Uses of Class
org.anchoranalysis.core.time.OperationContext

Packages that use OperationContext

Package	Description
org.anchoranalysis.annotation.io	Reading and writing annotations to the filesystem.
org.anchoranalysis.annotation.io.bean	Beans related to reading / writing / specifying annotations.
org.anchoranalysis.annotation.io.bean.comparer	What to compare an annotation (ground truth) against?
org.anchoranalysis.annotation.io.image	Reading and writing whole-image label annotations.
org.anchoranalysis.core.serialize	Utilities for serializing and deserializing objects.
org.anchoranalysis.image.bean.spatial.arrange	Beans to specify how to form a single-image by spatially combining other images.
org.anchoranalysis.image.bean.spatial.arrange.fill	Montages images together to completely fill the available space, while preserving aspect ratio.
org.anchoranalysis.image.bean.spatial.arrange.overlay	Combining other images through overlaying.
org.anchoranalysis.image.bean.spatial.arrange.tile	Combining other images through tiling.
org.anchoranalysis.image.io.bean.stack.metadata.reader	Bean classes for reading ImageMetadata from the file-system.
org.anchoranalysis.image.io.bean.stack.reader	Bean classes for reading raster-files from the filesystem.
org.anchoranalysis.image.io.object.input	Non-bean classes for reading an ObjectCollection from the filesystem.
org.anchoranalysis.image.io.stack.input	Non-bean classes for reading a Stack from the filesystem.
org.anchoranalysis.io.input.bean	Beans related to collecting inputs from the file-system for an experiment.
org.anchoranalysis.io.output.outputter	Classes for outputting to particular directories.
org.anchoranalysis.mpp.proposer	Non-bean classes for proposing Marks or other data-structures with particular attributes.
org.anchoranalysis.plugin.annotation.bean.comparer	Comparing the similarity of annotations from two images to each other.
org.anchoranalysis.plugin.annotation.bean.strategy	Strategies for how to annotate an image, such label per image etc.
org.anchoranalysis.plugin.image.feature.bean.object.combine	Features from combinations of ObjectMasks.
org.anchoranalysis.plugin.image.task.bean.combine	Combining multiple images together into a single image.
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.feature	Non-bean classes pertaining to Features as used in tasks.
org.anchoranalysis.plugin.image.task.stack	Non-bean classes pertaining to stacks and channels as used in tasks.
org.anchoranalysis.plugin.io.bean.metadata.reader	Implementations of ImageMetadataReader.
org.anchoranalysis.test	Testing utilities and fixtures with no greater downstream dependency than anchor-core.

Uses of OperationContext in org.anchoranalysis.annotation.io

Methods in org.anchoranalysis.annotation.io with parameters of type OperationContext

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.
Optional<T>	AnnotationReader.read(Path path, OperationContext context)	Reads an annotation, if possible, from the file-system.

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

Methods in org.anchoranalysis.annotation.io.bean with parameters of type OperationContext

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.

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

Methods in org.anchoranalysis.annotation.io.bean.comparer with parameters of type OperationContext

Modifier and Type	Method	Description
List<NameValue<Stack>>	MultipleComparer.createComparisonStacks(AnnotationWithMarks annotation, DisplayStack background, Path annotationPath, ColorScheme colorScheme, Path modelDirectory, OperationContext context, boolean debugMode)	Creates a Stack illustrating the comparison between annotation and each source in sources.
abstract Findable<ObjectCollection>	ComparableSource.loadAsObjects(Path reference, Dimensions dimensions, boolean debugMode, OperationContext context)	Loads the source of elements from the file-system and converts to a ObjectCollection.

Uses of OperationContext in org.anchoranalysis.annotation.io.image

Methods in org.anchoranalysis.annotation.io.image with parameters of type OperationContext

Modifier and Type	Method	Description
Optional<ImageLabelAnnotation>	ImageLabelAnnotationReader.read(Path path, OperationContext context)

Uses of OperationContext in org.anchoranalysis.core.serialize

Methods in org.anchoranalysis.core.serialize with parameters of type OperationContext

Modifier and Type	Method	Description
T	Deserializer.deserialize(Path filePath, OperationContext context)	Deserializes a representation of an object stored on the filesystem.
T	DictionaryDeserializer.deserialize(Path filePath, OperationContext context)
T	ObjectInputStreamDeserializer.deserialize(Path filePath, OperationContext context)
T	XStreamDeserializer.deserialize(Path filePath, OperationContext context)

Uses of OperationContext in org.anchoranalysis.image.bean.spatial.arrange

Methods in org.anchoranalysis.image.bean.spatial.arrange with parameters of type OperationContext

Modifier and Type	Method	Description
StackArrangement	Single.arrangeStacks(Iterator<Extent> extents, OperationContext context)
abstract StackArrangement	StackArranger.arrangeStacks(Iterator<Extent> extents, OperationContext context)	Arranges stacks to that they fit together in a single raster.
RGBStack	StackArranger.combine(List<RGBStack> stacks, VoxelsResizer resizer, OperationContext context)	Creates a new RGBStack of voxel data type unsigned byte that is a combination of other RGBStacks.
RGBStack	StackArranger.combine(List<RGBStack> stacks, VoxelsResizer resizer, ChannelFactorySingleType factory, OperationContext context)	Creates a new RGBStack that is a combination of other RGBStacks.

Uses of OperationContext in org.anchoranalysis.image.bean.spatial.arrange.fill

Methods in org.anchoranalysis.image.bean.spatial.arrange.fill with parameters of type OperationContext

Modifier and Type	Method	Description
StackArrangement	Fill.arrangeStacks(Iterator<Extent> extents, OperationContext context)

Uses of OperationContext in org.anchoranalysis.image.bean.spatial.arrange.overlay

Methods in org.anchoranalysis.image.bean.spatial.arrange.overlay with parameters of type OperationContext

Modifier and Type	Method	Description
StackArrangement	Overlay.arrangeStacks(Iterator<Extent> extents, OperationContext context)

Uses of OperationContext in org.anchoranalysis.image.bean.spatial.arrange.tile

Methods in org.anchoranalysis.image.bean.spatial.arrange.tile with parameters of type OperationContext

Modifier and Type	Method	Description
StackArrangement	Tile.arrangeStacks(Iterator<Extent> extents, OperationContext context)

Uses of OperationContext in org.anchoranalysis.image.io.bean.stack.metadata.reader

Methods in org.anchoranalysis.image.io.bean.stack.metadata.reader with parameters of type OperationContext

Modifier and Type	Method	Description
ImageMetadata	FromStackReader.openFile(Path path, StackReader defaultStackReader, OperationContext context)
abstract ImageMetadata	ImageMetadataReader.openFile(Path path, StackReader defaultStackReader, OperationContext context)	Opens a file containing one or more images but does not read an image.

Uses of OperationContext in org.anchoranalysis.image.io.bean.stack.reader

Methods in org.anchoranalysis.image.io.bean.stack.reader with parameters of type OperationContext

Modifier and Type	Method	Description
Stack	StackReader.readStack(Path path, OperationContext context)	Opens a file at path that should contain only a single-stack.

Uses of OperationContext in org.anchoranalysis.image.io.object.input

Methods in org.anchoranalysis.image.io.object.input with parameters of type OperationContext

Modifier and Type	Method	Description
static ObjectCollection	ObjectCollectionReader.createFromPath(Path path, OperationContext context)	Reads an object-collection from a path (or path prefix) trying different methods to read the objects.

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

Methods in org.anchoranalysis.image.io.stack.input with parameters of type OperationContext

Modifier and Type	Method	Description
static Mask	MaskReader.openMask(StackReader stackReader, Path path, BinaryValuesInt binaryValues, OperationContext context)	Utility functions for opening a single-channeled stack as a Mask.

Uses of OperationContext in org.anchoranalysis.io.input.bean

Methods in org.anchoranalysis.io.input.bean that return OperationContext

Modifier and Type	Method	Description
OperationContext	InputManagerParameters.getOperationContext()	Allows for logging and recording the execution-time of particular operations.

Constructors in org.anchoranalysis.io.input.bean with parameters of type OperationContext

Modifier	Constructor	Description
	InputManagerParameters(OperationContext operationContext)	Create with only a OperationContext, and using sensible default values for the other fields.
	InputManagerParameters(InputContextParameters inputContext, OperationContext operationContext)	Creates a new InputManagerParameters instance.

Uses of OperationContext in org.anchoranalysis.io.output.outputter

Methods in org.anchoranalysis.io.output.outputter that return OperationContext

Modifier and Type	Method	Description
default OperationContext	InputOutputContext.operationContext()	Creates a OperationContext based upon the state in this class.

Uses of OperationContext in org.anchoranalysis.mpp.proposer

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

Modifier and Type	Method	Description
OperationContext	ProposerContext.getOperationContext()	Operation context for the current operation.

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

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

Uses of OperationContext in org.anchoranalysis.plugin.annotation.bean.comparer

Methods in org.anchoranalysis.plugin.annotation.bean.comparer with parameters of type OperationContext

Modifier and Type	Method	Description
Findable<ObjectCollection>	MaskAsObject.loadAsObjects(Path reference, Dimensions dimensions, boolean debugMode, OperationContext context)
Findable<ObjectCollection>	Objects.loadAsObjects(Path filePathSource, Dimensions dimensions, boolean debugMode, OperationContext context)

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

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

Modifier and Type	Method	Description
Optional<String>	ImageLabelStrategy.annotationLabelFor(ProvidesStackInput item, OperationContext context)
Optional<String>	MarkProposerStrategy.annotationLabelFor(ProvidesStackInput item, OperationContext operationContext)
static Optional<ImageLabelAnnotation>	ReadAnnotationFromFile.readAssumeExists(Path path, OperationContext context)	Reads an ImageLabelAnnotation from a file, assuming the file exists.
static Optional<ImageLabelAnnotation>	ReadAnnotationFromFile.readCheckExists(Path path, OperationContext context)	Reads an ImageLabelAnnotation from a file if it exists.

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

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

Modifier and Type	Method	Description
ListWithThumbnails<T,ObjectCollection>	CombineObjectsForFeatures.deriveInputsStartBatch(ObjectCollection objects, EnergyStack energyStack, boolean thumbnailsEnabled, OperationContext context)	Derives a list of inputs (i.e. rows in a feature table) and starts a batch of related thumbnail generation.

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

Methods in org.anchoranalysis.plugin.image.task.bean.combine with parameters of type OperationContext

Modifier and Type	Method	Description
protected GroupMapByName<Channel,ChannelAggregator>	AggregateChannelTask.createGroupMap(ConsistentChannelChecker channelChecker, Optional<Stream<String>> groupIdentifiers, Optional<InputOutputContext> outputContext, OperationContext operationContext)

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

Methods in org.anchoranalysis.plugin.image.task.bean.grouped with parameters of type OperationContext

Modifier and Type	Method	Description
protected abstract GroupMapByName<S,T>	GroupedStackBase.createGroupMap(ConsistentChannelChecker channelChecker, Optional<Stream<String>> groupIdentifiers, Optional<InputOutputContext> outputContext, OperationContext operationContext)	Creates a map for the storing an aggregate-data-object for each group.

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

Methods in org.anchoranalysis.plugin.image.task.bean.grouped.histogram with parameters of type OperationContext

Modifier and Type	Method	Description
protected GroupMapByName<Histogram,Histogram>	ExportImageHistograms.createGroupMap(ConsistentChannelChecker channelChecker, Optional<Stream<String>> groupIdentifiers, Optional<InputOutputContext> outputContext, OperationContext operationContext)

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

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

Modifier and Type	Method	Description
OperationContext	FeatureCalculationContext.getOperationContext()	Gets the operation context.

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

Constructors in org.anchoranalysis.plugin.image.task.stack with parameters of type OperationContext

Modifier	Constructor	Description
	ImageSizePrereader(ImageMetadataReader imageMetadataReader, StackReader stackReader, OperationContext context)	Creates a new ImageSizePrereader instance.

Uses of OperationContext in org.anchoranalysis.plugin.io.bean.metadata.reader

Methods in org.anchoranalysis.plugin.io.bean.metadata.reader with parameters of type OperationContext

Modifier and Type	Method	Description
ImageMetadata	AlwaysReject.openFile(Path path, StackReader defaultStackReader, OperationContext context)
ImageMetadata	InferFromHeader.openFile(Path path, StackReader defaultStackReader, OperationContext context)

Uses of OperationContext in org.anchoranalysis.test

Methods in org.anchoranalysis.test that return OperationContext

Modifier and Type	Method	Description
static OperationContext	LoggerFixture.suppressedOperationContext()	An OperationContext containing a logger that doesn't output anything.