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

Class RasterTask<S,U>

Object

AnchorBean<Task<NamedChannelsInput,S>>

Task<NamedChannelsInput,S>

RasterTask<S,U>

Type Parameters:

S - shared-state type for entire task

U - shared-state type for current series i.e. for all stacks in one particular job

Direct Known Subclasses:

ConvertImageFormat

public abstract class RasterTask<S,U>
extends Task<NamedChannelsInput,S>

An experiment that takes (primarily) a series of raster images as an input.

An operation is executed independently on each stack in the series.

Author:

Owen Feehan

Constructor Summary

Constructors

Constructor	Description
RasterTask()

Method Summary

Modifier and Type	Method	Description
protected abstract U	createSharedStateJob(InputOutputContext context)	Creates a shared-state for the duration of a particular input-job.
void	doJobOnInput(InputBound<NamedChannelsInput,S> input)	Performs the task on a particular input.
abstract void	doStack(InputBound<NamedChannelsInput,S> input, U sharedStateJob, int seriesIndex, int numberSeries, InputOutputContext context)	Processes one stack from a series.
abstract void	endSeries(S sharedStateTask, U sharedStateJob, InputOutputContext context)	Ends processing of a series.
InputTypesExpected	inputTypesExpected()	Highest class(es) that will function as a valid input.
abstract void	startSeries(S sharedStateTask, U sharedStateJob, InputOutputContext context)	Starts processing of a series.

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

afterAllJobsAreExecuted, beforeAnyJobIsExecuted, defaultOutputs, executeJob, hasVeryQuickPerInputExecution, 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

RasterTask

public RasterTask()

Method Details

doJobOnInput

public void doJobOnInput(InputBound<NamedChannelsInput,S> input)
                  throws JobExecutionException

Description copied from class: Task

Performs the task on a particular input.

Specified by:

doJobOnInput in class Task<NamedChannelsInput,S>

Parameters:

input - the input for the job.

Throws:

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

createSharedStateJob

protected abstract U createSharedStateJob(InputOutputContext context)
                                   throws JobExecutionException

Creates a shared-state for the duration of a particular input-job.

This will exist across all stacks from the same series.

Parameters:

context - the input-output context associated with a particular job

Returns:

a newly created shared-state

Throws:

JobExecutionException - if an error occurs during job execution

startSeries

public abstract void startSeries(S sharedStateTask,
 U sharedStateJob,
 InputOutputContext context)
                          throws JobExecutionException

Starts processing of a series.

This corresponds to the start of an input job, before any stacks in the series are processed.

This should be called always once before all calls to doStack(org.anchoranalysis.experiment.task.InputBound<org.anchoranalysis.image.io.channel.input.NamedChannelsInput, S>, U, int, int, org.anchoranalysis.io.output.outputter.InputOutputContext).

Parameters:

sharedStateTask - shared-state across all jobs in task

sharedStateJob - shared-state across all stacks in a job (i.e. in all series)

context - input-output context

Throws:

JobExecutionException - if an error occurs during job execution

doStack

public abstract void doStack(InputBound<NamedChannelsInput,S> input,
 U sharedStateJob,
 int seriesIndex,
 int numberSeries,
 InputOutputContext context)
                      throws JobExecutionException

Processes one stack from a series.

This can be called many times in a job, once for each stack in the series.

It is assumed each job may have only one series.

Parameters:

input - the input-object corresponding to this stack (a set of named-channels)

sharedStateJob - shared-state across all stacks in a job (i.e. in all series)

seriesIndex - the index of the input that is being currently processed from the series

numberSeries - the total number of images in the series (constant for a given task)

context - IO context

Throws:

JobExecutionException - if an error occurs during job execution

endSeries

public abstract void endSeries(S sharedStateTask,
 U sharedStateJob,
 InputOutputContext context)
                        throws JobExecutionException

Ends processing of a series.

This corresponds to the end of an input job, after any stacks in the series are processed.

This should be called always once after all calls to doStack(org.anchoranalysis.experiment.task.InputBound<org.anchoranalysis.image.io.channel.input.NamedChannelsInput, S>, U, int, int, org.anchoranalysis.io.output.outputter.InputOutputContext).

Parameters:

sharedStateTask - shared-state across all jobs in task

sharedStateJob - shared-state across all stacks in a job (i.e. in all series)

context - input-output context

Throws:

JobExecutionException - if an error occurs during job execution

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<NamedChannelsInput,S>

Returns:

the input-types that a task expects.