visad.data.hdf5.hdf5objects
Class HDF5Dataset

java.lang.Object
  visad.data.hdf5.hdf5objects.HDF5Object
      visad.data.hdf5.hdf5objects.HDF5Dataset

All Implemented Interfaces:

Serializable

Direct Known Subclasses:

HDF5Attribute, HDF5DatasetAdapted

public class HDF5Dataset
extends HDF5Object

This class provides a mechanism to describe properties of datasets and to transfer data between memory and disk. A dataset is composed of a collection of raw data points and four classes of meta data to describe the data points.

The four classes of meta data are:

        Constant Meta Data
        Meta data that is created when the dataset is created and exists unchanged
                for the life of the dataset. For instance, the data type of stored array
                elements is defined when the dataset is created and cannot be subsequently
                changed.
        Persistent Meta Data
                Meta data that is an integral and permanent part of a dataset but can
                change over time. For instance, the size in any dimension can increase
                over time if such an increase is allowed when the dataset was created.
        Memory Meta Data
                Meta data that exists to describe how raw data is organized in the
                application's memory space. For instance, the data type of elements in
                an application array might not be the same as the data type of those
                elements as stored in the HDF5 file.
        Transport Meta Data
                Meta data that is used only during the transfer of raw data from one
                location to another. For instance, the number of processes participating
                in a collective I/O request or hints to the library to control caching
                of raw data.
  

For details of the HDF5 libraries, see the HDF5 Documentation at: http://hdf.ncsa.uiuc.edu/HDF5/doc/

See Also:

Serialized Form

Field Summary

protected long[]	count the selected subset of the dataset
protected Object	data the data array
protected HDF5Dataspace	dataspace the dataspace
protected HDF5Datatype	datatype the datatype
protected long[]	dims the dimensions of the dataset
protected long[]	maxdims the maximum dimensions of the dataset
protected Vector	member_names a list of member names of compound data
protected int	rank the rank of the dataset

Fields inherited from class visad.data.hdf5.hdf5objects.HDF5Object

ATTRIBUTE, DATASET, DATASPACE, DATATYPE, description, GROUP, HDF5FILE, id, LINK, name, shortName, type, UNKNOWN

Constructor Summary

HDF5Dataset()
Constructs a HDF5Dataset

HDF5Dataset(int loc_id, String set_name)
Opens a HDF5Dataset

HDF5Dataset(int loc_id, String set_name, int type_id, int space_id, int create_plist_id)
Creates a dataset at the specified location

HDF5Dataset(String name)
Constructs a HDF5Dataset

Method Summary

static Object	convertUnsignedData(Object data_in) convert unsigned data because Java does not support unsigned integers.
protected void	finalize() finalize() is called by the garbage collector on the object when garbage collection determines that there are no more references to the object.
long[]	getCount() Returns the selected counts of the data
Object	getData() Returns the data array
HDF5Dataspace	getDataspace() Returns the dataspace
HDF5Datatype	getDatatype() Returns the datatype
long[]	getDims() Returns the dimensions of the dataset
long[]	getMaxdims() Returns the maximum dimensions of the dataspace
int	getRank() Returns the rank of the dataset
void	init() initialize the HDF5Dataset: open HDF5 library.
Object	readData() Read the entire dataset from file
Object	readData(int mspace, int fspace) Read the data with specified memory and file space
String	toString() Converts this object to a String representation.
void	writeData(int mspace, int fspace, Object buf) write the data with specified memory and file space
void	writeData(Object buf) write the entire dataset from file

Methods inherited from class visad.data.hdf5.hdf5objects.HDF5Object

getDescription, getID, getName, getShortName, getType, setID, setShortName, setType

Methods inherited from class java.lang.Object

clone, equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

data

protected Object data

the data array

datatype

protected HDF5Datatype datatype

the datatype

dataspace

protected HDF5Dataspace dataspace

the dataspace

rank

protected int rank

the rank of the dataset

dims

protected long[] dims

the dimensions of the dataset

maxdims

protected long[] maxdims

the maximum dimensions of the dataset

count

protected long[] count

the selected subset of the dataset

member_names

protected Vector member_names

a list of member names of compound data

Constructor Detail

HDF5Dataset

public HDF5Dataset()

Constructs a HDF5Dataset

HDF5Dataset

public HDF5Dataset(String name)

Constructs a HDF5Dataset

HDF5Dataset

public HDF5Dataset(int loc_id,
                   String set_name,
                   int type_id,
                   int space_id,
                   int create_plist_id)

Creates a dataset at the specified location

Parameters:

loc_id - Identifier of the file or group to create the dataset within.

set_name - The name of the dataset to create.

type_id - Identifier of the datatype to use when creating the dataset.

space_id - Identifier of the dataspace to use when creating the dataset.

create_plist_id - Identifier of the set creation property list.

HDF5Dataset

public HDF5Dataset(int loc_id,
                   String set_name)

Opens a HDF5Dataset

Parameters:

loc_id - A file, group, or datatype identifier.

set_name - A datatset name.

Method Detail

init

public void init()
          throws HDF5Exception

initialize the HDF5Dataset:

1. open HDF5 library.
2. Set up datatype and dataspace.
3. Set up data ranks and dimensions.

Overrides:

init in class HDF5Object

Throws:

HDF5Exception

readData

public Object readData()
                throws HDF5Exception,
                       NullPointerException

Read the entire dataset from file

Returns:

the data array

Throws:

HDF5Exception

NullPointerException

readData

public Object readData(int mspace,
                       int fspace)
                throws HDF5Exception,
                       NullPointerException

Read the data with specified memory and file space

Parameters:

mspace - the memory space id

fspace - the file space id

Returns:

the data array

Throws:

HDF5Exception

NullPointerException

convertUnsignedData

public static Object convertUnsignedData(Object data_in)
                                  throws HDF5Exception

convert unsigned data because Java does not support unsigned integers.

Throws:

HDF5Exception

writeData

public void writeData(Object buf)
               throws HDF5Exception,
                      NullPointerException

write the entire dataset from file

Throws:

HDF5Exception

NullPointerException

writeData

public void writeData(int mspace,
                      int fspace,
                      Object buf)
               throws HDF5Exception,
                      NullPointerException

write the data with specified memory and file space

Throws:

HDF5Exception

NullPointerException

getData

public Object getData()

Returns the data array

getDatatype

public HDF5Datatype getDatatype()

Returns the datatype

getDataspace

public HDF5Dataspace getDataspace()

Returns the dataspace

getRank

public int getRank()

Returns the rank of the dataset

getDims

public long[] getDims()

Returns the dimensions of the dataset

getMaxdims

public long[] getMaxdims()

Returns the maximum dimensions of the dataspace

getCount

public long[] getCount()

Returns the selected counts of the data

toString

public String toString()

Converts this object to a String representation.

Overrides:

toString in class HDF5Object

Returns:

a string representation of this object

finalize

protected void finalize()
                 throws Throwable

finalize() is called by the garbage collector on the object when garbage collection determines that there are no more references to the object. It is used to dispose of system resources or to perform other cleanup as C++ destructors

Overrides:

finalize in class Object

Throws:

Throwable