com.bitplane.xt.img

Class ImarisCachedLabelImg<T extends NativeType<T>,A>

java.lang.Object

net.imglib2.img.AbstractImg<T>

net.imglib2.img.AbstractNativeImg<T,A>

net.imglib2.img.cell.AbstractCellImg<T,A,Cell<A>,LazyCellImg.LazyCells<Cell<A>>>

net.imglib2.img.cell.LazyCellImg<T,A>

net.imglib2.cache.img.CachedCellImg<T,A>

com.bitplane.xt.img.ImarisCachedLabelImg<T,A>

Type Parameters:

T - the pixel type

A - the underlying native access type

All Implemented Interfaces:

ImarisImg, Iterable<T>, Dimensions, EuclideanSpace, Img<T>, NativeImg<T,A>, Interval, IterableInterval<T>, IterableRealInterval<T>, RandomAccessible<T>, RandomAccessibleInterval<T>, RealInterval

public class ImarisCachedLabelImg<T extends NativeType<T>,A>
extends CachedCellImg<T,A>
implements ImarisImg

A LazyCellImg that creates empty Cells lazily when they are accessed and sends (modified) Cells to Imaris when memory runs full.

Integer labels on the ImgLib2 side are translated into channels on the Imaris side.

Author:

Tobias Pietzsch

Nested Class Summary

Nested classes/interfaces inherited from class net.imglib2.img.cell.LazyCellImg

LazyCellImg.Get<T>, LazyCellImg.LazyCells<T>

Nested classes/interfaces inherited from class net.imglib2.img.cell.AbstractCellImg

AbstractCellImg.CellImgSampler<C>

Field Summary

Fields inherited from class net.imglib2.img.cell.AbstractCellImg

cells, grid

Fields inherited from class net.imglib2.img.AbstractNativeImg

entitiesPerPixel, linkedType, numEntities

Fields inherited from class net.imglib2.img.AbstractImg

dimension, max, n, numPixels

Constructor Summary

Constructors

Constructor and Description
ImarisCachedLabelImg(ImarisCachedLabelImgFactory<T> factory, Imaris.IDataSetPrx dataset, CellGrid grid, Fraction entitiesPerPixel, Cache<Long,Cell<A>> cache, IoSync<?,?,?> iosync, A accessType)

Method Summary

Modifier and Type	Method and Description
ImgFactory<T>	factory()
ImarisApplication	getApplication() Get the ImarisApplication which holds (the backing cache for) this image.
Imaris.IDataSetPrx	getIDataSetPrx() Get the underlying IDataSet ICE proxy.
void	persist() Persist all changes back to Imaris
void	shutdown() Shutdown the internal IoSync to free resources via IoSync.shutdown().

Methods inherited from class net.imglib2.cache.img.CachedCellImg

getAccessType, getCache

Methods inherited from class net.imglib2.img.cell.LazyCellImg

copy

Methods inherited from class net.imglib2.img.cell.AbstractCellImg

copyDataTo, cursor, getCellGrid, getCells, iterationOrder, localizingCursor, randomAccess, update

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.RandomAccessible

getAt, getAt, getAt, randomAccess

Methods inherited from interface net.imglib2.IterableRealInterval

firstElement, size

Methods inherited from interface java.lang.Iterable

forEach, iterator, spliterator

Methods inherited from interface net.imglib2.Interval

dimension, max, max, max, maxAsLongArray, maxAsPoint, min, min, min, minAsLongArray, minAsPoint, realMax, realMin

Methods inherited from interface net.imglib2.RealInterval

maxAsDoubleArray, maxAsRealPoint, minAsDoubleArray, minAsRealPoint, realMax, realMax, realMin, realMin

Methods inherited from interface net.imglib2.Dimensions

allPositive, allPositive, dimensions, dimensions, dimensionsAsLongArray, dimensionsAsPoint, verify, verify, verifyAllPositive, verifyAllPositive

Methods inherited from interface net.imglib2.EuclideanSpace

numDimensions

Constructor Detail

ImarisCachedLabelImg

public ImarisCachedLabelImg(ImarisCachedLabelImgFactory<T> factory,
                            Imaris.IDataSetPrx dataset,
                            CellGrid grid,
                            Fraction entitiesPerPixel,
                            Cache<Long,Cell<A>> cache,
                            IoSync<?,?,?> iosync,
                            A accessType)

Method Detail

factory

public ImgFactory<T> factory()

Specified by:

factory in interface Img<T extends NativeType<T>>

Overrides:

factory in class CachedCellImg<T extends NativeType<T>,A>

shutdown

public void shutdown()

Shutdown the internal IoSync to free resources via IoSync.shutdown(). No data will be written to disk after shutdown.

persist

public void persist()

Persist all changes back to Imaris

Specified by:

persist in interface ImarisImg

getIDataSetPrx

public Imaris.IDataSetPrx getIDataSetPrx()

Description copied from interface: ImarisImg

Get the underlying IDataSet ICE proxy.

Specified by:

getIDataSetPrx in interface ImarisImg

getApplication

public ImarisApplication getApplication()

Description copied from interface: ImarisImg

Get the ImarisApplication which holds (the backing cache for) this image.

Specified by:

getApplication in interface ImarisImg