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Purpose:
Renamed old "HDF5 User's Guide" as "HDF5 User's Guide, Release 1.4.5".
Added navigation bar link to new user's guide on HDF server.
Changed release tag line (in old UG only) back to
"Describes HDF5 Release 1.4.5, February 200 3"
Platforms tested:
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652 lines
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<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
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<html>
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<head>
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<title>Reference (H5R) and Identifier Interfaces (H5I)</title>
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<!-- #BeginLibraryItem "/ed_libs/styles_UG.lbi" -->
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<!--
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* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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* Copyright by the Board of Trustees of the University of Illinois. *
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* All rights reserved. *
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* *
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* This file is part of HDF5. The full HDF5 copyright notice, including *
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* terms governing use, modification, and redistribution, is contained in *
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* the files COPYING and Copyright.html. COPYING can be found at the root *
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* of the source code distribution tree; Copyright.html can be found at the *
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* root level of an installed copy of the electronic HDF5 document set and *
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* is linked from the top-level documents page. It can also be found at *
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* http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
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* access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
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* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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-->
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<link href="ed_styles/UGelect.css" rel="stylesheet" type="text/css">
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<!-- #EndLibraryItem --></head>
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<body bgcolor="#FFFFFF">
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<!-- #BeginLibraryItem "/ed_libs/NavBar_UG.lbi" --><hr>
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<center>
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<table border=0 width=98%>
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<tr><td valign=top align=left>
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<a href="index.html">HDF5 documents and links</a> <br>
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<a href="H5.intro.html">Introduction to HDF5</a> <br>
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<a href="RM_H5Front.html">HDF5 Reference Manual</a> <br>
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<a href="http://hdf.ncsa.uiuc.edu/HDF5/doc/UG/index.html">HDF5 User's Guide for Release 1.6</a> <br>
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<!--
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<a href="Glossary.html">Glossary</a><br>
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-->
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</td>
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<td valign=top align=right>
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And in this document, the
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<a href="H5.user.html"><strong>HDF5 User's Guide from Release 1.4.5:</strong></a>
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<br>
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<a href="Files.html">Files</a>
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<a href="Datasets.html">Datasets</a>
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<a href="Datatypes.html">Datatypes</a>
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<a href="Dataspaces.html">Dataspaces</a>
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<a href="Groups.html">Groups</a>
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<br>
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<a href="References.html">References</a>
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<a href="Attributes.html">Attributes</a>
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<a href="Properties.html">Property Lists</a>
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<a href="Errors.html">Error Handling</a>
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<br>
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<a href="Filters.html">Filters</a>
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<a href="Caching.html">Caching</a>
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<a href="Chunking.html">Chunking</a>
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<a href="MountingFiles.html">Mounting Files</a>
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<br>
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<a href="Performance.html">Performance</a>
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<a href="Debugging.html">Debugging</a>
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<a href="Environment.html">Environment</a>
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<a href="ddl.html">DDL</a>
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</td></tr>
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</table>
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</center>
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<hr>
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<!-- #EndLibraryItem --><h1>The Reference Interface (H5R) and <br> the Identifier Interface (H5I)</h1>
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<h2>1. Introduction</h2>
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This document discusses the kinds of references implemented
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(and planned) in HDF5 and the functions implemented (and planned)
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to support them.
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<h2>2. References</h2>
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This section contains an overview of the kinds of references
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implemented, or planned for implementation, in HDF5.
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<p>
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<dl>
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<dt>Object reference
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<dd>Reference to an entire object in the current HDF5 file.
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<p>
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An object reference points to an entire object in the
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current HDF5 file by storing the relative file address
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(OID) of the object header for the object pointed to.
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The relative file address of an object header is
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constant for the life of the object.
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An object reference is of a fixed size in the file.
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<p>
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<dt>Dataset region reference
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<dd>Reference to a specific dataset region.
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<p>
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A dataset region reference points to a region of a
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dataset in the current HDF5 file by storing the OID
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of the dataset and the global heap offset of the
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region referenced. The region referenced is located
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by retrieving the coordinates of the areas in the
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region from the global heap. A dataset region
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reference is of a variable size in the file.
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</dl>
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<b>Note:</b> All references are treated as soft links for the
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purposes of reference counting. The library does not keep track of
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reference links and they may dangle if the object they refer to
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is deleted, moved, or not yet available.
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<h2>3. Reference Types</h2>
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Valid HDF5 reference types for use in the H5R functions
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are as follows:
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<center>
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<table>
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<tr><th align=left>Reference Type</th><th align=left>Value </th><th align=left>Description</th></tr>
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<!-- NOT USER-LEVEL INFORMATION; DELETED FROM HDF5 USER'S GUIDE
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<tr><td><code>H5R_BADTYPE</code></td>
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<td align=right><code>-1 </code></td>
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<td>Invalid reference type</td></tr>
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-->
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<tr><td><code>H5R_OBJECT</code></td>
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<td align=right><code>0 </code></td>
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<td>Object reference</td></tr>
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<tr><td><code>H5R_DATASET_REGION</code></td>
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<td align=right><code>1 </code></td>
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<td>Dataset region reference</td></tr>
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</table>
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</center>
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<h2>4. Functions</h2>
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Five functions, four in the H5R interface and one in the
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H5I interface, have been implemented to support references.
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The H5I function is also useful outside the context of references.
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<p>
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<dl>
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<dt><em>herr_t</em> <code>H5Rcreate(</code><em>void *</em><code>reference,</code>
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<em>hid_t</em> <code>loc_id,</code>
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<em>const char *</em><code>name,</code>
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<em>H5R_type_t</em> <code>type,</code>
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<em>hid_t</em> <code>space_id)</code>
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<dd><code>H5Rcreate</code> creates an object which is a
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particular type of reference (specified with the
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<code>type</code> parameter) to some file object and/or
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location specified with the <code>space_id</code> parameter.
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For dataset region references, the selection specified
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in the dataspace is the portion of the dataset which
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will be referred to.
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<p>
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<dt><em>hid_t</em> <code>H5Rdereference(</code><em>hid_t</em> <code>dset,</code>
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<em>H5R_type_t</em> <code>rtype,</code>
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<em>void *</em><code>reference)</code>
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<dd><code>H5Rdereference</code> opens the object referenced
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and returns an identifier for that object.
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The parameter <code>reference</code> specifies a reference of
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type <code>rtype</code> that is stored in the dataset
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<code>dset</code>.
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<p>
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<dt><em>int</em> <code>H5Rget_object_type(</code><em>hid_t</em> <code>obj_id,</code>
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<em>void *</em><code>reference)</code>
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<dd><code>H5Rget_object_type</code> retrieves the type of object
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that an object reference points to.
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The parameter <code>obj_id</code> specifies the dataset
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containing the reference object or the location identifier
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of the object that the dataset is located within.
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The parameter <code>reference</code> specifies the
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reference being queried.
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<p>
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<dt><em>H5S_t</em> <code>H5Rget_region(</code><em>H5D_t</em> <code>dataset,</code>
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<em>H5R_type_t</em> <code>type,</code>
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<em>void *</em><code>reference)</code>
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<dd><code>H5Rget_region</code> creates a copy of dataspace of
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the dataset that is pointed to and defines a selection in
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the copy which is the location (or region) pointed to.
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The parameter <code>ref</code> specifies a reference of
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type <code>rtype</code> that is stored in the dataset
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<code>dset</code>.
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<p>
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<dt><em>H5I_type_t</em> <code>H5Iget_type(</code><em>hid_t</em> <code>id)</code>
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<dd>Returns the type of object referred to by the
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identifier <code>id</code>. Valid return values appear
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in the following list:
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<center>
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<table>
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<tr valign=bottom><td><code>H5I_FILE</code></td>
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<td>File objects</td></tr>
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<tr valign=bottom><td><code>H5I_GROUP</code></td>
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<td>Group objects</td></tr>
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<tr valign=bottom><td><code>H5I_DATATYPE</code></td>
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<td>Datatype objects</td></tr>
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<tr valign=bottom><td><code>H5I_DATASPACE</code></td>
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<td>Dataspace objects</td></tr>
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<tr valign=bottom><td><code>H5I_DATASET</code></td>
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<td>Dataset objects</td></tr>
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<tr valign=bottom><td><code>H5I_ATTR</code></td>
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<td>Attribute objects</td></tr>
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</table>
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</center>
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<p>
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This function was inspired by the need of users to figure
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out which type of object closing function
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(<code>H5Dclose</code>, <code>H5Gclose</code>, etc.)
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to call after a call to <code>H5Rdereference</code>,
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but it is also of general use.
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<p>
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</dl>
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<h2>5. Examples</h2>
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<b>Object Reference Writing Example</b>
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<br>
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Create a dataset which has links to other datasets as part
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of its raw data and write the dataset to the file.
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<p>
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<pre>
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{
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hid_t file1;
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hid_t dataset1;
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hid_t datatype, dataspace;
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char buf[128];
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hobj_ref_t link;
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hobj_ref_t data[10][10];
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int rank;
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size_t dimsf[2];
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int i, j;
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/* Open the file */
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file1=H5Fopen("example.h5", H5F_ACC_RDWR, H5P_DEFAULT);
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/* Describe the size of the array and create the data space */
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rank=2;
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dimsf[0] = 10;
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dimsf[1] = 10;
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dataspace = H5Screate_simple(rank, dimsf, NULL);
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/* Define datatype */
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datatype = H5Tcopy(H5T_STD_REF_OBJ);
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/* Create a dataset */
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dataset1=H5Dcreate(file1,"Dataset One",datatype,dataspace,H5P_DEFAULT);
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/* Construct array of OIDs for other datasets in the file */
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/* somewhat hokey and artificial, but demonstrates the point */
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for(i=0; i<10; i++)
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for(j=0; j<10; i++)
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{
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sprintf(buf,"/Group/Linked Set %d-%d",i,j);
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if(H5Rcreate(&link,file1,buf,H5R_OBJECT,-1)>0)
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data[i][j]=link;
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} /* end for */
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/* Write the data to the dataset using default transfer properties. */
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H5Dwrite(dataset, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
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/* Close everything */
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H5Sclose(dataspace);
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H5Tclose(datatype);
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H5Dclose(dataset1);
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H5Fclose(file1);
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}
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</pre>
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<b>Object Reference Reading Example</b>
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<br>
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Open a dataset which has links to other datasets as part of
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its raw data and read in those links.
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<p>
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<pre>
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{
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hid_t file1;
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hid_t dataset1, tmp_dset;
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href_t data[10][10];
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int i, j;
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/* Open the file */
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file1=H5Fopen("example.h5", H5F_ACC_RDWR, H5P_DEFAULT);
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/* Open the dataset */
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dataset1=H5Dopen(file1,"Dataset One",H5P_DEFAULT);
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/*
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* Read the data to the dataset using default transfer properties.
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* (we are assuming the dataset is the same and not querying the
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* dimensions, etc.)
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*/
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H5Dread(dataset, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
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/* Analyze array of OIDs of linked datasets in the file */
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/* somewhat hokey and artificial, but demonstrates the point */
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for(i=0; i<10; i++)
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for(j=0; j<10; i++)
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{
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if((tmp_dset=H5Rdereference(dataset, H5T_STD_REF_OBJ, data[i][j]))>0)
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{
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<perform operations on linked dataset>
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} /* end if */
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H5Dclose(tmp_dset);
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} /* end for */
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/* Close everything */
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H5Dclose(dataset1);
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H5Fclose(file1);
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}
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</pre>
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<b>Dataset Region Reference Writing Example</b>
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<br>
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Create a dataset which has links to other dataset regions
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(single elements in this case) as part of its raw data and
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write the dataset to the file.
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<p>
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<pre>
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{
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hid_t file1;
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hid_t dataset1, dataset2;
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hid_t datatype, dataspace1, dataspace2;
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char buf[128];
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href_t link;
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href_t data[10][10]; /* HDF5 reference type */
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int rank;
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size_t dimsf[2];
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hssize_t start[3],count[3];
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int i, j;
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/* Open the file */
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file1=H5Fopen("example.h5", H5F_ACC_RDWR, H5P_DEFAULT);
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/* Describe the size of the array and create the data space */
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rank=2;
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dimsf[0] = 10;
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dimsf[1] = 10;
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dataspace1 = H5Screate_simple(rank, dimsf, NULL);
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/* Define Dataset Region Reference datatype */
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datatype = H5Tcopy(H5T_STD_REF_DATAREG);
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/* Create a dataset */
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dataset1=H5Dcreate(file1,"Dataset One",datatype,dataspace1,H5P_DEFAULT);
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/* Construct array of OIDs for other datasets in the file */
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/* (somewhat artificial, but demonstrates the point) */
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for(i=0; i<10; i++)
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for(j=0; j<10; i++)
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{
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sprintf(buf,"/Group/Linked Set %d-%d",i,j);
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/* Get the dataspace for the object to point to */
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dataset2=H5Dopen(file1,buf,H5P_DEFAULT);
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dataspace2=H5Dget_space(dataspace2);
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/* Select the region to point to */
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/* (could be different region for each pointer) */
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start[0]=5; start[1]=4; start[2]=3;
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count[0]=2; count[1]=4; count[2]=1;
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H5Sselect_hyperslab(dataspace2,H5S_SELECT_SET,start,NULL,count,NULL);
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if(H5Rcreate(&link,file1,buf,H5R_REF_DATAREG,dataspace2)>0)
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/* Store the reference */
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data[i][j]=link;
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H5Sclose(dataspace2);
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H5Dclose(dataspace2);
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} /* end for */
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/* Write the data to the dataset using default transfer properties. */
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H5Dwrite(dataset, H5T_STD_REF_DATAREG, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
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/* Close everything */
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H5Sclose(dataspace);
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H5Tclose(datatype);
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H5Dclose(dataset1);
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H5Fclose(file1);
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}
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</pre>
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<b>Dataset Region Reference Reading Example</b>
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<br>
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Open a dataset which has links to other datasets regions
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(single elements in this case) as part of its raw data and
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read in those links.
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<p>
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<pre>
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{
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hid_t file1;
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hid_t dataset1, tmp_dset;
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hid_t dataspace;
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href_t data[10][10]; /* HDF5 reference type */
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int i, j;
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/* Open the file */
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file1=H5Fopen("example.h5", H5F_ACC_RDWR, H5P_DEFAULT);
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/* Open the dataset */
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dataset1=H5Dopen(file1,"Dataset One",H5P_DEFAULT);
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/*
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* Read the data to the dataset using default transfer properties.
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* (we are assuming the dataset is the same and not querying the
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* dimensions, etc.)
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*/
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H5Dread(dataset, H5T_STD_REF_DATAREG, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
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/* Analyze array of OIDs of linked datasets in the file */
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/* (somewhat artificial, but demonstrates the point) */
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for(i=0; i<10; i++)
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for(j=0; j<10; i++)
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{
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if((tmp_dset=H5Rdereference(dataset, H5D_STD_REF_DATAREG,data[i][j]))>0)
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{
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/* Get the dataspace with the pointed to region selected */
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dataspace=H5Rget_space(data[i][j]);
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<perform operation on linked dataset region>
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H5Sclose(dataspace);
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} /* end if */
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H5Dclose(tmp_dset);
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} /* end for */
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/* Close everything */
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H5Dclose(dataset1);
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H5Fclose(file1);
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}
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</pre>
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<!--
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<h1>Material to Be Omitted!!!</h1>
|
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|
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Additional material above will also need to be deleted or
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commented out.
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<p>
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<h2>"Kinds of Reference" Information</h2>
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<dl>
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<dt>Dataset Offset Reference
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<dd>Reference to a specific byte sequence in a dataset (3)
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<dt>Disk Offset Reference
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<dd>Reference to a specific byte sequence in a file (3)
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<dt>External Object Reference
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<dd>Reference to an entire object in another HDF5 file (3)
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<dt>External Dataset Region Reference
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|
<dd>Reference an a specific dataset region in another HDF5 file (3)
|
|
<dt>External Dataset Offset Reference
|
|
<dd>Reference to a specific byte sequence in a dataset in
|
|
another HDF5 file (3)
|
|
<dt>External Disk Offset Reference
|
|
<dd>Reference to a specific byte sequence in another HDF5 file (3)
|
|
<dt>Generic Reference
|
|
<dd>A reference which may be any of the types defined above. (3)
|
|
</dl>
|
|
|
|
Notes:
|
|
<ul>
|
|
<li>1 - Planned for in final release.
|
|
<li>2 - Most useful reference types to tackle next
|
|
<li>3 - Optional reference types.
|
|
</ul>
|
|
|
|
<h2>Comments</h2>
|
|
<pre>
|
|
Reference types are atomic types and may be included as fields in compound
|
|
datatypes.
|
|
|
|
There are (at least) three levels of reference strength:
|
|
Weak - We allow the user to store any type of reference in an array
|
|
of references. (u.e., the array of references in the example above
|
|
could be a mix of Object, Dataset Region and Internal references)
|
|
Medium - We force the user to stick with a particular type of
|
|
reference within a dataset, but the datasets pointed to (with
|
|
Object and Dataset Region references) may be of any datatype
|
|
or dataspace.
|
|
Strong - We force the user to stick with a particular type of
|
|
reference and Object and Dataset Region references must point to
|
|
datasets with the same datatype.
|
|
Extra Strong - We force the user to stick with a particular type of
|
|
reference and Object and Dataset Region references must point to
|
|
datasets with the same datatype <i>and</i> dataspace.
|
|
|
|
The library is currently implemented with "medium" strength references.
|
|
</pre>
|
|
|
|
|
|
<h2>Reference Type</h2>
|
|
|
|
<center>
|
|
<table>
|
|
<tr><td><code>H5R_MAXTYPE</code></td>
|
|
<td align=right><code>3 </code></td>
|
|
<td>Highest type in group (invalid as true type)</td></tr>
|
|
</table>
|
|
</center>
|
|
|
|
|
|
<h2>Information Regarding Specific Kinds of References</h2>
|
|
|
|
<dl>
|
|
<dt>Dataset Offset Reference
|
|
<dd>Points to a sequence of bytes within a dataset in
|
|
the current HDF5 file by storing the OID of the dataset and the byte
|
|
length and offset of the sequence within the dataset. The offset is
|
|
the logical byte offset within the dataset, meaning that the data is
|
|
de-compressed before returning the sequence of bytes requested. No
|
|
interpretation of the data at that location is provided. However,
|
|
if the dataset is extendible and the size of the dimensions are changed,
|
|
the element(s) that the sequence is located within may vary. Fixed size
|
|
in file.
|
|
|
|
<dt>Disk Offset Reference
|
|
<dd>Points to a sequence of bytes in the current
|
|
HDF5 file by storing the byte length and offset of the sequence within
|
|
the file, relative to the super block (as are all the other high-level
|
|
addresses used in the file). The offset is the absolute byte offset
|
|
within the file, no interpretation of the data at that location is
|
|
provided. Fixed size in file.
|
|
|
|
<dt>External Object Reference
|
|
<dd>Points to an entire object in another HDF5 file by
|
|
storing a global heap offset which points to the URL of the external
|
|
file and the OID of the object pointed to. Variable size in file.
|
|
|
|
<dt>External Dataset Region Reference
|
|
<dd>Points to a region of a dataset in
|
|
another HDF5 file by storing a global heap offset which points to the
|
|
URL of the external file, OID of the dataset and the coordinates of the
|
|
region. Variable size in file.
|
|
|
|
<dt>External Dataset Offset Reference
|
|
<dd>Points to a sequence of bytes within a
|
|
dataset in another HDF5 file by storing a global heap offset which
|
|
points to the URL of the external file, the OID of the dataset and the
|
|
byte length and offset of the sequence within the dataset. The offset
|
|
is the logical byte offset within the dataset, meaning that the data is
|
|
de-compressed before returning the sequence of bytes requested.
|
|
However, if the dataset is not stored contiguously and the size of the
|
|
dimensions are changed, the element(s) that the sequence is located
|
|
within may vary. Variable size in file.
|
|
|
|
<dt>External Disk Offset Reference
|
|
<dd>Points to a sequence of bytes in another
|
|
HDF5 file by storing a global heap reference which points to the URL
|
|
of the external file and the byte length and offset of the sequence
|
|
within the file. The offset is the absolute byte offset within the
|
|
file, no interpretation of the data at that location is provided.
|
|
Variable size in file.
|
|
|
|
<dt>Generic Reference
|
|
<dd>A reference which may contain any of the other
|
|
references defined above. (Mostly useful for implementing "weak"
|
|
strength pointers within the medium strength model we are using)
|
|
Variable size in file.
|
|
|
|
</dl>
|
|
|
|
<h2>Implementation Details</h2>
|
|
|
|
<dl>
|
|
<dt>File Storage
|
|
<dd>In order to efficiently index an array, each element must be the
|
|
same size when stored in the dataset on disk. Fixed-sized references
|
|
will be stored directly in the dataset array on disk; variable-sized
|
|
references will have a fixed-size head offset stored in the array on
|
|
disk with a file heap used to store the actual variable-sized
|
|
information stored in the heap.
|
|
|
|
<dt>Memory Storage
|
|
<dd>Each <code>href_t</code> object in memory is a struct containing
|
|
a pointer type and union of information required for each
|
|
pointer type.
|
|
Information in this structure is not designed for users to view.
|
|
Non-C APIs may have to mangle this structure in some way, in order
|
|
to provide users with access to references in a language-appropriate
|
|
way.
|
|
</dl>
|
|
|
|
-->
|
|
|
|
|
|
<!-- #BeginLibraryItem "/ed_libs/NavBar_UG.lbi" --><hr>
|
|
<center>
|
|
<table border=0 width=98%>
|
|
<tr><td valign=top align=left>
|
|
<a href="index.html">HDF5 documents and links</a> <br>
|
|
<a href="H5.intro.html">Introduction to HDF5</a> <br>
|
|
<a href="RM_H5Front.html">HDF5 Reference Manual</a> <br>
|
|
<a href="http://hdf.ncsa.uiuc.edu/HDF5/doc/UG/index.html">HDF5 User's Guide for Release 1.6</a> <br>
|
|
<!--
|
|
<a href="Glossary.html">Glossary</a><br>
|
|
-->
|
|
</td>
|
|
<td valign=top align=right>
|
|
And in this document, the
|
|
<a href="H5.user.html"><strong>HDF5 User's Guide from Release 1.4.5:</strong></a>
|
|
<br>
|
|
<a href="Files.html">Files</a>
|
|
<a href="Datasets.html">Datasets</a>
|
|
<a href="Datatypes.html">Datatypes</a>
|
|
<a href="Dataspaces.html">Dataspaces</a>
|
|
<a href="Groups.html">Groups</a>
|
|
<br>
|
|
<a href="References.html">References</a>
|
|
<a href="Attributes.html">Attributes</a>
|
|
<a href="Properties.html">Property Lists</a>
|
|
<a href="Errors.html">Error Handling</a>
|
|
<br>
|
|
<a href="Filters.html">Filters</a>
|
|
<a href="Caching.html">Caching</a>
|
|
<a href="Chunking.html">Chunking</a>
|
|
<a href="MountingFiles.html">Mounting Files</a>
|
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<br>
|
|
<a href="Performance.html">Performance</a>
|
|
<a href="Debugging.html">Debugging</a>
|
|
<a href="Environment.html">Environment</a>
|
|
<a href="ddl.html">DDL</a>
|
|
</td></tr>
|
|
</table>
|
|
</center>
|
|
<hr>
|
|
<!-- #EndLibraryItem --><!-- #BeginLibraryItem "/ed_libs/Footer.lbi" --><address>
|
|
<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
|
|
<br>
|
|
Describes HDF5 Release 1.4.5, February 2003
|
|
</address><!-- #EndLibraryItem -->
|
|
|
|
Last modified: 3 March 2000
|
|
|
|
</body>
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</html>
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