mirror of
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9fb77d56b8
Purpose:
Clean up RM formatting.
Modify RM HTML code to facilitate automated generation of PDF version.
Minor edits.
Description:
Reworked format of "Parameters" sections.
Added HTML tags (and pseudo-HTML tags) used by HTMLdoc to
generate PDF files.
Fixed the "Copyright" link on RM_H5Front.html.
Other minor copy edits.
Platforms tested:
IE 5
572 lines
22 KiB
HTML
572 lines
22 KiB
HTML
<html><head><title>
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HDF5 Glossary
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</title>
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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/GenElect.css" rel="stylesheet" type="text/css">
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<body>
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<!-- #BeginLibraryItem "/ed_libs/NavBar_ADevG.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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<!--
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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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<a href="http://hdf.ncsa.uiuc.edu/HDF5/doc/UG/index.html">HDF5 User's Guide</a> <br>
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<a href="RM_H5Front.html">HDF5 Reference Manual</a> <br>
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<a href="ADGuide.html">HDF5 Application Developer's Guide</a> <br>
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</td></tr>
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</table>
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</center>
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<hr><!-- #EndLibraryItem --><center>
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<h1>HDF5 Glossary</h1>
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</center>
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<center>
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<table width=90% border=0>
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<tr><td valign=top align=left width=33%>
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<dl>
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<dt><a href="#Glossary-AtomicDType">atomic datatype</a>
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<dt><a href="#Glossary-Attribute">attribute</a>
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<!--<dt><a href="#Glossary-BasicDType">basic datatype</a>-->
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<dt><a href="#Glossary-LayoutChunked">chunked layout</a>
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<dt><a href="#Glossary-Chunking">chunking</a>
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<!--<dt><a href="#Glossary-ComplexDType">complex datatype</a>-->
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<dt><a href="#Glossary-CompoundDType">compound datatype</a>
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<!--<dt>compound element-->
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<dt><a href="#Glossary-LayoutContig">contiguous layout</a>
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<!--<dt>conversion function-->
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<dt><a href="#Glossary-Dataset">dataset</a>
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<dt><a href="#Glossary-Dataspace">dataspace</a>
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<!--<dl>-->
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<!-- <dt>dimensions-->
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<!-- <dt>selection-->
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<!--</dl>-->
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<dt><a href="#Glossary-Datatype">datatype</a>
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<dl>
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<dt><a href="#Glossary-AtomicDType">atomic</a>
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<!-- <dt><a href="#Glossary-BasicDType">basic</a>-->
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<!-- <dt><a href="#Glossary-ComplexDType">complex</a>-->
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<dt><a href="#Glossary-CompoundDType">compound</a>
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<!-- <dt>conversion function-->
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<!-- <dt><a href="#Glossary-DiskIO">disk I/O</a>-->
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<dt><a href="#Glossary-DTypeEnum">enumeration</a>
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<dt><a href="#Glossary-DTypeNamed">named</a>
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<dt><a href="#Glossary-DTypeOpaque">opaque</a>
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<!-- <dt>transient-->
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<dt><a href="#Glossary-DTypeVLen">variable-length</a>
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</dl>
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<!--<dt>DDL-->
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<!--<dt>dimensions-->
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<!--<dt><a href="#Glossary-DiskIO">disk I/O datatype</a>-->
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<!--<dt>element-->
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<dt><a href="#Glossary-DTypeEnum">enumeration datatype</a>
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<dt><a href="#Glossary-File">file</a>
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<dl>
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<!-- <dt>compound element-->
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<!-- <dt>element-->
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<dt><a href="#Glossary-Group">group</a>
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<dt><a href="#Glossary-Path">path</a>
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<dt><a href="#Glossary-RootGroup">root group</a>
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<dt><a href="#Glossary-SuperBlock">super block</a>
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</dl>
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</dl>
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</td>
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<td valign=top align=left width=34%>
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<dl>
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<dt><a href="#Glossary-FileAccessMode">file access mode</a>
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<dt><a href="#Glossary-Group">group</a>
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<dl>
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<!-- <dt>element-->
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<dt><a href="#Glossary-GroupMember">member</a>
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<dt><a href="#Glossary-RootGroup">root group</a>
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</dl>
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<dt><a href="#Glossary-LinkHard">hard link</a>
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<!--<dt>HDF5-->
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<dt><a href="#Glossary-Hyperslab">hyperslab</a>
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<dt><a href="#Glossary-Identifier">identifier</a>
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<dt><a href="#Glossary-Link">link</a>
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<dl>
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<dt><a href="#Glossary-LinkHard">hard</a>
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<dt><a href="#Glossary-LinkSoft">soft</a>
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<!-- <dt><a href="#Glossary-LinkSoftName">soft link name</a>-->
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<!-- <dt>target-->
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</dl>
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<dt><a href="#Glossary-GroupMember">member</a>
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<dt><a href="#Glossary-Name">name</a>
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<dt><a href="#Glossary-DTypeNamed">named datatype</a>
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<dt><a href="#Glossary-DTypeOpaque">opaque datatype</a>
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<dt><a href="#Glossary-Path">path</a>
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<!--<dt>parallel I/O-->
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<dt><a href="#Glossary-PList">property list</a>
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<dl>
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<dt><a href="#Glossary-PListDataTransfer">data transfer</a>
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<dt><a href="#Glossary-PListDSetAccess">dataset access</a>
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<dt><a href="#Glossary-PListDSetCreate">dataset creation</a>
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<dt><a href="#Glossary-PListFileAccess">file access</a>
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<dt><a href="#Glossary-PListFileCreate">file creation</a>
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</dl>
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</dl>
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</td>
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<td valign=top align=left width=33%>
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<dl>
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<dt><a href="#Glossary-RootGroup">root group</a>
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<dt><a href="#Glossary-Selection">selection</a>
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<dl>
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<dt><a href="#Glossary-Hyperslab">hyperslab</a>
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<!-- <dt>point-->
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</dl>
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<dt><a href="#Glossary-Serialization">serialization</a>
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<dt><a href="#Glossary-LinkSoft">soft link</a>
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<!--<dt><a href="#Glossary-LinkSoftName">soft link name</a>-->
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<dt><a href="#Glossary-StorageLayout">storage layout</a>
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<dl>
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<dt><a href="#Glossary-LayoutChunked">chunked</a>
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<dt><a href="#Glossary-Chunking">chunking</a>
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<dt><a href="#Glossary-LayoutContig">contiguous</a>
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</dl>
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<dt><a href="#Glossary-SuperBlock">super block</a>
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<!--<dt>target-->
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<!--<dt>threadsafe-->
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<!--<dt>transient datatype-->
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<dt><a href="#Glossary-DTypeVLen">variable-length datatype</a>
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</dl>
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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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<DL>
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<dt><strong><a name="Glossary-AtomicDType">atomic datatype</a></strong>
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<dd>A datatype which cannot be decomposed into smaller units at the
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API level.
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<P>
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<DT><a name="Glossary-Attribute"><B>attribute</B></a>
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<DD>A small dataset that can be used to describe the nature and/or
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the intended usage of the object it is attached to.
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<P>
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<!--
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<dt><strong><a name="Glossary-Basic">basic datatypes</a></strong>
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<ul>
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<li>char - 8-bit character (only for ASCII information)
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<li>int8 - 8-bit signed integer
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<li>uint8 - 8-bit unsigned integer
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<li>int16 - 16-bit signed integer
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<li>uint16 - 16-bit unsigned integer
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<li>int32 - 32-bit signed integer
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<li>uint32 - 32-bit unsigned integer
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<li>intn - "native" signed integer
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<li>uintn - "native" unsigned integer
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<li>int64 - 64-bit signed integer (new)
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<li>uint64 - 64-bit unsigned integer (new)
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<li>float32 - 32-bit IEEE float
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<li>float64 - 64-bit IEEE float
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</ul>
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<P>
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-->
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<dt><strong><a name="Glossary-LayoutChunked">chunked layout</a></strong>
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<dd>The storage layout of a chunked dataset.
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<P>
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<dt><strong><a name="Glossary-Chunking">chunking</a></strong>
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<dd>A storage layout where a dataset is partitioned into fixed-size
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multi-dimensional chunks. Chunking tends to improve performance
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and facilitates dataset extensibility.
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<P>
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<dt><strong><a name="Glossary-CompoundDType">compound datatype</a></strong>
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<dd>A collection of one or more atomic types or small arrays of such types.
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Similar to a struct in C or a common block in Fortran.
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<P>
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<!--
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<dt><strong><a name="Glossary-ComplexDType">complex datatype</a></strong>
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<dd>A collection of one or more atomic types or small arrays of such types.
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<ul>
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<li>hid_t - 32-bit unsigned integer used as ID for memory objects
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<li>hoid_t - 32-bit unsigned integer (currently) used as ID for
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disk-based objects
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<li>hbool_t - boolean to indicate true/false/error codes from functions
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<li>herr_t - 32-bit integer to indicate succeed/fail codes from
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functions
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</ul>
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<P>
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-->
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<dt><strong><a name="Glossary-LayoutContig">contiguous layout</a></strong>
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<dd>The storage layout of a dataset that is not chunked, so that the entire
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data portion of the dataset is stored in a single contiguous block.
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<P>
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<DT><B><a name="Glossary-PListDataTransfer">data transfer property list</a></B>
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<DD>The data transfer property list is used to control various aspects
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of the I/O, such as caching hints or collective I/O information.
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<P>
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<DT><B><a name="Glossary-Dataset">dataset</a></B>
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<DD>A multi-dimensional array of data elements, together with
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supporting metadata.
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<P>
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<!-- NEW PAGE -->
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<DT><B><a name="Glossary-PListDSetAccess">dataset access property list</a></B>
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<DD>A property list containing information on how a dataset is to be accessed.
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<P>
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<DT><B><a name="Glossary-PListDSetCreate">dataset creation property list</a></B>
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<DD>A property list containing information on how
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raw data is organized on disk and how the raw data is compressed.
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<!--
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The dataset API partitions these terms by layout, compression,
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and external storage:
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<UL>
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<B> Layout:</B>
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<UL>
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<LI>H5D_COMPACT: Data is small and can be stored in object header (not
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implemented yet). This eliminates disk seek/read requests.
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<LI>H5D_CONTIGUOUS: (<B>default</B>) The data is large, non-extendible,
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non-compressible, non-sparse, and can be stored externally.
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<LI>H5D_CHUNKED: The data is large and can be extended in any dimension.
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It is partitioned into chunks so each chunk is the same logical size.
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</UL>
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<B>Compression:</B> (gzip compression)<BR>
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<B>External Storage Properties:</B> The data must be contiguous to be
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stored externally. It allows you to store
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the data in one or more non-HDF5 files.
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</UL>
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-->
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<P>
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<DT><B><a name="Glossary-Dataspace">dataspace</a></B>
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<DD>An object that describes the dimensionality of the data array.
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A dataspace is either a regular N-dimensional array of data points,
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called a simple dataspace, or a more general collection of data points
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organized in another manner, called a complex dataspace.
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<P>
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<DT><B><a name="Glossary-Datatype">datatype</a></B>
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<DD>An object that describes the storage format of the individual data
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points of a data set.
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There are two categories of datatypes: atomic and compound datatypes.
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An atomic type is a type which cannot be decomposed into smaller
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units at the API level. A compound datatype is a collection of one or
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more atomic types or small arrays of such types.
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<P>
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<!--
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<DT><B>DDL</B>
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<DD>A detailed description of the HDF5 format and objects, written in a
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Data Description Language using Backus-Naur Form.
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<P>
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-->
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<!--
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<dt><strong><a name="Glossary-DiskIO">disk I/O datatypes</a></strong>
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<ul>
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<li>hoff_t - (64-bit?) offset on disk in bytes
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<li>hlen_t - (64-bit?) length on disk in bytes
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</ul>
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<P>
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-->
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<dt><strong><a name="Glossary-DTypeEnum">enumeration datatype</a></strong>
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<dd>A one-to-one mapping between a set of symbols and a set of
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integer values, and an order is imposed on the symbols by their
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integer values. The symbols are passed between the application
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and library as character strings and all the values for a
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particular enumeration datatype are of the same integer type,
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which is not necessarily a native type.
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<P>
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<DT><B><a name="Glossary-File">file</a></B>
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<DD>A container for storing grouped collections of
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multi-dimensional arrays containing scientific data.
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<P>
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<DT><B><a name="Glossary-FileAccessMode">file access mode</a></B>
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<DD>Determines whether an existing file will be overwritten,
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opened for read-only access, or opened for read/write access.
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All newly created files are opened for both reading and
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writing.
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<!--
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Possible values are:
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<PRE>
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H5F_ACC_RDWR: Allow read and write access to file.
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H5F_ACC_RDONLY: Allow read-only access to file.
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H5F_ACC_TRUNC: Truncate file, if it already exists, erasing all data
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previously stored in the file.
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H5F_ACC_EXCL: Fail if file already exists.
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H5F_ACC_DEBUG: Print debug information.
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H5P_DEFAULT: Apply default file access and creation properties.
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</PRE>
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-->
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<P>
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<DT><B><a name="Glossary-PListFileAccess">file access property list</a></B>
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<DD>File access property lists are used to control different methods
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of performing I/O on files:
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<!--
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<UL>
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<B>Unbuffered I/O:</B> Local permanent files can be accessed with the
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functions described in Section 2 of the Posix manual, namely open(),
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lseek(), read(), write(), and close(). <BR>
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<B>Buffered I/O:</B> Local permanent files can be accessed with the
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functions declared in the stdio.h header file, namely fopen(),
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fseek(), fread(), fwrite(), and fclose().<BR>
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<B>Memory I/O:</B> Local temporary files can be created and accessed
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directly from memory without ever creating permanent storage.
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The library uses malloc() and free() to create storage space for the
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file<BR>
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<B>Parallel Files using MPI I/O:</B> This driver allows parallel access
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to a file through the MPI I/O library. The parameters which can be
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modified are the MPI communicator, the info object, and the access mode.
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The communicator and info object are saved and then passed to
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MPI_File_open() during file creation or open. The access_mode
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controls the kind of parallel access the application intends.<BR>
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<B>Data Alignment:</B> Sometimes file access is faster if certain things
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are aligned on file blocks. This can be controlled by setting alignment
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properties of a file access property list with the H5Pset_alignment()
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function.
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</UL>
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-->
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<P>
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<DT><B><a name="Glossary-PListFileCreate">file creation property list</a></B>
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<DD>The property list used to control file metadata.
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<!--
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The parameters that can be modified are:
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<UL>
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<B>User-Block Size:</B> The "user-block" is a fixed length block
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of data located at the beginning of the file which is ignored
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by the HDF5 library and may be used to store any data information
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found to be useful to applications.
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<BR>
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<B>Offset and Length Sizes:</B> The number of bytes used to store the
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offset and length of objects in the HDF5 file can be controlled
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with this parameter.
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<BR>
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<b>Symbol Table Parameters:</b> The size of symbol table B-trees can
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be controlled by setting the 1/2 rank and 1/2 node size
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parameters of the B-tree.
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<BR>
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<B>Indexed Storage Parameters:</B> The size of indexed storage
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B-trees can be controlled by setting the 1/2 rank and 1/2 node
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size parameters of the B-tree.
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</UL>
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-->
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<P>
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<DT><B><a name="Glossary-Group">group</a></B>
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<DD>A structure containing zero or more HDF5 objects,
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together with supporting metadata.
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The two primary HDF5 objects are datasets and groups.
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<P>
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<dt><strong><a name="Glossary-LinkHard">hard link</a></strong>
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<dd>A direct association between a name and the object where both exist
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in a single HDF5 address space.
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<P>
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<!--
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<DT><B>HDF5</B>
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<DD>HDF5 is an abbreviation for Hierarchical Data Format Version 5.
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This file format is intended to make it easy to write and read
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scientific data
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<P>
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<UL>
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<LI>by including the information needed to understand the data
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within the file
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<P>
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<LI>by providing a library of C, FORTRAN, and other language
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programs that reduce the work required to provide efficient
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writing and reading - even with parallel IO
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</UL>
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<P>
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-->
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<DT><B><a name="Glossary-Hyperslab">hyperslab</a></B>
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<DD>A portion of a dataset. A hyperslab selection can be a
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logically contiguous collection of points in a dataspace or
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a regular pattern of points or blocks in a dataspace.
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<P>
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<dt><strong><a name="Glossary-Identifier">identifier</a></strong>
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<dd>A unique entity provided by the HDF5 library and used to access
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an HDF5 object, such as a file, goup, dataset, datatype, etc.
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<P>
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<dt><strong><a name="Glossary-Link">link</a></strong>
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<dd>An association between a name and the object in an HDF5 file group.
|
|
<P>
|
|
|
|
<dt><strong><a name="Glossary-GroupMember">member</a></strong>
|
|
<dd>A group or dataset that is in another dataset, <i>dataset A</i>,
|
|
is a member of <i>dataset A</i>.
|
|
<P>
|
|
|
|
<DT><B><a name="Glossary-Name">name</a></B>
|
|
<DD>A slash-separated list of components that uniquely identifies an
|
|
element of an HDF5 file. A name begins that begins with a slash
|
|
is an absolute name which is accessed beginning with the root group
|
|
of the file; all other names are relative names and the associated
|
|
objects are accessed beginning with the current or specified group.
|
|
<P>
|
|
|
|
<dt><strong><a name="Glossary-DTypeNamed">named datatype</a></strong>
|
|
<dd>A datatype that is named and stored in a file. Naming is permanent;
|
|
a datatype cannot be changed after being named.
|
|
<P>
|
|
|
|
<dt><strong><a name="Glossary-DTypeOpaque">opaque datatype</a></strong>
|
|
<dd>A mechanism for describing data which cannot be otherwise described
|
|
by HDF5. The only properties associated with opaque types are a
|
|
size in bytes and an ASCII tag.
|
|
<P>
|
|
|
|
<!--
|
|
<DT><B>parallel I/O HDF5</B>
|
|
<DD>The parallel I/O version of HDF5 supports parallel file access using
|
|
MPI (Message Passing Interface).
|
|
<P>
|
|
-->
|
|
|
|
<dt><strong><a name="Glossary-Path">path</a></strong>
|
|
<dd>The slash-separated list of components that forms the name
|
|
uniquely identifying an element of an HDF5 file.
|
|
<P>
|
|
|
|
<dt><strong><a name="Glossary-PList">property list</a></strong>
|
|
<dd>A collection of name/value pairs that can be passed to other
|
|
HDF5 functions to control features that are typically unimportant
|
|
or whose default values are usually used.
|
|
<P>
|
|
|
|
<dt><strong><a name="Glossary-RootGroup">root group</a></strong>
|
|
<dd>The group that is the entry point to the group graph in an HDF5 file.
|
|
Every HDF5 file has exactly one root group.
|
|
<P>
|
|
|
|
<dt><strong><a name="Glossary-Selection">selection</a></strong>
|
|
<dd>(1) A subset of a dataset or a dataspace, up to the entire dataset or
|
|
dataspace.
|
|
(2) The elements of an array or dataset that are marked for I/O.
|
|
<P>
|
|
|
|
<dt><strong><a name="Glossary-Serialization">serialization</a></strong>
|
|
<dd>The flattening of an <em>N</em>-dimensional data object into a
|
|
1-dimensional object so that, for example, the data object can be
|
|
transmitted over the network as a 1-dimensional bitstream.
|
|
<P>
|
|
|
|
<dt><strong><a name="Glossary-LinkSoft">soft link</a></strong>
|
|
<dd>An indirect association between a name and an object in an
|
|
HDF5 file group.
|
|
<P>
|
|
|
|
<dt><strong><a name="Glossary-StorageLayout">storage layout</a></strong>
|
|
<dd>The manner in which a dataset is stored, either contiguous or
|
|
chunked, in the HDF5 file.
|
|
<P>
|
|
|
|
<DT><B><a name="Glossary-SuperBlock">super block</a></B>
|
|
<DD>A block of data containing the information required to portably access
|
|
HDF5 files on multiple platforms, followed by information about the groups
|
|
and datasets in the file.
|
|
The super block contains information about the size of offsets,
|
|
lengths of objects, the number of entries in group tables,
|
|
and additional version information for the file.
|
|
<P>
|
|
|
|
<!--
|
|
<DT><B>threadsafe</B>
|
|
<DD>A "thread-safe" version of HDF-5 (TSHDF5) is one that can be called
|
|
from any thread of a multi-threaded program. Any calls to HDF
|
|
can be made in any order, and each individual HDF call will perform
|
|
correctly. A calling program does not have to explicitly lock the HDF
|
|
library in order to do I/O. Applications programmers may assume that
|
|
the TSHDF5 guarantees the following:
|
|
<UL>
|
|
<LI>the HDF-5 library does not create or destroy threads.
|
|
<LI>the HDF-5 library uses modest amounts of per-thread
|
|
private memory.
|
|
<LI>the HDF-5 library only locks/unlocks it's own locks (no locks
|
|
are passed in or returned from HDF), and the internal locking
|
|
is guaranteed to be deadlock free.
|
|
</UL>
|
|
<P>
|
|
These properties mean that the TSHDF5 library will not interfere
|
|
with an application's use of threads. A TSHDF5 library is the same
|
|
library as regular HDF-5 library, with additional code to synchronize
|
|
access to the HDF-5 library's internal data structures.
|
|
<P>
|
|
-->
|
|
|
|
<dt><strong><a name="Glossary-DTypeVLen">variable-length datatype</a></strong>
|
|
<dd>A sequence of an existing datatype (atomic, variable-length (VL),
|
|
or compound) which are not fixed in length from one dataset location
|
|
to another.
|
|
<P>
|
|
|
|
</DL>
|
|
|
|
|
|
<!-- #BeginLibraryItem "/ed_libs/NavBar_ADevG.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="Glossary.html">Glossary</a><br>
|
|
-->
|
|
</td>
|
|
<td valign=top align=right>
|
|
<a href="http://hdf.ncsa.uiuc.edu/HDF5/doc/UG/index.html">HDF5 User's Guide</a> <br>
|
|
<a href="RM_H5Front.html">HDF5 Reference Manual</a> <br>
|
|
<a href="ADGuide.html">HDF5 Application Developer's Guide</a> <br>
|
|
</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 1.7, the unreleased development branch; working toward HDF5 Release 1.8.0
|
|
</address><!-- #EndLibraryItem --><SCRIPT LANGUAGE="JAVASCRIPT">
|
|
<!--
|
|
document.writeln("Last modified: 24 February 2004");
|
|
-->
|
|
</SCRIPT>
|
|
|
|
</body>
|
|
</html>
|