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

Class SingleRowPerInput<T extends InputFromManager,S extends FeatureInput>

Object

AnchorBean<FeatureSource<T,FeatureList<S>,S>>

FeatureSource<T,FeatureList<S>,S>

SingleRowPerInput<T,S>

Type Parameters:

T - input-manager type

S - feature-input type

Direct Known Subclasses:

FromHistogram, FromImage, FromImageMetadata

public abstract class SingleRowPerInput<T extends InputFromManager,S extends FeatureInput>
extends FeatureSource<T,FeatureList<S>,S>

Base class for exporting features, where features are calculated per-image using a NamedFeatureStore.

Author:

Owen Feehan

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	SingleRowPerInput(String headerIdentifier)	Creates with a single non-group header that should be describe an identifier.
	SingleRowPerInput(String[] nonGroupHeaders)	Creates a new SingleRowPerInput instance.

Method Summary

Modifier and Type	Method	Description
protected abstract Optional<String[]>	additionalLabelsFor(T input)	Additional labels for an input to include (after the identifier, and before any group labels).
void	calculateAndOutput(T input, FeatureCalculationContext<FeatureList<S>> context)	Processes one input to calculate feature-results and output them to the file-system.
protected abstract ResultsVectorWithThumbnail	calculateResultsForInput(T input, FeatureCalculationContext<FeatureList<S>> context)	Calculates feature-results for a particular input.
FeatureExporter<FeatureList<S>>	createExporter(LabelHeaders metadataHeaders, List<NamedBean<FeatureListProvider<S>>> features, FeatureOutputNames outputNames, Optional<InputGrouper> grouper, FeatureExporterContext context)	Creates the FeatureExporter to be used for calculating and exporting feature-results.
LabelHeaders	headers(boolean groupsEnabled)	Generates label-headers for the non-feature-result columns in the CSV.

Methods inherited from class org.anchoranalysis.plugin.image.task.bean.feature.source.FeatureSource

includeGroupInExperiment, inputTypesExpected

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

SingleRowPerInput

protected SingleRowPerInput(String headerIdentifier)

Creates with a single non-group header that should be describe an identifier.

Parameters:

headerIdentifier - the column-name to describe an identifier.

SingleRowPerInput

public SingleRowPerInput(String[] nonGroupHeaders)

Creates a new SingleRowPerInput instance.

Parameters:

nonGroupHeaders - The column names (not pertaining to groups), the first of which should refer to an identifier.

Method Details

createExporter

public FeatureExporter<FeatureList<S>> createExporter(LabelHeaders metadataHeaders,
 List<NamedBean<FeatureListProvider<S>>> features,
 FeatureOutputNames outputNames,
 Optional<InputGrouper> grouper,
 FeatureExporterContext context)
                                               throws CreateException

Description copied from class: FeatureSource

Creates the FeatureExporter to be used for calculating and exporting feature-results.

Specified by:

createExporter in class FeatureSource<T extends InputFromManager,FeatureList<S extends FeatureInput>,S extends FeatureInput>

Parameters:

metadataHeaders - headers to use for additional "metadata" before feature-results.

features - the features to calculate.

outputNames - the names of various kind of outputs.

grouper - when defined, assigns each input to a group.

context - IO-context.

Returns:

a newly created FeatureExporter as matches this source of features.

Throws:

CreateException - if it cannot be created.

headers

public LabelHeaders headers(boolean groupsEnabled)

Description copied from class: FeatureSource

Generates label-headers for the non-feature-result columns in the CSV.

Specified by:

headers in class FeatureSource<T extends InputFromManager,FeatureList<S extends FeatureInput>,S extends FeatureInput>

Parameters:

groupsEnabled - whether groups are enabled

Returns:

a LabelHeaders object for the non-feature-result columns

calculateAndOutput

public void calculateAndOutput(T input,
 FeatureCalculationContext<FeatureList<S>> context)
                        throws OperationFailedException

Description copied from class: FeatureSource

Processes one input to calculate feature-results and output them to the file-system.

Specified by:

calculateAndOutput in class FeatureSource<T extends InputFromManager,FeatureList<S extends FeatureInput>,S extends FeatureInput>

Parameters:

input - one particular input that will create one or more "rows" in a feature-table

context - the FeatureCalculationContext for calculation

Throws:

OperationFailedException - if the operation fails

calculateResultsForInput

protected abstract ResultsVectorWithThumbnail calculateResultsForInput(T input,
 FeatureCalculationContext<FeatureList<S>> context)
                                                                throws NamedFeatureCalculateException

Calculates feature-results for a particular input.

Parameters:

input - the input.

context - context for calculating features.

Returns:

the results, with optionally associated thumbnail.

Throws:

NamedFeatureCalculateException - if any feature cannot calculate.

additionalLabelsFor

protected abstract Optional<String[]> additionalLabelsFor(T input)
                                                   throws OperationFailedException

Additional labels for an input to include (after the identifier, and before any group labels).

These should always correspond (when appended to the identifier) exactly to the nonGroupHeaders.

Parameters:

input - the input.

Returns:

any additional labels for the input.

Throws:

OperationFailedException - if the operation fails