Hdf5ImageLoader (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- bdv.img.hdf5.Hdf5ImageLoader

All Implemented Interfaces:

ViewerImgLoader, BasicImgLoader, BasicMultiResolutionImgLoader, ImgLoader, MultiResolutionImgLoader
```
public class Hdf5ImageLoader
extends Object
implements ViewerImgLoader, MultiResolutionImgLoader
```

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

class Hdf5ImageLoader.SetupImgLoader

Nested Classes
Modifier and Type	Class and Description
`class`	`Hdf5ImageLoader.SetupImgLoader`

Field Summary

Fields
Modifier and Type	Field and Description
`protected VolatileGlobalCellCache`	`cache`
`protected HashMap<ViewLevelId,DimsAndExistence>`	`cachedDimsAndExistence` Maps `ViewLevelId` (timepoint, setup, level) to `DimsAndExistence`.
`protected ch.systemsx.cisd.hdf5.IHDF5Reader`	`existingHdf5Reader` The `Hdf5ImageLoader` can be constructed with an existing `IHDF5Reader` which if non-null will be used instead of creating a new one on `hdf5File`.
`protected FetcherThreads`	`fetchers`
`protected bdv.img.hdf5.IHDF5Access`	`hdf5Access`
`protected File`	`hdf5File`
`protected int`	`maxNumLevels`
`protected ArrayList<Partition>`	`partitions` List of partitions if the dataset is split across several files
`protected AbstractSequenceDescription<?,?,?>`	`sequenceDescription`
`protected HashMap<Integer,Hdf5ImageLoader.SetupImgLoader>`	`setupImgLoaders` Maps setup id to `Hdf5ImageLoader.SetupImgLoader`.
`protected Hdf5VolatileShortArrayLoader`	`shortLoader`

Constructor Summary

Constructors
Modifier	Constructor and Description
	`Hdf5ImageLoader(File hdf5File, ArrayList<Partition> hdf5Partitions, AbstractSequenceDescription<?,?,?> sequenceDescription)`
	`Hdf5ImageLoader(File hdf5File, ArrayList<Partition> hdf5Partitions, AbstractSequenceDescription<?,?,?> sequenceDescription, boolean doOpen)`
`protected`	`Hdf5ImageLoader(File hdf5File, ch.systemsx.cisd.hdf5.IHDF5Reader existingHdf5Reader, ArrayList<Partition> hdf5Partitions, AbstractSequenceDescription<?,?,?> sequenceDescription, boolean doOpen)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`close()` Clear the cache and close the hdf5 file.
`boolean`	`existsImageData(ViewLevelId id)` Checks whether the given image data is present in the hdf5.
`VolatileGlobalCellCache`	`getCacheControl()`
`DimsAndExistence`	`getDimsAndExistence(ViewLevelId id)`
`File`	`getHdf5File()`
`ArrayList<Partition>`	`getPartitions()`
`Hdf5ImageLoader.SetupImgLoader`	`getSetupImgLoader(int setupId)` Get the `BasicMultiResolutionSetupImgLoader` for the specified view setup.
`Hdf5VolatileShortArrayLoader`	`getShortArrayLoader()`
`void`	`initCachedDimensionsFromHdf5(boolean background)`
`void`	`printMipmapInfo()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - hdf5File
```
protected File hdf5File
```
  - existingHdf5Reader
```
protected ch.systemsx.cisd.hdf5.IHDF5Reader existingHdf5Reader
```
    The Hdf5ImageLoader can be constructed with an existing IHDF5Reader which if non-null will be used instead of creating a new one on hdf5File.
    Note that close() will not close the existingHdf5Reader!
  - hdf5Access
```
protected bdv.img.hdf5.IHDF5Access hdf5Access
```
  - cache
```
protected VolatileGlobalCellCache cache
```
  - fetchers
```
protected FetcherThreads fetchers
```
  - shortLoader
```
protected Hdf5VolatileShortArrayLoader shortLoader
```
  - setupImgLoaders
```
protected final HashMap<Integer,Hdf5ImageLoader.SetupImgLoader> setupImgLoaders
```
    Maps setup id to Hdf5ImageLoader.SetupImgLoader.
  - partitions
```
protected final ArrayList<Partition> partitions
```
    List of partitions if the dataset is split across several files
  - maxNumLevels
```
protected int maxNumLevels
```
  - cachedDimsAndExistence
```
protected final HashMap<ViewLevelId,DimsAndExistence> cachedDimsAndExistence
```
    Maps ViewLevelId (timepoint, setup, level) to DimsAndExistence. Every entry is either null or the existence and dimensions of one image. This is filled in when an image is loaded for the first time.
  - sequenceDescription
```
protected final AbstractSequenceDescription<?,?,?> sequenceDescription
```
- Constructor Detail
  - Hdf5ImageLoader
```
public Hdf5ImageLoader(File hdf5File,
                       ArrayList<Partition> hdf5Partitions,
                       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,
                       AbstractSequenceDescription<?,?,?> sequenceDescription,
                       boolean doOpen)
```
  - Hdf5ImageLoader
```
protected Hdf5ImageLoader(File hdf5File,
                          ch.systemsx.cisd.hdf5.IHDF5Reader existingHdf5Reader,
                          ArrayList<Partition> hdf5Partitions,
                          AbstractSequenceDescription<?,?,?> sequenceDescription,
                          boolean doOpen)
```
- Method Detail
  - close
```
public void close()
```
    Clear the cache and close the hdf5 file. Images that were obtained from this loader before close() will stop working. Requesting images after close() will cause the hdf5 file to be reopened (with a new cache).
  - initCachedDimensionsFromHdf5
```
public void initCachedDimensionsFromHdf5(boolean background)
```
  - getHdf5File
```
public File getHdf5File()
```
  - getPartitions
```
public ArrayList<Partition> getPartitions()
```
  - getCacheControl
```
public VolatileGlobalCellCache getCacheControl()
```
    Specified by:
    
    getCacheControl in interface ViewerImgLoader
  - getShortArrayLoader
```
public Hdf5VolatileShortArrayLoader getShortArrayLoader()
```
  - 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)
```
    Description copied from interface: BasicMultiResolutionImgLoader
    
    Get the BasicMultiResolutionSetupImgLoader for the specified view setup.
    
    Specified by:
    
    getSetupImgLoader in interface ViewerImgLoader
    
    Specified by:
    
    getSetupImgLoader in interface BasicImgLoader
    
    Specified by:
    
    getSetupImgLoader in interface BasicMultiResolutionImgLoader
    
    Specified by:
    
    getSetupImgLoader in interface ImgLoader
    
    Specified by:
    
    getSetupImgLoader in interface MultiResolutionImgLoader
    
    Parameters:
    
    setupId - view setup for which to get the BasicMultiResolutionSetupImgLoader.
    
    Returns:
    
    BasicMultiResolutionSetupImgLoader for the specified view setup.

Class Hdf5ImageLoader

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

hdf5File

existingHdf5Reader

hdf5Access

cache

fetchers

shortLoader

setupImgLoaders

partitions

maxNumLevels

cachedDimsAndExistence

sequenceDescription

Constructor Detail

Hdf5ImageLoader

Hdf5ImageLoader

Hdf5ImageLoader

Method Detail

close

initCachedDimensionsFromHdf5

getHdf5File

getPartitions

getCacheControl

getShortArrayLoader

existsImageData

getDimsAndExistence

printMipmapInfo

getSetupImgLoader