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)
SharedStateRememberConverted<U,S>	beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<T> inputs, ParametersExperiment parameters)
OutputEnabledMutable	defaultOutputs()
void	doJobOnInput(InputBound<T, SharedStateRememberConverted<U,S>> inputBound)
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()
InputTypesExpected	inputTypesExpected()
void	replaceTask(Task<U,S> taskToReplace)
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

Specified by:

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

Throws:

ExperimentExecutionException

doJobOnInput

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

Specified by:

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

Throws:

JobExecutionException

inputTypesExpected

public InputTypesExpected inputTypesExpected()

Specified by:

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

afterAllJobsAreExecuted

public void afterAllJobsAreExecuted(SharedStateRememberConverted<U,S> sharedState,
 InputOutputContext context)
                             throws ExperimentExecutionException

Specified by:

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

Throws:

ExperimentExecutionException

hasVeryQuickPerInputExecution

public boolean hasVeryQuickPerInputExecution()

Specified by:

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

replaceTask

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

Specified by:

replaceTask in interface ReplaceTask<T extends NamedChannelsInput, S>

Throws:

OperationFailedException

defaultOutputs

public OutputEnabledMutable defaultOutputs()

Overrides:

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

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.