Uses of Class
org.anchoranalysis.image.core.channel.Channel

Packages that use Channel

Package	Description
org.anchoranalysis.feature.energy	A particular stack used in feature-calculations called a EnergyStack together with related classes.
org.anchoranalysis.image.bean.channel	Base classes for performing operations on Channels.
org.anchoranalysis.image.bean.displayer
org.anchoranalysis.image.bean.nonbean	Classes that are used elsewhere in this package but which aren't themselves AnchorBeans.
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.segment.object	Base classes to segment a channel into objects.
org.anchoranalysis.image.core.channel	The Channel core data-class and related operations and converters.
org.anchoranalysis.image.core.channel.convert	Converts a channel to other data-types.
org.anchoranalysis.image.core.channel.convert.attached	Converts a channel to another data-type based upon another object to which it is attached.
org.anchoranalysis.image.core.channel.convert.attached.channel	Converts a channel to another data-type based upon a Channel to which it is attached.
org.anchoranalysis.image.core.channel.convert.attached.histogram	Converts a channel to another data-type based upon a Histogram to which it is attached.
org.anchoranalysis.image.core.channel.factory	Factory classes for creating Channel for various voxel data-types.
org.anchoranalysis.image.core.mask	An image with only two permissible states.
org.anchoranalysis.image.core.object	The key data entity org.anchoranalysis.image.voxel.object and related-classes and operations.
org.anchoranalysis.image.core.object.label	Labelling elements (object-masks or similar) with unique successive integers in a channel.
org.anchoranalysis.image.core.stack	Defines the key data object, Stack, and related classes.
org.anchoranalysis.image.io.channel.input	Non-bean classes for reading a Channel from the filesystem.
org.anchoranalysis.image.io.channel.map	Non-bean classes for a mapping of names to Channels.
org.anchoranalysis.image.io.channel.output	Non-bean classes for writing a Channel to the filesystem.
org.anchoranalysis.io.bioformats	Non-bean classes for filesystem I/O using Bioformats.
org.anchoranalysis.io.bioformats.copyconvert	Converts the byte stream opened by Bioformats into channels of particular data-type.
org.anchoranalysis.io.imagej.convert	Converts to and from ImageJ data-structures for images.
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.aggregator	Implementations of ConvertChannelTo and ConvertChannelToWithHistogram.
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.mask.provider	Implementations of MaskProvider.
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.segment	Implementations of MaskProvider where an ObjectCollection is created by segmenting a Channel.
org.anchoranalysis.plugin.image.bean.object.provider	Implementations of ObjectCollectionProvider.
org.anchoranalysis.plugin.image.bean.object.provider.segment	Implementations of ObjectCollectionProvider involving segmentation.
org.anchoranalysis.plugin.image.bean.object.segment.channel	Implementations of SegmentChannelIntoObjects.
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima	Minima imposition for a Watershed transformation.
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong	Implementation of a Watershed transformation based on Yeong et al. 2009.
org.anchoranalysis.plugin.image.bean.stack.provider.color	Implementations of StackProvider that color portions of an image.
org.anchoranalysis.plugin.image.channel	Non-beans for operations or calculations relating to Channels.
org.anchoranalysis.plugin.image.feature.bean.object.single.energy	Implementations of FeatureSingleObject that reference a particular Channel in the associated EnergyStack.
org.anchoranalysis.plugin.image.feature.bean.object.single.intensity	Implementations of FeatureSingleObject that measure an object's intensity on a corresponding Channel.
org.anchoranalysis.plugin.image.intensity	Non-bean for operations or calculations relating to intensity.
org.anchoranalysis.plugin.image.intensity.level	Non-beans for calculating a thresholding level from itensity values.
org.anchoranalysis.plugin.image.task.bean.combine	Combining multiple images together into a single image.
org.anchoranalysis.plugin.image.task.bean.grouped	Tasks that involved stacks (usually each channel from an image) that are somehow grouped-together.
org.anchoranalysis.plugin.image.task.bean.grouped.histogram	Task(s) to export histograms of intensity values.
org.anchoranalysis.plugin.image.task.channel.aggregator	Combines multiple Channels voxel-wise to form a single aggregated Channel.
org.anchoranalysis.plugin.image.task.grouped	Non-bean classes about grouping channels or other inputs.
org.anchoranalysis.plugin.image.task.stack	Non-bean classes pertaining to stacks and channels as used in tasks.
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.rank	Non-linear filters using ImageJ that use the statistical rank of the intensity values in the kernel.
org.anchoranalysis.plugin.imagej.bean.object.segment	Implementations of ObjectCollectionProvider that call ImageJ to perform segmentation.
org.anchoranalysis.plugin.imagej.channel.provider	Implementations of ChannelProvider that call ImageJ.
org.anchoranalysis.test.image	Testing utilities and fixtures with no greater downstream dependency than anchor-image-io or anchor-io-bioformats or anchor-imagej.
org.anchoranalysis.test.image.io	Utilities for testing-related reading and writing to the filesystem.

Uses of Channel in org.anchoranalysis.feature.energy

Methods in org.anchoranalysis.feature.energy that return Channel

Modifier and Type	Method	Description
Channel	EnergyStack.getChannel(int index)	Returns the channel at a particular position in the stack.
final Channel	EnergyStackWithoutParameters.getChannel(int index)	Returns the channel at a particular position in the stack.

Constructors in org.anchoranalysis.feature.energy with parameters of type Channel

Modifier	Constructor	Description
	EnergyStack(Channel channel)	Create from a single Channel.
	EnergyStackWithoutParameters(Channel channel)	Create a energy-stack comprised of a single channel

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

Methods in org.anchoranalysis.image.bean.channel that return Channel

Modifier and Type	Method	Description
Channel	ChannelAggregator.aggregatedChannel()	Retrieve or create a Channel with containing the aggregated values.
protected abstract Channel	ChannelAggregator.retrieveCreateAggregatedChannel()	Retrieve or create an aggregated-channel of type outputType.

Methods in org.anchoranalysis.image.bean.channel with parameters of type Channel

Modifier and Type	Method	Description
void	ChannelAggregator.addChannel(Channel channel, Logger logger)	Adds a Channel to the aggregation.
protected abstract void	ChannelAggregator.addChannelAfterCheck(Channel channel)	Adds a Channel to the aggregation - after checking channel has acceptable dimensions.

Uses of Channel in org.anchoranalysis.image.bean.displayer

Methods in org.anchoranalysis.image.bean.displayer that return types with arguments of type Channel

Modifier and Type	Method	Description
protected ChannelConverterAttached<Channel,UnsignedByteBuffer>	IntensityQuantiles.createConverterFor(VoxelDataType dataType)
protected abstract ChannelConverterAttached<Channel,UnsignedByteBuffer>	StackDisplayer.createConverterFor(VoxelDataType dataType)	Determines what kind of converter to use for a particular channel, to map it to an unsigned 8-bit channel.

Methods in org.anchoranalysis.image.bean.displayer with parameters of type Channel

Modifier and Type	Method	Description
DisplayStack	StackDisplayer.deriveFrom(Channel channel)	Creates from a Channel.

Uses of Channel in org.anchoranalysis.image.bean.nonbean

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

Modifier and Type	Method	Description
void	ConsistentChannelChecker.checkChannelType(Channel channel)	Checks that a channel has the same type (max value) as the others.

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

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

Modifier and Type	Method	Description
NamedProviderStore<Channel>	ImageInitialization.channels()	A collection of Channels, indexed by name.

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

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

Modifier and Type	Method	Description
protected abstract Channel	ChannelProviderUnary.createFromChannel(Channel channel)	Creates a Channel given the entity provided by the delegate.
Channel	ChannelProviderBinary.get()
Channel	ChannelProviderTernary.get()
Channel	ChannelProviderUnary.get()
protected abstract Channel	ChannelProviderBinary.process(Channel channel1, Channel channel2)	Creates a Channel given the two entities provided by the delegates.
protected abstract Channel	ChannelProviderTernary.process(Channel channel1, Channel channel2, Channel channel3)	Creates a Channel given the two entities provided by the delegates.

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

Modifier and Type	Method	Description
protected abstract Channel	ChannelProviderUnary.createFromChannel(Channel channel)	Creates a Channel given the entity provided by the delegate.
protected abstract Channel	ChannelProviderBinary.process(Channel channel1, Channel channel2)	Creates a Channel given the two entities provided by the delegates.
protected abstract Channel	ChannelProviderTernary.process(Channel channel1, Channel channel2, Channel channel3)	Creates a Channel given the two entities provided by the delegates.

Uses of Channel in org.anchoranalysis.image.bean.segment.object

Methods in org.anchoranalysis.image.bean.segment.object with parameters of type Channel

Modifier and Type	Method	Description
protected static void	SegmentChannelIntoObjects.checkUnsupported3D(Channel channel)	Throws an exception if the channel has more than one z-slice, as 3D is unsupported by the implementation.
abstract ObjectCollection	SegmentChannelIntoObjects.segment(Channel channel, Optional<ObjectMask> objectMask, Optional<ObjectCollection> seeds)	Segments a channel to produce an object-collection.
ObjectCollection	SegmentChannelIntoObjectsUnary.segment(Channel channel, Optional<ObjectMask> objectMask, Optional<ObjectCollection> seeds)
protected abstract ObjectCollection	SegmentChannelIntoObjectsUnary.segment(Channel channel, Optional<ObjectMask> object, Optional<ObjectCollection> seeds, SegmentChannelIntoObjects upstreamSegmenter)	Creates an ObjectCollection given the segmentation-results provided by the delegate.

Uses of Channel in org.anchoranalysis.image.core.channel

Methods in org.anchoranalysis.image.core.channel that return Channel

Modifier and Type	Method	Description
Channel	Channel.duplicate()	A deep-copy.
Channel	Channel.extractSlice(int sliceIndex)	Creates a new Channel containing only one particular slice.
Channel	Channel.projectMax()	A maximum-intensity projection across the z-slices.
Channel	Channel.projectMean()	A mean-intensity projection across the z-slices.
Channel	Channel.resizeXY(int x, int y, VoxelsResizer resizer)	Like resizeXY(Extent, VoxelsResizer) but specifies the size via int parameters.
Channel	Channel.resizeXY(Extent extentToAssign, VoxelsResizer resizer)	Resizes the dimensions of the channel, interpolating the existing voxel values to match.
Channel	Channel.scaleXY(ScaleFactor scaleFactor, VoxelsResizer resizer)	Resizes the dimensions of the channel, by scaling the existing size by a factor.

Methods in org.anchoranalysis.image.core.channel with parameters of type Channel

Modifier and Type	Method	Description
boolean	Channel.equalsDeep(Channel other, boolean compareResolution)	Are the two channels equal using a deep voxel by voxel comparison?

Uses of Channel in org.anchoranalysis.image.core.channel.convert

Methods in org.anchoranalysis.image.core.channel.convert that return Channel

Modifier and Type	Method	Description
Channel	ChannelConverter.convert(Channel channel, ConversionPolicy changeExisting)	Converts channel to have voxels with data-type T.
Channel	ChannelConverterMulti.convert(Channel channel, VoxelDataType outputVoxelType)	Converts a Channel's voxels to another type.

Methods in org.anchoranalysis.image.core.channel.convert with parameters of type Channel

Modifier and Type	Method	Description
Channel	ChannelConverter.convert(Channel channel, ConversionPolicy changeExisting)	Converts channel to have voxels with data-type T.
Channel	ChannelConverterMulti.convert(Channel channel, VoxelDataType outputVoxelType)	Converts a Channel's voxels to another type.

Uses of Channel in org.anchoranalysis.image.core.channel.convert.attached

Methods in org.anchoranalysis.image.core.channel.convert.attached that return Channel

Modifier and Type	Method	Description
Channel	ChannelConverterAttached.convert(Channel channel, ConversionPolicy changeExisting)	Converts the voxel-type in a Channel.

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

Modifier and Type	Method	Description
Channel	ChannelConverterAttached.convert(Channel channel, ConversionPolicy changeExisting)	Converts the voxel-type in a Channel.

Uses of Channel in org.anchoranalysis.image.core.channel.convert.attached.channel

Methods in org.anchoranalysis.image.core.channel.convert.attached.channel that return Channel

Modifier and Type	Method	Description
Channel	IntensityRange.convert(Channel channel, ConversionPolicy changeExisting)
Channel	MaxIntensity.convert(Channel channel, ConversionPolicy changeExisting)

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

Modifier and Type	Method	Description
void	IntensityRange.attachObject(Channel channel)
void	MaxIntensity.attachObject(Channel channel)
Channel	IntensityRange.convert(Channel channel, ConversionPolicy changeExisting)
Channel	MaxIntensity.convert(Channel channel, ConversionPolicy changeExisting)

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

Methods in org.anchoranalysis.image.core.channel.convert.attached.histogram that return Channel

Modifier and Type	Method	Description
Channel	MaxIntensityFromHistogram.convert(Channel channel, ConversionPolicy changeExisting)
Channel	QuantileIntensityFromHistogram.convert(Channel channel, ConversionPolicy changeExisting)
Channel	UpperLowerQuantileIntensityFromHistogram.convert(Channel channel, ConversionPolicy changeExisting)

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

Modifier and Type	Method	Description
Channel	MaxIntensityFromHistogram.convert(Channel channel, ConversionPolicy changeExisting)
Channel	QuantileIntensityFromHistogram.convert(Channel channel, ConversionPolicy changeExisting)
Channel	UpperLowerQuantileIntensityFromHistogram.convert(Channel channel, ConversionPolicy changeExisting)

Uses of Channel in org.anchoranalysis.image.core.channel.factory

Methods in org.anchoranalysis.image.core.channel.factory that return Channel

Modifier and Type	Method	Description
Channel	ChannelFactory.create(Dimensions dimensions, VoxelDataType channelDataType)	Creates an empty initialized channel for a particular data-type.
Channel	ChannelFactory.create(Voxels<?> voxels)	Create a Channel from particular voxels.
Channel	ChannelFactory.create(Voxels<?> voxels, Optional<Resolution> resolution)	Create a Channel from particular voxels.
Channel	ChannelFactorySingleType.create(Voxels<?> voxels, Optional<Resolution> resolution)	Create a Channel from voxels and a resolution.
Channel	ChannelFactorySingleType.createEmptyInitialised(Dimensions dimensions)	Create a Channel initialized with zero-valued voxel-buffers.
Channel	ChannelFactory.createEmptyInitialisedToSupportMaxValue(Dimensions dimensions, long maxIntensityValueNeeded)	Creates an empty initialized channel with discrete type with as minimal as needed data-type to support a maximum value.
Channel	ChannelFactorySingleType.createEmptyUninitialised(Dimensions dimensions)	Create a Channel without initialization with voxel-buffers.
Channel	ChannelFactory.createUninitialised(Dimensions dimensions, VoxelDataType channelDataType)	Create a Channel without initialization with voxel-buffers.

Uses of Channel in org.anchoranalysis.image.core.mask

Methods in org.anchoranalysis.image.core.mask that return Channel

Modifier and Type	Method	Description
Channel	Mask.channel()	The underlying channel which contains the binary-values.

Constructors in org.anchoranalysis.image.core.mask with parameters of type Channel

Modifier	Constructor	Description
	Mask(Channel channel)	Creates a mask from an existing channel using default values for off (0) and on (255).
	Mask(Channel channel, BinaryValuesInt binaryValues)	Creates a mask from an existing channel.

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

Methods in org.anchoranalysis.image.core.object with parameters of type Channel

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

Uses of Channel in org.anchoranalysis.image.core.object.label

Methods in org.anchoranalysis.image.core.object.label that return Channel

Modifier and Type	Method	Description
Channel	LabelObjects.createLabelledChannel(BoundedList<T> elements, Optional<Map<Integer,T>> mapLabels)	Creates a channel that contains a unique integer (label) for each element's object-representation.

Methods in org.anchoranalysis.image.core.object.label with parameters of type Channel

Modifier and Type	Method	Description
void	LabelObjects.labelElements(Channel channel, Iterable<T> elements, Optional<Map<Integer,T>> mapLabels)	Replaces the contents of the channel so that all element's voxels are labelled with successive unique integer identifiers 1,2,3 etc. and voxels in no element are 0.

Uses of Channel in org.anchoranalysis.image.core.stack

Methods in org.anchoranalysis.image.core.stack that return Channel

Modifier and Type	Method	Description
Channel	RGBStack.blue()	The blue channel.
Channel	DisplayStack.createChannel(int index, boolean alwaysNew)	Create Channel for a particular index after applying conversion.
Channel	DisplayStack.extractChannelForBoundingBox(int index, BoundingBox box)	Creates a new Channel that refers to only a BoundingBox portion of the DisplayStack.
Channel	RGBStack.getChannel(int index)	Returns the channel at a particular position in the stack.
final Channel	Stack.getChannel(int index)	Returns the channel at a particular position in the stack.
final Channel	StackNotUniformSized.getChannel(int index)	Returns the channel at a particular position in the stack.
Channel	RGBStack.green()	The green channel.
Channel	RGBStack.red()	The red channel.

Methods in org.anchoranalysis.image.core.stack that return types with arguments of type Channel

Modifier and Type	Method	Description
List<Channel>	Stack.asListChannels()	Derives a List of Channels from those in the Stack, preserving order.
List<Optional<ChannelConverterAttached<Channel,UnsignedByteBuffer>>>	DisplayStack.getConverters()	A list of optional converters that will be applied to the respective channel in stack if they exist.
Iterator<Channel>	RGBStack.iterator()
Iterator<Channel>	Stack.iterator()
Iterator<Channel>	StackNotUniformSized.iterator()

Methods in org.anchoranalysis.image.core.stack with parameters of type Channel

Modifier and Type	Method	Description
final void	Stack.addChannel(Channel channel)	Appends a channel to the stack, as the new final-most channel position-wise.
final void	StackNotUniformSized.addChannel(Channel channel)	Appends a channel to the stack, as the new final-most channel position-wise.

Method parameters in org.anchoranalysis.image.core.stack with type arguments of type Channel

Modifier and Type	Method	Description
void	ChannelMapper.consumeChannelIfSupported(int channelIndex, BiConsumer<Channel,ChannelConverterAttached<Channel,UnsignedByteBuffer>> consumer, Consumer<Channel> fallback)	Like ChannelMapper.mapChannelIfSupported(int, BiFunction, Function) but the mapping has no return-type.
void	ChannelMapper.consumeChannelIfSupported(int channelIndex, BiConsumer<Channel,ChannelConverterAttached<Channel,UnsignedByteBuffer>> consumer, Consumer<Channel> fallback)	Like ChannelMapper.mapChannelIfSupported(int, BiFunction, Function) but the mapping has no return-type.
void	ChannelMapper.consumeChannelIfSupported(int channelIndex, BiConsumer<Channel,ChannelConverterAttached<Channel,UnsignedByteBuffer>> consumer, Consumer<Channel> fallback)	Like ChannelMapper.mapChannelIfSupported(int, BiFunction, Function) but the mapping has no return-type.
RGBStack	RGBStack.mapChannel(CheckedUnaryOperator<Channel,OperationFailedException> mapping)	Produces a new stack with a particular mapping applied to each channel.
Stack	Stack.mapChannel(CheckedUnaryOperator<Channel,OperationFailedException> mapping)	Produces a new stack with a particular mapping applied to each channel.
<T> T	ChannelMapper.mapChannelIfSupported(int channelIndex, BiFunction<Channel,ChannelConverterAttached<Channel,UnsignedByteBuffer>,T> mapFunction, Function<Channel,T> fallback)	Maps a Channel with mapFunction if a corresponding converter exists, otherwise with fallback.
<T> T	ChannelMapper.mapChannelIfSupported(int channelIndex, BiFunction<Channel,ChannelConverterAttached<Channel,UnsignedByteBuffer>,T> mapFunction, Function<Channel,T> fallback)	Maps a Channel with mapFunction if a corresponding converter exists, otherwise with fallback.
<T> T	ChannelMapper.mapChannelIfSupported(int channelIndex, BiFunction<Channel,ChannelConverterAttached<Channel,UnsignedByteBuffer>,T> mapFunction, Function<Channel,T> fallback)	Maps a Channel with mapFunction if a corresponding converter exists, otherwise with fallback.
Stack	Stack.mapChannelWithIndex(CheckedBiFunction<Channel,Integer,Channel,OperationFailedException> mapping)	Produces a new stack with a particular mapping applied to each channel (with an index of the channel also available).
Stack	Stack.mapChannelWithIndex(CheckedBiFunction<Channel,Integer,Channel,OperationFailedException> mapping)	Produces a new stack with a particular mapping applied to each channel (with an index of the channel also available).

Constructors in org.anchoranalysis.image.core.stack with parameters of type Channel

Modifier	Constructor	Description
	RGBStack(Channel red, Channel green, Channel blue)	Create with Channels for each color.
	Stack(boolean rgb, Channel... channels)	Creates from a varying number of channels, and a flag to indicate if they represent an RGB image or not.
	Stack(Channel channel)	Creates a Stack with a single channel.
	StackNotUniformSized(Channel channel)	Creates from a single Channel.

Constructor parameters in org.anchoranalysis.image.core.stack with type arguments of type Channel

Modifier	Constructor	Description
	ChannelMapper(IntFunction<Channel> channelGetter, IntFunction<Optional<ChannelConverterAttached<Channel,UnsignedByteBuffer>>> converterGetter)	Creates a new ChannelMapper instance.
	DisplayStack(Stack stack, boolean eventuallyThree, Function<VoxelDataType,ChannelConverterAttached<Channel,UnsignedByteBuffer>> createConverter)	Create for a particular Stack that may needed to be converted.
	Stack(boolean rgb, Stream<Channel> stream)	Like Stack(Stream) but allows explicitly setting whether it should be interpreted as RGB or not.
	Stack(Stream<Channel> stream)	Create a Stack from a stream of Channels.
	StackNotUniformSized(Stream<Channel> channelStream)	Creates from a stream of Channels.

Uses of Channel in org.anchoranalysis.image.io.channel.input

Methods in org.anchoranalysis.image.io.channel.input that return Channel

Modifier and Type	Method	Description
Channel	ChannelGetter.getChannel(String channelName, int timeIndex, Logger logger)	Retrieve the Channel corresponding to channelName at a particular time-frame.

Uses of Channel in org.anchoranalysis.image.io.channel.map

Methods in org.anchoranalysis.image.io.channel.map that return Channel

Modifier and Type	Method	Description
Channel	NamedChannelsConcatenate.getChannel(String channelName, int timeIndex, Logger logger)
Channel	OpenedNamedChannels.getChannel(String channelName, int timeIndex, Logger logger)

Methods in org.anchoranalysis.image.io.channel.map that return types with arguments of type Channel

Modifier and Type	Method	Description
Optional<Channel>	NamedChannelsConcatenate.getChannelOptional(String channelName, int timeIndex, Logger logger)
Optional<Channel>	NamedChannelsMap.getChannelOptional(String channelName, int timeIndex, Logger logger)	Gets a channel if it exists, returning empty if it doesn't.
Optional<Channel>	OpenedNamedChannels.getChannelOptional(String channelName, int timeIndex, Logger logger)

Uses of Channel in org.anchoranalysis.image.io.channel.output

Methods in org.anchoranalysis.image.io.channel.output with parameters of type Channel

Modifier and Type	Method	Description
Stack	ChannelGenerator.transform(Channel element)

Uses of Channel in org.anchoranalysis.io.bioformats

Methods in org.anchoranalysis.io.bioformats that return Channel

Modifier and Type	Method	Description
Channel	DestinationChannelForIndex.get(int index)	Retrieves the channel corresponding to a particular index.

Uses of Channel in org.anchoranalysis.io.bioformats.copyconvert

Method parameters in org.anchoranalysis.io.bioformats.copyconvert with type arguments of type Channel

Modifier and Type	Method	Description
static void	CopyConvert.copyAllFrames(loci.formats.IFormatReader reader, List<Channel> destination, ImageFileShape targetShape, ConvertTo<?> convertTo, ReadOptions readOptions, OrientationChange orientationCorrection)	Copies all frames, channels, z-slices (in a byte-array) into a destination set of Channels converting them if necessary along the way.

Uses of Channel in org.anchoranalysis.io.imagej.convert

Methods in org.anchoranalysis.io.imagej.convert that return Channel

Modifier and Type	Method	Description
static Channel	ConvertFromImagePlus.toChannel(ij.ImagePlus imagePlus, Optional<Resolution> resolution)	Converts an ImagePlus to a Channel.

Methods in org.anchoranalysis.io.imagej.convert with parameters of type Channel

Modifier and Type	Method	Description
static ij.ImagePlus	ConvertToImagePlus.from(Channel channel)	Creates an ImagePlus from a Channel.

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

Methods in org.anchoranalysis.plugin.fiji.bean.channel.provider that return Channel

Modifier and Type	Method	Description
Channel	AnisotropicDiffusion.createFromChannel(Channel channel)
Channel	MinimumFilter.createFromChannel(Channel channel)

Methods in org.anchoranalysis.plugin.fiji.bean.channel.provider with parameters of type Channel

Modifier and Type	Method	Description
Channel	AnisotropicDiffusion.createFromChannel(Channel channel)
Channel	MinimumFilter.createFromChannel(Channel channel)

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

Methods in org.anchoranalysis.plugin.fiji.bean.channel.provider.distance that return Channel

Modifier and Type	Method	Description
protected Channel	DistanceTransformForEachObject3D.createFromDimensions(Dimensions dimensions)
protected Channel	DistanceTransform3D.createFromMask(Mask mask)

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

Methods in org.anchoranalysis.plugin.fiji.bean.mask.provider with parameters of type Channel

Modifier and Type	Method	Description
protected Mask	AutoLocalThreshold.createFromSource(Channel channel)

Uses of Channel in org.anchoranalysis.plugin.image.bean.channel.aggregator

Methods in org.anchoranalysis.plugin.image.bean.channel.aggregator that return Channel

Modifier and Type	Method	Description
protected Channel	ProjectableBufferAggregator.retrieveCreateAggregatedChannel()

Methods in org.anchoranalysis.plugin.image.bean.channel.aggregator with parameters of type Channel

Modifier and Type	Method	Description
protected void	ProjectableBufferAggregator.addChannelAfterCheck(Channel channel)

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

Methods in org.anchoranalysis.plugin.image.bean.channel.provider that return Channel

Modifier and Type	Method	Description
protected Channel	Duplicate.createFromChannel(Channel channel)
Channel	IfParamEquals.createFromChannel(Channel channel)
Channel	UnaryWithObjectsBase.createFromChannel(Channel channel)
protected abstract Channel	UnaryWithObjectsBase.createFromChannel(Channel channel, ObjectCollection objects)	Creates a new channel from an existing channel and a collection of objects.
Channel	UnaryWithValueBase.createFromChannel(Channel channel)
protected abstract Channel	UnaryWithValueBase.createFromChannelWithConstant(Channel channel, double value)	Creates a new channel from an existing channel and a scalar value.
protected Channel	CreateNew.createFromDimensions(Dimensions dimensions)
protected abstract Channel	FromDimensionsBase.createFromDimensions(Dimensions dimensions)	Creates a channel from the given dimensions.
Channel	FromDimensionsBase.get()
Channel	FromInput.get()
Channel	FromStack.get()
Channel	Reference.get()
protected Channel	TwoVoxelMappingBase.process(Channel channel1, Channel channel2)

Methods in org.anchoranalysis.plugin.image.bean.channel.provider with parameters of type Channel

Modifier and Type	Method	Description
protected Channel	Duplicate.createFromChannel(Channel channel)
Channel	IfParamEquals.createFromChannel(Channel channel)
Channel	UnaryWithObjectsBase.createFromChannel(Channel channel)
protected abstract Channel	UnaryWithObjectsBase.createFromChannel(Channel channel, ObjectCollection objects)	Creates a new channel from an existing channel and a collection of objects.
Channel	UnaryWithValueBase.createFromChannel(Channel channel)
protected abstract Channel	UnaryWithValueBase.createFromChannelWithConstant(Channel channel, double value)	Creates a new channel from an existing channel and a scalar value.
protected Channel	TwoVoxelMappingBase.process(Channel channel1, Channel channel2)

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

Methods in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic that return Channel

Modifier and Type	Method	Description
Channel	Invert.createFromChannel(Channel channel)
Channel	ArithmeticWithConstantBase.createFromChannelWithConstant(Channel channel, double value)
Channel	ArithmeticWithConstantConditionallyWriteBase.createFromChannelWithConstant(Channel channel, double value)
protected Channel	SubtractMean.createFromMaskedChannel(Channel channel, Mask mask)
protected Channel	MeanThreeChannels.process(Channel channel1, Channel channel2, Channel channel3)

Methods in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic with parameters of type Channel

Modifier and Type	Method	Description
Channel	Invert.createFromChannel(Channel channel)
Channel	ArithmeticWithConstantBase.createFromChannelWithConstant(Channel channel, double value)
Channel	ArithmeticWithConstantConditionallyWriteBase.createFromChannelWithConstant(Channel channel, double value)
protected Channel	SubtractMean.createFromMaskedChannel(Channel channel, Mask mask)
protected Channel	MeanThreeChannels.process(Channel channel1, Channel channel2, Channel channel3)

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

Methods in org.anchoranalysis.plugin.image.bean.channel.provider.assign that return Channel

Modifier and Type	Method	Description
Channel	AssignFromDictionary.createFromChannel(Channel channel)
Channel	AssignFromIntersectingObjects.createFromChannel(Channel channel)
protected Channel	AssignFromChannel.createFromMaskedChannel(Channel channel, Mask mask)
protected Channel	AssignValue.createFromMaskedChannel(Channel channel, Mask mask)

Methods in org.anchoranalysis.plugin.image.bean.channel.provider.assign with parameters of type Channel

Modifier and Type	Method	Description
Channel	AssignFromDictionary.createFromChannel(Channel channel)
Channel	AssignFromIntersectingObjects.createFromChannel(Channel channel)
protected Channel	AssignFromChannel.createFromMaskedChannel(Channel channel, Mask mask)
protected Channel	AssignValue.createFromMaskedChannel(Channel channel, Mask mask)

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

Methods in org.anchoranalysis.plugin.image.bean.channel.provider.convert that return Channel

Modifier and Type	Method	Description
Channel	Convert.createFromChannel(Channel channel)
Channel	ConvertWithHistogram.createFromChannel(Channel channel)

Methods in org.anchoranalysis.plugin.image.bean.channel.provider.convert with parameters of type Channel

Modifier and Type	Method	Description
Channel	Convert.createFromChannel(Channel channel)
Channel	ConvertWithHistogram.createFromChannel(Channel channel)

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

Methods in org.anchoranalysis.plugin.image.bean.channel.provider.gradient that return Channel

Modifier and Type	Method	Description
protected Channel	GradientBase.convertToOutputType(Channel channelToConvert)	Converts the input channel to the output type specified by GradientBase.outputShort.
Channel	GradientBaseAddSum.createFromChannel(Channel channelIn)
Channel	Sobel.createFromChannel(Channel channelIn)

Methods in org.anchoranalysis.plugin.image.bean.channel.provider.gradient with parameters of type Channel

Modifier and Type	Method	Description
protected Channel	GradientBase.convertToOutputType(Channel channelToConvert)	Converts the input channel to the output type specified by GradientBase.outputShort.
Channel	GradientBaseAddSum.createFromChannel(Channel channelIn)
Channel	Sobel.createFromChannel(Channel channelIn)

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

Methods in org.anchoranalysis.plugin.image.bean.channel.provider.intensity that return Channel

Modifier and Type	Method	Description
Channel	Blur.createFromChannel(Channel channel)
Channel	IfVoxelZero.createFromChannel(Channel channel)
Channel	Median.createFromChannel(Channel channel)
protected Channel	NormalizeDifferenceToMedian.createFromChannel(Channel channel, ObjectCollection objects)
protected Channel	NormalizeObjectIntensity.createFromChannel(Channel channel, ObjectCollection objects)
Channel	QuantileStretch.createFromChannel(Channel channel)
Channel	ScaleXY.createFromChannel(Channel channel)
static Channel	IfVoxelZero.mergeViaZeroCheck(Channel channel, Channel channelIfPixelZero, VoxelDataType combinedType, double multiplierIfNonZero)	Creates a new channel which is a merged version of two input channels according to rules.

Methods in org.anchoranalysis.plugin.image.bean.channel.provider.intensity with parameters of type Channel

Modifier and Type	Method	Description
Channel	Blur.createFromChannel(Channel channel)
Channel	IfVoxelZero.createFromChannel(Channel channel)
Channel	Median.createFromChannel(Channel channel)
protected Channel	NormalizeDifferenceToMedian.createFromChannel(Channel channel, ObjectCollection objects)
protected Channel	NormalizeObjectIntensity.createFromChannel(Channel channel, ObjectCollection objects)
Channel	QuantileStretch.createFromChannel(Channel channel)
Channel	ScaleXY.createFromChannel(Channel channel)
static Channel	IfVoxelZero.mergeViaZeroCheck(Channel channel, Channel channelIfPixelZero, VoxelDataType combinedType, double multiplierIfNonZero)	Creates a new channel which is a merged version of two input channels according to rules.

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

Methods in org.anchoranalysis.plugin.image.bean.channel.provider.mask that return Channel

Modifier and Type	Method	Description
Channel	UnaryWithMaskBase.createFromChannel(Channel channel)
protected Channel	FromMask.createFromMask(Mask mask)
protected abstract Channel	FromMaskBase.createFromMask(Mask mask)	Creates a Channel from the provided Mask.
protected abstract Channel	UnaryWithMaskBase.createFromMaskedChannel(Channel channel, Mask mask)	Creates a new Channel from the input channel and mask.
protected Channel	ZeroOutsideMask.createFromMaskedChannel(Channel channel, Mask mask)
Channel	FromMaskBase.get()

Methods in org.anchoranalysis.plugin.image.bean.channel.provider.mask with parameters of type Channel

Modifier and Type	Method	Description
Channel	UnaryWithMaskBase.createFromChannel(Channel channel)
protected abstract Channel	UnaryWithMaskBase.createFromMaskedChannel(Channel channel, Mask mask)	Creates a new Channel from the input channel and mask.
protected Channel	ZeroOutsideMask.createFromMaskedChannel(Channel channel, Mask mask)

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

Methods in org.anchoranalysis.plugin.image.bean.channel.provider.object that return Channel

Modifier and Type	Method	Description
Channel	LevelPerObjectBase.createFromChannel(Channel channel)

Methods in org.anchoranalysis.plugin.image.bean.channel.provider.object with parameters of type Channel

Modifier and Type	Method	Description
Channel	LevelPerObjectBase.createFromChannel(Channel channel)
protected abstract void	LevelPerObjectBase.writeLevelsForObjects(Channel input, ObjectCollection objects, Channel output)	Creates a channel with the levels for a set of objects.
protected void	LevelPerObjectIndependently.writeLevelsForObjects(Channel channelIntensity, ObjectCollection objects, Channel output)
protected void	LevelPerObjectNeighbors.writeLevelsForObjects(Channel channelIntensity, ObjectCollection objects, Channel output)

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

Methods in org.anchoranalysis.plugin.image.bean.channel.provider.score that return Channel

Modifier and Type	Method	Description
protected Channel	IdentifyObjects.createFromChannel(Channel channel, ObjectCollection objects)
protected Channel	ScoreObjects.createFromChannel(Channel channel, ObjectCollection objects)
Channel	ScoreVoxels.get()

Methods in org.anchoranalysis.plugin.image.bean.channel.provider.score with parameters of type Channel

Modifier and Type	Method	Description
protected Channel	IdentifyObjects.createFromChannel(Channel channel, ObjectCollection objects)
protected Channel	ScoreObjects.createFromChannel(Channel channel, ObjectCollection objects)

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

Methods in org.anchoranalysis.plugin.image.bean.channel.provider.slice that return Channel

Modifier and Type	Method	Description
Channel	ExtractCenterSlice.createFromChannel(Channel channel)
Channel	ExtractSliceRange.createFromChannel(Channel channel)
Channel	MaximumIntensityProjection.createFromChannel(Channel channel)
Channel	MeanIntensityProjection.createFromChannel(Channel channel)
protected Channel	RepeatSlice.createFromDimensions(Dimensions dimensions)

Methods in org.anchoranalysis.plugin.image.bean.channel.provider.slice with parameters of type Channel

Modifier and Type	Method	Description
Channel	ExtractCenterSlice.createFromChannel(Channel channel)
Channel	ExtractSliceRange.createFromChannel(Channel channel)
Channel	MaximumIntensityProjection.createFromChannel(Channel channel)
Channel	MeanIntensityProjection.createFromChannel(Channel channel)

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

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

Modifier and Type	Method	Description
protected abstract Mask	FromChannelBase.createFromSource(Channel source)	Creates a Mask from the source Channel.

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

Methods in org.anchoranalysis.plugin.image.bean.mask.provider.convert with parameters of type Channel

Modifier and Type	Method	Description
protected Mask	FromChannel.createFromSource(Channel source)

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

Methods in org.anchoranalysis.plugin.image.bean.mask.provider.segment with parameters of type Channel

Modifier and Type	Method	Description
protected Mask	SegmentChannel.createFromSource(Channel source)
protected Mask	Threshold.createFromSource(Channel source)

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

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

Modifier and Type	Method	Description
protected abstract ObjectCollection	WithChannelBase.createFromChannel(Channel channelSrc)	Creates an ObjectCollection from a source Channel.
protected abstract ObjectCollection	UnaryWithChannelBase.createFromObjects(ObjectCollection objectsSource, Channel channelSource)	Creates objects from a source collection and a channel.

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

Methods in org.anchoranalysis.plugin.image.bean.object.provider.segment with parameters of type Channel

Modifier and Type	Method	Description
protected ObjectCollection	SegmentChannel.createFromChannel(Channel channelSource)
protected ObjectCollection	SegmentWithSeeds.createFromChannel(Channel channel)
protected ObjectCollection	BinarySegmentByObject.createFromObjects(ObjectCollection objectsSource, Channel channelSource)
ObjectCollection	SegmentChannelByObject.createFromObjects(ObjectCollection objectsSource, Channel channelToSegment)

Uses of Channel in org.anchoranalysis.plugin.image.bean.object.segment.channel

Methods in org.anchoranalysis.plugin.image.bean.object.segment.channel with parameters of type Channel

Modifier and Type	Method	Description
ObjectCollection	AtScale.segment(Channel channel, Optional<ObjectMask> objectMask, Optional<ObjectCollection> seeds, SegmentChannelIntoObjects upstreamSegmenter)
ObjectCollection	ConnectedComponentsFromBinarySegmentation.segment(Channel channel, Optional<ObjectMask> objectMask, Optional<ObjectCollection> seeds)
ObjectCollection	Filter.segment(Channel channel, Optional<ObjectMask> object, Optional<ObjectCollection> seeds, SegmentChannelIntoObjects upstreamSegmenter)
ObjectCollection	ImposeMinima.segment(Channel channel, Optional<ObjectMask> objectMask, Optional<ObjectCollection> seeds, SegmentChannelIntoObjects upstreamSegmenter)
ObjectCollection	Mser.segment(Channel channel, Optional<ObjectMask> objectMask, Optional<ObjectCollection> seeds)
ObjectCollection	SegmentOnMaximumIntensityAndExpandInZ.segment(Channel channel, Optional<ObjectMask> objectMask, Optional<ObjectCollection> seeds, SegmentChannelIntoObjects upstreamSegmenter)

Uses of Channel in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima

Methods in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima that return Channel

Modifier and Type	Method	Description
abstract Channel	MinimaImposition.imposeMinima(Channel channel, ObjectCollection seeds, Optional<ObjectMask> containingMask)	Imposes minima on a channel based on seed objects and an optional containing mask.
Channel	MinimaImpositionGrayscaleReconstruction.imposeMinima(Channel channel, ObjectCollection seeds, Optional<ObjectMask> containingMask)

Methods in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima with parameters of type Channel

Modifier and Type	Method	Description
abstract Channel	MinimaImposition.imposeMinima(Channel channel, ObjectCollection seeds, Optional<ObjectMask> containingMask)	Imposes minima on a channel based on seed objects and an optional containing mask.
Channel	MinimaImpositionGrayscaleReconstruction.imposeMinima(Channel channel, ObjectCollection seeds, Optional<ObjectMask> containingMask)

Uses of Channel in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong

Methods in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong with parameters of type Channel

Modifier and Type	Method	Description
ObjectCollection	WatershedYeong.segment(Channel channel, Optional<ObjectMask> objectMask, Optional<ObjectCollection> seeds)

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

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

Modifier and Type	Method	Description
static Stack	ThreeChannels.createRGBStack(Channel channelRed, Channel channelGreen, Channel channelBlue, VoxelDataType outputType)	Creates an RGB stack from up to three channels.

Uses of Channel in org.anchoranalysis.plugin.image.channel

Methods in org.anchoranalysis.plugin.image.channel that return Channel

Modifier and Type	Method	Description
static Channel	DimensionsChecker.createSameSize(ChannelProvider provider, String providerName, Channel channelSameSize)	Creates a new channel from a provider, making sure it's the same size as an existing channel.

Methods in org.anchoranalysis.plugin.image.channel with parameters of type Channel

Modifier and Type	Method	Description
static void	DimensionsChecker.check(Channel channelToCheck, String channelToCheckName, Dimensions dimFromChannel)	Checks a channel to make sure it's the same size as an existing channel.
static void	DimensionsChecker.check(Channel channel, Mask mask)	Checks if a channel and a mask have the same dimensions.
static Channel	DimensionsChecker.createSameSize(ChannelProvider provider, String providerName, Channel channelSameSize)	Creates a new channel from a provider, making sure it's the same size as an existing channel.
static Mask	DimensionsChecker.createSameSize(MaskProvider provider, String providerName, Channel channelSameSize)	Creates a new mask from a provider, making sure it's the same size as an existing channel.

Uses of Channel in org.anchoranalysis.plugin.image.feature.bean.object.single.energy

Methods in org.anchoranalysis.plugin.image.feature.bean.object.single.energy with parameters of type Channel

Modifier and Type	Method	Description
protected double	CountEqual.calculateWithChannel(ObjectMask object, Channel channel)	Calculates the number of voxels in the object that have the specified intensity value in the channel.
protected abstract double	SpecificEnergyChannelBase.calculateWithChannel(ObjectMask object, Channel channel)	Calculates the feature value for a specific object and channel.

Uses of Channel in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity

Methods in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity with parameters of type Channel

Modifier and Type	Method	Description
protected abstract double	FeatureEnergyChannel.calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject> input, Channel channel)	Calculates the feature value for a specific channel in the energy stack.
protected double	Intensity.calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject> input, Channel channel)
protected double	IntensityMeanMaxSlice.calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject> input, Channel channel)	Calculates the maximum mean intensity across all slices of the object in the given channel.
protected double	IntensityMeanShellBase.calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject> input, Channel channel)
protected double	TextureScore.calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject> input, Channel channel)
protected double	IntensityMeanShell.calculateForShell(ObjectMask object, Channel channel)
protected abstract double	IntensityMeanShellBase.calculateForShell(ObjectMask shell, Channel channel)	Calculates the feature value for the given shell and channel.
protected double	IntensityMeanShellMaxSlice.calculateForShell(ObjectMask object, Channel channel)

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

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

Modifier and Type	Method	Description
static double	IntensityMeanCalculator.calculateMeanIntensityObject(Channel channel, ObjectMask object)	Calculates the mean intensity of an object in a channel.
static double	IntensityMeanCalculator.calculateMeanIntensityObject(Channel channel, ObjectMask object, boolean excludeZero)	Calculates the mean intensity of an object in a channel, with an option to exclude zero values.

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

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

Modifier and Type	Method	Description
static LevelResultCollection	LevelResultCollectionFactory.createCollection(Channel channel, ObjectCollection objects, CalculateLevel calculateLevel, int numberDilations, MessageLogger logger)	Creates a LevelResultCollection from a channel and object collection.

Uses of Channel in org.anchoranalysis.plugin.image.task.bean.combine

Methods in org.anchoranalysis.plugin.image.task.bean.combine that return types with arguments of type Channel

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

Methods in org.anchoranalysis.plugin.image.task.bean.combine with parameters of type Channel

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

Method parameters in org.anchoranalysis.plugin.image.task.bean.combine with type arguments of type Channel

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

Uses of Channel in org.anchoranalysis.plugin.image.task.bean.grouped

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

Modifier and Type	Method	Description
protected abstract CheckedFunction<Channel,S,CreateException>	GroupedStackBase.createChannelDeriver(ChannelSource source)	A function to derive the individual type used for aggregation from a Channel.

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

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

Modifier and Type	Method	Description
protected CheckedFunction<Channel,Histogram,CreateException>	ExportImageHistograms.createChannelDeriver(ChannelSource source)

Uses of Channel in org.anchoranalysis.plugin.image.task.channel.aggregator

Methods in org.anchoranalysis.plugin.image.task.channel.aggregator that return types with arguments of type Channel

Modifier and Type	Method	Description
Iterator<Map.Entry<String,Channel>>	NamedChannels.iterator()

Methods in org.anchoranalysis.plugin.image.task.channel.aggregator with parameters of type Channel

Modifier and Type	Method	Description
void	NamedChannels.add(String name, Channel channel)	Adds a Channel with a name.

Uses of Channel in org.anchoranalysis.plugin.image.task.grouped

Methods in org.anchoranalysis.plugin.image.task.grouped that return Channel

Modifier and Type	Method	Description
Channel	ChannelSource.extractChannel(String stackName, boolean checkType)	Extracts a Channel from a particular Stack in stackStore.
Channel	ChannelSource.extractChannel(String stackName, boolean checkType, int index)	Extracts a Channel from a particular Stack in stackStore.
Channel	ChannelSource.extractChannel(Stack stack, boolean checkType, int index)	Extracts a Channel from a given Stack.
Channel	NamedChannel.getChannel()	The Channel instance.

Constructors in org.anchoranalysis.plugin.image.task.grouped with parameters of type Channel

Modifier	Constructor	Description
	NamedChannel(String name, Channel channel)	Creates a new NamedChannel instance.

Uses of Channel in org.anchoranalysis.plugin.image.task.stack

Methods in org.anchoranalysis.plugin.image.task.stack that return Channel

Modifier and Type	Method	Description
Channel	ChannelGetterForTimepoint.getChannel(String channelName, Logger logger)	Retrieves a channel with the given name for the specified timepoint.

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

Methods in org.anchoranalysis.plugin.imagej.bean.channel.provider that return Channel

Modifier and Type	Method	Description
protected Channel	BackgroundSubtractor.createFromChannel(Channel channel, int radius)
Channel	WithFilterBase.createFromChannel(Channel channel, int radius)
Channel	WithRadiusBase.createFromChannel(Channel channel)
protected abstract Channel	WithRadiusBase.createFromChannel(Channel channel, int radius)	Creates a new channel from an existing channel and a radius.

Methods in org.anchoranalysis.plugin.imagej.bean.channel.provider with parameters of type Channel

Modifier and Type	Method	Description
protected Channel	BackgroundSubtractor.createFromChannel(Channel channel, int radius)
Channel	WithFilterBase.createFromChannel(Channel channel, int radius)
Channel	WithRadiusBase.createFromChannel(Channel channel)
protected abstract Channel	WithRadiusBase.createFromChannel(Channel channel, int radius)	Creates a new channel from an existing channel and a radius.

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

Methods in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter that return Channel

Modifier and Type	Method	Description
Channel	EdgeFilterIJ.createFromChannel(Channel channel)
Channel	GaussianBlur2D.createFromChannel(Channel channel)

Methods in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter with parameters of type Channel

Modifier and Type	Method	Description
Channel	EdgeFilterIJ.createFromChannel(Channel channel)
Channel	GaussianBlur2D.createFromChannel(Channel channel)

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

Methods in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank that return Channel

Modifier and Type	Method	Description
Channel	MedianFilter3D.createFromChannel(Channel channel)

Methods in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank with parameters of type Channel

Modifier and Type	Method	Description
Channel	MedianFilter3D.createFromChannel(Channel channel)

Uses of Channel in org.anchoranalysis.plugin.imagej.bean.object.segment

Methods in org.anchoranalysis.plugin.imagej.bean.object.segment with parameters of type Channel

Modifier and Type	Method	Description
ObjectCollection	FloodFillEachIntensityLevel.segment(Channel channel, Optional<ObjectMask> objectMask, Optional<ObjectCollection> seeds)

Uses of Channel in org.anchoranalysis.plugin.imagej.channel.provider

Methods in org.anchoranalysis.plugin.imagej.channel.provider that return Channel

Modifier and Type	Method	Description
static Channel	FilterHelper.applyRankFilter(Channel channel, int radius, int filterType)	Applies a 2D rank-filter to each slice independently of a Channel.

Methods in org.anchoranalysis.plugin.imagej.channel.provider with parameters of type Channel

Modifier and Type	Method	Description
static Channel	FilterHelper.applyRankFilter(Channel channel, int radius, int filterType)	Applies a 2D rank-filter to each slice independently of a Channel.
static void	FilterHelper.processEachSlice(Channel channel, Consumer<ij.process.ImageProcessor> consumer)	Applies a Consumer to each slice independently of a Channel.

Uses of Channel in org.anchoranalysis.test.image

Methods in org.anchoranalysis.test.image that return Channel

Modifier and Type	Method	Description
Channel	ChannelFixture.createChannel(Extent extent, ChannelFixture.IntensityFunction createIntensity, VoxelDataType channelVoxelType)	Creates a channel with specified extent, intensity function, and voxel data type.

Methods in org.anchoranalysis.test.image with parameters of type Channel

Modifier and Type	Method	Description
void	WriteIntoDirectory.writeChannel(String outputName, Channel channel)	Writes a Channel to the output directory.

Uses of Channel in org.anchoranalysis.test.image.io

Methods in org.anchoranalysis.test.image.io that return Channel

Modifier and Type	Method	Description
Channel	TestLoaderImage.openChannelFromFilePath(Path filePath)	Opens a channel from a file path.
Channel	TestLoaderImage.openChannelFromTestPath(String testPath)	Opens a channel from a test path.