io.scif.img

Class SCIFIOImgPlus<T>

java.lang.Object

net.imagej.space.AbstractAnnotatedSpace<A>

net.imagej.space.AbstractTypedSpace<A>

net.imagej.space.AbstractCalibratedSpace<A>

net.imagej.interval.AbstractCalibratedRealInterval<net.imagej.axis.CalibratedAxis>

net.imagej.ImgPlus<T>

io.scif.img.SCIFIOImgPlus<T>

All Implemented Interfaces:

Iterable<T>, net.imagej.ImageMetadata, net.imagej.ImgPlusMetadata, net.imagej.interval.CalibratedRealInterval<net.imagej.axis.CalibratedAxis>, net.imagej.interval.TypedRealInterval<net.imagej.axis.CalibratedAxis>, net.imagej.Sourced, net.imagej.space.AnnotatedSpace<net.imagej.axis.CalibratedAxis>, net.imagej.space.CalibratedSpace<net.imagej.axis.CalibratedAxis>, net.imagej.space.TypedSpace<net.imagej.axis.CalibratedAxis>, net.imglib2.Dimensions, net.imglib2.EuclideanSpace, net.imglib2.img.Img<T>, net.imglib2.img.WrappedImg<T>, net.imglib2.Interval, net.imglib2.IterableInterval<T>, net.imglib2.IterableRealInterval<T>, net.imglib2.RandomAccessible<T>, net.imglib2.RandomAccessibleInterval<T>, net.imglib2.RealInterval, net.imglib2.Typed<T>, org.scijava.Disposable, org.scijava.Named

public class SCIFIOImgPlus<T>
extends net.imagej.ImgPlus<T>
implements org.scijava.Disposable

SCIFIO extension of ImgPlus that adds getColorTable(int, int) API for specifying both the plane and image index.

Also provides direct access to the Metadata object associated with the underlying dataset.

Author:

Mark Hiner

Field Summary

Fields

Modifier and Type	Field and Description
static String	GLOBAL_META
static String	IMAGE_META

Constructor Summary

Constructors

Constructor and Description
SCIFIOImgPlus(net.imglib2.img.Img<T> img)
SCIFIOImgPlus(net.imglib2.img.Img<T> img, net.imagej.ImgPlusMetadata metadata)
SCIFIOImgPlus(net.imglib2.img.Img<T> img, String name)
SCIFIOImgPlus(net.imglib2.img.Img<T> img, String name, net.imagej.axis.AxisType[] axes)
SCIFIOImgPlus(net.imglib2.img.Img<T> img, String name, net.imagej.axis.AxisType[] axes, double[] cal)
SCIFIOImgPlus(net.imagej.ImgPlus<T> imgPlus)

Method Summary

Modifier and Type	Method and Description
SCIFIOImgPlus<T>	copy()
void	dispose()
net.imglib2.display.ColorTable	getColorTable(int planeIndex)
net.imglib2.display.ColorTable	getColorTable(int imageIndex, int planeIndex)
ImageMetadata	getImageMetadata()
Metadata	getMetadata()
void	setImageMetadata(ImageMetadata imageMeta) Sets the ImageMetadata object for this ImgPlus.
void	setMetadata(Metadata meta) Sets the Metadata object for this ImgPlus.

Methods inherited from class net.imagej.ImgPlus

cursor, dimension, dimensions, factory, firstElement, getChannelMaximum, getChannelMinimum, getColorTableCount, getCompositeChannelCount, getImg, getName, getProperties, getSource, getValidBits, imgFactory, initializeColorTables, iterationOrder, iterator, localizingCursor, max, max, max, min, min, min, randomAccess, randomAccess, realMax, realMax, realMax, realMin, realMin, realMin, setChannelMaximum, setChannelMinimum, setColorTable, setCompositeChannelCount, setName, setSource, setValidBits, size, wrap, wrap, wrapRAI, wrapToImg

Methods inherited from class net.imagej.interval.AbstractCalibratedRealInterval

averageScale

Methods inherited from class net.imagej.space.AbstractAnnotatedSpace

axes, axis, numDimensions, setAxis

Methods inherited from class java.lang.Object

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

Methods inherited from interface net.imglib2.RandomAccessibleInterval

view

Methods inherited from interface net.imglib2.RandomAccessible

getAt, getAt, getAt

Methods inherited from interface net.imglib2.IterableInterval

localizingSpliterator, spliterator

Methods inherited from interface net.imglib2.IterableRealInterval

getType, parallelStream, stream

Methods inherited from interface java.lang.Iterable

forEach

Methods inherited from interface net.imglib2.Interval

maxAsLongArray, maxAsPoint, minAsLongArray, minAsPoint

Methods inherited from interface net.imglib2.RealInterval

maxAsDoubleArray, maxAsRealPoint, minAsDoubleArray, minAsRealPoint

Methods inherited from interface net.imglib2.Dimensions

allPositive, allPositive, dimensions, dimensionsAsLongArray, dimensionsAsPoint, verify, verify, verifyAllPositive, verifyAllPositive

Methods inherited from interface net.imglib2.EuclideanSpace

numDimensions

Methods inherited from interface net.imagej.space.CalibratedSpace

averageScale

Methods inherited from interface net.imagej.space.TypedSpace

dimensionIndex

Methods inherited from interface net.imagej.space.AnnotatedSpace

axes, axis, setAxis

Field Detail

GLOBAL_META

public static final String GLOBAL_META

See Also:

Constant Field Values

IMAGE_META

public static final String IMAGE_META

See Also:

Constant Field Values

Constructor Detail

SCIFIOImgPlus

public SCIFIOImgPlus(net.imglib2.img.Img<T> img)

SCIFIOImgPlus

public SCIFIOImgPlus(net.imglib2.img.Img<T> img,
                     String name)

SCIFIOImgPlus

public SCIFIOImgPlus(net.imglib2.img.Img<T> img,
                     String name,
                     net.imagej.axis.AxisType[] axes)

SCIFIOImgPlus

public SCIFIOImgPlus(net.imglib2.img.Img<T> img,
                     net.imagej.ImgPlusMetadata metadata)

SCIFIOImgPlus

public SCIFIOImgPlus(net.imglib2.img.Img<T> img,
                     String name,
                     net.imagej.axis.AxisType[] axes,
                     double[] cal)

SCIFIOImgPlus

public SCIFIOImgPlus(net.imagej.ImgPlus<T> imgPlus)

Method Detail

getMetadata

public Metadata getMetadata()

Returns:

The SCIFIO Metadata object attached to this ImgPlus.

setMetadata

public void setMetadata(Metadata meta)

Sets the Metadata object for this ImgPlus.

getImageMetadata

public ImageMetadata getImageMetadata()

Returns:

The SCIFIO ImageMetadata object attached to this ImgPlus.

setImageMetadata

public void setImageMetadata(ImageMetadata imageMeta)

Sets the ImageMetadata object for this ImgPlus.

getColorTable

public net.imglib2.display.ColorTable getColorTable(int planeIndex)

Specified by:

getColorTable in interface net.imagej.ImageMetadata

Overrides:

getColorTable in class net.imagej.ImgPlus<T>

getColorTable

public net.imglib2.display.ColorTable getColorTable(int imageIndex,
                                                    int planeIndex)

Parameters:

imageIndex - - Image index to look up the color table

planeIndex - - Plane index of the desired color table

Returns:

The ColorTable of the underlying dataset at the specified indices.

copy

public SCIFIOImgPlus<T> copy()

Specified by:

copy in interface net.imglib2.img.Img<T>

Overrides:

copy in class net.imagej.ImgPlus<T>

dispose

public void dispose()

Specified by:

dispose in interface org.scijava.Disposable