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

Class ExportFeatures<T extends InputFromManager,S,U extends FeatureInput>

Object

AnchorBean<Task<T,FeatureExporter<S>>>

Task<T,FeatureExporter<S>>

ExportFeatures<T,S,U>

Type Parameters:

T - See Task

S - a source-of-features that is duplicated for each new thread (to prevent any concurrency issues)

U - feature-input type for features bean-field

public class ExportFeatures<T extends InputFromManager,S,U extends FeatureInput>
extends Task<T,FeatureExporter<S>>

Calculates features and exports them as a CSV file.

Aggregated-features (based upon a certain grouping) can also be calculated.

The following outputs are produced:

Output Name	Default?	Description
"features"	yes	a single CSV file of feature-calculations where each row is an object.
"features""Aggregated"	yes	a single CSV file of feature-calculations where each row is a group (with aggregated features of the objects within).
"features""Group"	no	a CSV file of feature-calculations per group, where each row is an object.
"features""AggregatedGroup"	no	a XML file of aggregated feature-calculations per group
outputs from a sub-class of FeatureSource as used in source.
	outputs from Task
		outputs from FeatureResultsAndThumbnails

Author:

Owen Feehan

Field Summary

Fields

Modifier and Type	Field	Description
static final FeatureOutputNames	OUTPUT_NAMES	Default names for various outputs from the task.

Constructor Summary

Constructors

Constructor	Description
ExportFeatures()

Method Summary

Modifier and Type	Method	Description
void	afterAllJobsAreExecuted(FeatureExporter<S> sharedState, InputOutputContext context)	Called once after all calls to Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>).
FeatureExporter<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,FeatureExporter<S>> input)	Performs the task on a particular input.
List<NamedBean<FeatureListProvider<U>>>	getFeatures()	The features to be exported (after possibly some manipulation or augmentation).
List<NamedBean<FeatureListProvider<FeatureInputResults>>>	getFeaturesAggregate()	Features applied to each group to aggregate values (accepting FeatureInputResults).
Grouper	getGroup()	Includes an additional group column in CSVs, and creates group-specific feature files.
DerivePath	getId()	Translates an input file name to a unique ID.
FeatureSource<T,S,U>	getSource()	Source of feature-values to be exported.
ExportFeaturesStyle	getStyle()	Visual style for how feature export occurs.
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	setFeatures(List<NamedBean<FeatureListProvider<U>>> features)	The features to be exported (after possibly some manipulation or augmentation).
void	setFeaturesAggregate(List<NamedBean<FeatureListProvider<FeatureInputResults>>> featuresAggregate)	Features applied to each group to aggregate values (accepting FeatureInputResults).
void	setGroup(Grouper group)	Includes an additional group column in CSVs, and creates group-specific feature files.
void	setId(DerivePath id)	Translates an input file name to a unique ID.
void	setSource(FeatureSource<T,S,U> source)	Source of feature-values to be exported.
void	setStyle(ExportFeaturesStyle style)	Visual style for how feature export occurs.

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

Field Details

OUTPUT_NAMES

public static final FeatureOutputNames OUTPUT_NAMES

Default names for various outputs from the task.

Constructor Details

ExportFeatures

public ExportFeatures()

Method Details

beforeAnyJobIsExecuted

public FeatureExporter<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 InputFromManager,FeatureExporter<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,FeatureExporter<S>> input)
                  throws JobExecutionException

Description copied from class: Task

Performs the task on a particular input.

Specified by:

doJobOnInput in class Task<T extends InputFromManager,FeatureExporter<S>>

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(FeatureExporter<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 InputFromManager,FeatureExporter<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.

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 InputFromManager,FeatureExporter<S>>

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<T extends InputFromManager,FeatureExporter<S>>

Returns:

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

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 InputFromManager,FeatureExporter<S>>

Returns:

the input-types that a task expects.

getSource

public FeatureSource<T,S,U> getSource()

Source of feature-values to be exported.

setSource

public void setSource(FeatureSource<T,S,U> source)

Source of feature-values to be exported.

getGroup

public Grouper getGroup()

Includes an additional group column in CSVs, and creates group-specific feature files.

setGroup

public void setGroup(Grouper group)

Includes an additional group column in CSVs, and creates group-specific feature files.

getId

public DerivePath getId()

Translates an input file name to a unique ID.

setId

public void setId(DerivePath id)

Translates an input file name to a unique ID.

getFeatures

public List<NamedBean<FeatureListProvider<U>>> getFeatures()

The features to be exported (after possibly some manipulation or augmentation).

setFeatures

public void setFeatures(List<NamedBean<FeatureListProvider<U>>> features)

The features to be exported (after possibly some manipulation or augmentation).

getFeaturesAggregate

public List<NamedBean<FeatureListProvider<FeatureInputResults>>> getFeaturesAggregate()

Features applied to each group to aggregate values (accepting FeatureInputResults).

If not specified, a default list of mean, standard-deviation, min, max etc. of every feature is used.

setFeaturesAggregate

public void setFeaturesAggregate(List<NamedBean<FeatureListProvider<FeatureInputResults>>> featuresAggregate)

Features applied to each group to aggregate values (accepting FeatureInputResults).

If not specified, a default list of mean, standard-deviation, min, max etc. of every feature is used.

getStyle

public ExportFeaturesStyle getStyle()

Visual style for how feature export occurs.

setStyle

public void setStyle(ExportFeaturesStyle style)

Visual style for how feature export occurs.