses of OperationFailedException in org.anchoranalysis.plugin.image.bean.object.filter.independent

Methods in org.anchoranalysis.plugin.image.bean.object.filter.independent that throw OperationFailedException

Modifier and Type	Method	Description
protected void	GreaterIntersectionWith.end()
protected void	IntensityGreaterEqualThan.end()
protected void	IntersectsWith.end()
protected void	NotTouchingSceneBorder.end()
protected void	ThresholdedFeature.end()
protected boolean	GreaterIntersectionWith.match(ObjectMask object, Optional<Dimensions> dimensions)
protected boolean	IntensityGreaterEqualThan.match(ObjectMask object, Optional<Dimensions> dimensions)
protected boolean	IntersectsWith.match(ObjectMask objectToIntersectWith, Optional<Dimensions> dimensions)
protected boolean	NotTouchingSceneBorder.match(ObjectMask object, Optional<Dimensions> dimensions)
protected boolean	ThresholdedFeature.match(ObjectMask object, Optional<Dimensions> dim, DoubleBiPredicate relation)
protected void	GreaterIntersectionWith.start(Optional<Dimensions> dimensions, ObjectCollection objectsToFilter)
protected void	IntensityGreaterEqualThan.start(Optional<Dimensions> dimensions, ObjectCollection objectsToFilter)
protected void	IntersectsWith.start(Optional<Dimensions> dimensions, ObjectCollection objectsToFilter)
protected void	ThresholdedFeature.start(Optional<Dimensions> dimensions, ObjectCollection objectsToFilter)
protected void	ThresholdedVolume.start(Optional<Dimensions> dimensions, ObjectCollection objectsToFilter)

Uses of OperationFailedException in org.anchoranalysis.plugin.image.bean.object.match

Methods in org.anchoranalysis.plugin.image.bean.object.match that throw OperationFailedException

Modifier and Type	Method	Description
List<MatchedObject>	Always.findMatch(ObjectCollection sourceObjects)
List<MatchedObject>	Bridge.findMatch(ObjectCollection sourceObjects)
List<MatchedObject>	Intersection.findMatch(ObjectCollection sourceObjects)

Uses of OperationFailedException in org.anchoranalysis.plugin.image.bean.object.provider.merge

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

Modifier and Type	Method	Description
protected PayloadCalculator	MergeToIncreaseObjectFeature.createPayloadCalculator()
protected abstract PayloadCalculator	MergeWithFeature.createPayloadCalculator()	Determines the payload for any given or potential vertex.
protected AssignPriority	MergePairs.createPrioritizer()
protected AssignPriority	MergeToIncreaseObjectFeature.createPrioritizer()
protected abstract AssignPriority	MergeWithFeature.createPrioritizer()	Determines the priority (and selection criteria) used to allow merges between neighbors.
protected ObjectCollection	MergeBase.mergeMultiplex(ObjectCollection objects, MergeBase.MergeObjects mergeFunc)	Merges objects either in a container or altogether.
ObjectCollection	MergeBase.MergeObjects.mergeObjects(ObjectCollection objects)	Merges a collection of objects.
protected Resolution	MergeBase.resolutionRequired()	Gets the required Resolution.
protected Optional<UnitConverter>	MergeBase.unitConvertOptional()	Gets an optional UnitConverter based on the image resolution.

Uses of OperationFailedException in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima

Methods in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima that throw OperationFailedException

Modifier and Type	Method	Description
abstract Channel	MinimaImposition.imposeMinima(Channel channel, ObjectCollection seeds, Optional<ObjectMask> containingMask)	Imposes minima on a channel based on seed objects and an optional containing mask.
Channel	MinimaImpositionGrayscaleReconstruction.imposeMinima(Channel channel, ObjectCollection seeds, Optional<ObjectMask> containingMask)

Uses of OperationFailedException in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction

Methods in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction that throw OperationFailedException

Modifier and Type	Method	Description
abstract VoxelsUntyped	GrayscaleReconstructionByErosion.reconstruction(VoxelsUntyped mask, VoxelsUntyped marker, Optional<ObjectMask> containingMask)	Performs grayscale reconstruction of a mask image from a marker image.

Uses of OperationFailedException in org.anchoranalysis.plugin.image.bean.object.segment.reduce

Methods in org.anchoranalysis.plugin.image.bean.object.segment.reduce that throw OperationFailedException

Modifier and Type	Method	Description
ReductionOutcome<LabelledWithConfidence<ObjectMask>>	ThresholdConfidence.reduce(List<LabelledWithConfidence<ObjectMask>> elements, Extent extent, ExecutionTimeRecorder executionTimeRecorder)

Uses of OperationFailedException in org.anchoranalysis.plugin.image.bean.scale

Methods in org.anchoranalysis.plugin.image.bean.scale that throw OperationFailedException

Modifier and Type	Method	Description
ScaleFactor	ConstantScaleFactor.calculate(Optional<Dimensions> dimensionsToBeScaled, Optional<ImageSizeSuggestion> suggestedSize)
ScaleFactor	FitTo.calculate(Optional<Dimensions> dimensionsToBeScaled, Optional<ImageSizeSuggestion> suggestedSize)
ScaleFactor	Invert.calculate(Optional<Dimensions> dimensionsToBeScaled, Optional<ImageSizeSuggestion> suggestedSize)
ScaleFactor	MinimumXYResolution.calculate(Optional<Dimensions> dimensionsToBeScaled, Optional<ImageSizeSuggestion> suggestedSize)
ScaleFactor	ToDimensions.calculate(Optional<Dimensions> dimensionsToBeScaled, Optional<ImageSizeSuggestion> suggestedSize)
ScaleFactor	ToSuggested.calculate(Optional<Dimensions> dimensionsToBeScaled, Optional<ImageSizeSuggestion> suggestedSize)

Uses of OperationFailedException in org.anchoranalysis.plugin.image.bean.thumbnail.object

Methods in org.anchoranalysis.plugin.image.bean.thumbnail.object that throw OperationFailedException

Modifier and Type	Method	Description
ThumbnailBatch<ObjectCollection>	OutlinePreserveRelativeSize.start(ObjectCollection objects, StreamableCollection<BoundingBox> boundingBoxes, Optional<Stack> backgroundSource, ExecutionTimeRecorder executionTimeRecorder)
abstract ThumbnailBatch<ObjectCollection>	ThumbnailFromObjects.start(ObjectCollection objects, StreamableCollection<BoundingBox> boundingBoxes, Optional<Stack> background, ExecutionTimeRecorder executionTimeRecorder)	Initializes a batch to create thumbnails.

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

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

Modifier and Type	Method	Description
protected abstract void	CalculateLevelBase.beforeCalcSetup(Histogram histogram, int level)	Performs setup operations before calculation.
protected void	DifferenceCalculateLevelStandardDeviation.beforeCalcSetup(Histogram histogram, int level)

Uses of OperationFailedException in org.anchoranalysis.plugin.image.feature.object.calculation.single

Methods in org.anchoranalysis.plugin.image.feature.object.calculation.single that throw OperationFailedException

Modifier and Type	Method	Description
protected abstract ObjectMask	CalculateIncrementalOperationMap.applyOperation(ObjectMask object, Extent extent, boolean do3D)	Applies the incremental operation to the input object.

Uses of OperationFailedException in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological

Methods in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological that throw OperationFailedException

Modifier and Type	Method	Description
protected ObjectMask	CalculateDilationMap.applyOperation(ObjectMask object, Extent extent, boolean do3D)
protected ObjectMask	CalculateErosionMap.applyOperation(ObjectMask object, Extent extent, boolean do3D)

Uses of OperationFailedException in org.anchoranalysis.plugin.image.intensity

Methods in org.anchoranalysis.plugin.image.intensity that throw OperationFailedException

Modifier and Type	Method	Description
static Histogram	HistogramThresholder.withCalculateLevel(Histogram histogram, CalculateLevel calculateLevel)	Retains the portion of the histogram greater or equal to the calculated-level.

Uses of OperationFailedException in org.anchoranalysis.plugin.image.object

Methods in org.anchoranalysis.plugin.image.object that throw OperationFailedException

Modifier and Type	Method	Description
void	ColoredObjectCollection.addObjectsWithColor(ObjectCollectionProvider provider, RGBColor color)	Adds objects from a ObjectCollectionProvider all with one specific color
static ObjectCollection	ObjectIntersectionRemover.removeIntersectingVoxels(ObjectCollection objects, Dimensions dimensions, boolean errorDisconnectedObjects)	Removes intersecting voxels from a collection of objects.

Uses of OperationFailedException in org.anchoranalysis.plugin.image.object.merge

Methods in org.anchoranalysis.plugin.image.object.merge that throw OperationFailedException

Modifier and Type	Method	Description
List<ObjectVertex>	MergeGraph.addObjectsToGraph(ObjectCollection objects)	Adds objects to the graph.
ObjectVertex	MergeGraph.merge(TypedEdge<ObjectVertex,PrioritisedVertex> bestImprovement)	Merges two vertices in the graph.

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

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

Modifier and Type	Method	Description
boolean	AfterCondition.accept(ObjectMask source, ObjectMask destination, ObjectMask merged)	Checks if the merged object satisfies the condition.
boolean	AndCondition.accept(ObjectMask destination)
boolean	BeforeCondition.accept(ObjectMask source, ObjectMask destination, Optional<UnitConverter> unitConverter)	Checks if the source and destination objects satisfy the condition for merging.
boolean	DistanceCondition.accept(ObjectMask source, ObjectMask destination, Optional<UnitConverter> unitConverter)
boolean	IncreaseFeatureCondition.accept(ObjectMask source, ObjectMask destination, ObjectMask merged)
boolean	UpdatableBeforeCondition.accept(ObjectMask destination)	Checks if the destination object should be merged with the previously set source object.
boolean	WrapAsUpdatable.accept(ObjectMask destination)
void	AndCondition.updateSourceObject(ObjectMask source, Optional<UnitConverter> unitConverter)
void	NeighborhoodCondition.updateSourceObject(ObjectMask source, Optional<UnitConverter> unitConverter)
void	UpdatableBeforeCondition.updateSourceObject(ObjectMask source, Optional<UnitConverter> unitConverter)	Updates the source object and performs any necessary pre-computations.
void	WrapAsUpdatable.updateSourceObject(ObjectMask source, Optional<UnitConverter> unitConverter)

Uses of OperationFailedException in org.anchoranalysis.plugin.image.object.merge.priority

Methods in org.anchoranalysis.plugin.image.object.merge.priority that throw OperationFailedException

Modifier and Type	Method	Description
PrioritisedVertex	AssignPriority.assignPriority(ObjectVertex source, ObjectVertex destination, GraphLogger logger)	Assigns a priority to a potential merge between two objects.
protected abstract PrioritisedVertex	AssignPriority.assignPriorityToEdge(ObjectVertex source, ObjectVertex destination, ObjectMask merge, ErrorReporter errorReporter)	Assigns a priority to an edge between two objects.
PrioritisedVertex	AssignPriorityFromImprovement.assignPriorityToEdge(ObjectVertex source, ObjectVertex destination, ObjectMask merged, ErrorReporter errorReporter)
PrioritisedVertex	AssignPriorityFromPair.assignPriorityToEdge(ObjectVertex source, ObjectVertex destination, ObjectMask merged, ErrorReporter errorReporter)
PrioritisedVertex	Prioritizer.createPriority(ObjectVertex source, ObjectVertex destination, Logger logger)	Creates a prioritized vertex based on the source and destination vertices.

Uses of OperationFailedException in org.anchoranalysis.plugin.image.task.bean.combine

Method parameters in org.anchoranalysis.plugin.image.task.bean.combine with type arguments of type OperationFailedException

Modifier and Type	Method	Description
protected void	AggregateChannelTask.processIndividual(String name, Channel individual, boolean partOfGroup, CheckedBiConsumer<String,Channel,OperationFailedException> consumeIndividual, InputOutputContext context)

Methods in org.anchoranalysis.plugin.image.task.bean.combine that throw OperationFailedException

Modifier and Type	Method	Description
protected CheckedFunction<Channel,Channel,CreateException>	AggregateChannelTask.createChannelDeriver(ChannelSource source)
protected void	AggregateChannelTask.processIndividual(String name, Channel individual, boolean partOfGroup, CheckedBiConsumer<String,Channel,OperationFailedException> consumeIndividual, InputOutputContext context)

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

Methods in org.anchoranalysis.plugin.image.task.bean.feature.source that throw OperationFailedException

Modifier and Type	Method	Description
protected Optional<String[]>	FromImageMetadata.additionalLabelsFor(ImageMetadataInput input)
protected abstract Optional<String[]>	SingleRowPerInput.additionalLabelsFor(T input)	Additional labels for an input to include (after the identifier, and before any group labels).
abstract void	FeatureSource.calculateAndOutput(T input, FeatureCalculationContext<S> context)	Processes one input to calculate feature-results and output them to the file-system.
void	SingleRowPerInput.calculateAndOutput(T input, FeatureCalculationContext<FeatureList<S>> context)

Uses of OperationFailedException in org.anchoranalysis.plugin.image.task.bean.format.convertstyle

Methods in org.anchoranalysis.plugin.image.task.bean.format.convertstyle that throw OperationFailedException

Modifier and Type	Method	Description
abstract NamedStacks	ChannelConvertStyle.convert(Set<String> channelNames, ChannelGetterForTimepoint channelGetter, Logger logger)	Converts a particular set of channels.
NamedStacks	ExtractToRGB.convert(Set<String> channelNames, ChannelGetterForTimepoint channelGetter, Logger logger)
NamedStacks	IndependentChannels.convert(Set<String> channelNames, ChannelGetterForTimepoint channelGetter, Logger logger)
NamedStacks	RGBIfNamesMatch.convert(Set<String> channelNames, ChannelGetterForTimepoint channelGetter, Logger logger)

Uses of OperationFailedException in org.anchoranalysis.plugin.image.task.bean.grouped

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

Modifier and Type	Method	Description
protected abstract void	GroupedStackBase.processIndividual(String name, S individual, boolean partOfGroup, CheckedBiConsumer<String,S,OperationFailedException> consumeIndividual, InputOutputContext context)	Processes each derived individual element from a Channel, calling consumeIndividual one or more times.

Methods in org.anchoranalysis.plugin.image.task.bean.grouped that throw OperationFailedException

Modifier and Type	Method	Description
protected abstract CheckedFunction<Channel,S,CreateException>	GroupedStackBase.createChannelDeriver(ChannelSource source)	A function to derive the individual type used for aggregation from a Channel.
protected abstract void	GroupedStackBase.processIndividual(String name, S individual, boolean partOfGroup, CheckedBiConsumer<String,S,OperationFailedException> consumeIndividual, InputOutputContext context)	Processes each derived individual element from a Channel, calling consumeIndividual one or more times.

Uses of OperationFailedException in org.anchoranalysis.plugin.image.task.bean.grouped.histogram

Method parameters in org.anchoranalysis.plugin.image.task.bean.grouped.histogram with type arguments of type OperationFailedException

Modifier and Type	Method	Description
protected void	ExportImageHistograms.processIndividual(String name, Histogram individual, boolean partOfGroup, CheckedBiConsumer<String,Histogram,OperationFailedException> consumeIndividual, InputOutputContext context)

Methods in org.anchoranalysis.plugin.image.task.bean.grouped.histogram that throw OperationFailedException

Modifier and Type	Method	Description
protected CheckedFunction<Channel,Histogram,CreateException>	ExportImageHistograms.createChannelDeriver(ChannelSource source)
protected void	ExportImageHistograms.processIndividual(String name, Histogram individual, boolean partOfGroup, CheckedBiConsumer<String,Histogram,OperationFailedException> consumeIndividual, InputOutputContext context)

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

Methods in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels that throw OperationFailedException

Modifier and Type	Method	Description
NamedChannels	All.selectChannels(ChannelSource source, boolean checkType)
abstract NamedChannels	FromStacks.selectChannels(ChannelSource source, boolean checkType)	Takes a stack-collection and extracts a set of references to particular channels (each with a name).
NamedChannels	One.selectChannels(ChannelSource source, boolean checkType)
NamedChannels	SpecificAndRename.selectChannels(ChannelSource source, boolean checkType)

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

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

Modifier and Type	Method	Description
String	BinaryClassifierImageLabeller.labelFor(NoSharedState sharedState, ProvidesStackInput input, InputOutputContext context)	Determines the label for a given input image.
String	DescriptiveNameContainsImageLabeller.labelFor(NoSharedState sharedState, ProvidesStackInput input, InputOutputContext context)
String	ImageCSVLabeller.labelFor(ImageCSVLabellerInitialization sharedState, ProvidesStackInput input, InputOutputContext context)
abstract String	ImageLabeller.labelFor(T sharedState, ProvidesStackInput input, InputOutputContext context)	Determines a particular group-identifier (label) for an input.
String	ImageLabellerStringMap.labelFor(ImageLabellerStringMapInitialization<T> sharedState, ProvidesStackInput input, InputOutputContext context)

Uses of OperationFailedException in org.anchoranalysis.plugin.image.task.bean.scale

Methods in org.anchoranalysis.plugin.image.task.bean.scale that throw OperationFailedException

Modifier and Type	Method	Description
protected abstract Stack	ScaleImage.scaleStack(Stack stack, Optional<ImageSizeSuggestion> suggestedSize, VoxelsResizer voxelsResizer, S sharedState)	Produce a scaled version of a Stack, mapping each channel to a scaled version of itself.
protected Stack	ScaleImageCommonSize.scaleStack(Stack stack, Optional<ImageSizeSuggestion> suggestedSize, VoxelsResizer voxelsResizer, CommonSize sharedState)
protected Stack	ScaleImageIndependently.scaleStack(Stack stack, Optional<ImageSizeSuggestion> suggestedSize, VoxelsResizer voxelsResizer, NoSharedState sharedState)

Uses of OperationFailedException in org.anchoranalysis.plugin.image.task.channel.aggregator

Methods in org.anchoranalysis.plugin.image.task.channel.aggregator that throw OperationFailedException

Modifier and Type	Method	Description
void	NamedChannels.add(String name, Channel channel)	Adds a Channel with a name.

Constructors in org.anchoranalysis.plugin.image.task.channel.aggregator that throw OperationFailedException

Modifier	Constructor	Description
	NamedChannels(Stream<NamedChannels> channelsToCombine)	Creates by combining multiple existing NamedChannels.

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

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

Modifier and Type	Method	Description
CheckedSupplier<ResultsVector,OperationFailedException>	ResultsVectorWithThumbnail.getResultsVector()	Supplier for the ResultsVector.
CheckedSupplier<Optional<DisplayStack>,OperationFailedException>	ResultsVectorWithThumbnail.getThumbnail()	Supplier for the optional thumbnail DisplayStack.

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

Modifier and Type	Method	Description
void	FeatureResultsAndThumbnails.add(CheckedSupplier<LabelledResultsVector,OperationFailedException> resultToAdd, CheckedSupplier<Optional<DisplayStack>,OperationFailedException> thumbnail)	Adds results, together with a thumbnail.

Methods in org.anchoranalysis.plugin.image.task.feature that throw OperationFailedException

Modifier and Type	Method	Description
void	FeatureResultsAndThumbnails.add(CheckedSupplier<LabelledResultsVector,OperationFailedException> resultToAdd, CheckedSupplier<Optional<DisplayStack>,OperationFailedException> thumbnail)	Adds results, together with a thumbnail.
LabelledResultsVector	LabelledResultsVectorWithThumbnail.withoutThumbnail()	Exposes as a LabelledResultsVector without a thumbnail.

Constructor parameters in org.anchoranalysis.plugin.image.task.feature with type arguments of type OperationFailedException

Modifier	Constructor	Description
	ResultsVectorWithThumbnail(CheckedSupplier<ResultsVector,OperationFailedException> resultsVector)	Creates a new instance with a results vector and no thumbnail.
	ResultsVectorWithThumbnail(CheckedSupplier<ResultsVector,OperationFailedException> resultsVector, CheckedSupplier<Optional<DisplayStack>,OperationFailedException> thumbnail)	Creates a new ResultsVectorWithThumbnail instance.

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

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

Modifier and Type	Method	Description
void	CalculateFeaturesForObjects.calculateForObjects(ObjectCollectionProvider provider, LabelsForInput labelsForInput)	Calculates features for objects provided by a ObjectCollectionProvider.
void	CalculateFeaturesForObjects.calculateForObjects(ObjectCollection objects, EnergyStack energyStack, LabelsForInput labelsForInput)	Calculates the feature-results for objects, and stores the results.
FeatureCalculatorSingle<T>	FeatureCalculatorFromProvider.calculatorSingleFromProvider(FeatureListProvider<T> provider, String providerName)	Calculates a single-feature that comes from a provider (but can reference the other features from the store).
static EnergyStack	FeatureCalculatorRepeated.extractStack(ProvidesStackInput input, StackProvider stackEnergy, InputOutputContext context)	Extracts an EnergyStack from the given input and stack provider.

Constructors in org.anchoranalysis.plugin.image.task.feature.calculator that throw OperationFailedException

Modifier	Constructor	Description
	CalculateFeaturesForObjects(CombineObjectsForFeatures<T> table, InitializationWithEnergyStack initialization, boolean suppressErrors, FeatureCalculationContext<FeatureTableCalculator<T>> context)	Creates a new CalculateFeaturesForObjects.
	FeatureCalculatorFromProvider(ProvidesStackInput stackInput, Optional<StackProvider> stackEnergy, InputOutputContext context)	Creates a new FeatureCalculatorFromProvider.

Uses of OperationFailedException in org.anchoranalysis.plugin.image.task.grouped

Methods in org.anchoranalysis.plugin.image.task.grouped that throw OperationFailedException

Modifier and Type	Method	Description
void	AddToAggregateItem.add(S individual, T aggregate)	Adds an individual item to an aggregate item.
void	GroupMapByName.add(Optional<String> groupIdentifier, List<org.apache.commons.math3.util.Pair<String,S>> singleItemsToAdd)	Adds an item with a non-group identifier, and also optionally a group identifier.
void	ConsistentChannelNamesChecker.checkChannelNames(Set<String> channelNames, boolean rgb)	Checks that the channel-names are consistent.
Channel	ChannelSource.extractChannel(String stackName, boolean checkType)	Extracts a Channel from a particular Stack in stackStore.
Channel	ChannelSource.extractChannel(String stackName, boolean checkType, int index)	Extracts a Channel from a particular Stack in stackStore.
Channel	ChannelSource.extractChannel(Stack stack, boolean checkType, int index)	Extracts a Channel from a given Stack.
void	GroupMapByName.outputAnyRemainingGroups()	Outputs any groups that have not already been outputted.

Constructor parameters in org.anchoranalysis.plugin.image.task.grouped with type arguments of type OperationFailedException

Modifier	Constructor	Description
protected	GroupMapByName(String nounT, Optional<Stream<String>> groupIdentifiers, Optional<InputOutputContext> outputContext, Supplier<T> createAggregator, CheckedBiConsumer<S,T,OperationFailedException> addSingleToAggregator)	Creates a group-map.

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

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

Modifier and Type	Method	Description
String	SharedStateFilteredImageOutput.labelFor(ProvidesStackInput input, InputOutputContext context)	Determines a particular group-identifier for an input.

Uses of OperationFailedException in org.anchoranalysis.plugin.image.task.slice

Methods in org.anchoranalysis.plugin.image.task.slice that throw OperationFailedException

Modifier and Type	Method	Description
void	MontageSharedState.drawAllLabels(double ratioHeightForLabel, BoxAligner aligner)	Draw all labels that have been queued during calls to MontageSharedState.copyStackInto(org.anchoranalysis.core.functional.checked.CheckedSupplier<org.anchoranalysis.image.core.stack.RGBStack, org.anchoranalysis.io.input.InputReadFailedException>, java.lang.String, java.nio.file.Path, java.util.Optional<java.lang.String>).

Uses of OperationFailedException in org.anchoranalysis.plugin.image.task.stack

Methods in org.anchoranalysis.plugin.image.task.stack that throw OperationFailedException

Modifier and Type	Method	Description
static ImageInitialization	InitializationFactory.createWithStacks(ProvidesStackInput input, InitializationContext context)	Creates an ImageInitialization with stacks added from the input.

Uses of OperationFailedException in org.anchoranalysis.plugin.imagej.bean.threshold

Methods in org.anchoranalysis.plugin.imagej.bean.threshold that throw OperationFailedException

Modifier and Type	Method	Description
BinaryVoxels<UnsignedByteBuffer>	ThresholderSimpleFillHoles2D.threshold(VoxelsUntyped inputBuffer, BinaryValuesByte binaryValues, Optional<Histogram> histogram, Optional<ObjectMask> objectMask)

Uses of OperationFailedException in org.anchoranalysis.plugin.imagej.channel.provider

Methods in org.anchoranalysis.plugin.imagej.channel.provider that throw OperationFailedException

Modifier and Type	Method	Description
static Channel	FilterHelper.applyRankFilter(Channel channel, int radius, int filterType)	Applies a 2D rank-filter to each slice independently of a Channel.

Uses of OperationFailedException in org.anchoranalysis.plugin.imagej.mask

Methods in org.anchoranalysis.plugin.imagej.mask that throw OperationFailedException

Modifier and Type	Method	Description
static BinaryVoxels<UnsignedByteBuffer>	ApplyImageJMorphologicalOperation.applyOperation(BinaryVoxels<UnsignedByteBuffer> voxels, String command, int iterations)	Applies a specified morphological operation to the given binary voxels.
static void	ApplyImageJMorphologicalOperation.fill(BinaryVoxels<UnsignedByteBuffer> voxels)	Applies the fill operation to the given binary voxels.

Uses of OperationFailedException in org.anchoranalysis.plugin.io.bean.file.copy.naming

Methods in org.anchoranalysis.plugin.io.bean.file.copy.naming that throw OperationFailedException

Modifier and Type	Method	Description
abstract T	CopyFilesNaming.beforeCopying(Path destinationDirectory, List<FileWithDirectoryInput> inputs)	To be called once before any calls to CopyFilesNaming.destinationPath(File, DirectoryWithPrefix, int, CopyContext).
NoSharedState	CopyFilesNamingOne.beforeCopying(Path destinationDirectory, List<FileWithDirectoryInput> inputs)
NoSharedState	CopyFilesNamingWithoutSharedState.beforeCopying(Path destinationDirectory, List<FileWithDirectoryInput> inputs)

Uses of OperationFailedException in org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster

Methods in org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster that throw OperationFailedException

Modifier and Type	Method	Description
ClusterMembership	ClusterByTimestamp.beforeCopying(Path destinationDirectory, List<FileWithDirectoryInput> inputs)
String	ClusterIdentifier.name()	Derives a name for the cluster, based upon its contents.

Uses of OperationFailedException in org.anchoranalysis.plugin.io.bean.input.stack

Methods in org.anchoranalysis.plugin.io.bean.input.stack that throw OperationFailedException

Modifier and Type	Method	Description
void	ConvertNamedChannelsInputToStack.addToStoreInferNames(NamedProviderStore<TimeSeries> stacks, int seriesIndex, Logger logger)
void	ConvertNamedChannelsInputToStack.addToStoreWithName(String name, NamedProviderStore<TimeSeries> stacks, int seriesIndex, Logger logger)
int	ConvertNamedChannelsInputToStack.numberFrames()

Uses of OperationFailedException in org.anchoranalysis.plugin.io.bean.summarizer

Methods in org.anchoranalysis.plugin.io.bean.summarizer that throw OperationFailedException

Modifier and Type	Method	Description
abstract void	Summarizer.add(T element)	Adds a element to the summary.
void	SummarizerAggregate.add(T element)
void	SummarizerListMultiline.add(T element)
void	SummarizerSplitMoreThan.add(T element)
void	Summarizer.addAll(Collection<T> elements)	Adds the elements to the summary.
abstract String	Summarizer.describe()	A string summarizing this item.
String	SummarizerAggregate.describe()
String	SummarizerListMultiline.describe()
String	SummarizerSplitMoreThan.describe()
abstract boolean	Summarizer.requiresImageMetadata()	Whether a ImageMetadataInput is required as an input.
boolean	SummarizerAggregate.requiresImageMetadata()
boolean	SummarizerSplitMoreThan.requiresImageMetadata()

Uses of OperationFailedException in org.anchoranalysis.plugin.io.bean.summarizer.image

Methods in org.anchoranalysis.plugin.io.bean.summarizer.image that throw OperationFailedException

Modifier and Type	Method	Description
void	ImageSize.add(ImageMetadataInput input)
void	SummarizerImageMetadataSimple.add(ImageMetadataInput element)
String	SummarizerImageMetadata.describe()

Uses of OperationFailedException in org.anchoranalysis.plugin.io.bean.summarizer.input

Methods in org.anchoranalysis.plugin.io.bean.summarizer.input that throw OperationFailedException

Modifier and Type	Method	Description
void	SummarizerInputFromManager.add(T element)
String	SummarizerInputFromManager.describe()

Uses of OperationFailedException in org.anchoranalysis.plugin.io.bean.summarizer.path

Methods in org.anchoranalysis.plugin.io.bean.summarizer.path that throw OperationFailedException

Modifier and Type	Method	Description
void	FilePathPattern.add(Path element)
void	FileSizeStatistics.add(Path filePath)
String	FilePathPattern.describe()
String	FileSizeStatistics.describe()

Constructors in org.anchoranalysis.plugin.io.bean.summarizer.path that throw OperationFailedException

Modifier	Constructor	Description
	FilePathPattern(String... paths)	Create with one or more paths.

Uses of OperationFailedException in org.anchoranalysis.plugin.io.file.copy

Methods in org.anchoranalysis.plugin.io.file.copy that throw OperationFailedException

Modifier and Type	Method	Description
void	ClusterMembership.associateFileWithCluster(File file, long timestamp, ClusterIdentifier clusterIdentifier)	Indicates a particular file is a member of a particular cluster.

Uses of OperationFailedException in org.anchoranalysis.plugin.io.input.path

Methods in org.anchoranalysis.plugin.io.input.path that throw OperationFailedException

Modifier and Type	Method	Description
void	RootPathMap.addFromXmlFile(Path path)	Adds root-paths contained in a list of XML Beans in an xml file

Uses of OperationFailedException in org.anchoranalysis.plugin.io.shared

Methods in org.anchoranalysis.plugin.io.shared that throw OperationFailedException

Modifier and Type	Method	Description
void	RecordingCounter.recordCopiedOutput(Path source, Optional<Path> destination, int index)	Records an copy operation in the log / CSV path mapping.

Constructors in org.anchoranalysis.plugin.io.shared that throw OperationFailedException

Modifier	Constructor	Description
	RecordingCounter(Counter counter, Outputter outputter, T namingSharedState)

Uses of OperationFailedException in org.anchoranalysis.plugin.mpp.bean.convert

Methods in org.anchoranalysis.plugin.mpp.bean.convert that throw OperationFailedException

Modifier and Type	Method	Description
void	ConvertNamedChannels.replaceTask(Task<U,S> taskToReplace)

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

Methods in org.anchoranalysis.plugin.mpp.bean.define that throw OperationFailedException

Modifier and Type	Method	Description
<S> void	DefineOutputter.process(InputBound<MultiInput,S> input, DefineOutputter.Processor<ImageInitialization> operation)	Processes the input using the provided operation.
void	DefineOutputter.Processor.process(T initialization)	Processes the initialization.
S	DefineOutputterWithEnergy.ProcessWithEnergyStack.process(T initialization, EnergyStack energyStack)	Processes the initialization with an energy stack.
<S> S	DefineOutputterWithEnergy.processInput(InitializationContext context, SharedObjects sharedObjects, Optional<Dictionary> dictionary, DefineOutputterWithEnergy.ProcessWithEnergyStack<ImageInitialization,S> operation)	Processes the input with an energy stack and shared objects.
<S> void	DefineOutputterWithEnergy.processInput(ExportSharedObjects input, InitializationContext context, DefineOutputterWithEnergy.ProcessWithEnergyStack<ImageInitialization,S> operation)	Processes the input with an energy stack.

Uses of OperationFailedException in org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.maskrcnn

Methods in org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.maskrcnn that throw OperationFailedException

Modifier and Type	Method	Description
List<LabelledWithConfidence<MultiScaleObject>>	DecodeMaskRCNN.decode(List<ai.onnxruntime.OnnxTensor> inferenceOutput, ImageInferenceContext context)

Uses of OperationFailedException in org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.text

Methods in org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.text that throw OperationFailedException

Modifier and Type	Method	Description
List<LabelledWithConfidence<MultiScaleObject>>	DecodeEAST.decode(List<ai.onnxruntime.OnnxTensor> inferenceOutput, ImageInferenceContext context)

Uses of OperationFailedException in org.anchoranalysis.plugin.onnx.bean.object.segment.stack

Methods in org.anchoranalysis.plugin.onnx.bean.object.segment.stack that throw OperationFailedException

Modifier and Type	Method	Description
protected ai.onnxruntime.OnnxTensor	SegmentObjectsFromONNXModel.deriveInput(Stack stack, Optional<double[]> subtractMeans)

Uses of OperationFailedException in org.anchoranalysis.plugin.onnx.model

Method parameters in org.anchoranalysis.plugin.onnx.model with type arguments of type OperationFailedException

Modifier and Type	Method	Description
<S> S	OnnxModel.performInference(ai.onnxruntime.OnnxTensor input, String inputName, List<String> outputNames, CheckedFunction<List<ai.onnxruntime.OnnxTensor>,S,OperationFailedException> convertFunction)

Methods in org.anchoranalysis.plugin.onnx.model that throw OperationFailedException

Modifier and Type	Method	Description
void	OnnxModel.close()
<S> S	OnnxModel.performInference(ai.onnxruntime.OnnxTensor input, String inputName, List<String> outputNames, CheckedFunction<List<ai.onnxruntime.OnnxTensor>,S,OperationFailedException> convertFunction)

Uses of OperationFailedException in org.anchoranalysis.plugin.opencv

Methods in org.anchoranalysis.plugin.opencv that throw OperationFailedException

Modifier and Type	Method	Description
static List<Contour>	CVFindContours.contoursForObject(ObjectMask object)	Calculates the extreme outer contours from an ObjectMask as OpenCV defines contours.

Uses of OperationFailedException in org.anchoranalysis.plugin.opencv.bean.object.segment.stack

Methods in org.anchoranalysis.plugin.opencv.bean.object.segment.stack that throw OperationFailedException

Modifier and Type	Method	Description
protected org.opencv.core.Mat	SegmentObjectsFromTensorFlowModel.deriveInput(Stack stack, Optional<double[]> subtractMeans)

Uses of OperationFailedException in org.anchoranalysis.plugin.opencv.convert

Methods in org.anchoranalysis.plugin.opencv.convert that throw OperationFailedException

Modifier and Type	Method	Description
static Stack	ConvertFromMat.toStack(org.opencv.core.Mat mat)	Convert from an OpenCV Mat to a Stack.
static VoxelBuffer<?>	VoxelBufferFromMat.toVoxelBuffer(org.opencv.core.Mat mat, Extent extent)	Converts a Mat to a VoxelBuffer.

Uses of OperationFailedException in org.anchoranalysis.plugin.opencv.segment

Method parameters in org.anchoranalysis.plugin.opencv.segment with type arguments of type OperationFailedException

Modifier and Type	Method	Description
<S> S	OpenCVModel.performInference(org.opencv.core.Mat input, String inputName, List<String> outputNames, CheckedFunction<List<org.opencv.core.Mat>,S,OperationFailedException> convertFunction)

Methods in org.anchoranalysis.plugin.opencv.segment that throw OperationFailedException

Modifier and Type	Method	Description
<S> S	OpenCVModel.performInference(org.opencv.core.Mat input, String inputName, List<String> outputNames, CheckedFunction<List<org.opencv.core.Mat>,S,OperationFailedException> convertFunction)

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

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

Modifier and Type	Method	Description
void	PointsFitterToMark.fitPointsToMark(List<Point3f> pointsForFitter, Mark mark, Dimensions dim)	Fits a list of points to a mark using the specified points fitter.

Uses of OperationFailedException in org.anchoranalysis.plugin.points.convexhull

Methods in org.anchoranalysis.plugin.points.convexhull that throw OperationFailedException

Modifier and Type	Method	Description
static List<Point2i>	ConvexHullUtilities.convexHull2D(List<Point2i> points)	Apply a convex-hull algorithm to filter a set of points using the default minimum number of points.
static List<Point2i>	ConvexHullUtilities.convexHull2D(List<Point2i> points, int minNumberPoints)	Apply a convex-hull algorithm to filter a set of points.

Uses of OperationFailedException in org.anchoranalysis.spatial.box

Methods in org.anchoranalysis.spatial.box that throw OperationFailedException

Modifier and Type	Method	Description
BoundingBox	PointRange.toBoundingBox()	Creates a BoundingBox to just cover the range of points that have been added.

Uses of OperationFailedException in org.anchoranalysis.spatial.orientation

Methods in org.anchoranalysis.spatial.orientation that throw OperationFailedException

Modifier and Type	Method	Description
Point3d	RotationMatrix.column(int columnIndex)	Extracts a column from the rotation-matrix as a point.

Uses of OperationFailedException in org.anchoranalysis.test.experiment.task

Methods in org.anchoranalysis.test.experiment.task that throw OperationFailedException

Modifier and Type	Method	Description
<T extends InputFromManager, S, V extends Task<T, S>> void	ExecuteTaskHelper.assertExpectedTaskOutputs(List<T> inputs, V task, Path pathDirectoryOutput, String pathDirectorySaved, Iterable<String> pathsFileToCompare)	Executes a task on a multiple inputs and asserts expected outputs - with task arguments.
<T extends InputFromManager, S, V extends Task<T, S>> void	ExecuteTaskHelper.assertExpectedTaskOutputs(T input, V task, Path pathDirectoryOutput, String pathDirectorySaved, Iterable<String> pathsFileToCompare)	Executes a task on a single-input.

Uses of OperationFailedException in org.anchoranalysis.test.feature.plugins.mockfeature

Method parameters in org.anchoranalysis.test.feature.plugins.mockfeature with type arguments of type OperationFailedException

Modifier and Type	Method	Description
static void	MockFeatureWithCalculationFixture.executeAndAssertCount(int expectedCountCalc, int expectedCountExecute, CheckedRunnable<OperationFailedException> operation)	Executes an operation and asserts the expected number of calls to internal methods.

Methods in org.anchoranalysis.test.feature.plugins.mockfeature that throw OperationFailedException

Modifier and Type	Method	Description
static void	MockFeatureWithCalculationFixture.executeAndAssertCount(int expectedCountCalc, int expectedCountExecute, CheckedRunnable<OperationFailedException> operation)	Executes an operation and asserts the expected number of calls to internal methods.