ch.systemsx.cisd.hdf5

Interface IHDF5OpaqueReader

All Known Subinterfaces:

IHDF5OpaqueWriter

All Known Implementing Classes:

HDF5OpaqueReader, HDF5OpaqueWriter

public interface IHDF5OpaqueReader

An interface that provides methods for reading any data sets as byte arrays (as 'opaque data', just like ordinary file systems treat files). This is particularly useful for opaque data types, which are "black boxes" to the HDF5 library.

Obtain an object implementing this interface by calling IHDF5Reader.opaque().

Method Summary

Modifier and Type	Method and Description
byte[]	getArrayAttr(java.lang.String objectPath, java.lang.String attributeName) Gets the byte array values of an attribute attributeName of object objectPath.
java.lang.Iterable<HDF5DataBlock<byte[]>>	getArrayNaturalBlocks(java.lang.String dataSetPath) Provides all natural blocks of this one-dimensional data set to iterate over.
byte[]	readArray(java.lang.String objectPath) Reads the data set objectPath as byte array.
byte[]	readArrayBlock(java.lang.String objectPath, int blockSize, long blockNumber) Reads a block from data set objectPath as byte array.
byte[]	readArrayBlockWithOffset(java.lang.String objectPath, int blockSize, long offset) Reads a block from data set objectPath as byte array.
int	readArrayToBlockWithOffset(java.lang.String objectPath, byte[] buffer, int blockSize, long offset, int memoryOffset) Reads a block from data set objectPath as byte array into buffer.
java.lang.String	tryGetOpaqueTag(java.lang.String objectPath) Returns the tag of the opaque data type associated with objectPath, or null, if objectPath is not of an opaque data type (i.e.
HDF5OpaqueType	tryGetOpaqueType(java.lang.String objectPath) Returns the opaque data type or null, if objectPath is not of such a data type.

Method Detail

tryGetOpaqueTag

java.lang.String tryGetOpaqueTag(java.lang.String objectPath)

Returns the tag of the opaque data type associated with objectPath, or null, if objectPath is not of an opaque data type (i.e. if reader.getDataSetInformation(objectPath).getTypeInformation().getDataClass() != HDF5DataClass.OPAQUE ).

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The tag of the opaque data type, or null.

tryGetOpaqueType

HDF5OpaqueType tryGetOpaqueType(java.lang.String objectPath)

Returns the opaque data type or null, if objectPath is not of such a data type.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The opaque data type, or null.

getArrayAttr

byte[] getArrayAttr(java.lang.String objectPath,
                    java.lang.String attributeName)

Gets the byte array values of an attribute attributeName of object objectPath. The bytes read will be in the native byte-order of the machine but will otherwise be unchanged.

readArray

byte[] readArray(java.lang.String objectPath)

Reads the data set objectPath as byte array. The bytes read will be in the native byte-order of the machine and will be ordered 'row-first' in the case of multi-dimensional data sets, but will otherwise be unchanged.

Parameters:

objectPath - The name (including path information) of the data set object in the file.

Returns:

The data read from the data set.

readArrayBlock

byte[] readArrayBlock(java.lang.String objectPath,
                      int blockSize,
                      long blockNumber)
               throws HDF5JavaException

Reads a block from data set objectPath as byte array. The bytes read will be in the native byte-order of the machine, but will otherwise be unchanged. Must not be called for data sets of rank other than 1 and must not be called on Strings!

Parameters:

objectPath - The name (including path information) of the data set object in the file.

blockSize - The block size in numbers of elements (this will be the length of the byte[] returned, divided by the size of one element).

blockNumber - The number of the block to read (starting with 0, offset: multiply with blockSize).

Returns:

The data block read from the data set.

Throws:

HDF5JavaException - If the data set is not of rank 1 or is a String.

readArrayBlockWithOffset

byte[] readArrayBlockWithOffset(java.lang.String objectPath,
                                int blockSize,
                                long offset)
                         throws HDF5JavaException

Reads a block from data set objectPath as byte array. The bytes read will be in the native byte-order of the machine, but will otherwise be unchanged. Must not be called for data sets of rank other than 1 and must not be called on Strings!

Parameters:

objectPath - The name (including path information) of the data set object in the file.

blockSize - The block size in numbers of elements (this will be the length of the byte[] returned, divided by the size of one element).

offset - The offset of the block to read as number of elements (starting with 0).

Returns:

The data block read from the data set.

Throws:

HDF5JavaException - If the data set is not of rank 1.

readArrayToBlockWithOffset

int readArrayToBlockWithOffset(java.lang.String objectPath,
                               byte[] buffer,
                               int blockSize,
                               long offset,
                               int memoryOffset)
                        throws HDF5JavaException

Reads a block from data set objectPath as byte array into buffer. The bytes read will be in the native byte-order of the machine, but will otherwise be unchanged. Must not be called for data sets of rank other than 1 and must not be called on Strings!

Parameters:

objectPath - The name (including path information) of the data set object in the file.

buffer - The buffer to read the values in.

blockSize - The block size in numbers of elements (this will be the length of the byte[] returned, divided by the size of one element).

offset - The offset of the block in the data set as number of elements (zero-based).

memoryOffset - The offset of the block in buffer as number of elements (zero-based).

Returns:

The effective block size.

Throws:

HDF5JavaException - If the data set is not of rank 1.

getArrayNaturalBlocks

java.lang.Iterable<HDF5DataBlock<byte[]>> getArrayNaturalBlocks(java.lang.String dataSetPath)
                                                         throws HDF5JavaException

Provides all natural blocks of this one-dimensional data set to iterate over. The bytes read will be in the native byte-order of the machine, but will otherwise be unchanged. Must not be called for data sets of rank other than 1 and must not be called on Strings!

Throws:

HDF5JavaException - If the data set is not of rank 1.

See Also:

HDF5DataBlock