1998-07-08 22:54:54 +08:00
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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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1999-12-14 04:39:48 +08:00
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<title>Group Interface (H5G)</title>
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</head>
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1998-12-22 06:52:56 +08:00
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<body bgcolor="#FFFFFF">
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<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="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="index.html">Other HDF5 documents and links</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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1999-12-14 04:39:48 +08:00
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<a href="H5.user.html"><strong>HDF5 User's Guide:</strong></a>
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<br>
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1999-12-14 04:39:48 +08:00
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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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Groups
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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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1999-12-14 04:39:48 +08:00
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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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<h1>The Group Interface (H5G)</h1>
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<h2>1. Introduction</h2>
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<p>An object in HDF5 consists of an object header at a fixed file
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address that contains messages describing various properties of
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the object such as its storage location, layout, compression,
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etc. and some of these messages point to other data such as the
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raw data of a dataset. The address of the object header is also
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known as an <em>OID</em> and HDF5 has facilities for translating
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names to OIDs.
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<p>Every HDF5 object has at least one name and a set of names can
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be stored together in a group. Each group implements a name
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space where the names are any length and unique with respect to
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other names in the group.
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<p>Since a group is a type of HDF5 object it has an object header
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and a name which exists as a member of some other group. In this
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way, groups can be linked together to form a directed graph.
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One particular group is called the <em>Root Group</em> and is
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the group to which the HDF5 file super block points. Its name is
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"/" by convention. The <em>full name</em> of an object is
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created by joining component names with slashes much like Unix.
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<p>
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<center>
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<img alt="Group Graph Example" src="group_p1.gif">
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</center>
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<p>However, unlike Unix which arranges directories hierarchically,
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HDF5 arranges groups in a directed graph. Therefore, there is
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no ".." entry in a group since a group can have more than one
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parent. There is no "." entry either but the library understands
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it internally.
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<h2>2. Names</h2>
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<p>HDF5 places few restrictions on names: component names may be
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any length except zero and may contain any character except
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slash ("/") and the null terminator. A full name may be
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composed of any number of component names separated by slashes,
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with any of the component names being the special name ".". A
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name which begins with a slash is an <em>absolute</em> name
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which is looked up beginning at the root group of the file while
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all other <em>relative</em> names are looked up beginning at the
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specified group.
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Multiple consecutive slashes in a full name are treated as
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single slashes and trailing slashes are not significant. A
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special case is the name "/" (or equivalent) which refers to the
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root group.
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<p>Functions which operate on names generally take a location
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identifier which is either a file ID or a group ID and perform
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the lookup with respect to that location. Some possibilities
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are:
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<p>
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<center>
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<table border cellpadding=4>
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<tr>
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<th>Location Type</th>
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<th>Object Name</th>
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<th>Description</th>
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</tr>
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<tr>
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<td>File ID</td>
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<td><code>/foo/bar</code></td>
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<td>The object <code>bar</code> in group <code>foo</code>
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in the root group.</td>
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</tr>
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<tr>
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<td>Group ID</td>
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<td><code>/foo/bar</code></td>
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<td>The object <code>bar</code> in group <code>foo</code>
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in the root group of the file containing the specified
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group. In other words, the group ID's only purpose is
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to supply a file.</td>
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</tr>
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<tr>
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<td>File ID</td>
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<td><code>/</code></td>
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<td>The root group of the specified file.</td>
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</tr>
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<tr>
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<td>Group ID</td>
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<td><code>/</code></td>
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<td>The root group of the file containing the specified
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group.</td>
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</tr>
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<tr>
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<td>File ID</td>
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<td><code>foo/bar</code></td>
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<td>The object <code>bar</code> in group <code>foo</code>
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in the specified group.</td>
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</tr>
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<tr>
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<td>Group ID</td>
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<td><code>foo/bar</code></td>
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<td>The object <code>bar</code> in group <code>foo</code>
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in the specified group.</td>
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</tr>
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<tr>
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<td>File ID</td>
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<td><code>.</code></td>
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<td>The root group of the file.</td>
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</tr>
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<tr>
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<td>Group ID</td>
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<td><code>.</code></td>
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<td>The specified group.</td>
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</tr>
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<tr>
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<td>Other ID</td>
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<td><code>.</code></td>
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<td>The specified object.</td>
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</tr>
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</table>
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</center>
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2000-03-09 06:20:27 +08:00
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<p>Note, however, that object names within a group must be unique.
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For example, <code>H5Dcreate</code> returns an error if a
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dataset with the dataset name specified in the parameter list
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already exists at the location specified in the parameter list.
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1998-07-08 22:54:54 +08:00
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<h2>3. Creating, Opening, and Closing Groups</h2>
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<p>Groups are created with the <code>H5Gcreate()</code> function,
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and existing groups can be access with
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<code>H5Gopen()</code>. Both functions return an object ID which
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should be eventually released by calling
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<code>H5Gclose()</code>.
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<dl>
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<dt><code>hid_t H5Gcreate (hid_t <em>location_id</em>, const char
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*<em>name</em>, size_t <em>size_hint</em>)</code>
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<dd>This function creates a new group with the specified
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name at the specified location which is either a file ID or a
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group ID. The name must not already be taken by some other
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object and all parent groups must already exist. The
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<em>size_hint</em> is a hint for the number of bytes to
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reserve to store the names which will be eventually added to
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the new group. Passing a value of zero for <em>size_hint</em>
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is usually adequate since the library is able to dynamically
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resize the name heap, but a correct hint may result in better
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performance. The return value is a handle for the open group
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and it should be closed by calling <code>H5Gclose()</code>
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when it's no longer needed. A negative value is returned for
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failure.
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<br><br>
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<dt><code>hid_t H5Gopen (hid_t <em>location_id</em>, const char
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*<em>name</em>)</code>
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<dd>This function opens an existing group with the specified
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name at the specified location which is either a file ID or a
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group ID and returns an object ID. The object ID should be
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released by calling <code>H5Gclose()</code> when it is no
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longer needed. A negative value is returned for failure.
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<br><br>
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<dt><code>herr_t H5Gclose (hid_t <em>group_id</em>)</code>
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<dd>This function releases resources used by an group which was
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opened by <code>H5Gcreate()</code> or
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<code>H5Gopen()</code>. After closing a group the
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<em>group_id</em> should not be used again. This function
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returns zero for success or a negative value for failure.
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</dl>
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1998-10-30 06:13:17 +08:00
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<h2>4. Objects with Multiple Names</h2>
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<p>An object (including a group) can have more than one
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name. Creating the object gives it the first name, and then
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functions described here can be used to give it additional
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names. The association between a name and the object is called
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a <em>link</em> and HDF5 supports two types of links: a <em>hard
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link</em> is a direct association between the name and the
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object where both exist in a single HDF5 address space, and a
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<em>soft link</em> is an indirect association.
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<p>
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<center>
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<img alt="Hard Link Example" src="group_p2.gif">
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</center>
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<p>
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<center>
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<img alt="Soft Link Example" src="group_p3.gif">
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</center>
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<dl>
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<dt>Object Creation</dt>
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<dd>The creation of an object creates a hard link which is
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indistinguishable from other hard links that might be added
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later.
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<br><br>
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<dt><code>herr_t H5Glink (hid_t <em>file_id</em>, H5G_link_t
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<em>link_type</em>, const char *<em>current_name</em>,
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const char *<em>new_name</em>)</code>
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<dd>Creates a new name for an object that has some current name
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(possibly one of many names it currently has). If the
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<em>link_type</em> is <code>H5G_LINK_HARD</code> then a new
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hard link is created. Otherwise if <em>link_type</em> is
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<code>H5T_LINK_SOFT</code> a soft link is created which is an
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alias for the <em>current_name</em>. When creating a soft
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link the object need not exist. This function returns zero
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for success or negative for failure.
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<br><br>
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<dt><code>herr_t H5Gunlink (hid_t <em>file_id</em>, const char
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*<em>name</em>)</code>
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<dd>This function removes an association between a name and an
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object. Object headers keep track of how many hard links refer
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to the object and when the hard link count reaches zero the
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object can be removed from the file (but objects which are
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open are not removed until all handles to the object are
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closed).
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</dl>
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1998-10-30 06:13:17 +08:00
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<h2>5. Comments</h2>
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1998-07-21 05:01:32 +08:00
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<p>Objects can have a comment associated with them. The comment
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is set and queried with these two functions:
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<dl>
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<dt><code>herr_t H5Gset_comment (hid_t <em>loc_id</em>, const
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char *<em>name</em>, const char *<em>comment</em>)</code>
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<dd>The previous comment (if any) for the specified object is
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replace with a new comment. If the <em>comment</em> argument
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is the empty string or a null pointer then the comment message
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is removed from the object. Comments should be relatively
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short, null-terminated, ASCII strings.
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<br><br>
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<dt><code>herr_t H5Gget_comment (hid_t <em>loc_id</em>, const
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char *<em>name</em>, size_t <em>bufsize</em>, char
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*<em>comment</em>)</code>
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<dd>The comment string for an object is returned through the
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<em>comment</em> buffer. At most <em>bufsize</em> characters
|
[svn-r537] Changes since 19980722
----------------------
./src/H5A.c
./src/H5Apublic.h
./test/tattr.c
Switched the order of the second and third argument of
H5Aget_name() to make it consistent with other functions that
take buffers and buffer sizes.
./src/H5G.c
./src/H5Gpublic.h
./src/H5Gprivate.h
The H5Gget_comment() function returns the size of the comment
including the null terminator. If the object has no comment
then zero is returned. If an error occurs then a negative
value is returned.
./MANIFEST
./tools/Makefile.in
./tools/h5tools.h [NEW]
./tools/h5dump.c [NEW]
Created a library for printing values of datasets in a way
that looks nice. It's not done yet, but I needed it for
debugging the contents of files from Jim Reus.
./tools/h5ls.c
Added the `-d' and `--dump' options which cause the contents
of a dataset to be printed. Added `-w N' and `--width=N'
options to control how wide the raw data output should be. If
you want single-column output then say `-w1'.
Printing dataset values can now handle datasets of any integer
or floating point atomic type. As a special case, integers
which are one byte wide are treated a character strings for
now.
Sample output:
$ h5ls --dump --width=60 banana.hdf
ARCHIVE 0:0:0:744 Dataset {52/Inf}
Data:
(0) "U struct complex { double R; double I; };\012V"
(43) " double;\012"
U 0:0:0:2500 Dataset {256/512}
Data: printing of compound data types is not implemented yet
V 0:0:0:3928 Dataset {256/512}
Data:
(0) 0, 0.015625, 0.03125, 0.046875, 0.0625,
(5) 0.078125, 0.09375, 0.109375, 0.125, 0.140625,
(10) 0.15625, 0.171875, 0.1875, 0.203125, 0.21875,
(15) 0.234375, 0.25, 0.265625, 0.28125, 0.296875,
...
1998-07-24 05:19:17 +08:00
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including a null terminator are copied, and the result is
|
1998-07-21 05:01:32 +08:00
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not null terminated if the comment is longer than the supplied
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buffer. If an object doesn't have a comment then the empty
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string is returned.
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</dl>
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|
2000-11-02 03:01:55 +08:00
|
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|
<a name="H5GUnlinkToCorrupt">
|
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|
<h2>6. Unlinking Datasets with H5Gmove and H5Gunlink</h2>
|
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|
</a>
|
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|
<p>Exercise caution in the use of <code>H5Gmove</code> and
|
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|
|
<code>H5Gunlink</code>.
|
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|
<p>Note that <code>H5Gmove</code> and <code>H5Gunlink</code>
|
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|
each include a step that unlinks pointers to a set or group.
|
|
|
|
|
If the link that is removed is on the only path leading
|
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|
|
to a dataset or group, that dataset or group will become
|
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|
|
inaccessible in the file.
|
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|
<p>Consider the following example. Assume that the group
|
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|
|
<code>group2</code> can only be accessed via the following path,
|
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|
|
where <code>top_group</code> is a member of the file's root group:
|
|
|
|
|
<pre>
|
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|
|
|
<code>/top_group/group1/group2/</code> </pre>
|
|
|
|
|
Using <code>H5Gmove</code>, <code>top_group</code> is renamed
|
|
|
|
|
to be a member of <code>group2</code>. At this point, since
|
|
|
|
|
<code>top_group</code> was the only route from the root group
|
|
|
|
|
to <code>group1</code>, there is no longer a path by which
|
|
|
|
|
one can access <code>group1</code>, <code>group2</code>, or
|
|
|
|
|
any member datasets.
|
|
|
|
|
<code>top_group</code> and any member datasets have also
|
|
|
|
|
become inaccessible.
|
|
|
|
|
|
1998-12-22 06:52:56 +08:00
|
|
|
|
|
|
|
|
<hr>
|
|
|
|
|
<center>
|
|
|
|
|
<table border=0 width=98%>
|
|
|
|
|
<tr><td valign=top align=left>
|
|
|
|
|
<a href="H5.intro.html">Introduction to HDF5</a> <br>
|
|
|
|
|
<a href="RM_H5Front.html">HDF5 Reference Manual</a> <br>
|
|
|
|
|
<a href="index.html">Other HDF5 documents and links</a> <br>
|
|
|
|
|
<!--
|
|
|
|
|
<a href="Glossary.html">Glossary</a><br>
|
|
|
|
|
-->
|
|
|
|
|
</td>
|
|
|
|
|
<td valign=top align=right>
|
|
|
|
|
And in this document, the
|
1999-12-14 04:39:48 +08:00
|
|
|
<a href="H5.user.html"><strong>HDF5 User's Guide:</strong></a>
|
1998-12-22 06:52:56 +08:00
|
|
|
<br>
|
1999-12-14 04:39:48 +08:00
|
|
|
<a href="Files.html">Files</a>
|
1998-12-22 06:52:56 +08:00
|
|
|
<a href="Datasets.html">Datasets</a>
|
1999-12-14 04:39:48 +08:00
|
|
|
<a href="Datatypes.html">Datatypes</a>
|
1998-12-22 06:52:56 +08:00
|
|
|
<a href="Dataspaces.html">Dataspaces</a>
|
|
|
|
|
Groups
|
|
|
|
|
<br>
|
1999-12-14 04:39:48 +08:00
|
|
|
<a href="References.html">References</a>
|
1998-12-22 06:52:56 +08:00
|
|
|
<a href="Attributes.html">Attributes</a>
|
|
|
|
|
<a href="Properties.html">Property Lists</a>
|
|
|
|
|
<a href="Errors.html">Error Handling</a>
|
1999-12-14 04:39:48 +08:00
|
|
|
<br>
|
1998-12-22 06:52:56 +08:00
|
|
|
<a href="Filters.html">Filters</a>
|
|
|
|
|
<a href="Caching.html">Caching</a>
|
|
|
|
|
<a href="Chunking.html">Chunking</a>
|
1999-12-14 04:39:48 +08:00
|
|
|
<a href="MountingFiles.html">Mounting Files</a>
|
|
|
|
|
<br>
|
|
|
|
|
<a href="Performance.html">Performance</a>
|
1998-12-22 06:52:56 +08:00
|
|
|
<a href="Debugging.html">Debugging</a>
|
|
|
|
|
<a href="Environment.html">Environment</a>
|
|
|
|
|
<a href="ddl.html">DDL</a>
|
|
|
|
|
</td></tr>
|
|
|
|
|
</table>
|
|
|
|
|
</center>
|
|
|
|
|
|
|
|
|
|
|
1998-09-10 06:48:37 +08:00
|
|
|
|
|
|
|
|
<hr>
|
|
|
|
|
<address>
|
|
|
|
|
<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
|
|
|
|
|
</address>
|
|
|
|
|
|
1999-12-14 04:39:48 +08:00
|
|
|
<!-- Created: Tue Jan 27 09:11:27 EST 1998 -->
|
|
|
|
|
<!-- hhmts start -->
|
2000-11-02 03:01:55 +08:00
|
|
|
Last modified: 1 November 2000
|
1999-12-14 04:39:48 +08:00
|
|
|
<!-- hhmts end -->
|
1998-09-10 06:48:37 +08:00
|
|
|
|
2000-12-09 06:12:36 +08:00
|
|
|
<br>
|
2001-04-19 06:03:09 +08:00
|
|
|
Describes HDF5 Release 1.5, Unreleased Development Branch
|
2000-12-09 06:12:36 +08:00
|
|
|
|
|
|
|
|
|
1998-07-08 22:54:54 +08:00
|
|
|
</body>
|
|
|
|
|
</html>
|
