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51  <h1>Source code for sas.dataloader.readers.nexus_reader</h1><div class="highlight"><pre>
52<span class="c">#####################################################################</span>
53<span class="c">#This software was developed by the University of Tennessee as part of the</span>
54<span class="c">#Distributed Data Analysis of Neutron Scattering Experiments (DANSE)</span>
55<span class="c">#project funded by the US National Science Foundation.</span>
56<span class="c">#See the license text in license.txt</span>
57<span class="c">#copyright 2012, University of Tennessee</span>
58<span class="c">######################################################################</span>
59<span class="sd">&quot;&quot;&quot;</span>
60<span class="sd">    Nexus reader for 2D data reduced by Mantid</span>
61<span class="sd">&quot;&quot;&quot;</span>
62<span class="kn">import</span> <span class="nn">os</span>
63<span class="kn">from</span> <span class="nn">sas.dataloader.data_info</span> <span class="kn">import</span> <span class="n">Data2D</span>
64
65
66<div class="viewcode-block" id="Reader"><a class="viewcode-back" href="../../../../dev/api/sas.dataloader.readers.html#sas.dataloader.readers.nexus_reader.Reader">[docs]</a><span class="k">class</span> <span class="nc">Reader</span><span class="p">:</span>
67    <span class="sd">&quot;&quot;&quot;</span>
68<span class="sd">        Nexus reader for 2D data reduced by Mantid</span>
69<span class="sd">    &quot;&quot;&quot;</span>
70    <span class="c">## File type</span>
71    <span class="n">type_name</span> <span class="o">=</span> <span class="s">&quot;NXS&quot;</span>
72    <span class="c">## Wildcards</span>
73    <span class="nb">type</span> <span class="o">=</span> <span class="p">[</span><span class="s">&quot;Nexus files (*.nxs)|*.nxs&quot;</span><span class="p">]</span>
74    <span class="c">## Extension</span>
75    <span class="n">ext</span> <span class="o">=</span> <span class="p">[</span><span class="s">&#39;.nxs&#39;</span><span class="p">]</span>
76       
77<div class="viewcode-block" id="Reader.read"><a class="viewcode-back" href="../../../../dev/api/sas.dataloader.readers.html#sas.dataloader.readers.nexus_reader.Reader.read">[docs]</a>    <span class="k">def</span> <span class="nf">read</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
78        <span class="sd">&quot;&quot;&quot;</span>
79<span class="sd">            Open and read the data in a file</span>
80<span class="sd">        </span>
81<span class="sd">            :param filename: path of the file</span>
82<span class="sd">        &quot;&quot;&quot;</span>
83        <span class="k">try</span><span class="p">:</span>
84            <span class="kn">import</span> <span class="nn">nxs</span>
85        <span class="k">except</span><span class="p">:</span>
86            <span class="n">msg</span> <span class="o">=</span> <span class="s">&quot;Error reading Nexus file: Nexus package is missing.</span><span class="se">\n</span><span class="s">&quot;</span>
87            <span class="n">msg</span> <span class="o">+=</span> <span class="s">&quot;  Get it from http://http://www.nexusformat.org/&quot;</span>
88            <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">,</span> <span class="n">msg</span>
89       
90        <span class="c"># Instantiate data object</span>
91        <span class="n">output</span> <span class="o">=</span> <span class="n">Data2D</span><span class="p">()</span>
92        <span class="n">output</span><span class="o">.</span><span class="n">filename</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
93
94        <span class="n">fd</span> <span class="o">=</span> <span class="n">nxs</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="s">&#39;rw&#39;</span><span class="p">)</span>
95       
96        <span class="c"># Read in the 2D data</span>
97        <span class="n">fd</span><span class="o">.</span><span class="n">opengroup</span><span class="p">(</span><span class="s">&#39;mantid_workspace_1&#39;</span><span class="p">)</span>
98        <span class="n">fd</span><span class="o">.</span><span class="n">opengroup</span><span class="p">(</span><span class="s">&#39;workspace&#39;</span><span class="p">)</span>
99        <span class="n">fd</span><span class="o">.</span><span class="n">opendata</span><span class="p">(</span><span class="s">&#39;values&#39;</span><span class="p">)</span>
100        <span class="n">output</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="n">fd</span><span class="o">.</span><span class="n">getdata</span><span class="p">()</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
101        <span class="n">fd</span><span class="o">.</span><span class="n">closedata</span><span class="p">()</span>
102       
103        <span class="c"># Read in the errors</span>
104        <span class="n">fd</span><span class="o">.</span><span class="n">opendata</span><span class="p">(</span><span class="s">&#39;errors&#39;</span><span class="p">)</span>
105        <span class="n">output</span><span class="o">.</span><span class="n">err_data</span> <span class="o">=</span> <span class="n">fd</span><span class="o">.</span><span class="n">getdata</span><span class="p">()</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
106        <span class="n">fd</span><span class="o">.</span><span class="n">closedata</span><span class="p">()</span>
107       
108        <span class="c"># Read in the values on each axis</span>
109        <span class="n">fd</span><span class="o">.</span><span class="n">opendata</span><span class="p">(</span><span class="s">&#39;axis1&#39;</span><span class="p">)</span>
110        <span class="n">output</span><span class="o">.</span><span class="n">x_bins</span> <span class="o">=</span> <span class="n">fd</span><span class="o">.</span><span class="n">getdata</span><span class="p">()</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
111        <span class="n">fd</span><span class="o">.</span><span class="n">closedata</span><span class="p">()</span>
112       
113        <span class="n">fd</span><span class="o">.</span><span class="n">opendata</span><span class="p">(</span><span class="s">&#39;axis2&#39;</span><span class="p">)</span>
114        <span class="n">output</span><span class="o">.</span><span class="n">y_bins</span> <span class="o">=</span> <span class="n">fd</span><span class="o">.</span><span class="n">getdata</span><span class="p">()</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
115        <span class="n">fd</span><span class="o">.</span><span class="n">closedata</span><span class="p">()</span>
116        <span class="n">fd</span><span class="o">.</span><span class="n">closegroup</span><span class="p">()</span>
117               
118        <span class="n">output</span><span class="o">.</span><span class="n">xmin</span> <span class="o">=</span> <span class="nb">min</span><span class="p">(</span><span class="n">output</span><span class="o">.</span><span class="n">x_bins</span><span class="p">)</span>
119        <span class="n">output</span><span class="o">.</span><span class="n">xmax</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="n">output</span><span class="o">.</span><span class="n">x_bins</span><span class="p">)</span>
120        <span class="n">output</span><span class="o">.</span><span class="n">ymin</span> <span class="o">=</span> <span class="nb">min</span><span class="p">(</span><span class="n">output</span><span class="o">.</span><span class="n">y_bins</span><span class="p">)</span>
121        <span class="n">output</span><span class="o">.</span><span class="n">ymax</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="n">output</span><span class="o">.</span><span class="n">y_bins</span><span class="p">)</span>
122       
123        <span class="n">output</span><span class="o">.</span><span class="n">xaxis</span><span class="p">(</span><span class="s">&quot;</span><span class="se">\\</span><span class="s">rm{Q_{x}}&quot;</span><span class="p">,</span> <span class="s">&#39;A^{-1}&#39;</span><span class="p">)</span>
124        <span class="n">output</span><span class="o">.</span><span class="n">yaxis</span><span class="p">(</span><span class="s">&quot;</span><span class="se">\\</span><span class="s">rm{Q_{y}}&quot;</span><span class="p">,</span> <span class="s">&#39;A^{-1}&#39;</span><span class="p">)</span>
125        <span class="n">output</span><span class="o">.</span><span class="n">zaxis</span><span class="p">(</span><span class="s">&quot;</span><span class="se">\\</span><span class="s">rm{Intensity}&quot;</span><span class="p">,</span> <span class="s">&quot;cm^{-1}&quot;</span><span class="p">)</span>
126
127        <span class="c"># Meta data</span>
128        <span class="n">fd</span><span class="o">.</span><span class="n">opendata</span><span class="p">(</span><span class="s">&#39;title&#39;</span><span class="p">)</span>
129        <span class="n">output</span><span class="o">.</span><span class="n">title</span> <span class="o">=</span> <span class="n">fd</span><span class="o">.</span><span class="n">getdata</span><span class="p">()</span>
130        <span class="n">fd</span><span class="o">.</span><span class="n">closedata</span><span class="p">()</span>
131       
132        <span class="n">fd</span><span class="o">.</span><span class="n">opengroup</span><span class="p">(</span><span class="s">&#39;instrument&#39;</span><span class="p">)</span>
133        <span class="n">fd</span><span class="o">.</span><span class="n">opendata</span><span class="p">(</span><span class="s">&#39;name&#39;</span><span class="p">)</span>
134        <span class="n">output</span><span class="o">.</span><span class="n">instrument</span> <span class="o">=</span> <span class="n">fd</span><span class="o">.</span><span class="n">getdata</span><span class="p">()</span>
135        <span class="n">fd</span><span class="o">.</span><span class="n">closedata</span><span class="p">()</span>
136        <span class="n">fd</span><span class="o">.</span><span class="n">closegroup</span><span class="p">()</span>
137
138        <span class="n">fd</span><span class="o">.</span><span class="n">opengroup</span><span class="p">(</span><span class="s">&#39;logs&#39;</span><span class="p">)</span>
139        <span class="n">fd</span><span class="o">.</span><span class="n">opengroup</span><span class="p">(</span><span class="s">&#39;run_number&#39;</span><span class="p">)</span>
140        <span class="n">fd</span><span class="o">.</span><span class="n">opendata</span><span class="p">(</span><span class="s">&#39;value&#39;</span><span class="p">)</span>
141        <span class="n">output</span><span class="o">.</span><span class="n">run</span> <span class="o">=</span> <span class="n">fd</span><span class="o">.</span><span class="n">getdata</span><span class="p">()</span>
142
143        <span class="n">fd</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
144
145        <span class="c"># Store loading process information</span>
146        <span class="n">output</span><span class="o">.</span><span class="n">meta_data</span><span class="p">[</span><span class="s">&#39;loader&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">type_name</span>
147        <span class="k">return</span> <span class="n">output</span></div></div>
148</pre></div>
149
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