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

Packages that use BinaryVoxels

Package	Description
org.anchoranalysis.image.bean.segment.binary	Base classes to perform binary-segmentation.
org.anchoranalysis.image.bean.threshold	Base classes for thresholding and calculating levels for thresholding.
org.anchoranalysis.image.core.mask	An image with only two permissible states.
org.anchoranalysis.image.core.mask.combine	Binary operations involving voxelwise combination of Mask.
org.anchoranalysis.image.inference.segment	Non-beans pertaining to segmentation of images via model inference.
org.anchoranalysis.image.voxel.binary	The BinaryVoxels class and related operations.
org.anchoranalysis.image.voxel.binary.connected	Creating an ObjectCollection that is a connected component labelling of a BinaryVoxels.
org.anchoranalysis.image.voxel.iterator	Utilities to iterate over voxel-locations in images and sub-regions of images.
org.anchoranalysis.image.voxel.iterator.neighbor.kernel	Routines for moving a KernelPointCursor around the neighboring voxels of the point.
org.anchoranalysis.image.voxel.kernel	Applying a kernel via convolution to voxels.
org.anchoranalysis.image.voxel.kernel.outline	Kernel to find outline voxels on an object.
org.anchoranalysis.image.voxel.object	The fundamental data class that is an ObjectMask and related structures.
org.anchoranalysis.image.voxel.object.morphological	Morphological operations applied to ObjectMasks.
org.anchoranalysis.image.voxel.object.morphological.predicate	Predicates to match certain voxels as used in org.anchoranalysis.image.voxel.object.morphological.
org.anchoranalysis.image.voxel.thresholder	Thresholding operations on voxels.
org.anchoranalysis.plugin.fiji.bean.channel.provider.distance	Euclidean Distance Transform implementations via FIJI.
org.anchoranalysis.plugin.fiji.bean.threshold	Implementations of Thresholder that use FIJI.
org.anchoranalysis.plugin.image.bean.segment.binary	Implementations of BinarySegmentation.
org.anchoranalysis.plugin.imagej.bean.threshold	Implementations of Thresholder that call ImageJ.
org.anchoranalysis.plugin.imagej.channel.provider	Implementations of ChannelProvider that call ImageJ.
org.anchoranalysis.plugin.imagej.mask	Non-bean classes involving ObjectMask that call ImageJ.
org.anchoranalysis.plugin.mpp.bean.contour.visitscheduler	The VisitScheduler and related classes, as used in TraverseOuterContourOnImage.
org.anchoranalysis.plugin.mpp.bean.segment.binary	Implementations of BinarySegmentation involving Mark or related classes.

Uses of BinaryVoxels in org.anchoranalysis.image.bean.segment.binary

Methods in org.anchoranalysis.image.bean.segment.binary that return BinaryVoxels

Modifier and Type	Method and Description
abstract BinaryVoxels<UnsignedByteBuffer>	BinarySegmentation.segment(VoxelsUntyped voxels, BinarySegmentationParameters parameters, Optional<ObjectMask> objectMask) Performs a segmentation on voxels so that each voxel has an on or off state after the operation.
BinaryVoxels<UnsignedByteBuffer>	BinarySegmentationThreshold.segment(VoxelsUntyped voxels, BinarySegmentationParameters parameters, Optional<ObjectMask> objectMask)
BinaryVoxels<UnsignedByteBuffer>	BinarySegmentationReference.segment(VoxelsUntyped voxels, BinarySegmentationParameters parameters, Optional<ObjectMask> objectMask)
BinaryVoxels<UnsignedByteBuffer>	BinarySegmentationUnary.segment(VoxelsUntyped voxels, BinarySegmentationParameters parameters, Optional<ObjectMask> objectMask)
protected abstract BinaryVoxels<UnsignedByteBuffer>	BinarySegmentationUnary.segmentFromExistingSegmentation(VoxelsUntyped voxels, BinarySegmentationParameters parameters, Optional<ObjectMask> objectMask, BinarySegmentation segment) Performs a binary-segmentation, in a similar manner to BinarySegmentation.segment(org.anchoranalysis.image.voxel.VoxelsUntyped, org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters, java.util.Optional<org.anchoranalysis.image.voxel.object.ObjectMask>) but with the delegate as additional argument.

Uses of BinaryVoxels in org.anchoranalysis.image.bean.threshold

Methods in org.anchoranalysis.image.bean.threshold that return BinaryVoxels

Modifier and Type	Method and Description
BinaryVoxels<UnsignedByteBuffer>	Thresholder.threshold(VoxelsUntyped voxels) Like Thresholder.threshold(VoxelsUntyped) but using default binary-values.
BinaryVoxels<UnsignedByteBuffer>	Thresholder.threshold(VoxelsUntyped voxels, BinaryValuesByte binaryValues) Like Thresholder.threshold(VoxelsUntyped, BinaryValuesByte, Optional, Optional) applying the thresholding to the entire set of voxels.
BinaryVoxels<UnsignedByteBuffer>	ThresholderGlobal.threshold(VoxelsUntyped inputBuffer, BinaryValuesByte bvOut, Optional<Histogram> histogram, Optional<ObjectMask> objectMask)
abstract BinaryVoxels<UnsignedByteBuffer>	Thresholder.threshold(VoxelsUntyped voxels, BinaryValuesByte binaryValues, Optional<Histogram> histogram, Optional<ObjectMask> objectMask) Thresholds voxels (across a range of values) so that they have only binary range (i.e.

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

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

Modifier and Type	Method and Description
BinaryVoxels<UnsignedByteBuffer>	Mask.binaryVoxels() The underlying voxels in the mask, exposed as BinaryVoxels.

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

Modifier and Type	Method and Description
void	Mask.replaceBy(BinaryVoxels<UnsignedByteBuffer> voxels) Replaces the underlying voxels in the mask with new voxels.

Constructors in org.anchoranalysis.image.core.mask with parameters of type BinaryVoxels

Constructor and Description
Mask(BinaryVoxels<UnsignedByteBuffer> voxels) Creates a mask from an existing binary-voxels using default image resolution.
Mask(BinaryVoxels<UnsignedByteBuffer> voxels, Optional<Resolution> resolution) Creates a mask from an existing binary-voxels and a specific image resolution.

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

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

Modifier and Type	Method and Description
static void	MaskXor.apply(BinaryVoxels<UnsignedByteBuffer> voxelsFirst, BinaryVoxels<UnsignedByteBuffer> voxelsSecond) Performs a logical xor (exclusive or) operation on each voxel in two Voxels (considered to be masks), writing the result onto the second mask.
static void	MaskXor.apply(BinaryVoxels<UnsignedByteBuffer> voxelsFirst, BinaryVoxels<UnsignedByteBuffer> voxelsSecond) Performs a logical xor (exclusive or) operation on each voxel in two Voxels (considered to be masks), writing the result onto the second mask.

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

Methods in org.anchoranalysis.image.inference.segment that return BinaryVoxels

Modifier and Type	Method and Description
static BinaryVoxels<UnsignedByteBuffer>	ScaleAndThresholdVoxels.scaleAndThreshold(Voxels<FloatBuffer> voxels, Extent targetSize, VoxelsResizer resizer, float maskMinValue) Scales voxels representing a mask to a target size, and then thresholds.

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

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

Modifier and Type	Method and Description
protected abstract BinaryVoxels<T>	BinaryVoxels.binaryVoxelsFor(Voxels<T> voxels, BinaryValuesInt binaryValues) Creates a BinaryVoxels corresponding to a particular voxels and BinaryValuesInt.
static BinaryVoxels<UnsignedByteBuffer>	BinaryVoxelsFactory.createEmptyOff(Extent extent) Creates binary-voxels using unsigned 8-bit byte type and with all voxels set to off (0).
static BinaryVoxels<?>	BinaryVoxelsFactory.createEmptyOff(Extent extent, VoxelDataType dataType) Creates an empty binary-voxels of a particular data-type with all voxels initialized to off.
static BinaryVoxels<UnsignedByteBuffer>	BinaryVoxelsFactory.createEmptyOn(Extent extent) Creates binary-voxels using unsigned 8-bit byte type and with all voxels set to on (255).
abstract BinaryVoxels<T>	BinaryVoxels.duplicate() Deep-copy of the object, including duplicating voxel buffers in memory.
static BinaryVoxels<UnsignedByteBuffer>	BinaryVoxelsFactory.reuseByte(Voxels<UnsignedByteBuffer> voxels) Like BinaryVoxelsFactory.reuseByte(org.anchoranalysis.image.voxel.Voxels<org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer>) but uses default binary-values for off (0) and on (255).
static BinaryVoxels<UnsignedByteBuffer>	BinaryVoxelsFactory.reuseByte(Voxels<UnsignedByteBuffer> voxels, BinaryValuesInt binaryValues) Reuses an existing voxel-buffer (of type unsigned byte) as a binary-version which should have only two intensity-values representing off and on.
static BinaryVoxels<UnsignedIntBuffer>	BinaryVoxelsFactory.reuseInt(Voxels<UnsignedIntBuffer> voxels, BinaryValuesInt binaryValues) Reuses an existing voxel-buffer (of type unsigned int) as a binary-version which should have only two intensity-values representing off and on.
BinaryVoxels<T>	BinaryVoxels.sliceBinary(int z) A particular z-slice, wrapped into a BinaryVoxels.

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

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

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

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

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

Modifier and Type	Method and Description
static void	IterateVoxelsBoundingBox.withCursor(BinaryVoxels<UnsignedByteBuffer> voxels, BoundingBox box, KernelApplicationParameters parameters, ProcessKernelPointCursor process) Iterate over each voxel in a bounding-box using a KernelPointCursor.
static void	IterateVoxelsAll.withCursor(BinaryVoxels<UnsignedByteBuffer> voxels, KernelApplicationParameters parameters, ProcessKernelPointCursor process) Iterate over each voxel using a KernelPointCursor.
static boolean	IterateVoxelsBoundingBox.withCursorUntil(BinaryVoxels<UnsignedByteBuffer> voxels, BoundingBox box, KernelApplicationParameters parameters, PredicateKernelPointCursor predicate) Iterate over each voxel in a bounding-box using a KernelPointCursor until a predicate returns true..

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

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

Modifier and Type	Method and Description
static void	IterateKernelHelper.overAll(Kernel kernel, BinaryVoxels<UnsignedByteBuffer> voxels, KernelApplicationParameters parameters, ProcessKernelPointCursor processor) Iterates over all voxels.
static void	IterateKernelHelper.overBox(Kernel kernel, BinaryVoxels<UnsignedByteBuffer> voxels, BoundingBox box, KernelApplicationParameters parameters, ProcessKernelPointCursor processor) Iterates over only voxels contained within a bounding-box.
static boolean	IterateKernelHelper.overBoxUntil(Kernel kernel, BinaryVoxels<UnsignedByteBuffer> voxels, BoundingBox box, KernelApplicationParameters parameters, PredicateKernelPointCursor predicate) Iterates over only voxels contained within a bounding-box until a predicate is matched on a voxel.

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

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

Modifier and Type	Method and Description
static BinaryVoxels<UnsignedByteBuffer>	ApplyKernel.apply(BinaryKernel kernel, BinaryVoxels<UnsignedByteBuffer> voxels, KernelApplicationParameters parameters) Apply the kernel to BinaryVoxels<UnsignedByteBuffer> using the same binary-values as voxels to calculate a value for each voxel.

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

Modifier and Type	Method and Description
static BinaryVoxels<UnsignedByteBuffer>	ApplyKernel.apply(BinaryKernel kernel, BinaryVoxels<UnsignedByteBuffer> voxels, KernelApplicationParameters parameters) Apply the kernel to BinaryVoxels<UnsignedByteBuffer> using the same binary-values as voxels to calculate a value for each voxel.
static int	ApplyKernel.applyForCount(BinaryKernel kernel, BinaryVoxels<UnsignedByteBuffer> voxels, KernelApplicationParameters parameters) Applies a BinaryKernel to voxels and counts how many true values occur en aggregate.
static int	ApplyKernel.applyForCount(CountKernel kernel, BinaryVoxels<UnsignedByteBuffer> voxels, BoundingBox box, KernelApplicationParameters parameters) Applies the kernel to voxels and sums the returned value.
static int	ApplyKernel.applyForCount(CountKernel kernel, BinaryVoxels<UnsignedByteBuffer> voxels, KernelApplicationParameters parameters) Applies the kernel to voxels and sums the returned value.
static boolean	ApplyKernel.applyUntilPositive(CountKernel kernel, BinaryVoxels<UnsignedByteBuffer> voxels, BoundingBox box, KernelApplicationParameters parameters) Applies the kernel to voxels until a positive value is returned, then exits with true.

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

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

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

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

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

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

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

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

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

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

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

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

Modifier and Type	Method and Description
static BinaryVoxels<UnsignedByteBuffer>	MorphologicalDilation.dilate(BinaryVoxels<UnsignedByteBuffer> voxels, int iterations, DilationContext context) Performs a morphological dilation operation.
static BinaryVoxels<UnsignedByteBuffer>	MorphologicalErosion.erode(BinaryVoxels<UnsignedByteBuffer> voxels, int iterations, boolean useZ, Optional<java.util.function.Predicate<Point3i>> precondition) Performs a morphological erosion on a BinaryVoxels<UnsignedByteBuffer> voxels.

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

Modifier and Type	Method and Description
static BinaryVoxels<UnsignedByteBuffer>	MorphologicalDilation.dilate(BinaryVoxels<UnsignedByteBuffer> voxels, int iterations, DilationContext context) Performs a morphological dilation operation.
static BinaryVoxels<UnsignedByteBuffer>	MorphologicalErosion.erode(BinaryVoxels<UnsignedByteBuffer> voxels, int iterations, boolean useZ, Optional<java.util.function.Predicate<Point3i>> precondition) Performs a morphological erosion on a BinaryVoxels<UnsignedByteBuffer> voxels.

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

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

Modifier and Type	Method and Description
boolean	AcceptIterationPredicate.accept(BinaryVoxels<UnsignedByteBuffer> voxels) Whether a particular voxels fulfills the condition or not.
boolean	AcceptIterationList.accept(BinaryVoxels<UnsignedByteBuffer> voxels)

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

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

Modifier and Type	Method and Description
static BinaryVoxels<UnsignedByteBuffer>	VoxelsThresholder.threshold(VoxelsUntyped voxels, float level, BinaryValuesByte binaryValues, Optional<ObjectMask> objectMask, boolean alwaysDuplicate) Applies thresholding to VoxelsUntyped.
static BinaryVoxels<UnsignedByteBuffer>	VoxelsThresholder.thresholdFloat(Voxels<FloatBuffer> voxels, float level, BinaryValuesByte binaryValues) Applies thresholding to Voxels of float data type.

Uses of BinaryVoxels in org.anchoranalysis.plugin.fiji.bean.channel.provider.distance

Methods in org.anchoranalysis.plugin.fiji.bean.channel.provider.distance with parameters of type BinaryVoxels

Modifier and Type	Method and Description
Voxels<UnsignedByteBuffer>	DistanceTransform3D.createDistanceMapForVoxels(BinaryVoxels<UnsignedByteBuffer> voxels, Optional<Resolution> resolution, float multiplyByZRes)

Uses of BinaryVoxels in org.anchoranalysis.plugin.fiji.bean.threshold

Methods in org.anchoranalysis.plugin.fiji.bean.threshold that return BinaryVoxels

Modifier and Type	Method and Description
BinaryVoxels<UnsignedByteBuffer>	ThresholderAutoIJ.threshold(VoxelsUntyped inputBuffer, BinaryValuesByte binaryValues, Optional<Histogram> histogram, Optional<ObjectMask> objectMask)

Uses of BinaryVoxels in org.anchoranalysis.plugin.image.bean.segment.binary

Methods in org.anchoranalysis.plugin.image.bean.segment.binary that return BinaryVoxels

Modifier and Type	Method and Description
BinaryVoxels<UnsignedByteBuffer>	Sequence.segment(VoxelsUntyped voxels, BinarySegmentationParameters parameters, Optional<ObjectMask> objectMask)
BinaryVoxels<UnsignedByteBuffer>	ThresholdAgainstChannel.segment(VoxelsUntyped voxels, BinarySegmentationParameters parameters, Optional<ObjectMask> object)
BinaryVoxels<UnsignedByteBuffer>	Repeat.segmentFromExistingSegmentation(VoxelsUntyped voxels, BinarySegmentationParameters parameters, Optional<ObjectMask> objectMask, BinarySegmentation segment)
BinaryVoxels<UnsignedByteBuffer>	Invert.segmentFromExistingSegmentation(VoxelsUntyped voxels, BinarySegmentationParameters parameters, Optional<ObjectMask> objectMask, BinarySegmentation segment)

Uses of BinaryVoxels in org.anchoranalysis.plugin.imagej.bean.threshold

Methods in org.anchoranalysis.plugin.imagej.bean.threshold that return BinaryVoxels

Modifier and Type	Method and Description
BinaryVoxels<UnsignedByteBuffer>	ThresholderSimpleFillHoles2D.threshold(VoxelsUntyped inputBuffer, BinaryValuesByte bvOut, Optional<Histogram> histogram, Optional<ObjectMask> objectMask)

Uses of BinaryVoxels in org.anchoranalysis.plugin.imagej.channel.provider

Methods in org.anchoranalysis.plugin.imagej.channel.provider with parameters of type BinaryVoxels

Modifier and Type	Method and Description
static void	FilterHelper.processEachSlice(BinaryVoxels<UnsignedByteBuffer> voxels, java.util.function.Consumer<ij.process.ImageProcessor> consumer) Applies a Consumer to each slice independently of a BinaryVoxels<UnsignedByteBuffer>.

Uses of BinaryVoxels in org.anchoranalysis.plugin.imagej.mask

Methods in org.anchoranalysis.plugin.imagej.mask that return BinaryVoxels

Modifier and Type	Method and Description
static BinaryVoxels<UnsignedByteBuffer>	ApplyImageJMorphologicalOperation.applyOperation(BinaryVoxels<UnsignedByteBuffer> voxels, String command, int iterations)

Methods in org.anchoranalysis.plugin.imagej.mask with parameters of type BinaryVoxels

Modifier and Type	Method and Description
static BinaryVoxels<UnsignedByteBuffer>	ApplyImageJMorphologicalOperation.applyOperation(BinaryVoxels<UnsignedByteBuffer> voxels, String command, int iterations)
static void	ApplyImageJMorphologicalOperation.fill(BinaryVoxels<UnsignedByteBuffer> voxels)

Uses of BinaryVoxels in org.anchoranalysis.plugin.mpp.bean.contour.visitscheduler

Methods in org.anchoranalysis.plugin.mpp.bean.contour.visitscheduler with parameters of type BinaryVoxels

Modifier and Type	Method and Description
static boolean	VisitSchedulerConvexAboutRoot.isPointConvexTo(Point3i root, Point3i point, BinaryVoxels<UnsignedByteBuffer> binaryValues)
static boolean	VisitSchedulerConvexAboutRoot.isPointConvexTo(Point3i root, Point3i destPoint, BinaryVoxels<UnsignedByteBuffer> voxels, boolean debug)

Uses of BinaryVoxels in org.anchoranalysis.plugin.mpp.bean.segment.binary

Methods in org.anchoranalysis.plugin.mpp.bean.segment.binary that return BinaryVoxels

Modifier and Type	Method and Description
BinaryVoxels<UnsignedByteBuffer>	SegmentThresholdAboveMinBound.segment(VoxelsUntyped voxels, BinarySegmentationParameters parameters, Optional<ObjectMask> objectMask)