io.scif.img.cell

Class SCIFIOCellImg<T extends net.imglib2.type.NativeType<T>,A extends net.imglib2.img.basictypeaccess.DataAccess>

java.lang.Object

net.imglib2.img.AbstractImg<T>

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

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

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

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

io.scif.img.cell.SCIFIOCellImg<T,A>

All Implemented Interfaces:

Iterable<T>, net.imglib2.Dimensions, net.imglib2.EuclideanSpace, net.imglib2.img.Img<T>, net.imglib2.img.NativeImg<T,A>, net.imglib2.Interval, net.imglib2.IterableInterval<T>, net.imglib2.IterableRealInterval<T>, net.imglib2.RandomAccessible<T>, net.imglib2.RandomAccessibleInterval<T>, net.imglib2.RealInterval, net.imglib2.Typed<T>, org.scijava.Disposable

public class SCIFIOCellImg<T extends net.imglib2.type.NativeType<T>,A extends net.imglib2.img.basictypeaccess.DataAccess>
extends net.imglib2.cache.img.CachedCellImg<T,A>
implements org.scijava.Disposable

CachedCellImg implementation backed by a SCIFIO Reader.

Author:

Mark Hiner, Tobias Pietzsch

Nested Class Summary

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

net.imglib2.img.cell.LazyCellImg.Get<T>, net.imglib2.img.cell.LazyCellImg.LazyCells<T extends net.imglib2.img.cell.Cell<?>>

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

net.imglib2.img.cell.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
SCIFIOCellImg(SCIFIOCellImgFactory<T> factory, net.imglib2.img.cell.CellGrid grid, net.imglib2.util.Fraction entitiesPerPixel, net.imglib2.cache.Cache<Long,net.imglib2.img.cell.Cell<A>> cache, A accessType, net.imglib2.cache.IoSync iosync)

Method Summary

Modifier and Type	Method and Description
SCIFIOCellImg<T,A>	copy()
void	dispose()
SCIFIOCellImgFactory<T>	factory()
net.imglib2.display.ColorTable	getColorTable(int imageIndex, int planeIndex) Returns the ColorTable of the specified image and plane index.
Reader	reader()
void	setLoader(SCIFIOArrayLoader<?> loader)

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

getAccessType, getCache

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

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

Methods inherited from class net.imglib2.img.AbstractNativeImg

createLinkedType, getType, setLinkedType

Methods inherited from class net.imglib2.img.AbstractImg

dimension, dimensions, 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.RandomAccessibleInterval

size, view

Methods inherited from interface net.imglib2.RandomAccessible

getAt, getAt, getAt, randomAccess

Methods inherited from interface net.imglib2.IterableRealInterval

firstElement, iterator, parallelStream, stream

Methods inherited from interface java.lang.Iterable

forEach

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

SCIFIOCellImg

public SCIFIOCellImg(SCIFIOCellImgFactory<T> factory,
                     net.imglib2.img.cell.CellGrid grid,
                     net.imglib2.util.Fraction entitiesPerPixel,
                     net.imglib2.cache.Cache<Long,net.imglib2.img.cell.Cell<A>> cache,
                     A accessType,
                     net.imglib2.cache.IoSync iosync)

Method Detail

getColorTable

public net.imglib2.display.ColorTable getColorTable(int imageIndex,
                                                    int planeIndex)
                                             throws FormatException,
                                                    IOException

Returns the ColorTable of the specified image and plane index.

NB: opens the underlying image.

Throws:

FormatException

IOException

factory

public SCIFIOCellImgFactory<T> factory()

Specified by:

factory in interface net.imglib2.img.Img<T extends net.imglib2.type.NativeType<T>>

Overrides:

factory in class net.imglib2.cache.img.CachedCellImg<T extends net.imglib2.type.NativeType<T>,A extends net.imglib2.img.basictypeaccess.DataAccess>

reader

public Reader reader()

setLoader

public void setLoader(SCIFIOArrayLoader<?> loader)

copy

public SCIFIOCellImg<T,A> copy()

Specified by:

copy in interface net.imglib2.img.Img<T extends net.imglib2.type.NativeType<T>>

Overrides:

copy in class net.imglib2.img.cell.LazyCellImg<T extends net.imglib2.type.NativeType<T>,A extends net.imglib2.img.basictypeaccess.DataAccess>

dispose

public void dispose()

Specified by:

dispose in interface org.scijava.Disposable