public class PlanarImg<T extends NativeType<T>,A extends ArrayDataAccess<A>> extends AbstractNativeImg<T,A> implements PlanarAccess<A>, SubIntervalIterable<T>
NativeImg that stores data in an list of primitive arrays, one per
image plane.
The PlanarImg provides access to the underlying data arrays via the
getPlane(int) method.
| Modifier and Type | Class and Description |
|---|---|
static interface |
PlanarImg.PlanarContainerSampler
This interface is implemented by all samplers on the
PlanarImg. |
| Modifier and Type | Field and Description |
|---|---|
protected int[] |
dimensions |
protected List<A> |
mirror |
protected int |
numSlices |
protected int[] |
sliceSteps |
entitiesPerPixel, linkedType, numEntitiesdimension, max, n, numPixels| Constructor and Description |
|---|
PlanarImg(List<A> slices,
long[] dim,
Fraction entitiesPerPixel) |
PlanarImg(long[] dim,
Fraction entitiesPerPixel)
Deprecated.
Use
PlanarImg(List, long[], Fraction) instead. |
| Modifier and Type | Method and Description |
|---|---|
PlanarImg<T,?> |
copy() |
PlanarCursor<T> |
cursor()
Returns a
RealCursor that iterates with optimal speed without
calculating the location at each iteration step. |
Cursor<T> |
cursor(Interval interval)
|
PlanarImgFactory<T> |
factory()
Get a
ImgFactory that creates Imgs of the same kind as
this one. |
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)
|
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) |
Object |
subIntervalIterationOrder(Interval interval)
Returns the iteration order given the interval.
|
boolean |
supportsOptimizedCursor(Interval interval)
|
A |
update(Object c)
called by type with cursor.
|
createLinkedType, setLinkedTypedimension, dimensions, firstElement, iterator, max, max, max, min, min, min, numDimensions, numElements, randomAccess, realMax, realMax, realMax, realMin, realMin, realMin, size, toStringclone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, waitgetAt, getAt, getAt, randomAccessfirstElement, sizeforEach, iterator, spliteratordimension, max, max, max, maxAsLongArray, maxAsPoint, min, min, min, minAsLongArray, minAsPoint, realMax, realMinmaxAsDoubleArray, maxAsRealPoint, minAsDoubleArray, minAsRealPoint, realMax, realMax, realMin, realMinallPositive, allPositive, dimensions, dimensions, dimensionsAsLongArray, dimensionsAsPoint, verify, verify, verifyAllPositive, verifyAllPositivenumDimensionsprotected final int numSlices
protected final int[] dimensions
protected final int[] sliceSteps
protected final List<A extends ArrayDataAccess<A>> mirror
@Deprecated public PlanarImg(long[] dim, Fraction entitiesPerPixel)
PlanarImg(List, long[], Fraction) instead.public A update(Object c)
NativeImgupdate in interface NativeImg<T extends NativeType<T>,A extends ArrayDataAccess<A>>c - cursorpublic int numSlices()
public final int getIndex(int[] l)
l - public void indexToGlobalPosition(int sliceIndex,
int indexInSlice,
int[] position)
sliceIndex - index of sliceindexInSlice - index of element within sliceposition - receives global position of element
TODO: move this method to AbstractPlanarCursor? (that seems to
be the only place where it is needed)public int indexToGlobalPosition(int sliceIndex,
int indexInSlice,
int dim)
sliceIndex - index of sliceindexInSlice - index of element within slicedim - which dimension of the position we are interested inpublic PlanarCursor<T> cursor()
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.
cursor in interface IterableInterval<T extends NativeType<T>>cursor in interface IterableRealInterval<T extends NativeType<T>>public PlanarLocalizingCursor<T> localizingCursor()
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.
localizingCursor in interface IterableInterval<T extends NativeType<T>>localizingCursor in interface IterableRealInterval<T extends NativeType<T>>public PlanarRandomAccess<T> randomAccess()
RandomAccessibleThe 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.
randomAccess in interface RandomAccessible<T extends NativeType<T>>public FlatIterationOrder iterationOrder()
IterableRealIntervalIterableRealInterval. 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.iterationOrder in interface IterableRealInterval<T extends NativeType<T>>IterableRealInterval.FlatIterationOrderpublic A getPlane(int no)
getPlane in interface PlanarAccess<A extends ArrayDataAccess<A>>public void setPlane(int no,
A plane)
setPlane in interface PlanarAccess<A extends ArrayDataAccess<A>>public PlanarImgFactory<T> factory()
ImgImgFactory 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.factory in interface Img<T extends NativeType<T>>public boolean supportsOptimizedCursor(Interval interval)
supportsOptimizedCursor in interface SubIntervalIterable<T extends NativeType<T>>interval - to be checkedCursor can be optimized given the
Intervalpublic Object subIntervalIterationOrder(Interval interval)
subIntervalIterationOrder in interface SubIntervalIterable<T extends NativeType<T>>interval - Interval over which to iterateIterableRealIntervalpublic Cursor<T> cursor(Interval interval)
cursor in interface SubIntervalIterable<T extends NativeType<T>>interval - Interval over which to iterateCursorpublic Cursor<T> localizingCursor(Interval interval)
localizingCursor in interface SubIntervalIterable<T extends NativeType<T>>interval - Interval over which to iterateCursorpublic static int numberOfSlices(long[] dimensions)
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