Uses of Class
org.anchoranalysis.experiment.bean.task.Task

Packages that use Task

Package	Description
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.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.processor	Non-bean classes related to JobProcessor.
org.anchoranalysis.launcher.run.tasks	Loading and displaying pre-defined tasks.
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	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.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.plugin.mpp.bean.define	Beans related to Define involving Mark or related classes.
org.anchoranalysis.test.experiment.task	Helper classes to execute Tasks in tests.

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

Methods in org.anchoranalysis.experiment.bean.io with parameters of type Task

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

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

Methods in org.anchoranalysis.experiment.bean.processor that return Task

Modifier and Type	Method	Description
Task<T,S>	JobProcessor.getTask()	The task to be applied to inputs.

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

Modifier and Type	Method	Description
void	JobProcessor.replaceTask(Task<T,S> taskToReplace)
void	JobProcessor.setTask(Task<T,S> task)	The task to be applied to inputs.

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

Subclasses of Task in org.anchoranalysis.experiment.bean.task

Modifier and Type	Class	Description
class	TaskWithoutSharedState<T extends InputFromManager>	A particular type of task that doesn't share-state between running jobs

Uses of Task in org.anchoranalysis.experiment.io

Methods in org.anchoranalysis.experiment.io with parameters of type Task

Modifier and Type	Method	Description
void	ReplaceTask.replaceTask(Task<T,S> taskToReplace)	Replace the currently-assigned Task with another.

Uses of Task in org.anchoranalysis.experiment.task.processor

Constructors in org.anchoranalysis.experiment.task.processor with parameters of type Task

Modifier	Constructor	Description
	CallableJob(Task<T,S> task, ParametersUnbound<T,S> parametersUnbound, JobStateMonitor stateMonitor, JobDescription jobDescription, ConcurrentJobMonitor monitor, Optional<MessageLogger> loggerMonitor, int showOngoingJobsLessThan)	Constructor.

Uses of Task in org.anchoranalysis.launcher.run.tasks

Subclasses of Task in org.anchoranalysis.launcher.run.tasks

Modifier and Type	Class	Description
class	HelloWorld<S extends InputFromManager>	A dummy task that simply writes a message to all log files, specifically: 1. log file for experiment 2. log file for each input-object

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

Subclasses of Task in org.anchoranalysis.plugin.annotation.bean.aggregate

Modifier and Type	Class	Description
class	AggregateAnnotations<S extends AnnotatorStrategy>	Aggregates many per-image annotations together in form of a CSV file.

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

Subclasses of Task in org.anchoranalysis.plugin.annotation.bean.comparison

Modifier and Type	Class	Description
class	CompareAnnotations<T extends Assignment<ObjectMask>>	Task to compare a set of annotations to a segmentation or another set of annotations.

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

Subclasses of Task in org.anchoranalysis.plugin.image.task.bean

Modifier and Type	Class	Description
class	RasterTask<S,U>	An experiment that takes (primarily) a series of raster images as an input.

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

Subclasses of Task in org.anchoranalysis.plugin.image.task.bean.combine

Modifier and Type	Class	Description
class	AggregateChannelTask	Creates a an aggregated-image for each group, where each voxel-value is aggregated across each channel in each image in the group.
class	Montage	Creates a montage of images, by tiling them side-by-side.

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

Subclasses of Task in org.anchoranalysis.plugin.image.task.bean.feature

Modifier and Type	Class	Description
class	ExportFeatures<T extends InputFromManager,S,U extends FeatureInput>	Calculates features and exports them as a CSV file.

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

Subclasses of Task in org.anchoranalysis.plugin.image.task.bean.format

Modifier and Type	Class	Description
class	ConvertImageFormat	Converts each input-image to an output format, optionally changing the bit depth.

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

Subclasses of Task in org.anchoranalysis.plugin.image.task.bean.grouped

Modifier and Type	Class	Description
class	GroupedStackBase<S,T>	Base class for stacks (usually each channel from an image) that are somehow grouped-together.

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

Subclasses of Task in org.anchoranalysis.plugin.image.task.bean.grouped.histogram

Modifier and Type	Class	Description
class	ExportImageHistograms	Exports a histogram of voxel intensities as a CSV file for each channel of an image.

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

Subclasses of Task in org.anchoranalysis.plugin.image.task.bean.labeller

Modifier and Type	Class	Description
class	ImageAssignLabel<T>	Assigns a label to each image and copies into subdirectories for each label, and creates a labelling CSV.

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

Subclasses of Task in org.anchoranalysis.plugin.image.task.bean.scale

Modifier and Type	Class	Description
class	ScaleImage<S>	Base class for tasks whose primary aim is to scale (resize) an image.
class	ScaleImageCommonSize	Creates a scaled copy of images, ensuring all images have identical output size.
class	ScaleImageIndependently	Creates a scaled copy of images, treating each image independently, and without any padding or alignment.

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

Subclasses of Task in org.anchoranalysis.plugin.image.task.bean.segment

Modifier and Type	Class	Description
class	SegmentInstanceWithModel<T extends InferenceModel>	Using a model-pool, performs instance segmentation on an image producing zero, one or more objects per image.

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

Subclasses of Task in org.anchoranalysis.plugin.image.task.bean.slice

Modifier and Type	Class	Description
class	ExtractSlice	Reduces a z-stack to a single-slice by taking the optima of a feature calculated for each slice.

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

Subclasses of Task in org.anchoranalysis.plugin.io.bean.task

Modifier and Type	Class	Description
class	CombineCSV	Combines multiple CSV files into a single CSV file.
class	CopyFiles<T>	Copy files to the output-directory, possibly changing the name or performing other operations like compression in the process.
class	SummarizeBase<T extends InputFromManager,S>
class	SummarizeInputs<T extends InputFromManager>

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

Subclasses of Task in org.anchoranalysis.plugin.mpp.bean.convert

Modifier and Type	Class	Description
class	ConvertNamedChannels<T extends NamedChannelsInput,S,U extends InputFromManager>	Converts NamedChannelsInput to a variety of others to match a delegate task.

Methods in org.anchoranalysis.plugin.mpp.bean.convert that return Task

Modifier and Type	Method	Description
Task<U,S>	ConvertNamedChannels.getTask()	The underlying task that will be called, perhaps with a different input-type.

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

Modifier and Type	Method	Description
void	ConvertNamedChannels.replaceTask(Task<U,S> taskToReplace)
void	ConvertNamedChannels.setTask(Task<U,S> task)	The underlying task that will be called, perhaps with a different input-type.

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

Subclasses of Task in org.anchoranalysis.plugin.mpp.bean.define

Modifier and Type	Class	Description
class	Develop	Derives various types of outputs (images, histograms etc.) from MultiInputs.

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

Methods in org.anchoranalysis.test.experiment.task with type parameters of type Task

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.