Uses of Class
org.anchoranalysis.spatial.box.BoundingBox

Packages that use BoundingBox

Package	Description
org.anchoranalysis.image.bean.nonbean.spatial.arrange	Non-beans to specify how to form a single-image by spatially combining other images.
org.anchoranalysis.image.bean.spatial.arrange.align	Aligning a BoundingBox to fit inside another BoundingBox.
org.anchoranalysis.image.core.channel	The Channel core data-class and related operations and converters.
org.anchoranalysis.image.core.dimensions	Classes to describe the size of images or components of images both in voxels and physically.
org.anchoranalysis.image.core.mask	An image with only two permissible states.
org.anchoranalysis.image.core.merge	Merges two or more entities.
org.anchoranalysis.image.core.object.properties	An ObjectCollection with associated key-value pairs.
org.anchoranalysis.image.core.object.scale	Scaling object-collections, or lists of elements with object-representations.
org.anchoranalysis.image.core.points	Operations that extract points from image data entities or vice versa.
org.anchoranalysis.image.core.stack	Defines the key data object, Stack, and related classes.
org.anchoranalysis.image.io.bean.object.draw	How to represent an object-mask in a raster that is being drawn.
org.anchoranalysis.image.io.stack	Non-bean classes for reading / writing a Stack from and to the filesystem.
org.anchoranalysis.image.io.stack.output.box	Base classes for generators that ultimately write only a bounding-box portion of a Stack to the filesystem.
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.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.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.object	The fundamental data class that is an ObjectMask and related structures.
org.anchoranalysis.mpp.mark	Non-bean classes related to Marks.
org.anchoranalysis.mpp.mark.conic	Marks implementing conic sections.
org.anchoranalysis.mpp.mark.points	Marks implementing structures based on points.
org.anchoranalysis.mpp.mark.voxelized	A mark after a voxel-representation has been inferred.
org.anchoranalysis.mpp.overlay	Any Overlay related to a Mark.
org.anchoranalysis.overlay	Overlays and related classes involving drawing entities on top of an image.
org.anchoranalysis.overlay.bean	Beans relating to drawing an Overlay on an image.
org.anchoranalysis.overlay.collection	Collections of Overlays.
org.anchoranalysis.overlay.object	An implementation of an Overlay that draws an ObjectMask on an image.
org.anchoranalysis.plugin.image.bean.thumbnail.object	Implementations of ThumbnailFromObjects.
org.anchoranalysis.plugin.image.feature.bean.object.combine	Features from combinations of ObjectMasks.
org.anchoranalysis.plugin.image.feature.bean.object.pair.touching	Features that calculate how many other objects an ObjectMask directly neighbors.
org.anchoranalysis.plugin.image.feature.bean.object.single.border	Implementations of FeatureSingleObject that determine if an object lies at the border of an image.
org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox	Implementations of FeatureSingleObject that consider an object's bounding-box.
org.anchoranalysis.spatial.box	Axis-aligned bounding-boxes and related operations.
org.anchoranalysis.spatial.rtree	R-Tree data structure and related operations.
org.anchoranalysis.test.image.segment	Fixtures or other helper classes for testing image segmentation algorithms.

Uses of BoundingBox in org.anchoranalysis.image.bean.nonbean.spatial.arrange

Methods in org.anchoranalysis.image.bean.nonbean.spatial.arrange that return BoundingBox

Modifier and Type	Method	Description
BoundingBox	BoundingBoxEnclosed.getBox()	The BoundingBox in which the image should be placed.
BoundingBox	BoundingBoxEnclosed.getEnclosing()	An enclosing box (equal to or larger than box covering all screen-space used for this entity, including padding.

Methods in org.anchoranalysis.image.bean.nonbean.spatial.arrange with parameters of type BoundingBox

Modifier and Type	Method	Description
void	StackArrangement.add(BoundingBox box)	Adds a new BoundingBox to the arrangement, with no padding.
static void	StackCopierAtBox.copyImageInto(Stack source, Stack destination, BoundingBox box)	Copies a source stack into a destination stack at a particular BoundingBox.

Constructors in org.anchoranalysis.image.bean.nonbean.spatial.arrange with parameters of type BoundingBox

Modifier	Constructor	Description
	BoundingBoxEnclosed(BoundingBox box)	Create with a box that has no padding.
	BoundingBoxEnclosed(BoundingBox box, BoundingBox enclosing)	Creates a new BoundingBoxEnclosed instance.
	StackArrangement(Extent extent, BoundingBox box)	Create with a single BoundingBox.

Uses of BoundingBox in org.anchoranalysis.image.bean.spatial.arrange.align

Methods in org.anchoranalysis.image.bean.spatial.arrange.align that return BoundingBox

Modifier and Type	Method	Description
BoundingBox	BoxAligner.align(BoundingBox smaller, BoundingBox larger)	Determines a BoundingBox to use for smaller BoundingBox so that it fits inside larger BoundingBox.
BoundingBox	BoxAligner.align(Extent smaller, BoundingBox larger)	Determines a BoundingBox to use for a smaller Extent so that it fits inside larger BoundingBox.
BoundingBox	BoxAligner.align(Extent smaller, Extent larger)	Determines a BoundingBox to use for a smaller Extent so that it fits inside larger Extent.
protected BoundingBox	Align.alignAfterCheck(BoundingBox smaller, BoundingBox larger)
protected BoundingBox	Align.alignAfterCheck(Extent smaller, BoundingBox larger)
protected BoundingBox	Align.alignAfterCheck(Extent smaller, Extent larger)
protected abstract BoundingBox	BoxAligner.alignAfterCheck(BoundingBox smaller, BoundingBox larger)	Determines a BoundingBox to use for smaller BoundingBox so that it fits inside larger BoundingBox.
protected abstract BoundingBox	BoxAligner.alignAfterCheck(Extent smaller, BoundingBox larger)	Determines a BoundingBox to use for smaller Extent so that it fits inside larger BoundingBox.
protected abstract BoundingBox	BoxAligner.alignAfterCheck(Extent smaller, Extent larger)	Determines a BoundingBox to use for smaller Extent so that it fits inside larger Extent.
protected BoundingBox	Grow.alignAfterCheck(BoundingBox smaller, BoundingBox larger)
protected BoundingBox	Grow.alignAfterCheck(Extent smaller, BoundingBox larger)
protected BoundingBox	Grow.alignAfterCheck(Extent smaller, Extent larger)

Methods in org.anchoranalysis.image.bean.spatial.arrange.align with parameters of type BoundingBox

Modifier and Type	Method	Description
BoundingBox	BoxAligner.align(BoundingBox smaller, BoundingBox larger)	Determines a BoundingBox to use for smaller BoundingBox so that it fits inside larger BoundingBox.
BoundingBox	BoxAligner.align(Extent smaller, BoundingBox larger)	Determines a BoundingBox to use for a smaller Extent so that it fits inside larger BoundingBox.
protected BoundingBox	Align.alignAfterCheck(BoundingBox smaller, BoundingBox larger)
protected BoundingBox	Align.alignAfterCheck(Extent smaller, BoundingBox larger)
protected abstract BoundingBox	BoxAligner.alignAfterCheck(BoundingBox smaller, BoundingBox larger)	Determines a BoundingBox to use for smaller BoundingBox so that it fits inside larger BoundingBox.
protected abstract BoundingBox	BoxAligner.alignAfterCheck(Extent smaller, BoundingBox larger)	Determines a BoundingBox to use for smaller Extent so that it fits inside larger BoundingBox.
protected BoundingBox	Grow.alignAfterCheck(BoundingBox smaller, BoundingBox larger)
protected BoundingBox	Grow.alignAfterCheck(Extent smaller, BoundingBox larger)
Point3i	Align.alignCorner(BoundingBox smaller, Extent larger)	The minimum corner at which the entity should be locate after alignment, ignoring the space to the left.

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

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

Modifier and Type	Method	Description
ObjectMask	Channel.equalMask(BoundingBox box, int equalValue)	Creates a ObjectMask representing all the voxels in box equal to equalValue.

Uses of BoundingBox in org.anchoranalysis.image.core.dimensions

Methods in org.anchoranalysis.image.core.dimensions with parameters of type BoundingBox

Modifier and Type	Method	Description
boolean	Dimensions.contains(BoundingBox box)	Is box entirely contained within the extent?

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

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

Modifier and Type	Method	Description
ObjectMask	Mask.region(BoundingBox box, boolean reuseIfPossible)	Creates an ObjectMask corresponding to the on/off state in a bounding-box.

Uses of BoundingBox in org.anchoranalysis.image.core.merge

Methods in org.anchoranalysis.image.core.merge that return BoundingBox

Modifier and Type	Method	Description
static BoundingBox	ObjectMaskMerger.mergeBoundingBoxes(Stream<ObjectMask> objects)	Merges all the bounding boxes of a stream of objects.
static BoundingBox	ObjectMaskMerger.mergeBoundingBoxes(ObjectCollection objects)	Merges all the bounding boxes of a collection of objects.

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

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

Modifier and Type	Method	Description
BoundingBox	ObjectWithProperties.boundingBox()	The bounding-box which gives a location for the object-mask on an image.

Constructors in org.anchoranalysis.image.core.object.properties with parameters of type BoundingBox

Modifier	Constructor	Description
	ObjectWithProperties(BoundingBox box)	Creates as a bounding-box with all corresponding mask voxels set to off.

Uses of BoundingBox in org.anchoranalysis.image.core.object.scale

Methods in org.anchoranalysis.image.core.object.scale that return BoundingBox

Modifier and Type	Method	Description
default BoundingBox	AccessObjectMask.boundingBoxFor(T element)	A bounding-box for a given element.

Uses of BoundingBox in org.anchoranalysis.image.core.points

Methods in org.anchoranalysis.image.core.points that return BoundingBox

Modifier and Type	Method	Description
static BoundingBox	BoundingBoxFromPoints.fromStream(Stream<Point3i> points)	Create from a stream of Point3is.
static BoundingBox	BoundingBoxFromPoints.fromTwoPoints(Point3d point1, Point3d point2)	Creates a bounding-box for two unordered points.

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

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

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.
Channel	DisplayStack.extractChannelForBoundingBox(int index, BoundingBox box)	Creates a new Channel that refers to only a BoundingBox portion of the DisplayStack.

Uses of BoundingBox in org.anchoranalysis.image.io.bean.object.draw

Methods in org.anchoranalysis.image.io.bean.object.draw with parameters of type BoundingBox

Modifier and Type	Method	Description
void	Filled.drawSingle(ObjectWithProperties object, RGBStack stack, ObjectDrawAttributes attributes, int iteration, BoundingBox restrictTo)
void	Flatten.drawSingle(ObjectWithProperties object, RGBStack stack, ObjectDrawAttributes attributes, int iteration, BoundingBox restrictTo)
void	IfElse.drawSingle(ObjectWithProperties object, RGBStack stack, ObjectDrawAttributes attributes, int iteration, BoundingBox restrictTo)
void	Outline.drawSingle(ObjectWithProperties object, RGBStack stack, ObjectDrawAttributes attributes, int iteration, BoundingBox restrictTo)

Uses of BoundingBox in org.anchoranalysis.image.io.stack

Methods in org.anchoranalysis.image.io.stack with parameters of type BoundingBox

Modifier and Type	Method	Description
static RGBStack	ConvertStackToRGB.convertCropped(DisplayStack stack, BoundingBox box)	Converts a bounding-box region in DisplayStack to a RGBStack.

Uses of BoundingBox in org.anchoranalysis.image.io.stack.output.box

Methods in org.anchoranalysis.image.io.stack.output.box with parameters of type BoundingBox

Modifier and Type	Method	Description
Stack	ScaleableBackground.extractRegionFromStack(BoundingBox box)	Extracts a portion of a stack (flattened and maybe scaled) corresponding to a bounding-box
Stack	ExtractBoundingBoxAreaFromStackGenerator.transform(BoundingBox element)

Method parameters in org.anchoranalysis.image.io.stack.output.box with type arguments of type BoundingBox

Modifier and Type	Method	Description
static DrawObjectOnStackGenerator	DrawObjectOnStackGenerator.createFromGenerator(TransformingGenerator<BoundingBox,Stack> backgroundGenerator, int outlineWidth, ColorIndex colors)	Creates an extracted-object generator that draws an outline - with default color green and flattened in Z.

Uses of BoundingBox in org.anchoranalysis.image.voxel

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

Modifier and Type	Method	Description
BoundingBox	BoundedVoxels.boundingBox()	A bounding-box that associates voxels to a particular part of an image.
BoundingBox	BoundedVoxels.dilate(boolean do3D, Optional<Extent> clipRegion)	Grow bounding-box by 1 pixel in all directions.

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

Modifier and Type	Method	Description
static void	ExtentMatchHelper.checkExtentMatch(BoundingBox box1, BoundingBox box2)	Checks that the Extents of two bounding boxes are identical.
void	VoxelsUntyped.copyVoxelsTo(ObjectMask objectSource, VoxelsUntyped destination, BoundingBox boxDestination)	Copies the voxels into a destination, but only those voxels inside an ObjectMask.
void	VoxelsUntyped.copyVoxelsTo(BoundingBox boxSource, VoxelsUntyped destination, BoundingBox boxDestination)	Copies the voxels into a destination, but only those voxels inside a bounding-box.
BoundedVoxels<T>	BoundedVoxels.mapBoundingBoxPreserveExtent(BoundingBox boundingBoxToAssign)	Applies a function to map the bounding-box to a new-value.
BoundedVoxels<T>	BoundedVoxels.region(BoundingBox box, boolean reuseIfPossible)	A (sub-)region of the voxels.
BoundedVoxels<T>	BoundedVoxels.regionIntersecting(BoundingBox box, int voxelValueForRest)	Like BoundedVoxels.region(org.anchoranalysis.spatial.box.BoundingBox, boolean) but only expects a bounding-box that intersects at least partially.

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

Modifier	Constructor	Description
	BoundedVoxels(BoundingBox boundingBox, Voxels<T> voxels)	Creates voxels with a corresponding bounding box.

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

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

Modifier and Type	Method	Description
void	VoxelsAssigner.toBox(BoundingBox box)	Assigns to only voxels inside a bounding-box
void	VoxelsAssigner.toEitherTwoObjects(ObjectMask object1, ObjectMask object2, BoundingBox restrictTo)	Sets voxels to a value if the position is on in either of two masks
void	VoxelsAssigner.toObject(ObjectMask object, BoundingBox restrictTo)	Sets voxels in a box to a particular value if they match a object-mask (but only a part of the object-mask)

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

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

Modifier and Type	Method	Description
void	VoxelsExtracter.boxCopyTo(BoundingBox from, Voxels<T> voxelsDestination, BoundingBox destinationBox)	Copies a bounding-box area to another Voxels.
void	VoxelsExtracter.objectCopyTo(ObjectMask from, Voxels<T> voxelsDestination, BoundingBox destinationBox)	Copies an area corresponding to an object-mask to another Voxels.
Voxels<T>	VoxelsExtracter.region(BoundingBox box, boolean reuseIfPossible)	A (sub-)region of the voxels.

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

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

Modifier and Type	Method	Description
ObjectMask	PredicateAtCorner.deriveObject(BoundingBox box)
ObjectMask	PredicateImplementation.deriveObject(BoundingBox box)
ObjectMask	VoxelsPredicate.deriveObject(BoundingBox box)	Creates an ObjectMask for all the voxels inside the bounding-box satisfying the predicate.

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

Methods in org.anchoranalysis.image.voxel.factory with parameters of type BoundingBox

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 BoundingBox in org.anchoranalysis.image.voxel.iterator

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

Modifier and Type	Method	Description
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 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..
static void	IterateVoxelsBoundingBox.withMatchingPoints(BoundingBox box, Predicate<Point3i> predicate, ProcessPoint process)	Iterate over each voxel in a bounding-box that matches a predicate.
static void	IterateVoxelsBoundingBox.withPoint(BoundingBox box, ProcessPoint process)	Iterate over each voxel in a bounding-box
static void	IterateVoxelsBoundingBox.withPointAndIndex(BoundingBox box, ProcessPointAndIndex process)	Iterate over each voxel in a bounding-box
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 <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	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.

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

Modifier and Type	Method	Description
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.

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

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

Modifier and Type	Method	Description
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 BoundingBox in org.anchoranalysis.image.voxel.kernel

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

Modifier and Type	Method	Description
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 BoundingBox in org.anchoranalysis.image.voxel.object

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

Modifier and Type	Method	Description
BoundingBox	ObjectMask.boundingBox()	The bounding-box which gives a location for the object-mask on an image.

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

Modifier and Type	Method	Description
Set<T>	IntersectingObjects.intersectsWith(BoundingBox box)	All elements that intersect with a particular bounding box.
ObjectMask	ObjectMask.mapBoundingBoxChangeExtent(BoundingBox boxToAssign)	Applies a function to map the bounding-box to a new-value (whose extent is expected to change in value).
ObjectCollection	ObjectMaskStream.mapBoundingBoxChangeExtent(BoundingBox boxToAssign)	Creates a new ObjectCollection after mapping the bounding-box on each object (while maybe changing the extent).
ObjectMask	ObjectMask.region(BoundingBox box, boolean reuseIfPossible)	A (sub-)region of the object-mask.
ObjectMask	ObjectMask.regionIntersecting(BoundingBox box)	Creates an object-mask covering the a bounding-box (that is required to intersect at least partially)
ObjectMask	ObjectMask.relativeMaskTo(BoundingBox box)	Creates a new object-mask with coordinates changed to be relative to another box.

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

Modifier and Type	Method	Description
ObjectMask	ObjectMask.mapBoundingBoxPreserveExtent(UnaryOperator<BoundingBox> mapOperation)	Applies a function to map the bounding-box to a new-value (whose extent should be unchanged in value).
ObjectCollection	ObjectMaskStream.mapBoundingBoxPreserveExtent(UnaryOperator<BoundingBox> mapFunction)	Creates a new ObjectCollection after mapping the bounding-box on each object (whose extent should remain unchanged).

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

Modifier	Constructor	Description
	ObjectMask(BoundingBox box)	Creates as a bounding-box with all corresponding mask voxels set to off.
	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 BoundingBox in org.anchoranalysis.mpp.mark

Methods in org.anchoranalysis.mpp.mark that return BoundingBox

Modifier and Type	Method	Description
abstract BoundingBox	Mark.box(Dimensions dimensions, int regionID)	Calculates the bounding box for a specific region of the mark.
abstract BoundingBox	Mark.boxAllRegions(Dimensions dimensions)	Calculates the bounding box for all regions of the mark.

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

Modifier and Type	Method	Description
List<BoundingBox>	MarkCollection.boxList(Dimensions dimensions, int regionID)	Creates a list of bounding boxes for all marks in the collection.

Method parameters in org.anchoranalysis.mpp.mark with type arguments of type BoundingBox

Modifier and Type	Method	Description
ColoredMarks	ColoredMarks.subsetWhereBBoxIntersects(Dimensions dimensions, int regionID, List<BoundingBox> intersectList)	Creates a subset of marks whose bounding boxes intersect with given boxes.

Uses of BoundingBox in org.anchoranalysis.mpp.mark.conic

Methods in org.anchoranalysis.mpp.mark.conic that return BoundingBox

Modifier and Type	Method	Description
BoundingBox	Ellipse.box(Dimensions dimensions, int regionID)
BoundingBox	Ellipsoid.box(Dimensions dimensions, int regionID)
BoundingBox	MarkWithPositionAndSingleRadius.box(Dimensions dimensions, int regionID)
BoundingBox	Ellipse.boxAllRegions(Dimensions dimensions)
BoundingBox	Ellipsoid.boxAllRegions(Dimensions dimensions)
BoundingBox	MarkWithPositionAndSingleRadius.boxAllRegions(Dimensions dimensions)
static BoundingBox	BoundingBoxCalculator.boxFromBounds(Point3d pos, double radius, boolean do3D, Dimensions dimensions)	Calculates a bounding box for a point with a scalar radius in all dimensions.
static BoundingBox	BoundingBoxCalculator.boxFromBounds(Point3d center, cern.colt.matrix.DoubleMatrix1D radiiMatrix, boolean do3D, Dimensions dimensions)	Calculates a bounding box for a point with varying radii in each dimension (that have already been resolved into a matrix)

Uses of BoundingBox in org.anchoranalysis.mpp.mark.points

Methods in org.anchoranalysis.mpp.mark.points that return BoundingBox

Modifier and Type	Method	Description
BoundingBox	LineSegment.box(Dimensions dimensions, int regionID)
protected BoundingBox	PointListBase.box()	Creates a bounding box from the min and max points.
BoundingBox	PointListBase.box(Dimensions dimensions, int regionID)
BoundingBox	RotatableBoundingBox.box(Dimensions dimensions, int regionID)
BoundingBox	LineSegment.boxAllRegions(Dimensions dimensions)
BoundingBox	PointList.boxAllRegions(Dimensions dimensions)
BoundingBox	Polygon.boxAllRegions(Dimensions dimensions)
BoundingBox	PolygonCurve.boxAllRegions(Dimensions dimensions)
BoundingBox	RotatableBoundingBox.boxAllRegions(Dimensions dimensions)

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

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

Modifier and Type	Method	Description
BoundingBox	VoxelizedMark.boundingBox()	Gets the bounding-box enclosing the voxelized representation of the mark.
BoundingBox	VoxelizedMark.boundingBoxFlattened()	Gets the bounding-box flattened in z dimension.

Uses of BoundingBox in org.anchoranalysis.mpp.overlay

Methods in org.anchoranalysis.mpp.overlay that return BoundingBox

Modifier and Type	Method	Description
BoundingBox	OverlayMark.box(DrawOverlay overlayWriter, Dimensions dim)

Uses of BoundingBox in org.anchoranalysis.overlay

Methods in org.anchoranalysis.overlay that return BoundingBox

Modifier and Type	Method	Description
abstract BoundingBox	Overlay.box(DrawOverlay overlayWriter, Dimensions dimensions)	A bounding-box around the overlay.

Uses of BoundingBox in org.anchoranalysis.overlay.bean

Methods in org.anchoranalysis.overlay.bean with parameters of type BoundingBox

Modifier and Type	Method	Description
void	DrawObject.drawCollection(ObjectCollectionWithProperties objects, RGBStack stack, ObjectDrawAttributes attributes, BoundingBox boxContainer)	Writes object-masks onto of a RGBStack - within a bounding box only.
abstract void	DrawObject.drawSingle(ObjectWithProperties object, RGBStack stack, ObjectDrawAttributes attributes, int iteration, BoundingBox restrictTo)	Draws a single-object on top of a RGB-stack.

Uses of BoundingBox in org.anchoranalysis.overlay.collection

Method parameters in org.anchoranalysis.overlay.collection with type arguments of type BoundingBox

Modifier and Type	Method	Description
ColoredOverlayCollection	ColoredOverlayCollection.subsetWhereBoxIntersects(Dimensions scene, DrawOverlay drawOverlay, List<BoundingBox> toIntersectWith)	Find overlays whose bounding-boxes intersect with any of the boxes in toIntersectWith.

Uses of BoundingBox in org.anchoranalysis.overlay.object

Methods in org.anchoranalysis.overlay.object that return BoundingBox

Modifier and Type	Method	Description
BoundingBox	OverlayObjectMask.box(DrawOverlay overlayWriter, Dimensions dimensions)

Uses of BoundingBox in org.anchoranalysis.plugin.image.bean.thumbnail.object

Method parameters in org.anchoranalysis.plugin.image.bean.thumbnail.object with type arguments of type BoundingBox

Modifier and Type	Method	Description
ThumbnailBatch<ObjectCollection>	OutlinePreserveRelativeSize.start(ObjectCollection objects, StreamableCollection<BoundingBox> boundingBoxes, Optional<Stack> backgroundSource, ExecutionTimeRecorder executionTimeRecorder)
abstract ThumbnailBatch<ObjectCollection>	ThumbnailFromObjects.start(ObjectCollection objects, StreamableCollection<BoundingBox> boundingBoxes, Optional<Stack> background, ExecutionTimeRecorder executionTimeRecorder)	Initializes a batch to create thumbnails.

Uses of BoundingBox in org.anchoranalysis.plugin.image.feature.bean.object.combine

Methods in org.anchoranalysis.plugin.image.feature.bean.object.combine that return BoundingBox

Modifier and Type	Method	Description
protected abstract BoundingBox	CombineObjectsForFeatures.boundingBoxThatSpansInput(T input)	Creates a bounding-box that tightly fits the input to a particular table row (could be for one or more objects).
protected BoundingBox	EachObjectIndependently.boundingBoxThatSpansInput(FeatureInputSingleObject input)
protected BoundingBox	PairNeighbors.boundingBoxThatSpansInput(FeatureInputPairObjects input)

Uses of BoundingBox in org.anchoranalysis.plugin.image.feature.bean.object.pair.touching

Methods in org.anchoranalysis.plugin.image.feature.bean.object.pair.touching with parameters of type BoundingBox

Modifier and Type	Method	Description
protected double	HasTouchingVoxels.calculateWithIntersection(ObjectMask first, ObjectMask second, BoundingBox boxIntersect)
protected double	NumberTouchingVoxelFaces.calculateWithIntersection(ObjectMask object1, ObjectMask object2, BoundingBox boxIntersect)
protected double	NumberTouchingVoxels.calculateWithIntersection(ObjectMask object1, ObjectMask object2, BoundingBox boxIntersect)
protected abstract double	TouchingVoxels.calculateWithIntersection(ObjectMask object1, ObjectMask object2, BoundingBox boxIntersect)	Calculates the feature value for the intersection of two objects.

Uses of BoundingBox in org.anchoranalysis.plugin.image.feature.bean.object.single.border

Methods in org.anchoranalysis.plugin.image.feature.bean.object.single.border with parameters of type BoundingBox

Modifier and Type	Method	Description
protected abstract boolean	AtBorderBase.isBoundingBoxAtBorder(BoundingBox boundingBox, Extent extent)	Checks if the bounding box of an object is at the border of the image.
protected boolean	AtBorderXY.isBoundingBoxAtBorder(BoundingBox boundingBox, Extent extent)
protected boolean	AtBorderZ.isBoundingBoxAtBorder(BoundingBox boundingBox, Extent extent)

Uses of BoundingBox in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox

Methods in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox with parameters of type BoundingBox

Modifier and Type	Method	Description
protected abstract ReadableTuple3i	BoundingBoxAlongAxisBase.extractTupleForBoundingBox(BoundingBox box)	Extracts a ReadableTuple3i from the given BoundingBox.
protected ReadableTuple3i	BoundingBoxExtentAlongAxis.extractTupleForBoundingBox(BoundingBox box)
protected ReadableTuple3i	BoundingBoxMaximumAlongAxis.extractTupleForBoundingBox(BoundingBox box)
protected ReadableTuple3i	BoundingBoxMinimumAlongAxis.extractTupleForBoundingBox(BoundingBox box)

Uses of BoundingBox in org.anchoranalysis.spatial.box

Methods in org.anchoranalysis.spatial.box that return BoundingBox

Modifier and Type	Method	Description
static BoundingBox	BoundingBoxFactory.at(int x, int y, int width, int height)	Short-hand factory method for creating a 2D bounding-box.
static BoundingBox	BoundingBoxFactory.at(int x, int y, int z, int width, int height, int depth)	Short-hand factory method for creating a 3D bounding-box.
BoundingBox	BoundedList.boundingBox()	A bounding-box that must contain all elements in the collection
BoundingBox	BoundingBox.changeExtent(UnaryOperator<Extent> extentOperator)	Creates a copied BoundingBox but with a different extent.
BoundingBox	BoundingBox.changeExtent(Extent extent)	Creates a copied BoundingBox but with a different extent.
BoundingBox	BoundingBox.changeExtentZ(int extentZ)	Creates a copied BoundingBox but with a different extent in the Z-dimension.
BoundingBox	BoundingBox.changeZ(int cornerZ, int extentZ)	Creates a copied BoundingBox but with a different corner and extent in the Z-dimension.
BoundingBox	BoundingBox.clampTo(Extent extent)	Ensures that the box fits inside a Extent by reducing any values to their limits in the respective dimension.
static BoundingBox	BoundingBox.createDuplicate(ReadableTuple3i cornerMin, Extent extent)	Creates a bounding-box from a corner and an extent - duplicating cornerMin.
static BoundingBox	BoundingBox.createDuplicate(ReadableTuple3i cornerMinInclusive, ReadableTuple3i cornerMaxInclusive)	Creates from two int points (a minimum corner and a maximum corner) - reusing cornerMinInclusive internally.
static BoundingBox	BoundingBox.createReuse(Point3d cornerMinInclusive, Point3d cornerMaxInclusive)	Creates from two double points (a minimum corner and a maximum corner).
static BoundingBox	BoundingBox.createReuse(ReadableTuple3i cornerMin, Extent extent)	Creates a bounding-box from a corner and an extent - reusing cornerMin internally.
static BoundingBox	BoundingBox.createReuse(ReadableTuple3i cornerMinInclusive, ReadableTuple3i cornerMaxInclusive)	Creates from two int points (a minimum corner and a maximum corner) - reusing cornerMinInclusive internally.
BoundingBox	BoundingBox.flattenZ()	Collapses the z-dimension of the box to a single voxel depth, and a corner at 0 voxels.
BoundingBox	BoundingBox.growBy(Tuple3i toAdd, Extent containingExtent)	Grow the bounding-box by toAdd amount in each dimension in both positive and negative directions.
static BoundingBox	BoundingBoxMerger.merge(Stream<BoundingBox> stream)	Merges all the bounding boxes in a stream.
BoundingBox	BoundingBox.reflectThroughOrigin()	Reflects the bounding box through the origin.
BoundingBox	BoundingBox.relativePositionToBox(BoundingBox other)	A new bounding-box using relative position coordinates to another box.
BoundingBox	BoundingBox.scale(ScaleFactor scaleFactor)	Scales the bounding-box, both the corner-point and the extent.
BoundingBox	BoundingBox.scale(ScaleFactor scaleFactor, Extent extentToAssign)	Scales the bounding-box corner-point, and assigns a new extent.
BoundingBox	BoundingBox.scaleClampTo(ScaleFactor scaleFactor, Extent clampTo)	Scales the bounding-box, both the corner-point and the extent - ensuring it remains inside a containing-extent.
BoundingBox	BoundingBox.shiftBackBy(ReadableTuple3i shift)	Shifts the bounding-box backwards.
BoundingBox	BoundingBox.shiftBy(ReadableTuple3i shift)	Shifts the bounding-box forwards.
BoundingBox	BoundingBox.shiftTo(ReadableTuple3i cornerMinToAssign)	Assigns a new corner-location to the bounding-box.
BoundingBox	BoundingBox.shiftToOrigin()	Moves the bounding-box to the origin (0,0,0) but preserves the extent.
BoundingBox	BoundingBox.shiftToZ(int cornerZToAssign)	Assigns a new z-slice corner-location to the bounding-box.
BoundingBox	PointRange.toBoundingBox()	Creates a BoundingBox to just cover the range of points that have been added.
BoundingBox	PointRange.toBoundingBoxNoCheck()	Like PointRange.toBoundingBox() but if no points exist, an exception is not thrown.
static BoundingBox	BoundingBoxFactory.uniform3D(int corner, int extent)	Short-hand factory method for creating a 3D bounding-box, where a coordinate is identical in each dimension.
BoundingBox	BoundingBoxUnion.with(BoundingBox other)	Performs a union with another box (immutably).

Methods in org.anchoranalysis.spatial.box that return types with arguments of type BoundingBox

Modifier and Type	Method	Description
Optional<BoundingBox>	BoundingBoxIntersection.with(BoundingBox other)	Finds the intersection with another bounding-box, if it exists.
Optional<BoundingBox>	BoundingBoxIntersection.withInside(BoundingBox other, Extent containingExtent)	Finds the intersection and clamp to a containing extent.

Methods in org.anchoranalysis.spatial.box with parameters of type BoundingBox

Modifier and Type	Method	Description
BoundedList<T>	BoundedList.assignBoundingBox(BoundingBox boxToAssign)	Assigns a new containing bounding-box.
BoundedList<T>	BoundedList.assignBoundingBoxAndMap(BoundingBox boxToAssign, UnaryOperator<T> mappingFunction)	Assigns a new containing bounding-box and maps each individual element.
boolean	BoundingBoxContains.box(BoundingBox maybeContainedInside)	Is this other bounding-box fully contained within this bounding box?
int	BoundingBox.compareTo(BoundingBox other)
boolean	Extent.contains(BoundingBox box)	Is box entirely contained within the extent?
static double	BoundingBoxDistance.distance(BoundingBox box1, BoundingBox box2, boolean includeZ)	Calculates the distance between two BoundingBoxes.
boolean	BoundingBoxIntersection.existsWith(BoundingBox other)	Does intersection exist with another bounding-box?
static double	IntersectionOverUnion.forBoxes(BoundingBox box1, BoundingBox box2)	Calculates the intersection-over-union score a pair of bounding-boxes.
Point3i	BoundingBox.relativePositionTo(BoundingBox other)	The relative position of the corner to another bounding box.
BoundingBox	BoundingBox.relativePositionToBox(BoundingBox other)	A new bounding-box using relative position coordinates to another box.
Optional<BoundingBox>	BoundingBoxIntersection.with(BoundingBox other)	Finds the intersection with another bounding-box, if it exists.
BoundingBox	BoundingBoxUnion.with(BoundingBox other)	Performs a union with another box (immutably).
Optional<BoundingBox>	BoundingBoxIntersection.withInside(BoundingBox other, Extent containingExtent)	Finds the intersection and clamp to a containing extent.

Method parameters in org.anchoranalysis.spatial.box with type arguments of type BoundingBox

Modifier and Type	Method	Description
static <T> BoundedList<T>	BoundedList.createFromList(List<T> list, Function<T,BoundingBox> extractBoundingBox)	Creates for a list, minimally fitting a bounding-box around all elements
static <T> BoundedList<T>	BoundedList.createSingle(T element, Function<T,BoundingBox> extractBoundingBox)	Creates for a single element using its current bounding-box.
boolean	BoundingBoxIntersection.existsWithAny(List<BoundingBox> others)	Does intersection exist with with any of the others in the list?
static BoundingBox	BoundingBoxMerger.merge(Stream<BoundingBox> stream)	Merges all the bounding boxes in a stream.

Constructors in org.anchoranalysis.spatial.box with parameters of type BoundingBox

Modifier	Constructor	Description
	BoundingBoxContains(BoundingBox box)	Create with the BoundingBox that is queried.
	BoundingBoxIntersection(BoundingBox box)
	BoundingBoxUnion(BoundingBox box)

Uses of BoundingBox in org.anchoranalysis.spatial.rtree

Methods in org.anchoranalysis.spatial.rtree with parameters of type BoundingBox

Modifier and Type	Method	Description
void	BoundingBoxRTree.add(BoundingBox box, T payload)	Adds a bounding-box with a corresponding payload.
Set<T>	BoundingBoxRTree.intersectsWith(BoundingBox toIntersectWith)	Which bounding-boxes intersect with another specific bounding box?
Stream<T>	BoundingBoxRTree.intersectsWithStream(BoundingBox toIntersectWith)	Like BoundingBoxRTree.intersectsWith(BoundingBox) but returns a Stream instead of a Set.
void	BoundingBoxRTree.remove(BoundingBox box, T payload)	Removes a particular item from the r-tree, identified by its bounding-box and payload.

Constructor parameters in org.anchoranalysis.spatial.rtree with type arguments of type BoundingBox

Modifier	Constructor	Description
	SpatiallySeparate(Function<T,BoundingBox> extractBoundingBox)	Creates a new SpatiallySeparate instance.

Uses of BoundingBox in org.anchoranalysis.test.image.segment

Methods in org.anchoranalysis.test.image.segment that return BoundingBox

Modifier and Type	Method	Description
protected abstract BoundingBox	InstanceSegmentationTestBase.targetBox()	The bounding-box we use to set an area where we expect segments to reside.