All Classes

Class	Description
ArbitraryInsidePoint	Calculates deterministically a point that is definitely inside the object-mask and outputs a selected axis value.
Area<T extends org.anchoranalysis.feature.input.FeatureInputEnergy>	Area of the stack (XY dimensions only, Z dimension is not considered).
AsObjectMask	Treats a channel as an object-mask, assuming binary values of 0 and 255 and calls an object-mask feature
AtBorderBase	Base class for features that check if an object is at the border of an image.
AtBorderXY	Checks if an object's bounding box is at the border of the image in the XY plane.
AtBorderZ	Checks if an object's bounding box is at the border of the image in the Z dimension.
BitDepthPerChannel	The bit-depth of the image per channel.
BoundingBoxAlongAxisBase	Base class for features that calculate a value along a specific axis of an object's bounding box.
BoundingBoxExtentAlongAxis	Calculates the extent of an object's bounding box along a specified axis.
BoundingBoxMaximumAlongAxis	Calculates the maximum coordinate of an object's bounding box along a specified axis.
BoundingBoxMinimumAlongAxis	Calculates the minimum coordinate of an object's bounding box along a specified axis.
BoundingBoxNumberVoxels	Calculates the number of voxels in the bounding box of an object.
CalculateDeriveObjectInput	Derives a FeatureInputSingleObject from a FeatureInputStack by extracting an object mask from a specific energy channel.
CalculateDilation	Calculates the dilation of an ObjectMask.
CalculateDilationMap	Calculates a map of dilated ObjectMasks for different iteration counts.
CalculateErosion	Calculates the erosion of an ObjectMask.
CalculateErosionMap	Calculates a map of eroded ObjectMasks for different iteration counts.
CalculateHistogram	Calculates a Histogram from a specific channel in a FeatureInputStack.
CalculateHistogramMasked	Calculated a histogram for a specific region on a channel, as identified by a mask in another channel
CalculateIncrementalOperationMap	Calculates incremental operations on ObjectMasks and stores the results in a map.
CalculateInputFromDelegate<S,T extends org.anchoranalysis.feature.input.FeatureInput,U>	A base class for CalculationParts that derive from an existing "delegate" calculation.
CalculateInputFromDelegateOption<S extends org.anchoranalysis.feature.input.FeatureInput,T extends org.anchoranalysis.feature.input.FeatureInput,U>	Like CalculateInputFromDelegate except assumes optional return value and no parameters.
CalculateIntersecting	Calculates a FeatureInputPairObjects from a FeatureInputSingleObject and an intersecting ObjectCollection.
CalculateLevel	Calculates a level score based on voxel intensity and a given threshold.
CalculateLevelBase	Base class for calculating a score based on a threshold level derived from a histogram.
CalculateObjectMask	Calculates an ObjectMask based on a specified number of iterations.
CalculateShellObjectMask	Calculates a shell ObjectMask by performing dilation and erosion operations.
CoefficientOfVariation	Calculates the coefficient of variation of all the values in the histogram.
CombineObjectsForFeatures<T extends org.anchoranalysis.feature.input.FeatureInput>	A way to combine (or not combine) objects so that they provide a feature-table.
CostOverlapWithinMidpointDistance	TODO the center-of-gravity calculation can be turned into a FeatureCalculation which is cacheable
Count	Counts the number of items in a histogram (posssibly in relation to a threshold: above, below etc.)
CountEqual	Counts the number of voxels in an object that have a specific intensity value in a channel.
DataTypeMaxIntensity<T extends org.anchoranalysis.feature.input.FeatureInputEnergy>	The maximum-intensity allowed by the data-type of the stack.
DerivedObject	A base class for features that operate on a derived object mask and calculate a feature on it.
DeriveFromPair	Embeds each feature in a FeatureDeriveFromPair feature (first, second or merge) and prepends with a string.
Difference
DifferenceCalculateLevelStandardDeviation	Similar to Difference but calculates the width as the standard-deviation of the histogram
EachObjectIndependently	Selects features and objects directly from the input list, treating each object independently.
Erode	A feature that erodes an object mask and then calculates another feature on the eroded object.
Extent<T extends org.anchoranalysis.feature.input.FeatureInputEnergy>	Width/height/depth of energy-stack in pixels depending on axis.
FeatureEnergyChannel	A feature that uses a channel from the energy-stack as identified by an index.
FeatureIntersectingObjects	An abstract base class for features that calculate values based on intersecting objects.
FeatureIntersectingObjectsSingleElement	A feature that calculates a value based on intersecting objects, considering each intersecting object individually.
FeatureIntersectingObjectsThreshold	An abstract feature that calculates a value based on intersecting objects, considering each intersecting object individually and applying a threshold.
FeatureListProviderAggregatePair	Calculates features on each part of a pair (first, second, merged etc.) and then reduces the calculation to a single number.
FeatureSingleObjectFromShared<T extends org.anchoranalysis.feature.input.FeatureInputEnergy>	Calculates object-masks from entities in shared, using the feature-input only for an energy-stack.
ForSpecificAxis<T extends org.anchoranalysis.feature.input.FeatureInputEnergy>	Dimensions-calculation for one specific axis only.
FromDictionaryBase	An abstract base class for features that require a Dictionary for initialization.
FromDimensionsBase<T extends org.anchoranalysis.feature.input.FeatureInputDimensions>	Base class for features that are calculated from Dimensions.
GradientMagnitude	Calculates the mean of the intensity-gradient defined by multiple Energy channels in a particular direction
GradientMeanForAxis	Calculates the mean of the intensity-gradient defined by multiple Energy channels in a particular direction
HasTouchingVoxels	A simple scheme for counting the touching voxels.
Identity	A voxel score that can optionally normalize and adjust the intensity values.
IdentityImposeValueRelationToHistogram	A voxel score that imposes a value relation to a histogram.
ImageMomentsBase	A base class for features that are calculated using image-moments.
Intensity	Calculates a statistic from the intensity values covered by a single object-mask in a channel.
Intensity	The intensity of a particular channel of the stack, by default the mean-intensity.
IntensityGradientBase	Base class for features that calculate intensity gradients from multiple channels.
IntensityMeanMaxSlice	Calculates the maximum mean intensity across all slices of an object in a channel.
IntensityMeanShell	Constructs a 'shell' around an object by a number of dilation/erosion operations (not including the original object-mask) and measures the mean intensity of this shell
IntensityMeanShellBase	Constructs a shell around an object-mask using a standard dilation and erosion process.
IntensityMeanShellMaxSlice	Constructs a 'shell' around an object by a number of dilation/erosion operations (not including the original object-mask) and measures the mean intensity of this shell
IntensityMoments	Calculate various moment-related statistics about the intensity of each channel of an image.
Intersection	Finds the intersection of two objects and calculates a feature on it
Kurtosis	Calculates the kurtosis of all the values in the histogram.
LevelFromHistogram	Calculates a level (a threshold-value) from a histogram.
ListWithThumbnails<T,S>	A list of items with an associated thumbnail-batch.
MaskAsSingleObject<T extends org.anchoranalysis.feature.input.FeatureInputEnergy>	Calculates a feature, treating a mask as a single-object on the energy-stack.
MaxFeatureIntersectingObjects	1.
Maximum	Calculates the maximum value in a histogram.
MaximumNumberContourVoxelsOnSlice	Maximum number of voxels on any slice's contour (edge voxels) across all slices.
MaximumNumberVoxelsOnSlice	Maximum number of voxels in the object-mask across all slices.
MeanAcrossObjects<T extends org.anchoranalysis.feature.input.FeatureInputEnergy>	Calculates the mean of a feature applied to each connected component
MeanRaisedToPower	Calculates the mean value in a Histogram, and raises it to a power.
Median	Calculates the median value in a Histogram.
MinFeatureIntersectingObjectsAboveThreshold	1.
Minimum	Calculates the minimum value in a Histogram.
Mode	Calculates the skewness of all the values in the histogram.
MorphologicalIterations	Specifies a certain number of iterations of the morphological operations of dilation and erosion.
NormalizeByConstant	Normalizes the voxel intensity by dividing it by a constant value.
NormalizeByMax	This assumes the histograms correspond to the energy channels exactly (in terms of indexing)
NumberChannels	The number of channels in an image.
NumberChannels	The number of channels in an image-stack.
NumberDistinctValues	Number of unique values in histogram.
NumberFrames	The number of frames in an image.
NumberIntersectingObjects	A feature that calculates the number of objects intersecting with the input object.
NumberIntersectingObjectsAboveThreshold	1.
NumberNeighboringVoxels	Calculates the number of voxels on the object that have a neighbor.
NumberObjects	Calculates the number of objects in a FeatureInputObjectCollection.
NumberRemovedVoxelsAfterClosing	How many pixels are removed after a morphological closing operation on the object-mask.
NumberResolutionLevels	The number of resolution-levels in an image in a file.
NumberSeries	The number of series in an image-file.
NumberTouchingVoxelFaces	A scheme for counting the touching voxels by intersection of object-masks
NumberTouchingVoxels	A scheme for counting touching voxels.
NumberVoxelsAtBorder	Calculates the number of voxels at the border of an object.
ObjectAggregationBase<T extends org.anchoranalysis.feature.input.FeatureInputEnergy>	Calculates a feature for a set of objects using this stack as an energy-stack, and aggregates.
ObjectRadiusStandardDeviation	Calculates the standard deviation of distances from surface voxels to the centroid of an ObjectMask.
OutlineKernelBase	Base class for features that apply a kernel to the outline of an object.
OutsideRange	Calculates a voxel score based on whether the voxel intensity is outside a specified range.
OverlapRelative	Expresses the number of intersecting pixels between two objects as a ratio to a denominator.
OverlapRelativeToFirst	Calculates the overlap ratio between two objects relative to the size of the first object.
OverlapRelativeToMaxVolume	Overlap ratio to the maximum number of pixels
OverlapRelativeToMerged	Calculates the overlap ratio between two objects relative to the size of the merged object.
OverlapRelativeToSecond	Calculates the overlap ratio between two objects relative to the size of the second object.
PairedWithMask	Evaluates the object as a pair-feature together with the binary-mask from the shared objects.
PairNeighbors	Creates a set of features, that creates pairs of neighboring-objects and applies a mixture of single-object features and pair features.
ParamFromCollection<T extends org.anchoranalysis.feature.input.FeatureInput>	Retrieves a parameter as stored in a Dictionary in SharedObjects.
PermuteDivideByParam<T extends org.anchoranalysis.feature.input.FeatureInputDictionary>	Similar to FeatureListProviderPermute but embeds the feature in a GaussianScore
PermuteFeature<S,T extends org.anchoranalysis.feature.input.FeatureInput>	Permutes one or more properties of a Feature, so as to create a set of Features
PermuteFeatureBase<T extends org.anchoranalysis.feature.input.FeatureInput>	Creates permutations of a feature by modifying a particular property of it in different ways.
PermuteFeatureSequenceInteger<T extends org.anchoranalysis.feature.input.FeatureInputDictionary>	Permutes a property on a feature with a sequence of integers.
PermuteFirstSecondOrder<T extends org.anchoranalysis.feature.input.FeatureInputDictionary>	Permutes a feature by applying first and second order statistical operations.
PermuteFirstSecondOrder.CreateFirstSecondOrder<T extends org.anchoranalysis.feature.input.FeatureInput>	Functional interface for creating first and second order statistical operations.
PermuteGaussianScore<T extends org.anchoranalysis.feature.input.FeatureInputDictionary>	Permutes a feature by embedding it in a GaussianCumulative score.
PermuteZScore<T extends org.anchoranalysis.feature.input.FeatureInputDictionary>	Permutes a feature by embedding it in a ZScore.
PrincipalAxisEccentricity	Calculates the eccentricity of the Principal Axes (as defined by Image Moments).
PrincipalAxisLength	The length of a principal-axis (as defined by Image Moments).
PrincipalAxisOrientation	An element from orientation of a principal-axis (as defined by Image Moments).
Quantile	Calculates a specified quantile value from a Histogram.
QuantileAcrossConnectedComponents	Calculates the median of a feature applied to each connected component
QuantileAcrossObjects<T extends org.anchoranalysis.feature.input.FeatureInputEnergy>	Calculates the quantile of a feature applied to each connected component
Range	The range (difference in values) between two quantiles
RatioNonMode	Calculates the ratio of non-mode pixels to total pixels in a Histogram.
RatioPrincipalAxisLength	Calculates the ratio of prinicpal-axis length using Image Moments.
RatioThreshold	Calculates the ratio of values in a Histogram that satisfy a specified threshold condition.
ReduceFirstAndSecond	Calculates the aggregate of a feature applied to both the first and second objects in a FeatureInputPairObjects.
ReduceRatioFirstAndSecond	Calculates the aggregate of the ratio of first:second and second :first for a FeatureInputPairObjects
RejectIfIntensityLessThan	Rejects voxels with intensity less than a specified minimum, otherwise calculates a score using another VoxelScore.
ShapeRegularityCenterSlice	Calculates the shape regularity of the center slice of an ObjectMask.
ShapeRegularityMaximumIntensityProjection	Calculates the shape regularity of the maximum intensity projection of an ObjectMask.
Shell	Creates a shell around an ObjectMask by applying morphological operations.
SingleChannel	A score that is calculated on a single channel only.
Skewness	Calculates the skewness of all the values in the histogram.
SpecificAxisBase	A feature based on one specific principal-axis as identified by image moments.
SpecificEnergyChannelBase	A base class for features that operate on a specific channel from the energy stack.
StandardDeviation	Calculates the standard deviation of values in a Histogram.
SubtractReducedFromMerged	Calculates merged - reduce(first,second) for a FeatureInputPairObjects
Sum	Calculates the sum of all values in a Histogram.
SurfaceNumberVoxelFaces	The number of voxel-faces along the surface (the faces of each voxel that touch outside)
SurfaceNumberVoxels	The number of voxels on the surface (all voxels on the exterior of the object)
SurfaceNumberVoxelsBase	A base class for features that calculate the number of voxels on the surface of an object.
TextureScore	From Page 727 from Lin et al (A Multi-Model Approach to Simultaneous Segmentation and Classification of Heterogeneous Populations of Cell Nuclei
ThresholdHistogram	Thresholds the histogram (using a weightedOtsu) and then applies a feature to the thresholded version.
TotalCount	Calculates the total count of all entries in a Histogram.
TouchingVoxels	Base class for features that calculate touching with a dilated bounding box intersection.
UnitsWithinRange<T extends org.anchoranalysis.feature.input.FeatureInputWithResolution>	Checks if a value lies within a range defined by units (a minimum and maximum boundary)
Variance	Calculates the variance of all the values in the histogram.
Volume<T extends org.anchoranalysis.feature.input.FeatureInputEnergy>	Calculates the volume (x, y and z dimensions) of the scene from the dimensions
VoxelPhysicalSize<T extends org.anchoranalysis.feature.input.FeatureInputEnergy>	The physical size of a pixel in a specific dimension.