Package | Description |
---|---|
org.anchoranalysis.image.core.channel.convert |
Converts a channel to other data-types.
|
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.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.projection |
Classes for calculating differnet kind of projections of voxel values across multiple buffers.
|
org.anchoranalysis.image.voxel.projection.extrema |
Classes for performing both a Maximum Intensity
Projection and a minimum projection.
|
org.anchoranalysis.image.voxel.resizer |
Different interpolator methods to use when scaling voxels.
|
org.anchoranalysis.io.bioformats.copyconvert.toshort |
Converts the byte stream opened by Bioformats into channels of
ShortBuffer . |
org.anchoranalysis.io.imagej.convert |
Converts to and from ImageJ data-structures for images.
|
org.anchoranalysis.io.imagej.resizer |
Image interpolation when scaling using ImageJ.
|
org.anchoranalysis.plugin.opencv.convert |
Conversion to/from OpenCV data-structures.
|
org.anchoranalysis.plugin.opencv.resizer |
Interpolation non-beans that use OpenCV.
|
Constructor and Description |
---|
ToUnsignedShort(VoxelsConverter<UnsignedShortBuffer> voxelsConverter)
Convert with a particular
VoxelsConverter . |
Modifier and Type | Method and Description |
---|---|
Voxels<UnsignedShortBuffer> |
VoxelsUntyped.asShort()
Casts to use a
UnsignedShortBuffer if the voxels contain this data-type, otherwise
throws a IncorrectVoxelTypeException . |
VoxelsExtracter<UnsignedShortBuffer> |
VoxelsUnsignedShort.extract() |
Constructor and Description |
---|
VoxelsUnsignedShort(SliceBufferIndex<UnsignedShortBuffer> buffer)
Create from a buffer, indexed by slice.
|
Modifier and Type | Method and Description |
---|---|
static VoxelsArithmetic |
VoxelsArithmeticFactory.createUnsignedShort(Extent extent,
java.util.function.IntFunction<UnsignedShortBuffer> bufferForSlice)
Create a
VoxelsArithmetic for UnsignedShortBuffer . |
Modifier and Type | Method and Description |
---|---|
static VoxelsAssigner |
VoxelsAssignerFactory.createUnsignedShort(Voxels<UnsignedShortBuffer> voxels,
int valueToAssign)
Create a
VoxelsAssigner for a UnsignedShortBuffer . |
Modifier and Type | Method and Description |
---|---|
static VoxelBuffer<UnsignedShortBuffer> |
VoxelBufferFactory.allocateUnsignedShort(int capacity)
Allocates a new unsigned short voxel-buffers of given size.
|
static VoxelBuffer<UnsignedShortBuffer> |
VoxelBufferWrap.unsignedShortArray(short[] array)
Wraps an existing array (encoding unsigned shorts as a signed array) as a voxel-buffer.
|
static VoxelBuffer<UnsignedShortBuffer> |
VoxelBufferWrap.unsignedShortBuffer(UnsignedShortBuffer buffer)
Wraps an unsigned-short buffer into a voxel-buffer.
|
static VoxelBuffer<UnsignedShortBuffer> |
VoxelBufferWrap.unsignedShortRaw(ShortBuffer buffer)
Wraps an unsigned-short buffer (represented by a NIO signed-buffer) into a voxel-buffer.
|
Modifier and Type | Method and Description |
---|---|
static VoxelBuffer<UnsignedShortBuffer> |
VoxelBufferWrap.unsignedShortBuffer(UnsignedShortBuffer buffer)
Wraps an unsigned-short buffer into a voxel-buffer.
|
Modifier and Type | Method and Description |
---|---|
static UnsignedShortBuffer |
UnsignedShortBuffer.allocate(int capacity)
Allocates a new (direct) buffer of unsigned-shorts.
|
static UnsignedShortBuffer |
UnsignedShortBuffer.wrapRaw(short[] array)
Exposes a raw short-array as a buffer with unsigned-shorts.
|
static UnsignedShortBuffer |
UnsignedShortBuffer.wrapRaw(ShortBuffer bufferRaw)
Exposes a raw
UnsignedShortBuffer as a buffer with unsigned-shorts. |
Modifier and Type | Method and Description |
---|---|
void |
UnsignedShortBuffer.put(UnsignedShortBuffer source)
Relative put-method from an unsigned short buffer, represented by a
UnsignedShortBuffer . |
Modifier and Type | Method and Description |
---|---|
static SliceBufferIndex<UnsignedShortBuffer> |
FromShort.createInitialized(Extent extent)
Create a buffer of a particular size, that has been initialized.
|
static SliceBufferIndex<UnsignedShortBuffer> |
FromShort.createUninitialized(Extent extent)
Create a buffer of a particular size, that has not been initialized.
|
VoxelBuffer<UnsignedShortBuffer> |
FromShort.slice(int z) |
Modifier and Type | Method and Description |
---|---|
void |
FromShort.replaceSlice(int z,
VoxelBuffer<UnsignedShortBuffer> sliceToAssign) |
Modifier and Type | Method and Description |
---|---|
protected void |
ToUnsignedShortNoScaling.convertFloat(FloatBuffer in,
UnsignedShortBuffer out) |
protected void |
ToUnsignedShortScaleByType.convertFloat(FloatBuffer in,
UnsignedShortBuffer out)
Converts the current position in a
FloatBuffer to the current position in a UnsignedShortBuffer . |
protected void |
ToUnsignedShortNoScaling.convertUnsignedByte(UnsignedByteBuffer in,
UnsignedShortBuffer out) |
protected void |
ToUnsignedShortScaleByType.convertUnsignedByte(UnsignedByteBuffer in,
UnsignedShortBuffer out) |
protected void |
ToUnsignedShortNoScaling.convertUnsignedInt(UnsignedIntBuffer in,
UnsignedShortBuffer out) |
protected void |
ToUnsignedShortScaleByType.convertUnsignedInt(UnsignedIntBuffer in,
UnsignedShortBuffer out) |
protected void |
ToFloatNoScaling.convertUnsignedShort(UnsignedShortBuffer in,
FloatBuffer out) |
protected abstract void |
VoxelsConverter.convertUnsignedShort(UnsignedShortBuffer in,
T out)
Copies a value from the current position in a
UnsignedShortBuffer to the current
position in a buffer of type T . |
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) |
protected void |
ToUnsignedInt.convertUnsignedShort(UnsignedShortBuffer in,
UnsignedIntBuffer out) |
protected void |
ToUnsignedShortNoScaling.convertUnsignedShort(UnsignedShortBuffer in,
UnsignedShortBuffer out) |
protected void |
ToUnsignedShortScaleByType.convertUnsignedShort(UnsignedShortBuffer in,
UnsignedShortBuffer out) |
Modifier and Type | Method and Description |
---|---|
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.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.UnsignedShortType> |
ConvertToImg.fromShort(VoxelBuffer<UnsignedShortBuffer> buffer,
Extent extent)
Creates an
Img from a VoxelBuffer with an unsigned short 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 |
---|---|
static VoxelsExtracter<UnsignedShortBuffer> |
VoxelsExtracterFactory.createUnsignedShort(Voxels<UnsignedShortBuffer> voxels)
Create voxels-extracter for
UnsignedShortBuffer . |
Modifier and Type | Method and Description |
---|---|
static VoxelsExtracter<UnsignedShortBuffer> |
VoxelsExtracterFactory.createUnsignedShort(Voxels<UnsignedShortBuffer> voxels)
Create voxels-extracter for
UnsignedShortBuffer . |
Modifier and Type | Method and Description |
---|---|
static VoxelsFactoryTypeBound<UnsignedShortBuffer> |
VoxelsFactory.getUnsignedShort()
A factory that creates voxels of type unsigned short.
|
Modifier and Type | Method and Description |
---|---|
static ProjectableBuffer<UnsignedShortBuffer> |
MeanIntensityProjection.createUnsignedShort(Extent extent)
Creates a buffer for a mean-intensity projection for unsigned short voxels.
|
static ProjectableBuffer<UnsignedShortBuffer> |
StandardDeviationIntensityProjection.createUnsignedShort(Extent extent)
Creates a buffer for a standard-deviation projection for unsigned short voxels.
|
Modifier and Type | Method and Description |
---|---|
static ProjectableBuffer<UnsignedShortBuffer> |
MaxIntensityProjection.createUnsignedShort(Extent extent)
Creates a buffer for a maximum-intensity projection for unsigned short voxels.
|
static ProjectableBuffer<UnsignedShortBuffer> |
MinIntensityProjection.createUnsignedShort(Extent extent)
Creates a buffer for a minimum-intensity projection for unsigned short voxels.
|
Modifier and Type | Method and Description |
---|---|
protected abstract VoxelBuffer<UnsignedShortBuffer> |
VoxelsResizer.resizeShort(VoxelBuffer<UnsignedShortBuffer> voxelsSource,
VoxelBuffer<UnsignedShortBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination)
Interpolates from
voxelsSource to voxelsDestination for unsigned 16-bit
buffers. |
VoxelBuffer<UnsignedShortBuffer> |
VoxelsResizerNone.resizeShort(VoxelBuffer<UnsignedShortBuffer> voxelsSource,
VoxelBuffer<UnsignedShortBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
VoxelBuffer<UnsignedShortBuffer> |
VoxelsResizerImgLib2.resizeShort(VoxelBuffer<UnsignedShortBuffer> voxelsSource,
VoxelBuffer<UnsignedShortBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
protected VoxelBuffer<UnsignedShortBuffer> |
VoxelsResizerExecutionTime.resizeShort(VoxelBuffer<UnsignedShortBuffer> voxelsSource,
VoxelBuffer<UnsignedShortBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
Modifier and Type | Method and Description |
---|---|
protected abstract VoxelBuffer<UnsignedShortBuffer> |
VoxelsResizer.resizeShort(VoxelBuffer<UnsignedShortBuffer> voxelsSource,
VoxelBuffer<UnsignedShortBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination)
Interpolates from
voxelsSource to voxelsDestination for unsigned 16-bit
buffers. |
protected abstract VoxelBuffer<UnsignedShortBuffer> |
VoxelsResizer.resizeShort(VoxelBuffer<UnsignedShortBuffer> voxelsSource,
VoxelBuffer<UnsignedShortBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination)
Interpolates from
voxelsSource to voxelsDestination for unsigned 16-bit
buffers. |
VoxelBuffer<UnsignedShortBuffer> |
VoxelsResizerNone.resizeShort(VoxelBuffer<UnsignedShortBuffer> voxelsSource,
VoxelBuffer<UnsignedShortBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
VoxelBuffer<UnsignedShortBuffer> |
VoxelsResizerNone.resizeShort(VoxelBuffer<UnsignedShortBuffer> voxelsSource,
VoxelBuffer<UnsignedShortBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
VoxelBuffer<UnsignedShortBuffer> |
VoxelsResizerImgLib2.resizeShort(VoxelBuffer<UnsignedShortBuffer> voxelsSource,
VoxelBuffer<UnsignedShortBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
VoxelBuffer<UnsignedShortBuffer> |
VoxelsResizerImgLib2.resizeShort(VoxelBuffer<UnsignedShortBuffer> voxelsSource,
VoxelBuffer<UnsignedShortBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
protected VoxelBuffer<UnsignedShortBuffer> |
VoxelsResizerExecutionTime.resizeShort(VoxelBuffer<UnsignedShortBuffer> voxelsSource,
VoxelBuffer<UnsignedShortBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
protected VoxelBuffer<UnsignedShortBuffer> |
VoxelsResizerExecutionTime.resizeShort(VoxelBuffer<UnsignedShortBuffer> voxelsSource,
VoxelBuffer<UnsignedShortBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
Modifier and Type | Method and Description |
---|---|
protected void |
ToUnsignedShort.copyChangeOrientation(ByteBuffer source,
boolean littleEndian,
int channelIndexRelative,
UnsignedShortBuffer destination,
OrientationChange orientationCorrection) |
protected void |
ToUnsignedShort.copyKeepOrientation(ByteBuffer source,
boolean littleEndian,
int channelIndexRelative,
UnsignedShortBuffer destination) |
Modifier and Type | Method and Description |
---|---|
static VoxelBuffer<UnsignedShortBuffer> |
ConvertToVoxelBuffer.asShort(ij.process.ImageProcessor processor)
Convert a
ImageProcessor to VoxelBuffer<UnsignedShortBuffer> |
Modifier and Type | Method and Description |
---|---|
static ij.process.ImageProcessor |
ConvertToImageProcessor.fromShort(SliceBufferIndex<UnsignedShortBuffer> pixelsForSlice,
int z)
|
static ij.process.ImageProcessor |
ConvertToImageProcessor.fromShort(VoxelBuffer<UnsignedShortBuffer> slice,
Extent extent)
Creates a
ImageProcessor from voxel-buffer (of type ShortBuffer ) that is
already a slice. |
Modifier and Type | Method and Description |
---|---|
VoxelBuffer<UnsignedShortBuffer> |
VoxelsResizerImageJ.resizeShort(VoxelBuffer<UnsignedShortBuffer> voxelsSource,
VoxelBuffer<UnsignedShortBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
Modifier and Type | Method and Description |
---|---|
VoxelBuffer<UnsignedShortBuffer> |
VoxelsResizerImageJ.resizeShort(VoxelBuffer<UnsignedShortBuffer> voxelsSource,
VoxelBuffer<UnsignedShortBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
VoxelBuffer<UnsignedShortBuffer> |
VoxelsResizerImageJ.resizeShort(VoxelBuffer<UnsignedShortBuffer> voxelsSource,
VoxelBuffer<UnsignedShortBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
Modifier and Type | Method and Description |
---|---|
static VoxelBuffer<UnsignedShortBuffer> |
VoxelBufferFromMat.unsignedShortFromMat(org.opencv.core.Mat mat,
Extent extent)
|
Modifier and Type | Method and Description |
---|---|
static org.opencv.core.Mat |
ConvertToMat.fromVoxelBufferShort(VoxelBuffer<UnsignedShortBuffer> voxelBuffer,
Extent extent)
|
static org.opencv.core.Mat |
ConvertToMat.fromVoxelsShort(Voxels<UnsignedShortBuffer> voxels)
|
Modifier and Type | Method and Description |
---|---|
protected VoxelBuffer<UnsignedShortBuffer> |
VoxelsResizerOpenCV.resizeShort(VoxelBuffer<UnsignedShortBuffer> voxelsSource,
VoxelBuffer<UnsignedShortBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
Modifier and Type | Method and Description |
---|---|
protected VoxelBuffer<UnsignedShortBuffer> |
VoxelsResizerOpenCV.resizeShort(VoxelBuffer<UnsignedShortBuffer> voxelsSource,
VoxelBuffer<UnsignedShortBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
protected VoxelBuffer<UnsignedShortBuffer> |
VoxelsResizerOpenCV.resizeShort(VoxelBuffer<UnsignedShortBuffer> voxelsSource,
VoxelBuffer<UnsignedShortBuffer> voxelsDestination,
Extent extentSource,
Extent extentDestination) |
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.