Module org.bigdataviewer.core

Package bdv.img.n5

Class N5ImageLoader

java.lang.Object

bdv.img.n5.N5ImageLoader

All Implemented Interfaces:

ViewerImgLoader, mpicbg.spim.data.generic.sequence.BasicImgLoader, mpicbg.spim.data.generic.sequence.BasicMultiResolutionImgLoader, mpicbg.spim.data.sequence.ImgLoader, mpicbg.spim.data.sequence.MultiResolutionImgLoader

public class N5ImageLoader
extends Object
implements ViewerImgLoader, mpicbg.spim.data.sequence.MultiResolutionImgLoader

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
class	N5ImageLoader.SetupImgLoader<T extends net.imglib2.type.NativeType<T>,V extends net.imglib2.Volatile<T> & net.imglib2.type.NativeType<V>>

Constructor Summary

Constructors

Constructor	Description
N5ImageLoader(File n5File, mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<?,?,?> sequenceDescription)
N5ImageLoader(URI n5URI, mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<?,?,?> sequenceDescription)
N5ImageLoader(org.janelia.saalfeldlab.n5.N5Reader n5Reader, URI n5URI, mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<?,?,?> sequenceDescription)

Method Summary

Modifier and Type	Method	Description
void	close()	Clear the cache.
static SimpleCacheArrayLoader<?>	createCacheArrayLoader(org.janelia.saalfeldlab.n5.N5Reader n5, String pathName)
protected N5Properties	createN5PropertiesInstance()	Create a new N5Properties (provides metadata and resolves dataset paths).
CacheControl	getCacheControl()
File	getN5File()
URI	getN5URI()
N5ImageLoader.SetupImgLoader<?,?>	getSetupImgLoader(int setupId)
protected org.janelia.saalfeldlab.n5.N5Reader	instantiateN5Reader()	Create a new N5Reader.
Future<Void>	prefetch(int parallelism)	Touch all metadata in advance in parallel so the N5-API caches them.
protected <T extends net.imglib2.type.NativeType<T>> net.imglib2.RandomAccessibleInterval<T>	prepareCachedImage(String datasetPath, int setupId, int timepointId, int level, net.imglib2.cache.volatiles.CacheHints cacheHints, T type)	Create a CellImg backed by the cache.
void	setCreatedSharedQueue(SharedQueue createdSharedQueue)	Use the given SharedQueue to asynchronously load blocks.
void	setNumFetcherThreads(int n)	Set the number of fetcher threads that will be created to asynchronously load blocks.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

N5ImageLoader

public N5ImageLoader(URI n5URI,
                     mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<?,?,?> sequenceDescription)

N5ImageLoader

public N5ImageLoader(File n5File,
                     mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<?,?,?> sequenceDescription)

N5ImageLoader

public N5ImageLoader(org.janelia.saalfeldlab.n5.N5Reader n5Reader,
                     URI n5URI,
                     mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<?,?,?> sequenceDescription)

Method Detail

getN5URI

public URI getN5URI()

getN5File

public File getN5File()

instantiateN5Reader

protected org.janelia.saalfeldlab.n5.N5Reader instantiateN5Reader()

Create a new N5Reader.

Can be overridden by subclasses (rather than only having the option to provide an instance at construction time).

Returns:

a new N5Reader instance

createN5PropertiesInstance

protected N5Properties createN5PropertiesInstance()

Create a new N5Properties (provides metadata and resolves dataset paths).

Can be overridden by subclasses to adapt to different metadata schemes and storage layouts.

Returns:

a new N5Properties instance.

prefetch

public Future<Void> prefetch(int parallelism)

Touch all metadata in advance in parallel so the N5-API caches them.

prefetch() completes immediately. The prefetching is done asynchronously in a new ForkJoinPool with the indicated parallelism level. The returned Future can be used to wait for completion of the async prefetching.

Parameters:

parallelism - the parallelism level

Returns:

represents completion of the prefetching

setNumFetcherThreads

public void setNumFetcherThreads(int n)

Description copied from interface: ViewerImgLoader

Set the number of fetcher threads that will be created to asynchronously load blocks. It is permitted to set n=0, but that means that the volatile versions of images may not work correctly.

This is an optional operation, i.e., some ImgLoader implementations may just ignore it.

This method should be called before using the image loader, otherwise it might not have the desired effect.

Specified by:

setNumFetcherThreads in interface ViewerImgLoader

setCreatedSharedQueue

public void setCreatedSharedQueue(SharedQueue createdSharedQueue)

Description copied from interface: ViewerImgLoader

Use the given SharedQueue to asynchronously load blocks.

This is an optional operation, i.e., some ImgLoader implementations may just ignore it.

This method should be called before using the image loader, otherwise it might not have the desired effect.

Specified by:

setCreatedSharedQueue in interface ViewerImgLoader

close

public void close()

Clear the cache. Images that were obtained from this loader before close() will stop working. Requesting images after close() will cause the n5 to be reopened (with a new cache).

getSetupImgLoader

public N5ImageLoader.SetupImgLoader<?,?> getSetupImgLoader(int setupId)

Specified by:

getSetupImgLoader in interface mpicbg.spim.data.generic.sequence.BasicImgLoader

Specified by:

getSetupImgLoader in interface mpicbg.spim.data.generic.sequence.BasicMultiResolutionImgLoader

Specified by:

getSetupImgLoader in interface mpicbg.spim.data.sequence.ImgLoader

Specified by:

getSetupImgLoader in interface mpicbg.spim.data.sequence.MultiResolutionImgLoader

Specified by:

getSetupImgLoader in interface ViewerImgLoader

getCacheControl

public CacheControl getCacheControl()

Specified by:

getCacheControl in interface ViewerImgLoader

prepareCachedImage

protected <T extends net.imglib2.type.NativeType<T>> net.imglib2.RandomAccessibleInterval<T> prepareCachedImage(String datasetPath,
                                                                                                                int setupId,
                                                                                                                int timepointId,
                                                                                                                int level,
                                                                                                                net.imglib2.cache.volatiles.CacheHints cacheHints,
                                                                                                                T type)

Create a CellImg backed by the cache.

createCacheArrayLoader

public static SimpleCacheArrayLoader<?> createCacheArrayLoader(org.janelia.saalfeldlab.n5.N5Reader n5,
                                                               String pathName)
                                                        throws IOException

Throws:

IOException