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

Class CalculateLevelBase

Object

AnchorBean<VoxelScore>

InitializableBean<VoxelScore,ImageInitialization>

ImageBean<VoxelScore>

VoxelScore

SingleChannel

CalculateLevelBase

Direct Known Subclasses:

CalculateLevel, DifferenceCalculateLevelStandardDeviation

public abstract class CalculateLevelBase
extends SingleChannel

Base class for calculating a score based on a threshold level derived from a histogram.

Constructor Summary

Constructors

Constructor	Description
CalculateLevelBase()

Method Summary

Modifier and Type	Method	Description
protected abstract void	beforeCalcSetup(Histogram histogram, int level)	Performs setup operations before calculation.
protected abstract double	calculateForVoxel(int voxelIntensity, int level)	Calculates a score for a single voxel based on its intensity and the threshold level.
protected double	deriveScoreFromVoxel(int voxelIntensity)	Derives a score from a single voxel intensity.
CalculateLevel	getCalculateLevel()	The method to calculate the threshold level.
int	getHistogramChannelIndex()	The index of the histogram channel to use for calculations.
void	initialize(List<Histogram> histograms, Optional<Dictionary> dictionary)	Initializes the voxels-score.
void	setCalculateLevel(CalculateLevel calculateLevel)	The method to calculate the threshold level.
void	setHistogramChannelIndex(int histogramChannelIndex)	The index of the histogram channel to use for calculations.

Methods inherited from class org.anchoranalysis.plugin.image.feature.bean.score.SingleChannel

calculate, getEnergyChannelIndex, setEnergyChannelIndex

Methods inherited from class org.anchoranalysis.bean.initializable.InitializableBean

getInitialization, getLogger, getPropertyInitializer, initialize, initializeRecursive, initRecursiveWithInitializer, isInitialized, onInitialization

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

CalculateLevelBase

public CalculateLevelBase()

Method Details

initialize

public void initialize(List<Histogram> histograms,
 Optional<Dictionary> dictionary)
                throws InitializeException

Description copied from class: VoxelScore

Initializes the voxels-score.

Must be called before VoxelScore.calculate(int[]).

Overrides:

initialize in class VoxelScore

Parameters:

histograms - one or more histograms associated with this calculation

dictionary - optional Dictionary associated with this calculation

Throws:

InitializeException - if anything goes wrong

deriveScoreFromVoxel

protected double deriveScoreFromVoxel(int voxelIntensity)

Description copied from class: SingleChannel

Derives a score from a single voxel intensity.

Specified by:

deriveScoreFromVoxel in class SingleChannel

Parameters:

voxelIntensity - the intensity of the voxel in the specified energy channel

Returns:

the calculated score for the voxel

beforeCalcSetup

protected abstract void beforeCalcSetup(Histogram histogram,
 int level)
                                 throws OperationFailedException

Performs setup operations before calculation.

Parameters:

histogram - the Histogram to use for setup

level - the calculated threshold level

Throws:

OperationFailedException - if the setup operation fails

calculateForVoxel

protected abstract double calculateForVoxel(int voxelIntensity,
 int level)

Calculates a score for a single voxel based on its intensity and the threshold level.

Parameters:

voxelIntensity - the intensity of the voxel

level - the threshold level

Returns:

a score for the voxel

getCalculateLevel

public CalculateLevel getCalculateLevel()

The method to calculate the threshold level.

setCalculateLevel

public void setCalculateLevel(CalculateLevel calculateLevel)

The method to calculate the threshold level.

getHistogramChannelIndex

public int getHistogramChannelIndex()

The index of the histogram channel to use for calculations.

setHistogramChannelIndex

public void setHistogramChannelIndex(int histogramChannelIndex)

The index of the histogram channel to use for calculations.