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<h1>
<fieldset>Chapter 3: HDF Object Model</fieldset></h1>
This chapter provides basic information of about the HDF object model. For more
details of the object model, visit the HDF Object Model website at <a href="../../hdf-object/"> /hdf-java-html/hdf-object/ </a>
<ul class="ul">
<li class="add"><a href="ug03objects.html#ug03overview">3.1 Overview</a></li>
<li class="add"><a href="ug03objects.html#ug03definition">3.2 The HDF Object Package</a></li>
<li class="add"><a href="ug03objects.html#ug03hierarchy">3.3 Class Hierarchy</a></li>
<li class="add"><a href="ug03objects.html#ug03application">3.4 Using the HDF Object Package</a></li>
</ul>
<hr noshade="noshade" size="1" />
<h2> <a name="ug03overview" id="ug03overview"></a>3.1 Overview</h2>
<p>HDF files may contain many types of data objects that a scientist
might need. HDFView displays the data objects appropriately according to their
types. For example, a two-dimension dataset with an associated palette
will be displayed as an image. When you open an HDF file with HDFView,
you see the tree structure of an HDF file, showing the objects and their
groupings. You can select an object from the tree to view its content.</p>
<p>
HDF4 (i.e. HDF version 4) is based on the original 1988 version of HDF.
Versions 1, 2, 3, and 4 of HDF were all backward compatible, and HDF4
can access files created by all earlier versions. HDF5 is a completely
new format and library. Although they are conceptually related, HDF5 files
cannot be read by the HDF4 library and vice versa. HDF5 was
designed to address some of the limitations of HDF4 and to address
and exploit current and anticipated requirements of modern systems and
applications.</p>
<p>
HDFView is built on a common HDF object model and suports both versions of HDF.
The HDF object model was designed in such a way that the HDF4 and HDF5 objects
interact with users through a common object layer so the user interface
design will be independent of the file format (HDF4 or HDF5). Such a design
allows the HDFView to support and convert objects of different formats
(HDF4 and HDF5).</p>
<hr noshade size=1 />
<h2>
<a name="ug03definition"></a>3.2 The HDF Object Package</h2>
<p>
The <b>HDF Object Package</b> is a Java package that implements HDF4 and
HDF5 data objects in an object-oriented form. The HDF Java Object Package
provides common standard Java APIs to access both HDF4 and HDF5 files.</p>
<p>The HDF Object Package is <b>NOT</b> a “wrapper” for the native HDF
libraries, and it requires the HDF4 and HDF5 wrappers.
The HDF4 and HDF5 wrappers are separate HDF Java products. For
details about the HDF4 and HDF5 native interfaces, read
<a href="../../JNI/jhi/index.html">
Java HDF Interface (JHI)</a>
and
<a href="../../JNI/jhi5/index.html">
Java HDF5 Interface (JHI5)</a>.</p>
<p>
The HDF Object Package implements higher
level APIs and encapsulates HDF library calls into an object-oriented fashion
for easy access to HDF files. For example, to retrieve data content from an
HDF5 dataset by using the HDF5 library APIs directly, you have to make many
calls, such as, get the datatype information (datatype class, size, sign,
and etc), get the dataspace information (number of dimension, dimension
sizes), and allocate the data buffer. The HDF Object Package puts all these
calls into a single call - read().</p>
<p>The HDF Object Package, <i>ncsa.hdf.object</i>, provides classes that
reflect fundamental concepts to the design of HDF objects. Objects
of HDF5 (group and dataset) and HDF4 (group, multi-dimension array, raster
image, vdata and annotation) are presented as Java classes.</p>
<p>The HDF Object Package has two major goals. First, it simplifies the
process of reading information from or writing data to a file because the
details of accessing the HDF library are encapsulated into respective
classes. Second, HDF4 and HDF5 objects are inherited from the same common object
and interface. Applications can use the HDF Object Package to access
objects from either HDF4 or HDF5 in a uniform way, without accessing the
libraries directly. The following diagram explains the relationship of the
object package, HDF JNI, and application.</p>
<p><b>
HDF Applications <==> HDF Object Package <==> HDF4/5 Java Wrapper (JNI4/5) <==> HDF File
</b></p>
<h2>
<a name="ug03hierarchy"></a>3.3 Class Hierarchy</h2>
<p>
The HDF Object Package implements an abstract data model, and the objects
of the HDF4 and HDF5 data models are represented as instances of the abstract
objects. The abstract class <b>HObject</b> has two fundamental abstract
classes, <b>Group</b> and <b>Dataset</b>, and all HDF5 and HDF4 objects
are a sub-type of one of these abstract classes.</p>
<p>The following figure shows the class hierarchy of the HDF Object Package. In the
following, we give a brief description of these Java classes of HDF objects.
For details, see the Java docs at
<a href="../../javadocs/">javadocs </a>.</p>
<p>
The classes at the top of the class hierarchy are interfaces and abstract
classes. These interfaces and abstract classes define all the necessary public
APIs to retrieve information and data from HDF files. The classes at the bottom
are the implementing classes, which implement the public APIs defined by the
top classes.</p>
<center>
<p><img src="images/class_diagram_object.jpg" />
<br /><b>The class hierarchy of HDF objects</b></p></center>
<br />
<table border="1" cellpadding="3" cellspacing="0" width="100%">
<tr bgcolor="#dbeaf5" class="TableHeadingColor">
<td colspan=2><h2>Interface Summary</h2></td>
</tr>
<tr bgcolor="white" class="TableRowColor">
<td width="15%"><b><i>DataFormat</i></b></td>
<td>DataFormat describes general I/O operations of a data object,
such as read data content or data attributes into memory, write
data content or data attributes onto disk.</td>
</tr>
<tr bgcolor="white" class="TableRowColor">
<td width="15%"><b><i>FileFormat</i></b></td>
<td>FileFormat defines general I/O accessing interface to file resources,
such as open/close a file, and retrieve the file structure.</td>
</tr>
<tr bgcolor="white" class="TableRowColor">
<td width="15%"><b><i>Metadata</i></b></td>
<td>Metadata is a general interface about supporting data.</td>
</tr>
</table>
<br />
<table border="1" cellpadding="3" cellspacing="0" width="100%">
<tr bgcolor="#dbeaf5" class="TableHeadingColor">
<td colspan=2>
<h2>Class Summary</h2></td>
</tr>
<tr bgcolor="white" class="TableRowColor">
<td width="15%"><b>Attribute</b></td>
<td>Attribute holds a (name, value) pair of an HDF4/5 attribute.</td>
</tr>
<tr bgcolor="white" class="TableRowColor">
<td width="15%"><b>CompoundDS</b></td>
<td>CompoundDS is the superclass for HDF4 and HDF5 Compound Dataset.</td>
</tr>
<tr bgcolor="white" class="TableRowColor">
<td width="15%"><b>Dataset</b></td>
<td>Dataset is the superclass for HDF4/5 Dataset, inheriting the HObject.</td>
</tr>
<tr bgcolor="white" class="TableRowColor">
<td width="15%"><b>Datatype</b></td>
<td>Datatype holds a (name, value) pair of an HDF4/5 attribute.</td>
</tr>
<tr bgcolor="white" class="TableRowColor">
<td width="15%"><b>Group</b></td>
<td>Group is the superclass for HDF4 and HDF5 group, inheriting the HObject.</td>
</tr>
<tr bgcolor="white" class="TableRowColor">
<td width="15%"><b>H4Datatype</b></td>
<td>H4Datatype holds a (name, value) pair of an HDF4/5 attribute.</td>
</tr>
<tr bgcolor="white" class="TableRowColor">
<td width="15%"><b>H4File</b></td>
<td>H4File provides file level APIs.</td>
</tr>
<tr bgcolor="white" class="TableRowColor">
<td width="15%"><b>H4GRImage</b></td>
<td>H4GRImage describes a HDF4 general raster(GR) image and operations performed on
the GR image.</td>
</tr>
<tr bgcolor="white" class="TableRowColor">
<td width="15%"><b>H4Group</b></td>
<td>H4Group is a vgroup in HDF4, inheriting from Group.</td>
</tr>
<tr bgcolor="white" class="TableRowColor">
<td width="15%"><b>H4SDS</b></td>
<td>H4SDS describes HDF4 Scientific Data Sets (SDS) and operations performed on
the SDS.</td>
</tr>
<tr bgcolor="white" class="TableRowColor">
<td width="15%"><b>H4Vdata</b></td>
<td>H4Vdata describes a multi-dimension array of HDF4 vdata, inheriting CompoundDS.</td>
</tr>
<tr bgcolor="white" class="TableRowColor">
<td width="15%"><b>H5CompoundDS</b></td>
<td>H5CompoundDS describes a multi-dimension array of HDF5 compound dataset,
inheriting CompoundDS.</td>
</tr>
<tr bgcolor="white" class="TableRowColor">
<td width="15%"><b>H5Datatype</b></td>
<td>H5Datatype holds a (name, value) pair of an HDF4/5 attribute.</td>
</tr>
<tr bgcolor="white" class="TableRowColor">
<td width="15%"><b>H5File</b></td>
<td>H4File provides file level APIs.</td>
</tr>
<tr bgcolor="white" class="TableRowColor">
<td width="15%"><b>H5Group</b></td>
<td>H5Group represents a HDF5 group, inheriting from Group.</td>
</tr>
<tr bgcolor="white" class="TableRowColor">
<td width="15%"><b>H5ScalarDS</b></td>
<td>H5ScalarDS describes a multi-dimension array of HDF5 scalar or atomic data
types and operations performed on the scalar dataset, such as byte, int,
short, long, float, double, and string.</td>
</tr>
<tr bgcolor="white" class="TableRowColor">
<td width="15%"><b>HObject</b></td>
<td>HObject is the superclass for the HDF data hierarchy, inheriting the DataFormat
interface.</td>
</tr>
<tr bgcolor="white" class="TableRowColor">
<td width="15%"><b>ScalarDS</b></td>
<td>ScalarDS is the superclass for HDF4/5 ScalarDS, inheriting Dataset.</td>
</tr>
</table>
<br />
<h2>
<a name="ug03application"></a>3.4 Using the HDF Object Package</h2>
<p>
The HDF Object Package is used by Java applications to access HDF4 and
HDF5 files without directly calling the HDF4 and HDF5 library APIs. Library
calls are encapsulated into respective classes. The HDF Object Package
requires the
<a href="../../JNI/jhi/index.html">
Java HDF Interface (JHI)</a>
and the
<a href="../../JNI/jhi5/index.html">
Java HDF5 Interface (JHI5)</a>.</p>
<center>
<p><img SRC="images/hdf-obj.jpg" />
<br><b>The software packages</b></p></center>
<br />
<p>
The following examples show how to retrieve file hierarchy using
the HDF Object Package.</p>
<h3>Example 3.1: Retrieve and print HDF5 objects </h3>
<pre>
import ncsa.hdf.object.*; // include the common HDF object package
import ncsa.hdf.object.h5.*; // include the HDF5 object package
import ncsa.hdf.hdf5lib.*; // include the Java HDF5 interface
/**
* Retreve and print HDF5 objects from file hdf5_test.h5
* @version 1.3.0 10/26/2001
* @author Peter X. Cao
*
*/
public class TestH5File
{
public static void main(String[] argv)
{
// create an H5File object
H5File h5file = new H5File("hdf5_test.h5", HDF5Constants.H5F_ACC_RDONLY);
try
{
// open file and retrieve the file structure
h5file.open();
}
catch (Exception ex)
{
System.out.println(ex);
}
javax.swing.tree.MutableTreeNode root = h5file.getRootNode();
if (root != null)
{
printNode(root, " ");
}
try { h5file.close(); }
catch (Exception ex ) {}
}
// print out the data object recusively
private static void printNode(javax.swing.tree.TreeNode node, String indent)
{
System.out.println(indent+node);
int n = node.getChildCount();
for (int i=0; i<n; i++)
{
printNode(node.getChildAt(i), indent+" ");
}
}
}
</pre>
<h3>Example 3.2: Retrieve and print HDF4 objects </h3>
<pre>
import ncsa.hdf.object.*; // include the common HDF object package
import ncsa.hdf.object.h4.*; // include the HDF4 object package
import ncsa.hdf.hdflib.*; // include the Java HDF5 interface
/**
* Retreve and print HDF4 objects from file annras.hdf.
* @version 1.3.0 10/26/2001
* @author Peter X. Cao
*
*/
public class TestH4File
{
public static void main(String[] argv)
{
// create an H4File object
H4File h4file = new H4File("annras.hdf", HDFConstants.DFACC_READ);
try
{
// open file and retrieve the file structure
h4file.open();
}
catch (Exception ex)
{
System.out.println(ex);
}
javax.swing.tree.MutableTreeNode root = h4file.getRootNode();
if (root != null)
{
printNode(root, " ");
}
try { h4file.close(); }
catch (Exception ex ) {}
}
// print out the data object recusively
private static void printNode(javax.swing.tree.TreeNode node, String indent)
{
System.out.println(indent+node);
int n = node.getChildCount();
for (int i=0; i<n; i++)
{
printNode(node.getChildAt(i), indent+" ");
}
}
}
</pre>
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