Module org.bigdataviewer.core

Package bdv.img.hdf5

Class Hdf5ImageLoader

java.lang.Object

bdv.img.hdf5.Hdf5ImageLoader

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 Hdf5ImageLoader
extends Object
implements ViewerImgLoader, mpicbg.spim.data.sequence.MultiResolutionImgLoader

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
class	Hdf5ImageLoader.SetupImgLoader<T extends net.imglib2.type.NativeType<T>,V extends net.imglib2.Volatile<T> & net.imglib2.type.NativeType<V>>

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	Hdf5ImageLoader(File hdf5File, ch.systemsx.cisd.hdf5.IHDF5Reader existingHdf5Reader, ArrayList<Partition> hdf5Partitions, mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<?,?,?> sequenceDescription, boolean doOpen)
	Hdf5ImageLoader(File hdf5File, ArrayList<Partition> hdf5Partitions, mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<?,?,?> sequenceDescription)
	Hdf5ImageLoader(File hdf5File, ArrayList<Partition> hdf5Partitions, mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<?,?,?> sequenceDescription, boolean doOpen)

Method Summary

Modifier and Type	Method	Description
void	close()	Clear the cache.
boolean	existsImageData(ViewLevelId id)	Checks whether the given image data is present in the hdf5.
CacheControl	getCacheControl()
DimsAndExistence	getDimsAndExistence(ViewLevelId id)
File	getHdf5File()
ArrayList<Partition>	getPartitions()
Hdf5ImageLoader.SetupImgLoader<?,?>	getSetupImgLoader(int setupId)
void	printMipmapInfo()
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

Hdf5ImageLoader

public Hdf5ImageLoader(File hdf5File,
                       ArrayList<Partition> hdf5Partitions,
                       mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<?,?,?> sequenceDescription)

Parameters:

hdf5File -

hdf5Partitions -

sequenceDescription - the AbstractSequenceDescription. When loading images, this may be used to retrieve additional information for a ViewId, such as setup name, Angle, Channel, etc.

Hdf5ImageLoader

public Hdf5ImageLoader(File hdf5File,
                       ArrayList<Partition> hdf5Partitions,
                       mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<?,?,?> sequenceDescription,
                       boolean doOpen)

Hdf5ImageLoader

protected Hdf5ImageLoader(File hdf5File,
                          ch.systemsx.cisd.hdf5.IHDF5Reader existingHdf5Reader,
                          ArrayList<Partition> hdf5Partitions,
                          mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<?,?,?> sequenceDescription,
                          boolean doOpen)

Method Detail

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).

getHdf5File

public File getHdf5File()

getPartitions

public ArrayList<Partition> getPartitions()

getCacheControl

public CacheControl getCacheControl()

Specified by:

getCacheControl in interface ViewerImgLoader

existsImageData

public boolean existsImageData(ViewLevelId id)

Checks whether the given image data is present in the hdf5. Missing data may be caused by missing partition files

Returns:

true, if the given image data is present.

getDimsAndExistence

public DimsAndExistence getDimsAndExistence(ViewLevelId id)

printMipmapInfo

public void printMipmapInfo()

getSetupImgLoader

public Hdf5ImageLoader.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