org.janelia.saalfeldlab.n5.shard

Interface DatasetAccess<T>

Type Parameters:

T - type of the data contained in the DataBlock

All Known Implementing Classes:

DefaultDatasetAccess

public interface DatasetAccess<T>

Wrap an instantiated DataBlock/block codec hierarchy to implement (single and batch) DataBlock read/write methods.

Method Summary

Modifier and Type	Method and Description
boolean	deleteChunk(PositionValueAccess pva, long[] gridPosition) Deletes the chunk at gridPosition.
boolean	deleteChunks(PositionValueAccess pva, List<long[]> gridPositions) Deletes the chunks at the given positions.
Nesting.NestedGrid	getGrid()
DataBlock<T>	readBlock(PositionValueAccess pva, long[] shardGridPosition, int level) Read a block at shardGridPosition at the given nesting level.
DataBlock<T>	readChunk(PositionValueAccess pva, long[] gridPosition) Read the chunk at the given gridPosition.
List<DataBlock<T>>	readChunks(PositionValueAccess pva, List<long[]> gridPositions) Read the chunks at the given gridPositions.
void	writeBlock(PositionValueAccess pva, DataBlock<T> dataBlock, int level) Write a full block at the given nesting level.
void	writeChunk(PositionValueAccess pva, DataBlock<T> chunk) Writes a chunk to the grid position specified by chunk.
void	writeChunks(PositionValueAccess pva, List<DataBlock<T>> chunks) Writes multiple chunks to the grid positions specified by the respective chunks.
void	writeRegion(PositionValueAccess pva, long[] min, long[] size, N5Writer.DataBlockSupplier<T> chunkSupplier, boolean writeFully)
void	writeRegion(PositionValueAccess pva, long[] min, long[] size, N5Writer.DataBlockSupplier<T> chunkSupplier, boolean writeFully, ExecutorService exec)

Method Detail

readChunk

DataBlock<T> readChunk(PositionValueAccess pva,
                       long[] gridPosition)
                throws N5Exception.N5IOException

Read the chunk at the given gridPosition.

If the requested chunk doesn't exist, then this method will return null. N5IOException will be thrown if something goes wrong reading or decoding data for an existing key.

Parameters:

pva - dataset storage

gridPosition - grid position of the chunks to read

Returns:

the DataBlock or null

Throws:

N5Exception.N5IOException - if any error occurs while reading or decoding the block

readChunks

List<DataBlock<T>> readChunks(PositionValueAccess pva,
                              List<long[]> gridPositions)
                       throws N5Exception.N5IOException

Read the chunks at the given gridPositions.

The returned List<DataBlock<T>> is in the same order as the requested gridPositions. That is, the DataBlock at index i has grid coordinates gridPositions.get(i).

If a requested chunk doesn't exist, then the corresponding element in the result list will be null. (N5IOException will only be thrown if something goes wrong reading or decoding data for an existing key.)

Parameters:

pva - dataset storage

gridPositions - list of grid positions of the chunks to read

Returns:

list of DataBlocks

Throws:

N5Exception.N5IOException - if any error occurs while reading or decoding blocks

writeChunk

void writeChunk(PositionValueAccess pva,
                DataBlock<T> chunk)
         throws N5Exception.N5IOException

Writes a chunk to the grid position specified by chunk.

Throws:

N5Exception.N5IOException

writeChunks

void writeChunks(PositionValueAccess pva,
                 List<DataBlock<T>> chunks)
          throws N5Exception.N5IOException

Writes multiple chunks to the grid positions specified by the respective chunks.

Throws:

N5Exception.N5IOException

deleteChunk

boolean deleteChunk(PositionValueAccess pva,
                    long[] gridPosition)
             throws N5Exception.N5IOException

Deletes the chunk at gridPosition.

Returns:

true if it existed and was deleted.

Throws:

N5Exception.N5IOException

deleteChunks

boolean deleteChunks(PositionValueAccess pva,
                     List<long[]> gridPositions)
              throws N5Exception.N5IOException

Deletes the chunks at the given positions.

Returns:

true if any existed and were deleted.

Throws:

N5Exception.N5IOException

writeRegion

void writeRegion(PositionValueAccess pva,
                 long[] min,
                 long[] size,
                 N5Writer.DataBlockSupplier<T> chunkSupplier,
                 boolean writeFully)
          throws N5Exception.N5IOException

Parameters:

pva -

min - min pixel coordinate of region to write

size - size in pixels of region to write

chunkSupplier - is asked to create chunks within the given region

writeFully - if false, merge existing data in blocks/chunks that overlap the region boundary. if true, override everything.

Throws:

N5Exception.N5IOException

writeRegion

void writeRegion(PositionValueAccess pva,
                 long[] min,
                 long[] size,
                 N5Writer.DataBlockSupplier<T> chunkSupplier,
                 boolean writeFully,
                 ExecutorService exec)
          throws N5Exception,
                 InterruptedException,
                 ExecutionException

Parameters:

pva -

min - min pixel coordinate of region to write

size - size in pixels of region to write

chunkSupplier - is asked to create chunks within the given region. must be thread-safe.

writeFully - if false, merge existing data in blocks/chunks that overlap the region boundary. if true, override everything.

exec - used to parallelize over chunks and blocks

Throws:

N5Exception

InterruptedException

ExecutionException

readBlock

DataBlock<T> readBlock(PositionValueAccess pva,
                       long[] shardGridPosition,
                       int level)
                throws N5Exception.N5IOException

Read a block at shardGridPosition at the given nesting level. The data is read as chunks and then rearranged and assembled into a (large) DataBlock.

The getGridPosition() of the returned DataBlock is the grid position with respect to level. For example, if level==1, then this refers to the position on the shard grid.

Parameters:

pva - dataset storage

shardGridPosition - position of the shard to read (on the shard grid at level)

level - grid level of the shard/block to write.

Returns:

Throws:

N5Exception.N5IOException

writeBlock

void writeBlock(PositionValueAccess pva,
                DataBlock<T> dataBlock,
                int level)
         throws N5Exception.N5IOException

Write a full block at the given nesting level. The block data is given as a (large) DataBlock that will be sliced, rearranged, and written as chunks (level-0 DataBlocks).

dataBlock.getGridPosition() is the grid position with respect to level. For example, if level==1, then this refers to the position on the level-1 shard grid.

Parameters:

pva - dataset storage

dataBlock - block to write

level - grid level of the block to write.

Throws:

N5Exception.N5IOException

getGrid

Nesting.NestedGrid getGrid()