Class PlanarImg<T extends NativeType<T>, A extends ArrayDataAccess<A>>

java.lang.Object

net.imglib2.img.AbstractImg<T>

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

net.imglib2.img.planar.PlanarImg<T,A>

All Implemented Interfaces:

Iterable<T>, Dimensions, EuclideanSpace, DataAccess, PlanarAccess<A>, Img<T>, NativeImg<T,A>, Interval, IterableInterval<T>, IterableRealInterval<T>, RandomAccessible<T>, RandomAccessibleInterval<T>, RealInterval, Typed<T>, SubIntervalIterable<T>

public class PlanarImg<T extends NativeType<T>, A extends ArrayDataAccess<A>>
extends AbstractNativeImg<T,A>
implements PlanarAccess<A>, SubIntervalIterable<T>

A NativeImg that stores data in a list of primitive arrays, one per image plane.

The PlanarImg provides access to the underlying data arrays via the getPlane(int) method.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static interface	PlanarImg.PlanarContainerSampler	This interface is implemented by all samplers on the PlanarImg.

Field Summary

Fields

Modifier and Type	Field	Description
protected final int[]	dimensions
(package private) final int	elementsPerSlice
protected final List<A>	mirror
protected final int	numSlices
protected final int[]	sliceSteps

Fields inherited from class AbstractNativeImg

entitiesPerPixel, linkedType, numEntities

Fields inherited from class AbstractImg

dimension, max, n, numPixels

Constructor Summary

Constructors

Constructor	Description
PlanarImg(long[] dim, Fraction entitiesPerPixel)	Deprecated. Use PlanarImg(List, long[], Fraction) instead.
PlanarImg(A creator, long[] dim, Fraction entitiesPerPixel)
PlanarImg(List<A> slices, long[] dim, Fraction entitiesPerPixel)

Method Summary

Modifier and Type	Method	Description
private static int[]	computeSliceSteps(long[] dimensions)
PlanarImg<T,?>	copy()
private boolean	correspondsToPlane(Interval interval)
private static <A extends ArrayDataAccess<A>> List<A>	createSlices(A creator, long[] dim, Fraction entitiesPerPixel)
PlanarCursor<T>	cursor()	Returns a RealCursor that iterates with optimal speed without calculating the location at each iteration step.
Cursor<T>	cursor(Interval interval)	Create a Cursor to iterate over the given Interval.
static int	elementsPerSlice(long[] dimensions)	What is the size of one plane in a PlanarImg with the given dimensions?
private static <A> List<A>	emptySlices(long[] dim)
PlanarImgFactory<T>	factory()	Get a ImgFactory that creates Imgs of the same kind as this one.
final int	getIndex(int[] l)	For a given ≥2d location, estimate the pixel index in the stack slice.
A	getPlane(int no)
int	indexToGlobalPosition(int sliceIndex, int indexInSlice, int dim)	Compute a global position from the index of a slice and an index within that slice.
void	indexToGlobalPosition(int sliceIndex, int indexInSlice, int[] position)	Compute a global position from the index of a slice and an index within that slice.
FlatIterationOrder	iterationOrder()	Returns the iteration order of this IterableRealInterval.
PlanarLocalizingCursor<T>	localizingCursor()	Returns a RealLocalizable Iterator that calculates its location at each iteration step.
Cursor<T>	localizingCursor(Interval interval)	Create a Cursor to iterate over the given Interval.
LocalizableSpliterator<T>	localizingSpliterator()	Creates a LocalizableSpliterator over the elements of this IterableInterval.
static int	numberOfSlices(long[] dimensions)	How many slices has a PlanarImg with the given dimensions?
int	numSlices()
PlanarRandomAccess<T>	randomAccess()	Create a random access sampler for integer coordinates.
void	setPlane(int no, A plane)
LocalizableSpliterator<T>	spliterator()	Creates a LocalizableSpliterator over the elements of this IterableInterval.
Object	subIntervalIterationOrder(Interval interval)	Returns the iteration order given the interval.
boolean	supportsOptimizedCursor(Interval interval)	Determine whether a Cursor can be created that iterates the given Interval.
A	update(Object c)	called by type with cursor.

Methods inherited from class AbstractNativeImg

createLinkedType, getType, setLinkedType

Methods inherited from class AbstractImg

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

Methods inherited from class Object

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

Methods inherited from interface DataAccess

createView

Methods inherited from interface Dimensions

dimensions, dimensions, dimensionsAsLongArray, dimensionsAsPoint

Methods inherited from interface EuclideanSpace

numDimensions

Methods inherited from interface Interval

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

Methods inherited from interface Iterable

forEach

Methods inherited from interface IterableRealInterval

firstElement, getType, iterator, parallelStream, stream

Methods inherited from interface RandomAccessible

getAt, getAt, getAt, randomAccess

Methods inherited from interface RandomAccessibleInterval

size

Methods inherited from interface RealInterval

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

Field Details

numSlices

protected final int numSlices

elementsPerSlice

final int elementsPerSlice

dimensions

protected final int[] dimensions

sliceSteps

protected final int[] sliceSteps

mirror

protected final List<A extends ArrayDataAccess<A>> mirror

Constructor Details

PlanarImg

public PlanarImg(List<A> slices,
 long[] dim,
 Fraction entitiesPerPixel)

PlanarImg

@Deprecated
public PlanarImg(long[] dim,
 Fraction entitiesPerPixel)

Deprecated.

Use PlanarImg(List, long[], Fraction) instead.

PlanarImg

PlanarImg(A creator,
 long[] dim,
 Fraction entitiesPerPixel)

Method Details

update

public A update(Object c)

Description copied from interface: NativeImg

called by type with cursor.

Specified by:

update in interface NativeImg<T extends NativeType<T>, A extends ArrayDataAccess<A>>

Parameters:

c - cursor

Returns:

DataAccess which is referred to by the updater

numSlices

public int numSlices()

Returns:

total number of image planes

getIndex

public final int getIndex(int[] l)

For a given ≥2d location, estimate the pixel index in the stack slice.

Parameters:

l -

Returns:

TODO: remove this method? (it doesn't seem to be used anywhere)

indexToGlobalPosition

public void indexToGlobalPosition(int sliceIndex,
 int indexInSlice,
 int[] position)

Compute a global position from the index of a slice and an index within that slice.

Parameters:

sliceIndex - index of slice

indexInSlice - index of element within slice

position - receives global position of element TODO: move this method to AbstractPlanarCursor? (that seems to be the only place where it is needed)

indexToGlobalPosition

public int indexToGlobalPosition(int sliceIndex,
 int indexInSlice,
 int dim)

Compute a global position from the index of a slice and an index within that slice.

Parameters:

sliceIndex - index of slice

indexInSlice - index of element within slice

dim - which dimension of the position we are interested in

Returns:

dimension dim of global position TODO: move this method to AbstractPlanarCursor? (that seems to be the only place where it is needed)

cursor

public PlanarCursor<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 PlanarLocalizingCursor<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

randomAccess

public PlanarRandomAccess<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

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

getPlane

public A getPlane(int no)

Specified by:

getPlane in interface PlanarAccess<T extends NativeType<T>>

setPlane

public void setPlane(int no,
 A plane)

Specified by:

setPlane in interface PlanarAccess<T extends NativeType<T>>

factory

public PlanarImgFactory<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 PlanarImg<T,?> copy()

Specified by:

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

Returns:

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

supportsOptimizedCursor

public boolean supportsOptimizedCursor(Interval interval)

Determine whether a Cursor can be created that iterates the given Interval.

Specified by:

supportsOptimizedCursor in interface SubIntervalIterable<T extends NativeType<T>>

Parameters:

interval - to be checked

Returns:

true if a Cursor can be optimized given the Interval

subIntervalIterationOrder

public Object subIntervalIterationOrder(Interval interval)

Returns the iteration order given the interval.

Specified by:

subIntervalIterationOrder in interface SubIntervalIterable<T extends NativeType<T>>

Parameters:

interval - Interval over which to iterate

Returns:

the iteration order object @see IterableRealInterval

cursor

public Cursor<T> cursor(Interval interval)

Create a Cursor to iterate over the given Interval.

Specified by:

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

Parameters:

interval - Interval over which to iterate

Returns:

Cursor

spliterator

public LocalizableSpliterator<T> spliterator()

Description copied from interface: IterableInterval

Creates a LocalizableSpliterator over the elements of this IterableInterval. The returned Spliterator iterates with optimal speed without calculating the location at each iteration step. Localization is performed on demand.

The default implementation wraps a Cursor on the interval. The created Spliterator reports Spliterator.SIZED, Spliterator.SUBSIZED, Spliterator.ORDERED and Spliterator.NONNULL.

Specified by:

spliterator in interface Iterable<T extends NativeType<T>>

Specified by:

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

Specified by:

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

localizingSpliterator

public LocalizableSpliterator<T> localizingSpliterator()

Description copied from interface: IterableInterval

Creates a LocalizableSpliterator over the elements of this IterableInterval. The returned Spliterator calculates its location at each iteration step. That is, localization is performed with optimal speed.

The default implementation wraps a localizing Cursor on the interval. The created Spliterator reports Spliterator.SIZED, Spliterator.SUBSIZED, Spliterator.ORDERED and Spliterator.NONNULL.

Specified by:

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

Specified by:

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

correspondsToPlane

private boolean correspondsToPlane(Interval interval)

localizingCursor

public Cursor<T> localizingCursor(Interval interval)

Create a Cursor to iterate over the given Interval.

Specified by:

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

Parameters:

interval - Interval over which to iterate

Returns:

Cursor

elementsPerSlice

public static int elementsPerSlice(long[] dimensions)

What is the size of one plane in a PlanarImg with the given dimensions?

numberOfSlices

public static int numberOfSlices(long[] dimensions)

How many slices has a PlanarImg with the given dimensions?

computeSliceSteps

private static int[] computeSliceSteps(long[] dimensions)

emptySlices

private static <A> List<A> emptySlices(long[] dim)

createSlices

private static <A extends ArrayDataAccess<A>>
List<A> createSlices(A creator,
 long[] dim,
 Fraction entitiesPerPixel)