Class ArrayImg<T extends NativeType<T>,A extends DataAccess>
- java.lang.Object
-
- net.imglib2.img.AbstractImg<T>
-
- net.imglib2.img.AbstractNativeImg<T,A>
-
- net.imglib2.img.array.ArrayImg<T,A>
-
- Type Parameters:
T-A-
- All Implemented Interfaces:
java.lang.Iterable<T>,Dimensions,EuclideanSpace,Img<T>,NativeImg<T,A>,Interval,IterableInterval<T>,IterableRealInterval<T>,RandomAccessible<T>,RandomAccessibleInterval<T>,RealInterval,Typed<T>,SubIntervalIterable<T>
- Direct Known Subclasses:
ARGBScreenImage,ArrayImgAWTScreenImage
public class ArrayImg<T extends NativeType<T>,A extends DataAccess> extends AbstractNativeImg<T,A> implements SubIntervalIterable<T>
ThisImgstores an image in a single linear array of basic types. By that, it provides the fastest possible access to data while limiting the number of basic types stored toInteger.MAX_VALUE. Keep in mind that this does not necessarily reflect the number of pixels, because a pixel can be stored in less than or more than a basic type entry.
-
-
Field Summary
Fields Modifier and Type Field Description private Adata(package private) int[]dim(package private) int[]steps-
Fields inherited from class net.imglib2.img.AbstractNativeImg
entitiesPerPixel, linkedType, numEntities
-
Fields inherited from class net.imglib2.img.AbstractImg
dimension, max, n, numPixels
-
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description ArrayImg<T,?>copy()ArrayCursor<T>cursor()Returns aRealCursorthat iterates with optimal speed without calculating the location at each iteration step.Cursor<T>cursor(Interval interval)ArrayImgFactory<T>factory()Get aImgFactorythat createsImgs of the same kind as this one.private intfastCursorAvailable(Interval interval)If method returns -1 no fast cursor is available, else the amount of dims (starting from zero) which can be iterated fast are returned.FlatIterationOrderiterationOrder()Returns the iteration order of thisIterableRealInterval.ArrayLocalizingCursor<T>localizingCursor()Returns aRealLocalizableIteratorthat calculates its location at each iteration step.Cursor<T>localizingCursor(Interval interval)LocalizableSpliterator<T>localizingSpliterator()Creates aLocalizableSpliteratorover the elements of thisIterableInterval.private longoffset(Interval interval)ArrayRandomAccess<T>randomAccess()Create a random access sampler for integer coordinates.ArrayRandomAccess<T>randomAccess(Interval interval)Create a random access sampler for integer coordinates.private longsize(Interval interval, int length)LocalizableSpliterator<T>spliterator()Creates aLocalizableSpliteratorover the elements of thisIterableInterval.java.lang.ObjectsubIntervalIterationOrder(Interval interval)Returns the iteration order given the interval.booleansupportsOptimizedCursor(Interval interval)Aupdate(java.lang.Object o)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, 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 net.imglib2.IterableRealInterval
firstElement, getType, iterator, parallelStream, stream
-
Methods inherited from interface net.imglib2.RandomAccessible
getAt, getAt, getAt
-
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
-
steps
final int[] steps
-
dim
final int[] dim
-
data
private final A extends DataAccess data
-
-
Constructor Detail
-
ArrayImg
@Deprecated public ArrayImg(java.lang.Object data, long[] dim, Fraction entitiesPerPixel)Deprecated.Deprecated constructor for binary compatibility when A was not bounded by DataAccess- Parameters:
data- - will be cast to DataAccess type Adim-entitiesPerPixel-
-
-
Method Detail
-
update
public A update(java.lang.Object o)
Description copied from interface:NativeImgcalled by type with cursor.- Specified by:
updatein interfaceNativeImg<T extends NativeType<T>,A extends DataAccess>- Parameters:
o- cursor- Returns:
DataAccesswhich is referred to by the updater
-
cursor
public ArrayCursor<T> cursor()
Description copied from interface:IterableRealIntervalReturns a
RealCursorthat 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:
cursorin interfaceIterableInterval<T extends NativeType<T>>- Specified by:
cursorin interfaceIterableRealInterval<T extends NativeType<T>>- Specified by:
cursorin interfaceRandomAccessibleInterval<T extends NativeType<T>>- Returns:
- fast iterating iterator
-
localizingCursor
public ArrayLocalizingCursor<T> localizingCursor()
Description copied from interface:IterableRealIntervalReturns a
RealLocalizableIteratorthat 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:
localizingCursorin interfaceIterableInterval<T extends NativeType<T>>- Specified by:
localizingCursorin interfaceIterableRealInterval<T extends NativeType<T>>- Specified by:
localizingCursorin interfaceRandomAccessibleInterval<T extends NativeType<T>>- Returns:
- fast localizing iterator
-
randomAccess
public ArrayRandomAccess<T> randomAccess()
Description copied from interface:RandomAccessibleCreate 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 (theirInterval), soRandomAccessible.randomAccess()is only guaranteed to cover this finite domain. This may lead to unexpected results when usingViews. In the following codeRandomAccessible<T> extended = Views.extendBorder( img ) RandomAccessibleInterval<T> cropped = Views.interval( extended, img ); RandomAccess<T> a1 = extended.randomAccess(); RandomAccess<T> a2 = cropped.randomAccess();
Theaccessa1on the extended image is valid everywhere. However, somewhat counter-intuitively, theaccessa2on the extended and cropped image is only valid on the intervalimgto which the extended image was cropped. The access is only required to cover this interval, because it is the domain of the cropped image.Viewsattempts 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 theRandomAccessibleInterval, and you know that theRandomAccessibleIntervalis actually defined beyond its interval boundaries, then use theRandomAccessible.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:
randomAccessin interfaceRandomAccessible<T extends NativeType<T>>- Returns:
- random access sampler
-
randomAccess
public ArrayRandomAccess<T> randomAccess(Interval interval)
Description copied from interface:RandomAccessibleCreate a random access sampler for integer coordinates.The returned random access is intended to be used in the specified interval only. Thus, the RandomAccessible may provide optimized versions. If the interval is completely contained in the domain, the random access is guaranteed to provide the same values as that obtained by
RandomAccessible.randomAccess()within the interval.- Specified by:
randomAccessin interfaceRandomAccessible<T extends NativeType<T>>- Overrides:
randomAccessin classAbstractImg<T extends NativeType<T>>- Parameters:
interval- in which interval you intend to use the random access.- Returns:
- random access sampler
-
iterationOrder
public FlatIterationOrder iterationOrder()
Description copied from interface:IterableRealIntervalReturns the iteration order of thisIterableRealInterval. If the returned object equals (Object.equals(Object)) the iteration order of anotherIterableRealIntervalf then they can be copied by synchronous iteration. That is, having anIteratoron this and anotherIteratoron 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:
iterationOrderin interfaceIterableRealInterval<T extends NativeType<T>>- Specified by:
iterationOrderin interfaceRandomAccessibleInterval<T extends NativeType<T>>- Returns:
- the iteration order of this
IterableRealInterval. - See Also:
FlatIterationOrder
-
factory
public ArrayImgFactory<T> factory()
Description copied from interface:ImgGet aImgFactorythat createsImgs 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:
factoryin interfaceImg<T extends NativeType<T>>- Returns:
- a factory for Imgs of the same kind as this one.
-
cursor
public Cursor<T> cursor(Interval interval)
- Specified by:
cursorin interfaceSubIntervalIterable<T extends NativeType<T>>- Parameters:
interval-Intervalover which to iterate- Returns:
Cursor
-
size
private long size(Interval interval, int length)
-
offset
private long offset(Interval interval)
-
fastCursorAvailable
private int fastCursorAvailable(Interval interval)
If method returns -1 no fast cursor is available, else the amount of dims (starting from zero) which can be iterated fast are returned.
-
localizingCursor
public Cursor<T> localizingCursor(Interval interval)
- Specified by:
localizingCursorin interfaceSubIntervalIterable<T extends NativeType<T>>- Parameters:
interval-Intervalover which to iterate- Returns:
Cursor
-
supportsOptimizedCursor
public boolean supportsOptimizedCursor(Interval interval)
- Specified by:
supportsOptimizedCursorin interfaceSubIntervalIterable<T extends NativeType<T>>- Parameters:
interval- to be checked- Returns:
- true if a
Cursorcan be optimized given theInterval
-
subIntervalIterationOrder
public java.lang.Object subIntervalIterationOrder(Interval interval)
Returns the iteration order given the interval.- Specified by:
subIntervalIterationOrderin interfaceSubIntervalIterable<T extends NativeType<T>>- Parameters:
interval-Intervalover which to iterate- Returns:
- the iteration order object @see
IterableRealInterval
-
spliterator
public LocalizableSpliterator<T> spliterator()
Description copied from interface:IterableIntervalCreates aLocalizableSpliteratorover the elements of thisIterableInterval. The returnedSpliteratoriterates with optimal speed without calculating the location at each iteration step. Localization is performed on demand.The default implementation wraps a
Cursoron the interval. The createdSpliteratorreportsSpliterator.SIZED,Spliterator.SUBSIZED,Spliterator.ORDEREDandSpliterator.NONNULL.- Specified by:
spliteratorin interfacejava.lang.Iterable<T extends NativeType<T>>- Specified by:
spliteratorin interfaceIterableInterval<T extends NativeType<T>>- Specified by:
spliteratorin interfaceIterableRealInterval<T extends NativeType<T>>
-
localizingSpliterator
public LocalizableSpliterator<T> localizingSpliterator()
Description copied from interface:IterableIntervalCreates aLocalizableSpliteratorover the elements of thisIterableInterval. The returnedSpliteratorcalculates its location at each iteration step. That is, localization is performed with optimal speed.The default implementation wraps a
localizingCursoron the interval. The createdSpliteratorreportsSpliterator.SIZED,Spliterator.SUBSIZED,Spliterator.ORDEREDandSpliterator.NONNULL.- Specified by:
localizingSpliteratorin interfaceIterableInterval<T extends NativeType<T>>- Specified by:
localizingSpliteratorin interfaceIterableRealInterval<T extends NativeType<T>>
-
-