Uses of Interface
org.anchoranalysis.io.output.outputter.InputOutputContext

Packages that use InputOutputContext

Package	Description
org.anchoranalysis.experiment.bean.task	Defines a task, which is a set of operations run on an input, that may or may not generate an output.
org.anchoranalysis.experiment.io	Interfaces for replacing attributes of an experiment: input, output, task etc.
org.anchoranalysis.experiment.task	Non-bean classes related to a Task.
org.anchoranalysis.feature.io.results	Writes feature-calculation results in different formats, also grouped results.
org.anchoranalysis.image.io	Reading and writing of image-related data objects to and from the filesystem.
org.anchoranalysis.image.io.bean.object.feature	Beans to specify the outputting of features into CSV from a ObjectCollection.
org.anchoranalysis.io.output.outputter	Classes for outputting to particular directories.
org.anchoranalysis.plugin.annotation.bean.aggregate	Beans to combine two or more annotations.
org.anchoranalysis.plugin.annotation.bean.comparison	Task to compare a set of annotations to a segmentation or another set of annotations.
org.anchoranalysis.plugin.annotation.bean.comparison.assigner	Pairs annotations from two different sets, creating an assignment of some type.
org.anchoranalysis.plugin.image.task.bean	A parent package for many different kinds of tasks.
org.anchoranalysis.plugin.image.task.bean.combine	Combining multiple images together into a single image.
org.anchoranalysis.plugin.image.task.bean.feature	Tasks pertaining to Features.
org.anchoranalysis.plugin.image.task.bean.format	Tasks for converting image-formats.
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.labeller	Associating labels with images.
org.anchoranalysis.plugin.image.task.bean.scale	Tasks to scale an image.
org.anchoranalysis.plugin.image.task.bean.segment	Tasks to segment an image.
org.anchoranalysis.plugin.image.task.bean.slice	Tasks that process on one or more slices from a z-stack.
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.segment	Non-bean classes for image-segmentation.
org.anchoranalysis.plugin.io.bean.task	Implementations of Task related to file-system I/O.
org.anchoranalysis.plugin.mpp.bean.convert	Converting from NamedChannelsInput to the input-type expected by a Task.
org.anchoranalysis.test.image	Testing utilities and fixtures with no greater downstream dependency than anchor-image-io or anchor-io-bioformats or anchor-imagej.

Uses of InputOutputContext in org.anchoranalysis.experiment.bean.task

Methods in org.anchoranalysis.experiment.bean.task with parameters of type InputOutputContext

Modifier and Type	Method	Description
abstract void	Task.afterAllJobsAreExecuted(S sharedState, InputOutputContext context)	Called once after all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).
final void	TaskWithoutSharedState.afterAllJobsAreExecuted(NoSharedState sharedState, InputOutputContext context)

Uses of InputOutputContext in org.anchoranalysis.experiment.io

Methods in org.anchoranalysis.experiment.io that return InputOutputContext

Modifier and Type	Method	Description
InputOutputContext	InitializationContext.getInputOutput()	The input-output context.

Constructors in org.anchoranalysis.experiment.io with parameters of type InputOutputContext

Modifier	Constructor	Description
	InitializationContext(InputOutputContext inputOutputContext)	Create with an InputOutputContext.
	InitializationContext(InputOutputContext inputOutput, Optional<ImageSizeSuggestion> suggestedSize)	Creates a new InitializationContext instance.

Uses of InputOutputContext in org.anchoranalysis.experiment.task

Classes in org.anchoranalysis.experiment.task that implement InputOutputContext

Modifier and Type	Class	Description
class	InputOutputContextStateful	This exists as an implementation of InputOutputContext that exposes a StatefulMessageLogger.

Uses of InputOutputContext in org.anchoranalysis.feature.io.results

Methods in org.anchoranalysis.feature.io.results with parameters of type InputOutputContext

Modifier and Type	Method	Description
void	LabelledResultsCollector.flushAndClose(Optional<NamedFeatureStore<FeatureInputResults>> featuresAggregate, boolean includeGroups, Function<InputOutputContext,FeatureCSVWriterFactory> csvWriterCreator, FeatureOutputMetadata outputMetadata, InputOutputContext context)	Writes any queued (but not yet written elements to the file-system), and closes open file-handles.

Method parameters in org.anchoranalysis.feature.io.results with type arguments of type InputOutputContext

Modifier and Type	Method	Description
void	LabelledResultsCollector.flushAndClose(Optional<NamedFeatureStore<FeatureInputResults>> featuresAggregate, boolean includeGroups, Function<InputOutputContext,FeatureCSVWriterFactory> csvWriterCreator, FeatureOutputMetadata outputMetadata, InputOutputContext context)	Writes any queued (but not yet written elements to the file-system), and closes open file-handles.

Uses of InputOutputContext in org.anchoranalysis.image.io

Methods in org.anchoranalysis.image.io with parameters of type InputOutputContext

Modifier and Type	Method	Description
static ImageInitialization	ImageInitializationFactory.create(InputOutputContext context)	Create from an InputOutputContext - without any suggested size.
static ImageInitialization	ImageInitializationFactory.create(InputOutputContext context, Optional<ImageSizeSuggestion> suggestedSize)	Create from an InputOutputContext - with a suggested size.

Uses of InputOutputContext in org.anchoranalysis.image.io.bean.object.feature

Methods in org.anchoranalysis.image.io.bean.object.feature with parameters of type InputOutputContext

Modifier and Type	Method	Description
void	OutputFeatureTable.output(InputOutputContext context)	Outputs the feature-table.

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

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

Modifier and Type	Method	Description
InputOutputContext	InputOutputContextSubdirectoryCache.get(Optional<String> subdirectoryName)	Gets (from the cache if it's already there) a context for a subdirectory of given-name
default InputOutputContext	InputOutputContext.maybeSubdirectory(Optional<String> subdirectoryName, boolean inheritOutputRulesAndRecording)	Optionally creates a new context like with subdirectory(java.lang.String, boolean) but only if a directory-name is defined
default InputOutputContext	InputOutputContext.subdirectory(String subdirectoryName, boolean inheritOutputRulesAndRecording)	Creates a new context that writes instead to a subdirectory.

Constructors in org.anchoranalysis.io.output.outputter with parameters of type InputOutputContext

Modifier	Constructor	Description
	InputOutputContextSubdirectoryCache(InputOutputContext parentContext, boolean inheritOutputRulesAndRecording)	Creates a new InputOutputContextSubdirectoryCache instance.

Uses of InputOutputContext in org.anchoranalysis.plugin.annotation.bean.aggregate

Methods in org.anchoranalysis.plugin.annotation.bean.aggregate with parameters of type InputOutputContext

Modifier and Type	Method	Description
void	AggregateAnnotations.afterAllJobsAreExecuted(AggregateSharedState sharedState, InputOutputContext context)

Uses of InputOutputContext in org.anchoranalysis.plugin.annotation.bean.comparison

Methods in org.anchoranalysis.plugin.annotation.bean.comparison with parameters of type InputOutputContext

Modifier and Type	Method	Description
void	CompareAnnotations.afterAllJobsAreExecuted(ComparisonSharedState<T> sharedState, InputOutputContext context)

Uses of InputOutputContext in org.anchoranalysis.plugin.annotation.bean.comparison.assigner

Methods in org.anchoranalysis.plugin.annotation.bean.comparison.assigner with parameters of type InputOutputContext

Modifier and Type	Method	Description
abstract T	AnnotationComparisonAssigner.createAssignment(ObjectsToCompare objectsToCompare, Dimensions dimensions, boolean useMIP, InputOutputContext context)	Creates an assignment based on the objects to compare.
OverlappingObjects	FeatureCostAssigner.createAssignment(ObjectsToCompare objectsToCompare, Dimensions dimensions, boolean useMIP, InputOutputContext context)
ObjectVoxelIntersection	MaskIntersectionAssigner.createAssignment(ObjectsToCompare objectsToCompare, Dimensions dimensions, boolean useMIP, InputOutputContext context)

Uses of InputOutputContext in org.anchoranalysis.plugin.image.task.bean

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

Modifier and Type	Method	Description
protected abstract U	RasterTask.createSharedStateJob(InputOutputContext context)	Creates a shared-state for the duration of a particular input-job.
abstract void	RasterTask.doStack(InputBound<NamedChannelsInput,S> input, U sharedStateJob, int seriesIndex, int numberSeries, InputOutputContext context)	Processes one stack from a series.
abstract void	RasterTask.endSeries(S sharedStateTask, U sharedStateJob, InputOutputContext context)	Ends processing of a series.
abstract void	RasterTask.startSeries(S sharedStateTask, U sharedStateJob, InputOutputContext context)	Starts processing of a series.

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

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

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

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

Methods in org.anchoranalysis.plugin.image.task.bean.feature with parameters of type InputOutputContext

Modifier and Type	Method	Description
void	ExportFeatures.afterAllJobsAreExecuted(FeatureExporter<S> sharedState, InputOutputContext context)
FeatureExporterContext	ExportFeaturesStyle.deriveContext(InputOutputContext context)	Derives a FeatureExporterContext from the current style and given context.

Uses of InputOutputContext in org.anchoranalysis.plugin.image.task.bean.format

Methods in org.anchoranalysis.plugin.image.task.bean.format with parameters of type InputOutputContext

Modifier and Type	Method	Description
void	ConvertImageFormat.afterAllJobsAreExecuted(NoSharedState sharedState, InputOutputContext context)
protected OutputSequenceIndexed<Stack,String>	ConvertImageFormat.createSharedStateJob(InputOutputContext context)	Sets a new output-sequence for the series.
void	ConvertImageFormat.doStack(InputBound<NamedChannelsInput,NoSharedState> input, OutputSequenceIndexed<Stack,String> sharedStateJob, int seriesIndex, int numberSeries, InputOutputContext context)
void	ConvertImageFormat.endSeries(NoSharedState sharedStateTask, OutputSequenceIndexed<Stack,String> sharedStateJob, InputOutputContext context)
void	ConvertImageFormat.startSeries(NoSharedState sharedStateTask, OutputSequenceIndexed<Stack,String> sharedStateJob, InputOutputContext context)

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

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

Modifier and Type	Method	Description
void	GroupedStackBase.afterAllJobsAreExecuted(GroupedSharedState<S,T> sharedState, InputOutputContext context)
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 InputOutputContext in org.anchoranalysis.plugin.image.task.bean.grouped.histogram

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

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

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

Methods in org.anchoranalysis.plugin.image.task.bean.labeller with parameters of type InputOutputContext

Modifier and Type	Method	Description
void	ImageAssignLabel.afterAllJobsAreExecuted(SharedStateFilteredImageOutput<T> sharedState, InputOutputContext context)
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 InputOutputContext in org.anchoranalysis.plugin.image.task.bean.scale

Methods in org.anchoranalysis.plugin.image.task.bean.scale with parameters of type InputOutputContext

Modifier and Type	Method	Description
void	ScaleImage.afterAllJobsAreExecuted(S sharedState, InputOutputContext context)

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

Methods in org.anchoranalysis.plugin.image.task.bean.segment with parameters of type InputOutputContext

Modifier and Type	Method	Description
void	SegmentInstanceWithModel.afterAllJobsAreExecuted(SharedStateSegmentInstance<T> sharedState, InputOutputContext context)

Uses of InputOutputContext in org.anchoranalysis.plugin.image.task.bean.slice

Methods in org.anchoranalysis.plugin.image.task.bean.slice with parameters of type InputOutputContext

Modifier and Type	Method	Description
void	ExtractSlice.afterAllJobsAreExecuted(SharedStateSelectedSlice sharedState, InputOutputContext context)

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

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

Modifier and Type	Method	Description
InputOutputContext	FeatureCalculationContext.getContext()	The input-output context for the operation.
InputOutputContext	FeatureExporterContext.getContext()	Context for reading from or writing outputs to the file-system.

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

Modifier and Type	Method	Description
void	FeatureExporter.closeAndWriteOutputs(Optional<NamedFeatureStore<FeatureInputResults>> featuresAggregate, boolean includeGroups, Function<InputOutputContext,FeatureCSVWriterFactory> csvWriterCreator, InputOutputContext context)	Writes all the results that have been collected as a CSV file, and closes open I/O handles and memory structures.
FeatureCalculationContext<S>	FeatureExporter.createCalculationContext(Optional<String> groupName, ExecutionTimeRecorder executionTimeRecorder, InputOutputContext ioContext)	Creates a FeatureCalculationContext for calculating features to later use this exporter.
void	FeatureResultsAndThumbnails.writeGroupedResults(Optional<NamedFeatureStore<FeatureInputResults>> featuresAggregate, boolean includeGroups, Function<InputOutputContext,FeatureCSVWriterFactory> csvWriterCreator, InputOutputContext context)	Writes all the results that have been collected as a CSV file.

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

Modifier and Type	Method	Description
void	FeatureExporter.closeAndWriteOutputs(Optional<NamedFeatureStore<FeatureInputResults>> featuresAggregate, boolean includeGroups, Function<InputOutputContext,FeatureCSVWriterFactory> csvWriterCreator, InputOutputContext context)	Writes all the results that have been collected as a CSV file, and closes open I/O handles and memory structures.
void	FeatureResultsAndThumbnails.writeGroupedResults(Optional<NamedFeatureStore<FeatureInputResults>> featuresAggregate, boolean includeGroups, Function<InputOutputContext,FeatureCSVWriterFactory> csvWriterCreator, InputOutputContext context)	Writes all the results that have been collected as a CSV file.

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

Modifier	Constructor	Description
	FeatureCalculationContext(FeatureResultsAndThumbnails results, S rowSource, FeatureNameList featureNames, Optional<String> groupGeneratorName, ExecutionTimeRecorder executionTimeRecorder, boolean suppressErrors, InputOutputContext context)	Creates a new FeatureCalculationContext.
	FeatureExporterContext(InputOutputContext context, boolean removeNaNColumns, boolean visuallyShortenDecimals, boolean suppressErrors)	Creates a new FeatureExporterContext instance.

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

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

Modifier and Type	Method	Description
static EnergyStack	FeatureCalculatorRepeated.extractStack(ProvidesStackInput input, StackProvider stackEnergy, InputOutputContext context)	Extracts an EnergyStack from the given input and stack provider.

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

Modifier	Constructor	Description
	FeatureCalculatorFromProvider(ProvidesStackInput stackInput, Optional<StackProvider> stackEnergy, InputOutputContext context)	Creates a new FeatureCalculatorFromProvider.

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

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

Modifier and Type	Method	Description
protected abstract void	GroupMapByName.outputGroupIntoSubdirectory(Collection<Map.Entry<String,T>> namedAggregators, Function<Boolean,InputOutputContext> createContext, Optional<String> outputNameSingle)	Output a particular group into a subdirectory.

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

Methods in org.anchoranalysis.plugin.image.task.labeller with parameters of type InputOutputContext

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

Uses of InputOutputContext in org.anchoranalysis.plugin.image.task.segment

Methods in org.anchoranalysis.plugin.image.task.segment with parameters of type InputOutputContext

Modifier and Type	Method	Description
FeatureCalculationContext<FeatureTableCalculator<FeatureInputSingleObject>>	SharedStateSegmentInstance.createCalculationContext(ExecutionTimeRecorder executionTimeRecorder, InputOutputContext ioContext)	Creates a FeatureCalculationContext for calculating features to later use this exporter.

Uses of InputOutputContext in org.anchoranalysis.plugin.io.bean.task

Methods in org.anchoranalysis.plugin.io.bean.task with parameters of type InputOutputContext

Modifier and Type	Method	Description
void	CombineCSV.afterAllJobsAreExecuted(CSVWriter writer, InputOutputContext context)
void	CopyFiles.afterAllJobsAreExecuted(RecordingCounter<T> sharedState, InputOutputContext context)
void	SummarizeBase.afterAllJobsAreExecuted(Summarizer<S> sharedState, InputOutputContext context)

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

Methods in org.anchoranalysis.plugin.mpp.bean.convert with parameters of type InputOutputContext

Modifier and Type	Method	Description
void	ConvertNamedChannels.afterAllJobsAreExecuted(SharedStateRememberConverted<U,S> sharedState, InputOutputContext context)

Uses of InputOutputContext in org.anchoranalysis.test.image

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

Modifier and Type	Method	Description
static InputOutputContext	InputOutputContextFixture.withLogger(Logger logger)	Creates an InputOutputContext with a specified logger.
static InputOutputContext	InputOutputContextFixture.withSuppressedLogger()	Creates an InputOutputContext with a suppressed logger.
static InputOutputContext	InputOutputContextFixture.withSuppressedLogger(Path modelDir)	Creates an InputOutputContext with a suppressed logger and a specified model directory.