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4050 lines
121 KiB
4050 lines
121 KiB
<html>
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<head>
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<title>
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HDF5 File Format Specification
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</title>
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</head>
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<body bgcolor="#FFFFFF">
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<center>
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<table border=0 width=90%>
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<tr>
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<td valign=top>
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<ol type="I">
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<li><a href="#Intro">Introduction</a>
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<li><a href="#BootBlock">Disk Format Level 0 - File Signature and Super Block</a>
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<li><a href="#Group">Disk Format Level 1 - File Infrastructure</a>
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<font size=-2>
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<ol type="A">
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<li><a href="#Btrees">Disk Format Level 1A - B-link Trees and B-tree Nodes</a>
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<li><a href="#SymbolTable">Disk Format Level 1B - Group</a>
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<li><a href="#SymbolTableEntry">Disk Format Level 1C - Group Entry</a>
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<li><a href="#LocalHeap">Disk Format Level 1D - Local Heaps</a>
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<li><a href="#GlobalHeap">Disk Format Level 1E - Global Heap</a>
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<li><a href="#FreeSpaceIndex">Disk Format Level 1F - Free-space Index</a>
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</ol>
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</font>
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<li><a href="#DataObject">Disk Format Level 2 - Data Objects</a>
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<font size=-2>
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<ol type="A">
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<li><a href="#ObjectHeader">Disk Format Level 2a - Data Object Headers</a>
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<ol type="1">
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<li><a href="#NILMessage">Name: NIL</a> <!-- 0x0000 -->
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<li><a href="#SimpleDataSpace">Name: Simple Dataspace</a> <!-- 0x0001 -->
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<!--
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<li><a href="#DataSpaceMessage">Name: Complex Dataspace</a> --> <!-- 0x0002 -->
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<li><a href="#DataTypeMessage">Name: Datatype</a> <!-- 0x0003 -->
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<li><a href="#FillValueMessage">Name: Data Storage - Fill Value</a> <!-- 0x0004 -->
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<li><a href="#ReservedMessage_0005">Name: Reserved - not assigned yet</a> <!-- 0x0005 -->
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</ol>
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</ol>
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</font>
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</ol>
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</td><td> </td><td valign=top>
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<ol type="I" start="4">
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<li><a href="#DataObject">Disk Format Level 2 - Data Objects</a>
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<font size=-2><i>(Continued)</i>
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<ol type="A">
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<li><a href="#ObjectHeader">Disk Format Level 2a - Data Object Headers</a><i>(Continued)</i>
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<ol type="1" start="6">
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<li><a href="#CompactDataStorageMessage">Name: Data Storage - Compact</a> <!-- 0x0006 -->
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<li><a href="#ExternalFileListMessage">Name: Data Storage - External Data Files</a> <!-- 0x0007 -->
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<li><a href="#LayoutMessage">Name: Data Storage - Layout</a> <!-- 0x0008 -->
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<li><a href="#ReservedMessage_0009">Name: Reserved - not assigned yet</a> <!-- 0x0009 -->
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<li><a href="#ReservedMessage_000A">Name: Reserved - not assigned yet</a> <!-- 0x000a -->
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<li><a href="#FilterMessage">Name: Data Storage - Filter Pipeline</a> <!-- 0x000b -->
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<li><a href="#AttributeMessage">Name: Attribute</a> <!-- 0x000c -->
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<li><a href="#NameMessage">Name: Object Name</a> <!-- 0x000d -->
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<li><a href="#ModifiedMessage">Name: Object Modification Date and Time</a> <!-- 0x000e -->
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<li><a href="#SharedMessage">Name: Shared Object Message</a> <!-- 0x000f -->
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<li><a href="#ContinuationMessage">Name: Object Header Continuation</a> <!-- 0x0010 -->
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<li><a href="#SymbolTableMessage">Name: Group Message</a> <!-- 0x0011 -->
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</ol>
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<li><a href="#SharedObjectHeader">Disk Format: Level 2b - Shared Data Object Headers</a>
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<li><a href="#DataStorage">Disk Format: Level 2c - Data Object Data Storage</a>
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</ol>
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</font>
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</ol>
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</td></tr>
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</table>
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</center>
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<br><br>
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<h2>Introduction</h2>
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<table align=right width=100>
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<tr><td> </td><td align=center>
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<hr>
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<img src="FF-IH_FileGroup.gif" alt="HDF5 Groups" hspace=15 vspace=15>
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</td><td> </td></tr>
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<tr><td> </td><td align=center>
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<strong>Figure 1:</strong> Relationships among the HDF5 root group, other groups, and objects
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<hr>
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</td><td> </td></tr>
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<tr><td> </td><td align=center>
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<img src="FF-IH_FileObject.gif" alt="HDF5 Objects" hspace=15 vspace=15>
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</td><td> </td></tr>
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<tr><td> </td><td align=center>
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<strong>Figure 2:</strong> HDF5 objects -- datasets, datatypes, or dataspaces
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<hr>
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</td><td> </td></tr>
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</table>
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<P>The format of an HDF5 file on disk encompasses several
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key ideas of the HDF4 and AIO file formats as well as
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addressing some shortcomings therein. The new format is
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more self-describing than the HDF4 format and is more
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uniformly applied to data objects in the file.
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<P>An HDF5 file appears to the user as a directed graph.
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The nodes of this graph are the higher-level HDF5 objects
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that are exposed by the HDF5 APIs:
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<ul>
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<li>Groups
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<li>Datasets
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<li>Datatypes
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<li>Dataspaces
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</ul>
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<P>At the lowest level, as information is actually written to the disk,
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an HDF5 file is made up of the following objects:
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<ul>
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<li>A super block
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<li>B-tree nodes (containing either symbol nodes or raw data chunks)
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<li>Object headers
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<li>Collections
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<li>Local heaps
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<li>Free space
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</ul>
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The HDF5 library uses these lower-level objects to represent the
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higher-level objects that are then presented to the user or
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to applications through the APIs.
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For instance, a group is an object header that contains a message that
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points to a local heap and to a B-tree which points to symbol nodes.
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A dataset is an object header that contains messages that describe
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datatype, space, layout, filters, external files, fill value, etc
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with the layout message pointing to either a raw data chunk or to a
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B-tree that points to raw data chunks.
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<h3>This Document</h3>
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<p>This document describes the lower-level data objects;
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the higher-level objects and their properties are described
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in the <a href="H5.user.html"><cite>HDF5 User Guide</cite></a>.
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<!--
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<blockquote>
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<pre>
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Elena> NOTE: give reference to the detailed discussion of the B-trees
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Elena> when needed. Right now we do not have specification (only general one)
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Elena> for the Symbol Table B-trees and B-trees used to manage chunked datasets.
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Elena> B-trees
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Elena> General Discussion
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Elena> Object related discussions
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Elena> Symbol Tables
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Elena> Global heap
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Elena> "Free-space object"
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</pre>
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</blockquote>
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-->
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<P>Three levels of information comprise the file format.
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Level 0 contains basic information for identifying and
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defining information about the file. Level 1 information contains
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the group information (stored as a B-tree) and is used as the
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index for all the objects in the file. Level 2 is the rest
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of the file and contains all of the data objects, with each object
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partitioned into header information, also known as
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<em>meta information</em>, and data.
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<p>The sizes of various fields in the following layout tables are
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determined by looking at the number of columns the field spans
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in the table. There are three exceptions: (1) The size may be
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overridden by specifying a size in parentheses, (2) the size of
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addresses is determined by the <em>Size of Offsets</em> field
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in the super block, and (3) the size of size fields is determined
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by the <em>Size of Lengths</em> field in the super block.
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<br><br>
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<br><br>
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<h2><a name="BootBlock">
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Disk Format: Level 0 - File Signature and Super Block</a></h2>
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<P>The super block may begin at certain predefined offsets within
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the HDF5 file, allowing a block of unspecified content for
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users to place additional information at the beginning (and
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end) of the HDF5 file without limiting the HDF5 library's
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ability to manage the objects within the file itself. This
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feature was designed to accommodate wrapping an HDF5 file in
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another file format or adding descriptive information to the
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file without requiring the modification of the actual file's
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information. The super block is located by searching for the
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HDF5 file signature at byte offset 0, byte offset 512 and at
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successive locations in the file, each a multiple of two of
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the previous location, i.e. 0, 512, 1024, 2048, etc.
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<P>The super block is composed of a file signature, followed by
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super block and group version numbers, information
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about the sizes of offset and length values used to describe
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items within the file, the size of each group page,
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and a group entry for the root object in the file.
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<p>
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<center>
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<table border align=center cellpadding=4 width="80%">
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<caption align=top>
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<B>HDF5 Super Block Layout</B>
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</caption>
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<tr align=center>
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<th width="25%">byte</th>
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<th width="25%">byte</th>
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<th width="25%">byte</th>
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<th width="25%">byte</th>
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</tr>
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<tr align=center>
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<td colspan=4><br>HDF5 File Signature (8 bytes)<br><br></td>
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</tr>
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<tr align=center>
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<td>Version # of Super Block</td>
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<td>Version # of Global Free-space Storage</td>
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<td>Version # of Group</td>
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<td>Reserved</td>
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</tr>
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<tr align=center>
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<td>Version # of Shared Header Message Format</td>
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<td>Size of Offsets</td>
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<td>Size of Lengths</td>
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<td>Reserved (zero)</td>
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</tr>
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<tr align=center>
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<td colspan=2>Group Leaf Node K</td>
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<td colspan=2>Group Internal Node K</td>
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</tr>
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<tr align=center>
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<td colspan=4>File Consistency Flags</td>
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</tr>
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<tr align=center>
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<td colspan=4>Base Address*</td>
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</tr>
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<tr align=center>
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<td colspan=4>Address of Global Free-space Heap*</td>
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</tr>
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<tr align=center>
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<td colspan=4>End of File Address*</td>
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</tr>
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<tr align=center>
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<td colspan=4>Driver Information Block Address*</td>
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</tr>
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<tr align=center>
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<td colspan=4>Root Group Address*</td>
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</tr>
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</table>
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<table width="80%" border=0>
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<tr><td>
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<div align=right>
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(Items marked with an asterisk (*) in the above table
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<br>
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are of the size specified in "Size of Offsets.")
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</div>
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</td></tr>
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</table>
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</center>
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<p>
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<center>
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<table width="80%">
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<tr>
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<th width="30%">Field Name</th>
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<th width="70%">Description</th>
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</tr>
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<tr valign=top>
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<td>File Signature</td>
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<td>This field contains a constant value and can be used to
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quickly identify a file as being an HDF5 file. The
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constant value is designed to allow easy identification of
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an HDF5 file and to allow certain types of data corruption
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to be detected. The file signature of an HDF5 file always
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contains the following values:
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<br><br><center>
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<table border align=center cellpadding=4 width="100%">
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<tr align=center>
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<td>decimal</td>
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<td width="8%">137</td>
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<td width="8%">72</td>
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<td width="8%">68</td>
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<td width="8%">70</td>
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<td width="8%">13</td>
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<td width="8%">10</td>
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<td width="8%">26</td>
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<td width="8%">10</td>
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</tr>
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<tr align=center>
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<td>hexadecimal</td>
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<td width="8%">89</td>
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<td width="8%">48</td>
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<td width="8%">44</td>
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<td width="8%">46</td>
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<td width="8%">0d</td>
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<td width="8%">0a</td>
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<td width="8%">1a</td>
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<td width="8%">0a</td>
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</tr>
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<tr align=center>
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<td>ASCII C Notation</td>
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<td width="8%">\211</td>
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<td width="8%">H</td>
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<td width="8%">D</td>
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<td width="8%">F</td>
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<td width="8%">\r</td>
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<td width="8%">\n</td>
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<td width="8%">\032</td>
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<td width="8%">\n</td>
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</tr>
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</table>
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</center>
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<br>
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This signature both identifies the file as an HDF5 file
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and provides for immediate detection of common
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file-transfer problems. The first two bytes distinguish
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HDF5 files on systems that expect the first two bytes to
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identify the file type uniquely. The first byte is
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chosen as a non-ASCII value to reduce the probability
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that a text file may be misrecognized as an HDF5 file;
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also, it catches bad file transfers that clear bit
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7. Bytes two through four name the format. The CR-LF
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sequence catches bad file transfers that alter newline
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sequences. The control-Z character stops file display
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under MS-DOS. The final line feed checks for the inverse
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of the CR-LF translation problem. (This is a direct
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descendent of the PNG file signature.)</td>
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</tr>
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<tr valign=top>
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<td>Version Number of the Super Block</td>
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<td>This value is used to determine the format of the
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information in the super block. When the format of the
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information in the super block is changed, the version number
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is incremented to the next integer and can be used to
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determine how the information in the super block is
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formatted.</td>
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</tr>
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<tr valign=top>
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<td>Version Number of the Global Free-space Heap</td>
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<td>This value is used to determine the format of the
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information in the Global Free-space Heap.</td>
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</tr>
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<tr valign=top>
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<td>Version Number of the Group</td>
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<td>This value is used to determine the format of the
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information in the Group. When the format of
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the information in the Group is changed, the
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version number is incremented to the next integer and can be
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used to determine how the information in the Group
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is formatted.</td>
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</tr>
|
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<tr valign=top>
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<td>Version Number of the Shared Header Message Format</td>
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<td>This value is used to determine the format of the
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information in a shared object header message, which is
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stored in the global small-data heap. Since the format
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of the shared header messages differs from the private
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header messages, a version number is used to identify changes
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in the format.</td>
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</tr>
|
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<tr valign=top>
|
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<td>Size of Offsets</td>
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<td>This value contains the number of bytes used to store
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addresses in the file. The values for the addresses of
|
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objects in the file are offsets relative to a base address,
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usually the address of the super block signature. This
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allows a wrapper to be added after the file is created
|
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without invalidating the internal offset locations.</td>
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</tr>
|
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|
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<tr valign=top>
|
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<td>Size of Lengths</td>
|
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<td>This value contains the number of bytes used to store
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the size of an object.</td>
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</tr>
|
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<tr valign=top>
|
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<td>Group Leaf Node K</td>
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<td>Each leaf node of a group B-tree will have at
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least this many entries but not more than twice this
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many. If a group has a single leaf node then it
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may have fewer entries.</td>
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</tr>
|
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|
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<tr valign=top>
|
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<td>Group Internal Node K</td>
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<td>Each internal node of a group B-tree will have
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at least K pointers to other nodes but not more than 2K
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pointers. If the group has only one internal
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node then it might have fewer than K pointers.</td>
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</tr>
|
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|
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<tr valign=top>
|
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<td>Bytes per B-tree Page</td>
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<td>This value contains the number of bytes used for symbol
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pairs per page of the B-trees used in the file. All
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B-tree pages will have the same size per page.
|
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<br>
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For 32-bit file offsets, 340 objects is the maximum
|
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per 4KB page; for 64-bit file offset, 254 objects will fit
|
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per 4KB page. In general, the equation is:
|
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<br>
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<code> <<i>number of objects</i>> =
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<br>
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FLOOR((<<i>page size</i>> - <<i>offset size</i>>) /
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<br>
|
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(<<i>Symbol size</i>> + <<i>offset size</i>>))
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- 1 </code></td>
|
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</tr>
|
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|
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<tr valign=top>
|
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<td>File Consistency Flags</td>
|
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<td>This value contains flags to indicate information
|
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about the consistency of the information contained
|
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within the file. Currently, the following bit flags are
|
|
defined:
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<ul>
|
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<li>Bit 0 set indicates that the file is opened for
|
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write-access.
|
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<li>Bit 1 set indicates that the file has
|
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been verified for consistency and is guaranteed to be
|
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consistent with the format defined in this document.
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<li>Bits 2-31 are reserved for future use.
|
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</ul>
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Bit 0 should be
|
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set as the first action when a file is opened for write
|
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access and should be cleared only as the final action
|
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when closing a file. Bit 1 should be cleared during
|
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normal access to a file and only set after the file's
|
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consistency is guaranteed by the library or a
|
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consistency utility.</td>
|
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</tr>
|
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|
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<tr valign=top>
|
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<td>Base Address</td>
|
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<td>This is the absolute file address of the first byte of
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the HDF5 data within the file. The library currently
|
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constrains this value to be the absolute file address
|
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of the super block itself when creating new files;
|
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future versions of the library may provide greater
|
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flexibility. Unless otherwise noted,
|
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all other file addresses are relative to this base
|
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address.</td>
|
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</tr>
|
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|
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<tr valign=top>
|
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<td>Address of Global Free-space Heap</td>
|
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<td>Free-space management is not yet defined in the HDF5
|
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file format and is not handled by the library.
|
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Currently this field always contains the
|
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undefined address <code>0xfff...ff</code>.
|
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<!--
|
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<td>This value contains the relative address of the B-tree
|
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used to manage the blocks of data which are unused in the
|
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file currently. The free-space heap is used to manage the
|
|
blocks of bytes at the file-level which become unused when
|
|
objects are moved within the file.</td>
|
|
-->
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>End of File Address</td>
|
|
<td>This is the relative file address of the first byte past
|
|
the end of all HDF5 data. It is used to determine whether a
|
|
file has been accidentally truncated and as an address where
|
|
file data allocation can occur if the free list is not
|
|
used.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Driver Information Block Address</td>
|
|
<td>This is the relative file address of the file driver
|
|
information block which contains driver-specific
|
|
information needed to reopen the file. If there is no
|
|
driver information block then this entry should be the
|
|
undefined address (all bits set).</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Root Group Address</td>
|
|
<td>This is the address of the root group (described later
|
|
in this document), which serves as the entry point into
|
|
the group graph.</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
|
|
<p>The <em>file driver information block</em> is an optional region of the
|
|
file which contains information needed by the file driver in
|
|
order to reopen a file. The format of the file driver information
|
|
block is:
|
|
|
|
<p>
|
|
<center>
|
|
<table border align=center cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<B>Driver Information Block</B>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td>Version</td>
|
|
<td colspan=3>Reserved (zero)</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Driver Information Size (4 bytes)</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br>Driver Identification (8 bytes)<br><br></td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br><br>Driver Information<br><br><br></td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table align=center width="80%">
|
|
<tr>
|
|
<th width="30%">Field Name</th>
|
|
<th width="70%">Description</th>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Version</td>
|
|
<td>The version number of the driver information block. The
|
|
file format documented here is version zero.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Driver Information Size</td>
|
|
<td>The size in bytes of the Driver Information part of this
|
|
structure.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Driver Identification</td>
|
|
<td>This is an eight-byte ASCII string without null
|
|
termination which identifies the driver and version number
|
|
of the Driver Information block. The predefined drivers
|
|
supplied with the HDF5 library are identified by the
|
|
letters <code>NCSA</code> followed by the first four characters of
|
|
the driver name. If the Driver Information block is not
|
|
the original version then the last letter(s) of the
|
|
identification will be replaced by a version number in
|
|
ASCII.
|
|
For example, the various versions of the <em>family driver</em>
|
|
will be identified by <code>NCSAfami</code>, <code>NCSAfam0</code>,
|
|
<code>NCSAfam1</code>, etc.
|
|
(<code>NCSAfami</code> is simply <code>NCSAfamily</code> truncated
|
|
to eight characters. Subsequent identifiers will be created by
|
|
substituting sequential numerical values for the final character,
|
|
starting with zero.)
|
|
<p>
|
|
Identification for user-defined drivers
|
|
is arbitrary but should be unique.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Driver Information</td>
|
|
<td>Driver information is stored in a format defined by the
|
|
file driver and encoded/decoded by the driver callbacks
|
|
invoked from the <code>H5FD_sb_encode</code> and
|
|
<code>H5FD_sb_decode</code> functions.</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
|
|
<br><br>
|
|
<br><br>
|
|
|
|
|
|
<h2><a name="Group">
|
|
Disk Format: Level 1 - File Infrastructure</a></h2>
|
|
<h3><a name="Btrees">Disk Format: Level 1A - B-link Trees and B-tree Nodes</a></h3>
|
|
|
|
<p>B-link trees allow flexible storage for objects which tend to grow
|
|
in ways that cause the object to be stored discontiguously. B-trees
|
|
are described in various algorithms books including "Introduction to
|
|
Algorithms" by Thomas H. Cormen, Charles E. Leiserson, and Ronald
|
|
L. Rivest. The B-link tree, in which the sibling nodes at a
|
|
particular level in the tree are stored in a doubly-linked list,
|
|
is described in the "Efficient Locking for Concurrent Operations
|
|
on B-trees" paper by Phillip Lehman and S. Bing Yao as published
|
|
in the <em>ACM Transactions on Database Systems</em>, Vol. 6,
|
|
No. 4, December 1981.
|
|
|
|
<p>The B-link trees implemented by the file format contain one more
|
|
key than the number of children. In other words, each child
|
|
pointer out of a B-tree node has a left key and a right key.
|
|
The pointers out of internal nodes point to sub-trees while
|
|
the pointers out of leaf nodes point to symbol nodes and
|
|
raw data chunks.
|
|
Aside from that difference, internal nodes and leaf nodes
|
|
are identical.
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<B>B-tree Nodes</B>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Node Signature</td>
|
|
|
|
<tr align=center>
|
|
<td>Node Type</td>
|
|
<td>Node Level</td>
|
|
<td colspan=2>Entries Used</td>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Address of Left Sibling</td>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Address of Right Sibling</td>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Key 0 (variable size)</td>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Address of Child 0</td>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Key 1 (variable size)</td>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Address of Child 1</td>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>...</td>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Key 2<em>K</em> (variable size)</td>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Address of Child 2<em>K</em></td>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Key 2<em>K</em>+1 (variable size)</td>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table align=center width="80%">
|
|
<tr>
|
|
<th width="30%">Field Name</th>
|
|
<th width="70%">Description</th>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Node Signature</td>
|
|
<td>The ASCII character string <code>TREE</code> is
|
|
used to indicate the
|
|
beginning of a B-link tree node. This gives file
|
|
consistency checking utilities a better chance of
|
|
reconstructing a damaged file.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Node Type</td>
|
|
<td>Each B-link tree points to a particular type of data.
|
|
This field indicates the type of data as well as
|
|
implying the maximum degree <em>K</em> of the tree and
|
|
the size of each Key field.
|
|
<br>
|
|
<dl compact>
|
|
<dt>0
|
|
<dd>This tree points to group nodes.
|
|
<dt>1
|
|
<dd>This tree points to a new data chunk.
|
|
</dl>
|
|
</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Node Level</td>
|
|
<td>The node level indicates the level at which this node
|
|
appears in the tree (leaf nodes are at level zero). Not
|
|
only does the level indicate whether child pointers
|
|
point to sub-trees or to data, but it can also be used
|
|
to help file consistency checking utilities reconstruct
|
|
damaged trees.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Entries Used</td>
|
|
<td>This determines the number of children to which this
|
|
node points. All nodes of a particular type of tree
|
|
have the same maximum degree, but most nodes will point
|
|
to less than that number of children. The valid child
|
|
pointers and keys appear at the beginning of the node
|
|
and the unused pointers and keys appear at the end of
|
|
the node. The unused pointers and keys have undefined
|
|
values.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Address of Left Sibling</td>
|
|
<td>This is the file address of the left sibling of the
|
|
current node relative to the super block. If the current
|
|
node is the left-most node at this level then this field
|
|
is the undefined address (all bits set).</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Address of Right Sibling</td>
|
|
<td>This is the file address of the right sibling of the
|
|
current node relative to the super block. If the current
|
|
node is the right-most node at this level then this
|
|
field is the undefined address (all bits set).</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Keys and Child Pointers</td>
|
|
<td>Each tree has 2<em>K</em>+1 keys with 2<em>K</em>
|
|
child pointers interleaved between the keys. The number
|
|
of keys and child pointers actually containing valid
|
|
values is determined by the <em>Entries Used</em> field. If
|
|
that field is <em>N</em> then the B-link tree contains
|
|
<em>N</em> child pointers and <em>N</em>+1 keys.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Key</td>
|
|
<td>The format and size of the key values is determined by
|
|
the type of data to which this tree points. The keys are
|
|
ordered and are boundaries for the contents of the child
|
|
pointer; that is, the key values represented by child
|
|
<em>N</em> fall between Key <em>N</em> and Key
|
|
<em>N</em>+1. Whether the interval is open or closed on
|
|
each end is determined by the type of data to which the
|
|
tree points.
|
|
<p>
|
|
The format of the key depends on the node type.
|
|
For nodes of node type 1, the key is formatted as follows:
|
|
<center>
|
|
<table>
|
|
<tr valign=top align=left>
|
|
<td width=40%>Bytes 1-4</td>
|
|
<td>Size of chunk in bytes.</td>
|
|
<tr valign=top align=left></tr>
|
|
<td>Bytes 4-8</td>
|
|
<td>Filter mask, a 32-bit bitfield indicating which
|
|
filters have been applied to that chunk.</td>
|
|
</tr><tr valign=top align=left>
|
|
<td><i>N</i> fields of 8 bytes each</td>
|
|
<td>A 64-bit index indicating the offset of the
|
|
chunk within the dataset where <i>N</i> is the number
|
|
of dimensions of the dataset. For example, if
|
|
a chunk in a 3-dimensional dataset begins at the
|
|
position <code>[5,5,5]</code>, there will be three
|
|
such 8-bit indices, each with the value of
|
|
<code>5</code>.</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
<p>
|
|
For nodes of node type 0, the key is formatted as follows:
|
|
<center>
|
|
<table>
|
|
<tr valign=top align=left>
|
|
<td width=40%>A single field of <i>Size of Lengths</i>
|
|
bytes</td>
|
|
<td>Indicates the byte offset into the local heap
|
|
for the first object name in the subtree which
|
|
that key describes.</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Child Pointers</td>
|
|
<td>The tree node contains file addresses of subtrees or
|
|
data depending on the node level. Nodes at Level 0 point
|
|
to data addresses, either data chunk or group nodes.
|
|
Nodes at non-zero levels point to other nodes of the
|
|
same B-tree.</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
Each B-tree node looks like this:
|
|
|
|
<center>
|
|
<table>
|
|
<tr valign=top align=center>
|
|
<td>key[0]</td><td> </td>
|
|
<td>child[0]</td><td> </td>
|
|
<td>key[1]</td><td> </td>
|
|
<td>child[1]</td><td> </td>
|
|
<td>key[2]</td><td> </td>
|
|
<td>...</td><td> </td>
|
|
<td>...</td><td> </td>
|
|
<td>key[<i>N</i>-1]</td><td> </td>
|
|
<td>child[<i>N</i>-1]</td><td> </td>
|
|
<td>key[<i>N</i>]</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
where child[<i>i</i>] is a pointer to a sub-tree (at a level
|
|
above Level 0) or to data (at Level 0).
|
|
Each key[<i>i</i>] describes an <i>item</i> stored by the B-tree
|
|
(a chunk or an object of a group node). The range of values
|
|
represented by child[<i>i</i>] are indicated by key[<i>i</i>]
|
|
and key[<i>i</i>+1].
|
|
|
|
|
|
<p>The following question must next be answered:
|
|
"Is the value described by key[<i>i</i>] contained in
|
|
child[<i>i</i>-1] or in child[<i>i</i>]?"
|
|
The answer depends on the type of tree.
|
|
In trees for groups (node type 0) the object described by
|
|
key[<i>i</i>] is the greatest object contained in
|
|
child[<i>i</i>-1] while in chunk trees (node type 1) the
|
|
chunk described by key[<i>i</i>] is the least chunk in
|
|
child[<i>i</i>].
|
|
|
|
<p>That means that key[0] for group trees is sometimes unused;
|
|
it points to offset zero in the heap, which is always the
|
|
empty string and compares as "less-than" any valid object name.
|
|
|
|
<p>And key[<i>N</i>] for chunk trees is sometimes unused;
|
|
it contains a chunk offset which compares as "greater-than"
|
|
any other chunk offset and has a chunk byte size of zero
|
|
to indicate that it is not actually allocated.
|
|
|
|
|
|
<h3><a name="SymbolTable">Disk Format: Level 1B - Group and Symbol Nodes</a></h3>
|
|
|
|
<p>A group is an object internal to the file that allows
|
|
arbitrary nesting of objects (including other groups).
|
|
A group maps a set of names to a set of file
|
|
address relative to the base address. Certain meta data
|
|
for an object to which the group points can be duplicated
|
|
in the group symbol table in addition to the object header.
|
|
|
|
<p>An HDF5 object name space can be stored hierarchically by
|
|
partitioning the name into components and storing each
|
|
component in a group. The group entry for a
|
|
non-ultimate component points to the group containing
|
|
the next component. The group entry for the last
|
|
component points to the object being named.
|
|
|
|
<p>A group is a collection of group nodes pointed
|
|
to by a B-link tree. Each group node contains entries
|
|
for one or more symbols. If an attempt is made to add a
|
|
symbol to an already full group node containing
|
|
2<em>K</em> entries, then the node is split and one node
|
|
contains <em>K</em> symbols and the other contains
|
|
<em>K</em>+1 symbols.
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<B>Group Node (A Leaf of a B-tree)</B>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Node Signature</td>
|
|
|
|
<tr align=center>
|
|
<td>Version Number</td>
|
|
<td>Reserved for Future Use</td>
|
|
<td colspan=2>Number of Symbols</td>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br><br>Group Entries<br><br><br></td>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table align=center width="80%">
|
|
<tr>
|
|
<th width="30%">Field Name</th>
|
|
<th width="70%">Description</th>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Node Signature</td>
|
|
<td>The ASCII character string <code>SNOD</code> is
|
|
used to indicate the
|
|
beginning of a group node. This gives file
|
|
consistency checking utilities a better chance of
|
|
reconstructing a damaged file.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Version Number</td>
|
|
<td>The version number for the group node. This
|
|
document describes version 1.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Number of Symbols</td>
|
|
<td>Although all group nodes have the same length,
|
|
most contain fewer than the maximum possible number of
|
|
symbol entries. This field indicates how many entries
|
|
contain valid data. The valid entries are packed at the
|
|
beginning of the group node while the remaining
|
|
entries contain undefined values.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Group Entries</td>
|
|
<td>Each symbol has an entry in the group node.
|
|
The format of the entry is described below.</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<h3><a name="SymbolTableEntry">
|
|
Disk Format: Level 1C - Group Entry </a></h3>
|
|
|
|
<p>Each group entry in a group node is designed
|
|
to allow for very fast browsing of stored objects.
|
|
Toward that design goal, the group entries
|
|
include space for caching certain constant meta data from the
|
|
object header.
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<B>Group Entry</B>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Name Offset (<size> bytes)</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Object Header Address</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Cache Type</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Reserved</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br><br>Scratch-pad Space (16 bytes)<br><br><br></td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table align=center width="80%">
|
|
<tr>
|
|
<th width="30%">Field Name</th>
|
|
<th width="70%">Description</th>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Name Offset</td>
|
|
<td>This is the byte offset into the group local
|
|
heap for the name of the object. The name is null
|
|
terminated.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Object Header Address</td>
|
|
<td>Every object has an object header which serves as a
|
|
permanent location for the object's meta data. In addition
|
|
to appearing in the object header, some meta data can be
|
|
cached in the scratch-pad space.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Cache Type</td>
|
|
<td>The cache type is determined from the object header.
|
|
It also determines the format for the scratch-pad space.
|
|
<br>
|
|
<dl compact>
|
|
<dt>0
|
|
<dd>No data is cached by the group entry. This
|
|
is guaranteed to be the case when an object header
|
|
has a link count greater than one.
|
|
|
|
<dt>1
|
|
<dd>Object header meta data is cached in the group
|
|
entry. This implies that the group
|
|
entry refers to another group.
|
|
|
|
<dt>2
|
|
<dd>The entry is a symbolic link. The first four bytes
|
|
of the scratch-pad space are the offset into the local
|
|
heap for the link value. The object header address
|
|
will be undefined.
|
|
|
|
<dt><em>N</em>
|
|
<dd>Other cache values can be defined later and
|
|
libraries that do not understand the new values will
|
|
still work properly.
|
|
</dl>
|
|
</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Reserved</td>
|
|
<td>These four bytes are present so that the scratch-pad
|
|
space is aligned on an eight-byte boundary. They are
|
|
always set to zero.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Scratch-pad Space</td>
|
|
<td>This space is used for different purposes, depending
|
|
on the value of the Cache Type field. Any meta-data
|
|
about a dataset object represented in the scratch-pad
|
|
space is duplicated in the object header for that
|
|
dataset. This meta data can include the datatype
|
|
and the size of the dataspace for a dataset whose datatype
|
|
is atomic and whose dataspace is fixed and less than
|
|
four dimensions.
|
|
Furthermore, no data is cached in the group
|
|
entry scratch-pad space if the object header for
|
|
the group entry has a link count greater than
|
|
one.</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<h4>Format of the Scratch-pad Space</h4>
|
|
|
|
<p>The group entry scratch-pad space is formatted
|
|
according to the value in the Cache Type field.
|
|
|
|
<p>If the Cache Type field contains the value zero
|
|
(<code>0</code>) then no information is
|
|
stored in the scratch-pad space.
|
|
|
|
<p>If the Cache Type field contains the value one
|
|
(<code>1</code>), then the scratch-pad space
|
|
contains cached meta data for another object header
|
|
in the following format:
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<B>Object Header Scratch-pad Format</B>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Address of B-tree</td>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Address of Name Heap</td>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table align=center width="80%">
|
|
<tr>
|
|
<th width="30%">Field Name</th>
|
|
<th width="70%">Description</th>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Address of B-tree</td>
|
|
<td>This is the file address for the root of the
|
|
group's B-tree.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Address of Name Heap</td>
|
|
<td>This is the file address for the group's local
|
|
heap, in which are stored the symbol names.</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
|
|
<p>If the Cache Type field contains the value two
|
|
(<code>2</code>), then the scratch-pad space
|
|
contains cached meta data for another symbolic link
|
|
in the following format:
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<B>Symbolic Link Scratch-pad Format</B>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Offset to Link Value</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table align=center width="80%">
|
|
<tr>
|
|
<th width="30%">Field Name</th>
|
|
<th width="70%">Description</th>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Offset to Link Value</td>
|
|
<td>The value of a symbolic link (that is, the name of the
|
|
thing to which it points) is stored in the local heap.
|
|
This field is the 4-byte offset into the local heap for
|
|
the start of the link value, which is null terminated.</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<h3><a name="LocalHeap">Disk Format: Level 1D - Local Heaps</a></h3>
|
|
|
|
<p>A heap is a collection of small heap objects. Objects can be
|
|
inserted and removed from the heap at any time.
|
|
The address of a heap does not change once the heap is created.
|
|
References to objects are stored in the group table;
|
|
the names of those objects are stored in the local heap.
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<b>Local Heaps</b>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Heap Signature</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Reserved (zero)</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Data Segment Size</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Offset to Head of Free-list (<size> bytes)</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Address of Data Segment</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table align=center width="80%">
|
|
<tr>
|
|
<th width="30%">Field Name</th>
|
|
<th width="70%">Description</th>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Heap Signature</td>
|
|
<td>The ASCII character string <code>HEAP</code>
|
|
is used to indicate the
|
|
beginning of a heap. This gives file consistency
|
|
checking utilities a better chance of reconstructing a
|
|
damaged file.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Data Segment Size</td>
|
|
<td>The total amount of disk memory allocated for the heap
|
|
data. This may be larger than the amount of space
|
|
required by the object stored in the heap. The extra
|
|
unused space holds a linked list of free blocks.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Offset to Head of Free-list</td>
|
|
<td>This is the offset within the heap data segment of the
|
|
first free block (or all 0xff bytes if there is no free
|
|
block). The free block contains <size> bytes that
|
|
are the offset of the next free chunk (or all 0xff bytes
|
|
if this is the last free chunk) followed by <size>
|
|
bytes that store the size of this free chunk.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Address of Data Segment</td>
|
|
<td>The data segment originally starts immediately after
|
|
the heap header, but if the data segment must grow as a
|
|
result of adding more objects, then the data segment may
|
|
be relocated, in its entirety, to another part of the
|
|
file.</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>Objects within the heap should be aligned on an 8-byte boundary.
|
|
|
|
<h3><a name="GlobalHeap">Disk Format: Level 1E - Global Heap</a></h3>
|
|
|
|
<p>Each HDF5 file has a global heap which stores various types of
|
|
information which is typically shared between datasets. The
|
|
global heap was designed to satisfy these goals:
|
|
|
|
<ol type="A">
|
|
<li>Repeated access to a heap object must be efficient without
|
|
resulting in repeated file I/O requests. Since global heap
|
|
objects will typically be shared among several datasets, it is
|
|
probable that the object will be accessed repeatedly.
|
|
|
|
<br><br>
|
|
<li>Collections of related global heap objects should result in
|
|
fewer and larger I/O requests. For instance, a dataset of
|
|
void pointers will have a global heap object for each
|
|
pointer. Reading the entire set of void pointer objects
|
|
should result in a few large I/O requests instead of one small
|
|
I/O request for each object.
|
|
|
|
<br><br>
|
|
<li>It should be possible to remove objects from the global heap
|
|
and the resulting file hole should be eligible to be reclaimed
|
|
for other uses.
|
|
<br><br>
|
|
</ol>
|
|
|
|
<p>The implementation of the heap makes use of the memory
|
|
management already available at the file level and combines that
|
|
with a new top-level object called a <em>collection</em> to
|
|
achieve Goal B. The global heap is the set of all collections.
|
|
Each global heap object belongs to exactly one collection and
|
|
each collection contains one or more global heap objects. For
|
|
the purposes of disk I/O and caching, a collection is treated as
|
|
an atomic object.
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<B>A Global Heap Collection</B>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Magic Number</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td>Version</td>
|
|
<td colspan=3>Reserved</td>
|
|
</td>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Collection Size</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br>Global Heap Object 1
|
|
<i>(described below)</i><br><br></td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br>Global Heap Object 2<br><br></td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br>...<br><br></td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br>Global Heap Object <em>N</em><br><br></td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br>Global Heap Object 0 (free space)<br><br></td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table align=center width="80%">
|
|
<tr>
|
|
<th width="30%">Field Name</th>
|
|
<th width="70%">Description</th>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Magic Number</td>
|
|
<td>The magic number for global heap collections are the
|
|
four bytes <code>G</code>, <code>C</code>, <code>O</code>,
|
|
and <code>L</code>.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Version</td>
|
|
<td>Each collection has its own version number so that new
|
|
collections can be added to old files. This document
|
|
describes version zero of the collections.
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Collection Data Size</td>
|
|
<td>This is the size in bytes of the entire collection
|
|
including this field. The default (and minimum)
|
|
collection size is 4096 bytes which is a typical file
|
|
system block size and which allows for 170 16-byte heap
|
|
objects plus their overhead.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Object 1 through <em>N</em></td>
|
|
<td>The objects are stored in any order with no
|
|
intervening unused space.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Object 0</td>
|
|
<td>Object 0 (zero), when present, represents the free space in
|
|
the collection. Free space always appears at the end of
|
|
the collection. If the free space is too small to store
|
|
the header for Object 0 (described below) then the
|
|
header is implied and the collection contains no free space.
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<B>Global Heap Object</B>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=2>Object ID</td>
|
|
<td colspan=2>Reference Count</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Reserved</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Object Data Size</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br>Object Data<br><br></td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table align=center width="80%">
|
|
<tr>
|
|
<th width="30%">Field Name</th>
|
|
<th width="70%">Description</th>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Object ID</td>
|
|
<td>Each object has a unique identification number within a
|
|
collection. The identification numbers are chosen so that
|
|
new objects have the smallest value possible with the
|
|
exception that the identifier <code>0</code> always refers to the
|
|
object which represents all free space within the
|
|
collection.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Reference Count</td>
|
|
<td>All heap objects have a reference count field. An
|
|
object which is referenced from some other part of the
|
|
file will have a positive reference count. The reference
|
|
count for Object 0 is always zero.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Reserved</td>
|
|
<td>Zero padding to align next field on an 8-byte
|
|
boundary.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Object Size</td> <td>This is the size of the fields
|
|
above plus the object data stored for the object. The
|
|
actual storage size is rounded up to a multiple of
|
|
eight.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Object Data</td>
|
|
<td>The object data is treated as a one-dimensional array
|
|
of bytes to be interpreted by the caller.</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<h3><a name="FreeSpaceIndex">Disk Format: Level 1F - Free-space Heap</a></h3>
|
|
|
|
<p>The Free-space Index is a collection of blocks of data,
|
|
dispersed throughout the file, which are currently not used by
|
|
any file objects.
|
|
|
|
<p>The super block contains a pointer to root of the free-space description;
|
|
that pointer is currently (i.e., in HDF5 Release 1.2) required
|
|
to be the undefined address <code>0xfff...ff</code>.
|
|
|
|
<p>The free-sapce index is not otherwise publicly defined at this time.
|
|
|
|
|
|
<!--
|
|
<p>The Free-space Index is a collection of blocks of data,
|
|
dispersed throughout the file, which are currently not used by
|
|
any file objects. The blocks of data are indexed by a B-tree of
|
|
their length within the file.
|
|
|
|
|
|
<p>Each B-tree page is composed of the following entries and
|
|
B-tree management information, organized as follows:
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=bottom>
|
|
<B>HDF5 Free-space Heap Page</B>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Free-space Heap Signature</td>
|
|
<tr align=center>
|
|
<td colspan=4>B-tree Left-link Offset</td>
|
|
<tr align=center>
|
|
<td colspan=4><br>Length of Free-block #1<br> <br></td>
|
|
<tr align=center>
|
|
<td colspan=4><br>Offset of Free-block #1<br> <br></td>
|
|
<tr align=center>
|
|
<td colspan=4>.<br>.<br>.<br></td>
|
|
<tr align=center>
|
|
<td colspan=4><br>Length of Free-block #n<br> <br></td>
|
|
<tr align=center>
|
|
<td colspan=4><br>Offset of Free-block #n<br> <br></td>
|
|
<tr align=center>
|
|
<td colspan=4>"High" Offset</td>
|
|
<tr align=center>
|
|
<td colspan=4>Right-link Offset</td>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<dl>
|
|
<dt> The elements of the free-space heap page are described below:
|
|
<dd>
|
|
<dl>
|
|
<dt>Free-space Heap Signature: (4 bytes)
|
|
<dd>The ASCII character string <code>FREE</code>
|
|
is used to indicate the
|
|
beginning of a free-space heap B-tree page. This gives
|
|
file consistency checking utilities a better chance of
|
|
reconstructing a damaged file.
|
|
|
|
<dt>B-tree Left-link Offset: (<offset> bytes)
|
|
<dd>This value is used to indicate the offset of all offsets
|
|
in the B-link-tree which are smaller than the value of the
|
|
offset in entry #1. This value is also used to indicate a
|
|
leaf node in the B-link-tree by being set to all ones.
|
|
|
|
<dt>Length of Free-block #n: (<length> bytes)
|
|
<dd>This value indicates the length of an unused block in
|
|
the file.
|
|
|
|
<dt>Offset of Free-block #n: (<offset> bytes)
|
|
<dd>This value indicates the offset in the file of an
|
|
unused block in the file.
|
|
|
|
<dt>"High" Offset: (4-bytes)
|
|
<dd>This offset is used as the upper bound on offsets
|
|
contained within a page when the page has been split.
|
|
|
|
<dt>Right-link Offset: (<offset> bytes)
|
|
<dd>This value is used to indicate the offset of the next
|
|
child to the right of the parent of this group
|
|
page. When there is no node to the right, this value is
|
|
all zeros.
|
|
</dl>
|
|
</dl>
|
|
|
|
<p>The algorithms for searching and inserting objects in the
|
|
B-tree pages are described fully in the Lehman and Yao paper,
|
|
which should be read to provide a full description of the
|
|
B-tree's usage.
|
|
-->
|
|
|
|
|
|
<br><br>
|
|
<br><br>
|
|
|
|
|
|
<h2><a name="DataObject">Disk Format: Level 2 - Data Objects </a></h2>
|
|
|
|
<p>Data objects contain the real information in the file. These
|
|
objects compose the scientific data and other information which
|
|
are generally thought of as "data" by the end-user. All the
|
|
other information in the file is provided as a framework for
|
|
these data objects.
|
|
|
|
<p>A data object is composed of header information and data
|
|
information. The header information contains the information
|
|
needed to interpret the data information for the data object as
|
|
well as additional "meta-data" or pointers to additional
|
|
"meta-data" used to describe or annotate each data object.
|
|
|
|
<h3><a name="ObjectHeader">
|
|
Disk Format: Level 2a - Data Object Headers</a></h3>
|
|
|
|
<p>The header information of an object is designed to encompass
|
|
all the information about an object which would be desired to be
|
|
known, except for the data itself. This information includes
|
|
the dimensionality, number-type, information about how the data
|
|
is stored on disk (in external files, compressed, broken up in
|
|
blocks, etc.), as well as other information used by the library
|
|
to speed up access to the data objects or maintain a file's
|
|
integrity. The header of each object is not necessarily located
|
|
immediately prior to the object's data in the file and in fact
|
|
may be located in any position in the file.
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<B>Object Headers</B>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=1 width="25%">Version # of Object Header</td>
|
|
<td colspan=1 width="25%">Reserved</td>
|
|
<td colspan=2 width="50%">Number of Header Messages</td>
|
|
</tr>
|
|
<tr align=center>
|
|
<td colspan=4>Object Reference Count</td>
|
|
</tr>
|
|
<tr align=center>
|
|
<td colspan=4><br>Total Object Header Size<br><br></td>
|
|
</tr>
|
|
<tr align=center>
|
|
<td colspan=2>Header Message Type #1</td>
|
|
<td colspan=2>Size of Header Message Data #1</td>
|
|
</tr>
|
|
<tr align=center>
|
|
<td>Flags</td>
|
|
<td colspan=3>Reserved</td>
|
|
</tr>
|
|
<tr align=center>
|
|
<td colspan=4><br>Header Message Data #1<br><br></td>
|
|
</tr>
|
|
<tr align=center>
|
|
<td colspan=4>.<br>.<br>.<br></td>
|
|
</tr>
|
|
<tr align=center>
|
|
<td colspan=2>Header Message Type #n</td>
|
|
<td colspan=2>Size of Header Message Data #n</td>
|
|
</tr>
|
|
<tr align=center>
|
|
<td>Flags</td>
|
|
<td colspan=3>Reserved</td>
|
|
</tr>
|
|
<tr align=center>
|
|
<td colspan=4><br>Header Message Data #n<br><br></td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table align=center width="80%">
|
|
<tr>
|
|
<th width="30%">Field Name</th>
|
|
<th width="70%">Description</th>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Version number of the object header</td>
|
|
<td>This value is used to determine the format of the
|
|
information in the object header. When the format of the
|
|
information in the object header is changed, the version number
|
|
is incremented and can be used to determine how the
|
|
information in the object header is formatted.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Reserved</td>
|
|
<td>Always set to zero.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Number of header messages</td>
|
|
<td>This value determines the number of messages listed in
|
|
this object header. This provides a fast way for software
|
|
to prepare storage for the messages in the header.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Object Reference Count</td>
|
|
<td>This value specifies the number of references to this
|
|
object within the current file. References to the
|
|
data object from external files are not tracked.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Total Object Header Size</td>
|
|
<td>This value specifies the total number of bytes of header
|
|
message data following this length field for the current
|
|
message as well as any continuation data located elsewhere
|
|
in the file.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Header Message Type</td>
|
|
<td>The header message type specifies the type of
|
|
information included in the header message data following
|
|
the type along with a small amount of other information.
|
|
Bit 15 of the message type is set if the message is
|
|
constant (constant messages cannot be changed since they
|
|
may be cached in group entries throughout the
|
|
file). The header message types for the pre-defined
|
|
header messages will be included in further discussion
|
|
below.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Size of Header Message Data</td>
|
|
<td>This value specifies the number of bytes of header
|
|
message data following the header message type and length
|
|
information for the current message. The size includes
|
|
padding bytes to make the message a multiple of eight
|
|
bytes.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Flags</td>
|
|
<td>This is a bit field with the following definition:
|
|
<dl>
|
|
<dt><code>0</code>
|
|
<dd>If set, the message data is constant. This is used
|
|
for messages like the datatype message of a dataset.
|
|
<dt><code>1</code>
|
|
<dd>If set, the message is stored in the global heap and
|
|
the Header Message Data field contains a Shared Object
|
|
message and the Size of Header Message Data field
|
|
contains the size of that Shared Object message.
|
|
<dt><code>2-7</code>
|
|
<dd>Reserved
|
|
</dl>
|
|
</td>
|
|
|
|
<tr valign=top>
|
|
<td>Header Message Data</td>
|
|
<td>The format and length of this field is determined by the
|
|
header message type and size respectively. Some header
|
|
message types do not require any data and this information
|
|
can be eliminated by setting the length of the message to
|
|
zero. The data is padded with enough zeros to make the
|
|
size a multiple of eight.</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>The header message types and the message data associated with
|
|
them compose the critical "meta-data" about each object. Some
|
|
header messages are required for each object while others are
|
|
optional. Some optional header messages may also be repeated
|
|
several times in the header itself, the requirements and number
|
|
of times allowed in the header will be noted in each header
|
|
message description below.
|
|
|
|
<P>The following is a list of currently defined header messages:
|
|
|
|
<hr>
|
|
<h4><a name="NILMessage">Name: NIL</a></h4>
|
|
<b>Type: </b>0x0000<br>
|
|
<b>Length:</b> varies<br>
|
|
<b>Status:</b> Optional, may be repeated.<br>
|
|
<b>Purpose and Description:</b> The NIL message is used to
|
|
indicate a message
|
|
which is to be ignored when reading the header messages for a data object.
|
|
[Probably one which has been deleted for some reason.]<br>
|
|
<b>Format of Data:</b> Unspecified.<br>
|
|
|
|
<!-- Delete examples throughout doc
|
|
<b>Examples:</b> None.
|
|
-->
|
|
|
|
|
|
<hr>
|
|
<h4><a name="SimpleDataSpace">Name: Simple Dataspace</a></h4>
|
|
|
|
<b>Type: </b>0x0001<br>
|
|
<b>Length:</b> Varies according to the number of dimensions,
|
|
as described in the following table<br>
|
|
<b>Status:</b> The <em>Simple Dataspace</em> message is required
|
|
and may not be repeated. This message is currently used with
|
|
datasets and named dataspaces.<br>
|
|
|
|
<p>The <em>Simple Dataspace</em> message describes the number
|
|
of dimensions and size of each dimension that the data object
|
|
has. This message is only used for datasets which have a
|
|
simple, rectilinear grid layout; datasets requiring a more
|
|
complex layout (irregularly structured or unstructured grids, etc.)
|
|
must use the <em>Complex Dataspace</em> message for expressing
|
|
the space the dataset inhabits.
|
|
<i>(Note: The <em>Complex Dataspace</em> functionality is
|
|
not yet implemented (as of HDF5 Release 1.2). It is not described
|
|
in this document.)</i>
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<b>Simple Dataspace Message</b>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td>Version</td>
|
|
<td>Dimensionality</td>
|
|
<td>Flags</td>
|
|
<td>Reserved</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Reserved</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Dimension Size #1 (<size> bytes)</td>
|
|
<tr align=center>
|
|
<td colspan=4>.<br>.<br>.<br></td>
|
|
<tr align=center>
|
|
<td colspan=4>Dimension Size #n (<size> bytes)</td>
|
|
<tr align=center>
|
|
<td colspan=4>Dimension Maximum #1 (<size> bytes)</td>
|
|
<tr align=center>
|
|
<td colspan=4>.<br>.<br>.<br></td>
|
|
<tr align=center>
|
|
<td colspan=4>Dimension Maximum #n (<size> bytes)</td>
|
|
<tr align=center>
|
|
<td colspan=4>Permutation Index #1</td>
|
|
<tr align=center>
|
|
<td colspan=4>.<br>.<br>.<br></td>
|
|
<tr align=center>
|
|
<td colspan=4>Permutation Index #n</td>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table align=center width="80%">
|
|
<tr>
|
|
<th width="30%">Field Name</th>
|
|
<th width="70%">Description</th>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Version </td>
|
|
<td>This value is used to determine the format of the
|
|
Simple Dataspace Message. When the format of the
|
|
information in the message is changed, the version number
|
|
is incremented and can be used to determine how the
|
|
information in the object header is formatted.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Dimensionality</td>
|
|
<td>This value is the number of dimensions that the data
|
|
object has.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Flags</td>
|
|
<td>This field is used to store flags to indicate the
|
|
presence of parts of this message. Bit 0 (the least
|
|
significant bit) is used to indicate that maximum
|
|
dimensions are present. Bit 1 is used to indicate that
|
|
permutation indices are present for each dimension.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Dimension Size #n (<size> bytes)</td>
|
|
<td>This value is the current size of the dimension of the
|
|
data as stored in the file. The first dimension stored in
|
|
the list of dimensions is the slowest changing dimension
|
|
and the last dimension stored is the fastest changing
|
|
dimension.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Dimension Maximum #n (<size> bytes)</td>
|
|
<td>This value is the maximum size of the dimension of the
|
|
data as stored in the file. This value may be the special
|
|
value <UNLIMITED> (all bits set) which indicates
|
|
that the data may expand along this dimension
|
|
indefinitely. If these values are not stored, the maximum
|
|
value of each dimension is assumed to be the same as the
|
|
current size value.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Permutation Index #n (4 bytes)</td>
|
|
<td>This value is the index permutation used to map
|
|
each dimension from the canonical representation to an
|
|
alternate axis for each dimension. If these values are
|
|
not stored, the first dimension stored in the list of
|
|
dimensions is the slowest changing dimension and the last
|
|
dimension stored is the fastest changing dimension.</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<!-- Delete examples throughout doc
|
|
<h4>Examples</h4>
|
|
<dl>
|
|
<dt> Example #1
|
|
<dd>A sample 640 horizontally by 480 vertically raster image
|
|
dimension header. The number of dimensions would be set to 2
|
|
and the first dimension's size and maximum would both be set
|
|
to 480. The second dimension's size and maximum would both be
|
|
set to 640
|
|
.
|
|
<dt>Example #2
|
|
<dd>A sample 4 dimensional scientific dataset which is composed
|
|
of 30x24x3 slabs of data being written out in an unlimited
|
|
series every several minutes as timestep data (currently there
|
|
are five slabs). The number of dimensions is 4. The first
|
|
dimension size is 5 and its maximum is <UNLIMITED>. The
|
|
second through fourth dimension's size and maximum value are
|
|
set to 3, 24, and 30 respectively.
|
|
|
|
<dt>Example #3
|
|
<dd>A sample unlimited length text string, currently of length
|
|
83. The number of dimensions is 1, the size of the first
|
|
dimension is 83 and the maximum of the first dimension is set
|
|
to <UNLIMITED>, allowing further text data to be
|
|
appended to the string or possibly the string to be replaced
|
|
with another string of a different size. (This could also be
|
|
stored as a scalar dataset with number-type set to "string")
|
|
</dl>
|
|
-->
|
|
|
|
<!-- DELETE ENTIRE DATASPACE SECTION -->
|
|
<!--
|
|
<hr>
|
|
<h4><a name="DataSpaceMessage">Name: Complex Dataspace (Fiber Bundle?)</a></h4>
|
|
<b>Type: </b>0x0002<br>
|
|
<b>Length:</b> varies<br>
|
|
|
|
<b>Status:</b> One of the <em>Simple Dataspace</em> or
|
|
<em>Complex Dataspace</em> messages is required (but not both) and may
|
|
not be repeated.<br> <b>Purpose and Description:</b> The
|
|
<em>Dataspace</em> message describes space that the dataset is
|
|
mapped onto in a more comprehensive way than the <em>Simple
|
|
Dimensionality</em> message is capable of handling. The
|
|
dataspace of a dataset encompasses the type of coordinate system
|
|
used to locate the dataset's elements as well as the structure and
|
|
regularity of the coordinate system. The dataspace also
|
|
describes the number of dimensions which the dataset inhabits as
|
|
well as a possible higher dimensional space in which the dataset
|
|
is located within.
|
|
|
|
<br>
|
|
<b>Format of Data:</b>
|
|
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=bottom>
|
|
<B>HDF5 Dataspace Message Layout</B>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Mesh Type</td>
|
|
<tr align=center>
|
|
<td colspan=4>Logical Dimensionality</td>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<dl>
|
|
<dt>The elements of the dimensionality message are described below:
|
|
<dd>
|
|
<dl>
|
|
<dt>Mesh Type: (unsigned 32-bit integer)
|
|
<dd>This value indicates whether the grid is
|
|
polar/spherical/cartesion,
|
|
structured/unstructured and regular/irregular. <br>
|
|
The mesh type value is broken up as follows: <br>
|
|
|
|
<P>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=bottom>
|
|
<B>HDF5 Mesh-type Layout</B>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
|
|
<tr align=center>
|
|
<td colspan=1>Mesh Embedding</td>
|
|
<td colspan=1>Coordinate System</td>
|
|
<td colspan=1>Structure</td>
|
|
<td colspan=1>Regularity</td>
|
|
</table>
|
|
</center>
|
|
The following are the definitions of mesh-type bytes:
|
|
<dl>
|
|
<dt>Mesh Embedding
|
|
<dd>This value indicates whether the dataset dataspace
|
|
is located within
|
|
another dataspace or not:
|
|
<dl> <dl>
|
|
<dt><STANDALONE>
|
|
<dd>The dataset mesh is self-contained and is not
|
|
embedded in another mesh.
|
|
<dt><EMBEDDED>
|
|
<dd>The dataset's dataspace is located within
|
|
another dataspace, as
|
|
described in information below.
|
|
</dl> </dl>
|
|
<dt>Coordinate System
|
|
<dd>This value defines the type of coordinate system
|
|
used for the mesh:
|
|
<dl> <dl>
|
|
<dt><POLAR>
|
|
<dd>The last two dimensions are in polar
|
|
coordinates, higher dimensions are
|
|
cartesian.
|
|
<dt><SPHERICAL>
|
|
<dd>The last three dimensions are in spherical
|
|
coordinates, higher dimensions
|
|
are cartesian.
|
|
<dt><CARTESIAN>
|
|
<dd>All dimensions are in cartesian coordinates.
|
|
</dl> </dl>
|
|
<dt>Structure
|
|
<dd>This value defines the locations of the grid-points
|
|
on the axes:
|
|
<dl> <dl>
|
|
<dt><STRUCTURED>
|
|
<dd>All grid-points are on integral, sequential
|
|
locations, starting from 0.
|
|
<dt><UNSTRUCTURED>
|
|
<dd>Grid-points locations in each dimension are
|
|
explicitly defined and
|
|
may be of any numeric datatype.
|
|
</dl> </dl>
|
|
<dt>Regularity
|
|
<dd>This value defines the locations of the dataset
|
|
points on the grid:
|
|
<dl> <dl>
|
|
<dt><REGULAR>
|
|
<dd>All dataset elements are located at the
|
|
grid-points defined.
|
|
<dt><IRREGULAR>
|
|
<dd>Each dataset element has a particular
|
|
grid-location defined.
|
|
</dl> </dl>
|
|
</dl>
|
|
<p>The following grid combinations are currently allowed:
|
|
<dl> <dl>
|
|
<dt><POLAR-STRUCTURED-REGULAR>
|
|
<dt><SPHERICAL-STRUCTURED-REGULAR>
|
|
<dt><CARTESIAN-STRUCTURED-REGULAR>
|
|
<dt><POLAR-UNSTRUCTURED-REGULAR>
|
|
<dt><SPHERICAL-UNSTRUCTURED-REGULAR>
|
|
<dt><CARTESIAN-UNSTRUCTURED-REGULAR>
|
|
<dt><CARTESIAN-UNSTRUCTURED-IRREGULAR>
|
|
</dl> </dl>
|
|
All of the above grid types can be embedded within another
|
|
dataspace.
|
|
<br> <br>
|
|
<dt>Logical Dimensionality: (unsigned 32-bit integer)
|
|
<dd>This value is the number of dimensions that the dataset occupies.
|
|
|
|
<P>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=bottom>
|
|
<B>HDF5 Dataspace Embedded Dimensionality Information</B>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Embedded Dimensionality</td>
|
|
<tr align=center>
|
|
<td colspan=4>Embedded Dimension Size #1</td>
|
|
<tr align=center>
|
|
<td colspan=4>.<br>.<br>.<br></td>
|
|
<tr align=center>
|
|
<td colspan=4>Embedded Dimension Size #n</td>
|
|
<tr align=center>
|
|
<td colspan=4>Embedded Origin Location #1</td>
|
|
<tr align=center>
|
|
<td colspan=4>.<br>.<br>.<br></td>
|
|
<tr align=center>
|
|
<td colspan=4>Embedded Origin Location #n</td>
|
|
</table>
|
|
</center>
|
|
|
|
<dt>Embedded Dimensionality: (unsigned 32-bit integer)
|
|
<dd>This value is the number of dimensions of the space the
|
|
dataset is located
|
|
within. i.e. a planar dataset located within a 3-D space,
|
|
or a 3-D dataset
|
|
which is a subset of another 3-D space, etc.
|
|
<dt>Embedded Dimension Size: (unsigned 32-bit integer)
|
|
<dd>These values are the sizes of the dimensions of the
|
|
embedded dataspace
|
|
that the dataset is located within.
|
|
<dt>Embedded Origin Location: (unsigned 32-bit integer)
|
|
<dd>These values comprise the location of the dataset's
|
|
origin within the embedded dataspace.
|
|
</dl>
|
|
</dl>
|
|
[Comment: need some way to handle different orientations of the
|
|
dataset dataspace
|
|
within the embedded dataspace]<br>
|
|
|
|
<P>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=bottom>
|
|
<B>HDF5 Dataspace Structured/Regular Grid Information</B>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Logical Dimension Size #1</td>
|
|
<tr align=center>
|
|
<td colspan=4>Logical Dimension Maximum #1</td>
|
|
<tr align=center>
|
|
<td colspan=4>.<br>.<br>.<br></td>
|
|
<tr align=center>
|
|
<td colspan=4>Logical Dimension Size #n</td>
|
|
<tr align=center>
|
|
<td colspan=4>Logical Dimension Maximum #n</td>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<dl>
|
|
<dt>The elements of the dimensionality message are described below:
|
|
<dd>
|
|
<dl>
|
|
<dt>Logical Dimension Size #n: (unsigned 32-bit integer)
|
|
<dd>This value is the current size of the dimension of the
|
|
data as stored in
|
|
the file. The first dimension stored in the list of
|
|
dimensions is the slowest
|
|
changing dimension and the last dimension stored is the
|
|
fastest changing
|
|
dimension.
|
|
<dt>Logical Dimension Maximum #n: (unsigned 32-bit integer)
|
|
<dd>This value is the maximum size of the dimension of the
|
|
data as stored in
|
|
the file. This value may be the special value
|
|
<UNLIMITED> which
|
|
indicates that the data may expand along this dimension
|
|
indefinitely.
|
|
</dl>
|
|
</dl>
|
|
<P>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=bottom>
|
|
<B>HDF5 Dataspace Structured/Irregular Grid Information</B>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
|
|
<tr align=center>
|
|
<td colspan=4># of Grid Points in Dimension #1</td>
|
|
<tr align=center>
|
|
<td colspan=4>.<br>.<br>.<br></td>
|
|
<tr align=center>
|
|
<td colspan=4># of Grid Points in Dimension #n</td>
|
|
<tr align=center>
|
|
<td colspan=4>Datatype of Grid Point Locations</td>
|
|
<tr align=center>
|
|
<td colspan=4>Location of Grid Points in Dimension #1</td>
|
|
<tr align=center>
|
|
<td colspan=4>.<br>.<br>.<br></td>
|
|
<tr align=center>
|
|
<td colspan=4>Location of Grid Points in Dimension #n</td>
|
|
</table>
|
|
</center>
|
|
|
|
<P>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=bottom>
|
|
<B>HDF5 Dataspace Unstructured Grid Information</B>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
|
|
<tr align=center>
|
|
<td colspan=4># of Grid Points</td>
|
|
<tr align=center>
|
|
<td colspan=4>Datatype of Grid Point Locations</td>
|
|
<tr align=center>
|
|
<td colspan=4>Grid Point Locations<br>.<br>.<br></td>
|
|
</table>
|
|
</center>
|
|
|
|
<h4><a name="DataSpaceExample">Examples:</a></h4>
|
|
Need some good examples, this is complex!
|
|
-->
|
|
|
|
|
|
<hr>
|
|
<h4><a name="DataTypeMessage">Name: Datatype</a></h4>
|
|
|
|
<b>Type:</b> 0x0003<br>
|
|
<b>Length:</b> variable<br>
|
|
<b>Status:</b> One required per dataset or named datatype<br>
|
|
|
|
<p>The datatype message defines the datatype for each data point
|
|
of a dataset. A datatype can describe an atomic type like a
|
|
fixed- or floating-point type or a compound type like a C
|
|
struct. A datatype does not, however, describe how data points
|
|
are combined to produce a dataset. Datatypes are stored on disk
|
|
as a datatype message, which is a list of datatype classes and
|
|
their associated properties.
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<b>Datatype Message</b>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td>Type Class and Version</td>
|
|
<td colspan=3>Class Bit Field</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Size in Bytes (4 bytes)</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br><br>Properties<br><br><br></td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>The Class Bit Field and Properties fields vary depending
|
|
on the Type Class, which is the low-order four bits of the Type
|
|
Class and Version field (the high-order four bits are the
|
|
version, which should be set to the value one). The type class
|
|
is one of 0 (fixed-point number), 1 (floating-point number),
|
|
2 (date and time), 3 (text string), 4 (bit field), 5 (opaque),
|
|
6 (compound), 7 (reference), 8 (enumeration), or 9 (variable-length).
|
|
The Class Bit Field is zero and the size of the
|
|
Properties field is zero except for the cases noted here.
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<b>Bit Field for Fixed-point Numbers (Class 0)</b>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="10%">Bits</th>
|
|
<th width="90%">Meaning</th>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>0</td>
|
|
<td><b>Byte Order.</b> If zero, byte order is little-endian;
|
|
otherwise, byte order is big endian.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>1, 2</td>
|
|
<td><b>Padding type.</b> Bit 1 is the lo_pad type and bit 2
|
|
is the hi_pad type. If a datum has unused bits at either
|
|
end, then the lo_pad or hi_pad bit is copied to those
|
|
locations.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>3</td>
|
|
<td><b>Signed.</b> If this bit is set then the fixed-point
|
|
number is in 2's complement form.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>4-23</td>
|
|
<td>Reserved (zero).</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<b>Properties for Fixed-point Numbers (Class 0)</b>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">Byte</th>
|
|
<th width="25%">Byte</th>
|
|
<th width="25%">Byte</th>
|
|
<th width="25%">Byte</th>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=2>Bit Offset</td>
|
|
<td colspan=2>Bit Precision</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<b>Bit Field for Floating-point Numbers (Class 1)</b>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="10%">Bits</th>
|
|
<th width="90%">Meaning</th>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>0</td>
|
|
<td><b>Byte Order.</b> If zero, byte order is little-endian;
|
|
otherwise, byte order is big endian.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>1, 2, 3</td>
|
|
<td><b>Padding type.</b> Bit 1 is the low bits pad type, bit 2
|
|
is the high bits pad type, and bit 3 is the internal bits
|
|
pad type. If a datum has unused bits at either or between
|
|
the sign bit, exponent, or mantissa, then the value of bit
|
|
1, 2, or 3 is copied to those locations.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>4-5</td>
|
|
<td><b>Normalization.</b> The value can be 0 if there is no
|
|
normalization, 1 if the most significant bit of the
|
|
mantissa is always set (except for 0.0), and 2 if the most
|
|
significant bit of the mantissa is not stored but is
|
|
implied to be set. The value 3 is reserved and will not
|
|
appear in this field.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>6-7</td>
|
|
<td>Reserved (zero).</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>8-15</td>
|
|
<td><b>Sign.</b> This is the bit position of the sign
|
|
bit.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>16-23</td>
|
|
<td>Reserved (zero).</td>
|
|
</tr>
|
|
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<b>Properties for Floating-point Numbers (Class 1)</b>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">Byte</th>
|
|
<th width="25%">Byte</th>
|
|
<th width="25%">Byte</th>
|
|
<th width="25%">Byte</th>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=2>Bit Offset</td>
|
|
<td colspan=2>Bit Precision</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td>Exponent Location</td>
|
|
<td>Exponent Size in Bits</td>
|
|
<td>Mantissa Location</td>
|
|
<td>Mantissa Size in Bits</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Exponent Bias</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<b>Bit Field for Strings (Class 3)</b>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="10%">Bits</th>
|
|
<th width="90%">Meaning</th>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>0-3</td>
|
|
<td><b>Padding type.</b> This four-bit value determines the
|
|
type of padding to use for the string. The values are:
|
|
|
|
<dl>
|
|
<dt><code>0</code> Null terminate.
|
|
<dd>A zero byte marks the end of the string and is
|
|
guaranteed to be present after converting a long
|
|
string to a short string. When converting a short
|
|
string to a long string the value is padded with
|
|
additional null characters as necessary.
|
|
|
|
<br><br>
|
|
<dt><code>1</code> Null pad.
|
|
<dd>Null characters are added to the end of the value
|
|
during conversions from short values to long values
|
|
but conversion in the opposite direction simply
|
|
truncates the value.
|
|
|
|
<br><br>
|
|
<dt><code>2</code> Space pad.
|
|
<dd>Space characters are added to the end of the value
|
|
during conversions from short values to long values
|
|
but conversion in the opposite direction simply
|
|
truncates the value. This is the Fortran
|
|
representation of the string.
|
|
|
|
<br><br>
|
|
<dt><code>3-15</code> Reserved.
|
|
<dd>These values are reserved for future use.
|
|
</dl>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>4-7</td>
|
|
<td><b>Character Set.</b> The character set to use for
|
|
encoding the string. The only character set supported is
|
|
the 8-bit ASCII (zero) so no translations have been defined
|
|
yet.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>8-23</td>
|
|
<td>Reserved (zero).</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<b>Bit Field for Bitfield Types (Class 4)</b>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="10%">Bits</th>
|
|
<th width="90%">Meaning</th>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>0</td>
|
|
<td><b>Byte Order.</b> If zero, byte order is little-endian;
|
|
otherwise, byte order is big endian.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>1, 2</td>
|
|
<td><b>Padding type.</b> Bit 1 is the lo_pad type and bit 2
|
|
is the hi_pad type. If a datum has unused bits at either
|
|
end, then the lo_pad or hi_pad bit is copied to those
|
|
locations.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>3-23</td>
|
|
<td>Reserved (zero).</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<b>Properties for Bitfield Types (Class 4)</b>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">Byte</th>
|
|
<th width="25%">Byte</th>
|
|
<th width="25%">Byte</th>
|
|
<th width="25%">Byte</th>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=2>Bit Offset</td>
|
|
<td colspan=2>Bit Precision</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<b>Bit Field for Opaque Types (Class 5)</b>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="10%">Bits</th>
|
|
<th width="90%">Meaning</th>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>0-23</td>
|
|
<td>Reserved (zero).</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<b>Properties for Opaque Types (Class 5)</b>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">Byte</th>
|
|
<th width="25%">Byte</th>
|
|
<th width="25%">Byte</th>
|
|
<th width="25%">Byte</th>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br>Null-terminated ASCII Tag<br>
|
|
(multiple of 8 bytes)<br><br></td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<b>Bit Field for Compound Types (Class 6)</b>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="10%">Bits</th>
|
|
<th width="90%">Meaning</th>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>0-15</td>
|
|
<td><b>Number of Members.</b> This field contains the number
|
|
of members defined for the compound datatype. The member
|
|
definitions are listed in the Properties field of the data
|
|
type message.
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>15-23</td>
|
|
<td>Reserved (zero).</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>The Properties field of a compound datatype is a list of the
|
|
member definitions of the compound datatype. The member
|
|
definitions appear one after another with no intervening bytes.
|
|
The member types are described with a recursive datatype
|
|
message.
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<b>Properties for Compound Types (Class 6)</b>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">Byte</th>
|
|
<th width="25%">Byte</th>
|
|
<th width="25%">Byte</th>
|
|
<th width="25%">Byte</th>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br><br>Name (null terminated, multiple of
|
|
eight bytes)<br><br><br></td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Byte Offset of Member in Compound Instance</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td>Dimensionality</td>
|
|
<td colspan=3>reserved</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Dimension Permutation</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Reserved</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Size of Dimension 0 (required)</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Size of Dimension 1 (required)</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Size of Dimension 2 (required)</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Size of Dimension 3 (required)</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br><br>Member Type Message<br><br><br></td>
|
|
</tr>
|
|
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<b>Bit Field for Enumeration Types (Class 8)</b>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="10%">Bits</th>
|
|
<th width="90%">Meaning</th>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>0-15</td>
|
|
<td><b>Number of Members.</b> The number of name/value
|
|
pairs defined for the enumeration type.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>16-23</td>
|
|
<td>Reserved (zero).</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<b>Properties for Enumeration Types (Class 8)</b>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">Byte</th>
|
|
<th width="25%">Byte</th>
|
|
<th width="25%">Byte</th>
|
|
<th width="25%">Byte</th>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br>Parent Type<br><br></td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br>Names<br><br></td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br>Values<br><br></td>
|
|
</tr>
|
|
|
|
</table>
|
|
</center>
|
|
|
|
<center>
|
|
<table border=0 cellpadding=4 width="80%">
|
|
<tr align=left valign=top>
|
|
<td valign=top width=20%>Parent Type:</td>
|
|
<td valign=top>Each enumeration type is based on some parent type,
|
|
usually an integer. The information for that parent type is
|
|
described recursively by this field.</td>
|
|
</tr><tr align=left valign=top>
|
|
<td valign=top>Names:</td>
|
|
<td valign=top>The name for each name/value pair. Each name is
|
|
stored as a null terminated ASCII string in a multiple of
|
|
eight bytes. The names are in no particular order.</td>
|
|
</tr><tr align=left valign=top>
|
|
<td valign=top>Values:</td>
|
|
<td valign=top>The list of values in the same order as the names.
|
|
The values are packed (no inter-value padding) and the
|
|
size of each value is determined by the parent type.</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<b>Bit Field for Variable-length Types (Class 9)</b>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="10%">Bits</th>
|
|
<th width="90%">Meaning</th>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>0-3</td>
|
|
<td><dl><dt><b>Type</b></dt>
|
|
<dt>0 Variable-length sequence</dt>
|
|
<dd>This variable-length datatype can be of any sequence
|
|
of data. Variable-length sequences do not have padding
|
|
or character set information.</dd>
|
|
<dt>1 Variable-length string</dt>
|
|
<dd>This variable-length datatype is composed of a series of
|
|
characters. Variable-length strings have padding and
|
|
character set information.</dd></dl>
|
|
</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>4-7</td>
|
|
<td><dl><dt><b>Padding type</b> (variable-length string only)</dt>
|
|
<dd>This four-bit value determines the type of padding
|
|
used for variable-length strings. The values are the same
|
|
as for the string padding type, as follows:</dd>
|
|
<dt>0 Null terminate</dt>
|
|
<dd>A zero byte marks the end of a string and is guaranteed
|
|
to be present after converting a long string to a short
|
|
string. When converting a short string to a long string,
|
|
the value is padded with additional null characters
|
|
as necessary.
|
|
<dt>1 Null pad</dt>
|
|
<dd>Null characters are added to the end of the value
|
|
during conversion from a short string to a longer string.
|
|
Conversion from a long string to a shorter string
|
|
simply truncates the value.</dd>
|
|
<dt>2 Space pad</dt>
|
|
<dd>Space characters are added to the end of the value
|
|
during conversion from a short string to a longer string.
|
|
Conversion from a long string to a shorter string simply
|
|
truncates the value.
|
|
This is the Fortran representation of the string.
|
|
</dd>
|
|
<dt>3-15 Reserved</dt>
|
|
<dd>These values are reserved for future use.</dd></dl>
|
|
</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>8-11</td>
|
|
<td><dl><dt><b>Character set</b> (variable-length string only)</dt>
|
|
<dd>This four-bit value specifies the character set
|
|
to be used for encoding the string.</dd>
|
|
<dt>0 8-bit ASCII</dt>
|
|
<dd>As of this writing (July 2002, Release 1.4.4),
|
|
8-bit ASCII is the only character set supported.
|
|
Therefore, no translations have been defined.</dd></dl>
|
|
</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>12-23</td>
|
|
<td>Reserved (zero).</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<b>Properties for Variable-length Types (Class 9)</b>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">Byte</th>
|
|
<th width="25%">Byte</th>
|
|
<th width="25%">Byte</th>
|
|
<th width="25%">Byte</th>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br>Parent Type<br><br></td>
|
|
</tr>
|
|
|
|
</table>
|
|
</center>
|
|
|
|
<center>
|
|
<table border=0 cellpadding=4 width="80%">
|
|
<tr align=left valign=top>
|
|
<td valign=top width=20%>Parent Type:</td>
|
|
<td valign=top>Each variable-length type is based on
|
|
some parent type. The information for that parent type is
|
|
described recursively by this field.</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
|
|
|
|
<p>
|
|
|
|
<!--
|
|
<p>Datatype examples are <a href="Datatypes.html">here</a>.
|
|
-->
|
|
|
|
|
|
<hr>
|
|
<h4><a name="FillValueMessage">Name: Data Storage - Fill Value</a></h4>
|
|
<b>Type:</b> 0x0004<br>
|
|
<b>Length:</b> varies<br>
|
|
<b>Status:</b> Optional, may not be repeated.<br>
|
|
|
|
<p>The fill value message stores a single data point value which
|
|
is returned to the application when an uninitialized data point
|
|
is read from the dataset. The fill value is interpreted with
|
|
the same datatype as the dataset. If no fill value message is
|
|
present then a fill value of all zero is assumed.
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<b>Fill Value Message</b>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Size (4 bytes)</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br>Fill Value<br><br></td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table align=center width="80%">
|
|
<tr>
|
|
<th width="30%">Field Name</th>
|
|
<th width="70%">Description</th>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Size (4 bytes)</td>
|
|
<td>This is the size of the Fill Value field in bytes.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Fill Value</td>
|
|
<td>The fill value. The bytes of the fill value are
|
|
interpreted using the same datatype as for the dataset.</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<hr>
|
|
<h4><a name="ReservedMessage_0005">Name: Reserved - Not Assigned Yet</a></h4>
|
|
<b>Type:</b> 0x0005<br>
|
|
<b>Length:</b> N/A<br>
|
|
<b>Status:</b> N/A<br>
|
|
|
|
|
|
|
|
<hr>
|
|
<h4><a name="CompactDataStorageMessage">Name: Data Storage - Compact</a></h4>
|
|
|
|
<b>Type:</b> 0x0006<br>
|
|
<b>Length:</b> varies<br>
|
|
<b>Status:</b> Optional, may not be repeated.<br>
|
|
|
|
<p>This message indicates that the data for the data object is
|
|
stored within the current HDF file by including the actual
|
|
data as the header data for this message. The data is
|
|
stored internally in
|
|
the <em>normal format</em>, i.e. in one chunk, uncompressed, etc.
|
|
|
|
<P>Note that one and only one of the <em>Data Storage</em> headers can be
|
|
stored for each data object.
|
|
|
|
<P><b>Format of Data:</b> The message data is actually composed
|
|
of dataset data, so the format will be determined by the dataset
|
|
format.
|
|
|
|
<!-- Delete examples throughout doc
|
|
<h4><a name="CompactDataStorageExample">Examples:</a></h4>
|
|
[very straightforward]
|
|
-->
|
|
|
|
<hr>
|
|
<h4><a name="ExternalFileListMessage">Name: Data Storage -
|
|
External Data Files</a></h4>
|
|
<b>Type:</b> 0x0007<BR>
|
|
<b>Length:</b> varies<BR>
|
|
<b>Status:</b> Optional, may not be repeated.<BR>
|
|
|
|
<p><b>Purpose and Description:</b> The external object message
|
|
indicates that the data for an object is stored outside the HDF5
|
|
file. The filename of the object is stored as a Universal
|
|
Resource Location (URL) of the actual filename containing the
|
|
data. An external file list record also contains the byte offset
|
|
of the start of the data within the file and the amount of space
|
|
reserved in the file for that data.
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<b>External File List Message</b>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td>Version</td>
|
|
<td colspan=3>Reserved</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=2>Allocated Slots</td>
|
|
<td colspan=2>Used Slots</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br>Heap Address<br><br></td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br>Slot Definitions...<br><br></td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table align=center width="80%">
|
|
<tr>
|
|
<th width="30%">Field Name</th>
|
|
<th width="70%">Description</th>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Version </td>
|
|
<td>This value is used to determine the format of the
|
|
External File List Message. When the format of the
|
|
information in the message is changed, the version number
|
|
is incremented and can be used to determine how the
|
|
information in the object header is formatted.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Reserved</td>
|
|
<td>This field is reserved for future use.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Allocated Slots</td>
|
|
<td>The total number of slots allocated in the message. Its
|
|
value must be at least as large as the value contained in
|
|
the Used Slots field.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Used Slots</td>
|
|
<td>The number of initial slots which contain valid
|
|
information. The remaining slots are zero filled.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Heap Address</td>
|
|
<td>This is the address of a local name heap which contains
|
|
the names for the external files. The name at offset zero
|
|
in the heap is always the empty string.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Slot Definitions</td>
|
|
<td>The slot definitions are stored in order according to
|
|
the array addresses they represent. If more slots have
|
|
been allocated than what has been used then the defined
|
|
slots are all at the beginning of the list.</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<b>External File List Slot</b>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br>Name Offset (<size> bytes)<br><br></td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br>File Offset (<size> bytes)<br><br></td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br>Size<br><br></td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table align=center width="80%">
|
|
<tr>
|
|
<th width="30%">Field Name</th>
|
|
<th width="70%">Description</th>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Name Offset (<size> bytes)</td>
|
|
<td>The byte offset within the local name heap for the name
|
|
of the file. File names are stored as a URL which has a
|
|
protocol name, a host name, a port number, and a file
|
|
name:
|
|
<code><em>protocol</em>:<em>port</em>//<em>host</em>/<em>file</em></code>.
|
|
If the protocol is omitted then "file:" is assumed. If
|
|
the port number is omitted then a default port for that
|
|
protocol is used. If both the protocol and the port
|
|
number are omitted then the colon can also be omitted. If
|
|
the double slash and host name are omitted then
|
|
"localhost" is assumed. The file name is the only
|
|
mandatory part, and if the leading slash is missing then
|
|
it is relative to the application's current working
|
|
directory (the use of relative names is not
|
|
recommended).</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>File Offset (<size> bytes)</td>
|
|
<td>This is the byte offset to the start of the data in the
|
|
specified file. For files that contain data for a single
|
|
dataset this will usually be zero.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Size</td>
|
|
<td>This is the total number of bytes reserved in the
|
|
specified file for raw data storage. For a file that
|
|
contains exactly one complete dataset which is not
|
|
extendable, the size will usually be the exact size of the
|
|
dataset. However, by making the size larger one allows
|
|
HDF5 to extend the dataset. The size can be set to a value
|
|
larger than the entire file since HDF5 will read zeros
|
|
past the end of the file without failing.</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
|
|
<hr>
|
|
<h4><a name="LayoutMessage">Name: Data Storage - Layout</a></h4>
|
|
|
|
<b>Type:</b> 0x0008<BR>
|
|
<b>Length:</b> varies<BR>
|
|
<b>Status:</b> Required for datasets, may not be repeated.
|
|
|
|
<p><b>Purpose and Description:</b> Data layout describes how the
|
|
elements of a multi-dimensional array are arranged in the linear
|
|
address space of the file. Two types of data layout are
|
|
supported:
|
|
|
|
<ol>
|
|
<li>The array can be stored in one contiguous area of the file.
|
|
The layout requires that the size of the array be constant and
|
|
does not permit chunking, compression, checksums, encryption,
|
|
etc. The message stores the total size of the array and the
|
|
offset of an element from the beginning of the storage area is
|
|
computed as in C.
|
|
|
|
<li>The array domain can be regularly decomposed into chunks and
|
|
each chunk is allocated separately. This layout supports
|
|
arbitrary element traversals, compression, encryption, and
|
|
checksums, and the chunks can be distributed across external
|
|
raw data files (these features are described in other
|
|
messages). The message stores the size of a chunk instead of
|
|
the size of the entire array; the size of the entire array can
|
|
be calculated by traversing the B-tree that stores the chunk
|
|
addresses.
|
|
</ol>
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<B>Data Layout Message</B>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td>Version</td>
|
|
<td>Dimensionality</td>
|
|
<td>Layout Class</td>
|
|
<td>Reserved</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Reserved</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br>Address<br><br></td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Dimension 0 (4-bytes)</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Dimension 1 (4-bytes)</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>...</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table align=center width="80%">
|
|
<tr>
|
|
<th width="30%">Field Name</th>
|
|
<th width="70%">Description</th>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Version</td>
|
|
<td>A version number for the layout message. This
|
|
documentation describes version one.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Dimensionality</td>
|
|
<td>An array has a fixed dimensionality. This field
|
|
specifies the number of dimension size fields later in the
|
|
message.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Layout Class</td>
|
|
<td>The layout class specifies how the other fields of the
|
|
layout message are to be interpreted. A value of one
|
|
indicates contiguous storage while a value of two
|
|
indicates chunked storage. Other values will be defined
|
|
in the future.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Address</td>
|
|
<td>For contiguous storage, this is the address of the first
|
|
byte of storage. For chunked storage this is the address
|
|
of the B-tree that is used to look up the addresses of the
|
|
chunks.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Dimensions</td>
|
|
<td>For contiguous storage the dimensions define the entire
|
|
size of the array while for chunked storage they define
|
|
the size of a single chunk.</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
|
|
<hr>
|
|
<h4><a name="ReservedMessage_0009">Name: Reserved - Not Assigned Yet</a></h4>
|
|
<b>Type:</b> 0x0009<BR>
|
|
<b>Length:</b> N/A<BR>
|
|
<b>Status:</b> N/A<BR>
|
|
<b>Purpose and Description:</b> N/A<BR>
|
|
<b>Format of Data:</b> N/A
|
|
|
|
<hr>
|
|
<h4><a name="ReservedMessage_000A">Name: Reserved - Not Assigned Yet</a></h4>
|
|
<b>Type:</b> 0x000A<BR>
|
|
<b>Length:</b> N/A<BR>
|
|
<b>Status:</b> N/A<BR>
|
|
<b>Purpose and Description:</b> N/A<BR>
|
|
<b>Format of Data:</b> N/A
|
|
|
|
<hr>
|
|
<h4><a name="FilterMessage">Name: Data Storage - Filter Pipeline</a></h4>
|
|
<b>Type:</b> 0x000B<BR>
|
|
<b>Length:</b> varies<BR>
|
|
<b>Status:</b> Optional, may not be repeated.
|
|
|
|
<p><b>Purpose and Description:</b> This message describes the
|
|
filter pipeline which should be applied to the data stream by
|
|
providing filter identification numbers, flags, a name, an
|
|
client data.
|
|
|
|
<p>
|
|
<center>
|
|
<table border align=center cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<b>Filter Pipeline Message</b>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td>Version</td>
|
|
<td>Number of Filters</td>
|
|
<td colspan=2>Reserved</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Reserved</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br>Filter List<br><br></td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table align=center width="80%">
|
|
<tr>
|
|
<th width="30%">Field Name</th>
|
|
<th width="70%">Description</th>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Version</td>
|
|
<td>The version number for this message. This document
|
|
describes version one.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Number of Filters</td>
|
|
<td>The total number of filters described by this
|
|
message. The maximum possible number of filters in a
|
|
message is 32.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Filter List</td>
|
|
<td>A description of each filter. A filter description
|
|
appears in the next table.</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table border align=center cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<b>Filter Pipeline Message</b>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=2>Filter Identification</td>
|
|
<td colspan=2>Name Length</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=2>Flags</td>
|
|
<td colspan=2>Client Data Number of Values</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br>Name<br><br></td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br>Client Data<br><br></td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Padding</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table align=center width="80%">
|
|
<tr>
|
|
<th width="30%">Field Name</th>
|
|
<th width="70%">Description</th>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Filter Identification</td>
|
|
<td>This is a unique (except in the case of testing)
|
|
identifier for the filter. Values from zero through 255
|
|
are reserved for filters defined by the NCSA HDF5
|
|
library. Values 256 through 511 have been set aside for
|
|
use when developing/testing new filters. The remaining
|
|
values are allocated to specific filters by contacting the
|
|
<a href="mailto:hdf5dev@ncsa.uiuc.edu">HDF5 Development
|
|
Team</a>.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Name Length</td>
|
|
<td>Each filter has an optional null-terminated ASCII name
|
|
and this field holds the length of the name including the
|
|
null termination padded with nulls to be a multiple of
|
|
eight. If the filter has no name then a value of zero is
|
|
stored in this field.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Flags</td>
|
|
<td>The flags indicate certain properties for a filter. The
|
|
bit values defined so far are:
|
|
|
|
<dl>
|
|
<dt><code>bit 1</code>
|
|
<dd>If set then the filter is an optional filter.
|
|
During output, if an optional filter fails it will be
|
|
silently removed from the pipeline.
|
|
</dl>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Client Data Number of Values</td>
|
|
<td>Each filter can store a few integer values to control
|
|
how the filter operates. The number of entries in the
|
|
Client Data array is stored in this field.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Name</td>
|
|
<td>If the Name Length field is non-zero then it will
|
|
contain the size of this field, a multiple of eight. This
|
|
field contains a null-terminated, ASCII character
|
|
string to serve as a comment/name for the filter.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Client Data</td>
|
|
<td>This is an array of four-byte integers which will be
|
|
passed to the filter function. The Client Data Number of
|
|
Values determines the number of elements in the
|
|
array.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Padding</td>
|
|
<td>Four bytes of zeros are added to the message at this
|
|
point if the Client Data Number of Values field contains
|
|
an odd number.</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<hr>
|
|
<h4><a name="AttributeMessage">Name: Attribute</a></h4>
|
|
<b>Type:</b> 0x000C<BR>
|
|
<b>Length:</b> varies<BR>
|
|
<b>Status:</b> Optional, may be repeated.<BR>
|
|
|
|
<p><b>Purpose and Description:</b> The <em>Attribute</em>
|
|
message is used to list objects in the HDF file which are used
|
|
as attributes, or "meta-data" about the current object. An
|
|
attribute is a small dataset; it has a name, a datatype, a data
|
|
space, and raw data. Since attributes are stored in the object
|
|
header they must be relatively small (<64kb) and can be
|
|
associated with any type of object which has an object header
|
|
(groups, datasets, named types and spaces, etc.).
|
|
|
|
<p>
|
|
<center>
|
|
<table border align=center cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<b>Attribute Message</b>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td>Version</td>
|
|
<td>Reserved</td>
|
|
<td colspan=2>Name Size</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=2>Type Size</td>
|
|
<td colspan=2>Space Size</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br>Name<br><br></td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br>Type<br><br></td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br>Space<br><br></td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br>Data<br><br></td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table align=center width="80%">
|
|
<tr>
|
|
<th width="30%">Field Name</th>
|
|
<th width="70%">Description</th>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Version</td>
|
|
<td>Version number for the message. This document describes
|
|
version 1 of attribute messages.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Reserved</td>
|
|
<td>This field is reserved for later use and is set to
|
|
zero.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Name Size</td>
|
|
<td>The length of the attribute name in bytes including the
|
|
null terminator. Note that the Name field below may
|
|
contain additional padding not represented by this
|
|
field.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Type Size</td>
|
|
<td>The length of the datatype description in the Type
|
|
field below. Note that the Type field may contain
|
|
additional padding not represented by this field.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Space Size</td>
|
|
<td>The length of the dataspace description in the Space
|
|
field below. Note that the Space field may contain
|
|
additional padding not represented by this field.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Name</td>
|
|
<td>The null-terminated attribute name. This field is
|
|
padded with additional null characters to make it a
|
|
multiple of eight bytes.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Type</td>
|
|
<td>The datatype description follows the same format as
|
|
described for the datatype object header message. This
|
|
field is padded with additional zero bytes to make it a
|
|
multiple of eight bytes.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Space</td>
|
|
<td>The dataspace description follows the same format as
|
|
described for the dataspace object header message. This
|
|
field is padded with additional zero bytes to make it a
|
|
multiple of eight bytes.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Data</td>
|
|
<td>The raw data for the attribute. The size is determined
|
|
from the datatype and dataspace descriptions. This
|
|
field is <em>not</em> padded with additional zero
|
|
bytes.</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<hr>
|
|
<h4><a name="NameMessage">Name: Object Name</a></h4>
|
|
|
|
<p><b>Type:</b> 0x000D<br>
|
|
<b>Length:</b> varies<br>
|
|
<b>Status:</b> Optional, may not be repeated.
|
|
|
|
<p><b>Purpose and Description:</b> The object name or comment is
|
|
designed to be a short description of an object. An object name
|
|
is a sequence of non-zero (<code>\0</code>) ASCII characters with no other
|
|
formatting included by the library.
|
|
|
|
<p>
|
|
<center>
|
|
<table border align=center cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<b>Name Message</b>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br>Name<br><br></td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table align=center width="80%">
|
|
<tr>
|
|
<th width="30%">Field Name</th>
|
|
<th width="70%">Description</th>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Name</td>
|
|
<td>A null terminated ASCII character string.</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<hr>
|
|
<h4><a name="ModifiedMessage">Name: Object Modification Date & Time</a></h4>
|
|
|
|
<p><b>Type:</b> 0x000E<br>
|
|
<b>Length:</b> fixed<br>
|
|
<b>Status:</b> Optional, may not be repeated.
|
|
|
|
<p><b>Purpose and Description:</b> The object modification date
|
|
and time is a timestamp which indicates (using ISO-8601 date and
|
|
time format) the last modification of an object. The time is
|
|
updated when any object header message changes according to the
|
|
system clock where the change was posted.
|
|
|
|
<p>
|
|
<center>
|
|
<table border align=center cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<b>Modification Time Message</b>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Year</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=2>Month</td>
|
|
<td colspan=2>Day of Month</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=2>Hour</td>
|
|
<td colspan=2>Minute</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=2>Second</td>
|
|
<td colspan=2>Reserved</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table align=center width="80%">
|
|
<tr>
|
|
<th width="30%">Field Name</th>
|
|
<th width="70%">Description</th>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Year</td>
|
|
<td>The four-digit year as an ASCII string. For example,
|
|
<code>1998</code>. All fields of this message should be interpreted
|
|
as coordinated universal time (UTC)</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Month</td>
|
|
<td>The month number as a two digit ASCII string where
|
|
January is <code>01</code> and December is <code>12</code>.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Day of Month</td>
|
|
<td>The day number within the month as a two digit ASCII
|
|
string. The first day of the month is <code>01</code>.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Hour</td>
|
|
<td>The hour of the day as a two digit ASCII string where
|
|
midnight is <code>00</code> and 11:00pm is <code>23</code>.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Minute</td>
|
|
<td>The minute of the hour as a two digit ASCII string where
|
|
the first minute of the hour is <code>00</code> and
|
|
the last is <code>59</code>.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Second</td>
|
|
<td>The second of the minute as a two digit ASCII string
|
|
where the first second of the minute is <code>00</code>
|
|
and the last is <code>59</code>.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Reserved</td>
|
|
<td>This field is reserved and should always be zero.</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<hr>
|
|
<h4><a name="SharedMessage">Name: Shared Object Message</a></h4>
|
|
<b>Type:</b> 0x000F<br>
|
|
<b>Length:</b> 4 Bytes<br>
|
|
<b>Status:</b> Optional, may be repeated.
|
|
|
|
<p>A constant message can be shared among several object headers
|
|
by writing that message in the global heap and having the object
|
|
headers all point to it. The pointing is accomplished with a
|
|
Shared Object message which is understood directly by the object
|
|
header layer of the library. It is also possible to have a
|
|
message of one object header point to a message in some other
|
|
object header, but care must be exercised to prevent cycles.
|
|
|
|
<p>If a message is shared, then the message appears in the global
|
|
heap and its message ID appears in the Header Message Type
|
|
field of the object header. Also, the Flags field in the object
|
|
header for that message will have bit two set (the
|
|
<code>H5O_FLAG_SHARED</code> bit). The message body in the
|
|
object header will be that of a Shared Object message defined
|
|
here and not that of the pointed-to message.
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=top>
|
|
<b>Shared Message Message</b>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">byte</td>
|
|
<th width="25%">byte</td>
|
|
<th width="25%">byte</td>
|
|
<th width="25%">byte</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td>Version</td>
|
|
<td>Flags</td>
|
|
<td colspan=2>Reserved</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Reserved</td>
|
|
</tr>
|
|
|
|
<tr align=center>
|
|
<td colspan=4><br>Pointer<br><br></td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<center>
|
|
<table align=center width="80%">
|
|
<tr>
|
|
<th width="30%">Field Name</th>
|
|
<th width="70%">Description</th>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Version</td>
|
|
<td>The version number for the message. This document
|
|
describes version one of shared messages.</td>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Flags</td>
|
|
<td>The Shared Message message points to a message which is
|
|
shared among multiple object headers. The Flags field
|
|
describes the type of sharing:
|
|
|
|
<dl>
|
|
<dt><code>Bit 0</code>
|
|
<dd>If this bit is clear then the actual message is the
|
|
first message in some other object header; otherwise
|
|
the actual message is stored in the global heap.
|
|
|
|
<dt><code>Bits 2-7</code>
|
|
<dd>Reserved (always zero)
|
|
</dl>
|
|
</tr>
|
|
|
|
<tr valign=top>
|
|
<td>Pointer</td>
|
|
<td>This field points to the actual message. The format of
|
|
the pointer depends on the value of the Flags field. If
|
|
the actual message is in the global heap then the pointer
|
|
is the file address of the global heap collection that
|
|
holds the message, and a four-byte index into that
|
|
collection. Otherwise the pointer is a group entry
|
|
that points to some other object header.</td>
|
|
</tr>
|
|
</table>
|
|
</center>
|
|
|
|
|
|
<hr>
|
|
<h4><a name="ContinuationMessage">Name: Object Header Continuation</a></h4>
|
|
<b>Type:</b> 0x0010<BR>
|
|
<b>Length:</b> fixed<BR>
|
|
<b>Status:</b> Optional, may be repeated.<BR>
|
|
<b>Purpose and Description:</b> The object header continuation is the location
|
|
in the file of more header messages for the current data object. This can be
|
|
used when header blocks are large, or likely to change over time.<BR>
|
|
<b>Format of Data:</b><p>
|
|
The object header continuation is formatted as follows (assuming a 4-byte
|
|
length & offset are being used in the current file):
|
|
|
|
<P>
|
|
<center>
|
|
<table border cellpadding=4 width=60%>
|
|
<caption align=bottom>
|
|
<B>HDF5 Object Header Continuation Message Layout</B>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width=25%>byte</th>
|
|
<th width=25%>byte</th>
|
|
<th width=25%>byte</th>
|
|
<th width=25%>byte</th>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Header Continuation Offset</td>
|
|
<tr align=center>
|
|
<td colspan=4>Header Continuation Length</td>
|
|
</table>
|
|
</center>
|
|
|
|
<P>
|
|
<dl>
|
|
<dt>The elements of the Header Continuation Message are described below:
|
|
<dd>
|
|
<dl>
|
|
<dt>Header Continuation Offset: (<offset> bytes)
|
|
<dd>This value is the offset in bytes from the beginning of the file where the
|
|
header continuation information is located.
|
|
<dt>Header Continuation Length: (<length> bytes)
|
|
<dd>This value is the length in bytes of the header continuation information in
|
|
the file.
|
|
</dl>
|
|
</dl>
|
|
|
|
<!-- Delete examples throughout doc
|
|
<h4><a name="ContinuationExample">Examples:</a></h4>
|
|
[straightforward]
|
|
-->
|
|
|
|
<hr>
|
|
<h4><a name="SymbolTableMessage">Name: Group Message</a></h4>
|
|
<b>Type:</b> 0x0011<BR>
|
|
<b>Length:</b> fixed<BR>
|
|
<b>Status:</b> Required for groups, may not be repeated.<BR>
|
|
<b>Purpose and Description:</b> Each group has a B-tree and a
|
|
name heap which are pointed to by this message.<BR>
|
|
<b>Format of data:</b>
|
|
<p>The group message is formatted as follows:
|
|
|
|
<p>
|
|
<center>
|
|
<table border cellpadding=4 width="80%">
|
|
<caption align=bottom>
|
|
<b>HDF5 Object Header Group Message Layout</b>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
<th width="25%">byte</th>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>B-tree Address</td>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Heap Address</td>
|
|
</table>
|
|
</center>
|
|
|
|
<P>
|
|
<dl>
|
|
<dt>The elements of the Group Message are described below:
|
|
<dd>
|
|
<dl>
|
|
<dt>B-tree Address (<offset> bytes)
|
|
<dd>This value is the offset in bytes from the beginning of the file
|
|
where the B-tree is located.
|
|
<dt>Heap Address (<offset> bytes)
|
|
<dd>This value is the offset in bytes from the beginning of the file
|
|
where the group name heap is located.
|
|
</dl>
|
|
</dl>
|
|
|
|
<h3><a name="SharedObjectHeader">Disk Format: Level 2b - Shared Data Object Headers</a></h3>
|
|
<P>In order to share header messages between several dataset objects, object
|
|
header messages may be placed into the global heap. Since these
|
|
messages require additional information beyond the basic object header message
|
|
information, the format of the shared message is detailed below.
|
|
|
|
<BR> <BR>
|
|
<center>
|
|
<table border cellpadding=4 width=60%>
|
|
<caption align=bottom>
|
|
<B>HDF5 Shared Object Header Message</B>
|
|
</caption>
|
|
|
|
<tr align=center>
|
|
<th width=25%>byte</th>
|
|
<th width=25%>byte</th>
|
|
<th width=25%>byte</th>
|
|
<th width=25%>byte</th>
|
|
|
|
<tr align=center>
|
|
<td colspan=4>Reference Count of Shared Header Message</td>
|
|
<tr align=center>
|
|
<td colspan=4><br> Shared Object Header Message<br> <br></td>
|
|
</table>
|
|
</center>
|
|
|
|
<p>
|
|
<dl>
|
|
<dt> The elements of the shared object header message are described below:
|
|
<dd>
|
|
<dl>
|
|
<dt>Reference Count of Shared Header Message: (32-bit unsigned integer)
|
|
<dd>This value is used to keep a count of the number of dataset objects which
|
|
refer to this message from their dataset headers. When this count reaches zero,
|
|
the shared message header may be removed from the global heap.
|
|
<dt>Shared Object Header Message: (various lengths)
|
|
<dd>The data stored for the shared object header message is formatted in the
|
|
same way as the private object header messages described in the object header
|
|
description earlier in this document and begins with the header message Type.
|
|
</dl>
|
|
</dl>
|
|
|
|
|
|
<h3><a name="DataStorage">Disk Format: Level 2c - Data Object Data Storage</a></h3>
|
|
<P>The data for an object is stored separately from the header
|
|
information in the file and may not actually be located in the HDF5 file
|
|
itself if the header indicates that the data is stored externally. The
|
|
information for each record in the object is stored according to the
|
|
dimensionality of the object (indicated in the dimensionality header message).
|
|
Multi-dimensional data is stored in C order [same as current scheme], i.e. the
|
|
"last" dimension changes fastest.
|
|
<P>Data whose elements are composed of simple number-types are stored in
|
|
native-endian IEEE format, unless they are specifically defined as being stored
|
|
in a different machine format with the architecture-type information from the
|
|
number-type header message. This means that each architecture will need to
|
|
[potentially] byte-swap data values into the internal representation for that
|
|
particular machine.
|
|
<P> Data with a "variable" sized number-type is stored in a data heap
|
|
internal to the HDF5 file. Global heap identifiers are stored in the
|
|
data object storage.
|
|
<P>Data whose elements are composed of pointer number-types are stored in several
|
|
different ways depending on the particular pointer type involved. Simple
|
|
pointers are just stored as the dataset offset of the object being pointed to with the
|
|
size of the pointer being the same number of bytes as offsets in the file.
|
|
Partial-object pointers are stored as a heap-ID which points to the following
|
|
information within the file-heap: an offset of the object pointed to, number-type
|
|
information (same format as header message), dimensionality information (same
|
|
format as header message), sub-set start and end information (i.e. a coordinate
|
|
location for each), and field start and end names (i.e. a [pointer to the]
|
|
string indicating the first field included and a [pointer to the] string name
|
|
for the last field).
|
|
|
|
<P>Data of a compound datatype is stored as a contiguous stream of the items
|
|
in the structure, with each item formatted according to its datatype.
|
|
|
|
</body>
|
|
</html>
|
|
|