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hdf5/doc/html/H5.format.html
Quincey Koziol 427ff7da28 [svn-r9727] Purpose: 
Bug Fix/Code Cleanup/Doc Cleanup/Optimization/Branch Sync :-)

Description:
    Generally speaking, this is the "signed->unsigned" change to selections.
However, in the process of merging code back, things got stickier and stickier
until I ended up doing a big "sync the two branches up" operation.  So... I
brought back all the "infrastructure" fixes from the development branch to the
release branch (which I think were actually making some improvement in
performance) as well as fixed several bugs which had been fixed in one branch,
but not the other.

    I've also tagged the repository before making this checkin with the label
"before_signed_unsigned_changes".

Platforms tested:
    FreeBSD 4.10 (sleipnir) w/parallel & fphdf5
    FreeBSD 4.10 (sleipnir) w/threadsafe
    FreeBSD 4.10 (sleipnir) w/backward compatibility
    Solaris 2.7 (arabica) w/"purify options"
    Solaris 2.8 (sol) w/FORTRAN & C++
    AIX 5.x (copper) w/parallel & FORTRAN
    IRIX64 6.5 (modi4) w/FORTRAN
    Linux 2.4 (heping) w/FORTRAN & C++


Misc. update:
2004-12-29 09:26:20 -05:00

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<html>
<head>
<title>
HDF5 File Format Specification
</title>
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<center>
<table border=0 width=98%>
<tr><td valign=top align=left>
<a href="index.html">HDF5 documents and links</a>&nbsp;<br>
<a href="H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
<!--
<a href="Glossary.html">Glossary</a><br>
-->
</td>
<td valign=top align=right>
<a href="http://hdf.ncsa.uiuc.edu/HDF5/doc/UG/index.html">HDF5 User's Guide</a>&nbsp;<br>
<a href="RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
<a href="ADGuide.html">HDF5 Application Developer's Guide</a>&nbsp;<br>
</td></tr>
</table>
</center>
<hr>
<!-- #EndLibraryItem --><center><h1>HDF5 File Format Specification</h1></center>
<center>
<table border=0 width=90%>
<tr>
<td valign=top>
<ol type=I>
<li><a href="#Intro">Introduction</a>
<li><a href="#FileMetaData">Disk Format Level 0 - File Metadata</a>
<font size=-2>
<ol type=A>
<li><a href="#SuperBlock">Disk Format Level 0A - File Signature and Super Block</a>
<li><a href="#DriverInfo">Disk Format Level 0B - File Driver Info</a>
</ol>
</font>
<li><a href="#FileInfra">Disk Format Level 1 - File Infrastructure</a>
<font size=-2>
<ol type=A>
<li><a href="#Btrees">Disk Format Level 1A - B-link Trees and B-tree Nodes</a>
<li><a href="#SymbolTable">Disk Format Level 1B - Group</a>
<li><a href="#SymbolTableEntry">Disk Format Level 1C - Group Entry</a>
<li><a href="#LocalHeap">Disk Format Level 1D - Local Heaps</a>
<li><a href="#GlobalHeap">Disk Format Level 1E - Global Heap</a>
<li><a href="#FreeSpaceIndex">Disk Format Level 1F - Free-space Index</a>
</ol>
</font>
<li><a href="#DataObject">Disk Format Level 2 - Data Objects</a>
<font size=-2>
<ol type=A>
<li><a href="#ObjectHeader">Disk Format Level 2a - Data Object Headers</a>
<ol type=1>
<li><a href="#NILMessage">Name: NIL</a> <!-- 0x0000 -->
<li><a href="#SimpleDataSpace">Name: Simple Dataspace</a> <!-- 0x0001 -->
<!-- <li><a href="#DataSpaceMessage">Name: Complex Dataspace</a> --> <!-- 0x0002 -->
<li><a href="#ReservedMessage_0002">Name: Reserved - not assigned yet</a> <!-- 0x0002 -->
<li><a href="#DataTypeMessage">Name: Datatype</a> <!-- 0x0003 -->
<li><a href="#OldFillValueMessage">Name: Data Storage - Fill Value (Old)</a> <!-- 0x0004 -->
<li><a href="#FillValueMessage">Name: Data Storage - Fill Value</a> <!-- 0x0005 -->
</ol>
</ol>
</font>
</ol>
</td><td>&nbsp;&nbsp;</td><td valign=top>
<ol type=I start=4>
<li><a href="#DataObject">Disk Format Level 2 - Data Objects</a>
<font size=-2><i>(Continued)</i>
<ol type=A>
<li><a href="#ObjectHeader">Disk Format Level 2a - Data Object Headers</a><i>(Continued)</i>
<ol type=1 start=6>
<!-- <li><a href="#CompactDataStorageMessage">Name: Data Storage - Compact</a> --> <!-- 0x0006 -->
<li><a href="#ReservedMessage_0006">Name: Reserved - not assigned yet</a> <!-- 0x0006 -->
<li><a href="#ExternalFileListMessage">Name: Data Storage - External Data Files</a> <!-- 0x0007 -->
<li><a href="#LayoutMessage">Name: Data Storage - Layout</a> <!-- 0x0008 -->
<li><a href="#ReservedMessage_0009">Name: Reserved - not assigned yet</a> <!-- 0x0009 -->
<li><a href="#ReservedMessage_000A">Name: Reserved - not assigned yet</a> <!-- 0x000a -->
<li><a href="#FilterMessage">Name: Data Storage - Filter Pipeline</a> <!-- 0x000b -->
<li><a href="#AttributeMessage">Name: Attribute</a> <!-- 0x000c -->
<li><a href="#CommentMessage">Name: Object Comment</a> <!-- 0x000d -->
<li><a href="#OldModifiedMessage">Name: Object Modification Date and Time (Old)</a> <!-- 0x000e -->
<li><a href="#SharedMessage">Name: Shared Object Message</a> <!-- 0x000f -->
<li><a href="#ContinuationMessage">Name: Object Header Continuation</a> <!-- 0x0010 -->
<li><a href="#SymbolTableMessage">Name: Group Message</a> <!-- 0x0011 -->
<li><a href="#ModifiedMessage">Name: Object Modification Date and Time</a> <!-- 0x0012 -->
</ol>
<li><a href="#SharedObjectHeader">Disk Format: Level 2b - Shared Data Object Headers</a>
<li><a href="#DataStorage">Disk Format: Level 2c - Data Object Data Storage</a>
</ol>
</font>
<LI><A href="#Appendix">Appendix</A>
</ol>
</td></tr>
</table>
</center>
<BR>
<HR>
<h2>Introduction</h2>
<table align=right width=100>
<tr><td>&nbsp;</td><td align=center>
<hr>
<img src="FF-IH_FileGroup.gif" alt="HDF5 Groups" hspace=15 vspace=15>
</td><td>&nbsp;</td></tr>
<tr><td>&nbsp;</td><td align=center>
<strong>Figure 1:</strong> Relationships among the HDF5 root group, other groups, and objects
<hr>
</td><td>&nbsp;</td></tr>
<tr><td>&nbsp;</td><td align=center>
<img src="FF-IH_FileObject.gif" alt="HDF5 Objects" hspace=15 vspace=15>
</td><td>&nbsp;</td></tr>
<tr><td>&nbsp;</td><td align=center>
<strong>Figure 2:</strong> HDF5 objects -- datasets, datatypes, or dataspaces
<hr>
</td><td>&nbsp;</td></tr>
</table>
<P>The format of an HDF5 file on disk encompasses several
key ideas of the HDF4 and AIO file formats as well as
addressing some shortcomings therein. The new format is
more self-describing than the HDF4 format and is more
uniformly applied to data objects in the file.
<P>An HDF5 file appears to the user as a directed graph.
The nodes of this graph are the higher-level HDF5 objects
that are exposed by the HDF5 APIs:
<ul>
<li>Groups
<li>Datasets
<li>Named datatypes
</ul>
<P>At the lowest level, as information is actually written to the disk,
an HDF5 file is made up of the following objects:
<ul>
<li>A super block
<li>B-tree nodes (containing either symbol nodes or raw data chunks)
<li>Object headers
<li>A global heap
<li>Local heaps
<li>Free space
</ul>
<P>The HDF5 library uses these low-level objects to represent the
higher-level objects that are then presented to the user or
to applications through the APIs.
For instance, a group is an object header that contains a message that
points to a local heap and to a B-tree which points to symbol nodes.
A dataset is an object header that contains messages that describe
datatype, space, layout, filters, external files, fill value, etc
with the layout message pointing to either a raw data chunk or to a
B-tree that points to raw data chunks.
<h3>This Document</h3>
<p>This document describes the lower-level data objects;
the higher-level objects and their properties are described
in the <a href="H5.user.html"><cite>HDF5 User's Guide</cite></a>.
<P>Three levels of information comprise the file format.
Level 0 contains basic information for identifying and
defining information about the file. Level 1 information contains
the information about the pieces of a file shared by many objects
in the file (such as a B-trees and heaps). Level 2 is the rest
of the file and contains all of the data objects, with each object
partitioned into header information, also known as
<em>metadata</em>, and data.
<p>The sizes of various fields in the following layout tables are
determined by looking at the number of columns the field spans
in the table. There are three exceptions: (1) The size may be
overridden by specifying a size in parentheses, (2) the size of
addresses is determined by the <em>Size of Offsets</em> field
in the super block and is indicated in this document with a
superscripted 'O', and (3) the size of length fields is determined
by the <em>Size of Lengths</em> field in the super block and is
indicated in this document with a superscripted 'L'.
<P>Values for all fields in this document should be treated as unsigned
integers, unless otherwise noted in the description of a field.
Additionally, all metadata fields are stored in little-endian byte
order.
</P>
<BR>
<HR>
<h2><a name="FileMetaData">
Disk Format: Level 0 - File Metadata</a></h2>
<H3><A name="SuperBlock">
Disk Format: Level 0A - File Signature and Super Block</A></H3>
<P>The super block may begin at certain predefined offsets within
the HDF5 file, allowing a block of unspecified content for
users to place additional information at the beginning (and
end) of the HDF5 file without limiting the HDF5 library's
ability to manage the objects within the file itself. This
feature was designed to accommodate wrapping an HDF5 file in
another file format or adding descriptive information to the
file without requiring the modification of the actual file's
information. The super block is located by searching for the
HDF5 file signature at byte offset 0, byte offset 512 and at
successive locations in the file, each a multiple of two of
the previous location, i.e. 0, 512, 1024, 2048, etc.
<P>The super block is composed of a file signature, followed by
super block and group version numbers, information
about the sizes of offset and length values used to describe
items within the file, the size of each group page,
and a group entry for the root object in the file.
<br>
<div align=center>
<table class=format>
<caption>
HDF5 Super Block Layout
</caption>
<tr>
<th>byte</th>
<th>byte</th>
<th>byte</th>
<th>byte</th>
</tr>
<tr>
<td colspan=4><br>HDF5 File Signature (8 bytes)<br><br></td>
</tr>
<tr>
<td>Version # of Super Block</td>
<td>Version # of Global Free-space Storage</td>
<td>Version # of Root Group Symbol Table Entry</td>
<td>Reserved (zero)</td>
</tr>
<tr>
<td>Version # of Shared Header Message Format</td>
<td>Size of Offsets</td>
<td>Size of Lengths</td>
<td>Reserved (zero)</td>
</tr>
<tr>
<td colspan=2>Group Leaf Node K</td>
<td colspan=2>Group Internal Node K</td>
</tr>
<tr>
<td colspan=4>File Consistency Flags</td>
</tr>
<tr>
<td colspan=2 style="border:dotted;">Indexed Storage Internal Node K<sup>1</sup></td>
<td colspan=2 style="border:dotted;">Reserved (zero)<sup>1</sup></td>
</tr>
<tr>
<td colspan=4>Base Address<sup>O</sup></td>
</tr>
<tr>
<td colspan=4>Address of Global Free-space Heap<sup>O</sup></td>
</tr>
<tr>
<td colspan=4>End of File Address<sup>O</sup></td>
</tr>
<tr>
<td colspan=4>Driver Information Block Address<sup>O</sup></td>
</tr>
<tr>
<td colspan=4>Root Group Symbol Table Entry</td>
</tr>
</table>
<table class=note>
<tr><td>
(Items marked with an 'O' the above table are
<br>
of the size specified in "Size of Offsets.")
</td></tr>
<tr><td>
(Items marked with an '1' the above table are
<br>
new in version 1 of the superblock)
</td></tr>
</table>
</div>
<br>
<div align=center>
<table class=desc>
<tr>
<th width="30%">Field Name</th>
<th>Description</th>
</tr>
<tr>
<td>HDF5 File Signature</td>
<td>
<P>This field contains a constant value and can be used to
quickly identify a file as being an HDF5 file. The
constant value is designed to allow easy identification of
an HDF5 file and to allow certain types of data corruption
to be detected. The file signature of an HDF5 file always
contains the following values:
</P>
<center>
<table border align=center cellpadding=4>
<tr align=center>
<td align=right>Decimal:</td>
<td width="8%">137</td>
<td width="8%">72</td>
<td width="8%">68</td>
<td width="8%">70</td>
<td width="8%">13</td>
<td width="8%">10</td>
<td width="8%">26</td>
<td width="8%">10</td>
</tr>
<tr align=center>
<td align=right>Hexadecimal:</td>
<td>89</td>
<td>48</td>
<td>44</td>
<td>46</td>
<td>0d</td>
<td>0a</td>
<td>1a</td>
<td>0a</td>
</tr>
<tr align=center>
<td align=right>ASCII C Notation:</td>
<td>\211</td>
<td>H</td>
<td>D</td>
<td>F</td>
<td>\r</td>
<td>\n</td>
<td>\032</td>
<td>\n</td>
</tr>
</table>
</center>
<br>
<P>This signature both identifies the file as an HDF5 file
and provides for immediate detection of common
file-transfer problems. The first two bytes distinguish
HDF5 files on systems that expect the first two bytes to
identify the file type uniquely. The first byte is
chosen as a non-ASCII value to reduce the probability
that a text file may be misrecognized as an HDF5 file;
also, it catches bad file transfers that clear bit
7. Bytes two through four name the format. The CR-LF
sequence catches bad file transfers that alter newline
sequences. The control-Z character stops file display
under MS-DOS. The final line feed checks for the inverse
of the CR-LF translation problem. (This is a direct
descendent of the <A href="http://www.libpng.org/pub/png/spec/PNG-Rationale.html#R.PNG-file-signature">PNG</A> file
signature.)
</P>
<P><EM>This field is present in version 0+ of the superblock.</EM>
</P>
</td>
</tr>
<tr>
<td>Version Number of the Super Block</td>
<td>
<P>This value is used to determine the format of the
information in the super block. When the format of the
information in the super block is changed, the version number
is incremented to the next integer and can be used to
determine how the information in the super block is
formatted.
</P>
<P>Values of 0 and 1 are defined for this field.
</P>
<P><EM>This field is present in version 0+ of the superblock.</EM>
</P>
</td>
</tr>
<tr>
<td>Version Number of the File Free-space Information</td>
<td>
<P>This value is used to determine the format of the
information in the File Free-space Information.
</P>
<P>The only value currently valid in this field is '0', which
indicates that the free space index is formatted as described
<A href="#FreeSpaceIndex">below</A>.
</P>
<P><EM>This field is present in version 0+ of the superblock.</EM>
</P>
</td>
</tr>
<tr>
<td>Version Number of the Root Group Symbol Table Entry</td>
<td>
<P>This value is used to determine the format of the
information in the Root Group Symbol Table Entry. When the
format of the information in that field is changed, the
version number is incremented to the next integer and can be
used to determine how the information in the field
is formatted.
</P>
<P>The only value currently valid in this field is '0', which
indicates that the root group symbol table entry is formatted as
described <A href="#SymbolTableEntry">below</A>.
</P>
<P><EM>This field is present in version 0+ of the superblock.</EM>
</P>
</td>
</tr>
<tr>
<td>Version Number of the Shared Header Message Format</td>
<td>
<P>This value is used to determine the format of the
information in a shared object header message, which is
stored in the global small-data heap. Since the format
of the shared header messages differs from the private
header messages, a version number is used to identify changes
in the format.
</P>
<P>The only value currently valid in this field is '0', which
indicates that shared header messages are formatted as
described <A href="#SharedObjectHeader">below</A>.
</P>
<P><EM>This field is present in version 0+ of the superblock.</EM>
</P>
</td>
</tr>
<tr>
<td>Size of Offsets</td>
<td>
<P>This value contains the number of bytes used to store
addresses in the file. The values for the addresses of
objects in the file are offsets relative to a base address,
usually the address of the super block signature. This
allows a wrapper to be added after the file is created
without invalidating the internal offset locations.
</P>
<P><EM>This field is present in version 0+ of the superblock.</EM>
</P>
</td>
</tr>
<tr>
<td>Size of Lengths</td>
<td>
<P>This value contains the number of bytes used to store
the size of an object.
</P>
<P><EM>This field is present in version 0+ of the superblock.</EM>
</P>
</td>
</tr>
<tr>
<td>Group Leaf Node K</td>
<td>
<P>Each leaf node of a group B-tree will have at
least this many entries but not more than twice this
many. If a group has a single leaf node then it
may have fewer entries.
</P>
<P>This value must be greater than zero.
</P>
<P>See the <A href="#Btrees">description</A> of B-trees below.
</P>
<P><EM>This field is present in version 0+ of the superblock.</EM>
</P>
</td>
</tr>
<tr>
<td>Group Internal Node K</td>
<td>
<P>Each internal node of a group B-tree will have at
least this many entries but not more than twice this
many. If the group has only one internal
node then it might have fewer entries.
</P>
<P>This value must be greater than zero.
</P>
<P>See the <A href="#Btrees">description</A> of B-trees below.
</P>
<P><EM>This field is present in version 0+ of the superblock.</EM>
</P>
</td>
</tr>
<tr>
<td>File Consistency Flags</td>
<td>
<P>This value contains flags to indicate information
about the consistency of the information contained
within the file. Currently, the following bit flags are
defined:
<ul>
<li>Bit 0 set indicates that the file is opened for
write-access.
<li>Bit 1 set indicates that the file has
been verified for consistency and is guaranteed to be
consistent with the format defined in this document.
<li>Bits 2-31 are reserved for future use.
</ul>
Bit 0 should be
set as the first action when a file is opened for write
access and should be cleared only as the final action
when closing a file. Bit 1 should be cleared during
normal access to a file and only set after the file's
consistency is guaranteed by the library or a
consistency utility.
</P>
<P><EM>This field is present in version 0+ of the superblock.</EM>
</P>
</td>
</tr>
<tr>
<td>Indexed Storage Internal Node K</td>
<td>
<P>Each internal node of a indexed storage B-tree will have at
least this many entries but not more than twice this
many. If the group has only one internal
node then it might have fewer entries.
</P>
<P>This value must be greater than zero.
</P>
<P>See the <A href="#Btrees">description</A> of B-trees below.
</P>
<P><EM>This field is present in version 1+ of the superblock.</EM>
</P>
</td>
</tr>
<tr>
<td>Base Address</td>
<td>
<P>This is the absolute file address of the first byte of
the HDF5 data within the file. The library currently
constrains this value to be the absolute file address
of the super block itself when creating new files;
future versions of the library may provide greater
flexibility. When opening an existing file and this address does
not match the offset of the superblock, the library assumes
that the entire contents of the HDF5 file have been adjusted in
the file and adjusts the base address and end of file address to
reflect their new positions in the file. Unless otherwise noted,
all other file addresses are relative to this base
address.
</P>
<P><EM>This field is present in version 0+ of the superblock.</EM>
</P>
</td>
</tr>
<tr>
<td>Address of Global Free-space Index</td>
<td>
<P>Free-space management is not yet defined in the HDF5
file format and is not handled by the library.
Currently this field always contains the
<A href="#UndefinedAddress">undefined address</A>.
</P>
<P><EM>This field is present in version 0+ of the superblock.</EM>
</P>
</td>
</tr>
<tr>
<td>End of File Address</td>
<td>
<P>This is the absolute file address of the first byte past
the end of all HDF5 data. It is used to determine whether a
file has been accidently truncated and as an address where
file data allocation can occur if space from the free list is
not used.
</P>
<P><EM>This field is present in version 0+ of the superblock.</EM>
</P>
</td>
</tr>
<tr>
<td>Driver Information Block Address</td>
<td>
<P>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
<A href="#UndefinedAddress">undefined address</A>.
</P>
<P><EM>This field is present in version 0+ of the superblock.</EM>
</P>
</td>
</tr>
<tr>
<td>Root Group Symbol Table Entry</td>
<td>
<P>This is the <A href="#SymbolTableEntry">symbol table entry</A>
of the root group, which serves as the entry point into
the group graph for the file.
</P>
<P><EM>This field is present in version 0+ of the superblock.</EM>
</P>
</td>
</tr>
</table>
</div>
<H3><A name="DriverInfo">
Disk Format: Level 0B - File Driver Info</A></H3>
<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:
<br>
<div align=center>
<table class=format>
<caption>
Driver Information Block
</caption>
<tr>
<th>byte</th>
<th>byte</th>
<th>byte</th>
<th>byte</th>
</tr>
<tr>
<td>Version</td>
<td colspan=3>Reserved (zero)</td>
</tr>
<tr>
<td colspan=4>Driver Information Size (4 bytes)</td>
</tr>
<tr>
<td colspan=4><br>Driver Identification (8 bytes)<br><br></td>
</tr>
<tr>
<td colspan=4><br><br>Driver Information (<em>n</em> bytes)<br><br><br></td>
</tr>
</table>
</div>
<br>
<div align=center>
<table class=desc>
<tr>
<th width="30%">Field Name</th>
<th>Description</th>
</tr>
<tr>
<td>Version</td>
<td>
<P>The version number of the driver information block. The
file format documented here is version zero.
</P>
</td>
</tr>
<tr>
<td>Driver Information Size</td>
<td>
<P>The size in bytes of the Driver Information part of this
structure.
</P>
</td>
</tr>
<tr>
<td>Driver Identification</td>
<td>
<P>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.
</P>
<P>
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>
<P>
Identification for user-defined drivers
is arbitrary but should be unique and avoid the four character
prefix "NCSA".
</P>
</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>
</div>
<BR>
<HR>
<h2><a name="FileInfra">
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 <cite>ACM Transactions on Database Systems</cite>, 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.
<br>
<div align=center>
<table class=format>
<caption>
B-tree Nodes
</caption>
<tr>
<th>byte</th>
<th>byte</th>
<th>byte</th>
<th>byte</th>
<tr>
<td colspan=4>Signature</td>
<tr>
<td>Node Type</td>
<td>Node Level</td>
<td colspan=2>Entries Used</td>
<tr>
<td colspan=4>Address of Left Sibling<sup>O</sup></td>
<tr>
<td colspan=4>Address of Right Sibling<sup>O</sup></td>
<tr>
<td colspan=4>Key 0 (variable size)</td>
<tr>
<td colspan=4>Address of Child 0<sup>O</sup></td>
<tr>
<td colspan=4>Key 1 (variable size)</td>
<tr>
<td colspan=4>Address of Child 1<sup>O</sup></td>
<tr>
<td colspan=4>...</td>
<tr>
<td colspan=4>Key 2<em>K</em> (variable size)</td>
<tr>
<td colspan=4>Address of Child 2<em>K</em><sup>O</sup></td>
<tr>
<td colspan=4>Key 2<em>K</em>+1 (variable size)</td>
</table>
<table class=note>
<tr><td>
(Items marked with an 'O' the above table are
<br>
of the size specified in "Size of Offsets.")
</td></tr>
</table>
</div>
<br>
<div align=center>
<table class=desc>
<tr>
<th width="30%">Field Name</th>
<th>Description</th>
</tr>
<tr>
<td>Signature</td>
<td>
<P>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.
</P>
</td>
</tr>
<tr>
<td>Node Type</td>
<td>
<P>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.
</P>
<table class=list>
<tr>
<th width="30%">Node Type</th>
<th align=left>Description</th>
</tr>
<tr>
<td align=center>0</td>
<td>This tree points to group nodes.</td>
</tr>
<tr>
<td align=center>1</td>
<td>This tree points to raw data chunk nodes.</td>
</tr>
</table>
</td>
</tr>
<tr>
<td>Node Level</td>
<td>
<P>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
damanged trees.
</P>
</td>
</tr>
<tr valign=top>
<td>Entries Used</td>
<td>
<P>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.
</P>
</td>
</tr>
<tr valign=top>
<td>Address of Left Sibling</td>
<td>
<P>This is the relative file address of the left sibling of
the current node. If the current
node is the left-most node at this level then this field
is the <A href="#UndefinedAddress">undefined address</A>.
</P>
</td>
</tr>
<tr valign=top>
<td>Address of Right Sibling</td>
<td>
<P>This is the relative file address of the right sibling of
the current node. If the current
node is the right-most node at this level then this
field is the <A href="#UndefinedAddress">undefined address</A>.
</P>
</td>
</tr>
<tr valign=top>
<td>Keys and Child Pointers</td>
<td>
<P>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 node's <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.
</P>
</td>
</tr>
<tr valign=top>
<td>Key</td>
<td>
<P>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>
<P>
The format of the key depends on the node type.
For nodes of node type 0 (group nodes), the key is formatted as
follows:
<center>
<table class=list>
<tr>
<td width=30%>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>
</P>
<P>
For nodes of node type 1 (chunked raw data nodes), the key is
formatted as follows:
<center>
<table class=list>
<tr>
<td width=30%>Bytes 1-4:</td>
<td>Size of chunk in bytes.</td>
</tr>
<tr>
<td>Bytes 4-8:</td>
<td>Filter mask, a 32-bit bitfield indicating which
filters have been skipped for this chunk. Each filter
has an index number in the pipeline (starting at 0, with
the first filter to apply) and if that filter is skipped,
the bit corresponding to it's index is set.</td>
</tr>
<tr>
<td><em>N</em> 64-bit fields:</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 64-bit indices, each with the value of
<code>5</code>.</td>
</tr>
</table>
</center>
</P>
</td>
</tr>
<tr valign=top>
<td>Child Pointer</td>
<td>
<P>The tree node contains file addresses of subtrees or
data depending on the node level. Nodes at Level 0 point
to data addresses, either raw data chunk or group nodes.
Nodes at non-zero levels point to other nodes of the
same B-tree.
</P>
<P>For raw data chunk nodes, the child pointer is the address
of a single raw data chunk. For group nodes, the child pointer
points to a <A href="#SymbolTable">symbol table</A>, which contains
information for multiple symbol table entries.
</P>
</td>
</tr>
</table>
</div>
<p>
Conceptually, each B-tree node looks like this:
<center>
<table>
<tr valign=top align=center>
<td>key[0]</td><td>&nbsp;</td>
<td>child[0]</td><td>&nbsp;</td>
<td>key[1]</td><td>&nbsp;</td>
<td>child[1]</td><td>&nbsp;</td>
<td>key[2]</td><td>&nbsp;</td>
<td>...</td><td>&nbsp;</td>
<td>...</td><td>&nbsp;</td>
<td>key[<i>N</i>-1]</td><td>&nbsp;</td>
<td>child[<i>N</i>-1]</td><td>&nbsp;</td>
<td>key[<i>N</i>]</td>
</tr>
</table>
</center>
<br>
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>] is 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 within the file (including other groups).
A group maps a set of names in the group to a set of relative
file addresses where objects with those names are located in
the file. Certain metadata for an object to which the group points
can be cached in the group's symbol table in addition to the
object's 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.
<br>
<div align=center>
<table class=format>
<caption>
Group Node (A Leaf of a B-tree)
</caption>
<tr>
<th>byte</th>
<th>byte</th>
<th>byte</th>
<th>byte</th>
<tr>
<td colspan=4>Signature</td>
<tr>
<td>Version Number</td>
<td>Reserved (0)</td>
<td colspan=2>Number of Symbols</td>
<tr>
<td colspan=4><br><br>Group Entries<br><br><br></td>
</table>
</div>
<br>
<div align=center>
<table class=desc>
<tr>
<th width="30%">Field Name</th>
<th>Description</th>
</tr>
<tr>
<td>Signature</td>
<td>
<P>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.
</P>
</td>
</tr>
<tr>
<td>Version Number</td>
<td>
<P>The version number for the group node. This
document describes version 1. (There is no version '0'
of the group node)
</P>
</td>
</tr>
<tr>
<td>Number of Symbols</td>
<td>
<P>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.
</P>
</td>
</tr>
<tr>
<td>Group Entries</td>
<td>
<P>Each symbol has an entry in the group node.
The format of the entry is described below.
There are 2<EM>K</EM> entries in each group node, where
<EM>K</EM> is the "Group Leaf Node K" value from the
<A href="#SuperBlock">super block</A>.
</P>
</td>
</tr>
</table>
</div>
<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 metadata from the
object header.
<br>
<div align=center>
<table class=format>
<caption>
Group Entry
</caption>
<tr>
<th>byte</th>
<th>byte</th>
<th>byte</th>
<th>byte</th>
</tr>
<tr>
<td colspan=4>Name Offset<sup>O</sup></td>
</tr>
<tr>
<td colspan=4>Object Header Address<sup>O</sup></td>
</tr>
<tr>
<td colspan=4>Cache Type</td>
</tr>
<tr>
<td colspan=4>Reserved</td>
</tr>
<tr>
<td colspan=4><br><br>Scratch-pad Space (16 bytes)<br><br><br></td>
</tr>
</table>
<table class=note>
<tr><td>
(Items marked with an 'O' the above table are
<br>
of the size specified in "Size of Offsets.")
</td></tr>
</table>
</div>
<br>
<div align=center>
<table class=desc>
<tr>
<th width="30%">Field Name</th>
<th>Description</th>
</tr>
<tr>
<td>Name Offset</td>
<td>
<P>This is the byte offset into the group local
heap for the name of the object. The name is null
terminated.
</P>
</td>
</tr>
<tr>
<td>Object Header Address</td>
<td>
<P>Every object has an object header which serves as a
permanent location for the object's metadata. In addition
to appearing in the object header, some metadata can be
cached in the scratch-pad space.
</P>
</td>
</tr>
<tr>
<td>Cache Type</td>
<td>
<P>The cache type is determined from the object header.
It also determines the format for the scratch-pad space:
<br>
<table class=list>
<tr align=left>
<th>Type:</th>
<th>Description:</th>
</tr>
<tr>
<td width="10%" align=center>0</td>
<td>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.
</td>
</tr>
<tr>
<td align=center>1</td>
<td>Object header metadata is cached in the group
entry. This implies that the group
entry refers to another group.
</td>
</tr>
<tr>
<td align=center>2</td>
<td>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.
</td>
</tr>
<tr>
<td align=center><em>N</em></td>
<td>Other cache values can be defined later and
libraries that do not understand the new values will
still work properly.
</td>
</tr>
</table>
</P>
</td>
</tr>
<tr>
<td>Reserved</td>
<td>
<P>These four bytes are present so that the scratch-pad
space is aligned on an eight-byte boundary. They are
always set to zero.
</P>
</td>
</tr>
<tr>
<td>Scratch-pad Space</td>
<td>
<P>This space is used for different purposes, depending
on the value of the Cache Type field. Any metadata
about a dataset object represented in the scratch-pad
space is duplicated in the object header for that
dataset. This metadata 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.
</P>
<P>
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.
</P>
</td>
</tr>
</table>
</div>
<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 metadata for another object header
in the following format:
<br>
<div align=center>
<table class=format>
<caption>
Object Header Scratch-pad Format
</caption>
<tr>
<th>byte</th>
<th>byte</th>
<th>byte</th>
<th>byte</th>
<tr>
<td colspan=4>Address of B-tree<sup>O</sup></td>
<tr>
<td colspan=4>Address of Name Heap<sup>O</sup></td>
</table>
<table class=note>
<tr><td>
(Items marked with an 'O' the above table are
<br>
of the size specified in "Size of Offsets.")
</td></tr>
</table>
</div>
<br>
<div align=center>
<table class=desc>
<tr>
<th width="30%">Field Name</th>
<th>Description</th>
</tr>
<tr>
<td>Address of B-tree</td>
<td>
<P>This is the file address for the root of the
group's B-tree.
</P>
</td>
</tr>
<tr>
<td>Address of Name Heap</td>
<td>
<P>This is the file address for the group's local
heap, in which are stored the group's symbol names.
</P>
</td>
</tr>
</table>
</div>
<P>If the Cache Type field contains the value two
<code>(2)</code>, then the scratch-pad space
contains cached metadata for another symbolic link
in the following format:
<br>
<div align=center>
<table class=format>
<caption>
Symbolic Link Scratch-pad Format
</caption>
<tr>
<th>byte</th>
<th>byte</th>
<th>byte</th>
<th>byte</th>
</tr>
<tr>
<td colspan=4>Offset to Link Value</td>
</tr>
</table>
</div>
<br>
<div align=center>
<table class=desc>
<tr>
<th width="30%">Field Name</th>
<th>Description</th>
</tr>
<tr>
<td>Offset to Link Value</td>
<td>
<P>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.
</P>
</td>
</tr>
</table>
</div>
<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>
<br>
<div align=center>
<table class=format>
<caption>
Local Heap
</caption>
<tr>
<th>byte</th>
<th>byte</th>
<th>byte</th>
<th>byte</th>
</tr>
<tr>
<td colspan=4>Signature</td>
</tr>
<tr>
<td>Version</td>
<td colspan=3>Reserved (zero)</td>
</td>
<tr>
<td colspan=4>Data Segment Size<sup>L</sup></td>
</tr>
<tr>
<td colspan=4>Offset to Head of Free-list<sup>L</sup></td>
</tr>
<tr>
<td colspan=4>Address of Data Segment<sup>O</sup></td>
</tr>
</table>
<table class=note>
<tr><td>
(Items marked with an 'L' the above table are
<br>
of the size specified in "Size of Lengths.")
</td></tr>
<tr><td>
(Items marked with an 'O' the above table are
<br>
of the size specified in "Size of Offsets.")
</td></tr>
</table>
</div>
<p>
<center>
<table class=desc>
<tr>
<th width="30%">Field Name</th>
<th>Description</th>
</tr>
<tr>
<td>Signature</td>
<td>
<P>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.
</P>
</td>
</tr>
<tr>
<td>Version</td>
<td>
<P>Each local heap has its own version number so that new
heaps can be added to old files. This document
describes version zero (0) of the local heap.
</P>
</td>
</tr>
<tr>
<td>Data Segment Size</td>
<td>
<P>The total amount of disk memory allocated for the heap
data. This may be larger than the amount of space
required by the objects stored in the heap. The extra
unused space in the heap holds a linked list of free blocks.
</P>
</td>
</tr>
<tr>
<td>Offset to Head of Free-list</td>
<td>
<P>This is the offset within the heap data segment of the
first free block (or the
<A href="#UndefinedAddress">undefined address</A> if there is no
free block). The free block contains "Size of Lengths" bytes that
are the offset of the next free block (or the
value '1' if this is the
last free block) followed by "Size of Lengths" bytes that store
the size of this free block. The size of the free block includes
the space used to store the offset of the next free block and
the of the current block, making the minimum size of a free block
2 * "Size of Lengths".
</P>
</td>
</tr>
<tr>
<td>Address of Data Segment</td>
<td>
<P>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.
</P>
</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.
<li>Collections of related global heap objects should result in
fewer and larger I/O requests. For instance, a dataset of
object references will have a global heap object for each
reference. Reading the entire set of object references
should result in a few large I/O requests instead of one small
I/O request for each reference.
<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.
</ol>
</P>
<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>
<P>The HDF5 library creates global heap collections as needed, so there may
be multiple collections throughout the file. The set of all of them is
abstractly called the "global heap", although they don't actually link
to each other, and there is no global place in the file where you can
discover all of the collections. The collections are found simply by
finding a reference to one through another object in the file (eg.
variable-length datatype elements, etc).
</P>
<br>
<div align=center>
<table class=format>
<caption>
A Global Heap Collection
</caption>
<tr>
<th>byte</th>
<th>byte</th>
<th>byte</th>
<th>byte</th>
</tr>
<tr>
<td colspan=4>Signature</td>
</tr>
<tr>
<td>Version</td>
<td colspan=3>Reserved (zero)</td>
</td>
<tr>
<td colspan=4>Collection Size<sup>L</sup></td>
</tr>
<tr>
<td colspan=4><br>Global Heap Object 1<br><br></td>
</tr>
<tr>
<td colspan=4><br>Global Heap Object 2<br><br></td>
</tr>
<tr>
<td colspan=4><br>...<br><br></td>
</tr>
<tr>
<td colspan=4><br>Global Heap Object <em>N</em><br><br></td>
</tr>
<tr>
<td colspan=4><br>Global Heap Object 0 (free space)<br><br></td>
</tr>
</table>
<table class=note>
<tr><td>
(Items marked with an 'L' the above table are
<br>
of the size specified in "Size of Lengths.")
</td></tr>
</table>
</div>
<br>
<div align=center>
<table class=desc>
<tr>
<th width="30%">Field Name</th>
<th>Description</th>
</tr>
<tr>
<td>Signature</td>
<td>
<P>The ASCII character string "<code>GCOL</code>"
is used to indicate the
beginning of a collection. This gives file consistency
checking utilities a better chance of reconstructing a
damaged file.
</P>
</td>
</tr>
<tr>
<td>Version</td>
<td>
<P>Each collection has its own version number so that new
collections can be added to old files. This document
describes version one (1) of the collections (there is no
version zero (0)).
</P>
</td>
</tr>
<tr>
<td>Collection Size</td>
<td>
<P>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. This allows for 127 16-byte heap
objects plus their overhead (the collection header of 16 bytes
and the 16 bytes of information about each heap object).
</P>
</td>
</tr>
<tr>
<td>Global Heap Object 1 through <em>N</em></td>
<td>
<P>The objects are stored in any order with no
intervening unused space.
</P>
</td>
</tr>
<tr>
<td>Global Heap Object 0</td>
<td>
<P>Global Heap 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.
</P>
</td>
</table>
</div>
<br>
<div align=center>
<table class=format>
<caption>
Global Heap Object
</caption>
<tr>
<th>byte</th>
<th>byte</th>
<th>byte</th>
<th>byte</th>
</tr>
<tr>
<td colspan=2>Heap Object ID</td>
<td colspan=2>Reference Count</td>
</tr>
<tr>
<td colspan=4>Reserved</td>
</tr>
<tr>
<td colspan=4>Object Size<sup>L</sup></td>
</tr>
<tr>
<td colspan=4><br>Object Data<br><br></td>
</tr>
</table>
<table class=note>
<tr><td>
(Items marked with an 'L' the above table are
<br>
of the size specified in "Size of Lengths.")
</td></tr>
</table>
</div>
<br>
<div align=center>
<table class=desc>
<tr>
<th width="30%">Field Name</th>
<th>Description</th>
</tr>
<tr>
<td>Heap Object ID</td>
<td>
<P>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.
</P>
</td>
</tr>
<tr>
<td>Reference Count</td>
<td>
<P>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.
</P>
</td>
</tr>
<tr>
<td>Reserved</td>
<td>
<P>Zero padding to align next field on an 8-byte boundary.
</P>
</td>
</tr>
<tr>
<td>Object Size</td>
<td>
<P>This is the size of the object data stored for the object.
The actual storage space allocated for the object data is rounded
up to a multiple of eight.
</P>
</td>
</tr>
<tr>
<td>Object Data</td>
<td>
<P>The object data is treated as a one-dimensional array
of bytes to be interpreted by the caller.
</P>
</td>
</tr>
</table>
</div>
<h3><a name="FreeSpaceIndex">Disk Format: Level 1F - Free-space Index</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 required to be the
<A href="#UndefinedAddress">undefined address</A>.
<p>The format of the free-space index is not 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>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>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: (&lt;offset&gt; 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: (&lt;length&gt; bytes)
<dd>This value indicates the length of an unused block in
the file.
<dt>Offset of Free-block #n: (&lt;offset&gt; 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: (&lt;offset&gt; 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>
<HR>
<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>
<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 "metadata" or pointers to additional
"metadata" used to describe or annotate each data object.
</P>
<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, except for the data itself.
This information includes
the dataspace, datatype, 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. Information stored by user applications as attributes
is also stored in the object's header. 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. The order
of the messages in an object header is not significant.
</P>
<P>Header messages are aligned on 8-byte boundaries.
</P>
<br>
<div align=center>
<table class=format>
<caption>
Object Headers
</caption>
<tr>
<th>byte</th>
<th>byte</th>
<th>byte</th>
<th>byte</th>
</tr>
<tr>
<td>Version</td>
<td>Reserved (zero)</td>
<td colspan=2>Number of Header Messages</td>
</tr>
<tr>
<td colspan=4>Object Reference Count</td>
</tr>
<tr>
<td colspan=4>Object Header Size</td>
</tr>
<tr>
<td colspan=2>Header Message Type #1</td>
<td colspan=2>Size of Header Message Data #1</td>
</tr>
<tr>
<td>Header Message #1 Flags</td>
<td colspan=3>Reserved (zero)</td>
</tr>
<tr>
<td colspan=4><br>Header Message Data #1<br><br></td>
</tr>
<tr>
<td colspan=4>.<br>.<br>.<br></td>
</tr>
<tr>
<td colspan=2>Header Message Type #n</td>
<td colspan=2>Size of Header Message Data #n</td>
</tr>
<tr>
<td>Header Message #n Flags</td>
<td colspan=3>Reserved (zero)</td>
</tr>
<tr>
<td colspan=4><br>Header Message Data #n<br><br></td>
</tr>
</table>
</div>
<br>
<div align=center>
<table class=desc>
<tr>
<th width="30%">Field Name</th>
<th>Description</th>
</tr>
<tr>
<td>Version</td>
<td>
<P>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. This
document describes version one (1) (there was no version
zero (0)).
</P>
</td>
</tr>
<tr>
<td>Number of Header Messages</td>
<td>
<P>This value determines the number of messages listed in
object headers for this object. This value includes the messages
in continuation messages for this object.
</P>
</td>
</tr>
<tr>
<td>Object Reference Count</td>
<td>
<P>This value specifies the number of "hard links" to this object
within the current file. References to the object from external
files, "soft links" in this file and object references in this
file are not tracked.
</P>
</td>
</tr>
<tr>
<td>Object Header Size</td>
<td>
<P>This value specifies the number of bytes of header message data
following this length field that contain object header messages
for this object header. This value does not include the size of
object header continuation blocks for this object elsewhere in the
file.
</P>
</td>
</tr>
<tr>
<td>Header Message Type</td>
<td>
<P>This value specifies the type of information included in the
following header message data. The header message types for the
pre-defined header messages are included in sections below.
</P>
</td>
</tr>
<tr>
<td>Size of Header Message Data</td>
<td>
<P>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.
</P>
</td>
</tr>
<tr>
<td>Header Message Flags</td>
<td>
<P>This is a bit field with the following definition:
<table class=list>
<tr>
<th width="30%">Bit</th>
<th align=left>Description</th>
</tr>
<tr>
<td align=center><code>0</code></td>
<td>If set, the message data is constant. This is used
for messages like the datatype message of a dataset.
</td>
</tr>
<tr>
<td align=center><code>1</code></td>
<td>If set, the message is stored in the global heap.
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.
</td>
</tr>
<tr>
<td align=center><code>2-7</code></td>
<td>Reserved</td>
</tr>
</table>
</P>
</td>
</tr>
<tr>
<td>Header Message Data</td>
<td>
<P>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.
</P>
</td>
</tr>
</table>
</div>
<P>The header message types and the message data associated with
them compose the critical "metadata" 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>
<P>The following is a list of currently defined header messages:
</P>
<hr>
<h4><a name="NILMessage">Name: NIL</a></h4>
<P class=item><B>Header Message Type: </B>0x0000
</P>
<P class=item><B>Length:</B> varies
</P>
<P class=item><B>Status:</B> Optional, may be repeated.
</P>
<P class=item><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. [Possibly one which has been deleted for some reason.]
</P>
<P class=item><B>Format of Data:</B> Unspecified.
</P>
<hr>
<h4><a name="SimpleDataSpace">Name: Simple Dataspace</a></h4>
<P class=item><B>Header Message Type: </B>0x0001
</P>
<P class=item><B>Length:</B> Varies according to the number of dimensions,
as described in the following table.
</P>
<P class=item><B>Status:</B> Required for dataset objects, may not be
repeated.
</P>
<P class=item><B>Description:</B> The simple dataspace message describes the
number of dimensions (i.e. "rank") 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 and it is not described in this
document.)</i>
</P>
<P class=item><B>Format of Data:</B>
<br>
<div align=center>
<table class=format>
<caption>
Simple Dataspace Message
</caption>
<tr>
<th>byte</th>
<th>byte</th>
<th>byte</th>
<th>byte</th>
</tr>
<tr>
<td>Version</td>
<td>Dimensionality</td>
<td>Flags</td>
<td>Reserved</td>
</tr>
<tr>
<td colspan=4>Reserved</td>
</tr>
<tr>
<td colspan=4>Dimension #1 Size<sup>L</sup></td>
<tr>
<td colspan=4>.<br>.<br>.<br></td>
<tr>
<td colspan=4>Dimension #n Size<sup>L</sup></td>
<tr>
<td colspan=4>Dimension #1 Maximum Size<sup>L</sup></td>
<tr>
<td colspan=4>.<br>.<br>.<br></td>
<tr>
<td colspan=4>Dimension #n Maximum Size<sup>L</sup></td>
<tr>
<td colspan=4>Permutation Index #1<sup>L</sup></td>
<tr>
<td colspan=4>.<br>.<br>.<br></td>
<tr>
<td colspan=4>Permutation Index #n<sup>L</sup></td>
</table>
<table class=note>
<tr><td>
(Items marked with an 'L' the above table are
<br>
of the size specified in "Size of Lengths.")
</td></tr>
</table>
</div>
<br>
<div align=center>
<table class=desc>
<tr>
<th width="30%">Field Name</th>
<th>Description</th>
</tr>
<tr>
<td>Version</td>
<td>
<P>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. This
document describes version one (1) (there was no version
zero (0)).
</P>
</td>
</tr>
<tr>
<td>Dimensionality</td>
<td>
<P>This value is the number of dimensions that the data
object has.
</P>
</td>
</tr>
<tr>
<td>Flags</td>
<td>
<P>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.
</P>
</td>
</tr>
<tr>
<td>Dimension #n Size</td>
<td>
<P>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.
</P>
</td>
</tr>
<tr>
<td>Dimension #n Maximum Size</td>
<td>
<P>This value is the maximum size of the dimension of the
data as stored in the file. This value may be the special
"<A href="#UnlimitedDim">unlimited</A>" size which indicates
that the data may expand along this dimension indefinitely.
If these values are not stored, the maximum size of each
dimension is assumed to be the dimension's current size.
</P>
</td>
</tr>
<tr>
<td>Permutation Index #n</td>
<td>
<P>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.
</P>
</td>
</tr>
</table>
</div>
</P>
<!--
<hr>
<h4><a name="DataSpaceMessage">Name: Complex Dataspace (Fiber Bundle?)</a></h4>
<b>Header Message 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>&lt;STANDALONE&gt;
<dd>The dataset mesh is self-contained and is not
embedded in another mesh.
<dt>&lt;EMBEDDED&gt;
<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>&lt;POLAR&gt;
<dd>The last two dimensions are in polar
coordinates, higher dimensions are
cartesian.
<dt>&lt;SPHERICAL&gt;
<dd>The last three dimensions are in spherical
coordinates, higher dimensions
are cartesian.
<dt>&lt;CARTESIAN&gt;
<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>&lt;STRUCTURED&gt;
<dd>All grid-points are on integral, sequential
locations, starting from 0.
<dt>&lt;UNSTRUCTURED&gt;
<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>&lt;REGULAR&gt;
<dd>All dataset elements are located at the
grid-points defined.
<dt>&lt;IRREGULAR&gt;
<dd>Each dataset element has a particular
grid-location defined.
</dl> </dl>
</dl>
<p>The following grid combinations are currently allowed:
<dl> <dl>
<dt>&lt;POLAR-STRUCTURED-REGULAR&gt;
<dt>&lt;SPHERICAL-STRUCTURED-REGULAR&gt;
<dt>&lt;CARTESIAN-STRUCTURED-REGULAR&gt;
<dt>&lt;POLAR-UNSTRUCTURED-REGULAR&gt;
<dt>&lt;SPHERICAL-UNSTRUCTURED-REGULAR&gt;
<dt>&lt;CARTESIAN-UNSTRUCTURED-REGULAR&gt;
<dt>&lt;CARTESIAN-UNSTRUCTURED-IRREGULAR&gt;
</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
&lt;UNLIMITED&gt; 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>
-->
<hr>
<h4><a name="ReservedMessage_0002">Name: Reserved - Not Assigned Yet</a></h4>
<b>Header Message Type:</b> 0x0002<BR>
<b>Length:</b> N/A<BR>
<b>Status:</b> N/A<BR>
<b>Format of Data:</b> N/A<BR>
<p><b>Purpose and Description:</b> This message type was skipped during
the initial specification of the file format and may be used in a
future expansion to the format.
<hr>
<h4><a name="DataTypeMessage">Name: Datatype</a></h4>
<P class=item><B>Header Message Type:</B> 0x0003
</P>
<P class=item><B>Length:</B> variable
</P>
<P class=item><B>Status:</B> Required for dataset or named datatype objects,
may not be repeated.
</P>
<P class=item><B>Description:</B> The datatype message defines the datatype
for each element 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.
Datatypes messages are stored
as a list of datatype classes and
their associated properties.
</P>
<P class=item2>Datatype messages that are part of a dataset object,
do not describe how elements are related to one another, the dataspace
message is used for that purpose. Datatype messages that are part of
a named datatype message describe an "abstract" datatype that can be
used by other objects in the file.
</P>
<P class=item><B>Format of Data:</B>
<br>
<div align=center>
<table class=format>
<caption>
Datatype Message
</caption>
<tr>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
</tr>
<tr>
<td>Class and Version</td>
<td>Class Bit Field, Bits 0-7</td>
<td>Class Bit Field, Bits 8-15</td>
<td>Class Bit Field, Bits 16-23</td>
</tr>
<tr>
<td colspan=4>Size</td>
</tr>
<tr>
<td colspan=4><br><br>Properties<br><br><br></td>
</tr>
</table>
</div>
<br>
<div align=center>
<table class=desc>
<tr>
<th width="30%">Field Name</th>
<th>Description</th>
</tr>
<tr>
<td>Class and Version</td>
<td>
<P>The version of the datatype message and the datatype's class
information are packed together in this field. The version
number is packed in the top 4 bits of the field and the class
is contained in the bottom 4 bits.
</P>
<P>The version number information is used for changes in the
format of the datatype message and is described here:
<table class=list>
<tr>
<th width="30%">Version</th>
<th align=left>Description</th>
</tr>
<tr>
<td align=center><code>0</code></td>
<td>Never used
</td>
</tr>
<tr>
<td align=center><code>1</code></td>
<td>Used by early versions of the library to encode
compound datatypes with explicit array fields.
See the compound datatype description below for
further details.
</td>
</tr>
<tr>
<td align=center><code>2</code></td>
<td>The current version used by the library.
</td>
</tr>
</table>
</P>
<P>The class of the datatype determines the format for the class
bit field and properties portion of the datatype message, which
are described below. The
following classes are currently defined:
<table width=100% class=list>
<tr>
<th width="30%">Value</th>
<th align=left>Description</th>
</tr>
<tr>
<td align=center><code>0</code></td>
<td>Fixed-Point</td>
</tr>
<tr>
<td align=center><code>1</code></td>
<td>Floating-Point</td>
</tr>
<tr>
<td align=center><code>2</code></td>
<td>Time</td>
</tr>
<tr>
<td align=center><code>3</code></td>
<td>String</td>
</tr>
<tr>
<td align=center><code>4</code></td>
<td>Bitfield</td>
</tr>
<tr>
<td align=center><code>5</code></td>
<td>Opaque</td>
</tr>
<tr>
<td align=center><code>6</code></td>
<td>Compound</td>
</tr>
<tr>
<td align=center><code>7</code></td>
<td>Reference</td>
</tr>
<tr>
<td align=center><code>8</code></td>
<td>Enumerated</td>
</tr>
<tr>
<td align=center><code>9</code></td>
<td>Variable-Length</td>
</tr>
<tr>
<td align=center><code>10</code></td>
<td>Array</td>
</tr>
</table>
</P>
</td>
</tr>
<tr>
<td>Class Bit Fields</td>
<td>
<P>The information in these bit fields is specific to each datatype
class and is described below. All bits not defined for a
datatype class are set to zero.
</P>
</td>
</tr>
<tr>
<td>Size</td>
<td>
<P>The size of the datatype in bytes.
</P>
</td>
</tr>
<tr>
<td>Properties</td>
<td>
<P>This variable-sized field encodes information specific to each
datatype class and is described below. If there is no
property information specified for a datatype class, the size
of this field is zero.
</P>
</td>
</tr>
</table>
</div>
</P>
<P>Class specific information for Fixed-Point Numbers (Class 0):
<br>
<div align=center>
<table class=desc>
<caption>
Bit Field Description
</caption>
<tr>
<th width="10%">Bits</th>
<th>Meaning</th>
</tr>
<tr>
<td>0</td>
<td><b>Byte Order.</b> If zero, byte order is little-endian;
otherwise, byte order is big endian.</td>
</tr>
<tr>
<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>
<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>
<td>4-23</td>
<td>Reserved (zero).</td>
</tr>
</table>
</div>
<br>
<div align=center>
<table class=format>
<caption>
Property Descriptions
</caption>
<tr>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
</tr>
<tr>
<td colspan=2>Bit Offset</td>
<td colspan=2>Bit Precision</td>
</tr>
</table>
</div>
<br>
<div align=center>
<table class=desc>
<tr>
<th width="30%">Field Name</th>
<th>Description</th>
</tr>
<tr>
<td>Bit Offset</td>
<td>
<P>The bit offset of the first significant bit of the fixed-point
value within the datatype. The bit offset specifies the number
of bits "to the right of" the value.
</P>
</td>
</tr>
<tr>
<td>Bit Precision</td>
<td>
<P>The number of bits of precision of the fixed-point value
within the datatype.
</P>
</td>
</tr>
</table>
</div>
</P>
<P>Class specific information for Floating-Point Numbers (Class 1):
<br>
<div align=center>
<table class=desc>
<caption>
Bit Field Description
</caption>
<tr>
<th width="10%">Bits</th>
<th>Meaning</th>
</tr>
<tr>
<td>0</td>
<td><b>Byte Order.</b> If zero, byte order is little-endian;
otherwise, byte order is big endian.</td>
</tr>
<tr>
<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 end 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>
<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
signficant 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>
<td>6-7</td>
<td>Reserved (zero).</td>
</tr>
<tr>
<td>8-15</td>
<td><b>Sign Location.</b> This is the bit position of the sign
bit. Bits are numbered with the least significant bit zero.</td>
</tr>
<tr>
<td>16-23</td>
<td>Reserved (zero).</td>
</tr>
</table>
</div>
<br>
<div align=center>
<table class=format>
<caption>
Property Descriptions
</caption>
<tr>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
</tr>
<tr>
<td colspan=2>Bit Offset</td>
<td colspan=2>Bit Precision</td>
</tr>
<tr>
<td>Exponent Location</td>
<td>Exponent Size</td>
<td>Mantissa Location</td>
<td>Mantissa Size</td>
</tr>
<tr>
<td colspan=4>Exponent Bias</td>
</tr>
</table>
</div>
<br>
<div align=center>
<table class=desc>
<tr>
<th width="30%">Field Name</th>
<th>Description</th>
</tr>
<tr>
<td>Bit Offset</td>
<td>
<P>The bit offset of the first significant bit of the floating-point
value within the datatype. The bit offset specifies the number
of bits "to the right of" the value.
</P>
</td>
</tr>
<tr>
<td>Bit Precision</td>
<td>
<P>The number of bits of precision of the floating-point value
within the datatype.
</P>
</td>
</tr>
<tr>
<td>Exponent Location</td>
<td>
<P>The bit position of the exponent field. Bits are numbered with
the least significant bit number zero.
</P>
</td>
</tr>
<tr>
<td>Exponent Size</td>
<td>
<P>The size of the exponent field in bits.
</P>
</td>
</tr>
<tr>
<td>Mantissa Location</td>
<td>
<P>The bit position of the mantissa field. Bits are numbered with
the least significant bit number zero.
</P>
</td>
</tr>
<tr>
<td>Mantissa Size</td>
<td>
<P>The size of the mantissa field in bits.
</P>
</td>
</tr>
<tr>
<td>Exponent Bias</td>
<td>
<P>The bias of the exponent field.
</P>
</td>
</tr>
</table>
</div>
</P>
<P>Class specific information for Time (Class 2):
<br>
<div align=center>
<table class=desc>
<caption>
Bit Field Description
</caption>
<tr>
<th width="10%">Bits</th>
<th>Meaning</th>
</tr>
<tr>
<td>0</td>
<td><b>Byte Order.</b> If zero, byte order is little-endian;
otherwise, byte order is big endian.</td>
</tr>
<tr>
<td>1-23</td>
<td>Reserved (zero).</td>
</tr>
</table>
</div>
<br>
<div align=center>
<table class=format>
<caption>
Property Descriptions
</caption>
<tr>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
</tr>
<tr>
<td colspan=2>Bit Precision</td>
</tr>
</table>
</div>
<br>
<div align=center>
<table class=desc>
<tr>
<th width="30%">Field Name</th>
<th>Description</th>
</tr>
<tr>
<td>Bit Precision</td>
<td>
<P>The number of bits of precision of the time value.
</P>
</td>
</tr>
</table>
</div>
</P>
<P>Class specific information for Strings (Class 3):
<br>
<div align=center>
<table class=desc>
<caption>
Bit Field Description
</caption>
<tr>
<th width="10%">Bits</th>
<th>Meaning</th>
</tr>
<tr>
<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:
<table width=100% class=list>
<tr>
<th width="30%">Value</th>
<th align=left>Description</th>
</tr>
<tr>
<td align=center><code>0</code></td>
<td>Null Terminate: 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.
</td>
</tr>
<tr>
<td align=center><code>1</code></td>
<td>Null Pad: 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.
</td>
</tr>
<tr>
<td align=center><code>2</code></td>
<td>Space Pad: 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.
</td>
</tr>
<tr>
<td align=center><code>3-15</code></td>
<td>Reserved
</td>
</tr>
</table>
</tr>
<tr>
<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>
<td>8-23</td>
<td>Reserved (zero).</td>
</tr>
</table>
</div>
<P>There are no properties defined for the string class.
</P>
</P>
<P>Class specific information for Bitfields (Class 4):
<br>
<div align=center>
<table class=desc>
<caption>
Bit Field Description
</caption>
<tr>
<th width="10%">Bits</th>
<th>Meaning</th>
</tr>
<tr>
<td>0</td>
<td><b>Byte Order.</b> If zero, byte order is little-endian;
otherwise, byte order is big endian.</td>
</tr>
<tr>
<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>
<td>3-23</td>
<td>Reserved (zero).</td>
</tr>
</table>
</div>
<br>
<div align=center>
<table class=format>
<caption>
Property Description
</caption>
<tr>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
</tr>
<tr>
<td colspan=2>Bit Offset</td>
<td colspan=2>Bit Precision</td>
</tr>
</table>
</div>
<br>
<div align=center>
<table class=desc>
<tr>
<th width="30%">Field Name</th>
<th>Description</th>
</tr>
<tr>
<td>Bit Offset</td>
<td>
<P>The bit offset of the first significant bit of the bitfield
within the datatype. The bit offset specifies the number
of bits "to the right of" the value.
</P>
</td>
</tr>
<tr>
<td>Bit Precision</td>
<td>
<P>The number of bits of precision of the bitfield
within the datatype.
</P>
</td>
</tr>
</table>
</div>
</P>
<P>Class specific information for Opaque (Class 5):
<br>
<div align=center>
<table class=desc>
<caption>
Bit Field Description
</caption>
<tr>
<th width="10%">Bits</th>
<th>Meaning</th>
</tr>
<tr>
<td>0-7</td>
<td>Length of ASCII tag in bytes.</td>
</tr>
<tr>
<td>8-23</td>
<td>Reserved (zero).</td>
</tr>
</table>
</div>
<br>
<div align=center>
<table class=format>
<caption>
Property Description
</caption>
<tr>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
</tr>
<tr>
<td colspan=4><br>ASCII Tag<br>
<br></td>
</tr>
</table>
</div>
<br>
<div align=center>
<table class=desc>
<tr>
<th width="30%">Field Name</th>
<th>Description</th>
</tr>
<tr>
<td>ASCII Tag</td>
<td>
<P>This NUL-terminated string provides a description for the
opaque type. It is NUL-padded to a multiple of 8 bytes.
</P>
</td>
</tr>
</table>
</div>
</P>
<P>Class specific information for Compound (Class 6):
<br>
<div align=center>
<table class=desc>
<caption>
Bit Field Description
</caption>
<tr>
<th width="10%">Bits</th>
<th>Meaning</th>
</tr>
<tr>
<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>
<td>15-23</td>
<td>Reserved (zero).</td>
</tr>
</table>
</div>
</P>
<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>Note that the property descriptions are different for different
versions of the datatype version. Additionally note that the version
0 properties are deprecated and have been replaced with the version
1 properties in versions of the HDF5 library from the 1.4 release
onward.
<br>
<div align=center>
<table class=format>
<caption>
Properties Description for Datatype Version 1
</caption>
<tr>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
</tr>
<tr>
<td colspan=4><br>Name<br><br></td>
</tr>
<tr>
<td colspan=4>Byte Offset of Member</td>
</tr>
<tr>
<td>Dimensionality</td>
<td colspan=3>Reserved (zero)</td>
</tr>
<tr>
<td colspan=4>Dimension Permutation</td>
</tr>
<tr>
<td colspan=4>Reserved (zero)</td>
</tr>
<tr>
<td colspan=4>Dimension #1 Size (required)</td>
</tr>
<tr>
<td colspan=4>Dimension #2 Size (required)</td>
</tr>
<tr>
<td colspan=4>Dimension #3 Size (required)</td>
</tr>
<tr>
<td colspan=4>Dimension #4 Size (required)</td>
</tr>
<tr>
<td colspan=4><br>Member Type Message<br><br></td>
</tr>
</table>
</div>
<br>
<div align=center>
<table class=desc>
<tr>
<th width="30%">Field Name</th>
<th>Description</th>
</tr>
<tr>
<td>Name</td>
<td>
<P>This NUL-terminated string provides a description for the
opaque type. It is NUL-padded to a multiple of 8 bytes.
</P>
</td>
</tr>
<tr>
<td>Byte Offset of Member</td>
<td>
<P>This is the byte offset of the member within the datatype.
</P>
</td>
</tr>
<tr>
<td>Dimensionality</td>
<td>
<P>If set to zero, this field indicates a scalar member. If set
to a value greater than zero, this field indicates that the
member is an array of values. For array members, the size of
the array is indicated by the 'Size of Dimension n' field in
this message.
</P>
</td>
</tr>
<tr>
<td>Dimension Permutation</td>
<td>
<P>This field was intended to allow an array field to have
it's dimensions permuted, but this was never implemented.
This field should always be set to zero.
</P>
</td>
</tr>
<tr>
<td>Dimension #n Size</td>
<td>
<P>This field is the size of a dimension of the array field 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.
</P>
</td>
</tr>
<tr>
<td>Member Type Message</td>
<td>
<P>This field is a datatype message describing the datatype of
the member.
</P>
</td>
</tr>
</table>
</div>
<br>
<div align=center>
<table class=format>
<caption>
Properties Description for Datatype Version 2
</caption>
<tr>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
</tr>
<tr>
<td colspan=4><br>Name<br><br></td>
</tr>
<tr>
<td colspan=4>Byte Offset of Member</td>
</tr>
<tr>
<td colspan=4><br>Member Type Message<br><br></td>
</tr>
</table>
</div>
<br>
<div align=center>
<table class=desc>
<tr>
<th width="30%">Field Name</th>
<th>Description</th>
</tr>
<tr>
<td>Name</td>
<td>
<P>This NUL-terminated string provides a description for the
opaque type. It is NUL-padded to a multiple of 8 bytes.
</P>
</td>
</tr>
<tr>
<td>Byte Offset of Member</td>
<td>
<P>This is the byte offset of the member within the datatype.
</P>
</td>
</tr>
<tr>
<td>Member Type Message</td>
<td>
<P>This field is a datatype message describing the datatype of
the member.
</P>
</td>
</tr>
</table>
</div>
</P>
<P>Class specific information for Reference (Class 7):
<br>
<div align=center>
<table class=desc>
<caption>
Bit Field Description
</caption>
<tr>
<th width="10%">Bits</th>
<th>Meaning</th>
</tr>
<tr>
<td>0-3</td>
<td><b>Type.</b> This four-bit value contains the type of reference
described. The values defined are:
<table width=100% class=list>
<tr>
<th width="30%">Value</th>
<th align=left>Description</th>
</tr>
<tr>
<td align=center><code>0</code></td>
<td>Object Reference: A reference to another object in this
HDF5 file.
</td>
</tr>
<tr>
<td align=center><code>1</code></td>
<td>Dataset Region Reference: A reference to a region within
a dataset in this HDF5 file.
</td>
</tr>
<tr>
<td align=center><code>2</code></td>
<td>Internal Reference: A reference to a region within the
current dataset. (Not currently implemented)
</td>
</tr>
<tr>
<td align=center><code>3-15</code></td>
<td>Reserved
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td>15-23</td>
<td>Reserved (zero).</td>
</tr>
</table>
</div>
<P>There are no properties defined for the reference class.
</P>
</P>
<P>Class specific information for Enumeration (Class 8):
<br>
<div align=center>
<table class=desc>
<caption>
Bit Field Description
</caption>
<tr>
<th width="10%">Bits</th>
<th>Meaning</th>
</tr>
<tr>
<td>0-15</td>
<td><b>Number of Members.</b> The number of name/value
pairs defined for the enumeration type.</td>
</tr>
<tr>
<td>16-23</td>
<td>Reserved (zero).</td>
</tr>
</table>
</div>
<br>
<div align=center>
<table class=format>
<caption>
Property Description
</caption>
<tr>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
</tr>
<tr>
<td colspan=4><br>Base Type<br><br></td>
</tr>
<tr>
<td colspan=4><br>Names<br><br></td>
</tr>
<tr>
<td colspan=4><br>Values<br><br></td>
</tr>
</table>
</div>
<br>
<div align=center>
<table class=desc>
<tr>
<th width="30%">Field Name</th>
<th>Description</th>
</tr>
<tr>
<td>Base Type</td>
<td>
<P>Each enumeration type is based on some parent type, usually an
integer. The information for that parent type is described
recursively by this field.
</P>
</td>
</tr>
<tr>
<td>Names</td>
<td>
<P>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.
</P>
</td>
</tr>
<tr>
<td>Values</td>
<td>
<P>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.
</P>
</td>
</tr>
</table>
</div>
</P>
<P>Class specific information for Variable-Length (Class 9):
<br>
<div align=center>
<table class=desc>
<caption>
Bit Field Description
</caption>
<tr>
<th width="10%">Bits</th>
<th>Meaning</th>
</tr>
<tr>
<td>0-3</td>
<td><b>Type.</b> This four-bit value contains the type of
variable-length datatype described. The values defined are:
<table width=100% class=list>
<tr>
<th width="30%">Value</th>
<th align=left>Description</th>
</tr>
<tr>
<td align=center><code>0</code></td>
<td>Sequence: A variable-length sequence of any sequence of
data. Variable-length sequences do not have padding or
character set information.
</td>
</tr>
<tr>
<td align=center><code>1</code></td>
<td>String: A variable-length sequence of characters.
Variable-length strings have padding and character set
information.
</td>
</tr>
<tr>
<td align=center><code>2-15</code></td>
<td>Reserved
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td>4-7</td>
<td><b>Padding type.</b> (variable-length string only)
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:
<table width=100% class=list>
<tr>
<th width="30%">Value</th>
<th align=left>Description</th>
</tr>
<tr>
<td align=center><code>0</code></td>
<td>Null terminate: 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.
</td>
</tr>
<tr>
<td align=center><code>1</code></td>
<td>Null pad: 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.
</td>
</tr>
<tr>
<td align=center><code>2</code></td>
<td>Space pad: 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.
</td>
</tr>
<tr>
<td align=center><code>3-15</code></td>
<td>Reserved
</td>
</tr>
</table>
This value is set to zero for variable-length sequences.
</td>
</tr>
<tr>
<td>8-11</td>
<td><b>Character Set.</b> (variable-length string only)
This four-bit value specifies the character set
to be used for encoding the string:
<table width=100% class=list>
<tr>
<th width="30%">Value</th>
<th align=left>Description</th>
</tr>
<tr>
<td align=center><code>0</code></td>
<td>ASCII: As of this writing (July 2003, Release 1.6.0),
8-bit ASCII is the only character set supported. Therefore,
no translations have been defined.
</td>
</tr>
<tr>
<td align=center><code>1-15</code></td>
<td>Reserved
</td>
</tr>
</table>
This value is set to zero for variable-length sequences.
</td>
</tr>
<tr>
<td>12-23</td>
<td>Reserved (zero).</td>
</tr>
</table>
</div>
<br>
<div align=center>
<table class=format>
<caption>
Property Description
</caption>
<tr>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
</tr>
<tr>
<td colspan=4><br>Base Type<br><br></td>
</tr>
</table>
</div>
<br>
<div align=center>
<table class=desc>
<tr>
<th width="30%">Field Name</th>
<th>Description</th>
</tr>
<tr>
<td>Base Type</td>
<td>
<P>Each variable-length type is based on some parent type. The
information for that parent type is described recursively by
this field.
</P>
</td>
</tr>
</table>
</div>
</P>
<P>Class specific information for Array (Class 10):
<P>There are no bit fields defined for the array class.
</P>
<P>Note that the dimension information defined in the property for this
datatype class is independent of dataspace information for a dataset.
The dimension information here describes the dimensionality of the
information within a data element (or a component of an element, if the
array datatype is nested within another datatype) and the dataspace for a
dataset describes the location of the elements in a dataset.
</P>
<br>
<div align=center>
<table class=format>
<caption>
Property Description
</caption>
<tr>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
</tr>
<tr>
<td>Dimensionality</td>
<td colspan=3>Reserved (zero)</td>
</tr>
<tr>
<td colspan=4>Dimension #1 Size</td>
</tr>
<tr>
<td colspan=4>.<br>.<br>.<br></td>
</tr>
<tr>
<td colspan=4>Dimension #n Size</td>
</tr>
<tr>
<td colspan=4>Permutation Index #1</td>
</tr>
<tr>
<td colspan=4>.<br>.<br>.<br></td>
</tr>
<tr>
<td colspan=4>Permutation Index #n</td>
</tr>
<tr>
<td colspan=4><br>Base Type<br><br></td>
</tr>
</table>
</div>
<br>
<div align=center>
<table class=desc>
<tr>
<th width="30%">Field Name</th>
<th>Description</th>
</tr>
<tr>
<td>Dimensionality</td>
<td>
<P>This value is the number of dimensions that the array has.
</P>
</td>
</tr>
<tr>
<td>Dimension #n Size</td>
<td>
<P>This value is the size of the dimension of the array
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.
</P>
</td>
</tr>
<tr>
<td>Permutation Index #n</td>
<td>
<P>This value is the index permutation used to map
each dimension from the canonical representation to an
alternate axis for each dimension. Currently, dimension
permutations are not supported and these indices should be set
to the index position minus one (i.e. the first dimension should
be set to 0, the second dimension should be set to 1, etc.)
</P>
</td>
</tr>
<tr>
<td>Base Type</td>
<td>
<P>Each array type is based on some parent type. The
information for that parent type is described recursively by
this field.
</P>
</td>
</tr>
</table>
</div>
</P>
<hr>
<h4><a name="OldFillValueMessage">Name: Data Storage - Fill Value (Old)</a></h4>
<P class=item><B>Header Message Type:</B> 0x0004
</P>
<P class=item><B>Length:</B> varies
</P>
<P class=item><B>Status:</B> Optional, may not be repeated.
</P>
<P class=item><B>Description:</B> The fill value message stores a single
data value which is returned to the application when an uninitialized
data element is read from a 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 bytes is assumed.
</P>
<P class=item2>This fill value message is deprecated in favor of the "new"
fill value message (Message Type 0x0005) and is only written to the
file for forward compatibility with versions of the HDF5 library before
the 1.6.0 version. Additionally, it only appears for datasets with a
user defined fill value (as opposed to the library default fill value
or an explicitly set "undefined" fill value).
</P>
<P class=item><B>Format of Data:</B>
<br>
<div align=center>
<table class=format>
<caption>
Fill Value Message (Old)
</caption>
<tr>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
</tr>
<tr>
<td colspan=4>Size</td>
</tr>
<tr>
<td colspan=4><br>Fill Value<br><br></td>
</tr>
</table>
</div>
<br>
<div align=center>
<table class=desc>
<tr>
<th width="30%">Field Name</th>
<th>Description</th>
</tr>
<tr>
<td>Size</td>
<td>
<P>This is the size of the Fill Value field in bytes.
</P>
</td>
</tr>
<tr>
<td>Fill Value</td>
<td>
<P>The fill value. The bytes of the fill value are interpreted
using the same datatype as for the dataset.
</P>
</td>
</tr>
</table>
</div>
</P>
<hr>
<h4><a name="FillValueMessage">Name: Data Storage - Fill Value </a></h4>
<P class=item><B>Header Message Type:</B> 0x0005
</P>
<P class=item><B>Length:</B> varies
</P>
<P class=item><B>Status:</B> Required for dataset objects, may not be repeated.
</P>
<P class=item><B>Description:</B> The fill value message stores a single
data value which is returned to the application when an uninitialized
data element is read from a dataset. The fill value is interpreted
with the same datatype as the dataset.
</P>
<P class=item><B>Format of Data:</B>
<br>
<div align=center>
<table class=format>
<caption>
Fill Value Message
</caption>
<tr>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
</tr>
<tr>
<td>Version</td>
<td>Space Allocation Time</td>
<td>Fill Value Write Time</td>
<td>Fill Value Defined</td>
</tr>
<tr>
<td colspan=4>Size</td>
</tr>
<tr>
<td colspan=4><br>Fill Value<br><br></td>
</tr>
</table>
</div>
<br>
<div align=center>
<table class=desc>
<tr>
<th width="30%">Field Name</th>
<th>Description</th>
</tr>
<tr>
<td>Version</td>
<td>
<P>The version number information is used for changes in the
format of the fill value message and is described here:
<table class=list>
<tr>
<th width="30%">Version</th>
<th align=left>Description</th>
</tr>
<tr>
<td align=center><code>0</code></td>
<td>Never used
</td>
</tr>
<tr>
<td align=center><code>1</code></td>
<td>Used by version 1.6.x of the library to encode
fill values. In this version, the Size field is
always present.
</td>
</tr>
<tr>
<td align=center><code>2</code></td>
<td>The current version used by the library (version
1.7.3 or later). In this version, the Size and
Fill Value fields are
only present if the Fill Value Defined field is set
to 1.
</td>
</tr>
</table>
</P>
</td>
</tr>
<tr>
<td>Space Allocation Time</td>
<td>
<P>When the storage space for the dataset's raw data will be
allocated. The allowed values are:
<table class=list>
<tr>
<th width="30%">Value</th>
<th align=left>Description</th>
</tr>
<tr>
<td align=center><code>1</code></td>
<td>Early allocation. Storage space for the entire dataset
should be allocated in the file when the dataset is
created.
</td>
</tr>
<tr>
<td align=center><code>2</code></td>
<td>Late allocation. Storage space for the entire dataset
should not be allocated until the dataset is written
to.
</td>
</tr>
<tr>
<td align=center><code>3</code></td>
<td>Incremental allocation. Storage space for the
dataset should not be allocated until the portion
of the dataset is written to. This is currently
used in conjunction with chunked data storage for
datasets.
</td>
</tr>
</table>
</P>
</td>
</tr>
<tr>
<td>Fill Value Write Time</td>
<td>
<P>At the time that storage space for the dataset's raw data is
allocated, this value indicates whether the fill value should
be written to the raw data storage elements. The allowed values
are:
<table class=list>
<tr>
<th width="30%">Value</th>
<th align=left>Description</th>
</tr>
<tr>
<td align=center><code>0</code></td>
<td>On allocation. The fill value is always written to
the raw data storage when the storage space is allocated.
</td>
</tr>
<tr>
<td align=center><code>1</code></td>
<td>Never. The fill value should never be written to
the raw data storage.
</td>
</tr>
<tr>
<td align=center><code>2</code></td>
<td>Fill value written if set by user. The fill value
will be written to the raw data storage when the storage
space is allocated only if the user explicitly set
the fill value. If the fill value is the library
default or is undefined, it will not be written to
the raw data storage.
</td>
</tr>
</table>
</P>
</td>
</tr>
<tr>
<td>Fill Value Defined</td>
<td>
<P>This value indicates if a fill value is defined for this
dataset. If this value is 0, the fill value is undefined.
If this value is 1, a fill value is defined for this dataset.
For version 2 or later of the fill value message, this value
controls the presence of the Size field.
</P>
</td>
</tr>
<tr>
<td>Size</td>
<td>
<P>This is the size of the Fill Value field in bytes. This field
is not present if the Version field is >1 and the Fill Value
Defined field is set to 0.
</P>
</td>
</tr>
<tr>
<td>Fill Value</td>
<td>
<P>The fill value. The bytes of the fill value are interpreted
using the same datatype as for the dataset. This field is
not present if the Version field is >1 and the Fill Value
Defined field is set to 0.
</P>
</td>
</tr>
</table>
</div>
</P>
<!--
<hr>
<h4><a name="CompactDataStorageMessage">Name: Data Storage - Compact</a></h4>
<b>Header Message 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.
-->
<hr>
<h4><a name="ReservedMessage_0006">Name: Reserved - Not Assigned Yet</a></h4>
<b>Header Message Type:</b> 0x0006<BR>
<b>Length:</b> N/A<BR>
<b>Status:</b> N/A<BR>
<b>Format of Data:</b> N/A<BR>
<p><b>Purpose and Description:</b> This message type was skipped during
the initial specification of the file format and may be used in a
future expansion to the format.
<hr>
<h4><a name="ExternalFileListMessage">Name: Data Storage -
External Data Files</a></h4>
<b>Header Message 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 align=left>
<th width="30%"><U><font size=+1>Field Name</font></U></th>
<th><U><font size=+1>Description</font></U></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 (&lt;size&gt; bytes)<br><br></td>
</tr>
<tr align=center>
<td colspan=4><br>File Offset (&lt;size&gt; 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 align=left>
<th width="30%"><U><font size=+1>Field Name</font></U></th>
<th><U><font size=+1>Description</font></U></th>
</tr>
<tr valign=top>
<td>Name Offset (&lt;size&gt; 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 (&lt;size&gt; 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>Header Message 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. Three 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.
<li>The array can be stored in one contiguous block, as part of
this object header message (this is called "compact" storage below).
</ol>
<P>Version 3 of this message re-structured the format into specific
properties that are required for each layout class.
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<B>Data Layout Message, Versions 1 and 2</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>
<tr align=center>
<td colspan=4>Compact Data Size (4-bytes)</td>
</tr>
<tr align=center>
<td colspan=4>Compact Data</td>
</tr>
<tr align=center>
<td colspan=4>...</td>
</tr>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr align=left>
<th width="30%"><U><font size=+1>Field Name</font></U></th>
<th><U><font size=+1>Description</font></U></th>
</tr>
<tr valign=top>
<td>Version</td>
<td>A version number for the layout message. This value can be
either 1 or 2.</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, a value of two
indicates chunked storage,
while a value of zero
indicates compact 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. This field is not present for compact storage.
If the version for this message is set to 2, the address
may have the "undefined address" value, to indicate that
storage has not yet been allocated for this array.</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>
<tr valign=top>
<td>Compact Data Size</td>
<td>This field is only present for compact data storage.
It contains the size of the raw data for the dataset array.</td>
<tr valign=top>
<td>Compact Data</td>
<td>This field is only present for compact data storage.
It contains the raw data for the dataset array.</td>
</tr>
</table>
</center>
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<B>Data Layout Message, Version 3</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>Layout Class</td>
</tr>
<tr align=center>
<td colspan=4>Properties</td>
</tr>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr align=left>
<th width="30%"><U><font size=+1>Field Name</font></U></th>
<th><U><font size=+1>Description</font></U></th>
</tr>
<tr valign=top>
<td>Version</td>
<td>A version number for the layout message. This value can be
either 1, 2 or 3.</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, a value of two
indicates chunked storage,
while a value of three
indicates compact storage.</td>
</tr>
<tr valign=top>
<td>Properties</td>
<td>This variable-sized field encodes information specific to each
layout class and is described below. If there is no property
information specified for a layout class, the size of this field
is zero bytes.</td>
</tr>
</table>
</center>
<P>Class-specific information for contiguous layout (Class 0):
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<B>Property Descriptions</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>Address<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 align=left>
<th width="30%"><U><font size=+1>Field Name</font></U></th>
<th><U><font size=+1>Description</font></U></th>
</tr>
<tr valign=top>
<td>Address</td>
<td>This is the address of the first byte of raw data storage.
The address may have the "undefined address" value, to indicate
that storage has not yet been allocated for this array.</td>
</tr>
<tr valign=top>
<td>Size</td>
<td>This field contains the size allocated to store the raw data.</td>
</table>
</center>
<P>Class-specific information for chunked layout (Class 1):
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<B>Property Descriptions</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>Dimensionality</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 align=left>
<th width="30%"><U><font size=+1>Field Name</font></U></th>
<th><U><font size=+1>Description</font></U></th>
</tr>
<tr valign=top>
<td>Dimensionality</td>
<td>A chunk has a fixed dimensionality. This field
specifies the number of dimension size fields later in the
message.</td>
</tr>
<tr valign=top>
<td>Address</td>
<td>This is the address
of the B-tree that is used to look up the addresses of the
chunks.
The address
may have the "undefined address" value, to indicate that
storage has not yet been allocated for this array.</td>
</tr>
<tr valign=top>
<td>Dimensions</td>
<td>The dimension sizes define the size of a single chunk.</td>
</tr>
</table>
</center>
<P>Class-specific information for compact layout (Class 2):
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<B>Property Descriptions</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>Size</td>
</tr>
<tr align=center>
<td colspan=4>Raw Data</td>
</tr>
<tr align=center>
<td colspan=4>...</td>
</tr>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr align=left>
<th width="30%"><U><font size=+1>Field Name</font></U></th>
<th><U><font size=+1>Description</font></U></th>
</tr>
<tr valign=top>
<td>Size</td>
<td>This field contains the size of the raw data for the dataset array.</td>
<tr valign=top>
<td>Raw Data</td>
<td>This field contains the raw data for the dataset array.</td>
</tr>
</table>
</center>
<hr>
<h4><a name="ReservedMessage_0009">Name: Reserved - Not Assigned Yet</a></h4>
<b>Header Message Type:</b> 0x0009<BR>
<b>Length:</b> N/A<BR>
<b>Status:</b> N/A<BR>
<b>Format of Data:</b> N/A<BR>
<p><b>Purpose and Description:</b> This message type was skipped during
the initial specification of the file format and may be used in a
future expansion to the format.
<hr>
<h4><a name="ReservedMessage_000A">Name: Reserved - Not Assigned Yet</a></h4>
<b>Header Message Type:</b> 0x000A<BR>
<b>Length:</b> N/A<BR>
<b>Status:</b> N/A<BR>
<b>Format of Data:</b> N/A<BR>
<p><b>Purpose and Description:</b> This message type was skipped during
the initial specification of the file format and may be used in a
future expansion to the format.
<hr>
<h4><a name="FilterMessage">Name: Data Storage - Filter Pipeline</a></h4>
<b>Header Message 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 align=left>
<th width="30%"><U><font size=+1>Field Name</font></U></th>
<th><U><font size=+1>Description</font></U></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 align=left>
<th width="30%"><U><font size=+1>Field Name</font></U></th>
<th><U><font size=+1>Description</font></U></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>Header Message 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 "metadata" 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>Note: Attributes on an object must have unique names. (The HDF5 library
currently enforces this by causing the creation of an attribute with
a duplicate name to fail)
Attributes on different objects may have the same name, however.
<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 align=left>
<th width="30%"><U><font size=+1>Field Name</font></U></th>
<th><U><font size=+1>Description</font></U></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="CommentMessage">Name: Object Comment</a></h4>
<p><b>Header Message 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 comment is
designed to be a short description of an object. An object comment
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>Comment<br><br></td>
</tr>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr align=left>
<th width="30%"><U><font size=+1>Field Name</font></U></th>
<th><U><font size=+1>Description</font></U></th>
</tr>
<tr valign=top>
<td>Name</td>
<td>A null terminated ASCII character string.</td>
</tr>
</table>
</center>
<hr>
<h4><a name="OldModifiedMessage">Name: Object Modification Date &amp; Time (Old)</a></h4>
<p><b>Header Message 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>This modification time message is deprecated in favor of the "new"
modification time message (Message Type 0x0012) and is no longer written
to the file in versions of the HDF5 library after the 1.6.0 version.
</p>
<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 align=left>
<th width="30%"><U><font size=+1>Field Name</font></U></th>
<th><U><font size=+1>Description</font></U></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>Header Message 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 align=left>
<th width="30%"><U><font size=+1>Field Name</font></U></th>
<th><U><font size=+1>Description</font></U></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>Header Message 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 &amp; 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: (&lt;offset&gt; 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: (&lt;length&gt; bytes)
<dd>This value is the length in bytes of the header continuation information in
the file.
</dl>
</dl>
<hr>
<h4><a name="SymbolTableMessage">Name: Group Message</a></h4>
<b>Header Message 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 (&lt;offset&gt; bytes)
<dd>This value is the offset in bytes from the beginning of the file
where the B-tree is located.
<dt>Heap Address (&lt;offset&gt; bytes)
<dd>This value is the offset in bytes from the beginning of the file
where the group name heap is located.
</dl>
</dl>
<hr>
<h4><a name="ModifiedMessage">Name: Object Modification Date &amp; Time</a></h4>
<P class=item><B>Header Message Type:</B> 0x0012
</P>
<P class=item><B>Length:</B> Fixed
</P>
<P class=item><B>Status:</B> Optional, may not be repeated.
</P>
<P class=item><B>Description:</B> The object modification date
and time is a timestamp which indicates
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>
<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=1>Version</td>
<td colspan=3>Reserved</td>
</tr>
<tr align=center>
<td colspan=4>Seconds After Epoch</td>
</tr>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr align=left>
<th width="30%"><U><font size=+1>Field Name</font></U></th>
<th><U><font size=+1>Description</font></U></th>
</tr>
<tr valign=top>
<td>Version</td>
<td>The version number for the message. This document
describes version one of the new modification time message.</td>
</tr>
<tr valign=top>
<td>Reserved</td>
<td>This field is reserved and should always be zero.</td>
</tr>
<tr valign=top>
<td>Seconds After Epoch</td>
<td>The number of seconds since 0 hours, 0
minutes, 0 seconds, January 1, 1970, Coordinated Universal Time.
</tr>
</table>
</center>
<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-length datatype is stored in the global heap
of 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.
Dataset region references 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.</p>
<h3><a name="Appendix">Appendix</a></h3>
<P>Definitions of various terms used in this document.
</P>
<P>The <A name="UndefinedAddress">"undefined address"</A> for a file is a
file address with all bits set, i.e. <code>0xffff...ff</code>.
<P>The <A name="UnlimitedDim">"unlimited size"</A> for a size is a
value with all bits set, i.e. <code>0xffff...ff</code>.
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<address><a href="mailto:koziol@ncsa.uiuc.edu">Quincey Koziol</a></address>
<address><a href="mailto:matzke@llnl.gov">Robb Matzke</a></address>
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<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
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Describes HDF5 Release 1.7, the unreleased development branch; working toward HDF5 Release 1.8.0
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