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50  <h1>Source code for G2sfact</h1><div class="highlight"><pre>
51<span class="c"># -*- coding: utf-8 -*-</span>
52<span class="c">########### SVN repository information ###################</span>
53<span class="c"># $Date: 2015-07-09 17:00:23 -0500 (Thu, 09 Jul 2015) $</span>
54<span class="c"># $Author: vondreele $</span>
55<span class="c"># $Revision: 1924 $</span>
56<span class="c"># $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/imports/G2sfact.py $</span>
57<span class="c"># $Id: G2sfact.py 1924 2015-07-09 22:00:23Z vondreele $</span>
58<span class="c">########### SVN repository information ###################</span>
59<span class="sd">&#39;&#39;&#39;</span>
60<span class="sd">*Module G2sfact: simple HKL import*</span>
61<span class="sd">-----------------------------------</span>
62<span class="sd">Read structure factors from a simple hkl file. Two routines are</span>
63<span class="sd">provided to read from files containing F or F\ :sup:`2` values.</span>
64
65<span class="sd">&#39;&#39;&#39;</span>
66<span class="kn">import</span> <span class="nn">sys</span>
67<span class="kn">import</span> <span class="nn">numpy</span> <span class="kn">as</span> <span class="nn">np</span>
68<span class="kn">import</span> <span class="nn">copy</span>
69<span class="kn">import</span> <span class="nn">GSASIIIO</span> <span class="kn">as</span> <span class="nn">G2IO</span>
70<span class="kn">import</span> <span class="nn">GSASIIpath</span>
71<span class="n">GSASIIpath</span><span class="o">.</span><span class="n">SetVersionNumber</span><span class="p">(</span><span class="s">&quot;$Revision: 1924 $&quot;</span><span class="p">)</span>
72
73<div class="viewcode-block" id="ColumnValidator"><a class="viewcode-back" href="../imports.html#G2sfact.ColumnValidator">[docs]</a><span class="k">def</span> <span class="nf">ColumnValidator</span><span class="p">(</span><span class="n">parent</span><span class="p">,</span> <span class="n">filepointer</span><span class="p">,</span><span class="n">nCol</span><span class="o">=</span><span class="mi">5</span><span class="p">):</span>
74    <span class="s">&#39;Validate a file to check that it contains columns of numbers&#39;</span>
75    <span class="n">l</span> <span class="o">=</span> <span class="n">filepointer</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>
76    <span class="n">line</span> <span class="o">=</span> <span class="mi">1</span>
77    <span class="k">while</span> <span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="p">[</span><span class="s">&#39;#&#39;</span><span class="p">,</span><span class="s">&#39;(&#39;</span><span class="p">]:</span>        <span class="c">#get past comments &amp; fortran formats, if any</span>
78        <span class="n">l</span> <span class="o">=</span> <span class="n">filepointer</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>       
79        <span class="n">line</span> <span class="o">+=</span> <span class="mi">1</span>
80    <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">10</span><span class="p">):</span> <span class="c"># scan a few lines</span>
81        <span class="n">S</span> <span class="o">=</span> <span class="n">l</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
82        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">S</span><span class="p">)</span> <span class="o">&lt;</span> <span class="n">nCol</span><span class="p">:</span>
83            <span class="n">parent</span><span class="o">.</span><span class="n">errors</span> <span class="o">=</span> <span class="s">&#39;line &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">line</span><span class="p">)</span><span class="o">+</span><span class="s">&#39;: invalid input</span><span class="se">\n</span><span class="s">&#39;</span><span class="o">+</span><span class="n">l</span>
84            <span class="k">return</span> <span class="bp">False</span>
85        <span class="k">for</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">S</span><span class="p">[:</span><span class="n">nCol</span><span class="p">]:</span>
86            <span class="k">try</span><span class="p">:</span>
87                <span class="nb">float</span><span class="p">(</span><span class="n">v</span><span class="p">)</span>
88            <span class="k">except</span> <span class="ne">ValueError</span><span class="p">:</span>
89                <span class="n">parent</span><span class="o">.</span><span class="n">errors</span> <span class="o">=</span> <span class="s">&#39;line &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">line</span><span class="p">)</span><span class="o">+</span><span class="s">&#39;: string found where a number is expected</span><span class="se">\n</span><span class="s">&#39;</span><span class="o">+</span><span class="n">l</span>
90                <span class="k">return</span> <span class="bp">False</span>           
91        <span class="n">l</span> <span class="o">=</span> <span class="n">filepointer</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>
92        <span class="n">line</span> <span class="o">+=</span> <span class="mi">1</span>
93    <span class="k">return</span> <span class="bp">True</span>
94
95</div>
96<div class="viewcode-block" id="HKLF_ReaderClass"><a class="viewcode-back" href="../imports.html#G2sfact.HKLF_ReaderClass">[docs]</a><span class="k">class</span> <span class="nc">HKLF_ReaderClass</span><span class="p">(</span><span class="n">G2IO</span><span class="o">.</span><span class="n">ImportStructFactor</span><span class="p">):</span>
97    <span class="s">&#39;Routines to import F, sig(F) reflections from a HKLF file&#39;</span>
98    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
99        <span class="nb">super</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">__class__</span><span class="p">,</span><span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span> <span class="c"># fancy way to self-reference</span>
100            <span class="n">extensionlist</span><span class="o">=</span><span class="p">(</span><span class="s">&#39;.hkl&#39;</span><span class="p">,</span><span class="s">&#39;.HKL&#39;</span><span class="p">),</span>
101            <span class="n">strictExtension</span><span class="o">=</span><span class="bp">False</span><span class="p">,</span>
102            <span class="n">formatName</span> <span class="o">=</span> <span class="s">&#39;HKL F&#39;</span><span class="p">,</span>
103            <span class="n">longFormatName</span> <span class="o">=</span> <span class="s">&#39;Simple [hkl, Fo, sig(Fo)] Structure factor text file&#39;</span>
104            <span class="p">)</span>
105
106<div class="viewcode-block" id="HKLF_ReaderClass.ContentsValidator"><a class="viewcode-back" href="../imports.html#G2sfact.HKLF_ReaderClass.ContentsValidator">[docs]</a>    <span class="k">def</span> <span class="nf">ContentsValidator</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filepointer</span><span class="p">):</span>
107        <span class="s">&#39;Make sure file contains the expected columns on numbers&#39;</span>
108        <span class="k">return</span> <span class="n">ColumnValidator</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filepointer</span><span class="p">)</span>
109</div>
110<div class="viewcode-block" id="HKLF_ReaderClass.Reader"><a class="viewcode-back" href="../imports.html#G2sfact.HKLF_ReaderClass.Reader">[docs]</a>    <span class="k">def</span> <span class="nf">Reader</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">filename</span><span class="p">,</span><span class="n">filepointer</span><span class="p">,</span> <span class="n">ParentFrame</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="o">**</span><span class="n">unused</span><span class="p">):</span>
111        <span class="s">&#39;Read the file&#39;</span>
112        <span class="k">try</span><span class="p">:</span>
113            <span class="k">for</span> <span class="n">line</span><span class="p">,</span><span class="n">S</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">filepointer</span><span class="p">):</span>
114                <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">=</span> <span class="s">&#39;  Error reading line &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">line</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span>
115                <span class="k">if</span> <span class="n">S</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;#&#39;</span><span class="p">:</span> <span class="k">continue</span>       <span class="c">#ignore comments, if any</span>
116                <span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span><span class="n">Fo</span><span class="p">,</span><span class="n">sigFo</span> <span class="o">=</span> <span class="n">S</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
117                <span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span> <span class="o">=</span> <span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">h</span><span class="p">),</span><span class="nb">int</span><span class="p">(</span><span class="n">k</span><span class="p">),</span><span class="nb">int</span><span class="p">(</span><span class="n">l</span><span class="p">)]</span>
118                <span class="k">if</span> <span class="ow">not</span> <span class="nb">any</span><span class="p">([</span><span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">]):</span>
119                    <span class="k">break</span>
120                <span class="n">Fo</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">Fo</span><span class="p">)</span>
121                <span class="n">sigFo</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">sigFo</span><span class="p">)</span>
122                <span class="c"># h,k,l,m,dsp,Fo2,sig,Fc2,Fot2,Fct2,phase,...</span>
123                <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;RefList&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span><span class="mi">1</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">Fo</span><span class="o">**</span><span class="mi">2</span><span class="p">,</span><span class="mf">2.</span><span class="o">*</span><span class="n">Fo</span><span class="o">*</span><span class="n">sigFo</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">Fo</span><span class="o">**</span><span class="mi">2</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">])</span>
124            <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">=</span> <span class="s">&#39;Error after reading reflections (unexpected!)&#39;</span>
125            <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;RefList&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;RefList&#39;</span><span class="p">])</span>
126            <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;Type&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s">&#39;SXC&#39;</span>
127            <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;Super&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>
128            <span class="bp">self</span><span class="o">.</span><span class="n">UpdateParameters</span><span class="p">(</span><span class="n">Type</span><span class="o">=</span><span class="s">&#39;SXC&#39;</span><span class="p">,</span><span class="n">Wave</span><span class="o">=</span><span class="bp">None</span><span class="p">)</span> <span class="c"># histogram type</span>
129            <span class="k">return</span> <span class="bp">True</span>
130        <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">detail</span><span class="p">:</span>
131            <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">+=</span> <span class="s">&#39;</span><span class="se">\n</span><span class="s">  &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">detail</span><span class="p">)</span>
132            <span class="k">print</span> <span class="s">&#39;</span><span class="se">\n\n</span><span class="s">&#39;</span><span class="o">+</span><span class="bp">self</span><span class="o">.</span><span class="n">formatName</span><span class="o">+</span><span class="s">&#39; read error: &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">detail</span><span class="p">)</span> <span class="c"># for testing</span>
133            <span class="kn">import</span> <span class="nn">traceback</span>
134            <span class="n">traceback</span><span class="o">.</span><span class="n">print_exc</span><span class="p">(</span><span class="nb">file</span><span class="o">=</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">)</span>
135            <span class="k">return</span> <span class="bp">False</span>
136</div></div>
137<div class="viewcode-block" id="SHELX4_ReaderClass"><a class="viewcode-back" href="../imports.html#G2sfact.SHELX4_ReaderClass">[docs]</a><span class="k">class</span> <span class="nc">SHELX4_ReaderClass</span><span class="p">(</span><span class="n">G2IO</span><span class="o">.</span><span class="n">ImportStructFactor</span><span class="p">):</span>
138    <span class="s">&#39;Routines to import F**2, sig(F**2) reflections from a Shelx HKLF 4 file&#39;</span>
139    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
140        <span class="k">if</span> <span class="s">&#39;linux&#39;</span> <span class="ow">in</span> <span class="n">sys</span><span class="o">.</span><span class="n">platform</span><span class="p">:</span>  <span class="c"># wx 3.0.0.0 on gtk does not like Unicode in menus</span>
141            <span class="n">formatName</span> <span class="o">=</span> <span class="s">&#39;HKLF 4&#39;</span>
142            <span class="n">longFormatName</span> <span class="o">=</span> <span class="s">&#39;Shelx HKLF 4 [hkl, Fo2, sig(Fo2)] Structure factor text file&#39;</span>
143        <span class="k">else</span><span class="p">:</span>
144            <span class="n">formatName</span> <span class="o">=</span> <span class="s">u&#39;Shelx HKLF 4 F</span><span class="se">\u00b2</span><span class="s">&#39;</span>
145            <span class="n">longFormatName</span> <span class="o">=</span> <span class="s">u&#39;Shelx HKLF 4 [hkl, Fo</span><span class="se">\u00b2</span><span class="s">, sig(Fo</span><span class="se">\u00b2</span><span class="s">)] Structure factor text file&#39;</span>
146        <span class="nb">super</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">__class__</span><span class="p">,</span><span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span> <span class="c"># fancy way to self-reference</span>
147            <span class="n">extensionlist</span><span class="o">=</span><span class="p">(</span><span class="s">&#39;.hkl&#39;</span><span class="p">,</span><span class="s">&#39;.HKL&#39;</span><span class="p">),</span>
148            <span class="n">strictExtension</span><span class="o">=</span><span class="bp">False</span><span class="p">,</span>
149            <span class="n">formatName</span><span class="o">=</span><span class="n">formatName</span><span class="p">,</span>
150            <span class="n">longFormatName</span><span class="o">=</span><span class="n">longFormatName</span><span class="p">)</span>
151
152<div class="viewcode-block" id="SHELX4_ReaderClass.ContentsValidator"><a class="viewcode-back" href="../imports.html#G2sfact.SHELX4_ReaderClass.ContentsValidator">[docs]</a>    <span class="k">def</span> <span class="nf">ContentsValidator</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filepointer</span><span class="p">):</span>
153        <span class="s">&#39;Make sure file contains the expected columns on numbers&#39;</span>
154        <span class="k">return</span> <span class="n">ColumnValidator</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filepointer</span><span class="p">)</span>
155</div>
156<div class="viewcode-block" id="SHELX4_ReaderClass.Reader"><a class="viewcode-back" href="../imports.html#G2sfact.SHELX4_ReaderClass.Reader">[docs]</a>    <span class="k">def</span> <span class="nf">Reader</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">filename</span><span class="p">,</span><span class="n">filepointer</span><span class="p">,</span> <span class="n">ParentFrame</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="o">**</span><span class="n">unused</span><span class="p">):</span>
157        <span class="s">&#39;Read the file&#39;</span>
158        <span class="k">try</span><span class="p">:</span>
159            <span class="k">for</span> <span class="n">line</span><span class="p">,</span><span class="n">S</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">filepointer</span><span class="p">):</span>
160                <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">=</span> <span class="s">&#39;  Error reading line &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">line</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span>
161                <span class="k">if</span> <span class="n">S</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;#&#39;</span><span class="p">:</span> <span class="k">continue</span>       <span class="c">#ignore comments, if any</span>
162                <span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span><span class="n">Fo</span><span class="p">,</span><span class="n">sigFo</span> <span class="o">=</span> <span class="n">S</span><span class="p">[:</span><span class="mi">4</span><span class="p">],</span><span class="n">S</span><span class="p">[</span><span class="mi">4</span><span class="p">:</span><span class="mi">8</span><span class="p">],</span><span class="n">S</span><span class="p">[</span><span class="mi">8</span><span class="p">:</span><span class="mi">12</span><span class="p">],</span><span class="n">S</span><span class="p">[</span><span class="mi">12</span><span class="p">:</span><span class="mi">20</span><span class="p">],</span><span class="n">S</span><span class="p">[</span><span class="mi">20</span><span class="p">:</span><span class="mi">28</span><span class="p">]</span>
163                <span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span> <span class="o">=</span> <span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">h</span><span class="p">),</span><span class="nb">int</span><span class="p">(</span><span class="n">k</span><span class="p">),</span><span class="nb">int</span><span class="p">(</span><span class="n">l</span><span class="p">)]</span>
164                <span class="k">if</span> <span class="ow">not</span> <span class="nb">any</span><span class="p">([</span><span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">]):</span>
165                    <span class="k">break</span>
166                <span class="n">Fo</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">Fo</span><span class="p">)</span>
167                <span class="n">sigFo</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">sigFo</span><span class="p">)</span>
168                <span class="c"># h,k,l,m,dsp,Fo2,sig,Fc2,Fot2,Fct2,phase,...</span>
169                <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;RefList&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span><span class="mi">1</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">Fo</span><span class="p">,</span><span class="n">sigFo</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">Fo</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">])</span>
170                <span class="c">#self.RefDict[&#39;FF&#39;].append({}) # now done in OnImportSfact</span>
171            <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">=</span> <span class="s">&#39;Error after reading reflections (unexpected!)&#39;</span>
172            <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;RefList&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;RefList&#39;</span><span class="p">])</span>
173            <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;Type&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s">&#39;SXC&#39;</span>
174            <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;Super&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>
175            <span class="bp">self</span><span class="o">.</span><span class="n">UpdateParameters</span><span class="p">(</span><span class="n">Type</span><span class="o">=</span><span class="s">&#39;SXC&#39;</span><span class="p">,</span><span class="n">Wave</span><span class="o">=</span><span class="bp">None</span><span class="p">)</span> <span class="c"># histogram type</span>
176            <span class="k">return</span> <span class="bp">True</span>
177        <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">detail</span><span class="p">:</span>
178            <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">+=</span> <span class="s">&#39;</span><span class="se">\n</span><span class="s">  &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">detail</span><span class="p">)</span>
179            <span class="k">print</span> <span class="s">&#39;</span><span class="se">\n\n</span><span class="s">&#39;</span><span class="o">+</span><span class="bp">self</span><span class="o">.</span><span class="n">formatName</span><span class="o">+</span><span class="s">&#39; read error: &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">detail</span><span class="p">)</span> <span class="c"># for testing</span>
180            <span class="kn">import</span> <span class="nn">traceback</span>
181            <span class="n">traceback</span><span class="o">.</span><span class="n">print_exc</span><span class="p">(</span><span class="nb">file</span><span class="o">=</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">)</span>
182            <span class="k">return</span> <span class="bp">False</span>
183            </div></div>
184<div class="viewcode-block" id="SHELX5_ReaderClass"><a class="viewcode-back" href="../imports.html#G2sfact.SHELX5_ReaderClass">[docs]</a><span class="k">class</span> <span class="nc">SHELX5_ReaderClass</span><span class="p">(</span><span class="n">G2IO</span><span class="o">.</span><span class="n">ImportStructFactor</span><span class="p">):</span>
185    <span class="s">&#39;Routines to import F**2, sig(F**2) twin/incommensurate reflections from a fixed format SHELX HKLF5 file&#39;</span>
186    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
187        <span class="k">if</span> <span class="s">&#39;linux&#39;</span> <span class="ow">in</span> <span class="n">sys</span><span class="o">.</span><span class="n">platform</span><span class="p">:</span>  <span class="c"># wx 3.0.0.0 on gtk does not like Unicode in menus</span>
188            <span class="n">formatName</span> <span class="o">=</span> <span class="s">&#39;Shelx HKLF 5 F2 Tw/Incom&#39;</span>
189            <span class="n">longFormatName</span> <span class="o">=</span> <span class="s">&#39;Shelx HKLF 5 [hklm, Fo2, sig(Fo2), Tind] Twin/incommensurate structure factor text file&#39;</span>
190        <span class="k">else</span><span class="p">:</span>
191            <span class="n">formatName</span> <span class="o">=</span> <span class="s">u&#39;Shelx HKLF 5 F</span><span class="se">\u00b2</span><span class="s"> Tw/Incom&#39;</span>
192            <span class="n">longFormatName</span> <span class="o">=</span> <span class="s">u&#39;Shelx HKLF 5 [hklm, Fo</span><span class="se">\u00b2</span><span class="s">, sig(Fo</span><span class="se">\u00b2</span><span class="s">), Tind] Twin/incommensurate structure factor text file&#39;</span>       
193        <span class="nb">super</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">__class__</span><span class="p">,</span><span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span> <span class="c"># fancy way to self-reference</span>
194            <span class="n">extensionlist</span><span class="o">=</span><span class="p">(</span><span class="s">&#39;.hkl&#39;</span><span class="p">,</span><span class="s">&#39;.HKL&#39;</span><span class="p">),</span>
195            <span class="n">strictExtension</span><span class="o">=</span><span class="bp">False</span><span class="p">,</span>
196            <span class="n">formatName</span><span class="o">=</span><span class="n">formatName</span><span class="p">,</span>
197            <span class="n">longFormatName</span><span class="o">=</span><span class="n">longFormatName</span><span class="p">)</span>
198        <span class="bp">self</span><span class="o">.</span><span class="n">Super</span> <span class="o">=</span> <span class="mi">0</span>
199
200<div class="viewcode-block" id="SHELX5_ReaderClass.ContentsValidator"><a class="viewcode-back" href="../imports.html#G2sfact.SHELX5_ReaderClass.ContentsValidator">[docs]</a>    <span class="k">def</span> <span class="nf">ContentsValidator</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filepointer</span><span class="p">):</span>
201        <span class="sd">&#39;&#39;&#39;Discover how many columns before F^2 are in the SHELX HKL5 file </span>
202<span class="sd">        - could be 3-6 depending on satellites&#39;&#39;&#39;</span>
203        <span class="n">numCols</span> <span class="o">=</span> <span class="mi">0</span>
204        <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">filepointer</span><span class="p">):</span>
205            <span class="k">for</span> <span class="n">j</span><span class="p">,</span><span class="n">item</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()):</span>  <span class="c">#find 1st col with &#39;.&#39;; has F^2</span>
206                <span class="k">if</span> <span class="s">&#39;.&#39;</span> <span class="ow">in</span> <span class="n">item</span><span class="p">:</span>
207                    <span class="n">numCols</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="n">numCols</span><span class="p">,</span><span class="n">j</span><span class="p">)</span>
208                    <span class="k">break</span>
209            <span class="k">if</span> <span class="n">i</span> <span class="o">&gt;</span> <span class="mi">20</span><span class="p">:</span>
210                <span class="k">break</span>
211        <span class="bp">self</span><span class="o">.</span><span class="n">Super</span> <span class="o">=</span> <span class="n">numCols</span><span class="o">-</span><span class="mi">3</span>     <span class="c">#= 0,1,2,or 3</span>
212        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">Super</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
213            <span class="k">raise</span> <span class="bp">self</span><span class="o">.</span><span class="n">ImportException</span><span class="p">(</span><span class="s">&quot;Supersymmetry too high; GSAS-II limited to (3+1) supersymmetry&quot;</span><span class="p">)</span>           
214        <span class="k">return</span> <span class="bp">True</span>
215</div>
216<div class="viewcode-block" id="SHELX5_ReaderClass.Reader"><a class="viewcode-back" href="../imports.html#G2sfact.SHELX5_ReaderClass.Reader">[docs]</a>    <span class="k">def</span> <span class="nf">Reader</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">filename</span><span class="p">,</span><span class="n">filepointer</span><span class="p">,</span> <span class="n">ParentFrame</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="o">**</span><span class="n">unused</span><span class="p">):</span>
217        <span class="s">&#39;Read the file&#39;</span>
218        <span class="n">TwDict</span> <span class="o">=</span> <span class="p">{}</span>
219        <span class="n">TwSet</span> <span class="o">=</span> <span class="p">{}</span>
220        <span class="n">TwMax</span> <span class="o">=</span> <span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">,[]]</span>
221        <span class="n">first</span> <span class="o">=</span> <span class="bp">True</span>
222        <span class="k">try</span><span class="p">:</span>
223            <span class="k">for</span> <span class="n">line</span><span class="p">,</span><span class="n">S</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">filepointer</span><span class="p">):</span>
224                <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">=</span> <span class="s">&#39;  Error reading line &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">line</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span>
225                <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">Super</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
226                    <span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span><span class="n">Fo</span><span class="p">,</span><span class="n">sigFo</span><span class="p">,</span><span class="n">Tw</span> <span class="o">=</span> <span class="n">S</span><span class="p">[:</span><span class="mi">4</span><span class="p">],</span><span class="n">S</span><span class="p">[</span><span class="mi">4</span><span class="p">:</span><span class="mi">8</span><span class="p">],</span><span class="n">S</span><span class="p">[</span><span class="mi">8</span><span class="p">:</span><span class="mi">12</span><span class="p">],</span><span class="n">S</span><span class="p">[</span><span class="mi">12</span><span class="p">:</span><span class="mi">20</span><span class="p">],</span><span class="n">S</span><span class="p">[</span><span class="mi">20</span><span class="p">:</span><span class="mi">28</span><span class="p">],</span><span class="n">S</span><span class="p">[</span><span class="mi">28</span><span class="p">:</span><span class="mi">32</span><span class="p">]</span>
227                    <span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span> <span class="o">=</span> <span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">h</span><span class="p">),</span><span class="nb">int</span><span class="p">(</span><span class="n">k</span><span class="p">),</span><span class="nb">int</span><span class="p">(</span><span class="n">l</span><span class="p">)]</span>
228                <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">Super</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
229                    <span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span><span class="n">m1</span><span class="p">,</span><span class="n">Fo</span><span class="p">,</span><span class="n">sigFo</span><span class="p">,</span><span class="n">Tw</span> <span class="o">=</span> <span class="n">S</span><span class="p">[:</span><span class="mi">4</span><span class="p">],</span><span class="n">S</span><span class="p">[</span><span class="mi">4</span><span class="p">:</span><span class="mi">8</span><span class="p">],</span><span class="n">S</span><span class="p">[</span><span class="mi">8</span><span class="p">:</span><span class="mi">12</span><span class="p">],</span><span class="n">S</span><span class="p">[</span><span class="mi">12</span><span class="p">:</span><span class="mi">16</span><span class="p">],</span><span class="n">S</span><span class="p">[</span><span class="mi">16</span><span class="p">:</span><span class="mi">24</span><span class="p">],</span><span class="n">S</span><span class="p">[</span><span class="mi">24</span><span class="p">:</span><span class="mi">32</span><span class="p">],</span><span class="n">S</span><span class="p">[</span><span class="mi">32</span><span class="p">:</span><span class="mi">36</span><span class="p">]</span>
230                    <span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span><span class="n">m1</span> <span class="o">=</span> <span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">h</span><span class="p">),</span><span class="nb">int</span><span class="p">(</span><span class="n">k</span><span class="p">),</span><span class="nb">int</span><span class="p">(</span><span class="n">l</span><span class="p">),</span><span class="nb">int</span><span class="p">(</span><span class="n">m1</span><span class="p">)]</span>
231                <span class="n">Tw</span> <span class="o">=</span> <span class="n">Tw</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
232                <span class="k">if</span> <span class="n">Tw</span> <span class="ow">in</span> <span class="p">[</span><span class="s">&#39;&#39;</span><span class="p">,</span><span class="s">&#39;0&#39;</span><span class="p">]:</span>
233                    <span class="n">Tw</span> <span class="o">=</span> <span class="s">&#39;1&#39;</span>
234                <span class="k">if</span> <span class="ow">not</span> <span class="nb">any</span><span class="p">([</span><span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">]):</span>
235                    <span class="k">break</span>
236                <span class="k">if</span> <span class="s">&#39;-&#39;</span> <span class="ow">in</span> <span class="n">Tw</span><span class="p">:</span>
237                    <span class="k">if</span> <span class="n">Tw</span> <span class="o">==</span> <span class="s">&#39;-1&#39;</span><span class="p">:</span>  <span class="c">#fix reversed twin ids</span>
238                        <span class="n">Tw</span> <span class="o">=</span> <span class="s">&#39;-2&#39;</span>
239                        <span class="k">if</span> <span class="n">first</span><span class="p">:</span>
240                            <span class="bp">self</span><span class="o">.</span><span class="n">warnings</span> <span class="o">+=</span> <span class="s">&#39;</span><span class="se">\n</span><span class="s">Primary twin id changed to 1&#39;</span>
241                            <span class="n">first</span> <span class="o">=</span> <span class="bp">False</span>
242                    <span class="n">TwId</span> <span class="o">=</span> <span class="o">-</span><span class="nb">int</span><span class="p">(</span><span class="n">Tw</span><span class="p">)</span><span class="o">-</span><span class="mi">1</span>
243                    <span class="n">TwSet</span><span class="p">[</span><span class="n">TwId</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">])</span>
244                    <span class="k">if</span> <span class="n">TwId</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">TwMax</span><span class="p">[</span><span class="mi">1</span><span class="p">]:</span>
245                        <span class="n">TwMax</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">TwId</span><span class="p">)</span>
246                <span class="k">else</span><span class="p">:</span>
247                    <span class="k">if</span> <span class="n">Tw</span> <span class="o">!=</span> <span class="s">&#39;1&#39;</span><span class="p">:</span>  <span class="c">#fix reversed twin ids</span>
248                        <span class="k">if</span> <span class="n">first</span><span class="p">:</span>
249                            <span class="bp">self</span><span class="o">.</span><span class="n">warnings</span> <span class="o">+=</span> <span class="s">&#39;</span><span class="se">\n</span><span class="s">Primary twin id changed to 1</span><span class="se">\n</span><span class="s">NB: multiple primary twins not working&#39;</span>
250                            <span class="n">first</span> <span class="o">=</span> <span class="bp">False</span>
251                        <span class="n">Tw</span> <span class="o">=</span> <span class="s">&#39;1&#39;</span>
252                    <span class="n">TwId</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">Tw</span><span class="p">)</span><span class="o">-</span><span class="mi">1</span>
253                    <span class="k">if</span> <span class="n">TwSet</span><span class="p">:</span>
254                        <span class="n">TwDict</span><span class="p">[</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;RefList&#39;</span><span class="p">])]</span> <span class="o">=</span> <span class="n">TwSet</span>
255                        <span class="n">TwSet</span> <span class="o">=</span> <span class="p">{}</span>   
256                    <span class="n">Fo</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">Fo</span><span class="p">)</span>
257                    <span class="n">sigFo</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">sigFo</span><span class="p">)</span>
258                    <span class="c"># h,k,l,m,dsp,Fo2,sig,Fc2,Fot2,Fct2,phase,...</span>
259                    <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">Super</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
260                        <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;RefList&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span><span class="nb">int</span><span class="p">(</span><span class="n">Tw</span><span class="p">),</span><span class="mi">0</span><span class="p">,</span><span class="n">Fo</span><span class="p">,</span><span class="n">sigFo</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">Fo</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">])</span>
261                    <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">Super</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
262                        <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;RefList&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span><span class="n">m1</span><span class="p">,</span><span class="nb">int</span><span class="p">(</span><span class="n">Tw</span><span class="p">),</span><span class="mi">0</span><span class="p">,</span><span class="n">Fo</span><span class="p">,</span><span class="n">sigFo</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">Fo</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">])</span>
263                <span class="n">TwMax</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="n">TwMax</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span><span class="n">TwId</span><span class="p">)</span>
264            <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">=</span> <span class="s">&#39;Error after reading reflections (unexpected!)&#39;</span>
265            <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;RefList&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;RefList&#39;</span><span class="p">])</span>
266            <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;Type&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s">&#39;SXC&#39;</span>
267            <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;Super&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">Super</span>
268            <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;TwDict&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">TwDict</span>
269            <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;TwMax&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">TwMax</span>
270            <span class="bp">self</span><span class="o">.</span><span class="n">UpdateParameters</span><span class="p">(</span><span class="n">Type</span><span class="o">=</span><span class="s">&#39;SXC&#39;</span><span class="p">,</span><span class="n">Wave</span><span class="o">=</span><span class="bp">None</span><span class="p">)</span> <span class="c"># histogram type</span>
271            <span class="k">return</span> <span class="bp">True</span>
272        <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">detail</span><span class="p">:</span>
273            <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">+=</span> <span class="s">&#39;</span><span class="se">\n</span><span class="s">  &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">detail</span><span class="p">)</span>
274            <span class="k">print</span> <span class="s">&#39;</span><span class="se">\n\n</span><span class="s">&#39;</span><span class="o">+</span><span class="bp">self</span><span class="o">.</span><span class="n">formatName</span><span class="o">+</span><span class="s">&#39; read error: &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">detail</span><span class="p">)</span> <span class="c"># for testing</span>
275            <span class="kn">import</span> <span class="nn">traceback</span>
276            <span class="n">traceback</span><span class="o">.</span><span class="n">print_exc</span><span class="p">(</span><span class="nb">file</span><span class="o">=</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">)</span>
277            <span class="k">return</span> <span class="bp">False</span>
278</div></div>
279<div class="viewcode-block" id="M90_ReaderClass"><a class="viewcode-back" href="../imports.html#G2sfact.M90_ReaderClass">[docs]</a><span class="k">class</span> <span class="nc">M90_ReaderClass</span><span class="p">(</span><span class="n">G2IO</span><span class="o">.</span><span class="n">ImportStructFactor</span><span class="p">):</span>
280    <span class="s">&#39;Routines to import F**2, sig(F**2) reflections from a JANA M90 file&#39;</span>
281    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
282        <span class="k">if</span> <span class="s">&#39;linux&#39;</span> <span class="ow">in</span> <span class="n">sys</span><span class="o">.</span><span class="n">platform</span><span class="p">:</span>  <span class="c"># wx 3.0.0.0 on gtk does not like Unicode in menus</span>
283            <span class="n">longFormatName</span> <span class="o">=</span> <span class="s">&#39;JANA [hkl, Fo2, sig(Fo2)] Structure factor text file&#39;</span>
284        <span class="k">else</span><span class="p">:</span>
285            <span class="n">longFormatName</span> <span class="o">=</span> <span class="s">u&#39;JANA [hkl, Fo</span><span class="se">\u00b2</span><span class="s">, sig(Fo</span><span class="se">\u00b2</span><span class="s">)] Structure factor text file&#39;</span>
286        <span class="nb">super</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">__class__</span><span class="p">,</span><span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span> <span class="c"># fancy way to self-reference</span>
287            <span class="n">extensionlist</span><span class="o">=</span><span class="p">(</span><span class="s">&#39;.m90&#39;</span><span class="p">,</span><span class="s">&#39;.M90&#39;</span><span class="p">),</span>
288            <span class="n">strictExtension</span><span class="o">=</span><span class="bp">False</span><span class="p">,</span>
289            <span class="n">formatName</span> <span class="o">=</span> <span class="s">u&#39;JANA M90&#39;</span><span class="p">,</span>
290            <span class="n">longFormatName</span> <span class="o">=</span> <span class="n">longFormatName</span>
291            <span class="p">)</span>
292        <span class="bp">self</span><span class="o">.</span><span class="n">Super</span> <span class="o">=</span> <span class="mi">0</span>
293
294<div class="viewcode-block" id="M90_ReaderClass.ContentsValidator"><a class="viewcode-back" href="../imports.html#G2sfact.M90_ReaderClass.ContentsValidator">[docs]</a>    <span class="k">def</span> <span class="nf">ContentsValidator</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filepointer</span><span class="p">):</span>
295        <span class="s">&#39;Discover how many columns are in the m90 file - could be 9-12 depending on satellites&#39;</span>
296        <span class="n">numCols</span> <span class="o">=</span> <span class="mi">0</span>
297        <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">filepointer</span><span class="p">):</span>
298            <span class="k">if</span> <span class="s">&#39;Data&#39;</span> <span class="ow">in</span> <span class="n">line</span><span class="p">:</span>
299                <span class="n">startData</span> <span class="o">=</span> <span class="n">i</span>
300                <span class="k">break</span>
301        <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">filepointer</span><span class="p">):</span>
302            <span class="k">if</span> <span class="n">i</span> <span class="o">&gt;</span> <span class="n">startData</span><span class="p">:</span>
303                <span class="n">numCols</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="n">numCols</span><span class="p">,</span><span class="nb">len</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()))</span>
304            <span class="k">if</span> <span class="n">i</span> <span class="o">&gt;</span> <span class="n">startData</span><span class="o">+</span><span class="mi">20</span><span class="p">:</span>
305                <span class="k">break</span>
306        <span class="bp">self</span><span class="o">.</span><span class="n">Super</span> <span class="o">=</span> <span class="n">numCols</span><span class="o">-</span><span class="mi">9</span>     <span class="c">#= 0,1,2,or 3</span>
307        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">Super</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
308            <span class="k">raise</span> <span class="bp">self</span><span class="o">.</span><span class="n">ImportException</span><span class="p">(</span><span class="s">&quot;Supersymmetry too high; GSAS-II limited to (3+1) supersymmetry&quot;</span><span class="p">)</span>           
309        <span class="k">return</span> <span class="bp">True</span> <span class="c">#ColumnValidator(self, filepointer)</span>
310</div>
311<div class="viewcode-block" id="M90_ReaderClass.Reader"><a class="viewcode-back" href="../imports.html#G2sfact.M90_ReaderClass.Reader">[docs]</a>    <span class="k">def</span> <span class="nf">Reader</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">filename</span><span class="p">,</span><span class="n">filepointer</span><span class="p">,</span> <span class="n">ParentFrame</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="o">**</span><span class="n">unused</span><span class="p">):</span>
312        <span class="s">&#39;Read the file&#39;</span>
313        <span class="k">try</span><span class="p">:</span>
314            <span class="k">for</span> <span class="n">line</span><span class="p">,</span><span class="n">S</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">filepointer</span><span class="p">):</span>
315                <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">=</span> <span class="s">&#39;  Error reading line &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">line</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span>
316                <span class="k">if</span> <span class="n">S</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;#&#39;</span><span class="p">:</span> <span class="k">continue</span>       <span class="c">#ignore comments, if any</span>
317                <span class="k">try</span><span class="p">:</span>
318                    <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">Super</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
319                        <span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span><span class="n">Fo</span><span class="p">,</span><span class="n">sigFo</span> <span class="o">=</span> <span class="n">S</span><span class="o">.</span><span class="n">split</span><span class="p">()[:</span><span class="mi">5</span><span class="p">]</span>
320                        <span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span> <span class="o">=</span> <span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">h</span><span class="p">),</span><span class="nb">int</span><span class="p">(</span><span class="n">k</span><span class="p">),</span><span class="nb">int</span><span class="p">(</span><span class="n">l</span><span class="p">)]</span>
321                    <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">Super</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
322                        <span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span><span class="n">m1</span><span class="p">,</span><span class="n">Fo</span><span class="p">,</span><span class="n">sigFo</span> <span class="o">=</span> <span class="n">S</span><span class="o">.</span><span class="n">split</span><span class="p">()[:</span><span class="mi">6</span><span class="p">]</span>
323                        <span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span><span class="n">m1</span> <span class="o">=</span> <span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">h</span><span class="p">),</span><span class="nb">int</span><span class="p">(</span><span class="n">k</span><span class="p">),</span><span class="nb">int</span><span class="p">(</span><span class="n">l</span><span class="p">),</span><span class="nb">int</span><span class="p">(</span><span class="n">m1</span><span class="p">)]</span>
324                <span class="k">except</span> <span class="ne">ValueError</span><span class="p">:</span>  <span class="c">#skipping text at front</span>
325                    <span class="k">if</span> <span class="ow">not</span> <span class="n">S</span><span class="p">:</span>
326                        <span class="k">break</span>
327                    <span class="n">text</span> <span class="o">=</span> <span class="n">S</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
328                    <span class="k">if</span> <span class="n">text</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;lambda&#39;</span><span class="p">:</span>
329                        <span class="n">wave</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">text</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
330                    <span class="k">continue</span>
331                <span class="n">Fo</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">Fo</span><span class="p">)</span>
332                <span class="n">sigFo</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">sigFo</span><span class="p">)</span>
333                <span class="c"># h,k,l,m,dsp,Fo2,sig,Fc2,Fot2,Fct2,phase,...</span>
334                <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">Super</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
335                    <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;RefList&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span><span class="mi">1</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">Fo</span><span class="p">,</span><span class="n">sigFo</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">Fo</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">])</span>
336                <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">Super</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
337                    <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;RefList&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span><span class="n">m1</span><span class="p">,</span><span class="mi">1</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">Fo</span><span class="p">,</span><span class="n">sigFo</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">Fo</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">])</span>
338            <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">=</span> <span class="s">&#39;Error after reading reflections (unexpected!)&#39;</span>
339            <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;RefList&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;RefList&#39;</span><span class="p">])</span>
340            <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;Type&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s">&#39;SXC&#39;</span>
341            <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;Super&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">Super</span>
342            <span class="bp">self</span><span class="o">.</span><span class="n">UpdateParameters</span><span class="p">(</span><span class="n">Type</span><span class="o">=</span><span class="s">&#39;SXC&#39;</span><span class="p">,</span><span class="n">Wave</span><span class="o">=</span><span class="n">wave</span><span class="p">)</span> <span class="c"># histogram type</span>
343            <span class="k">return</span> <span class="bp">True</span>
344        <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">detail</span><span class="p">:</span>
345            <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">+=</span> <span class="s">&#39;</span><span class="se">\n</span><span class="s">  &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">detail</span><span class="p">)</span>
346            <span class="k">print</span> <span class="s">&#39;</span><span class="se">\n\n</span><span class="s">&#39;</span><span class="o">+</span><span class="bp">self</span><span class="o">.</span><span class="n">formatName</span><span class="o">+</span><span class="s">&#39; read error: &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">detail</span><span class="p">)</span> <span class="c"># for testing</span>
347            <span class="kn">import</span> <span class="nn">traceback</span>
348            <span class="n">traceback</span><span class="o">.</span><span class="n">print_exc</span><span class="p">(</span><span class="nb">file</span><span class="o">=</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">)</span>
349            <span class="k">return</span> <span class="bp">False</span>
350            </div></div>
351<div class="viewcode-block" id="NT_HKLF2_ReaderClass"><a class="viewcode-back" href="../imports.html#G2sfact.NT_HKLF2_ReaderClass">[docs]</a><span class="k">class</span> <span class="nc">NT_HKLF2_ReaderClass</span><span class="p">(</span><span class="n">G2IO</span><span class="o">.</span><span class="n">ImportStructFactor</span><span class="p">):</span>
352    <span class="s">&#39;Routines to import neutron TOF F**2, sig(F**2) reflections from a HKLF file&#39;</span>
353    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
354        <span class="k">if</span> <span class="s">&#39;linux&#39;</span> <span class="ow">in</span> <span class="n">sys</span><span class="o">.</span><span class="n">platform</span><span class="p">:</span>  <span class="c"># wx 3.0.0.0 on gtk does not like Unicode in menus</span>
355            <span class="n">formatName</span> <span class="o">=</span> <span class="s">&#39;Neutron TOF HKL F2&#39;</span>
356            <span class="n">longFormatName</span> <span class="o">=</span> <span class="s">&#39;Neutron TOF [hkl, Fo2, sig(Fo2),...] Structure factor text file&#39;</span>
357        <span class="k">else</span><span class="p">:</span>
358            <span class="n">formatName</span> <span class="o">=</span> <span class="s">u&#39;Neutron TOF HKL F</span><span class="se">\u00b2</span><span class="s">&#39;</span>
359            <span class="n">longFormatName</span> <span class="o">=</span> <span class="s">u&#39;Neutron TOF [hkl, Fo</span><span class="se">\u00b2</span><span class="s">, sig(Fo</span><span class="se">\u00b2</span><span class="s">),...] Structure factor text file&#39;</span>
360        <span class="nb">super</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">__class__</span><span class="p">,</span><span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span> <span class="c"># fancy way to self-reference</span>
361            <span class="n">extensionlist</span><span class="o">=</span><span class="p">(</span><span class="s">&#39;.hkl&#39;</span><span class="p">,</span><span class="s">&#39;.HKL&#39;</span><span class="p">),</span>
362            <span class="n">strictExtension</span><span class="o">=</span><span class="bp">False</span><span class="p">,</span>
363            <span class="n">formatName</span><span class="o">=</span><span class="n">formatName</span><span class="p">,</span>
364            <span class="n">longFormatName</span><span class="o">=</span><span class="n">longFormatName</span><span class="p">)</span>
365
366<div class="viewcode-block" id="NT_HKLF2_ReaderClass.ContentsValidator"><a class="viewcode-back" href="../imports.html#G2sfact.NT_HKLF2_ReaderClass.ContentsValidator">[docs]</a>    <span class="k">def</span> <span class="nf">ContentsValidator</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filepointer</span><span class="p">):</span>
367        <span class="s">&#39;Make sure file contains the expected columns on numbers &amp; count number of data blocks - &quot;Banks&quot;&#39;</span>
368        <span class="n">oldNo</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
369        <span class="k">for</span> <span class="n">line</span><span class="p">,</span><span class="n">S</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">filepointer</span><span class="p">):</span>
370            <span class="k">if</span> <span class="ow">not</span> <span class="n">S</span><span class="p">:</span>   <span class="c">#empty line terminates read</span>
371                <span class="k">break</span>
372            <span class="k">if</span> <span class="n">S</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;#&#39;</span><span class="p">:</span> <span class="k">continue</span>       <span class="c">#ignore comments, if any</span>
373            <span class="k">if</span> <span class="n">S</span><span class="o">.</span><span class="n">split</span><span class="p">()[:</span><span class="mi">3</span><span class="p">]</span> <span class="o">==</span> <span class="p">[</span><span class="s">&#39;0&#39;</span><span class="p">,</span><span class="s">&#39;0&#39;</span><span class="p">,</span><span class="s">&#39;0&#39;</span><span class="p">]:</span>
374                <span class="k">break</span>
375            <span class="n">bankNo</span> <span class="o">=</span> <span class="n">S</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">5</span><span class="p">]</span>
376            <span class="k">if</span> <span class="n">bankNo</span> <span class="o">!=</span> <span class="n">oldNo</span><span class="p">:</span>
377                <span class="bp">self</span><span class="o">.</span><span class="n">Banks</span><span class="o">.</span><span class="n">append</span><span class="p">({</span><span class="s">&#39;RefDict&#39;</span><span class="p">:{</span><span class="s">&#39;RefList&#39;</span><span class="p">:[],}})</span>
378                <span class="n">oldNo</span> <span class="o">=</span> <span class="n">bankNo</span>
379        <span class="n">filepointer</span><span class="o">.</span><span class="n">seek</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
380        <span class="k">return</span> <span class="n">ColumnValidator</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filepointer</span><span class="p">,</span><span class="n">nCol</span><span class="o">=</span><span class="mi">8</span><span class="p">)</span>
381</div>
382<div class="viewcode-block" id="NT_HKLF2_ReaderClass.Reader"><a class="viewcode-back" href="../imports.html#G2sfact.NT_HKLF2_ReaderClass.Reader">[docs]</a>    <span class="k">def</span> <span class="nf">Reader</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">filename</span><span class="p">,</span><span class="n">filepointer</span><span class="p">,</span> <span class="n">ParentFrame</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="o">**</span><span class="n">unused</span><span class="p">):</span>
383        <span class="s">&#39;Read the file&#39;</span>
384        <span class="n">filepointer</span><span class="o">.</span><span class="n">seek</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
385        <span class="k">try</span><span class="p">:</span>
386            <span class="k">for</span> <span class="n">line</span><span class="p">,</span><span class="n">S</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">filepointer</span><span class="p">):</span>
387                <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">=</span> <span class="s">&#39;  Error reading line &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">line</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span>
388                <span class="k">if</span> <span class="n">S</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;#&#39;</span><span class="p">:</span> <span class="k">continue</span>       <span class="c">#ignore comments, if any</span>
389                <span class="n">data</span> <span class="o">=</span> <span class="n">S</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
390                <span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span><span class="n">Fo</span><span class="p">,</span><span class="n">sigFo</span><span class="p">,</span><span class="n">bN</span><span class="p">,</span><span class="n">wave</span><span class="p">,</span><span class="n">tbar</span> <span class="o">=</span> <span class="n">data</span><span class="p">[:</span><span class="mi">8</span><span class="p">]</span>  <span class="c">#bN = 1..., 6 dir cos next                    </span>
391                <span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span> <span class="o">=</span> <span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">h</span><span class="p">),</span><span class="nb">int</span><span class="p">(</span><span class="n">k</span><span class="p">),</span><span class="nb">int</span><span class="p">(</span><span class="n">l</span><span class="p">)]</span>
392                <span class="k">if</span> <span class="ow">not</span> <span class="nb">any</span><span class="p">([</span><span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">]):</span>
393                    <span class="k">break</span>
394                <span class="n">Fo</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">Fo</span><span class="p">)</span>
395                <span class="n">sigFo</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">sigFo</span><span class="p">)</span>
396                <span class="n">wave</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">wave</span><span class="p">)</span>
397                <span class="n">tbar</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">tbar</span><span class="p">)</span>
398                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">Banks</span><span class="p">):</span>
399                    <span class="bp">self</span><span class="o">.</span><span class="n">Banks</span><span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">bN</span><span class="p">)</span><span class="o">-</span><span class="mi">1</span><span class="p">][</span><span class="s">&#39;RefDict&#39;</span><span class="p">][</span><span class="s">&#39;RefList&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span><span class="mi">1</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">Fo</span><span class="p">,</span><span class="n">sigFo</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">Fo</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">wave</span><span class="p">,</span><span class="n">tbar</span><span class="p">])</span>
400                <span class="k">else</span><span class="p">:</span>
401                <span class="c"># h,k,l,m,dsp,Fo2,sig,Fc2,Fot2,Fct2,phase,...</span>
402                    <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;RefList&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span><span class="mi">1</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">Fo</span><span class="p">,</span><span class="n">sigFo</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">Fo</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">wave</span><span class="p">,</span><span class="n">tbar</span><span class="p">])</span>
403            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">Banks</span><span class="p">):</span>
404                <span class="bp">self</span><span class="o">.</span><span class="n">UpdateParameters</span><span class="p">(</span><span class="n">Type</span><span class="o">=</span><span class="s">&#39;SNT&#39;</span><span class="p">,</span><span class="n">Wave</span><span class="o">=</span><span class="bp">None</span><span class="p">)</span> <span class="c"># histogram type</span>
405                <span class="k">for</span> <span class="n">Bank</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">Banks</span><span class="p">:</span>
406                    <span class="n">Bank</span><span class="p">[</span><span class="s">&#39;RefDict&#39;</span><span class="p">][</span><span class="s">&#39;RefList&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">Bank</span><span class="p">[</span><span class="s">&#39;RefDict&#39;</span><span class="p">][</span><span class="s">&#39;RefList&#39;</span><span class="p">])</span>
407                    <span class="n">Bank</span><span class="p">[</span><span class="s">&#39;RefDict&#39;</span><span class="p">][</span><span class="s">&#39;Type&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s">&#39;SNT&#39;</span>                   
408                    <span class="n">Bank</span><span class="p">[</span><span class="s">&#39;RefDict&#39;</span><span class="p">][</span><span class="s">&#39;Super&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>
409            <span class="k">else</span><span class="p">:</span>
410                <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;RefList&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;RefList&#39;</span><span class="p">])</span>
411                <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;Type&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s">&#39;SNT&#39;</span>
412                <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;Super&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>
413                <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">=</span> <span class="s">&#39;Error after reading reflections (unexpected!)&#39;</span>
414                <span class="bp">self</span><span class="o">.</span><span class="n">UpdateParameters</span><span class="p">(</span><span class="n">Type</span><span class="o">=</span><span class="s">&#39;SNT&#39;</span><span class="p">,</span><span class="n">Wave</span><span class="o">=</span><span class="bp">None</span><span class="p">)</span> <span class="c"># histogram type</span>
415            <span class="k">return</span> <span class="bp">True</span>
416        <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">detail</span><span class="p">:</span>
417            <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">+=</span> <span class="s">&#39;</span><span class="se">\n</span><span class="s">  &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">detail</span><span class="p">)</span>
418            <span class="k">print</span> <span class="s">&#39;</span><span class="se">\n\n</span><span class="s">&#39;</span><span class="o">+</span><span class="bp">self</span><span class="o">.</span><span class="n">formatName</span><span class="o">+</span><span class="s">&#39; read error: &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">detail</span><span class="p">)</span> <span class="c"># for testing</span>
419            <span class="kn">import</span> <span class="nn">traceback</span>
420            <span class="n">traceback</span><span class="o">.</span><span class="n">print_exc</span><span class="p">(</span><span class="nb">file</span><span class="o">=</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">)</span>
421            <span class="k">return</span> <span class="bp">False</span>
422</div></div>
423<div class="viewcode-block" id="NT_JANA2K_ReaderClass"><a class="viewcode-back" href="../imports.html#G2sfact.NT_JANA2K_ReaderClass">[docs]</a><span class="k">class</span> <span class="nc">NT_JANA2K_ReaderClass</span><span class="p">(</span><span class="n">G2IO</span><span class="o">.</span><span class="n">ImportStructFactor</span><span class="p">):</span>
424    <span class="s">&#39;Routines to import neutron TOF F**2, sig(F**2) reflections from a JANA2000 file&#39;</span>
425    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
426        <span class="k">if</span> <span class="s">&#39;linux&#39;</span> <span class="ow">in</span> <span class="n">sys</span><span class="o">.</span><span class="n">platform</span><span class="p">:</span>  <span class="c"># wx 3.0.0.0 on gtk does not like Unicode in menus</span>
427            <span class="n">formatName</span> <span class="o">=</span> <span class="s">&#39;Neutron TOF JANA2000 F2&#39;</span>
428            <span class="n">longFormatName</span> <span class="o">=</span> <span class="s">&#39;Neutron TOF [hkl, Fo2, sig(Fo2),...] Structure factor text file&#39;</span>
429        <span class="k">else</span><span class="p">:</span>
430            <span class="n">formatName</span> <span class="o">=</span> <span class="s">u&#39;Neutron TOF JANA2000 F</span><span class="se">\u00b2</span><span class="s">&#39;</span>
431            <span class="n">longFormatName</span> <span class="o">=</span> <span class="s">u&#39;Neutron TOF [hkl, Fo</span><span class="se">\u00b2</span><span class="s">, sig(Fo</span><span class="se">\u00b2</span><span class="s">),...] Structure factor text file&#39;</span>
432        <span class="nb">super</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">__class__</span><span class="p">,</span><span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span> <span class="c"># fancy way to self-reference</span>
433            <span class="n">extensionlist</span><span class="o">=</span><span class="p">(</span><span class="s">&#39;.int&#39;</span><span class="p">,</span><span class="s">&#39;.INT&#39;</span><span class="p">),</span>
434            <span class="n">strictExtension</span><span class="o">=</span><span class="bp">False</span><span class="p">,</span>
435            <span class="n">formatName</span><span class="o">=</span><span class="n">formatName</span><span class="p">,</span>
436            <span class="n">longFormatName</span><span class="o">=</span><span class="n">longFormatName</span><span class="p">)</span>
437
438<div class="viewcode-block" id="NT_JANA2K_ReaderClass.ContentsValidator"><a class="viewcode-back" href="../imports.html#G2sfact.NT_JANA2K_ReaderClass.ContentsValidator">[docs]</a>    <span class="k">def</span> <span class="nf">ContentsValidator</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filepointer</span><span class="p">):</span>
439        <span class="s">&#39;Make sure file contains the expected columns on numbers &amp; count number of data blocks - &quot;Banks&quot;&#39;</span>
440        <span class="n">oldNo</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
441        <span class="k">for</span> <span class="n">line</span><span class="p">,</span><span class="n">S</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">filepointer</span><span class="p">):</span>
442            <span class="k">if</span> <span class="ow">not</span> <span class="n">S</span><span class="p">:</span>   <span class="c">#empty line terminates read</span>
443                <span class="k">break</span>
444            <span class="k">if</span> <span class="n">S</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="p">[</span><span class="s">&#39;#&#39;</span><span class="p">,</span><span class="s">&#39;(&#39;</span><span class="p">]:</span> <span class="k">continue</span>       <span class="c">#ignore comments &amp; fortran format line</span>
445            <span class="n">bankNo</span> <span class="o">=</span> <span class="n">S</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">5</span><span class="p">]</span>
446            <span class="k">if</span> <span class="n">bankNo</span> <span class="o">!=</span> <span class="n">oldNo</span><span class="p">:</span>
447                <span class="bp">self</span><span class="o">.</span><span class="n">Banks</span><span class="o">.</span><span class="n">append</span><span class="p">({</span><span class="s">&#39;RefDict&#39;</span><span class="p">:{</span><span class="s">&#39;RefList&#39;</span><span class="p">:[],}})</span>
448                <span class="n">oldNo</span> <span class="o">=</span> <span class="n">bankNo</span>
449        <span class="n">filepointer</span><span class="o">.</span><span class="n">seek</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
450        <span class="k">return</span> <span class="n">ColumnValidator</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filepointer</span><span class="p">,</span><span class="n">nCol</span><span class="o">=</span><span class="mi">10</span><span class="p">)</span>
451</div>
452<div class="viewcode-block" id="NT_JANA2K_ReaderClass.Reader"><a class="viewcode-back" href="../imports.html#G2sfact.NT_JANA2K_ReaderClass.Reader">[docs]</a>    <span class="k">def</span> <span class="nf">Reader</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">filename</span><span class="p">,</span><span class="n">filepointer</span><span class="p">,</span> <span class="n">ParentFrame</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="o">**</span><span class="n">unused</span><span class="p">):</span>
453        <span class="s">&#39;Read the file&#39;</span>
454        <span class="n">filepointer</span><span class="o">.</span><span class="n">seek</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
455        <span class="k">try</span><span class="p">:</span>
456            <span class="k">for</span> <span class="n">line</span><span class="p">,</span><span class="n">S</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">filepointer</span><span class="p">):</span>
457                <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">=</span> <span class="s">&#39;  Error reading line &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">line</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span>
458                <span class="k">if</span> <span class="n">S</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="p">[</span><span class="s">&#39;#&#39;</span><span class="p">,</span><span class="s">&#39;(&#39;</span><span class="p">]:</span> <span class="k">continue</span>       <span class="c">#ignore comments &amp; fortran format line</span>
459                <span class="n">data</span> <span class="o">=</span> <span class="n">S</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
460                <span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span><span class="n">Fo</span><span class="p">,</span><span class="n">sigFo</span><span class="p">,</span><span class="n">bN</span><span class="p">,</span><span class="n">wave</span><span class="p">,</span><span class="n">x</span><span class="p">,</span><span class="n">x</span><span class="p">,</span><span class="n">tbar</span> <span class="o">=</span> <span class="n">data</span><span class="p">[:</span><span class="mi">10</span><span class="p">]</span>  <span class="c">#bN = 1..., 6 dir cos next                    </span>
461                <span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span> <span class="o">=</span> <span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">h</span><span class="p">),</span><span class="nb">int</span><span class="p">(</span><span class="n">k</span><span class="p">),</span><span class="nb">int</span><span class="p">(</span><span class="n">l</span><span class="p">)]</span>
462                <span class="k">if</span> <span class="ow">not</span> <span class="nb">any</span><span class="p">([</span><span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">]):</span>
463                    <span class="k">break</span>
464                <span class="n">Fo</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">Fo</span><span class="p">)</span>
465                <span class="n">sigFo</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">sigFo</span><span class="p">)</span>
466                <span class="n">wave</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">wave</span><span class="p">)</span>
467                <span class="n">tbar</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">tbar</span><span class="p">)</span>
468                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">Banks</span><span class="p">):</span>
469                    <span class="bp">self</span><span class="o">.</span><span class="n">Banks</span><span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">bN</span><span class="p">)</span><span class="o">-</span><span class="mi">1</span><span class="p">][</span><span class="s">&#39;RefDict&#39;</span><span class="p">][</span><span class="s">&#39;RefList&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span><span class="mi">1</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">Fo</span><span class="p">,</span><span class="n">sigFo</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">Fo</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">wave</span><span class="p">,</span><span class="n">tbar</span><span class="p">])</span>
470                <span class="k">else</span><span class="p">:</span>
471                <span class="c"># h,k,l,m,dsp,Fo2,sig,Fc2,Fot2,Fct2,phase,...</span>
472                    <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;RefList&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span><span class="mi">1</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">Fo</span><span class="p">,</span><span class="n">sigFo</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">Fo</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">wave</span><span class="p">,</span><span class="n">tbar</span><span class="p">])</span>
473            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">Banks</span><span class="p">):</span>
474                <span class="bp">self</span><span class="o">.</span><span class="n">UpdateParameters</span><span class="p">(</span><span class="n">Type</span><span class="o">=</span><span class="s">&#39;SNT&#39;</span><span class="p">,</span><span class="n">Wave</span><span class="o">=</span><span class="bp">None</span><span class="p">)</span> <span class="c"># histogram type</span>
475                <span class="k">for</span> <span class="n">Bank</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">Banks</span><span class="p">:</span>
476                    <span class="n">Bank</span><span class="p">[</span><span class="s">&#39;RefDict&#39;</span><span class="p">][</span><span class="s">&#39;RefList&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">Bank</span><span class="p">[</span><span class="s">&#39;RefDict&#39;</span><span class="p">][</span><span class="s">&#39;RefList&#39;</span><span class="p">])</span>
477                    <span class="n">Bank</span><span class="p">[</span><span class="s">&#39;RefDict&#39;</span><span class="p">][</span><span class="s">&#39;Type&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s">&#39;SNT&#39;</span>                   
478                    <span class="n">Bank</span><span class="p">[</span><span class="s">&#39;RefDict&#39;</span><span class="p">][</span><span class="s">&#39;Super&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>        <span class="c">#for now                    </span>
479            <span class="k">else</span><span class="p">:</span>
480                <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;RefList&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;RefList&#39;</span><span class="p">])</span>
481                <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;Type&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s">&#39;SNT&#39;</span>
482                <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;Super&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>   <span class="c">#for now</span>
483                <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">=</span> <span class="s">&#39;Error after reading reflections (unexpected!)&#39;</span>
484                <span class="bp">self</span><span class="o">.</span><span class="n">UpdateParameters</span><span class="p">(</span><span class="n">Type</span><span class="o">=</span><span class="s">&#39;SNT&#39;</span><span class="p">,</span><span class="n">Wave</span><span class="o">=</span><span class="bp">None</span><span class="p">)</span> <span class="c"># histogram type</span>
485            <span class="k">return</span> <span class="bp">True</span>
486        <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">detail</span><span class="p">:</span>
487            <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">+=</span> <span class="s">&#39;</span><span class="se">\n</span><span class="s">  &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">detail</span><span class="p">)</span>
488            <span class="k">print</span> <span class="s">&#39;</span><span class="se">\n\n</span><span class="s">&#39;</span><span class="o">+</span><span class="bp">self</span><span class="o">.</span><span class="n">formatName</span><span class="o">+</span><span class="s">&#39; read error: &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">detail</span><span class="p">)</span> <span class="c"># for testing</span>
489            <span class="kn">import</span> <span class="nn">traceback</span>
490            <span class="n">traceback</span><span class="o">.</span><span class="n">print_exc</span><span class="p">(</span><span class="nb">file</span><span class="o">=</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">)</span>
491            <span class="k">return</span> <span class="bp">False</span>
492</div></div>
493<div class="viewcode-block" id="ISIS_SXD_INT_ReaderClass"><a class="viewcode-back" href="../imports.html#G2sfact.ISIS_SXD_INT_ReaderClass">[docs]</a><span class="k">class</span> <span class="nc">ISIS_SXD_INT_ReaderClass</span><span class="p">(</span><span class="n">G2IO</span><span class="o">.</span><span class="n">ImportStructFactor</span><span class="p">):</span>
494    <span class="s">&#39;Routines to import neutron TOF F**2, sig(F**2) reflections from a ISIS int file&#39;</span>
495    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
496        <span class="k">if</span> <span class="s">&#39;linux&#39;</span> <span class="ow">in</span> <span class="n">sys</span><span class="o">.</span><span class="n">platform</span><span class="p">:</span>  <span class="c"># wx 3.0.0.0 on gtk does not like Unicode in menus</span>
497            <span class="n">formatName</span> <span class="o">=</span> <span class="s">u&#39;Neutron SXD TOF HKL F2&#39;</span>
498            <span class="n">longFormatName</span> <span class="o">=</span> <span class="s">u&#39;Neutron SXD TOF [hkl, Fo2, sig(Fo2),...] Structure factor text file&#39;</span>
499        <span class="k">else</span><span class="p">:</span>
500            <span class="n">formatName</span> <span class="o">=</span> <span class="s">u&#39;Neutron SXD TOF HKL F</span><span class="se">\u00b2</span><span class="s">&#39;</span>
501            <span class="n">longFormatName</span> <span class="o">=</span> <span class="s">u&#39;Neutron SXD TOF [hkl, Fo</span><span class="se">\u00b2</span><span class="s">, sig(Fo</span><span class="se">\u00b2</span><span class="s">),...] Structure factor text file&#39;</span>
502        <span class="nb">super</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">__class__</span><span class="p">,</span><span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span> <span class="c"># fancy way to self-reference</span>
503            <span class="n">extensionlist</span><span class="o">=</span><span class="p">(</span><span class="s">&#39;.int&#39;</span><span class="p">,</span><span class="s">&#39;.INT&#39;</span><span class="p">),</span>
504            <span class="n">strictExtension</span><span class="o">=</span><span class="bp">False</span><span class="p">,</span>
505            <span class="n">formatName</span><span class="o">=</span><span class="n">formatName</span><span class="p">,</span>
506            <span class="n">longFormatName</span><span class="o">=</span><span class="n">longFormatName</span><span class="p">)</span>
507
508<div class="viewcode-block" id="ISIS_SXD_INT_ReaderClass.ContentsValidator"><a class="viewcode-back" href="../imports.html#G2sfact.ISIS_SXD_INT_ReaderClass.ContentsValidator">[docs]</a>    <span class="k">def</span> <span class="nf">ContentsValidator</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filepointer</span><span class="p">):</span>
509        <span class="s">&#39;Make sure file contains the expected columns on numbers &amp; count number of data blocks - &quot;Banks&quot;&#39;</span>
510        <span class="n">oldNo</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
511        <span class="k">for</span> <span class="n">line</span><span class="p">,</span><span class="n">S</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">filepointer</span><span class="p">):</span>
512            <span class="k">if</span> <span class="ow">not</span> <span class="n">S</span><span class="p">:</span>   <span class="c">#empty line terminates read</span>
513                <span class="k">break</span>
514            <span class="k">if</span> <span class="n">S</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;#&#39;</span><span class="p">:</span> <span class="k">continue</span>       <span class="c">#ignore comments, if any</span>
515            <span class="k">if</span> <span class="n">S</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;(&#39;</span><span class="p">:</span> <span class="k">continue</span>        <span class="c">#ignore format line</span>
516            <span class="n">bankNo</span> <span class="o">=</span> <span class="n">S</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">5</span><span class="p">]</span>
517            <span class="k">if</span> <span class="n">bankNo</span> <span class="o">!=</span> <span class="n">oldNo</span><span class="p">:</span>
518                <span class="bp">self</span><span class="o">.</span><span class="n">Banks</span><span class="o">.</span><span class="n">append</span><span class="p">({</span><span class="s">&#39;RefDict&#39;</span><span class="p">:{</span><span class="s">&#39;RefList&#39;</span><span class="p">:[],}})</span>
519                <span class="n">oldNo</span> <span class="o">=</span> <span class="n">bankNo</span>
520        <span class="n">filepointer</span><span class="o">.</span><span class="n">seek</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
521        <span class="k">return</span> <span class="n">ColumnValidator</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filepointer</span><span class="p">,</span><span class="n">nCol</span><span class="o">=</span><span class="mi">8</span><span class="p">)</span>
522</div>
523<div class="viewcode-block" id="ISIS_SXD_INT_ReaderClass.Reader"><a class="viewcode-back" href="../imports.html#G2sfact.ISIS_SXD_INT_ReaderClass.Reader">[docs]</a>    <span class="k">def</span> <span class="nf">Reader</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">filename</span><span class="p">,</span><span class="n">filepointer</span><span class="p">,</span> <span class="n">ParentFrame</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="o">**</span><span class="n">unused</span><span class="p">):</span>
524        <span class="s">&#39;Read the file&#39;</span>
525        <span class="n">filepointer</span><span class="o">.</span><span class="n">seek</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
526        <span class="k">try</span><span class="p">:</span>
527            <span class="k">for</span> <span class="n">line</span><span class="p">,</span><span class="n">S</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">filepointer</span><span class="p">):</span>
528                <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">=</span> <span class="s">&#39;  Error reading line &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">line</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span>
529                <span class="k">if</span> <span class="n">S</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;#&#39;</span><span class="p">:</span> <span class="k">continue</span>       <span class="c">#ignore comments, if any</span>
530                <span class="k">if</span> <span class="n">S</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;(&#39;</span><span class="p">:</span> <span class="k">continue</span>        <span class="c">#ignore the format line</span>
531                <span class="n">data</span> <span class="o">=</span> <span class="n">S</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
532                <span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span><span class="n">Fo</span><span class="p">,</span><span class="n">sigFo</span><span class="p">,</span><span class="n">bN</span><span class="p">,</span><span class="n">wave</span><span class="p">,</span><span class="n">x</span><span class="p">,</span><span class="n">x</span><span class="p">,</span><span class="n">tbar</span> <span class="o">=</span> <span class="n">data</span><span class="p">[:</span><span class="mi">10</span><span class="p">]</span>                   
533                <span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span> <span class="o">=</span> <span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">h</span><span class="p">),</span><span class="nb">int</span><span class="p">(</span><span class="n">k</span><span class="p">),</span><span class="nb">int</span><span class="p">(</span><span class="n">l</span><span class="p">)]</span>
534                <span class="k">if</span> <span class="ow">not</span> <span class="nb">any</span><span class="p">([</span><span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">]):</span>
535                    <span class="k">break</span>
536                <span class="n">Fo</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">Fo</span><span class="p">)</span>
537                <span class="n">sigFo</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">sigFo</span><span class="p">)</span>
538                <span class="n">wave</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">wave</span><span class="p">)</span>
539                <span class="n">tbar</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">tbar</span><span class="p">)</span>
540                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">Banks</span><span class="p">):</span>
541                    <span class="bp">self</span><span class="o">.</span><span class="n">Banks</span><span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">bN</span><span class="p">)</span><span class="o">-</span><span class="mi">1</span><span class="p">][</span><span class="s">&#39;RefDict&#39;</span><span class="p">][</span><span class="s">&#39;RefList&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span><span class="mi">1</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">Fo</span><span class="p">,</span><span class="n">sigFo</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">Fo</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">wave</span><span class="p">,</span><span class="n">tbar</span><span class="p">])</span>
542                <span class="k">else</span><span class="p">:</span>
543                <span class="c"># h,k,l,m,dsp,Fo2,sig,Fc2,Fot2,Fct2,phase,...</span>
544                    <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;RefList&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">h</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">l</span><span class="p">,</span><span class="mi">1</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">Fo</span><span class="p">,</span><span class="n">sigFo</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">Fo</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">wave</span><span class="p">,</span><span class="n">tbar</span><span class="p">])</span>
545            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">Banks</span><span class="p">):</span>
546                <span class="bp">self</span><span class="o">.</span><span class="n">UpdateParameters</span><span class="p">(</span><span class="n">Type</span><span class="o">=</span><span class="s">&#39;SNT&#39;</span><span class="p">,</span><span class="n">Wave</span><span class="o">=</span><span class="bp">None</span><span class="p">)</span> <span class="c"># histogram type</span>
547                <span class="k">for</span> <span class="n">Bank</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">Banks</span><span class="p">:</span>
548                    <span class="n">Bank</span><span class="p">[</span><span class="s">&#39;RefDict&#39;</span><span class="p">][</span><span class="s">&#39;RefList&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">Bank</span><span class="p">[</span><span class="s">&#39;RefDict&#39;</span><span class="p">][</span><span class="s">&#39;RefList&#39;</span><span class="p">])</span>
549                    <span class="n">Bank</span><span class="p">[</span><span class="s">&#39;RefDict&#39;</span><span class="p">][</span><span class="s">&#39;Type&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s">&#39;SNT&#39;</span>                   
550                    <span class="n">Bank</span><span class="p">[</span><span class="s">&#39;RefDict&#39;</span><span class="p">][</span><span class="s">&#39;Super&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>
551            <span class="k">else</span><span class="p">:</span>
552                <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;RefList&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;RefList&#39;</span><span class="p">])</span>
553                <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;Type&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s">&#39;SNT&#39;</span>
554                <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span><span class="p">[</span><span class="s">&#39;Super&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>
555                <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">=</span> <span class="s">&#39;Error after reading reflections (unexpected!)&#39;</span>
556                <span class="bp">self</span><span class="o">.</span><span class="n">UpdateParameters</span><span class="p">(</span><span class="n">Type</span><span class="o">=</span><span class="s">&#39;SNT&#39;</span><span class="p">,</span><span class="n">Wave</span><span class="o">=</span><span class="bp">None</span><span class="p">)</span> <span class="c"># histogram type</span>
557            <span class="k">return</span> <span class="bp">True</span>
558        <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">detail</span><span class="p">:</span>
559            <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">+=</span> <span class="s">&#39;</span><span class="se">\n</span><span class="s">  &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">detail</span><span class="p">)</span>
560            <span class="k">print</span> <span class="s">&#39;</span><span class="se">\n\n</span><span class="s">&#39;</span><span class="o">+</span><span class="bp">self</span><span class="o">.</span><span class="n">formatName</span><span class="o">+</span><span class="s">&#39; read error: &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">detail</span><span class="p">)</span> <span class="c"># for testing</span>
561            <span class="kn">import</span> <span class="nn">traceback</span>
562            <span class="n">traceback</span><span class="o">.</span><span class="n">print_exc</span><span class="p">(</span><span class="nb">file</span><span class="o">=</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">)</span>
563            <span class="k">return</span> <span class="bp">False</span>
564</pre></div></div></div>
565
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