Package | Description |
---|---|
org.anchoranalysis.annotation.io.assignment |
A pairing of objects from two collections (bipartite matching).
|
org.anchoranalysis.feature.energy |
A particular stack used in feature-calculations called a
EnergyStack together with related classes. |
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 |
Beans to define entities or operate that consider Euclidian space.
|
org.anchoranalysis.image.bean.spatial.arrange |
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.bean.spatial.arrange.fill |
Montages images together to completely fill the available space, while preserving aspect ratio.
|
org.anchoranalysis.image.bean.spatial.arrange.overlay |
Combining other images through overlaying.
|
org.anchoranalysis.image.bean.spatial.arrange.tile |
Combining other images through tiling.
|
org.anchoranalysis.image.core.bufferedimage |
Conversions and operations involving Java AWT's
BufferedImage . |
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.dimensions.size.suggestion |
Suggestions on a size for an image.
|
org.anchoranalysis.image.core.mask |
An image with only two permissible states.
|
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.inference.bean.reduce |
Beans to reduce the number of results that are returned from inference, by removing overlaping
entities etc.
|
org.anchoranalysis.image.inference.bean.segment.reduce |
Non-bean classes to reduce the number of results that are returned from inference, by removing
overlapping entities etc.
|
org.anchoranalysis.image.inference.segment |
Non-beans pertaining to segmentation of images via model inference.
|
org.anchoranalysis.image.io.bean.stack.combine |
Beans to combine multiple stacks into a single stack before outputting.
|
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.arithmetic |
Arithmetic operations for
Voxels . |
org.anchoranalysis.image.voxel.binary |
The
BinaryVoxels class and related operations. |
org.anchoranalysis.image.voxel.buffer |
A buffer of voxel-values, usually corresponding to a single z-slice in
Voxels . |
org.anchoranalysis.image.voxel.buffer.slice |
A container with voxel-buffers for each z-slice.
|
org.anchoranalysis.image.voxel.convert.imglib2 |
Converts anchor data-structures to those used by ImgLib2.
|
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 |
Iterating over a point's neighboring voxels.
|
org.anchoranalysis.image.voxel.kernel |
Applying a kernel via
convolution to voxels.
|
org.anchoranalysis.image.voxel.neighborhood |
A region in proximity to a voxel, encompassing this voxel as well as others.
|
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
ObjectMask s. |
org.anchoranalysis.image.voxel.projection |
Classes for calculating differnet kind of projections of voxel values across multiple buffers.
|
org.anchoranalysis.image.voxel.projection.extrema |
Classes for performing both a Maximum Intensity
Projection and a minimum projection.
|
org.anchoranalysis.image.voxel.resizer |
Different interpolator methods to use when scaling voxels.
|
org.anchoranalysis.io.bioformats.copyconvert |
Converts the byte stream opened by Bioformats into channels of particular data-type.
|
org.anchoranalysis.io.bioformats.metadata |
Reading metadata information from files using EXIF and/or other metadata headers.
|
org.anchoranalysis.io.imagej.convert |
Converts to and from ImageJ data-structures for images.
|
org.anchoranalysis.io.imagej.resizer |
Image interpolation when scaling using ImageJ.
|
org.anchoranalysis.plugin.image.bean.channel.aggregator |
Implementations of
ConvertChannelTo and ConvertChannelToWithHistogram . |
org.anchoranalysis.plugin.image.bean.object.provider.morphological |
Implementations of
ObjectCollectionProvider
involving morphological operations. |
org.anchoranalysis.plugin.image.bean.object.segment.reduce |
Strategies for reducing the number of elements with a list by merging/removing lower-confidence
elements that overlap.
|
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.object.calculation.single |
Implementations of
CalculationPart that that
process a single ObjectMask . |
org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological |
Implementations of
CalculationPart that that
process a single ObjectMask - with morphological operations. |
org.anchoranalysis.plugin.image.segment.watershed.encoding |
Encoding voxels in a watershed-transformation implementation.
|
org.anchoranalysis.plugin.image.task.size |
Non-bean classes pertaining to determining the size of an image.
|
org.anchoranalysis.plugin.image.task.slice |
Non-bean classes pertaining to combining stacks into a single stack.
|
org.anchoranalysis.plugin.io.multifile |
Non-bean classes to help use multiple files to represent a single
Stack . |
org.anchoranalysis.plugin.opencv.bean.feature |
Extracting features using OpenCV.
|
org.anchoranalysis.plugin.opencv.convert |
Conversion to/from OpenCV data-structures.
|
org.anchoranalysis.plugin.opencv.resizer |
Interpolation non-beans that use OpenCV.
|
org.anchoranalysis.spatial.box |
Axis-aligned bounding-boxes and related operations.
|
org.anchoranalysis.spatial.scale |
How to much to scale an entity in Cartesian space by.
|
org.anchoranalysis.test.image |
Testing utilities and fixtures with no greater downstream dependency than anchor-image-io
or anchor-io-bioformats or anchor-imagej.
|
org.anchoranalysis.test.image.object |
Fixtures for creating object-masks.
|
Modifier and Type | Method and Description |
---|---|
void |
OverlappingObjects.removeTouchingBorderXY(Extent extent)
Removes any objects from the assignment if they touch the X or Y scene border.
|
Modifier and Type | Method and Description |
---|---|
Extent |
EnergyStackWithoutParameters.extent()
The width and height and depth of all
Channel s in the stack. |
Extent |
EnergyStack.extent()
The width and height and depth of all
Channel s in the stack. |
Modifier and Type | Method and Description |
---|---|
Extent |
StackArrangement.extent()
The size of the larger image in which all the
BoundingBox es in list must
fully reside. |
Constructor and Description |
---|
StackArrangement(Extent extent)
Create with the overall
Extent and no boxes. |
StackArrangement(Extent extent,
BoundingBox box)
Create with a single
BoundingBox . |
StackArrangement(Extent extent,
List<BoundingBoxEnclosed> boxes) |
Modifier and Type | Method and Description |
---|---|
Extent |
SizeXY.asExtent()
Creates an extent with identical width and height and depth (z-extent) of 1.
|
Extent |
SizeXY.asExtent(int depth)
Creates an extent with identical width and height and a specific depth (z-extent).
|
Constructor and Description |
---|
SizeXY(Extent extent)
Create form an
Extent . |
Modifier and Type | Method and Description |
---|---|
StackArrangement |
Single.arrangeStacks(Iterator<Extent> extents,
OperationContext context) |
abstract StackArrangement |
StackArranger.arrangeStacks(Iterator<Extent> extents,
OperationContext context)
Arranges stacks to that they fit together in a single raster.
|
Modifier and Type | Method and Description |
---|---|
BoundingBox |
BoxAligner.align(Extent smaller,
BoundingBox larger)
|
BoundingBox |
BoxAligner.align(Extent smaller,
Extent 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)
|
protected BoundingBox |
Grow.alignAfterCheck(Extent smaller,
Extent larger) |
protected BoundingBox |
Align.alignAfterCheck(Extent smaller,
Extent larger) |
protected abstract BoundingBox |
BoxAligner.alignAfterCheck(Extent smaller,
Extent 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 |
---|---|
Extent |
ExtentToArrange.getExtent()
The
Extent . |
static Extent |
FitCombinedScaler.scaleToWidth(List<List<ExtentToArrange>> partitions,
boolean permitPartialFinalRow,
int width)
Calculates the size of the combined image to use for the montage, and scales the associated
Extent each to match. |
Modifier and Type | Method and Description |
---|---|
StackArrangement |
Fill.arrangeStacks(Iterator<Extent> extents,
OperationContext context) |
Constructor and Description |
---|
ExtentToArrange(int index,
Extent extent)
Create with a particular index and size.
|
Modifier and Type | Method and Description |
---|---|
StackArrangement |
Overlay.arrangeStacks(Iterator<Extent> extents,
OperationContext context) |
Modifier and Type | Method and Description |
---|---|
StackArrangement |
Tile.arrangeStacks(Iterator<Extent> extents,
OperationContext context) |
Modifier and Type | Method and Description |
---|---|
static BufferedImage |
BufferedImageFromStack.createRGB(Voxels<UnsignedByteBuffer> red,
Voxels<UnsignedByteBuffer> green,
Voxels<UnsignedByteBuffer> blue,
Extent extent)
Creates a
BufferedImage from three Voxels<UnsignedByteBuffer> representing
respectively, red, green, blue color components. |
Modifier and Type | Method and Description |
---|---|
Extent |
Channel.extent()
The size of the voxels across three dimensions.
|
Modifier and Type | Method and Description |
---|---|
Channel |
Channel.resizeXY(Extent extentToAssign,
VoxelsResizer resizer)
Resizes the dimensions of the channel, interpolating the existing voxel values to match.
|
Modifier and Type | Method and Description |
---|---|
Extent |
Dimensions.extent()
The width and height and depth of the image.
|
abstract Extent |
OrientationChange.extent(Extent extent)
A
Extent that describes extent after the orientation change. |
Modifier and Type | Method and Description |
---|---|
Dimensions |
Dimensions.duplicateChangeExtent(Extent extentToAssign)
Deep-copies the current object, but assigns a different
Extent . |
abstract Extent |
OrientationChange.extent(Extent extent)
A
Extent that describes extent after the orientation change. |
abstract int |
OrientationChange.index(int x,
int y,
Extent extent)
Determines the index in a output-array to put an element after applying the
orientation-change.
|
abstract int |
OrientationChange.index(int existingIndex,
int x,
int y,
Extent extent)
Like {#link determineOutputIndex(int,int,Extent)} but also accepts an index.
|
Constructor and Description |
---|
Dimensions(Extent extent)
Construct with an explicit extent and no resolution.
|
Dimensions(Extent extent,
Optional<Resolution> resolution) |
Modifier and Type | Method and Description |
---|---|
ScaleFactor |
ImageSizeSuggestion.calculateScaleFactor(Optional<Extent> extentToBeScaled)
Calculates the scaling factor.
|
Modifier and Type | Method and Description |
---|---|
Extent |
Mask.extent()
The size of the voxels across three dimensions.
|
Modifier and Type | Method and Description |
---|---|
ObjectMask |
AccessObjectMaskSimple.clipTo(ObjectMask element,
Extent extent) |
T |
AccessObjectMask.clipTo(T element,
Extent extent)
Ensures the element lies within a certain extent.
|
static <T> ScaledElements<T> |
Scaler.scaleElements(List<T> elements,
ScaleFactor factor,
boolean overlappingObjects,
Extent clipTo,
AccessObjectMask<T> access)
Scales every element in a list collectively, ensuring the results remain inside a particular
region.
|
static ScaledElements<ObjectMask> |
Scaler.scaleObjects(ObjectCollection objects,
ScaleFactor factor,
boolean overlappingObjects,
Extent clipTo)
Scales every object-mask in a collection collectively, ensuring the results remain
inside a particular region.
|
Modifier and Type | Method and Description |
---|---|
Extent |
RGBStack.extent()
The width and height and depth of the image.
|
Extent |
DisplayStack.extent()
The width and height and depth of all channels in the
Stack . |
Extent |
Stack.extent()
The width and height and depth of the image.
|
Constructor and Description |
---|
RGBStack(Extent extent)
Creates a particularly-sized stack with unsigned byte voxel data type, with all voxels
initialized to 0.
|
RGBStack(Extent extent,
ChannelFactorySingleType factory)
Creates a particularly-sized stack with all channels initialized to 0.
|
RGBStack(Extent extent,
Color color)
Creates a particularly-sized stack with unsigned byte voxel data type, with all voxels
initialized to a specific
Color . |
RGBStack(Extent extent,
RGBColor color)
Creates a particularly-sized stack with unsigned byte voxel data type, with all voxels
initialized to a specific
RGBColor . |
Stack(Extent extent)
Creates a
Stack with a single unsigned-byte channel of size channel . |
Modifier and Type | Method and Description |
---|---|
ReductionOutcome<LabelledWithConfidence<ObjectMask>> |
ReduceElementsGreedy.reduce(List<LabelledWithConfidence<ObjectMask>> elements,
Extent extent,
ExecutionTimeRecorder executionTimeRecorder) |
Modifier and Type | Method and Description |
---|---|
abstract ReductionOutcome<LabelledWithConfidence<T>> |
ReduceElements.reduce(List<LabelledWithConfidence<T>> elements,
Extent extent,
ExecutionTimeRecorder executionTimeRecorder)
Reduce a list of elements (each with a confidence score and a label) to a
smaller-list.
|
Modifier and Type | Method and Description |
---|---|
Extent |
SegmentedObjectsAtScale.extent()
The width and height and depth of the background image, associated with the objects.
|
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.
|
Modifier and Type | Method and Description |
---|---|
void |
TextStyle.drawText(String textToDraw,
BufferedImage image,
Extent extent)
Draws text on a
BufferedImage . |
Modifier and Type | Method and Description |
---|---|
Extent |
ScaleableBackground.sizeAfterAnyScaling()
The size of the background after any scaling has occurred.
|
Modifier and Type | Field and Description |
---|---|
static Extent |
Voxels.MAX_IN_TO_STRING
The maximum number of rows/columns/slices to show in
Voxels.toString() . |
Modifier and Type | Method and Description |
---|---|
Extent |
VoxelsUntyped.extent()
The size of the voxels across three dimensions.
|
Extent |
BoundedVoxels.extent()
The size of the voxels across three dimensions, and also the size of the associated
bounding-box.
|
Extent |
Voxels.extent()
The size of the voxels across three dimensions.
|
Modifier and Type | Method and Description |
---|---|
BoundingBox |
BoundedVoxels.dilate(boolean do3D,
Optional<Extent> clipRegion)
Grow bounding-box by 1 pixel in all directions.
|
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.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 |
---|---|
static VoxelsArithmetic |
VoxelsArithmeticFactory.createFloat(Extent extent,
java.util.function.IntFunction<FloatBuffer> bufferForSlice)
Create a
VoxelsArithmetic for FloatBuffer . |
static VoxelsArithmetic |
VoxelsArithmeticFactory.createUnsignedByte(Extent extent,
java.util.function.IntFunction<UnsignedByteBuffer> bufferForSlice)
Create a
VoxelsArithmetic for UnsignedByteBuffer . |
static VoxelsArithmetic |
VoxelsArithmeticFactory.createUnsignedInt(Extent extent,
java.util.function.IntFunction<UnsignedIntBuffer> bufferForSlice)
Create a
VoxelsArithmetic for UnsignedIntBuffer . |
static VoxelsArithmetic |
VoxelsArithmeticFactory.createUnsignedShort(Extent extent,
java.util.function.IntFunction<UnsignedShortBuffer> bufferForSlice)
Create a
VoxelsArithmetic for UnsignedShortBuffer . |
Modifier and Type | Method and Description |
---|---|
Extent |
BinaryVoxels.extent()
The size of the voxels across three dimensions.
|
Modifier and Type | Method and Description |
---|---|
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).
|
Modifier and Type | Method and Description |
---|---|
Extent |
SlidingBuffer.extent()
The size of the voxels across three dimensions.
|
Modifier and Type | Method and Description |
---|---|
Extent |
FromShort.extent() |
Extent |
FromFloat.extent() |
Extent |
FromByte.extent() |
Extent |
SliceBufferIndex.extent()
The size of each buffer.
|
Extent |
FromInt.extent() |
Modifier and Type | Method and Description |
---|---|
static SliceBufferIndex<UnsignedShortBuffer> |
FromShort.createInitialized(Extent extent)
Create a buffer of a particular size, that has been initialized.
|
static SliceBufferIndex<FloatBuffer> |
FromFloat.createInitialized(Extent extent)
Create a buffer of a particular size, that has been initialized.
|
static SliceBufferIndex<UnsignedByteBuffer> |
FromByte.createInitialized(Extent extent)
Create a buffer of a particular size, that has been initialized.
|
static SliceBufferIndex<UnsignedIntBuffer> |
FromInt.createInitialized(Extent extent)
Create a buffer of a particular size, that has been initialized.
|
static SliceBufferIndex<UnsignedShortBuffer> |
FromShort.createUninitialized(Extent extent)
Create a buffer of a particular size, that has not been initialized.
|
static SliceBufferIndex<FloatBuffer> |
FromFloat.createUninitialized(Extent extent)
Create a buffer of a particular size, that has not been initialized.
|
static SliceBufferIndex<UnsignedByteBuffer> |
FromByte.createUninitialized(Extent extent)
Create a buffer of a particular size, that has not been initialized.
|
static SliceBufferIndex<UnsignedIntBuffer> |
FromInt.createUninitialized(Extent extent)
Create a buffer of a particular size, that has not been initialized.
|
Modifier and Type | Method and Description |
---|---|
static net.imglib2.img.Img<net.imglib2.type.numeric.integer.UnsignedByteType> |
ConvertToImg.fromByte(VoxelBuffer<UnsignedByteBuffer> buffer,
Extent extent)
Creates an
Img from a VoxelBuffer with an unsigned byte data-type. |
static net.imglib2.img.Img<net.imglib2.type.numeric.real.FloatType> |
ConvertToImg.fromFloat(VoxelBuffer<FloatBuffer> buffer,
Extent extent)
Creates an
Img from a VoxelBuffer with a float data-type. |
static net.imglib2.img.Img<net.imglib2.type.numeric.integer.UnsignedShortType> |
ConvertToImg.fromShort(VoxelBuffer<UnsignedShortBuffer> buffer,
Extent extent)
Creates an
Img from a VoxelBuffer with an unsigned short data-type. |
Modifier and Type | Method and Description |
---|---|
VoxelsUntyped |
VoxelsFactory.createEmpty(Extent extent,
VoxelDataType dataType)
Creates empty voxels to match a particular size.
|
default Voxels<T> |
VoxelsFactoryTypeBound.createForVoxelBuffer(VoxelBuffer<T> buffer,
Extent extent)
Create a new
Voxels that has been initialized with a single-slice's memory
buffers. |
Voxels<T> |
VoxelsFactoryTypeBound.createInitialized(Extent extent)
Create a new
Voxels that has been initialized with memory buffers. |
Voxels<T> |
VoxelsFactoryTypeBound.createUninitialized(Extent extent)
Create a new
Voxels that has not yet been initialized with memory buffers. |
Modifier and Type | Method and Description |
---|---|
static void |
IterateVoxelsAll.withPoint(Extent extent,
ProcessPoint process)
Iterate over each voxel in an
Extent |
static void |
IterateVoxelsObjectMaskOptional.withPoint(Optional<ObjectMask> objectMask,
Extent extent,
ProcessPoint process)
Iterate over all points that are located on a object-mask or else all points in an extent.
|
static void |
IterateVoxelsAll.withPointAndIndex(Extent extent,
ProcessPointAndIndex process)
Iterate over each voxel in an
Extent . |
Modifier and Type | Method and Description |
---|---|
Extent |
ProcessVoxelNeighborAbsoluteWithSlidingBuffer.extent()
The size of the associated
SlidingBuffer . |
Modifier and Type | Method and Description |
---|---|
static <T> ProcessVoxelNeighbor<T> |
ProcessVoxelNeighborFactory.within(Optional<ObjectMask> containingMask,
Extent extentFallback,
ProcessVoxelNeighborAbsolute<T> process)
Creates to process neighbors that must lie within either an object-mask or an extent (as a
fallback).
|
Modifier and Type | Method and Description |
---|---|
Extent |
KernelPointCursor.getExtent()
The size of the image the kernel iterates over.
|
Constructor and Description |
---|
KernelPointCursor(int index,
Point3i point,
Extent extent,
BinaryValuesByte binaryValues,
KernelApplicationParameters parameters)
Creates to be focused around a particular point in the image.
|
Modifier and Type | Method and Description |
---|---|
static <V> GraphWithPayload<V,Integer> |
NeighborGraph.create(List<V> vertices,
java.util.function.Function<V,ObjectMask> vertexToObject,
Extent sceneExtent,
boolean preventObjectIntersection,
boolean do3D)
Like
NeighborGraph.create(ObjectCollection, Extent, boolean, boolean) but extracts objects from a
list of elements which form the vertices. |
static GraphWithPayload<ObjectMask,Integer> |
NeighborGraph.create(ObjectCollection objects,
Extent sceneExtent,
boolean preventObjectIntersection,
boolean do3D)
Create the graph with object-masks as vertices, where edges represent the number of
neighboring voxels between objects.
|
Modifier and Type | Method and Description |
---|---|
Extent |
ObjectMask.extent()
The size of the object-mask's bounding-box across three dimensions.
|
Modifier and Type | Method and Description |
---|---|
ObjectMask |
ObjectMask.clampTo(Extent extent)
Makes sure an object fits inside an extent, removing any parts which do not.
|
Optional<ObjectMask> |
ObjectMask.intersect(ObjectMask other,
Extent extent)
Intersects this object-mask with another
|
Modifier and Type | Method and Description |
---|---|
ObjectMask |
ObjectMask.growBuffer(Point3i growthNegative,
Point3i growthPositive,
Optional<Extent> clipRegion)
Grows the object-mask's voxel buffers in the positive and negative directions by a certain
amount.
|
ObjectMask |
ObjectMask.scale(ScaleFactor factor,
Optional<Extent> clipTo)
Produces a scaled-version of an object-mask.
|
Modifier and Type | Method and Description |
---|---|
static ObjectMask |
MorphologicalDilation.dilate(ObjectMask object,
Optional<Extent> extent,
boolean useZ,
int iterations,
boolean bigNeighborhood)
Dilates an
ObjectMask , growing the bounding-box as necessary. |
Modifier and Type | Method and Description |
---|---|
static <T> ProjectableBuffer<T> |
MeanIntensityProjection.create(VoxelDataType dataType,
Extent extent)
Creates a buffer for a mean-intensity projection for unsigned byte voxels.
|
static <T> ProjectableBuffer<T> |
StandardDeviationIntensityProjection.create(VoxelDataType dataType,
Extent extent)
Creates a buffer for a standard-deviation projection for unsigned byte voxels.
|
static ProjectableBuffer<FloatBuffer> |
MeanIntensityProjection.createFloat(Extent extent)
Creates a buffer for a mean-intensity projection for float voxels.
|
static ProjectableBuffer<FloatBuffer> |
StandardDeviationIntensityProjection.createFloat(Extent extent)
Creates a buffer for a standard-deviation projection for float voxels.
|
static ProjectableBuffer<UnsignedByteBuffer> |
MeanIntensityProjection.createUnsignedByte(Extent extent)
Creates a buffer for a mean-intensity projection for unsigned byte voxels.
|
static ProjectableBuffer<UnsignedByteBuffer> |
StandardDeviationIntensityProjection.createUnsignedByte(Extent extent)
Creates a buffer for a standard-deviation projection for unsigned byte voxels.
|
static ProjectableBuffer<UnsignedIntBuffer> |
MeanIntensityProjection.createUnsignedInt(Extent extent)
Creates a buffer for a mean-intensity projection for unsigned int voxels.
|
static ProjectableBuffer<UnsignedIntBuffer> |
StandardDeviationIntensityProjection.createUnsignedInt(Extent extent)
Creates a buffer for a standard-deviation projection for unsigned int voxels.
|
static ProjectableBuffer<UnsignedShortBuffer> |
MeanIntensityProjection.createUnsignedShort(Extent extent)
Creates a buffer for a mean-intensity projection for unsigned short voxels.
|
static ProjectableBuffer<UnsignedShortBuffer> |
StandardDeviationIntensityProjection.createUnsignedShort(Extent extent)
Creates a buffer for a standard-deviation projection for unsigned short voxels.
|
Modifier and Type | Method and Description |
---|---|
static <T> ProjectableBuffer<T> |
MaxIntensityProjection.create(VoxelDataType dataType,
Extent extent)
Creates a buffer for a maximum-intensity projection for unsigned byte voxels.
|
static <T> ProjectableBuffer<T> |
MinIntensityProjection.create(VoxelDataType dataType,
Extent extent)
Creates a buffer for a minimum-intensity projection for unsigned byte voxels.
|
static ProjectableBuffer<FloatBuffer> |
MaxIntensityProjection.createFloat(Extent extent)
Creates a buffer for a maximum-intensity projection for float voxels.
|
static ProjectableBuffer<FloatBuffer> |
MinIntensityProjection.createFloat(Extent extent)
Creates a buffer for a minimum-intensity projection for float voxels.
|
static ProjectableBuffer<UnsignedByteBuffer> |
MaxIntensityProjection.createUnsignedByte(Extent extent)
Creates a buffer for a maximum-intensity projection for unsigned byte voxels.
|
static ProjectableBuffer<UnsignedByteBuffer> |
MinIntensityProjection.createUnsignedByte(Extent extent)
Creates a buffer for a minimum-intensity projection for unsigned byte voxels.
|
static ProjectableBuffer<UnsignedIntBuffer> |
MaxIntensityProjection.createUnsignedInt(Extent extent)
Creates a buffer for a maximum-intensity projection for unsigned int voxels.
|
static ProjectableBuffer<UnsignedIntBuffer> |
MinIntensityProjection.createUnsignedInt(Extent extent)
Creates a buffer for a minimum-intensity projection for unsigned int voxels.
|
static ProjectableBuffer<UnsignedShortBuffer> |
MaxIntensityProjection.createUnsignedShort(Extent extent)
Creates a buffer for a maximum-intensity projection for unsigned short voxels.
|
static ProjectableBuffer<UnsignedShortBuffer> |
MinIntensityProjection.createUnsignedShort(Extent extent)
Creates a buffer for a minimum-intensity projection for unsigned short voxels.
|
Modifier and Type | Method and Description |
---|---|
protected abstract VoxelBuffer<UnsignedByteBuffer> |
VoxelsResizer.resizeByte(VoxelBuffer<UnsignedByteBuffer> voxelsSource,
VoxelBuffer<UnsignedByteBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination)
Interpolates from
voxelsSource to voxelsDestination for unsigned 8-bit
buffers. |
VoxelBuffer<UnsignedByteBuffer> |
VoxelsResizerNone.resizeByte(VoxelBuffer<UnsignedByteBuffer> voxelsSource,
VoxelBuffer<UnsignedByteBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
VoxelBuffer<UnsignedByteBuffer> |
VoxelsResizerImgLib2.resizeByte(VoxelBuffer<UnsignedByteBuffer> voxelsSource,
VoxelBuffer<UnsignedByteBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
protected VoxelBuffer<UnsignedByteBuffer> |
VoxelsResizerExecutionTime.resizeByte(VoxelBuffer<UnsignedByteBuffer> voxelsSource,
VoxelBuffer<UnsignedByteBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
protected abstract VoxelBuffer<FloatBuffer> |
VoxelsResizer.resizeFloat(VoxelBuffer<FloatBuffer> voxelsSource,
VoxelBuffer<FloatBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination)
Interpolates from
voxelsSource to voxelsDestination for float buffers. |
VoxelBuffer<FloatBuffer> |
VoxelsResizerNone.resizeFloat(VoxelBuffer<FloatBuffer> voxelsSource,
VoxelBuffer<FloatBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
VoxelBuffer<FloatBuffer> |
VoxelsResizerImgLib2.resizeFloat(VoxelBuffer<FloatBuffer> voxelsSource,
VoxelBuffer<FloatBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
protected VoxelBuffer<FloatBuffer> |
VoxelsResizerExecutionTime.resizeFloat(VoxelBuffer<FloatBuffer> voxelsSource,
VoxelBuffer<FloatBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
protected abstract VoxelBuffer<UnsignedShortBuffer> |
VoxelsResizer.resizeShort(VoxelBuffer<UnsignedShortBuffer> voxelsSource,
VoxelBuffer<UnsignedShortBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination)
Interpolates from
voxelsSource to voxelsDestination for unsigned 16-bit
buffers. |
VoxelBuffer<UnsignedShortBuffer> |
VoxelsResizerNone.resizeShort(VoxelBuffer<UnsignedShortBuffer> voxelsSource,
VoxelBuffer<UnsignedShortBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
VoxelBuffer<UnsignedShortBuffer> |
VoxelsResizerImgLib2.resizeShort(VoxelBuffer<UnsignedShortBuffer> voxelsSource,
VoxelBuffer<UnsignedShortBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
protected VoxelBuffer<UnsignedShortBuffer> |
VoxelsResizerExecutionTime.resizeShort(VoxelBuffer<UnsignedShortBuffer> voxelsSource,
VoxelBuffer<UnsignedShortBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
Modifier and Type | Field and Description |
---|---|
protected Extent |
ConvertTo.extent
The size of the source and destination buffers.
|
Modifier and Type | Method and Description |
---|---|
static Optional<Extent> |
ReadMetadataUtilities.readFromWidthHeightTags(com.drew.metadata.Directory directory,
int tagWidth,
int tagHeight)
Reads two metadata entries, representing width and height, and use them to form a
Extent . |
static <T extends com.drew.metadata.Directory> |
ReadMetadataUtilities.readFromWidthHeightTags(com.drew.metadata.Metadata metadata,
Class<T> directoryType,
int tagWidth,
int tagHeight)
Reads two metadata entries, representing width and height, and use them to form a
Extent . |
Modifier and Type | Method and Description |
---|---|
static ij.process.ImageProcessor |
ConvertToImageProcessor.fromByte(VoxelBuffer<UnsignedByteBuffer> slice,
Extent extent)
Creates a
ImageProcessor from voxel-buffer (of type ByteBuffer ) that is
already a slice. |
static ij.process.ImageProcessor |
ConvertToImageProcessor.fromFloat(VoxelBuffer<FloatBuffer> slice,
Extent extent)
Creates a
ImageProcessor from voxel-buffer (of type FloatBuffer ) that is
already a slice. |
static ij.process.ImageProcessor |
ConvertToImageProcessor.fromShort(VoxelBuffer<UnsignedShortBuffer> slice,
Extent extent)
Creates a
ImageProcessor from voxel-buffer (of type ShortBuffer ) that is
already a slice. |
Modifier and Type | Method and Description |
---|---|
VoxelBuffer<UnsignedByteBuffer> |
VoxelsResizerImageJ.resizeByte(VoxelBuffer<UnsignedByteBuffer> voxelsSource,
VoxelBuffer<UnsignedByteBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
VoxelBuffer<FloatBuffer> |
VoxelsResizerImageJ.resizeFloat(VoxelBuffer<FloatBuffer> voxelsSource,
VoxelBuffer<FloatBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
VoxelBuffer<UnsignedShortBuffer> |
VoxelsResizerImageJ.resizeShort(VoxelBuffer<UnsignedShortBuffer> voxelsSource,
VoxelBuffer<UnsignedShortBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
Modifier and Type | Method and Description |
---|---|
protected abstract ProjectableBuffer<T> |
ProjectableBufferAggregator.create(VoxelDataType dataType,
Extent extent)
Creates the
ProjectableBuffer used for aggregation. |
protected ProjectableBuffer<T> |
MeanProjection.create(VoxelDataType dataType,
Extent extent) |
protected ProjectableBuffer<T> |
MinProjection.create(VoxelDataType dataType,
Extent extent) |
protected ProjectableBuffer<T> |
MaxProjection.create(VoxelDataType dataType,
Extent extent) |
protected ProjectableBuffer<T> |
StandardDeviationProjection.create(VoxelDataType dataType,
Extent extent) |
Modifier and Type | Method and Description |
---|---|
protected Optional<Extent> |
ObjectCollectionProviderMorphological.deriveExtent() |
Modifier and Type | Method and Description |
---|---|
protected ObjectMask |
Dilate.applyMorphologicalOperation(ObjectMask object,
Optional<Extent> extent) |
protected abstract ObjectMask |
ObjectCollectionProviderMorphological.applyMorphologicalOperation(ObjectMask object,
Optional<Extent> extent) |
protected ObjectMask |
Erode.applyMorphologicalOperation(ObjectMask object,
Optional<Extent> extent) |
Modifier and Type | Method and Description |
---|---|
ReductionOutcome<LabelledWithConfidence<ObjectMask>> |
ThresholdConfidence.reduce(List<LabelledWithConfidence<ObjectMask>> elements,
Extent extent,
ExecutionTimeRecorder executionTimeRecorder) |
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 abstract ObjectMask |
CalculateIncrementalOperationMap.applyOperation(ObjectMask object,
Extent extent,
boolean do3D) |
Modifier and Type | Method and Description |
---|---|
protected ObjectMask |
CalculateErosionMap.applyOperation(ObjectMask object,
Extent extent,
boolean do3D) |
protected ObjectMask |
CalculateDilationMap.applyOperation(ObjectMask object,
Extent extent,
boolean do3D) |
Modifier and Type | Method and Description |
---|---|
Extent |
EncodedVoxels.extent() |
Modifier and Type | Method and Description |
---|---|
Extent |
CommonSize.extent()
The common-size of all images.
|
Extent |
SizeMapping.getExtent()
The size.
|
Modifier and Type | Method and Description |
---|---|
void |
SizeMapping.assignExtent(Extent extent)
Replace the existing
Extent with a new value. |
Constructor and Description |
---|
CommonSize(Extent extent) |
SizeMapping(Path path,
Extent extent) |
Constructor and Description |
---|
MontageSharedState(Map<Path,BoundingBoxEnclosed> boxes,
Extent sizeCombined,
VoxelsResizer resizer,
ExecutionTimeRecorder executionTimeRecorder)
Create with a mapping from
Path s to boxes. |
Modifier and Type | Method and Description |
---|---|
Extent |
SizeExtents.toExtent() |
Modifier and Type | Method and Description |
---|---|
void |
HOGParameters.checkSize(Extent extent)
Throws an exception if an image of size
extent cannot be described by these
parameters. |
org.opencv.objdetect.HOGDescriptor |
HOGParameters.createDescriptor(Extent imageSize)
Creates an empty
HOGDescriptor to describe an image of a particular size. |
int |
HOGParameters.sizeDescriptor(Extent imageSize)
Calculates the size of the descriptor will be for a given image.
|
Modifier and Type | Method and Description |
---|---|
static org.opencv.core.Mat |
ConvertToMat.createEmptyMat(Extent extent,
int type)
Creates a
Mat which contains only zero-values. |
static VoxelBuffer<FloatBuffer> |
VoxelBufferFromMat.floatFromMat(org.opencv.core.Mat mat,
Extent extent)
|
static org.opencv.core.Mat |
ConvertToMat.fromVoxelBufferByte(VoxelBuffer<UnsignedByteBuffer> voxelBuffer,
Extent extent)
|
static org.opencv.core.Mat |
ConvertToMat.fromVoxelBufferFloat(VoxelBuffer<FloatBuffer> voxelBuffer,
Extent extent)
|
static org.opencv.core.Mat |
ConvertToMat.fromVoxelBufferShort(VoxelBuffer<UnsignedShortBuffer> voxelBuffer,
Extent extent)
|
static VoxelBuffer<?> |
VoxelBufferFromMat.toVoxelBuffer(org.opencv.core.Mat mat,
Extent extent)
Converts a
Mat to a VoxelBuffer . |
static VoxelBuffer<UnsignedByteBuffer> |
VoxelBufferFromMat.unsignedByteFromMat(org.opencv.core.Mat mat,
Extent extent)
|
static VoxelBuffer<UnsignedShortBuffer> |
VoxelBufferFromMat.unsignedShortFromMat(org.opencv.core.Mat mat,
Extent extent)
|
Modifier and Type | Method and Description |
---|---|
protected VoxelBuffer<UnsignedByteBuffer> |
VoxelsResizerOpenCV.resizeByte(VoxelBuffer<UnsignedByteBuffer> voxelsSource,
VoxelBuffer<UnsignedByteBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
protected VoxelBuffer<FloatBuffer> |
VoxelsResizerOpenCV.resizeFloat(VoxelBuffer<FloatBuffer> voxelsSource,
VoxelBuffer<FloatBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
protected VoxelBuffer<UnsignedShortBuffer> |
VoxelsResizerOpenCV.resizeShort(VoxelBuffer<UnsignedShortBuffer> voxelsSource,
VoxelBuffer<UnsignedShortBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
Modifier and Type | Method and Description |
---|---|
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. |
Extent |
Extent.duplicateChangeX(int xToAssign)
Creates a copy of the current
Extent with the value for the X-dimension changed. |
Extent |
Extent.duplicateChangeY(int yToAssign)
Creates a copy of the current
Extent with the value for the Y-dimension changed. |
Extent |
Extent.duplicateChangeZ(int zToAssign)
Creates a copy of the current
Extent with the value for the Z-dimension changed. |
Extent |
BoundingBox.extent()
Dimensions in pixels needed to represent the bounding box.
|
Extent |
Extent.flattenZ()
Collapses the Z dimension.
|
Extent |
Extent.growBy(int toAdd)
Creates a new
Extent with toAdd size added to each dimension. |
Extent |
Extent.growBy(ReadableTuple3i toAdd)
Creates a new
Extent with toAdd size added to each respective
dimension. |
Extent |
Extent.intersectWith(Extent other)
Intersects this extent with another (i.e.
|
Extent |
Extent.minimum(Extent extent)
An extent that contains the minimum of two extents for each dimension respectively.
|
Extent |
Extent.scaleXYBy(double scaleFactor,
boolean round)
Scales all dimensions by a scaling-factor.
|
Extent |
Extent.scaleXYBy(ScaleFactor scaleFactor,
boolean round)
Scales the X- and Y- dimensions by a scaling-factor.
|
Extent |
Extent.shrinkBy(ReadableTuple3i toSubtract)
Creates a new
Extent with toSubtract size subtracted from each
respective dimension. |
Modifier and Type | Method and Description |
---|---|
boolean |
Extent.anyDimensionIsLargerThan(Extent other)
Returns true if any dimension in this extent is larger than the corresponding dimension in
other extent. |
boolean |
BoundingBox.atBorder(Extent extent)
Does the bounding-box have an edge at the border of an image of size
extent ? |
boolean |
BoundingBox.atBorderXY(Extent extent)
Like
BoundingBox.atBorder(Extent) but considers only the X- and Y- dimensions. |
boolean |
BoundingBox.atBorderZ(Extent extent)
Like
BoundingBox.atBorder(Extent) but considers only the Z-dimension. |
BoundingBox |
BoundingBox.changeExtent(Extent extent)
Creates a copied
BoundingBox but with a different extent. |
BoundingBox |
BoundingBox.clampTo(Extent extent)
Ensures that the box fits inside a
Extent by reducing any values to their limits in
the respective dimension. |
int |
Extent.compareTo(Extent other) |
static BoundingBox |
BoundingBox.createDuplicate(ReadableTuple3i cornerMin,
Extent extent)
Creates a bounding-box from a corner and an extent - duplicating
cornerMin . |
static BoundingBox |
BoundingBox.createReuse(ReadableTuple3i cornerMin,
Extent extent)
Creates a bounding-box from a corner and an extent - reusing
cornerMin internally. |
boolean |
Extent.equalsIgnoreZ(Extent other)
Checks for equality with another extent ignoring any differences in the Z dimension.
|
BoundingBox |
BoundingBox.growBy(Tuple3i toAdd,
Extent containingExtent)
Grow the bounding-box by
toAdd amount in each dimension in both positive and negative
directions. |
Extent |
Extent.intersectWith(Extent other)
Intersects this extent with another (i.e.
|
Extent |
Extent.minimum(Extent extent)
An extent that contains the minimum of two extents for each dimension respectively.
|
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.
|
Optional<BoundingBox> |
BoundingBoxIntersection.withInside(BoundingBox other,
Extent containingExtent)
Finds the intersection and clamp to a containing extent.
|
Modifier and Type | Method and Description |
---|---|
BoundingBox |
BoundingBox.changeExtent(java.util.function.UnaryOperator<Extent> extentOperator)
Creates a copied
BoundingBox but with a different extent. |
Constructor and Description |
---|
BoundingBox(Extent extent)
Constructs a bounding-box to cover the entirety of a certain extent.
|
Modifier and Type | Method and Description |
---|---|
Extent |
ScaleFactorInt.scale(Extent extent)
Multiplies an
Extent by the respective scaling-factor in each dimension. |
Modifier and Type | Method and Description |
---|---|
static ScaleFactor |
RelativeScaleCalculator.relativeScale(Extent source,
Extent target)
Calculates a scaling factor so as to scale
source to target . |
static ScaleFactor |
RelativeScaleCalculator.relativeScale(Extent source,
Extent target,
boolean preserveAspectRatio)
|
static ScaleFactor |
RelativeScaleCalculator.relativeScalePreserveAspectRatio(Extent source,
Extent target)
Calculates a scaling factor so as to maximally scale
source to target -
while preserving the aspect ratio. |
Extent |
ScaleFactorInt.scale(Extent extent)
Multiplies an
Extent by the respective scaling-factor in each dimension. |
Modifier and Type | Field and Description |
---|---|
static Extent |
ChannelFixture.LARGE_2D |
static Extent |
ChannelFixture.LARGE_3D |
static Extent |
ChannelFixture.MEDIUM_2D |
static Extent |
ChannelFixture.MEDIUM_3D |
static Extent |
ChannelFixture.SMALL_2D |
static Extent |
ChannelFixture.SMALL_3D |
Modifier and Type | Method and Description |
---|---|
static Extent |
MaskFixture.maskExtent(boolean do3D) |
Modifier and Type | Method and Description |
---|---|
Stack |
StackFixture.create(ChannelSpecification channelSpecification,
Extent extent)
Creates a stack with a particular number of the channels of particular size.
|
Channel |
ChannelFixture.createChannel(Extent extent,
ChannelFixture.IntensityFunction createIntensity,
VoxelDataType channelVoxelType) |
Constructor and Description |
---|
CutOffCorners(int edgeXY,
int edgeZ,
Extent extent) |
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.