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