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
net.imglib2.img.AbstractImg<T>
net.imglib2.img.AbstractNativeImg<T,A>
net.imglib2.img.cell.AbstractCellImg<T,A,C,I>
All Implemented Interfaces:
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 for Img types that divide their underlying data into cells.
Author:
Mark Hiner, Tobias Pietzsch

  • Field Details

  • Constructor Details

    • AbstractCellImg

      public AbstractCellImg(CellGrid grid, I imgOfCells, Fraction entitiesPerPixel)

  • Method Details

    • update

      public A update(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

    • 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

    • 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

    • 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: 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.
      Returns:
      random access sampler

    • iterationOrder

      public CellIterationOrder 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.
      Returns:
      the iteration order of this IterableRealInterval.
      See Also:

    • getCells

      public I getCells()
      Get the underlying image of cells which gives access to the individual Cells through Cursors and RandomAccesses.
      Returns:
      the image of cells.

    • getCellGrid

      public CellGrid getCellGrid()
      Get the CellGrid which describes the layout of the AbstractCellImg. 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.

    • copyDataTo

      protected void copyDataTo(AbstractCellImg<T,?,?,?> copy)