net.imglib2.blocks

Interface PrimitiveBlocks<T extends NativeType<T>>

Type Parameters:

T - pixel type

All Superinterfaces:

EuclideanSpace, Typed<T>

public interface PrimitiveBlocks<T extends NativeType<T>>
extends Typed<T>, EuclideanSpace

Copy blocks of data out of a NativeType<T> source into primitive arrays (of the appropriate type).

Use the static method PrimitiveBlocks.of to create a PrimitiveBlocks accessor for an arbitrary RandomAccessible source. Then use the copy(net.imglib2.Interval, java.lang.Object) method, to copy blocks out of the source into flat primitive arrays.

PrimitiveBlocks.of understands a lot of View constructions (that ultimately end in CellImg, ArrayImg, etc) and will try to build an optimized copier. For example, the following will work:

 		CellImg< UnsignedByteType, ? > cellImg3D;
 		RandomAccessible< FloatType > view = Converters.convert(
 				Views.extendBorder(
 						Views.hyperSlice(
 								Views.zeroMin(
 										Views.rotate( cellImg3D, 1, 0 )
 								),
 								2, 80 )
 				),
 				new RealFloatConverter<>(),
 				new FloatType()
 		);
 		PrimitiveBlocks< FloatType > blocks = PrimitiveBlocks.of( view );

 		final float[] data = new float[ 40 * 50 ];
 		blocks.copy( new int[] { 10, 20 }, data, new int[] { 40, 50 } );
 

If a source RandomAccessible cannot be understood, PrimitiveBlocks.of will return a fall-back implementation (based on LoopBuilder).

With the optional OnFallback argument to PrimitiveBlocks.of it can be configured, whether fall-back should be silently accepted (ACCEPT), a warning should be printed (WARN), or an IllegalArgumentException thrown (FAIL). The warning/exception message explains why the input RandomAccessible requires fall-back.

The only really un-supported case is if the pixel type T does not map one-to-one to a primitive type. (For example, ComplexDoubleType or Unsigned4BitType are not supported.)

Implementations are not thread-safe in general. Use threadSafe() to obtain a thread-safe instance (implemented using ThreadLocal copies). E.g.,

 		PrimitiveBlocks< FloatType > blocks = PrimitiveBlocks.of( view ).threadSafe();
 

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static class	PrimitiveBlocks.OnFallback

Method Summary

Modifier and Type	Method and Description
default void	copy(int[] srcPos, Object dest, int[] size) Copy a block from the (T-typed) source into primitive arrays (of the appropriate type).
void	copy(Interval interval, Object dest) Copy a block from the (T-typed) source into primitive arrays (of the appropriate type).
default void	copy(long[] srcPos, Object dest, int[] size) Copy a block from the (T-typed) source into primitive arrays (of the appropriate type).
PrimitiveBlocks<T>	independentCopy()
static <T extends NativeType<T>> PrimitiveBlocks<T>	of(RandomAccessible<T> ra) Create a PrimitiveBlocks accessor for an arbitrary RandomAccessible source.
static <T extends NativeType<T>> PrimitiveBlocks<T>	of(RandomAccessible<T> ra, PrimitiveBlocks.OnFallback onFallback) Create a PrimitiveBlocks accessor for an arbitrary RandomAccessible source.
PrimitiveBlocks<T>	threadSafe() Get a thread-safe version of this PrimitiveBlocks.

Methods inherited from interface net.imglib2.Typed

getType

Methods inherited from interface net.imglib2.EuclideanSpace

numDimensions

Method Detail

copy

void copy(Interval interval,
          Object dest)

Copy a block from the (T-typed) source into primitive arrays (of the appropriate type).

Parameters:

interval - position and size of the block to copy

dest - primitive array to copy into. Must correspond to T, for example, if T is UnsignedByteType then dest must be byte[].

copy

default void copy(long[] srcPos,
                  Object dest,
                  int[] size)

Copy a block from the (T-typed) source into primitive arrays (of the appropriate type).

Parameters:

srcPos - min coordinate of the block to copy

dest - primitive array to copy into. Must correspond to T, for example, if T is UnsignedByteType then dest must be byte[].

size - the size of the block to copy

copy

default void copy(int[] srcPos,
                  Object dest,
                  int[] size)

Copy a block from the (T-typed) source into primitive arrays (of the appropriate type).

Parameters:

srcPos - min coordinate of the block to copy

dest - primitive array to copy into. Must correspond to T, for example, if T is UnsignedByteType then dest must be byte[].

size - the size of the block to copy

threadSafe

PrimitiveBlocks<T> threadSafe()

Get a thread-safe version of this PrimitiveBlocks. (Implemented as a wrapper that makes ThreadLocal copies).

independentCopy

PrimitiveBlocks<T> independentCopy()

of

static <T extends NativeType<T>> PrimitiveBlocks<T> of(RandomAccessible<T> ra)

Create a PrimitiveBlocks accessor for an arbitrary RandomAccessible source. Many View constructions (that ultimately end in CellImg, ArrayImg, etc.) are understood and will be handled by an optimized copier.

If the source RandomAccessible cannot be understood, a warning is printed, and a fall-back implementation (based on LoopBuilder) is returned.

The returned PrimitiveBlocks is not thread-safe in general. Use threadSafe() to obtain a thread-safe instance, e.g., PrimitiveBlocks.of(view).threadSafe().

Type Parameters:

T - pixel type

Parameters:

ra - the source

Returns:

a PrimitiveBlocks accessor for ra.

of

static <T extends NativeType<T>> PrimitiveBlocks<T> of(RandomAccessible<T> ra,
                                                       PrimitiveBlocks.OnFallback onFallback)

Create a PrimitiveBlocks accessor for an arbitrary RandomAccessible source. Many View constructions (that ultimately end in CellImg, ArrayImg, etc.) are understood and will be handled by an optimized copier.

If the source RandomAccessible cannot be understood, a fall-back implementation (based on LoopBuilder) has to be used. The onFallback argument specifies how to handle this case:

• ACCEPT: silently accept fall-back
• WARN: accept fall-back, but print a warning explaining why the input ra requires fall-back
• FAIL: throw IllegalArgumentException explaining why the input ra requires fall-back

The returned PrimitiveBlocks is not thread-safe in general. Use threadSafe() to obtain a thread-safe instance, e.g., PrimitiveBlocks.of(view).threadSafe().

Type Parameters:

T - pixel type

Parameters:

ra - the source

Returns:

a PrimitiveBlocks accessor for ra.