Index (anchor-image-feature 1.0.0 API)

B C D E F G H I M N O P R S T V W
All Classes and Interfaces|All Packages

B

beforeCalc(FeatureInitialization) - Method in class org.anchoranalysis.image.feature.bean.physical.ConvertToPhysicalDistance: Initializes the direction vector before calculation.

C

CACHE_NAME_FIRST - Static variable in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair: Cache name for the first object in the pair.
CACHE_NAME_MERGED - Static variable in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair: Cache name for the merged object from the pair.
CACHE_NAME_SECOND - Static variable in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair: Cache name for the second object in the pair.
calculate(int[]) - Method in class org.anchoranalysis.image.feature.bean.VoxelScore: Calculates a score for a set of voxel intensities.
calculate(FeatureCalculationInput<FeatureInputHistogram>) - Method in class org.anchoranalysis.image.feature.bean.histogram.FeatureHistogramStatistic
calculate(FeatureCalculationInput<FeatureInputImageMetadata>) - Method in class org.anchoranalysis.image.feature.bean.FeatureImageMetadata
calculate(FeatureCalculationInput<FeatureInputObjectCollection>) - Method in class org.anchoranalysis.image.feature.bean.object.collection.FeatureObjectCollection
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.First
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.Merged
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.Minimum
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.RatioFirstToSecond
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.Second
calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.SubtractSecondFromFirst
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity
calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.image.feature.bean.object.single.NumberVoxels
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.image.feature.bean.physical.WithResolutionBase: Calculates the feature value, handling cases where resolution might be missing.
calculate(ImageMetadata) - Method in class org.anchoranalysis.image.feature.bean.FeatureImageMetadata: Calculates the feature-value for a given ImageMetadata.
calculate(FeatureInputObjectCollection) - Method in class org.anchoranalysis.image.feature.bean.object.collection.FeatureObjectCollection: Calculates the feature-value for a given FeatureInputObjectCollection.
calculate(FeatureInputPairObjects) - Method in class org.anchoranalysis.image.feature.calculator.merged.PairsTableCalculator
calculate(FeatureInputPairObjects, FeatureList<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.calculator.merged.PairsTableCalculator
calculate(FeatureInputSingleObject) - Method in class org.anchoranalysis.image.feature.calculator.SingleTableCalculator
calculate(FeatureInputSingleObject, FeatureList<FeatureInputSingleObject>) - Method in class org.anchoranalysis.image.feature.calculator.SingleTableCalculator
CalculateInputFromPair - Class in org.anchoranalysis.image.feature.calculation: Calculates a single-input from a pair of objects.
CalculateInputFromPair(CalculateInputFromPair.Extract) - Constructor for class org.anchoranalysis.image.feature.calculation.CalculateInputFromPair: Creates a new CalculateInputFromPair instance.
CalculateInputFromPair.Extract - Enum Class in org.anchoranalysis.image.feature.calculation: Defines the extraction mode for the calculation.
calculateMaybeSuppressErrors(FeatureInputPairObjects, ErrorReporter) - Method in class org.anchoranalysis.image.feature.calculator.merged.PairsTableCalculator: Calculates features for the input, optionally suppressing errors.
CalculateNumberVoxels - Class in org.anchoranalysis.image.feature.calculation: Calculates the number of voxels in a single object, optionally flattening in the Z-dimension.
CalculateNumberVoxels(boolean) - Constructor for class org.anchoranalysis.image.feature.calculation.CalculateNumberVoxels: Creates a new CalculateNumberVoxels instance.
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.image.feature.bean.histogram.FeatureHistogramStatistic: Calculates the statistic from the histogram, that is subsequently returned as the feature-value.
calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.image.feature.bean.histogram.Mean
calculateSuppressErrors(FeatureInputPairObjects, ErrorReporter) - Method in class org.anchoranalysis.image.feature.calculator.merged.PairsTableCalculator
calculateSuppressErrors(FeatureInputSingleObject, ErrorReporter) - Method in class org.anchoranalysis.image.feature.calculator.SingleTableCalculator
calculateWithResolution(double, Resolution) - Method in class org.anchoranalysis.image.feature.bean.physical.FeatureConvertUnits: Calculates the feature value with resolution information.
calculateWithResolution(double, Resolution) - Method in class org.anchoranalysis.image.feature.bean.physical.WithResolutionBase: Calculates the feature value using the provided value and resolution.
canEqual(Object) - Method in class org.anchoranalysis.image.feature.calculation.CalculateInputFromPair
canEqual(Object) - Method in class org.anchoranalysis.image.feature.calculation.CalculateNumberVoxels
canEqual(Object) - Method in class org.anchoranalysis.image.feature.input.FeatureInputImageMetadata
canEqual(Object) - Method in class org.anchoranalysis.image.feature.input.FeatureInputObjectCollection
canEqual(Object) - Method in class org.anchoranalysis.image.feature.input.FeatureInputPairObjects
canEqual(Object) - Method in class org.anchoranalysis.image.feature.input.FeatureInputSingleObject
canEqual(Object) - Method in class org.anchoranalysis.image.feature.input.FeatureInputStack
CenterOfGravity - Class in org.anchoranalysis.image.feature.bean.object.single: Calculates the center of gravity of a single object along a specified axis.
CenterOfGravity() - Constructor for class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity
CenterOfGravity(Axis) - Constructor for class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity: Creates a CenterOfGravity feature for a specific axis.
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator
ConvertFromPhysicalVolume<T> - Class in org.anchoranalysis.image.feature.bean.physical: Converts a feature from physical volume units to voxel units.
ConvertFromPhysicalVolume() - Constructor for class org.anchoranalysis.image.feature.bean.physical.ConvertFromPhysicalVolume
convertToPhysical(double, UnitConverter) - Method in class org.anchoranalysis.image.feature.bean.physical.ConvertFromPhysicalVolume: Converts the input value from physical volume units to voxel units.
convertToPhysical(double, UnitConverter) - Method in class org.anchoranalysis.image.feature.bean.physical.ConvertToPhysicalAreaXY: Converts the input value from pixel units to physical area units in an isometric XY plane.
convertToPhysical(double, UnitConverter) - Method in class org.anchoranalysis.image.feature.bean.physical.ConvertToPhysicalDistance: Converts the input value to physical distance along the specified direction.
convertToPhysical(double, UnitConverter) - Method in class org.anchoranalysis.image.feature.bean.physical.ConvertToPhysicalVolume: Converts the input value from voxel units to physical volume units.
convertToPhysical(double, UnitConverter) - Method in class org.anchoranalysis.image.feature.bean.physical.FeatureConvertUnits: Converts the input value to physical units.
ConvertToPhysicalAreaXY<T> - Class in org.anchoranalysis.image.feature.bean.physical: Converts a feature value representing area in pixel units to physical area units in an isometric XY plane.
ConvertToPhysicalAreaXY() - Constructor for class org.anchoranalysis.image.feature.bean.physical.ConvertToPhysicalAreaXY
ConvertToPhysicalDistance<T> - Class in org.anchoranalysis.image.feature.bean.physical: Converts a distance feature to physical units along a specified direction.
ConvertToPhysicalDistance() - Constructor for class org.anchoranalysis.image.feature.bean.physical.ConvertToPhysicalDistance
ConvertToPhysicalDistance(Feature<T>, SpatialUnits.UnitSuffix, DirectionVector) - Constructor for class org.anchoranalysis.image.feature.bean.physical.ConvertToPhysicalDistance: Creates a new instance with specified feature, unit type, and direction vector.
ConvertToPhysicalVolume<T> - Class in org.anchoranalysis.image.feature.bean.physical: Converts a feature value representing volume in voxel units to physical volume units.
ConvertToPhysicalVolume() - Constructor for class org.anchoranalysis.image.feature.bean.physical.ConvertToPhysicalVolume
create(Optional<SharedObjects>, Optional<EnergyStack>) - Static method in class org.anchoranalysis.image.feature.calculator.InitializationFactory: Creates a FeatureInitialization object from optional SharedObjects and EnergyStack.
createCalculator(CreateCalculatorHelper, ImageInitialization, BoundReplaceStrategy<FeatureInputStack, ? extends ReplaceStrategy<FeatureInputStack>>) - Method in class org.anchoranalysis.image.feature.calculator.merged.MergedPairsFeatures: Creates a feature calculator for stack features.
createFeatureNames() - Method in interface org.anchoranalysis.image.feature.calculator.FeatureTableCalculator: Creates a list of names for each feature (columns of the table).
createFeatureNames() - Method in class org.anchoranalysis.image.feature.calculator.merged.PairsTableCalculator
createFeatureNames() - Method in class org.anchoranalysis.image.feature.calculator.SingleTableCalculator
createFeatureSession() - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator: Creates session for evaluating feature optionally adding an energy-stack.
createFeatureSession(UnaryOperator<FeatureList<T>>, SharedObjects) - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureListEvaluator: Creates session for evaluating features.
createPair(CreateCalculatorHelper, ImageInitialization, CacheTransferSourceCollection) - Method in class org.anchoranalysis.image.feature.calculator.merged.MergedPairsFeatures: Creates a feature calculator for pair object features.
createSingle(CreateCalculatorHelper, ImageInitialization, BoundReplaceStrategy<FeatureInputSingleObject, CacheAndReuseStrategy<FeatureInputSingleObject>>) - Method in class org.anchoranalysis.image.feature.calculator.merged.MergedPairsFeatures: Creates a feature calculator for single object features.

D

dimensions() - Method in class org.anchoranalysis.image.feature.input.FeatureInputImageMetadata
duplicate() - Method in class org.anchoranalysis.image.feature.calculator.merged.MergedPairsFeatures: Creates a duplicate of this MergedPairsFeatures instance.
duplicateForNewThread() - Method in interface org.anchoranalysis.image.feature.calculator.FeatureTableCalculator: Makes a copy of the feature-store for a new thread.
duplicateForNewThread() - Method in class org.anchoranalysis.image.feature.calculator.merged.PairsTableCalculator
duplicateForNewThread() - Method in class org.anchoranalysis.image.feature.calculator.SingleTableCalculator

E

energyStack() - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator: The specified energy stack.
equals(Object) - Method in class org.anchoranalysis.image.feature.calculation.CalculateInputFromPair
equals(Object) - Method in class org.anchoranalysis.image.feature.calculation.CalculateNumberVoxels
equals(Object) - Method in class org.anchoranalysis.image.feature.calculator.NamedFeatureCalculatorMulti
equals(Object) - Method in class org.anchoranalysis.image.feature.input.FeatureInputImageMetadata
equals(Object) - Method in class org.anchoranalysis.image.feature.input.FeatureInputObjectCollection
equals(Object) - Method in class org.anchoranalysis.image.feature.input.FeatureInputPairObjects
equals(Object) - Method in class org.anchoranalysis.image.feature.input.FeatureInputSingleObject
equals(Object) - Method in class org.anchoranalysis.image.feature.input.FeatureInputStack
execute(FeatureInputPairObjects) - Method in class org.anchoranalysis.image.feature.calculation.CalculateInputFromPair: Executes the calculation to extract a single object from the pair.
execute(FeatureInputSingleObject) - Method in class org.anchoranalysis.image.feature.calculation.CalculateNumberVoxels: Executes the calculation to count the number of voxels in the object.

F

FeatureConvertUnits<T> - Class in org.anchoranalysis.image.feature.bean.physical: An abstract base class for features that convert units between physical and voxel space.
FeatureConvertUnits() - Constructor for class org.anchoranalysis.image.feature.bean.physical.FeatureConvertUnits
FeatureConvertUnits(Feature<T>, SpatialUnits.UnitSuffix) - Constructor for class org.anchoranalysis.image.feature.bean.physical.FeatureConvertUnits: Constructs a FeatureConvertUnits with a specified feature and unit type.
FeatureDeriveFromPair - Class in org.anchoranalysis.image.feature.bean.object.pair: Base class for evaluating FeaturePairObjects in terms of another feature that operates on elements (first, second, merged etc.).
FeatureDeriveFromPair() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair
FeatureDeriveFromPair(Feature<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair: Creates a new FeatureDeriveFromPair instance.
FeatureEnergy<T> - Class in org.anchoranalysis.image.feature.bean: A base class for features that only require an input that extends from FeatureInputEnergy
FeatureEnergy() - Constructor for class org.anchoranalysis.image.feature.bean.FeatureEnergy
FeatureEvaluator<T> - Class in org.anchoranalysis.image.feature.bean.evaluator: Defines a feature and provides a means to calculate inputs for it, a session.
FeatureEvaluator() - Constructor for class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator
FeatureHistogram - Class in org.anchoranalysis.image.feature.bean: A base class for features that accept a histogram as input.
FeatureHistogram() - Constructor for class org.anchoranalysis.image.feature.bean.FeatureHistogram
FeatureHistogramStatistic - Class in org.anchoranalysis.image.feature.bean.histogram: Base class for FeatureHistogram implementations that calculate a statistic from the Histogram.
FeatureHistogramStatistic() - Constructor for class org.anchoranalysis.image.feature.bean.histogram.FeatureHistogramStatistic
FeatureImageMetadata - Class in org.anchoranalysis.image.feature.bean: A base class for a feature that accepts a FeatureInputImageMetadata as input.
FeatureImageMetadata() - Constructor for class org.anchoranalysis.image.feature.bean.FeatureImageMetadata
FeatureInputHistogram - Class in org.anchoranalysis.image.feature.input: A feature input that contains a histogram and optional resolution information.
FeatureInputHistogram(Histogram, Optional<Resolution>) - Constructor for class org.anchoranalysis.image.feature.input.FeatureInputHistogram: Creates a new FeatureInputHistogram instance.
FeatureInputImageMetadata - Class in org.anchoranalysis.image.feature.input: A FeatureInput that provides ImageMetadata.
FeatureInputImageMetadata(ImageMetadata) - Constructor for class org.anchoranalysis.image.feature.input.FeatureInputImageMetadata: Creates a new FeatureInputImageMetadata instance.
FeatureInputObjectCollection - Class in org.anchoranalysis.image.feature.input: A feature input representing a collection of objects, optionally associated with an energy stack.
FeatureInputObjectCollection(ObjectCollection) - Constructor for class org.anchoranalysis.image.feature.input.FeatureInputObjectCollection: Constructs a FeatureInputObjectCollection with a collection of objects.
FeatureInputObjectCollection(ObjectCollection, Optional<EnergyStack>) - Constructor for class org.anchoranalysis.image.feature.input.FeatureInputObjectCollection: Constructs a FeatureInputObjectCollection with a collection of objects and an optional energy stack.
FeatureInputPairObjects - Class in org.anchoranalysis.image.feature.input: A pair of objects (first and second) and optionally a merged version of both.
FeatureInputPairObjects(FeatureInputPairObjects) - Constructor for class org.anchoranalysis.image.feature.input.FeatureInputPairObjects: Copy constructor for FeatureInputPairObjects.
FeatureInputPairObjects(ObjectMask, ObjectMask) - Constructor for class org.anchoranalysis.image.feature.input.FeatureInputPairObjects: Constructs a FeatureInputPairObjects with two ObjectMasks.
FeatureInputPairObjects(ObjectMask, ObjectMask, Optional<EnergyStack>) - Constructor for class org.anchoranalysis.image.feature.input.FeatureInputPairObjects: Constructs a FeatureInputPairObjects with two ObjectMasks and an optional EnergyStack.
FeatureInputPairObjects(ObjectMask, ObjectMask, Optional<EnergyStack>, Optional<ObjectMask>) - Constructor for class org.anchoranalysis.image.feature.input.FeatureInputPairObjects: Constructs a FeatureInputPairObjects with two ObjectMasks, an optional EnergyStack, and an optional merged ObjectMask.
FeatureInputPairObjects(ObjectMask, ObjectMask, EnergyStack) - Constructor for class org.anchoranalysis.image.feature.input.FeatureInputPairObjects: Constructs a FeatureInputPairObjects with two ObjectMasks and an EnergyStack.
FeatureInputSingleObject - Class in org.anchoranalysis.image.feature.input: An input representing a single object-mask (with maybe an energy-stack associated).
FeatureInputSingleObject(ObjectMask) - Constructor for class org.anchoranalysis.image.feature.input.FeatureInputSingleObject: Constructs a FeatureInputSingleObject with an ObjectMask.
FeatureInputSingleObject(ObjectMask, Optional<EnergyStack>) - Constructor for class org.anchoranalysis.image.feature.input.FeatureInputSingleObject: Constructs a FeatureInputSingleObject with an ObjectMask and an optional EnergyStack.
FeatureInputSingleObject(ObjectMask, EnergyStack) - Constructor for class org.anchoranalysis.image.feature.input.FeatureInputSingleObject: Constructs a FeatureInputSingleObject with an ObjectMask and an EnergyStack.
FeatureInputStack - Class in org.anchoranalysis.image.feature.input: A feature input that represents an energy stack.
FeatureInputStack() - Constructor for class org.anchoranalysis.image.feature.input.FeatureInputStack: Constructs a FeatureInputStack with an empty energy stack.
FeatureInputStack(Optional<EnergyStackWithoutParameters>) - Constructor for class org.anchoranalysis.image.feature.input.FeatureInputStack: Constructs a FeatureInputStack with an optional energy stack.
FeatureInputStack(EnergyStackWithoutParameters) - Constructor for class org.anchoranalysis.image.feature.input.FeatureInputStack: Constructs a FeatureInputStack with the given energy stack.
FeatureListEvaluator<T> - Class in org.anchoranalysis.image.feature.bean.evaluator: Defines a list of features and provides a means to calculate inputs for it, a session.
FeatureListEvaluator() - Constructor for class org.anchoranalysis.image.feature.bean.evaluator.FeatureListEvaluator
FeatureObjectCollection - Class in org.anchoranalysis.image.feature.bean.object.collection: A base class for a feature that accepts a ObjectCollection as input.
FeatureObjectCollection() - Constructor for class org.anchoranalysis.image.feature.bean.object.collection.FeatureObjectCollection
FeaturePairObjects - Class in org.anchoranalysis.image.feature.bean.object.pair: An abstract base class for features that operate on pairs of objects.
FeaturePairObjects() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.FeaturePairObjects
FeatureSingleObject - Class in org.anchoranalysis.image.feature.bean.object.single: An abstract base class for features that operate on a single object.
FeatureSingleObject() - Constructor for class org.anchoranalysis.image.feature.bean.object.single.FeatureSingleObject
FeatureStack - Class in org.anchoranalysis.image.feature.bean: An abstract base class for features that operate on image stacks.
FeatureStack() - Constructor for class org.anchoranalysis.image.feature.bean.FeatureStack
FeatureTableCalculator<T> - Interface in org.anchoranalysis.image.feature.calculator: A feature-calculator with additional functions for encoding the output in a tabular format with column names.
First - Class in org.anchoranalysis.image.feature.bean.object.pair: Evaluates a feature on the first object in a pair of objects.
First() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.First
First(Feature<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.First: Creates a new instance that will evaluate the given feature on the first object of a pair.
FIRST - Enum constant in enum class org.anchoranalysis.image.feature.calculation.CalculateInputFromPair.Extract: Extract the first object from the pair.

G

getAxis() - Method in class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity: The axis along which to calculate the center of gravity.
getCalculator() - Method in class org.anchoranalysis.image.feature.calculator.NamedFeatureCalculatorMulti: The multi-feature calculator.
getDictionary() - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator: Parameters to optionally associated with stackEnergy, and meaningless if stackEnergy is not specified.
getDirection() - Method in class org.anchoranalysis.image.feature.bean.physical.ConvertToPhysicalDistance: Direction of the distance being converted, defaults to a unit vector along the X-axis.
getEmptyValue() - Method in class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity: The value to return if the center of gravity calculation results in NaN.
getFeature() - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator: The single feature that will be calculated (possibly repeatedly) in the session.
getFeatureProvider() - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator: The single feature that will be calculated (possibly repeatedly) in the session
getFeatures() - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureListEvaluator: A list of providers, combined together to form a list of features, to be calculated in a session.
getFirst() - Method in class org.anchoranalysis.image.feature.input.FeatureInputPairObjects: Gets the first ObjectMask.
getHistogram() - Method in class org.anchoranalysis.image.feature.input.FeatureInputHistogram: The histogram associated with this feature input.
getImage() - Method in class org.anchoranalysis.image.feature.calculator.merged.MergedPairsFeatures
getItem() - Method in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair: The feature to be applied to individual objects.
getMerged() - Method in class org.anchoranalysis.image.feature.input.FeatureInputPairObjects: Returns a merged version of the two objects.
getMergedOptional() - Method in class org.anchoranalysis.image.feature.input.FeatureInputPairObjects: Gets the optional merged ObjectMask.
getMetadata() - Method in class org.anchoranalysis.image.feature.input.FeatureInputImageMetadata: The image metadata.
getNames() - Method in class org.anchoranalysis.image.feature.calculator.NamedFeatureCalculatorMulti: The list of feature names associated with the calculator.
getObject() - Method in class org.anchoranalysis.image.feature.input.FeatureInputSingleObject: The object mask associated with this input.
getObjects() - Method in class org.anchoranalysis.image.feature.input.FeatureInputObjectCollection: The collection of objects associated with this feature input.
getPair() - Method in class org.anchoranalysis.image.feature.calculator.merged.MergedPairsFeatures
getResolutionOptional() - Method in class org.anchoranalysis.image.feature.input.FeatureInputHistogram: Gets the optional resolution information.
getSecond() - Method in class org.anchoranalysis.image.feature.input.FeatureInputPairObjects: Gets the second ObjectMask.
getSingle() - Method in class org.anchoranalysis.image.feature.calculator.merged.MergedPairsFeatures
getStackEnergy() - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator: Optionally specifies an energy-stack to be associated with every calculation input.
getUnitType() - Method in class org.anchoranalysis.image.feature.bean.physical.FeatureConvertUnits: The type of unit to convert to, represented as a string (e.g., "um" for micrometers).
getValueIfEmpty() - Method in class org.anchoranalysis.image.feature.bean.histogram.FeatureHistogramStatistic: The value to return iff exceptionifEmpty is false.

H

hashCode() - Method in class org.anchoranalysis.image.feature.calculation.CalculateInputFromPair
hashCode() - Method in class org.anchoranalysis.image.feature.calculation.CalculateNumberVoxels
hashCode() - Method in class org.anchoranalysis.image.feature.calculator.NamedFeatureCalculatorMulti
hashCode() - Method in class org.anchoranalysis.image.feature.input.FeatureInputImageMetadata
hashCode() - Method in class org.anchoranalysis.image.feature.input.FeatureInputObjectCollection
hashCode() - Method in class org.anchoranalysis.image.feature.input.FeatureInputPairObjects
hashCode() - Method in class org.anchoranalysis.image.feature.input.FeatureInputSingleObject
hashCode() - Method in class org.anchoranalysis.image.feature.input.FeatureInputStack

I

includeFirst() - Method in class org.anchoranalysis.image.feature.calculator.merged.MergedPairsInclude: Checks if the first object should be included.
includeFirstOrSecond() - Method in class org.anchoranalysis.image.feature.calculator.merged.MergedPairsInclude: Checks if either the first or second object should be included.
includeMerged() - Method in class org.anchoranalysis.image.feature.calculator.merged.MergedPairsInclude: Checks if the merged object should be included.
includeSecond() - Method in class org.anchoranalysis.image.feature.calculator.merged.MergedPairsInclude: Checks if the second object should be included.
InitializationFactory - Class in org.anchoranalysis.image.feature.calculator: A factory for creating FeatureInitialization objects.
initialize(List<Histogram>, Optional<Dictionary>) - Method in class org.anchoranalysis.image.feature.bean.VoxelScore: Initializes the voxels-score.
inputType() - Method in class org.anchoranalysis.image.feature.bean.FeatureEnergy
inputType() - Method in class org.anchoranalysis.image.feature.bean.FeatureHistogram
inputType() - Method in class org.anchoranalysis.image.feature.bean.FeatureImageMetadata
inputType() - Method in class org.anchoranalysis.image.feature.bean.FeatureStack
inputType() - Method in class org.anchoranalysis.image.feature.bean.object.collection.FeatureObjectCollection
inputType() - Method in class org.anchoranalysis.image.feature.bean.object.pair.FeaturePairObjects
inputType() - Method in class org.anchoranalysis.image.feature.bean.object.single.FeatureSingleObject
isAcceptMissingResolution() - Method in class org.anchoranalysis.image.feature.bean.physical.WithResolutionBase: Whether to return Double.NaN (if true) or throw an exception (if false) when image resolution is missing.
isExceptionIfEmpty() - Method in class org.anchoranalysis.image.feature.bean.histogram.FeatureHistogramStatistic: If true, then an exception is thrown if the histogram is empty, otherwise FeatureHistogramStatistic.valueIfEmpty is returned.
isMip() - Method in class org.anchoranalysis.image.feature.bean.object.single.NumberVoxels: If true, calculates the number of voxels in the maximum intensity projection (MIP) of the object.

M

mapCalculator(UnaryOperator<FeatureCalculatorMulti<T>>) - Method in class org.anchoranalysis.image.feature.calculator.NamedFeatureCalculatorMulti: Creates a new instance by applying a mapping function to the calculator.
Mean - Class in org.anchoranalysis.image.feature.bean.histogram: Calculates the mean value of a histogram.
Mean() - Constructor for class org.anchoranalysis.image.feature.bean.histogram.Mean
Merged - Class in org.anchoranalysis.image.feature.bean.object.pair: Evaluates a feature on the merged object created from a pair of objects.
Merged() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.Merged
Merged(Feature<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.Merged: Creates a new instance that will evaluate the given feature on the merged object of a pair.
MERGED - Enum constant in enum class org.anchoranalysis.image.feature.calculation.CalculateInputFromPair.Extract: Extract the merged object from the pair.
MergedPairsFeatures - Class in org.anchoranalysis.image.feature.calculator.merged: The list of features that can be used in a PairsTableCalculator
MergedPairsFeatures(FeatureList<FeatureInputPairObjects>) - Constructor for class org.anchoranalysis.image.feature.calculator.merged.MergedPairsFeatures: Creates to only calculate pair features.
MergedPairsFeatures(FeatureList<FeatureInputStack>, FeatureList<FeatureInputSingleObject>, FeatureList<FeatureInputPairObjects>) - Constructor for class org.anchoranalysis.image.feature.calculator.merged.MergedPairsFeatures: Creates with features for single, pair and image as a whole.
MergedPairsInclude - Class in org.anchoranalysis.image.feature.calculator.merged: Specifies which parts of a merged pair to include in calculations.
MergedPairsInclude() - Constructor for class org.anchoranalysis.image.feature.calculator.merged.MergedPairsInclude: Constructs a MergedPairsInclude with all options set to true.
MergedPairsInclude(boolean, boolean, boolean) - Constructor for class org.anchoranalysis.image.feature.calculator.merged.MergedPairsInclude: Constructs a MergedPairsInclude with specified inclusion options.
Minimum - Class in org.anchoranalysis.image.feature.bean.object.pair: Calculates the minimum value of a feature applied to both objects in a pair.
Minimum() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.Minimum
Minimum(Feature<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.Minimum: Creates a new instance that will calculate the minimum feature value from a pair of objects.

N

NamedFeatureCalculatorMulti<T> - Class in org.anchoranalysis.image.feature.calculator: A FeatureCalculatorMulti with associated feature-names.
NamedFeatureCalculatorMulti(FeatureCalculatorMulti<T>, FeatureNameList) - Constructor for class org.anchoranalysis.image.feature.calculator.NamedFeatureCalculatorMulti: Creates a new NamedFeatureCalculatorMulti instance.
numberImageFeatures() - Method in class org.anchoranalysis.image.feature.calculator.merged.MergedPairsFeatures: Gets the number of image features.
numberPairFeatures() - Method in class org.anchoranalysis.image.feature.calculator.merged.MergedPairsFeatures: Gets the number of pair features.
numberSingleFeatures() - Method in class org.anchoranalysis.image.feature.calculator.merged.MergedPairsFeatures: Gets the number of single object features.
NumberVoxels - Class in org.anchoranalysis.image.feature.bean.object.single: Calculates the number of voxels in a single object.
NumberVoxels() - Constructor for class org.anchoranalysis.image.feature.bean.object.single.NumberVoxels

O

org.anchoranalysis.image.feature.bean - package org.anchoranalysis.image.feature.bean: Beans pertaining to feature definition and calculation.
org.anchoranalysis.image.feature.bean.evaluator - package org.anchoranalysis.image.feature.bean.evaluator: Beans that define context (which feature, which energy-stack) for evaluating feature-inputs.
org.anchoranalysis.image.feature.bean.histogram - package org.anchoranalysis.image.feature.bean.histogram: Features that operate on a Histogram.
org.anchoranalysis.image.feature.bean.object.collection - package org.anchoranalysis.image.feature.bean.object.collection: Features that operate on a ObjectCollection.
org.anchoranalysis.image.feature.bean.object.pair - package org.anchoranalysis.image.feature.bean.object.pair: Features that operate on a pair of ObjectMasks.
org.anchoranalysis.image.feature.bean.object.single - package org.anchoranalysis.image.feature.bean.object.single: Features that operate on a single ObjectMask.
org.anchoranalysis.image.feature.bean.physical - package org.anchoranalysis.image.feature.bean.physical: Features that convert to/from physical spatial units (e.g.
org.anchoranalysis.image.feature.calculation - package org.anchoranalysis.image.feature.calculation: Reusable implementations of CalculationPart related to images.
org.anchoranalysis.image.feature.calculator - package org.anchoranalysis.image.feature.calculator: Implementations of FeatureCalculatorMulti related to images, especially to create tables of feature-calculations.
org.anchoranalysis.image.feature.calculator.merged - package org.anchoranalysis.image.feature.calculator.merged: A particular implementation of FeatureCalculatorMulti for feature-calculations based upon pairs of image-objects.
org.anchoranalysis.image.feature.input - package org.anchoranalysis.image.feature.input: Image-related implementations of FeatureInput.

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PairsTableCalculator - Class in org.anchoranalysis.image.feature.calculator.merged: A feature-session to evaluate pairs of objects.
PairsTableCalculator(MergedPairsFeatures) - Constructor for class org.anchoranalysis.image.feature.calculator.merged.PairsTableCalculator: Constructs a PairsTableCalculator with default inclusion and error suppression.
PairsTableCalculator(MergedPairsFeatures, MergedPairsInclude, boolean) - Constructor for class org.anchoranalysis.image.feature.calculator.merged.PairsTableCalculator

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RatioFirstToSecond - Class in org.anchoranalysis.image.feature.bean.object.pair: Ratio of first-object to second-object in a pair.
RatioFirstToSecond() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.RatioFirstToSecond

S

Second - Class in org.anchoranalysis.image.feature.bean.object.pair: Evaluates a feature on the second object in a pair of objects.
Second() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.Second
Second(Feature<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.Second: Creates a new instance that will evaluate the given feature on the second object of a pair.
SECOND - Enum constant in enum class org.anchoranalysis.image.feature.calculation.CalculateInputFromPair.Extract: Extract the second object from the pair.
setAcceptMissingResolution(boolean) - Method in class org.anchoranalysis.image.feature.bean.physical.WithResolutionBase: Whether to return Double.NaN (if true) or throw an exception (if false) when image resolution is missing.
setAxis(String) - Method in class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity: The axis along which to calculate the center of gravity.
setDictionary(DictionaryProvider) - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator: Parameters to optionally associated with stackEnergy, and meaningless if stackEnergy is not specified.
setDirection(DirectionVectorBean) - Method in class org.anchoranalysis.image.feature.bean.physical.ConvertToPhysicalDistance: Direction of the distance being converted, defaults to a unit vector along the X-axis.
setEmptyValue(double) - Method in class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity: The value to return if the center of gravity calculation results in NaN.
setExceptionIfEmpty(boolean) - Method in class org.anchoranalysis.image.feature.bean.histogram.FeatureHistogramStatistic: If true, then an exception is thrown if the histogram is empty, otherwise FeatureHistogramStatistic.valueIfEmpty is returned.
setFeature(Feature<T>) - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator: The single feature that will be calculated (possibly repeatedly) in the session.
setFeatureProvider(FeatureProvider<T>) - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator: The single feature that will be calculated (possibly repeatedly) in the session
setFeatures(List<FeatureProvider<T>>) - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureListEvaluator: A list of providers, combined together to form a list of features, to be calculated in a session.
setItem(Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair: The feature to be applied to individual objects.
setMip(boolean) - Method in class org.anchoranalysis.image.feature.bean.object.single.NumberVoxels: If true, calculates the number of voxels in the maximum intensity projection (MIP) of the object.
setStackEnergy(Provider<Stack>) - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator: Optionally specifies an energy-stack to be associated with every calculation input.
setUnitType(String) - Method in class org.anchoranalysis.image.feature.bean.physical.FeatureConvertUnits: The type of unit to convert to, represented as a string (e.g., "um" for micrometers).
setValueIfEmpty(double) - Method in class org.anchoranalysis.image.feature.bean.histogram.FeatureHistogramStatistic: The value to return iff exceptionifEmpty is false.
SingleTableCalculator - Class in org.anchoranalysis.image.feature.calculator: A feature table calculator for single objects.
SingleTableCalculator(NamedFeatureStore<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.image.feature.calculator.SingleTableCalculator: Creates a new SingleTableCalculator instance.
sizeFeatures() - Method in class org.anchoranalysis.image.feature.calculator.merged.PairsTableCalculator
sizeFeatures() - Method in class org.anchoranalysis.image.feature.calculator.SingleTableCalculator
start(ImageInitialization, Optional<EnergyStack>, Logger) - Method in interface org.anchoranalysis.image.feature.calculator.FeatureTableCalculator: Initializes a feature store that has the same structure as that previously created by createFeatures() from the same object.
start(ImageInitialization, Optional<EnergyStack>, Logger) - Method in class org.anchoranalysis.image.feature.calculator.merged.PairsTableCalculator
start(ImageInitialization, Optional<EnergyStack>, Logger) - Method in class org.anchoranalysis.image.feature.calculator.SingleTableCalculator
SubtractSecondFromFirst - Class in org.anchoranalysis.image.feature.bean.object.pair: Subtract second-object from first-object in a pair.
SubtractSecondFromFirst() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.SubtractSecondFromFirst

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toString() - Method in class org.anchoranalysis.image.feature.calculator.NamedFeatureCalculatorMulti
toString() - Method in class org.anchoranalysis.image.feature.input.FeatureInputPairObjects: Returns a string representation of the object.
toString() - Method in class org.anchoranalysis.image.feature.input.FeatureInputSingleObject: Returns a string representation of the object.

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valueFromFirst(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair: Calculates the feature value for the first object in the pair.
valueFromMerged(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair: Calculates the feature value for the merged object from the pair.
valueFromSecond(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair: Calculates the feature value for the second object in the pair.
valueOf(String) - Static method in enum class org.anchoranalysis.image.feature.calculation.CalculateInputFromPair.Extract: Returns the enum constant of this class with the specified name.
values() - Static method in enum class org.anchoranalysis.image.feature.calculation.CalculateInputFromPair.Extract: Returns an array containing the constants of this enum class, in the order they are declared.
VoxelScore - Class in org.anchoranalysis.image.feature.bean: Calculates a per-voxel score.
VoxelScore() - Constructor for class org.anchoranalysis.image.feature.bean.VoxelScore

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WithResolutionBase<T> - Class in org.anchoranalysis.image.feature.bean.physical: Base class for a feature that requires input resolution to be calculated.
WithResolutionBase() - Constructor for class org.anchoranalysis.image.feature.bean.physical.WithResolutionBase
WithResolutionBase(Feature<T>) - Constructor for class org.anchoranalysis.image.feature.bean.physical.WithResolutionBase: Creates a new instance with a specified feature.

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