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509 lines
18 KiB
HTML
<html>
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<head><title>
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HDF5/Tools API Specification
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</title></head>
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<body bgcolor="#FFFFFF">
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<hr>
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<center>
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<table border=0 width=98%>
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<tr><td valign=top align=left>
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<a href="H5.intro.html">Introduction to HDF5</a> <br>
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<a href="H5.user.html">HDF5 User Guide</a> <br>
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<a href="index.html">Other HDF5 documents and links</a> <br>
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<!--
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<a href="Glossary.html">Glossary</a><br>
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-->
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</td>
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<td valign=top align=right>
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And in this document, the
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<a href="RM_H5Front.html">HDF5 Reference Manual</a>
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<br>
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<a href="RM_H5.html">H5</a>
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<a href="RM_H5A.html">H5A</a>
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<a href="RM_H5D.html">H5D</a>
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<a href="RM_H5E.html">H5E</a>
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<a href="RM_H5F.html">H5F</a>
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<a href="RM_H5G.html">H5G</a>
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<a href="RM_H5I.html">H5I</a>
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<br>
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<a href="RM_H5P.html">H5P</a>
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<a href="RM_H5R.html">H5R</a>
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<a href="RM_H5RA.html">H5RA</a>
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<a href="RM_H5S.html">H5S</a>
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<a href="RM_H5T.html">H5T</a>
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<a href="RM_H5Z.html">H5Z</a>
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Tools
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</td></tr>
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</table>
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</center>
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<hr>
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<center>
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<h1>HDF5 Tools</h1>
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</center>
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<h2>HDF5 Tool Interfaces</h2>
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<p>
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These tools enable the user to examine HDF5 files interactively.
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<table border=0>
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<tr><td valign=top>
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<ul>
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<li><a href="#Tools-Dump">h5dump</a> -- A tool for displaying
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HDF5 file contents
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<li><a href="#Tools-Ls">h5ls</a> -- A tool for listing specified
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features of HDF5 file contents
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<li><a href="#Tools-Repart">h5repart</a> -- A tool for repartitioning
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a file, creating a family of files
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<li><a href="#Tools-H5toh4">h5toh4</a> -- A tool for converting an
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HDF5 file to an HDF4 file.
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</ul>
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</td></tr>
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</table>
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<p>
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<hr>
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<dl>
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<dt><strong>Tool Name:</strong> <a name="Tools-Dump">h5dump</a>
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<dt><strong>Syntax:</strong>
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<dd><code>h5dump
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[-h]
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[-bb]
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[-header]
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[-v]
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[-V]
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[-a </code><em>names</em><code>]
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[-d </code><em>names</em><code>]
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[-g </code><em>names</em><code>]
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[-l </code><em>names</em><code>]
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[-o </code><em>fname</em><code>]
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[-t </code><em>names</em><code>]
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[-w </code><em>number</em><code>]</code>
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<em>file</em>
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<dt><strong>Purpose:</strong>
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<dd>Displays HDF5 file contents.
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<dt><strong>Description:</strong>
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<dd><code>h5dump</code> enables the user to interactively examine
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the contents of an HDF5 file and dump those contents,
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in human readable form, to an ASCII file.
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<p>
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<code>h5dump</code> displays HDF5 file content on
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standard output. It may display the content of the
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whole HDF5 file or selected objects, which can be groups,
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datasets, links, attributes, or data types.
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<p>
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The <code>-header</code> option displays object
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header information only.
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<p>
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Names are the absolute names of the objects.
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<code>h5dump</code> displays objects in the order same as the
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command order. If a name does not start with a slash,
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<code>h5dump</code> begins searching for the specified object
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starting at the root group.
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<p>
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If an object is hard linked with multiple names,
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<code>h5dump</code> displays the content of the object in the
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first occurrence. Only the link information is displayed in
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later occurrences.
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<p>
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<code>h5dump</code> assigns a name for any unnamed data type in
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the form of <code>#</code><em>oid1</em><code>:</code><em>oid2</em>,
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where <em>oid1</em> and <em>oid2</em> are the object identifiers
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assigned by the library. The unnamed types are displayed within
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the root group.
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<p>
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Data types are displayed with standard type names. For example,
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if a data set is created with <code>H5T_NATIVE_INT</code> type
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and the standard type name for integer on that machine is
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<code>H5T_STD_I32BE</code>, <code>h5dump</code> displays
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<code>H5T_STD_I32BE</code> as the type of the data set.
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<p>
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The <code>h5dump</code> output is described in detail in the
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<a href="ddl.html"><cite>DDL for HDF5</cite></a>, the
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<cite>Data Description Language</cite> document.
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<dt><strong>Options and Parameters:</strong>
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<dl>
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<dt><code>-h</code>
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<dd>Prints information on this command and exits.
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<dt><code>-bb</code>
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<dd>Displays the contents of the super block. The default is
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not to display.
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<BR>
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<em>(This option is not yet implemented.)</em>
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<dt><code>-header</code>
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<dd>Displays header information only; no data is displayed.
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<dt><code>-v</code>
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<dd>Displays the object ids.
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<dt><code>-V</code>
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<dd>Displays version information and exits.
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<dt><code>-a</code> <em>names</em>
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<dd>Displays the specified attribute(s).
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<dt><code>-d</code> <em>names</em>
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<dd>Displays the specified dataset(s).
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<dt><code>-g</code> <em>names</em>
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<dd>Displays the specified group(s) and all the members.
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<dt><code>-l</code> <em>names</em>
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<dd>Displays the values of the specified soft link(s).
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<dt><code>-t</code> <em>names</em>
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<dd>Displays the specified named data type(s).
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<dt><code>-w</code> <em>number</em>
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<dd>Displays the information with the specified number of columns.
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<dt><code>-o</code> <em>filename</em>
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<dd>Output the raw data of datasets to a separate file <code>filename</code>.
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<dt><em>file</em>
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<dd>The file to be examined.
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</dl>
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<dt><strong>Examples:</strong>
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<ol>
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<li>Dumping the group <code>/GroupFoo/GroupBar</code> in the file
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<code>quux.h5</code>:
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<blockquote>
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<code>h5dump -g /GroupFoo/GroupBar quux.h5</code>
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</blockquote></li>
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<li>Dumping the dataset <code>Fnord</code> in the group
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<code>/GroupFoo/GroupBar</code> in the file <code>quux.h5</code>:
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<blockquote>
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<code>h5dump -d /GroupFoo/GroupBar/Fnord quux.h5</code>
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</blockquote></li>
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<li>Dumping the attribute <code>metadata</code> of the dataset
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<code>Fnord</code> which is in group
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<code>/GroupFoo/GroupBar</code> in the file <code>quux.h5</code>:
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<blockquote>
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<code>h5dump -a /GroupFoo/GroupBar/Fnord/metadata quux.h5</code>
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</blockquote></li>
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<li>Dumping the attribute <code>metadata</code> which is an
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attribute of the root group in the file <code>quux.h5</code>:
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<blockquote>
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<code>h5dump -a /metadata quux.h5</code>
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</blockquote></li>
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</ol>
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<dt><strong>Current Status:</strong>
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<dd>The current version of <code>h5dump</code> displays the
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following information:
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<ul>
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<li>Group
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<ul>
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<li>group attribute (see Attribute)
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<li>group member
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</ul>
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<li>Dataset
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<ul>
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<li>dataset attribute (see Attribute)
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<li>dataset type (see Data type)
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<li>dataset space (see Data space)
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<li>dataset data
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</ul>
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<li>Attribute
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<ul>
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<li>attribute type (see Data type)
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<li>attribute space (see Data space)
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<li>attribute data
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</ul>
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<li>Data type
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<ul>
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<li>integer type
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<dt>- H5T_STD_I8BE, H5T_STD_I8LE, H5T_STD_I16BE, ...
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<li>floating point type
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<dt>- H5T_IEEE_F32BE, H5T_IEEE_F32LE, H5T_IEEE_F64BE, ...
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<li>string type
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<li>compound type
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<dt>- named, unnamed and transient compound type
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<dt>- integer, floating or string type member
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<li>opaque types
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<li>reference type
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<dt>- object references
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<dt>- data regions
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<li>enum type
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<li>variable-length datatypes
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<dt>- atomic types only
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<dt>- scalar or single dimensional array of variable-length
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types supported
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</ul>
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<li>Data space
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<ul>
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<li>scalar and simple space
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</ul>
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<li>Soft link
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<li>Hard link
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<li>Loop detection
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</ul>
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<dt><strong>See Also:</strong>
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<dd>HDF5 Data Description Language syntax
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(<a href="ddl.html"><cite>DDL for HDF5</cite></a>)
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</dl>
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<hr>
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<dl>
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<dt><strong>Tool Name:</strong> <a name="Tools-Ls">h5ls</a>
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<dt><strong>Syntax:</strong>
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<dd><code>h5ls
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[</code><em>options</em><code>]</code><em>
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file</em><code>
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[</code><em>objects...</em><code>]</code>
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<dt><strong>Purpose:</strong>
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<dd>Prints information about a file or dataset.
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<dt><strong>Description:</strong>
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<dd><code>h5ls</code> prints selected information about file objects
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in the specified format.
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<dt><strong>Options and Parameters:</strong>
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<dl>
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<dt><code>-h</code> or <code>-?</code> or <code>--help</code>
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<dd>Print a usage message and exit.
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<dt><code>-a</code> or <code>--address</code>
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<dd>Primt addresses for raw data.
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<dt><code>-d</code> or <code>--data</code>
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<dd>Print the values of datasets.
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<dt><code>-e</code> or <code>--errors</code>
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<dd>Show all HDF5 error reporting.
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<dt><code>-f</code> or <code>--full</code>
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<dd>Print full path names instead of base names.
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<dt><code>-g</code> or <code>--group</code>
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<dd>Show information about a group, not its contents.
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<dt><code>-l</code> or <code>--label</code>
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<dd>Label members of compound datasets.
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<dt><code>-r</code> or <code>--recursive</code>
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<dd>List all groups recursively, avoiding cycles.
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<dt><code>-s</code> or <code>--string</code>
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<dd>Print 1-bytes integer datasets as ASCII.
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<dt><code>-S</code> or <code>--simple</code>
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<dd>Use a machine-readable output format.
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<dt><code>-w</code><em>N</em> or <code>--width=</code><em>N</em>
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<dd>Set the number of columns of output.
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<dt><code>-v</code> or <code>--verbose</code>
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<dd>Generate more verbose output.
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<dt><code>-V</code> or <code>--version</code>
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<dd>Print version number and exit.
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<dt><code>-x</code> or <code>--hexdump</code>
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<dd>Show raw data in hexadecimal format.
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<dt><em>file</em>
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<dd>The file name may include a printf(3C) integer format
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such as <code>%%05d</code> to open a file family.
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<dt><em>objects</em>
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<dd>Each object consists of an HDF5 file name optionally
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followed by a slash and an object name within the file
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(if no object is specified within the file then the
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contents of the root group are displayed). The file name
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may include a <code>printf(3C)</code> integer format such
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as "%05d" to open a file family.
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</dl>
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<!--
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<dt><strong>Current Status:</strong>
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<dd>
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<dt><strong>See Also:</strong>
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<dd>
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-->
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</dl>
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<hr>
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<dl>
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<dt><strong>Tool Name:</strong> <a name="Tools-Repart">h5repart</a>
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<dt><strong>Syntax:</strong>
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<dd><code>h5repart
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[-v]
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[-V]
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[-[b|m]</code><em>N</em><code>[g|m|k]]</code>
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<em>source_file
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dest_file</em>
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<dt><strong>Purpose:</strong>
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<dd>Repartitions a file or family of files.
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<dt><strong>Description:</strong>
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<dd><code>h5repart</code> splits a single file into a family of
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files, joins a family of files into a single file, or copies
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one family of files to another while changing the size of the
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family members. <code>h5repart</code> can also be used to
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copy a single file to a single file with holes.
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<p>
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Sizes associated with the <code>-b</code> and <code>-m</code>
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options may be suffixed with <code>g</code> for gigabytes,
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<code>m</code> for megabytes, or <code>k</code> for kilobytes.
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<p>
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File family names include an integer <code>printf</code>
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format such as <code>%d</code>.
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<dt><strong>Options and Parameters:</strong>
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<dl>
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<dt><code>-v</code>
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<dd>Produce verbose output.
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<dt><code>-V</code>
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<dd>Print a version number and exit.
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<dt><code>-b</code><em>N</em>
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<dd>The I/O block size, defaults to 1kB
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<dt><code>-m</code><em>N</em>
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<dd>The destination member size or 1GB
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<dt><em>source_file</em>
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<dd>The name of the source file
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<dt><em>dest_file</em>
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<dd>The name of the destination files
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</dl>
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<!--
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<dt><strong>Current Status:</strong>
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<dd>
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<dt><strong>See Also:</strong>
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<dd>
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-->
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</dl>
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<hr>
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<dl>
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<dt><strong>Tool Name:</strong> <a name="Tools-H5toh4">h5toh4</a>
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<dt><strong>Syntax:</strong>
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<dd><code>h5toh4 -h</code><br>
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<code>h5toh4 </code><em>
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h5file
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h4file</em><br>
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<code>h5toh4 </code><em>
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h5file</em><br>
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<code>h5toh4 -m </code><em>
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h5file1
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h5file2
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h5file3</em> ...
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<dt><strong>Purpose:</strong>
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<dd>Converts an HDF5 file into an HDF4 file.
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<dt><strong>Description:</strong>
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<dd><code>h5toh4</code> is an HDF5 utility which reads
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an HDF5 file, <em>h5file</em>, and converts all
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supported objects and pathways to produce an HDF4 file,
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<em>h4file</em>. If <em>h4file</em> already exists,
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it will be replaced.
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<p>
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If only one file name is given, the name must end in
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<code>.h5</code> and is assumed to represent the
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HDF5 input file. <code>h5toh4</code> replaces the
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<code>.h5</code> suffix with <code>.hdf</code> to form
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the name of the resulting HDF4 file and proceeds as above.
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If a file with the name of the intended HDF4 file already
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exists, <code>h5toh4</code> exits with an error without
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changing the contents of any file.
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<p>
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The <code>-m</code> option allows multiple HDF5 file
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arguments. Each file name is treated the same as the
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single file name case above.
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<p>
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The <code>-h</code> option causes the following
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syntax summary to be displayed:<br>
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<pre> h5toh4 file.h5 file.hdf
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h5toh4 file.h5
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h5toh4 -m file1.h5 file2.h5 ...</pre>
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<p>
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The following HDF5 objects occurring in an HDF5 file are
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converted to HDF4 objects in the HDF4 file:
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<ul>
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<li>HDF5 group objects are converted into HDF4 Vgroup
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objects. HDF5 hardlinks and softlinks pointing to
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objects are converted to HDF4 Vgroup references.
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<li>HDF5 dataset objects of integer datatype are
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converted into HDF4 SDS objects. These datasets
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may have up to 32 fixed dimensions.
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The slowest varying dimension may be extendable.
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8-bit, 16-bit, and 32-bit integer datatypes are
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supported.
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<li>HDF5 dataset objects of floating point datatype
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are converted into HDF4 SDS objects.
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These datasets may have up to 32 fixed dimensions.
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The slowest varying dimension may be extendable.
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32-bit and 64-bit floating point datatypes are
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supported.
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<li>HDF5 dataset objects of single dimension and
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compound datatype are converted into HDF4 Vdata
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objects. The length of that single dimension may
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be fixed or extendable. The members of the
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compound datatype are constrained to be no more
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than rank 4.
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<li>HDF5 dataset objects of single dimension and fixed length string
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datatype are converted into HDF4 Vdata objects. The HDF4 Vdata is a
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single field whose order is the length of the HDF5 string type. The
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number of records of the Vdata is the length of the single dimension
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which may be fixed or extendable.
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</ul>
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Other objects are not converted and are not recorded
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in the resulting <em>h4file</em>.
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<p>
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Attributes associated with any of the supported HDF5
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objects are carried over to the HDF4 objects.
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Attributes may be of integer, floating point, or fixed length string datatype
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and they may have up to 32 fixed dimensions.
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<p>
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All datatypes are converted to big-endian.
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Floating point datatypes are converted to IEEE format.
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|
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<dt><strong>Options and Parameters:</strong>
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<dl>
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<dt><code>-h</code>
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<dd>Displays a syntax summary.
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<dt><code>-m</code>
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<dd>Converts multiple HDF5 files to multiple HDF4 files.
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<dt><em>h5file</em>
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<dd>The HDF5 file to be converted.
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<dt><em>h4file</em>
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<dd>The HDF4 file to be created.
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</dl>
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<!--
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<dt><strong>Current Status:</strong>
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<dd>
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<dt><strong>See Also:</strong>
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<dd>
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-->
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</dl>
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<hr>
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<center>
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<table border=0 width=98%>
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<tr><td valign=top align=left>
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<a href="H5.intro.html">Introduction to HDF5</a> <br>
|
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<a href="H5.user.html">HDF5 User Guide</a> <br>
|
|
<a href="index.html">Other HDF5 documents and links</a> <br>
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|
<!--
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<a href="Glossary.html">Glossary</a><br>
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-->
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</td>
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<td valign=top align=right>
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|
And in this document, the
|
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<a href="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>
|
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<a href="RM_H5F.html">H5F</a>
|
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<a href="RM_H5G.html">H5G</a>
|
|
<a href="RM_H5I.html">H5I</a>
|
|
<br>
|
|
<a href="RM_H5P.html">H5P</a>
|
|
<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
|
|
</td></tr>
|
|
</table>
|
|
</center>
|
|
<hr>
|
|
|
|
|
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<address>
|
|
<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
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<br>
|
|
Last modified: 17 November 2000
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