Uses of Class
org.anchoranalysis.image.voxel.binary.BinaryVoxels

Packages that use BinaryVoxels

Package	Description
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.iterator	Utilities to iterate over voxel-locations in images and sub-regions of images.
org.anchoranalysis.image.voxel.iterator.neighbor.kernel	Routines for moving a KernelPointCursor around the neighboring voxels of the point.
org.anchoranalysis.image.voxel.kernel	Applying a kernel via convolution to voxels.
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.thresholder	Thresholding operations on voxels.

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

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

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.createEmptyOff(Extent extent)	Creates binary-voxels using unsigned 8-bit byte type and with all voxels set to off (0).
static BinaryVoxels<?>	BinaryVoxelsFactory.createEmptyOff(Extent extent, VoxelDataType dataType)	Creates an empty binary-voxels of a particular data-type with all voxels initialized to off.
static BinaryVoxels<UnsignedByteBuffer>	BinaryVoxelsFactory.createEmptyOn(Extent extent)	Creates binary-voxels using unsigned 8-bit byte type and with all voxels set to on (255).
abstract BinaryVoxels<T>	BinaryVoxels.duplicate()	Deep-copy of the object, including duplicating voxel buffers in memory.
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.
BinaryVoxels<T>	BinaryVoxels.sliceBinary(int z)	A particular z-slice, wrapped into a BinaryVoxels.

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

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

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

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

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

Modifier and Type	Method	Description
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 BinaryVoxels in org.anchoranalysis.image.voxel.iterator.neighbor.kernel

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

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.

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

Methods in org.anchoranalysis.image.voxel.kernel that return BinaryVoxels

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.

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

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.

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

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

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

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

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

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

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

Modifier and Type	Method	Description
static ObjectCollection	ObjectCollectionFactory.of(BinaryVoxels<UnsignedByteBuffer>... masks)	Creates a new collection with elements from the parameter-list of BinaryVoxels converting the voxels in their entirety to an object-mask at the origin.

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

Modifier	Constructor	Description
	ObjectMask(BinaryVoxels<UnsignedByteBuffer> voxels)	Creates from a BinaryVoxels to be located at the origin.
	ObjectMask(BoundingBox box, BinaryVoxels<UnsignedByteBuffer> voxels)	Creates from a BinaryVoxels and a corresponding bounding-box.

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

Methods in org.anchoranalysis.image.voxel.object.morphological that return BinaryVoxels

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.

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

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 BinaryVoxels in org.anchoranalysis.image.voxel.object.morphological.predicate

Methods in org.anchoranalysis.image.voxel.object.morphological.predicate with parameters of type BinaryVoxels

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 BinaryVoxels in org.anchoranalysis.image.voxel.thresholder

Methods in org.anchoranalysis.image.voxel.thresholder that return BinaryVoxels

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.