Package org.anchoranalysis.plugin.mpp.bean.convert

Class ConvertNamedChannels<T extends NamedChannelsInput,S,U extends InputFromManager>

Object

AnchorBean<Task<T,SharedStateRememberConverted<U,S>>>

Task<T,SharedStateRememberConverted<U,S>>

ConvertNamedChannels<T,S,U>

Type Parameters:

T - the named-channels-input we expect to receive

S - shared-state of the task

U - the named-channels-input the delegate task contains

All Implemented Interfaces:

ReplaceTask<U,S>

public class ConvertNamedChannels<T extends NamedChannelsInput,S,U extends InputFromManager>
extends Task<T,SharedStateRememberConverted<U,S>>
implements ReplaceTask<U,S>

Converts NamedChannelsInput to a variety of others to match a delegate task.

The other types, to which a NamedChannelsInput will be converted are:

1. MultiInput
2. StackSequenceInput
3. FileWithDirectoryInput
4. ImageMetadataInput

Note that the presence of ReplaceTask gives special behavior to this task in the JobProcessor.

Author:

Owen Feehan

Constructor Summary

Constructors

Constructor	Description
ConvertNamedChannels()

Method Summary

Modifier and Type	Method	Description
void	afterAllJobsAreExecuted(SharedStateRememberConverted<U,S> sharedState, InputOutputContext context)	Called once after all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).
SharedStateRememberConverted<U,S>	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>).
OutputEnabledMutable	defaultOutputs()	If specified, default rules for determine which outputs are enabled or not.
void	doJobOnInput(InputBound<T,SharedStateRememberConverted<U,S>> inputBound)	Performs the task on a particular input.
StackReader	getDefaultStackReaderForMetadata()	Supplies to the imageMetadataReader to use, if no other reader is specified.
ImageMetadataReader	getImageMetadataReader()	How to read the ImageMetadata from the file-system.
Task<U,S>	getTask()	The underlying task that will be called, perhaps with a different input-type.
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	replaceTask(Task<U,S> taskToReplace)	Replace the currently-assigned Task with another.
void	setDefaultStackReaderForMetadata(StackReader defaultStackReaderForMetadata)	Supplies to the imageMetadataReader to use, if no other reader is specified.
void	setImageMetadataReader(ImageMetadataReader imageMetadataReader)	How to read the ImageMetadata from the file-system.
void	setTask(Task<U,S> task)	The underlying task that will be called, perhaps with a different input-type.

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

ConvertNamedChannels

public ConvertNamedChannels()

Method Details

beforeAnyJobIsExecuted

public SharedStateRememberConverted<U,S> beforeAnyJobIsExecuted(Outputter outputter,
 ConcurrencyPlan concurrencyPlan,
 List<T> 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<T extends NamedChannelsInput,SharedStateRememberConverted<U extends InputFromManager,S>>

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.

doJobOnInput

public void doJobOnInput(InputBound<T,SharedStateRememberConverted<U,S>> inputBound)
                  throws JobExecutionException

Description copied from class: Task

Performs the task on a particular input.

Specified by:

doJobOnInput in class Task<T extends NamedChannelsInput,SharedStateRememberConverted<U extends InputFromManager,S>>

Parameters:

inputBound - the input for the job.

Throws:

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

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<T extends NamedChannelsInput,SharedStateRememberConverted<U extends InputFromManager,S>>

Returns:

the input-types that a task expects.

afterAllJobsAreExecuted

public void afterAllJobsAreExecuted(SharedStateRememberConverted<U,S> 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<T extends NamedChannelsInput,SharedStateRememberConverted<U extends InputFromManager,S>>

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.

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<T extends NamedChannelsInput,SharedStateRememberConverted<U extends InputFromManager,S>>

Returns:

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

replaceTask

public void replaceTask(Task<U,S> taskToReplace)
                 throws OperationFailedException

Description copied from interface: ReplaceTask

Replace the currently-assigned Task with another.

Specified by:

replaceTask in interface ReplaceTask<T extends NamedChannelsInput,S>

Parameters:

taskToReplace - the task to replace.

Throws:

OperationFailedException - if the task cannot be successfully replaced.

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<T extends NamedChannelsInput,SharedStateRememberConverted<U extends InputFromManager,S>>

Returns:

the default rules if they exist.

getTask

public Task<U,S> getTask()

The underlying task that will be called, perhaps with a different input-type.

setTask

public void setTask(Task<U,S> task)

The underlying task that will be called, perhaps with a different input-type.

getImageMetadataReader

public ImageMetadataReader getImageMetadataReader()

How to read the ImageMetadata from the file-system.

setImageMetadataReader

public void setImageMetadataReader(ImageMetadataReader imageMetadataReader)

How to read the ImageMetadata from the file-system.

getDefaultStackReaderForMetadata

public StackReader getDefaultStackReaderForMetadata()

Supplies to the imageMetadataReader to use, if no other reader is specified.

setDefaultStackReaderForMetadata

public void setDefaultStackReaderForMetadata(StackReader defaultStackReaderForMetadata)

Supplies to the imageMetadataReader to use, if no other reader is specified.