Package | Description |
---|---|
org.anchoranalysis.image.bean.nonbean.spatial.arrange |
Non-beans to specify how to form a single-image by spatially combining other images.
|
org.anchoranalysis.image.bean.spatial.arrange.align |
Aligning a
BoundingBox to fit inside another BoundingBox . |
org.anchoranalysis.image.core.channel |
The
Channel core data-class and related operations
and converters. |
org.anchoranalysis.image.core.dimensions |
Classes to describe the size of images or components of images both in voxels and physically.
|
org.anchoranalysis.image.core.mask |
An image with only two permissible states.
|
org.anchoranalysis.image.core.merge |
Merges two or more entities.
|
org.anchoranalysis.image.core.object.properties |
An
ObjectCollection with associated key-value
pairs. |
org.anchoranalysis.image.core.object.scale |
Scaling object-collections, or lists of elements with object-representations.
|
org.anchoranalysis.image.core.points |
Operations that extract points from image data entities or vice versa.
|
org.anchoranalysis.image.core.stack |
Defines the key data object,
Stack , and related
classes. |
org.anchoranalysis.image.io.bean.object.draw |
How to represent an object-mask in a raster that is being drawn.
|
org.anchoranalysis.image.io.stack |
Non-bean classes for reading / writing a
Stack from
and to the filesystem. |
org.anchoranalysis.image.io.stack.output.box |
Base classes for generators that ultimately write only a bounding-box portion of a
Stack to the filesystem. |
org.anchoranalysis.image.voxel |
Data-structures to store and manipulate image raster-data or voxels.
|
org.anchoranalysis.image.voxel.assigner |
Assigns values to some or all voxels.
|
org.anchoranalysis.image.voxel.extracter |
Methods to read/copy/duplicate portions of voxels.
|
org.anchoranalysis.image.voxel.extracter.predicate |
Methods to find or count voxels that satisfy a predicate.
|
org.anchoranalysis.image.voxel.factory |
Creates new instances of
Voxels and VoxelsUntyped with specific data-types. |
org.anchoranalysis.image.voxel.iterator |
Utilities to iterate over voxel-locations in images and sub-regions of images.
|
org.anchoranalysis.image.voxel.iterator.neighbor.kernel |
Routines for moving a
KernelPointCursor around the
neighboring voxels of the point. |
org.anchoranalysis.image.voxel.kernel |
Applying a kernel via
convolution to voxels.
|
org.anchoranalysis.image.voxel.object |
The fundamental data class that is an
ObjectMask
and related structures. |
org.anchoranalysis.mpp.mark |
Non-bean classes related to
Mark s. |
org.anchoranalysis.mpp.mark.conic |
Mark s implementing conic sections. |
org.anchoranalysis.mpp.mark.points |
Mark s implementing structures based on points. |
org.anchoranalysis.mpp.mark.voxelized |
A mark after a voxel-representation has been inferred.
|
org.anchoranalysis.mpp.overlay | |
org.anchoranalysis.overlay |
Overlay s and related classes involving drawing entities on top
of an image. |
org.anchoranalysis.overlay.bean |
Beans relating to drawing an
Overlay on an image. |
org.anchoranalysis.overlay.collection |
Collections of
Overlay s. |
org.anchoranalysis.overlay.object |
An implementation of an
Overlay that draws an ObjectMask on an image. |
org.anchoranalysis.plugin.image.bean.thumbnail.object |
Implementations of
ThumbnailFromObjects . |
org.anchoranalysis.plugin.image.feature.bean.object.combine |
Features from combinations of
ObjectMask s. |
org.anchoranalysis.plugin.image.feature.bean.object.pair.touching |
Features that calculate how many other objects an
ObjectMask directly neighbors. |
org.anchoranalysis.plugin.image.feature.bean.object.single.border |
Implementations of
FeatureSingleObject that determine if an
object lies at the border of an image. |
org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox |
Implementations of
FeatureSingleObject that consider an
object's bounding-box. |
org.anchoranalysis.plugin.mpp.bean.region |
Implementations of
MarkRegion . |
org.anchoranalysis.plugin.mpp.feature.bean.memo.pair |
Implementations of
FeaturePairMemo . |
org.anchoranalysis.spatial.box |
Axis-aligned bounding-boxes and related operations.
|
org.anchoranalysis.spatial.rtree |
R-Tree data structure and related operations.
|
org.anchoranalysis.test.image.segment |
Fixtures or other helper classes for testing image segmentation algorithms.
|
Modifier and Type | Method and Description |
---|---|
BoundingBox |
BoundingBoxEnclosed.getBox()
The
BoundingBox in which the image should be placed. |
BoundingBox |
BoundingBoxEnclosed.getEnclosing()
An enclosing box (equal to or larger than
box covering all screen-space used for this
entity, including padding. |
Modifier and Type | Method and Description |
---|---|
void |
StackArrangement.add(BoundingBox box)
Adds a new
BoundingBox to the arrangement, with no padding. |
static void |
StackCopierAtBox.copyImageInto(Stack source,
Stack destination,
BoundingBox box)
|
Constructor and Description |
---|
BoundingBoxEnclosed(BoundingBox box)
Create with a box that has no padding.
|
BoundingBoxEnclosed(BoundingBox box,
BoundingBox enclosing) |
StackArrangement(Extent extent,
BoundingBox box)
Create with a single
BoundingBox . |
Modifier and Type | Method and Description |
---|---|
BoundingBox |
BoxAligner.align(BoundingBox smaller,
BoundingBox larger)
|
BoundingBox |
BoxAligner.align(Extent smaller,
BoundingBox larger)
|
protected BoundingBox |
Grow.alignAfterCheck(BoundingBox smaller,
BoundingBox larger) |
protected BoundingBox |
Align.alignAfterCheck(BoundingBox smaller,
BoundingBox larger) |
protected abstract BoundingBox |
BoxAligner.alignAfterCheck(BoundingBox smaller,
BoundingBox larger)
|
protected BoundingBox |
Grow.alignAfterCheck(Extent smaller,
BoundingBox larger) |
protected BoundingBox |
Align.alignAfterCheck(Extent smaller,
BoundingBox larger) |
protected abstract BoundingBox |
BoxAligner.alignAfterCheck(Extent smaller,
BoundingBox larger)
|
Point3i |
Align.alignCorner(BoundingBox smaller,
Extent larger)
The minimum corner at which the entity should be locate after alignment, ignoring the space
to the left.
|
Modifier and Type | Method and Description |
---|---|
ObjectMask |
Channel.equalMask(BoundingBox box,
int equalValue)
|
Modifier and Type | Method and Description |
---|---|
boolean |
Dimensions.contains(BoundingBox box)
Is
box entirely contained within the extent? |
Modifier and Type | Method and Description |
---|---|
ObjectMask |
Mask.region(BoundingBox box,
boolean reuseIfPossible)
Creates an
ObjectMask corresponding to the on/off state in a bounding-box. |
Modifier and Type | Method and Description |
---|---|
static BoundingBox |
ObjectMaskMerger.mergeBoundingBoxes(ObjectCollection objects)
Merges all the bounding boxes of a collection of objects.
|
static BoundingBox |
ObjectMaskMerger.mergeBoundingBoxes(java.util.stream.Stream<ObjectMask> objects)
Merges all the bounding boxes of a stream of objects.
|
Modifier and Type | Method and Description |
---|---|
BoundingBox |
ObjectWithProperties.boundingBox()
The bounding-box which gives a location for the object-mask on an image.
|
Constructor and Description |
---|
ObjectWithProperties(BoundingBox box)
Creates as a bounding-box with all corresponding mask voxels set to off.
|
Modifier and Type | Method and Description |
---|---|
default BoundingBox |
AccessObjectMask.boundingBoxFor(T element)
A bounding-box for a given element.
|
Modifier and Type | Method and Description |
---|---|
static BoundingBox |
BoundingBoxFromPoints.fromStream(java.util.stream.Stream<Point3i> points)
Create from a stream of
Point3i s. |
static BoundingBox |
BoundingBoxFromPoints.fromTwoPoints(Point3d point1,
Point3d point2)
Creates a bounding-box for two unordered points.
|
Modifier and Type | Method and Description |
---|---|
void |
DisplayStack.copyPixelsTo(int channelIndex,
BoundingBox sourceBox,
Voxels<UnsignedByteBuffer> destinationVoxels,
BoundingBox destinationBox)
Copies pixels from a particular channel to an output buffer.
|
Channel |
DisplayStack.extractChannelForBoundingBox(int index,
BoundingBox box)
|
Modifier and Type | Method and Description |
---|---|
void |
IfElse.drawSingle(ObjectWithProperties object,
RGBStack stack,
ObjectDrawAttributes attributes,
int iteration,
BoundingBox restrictTo) |
void |
Outline.drawSingle(ObjectWithProperties object,
RGBStack stack,
ObjectDrawAttributes attributes,
int iteration,
BoundingBox restrictTo) |
void |
Flatten.drawSingle(ObjectWithProperties object,
RGBStack stack,
ObjectDrawAttributes attributes,
int iteration,
BoundingBox restrictTo) |
void |
Filled.drawSingle(ObjectWithProperties object,
RGBStack stack,
ObjectDrawAttributes attributes,
int iteration,
BoundingBox restrictTo) |
Modifier and Type | Method and Description |
---|---|
static RGBStack |
ConvertStackToRGB.convertCropped(DisplayStack stack,
BoundingBox box)
Converts a bounding-box region in
DisplayStack to a RGBStack . |
Modifier and Type | Method and Description |
---|---|
Stack |
ScaleableBackground.extractRegionFromStack(BoundingBox box)
Extracts a portion of a stack (flattened and maybe scaled) corresponding to a bounding-box
|
Stack |
ExtractBoundingBoxAreaFromStackGenerator.transform(BoundingBox element) |
Modifier and Type | Method and Description |
---|---|
static DrawObjectOnStackGenerator |
DrawObjectOnStackGenerator.createFromGenerator(TransformingGenerator<BoundingBox,Stack> backgroundGenerator,
int outlineWidth,
ColorIndex colors)
Creates an extracted-object generator that draws an outline - with default color green and
flattened in Z.
|
Modifier and Type | Method and Description |
---|---|
BoundingBox |
BoundedVoxels.boundingBox()
A bounding-box that associates voxels to a particular part of an image.
|
BoundingBox |
BoundedVoxels.dilate(boolean do3D,
Optional<Extent> clipRegion)
Grow bounding-box by 1 pixel in all directions.
|
Modifier and Type | Method and Description |
---|---|
static void |
ExtentMatchHelper.checkExtentMatch(BoundingBox box1,
BoundingBox box2)
Checks that the
Extent s of two bounding boxes are identical. |
void |
VoxelsUntyped.copyVoxelsTo(BoundingBox boxSource,
VoxelsUntyped destination,
BoundingBox boxDestination)
Copies the voxels into a
destination , but only those voxels inside a bounding-box. |
void |
VoxelsUntyped.copyVoxelsTo(ObjectMask objectSource,
VoxelsUntyped destination,
BoundingBox boxDestination)
Copies the voxels into a
destination , but only those voxels inside an ObjectMask . |
BoundedVoxels<T> |
BoundedVoxels.mapBoundingBoxPreserveExtent(BoundingBox boundingBoxToAssign)
Applies a function to map the bounding-box to a new-value.
|
BoundedVoxels<T> |
BoundedVoxels.region(BoundingBox box,
boolean reuseIfPossible)
A (sub-)region of the voxels.
|
BoundedVoxels<T> |
BoundedVoxels.regionIntersecting(BoundingBox box,
int voxelValueForRest)
Like
BoundedVoxels.region(org.anchoranalysis.spatial.box.BoundingBox, boolean) but only expects a bounding-box that intersects at least partially. |
Constructor and Description |
---|
BoundedVoxels(BoundingBox boundingBox,
Voxels<T> voxels)
Creates voxels with a corresponding bounding box.
|
Modifier and Type | Method and Description |
---|---|
void |
VoxelsAssigner.toBox(BoundingBox box)
Assigns to only voxels inside a bounding-box
|
void |
VoxelsAssigner.toEitherTwoObjects(ObjectMask object1,
ObjectMask object2,
BoundingBox restrictTo)
Sets voxels to a value if the position is on in either of two masks
|
void |
VoxelsAssigner.toObject(ObjectMask object,
BoundingBox restrictTo)
Sets voxels in a box to a particular value if they match a object-mask (but only a part of
the object-mask)
|
Modifier and Type | Method and Description |
---|---|
void |
VoxelsExtracter.boxCopyTo(BoundingBox from,
Voxels<T> voxelsDestination,
BoundingBox destinationBox)
Copies a bounding-box area to another
Voxels . |
void |
VoxelsExtracter.objectCopyTo(ObjectMask from,
Voxels<T> voxelsDestination,
BoundingBox destinationBox)
Copies an area corresponding to an object-mask to another
Voxels . |
Voxels<T> |
VoxelsExtracter.region(BoundingBox box,
boolean reuseIfPossible)
A (sub-)region of the voxels.
|
Modifier and Type | Method and Description |
---|---|
ObjectMask |
VoxelsPredicate.deriveObject(BoundingBox box)
Creates an
ObjectMask for all the voxels inside the bounding-box satisfying the
predicate. |
ObjectMask |
PredicateImplementation.deriveObject(BoundingBox box) |
ObjectMask |
PredicateAtCorner.deriveObject(BoundingBox box) |
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 <T> void |
IterateVoxelsBoundingBox.withBuffer(BoundingBox box,
Voxels<T> voxels,
ProcessBufferUnary<T> process)
Iterate over each voxel in a bounding-box - with one associated buffer for each slice
|
static void |
IterateVoxelsBoundingBox.withCursor(BinaryVoxels<UnsignedByteBuffer> voxels,
BoundingBox box,
KernelApplicationParameters parameters,
ProcessKernelPointCursor process)
Iterate over each voxel in a bounding-box using a
KernelPointCursor . |
static boolean |
IterateVoxelsBoundingBox.withCursorUntil(BinaryVoxels<UnsignedByteBuffer> voxels,
BoundingBox box,
KernelApplicationParameters parameters,
PredicateKernelPointCursor predicate)
Iterate over each voxel in a bounding-box using a
KernelPointCursor until a predicate
returns true.. |
static void |
IterateVoxelsBoundingBox.withMatchingPoints(BoundingBox box,
java.util.function.Predicate<Point3i> predicate,
ProcessPoint process)
Iterate over each voxel in a bounding-box that matches a predicate.
|
static void |
IterateVoxelsBoundingBox.withPoint(BoundingBox box,
ProcessPoint process)
Iterate over each voxel in a bounding-box
|
static void |
IterateVoxelsBoundingBox.withPointAndIndex(BoundingBox box,
ProcessPointAndIndex process)
Iterate over each voxel in a bounding-box
|
static <T> void |
IterateVoxelsBoundingBox.withThreeBuffers(BoundingBox box,
ReadableTuple3i shiftForSecond,
ReadableTuple3i shiftForThird,
Voxels<T> voxels1,
Voxels<T> voxels2,
Voxels<T> voxels3,
ProcessBufferTernary<T> process)
Iterate over each voxel in a bounding-box - with three associated buffers for each
slice.
|
static <T> void |
IterateVoxelsBoundingBox.withTwoBuffers(BoundingBox box,
ReadableTuple3i shiftForSecond,
Voxels<T> voxels1,
Voxels<T> voxels2,
ProcessBufferBinary<T,T> process)
Iterate over each voxel in a bounding-box - with two associated buffers for each
slice, one
VoxelBuffer and one Buffer |
static <T> Optional<Point3i> |
IterateVoxelsBoundingBox.withTwoBuffersUntil(BoundingBox box,
ReadableTuple3i shiftForSecond,
Voxels<T> voxels1,
Voxels<T> voxels2,
PredicateBufferBinary<T> predicate)
Iterate over each voxel in a bounding-box - with two associated buffers for each slice
- until a predicate evaluates to true.
|
static <S,T> void |
IterateVoxelsBoundingBox.withTwoMixedBuffers(BoundingBox box,
ReadableTuple3i shiftForSecond,
Voxels<S> voxels1,
Voxels<T> voxels2,
ProcessBufferBinaryMixed<S,T> process)
Iterate over each voxel in a bounding-box - with two associated buffers for each
slice.
|
Modifier and Type | Method and Description |
---|---|
static <T> void |
IterateVoxelsObjectMask.withVoxelBuffer(ObjectMask object,
Voxels<T> voxels,
Optional<BoundingBox> restrictTo,
ProcessVoxelBufferUnary<T> process)
Iterate over each voxel on an object-mask with one associated
VoxelBuffer . |
Modifier and Type | Method and Description |
---|---|
static void |
IterateKernelHelper.overBox(Kernel kernel,
BinaryVoxels<UnsignedByteBuffer> voxels,
BoundingBox box,
KernelApplicationParameters parameters,
ProcessKernelPointCursor processor)
Iterates over only voxels contained within a bounding-box.
|
static boolean |
IterateKernelHelper.overBoxUntil(Kernel kernel,
BinaryVoxels<UnsignedByteBuffer> voxels,
BoundingBox box,
KernelApplicationParameters parameters,
PredicateKernelPointCursor predicate)
Iterates over only voxels contained within a bounding-box until a predicate is matched
on a voxel.
|
Modifier and Type | Method and Description |
---|---|
static int |
ApplyKernel.applyForCount(CountKernel kernel,
BinaryVoxels<UnsignedByteBuffer> voxels,
BoundingBox box,
KernelApplicationParameters parameters)
Applies the kernel to voxels and sums the returned value.
|
static boolean |
ApplyKernel.applyUntilPositive(CountKernel kernel,
BinaryVoxels<UnsignedByteBuffer> voxels,
BoundingBox box,
KernelApplicationParameters parameters)
Applies the kernel to voxels until a positive value is returned, then exits with true.
|
Modifier and Type | Method and Description |
---|---|
BoundingBox |
ObjectMask.boundingBox()
The bounding-box which gives a location for the object-mask on an image.
|
Modifier and Type | Method and Description |
---|---|
Set<T> |
IntersectingObjects.intersectsWith(BoundingBox box)
All elements that intersect with a particular bounding box.
|
ObjectMask |
ObjectMask.mapBoundingBoxChangeExtent(BoundingBox boxToAssign)
Applies a function to map the bounding-box to a new-value (whose extent is expected to change
in value).
|
ObjectCollection |
ObjectMaskStream.mapBoundingBoxChangeExtent(BoundingBox boxToAssign)
Creates a new
ObjectCollection after mapping the bounding-box on each object (while
maybe changing the extent). |
ObjectMask |
ObjectMask.region(BoundingBox box,
boolean reuseIfPossible)
A (sub-)region of the object-mask.
|
ObjectMask |
ObjectMask.regionIntersecting(BoundingBox box)
Creates an object-mask covering the a bounding-box (that is required to intersect at least
partially)
|
ObjectMask |
ObjectMask.relativeMaskTo(BoundingBox box)
Creates a new object-mask with coordinates changed to be relative to another box.
|
Modifier and Type | Method and Description |
---|---|
ObjectMask |
ObjectMask.mapBoundingBoxPreserveExtent(java.util.function.UnaryOperator<BoundingBox> mapOperation)
Applies a function to map the bounding-box to a new-value (whose extent should be unchanged
in value).
|
ObjectCollection |
ObjectMaskStream.mapBoundingBoxPreserveExtent(java.util.function.UnaryOperator<BoundingBox> mapFunction)
Creates a new
ObjectCollection after mapping the bounding-box on each object (whose
extent should remain unchanged). |
Constructor and Description |
---|
ObjectMask(BoundingBox box)
Creates as a bounding-box with all corresponding mask voxels set to off.
|
ObjectMask(BoundingBox box,
BinaryVoxels<UnsignedByteBuffer> voxels)
Creates from a
BinaryVoxels and a corresponding bounding-box. |
ObjectMask(BoundingBox box,
Voxels<UnsignedByteBuffer> voxels)
|
ObjectMask(BoundingBox box,
Voxels<UnsignedByteBuffer> voxels,
BinaryValuesByte binaryValues)
Like
ObjectMask(BoundingBox, Voxels, BinaryValuesInt) but specifies the
binary-values as bytes. |
ObjectMask(BoundingBox box,
Voxels<UnsignedByteBuffer> voxels,
BinaryValuesInt binaryValues)
|
Modifier and Type | Method and Description |
---|---|
abstract BoundingBox |
Mark.box(Dimensions dimensions,
int regionID) |
abstract BoundingBox |
Mark.boxAllRegions(Dimensions dimensions) |
Modifier and Type | Method and Description |
---|---|
List<BoundingBox> |
MarkCollection.boxList(Dimensions dimensions,
int regionID) |
Modifier and Type | Method and Description |
---|---|
ColoredMarks |
ColoredMarks.subsetWhereBBoxIntersects(Dimensions dimensions,
int regionID,
List<BoundingBox> intersectList) |
Modifier and Type | Method and Description |
---|---|
BoundingBox |
MarkWithPositionAndSingleRadius.box(Dimensions dimensions,
int regionID) |
BoundingBox |
Ellipsoid.box(Dimensions dimensions,
int regionID) |
BoundingBox |
Ellipse.box(Dimensions dimensions,
int regionID) |
BoundingBox |
MarkWithPositionAndSingleRadius.boxAllRegions(Dimensions dimensions) |
BoundingBox |
Ellipsoid.boxAllRegions(Dimensions dimensions) |
BoundingBox |
Ellipse.boxAllRegions(Dimensions dimensions) |
static BoundingBox |
BoundingBoxCalculator.boxFromBounds(Point3d pos,
double radius,
boolean do3D,
Dimensions dimensions)
Calculates a bounding box for a point with a scalar radius in all dimensions.
|
static BoundingBox |
BoundingBoxCalculator.boxFromBounds(Point3d center,
cern.colt.matrix.DoubleMatrix1D radiiMatrix,
boolean do3D,
Dimensions dimensions)
Calculates a bounding box for a point with varying radii in each dimension (that have already
been resolved into a matrix)
|
Modifier and Type | Method and Description |
---|---|
protected BoundingBox |
PointListBase.box() |
BoundingBox |
RotatableBoundingBox.box(Dimensions dimensions,
int regionID) |
BoundingBox |
PointListBase.box(Dimensions dimensions,
int regionID) |
BoundingBox |
LineSegment.box(Dimensions dimensions,
int regionID) |
BoundingBox |
PointList.boxAllRegions(Dimensions dimensions) |
BoundingBox |
RotatableBoundingBox.boxAllRegions(Dimensions dimensions) |
BoundingBox |
PolygonCurve.boxAllRegions(Dimensions dimensions) |
BoundingBox |
Polygon.boxAllRegions(Dimensions dimensions) |
BoundingBox |
LineSegment.boxAllRegions(Dimensions dimensions) |
Modifier and Type | Method and Description |
---|---|
BoundingBox |
VoxelizedMark.boundingBox()
A bounding-box enclosing the voxelized representation of the mark
|
BoundingBox |
VoxelizedMark.boundingBoxFlattened()
The bounding-box flattened in z dimension
|
Modifier and Type | Method and Description |
---|---|
BoundingBox |
OverlayMark.box(DrawOverlay overlayWriter,
Dimensions dim) |
Modifier and Type | Method and Description |
---|---|
abstract BoundingBox |
Overlay.box(DrawOverlay overlayWriter,
Dimensions dimensions)
A bounding-box around the overlay.
|
Modifier and Type | Method and Description |
---|---|
void |
DrawObject.drawCollection(ObjectCollectionWithProperties objects,
RGBStack stack,
ObjectDrawAttributes attributes,
BoundingBox boxContainer)
Writes object-masks onto of a
RGBStack - within a bounding box only. |
abstract void |
DrawObject.drawSingle(ObjectWithProperties object,
RGBStack stack,
ObjectDrawAttributes attributes,
int iteration,
BoundingBox restrictTo)
Draws a single-object on top of a RGB-stack.
|
Modifier and Type | Method and Description |
---|---|
ColoredOverlayCollection |
ColoredOverlayCollection.subsetWhereBoxIntersects(Dimensions scene,
DrawOverlay drawOverlay,
List<BoundingBox> toIntersectWith)
Find overlays whose bounding-boxes intersect with any of the boxes in
toIntersectWith . |
Modifier and Type | Method and Description |
---|---|
BoundingBox |
OverlayObjectMask.box(DrawOverlay overlayWriter,
Dimensions dimensions) |
Modifier and Type | Method and Description |
---|---|
abstract ThumbnailBatch<ObjectCollection> |
ThumbnailFromObjects.start(ObjectCollection objects,
StreamableCollection<BoundingBox> boundingBoxes,
Optional<Stack> background,
ExecutionTimeRecorder executionTimeRecorder)
Initializes a batch to create thumbnails.
|
ThumbnailBatch<ObjectCollection> |
OutlinePreserveRelativeSize.start(ObjectCollection objects,
StreamableCollection<BoundingBox> boundingBoxes,
Optional<Stack> backgroundSource,
ExecutionTimeRecorder executionTimeRecorder) |
Modifier and Type | Method and Description |
---|---|
protected BoundingBox |
PairNeighbors.boundingBoxThatSpansInput(FeatureInputPairObjects input) |
protected BoundingBox |
EachObjectIndependently.boundingBoxThatSpansInput(FeatureInputSingleObject input) |
protected abstract BoundingBox |
CombineObjectsForFeatures.boundingBoxThatSpansInput(T input)
Creates a bounding-box that tightly fits the input to a particular table row (could be for
one or more objects)
|
Modifier and Type | Method and Description |
---|---|
protected double |
HasTouchingVoxels.calculateWithIntersection(ObjectMask first,
ObjectMask second,
BoundingBox boxIntersect) |
protected abstract double |
TouchingVoxels.calculateWithIntersection(ObjectMask object1,
ObjectMask object2,
BoundingBox boxIntersect) |
protected double |
NumberTouchingVoxels.calculateWithIntersection(ObjectMask object1,
ObjectMask object2,
BoundingBox boxIntersect) |
protected double |
NumberTouchingVoxelFaces.calculateWithIntersection(ObjectMask object1,
ObjectMask object2,
BoundingBox boxIntersect) |
Modifier and Type | Method and Description |
---|---|
protected boolean |
AtBorderXY.isBoundingBoxAtBorder(BoundingBox boundingBox,
Extent extent) |
protected boolean |
AtBorderZ.isBoundingBoxAtBorder(BoundingBox boundingBox,
Extent extent) |
protected abstract boolean |
AtBorderBase.isBoundingBoxAtBorder(BoundingBox boundingBox,
Extent extent) |
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 |
---|---|
protected BoundingBox |
IndexedRegionBase.boundingBoxForRegion(VoxelizedMark vozelized) |
Modifier and Type | Method and Description |
---|---|
protected VoxelStatistics |
CenterSliceWindow.createStatisticsForBBox(VoxelizedMark mark,
Dimensions dimensions,
BoundingBox box,
int zCenter) |
protected abstract VoxelStatistics |
CenterSliceBase.createStatisticsForBBox(VoxelizedMark mark,
Dimensions dimensions,
BoundingBox box,
int zCenter) |
protected VoxelStatistics |
CenterSlice.createStatisticsForBBox(VoxelizedMark mark,
Dimensions dimensions,
BoundingBox box,
int zCenter) |
Modifier and Type | Method and Description |
---|---|
protected BoundingBox |
FeaturePairMemoSingleRegion.box(FeatureInputPairMemo input,
java.util.function.Function<FeatureInputPairMemo,VoxelizedMarkMemo> funcExtract) |
Modifier and Type | Method and Description |
---|---|
static BoundingBox |
BoundingBoxFactory.at(int x,
int y,
int width,
int height)
Short-hand factory method for creating a 2D bounding-box.
|
static BoundingBox |
BoundingBoxFactory.at(int x,
int y,
int z,
int width,
int height,
int depth)
Short-hand factory method for creating a 3D bounding-box.
|
BoundingBox |
BoundedList.boundingBox()
A bounding-box that must contain all elements in the collection
|
BoundingBox |
BoundingBox.changeExtent(Extent extent)
Creates a copied
BoundingBox but with a different extent. |
BoundingBox |
BoundingBox.changeExtent(java.util.function.UnaryOperator<Extent> extentOperator)
Creates a copied
BoundingBox but with a different extent. |
BoundingBox |
BoundingBox.changeExtentZ(int extentZ)
Creates a copied
BoundingBox but with a different extent in the Z-dimension. |
BoundingBox |
BoundingBox.changeZ(int cornerZ,
int extentZ)
Creates a copied
BoundingBox but with a different corner and extent in the
Z-dimension. |
BoundingBox |
BoundingBox.clampTo(Extent extent)
Ensures that the box fits inside a
Extent by reducing any values to their limits in
the respective dimension. |
static BoundingBox |
BoundingBox.createDuplicate(ReadableTuple3i cornerMin,
Extent extent)
Creates a bounding-box from a corner and an extent - duplicating
cornerMin . |
static BoundingBox |
BoundingBox.createDuplicate(ReadableTuple3i cornerMinInclusive,
ReadableTuple3i cornerMaxInclusive)
Creates from two
int points (a minimum corner and a maximum corner) - reusing cornerMinInclusive internally. |
static BoundingBox |
BoundingBox.createReuse(Point3d cornerMinInclusive,
Point3d cornerMaxInclusive)
Creates from two
double points (a minimum corner and a maximum corner). |
static BoundingBox |
BoundingBox.createReuse(ReadableTuple3i cornerMin,
Extent extent)
Creates a bounding-box from a corner and an extent - reusing
cornerMin internally. |
static BoundingBox |
BoundingBox.createReuse(ReadableTuple3i cornerMinInclusive,
ReadableTuple3i cornerMaxInclusive)
Creates from two
int points (a minimum corner and a maximum corner) - reusing cornerMinInclusive internally. |
BoundingBox |
BoundingBox.flattenZ()
Collapses the z-dimension of the box to a single voxel depth, and a corner at
0
voxels. |
BoundingBox |
BoundingBox.growBy(Tuple3i toAdd,
Extent containingExtent)
Grow the bounding-box by
toAdd amount in each dimension in both positive and negative
directions. |
static BoundingBox |
BoundingBoxMerger.merge(java.util.stream.Stream<BoundingBox> stream)
Merges all the bounding boxes in a stream.
|
BoundingBox |
BoundingBox.reflectThroughOrigin()
Reflects the bounding box through the origin.
|
BoundingBox |
BoundingBox.relativePositionToBox(BoundingBox other)
A new bounding-box using relative position coordinates to another box.
|
BoundingBox |
BoundingBox.scale(ScaleFactor scaleFactor)
Scales the bounding-box, both the corner-point and the extent.
|
BoundingBox |
BoundingBox.scale(ScaleFactor scaleFactor,
Extent extentToAssign)
Scales the bounding-box corner-point, and assigns a new extent.
|
BoundingBox |
BoundingBox.scaleClampTo(ScaleFactor scaleFactor,
Extent clampTo)
Scales the bounding-box, both the corner-point and the extent - ensuring it remains inside a
containing-extent.
|
BoundingBox |
BoundingBox.shiftBackBy(ReadableTuple3i shift)
Shifts the bounding-box backwards.
|
BoundingBox |
BoundingBox.shiftBy(ReadableTuple3i shift)
Shifts the bounding-box forwards.
|
BoundingBox |
BoundingBox.shiftTo(ReadableTuple3i cornerMinToAssign)
Assigns a new corner-location to the bounding-box.
|
BoundingBox |
BoundingBox.shiftToOrigin()
Moves the bounding-box to the origin (0,0,0) but preserves the extent.
|
BoundingBox |
BoundingBox.shiftToZ(int cornerZToAssign)
Assigns a new z-slice corner-location to the bounding-box.
|
BoundingBox |
PointRange.toBoundingBox()
Creates a
BoundingBox to just cover the range of points that have been added. |
BoundingBox |
PointRange.toBoundingBoxNoCheck()
Like
PointRange.toBoundingBox() but if no points exist, an exception is not thrown. |
static BoundingBox |
BoundingBoxFactory.uniform3D(int corner,
int extent)
Short-hand factory method for creating a 3D bounding-box, where a coordinate is identical in
each dimension.
|
BoundingBox |
BoundingBoxUnion.with(BoundingBox other)
Performs a union with another box (immutably).
|
Modifier and Type | Method and Description |
---|---|
Optional<BoundingBox> |
BoundingBoxIntersection.with(BoundingBox other)
Finds the intersection with another bounding-box, if it exists.
|
Optional<BoundingBox> |
BoundingBoxIntersection.withInside(BoundingBox other,
Extent containingExtent)
Finds the intersection and clamp to a containing extent.
|
Modifier and Type | Method and Description |
---|---|
BoundedList<T> |
BoundedList.assignBoundingBox(BoundingBox boxToAssign)
Assigns a new containing bounding-box.
|
BoundedList<T> |
BoundedList.assignBoundingBoxAndMap(BoundingBox boxToAssign,
java.util.function.UnaryOperator<T> mappingFunction)
Assigns a new containing bounding-box and maps each individual element.
|
boolean |
BoundingBoxContains.box(BoundingBox maybeContainedInside)
Is this other bounding-box fully contained within this bounding box?
|
int |
BoundingBox.compareTo(BoundingBox other) |
boolean |
Extent.contains(BoundingBox box)
Is
box entirely contained within the extent? |
static double |
BoundingBoxDistance.distance(BoundingBox box1,
BoundingBox box2,
boolean includeZ)
Calculates the distance between two
BoundingBox es. |
boolean |
BoundingBoxIntersection.existsWith(BoundingBox other)
Does intersection exist with another bounding-box?
|
static double |
IntersectionOverUnion.forBoxes(BoundingBox box1,
BoundingBox box2)
Calculates the intersection-over-union score a pair of bounding-boxes.
|
Point3i |
BoundingBox.relativePositionTo(BoundingBox other)
The relative position of the corner to another bounding box.
|
BoundingBox |
BoundingBox.relativePositionToBox(BoundingBox other)
A new bounding-box using relative position coordinates to another box.
|
BoundingBox |
BoundingBoxUnion.with(BoundingBox other)
Performs a union with another box (immutably).
|
Optional<BoundingBox> |
BoundingBoxIntersection.with(BoundingBox other)
Finds the intersection with another bounding-box, if it exists.
|
Optional<BoundingBox> |
BoundingBoxIntersection.withInside(BoundingBox other,
Extent containingExtent)
Finds the intersection and clamp to a containing extent.
|
Modifier and Type | Method and Description |
---|---|
static <T> BoundedList<T> |
BoundedList.createFromList(List<T> list,
java.util.function.Function<T,BoundingBox> extractBoundingBox)
Creates for a list, minimally fitting a bounding-box around all elements
|
static <T> BoundedList<T> |
BoundedList.createSingle(T element,
java.util.function.Function<T,BoundingBox> extractBoundingBox)
Creates for a single element using its current bounding-box.
|
boolean |
BoundingBoxIntersection.existsWithAny(List<BoundingBox> others)
Does intersection exist with with any of the others in the list?
|
static BoundingBox |
BoundingBoxMerger.merge(java.util.stream.Stream<BoundingBox> stream)
Merges all the bounding boxes in a stream.
|
Constructor and Description |
---|
BoundingBoxContains(BoundingBox box)
Create with the
BoundingBox that is queried. |
BoundingBoxIntersection(BoundingBox box) |
BoundingBoxUnion(BoundingBox box) |
Modifier and Type | Method and Description |
---|---|
void |
BoundingBoxRTree.add(BoundingBox box,
T payload)
Adds a bounding-box with a corresponding payload.
|
Set<T> |
BoundingBoxRTree.intersectsWith(BoundingBox toIntersectWith)
Which bounding-boxes intersect with another specific bounding box?
|
java.util.stream.Stream<T> |
BoundingBoxRTree.intersectsWithStream(BoundingBox toIntersectWith)
|
void |
BoundingBoxRTree.remove(BoundingBox box,
T payload)
Removes a particular item from the r-tree, identified by its bounding-box and payload.
|
Constructor and Description |
---|
SpatiallySeparate(java.util.function.Function<T,BoundingBox> extractBoundingBox) |
Modifier and Type | Method and Description |
---|---|
protected abstract BoundingBox |
InstanceSegmentationTestBase.targetBox()
The bounding-box we use to set an area where we expect segments to reside.
|
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.