Uses of Class
org.anchoranalysis.image.voxel.Voxels

Packages that use Voxels

Package	Description
org.anchoranalysis.image.core.bufferedimage	Conversions and operations involving Java AWT's BufferedImage.
org.anchoranalysis.image.core.channel	The Channel core data-class and related operations and converters.
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.mask.combine	Binary operations involving voxelwise combination of Mask.
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.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.assigner	Assigns values to some or all voxels.
org.anchoranalysis.image.voxel.binary	The BinaryVoxels class and related operations.
org.anchoranalysis.image.voxel.buffer	A buffer of voxel-values, usually corresponding to a single z-slice in Voxels.
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.extracter.predicate	Methods to find or count voxels that satisfy a predicate.
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.kernel	Applying a kernel via convolution to voxels.
org.anchoranalysis.image.voxel.object	The fundamental data class that is an ObjectMask and related structures.
org.anchoranalysis.image.voxel.projection	Classes for calculating differnet kind of projections of voxel values across multiple buffers.
org.anchoranalysis.image.voxel.thresholder	Thresholding operations on voxels.
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.mpp.overlap	Calculating overlaps between two Marks.
org.anchoranalysis.plugin.fiji.bean.channel.provider.distance	Euclidean Distance Transform implementations via FIJI.
org.anchoranalysis.plugin.image.segment.thresholder.slice	Non-beans pertaining to segmenting a z-stack slice-by-slice.
org.anchoranalysis.plugin.image.segment.watershed.encoding	Encoding voxels in a watershed-transformation implementation.
org.anchoranalysis.plugin.opencv.convert	Conversion to/from OpenCV data-structures.
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 Voxels in org.anchoranalysis.image.core.bufferedimage

Methods in org.anchoranalysis.image.core.bufferedimage with parameters of type Voxels

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 Voxels in org.anchoranalysis.image.core.channel

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

Modifier and Type	Method	Description
void	Channel.replaceVoxels(Voxels<?> voxelsToAssign)	Assigns new voxels to replace the existing voxels.

Constructors in org.anchoranalysis.image.core.channel with parameters of type Voxels

Modifier	Constructor	Description
	Channel(Voxels<?> voxels, Optional<Resolution> resolution)	Creates for particular voxels and resolution.

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

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

Modifier and Type	Method	Description
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.

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

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

Modifier and Type	Method	Description
Voxels<UnsignedByteBuffer>	Mask.voxels()	The underlying voxels in the mask.

Methods in org.anchoranalysis.image.core.mask with parameters of type Voxels

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
static <T> void	IterateVoxelsMask.withBuffer(Mask mask, Voxels<T> voxels, ProcessBufferUnary<T> process)	Iterate over each voxel in a mask - with an associated buffer for each slice from a voxel-bo

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

Methods in org.anchoranalysis.image.core.mask.combine with parameters of type Voxels

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.

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

Constructors in org.anchoranalysis.image.core.object.label with parameters of type Voxels

Modifier	Constructor	Description
	DecodeLabels(Voxels<?> voxels, int minLabelInclusive, int maxLabelInclusive, DecodeLabels.CreateElementFromScaledObject<T> createScaledElement)	Creates a new DecodeLabels instance.

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

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

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

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

Methods in org.anchoranalysis.image.inference.segment with parameters of type Voxels

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 Voxels in org.anchoranalysis.image.voxel

Subclasses of Voxels in org.anchoranalysis.image.voxel

Modifier and Type	Class	Description
final class	VoxelsFloat	Implementation of Voxels whose voxels are of type float.
final class	VoxelsUnsignedByte	Implementation of Voxels whose voxels are of type unsigned byte (8-bit).
final class	VoxelsUnsignedInt	Implementation of Voxels whose voxels are of type unsigned int (32-bit).
final class	VoxelsUnsignedShort	Implementation of Voxels whose voxels are of type unsigned short (16-bit).

Methods in org.anchoranalysis.image.voxel that return Voxels

Modifier and Type	Method	Description
Voxels<?>	VoxelsUntyped.any()	Exposes without any specific buffer type.
Voxels<UnsignedByteBuffer>	VoxelsUntyped.asByte()	Casts to use a UnsignedByteBuffer if the voxels contain this data-type, otherwise throws a IncorrectVoxelTypeException.
Voxels<FloatBuffer>	VoxelsUntyped.asFloat()	Casts to use a FloatBuffer if the voxels contain this data-type, otherwise throws a IncorrectVoxelTypeException.
Voxels<UnsignedIntBuffer>	VoxelsUntyped.asInt()	Casts to use a UnsignedIntBuffer if the voxels contain this data-type, otherwise throws a IncorrectVoxelTypeException.
Voxels<UnsignedShortBuffer>	VoxelsUntyped.asShort()	Casts to use a UnsignedShortBuffer if the voxels contain this data-type, otherwise throws a IncorrectVoxelTypeException.
Voxels<?>	VoxelsUntyped.checkIdenticalDataType(VoxelDataType match)	Do the voxels have a data-type that is equal to match?
Voxels<T>	Voxels.duplicate()	A deep-copy.
Voxels<T>	BoundedVoxels.voxels()	Voxel-data that fits inside the bounding-box (its extent is invariant with the extent of the bounding-box).

Methods in org.anchoranalysis.image.voxel with parameters of type Voxels

Modifier and Type	Method	Description
boolean	Voxels.equalsDeep(Voxels<?> other)	Are the voxels identical to another voxels (deep equals)?
BoundedVoxels<T>	BoundedVoxels.replaceVoxels(Voxels<T> voxelsToAssign)	Replaces the voxels in the box.

Constructors in org.anchoranalysis.image.voxel with parameters of type Voxels

Modifier	Constructor	Description
	BoundedVoxels(Voxels<T> voxels)	Creates voxels bounded to match the entire voxel-data at the origin.
	BoundedVoxels(BoundingBox boundingBox, Voxels<T> voxels)	Creates voxels with a corresponding bounding box.
	VoxelsUntyped(Voxels<?> voxels)	Creates to wrap a Voxels of unspecified type.

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

Methods in org.anchoranalysis.image.voxel.assigner with parameters of type Voxels

Modifier and Type	Method	Description
static VoxelsAssigner	VoxelsAssignerFactory.createFloat(Voxels<FloatBuffer> voxels, int valueToAssign)	Create a VoxelsAssigner for a FloatBuffer.
static VoxelsAssigner	VoxelsAssignerFactory.createUnsignedByte(Voxels<UnsignedByteBuffer> voxels, int valueToAssign)	Create a VoxelsAssigner for a UnsignedByteBuffer.
static VoxelsAssigner	VoxelsAssignerFactory.createUnsignedInt(Voxels<UnsignedIntBuffer> voxels, int valueToAssign)	Create a a VoxelsAssigner for a UnsignedIntBuffer.
static VoxelsAssigner	VoxelsAssignerFactory.createUnsignedShort(Voxels<UnsignedShortBuffer> voxels, int valueToAssign)	Create a VoxelsAssigner for a UnsignedShortBuffer.

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

Methods in org.anchoranalysis.image.voxel.binary that return Voxels

Modifier and Type	Method	Description
Voxels<T>	BinaryVoxels.voxels()	Voxels that should only have two intensity-values (representing on and off states).

Methods in org.anchoranalysis.image.voxel.binary with parameters of type Voxels

Modifier and Type	Method	Description
protected abstract BinaryVoxels<T>	BinaryVoxels.binaryVoxelsFor(Voxels<T> voxels, BinaryValuesInt binaryValues)	Creates a BinaryVoxels corresponding to a particular voxels and BinaryValuesInt.
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.
static BinaryVoxels<UnsignedIntBuffer>	BinaryVoxelsFactory.reuseInt(Voxels<UnsignedIntBuffer> voxels, BinaryValuesInt binaryValues)	Reuses an existing voxel-buffer (of type unsigned int) as a binary-version which should have only two intensity-values representing off and on.

Constructors in org.anchoranalysis.image.voxel.binary with parameters of type Voxels

Modifier	Constructor	Description
	BinaryVoxels(Voxels<T> voxels, BinaryValuesInt binaryValues)	Creates a new BinaryVoxels instance.

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

Methods in org.anchoranalysis.image.voxel.buffer that return Voxels

Modifier and Type	Method	Description
Voxels<T>	ProjectableBuffer.completeProjection()	Performs any final operation before turning the projected buffer.
Voxels<T>	SlidingBuffer.getVoxels()	The voxels from which buffers corresponding to slices are extracted.

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

Modifier and Type	Method	Description
void	ProjectableBuffer.addVoxels(Voxels<T> voxels)	Adds a Voxels to the projection, as a single entity.

Constructors in org.anchoranalysis.image.voxel.buffer with parameters of type Voxels

Modifier	Constructor	Description
	SlidingBuffer(Voxels<T> voxels)	Create for particular voxels.

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

Methods in org.anchoranalysis.image.voxel.convert that return Voxels

Modifier and Type	Method	Description
<S, T> Voxels<S>	VoxelsConverterMulti.convert(VoxelsUntyped voxels, VoxelsFactoryTypeBound<T> outputVoxelsFactory)	Converts a Voxels to another type.
Voxels<T>	VoxelsConverter.convertFrom(VoxelsUntyped from, VoxelsFactoryTypeBound<T> factory)	Creates a new voxels of type T and copies the voxels from from.

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

Modifier and Type	Method	Description
void	VoxelsConverter.copyFrom(VoxelsUntyped from, Voxels<T> to)	Copies voxels from a source (of any type) to voxels of type T.
void	VoxelsConverter.copyFromFloat(Voxels<FloatBuffer> from, Voxels<T> to)	Copies voxels from a source of type @{link FloatBuffer} to voxels of type T.
void	VoxelsConverter.copyFromUnsignedByte(Voxels<UnsignedByteBuffer> from, Voxels<T> to)	Copies voxels from a source of type @{link UnsignedByteBuffer} to voxels of type T.
void	VoxelsConverter.copyFromUnsignedInt(Voxels<UnsignedIntBuffer> from, Voxels<T> to)	Copies voxels from a source of type @{link UnsignedIntBuffer} to voxels of type T.
void	VoxelsConverter.copyFromUnsignedShort(Voxels<UnsignedShortBuffer> from, Voxels<T> to)	Copies voxels from a source of type @{link UnsignedShortBuffer} to voxels of type T.

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

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

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

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

Methods in org.anchoranalysis.image.voxel.convert.imglib2 with parameters of type Voxels

Modifier and Type	Method	Description
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.
static net.imglib2.img.Img<net.imglib2.type.numeric.real.FloatType>	ConvertToImg.fromFloat(Voxels<FloatBuffer> voxels)	Creates an Img from Voxels with a float data-type.
static net.imglib2.img.NativeImg<net.imglib2.type.numeric.real.FloatType,net.imglib2.img.basictypeaccess.array.FloatArray>	ConvertToNativeImg.fromFloat(Voxels<FloatBuffer> voxels)	Creates an NativeImg from Voxels with a float data-type.
static net.imglib2.img.Img<net.imglib2.type.numeric.integer.UnsignedShortType>	ConvertToImg.fromShort(Voxels<UnsignedShortBuffer> voxels)	Creates an Img from Voxels with an unsigned short data-type.
static net.imglib2.img.NativeImg<net.imglib2.type.numeric.integer.UnsignedShortType,net.imglib2.img.basictypeaccess.array.ShortArray>	ConvertToNativeImg.fromShort(Voxels<UnsignedShortBuffer> voxels)	Creates an NativeImg from Voxels with an unsigned short data-type.

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

Methods in org.anchoranalysis.image.voxel.extracter that return Voxels

Modifier and Type	Method	Description
Voxels<T>	VoxelsExtracter.projectMax()	A maximum intensity projection of all slices
Voxels<T>	VoxelsExtracter.projectMean()	A mean intensity projection of all slices.
Voxels<T>	VoxelsExtracter.region(BoundingBox box, boolean reuseIfPossible)	A (sub-)region of the voxels.
Voxels<T>	VoxelsExtracter.resizedXY(int sizeX, int sizeY, VoxelsResizer resizer)	Creates a new voxels that are a resized version of the current voxels (only in X and Y dimensions), interpolating as needed.
Voxels<T>	VoxelsExtracter.slice(int sliceIndex)	Creates a new Voxels with only particular slice.

Methods in org.anchoranalysis.image.voxel.extracter with parameters of type Voxels

Modifier and Type	Method	Description
void	VoxelsExtracter.boxCopyTo(BoundingBox from, Voxels<T> voxelsDestination, BoundingBox destinationBox)	Copies a bounding-box area to another Voxels.
static VoxelsExtracter<FloatBuffer>	VoxelsExtracterFactory.createFloat(Voxels<FloatBuffer> voxels)	Create voxels-extracter for FloatBuffer.
static VoxelsExtracter<UnsignedByteBuffer>	VoxelsExtracterFactory.createUnsignedByte(Voxels<UnsignedByteBuffer> voxels)	Create voxels-extracter for UnsignedByteBuffer.
static VoxelsExtracter<UnsignedIntBuffer>	VoxelsExtracterFactory.createUnsignedInt(Voxels<UnsignedIntBuffer> voxels)	Create voxels-extracter for UnsignedIntBuffer.
static VoxelsExtracter<UnsignedShortBuffer>	VoxelsExtracterFactory.createUnsignedShort(Voxels<UnsignedShortBuffer> voxels)	Create voxels-extracter for UnsignedShortBuffer.
void	VoxelsExtracter.objectCopyTo(ObjectMask from, Voxels<T> voxelsDestination, BoundingBox destinationBox)	Copies an area corresponding to an object-mask to another Voxels.

Uses of Voxels in org.anchoranalysis.image.voxel.extracter.predicate

Constructors in org.anchoranalysis.image.voxel.extracter.predicate with parameters of type Voxels

Modifier	Constructor	Description
	PredicateImplementation(Voxels<T> voxels, Predicate<T> predicate)	Creates a new PredicateImplementation instance.

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

Methods in org.anchoranalysis.image.voxel.factory that return Voxels

Modifier and Type	Method	Description
Voxels<T>	VoxelsFactoryTypeBound.create(SliceBufferIndex<T> voxels)	Create a new Voxels that has been initialized with buffers from SliceBufferIndex.
default Voxels<T>	VoxelsFactoryTypeBound.createForVoxelBuffer(VoxelBuffer<T> buffer, Extent extent)	Create a new Voxels that has been initialized with a single-slice's memory buffers.
Voxels<T>	VoxelsFactoryTypeBound.createInitialized(Extent extent)	Create a new Voxels that has been initialized with memory buffers.
Voxels<T>	VoxelsFactoryTypeBound.createUninitialized(Extent extent)	Create a new Voxels that has not yet been initialized with memory buffers.

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

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

Modifier and Type	Method	Description
static <T> boolean	IterateVoxelsObjectMask.allMatchIntensity(ObjectMask object, Voxels<T> voxels, IntPredicate predicate)	Do all points on an object-mask match a predicate on the point's voxel-intensity?
static <T> boolean	IterateVoxelsAll.anyPredicateMatch(Voxels<T> voxels, Predicate<T> predicate)	Tries to apply a predicate to all the remaining buffer locations, returning true if the predicate matches.
static void	IterateVoxelsAll.assignEachMatchingPoint(Voxels<?> voxels, IntPredicate predicate, int valueToAssign)	Assigns a value to any voxel whose intensity matches a predicate, reading and writing the buffer as an int.
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	IterateVoxelsAll.changeIntensity(Voxels<?> voxels, IntUnaryOperator operator)	Changes each voxel, reading and writing the buffer as an int.
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 <T extends UnsignedBufferAsInt> int	IterateVoxelsAll.intensityMax(Voxels<T> voxels)	Finds the maximum intensity-value (as an int) among all voxels.
static <T extends UnsignedBufferAsInt> int	IterateVoxelsAll.intensityMin(Voxels<T> voxels)	Finds the minimum intensity-value (as an int) among all voxels.
static <T extends UnsignedBufferAsInt> MinMaxRange	IterateVoxelsAll.intensityMinMax(Voxels<T> voxels)	Finds the maximum intensity-value (as an int) among all voxels.
static <T> void	IterateVoxelsAll.withBuffer(Voxels<T> voxels, ProcessBufferUnary<T> process)	Iterate over each voxel - with one associated buffer for each slice.
static <T> void	IterateVoxelsBoundingBox.withBuffer(BoundingBox box, Voxels<T> voxels, ProcessBufferUnary<T> process)	Iterate over each voxel in a bounding-box - with one associated buffer for each slice
static <T> void	IterateVoxelsObjectMask.withBuffer(ObjectMask object, Voxels<T> voxels, ProcessBufferUnary<T> process)	Iterate over each voxel in an object-mask - with one associated buffer for each slice from Voxels.
static <T> void	IterateVoxelsObjectMaskOptional.withBuffer(Optional<ObjectMask> objectMask, Voxels<T> voxels, ProcessBufferUnary<T> process)	Iterate over each voxel (or optionally only on object-mask) with one associated buffer.
static <T> void	IterateVoxelsAll.withThreeBuffers(Voxels<T> voxels1, Voxels<T> voxels2, Voxels<T> voxels3, ProcessBufferTernary<T> process)	Iterate over each voxel - with three associated buffers for each slice.
static <T> void	IterateVoxelsBoundingBox.withThreeBuffers(BoundingBox box, ReadableTuple3i shiftForSecond, ReadableTuple3i shiftForThird, Voxels<T> voxels1, Voxels<T> voxels2, Voxels<T> voxels3, ProcessBufferTernary<T> process)	Iterate over each voxel in a bounding-box - with three associated buffers for each slice.
static <T> void	IterateVoxelsBoundingBox.withTwoBuffers(BoundingBox box, ReadableTuple3i shiftForSecond, Voxels<T> voxels1, Voxels<T> voxels2, ProcessBufferBinary<T,T> process)	Iterate over each voxel in a bounding-box - with two associated buffers for each slice, one VoxelBuffer and one Buffer
static <S, T> void	IterateVoxelsObjectMask.withTwoBuffers(ObjectMask object, Voxels<S> voxels1, Voxels<T> voxels2, ProcessBufferBinary<S,T> process)	Iterate over each voxel with a corresponding on value in an object-mask - and with two associated buffers for each slice covering the all the global space i.e. the entire image.
static <S, T> void	IterateVoxelsObjectMaskOptional.withTwoBuffers(Optional<ObjectMask> objectMask, Voxels<S> voxels1, Voxels<T> voxels2, ProcessBufferBinary<S,T> process)	Iterate over each voxel (or optionally only on object-mask) with two associated buffers.
static <S, T> void	IterateVoxelsAll.withTwoBuffersAndPoint(Voxels<S> voxels1, Voxels<T> voxels2, ProcessBufferBinary<S,T> process)	Iterate over each voxel - with two associated buffers for each slice
static <T> Optional<Point3i>	IterateVoxelsBoundingBox.withTwoBuffersUntil(BoundingBox box, ReadableTuple3i shiftForSecond, Voxels<T> voxels1, Voxels<T> voxels2, PredicateBufferBinary<T> predicate)	Iterate over each voxel in a bounding-box - with two associated buffers for each slice - until a predicate evaluates to true.
static <S, T> void	IterateVoxelsAll.withTwoMixedBuffers(Voxels<S> voxels1, Voxels<T> voxels2, ProcessVoxelBufferBinaryMixed<S,T> process)	Iterate over each voxel in a bounding-box - with one associated voxel-buffer and one associated buffer for each slice.
static <S, T> void	IterateVoxelsBoundingBox.withTwoMixedBuffers(BoundingBox box, ReadableTuple3i shiftForSecond, Voxels<S> voxels1, Voxels<T> voxels2, ProcessBufferBinaryMixed<S,T> process)	Iterate over each voxel in a bounding-box - with two associated buffers for each slice.
static <S, T> void	IterateVoxelsObjectMask.withTwoMixedBuffers(ObjectMask object, Voxels<S> voxels1, Voxels<T> voxels2, ProcessVoxelBufferBinaryMixed<S,T> process)	Iterate over each voxel in an object-mask - with one associated voxel-buffer and one associated buffer for each slice.
static <S, T> void	IterateVoxelsAll.withTwoVoxelBuffers(Voxels<S> voxels1, Voxels<T> voxels2, ProcessVoxelBufferBinary<S,T> process)	Iterate over each voxel in a bounding-box - with two associated voxel-buffers for each slice
static <S, T> void	IterateVoxelsObjectMask.withTwoVoxelBuffers(ObjectMask object, Voxels<S> voxels1, Voxels<T> voxels2, ProcessVoxelBufferBinary<S,T> process)	Iterate over each voxel in an object-mask - with two associated voxel-buffers and for each slice.
static <T> void	IterateVoxelsAll.withVoxelBuffer(Voxels<T> voxels, ProcessVoxelBufferUnary<T> process)	Iterate over each voxel - with one associated voxel-buffer for each slice.
static <T, E extends Exception> void	IterateVoxelsAll.withVoxelBuffer(Voxels<T> voxels, ProcessVoxelBufferUnaryWithPoint<T,E> process)	Iterate over each voxel - with one associated voxel-buffer for each slice.
static <T> void	IterateVoxelsObjectMask.withVoxelBuffer(ObjectMask object, Voxels<T> voxels, Optional<BoundingBox> restrictTo, ProcessVoxelBufferUnary<T> process)	Iterate over each voxel on an object-mask with one associated VoxelBuffer.
static <T> void	IterateVoxelsObjectMask.withVoxelBuffer(ObjectMask object, Voxels<T> voxels, ProcessVoxelBufferUnary<T> process)	Iterate over each voxel on an object-mask with one associated VoxelBuffer.

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

Methods in org.anchoranalysis.image.voxel.iterator.intersecting with parameters of type Voxels

Modifier and Type	Method	Description
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.

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

Constructors in org.anchoranalysis.image.voxel.kernel with parameters of type Voxels

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

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

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

Modifier and Type	Method	Description
Voxels<UnsignedByteBuffer>	ObjectMask.voxels()	The underlying voxel memory buffers for the object-mask, exposed via Voxels.

Methods in org.anchoranalysis.image.voxel.object with parameters of type Voxels

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

Constructors in org.anchoranalysis.image.voxel.object with parameters of type Voxels

Modifier	Constructor	Description
	ObjectMask(Voxels<UnsignedByteBuffer> voxels)	Creates from a Voxels mask that is cornered at the origin.
	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 Voxels in org.anchoranalysis.image.voxel.projection

Fields in org.anchoranalysis.image.voxel.projection declared as Voxels

Modifier and Type	Field	Description
protected final Voxels<FloatBuffer>	CountedProjectableBuffer.voxelsSum	Accumulates the sum of voxel values.

Methods in org.anchoranalysis.image.voxel.projection that return Voxels

Modifier and Type	Method	Description
protected Voxels<T>	CountedProjectableBuffer.flattenFrom(Voxels<FloatBuffer> voxels)	Flattens the accumulated voxels to the target type.

Methods in org.anchoranalysis.image.voxel.projection with parameters of type Voxels

Modifier and Type	Method	Description
void	CountedProjectableBuffer.addVoxels(Voxels<T> voxels)
protected void	CountedProjectableBuffer.divideVoxelsByCount(Voxels<FloatBuffer> voxels)	Divides all voxel values by the count of added voxels.
protected Voxels<T>	CountedProjectableBuffer.flattenFrom(Voxels<FloatBuffer> voxels)	Flattens the accumulated voxels to the target type.

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

Methods in org.anchoranalysis.image.voxel.thresholder with parameters of type Voxels

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.
static BinaryVoxels<UnsignedByteBuffer>	VoxelsThresholder.thresholdFloat(Voxels<FloatBuffer> voxels, float level, BinaryValuesByte binaryValues)	Applies thresholding to Voxels of float data type.

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

Constructor parameters in org.anchoranalysis.io.bioformats.copyconvert with type arguments of type Voxels

Modifier	Constructor	Description
	ConvertTo(Function<VoxelsUntyped,Voxels<T>> functionCast, IntFunction<T> allocateBuffer, Function<T,VoxelBuffer<T>> wrapBuffer)	Creates a new ConvertTo instance.

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

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

Modifier and Type	Method	Description
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 Voxels in org.anchoranalysis.mpp.overlap

Methods in org.anchoranalysis.mpp.overlap with parameters of type Voxels

Modifier and Type	Method	Description
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 Voxels in org.anchoranalysis.plugin.fiji.bean.channel.provider.distance

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

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 Voxels in org.anchoranalysis.plugin.image.segment.thresholder.slice

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

Modifier and Type	Method	Description
abstract void	SliceThresholder.segmentAll(Voxels<?> voxelsIn, Voxels<?> voxelsThreshold, Voxels<UnsignedByteBuffer> voxelsOut)	Segments all slices in the input voxels.
void	SliceThresholderMask.segmentAll(Voxels<?> voxelsIn, Voxels<?> voxelsThreshold, Voxels<UnsignedByteBuffer> voxelsOut)
void	SliceThresholderWithoutMask.segmentAll(Voxels<?> voxelsIn, Voxels<?> voxelsThreshold, Voxels<UnsignedByteBuffer> voxelsOut)

Uses of Voxels in org.anchoranalysis.plugin.image.segment.watershed.encoding

Methods in org.anchoranalysis.plugin.image.segment.watershed.encoding that return Voxels

Modifier and Type	Method	Description
Voxels<UnsignedIntBuffer>	EncodedVoxels.voxels()	The voxels containing encoded information.

Constructors in org.anchoranalysis.plugin.image.segment.watershed.encoding with parameters of type Voxels

Modifier	Constructor	Description
	EncodedVoxels(Voxels<UnsignedIntBuffer> voxels)	Creates a new EncodedVoxels instance.

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

Methods in org.anchoranalysis.plugin.opencv.convert with parameters of type Voxels

Modifier and Type	Method	Description
static org.opencv.core.Mat	ConvertToMat.fromVoxelsByte(Voxels<UnsignedByteBuffer> voxels)	Converts a Voxels of type UnsignedByteBuffer to a Mat.
static org.opencv.core.Mat	ConvertToMat.fromVoxelsFloat(Voxels<FloatBuffer> voxels)	Converts a Voxels of type FloatBuffer to a Mat.
static org.opencv.core.Mat	ConvertToMat.fromVoxelsShort(Voxels<UnsignedShortBuffer> voxels)	Converts a Voxels of type UnsignedShortBuffer to a Mat.

Uses of Voxels in org.anchoranalysis.test.image

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

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