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HDF5/Tools API Specification
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Tools
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<center>
<h1>HDF5 Tools</h1>
</center>
<h2>HDF5 Tool Interfaces</h2>
<p>
These tools enable the user to examine HDF5 files interactively.
<table border=0>
<tr><td valign=top>
<ul>
<li><a href="#Tools-Dump">h5dump</a> --
A tool for displaying HDF5 file contents
<li><a href="#Tools-Ls">h5ls</a> --
A tool for listing specified features of HDF5 file contents
<li><a href="#Tools-Repart">h5repart</a> --
A tool for repartitioning a file, creating a family of files
<li><a href="#Tools-H5toh4">h5toh4</a> --
A tool for converting an HDF5 file to an HDF4 file
<li><a href="#Tools-H4toh5">h4toh5</a> --
A tool for converting an HDF4 file to an HDF5 file
</ul>
</td></tr>
</table>
<p>
<hr>
<dl>
<dt><strong>Tool Name:</strong> <a name="Tools-Dump">h5dump</a>
<dt><strong>Syntax:</strong>
<dd><code>h5dump
[</code><em>OPTIONS</em><code>]</code> <em>file</em>
<dt><strong>Purpose:</strong>
<dd>Displays HDF5 file contents.
<dt><strong>Description:</strong>
<dd><code>h5dump</code> enables the user to interactively examine
the contents of an HDF5 file and dump those contents, in human
readable form, to an ASCII file.
<p>
<code>h5dump</code> displays HDF5 file content on standard
output. It may display the content of the whole HDF5 file or
selected objects, which can be groups, datasets, links,
attributes, or data types.
</p>
<p>
The <code>--header</code> option displays object header
information only.
</p>
<p>
Names are the absolute names of the objects. <code>h5dump</code>
displays objects in the order same as the command order. If a
name does not start with a slash, <code>h5dump</code> begins
searching for the specified object starting at the root group.
</p>
<p>
If an object is hard linked with multiple names,
<code>h5dump</code> displays the content of the object in the
first occurrence. Only the link information is displayed in later
occurrences.
</p>
<p>
<code>h5dump</code> assigns a name for any unnamed data type in
the form of
<code>#</code><em>oid1</em><code>:</code><em>oid2</em>, where
<em>oid1</em> and <em>oid2</em> are the object identifiers
assigned by the library. The unnamed types are displayed within
the root group.
</p>
<p>
Data types are displayed with standard type names. For example,
if a data set is created with <code>H5T_NATIVE_INT</code> type
and the standard type name for integer on that machine is
<code>H5T_STD_I32BE</code>, <code>h5dump</code> displays
<code>H5T_STD_I32BE</code> as the type of the data set.
</p>
<p>
The <code>h5dump</code> output is described in detail in the <a
href="ddl.html"><cite>DDL for HDF5</cite></a>, the <cite>Data
Description Language</cite> document.
</p>
<p>
<em>Note</em>: It is no longer permissable to specify multiple
attributes, datasets, data types, groups, or soft links with one
flag. For example, before one could issue the command:
</p>
<blockquote>
<code>h5dump -a /attr1 /attr2 foo.h5</code>
</blockquote>
<p>
and both <code>/attr1</code> and <code>/attr2</code> would be
dumped. In order to do this now, one must issue the command:
</p>
<blockquote>
<code>h5dump -a /attr1 -a /attr2 foo.h5</code>
</blockquote>
<dt><strong>Options and Parameters:</strong>
<dl>
<dt><code>-h</code> or
<code>--help</code></dt>
<dd>Print a usage message and exit.</dd>
<dt><code>-B</code> or
<code>--bootblock</code></dt>
<dd>Print the content of the boot block.<br>
<em>(This option is not yet implemented.)</em></dd>
<dt><code>-H</code> or
<code>--header</code></dt>
<dd>Print the header only; no data is displayed.</dd>
<dt><code>-i</code> or
<code>--object-ids</code></dt>
<dd>Print the object ids.</dd>
<dt><code>-V</code> or
<code>--version</code></dt>
<dd>Print version number and exit.</dd>
<dt><code>-a <em>P</em></code> or
<code>--attribute=<em>P<em></code></dt>
<dd>Print the specified attribute.</dd>
<dt><code>-d <em>P</em></code> or
<code>--dataset=<em>P<em></code></dt>
<dd>Print the specified dataset.</dd>
<dt><code>-g <em>P</em></code> or
<code>--group=<em>P<em></code></dt>
<dd>Print the specified group and all members.</dd>
<dt><code>-l <em>P</em></code> or
<code>--soft-link=<em>P<em></code></dt>
<dd>Print the value(s) of the specified soft link.</dd>
<dt><code>-o <em>P</em></code> or
<code>--output=<em>F<em></code></dt>
<dd>Output raw data into file F.</dd>
<dt><code>-t <em>P</em></code> or
<code>--datatype=<em>T<em></code></dt>
<dd>Print the specified named data type.</dd>
<dt><code>-w <em>P</em></code> or
<code>--width=<em>#<em></code></dt>
<dd>Set the number of columns of output.</dd>
<dt><em>file</em></dt>
<dd>The file to be examined.</dd>
</dl>
<ul>
<li><em>P</em> - is the full path from the root group to the
object.</li>
<li><em>T</em> - is the name of the data type.</li>
<li><em>F</em> - is a filename.</li>
<li><em>#</em> - is an integer greater than 1.</li>
</ul>
<dt><strong>Examples:</strong>
<ol>
<li>Dumping the group <code>/GroupFoo/GroupBar</code> in the file
<code>quux.h5</code>:
<blockquote>
<code>h5dump -g /GroupFoo/GroupBar quux.h5</code>
</blockquote>
<li>Dumping the dataset <code>Fnord</code> in the group
<code>/GroupFoo/GroupBar</code> in the file <code>quux.h5</code>:
<blockquote>
<code>h5dump -d /GroupFoo/GroupBar/Fnord quux.h5</code>
</blockquote>
<li>Dumping the attribute <code>metadata</code> of the dataset
<code>Fnord</code> which is in group
<code>/GroupFoo/GroupBar</code> in the file <code>quux.h5</code>:
<blockquote>
<code>h5dump -a /GroupFoo/GroupBar/Fnord/metadata quux.h5</code>
</blockquote>
<li>Dumping the attribute <code>metadata</code> which is an
attribute of the root group in the file <code>quux.h5</code>:
<blockquote>
<code>h5dump -a /metadata quux.h5</code>
</blockquote>
</ol>
<dt><strong>Current Status:</strong>
<dd>The current version of <code>h5dump</code> displays the
following information:
<ul>
<li>Group
<ul>
<li>group attribute (see Attribute)
<li>group member
</ul>
<li>Dataset
<ul>
<li>dataset attribute (see Attribute)
<li>dataset type (see Data type)
<li>dataset space (see Data space)
<li>dataset data
</ul>
<li>Attribute
<ul>
<li>attribute type (see Data type)
<li>attribute space (see Data space)
<li>attribute data
</ul>
<li>Data type
<ul>
<li>integer type
<dt>- H5T_STD_I8BE, H5T_STD_I8LE, H5T_STD_I16BE, ...
<li>floating point type
<dt>- H5T_IEEE_F32BE, H5T_IEEE_F32LE, H5T_IEEE_F64BE, ...
<li>string type
<li>compound type
<dt>- named, unnamed and transient compound type
<dt>- integer, floating or string type member
<li>opaque types
<li>reference type
<dt>- object references
<dt>- data regions
<li>enum type
<li>variable-length datatypes
<dt>- atomic types only
<dt>- scalar or single dimensional array of variable-length
types supported
</ul>
<li>Data space
<ul>
<li>scalar and simple space
</ul>
<li>Soft link
<li>Hard link
<li>Loop detection
</ul>
<dt><strong>See Also:</strong>
<dd>HDF5 Data Description Language syntax
(<a href="ddl.html"><cite>DDL for HDF5</cite></a>)
</dl>
<hr>
<dl>
<dt><strong>Tool Name:</strong> <a name="Tools-Ls">h5ls</a>
<dt><strong>Syntax:</strong>
<dd><code>h5ls
[</code><em>OPTIONS</em><code>]</code><em>
file</em><code>
[</code><em>OBJECTS...</em><code>]</code>
<dt><strong>Purpose:</strong>
<dd>Prints information about a file or dataset.
<dt><strong>Description:</strong>
<dd><code>h5ls</code> prints selected information about file objects
in the specified format.
<dt><strong>Options and Parameters:</strong>
<dl>
<dt><code>-h</code> or
<code>-?</code> or
<code>--help</code>
<dd>Print a usage message and exit.
<dt><code>-a</code> or
<code>--address</code>
<dd>Print addresses for raw data.
<dt><code>-d</code> or <code>--data</code>
<dd>Print the values of datasets.
<dt><code>-e</code> or
<code>--errors</code>
<dd>Show all HDF5 error reporting.
<dt><code>-f</code> or
<code>--full</code>
<dd>Print full path names instead of base names.
<dt><code>-g</code> or
<code>--group</code>
<dd>Show information about a group, not its contents.
<dt><code>-l</code> or
<code>--label</code>
<dd>Label members of compound datasets.
<dt><code>-r</code> or
<code>--recursive</code>
<dd>List all groups recursively, avoiding cycles.
<dt><code>-s</code> or
<code>--string</code>
<dd>Print 1-bytes integer datasets as ASCII.
<dt><code>-S</code> or
<code>--simple</code>
<dd>Use a machine-readable output format.
<dt><code>-w</code><em>N</em> or
<code>--width=</code><em>N</em>
<dd>Set the number of columns of output.
<dt><code>-v</code> or
<code>--verbose</code>
<dd>Generate more verbose output.
<dt><code>-V</code> or
<code>--version</code>
<dd>Print version number and exit.
<dt><code>-x</code> or
<code>--hexdump</code>
<dd>Show raw data in hexadecimal format.
<dt><em>file</em>
<dd>The file name may include a printf(3C) integer format
such as <code>%%05d</code> to open a file family.
<dt><em>objects</em>
<dd>Each object consists of an HDF5 file name optionally
followed by a slash and an object name within the file
(if no object is specified within the file then the
contents of the root group are displayed). The file name
may include a <code>printf(3C)</code> integer format such
as "%05d" to open a file family.
</dl>
<!--
<dt><strong>Current Status:</strong>
<dd>
<dt><strong>See Also:</strong>
<dd>
-->
</dl>
<hr>
<dl>
<dt><strong>Tool Name:</strong> <a name="Tools-Repart">h5repart</a>
<dt><strong>Syntax:</strong>
<dd><code>h5repart
[-v]
[-V]
[-[b|m]</code><em>N</em><code>[g|m|k]]</code>
<em>source_file
dest_file</em>
<dt><strong>Purpose:</strong>
<dd>Repartitions a file or family of files.
<dt><strong>Description:</strong>
<dd><code>h5repart</code> splits a single file into a family of
files, joins a family of files into a single file, or copies
one family of files to another while changing the size of the
family members. <code>h5repart</code> can also be used to
copy a single file to a single file with holes.
<p>
Sizes associated with the <code>-b</code> and <code>-m</code>
options may be suffixed with <code>g</code> for gigabytes,
<code>m</code> for megabytes, or <code>k</code> for kilobytes.
<p>
File family names include an integer <code>printf</code>
format such as <code>%d</code>.
<dt><strong>Options and Parameters:</strong>
<dl>
<dt><code>-v</code>
<dd>Produce verbose output.
<dt><code>-V</code>
<dd>Print a version number and exit.
<dt><code>-b</code><em>N</em>
<dd>The I/O block size, defaults to 1kB
<dt><code>-m</code><em>N</em>
<dd>The destination member size or 1GB
<dt><em>source_file</em>
<dd>The name of the source file
<dt><em>dest_file</em>
<dd>The name of the destination files
</dl>
<!--
<dt><strong>Current Status:</strong>
<dd>
<dt><strong>See Also:</strong>
<dd>
-->
</dl>
<hr>
<dl>
<dt><strong>Tool Name:</strong> <a name="Tools-H5toh4">h5toh4</a>
<dt><strong>Syntax:</strong>
<dd><code>h5toh4 -h</code><br>
<code>h5toh4 </code><em>
h5file
h4file</em><br>
<code>h5toh4 </code><em>
h5file</em><br>
<code>h5toh4 -m </code><em>
h5file1
h5file2
h5file3</em> ...
<dt><strong>Purpose:</strong>
<dd>Converts an HDF5 file into an HDF4 file.
<dt><strong>Description:</strong>
<dd><code>h5toh4</code> is an HDF5 utility which reads
an HDF5 file, <em>h5file</em>, and converts all
supported objects and pathways to produce an HDF4 file,
<em>h4file</em>. If <em>h4file</em> already exists,
it will be replaced.
<p>
If only one file name is given, the name must end in
<code>.h5</code> and is assumed to represent the
HDF5 input file. <code>h5toh4</code> replaces the
<code>.h5</code> suffix with <code>.hdf</code> to form
the name of the resulting HDF4 file and proceeds as above.
If a file with the name of the intended HDF4 file already
exists, <code>h5toh4</code> exits with an error without
changing the contents of any file.
<p>
The <code>-m</code> option allows multiple HDF5 file
arguments. Each file name is treated the same as the
single file name case above.
<p>
The <code>-h</code> option causes the following
syntax summary to be displayed:
<pre> h5toh4 file.h5 file.hdf
h5toh4 file.h5
h5toh4 -m file1.h5 file2.h5 ...</pre>
<p>
The following HDF5 objects occurring in an HDF5 file are
converted to HDF4 objects in the HDF4 file:
<ul>
<li>HDF5 group objects are converted into HDF4 Vgroup
objects. HDF5 hardlinks and softlinks pointing to
objects are converted to HDF4 Vgroup references.
<li>HDF5 dataset objects of integer datatype are
converted into HDF4 SDS objects. These datasets
may have up to 32 fixed dimensions.
The slowest varying dimension may be extendable.
8-bit, 16-bit, and 32-bit integer datatypes are
supported.
<li>HDF5 dataset objects of floating point datatype
are converted into HDF4 SDS objects.
These datasets may have up to 32 fixed dimensions.
The slowest varying dimension may be extendable.
32-bit and 64-bit floating point datatypes are
supported.
<li>HDF5 dataset objects of single dimension and
compound datatype are converted into HDF4 Vdata
objects. The length of that single dimension may
be fixed or extendable. The members of the
compound datatype are constrained to be no more
than rank 4.
<li>HDF5 dataset objects of single dimension and fixed length string
datatype are converted into HDF4 Vdata objects. The HDF4 Vdata
is a single field whose order is the length of the HDF5 string
type. The number of records of the Vdata is the length of the
single dimension which may be fixed or extendable.
</ul>
Other objects are not converted and are not recorded
in the resulting <em>h4file</em>.
<p>
Attributes associated with any of the supported HDF5
objects are carried over to the HDF4 objects.
Attributes may be of integer, floating point, or fixed length
string datatype and they may have up to 32 fixed dimensions.
<p>
All datatypes are converted to big-endian.
Floating point datatypes are converted to IEEE format.
<dt><strong>Options and Parameters:</strong>
<dl>
<dt><code>-h</code>
<dd>Displays a syntax summary.
<dt><code>-m</code>
<dd>Converts multiple HDF5 files to multiple HDF4 files.
<dt><em>h5file</em>
<dd>The HDF5 file to be converted.
<dt><em>h4file</em>
<dd>The HDF4 file to be created.
</dl>
<!--
<dt><strong>Current Status:</strong>
<dd>
<dt><strong>See Also:</strong>
<dd>
-->
</dl>
<hr>
<dl>
<dt><strong>Tool Name:</strong> <a name="Tools-H4toh5">h4toh5</a>
<dt><strong>Syntax:</strong>
<dd><code>h4toh5 -h</code><br>
<code>h4toh5 </code><em>
h4file
h5file</em><br>
<code>h4toh5 </code><em>
h4file</em><br>
<!-- currently no -m option
<code>h4toh5 -m </code><em>
h4file1
h4file2
h4file3</em> ...
-->
<dt><strong>Purpose:</strong>
<dd>Converts an HDF4 file to an HDF5 file.
<dt><strong>Description:</strong>
<dd><code>h4toh5</code> is a file conversion utility that reads
an HDF4 file, <em>h4file</em> (<code>input.hdf</code> for example),
and writes an HDF5 file, <em>h5file</em> (<code>output.h5</code>
for example), containing the same data.
<p>
If no output file <em>h5file</em> is specified,
<code>h4toh5</code> uses the input filename to designate
the output file, replacing the extension <code>.hdf</code>
with <code>.h5</code>.
For example, if the input file <code>scheme3.hdf</code> is
specified with no output filename, <code>h4toh5</code> will
name the output file <code>scheme3.h5</code>.
<p>
<!-- currently no -m option
The <code>-m</code> option allows multiple HDF5 file
arguments. Each file name is treated the same as the
single file name case above.
<p>
-->
The <code>-h</code> option causes a syntax summary
similar to the following to be displayed:
<pre> h4toh5 inputfile.hdf outputfile.h5
h5toh4 inputfile.hdf <!-- currently no -m option
h5toh4 -m inputfile1.hdf inputfile2.hdf ... --> </pre>
<p>
Each object in the HDF4 file is converted to an equivalent
HDF5 object, according to the mapping described in
<a href="ADGuide/H4toH5Mapping.pdf" target=ExternalWinA>
<cite>Mapping HDF4 Objects to HDF5 Objects</cite></a>.
(If this mapping changes between HDF5 Library releases, a more up-to-date
version may be available at
<a href="http://hdf.ncsa.uiuc.edu/HDF5/papers/h4toh5/H4-to-H5MappingGuidelines.pdf" target=ExternalWinB>
<cite>Mapping HDF4 Objects to HDF5 Objects</cite> on the HDF FTP server</a>.)
<p>
In this inital version, <code>h4toh5</code> converts the following
HDF4 objects:
<center>
<table width=75% border=0>
<tr><th width=40% valign=top align=left>
HDF4 Object
</td><th width=60% valign=top align=left>
Resulting HDF5 Object
</td></tr>
<tr><td width=40% valign=top align=left>
SDS
</td><td width=60% valign=top align=left>
Dataset
</td></tr>
<tr><td width=40% valign=top align=left>
GR, RI8, and RI24 image
</td><td width=60% valign=top align=left>
Dataset
</td></tr>
<tr><td width=40% valign=top align=left>
Vdata
</td><td width=60% valign=top align=left>
Dataset
</td></tr>
<tr><td width=40% valign=top align=left>
Vgroup
</td><td width=60% valign=top align=left>
Group
</td></tr>
<tr><td width=40% valign=top align=left>
Annotation
</td><td width=60% valign=top align=left>
Attribute
</td></tr>
<tr><td width=40% valign=top align=left>
Palette
</td><td width=60% valign=top align=left>
Dataset
</td></tr>
</table>
</center>
<dt><strong>Options and Parameters:</strong>
<dl>
<dt><code>-h</code>
<dd>Displays a syntax summary.
<!-- currently no -m option
<dt><code>-m</code>
<dd>Converts multiple HDF4 files to multiple HDF5 files.
-->
<dt><em>h4file</em>
<dd>The HDF4 file to be converted.
<dt><em>h5file</em>
<dd>The HDF5 file to be created.
</dl>
<!--
<dt><strong>Current Status:</strong>
<dd>
<dt><strong>See Also:</strong>
<dd>
-->
</dl>
<!-- Template, next 40 lines -->
<!-- Template, next 40 lines -->
<!-- Template, next 40 lines
<hr>
<dl>
<dt><strong>Tool Name:</strong> <a name="Tools-H5toh4">h5toh4</a>
<dt><strong>Syntax:</strong>
<dd><code>h5toh4 -h</code><br>
<code>h5toh4 </code><em>
h5file
h4file</em><br>
<code>h5toh4 </code><em>
h5file</em><br>
<code>h5toh4 -m </code><em>
h5file1
h5file2
h5file3</em> ...
<dt><strong>Purpose:</strong>
<dd>Purpose...
<dt><strong>Description:</strong>
<dd><code>TOOL</code> is an HDF5 utility which ...
Paragraph
<pre> sample code
sample code
sample code </pre>
<p>
Paragraph
<p>
Paragraph
<dt><strong>Options and Parameters:</strong>
<dl>
<dt><code>-option</code>
<dd>Description
<dt><em>parameter</em>
<dd>Description
</dl>
<dt><strong>Current Status:</strong>
<dd>
<dt><strong>See Also:</strong>
<dd>
</dl>
-->
<hr>
<center>
<table border=0 width=98%>
<tr><td valign=top align=left>
<a href="H5.intro.html">Introduction to HDF5</a> <br>
<a href="H5.user.html">HDF5 User Guide</a> <br>
<a href="index.html">Other HDF5 documents and links</a> <br>
<!--
<a href="Glossary.html">Glossary</a><br>
-->
</td>
<td valign=top align=right>
And in this document, the
<a href="RM_H5Front.html">HDF5 Reference Manual</a>
<br>
<a href="RM_H5.html">H5</a>
<a href="RM_H5A.html">H5A</a>
<a href="RM_H5D.html">H5D</a>
<a href="RM_H5E.html">H5E</a>
<a href="RM_H5F.html">H5F</a>
<a href="RM_H5G.html">H5G</a>
<a href="RM_H5I.html">H5I</a>
<a href="RM_H5P.html">H5P</a>
<br>
<a href="RM_H5R.html">H5R</a>
<a href="RM_H5RA.html">H5RA</a>
<a href="RM_H5S.html">H5S</a>
<a href="RM_H5T.html">H5T</a>
<a href="RM_H5Z.html">H5Z</a>
Tools
<a href="PredefDTypes.html">Datatypes</a>
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<address>
<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
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Last modified: 15 December 2000
<br>
Describes HDF5 Release 1.4 Beta, December 2000
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