Package | Description |
---|---|
org.anchoranalysis.image.bean.displayer | |
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.bufferedimage |
Conversions and operations involving Java AWT's
BufferedImage . |
org.anchoranalysis.image.core.channel.convert |
Converts a channel to other data-types.
|
org.anchoranalysis.image.core.channel.convert.attached.channel |
Converts a channel to another data-type based upon a
Channel to which it is attached. |
org.anchoranalysis.image.core.channel.convert.attached.histogram |
Converts a channel to another data-type based upon a
Histogram to which it is attached. |
org.anchoranalysis.image.core.mask |
An image with only two permissible states.
|
org.anchoranalysis.image.core.mask.combine |
Binary operations involving voxelwise combination of
Mask . |
org.anchoranalysis.image.core.object.properties |
An
ObjectCollection with associated key-value
pairs. |
org.anchoranalysis.image.core.stack |
Defines the key data object,
Stack , and related
classes. |
org.anchoranalysis.image.inference.segment |
Non-beans pertaining to segmentation of images via model inference.
|
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.assigner |
Assigns values to some or all voxels.
|
org.anchoranalysis.image.voxel.binary |
The
BinaryVoxels class and related operations. |
org.anchoranalysis.image.voxel.binary.connected | |
org.anchoranalysis.image.voxel.buffer |
A buffer of voxel-values, usually corresponding to a single z-slice in
Voxels . |
org.anchoranalysis.image.voxel.buffer.primitive |
Conversion of both primitive data types and image structures between Anchor's data-structures and
other representations.
|
org.anchoranalysis.image.voxel.buffer.slice |
A container with voxel-buffers for each z-slice.
|
org.anchoranalysis.image.voxel.convert |
Converting
Voxels to different data-types. |
org.anchoranalysis.image.voxel.convert.bufferedimage |
Converts anchor data-structures to the
BufferedImage used by Java's AWT. |
org.anchoranalysis.image.voxel.convert.imglib2 |
Converts anchor data-structures to those used by ImgLib2.
|
org.anchoranalysis.image.voxel.extracter |
Methods to read/copy/duplicate portions of voxels.
|
org.anchoranalysis.image.voxel.factory |
Creates new instances of
Voxels and VoxelsUntyped with specific data-types. |
org.anchoranalysis.image.voxel.iterator |
Utilities to iterate over voxel-locations in images and sub-regions of images.
|
org.anchoranalysis.image.voxel.iterator.intersecting |
Like
org.anchoranalysis.image.voxel.iterator but refers to iterators that operation over
the intersecting regions of two entities. |
org.anchoranalysis.image.voxel.iterator.neighbor |
Iterating over a point's neighboring voxels.
|
org.anchoranalysis.image.voxel.iterator.neighbor.kernel |
Routines for moving a
KernelPointCursor around the
neighboring voxels of the point. |
org.anchoranalysis.image.voxel.iterator.predicate |
Functional-interfaces for processing different combinations of points and buffers that return a
boolean.
|
org.anchoranalysis.image.voxel.kernel |
Applying a kernel via
convolution to voxels.
|
org.anchoranalysis.image.voxel.kernel.morphological |
Kernels that apply morphological operations.
|
org.anchoranalysis.image.voxel.kernel.outline |
Kernel to find outline voxels on an object.
|
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.object.morphological.predicate |
Predicates to match certain voxels as used in
org.anchoranalysis.image.voxel.object.morphological . |
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.image.voxel.thresholder |
Thresholding operations on voxels.
|
org.anchoranalysis.io.bioformats.copyconvert.tobyte |
Converts the byte stream opened by Bioformats into channels of
ByteBuffer . |
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.mpp.mark.voxelized |
A mark after a voxel-representation has been inferred.
|
org.anchoranalysis.mpp.overlap |
Calculating overlaps between two
Mark s. |
org.anchoranalysis.plugin.fiji.bean.channel.provider.distance |
Euclidean Distance Transform
implementations via FIJI.
|
org.anchoranalysis.plugin.fiji.bean.threshold |
Implementations of
Thresholder that use FIJI. |
org.anchoranalysis.plugin.image.bean.channel.convert |
Implementations of
ConvertChannelTo and ConvertChannelToWithHistogram . |
org.anchoranalysis.plugin.image.bean.segment.binary |
Implementations of
BinarySegmentation . |
org.anchoranalysis.plugin.image.segment.thresholder.slice |
Non-beans pertaining to segmenting a z-stack slice-by-slice.
|
org.anchoranalysis.plugin.imagej.bean.threshold |
Implementations of
Thresholder that call ImageJ. |
org.anchoranalysis.plugin.imagej.channel.provider |
Implementations of
ChannelProvider that call ImageJ. |
org.anchoranalysis.plugin.imagej.mask |
Non-bean classes involving
ObjectMask that call ImageJ. |
org.anchoranalysis.plugin.mpp.bean.contour.visitscheduler |
The
VisitScheduler and related
classes, as used in TraverseOuterContourOnImage . |
org.anchoranalysis.plugin.mpp.bean.segment.binary |
Implementations of
BinarySegmentation
involving Mark or related classes. |
org.anchoranalysis.plugin.mpp.feature.overlap |
Implementations of
CalculationPart to calculate
overlap between two entities. |
org.anchoranalysis.plugin.opencv.convert |
Conversion to/from OpenCV data-structures.
|
org.anchoranalysis.plugin.opencv.resizer |
Interpolation non-beans that use OpenCV.
|
org.anchoranalysis.test.image |
Testing utilities and fixtures with no greater downstream dependency than anchor-image-io
or anchor-io-bioformats or anchor-imagej.
|
Modifier and Type | Method and Description |
---|---|
protected abstract ChannelConverterAttached<Channel,UnsignedByteBuffer> |
StackDisplayer.createConverterFor(VoxelDataType dataType)
Determines what kind of converter to use for a particular channel, to map it to an unsigned
8-bit channel.
|
protected ChannelConverterAttached<Channel,UnsignedByteBuffer> |
IntensityQuantiles.createConverterFor(VoxelDataType dataType) |
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 |
---|---|
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. |
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. |
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. |
Constructor and Description |
---|
ToUnsignedByte(VoxelsConverter<UnsignedByteBuffer> voxelsConverter)
Convert with a particular
VoxelsConverter . |
Modifier and Type | Method and Description |
---|---|
VoxelsConverter<UnsignedByteBuffer> |
IntensityRange.getVoxelsConverter() |
VoxelsConverter<UnsignedByteBuffer> |
MaxIntensity.getVoxelsConverter() |
Modifier and Type | Method and Description |
---|---|
VoxelsConverter<UnsignedByteBuffer> |
QuantileIntensityFromHistogram.getVoxelsConverter() |
VoxelsConverter<UnsignedByteBuffer> |
MaxIntensityFromHistogram.getVoxelsConverter() |
VoxelsConverter<UnsignedByteBuffer> |
UpperLowerQuantileIntensityFromHistogram.getVoxelsConverter() |
Modifier and Type | Method and Description |
---|---|
UnsignedByteBuffer |
Mask.sliceBuffer(int z)
A buffer corresponding to a particular z-slice.
|
Modifier and Type | Method and Description |
---|---|
BinaryVoxels<UnsignedByteBuffer> |
Mask.binaryVoxels()
The underlying voxels in the mask, exposed as
BinaryVoxels . |
Voxels<UnsignedByteBuffer> |
Mask.voxels()
The underlying voxels in the mask.
|
Modifier and Type | Method and Description |
---|---|
static RunningSum |
IterateVoxelsMask.calculateRunningSum(Mask mask,
Voxels<UnsignedByteBuffer> voxelsIntensity)
Calculates the sum and count across voxels intensity that correspond to on voxels on a
mask
|
void |
Mask.replaceBy(BinaryVoxels<UnsignedByteBuffer> voxels)
Replaces the underlying voxels in the mask with new voxels.
|
Constructor and Description |
---|
Mask(BinaryVoxels<UnsignedByteBuffer> voxels)
Creates a mask from an existing binary-voxels using default image resolution.
|
Mask(BinaryVoxels<UnsignedByteBuffer> voxels,
Optional<Resolution> resolution)
Creates a mask from an existing binary-voxels and a specific image resolution.
|
Modifier and Type | Method and Description |
---|---|
static void |
MaskXor.apply(BinaryVoxels<UnsignedByteBuffer> voxelsFirst,
BinaryVoxels<UnsignedByteBuffer> voxelsSecond)
Performs a logical xor (exclusive or) operation on each voxel in two
Voxels
(considered to be masks), writing the result onto the second mask. |
static void |
MaskXor.apply(BinaryVoxels<UnsignedByteBuffer> voxelsFirst,
BinaryVoxels<UnsignedByteBuffer> voxelsSecond)
Performs a logical xor (exclusive or) operation on each voxel in two
Voxels
(considered to be masks), writing the result onto the second mask. |
static void |
MaskAnd.apply(Voxels<UnsignedByteBuffer> voxelsFirst,
Voxels<UnsignedByteBuffer> voxelsSecond,
BinaryValuesByte binaryValuesFirst,
BinaryValuesByte binaryValuesSecond)
Performs a logical and operation on each voxel in two
Voxels (considered to be
masks), writing the result onto the second mask. |
static void |
MaskAnd.apply(Voxels<UnsignedByteBuffer> voxelsFirst,
Voxels<UnsignedByteBuffer> voxelsSecond,
BinaryValuesByte binaryValuesFirst,
BinaryValuesByte binaryValuesSecond)
Performs a logical and operation on each voxel in two
Voxels (considered to be
masks), writing the result onto the second mask. |
Modifier and Type | Method and Description |
---|---|
UnsignedByteBuffer |
ObjectWithProperties.sliceBufferLocal(int sliceIndexRelative)
A slice buffer with local coordinates.
|
Modifier and Type | Method and Description |
---|---|
UnsignedByteBuffer |
RGBStack.sliceBuffer(int channelIndex,
int zIndex)
A buffer corresponding to a particular z-slice of a particular channel.
|
Modifier and Type | Method and Description |
---|---|
List<Optional<ChannelConverterAttached<Channel,UnsignedByteBuffer>>> |
DisplayStack.getConverters()
A list of optional converters that will be applied to the respective channel in
stack
if they exist. |
Modifier and Type | Method and Description |
---|---|
void |
ChannelMapper.consumeChannelIfSupported(int channelIndex,
java.util.function.BiConsumer<Channel,ChannelConverterAttached<Channel,UnsignedByteBuffer>> consumer,
java.util.function.Consumer<Channel> fallback)
Like
ChannelMapper.mapChannelIfSupported(int, BiFunction, Function) but the mapping has no
return-type. |
void |
DisplayStack.copyPixelsTo(int channelIndex,
BoundingBox sourceBox,
Voxels<UnsignedByteBuffer> destinationVoxels,
BoundingBox destinationBox)
Copies pixels from a particular channel to an output buffer.
|
<T> T |
ChannelMapper.mapChannelIfSupported(int channelIndex,
java.util.function.BiFunction<Channel,ChannelConverterAttached<Channel,UnsignedByteBuffer>,T> mapFunction,
java.util.function.Function<Channel,T> fallback)
|
Constructor and Description |
---|
ChannelMapper(java.util.function.IntFunction<Channel> channelGetter,
java.util.function.IntFunction<Optional<ChannelConverterAttached<Channel,UnsignedByteBuffer>>> converterGetter) |
DisplayStack(Stack stack,
boolean eventuallyThree,
java.util.function.Function<VoxelDataType,ChannelConverterAttached<Channel,UnsignedByteBuffer>> createConverter)
Create for a particular
Stack that may needed to be converted. |
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 |
---|---|
Voxels<UnsignedByteBuffer> |
VoxelsUntyped.asByte()
Casts to use a
UnsignedByteBuffer if the voxels contain this data-type, otherwise
throws a IncorrectVoxelTypeException . |
VoxelsExtracter<UnsignedByteBuffer> |
VoxelsUnsignedByte.extract() |
Constructor and Description |
---|
VoxelsUnsignedByte(SliceBufferIndex<UnsignedByteBuffer> buffer)
Create from a buffer, indexed by slice.
|
Modifier and Type | Method and Description |
---|---|
static VoxelsArithmetic |
VoxelsArithmeticFactory.createUnsignedByte(Extent extent,
java.util.function.IntFunction<UnsignedByteBuffer> bufferForSlice)
Create a
VoxelsArithmetic for UnsignedByteBuffer . |
Modifier and Type | Method and Description |
---|---|
static VoxelsAssigner |
VoxelsAssignerFactory.createUnsignedByte(Voxels<UnsignedByteBuffer> voxels,
int valueToAssign)
Create a
VoxelsAssigner for a UnsignedByteBuffer . |
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<UnsignedByteBuffer> |
BinaryVoxelsFactory.createEmptyOn(Extent extent)
Creates binary-voxels using unsigned 8-bit byte type and with all voxels set to on
(255).
|
static BinaryVoxels<UnsignedByteBuffer> |
BinaryVoxelsFactory.reuseByte(Voxels<UnsignedByteBuffer> voxels)
Like
BinaryVoxelsFactory.reuseByte(org.anchoranalysis.image.voxel.Voxels<org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer>) but uses default binary-values for off (0) and on
(255). |
static BinaryVoxels<UnsignedByteBuffer> |
BinaryVoxelsFactory.reuseByte(Voxels<UnsignedByteBuffer> voxels,
BinaryValuesInt binaryValues)
Reuses an existing voxel-buffer (of type unsigned byte) as a binary-version which should have
only two intensity-values representing off and on.
|
Modifier and Type | Method and Description |
---|---|
static BinaryVoxels<UnsignedByteBuffer> |
BinaryVoxelsFactory.reuseByte(Voxels<UnsignedByteBuffer> voxels)
Like
BinaryVoxelsFactory.reuseByte(org.anchoranalysis.image.voxel.Voxels<org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer>) but uses default binary-values for off (0) and on
(255). |
static BinaryVoxels<UnsignedByteBuffer> |
BinaryVoxelsFactory.reuseByte(Voxels<UnsignedByteBuffer> voxels,
BinaryValuesInt binaryValues)
Reuses an existing voxel-buffer (of type unsigned byte) as a binary-version which should have
only two intensity-values representing off and on.
|
Modifier and Type | Method and Description |
---|---|
ObjectCollection |
ObjectsFromConnectedComponentsFactory.createUnsignedByte(BinaryVoxels<UnsignedByteBuffer> voxels)
Finds the connected-components in unsigned byte voxels.
|
Modifier and Type | Method and Description |
---|---|
static VoxelBuffer<UnsignedByteBuffer> |
VoxelBufferFactory.allocateUnsignedByte(int capacity)
Allocates a new unsigned byte voxel-buffer of given size.
|
static VoxelBuffer<UnsignedByteBuffer> |
VoxelBufferWrap.unsignedByteArray(byte[] array)
Wraps an existing array (encoding unsigned bytes as a signed array) as a voxel-buffer.
|
static VoxelBuffer<UnsignedByteBuffer> |
VoxelBufferWrap.unsignedByteBuffer(UnsignedByteBuffer buffer)
Wraps an unsigned-byte buffer into a voxel-buffer.
|
static VoxelBuffer<UnsignedByteBuffer> |
VoxelBufferWrap.unsignedByteRaw(ByteBuffer buffer)
Wraps an unsigned-byte buffer (represented by a NIO signed-buffer) into a voxel-buffer.
|
Modifier and Type | Method and Description |
---|---|
static VoxelBuffer<UnsignedByteBuffer> |
VoxelBufferWrap.unsignedByteBuffer(UnsignedByteBuffer buffer)
Wraps an unsigned-byte buffer into a voxel-buffer.
|
Modifier and Type | Method and Description |
---|---|
static UnsignedByteBuffer |
UnsignedByteBuffer.allocate(int capacity)
Allocates a new buffer of unsigned-bytes.
|
static UnsignedByteBuffer |
UnsignedByteBuffer.wrapRaw(byte[] array)
Exposes a raw byte-array as a buffer with unsigned-bytes.
|
static UnsignedByteBuffer |
UnsignedByteBuffer.wrapRaw(ByteBuffer bufferRaw)
Exposes a raw
ByteBuffer as a buffer with unsigned-bytes. |
Modifier and Type | Method and Description |
---|---|
void |
UnsignedByteBuffer.put(UnsignedByteBuffer source)
Relative put-method from an unsigned byte buffer, represented by a
UnsignedByteBuffer . |
Modifier and Type | Method and Description |
---|---|
static SliceBufferIndex<UnsignedByteBuffer> |
FromByte.createInitialized(Extent extent)
Create a buffer of a particular size, that has been initialized.
|
static SliceBufferIndex<UnsignedByteBuffer> |
FromByte.createUninitialized(Extent extent)
Create a buffer of a particular size, that has not been initialized.
|
VoxelBuffer<UnsignedByteBuffer> |
FromByte.slice(int z) |
Modifier and Type | Method and Description |
---|---|
void |
FromByte.replaceSlice(int z,
VoxelBuffer<UnsignedByteBuffer> sliceToAssign) |
Modifier and Type | Method and Description |
---|---|
protected void |
ToUnsignedByteScaleByType.convertFloat(FloatBuffer in,
UnsignedByteBuffer out)
Converts the current position in a
FloatBuffer to the current position in a UnsignedShortBuffer . |
protected void |
ToUnsignedByteNoScaling.convertFloat(FloatBuffer in,
UnsignedByteBuffer out) |
protected void |
ToUnsignedByteScaleByMaxValue.convertFloat(FloatBuffer in,
UnsignedByteBuffer out) |
protected void |
ToUnsignedByteScaleByMinMaxValue.convertFloat(FloatBuffer in,
UnsignedByteBuffer out) |
protected void |
ToFloatNoScaling.convertUnsignedByte(UnsignedByteBuffer in,
FloatBuffer out) |
protected abstract void |
VoxelsConverter.convertUnsignedByte(UnsignedByteBuffer in,
T out)
Copies a value from the current position in a
UnsignedByteBuffer to the current
position in a buffer of type T . |
protected void |
ToUnsignedByte.convertUnsignedByte(UnsignedByteBuffer in,
UnsignedByteBuffer out) |
protected void |
ToUnsignedInt.convertUnsignedByte(UnsignedByteBuffer in,
UnsignedIntBuffer out) |
protected void |
ToUnsignedShortNoScaling.convertUnsignedByte(UnsignedByteBuffer in,
UnsignedShortBuffer out) |
protected void |
ToUnsignedShortScaleByType.convertUnsignedByte(UnsignedByteBuffer in,
UnsignedShortBuffer out) |
protected void |
ToUnsignedByteScaleByType.convertUnsignedInt(UnsignedIntBuffer in,
UnsignedByteBuffer out) |
protected void |
ToUnsignedByteNoScaling.convertUnsignedInt(UnsignedIntBuffer in,
UnsignedByteBuffer out) |
protected void |
ToUnsignedByteScaleByMaxValue.convertUnsignedInt(UnsignedIntBuffer in,
UnsignedByteBuffer out) |
protected void |
ToUnsignedByteScaleByMinMaxValue.convertUnsignedInt(UnsignedIntBuffer in,
UnsignedByteBuffer out) |
protected void |
ToUnsignedByteScaleByType.convertUnsignedShort(UnsignedShortBuffer in,
UnsignedByteBuffer out) |
protected void |
ToUnsignedByteNoScaling.convertUnsignedShort(UnsignedShortBuffer in,
UnsignedByteBuffer out) |
protected void |
ToUnsignedByteScaleByMaxValue.convertUnsignedShort(UnsignedShortBuffer in,
UnsignedByteBuffer out) |
protected void |
ToUnsignedByteScaleByMinMaxValue.convertUnsignedShort(UnsignedShortBuffer in,
UnsignedByteBuffer out) |
Modifier and Type | Method and Description |
---|---|
void |
VoxelsConverter.copyFromUnsignedByte(Voxels<UnsignedByteBuffer> from,
Voxels<T> to)
Copies voxels from a source of type @{link UnsignedByteBuffer} to voxels of type
T . |
Modifier and Type | Method and Description |
---|---|
static BufferedImage |
BufferedImageFromVoxels.createGrayscaleByte(Voxels<UnsignedByteBuffer> voxels)
Creates a
BufferedImage from a Voxels<UnsignedByteBuffer> . |
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.integer.UnsignedByteType> |
ConvertToImg.fromByte(Voxels<UnsignedByteBuffer> voxels)
Creates an
Img from Voxels with an unsigned byte data-type. |
static net.imglib2.img.NativeImg<net.imglib2.type.numeric.integer.UnsignedByteType,net.imglib2.img.basictypeaccess.array.ByteArray> |
ConvertToNativeImg.fromByte(Voxels<UnsignedByteBuffer> voxels)
Creates an
NativeImg from Voxels with an unsigned byte data-type. |
Modifier and Type | Method and Description |
---|---|
static VoxelsExtracter<UnsignedByteBuffer> |
VoxelsExtracterFactory.createUnsignedByte(Voxels<UnsignedByteBuffer> voxels)
Create voxels-extracter for
UnsignedByteBuffer . |
Modifier and Type | Method and Description |
---|---|
static VoxelsExtracter<UnsignedByteBuffer> |
VoxelsExtracterFactory.createUnsignedByte(Voxels<UnsignedByteBuffer> voxels)
Create voxels-extracter for
UnsignedByteBuffer . |
Modifier and Type | Method and Description |
---|---|
static VoxelsFactoryTypeBound<UnsignedByteBuffer> |
VoxelsFactory.getUnsignedByte()
A factory that creates voxels of type unsigned byte.
|
Modifier and Type | Method and Description |
---|---|
static void |
IterateVoxelsAll.binaryOperation(Voxels<UnsignedByteBuffer> voxelsIn1,
Voxels<UnsignedByteBuffer> voxelsIn2,
Voxels<UnsignedByteBuffer> voxelsOut,
java.util.function.IntBinaryOperator operation)
Iterate over each voxel in a bounding-box - applying a binary operation with values from
two input
Voxels<UnsignedByteBuffer> for each slice and writing it into an
output Voxels<UnsignedByteBuffer> . |
static void |
IterateVoxelsAll.binaryOperation(Voxels<UnsignedByteBuffer> voxelsIn1,
Voxels<UnsignedByteBuffer> voxelsIn2,
Voxels<UnsignedByteBuffer> voxelsOut,
java.util.function.IntBinaryOperator operation)
Iterate over each voxel in a bounding-box - applying a binary operation with values from
two input
Voxels<UnsignedByteBuffer> for each slice and writing it into an
output Voxels<UnsignedByteBuffer> . |
static void |
IterateVoxelsAll.binaryOperation(Voxels<UnsignedByteBuffer> voxelsIn1,
Voxels<UnsignedByteBuffer> voxelsIn2,
Voxels<UnsignedByteBuffer> voxelsOut,
java.util.function.IntBinaryOperator operation)
Iterate over each voxel in a bounding-box - applying a binary operation with values from
two input
Voxels<UnsignedByteBuffer> for each slice and writing it into an
output Voxels<UnsignedByteBuffer> . |
static void |
IterateVoxelsEqualTo.equalToPrimitive(Voxels<UnsignedByteBuffer> voxels,
byte equalToValue,
ScalarThreeDimensionalConsumer consumer)
Iterates through all points with a specific voxel intensity-value, passing coordinates as
primitive types.
|
static void |
IterateVoxelsEqualTo.equalToPrimitiveSlice(Voxels<UnsignedByteBuffer> voxels,
int sliceIndex,
byte equalToValue,
ScalarThreeDimensionalConsumer consumer)
|
static void |
IterateVoxelsEqualTo.equalToReusePoint(Voxels<UnsignedByteBuffer> voxels,
byte equalToValue,
java.util.function.Consumer<Point3i> consumer)
Iterates all points with a specific voxel intensity-value, reusing the
Point3i in
each iteration. |
static Optional<Point3i> |
IterateVoxelsEqualTo.untilFirstIntensityEqualTo(BoundedVoxels<UnsignedByteBuffer> voxels,
byte equalToValue)
Iterates each voxel until a specific intensity value is found.
|
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 void |
IterateVoxelsAll.withCursor(BinaryVoxels<UnsignedByteBuffer> voxels,
KernelApplicationParameters parameters,
ProcessKernelPointCursor process)
Iterate over each voxel 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.. |
Modifier and Type | Method and Description |
---|---|
static int |
CountVoxelsIntersectingBounded.countByte(BoundedVoxels<UnsignedByteBuffer> voxels1,
BoundedVoxels<UnsignedByteBuffer> voxels2,
PredicateTwoBytes predicate)
Counts all voxels in the intersection of two bounded-voxels of type
BoundedVoxels
that match a predicate. |
static int |
CountVoxelsIntersectingBounded.countByte(BoundedVoxels<UnsignedByteBuffer> voxels1,
BoundedVoxels<UnsignedByteBuffer> voxels2,
PredicateTwoBytes predicate)
Counts all voxels in the intersection of two bounded-voxels of type
BoundedVoxels
that match a predicate. |
static int |
CountVoxelsIntersectingBounded.countByteMasked(Voxels<UnsignedByteBuffer> maskGlobal,
byte onMaskGlobal,
BoundedVoxels<UnsignedByteBuffer> voxels1,
BoundedVoxels<UnsignedByteBuffer> voxels2,
PredicateTwoBytes predicate)
Counts all voxels intersection of two bounded-voxels of type
BoundedVoxels but only
voxels that lie on an object-mask and match a predicate. |
static int |
CountVoxelsIntersectingBounded.countByteMasked(Voxels<UnsignedByteBuffer> maskGlobal,
byte onMaskGlobal,
BoundedVoxels<UnsignedByteBuffer> voxels1,
BoundedVoxels<UnsignedByteBuffer> voxels2,
PredicateTwoBytes predicate)
Counts all voxels intersection of two bounded-voxels of type
BoundedVoxels but only
voxels that lie on an object-mask and match a predicate. |
static int |
CountVoxelsIntersectingBounded.countByteMasked(Voxels<UnsignedByteBuffer> maskGlobal,
byte onMaskGlobal,
BoundedVoxels<UnsignedByteBuffer> voxels1,
BoundedVoxels<UnsignedByteBuffer> voxels2,
PredicateTwoBytes predicate)
Counts all voxels intersection of two bounded-voxels of type
BoundedVoxels but only
voxels that lie on an object-mask and match a predicate. |
static void |
IterateVoxelsIntersectingBounded.withTwoBuffers(Voxels<UnsignedByteBuffer> maskGlobal,
byte onMaskGlobal,
BoundedVoxels<UnsignedByteBuffer> voxels1,
BoundedVoxels<UnsignedByteBuffer> voxels2,
ProcessBufferBinary<UnsignedByteBuffer,UnsignedByteBuffer> process)
Iterates over the intersection of two bounded-voxels of type
BoundedVoxels but only
voxels that lie on an object-mask. |
static void |
IterateVoxelsIntersectingBounded.withTwoBuffers(Voxels<UnsignedByteBuffer> maskGlobal,
byte onMaskGlobal,
BoundedVoxels<UnsignedByteBuffer> voxels1,
BoundedVoxels<UnsignedByteBuffer> voxels2,
ProcessBufferBinary<UnsignedByteBuffer,UnsignedByteBuffer> process)
Iterates over the intersection of two bounded-voxels of type
BoundedVoxels but only
voxels that lie on an object-mask. |
static void |
IterateVoxelsIntersectingBounded.withTwoBuffers(Voxels<UnsignedByteBuffer> maskGlobal,
byte onMaskGlobal,
BoundedVoxels<UnsignedByteBuffer> voxels1,
BoundedVoxels<UnsignedByteBuffer> voxels2,
ProcessBufferBinary<UnsignedByteBuffer,UnsignedByteBuffer> process)
Iterates over the intersection of two bounded-voxels of type
BoundedVoxels but only
voxels that lie on an object-mask. |
static void |
IterateVoxelsIntersectingBounded.withTwoBuffers(Voxels<UnsignedByteBuffer> maskGlobal,
byte onMaskGlobal,
BoundedVoxels<UnsignedByteBuffer> voxels1,
BoundedVoxels<UnsignedByteBuffer> voxels2,
ProcessBufferBinary<UnsignedByteBuffer,UnsignedByteBuffer> process)
Iterates over the intersection of two bounded-voxels of type
BoundedVoxels but only
voxels that lie on an object-mask. |
static void |
IterateVoxelsIntersectingBounded.withTwoBuffers(Voxels<UnsignedByteBuffer> maskGlobal,
byte onMaskGlobal,
BoundedVoxels<UnsignedByteBuffer> voxels1,
BoundedVoxels<UnsignedByteBuffer> voxels2,
ProcessBufferBinary<UnsignedByteBuffer,UnsignedByteBuffer> process)
Iterates over the intersection of two bounded-voxels of type
BoundedVoxels but only
voxels that lie on an object-mask. |
Modifier and Type | Method and Description |
---|---|
default void |
ProcessChangedPointAbsoluteMasked.notifyChangeZ(int zChange,
int z,
UnsignedByteBuffer objectMaskBuffer)
Notifies the processor that there has been a change in z-coordinate.
|
Modifier and Type | Method and Description |
---|---|
void |
WalkRunnable.walk(UnsignedByteBuffer buffer,
BufferRetriever bufferRetriever)
Walks in X and Y direction, and Z direction if enabled.
|
boolean |
WalkPredicate.walk(UnsignedByteBuffer buffer,
BufferRetriever bufferRetriever)
Do any neighboring voxels in any direction satisfy the predicate?
|
Modifier and Type | Method and Description |
---|---|
static void |
IterateKernelHelper.overAll(Kernel kernel,
BinaryVoxels<UnsignedByteBuffer> voxels,
KernelApplicationParameters parameters,
ProcessKernelPointCursor processor)
Iterates over all voxels.
|
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.
|
boolean |
NeighborPredicate.test(boolean inside,
KernelPointCursor point,
java.util.function.Supplier<UnsignedByteBuffer> buffer,
int zShift)
Tests if a neighbor satisfies a condition.
|
Modifier and Type | Method and Description |
---|---|
default PredicateBufferBinary<UnsignedByteBuffer> |
PredicateTwoBytes.deriveUnsignedBytePredicate()
Derives a predicate with a different interface for operating on
UnsignedByteBuffer . |
default ProcessBufferBinary<UnsignedByteBuffer,UnsignedByteBuffer> |
PredicateTwoBytes.deriveUnsignedByteProcessor()
Derives a processor with a different interface for operating on
UnsignedByteBuffer . |
default ProcessBufferBinary<UnsignedByteBuffer,UnsignedByteBuffer> |
PredicateTwoBytes.deriveUnsignedByteProcessor()
Derives a processor with a different interface for operating on
UnsignedByteBuffer . |
Modifier and Type | Method and Description |
---|---|
static BinaryVoxels<UnsignedByteBuffer> |
ApplyKernel.apply(BinaryKernel kernel,
BinaryVoxels<UnsignedByteBuffer> voxels,
KernelApplicationParameters parameters)
Apply the kernel to
BinaryVoxels<UnsignedByteBuffer> using the same binary-values as
voxels to calculate a value for each voxel. |
Optional<UnsignedByteBuffer> |
LocalSlices.getLocal(int relativeZIndex) |
Optional<UnsignedByteBuffer> |
BufferRetriever.getLocal(int relativeZIndex)
Get a buffer at a particular index in the z-dimension.
|
Modifier and Type | Method and Description |
---|---|
boolean |
KernelPointCursor.isBufferOff(UnsignedByteBuffer buffer)
Is the value at the current index in this buffer corresponding to an off state?
|
boolean |
KernelPointCursor.isBufferOn(UnsignedByteBuffer buffer)
Is the value at the current index in this buffer corresponding to an on state?
|
Modifier and Type | Method and Description |
---|---|
static BinaryVoxels<UnsignedByteBuffer> |
ApplyKernel.apply(BinaryKernel kernel,
BinaryVoxels<UnsignedByteBuffer> voxels,
KernelApplicationParameters parameters)
Apply the kernel to
BinaryVoxels<UnsignedByteBuffer> using the same binary-values as
voxels to calculate a value for each voxel. |
static int |
ApplyKernel.applyForCount(BinaryKernel kernel,
BinaryVoxels<UnsignedByteBuffer> voxels,
KernelApplicationParameters parameters)
Applies a
BinaryKernel to voxels and counts how many true values occur en aggregate. |
static int |
ApplyKernel.applyForCount(CountKernel kernel,
BinaryVoxels<UnsignedByteBuffer> voxels,
BoundingBox box,
KernelApplicationParameters parameters)
Applies the kernel to voxels and sums the returned value.
|
static int |
ApplyKernel.applyForCount(CountKernel kernel,
BinaryVoxels<UnsignedByteBuffer> voxels,
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.
|
Constructor and Description |
---|
LocalSlices(int z,
int windowSize,
Voxels<UnsignedByteBuffer> voxels)
Create with focus around a particular slice.
|
Modifier and Type | Method and Description |
---|---|
protected abstract boolean |
BinaryKernelMorphological.firstCheck(KernelPointCursor point,
UnsignedByteBuffer buffer)
The first check done on the kernel center-point, before checking any neighbors.
|
protected boolean |
DilationKernel.firstCheck(KernelPointCursor point,
UnsignedByteBuffer buffer) |
protected boolean |
ErosionKernel.firstCheck(KernelPointCursor point,
UnsignedByteBuffer buffer) |
Modifier and Type | Method and Description |
---|---|
protected abstract boolean |
BinaryKernelMorphological.doesNeighborQualify(boolean inside,
KernelPointCursor point,
java.util.function.Supplier<UnsignedByteBuffer> buffer,
int zShift)
Does a particular neighboring-point satisfy the conditions.
|
protected boolean |
DilationKernel.doesNeighborQualify(boolean inside,
KernelPointCursor point,
java.util.function.Supplier<UnsignedByteBuffer> buffer,
int zShift) |
protected boolean |
ErosionKernel.doesNeighborQualify(boolean inside,
KernelPointCursor point,
java.util.function.Supplier<UnsignedByteBuffer> buffer,
int zShift)
Checks whether a particular neighbor voxel qualifies to make the current voxel an outline
voxel.
|
Modifier and Type | Method and Description |
---|---|
protected boolean |
OutlineKernelBase.firstCheck(KernelPointCursor point,
UnsignedByteBuffer buffer) |
Modifier and Type | Method and Description |
---|---|
protected boolean |
OutlineKernelNeighborMatchValue.doesNeighborQualify(boolean inside,
KernelPointCursor point,
java.util.function.Supplier<UnsignedByteBuffer> buffer,
int zShift)
Checks whether a particular neighbor voxel qualifies to make the current voxel an outline
voxel.
|
protected boolean |
OutlineKernel.doesNeighborQualify(boolean inside,
KernelPointCursor point,
java.util.function.Supplier<UnsignedByteBuffer> buffer,
int zShift)
Checks whether a particular neighbor voxel qualifies to make the current voxel an outline
voxel.
|
Constructor and Description |
---|
OutlineKernelNeighborMatchValue(BinaryVoxels<UnsignedByteBuffer> mask)
Creates for an object.
|
Modifier and Type | Method and Description |
---|---|
UnsignedByteBuffer |
ObjectMask.sliceBufferGlobal(int sliceIndexGlobal)
A slice buffer with global coordinates.
|
UnsignedByteBuffer |
ObjectMask.sliceBufferLocal(int sliceIndexRelative)
A slice buffer with local coordinates.
|
Modifier and Type | Method and Description |
---|---|
BinaryVoxels<UnsignedByteBuffer> |
ObjectMask.binaryVoxels()
The underlying voxel memory buffers for the object-mask, exposed via a
BinaryVoxels . |
BoundedVoxels<UnsignedByteBuffer> |
ObjectMask.boundedVoxels()
The underlying voxel memory buffers for the object-mask, exposed via
BoundedVoxels . |
VoxelsExtracter<UnsignedByteBuffer> |
ObjectMask.extract()
Provides methods to read/copy/duplicate regions of voxels.
|
Voxels<UnsignedByteBuffer> |
ObjectMask.voxels()
The underlying voxel memory buffers for the object-mask, exposed via
Voxels . |
Modifier and Type | Method and Description |
---|---|
ObjectMask |
ObjectMask.replaceVoxels(Voxels<UnsignedByteBuffer> voxelsToAssign)
Replaces the voxels in the object-mask.
|
Modifier and Type | Method and Description |
---|---|
static BinaryVoxels<UnsignedByteBuffer> |
MorphologicalDilation.dilate(BinaryVoxels<UnsignedByteBuffer> voxels,
int iterations,
DilationContext context)
Performs a morphological dilation operation.
|
static BinaryVoxels<UnsignedByteBuffer> |
MorphologicalErosion.erode(BinaryVoxels<UnsignedByteBuffer> voxels,
int iterations,
boolean useZ,
Optional<java.util.function.Predicate<Point3i>> precondition)
Performs a morphological erosion on a
BinaryVoxels<UnsignedByteBuffer> voxels . |
Modifier and Type | Method and Description |
---|---|
static BinaryVoxels<UnsignedByteBuffer> |
MorphologicalDilation.dilate(BinaryVoxels<UnsignedByteBuffer> voxels,
int iterations,
DilationContext context)
Performs a morphological dilation operation.
|
static BinaryVoxels<UnsignedByteBuffer> |
MorphologicalErosion.erode(BinaryVoxels<UnsignedByteBuffer> voxels,
int iterations,
boolean useZ,
Optional<java.util.function.Predicate<Point3i>> precondition)
Performs a morphological erosion on a
BinaryVoxels<UnsignedByteBuffer> voxels . |
Modifier and Type | Method and Description |
---|---|
boolean |
AcceptIterationPredicate.accept(BinaryVoxels<UnsignedByteBuffer> voxels)
Whether a particular
voxels fulfills the condition or not. |
boolean |
AcceptIterationList.accept(BinaryVoxels<UnsignedByteBuffer> voxels) |
Modifier and Type | Method and Description |
---|---|
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.
|
Modifier and Type | Method and Description |
---|---|
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.
|
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) |
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. |
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> |
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) |
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 VoxelBuffer<UnsignedByteBuffer> |
VoxelsResizerExecutionTime.resizeByte(VoxelBuffer<UnsignedByteBuffer> voxelsSource,
VoxelBuffer<UnsignedByteBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
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 . |
static BinaryVoxels<UnsignedByteBuffer> |
VoxelsThresholder.thresholdFloat(Voxels<FloatBuffer> voxels,
float level,
BinaryValuesByte binaryValues)
Applies thresholding to
Voxels of float data type. |
Modifier and Type | Method and Description |
---|---|
static void |
VoxelsThresholder.thresholdByte(Voxels<UnsignedByteBuffer> voxels,
int level,
BinaryValuesByte binaryValues)
Applies thresholding to
Voxels of unsigned byte data type. |
Modifier and Type | Method and Description |
---|---|
protected UnsignedByteBuffer |
UnsignedByteFromUnsignedByte.convert(ByteBuffer source,
int channelIndexRelative,
OrientationChange orientationCorrection,
boolean littleEndian) |
Modifier and Type | Method and Description |
---|---|
protected void |
ToUnsignedByteWithScaling.copyChangeOrientation(ByteBuffer source,
boolean littleEndian,
int channelIndexRelative,
UnsignedByteBuffer destination,
OrientationChange orientationCorrection) |
protected void |
UnsignedByteFromFloat.copyChangeOrientation(ByteBuffer source,
boolean littleEndian,
int channelIndexRelative,
UnsignedByteBuffer destination,
OrientationChange orientationCorrection) |
protected void |
UnsignedByteFromUnsignedByteNoInterleaving.copyChangeOrientation(ByteBuffer source,
boolean littleEndian,
int channelIndexRelative,
UnsignedByteBuffer destination,
OrientationChange orientationCorrection) |
protected void |
UnsignedByteFromUnsignedByteInterleaving.copyChangeOrientation(ByteBuffer source,
boolean littleEndian,
int channelIndexRelative,
UnsignedByteBuffer destination,
OrientationChange orientationCorrection) |
protected void |
ToUnsignedByteWithScaling.copyKeepOrientation(ByteBuffer source,
boolean littleEndian,
int channelIndexRelative,
UnsignedByteBuffer destination) |
protected void |
UnsignedByteFromFloat.copyKeepOrientation(ByteBuffer source,
boolean littleEndian,
int channelIndexRelative,
UnsignedByteBuffer destination) |
protected void |
UnsignedByteFromUnsignedByteNoInterleaving.copyKeepOrientation(ByteBuffer source,
boolean littleEndian,
int channelIndexRelative,
UnsignedByteBuffer destination) |
protected void |
UnsignedByteFromUnsignedByteInterleaving.copyKeepOrientation(ByteBuffer source,
boolean littleEndian,
int channelIndexRelative,
UnsignedByteBuffer destination) |
Modifier and Type | Method and Description |
---|---|
static VoxelBuffer<UnsignedByteBuffer> |
ConvertToVoxelBuffer.asByte(ij.process.ImageProcessor processor)
Convert a
ImageProcessor to VoxelBuffer<UnsignedByteBuffer> |
Modifier and Type | Method and Description |
---|---|
static ij.process.ImageProcessor |
ConvertToImageProcessor.fromByte(SliceBufferIndex<UnsignedByteBuffer> pixelsForSlice,
int z)
|
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.ImagePlus |
ConvertToImagePlus.fromSlice(Voxels<UnsignedByteBuffer> voxels,
int sliceIndex,
String name)
Creates an
ImagePlus from one slice of a Voxels<UnsignedByteBuffer>
voxels . |
Modifier and Type | Method and Description |
---|---|
VoxelBuffer<UnsignedByteBuffer> |
VoxelsResizerImageJ.resizeByte(VoxelBuffer<UnsignedByteBuffer> voxelsSource,
VoxelBuffer<UnsignedByteBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
Modifier and Type | Method and Description |
---|---|
VoxelBuffer<UnsignedByteBuffer> |
VoxelsResizerImageJ.resizeByte(VoxelBuffer<UnsignedByteBuffer> voxelsSource,
VoxelBuffer<UnsignedByteBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
VoxelBuffer<UnsignedByteBuffer> |
VoxelsResizerImageJ.resizeByte(VoxelBuffer<UnsignedByteBuffer> voxelsSource,
VoxelBuffer<UnsignedByteBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
Modifier and Type | Method and Description |
---|---|
BoundedVoxels<UnsignedByteBuffer> |
VoxelizedMark.voxels() |
BoundedVoxels<UnsignedByteBuffer> |
VoxelizedMark.voxelsMaximumIntensityProjection() |
Modifier and Type | Method and Description |
---|---|
int |
CountIntersectingVoxels.count(BoundedVoxels<UnsignedByteBuffer> voxels1,
BoundedVoxels<UnsignedByteBuffer> voxels2) |
int |
CountIntersectingVoxels.count(BoundedVoxels<UnsignedByteBuffer> voxels1,
BoundedVoxels<UnsignedByteBuffer> voxels2) |
int |
CountIntersectingVoxels.countMasked(BoundedVoxels<UnsignedByteBuffer> voxels1,
BoundedVoxels<UnsignedByteBuffer> voxels2,
Voxels<UnsignedByteBuffer> maskGlobal,
byte onMaskGlobal) |
int |
CountIntersectingVoxels.countMasked(BoundedVoxels<UnsignedByteBuffer> voxels1,
BoundedVoxels<UnsignedByteBuffer> voxels2,
Voxels<UnsignedByteBuffer> maskGlobal,
byte onMaskGlobal) |
int |
CountIntersectingVoxels.countMasked(BoundedVoxels<UnsignedByteBuffer> voxels1,
BoundedVoxels<UnsignedByteBuffer> voxels2,
Voxels<UnsignedByteBuffer> maskGlobal,
byte onMaskGlobal) |
static double |
OverlapUtilities.overlapWithMaskGlobal(VoxelizedMarkMemo pmm1,
VoxelizedMarkMemo pmm2,
int regionID,
Voxels<UnsignedByteBuffer> globalMask,
byte onGlobalMask)
Counts the number of overlapping voxels between two
VoxelizedMarkMemo |
Modifier and Type | Method and Description |
---|---|
Voxels<UnsignedByteBuffer> |
DistanceTransform3D.createDistanceMapForVoxels(BinaryVoxels<UnsignedByteBuffer> voxels,
Optional<Resolution> resolution,
float multiplyByZRes) |
Modifier and Type | Method and Description |
---|---|
Voxels<UnsignedByteBuffer> |
DistanceTransform3D.createDistanceMapForVoxels(BinaryVoxels<UnsignedByteBuffer> voxels,
Optional<Resolution> resolution,
float multiplyByZRes) |
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 |
---|---|
ChannelConverter<UnsignedByteBuffer> |
ScaleByMinMaxValue.createConverter() |
ChannelConverter<UnsignedByteBuffer> |
ScaleByTypeToByte.createConverter() |
ChannelConverter<UnsignedByteBuffer> |
ToByte.createConverter() |
ChannelConverter<UnsignedByteBuffer> |
ScaleByDictionary.createConverter() |
ChannelConverterAttached<Histogram,UnsignedByteBuffer> |
ToByteUpperLowerQuantileIntensity.createConverter() |
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 |
---|---|
protected void |
SliceThresholder.writeOffByte(int offset,
UnsignedByteBuffer bufferOut) |
protected void |
SliceThresholder.writeThresholdedByte(int offset,
UnsignedByteBuffer bufferOut,
VoxelBuffer<?> bufferIn,
VoxelBuffer<?> bufferThreshold) |
Modifier and Type | Method and Description |
---|---|
abstract void |
SliceThresholder.segmentAll(Voxels<?> voxelsIn,
Voxels<?> voxelsThreshold,
Voxels<UnsignedByteBuffer> voxelsOut) |
void |
SliceThresholderWithoutMask.segmentAll(Voxels<?> voxelsIn,
Voxels<?> voxelsThreshold,
Voxels<UnsignedByteBuffer> voxelsOut) |
void |
SliceThresholderMask.segmentAll(Voxels<?> voxelsIn,
Voxels<?> voxelsThrshld,
Voxels<UnsignedByteBuffer> voxelsOut) |
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 |
---|---|
static void |
FilterHelper.processEachSlice(BinaryVoxels<UnsignedByteBuffer> voxels,
java.util.function.Consumer<ij.process.ImageProcessor> consumer)
Applies a
Consumer to each slice independently of a BinaryVoxels<UnsignedByteBuffer> . |
Modifier and Type | Method and Description |
---|---|
static BinaryVoxels<UnsignedByteBuffer> |
ApplyImageJMorphologicalOperation.applyOperation(BinaryVoxels<UnsignedByteBuffer> voxels,
String command,
int iterations) |
Modifier and Type | Method and Description |
---|---|
static BinaryVoxels<UnsignedByteBuffer> |
ApplyImageJMorphologicalOperation.applyOperation(BinaryVoxels<UnsignedByteBuffer> voxels,
String command,
int iterations) |
static void |
ApplyImageJMorphologicalOperation.fill(BinaryVoxels<UnsignedByteBuffer> voxels) |
Modifier and Type | Method and Description |
---|---|
static boolean |
VisitSchedulerConvexAboutRoot.isPointConvexTo(Point3i root,
Point3i point,
BinaryVoxels<UnsignedByteBuffer> binaryValues) |
static boolean |
VisitSchedulerConvexAboutRoot.isPointConvexTo(Point3i root,
Point3i destPoint,
BinaryVoxels<UnsignedByteBuffer> voxels,
boolean debug) |
Modifier and Type | Method and Description |
---|---|
BinaryVoxels<UnsignedByteBuffer> |
SegmentThresholdAboveMinBound.segment(VoxelsUntyped voxels,
BinarySegmentationParameters parameters,
Optional<ObjectMask> objectMask) |
Constructor and Description |
---|
MaxIntensityProjectionPair(BoundedVoxels<UnsignedByteBuffer> voxels1,
BoundedVoxels<UnsignedByteBuffer> voxels2,
RegionMembershipWithFlags rmFlags1,
RegionMembershipWithFlags rmFlags2) |
MaxIntensityProjectionPair(BoundedVoxels<UnsignedByteBuffer> voxels1,
BoundedVoxels<UnsignedByteBuffer> voxels2,
RegionMembershipWithFlags rmFlags1,
RegionMembershipWithFlags rmFlags2) |
Modifier and Type | Method and Description |
---|---|
static VoxelBuffer<UnsignedByteBuffer> |
VoxelBufferFromMat.unsignedByteFromMat(org.opencv.core.Mat mat,
Extent extent)
|
Modifier and Type | Method and Description |
---|---|
static org.opencv.core.Mat |
ConvertToMat.fromVoxelBufferByte(VoxelBuffer<UnsignedByteBuffer> voxelBuffer,
Extent extent)
|
static org.opencv.core.Mat |
ConvertToMat.fromVoxelsByte(Voxels<UnsignedByteBuffer> voxels)
|
Modifier and Type | Method and Description |
---|---|
protected VoxelBuffer<UnsignedByteBuffer> |
VoxelsResizerOpenCV.resizeByte(VoxelBuffer<UnsignedByteBuffer> voxelsSource,
VoxelBuffer<UnsignedByteBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
Modifier and Type | Method and Description |
---|---|
protected VoxelBuffer<UnsignedByteBuffer> |
VoxelsResizerOpenCV.resizeByte(VoxelBuffer<UnsignedByteBuffer> voxelsSource,
VoxelBuffer<UnsignedByteBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
protected VoxelBuffer<UnsignedByteBuffer> |
VoxelsResizerOpenCV.resizeByte(VoxelBuffer<UnsignedByteBuffer> voxelsSource,
VoxelBuffer<UnsignedByteBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
Modifier and Type | Method and Description |
---|---|
void |
WriteIntoDirectory.writeVoxels(String outputName,
Voxels<UnsignedByteBuffer> voxels) |
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.