Package net.imglib2.img.cell
Class AbstractCellImg<T extends NativeType<T>,A,C extends Cell<A>,I extends RandomAccessible<C> & IterableInterval<C>>
- java.lang.Object
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- net.imglib2.img.AbstractImg<T>
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- net.imglib2.img.AbstractNativeImg<T,A>
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- net.imglib2.img.cell.AbstractCellImg<T,A,C,I>
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- All Implemented Interfaces:
java.lang.Iterable<T>
,Dimensions
,EuclideanSpace
,Img<T>
,NativeImg<T,A>
,Interval
,IterableInterval<T>
,IterableRealInterval<T>
,RandomAccessible<T>
,RandomAccessibleInterval<T>
,RealInterval
- Direct Known Subclasses:
CellImg
,LazyCellImg
public abstract class AbstractCellImg<T extends NativeType<T>,A,C extends Cell<A>,I extends RandomAccessible<C> & IterableInterval<C>> extends AbstractNativeImg<T,A>
Abstract superclass forImg
types that divide their underlying data into cells.- Author:
- Mark Hiner, Tobias Pietzsch
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Nested Class Summary
Nested Classes Modifier and Type Class Description static interface
AbstractCellImg.CellImgSampler<C>
This interface is implemented by all samplers on theAbstractCellImg
.
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Field Summary
Fields Modifier and Type Field Description protected I
cells
protected CellGrid
grid
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Fields inherited from class net.imglib2.img.AbstractNativeImg
entitiesPerPixel, linkedType, numEntities
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Fields inherited from class net.imglib2.img.AbstractImg
dimension, max, n, numPixels
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Constructor Summary
Constructors Constructor Description AbstractCellImg(CellGrid grid, I imgOfCells, Fraction entitiesPerPixel)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
copyDataTo(AbstractCellImg<T,?,?,?> copy)
CellCursor<T,C>
cursor()
Returns aRealCursor
that iterates with optimal speed without calculating the location at each iteration step.CellGrid
getCellGrid()
Get theCellGrid
which describes the layout of theAbstractCellImg
.I
getCells()
Get the underlying image of cells which gives access to the individualCell
s through Cursors and RandomAccesses.CellIterationOrder
iterationOrder()
Returns the iteration order of thisIterableRealInterval
.CellLocalizingCursor<T,C>
localizingCursor()
Returns aRealLocalizable
Iterator
that calculates its location at each iteration step.CellRandomAccess<T,C>
randomAccess()
Create a random access sampler for integer coordinates.A
update(java.lang.Object cursor)
called by type with cursor.-
Methods inherited from class net.imglib2.img.AbstractNativeImg
createLinkedType, setLinkedType
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Methods inherited from class net.imglib2.img.AbstractImg
dimension, dimensions, firstElement, iterator, max, max, max, min, min, min, numDimensions, numElements, randomAccess, realMax, realMax, realMax, realMin, realMin, realMin, size, toString
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
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Methods inherited from interface net.imglib2.Dimensions
dimension, dimensions
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Methods inherited from interface net.imglib2.EuclideanSpace
numDimensions
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Methods inherited from interface net.imglib2.IterableRealInterval
firstElement, size
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Methods inherited from interface net.imglib2.RandomAccessible
randomAccess
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Field Detail
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grid
protected final CellGrid grid
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cells
protected final I extends RandomAccessible<C> & IterableInterval<C> cells
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Method Detail
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update
public A update(java.lang.Object cursor)
Description copied from interface:NativeImg
called by type with cursor.- Parameters:
cursor
- cursor- Returns:
- native array which is referred to by the updater
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cursor
public CellCursor<T,C> 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.
- Returns:
- fast iterating iterator
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localizingCursor
public CellLocalizingCursor<T,C> 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.
- Returns:
- fast localizing iterator
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randomAccess
public CellRandomAccess<T,C> 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:RandomAccessibleInterval
s 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();
Theaccess
a1
on the extended image is valid everywhere. However, somewhat counter-intuitively, theaccess
a2
on the extended and cropped image is only valid on the intervalimg
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 theRandomAccessibleInterval
, and you know that theRandomAccessibleInterval
is 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.- Returns:
- random access sampler
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iterationOrder
public CellIterationOrder iterationOrder()
Description copied from interface:IterableRealInterval
Returns the iteration order of thisIterableRealInterval
. If the returned object equals (Object.equals(Object)
) the iteration order of anotherIterableRealInterval
f then they can be copied by synchronous iteration. That is, having anIterator
on this and anotherIterator
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.- Returns:
- the iteration order of this
IterableRealInterval
. - See Also:
FlatIterationOrder
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getCells
public I getCells()
Get the underlying image of cells which gives access to the individualCell
s through Cursors and RandomAccesses.- Returns:
- the image of cells.
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getCellGrid
public CellGrid getCellGrid()
Get theCellGrid
which describes the layout of theAbstractCellImg
. The grid provides the dimensions of the image, the number of cells in each dimension, and the dimensions of individual cells.- Returns:
- the cell grid layout.
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copyDataTo
protected void copyDataTo(AbstractCellImg<T,?,?,?> copy)
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