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<div class="headertitle"><div class="title">PNeXus.h File Reference</div></div>
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<div class="contents">
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<p>NeXus HDF4/HDF5 file reader and writer for muon spin rotation data.
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<a href="#details">More...</a></p>
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<div class="textblock"><code>#include <string></code><br />
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<code>#include <vector></code><br />
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<code>#include <map></code><br />
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<code>#include <cctype></code><br />
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<code>#include <algorithm></code><br />
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<code>#include <any></code><br />
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<code>#include <cstdint></code><br />
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<code>#include "Minuit2/FCNBase.h"</code><br />
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<code>#include <mfhdf.h></code><br />
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<code>#include <hdf.h></code><br />
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<code>#include <H5Cpp.h></code><br />
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</div><div class="textblock"><div class="dynheader">
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Include dependency graph for PNeXus.h:</div>
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<div class="dyncontent">
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<div class="center"><img src="PNeXus_8h__incl.png" border="0" usemap="#a_2workspace_2LMU_2musrfit_2src_2external_2nexus_2PNeXus_8h" alt=""/></div>
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This graph shows which files directly or indirectly include this file:</div>
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<div class="dyncontent">
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<div class="center"><img src="PNeXus_8h__dep__incl.png" border="0" usemap="#a_2workspace_2LMU_2musrfit_2src_2external_2nexus_2PNeXus_8hdep" alt=""/></div>
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<area shape="rect" title="NeXus HDF4/HDF5 file reader and writer for muon spin rotation data." alt="" coords="12,5,211,50"/>
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<p><a href="PNeXus_8h_source.html">Go to the source code of this file.</a></p>
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<table class="memberdecls">
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="nested-classes" name="nested-classes"></a>
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Classes</h2></td></tr>
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<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="classnxH4_1_1PNeXusDeadTime.html">nxH4::PNeXusDeadTime</a></td></tr>
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<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">Dead time correction calculator for muon detector data. <a href="classnxH4_1_1PNeXusDeadTime.html#details">More...</a><br /></td></tr>
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<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="classnxH4_1_1PNXdata.html">nxH4::PNXdata< T ></a></td></tr>
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<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">Template class for storing HDF4 dataset content with attributes. <a href="classnxH4_1_1PNXdata.html#details">More...</a><br /></td></tr>
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<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="classnxH4_1_1PNeXus.html">nxH4::PNeXus</a></td></tr>
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<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">NeXus HDF4 file reader with case-insensitive path lookup. <a href="classnxH4_1_1PNeXus.html#details">More...</a><br /></td></tr>
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<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="classnxH5_1_1PNeXusDeadTime.html">nxH5::PNeXusDeadTime</a></td></tr>
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<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">Dead time correction calculator for muon detector data. <a href="classnxH5_1_1PNeXusDeadTime.html#details">More...</a><br /></td></tr>
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<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="classnxH5_1_1PNXdata.html">nxH5::PNXdata< T ></a></td></tr>
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<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">Template class for storing HDF5 dataset content with attributes. <a href="classnxH5_1_1PNXdata.html#details">More...</a><br /></td></tr>
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<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="classnxH5_1_1PNeXus.html">nxH5::PNeXus</a></td></tr>
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<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">NeXus HDF5 file reader with case-insensitive path lookup. <a href="classnxH5_1_1PNeXus.html#details">More...</a><br /></td></tr>
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<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
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</table><table class="memberdecls">
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="namespaces" name="namespaces"></a>
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Namespaces</h2></td></tr>
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<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">namespace  </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacenxs.html">nxs</a></td></tr>
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<tr class="memdesc:namespacenxs"><td class="mdescLeft"> </td><td class="mdescRight">Common utilities for NeXus file handling. <br /></td></tr>
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<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">namespace  </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacenxH4.html">nxH4</a></td></tr>
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<tr class="memdesc:namespacenxH4"><td class="mdescLeft"> </td><td class="mdescRight">HDF4 implementation of the NeXus file reader/writer. <br /></td></tr>
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<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">namespace  </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacenxH5.html">nxH5</a></td></tr>
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<tr class="memdesc:namespacenxH5"><td class="mdescLeft"> </td><td class="mdescRight">HDF5 implementation of the NeXus file reader/writer. <br /></td></tr>
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<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
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</table><table class="memberdecls">
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="enum-members" name="enum-members"></a>
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Enumerations</h2></td></tr>
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<tr class="memitem:a5c87400a55867e90d3f6f95d2d37b6d8" id="r_a5c87400a55867e90d3f6f95d2d37b6d8"><td class="memItemLeft" align="right" valign="top">enum class  </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacenxs.html#a5c87400a55867e90d3f6f95d2d37b6d8">nxs::HDFType</a> { <a class="el" href="namespacenxs.html#a5c87400a55867e90d3f6f95d2d37b6d8a8aee0c0676a2b00f33deaa1be0be783d">nxs::HDF4</a>
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, <a class="el" href="namespacenxs.html#a5c87400a55867e90d3f6f95d2d37b6d8a86459eb6a9c3edb9d09e9d6fe8d5b9fa">nxs::HDF5</a>
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, <a class="el" href="namespacenxs.html#a5c87400a55867e90d3f6f95d2d37b6d8a88183b946cc5f0e8c96b2e66e1c74a7e">nxs::Unknown</a>
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}</td></tr>
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<tr class="memdesc:a5c87400a55867e90d3f6f95d2d37b6d8"><td class="mdescLeft"> </td><td class="mdescRight">Enumeration of supported HDF file types. <a href="namespacenxs.html#a5c87400a55867e90d3f6f95d2d37b6d8">More...</a><br /></td></tr>
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<tr class="separator:a5c87400a55867e90d3f6f95d2d37b6d8"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a61bdb83ae066acbabf15ac914adee440" id="r_a61bdb83ae066acbabf15ac914adee440"><td class="memItemLeft" align="right" valign="top">enum class  </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacenxH4.html#a61bdb83ae066acbabf15ac914adee440">nxH4::H4DataType</a> { <br />
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  <a class="el" href="namespacenxH4.html#a61bdb83ae066acbabf15ac914adee440abd073fcbb15020b25a70e2cd95f9f4a9">nxH4::kINT32</a>
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, <a class="el" href="namespacenxH4.html#a61bdb83ae066acbabf15ac914adee440a301f3a167870b9b96bb0cef222e840ca">nxH4::kFLOAT32</a>
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, <a class="el" href="namespacenxH4.html#a61bdb83ae066acbabf15ac914adee440aaf8ee424b90f9be92f84682951a40030">nxH4::kFLOAT64</a>
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, <a class="el" href="namespacenxH4.html#a61bdb83ae066acbabf15ac914adee440a7189f5544734341eb25e4f123da788e5">nxH4::kCHAR8</a>
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, <br />
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  <a class="el" href="namespacenxH4.html#a61bdb83ae066acbabf15ac914adee440a4ff321e2f4f9df8e42f5ab2409b1a4d2">nxH4::kUINT32</a>
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, <a class="el" href="namespacenxH4.html#a61bdb83ae066acbabf15ac914adee440a4995a8359faf06dc440d65fa64b3410b">nxH4::kINT16</a>
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, <a class="el" href="namespacenxH4.html#a61bdb83ae066acbabf15ac914adee440a3500227c188f1328650855b481471a8c">nxH4::kUINT16</a>
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, <a class="el" href="namespacenxH4.html#a61bdb83ae066acbabf15ac914adee440a69c1a4a69db0e50820cf63122f90ad09">nxH4::kINT8</a>
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, <br />
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  <a class="el" href="namespacenxH4.html#a61bdb83ae066acbabf15ac914adee440a159244e0ab6cea87daa7eaa8f6e19937">nxH4::kUINT8</a>
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<br />
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}</td></tr>
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<tr class="memdesc:a61bdb83ae066acbabf15ac914adee440"><td class="mdescLeft"> </td><td class="mdescRight">HDF4 data type enumeration. <a href="namespacenxH4.html#a61bdb83ae066acbabf15ac914adee440">More...</a><br /></td></tr>
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<tr class="separator:a61bdb83ae066acbabf15ac914adee440"><td class="memSeparator" colspan="2"> </td></tr>
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</table><table class="memberdecls">
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="func-members" name="func-members"></a>
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Functions</h2></td></tr>
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<tr class="memitem:aec53b94446678ee1597e48358b74a82b" id="r_aec53b94446678ee1597e48358b74a82b"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespacenxs.html#a5c87400a55867e90d3f6f95d2d37b6d8">HDFType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacenxs.html#aec53b94446678ee1597e48358b74a82b">nxs::checkHDFType</a> (const std::string &filename)</td></tr>
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<tr class="memdesc:aec53b94446678ee1597e48358b74a82b"><td class="mdescLeft"> </td><td class="mdescRight">Determine the HDF format type of a file by reading its header. <br /></td></tr>
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<tr class="separator:aec53b94446678ee1597e48358b74a82b"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:af0448f2057fce5a84ee483768d21e2f6" id="r_af0448f2057fce5a84ee483768d21e2f6"><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="namespacenxs.html#af0448f2057fce5a84ee483768d21e2f6">nxs::getIso8601TimestampLocal</a> ()</td></tr>
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<tr class="memdesc:af0448f2057fce5a84ee483768d21e2f6"><td class="mdescLeft"> </td><td class="mdescRight">get the current time and return it as na IOS8601 time stamp. <br /></td></tr>
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<tr class="separator:af0448f2057fce5a84ee483768d21e2f6"><td class="memSeparator" colspan="2"> </td></tr>
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</table>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
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<div class="textblock"><p>NeXus HDF4/HDF5 file reader and writer for muon spin rotation data. </p>
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<p>This header file defines the PNeXus library for reading and writing NeXus files in both HDF4 and HDF5 formats. The library is specifically designed for ISIS muon NeXus files but can be adapted for other NeXus data.</p>
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<p>The library provides:</p><ul>
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<li><b>Dual format support</b>: Both HDF4 (<a class="el" href="namespacenxH4.html" title="HDF4 implementation of the NeXus file reader/writer.">nxH4</a> namespace) and HDF5 (<a class="el" href="namespacenxH5.html" title="HDF5 implementation of the NeXus file reader/writer.">nxH5</a> namespace)</li>
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<li><b>Case-insensitive path lookup</b>: Handles varying path casings in NeXus files</li>
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<li><b>Type-safe data handling</b>: Template-based PNXdata class with type preservation</li>
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<li><b>IDF version support</b>: Handles both IDF version 1 and version 2 file structures</li>
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<li><b>Dead time correction</b>: Built-in muon spectrometry dead time analysis</li>
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</ul>
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<h2><a class="anchor" id="autotoc_md0"></a>
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Architecture</h2>
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<p>The library is organized into three namespaces:</p><ul>
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<li><b>nxs</b>: Common utilities (HDFType enum, checkHDFType function)</li>
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<li><b><a class="el" href="namespacenxH4.html" title="HDF4 implementation of the NeXus file reader/writer.">nxH4</a></b>: HDF4-specific implementation (conditional, requires HAVE_HDF4)</li>
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<li><b><a class="el" href="namespacenxH5.html" title="HDF5 implementation of the NeXus file reader/writer.">nxH5</a></b>: HDF5-specific implementation (always available)</li>
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</ul>
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<h2><a class="anchor" id="autotoc_md1"></a>
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Data Organization</h2>
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<p>NeXus files follow the ISIS muon format with structure: </p><pre class="fragment">* /raw_data_1/ (NXentry)
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* ├── IDF_version
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* ├── beamline, definition, run_number, title
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* ├── start_time, end_time, good_frames
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* ├── detector_1/ (NXdata)
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* │ ├── counts (multi-dimensional)
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* │ ├── raw_time
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* │ └── attributes (signal, axes, units, etc.)
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* └── instrument/ (NXinstrument)
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* ├── name, source/
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* └── detector_1/ (NXdetector)
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* ├── counts, raw_time
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* ├── resolution, spectrum_index
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* └── dead_time
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* </pre><h2><a class="anchor" id="autotoc_md2"></a>
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Usage Example</h2>
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<div class="fragment"><div class="line"><span class="preprocessor">#include "<a class="code" href="PNeXus_8h.html">PNeXus.h</a>"</span></div>
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<div class="line"> </div>
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<div class="line"><span class="comment">// Check file type</span></div>
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<div class="line"><a class="code hl_enumeration" href="namespacenxs.html#a5c87400a55867e90d3f6f95d2d37b6d8">nxs::HDFType</a> type = <a class="code hl_function" href="namespacenxs.html#aec53b94446678ee1597e48358b74a82b">nxs::checkHDFType</a>(<span class="stringliteral">"file.nxs"</span>);</div>
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<div class="line"> </div>
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<div class="line"><span class="keywordflow">if</span> (type == <a class="code hl_enumvalue" href="namespacenxs.html#a5c87400a55867e90d3f6f95d2d37b6d8a86459eb6a9c3edb9d09e9d6fe8d5b9fa">nxs::HDFType::HDF5</a>) {</div>
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<div class="line"> <span class="comment">// Read HDF5 NeXus file</span></div>
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<div class="line"> <a class="code hl_class" href="classnxH5_1_1PNeXus.html">nxH5::PNeXus</a> nexus(<span class="stringliteral">"file.nxs"</span>);</div>
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<div class="line"> nexus.Dump();</div>
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<div class="line"> </div>
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<div class="line"> <span class="comment">// Access data</span></div>
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<div class="line"> <span class="keyword">auto</span> counts = nexus.GetDataset<<span class="keywordtype">int</span>>(<span class="stringliteral">"/raw_data_1/detector_1/counts"</span>);</div>
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<div class="line"> <span class="keyword">auto</span> dims = counts.GetDimensions();</div>
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<div class="line">}</div>
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<div class="ttc" id="aPNeXus_8h_html"><div class="ttname"><a href="PNeXus_8h.html">PNeXus.h</a></div><div class="ttdoc">NeXus HDF4/HDF5 file reader and writer for muon spin rotation data.</div></div>
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<div class="ttc" id="aclassnxH5_1_1PNeXus_html"><div class="ttname"><a href="classnxH5_1_1PNeXus.html">nxH5::PNeXus</a></div><div class="ttdoc">NeXus HDF5 file reader with case-insensitive path lookup.</div><div class="ttdef"><b>Definition</b> <a href="PNeXus_8h_source.html#l01463">PNeXus.h:1463</a></div></div>
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|
<div class="ttc" id="anamespacenxs_html_a5c87400a55867e90d3f6f95d2d37b6d8"><div class="ttname"><a href="namespacenxs.html#a5c87400a55867e90d3f6f95d2d37b6d8">nxs::HDFType</a></div><div class="ttdeci">HDFType</div><div class="ttdoc">Enumeration of supported HDF file types.</div><div class="ttdef"><b>Definition</b> <a href="PNeXus_8h_source.html#l00141">PNeXus.h:141</a></div></div>
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<div class="ttc" id="anamespacenxs_html_a5c87400a55867e90d3f6f95d2d37b6d8a86459eb6a9c3edb9d09e9d6fe8d5b9fa"><div class="ttname"><a href="namespacenxs.html#a5c87400a55867e90d3f6f95d2d37b6d8a86459eb6a9c3edb9d09e9d6fe8d5b9fa">nxs::HDFType::HDF5</a></div><div class="ttdeci">@ HDF5</div><div class="ttdoc">HDF5 format (magic: 0x89 'H' 'D' 'F' 0x0d 0x0a 0x1a 0x0a)</div><div class="ttdef"><b>Definition</b> <a href="PNeXus_8h_source.html#l00143">PNeXus.h:143</a></div></div>
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|
<div class="ttc" id="anamespacenxs_html_aec53b94446678ee1597e48358b74a82b"><div class="ttname"><a href="namespacenxs.html#aec53b94446678ee1597e48358b74a82b">nxs::checkHDFType</a></div><div class="ttdeci">HDFType checkHDFType(const std::string &filename)</div><div class="ttdoc">Determine the HDF format type of a file by reading its header.</div><div class="ttdef"><b>Definition</b> <a href="PNeXus_8cpp_source.html#l00100">PNeXus.cpp:100</a></div></div>
|
|
</div><!-- fragment --><dl class="section author"><dt>Author</dt><dd>Andreas Suter </dd></dl>
|
|
<dl class="section date"><dt>Date</dt><dd>2007-2026 </dd></dl>
|
|
<dl class="section copyright"><dt>Copyright</dt><dd>GNU General Public License v2 </dd></dl>
|
|
<dl class="section version"><dt>Version</dt><dd>1.0</dd></dl>
|
|
<dl class="section see"><dt>See also</dt><dd><a class="el" href="namespacenxs.html#aec53b94446678ee1597e48358b74a82b" title="Determine the HDF format type of a file by reading its header.">nxs::checkHDFType()</a> </dd>
|
|
<dd>
|
|
<a class="el" href="classnxH4_1_1PNeXus.html" title="NeXus HDF4 file reader with case-insensitive path lookup.">nxH4::PNeXus</a> </dd>
|
|
<dd>
|
|
<a class="el" href="classnxH5_1_1PNeXus.html" title="NeXus HDF5 file reader with case-insensitive path lookup.">nxH5::PNeXus</a> </dd></dl>
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<p class="definition">Definition in file <a class="el" href="PNeXus_8h_source.html">PNeXus.h</a>.</p>
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</div></div><!-- contents -->
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