net.imagej

Class ImgPlus<T>

java.lang.Object

net.imagej.space.AbstractAnnotatedSpace<A>

net.imagej.space.AbstractTypedSpace<A>

net.imagej.space.AbstractCalibratedSpace<A>

net.imagej.interval.AbstractCalibratedRealInterval<CalibratedAxis>

net.imagej.ImgPlus<T>

All Implemented Interfaces:

Iterable<T>, ImageMetadata, ImgPlusMetadata, CalibratedRealInterval<CalibratedAxis>, TypedRealInterval<CalibratedAxis>, Sourced, AnnotatedSpace<CalibratedAxis>, CalibratedSpace<CalibratedAxis>, TypedSpace<CalibratedAxis>, Dimensions, EuclideanSpace, Img<T>, WrappedImg<T>, Interval, IterableInterval<T>, IterableRealInterval<T>, RandomAccessible<T>, RandomAccessibleInterval<T>, RealInterval, Typed<T>, Named

public class ImgPlus<T>
extends AbstractCalibratedRealInterval<CalibratedAxis>
implements Img<T>, WrappedImg<T>, ImgPlusMetadata

A simple container for storing an Img together with its metadata. Metadata includes name, dimensional axes and calibration information.

NOTE: This class is slated for redesign soon. Use at your own risk! If you need future stability, use ImgLib2 and/or ImageJ 1.x classes.

Author:

Curtis Rueden

Constructor Summary

Constructors

Constructor and Description
ImgPlus(Img<T> img)
ImgPlus(Img<T> img, ImgPlusMetadata metadata)
ImgPlus(Img<T> img, ImgPlusMetadata metadata, boolean axesOnly) As ImgPlus(Img, ImgPlusMetadata) but with a flag to determine if metadata beyond axis information is copied.
ImgPlus(Img<T> img, String name)
ImgPlus(Img<T> img, String name, AxisType[] axes)
ImgPlus(Img<T> img, String name, AxisType[] axisTypes, double[] cal)
ImgPlus(Img<T> img, String name, AxisType[] axisTypes, double[] cal, String[] units)
ImgPlus(Img<T> img, String name, CalibratedAxis... axes)

Method Summary

Modifier and Type	Method and Description
ImgPlus<T>	copy()
Cursor<T>	cursor()
long	dimension(int d)
void	dimensions(long[] dimensions)
ImgFactory<T>	factory()
T	firstElement()
double	getChannelMaximum(int c) Gets the maximum actual pixel value for the given channel.
double	getChannelMinimum(int c) Gets the minimum actual pixel value for the given channel.
ColorTable	getColorTable(int no) Gets the color table at the given position.
int	getColorTableCount() Gets the number of available ColorTables.
int	getCompositeChannelCount() Gets the number of channels intended to be displayed together.
Img<T>	getImg() Gets the backing Img of this ImgPlus.
String	getName()
Map<String,Object>	getProperties() Gets a table of key/value pairs associated with the image.
String	getSource() Gets the source String
int	getValidBits() Gets the number of valid bits (if applicable to this Img).
static <T> ImgFactory<T>	imgFactory(RandomAccessibleInterval<T> rai) Gets an ImgFactory suitable for creating Imgs of the given RandomAccessibleInterval's container, type, and dimensions.
void	initializeColorTables(int count) Sets the number of available color tables to the given value.
Object	iterationOrder()
Iterator<T>	iterator()
Cursor<T>	localizingCursor()
long	max(int d)
void	max(long[] max)
void	max(Positionable max)
long	min(int d)
void	min(long[] min)
void	min(Positionable min)
RandomAccess<T>	randomAccess()
RandomAccess<T>	randomAccess(Interval interval)
void	realMax(double[] max)
double	realMax(int d)
void	realMax(RealPositionable max)
void	realMin(double[] min)
double	realMin(int d)
void	realMin(RealPositionable min)
void	setChannelMaximum(int c, double max) Sets the maximum actual pixel value for the given channel.
void	setChannelMinimum(int c, double min) Sets the minimum actual pixel value for the given channel.
void	setColorTable(ColorTable cT, int no) Sets the color table at the given position.
void	setCompositeChannelCount(int value) Sets the number of channels intended to be displayed together.
void	setName(String name)
void	setSource(String source) Sets the source String
void	setValidBits(int bits) Sets the number of valid bits.
long	size()
static <T> ImgPlus<T>	wrap(Img<T> img) Ensures the given Img is an ImgPlus, wrapping if necessary.
static <T> ImgPlus<T>	wrap(Img<T> img, ImgPlusMetadata metadata) Ensures the given Img is an ImgPlus, wrapping if necessary.
static <T extends Type<T>> ImgPlus<T>	wrapRAI(RandomAccessibleInterval<T> rai) Wraps a RandomAccessibleInterval into an ImgPlus.
static <T extends Type<T>> Img<T>	wrapToImg(RandomAccessibleInterval<T> rai) Wraps a RandomAccessibleInterval into an Img.

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

Constructor Detail

ImgPlus

public ImgPlus(Img<T> img)

ImgPlus

public ImgPlus(Img<T> img,
               String name)

ImgPlus

public ImgPlus(Img<T> img,
               String name,
               AxisType[] axes)

ImgPlus

public ImgPlus(Img<T> img,
               ImgPlusMetadata metadata)

ImgPlus

public ImgPlus(Img<T> img,
               ImgPlusMetadata metadata,
               boolean axesOnly)

As ImgPlus(Img, ImgPlusMetadata) but with a flag to determine if metadata beyond axis information is copied.

Parameters:

axesOnly - - if true, only axis metadata is copied.

ImgPlus

public ImgPlus(Img<T> img,
               String name,
               AxisType[] axisTypes,
               double[] cal)

ImgPlus

public ImgPlus(Img<T> img,
               String name,
               AxisType[] axisTypes,
               double[] cal,
               String[] units)

ImgPlus

public ImgPlus(Img<T> img,
               String name,
               CalibratedAxis... axes)

Method Detail

wrapRAI

public static <T extends Type<T>> ImgPlus<T> wrapRAI(RandomAccessibleInterval<T> rai)

Wraps a RandomAccessibleInterval into an ImgPlus.

wrapToImg

public static <T extends Type<T>> Img<T> wrapToImg(RandomAccessibleInterval<T> rai)

Wraps a RandomAccessibleInterval into an Img.

imgFactory

public static <T> ImgFactory<T> imgFactory(RandomAccessibleInterval<T> rai)

Gets an ImgFactory suitable for creating Imgs of the given RandomAccessibleInterval's container, type, and dimensions.

getImg

public Img<T> getImg()

Gets the backing Img of this ImgPlus.

Note that most of the time, you do not need to call this method. Rather, you can use the ImgPlus directly because it implements all of the same interfaces. However, there are legitimate cases where you may need access to the backing container (e.g., for performance, to cast to the appropriate Img implementation such as ArrayImg).

Specified by:

getImg in interface WrappedImg<T>

randomAccess

public RandomAccess<T> randomAccess()

Specified by:

randomAccess in interface RandomAccessible<T>

randomAccess

public RandomAccess<T> randomAccess(Interval interval)

Specified by:

randomAccess in interface RandomAccessible<T>

min

public long min(int d)

Specified by:

min in interface Interval

min

public void min(long[] min)

Specified by:

min in interface Interval

min

public void min(Positionable min)

Specified by:

min in interface Interval

max

public long max(int d)

Specified by:

max in interface Interval

max

public void max(long[] max)

Specified by:

max in interface Interval

max

public void max(Positionable max)

Specified by:

max in interface Interval

dimensions

public void dimensions(long[] dimensions)

Specified by:

dimensions in interface Dimensions

dimension

public long dimension(int d)

Specified by:

dimension in interface Dimensions

Specified by:

dimension in interface Interval

realMin

public double realMin(int d)

Specified by:

realMin in interface Interval

Specified by:

realMin in interface RealInterval

Overrides:

realMin in class AbstractCalibratedRealInterval<CalibratedAxis>

realMin

public void realMin(double[] min)

Specified by:

realMin in interface RealInterval

Overrides:

realMin in class AbstractCalibratedRealInterval<CalibratedAxis>

realMin

public void realMin(RealPositionable min)

Specified by:

realMin in interface RealInterval

Overrides:

realMin in class AbstractCalibratedRealInterval<CalibratedAxis>

realMax

public double realMax(int d)

Specified by:

realMax in interface Interval

Specified by:

realMax in interface RealInterval

Overrides:

realMax in class AbstractCalibratedRealInterval<CalibratedAxis>

realMax

public void realMax(double[] max)

Specified by:

realMax in interface RealInterval

Overrides:

realMax in class AbstractCalibratedRealInterval<CalibratedAxis>

realMax

public void realMax(RealPositionable max)

Specified by:

realMax in interface RealInterval

Overrides:

realMax in class AbstractCalibratedRealInterval<CalibratedAxis>

cursor

public Cursor<T> cursor()

Specified by:

cursor in interface IterableInterval<T>

Specified by:

cursor in interface IterableRealInterval<T>

Specified by:

cursor in interface RandomAccessibleInterval<T>

localizingCursor

public Cursor<T> localizingCursor()

Specified by:

localizingCursor in interface IterableInterval<T>

Specified by:

localizingCursor in interface IterableRealInterval<T>

Specified by:

localizingCursor in interface RandomAccessibleInterval<T>

size

public long size()

Specified by:

size in interface IterableRealInterval<T>

Specified by:

size in interface RandomAccessibleInterval<T>

firstElement

public T firstElement()

Specified by:

firstElement in interface IterableRealInterval<T>

iterationOrder

public Object iterationOrder()

Specified by:

iterationOrder in interface IterableRealInterval<T>

Specified by:

iterationOrder in interface RandomAccessibleInterval<T>

iterator

public Iterator<T> iterator()

Specified by:

iterator in interface Iterable<T>

Specified by:

iterator in interface IterableRealInterval<T>

factory

public ImgFactory<T> factory()

Specified by:

factory in interface Img<T>

copy

public ImgPlus<T> copy()

Specified by:

copy in interface Img<T>

getName

public String getName()

Specified by:

getName in interface Named

setName

public void setName(String name)

Specified by:

setName in interface Named

getValidBits

public int getValidBits()

Description copied from interface: ImageMetadata

Gets the number of valid bits (if applicable to this Img).

Specified by:

getValidBits in interface ImageMetadata

setValidBits

public void setValidBits(int bits)

Description copied from interface: ImageMetadata

Sets the number of valid bits.

Specified by:

setValidBits in interface ImageMetadata

getChannelMinimum

public double getChannelMinimum(int c)

Description copied from interface: ImageMetadata

Gets the minimum actual pixel value for the given channel.

Specified by:

getChannelMinimum in interface ImageMetadata

setChannelMinimum

public void setChannelMinimum(int c,
                              double min)

Description copied from interface: ImageMetadata

Sets the minimum actual pixel value for the given channel.

Specified by:

setChannelMinimum in interface ImageMetadata

getChannelMaximum

public double getChannelMaximum(int c)

Description copied from interface: ImageMetadata

Gets the maximum actual pixel value for the given channel.

Specified by:

getChannelMaximum in interface ImageMetadata

setChannelMaximum

public void setChannelMaximum(int c,
                              double max)

Description copied from interface: ImageMetadata

Sets the maximum actual pixel value for the given channel.

Specified by:

setChannelMaximum in interface ImageMetadata

getCompositeChannelCount

public int getCompositeChannelCount()

Description copied from interface: ImageMetadata

Gets the number of channels intended to be displayed together.

Specified by:

getCompositeChannelCount in interface ImageMetadata

setCompositeChannelCount

public void setCompositeChannelCount(int value)

Description copied from interface: ImageMetadata

Sets the number of channels intended to be displayed together.

Specified by:

setCompositeChannelCount in interface ImageMetadata

getColorTable

public ColorTable getColorTable(int no)

Description copied from interface: ImageMetadata

Gets the color table at the given position.

Specified by:

getColorTable in interface ImageMetadata

setColorTable

public void setColorTable(ColorTable cT,
                          int no)

Description copied from interface: ImageMetadata

Sets the color table at the given position.

Specified by:

setColorTable in interface ImageMetadata

Parameters:

cT - The color table to store.

no - The position of the color table, typically (but not necessarily) a 1D dimensional planar index rasterized from an N-dimensional planar position array.

initializeColorTables

public void initializeColorTables(int count)

Description copied from interface: ImageMetadata

Sets the number of available color tables to the given value.

Specified by:

initializeColorTables in interface ImageMetadata

getColorTableCount

public int getColorTableCount()

Description copied from interface: ImageMetadata

Gets the number of available ColorTables. For Imgs, this number typically matches the total number of planes.

Specified by:

getColorTableCount in interface ImageMetadata

getSource

public String getSource()

Description copied from interface: Sourced

Gets the source String

Specified by:

getSource in interface Sourced

setSource

public void setSource(String source)

Description copied from interface: Sourced

Sets the source String

Specified by:

setSource in interface Sourced

wrap

public static <T> ImgPlus<T> wrap(Img<T> img)

Ensures the given Img is an ImgPlus, wrapping if necessary.

wrap

public static <T> ImgPlus<T> wrap(Img<T> img,
                                  ImgPlusMetadata metadata)

Ensures the given Img is an ImgPlus, wrapping if necessary.

getProperties

public Map<String,Object> getProperties()

Description copied from interface: ImageMetadata

Gets a table of key/value pairs associated with the image.

Specified by:

getProperties in interface ImageMetadata