Index (anchor-image-voxel 0.2.1 API)

A B C D E F G H I K L M N O P Q R S T U V W Z
All Classes All Packages

A

accept(BinaryVoxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.object.morphological.predicate.AcceptIterationList
accept(BinaryVoxels<UnsignedByteBuffer>) - Method in interface org.anchoranalysis.image.voxel.object.morphological.predicate.AcceptIterationPredicate: Whether a particular voxels fulfills the condition or not.
AcceptIterationList - Class in org.anchoranalysis.image.voxel.object.morphological.predicate: The condition is accepted if any one of a list of AcceptIterationPredicate fulfills the condition.
AcceptIterationList() - Constructor for class org.anchoranalysis.image.voxel.object.morphological.predicate.AcceptIterationList
AcceptIterationPredicate - Interface in org.anchoranalysis.image.voxel.object.morphological.predicate: A condition that must be fulfilled for a particular iteration of a morphological operation to be accepted.
add(AcceptIterationPredicate) - Method in class org.anchoranalysis.image.voxel.object.morphological.predicate.AcceptIterationList: Adds an item to the list of predicates.
add(VoxelStatistics) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined: Adds an element.
add(ReadableTuple3i) - Method in class org.anchoranalysis.image.voxel.object.DeriveObjectFromPoints: Adds a point to the object.
addTo(ObjectMask, int) - Method in interface org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmetic: Adds a constant-value to each voxel but only for voxels inside an object-mask.
addVoxelBuffer(VoxelBuffer<T>) - Method in interface org.anchoranalysis.image.voxel.buffer.ProjectableBuffer: Adds a VoxelBuffer to the projection, as a single entity.
addVoxels(Voxels<T>) - Method in interface org.anchoranalysis.image.voxel.buffer.ProjectableBuffer: Adds a Voxels to the projection, as a single entity.
allMatchIntensity(ObjectMask, Voxels<T>, IntPredicate) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask: Do all points on an object-mask match a predicate on the point's voxel-intensity?
allocate(int) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Allocates a new buffer of unsigned-bytes.
allocate(int) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Allocates a new (direct) buffer of unsigned-ints.
allocate(int) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Allocates a new (direct) buffer of unsigned-shorts.
allocateFloat(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory: Allocates a new float voxel-buffers of given size.
allocateFloatArray(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory: Creates an array of float voxel-buffers of given size.
allocateUnsignedByte(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory: Allocates a new unsigned byte voxel-buffer of given size.
allocateUnsignedByteArray(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory: Creates an array of unsigned byte voxel-buffers of given size.
allocateUnsignedInt(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory: Allocates a new unsigned int voxel-buffers of given size.
allocateUnsignedIntArray(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory: Creates an array of unsigned int voxel-buffers of given size.
allocateUnsignedShort(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory: Allocates a new unsigned short voxel-buffers of given size.
allocateUnsignedShortArray(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory: Creates an array of unsigned short voxel-buffers of given size.
AndKernel - Class in org.anchoranalysis.image.voxel.kernel: Combines two BinaryKernels so that they only a true value exists only at a point where both kernels return true.
AndKernel(BinaryKernel, BinaryKernel) - Constructor for class org.anchoranalysis.image.voxel.kernel.AndKernel: Create for the two kernels.
any() - Method in class org.anchoranalysis.image.voxel.VoxelsUntyped: Exposes without any specific buffer type.
anyExists() - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
anyExists() - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
anyExists() - Method in interface org.anchoranalysis.image.voxel.extracter.predicate.VoxelsPredicate: Does at least one value satisfy the predicate - across all voxels?
anyMatch(Predicate<ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Does the predicate evaluate to true on any object in the collection?
anyPredicateMatch(Voxels<T>, Predicate<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Tries to apply a predicate to all the remaining buffer locations, returning true if the predicate matches.
apply(BinaryKernel, BinaryVoxels<UnsignedByteBuffer>, KernelApplicationParameters) - Static method in class org.anchoranalysis.image.voxel.kernel.ApplyKernel: Apply the kernel to BinaryVoxels<UnsignedByteBuffer> using the same binary-values as voxels to calculate a value for each voxel.
applyForCount(BinaryKernel, BinaryVoxels<UnsignedByteBuffer>, KernelApplicationParameters) - Static method in class org.anchoranalysis.image.voxel.kernel.ApplyKernel: Applies a BinaryKernel to voxels and counts how many true values occur en aggregate.
applyForCount(CountKernel, BinaryVoxels<UnsignedByteBuffer>, KernelApplicationParameters) - Static method in class org.anchoranalysis.image.voxel.kernel.ApplyKernel: Applies the kernel to voxels and sums the returned value.
applyForCount(CountKernel, BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters) - Static method in class org.anchoranalysis.image.voxel.kernel.ApplyKernel: Applies the kernel to voxels and sums the returned value.
ApplyKernel - Class in org.anchoranalysis.image.voxel.kernel: Applies various kinds of Kernel to BinaryVoxels.
applyUntilPositive(CountKernel, BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters) - Static method in class org.anchoranalysis.image.voxel.kernel.ApplyKernel: Applies the kernel to voxels until a positive value is returned, then exits with true.
arithmetic() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Interface that allows manipulation of voxel intensities via arithmetic operations.
arithmetic() - Method in class org.anchoranalysis.image.voxel.Voxels: Interface that allows manipulation of voxel intensities via arithmetic operations.
arithmetic() - Method in class org.anchoranalysis.image.voxel.VoxelsUntyped: Interface that allows manipulation of voxel intensities via arithmetic operations.
array() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: The array of the buffer ala ByteBuffer.array().
array() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: The array of the buffer ala IntBuffer.array().
array() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: The array of the buffer ala ShortBuffer.array().
as(boolean) - Static method in enum org.anchoranalysis.image.voxel.kernel.OutsideKernelPolicy: Multiplexes between OutsideKernelPolicy.AS_ON and OutsideKernelPolicy.AS_OFF.
AS_OFF - org.anchoranalysis.image.voxel.kernel.OutsideKernelPolicy: Pretend any parts of the neighborhood that lie outside the scene are being off-valued.
AS_ON - org.anchoranalysis.image.voxel.kernel.OutsideKernelPolicy: Pretend any parts of the neighborhood that lie outside the scene are being on-valued.
asByte() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesInt: Derives a BinaryValuesByte representation from the current values.
asByte() - Method in class org.anchoranalysis.image.voxel.VoxelsUntyped: Casts to use a UnsignedByteBuffer if the voxels contain this data-type, otherwise throws a IncorrectVoxelTypeException.
asFloat() - Method in class org.anchoranalysis.image.voxel.VoxelsUntyped: Casts to use a FloatBuffer if the voxels contain this data-type, otherwise throws a IncorrectVoxelTypeException.
asGraph() - Method in class org.anchoranalysis.image.voxel.object.IntersectingObjects: Constructs a graph where each vertex is an element and an edge exists between any elements that intersect.
asInt() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte: Derives a BinaryValuesInt representation from the current values.
asInt() - Method in class org.anchoranalysis.image.voxel.VoxelsUntyped: Casts to use a UnsignedIntBuffer if the voxels contain this data-type, otherwise throws a IncorrectVoxelTypeException.
asList() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: Exposes the underlying objects as a ArrayList.
asShort() - Method in class org.anchoranalysis.image.voxel.VoxelsUntyped: Casts to use a UnsignedShortBuffer if the voxels contain this data-type, otherwise throws a IncorrectVoxelTypeException.
assignEachMatchingPoint(Voxels<?>, IntPredicate, int) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Assigns a value to any voxel whose intensity matches a predicate, reading and writing the buffer as an int.
assignOff() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: Creates an assigner that may set the off state in subsequently specified regions of the voxels.
assignOff() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Assigns the off value to voxels, expecting global coordinates.
assignOn() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: Creates an assigner that may set the on state in subsequently specified regions of the voxels.
assignOn() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Assigns the on value to voxels, expecting global coordinates.
assignValue(int) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Assigns a value to a bounded-voxels accepting global coordinates for objects, boxes etc.
assignValue(int) - Method in class org.anchoranalysis.image.voxel.Voxels: Interface that allows assignment of a particular value to all or subsets of the voxels.
assignValue(int) - Method in class org.anchoranalysis.image.voxel.VoxelsFloat
assignValue(int) - Method in class org.anchoranalysis.image.voxel.VoxelsUnsignedByte
assignValue(int) - Method in class org.anchoranalysis.image.voxel.VoxelsUnsignedInt
assignValue(int) - Method in class org.anchoranalysis.image.voxel.VoxelsUnsignedShort
assignValue(int) - Method in class org.anchoranalysis.image.voxel.VoxelsUntyped: Interface that allows assignment of a particular value to all or subsets of the voxels.
atCorner(ReadableTuple3i, VoxelsExtracter<T>) - Static method in class org.anchoranalysis.image.voxel.extracter.VoxelsExtracterFactory: Projects a VoxelsExtracter to a corner in a larger global space.

B

BinaryKernel - Class in org.anchoranalysis.image.voxel.kernel: Base class for kernels that return a boolean for every voxel.
BinaryKernel(int) - Constructor for class org.anchoranalysis.image.voxel.kernel.BinaryKernel: Creates with a specific kernel-size.
BinaryKernelMorphological - Class in org.anchoranalysis.image.voxel.kernel.morphological: A parent class for any BinaryKernel that implements a morphological operation.
BinaryKernelMorphological(boolean, boolean, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.morphological.BinaryKernelMorphological: Creates with a flag for big-neighborhood, and boolean outcomes for certain cases.
BinaryOnOffSetter - Interface in org.anchoranalysis.image.voxel.binary: Getters and setters for reading and assigning binary state to voxels.
binaryOperation(Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, IntBinaryOperator) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: 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>.
binaryResizer(int) - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizerFactory: A VoxelsResizer that is suitable for resizing a binary raster-image, restricted to two possible intensity values only.
binaryValues() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: Which two intensity values represent off and on states.
binaryValues() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: What values constitute an on and off state in voxels - as ints.
binaryValuesByte() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: What values constitute an on and off state in voxels - as bytes.
BinaryValuesByte - Class in org.anchoranalysis.image.voxel.binary.values: Two values representing byte binary states in an UnsignedByteBuffer.
BinaryValuesByte(byte, byte) - Constructor for class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
BinaryValuesByte(int, int) - Constructor for class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte: Create with int values for off and on states.
BinaryValuesInt - Class in org.anchoranalysis.image.voxel.binary.values: Two values representing int binary states in an unsigned-byte buffer.
BinaryValuesInt(int, int) - Constructor for class org.anchoranalysis.image.voxel.binary.values.BinaryValuesInt
binaryVoxels() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: The underlying voxel memory buffers for the object-mask, exposed via a BinaryVoxels.
BinaryVoxels<T> - Class in org.anchoranalysis.image.voxel.binary: Like Voxels but should only contain two distinct intensity-values representing on and off.
BinaryVoxels(Voxels<T>, BinaryValuesInt) - Constructor for class org.anchoranalysis.image.voxel.binary.BinaryVoxels
BinaryVoxelsFactory - Class in org.anchoranalysis.image.voxel.binary: Creates BinaryVoxels parameterized by size and initial state.
binaryVoxelsFor(Voxels<T>, BinaryValuesInt) - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: Creates a BinaryVoxels corresponding to a particular voxels and BinaryValuesInt.
BIT_DEPTH - Static variable in class org.anchoranalysis.image.voxel.datatype.FloatVoxelType: How many bits to represent this voxel-type.
BIT_DEPTH - Static variable in class org.anchoranalysis.image.voxel.datatype.SignedShortVoxelType: How many bits to represent this voxel-type.
BIT_DEPTH - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedByteVoxelType: How many bits to represent this voxel-type.
BIT_DEPTH - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedIntVoxelType: How many bits to represent this voxel-type.
BIT_DEPTH - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedShortVoxelType: How many bits to represent this voxel-type.
bitDepth() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType: The number of bits required to represent a voxel.
boundedVoxels() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: The underlying voxel memory buffers for the object-mask, exposed via BoundedVoxels.
BoundedVoxels<T> - Class in org.anchoranalysis.image.voxel: Voxels that exist within a particular bounding-box in an image.
BoundedVoxels(BoundedVoxels<T>) - Constructor for class org.anchoranalysis.image.voxel.BoundedVoxels: Copy constructor.
BoundedVoxels(Voxels<T>) - Constructor for class org.anchoranalysis.image.voxel.BoundedVoxels: Creates voxels bounded to match the entire voxel-data at the origin.
BoundedVoxels(BoundingBox, Voxels<T>) - Constructor for class org.anchoranalysis.image.voxel.BoundedVoxels: Creates voxels with a corresponding bounding box.
boundingBox() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: A bounding-box that associates voxels to a particular part of an image.
boundingBox() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: The bounding-box which gives a location for the object-mask on an image.
boxCopyTo(BoundingBox, Voxels<T>, BoundingBox) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: Copies a bounding-box area to another Voxels.
buffer() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: The associated buffer for storing the voxels.
buffer() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferUnsigned
BufferedImageFromVoxels - Class in org.anchoranalysis.image.voxel.convert.bufferedimage: Converts a Voxels instance into an AWT BufferedImage.
bufferRelative(int) - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer: Returns the corresponding buffer at a relative z-slice index to the current focused z-slice.
BufferRetriever - Interface in org.anchoranalysis.image.voxel.kernel: Retrieves a buffer corresponding to a relative index in the z-dimension.

C

calculateAt(KernelPointCursor) - Method in class org.anchoranalysis.image.voxel.kernel.AndKernel
calculateAt(KernelPointCursor) - Method in class org.anchoranalysis.image.voxel.kernel.BinaryKernel: Calculates the boolean at a particular point.
calculateAt(KernelPointCursor) - Method in class org.anchoranalysis.image.voxel.kernel.ConditionalKernel
calculateAt(KernelPointCursor) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernel: Calculates the count at a particular point.
calculateAt(KernelPointCursor) - Method in class org.anchoranalysis.image.voxel.kernel.morphological.BinaryKernelMorphological
callEachPointInNeighborhood(Point3i, Neighborhood, boolean, ProcessVoxelNeighbor<T>, int, int) - Static method in class org.anchoranalysis.image.voxel.iterator.neighbor.IterateVoxelsNeighbors: Iterate over each point in the neighborhood of an existing point.
canEqual(Object) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
canEqual(Object) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt
canEqual(Object) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
canEqual(Object) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
canEqual(Object) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
canValueRangeChange() - Method in class org.anchoranalysis.image.voxel.resizer.Lanczos
canValueRangeChange() - Method in class org.anchoranalysis.image.voxel.resizer.Linear
canValueRangeChange() - Method in class org.anchoranalysis.image.voxel.resizer.NearestNeighbor
canValueRangeChange() - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizer: Returns true if it's possible for values to be created after interpolation that aren't found in the input-image.
canValueRangeChange() - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizerExecutionTime
canValueRangeChange() - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizerNone
capacity() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: The capacity of the buffer ala Buffer.capacity.
capacity() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: The capacity (i.e.
capacity() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferUnsigned
centerOfGravity() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Calculates center-of-gravity across all axes.
centerOfGravity(Axis) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Calculates center-of-gravity for one specific axis only.
changedOffset(int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer: Calculates the offset in the buffer for a voxel, indicated by its relative-change in position.
changeIntensity(Voxels<?>, IntUnaryOperator) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Changes each voxel, reading and writing the buffer as an int.
checkExtentMatch(BoundingBox, BoundingBox) - Static method in class org.anchoranalysis.image.voxel.ExtentMatchHelper: Checks that the Extents of two bounding boxes are identical.
checkIdenticalDataType(VoxelDataType) - Method in class org.anchoranalysis.image.voxel.VoxelsUntyped: Do the voxels have a data-type that is equal to match?
checkIfConnected() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Determines if an object-mask is connected.
clampTo(Extent) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Makes sure an object fits inside an extent, removing any parts which do not.
clear() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: Clears the buffer ala Buffer.clear().
collectResult() - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessChangedPointAbsoluteMasked: Collects the result of the operation after processing neighbor voxels.
collectResult() - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighbor: Collects the result of the operation after processing neighbor pixels.
collectResult() - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsolute: Collects the result of the operation after processing neighbor voxels.
combineTypes(VoxelDataType, VoxelDataType) - Static method in class org.anchoranalysis.image.voxel.datatype.CombineTypes: What data-type to use to represent voxels of both type1 and type2?
CombineTypes - Class in org.anchoranalysis.image.voxel.datatype: Calculates which VoxelDataType to use when combining two other voxel-data types, but without losing precision.
commonType(Stream<VoxelDataType>) - Static method in class org.anchoranalysis.image.voxel.datatype.FindCommonVoxelType: Finds a common type to represent (ideally without loss of precision} of a stream of types.
commonType(VoxelDataType, VoxelDataType) - Static method in class org.anchoranalysis.image.voxel.datatype.FindCommonVoxelType: Finds a common type to represent (ideally without loss of precision} both first and second.
completeProjection() - Method in interface org.anchoranalysis.image.voxel.buffer.ProjectableBuffer: Performs any final operation before turning the projected buffer.
ConditionalKernel - Class in org.anchoranalysis.image.voxel.kernel: Executes another BinaryKernel iff a predicate is satisfied for a particular point.
ConditionalKernel(BinaryKernel, Predicate<Point3i>) - Constructor for class org.anchoranalysis.image.voxel.kernel.ConditionalKernel: Creates with a particular delegate BinaryKernel and a predicate that tests each point.
contains(Point3i) - Method in class org.anchoranalysis.image.voxel.object.IntersectingObjects: All elements that contain a particular point.
contains(Point3i) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Whether a particular point exists within the object-mask?
convert(VoxelsUntyped, VoxelsFactoryTypeBound<T>) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverterMulti: Converts a Voxels to another type.
convertFloat(FloatBuffer, FloatBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToFloatNoScaling
convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedByteNoScaling
convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedByteScaleByMaxValue
convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedByteScaleByMinMaxValue
convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedByteScaleByType: Converts the current position in a FloatBuffer to the current position in a UnsignedShortBuffer.
convertFloat(FloatBuffer, UnsignedIntBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedInt
convertFloat(FloatBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedShortNoScaling
convertFloat(FloatBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedShortScaleByType: Converts the current position in a FloatBuffer to the current position in a UnsignedShortBuffer.
convertFloat(FloatBuffer, T) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter: Copies a value from the current position in a FloatBuffer to the current position in a buffer of type T.
convertFrom(VoxelsUntyped, VoxelsFactoryTypeBound<T>) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter: Creates a new voxels of type T and copies the voxels from from.
ConvertToImg - Class in org.anchoranalysis.image.voxel.convert.imglib2: Converts the Voxels and VoxelBuffer data-types used in Anchor to the Img used in ImgLib2.
ConvertToNativeImg - Class in org.anchoranalysis.image.voxel.convert.imglib2: Converts the Voxels and VoxelBuffer data-types used in Anchor to the NativeImg used in ImgLib2.
convertUnsignedByte(UnsignedByteBuffer, FloatBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToFloatNoScaling
convertUnsignedByte(UnsignedByteBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedByte
convertUnsignedByte(UnsignedByteBuffer, UnsignedIntBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedInt
convertUnsignedByte(UnsignedByteBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedShortNoScaling
convertUnsignedByte(UnsignedByteBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedShortScaleByType
convertUnsignedByte(UnsignedByteBuffer, T) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter: Copies a value from the current position in a UnsignedByteBuffer to the current position in a buffer of type T.
convertUnsignedInt(UnsignedIntBuffer, FloatBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToFloatNoScaling
convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedByteNoScaling
convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedByteScaleByMaxValue
convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedByteScaleByMinMaxValue
convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedByteScaleByType
convertUnsignedInt(UnsignedIntBuffer, UnsignedIntBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedInt
convertUnsignedInt(UnsignedIntBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedShortNoScaling
convertUnsignedInt(UnsignedIntBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedShortScaleByType
convertUnsignedInt(UnsignedIntBuffer, T) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter: Copies a value from the current position in a UnsignedIntBuffer to the current position in a buffer of type T.
convertUnsignedShort(UnsignedShortBuffer, FloatBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToFloatNoScaling
convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedByteNoScaling
convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedByteScaleByMaxValue
convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedByteScaleByMinMaxValue
convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedByteScaleByType
convertUnsignedShort(UnsignedShortBuffer, UnsignedIntBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedInt
convertUnsignedShort(UnsignedShortBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedShortNoScaling
convertUnsignedShort(UnsignedShortBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedShortScaleByType
convertUnsignedShort(UnsignedShortBuffer, T) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter: Copies a value from the current position in a UnsignedShortBuffer to the current position in a buffer of type T.
copyFrom(VoxelsUntyped, Voxels<T>) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter: Copies voxels from a source (of any type) to voxels of type T.
copyFromFloat(Voxels<FloatBuffer>, Voxels<T>) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter: Copies voxels from a source of type @{link FloatBuffer} to voxels of type T.
copyFromUnsignedByte(Voxels<UnsignedByteBuffer>, Voxels<T>) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter: Copies voxels from a source of type @{link UnsignedByteBuffer} to voxels of type T.
copyFromUnsignedInt(Voxels<UnsignedIntBuffer>, Voxels<T>) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter: Copies voxels from a source of type @{link UnsignedIntBuffer} to voxels of type T.
copyFromUnsignedShort(Voxels<UnsignedShortBuffer>, Voxels<T>) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter: Copies voxels from a source of type @{link UnsignedShortBuffer} to voxels of type T.
copyVoxelFrom(int, VoxelBuffer<T>, int) - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: Copies one particular intensity-value from another VoxelBuffer into this buffer.
copyVoxelsTo(ObjectMask, VoxelsUntyped, BoundingBox) - Method in class org.anchoranalysis.image.voxel.VoxelsUntyped: Copies the voxels into a destination, but only those voxels inside an ObjectMask.
copyVoxelsTo(BoundingBox, VoxelsUntyped, BoundingBox) - Method in class org.anchoranalysis.image.voxel.VoxelsUntyped: Copies the voxels into a destination, but only those voxels inside a bounding-box.
cornerMin() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: The minimum corner of the bounding box in each dimension.
count() - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
count() - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
count() - Method in interface org.anchoranalysis.image.voxel.extracter.predicate.VoxelsPredicate: Counts the number of values satisfying the predicate - across all voxels.
countByte(BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, PredicateTwoBytes) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.CountVoxelsIntersectingBounded: Counts all voxels in the intersection of two bounded-voxels of type BoundedVoxels that match a predicate.
countByteMasked(Voxels<UnsignedByteBuffer>, byte, BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, PredicateTwoBytes) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.CountVoxelsIntersectingBounded: Counts all voxels intersection of two bounded-voxels of type BoundedVoxels but only voxels that lie on an object-mask and match a predicate.
countForObject(ObjectMask) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
countForObject(ObjectMask) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
countForObject(ObjectMask) - Method in interface org.anchoranalysis.image.voxel.extracter.predicate.VoxelsPredicate: Counts the number of values satisfying the predicate - but restricted to voxels corresponding to on in an object-mask.
countIntersectingVoxels(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Counts the number of intersecting-voxels between two object-masks.
countIntersectingVoxels(ObjectMask, ObjectMask) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.CountVoxelsIntersectingObjects: Counts the number of intersecting-voxels between two object-masks.
CountKernel - Class in org.anchoranalysis.image.voxel.kernel.count: Base class for kernels that return a count (positive integer) for every voxel.
CountKernel() - Constructor for class org.anchoranalysis.image.voxel.kernel.count.CountKernel: Creates with a kernel-size of three.
CountKernelNeighborhood - Class in org.anchoranalysis.image.voxel.kernel.count: For every voxel on the outline, count all neighbors that are adjacent.
CountKernelNeighborhood() - Constructor for class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhood
CountKernelNeighborhoodMask - Class in org.anchoranalysis.image.voxel.kernel.count: The number of touching-faces of a voxel with a neighbor, so long as the neighbor is part of an ObjectMask.
CountKernelNeighborhoodMask(ObjectMask) - Constructor for class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodMask: Create with object-mask.
countOff() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: Counts the number of voxels with an off state.
countOn() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: Counts the number of voxels with an on state.
countThreshold(RelationToThreshold) - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics: Counts the number of voxels that exist, relative to a threshold.
countThreshold(RelationToThreshold) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
countThreshold(RelationToThreshold) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
CountVoxelsIntersectingBounded - Class in org.anchoranalysis.image.voxel.iterator.intersecting: Like IterateVoxelsBoundingBox but counts voxels matching a predicate rather than iterating.
CountVoxelsIntersectingObjects - Class in org.anchoranalysis.image.voxel.iterator.intersecting: Like CountVoxelsIntersectingBounded but specifically counts areas of intersection between two ObjectMasks.
create(List<V>, Function<V, ObjectMask>, Extent, boolean, boolean) - Static method in class org.anchoranalysis.image.voxel.neighborhood.NeighborGraph: Like NeighborGraph.create(ObjectCollection, Extent, boolean, boolean) but extracts objects from a list of elements which form the vertices.
create(SliceBufferIndex<T>) - Method in interface org.anchoranalysis.image.voxel.factory.VoxelsFactoryTypeBound: Create a new Voxels that has been initialized with buffers from SliceBufferIndex.
create(VoxelDataType, Extent) - Static method in class org.anchoranalysis.image.voxel.projection.extrema.MaxIntensityProjection: Creates a buffer for a maximum-intensity projection for unsigned byte voxels.
create(VoxelDataType, Extent) - Static method in class org.anchoranalysis.image.voxel.projection.extrema.MinIntensityProjection: Creates a buffer for a minimum-intensity projection for unsigned byte voxels.
create(VoxelDataType, Extent) - Static method in class org.anchoranalysis.image.voxel.projection.MeanIntensityProjection: Creates a buffer for a mean-intensity projection for unsigned byte voxels.
create(VoxelDataType, Extent) - Static method in class org.anchoranalysis.image.voxel.projection.StandardDeviationIntensityProjection: Creates a buffer for a standard-deviation projection for unsigned byte voxels.
create(ObjectCollection) - Static method in class org.anchoranalysis.image.voxel.object.IntersectingObjects: Creates from an ObjectCollection.
create(ObjectCollection, Extent, boolean, boolean) - Static method in class org.anchoranalysis.image.voxel.neighborhood.NeighborGraph: Create the graph with object-masks as vertices, where edges represent the number of neighboring voxels between objects.
createBounded(BoundingBox) - Method in interface org.anchoranalysis.image.voxel.factory.VoxelsFactoryTypeBound: Creates and initializes voxels that correspond to a particular bounding-box region.
createEmpty(Extent, VoxelDataType) - Method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory: Creates empty voxels to match a particular size.
createEmptyOff(Extent) - Static method in class org.anchoranalysis.image.voxel.binary.BinaryVoxelsFactory: Creates binary-voxels using unsigned 8-bit byte type and with all voxels set to off (0).
createEmptyOff(Extent, VoxelDataType) - Static method in class org.anchoranalysis.image.voxel.binary.BinaryVoxelsFactory: Creates an empty binary-voxels of a particular data-type with all voxels initialized to off.
createEmptyOn(Extent) - Static method in class org.anchoranalysis.image.voxel.binary.BinaryVoxelsFactory: Creates binary-voxels using unsigned 8-bit byte type and with all voxels set to on (255).
createFloat(Voxels<FloatBuffer>) - Static method in class org.anchoranalysis.image.voxel.extracter.VoxelsExtracterFactory: Create voxels-extracter for FloatBuffer.
createFloat(Voxels<FloatBuffer>, int) - Static method in class org.anchoranalysis.image.voxel.assigner.VoxelsAssignerFactory: Create a VoxelsAssigner for a FloatBuffer.
createFloat(Extent) - Static method in class org.anchoranalysis.image.voxel.projection.extrema.MaxIntensityProjection: Creates a buffer for a maximum-intensity projection for float voxels.
createFloat(Extent) - Static method in class org.anchoranalysis.image.voxel.projection.extrema.MinIntensityProjection: Creates a buffer for a minimum-intensity projection for float voxels.
createFloat(Extent) - Static method in class org.anchoranalysis.image.voxel.projection.MeanIntensityProjection: Creates a buffer for a mean-intensity projection for float voxels.
createFloat(Extent) - Static method in class org.anchoranalysis.image.voxel.projection.StandardDeviationIntensityProjection: Creates a buffer for a standard-deviation projection for float voxels.
createFloat(Extent, IntFunction<FloatBuffer>) - Static method in class org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmeticFactory: Create a VoxelsArithmetic for FloatBuffer.
createForVoxelBuffer(VoxelBuffer<T>, Extent) - Method in interface org.anchoranalysis.image.voxel.factory.VoxelsFactoryTypeBound: Create a new Voxels that has been initialized with a single-slice's memory buffers.
createFrom(SliceBufferIndex<T>, VoxelDataType) - Method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory: Creates voxels from a particular SliceBufferIndex with specified type.
createFrom(VoxelBuffer<?>) - Static method in class org.anchoranalysis.image.voxel.statistics.HistogramFactory: Creates a Histogram of the aggregated voxel intensities in a VoxelBuffer.
createFrom(VoxelsUntyped) - Static method in class org.anchoranalysis.image.voxel.statistics.HistogramFactory: Creates a Histogram of the aggregated voxel intensities in a VoxelsUntyped.
createGrayscaleByte(Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.bufferedimage.BufferedImageFromVoxels: Creates a BufferedImage from a Voxels<UnsignedByteBuffer>.
createGrayscaleShort(Voxels<UnsignedShortBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.bufferedimage.BufferedImageFromVoxels: Creates a BufferedImage from a Voxels<UnsignedShortBuffer>.
createInitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.buffer.slice.FromByte: Create a buffer of a particular size, that has been initialized.
createInitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.buffer.slice.FromFloat: Create a buffer of a particular size, that has been initialized.
createInitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.buffer.slice.FromInt: Create a buffer of a particular size, that has been initialized.
createInitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.buffer.slice.FromShort: Create a buffer of a particular size, that has been initialized.
createInitialized(Extent) - Method in interface org.anchoranalysis.image.voxel.factory.VoxelsFactoryTypeBound: Create a new Voxels that has been initialized with memory buffers.
createInverted() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesInt: Inverts the values so off becomes on, and vice-versa.
createKernel() - Method in class org.anchoranalysis.image.voxel.kernel.morphological.DilationContext: Creates a kernel for performing the dilation.
createSubset(Collection<Integer>) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: A subset of the collection identified by particular indices.
createUninitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.buffer.slice.FromByte: Create a buffer of a particular size, that has not been initialized.
createUninitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.buffer.slice.FromFloat: Create a buffer of a particular size, that has not been initialized.
createUninitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.buffer.slice.FromInt: Create a buffer of a particular size, that has not been initialized.
createUninitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.buffer.slice.FromShort: Create a buffer of a particular size, that has not been initialized.
createUninitialized(Extent) - Method in interface org.anchoranalysis.image.voxel.factory.VoxelsFactoryTypeBound: Create a new Voxels that has not yet been initialized with memory buffers.
createUnsignedByte(BinaryVoxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.binary.connected.ObjectsFromConnectedComponentsFactory: Finds the connected-components in unsigned byte voxels.
createUnsignedByte(Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.extracter.VoxelsExtracterFactory: Create voxels-extracter for UnsignedByteBuffer.
createUnsignedByte(Voxels<UnsignedByteBuffer>, int) - Static method in class org.anchoranalysis.image.voxel.assigner.VoxelsAssignerFactory: Create a VoxelsAssigner for a UnsignedByteBuffer.
createUnsignedByte(Extent) - Static method in class org.anchoranalysis.image.voxel.projection.extrema.MaxIntensityProjection: Creates a buffer for a maximum-intensity projection for unsigned byte voxels.
createUnsignedByte(Extent) - Static method in class org.anchoranalysis.image.voxel.projection.extrema.MinIntensityProjection: Creates a buffer for a minimum-intensity projection for unsigned byte voxels.
createUnsignedByte(Extent) - Static method in class org.anchoranalysis.image.voxel.projection.MeanIntensityProjection: Creates a buffer for a mean-intensity projection for unsigned byte voxels.
createUnsignedByte(Extent) - Static method in class org.anchoranalysis.image.voxel.projection.StandardDeviationIntensityProjection: Creates a buffer for a standard-deviation projection for unsigned byte voxels.
createUnsignedByte(Extent, IntFunction<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmeticFactory: Create a VoxelsArithmetic for UnsignedByteBuffer.
createUnsignedInt(BinaryVoxels<UnsignedIntBuffer>) - Method in class org.anchoranalysis.image.voxel.binary.connected.ObjectsFromConnectedComponentsFactory: Finds the connected-components in unsigned int voxels.
createUnsignedInt(Voxels<UnsignedIntBuffer>) - Static method in class org.anchoranalysis.image.voxel.extracter.VoxelsExtracterFactory: Create voxels-extracter for UnsignedIntBuffer.
createUnsignedInt(Voxels<UnsignedIntBuffer>, int) - Static method in class org.anchoranalysis.image.voxel.assigner.VoxelsAssignerFactory: Create a a VoxelsAssigner for a UnsignedIntBuffer.
createUnsignedInt(Extent) - Static method in class org.anchoranalysis.image.voxel.projection.extrema.MaxIntensityProjection: Creates a buffer for a maximum-intensity projection for unsigned int voxels.
createUnsignedInt(Extent) - Static method in class org.anchoranalysis.image.voxel.projection.extrema.MinIntensityProjection: Creates a buffer for a minimum-intensity projection for unsigned int voxels.
createUnsignedInt(Extent) - Static method in class org.anchoranalysis.image.voxel.projection.MeanIntensityProjection: Creates a buffer for a mean-intensity projection for unsigned int voxels.
createUnsignedInt(Extent) - Static method in class org.anchoranalysis.image.voxel.projection.StandardDeviationIntensityProjection: Creates a buffer for a standard-deviation projection for unsigned int voxels.
createUnsignedInt(Extent, IntFunction<UnsignedIntBuffer>) - Static method in class org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmeticFactory: Create a VoxelsArithmetic for UnsignedIntBuffer.
createUnsignedShort(Voxels<UnsignedShortBuffer>) - Static method in class org.anchoranalysis.image.voxel.extracter.VoxelsExtracterFactory: Create voxels-extracter for UnsignedShortBuffer.
createUnsignedShort(Voxels<UnsignedShortBuffer>, int) - Static method in class org.anchoranalysis.image.voxel.assigner.VoxelsAssignerFactory: Create a VoxelsAssigner for a UnsignedShortBuffer.
createUnsignedShort(Extent) - Static method in class org.anchoranalysis.image.voxel.projection.extrema.MaxIntensityProjection: Creates a buffer for a maximum-intensity projection for unsigned short voxels.
createUnsignedShort(Extent) - Static method in class org.anchoranalysis.image.voxel.projection.extrema.MinIntensityProjection: Creates a buffer for a minimum-intensity projection for unsigned short voxels.
createUnsignedShort(Extent) - Static method in class org.anchoranalysis.image.voxel.projection.MeanIntensityProjection: Creates a buffer for a mean-intensity projection for unsigned short voxels.
createUnsignedShort(Extent) - Static method in class org.anchoranalysis.image.voxel.projection.StandardDeviationIntensityProjection: Creates a buffer for a standard-deviation projection for unsigned short voxels.
createUnsignedShort(Extent, IntFunction<UnsignedShortBuffer>) - Static method in class org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmeticFactory: Create a VoxelsArithmetic for UnsignedShortBuffer.

D

dataType() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: Data-type of each voxel in the buffer.
dataType() - Method in interface org.anchoranalysis.image.voxel.factory.VoxelsFactoryTypeBound: The data-type of the voxels, as created by this factory.
dataType() - Method in class org.anchoranalysis.image.voxel.Voxels: The underlying data-type of the voxels, represented by a VoxelDataType instance.
decrementX() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Decrements the point and associated index by one in the X dimension.
decrementY() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Decrements the point and associated index by one in the Y dimension.
decrementYTwice() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Decrements the point and associated index by two in the Y dimension.
decrementZ() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Decrements the point by one in the Z dimension.
deriveObject() - Method in class org.anchoranalysis.image.voxel.object.DeriveObjectFromPoints: Derives an ObjectMask that includes all points that were previously added.
deriveObject(BoundingBox) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
deriveObject(BoundingBox) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
deriveObject(BoundingBox) - Method in interface org.anchoranalysis.image.voxel.extracter.predicate.VoxelsPredicate: Creates an ObjectMask for all the voxels inside the bounding-box satisfying the predicate.
DeriveObjectFromPoints - Class in org.anchoranalysis.image.voxel.object: Derive an ObjectMask by incrementally adding points.
DeriveObjectFromPoints() - Constructor for class org.anchoranalysis.image.voxel.object.DeriveObjectFromPoints
deriveObjectTight() - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
deriveObjectTight() - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
deriveObjectTight() - Method in interface org.anchoranalysis.image.voxel.extracter.predicate.VoxelsPredicate: Creates an ObjectMask for all the voxels satisfying the predicate, minimally fitting the bounding-box to the on voxels only.
derivePointsLocal() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Creates a list of all on voxels as points, using local coordinates i.e.
deriveUnsignedBytePredicate() - Method in interface org.anchoranalysis.image.voxel.iterator.predicate.PredicateTwoBytes: Derives a predicate with a different interface for operating on UnsignedByteBuffer.
deriveUnsignedByteProcessor() - Method in interface org.anchoranalysis.image.voxel.iterator.predicate.PredicateTwoBytes: Derives a processor with a different interface for operating on UnsignedByteBuffer.
dilate(boolean, Optional<Extent>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Grow bounding-box by 1 pixel in all directions.
dilate(BinaryVoxels<UnsignedByteBuffer>, int, DilationContext) - Static method in class org.anchoranalysis.image.voxel.object.morphological.MorphologicalDilation: Performs a morphological dilation operation.
dilate(ObjectMask, Optional<Extent>, boolean, int, boolean) - Static method in class org.anchoranalysis.image.voxel.object.morphological.MorphologicalDilation: Dilates an ObjectMask, growing the bounding-box as necessary.
DilationContext - Class in org.anchoranalysis.image.voxel.kernel.morphological: Additional parameters for influencing a morphologicla dilation opperation.
DilationContext(OutsideKernelPolicy, boolean, boolean, Optional<Predicate<Point3i>>) - Constructor for class org.anchoranalysis.image.voxel.kernel.morphological.DilationContext: Create without a post-condition.
DilationContext(OutsideKernelPolicy, boolean, boolean, Optional<Predicate<Point3i>>, Optional<AcceptIterationPredicate>) - Constructor for class org.anchoranalysis.image.voxel.kernel.morphological.DilationContext: Create with a post-condition.
DilationKernel - Class in org.anchoranalysis.image.voxel.kernel.morphological: Morphological dilation with a 3x3 or 3x3x3 kernel size.
DilationKernel(boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.morphological.DilationKernel: Creates with a type of neighborhood.
divideBy(int) - Method in interface org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmetic: Divides the value of all voxels by a scalar constant.
doesNeighborQualify(boolean, KernelPointCursor, Supplier<UnsignedByteBuffer>, int) - Method in class org.anchoranalysis.image.voxel.kernel.morphological.BinaryKernelMorphological: Does a particular neighboring-point satisfy the conditions.
doesNeighborQualify(boolean, KernelPointCursor, Supplier<UnsignedByteBuffer>, int) - Method in class org.anchoranalysis.image.voxel.kernel.morphological.DilationKernel
doesNeighborQualify(boolean, KernelPointCursor, Supplier<UnsignedByteBuffer>, int) - Method in class org.anchoranalysis.image.voxel.kernel.morphological.ErosionKernel: Checks whether a particular neighbor voxel qualifies to make the current voxel an outline voxel.
doesNeighborQualify(boolean, KernelPointCursor, Supplier<UnsignedByteBuffer>, int) - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernel: Checks whether a particular neighbor voxel qualifies to make the current voxel an outline voxel.
doesNeighborQualify(boolean, KernelPointCursor, Supplier<UnsignedByteBuffer>, int) - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernelNeighborMatchValue: Checks whether a particular neighbor voxel qualifies to make the current voxel an outline voxel.
doesNeighborVoxelQualify(Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernel: Whether a particular neighboring voxel is accepted or not.
doesNeighborVoxelQualify(Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhood
doesNeighborVoxelQualify(Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodMask
duplicate() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: Deep-copy of the object, including duplicating voxel buffers in memory.
duplicate() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: A deep-copy of the current structure.
duplicate() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: Creates a deep copy of the current object, including deep-copying the associated buffer.
duplicate() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: Deep copy, including duplicating ObjectMasks.
duplicate() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Creates a deep-copy of the current object-mask.
duplicate() - Method in class org.anchoranalysis.image.voxel.Voxels: A deep-copy.
duplicateShallow() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: Shallow copy of objects.

E

empty() - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a newly created object-collection that is empty.
equals(Object) - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
equals(Object) - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesInt
equals(Object) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
equals(Object) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt
equals(Object) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
equals(Object) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
equals(Object) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
equals(Object) - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType
equals(Object) - Method in class org.anchoranalysis.image.voxel.iterator.MinMaxRange
equals(Object) - Method in class org.anchoranalysis.image.voxel.kernel.KernelApplicationParameters
equals(Object) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: Checks if two collections are equal in a shallow way.
equalsDeep(BoundedVoxels<?>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Performs a deep equality check, that includes checking that each voxel has an identical value.
equalsDeep(ObjectCollection) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: Checks if two collections are equal in a deeper way.
equalsDeep(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: A deep equality check with another ObjectMask.
equalsDeep(Voxels<?>) - Method in class org.anchoranalysis.image.voxel.Voxels: Are the voxels identical to another voxels (deep equals)?
equalToPrimitive(Voxels<UnsignedByteBuffer>, byte, ScalarThreeDimensionalConsumer) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsEqualTo: Iterates through all points with a specific voxel intensity-value, passing coordinates as primitive types.
equalToPrimitiveSlice(Voxels<UnsignedByteBuffer>, int, byte, ScalarThreeDimensionalConsumer) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsEqualTo: 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.
equalToReusePoint(Voxels<UnsignedByteBuffer>, byte, Consumer<Point3i>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsEqualTo: Iterates all points with a specific voxel intensity-value, reusing the Point3i in each iteration.
erode(BinaryVoxels<UnsignedByteBuffer>, int, boolean, Optional<Predicate<Point3i>>) - Static method in class org.anchoranalysis.image.voxel.object.morphological.MorphologicalErosion: Performs a morphological erosion on a BinaryVoxels<UnsignedByteBuffer> voxels.
erode(ObjectMask, int, boolean) - Static method in class org.anchoranalysis.image.voxel.object.morphological.MorphologicalErosion: Performs a morphological erosion on an ObjectMask.
erode(ObjectMask, int, boolean, Optional<AcceptIterationPredicate>) - Static method in class org.anchoranalysis.image.voxel.object.morphological.MorphologicalErosion: Performs a morphological erosion on an ObjectMask - with a postcondition.
ErosionKernel - Class in org.anchoranalysis.image.voxel.kernel.morphological: Erosion with a 3x3 or 3x3x3 kernel size.
ErosionKernel() - Constructor for class org.anchoranalysis.image.voxel.kernel.morphological.ErosionKernel: Default constructor.
extendWith(int) - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizerImgLib2: Switches to extend constant-value out-of-bounds strategy
extent() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: The size of the voxels across three dimensions.
extent() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: The size of the voxels across three dimensions, and also the size of the associated bounding-box.
extent() - Method in class org.anchoranalysis.image.voxel.buffer.slice.FromByte
extent() - Method in class org.anchoranalysis.image.voxel.buffer.slice.FromFloat
extent() - Method in class org.anchoranalysis.image.voxel.buffer.slice.FromInt
extent() - Method in class org.anchoranalysis.image.voxel.buffer.slice.FromShort
extent() - Method in interface org.anchoranalysis.image.voxel.buffer.slice.SliceBufferIndex: The size of each buffer.
extent() - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer: The size of the voxels across three dimensions.
extent() - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer: The size of the associated SlidingBuffer.
extent() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: The size of the object-mask's bounding-box across three dimensions.
extent() - Method in class org.anchoranalysis.image.voxel.Voxels: The size of the voxels across three dimensions.
extent() - Method in class org.anchoranalysis.image.voxel.VoxelsUntyped: The size of the voxels across three dimensions.
ExtentMatchHelper - Class in org.anchoranalysis.image.voxel: Checks if the Extents of two BoundingBoxes are identical.
extract() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: Interface that allows read/copy/duplication operations to be performed regarding the voxels intensities.
extract() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Extracts value from voxels using global coordinates (relative to the image as a whole).
extract() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Provides methods to read/copy/duplicate regions of voxels.
extract() - Method in class org.anchoranalysis.image.voxel.Voxels: Interface that allows read/copy/duplication operations to be performed regarding the voxels intensities.
extract() - Method in class org.anchoranalysis.image.voxel.VoxelsFloat
extract() - Method in class org.anchoranalysis.image.voxel.VoxelsUnsignedByte
extract() - Method in class org.anchoranalysis.image.voxel.VoxelsUnsignedInt
extract() - Method in class org.anchoranalysis.image.voxel.VoxelsUnsignedShort
extract() - Method in class org.anchoranalysis.image.voxel.VoxelsUntyped: Interface that allows read/copy/duplication operations to be performed regarding the voxels intensities.
extractSlice(int) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Extracts a particular slice.
extractSlice(int, boolean) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Extracts one particular slice as an object-mask

F

factory() - Method in class org.anchoranalysis.image.voxel.Voxels: A factory for creating voxels with a particular buffer-type.
filter(Predicate<ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Filters a ObjectCollection to include certain items based on a predicate
filter(CheckedPredicate<ObjectMask, E>, Class<? extends Exception>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Filters a ObjectCollection to include certain items based on a predicate
filterAndMap(Predicate<ObjectMask>, UnaryOperator<ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Performs a ObjectMaskStream.filter(java.util.function.Predicate<org.anchoranalysis.image.voxel.object.ObjectMask>) and then a ObjectMaskStream.map(org.anchoranalysis.core.functional.checked.CheckedFunction<org.anchoranalysis.image.voxel.object.ObjectMask, org.anchoranalysis.image.voxel.object.ObjectMask, E>).
filterAndMapFrom(Collection<T>, Predicate<T>, Class<? extends E>, CheckedFunction<T, ObjectMask, E>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by filtering an iterable and then mapping it to ObjectMask.
filterAndMapFrom(Collection<T>, Predicate<T>, Function<T, ObjectMask>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by filtering an iterable and then mapping it to ObjectMask.
filterAndMapWithIndexFrom(List<T>, Predicate<T>, Class<? extends E>, CheckedBiFunction<T, Integer, ObjectMask, E>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by filtering a list and then mapping from it to ObjectMask.
filterExclude(Predicate<ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Filters a ObjectCollection to exclude certain items based on a predicate
filterSubset(Predicate<ObjectMask>, Collection<Integer>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Like ObjectMaskStream.filter(java.util.function.Predicate<org.anchoranalysis.image.voxel.object.ObjectMask>) but only operates on certain indices of the collection.
filterSubsetStream(Predicate<ObjectMask>, Collection<Integer>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Like ObjectMaskStream.filterSubset(java.util.function.Predicate<org.anchoranalysis.image.voxel.object.ObjectMask>, java.util.Collection<java.lang.Integer>) but returns a stream rather than a ObjectCollection.
findArbitraryOnVoxel() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Finds any arbitrary on voxel on the object.
FindCommonVoxelType - Class in org.anchoranalysis.image.voxel.datatype: Finds a common voxel-data type to represent two types.
firstCheck(KernelPointCursor, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.kernel.morphological.BinaryKernelMorphological: The first check done on the kernel center-point, before checking any neighbors.
firstCheck(KernelPointCursor, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.kernel.morphological.DilationKernel
firstCheck(KernelPointCursor, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.kernel.morphological.ErosionKernel
firstCheck(KernelPointCursor, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernelBase
flatMap(Class<? extends Exception>, CheckedFunction<ObjectMask, ObjectCollection, E>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Like a typical flatMap() operation but accepts a mapping function that throws a checked exception.
flatMap(Function<ObjectMask, ObjectCollection>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Creates a new ObjectCollection after mapping each item to several others.
flatMapFrom(Collection<T>, Function<T, ObjectCollection>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by flat-mapping an incoming stream to ObjectCollection.
flatMapFrom(Stream<T>, Class<? extends Exception>, CheckedFunction<T, ObjectCollection, E>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by flat-mapping an incoming stream to ObjectCollection and rethrowing any exception during mapping.
flatMapFromCollection(Stream<T>, Class<? extends Exception>, CheckedFunction<T, Stream<? extends ObjectMask>, E>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new ObjectCollection by flatMapping an incoming stream to Collection<ObjectMask> and rethrowing any exception during mapping.
flatMapFromRange(int, int, Class<? extends Exception>, CheckedIntFunction<ObjectCollection, E>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by flat-mapping integers (from a range) each to a ObjectCollection.
flatMapFromRange(int, int, IntFunction<ObjectCollection>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by flat-mapping integers (from a range) each to a ObjectCollection.
flatMapFromStream(Stream<T>, Class<? extends Exception>, CheckedFunction<T, Stream<ObjectMask>, E>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by flat-mapping an incoming stream to ObjectCollection and rethrowing any exception during mapping.
flattenZ() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: A maximum-intensity projection.
floatArray(float[]) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap: Wraps an float-array into a voxel-buffer.
floatBuffer(FloatBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap: Wraps a float buffer into a voxel-buffer.
FloatVoxelType - Class in org.anchoranalysis.image.voxel.datatype: A 32-bit voxel data-type representing floating-point numbers, as per the Java primitive float type.
from(VoxelsUntyped) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg: Converts from a VoxelsUntyped (Anchor structure) to a Img (ImgLib2 structure).
fromByte(VoxelBuffer<UnsignedByteBuffer>, Extent) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg: Creates an Img from a VoxelBuffer with an unsigned byte data-type.
fromByte(Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg: Creates an Img from Voxels with an unsigned byte data-type.
fromByte(Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToNativeImg: Creates an NativeImg from Voxels with an unsigned byte data-type.
FromByte - Class in org.anchoranalysis.image.voxel.buffer.slice: Implementation of SliceBufferIndex with voxels of type unsigned byte.
fromFloat(VoxelBuffer<FloatBuffer>, Extent) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg: Creates an Img from a VoxelBuffer with a float data-type.
fromFloat(Voxels<FloatBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg: Creates an Img from Voxels with a float data-type.
fromFloat(Voxels<FloatBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToNativeImg: Creates an NativeImg from Voxels with a float data-type.
FromFloat - Class in org.anchoranalysis.image.voxel.buffer.slice: Implementation of SliceBufferIndex with voxels of type float.
FromInt - Class in org.anchoranalysis.image.voxel.buffer.slice: Implementation of SliceBufferIndex with voxels of type unsigned int.
fromRepeated(int, Supplier<ObjectMask>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by repeatedly calling a function to create a single ObjectMask.
fromSet(Set<ObjectMask>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection from a set of ObjectMask.
fromShort(VoxelBuffer<UnsignedShortBuffer>, Extent) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg: Creates an Img from a VoxelBuffer with an unsigned short data-type.
fromShort(Voxels<UnsignedShortBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg: Creates an Img from Voxels with an unsigned short data-type.
fromShort(Voxels<UnsignedShortBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToNativeImg: Creates an NativeImg from Voxels with an unsigned short data-type.
FromShort - Class in org.anchoranalysis.image.voxel.buffer.slice: Implementation of SliceBufferIndex with voxels of type unsigned short.
fromSlice(VoxelsUntyped, int) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg: Creates an Img from a single z-slice of a VoxelsUntyped.

G

get(int) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: Get an ObjectMask at a particular position in the collection.
get(VoxelDataType) - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataTypeFactoryMultiplexer: Multiplexes one of the factories according to data-type
getCenter() - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer: The buffer for the currently selected slice.
getDefault() - Static method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte: Default values to use, if not otherwise specified.
getDefault() - Static method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesInt: Default values to use, if not otherwise specified.
getDelegate() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: The underlying storage buffer, to which calls are delegated with our without conversion.
getDelegate() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: The underlying storage buffer, to which calls are delegated with our without conversion.
getDelegate() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: The underlying storage buffer, to which calls are delegated with our without conversion.
getExtent() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: The size of the image the kernel iterates over.
getFirstBinaryValues() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: The BinaryValuesInt associated with the first object in the collection.
getFirstBinaryValuesByte() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: The BinaryValuesByte associated with the first object in the collection.
getFloat() - Static method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory: A factory that creates voxels of type float.
getIndex() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: The index in the buffer that the kernel currently is focussed on.
getInstance() - Static method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizerFactory: Singleton instance of VoxelsResizerFactory.
getInt(int) - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: Gets an element from the buffer at a particular position, converting, if necessary, to an int.
getInt(int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer: Get a value from the buffer at a particular absolute position.
getInt(int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer: Get a value from the buffer at a particular relative position.
getKernelApplication() - Method in class org.anchoranalysis.image.voxel.kernel.morphological.DilationContext: How the kernel is applied to the scene.
getLocal(int) - Method in interface org.anchoranalysis.image.voxel.kernel.BufferRetriever: Get a buffer at a particular index in the z-dimension.
getLocal(int) - Method in class org.anchoranalysis.image.voxel.kernel.LocalSlices
getMax() - Method in class org.anchoranalysis.image.voxel.iterator.MinMaxRange: The maximum value.
getMin() - Method in class org.anchoranalysis.image.voxel.iterator.MinMaxRange: The minimum value.
getMinusOne() - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer: The voxel-buffer for the slice with the currently selected slice's index -1 or null if it's the first slice.
getOff() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte: The byte representation of the value for off.
getOff() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesInt: The integer representation of the value for off.
getOn() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte: The byte representation of the value for on.
getOn() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesInt: The integer representation of the value for on.
getOutsideKernelPolicy() - Method in class org.anchoranalysis.image.voxel.kernel.KernelApplicationParameters: How to handle voxels that appear in a neighborhood that lies outside the scene boundaries.
getPlusOne() - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer: The voxel-buffer for the slice with the currently selected slice's index +1 or null if it's the final slice.
getPoint() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: The point around which the cursor may iterate.
getPostcondition() - Method in class org.anchoranalysis.image.voxel.kernel.morphological.DilationContext: If defined, a condition which must be satisfied after an iteration occurs, otherwise no more iterations occur.
getRaw() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Gets an unsigned-byte (represented as a byte) at the current buffer position.
getRaw() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Gets an unsigned-int (represented as an int) at the current buffer position.
getRaw() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Gets an unsigned-short (represented as a short) at the current buffer position.
getRaw(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Gets an unsigned-byte (represented as a byte) at a particular buffer position.
getRaw(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Gets an unsigned-int (represented as a int) at a particular buffer position.
getRaw(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Gets an unsigned-short (represented as a short) at a particular buffer position.
getSize() - Method in class org.anchoranalysis.image.voxel.kernel.Kernel: The size of the kernel-matrix in one dimension, either X or Y.
getUnsigned() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt: Gets an unsigned-byte (represented as a int) at the current buffer position.
getUnsigned() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
getUnsigned() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Gets an unsigned-int (represented as a long) at the current buffer position.
getUnsigned() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
getUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt: Gets an unsigned-byte (represented as a int) at a particular buffer position.
getUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
getUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Gets an unsigned-int (represented as a long) at a particular buffer position.
getUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
getUnsignedByte() - Static method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory: A factory that creates voxels of type unsigned byte.
getUnsignedInt() - Static method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory: A factory that creates voxels of type unsigned int.
getUnsignedShort() - Static method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory: A factory that creates voxels of type unsigned short.
getVoxelDataType() - Method in class org.anchoranalysis.image.voxel.VoxelsUntyped: The underlying data-type of the voxels, represented by a VoxelDataType instance.
getVoxels() - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer: The voxels from which buffers corresponding to slices are extracted.
growBuffer(Point3i, Point3i, Optional<Extent>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Grows the object-mask's voxel buffers in the positive and negative directions by a certain amount.
growBuffer(Point3i, Point3i, Optional<Extent>, VoxelsFactoryTypeBound<T>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Grows the voxel buffer in the positive and negative directions by a certain amount.
growToZ(int) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Grows a single z-sliced ObjectMask by duplicating the slice across the z-dimension sizeZ number of times.
growToZ(int, VoxelsFactoryTypeBound<T>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Grows a single z-sliced BoundedVoxels by duplicating the slice across the z-dimension sizeZ number of times.

H

hasArray() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: Whether the buffer has an array?
hashCode() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
hashCode() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesInt
hashCode() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
hashCode() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt
hashCode() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
hashCode() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
hashCode() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
hashCode() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType
hashCode() - Method in class org.anchoranalysis.image.voxel.iterator.MinMaxRange
hashCode() - Method in class org.anchoranalysis.image.voxel.kernel.KernelApplicationParameters
hashCode() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
hasIntersectingVoxels(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Determines whether there are any intersecting voxels on two object-masks.
hasIntersectingVoxels(ObjectMask, ObjectMask) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.CountVoxelsIntersectingObjects: Determines whether there are any intersecting voxels on two object-masks.
hasOffVoxel() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: At least one voxel exists with an off value.
hasOnVoxel() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: At least one voxel exists with an on value.
hasRemaining() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: Whether there are elements between the current position and the limit Buffer.hasRemaining().
hasRemaining() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: Are there voxels remaining in a buffer?
hasRemaining() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferUnsigned
higherCountExistsThan(int) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
higherCountExistsThan(int) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
higherCountExistsThan(int) - Method in interface org.anchoranalysis.image.voxel.extracter.predicate.VoxelsPredicate: Whether the count is greater than a particular threshold.
histogram() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics: A Histogram of all voxel values.
histogram() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
histogram() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
HistogramFactory - Class in org.anchoranalysis.image.voxel.statistics: Creates a Histogram to describe the intensity values of voxels in aggregate.

I

IGNORE_OUTSIDE - org.anchoranalysis.image.voxel.kernel.OutsideKernelPolicy: Ignore any parts of the neighborhood that lie outside the scene.
IncorrectVoxelTypeException - Exception in org.anchoranalysis.image.voxel.datatype: When an unexpected VoxelDataType is encountered.
IncorrectVoxelTypeException(String) - Constructor for exception org.anchoranalysis.image.voxel.datatype.IncorrectVoxelTypeException: Create with only a message.
IncorrectVoxelTypeException(Throwable) - Constructor for exception org.anchoranalysis.image.voxel.datatype.IncorrectVoxelTypeException: Create with only a cause.
incrementIndexOnly() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Increments the current index state by one, without changing the current point state.
incrementX() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Increments the point and associated index by one in the X dimension.
incrementXTwice() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Increments the point and associated index by two in the X dimension.
incrementY() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Increments the point and associated index by one in the Y dimension.
incrementYTwice() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Increments the point and associated index by two in the Y dimension.
incrementZ() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Increments the point by one in the Z dimension.
incrementZTwice() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Increments the point by two in the Z dimension.
initSource(int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessChangedPointAbsoluteMasked: The value and offset for the source point (around which we process neighbors).
initSource(int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsolute: The value and offset for the source point (around which we process neighbors).
initSource(int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
initSource(Point3i, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighbor: Specify the source-point (of which all the processed points are neighbors).
instance() - Static method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory: Singleton instance.
INSTANCE - Static variable in class org.anchoranalysis.image.voxel.datatype.FloatVoxelType: A singleton instance of the type.
INSTANCE - Static variable in class org.anchoranalysis.image.voxel.datatype.SignedShortVoxelType: A singleton instance of the type.
INSTANCE - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedByteVoxelType: A singleton instance of the type.
INSTANCE - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedIntVoxelType: A singleton instance of the type.
INSTANCE - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedShortVoxelType: A singleton instance of the type.
intensityMax(Voxels<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Finds the maximum intensity-value (as an int) among all voxels.
intensityMin(Voxels<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Finds the minimum intensity-value (as an int) among all voxels.
intensityMinMax(Voxels<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Finds the maximum intensity-value (as an int) among all voxels.
intersect(ObjectMask, Extent) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Intersects this object-mask with another
IntersectingObjects<T> - Class in org.anchoranalysis.image.voxel.object: A data-structure to efficiently determine which object-masks intersect in a collection.
IntersectingObjects(Collection<T>, Function<T, ObjectMask>) - Constructor for class org.anchoranalysis.image.voxel.object.IntersectingObjects: Creates an r-tree for particular objects, as extracted from elements.
intersectsWith(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.IntersectingObjects: All elements that intersect with a particular object.
intersectsWith(BoundingBox) - Method in class org.anchoranalysis.image.voxel.object.IntersectingObjects: All elements that intersect with a particular bounding box.
intersectsWithStream(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.IntersectingObjects: Like IntersectingObjects.intersectsWith(ObjectMask) but returns the objects as a Stream rather than a Set.
invert() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: Changes the off state to be the on state and vice-versa.
invert() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte: Inverts the values so off becomes on, and vice-versa.
invert() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Produces a new object-mask that uses the same voxel-buffer but switches the off and on mapping.
isBufferOff(UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Is the value at the current index in this buffer corresponding to an off state?
isBufferOn(UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Is the value at the current index in this buffer corresponding to an on state?
isDirect() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: Is this buffer direct or non-direct?
isDirect() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: Is this buffer direct or non-direct?
isDirect() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferUnsigned
isEmpty() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: Whether the collection contains no objects.
isIgnoreOutside() - Method in class org.anchoranalysis.image.voxel.kernel.KernelApplicationParameters: When true, any parts of the neighborhood that lie outside the scene are not considered in kernel neighborhoods.
isIgnoreOutside() - Method in enum org.anchoranalysis.image.voxel.kernel.OutsideKernelPolicy: When true, any parts of the neighborhood that lie outside the scene are not considered in kernel neighborhoods.
isInteger() - Method in class org.anchoranalysis.image.voxel.datatype.FloatVoxelType
isInteger() - Method in class org.anchoranalysis.image.voxel.datatype.SignedVoxelType
isInteger() - Method in class org.anchoranalysis.image.voxel.datatype.UnsignedVoxelType
isInteger() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType: Whether the data-type represents an integer or floating-point?
isOff(byte) - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte: Does a particular value correspond to the off state?
isOff(int, int, int) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter: Does the voxel at this point have an off state?
isOff(Point3i) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter: Does the voxel at this point have an off state?
isOn(byte) - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte: Does a particular value correspond to the on state?
isOn(int, int, int) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter: Does the voxel at this point have an on state?
isOn(Point3i) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter: Does the voxel at this point have an on state?
isOutsideOffUnignored() - Method in class org.anchoranalysis.image.voxel.kernel.KernelApplicationParameters: True only when voxels outside the scene should not be ignored and considered as off.
isOutsideOffUnignored() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: True only when voxels outside the scene should not be ignored and considered as off.
isOutsideOn() - Method in class org.anchoranalysis.image.voxel.kernel.KernelApplicationParameters: In cases where KernelApplicationParameters.isIgnoreOutside() is false, then whether to treat voxels that lie outside the scene as on (if true) or off (if false).
isOutsideOn() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Whether to treat voxels that lie outside the scene as on (if true) or off (if false).
isOutsideOn() - Method in enum org.anchoranalysis.image.voxel.kernel.OutsideKernelPolicy: In cases where OutsideKernelPolicy.isIgnoreOutside() is false, then whether to treat voxels that lie outside the scene as on (if true) or off (if false).
isOutsideOnUnignored() - Method in class org.anchoranalysis.image.voxel.kernel.KernelApplicationParameters: True only when voxels outside the scene should not be ignored and considered as on.
isUnsigned() - Method in class org.anchoranalysis.image.voxel.datatype.FloatVoxelType
isUnsigned() - Method in class org.anchoranalysis.image.voxel.datatype.SignedVoxelType
isUnsigned() - Method in class org.anchoranalysis.image.voxel.datatype.UnsignedVoxelType
isUnsigned() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType: Whether the data-type is unsigned?
isUseZ() - Method in class org.anchoranalysis.image.voxel.kernel.KernelApplicationParameters: Whether to additionally apply the kernel along the Z dimension, as well as X and Y?
isUseZ() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Whether to additionally apply the kernel along the Z dimension, as well as X and Y?
IterateKernelHelper - Class in org.anchoranalysis.image.voxel.iterator.neighbor.kernel: Routines to iterate a Kernel over some or all of the voxels in a BinaryVoxels.
iterateOverSlices(Consumer<VoxelBuffer<T>>) - Method in interface org.anchoranalysis.image.voxel.buffer.slice.SliceBufferIndex: Calls sliceConsumer once for each slice with the respective buffer.
iterateOverSlicesAndOffsets(ProcessVoxelBufferUnary<T>) - Method in interface org.anchoranalysis.image.voxel.buffer.slice.SliceBufferIndex: Calls process for each offset in each slice.
IterateVoxelsAll - Class in org.anchoranalysis.image.voxel.iterator: Utilities for iterating over all voxels in one or more Voxels.
IterateVoxelsBoundingBox - Class in org.anchoranalysis.image.voxel.iterator: Utilities for iterating over the subset of image voxels within a bounding-box.
IterateVoxelsEqualTo - Class in org.anchoranalysis.image.voxel.iterator: Like IterateVoxelsAll but specifically for equal-to operations on Voxels of type UnsignedByteBuffer.
IterateVoxelsIntersectingBounded - Class in org.anchoranalysis.image.voxel.iterator.intersecting: Like IterateVoxelsBoundingBox but specifically for processing areas of intersection between BoundedVoxels of type UnsignedByteBuffer.
IterateVoxelsNeighbors - Class in org.anchoranalysis.image.voxel.iterator.neighbor: Utilities for iterating over the neighboring voxels to a given point.
IterateVoxelsObjectMask - Class in org.anchoranalysis.image.voxel.iterator: Utilities for iterating over the subset of voxels corresponding to an on state in an ObjectMask.
IterateVoxelsObjectMaskOptional - Class in org.anchoranalysis.image.voxel.iterator: Utilities for iterating over the subset of voxels corresponding to an on state in an optional ObjectMask.
IterateVoxelsRemaining - Class in org.anchoranalysis.image.voxel.iterator: Utilities for iterating over remaining voxels in one or more VoxelBuffers.
iterator() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection

K

Kernel - Class in org.anchoranalysis.image.voxel.kernel: A small matrix that is convolved with or otherwise combined across each voxel in an image.
Kernel(int) - Constructor for class org.anchoranalysis.image.voxel.kernel.Kernel: Creates a kernel with a given size in the X and Y dimensions.
KernelApplicationParameters - Class in org.anchoranalysis.image.voxel.kernel: Parameters used for applying a Kernel to a BinaryVoxels.
KernelApplicationParameters(OutsideKernelPolicy, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.KernelApplicationParameters
KernelPointCursor - Class in org.anchoranalysis.image.voxel.kernel: A mutable context around determining whether a particular point should be on or off with a BinaryKernel.
KernelPointCursor(int, Point3i, Extent, BinaryValuesByte, KernelApplicationParameters) - Constructor for class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Creates to be focused around a particular point in the image.

L

Lanczos - Class in org.anchoranalysis.image.voxel.resizer: Resizes with an interpolator that uses Lanczos resampling as implemented in Imglib2.
Lanczos() - Constructor for class org.anchoranalysis.image.voxel.resizer.Lanczos: Default constructor.
lessThanMaxX() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Whether the current point is less than the image's extent in the X-dimension?
lessThanMaxY() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Whether the current point is less than the image's extent in the Y-dimension?
Linear - Class in org.anchoranalysis.image.voxel.resizer: Resizes with an interpolator that uses linear interpolation as implemented in Imglib2.
Linear() - Constructor for class org.anchoranalysis.image.voxel.resizer.Linear: Default constructor.
LocalSlices - Class in org.anchoranalysis.image.voxel.kernel: Caches a small number of slices around which we wish to work, so the memory is efficiently accessed.
LocalSlices(int, int, Voxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.kernel.LocalSlices: Create with focus around a particular slice.
lowerCountExistsThan(int) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
lowerCountExistsThan(int) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
lowerCountExistsThan(int) - Method in interface org.anchoranalysis.image.voxel.extracter.predicate.VoxelsPredicate: Whether the count is less than a particular threshold.

M

map(CheckedFunction<ObjectMask, ObjectMask, E>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Creates a new ObjectCollection after mapping each item to another.
mapBoundingBoxChangeExtent(BoundingBox) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Applies a function to map the bounding-box to a new-value (whose extent is expected to change in value).
mapBoundingBoxChangeExtent(BoundingBox) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Creates a new ObjectCollection after mapping the bounding-box on each object (while maybe changing the extent).
mapBoundingBoxPreserveExtent(UnaryOperator<BoundingBox>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Applies a function to map the bounding-box to a new-value (whose extent should be unchanged in value).
mapBoundingBoxPreserveExtent(UnaryOperator<BoundingBox>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Creates a new ObjectCollection after mapping the bounding-box on each object (whose extent should remain unchanged).
mapBoundingBoxPreserveExtent(BoundingBox) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Applies a function to map the bounding-box to a new-value.
mapFrom(Iterable<T>, Class<? extends E>, CheckedFunction<T, ObjectMask, E>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by mapping an Iterable to ObjectMask.
mapFrom(Iterable<T>, Function<T, ObjectMask>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by mapping an Iterable to ObjectMask.
mapFromOptional(Iterable<T>, Class<? extends Exception>, CheckedFunction<T, Optional<ObjectMask>, E>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by mapping an Iterable to Optional.
mapFromOptional(Iterable<T>, Function<T, Optional<ObjectMask>>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by mapping an Iterable to Optional.
mapFromOptional(Iterator<T>, Class<? extends Exception>, CheckedFunction<T, Optional<ObjectMask>, E>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by mapping an Iterator to Optional.
mapFromOptional(Iterator<T>, Function<T, Optional<ObjectMask>>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by mapping an Iterator to Optional.
mapFromRange(int, int, Class<? extends Exception>, CheckedIntFunction<ObjectMask, E>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by mapping integers (from a range) each to a ObjectMask.
mapFromRange(int, int, IntFunction<ObjectMask>) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection by mapping integers (from a range) each to a ObjectMask.
mapToList(CheckedFunction<ObjectMask, T, E>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Creates a new List after mapping each item to another type.
mapToListOptional(CheckedFunction<ObjectMask, Optional<T>, E>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Creates a new List after mapping each item to another (optional) type
mapToSortedSet(CheckedFunction<ObjectMask, T, E>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Creates a new SortedSet after mapping each item to another type.
MAX_IN_TO_STRING - Static variable in class org.anchoranalysis.image.voxel.Voxels: The maximum number of rows/columns/slices to show in Voxels.toString().
MAX_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.FloatVoxelType: Minimum supported value for the type.
MAX_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.SignedShortVoxelType: Maximum supported value for the type.
MAX_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedByteVoxelType: Minimum supported value for the type, as a long.
MAX_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedIntVoxelType: Maximum supported value for the type.
MAX_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedShortVoxelType: Minimum supported value for the type, as a long.
MAX_VALUE_INT - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedByteVoxelType: Maximum supported value for the type, as an int.
MAX_VALUE_INT - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedShortVoxelType: Maximum supported value for the type, as an int.
maxAsInt(ToIntFunction<ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Finds the maximum value of a function applied to each object in the collection.
MaxIntensityProjection - Class in org.anchoranalysis.image.voxel.projection.extrema: Creates buffers for performing a Maximum Intensity Projection.
maxValue() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType: The maximum value this type can represent, or VoxelDataType.VALUE_NOT_COMPATIBLE if it cannot be represented in a long.
mean() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics: The mean of all voxel values.
MeanIntensityProjection - Class in org.anchoranalysis.image.voxel.projection: Creates buffers for performing a mean-intensity-projection.
MIN_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.FloatVoxelType: Maximum supported value for the type.
MIN_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.SignedShortVoxelType: Minimum supported value for the type.
minAsInt(ToIntFunction<ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Finds the minimum value of a function applied to each object in the collection.
MinIntensityProjection - Class in org.anchoranalysis.image.voxel.projection.extrema: Creates buffers for performing a minimum intensity projection, similarly to MaxIntensityProjection but calculating the minimum.
MinMaxRange - Class in org.anchoranalysis.image.voxel.iterator: The minimum and maximum associated with a range of values.
MinMaxRange(long, long) - Constructor for class org.anchoranalysis.image.voxel.iterator.MinMaxRange
minValue() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType: The minimum value this type can represent, or VoxelDataType.VALUE_NOT_COMPATIBLE if it cannot be represented in a long.
MorphologicalDilation - Class in org.anchoranalysis.image.voxel.object.morphological: Performs morphological dilation on an ObjectMask or BinaryVoxels.
MorphologicalErosion - Class in org.anchoranalysis.image.voxel.object.morphological: Performs morphological erosion operation on an ObjectMask or BinaryVoxels.
multiplex(int, int, int) - Method in enum org.anchoranalysis.image.voxel.kernel.OutsideKernelPolicy: Multiplexes between three-values depending on which policy is currently selected.
multiplyBy(double) - Method in interface org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmetic: Multiplies the value of all voxels by a factor.
multiplyBy(ObjectMask, double) - Method in interface org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmetic: Multiplies each voxel by constant factor but only for voxels inside an ObjectMask.

N

NearestNeighbor - Class in org.anchoranalysis.image.voxel.resizer: Resizes with an interpolator that uses nearest neighbor interpolation as implemented in Imglib2.
NearestNeighbor() - Constructor for class org.anchoranalysis.image.voxel.resizer.NearestNeighbor: Default constructor.
NeighborGraph - Class in org.anchoranalysis.image.voxel.neighborhood: Creates a graph where each vertex represents an ObjectMask and edges between indicate that two objects neighbor each other.
Neighborhood - Interface in org.anchoranalysis.image.voxel.neighborhood: A region in proximity to a voxel, encompassing this voxel as well as others.
NeighborhoodFactory - Class in org.anchoranalysis.image.voxel.neighborhood: Creates either a big voxel-neighborhood or a small voxel-neighborhood.
NeighborPredicate - Interface in org.anchoranalysis.image.voxel.iterator.neighbor.kernel: A predicate on whether a neighbor satisfies a condition in relation to a particular point that it neighbors.
noInterpolation() - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizerFactory: A VoxelsResizer that is effectively disabled, and performs no interpolation, copying a single (minimal corner) value for each voxel.
nonNegativeX() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Whether the current point is non-negative in the X-dimension?
nonNegativeY() - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: Whether the current point is non-negative in the Y-dimension?
notifyBuffer(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.AndKernel
notifyBuffer(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.ConditionalKernel
notifyBuffer(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernel
notifyBuffer(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.Kernel: Called to inform the Kernel of buffers that are currently being processed.
notifyBuffer(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.morphological.BinaryKernelMorphological
notifyBuffer(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernelNeighborMatchValue
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.predicate.PredicateBufferBinary: Notifies the processor that there has been a change in slice (z global coordinate).
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.predicate.PredicateKernelPointCursor: Notifies the processor that there has been a change in z-coordinate.
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferBinary: Notifies the processor that there has been a change in slice.
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferBinaryMixed: Notifies the processor that there has been a change in slice.
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferBinaryWithoutOffset: Notifies the processor that there has been a change in slice.
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferTernary: Notifies the processor that there has been a change in slice.
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferUnary: Notifies the processor that there has been a change in slice.
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.ProcessKernelPointCursor: Notifies the processor that there has been a change in z-coordinate.
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.ProcessPoint: Notifies the processor that there has been a change in Z-coordinate.
notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.ProcessPointAndIndex: Notifies the processor that there has been a change in Z-coordinate.
notifyChangeY(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.ProcessPoint: Notifies the processor that there has been a change in Y-coordinate.
notifyChangeY(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.ProcessPointAndIndex: Notifies the processor that there has been a change in Y-coordinate.
notifyChangeZ(int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighbor: Notifies the processor that there has been a change in z-coordinate.
notifyChangeZ(int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsolute: Notifies the processor that there has been a change in z-coordinate.
notifyChangeZ(int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
notifyChangeZ(int, int, UnsignedByteBuffer) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessChangedPointAbsoluteMasked: Notifies the processor that there has been a change in z-coordinate.
numberBytes() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType: The number of bytes needed to represent this data-type.
numberVoxelsOn() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: The number of on voxels on the object-mask.

O

ObjectCollection - Class in org.anchoranalysis.image.voxel.object: A collection of ObjectMasks.
ObjectCollection(ArrayList<ObjectMask>) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectCollection: Creates with the underlying list.
ObjectCollection(Stream<ObjectMask>) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectCollection: Creates with elements from a stream.
ObjectCollectionFactory - Class in org.anchoranalysis.image.voxel.object: Creates ObjectCollection using various utility and helper methods.
objectCopyTo(ObjectMask, Voxels<T>, BoundingBox) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: Copies an area corresponding to an object-mask to another Voxels.
ObjectMask - Class in org.anchoranalysis.image.voxel.object: A localized-mask in an image, expressed as a BoundingBox, with a corresponding mask sized to match the bounding-box.
ObjectMask(BinaryVoxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask: Creates from a BinaryVoxels to be located at the origin.
ObjectMask(BoundedVoxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask: Creates from a BoundedVoxels with UnsignedByteBuffer.
ObjectMask(BoundedVoxels<UnsignedByteBuffer>, BinaryValuesInt) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask: Creates from BoundedVoxels and corresponding BinaryValuesInt.
ObjectMask(Voxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask: Creates from a Voxels mask that is cornered at the origin.
ObjectMask(BoundingBox) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask: Creates as a bounding-box with all corresponding mask voxels set to off.
ObjectMask(BoundingBox, BinaryVoxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask: Creates from a BinaryVoxels and a corresponding bounding-box.
ObjectMask(BoundingBox, Voxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask: Creates from Voxels and a BoundingBox with default BinaryValuesInt.
ObjectMask(BoundingBox, Voxels<UnsignedByteBuffer>, BinaryValuesByte) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask: Like ObjectMask(BoundingBox, Voxels, BinaryValuesInt) but specifies the binary-values as bytes.
ObjectMask(BoundingBox, Voxels<UnsignedByteBuffer>, BinaryValuesInt) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask: Creates from Voxels and a corresponding BoundingBox and BinaryValuesInt.
ObjectMaskStream - Class in org.anchoranalysis.image.voxel.object: A custom "stream" like class for various functional-programming operations on ObjectCollection
ObjectMaskStream(ObjectCollection) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMaskStream
ObjectsFromConnectedComponentsFactory - Class in org.anchoranalysis.image.voxel.binary.connected: Creates a ObjectCollection from the connected-components of a mask or binary-voxels.
ObjectsFromConnectedComponentsFactory() - Constructor for class org.anchoranalysis.image.voxel.binary.connected.ObjectsFromConnectedComponentsFactory: Creates to use a small-neighborhood.
ObjectsFromConnectedComponentsFactory(boolean) - Constructor for class org.anchoranalysis.image.voxel.binary.connected.ObjectsFromConnectedComponentsFactory: Creates to use a specified type of neighborhood.
ObjectsFromConnectedComponentsFactory(boolean, int) - Constructor for class org.anchoranalysis.image.voxel.binary.connected.ObjectsFromConnectedComponentsFactory: Creates to use a specified type of neighborhood, and minimum number of voxels.
ObjectsFromConnectedComponentsFactory(int) - Constructor for class org.anchoranalysis.image.voxel.binary.connected.ObjectsFromConnectedComponentsFactory: Creates to use a minimum number of voxels for each connected component.
of(boolean) - Static method in class org.anchoranalysis.image.voxel.neighborhood.NeighborhoodFactory: Gets an appropriate neighborhood
of(boolean, boolean) - Static method in enum org.anchoranalysis.image.voxel.kernel.OutsideKernelPolicy: Multiplexes between all three possible enums.
of(Collection<ObjectMask>...) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection with elements copied from existing collections.
of(Optional<ObjectCollection>...) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection with elements copied from existing collections, if they exist.
of(BinaryVoxels<UnsignedByteBuffer>...) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: 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.
of(ObjectCollection...) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection with elements copied from existing collections.
of(ObjectMask...) - Static method in class org.anchoranalysis.image.voxel.object.ObjectCollectionFactory: Creates a new collection with elements from the parameter-list.
offsetGlobal(int, int) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Calculates an offset for locating a voxel inside the buffer, with global encoding of coordinates.
offsetRelative(int, int) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Calculates an offset for locating a voxel inside the buffer, with local encoding of coordinates.
org.anchoranalysis.image.voxel - package org.anchoranalysis.image.voxel: Data-structures to store and manipulate image raster-data or voxels.
org.anchoranalysis.image.voxel.arithmetic - package org.anchoranalysis.image.voxel.arithmetic: Arithmetic operations for Voxels.
org.anchoranalysis.image.voxel.assigner - package org.anchoranalysis.image.voxel.assigner: Assigns values to some or all voxels.
org.anchoranalysis.image.voxel.binary - package org.anchoranalysis.image.voxel.binary: The BinaryVoxels class and related operations.
org.anchoranalysis.image.voxel.binary.connected - package org.anchoranalysis.image.voxel.binary.connected: Creating an ObjectCollection that is a connected component labelling of a BinaryVoxels.
org.anchoranalysis.image.voxel.binary.values - package org.anchoranalysis.image.voxel.binary.values: Defining on and off intensity-values to interpret an image in a binary way.
org.anchoranalysis.image.voxel.buffer - package org.anchoranalysis.image.voxel.buffer: A buffer of voxel-values, usually corresponding to a single z-slice in Voxels.
org.anchoranalysis.image.voxel.buffer.primitive - package org.anchoranalysis.image.voxel.buffer.primitive: Conversion of both primitive data types and image structures between Anchor's data-structures and other representations.
org.anchoranalysis.image.voxel.buffer.slice - package org.anchoranalysis.image.voxel.buffer.slice: A container with voxel-buffers for each z-slice.
org.anchoranalysis.image.voxel.convert - package org.anchoranalysis.image.voxel.convert: Converting Voxels to different data-types.
org.anchoranalysis.image.voxel.convert.bufferedimage - package org.anchoranalysis.image.voxel.convert.bufferedimage: Converts anchor data-structures to the BufferedImage used by Java's AWT.
org.anchoranalysis.image.voxel.convert.imglib2 - package org.anchoranalysis.image.voxel.convert.imglib2: Converts anchor data-structures to those used by ImgLib2.
org.anchoranalysis.image.voxel.datatype - package org.anchoranalysis.image.voxel.datatype: The different data-types that can be used to represent voxels.
org.anchoranalysis.image.voxel.extracter - package org.anchoranalysis.image.voxel.extracter: Methods to read/copy/duplicate portions of voxels.
org.anchoranalysis.image.voxel.extracter.predicate - package org.anchoranalysis.image.voxel.extracter.predicate: Methods to find or count voxels that satisfy a predicate.
org.anchoranalysis.image.voxel.factory - package org.anchoranalysis.image.voxel.factory: Creates new instances of Voxels and VoxelsUntyped with specific data-types.
org.anchoranalysis.image.voxel.iterator - package org.anchoranalysis.image.voxel.iterator: Utilities to iterate over voxel-locations in images and sub-regions of images.
org.anchoranalysis.image.voxel.iterator.intersecting - package org.anchoranalysis.image.voxel.iterator.intersecting: Like org.anchoranalysis.image.voxel.iterator but refers to iterators that operation over the intersecting regions of two entities.
org.anchoranalysis.image.voxel.iterator.neighbor - package org.anchoranalysis.image.voxel.iterator.neighbor: Iterating over a point's neighboring voxels.
org.anchoranalysis.image.voxel.iterator.neighbor.kernel - package org.anchoranalysis.image.voxel.iterator.neighbor.kernel: Routines for moving a KernelPointCursor around the neighboring voxels of the point.
org.anchoranalysis.image.voxel.iterator.predicate - package org.anchoranalysis.image.voxel.iterator.predicate: Functional-interfaces for processing different combinations of points and buffers that return a boolean.
org.anchoranalysis.image.voxel.iterator.process - package org.anchoranalysis.image.voxel.iterator.process: Functional-interfaces for processing different combinations of points and buffers that do not return a value.
org.anchoranalysis.image.voxel.iterator.process.buffer - package org.anchoranalysis.image.voxel.iterator.process.buffer: Functional-interfaces for processing different combinations of points and raw buffers, but not VoxelBuffer.
org.anchoranalysis.image.voxel.iterator.process.voxelbuffer - package org.anchoranalysis.image.voxel.iterator.process.voxelbuffer: Functional-interfaces for processing different combinations of points and VoxelBuffer but not raw buffers.
org.anchoranalysis.image.voxel.kernel - package org.anchoranalysis.image.voxel.kernel: Applying a kernel via convolution to voxels.
org.anchoranalysis.image.voxel.kernel.count - package org.anchoranalysis.image.voxel.kernel.count: Kernels to count the number of voxels that are equal to a particular value.
org.anchoranalysis.image.voxel.kernel.morphological - package org.anchoranalysis.image.voxel.kernel.morphological: Kernels that apply morphological operations.
org.anchoranalysis.image.voxel.kernel.outline - package org.anchoranalysis.image.voxel.kernel.outline: Kernel to find outline voxels on an object.
org.anchoranalysis.image.voxel.neighborhood - package org.anchoranalysis.image.voxel.neighborhood: A region in proximity to a voxel, encompassing this voxel as well as others.
org.anchoranalysis.image.voxel.object - package org.anchoranalysis.image.voxel.object: The fundamental data class that is an ObjectMask and related structures.
org.anchoranalysis.image.voxel.object.morphological - package org.anchoranalysis.image.voxel.object.morphological: Morphological operations applied to ObjectMasks.
org.anchoranalysis.image.voxel.object.morphological.predicate - package org.anchoranalysis.image.voxel.object.morphological.predicate: Predicates to match certain voxels as used in org.anchoranalysis.image.voxel.object.morphological.
org.anchoranalysis.image.voxel.projection - package org.anchoranalysis.image.voxel.projection: Classes for calculating differnet kind of projections of voxel values across multiple buffers.
org.anchoranalysis.image.voxel.projection.extrema - package org.anchoranalysis.image.voxel.projection.extrema: Classes for performing both a Maximum Intensity Projection and a minimum projection.
org.anchoranalysis.image.voxel.resizer - package org.anchoranalysis.image.voxel.resizer: Different interpolator methods to use when scaling voxels.
org.anchoranalysis.image.voxel.statistics - package org.anchoranalysis.image.voxel.statistics: Statistics about aggregated voxel intensities.
org.anchoranalysis.image.voxel.thresholder - package org.anchoranalysis.image.voxel.thresholder: Thresholding operations on voxels.
OutlineKernel - Class in org.anchoranalysis.image.voxel.kernel.outline: Sets voxels on the outline of an object to be on and otherwise off.
OutlineKernel() - Constructor for class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernel
OutlineKernelBase - Class in org.anchoranalysis.image.voxel.kernel.outline: A base class for kernels that find the outline of an ObjectMask.
OutlineKernelBase() - Constructor for class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernelBase: Default constructor.
OutlineKernelNeighborMatchValue - Class in org.anchoranalysis.image.voxel.kernel.outline: Outputs the outline of an object-mask, but only for voxels on the exterior which neighbor a binary-mask.
OutlineKernelNeighborMatchValue(BinaryVoxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernelNeighborMatchValue: Creates for an object.
OutsideKernelPolicy - Enum in org.anchoranalysis.image.voxel.kernel: How to handle voxels whose neighbors are outside the scene.
overAll(Kernel, BinaryVoxels<UnsignedByteBuffer>, KernelApplicationParameters, ProcessKernelPointCursor) - Static method in class org.anchoranalysis.image.voxel.iterator.neighbor.kernel.IterateKernelHelper: Iterates over all voxels.
overBox(Kernel, BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters, ProcessKernelPointCursor) - Static method in class org.anchoranalysis.image.voxel.iterator.neighbor.kernel.IterateKernelHelper: Iterates over only voxels contained within a bounding-box.
overBoxUntil(Kernel, BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters, PredicateKernelPointCursor) - Static method in class org.anchoranalysis.image.voxel.iterator.neighbor.kernel.IterateKernelHelper: Iterates over only voxels contained within a bounding-box until a predicate is matched on a voxel.

P

position() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: The position of the buffer ala Buffer.position.
position(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: Assigns a new position to the buffer.
position(int) - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: Assigns a new position to the buffer.
position(int) - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferUnsigned
PredicateAtCorner - Class in org.anchoranalysis.image.voxel.extracter.predicate: Projects a VoxelsPredicate to a corner in a larger global space
PredicateAtCorner(ReadableTuple3i, VoxelsPredicate) - Constructor for class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
PredicateBufferBinary<T> - Interface in org.anchoranalysis.image.voxel.iterator.predicate: Like ProcessBufferBinary but returns a boolean.
PredicateImplementation<T> - Class in org.anchoranalysis.image.voxel.extracter.predicate: Implementation of VoxelsPredicate for a particular Voxels.
PredicateImplementation(Voxels<T>, Predicate<T>) - Constructor for class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
PredicateKernelPointCursor - Interface in org.anchoranalysis.image.voxel.iterator.predicate: Processes a KernelPointCursor and evaluates a predicate on the current position.
PredicateTwoBytes - Interface in org.anchoranalysis.image.voxel.iterator.predicate: Like Predicate but takes two bytes as argument.
PrimitiveConverter - Class in org.anchoranalysis.image.voxel.buffer.primitive: Type conversion between primitive data types.
process(byte, byte) - Method in interface org.anchoranalysis.image.voxel.iterator.process.ProcessTwoBytes: Performs the processing.
process(VoxelBuffer<S>, VoxelBuffer<T>) - Method in interface org.anchoranalysis.image.voxel.iterator.process.voxelbuffer.ProcessVoxelBufferBinaryWithoutOffset: Processes a voxel location in a buffer
process(VoxelBuffer<S>, VoxelBuffer<T>, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.voxelbuffer.ProcessVoxelBufferBinary: Processes a voxel location in a buffer
process(VoxelBuffer<T>, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.voxelbuffer.ProcessVoxelBufferUnary: Processes a voxel location in a buffer.
process(KernelPointCursor) - Method in interface org.anchoranalysis.image.voxel.iterator.process.ProcessKernelPointCursor: Processes a particular point.
process(Point3i) - Method in interface org.anchoranalysis.image.voxel.iterator.process.ProcessPoint: Processes a particular point.
process(Point3i, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.ProcessPointAndIndex: Processes a particular point.
process(Point3i, VoxelBuffer<S>, T, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.voxelbuffer.ProcessVoxelBufferBinaryMixed: Processes a voxel location in a buffer
process(Point3i, VoxelBuffer<S>, T, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferBinaryMixed: Processes a voxel location in two buffers.
process(Point3i, VoxelBuffer<T>, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.voxelbuffer.ProcessVoxelBufferUnaryWithPoint: Processes a voxel location in a buffer.
process(Point3i, S, T, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferBinary: Processes a voxel location in two buffers.
process(Point3i, T, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferUnary: Processes a voxel location in a buffer.
process(Point3i, T, T, T, int, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferTernary: Processes a voxel location in a buffer.
process(S, T) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferBinaryWithoutOffset: Processes a voxel location in a buffer.
ProcessBufferBinary<S,T> - Interface in org.anchoranalysis.image.voxel.iterator.process.buffer: Processes a 3D point like ProcessPoint but also retrieves two Buffer for the current z-slice.
ProcessBufferBinaryMixed<S,T> - Interface in org.anchoranalysis.image.voxel.iterator.process.buffer: Processes a 3D point like ProcessPoint but also retrieves both one VoxelBuffer for the current z-slice and one Buffer for the current z-slice.
ProcessBufferBinaryWithoutOffset<S,T> - Interface in org.anchoranalysis.image.voxel.iterator.process.buffer: Processes two buffers for each z-slice jointly, without any offset or point.
ProcessBufferTernary<T> - Interface in org.anchoranalysis.image.voxel.iterator.process.buffer: Processes a 3D point like ProcessPoint but also retrieves three buffers for the current z-slice.
ProcessBufferUnary<T> - Interface in org.anchoranalysis.image.voxel.iterator.process.buffer: Processes a 3D point like ProcessPoint but also retrieves a buffer for the current z-slice.
ProcessChangedPointAbsoluteMasked<T> - Interface in org.anchoranalysis.image.voxel.iterator.neighbor: Processes a point which has been translated (changed) relative to another point - and includes global coordinates and includes an object-mask buffer.
ProcessKernelPointCursor - Interface in org.anchoranalysis.image.voxel.iterator.process: Processes a KernelPointCursor which includes a Point3i.
processNeighborhoodPoints(boolean, ProcessVoxelNeighbor<?>) - Method in interface org.anchoranalysis.image.voxel.neighborhood.Neighborhood: Calls ProcessVoxelNeighbor for each voxel in the neighborhood of the current state of ProcessVoxelNeighbor.
processPoint(int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighbor: Processes a particular point.
processPoint(int, int, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsolute: Processes a particular point.
processPoint(int, int, int, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessChangedPointAbsoluteMasked: Processes a particular point.
ProcessPoint - Interface in org.anchoranalysis.image.voxel.iterator.process: Processes a 3D point.
ProcessPointAndIndex - Interface in org.anchoranalysis.image.voxel.iterator.process: Processes a Point3i also including an index.
ProcessTwoBytes - Interface in org.anchoranalysis.image.voxel.iterator.process: Processes two bytes.
ProcessVoxelBufferBinary<S,T> - Interface in org.anchoranalysis.image.voxel.iterator.process.voxelbuffer: Processes a 3D point like ProcessPoint but also retrieves two VoxelBuffers for the current z-slice.
ProcessVoxelBufferBinaryMixed<S,T> - Interface in org.anchoranalysis.image.voxel.iterator.process.voxelbuffer: Processes a 3D point like ProcessVoxelBufferBinary but rather has one VoxelBuffer and one buffer, and also exposes a Point3i.
ProcessVoxelBufferBinaryWithoutOffset<S,T> - Interface in org.anchoranalysis.image.voxel.iterator.process.voxelbuffer: Processes two voxel-buffers for each z-slice jointly, without any offset or point.
ProcessVoxelBufferUnary<T> - Interface in org.anchoranalysis.image.voxel.iterator.process.voxelbuffer: Processes a 3D point like ProcessPoint but also retrieves a VoxelBuffer for the current z-slice.
ProcessVoxelBufferUnaryWithPoint<T,E extends Exception> - Interface in org.anchoranalysis.image.voxel.iterator.process.voxelbuffer: Processes a 3D point like ProcessVoxelBufferUnary but also exposes a Point3i.
ProcessVoxelNeighbor<T> - Interface in org.anchoranalysis.image.voxel.iterator.neighbor: Processes a point that is an neighbor of another.
ProcessVoxelNeighborAbsolute<T> - Interface in org.anchoranalysis.image.voxel.iterator.neighbor: Processes a point that is a neighbor of another - includes global (absolute) coordinates for this point.
ProcessVoxelNeighborAbsoluteWithSlidingBuffer<T> - Class in org.anchoranalysis.image.voxel.iterator.neighbor: Like ProcessVoxelNeighborAbsolute but additionally includes a SlidingBuffer.
ProcessVoxelNeighborAbsoluteWithSlidingBuffer(SlidingBuffer<?>) - Constructor for class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer: Creates for a particular sliding buffer.
ProcessVoxelNeighborFactory - Class in org.anchoranalysis.image.voxel.iterator.neighbor: Creates ProcessVoxelNeighbor to match certain circumstances.
ProjectableBuffer<T> - Interface in org.anchoranalysis.image.voxel.buffer: A buffer to which slices may be added to form a projection.
projectMax() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: A maximum-intensity projection (flattens in z dimension)
projectMax() - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: A maximum intensity projection of all slices
projectMean() - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: A mean intensity projection of all slices.
put(ByteBuffer) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Relative put-method from an unsigned byte buffer, represented by a ByteBuffer.
put(ShortBuffer) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Relative put-method from an unsigned short buffer, represented by a ShortBuffer.
put(UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Relative put-method from an unsigned byte buffer, represented by a UnsignedByteBuffer.
put(UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Relative put-method from an unsigned short buffer, represented by a UnsignedShortBuffer.
putByte(int, byte) - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: Puts a byte in the buffer at a particular position, converting, if necessary, to the buffer type.
putDouble(double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: Puts a double at the current buffer position.
putDouble(double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
putDouble(double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
putDouble(double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
putDouble(int, double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: Puts a double at a particular buffer position.
putDouble(int, double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
putDouble(int, double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
putDouble(int, double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
putDoubleClamped(double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Puts a double at the current buffer position, clamping to ensure the value is within the range (0,255).
putFloat(float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: Puts a float at the current buffer position.
putFloat(float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
putFloat(float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
putFloat(float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
putFloat(int, float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: Puts a float at a particular buffer position.
putFloat(int, float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
putFloat(int, float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
putFloat(int, float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
putFloatClamped(float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Puts a float at the current buffer position, clamping to ensure the value is within the range (0,255).
putFloatClamped(float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Puts a float at the current buffer position, clamping to ensure the value is within the range (0,255).
putInt(int, int) - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: Puts a int in the buffer at a particular position, converting, if necessary, to the buffer type.
putInt(int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer: Assign a value to the buffer at a particular absolute position.
putLong(long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer: Puts a long at the current buffer position.
putLong(long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
putLong(long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
putLong(long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
putLongClamped(long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Puts a long at the current buffer position, clamping to ensure the value is within the range (0,255).
putRaw(byte) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Puts an unsigned-byte (represented as a byte) at the current buffer position.
putRaw(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Puts an unsigned-int (represented as a int) at the current buffer position.
putRaw(int, byte) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Puts an unsigned-byte (represented as a byte) a particular buffer position.
putRaw(int, int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Puts an unsigned-int (represented as a int) a particular buffer position.
putRaw(int, short) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Puts an unsigned-short (represented as a short) a particular buffer position.
putRaw(short) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Puts an unsigned-short (represented as a short) at the current buffer position.
putUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt: Puts an unsigned-byte (represented by an int) at current buffer position.
putUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
putUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
putUnsigned(int, int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt: Puts an unsigned-byte (represented as a int) a particular buffer position.
putUnsigned(int, int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
putUnsigned(int, int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
putUnsigned(int, long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Puts an unsigned-int (represented as a long) a particular buffer position.
putUnsigned(long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Puts an unsigned-int (represented by a long) at current buffer position.
putUnsignedClamped(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Puts a long at the current buffer position, clamping to ensure the value is within the range (0,255).
putUnsignedInt(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Puts an unsigned-int (represented by a int) at current buffer position.

Q

quantile(double) - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics: The voxel value corresponding to a particular quantile.
quantile(double) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
quantile(double) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram

R

region(BoundingBox, boolean) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: A (sub-)region of the voxels.
region(BoundingBox, boolean) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: A (sub-)region of the voxels.
region(BoundingBox, boolean) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: A (sub-)region of the object-mask.
regionIntersecting(BoundingBox) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Creates an object-mask covering the a bounding-box (that is required to intersect at least partially)
regionIntersecting(BoundingBox, int) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Like BoundedVoxels.region(org.anchoranalysis.spatial.box.BoundingBox, boolean) but only expects a bounding-box that intersects at least partially.
regionZ(int, int) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Creates an object-mask with a subrange of the slices.
regionZ(int, int, VoxelsFactoryTypeBound<T>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Creates an box with a subrange of the slices.
relativeMaskTo(BoundingBox) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Creates a new object-mask with coordinates changed to be relative to another box.
remove(T) - Method in class org.anchoranalysis.image.voxel.object.IntersectingObjects: Removes an object-mask, so that it is no longer considered in queries.
replaceSlice(int, VoxelBuffer<FloatBuffer>) - Method in class org.anchoranalysis.image.voxel.buffer.slice.FromFloat
replaceSlice(int, VoxelBuffer<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.buffer.slice.FromByte
replaceSlice(int, VoxelBuffer<UnsignedIntBuffer>) - Method in class org.anchoranalysis.image.voxel.buffer.slice.FromInt
replaceSlice(int, VoxelBuffer<UnsignedShortBuffer>) - Method in class org.anchoranalysis.image.voxel.buffer.slice.FromShort
replaceSlice(int, VoxelBuffer<T>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Assigns a new buffer for a slice.
replaceSlice(int, VoxelBuffer<T>) - Method in interface org.anchoranalysis.image.voxel.buffer.slice.SliceBufferIndex: Replaces the voxels for a particular z-slice.
replaceSlice(int, VoxelBuffer<T>) - Method in class org.anchoranalysis.image.voxel.Voxels: Assigns a new buffer for a particular slice.
replaceSlice(int, VoxelsUntyped, int, boolean) - Method in class org.anchoranalysis.image.voxel.VoxelsUntyped: Copies one particular z-slice of voxels from a source into the current voxels.
replaceVoxels(Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Replaces the voxels in the object-mask.
replaceVoxels(Voxels<T>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Replaces the voxels in the box.
resize(VoxelsUntyped, VoxelsUntyped) - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizer: Copies voxels slice-by-slice from source to destination performing necessary interpolation.
resizeByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizer: Interpolates from voxelsSource to voxelsDestination for unsigned 8-bit buffers.
resizeByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizerExecutionTime
resizeByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizerImgLib2
resizeByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizerNone
resizedXY(int, int, VoxelsResizer) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: Creates a new voxels that are a resized version of the current voxels (only in X and Y dimensions), interpolating as needed.
resizeFloat(VoxelBuffer<FloatBuffer>, VoxelBuffer<FloatBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizer: Interpolates from voxelsSource to voxelsDestination for float buffers.
resizeFloat(VoxelBuffer<FloatBuffer>, VoxelBuffer<FloatBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizerExecutionTime
resizeFloat(VoxelBuffer<FloatBuffer>, VoxelBuffer<FloatBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizerImgLib2
resizeFloat(VoxelBuffer<FloatBuffer>, VoxelBuffer<FloatBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizerNone
resizeShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizer: Interpolates from voxelsSource to voxelsDestination for unsigned 16-bit buffers.
resizeShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizerExecutionTime
resizeShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizerImgLib2
resizeShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.resizer.VoxelsResizerNone
reuseByte(Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.binary.BinaryVoxelsFactory: 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).
reuseByte(Voxels<UnsignedByteBuffer>, BinaryValuesInt) - Static method in class org.anchoranalysis.image.voxel.binary.BinaryVoxelsFactory: Reuses an existing voxel-buffer (of type unsigned byte) as a binary-version which should have only two intensity-values representing off and on.
reuseInt(Voxels<UnsignedIntBuffer>, BinaryValuesInt) - Static method in class org.anchoranalysis.image.voxel.binary.BinaryVoxelsFactory: Reuses an existing voxel-buffer (of type unsigned int) as a binary-version which should have only two intensity-values representing off and on.
rewind() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Rewinds the buffer ala ByteBuffer.rewind().

S

scale(ScaleFactor) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Produces a scaled-version of an object-mask.
scale(ScaleFactor, Optional<Extent>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Produces a scaled-version of an object-mask.
scale(ScaleFactor, VoxelsResizer, Optional<Extent>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Creates a scaled-version (in XY dimensions only) of the current bounding-box.
seek(int) - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer: Moves buffer to a particular z-slice.
setIndex(int) - Method in class org.anchoranalysis.image.voxel.kernel.KernelPointCursor: The index in the buffer that the kernel currently is focussed on.
setMaxValue(long) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedByteScaleByMaxValue: Assigns the maximum-value that will be represented in the scaled-values.
setMinMaxValues(long, long) - Method in class org.anchoranalysis.image.voxel.convert.ToUnsignedByteScaleByMinMaxValue: Assigns the minimum- and maximum-values which existing values are scaled against.
setOff(int, int, int) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter: Assigns an off state to a voxel at a particular point.
setOff(Point3i) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter: Assigns an off state to a voxel at a particular point.
setOn(int, int, int) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter: Assigns an on state to a voxel at a particular point.
setOn(Point3i) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter: Assigns an on state to a voxel at a particular point.
shift() - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer: Increments the slice number by one.
shiftBackBy(VoxelsAssigner, ReadableTuple3i) - Static method in class org.anchoranalysis.image.voxel.assigner.VoxelsAssignerFactory: Shifts all coordinates backwards before passing to another VoxelsAssigner.
shiftBackBy(ReadableTuple3i) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Shifts the object-mask by moving its bounding-box backwards.
shiftBy(ReadableTuple3i) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: Shifts the bounding-box of each object by adding to it.
shiftBy(ReadableTuple3i) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Shifts the object-mask by moving its bounding-box forwards.
shiftToOrigin() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Creates a new object-mask with identical voxels but with the bounding-box beginning at the origin (0,0,0).
SignedShortVoxelType - Class in org.anchoranalysis.image.voxel.datatype: A 16-bit voxel data-type representing signed-short numbers.
SignedVoxelType - Class in org.anchoranalysis.image.voxel.datatype: Base class for voxel-data-types that are signed and integral.
SignedVoxelType(int, String, long, long) - Constructor for class org.anchoranalysis.image.voxel.datatype.SignedVoxelType: Construct for a particular number of bits, with a unique identifier, and with bounds on the values.
size() - Method in class org.anchoranalysis.image.voxel.object.IntersectingObjects: Number of items in the r-tree.
size() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: The number of objects in the collection.
size() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics: The total count.
size() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
size() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
slice(int) - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: A VoxelBuffer corresponding to a particular z-slice.
slice(int) - Method in class org.anchoranalysis.image.voxel.buffer.slice.FromByte
slice(int) - Method in class org.anchoranalysis.image.voxel.buffer.slice.FromFloat
slice(int) - Method in class org.anchoranalysis.image.voxel.buffer.slice.FromInt
slice(int) - Method in class org.anchoranalysis.image.voxel.buffer.slice.FromShort
slice(int) - Method in interface org.anchoranalysis.image.voxel.buffer.slice.SliceBufferIndex: A VoxelBuffer corresponding to a particular z-slice.
slice(int) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: Creates a new Voxels with only particular slice.
slice(int) - Method in class org.anchoranalysis.image.voxel.Voxels: A VoxelBuffer corresponding to a particular z-slice.
slice(int) - Method in class org.anchoranalysis.image.voxel.VoxelsUntyped: A VoxelBuffer corresponding to a particular z-slice.
sliceBinary(int) - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: A particular z-slice, wrapped into a BinaryVoxels.
sliceBuffer(int) - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: A buffer corresponding to a particular z-slice.
sliceBuffer(int) - Method in interface org.anchoranalysis.image.voxel.buffer.slice.SliceBufferIndex: The underlying buffer corresponding to a particular z-slice.
sliceBuffer(int) - Method in class org.anchoranalysis.image.voxel.Voxels: A buffer corresponding to a particular z-slice.
sliceBufferGlobal(int) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: A slice buffer with global coordinates.
sliceBufferGlobal(int) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: A slice buffer with global coordinates.
SliceBufferIndex<T> - Interface in org.anchoranalysis.image.voxel.buffer.slice: A container with voxel-buffers for each z-slice.
sliceBufferLocal(int) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: A slice buffer with local coordinates.
sliceBufferLocal(int) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: A slice buffer with local coordinates.
slices() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: An index mapping slice of voxels (in the z dimension) to a particular buffer with the corresponding voxel intensities.
slices() - Method in class org.anchoranalysis.image.voxel.Voxels: An index mapping slice of voxels (in the z dimension) to a particular buffer with the corresponding voxel intensities.
SlidingBuffer<T> - Class in org.anchoranalysis.image.voxel.buffer: An index that places a particular z-slice in local context.
SlidingBuffer(Voxels<T>) - Constructor for class org.anchoranalysis.image.voxel.buffer.SlidingBuffer: Create for particular voxels.
sourceValue - Variable in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer: The intensity value of the source voxel.
spatiallySeparate() - Method in class org.anchoranalysis.image.voxel.object.IntersectingObjects: Splits the collection of objects into spatially separate clusters.
StandardDeviationIntensityProjection - Class in org.anchoranalysis.image.voxel.projection: Creates buffers for projecting the standard-deviation.
stdDev() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics: The standard-deviation of all voxel values.
stream() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: Provides various functional-programming operations on the object-collection.
streamIndices(Collection<Integer>) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: Streams only objects at specific indices.
streamStandardJava() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: A stream of object-masks as per Java's standard collections interface.
subtractFrom(int) - Method in interface org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmetic: Subtracts all current voxel-values from a constant-value.
subtractFromMaxValue() - Method in class org.anchoranalysis.image.voxel.VoxelsUntyped: Subtracts all voxel-values from the maximum value associated with the data-type.
sum() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics: The sum of all voxel values.
sum() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
sum() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
sumOfSquares() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics: The sum of the square of all voxel values.
sumOfSquares() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
sumOfSquares() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram

T

test(boolean, KernelPointCursor, Supplier<UnsignedByteBuffer>, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.kernel.NeighborPredicate: Tests if a neighbor satisfies a condition.
test(byte, byte) - Method in interface org.anchoranalysis.image.voxel.iterator.predicate.PredicateTwoBytes: Do the combination of two arguments fulfill the predicate?
test(KernelPointCursor) - Method in interface org.anchoranalysis.image.voxel.iterator.predicate.PredicateKernelPointCursor: Whether the condition is satisfied for a particular point?
test(Point3i, T, T, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.predicate.PredicateBufferBinary: Tests a voxel location in two buffers.
threshold(RelationToThreshold) - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics: Derives statistics only of the voxels that satisfy a condition, relative to a threshold.
threshold(RelationToThreshold) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
threshold(RelationToThreshold) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
threshold(VoxelsUntyped, float, BinaryValuesByte, Optional<ObjectMask>, boolean) - Static method in class org.anchoranalysis.image.voxel.thresholder.VoxelsThresholder: Applies thresholding to VoxelsUntyped.
thresholdByte(Voxels<UnsignedByteBuffer>, int, BinaryValuesByte) - Static method in class org.anchoranalysis.image.voxel.thresholder.VoxelsThresholder: Applies thresholding to Voxels of unsigned byte data type.
thresholdFloat(Voxels<FloatBuffer>, float, BinaryValuesByte) - Static method in class org.anchoranalysis.image.voxel.thresholder.VoxelsThresholder: Applies thresholding to Voxels of float data type.
toAll() - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner: Assigns to all the voxels
toBox(BoundingBox) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner: Assigns to only voxels inside a bounding-box
toEitherTwoObjects(ObjectMask, ObjectMask, BoundingBox) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner: Sets voxels to a value if the position is on in either of two masks
ToFloatNoScaling - Class in org.anchoranalysis.image.voxel.convert: Converts voxel buffers to a FloatBuffer without scaling any values.
ToFloatNoScaling() - Constructor for class org.anchoranalysis.image.voxel.convert.ToFloatNoScaling
toObject(ObjectMask) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner: Sets voxels in a box to a particular value if they match an object-mask
toObject(ObjectMask, BoundingBox) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner: Sets voxels in a box to a particular value if they match a object-mask (but only a part of the object-mask)
toObjectIf(ObjectMask, IntPredicate) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner: Sets voxels in a box to a particular value if they match an object-mask and a voxel matches a predicate
toObjectWhile(ObjectMask, IntPredicate) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner: Sets voxels in a box to a particular value if they match an object-mask and each voxel matches a predicate
toSet() - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream: Converts to a HashSet.
toString() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
toString() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
toString() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt: Print a description and the the first {link #MAX_NUMBER_ROWS_COLUMNS_IN_TO_STRING} rows and columns as values.
toString() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
toString() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType
toString() - Method in class org.anchoranalysis.image.voxel.iterator.MinMaxRange
toString() - Method in class org.anchoranalysis.image.voxel.kernel.KernelApplicationParameters
toString() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: Default string representation of the collection, one line with each object described by its center-of-gravity.
toString() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: A string representation of the object-mask showing: the center-of-gravity.
toString() - Method in class org.anchoranalysis.image.voxel.Voxels: Print a description and the the first Voxels.MAX_IN_TO_STRING (if they exist) rows and columns as values.
toString(boolean, boolean) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection: A string representation of all objects in the collection using their center of gravities (and optionally indices).
ToUnsignedByte - Class in org.anchoranalysis.image.voxel.convert: Base class for conversion to unsigned 8-bit.
ToUnsignedByte() - Constructor for class org.anchoranalysis.image.voxel.convert.ToUnsignedByte
ToUnsignedByteNoScaling - Class in org.anchoranalysis.image.voxel.convert: Converts voxel buffers to an unsigned 8-bit buffer without scaling any values.
ToUnsignedByteNoScaling() - Constructor for class org.anchoranalysis.image.voxel.convert.ToUnsignedByteNoScaling
ToUnsignedByteScaleByMaxValue - Class in org.anchoranalysis.image.voxel.convert: Converts voxel buffers to an unsigned 8-bit buffer linearly scaling against the maximum constant value.
ToUnsignedByteScaleByMaxValue(int) - Constructor for class org.anchoranalysis.image.voxel.convert.ToUnsignedByteScaleByMaxValue: Creates with the maximum-value which existing values are scaled against.
ToUnsignedByteScaleByMinMaxValue - Class in org.anchoranalysis.image.voxel.convert: Converts voxel buffers to an unsigned 8-bit buffer scaling against a the minimum and maximum constant.
ToUnsignedByteScaleByMinMaxValue(long, long) - Constructor for class org.anchoranalysis.image.voxel.convert.ToUnsignedByteScaleByMinMaxValue: Creates with the minimum- and maximum-values which existing values are scaled against.
ToUnsignedByteScaleByType - Class in org.anchoranalysis.image.voxel.convert: Converts voxel buffers to a UnsignedByteBuffer scaling against the maximum value in each buffer.
ToUnsignedByteScaleByType() - Constructor for class org.anchoranalysis.image.voxel.convert.ToUnsignedByteScaleByType
ToUnsignedInt - Class in org.anchoranalysis.image.voxel.convert: Base class for conversion to unsigned 32-bit.
ToUnsignedInt() - Constructor for class org.anchoranalysis.image.voxel.convert.ToUnsignedInt
ToUnsignedShortNoScaling - Class in org.anchoranalysis.image.voxel.convert: Converts voxel buffers to an unsigned 16-bit buffer without scaling any values.
ToUnsignedShortNoScaling() - Constructor for class org.anchoranalysis.image.voxel.convert.ToUnsignedShortNoScaling
ToUnsignedShortScaleByType - Class in org.anchoranalysis.image.voxel.convert: Converts voxel buffers to an unsigned 16-bit buffer, scaling against the maximum value in each data-type.
ToUnsignedShortScaleByType() - Constructor for class org.anchoranalysis.image.voxel.convert.ToUnsignedShortScaleByType
toVoxel(int, int, int) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner: Assigns one particular voxel
toVoxel(Point3i) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner: Assigns one particular voxel

U

underlyingBytes() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer: THe underlying bytes that describe the voxels.
UnsignedBuffer - Class in org.anchoranalysis.image.voxel.buffer.primitive: Base class for buffers that represent an unsigned-type in the signed-equivalent-type NIO Buffer.
UnsignedBuffer(Buffer) - Constructor for class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
UnsignedBufferAsInt - Class in org.anchoranalysis.image.voxel.buffer.primitive: A UnsignedBuffer that exposes its internal types as int.
UnsignedBufferAsInt(Buffer) - Constructor for class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt: Construct with a delegate buffer.
unsignedByteArray(byte[]) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap: Wraps an existing array (encoding unsigned bytes as a signed array) as a voxel-buffer.
unsignedByteBuffer(UnsignedByteBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap: Wraps an unsigned-byte buffer into a voxel-buffer.
UnsignedByteBuffer - Class in org.anchoranalysis.image.voxel.buffer.primitive: Wraps a ByteBuffer but automatically performs conversion to int.
unsignedByteRaw(ByteBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap: Wraps an unsigned-byte buffer (represented by a NIO signed-buffer) into a voxel-buffer.
unsignedByteToInt(byte) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.PrimitiveConverter: Converts an unsigned-byte value to a signed int.
unsignedByteToShort(byte) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.PrimitiveConverter: Converts an unsigned-byte value to a signed short.
UnsignedByteVoxelType - Class in org.anchoranalysis.image.voxel.datatype: A 8-bit voxel data-type representing unsigned-byte numbers.
unsignedIntArray(int[]) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap: Wraps an unsigned-int buffer into a voxel-buffer.
unsignedIntBuffer(UnsignedIntBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap: Wraps an unsigned-int buffer (represented by a NIO signed-buffer) into a voxel-buffer.
UnsignedIntBuffer - Class in org.anchoranalysis.image.voxel.buffer.primitive: Wraps an IntBuffer but automatically performs conversion to long.
unsignedIntToInt(int) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.PrimitiveConverter: Converts an unsigned-int value to a signed int.
unsignedIntToLong(int) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.PrimitiveConverter: Converts an unsigned-int value to a signed long.
unsignedIntToShort(int) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.PrimitiveConverter: Converts an unsigned-int value to a signed int.
UnsignedIntVoxelType - Class in org.anchoranalysis.image.voxel.datatype: A 32-bit voxel data-type representing unsigned-int numbers.
unsignedShortArray(short[]) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap: Wraps an existing array (encoding unsigned shorts as a signed array) as a voxel-buffer.
unsignedShortBuffer(UnsignedShortBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap: Wraps an unsigned-short buffer into a voxel-buffer.
UnsignedShortBuffer - Class in org.anchoranalysis.image.voxel.buffer.primitive: Wraps a ShortBuffer but automatically performs conversion to int.
unsignedShortRaw(ShortBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap: Wraps an unsigned-short buffer (represented by a NIO signed-buffer) into a voxel-buffer.
unsignedShortToInt(short) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.PrimitiveConverter: Converts an unsigned-short value to a signed int.
UnsignedShortVoxelType - Class in org.anchoranalysis.image.voxel.datatype: A 16-bit voxel data-type representing unsigned-short numbers.
UnsignedVoxelType - Class in org.anchoranalysis.image.voxel.datatype: Base class for voxel-data-types that are unsigned and integral.
UnsignedVoxelType(int, String, long) - Constructor for class org.anchoranalysis.image.voxel.datatype.UnsignedVoxelType: Construct for a particular number of bits, with a unique identifier, and with bounds on the values.
untilFirstIntensityEqualTo(BoundedVoxels<UnsignedByteBuffer>, byte) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsEqualTo: Iterates each voxel until a specific intensity value is found.

V

VALUE_NOT_COMPATIBLE - Static variable in class org.anchoranalysis.image.voxel.datatype.VoxelDataType: A placeholder value for maxValue or minValue if the true maximum or minimum value cannot be expressed as a long.
valueOf(String) - Static method in enum org.anchoranalysis.image.voxel.kernel.OutsideKernelPolicy: Returns the enum constant of this type with the specified name.
values() - Static method in enum org.anchoranalysis.image.voxel.kernel.OutsideKernelPolicy: Returns an array containing the constants of this enum type, in the order they are declared.
variance() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics: The variance of all voxel values.
voxel(int, int) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: Gets the value of one particular voxel.
voxel(int, int, int) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: Gets the value of one particular voxel.
voxel(ReadableTuple3i) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: Gets the value of one particular voxel.
VoxelBuffer<T> - Class in org.anchoranalysis.image.voxel.buffer: A buffer of voxel-values, usually corresponding to a single z-slice in Voxels.
VoxelBuffer() - Constructor for class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
VoxelBufferFactory - Class in org.anchoranalysis.image.voxel.buffer: Creating voxel-buffers and arrays of voxel-buffers of various types.
VoxelBufferUnsigned<T extends UnsignedBuffer> - Class in org.anchoranalysis.image.voxel.buffer: A parent class for VoxelBuffer that accepts unsigned-buffers and implements some common operations.
VoxelBufferUnsigned(T) - Constructor for class org.anchoranalysis.image.voxel.buffer.VoxelBufferUnsigned
VoxelBufferWrap - Class in org.anchoranalysis.image.voxel.buffer: Wraps arrays and buffers of primitive-types into VoxelBuffer.
VoxelDataType - Class in org.anchoranalysis.image.voxel.datatype: The type of data that a single voxel represents in an image or related buffer.
VoxelDataType(int, String, long, long) - Constructor for class org.anchoranalysis.image.voxel.datatype.VoxelDataType
VoxelDataTypeFactoryMultiplexer<T> - Class in org.anchoranalysis.image.voxel.datatype: Multiplexes between factories for the various VoxelDataTypes.
VoxelDataTypeFactoryMultiplexer(T, T, T, T) - Constructor for class org.anchoranalysis.image.voxel.datatype.VoxelDataTypeFactoryMultiplexer
voxels() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels: Voxels that should only have two intensity-values (representing on and off states).
voxels() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels: Voxel-data that fits inside the bounding-box (its extent is invariant with the extent of the bounding-box).
voxels() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: The underlying voxel memory buffers for the object-mask, exposed via Voxels.
Voxels<T> - Class in org.anchoranalysis.image.voxel: A box (3-dimensions) with voxel-data.
Voxels(SliceBufferIndex<T>, VoxelsFactoryTypeBound<T>, VoxelsArithmetic) - Constructor for class org.anchoranalysis.image.voxel.Voxels
VoxelsArithmetic - Interface in org.anchoranalysis.image.voxel.arithmetic: Allows manipulation of voxel intensities via arithmetic operations.
VoxelsArithmeticFactory - Class in org.anchoranalysis.image.voxel.arithmetic: Creates VoxelsArithmetic for buffers of different types.
VoxelsAssigner - Interface in org.anchoranalysis.image.voxel.assigner: Assigns values to some or all voxels.
VoxelsAssignerFactory - Class in org.anchoranalysis.image.voxel.assigner: Creates VoxelsAssigner for buffers of different types.
VoxelsConverter<T> - Class in org.anchoranalysis.image.voxel.convert: Converts voxels from one data-type to another.
VoxelsConverter() - Constructor for class org.anchoranalysis.image.voxel.convert.VoxelsConverter
VoxelsConverterMulti - Class in org.anchoranalysis.image.voxel.convert: Converts a channel from one voxel data-type to one of multiple other types.
VoxelsConverterMulti() - Constructor for class org.anchoranalysis.image.voxel.convert.VoxelsConverterMulti
voxelsEqualTo(int) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: Operations on whether particular voxels are equal to a particular value.
VoxelsExtracter<T> - Interface in org.anchoranalysis.image.voxel.extracter: Provides methods to read/copy/duplicate regions of voxels.
VoxelsExtracterFactory - Class in org.anchoranalysis.image.voxel.extracter: Creates VoxelsExtracter corresponding to Voxels of differing data-type.
VoxelsFactory - Class in org.anchoranalysis.image.voxel.factory: Creates VoxelsUntyped and provides a singleton location for implementations of VoxelsFactoryTypeBound for different types.
VoxelsFactoryTypeBound<T> - Interface in org.anchoranalysis.image.voxel.factory: A factory for creating voxels with a particular buffer-type.
VoxelsFloat - Class in org.anchoranalysis.image.voxel: Implementation of Voxels whose voxels are of type float.
VoxelsFloat(SliceBufferIndex<FloatBuffer>) - Constructor for class org.anchoranalysis.image.voxel.VoxelsFloat: Create from a buffer, indexed by slice.
voxelsGreaterThan(int) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: Operations on whether particular voxels are greater than a threshold (but not equal to).
voxelsOff() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Provides a VoxelsPredicate that finds or counts all off voxels in the object-mask.
voxelsOn() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask: Provides a VoxelsPredicate that finds or counts all on voxels in the object-mask.
VoxelsPredicate - Interface in org.anchoranalysis.image.voxel.extracter.predicate: Methods to find or count voxels that satisfy a predicate.
VoxelsResizer - Class in org.anchoranalysis.image.voxel.resizer: Copies voxels while performing interpolation.
VoxelsResizer() - Constructor for class org.anchoranalysis.image.voxel.resizer.VoxelsResizer
VoxelsResizerExecutionTime - Class in org.anchoranalysis.image.voxel.resizer: Calls another VoxelsResizer recording each resize call via a ExecutionTimeRecorder.
VoxelsResizerExecutionTime(VoxelsResizer, ExecutionTimeRecorder, String) - Constructor for class org.anchoranalysis.image.voxel.resizer.VoxelsResizerExecutionTime: Creates with an VoxelsResizer and ExecutionTimeRecorder.
VoxelsResizerFactory - Class in org.anchoranalysis.image.voxel.resizer: Creates instances of VoxelsResizer to match particular circumstances.
VoxelsResizerImgLib2 - Class in org.anchoranalysis.image.voxel.resizer: Performs resizing of VoxelBuffers using ImgLib2's interpolation.
VoxelsResizerImgLib2(InterpolatorFactory<UnsignedByteType, RandomAccessible<UnsignedByteType>>, InterpolatorFactory<UnsignedShortType, RandomAccessible<UnsignedShortType>>, InterpolatorFactory<FloatType, RandomAccessible<FloatType>>) - Constructor for class org.anchoranalysis.image.voxel.resizer.VoxelsResizerImgLib2
VoxelsResizerNone - Class in org.anchoranalysis.image.voxel.resizer: Doesn't do any interpolation, just copies a single value for each voxel.
VoxelsResizerNone() - Constructor for class org.anchoranalysis.image.voxel.resizer.VoxelsResizerNone
VoxelStatistics - Interface in org.anchoranalysis.image.voxel.statistics: Allows retrieval of statistics about voxel values.
VoxelStatisticsCombined - Class in org.anchoranalysis.image.voxel.statistics: Aggregates statistics of a list of VoxelStatistics as if they were one.
VoxelStatisticsCombined() - Constructor for class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
VoxelStatisticsFromHistogram - Class in org.anchoranalysis.image.voxel.statistics: Calculates statistics from a Histogram of voxel intensities.
VoxelStatisticsFromHistogram(Histogram) - Constructor for class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
VoxelsThresholder - Class in org.anchoranalysis.image.voxel.thresholder: Performs a thresholding operation on voxels.
VoxelsUnsignedByte - Class in org.anchoranalysis.image.voxel: Implementation of Voxels whose voxels are of type unsigned byte (8-bit).
VoxelsUnsignedByte(SliceBufferIndex<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.VoxelsUnsignedByte: Create from a buffer, indexed by slice.
VoxelsUnsignedInt - Class in org.anchoranalysis.image.voxel: Implementation of Voxels whose voxels are of type unsigned int (32-bit).
VoxelsUnsignedInt(SliceBufferIndex<UnsignedIntBuffer>) - Constructor for class org.anchoranalysis.image.voxel.VoxelsUnsignedInt: Create from a buffer, indexed by slice.
VoxelsUnsignedShort - Class in org.anchoranalysis.image.voxel: Implementation of Voxels whose voxels are of type unsigned short (16-bit).
VoxelsUnsignedShort(SliceBufferIndex<UnsignedShortBuffer>) - Constructor for class org.anchoranalysis.image.voxel.VoxelsUnsignedShort: Create from a buffer, indexed by slice.
VoxelsUntyped - Class in org.anchoranalysis.image.voxel: Stores memory buffers representing image voxels, without explicit typing of buffers.
VoxelsUntyped(Voxels<?>) - Constructor for class org.anchoranalysis.image.voxel.VoxelsUntyped: Creates to wrap a Voxels of unspecified type.
voxelsWithMinMaxIntensity() - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: Finds the minimum-value and maximum of any voxel.
voxelWithMaxIntensity() - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: Finds the maximum-value of any voxel and rounding up (ceiling) to the nearest long.
voxelWithMinIntensity() - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter: Finds the minimum-value of any voxel and rounding down (floor) to the nearest long.

W

walk(UnsignedByteBuffer, BufferRetriever) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.kernel.WalkPredicate: Do any neighboring voxels in any direction satisfy the predicate?
walk(UnsignedByteBuffer, BufferRetriever) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.kernel.WalkRunnable: Walks in X and Y direction, and Z direction if enabled.
WalkPredicate - Class in org.anchoranalysis.image.voxel.iterator.neighbor.kernel: Walks in X, Y and Z directions from a point, test a NeighborPredicate to determine if a neighbor satisfies conditions.
WalkPredicate(KernelPointCursor, NeighborPredicate, boolean) - Constructor for class org.anchoranalysis.image.voxel.iterator.neighbor.kernel.WalkPredicate
WalkRunnable - Class in org.anchoranalysis.image.voxel.iterator.neighbor.kernel: Walks in X, Y and Z directions from a point, executing a Runnable if the neighbor satisfies conditions.
WalkRunnable(KernelPointCursor, Predicate<Point3i>, Runnable) - Constructor for class org.anchoranalysis.image.voxel.iterator.neighbor.kernel.WalkRunnable
withBuffer(Optional<ObjectMask>, Voxels<T>, ProcessBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMaskOptional: Iterate over each voxel (or optionally only on object-mask) with one associated buffer.
withBuffer(ObjectMask, Voxels<T>, ProcessBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask: Iterate over each voxel in an object-mask - with one associated buffer for each slice from Voxels.
withBuffer(Voxels<T>, ProcessBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Iterate over each voxel - with one associated buffer for each slice.
withBuffer(BoundingBox, Voxels<T>, ProcessBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox: Iterate over each voxel in a bounding-box - with one associated buffer for each slice
withCursor(BinaryVoxels<UnsignedByteBuffer>, KernelApplicationParameters, ProcessKernelPointCursor) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Iterate over each voxel using a KernelPointCursor.
withCursor(BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters, ProcessKernelPointCursor) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox: Iterate over each voxel in a bounding-box using a KernelPointCursor.
withCursorUntil(BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters, PredicateKernelPointCursor) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox: Iterate over each voxel in a bounding-box using a KernelPointCursor until a predicate returns true..
within(Optional<ObjectMask>, Extent, ProcessVoxelNeighborAbsolute<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborFactory: Creates to process neighbors that must lie within either an object-mask or an extent (as a fallback).
withinExtent(ProcessVoxelNeighborAbsoluteWithSlidingBuffer<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborFactory: Creates to process neighbors that must lie within an extent.
withinMask(ObjectMask, ProcessChangedPointAbsoluteMasked<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborFactory: Creates to process neighbors that must lie within an ObjectMask.
withinMask(ObjectMask, ProcessVoxelNeighborAbsolute<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborFactory: Creates to process neighbors that must lie within an ObjectMask.
withMatchingPoints(BoundingBox, Predicate<Point3i>, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox: Iterate over each voxel in a bounding-box that matches a predicate.
withPoint(Optional<ObjectMask>, Extent, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMaskOptional: Iterate over all points that are located on a object-mask or else all points in an extent.
withPoint(ObjectMask, Optional<ObjectMask>, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask: Iterate over each point that is located on an object-mask AND optionally a second-mask
withPoint(ObjectMask, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask: Iterate over each voxel that is located on an object-mask
withPoint(BoundingBox, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox: Iterate over each voxel in a bounding-box
withPoint(Extent, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Iterate over each voxel in an Extent
withPointAndIndex(BoundingBox, ProcessPointAndIndex) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox: Iterate over each voxel in a bounding-box
withPointAndIndex(Extent, ProcessPointAndIndex) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Iterate over each voxel in an Extent.
withSlidingBuffer(Optional<ObjectMask>, SlidingBuffer<?>, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMaskOptional: Iterate over each voxel in a sliding-buffer, optionally restricting it to be only voxels in a certain object
withThreeBuffers(Voxels<T>, Voxels<T>, Voxels<T>, ProcessBufferTernary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Iterate over each voxel - with three associated buffers for each slice.
withThreeBuffers(BoundingBox, ReadableTuple3i, ReadableTuple3i, Voxels<T>, Voxels<T>, Voxels<T>, ProcessBufferTernary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox: Iterate over each voxel in a bounding-box - with three associated buffers for each slice.
withTwoBuffers(Optional<ObjectMask>, Voxels<S>, Voxels<T>, ProcessBufferBinary<S, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMaskOptional: Iterate over each voxel (or optionally only on object-mask) with two associated buffers.
withTwoBuffers(BoundedVoxels<T>, BoundedVoxels<T>, ProcessBufferBinary<T, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.IterateVoxelsIntersectingBounded: Iterates over the intersection of two bounded-voxels of type BoundedVoxels.
withTwoBuffers(ObjectMask, Voxels<S>, Voxels<T>, ProcessBufferBinary<S, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask: 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.
withTwoBuffers(Voxels<UnsignedByteBuffer>, byte, BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, ProcessBufferBinary<UnsignedByteBuffer, UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.IterateVoxelsIntersectingBounded: Iterates over the intersection of two bounded-voxels of type BoundedVoxels but only voxels that lie on an object-mask.
withTwoBuffers(BoundingBox, ReadableTuple3i, Voxels<T>, Voxels<T>, ProcessBufferBinary<T, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox: Iterate over each voxel in a bounding-box - with two associated buffers for each slice, one VoxelBuffer and one Buffer
withTwoBuffersAndPoint(Voxels<S>, Voxels<T>, ProcessBufferBinary<S, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Iterate over each voxel - with two associated buffers for each slice
withTwoBuffersUntil(BoundedVoxels<T>, BoundedVoxels<T>, PredicateBufferBinary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.IterateVoxelsIntersectingBounded: Iterates over the intersection of two bounded-voxels of type BoundedVoxels until a predicate is satisfied.
withTwoBuffersUntil(BoundingBox, ReadableTuple3i, Voxels<T>, Voxels<T>, PredicateBufferBinary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox: Iterate over each voxel in a bounding-box - with two associated buffers for each slice - until a predicate evaluates to true.
withTwoBuffersWithoutOffset(VoxelBuffer<S>, VoxelBuffer<T>, ProcessBufferBinaryWithoutOffset<S, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsRemaining: Iterate over remaining voxels each voxel - with two associated buffers for each slice.
withTwoMixedBuffers(ObjectMask, Voxels<S>, Voxels<T>, ProcessVoxelBufferBinaryMixed<S, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask: Iterate over each voxel in an object-mask - with one associated voxel-buffer and one associated buffer for each slice.
withTwoMixedBuffers(Voxels<S>, Voxels<T>, ProcessVoxelBufferBinaryMixed<S, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Iterate over each voxel in a bounding-box - with one associated voxel-buffer and one associated buffer for each slice.
withTwoMixedBuffers(BoundingBox, ReadableTuple3i, Voxels<S>, Voxels<T>, ProcessBufferBinaryMixed<S, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox: Iterate over each voxel in a bounding-box - with two associated buffers for each slice.
withTwoVoxelBuffers(ObjectMask, Voxels<S>, Voxels<T>, ProcessVoxelBufferBinary<S, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask: Iterate over each voxel in an object-mask - with two associated voxel-buffers and for each slice.
withTwoVoxelBuffers(Voxels<S>, Voxels<T>, ProcessVoxelBufferBinary<S, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Iterate over each voxel in a bounding-box - with two associated voxel-buffers for each slice
withVoxelBuffer(ObjectMask, Voxels<T>, Optional<BoundingBox>, ProcessVoxelBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask: Iterate over each voxel on an object-mask with one associated VoxelBuffer.
withVoxelBuffer(ObjectMask, Voxels<T>, ProcessVoxelBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask: Iterate over each voxel on an object-mask with one associated VoxelBuffer.
withVoxelBuffer(Voxels<T>, ProcessVoxelBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Iterate over each voxel - with one associated voxel-buffer for each slice.
withVoxelBuffer(Voxels<T>, ProcessVoxelBufferUnaryWithPoint<T, E>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll: Iterate over each voxel - with one associated voxel-buffer for each slice.
wrapRaw(byte[]) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Exposes a raw byte-array as a buffer with unsigned-bytes.
wrapRaw(int[]) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Exposes a raw int-array as a buffer with unsigned-ints.
wrapRaw(short[]) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Exposes a raw short-array as a buffer with unsigned-shorts.
wrapRaw(ByteBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer: Exposes a raw ByteBuffer as a buffer with unsigned-bytes.
wrapRaw(IntBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer: Exposes a raw UnsignedIntBuffer as a buffer with unsigned-ints.
wrapRaw(ShortBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer: Exposes a raw UnsignedShortBuffer as a buffer with unsigned-shorts.

Z

zChange - Variable in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer: The change in the Z-dimension to reach this neighbor relative to the source coordinate.

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