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Timestamp:
Oct 10, 2015 9:59:34 PM (10 years ago)
Author:
toby
Message:

rebuild docs

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  • TabularUnified sphinxdocs/build/html/_modules/GSASII.html

    r1832 r1998  
    5353<span class="c">#GSASII</span>
    5454<span class="c">########### SVN repository information ###################</span>
    55 <span class="c"># $Date: 2015-05-01 18:38:23 -0500 (Fri, 01 May 2015) $</span>
     55<span class="c"># $Date: 2015-10-10 11:58:12 -0500 (Sat, 10 Oct 2015) $</span>
    5656<span class="c"># $Author: toby $</span>
    57 <span class="c"># $Revision: 1831 $</span>
     57<span class="c"># $Revision: 1997 $</span>
    5858<span class="c"># $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/GSASII.py $</span>
    59 <span class="c"># $Id: GSASII.py 1831 2015-05-01 23:38:23Z toby $</span>
     59<span class="c"># $Id: GSASII.py 1997 2015-10-10 16:58:12Z toby $</span>
    6060<span class="c">########### SVN repository information ###################</span>
    6161<span class="sd">&#39;&#39;&#39;</span>
    … …  
    115115<span class="c"># load the GSAS routines</span>
    116116<span class="kn">import</span> <span class="nn">GSASIIpath</span>
    117 <span class="n">GSASIIpath</span><span class="o">.</span><span class="n">SetVersionNumber</span><span class="p">(</span><span class="s">&quot;$Revision: 1831 $&quot;</span><span class="p">)</span>
     117<span class="n">GSASIIpath</span><span class="o">.</span><span class="n">SetVersionNumber</span><span class="p">(</span><span class="s">&quot;$Revision: 1997 $&quot;</span><span class="p">)</span>
    118118<span class="kn">import</span> <span class="nn">GSASIIIO</span> <span class="kn">as</span> <span class="nn">G2IO</span>
    119119<span class="kn">import</span> <span class="nn">GSASIIgrid</span> <span class="kn">as</span> <span class="nn">G2gd</span>
    … …  
    122122<span class="kn">import</span> <span class="nn">GSASIIpwd</span> <span class="kn">as</span> <span class="nn">G2pwd</span>
    123123<span class="kn">import</span> <span class="nn">GSASIIpwdGUI</span> <span class="kn">as</span> <span class="nn">G2pdG</span>
     124<span class="kn">import</span> <span class="nn">GSASIIphsGUI</span> <span class="kn">as</span> <span class="nn">G2phsG</span>
    124125<span class="kn">import</span> <span class="nn">GSASIIspc</span> <span class="kn">as</span> <span class="nn">G2spc</span>
    125126<span class="kn">import</span> <span class="nn">GSASIIstrMain</span> <span class="kn">as</span> <span class="nn">G2stMn</span>
    … …  
    145146            <span class="s">&#39;Babinet&#39;</span><span class="p">:{</span><span class="s">&#39;BabA&#39;</span><span class="p">:[</span><span class="mf">0.0</span><span class="p">,</span><span class="bp">False</span><span class="p">],</span><span class="s">&#39;BabU&#39;</span><span class="p">:[</span><span class="mf">0.0</span><span class="p">,</span><span class="bp">False</span><span class="p">]},</span>
    146147            <span class="s">&#39;Extinction&#39;</span><span class="p">:[</span><span class="s">&#39;Lorentzian&#39;</span><span class="p">,</span><span class="s">&#39;None&#39;</span><span class="p">,</span> <span class="p">{</span><span class="s">&#39;Tbar&#39;</span><span class="p">:</span><span class="mf">0.1</span><span class="p">,</span><span class="s">&#39;Cos2TM&#39;</span><span class="p">:</span><span class="mf">0.955</span><span class="p">,</span>
    147             <span class="s">&#39;Eg&#39;</span><span class="p">:[</span><span class="mf">1.e-10</span><span class="p">,</span><span class="bp">False</span><span class="p">],</span><span class="s">&#39;Es&#39;</span><span class="p">:[</span><span class="mf">1.e-10</span><span class="p">,</span><span class="bp">False</span><span class="p">],</span><span class="s">&#39;Ep&#39;</span><span class="p">:[</span><span class="mf">1.e-10</span><span class="p">,</span><span class="bp">False</span><span class="p">]}]}</span>
     148            <span class="s">&#39;Eg&#39;</span><span class="p">:[</span><span class="mf">1.e-10</span><span class="p">,</span><span class="bp">False</span><span class="p">],</span><span class="s">&#39;Es&#39;</span><span class="p">:[</span><span class="mf">1.e-10</span><span class="p">,</span><span class="bp">False</span><span class="p">],</span><span class="s">&#39;Ep&#39;</span><span class="p">:[</span><span class="mf">1.e-10</span><span class="p">,</span><span class="bp">False</span><span class="p">]}],</span>
     149            <span class="s">&#39;Flack&#39;</span><span class="p">:[</span><span class="mf">0.0</span><span class="p">,</span><span class="bp">False</span><span class="p">]}</span>
    148150    <span class="k">elif</span> <span class="n">dType</span> <span class="o">==</span> <span class="s">&#39;SNT&#39;</span><span class="p">:</span>
    149151        <span class="k">return</span> <span class="p">{</span><span class="s">&#39;Histogram&#39;</span><span class="p">:</span><span class="n">histoName</span><span class="p">,</span><span class="s">&#39;Show&#39;</span><span class="p">:</span><span class="bp">False</span><span class="p">,</span><span class="s">&#39;Scale&#39;</span><span class="p">:[</span><span class="mf">1.0</span><span class="p">,</span><span class="bp">True</span><span class="p">],</span>
    … …  
    228230            <span class="n">help</span><span class="o">=</span><span class="s">&#39;&#39;</span><span class="p">,</span><span class="nb">id</span><span class="o">=</span><span class="n">wx</span><span class="o">.</span><span class="n">ID_ANY</span><span class="p">,</span>
    229231            <span class="n">kind</span><span class="o">=</span><span class="n">wx</span><span class="o">.</span><span class="n">ITEM_NORMAL</span><span class="p">,</span>
    230             <span class="n">text</span><span class="o">=</span><span class="s">&#39;Add phase&#39;</span><span class="p">)</span>
     232            <span class="n">text</span><span class="o">=</span><span class="s">&#39;Add new phase&#39;</span><span class="p">)</span>
    231233        <span class="bp">self</span><span class="o">.</span><span class="n">Bind</span><span class="p">(</span><span class="n">wx</span><span class="o">.</span><span class="n">EVT_MENU</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">OnAddPhase</span><span class="p">,</span> <span class="nb">id</span><span class="o">=</span><span class="n">item</span><span class="o">.</span><span class="n">GetId</span><span class="p">())</span>
    232234        <span class="n">item</span> <span class="o">=</span> <span class="n">parent</span><span class="o">.</span><span class="n">Append</span><span class="p">(</span>
    … …  
    332334            <span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
    333335                <span class="k">print</span> <span class="s">&#39;Import_&#39;</span><span class="o">+</span><span class="n">errprefix</span><span class="o">+</span><span class="s">&#39;: Attribute Error &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
    334                 <span class="k">pass</span>
    335             <span class="k">except</span> <span class="ne">ImportError</span><span class="p">:</span>
    336                 <span class="k">print</span> <span class="s">&#39;Import_&#39;</span><span class="o">+</span><span class="n">errprefix</span><span class="o">+</span><span class="s">&#39;: Error importing file &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
    337                 <span class="k">pass</span>
     336            <span class="c">#except ImportError:</span>
     337            <span class="c">#    print &#39;Import_&#39;+errprefix+&#39;: Error importing file &#39;+str(filename)</span>
     338            <span class="k">except</span> <span class="ne">Exception</span><span class="p">,</span><span class="n">errmsg</span><span class="p">:</span>
     339                <span class="k">print</span><span class="p">(</span><span class="s">&#39;</span><span class="se">\n</span><span class="s">Import_&#39;</span><span class="o">+</span><span class="n">errprefix</span><span class="o">+</span><span class="s">&#39;: Error importing file &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">filename</span><span class="p">))</span>
     340                <span class="k">print</span><span class="p">(</span><span class="s">&#39;Error message: &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">errmsg</span><span class="p">)</span><span class="o">+</span><span class="s">&#39;</span><span class="se">\n</span><span class="s">&#39;</span><span class="p">)</span>
    338341            <span class="k">if</span> <span class="n">fp</span><span class="p">:</span> <span class="n">fp</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
    339342
    … …  
    745748                            <span class="n">H</span> <span class="o">=</span> <span class="n">hkl</span>
    746749                        <span class="n">ref</span><span class="p">[</span><span class="mi">4</span><span class="o">+</span><span class="n">Super</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="mf">1.</span><span class="o">/</span><span class="n">G2lat</span><span class="o">.</span><span class="n">calc_rDsq2</span><span class="p">(</span><span class="n">H</span><span class="p">,</span><span class="n">G</span><span class="p">))</span>
    747                         <span class="n">iabsnt</span><span class="p">,</span><span class="n">ref</span><span class="p">[</span><span class="mi">3</span><span class="o">+</span><span class="n">Super</span><span class="p">],</span><span class="n">Uniq</span><span class="p">,</span><span class="n">phi</span> <span class="o">=</span> <span class="n">G2spc</span><span class="o">.</span><span class="n">GenHKLf</span><span class="p">(</span><span class="n">H</span><span class="p">,</span><span class="n">SGData</span><span class="p">)</span>
     750                        <span class="n">iabsnt</span> <span class="o">=</span> <span class="n">G2spc</span><span class="o">.</span><span class="n">GenHKLf</span><span class="p">(</span><span class="n">H</span><span class="p">,</span><span class="n">SGData</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
    748751                        <span class="k">if</span> <span class="n">iabsnt</span><span class="p">:</span>  <span class="c">#flag space gp. absences</span>
    749                             <span class="n">ref</span><span class="p">[</span><span class="mi">3</span><span class="o">+</span><span class="n">Super</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>
     752                            <span class="k">if</span> <span class="n">Super</span><span class="p">:</span>
     753                                <span class="k">if</span> <span class="ow">not</span> <span class="n">ref</span><span class="p">[</span><span class="mi">2</span><span class="o">+</span><span class="n">Super</span><span class="p">]:</span>
     754                                    <span class="n">ref</span><span class="p">[</span><span class="mi">3</span><span class="o">+</span><span class="n">Super</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>
     755                                <span class="k">else</span><span class="p">:</span>
     756                                    <span class="n">ref</span><span class="p">[</span><span class="mi">3</span><span class="o">+</span><span class="n">Super</span><span class="p">]</span> <span class="o">=</span> <span class="mi">1</span>    <span class="c">#twin id?</span>
     757                            <span class="k">else</span><span class="p">:</span>
     758                                <span class="n">ref</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>
    750759                    <span class="n">UseList</span><span class="p">[</span><span class="n">histoName</span><span class="p">]</span> <span class="o">=</span> <span class="n">SetDefaultDData</span><span class="p">(</span><span class="n">reflData</span><span class="p">[</span><span class="s">&#39;Type&#39;</span><span class="p">],</span><span class="n">histoName</span><span class="p">)</span>
    751760                <span class="k">elif</span> <span class="n">histoName</span> <span class="ow">in</span> <span class="n">PWDRlist</span><span class="p">:</span>
    … …  
    753762                    <span class="n">refList</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">GetItemPyData</span><span class="p">(</span>
    754763                        <span class="n">G2gd</span><span class="o">.</span><span class="n">GetPatternTreeItemId</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">Id</span><span class="p">,</span><span class="s">&#39;Reflection Lists&#39;</span><span class="p">))</span>
    755                     <span class="n">refList</span><span class="p">[</span><span class="n">generalData</span><span class="p">[</span><span class="s">&#39;Name&#39;</span><span class="p">]]</span> <span class="o">=</span> <span class="p">[]</span>
     764                    <span class="n">refList</span><span class="p">[</span><span class="n">generalData</span><span class="p">[</span><span class="s">&#39;Name&#39;</span><span class="p">]]</span> <span class="o">=</span> <span class="p">{}</span>
    756765                    <span class="n">UseList</span><span class="p">[</span><span class="n">histoName</span><span class="p">]</span> <span class="o">=</span> <span class="n">SetDefaultDData</span><span class="p">(</span><span class="s">&#39;PWDR&#39;</span><span class="p">,</span><span class="n">histoName</span><span class="p">,</span><span class="n">NShkl</span><span class="o">=</span><span class="n">NShkl</span><span class="p">,</span><span class="n">NDij</span><span class="o">=</span><span class="n">NDij</span><span class="p">)</span>
    757766                <span class="k">else</span><span class="p">:</span>
    … …  
    826835                    <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">SetItemPyData</span><span class="p">(</span><span class="n">Sub</span><span class="p">,</span><span class="n">copy</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="n">rd</span><span class="o">.</span><span class="n">Parameters</span><span class="p">))</span>
    827836                    <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">SetItemPyData</span><span class="p">(</span>
    828                         <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">AppendItem</span><span class="p">(</span><span class="n">Id</span><span class="p">,</span><span class="n">text</span><span class="o">=</span><span class="s">&#39;Reflection List&#39;</span><span class="p">),[])</span>  <span class="c">#dummy entry for GUI use</span>
     837                        <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">AppendItem</span><span class="p">(</span><span class="n">Id</span><span class="p">,</span><span class="n">text</span><span class="o">=</span><span class="s">&#39;Reflection List&#39;</span><span class="p">),{})</span>  <span class="c">#dummy entry for GUI use</span>
    829838                    <span class="n">newHistList</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">HistName</span><span class="p">)</span>
    830839            <span class="k">else</span><span class="p">:</span>
    … …  
    839848                <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">SetItemPyData</span><span class="p">(</span><span class="n">Sub</span><span class="p">,</span><span class="n">rd</span><span class="o">.</span><span class="n">Parameters</span><span class="p">)</span>
    840849                <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">SetItemPyData</span><span class="p">(</span>
    841                     <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">AppendItem</span><span class="p">(</span><span class="n">Id</span><span class="p">,</span><span class="n">text</span><span class="o">=</span><span class="s">&#39;Reflection List&#39;</span><span class="p">),[])</span>  <span class="c">#dummy entry for GUI use</span>
     850                    <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">AppendItem</span><span class="p">(</span><span class="n">Id</span><span class="p">,</span><span class="n">text</span><span class="o">=</span><span class="s">&#39;Reflection List&#39;</span><span class="p">),{})</span>  <span class="c">#dummy entry for GUI use</span>
    842851                <span class="n">newHistList</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">HistName</span><span class="p">)</span>
    843852               
    … …  
    882891                <span class="n">UseList</span><span class="p">[</span><span class="n">histoName</span><span class="p">]</span> <span class="o">=</span> <span class="n">SetDefaultDData</span><span class="p">(</span><span class="n">reflData</span><span class="p">[</span><span class="s">&#39;Type&#39;</span><span class="p">],</span><span class="n">histoName</span><span class="p">)</span>
    883892                <span class="n">G</span><span class="p">,</span><span class="n">g</span> <span class="o">=</span> <span class="n">G2lat</span><span class="o">.</span><span class="n">cell2Gmat</span><span class="p">(</span><span class="n">generalData</span><span class="p">[</span><span class="s">&#39;Cell&#39;</span><span class="p">][</span><span class="mi">1</span><span class="p">:</span><span class="mi">7</span><span class="p">])</span>
     893                <span class="k">if</span> <span class="s">&#39;TwMax&#39;</span> <span class="ow">in</span> <span class="n">reflData</span><span class="p">:</span>     <span class="c">#nonmerohedral twins present</span>
     894                    <span class="n">UseList</span><span class="p">[</span><span class="n">histoName</span><span class="p">][</span><span class="s">&#39;Twins&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
     895                    <span class="k">for</span> <span class="n">iT</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">reflData</span><span class="p">[</span><span class="s">&#39;TwMax&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="mi">1</span><span class="p">):</span>
     896                        <span class="k">if</span> <span class="n">iT</span> <span class="ow">in</span> <span class="n">reflData</span><span class="p">[</span><span class="s">&#39;TwMax&#39;</span><span class="p">][</span><span class="mi">1</span><span class="p">]:</span>
     897                            <span class="n">UseList</span><span class="p">[</span><span class="n">histoName</span><span class="p">][</span><span class="s">&#39;Twins&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="bp">False</span><span class="p">,</span><span class="mf">0.0</span><span class="p">])</span>
     898                        <span class="k">else</span><span class="p">:</span>
     899                            <span class="n">UseList</span><span class="p">[</span><span class="n">histoName</span><span class="p">][</span><span class="s">&#39;Twins&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">np</span><span class="o">.</span><span class="n">array</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="mi">0</span><span class="p">],[</span><span class="mi">0</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="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">1</span><span class="p">]]),[</span><span class="mf">1.0</span><span class="p">,</span><span class="bp">False</span><span class="p">,</span><span class="n">reflData</span><span class="p">[</span><span class="s">&#39;TwMax&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">]]])</span>
     900                <span class="k">else</span><span class="p">:</span>   <span class="c">#no nonmerohedral twins</span>
     901                    <span class="n">UseList</span><span class="p">[</span><span class="n">histoName</span><span class="p">][</span><span class="s">&#39;Twins&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[[</span><span class="n">np</span><span class="o">.</span><span class="n">array</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="mi">0</span><span class="p">],[</span><span class="mi">0</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="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">1</span><span class="p">]]),[</span><span class="mf">1.0</span><span class="p">,</span><span class="bp">False</span><span class="p">,</span><span class="mi">0</span><span class="p">]],]</span>
    884902                <span class="k">for</span> <span class="n">iref</span><span class="p">,</span><span class="n">ref</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">reflData</span><span class="p">[</span><span class="s">&#39;RefList&#39;</span><span class="p">]):</span>
    885903                    <span class="n">hkl</span> <span class="o">=</span> <span class="n">ref</span><span class="p">[:</span><span class="mi">3</span><span class="p">]</span>
    … …  
    889907                        <span class="n">H</span> <span class="o">=</span> <span class="n">hkl</span>
    890908                    <span class="n">ref</span><span class="p">[</span><span class="mi">4</span><span class="o">+</span><span class="n">Super</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="mf">1.</span><span class="o">/</span><span class="n">G2lat</span><span class="o">.</span><span class="n">calc_rDsq2</span><span class="p">(</span><span class="n">H</span><span class="p">,</span><span class="n">G</span><span class="p">))</span>
    891                     <span class="n">iabsnt</span><span class="p">,</span><span class="n">ref</span><span class="p">[</span><span class="mi">3</span><span class="o">+</span><span class="n">Super</span><span class="p">],</span><span class="n">Uniq</span><span class="p">,</span><span class="n">phi</span> <span class="o">=</span> <span class="n">G2spc</span><span class="o">.</span><span class="n">GenHKLf</span><span class="p">(</span><span class="n">H</span><span class="p">,</span><span class="n">SGData</span><span class="p">)</span>
     909                    <span class="n">iabsnt</span><span class="p">,</span><span class="n">mul</span><span class="p">,</span><span class="n">Uniq</span><span class="p">,</span><span class="n">phi</span> <span class="o">=</span> <span class="n">G2spc</span><span class="o">.</span><span class="n">GenHKLf</span><span class="p">(</span><span class="n">H</span><span class="p">,</span><span class="n">SGData</span><span class="p">)</span>
    892910                    <span class="k">if</span> <span class="n">iabsnt</span><span class="p">:</span>  <span class="c">#flag space gp. absences</span>
    893                         <span class="n">ref</span><span class="p">[</span><span class="mi">3</span><span class="o">+</span><span class="n">Super</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>
     911                        <span class="k">if</span> <span class="n">Super</span><span class="p">:</span>
     912                            <span class="k">if</span> <span class="ow">not</span> <span class="n">ref</span><span class="p">[</span><span class="mi">2</span><span class="o">+</span><span class="n">Super</span><span class="p">]:</span>
     913                                <span class="n">ref</span><span class="p">[</span><span class="mi">3</span><span class="o">+</span><span class="n">Super</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>
     914                            <span class="k">else</span><span class="p">:</span>
     915                                <span class="n">ref</span><span class="p">[</span><span class="mi">3</span><span class="o">+</span><span class="n">Super</span><span class="p">]</span> <span class="o">=</span> <span class="mi">1</span>    <span class="c">#twin id?</span>
     916                        <span class="k">else</span><span class="p">:</span>
     917                            <span class="n">ref</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>
    894918        <span class="n">wx</span><span class="o">.</span><span class="n">EndBusyCursor</span><span class="p">()</span>
    895919       
    … …  
    13761400                <span class="n">rd</span><span class="o">.</span><span class="n">powderdata</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">rd</span><span class="o">.</span><span class="n">powderdata</span><span class="p">[</span><span class="mi">0</span><span class="p">][:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">+</span><span class="n">cw</span><span class="o">/</span><span class="mf">2.</span>
    13771401                <span class="k">if</span> <span class="n">rd</span><span class="o">.</span><span class="n">GSAS</span><span class="p">:</span>     <span class="c">#NB: old GSAS wanted intensities*CW even if normalized!</span>
    1378                     <span class="n">rd</span><span class="o">.</span><span class="n">powderdata</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">rd</span><span class="o">.</span><span class="n">powderdata</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">/</span><span class="n">cw</span><span class="p">[:</span><span class="nb">len</span><span class="p">(</span><span class="n">rd</span><span class="o">.</span><span class="n">powderdata</span><span class="p">[</span><span class="mi">1</span><span class="p">])]</span>
    1379                     <span class="n">rd</span><span class="o">.</span><span class="n">powderdata</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="n">rd</span><span class="o">.</span><span class="n">powderdata</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">*</span><span class="n">cw</span><span class="p">[:</span><span class="nb">len</span><span class="p">(</span><span class="n">rd</span><span class="o">.</span><span class="n">powderdata</span><span class="p">[</span><span class="mi">1</span><span class="p">])]</span><span class="o">**</span><span class="mi">2</span>  <span class="c">#1/var=w at this point</span>
     1402                    <span class="n">npts</span> <span class="o">=</span> <span class="nb">min</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">rd</span><span class="o">.</span><span class="n">powderdata</span><span class="p">[</span><span class="mi">0</span><span class="p">]),</span><span class="nb">len</span><span class="p">(</span><span class="n">rd</span><span class="o">.</span><span class="n">powderdata</span><span class="p">[</span><span class="mi">1</span><span class="p">]),</span><span class="nb">len</span><span class="p">(</span><span class="n">cw</span><span class="p">))</span>
     1403                    <span class="n">rd</span><span class="o">.</span><span class="n">powderdata</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">rd</span><span class="o">.</span><span class="n">powderdata</span><span class="p">[</span><span class="mi">1</span><span class="p">][:</span><span class="n">npts</span><span class="p">]</span><span class="o">/</span><span class="n">cw</span><span class="p">[:</span><span class="n">npts</span><span class="p">]</span>
     1404                    <span class="n">rd</span><span class="o">.</span><span class="n">powderdata</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="n">rd</span><span class="o">.</span><span class="n">powderdata</span><span class="p">[</span><span class="mi">2</span><span class="p">][:</span><span class="n">npts</span><span class="p">]</span><span class="o">*</span><span class="n">cw</span><span class="p">[:</span><span class="n">npts</span><span class="p">]</span><span class="o">**</span><span class="mi">2</span>  <span class="c">#1/var=w at this point</span>
    13801405                <span class="k">else</span><span class="p">:</span>       <span class="c">#NB: from topas/fullprof type files</span>
    13811406                    <span class="n">rd</span><span class="o">.</span><span class="n">powderdata</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">rd</span><span class="o">.</span><span class="n">powderdata</span><span class="p">[</span><span class="mi">1</span><span class="p">][:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
    … …  
    16441669            <span class="n">refList</span><span class="p">[</span><span class="n">generalData</span><span class="p">[</span><span class="s">&#39;Name&#39;</span><span class="p">]]</span> <span class="o">=</span> <span class="p">[]</span>
    16451670        <span class="k">return</span> <span class="c"># success</span>
     1671        </div>
     1672<div class="viewcode-block" id="GSASII.OnPreferences"><a class="viewcode-back" href="../GSASII.html#GSASII.GSASII.OnPreferences">[docs]</a>    <span class="k">def</span> <span class="nf">OnPreferences</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">event</span><span class="p">):</span>
     1673        <span class="s">&#39;Edit the GSAS-II configuration variables&#39;</span>
     1674        <span class="n">dlg</span> <span class="o">=</span> <span class="n">G2G</span><span class="o">.</span><span class="n">SelectConfigSetting</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
     1675        <span class="n">dlg</span><span class="o">.</span><span class="n">ShowModal</span><span class="p">()</span> <span class="o">==</span> <span class="n">wx</span><span class="o">.</span><span class="n">ID_OK</span>
     1676        <span class="n">dlg</span><span class="o">.</span><span class="n">Destroy</span><span class="p">()</span>
    16461677</div>
    16471678    <span class="k">def</span> <span class="nf">_Add_ImportMenu_smallangle</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">parent</span><span class="p">):</span>
    … …  
    19211952                <span class="n">filelist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>   
    19221953        <span class="n">filelist</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">filelist</span><span class="p">)))</span> <span class="c"># remove duplicates</span>
    1923         <span class="n">exporterlist</span> <span class="o">=</span> <span class="p">[]</span>
     1954        <span class="bp">self</span><span class="o">.</span><span class="n">exporterlist</span> <span class="o">=</span> <span class="p">[]</span>
    19241955        <span class="c"># go through the routines and import them, saving objects that</span>
    19251956        <span class="c"># have export routines (method Exporter)</span>
    … …  
    19401971                        <span class="k">else</span><span class="p">:</span>
    19411972                            <span class="n">exporter</span> <span class="o">=</span> <span class="n">clss</span><span class="p">[</span><span class="mi">1</span><span class="p">](</span><span class="bp">self</span><span class="p">)</span> <span class="c"># create an export instance</span>
    1942                             <span class="n">exporterlist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">exporter</span><span class="p">)</span>
     1973                            <span class="bp">self</span><span class="o">.</span><span class="n">exporterlist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">exporter</span><span class="p">)</span>
    19431974            <span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
    19441975                <span class="k">print</span> <span class="s">&#39;Import_&#39;</span><span class="o">+</span><span class="n">errprefix</span><span class="o">+</span><span class="s">&#39;: Attribute Error&#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
    … …  
    19491980            <span class="k">if</span> <span class="n">fp</span><span class="p">:</span> <span class="n">fp</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
    19501981        <span class="c"># Add submenu item(s) for each Exporter by its self-declared type (can be more than one)</span>
    1951         <span class="k">for</span> <span class="n">obj</span> <span class="ow">in</span> <span class="n">exporterlist</span><span class="p">:</span>
     1982        <span class="k">for</span> <span class="n">obj</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">exporterlist</span><span class="p">:</span>
    19521983            <span class="c">#print &#39;exporter&#39;,obj</span>
    19531984            <span class="k">for</span> <span class="n">typ</span> <span class="ow">in</span> <span class="n">obj</span><span class="o">.</span><span class="n">exporttype</span><span class="p">:</span>
    … …  
    20442075        <span class="bp">self</span><span class="o">.</span><span class="n">_Add_ImportMenu_Sfact</span><span class="p">(</span><span class="n">Import</span><span class="p">)</span>
    20452076        <span class="bp">self</span><span class="o">.</span><span class="n">_Add_ImportMenu_smallangle</span><span class="p">(</span><span class="n">Import</span><span class="p">)</span>
     2077        <span class="n">item</span> <span class="o">=</span> <span class="n">File</span><span class="o">.</span><span class="n">Append</span><span class="p">(</span><span class="n">wx</span><span class="o">.</span><span class="n">ID_PREFERENCES</span><span class="p">,</span> <span class="n">text</span> <span class="o">=</span> <span class="s">&quot;&amp;Preferences&quot;</span><span class="p">)</span>
     2078        <span class="bp">self</span><span class="o">.</span><span class="n">Bind</span><span class="p">(</span><span class="n">wx</span><span class="o">.</span><span class="n">EVT_MENU</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">OnPreferences</span><span class="p">,</span> <span class="n">item</span><span class="p">)</span>
     2079
    20462080        <span class="c">#======================================================================</span>
    20472081        <span class="c"># Code to help develop/debug an importer, much is hard-coded below</span>
    … …  
    23732407        <span class="n">dlg</span> <span class="o">=</span> <span class="n">wx</span><span class="o">.</span><span class="n">FileDialog</span><span class="p">(</span>
    23742408            <span class="bp">self</span><span class="p">,</span> <span class="s">&#39;Choose image files&#39;</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>
    2375             <span class="s">&#39;Any supported image file (*.edf;*.tif;*.tiff;*.mar*;*.ge*;*.avg;*.sum;*.img;*.G2img;*.png)|&#39;</span>
    2376             <span class="s">&#39;*.edf;*.tif;*.tiff;*.mar*;*.ge*;*.avg;*.sum;*.img;*.G2img;*.png;*.zip|&#39;</span>
     2409            <span class="s">&#39;Any supported image file (*.edf;*.tif;*.tiff;*.mar*;*.ge*;*.avg;*.sum;*.img;*.stl;*.G2img;*.png)|&#39;</span>
     2410            <span class="s">&#39;*.edf;*.tif;*.tiff;*.mar*;*.ge*;*.avg;*.sum;*.img;*.stl;*.G2img;*.png;*.zip|&#39;</span>
    23772411            <span class="s">&#39;European detector file (*.edf)|*.edf|&#39;</span>
    23782412            <span class="s">&#39;Any detector tif (*.tif;*.tiff)|*.tif;*.tiff|&#39;</span>
    … …  
    23802414            <span class="s">&#39;GE Image (*.ge*;*.avg;*.sum)|*.ge*;*.avg;*.sum|&#39;</span>
    23812415            <span class="s">&#39;ADSC Image (*.img)|*.img|&#39;</span>
     2416            <span class="s">&#39;Rigaku R-Axis IV (*.stl)|*.stl|&#39;</span>
    23822417            <span class="s">&#39;GSAS-II Image (*.G2img)|*.G2img|&#39;</span>
    23832418            <span class="s">&#39;Portable Network Graphics image (*.png)|*.png|&#39;</span>
    … …  
    23902425                <span class="n">imagefiles</span><span class="o">.</span><span class="n">sort</span><span class="p">()</span>
    23912426                <span class="k">for</span> <span class="n">imagefile</span> <span class="ow">in</span> <span class="n">imagefiles</span><span class="p">:</span>
    2392                     <span class="c"># if a zip file, open and extract</span>
    2393                     <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">imagefile</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s">&#39;.zip&#39;</span><span class="p">:</span>
    2394                         <span class="n">extractedfile</span> <span class="o">=</span> <span class="n">G2IO</span><span class="o">.</span><span class="n">ExtractFileFromZip</span><span class="p">(</span><span class="n">imagefile</span><span class="p">,</span><span class="n">parent</span><span class="o">=</span><span class="bp">self</span><span class="p">)</span>
    2395                         <span class="k">if</span> <span class="n">extractedfile</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span> <span class="ow">and</span> <span class="n">extractedfile</span> <span class="o">!=</span> <span class="n">imagefile</span><span class="p">:</span>
    2396                             <span class="n">imagefile</span> <span class="o">=</span> <span class="n">extractedfile</span>
    2397                     <span class="n">Comments</span><span class="p">,</span><span class="n">Data</span><span class="p">,</span><span class="n">Npix</span><span class="p">,</span><span class="n">Image</span> <span class="o">=</span> <span class="n">G2IO</span><span class="o">.</span><span class="n">GetImageData</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">imagefile</span><span class="p">)</span>
    2398                     <span class="k">if</span> <span class="n">Comments</span><span class="p">:</span>
    2399                         <span class="n">Id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">AppendItem</span><span class="p">(</span><span class="n">parent</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">root</span><span class="p">,</span><span class="n">text</span><span class="o">=</span><span class="s">&#39;IMG &#39;</span><span class="o">+</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">imagefile</span><span class="p">))</span>
    2400                         <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">SetItemPyData</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">AppendItem</span><span class="p">(</span><span class="n">Id</span><span class="p">,</span><span class="n">text</span><span class="o">=</span><span class="s">&#39;Comments&#39;</span><span class="p">),</span><span class="n">Comments</span><span class="p">)</span>
    2401                         <span class="n">Imax</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">amax</span><span class="p">(</span><span class="n">Image</span><span class="p">)</span>
    2402                         <span class="n">Imin</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span><span class="n">np</span><span class="o">.</span><span class="n">amin</span><span class="p">(</span><span class="n">Image</span><span class="p">))</span>          <span class="c">#force positive</span>
    2403                         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">imageDefault</span><span class="p">:</span>
    2404                             <span class="n">Data</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">imageDefault</span><span class="p">)</span>
    2405                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;showLines&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">True</span>
    2406                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;ring&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
    2407                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;rings&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
    2408                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;cutoff&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">10</span>
    2409                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;pixLimit&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">20</span>
    2410                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;edgemin&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">100000000</span>
    2411                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;calibdmin&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mf">0.5</span>
    2412                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;calibskip&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>
    2413                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;ellipses&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
    2414                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;calibrant&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s">&#39;&#39;</span>
    2415                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;GonioAngles&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mf">0.</span><span class="p">,</span><span class="mf">0.</span><span class="p">,</span><span class="mf">0.</span><span class="p">]</span>
    2416                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;DetDepthRef&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">False</span>
    2417                         <span class="k">else</span><span class="p">:</span>
    2418                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;type&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s">&#39;PWDR&#39;</span>
    2419                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;color&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s">&#39;Paired&#39;</span>
    2420                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;tilt&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mf">0.0</span>
    2421                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;rotation&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mf">0.0</span>
    2422                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;showLines&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">False</span>
    2423                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;ring&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
    2424                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;rings&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
    2425                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;cutoff&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">10</span>
    2426                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;pixLimit&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">20</span>
    2427                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;calibdmin&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mf">0.5</span>
    2428                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;calibskip&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>
    2429                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;edgemin&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">100000000</span>
    2430                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;ellipses&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
    2431                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;GonioAngles&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mf">0.</span><span class="p">,</span><span class="mf">0.</span><span class="p">,</span><span class="mf">0.</span><span class="p">]</span>
    2432                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;DetDepth&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mf">0.</span>
    2433                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;DetDepthRef&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">False</span>
    2434                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;calibrant&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s">&#39;&#39;</span>
    2435                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;IOtth&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mf">2.0</span><span class="p">,</span><span class="mf">5.0</span><span class="p">]</span>
    2436                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;LRazimuth&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mi">135</span><span class="p">,</span><span class="mi">225</span><span class="p">]</span>
    2437                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;azmthOff&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mf">0.0</span>
    2438                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;outChannels&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">2500</span>
    2439                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;outAzimuths&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">1</span>
    2440                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;centerAzm&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">False</span>
    2441                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;fullIntegrate&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">False</span>
    2442                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;setRings&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">False</span>
    2443                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;background image&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="s">&#39;&#39;</span><span class="p">,</span><span class="o">-</span><span class="mf">1.0</span><span class="p">]</span>                           
    2444                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;dark image&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="s">&#39;&#39;</span><span class="p">,</span><span class="o">-</span><span class="mf">1.0</span><span class="p">]</span>
    2445                             <span class="n">Data</span><span class="p">[</span><span class="s">&#39;Flat Bkg&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mf">0.0</span>
    2446                         <span class="n">Data</span><span class="p">[</span><span class="s">&#39;setDefault&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">False</span>
    2447                         <span class="n">Data</span><span class="p">[</span><span class="s">&#39;range&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[(</span><span class="n">Imin</span><span class="p">,</span><span class="n">Imax</span><span class="p">),[</span><span class="n">Imin</span><span class="p">,</span><span class="n">Imax</span><span class="p">]]</span>
    2448                         <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">SetItemPyData</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">AppendItem</span><span class="p">(</span><span class="n">Id</span><span class="p">,</span><span class="n">text</span><span class="o">=</span><span class="s">&#39;Image Controls&#39;</span><span class="p">),</span><span class="n">Data</span><span class="p">)</span>
    2449                         <span class="n">Masks</span> <span class="o">=</span> <span class="p">{</span><span class="s">&#39;Points&#39;</span><span class="p">:[],</span><span class="s">&#39;Rings&#39;</span><span class="p">:[],</span><span class="s">&#39;Arcs&#39;</span><span class="p">:[],</span><span class="s">&#39;Polygons&#39;</span><span class="p">:[],</span><span class="s">&#39;Frames&#39;</span><span class="p">:[],</span><span class="s">&#39;Thresholds&#39;</span><span class="p">:[(</span><span class="n">Imin</span><span class="p">,</span><span class="n">Imax</span><span class="p">),[</span><span class="n">Imin</span><span class="p">,</span><span class="n">Imax</span><span class="p">]]}</span>
    2450                         <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">SetItemPyData</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">AppendItem</span><span class="p">(</span><span class="n">Id</span><span class="p">,</span><span class="n">text</span><span class="o">=</span><span class="s">&#39;Masks&#39;</span><span class="p">),</span><span class="n">Masks</span><span class="p">)</span>
    2451                         <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">SetItemPyData</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">AppendItem</span><span class="p">(</span><span class="n">Id</span><span class="p">,</span><span class="n">text</span><span class="o">=</span><span class="s">&#39;Stress/Strain&#39;</span><span class="p">),</span>
    2452                             <span class="p">{</span><span class="s">&#39;Type&#39;</span><span class="p">:</span><span class="s">&#39;True&#39;</span><span class="p">,</span><span class="s">&#39;d-zero&#39;</span><span class="p">:[],</span><span class="s">&#39;Sample phi&#39;</span><span class="p">:</span><span class="mf">0.0</span><span class="p">,</span><span class="s">&#39;Sample z&#39;</span><span class="p">:</span><span class="mf">0.0</span><span class="p">,</span><span class="s">&#39;Sample load&#39;</span><span class="p">:</span><span class="mf">0.0</span><span class="p">})</span>
    2453                         <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">SetItemPyData</span><span class="p">(</span><span class="n">Id</span><span class="p">,[</span><span class="n">Npix</span><span class="p">,</span><span class="n">imagefile</span><span class="p">])</span>
    2454                         <span class="bp">self</span><span class="o">.</span><span class="n">PickId</span> <span class="o">=</span> <span class="n">Id</span>
    2455                         <span class="bp">self</span><span class="o">.</span><span class="n">PickIdText</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">GetTreeItemsList</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">PickId</span><span class="p">)</span>
    2456                         <span class="bp">self</span><span class="o">.</span><span class="n">Image</span> <span class="o">=</span> <span class="n">Id</span>
    2457                 <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="n">dlg</span><span class="o">.</span><span class="n">GetDirectory</span><span class="p">())</span>           <span class="c"># to get Mac/Linux to change directory!                </span>
    2458                 <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">SelectItem</span><span class="p">(</span><span class="n">G2gd</span><span class="o">.</span><span class="n">GetPatternTreeItemId</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">Id</span><span class="p">,</span><span class="s">&#39;Image Controls&#39;</span><span class="p">))</span>             <span class="c">#show last one</span>
     2427                    <span class="n">G2IO</span><span class="o">.</span><span class="n">ReadLoadImage</span><span class="p">(</span><span class="n">imagefile</span><span class="p">,</span><span class="bp">self</span><span class="p">)</span>
     2428                <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="n">dlg</span><span class="o">.</span><span class="n">GetDirectory</span><span class="p">())</span>           <span class="c"># to get Mac/Linux to change directory!</span>
     2429                <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">SelectItem</span><span class="p">(</span><span class="n">G2gd</span><span class="o">.</span><span class="n">GetPatternTreeItemId</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="bp">self</span><span class="o">.</span><span class="n">Image</span><span class="p">,</span><span class="s">&#39;Image Controls&#39;</span><span class="p">))</span>             <span class="c">#show last image to be read</span>
    24592430        <span class="k">finally</span><span class="p">:</span>
    24602431            <span class="n">path</span> <span class="o">=</span> <span class="n">dlg</span><span class="o">.</span><span class="n">GetDirectory</span><span class="p">()</span>           <span class="c"># to get Mac/Linux to change directory!</span>
    … …  
    24642435<div class="viewcode-block" id="GSASII.CheckNotebook"><a class="viewcode-back" href="../GSASII.html#GSASII.GSASII.CheckNotebook">[docs]</a>    <span class="k">def</span> <span class="nf">CheckNotebook</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
    24652436        <span class="sd">&#39;&#39;&#39;Make sure the data tree has the minimally expected controls.</span>
    2466 <span class="sd">        (BHT) correct?</span>
    24672437<span class="sd">        &#39;&#39;&#39;</span>
    24682438        <span class="k">if</span> <span class="ow">not</span> <span class="n">G2gd</span><span class="o">.</span><span class="n">GetPatternTreeItemId</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="bp">self</span><span class="o">.</span><span class="n">root</span><span class="p">,</span><span class="s">&#39;Notebook&#39;</span><span class="p">):</span>
    … …  
    28772847                                        <span class="k">del</span><span class="p">(</span><span class="n">refList</span><span class="p">[</span><span class="n">item</span><span class="p">])</span>
    28782848                            <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">SetItemPyData</span><span class="p">(</span><span class="n">Id</span><span class="p">,</span><span class="n">refList</span><span class="p">)</span>
     2849                        <span class="k">elif</span> <span class="s">&#39;HKLF&#39;</span> <span class="ow">in</span> <span class="n">name</span><span class="p">:</span>
     2850                            <span class="n">data</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">GetItemPyData</span><span class="p">(</span><span class="n">item</span><span class="p">)</span>
     2851                            <span class="n">data</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
     2852                            <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">SetItemPyData</span><span class="p">(</span><span class="n">item</span><span class="p">,</span><span class="n">data</span><span class="p">)</span>
     2853                           
    28792854                        <span class="n">item</span><span class="p">,</span> <span class="n">cookie</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">GetNextChild</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">root</span><span class="p">,</span> <span class="n">cookie</span><span class="p">)</span>
    28802855            <span class="k">finally</span><span class="p">:</span>
    … …  
    29912966                    <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">DeleteChildren</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">root</span><span class="p">)</span>
    29922967                    <span class="bp">self</span><span class="o">.</span><span class="n">GSASprojectfile</span> <span class="o">=</span> <span class="s">&#39;&#39;</span>
    2993                     <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">HKL</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">HKL</span> <span class="o">=</span> <span class="p">[]</span>
     2968                    <span class="bp">self</span><span class="o">.</span><span class="n">HKL</span> <span class="o">=</span> <span class="p">[]</span>
    29942969                    <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">G2plotNB</span><span class="o">.</span><span class="n">plotList</span><span class="p">:</span>
    29952970                        <span class="bp">self</span><span class="o">.</span><span class="n">G2plotNB</span><span class="o">.</span><span class="n">clear</span><span class="p">()</span>
    … …  
    30773052        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">GSASprojectfile</span><span class="p">:</span>
    30783053            <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">SetItemText</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">root</span><span class="p">,</span><span class="s">&#39;Loaded Data: &#39;</span><span class="o">+</span><span class="bp">self</span><span class="o">.</span><span class="n">GSASprojectfile</span><span class="p">)</span>
     3054            <span class="bp">self</span><span class="o">.</span><span class="n">CheckNotebook</span><span class="p">()</span>
    30793055            <span class="n">G2IO</span><span class="o">.</span><span class="n">ProjFileSave</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
    30803056        <span class="k">else</span><span class="p">:</span>
    … …  
    30933069                <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">SetItemText</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">root</span><span class="p">,</span><span class="s">&#39;Saving project as&#39;</span><span class="o">+</span><span class="bp">self</span><span class="o">.</span><span class="n">GSASprojectfile</span><span class="p">)</span>
    30943070                <span class="bp">self</span><span class="o">.</span><span class="n">SetTitle</span><span class="p">(</span><span class="s">&quot;GSAS-II data tree: &quot;</span><span class="o">+</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">GSASprojectfile</span><span class="p">)[</span><span class="mi">1</span><span class="p">])</span>
     3071                <span class="bp">self</span><span class="o">.</span><span class="n">CheckNotebook</span><span class="p">()</span>
    30953072                <span class="n">G2IO</span><span class="o">.</span><span class="n">ProjFileSave</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
    30963073                <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="n">dlg</span><span class="o">.</span><span class="n">GetDirectory</span><span class="p">())</span>           <span class="c"># to get Mac/Linux to change directory!</span>
    … …  
    31353112                                <span class="k">for</span> <span class="n">peak</span> <span class="ow">in</span> <span class="n">peaks</span><span class="p">:</span>
    31363113                                    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">peak</span><span class="p">)</span> <span class="o">==</span> <span class="mi">8</span><span class="p">:</span>  <span class="c">#CW</span>
    3137                                         <span class="n">FWHM</span> <span class="o">=</span> <span class="n">G2pwd</span><span class="o">.</span><span class="n">getgamFW</span><span class="p">(</span><span class="n">peak</span><span class="p">[</span><span class="mi">6</span><span class="p">],</span><span class="n">peak</span><span class="p">[</span><span class="mi">4</span><span class="p">])</span>
     3114                                        <span class="n">FWHM</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="n">G2pwd</span><span class="o">.</span><span class="n">getgamFW</span><span class="p">(</span><span class="n">peak</span><span class="p">[</span><span class="mi">6</span><span class="p">],</span><span class="n">peak</span><span class="p">[</span><span class="mi">4</span><span class="p">])</span>      <span class="c">#to get delta-2-theta in deg. from Gam(peak)</span>
    31383115                                        <span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">&quot;</span><span class="si">%10.5f</span><span class="s"> </span><span class="si">%12.2f</span><span class="s"> </span><span class="si">%10.5f</span><span class="s"> </span><span class="si">%10.5f</span><span class="s"> </span><span class="si">%10.5f</span><span class="s"> </span><span class="se">\n</span><span class="s">&quot;</span> <span class="o">%</span> \
    31393116                                            <span class="p">(</span><span class="n">peak</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span><span class="n">peak</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span><span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="nb">max</span><span class="p">(</span><span class="mf">0.0001</span><span class="p">,</span><span class="n">peak</span><span class="p">[</span><span class="mi">4</span><span class="p">]))</span><span class="o">/</span><span class="mf">100.</span><span class="p">,</span><span class="n">peak</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span><span class="o">/</span><span class="mf">100.</span><span class="p">,</span><span class="n">FWHM</span><span class="o">/</span><span class="mf">100.</span><span class="p">))</span> <span class="c">#convert to deg</span>
    31403117                                    <span class="k">else</span><span class="p">:</span>               <span class="c">#TOF - more cols</span>
    3141                                         <span class="n">FWHM</span> <span class="o">=</span> <span class="n">G2pwd</span><span class="o">.</span><span class="n">getgamFW</span><span class="p">(</span><span class="n">peak</span><span class="p">[</span><span class="mi">10</span><span class="p">],</span><span class="n">peak</span><span class="p">[</span><span class="mi">8</span><span class="p">])</span>
     3118                                        <span class="n">FWHM</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="n">G2pwd</span><span class="o">.</span><span class="n">getgamFW</span><span class="p">(</span><span class="n">peak</span><span class="p">[</span><span class="mi">10</span><span class="p">],</span><span class="n">peak</span><span class="p">[</span><span class="mi">8</span><span class="p">])</span>      <span class="c">#to get delta-TOF from Gam(peak)</span>
    31423119                                        <span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">&quot;</span><span class="si">%10.5f</span><span class="s"> </span><span class="si">%12.2f</span><span class="s"> </span><span class="si">%10.3f</span><span class="s"> </span><span class="si">%10.3f</span><span class="s"> </span><span class="si">%10.3f</span><span class="s"> </span><span class="si">%10.3f</span><span class="s"> </span><span class="si">%10.3f</span><span class="se">\n</span><span class="s">&quot;</span> <span class="o">%</span> \
    3143                                             <span class="p">(</span><span class="n">peak</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span><span class="n">peak</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span><span class="n">peak</span><span class="p">[</span><span class="mi">4</span><span class="p">],</span><span class="n">peak</span><span class="p">[</span><span class="mi">6</span><span class="p">],</span><span class="n">peak</span><span class="p">[</span><span class="mi">8</span><span class="p">],</span><span class="n">peak</span><span class="p">[</span><span class="mi">10</span><span class="p">],</span><span class="n">FWHM</span><span class="p">))</span>
     3120                                            <span class="p">(</span><span class="n">peak</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span><span class="n">peak</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span><span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="nb">max</span><span class="p">(</span><span class="mf">0.0001</span><span class="p">,</span><span class="n">peak</span><span class="p">[</span><span class="mi">4</span><span class="p">])),</span><span class="n">peak</span><span class="p">[</span><span class="mi">6</span><span class="p">],</span><span class="n">peak</span><span class="p">[</span><span class="mi">8</span><span class="p">],</span><span class="n">peak</span><span class="p">[</span><span class="mi">10</span><span class="p">],</span><span class="n">FWHM</span><span class="p">))</span>
    31443121                            <span class="n">item2</span><span class="p">,</span> <span class="n">cookie2</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">GetNextChild</span><span class="p">(</span><span class="n">item</span><span class="p">,</span> <span class="n">cookie2</span><span class="p">)</span>                           
    31453122                    <span class="n">item</span><span class="p">,</span> <span class="n">cookie</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">GetNextChild</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">root</span><span class="p">,</span> <span class="n">cookie</span><span class="p">)</span>                           
    … …  
    31743151                                        <span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">&#39;</span><span class="si">%s</span><span class="s"> </span><span class="se">\n</span><span class="s">&#39;</span><span class="o">%</span><span class="p">(</span><span class="s">&#39;   h   k   l   m    d-space   2-theta       wid        F**2&#39;</span><span class="p">))</span>
    31753152                                    <span class="k">for</span> <span class="n">peak</span> <span class="ow">in</span> <span class="n">peaks</span><span class="p">[</span><span class="s">&#39;RefList&#39;</span><span class="p">]:</span>
    3176                                         <span class="n">FWHM</span> <span class="o">=</span> <span class="n">G2pwd</span><span class="o">.</span><span class="n">getgamFW</span><span class="p">(</span><span class="n">peak</span><span class="p">[</span><span class="mi">7</span><span class="p">],</span><span class="n">peak</span><span class="p">[</span><span class="mi">6</span><span class="p">])</span><span class="o">/</span><span class="mf">50.</span>      <span class="c">#to get delta-2-theta in deg.</span>
     3153                                        <span class="n">FWHM</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="n">G2pwd</span><span class="o">.</span><span class="n">getgamFW</span><span class="p">(</span><span class="n">peak</span><span class="p">[</span><span class="mi">7</span><span class="p">],</span><span class="n">peak</span><span class="p">[</span><span class="mi">6</span><span class="p">])</span>
    31773154                                        <span class="k">if</span> <span class="s">&#39;T&#39;</span> <span class="ow">in</span> <span class="n">peaks</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">&#39;Type&#39;</span><span class="p">,</span><span class="s">&#39;PXC&#39;</span><span class="p">):</span>
    31783155                                            <span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">&quot; </span><span class="si">%3d</span><span class="s"> </span><span class="si">%3d</span><span class="s"> </span><span class="si">%3d</span><span class="s"> </span><span class="si">%3d</span><span class="s"> </span><span class="si">%10.5f</span><span class="s"> </span><span class="si">%10.2f</span><span class="s"> </span><span class="si">%10.5f</span><span class="s"> </span><span class="si">%10.3f</span><span class="s"> </span><span class="se">\n</span><span class="s">&quot;</span> <span class="o">%</span> \
    … …  
    31803157                                        <span class="k">else</span><span class="p">:</span>
    31813158                                            <span class="nb">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">&quot; </span><span class="si">%3d</span><span class="s"> </span><span class="si">%3d</span><span class="s"> </span><span class="si">%3d</span><span class="s"> </span><span class="si">%3d</span><span class="s"> </span><span class="si">%10.5f</span><span class="s"> </span><span class="si">%10.5f</span><span class="s"> </span><span class="si">%10.5f</span><span class="s"> </span><span class="si">%10.3f</span><span class="s"> </span><span class="se">\n</span><span class="s">&quot;</span> <span class="o">%</span> \
    3182                                                 <span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">peak</span><span class="p">[</span><span class="mi">0</span><span class="p">]),</span><span class="nb">int</span><span class="p">(</span><span class="n">peak</span><span class="p">[</span><span class="mi">1</span><span class="p">]),</span><span class="nb">int</span><span class="p">(</span><span class="n">peak</span><span class="p">[</span><span class="mi">2</span><span class="p">]),</span><span class="nb">int</span><span class="p">(</span><span class="n">peak</span><span class="p">[</span><span class="mi">3</span><span class="p">]),</span><span class="n">peak</span><span class="p">[</span><span class="mi">4</span><span class="p">],</span><span class="n">peak</span><span class="p">[</span><span class="mi">5</span><span class="p">],</span><span class="n">FWHM</span><span class="p">,</span><span class="n">peak</span><span class="p">[</span><span class="mi">8</span><span class="p">]))</span>
     3159                                                <span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">peak</span><span class="p">[</span><span class="mi">0</span><span class="p">]),</span><span class="nb">int</span><span class="p">(</span><span class="n">peak</span><span class="p">[</span><span class="mi">1</span><span class="p">]),</span><span class="nb">int</span><span class="p">(</span><span class="n">peak</span><span class="p">[</span><span class="mi">2</span><span class="p">]),</span><span class="nb">int</span><span class="p">(</span><span class="n">peak</span><span class="p">[</span><span class="mi">3</span><span class="p">]),</span><span class="n">peak</span><span class="p">[</span><span class="mi">4</span><span class="p">],</span><span class="n">peak</span><span class="p">[</span><span class="mi">5</span><span class="p">],</span><span class="n">FWHM</span><span class="o">/</span><span class="mf">100.</span><span class="p">,</span><span class="n">peak</span><span class="p">[</span><span class="mi">8</span><span class="p">]))</span>
    31833160                            <span class="n">item2</span><span class="p">,</span> <span class="n">cookie2</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">GetNextChild</span><span class="p">(</span><span class="n">item</span><span class="p">,</span> <span class="n">cookie2</span><span class="p">)</span>                           
    31843161                    <span class="n">item</span><span class="p">,</span> <span class="n">cookie</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">GetNextChild</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">root</span><span class="p">,</span> <span class="n">cookie</span><span class="p">)</span>                           
    … …  
    35313508                <span class="n">dlg</span><span class="o">.</span><span class="n">Destroy</span><span class="p">()</span>
    35323509                <span class="k">return</span>
    3533 
    35343510        <span class="bp">self</span><span class="o">.</span><span class="n">OnFileSave</span><span class="p">(</span><span class="n">event</span><span class="p">)</span>
    35353511        <span class="c"># check that constraints are OK here</span>
    35363512        <span class="n">errmsg</span><span class="p">,</span> <span class="n">warnmsg</span> <span class="o">=</span> <span class="n">G2stIO</span><span class="o">.</span><span class="n">ReadCheckConstraints</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">GSASprojectfile</span><span class="p">)</span>
    35373513        <span class="k">if</span> <span class="n">errmsg</span><span class="p">:</span>
    3538             <span class="bp">self</span><span class="o">.</span><span class="n">ErrorDialog</span><span class="p">(</span><span class="s">&#39;Constraint Error&#39;</span><span class="p">,</span>
    3539                              <span class="s">&#39;Error in constraints. Refinement not possible.&#39;</span><span class="o">+</span>
    3540                              <span class="s">&#39;</span><span class="se">\n</span><span class="s">See console error message for details.&#39;</span><span class="p">)</span>
     3514            <span class="bp">self</span><span class="o">.</span><span class="n">ErrorDialog</span><span class="p">(</span><span class="s">&#39;Refinement error&#39;</span><span class="p">,</span><span class="n">errmsg</span><span class="p">)</span>
    35413515            <span class="k">return</span>
    35423516        <span class="k">if</span> <span class="n">warnmsg</span><span class="p">:</span>
    35433517            <span class="k">print</span><span class="p">(</span><span class="s">&#39;Conflict between refinment flag settings and constraints:</span><span class="se">\n</span><span class="s">&#39;</span><span class="o">+</span>
    3544                   <span class="n">warnmsg</span><span class="o">+</span><span class="s">&#39;</span><span class="se">\n</span><span class="s">Refinement not possible&#39;</span><span class="p">)</span>
     3518                <span class="n">warnmsg</span><span class="o">+</span><span class="s">&#39;</span><span class="se">\n</span><span class="s">Refinement not possible&#39;</span><span class="p">)</span>
    35453519            <span class="bp">self</span><span class="o">.</span><span class="n">ErrorDialog</span><span class="p">(</span><span class="s">&#39;Refinement Flag Error&#39;</span><span class="p">,</span>
    3546                              <span class="s">&#39;Conflict between refinement flag settings and constraints:</span><span class="se">\n</span><span class="s">&#39;</span><span class="o">+</span>
    3547                              <span class="n">warnmsg</span><span class="o">+</span>
    3548                              <span class="s">&#39;</span><span class="se">\n</span><span class="s">Refinement not possible&#39;</span><span class="p">)</span>
     3520                <span class="s">&#39;Conflict between refinement flag settings and constraints:</span><span class="se">\n</span><span class="s">&#39;</span><span class="o">+</span>
     3521                <span class="n">warnmsg</span><span class="o">+</span><span class="s">&#39;</span><span class="se">\n</span><span class="s">Refinement not possible&#39;</span><span class="p">)</span>
    35493522            <span class="k">return</span>
    35503523        <span class="n">dlg</span> <span class="o">=</span> <span class="n">wx</span><span class="o">.</span><span class="n">ProgressDialog</span><span class="p">(</span><span class="s">&#39;Residual&#39;</span><span class="p">,</span><span class="s">&#39;All data Rw =&#39;</span><span class="p">,</span><span class="mf">101.0</span><span class="p">,</span>
    … …  
    35783551                    <span class="n">Id</span> <span class="o">=</span> <span class="mi">0</span>
    35793552                    <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">DeleteChildren</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">root</span><span class="p">)</span>
    3580                     <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">HKL</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">HKL</span> <span class="o">=</span> <span class="p">[]</span>
    3581                     <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">G2plotNB</span><span class="o">.</span><span class="n">plotList</span><span class="p">:</span>
    3582                         <span class="bp">self</span><span class="o">.</span><span class="n">G2plotNB</span><span class="o">.</span><span class="n">clear</span><span class="p">()</span>
     3553                    <span class="bp">self</span><span class="o">.</span><span class="n">HKL</span> <span class="o">=</span> <span class="p">[]</span>
     3554<span class="c">#                    if self.G2plotNB.plotList:</span>
     3555<span class="c">#                        self.G2plotNB.clear()</span>
    35833556                    <span class="n">G2IO</span><span class="o">.</span><span class="n">ProjFileOpen</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
    35843557                    <span class="n">item</span><span class="p">,</span> <span class="n">cookie</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">GetFirstChild</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">root</span><span class="p">)</span>
    … …  
    35883561                            <span class="n">Id</span> <span class="o">=</span> <span class="n">item</span>
    35893562                        <span class="n">item</span><span class="p">,</span> <span class="n">cookie</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">GetNextChild</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">root</span><span class="p">,</span> <span class="n">cookie</span><span class="p">)</span>               
    3590                     <span class="k">if</span> <span class="n">Id</span><span class="p">:</span>
    3591                         <span class="bp">self</span><span class="o">.</span><span class="n">PickIdText</span> <span class="o">=</span> <span class="bp">None</span>  <span class="c">#force reload of PickId contents</span>
    3592                         <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">SelectItem</span><span class="p">(</span><span class="n">Id</span><span class="p">)</span>
    35933563                    <span class="k">if</span> <span class="n">parentName</span><span class="p">:</span>
    35943564                        <span class="n">parentId</span> <span class="o">=</span> <span class="n">G2gd</span><span class="o">.</span><span class="n">GetPatternTreeItemId</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">root</span><span class="p">,</span> <span class="n">parentName</span><span class="p">)</span>
    … …  
    35993569                        <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">SelectItem</span><span class="p">(</span><span class="n">itemId</span><span class="p">)</span>
    36003570                    <span class="k">if</span> <span class="s">&#39;Phases&#39;</span> <span class="ow">in</span> <span class="n">parentName</span><span class="p">:</span>
     3571                        <span class="n">data</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">GetItemPyData</span><span class="p">(</span><span class="n">itemId</span><span class="p">)</span>
     3572                        <span class="k">if</span> <span class="n">data</span><span class="p">[</span><span class="s">&#39;Drawing&#39;</span><span class="p">]:</span>
     3573                            <span class="n">data</span><span class="p">[</span><span class="s">&#39;Drawing&#39;</span><span class="p">][</span><span class="s">&#39;Atoms&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
     3574                            <span class="bp">self</span><span class="o">.</span><span class="n">dataDisplay</span><span class="o">.</span><span class="n">SetSelection</span><span class="p">(</span><span class="mi">4</span><span class="p">)</span>    <span class="c">#location of Drawing Data</span>
    36013575                        <span class="bp">self</span><span class="o">.</span><span class="n">dataDisplay</span><span class="o">.</span><span class="n">SetSelection</span><span class="p">(</span><span class="n">tabId</span><span class="p">)</span>
     3576                    <span class="k">elif</span> <span class="n">Id</span><span class="p">:</span>
     3577                        <span class="bp">self</span><span class="o">.</span><span class="n">PickIdText</span> <span class="o">=</span> <span class="bp">None</span>  <span class="c">#force reload of PickId contents</span>
     3578                        <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">SelectItem</span><span class="p">(</span><span class="n">Id</span><span class="p">)</span>
     3579
    36023580            <span class="k">finally</span><span class="p">:</span>
    36033581                <span class="n">dlg2</span><span class="o">.</span><span class="n">Destroy</span><span class="p">()</span>
    … …  
    36193597        <span class="n">errmsg</span><span class="p">,</span> <span class="n">warnmsg</span> <span class="o">=</span> <span class="n">G2stIO</span><span class="o">.</span><span class="n">ReadCheckConstraints</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">GSASprojectfile</span><span class="p">)</span>
    36203598        <span class="k">if</span> <span class="n">errmsg</span><span class="p">:</span>
    3621             <span class="bp">self</span><span class="o">.</span><span class="n">ErrorDialog</span><span class="p">(</span><span class="s">&#39;Constraint Error&#39;</span><span class="p">,</span>
    3622                              <span class="s">&#39;Error in constraints:</span><span class="se">\n</span><span class="s">&#39;</span><span class="o">+</span><span class="n">errmsg</span><span class="o">+</span>
    3623                              <span class="s">&#39;</span><span class="se">\n</span><span class="s">Refinement not possible&#39;</span><span class="p">)</span>
     3599            <span class="bp">self</span><span class="o">.</span><span class="n">ErrorDialog</span><span class="p">(</span><span class="s">&#39;Refinement error&#39;</span><span class="p">,</span><span class="n">errmsg</span><span class="p">)</span>
    36243600            <span class="k">return</span>
    36253601        <span class="k">if</span> <span class="n">warnmsg</span><span class="p">:</span>
    … …  
    36503626                    <span class="bp">self</span><span class="o">.</span><span class="n">PickIdText</span> <span class="o">=</span> <span class="bp">None</span>  <span class="c">#force reload of PickId contents</span>
    36513627                    <span class="bp">self</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">DeleteChildren</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">root</span><span class="p">)</span>
    3652                     <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">HKL</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">HKL</span> <span class="o">=</span> <span class="p">[]</span>
     3628                    <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">HKL</span><span class="p">):</span> <span class="bp">self</span><span class="o">.</span><span class="n">HKL</span> <span class="o">=</span> <span class="p">[]</span>
    36533629                    <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">G2plotNB</span><span class="o">.</span><span class="n">plotList</span><span class="p">:</span>
    36543630                        <span class="bp">self</span><span class="o">.</span><span class="n">G2plotNB</span><span class="o">.</span><span class="n">clear</span><span class="p">()</span>
    … …  
    36863662        <span class="k">if</span> <span class="s">&#39;2.7&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">sys</span><span class="o">.</span><span class="n">version</span><span class="p">[:</span><span class="mi">5</span><span class="p">]:</span>
    36873663            <span class="n">dlg</span> <span class="o">=</span> <span class="n">wx</span><span class="o">.</span><span class="n">MessageDialog</span><span class="p">(</span><span class="bp">None</span><span class="p">,</span>
    3688                 <span class="s">&#39;GSAS-II requires Python 2.7.x</span><span class="se">\n</span><span class="s"> Yours is &#39;</span><span class="o">+</span><span class="n">sys</span><span class="o">.</span><span class="n">version</span><span class="p">[:</span><span class="mi">5</span><span class="p">],</span>
     3664                <span class="s">&#39;GSAS-II requires Python 2.7.x</span><span class="se">\n</span><span class="s"> Yours is &#39;</span><span class="o">+</span><span class="n">sys</span><span class="o">.</span><span class="n">version</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">0</span><span class="p">],</span>
    36893665                <span class="s">&#39;Python version error&#39;</span><span class="p">,</span>  <span class="n">wx</span><span class="o">.</span><span class="n">OK</span><span class="p">)</span>
    36903666            <span class="k">try</span><span class="p">:</span>
    … …  
    36963672        <span class="bp">self</span><span class="o">.</span><span class="n">main</span><span class="o">.</span><span class="n">Show</span><span class="p">()</span>
    36973673        <span class="bp">self</span><span class="o">.</span><span class="n">SetTopWindow</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">main</span><span class="p">)</span>
     3674        <span class="c"># save the current package versions</span>
     3675        <span class="bp">self</span><span class="o">.</span><span class="n">main</span><span class="o">.</span><span class="n">PackageVersions</span> <span class="o">=</span> <span class="p">[]</span>
     3676        <span class="bp">self</span><span class="o">.</span><span class="n">main</span><span class="o">.</span><span class="n">PackageVersions</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="s">&#39;Python&#39;</span><span class="p">,</span><span class="n">sys</span><span class="o">.</span><span class="n">version</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">0</span><span class="p">]])</span>
     3677        <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="p">(</span><span class="n">wx</span><span class="p">,</span><span class="n">mpl</span><span class="p">,</span><span class="n">np</span><span class="p">,</span><span class="n">sp</span><span class="p">,</span><span class="n">ogl</span><span class="p">):</span>
     3678            <span class="bp">self</span><span class="o">.</span><span class="n">main</span><span class="o">.</span><span class="n">PackageVersions</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">p</span><span class="o">.</span><span class="n">__name__</span><span class="p">,</span><span class="n">p</span><span class="o">.</span><span class="n">__version__</span><span class="p">])</span>
     3679        <span class="k">try</span><span class="p">:</span>
     3680            <span class="bp">self</span><span class="o">.</span><span class="n">main</span><span class="o">.</span><span class="n">PackageVersions</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">Image</span><span class="o">.</span><span class="n">__name__</span><span class="p">,</span><span class="n">Image</span><span class="o">.</span><span class="n">VERSION</span><span class="p">])</span>
     3681        <span class="k">except</span><span class="p">:</span>
     3682            <span class="k">try</span><span class="p">:</span>
     3683                <span class="kn">from</span> <span class="nn">PIL</span> <span class="kn">import</span> <span class="n">PILLOW_VERSION</span>
     3684                <span class="bp">self</span><span class="o">.</span><span class="n">main</span><span class="o">.</span><span class="n">PackageVersions</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">Image</span><span class="o">.</span><span class="n">__name__</span><span class="p">,</span><span class="n">PILLOW_VERSION</span><span class="p">])</span>
     3685            <span class="k">except</span><span class="p">:</span>
     3686                <span class="k">pass</span>
     3687        <span class="bp">self</span><span class="o">.</span><span class="n">main</span><span class="o">.</span><span class="n">PackageVersions</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="s">&#39; Platform&#39;</span><span class="p">,</span><span class="n">sys</span><span class="o">.</span><span class="n">platform</span><span class="o">+</span><span class="s">&#39; &#39;</span><span class="o">+</span><span class="n">platform</span><span class="o">.</span><span class="n">architecture</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="o">+</span><span class="n">platform</span><span class="o">.</span><span class="n">machine</span><span class="p">()])</span>
     3688       
     3689<span class="c">#        self.main.PackageVersions = {}</span>
     3690<span class="c">#        self.main.PackageVersions[&#39;Python&#39;] = sys.version.split()[0]</span>
     3691<span class="c">#        for p in (wx,mpl,np,sp,ogl):</span>
     3692<span class="c">#            self.main.PackageVersions[p.__name__] = p.__version__</span>
     3693<span class="c">#        try:</span>
     3694<span class="c">#            self.main.PackageVersions[Image.__name__] = Image.VERSION</span>
     3695<span class="c">#        except:</span>
     3696<span class="c">#            try:</span>
     3697<span class="c">#                from PIL import PILLOW_VERSION</span>
     3698<span class="c">#                self.main.PackageVersions[Image.__name__] = PILLOW_VERSION</span>
     3699<span class="c">#            except:</span>
     3700<span class="c">#                pass</span>
     3701<span class="c">#        self.main.PackageVersions[&#39; Platform&#39;] = sys.platform+&#39; &#39;+platform.architecture()[0]+&#39; &#39;+platform.machine()</span>
    36983702        <span class="c"># DEBUG: jump to sequential results</span>
    36993703        <span class="c">#Id = G2gd.GetPatternTreeItemId(self.main,self.main.root,&#39;Sequential results&#39;)</span>
    … …  
    37123716    <span class="c">#     self.main.OnFileOpen(None,filename)</span>
    37133717    <span class="c"># removed because this gets triggered when a file is on the command line in canopy 1.4 -- not likely used anyway</span>
    3714     </div></div>
     3718       </div></div>
    37153719<div class="viewcode-block" id="main"><a class="viewcode-back" href="../GSASII.html#GSASII.main">[docs]</a><span class="k">def</span> <span class="nf">main</span><span class="p">():</span>
    37163720    <span class="sd">&#39;&#39;&#39;Start up the GSAS-II application&#39;&#39;&#39;</span>
    … …  
    37283732    <span class="c"># print versions</span>
    37293733    <span class="k">print</span> <span class="s">&quot;Python module versions loaded:&quot;</span>
    3730     <span class="k">print</span> <span class="s">&quot;python:     &quot;</span><span class="p">,</span><span class="n">sys</span><span class="o">.</span><span class="n">version</span><span class="p">[:</span><span class="mi">5</span><span class="p">]</span>
     3734    <span class="k">print</span> <span class="s">&quot;python:     &quot;</span><span class="p">,</span><span class="n">sys</span><span class="o">.</span><span class="n">version</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
    37313735    <span class="k">print</span> <span class="s">&quot;wxpython:   &quot;</span><span class="p">,</span><span class="n">wx</span><span class="o">.</span><span class="n">__version__</span>
    37323736    <span class="k">print</span> <span class="s">&quot;matplotlib: &quot;</span><span class="p">,</span><span class="n">mpl</span><span class="o">.</span><span class="n">__version__</span>
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