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

Packages that use BoundedVoxels

Package	Description
org.anchoranalysis.image.voxel	Data-structures to store and manipulate image raster-data or 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.object	The fundamental data class that is an ObjectMask and related structures.
org.anchoranalysis.mpp.mark.voxelized	A mark after a voxel-representation has been inferred.
org.anchoranalysis.mpp.overlap	Calculating overlaps between two Marks.

Uses of BoundedVoxels in org.anchoranalysis.image.voxel

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

Modifier and Type	Method	Description
BoundedVoxels<T>	BoundedVoxels.duplicate()	A deep-copy of the current structure.
BoundedVoxels<T>	BoundedVoxels.extractSlice(int sliceIndex)	Extracts a particular slice.
BoundedVoxels<T>	BoundedVoxels.growBuffer(Point3i growthNegative, Point3i growthPositive, Optional<Extent> clipRegion, VoxelsFactoryTypeBound<T> factory)	Grows the voxel buffer in the positive and negative directions by a certain amount.
BoundedVoxels<T>	BoundedVoxels.growToZ(int sizeZ, VoxelsFactoryTypeBound<T> factory)	Grows a single z-sliced BoundedVoxels by duplicating the slice across the z-dimension sizeZ number of times.
BoundedVoxels<T>	BoundedVoxels.mapBoundingBoxPreserveExtent(BoundingBox boundingBoxToAssign)	Applies a function to map the bounding-box to a new-value.
BoundedVoxels<T>	BoundedVoxels.projectMax()	A maximum-intensity projection (flattens in z dimension)
BoundedVoxels<T>	BoundedVoxels.region(BoundingBox box, boolean reuseIfPossible)	A (sub-)region of the voxels.
BoundedVoxels<T>	BoundedVoxels.regionIntersecting(BoundingBox box, int voxelValueForRest)	Like region(org.anchoranalysis.spatial.box.BoundingBox, boolean) but only expects a bounding-box that intersects at least partially.
BoundedVoxels<T>	BoundedVoxels.regionZ(int zMin, int zMax, VoxelsFactoryTypeBound<T> factory)	Creates an box with a subrange of the slices.
BoundedVoxels<T>	BoundedVoxels.replaceVoxels(Voxels<T> voxelsToAssign)	Replaces the voxels in the box.
BoundedVoxels<T>	BoundedVoxels.scale(ScaleFactor scaleFactor, VoxelsResizer resizer, Optional<Extent> clipTo)	Creates a scaled-version (in XY dimensions only) of the current bounding-box.

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

Modifier and Type	Method	Description
boolean	BoundedVoxels.equalsDeep(BoundedVoxels<?> other)	Performs a deep equality check, that includes checking that each voxel has an identical value.

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

Modifier	Constructor	Description
	BoundedVoxels(BoundedVoxels<T> source)	Copy constructor.

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

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

Modifier and Type	Method	Description
default BoundedVoxels<T>	VoxelsFactoryTypeBound.createBounded(BoundingBox box)	Creates and initializes voxels that correspond to a particular bounding-box region.

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

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

Modifier and Type	Method	Description
static Optional<Point3i>	IterateVoxelsEqualTo.untilFirstIntensityEqualTo(BoundedVoxels<UnsignedByteBuffer> voxels, byte equalToValue)	Iterates each voxel until a specific intensity value is found.

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

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

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 <T> void	IterateVoxelsIntersectingBounded.withTwoBuffers(BoundedVoxels<T> voxels1, BoundedVoxels<T> voxels2, ProcessBufferBinary<T,T> process)	Iterates over the intersection of two bounded-voxels of type BoundedVoxels.
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 <T> Optional<Point3i>	IterateVoxelsIntersectingBounded.withTwoBuffersUntil(BoundedVoxels<T> voxels1, BoundedVoxels<T> voxels2, PredicateBufferBinary<T> predicate)	Iterates over the intersection of two bounded-voxels of type BoundedVoxels until a predicate is satisfied.

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

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

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

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

Modifier	Constructor	Description
	ObjectMask(BoundedVoxels<UnsignedByteBuffer> voxels)	Creates from a BoundedVoxels with UnsignedByteBuffer.
	ObjectMask(BoundedVoxels<UnsignedByteBuffer> voxels, BinaryValuesInt binaryValues)	Creates from BoundedVoxels and corresponding BinaryValuesInt.

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

Methods in org.anchoranalysis.mpp.mark.voxelized that return BoundedVoxels

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 BoundedVoxels in org.anchoranalysis.mpp.overlap

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

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.