Uses of Interface
org.anchoranalysis.io.input.InputFromManager

Packages that use InputFromManager

Package	Description
org.anchoranalysis.annotation.io	Reading and writing annotations to the filesystem.
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	Non-bean classes related to a Task.
org.anchoranalysis.experiment.task.processor	Non-bean classes related to JobProcessor.
org.anchoranalysis.image.io.bean.stack.reader	Bean classes for reading raster-files from the filesystem.
org.anchoranalysis.image.io.channel.input	Non-bean classes for reading a Channel from the filesystem.
org.anchoranalysis.image.io.stack.input	Non-bean classes for reading a Stack from the filesystem.
org.anchoranalysis.io.input	Classes relating to creating inputs for an experiment / task.
org.anchoranalysis.io.input.bean	Beans related to collecting inputs from the file-system for an experiment.
org.anchoranalysis.io.input.file	Non-bean classes that relate to using files during inputting.
org.anchoranalysis.launcher.run.tasks	Loading and displaying pre-defined tasks.
org.anchoranalysis.mpp.io.input	Non-beans for reading data structures related to marked point processes from the file system.
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.comparison	Non-bean classes for comparing two sets of annotations.
org.anchoranalysis.plugin.image.task.bean.feature	Tasks pertaining to Features.
org.anchoranalysis.plugin.image.task.bean.feature.source	Source of rows in feature-tables with FeatureSource and derived classes.
org.anchoranalysis.plugin.io.bean.input	Implementations of InputManager.
org.anchoranalysis.plugin.io.bean.input.files	InputManagers that accept a set of named-files.
org.anchoranalysis.plugin.io.bean.input.filter	Implementations of InputManager that filter inputs.
org.anchoranalysis.plugin.io.bean.input.stack	Implementations of InputManager that process Stacks.
org.anchoranalysis.plugin.io.bean.summarizer.input	Implementations of Summarizer that summarize generically InputFromManagers.
org.anchoranalysis.plugin.io.bean.task	Implementations of Task related to file-system I/O.
org.anchoranalysis.plugin.io.input.filter	Non-bean classes to help tasks in org.anchoranalysis.plugin.io.bean.input.filter.
org.anchoranalysis.plugin.mpp.bean.convert	Converting from NamedChannelsInput to the input-type expected by a Task.
org.anchoranalysis.plugin.mpp.shared	Shared-state use across tasks in this JAR.
org.anchoranalysis.test.experiment.task	Helper classes to execute Tasks in tests.

Uses of InputFromManager in org.anchoranalysis.annotation.io

Classes in org.anchoranalysis.annotation.io that implement InputFromManager

Modifier and Type	Class	Description
class	AnnotationWithStrategy<T extends AnnotatorStrategy>	One particular annotation, associated with its strategy.

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

Classes in org.anchoranalysis.experiment.bean.io with type parameters of type InputFromManager

Modifier and Type	Class	Description
class	InputOutputExperiment<T extends InputFromManager,S>	An experiment that uses both an InputManager to specify inputs and a OutputManager to specify outputting.

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

Classes in org.anchoranalysis.experiment.bean.processor with type parameters of type InputFromManager

Modifier and Type	Class	Description
class	DebugDependentProcessor<T extends InputFromManager,S>	Executes different processors depending on whether we are in debug mode or not.
class	JobProcessor<T extends InputFromManager,S>	Base class for a method to apply a task on inputs.
class	ParallelProcessor<T extends InputFromManager,S>	Executes jobs in parallel across cores on the system.
class	SequentialProcessor<T extends InputFromManager,S>	Executes jobs sequentially, without any parallelism.

Method parameters in org.anchoranalysis.experiment.bean.processor with type arguments of type InputFromManager

Modifier and Type	Method	Description
boolean	JobProcessor.isInputCompatibleWith(Class<? extends InputFromManager> inputClass)	Is an input-type compatible with this particular task?

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

Classes in org.anchoranalysis.experiment.bean.task with type parameters of type InputFromManager

Modifier and Type	Class	Description
class	Task<T extends InputFromManager,S>	Encapsulates some kind of processing to be performed on a set of inputs.
class	TaskWithoutSharedState<T extends InputFromManager>	A particular type of task that doesn't share-state between running jobs

Method parameters in org.anchoranalysis.experiment.bean.task with type arguments of type InputFromManager

Modifier and Type	Method	Description
boolean	Task.isInputCompatibleWith(Class<? extends InputFromManager> inputClass)	Is an input-object type compatible with this particular task?

Uses of InputFromManager in org.anchoranalysis.experiment.io

Classes in org.anchoranalysis.experiment.io with type parameters of type InputFromManager

Modifier and Type	Interface	Description
interface	ReplaceInputManager<T extends InputFromManager>	Indicates and provides a mechanism that the InputManager can be replaced.
interface	ReplaceTask<T extends InputFromManager,S>	Indicates and provides a mechanism that the Task can be replaced.

Uses of InputFromManager in org.anchoranalysis.experiment.task

Method parameters in org.anchoranalysis.experiment.task with type arguments of type InputFromManager

Modifier and Type	Method	Description
void	InputTypesExpected.add(Class<? extends InputFromManager> inputTypeClass)	Appends an input-type class to the existing list.
boolean	InputTypesExpected.doesClassInheritFromAny(Class<? extends InputFromManager> childClass)	Does the child-class inherit from any one of expected input-types?

Constructor parameters in org.anchoranalysis.experiment.task with type arguments of type InputFromManager

Modifier	Constructor	Description
	InputTypesExpected(Class<? extends InputFromManager> inputTypeClass)	Creates with the class of the input-type.

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

Classes in org.anchoranalysis.experiment.task.processor with type parameters of type InputFromManager

Modifier and Type	Class	Description
class	CallableJob<T extends InputFromManager,S>	A job derived from a Task that can be placed on different threads

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

Classes in org.anchoranalysis.image.io.bean.stack.reader with type parameters of type InputFromManager

Modifier and Type	Class	Description
class	InputManagerWithStackReader<T extends InputFromManager>	Extends an InputManager to add a StackReader bean property.

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

Classes in org.anchoranalysis.image.io.channel.input that implement InputFromManager

Modifier and Type	Class	Description
class	NamedChannelsInput	Provides a set of channels as an input, with each channel having a name.
class	NamedChannelsInputPart	One part of a NamedChannelsInput that can be combined with others.

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

Subinterfaces of InputFromManager in org.anchoranalysis.image.io.stack.input

Modifier and Type	Interface	Description
interface	ProvidesStackInput	Base class for inputs which somehow eventually send up providing stacks, with or without names.
interface	StackSequenceInput	Provides a single stack (or a time series of such stacks) as an input

Classes in org.anchoranalysis.image.io.stack.input that implement InputFromManager

Modifier and Type	Class	Description
class	ImageMetadataInput	An input that provides a ImageMetadata but only lazily when first called.

Uses of InputFromManager in org.anchoranalysis.io.input

Classes in org.anchoranalysis.io.input with type parameters of type InputFromManager

Modifier and Type	Class	Description
class	InputFromManagerDelegate<T extends InputFromManager>	A base class for InputFromManager-implementing classes that delegate to another.
class	InputsWithDirectory<T extends InputFromManager>	All inputs for an experiment, together with any parent directory which is specified as a parent for these inputs.

Classes in org.anchoranalysis.io.input that implement InputFromManager

Modifier and Type	Class	Description
class	InputFromManagerDelegate<T extends InputFromManager>	A base class for InputFromManager-implementing classes that delegate to another.

Methods in org.anchoranalysis.io.input with type parameters of type InputFromManager

Modifier and Type	Method	Description
<S extends InputFromManager> InputsWithDirectory<S>	InputsWithDirectory.map(Function<T,S> mapFunction)	Creates a new InputsWithDirectory which is the result of mapping the existing inputs.
<S extends InputFromManager, E extends Exception> InputsWithDirectory<S>	InputsWithDirectory.map(CheckedFunction<T,S,E> mapFunction, Class<? extends E> throwableClass)	Creates a new InputsWithDirectory which is the result of mapping the existing inputs.
<S extends InputFromManager> InputsWithDirectory<S>	InputsWithDirectory.withInputs(List<S> inputsToAssign)	Changes the inputs, but preserves the directory.

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

Classes in org.anchoranalysis.io.input.bean with type parameters of type InputFromManager

Modifier and Type	Class	Description
class	InputManager<T extends InputFromManager>	Base class for describing the inputs.
class	InputManagerUnary<T extends InputFromManager>	Base class for an InputManager that delegates to another InputManager with the same input-type.

Uses of InputFromManager in org.anchoranalysis.io.input.file

Classes in org.anchoranalysis.io.input.file that implement InputFromManager

Modifier and Type	Class	Description
class	FileInput	An input pertaining to a single file on the file-system.
class	FileWithDirectoryInput	An input pertaining to a single file on the file-system - and a directory in which it resides.
class	SingleFileInputBase	A base class for inputs that refer to a single file.

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

Classes in org.anchoranalysis.launcher.run.tasks with type parameters of type InputFromManager

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 InputFromManager in org.anchoranalysis.mpp.io.input

Classes in org.anchoranalysis.mpp.io.input that implement InputFromManager

Modifier and Type	Class	Description
class	MultiInput	An input to an experiment that combines a particular Stack with other types of entities.

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

Classes in org.anchoranalysis.plugin.annotation.bean.comparison with type parameters of type InputFromManager

Modifier and Type	Class	Description
class	AnnotationComparisonInputManager<T extends InputFromManager>	An input manager for annotation comparison that extends InputManagerWithStackReader.

Uses of InputFromManager in org.anchoranalysis.plugin.annotation.comparison

Classes in org.anchoranalysis.plugin.annotation.comparison with type parameters of type InputFromManager

Modifier and Type	Class	Description
class	AnnotationComparisonInput<T extends InputFromManager>	Input for annotation comparison, containing sources to compare and associated metadata.

Classes in org.anchoranalysis.plugin.annotation.comparison that implement InputFromManager

Modifier and Type	Class	Description
class	AnnotationComparisonInput<T extends InputFromManager>	Input for annotation comparison, containing sources to compare and associated metadata.

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

Classes in org.anchoranalysis.plugin.image.task.bean.feature with type parameters of type InputFromManager

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 InputFromManager in org.anchoranalysis.plugin.image.task.bean.feature.source

Classes in org.anchoranalysis.plugin.image.task.bean.feature.source with type parameters of type InputFromManager

Modifier and Type	Class	Description
class	FeatureSource<T extends InputFromManager,S,U extends FeatureInput>	Extracts features from some kind of inputs to produce one or more rows in a feature-table.
class	SingleRowPerInput<T extends InputFromManager,S extends FeatureInput>	Base class for exporting features, where features are calculated per-image using a NamedFeatureStore.

Uses of InputFromManager in org.anchoranalysis.plugin.io.bean.input

Classes in org.anchoranalysis.plugin.io.bean.input with type parameters of type InputFromManager

Modifier and Type	Class	Description
class	BranchIfDebug<T extends InputFromManager>	Uses one input-manager normally, but a different one if in debug mode.
class	Concatenate<T extends InputFromManager>	Concatenates the inputs from multiple InputManagers that all provide the same input-type.
class	Exclude<T extends InputFromManager>	Excludes all inputs whose identifiers match a regular expression.
class	Limit<T extends InputFromManager>	Limits the number of input-objects to a certain hard-maximum
class	LimitIfRequested<T extends InputFromManager>	Like Limit if it is requested in the InputContextParameters, makes no change to the inputs.
class	Shuffle<T extends InputFromManager>	Randomly shuffles the order of the inputs.
class	ShuffleIfRequested<T extends InputFromManager>	Like Shuffle if requested in the InputContextParameters otherwise makes no change to the inputs.
class	SortAlphabetically<T extends InputFromManager>	Sorts the input-items in alphabetical order of their input-name.

Uses of InputFromManager in org.anchoranalysis.plugin.io.bean.input.files

Classes in org.anchoranalysis.plugin.io.bean.input.files with type parameters of type InputFromManager

Modifier and Type	Class	Description
class	NamedFilesBase<T extends InputFromManager>	Base class for an InputManager that produces inputs that are created from a NamedFile.

Uses of InputFromManager in org.anchoranalysis.plugin.io.bean.input.filter

Classes in org.anchoranalysis.plugin.io.bean.input.filter with type parameters of type InputFromManager

Modifier and Type	Class	Description
class	FilterCSVColumn<T extends InputFromManager>	Finds a CSV file with the names of an input as the first-column.
class	FilterDescriptiveName<T extends InputFromManager>	Filters all the input objects for only those with certain types of descriptive-names.
class	FilterIfDebug<T extends InputFromManager>	Filters a list of inputs when in debug-mode

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

Classes in org.anchoranalysis.plugin.io.bean.input.stack that implement InputFromManager

Modifier and Type	Class	Description
class	ConvertNamedChannelsInputToStack	An input object that converts NamedChannelsInput to StackSequenceInput.

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

Classes in org.anchoranalysis.plugin.io.bean.summarizer.input with type parameters of type InputFromManager

Modifier and Type	Class	Description
class	ExtractIdentifier<T extends InputFromManager>	Extracts the identifier from an InputFromManager to summarize further.
class	ExtractIdentifierAndPath<T extends InputFromManager>	Extracts the identifier and path from an InputFromManager to summarize further.
class	ExtractPath<T extends InputFromManager>	Extracts a Path from an input to summarize further.
class	SummarizerInputFromManager<T extends InputFromManager,S>	Extracts a particular item from an InputFromManager for further summarization downstream.

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

Classes in org.anchoranalysis.plugin.io.bean.task with type parameters of type InputFromManager

Modifier and Type	Class	Description
class	SummarizeBase<T extends InputFromManager,S>
class	SummarizeInputs<T extends InputFromManager>

Uses of InputFromManager in org.anchoranalysis.plugin.io.input.filter

Methods in org.anchoranalysis.plugin.io.input.filter with type parameters of type InputFromManager

Modifier and Type	Method	Description
<T extends InputFromManager> List<T>	FilterDescriptiveNameEqualsContains.removeNonMatching(List<T> in)	Removes items from the input list that don't match the filter criteria.

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

Classes in org.anchoranalysis.plugin.mpp.bean.convert with type parameters of type InputFromManager

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.

Uses of InputFromManager in org.anchoranalysis.plugin.mpp.shared

Classes in org.anchoranalysis.plugin.mpp.shared with type parameters of type InputFromManager

Modifier and Type	Class	Description
final class	ConvertedInput<U extends InputFromManager>	A converted-input, together with any logged messages associated with it.
class	SharedStateRememberConverted<U extends InputFromManager,S>	Shared-state that remembers converted inputs for corresponding unconverted inputs.

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

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

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.