Ignore:
Timestamp:
Mar 14, 2015 5:35:03 PM (8 years ago)
Author:
toby
Message:

change sphinx docs links; rebuild & fixing minor formatting

File:
1 edited

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  • sphinxdocs/build/html/_modules/GSASIIIO.html

    r1513 r1709  
    5151<span class="c"># -*- coding: utf-8 -*-</span>
    5252<span class="c">########### SVN repository information ###################</span>
    53 <span class="c"># $Date: 2014-09-26 10:52:52 -0500 (Fri, 26 Sep 2014) $</span>
    54 <span class="c"># $Author: vondreele $</span>
    55 <span class="c"># $Revision: 1507 $</span>
     53<span class="c"># $Date: 2015-03-12 17:09:00 -0500 (Thu, 12 Mar 2015) $</span>
     54<span class="c"># $Author: toby $</span>
     55<span class="c"># $Revision: 1698 $</span>
    5656<span class="c"># $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/GSASIIIO.py $</span>
    57 <span class="c"># $Id: GSASIIIO.py 1507 2014-09-26 15:52:52Z vondreele $</span>
     57<span class="c"># $Id: GSASIIIO.py 1698 2015-03-12 22:09:00Z toby $</span>
    5858<span class="c">########### SVN repository information ###################</span>
    5959<span class="sd">&#39;&#39;&#39;</span>
    … …  
    8080<span class="kn">import</span> <span class="nn">random</span> <span class="kn">as</span> <span class="nn">ran</span>
    8181<span class="kn">import</span> <span class="nn">GSASIIpath</span>
    82 <span class="n">GSASIIpath</span><span class="o">.</span><span class="n">SetVersionNumber</span><span class="p">(</span><span class="s">&quot;$Revision: 1507 $&quot;</span><span class="p">)</span>
     82<span class="n">GSASIIpath</span><span class="o">.</span><span class="n">SetVersionNumber</span><span class="p">(</span><span class="s">&quot;$Revision: 1698 $&quot;</span><span class="p">)</span>
    8383<span class="kn">import</span> <span class="nn">GSASIIgrid</span> <span class="kn">as</span> <span class="nn">G2gd</span>
    8484<span class="kn">import</span> <span class="nn">GSASIIspc</span> <span class="kn">as</span> <span class="nn">G2spc</span>
    8585<span class="kn">import</span> <span class="nn">GSASIIlattice</span> <span class="kn">as</span> <span class="nn">G2lat</span>
    8686<span class="kn">import</span> <span class="nn">GSASIIpwdGUI</span> <span class="kn">as</span> <span class="nn">G2pdG</span>
     87<span class="kn">import</span> <span class="nn">GSASIIimage</span> <span class="kn">as</span> <span class="nn">G2img</span>
    8788<span class="kn">import</span> <span class="nn">GSASIIElem</span> <span class="kn">as</span> <span class="nn">G2el</span>
    8889<span class="kn">import</span> <span class="nn">GSASIIstrIO</span> <span class="kn">as</span> <span class="nn">G2stIO</span>
    8990<span class="kn">import</span> <span class="nn">GSASIImapvars</span> <span class="kn">as</span> <span class="nn">G2mv</span>
     91<span class="kn">import</span> <span class="nn">GSASIIctrls</span> <span class="kn">as</span> <span class="nn">G2G</span>
    9092<span class="kn">import</span> <span class="nn">os</span>
    9193<span class="kn">import</span> <span class="nn">os.path</span> <span class="kn">as</span> <span class="nn">ospath</span>
    … …  
    186188
    187189<span class="sd">    &#39;&#39;&#39;</span>
    188     <span class="k">if</span> <span class="ow">not</span> <span class="n">ospath</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">imagefile</span><span class="p">):</span>
    189         <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><span class="n">G2frame</span><span class="p">,</span> <span class="s">&#39;Bad image file name; choose name&#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>\
     190    <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">imagefile</span><span class="p">):</span>
     191        <span class="k">print</span> <span class="s">&#39;Image file &#39;</span><span class="o">+</span><span class="n">imagefile</span><span class="o">+</span><span class="s">&#39; not found&#39;</span>
     192        <span class="n">fil</span> <span class="o">=</span> <span class="n">imagefile</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">&#39;</span><span class="se">\\</span><span class="s">&#39;</span><span class="p">,</span><span class="s">&#39;/&#39;</span><span class="p">)</span> <span class="c"># windows?!</span>
     193        <span class="c"># see if we can find a file with same name or in a similarly named sub-dir</span>
     194        <span class="n">pth</span><span class="p">,</span><span class="n">fil</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="n">fil</span><span class="p">)</span>
     195        <span class="n">prevpth</span> <span class="o">=</span> <span class="bp">None</span>
     196        <span class="k">while</span> <span class="n">pth</span> <span class="ow">and</span> <span class="n">pth</span> <span class="o">!=</span> <span class="n">prevpth</span><span class="p">:</span>
     197            <span class="n">prevpth</span> <span class="o">=</span> <span class="n">pth</span>
     198            <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">exists</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">G2frame</span><span class="o">.</span><span class="n">dirname</span><span class="p">,</span><span class="n">fil</span><span class="p">)):</span>
     199                <span class="k">print</span> <span class="s">&#39;found image file &#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">join</span><span class="p">(</span><span class="n">G2frame</span><span class="o">.</span><span class="n">dirname</span><span class="p">,</span><span class="n">fil</span><span class="p">)</span>
     200                <span class="k">return</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">G2frame</span><span class="o">.</span><span class="n">dirname</span><span class="p">,</span><span class="n">fil</span><span class="p">)</span>
     201            <span class="n">pth</span><span class="p">,</span><span class="n">enddir</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="n">pth</span><span class="p">)</span>
     202            <span class="n">fil</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">join</span><span class="p">(</span><span class="n">enddir</span><span class="p">,</span><span class="n">fil</span><span class="p">)</span>
     203        <span class="c"># not found as a subdirectory, drop common parts of path for last saved &amp; image file names</span>
     204        <span class="c">#    if image was .../A/B/C/imgs/ima.ge</span>
     205        <span class="c">#      &amp; GPX was  .../A/B/C/refs/fil.gpx but is now .../NEW/TEST/TEST1</span>
     206        <span class="c">#    will look for .../NEW/TEST/TEST1/imgs/ima.ge, .../NEW/TEST/imgs/ima.ge, .../NEW/imgs/ima.ge and so on</span>
     207        <span class="n">Controls</span> <span class="o">=</span> <span class="n">G2frame</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">G2gd</span><span class="o">.</span><span class="n">GetPatternTreeItemId</span><span class="p">(</span><span class="n">G2frame</span><span class="p">,</span><span class="n">G2frame</span><span class="o">.</span><span class="n">root</span><span class="p">,</span> <span class="s">&#39;Controls&#39;</span><span class="p">))</span>
     208        <span class="n">gpxPath</span> <span class="o">=</span> <span class="n">Controls</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">&#39;LastSavedAs&#39;</span><span class="p">,</span><span class="s">&#39;&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">&#39;</span><span class="se">\\</span><span class="s">&#39;</span><span class="p">,</span><span class="s">&#39;/&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">&#39;/&#39;</span><span class="p">)</span> <span class="c"># blank in older .GPX files</span>
     209        <span class="n">imgPath</span> <span class="o">=</span> <span class="n">imagefile</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">&#39;</span><span class="se">\\</span><span class="s">&#39;</span><span class="p">,</span><span class="s">&#39;/&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">&#39;/&#39;</span><span class="p">)</span>
     210        <span class="k">for</span> <span class="n">p1</span><span class="p">,</span><span class="n">p2</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">gpxPath</span><span class="p">,</span><span class="n">imgPath</span><span class="p">):</span>
     211            <span class="k">if</span> <span class="n">p1</span> <span class="o">==</span> <span class="n">p2</span><span class="p">:</span>
     212                <span class="n">gpxPath</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="mi">0</span><span class="p">),</span><span class="n">imgPath</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
     213            <span class="k">else</span><span class="p">:</span>
     214                <span class="k">break</span>
     215        <span class="n">fil</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">join</span><span class="p">(</span><span class="o">*</span><span class="n">imgPath</span><span class="p">)</span> <span class="c"># file with non-common prefix elements</span>
     216        <span class="n">prevpth</span> <span class="o">=</span> <span class="bp">None</span>
     217        <span class="n">pth</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">abspath</span><span class="p">(</span><span class="n">G2frame</span><span class="o">.</span><span class="n">dirname</span><span class="p">)</span>
     218        <span class="k">while</span> <span class="n">pth</span> <span class="ow">and</span> <span class="n">pth</span> <span class="o">!=</span> <span class="n">prevpth</span><span class="p">:</span>
     219            <span class="n">prevpth</span> <span class="o">=</span> <span class="n">pth</span>
     220            <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">exists</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">pth</span><span class="p">,</span><span class="n">fil</span><span class="p">)):</span>
     221                <span class="k">print</span> <span class="s">&#39;found image file &#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">join</span><span class="p">(</span><span class="n">pth</span><span class="p">,</span><span class="n">fil</span><span class="p">)</span>
     222                <span class="k">return</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">pth</span><span class="p">,</span><span class="n">fil</span><span class="p">)</span>
     223            <span class="n">pth</span><span class="p">,</span><span class="n">enddir</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="n">pth</span><span class="p">)</span>
     224        <span class="n">GSASIIpath</span><span class="o">.</span><span class="n">IPyBreak</span><span class="p">()</span>
     225
     226    <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">imagefile</span><span class="p">):</span>
     227        <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><span class="n">G2frame</span><span class="p">,</span> <span class="s">&#39;Previous image file not found; open here&#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>\
    190228        <span class="s">&#39;Any image file (*.edf;*.tif;*.tiff;*.mar*;*.ge*;*.avg;*.sum;*.img)</span><span class="se">\</span>
    191229<span class="s">        |*.edf;*.tif;*.tiff;*.mar*;*.ge*;*.avg;*.sum;*.img|</span><span class="se">\</span>
    … …  
    220258    <span class="n">vsizer</span><span class="o">.</span><span class="n">Add</span><span class="p">(</span><span class="n">wx</span><span class="o">.</span><span class="n">StaticText</span><span class="p">(</span><span class="n">dlg</span><span class="p">,</span><span class="n">wx</span><span class="o">.</span><span class="n">ID_ANY</span><span class="p">,</span><span class="s">u&#39;Wavelength (</span><span class="se">\xC5</span><span class="s">) &#39;</span><span class="p">),</span>
    221259               <span class="mi">0</span><span class="p">,</span><span class="n">wx</span><span class="o">.</span><span class="n">ALIGN_LEFT</span><span class="o">|</span><span class="n">wx</span><span class="o">.</span><span class="n">ALL</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
    222     <span class="n">wdgt</span> <span class="o">=</span> <span class="n">G2gd</span><span class="o">.</span><span class="n">ValidatedTxtCtrl</span><span class="p">(</span><span class="n">dlg</span><span class="p">,</span><span class="n">Data</span><span class="p">,</span><span class="s">&#39;wavelength&#39;</span><span class="p">)</span>
     260    <span class="n">wdgt</span> <span class="o">=</span> <span class="n">G2G</span><span class="o">.</span><span class="n">ValidatedTxtCtrl</span><span class="p">(</span><span class="n">dlg</span><span class="p">,</span><span class="n">Data</span><span class="p">,</span><span class="s">&#39;wavelength&#39;</span><span class="p">)</span>
    223261    <span class="n">vsizer</span><span class="o">.</span><span class="n">Add</span><span class="p">(</span><span class="n">wdgt</span><span class="p">)</span>
    224262    <span class="n">mainsizer</span><span class="o">.</span><span class="n">Add</span><span class="p">(</span><span class="n">vsizer</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">wx</span><span class="o">.</span><span class="n">ALIGN_LEFT</span><span class="o">|</span><span class="n">wx</span><span class="o">.</span><span class="n">ALL</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
    … …  
    227265    <span class="n">vsizer</span><span class="o">.</span><span class="n">Add</span><span class="p">(</span><span class="n">wx</span><span class="o">.</span><span class="n">StaticText</span><span class="p">(</span><span class="n">dlg</span><span class="p">,</span><span class="n">wx</span><span class="o">.</span><span class="n">ID_ANY</span><span class="p">,</span><span class="s">u&#39;Pixel size (</span><span class="se">\xb5</span><span class="s">m). Width &#39;</span><span class="p">),</span>
    228266               <span class="mi">0</span><span class="p">,</span><span class="n">wx</span><span class="o">.</span><span class="n">ALIGN_LEFT</span><span class="o">|</span><span class="n">wx</span><span class="o">.</span><span class="n">ALL</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
    229     <span class="n">wdgt</span> <span class="o">=</span> <span class="n">G2gd</span><span class="o">.</span><span class="n">ValidatedTxtCtrl</span><span class="p">(</span><span class="n">dlg</span><span class="p">,</span><span class="n">Data</span><span class="p">[</span><span class="s">&#39;pixelSize&#39;</span><span class="p">],</span><span class="mi">0</span><span class="p">,</span>
     267    <span class="n">wdgt</span> <span class="o">=</span> <span class="n">G2G</span><span class="o">.</span><span class="n">ValidatedTxtCtrl</span><span class="p">(</span><span class="n">dlg</span><span class="p">,</span><span class="n">Data</span><span class="p">[</span><span class="s">&#39;pixelSize&#39;</span><span class="p">],</span><span class="mi">0</span><span class="p">,</span>
    230268                                 <span class="n">size</span><span class="o">=</span><span class="p">(</span><span class="mi">50</span><span class="p">,</span><span class="o">-</span><span class="mi">1</span><span class="p">))</span>
    231269    <span class="n">vsizer</span><span class="o">.</span><span class="n">Add</span><span class="p">(</span><span class="n">wdgt</span><span class="p">)</span>
    232270    <span class="n">vsizer</span><span class="o">.</span><span class="n">Add</span><span class="p">(</span><span class="n">wx</span><span class="o">.</span><span class="n">StaticText</span><span class="p">(</span><span class="n">dlg</span><span class="p">,</span><span class="n">wx</span><span class="o">.</span><span class="n">ID_ANY</span><span class="p">,</span><span class="s">u&#39;  Height &#39;</span><span class="p">),</span>
    233271               <span class="n">wx</span><span class="o">.</span><span class="n">ALIGN_LEFT</span><span class="o">|</span><span class="n">wx</span><span class="o">.</span><span class="n">ALL</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
    234     <span class="n">wdgt</span> <span class="o">=</span> <span class="n">G2gd</span><span class="o">.</span><span class="n">ValidatedTxtCtrl</span><span class="p">(</span><span class="n">dlg</span><span class="p">,</span><span class="n">Data</span><span class="p">[</span><span class="s">&#39;pixelSize&#39;</span><span class="p">],</span><span class="mi">1</span><span class="p">,</span>
     272    <span class="n">wdgt</span> <span class="o">=</span> <span class="n">G2G</span><span class="o">.</span><span class="n">ValidatedTxtCtrl</span><span class="p">(</span><span class="n">dlg</span><span class="p">,</span><span class="n">Data</span><span class="p">[</span><span class="s">&#39;pixelSize&#39;</span><span class="p">],</span><span class="mi">1</span><span class="p">,</span>
    235273                                 <span class="n">size</span><span class="o">=</span><span class="p">(</span><span class="mi">50</span><span class="p">,</span><span class="o">-</span><span class="mi">1</span><span class="p">))</span>
    236274    <span class="n">vsizer</span><span class="o">.</span><span class="n">Add</span><span class="p">(</span><span class="n">wdgt</span><span class="p">)</span>
    … …  
    240278    <span class="n">vsizer</span><span class="o">.</span><span class="n">Add</span><span class="p">(</span><span class="n">wx</span><span class="o">.</span><span class="n">StaticText</span><span class="p">(</span><span class="n">dlg</span><span class="p">,</span><span class="n">wx</span><span class="o">.</span><span class="n">ID_ANY</span><span class="p">,</span><span class="s">u&#39;Sample to detector (mm) &#39;</span><span class="p">),</span>
    241279               <span class="mi">0</span><span class="p">,</span><span class="n">wx</span><span class="o">.</span><span class="n">ALIGN_LEFT</span><span class="o">|</span><span class="n">wx</span><span class="o">.</span><span class="n">ALL</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
    242     <span class="n">wdgt</span> <span class="o">=</span> <span class="n">G2gd</span><span class="o">.</span><span class="n">ValidatedTxtCtrl</span><span class="p">(</span><span class="n">dlg</span><span class="p">,</span><span class="n">Data</span><span class="p">,</span><span class="s">&#39;distance&#39;</span><span class="p">)</span>
     280    <span class="n">wdgt</span> <span class="o">=</span> <span class="n">G2G</span><span class="o">.</span><span class="n">ValidatedTxtCtrl</span><span class="p">(</span><span class="n">dlg</span><span class="p">,</span><span class="n">Data</span><span class="p">,</span><span class="s">&#39;distance&#39;</span><span class="p">)</span>
    243281    <span class="n">vsizer</span><span class="o">.</span><span class="n">Add</span><span class="p">(</span><span class="n">wdgt</span><span class="p">)</span>
    244282    <span class="n">mainsizer</span><span class="o">.</span><span class="n">Add</span><span class="p">(</span><span class="n">vsizer</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">wx</span><span class="o">.</span><span class="n">ALIGN_LEFT</span><span class="o">|</span><span class="n">wx</span><span class="o">.</span><span class="n">ALL</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
    … …  
    247285    <span class="n">vsizer</span><span class="o">.</span><span class="n">Add</span><span class="p">(</span><span class="n">wx</span><span class="o">.</span><span class="n">StaticText</span><span class="p">(</span><span class="n">dlg</span><span class="p">,</span><span class="n">wx</span><span class="o">.</span><span class="n">ID_ANY</span><span class="p">,</span><span class="s">u&#39;Beam center (pixels). X = &#39;</span><span class="p">),</span>
    248286               <span class="mi">0</span><span class="p">,</span><span class="n">wx</span><span class="o">.</span><span class="n">ALIGN_LEFT</span><span class="o">|</span><span class="n">wx</span><span class="o">.</span><span class="n">ALL</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
    249     <span class="n">wdgt</span> <span class="o">=</span> <span class="n">G2gd</span><span class="o">.</span><span class="n">ValidatedTxtCtrl</span><span class="p">(</span><span class="n">dlg</span><span class="p">,</span><span class="n">Data</span><span class="p">[</span><span class="s">&#39;center&#39;</span><span class="p">],</span><span class="mi">0</span><span class="p">,</span>
     287    <span class="n">wdgt</span> <span class="o">=</span> <span class="n">G2G</span><span class="o">.</span><span class="n">ValidatedTxtCtrl</span><span class="p">(</span><span class="n">dlg</span><span class="p">,</span><span class="n">Data</span><span class="p">[</span><span class="s">&#39;center&#39;</span><span class="p">],</span><span class="mi">0</span><span class="p">,</span>
    250288                                 <span class="n">size</span><span class="o">=</span><span class="p">(</span><span class="mi">75</span><span class="p">,</span><span class="o">-</span><span class="mi">1</span><span class="p">))</span>
    251289    <span class="n">vsizer</span><span class="o">.</span><span class="n">Add</span><span class="p">(</span><span class="n">wdgt</span><span class="p">)</span>
    252290    <span class="n">vsizer</span><span class="o">.</span><span class="n">Add</span><span class="p">(</span><span class="n">wx</span><span class="o">.</span><span class="n">StaticText</span><span class="p">(</span><span class="n">dlg</span><span class="p">,</span><span class="n">wx</span><span class="o">.</span><span class="n">ID_ANY</span><span class="p">,</span><span class="s">u&#39;  Y = &#39;</span><span class="p">),</span>
    253291               <span class="n">wx</span><span class="o">.</span><span class="n">ALIGN_LEFT</span><span class="o">|</span><span class="n">wx</span><span class="o">.</span><span class="n">ALL</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
    254     <span class="n">wdgt</span> <span class="o">=</span> <span class="n">G2gd</span><span class="o">.</span><span class="n">ValidatedTxtCtrl</span><span class="p">(</span><span class="n">dlg</span><span class="p">,</span><span class="n">Data</span><span class="p">[</span><span class="s">&#39;center&#39;</span><span class="p">],</span><span class="mi">1</span><span class="p">,</span>
     292    <span class="n">wdgt</span> <span class="o">=</span> <span class="n">G2G</span><span class="o">.</span><span class="n">ValidatedTxtCtrl</span><span class="p">(</span><span class="n">dlg</span><span class="p">,</span><span class="n">Data</span><span class="p">[</span><span class="s">&#39;center&#39;</span><span class="p">],</span><span class="mi">1</span><span class="p">,</span>
    255293                                 <span class="n">size</span><span class="o">=</span><span class="p">(</span><span class="mi">75</span><span class="p">,</span><span class="o">-</span><span class="mi">1</span><span class="p">))</span>
    256294    <span class="n">vsizer</span><span class="o">.</span><span class="n">Add</span><span class="p">(</span><span class="n">wdgt</span><span class="p">)</span>
    … …  
    260298    <span class="n">vsizer</span><span class="o">.</span><span class="n">Add</span><span class="p">(</span><span class="n">wx</span><span class="o">.</span><span class="n">StaticText</span><span class="p">(</span><span class="n">dlg</span><span class="p">,</span><span class="n">wx</span><span class="o">.</span><span class="n">ID_ANY</span><span class="p">,</span><span class="s">u&#39;Comments &#39;</span><span class="p">),</span>
    261299               <span class="mi">0</span><span class="p">,</span><span class="n">wx</span><span class="o">.</span><span class="n">ALIGN_LEFT</span><span class="o">|</span><span class="n">wx</span><span class="o">.</span><span class="n">ALL</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
    262     <span class="n">wdgt</span> <span class="o">=</span> <span class="n">G2gd</span><span class="o">.</span><span class="n">ValidatedTxtCtrl</span><span class="p">(</span><span class="n">dlg</span><span class="p">,</span><span class="n">Comments</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">size</span><span class="o">=</span><span class="p">(</span><span class="mi">250</span><span class="p">,</span><span class="o">-</span><span class="mi">1</span><span class="p">))</span>
     300    <span class="n">wdgt</span> <span class="o">=</span> <span class="n">G2G</span><span class="o">.</span><span class="n">ValidatedTxtCtrl</span><span class="p">(</span><span class="n">dlg</span><span class="p">,</span><span class="n">Comments</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">size</span><span class="o">=</span><span class="p">(</span><span class="mi">250</span><span class="p">,</span><span class="o">-</span><span class="mi">1</span><span class="p">))</span>
    263301    <span class="n">vsizer</span><span class="o">.</span><span class="n">Add</span><span class="p">(</span><span class="n">wdgt</span><span class="p">)</span>
    264302    <span class="n">mainsizer</span><span class="o">.</span><span class="n">Add</span><span class="p">(</span><span class="n">vsizer</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">wx</span><span class="o">.</span><span class="n">ALIGN_LEFT</span><span class="o">|</span><span class="n">wx</span><span class="o">.</span><span class="n">ALL</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
    … …  
    292330    <span class="n">ext</span> <span class="o">=</span> <span class="n">ospath</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>
    293331    <span class="n">Comments</span> <span class="o">=</span> <span class="p">[]</span>
     332    <span class="n">Image</span> <span class="o">=</span> <span class="bp">None</span>
    294333    <span class="k">if</span> <span class="n">ext</span> <span class="o">==</span> <span class="s">&#39;.tif&#39;</span> <span class="ow">or</span> <span class="n">ext</span> <span class="o">==</span> <span class="s">&#39;.tiff&#39;</span><span class="p">:</span>
    295334        <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">GetTifData</span><span class="p">(</span><span class="n">imagefile</span><span class="p">)</span>
    … …  
    320359        <span class="k">if</span> <span class="ow">not</span> <span class="n">imageOnly</span><span class="p">:</span>
    321360            <span class="n">EditImageParms</span><span class="p">(</span><span class="n">G2frame</span><span class="p">,</span><span class="n">Data</span><span class="p">,</span><span class="n">Comments</span><span class="p">,</span><span class="n">Image</span><span class="p">,</span><span class="n">imagefile</span><span class="p">)</span>
     361    <span class="k">else</span><span class="p">:</span>
     362        <span class="k">print</span> <span class="s">&#39;Extension for file &#39;</span><span class="o">+</span><span class="n">imagefile</span><span class="o">+</span><span class="s">&#39; not recognized&#39;</span>
     363    <span class="k">if</span> <span class="n">Image</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
     364        <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">&#39;No image read&#39;</span><span class="p">)</span>
    322365    <span class="k">if</span> <span class="n">imageOnly</span><span class="p">:</span>
    323366        <span class="k">if</span> <span class="n">TRANSP</span><span class="p">:</span>
    … …  
    396439        <span class="n">image</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">ar</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="s">&#39;L&#39;</span><span class="p">,</span><span class="n">File</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="n">imSize</span><span class="p">)),</span><span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">int32</span><span class="p">)</span>
    397440    <span class="k">elif</span> <span class="n">dType</span> <span class="o">==</span> <span class="s">&#39;UnsignedLong&#39;</span><span class="p">:</span>
    398         <span class="n">image</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">ar</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="s">&#39;L&#39;</span><span class="p">,</span><span class="n">File</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="n">imSize</span><span class="p">)),</span><span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">int32</span><span class="p">)</span>       
     441        <span class="n">image</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">ar</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="s">&#39;L&#39;</span><span class="p">,</span><span class="n">File</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="n">imSize</span><span class="p">)),</span><span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">int32</span><span class="p">)</span>
     442    <span class="k">elif</span> <span class="n">dType</span> <span class="o">==</span> <span class="s">&#39;SignedInteger&#39;</span><span class="p">:</span>
     443        <span class="n">image</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">ar</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="s">&#39;l&#39;</span><span class="p">,</span><span class="n">File</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="n">imSize</span><span class="p">)),</span><span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">int32</span><span class="p">)</span>
    399444    <span class="n">image</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="n">image</span><span class="p">,(</span><span class="n">sizexy</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span><span class="n">sizexy</span><span class="p">[</span><span class="mi">0</span><span class="p">]))</span>
    400445    <span class="n">data</span> <span class="o">=</span> <span class="p">{</span><span class="s">&#39;pixelSize&#39;</span><span class="p">:</span><span class="n">pixSize</span><span class="p">,</span><span class="s">&#39;wavelength&#39;</span><span class="p">:</span><span class="n">wave</span><span class="p">,</span><span class="s">&#39;distance&#39;</span><span class="p">:</span><span class="n">dist</span><span class="p">,</span><span class="s">&#39;center&#39;</span><span class="p">:</span><span class="n">cent</span><span class="p">,</span><span class="s">&#39;size&#39;</span><span class="p">:</span><span class="n">sizexy</span><span class="p">}</span>
    … …  
    724769                <span class="k">else</span><span class="p">:</span>
    725770                    <span class="n">image</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">ar</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="s">&#39;I&#39;</span><span class="p">,</span><span class="n">File</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="mi">4</span><span class="o">*</span><span class="n">Npix</span><span class="p">)),</span><span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">int32</span><span class="p">)</span>
    726                
     771            <span class="k">elif</span> <span class="n">IFD</span><span class="p">[</span><span class="mi">258</span><span class="p">][</span><span class="mi">2</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="mi">16</span><span class="p">:</span>
     772                <span class="n">tifType</span> <span class="o">=</span> <span class="s">&#39;MedOptics D1&#39;</span>
     773                <span class="n">pixy</span> <span class="o">=</span> <span class="p">[</span><span class="mf">46.9</span><span class="p">,</span><span class="mf">46.9</span><span class="p">]</span>
     774                <span class="n">File</span><span class="o">.</span><span class="n">seek</span><span class="p">(</span><span class="mi">8</span><span class="p">)</span>
     775                <span class="k">if</span> <span class="ow">not</span> <span class="n">imageOnly</span><span class="p">:</span>
     776                    <span class="k">print</span> <span class="s">&#39;Read MedOptics D1 tiff file: &#39;</span><span class="p">,</span><span class="n">filename</span>
     777                <span class="n">image</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">ar</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="s">&#39;H&#39;</span><span class="p">,</span><span class="n">File</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="mi">2</span><span class="o">*</span><span class="n">Npix</span><span class="p">)),</span><span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">int32</span><span class="p">)</span>
     778                 
    727779        <span class="k">elif</span> <span class="n">IFD</span><span class="p">[</span><span class="mi">273</span><span class="p">][</span><span class="mi">2</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="mi">4096</span><span class="p">:</span>
    728780            <span class="k">if</span> <span class="n">sizexy</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="mi">3072</span><span class="p">:</span>
    … …  
    9901042        <span class="nb">file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">G2frame</span><span class="o">.</span><span class="n">GSASprojectfile</span><span class="p">,</span><span class="s">&#39;wb&#39;</span><span class="p">)</span>
    9911043        <span class="k">print</span> <span class="s">&#39;save to file: &#39;</span><span class="p">,</span><span class="n">G2frame</span><span class="o">.</span><span class="n">GSASprojectfile</span>
     1044        <span class="c"># stick the file name into the tree, if possible</span>
     1045        <span class="k">try</span><span class="p">:</span>
     1046            <span class="n">Controls</span> <span class="o">=</span> <span class="n">G2frame</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">GetItemPyData</span><span class="p">(</span>
     1047                <span class="n">G2gd</span><span class="o">.</span><span class="n">GetPatternTreeItemId</span><span class="p">(</span><span class="n">G2frame</span><span class="p">,</span><span class="n">G2frame</span><span class="o">.</span><span class="n">root</span><span class="p">,</span> <span class="s">&#39;Controls&#39;</span><span class="p">))</span>
     1048            <span class="n">Controls</span><span class="p">[</span><span class="s">&#39;LastSavedAs&#39;</span><span class="p">]</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">abspath</span><span class="p">(</span><span class="n">G2frame</span><span class="o">.</span><span class="n">GSASprojectfile</span><span class="p">)</span>
     1049        <span class="k">except</span><span class="p">:</span>
     1050            <span class="k">pass</span>
    9921051        <span class="n">wx</span><span class="o">.</span><span class="n">BeginBusyCursor</span><span class="p">()</span>
    9931052        <span class="k">try</span><span class="p">:</span>
    … …  
    10321091    <span class="k">else</span><span class="p">:</span>
    10331092        <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">azm</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">azms</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">]):</span>
    1034             <span class="n">Azms</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">azms</span><span class="p">[</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">]</span><span class="o">+</span><span class="n">azm</span><span class="p">)</span><span class="o">/</span><span class="mf">2.</span><span class="p">)</span>
     1093            <span class="n">Azms</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">G2img</span><span class="o">.</span><span class="n">meanAzm</span><span class="p">(</span><span class="n">azm</span><span class="p">,</span><span class="n">azms</span><span class="p">[</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">]))</span>
    10351094    <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">azm</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">azms</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">]):</span>
    10361095        <span class="n">Aname</span> <span class="o">=</span> <span class="n">name</span><span class="o">+</span><span class="s">&quot; Azm= </span><span class="si">%.2f</span><span class="s">&quot;</span><span class="o">%</span><span class="p">(</span><span class="n">Azms</span><span class="p">[</span><span class="n">i</span><span class="p">])</span>
    … …  
    10681127        <span class="k">if</span> <span class="s">&#39;PWDR&#39;</span> <span class="ow">in</span> <span class="n">Aname</span><span class="p">:</span>
    10691128            <span class="n">G2frame</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">G2frame</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;Sample Parameters&#39;</span><span class="p">),</span><span class="n">Sample</span><span class="p">)</span>
    1070             <span class="n">G2frame</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">G2frame</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;Peak List&#39;</span><span class="p">),[])</span>
    1071             <span class="n">G2frame</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">G2frame</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;Index Peak List&#39;</span><span class="p">),[])</span>
     1129            <span class="n">G2frame</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">G2frame</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;Peak List&#39;</span><span class="p">),{</span><span class="s">&#39;sigDict&#39;</span><span class="p">:{},</span><span class="s">&#39;peaks&#39;</span><span class="p">:[]})</span>
     1130            <span class="n">G2frame</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">G2frame</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;Index Peak List&#39;</span><span class="p">),[[],[]])</span>
    10721131            <span class="n">G2frame</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">G2frame</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;Unit Cells List&#39;</span><span class="p">),[])</span>
    10731132            <span class="n">G2frame</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">G2frame</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 Lists&#39;</span><span class="p">),{})</span>
    … …  
    10801139            <span class="s">&#39;Dummy&#39;</span><span class="p">:</span><span class="bp">False</span><span class="p">,</span>
    10811140            <span class="s">&#39;ranId&#39;</span><span class="p">:</span><span class="n">ran</span><span class="o">.</span><span class="n">randint</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="n">sys</span><span class="o">.</span><span class="n">maxint</span><span class="p">),</span>
     1141            <span class="s">&#39;Offset&#39;</span><span class="p">:[</span><span class="mf">0.0</span><span class="p">,</span><span class="mf">0.0</span><span class="p">],</span><span class="s">&#39;delOffset&#39;</span><span class="p">:</span><span class="mf">0.02</span><span class="p">,</span><span class="s">&#39;refOffset&#39;</span><span class="p">:</span><span class="o">-</span><span class="mf">1.0</span><span class="p">,</span><span class="s">&#39;refDelt&#39;</span><span class="p">:</span><span class="mf">0.01</span><span class="p">,</span>
     1142            <span class="s">&#39;qPlot&#39;</span><span class="p">:</span><span class="bp">False</span><span class="p">,</span><span class="s">&#39;dPlot&#39;</span><span class="p">:</span><span class="bp">False</span><span class="p">,</span><span class="s">&#39;sqrtPlot&#39;</span><span class="p">:</span><span class="bp">False</span>
    10821143            <span class="p">}</span>
    10831144        <span class="n">G2frame</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">SetItemPyData</span><span class="p">(</span>
    … …  
    12041265    <span class="k">print</span> <span class="s">&#39;index peak list saved&#39;</span>
    12051266    </div>
    1206 <div class="viewcode-block" id="SetNewPhase"><a class="viewcode-back" href="../GSASIIGUIr.html#GSASIIIO.SetNewPhase">[docs]</a><span class="k">def</span> <span class="nf">SetNewPhase</span><span class="p">(</span><span class="n">Name</span><span class="o">=</span><span class="s">&#39;New Phase&#39;</span><span class="p">,</span><span class="n">SGData</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span><span class="n">cell</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
     1267<div class="viewcode-block" id="SetNewPhase"><a class="viewcode-back" href="../GSASIIGUIr.html#GSASIIIO.SetNewPhase">[docs]</a><span class="k">def</span> <span class="nf">SetNewPhase</span><span class="p">(</span><span class="n">Name</span><span class="o">=</span><span class="s">&#39;New Phase&#39;</span><span class="p">,</span><span class="n">SGData</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span><span class="n">cell</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span><span class="n">Super</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
    12071268    <span class="sd">&#39;&#39;&#39;Create a new phase dict with default values for various parameters</span>
    12081269
    … …  
    12451306        <span class="s">&#39;RBModels&#39;</span><span class="p">:{},</span>
    12461307        <span class="p">}</span>
     1308    <span class="k">if</span> <span class="n">Super</span> <span class="ow">and</span> <span class="n">Super</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">&#39;Use&#39;</span><span class="p">,</span><span class="bp">False</span><span class="p">):</span>
     1309        <span class="n">phaseData</span><span class="p">[</span><span class="s">&#39;General&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s">&#39;Type&#39;</span><span class="p">:</span><span class="s">&#39;modulated&#39;</span><span class="p">,</span><span class="s">&#39;Super&#39;</span><span class="p">:</span><span class="bp">True</span><span class="p">,</span><span class="s">&#39;SuperSg&#39;</span><span class="p">:</span><span class="n">Super</span><span class="p">[</span><span class="s">&#39;ssSymb&#39;</span><span class="p">]})</span>
     1310        <span class="n">phaseData</span><span class="p">[</span><span class="s">&#39;General&#39;</span><span class="p">][</span><span class="s">&#39;SSGData&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">G2spc</span><span class="o">.</span><span class="n">SSpcGroup</span><span class="p">(</span><span class="n">SGData</span><span class="p">,</span><span class="n">Super</span><span class="p">[</span><span class="s">&#39;ssSymb&#39;</span><span class="p">])</span>
     1311        <span class="n">phaseData</span><span class="p">[</span><span class="s">&#39;General&#39;</span><span class="p">][</span><span class="s">&#39;SuperVec&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="n">Super</span><span class="p">[</span><span class="s">&#39;ModVec&#39;</span><span class="p">],</span><span class="bp">False</span><span class="p">,</span><span class="n">Super</span><span class="p">[</span><span class="s">&#39;maxH&#39;</span><span class="p">]]</span>
     1312
    12471313    <span class="k">return</span> <span class="n">phaseData</span>
    12481314       </div>
    … …  
    16741740        <span class="s">&#39;self.Parameters is a list with two dicts for data parameter settings&#39;</span>
    16751741        <span class="bp">self</span><span class="o">.</span><span class="n">InitParameters</span><span class="p">()</span>
    1676         <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span> <span class="o">=</span> <span class="p">{</span><span class="s">&#39;RefList&#39;</span><span class="p">:[],</span><span class="s">&#39;FF&#39;</span><span class="p">:[],</span><span class="s">&#39;Super&#39;</span><span class="p">:</span><span class="mi">0</span><span class="p">}</span>
     1742        <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span> <span class="o">=</span> <span class="p">{</span><span class="s">&#39;RefList&#39;</span><span class="p">:[],</span><span class="s">&#39;FF&#39;</span><span class="p">:{},</span><span class="s">&#39;Super&#39;</span><span class="p">:</span><span class="mi">0</span><span class="p">}</span>
    16771743        <span class="bp">self</span><span class="o">.</span><span class="n">Banks</span> <span class="o">=</span> <span class="p">[]</span>             <span class="c">#for multi bank data (usually TOF)</span>
    16781744        <span class="sd">&#39;&#39;&#39;self.RefDict is a dict containing the reflection information, as read from the file.</span>
    … …  
    16881754        <span class="bp">self</span><span class="o">.</span><span class="n">InitParameters</span><span class="p">()</span>
    16891755        <span class="bp">self</span><span class="o">.</span><span class="n">Banks</span> <span class="o">=</span> <span class="p">[]</span>             <span class="c">#for multi bank data (usually TOF)</span>
    1690         <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span> <span class="o">=</span> <span class="p">{</span><span class="s">&#39;RefList&#39;</span><span class="p">:[],</span><span class="s">&#39;FF&#39;</span><span class="p">:[],</span><span class="s">&#39;Super&#39;</span><span class="p">:</span><span class="mi">0</span><span class="p">}</span>
     1756        <span class="bp">self</span><span class="o">.</span><span class="n">RefDict</span> <span class="o">=</span> <span class="p">{</span><span class="s">&#39;RefList&#39;</span><span class="p">:[],</span><span class="s">&#39;FF&#39;</span><span class="p">:{},</span><span class="s">&#39;Super&#39;</span><span class="p">:</span><span class="mi">0</span><span class="p">}</span>
    16911757        </div>
    16921758<div class="viewcode-block" id="ImportStructFactor.InitParameters"><a class="viewcode-back" href="../GSASIIGUIr.html#GSASIIIO.ImportStructFactor.InitParameters">[docs]</a>    <span class="k">def</span> <span class="nf">InitParameters</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
    … …  
    17431809        <span class="bp">self</span><span class="o">.</span><span class="n">comments</span> <span class="o">=</span> <span class="p">[]</span>
    17441810        <span class="bp">self</span><span class="o">.</span><span class="n">idstring</span> <span class="o">=</span> <span class="s">&#39;&#39;</span>
    1745         <span class="bp">self</span><span class="o">.</span><span class="n">Sample</span> <span class="o">=</span> <span class="n">G2pdG</span><span class="o">.</span><span class="n">SetDefaultSample</span><span class="p">()</span>
     1811        <span class="bp">self</span><span class="o">.</span><span class="n">Sample</span> <span class="o">=</span> <span class="n">G2pdG</span><span class="o">.</span><span class="n">SetDefaultSample</span><span class="p">()</span> <span class="c"># default sample parameters</span>
     1812        <span class="bp">self</span><span class="o">.</span><span class="n">Controls</span> <span class="o">=</span> <span class="p">{}</span>  <span class="c"># items to be placed in top-level Controls </span>
    17461813        <span class="bp">self</span><span class="o">.</span><span class="n">GSAS</span> <span class="o">=</span> <span class="bp">None</span>     <span class="c"># used in TOF</span>
    17471814        <span class="bp">self</span><span class="o">.</span><span class="n">repeat_instparm</span> <span class="o">=</span> <span class="bp">True</span> <span class="c"># Should a parm file be</span>
    … …  
    17541821        <span class="bp">self</span><span class="o">.</span><span class="n">numbanks</span> <span class="o">=</span> <span class="mi">1</span>
    17551822        <span class="bp">self</span><span class="o">.</span><span class="n">instdict</span> <span class="o">=</span> <span class="p">{}</span> <span class="c"># place items here that will be transferred to the instrument parameters</span>
     1823        <span class="bp">self</span><span class="o">.</span><span class="n">pwdparms</span> <span class="o">=</span> <span class="p">{}</span> <span class="c"># place parameters that are transferred directly to the tree</span>
     1824                           <span class="c"># here (typically from an existing GPX file)</span>
    17561825<span class="c">######################################################################</span></div></div>
    17571826<div class="viewcode-block" id="ImportSmallAngleData"><a class="viewcode-back" href="../GSASIIGUIr.html#GSASIIIO.ImportSmallAngleData">[docs]</a><span class="k">class</span> <span class="nc">ImportSmallAngleData</span><span class="p">(</span><span class="n">ImportBaseclass</span><span class="p">):</span>
    … …  
    20512120        <span class="bp">self</span><span class="o">.</span><span class="n">parmDict</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">rbDict</span><span class="p">)</span>
    20522121        <span class="n">rbIds</span> <span class="o">=</span> <span class="n">rigidbodyDict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">&#39;RBIds&#39;</span><span class="p">,{</span><span class="s">&#39;Vector&#39;</span><span class="p">:[],</span><span class="s">&#39;Residue&#39;</span><span class="p">:[]})</span>
    2053         <span class="n">Natoms</span><span class="p">,</span><span class="n">atomIndx</span><span class="p">,</span><span class="n">phaseVary</span><span class="p">,</span><span class="n">phaseDict</span><span class="p">,</span><span class="n">pawleyLookup</span><span class="p">,</span><span class="n">FFtables</span><span class="p">,</span><span class="n">BLtables</span> <span class="o">=</span>  <span class="n">G2stIO</span><span class="o">.</span><span class="n">GetPhaseData</span><span class="p">(</span>
     2122        <span class="n">Natoms</span><span class="p">,</span><span class="n">atomIndx</span><span class="p">,</span><span class="n">phaseVary</span><span class="p">,</span><span class="n">phaseDict</span><span class="p">,</span><span class="n">pawleyLookup</span><span class="p">,</span><span class="n">FFtables</span><span class="p">,</span><span class="n">BLtables</span><span class="p">,</span><span class="n">maxSSwave</span> <span class="o">=</span>  <span class="n">G2stIO</span><span class="o">.</span><span class="n">GetPhaseData</span><span class="p">(</span>
    20542123            <span class="n">Phases</span><span class="p">,</span><span class="n">RestraintDict</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span><span class="n">rbIds</span><span class="o">=</span><span class="n">rbIds</span><span class="p">,</span><span class="n">Print</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span>
    20552124        <span class="bp">self</span><span class="o">.</span><span class="n">parmDict</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">phaseDict</span><span class="p">)</span>
    … …  
    23172386            <span class="n">pfx</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">phasedict</span><span class="p">[</span><span class="s">&#39;pId&#39;</span><span class="p">])</span><span class="o">+</span><span class="s">&#39;::&#39;</span>
    23182387            <span class="n">A</span><span class="p">,</span><span class="n">sigA</span> <span class="o">=</span> <span class="n">G2stIO</span><span class="o">.</span><span class="n">cellFill</span><span class="p">(</span><span class="n">pfx</span><span class="p">,</span><span class="n">phasedict</span><span class="p">[</span><span class="s">&#39;General&#39;</span><span class="p">][</span><span class="s">&#39;SGData&#39;</span><span class="p">],</span><span class="bp">self</span><span class="o">.</span><span class="n">parmDict</span><span class="p">,</span><span class="bp">self</span><span class="o">.</span><span class="n">sigDict</span><span class="p">)</span>
    2319             <span class="n">cellSig</span> <span class="o">=</span> <span class="n">G2stIO</span><span class="o">.</span><span class="n">getCellEsd</span><span class="p">(</span><span class="n">pfx</span><span class="p">,</span>
    2320                                         <span class="n">phasedict</span><span class="p">[</span><span class="s">&#39;General&#39;</span><span class="p">][</span><span class="s">&#39;SGData&#39;</span><span class="p">],</span><span class="n">A</span><span class="p">,</span>
    2321                                         <span class="bp">self</span><span class="o">.</span><span class="n">OverallParms</span><span class="p">[</span><span class="s">&#39;Covariance&#39;</span><span class="p">])</span>  <span class="c"># returns 7 vals, includes sigVol</span>
     2388            <span class="n">cellSig</span> <span class="o">=</span> <span class="n">G2stIO</span><span class="o">.</span><span class="n">getCellEsd</span><span class="p">(</span><span class="n">pfx</span><span class="p">,</span><span class="n">phasedict</span><span class="p">[</span><span class="s">&#39;General&#39;</span><span class="p">][</span><span class="s">&#39;SGData&#39;</span><span class="p">],</span><span class="n">A</span><span class="p">,</span>
     2389                <span class="bp">self</span><span class="o">.</span><span class="n">OverallParms</span><span class="p">[</span><span class="s">&#39;Covariance&#39;</span><span class="p">])</span>  <span class="c"># returns 7 vals, includes sigVol</span>
    23222390            <span class="n">cellList</span> <span class="o">=</span> <span class="n">G2lat</span><span class="o">.</span><span class="n">A2cell</span><span class="p">(</span><span class="n">A</span><span class="p">)</span> <span class="o">+</span> <span class="p">(</span><span class="n">G2lat</span><span class="o">.</span><span class="n">calc_V</span><span class="p">(</span><span class="n">A</span><span class="p">),)</span>
    23232391            <span class="k">return</span> <span class="n">cellList</span><span class="p">,</span><span class="n">cellSig</span>
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