Uses of Class
org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer

Packages that use UnsignedByteBuffer

Package	Description
org.anchoranalysis.image.bean.displayer
org.anchoranalysis.image.bean.segment.binary	Base classes to perform binary-segmentation.
org.anchoranalysis.image.bean.threshold	Base classes for thresholding and calculating levels for thresholding.
org.anchoranalysis.image.core.bufferedimage	Conversions and operations involving Java AWT's BufferedImage.
org.anchoranalysis.image.core.channel.convert	Converts a channel to other data-types.
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.mask	An image with only two permissible states.
org.anchoranalysis.image.core.mask.combine	Binary operations involving voxelwise combination of Mask.
org.anchoranalysis.image.core.object.properties	An ObjectCollection with associated key-value pairs.
org.anchoranalysis.image.core.stack	Defines the key data object, Stack, and related classes.
org.anchoranalysis.image.inference.segment	Non-beans pertaining to segmentation of images via model inference.
org.anchoranalysis.image.voxel	Data-structures to store and manipulate image raster-data or voxels.
org.anchoranalysis.image.voxel.arithmetic	Arithmetic operations for Voxels.
org.anchoranalysis.image.voxel.assigner	Assigns values to some or all voxels.
org.anchoranalysis.image.voxel.binary	The BinaryVoxels class and related operations.
org.anchoranalysis.image.voxel.binary.connected	Creating an ObjectCollection that is a connected component labelling of a BinaryVoxels.
org.anchoranalysis.image.voxel.buffer	A buffer of voxel-values, usually corresponding to a single z-slice in Voxels.
org.anchoranalysis.image.voxel.buffer.primitive	Conversion of both primitive data types and image structures between Anchor's data-structures and other representations.
org.anchoranalysis.image.voxel.buffer.slice	A container with voxel-buffers for each z-slice.
org.anchoranalysis.image.voxel.convert	Converting Voxels to different data-types.
org.anchoranalysis.image.voxel.convert.bufferedimage	Converts anchor data-structures to the BufferedImage used by Java's AWT.
org.anchoranalysis.image.voxel.convert.imglib2	Converts anchor data-structures to those used by ImgLib2.
org.anchoranalysis.image.voxel.extracter	Methods to read/copy/duplicate portions of voxels.
org.anchoranalysis.image.voxel.factory	Creates new instances of Voxels and VoxelsUntyped with specific data-types.
org.anchoranalysis.image.voxel.iterator	Utilities to iterate over voxel-locations in images and sub-regions of images.
org.anchoranalysis.image.voxel.iterator.intersecting	Like org.anchoranalysis.image.voxel.iterator but refers to iterators that operation over the intersecting regions of two entities.
org.anchoranalysis.image.voxel.iterator.neighbor	Iterating over a point's neighboring voxels.
org.anchoranalysis.image.voxel.iterator.neighbor.kernel	Routines for moving a KernelPointCursor around the neighboring voxels of the point.
org.anchoranalysis.image.voxel.iterator.predicate	Functional-interfaces for processing different combinations of points and buffers that return a boolean.
org.anchoranalysis.image.voxel.kernel	Applying a kernel via convolution to voxels.
org.anchoranalysis.image.voxel.kernel.morphological	Kernels that apply morphological operations.
org.anchoranalysis.image.voxel.kernel.outline	Kernel to find outline voxels on an object.
org.anchoranalysis.image.voxel.object	The fundamental data class that is an ObjectMask and related structures.
org.anchoranalysis.image.voxel.object.morphological	Morphological operations applied to ObjectMasks.
org.anchoranalysis.image.voxel.object.morphological.predicate	Predicates to match certain voxels as used in org.anchoranalysis.image.voxel.object.morphological.
org.anchoranalysis.image.voxel.projection	Classes for calculating differnet kind of projections of voxel values across multiple buffers.
org.anchoranalysis.image.voxel.projection.extrema	Classes for performing both a Maximum Intensity Projection and a minimum projection.
org.anchoranalysis.image.voxel.resizer	Different interpolator methods to use when scaling voxels.
org.anchoranalysis.image.voxel.thresholder	Thresholding operations on voxels.
org.anchoranalysis.io.bioformats.copyconvert.tobyte	Converts the byte stream opened by Bioformats into channels of ByteBuffer.
org.anchoranalysis.io.imagej.convert	Converts to and from ImageJ data-structures for images.
org.anchoranalysis.io.imagej.resizer	Image interpolation when scaling using ImageJ.
org.anchoranalysis.mpp.mark.voxelized	A mark after a voxel-representation has been inferred.
org.anchoranalysis.mpp.overlap	Calculating overlaps between two Marks.
org.anchoranalysis.plugin.fiji.bean.channel.provider.distance	Euclidean Distance Transform implementations via FIJI.
org.anchoranalysis.plugin.fiji.bean.threshold	Implementations of Thresholder that use FIJI.
org.anchoranalysis.plugin.image.bean.channel.convert	Implementations of ConvertChannelTo and ConvertChannelToWithHistogram.
org.anchoranalysis.plugin.image.bean.segment.binary	Implementations of BinarySegmentation.
org.anchoranalysis.plugin.image.segment.thresholder.slice	Non-beans pertaining to segmenting a z-stack slice-by-slice.
org.anchoranalysis.plugin.imagej.bean.threshold	Implementations of Thresholder that call ImageJ.
org.anchoranalysis.plugin.imagej.channel.provider	Implementations of ChannelProvider that call ImageJ.
org.anchoranalysis.plugin.imagej.mask	Non-bean classes involving ObjectMask that call ImageJ.
org.anchoranalysis.plugin.opencv.convert	Conversion to/from OpenCV data-structures.
org.anchoranalysis.plugin.opencv.resizer	Interpolation non-beans that use OpenCV.
org.anchoranalysis.test.image	Testing utilities and fixtures with no greater downstream dependency than anchor-image-io or anchor-io-bioformats or anchor-imagej.

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

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

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.

Uses of UnsignedByteBuffer in org.anchoranalysis.image.bean.segment.binary

Methods in org.anchoranalysis.image.bean.segment.binary that return types with arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
abstract BinaryVoxels<UnsignedByteBuffer>	BinarySegmentation.segment(VoxelsUntyped voxels, BinarySegmentationParameters parameters, Optional<ObjectMask> objectMask)	Performs a segmentation on voxels so that each voxel has an on or off state after the operation.
BinaryVoxels<UnsignedByteBuffer>	BinarySegmentationReference.segment(VoxelsUntyped voxels, BinarySegmentationParameters parameters, Optional<ObjectMask> objectMask)
BinaryVoxels<UnsignedByteBuffer>	BinarySegmentationThreshold.segment(VoxelsUntyped voxels, BinarySegmentationParameters parameters, Optional<ObjectMask> objectMask)
BinaryVoxels<UnsignedByteBuffer>	BinarySegmentationUnary.segment(VoxelsUntyped voxels, BinarySegmentationParameters parameters, Optional<ObjectMask> objectMask)
protected abstract BinaryVoxels<UnsignedByteBuffer>	BinarySegmentationUnary.segmentFromExistingSegmentation(VoxelsUntyped voxels, BinarySegmentationParameters parameters, Optional<ObjectMask> objectMask, BinarySegmentation segment)	Performs a binary-segmentation, in a similar manner to BinarySegmentation.segment(org.anchoranalysis.image.voxel.VoxelsUntyped, org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters, java.util.Optional<org.anchoranalysis.image.voxel.object.ObjectMask>) but with the delegate as additional argument.

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

Methods in org.anchoranalysis.image.bean.threshold that return types with arguments of type UnsignedByteBuffer

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

Uses of UnsignedByteBuffer in org.anchoranalysis.image.core.bufferedimage

Method parameters in org.anchoranalysis.image.core.bufferedimage with type arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
static BufferedImage	BufferedImageFromStack.createRGB(Voxels<UnsignedByteBuffer> red, Voxels<UnsignedByteBuffer> green, Voxels<UnsignedByteBuffer> blue, Extent extent)	Creates a BufferedImage from three Voxels<UnsignedByteBuffer> representing respectively, red, green, blue color components.

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

Constructor parameters in org.anchoranalysis.image.core.channel.convert with type arguments of type UnsignedByteBuffer

Modifier	Constructor	Description
	ToUnsignedByte(VoxelsConverter<UnsignedByteBuffer> voxelsConverter)	Convert with a particular VoxelsConverter.

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

Methods in org.anchoranalysis.image.core.channel.convert.attached.channel that return types with arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
VoxelsConverter<UnsignedByteBuffer>	IntensityRange.getVoxelsConverter()
VoxelsConverter<UnsignedByteBuffer>	MaxIntensity.getVoxelsConverter()

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

Methods in org.anchoranalysis.image.core.channel.convert.attached.histogram that return types with arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
VoxelsConverter<UnsignedByteBuffer>	MaxIntensityFromHistogram.getVoxelsConverter()
VoxelsConverter<UnsignedByteBuffer>	QuantileIntensityFromHistogram.getVoxelsConverter()
VoxelsConverter<UnsignedByteBuffer>	UpperLowerQuantileIntensityFromHistogram.getVoxelsConverter()

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

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

Modifier and Type	Method	Description
UnsignedByteBuffer	Mask.sliceBuffer(int z)	A buffer corresponding to a particular z-slice.

Methods in org.anchoranalysis.image.core.mask that return types with arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
BinaryVoxels<UnsignedByteBuffer>	Mask.binaryVoxels()	The underlying voxels in the mask, exposed as BinaryVoxels.
Voxels<UnsignedByteBuffer>	Mask.voxels()	The underlying voxels in the mask.

Method parameters in org.anchoranalysis.image.core.mask with type arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
static RunningSum	IterateVoxelsMask.calculateRunningSum(Mask mask, Voxels<UnsignedByteBuffer> voxelsIntensity)	Calculates the sum and count across voxels intensity that correspond to on voxels on a mask
void	Mask.replaceBy(BinaryVoxels<UnsignedByteBuffer> voxels)	Replaces the underlying voxels in the mask with new voxels.

Constructor parameters in org.anchoranalysis.image.core.mask with type arguments of type UnsignedByteBuffer

Modifier	Constructor	Description
	Mask(BinaryVoxels<UnsignedByteBuffer> voxels)	Creates a mask from an existing binary-voxels using default image resolution.
	Mask(BinaryVoxels<UnsignedByteBuffer> voxels, Optional<Resolution> resolution)	Creates a mask from an existing binary-voxels and a specific image resolution.

Uses of UnsignedByteBuffer in org.anchoranalysis.image.core.mask.combine

Method parameters in org.anchoranalysis.image.core.mask.combine with type arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
static void	MaskAnd.apply(Voxels<UnsignedByteBuffer> voxelsFirst, Voxels<UnsignedByteBuffer> voxelsSecond, BinaryValuesByte binaryValuesFirst, BinaryValuesByte binaryValuesSecond)	Performs a logical and operation on each voxel in two Voxels (considered to be masks), writing the result onto the second mask.
static void	MaskXor.apply(BinaryVoxels<UnsignedByteBuffer> voxelsFirst, BinaryVoxels<UnsignedByteBuffer> voxelsSecond)	Performs a logical xor (exclusive or) operation on each voxel in two Voxels (considered to be masks), writing the result onto the second mask.

Uses of UnsignedByteBuffer in org.anchoranalysis.image.core.object.properties

Methods in org.anchoranalysis.image.core.object.properties that return UnsignedByteBuffer

Modifier and Type	Method	Description
UnsignedByteBuffer	ObjectWithProperties.sliceBufferLocal(int sliceIndexRelative)	A slice buffer with local coordinates.

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

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

Modifier and Type	Method	Description
UnsignedByteBuffer	RGBStack.sliceBuffer(int channelIndex, int zIndex)	A buffer corresponding to a particular z-slice of a particular channel.

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

Modifier and Type	Method	Description
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.

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

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	DisplayStack.copyPixelsTo(int channelIndex, BoundingBox sourceBox, Voxels<UnsignedByteBuffer> destinationVoxels, BoundingBox destinationBox)	Copies pixels from a particular channel to an output buffer.
<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.

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

Modifier	Constructor	Description
	DisplayStack(Stack stack, boolean eventuallyThree, Function<VoxelDataType,ChannelConverterAttached<Channel,UnsignedByteBuffer>> createConverter)	Create for a particular Stack that may needed to be converted.

Uses of UnsignedByteBuffer in org.anchoranalysis.image.inference.segment

Methods in org.anchoranalysis.image.inference.segment that return types with arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
static BinaryVoxels<UnsignedByteBuffer>	ScaleAndThresholdVoxels.scaleAndThreshold(Voxels<FloatBuffer> voxels, Extent targetSize, VoxelsResizer resizer, float maskMinValue)	Scales voxels representing a mask to a target size, and then thresholds.

Uses of UnsignedByteBuffer in org.anchoranalysis.image.voxel

Methods in org.anchoranalysis.image.voxel that return types with arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
Voxels<UnsignedByteBuffer>	VoxelsUntyped.asByte()	Casts to use a UnsignedByteBuffer if the voxels contain this data-type, otherwise throws a IncorrectVoxelTypeException.
VoxelsExtracter<UnsignedByteBuffer>	VoxelsUnsignedByte.extract()

Constructor parameters in org.anchoranalysis.image.voxel with type arguments of type UnsignedByteBuffer

Modifier	Constructor	Description
	VoxelsUnsignedByte(SliceBufferIndex<UnsignedByteBuffer> buffer)	Create from a buffer, indexed by slice.

Uses of UnsignedByteBuffer in org.anchoranalysis.image.voxel.arithmetic

Method parameters in org.anchoranalysis.image.voxel.arithmetic with type arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
static VoxelsArithmetic	VoxelsArithmeticFactory.createUnsignedByte(Extent extent, IntFunction<UnsignedByteBuffer> bufferForSlice)	Create a VoxelsArithmetic for UnsignedByteBuffer.

Uses of UnsignedByteBuffer in org.anchoranalysis.image.voxel.assigner

Method parameters in org.anchoranalysis.image.voxel.assigner with type arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
static VoxelsAssigner	VoxelsAssignerFactory.createUnsignedByte(Voxels<UnsignedByteBuffer> voxels, int valueToAssign)	Create a VoxelsAssigner for a UnsignedByteBuffer.

Uses of UnsignedByteBuffer in org.anchoranalysis.image.voxel.binary

Methods in org.anchoranalysis.image.voxel.binary that return types with arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
static BinaryVoxels<UnsignedByteBuffer>	BinaryVoxelsFactory.createEmptyOff(Extent extent)	Creates binary-voxels using unsigned 8-bit byte type and with all voxels set to off (0).
static BinaryVoxels<UnsignedByteBuffer>	BinaryVoxelsFactory.createEmptyOn(Extent extent)	Creates binary-voxels using unsigned 8-bit byte type and with all voxels set to on (255).
static BinaryVoxels<UnsignedByteBuffer>	BinaryVoxelsFactory.reuseByte(Voxels<UnsignedByteBuffer> voxels)	Like BinaryVoxelsFactory.reuseByte(org.anchoranalysis.image.voxel.Voxels<org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer>) but uses default binary-values for off (0) and on (255).
static BinaryVoxels<UnsignedByteBuffer>	BinaryVoxelsFactory.reuseByte(Voxels<UnsignedByteBuffer> voxels, BinaryValuesInt binaryValues)	Reuses an existing voxel-buffer (of type unsigned byte) as a binary-version which should have only two intensity-values representing off and on.

Method parameters in org.anchoranalysis.image.voxel.binary with type arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
static BinaryVoxels<UnsignedByteBuffer>	BinaryVoxelsFactory.reuseByte(Voxels<UnsignedByteBuffer> voxels)	Like BinaryVoxelsFactory.reuseByte(org.anchoranalysis.image.voxel.Voxels<org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer>) but uses default binary-values for off (0) and on (255).
static BinaryVoxels<UnsignedByteBuffer>	BinaryVoxelsFactory.reuseByte(Voxels<UnsignedByteBuffer> voxels, BinaryValuesInt binaryValues)	Reuses an existing voxel-buffer (of type unsigned byte) as a binary-version which should have only two intensity-values representing off and on.

Uses of UnsignedByteBuffer in org.anchoranalysis.image.voxel.binary.connected

Method parameters in org.anchoranalysis.image.voxel.binary.connected with type arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
ObjectCollection	ObjectsFromConnectedComponentsFactory.createUnsignedByte(BinaryVoxels<UnsignedByteBuffer> voxels)	Finds the connected-components in unsigned byte voxels.

Uses of UnsignedByteBuffer in org.anchoranalysis.image.voxel.buffer

Methods in org.anchoranalysis.image.voxel.buffer that return types with arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
static VoxelBuffer<UnsignedByteBuffer>	VoxelBufferFactory.allocateUnsignedByte(int capacity)	Allocates a new unsigned byte voxel-buffer of given size.
static VoxelBuffer<UnsignedByteBuffer>[]	VoxelBufferFactory.allocateUnsignedByteArray(int size)	Creates an array of unsigned byte voxel-buffers of given size.
static VoxelBuffer<UnsignedByteBuffer>	VoxelBufferWrap.unsignedByteArray(byte[] array)	Wraps an existing array (encoding unsigned bytes as a signed array) as a voxel-buffer.
static VoxelBuffer<UnsignedByteBuffer>	VoxelBufferWrap.unsignedByteBuffer(UnsignedByteBuffer buffer)	Wraps an unsigned-byte buffer into a voxel-buffer.
static VoxelBuffer<UnsignedByteBuffer>	VoxelBufferWrap.unsignedByteRaw(ByteBuffer buffer)	Wraps an unsigned-byte buffer (represented by a NIO signed-buffer) into a voxel-buffer.

Methods in org.anchoranalysis.image.voxel.buffer with parameters of type UnsignedByteBuffer

Modifier and Type	Method	Description
static VoxelBuffer<UnsignedByteBuffer>	VoxelBufferWrap.unsignedByteBuffer(UnsignedByteBuffer buffer)	Wraps an unsigned-byte buffer into a voxel-buffer.

Uses of UnsignedByteBuffer in org.anchoranalysis.image.voxel.buffer.primitive

Methods in org.anchoranalysis.image.voxel.buffer.primitive that return UnsignedByteBuffer

Modifier and Type	Method	Description
static UnsignedByteBuffer	UnsignedByteBuffer.allocate(int capacity)	Allocates a new buffer of unsigned-bytes.
static UnsignedByteBuffer	UnsignedByteBuffer.wrapRaw(byte[] array)	Exposes a raw byte-array as a buffer with unsigned-bytes.
static UnsignedByteBuffer	UnsignedByteBuffer.wrapRaw(ByteBuffer bufferRaw)	Exposes a raw ByteBuffer as a buffer with unsigned-bytes.

Methods in org.anchoranalysis.image.voxel.buffer.primitive with parameters of type UnsignedByteBuffer

Modifier and Type	Method	Description
void	UnsignedByteBuffer.put(UnsignedByteBuffer source)	Relative put-method from an unsigned byte buffer, represented by a UnsignedByteBuffer.

Uses of UnsignedByteBuffer in org.anchoranalysis.image.voxel.buffer.slice

Methods in org.anchoranalysis.image.voxel.buffer.slice that return types with arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
static SliceBufferIndex<UnsignedByteBuffer>	FromByte.createInitialized(Extent extent)	Create a buffer of a particular size, that has been initialized.
static SliceBufferIndex<UnsignedByteBuffer>	FromByte.createUninitialized(Extent extent)	Create a buffer of a particular size, that has not been initialized.
VoxelBuffer<UnsignedByteBuffer>	FromByte.slice(int z)

Method parameters in org.anchoranalysis.image.voxel.buffer.slice with type arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
void	FromByte.replaceSlice(int z, VoxelBuffer<UnsignedByteBuffer> sliceToAssign)

Uses of UnsignedByteBuffer in org.anchoranalysis.image.voxel.convert

Methods in org.anchoranalysis.image.voxel.convert with parameters of type UnsignedByteBuffer

Modifier and Type	Method	Description
protected void	ToUnsignedByteNoScaling.convertFloat(FloatBuffer in, UnsignedByteBuffer out)
protected void	ToUnsignedByteScaleByMaxValue.convertFloat(FloatBuffer in, UnsignedByteBuffer out)
protected void	ToUnsignedByteScaleByMinMaxValue.convertFloat(FloatBuffer in, UnsignedByteBuffer out)
protected void	ToUnsignedByteScaleByType.convertFloat(FloatBuffer in, UnsignedByteBuffer out)	Converts the current position in a FloatBuffer to the current position in a UnsignedShortBuffer.
protected void	ToFloatNoScaling.convertUnsignedByte(UnsignedByteBuffer in, FloatBuffer out)
protected void	ToUnsignedByte.convertUnsignedByte(UnsignedByteBuffer in, UnsignedByteBuffer out)
protected void	ToUnsignedInt.convertUnsignedByte(UnsignedByteBuffer in, UnsignedIntBuffer out)
protected void	ToUnsignedShortNoScaling.convertUnsignedByte(UnsignedByteBuffer in, UnsignedShortBuffer out)
protected void	ToUnsignedShortScaleByType.convertUnsignedByte(UnsignedByteBuffer in, UnsignedShortBuffer out)
protected abstract void	VoxelsConverter.convertUnsignedByte(UnsignedByteBuffer in, T out)	Copies a value from the current position in a UnsignedByteBuffer to the current position in a buffer of type T.
protected void	ToUnsignedByteNoScaling.convertUnsignedInt(UnsignedIntBuffer in, UnsignedByteBuffer out)
protected void	ToUnsignedByteScaleByMaxValue.convertUnsignedInt(UnsignedIntBuffer in, UnsignedByteBuffer out)
protected void	ToUnsignedByteScaleByMinMaxValue.convertUnsignedInt(UnsignedIntBuffer in, UnsignedByteBuffer out)
protected void	ToUnsignedByteScaleByType.convertUnsignedInt(UnsignedIntBuffer in, UnsignedByteBuffer out)
protected void	ToUnsignedByteNoScaling.convertUnsignedShort(UnsignedShortBuffer in, UnsignedByteBuffer out)
protected void	ToUnsignedByteScaleByMaxValue.convertUnsignedShort(UnsignedShortBuffer in, UnsignedByteBuffer out)
protected void	ToUnsignedByteScaleByMinMaxValue.convertUnsignedShort(UnsignedShortBuffer in, UnsignedByteBuffer out)
protected void	ToUnsignedByteScaleByType.convertUnsignedShort(UnsignedShortBuffer in, UnsignedByteBuffer out)

Method parameters in org.anchoranalysis.image.voxel.convert with type arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
void	VoxelsConverter.copyFromUnsignedByte(Voxels<UnsignedByteBuffer> from, Voxels<T> to)	Copies voxels from a source of type @{link UnsignedByteBuffer} to voxels of type T.

Uses of UnsignedByteBuffer in org.anchoranalysis.image.voxel.convert.bufferedimage

Method parameters in org.anchoranalysis.image.voxel.convert.bufferedimage with type arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
static BufferedImage	BufferedImageFromVoxels.createGrayscaleByte(Voxels<UnsignedByteBuffer> voxels)	Creates a BufferedImage from a Voxels<UnsignedByteBuffer>.

Uses of UnsignedByteBuffer in org.anchoranalysis.image.voxel.convert.imglib2

Method parameters in org.anchoranalysis.image.voxel.convert.imglib2 with type arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
static net.imglib2.img.Img<net.imglib2.type.numeric.integer.UnsignedByteType>	ConvertToImg.fromByte(VoxelBuffer<UnsignedByteBuffer> buffer, Extent extent)	Creates an Img from a VoxelBuffer with an unsigned byte data-type.
static net.imglib2.img.Img<net.imglib2.type.numeric.integer.UnsignedByteType>	ConvertToImg.fromByte(Voxels<UnsignedByteBuffer> voxels)	Creates an Img from Voxels with an unsigned byte data-type.
static net.imglib2.img.NativeImg<net.imglib2.type.numeric.integer.UnsignedByteType,net.imglib2.img.basictypeaccess.array.ByteArray>	ConvertToNativeImg.fromByte(Voxels<UnsignedByteBuffer> voxels)	Creates an NativeImg from Voxels with an unsigned byte data-type.

Uses of UnsignedByteBuffer in org.anchoranalysis.image.voxel.extracter

Methods in org.anchoranalysis.image.voxel.extracter that return types with arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
static VoxelsExtracter<UnsignedByteBuffer>	VoxelsExtracterFactory.createUnsignedByte(Voxels<UnsignedByteBuffer> voxels)	Create voxels-extracter for UnsignedByteBuffer.

Method parameters in org.anchoranalysis.image.voxel.extracter with type arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
static VoxelsExtracter<UnsignedByteBuffer>	VoxelsExtracterFactory.createUnsignedByte(Voxels<UnsignedByteBuffer> voxels)	Create voxels-extracter for UnsignedByteBuffer.

Uses of UnsignedByteBuffer in org.anchoranalysis.image.voxel.factory

Methods in org.anchoranalysis.image.voxel.factory that return types with arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
static VoxelsFactoryTypeBound<UnsignedByteBuffer>	VoxelsFactory.getUnsignedByte()	A factory that creates voxels of type unsigned byte.

Uses of UnsignedByteBuffer in org.anchoranalysis.image.voxel.iterator

Method parameters in org.anchoranalysis.image.voxel.iterator with type arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
static void	IterateVoxelsAll.binaryOperation(Voxels<UnsignedByteBuffer> voxelsIn1, Voxels<UnsignedByteBuffer> voxelsIn2, Voxels<UnsignedByteBuffer> voxelsOut, IntBinaryOperator operation)	Iterate over each voxel in a bounding-box - applying a binary operation with values from two input Voxels<UnsignedByteBuffer> for each slice and writing it into an output Voxels<UnsignedByteBuffer>.
static void	IterateVoxelsEqualTo.equalToPrimitive(Voxels<UnsignedByteBuffer> voxels, byte equalToValue, ScalarThreeDimensionalConsumer consumer)	Iterates through all points with a specific voxel intensity-value, passing coordinates as primitive types.
static void	IterateVoxelsEqualTo.equalToPrimitiveSlice(Voxels<UnsignedByteBuffer> voxels, int sliceIndex, byte equalToValue, ScalarThreeDimensionalConsumer consumer)	Like IterateVoxelsEqualTo.equalToPrimitive(org.anchoranalysis.image.voxel.Voxels<org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer>, byte, org.anchoranalysis.spatial.point.consumer.ScalarThreeDimensionalConsumer) but only iterates over one specific z-slice.
static void	IterateVoxelsEqualTo.equalToReusePoint(Voxels<UnsignedByteBuffer> voxels, byte equalToValue, Consumer<Point3i> consumer)	Iterates all points with a specific voxel intensity-value, reusing the Point3i in each iteration.
static Optional<Point3i>	IterateVoxelsEqualTo.untilFirstIntensityEqualTo(BoundedVoxels<UnsignedByteBuffer> voxels, byte equalToValue)	Iterates each voxel until a specific intensity value is found.
static void	IterateVoxelsAll.withCursor(BinaryVoxels<UnsignedByteBuffer> voxels, KernelApplicationParameters parameters, ProcessKernelPointCursor process)	Iterate over each voxel using a KernelPointCursor.
static void	IterateVoxelsBoundingBox.withCursor(BinaryVoxels<UnsignedByteBuffer> voxels, BoundingBox box, KernelApplicationParameters parameters, ProcessKernelPointCursor process)	Iterate over each voxel in a bounding-box using a KernelPointCursor.
static boolean	IterateVoxelsBoundingBox.withCursorUntil(BinaryVoxels<UnsignedByteBuffer> voxels, BoundingBox box, KernelApplicationParameters parameters, PredicateKernelPointCursor predicate)	Iterate over each voxel in a bounding-box using a KernelPointCursor until a predicate returns true..

Uses of UnsignedByteBuffer in org.anchoranalysis.image.voxel.iterator.intersecting

Method parameters in org.anchoranalysis.image.voxel.iterator.intersecting with type arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
static int	CountVoxelsIntersectingBounded.countByte(BoundedVoxels<UnsignedByteBuffer> voxels1, BoundedVoxels<UnsignedByteBuffer> voxels2, PredicateTwoBytes predicate)	Counts all voxels in the intersection of two bounded-voxels of type BoundedVoxels that match a predicate.
static int	CountVoxelsIntersectingBounded.countByteMasked(Voxels<UnsignedByteBuffer> maskGlobal, byte onMaskGlobal, BoundedVoxels<UnsignedByteBuffer> voxels1, BoundedVoxels<UnsignedByteBuffer> voxels2, PredicateTwoBytes predicate)	Counts all voxels intersection of two bounded-voxels of type BoundedVoxels but only voxels that lie on an object-mask and match a predicate.
static int	CountVoxelsIntersectingBounded.countByteMasked(Voxels<UnsignedByteBuffer> maskGlobal, byte onMaskGlobal, BoundedVoxels<UnsignedByteBuffer> voxels1, BoundedVoxels<UnsignedByteBuffer> voxels2, PredicateTwoBytes predicate)	Counts all voxels intersection of two bounded-voxels of type BoundedVoxels but only voxels that lie on an object-mask and match a predicate.
static void	IterateVoxelsIntersectingBounded.withTwoBuffers(Voxels<UnsignedByteBuffer> maskGlobal, byte onMaskGlobal, BoundedVoxels<UnsignedByteBuffer> voxels1, BoundedVoxels<UnsignedByteBuffer> voxels2, ProcessBufferBinary<UnsignedByteBuffer,UnsignedByteBuffer> process)	Iterates over the intersection of two bounded-voxels of type BoundedVoxels but only voxels that lie on an object-mask.
static void	IterateVoxelsIntersectingBounded.withTwoBuffers(Voxels<UnsignedByteBuffer> maskGlobal, byte onMaskGlobal, BoundedVoxels<UnsignedByteBuffer> voxels1, BoundedVoxels<UnsignedByteBuffer> voxels2, ProcessBufferBinary<UnsignedByteBuffer,UnsignedByteBuffer> process)	Iterates over the intersection of two bounded-voxels of type BoundedVoxels but only voxels that lie on an object-mask.
static void	IterateVoxelsIntersectingBounded.withTwoBuffers(Voxels<UnsignedByteBuffer> maskGlobal, byte onMaskGlobal, BoundedVoxels<UnsignedByteBuffer> voxels1, BoundedVoxels<UnsignedByteBuffer> voxels2, ProcessBufferBinary<UnsignedByteBuffer,UnsignedByteBuffer> process)	Iterates over the intersection of two bounded-voxels of type BoundedVoxels but only voxels that lie on an object-mask.
static void	IterateVoxelsIntersectingBounded.withTwoBuffers(Voxels<UnsignedByteBuffer> maskGlobal, byte onMaskGlobal, BoundedVoxels<UnsignedByteBuffer> voxels1, BoundedVoxels<UnsignedByteBuffer> voxels2, ProcessBufferBinary<UnsignedByteBuffer,UnsignedByteBuffer> process)	Iterates over the intersection of two bounded-voxels of type BoundedVoxels but only voxels that lie on an object-mask.

Uses of UnsignedByteBuffer in org.anchoranalysis.image.voxel.iterator.neighbor

Methods in org.anchoranalysis.image.voxel.iterator.neighbor with parameters of type UnsignedByteBuffer

Modifier and Type	Method	Description
default void	ProcessChangedPointAbsoluteMasked.notifyChangeZ(int zChange, int z, UnsignedByteBuffer objectMaskBuffer)	Notifies the processor that there has been a change in z-coordinate.

Uses of UnsignedByteBuffer in org.anchoranalysis.image.voxel.iterator.neighbor.kernel

Methods in org.anchoranalysis.image.voxel.iterator.neighbor.kernel with parameters of type UnsignedByteBuffer

Modifier and Type	Method	Description
boolean	WalkPredicate.walk(UnsignedByteBuffer buffer, BufferRetriever bufferRetriever)	Do any neighboring voxels in any direction satisfy the predicate?
void	WalkRunnable.walk(UnsignedByteBuffer buffer, BufferRetriever bufferRetriever)	Walks in X and Y direction, and Z direction if enabled.

Method parameters in org.anchoranalysis.image.voxel.iterator.neighbor.kernel with type arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
static void	IterateKernelHelper.overAll(Kernel kernel, BinaryVoxels<UnsignedByteBuffer> voxels, KernelApplicationParameters parameters, ProcessKernelPointCursor processor)	Iterates over all voxels.
static void	IterateKernelHelper.overBox(Kernel kernel, BinaryVoxels<UnsignedByteBuffer> voxels, BoundingBox box, KernelApplicationParameters parameters, ProcessKernelPointCursor processor)	Iterates over only voxels contained within a bounding-box.
static boolean	IterateKernelHelper.overBoxUntil(Kernel kernel, BinaryVoxels<UnsignedByteBuffer> voxels, BoundingBox box, KernelApplicationParameters parameters, PredicateKernelPointCursor predicate)	Iterates over only voxels contained within a bounding-box until a predicate is matched on a voxel.
boolean	NeighborPredicate.test(boolean inside, KernelPointCursor point, Supplier<UnsignedByteBuffer> buffer, int zShift)	Tests if a neighbor satisfies a condition.

Uses of UnsignedByteBuffer in org.anchoranalysis.image.voxel.iterator.predicate

Methods in org.anchoranalysis.image.voxel.iterator.predicate that return types with arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
default PredicateBufferBinary<UnsignedByteBuffer>	PredicateTwoBytes.deriveUnsignedBytePredicate()	Derives a predicate with a different interface for operating on UnsignedByteBuffer.
default ProcessBufferBinary<UnsignedByteBuffer,UnsignedByteBuffer>	PredicateTwoBytes.deriveUnsignedByteProcessor()	Derives a processor with a different interface for operating on UnsignedByteBuffer.
default ProcessBufferBinary<UnsignedByteBuffer,UnsignedByteBuffer>	PredicateTwoBytes.deriveUnsignedByteProcessor()	Derives a processor with a different interface for operating on UnsignedByteBuffer.

Uses of UnsignedByteBuffer in org.anchoranalysis.image.voxel.kernel

Methods in org.anchoranalysis.image.voxel.kernel that return types with arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
static BinaryVoxels<UnsignedByteBuffer>	ApplyKernel.apply(BinaryKernel kernel, BinaryVoxels<UnsignedByteBuffer> voxels, KernelApplicationParameters parameters)	Apply the kernel to BinaryVoxels<UnsignedByteBuffer> using the same binary-values as voxels to calculate a value for each voxel.
Optional<UnsignedByteBuffer>	BufferRetriever.getLocal(int relativeZIndex)	Get a buffer at a particular index in the z-dimension.
Optional<UnsignedByteBuffer>	LocalSlices.getLocal(int relativeZIndex)

Methods in org.anchoranalysis.image.voxel.kernel with parameters of type UnsignedByteBuffer

Modifier and Type	Method	Description
boolean	KernelPointCursor.isBufferOff(UnsignedByteBuffer buffer)	Is the value at the current index in this buffer corresponding to an off state?
boolean	KernelPointCursor.isBufferOn(UnsignedByteBuffer buffer)	Is the value at the current index in this buffer corresponding to an on state?

Method parameters in org.anchoranalysis.image.voxel.kernel with type arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
static BinaryVoxels<UnsignedByteBuffer>	ApplyKernel.apply(BinaryKernel kernel, BinaryVoxels<UnsignedByteBuffer> voxels, KernelApplicationParameters parameters)	Apply the kernel to BinaryVoxels<UnsignedByteBuffer> using the same binary-values as voxels to calculate a value for each voxel.
static int	ApplyKernel.applyForCount(BinaryKernel kernel, BinaryVoxels<UnsignedByteBuffer> voxels, KernelApplicationParameters parameters)	Applies a BinaryKernel to voxels and counts how many true values occur en aggregate.
static int	ApplyKernel.applyForCount(CountKernel kernel, BinaryVoxels<UnsignedByteBuffer> voxels, KernelApplicationParameters parameters)	Applies the kernel to voxels and sums the returned value.
static int	ApplyKernel.applyForCount(CountKernel kernel, BinaryVoxels<UnsignedByteBuffer> voxels, BoundingBox box, KernelApplicationParameters parameters)	Applies the kernel to voxels and sums the returned value.
static boolean	ApplyKernel.applyUntilPositive(CountKernel kernel, BinaryVoxels<UnsignedByteBuffer> voxels, BoundingBox box, KernelApplicationParameters parameters)	Applies the kernel to voxels until a positive value is returned, then exits with true.

Constructor parameters in org.anchoranalysis.image.voxel.kernel with type arguments of type UnsignedByteBuffer

Modifier	Constructor	Description
	LocalSlices(int z, int windowSize, Voxels<UnsignedByteBuffer> voxels)	Create with focus around a particular slice.

Uses of UnsignedByteBuffer in org.anchoranalysis.image.voxel.kernel.morphological

Methods in org.anchoranalysis.image.voxel.kernel.morphological with parameters of type UnsignedByteBuffer

Modifier and Type	Method	Description
protected abstract boolean	BinaryKernelMorphological.firstCheck(KernelPointCursor point, UnsignedByteBuffer buffer)	The first check done on the kernel center-point, before checking any neighbors.
protected boolean	DilationKernel.firstCheck(KernelPointCursor point, UnsignedByteBuffer buffer)
protected boolean	ErosionKernel.firstCheck(KernelPointCursor point, UnsignedByteBuffer buffer)

Method parameters in org.anchoranalysis.image.voxel.kernel.morphological with type arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
protected abstract boolean	BinaryKernelMorphological.doesNeighborQualify(boolean inside, KernelPointCursor point, Supplier<UnsignedByteBuffer> buffer, int zShift)	Does a particular neighboring-point satisfy the conditions.
protected boolean	DilationKernel.doesNeighborQualify(boolean inside, KernelPointCursor point, Supplier<UnsignedByteBuffer> buffer, int zShift)
protected boolean	ErosionKernel.doesNeighborQualify(boolean inside, KernelPointCursor point, Supplier<UnsignedByteBuffer> buffer, int zShift)	Checks whether a particular neighbor voxel qualifies to make the current voxel an outline voxel.

Uses of UnsignedByteBuffer in org.anchoranalysis.image.voxel.kernel.outline

Methods in org.anchoranalysis.image.voxel.kernel.outline with parameters of type UnsignedByteBuffer

Modifier and Type	Method	Description
protected boolean	OutlineKernelBase.firstCheck(KernelPointCursor point, UnsignedByteBuffer buffer)

Method parameters in org.anchoranalysis.image.voxel.kernel.outline with type arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
protected boolean	OutlineKernel.doesNeighborQualify(boolean inside, KernelPointCursor point, Supplier<UnsignedByteBuffer> buffer, int zShift)	Checks whether a particular neighbor voxel qualifies to make the current voxel an outline voxel.
protected boolean	OutlineKernelNeighborMatchValue.doesNeighborQualify(boolean inside, KernelPointCursor point, Supplier<UnsignedByteBuffer> buffer, int zShift)	Checks whether a particular neighbor voxel qualifies to make the current voxel an outline voxel.

Constructor parameters in org.anchoranalysis.image.voxel.kernel.outline with type arguments of type UnsignedByteBuffer

Modifier	Constructor	Description
	OutlineKernelNeighborMatchValue(BinaryVoxels<UnsignedByteBuffer> mask)	Creates for an object.

Uses of UnsignedByteBuffer in org.anchoranalysis.image.voxel.object

Methods in org.anchoranalysis.image.voxel.object that return UnsignedByteBuffer

Modifier and Type	Method	Description
UnsignedByteBuffer	ObjectMask.sliceBufferGlobal(int sliceIndexGlobal)	A slice buffer with global coordinates.
UnsignedByteBuffer	ObjectMask.sliceBufferLocal(int sliceIndexRelative)	A slice buffer with local coordinates.

Methods in org.anchoranalysis.image.voxel.object that return types with arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
BinaryVoxels<UnsignedByteBuffer>	ObjectMask.binaryVoxels()	The underlying voxel memory buffers for the object-mask, exposed via a BinaryVoxels.
BoundedVoxels<UnsignedByteBuffer>	ObjectMask.boundedVoxels()	The underlying voxel memory buffers for the object-mask, exposed via BoundedVoxels.
VoxelsExtracter<UnsignedByteBuffer>	ObjectMask.extract()	Provides methods to read/copy/duplicate regions of voxels.
Voxels<UnsignedByteBuffer>	ObjectMask.voxels()	The underlying voxel memory buffers for the object-mask, exposed via Voxels.

Method parameters in org.anchoranalysis.image.voxel.object with type arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
ObjectMask	ObjectMask.replaceVoxels(Voxels<UnsignedByteBuffer> voxelsToAssign)	Replaces the voxels in the object-mask.

Constructor parameters in org.anchoranalysis.image.voxel.object with type arguments of type UnsignedByteBuffer

Modifier	Constructor	Description
	ObjectMask(BinaryVoxels<UnsignedByteBuffer> voxels)	Creates from a BinaryVoxels to be located at the origin.
	ObjectMask(BoundedVoxels<UnsignedByteBuffer> voxels)	Creates from a BoundedVoxels with UnsignedByteBuffer.
	ObjectMask(BoundedVoxels<UnsignedByteBuffer> voxels, BinaryValuesInt binaryValues)	Creates from BoundedVoxels and corresponding BinaryValuesInt.
	ObjectMask(Voxels<UnsignedByteBuffer> voxels)	Creates from a Voxels mask that is cornered at the origin.
	ObjectMask(BoundingBox box, BinaryVoxels<UnsignedByteBuffer> voxels)	Creates from a BinaryVoxels and a corresponding bounding-box.
	ObjectMask(BoundingBox box, Voxels<UnsignedByteBuffer> voxels)	Creates from Voxels and a BoundingBox with default BinaryValuesInt.
	ObjectMask(BoundingBox box, Voxels<UnsignedByteBuffer> voxels, BinaryValuesByte binaryValues)	Like ObjectMask(BoundingBox, Voxels, BinaryValuesInt) but specifies the binary-values as bytes.
	ObjectMask(BoundingBox box, Voxels<UnsignedByteBuffer> voxels, BinaryValuesInt binaryValues)	Creates from Voxels and a corresponding BoundingBox and BinaryValuesInt.

Uses of UnsignedByteBuffer in org.anchoranalysis.image.voxel.object.morphological

Methods in org.anchoranalysis.image.voxel.object.morphological that return types with arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
static BinaryVoxels<UnsignedByteBuffer>	MorphologicalDilation.dilate(BinaryVoxels<UnsignedByteBuffer> voxels, int iterations, DilationContext context)	Performs a morphological dilation operation.
static BinaryVoxels<UnsignedByteBuffer>	MorphologicalErosion.erode(BinaryVoxels<UnsignedByteBuffer> voxels, int iterations, boolean useZ, Optional<Predicate<Point3i>> precondition)	Performs a morphological erosion on a BinaryVoxels<UnsignedByteBuffer> voxels.

Method parameters in org.anchoranalysis.image.voxel.object.morphological with type arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
static BinaryVoxels<UnsignedByteBuffer>	MorphologicalDilation.dilate(BinaryVoxels<UnsignedByteBuffer> voxels, int iterations, DilationContext context)	Performs a morphological dilation operation.
static BinaryVoxels<UnsignedByteBuffer>	MorphologicalErosion.erode(BinaryVoxels<UnsignedByteBuffer> voxels, int iterations, boolean useZ, Optional<Predicate<Point3i>> precondition)	Performs a morphological erosion on a BinaryVoxels<UnsignedByteBuffer> voxels.

Uses of UnsignedByteBuffer in org.anchoranalysis.image.voxel.object.morphological.predicate

Method parameters in org.anchoranalysis.image.voxel.object.morphological.predicate with type arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
boolean	AcceptIterationList.accept(BinaryVoxels<UnsignedByteBuffer> voxels)
boolean	AcceptIterationPredicate.accept(BinaryVoxels<UnsignedByteBuffer> voxels)	Whether a particular voxels fulfills the condition or not.

Uses of UnsignedByteBuffer in org.anchoranalysis.image.voxel.projection

Methods in org.anchoranalysis.image.voxel.projection that return types with arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
ProjectableBuffer<UnsignedByteBuffer>	MeanIntensityProjection.createUnsignedByte(Extent extent)
abstract ProjectableBuffer<UnsignedByteBuffer>	Projection.createUnsignedByte(Extent extent)	Creates a buffer for a maximum-intensity projection for unsigned byte voxels.
ProjectableBuffer<UnsignedByteBuffer>	StandardDeviationIntensityProjection.createUnsignedByte(Extent extent)

Uses of UnsignedByteBuffer in org.anchoranalysis.image.voxel.projection.extrema

Methods in org.anchoranalysis.image.voxel.projection.extrema that return types with arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
ProjectableBuffer<UnsignedByteBuffer>	ComparisonProjection.createUnsignedByte(Extent extent)

Uses of UnsignedByteBuffer in org.anchoranalysis.image.voxel.resizer

Methods in org.anchoranalysis.image.voxel.resizer that return types with arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
protected abstract VoxelBuffer<UnsignedByteBuffer>	VoxelsResizer.resizeByte(VoxelBuffer<UnsignedByteBuffer> voxelsSource, VoxelBuffer<UnsignedByteBuffer> voxelsDestination, Extent extentSource, Extent extentDestination)	Interpolates from voxelsSource to voxelsDestination for unsigned 8-bit buffers.
protected VoxelBuffer<UnsignedByteBuffer>	VoxelsResizerExecutionTime.resizeByte(VoxelBuffer<UnsignedByteBuffer> voxelsSource, VoxelBuffer<UnsignedByteBuffer> voxelsDestination, Extent extentSource, Extent extentDestination)
VoxelBuffer<UnsignedByteBuffer>	VoxelsResizerImgLib2.resizeByte(VoxelBuffer<UnsignedByteBuffer> voxelsSource, VoxelBuffer<UnsignedByteBuffer> voxelsDestination, Extent extentSource, Extent extentDestination)
VoxelBuffer<UnsignedByteBuffer>	VoxelsResizerNone.resizeByte(VoxelBuffer<UnsignedByteBuffer> voxelsSource, VoxelBuffer<UnsignedByteBuffer> voxelsDestination, Extent extentSource, Extent extentDestination)

Method parameters in org.anchoranalysis.image.voxel.resizer with type arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
protected abstract VoxelBuffer<UnsignedByteBuffer>	VoxelsResizer.resizeByte(VoxelBuffer<UnsignedByteBuffer> voxelsSource, VoxelBuffer<UnsignedByteBuffer> voxelsDestination, Extent extentSource, Extent extentDestination)	Interpolates from voxelsSource to voxelsDestination for unsigned 8-bit buffers.
protected VoxelBuffer<UnsignedByteBuffer>	VoxelsResizerExecutionTime.resizeByte(VoxelBuffer<UnsignedByteBuffer> voxelsSource, VoxelBuffer<UnsignedByteBuffer> voxelsDestination, Extent extentSource, Extent extentDestination)
VoxelBuffer<UnsignedByteBuffer>	VoxelsResizerImgLib2.resizeByte(VoxelBuffer<UnsignedByteBuffer> voxelsSource, VoxelBuffer<UnsignedByteBuffer> voxelsDestination, Extent extentSource, Extent extentDestination)
VoxelBuffer<UnsignedByteBuffer>	VoxelsResizerNone.resizeByte(VoxelBuffer<UnsignedByteBuffer> voxelsSource, VoxelBuffer<UnsignedByteBuffer> voxelsDestination, Extent extentSource, Extent extentDestination)

Uses of UnsignedByteBuffer in org.anchoranalysis.image.voxel.thresholder

Methods in org.anchoranalysis.image.voxel.thresholder that return types with arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
static BinaryVoxels<UnsignedByteBuffer>	VoxelsThresholder.threshold(VoxelsUntyped voxels, float level, BinaryValuesByte binaryValues, Optional<ObjectMask> objectMask, boolean alwaysDuplicate)	Applies thresholding to VoxelsUntyped.
static BinaryVoxels<UnsignedByteBuffer>	VoxelsThresholder.thresholdFloat(Voxels<FloatBuffer> voxels, float level, BinaryValuesByte binaryValues)	Applies thresholding to Voxels of float data type.

Method parameters in org.anchoranalysis.image.voxel.thresholder with type arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
static void	VoxelsThresholder.thresholdByte(Voxels<UnsignedByteBuffer> voxels, int level, BinaryValuesByte binaryValues)	Applies thresholding to Voxels of unsigned byte data type.

Uses of UnsignedByteBuffer in org.anchoranalysis.io.bioformats.copyconvert.tobyte

Methods in org.anchoranalysis.io.bioformats.copyconvert.tobyte that return UnsignedByteBuffer

Modifier and Type	Method	Description
protected UnsignedByteBuffer	UnsignedByteFromUnsignedByte.convert(ByteBuffer source, int channelIndexRelative, OrientationChange orientationCorrection, boolean littleEndian)

Methods in org.anchoranalysis.io.bioformats.copyconvert.tobyte with parameters of type UnsignedByteBuffer

Modifier and Type	Method	Description
protected void	ToUnsignedByteWithScaling.copyChangeOrientation(ByteBuffer source, boolean littleEndian, int channelIndexRelative, UnsignedByteBuffer destination, OrientationChange orientationCorrection)
protected void	UnsignedByteFromFloat.copyChangeOrientation(ByteBuffer source, boolean littleEndian, int channelIndexRelative, UnsignedByteBuffer destination, OrientationChange orientationCorrection)
protected void	UnsignedByteFromUnsignedByteInterleaving.copyChangeOrientation(ByteBuffer source, boolean littleEndian, int channelIndexRelative, UnsignedByteBuffer destination, OrientationChange orientationCorrection)
protected void	UnsignedByteFromUnsignedByteNoInterleaving.copyChangeOrientation(ByteBuffer source, boolean littleEndian, int channelIndexRelative, UnsignedByteBuffer destination, OrientationChange orientationCorrection)
protected void	ToUnsignedByteWithScaling.copyKeepOrientation(ByteBuffer source, boolean littleEndian, int channelIndexRelative, UnsignedByteBuffer destination)
protected void	UnsignedByteFromFloat.copyKeepOrientation(ByteBuffer source, boolean littleEndian, int channelIndexRelative, UnsignedByteBuffer destination)
protected void	UnsignedByteFromUnsignedByteInterleaving.copyKeepOrientation(ByteBuffer source, boolean littleEndian, int channelIndexRelative, UnsignedByteBuffer destination)
protected void	UnsignedByteFromUnsignedByteNoInterleaving.copyKeepOrientation(ByteBuffer source, boolean littleEndian, int channelIndexRelative, UnsignedByteBuffer destination)

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

Methods in org.anchoranalysis.io.imagej.convert that return types with arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
static VoxelBuffer<UnsignedByteBuffer>	ConvertToVoxelBuffer.asByte(ij.process.ImageProcessor processor)	Convert a ImageProcessor to VoxelBuffer<UnsignedByteBuffer>

Method parameters in org.anchoranalysis.io.imagej.convert with type arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
static ij.process.ImageProcessor	ConvertToImageProcessor.fromByte(SliceBufferIndex<UnsignedByteBuffer> pixelsForSlice, int z)	Creates a ImageProcessor by extracting a slice from a SliceBufferIndex of type UnsignedByteBuffer.
static ij.process.ImageProcessor	ConvertToImageProcessor.fromByte(VoxelBuffer<UnsignedByteBuffer> slice, Extent extent)	Creates a ImageProcessor from voxel-buffer (of type ByteBuffer) that is already a slice.
static ij.ImagePlus	ConvertToImagePlus.fromSlice(Voxels<UnsignedByteBuffer> voxels, int sliceIndex, String name)	Creates an ImagePlus from one slice of a Voxels<UnsignedByteBuffer> voxels.

Uses of UnsignedByteBuffer in org.anchoranalysis.io.imagej.resizer

Methods in org.anchoranalysis.io.imagej.resizer that return types with arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
VoxelBuffer<UnsignedByteBuffer>	VoxelsResizerImageJ.resizeByte(VoxelBuffer<UnsignedByteBuffer> voxelsSource, VoxelBuffer<UnsignedByteBuffer> voxelsDestination, Extent extentSource, Extent extentDestination)

Method parameters in org.anchoranalysis.io.imagej.resizer with type arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
VoxelBuffer<UnsignedByteBuffer>	VoxelsResizerImageJ.resizeByte(VoxelBuffer<UnsignedByteBuffer> voxelsSource, VoxelBuffer<UnsignedByteBuffer> voxelsDestination, Extent extentSource, Extent extentDestination)

Uses of UnsignedByteBuffer in org.anchoranalysis.mpp.mark.voxelized

Methods in org.anchoranalysis.mpp.mark.voxelized that return types with arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
BoundedVoxels<UnsignedByteBuffer>	VoxelizedMark.voxels()	Gets the voxel representation of the mark.
BoundedVoxels<UnsignedByteBuffer>	VoxelizedMark.voxelsMaximumIntensityProjection()	Gets the maximum intensity projection of the voxelized mark.

Uses of UnsignedByteBuffer in org.anchoranalysis.mpp.overlap

Method parameters in org.anchoranalysis.mpp.overlap with type arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
int	CountIntersectingVoxels.count(BoundedVoxels<UnsignedByteBuffer> voxels1, BoundedVoxels<UnsignedByteBuffer> voxels2)	Counts the number of intersecting voxels between two bounded voxel sets.
int	CountIntersectingVoxels.countMasked(BoundedVoxels<UnsignedByteBuffer> voxels1, BoundedVoxels<UnsignedByteBuffer> voxels2, Voxels<UnsignedByteBuffer> maskGlobal, byte onMaskGlobal)	Counts the number of intersecting voxels between two bounded voxel sets, considering a global mask.
int	CountIntersectingVoxels.countMasked(BoundedVoxels<UnsignedByteBuffer> voxels1, BoundedVoxels<UnsignedByteBuffer> voxels2, Voxels<UnsignedByteBuffer> maskGlobal, byte onMaskGlobal)	Counts the number of intersecting voxels between two bounded voxel sets, considering a global mask.
static double	OverlapUtilities.overlapWithMaskGlobal(VoxelizedMarkMemo memo1, VoxelizedMarkMemo memo2, int regionID, Voxels<UnsignedByteBuffer> globalMask, byte onGlobalMask)	Counts the number of overlapping voxels between two VoxelizedMarkMemo objects, considering a global mask.

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

Methods in org.anchoranalysis.plugin.fiji.bean.channel.provider.distance that return types with arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
Voxels<UnsignedByteBuffer>	DistanceTransform3D.createDistanceMapForVoxels(BinaryVoxels<UnsignedByteBuffer> voxels, Optional<Resolution> resolution, float multiplyByZRes)	Creates a distance map for binary voxels.

Method parameters in org.anchoranalysis.plugin.fiji.bean.channel.provider.distance with type arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
Voxels<UnsignedByteBuffer>	DistanceTransform3D.createDistanceMapForVoxels(BinaryVoxels<UnsignedByteBuffer> voxels, Optional<Resolution> resolution, float multiplyByZRes)	Creates a distance map for binary voxels.

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

Methods in org.anchoranalysis.plugin.fiji.bean.threshold that return types with arguments of type UnsignedByteBuffer

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

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

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

Modifier and Type	Method	Description
ChannelConverter<UnsignedByteBuffer>	ScaleByDictionary.createConverter()
ChannelConverter<UnsignedByteBuffer>	ScaleByMinMaxValue.createConverter()
ChannelConverter<UnsignedByteBuffer>	ScaleByTypeToByte.createConverter()
ChannelConverter<UnsignedByteBuffer>	ToByte.createConverter()
ChannelConverterAttached<Histogram,UnsignedByteBuffer>	ToByteUpperLowerQuantileIntensity.createConverter()

Uses of UnsignedByteBuffer in org.anchoranalysis.plugin.image.bean.segment.binary

Methods in org.anchoranalysis.plugin.image.bean.segment.binary that return types with arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
BinaryVoxels<UnsignedByteBuffer>	Sequence.segment(VoxelsUntyped voxels, BinarySegmentationParameters parameters, Optional<ObjectMask> objectMask)
BinaryVoxels<UnsignedByteBuffer>	ThresholdAgainstChannel.segment(VoxelsUntyped voxels, BinarySegmentationParameters parameters, Optional<ObjectMask> object)
BinaryVoxels<UnsignedByteBuffer>	Invert.segmentFromExistingSegmentation(VoxelsUntyped voxels, BinarySegmentationParameters parameters, Optional<ObjectMask> objectMask, BinarySegmentation segment)
BinaryVoxels<UnsignedByteBuffer>	Repeat.segmentFromExistingSegmentation(VoxelsUntyped voxels, BinarySegmentationParameters parameters, Optional<ObjectMask> objectMask, BinarySegmentation segment)

Uses of UnsignedByteBuffer in org.anchoranalysis.plugin.image.segment.thresholder.slice

Methods in org.anchoranalysis.plugin.image.segment.thresholder.slice with parameters of type UnsignedByteBuffer

Modifier and Type	Method	Description
protected final void	SliceThresholder.writeOffByte(int offset, UnsignedByteBuffer bufferOut)	Writes the 'off' binary value to the output buffer at the specified offset.
protected final void	SliceThresholder.writeThresholdedByte(int offset, UnsignedByteBuffer bufferOut, VoxelBuffer<?> bufferIn, VoxelBuffer<?> bufferThreshold)	Writes a thresholded value to the output buffer based on the input and threshold buffers.

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

Methods in org.anchoranalysis.plugin.imagej.bean.threshold that return types with arguments of type UnsignedByteBuffer

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

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

Method parameters in org.anchoranalysis.plugin.imagej.channel.provider with type arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
static void	FilterHelper.processEachSlice(BinaryVoxels<UnsignedByteBuffer> voxels, Consumer<ij.process.ImageProcessor> consumer)	Applies a Consumer to each slice independently of a BinaryVoxels with UnsignedByteBuffer.

Uses of UnsignedByteBuffer in org.anchoranalysis.plugin.imagej.mask

Methods in org.anchoranalysis.plugin.imagej.mask that return types with arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
static BinaryVoxels<UnsignedByteBuffer>	ApplyImageJMorphologicalOperation.applyOperation(BinaryVoxels<UnsignedByteBuffer> voxels, String command, int iterations)	Applies a specified morphological operation to the given binary voxels.

Method parameters in org.anchoranalysis.plugin.imagej.mask with type arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
static BinaryVoxels<UnsignedByteBuffer>	ApplyImageJMorphologicalOperation.applyOperation(BinaryVoxels<UnsignedByteBuffer> voxels, String command, int iterations)	Applies a specified morphological operation to the given binary voxels.
static void	ApplyImageJMorphologicalOperation.fill(BinaryVoxels<UnsignedByteBuffer> voxels)	Applies the fill operation to the given binary voxels.

Uses of UnsignedByteBuffer in org.anchoranalysis.plugin.opencv.convert

Methods in org.anchoranalysis.plugin.opencv.convert that return types with arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
static VoxelBuffer<UnsignedByteBuffer>	VoxelBufferFromMat.unsignedByteFromMat(org.opencv.core.Mat mat, Extent extent)	Converts a Mat to a VoxelBuffer with voxel data-type UnsignedByteBuffer.

Method parameters in org.anchoranalysis.plugin.opencv.convert with type arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
static org.opencv.core.Mat	ConvertToMat.fromVoxelBufferByte(VoxelBuffer<UnsignedByteBuffer> voxelBuffer, Extent extent)	Converts a VoxelBuffer of type UnsignedByteBuffer to a Mat.
static org.opencv.core.Mat	ConvertToMat.fromVoxelsByte(Voxels<UnsignedByteBuffer> voxels)	Converts a Voxels of type UnsignedByteBuffer to a Mat.

Uses of UnsignedByteBuffer in org.anchoranalysis.plugin.opencv.resizer

Methods in org.anchoranalysis.plugin.opencv.resizer that return types with arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
protected VoxelBuffer<UnsignedByteBuffer>	VoxelsResizerOpenCV.resizeByte(VoxelBuffer<UnsignedByteBuffer> voxelsSource, VoxelBuffer<UnsignedByteBuffer> voxelsDestination, Extent extentSource, Extent extentDestination)

Method parameters in org.anchoranalysis.plugin.opencv.resizer with type arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
protected VoxelBuffer<UnsignedByteBuffer>	VoxelsResizerOpenCV.resizeByte(VoxelBuffer<UnsignedByteBuffer> voxelsSource, VoxelBuffer<UnsignedByteBuffer> voxelsDestination, Extent extentSource, Extent extentDestination)

Uses of UnsignedByteBuffer in org.anchoranalysis.test.image

Method parameters in org.anchoranalysis.test.image with type arguments of type UnsignedByteBuffer

Modifier and Type	Method	Description
void	WriteIntoDirectory.writeVoxels(String outputName, Voxels<UnsignedByteBuffer> voxels)	Writes Voxels to the output directory.