Package | Description |
---|---|
org.anchoranalysis.image.bean.segment.binary |
Base classes to perform binary-segmentation.
|
org.anchoranalysis.image.bean.threshold |
Base classes for thresholding and calculating levels for thresholding.
|
org.anchoranalysis.image.core.channel |
The
Channel core data-class and related operations
and converters. |
org.anchoranalysis.image.core.object |
The key data entity
org.anchoranalysis.image.voxel.object and related-classes and
operations. |
org.anchoranalysis.image.voxel |
Data-structures to store and manipulate image raster-data or voxels.
|
org.anchoranalysis.image.voxel.convert |
Converting
Voxels to different data-types. |
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.resizer |
Different interpolator methods to use when scaling voxels.
|
org.anchoranalysis.image.voxel.statistics |
Statistics about aggregated voxel intensities.
|
org.anchoranalysis.image.voxel.thresholder |
Thresholding operations on voxels.
|
org.anchoranalysis.io.bioformats.copyconvert |
Converts the byte stream opened by Bioformats into channels of particular data-type.
|
org.anchoranalysis.io.imagej.convert |
Converts to and from ImageJ data-structures for images.
|
org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction |
Morphological grayscale-reconstruction algorithm.
|
org.anchoranalysis.plugin.fiji.bean.threshold |
Implementations of
Thresholder that use FIJI. |
org.anchoranalysis.plugin.image.bean.blur |
Filters that perform blurring.
|
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction |
Grayscale reconstruction to support the Watershed transformation.
|
org.anchoranalysis.plugin.image.bean.segment.binary |
Implementations of
BinarySegmentation . |
org.anchoranalysis.plugin.imagej.bean.threshold |
Implementations of
Thresholder that call ImageJ. |
org.anchoranalysis.plugin.mpp.bean.segment.binary |
Implementations of
BinarySegmentation
involving Mark or related classes. |
Modifier and Type | Method and Description |
---|---|
BinaryVoxels<UnsignedByteBuffer> |
Thresholder.threshold(VoxelsUntyped voxels)
Like
Thresholder.threshold(VoxelsUntyped) but using default binary-values. |
BinaryVoxels<UnsignedByteBuffer> |
Thresholder.threshold(VoxelsUntyped voxels,
BinaryValuesByte binaryValues)
Like
Thresholder.threshold(VoxelsUntyped, BinaryValuesByte, Optional, Optional) applying the
thresholding to the entire set of voxels. |
BinaryVoxels<UnsignedByteBuffer> |
ThresholderGlobal.threshold(VoxelsUntyped inputBuffer,
BinaryValuesByte bvOut,
Optional<Histogram> histogram,
Optional<ObjectMask> objectMask) |
abstract BinaryVoxels<UnsignedByteBuffer> |
Thresholder.threshold(VoxelsUntyped voxels,
BinaryValuesByte binaryValues,
Optional<Histogram> histogram,
Optional<ObjectMask> objectMask)
Thresholds voxels (across a range of values) so that they have only binary range (i.e.
|
Modifier and Type | Method and Description |
---|---|
VoxelsUntyped |
Channel.voxels()
The underlying voxels in the channel.
|
Modifier and Type | Method and Description |
---|---|
static Histogram |
HistogramFromObjectsFactory.createFrom(VoxelsUntyped voxels,
Optional<ObjectMask> object)
|
Modifier and Type | Method and Description |
---|---|
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 . |
void |
VoxelsUntyped.replaceSlice(int sliceIndexToUpdate,
VoxelsUntyped sourceVoxels,
int sliceIndexSource,
boolean duplicate)
Copies one particular z-slice of voxels from a source into the current voxels.
|
Modifier and Type | Method and Description |
---|---|
<S,T> Voxels<S> |
VoxelsConverterMulti.convert(VoxelsUntyped voxels,
VoxelsFactoryTypeBound<T> outputVoxelsFactory)
Converts a
Voxels to another type. |
Voxels<T> |
VoxelsConverter.convertFrom(VoxelsUntyped from,
VoxelsFactoryTypeBound<T> factory)
Creates a new voxels of type
T and copies the voxels from from . |
void |
VoxelsConverter.copyFrom(VoxelsUntyped from,
Voxels<T> to)
Copies voxels from a source (of any type) to voxels of type
T . |
Modifier and Type | Method and Description |
---|---|
static net.imglib2.img.Img<? extends net.imglib2.type.numeric.RealType<?>> |
ConvertToImg.from(VoxelsUntyped voxels)
Converts from a
VoxelsUntyped (Anchor structure) to a Img (ImgLib2
structure). |
static net.imglib2.img.Img<? extends net.imglib2.type.numeric.RealType<?>> |
ConvertToImg.fromSlice(VoxelsUntyped voxels,
int sliceIndex)
Creates an
Img from a single z-slice of a VoxelsUntyped . |
Modifier and Type | Method and Description |
---|---|
VoxelsUntyped |
VoxelsFactory.createEmpty(Extent extent,
VoxelDataType dataType)
Creates empty voxels to match a particular size.
|
<T> VoxelsUntyped |
VoxelsFactory.createFrom(SliceBufferIndex<T> buffer,
VoxelDataType dataType)
Creates voxels from a particular
SliceBufferIndex with specified type. |
Modifier and Type | Method and Description |
---|---|
void |
VoxelsResizer.resize(VoxelsUntyped source,
VoxelsUntyped destination)
Copies voxels slice-by-slice from
source to destination performing necessary
interpolation. |
Modifier and Type | Method and Description |
---|---|
static Histogram |
HistogramFactory.createFrom(VoxelsUntyped voxels)
Creates a
Histogram of the aggregated voxel intensities in a VoxelsUntyped . |
Modifier and Type | Method and Description |
---|---|
static BinaryVoxels<UnsignedByteBuffer> |
VoxelsThresholder.threshold(VoxelsUntyped voxels,
float level,
BinaryValuesByte binaryValues,
Optional<ObjectMask> objectMask,
boolean alwaysDuplicate)
Applies thresholding to
VoxelsUntyped . |
Constructor and Description |
---|
ConvertTo(java.util.function.Function<VoxelsUntyped,Voxels<T>> functionCast,
java.util.function.IntFunction<T> allocateBuffer,
java.util.function.Function<T,VoxelBuffer<T>> wrapBuffer) |
Modifier and Type | Method and Description |
---|---|
static VoxelsUntyped |
ConvertFromImagePlus.toVoxels(ij.ImagePlus image)
Converts an
ImagePlus to a VoxelsUntyped . |
Modifier and Type | Method and Description |
---|---|
static ij.ImagePlus |
ConvertToImagePlus.from(VoxelsUntyped voxels)
Creates an
ImagePlus from a VoxelsUntyped . |
static ij.process.ImageProcessor |
ConvertToImageProcessor.from(VoxelsUntyped voxels,
int z)
Creates a
ImageProcessor by extracting a slice from a VoxelsUntyped . |
Modifier and Type | Method and Description |
---|---|
VoxelsUntyped |
GrayscaleReconstruction2DIJ.reconstruction(VoxelsUntyped mask,
VoxelsUntyped marker,
Optional<ObjectMask> containingMask) |
Modifier and Type | Method and Description |
---|---|
VoxelsUntyped |
GrayscaleReconstruction2DIJ.reconstruction(VoxelsUntyped mask,
VoxelsUntyped marker,
Optional<ObjectMask> containingMask) |
Modifier and Type | Method and Description |
---|---|
BinaryVoxels<UnsignedByteBuffer> |
ThresholderAutoIJ.threshold(VoxelsUntyped inputBuffer,
BinaryValuesByte binaryValues,
Optional<Histogram> histogram,
Optional<ObjectMask> objectMask) |
Modifier and Type | Method and Description |
---|---|
abstract void |
BlurStrategy.blur(VoxelsUntyped voxels,
Dimensions dimensions,
MessageLogger logger) |
void |
BlurGaussian3D.blur(VoxelsUntyped voxels,
Dimensions dimensions,
MessageLogger logger) |
void |
BlurGaussianEachSlice2D.blur(VoxelsUntyped voxels,
Dimensions dimensions,
MessageLogger logger) |
Modifier and Type | Method and Description |
---|---|
abstract VoxelsUntyped |
GrayscaleReconstructionByErosion.reconstruction(VoxelsUntyped mask,
VoxelsUntyped marker,
Optional<ObjectMask> containingMask) |
VoxelsUntyped |
GrayscaleReconstructionRobinson.reconstruction(VoxelsUntyped mask,
VoxelsUntyped marker,
Optional<ObjectMask> containingMask) |
Modifier and Type | Method and Description |
---|---|
abstract VoxelsUntyped |
GrayscaleReconstructionByErosion.reconstruction(VoxelsUntyped mask,
VoxelsUntyped marker,
Optional<ObjectMask> containingMask) |
VoxelsUntyped |
GrayscaleReconstructionRobinson.reconstruction(VoxelsUntyped mask,
VoxelsUntyped marker,
Optional<ObjectMask> containingMask) |
Modifier and Type | Method and Description |
---|---|
BinaryVoxels<UnsignedByteBuffer> |
Sequence.segment(VoxelsUntyped voxels,
BinarySegmentationParameters parameters,
Optional<ObjectMask> objectMask) |
BinaryVoxels<UnsignedByteBuffer> |
ThresholdAgainstChannel.segment(VoxelsUntyped voxels,
BinarySegmentationParameters parameters,
Optional<ObjectMask> object) |
BinaryVoxels<UnsignedByteBuffer> |
Repeat.segmentFromExistingSegmentation(VoxelsUntyped voxels,
BinarySegmentationParameters parameters,
Optional<ObjectMask> objectMask,
BinarySegmentation segment) |
BinaryVoxels<UnsignedByteBuffer> |
Invert.segmentFromExistingSegmentation(VoxelsUntyped voxels,
BinarySegmentationParameters parameters,
Optional<ObjectMask> objectMask,
BinarySegmentation segment) |
Modifier and Type | Method and Description |
---|---|
BinaryVoxels<UnsignedByteBuffer> |
ThresholderSimpleFillHoles2D.threshold(VoxelsUntyped inputBuffer,
BinaryValuesByte bvOut,
Optional<Histogram> histogram,
Optional<ObjectMask> objectMask) |
Modifier and Type | Method and Description |
---|---|
BinaryVoxels<UnsignedByteBuffer> |
SegmentThresholdAboveMinBound.segment(VoxelsUntyped voxels,
BinarySegmentationParameters parameters,
Optional<ObjectMask> objectMask) |
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.