Module net.imglib2.imagej

Package net.imglib2.imagej

Class ImagePlusToImg

java.lang.Object

net.imglib2.imagej.ImagePlusToImg

public class ImagePlusToImg
extends Object

Provides convenience functions to wrap ImageJ 1.x data structures as ImgLib2 ones.

Author:

Stephan Preibisch, Stephan Saalfeld, Matthias Arzt, Gabriel Selzer

Constructor Summary

Constructors

Constructor	Description
ImagePlusToImg()

Method Summary

Modifier and Type	Method	Description
static net.imglib2.img.planar.PlanarImg<net.imglib2.type.numeric.integer.UnsignedByteType,net.imglib2.img.basictypeaccess.array.ByteArray>	wrapByteCached(ij.ImagePlus image)	Wraps an 8 bit ImagePlus, into an PlanarImg, that is backed by a PlanarImg.
static net.imglib2.img.planar.PlanarImg<net.imglib2.type.numeric.integer.UnsignedByteType,?>	wrapByteDirect(ij.ImagePlus imp)	Wraps an ImagePlus into a PlanarImg of unsigned bytes.
static net.imglib2.img.planar.PlanarImg<?,?>	wrapCached(ij.ImagePlus image)	Wraps an ImagePlus, into an PlanarImg, that is backed by a PlanarImg.
static net.imglib2.img.planar.PlanarImg<?,?>	wrapDirect(ij.ImagePlus imp)	Wraps an ImagePlus into a PlanarImg.
static net.imglib2.img.planar.PlanarImg<net.imglib2.type.numeric.real.FloatType,net.imglib2.img.basictypeaccess.array.FloatArray>	wrapFloatCached(ij.ImagePlus image)	Wraps a 32 bit ImagePlus, into an PlanarImg, that is backed by a PlanarImg.
static net.imglib2.img.planar.PlanarImg<net.imglib2.type.numeric.real.FloatType,?>	wrapFloatDirect(ij.ImagePlus imp)	Wraps an ImagePlus into a PlanarImg of floats.
static net.imglib2.img.planar.PlanarImg<net.imglib2.type.numeric.ARGBType,net.imglib2.img.basictypeaccess.array.IntArray>	wrapRGBACached(ij.ImagePlus image)	Wraps a 24 bit ImagePlus, into an PlanarImg, that is backed by a PlanarImg.
static net.imglib2.img.planar.PlanarImg<net.imglib2.type.numeric.ARGBType,?>	wrapRGBADirect(ij.ImagePlus imp)	Wraps an ImagePlus into a PlanarImg of RGBA tuples.
static net.imglib2.img.planar.PlanarImg<net.imglib2.type.numeric.integer.UnsignedShortType,net.imglib2.img.basictypeaccess.array.ShortArray>	wrapShortCached(ij.ImagePlus image)	Wraps a 16 bit ImagePlus, into an PlanarImg, that is backed by a PlanarImg.
static net.imglib2.img.planar.PlanarImg<net.imglib2.type.numeric.integer.UnsignedShortType,?>	wrapShortDirect(ij.ImagePlus imp)	Wraps an ImagePlus into a PlanarImg of unsigned shorts.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ImagePlusToImg

public ImagePlusToImg()

Method Detail

wrapDirect

public static net.imglib2.img.planar.PlanarImg<?,?> wrapDirect(ij.ImagePlus imp)

Wraps an ImagePlus into a PlanarImg.

Under the hood, each ImageProcessor's backing array is wrapped into an ArrayDataAccess. The resulting List of ArrayDataAccesses is used to form a PlanarImg.

Parameters:

imp - the ImagePlus to wrap

Returns:

a PlanarImg directly wrapping imp

wrapByteDirect

public static net.imglib2.img.planar.PlanarImg<net.imglib2.type.numeric.integer.UnsignedByteType,?> wrapByteDirect(ij.ImagePlus imp)

Wraps an ImagePlus into a PlanarImg of unsigned bytes.

Under the hood, each ImageProcessor's backing array is wrapped into an ByteArray. The resulting List of ArrayDataAccesses is used to form a PlanarImg.

Parameters:

imp - the ImagePlus to wrap

Returns:

a PlanarImg of unsigned bytes directly wrapping imp

wrapShortDirect

public static net.imglib2.img.planar.PlanarImg<net.imglib2.type.numeric.integer.UnsignedShortType,?> wrapShortDirect(ij.ImagePlus imp)

Wraps an ImagePlus into a PlanarImg of unsigned shorts.

Under the hood, each ImageProcessor's backing array is wrapped into an ShortArray. The resulting List of ArrayDataAccesses is used to form a PlanarImg.

Parameters:

imp - the ImagePlus to wrap

Returns:

a PlanarImg of unsigned shorts directly wrapping imp

wrapRGBADirect

public static net.imglib2.img.planar.PlanarImg<net.imglib2.type.numeric.ARGBType,?> wrapRGBADirect(ij.ImagePlus imp)

Wraps an ImagePlus into a PlanarImg of RGBA tuples.

Under the hood, each ImageProcessor's backing array is wrapped into an IntArray. The resulting List of ArrayDataAccesses is used to form a PlanarImg.

Parameters:

imp - the ImagePlus to wrap

Returns:

a PlanarImg of ARGB tuples directly wrapping imp

wrapFloatDirect

public static net.imglib2.img.planar.PlanarImg<net.imglib2.type.numeric.real.FloatType,?> wrapFloatDirect(ij.ImagePlus imp)

Wraps an ImagePlus into a PlanarImg of floats.

Under the hood, each ImageProcessor's backing array is wrapped into an FloatArray. The resulting List of ArrayDataAccesses is used to form a PlanarImg.

Parameters:

imp - the ImagePlus to wrap

Returns:

a PlanarImg of floats directly wrapping imp

wrapByteCached

public static net.imglib2.img.planar.PlanarImg<net.imglib2.type.numeric.integer.UnsignedByteType,net.imglib2.img.basictypeaccess.array.ByteArray> wrapByteCached(ij.ImagePlus image)

Wraps an 8 bit ImagePlus, into an PlanarImg, that is backed by a PlanarImg. The PlanarImg loads the planes only if needed, and caches them.

Parameters:

image - the ImagePlus to wrap. Must contain unsigned bytes.

Returns:

a PlanarImg wrapping image.

wrapShortCached

public static net.imglib2.img.planar.PlanarImg<net.imglib2.type.numeric.integer.UnsignedShortType,net.imglib2.img.basictypeaccess.array.ShortArray> wrapShortCached(ij.ImagePlus image)

Wraps a 16 bit ImagePlus, into an PlanarImg, that is backed by a PlanarImg. The PlanarImg loads the planes only if needed, and caches them.

Parameters:

image - the ImagePlus to wrap. Must contain unsigned shorts.

Returns:

a PlanarImg wrapping image.

wrapFloatCached

public static net.imglib2.img.planar.PlanarImg<net.imglib2.type.numeric.real.FloatType,net.imglib2.img.basictypeaccess.array.FloatArray> wrapFloatCached(ij.ImagePlus image)

Wraps a 32 bit ImagePlus, into an PlanarImg, that is backed by a PlanarImg. The PlanarImg loads the planes only if needed, and caches them.

Parameters:

image - the ImagePlus to wrap. Must contain floats.

Returns:

a PlanarImg wrapping image.

wrapRGBACached

public static net.imglib2.img.planar.PlanarImg<net.imglib2.type.numeric.ARGBType,net.imglib2.img.basictypeaccess.array.IntArray> wrapRGBACached(ij.ImagePlus image)

Wraps a 24 bit ImagePlus, into an PlanarImg, that is backed by a PlanarImg. The PlanarImg loads the planes only if needed, and caches them.

Parameters:

image - the ImagePlus to wrap. Must contain RGB tuples.

Returns:

a PlanarImg wrapping image.

wrapCached

public static net.imglib2.img.planar.PlanarImg<?,?> wrapCached(ij.ImagePlus image)

Wraps an ImagePlus, into an PlanarImg, that is backed by a PlanarImg. The PlanarImg loads the planes only if needed, and caches them. The pixel type of the returned image depends on the type of the ImagePlus.

Parameters:

image - the ImagePlus to wrap

Returns:

a PlanarImg wrapping image.