ncsa.hdf.object.h5
Class H5CompoundDS

java.lang.Object
  extended byncsa.hdf.object.HObject
      extended byncsa.hdf.object.Dataset
          extended byncsa.hdf.object.CompoundDS
              extended byncsa.hdf.object.h5.H5CompoundDS
All Implemented Interfaces:
DataFormat, java.io.Serializable

public class H5CompoundDS
extends CompoundDS

H5CompoundDS describes a multi-dimension array of HDF5 compound dataset, inheriting CompoundDS.

A HDF5 compound datatype is similar to a struct in C or a common block in Fortran: it is a collection of one or more atomic types or small arrays of such types. Each member of a compound type has a name which is unique within that type, and a byte offset that determines the first byte (smallest byte address) of that member in a compound datum.

There are two basic types of compound datasets, simple compound data and nested compound data. Members of a simple compound dataset are scalar data or array of scalar data. Members of a nested compound dataset can be compound or array of compound data. The current implementation of H5CompoundDS only supports simple compound datasets.

A special case of compound dataset is the one-dimension simple compound data. An one-dimension HDF5 compound array is like an HDF5 Vdata table. Members of the compound dataset are similar to fileds of HDF4 VData table.

ARRAY of compound dataset is not supported in this implementation. ARRAY of compound dataset requires to read the whole data structure instead of read field by field.

How to Select a Subset

Dataset defines APIs for read, write and subet a dataset. No function is defined to select a subset of a data array. The selection is done in an implicit way. Function calls to dimension information such as getSelectedDims() return an array of dimension values, which is a reference to the array in the dataset object. Changes of the array outside the dataset object directly change the values of the array in the dataset object. It is like pointers in C.

The following is an example of how to make a subset. In the example, the dataset is a 4-dimension with size of [200][100][50][10], i.e. dims[0]=200; dims[1]=100; dims[2]=50; dims[3]=10;
We want to select every other data points in dims[1] and dims[2]

     int rank = dataset.getRank();   // number of dimension of the dataset
     long[] dims = dataset.getDims(); // the dimension sizes of the dataset
     long[] selected = dataset.getSelectedDims(); // the selected size of the dataet
     long[] start = dataset.getStartDims(); // the off set of the selection
     long[] stride = dataset.getStride(); // the stride of the dataset
     int[]  selectedIndex = dataset.getSelectedIndex(); // the selected dimensions for display

     // select dim1 and dim2 as 2D data for display,and slice through dim0
     selectedIndex[0] = 1;
     selectedIndex[1] = 2;
     selectedIndex[1] = 0;

     // reset the selection arrays
     for (int i=0; i

 

See Also:
Serialized Form

Field Summary
 
Fields inherited from class ncsa.hdf.object.CompoundDS
isMemberSelected, memberDims, memberNames, memberOrders, memberTypes, numberOfMembers
 
Fields inherited from class ncsa.hdf.object.Dataset
chunkSize, compression, data, datatype, dimNames, dims, H5Z_FILTER_CONFIG_DECODE_ENABLED, H5Z_FILTER_CONFIG_ENCODE_ENABLED, rank, selectedDims, selectedIndex, selectedStride, startDims
 
Fields inherited from class ncsa.hdf.object.HObject
hasAttribute, oid, separator
 
Constructor Summary
H5CompoundDS(FileFormat fileFormat, java.lang.String name, java.lang.String path)
           
H5CompoundDS(FileFormat fileFormat, java.lang.String name, java.lang.String path, long[] oid)
          Creates a H5CompoundDS object with specific name and path.
 
Method Summary
 void close(int did)
          Closes access to this object.
 Dataset copy(Group pgroup, java.lang.String name, long[] dims, java.lang.Object data)
          Copy this dataset to another group.
static Dataset create(java.lang.String name, Group pgroup, long[] dims, java.lang.String[] memberNames, Datatype[] memberDatatypes, int[] memberRanks, int[][] memberDims, java.lang.Object data)
           
static Dataset create(java.lang.String name, Group pgroup, long[] dims, java.lang.String[] memberNames, Datatype[] memberDatatypes, int[] memberSizes, java.lang.Object data)
          creates a new compound dataset
 Datatype getDatatype()
          returns the datatype of this dataset.
 java.util.List getMetadata()
          Loads the metadata such as attributes and type of the the data object into memory if the metadata is not loaded.
 void init()
          Retrieve and initialize dimensions and member information.
 int open()
          Opens access to this object.
 java.lang.Object read()
          Loads the content of this data object into memory if the data of the object is not loaded.
 byte[] readBytes()
          Read data values of this dataset into byte array.
 void removeMetadata(java.lang.Object info)
          Deletes an attribute from this dataset.
 void setName(java.lang.String newName)
          Sets the name of the data object.
 void write(java.lang.Object buf)
          Write data values into file.
 void writeMetadata(java.lang.Object info)
          Creates a new attribute and attached to this dataset if attribute does not exist.
 
Methods inherited from class ncsa.hdf.object.CompoundDS
getMemberCount, getMemberNames, getMemberOrders, getMemberTypes, getMemeberDims, getSelectedMemberCount, getSelectedMemberOrders, isMemberSelected, selectMember, setMemberSelection
 
Methods inherited from class ncsa.hdf.object.Dataset
byteToString, clearData, convertFromUnsignedC, convertToUnsignedC, getChunkSize, getCompression, getData, getDimNames, getDims, getHeight, getRank, getSelectedDims, getSelectedIndex, getStartDims, getStride, getWidth, setData, stringToByte, write
 
Methods inherited from class ncsa.hdf.object.HObject
equalsOID, getFID, getFile, getFileFormat, getName, getOID, getPath, hasAttribute, setPath, toString
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

H5CompoundDS

public H5CompoundDS(FileFormat fileFormat,
                    java.lang.String name,
                    java.lang.String path)

H5CompoundDS

public H5CompoundDS(FileFormat fileFormat,
                    java.lang.String name,
                    java.lang.String path,
                    long[] oid)
Creates a H5CompoundDS object with specific name and path.

Parameters:
fileFormat - the HDF file.
name - the name of this H5CompoundDS.
path - the full path of this H5CompoundDS.
oid - the unique identifier of this data object.
Method Detail

getDatatype

public Datatype getDatatype()
Description copied from class: Dataset
returns the datatype of this dataset.

Specified by:
getDatatype in class Dataset

readBytes

public byte[] readBytes()
                 throws HDF5Exception
Description copied from class: Dataset
Read data values of this dataset into byte array. readBytes() loads data as arry of bytes instead of array of its datatype. For example, for an one-dimension 32-bit integer dataset of size 5, the readBytes() returns of a byte array of size 20 instead of a int array of 5.

readBytes() is most used for copy data values, at which case, data do not need to be changed or displayed.

Specified by:
readBytes in class Dataset
Throws:
HDF5Exception

read

public java.lang.Object read()
                      throws HDF5Exception
Loads the content of this data object into memory if the data of the object is not loaded. If the content is already loaded, it returns the content. It returns null if the data object has no content or it fails to load the data content.

Data is read from file member by member and stored into a list by members. Each member data is an one-dimension array. The array type is determined by the datatype of the member. The data list contains only the data of selected members.

For example, if compound dataset "A" has the following nested structure, and memeber datatypes

 A --> m01 (int)
 A --> m02 (float)
 A --> nest1 --> m11 (char)
 A --> nest1 --> m12 (String)
 A --> nest1 --> nest2 --> m21 (long)
 A --> nest1 --> nest2 --> m22 (double)
 
read() returns a List contains arrays of int, float, char, Stirng, long and double.

Specified by:
read in class Dataset
Returns:
the array of data List.
Throws:
HDF5Exception

write

public void write(java.lang.Object buf)
           throws HDF5Exception
Description copied from class: Dataset
Write data values into file.

Specified by:
write in class Dataset
Parameters:
buf - the data to write
Throws:
HDF5Exception

copy

public Dataset copy(Group pgroup,
                    java.lang.String name,
                    long[] dims,
                    java.lang.Object data)
             throws java.lang.Exception
Description copied from class: Dataset
Copy this dataset to another group.

Specified by:
copy in class Dataset
Parameters:
pgroup - the group which the dataset is copied to.
name - the name of the new dataset.
dims - the dimension sizes of the the new dataset.
data - the data to be copied.
Returns:
the new dataset.
Throws:
java.lang.Exception

getMetadata

public java.util.List getMetadata()
                           throws HDF5Exception
Description copied from interface: DataFormat
Loads the metadata such as attributes and type of the the data object into memory if the metadata is not loaded. If the metadata is loaded, it returns the metadata. The metadata is stored as a collection of metadata ojbects in a List.

Returns:
the list of metadata objects.
Throws:
HDF5Exception
See Also:
List

writeMetadata

public void writeMetadata(java.lang.Object info)
                   throws java.lang.Exception
Creates a new attribute and attached to this dataset if attribute does not exist. Otherwise, just update the value of the attribute.

Parameters:
info - the atribute to attach
Throws:
java.lang.Exception

removeMetadata

public void removeMetadata(java.lang.Object info)
                    throws HDF5Exception
Deletes an attribute from this dataset.

Parameters:
info - the attribute to delete.
Throws:
HDF5Exception

open

public int open()
Description copied from class: HObject
Opens access to this object.

Sub-classes have to implement this interface so that different data objects have their own ways of how the data resources are opened.

Specified by:
open in class HObject
Returns:
the interface identifier for access this object.

close

public void close(int did)
Description copied from class: HObject
Closes access to this object.

Specified by:
close in class HObject
Parameters:
did - the object identifier. Sub-classes have to implement this interface so that different data objects have their own ways of how the data resources are closed.

init

public void init()
Retrieve and initialize dimensions and member information.

Specified by:
init in class Dataset

setName

public void setName(java.lang.String newName)
             throws java.lang.Exception
Sets the name of the data object.

Overrides:
setName in class HObject
Parameters:
newName - the new name of the object.
Throws:
java.lang.Exception

create

public static Dataset create(java.lang.String name,
                             Group pgroup,
                             long[] dims,
                             java.lang.String[] memberNames,
                             Datatype[] memberDatatypes,
                             int[] memberSizes,
                             java.lang.Object data)
                      throws java.lang.Exception
creates a new compound dataset

Parameters:
name - the name of the dataset
pgroup - the parent group
dims - the dimension size
memberNames - the names of compound datatype
memberDatatypes - the datatypes of the compound datatype
memberSizes - the sizes of memeber array
data - the initial data
Returns:
the new compound dataset or null if failed
Throws:
java.lang.Exception

create

public static Dataset create(java.lang.String name,
                             Group pgroup,
                             long[] dims,
                             java.lang.String[] memberNames,
                             Datatype[] memberDatatypes,
                             int[] memberRanks,
                             int[][] memberDims,
                             java.lang.Object data)
                      throws java.lang.Exception
Throws:
java.lang.Exception