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Purpose: Feature Description Description: Added the description of the --filedriver option to the h5dump explanation section. Platforms tested: w3m
1015 lines
38 KiB
HTML
1015 lines
38 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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<a href="RM_H5P.html">H5P</a>
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<br>
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<a href="RM_H5R.html">H5R</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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<a href="PredefDTypes.html">Datatypes</a>
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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 file contents,
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to modify HDF5 file contents in a carefully prescribed manner, and
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to convert files from HDF4 format to HDF5 format and vice versa.
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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> --
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A tool for displaying HDF5 file contents
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<li><a href="#Tools-Ls">h5ls</a> --
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A tool for listing specified features of HDF5 file contents
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<li><a href="#Tools-Repart">h5repart</a> --
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A tool for repartitioning a file, creating a family of files
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<li><a href="#Tools-GIF2H5">gif2h5</a> --
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A tool for converting a GIF file to an HDF5 file
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<li><a href="#Tools-H52GIF">h52gif</a> --
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A tool for converting images in an HDF5 file to a GIF file
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<li><a href="#Tools-H5toh4">h5toh4</a> --
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A tool for converting an HDF5 file to an HDF4 file
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<li><a href="#Tools-H4toh5">h4toh5</a> --
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A tool for converting an HDF4 file to an HDF5 file
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<li><a href="#Tools-H5CC">h5cc</a> --
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A tool for compiling HDF5 programs
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<li><a href="http://hdf.ncsa.uiuc.edu/java-hdf5-html/">Java-based tools for HDF5</a> --
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<em>(at <code>http://hdf.ncsa.uiuc.edu/java-hdf5-html/</code>)</em>
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<br>
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Java-based tools for viewing, manipulating, and generating HDF5
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files (distributed separately)
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<br>
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Includes <code>H5view</code>, <code>H5gen</code>, Java HDF5
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Interface (JHI5), and HDF5 VisAD Data Adapter
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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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[</code><em>OPTIONS</em><code>]</code> <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 examine
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the contents of an HDF5 file and dump those contents, in human
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readable form, to an ASCII file.
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<p>
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<code>h5dump</code> dumps HDF5 file content to standard output.
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It can display the contents of the entire HDF5 file or
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selected objects, which can be groups, datasets, a subset of a
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dataset, links, attributes, or datatypes.
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</p>
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<p>
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The <code>--header</code> option displays object header
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information only.
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</p>
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<p>
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Names are the absolute names of the objects. <code>h5dump</code>
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displays objects in the order same as the command order. If a
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name does not start with a slash, <code>h5dump</code> begins
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searching for the specified object starting at the root group.
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</p>
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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 later
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occurrences.
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</p>
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<p>
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<code>h5dump</code> assigns a name for any unnamed datatype in
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the form of
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<code>#</code><em>oid1</em><code>:</code><em>oid2</em>, where
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<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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<p>
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Datatypes are displayed with standard type names. For example,
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if a dataset 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 dataset.
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</p>
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<p>
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<code>h5dump</code> can also dump a subset of a dataset.
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This feature operates in much the same way as hyperslabs in HDF5;
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the parameters specified on the commnd line are passed to the
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function <a href="RM_H5S.html#Dataspace-SelectHyperslab">
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<code>H5Sselect_hyperslab</code></a> and the resulting selection
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is displayed.
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</p>
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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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</p>
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<p>
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<em>Note</em>: It is not permissable to specify multiple
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attributes, datasets, datatypes, groups, or soft links with one
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flag. For example, one may not issue the command
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<br>
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<font size=-1>WRONG:</font>
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<code>h5dump -a /attr1 /attr2 foo.h5</code>
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</br>
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to display both <code>/attr1</code> and <code>/attr2</code>.
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One must issue the following command:
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<br>
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<font size=-1>CORRECT:</font>
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<code>h5dump -a /attr1 -a /attr2 foo.h5</code>
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</br>
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</p>
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<p>
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It's possible to select the file driver with which to open the
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HDF5 file by using the --filedriver (-f) command-line option.
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Acceptable values for the --filedriver option are: "sec2",
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"family", "split", "multi", and "stream". If the file driver flag
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isn't specified, then the file will be opened with each driver in
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turn and in the order specified above until one driver succeeds
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in opening the file.
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</p>
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<dt><strong>XML Output:</strong>
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<dd>With the <code>--xml</code> option, <code>h5dump</code> generates
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XML output. This output contains a complete description of the file,
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marked up in XML. The XML conforms to the HDF5 Document Type
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Definition (DTD) available at
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<a href="http://hdf.ncsa.uiuc.edu/DTDs/HDF5-File.dtd">
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<code>http://hdf.ncsa.uiuc.edu/DTDs/HDF5-File.dtd</code></a>.
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<p>
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The XML output is suitable for use with other tools, including the
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<a href="http://hdf.ncsa.uiuc.edu/java-hdf5-html">HDF5 Java Tools</a>.
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<dt><strong>Options and Parameters:</strong>
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<dl>
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<dt><code>-h</code> or
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<code>--help</code></dt>
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<dd>Print a usage message and exit.</dd>
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<dt><code>-B</code> or
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<code>--bootblock</code></dt>
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<dd>Print the content of the boot block.<br>
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<em>(This option is not yet implemented.)</em></dd>
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<dt><code>-H</code> or
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<code>--header</code></dt>
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<dd>Print the header only; no data is displayed.</dd>
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<dt><code>-i</code> or
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<code>--object-ids</code></dt>
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<dd>Print the object ids.</dd>
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<dt><code>-V</code> or
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<code>--version</code></dt>
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<dd>Print version number and exit.</dd>
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<dt><code>-a <em>P</em></code> or
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<code>--attribute=<em>P</em></code></dt>
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<dd>Print the specified attribute.</dd>
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<dt><code>-d <em>P</em></code> or
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<code>--dataset=<em>P</em></code></dt>
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<dd>Print the specified dataset.</dd>
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<dt><code>-f <em>D</em></code> or
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<code>--filedriver=<em>D</em></code></dt>
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<dd>Specify which driver to open the file with.</dd>
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<dt><code>-g <em>P</em></code> or
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<code>--group=<em>P</em></code></dt>
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<dd>Print the specified group and all members.</dd>
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<dt><code>-l <em>P</em></code> or
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<code>--soft-link=<em>P</em></code></dt>
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<dd>Print the value(s) of the specified soft link.</dd>
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<dt><code>-o <em>F</em></code> or
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<code>--output=<em>F</em></code></dt>
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<dd>Output raw data into file F.</dd>
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<dt><code>-t <em>T</em></code> or
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<code>--datatype=<em>T</em></code></dt>
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<dd>Print the specified named datatype.</dd>
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<dt><code>-w <em>N</em></code> or
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<code>--width=<em>N</em></code></dt>
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<dd>Set the number of columns of output.</dd>
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<dt><code>-x <em>U</em></code> or
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<code>--xml</code></dt>
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<dd>Output XML instead of DDL.</dd>
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<dt><code>-D <em>U</em></code> or
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<code>--xml-dtd=<em>U</em></code></dt>
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<dd>In XML output, refer to the DTD at <em>U</em>
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instead of the default DTD.</dd>
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<dt><code>-s <em>L</em></code> or
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<code>--start=<em>L</em></code></dt>
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<dd>Offset of start of subsetting selection.
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<br>
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Default: the beginning of the dataset.</dd>
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<dt><code>-S <em>L</em></code> or
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<code>--stride=<em>L</em></code></dt>
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<dd>Hyperslab stride.
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<br>
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Default: 1 in all dimensions.</dd>
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<dt><code>-c <em>L</em></code> or
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<code>--count=<em>L</em></code></dt>
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<dd>Number of blocks to include in the selection.</dd>
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<dt><code>-k <em>L</em></code> or
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<code>--block=<em>L</em></code></dt>
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<dd>Size of block in hyperslab.
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<br>
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Default: 1 in all dimensions.</dd>
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<dt><em>file</em></dt>
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<dd>The file to be examined.</dd>
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<br><br>
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<dt>The option parameters listed above are defined as follows:
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<dd><em>D</em> -- which file driver to use in opening the
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file. Acceptable values are "sec2", "family", "split",
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"multi", and "stream". Without the file driver flag the
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file will be opened with each driver in turn and in the
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order specified above until one driver succeeds in
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opening the file.</dd>
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<dd><em>P</em> -- The full path from the root group to
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the object</dd>
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<dd><em>T</em> -- The name of the datatype</dd>
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<dd><em>F</em> -- A filename</dd>
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<dd><em>N</em> -- An integer greater than 1</dd>
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<dd><em>L</em> -- A list of integers, the number of which is
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equal to the number of dimensions in the dataspace being
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queried</dd>
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<dd><em>U</em> -- A URI (as defined in
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[<a href="http://www.ietf.org/rfc/rfc2396.txt">IETF RFC 2396</a>],
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updated by
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[<a href="http://www.ietf.org/rfc/rfc2732.txt">IETF RFC 2732</a>])
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that refers to the DTD to be used to validate the XML</dd>
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<br><br>
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<dt>Subsetting paramaters can also be expressed in a convenient
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compact form, as follows:
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<br>
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<code>--dataset="/foo/mydataset[START;STRIDE;COUNT;BLOCK]"</code>
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<br>
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All of the semicolons (<code>;</code>) are required, even when
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a parameter value is not specified.
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When not specified, default parameter values are used.
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</dl>
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<p>
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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>
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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>
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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>
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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>
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<li>Producing an XML listing of the file <code>bobo.h5</code>:
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<blockquote>
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<code>h5dump --xml bobo.h5 > bobo.h5.xml</code>
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</blockquote>
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<li>Dumping a subset of the dataset <code>/GroupFoo/databar/</code>
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in the file <code>quux.h5</code>
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<blockquote>
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<code>h5dump -d /GroupFoo/databar --start="1,1" --stride="2,3"
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<br>
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--count="3,19" --block="1,1" quux.h5</code>
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</blockquote>
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<li>The same example using the short form to specify the
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subsetting parameters:
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<blockquote>
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<code>h5dump -d "/GroupFoo/databar[1,1;2,3;3,19;1,1]" quux.h5</code>
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</blockquote>
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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 Datatype)
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<li>dataset space (see Dataspace)
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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 Datatype)
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<li>attribute space (see Dataspace)
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<li>attribute data
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</ul>
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<li>Datatype
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<ul>
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<li>integer type
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<br>
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- H5T_STD_I8BE, H5T_STD_I8LE, H5T_STD_I16BE, ...
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<li>floating point type
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<br>
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- 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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<br>
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- named, unnamed and transient compound type
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<br>
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- integer, floating or string type member
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<li>opaque types
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<li>reference type
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<br>
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- object references
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<br>
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- data regions
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<li>enum type
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<li>variable-length datatypes
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<br>
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- atomic types only
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<br>
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- scalar or single dimensional array of variable-length
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types supported
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</ul>
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<li>Dataspace
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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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<ul>
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<li>HDF5 Data Description Language syntax at
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<a href="ddl.html"><cite>DDL for HDF5</cite></a>
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<li>HDF5 XML DTD at
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<a href="http://hdf.ncsa.uiuc.edu/DTDs/HDF5-File.dtd">http://hdf.ncsa.uiuc.edu/DTDs/HDF5-File.dtd</a>
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<li>HDF5 XML information at
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<a href="http://hdf.ncsa.uiuc.edu/HDF5/XML">http://hdf.ncsa.uiuc.edu/HDF5/XML/</a>
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</ul>
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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
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<code>-?</code> or
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<code>--help</code>
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<dd>Print a usage message and exit.
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<dt><code>-a</code> or
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<code>--address</code>
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<dd>Print 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>
|
|
<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-GIF2H5">gif2h5</a>
|
|
<dt><strong>Syntax:</strong>
|
|
<dd><code>gif2h5</code>
|
|
<em>gif_file</em> <em>h5_file</em>
|
|
<dt><strong>Purpose:</strong>
|
|
<dd>Converts a GIF file to an HDF5 file.
|
|
<dt><strong>Description:</strong>
|
|
<dd><code>gif2h5</code> accepts as input the GIF file <em>gif_file</em>
|
|
and produces the HDF5 file <em>h5_file</em> as output.
|
|
|
|
<dt><strong>Options and Parameters:</strong>
|
|
<dl>
|
|
<dt><em>gif_file</em>
|
|
<dd>The name of the input GIF file
|
|
<dt><em>h5_file</em>
|
|
<dd>The name of the output HDF5 file
|
|
</dl>
|
|
<!--
|
|
<dt><strong>Current Status:</strong>
|
|
<dd>
|
|
<dt><strong>See Also:</strong>
|
|
<dd>
|
|
-->
|
|
</dl>
|
|
|
|
|
|
<hr>
|
|
<dl>
|
|
<dt><strong>Tool Name:</strong> <a name="Tools-H52GIF">h52gif</a>
|
|
<dt><strong>Syntax:</strong>
|
|
<dd><code>h52gif</code>
|
|
<em>h5_file</em> <em>gif_file</em>
|
|
<code>-i</code> <em>h5_image</em>
|
|
<code>[-p</code> <em>h5_palette</em><code>]</code>
|
|
<dt><strong>Purpose:</strong>
|
|
<dd>Converts an HDF5 file to a GIF file.
|
|
<dt><strong>Description:</strong>
|
|
<dd><code>h52gif</code> accepts as input the HDF5 file <em>h5_file</em>
|
|
and the names of images and associated palettes within that file
|
|
as input and produces the GIF file <em>gif_file</em>,
|
|
containing those images, as output.
|
|
<p>
|
|
<code>h52gif</code> expects <em>at least</em>
|
|
one <em>h5_image</em>.
|
|
You may repeat
|
|
<br>
|
|
|
|
<code>-i</code> <em>h5_image</em>
|
|
<code>[-p</code> <em>h5_palette</em><code>]</code>
|
|
<br>
|
|
up to 50 times, for a maximum of 50 images.
|
|
|
|
<dt><strong>Options and Parameters:</strong>
|
|
<dl>
|
|
<dt><em>h5_file</em>
|
|
<dd>The name of the input HDF5 file
|
|
<dt><em>gif_file</em>
|
|
<dd>The name of the output GIF file
|
|
<dt><code>-i</code> <em>h5_image</em>
|
|
<dd>Image option, specifying the name of an HDF5 image or
|
|
dataset containing an image to be converted
|
|
<dt><code>-p</code> <em>h5_palette</em>
|
|
<dd>Palette option, specifying the name of an HDF5 dataset
|
|
containing a palette to be used in an image conversion
|
|
</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>
|
|
|
|
<hr>
|
|
<dl>
|
|
<dt><strong>Tool Name:</strong> <a name="Tools-H5CC">h5cc</a>
|
|
<dt><strong>Syntax:</strong>
|
|
<dd><code>h5cc
|
|
[</code><em>OPTIONS</em><code>]</code> <em><compile line></em>
|
|
<dt><strong>Purpose:</strong>
|
|
<dd>Helper script to compile HDF5 applications.
|
|
<dt><strong>Description:</strong>
|
|
<dd><p>
|
|
<code>h5cc</code> can be used in much the same way MPIch is used
|
|
to compile HDF5 program. It takes care of specifying where the
|
|
HDF5 header files and libraries are on the commandline.
|
|
</p>
|
|
|
|
<p>
|
|
<code>h5cc</code> supercedes all other compiler scripts in that
|
|
if you've used them to compile the HDF5 library, then
|
|
<code>h5cc</code> also uses those scripts. For examples, when
|
|
compiling an MPIch program, you use the <code>mpicc</code>
|
|
script. If you've built HDF5 using MPIch, then <code>h5cc</code>
|
|
uses the MPIch program for compilation.
|
|
</p>
|
|
|
|
<p>
|
|
Some programs use HDF5 in only a few modules. It isn't necessary
|
|
to use <code>h5cc</code> to compile those modules which don't use
|
|
HDF5. In fact, since <code>h5cc</code> is only a convenience
|
|
script, you are still able to compile HDF5 modules in the normal
|
|
way. In that case, you will have to specify the HDF5 libraries
|
|
and include paths yourself.
|
|
</p>
|
|
|
|
<p>
|
|
An example of how to use HDF5 to compile the program
|
|
<code>hdf_prog</code> which consists of modules
|
|
<code>prog1.c</code> and <code>prog2.c</code> and uses the HDF5
|
|
shared library:
|
|
|
|
<pre>
|
|
# h5cc -c prog1.c
|
|
# h5cc -c prog2.c
|
|
# h5cc -shlib -o hdf_prog prog1.o prog2.o
|
|
</pre>
|
|
<p>
|
|
<dt><strong>Options and Parameters:</strong>
|
|
<dl>
|
|
<dt><code>-help</code>
|
|
<dd>Prints a help message.
|
|
<dt><code>-echo</code>
|
|
<dd>Show all the shell commands executed.
|
|
<dt><code>-prefix=DIR</code>
|
|
<dd>Use the directory DIR to find HDF5 lib/ and include/
|
|
subdirectories [default: prefix specified when
|
|
configuring HDF5].
|
|
<dt><code>-show</code>
|
|
<dd>Show the commands without executing them.
|
|
<dt><code>-shlib</code>
|
|
<dd>Compile using shared HDF5 libraries.
|
|
<dt><code>-noshlib</code>
|
|
<dd>Compile using static HDF5 libraries [default].
|
|
<dt><em><compile line></em>
|
|
<dd>The normal compile line options for your compiler. h5cc
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uses the same compiler you used to compile HDF5. Check
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with your compiler's manual for more information on which
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options are needed.
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</dl>
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<p>
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<dt><strong>Environment Variables:</strong>
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<br>
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When set, these environment variables override some of the built-in
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defaults of <code>h5cc</code>.
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<dl>
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<dt><code>HDF5_CC</code>
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<dd>Use a different C compiler.
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<dt><code>HDF5_CLINKER</code>
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<dd>Use a different linker.
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<dt><code>HDF5_USE_SHLIB=[yes|no]</code>
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<dd>Use shared version of the HDF5 library [default: no].
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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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|
|
|
<!-- Template, next 40 lines -->
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<!-- Template, next 40 lines -->
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<!-- Template, next 40 lines
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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>
|
|
h5file1
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|
h5file2
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|
h5file3</em> ...
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|
<dt><strong>Purpose:</strong>
|
|
<dd>Purpose...
|
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<dt><strong>Description:</strong>
|
|
<dd><code>TOOL</code> is an HDF5 utility which ...
|
|
Paragraph
|
|
<pre> sample code
|
|
sample code
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|
sample code </pre>
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|
<p>
|
|
Paragraph
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|
<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>
|
|
|
|
|
|
-->
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|
|
|
|
|
<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>
|
|
<!--
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|
<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_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>
|
|
</td></tr>
|
|
</table>
|
|
</center>
|
|
<hr>
|
|
|
|
|
|
<address>
|
|
<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
|
|
|
|
<br>
|
|
Last modified: 13. September 2001
|
|
|
|
<br>
|
|
Describes HDF5 Release 1.5, Unreleased Development Branch
|
|
|
|
|
|
</body>
|
|
</html>
|