Hdf5ImageLoader.SetupImgLoader (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- bdv.AbstractViewerSetupImgLoader<UnsignedShortType,VolatileUnsignedShortType>
- - bdv.img.hdf5.Hdf5ImageLoader.SetupImgLoader

All Implemented Interfaces:

ViewerSetupImgLoader<UnsignedShortType,VolatileUnsignedShortType>, BasicMultiResolutionSetupImgLoader<UnsignedShortType>, BasicSetupImgLoader<UnsignedShortType>, MultiResolutionSetupImgLoader<UnsignedShortType>, SetupImgLoader<UnsignedShortType>

Enclosing class:

Hdf5ImageLoader
```
public class Hdf5ImageLoader.SetupImgLoader
extends AbstractViewerSetupImgLoader<UnsignedShortType,VolatileUnsignedShortType>
implements MultiResolutionSetupImgLoader<UnsignedShortType>
```

Field Summary
- Fields inherited from class bdv.AbstractViewerSetupImgLoader
  type, volatileType

Constructor Summary

Constructors
Modifier Constructor and Description

protected SetupImgLoader(int setupId, MipmapInfo mipmapInfo)

Constructors
Modifier	Constructor and Description
`protected`	`SetupImgLoader(int setupId, MipmapInfo mipmapInfo)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`RandomAccessibleInterval<UnsignedShortType>`	`getImage(int timepointId, int level, ImgLoaderHint... hints)` Get the image at the specified timepoint and resolution level.
`Dimensions`	`getImageSize(int timepointId, int level)` Get the size of an image.
`MipmapInfo`	`getMipmapInfo()`
`double[][]`	`getMipmapResolutions()` Get the sub-sampling factors, indexed by resolution level and dimension.
`AffineTransform3D[]`	`getMipmapTransforms()` Get the transformation from coordinates of the sub-sampled image of a a resolution level to coordinates of the full resolution image.
`protected <T> RandomAccessibleInterval<T>`	`getMissingDataImage(ViewLevelId id, T constant)` For images that are missing in the hdf5, a constant image is created.
`RandomAccessibleInterval<VolatileUnsignedShortType>`	`getVolatileImage(int timepointId, int level, ImgLoaderHint... hints)`
`VoxelDimensions`	`getVoxelSize(int timepointId)` Get the voxel size of an image.
`int`	`numMipmapLevels()` Get number of resolution levels.
`protected <T extends NativeType<T>> RandomAccessibleInterval<T>`	`prepareCachedImage(int timepointId, int level, LoadingStrategy loadingStrategy, T type)` Create a `CellImg` backed by the cache.

Methods inherited from class bdv.AbstractViewerSetupImgLoader
getImage, getImageType, getVolatileImageType

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

Methods inherited from interface mpicbg.spim.data.sequence.MultiResolutionSetupImgLoader
getFloatImage, getFloatImage, getImageSize

Methods inherited from interface mpicbg.spim.data.generic.sequence.BasicSetupImgLoader
getImage, getImageType

- Constructor Detail
  - SetupImgLoader
```
protected SetupImgLoader(int setupId,
                         MipmapInfo mipmapInfo)
```
- Method Detail
  - getImage
```
public RandomAccessibleInterval<UnsignedShortType> getImage(int timepointId,
                                                            int level,
                                                            ImgLoaderHint... hints)
```
    Description copied from interface: BasicMultiResolutionSetupImgLoader
    
    Get the image at the specified timepoint and resolution level.
    The returned image has pixel type T (an instance of T may be obtained by BasicSetupImgLoader.getImageType()).
    
    Specified by:
    
    getImage in interface BasicMultiResolutionSetupImgLoader<UnsignedShortType>
    
    Parameters:
    
    timepointId - timepoint for which to retrieve the image.
    
    level - resolution level for which to retrieve the image.
    
    hints - optional hints regarding how to load the image.
    
    Returns:
    
    image of type T.
  - getVolatileImage
```
public RandomAccessibleInterval<VolatileUnsignedShortType> getVolatileImage(int timepointId,
                                                                            int level,
                                                                            ImgLoaderHint... hints)
```
    Specified by:
    
    getVolatileImage in interface ViewerSetupImgLoader<UnsignedShortType,VolatileUnsignedShortType>
  - prepareCachedImage
```
protected <T extends NativeType<T>> RandomAccessibleInterval<T> prepareCachedImage(int timepointId,
                                                                                   int level,
                                                                                   LoadingStrategy loadingStrategy,
                                                                                   T type)
```
    Create a CellImg backed by the cache.
  - getMissingDataImage
```
protected <T> RandomAccessibleInterval<T> getMissingDataImage(ViewLevelId id,
                                                              T constant)
```
    For images that are missing in the hdf5, a constant image is created. If the dimension of the missing image is known (see Hdf5ImageLoader.getDimsAndExistence(ViewLevelId)) then use that. Otherwise create a 1x1x1 image.
  - getMipmapInfo
```
public MipmapInfo getMipmapInfo()
```
  - getMipmapResolutions
```
public double[][] getMipmapResolutions()
```
    Description copied from interface: BasicMultiResolutionSetupImgLoader
    
    Get the sub-sampling factors, indexed by resolution level and dimension. For example, a sub-sampling factor of 2 means the respective resolution level is scaled by 0.5 in the respective dimension.
    
    Specified by:
    
    getMipmapResolutions in interface BasicMultiResolutionSetupImgLoader<UnsignedShortType>
    
    Returns:
    
    sub-sampling factors, indexed by resolution level and dimension.
  - getMipmapTransforms
```
public AffineTransform3D[] getMipmapTransforms()
```
    Description copied from interface: BasicMultiResolutionSetupImgLoader
    
    Get the transformation from coordinates of the sub-sampled image of a a resolution level to coordinates of the full resolution image. The array of transforms is indexed by resolution level.
    
    Specified by:
    
    getMipmapTransforms in interface BasicMultiResolutionSetupImgLoader<UnsignedShortType>
    
    Returns:
    
    array with one transformation for each mipmap level.
  - numMipmapLevels
```
public int numMipmapLevels()
```
    Description copied from interface: BasicMultiResolutionSetupImgLoader
    
    Get number of resolution levels.
    
    Specified by:
    
    numMipmapLevels in interface BasicMultiResolutionSetupImgLoader<UnsignedShortType>
    
    Returns:
    
    number of resolution levels.
  - getImageSize
```
public Dimensions getImageSize(int timepointId,
                               int level)
```
    Description copied from interface: MultiResolutionSetupImgLoader
    
    Get the size of an image. If possible, load only the meta-data for the specified image. Note, that this should not get the meta-data from the SequenceDescription but pull it from the image file.
    
    Specified by:
    
    getImageSize in interface MultiResolutionSetupImgLoader<UnsignedShortType>
    
    Parameters:
    
    timepointId - timepoint for which to retrieve the image size.
    
    level - resolution level for which to retrieve the image size.
    
    Returns:
    
    the image size, or null if it could not be determined.
  - getVoxelSize
```
public VoxelDimensions getVoxelSize(int timepointId)
```
    Description copied from interface: SetupImgLoader
    
    Get the voxel size of an image. If possible, load only the meta-data for the specified image. Note, that this should not get the meta-data from the SequenceDescription but pull it from the image file.
    
    Specified by:
    
    getVoxelSize in interface SetupImgLoader<UnsignedShortType>
    
    Parameters:
    
    timepointId - timepoint for which to retrieve the voxel size.
    
    Returns:
    
    the voxel size, or null if it could not be determined.

Class Hdf5ImageLoader.SetupImgLoader

Field Summary

Fields inherited from class bdv.AbstractViewerSetupImgLoader

Constructor Summary

Method Summary

Methods inherited from class bdv.AbstractViewerSetupImgLoader

Methods inherited from class java.lang.Object

Methods inherited from interface mpicbg.spim.data.sequence.MultiResolutionSetupImgLoader

Methods inherited from interface mpicbg.spim.data.generic.sequence.BasicSetupImgLoader

Constructor Detail

SetupImgLoader

Method Detail

getImage

getVolatileImage

prepareCachedImage

getMissingDataImage

getMipmapInfo

getMipmapResolutions

getMipmapTransforms

numMipmapLevels

getImageSize

getVoxelSize