Package net.imglib2.img.planar

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

    • Field Detail

      • numSlices

        protected final int numSlices

      • elementsPerSlice

        final int elementsPerSlice

      • dimensions

        protected final int[] dimensions

      • sliceSteps

        protected final int[] sliceSteps

    • Constructor Detail

      • PlanarImg

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

      • PlanarImg

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

    • Method Detail

      • 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)

      • 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

      • 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

      • correspondsToPlane

        private boolean correspondsToPlane​(Interval interval)

      • 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> java.util.List<A> emptySlices​(long[] dim)

      • createSlices

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