Package | Description |
---|---|
org.anchoranalysis.image.core.dimensions |
Classes to describe the size of images or components of images both in voxels and physically.
|
org.anchoranalysis.image.core.object.label |
Labelling elements (object-masks or similar) with unique successive integers in a channel.
|
org.anchoranalysis.image.core.object.scale |
Scaling object-collections, or lists of elements with object-representations.
|
org.anchoranalysis.image.core.stack |
Defines the key data object,
Stack , and related
classes. |
org.anchoranalysis.image.voxel |
Data-structures to store and manipulate image raster-data or voxels.
|
org.anchoranalysis.image.voxel.assigner |
Assigns values to some or all voxels.
|
org.anchoranalysis.image.voxel.extracter |
Methods to read/copy/duplicate portions of voxels.
|
org.anchoranalysis.image.voxel.extracter.predicate |
Methods to find or count voxels that satisfy a predicate.
|
org.anchoranalysis.image.voxel.iterator |
Utilities to iterate over voxel-locations in images and sub-regions of images.
|
org.anchoranalysis.image.voxel.object |
The fundamental data class that is an
ObjectMask
and related structures. |
org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox |
Implementations of
FeatureSingleObject that consider an
object's bounding-box. |
org.anchoranalysis.plugin.mpp.contour.path |
A set of contiguously neighboring points along the outline of an object.
|
org.anchoranalysis.spatial.box |
Axis-aligned bounding-boxes and related operations.
|
org.anchoranalysis.spatial.point |
A cartesian-coordinate, across varying primitive types, in 2D and 3D space.
|
org.anchoranalysis.spatial.rtree |
R-Tree data structure and related operations.
|
Constructor and Description |
---|
Dimensions(ReadableTuple3i extent)
Construct with an explicit extent and no resolution.
|
Constructor and Description |
---|
LabelObjects(java.util.function.Function<T,ObjectMask> extractObject,
java.util.function.BiFunction<T,ReadableTuple3i,T> shiftElement) |
LabelObjects(Optional<java.util.function.UnaryOperator<T>> operationBeforeLabelling,
Optional<java.util.function.Consumer<OverlappingObject<T>>> overlappingObjectConsumer,
java.util.function.Function<T,ObjectMask> extractObject,
java.util.function.BiFunction<T,ReadableTuple3i,T> shiftElement) |
Modifier and Type | Method and Description |
---|---|
ObjectMask |
AccessObjectMaskSimple.shiftBy(ObjectMask element,
ReadableTuple3i quantity) |
T |
AccessObjectMask.shiftBy(T element,
ReadableTuple3i quantity)
Positionally-shifts an element by a given quantity in the positive direction.
|
Modifier and Type | Method and Description |
---|---|
RGBColor |
RGBStack.colorAtVoxel(ReadableTuple3i point)
Gets the color at a particular voxel.
|
Modifier and Type | Method and Description |
---|---|
ReadableTuple3i |
BoundedVoxels.cornerMin()
The minimum corner of the bounding box in each dimension.
|
Modifier and Type | Method and Description |
---|---|
static VoxelsAssigner |
VoxelsAssignerFactory.shiftBackBy(VoxelsAssigner voxelsAssigner,
ReadableTuple3i shift)
Shifts all coordinates backwards before passing to another
VoxelsAssigner . |
Modifier and Type | Method and Description |
---|---|
static <T> VoxelsExtracter<T> |
VoxelsExtracterFactory.atCorner(ReadableTuple3i corner,
VoxelsExtracter<T> delegate)
Projects a
VoxelsExtracter to a corner in a larger global space. |
int |
VoxelsExtracter.voxel(ReadableTuple3i point)
Gets the value of one particular voxel.
|
Constructor and Description |
---|
PredicateAtCorner(ReadableTuple3i corner,
VoxelsPredicate delegate) |
Modifier and Type | Method and Description |
---|---|
static <T> void |
IterateVoxelsBoundingBox.withThreeBuffers(BoundingBox box,
ReadableTuple3i shiftForSecond,
ReadableTuple3i shiftForThird,
Voxels<T> voxels1,
Voxels<T> voxels2,
Voxels<T> voxels3,
ProcessBufferTernary<T> process)
Iterate over each voxel in a bounding-box - with three associated buffers for each
slice.
|
static <T> void |
IterateVoxelsBoundingBox.withTwoBuffers(BoundingBox box,
ReadableTuple3i shiftForSecond,
Voxels<T> voxels1,
Voxels<T> voxels2,
ProcessBufferBinary<T,T> process)
Iterate over each voxel in a bounding-box - with two associated buffers for each
slice, one
VoxelBuffer and one Buffer |
static <T> Optional<Point3i> |
IterateVoxelsBoundingBox.withTwoBuffersUntil(BoundingBox box,
ReadableTuple3i shiftForSecond,
Voxels<T> voxels1,
Voxels<T> voxels2,
PredicateBufferBinary<T> predicate)
Iterate over each voxel in a bounding-box - with two associated buffers for each slice
- until a predicate evaluates to true.
|
static <S,T> void |
IterateVoxelsBoundingBox.withTwoMixedBuffers(BoundingBox box,
ReadableTuple3i shiftForSecond,
Voxels<S> voxels1,
Voxels<T> voxels2,
ProcessBufferBinaryMixed<S,T> process)
Iterate over each voxel in a bounding-box - with two associated buffers for each
slice.
|
Modifier and Type | Method and Description |
---|---|
void |
DeriveObjectFromPoints.add(ReadableTuple3i point)
Adds a point to the object.
|
ObjectMask |
ObjectMask.shiftBackBy(ReadableTuple3i shift)
Shifts the object-mask by moving its bounding-box backwards.
|
ObjectCollection |
ObjectCollection.shiftBy(ReadableTuple3i shiftBy)
Shifts the bounding-box of each object by adding to it.
|
ObjectMask |
ObjectMask.shiftBy(ReadableTuple3i shift)
Shifts the object-mask by moving its bounding-box forwards.
|
Modifier and Type | Method and Description |
---|---|
protected ReadableTuple3i |
BoundingBoxExtentAlongAxis.extractTupleForBoundingBox(BoundingBox box) |
protected abstract ReadableTuple3i |
BoundingBoxAlongAxisBase.extractTupleForBoundingBox(BoundingBox box) |
protected ReadableTuple3i |
BoundingBoxMinimumAlongAxis.extractTupleForBoundingBox(BoundingBox box) |
protected ReadableTuple3i |
BoundingBoxMaximumAlongAxis.extractTupleForBoundingBox(BoundingBox box) |
Modifier and Type | Method and Description |
---|---|
List<Point3i> |
ContiguousVoxelPath.addShift(ReadableTuple3i shift)
Adds a shift to each point (modifying the existing points in memory), and returns them as a
list
|
Modifier and Type | Method and Description |
---|---|
ReadableTuple3i |
Extent.asTuple()
Exposes the extent as a tuple.
|
ReadableTuple3i |
BoundingBox.calculateCornerMaxExclusive()
The maximum (right-most) point just outside the box.
|
ReadableTuple3i |
BoundingBox.calculateCornerMaxInclusive()
The maximum (right-most) point inside the box.
|
ReadableTuple3i |
BoundingBox.cornerMin()
The minimum corner of the bounding box in each dimension.
|
Modifier and Type | Method and Description |
---|---|
void |
PointRange.add(ReadableTuple3i point)
Adds a new point to be considered in the range.
|
boolean |
Extent.contains(ReadableTuple3i point)
Is a point of type
ReadableTuple3i contained within the extent? |
static BoundingBox |
BoundingBox.createDuplicate(ReadableTuple3i cornerMin,
Extent extent)
Creates a bounding-box from a corner and an extent - duplicating
cornerMin . |
static BoundingBox |
BoundingBox.createDuplicate(ReadableTuple3i cornerMinInclusive,
ReadableTuple3i cornerMaxInclusive)
Creates from two
int points (a minimum corner and a maximum corner) - reusing cornerMinInclusive internally. |
static Extent |
Extent.createFromTupleDuplicate(ReadableTuple3i tuple)
Creates from a
ReadableTuple3i representing the sizes in each dimension, where the
tuple is not used internally. |
static Extent |
Extent.createFromTupleReuse(ReadableTuple3i tuple)
Creates from a
ReadableTuple3i representing the sizes in each dimension, where the
tuple is used internally. |
static BoundingBox |
BoundingBox.createReuse(ReadableTuple3i cornerMin,
Extent extent)
Creates a bounding-box from a corner and an extent - reusing
cornerMin internally. |
static BoundingBox |
BoundingBox.createReuse(ReadableTuple3i cornerMinInclusive,
ReadableTuple3i cornerMaxInclusive)
Creates from two
int points (a minimum corner and a maximum corner) - reusing cornerMinInclusive internally. |
Extent |
Extent.growBy(ReadableTuple3i toAdd)
Creates a new
Extent with toAdd size added to each respective
dimension. |
int |
Extent.offset(ReadableTuple3i point)
Calculates a XYZ-offset of a point in a buffer whose dimensions are this extent.
|
int |
Extent.offsetSlice(ReadableTuple3i point)
Calculates a XY-offset of a point in a buffer whose dimensions are this extent.
|
boolean |
BoundingBoxContains.point(ReadableTuple3i point)
Is this point within the bounding-box?
|
BoundingBox |
BoundingBox.shiftBackBy(ReadableTuple3i shift)
Shifts the bounding-box backwards.
|
BoundingBox |
BoundingBox.shiftBy(ReadableTuple3i shift)
Shifts the bounding-box forwards.
|
BoundingBox |
BoundingBox.shiftTo(ReadableTuple3i cornerMinToAssign)
Assigns a new corner-location to the bounding-box.
|
Extent |
Extent.shrinkBy(ReadableTuple3i toSubtract)
Creates a new
Extent with toSubtract size subtracted from each
respective dimension. |
Modifier and Type | Class and Description |
---|---|
class |
Point3i
A three-dimensional point of int values.
|
class |
Tuple3i
A three-dimensional tuple of int values.
|
Modifier and Type | Method and Description |
---|---|
ReadableTuple3i |
ReadableTuple3i.duplicateChangeZ(int zValueToAssign)
Creates a copy of the current tuple, but with a different Z-component value.
|
Modifier and Type | Method and Description |
---|---|
void |
Tuple3i.add(ReadableTuple3i toAdd)
Arithmetically adds a
ReadableTuple3i 's values across each dimension. |
void |
Tuple3d.add(ReadableTuple3i toAdd)
Arithmetically adds a
ReadableTuple3i 's values across each dimension. |
default int |
ReadableTuple3i.compareTo(ReadableTuple3i other) |
static Point3d |
PointConverter.doubleFromInt(ReadableTuple3i point)
Convert a
ReadableTuple3i to a Point3d . |
static Point3i |
Point3i.elementwiseOperation(ReadableTuple3i tuple1,
ReadableTuple3i tuple2,
java.util.function.IntBinaryOperator operator)
Creates a new point by applying a pairwise operation to each dimension's values for two
tuples.
|
static Point3f |
PointConverter.floatFromInt(ReadableTuple3i point)
Convert a
ReadableTuple3i to a Point3f . |
static Point3f |
PointConverter.floatFromIntDropZ(ReadableTuple3i point)
Creates a
ReadableTuple3i to a Point3f , preserving X- and Y-components but
set setting the Z-component to be 0 . |
static Point3i |
Point3i.immutableAdd(ReadableTuple3i tuple,
int x,
int y,
int z)
Adds values to a tuple immutably.
|
static Point3i |
Point3i.immutableAdd(ReadableTuple3i tuple1,
ReadableTuple3i tuple2)
Adds two tuples immutably.
|
static Point3i |
Point3i.immutableAdd(ReadableTuple3i tuple1,
ReadableTuple3i tuple2,
ReadableTuple3i tuple3)
Adds three tuples immutably.
|
static Point3i |
Point3i.immutableScale(ReadableTuple3i point,
int factor)
Multiplies each component by
factor without changing any values in an existing point. |
static Point3i |
Point3i.immutableSubtract(ReadableTuple3i tuple,
ReadableTuple3i toSubtract)
Subtracts two tuples immutably.
|
default boolean |
ReadableTuple3i.matchAllDimensions(ReadableTuple3i point,
IntBinaryPredicate predicate)
Whether the values in each dimension satisfy a predicate, where the value in the current
object is the left argument, and the corresponding value in
point forms the right
argument. |
Point3i |
Tuple3i.max(ReadableTuple3i point)
Element-wise maximum between this point and another.
|
Point3d |
Point3d.min(ReadableTuple3i point)
Element-wise minimum between this point and another.
|
Point3i |
Tuple3i.min(ReadableTuple3i point)
Element-wise minimum between this point and another.
|
void |
Tuple3i.subtract(ReadableTuple3i valueToSubtract)
Arithmetically subtracts a value across each dimension.
|
Constructor and Description |
---|
Point3i(ReadableTuple3i point)
Creates with the same values as an existing
ReadableTuple3i . |
Modifier and Type | Method and Description |
---|---|
Set<T> |
BoundingBoxRTree.contains(ReadableTuple3i point)
Which objects contain a particular point?
|
java.util.stream.Stream<T> |
BoundingBoxRTree.containsStream(ReadableTuple3i point)
Like
BoundingBoxRTree.contains(org.anchoranalysis.spatial.point.ReadableTuple3i) but returns a Stream instead of a Set . |
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.