Package net.imglib2.img.planar
Class PlanarImg<T extends NativeType<T>,A extends ArrayDataAccess<A>>
java.lang.Object
net.imglib2.img.AbstractImg<T>
net.imglib2.img.AbstractNativeImg<T,A>
net.imglib2.img.planar.PlanarImg<T,A>
- All Implemented Interfaces:
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>
A
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.
- Author:
- Jan Funke, Stephan Preibisch, Stephan Saalfeld, Johannes Schindelin, Tobias Pietzsch
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic interface
This interface is implemented by all samplers on thePlanarImg
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected final int[]
protected final int
protected final int[]
Fields inherited from class net.imglib2.img.AbstractNativeImg
entitiesPerPixel, linkedType, numEntities
Fields inherited from class net.imglib2.img.AbstractImg
dimension, max, n, numPixels
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptioncopy()
cursor()
Returns aRealCursor
that iterates with optimal speed without calculating the location at each iteration step.factory()
Get aImgFactory
that createsImg
s of the same kind as this one.final int
getIndex
(int[] l) For a given ≥2d location, estimate the pixel index in the stack slice.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.Returns the iteration order of thisIterableRealInterval
.Returns aRealLocalizable
Iterator
that calculates its location at each iteration step.localizingCursor
(Interval interval) int
Create a random access sampler for integer coordinates.void
subIntervalIterationOrder
(Interval interval) Returns the iteration order given the interval.boolean
supportsOptimizedCursor
(Interval interval) called by type with cursor.Methods inherited from class net.imglib2.img.AbstractNativeImg
createLinkedType, setLinkedType
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
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
Methods inherited from interface net.imglib2.Dimensions
dimension, dimensions
Methods inherited from interface net.imglib2.EuclideanSpace
numDimensions
Methods inherited from interface java.lang.Iterable
forEach, iterator, spliterator
Methods inherited from interface net.imglib2.IterableRealInterval
firstElement, size
Methods inherited from interface net.imglib2.RandomAccessible
randomAccess
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Field Details
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numSlices
protected final int numSlices -
dimensions
protected final int[] dimensions -
sliceSteps
protected final int[] sliceSteps -
mirror
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Constructor Details
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PlanarImg
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Method Details
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update
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
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
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
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
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:
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getPlane
- Specified by:
getPlane
in interfacePlanarAccess<T extends NativeType<T>>
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setPlane
- Specified by:
setPlane
in interfacePlanarAccess<T extends NativeType<T>>
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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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copy
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supportsOptimizedCursor
- 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
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
- Specified by:
cursor
in interfaceSubIntervalIterable<T extends NativeType<T>>
- Parameters:
interval
-Interval
over which to iterate- Returns:
Cursor
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localizingCursor
- Specified by:
localizingCursor
in interfaceSubIntervalIterable<T extends NativeType<T>>
- Parameters:
interval
-Interval
over which to iterate- Returns:
Cursor
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