Package | Description |
---|---|
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.channel.factory |
Factory classes for creating
Channel for various
voxel data-types. |
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.label |
Labelling elements (object-masks or similar) with unique successive integers in a channel.
|
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.assigner |
Assigns values to some or all 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.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.extracter.predicate |
Methods to find or count voxels that satisfy a predicate.
|
org.anchoranalysis.image.voxel.factory |
Creates new instances of
Voxels and VoxelsUntyped with specific data-types. |
org.anchoranalysis.image.voxel.iterator |
Utilities to iterate over voxel-locations in images and sub-regions of images.
|
org.anchoranalysis.image.voxel.iterator.intersecting |
Like
org.anchoranalysis.image.voxel.iterator but refers to iterators that operation over
the intersecting regions of two entities. |
org.anchoranalysis.image.voxel.kernel |
Applying a kernel via
convolution to voxels.
|
org.anchoranalysis.image.voxel.object |
The fundamental data class that is an
ObjectMask
and related structures. |
org.anchoranalysis.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.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.image.segment.thresholder.slice |
Non-beans pertaining to segmenting a z-stack slice-by-slice.
|
org.anchoranalysis.plugin.image.segment.watershed.encoding |
Encoding voxels in a watershed-transformation implementation.
|
org.anchoranalysis.plugin.opencv.convert |
Conversion to/from OpenCV data-structures.
|
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 |
---|---|
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. |
Modifier and Type | Method and Description |
---|---|
void |
Channel.replaceVoxels(Voxels<?> voxelsToAssign)
Assigns new voxels to replace the existing voxels.
|
Constructor and Description |
---|
Channel(Voxels<?> voxels,
Optional<Resolution> resolution)
Creates for particular voxels and resolution.
|
Modifier and Type | Method and Description |
---|---|
Channel |
ChannelFactory.create(Voxels<?> voxels)
Create a
Channel from particular voxels. |
Channel |
ChannelFactory.create(Voxels<?> voxels,
Optional<Resolution> resolution)
Create a
Channel from particular voxels. |
Channel |
ChannelFactorySingleType.create(Voxels<?> voxels,
Optional<Resolution> resolution)
Create a
Channel from voxels and a resolution. |
Modifier and Type | Method and Description |
---|---|
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
|
static <T> void |
IterateVoxelsMask.withBuffer(Mask mask,
Voxels<T> voxels,
ProcessBufferUnary<T> process)
Iterate over each voxel in a mask - with an associated buffer for each slice from a voxel-bo
|
Modifier and Type | Method and Description |
---|---|
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. |
Constructor and Description |
---|
DecodeLabels(Voxels<?> voxels,
int minLabelInclusive,
int maxLabelInclusive,
DecodeLabels.CreateElementFromScaledObject<T> createScaledElement) |
Modifier and Type | Method and Description |
---|---|
void |
DisplayStack.copyPixelsTo(int channelIndex,
BoundingBox sourceBox,
Voxels<UnsignedByteBuffer> destinationVoxels,
BoundingBox destinationBox)
Copies pixels from a particular channel to an output buffer.
|
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 | Class and Description |
---|---|
class |
VoxelsFloat
Implementation of
Voxels whose voxels are of type float. |
class |
VoxelsUnsignedByte
Implementation of
Voxels whose voxels are of type unsigned byte (8-bit). |
class |
VoxelsUnsignedInt
Implementation of
Voxels whose voxels are of type unsigned int (32-bit). |
class |
VoxelsUnsignedShort
Implementation of
Voxels whose voxels are of type unsigned short (16-bit). |
Modifier and Type | Method and Description |
---|---|
Voxels<?> |
VoxelsUntyped.any()
Exposes without any specific buffer type.
|
Voxels<UnsignedByteBuffer> |
VoxelsUntyped.asByte()
Casts to use a
UnsignedByteBuffer if the voxels contain this data-type, otherwise
throws a IncorrectVoxelTypeException . |
Voxels<FloatBuffer> |
VoxelsUntyped.asFloat()
Casts to use a
FloatBuffer if the voxels contain this data-type, otherwise throws a
IncorrectVoxelTypeException . |
Voxels<UnsignedIntBuffer> |
VoxelsUntyped.asInt()
Casts to use a
UnsignedIntBuffer if the voxels contain this data-type, otherwise
throws a IncorrectVoxelTypeException . |
Voxels<UnsignedShortBuffer> |
VoxelsUntyped.asShort()
Casts to use a
UnsignedShortBuffer if the voxels contain this data-type, otherwise
throws a IncorrectVoxelTypeException . |
Voxels<?> |
VoxelsUntyped.checkIdenticalDataType(VoxelDataType match)
Do the voxels have a data-type that is equal to
match ? |
Voxels<T> |
Voxels.duplicate()
A deep-copy.
|
Voxels<T> |
BoundedVoxels.voxels()
Voxel-data that fits inside the bounding-box (its extent is invariant with the extent of the
bounding-box).
|
Modifier and Type | Method and Description |
---|---|
boolean |
Voxels.equalsDeep(Voxels<?> other)
Are the voxels identical to another voxels (deep equals)?
|
BoundedVoxels<T> |
BoundedVoxels.replaceVoxels(Voxels<T> voxelsToAssign)
Replaces the voxels in the box.
|
Constructor and Description |
---|
BoundedVoxels(BoundingBox boundingBox,
Voxels<T> voxels)
Creates voxels with a corresponding bounding box.
|
BoundedVoxels(Voxels<T> voxels)
Creates voxels bounded to match the entire voxel-data at the origin.
|
VoxelsUntyped(Voxels<?> voxels)
Creates to wrap a
Voxels of unspecified type. |
Modifier and Type | Method and Description |
---|---|
static VoxelsAssigner |
VoxelsAssignerFactory.createFloat(Voxels<FloatBuffer> voxels,
int valueToAssign)
Create a
VoxelsAssigner for a FloatBuffer . |
static VoxelsAssigner |
VoxelsAssignerFactory.createUnsignedByte(Voxels<UnsignedByteBuffer> voxels,
int valueToAssign)
Create a
VoxelsAssigner for a UnsignedByteBuffer . |
static VoxelsAssigner |
VoxelsAssignerFactory.createUnsignedInt(Voxels<UnsignedIntBuffer> voxels,
int valueToAssign)
Create a a
VoxelsAssigner for a UnsignedIntBuffer . |
static VoxelsAssigner |
VoxelsAssignerFactory.createUnsignedShort(Voxels<UnsignedShortBuffer> voxels,
int valueToAssign)
Create a
VoxelsAssigner for a UnsignedShortBuffer . |
Modifier and Type | Method and Description |
---|---|
Voxels<T> |
BinaryVoxels.voxels()
Voxels that should only have two intensity-values (representing on and off
states).
|
Modifier and Type | Method and Description |
---|---|
protected abstract BinaryVoxels<T> |
BinaryVoxels.binaryVoxelsFor(Voxels<T> voxels,
BinaryValuesInt binaryValues)
Creates a
BinaryVoxels corresponding to a particular voxels and BinaryValuesInt . |
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.
|
static BinaryVoxels<UnsignedIntBuffer> |
BinaryVoxelsFactory.reuseInt(Voxels<UnsignedIntBuffer> voxels,
BinaryValuesInt binaryValues)
Reuses an existing voxel-buffer (of type unsigned int) as a binary-version which should have
only two intensity-values representing off and on.
|
Constructor and Description |
---|
BinaryVoxels(Voxels<T> voxels,
BinaryValuesInt binaryValues) |
Modifier and Type | Method and Description |
---|---|
Voxels<T> |
ProjectableBuffer.completeProjection()
Performs any final operation before turning the projected buffer.
|
Voxels<T> |
SlidingBuffer.getVoxels()
The voxels from which buffers corresponding to slices are extracted.
|
Modifier and Type | Method and Description |
---|---|
void |
ProjectableBuffer.addVoxels(Voxels<T> voxels)
Adds a
Voxels to the projection, as a single entity. |
Constructor and Description |
---|
SlidingBuffer(Voxels<T> voxels)
Create for particular 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 . |
Modifier and Type | Method and Description |
---|---|
void |
VoxelsConverter.copyFrom(VoxelsUntyped from,
Voxels<T> to)
Copies voxels from a source (of any type) to voxels of type
T . |
void |
VoxelsConverter.copyFromFloat(Voxels<FloatBuffer> from,
Voxels<T> to)
Copies voxels from a source of type @{link FloatBuffer} to voxels of type
T . |
void |
VoxelsConverter.copyFromFloat(Voxels<FloatBuffer> from,
Voxels<T> to)
Copies voxels from a source of type @{link FloatBuffer} to voxels of type
T . |
void |
VoxelsConverter.copyFromUnsignedByte(Voxels<UnsignedByteBuffer> from,
Voxels<T> to)
Copies voxels from a source of type @{link UnsignedByteBuffer} to voxels of type
T . |
void |
VoxelsConverter.copyFromUnsignedByte(Voxels<UnsignedByteBuffer> from,
Voxels<T> to)
Copies voxels from a source of type @{link UnsignedByteBuffer} to voxels of type
T . |
void |
VoxelsConverter.copyFromUnsignedInt(Voxels<UnsignedIntBuffer> from,
Voxels<T> to)
Copies voxels from a source of type @{link UnsignedIntBuffer} to voxels of type
T . |
void |
VoxelsConverter.copyFromUnsignedInt(Voxels<UnsignedIntBuffer> from,
Voxels<T> to)
Copies voxels from a source of type @{link UnsignedIntBuffer} to voxels of type
T . |
void |
VoxelsConverter.copyFromUnsignedShort(Voxels<UnsignedShortBuffer> from,
Voxels<T> to)
Copies voxels from a source of type @{link UnsignedShortBuffer} to voxels of type
T . |
void |
VoxelsConverter.copyFromUnsignedShort(Voxels<UnsignedShortBuffer> from,
Voxels<T> to)
Copies voxels from a source of type @{link UnsignedShortBuffer} 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> . |
static BufferedImage |
BufferedImageFromVoxels.createGrayscaleShort(Voxels<UnsignedShortBuffer> voxels)
Creates a
BufferedImage from a Voxels<UnsignedShortBuffer> . |
Modifier and Type | Method and Description |
---|---|
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. |
static net.imglib2.img.Img<net.imglib2.type.numeric.real.FloatType> |
ConvertToImg.fromFloat(Voxels<FloatBuffer> voxels)
Creates an
Img from Voxels with a float data-type. |
static net.imglib2.img.NativeImg<net.imglib2.type.numeric.real.FloatType,net.imglib2.img.basictypeaccess.array.FloatArray> |
ConvertToNativeImg.fromFloat(Voxels<FloatBuffer> voxels)
Creates an
NativeImg from Voxels with a float data-type. |
static net.imglib2.img.Img<net.imglib2.type.numeric.integer.UnsignedShortType> |
ConvertToImg.fromShort(Voxels<UnsignedShortBuffer> voxels)
Creates an
Img from Voxels with an unsigned short data-type. |
static net.imglib2.img.NativeImg<net.imglib2.type.numeric.integer.UnsignedShortType,net.imglib2.img.basictypeaccess.array.ShortArray> |
ConvertToNativeImg.fromShort(Voxels<UnsignedShortBuffer> voxels)
Creates an
NativeImg from Voxels with an unsigned short data-type. |
Modifier and Type | Method and Description |
---|---|
Voxels<T> |
VoxelsExtracter.projectMax()
A maximum intensity projection of all slices
|
Voxels<T> |
VoxelsExtracter.projectMean()
A mean intensity projection of all slices.
|
Voxels<T> |
VoxelsExtracter.region(BoundingBox box,
boolean reuseIfPossible)
A (sub-)region of the voxels.
|
Voxels<T> |
VoxelsExtracter.resizedXY(int sizeX,
int sizeY,
VoxelsResizer resizer)
Creates a new voxels that are a resized version of the current voxels (only in X and Y
dimensions), interpolating as needed.
|
Voxels<T> |
VoxelsExtracter.slice(int sliceIndex)
Creates a new
Voxels with only particular slice. |
Modifier and Type | Method and Description |
---|---|
void |
VoxelsExtracter.boxCopyTo(BoundingBox from,
Voxels<T> voxelsDestination,
BoundingBox destinationBox)
Copies a bounding-box area to another
Voxels . |
static VoxelsExtracter<FloatBuffer> |
VoxelsExtracterFactory.createFloat(Voxels<FloatBuffer> voxels)
Create voxels-extracter for
FloatBuffer . |
static VoxelsExtracter<UnsignedByteBuffer> |
VoxelsExtracterFactory.createUnsignedByte(Voxels<UnsignedByteBuffer> voxels)
Create voxels-extracter for
UnsignedByteBuffer . |
static VoxelsExtracter<UnsignedIntBuffer> |
VoxelsExtracterFactory.createUnsignedInt(Voxels<UnsignedIntBuffer> voxels)
Create voxels-extracter for
UnsignedIntBuffer . |
static VoxelsExtracter<UnsignedShortBuffer> |
VoxelsExtracterFactory.createUnsignedShort(Voxels<UnsignedShortBuffer> voxels)
Create voxels-extracter for
UnsignedShortBuffer . |
void |
VoxelsExtracter.objectCopyTo(ObjectMask from,
Voxels<T> voxelsDestination,
BoundingBox destinationBox)
Copies an area corresponding to an object-mask to another
Voxels . |
Constructor and Description |
---|
PredicateImplementation(Voxels<T> voxels,
java.util.function.Predicate<T> predicate) |
Modifier and Type | Method and Description |
---|---|
Voxels<T> |
VoxelsFactoryTypeBound.create(SliceBufferIndex<T> voxels)
Create a new
Voxels that has been initialized with buffers from SliceBufferIndex . |
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 <T> boolean |
IterateVoxelsObjectMask.allMatchIntensity(ObjectMask object,
Voxels<T> voxels,
java.util.function.IntPredicate predicate)
Do all points on an object-mask match a predicate on the point's voxel-intensity?
|
static <T> boolean |
IterateVoxelsAll.anyPredicateMatch(Voxels<T> voxels,
java.util.function.Predicate<T> predicate)
Tries to apply a predicate to all the remaining buffer locations, returning true if the
predicate matches.
|
static void |
IterateVoxelsAll.assignEachMatchingPoint(Voxels<?> voxels,
java.util.function.IntPredicate predicate,
int valueToAssign)
Assigns a value to any voxel whose intensity matches a predicate, reading and writing the
buffer as an
int . |
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 |
IterateVoxelsAll.changeIntensity(Voxels<?> voxels,
java.util.function.IntUnaryOperator operator)
Changes each voxel, reading and writing the buffer as an
int . |
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 <T extends UnsignedBufferAsInt> |
IterateVoxelsAll.intensityMax(Voxels<T> voxels)
Finds the maximum intensity-value (as an int) among all voxels.
|
static <T extends UnsignedBufferAsInt> |
IterateVoxelsAll.intensityMin(Voxels<T> voxels)
Finds the minimum intensity-value (as an int) among all voxels.
|
static <T extends UnsignedBufferAsInt> |
IterateVoxelsAll.intensityMinMax(Voxels<T> voxels)
Finds the maximum intensity-value (as an int) among all voxels.
|
static <T> void |
IterateVoxelsBoundingBox.withBuffer(BoundingBox box,
Voxels<T> voxels,
ProcessBufferUnary<T> process)
Iterate over each voxel in a bounding-box - with one associated buffer for each slice
|
static <T> void |
IterateVoxelsObjectMask.withBuffer(ObjectMask object,
Voxels<T> voxels,
ProcessBufferUnary<T> process)
Iterate over each voxel in an object-mask - with one associated buffer for each
slice from
Voxels . |
static <T> void |
IterateVoxelsObjectMaskOptional.withBuffer(Optional<ObjectMask> objectMask,
Voxels<T> voxels,
ProcessBufferUnary<T> process)
Iterate over each voxel (or optionally only on object-mask) with one associated
buffer.
|
static <T> void |
IterateVoxelsAll.withBuffer(Voxels<T> voxels,
ProcessBufferUnary<T> process)
Iterate over each voxel - with one associated buffer for each slice.
|
static <T> void |
IterateVoxelsBoundingBox.withThreeBuffers(BoundingBox box,
ReadableTuple3i shiftForSecond,
ReadableTuple3i shiftForThird,
Voxels<T> voxels1,
Voxels<T> voxels2,
Voxels<T> voxels3,
ProcessBufferTernary<T> process)
Iterate over each voxel in a bounding-box - with three associated buffers for each
slice.
|
static <T> void |
IterateVoxelsBoundingBox.withThreeBuffers(BoundingBox box,
ReadableTuple3i shiftForSecond,
ReadableTuple3i shiftForThird,
Voxels<T> voxels1,
Voxels<T> voxels2,
Voxels<T> voxels3,
ProcessBufferTernary<T> process)
Iterate over each voxel in a bounding-box - with three associated buffers for each
slice.
|
static <T> void |
IterateVoxelsBoundingBox.withThreeBuffers(BoundingBox box,
ReadableTuple3i shiftForSecond,
ReadableTuple3i shiftForThird,
Voxels<T> voxels1,
Voxels<T> voxels2,
Voxels<T> voxels3,
ProcessBufferTernary<T> process)
Iterate over each voxel in a bounding-box - with three associated buffers for each
slice.
|
static <T> void |
IterateVoxelsAll.withThreeBuffers(Voxels<T> voxels1,
Voxels<T> voxels2,
Voxels<T> voxels3,
ProcessBufferTernary<T> process)
Iterate over each voxel - with three associated buffers for each slice.
|
static <T> void |
IterateVoxelsAll.withThreeBuffers(Voxels<T> voxels1,
Voxels<T> voxels2,
Voxels<T> voxels3,
ProcessBufferTernary<T> process)
Iterate over each voxel - with three associated buffers for each slice.
|
static <T> void |
IterateVoxelsAll.withThreeBuffers(Voxels<T> voxels1,
Voxels<T> voxels2,
Voxels<T> voxels3,
ProcessBufferTernary<T> process)
Iterate over each voxel - with three associated buffers for each slice.
|
static <T> void |
IterateVoxelsBoundingBox.withTwoBuffers(BoundingBox box,
ReadableTuple3i shiftForSecond,
Voxels<T> voxels1,
Voxels<T> voxels2,
ProcessBufferBinary<T,T> process)
Iterate over each voxel in a bounding-box - with two associated buffers for each
slice, one
VoxelBuffer and one Buffer |
static <T> void |
IterateVoxelsBoundingBox.withTwoBuffers(BoundingBox box,
ReadableTuple3i shiftForSecond,
Voxels<T> voxels1,
Voxels<T> voxels2,
ProcessBufferBinary<T,T> process)
Iterate over each voxel in a bounding-box - with two associated buffers for each
slice, one
VoxelBuffer and one Buffer |
static <S,T> void |
IterateVoxelsObjectMask.withTwoBuffers(ObjectMask object,
Voxels<S> voxels1,
Voxels<T> voxels2,
ProcessBufferBinary<S,T> process)
Iterate over each voxel with a corresponding on value in an object-mask - and with
two associated buffers for each slice covering the all the global space
i.e.
|
static <S,T> void |
IterateVoxelsObjectMask.withTwoBuffers(ObjectMask object,
Voxels<S> voxels1,
Voxels<T> voxels2,
ProcessBufferBinary<S,T> process)
Iterate over each voxel with a corresponding on value in an object-mask - and with
two associated buffers for each slice covering the all the global space
i.e.
|
static <S,T> void |
IterateVoxelsObjectMaskOptional.withTwoBuffers(Optional<ObjectMask> objectMask,
Voxels<S> voxels1,
Voxels<T> voxels2,
ProcessBufferBinary<S,T> process)
Iterate over each voxel (or optionally only on object-mask) with two associated
buffers.
|
static <S,T> void |
IterateVoxelsObjectMaskOptional.withTwoBuffers(Optional<ObjectMask> objectMask,
Voxels<S> voxels1,
Voxels<T> voxels2,
ProcessBufferBinary<S,T> process)
Iterate over each voxel (or optionally only on object-mask) with two associated
buffers.
|
static <S,T> void |
IterateVoxelsAll.withTwoBuffersAndPoint(Voxels<S> voxels1,
Voxels<T> voxels2,
ProcessBufferBinary<S,T> process)
Iterate over each voxel - with two associated buffers for each slice
|
static <S,T> void |
IterateVoxelsAll.withTwoBuffersAndPoint(Voxels<S> voxels1,
Voxels<T> voxels2,
ProcessBufferBinary<S,T> process)
Iterate over each voxel - with two associated buffers for each slice
|
static <T> Optional<Point3i> |
IterateVoxelsBoundingBox.withTwoBuffersUntil(BoundingBox box,
ReadableTuple3i shiftForSecond,
Voxels<T> voxels1,
Voxels<T> voxels2,
PredicateBufferBinary<T> predicate)
Iterate over each voxel in a bounding-box - with two associated buffers for each slice
- until a predicate evaluates to true.
|
static <T> Optional<Point3i> |
IterateVoxelsBoundingBox.withTwoBuffersUntil(BoundingBox box,
ReadableTuple3i shiftForSecond,
Voxels<T> voxels1,
Voxels<T> voxels2,
PredicateBufferBinary<T> predicate)
Iterate over each voxel in a bounding-box - with two associated buffers for each slice
- until a predicate evaluates to true.
|
static <S,T> void |
IterateVoxelsBoundingBox.withTwoMixedBuffers(BoundingBox box,
ReadableTuple3i shiftForSecond,
Voxels<S> voxels1,
Voxels<T> voxels2,
ProcessBufferBinaryMixed<S,T> process)
Iterate over each voxel in a bounding-box - with two associated buffers for each
slice.
|
static <S,T> void |
IterateVoxelsBoundingBox.withTwoMixedBuffers(BoundingBox box,
ReadableTuple3i shiftForSecond,
Voxels<S> voxels1,
Voxels<T> voxels2,
ProcessBufferBinaryMixed<S,T> process)
Iterate over each voxel in a bounding-box - with two associated buffers for each
slice.
|
static <S,T> void |
IterateVoxelsObjectMask.withTwoMixedBuffers(ObjectMask object,
Voxels<S> voxels1,
Voxels<T> voxels2,
ProcessVoxelBufferBinaryMixed<S,T> process)
Iterate over each voxel in an object-mask - with one associated voxel-buffer and
one associated buffer for each slice.
|
static <S,T> void |
IterateVoxelsObjectMask.withTwoMixedBuffers(ObjectMask object,
Voxels<S> voxels1,
Voxels<T> voxels2,
ProcessVoxelBufferBinaryMixed<S,T> process)
Iterate over each voxel in an object-mask - with one associated voxel-buffer and
one associated buffer for each slice.
|
static <S,T> void |
IterateVoxelsAll.withTwoMixedBuffers(Voxels<S> voxels1,
Voxels<T> voxels2,
ProcessVoxelBufferBinaryMixed<S,T> process)
Iterate over each voxel in a bounding-box - with one associated voxel-buffer and
one associated buffer for each slice.
|
static <S,T> void |
IterateVoxelsAll.withTwoMixedBuffers(Voxels<S> voxels1,
Voxels<T> voxels2,
ProcessVoxelBufferBinaryMixed<S,T> process)
Iterate over each voxel in a bounding-box - with one associated voxel-buffer and
one associated buffer for each slice.
|
static <S,T> void |
IterateVoxelsObjectMask.withTwoVoxelBuffers(ObjectMask object,
Voxels<S> voxels1,
Voxels<T> voxels2,
ProcessVoxelBufferBinary<S,T> process)
Iterate over each voxel in an object-mask - with two associated voxel-buffers and for
each slice.
|
static <S,T> void |
IterateVoxelsObjectMask.withTwoVoxelBuffers(ObjectMask object,
Voxels<S> voxels1,
Voxels<T> voxels2,
ProcessVoxelBufferBinary<S,T> process)
Iterate over each voxel in an object-mask - with two associated voxel-buffers and for
each slice.
|
static <S,T> void |
IterateVoxelsAll.withTwoVoxelBuffers(Voxels<S> voxels1,
Voxels<T> voxels2,
ProcessVoxelBufferBinary<S,T> process)
Iterate over each voxel in a bounding-box - with two associated voxel-buffers
for each slice
|
static <S,T> void |
IterateVoxelsAll.withTwoVoxelBuffers(Voxels<S> voxels1,
Voxels<T> voxels2,
ProcessVoxelBufferBinary<S,T> process)
Iterate over each voxel in a bounding-box - with two associated voxel-buffers
for each slice
|
static <T> void |
IterateVoxelsObjectMask.withVoxelBuffer(ObjectMask object,
Voxels<T> voxels,
Optional<BoundingBox> restrictTo,
ProcessVoxelBufferUnary<T> process)
Iterate over each voxel on an object-mask with one associated
VoxelBuffer . |
static <T> void |
IterateVoxelsObjectMask.withVoxelBuffer(ObjectMask object,
Voxels<T> voxels,
ProcessVoxelBufferUnary<T> process)
Iterate over each voxel on an object-mask with one associated
VoxelBuffer . |
static <T> void |
IterateVoxelsAll.withVoxelBuffer(Voxels<T> voxels,
ProcessVoxelBufferUnary<T> process)
Iterate over each voxel - with one associated voxel-buffer for each slice.
|
static <T,E extends Exception> |
IterateVoxelsAll.withVoxelBuffer(Voxels<T> voxels,
ProcessVoxelBufferUnaryWithPoint<T,E> process)
Iterate over each voxel - with one associated voxel-buffer for each slice.
|
Modifier and Type | Method and Description |
---|---|
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. |
Constructor and Description |
---|
LocalSlices(int z,
int windowSize,
Voxels<UnsignedByteBuffer> voxels)
Create with focus around a particular slice.
|
Modifier and Type | Method and Description |
---|---|
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.
|
Constructor and Description |
---|
ObjectMask(BoundingBox box,
Voxels<UnsignedByteBuffer> voxels)
|
ObjectMask(BoundingBox box,
Voxels<UnsignedByteBuffer> voxels,
BinaryValuesByte binaryValues)
Like
ObjectMask(BoundingBox, Voxels, BinaryValuesInt) but specifies the
binary-values as bytes. |
ObjectMask(BoundingBox box,
Voxels<UnsignedByteBuffer> voxels,
BinaryValuesInt binaryValues)
|
ObjectMask(Voxels<UnsignedByteBuffer> voxels)
Creates from a
Voxels mask that is cornered at the origin. |
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. |
static BinaryVoxels<UnsignedByteBuffer> |
VoxelsThresholder.thresholdFloat(Voxels<FloatBuffer> voxels,
float level,
BinaryValuesByte binaryValues)
Applies thresholding to
Voxels of float data type. |
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 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 |
---|---|
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 |
---|---|
abstract void |
SliceThresholder.segmentAll(Voxels<?> voxelsIn,
Voxels<?> voxelsThreshold,
Voxels<UnsignedByteBuffer> voxelsOut) |
abstract void |
SliceThresholder.segmentAll(Voxels<?> voxelsIn,
Voxels<?> voxelsThreshold,
Voxels<UnsignedByteBuffer> voxelsOut) |
abstract void |
SliceThresholder.segmentAll(Voxels<?> voxelsIn,
Voxels<?> voxelsThreshold,
Voxels<UnsignedByteBuffer> voxelsOut) |
void |
SliceThresholderWithoutMask.segmentAll(Voxels<?> voxelsIn,
Voxels<?> voxelsThreshold,
Voxels<UnsignedByteBuffer> voxelsOut) |
void |
SliceThresholderWithoutMask.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) |
void |
SliceThresholderMask.segmentAll(Voxels<?> voxelsIn,
Voxels<?> voxelsThrshld,
Voxels<UnsignedByteBuffer> voxelsOut) |
void |
SliceThresholderMask.segmentAll(Voxels<?> voxelsIn,
Voxels<?> voxelsThrshld,
Voxels<UnsignedByteBuffer> voxelsOut) |
Modifier and Type | Method and Description |
---|---|
Voxels<UnsignedIntBuffer> |
EncodedVoxels.voxels() |
Constructor and Description |
---|
EncodedVoxels(Voxels<UnsignedIntBuffer> voxels) |
Modifier and Type | Method and Description |
---|---|
static org.opencv.core.Mat |
ConvertToMat.fromVoxelsByte(Voxels<UnsignedByteBuffer> voxels)
|
static org.opencv.core.Mat |
ConvertToMat.fromVoxelsFloat(Voxels<FloatBuffer> voxels)
|
static org.opencv.core.Mat |
ConvertToMat.fromVoxelsShort(Voxels<UnsignedShortBuffer> voxels)
|
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.