ImgPlus (ImageJ2 Javadocs 0-SNAPSHOT API)

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, 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

All Methods Static Methods Instance Methods Concrete Methods
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 `ColorTable`s.
`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`).
`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.

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.RandomAccessible
getAt, getAt, getAt

Methods inherited from interface java.lang.Iterable
forEach, spliterator

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.imagej.space.CalibratedSpace
averageScale

Methods inherited from interface net.imagej.space.TypedSpace
dimensionIndex

Methods inherited from interface net.imagej.space.AnnotatedSpace
axes, axis, setAxis

Methods inherited from interface net.imglib2.EuclideanSpace
numDimensions

- 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
  - 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>
  - localizingCursor
```
public Cursor<T> localizingCursor()
```
    Specified by:
    
    localizingCursor in interface IterableInterval<T>
    
    Specified by:
    
    localizingCursor in interface IterableRealInterval<T>
  - size
```
public long size()
```
    Specified by:
    
    size in interface IterableRealInterval<T>
  - firstElement
```
public T firstElement()
```
    Specified by:
    
    firstElement in interface IterableRealInterval<T>
  - iterationOrder
```
public Object iterationOrder()
```
    Specified by:
    
    iterationOrder in interface IterableRealInterval<T>
  - iterator
```
public Iterator<T> iterator()
```
    Specified by:
    
    iterator in interface Iterable<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

Class ImgPlus<T>

Constructor Summary

Method Summary

Methods inherited from class net.imagej.interval.AbstractCalibratedRealInterval

Methods inherited from class net.imagej.space.AbstractAnnotatedSpace

Methods inherited from class java.lang.Object

Methods inherited from interface net.imglib2.RandomAccessible

Methods inherited from interface java.lang.Iterable

Methods inherited from interface net.imglib2.Interval

Methods inherited from interface net.imglib2.RealInterval

Methods inherited from interface net.imglib2.Dimensions

Methods inherited from interface net.imagej.space.CalibratedSpace

Methods inherited from interface net.imagej.space.TypedSpace

Methods inherited from interface net.imagej.space.AnnotatedSpace

Methods inherited from interface net.imglib2.EuclideanSpace

Constructor Detail

ImgPlus

ImgPlus

ImgPlus

ImgPlus

ImgPlus

ImgPlus

ImgPlus

ImgPlus

Method Detail

getImg

randomAccess

randomAccess

min

min

min

max

max

max

dimensions

dimension

realMin

realMin

realMin

realMax

realMax

realMax

cursor

localizingCursor

size

firstElement

iterationOrder

iterator

factory

copy

getName

setName

getValidBits

setValidBits

getChannelMinimum

setChannelMinimum

getChannelMaximum

setChannelMaximum

getCompositeChannelCount

setCompositeChannelCount

getColorTable

setColorTable

initializeColorTables

getColorTableCount

getSource

setSource

wrap

wrap

getProperties