Module net.imglib2.imagej

Package net.imglib2.imagej

Class RAIToImagePlus

java.lang.Object

net.imglib2.imagej.RAIToImagePlus

public class RAIToImagePlus
extends Object

Utilities for wrapping RandomAccessibleIntervals into ImagePluses.

Under the hood, conversion utilizes ImageJVirtualStack, allowing read/write operations to the backing RandomAccessibleInterval.

Author:

Tobis Pietzsch, Stephan Preibisch, Stephan Saalfeld, Gabriel Selzer

Method Summary

Modifier and Type	Method	Description
static <T extends net.imglib2.type.numeric.RealType<T>> ij.ImagePlus	convertRGB(net.imglib2.RandomAccessibleInterval<T> img, String title)	Create a 24bit RGB ImagePlus from a RandomAccessibleInterval a using a default Converter.
static <T extends net.imglib2.type.numeric.NumericType<T>> ij.ImagePlus	wrap(net.imglib2.RandomAccessibleInterval<T> img, String title)	Create a single channel ImagePlus from a RandomAccessibleInterval.
static <T extends net.imglib2.type.numeric.NumericType<T>> ij.ImagePlus	wrap(net.imglib2.RandomAccessibleInterval<T> img, String title, ExecutorService service)	Create a single channel ImagePlus from a RandomAccessibleInterval.
static <B extends net.imglib2.type.BooleanType<B>> ij.ImagePlus	wrapAndScaleBoolean(net.imglib2.RandomAccessibleInterval<B> img, String title)	Create a single channel 8-bit unsigned integer ImagePlus from a BooleanType RandomAccessibleInterval using a custom Converter.
static <B extends net.imglib2.type.BooleanType<B>> ij.ImagePlus	wrapAndScaleBoolean(net.imglib2.RandomAccessibleInterval<B> img, String title, ExecutorService service)	Create a single channel 8-bit unsigned integer ImagePlus from a BooleanType RandomAccessibleInterval using a custom Converter.
static <B extends net.imglib2.type.BooleanType<B>> ij.ImagePlus	wrapBoolean(net.imglib2.RandomAccessibleInterval<B> img, String title)	Create a single channel 8-bit unsigned integer ImagePlus from a BooleanType RandomAccessibleInterval using a custom Converter.
static <B extends net.imglib2.type.BooleanType<B>> ij.ImagePlus	wrapBoolean(net.imglib2.RandomAccessibleInterval<B> img, String title, ExecutorService service)	Create a single channel 8-bit unsigned integer ImagePlus from a BooleanType RandomAccessibleInterval using a custom Converter.
static <T extends net.imglib2.type.numeric.RealType<T>> ij.ImagePlus	wrapFloat(net.imglib2.RandomAccessibleInterval<T> img, String title)	Create a single channel 32-bit float ImagePlus from a RandomAccessibleInterval using a default Converter.
static <T extends net.imglib2.type.numeric.RealType<T>> ij.ImagePlus	wrapFloat(net.imglib2.RandomAccessibleInterval<T> img, String title, ExecutorService service)	Create a single channel 32-bit float ImagePlus from a RandomAccessibleInterval using a default Converter.
static <T> ij.ImagePlus	wrapFloat(net.imglib2.RandomAccessibleInterval<T> img, net.imglib2.converter.Converter<T,net.imglib2.type.numeric.real.FloatType> converter, String title)	Create a single channel 32-bit float ImagePlus from a RandomAccessibleInterval using a custom Converter.
static <T> ij.ImagePlus	wrapFloat(net.imglib2.RandomAccessibleInterval<T> img, net.imglib2.converter.Converter<T,net.imglib2.type.numeric.real.FloatType> converter, String title, ExecutorService service)	Create a single channel 32-bit float ImagePlus from a RandomAccessibleInterval using a custom Converter.
static ij.ImagePlus	wrapRGB(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.ARGBType> img, String title)	Create a 24bit RGB ImagePlus wrapping a RandomAccessibleInterval with ARGBType elements.
static ij.ImagePlus	wrapRGB(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.ARGBType> img, String title, ExecutorService service)	Create a 24bit RGB ImagePlus from a RandomAccessibleInterval with ARGBType elements.
static <T extends net.imglib2.type.numeric.RealType<T>> ij.ImagePlus	wrapUnsignedByte(net.imglib2.RandomAccessibleInterval<T> img, String title)	Create a single channel 8-bit unsigned integer ImagePlus from a RandomAccessibleInterval using a custom Converter.
static <T extends net.imglib2.type.numeric.RealType<T>> ij.ImagePlus	wrapUnsignedByte(net.imglib2.RandomAccessibleInterval<T> img, String title, ExecutorService service)	Create a single channel 8-bit unsigned integer ImagePlus from a RandomAccessibleInterval using a custom Converter.
static <T> ij.ImagePlus	wrapUnsignedByte(net.imglib2.RandomAccessibleInterval<T> img, net.imglib2.converter.Converter<T,net.imglib2.type.numeric.integer.UnsignedByteType> converter, String title)	Create a single channel 8-bit unsigned integer ImagePlus from a RandomAccessibleInterval using a custom Converter.
static <T> ij.ImagePlus	wrapUnsignedByte(net.imglib2.RandomAccessibleInterval<T> img, net.imglib2.converter.Converter<T,net.imglib2.type.numeric.integer.UnsignedByteType> converter, String title, ExecutorService service)	Create a single channel 8-bit unsigned integer ImagePlus from a RandomAccessibleInterval using a custom Converter.
static <T extends net.imglib2.type.numeric.RealType<T>> ij.ImagePlus	wrapUnsignedShort(net.imglib2.RandomAccessibleInterval<T> img, String title)	Create a single channel 16-bit unsigned integer ImagePlus from a RandomAccessibleInterval using a default Converter (clamp values to range [0, 65535]).
static <T extends net.imglib2.type.numeric.RealType<T>> ij.ImagePlus	wrapUnsignedShort(net.imglib2.RandomAccessibleInterval<T> img, String title, ExecutorService service)	Create a single channel 16-bit unsigned integer ImagePlus from a RandomAccessibleInterval using a default Converter (clamp values to range [0, 65535]).
static <T> ij.ImagePlus	wrapUnsignedShort(net.imglib2.RandomAccessibleInterval<T> img, net.imglib2.converter.Converter<T,net.imglib2.type.numeric.integer.UnsignedShortType> converter, String title)	Create a single channel 16-bit unsigned integer ImagePlus from a RandomAccessibleInterval using a custom Converter.
static <T> ij.ImagePlus	wrapUnsignedShort(net.imglib2.RandomAccessibleInterval<T> img, net.imglib2.converter.Converter<T,net.imglib2.type.numeric.integer.UnsignedShortType> converter, String title, ExecutorService service)	Create a single channel 16-bit unsigned integer ImagePlus from a RandomAccessibleInterval using a custom Converter.
static ij.ImagePlus	wrapVirtualStack(net.imglib2.RandomAccessibleInterval<?> rai, String title)	Wraps an RandomAccessibleInterval into an ImagePlus.
static <B extends net.imglib2.type.BooleanType<B>> ij.ImagePlus	wrapVirtualStackAndScaleBooleanType(net.imglib2.RandomAccessibleInterval<B> rai, String title)	Similar to wrapVirtualStack(RandomAccessibleInterval, String), but works only for RandomAccessibleIntervals of BitType.

Methods inherited from class java.lang.Object

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

Method Detail

wrap

public static <T extends net.imglib2.type.numeric.NumericType<T>> ij.ImagePlus wrap(net.imglib2.RandomAccessibleInterval<T> img,
                                                                                    String title,
                                                                                    ExecutorService service)

Create a single channel ImagePlus from a RandomAccessibleInterval. The image type of the result (ImagePlus.GRAY8, ImagePlus.GRAY16, ImagePlus.GRAY32, ImagePlus.COLOR_256 or ImagePlus.COLOR_RGB) is inferred from the generic type of the input RandomAccessibleInterval.

Type Parameters:

T - element type in source image

Parameters:

img - the RandomAccessibleInterval to wrap

title - the name to assign to the wrapped ImagePlus

service - an ExecutorService to manage asynchronous tasks

Returns:

an ImagePlus wrapping img named title

wrap

public static <T extends net.imglib2.type.numeric.NumericType<T>> ij.ImagePlus wrap(net.imglib2.RandomAccessibleInterval<T> img,
                                                                                    String title)

Create a single channel ImagePlus from a RandomAccessibleInterval. The image type of the result (ImagePlus.GRAY8, ImagePlus.GRAY16, ImagePlus.GRAY32, ImagePlus.COLOR_256 or ImagePlus.COLOR_RGB) is inferred from the generic type of the input RandomAccessibleInterval.

Type Parameters:

T - element type in source image

Parameters:

img - the RandomAccessibleInterval to wrap

title - the name to assign to the wrapped ImagePlus

Returns:

an ImagePlus wrapping img named title

wrapFloat

public static <T extends net.imglib2.type.numeric.RealType<T>> ij.ImagePlus wrapFloat(net.imglib2.RandomAccessibleInterval<T> img,
                                                                                      String title,
                                                                                      ExecutorService service)

Create a single channel 32-bit float ImagePlus from a RandomAccessibleInterval using a default Converter.

Type Parameters:

T - element type in source image

Parameters:

img - the data to wrap.

title - the title to set on the resulting ImagePlus.

service - an ExecutorService used for processing.

Returns:

an RGB ImagePlus wrapping img

wrapFloat

public static <T extends net.imglib2.type.numeric.RealType<T>> ij.ImagePlus wrapFloat(net.imglib2.RandomAccessibleInterval<T> img,
                                                                                      String title)

Create a single channel 32-bit float ImagePlus from a RandomAccessibleInterval using a default Converter.

Type Parameters:

T - element type in source image

Parameters:

img - the data to wrap.

title - the title to set on the resulting ImagePlus.

Returns:

an RGB ImagePlus wrapping img

wrapFloat

public static <T> ij.ImagePlus wrapFloat(net.imglib2.RandomAccessibleInterval<T> img,
                                         net.imglib2.converter.Converter<T,net.imglib2.type.numeric.real.FloatType> converter,
                                         String title,
                                         ExecutorService service)

Create a single channel 32-bit float ImagePlus from a RandomAccessibleInterval using a custom Converter.

Type Parameters:

T - element type in source image

Parameters:

img - the data to wrap.

converter - a Converter turning RAIToImagePlus into a an FloatType

title - the title to set on the resulting ImagePlus.

service - an ExecutorService used for processing.

Returns:

an RGB ImagePlus wrapping img

wrapFloat

public static <T> ij.ImagePlus wrapFloat(net.imglib2.RandomAccessibleInterval<T> img,
                                         net.imglib2.converter.Converter<T,net.imglib2.type.numeric.real.FloatType> converter,
                                         String title)

Create a single channel 32-bit float ImagePlus from a RandomAccessibleInterval using a custom Converter.

Type Parameters:

T - element type in source image

Parameters:

img - the data to wrap.

converter - a Converter turning RAIToImagePlus into a an FloatType

title - the title to set on the resulting ImagePlus.

Returns:

an RGB ImagePlus wrapping img

wrapRGB

public static ij.ImagePlus wrapRGB(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.ARGBType> img,
                                   String title,
                                   ExecutorService service)

Create a 24bit RGB ImagePlus from a RandomAccessibleInterval with ARGBType elements.

Parameters:

img - the data to wrap.

title - the title to set on the resulting ImagePlus.

service - an ExecutorService used for processing.

Returns:

an RGB ImagePlus wrapping img

wrapRGB

public static ij.ImagePlus wrapRGB(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.ARGBType> img,
                                   String title)

Create a 24bit RGB ImagePlus wrapping a RandomAccessibleInterval with ARGBType elements.

Parameters:

img - the RandomAccessibleInterval to wrap

title - the name assigned to the resulting ImagePlus

Returns:

an RGB ImagePlus wrapping img

convertRGB

public static <T extends net.imglib2.type.numeric.RealType<T>> ij.ImagePlus convertRGB(net.imglib2.RandomAccessibleInterval<T> img,
                                                                                       String title)

Create a 24bit RGB ImagePlus from a RandomAccessibleInterval a using a default Converter.

Type Parameters:

T - element type in source image

Parameters:

img - the RandomAccessibleInterval to wrap

title - the name assigned to the resulting ImagePlus

Returns:

an RGB ImagePlus wrapping img

wrapUnsignedByte

public static <T extends net.imglib2.type.numeric.RealType<T>> ij.ImagePlus wrapUnsignedByte(net.imglib2.RandomAccessibleInterval<T> img,
                                                                                             String title,
                                                                                             ExecutorService service)

Create a single channel 8-bit unsigned integer ImagePlus from a RandomAccessibleInterval using a custom Converter.

Type Parameters:

T - element type in source image

Parameters:

img - the RandomAccessibleInterval to wrap

title - the name assigned to the resulting ImagePlus

service - the ExecutorService used for processing.

Returns:

an ImagePlus wrapping img

wrapUnsignedByte

public static <T extends net.imglib2.type.numeric.RealType<T>> ij.ImagePlus wrapUnsignedByte(net.imglib2.RandomAccessibleInterval<T> img,
                                                                                             String title)

Create a single channel 8-bit unsigned integer ImagePlus from a RandomAccessibleInterval using a custom Converter.

Type Parameters:

T - element type in source image

Parameters:

img - the RandomAccessibleInterval to wrap

title - the name assigned to the resulting ImagePlus

Returns:

an ImagePlus wrapping img

wrapUnsignedByte

public static <T> ij.ImagePlus wrapUnsignedByte(net.imglib2.RandomAccessibleInterval<T> img,
                                                net.imglib2.converter.Converter<T,net.imglib2.type.numeric.integer.UnsignedByteType> converter,
                                                String title,
                                                ExecutorService service)

Create a single channel 8-bit unsigned integer ImagePlus from a RandomAccessibleInterval using a custom Converter.

Type Parameters:

T - element type in source image

Parameters:

img - the RandomAccessibleInterval to wrap

converter - a Converter turning RAIToImagePlus into a an UnsignedByteType

title - the name assigned to the resulting ImagePlus

service - the ExecutorService used for processing.

Returns:

an ImagePlus wrapping img

wrapUnsignedByte

public static <T> ij.ImagePlus wrapUnsignedByte(net.imglib2.RandomAccessibleInterval<T> img,
                                                net.imglib2.converter.Converter<T,net.imglib2.type.numeric.integer.UnsignedByteType> converter,
                                                String title)

Create a single channel 8-bit unsigned integer ImagePlus from a RandomAccessibleInterval using a custom Converter.

Type Parameters:

T - element type in source image

Parameters:

img - the RandomAccessibleInterval to wrap

converter - a Converter turning RAIToImagePlus into a an UnsignedByteType

title - the name assigned to the resulting ImagePlus

Returns:

an ImagePlus wrapping img

wrapUnsignedShort

public static <T extends net.imglib2.type.numeric.RealType<T>> ij.ImagePlus wrapUnsignedShort(net.imglib2.RandomAccessibleInterval<T> img,
                                                                                              String title,
                                                                                              ExecutorService service)

Create a single channel 16-bit unsigned integer ImagePlus from a RandomAccessibleInterval using a default Converter (clamp values to range [0, 65535]).

Type Parameters:

T - element type in source image

Parameters:

img - the RandomAccessibleInterval to wrap

title - the name assigned to the resulting ImagePlus

service - the ExecutorService used for processing.

Returns:

an ImagePlus wrapping img

wrapUnsignedShort

public static <T extends net.imglib2.type.numeric.RealType<T>> ij.ImagePlus wrapUnsignedShort(net.imglib2.RandomAccessibleInterval<T> img,
                                                                                              String title)

Create a single channel 16-bit unsigned integer ImagePlus from a RandomAccessibleInterval using a default Converter (clamp values to range [0, 65535]).

Type Parameters:

T - element type in source image

Parameters:

img - the RandomAccessibleInterval to wrap

title - the name assigned to the resulting ImagePlus

Returns:

an ImagePlus wrapping img

wrapUnsignedShort

public static <T> ij.ImagePlus wrapUnsignedShort(net.imglib2.RandomAccessibleInterval<T> img,
                                                 net.imglib2.converter.Converter<T,net.imglib2.type.numeric.integer.UnsignedShortType> converter,
                                                 String title,
                                                 ExecutorService service)

Create a single channel 16-bit unsigned integer ImagePlus from a RandomAccessibleInterval using a custom Converter.

Type Parameters:

T - element type in source image

Parameters:

img - the RandomAccessibleInterval to wrap

converter - a Converter turning RAIToImagePlus into a an UnsignedShortType

title - the name assigned to the resulting ImagePlus

service - the ExecutorService used for processing.

Returns:

an ImagePlus wrapping img

wrapUnsignedShort

public static <T> ij.ImagePlus wrapUnsignedShort(net.imglib2.RandomAccessibleInterval<T> img,
                                                 net.imglib2.converter.Converter<T,net.imglib2.type.numeric.integer.UnsignedShortType> converter,
                                                 String title)

Create a single channel 16-bit unsigned integer ImagePlus from a RandomAccessibleInterval using a custom Converter.

Type Parameters:

T - element type in source image

Parameters:

img - the RandomAccessibleInterval to wrap

converter - a Converter turning RAIToImagePlus into a an UnsignedShortType

title - the name assigned to the resulting ImagePlus

Returns:

an ImagePlus wrapping img

wrapBoolean

public static <B extends net.imglib2.type.BooleanType<B>> ij.ImagePlus wrapBoolean(net.imglib2.RandomAccessibleInterval<B> img,
                                                                                   String title,
                                                                                   ExecutorService service)

Create a single channel 8-bit unsigned integer ImagePlus from a BooleanType RandomAccessibleInterval using a custom Converter.

Type Parameters:

B - element type in source image

Parameters:

img - the RandomAccessibleInterval to wrap

title - the name assigned to the resulting ImagePlus

service - the ExecutorService used for processing.

Returns:

an ImagePlus wrapping img

See Also:

for wrapping with scaling.

wrapBoolean

public static <B extends net.imglib2.type.BooleanType<B>> ij.ImagePlus wrapBoolean(net.imglib2.RandomAccessibleInterval<B> img,
                                                                                   String title)

Create a single channel 8-bit unsigned integer ImagePlus from a BooleanType RandomAccessibleInterval using a custom Converter.

Type Parameters:

B - element type in source image

Parameters:

img - the RandomAccessibleInterval to wrap

title - the name assigned to the resulting ImagePlus

Returns:

an ImagePlus wrapping img

See Also:

for wrapping with scaling.

wrapAndScaleBoolean

public static <B extends net.imglib2.type.BooleanType<B>> ij.ImagePlus wrapAndScaleBoolean(net.imglib2.RandomAccessibleInterval<B> img,
                                                                                           String title,
                                                                                           ExecutorService service)

Create a single channel 8-bit unsigned integer ImagePlus from a BooleanType RandomAccessibleInterval using a custom Converter.

Note that this method scales the result such that true values in img are mapped to 255 in the resulting ImagePlus.

Type Parameters:

B - element type in source image

Parameters:

img - the RandomAccessibleInterval to wrap

title - the name assigned to the resulting ImagePlus

service - the ExecutorService used for processing.

Returns:

an ImagePlus wrapping img

See Also:

for wrapping without scaling.

wrapAndScaleBoolean

public static <B extends net.imglib2.type.BooleanType<B>> ij.ImagePlus wrapAndScaleBoolean(net.imglib2.RandomAccessibleInterval<B> img,
                                                                                           String title)

Create a single channel 8-bit unsigned integer ImagePlus from a BooleanType RandomAccessibleInterval using a custom Converter.

Note that this method scales the result such that true values in img are mapped to 255 in the resulting ImagePlus.

Type Parameters:

B - element type in source image

Parameters:

img - the RandomAccessibleInterval to wrap

title - the name assigned to the resulting ImagePlus

Returns:

an ImagePlus wrapping img

See Also:

for wrapping without scaling.

wrapVirtualStack

public static ij.ImagePlus wrapVirtualStack(net.imglib2.RandomAccessibleInterval<?> rai,
                                            String title)

Wraps an RandomAccessibleInterval into an ImagePlus. The image can be RealType or ARGBType. The ImagePlus is backed by a special VirtualStack, which copies an plane from the given image, instead of it plane from a file.

Only up to five dimensions are supported. Axes can might be arbitrary. The image title and calibration are derived from the given image.

Parameters:

rai - the RandomAccessibleInterval to convert

title - the title to assign to the output

Returns:

an ImagePlus wrapping rai

See Also:

ArrayImgToImagePlus

wrapVirtualStackAndScaleBooleanType

public static <B extends net.imglib2.type.BooleanType<B>> ij.ImagePlus wrapVirtualStackAndScaleBooleanType(net.imglib2.RandomAccessibleInterval<B> rai,
                                                                                                           String title)

Similar to wrapVirtualStack(RandomAccessibleInterval, String), but works only for RandomAccessibleIntervals of BitType. The pixel values of 0 and 1 are scaled to 0 and 255.

Parameters:

rai - the RandomAccessibleInterval to convert. Must contain bits.

title - the title to assign to the output

Returns:

an ImagePlus wrapping rai

See Also:

ArrayImgToImagePlus