Package net.imglib2.img.planar
Class PlanarImg<T extends NativeType<T>,A extends ArrayDataAccess<A>>
- 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.planar.PlanarImg<T,A>
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- All Implemented Interfaces:
java.lang.Iterable<T>
,Dimensions
,EuclideanSpace
,PlanarAccess<A>
,Img<T>
,NativeImg<T,A>
,Interval
,IterableInterval<T>
,IterableRealInterval<T>
,RandomAccessible<T>
,RandomAccessibleInterval<T>
,RealInterval
,SubIntervalIterable<T>
public class PlanarImg<T extends NativeType<T>,A extends ArrayDataAccess<A>> extends AbstractNativeImg<T,A> implements PlanarAccess<A>, SubIntervalIterable<T>
ANativeImg
that stores data in an list of primitive arrays, one per image plane.The
PlanarImg
provides access to the underlying data arrays via thegetPlane(int)
method.- Author:
- Jan Funke, Stephan Preibisch, Stephan Saalfeld, Johannes Schindelin, Tobias Pietzsch
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Nested Class Summary
Nested Classes Modifier and Type Class Description static interface
PlanarImg.PlanarContainerSampler
This interface is implemented by all samplers on thePlanarImg
.
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Field Summary
Fields Modifier and Type Field Description protected int[]
dimensions
protected java.util.ArrayList<A>
mirror
protected int
numSlices
protected int[]
sliceSteps
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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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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description PlanarImg<T,?>
copy()
PlanarCursor<T>
cursor()
Returns aRealCursor
that iterates with optimal speed without calculating the location at each iteration step.Cursor<T>
cursor(Interval interval)
PlanarImgFactory<T>
factory()
Get aImgFactory
that createsImg
s 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 thisIterableRealInterval
.PlanarLocalizingCursor<T>
localizingCursor()
Returns aRealLocalizable
Iterator
that calculates its location at each iteration step.Cursor<T>
localizingCursor(Interval interval)
int
numSlices()
PlanarRandomAccess<T>
randomAccess()
Create a random access sampler for integer coordinates.void
setPlane(int no, A plane)
java.lang.Object
subIntervalIterationOrder(Interval interval)
Returns the iteration order given the interval.boolean
supportsOptimizedCursor(Interval interval)
A
update(java.lang.Object c)
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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numSlices
protected final int numSlices
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dimensions
protected final int[] dimensions
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sliceSteps
protected final int[] sliceSteps
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mirror
protected final java.util.ArrayList<A extends ArrayDataAccess<A>> mirror
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Constructor Detail
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PlanarImg
public PlanarImg(long[] dim, Fraction entitiesPerPixel)
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Method Detail
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update
public A update(java.lang.Object c)
Description copied from interface:NativeImg
called by type with cursor.- Specified by:
update
in interfaceNativeImg<T extends NativeType<T>,A extends ArrayDataAccess<A>>
- Parameters:
c
- cursor- Returns:
- native array which is referred to by the updater
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numSlices
public int numSlices()
- Returns:
- total number of image planes
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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)
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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 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)
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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 sliceindexInSlice
- index of element within slicedim
- 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)
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cursor
public PlanarCursor<T> 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.
- Specified by:
cursor
in interfaceIterableInterval<T extends NativeType<T>>
- Specified by:
cursor
in interfaceIterableRealInterval<T extends NativeType<T>>
- Returns:
- fast iterating iterator
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localizingCursor
public PlanarLocalizingCursor<T> 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.
- Specified by:
localizingCursor
in interfaceIterableInterval<T extends NativeType<T>>
- Specified by:
localizingCursor
in interfaceIterableRealInterval<T extends NativeType<T>>
- Returns:
- fast localizing iterator
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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: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.- Specified by:
randomAccess
in interfaceRandomAccessible<T extends NativeType<T>>
- Returns:
- random access sampler
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iterationOrder
public FlatIterationOrder 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.- Specified by:
iterationOrder
in interfaceIterableRealInterval<T extends NativeType<T>>
- Returns:
- the iteration order of this
IterableRealInterval
. - See Also:
FlatIterationOrder
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getPlane
public A getPlane(int no)
- Specified by:
getPlane
in interfacePlanarAccess<T extends NativeType<T>>
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setPlane
public void setPlane(int no, A plane)
- Specified by:
setPlane
in interfacePlanarAccess<T extends NativeType<T>>
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factory
public PlanarImgFactory<T> factory()
Description copied from interface:Img
Get aImgFactory
that createsImg
s 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 interfaceImg<T extends NativeType<T>>
- Returns:
- a factory for Imgs of the same kind as this one.
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supportsOptimizedCursor
public boolean supportsOptimizedCursor(Interval interval)
- Specified by:
supportsOptimizedCursor
in interfaceSubIntervalIterable<T extends NativeType<T>>
- Parameters:
interval
- to be checked- Returns:
- true if a
Cursor
can be optimized given theInterval
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subIntervalIterationOrder
public java.lang.Object subIntervalIterationOrder(Interval interval)
Returns the iteration order given the interval.- Specified by:
subIntervalIterationOrder
in interfaceSubIntervalIterable<T extends NativeType<T>>
- Parameters:
interval
-Interval
over which to iterate- Returns:
- the iteration order object @see
IterableRealInterval
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cursor
public Cursor<T> cursor(Interval interval)
- Specified by:
cursor
in interfaceSubIntervalIterable<T extends NativeType<T>>
- Parameters:
interval
-Interval
over which to iterate- Returns:
Cursor
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localizingCursor
public Cursor<T> localizingCursor(Interval interval)
- Specified by:
localizingCursor
in interfaceSubIntervalIterable<T extends NativeType<T>>
- Parameters:
interval
-Interval
over which to iterate- Returns:
Cursor
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