Package org.anchoranalysis.plugin.image.task.bean.labeller

Class ImageAssignLabel<T>

Object

AnchorBean<Task<ProvidesStackInput,SharedStateFilteredImageOutput<T>>>

Task<ProvidesStackInput,SharedStateFilteredImageOutput<T>>

ImageAssignLabel<T>

Type Parameters:

T - type of initialization associated with the filter.

public class ImageAssignLabel<T>
extends Task<ProvidesStackInput,SharedStateFilteredImageOutput<T>>

Assigns a label to each image and copies into subdirectories for each label, and creates a labelling CSV.

The following outputs are produced:

Output Name	Default?	Description
"images"	yes	a directory where copies of input images are placed in subdirectories corresponding to their label.
"mapping"	yes	a single CSV file where each row is an image-label correspondence.
inherited from Task

Author:

Owen Feehan

Constructor Summary

Constructors

Constructor	Description
ImageAssignLabel()

Method Summary

Modifier and Type	Method	Description
void	afterAllJobsAreExecuted(SharedStateFilteredImageOutput<T> sharedState, InputOutputContext context)	Called once after all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).
SharedStateFilteredImageOutput<T>	beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<ProvidesStackInput> inputs, ParametersExperiment parameters)	Called once before all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).
OutputEnabledMutable	defaultOutputs()	If specified, default rules for determine which outputs are enabled or not.
void	doJobOnInput(InputBound<ProvidesStackInput,SharedStateFilteredImageOutput<T>> input)	Performs the task on a particular input.
ImageLabeller<T>	getImageLabeller()	Maps a label to an image
StackProvider	getOutputStackProvider()	If it's set, a stack is generated that is outputted into subdirectory corresponding to the groupIdentifier.
boolean	hasVeryQuickPerInputExecution()	Is the execution-time of the task per-input expected to be very quick to execute?
InputTypesExpected	inputTypesExpected()	Highest class(es) that will function as a valid input.
void	setImageLabeller(ImageLabeller<T> imageLabeller)	Maps a label to an image
void	setOutputStackProvider(StackProvider outputStackProvider)	If it's set, a stack is generated that is outputted into subdirectory corresponding to the groupIdentifier.

Methods inherited from class org.anchoranalysis.experiment.bean.task.Task

executeJob, isInputCompatibleWith

Methods inherited from class org.anchoranalysis.bean.AnchorBean

checkMisconfigured, describeBean, describeChildren, duplicateBean, fields, findFieldsOfClass, getBeanName, getLocalPath, localise, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Details

ImageAssignLabel

public ImageAssignLabel()

Method Details

beforeAnyJobIsExecuted

public SharedStateFilteredImageOutput<T> beforeAnyJobIsExecuted(Outputter outputter,
 ConcurrencyPlan concurrencyPlan,
 List<ProvidesStackInput> inputs,
 ParametersExperiment parameters)
                                                         throws ExperimentExecutionException

Description copied from class: Task

Called once before all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).

Specified by:

beforeAnyJobIsExecuted in class Task<ProvidesStackInput,SharedStateFilteredImageOutput<T>>

Parameters:

outputter - the output-manager for the experiment (not for an individual job)

concurrencyPlan - available numbers of processors that can call Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>)

inputs - a list of inputs, each will result in at least one call to Task.executeJob(ParametersUnbound).

parameters - the experiment-parameters.

Returns:

the shared-state that is passed to each call to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>) and to Task.afterAllJobsAreExecuted(S, org.anchoranalysis.io.output.outputter.InputOutputContext).

Throws:

ExperimentExecutionException - if a fatal error occurs executing this step of the experiment.

defaultOutputs

public OutputEnabledMutable defaultOutputs()

Description copied from class: Task

If specified, default rules for determine which outputs are enabled or not.

Overrides:

defaultOutputs in class Task<ProvidesStackInput,SharedStateFilteredImageOutput<T>>

Returns:

the default rules if they exist.

inputTypesExpected

public InputTypesExpected inputTypesExpected()

Description copied from class: Task

Highest class(es) that will function as a valid input.

This is usually the class of T (or sometimes the absolute base class InputFromManager).

Specified by:

inputTypesExpected in class Task<ProvidesStackInput,SharedStateFilteredImageOutput<T>>

Returns:

the input-types that a task expects.

doJobOnInput

public void doJobOnInput(InputBound<ProvidesStackInput,SharedStateFilteredImageOutput<T>> input)
                  throws JobExecutionException

Description copied from class: Task

Performs the task on a particular input.

Specified by:

doJobOnInput in class Task<ProvidesStackInput,SharedStateFilteredImageOutput<T>>

Parameters:

input - the input for the job.

Throws:

JobExecutionException - if an error occurs executing a particular job, that is not otherwise suppressed.

hasVeryQuickPerInputExecution

public boolean hasVeryQuickPerInputExecution()

Description copied from class: Task

Is the execution-time of the task per-input expected to be very quick to execute?

Specified by:

hasVeryQuickPerInputExecution in class Task<ProvidesStackInput,SharedStateFilteredImageOutput<T>>

Returns:

true iff the execution is expected to be very quick, false otherwise.

afterAllJobsAreExecuted

public void afterAllJobsAreExecuted(SharedStateFilteredImageOutput<T> sharedState,
 InputOutputContext context)
                             throws ExperimentExecutionException

Description copied from class: Task

Called once after all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).

Specified by:

afterAllJobsAreExecuted in class Task<ProvidesStackInput,SharedStateFilteredImageOutput<T>>

Parameters:

sharedState - the shared-state

context - IO-context for experiment (not for an individual job)

Throws:

ExperimentExecutionException - if a fatal error occurs executing this step of the experiment.

getImageLabeller

public ImageLabeller<T> getImageLabeller()

Maps a label to an image

setImageLabeller

public void setImageLabeller(ImageLabeller<T> imageLabeller)

Maps a label to an image

getOutputStackProvider

public StackProvider getOutputStackProvider()

If it's set, a stack is generated that is outputted into subdirectory corresponding to the groupIdentifier.

setOutputStackProvider

public void setOutputStackProvider(StackProvider outputStackProvider)

If it's set, a stack is generated that is outputted into subdirectory corresponding to the groupIdentifier.