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

Class FromHistogram

Object

AnchorBean<FeatureSource<FileInput,FeatureList<FeatureInputHistogram>,FeatureInputHistogram>>

FeatureSource<FileInput,FeatureList<FeatureInputHistogram>,FeatureInputHistogram>

SingleRowPerInput<FileInput,FeatureInputHistogram>

FromHistogram

public class FromHistogram
extends SingleRowPerInput<FileInput,FeatureInputHistogram>

Each input-file describes a histogram that produces one row of features.

Optionally, additionally extracted features are written in a XML model.

Author:

Owen Feehan

Constructor Summary

Constructors

Constructor	Description
FromHistogram()	Creates a new FromHistogram instance.

Method Summary

Modifier and Type	Method	Description
protected Optional<String[]>	additionalLabelsFor(FileInput input)	Additional labels for an input to include (after the identifier, and before any group labels).
protected ResultsVectorWithThumbnail	calculateResultsForInput(FileInput input, FeatureCalculationContext<FeatureList<FeatureInputHistogram>> context)	Calculates feature-results for a particular input.
HistogramProvider	getHistogram()	If non-null, a histogram is extracted from this provider rather than the histogram from the inputted CSV.
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	setHistogram(HistogramProvider histogram)	If non-null, a histogram is extracted from this provider rather than the histogram from the inputted CSV.

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

FromHistogram

public FromHistogram()

Creates a new FromHistogram 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<FileInput,FeatureList<FeatureInputHistogram>,FeatureInputHistogram>

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<FileInput,FeatureList<FeatureInputHistogram>,FeatureInputHistogram>

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(FileInput input,
 FeatureCalculationContext<FeatureList<FeatureInputHistogram>> context)
                                                       throws NamedFeatureCalculateException

Description copied from class: SingleRowPerInput

Calculates feature-results for a particular input.

Specified by:

calculateResultsForInput in class SingleRowPerInput<FileInput,FeatureInputHistogram>

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(FileInput 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<FileInput,FeatureInputHistogram>

Parameters:

input - the input.

Returns:

any additional labels for the input.

getHistogram

public HistogramProvider getHistogram()

If non-null, a histogram is extracted from this provider rather than the histogram from the inputted CSV.

The histogram from the inputted CSV is available in the SharedObjects as "input".

In this way, histogram can approximate a function of the original histogram.

setHistogram

public void setHistogram(HistogramProvider histogram)

If non-null, a histogram is extracted from this provider rather than the histogram from the inputted CSV.

The histogram from the inputted CSV is available in the SharedObjects as "input".

In this way, histogram can approximate a function of the original histogram.