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

Class FromImage

Object

AnchorBean<FeatureSource<ProvidesStackInput,FeatureList<FeatureInputStack>,FeatureInputStack>>

FeatureSource<ProvidesStackInput,FeatureList<FeatureInputStack>,FeatureInputStack>

SingleRowPerInput<ProvidesStackInput,FeatureInputStack>

FromImage

public class FromImage
extends SingleRowPerInput<ProvidesStackInput,FeatureInputStack>

Calculates features from a single image.

Each image produces a single row of features.

Constructor Summary

Constructors

Constructor	Description
FromImage()	Creates a new FromImage instance.

Method Summary

Modifier and Type	Method	Description
protected Optional<String[]>	additionalLabelsFor(ProvidesStackInput input)	Additional labels for an input to include (after the identifier, and before any group labels).
protected ResultsVectorWithThumbnail	calculateResultsForInput(ProvidesStackInput input, FeatureCalculationContext<FeatureList<FeatureInputStack>> context)	Calculates feature-results for a particular input.
StackProvider	getStackEnergy()	Optionally defines an energy-stack for feature calculation (if not set, the energy-stack is considered to be the input stacks).
ThumbnailFromStack	getThumbnail()	Method to generate a thumbnail for images.
boolean	includeGroupInExperiment(boolean groupGeneratorDefined)	Determines if group columns should be added to the CSV exports and other group exports may occur in sub-directories.
InputTypesExpected	inputTypesExpected()	Specifies the highest class(es) that will function as a valid input.
void	setStackEnergy(StackProvider stackEnergy)	Optionally defines an energy-stack for feature calculation (if not set, the energy-stack is considered to be the input stacks).
void	setThumbnail(ThumbnailFromStack thumbnail)	Method to generate a thumbnail for images.

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

calculateAndOutput, createExporter, headers

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

FromImage

public FromImage()

Creates a new FromImage instance.

Method Details

inputTypesExpected

public InputTypesExpected inputTypesExpected()

Description copied from class: FeatureSource

Specifies the 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 FeatureSource<ProvidesStackInput,FeatureList<FeatureInputStack>,FeatureInputStack>

Returns:

an InputTypesExpected object specifying the expected input types

includeGroupInExperiment

public boolean includeGroupInExperiment(boolean groupGeneratorDefined)

Description copied from class: FeatureSource

Determines if group columns should be added to the CSV exports and other group exports may occur in sub-directories.

Specified by:

includeGroupInExperiment in class FeatureSource<ProvidesStackInput,FeatureList<FeatureInputStack>,FeatureInputStack>

Parameters:

groupGeneratorDefined - has a group-generator been defined for this experiment?

Returns:

true if a group-generator has been defined, false otherwise

calculateResultsForInput

protected ResultsVectorWithThumbnail calculateResultsForInput(ProvidesStackInput input,
 FeatureCalculationContext<FeatureList<FeatureInputStack>> context)
                                                       throws NamedFeatureCalculateException

Description copied from class: SingleRowPerInput

Calculates feature-results for a particular input.

Specified by:

calculateResultsForInput in class SingleRowPerInput<ProvidesStackInput,FeatureInputStack>

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 Optional<String[]> additionalLabelsFor(ProvidesStackInput input)

Description copied from class: SingleRowPerInput

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.

Specified by:

additionalLabelsFor in class SingleRowPerInput<ProvidesStackInput,FeatureInputStack>

Parameters:

input - the input.

Returns:

any additional labels for the input.

getStackEnergy

public StackProvider getStackEnergy()

Optionally defines an energy-stack for feature calculation (if not set, the energy-stack is considered to be the input stacks).

setStackEnergy

public void setStackEnergy(StackProvider stackEnergy)

Optionally defines an energy-stack for feature calculation (if not set, the energy-stack is considered to be the input stacks).

getThumbnail

public ThumbnailFromStack getThumbnail()

Method to generate a thumbnail for images.

setThumbnail

public void setThumbnail(ThumbnailFromStack thumbnail)

Method to generate a thumbnail for images.