2c7f74e088
Bug fix Description: The documentation on how to dump attribute data was not complete enough. Some people got confused on the commandline syntax (you have to specify the "path" from the root group to the attribute to dump it). I put some examples in to show how to correctly dump attributes. Platforms tested: Viewed with Netscrape.
479 lines
17 KiB
HTML
479 lines
17 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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[-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><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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</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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</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>-d</code> or <code>--dump</code>
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<dd>Print the values of datasets.
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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><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>The names of zero or more objects about which information
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should be displayed. If a group is mentioned then
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information about each of its members is displayed.
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If no object names are specified then information about
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all of the objects in the root group is displayed.
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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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<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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|
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<hr>
|
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<center>
|
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<table border=0 width=98%>
|
|
<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>
|
|
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>
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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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<address>
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<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
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<br>
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Last modified: 29 April 1999
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</body>
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</html>
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