Uses of Class
org.anchoranalysis.math.histogram.Histogram

Packages that use Histogram

Package	Description
org.anchoranalysis.image.bean.channel	Base classes for performing operations on Channels.
org.anchoranalysis.image.bean.nonbean.init	Classes that aren't AnchorBeans that pertain to the initialization of image-related beans.
org.anchoranalysis.image.bean.nonbean.segment	Non-bean classes relating to image-segmentation.
org.anchoranalysis.image.bean.provider	Base classes for providers of different core data entities related to images.
org.anchoranalysis.image.bean.threshold	Base classes for thresholding and calculating levels for thresholding.
org.anchoranalysis.image.core.channel.convert.attached.histogram	Converts a channel to another data-type based upon a Histogram to which it is attached.
org.anchoranalysis.image.core.object	The key data entity org.anchoranalysis.image.voxel.object and related-classes and operations.
org.anchoranalysis.image.feature.bean	Beans pertaining to feature definition and calculation.
org.anchoranalysis.image.feature.bean.histogram	Features that operate on a Histogram.
org.anchoranalysis.image.feature.input	Image-related implementations of FeatureInput.
org.anchoranalysis.image.io.histogram.input	Non-bean classes for reading a Histogram from the filesystem.
org.anchoranalysis.image.io.histogram.output	Non-bean classes for writing a Histogram to the filesystem.
org.anchoranalysis.image.voxel.statistics	Statistics about aggregated voxel intensities.
org.anchoranalysis.math.histogram	The Histogram data class and related operations.
org.anchoranalysis.mpp.index	Indexing voxel-values in different ways.
org.anchoranalysis.mpp.index.factory	Factories for classes in org.anchoranalysis.mpp.index.
org.anchoranalysis.mpp.io.input	Non-beans for reading data structures related to marked point processes from the file system.
org.anchoranalysis.plugin.fiji.bean.threshold	Implementations of Thresholder that use FIJI.
org.anchoranalysis.plugin.image.bean.channel.convert	Implementations of ConvertChannelTo and ConvertChannelToWithHistogram.
org.anchoranalysis.plugin.image.bean.histogram.provider	Implementations of HistogramProvider.
org.anchoranalysis.plugin.image.bean.histogram.threshold	Thresholding of intensity values represented in at Histogram.
org.anchoranalysis.plugin.image.feature.bean.histogram.statistic	Implementations of FeatureHistogram that calculate statistics.
org.anchoranalysis.plugin.image.feature.bean.histogram.threshold	Implementations of FeatureHistogram that perform thresholding.
org.anchoranalysis.plugin.image.feature.bean.score	Implementations of VoxelScore.
org.anchoranalysis.plugin.image.feature.stack.calculation	Implementations of CalculationPart that process Stacks as used by features elsewhere in this package.
org.anchoranalysis.plugin.image.intensity	Non-bean for operations or calculations relating to intensity.
org.anchoranalysis.plugin.image.intensity.level	Non-beans for calculating a thresholding level from itensity values.
org.anchoranalysis.plugin.image.task.bean.grouped.histogram	Task(s) to export histograms of intensity values.
org.anchoranalysis.plugin.imagej.bean.threshold	Implementations of Thresholder that call ImageJ.
org.anchoranalysis.test.feature.plugins	Testing utilities and fixtures with no greater downstream dependency than anchor-image-feature or anchor-mpp.

Uses of Histogram in org.anchoranalysis.image.bean.channel

Methods in org.anchoranalysis.image.bean.channel that return types with arguments of type Histogram

Modifier and Type	Method	Description
abstract ChannelConverterAttached<Histogram,T>	ConvertChannelToWithHistogram.createConverter()	Creates the converter.

Uses of Histogram in org.anchoranalysis.image.bean.nonbean.init

Methods in org.anchoranalysis.image.bean.nonbean.init that return types with arguments of type Histogram

Modifier and Type	Method	Description
NamedProviderStore<Histogram>	ImageInitialization.histograms()	A collection of Histograms, indexed by name.

Uses of Histogram in org.anchoranalysis.image.bean.nonbean.segment

Methods in org.anchoranalysis.image.bean.nonbean.segment that return types with arguments of type Histogram

Modifier and Type	Method	Description
Optional<Histogram>	BinarySegmentationParameters.getIntensityHistogram()	A histogram of the intensity values of the voxels that are being segmented.

Constructor parameters in org.anchoranalysis.image.bean.nonbean.segment with type arguments of type Histogram

Modifier	Constructor	Description
	BinarySegmentationParameters(Optional<Histogram> intensityHistogram, Optional<Resolution> resolution)	Creates a new BinarySegmentationParameters instance.
	BinarySegmentationParameters(Resolution resolution, Optional<Histogram> intensityHistogram)	Creates with a specific resolution and intensity-histogram.

Uses of Histogram in org.anchoranalysis.image.bean.provider

Methods in org.anchoranalysis.image.bean.provider that return Histogram

Modifier and Type	Method	Description
protected abstract Histogram	HistogramProviderUnary.createFromHistogram(Histogram histogram)	Creates a Histogram given the entity provided by the delegate.
Histogram	HistogramProviderUnary.get()

Methods in org.anchoranalysis.image.bean.provider with parameters of type Histogram

Modifier and Type	Method	Description
protected abstract Histogram	HistogramProviderUnary.createFromHistogram(Histogram histogram)	Creates a Histogram given the entity provided by the delegate.

Uses of Histogram in org.anchoranalysis.image.bean.threshold

Methods in org.anchoranalysis.image.bean.threshold with parameters of type Histogram

Modifier and Type	Method	Description
abstract int	CalculateLevel.calculateLevel(Histogram histogram)	Determines a voxel intensity that can be used for thresholding.
protected int	CalculateLevelUnary.calculateLevelFromDelegate(Histogram histogram)	Determines a voxel intensity that can be used for thresholding from the delegate calculateLevel.

Method parameters in org.anchoranalysis.image.bean.threshold with type arguments of type Histogram

Modifier and Type	Method	Description
abstract BinaryVoxels<UnsignedByteBuffer>	Thresholder.threshold(VoxelsUntyped voxels, BinaryValuesByte binaryValues, Optional<Histogram> histogram, Optional<ObjectMask> objectMask)	Thresholds voxels (across a range of values) so that they have only binary range (i.e. two voxel values representing on and off).
BinaryVoxels<UnsignedByteBuffer>	ThresholderGlobal.threshold(VoxelsUntyped inputBuffer, BinaryValuesByte bvOut, Optional<Histogram> histogram, Optional<ObjectMask> objectMask)

Uses of Histogram in org.anchoranalysis.image.core.channel.convert.attached.histogram

Methods in org.anchoranalysis.image.core.channel.convert.attached.histogram with parameters of type Histogram

Modifier and Type	Method	Description
void	MaxIntensityFromHistogram.attachObject(Histogram histogram)
void	QuantileIntensityFromHistogram.attachObject(Histogram object)
void	UpperLowerQuantileIntensityFromHistogram.attachObject(Histogram histogram)

Uses of Histogram in org.anchoranalysis.image.core.object

Methods in org.anchoranalysis.image.core.object that return Histogram

Modifier and Type	Method	Description
static Histogram	HistogramFromObjectsFactory.createFrom(Channel channel, Optional<Mask> mask)	Creates a Histogram of all voxel intensity values in channel, or only those in mask if it is dfined.
static Histogram	HistogramFromObjectsFactory.createFrom(Channel channel, Mask mask)	Creates a Histogram of all voxel intensity values in channel corresponding to Mask.
static Histogram	HistogramFromObjectsFactory.createFrom(Channel channel, ObjectCollection objects)	Creates a Histogram of voxel intensity values in channel corresponding to objects.
static Histogram	HistogramFromObjectsFactory.createFrom(Channel channel, ObjectMask object)	Creates a Histogram of voxel intensity values in channel corresponding to object.
static Histogram	HistogramFromObjectsFactory.createFrom(VoxelsUntyped voxels, Optional<ObjectMask> object)	Creates a Histogram of voxel intensity values in voxels, all or only those in object.

Uses of Histogram in org.anchoranalysis.image.feature.bean

Method parameters in org.anchoranalysis.image.feature.bean with type arguments of type Histogram

Modifier and Type	Method	Description
void	VoxelScore.initialize(List<Histogram> histograms, Optional<Dictionary> dictionary)	Initializes the voxels-score.

Uses of Histogram in org.anchoranalysis.image.feature.bean.histogram

Methods in org.anchoranalysis.image.feature.bean.histogram with parameters of type Histogram

Modifier and Type	Method	Description
protected abstract double	FeatureHistogramStatistic.calculateStatisticFrom(Histogram histogram)	Calculates the statistic from the histogram, that is subsequently returned as the feature-value.
protected double	Mean.calculateStatisticFrom(Histogram histogram)

Uses of Histogram in org.anchoranalysis.image.feature.input

Methods in org.anchoranalysis.image.feature.input that return Histogram

Modifier and Type	Method	Description
Histogram	FeatureInputHistogram.getHistogram()	The histogram associated with this feature input.

Constructors in org.anchoranalysis.image.feature.input with parameters of type Histogram

Modifier	Constructor	Description
	FeatureInputHistogram(Histogram histogram, Optional<Resolution> resolution)	Creates a new FeatureInputHistogram instance.

Uses of Histogram in org.anchoranalysis.image.io.histogram.input

Methods in org.anchoranalysis.image.io.histogram.input that return Histogram

Modifier and Type	Method	Description
static Histogram	HistogramCSVReader.readHistogramFromFile(Path filePath)	Reads a CSV file from the file-system that describes a histogram of voxel values.

Uses of Histogram in org.anchoranalysis.image.io.histogram.output

Methods in org.anchoranalysis.image.io.histogram.output with parameters of type Histogram

Modifier and Type	Method	Description
void	HistogramCSVGenerator.writeToFile(Histogram element, OutputWriteSettings settings, Path filePath)

Uses of Histogram in org.anchoranalysis.image.voxel.statistics

Methods in org.anchoranalysis.image.voxel.statistics that return Histogram

Modifier and Type	Method	Description
static Histogram	HistogramFactory.createFrom(VoxelBuffer<?> buffer)	Creates a Histogram of the aggregated voxel intensities in a VoxelBuffer.
static Histogram	HistogramFactory.createFrom(VoxelsUntyped voxels)	Creates a Histogram of the aggregated voxel intensities in a VoxelsUntyped.
Histogram	VoxelStatistics.histogram()	A Histogram of all voxel values.
Histogram	VoxelStatisticsCombined.histogram()
Histogram	VoxelStatisticsFromHistogram.histogram()

Constructors in org.anchoranalysis.image.voxel.statistics with parameters of type Histogram

Modifier	Constructor	Description
	VoxelStatisticsFromHistogram(Histogram histogram)	Creates a new VoxelStatisticsFromHistogram instance.

Uses of Histogram in org.anchoranalysis.math.histogram

Methods in org.anchoranalysis.math.histogram that return Histogram

Modifier and Type	Method	Description
Histogram	Histogram.cropRemoveLargerValues(long maxCount)	Like cropRemoveSmallerValues(long) but larger values are removed rather than smaller values if the total count is too high.
Histogram	Histogram.cropRemoveSmallerValues(long maxCount)	Creates a Histogram reusing the bins in the current histogram, but with an upper limit on the total count.
Histogram	Histogram.duplicate()	Creates a deep-copy of the current object.
Histogram	Histogram.threshold(DoublePredicate predicate)	Generates a new histogram containing only values that match a predicate.

Methods in org.anchoranalysis.math.histogram with parameters of type Histogram

Modifier and Type	Method	Description
void	Histogram.addHistogram(Histogram other)	Adds the counts from another histogram to the current object.
static double	HistogramStatistics.coefficientOfVariation(Histogram histogram)	Calculates the coefficient-of-variation of a distribution of values, represented by their histogram.
static double	HistogramStatistics.kurtosis(Histogram histogram)	Calculates the kurtosis of a distribution of values, represented by their histogram.
static double	HistogramStatistics.skewness(Histogram histogram)	Calculates the skewness of a distribution of values, represented by their histogram.

Uses of Histogram in org.anchoranalysis.mpp.index

Methods in org.anchoranalysis.mpp.index that return Histogram

Modifier and Type	Method	Description
Histogram	VoxelPartitionHistogram.getCombined()
Histogram	VoxelPartitionHistogram.getSlice(int sliceID)

Method parameters in org.anchoranalysis.mpp.index with type arguments of type Histogram

Modifier and Type	Method	Description
void	VoxelPartitionHistogram.cleanUp(VoxelPartitionFactory<Histogram> factory)

Constructor parameters in org.anchoranalysis.mpp.index with type arguments of type Histogram

Modifier	Constructor	Description
	VoxelPartitionHistogram(int numberSlices, Supplier<Histogram> histogramFactory)	Constructs a VoxelPartitionHistogram with a specified number of slices.

Uses of Histogram in org.anchoranalysis.mpp.index.factory

Methods in org.anchoranalysis.mpp.index.factory that return types with arguments of type Histogram

Modifier and Type	Method	Description
VoxelPartition<Histogram>	VoxelPartitonFactoryHistogram.create(int numSlices)	Creates a new VoxelPartitionHistogram with the specified number of slices.

Methods in org.anchoranalysis.mpp.index.factory with parameters of type Histogram

Modifier and Type	Method	Description
void	VoxelPartitonFactoryHistogram.addUnused(Histogram part)	Adds an unused histogram to the factory.

Uses of Histogram in org.anchoranalysis.mpp.io.input

Methods in org.anchoranalysis.mpp.io.input that return types with arguments of type Histogram

Modifier and Type	Method	Description
MultiInputSubMap<Histogram>	MultiInput.histogram()	Gets the map of Histograms.

Uses of Histogram in org.anchoranalysis.plugin.fiji.bean.threshold

Method parameters in org.anchoranalysis.plugin.fiji.bean.threshold with type arguments of type Histogram

Modifier and Type	Method	Description
BinaryVoxels<UnsignedByteBuffer>	ThresholderAutoIJ.threshold(VoxelsUntyped inputBuffer, BinaryValuesByte binaryValues, Optional<Histogram> histogram, Optional<ObjectMask> objectMask)

Uses of Histogram in org.anchoranalysis.plugin.image.bean.channel.convert

Methods in org.anchoranalysis.plugin.image.bean.channel.convert that return types with arguments of type Histogram

Modifier and Type	Method	Description
ChannelConverterAttached<Histogram,UnsignedByteBuffer>	ToByteUpperLowerQuantileIntensity.createConverter()

Uses of Histogram in org.anchoranalysis.plugin.image.bean.histogram.provider

Methods in org.anchoranalysis.plugin.image.bean.histogram.provider that return Histogram

Modifier and Type	Method	Description
Histogram	CutBelowThreshold.createFromHistogram(Histogram histogram)
Histogram	GreaterThanThreshold.createFromHistogram(Histogram histogram)
Histogram	FromChannel.get()
Histogram	Reference.get()

Methods in org.anchoranalysis.plugin.image.bean.histogram.provider with parameters of type Histogram

Modifier and Type	Method	Description
Histogram	CutBelowThreshold.createFromHistogram(Histogram histogram)
Histogram	GreaterThanThreshold.createFromHistogram(Histogram histogram)

Uses of Histogram in org.anchoranalysis.plugin.image.bean.histogram.threshold

Methods in org.anchoranalysis.plugin.image.bean.histogram.threshold with parameters of type Histogram

Modifier and Type	Method	Description
int	CalculateLevelRelativeToThreshold.calculateLevel(Histogram histogram)
int	ClampHistogramMax.calculateLevel(Histogram histogram)
int	Constant.calculateLevel(Histogram histogram)
int	EmptyHistogramConstant.calculateLevel(Histogram histogram)
int	Maximum.calculateLevel(Histogram h)
int	Minimum.calculateLevel(Histogram h)
int	Otsu.calculateLevel(Histogram histogram)
int	OtsuWeighted.calculateLevel(Histogram histogram)
int	Quantile.calculateLevel(Histogram histogram)

Uses of Histogram in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic

Methods in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic with parameters of type Histogram

Modifier and Type	Method	Description
protected double	CoefficientOfVariation.calculateStatisticFrom(Histogram histogram)
protected double	Count.calculateStatisticFrom(Histogram histogram)
protected double	Kurtosis.calculateStatisticFrom(Histogram histogram)
protected double	Maximum.calculateStatisticFrom(Histogram histogram)
protected double	MeanRaisedToPower.calculateStatisticFrom(Histogram histogram)
protected double	Median.calculateStatisticFrom(Histogram histogram)
protected double	Minimum.calculateStatisticFrom(Histogram histogram)
protected double	Mode.calculateStatisticFrom(Histogram histogram)
protected double	NumberDistinctValues.calculateStatisticFrom(Histogram histogram)
protected double	Quantile.calculateStatisticFrom(Histogram histogram)
protected double	Range.calculateStatisticFrom(Histogram histogram)
protected double	RatioNonMode.calculateStatisticFrom(Histogram histogram)
protected double	Skewness.calculateStatisticFrom(Histogram histogram)
protected double	StandardDeviation.calculateStatisticFrom(Histogram histogram)
protected double	Sum.calculateStatisticFrom(Histogram histogram)
protected double	TotalCount.calculateStatisticFrom(Histogram histogram)
protected double	Variance.calculateStatisticFrom(Histogram histogram)

Uses of Histogram in org.anchoranalysis.plugin.image.feature.bean.histogram.threshold

Methods in org.anchoranalysis.plugin.image.feature.bean.histogram.threshold with parameters of type Histogram

Modifier and Type	Method	Description
protected double	RatioThreshold.calculateStatisticFrom(Histogram histogram)

Uses of Histogram in org.anchoranalysis.plugin.image.feature.bean.score

Methods in org.anchoranalysis.plugin.image.feature.bean.score with parameters of type Histogram

Modifier and Type	Method	Description
protected void	CalculateLevel.beforeCalcSetup(Histogram histogram, int level)
protected abstract void	CalculateLevelBase.beforeCalcSetup(Histogram histogram, int level)	Performs setup operations before calculation.
protected void	DifferenceCalculateLevelStandardDeviation.beforeCalcSetup(Histogram histogram, int level)

Method parameters in org.anchoranalysis.plugin.image.feature.bean.score with type arguments of type Histogram

Modifier and Type	Method	Description
void	CalculateLevelBase.initialize(List<Histogram> histograms, Optional<Dictionary> dictionary)
void	FromDictionaryBase.initialize(List<Histogram> histograms, Optional<Dictionary> dictionary)	Initializes the feature with histograms and a dictionary.
void	IdentityImposeValueRelationToHistogram.initialize(List<Histogram> histograms, Optional<Dictionary> dictionary)
void	NormalizeByMax.initialize(List<Histogram> histograms, Optional<Dictionary> dictionary)

Uses of Histogram in org.anchoranalysis.plugin.image.feature.stack.calculation

Methods in org.anchoranalysis.plugin.image.feature.stack.calculation that return Histogram

Modifier and Type	Method	Description
protected Histogram	CalculateHistogram.execute(FeatureInputStack input)
protected Histogram	CalculateHistogramMasked.execute(FeatureInputStack input)

Uses of Histogram in org.anchoranalysis.plugin.image.intensity

Methods in org.anchoranalysis.plugin.image.intensity that return Histogram

Modifier and Type	Method	Description
static Histogram	HistogramThresholder.withCalculateLevel(Histogram histogram, CalculateLevel calculateLevel)	Retains the portion of the histogram greater or equal to the calculated-level.

Methods in org.anchoranalysis.plugin.image.intensity with parameters of type Histogram

Modifier and Type	Method	Description
static Histogram	HistogramThresholder.withCalculateLevel(Histogram histogram, CalculateLevel calculateLevel)	Retains the portion of the histogram greater or equal to the calculated-level.

Uses of Histogram in org.anchoranalysis.plugin.image.intensity.level

Methods in org.anchoranalysis.plugin.image.intensity.level that return Histogram

Modifier and Type	Method	Description
Histogram	LevelResult.getHistogram()	The Histogram of intensity values for this level.

Constructors in org.anchoranalysis.plugin.image.intensity.level with parameters of type Histogram

Modifier	Constructor	Description
	LevelResult(int level, ObjectMask object, Histogram histogram)	Creates a new LevelResult instance.

Uses of Histogram in org.anchoranalysis.plugin.image.task.bean.grouped.histogram

Methods in org.anchoranalysis.plugin.image.task.bean.grouped.histogram that return types with arguments of type Histogram

Modifier and Type	Method	Description
protected CheckedFunction<Channel,Histogram,CreateException>	ExportImageHistograms.createChannelDeriver(ChannelSource source)
protected GroupMapByName<Histogram,Histogram>	ExportImageHistograms.createGroupMap(ConsistentChannelChecker channelChecker, Optional<Stream<String>> groupIdentifiers, Optional<InputOutputContext> outputContext, OperationContext operationContext)
protected GroupMapByName<Histogram,Histogram>	ExportImageHistograms.createGroupMap(ConsistentChannelChecker channelChecker, Optional<Stream<String>> groupIdentifiers, Optional<InputOutputContext> outputContext, OperationContext operationContext)

Methods in org.anchoranalysis.plugin.image.task.bean.grouped.histogram with parameters of type Histogram

Modifier and Type	Method	Description
protected void	ExportImageHistograms.processIndividual(String name, Histogram individual, boolean partOfGroup, CheckedBiConsumer<String,Histogram,OperationFailedException> consumeIndividual, InputOutputContext context)

Method parameters in org.anchoranalysis.plugin.image.task.bean.grouped.histogram with type arguments of type Histogram

Modifier and Type	Method	Description
protected void	ExportImageHistograms.processIndividual(String name, Histogram individual, boolean partOfGroup, CheckedBiConsumer<String,Histogram,OperationFailedException> consumeIndividual, InputOutputContext context)

Uses of Histogram in org.anchoranalysis.plugin.imagej.bean.threshold

Method parameters in org.anchoranalysis.plugin.imagej.bean.threshold with type arguments of type Histogram

Modifier and Type	Method	Description
BinaryVoxels<UnsignedByteBuffer>	ThresholderSimpleFillHoles2D.threshold(VoxelsUntyped inputBuffer, BinaryValuesByte binaryValues, Optional<Histogram> histogram, Optional<ObjectMask> objectMask)

Uses of Histogram in org.anchoranalysis.test.feature.plugins

Methods in org.anchoranalysis.test.feature.plugins that return Histogram

Modifier and Type	Method	Description
static Histogram	HistogramFixture.createAscending()	Creates an ascending histogram from 0 to 255 (inclusive).
static Histogram	HistogramFixture.createDescending()	Creates a descending histogram from 0 to 255 (inclusive).