public class HDF5ReferenceReader extends java.lang.Object implements IHDF5ReferenceReader
Modifier and Type | Method and Description |
---|---|
java.lang.String[] |
getArrayAttr(java.lang.String objectPath,
java.lang.String attributeName)
Reads a 1D object reference array attribute named attributeName from the object
objectPath, resolving the names of the objects.
|
java.lang.String[] |
getArrayAttr(java.lang.String objectPath,
java.lang.String attributeName,
boolean resolveName)
Reads a 1D object reference array attribute named attributeName from the object
objectPath.
|
java.lang.Iterable<HDF5DataBlock<java.lang.String[]>> |
getArrayNaturalBlocks(java.lang.String dataSetPath)
Provides all natural blocks of this one-dimensional data set to iterate over.
|
java.lang.Iterable<HDF5DataBlock<java.lang.String[]>> |
getArrayNaturalBlocks(java.lang.String dataSetPath,
boolean resolveName)
Provides all natural blocks of this one-dimensional data set to iterate over.
|
java.lang.String |
getAttr(java.lang.String objectPath,
java.lang.String attributeName)
Reads an object reference attribute named attributeName from the object
objectPath, resolving the name of the object.
|
java.lang.String |
getAttr(java.lang.String objectPath,
java.lang.String attributeName,
boolean resolveName)
Reads an object reference attribute named attributeName from the object
objectPath.
|
ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> |
getMDArrayAttr(java.lang.String objectPath,
java.lang.String attributeName)
Reads an object reference array attribute named attributeName from the object
objectPath, resolving the names of the objects.
|
ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> |
getMDArrayAttr(java.lang.String objectPath,
java.lang.String attributeName,
boolean resolveName)
Reads an object reference array attribute named attributeName from the object
objectPath.
|
java.lang.Iterable<HDF5MDDataBlock<ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String>>> |
getMDArrayNaturalBlocks(java.lang.String dataSetPath)
Provides all natural blocks of this multi-dimensional data set to iterate over.
|
java.lang.Iterable<HDF5MDDataBlock<ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String>>> |
getMDArrayNaturalBlocks(java.lang.String dataSetPath,
boolean resolveName)
Provides all natural blocks of this multi-dimensional data set to iterate over.
|
java.lang.String |
read(java.lang.String objectPath)
Reads an object reference from the object objectPath, resolving the name of the
object.
|
java.lang.String |
read(java.lang.String objectPath,
boolean resolveName)
Reads an object reference from the object objectPath.
|
java.lang.String[] |
readArray(java.lang.String objectPath)
Reads an array of object references from the object objectPath, resolving the
names of the objects.
|
java.lang.String[] |
readArray(java.lang.String objectPath,
boolean resolveName)
Reads an array of object references from the object objectPath.
|
java.lang.String[] |
readArrayBlock(java.lang.String objectPath,
int blockSize,
long blockNumber)
Reads a block from an array (of rank 1) of object references from the data set
objectPath, resolving the names of the objects.
|
java.lang.String[] |
readArrayBlock(java.lang.String objectPath,
int blockSize,
long blockNumber,
boolean resolveName)
Reads a block from an array (of rank 1) of object references from the data set
objectPath.
|
java.lang.String[] |
readArrayBlockWithOffset(java.lang.String objectPath,
int blockSize,
long offset)
Reads a block from an array (of rank 1) of object references from the data set
objectPath, resolving the names of the objects.
|
java.lang.String[] |
readArrayBlockWithOffset(java.lang.String objectPath,
int blockSize,
long offset,
boolean resolveName)
Reads a block from an array (of rank 1) of object references from the data set
objectPath.
|
ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> |
readMDArray(java.lang.String objectPath)
Reads an array (or rank N) of object references from the object objectPath,
resolving the names of the objects.
|
ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> |
readMDArray(java.lang.String objectPath,
boolean resolveName)
Reads an array (or rank N) of object references from the object objectPath.
|
ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> |
readMDArrayBlock(java.lang.String objectPath,
int[] blockDimensions,
long[] blockNumber)
Reads a multi-dimensional array of object references from the data set objectPath,
resolving the names of the objects.
|
ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> |
readMDArrayBlock(java.lang.String objectPath,
int[] blockDimensions,
long[] blockNumber,
boolean resolveName)
Reads a multi-dimensional array of object references from the data set objectPath.
|
ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> |
readMDArrayBlockWithOffset(java.lang.String objectPath,
int[] blockDimensions,
long[] offset)
Reads a multi-dimensional array of object references from the data set objectPath,
resolving the names of the objects.
|
ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> |
readMDArrayBlockWithOffset(java.lang.String objectPath,
int[] blockDimensions,
long[] offset,
boolean resolveName)
Reads a multi-dimensional array of object references from the data set objectPath.
|
java.lang.String |
resolvePath(java.lang.String reference)
Resolves the path of a reference which has been read without name resolution.
|
public java.lang.String resolvePath(java.lang.String reference)
IHDF5ReferenceReader
resolvePath
in interface IHDF5ReferenceReader
reference
- Reference encoded as string.IHDF5ReferenceReader.readArray(String, boolean)
public java.lang.String getAttr(java.lang.String objectPath, java.lang.String attributeName)
IHDF5ReferenceReader
IHDF5ReaderConfigurator.noAutoDereference()
).getAttr
in interface IHDF5ReferenceReader
objectPath
- The name (including path information) of the data set object in the file.attributeName
- The name of the attribute to read.public java.lang.String getAttr(java.lang.String objectPath, java.lang.String attributeName, boolean resolveName)
IHDF5ReferenceReader
IHDF5ReaderConfigurator.noAutoDereference()
), a reference can be provided in all
places where an object path is expected. This is considerably faster than resolving the
name/path of the reference if the name/path by itself is not needed.getAttr
in interface IHDF5ReferenceReader
objectPath
- The name (including path information) of the data set object in the file.attributeName
- The name of the attribute to read.resolveName
- If true
, resolves the name of the object referenced,
otherwise returns the references itself.public java.lang.String[] getArrayAttr(java.lang.String objectPath, java.lang.String attributeName)
IHDF5ReferenceReader
IHDF5ReaderConfigurator.noAutoDereference()
).getArrayAttr
in interface IHDF5ReferenceReader
objectPath
- The name (including path information) of the data set object in the file.attributeName
- The name of the attribute to read.public java.lang.String[] getArrayAttr(java.lang.String objectPath, java.lang.String attributeName, boolean resolveName)
IHDF5ReferenceReader
IHDF5ReaderConfigurator.noAutoDereference()
), a reference can be provided in all
places where an object path is expected. This is considerably faster than resolving the
name/path of the reference if the name/path by itself is not needed.getArrayAttr
in interface IHDF5ReferenceReader
objectPath
- The name (including path information) of the data set object in the file.attributeName
- The name of the attribute to read.resolveName
- If true
, resolves the names of the objects referenced,
otherwise returns the references itself.public ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> getMDArrayAttr(java.lang.String objectPath, java.lang.String attributeName)
IHDF5ReferenceReader
IHDF5ReaderConfigurator.noAutoDereference()
).getMDArrayAttr
in interface IHDF5ReferenceReader
objectPath
- The name (including path information) of the data set object in the file.attributeName
- The name of the attribute to read.public ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> getMDArrayAttr(java.lang.String objectPath, java.lang.String attributeName, boolean resolveName)
IHDF5ReferenceReader
IHDF5ReaderConfigurator.noAutoDereference()
), a reference can be provided in all
places where an object path is expected. This is considerably faster than resolving the
name/path of the reference if the name/path by itself is not needed.getMDArrayAttr
in interface IHDF5ReferenceReader
objectPath
- The name (including path information) of the data set object in the file.attributeName
- The name of the attribute to read.resolveName
- If true
, resolves the names of the objects referenced,
otherwise returns the references itself.public java.lang.String read(java.lang.String objectPath)
IHDF5ReferenceReader
IHDF5ReaderConfigurator.noAutoDereference()
).read
in interface IHDF5ReferenceReader
objectPath
- The name (including path information) of the data set object in the file.public java.lang.String read(java.lang.String objectPath, boolean resolveName)
IHDF5ReferenceReader
IHDF5ReaderConfigurator.noAutoDereference()
), a reference can be provided in all
places where an object path is expected. This is considerably faster than resolving the
name/path of the reference if the name/path by itself is not needed.read
in interface IHDF5ReferenceReader
objectPath
- The name (including path information) of the data set object in the file.resolveName
- If true
, resolves the name of the object referenced,
otherwise returns the references itself.public java.lang.String[] readArray(java.lang.String objectPath)
IHDF5ReferenceReader
IHDF5ReaderConfigurator.noAutoDereference()
).readArray
in interface IHDF5ReferenceReader
objectPath
- The name (including path information) of the data set object in the file.public java.lang.String[] readArray(java.lang.String objectPath, boolean resolveName)
IHDF5ReferenceReader
IHDF5ReaderConfigurator.noAutoDereference()
), a reference can be provided in all
places where an object path is expected. This is considerably faster than resolving the
name/path of the reference if the name/path by itself is not needed.readArray
in interface IHDF5ReferenceReader
objectPath
- The name (including path information) of the data set object in the file.resolveName
- If true
, resolves the names of the objects referenced,
otherwise returns the references itself.public java.lang.String[] readArrayBlock(java.lang.String objectPath, int blockSize, long blockNumber)
IHDF5ReferenceReader
IHDF5ReaderConfigurator.noAutoDereference()
).readArrayBlock
in interface IHDF5ReferenceReader
objectPath
- The name (including path information) of the data set object in the file.blockSize
- The block size (this will be the length of the long[]
returned
if the data set is long enough).blockNumber
- The number of the block to read (starting with 0, offset: multiply with
blockSize).public java.lang.String[] readArrayBlock(java.lang.String objectPath, int blockSize, long blockNumber, boolean resolveName)
IHDF5ReferenceReader
IHDF5ReaderConfigurator.noAutoDereference()
), a reference can be provided in all
places where an object path is expected. This is considerably faster than resolving the
name/path of the reference if the name/path by itself is not needed.readArrayBlock
in interface IHDF5ReferenceReader
objectPath
- The name (including path information) of the data set object in the file.blockSize
- The block size (this will be the length of the long[]
returned
if the data set is long enough).blockNumber
- The number of the block to read (starting with 0, offset: multiply with
blockSize).resolveName
- If true
, resolves the names of the objects referenced,
otherwise returns the references itself.public java.lang.String[] readArrayBlockWithOffset(java.lang.String objectPath, int blockSize, long offset)
IHDF5ReferenceReader
IHDF5ReaderConfigurator.noAutoDereference()
).readArrayBlockWithOffset
in interface IHDF5ReferenceReader
objectPath
- The name (including path information) of the data set object in the file.blockSize
- The block size (this will be the length of the long[]
returned).offset
- The offset of the block in the data set to start reading from (starting with
0).public java.lang.String[] readArrayBlockWithOffset(java.lang.String objectPath, int blockSize, long offset, boolean resolveName)
IHDF5ReferenceReader
IHDF5ReaderConfigurator.noAutoDereference()
), a reference can be provided in all
places where an object path is expected. This is considerably faster than resolving the
name/path of the reference if the name/path by itself is not needed.readArrayBlockWithOffset
in interface IHDF5ReferenceReader
objectPath
- The name (including path information) of the data set object in the file.blockSize
- The block size (this will be the length of the long[]
returned).offset
- The offset of the block in the data set to start reading from (starting with
0).resolveName
- If true
, resolves the names of the objects referenced,
otherwise returns the references itself.public ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> readMDArray(java.lang.String objectPath)
IHDF5ReferenceReader
IHDF5ReaderConfigurator.noAutoDereference()
).readMDArray
in interface IHDF5ReferenceReader
objectPath
- The name (including path information) of the data set object in the file.public ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> readMDArray(java.lang.String objectPath, boolean resolveName)
IHDF5ReferenceReader
IHDF5ReaderConfigurator.noAutoDereference()
), a reference can be provided in all
places where an object path is expected. This is considerably faster than resolving the
name/path of the reference if the name/path by itself is not needed.readMDArray
in interface IHDF5ReferenceReader
objectPath
- The name (including path information) of the data set object in the file.resolveName
- If true
, resolves the names of the objects referenced,
otherwise returns the references itself.public ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> readMDArrayBlock(java.lang.String objectPath, int[] blockDimensions, long[] blockNumber)
IHDF5ReferenceReader
IHDF5ReaderConfigurator.noAutoDereference()
).readMDArrayBlock
in interface IHDF5ReferenceReader
objectPath
- The name (including path information) of the data set object in the file.blockDimensions
- The extent of the block in each dimension.blockNumber
- The block number in each dimension (offset: multiply with the
blockDimensions in the according dimension).public ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> readMDArrayBlock(java.lang.String objectPath, int[] blockDimensions, long[] blockNumber, boolean resolveName)
IHDF5ReferenceReader
IHDF5ReaderConfigurator.noAutoDereference()
), a reference can be provided in all
places where an object path is expected. This is considerably faster than resolving the
name/path of the reference if the name/path by itself is not needed.readMDArrayBlock
in interface IHDF5ReferenceReader
objectPath
- The name (including path information) of the data set object in the file.blockDimensions
- The extent of the block in each dimension.blockNumber
- The block number in each dimension (offset: multiply with the
blockDimensions in the according dimension).resolveName
- If true
, resolves the names of the objects referenced,
otherwise returns the references itself.public ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> readMDArrayBlockWithOffset(java.lang.String objectPath, int[] blockDimensions, long[] offset)
IHDF5ReferenceReader
IHDF5ReaderConfigurator.noAutoDereference()
).readMDArrayBlockWithOffset
in interface IHDF5ReferenceReader
objectPath
- The name (including path information) of the data set object in the file.blockDimensions
- The extent of the block in each dimension.offset
- The offset in the data set to start reading from in each dimension.public ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String> readMDArrayBlockWithOffset(java.lang.String objectPath, int[] blockDimensions, long[] offset, boolean resolveName)
IHDF5ReferenceReader
IHDF5ReaderConfigurator.noAutoDereference()
), a reference can be provided in all
places where an object path is expected. This is considerably faster than resolving the
name/path of the reference if the name/path by itself is not needed.readMDArrayBlockWithOffset
in interface IHDF5ReferenceReader
objectPath
- The name (including path information) of the data set object in the file.blockDimensions
- The extent of the block in each dimension.offset
- The offset in the data set to start reading from in each dimension.resolveName
- If true
, resolves the names of the objects referenced,
otherwise returns the references itself.public java.lang.Iterable<HDF5DataBlock<java.lang.String[]>> getArrayNaturalBlocks(java.lang.String dataSetPath) throws HDF5JavaException
IHDF5ReferenceReader
getArrayNaturalBlocks
in interface IHDF5ReferenceReader
HDF5JavaException
- If the data set is not of rank 1.HDF5DataBlock
public java.lang.Iterable<HDF5DataBlock<java.lang.String[]>> getArrayNaturalBlocks(java.lang.String dataSetPath, boolean resolveName) throws HDF5JavaException
IHDF5ReferenceReader
getArrayNaturalBlocks
in interface IHDF5ReferenceReader
HDF5JavaException
- If the data set is not of rank 1.HDF5DataBlock
public java.lang.Iterable<HDF5MDDataBlock<ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String>>> getMDArrayNaturalBlocks(java.lang.String dataSetPath)
IHDF5ReferenceReader
getMDArrayNaturalBlocks
in interface IHDF5ReferenceReader
HDF5MDDataBlock
public java.lang.Iterable<HDF5MDDataBlock<ch.systemsx.cisd.base.mdarray.MDArray<java.lang.String>>> getMDArrayNaturalBlocks(java.lang.String dataSetPath, boolean resolveName)
IHDF5ReferenceReader
getMDArrayNaturalBlocks
in interface IHDF5ReferenceReader
HDF5MDDataBlock