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Groups.html Added note that object names (in Groups.html) or dataset names (in Datasets.html) must be unique. Changed 'boot block' to 'super block'. (Groups.html only) Files.html Minor formatting fixes. Datatypes.html H5Tconvert: Added plist_id parameter. References.html Deleted "not implemented" and related messages. Added description of H5Rget_object_type. Deleted all material about internal dataset region references. [Unlikely to be implemented (QK) and there was very little info.] Commented out references to H5R_BADTYPE. [This appeared in the list of "valid types", which it is not. And user is instructed to test for 'a negative value' rather than 'H5R_BADTYPE'. So this was deemed not to be user-level information.] Changed 'boot block' to 'super block'. Other minor editing changes.
642 lines
22 KiB
HTML
642 lines
22 KiB
HTML
<!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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</head>
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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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<a href="H5.user.html"><strong>HDF5 User's Guide:</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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References
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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="Palettes.html">Palettes</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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<br>
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<a href="Ragged.html">Ragged Arrays</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 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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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)
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<dt>External Dataset Offset Reference
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<dd>Reference to a specific byte sequence in a dataset in
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another HDF5 file (3)
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<dt>External Disk Offset Reference
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<dd>Reference to a specific byte sequence in another HDF5 file (3)
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<dt>Generic Reference
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<dd>A reference which may be any of the types defined above. (3)
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</dl>
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Notes:
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<ul>
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<li>1 - Planned for in final release.
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<li>2 - Most useful reference types to tackle next
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<li>3 - Optional reference types.
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</ul>
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<h2>Comments</h2>
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<pre>
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Reference types are atomic types and may be included as fields in compound
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datatypes.
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There are (at least) three levels of reference strength:
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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>
|
|
|
|
-->
|
|
|
|
<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
|
|
<a href="H5.user.html"><strong>HDF5 User's Guide:</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>
|
|
References
|
|
<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="Palettes.html">Palettes</a>
|
|
<a href="Caching.html">Caching</a>
|
|
<a href="Chunking.html">Chunking</a>
|
|
<a href="MountingFiles.html">Mounting Files</a>
|
|
<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>
|
|
<br>
|
|
<a href="Ragged.html">Ragged Arrays</a>
|
|
</td></tr>
|
|
</table>
|
|
</center>
|
|
|
|
|
|
<hr>
|
|
<address>
|
|
<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
|
|
</address>
|
|
|
|
Last modified: 14 October 1999
|
|
|
|
</body>
|
|
</html>
|