Package net.imglib2.img.sparse

Class NtreeImg<T extends NativeType<T>,A extends NtreeAccess<?,A>>

java.lang.Object

net.imglib2.img.AbstractImg<T>

net.imglib2.img.AbstractNativeImg<T,A>

net.imglib2.img.sparse.NtreeImg<T,A>

All Implemented Interfaces:

java.io.Serializable, java.lang.Iterable<T>, Dimensions, EuclideanSpace, Img<T>, NativeImg<T,A>, Interval, IterableInterval<T>, IterableRealInterval<T>, RandomAccessible<T>, RandomAccessibleInterval<T>, RealInterval, Typed<T>

public final class NtreeImg<T extends NativeType<T>,A extends NtreeAccess<?,A>>
extends AbstractNativeImg<T,A>
implements java.io.Serializable

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static interface	NtreeImg.PositionProvider

Field Summary

Fields

Modifier and Type	Field	Description
(package private) A	data
private static long	serialVersionUID	TODO: remove with proper serialization

Fields inherited from class net.imglib2.img.AbstractNativeImg

entitiesPerPixel, linkedType, numEntities

Fields inherited from class net.imglib2.img.AbstractImg

dimension, max, n, numPixels

Constructor Summary

Constructors

Modifier	Constructor	Description
	NtreeImg(A data, long[] dim, Fraction entitiesPerPixel)
private	NtreeImg(NtreeImg<T,A> img)

Method Summary

Modifier and Type	Method	Description
NtreeImg<T,A>	copy()
NtreeCursor<T>	cursor()	Returns a RealCursor that iterates with optimal speed without calculating the location at each iteration step.
ImgFactory<T>	factory()	Get a ImgFactory that creates Imgs of the same kind as this one.
FlatIterationOrder	iterationOrder()	Returns the iteration order of this IterableRealInterval.
NtreeCursor<T>	localizingCursor()	Returns a RealLocalizable Iterator that calculates its location at each iteration step.
NtreeRandomAccess<T>	randomAccess()	Create a random access sampler for integer coordinates.
A	update(java.lang.Object updater)	called by type with cursor.

Methods inherited from class net.imglib2.img.AbstractNativeImg

createLinkedType, getType, setLinkedType

Methods inherited from class net.imglib2.img.AbstractImg

dimension, dimensions, max, max, max, min, min, min, numDimensions, numElements, randomAccess, realMax, realMax, realMax, realMin, realMin, realMin, size, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface net.imglib2.Dimensions

dimensions, dimensions, dimensionsAsLongArray, dimensionsAsPoint

Methods inherited from interface net.imglib2.EuclideanSpace

numDimensions

Methods inherited from interface net.imglib2.Interval

dimension, max, max, max, maxAsLongArray, maxAsPoint, min, min, min, minAsLongArray, minAsPoint, realMax, realMin

Methods inherited from interface java.lang.Iterable

forEach

Methods inherited from interface net.imglib2.IterableInterval

localizingSpliterator, spliterator

Methods inherited from interface net.imglib2.IterableRealInterval

firstElement, iterator, parallelStream, stream

Methods inherited from interface net.imglib2.RandomAccessible

getAt, getAt, getAt, randomAccess

Methods inherited from interface net.imglib2.RandomAccessibleInterval

size

Methods inherited from interface net.imglib2.RealInterval

maxAsDoubleArray, maxAsRealPoint, minAsDoubleArray, minAsRealPoint, realMax, realMax, realMin, realMin

Field Detail

serialVersionUID

private static final long serialVersionUID

TODO: remove with proper serialization

See Also:

Constant Field Values

data

final A extends NtreeAccess<?,A> data

Constructor Detail

NtreeImg

public NtreeImg(A data,
                long[] dim,
                Fraction entitiesPerPixel)

NtreeImg

private NtreeImg(NtreeImg<T,A> img)

Method Detail

update

public A update(java.lang.Object updater)

Description copied from interface: NativeImg

called by type with cursor.

Specified by:

update in interface NativeImg<T extends NativeType<T>,A extends NtreeAccess<?,A>>

Parameters:

updater - cursor

Returns:

DataAccess which is referred to by the updater

randomAccess

public NtreeRandomAccess<T> randomAccess()

Description copied from interface: RandomAccessible

Create a random access sampler for integer coordinates.

The returned random access covers as much of the domain as possible.

Please note: RandomAccessibleIntervals have a finite domain (their Interval), so RandomAccessible.randomAccess() is only guaranteed to cover this finite domain. This may lead to unexpected results when using Views. In the following code

 RandomAccessible<T> extended = Views.extendBorder( img )
 RandomAccessibleInterval<T> cropped = Views.interval( extended, img );
 RandomAccess<T> a1 = extended.randomAccess();
 RandomAccess<T> a2 = cropped.randomAccess();
 

The access a1 on the extended image is valid everywhere. However, somewhat counter-intuitively, the access a2 on the extended and cropped image is only valid on the interval img to which the extended image was cropped. The access is only required to cover this interval, because it is the domain of the cropped image. Views attempts to provide the fastest possible access that meets this requirement, and will therefore strip the extension. To deal with this, if you know that you need to access pixels outside the domain of the RandomAccessibleInterval, and you know that the RandomAccessibleInterval is actually defined beyond its interval boundaries, then use the RandomAccessible.randomAccess(Interval) variant and specify which interval you actually want to access. In the above example,

 RandomAccess<T> a2 = cropped.randomAccess( Intervals.expand( img, 10 ) );
 

will provide the extended access as expected.

Specified by:

randomAccess in interface RandomAccessible<T extends NativeType<T>>

Returns:

random access sampler

cursor

public NtreeCursor<T> cursor()

Description copied from interface: IterableRealInterval

Returns a RealCursor that iterates with optimal speed without calculating the location at each iteration step. Localization is performed on demand.

Use this where localization is required rarely/ not for each iteration.

Specified by:

cursor in interface IterableInterval<T extends NativeType<T>>

Specified by:

cursor in interface IterableRealInterval<T extends NativeType<T>>

Specified by:

cursor in interface RandomAccessibleInterval<T extends NativeType<T>>

Returns:

fast iterating iterator

localizingCursor

public NtreeCursor<T> localizingCursor()

Description copied from interface: IterableRealInterval

Returns a RealLocalizable Iterator that calculates its location at each iteration step. That is, localization is performed with optimal speed.

Use this where localization is required often/ for each iteration.

Specified by:

localizingCursor in interface IterableInterval<T extends NativeType<T>>

Specified by:

localizingCursor in interface IterableRealInterval<T extends NativeType<T>>

Specified by:

localizingCursor in interface RandomAccessibleInterval<T extends NativeType<T>>

Returns:

fast localizing iterator

factory

public ImgFactory<T> factory()

Description copied from interface: Img

Get a ImgFactory that creates Imgs of the same kind as this one. This is useful to create Imgs for temporary storage in generic methods where the specific Img type is unknown. Note, that the factory can be used even if all references to this Img have been invalidated.

Specified by:

factory in interface Img<T extends NativeType<T>>

Returns:

a factory for Imgs of the same kind as this one.

copy

public NtreeImg<T,A> copy()

Specified by:

copy in interface Img<T extends NativeType<T>>

Returns:

- A copy of the current Img instance, all pixels are duplicated

iterationOrder

public FlatIterationOrder iterationOrder()

Description copied from interface: IterableRealInterval

Returns the iteration order of this IterableRealInterval. If the returned object equals (Object.equals(Object)) the iteration order of another IterableRealInterval f then they can be copied by synchronous iteration. That is, having an Iterator on this and another Iterator on f, moving both in synchrony will point both of them to corresponding locations in their source domain. In other words, this and f have the same iteration order and means and the same number of elements.

Specified by:

iterationOrder in interface IterableRealInterval<T extends NativeType<T>>

Specified by:

iterationOrder in interface RandomAccessibleInterval<T extends NativeType<T>>

Returns:

the iteration order of this IterableRealInterval.

See Also:

FlatIterationOrder