Uses of Interface
org.anchoranalysis.bean.Provider

Packages that use Provider

Package	Description
org.anchoranalysis.bean	Defining, loading, initializing Anchor Beans.
org.anchoranalysis.bean.shared.dictionary	Setting, referencing and initializing key-value parameters.
org.anchoranalysis.feature.bean.list	A feature-list (custom list type for features) and associated providers.
org.anchoranalysis.feature.bean.provider	Provider of a single feature.
org.anchoranalysis.image.bean.nonbean.init	Classes that aren't AnchorBeans that pertain to the initialization of image-related beans.
org.anchoranalysis.image.bean.provider	Base classes for providers of different core data entities related to images.
org.anchoranalysis.image.bean.provider.stack	A provider of Stacks.
org.anchoranalysis.image.feature.bean.evaluator	Beans that define context (which feature, which energy-stack) for evaluating feature-inputs.
org.anchoranalysis.image.io.bean.stack.combine	Beans to combine multiple stacks into a single stack before outputting.
org.anchoranalysis.io.input.bean.dictionary	Methods to provide a Dictionary.
org.anchoranalysis.io.input.bean.path.provider	Methods to provide a single file-path.
org.anchoranalysis.mpp.bean.provider	Implementations of Provider involving Marks.
org.anchoranalysis.plugin.fiji.bean.channel.provider	Implementations of ChannelProvider that use FIJI.
org.anchoranalysis.plugin.fiji.bean.channel.provider.distance	Euclidean Distance Transform implementations via FIJI.
org.anchoranalysis.plugin.fiji.bean.mask.provider	Implementations of MaskProvider that use FIJI.
org.anchoranalysis.plugin.image.bean.channel.provider	Implementations of ChannelProvider that are generic base-classes or otherwise abstract or general.
org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic	Implementations of ChannelProvider that perform arithmetic on voxels in one or more Channels.
org.anchoranalysis.plugin.image.bean.channel.provider.assign	Implementations of ChannelProvider that sets the values of the voxels in a Channel.
org.anchoranalysis.plugin.image.bean.channel.provider.convert	Implementations of ChannelProvider that converts a Channel from one voxel-type to another.
org.anchoranalysis.plugin.image.bean.channel.provider.gradient	Implementations of ChannelProvider that calculate the gradient of a Channel's voxels in one or more dimensions.
org.anchoranalysis.plugin.image.bean.channel.provider.intensity	Implementations of ChannelProvider that manipulate the intensity-values of the voxels of a Channel's voxels.
org.anchoranalysis.plugin.image.bean.channel.provider.mask	Implementations of ChannelProvider that involve conversion from or application of Masks.
org.anchoranalysis.plugin.image.bean.channel.provider.object	Implementations of ChannelProvider that involve conversion from or application of ObjectMasks.
org.anchoranalysis.plugin.image.bean.channel.provider.score	Implementations of ChannelProvider that assign a score to particular subregions of a channel.
org.anchoranalysis.plugin.image.bean.channel.provider.slice	Implementations of ChannelProvider that process 3D channels slice-by-slice.
org.anchoranalysis.plugin.image.bean.color.provider	Implementations of ColorProvider.
org.anchoranalysis.plugin.image.bean.dimensions.provider	Implementations of DimensionsProvider.
org.anchoranalysis.plugin.image.bean.histogram.provider	Implementations of HistogramProvider.
org.anchoranalysis.plugin.image.bean.mask.provider	Implementations of MaskProvider.
org.anchoranalysis.plugin.image.bean.mask.provider.combine	Implementations of MaskProvider that combine existing providers.
org.anchoranalysis.plugin.image.bean.mask.provider.convert	Implementations of MaskProvider that convert providers of other types to ObjectMasks.
org.anchoranalysis.plugin.image.bean.mask.provider.morphological	Implementations of MaskProvider that implement morphological operations.
org.anchoranalysis.plugin.image.bean.mask.provider.predicate	Provides if-else conditions to a MaskProvider.
org.anchoranalysis.plugin.image.bean.mask.provider.segment	Implementations of MaskProvider where an ObjectCollection is created by segmenting a Channel.
org.anchoranalysis.plugin.image.bean.mask.provider.slice	Implementations of MaskProvider that process 3D masks slice-by-slice.
org.anchoranalysis.plugin.image.bean.object.provider	Implementations of ObjectCollectionProvider.
org.anchoranalysis.plugin.image.bean.object.provider.connected	Implementations of ObjectCollectionProvider involving connected-components.
org.anchoranalysis.plugin.image.bean.object.provider.feature	Implementations of ObjectCollectionProvider involving feature calculation.
org.anchoranalysis.plugin.image.bean.object.provider.filter	Implementations of ObjectCollectionProvider that filter objects.
org.anchoranalysis.plugin.image.bean.object.provider.mask	Implementations of ObjectCollectionProvider involving a Mask.
org.anchoranalysis.plugin.image.bean.object.provider.merge	Implementations of ObjectCollectionProvider involving merging objects together.
org.anchoranalysis.plugin.image.bean.object.provider.morphological	Implementations of ObjectCollectionProvider involving morphological operations.
org.anchoranalysis.plugin.image.bean.object.provider.segment	Implementations of ObjectCollectionProvider involving segmentation.
org.anchoranalysis.plugin.image.bean.object.provider.slice	Implementations of ObjectCollectionProvider involving z-slice processing.
org.anchoranalysis.plugin.image.bean.object.provider.split	Implementations of ObjectCollectionProvider involving splitting objects into smaller objects.
org.anchoranalysis.plugin.image.bean.stack.provider	Implementations of StackProvider.
org.anchoranalysis.plugin.image.bean.stack.provider.color	Implementations of StackProvider that color portions of an image.
org.anchoranalysis.plugin.image.feature.bean.list	Implementations of FeatureListProvider.
org.anchoranalysis.plugin.image.feature.bean.list.pair	Implementations of FeatureListProvider with input-type FeatureInputPairObjects.
org.anchoranalysis.plugin.image.feature.bean.list.permute	Implementations of FeatureListProvider that derive new features with permuted property-values.
org.anchoranalysis.plugin.imagej.bean.channel.provider	Implementations of ChannelProvider that call ImageJ.
org.anchoranalysis.plugin.imagej.bean.channel.provider.filter	Filters using ImageJ.
org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments	Non-linear filters using ImageJ that use the statistical moments of the intensity values in the kernel.
org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank	Non-linear filters using ImageJ that use the statistical rank of the intensity values in the kernel.
org.anchoranalysis.plugin.imagej.bean.mask.provider	Implementations of MaskProvider that call ImageJ.
org.anchoranalysis.plugin.imagej.bean.object.provider	Implementations of ObjectCollectionProvider that call ImageJ.
org.anchoranalysis.plugin.imagej.bean.stack.provider	Implementations of StackProvider that call ImageJ.
org.anchoranalysis.plugin.mpp.bean.object.provider	Implementations of ObjectCollectionProvider.
org.anchoranalysis.plugin.mpp.bean.provider.collection	Implementation of MarkCollectionProvider.
org.anchoranalysis.plugin.mpp.bean.stack.provider	Implementations of StackProvider involving Mark or related classes.
org.anchoranalysis.plugin.opencv.bean.color	Operations involving color-spaces and OpenCV.
org.anchoranalysis.plugin.opencv.bean.feature	Extracting features using OpenCV.
org.anchoranalysis.plugin.points.bean	Beans that fit or otherwise manipulate sets of points.
org.anchoranalysis.plugin.points.bean.convexhull	Convex hull operations.

Uses of Provider in org.anchoranalysis.bean

Methods in org.anchoranalysis.bean with parameters of type Provider

Modifier and Type	Method	Description
static <T> Optional<T>	OptionalProviderFactory.create(Provider<T> provider)	Creates from a provider if non-null.

Uses of Provider in org.anchoranalysis.bean.shared.dictionary

Classes in org.anchoranalysis.bean.shared.dictionary that implement Provider

Modifier and Type	Class	Description
class	DictionaryProvider	Base class for beans that implement Provider to provide a Dictionary.
class	DictionaryProviderReference	References a particular Dictionary in shared-object-space.

Uses of Provider in org.anchoranalysis.feature.bean.list

Classes in org.anchoranalysis.feature.bean.list that implement Provider

Modifier and Type	Class	Description
class	Define<T extends FeatureInput>	Specifies a list of features directly without assigning any custom-naming.
class	DefinedNamed<T extends FeatureInput>	Specifies features via a list of names and associated with features.
class	DefineSingle<T extends FeatureInput>	Specifies a single feature directly without assigning any custom-naming.
class	FeatureListProvider<T extends FeatureInput>	Provides a list of Features with identical input-type.
class	PrependName	Prepends a string to the custom-name of each feature in a list.
class	ReferencingFeatureListProvider<T extends FeatureInput>	A base class for implementations of FeatureListProvider that may reference features created elsewhere.

Methods in org.anchoranalysis.feature.bean.list with parameters of type Provider

Modifier and Type	Method	Description
static <T extends FeatureInput> FeatureList<T>	FeatureListFactory.fromProvider(Provider<Feature<T>> featureProvider)	Creates a list for a single-feature created from a provider

Uses of Provider in org.anchoranalysis.feature.bean.provider

Classes in org.anchoranalysis.feature.bean.provider that implement Provider

Modifier and Type	Class	Description
class	FeatureProvider<T extends FeatureInput>	Provides a single Feature.
class	FeatureProviderBean<B,P>	Base class for FeatureRelatedBeans that implement Provider to provide an object of type S.
class	FeatureProviderDefine<T extends FeatureInput>	Defines a single Feature to provide via a bean property.
class	FeatureProviderReference	Provides an existing Feature identified by its name and optionally a feature-list in which is resides.

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

Methods in org.anchoranalysis.image.bean.nonbean.init with type parameters of type Provider

Modifier and Type	Method	Description
<S extends InitializableBean<?, V> & Provider<T>, T> void	PopulateStoreFromDefine.copyProviderInitialize(Class<?> defineClass, NamedProviderStore<T> destination)	Copies objects of a particular class (which must be a Provider) from define and initializes each.

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

Classes in org.anchoranalysis.image.bean.provider that implement Provider

Modifier and Type	Class	Description
class	BeanProviderAsStackBase<T,S>	A provider base-class that as well as providing type S, also provides a Stack.
class	ChannelProvider	Base class for beans that implement Provider to provide a Channel and associated Stack.
class	ChannelProviderBinary	Implementation of ChannelProvider that calls two ChannelProviders that must provide Channels of the same dimensions.
class	ChannelProviderTernary	Implementation of ChannelProvider that calls three ChannelProviders that must provide Channels of the same dimensions.
class	ChannelProviderUnary	Implementation of ChannelProvider that calls a single delegate ChannelProvider.
class	ColorProvider	Base class for beans that implement Provider to provide a ColorList.
class	DimensionsProvider	Base class for beans that implement Provider to provide Dimensions.
class	HistogramProvider	Base class for beans that implement Provider to provide a Histogram.
class	HistogramProviderUnary	Implementation of HistogramProvider that calls a single delegate HistogramProvider.
class	MaskProvider	Base class for beans that implement Provider to provide a Mask and associated Stack.
class	MaskProviderUnary	Implementation of MaskProvider that calls a single delegate MaskProvider.
class	ObjectCollectionProvider	Base class for beans that implement Provider to provide an ObjectCollection.
class	ObjectCollectionProviderUnary	Implementation of ObjectCollectionProvider that calls a single delegate Provider<ObjectCollection>.

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

Modifier and Type	Method	Description
Provider<Mask>	MaskProviderUnary.getMask()	The delegate Provider<Mask> that is called.
Provider<ObjectCollection>	ObjectCollectionProviderUnary.getObjects()	The delegate Provider<ObjectCollection> that is called.

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

Modifier and Type	Method	Description
void	MaskProviderUnary.setMask(Provider<Mask> mask)	The delegate Provider<Mask> that is called.
void	ObjectCollectionProviderUnary.setObjects(Provider<ObjectCollection> objects)	The delegate Provider<ObjectCollection> that is called.

Uses of Provider in org.anchoranalysis.image.bean.provider.stack

Classes in org.anchoranalysis.image.bean.provider.stack that implement Provider

Modifier and Type	Class	Description
class	Arrange	Creates a stack that combines other stacks.
class	StackProvider	Base class for beans that implement Provider to provide a Stack.
class	StackProviderUnary	Implementation of StackProvider that calls a single delegate Provider<Stack>.

Methods in org.anchoranalysis.image.bean.provider.stack that return Provider

Modifier and Type	Method	Description
Provider<Stack>	StackProviderUnary.getStack()	The delegate Provider<Stack> that is called.

Methods in org.anchoranalysis.image.bean.provider.stack that return types with arguments of type Provider

Modifier and Type	Method	Description
List<Provider<Stack>>	Arrange.getList()	The stacks that are passed in respect order into arrange.

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

Modifier and Type	Method	Description
void	Arrange.addStack(Provider<Stack> provider)	Adds a stack to the existing list of stack-providers.
void	StackProviderUnary.setStack(Provider<Stack> stack)	The delegate Provider<Stack> that is called.

Method parameters in org.anchoranalysis.image.bean.provider.stack with type arguments of type Provider

Modifier and Type	Method	Description
void	Arrange.setList(List<Provider<Stack>> list)	The stacks that are passed in respect order into arrange.

Uses of Provider in org.anchoranalysis.image.feature.bean.evaluator

Methods in org.anchoranalysis.image.feature.bean.evaluator that return Provider

Modifier and Type	Method	Description
Provider<Stack>	FeatureEvaluator.getStackEnergy()	Optionally specifies an energy-stack to be associated with every calculation input.

Methods in org.anchoranalysis.image.feature.bean.evaluator with parameters of type Provider

Modifier and Type	Method	Description
void	FeatureEvaluator.setStackEnergy(Provider<Stack> stackEnergy)	Optionally specifies an energy-stack to be associated with every calculation input.

Uses of Provider in org.anchoranalysis.image.io.bean.stack.combine

Classes in org.anchoranalysis.image.io.bean.stack.combine that implement Provider

Modifier and Type	Class	Description
class	TileWithLabels	Tiles a number of StackProviderWithLabels as a single StackProvider.
class	WriteText	Creates an image that contains text only.

Methods in org.anchoranalysis.image.io.bean.stack.combine that return Provider

Modifier and Type	Method	Description
Provider<Stack>	WriteText.getRepeatZProvider()	Repeats the generated (2D) string in z, so it's the same z-size as intensityProvider
Provider<Stack>	StackProviderWithLabel.getStack()	Provides the stack.

Methods in org.anchoranalysis.image.io.bean.stack.combine with parameters of type Provider

Modifier and Type	Method	Description
void	WriteText.setRepeatZProvider(Provider<Stack> repeatZProvider)	Repeats the generated (2D) string in z, so it's the same z-size as intensityProvider
void	StackProviderWithLabel.setStack(Provider<Stack> stack)	Provides the stack.

Uses of Provider in org.anchoranalysis.io.input.bean.dictionary

Classes in org.anchoranalysis.io.input.bean.dictionary that implement Provider

Modifier and Type	Class	Description
class	ReadFromFile	Reads a Dictionary from a file in Java properties format.

Uses of Provider in org.anchoranalysis.io.input.bean.path.provider

Classes in org.anchoranalysis.io.input.bean.path.provider that implement Provider

Modifier and Type	Class	Description
class	FilePathProvider	Base class for beans that implement Provider to provide a Path.
class	FilePathProviderReference	Calls an existing FilePathProvider indirectly to provide an identical result.
class	FromFiles	Extracts a path from a FilesProvider.

Uses of Provider in org.anchoranalysis.mpp.bean.provider

Classes in org.anchoranalysis.mpp.bean.provider that implement Provider

Modifier and Type	Class	Description
class	MarkBoundsProvider	An abstract provider for MarkBounds.
class	MarkCollectionProvider	Provides a collection of marks
class	MarksBaseProvider<T,S>	Base class for MarksBean that implements Provider to provide an object of type S.
class	SingleMarkProvider	Provides (maybe) a single mark

Uses of Provider in org.anchoranalysis.plugin.fiji.bean.channel.provider

Classes in org.anchoranalysis.plugin.fiji.bean.channel.provider that implement Provider

Modifier and Type	Class	Description
class	AnisotropicDiffusion	Performs Perona-Malik Anisotropic Diffusion.
class	MinimumFilter	Applies a minimum filter to a channel using ImageJ's MinMaxMedian plugin.

Uses of Provider in org.anchoranalysis.plugin.fiji.bean.channel.provider.distance

Classes in org.anchoranalysis.plugin.fiji.bean.channel.provider.distance that implement Provider

Modifier and Type	Class	Description
class	DistanceTransform3D	Euclidian Distance Transform from ImageJ that works on 2D as well as 3D z-stacks.
class	DistanceTransformForEachObject3D	Like DistanceTransform3D but applies the distance transform separately for each object in a collection.

Uses of Provider in org.anchoranalysis.plugin.fiji.bean.mask.provider

Classes in org.anchoranalysis.plugin.fiji.bean.mask.provider that implement Provider

Modifier and Type	Class	Description
class	AutoLocalThreshold	Applies local thresholding algorithm using Fiji's {link Auto_Local_Threshold} plugin

Uses of Provider in org.anchoranalysis.plugin.image.bean.channel.provider

Classes in org.anchoranalysis.plugin.image.bean.channel.provider that implement Provider

Modifier and Type	Class	Description
class	CreateNew	Creates a new channel with all values initialized to a constant (by default zero)
class	Duplicate	Creates a duplicate of the input channel.
class	FromDimensionsBase	An abstract base class for creating a channel from specified dimensions.
class	FromInput	Finds the input-stack using a conventional name of input_image - and extracts the first channel
class	FromStack	Extracts a channel from a provider of a stack.
class	IfParamEquals	Provides a channel based on a condition from a dictionary.
class	Reference	Provides a channel by referencing it from a a set of named-channels.
class	TwoVoxelMappingBase	Takes the two channels and creates a NEW third channel whose pixels are a function of the two channels
class	UnaryWithObjectsBase	An abstract base class for creating a channel from an existing channel and a collection of objects.
class	UnaryWithValueBase	A ChannelProviderUnary which has a scalar value field.

Uses of Provider in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic

Classes in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic that implement Provider

Modifier and Type	Class	Description
final class	AddConstant	Adds a constant value to each voxel in a channel.
class	ArithmeticWithConstantBase	Base-class for operations that perform a binary arithmetic operation with each voxel-value and a constant.
class	ArithmeticWithConstantConditionallyWriteBase	Base class for arithmetic operations that conditionally overwrite voxel values with a constant.
class	Invert	Inverts the intensity values of a Channel by subtracting each voxel from the maximum value for the channel's data type.
class	MaxTwoChannels	Creates a new channel by taking the maximum value of corresponding voxels from two input channels.
class	MaxWithConstant	Replaces voxel values with a constant value if the constant is greater than the original voxel value.
class	MeanThreeChannels	Creates a new channel that is the mean of three input channels.
class	MinTwoChannels	Creates a new channel by taking the minimum value of corresponding voxels from two input channels.
class	MinWithConstant	Replaces voxel values with a constant value if the constant is less than the original voxel value.
class	MultiplyConstant	Multiplies each voxel value in a channel by a constant value.
class	MultiplyTwoChannels	Creates a new channel by multiplying corresponding voxels from two input channels.
class	SubtractFromConstant	Subtracts each voxel value in a channel from a constant value.
class	SubtractMean	Subtracts the mean intensity (of the entire channel or a masked portion thereof) from every voxel.
class	SubtractTwoChannels	Creates a new channel by subtracting corresponding voxels of the second channel from the first channel.

Uses of Provider in org.anchoranalysis.plugin.image.bean.channel.provider.assign

Classes in org.anchoranalysis.plugin.image.bean.channel.provider.assign that implement Provider

Modifier and Type	Class	Description
class	AssignFromChannel	Copies the pixels from channelAssignFrom to channel (possibly masking).
class	AssignFromDictionary	Assigns a value from a dictionary to all voxels in a channel.
class	AssignFromIntersectingObjects	Matches source-objects to target objects, based upon intersection, and assigns the value in the respective source object to the target object
class	AssignValue	Assigns a constant (scalar) value to the portion of the image covered by a mask

Uses of Provider in org.anchoranalysis.plugin.image.bean.channel.provider.convert

Classes in org.anchoranalysis.plugin.image.bean.channel.provider.convert that implement Provider

Modifier and Type	Class	Description
class	Convert<T>	Converts a channel by applying a converter (no histogram is involved in the conversion).
class	ConvertBase	Base class for channel providers that perform conversions on a single input channel.
class	ConvertWithHistogram<T>	Converts a channel to a different voxel data-type by applying a converter with an associated histogram.

Uses of Provider in org.anchoranalysis.plugin.image.bean.channel.provider.gradient

Classes in org.anchoranalysis.plugin.image.bean.channel.provider.gradient that implement Provider

Modifier and Type	Class	Description
class	GradientBase	Base class to calculate the gradient of the voxels in a Channel.
class	GradientBaseAddSum	Like GradientBase but allows an arbitrary constant to be added to voxels storing the gradient.
class	GradientForAxis	Extracts the gradient in the direction of a particular axis (identified by an index)
class	GradientXY	Calculates a Channel's gradient along the x and y axes.
class	Sobel	3x3 Sobel Filter

Uses of Provider in org.anchoranalysis.plugin.image.bean.channel.provider.intensity

Classes in org.anchoranalysis.plugin.image.bean.channel.provider.intensity that implement Provider

Modifier and Type	Class	Description
class	Blur	Blurs an image using a particular strategy (defaults to a gaussian blur in each slice)
class	IfVoxelZero	Creates a new channel which is a merged version of two input channels according to rules.
class	Median	Applies a median-filter with square kernel
class	NormalizeDifferenceToMedian	Corrects a channel in the following way
class	NormalizeObjectIntensity	Rewrites the intensity for each object-mask (assume no overlap) so that its mean is 128
class	QuantileStretch	Changes the voxel values to map the range of 0th quantile to xth quantile across the entire voxel data range
class	ScaleXY	Scales the channel in the X and Y dimensions.

Uses of Provider in org.anchoranalysis.plugin.image.bean.channel.provider.mask

Classes in org.anchoranalysis.plugin.image.bean.channel.provider.mask that implement Provider

Modifier and Type	Class	Description
class	FromMask	Creates a Channel directly from a Mask without any modification.
class	FromMaskBase	A base class for a ChannelProvider which also uses a binary-mask, but which doesn't use any other ChannelProvider as an input.
class	UnaryWithMaskBase	A base class for a ChannelProviderUnary which also uses a binary mask.
class	ZeroOutsideMask	Set pixels NOT IN the mask to 0, but keep pixels IN the mask identical.

Uses of Provider in org.anchoranalysis.plugin.image.bean.channel.provider.object

Classes in org.anchoranalysis.plugin.image.bean.channel.provider.object that implement Provider

Modifier and Type	Class	Description
class	LevelPerObjectBase	Creates a channel with a level calculated for each object using various methods.
class	LevelPerObjectIndependently	Creates a channel with different threshold-levels for each object, calculating the level only from the histogram of the particular object.
class	LevelPerObjectNeighbors	Calculates a threshold-level for each object collectively based on other objects

Uses of Provider in org.anchoranalysis.plugin.image.bean.channel.provider.score

Classes in org.anchoranalysis.plugin.image.bean.channel.provider.score that implement Provider

Modifier and Type	Class	Description
class	IdentifyObjects	Assigns a unique id number to each object.
class	ScoreObjects	Creates a channel by scoring objects based on a feature calculation.
class	ScoreVoxels	Assigns a score (a value indicating how probable something is) to each voxel

Uses of Provider in org.anchoranalysis.plugin.image.bean.channel.provider.slice

Classes in org.anchoranalysis.plugin.image.bean.channel.provider.slice that implement Provider

Modifier and Type	Class	Description
class	ExtractCenterSlice	Extracts the slice at the center (rounding down) of the range of z-stacks.
class	ExtractSliceRange	Extracts slices from sliceStart (inclusive) to sliceEnd (inclusive).
class	MaximumIntensityProjection	Creates a maximum intensity projection of a 3D Channel.
class	MeanIntensityProjection	Creates a mean intensity projection of a 3D Channel.
class	RepeatSlice	Creates a new channel with specific dimensions that repeatedly duplicates a slice from an existing channel

Uses of Provider in org.anchoranalysis.plugin.image.bean.color.provider

Classes in org.anchoranalysis.plugin.image.bean.color.provider that implement Provider

Modifier and Type	Class	Description
class	Concatenate	Combines one or more ColorProviders into a unitary ColorProvider.
class	GenerateToMatchObjects	Generates colors to match the size of an object-collection.

Uses of Provider in org.anchoranalysis.plugin.image.bean.dimensions.provider

Classes in org.anchoranalysis.plugin.image.bean.dimensions.provider that implement Provider

Modifier and Type	Class	Description
class	FromChannel	Creates image-dimensions by referencing them from a ChannelProvider.
class	GuessDimensions	Guesses dimensions from an input-image if it exists.
class	SpecifyDimensions	Specifies dimensions explicitly via bean properties.

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

Classes in org.anchoranalysis.plugin.image.bean.histogram.provider that implement Provider

Modifier and Type	Class	Description
class	CutBelowThreshold	This cuts a Histogram below a threshold BUT TRANSFERS ALL THE COUNT greater than equal to the threshold into the bin just below the threshold value
class	FromChannel	Creates a Histogram from a Channel, optionally using a mask.
class	GreaterThanThreshold	Thresholds a histogram using a CalculateLevel keeping only the values greater equal than the threshold
class	Reference	A provider that references an existing Histogram by its identifier.

Uses of Provider in org.anchoranalysis.plugin.image.bean.mask.provider

Classes in org.anchoranalysis.plugin.image.bean.mask.provider that implement Provider

Modifier and Type	Class	Description
class	AllValuesOff	Creates a new mask of particular dimensionality where all values are off.
class	AllValuesOn	Creates a new mask of particular dimensionality where all values are on.
class	Duplicate	A provider that creates a duplicate of a given Mask.
class	FromChannelBase	Base-class for MaskProviders that accept a Channel as input.
class	FromDimensionsBase	Base class for MaskProviders that create a mask based on given dimensions.
class	Invert	Switches on voxels to off and vice-versa.
class	Reference	A provider that references an existing Mask by its identifier.
class	ScaleXY	Scales the mask in XY dimensions, but not in Z dimension.

Uses of Provider in org.anchoranalysis.plugin.image.bean.mask.provider.combine

Classes in org.anchoranalysis.plugin.image.bean.mask.provider.combine that implement Provider

Modifier and Type	Class	Description
class	And	Outputs the logical operation and voxelwise on both masks, modifying {mask} with the result.
class	CombineBase	Base class for combining two masks.
class	IfHighLow	Outputs the logical operation iff first==HIGH and second==LOW then LOW voxelwise on both masks, modifying {mask} with the result.
class	Or	Outputs the logical operation or voxelwise on both masks, modifying {mask} with the result.
class	Xor	Outputs the logical operation xor (exclusive or) voxelwise on both masks, modifying {mask} with the result.

Uses of Provider in org.anchoranalysis.plugin.image.bean.mask.provider.convert

Classes in org.anchoranalysis.plugin.image.bean.mask.provider.convert that implement Provider

Modifier and Type	Class	Description
class	FromChannel	Creates a mask from an existing channel, reusing the channel's buffer and considering all 0 values as off, and 255 values as on.
class	FromObjects	Creates a Mask from a collection of object-masks.
class	FromStackChannel	Creates a Mask from a specific channel in a stack.

Uses of Provider in org.anchoranalysis.plugin.image.bean.mask.provider.morphological

Classes in org.anchoranalysis.plugin.image.bean.mask.provider.morphological that implement Provider

Modifier and Type	Class	Description
class	Box	Creates a Mask where all pixels are on within a box region.
class	Dilate	Performs a dilation morphological operation on BinaryVoxels.
class	Erode	Performs an erosion morphological operation on BinaryVoxels.
class	ExteriorContour	Finds the exterior outer contour for a Mask that forms its outline.
class	FitBoxToOnVoxels	Fits a box around the on voxels.
class	MorphologicalOperatorBase	Base class for performing morphological operations on BinaryVoxels.

Uses of Provider in org.anchoranalysis.plugin.image.bean.mask.provider.predicate

Classes in org.anchoranalysis.plugin.image.bean.mask.provider.predicate that implement Provider

Modifier and Type	Class	Description
class	IfKeyValueCondition	The current mask is returned if a condition on key-values is satisfied otherwise maskElse is returned.
class	IfNotEmpty	The current mask is returned if it's non-empty (at least one on voxel) otherwise maskElse is returned.
class	IfObjectFilter	The current mask is returned if the mask (treated as an object) passed an object-filter, otherwise maskElse is returned.
class	IfPredicateBase	Base class which multiplexes between the current mask and an alternative depending if a condition is met.
class	IfStackExists	The current mask is a particular stack exists (at least one on voxel) otherwise maskElse is returned.

Uses of Provider in org.anchoranalysis.plugin.image.bean.mask.provider.segment

Classes in org.anchoranalysis.plugin.image.bean.mask.provider.segment that implement Provider

Modifier and Type	Class	Description
class	SegmentChannel	Applies a BinarySegmentation algorithm to derive a mask from a channel
class	Threshold	Thresholds a channel to produce a mask, reusing (and modifying) the input-buffers of the channel if possible.

Uses of Provider in org.anchoranalysis.plugin.image.bean.mask.provider.slice

Classes in org.anchoranalysis.plugin.image.bean.mask.provider.slice that implement Provider

Modifier and Type	Class	Description
class	FlattenZ	Flattens a mask in the z-dimension, so it is 2D instead of 3D (like a maximum intensity projection).
class	RepeatSlice	Creates a new mask with specific dimensions that repeatedly duplicates a slice from an existing mask

Uses of Provider in org.anchoranalysis.plugin.image.bean.object.provider

Classes in org.anchoranalysis.plugin.image.bean.object.provider that implement Provider

Modifier and Type	Class	Description
class	AtIndex	Extract a single ObjectMask into a new collection.
class	Concatenate	An ObjectCollectionProvider that concatenates multiple ObjectCollections from a list of providers.
class	Duplicate	Duplicates (deep copy) an object-collection.
class	Empty	Creates an empty object-collection.
class	IfParamEqual	Multiplexes between two object-collection-providers depending on whether a parameter value equals a particular string
class	Permute	Permutes some changes over an ObjectCollectionProvider and collects all the results in an ObjectCollection
class	Reference	An ObjectCollectionProvider that references an existing ObjectCollection by its identifier.
class	ReferenceOrElse	Returns a object-collection by name if it exists, or else calls objectsElse if it doesn't exist.
class	Scale	Scales all the objects in the collection by a particular scale-factor.
class	UnaryWithChannelBase	Base class for ObjectCollectionProviderUnary that also requires a Channel.
class	WithChannelBase	Base class for ObjectCollectionProviders that create objects from a Channel.
class	WithContainerBase	Base class for ObjectCollectionProviderUnary that take an optional objectsContainer bean-field.
class	WithDimensionsBase	Base class for ObjectCollectionProviderUnary classes that require dimensions to be specified.
class	WithOptionalDimensionsBase	Base class for ObjectCollectionProviderUnary classes that offer an optional means to specify dimensions.

Uses of Provider in org.anchoranalysis.plugin.image.bean.object.provider.connected

Classes in org.anchoranalysis.plugin.image.bean.object.provider.connected that implement Provider

Modifier and Type	Class	Description
class	ConnectedComponentsFromMask	Converts a binary-mask into its connected components
class	DecomposeIntoConnectedComponents	Ensures each object in a collection is a connected-component, decomposing it if necessary into multiple objects.
class	RejectIfNotConnected	Rejects a set of objects, if any object is not fully connected (pixels form two or more separate connected components)

Methods in org.anchoranalysis.plugin.image.bean.object.provider.connected that return Provider

Modifier and Type	Method	Description
Provider<Mask>	ConnectedComponentsFromMask.getMask()

Methods in org.anchoranalysis.plugin.image.bean.object.provider.connected with parameters of type Provider

Modifier and Type	Method	Description
void	ConnectedComponentsFromMask.setMask(Provider<Mask> mask)

Uses of Provider in org.anchoranalysis.plugin.image.bean.object.provider.feature

Classes in org.anchoranalysis.plugin.image.bean.object.provider.feature that implement Provider

Modifier and Type	Class	Description
class	ObjectCollectionProviderWithFeature	An abstract base class for object collection providers that use a feature evaluator.
class	ObjectWithMaximumFeature	Finds the object with the maximum feature-value from a collection.
class	ObjectWithMaximumFeatureFromEachMatchedCollection	Finds the object with the maximum feature among a group of matches for each object.
class	SortByFeature	Creates a new object-collection with objects sorted by a derived feature-value (in ascending order)

Uses of Provider in org.anchoranalysis.plugin.image.bean.object.provider.filter

Classes in org.anchoranalysis.plugin.image.bean.object.provider.filter that implement Provider

Modifier and Type	Class	Description
class	Filter	Filters an ObjectCollection using the specified ObjectFilter.
class	FilterByGroup	Filters an ObjectCollection by grouping objects and then applying a filter to each group.
class	IntersectsWithContainer	Returns only the objects that intersect with at least one object in the container
class	Match	Provides an ObjectCollection by matching objects using a specified ObjectMatcher.
class	NotInContainer	Filters objects to keep only those which are NOT in the container.
class	ObjectCollectionProviderFilterBase	Base class for object collection providers that apply a filter to the objects.
class	RemoveTouchingBorder	Considers all possible pairs of objects in a provider, and removes those that touch the border.

Uses of Provider in org.anchoranalysis.plugin.image.bean.object.provider.mask

Classes in org.anchoranalysis.plugin.image.bean.object.provider.mask that implement Provider

Modifier and Type	Class	Description
class	AndObjectsWithMasks	Reduce the size of individual objects (if neccessary, and minimally) to fit within a binary-mask.
class	FromMask	Converts a binary-mask to an object-collection (containing a single object)

Methods in org.anchoranalysis.plugin.image.bean.object.provider.mask that return Provider

Modifier and Type	Method	Description
Provider<Mask>	FromMask.getMask()

Methods in org.anchoranalysis.plugin.image.bean.object.provider.mask with parameters of type Provider

Modifier and Type	Method	Description
void	FromMask.setMask(Provider<Mask> mask)

Uses of Provider in org.anchoranalysis.plugin.image.bean.object.provider.merge

Classes in org.anchoranalysis.plugin.image.bean.object.provider.merge that implement Provider

Modifier and Type	Class	Description
class	MergeBase	A base class for algorithms that merge object-masks.
class	MergeGreedyToIncreaseObjectFeature	Naive greedy merge strategy when any two neighboring objects are merged if it increases a feature.
class	MergePairs	Merges objects if a pair feature value satisfies a condition.
class	MergeToIncreaseObjectFeature	Merges neighboring objects if it results in an increase in the average feature-value calculated on each single object.
class	MergeTwoCollectionsItemwise	Merges itemwise objects from two collections.
class	MergeWithFeature	Base class for object-merging strategies that involve calculating a feature.
class	MergeWithOptionalDistanceConstraint	Expands MergeBase by optionally imposing a maximum-distance requirement between objects that are possibly merged.

Uses of Provider in org.anchoranalysis.plugin.image.bean.object.provider.morphological

Classes in org.anchoranalysis.plugin.image.bean.object.provider.morphological that implement Provider

Modifier and Type	Class	Description
class	Dilate	Dilates each object in the collection, growing bounding-boxes as necessary in relevant dimensions.
class	Erode	Erodes each object in the collection, growing bounding-boxes as necessary in relevant dimensions.
class	ObjectCollectionProviderMorphological	Base class for providers that apply morphological operations to an ObjectCollection.

Uses of Provider in org.anchoranalysis.plugin.image.bean.object.provider.segment

Classes in org.anchoranalysis.plugin.image.bean.object.provider.segment that implement Provider

Modifier and Type	Class	Description
class	BinarySegmentByObject	Performs a binary-segmentation using the upstream objects as masks.
class	SegmentChannel	Segments a channel into objects using a specified segmentation algorithm.
class	SegmentChannelByObject	Performs segmentation of a channel using each object in the upstream collection as a mask.
class	SegmentStack<T extends InferenceModel>	Segments a stack into objects.
class	SegmentWithSeeds	Takes each object one-by-one from objectsSource, and finds matching seeds from objectsSeeds

Uses of Provider in org.anchoranalysis.plugin.image.bean.object.provider.slice

Classes in org.anchoranalysis.plugin.image.bean.object.provider.slice that implement Provider

Modifier and Type	Class	Description
class	ExtendInZ	Creates a 3D version of an object by replicating each input-object across the z-dimension to meet (3D) dimensions.
class	ExtendInZWithinContainer	Extends an object (2D/3D) as much as it can within the z-slices of a containing object
class	FlattenZ	Flattens all object-masks in the z-dimension, so it is 2D instead of 3D (like a maximum intensity projection).
class	SliceAt	Extracts a specific slice from a collection of 3D objects.

Uses of Provider in org.anchoranalysis.plugin.image.bean.object.provider.split

Classes in org.anchoranalysis.plugin.image.bean.object.provider.split that implement Provider

Modifier and Type	Class	Description
class	RemoveIntersectingVoxels	Considers all possible pairs of objects in a provider, and removes any intersecting pixels
class	SplitByObjects	Splits objects in a collection based on intersections with another set of objects.
class	SplitIntoSquares	Splits objects into sub-objects by cutting by an orthogonal square lattice (like a chessboard).

Uses of Provider in org.anchoranalysis.plugin.image.bean.stack.provider

Classes in org.anchoranalysis.plugin.image.bean.stack.provider that implement Provider

Modifier and Type	Class	Description
class	Concatenate	Combines all the channels from one or more sources (stacks, channels etc.)
class	FromChannelOrMask	Creates a Stack from a Channel or Mask (reusing the voxel buffers).
class	FromInput	Finds the input-stack using a conventional name of input_image
class	Reference	Retrieves an existing stack.

Methods in org.anchoranalysis.plugin.image.bean.stack.provider that return Provider

Modifier and Type	Method	Description
Provider<Mask>	FromChannelOrMask.getMask()	A mask that is provided to the stack.

Methods in org.anchoranalysis.plugin.image.bean.stack.provider with parameters of type Provider

Modifier and Type	Method	Description
void	FromChannelOrMask.setMask(Provider<Mask> mask)	A mask that is provided to the stack.

Uses of Provider in org.anchoranalysis.plugin.image.bean.stack.provider.color

Classes in org.anchoranalysis.plugin.image.bean.stack.provider.color that implement Provider

Modifier and Type	Class	Description
class	ColoredBase	Base class for providers that draw entities (an outline or filled) on a background.
class	ColoredBaseWithGenerator	Like ColoredBase but uses a generator to determine the colors for the objects.
class	ColoredMask	Draws a colored representation (outline or filled) of a ObjectMask on a background
class	ColoredObjects	Draws a colored representation (outline or filled) of an ObjectCollection on a background
class	ThreeChannels	Provides a Stack by combining up to three channels (red, green, blue) into an RGB image.
class	ThreeColoredObjects	Colors three collections of objects in RED, GREEN, BLUE channels on top of a background.

Uses of Provider in org.anchoranalysis.plugin.image.feature.bean.list

Classes in org.anchoranalysis.plugin.image.feature.bean.list that implement Provider

Modifier and Type	Class	Description
class	IntensityMoments	Calculate various moment-related statistics about the intensity of each channel of an image.

Uses of Provider in org.anchoranalysis.plugin.image.feature.bean.list.pair

Classes in org.anchoranalysis.plugin.image.feature.bean.list.pair that implement Provider

Modifier and Type	Class	Description
class	DeriveFromPair	Embeds each feature in a FeatureDeriveFromPair feature (first, second or merge) and prepends with a string.
class	FeatureListProviderAggregatePair	Calculates features on each part of a pair (first, second, merged etc.) and then reduces the calculation to a single number.
class	ReduceFirstAndSecond	Calculates the aggregate of a feature applied to both the first and second objects in a FeatureInputPairObjects.
class	ReduceRatioFirstAndSecond	Calculates the aggregate of the ratio of first:second and second :first for a FeatureInputPairObjects
class	SubtractReducedFromMerged	Calculates merged - reduce(first,second) for a FeatureInputPairObjects

Uses of Provider in org.anchoranalysis.plugin.image.feature.bean.list.permute

Classes in org.anchoranalysis.plugin.image.feature.bean.list.permute that implement Provider

Modifier and Type	Class	Description
class	PermuteDivideByParam<T extends FeatureInputDictionary>	Similar to FeatureListProviderPermute but embeds the feature in a GaussianScore
class	PermuteFeature<S,T extends FeatureInput>	Permutes one or more properties of a Feature, so as to create a set of Features
class	PermuteFeatureBase<T extends FeatureInput>	Creates permutations of a feature by modifying a particular property of it in different ways.
class	PermuteFeatureSequenceInteger<T extends FeatureInputDictionary>	Permutes a property on a feature with a sequence of integers.
class	PermuteFirstSecondOrder<T extends FeatureInputDictionary>	Permutes a feature by applying first and second order statistical operations.
class	PermuteGaussianScore<T extends FeatureInputDictionary>	Permutes a feature by embedding it in a GaussianCumulative score.
class	PermuteZScore<T extends FeatureInputDictionary>	Permutes a feature by embedding it in a ZScore.

Uses of Provider in org.anchoranalysis.plugin.imagej.bean.channel.provider

Classes in org.anchoranalysis.plugin.imagej.bean.channel.provider that implement Provider

Modifier and Type	Class	Description
class	BackgroundSubtractor	Subtracts background from a channel using ImageJ's BackgroundSubtracter.
class	WithFilterBase	A base class for applying ImageJ rank filters to channels.
class	WithRadiusBase	A ChannelProviderUnary with a 'radius' parameter.

Uses of Provider in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter

Classes in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter that implement Provider

Modifier and Type	Class	Description
class	EdgeFilterIJ	Applies an edge detection filter to each slice of a Channel independently using ImageJ's FIND_EDGES filter.
class	GaussianBlur2D	Applies a 2D Gaussian blur filter to each slice of a Channel independently.

Uses of Provider in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments

Classes in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments that implement Provider

Modifier and Type	Class	Description
class	MeanFilter2D	Applies a 2D mean filter to a channel using ImageJ's RankFilters.
class	VarianceFilter2D	Applies a 2D variance filter to a channel using ImageJ's RankFilters.

Uses of Provider in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank

Classes in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank that implement Provider

Modifier and Type	Class	Description
class	MedianFilter2D	Applies a 2D median filter to a channel using ImageJ's RankFilters.
class	MedianFilter3D	Applies a 3D median filter to a channel using a hybrid 3D median filter ImageJ plugin.

Uses of Provider in org.anchoranalysis.plugin.imagej.bean.mask.provider

Classes in org.anchoranalysis.plugin.imagej.bean.mask.provider that implement Provider

Modifier and Type	Class	Description
class	FillHoles	Fills holes in a mask, with options to skip holes touching the border or exceeding a maximum volume.
class	MorphologicalOperation	Applies an ImageJ (2D) morphological operation to each slice

Uses of Provider in org.anchoranalysis.plugin.imagej.bean.object.provider

Classes in org.anchoranalysis.plugin.imagej.bean.object.provider that implement Provider

Modifier and Type	Class	Description
class	DrawLineAlongConvexHull	Draws a lines between successive points on the convex-hull of an object.
class	FillHoles	Fills holes in an object.

Uses of Provider in org.anchoranalysis.plugin.imagej.bean.stack.provider

Classes in org.anchoranalysis.plugin.imagej.bean.stack.provider that implement Provider

Modifier and Type	Class	Description
class	MontageSlices	Creates a montage of slices from a stack.

Uses of Provider in org.anchoranalysis.plugin.mpp.bean.object.provider

Classes in org.anchoranalysis.plugin.mpp.bean.object.provider that implement Provider

Modifier and Type	Class	Description
class	FromMarks	Creates object-masks from a MarkCollection where (a particular region of) each mark creates an object.

Uses of Provider in org.anchoranalysis.plugin.mpp.bean.provider.collection

Classes in org.anchoranalysis.plugin.mpp.bean.provider.collection that implement Provider

Modifier and Type	Class	Description
class	CreateNew	Creates a new empty collection of marks
class	FromSingleMark	Creates a MarkCollection from a single mark provided by a SingleMarkProvider.
class	PointsFromObjects	Creates a MarkCollection of point marks from an ObjectCollection.
class	Reference	Provides a MarkCollection by referencing it from the initialization context using an ID.
class	ReferenceOrEmpty	Returns an existing marks-collection or an empty set if it doesn't exist
class	ScaleXY	Scales the X and Y coordinates of marks in a MarkCollection using a ScaleCalculator.

Uses of Provider in org.anchoranalysis.plugin.mpp.bean.stack.provider

Classes in org.anchoranalysis.plugin.mpp.bean.stack.provider that implement Provider

Modifier and Type	Class	Description
class	ColoredMarks	Draws a colored representation (outline or filled) of an MarkCollection on a background

Uses of Provider in org.anchoranalysis.plugin.opencv.bean.color

Classes in org.anchoranalysis.plugin.opencv.bean.color that implement Provider

Modifier and Type	Class	Description
class	ColorConverterBase	Converts a RGB stack into another color space using OpenCV.
class	ConvertRGBToHSV	Converts a RGB image to the HSV color space.
class	ConvertRGBToLab	Converts a RGB image to the Lab color space.

Uses of Provider in org.anchoranalysis.plugin.opencv.bean.feature

Classes in org.anchoranalysis.plugin.opencv.bean.feature that implement Provider

Modifier and Type	Class	Description
class	HOGDescriptor	Creates the entire HOG descriptor for an image.

Uses of Provider in org.anchoranalysis.plugin.points.bean

Classes in org.anchoranalysis.plugin.points.bean that implement Provider

Modifier and Type	Class	Description
class	FitPointsFromObjects	A MarkCollectionProvider that fits points from objects to create marks.
class	SplitContourAtSaddlePoints	Splits a 2D contour represented by an object-mask into several contours, splitting at "turn" points.

Uses of Provider in org.anchoranalysis.plugin.points.bean.convexhull

Classes in org.anchoranalysis.plugin.points.bean.convexhull that implement Provider

Modifier and Type	Class	Description
class	ConvexHull2D	Sets particular voxels to high only if they exist on the convex-hull of the outline of a mask.
class	ConvexHull3D	Calculates a 3D convex hull from a binary mask.
class	ConvexHullBase	Base class for convex hull implementations.