Uses of Class
org.anchoranalysis.io.output.outputter.Outputter

Packages that use Outputter

Package	Description
org.anchoranalysis.experiment.bean.processor	How a task is executed on multiple inputs.
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.csv	Metadata for writing feature calculation-results in CSV format.
org.anchoranalysis.io.output.outputter	Classes for outputting to particular directories.
org.anchoranalysis.io.output.writer	Allows a generators to write element(s) to the filesystem.
org.anchoranalysis.mpp.io.output	Non-beans for writing data structures related to marked point processes from the file system.
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.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.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.labeller	Non-bean classes about labelling images.
org.anchoranalysis.plugin.image.task.stack	Non-bean classes pertaining to stacks and channels as used in tasks.
org.anchoranalysis.plugin.io.bean.task	Implementations of Task related to file-system I/O.
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.test.image.io	Utilities for testing-related reading and writing to the filesystem.

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

Methods in org.anchoranalysis.experiment.bean.processor with parameters of type Outputter

Modifier and Type	Method	Description
protected TaskStatistics	DebugDependentProcessor.execute(Outputter rootOutputter, List<T> inputs, ParametersExperiment parametersExperiment)
protected abstract TaskStatistics	JobProcessor.execute(Outputter rootOutputter, List<T> inputs, ParametersExperiment parametersExperiment)	Executes the task on all inputs.
protected TaskStatistics	ParallelProcessor.execute(Outputter rootOutputter, List<T> inputs, ParametersExperiment parametersExperiment)
protected TaskStatistics	SequentialProcessor.execute(Outputter rootOutputter, List<T> inputs, ParametersExperiment parametersExperiment)
TaskStatistics	JobProcessor.executeLogStatistics(Outputter rootOutputter, List<T> inputs, ParametersExperiment parametersExperiment)	Executes the task on all inputs and logs statistics about this to the file-systen.

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

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

Modifier and Type	Method	Description
abstract S	Task.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<T> inputs, ParametersExperiment parameters)	Called once before all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).
final NoSharedState	TaskWithoutSharedState.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<T> inputs, ParametersExperiment parameters)

Uses of Outputter in org.anchoranalysis.experiment.io

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

Modifier and Type	Method	Description
Outputter	InitializationContext.getOutputter()	An outputter that writes to the particular output-directory.

Uses of Outputter in org.anchoranalysis.experiment.task

Methods in org.anchoranalysis.experiment.task that return Outputter

Modifier and Type	Method	Description
Outputter	InputBound.getOutputter()	The Outputter associated with this input, as it is being processed as a job.
Outputter	InputOutputContextStateful.getOutputter()
Outputter	ParametersExperiment.getOutputter()	An outputter that writes to the particular output-directory.

Constructors in org.anchoranalysis.experiment.task with parameters of type Outputter

Modifier	Constructor	Description
	InputOutputContextStateful(ExecutionArguments executionArguments, Outputter outputter, ExecutionTimeRecorder executionTimeRecorder, StatefulMessageLogger logger, ErrorReporter errorReporter)	Creates with initialization arguments.

Uses of Outputter in org.anchoranalysis.feature.io.csv

Methods in org.anchoranalysis.feature.io.csv with parameters of type Outputter

Modifier and Type	Method	Description
static Optional<FeatureCSVWriter>	FeatureCSVWriter.create(FeatureCSVMetadata metadata, Outputter outputter, boolean visuallyShortenedDecimals)	Maybe creates a FeatureCSVWriter depending if the output is allowed.

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

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

Modifier and Type	Method	Description
Outputter	Outputter.deriveSubdirectory(String subdirectoryName, boolean inheritOutputRulesAndRecording)	Creates a new Outputter by appending a relative folder-path to the current Outputter
Outputter	InputOutputContext.getOutputter()	An outputter that writes to the particular output-directory.

Uses of Outputter in org.anchoranalysis.io.output.writer

Methods in org.anchoranalysis.io.output.writer that return types with arguments of type Outputter

Modifier and Type	Method	Description
Optional<Outputter>	WriterRouterErrors.createSubdirectory(String outputName, boolean inheritOutputRulesAndRecording)	Maybe creates a subdirectory for writing to.

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

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

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

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

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

Modifier and Type	Method	Description
AggregateSharedState	AggregateAnnotations.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<AnnotationWithStrategy<S>> inputs, ParametersExperiment parameters)

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

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

Modifier and Type	Method	Description
ComparisonSharedState<T>	CompareAnnotations.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<AnnotationComparisonInput<ProvidesStackInput>> inputs, ParametersExperiment parameters)

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

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

Modifier and Type	Method	Description
MontageSharedState	Montage.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<StackSequenceInput> inputs, ParametersExperiment parameters)

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

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

Modifier and Type	Method	Description
FeatureExporter<S>	ExportFeatures.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<T> inputs, ParametersExperiment parameters)

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

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

Modifier and Type	Method	Description
NoSharedState	ConvertImageFormat.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<NamedChannelsInput> inputs, ParametersExperiment parameters)

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

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

Modifier and Type	Method	Description
GroupedSharedState<S,T>	GroupedStackBase.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<ProvidesStackInput> inputs, ParametersExperiment parameters)

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

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

Modifier and Type	Method	Description
SharedStateFilteredImageOutput<T>	ImageAssignLabel.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<ProvidesStackInput> inputs, ParametersExperiment parameters)

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

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

Modifier and Type	Method	Description
CommonSize	ScaleImageCommonSize.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<StackSequenceInput> inputs, ParametersExperiment parameters)
NoSharedState	ScaleImageIndependently.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<StackSequenceInput> inputs, ParametersExperiment parameters)

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

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

Modifier and Type	Method	Description
SharedStateSegmentInstance<T>	SegmentInstanceWithModel.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan plan, List<StackSequenceInput> inputs, ParametersExperiment parameters)

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

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

Modifier and Type	Method	Description
SharedStateSelectedSlice	ExtractSlice.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<NamedChannelsInput> inputs, ParametersExperiment parameters)

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

Methods in org.anchoranalysis.plugin.image.task.labeller that return types with arguments of type Outputter

Modifier and Type	Method	Description
Optional<Outputter>	SharedStateFilteredImageOutput.getOutputterFor(String groupIdentifier)	Gets the outputter for a specific group identifier.

Constructors in org.anchoranalysis.plugin.image.task.labeller with parameters of type Outputter

Modifier	Constructor	Description
	SharedStateFilteredImageOutput(Outputter baseOutputter, ImageLabeller<T> filter, String outputNameMapping, String outputNameImages)	Creates a new SharedStateFilteredImageOutput.

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

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

Modifier	Constructor	Description
	SharedStateSelectedSlice(Outputter baseOutputter)	Creates a new instance of SharedStateSelectedSlice.

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

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

Modifier and Type	Method	Description
CSVWriter	CombineCSV.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<FileInput> inputs, ParametersExperiment parameters)
RecordingCounter<T>	CopyFiles.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<FileWithDirectoryInput> inputs, ParametersExperiment parameters)
Summarizer<S>	SummarizeBase.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<T> inputs, ParametersExperiment parameters)

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

Constructors in org.anchoranalysis.plugin.io.shared with parameters of type Outputter

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

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

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

Modifier and Type	Method	Description
SharedStateRememberConverted<U,S>	ConvertNamedChannels.beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<T> inputs, ParametersExperiment parameters)

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

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

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

Uses of Outputter in org.anchoranalysis.test.image.io

Methods in org.anchoranalysis.test.image.io that return Outputter

Modifier and Type	Method	Description
static Outputter	OutputterFixture.outputter(Optional<Path> pathTempDirectory)	Creates an Outputter instance with optionally a path to a temporary directory for outtputting files.
static Outputter	OutputterFixture.outputter(OutputManager outputManager, OutputEnabledRules outputsEnabled)	Creates an Outputter instance with a specified OutputManager and OutputEnabledRules.