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

Class ExtractSlice

Object

AnchorBean<Task<NamedChannelsInput,SharedStateSelectedSlice>>

Task<NamedChannelsInput,SharedStateSelectedSlice>

ExtractSlice

public class ExtractSlice
extends Task<NamedChannelsInput,SharedStateSelectedSlice>

Reduces a z-stack to a single-slice by taking the optima of a feature calculated for each slice.

Expects a second-level output "stack" to determine which slices are outputted or not.

Author:

Owen Feehan

Constructor Summary

Constructors

Constructor	Description
ExtractSlice()

Method Summary

Modifier and Type	Method	Description
void	afterAllJobsAreExecuted(SharedStateSelectedSlice sharedState, InputOutputContext context)	Called once after all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).
SharedStateSelectedSlice	beforeAnyJobIsExecuted(Outputter outputter, ConcurrencyPlan concurrencyPlan, List<NamedChannelsInput> 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<NamedChannelsInput,SharedStateSelectedSlice> input)	Performs the task on a particular input.
FeatureListProvider<FeatureInputStack>	getScoreProvider()
StackProvider	getStackEnergy()
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.
boolean	isFindMaxima()	If true, the maxima of the score is searched for.
void	setFindMaxima(boolean findMaxima)	If true, the maxima of the score is searched for.
void	setScoreProvider(FeatureListProvider<FeatureInputStack> scoreProvider)
void	setStackEnergy(StackProvider stackEnergy)

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

ExtractSlice

public ExtractSlice()

Method Details

beforeAnyJobIsExecuted

public SharedStateSelectedSlice beforeAnyJobIsExecuted(Outputter outputter,
 ConcurrencyPlan concurrencyPlan,
 List<NamedChannelsInput> 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<NamedChannelsInput,SharedStateSelectedSlice>

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.

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,SharedStateSelectedSlice>

Returns:

the input-types that a task expects.

doJobOnInput

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

Description copied from class: Task

Performs the task on a particular input.

Specified by:

doJobOnInput in class Task<NamedChannelsInput,SharedStateSelectedSlice>

Parameters:

input - the input for the job.

Throws:

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

afterAllJobsAreExecuted

public void afterAllJobsAreExecuted(SharedStateSelectedSlice 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<NamedChannelsInput,SharedStateSelectedSlice>

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.

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<NamedChannelsInput,SharedStateSelectedSlice>

Returns:

the default rules if they exist.

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<NamedChannelsInput,SharedStateSelectedSlice>

Returns:

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

getScoreProvider

public FeatureListProvider<FeatureInputStack> getScoreProvider()

setScoreProvider

public void setScoreProvider(FeatureListProvider<FeatureInputStack> scoreProvider)

getStackEnergy

public StackProvider getStackEnergy()

setStackEnergy

public void setStackEnergy(StackProvider stackEnergy)

isFindMaxima

public boolean isFindMaxima()

If true, the maxima of the score is searched for. If false, rather the minima.

setFindMaxima

public void setFindMaxima(boolean findMaxima)

If true, the maxima of the score is searched for. If false, rather the minima.