Package | Description |
---|---|
org.anchoranalysis.image.voxel |
Data-structures to store and manipulate image raster-data or voxels.
|
org.anchoranalysis.image.voxel.factory |
Creates new instances of
Voxels and VoxelsUntyped with specific data-types. |
org.anchoranalysis.image.voxel.iterator |
Utilities to iterate over voxel-locations in images and sub-regions of images.
|
org.anchoranalysis.image.voxel.iterator.intersecting |
Like
org.anchoranalysis.image.voxel.iterator but refers to iterators that operation over
the intersecting regions of two entities. |
org.anchoranalysis.image.voxel.object |
The fundamental data class that is an
ObjectMask
and related structures. |
org.anchoranalysis.mpp.mark.voxelized |
A mark after a voxel-representation has been inferred.
|
org.anchoranalysis.mpp.overlap |
Calculating overlaps between two
Mark s. |
org.anchoranalysis.plugin.mpp.feature.overlap |
Implementations of
CalculationPart to calculate
overlap between two entities. |
Modifier and Type | Method and Description |
---|---|
BoundedVoxels<T> |
BoundedVoxels.duplicate()
A deep-copy of the current structure.
|
BoundedVoxels<T> |
BoundedVoxels.extractSlice(int sliceIndex)
Extracts a particular slice.
|
BoundedVoxels<T> |
BoundedVoxels.growBuffer(Point3i growthNegative,
Point3i growthPositive,
Optional<Extent> clipRegion,
VoxelsFactoryTypeBound<T> factory)
Grows the voxel buffer in the positive and negative directions by a certain amount.
|
BoundedVoxels<T> |
BoundedVoxels.growToZ(int sizeZ,
VoxelsFactoryTypeBound<T> factory)
Grows a single z-sliced
BoundedVoxels by duplicating the slice across the z-dimension
sizeZ number of times. |
BoundedVoxels<T> |
BoundedVoxels.mapBoundingBoxPreserveExtent(BoundingBox boundingBoxToAssign)
Applies a function to map the bounding-box to a new-value.
|
BoundedVoxels<T> |
BoundedVoxels.projectMax()
A maximum-intensity projection (flattens in z dimension)
|
BoundedVoxels<T> |
BoundedVoxels.region(BoundingBox box,
boolean reuseIfPossible)
A (sub-)region of the voxels.
|
BoundedVoxels<T> |
BoundedVoxels.regionIntersecting(BoundingBox box,
int voxelValueForRest)
Like
region(org.anchoranalysis.spatial.box.BoundingBox, boolean) but only expects a bounding-box that intersects at least partially. |
BoundedVoxels<T> |
BoundedVoxels.regionZ(int zMin,
int zMax,
VoxelsFactoryTypeBound<T> factory)
Creates an box with a subrange of the slices.
|
BoundedVoxels<T> |
BoundedVoxels.replaceVoxels(Voxels<T> voxelsToAssign)
Replaces the voxels in the box.
|
BoundedVoxels<T> |
BoundedVoxels.scale(ScaleFactor scaleFactor,
VoxelsResizer resizer,
Optional<Extent> clipTo)
Creates a scaled-version (in XY dimensions only) of the current bounding-box.
|
Modifier and Type | Method and Description |
---|---|
boolean |
BoundedVoxels.equalsDeep(BoundedVoxels<?> other)
Performs a deep equality check, that includes checking that each voxel has an
identical value.
|
Constructor and Description |
---|
BoundedVoxels(BoundedVoxels<T> source)
Copy constructor.
|
Modifier and Type | Method and Description |
---|---|
default BoundedVoxels<T> |
VoxelsFactoryTypeBound.createBounded(BoundingBox box)
Creates and initializes voxels that correspond to a particular bounding-box region.
|
Modifier and Type | Method and Description |
---|---|
static Optional<Point3i> |
IterateVoxelsEqualTo.untilFirstIntensityEqualTo(BoundedVoxels<UnsignedByteBuffer> voxels,
byte equalToValue)
Iterates each voxel until a specific intensity value is found.
|
Modifier and Type | Method and Description |
---|---|
static int |
CountVoxelsIntersectingBounded.countByte(BoundedVoxels<UnsignedByteBuffer> voxels1,
BoundedVoxels<UnsignedByteBuffer> voxels2,
PredicateTwoBytes predicate)
Counts all voxels in the intersection of two bounded-voxels of type
BoundedVoxels
that match a predicate. |
static int |
CountVoxelsIntersectingBounded.countByte(BoundedVoxels<UnsignedByteBuffer> voxels1,
BoundedVoxels<UnsignedByteBuffer> voxels2,
PredicateTwoBytes predicate)
Counts all voxels in the intersection of two bounded-voxels of type
BoundedVoxels
that match a predicate. |
static int |
CountVoxelsIntersectingBounded.countByteMasked(Voxels<UnsignedByteBuffer> maskGlobal,
byte onMaskGlobal,
BoundedVoxels<UnsignedByteBuffer> voxels1,
BoundedVoxels<UnsignedByteBuffer> voxels2,
PredicateTwoBytes predicate)
Counts all voxels intersection of two bounded-voxels of type
BoundedVoxels but only
voxels that lie on an object-mask and match a predicate. |
static int |
CountVoxelsIntersectingBounded.countByteMasked(Voxels<UnsignedByteBuffer> maskGlobal,
byte onMaskGlobal,
BoundedVoxels<UnsignedByteBuffer> voxels1,
BoundedVoxels<UnsignedByteBuffer> voxels2,
PredicateTwoBytes predicate)
Counts all voxels intersection of two bounded-voxels of type
BoundedVoxels but only
voxels that lie on an object-mask and match a predicate. |
static <T> void |
IterateVoxelsIntersectingBounded.withTwoBuffers(BoundedVoxels<T> voxels1,
BoundedVoxels<T> voxels2,
ProcessBufferBinary<T,T> process)
Iterates over the intersection of two bounded-voxels of type
BoundedVoxels . |
static <T> void |
IterateVoxelsIntersectingBounded.withTwoBuffers(BoundedVoxels<T> voxels1,
BoundedVoxels<T> voxels2,
ProcessBufferBinary<T,T> process)
Iterates over the intersection of two bounded-voxels of type
BoundedVoxels . |
static void |
IterateVoxelsIntersectingBounded.withTwoBuffers(Voxels<UnsignedByteBuffer> maskGlobal,
byte onMaskGlobal,
BoundedVoxels<UnsignedByteBuffer> voxels1,
BoundedVoxels<UnsignedByteBuffer> voxels2,
ProcessBufferBinary<UnsignedByteBuffer,UnsignedByteBuffer> process)
Iterates over the intersection of two bounded-voxels of type
BoundedVoxels but only
voxels that lie on an object-mask. |
static void |
IterateVoxelsIntersectingBounded.withTwoBuffers(Voxels<UnsignedByteBuffer> maskGlobal,
byte onMaskGlobal,
BoundedVoxels<UnsignedByteBuffer> voxels1,
BoundedVoxels<UnsignedByteBuffer> voxels2,
ProcessBufferBinary<UnsignedByteBuffer,UnsignedByteBuffer> process)
Iterates over the intersection of two bounded-voxels of type
BoundedVoxels but only
voxels that lie on an object-mask. |
static <T> Optional<Point3i> |
IterateVoxelsIntersectingBounded.withTwoBuffersUntil(BoundedVoxels<T> voxels1,
BoundedVoxels<T> voxels2,
PredicateBufferBinary<T> predicate)
Iterates over the intersection of two bounded-voxels of type
BoundedVoxels until a
predicate is satisfied. |
static <T> Optional<Point3i> |
IterateVoxelsIntersectingBounded.withTwoBuffersUntil(BoundedVoxels<T> voxels1,
BoundedVoxels<T> voxels2,
PredicateBufferBinary<T> predicate)
Iterates over the intersection of two bounded-voxels of type
BoundedVoxels until a
predicate is satisfied. |
Modifier and Type | Method and Description |
---|---|
BoundedVoxels<UnsignedByteBuffer> |
ObjectMask.boundedVoxels()
The underlying voxel memory buffers for the object-mask, exposed via
BoundedVoxels . |
Constructor and Description |
---|
ObjectMask(BoundedVoxels<UnsignedByteBuffer> voxels)
Creates from a
BoundedVoxels with UnsignedByteBuffer . |
ObjectMask(BoundedVoxels<UnsignedByteBuffer> voxels,
BinaryValuesInt binaryValues)
Creates from
BoundedVoxels and corresponding BinaryValuesInt . |
Modifier and Type | Method and Description |
---|---|
BoundedVoxels<UnsignedByteBuffer> |
VoxelizedMark.voxels() |
BoundedVoxels<UnsignedByteBuffer> |
VoxelizedMark.voxelsMaximumIntensityProjection() |
Modifier and Type | Method and Description |
---|---|
int |
CountIntersectingVoxels.count(BoundedVoxels<UnsignedByteBuffer> voxels1,
BoundedVoxels<UnsignedByteBuffer> voxels2) |
int |
CountIntersectingVoxels.count(BoundedVoxels<UnsignedByteBuffer> voxels1,
BoundedVoxels<UnsignedByteBuffer> voxels2) |
int |
CountIntersectingVoxels.countMasked(BoundedVoxels<UnsignedByteBuffer> voxels1,
BoundedVoxels<UnsignedByteBuffer> voxels2,
Voxels<UnsignedByteBuffer> maskGlobal,
byte onMaskGlobal) |
int |
CountIntersectingVoxels.countMasked(BoundedVoxels<UnsignedByteBuffer> voxels1,
BoundedVoxels<UnsignedByteBuffer> voxels2,
Voxels<UnsignedByteBuffer> maskGlobal,
byte onMaskGlobal) |
Constructor and Description |
---|
MaxIntensityProjectionPair(BoundedVoxels<UnsignedByteBuffer> voxels1,
BoundedVoxels<UnsignedByteBuffer> voxels2,
RegionMembershipWithFlags rmFlags1,
RegionMembershipWithFlags rmFlags2) |
MaxIntensityProjectionPair(BoundedVoxels<UnsignedByteBuffer> voxels1,
BoundedVoxels<UnsignedByteBuffer> voxels2,
RegionMembershipWithFlags rmFlags1,
RegionMembershipWithFlags rmFlags2) |
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.