Image (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- mpicbg.imglib.image.Image<T>

All Implemented Interfaces:

Iterable<T>, Collection<T>, ImageProperties, Dimensionality

Direct Known Subclasses:

AbstractAffine3D, AbstractNormalize, BandpassFilter, Dither, Downsample, FFT, Gauss, HoughLineTransform, InverseFFT, Labeling, MedianFilter, Morph, NormalizeSum, Resample, StructuringElement
```
public class Image<T extends Type<T>>
extends Object
implements ImageProperties, Dimensionality, Collection<T>
```
TODO

Author:

Stephan Preibisch, Stephan Saalfeld

Field Summary

Fields
Modifier and Type Field and Description

protected float[] calibration

protected ArrayList<Cursor<T>> cursors

protected Display<T> display

protected String name

Fields
Modifier and Type	Field and Description
`protected float[]`	`calibration`
`protected ArrayList<Cursor<T>>`	`cursors`
`protected Display<T>`	`display`
`protected String`	`name`

Constructor Summary

Constructors
Modifier	Constructor and Description
	`Image(Container<T> container, T type)`
	`Image(Container<T> container, T type, String name)`
`protected`	`Image(ImageFactory<T> imageFactory, int[] dim, String name)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`add(T e)`
`boolean`	`addAll(Collection<? extends T> c)`
`protected void`	`addCursor(Cursor<T> c)` Adds a `Cursor` to the `ArrayList` of instantiated `Cursor`s.
`void`	`clear()`
`Image<T>`	`clone()` Clones this `Image`, i.e.
`void`	`close()` Closes the `Image` by closing all `Cursor`s and the `Container`
`void`	`closeAllCursors()` Closes all `Cursor`s operating on this `Image`.
`boolean`	`contains(Object o)`
`boolean`	`containsAll(Collection<?> c)`
`Cursor<T>`	`createCursor()` Return a `Cursor` that will traverse the image's pixel data in a memory-optimized fashion.
`Interpolator<T>`	`createInterpolator(InterpolatorFactory<T> factory)` Creates and `Interpolator` on this `Image` given a certain `InterpolatorFactory`.
`LocalizableByDimCursor<T>`	`createLocalizableByDimCursor()` Creates a `LocalizableByDimCursor` which is able to move freely within the `Image`.
`LocalizableByDimCursor<T>`	`createLocalizableByDimCursor(OutOfBoundsStrategyFactory<T> factory)` Creates a `LocalizableByDimCursor` which is able to move freely within and out of `Image` bounds.
`LocalizableCursor<T>`	`createLocalizableCursor()` Return a `LocalizableCursor` that will traverse the image's pixel data in a memory-optimized fashion and keeps track of its position
`LocalizablePlaneCursor<T>`	`createLocalizablePlaneCursor()` Creates a `LocalizablePlaneCursor` which is optimized to iterate arbitrary 2-dimensional planes within an `Image`.
`Image<T>`	`createNewImage()` Creates a new `Image` with the same dimensions, `ContainerFactory` and `Type` as this one, the name is given automatically.
`Image<T>`	`createNewImage(int[] dimensions)` Creates a new `Image` with the same `ContainerFactory` and `Type` as this one, the name is given automatically.
`Image<T>`	`createNewImage(int[] dimensions, String name)` Creates a new `Image` with the same `ContainerFactory` and `Type` as this one.
`Image<T>`	`createNewImage(String name)` Creates a new `Image` with the same dimensions, `ContainerFactory` and `Type` as this one as this one.
`int[]`	`createPositionArray()` Creates an int array of the same dimensionality as this `Image` which can be used for addressing `Cursor`s.
`T`	`createType()` Creates a `Type` that the `Image` is typed with.
`static long`	`createUniqueId()`
`ArrayList<Cursor<T>>`	`getActiveCursors()` Return all active `Cursor`s currently instantiated for this `Image`.
`float[]`	`getCalibration()`
`float`	`getCalibration(int dim)`
`Container<T>`	`getContainer()` Returns the `Container` that is used for storing the image data.
`ContainerFactory`	`getContainerFactory()` Returns the `ContainerFactory` of this `Image`.
`ArrayList<Cursor<T>>`	`getCursors()` Return all `Cursor`s currently instantiated for this `Image` in a new `ArrayList`.
`void`	`getCursors(Collection<Cursor<T>> collection)` Put all `Cursor`s currently instantiated into a `Collection`.
`int`	`getDimension(int dim)`
`int[]`	`getDimensions()`
`void`	`getDimensions(int[] dimensions)`
`Display<T>`	`getDisplay()` Return the current `Display` of the `Image`
`ImageFactory<T>`	`getImageFactory()` Returns the `ImageFactory` of this `Image`.
`String`	`getName()`
`int`	`getNumActiveCursors()` Returns the number of active `Cursor`s instantiated on this `Image`.
`int`	`getNumCursors()` Returns the number of `Cursor`s instantiated on this `Image`.
`int`	`getNumDimensions()`
`int`	`getNumPixels()`
`boolean`	`isEmpty()`
`Iterator<T>`	`iterator()`
`boolean`	`remove(Object o)`
`boolean`	`removeAll(Collection<?> c)`
`void`	`removeAllCursors()` Remove all cursors
`protected void`	`removeCursor(Cursor<T> c)` Remove a `Cursor` from the `ArrayList` of instantiated `Cursor`s.
`boolean`	`retainAll(Collection<?> c)`
`void`	`setCalibration(float[] calibration)`
`void`	`setCalibration(float calibration, int dim)`
`void`	`setDefaultDisplay()` Sets the default `Display` of this `Image` as defined by the `Type`
`void`	`setDisplay(Display<T> display)` Sets the `Display` associated with this `Image`.
`void`	`setName(String name)`
`int`	`size()`
`T[]`	`toArray()`
`<E> E[]`	`toArray(E[] a)`
`String`	`toString()`

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.Collection
equals, hashCode, parallelStream, removeIf, spliterator, stream

Methods inherited from interface java.lang.Iterable
forEach

- Field Detail
  - cursors
```
protected final ArrayList<Cursor<T extends Type<T>>> cursors
```
  - name
```
protected String name
```
  - calibration
```
protected final float[] calibration
```
  - display
```
protected Display<T extends Type<T>> display
```
- Constructor Detail
  - Image
```
public Image(Container<T> container,
             T type)
```
  - Image
```
public Image(Container<T> container,
             T type,
             String name)
```
  - Image
```
protected Image(ImageFactory<T> imageFactory,
                int[] dim,
                String name)
```
- Method Detail
  - createNewImage
```
public Image<T> createNewImage(int[] dimensions,
                               String name)
```
    Creates a new Image with the same ContainerFactory and Type as this one.
    
    Parameters:
    
    dimensions - - the dimensions of the Image
    
    Returns:
    
    - a new empty Image
  - createNewImage
```
public Image<T> createNewImage(int[] dimensions)
```
    Creates a new Image with the same ContainerFactory and Type as this one, the name is given automatically.
    
    Parameters:
    
    dimensions - - the dimensions of the Image
    
    Returns:
    
    - a new empty Image
  - createNewImage
```
public Image<T> createNewImage(String name)
```
    Creates a new Image with the same dimensions, ContainerFactory and Type as this one as this one.
    
    Returns:
    
    - a new empty Image
  - createNewImage
```
public Image<T> createNewImage()
```
    Creates a new Image with the same dimensions, ContainerFactory and Type as this one, the name is given automatically.
    
    Returns:
    
    - a new empty Image
  - getCalibration
```
public float[] getCalibration()
```
  - getCalibration
```
public float getCalibration(int dim)
```
  - setCalibration
```
public void setCalibration(float[] calibration)
```
  - setCalibration
```
public void setCalibration(float calibration,
                           int dim)
```
  - getContainer
```
public Container<T> getContainer()
```
    Returns the Container that is used for storing the image data.
    
    Returns:
    
    Container - the typed Container
  - createType
```
public T createType()
```
    Creates a Type that the Image is typed with.
    
    Returns:
    
    T - an instance of Type for computing
  - createCursor
```
public Cursor<T> createCursor()
```
    Return a Cursor that will traverse the image's pixel data in a memory-optimized fashion.
    
    Returns:
    
    Cursor - the typed Cursor
  - createLocalizableCursor
```
public LocalizableCursor<T> createLocalizableCursor()
```
    Return a LocalizableCursor that will traverse the image's pixel data in a memory-optimized fashion and keeps track of its position
    
    Returns:
    
    LocalizableCursor - the typed LocalizableCursor
  - createLocalizablePlaneCursor
```
public LocalizablePlaneCursor<T> createLocalizablePlaneCursor()
```
    Creates a LocalizablePlaneCursor which is optimized to iterate arbitrary 2-dimensional planes within an Image. This is very important for the Display.
    
    Returns:
    
    - LocalizablePlaneCursor
  - createLocalizableByDimCursor
```
public LocalizableByDimCursor<T> createLocalizableByDimCursor()
```
    Creates a LocalizableByDimCursor which is able to move freely within the Image. When exiting the Image this LocalizableByDimCursor will fail!! Therefore it is faster.
    
    Returns:
    
    - a LocalizableByDimCursor that cannot leave the Image
  - createLocalizableByDimCursor
```
public LocalizableByDimCursor<T> createLocalizableByDimCursor(OutOfBoundsStrategyFactory<T> factory)
```
    Creates a LocalizableByDimCursor which is able to move freely within and out of Image bounds. given a OutOfBoundsStrategyFactory which defines the behaviour out of Image bounds.
    
    Parameters:
    
    factory - - the OutOfBoundsStrategyFactory
    
    Returns:
    
    - a LocalizableByDimCursor that can leave the Image
  - createInterpolator
```
public Interpolator<T> createInterpolator(InterpolatorFactory<T> factory)
```
    Creates and Interpolator on this Image given a certain InterpolatorFactory.
    
    Parameters:
    
    factory - - the InterpolatorFactory to use
    
    Returns:
    
    Interpolator
  - setDefaultDisplay
```
public void setDefaultDisplay()
```
    Sets the default Display of this Image as defined by the Type
  - getDisplay
```
public Display<T> getDisplay()
```
    Return the current Display of the Image
    
    Returns:
    
    - the Display
  - setDisplay
```
public void setDisplay(Display<T> display)
```
    Sets the Display associated with this Image.
    
    Parameters:
    
    display - - the Display
  - createUniqueId
```
public static final long createUniqueId()
```
  - close
```
public void close()
```
    Closes the Image by closing all Cursors and the Container
  - createPositionArray
```
public int[] createPositionArray()
```
    Creates an int array of the same dimensionality as this Image which can be used for addressing Cursors.
    
    Returns:
    
    - empty int[] TODO Do we really need this? I just replaces int[] t = new int[ img1.getNumDimensions() ]; by int[] t = img1.getPositionArray() Saalfeld: remove! ;) Preibisch: keep (esoteric reasons)
  - getNumDimensions
```
public int getNumDimensions()
```
    Specified by:
    
    getNumDimensions in interface ImageProperties
    
    Specified by:
    
    getNumDimensions in interface Dimensionality
  - getDimensions
```
public int[] getDimensions()
```
    Specified by:
    
    getDimensions in interface ImageProperties
    
    Specified by:
    
    getDimensions in interface Dimensionality
  - getNumPixels
```
public int getNumPixels()
```
    Specified by:
    
    getNumPixels in interface ImageProperties
  - getName
```
public String getName()
```
    Specified by:
    
    getName in interface ImageProperties
  - setName
```
public void setName(String name)
```
    Specified by:
    
    setName in interface ImageProperties
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - getDimensions
```
public void getDimensions(int[] dimensions)
```
    Specified by:
    
    getDimensions in interface ImageProperties
    
    Specified by:
    
    getDimensions in interface Dimensionality
  - getDimension
```
public int getDimension(int dim)
```
    Specified by:
    
    getDimension in interface ImageProperties
  - clone
```
public Image<T> clone()
```
    Clones this Image, i.e. creates this Image containing the same content. No Cursors will be instantiated and the name will be given automatically.
    
    Overrides:
    
    clone in class Object
  - getContainerFactory
```
public ContainerFactory getContainerFactory()
```
    Returns the ContainerFactory of this Image.
    
    Returns:
    
    - ContainerFactory
  - getImageFactory
```
public ImageFactory<T> getImageFactory()
```
    Returns the ImageFactory of this Image.
    
    Returns:
    
    - ImageFactory
  - removeAllCursors
```
public void removeAllCursors()
```
    Remove all cursors
  - closeAllCursors
```
public void closeAllCursors()
```
    Closes all Cursors operating on this Image.
  - getCursors
```
public void getCursors(Collection<Cursor<T>> collection)
```
    Put all Cursors currently instantiated into a Collection.
  - getCursors
```
public ArrayList<Cursor<T>> getCursors()
```
    Return all Cursors currently instantiated for this Image in a new ArrayList.
    
    Returns:
    
    - ArrayList containing the Cursors
  - getActiveCursors
```
public ArrayList<Cursor<T>> getActiveCursors()
```
    Return all active Cursors currently instantiated for this Image.
    
    Returns:
    
    - ArrayList containing the Cursors
  - addCursor
```
protected void addCursor(Cursor<T> c)
```
    Adds a Cursor to the ArrayList of instantiated Cursors.
    
    Parameters:
    
    c - - new Cursor
  - removeCursor
```
protected void removeCursor(Cursor<T> c)
```
    Remove a Cursor from the ArrayList of instantiated Cursors.
    
    Parameters:
    
    c - - Cursor to be removed
  - getNumCursors
```
public int getNumCursors()
```
    Returns the number of Cursors instantiated on this Image.
    
    Returns:
    
    - the number of Cursors
  - getNumActiveCursors
```
public int getNumActiveCursors()
```
    Returns the number of active Cursors instantiated on this Image.
    
    Returns:
    
    - the number of active Cursors
  - add
```
public boolean add(T e)
```
    Specified by:
    
    add in interface Collection<T extends Type<T>>
  - addAll
```
public boolean addAll(Collection<? extends T> c)
```
    Specified by:
    
    addAll in interface Collection<T extends Type<T>>
  - clear
```
public void clear()
```
    Specified by:
    
    clear in interface Collection<T extends Type<T>>
  - contains
```
public boolean contains(Object o)
```
    Specified by:
    
    contains in interface Collection<T extends Type<T>>
  - containsAll
```
public boolean containsAll(Collection<?> c)
```
    Specified by:
    
    containsAll in interface Collection<T extends Type<T>>
  - isEmpty
```
public boolean isEmpty()
```
    Specified by:
    
    isEmpty in interface Collection<T extends Type<T>>
  - iterator
```
public Iterator<T> iterator()
```
    Specified by:
    
    iterator in interface Iterable<T extends Type<T>>
    
    Specified by:
    
    iterator in interface Collection<T extends Type<T>>
  - remove
```
public boolean remove(Object o)
```
    Specified by:
    
    remove in interface Collection<T extends Type<T>>
  - removeAll
```
public boolean removeAll(Collection<?> c)
```
    Specified by:
    
    removeAll in interface Collection<T extends Type<T>>
  - retainAll
```
public boolean retainAll(Collection<?> c)
```
    Specified by:
    
    retainAll in interface Collection<T extends Type<T>>
  - size
```
public int size()
```
    Specified by:
    
    size in interface Collection<T extends Type<T>>
  - toArray
```
public T[] toArray()
```
    Specified by:
    
    toArray in interface Collection<T extends Type<T>>
  - toArray
```
public <E> E[] toArray(E[] a)
```
    Specified by:
    
    toArray in interface Collection<T extends Type<T>>

Class Image<T extends Type<T>>

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface java.util.Collection

Methods inherited from interface java.lang.Iterable

Field Detail

cursors

name

calibration

display

Constructor Detail

Image

Image

Image

Method Detail

createNewImage

createNewImage

createNewImage

createNewImage

getCalibration

getCalibration

setCalibration

setCalibration

getContainer

createType

createCursor

createLocalizableCursor

createLocalizablePlaneCursor

createLocalizableByDimCursor

createLocalizableByDimCursor

createInterpolator

setDefaultDisplay

getDisplay

setDisplay

createUniqueId

close

createPositionArray

getNumDimensions

getDimensions

getNumPixels

getName

setName

toString

getDimensions

getDimension

clone

getContainerFactory

getImageFactory

removeAllCursors

closeAllCursors

getCursors

getCursors

getActiveCursors

addCursor

removeCursor

getNumCursors

getNumActiveCursors

add

addAll

clear

contains

containsAll

isEmpty

iterator

remove

removeAll

retainAll

size

toArray

toArray