ncsa.hdf.object.h4
Class H4Vdata

java.lang.Object
  ncsa.hdf.object.HObject
      ncsa.hdf.object.Dataset
          ncsa.hdf.object.CompoundDS
              ncsa.hdf.object.h4.H4Vdata

All Implemented Interfaces:

java.io.Serializable, DataFormat

public class H4Vdata
extends CompoundDS

H4Vdata describes a multi-dimension array of HDF4 vdata, inheriting CompoundDS.

A vdata is like a table that consists of a collection of records whose values are stored in fixed-length fields. All records have the same structure and all values in each field have the same data type. Vdatas are uniquely identified by a name, a class, and a series of individual field names.

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

 





Version:
  
1.1 9/4/2007
Author:
  
Peter X. Cao
See Also:
Serialized Form






Field Summary




static long
serialVersionUID



           


 
Fields inherited from class ncsa.hdf.object.CompoundDS
separator
 



Constructor Summary
H4Vdata(FileFormat theFile,
        java.lang.String name,
        java.lang.String path)



           
H4Vdata(FileFormat theFile,
        java.lang.String name,
        java.lang.String path,
        long[] oid)



          Creates an H4Vdata object with specific name and path.
 



Method Summary




 void
close(int vsid)



          Closes access to the object.



 Datatype
getDatatype()



          Returns the datatype object of the dataset.



 int
getFieldCount()



          Returns the number of fields.



 int[]
getFieldOrders()



          Returns the orders of fields



 java.util.List
getMetadata()



          Retrieves the metadata such as attributes from file.



 java.util.List
getMetadata(int... attrPropList)



           



 int
getRecordCount()



          Returns the number of records.



 boolean
hasAttribute()



          Check if the object has any attributes attached.



 void
init()



          Initializes the H4Vdata such as dimension sizes of this dataset.



 int
open()



          Opens an existing object such as dataset or group for access.



 java.lang.Object
read()



          Reads the data from file.



 byte[]
readBytes()



          Reads the raw data of the dataset from file to a byte array.



 void
removeMetadata(java.lang.Object info)



          Deletes an existing metadata from this data object.



 void
write(java.lang.Object buf)



          Writes a memory buffer to the dataset in file.



 void
writeMetadata(java.lang.Object info)



          Writes a specific metadata (such as attribute) into file.


 
Methods inherited from class ncsa.hdf.object.CompoundDS
copy, getMemberCount, getMemberNames, getMemberOrders, getMemberTypes, getMemeberDims, getSelectedMemberCount, getSelectedMemberOrders, getSelectedMemberTypes, isMemberSelected, selectMember, setMemberSelection
 
Methods inherited from class ncsa.hdf.object.Dataset
byteToString, clear, clearData, convertFromUnsignedC, convertFromUnsignedC, convertToUnsignedC, convertToUnsignedC, getChunkSize, getCompression, getConvertByteToString, getData, getDimNames, getDims, getHeight, getMaxDims, getRank, getSelectedDims, getSelectedIndex, getSize, getStartDims, getStride, getWidth, isEnumConverted, isString, setConvertByteToString, setData, setEnumConverted, stringToByte, write
 
Methods inherited from class ncsa.hdf.object.HObject
equalsOID, getFID, getFile, getFileFormat, getFullName, getLinkTargetObjName, getName, getOID, getPath, setLinkTargetObjName, setName, setPath, toString
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
 





Field Detail



serialVersionUID
public static final long serialVersionUID


See Also:
Constant Field Values





Constructor Detail



H4Vdata
public H4Vdata(FileFormat theFile,
               java.lang.String name,
               java.lang.String path)





H4Vdata
public H4Vdata(FileFormat theFile,
               java.lang.String name,
               java.lang.String path,
               long[] oid)

Creates an H4Vdata object with specific name and path.
 



Parameters:
theFile - the HDF file.
name - the name of this H4Vdata.
path - the full path of this H4Vdata.
oid - the unique identifier of this data object.





Method Detail



hasAttribute
public boolean hasAttribute()

Description copied from interface: DataFormat
Check if the object has any attributes attached.



Returns:
true if it has any attribute(s), false otherwise.





getDatatype
public Datatype getDatatype()

Description copied from class: Dataset
Returns the datatype object of the dataset.


Specified by:
getDatatype in class Dataset



Returns:
the datatype object of the dataset.





readBytes
public byte[] readBytes()
                 throws HDFException

Description copied from class: Dataset
Reads the raw data of the dataset from file to a byte array.
 

 readBytes() reads raw data to an array 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 an
 int array of 5.
 

 readBytes() can be used to copy data from one dataset to another
 efficiently because the raw data is not converted to its native type, it
 saves memory space and CPU time.


Specified by:
readBytes in class Dataset



Returns:
the byte array of the raw data.
Throws:
HDFException





read
public java.lang.Object read()
                      throws HDFException

Description copied from class: Dataset
Reads the data from file.
 

 read() reads the data from file to a memory buffer and returns the memory
 buffer. The dataset object does not hold the memobry buffer. To store the
 memory buffer in the dataset object, one must call getData().
 

 By default, the whole dataset is read into memory. Users can also select
 subset to read. Subsetting is done in an implicit way.
 

 How to Select a Subset
 

 A selection is specified by three arrays: start, stride and count.
 

 
start: offset of a selection
 
stride: determining how many elements to move in each dimension
 
count: number of elements to select in each dimension
 
 getStartDims(), getStartDims() and getSelectedDims() returns the start,
 stride and count arrays respectively. Applications can make a selection
 by changing the values of the arrays.
 

 The following example shows how to make a subset. In the example, the
 dataset is a 4-dimensional array 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 point 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 < rank; i++) {
     start[i] = 0;
     selected[i] = 1;
     stride[i] = 1;
 }
 
 // set stride to 2 on dim1 and dim2 so that every other data points are selected.
 stride[1] = 2;
 stride[2] = 2;
 
 // set the selection size of dim1 and dim2
 selected[1] = dims[1] / stride[1];
 selected[2] = dims[1] / stride[2];
 
 // when dataset.getData() is called, the slection above will be used since
 // the dimension arrays are passed by reference. Changes of these arrays
 // outside the dataset object directly change the values of these array
 // in the dataset object.
 
 

 For ScalarDS, the memory data buffer is an one-dimensional array of byte,
 short, int, float, double or String type based on the datatype of the
 dataset.
 

 For CompoundDS, the meory data object is an java.util.List object. Each
 element of the list is a data array that corresponds to a compound field.
 

 For example, if compound dataset "comp" has the following nested
 structure, and memeber datatypes
 
 
 comp --> m01 (int)
 comp --> m02 (float)
 comp --> nest1 --> m11 (char)
 comp --> nest1 --> m12 (String)
 comp --> nest1 --> nest2 --> m21 (long)
 comp --> nest1 --> nest2 --> m22 (double)
 
 
 getData() returns a list of six arrays: {int[], float[], char[],
 Stirng[], long[] and double[]}.


Specified by:
read in class Dataset



Returns:
the data read from file.
Throws:
HDFException
See Also:
#getData()}





write
public void write(java.lang.Object buf)
           throws HDFException

Description copied from class: Dataset
Writes a memory buffer to the dataset in file.


Specified by:
write in class Dataset


Parameters:
buf - the data to write
Throws:
HDFException





getMetadata
public java.util.List getMetadata()
                           throws HDFException

Description copied from interface: DataFormat
Retrieves the metadata such as attributes from file.
 

 Metadata such as attributes are stored in a List.



Returns:
the list of metadata objects.
Throws:
HDFException





writeMetadata
public void writeMetadata(java.lang.Object info)
                   throws java.lang.Exception

Description copied from interface: DataFormat
Writes a specific metadata (such as attribute) into file.
 
 

 If an HDF(4&5) attribute exists in file, the method updates its value. 
 If the attribute does not exists in file, it creates the attribute in 
 file and attaches it to the object.
 It will fail to write a new attribute to the object where an attribute 
 with the same name already exists.  
 To update the value of an existing attribute in file, one needs to get 
 the instance of the attribute by getMetadata(), change its values, 
 and use writeMetadata() to write the value.


Parameters:
info - the metadata to write.
Throws:
java.lang.Exception





removeMetadata
public void removeMetadata(java.lang.Object info)
                    throws HDFException

Description copied from interface: DataFormat
Deletes an existing metadata from this data object.


Parameters:
info - the metadata to delete.
Throws:
HDFException





open
public int open()

Description copied from class: HObject
Opens an existing object such as dataset or group for access.
 
 The return value is an object identifier obtained by implementing classes
 such as H5.H5Dopen(). This function is needed to allow other objects to
 be able to access the object. For instance, H5File class uses the open()
 function to obtain object identifier for copyAttributes(int src_id, int
 dst_id) and other purposes. The open() function should be used in pair
 with close(int) function.


Specified by:
open in class HObject



Returns:
the object identifier if successful; otherwise returns a negative
         value.
See Also:
HObject.close(int)





close
public void close(int vsid)

Description copied from class: HObject
Closes access to the object.
 

 Sub-classes must implement this interface because different data objects
 have their own ways of how the data resources are closed.
 

 For example, H5Group.close() calls the ncsa.hdf.hdf5lib.H5.H5Gclose()
 method and closes the group resource specified by the group id.


Specified by:
close in class HObject


Parameters:
vsid - The object identifier.





init
public void init()

Initializes the H4Vdata such as dimension sizes of this dataset.


Specified by:
init in class Dataset








getRecordCount
public int getRecordCount()

Returns the number of records.








getFieldCount
public int getFieldCount()

Returns the number of fields.








getFieldOrders
public int[] getFieldOrders()

Returns the orders of fields








getMetadata
public java.util.List getMetadata(int... attrPropList)
                           throws java.lang.Exception



Throws:
java.lang.Exception