Changeset 2010 for sphinxdocs/build/html


Ignore:
Timestamp:
Oct 16, 2015 11:13:04 AM (7 years ago)
Author:
toby
Message:

update docs

Location:
sphinxdocs/build/html
Files:
16 edited

Legend:

Unmodified
Added
Removed
  • sphinxdocs/build/html/GSASII.html

    r1998 r2010  
    381381<dl class="method">
    382382<dt id="GSASII.GSASII.OnImportGeneric">
    383 <tt class="descclassname">GSASII.</tt><tt class="descname">OnImportGeneric</tt><big>(</big><em>reader</em>, <em>readerlist</em>, <em>label</em>, <em>multiple=False</em>, <em>usedRanIdList=</em><span class="optional">[</span><span class="optional">]</span><big>)</big><a class="reference internal" href="_modules/GSASII.html#GSASII.OnImportGeneric"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASII.GSASII.OnImportGeneric" title="Permalink to this definition">¶</a></dt>
    384 <dd><p>Used to import Phases, powder dataset or single
    385 crystal datasets (structure factor tables) using reader objects
    386 subclassed from <a class="reference internal" href="GSASIIGUIr.html#GSASIIIO.ImportPhase" title="GSASIIIO.ImportPhase"><tt class="xref py py-class docutils literal"><span class="pre">GSASIIIO.ImportPhase</span></tt></a>, <a class="reference internal" href="GSASIIGUIr.html#GSASIIIO.ImportStructFactor" title="GSASIIIO.ImportStructFactor"><tt class="xref py py-class docutils literal"><span class="pre">GSASIIIO.ImportStructFactor</span></tt></a>
    387 or <a class="reference internal" href="GSASIIGUIr.html#GSASIIIO.ImportPowderData" title="GSASIIIO.ImportPowderData"><tt class="xref py py-class docutils literal"><span class="pre">GSASIIIO.ImportPowderData</span></tt></a>. If a reader is specified, only
    388 that will be attempted, but if no reader is specified, every one
    389 that is potentially compatible (by file extension) will
    390 be tried on the selected file(s).</p>
     383<tt class="descclassname">GSASII.</tt><tt class="descname">OnImportGeneric</tt><big>(</big><em>reader</em>, <em>readerlist</em>, <em>label</em>, <em>multiple=False</em>, <em>usedRanIdList=</em>, <span class="optional">[</span><span class="optional">]</span><em>Preview=True</em><big>)</big><a class="reference internal" href="_modules/GSASII.html#GSASII.OnImportGeneric"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASII.GSASII.OnImportGeneric" title="Permalink to this definition">¶</a></dt>
     384<dd><p>Used to import Phases or datasets using reader objects
     385subclassed from <a class="reference internal" href="GSASIIGUIr.html#GSASIIIO.ImportPhase" title="GSASIIIO.ImportPhase"><tt class="xref py py-class docutils literal"><span class="pre">GSASIIIO.ImportPhase</span></tt></a>,
     386<a class="reference internal" href="GSASIIGUIr.html#GSASIIIO.ImportStructFactor" title="GSASIIIO.ImportStructFactor"><tt class="xref py py-class docutils literal"><span class="pre">GSASIIIO.ImportStructFactor</span></tt></a>,
     387<a class="reference internal" href="GSASIIGUIr.html#GSASIIIO.ImportPowderData" title="GSASIIIO.ImportPowderData"><tt class="xref py py-class docutils literal"><span class="pre">GSASIIIO.ImportPowderData</span></tt></a>,
     388<a class="reference internal" href="GSASIIGUIr.html#GSASIIIO.ImportSmallAngleData" title="GSASIIIO.ImportSmallAngleData"><tt class="xref py py-class docutils literal"><span class="pre">GSASIIIO.ImportSmallAngleData</span></tt></a> or
     389<a class="reference internal" href="GSASIIGUIr.html#GSASIIIO.ImportImage" title="GSASIIIO.ImportImage"><tt class="xref py py-class docutils literal"><span class="pre">GSASIIIO.ImportImage</span></tt></a>.
     390If a specific reader is specified, only that method will be called,
     391but if no reader is specified, every one that is potentially
     392compatible (by file extension) will be tried on the file(s)
     393selected in the Open File dialog.</p>
    391394<table class="docutils field-list" frame="void" rules="none">
    392395<col class="field-name" />
     
    410413<li><strong>usedRanIdList</strong> (<em>list</em>) &#8211; an optional list of random Ids that
    411414have been used and should not be reused</li>
     415<li><strong>Preview</strong> (<em>bool</em>) &#8211; indicates if a preview of the file should
     416be shown. Default is True, but set to False for image files
     417which are all binary.</li>
    412418</ul>
    413419</td>
     
    419425</tbody>
    420426</table>
     427</dd></dl>
     428
     429<dl class="method">
     430<dt id="GSASII.GSASII.OnImportImage">
     431<tt class="descclassname">GSASII.</tt><tt class="descname">OnImportImage</tt><big>(</big><em>event</em><big>)</big><a class="reference internal" href="_modules/GSASII.html#GSASII.OnImportImage"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASII.GSASII.OnImportImage" title="Permalink to this definition">¶</a></dt>
     432<dd><p>Called in response to an Import/Image/... menu item
     433to read an image from a file. Like all the other imports,
     434dict self.ImportMenuId is used to look up the specific
     435reader item associated with the menu item, which will be
     436None for the last menu item, which is the &#8220;guess&#8221; option
     437where all appropriate formats will be tried.</p>
     438<p>A reader object is filled each time an image is read.</p>
    421439</dd></dl>
    422440
     
    573591</tbody>
    574592</table>
     593</dd></dl>
     594
     595<dl class="method">
     596<dt id="GSASII.GSASII.PreviewFile">
     597<tt class="descclassname">GSASII.</tt><tt class="descname">PreviewFile</tt><big>(</big><em>filename</em>, <em>fp</em><big>)</big><a class="reference internal" href="_modules/GSASII.html#GSASII.PreviewFile"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASII.GSASII.PreviewFile" title="Permalink to this definition">¶</a></dt>
     598<dd><p>confirm we have the right file</p>
    575599</dd></dl>
    576600
  • sphinxdocs/build/html/GSASIIGUIr.html

    r1998 r2010  
    16261626<dt id="GSASIIIO.CheckImageFile">
    16271627<tt class="descclassname">GSASIIIO.</tt><tt class="descname">CheckImageFile</tt><big>(</big><em>G2frame</em>, <em>imagefile</em><big>)</big><a class="reference internal" href="_modules/GSASIIIO.html#CheckImageFile"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIIO.CheckImageFile" title="Permalink to this definition">¶</a></dt>
    1628 <dd><p>Get an new image file name if the specified one does not
    1629 exist</p>
     1628<dd><p>Try to locate an image file if the project and image have been moved
     1629together. If the image file cannot be found, request the location from
     1630the user.</p>
    16301631<table class="docutils field-list" frame="void" rules="none">
    16311632<col class="field-name" />
     
    21172118<tt class="descclassname">ImportBaseclass.</tt><tt class="descname">ReInitialize</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/GSASIIIO.html#ImportBaseclass.ReInitialize"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIIO.ImportBaseclass.ReInitialize" title="Permalink to this definition">¶</a></dt>
    21182119<dd><p>Reinitialize the Reader to initial settings</p>
     2120</dd></dl>
     2121
     2122</dd></dl>
     2123
     2124<dl class="class">
     2125<dt id="GSASIIIO.ImportImage">
     2126<em class="property">class </em><tt class="descclassname">GSASIIIO.</tt><tt class="descname">ImportImage</tt><big>(</big><em>formatName</em>, <em>longFormatName=None</em>, <em>extensionlist=</em>, <span class="optional">[</span><span class="optional">]</span><em>strictExtension=False</em><big>)</big><a class="reference internal" href="_modules/GSASIIIO.html#ImportImage"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIIO.ImportImage" title="Permalink to this definition">¶</a></dt>
     2127<dd><p>Defines a base class for the reading of images</p>
     2128<p>Structure factors are read with a call to <a class="reference internal" href="GSASII.html#GSASII.GSASII.OnImportImage" title="GSASII.GSASII.OnImportImage"><tt class="xref py py-meth docutils literal"><span class="pre">GSASII.GSASII.OnImportImage()</span></tt></a>
     2129which in turn calls <a class="reference internal" href="GSASII.html#GSASII.GSASII.OnImportGeneric" title="GSASII.GSASII.OnImportGeneric"><tt class="xref py py-meth docutils literal"><span class="pre">GSASII.GSASII.OnImportGeneric()</span></tt></a>, which calls
     2130methods <tt class="xref py py-meth docutils literal"><span class="pre">ExtensionValidator()</span></tt>, <tt class="xref py py-meth docutils literal"><span class="pre">ContentsValidator()</span></tt> and
     2131<tt class="xref py py-meth docutils literal"><span class="pre">Reader()</span></tt>.</p>
     2132<p>See <a class="reference internal" href="imports.html#import-routines"><em>Writing a Import Routine</em></a>
     2133for an explanation on how to use import classes in general. The specifics
     2134for reading an image requires that the <tt class="docutils literal"><span class="pre">Reader()</span></tt> routine in the import
     2135class need to do only a few things:...</p>
     2136<p>(should load <tt class="xref py py-attr docutils literal"><span class="pre">RefDict</span></tt> item <tt class="docutils literal"><span class="pre">'RefList'</span></tt> with the reflection list,
     2137(and set <tt class="xref py py-attr docutils literal"><span class="pre">Parameters</span></tt> with the instrument parameters
     2138(initialized with <a class="reference internal" href="#GSASIIIO.ImportImage.InitParameters" title="GSASIIIO.ImportImage.InitParameters"><tt class="xref py py-meth docutils literal"><span class="pre">InitParameters()</span></tt></a> and set with <tt class="xref py py-meth docutils literal"><span class="pre">UpdateParameters()</span></tt>).</p>
     2139<dl class="method">
     2140<dt id="GSASIIIO.ImportImage.InitParameters">
     2141<tt class="descname">InitParameters</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/GSASIIIO.html#ImportImage.InitParameters"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIIO.ImportImage.InitParameters" title="Permalink to this definition">¶</a></dt>
     2142<dd><p>initialize the instrument parameters structure</p>
     2143</dd></dl>
     2144
     2145<dl class="method">
     2146<dt id="GSASIIIO.ImportImage.ReInitialize">
     2147<tt class="descname">ReInitialize</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/GSASIIIO.html#ImportImage.ReInitialize"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIIO.ImportImage.ReInitialize" title="Permalink to this definition">¶</a></dt>
     2148<dd><p>Reinitialize the Reader to initial settings &#8211; not used at present</p>
    21192149</dd></dl>
    21202150
     
    22282258</dd></dl>
    22292259
     2260<dl class="function">
     2261<dt id="GSASIIIO.LoadImage">
     2262<tt class="descclassname">GSASIIIO.</tt><tt class="descname">LoadImage</tt><big>(</big><em>imagefile</em>, <em>G2frame</em>, <em>Comments</em>, <em>Data</em>, <em>Npix</em>, <em>Image</em><big>)</big><a class="reference internal" href="_modules/GSASIIIO.html#LoadImage"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIIO.LoadImage" title="Permalink to this definition">¶</a></dt>
     2263<dd><p>Load an image into the tree</p>
     2264</dd></dl>
     2265
    22302266<dl class="class">
    22312267<dt id="GSASIIIO.MultipleChoicesDialog">
     
    22892325</tr>
    22902326<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">a PyCifRW CIF object.</td>
     2327</tr>
     2328</tbody>
     2329</table>
     2330</dd></dl>
     2331
     2332<dl class="function">
     2333<dt id="GSASIIIO.ReadImageData">
     2334<tt class="descclassname">GSASIIIO.</tt><tt class="descname">ReadImageData</tt><big>(</big><em>G2frame</em>, <em>imagefile</em>, <em>imageOnly=False</em><big>)</big><a class="reference internal" href="_modules/GSASIIIO.html#ReadImageData"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIIO.ReadImageData" title="Permalink to this definition">¶</a></dt>
     2335<dd><p>Read a single image with an image importer. replacement for GetImageData</p>
     2336<table class="docutils field-list" frame="void" rules="none">
     2337<col class="field-name" />
     2338<col class="field-body" />
     2339<tbody valign="top">
     2340<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
     2341<li><strong>G2frame</strong> (<em>wx.Frame</em>) &#8211; main GSAS-II Frame and data object.</li>
     2342<li><strong>imagefile</strong> (<em>str</em>) &#8211; name of image file</li>
     2343<li><strong>imageOnly</strong> (<em>bool</em>) &#8211; If True return only the image,
     2344otherwise  (default) return more (see below)</li>
     2345</ul>
     2346</td>
     2347</tr>
     2348<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">an image as a numpy array or a list of four items:
     2349Comments, Data, Npix and the Image, as selected by imageOnly</p>
     2350</td>
    22912351</tr>
    22922352</tbody>
  • sphinxdocs/build/html/GSASIIutil.html

    r1998 r2010  
    645645
    646646<dl class="data">
     647<dt id="config_example.Transpose">
     648<tt class="descclassname">config_example.</tt><tt class="descname">Transpose</tt><em class="property"> = False</em><a class="headerlink" href="#config_example.Transpose" title="Permalink to this definition">¶</a></dt>
     649<dd><p>Set to True to cause images to be Transposed when read (for code development)</p>
     650</dd></dl>
     651
     652<dl class="data">
    647653<dt id="config_example.Tutorial_location">
    648654<tt class="descclassname">config_example.</tt><tt class="descname">Tutorial_location</tt><em class="property"> = None</em><a class="headerlink" href="#config_example.Tutorial_location" title="Permalink to this definition">¶</a></dt>
     
    16681674<dl class="data">
    16691675<dt id="GSASIIlattice.selftestlist">
    1670 <tt class="descclassname">GSASIIlattice.</tt><tt class="descname">selftestlist</tt><em class="property"> = [&lt;function test0 at 0x10999caa0&gt;, &lt;function test1 at 0x10999cb18&gt;, &lt;function test2 at 0x10999cb90&gt;, &lt;function test3 at 0x10999cc08&gt;, &lt;function test4 at 0x10999cc80&gt;, &lt;function test5 at 0x10999ccf8&gt;, &lt;function test6 at 0x10999cd70&gt;, &lt;function test7 at 0x10999cde8&gt;, &lt;function test8 at 0x10999ce60&gt;, &lt;function test9 at 0x10999ced8&gt;]</em><a class="headerlink" href="#GSASIIlattice.selftestlist" title="Permalink to this definition">¶</a></dt>
     1676<tt class="descclassname">GSASIIlattice.</tt><tt class="descname">selftestlist</tt><em class="property"> = [&lt;function test0 at 0x108faaaa0&gt;, &lt;function test1 at 0x108faab18&gt;, &lt;function test2 at 0x108faab90&gt;, &lt;function test3 at 0x108faac08&gt;, &lt;function test4 at 0x108faac80&gt;, &lt;function test5 at 0x108faacf8&gt;, &lt;function test6 at 0x108faad70&gt;, &lt;function test7 at 0x108faade8&gt;, &lt;function test8 at 0x108faae60&gt;, &lt;function test9 at 0x108faaed8&gt;]</em><a class="headerlink" href="#GSASIIlattice.selftestlist" title="Permalink to this definition">¶</a></dt>
    16711677<dd><p>Defines a list of self-tests</p>
    16721678</dd></dl>
     
    22542260<dl class="data">
    22552261<dt id="GSASIIspc.selftestlist">
    2256 <tt class="descclassname">GSASIIspc.</tt><tt class="descname">selftestlist</tt><em class="property"> = [&lt;function test0 at 0x109992320&gt;, &lt;function test1 at 0x109992398&gt;, &lt;function test2 at 0x109992410&gt;, &lt;function test3 at 0x109992488&gt;]</em><a class="headerlink" href="#GSASIIspc.selftestlist" title="Permalink to this definition">¶</a></dt>
     2262<tt class="descclassname">GSASIIspc.</tt><tt class="descname">selftestlist</tt><em class="property"> = [&lt;function test0 at 0x108fa1320&gt;, &lt;function test1 at 0x108fa1398&gt;, &lt;function test2 at 0x108fa1410&gt;, &lt;function test3 at 0x108fa1488&gt;]</em><a class="headerlink" href="#GSASIIspc.selftestlist" title="Permalink to this definition">¶</a></dt>
    22572263<dd><p>Defines a list of self-tests</p>
    22582264</dd></dl>
  • sphinxdocs/build/html/_modules/GSASII.html

    r1998 r2010  
    5353<span class="c">#GSASII</span>
    5454<span class="c">########### SVN repository information ###################</span>
    55 <span class="c"># $Date: 2015-10-10 11:58:12 -0500 (Sat, 10 Oct 2015) $</span>
     55<span class="c"># $Date: 2015-10-12 17:31:16 -0500 (Mon, 12 Oct 2015) $</span>
    5656<span class="c"># $Author: toby $</span>
    57 <span class="c"># $Revision: 1997 $</span>
     57<span class="c"># $Revision: 2003 $</span>
    5858<span class="c"># $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/GSASII.py $</span>
    59 <span class="c"># $Id: GSASII.py 1997 2015-10-10 16:58:12Z toby $</span>
     59<span class="c"># $Id: GSASII.py 2003 2015-10-12 22:31:16Z 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: 1997 $&quot;</span><span class="p">)</span>
     117<span class="n">GSASIIpath</span><span class="o">.</span><span class="n">SetVersionNumber</span><span class="p">(</span><span class="s">&quot;$Revision: 2003 $&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>
     
    292292        <span class="bp">self</span><span class="o">.</span><span class="n">ImportSmallAngleReaderlist</span> <span class="o">=</span> <span class="p">[]</span>
    293293        <span class="bp">self</span><span class="o">.</span><span class="n">_init_Import_routines</span><span class="p">(</span><span class="s">&#39;sad&#39;</span><span class="p">,</span><span class="bp">self</span><span class="o">.</span><span class="n">ImportSmallAngleReaderlist</span><span class="p">,</span><span class="s">&#39;SmallAngle_Data&#39;</span><span class="p">)</span>
     294        <span class="bp">self</span><span class="o">.</span><span class="n">ImportImageReaderlist</span> <span class="o">=</span> <span class="p">[]</span>
     295        <span class="bp">self</span><span class="o">.</span><span class="n">_init_Import_routines</span><span class="p">(</span><span class="s">&#39;img&#39;</span><span class="p">,</span><span class="bp">self</span><span class="o">.</span><span class="n">ImportImageReaderlist</span><span class="p">,</span><span class="s">&#39;Images&#39;</span><span class="p">)</span>
    294296        <span class="bp">self</span><span class="o">.</span><span class="n">ImportMenuId</span> <span class="o">=</span> <span class="p">{}</span>
    295297
     
    351353            <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">SeqRefine</span><span class="p">:</span> <span class="n">i</span><span class="o">.</span><span class="n">Enable</span><span class="p">(</span><span class="bp">False</span><span class="p">)</span>
    352354</div>
    353 <div class="viewcode-block" id="GSASII.OnImportGeneric"><a class="viewcode-back" href="../GSASII.html#GSASII.GSASII.OnImportGeneric">[docs]</a>    <span class="k">def</span> <span class="nf">OnImportGeneric</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">reader</span><span class="p">,</span><span class="n">readerlist</span><span class="p">,</span><span class="n">label</span><span class="p">,</span><span class="n">multiple</span><span class="o">=</span><span class="bp">False</span><span class="p">,</span><span class="n">usedRanIdList</span><span class="o">=</span><span class="p">[]):</span>
    354         <span class="sd">&#39;&#39;&#39;Used to import Phases, powder dataset or single</span>
    355 <span class="sd">        crystal datasets (structure factor tables) using reader objects</span>
    356 <span class="sd">        subclassed from :class:`GSASIIIO.ImportPhase`, :class:`GSASIIIO.ImportStructFactor`</span>
    357 <span class="sd">        or :class:`GSASIIIO.ImportPowderData`. If a reader is specified, only</span>
    358 <span class="sd">        that will be attempted, but if no reader is specified, every one</span>
    359 <span class="sd">        that is potentially compatible (by file extension) will</span>
    360 <span class="sd">        be tried on the selected file(s). </span>
     355<div class="viewcode-block" id="GSASII.PreviewFile"><a class="viewcode-back" href="../GSASII.html#GSASII.GSASII.PreviewFile">[docs]</a>    <span class="k">def</span> <span class="nf">PreviewFile</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">filename</span><span class="p">,</span><span class="n">fp</span><span class="p">):</span>
     356        <span class="s">&#39;confirm we have the right file&#39;</span>
     357        <span class="n">rdmsg</span> <span class="o">=</span> <span class="s">&#39;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><span class="o">+</span><span class="s">&#39; begins:</span><span class="se">\n\n</span><span class="s">&#39;</span>
     358        <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">3</span><span class="p">):</span>
     359            <span class="n">rdmsg</span> <span class="o">+=</span> <span class="n">fp</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>
     360        <span class="n">rdmsg</span> <span class="o">+=</span> <span class="s">&#39;</span><span class="se">\n\n</span><span class="s">Do you want to read this file?&#39;</span>
     361        <span class="k">if</span> <span class="ow">not</span> <span class="nb">all</span><span class="p">([</span><span class="nb">ord</span><span class="p">(</span><span class="n">c</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">128</span> <span class="ow">and</span> <span class="nb">ord</span><span class="p">(</span><span class="n">c</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">0</span> <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">rdmsg</span><span class="p">]):</span> <span class="c"># show only if ASCII</span>
     362            <span class="n">rdmsg</span> <span class="o">=</span> <span class="s">&#39;File &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span>
     363                <span class="n">filename</span><span class="p">)</span><span class="o">+</span><span class="s">&#39; is a binary file. Do you want to read this file?&#39;</span>
     364        <span class="c"># it would be better to use something that</span>
     365        <span class="c"># would resize better, but this will do for now</span>
     366        <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>
     367            <span class="bp">self</span><span class="p">,</span> <span class="n">rdmsg</span><span class="p">,</span>
     368            <span class="s">&#39;Is this the file you want?&#39;</span><span class="p">,</span>
     369            <span class="n">wx</span><span class="o">.</span><span class="n">YES_NO</span> <span class="o">|</span> <span class="n">wx</span><span class="o">.</span><span class="n">ICON_QUESTION</span><span class="p">,</span>
     370            <span class="p">)</span>
     371        <span class="n">dlg</span><span class="o">.</span><span class="n">SetSize</span><span class="p">((</span><span class="mi">700</span><span class="p">,</span><span class="mi">300</span><span class="p">))</span> <span class="c"># does not resize on Mac</span>
     372        <span class="n">result</span> <span class="o">=</span> <span class="n">wx</span><span class="o">.</span><span class="n">ID_NO</span>
     373        <span class="k">try</span><span class="p">:</span>
     374            <span class="n">result</span> <span class="o">=</span> <span class="n">dlg</span><span class="o">.</span><span class="n">ShowModal</span><span class="p">()</span>
     375        <span class="k">finally</span><span class="p">:</span>
     376            <span class="n">dlg</span><span class="o">.</span><span class="n">Destroy</span><span class="p">()</span>
     377        <span class="k">if</span> <span class="n">result</span> <span class="o">==</span> <span class="n">wx</span><span class="o">.</span><span class="n">ID_NO</span><span class="p">:</span> <span class="k">return</span> <span class="bp">True</span>
     378        <span class="k">return</span> <span class="bp">False</span>
     379    </div>
     380<div class="viewcode-block" id="GSASII.OnImportGeneric"><a class="viewcode-back" href="../GSASII.html#GSASII.GSASII.OnImportGeneric">[docs]</a>    <span class="k">def</span> <span class="nf">OnImportGeneric</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">reader</span><span class="p">,</span><span class="n">readerlist</span><span class="p">,</span><span class="n">label</span><span class="p">,</span><span class="n">multiple</span><span class="o">=</span><span class="bp">False</span><span class="p">,</span>
     381                        <span class="n">usedRanIdList</span><span class="o">=</span><span class="p">[],</span><span class="n">Preview</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
     382        <span class="sd">&#39;&#39;&#39;Used to import Phases or datasets using reader objects</span>
     383<span class="sd">        subclassed from :class:`GSASIIIO.ImportPhase`,</span>
     384<span class="sd">        :class:`GSASIIIO.ImportStructFactor`,</span>
     385<span class="sd">        :class:`GSASIIIO.ImportPowderData`,</span>
     386<span class="sd">        :class:`GSASIIIO.ImportSmallAngleData` or</span>
     387<span class="sd">        :class:`GSASIIIO.ImportImage`.</span>
     388<span class="sd">        If a specific reader is specified, only that method will be called,</span>
     389<span class="sd">        but if no reader is specified, every one that is potentially</span>
     390<span class="sd">        compatible (by file extension) will be tried on the file(s)</span>
     391<span class="sd">        selected in the Open File dialog.</span>
    361392
    362393<span class="sd">        :param readerobject reader: This will be a reference to</span>
     
    380411<span class="sd">        :param list usedRanIdList: an optional list of random Ids that </span>
    381412<span class="sd">          have been used and should not be reused</span>
     413
     414<span class="sd">        :param bool Preview: indicates if a preview of the file should</span>
     415<span class="sd">          be shown. Default is True, but set to False for image files</span>
     416<span class="sd">          which are all binary. </span>
    382417
    383418<span class="sd">        :returns: a list of reader objects (rd_list) that were able</span>
     
    447482                <span class="k">if</span> <span class="n">extractedfile</span> <span class="o">!=</span> <span class="n">filename</span><span class="p">:</span>
    448483                    <span class="n">filename</span><span class="p">,</span><span class="bp">self</span><span class="o">.</span><span class="n">zipfile</span> <span class="o">=</span> <span class="n">extractedfile</span><span class="p">,</span><span class="n">filename</span> <span class="c"># now use the file that was created</span>
    449             <span class="c"># set what formats are compatible with this file</span>
     484            <span class="c"># determine which formats are compatible with this file</span>
    450485            <span class="n">primaryReaders</span> <span class="o">=</span> <span class="p">[]</span>
    451486            <span class="n">secondaryReaders</span> <span class="o">=</span> <span class="p">[]</span>
     
    456491                <span class="k">elif</span> <span class="n">flag</span><span class="p">:</span>
    457492                    <span class="n">primaryReaders</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">rd</span><span class="p">)</span>
    458             <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">secondaryReaders</span><span class="p">)</span> <span class="o">+</span> <span class="nb">len</span><span class="p">(</span><span class="n">primaryReaders</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
     493            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">secondaryReaders</span><span class="p">)</span> <span class="o">+</span> <span class="nb">len</span><span class="p">(</span><span class="n">primaryReaders</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span> <span class="ow">and</span> <span class="n">reader</span><span class="p">:</span>
     494                <span class="bp">self</span><span class="o">.</span><span class="n">ErrorDialog</span><span class="p">(</span><span class="s">&#39;Not supported&#39;</span><span class="p">,</span><span class="s">&#39;The selected reader cannot read file &#39;</span><span class="o">+</span><span class="n">filename</span><span class="p">)</span>
     495                <span class="k">return</span> <span class="p">[]</span>
     496            <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">secondaryReaders</span><span class="p">)</span> <span class="o">+</span> <span class="nb">len</span><span class="p">(</span><span class="n">primaryReaders</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
    459497                <span class="bp">self</span><span class="o">.</span><span class="n">ErrorDialog</span><span class="p">(</span><span class="s">&#39;No Format&#39;</span><span class="p">,</span><span class="s">&#39;No matching format for file &#39;</span><span class="o">+</span><span class="n">filename</span><span class="p">)</span>
    460498                <span class="k">return</span> <span class="p">[]</span>
     
    462500            <span class="n">fp</span> <span class="o">=</span> <span class="bp">None</span>
    463501            <span class="n">msg</span> <span class="o">=</span> <span class="s">&#39;&#39;</span>
    464             <span class="k">try</span><span class="p">:</span>
    465                 <span class="n">fp</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span><span class="s">&#39;Ur&#39;</span><span class="p">)</span>
    466                 <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">filelist</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
    467                     <span class="c"># confirm we have the right file</span>
    468                     <span class="n">rdmsg</span> <span class="o">=</span> <span class="s">&#39;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><span class="o">+</span><span class="s">&#39; begins:</span><span class="se">\n\n</span><span class="s">&#39;</span>
    469                     <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">3</span><span class="p">):</span>
    470                         <span class="n">rdmsg</span> <span class="o">+=</span> <span class="n">fp</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>
    471                     <span class="n">rdmsg</span> <span class="o">+=</span> <span class="s">&#39;</span><span class="se">\n\n</span><span class="s">Do you want to read this file?&#39;</span>
    472                     <span class="k">if</span> <span class="ow">not</span> <span class="nb">all</span><span class="p">([</span><span class="nb">ord</span><span class="p">(</span><span class="n">c</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">128</span> <span class="ow">and</span> <span class="nb">ord</span><span class="p">(</span><span class="n">c</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">0</span> <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">rdmsg</span><span class="p">]):</span> <span class="c"># show only if ASCII</span>
    473                         <span class="n">rdmsg</span> <span class="o">=</span> <span class="s">&#39;File &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span>
    474                             <span class="n">filename</span><span class="p">)</span><span class="o">+</span><span class="s">&#39; is a binary file. Do you want to read this file?&#39;</span>
    475                     <span class="n">result</span> <span class="o">=</span> <span class="n">wx</span><span class="o">.</span><span class="n">ID_NO</span>
    476                     <span class="c"># it would be better to use something that</span>
    477                     <span class="c"># would resize better, but this will do for now</span>
    478                     <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>
    479                         <span class="bp">self</span><span class="p">,</span> <span class="n">rdmsg</span><span class="p">,</span>
    480                         <span class="s">&#39;Is this the file you want?&#39;</span><span class="p">,</span>
    481                         <span class="n">wx</span><span class="o">.</span><span class="n">YES_NO</span> <span class="o">|</span> <span class="n">wx</span><span class="o">.</span><span class="n">ICON_QUESTION</span><span class="p">,</span>
    482                         <span class="p">)</span>
    483                     <span class="n">dlg</span><span class="o">.</span><span class="n">SetSize</span><span class="p">((</span><span class="mi">700</span><span class="p">,</span><span class="mi">300</span><span class="p">))</span> <span class="c"># does not resize on Mac</span>
    484                     <span class="k">try</span><span class="p">:</span>
    485                         <span class="n">result</span> <span class="o">=</span> <span class="n">dlg</span><span class="o">.</span><span class="n">ShowModal</span><span class="p">()</span>
    486                     <span class="k">finally</span><span class="p">:</span>
    487                         <span class="n">dlg</span><span class="o">.</span><span class="n">Destroy</span><span class="p">()</span>
    488                     <span class="k">if</span> <span class="n">result</span> <span class="o">==</span> <span class="n">wx</span><span class="o">.</span><span class="n">ID_NO</span><span class="p">:</span> <span class="k">return</span> <span class="p">[]</span>
    489                            
    490                 <span class="bp">self</span><span class="o">.</span><span class="n">lastimport</span> <span class="o">=</span> <span class="n">filename</span> <span class="c"># this is probably not what I want to do -- it saves only the</span>
    491                 <span class="c"># last name in a series. See rd.readfilename for a better name.</span>
    492                
    493                 <span class="c"># try the file first with Readers that specify the</span>
    494                 <span class="c"># file&#39;s extension and later with ones that merely allow it</span>
    495                 <span class="n">errorReport</span> <span class="o">=</span> <span class="s">&#39;&#39;</span>
    496                 <span class="k">for</span> <span class="n">rd</span> <span class="ow">in</span> <span class="n">primaryReaders</span><span class="o">+</span><span class="n">secondaryReaders</span><span class="p">:</span>
    497                     <span class="n">rd</span><span class="o">.</span><span class="n">ReInitialize</span><span class="p">()</span> <span class="c"># purge anything from a previous read</span>
     502            <span class="n">fp</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span><span class="s">&#39;Ur&#39;</span><span class="p">)</span>
     503            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">filelist</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">and</span> <span class="n">Preview</span><span class="p">:</span>
     504                <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">PreviewFile</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span><span class="n">fp</span><span class="p">):</span> <span class="k">return</span> <span class="p">[]</span>
     505            <span class="bp">self</span><span class="o">.</span><span class="n">lastimport</span> <span class="o">=</span> <span class="n">filename</span> <span class="c"># this is probably not what I want to do -- it saves only the</span>
     506            <span class="c"># last name in a series. See rd.readfilename for a better name.</span>
     507
     508            <span class="c"># try the file first with Readers that specify the</span>
     509            <span class="c"># file&#39;s extension and later with ones that merely allow it</span>
     510            <span class="n">errorReport</span> <span class="o">=</span> <span class="s">&#39;&#39;</span>
     511            <span class="k">for</span> <span class="n">rd</span> <span class="ow">in</span> <span class="n">primaryReaders</span><span class="o">+</span><span class="n">secondaryReaders</span><span class="p">:</span>
     512                <span class="n">rd</span><span class="o">.</span><span class="n">ReInitialize</span><span class="p">()</span> <span class="c"># purge anything from a previous read</span>
     513                <span class="n">fp</span><span class="o">.</span><span class="n">seek</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>  <span class="c"># rewind</span>
     514                <span class="n">rd</span><span class="o">.</span><span class="n">errors</span> <span class="o">=</span> <span class="s">&quot;&quot;</span> <span class="c"># clear out any old errors</span>
     515                <span class="k">if</span> <span class="ow">not</span> <span class="n">rd</span><span class="o">.</span><span class="n">ContentsValidator</span><span class="p">(</span><span class="n">fp</span><span class="p">):</span> <span class="c"># rejected on cursory check</span>
     516                    <span class="n">errorReport</span> <span class="o">+=</span> <span class="s">&quot;</span><span class="se">\n</span><span class="s">  &quot;</span><span class="o">+</span><span class="n">rd</span><span class="o">.</span><span class="n">formatName</span> <span class="o">+</span> <span class="s">&#39; validator error&#39;</span>
     517                    <span class="k">if</span> <span class="n">rd</span><span class="o">.</span><span class="n">errors</span><span class="p">:</span>
     518                        <span class="n">errorReport</span> <span class="o">+=</span> <span class="s">&#39;: &#39;</span><span class="o">+</span><span class="n">rd</span><span class="o">.</span><span class="n">errors</span>
     519                    <span class="k">continue</span>
     520                <span class="n">repeat</span> <span class="o">=</span> <span class="bp">True</span>
     521                <span class="n">rdbuffer</span> <span class="o">=</span> <span class="p">{}</span> <span class="c"># create temporary storage for file reader</span>
     522                <span class="n">block</span> <span class="o">=</span> <span class="mi">0</span>
     523                <span class="k">while</span> <span class="n">repeat</span><span class="p">:</span> <span class="c"># loop if the reader asks for another pass on the file</span>
     524                    <span class="n">block</span> <span class="o">+=</span> <span class="mi">1</span>
     525                    <span class="n">repeat</span> <span class="o">=</span> <span class="bp">False</span>
    498526                    <span class="n">fp</span><span class="o">.</span><span class="n">seek</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>  <span class="c"># rewind</span>
    499                     <span class="n">rd</span><span class="o">.</span><span class="n">errors</span> <span class="o">=</span> <span class="s">&quot;&quot;</span> <span class="c"># clear out any old errors</span>
    500                     <span class="k">if</span> <span class="ow">not</span> <span class="n">rd</span><span class="o">.</span><span class="n">ContentsValidator</span><span class="p">(</span><span class="n">fp</span><span class="p">):</span> <span class="c"># rejected on cursory check</span>
    501                         <span class="n">errorReport</span> <span class="o">+=</span> <span class="s">&quot;</span><span class="se">\n</span><span class="s">  &quot;</span><span class="o">+</span><span class="n">rd</span><span class="o">.</span><span class="n">formatName</span> <span class="o">+</span> <span class="s">&#39; validator error&#39;</span>
    502                         <span class="k">if</span> <span class="n">rd</span><span class="o">.</span><span class="n">errors</span><span class="p">:</span>
    503                             <span class="n">errorReport</span> <span class="o">+=</span> <span class="s">&#39;: &#39;</span><span class="o">+</span><span class="n">rd</span><span class="o">.</span><span class="n">errors</span>
    504                         <span class="k">continue</span>
    505                     <span class="n">repeat</span> <span class="o">=</span> <span class="bp">True</span>
    506                     <span class="n">rdbuffer</span> <span class="o">=</span> <span class="p">{}</span> <span class="c"># create temporary storage for file reader</span>
    507                     <span class="n">block</span> <span class="o">=</span> <span class="mi">0</span>
    508                     <span class="k">while</span> <span class="n">repeat</span><span class="p">:</span> <span class="c"># loop if the reader asks for another pass on the file</span>
    509                         <span class="n">block</span> <span class="o">+=</span> <span class="mi">1</span>
    510                         <span class="n">repeat</span> <span class="o">=</span> <span class="bp">False</span>
    511                         <span class="n">fp</span><span class="o">.</span><span class="n">seek</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>  <span class="c"># rewind</span>
    512                         <span class="n">rd</span><span class="o">.</span><span class="n">objname</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
    513                         <span class="n">flag</span> <span class="o">=</span> <span class="bp">False</span>
     527                    <span class="n">rd</span><span class="o">.</span><span class="n">objname</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
     528                    <span class="n">flag</span> <span class="o">=</span> <span class="bp">False</span>
     529                    <span class="k">if</span> <span class="n">GSASIIpath</span><span class="o">.</span><span class="n">GetConfigValue</span><span class="p">(</span><span class="s">&#39;debug&#39;</span><span class="p">):</span>
     530                        <span class="n">flag</span> <span class="o">=</span> <span class="n">rd</span><span class="o">.</span><span class="n">Reader</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span><span class="n">fp</span><span class="p">,</span><span class="bp">self</span><span class="p">,</span>
     531                                         <span class="nb">buffer</span><span class="o">=</span><span class="n">rdbuffer</span><span class="p">,</span>
     532                                         <span class="n">blocknum</span><span class="o">=</span><span class="n">block</span><span class="p">,</span>
     533                                         <span class="n">usedRanIdList</span><span class="o">=</span><span class="n">usedRanIdList</span><span class="p">,</span>
     534                                         <span class="p">)</span>
     535                    <span class="k">else</span><span class="p">:</span>
    514536                        <span class="k">try</span><span class="p">:</span>
    515537                            <span class="n">flag</span> <span class="o">=</span> <span class="n">rd</span><span class="o">.</span><span class="n">Reader</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span><span class="n">fp</span><span class="p">,</span><span class="bp">self</span><span class="p">,</span>
     
    524546                            <span class="n">rd</span><span class="o">.</span><span class="n">errors</span> <span class="o">+=</span> <span class="s">&quot;</span><span class="se">\n</span><span class="s">  Unhandled read exception: &quot;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">detail</span><span class="p">)</span>
    525547                            <span class="n">rd</span><span class="o">.</span><span class="n">errors</span> <span class="o">+=</span> <span class="s">&quot;</span><span class="se">\n</span><span class="s">  Traceback info:</span><span class="se">\n</span><span class="s">&quot;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">traceback</span><span class="o">.</span><span class="n">format_exc</span><span class="p">())</span>
    526                         <span class="k">if</span> <span class="n">flag</span><span class="p">:</span> <span class="c"># this read succeeded</span>
    527                             <span class="n">rd</span><span class="o">.</span><span class="n">readfilename</span> <span class="o">=</span> <span class="n">filename</span>
    528                             <span class="n">rd_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">rd</span><span class="p">))</span> <span class="c"># save the result before it is written over</span>
    529                             <span class="k">if</span> <span class="n">rd</span><span class="o">.</span><span class="n">repeat</span><span class="p">:</span>
    530                                 <span class="n">repeat</span> <span class="o">=</span> <span class="bp">True</span>
    531                             <span class="k">continue</span>
    532                         <span class="n">errorReport</span> <span class="o">+=</span> <span class="s">&#39;</span><span class="se">\n</span><span class="s">&#39;</span><span class="o">+</span><span class="n">rd</span><span class="o">.</span><span class="n">formatName</span> <span class="o">+</span> <span class="s">&#39; read error&#39;</span>
    533                         <span class="k">if</span> <span class="n">rd</span><span class="o">.</span><span class="n">errors</span><span class="p">:</span>
    534                             <span class="n">errorReport</span> <span class="o">+=</span> <span class="s">&#39;: &#39;</span><span class="o">+</span><span class="n">rd</span><span class="o">.</span><span class="n">errors</span>
    535                     <span class="k">if</span> <span class="n">rd_list</span><span class="p">:</span> <span class="c"># read succeeded, was there a warning or any errors? </span>
    536                         <span class="k">if</span> <span class="n">rd</span><span class="o">.</span><span class="n">warnings</span><span class="p">:</span>
    537                             <span class="bp">self</span><span class="o">.</span><span class="n">ErrorDialog</span><span class="p">(</span><span class="s">&#39;Read Warning&#39;</span><span class="p">,</span><span class="s">&#39;The &#39;</span><span class="o">+</span> <span class="n">rd</span><span class="o">.</span><span class="n">formatName</span><span class="o">+</span>
    538                                              <span class="s">&#39; reader reported a warning message:</span><span class="se">\n\n</span><span class="s">&#39;</span><span class="o">+</span>
    539                                              <span class="n">rd</span><span class="o">.</span><span class="n">warnings</span><span class="p">)</span>
    540                         <span class="k">break</span> <span class="c"># success in reading, try no further</span>
     548                    <span class="k">if</span> <span class="n">flag</span><span class="p">:</span> <span class="c"># this read succeeded</span>
     549                        <span class="n">rd</span><span class="o">.</span><span class="n">readfilename</span> <span class="o">=</span> <span class="n">filename</span>
     550                        <span class="n">rd_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">rd</span><span class="p">))</span> <span class="c"># save the result before it is written over</span>
     551                        <span class="k">if</span> <span class="n">rd</span><span class="o">.</span><span class="n">repeat</span><span class="p">:</span>
     552                            <span class="n">repeat</span> <span class="o">=</span> <span class="bp">True</span>
     553                        <span class="k">continue</span>
     554                    <span class="n">errorReport</span> <span class="o">+=</span> <span class="s">&#39;</span><span class="se">\n</span><span class="s">&#39;</span><span class="o">+</span><span class="n">rd</span><span class="o">.</span><span class="n">formatName</span> <span class="o">+</span> <span class="s">&#39; read error&#39;</span>
     555                    <span class="k">if</span> <span class="n">rd</span><span class="o">.</span><span class="n">errors</span><span class="p">:</span>
     556                        <span class="n">errorReport</span> <span class="o">+=</span> <span class="s">&#39;: &#39;</span><span class="o">+</span><span class="n">rd</span><span class="o">.</span><span class="n">errors</span>
     557                <span class="k">if</span> <span class="n">rd_list</span><span class="p">:</span> <span class="c"># read succeeded, was there a warning or any errors? </span>
     558                    <span class="k">if</span> <span class="n">rd</span><span class="o">.</span><span class="n">warnings</span><span class="p">:</span>
     559                        <span class="bp">self</span><span class="o">.</span><span class="n">ErrorDialog</span><span class="p">(</span><span class="s">&#39;Read Warning&#39;</span><span class="p">,</span><span class="s">&#39;The &#39;</span><span class="o">+</span> <span class="n">rd</span><span class="o">.</span><span class="n">formatName</span><span class="o">+</span>
     560                                         <span class="s">&#39; reader reported a warning message:</span><span class="se">\n\n</span><span class="s">&#39;</span><span class="o">+</span>
     561                                         <span class="n">rd</span><span class="o">.</span><span class="n">warnings</span><span class="p">)</span>
     562                    <span class="k">break</span> <span class="c"># success in reading, try no further</span>
     563            <span class="k">else</span><span class="p">:</span>
     564                <span class="k">if</span> <span class="n">singlereader</span><span class="p">:</span>
     565                    <span class="bp">self</span><span class="o">.</span><span class="n">ErrorDialog</span><span class="p">(</span><span class="s">&#39;Read Error&#39;</span><span class="p">,</span><span class="s">&#39;The &#39;</span><span class="o">+</span> <span class="n">rd</span><span class="o">.</span><span class="n">formatName</span><span class="o">+</span>
     566                                     <span class="s">&#39; reader was not able to read file &#39;</span><span class="o">+</span><span class="n">filename</span><span class="o">+</span><span class="n">msg</span><span class="o">+</span>
     567                                     <span class="s">&#39;</span><span class="se">\n\n</span><span class="s">Error message(s):</span><span class="se">\n</span><span class="s">&#39;</span><span class="o">+</span><span class="n">errorReport</span>
     568                                     <span class="p">)</span>
    541569                <span class="k">else</span><span class="p">:</span>
    542                     <span class="k">if</span> <span class="n">singlereader</span><span class="p">:</span>
    543                         <span class="bp">self</span><span class="o">.</span><span class="n">ErrorDialog</span><span class="p">(</span><span class="s">&#39;Read Error&#39;</span><span class="p">,</span><span class="s">&#39;The &#39;</span><span class="o">+</span> <span class="n">rd</span><span class="o">.</span><span class="n">formatName</span><span class="o">+</span>
    544                                          <span class="s">&#39; reader was not able to read file &#39;</span><span class="o">+</span><span class="n">filename</span><span class="o">+</span><span class="n">msg</span><span class="o">+</span>
    545                                          <span class="s">&#39;</span><span class="se">\n\n</span><span class="s">Error message(s):</span><span class="se">\n</span><span class="s">&#39;</span><span class="o">+</span><span class="n">errorReport</span>
    546                                          <span class="p">)</span>
    547                     <span class="k">else</span><span class="p">:</span>
    548                         <span class="bp">self</span><span class="o">.</span><span class="n">ErrorDialog</span><span class="p">(</span><span class="s">&#39;Read Error&#39;</span><span class="p">,</span><span class="s">&#39;No reader was able to read file &#39;</span><span class="o">+</span><span class="n">filename</span><span class="o">+</span><span class="n">msg</span><span class="o">+</span>
    549                                          <span class="s">&#39;</span><span class="se">\n\n</span><span class="s">Error messages:</span><span class="se">\n</span><span class="s">&#39;</span><span class="o">+</span><span class="n">errorReport</span>
    550                                          <span class="p">)</span>
    551             <span class="k">except</span><span class="p">:</span>
    552                 <span class="kn">import</span> <span class="nn">traceback</span>
    553                 <span class="k">print</span> <span class="n">traceback</span><span class="o">.</span><span class="n">format_exc</span><span class="p">()</span>
    554                 <span class="bp">self</span><span class="o">.</span><span class="n">ErrorDialog</span><span class="p">(</span><span class="s">&#39;Open Error&#39;</span><span class="p">,</span><span class="s">&#39;Unexpected error trying to open or read file &#39;</span><span class="o">+</span><span class="n">filename</span><span class="p">)</span>
     570                    <span class="bp">self</span><span class="o">.</span><span class="n">ErrorDialog</span><span class="p">(</span><span class="s">&#39;Read Error&#39;</span><span class="p">,</span><span class="s">&#39;No reader was able to read file &#39;</span><span class="o">+</span><span class="n">filename</span><span class="o">+</span><span class="n">msg</span><span class="o">+</span>
     571                                     <span class="s">&#39;</span><span class="se">\n\n</span><span class="s">Error messages:</span><span class="se">\n</span><span class="s">&#39;</span><span class="o">+</span><span class="n">errorReport</span>
     572                                     <span class="p">)</span>
    555573            <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>
    556574        <span class="k">return</span> <span class="n">rd_list</span>
     
    604622        <span class="k">finally</span><span class="p">:</span>
    605623            <span class="n">dlg</span><span class="o">.</span><span class="n">Destroy</span><span class="p">()</span>
    606         <span class="k">return</span> <span class="n">filelist</span>
    607             </div>
     624        <span class="k">return</span> <span class="n">filelist</span>           
     625        </div>
    608626<div class="viewcode-block" id="GSASII.OnImportPhase"><a class="viewcode-back" href="../GSASII.html#GSASII.GSASII.OnImportPhase">[docs]</a>    <span class="k">def</span> <span class="nf">OnImportPhase</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">event</span><span class="p">):</span>
    609627        <span class="sd">&#39;&#39;&#39;Called in response to an Import/Phase/... menu item</span>
     
    769787        <span class="k">return</span> <span class="c"># success</span>
    770788        </div>
     789    <span class="k">def</span> <span class="nf">_Add_ImportMenu_Image</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">parent</span><span class="p">):</span>
     790        <span class="sd">&#39;&#39;&#39;configure the Import Image menus accord to the readers found in _init_Imports</span>
     791<span class="sd">        &#39;&#39;&#39;</span>
     792        <span class="n">submenu</span> <span class="o">=</span> <span class="n">wx</span><span class="o">.</span><span class="n">Menu</span><span class="p">()</span>
     793        <span class="n">item</span> <span class="o">=</span> <span class="n">parent</span><span class="o">.</span><span class="n">AppendMenu</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">&#39;Image&#39;</span><span class="p">,</span>
     794            <span class="n">submenu</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s">&#39;Import image file&#39;</span><span class="p">)</span>
     795        <span class="k">for</span> <span class="n">reader</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">ImportImageReaderlist</span><span class="p">:</span>
     796            <span class="n">item</span> <span class="o">=</span> <span class="n">submenu</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_ANY</span><span class="p">,</span><span class="n">help</span><span class="o">=</span><span class="n">reader</span><span class="o">.</span><span class="n">longFormatName</span><span class="p">,</span>
     797                <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><span class="n">text</span><span class="o">=</span><span class="s">&#39;from &#39;</span><span class="o">+</span><span class="n">reader</span><span class="o">.</span><span class="n">formatName</span><span class="o">+</span><span class="s">&#39; file&#39;</span><span class="p">)</span>
     798            <span class="bp">self</span><span class="o">.</span><span class="n">ImportMenuId</span><span class="p">[</span><span class="n">item</span><span class="o">.</span><span class="n">GetId</span><span class="p">()]</span> <span class="o">=</span> <span class="n">reader</span>
     799            <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">OnImportImage</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>
     800        <span class="n">item</span> <span class="o">=</span> <span class="n">submenu</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_ANY</span><span class="p">,</span>
     801                              <span class="n">help</span><span class="o">=</span><span class="s">&#39;Import image data, use file to try to determine format&#39;</span><span class="p">,</span>
     802                              <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>
     803                              <span class="n">text</span><span class="o">=</span><span class="s">&#39;guess format from file&#39;</span><span class="p">)</span>
     804        <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">OnImportImage</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>
     805       
     806<div class="viewcode-block" id="GSASII.OnImportImage"><a class="viewcode-back" href="../GSASII.html#GSASII.GSASII.OnImportImage">[docs]</a>    <span class="k">def</span> <span class="nf">OnImportImage</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">event</span><span class="p">):</span>
     807        <span class="sd">&#39;&#39;&#39;Called in response to an Import/Image/... menu item</span>
     808<span class="sd">        to read an image from a file. Like all the other imports,</span>
     809<span class="sd">        dict self.ImportMenuId is used to look up the specific</span>
     810<span class="sd">        reader item associated with the menu item, which will be</span>
     811<span class="sd">        None for the last menu item, which is the &quot;guess&quot; option</span>
     812<span class="sd">        where all appropriate formats will be tried.</span>
     813
     814<span class="sd">        A reader object is filled each time an image is read. </span>
     815<span class="sd">        &#39;&#39;&#39;</span>
     816        <span class="c"># look up which format was requested</span>
     817        <span class="n">reqrdr</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ImportMenuId</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">event</span><span class="o">.</span><span class="n">GetId</span><span class="p">())</span>
     818        <span class="n">rdlist</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">OnImportGeneric</span><span class="p">(</span><span class="n">reqrdr</span><span class="p">,</span>
     819                                  <span class="bp">self</span><span class="o">.</span><span class="n">ImportImageReaderlist</span><span class="p">,</span>
     820                                  <span class="s">&#39;image&#39;</span><span class="p">,</span><span class="n">multiple</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span><span class="n">Preview</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span>
     821        <span class="k">if</span> <span class="ow">not</span> <span class="n">rdlist</span><span class="p">:</span> <span class="k">return</span>
     822        <span class="n">first</span> <span class="o">=</span> <span class="bp">True</span>
     823        <span class="k">for</span> <span class="n">rd</span> <span class="ow">in</span> <span class="n">rdlist</span><span class="p">:</span>
     824            <span class="k">if</span> <span class="n">first</span><span class="p">:</span>
     825                <span class="n">first</span> <span class="o">=</span> <span class="bp">False</span>
     826                <span class="bp">self</span><span class="o">.</span><span class="n">CheckNotebook</span><span class="p">()</span>
     827            <span class="n">G2IO</span><span class="o">.</span><span class="n">LoadImage</span><span class="p">(</span><span class="n">rd</span><span class="o">.</span><span class="n">readfilename</span><span class="p">,</span><span class="bp">self</span><span class="p">,</span><span class="n">rd</span><span class="o">.</span><span class="n">Comments</span><span class="p">,</span><span class="n">rd</span><span class="o">.</span><span class="n">Data</span><span class="p">,</span><span class="n">rd</span><span class="o">.</span><span class="n">Npix</span><span class="p">,</span><span class="n">rd</span><span class="o">.</span><span class="n">Image</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">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 have beeen read</span>
     829        <span class="c"># replace G2IO.GetImageData with something using imports</span>
     830        <span class="c"># look over G2IO.ReadLoadImage</span>
     831                    </div>
    771832    <span class="k">def</span> <span class="nf">_Add_ImportMenu_Sfact</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">parent</span><span class="p">):</span>
    772833        <span class="sd">&#39;&#39;&#39;configure the Import Structure Factor menus accord to the readers found in _init_Imports</span>
     
    20712132        <span class="n">Import</span> <span class="o">=</span> <span class="n">wx</span><span class="o">.</span><span class="n">Menu</span><span class="p">(</span><span class="n">title</span><span class="o">=</span><span class="s">&#39;&#39;</span><span class="p">)</span>       
    20722133        <span class="n">menubar</span><span class="o">.</span><span class="n">Append</span><span class="p">(</span><span class="n">menu</span><span class="o">=</span><span class="n">Import</span><span class="p">,</span> <span class="n">title</span><span class="o">=</span><span class="s">&#39;Import&#39;</span><span class="p">)</span>
     2134        <span class="bp">self</span><span class="o">.</span><span class="n">_Add_ImportMenu_Image</span><span class="p">(</span><span class="n">Import</span><span class="p">)</span>
    20732135        <span class="bp">self</span><span class="o">.</span><span class="n">_Add_ImportMenu_Phase</span><span class="p">(</span><span class="n">Import</span><span class="p">)</span>
    20742136        <span class="bp">self</span><span class="o">.</span><span class="n">_Add_ImportMenu_powder</span><span class="p">(</span><span class="n">Import</span><span class="p">)</span>
  • sphinxdocs/build/html/_modules/GSASIIIO.html

    r1998 r2010  
    5151<span class="c"># -*- coding: utf-8 -*-</span>
    5252<span class="c">########### SVN repository information ###################</span>
    53 <span class="c"># $Date: 2015-10-10 11:58:12 -0500 (Sat, 10 Oct 2015) $</span>
     53<span class="c"># $Date: 2015-10-12 17:31:16 -0500 (Mon, 12 Oct 2015) $</span>
    5454<span class="c"># $Author: toby $</span>
    55 <span class="c"># $Revision: 1997 $</span>
     55<span class="c"># $Revision: 2003 $</span>
    5656<span class="c"># $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/GSASIIIO.py $</span>
    57 <span class="c"># $Id: GSASIIIO.py 1997 2015-10-10 16:58:12Z toby $</span>
     57<span class="c"># $Id: GSASIIIO.py 2003 2015-10-12 22:31:16Z 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: 1997 $&quot;</span><span class="p">)</span>
     82<span class="n">GSASIIpath</span><span class="o">.</span><span class="n">SetVersionNumber</span><span class="p">(</span><span class="s">&quot;$Revision: 2003 $&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>
     
    9696<span class="n">DEBUG</span> <span class="o">=</span> <span class="bp">False</span>       <span class="c">#=True for various prints</span>
    9797<span class="n">TRANSP</span> <span class="o">=</span> <span class="bp">False</span>      <span class="c">#=true to transpose images for testing</span>
     98<span class="k">if</span> <span class="n">GSASIIpath</span><span class="o">.</span><span class="n">GetConfigValue</span><span class="p">(</span><span class="s">&#39;Transpose&#39;</span><span class="p">):</span> <span class="n">TRANSP</span> <span class="o">=</span> <span class="bp">True</span>
    9899<span class="n">npsind</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">x</span><span class="o">*</span><span class="n">np</span><span class="o">.</span><span class="n">pi</span><span class="o">/</span><span class="mf">180.</span><span class="p">)</span>
    99100
     
    180181</div>
    181182<div class="viewcode-block" id="CheckImageFile"><a class="viewcode-back" href="../GSASIIGUIr.html#GSASIIIO.CheckImageFile">[docs]</a><span class="k">def</span> <span class="nf">CheckImageFile</span><span class="p">(</span><span class="n">G2frame</span><span class="p">,</span><span class="n">imagefile</span><span class="p">):</span>
    182     <span class="sd">&#39;&#39;&#39;Get an new image file name if the specified one does not</span>
    183 <span class="sd">    exist</span>
     183    <span class="sd">&#39;&#39;&#39;Try to locate an image file if the project and image have been moved</span>
     184<span class="sd">    together. If the image file cannot be found, request the location from</span>
     185<span class="sd">    the user.</span>
    184186
    185187<span class="sd">    :param wx.Frame G2frame: main GSAS-II Frame and data object</span>
    186 
    187188<span class="sd">    :param str imagefile: name of image file</span>
    188 
    189189<span class="sd">    :returns: imagefile, if it exists, or the name of a file</span>
    190190<span class="sd">      that does exist or False if the user presses Cancel</span>
     
    320320    <span class="sd">&#39;&#39;&#39;Read a GSAS-II image file and load it into the data tree</span>
    321321<span class="sd">    &#39;&#39;&#39;</span>
    322     <span class="c"># get a list of existing Image entries</span>
    323     <span class="n">ImgNames</span> <span class="o">=</span> <span class="p">[]</span>
    324     <span class="k">if</span> <span class="n">G2frame</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">GetCount</span><span class="p">():</span>
    325         <span class="n">item</span><span class="p">,</span> <span class="n">cookie</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">GetFirstChild</span><span class="p">(</span><span class="n">G2frame</span><span class="o">.</span><span class="n">root</span><span class="p">)</span>
    326         <span class="k">while</span> <span class="n">item</span><span class="p">:</span>
    327             <span class="n">name</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">GetItemText</span><span class="p">(</span><span class="n">item</span><span class="p">)</span>
    328             <span class="k">if</span> <span class="n">name</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s">&#39;IMG&#39;</span><span class="p">):</span> <span class="n">ImgNames</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">name</span><span class="p">)</span>       
    329             <span class="n">item</span><span class="p">,</span> <span class="n">cookie</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">GetNextChild</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="n">cookie</span><span class="p">)</span>
    330322    <span class="c"># if a zip file, open and extract</span>
    331323    <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>
     
    335327    <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">GetImageData</span><span class="p">(</span><span class="n">G2frame</span><span class="p">,</span><span class="n">imagefile</span><span class="p">)</span>
    336328    <span class="k">if</span> <span class="n">Comments</span><span class="p">:</span>
    337         <span class="n">TreeName</span> <span class="o">=</span> <span class="n">G2obj</span><span class="o">.</span><span class="n">MakeUniqueLabel</span><span class="p">(</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><span class="n">ImgNames</span><span class="p">)</span>
    338         <span class="k">print</span> <span class="s">&#39;b=&#39;</span><span class="p">,</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>
    339         <span class="k">print</span> <span class="s">&#39;a=&#39;</span><span class="p">,</span><span class="n">TreeName</span>
    340         <span class="n">Id</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">AppendItem</span><span class="p">(</span><span class="n">parent</span><span class="o">=</span><span class="n">G2frame</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="n">TreeName</span><span class="p">)</span>
    341         <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;Comments&#39;</span><span class="p">),</span><span class="n">Comments</span><span class="p">)</span>
    342         <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>
    343         <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>
    344         <span class="k">if</span> <span class="n">G2frame</span><span class="o">.</span><span class="n">imageDefault</span><span class="p">:</span>
    345             <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="n">G2frame</span><span class="o">.</span><span class="n">imageDefault</span><span class="p">)</span>
    346             <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>
    347             <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>
    348             <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>
    349             <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>
    350             <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>
    351             <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>
    352             <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>
    353             <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>
    354             <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>
    355             <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>
    356             <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>
    357             <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>
     329        <span class="n">LoadImage</span><span class="p">(</span><span class="n">imagefile</span><span class="p">,</span><span class="n">G2frame</span><span class="p">,</span><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="p">)</span>
     330    </div>
     331<div class="viewcode-block" id="LoadImage"><a class="viewcode-back" href="../GSASIIGUIr.html#GSASIIIO.LoadImage">[docs]</a><span class="k">def</span> <span class="nf">LoadImage</span><span class="p">(</span><span class="n">imagefile</span><span class="p">,</span><span class="n">G2frame</span><span class="p">,</span><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="p">):</span>
     332    <span class="sd">&#39;&#39;&#39;Load an image into the tree</span>
     333<span class="sd">    &#39;&#39;&#39;</span>
     334   
     335    <span class="n">ImgNames</span> <span class="o">=</span> <span class="p">[]</span>
     336    <span class="k">if</span> <span class="n">G2frame</span><span class="o">.</span><span class="n">PatternTree</span><span class="o">.</span><span class="n">GetCount</span><span class="p">():</span> <span class="c"># get a list of existing Image entries</span>
     337        <span class="n">item</span><span class="p">,</span> <span class="n">cookie</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">GetFirstChild</span><span class="p">(</span><span class="n">G2frame</span><span class="o">.</span><span class="n">root</span><span class="p">)</span>
     338        <span class="k">while</span> <span class="n">item</span><span class="p">:</span>
     339            <span class="n">name</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">GetItemText</span><span class="p">(</span><span class="n">item</span><span class="p">)</span>
     340            <span class="k">if</span> <span class="n">name</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s">&#39;IMG&#39;</span><span class="p">):</span> <span class="n">ImgNames</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">name</span><span class="p">)</span>       
     341            <span class="n">item</span><span class="p">,</span> <span class="n">cookie</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">GetNextChild</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="n">cookie</span><span class="p">)</span>
     342    <span class="n">TreeName</span> <span class="o">=</span> <span class="n">G2obj</span><span class="o">.</span><span class="n">MakeUniqueLabel</span><span class="p">(</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><span class="n">ImgNames</span><span class="p">)</span>
     343    <span class="n">Id</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">AppendItem</span><span class="p">(</span><span class="n">parent</span><span class="o">=</span><span class="n">G2frame</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="n">TreeName</span><span class="p">)</span>
     344    <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;Comments&#39;</span><span class="p">),</span><span class="n">Comments</span><span class="p">)</span>
     345    <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>
     346    <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>
     347    <span class="k">if</span> <span class="n">G2frame</span><span class="o">.</span><span class="n">imageDefault</span><span class="p">:</span>
     348        <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="n">G2frame</span><span class="o">.</span><span class="n">imageDefault</span><span class="p">)</span>
     349        <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>
     350        <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>
     351        <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>
     352        <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>
     353        <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>
     354        <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>
     355        <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>
     356        <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>
     357        <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>
     358        <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>
     359        <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>
     360        <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>
     361    <span class="k">else</span><span class="p">:</span>
     362        <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>
     363        <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>
     364        <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>
     365        <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>
     366        <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>
     367        <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>
     368        <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>
     369        <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>
     370        <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>
     371        <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>
     372        <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>
     373        <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>
     374        <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>
     375        <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>
     376        <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>
     377        <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>
     378        <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>
     379        <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>
     380        <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>
     381        <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>
     382        <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>
     383        <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>
     384        <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>
     385        <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>
     386        <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>
     387        <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>                           
     388        <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>
     389        <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>
     390    <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>
     391    <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>
     392    <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;Image Controls&#39;</span><span class="p">),</span><span class="n">Data</span><span class="p">)</span>
     393    <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>
     394    <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;Masks&#39;</span><span class="p">),</span><span class="n">Masks</span><span class="p">)</span>
     395    <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;Stress/Strain&#39;</span><span class="p">),</span>
     396        <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>
     397    <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">Id</span><span class="p">,[</span><span class="n">Npix</span><span class="p">,</span><span class="n">imagefile</span><span class="p">])</span>
     398    <span class="n">G2frame</span><span class="o">.</span><span class="n">PickId</span> <span class="o">=</span> <span class="n">Id</span>
     399    <span class="n">G2frame</span><span class="o">.</span><span class="n">PickIdText</span> <span class="o">=</span> <span class="n">G2frame</span><span class="o">.</span><span class="n">GetTreeItemsList</span><span class="p">(</span><span class="n">G2frame</span><span class="o">.</span><span class="n">PickId</span><span class="p">)</span>
     400    <span class="n">G2frame</span><span class="o">.</span><span class="n">Image</span> <span class="o">=</span> <span class="n">Id</span>
     401    </div>
     402<div class="viewcode-block" id="ReadImageData"><a class="viewcode-back" href="../GSASIIGUIr.html#GSASIIIO.ReadImageData">[docs]</a><span class="k">def</span> <span class="nf">ReadImageData</span><span class="p">(</span><span class="n">G2frame</span><span class="p">,</span><span class="n">imagefile</span><span class="p">,</span><span class="n">imageOnly</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
     403    <span class="sd">&#39;&#39;&#39;Read a single image with an image importer. replacement for GetImageData</span>
     404
     405<span class="sd">    :param wx.Frame G2frame: main GSAS-II Frame and data object.</span>
     406<span class="sd">    :param str imagefile: name of image file</span>
     407<span class="sd">    :param bool imageOnly: If True return only the image,</span>
     408<span class="sd">      otherwise  (default) return more (see below)</span>
     409
     410<span class="sd">    :returns: an image as a numpy array or a list of four items:</span>
     411<span class="sd">      Comments, Data, Npix and the Image, as selected by imageOnly</span>
     412
     413<span class="sd">    &#39;&#39;&#39;</span>
     414    <span class="c"># determine which formats are compatible with this file</span>
     415    <span class="k">print</span> <span class="s">&#39;Debug: using ReadImageData&#39;</span>
     416    <span class="n">primaryReaders</span> <span class="o">=</span> <span class="p">[]</span>
     417    <span class="n">secondaryReaders</span> <span class="o">=</span> <span class="p">[]</span>
     418    <span class="k">for</span> <span class="n">rd</span> <span class="ow">in</span> <span class="n">G2frame</span><span class="o">.</span><span class="n">ImportImageReaderlist</span><span class="p">:</span>
     419        <span class="n">flag</span> <span class="o">=</span> <span class="n">rd</span><span class="o">.</span><span class="n">ExtensionValidator</span><span class="p">(</span><span class="n">imagefile</span><span class="p">)</span>
     420        <span class="k">if</span> <span class="n">flag</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
     421            <span class="n">secondaryReaders</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">rd</span><span class="p">)</span>
     422        <span class="k">elif</span> <span class="n">flag</span><span class="p">:</span>
     423            <span class="n">primaryReaders</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">rd</span><span class="p">)</span>
     424    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">secondaryReaders</span><span class="p">)</span> <span class="o">+</span> <span class="nb">len</span><span class="p">(</span><span class="n">primaryReaders</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
     425        <span class="k">print</span><span class="p">(</span><span class="s">&#39;Error: No matching format for file &#39;</span><span class="o">+</span><span class="n">filename</span><span class="p">)</span>
     426        <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>
     427    <span class="n">fp</span> <span class="o">=</span> <span class="bp">None</span>
     428    <span class="n">errorReport</span> <span class="o">=</span> <span class="s">&#39;&#39;</span>
     429    <span class="n">fp</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">imagefile</span><span class="p">,</span><span class="s">&#39;Ur&#39;</span><span class="p">)</span>
     430    <span class="k">for</span> <span class="n">rd</span> <span class="ow">in</span> <span class="n">primaryReaders</span><span class="o">+</span><span class="n">secondaryReaders</span><span class="p">:</span>
     431        <span class="n">rd</span><span class="o">.</span><span class="n">ReInitialize</span><span class="p">()</span> <span class="c"># purge anything from a previous read</span>
     432        <span class="n">fp</span><span class="o">.</span><span class="n">seek</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>  <span class="c"># rewind</span>
     433        <span class="n">rd</span><span class="o">.</span><span class="n">errors</span> <span class="o">=</span> <span class="s">&quot;&quot;</span> <span class="c"># clear out any old errors</span>
     434        <span class="k">if</span> <span class="ow">not</span> <span class="n">rd</span><span class="o">.</span><span class="n">ContentsValidator</span><span class="p">(</span><span class="n">fp</span><span class="p">):</span> <span class="c"># rejected on cursory check</span>
     435            <span class="n">errorReport</span> <span class="o">+=</span> <span class="s">&quot;</span><span class="se">\n</span><span class="s">  &quot;</span><span class="o">+</span><span class="n">rd</span><span class="o">.</span><span class="n">formatName</span> <span class="o">+</span> <span class="s">&#39; validator error&#39;</span>
     436            <span class="k">if</span> <span class="n">rd</span><span class="o">.</span><span class="n">errors</span><span class="p">:</span>
     437                <span class="n">errorReport</span> <span class="o">+=</span> <span class="s">&#39;: &#39;</span><span class="o">+</span><span class="n">rd</span><span class="o">.</span><span class="n">errors</span>
     438                <span class="k">continue</span>
     439        <span class="n">rdbuffer</span> <span class="o">=</span> <span class="p">{}</span> <span class="c"># create temporary storage for file reader</span>
     440        <span class="k">if</span> <span class="n">GSASIIpath</span><span class="o">.</span><span class="n">GetConfigValue</span><span class="p">(</span><span class="s">&#39;debug&#39;</span><span class="p">):</span>
     441            <span class="n">flag</span> <span class="o">=</span> <span class="n">rd</span><span class="o">.</span><span class="n">Reader</span><span class="p">(</span><span class="n">imagefile</span><span class="p">,</span><span class="n">fp</span><span class="p">,</span><span class="n">G2frame</span><span class="p">)</span>
    358442        <span class="k">else</span><span class="p">:</span>
    359             <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>
    360             <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>
    361             <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>
    362             <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>
    363             <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>
    364             <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>
    365             <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>
    366             <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>
    367             <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>
    368             <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>
    369             <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>
    370             <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>
    371             <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>
    372             <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>
    373             <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>
    374             <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>
    375             <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>
    376             <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>
    377             <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>
    378             <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>
    379             <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>
    380             <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>
    381             <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>
    382             <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>
    383             <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>
    384             <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>                           
    385             <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>
    386             <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>
    387         <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>
    388         <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>
    389         <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;Image Controls&#39;</span><span class="p">),</span><span class="n">Data</span><span class="p">)</span>
    390         <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>
    391         <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;Masks&#39;</span><span class="p">),</span><span class="n">Masks</span><span class="p">)</span>
    392         <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;Stress/Strain&#39;</span><span class="p">),</span>
    393             <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>
    394         <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">Id</span><span class="p">,[</span><span class="n">Npix</span><span class="p">,</span><span class="n">imagefile</span><span class="p">])</span>
    395         <span class="n">G2frame</span><span class="o">.</span><span class="n">PickId</span> <span class="o">=</span> <span class="n">Id</span>
    396         <span class="n">G2frame</span><span class="o">.</span><span class="n">PickIdText</span> <span class="o">=</span> <span class="n">G2frame</span><span class="o">.</span><span class="n">GetTreeItemsList</span><span class="p">(</span><span class="n">G2frame</span><span class="o">.</span><span class="n">PickId</span><span class="p">)</span>
    397         <span class="n">G2frame</span><span class="o">.</span><span class="n">Image</span> <span class="o">=</span> <span class="n">Id</span>
     443            <span class="n">flag</span> <span class="o">=</span> <span class="bp">False</span>
     444            <span class="k">try</span><span class="p">:</span>
     445                <span class="n">flag</span> <span class="o">=</span> <span class="n">rd</span><span class="o">.</span><span class="n">Reader</span><span class="p">(</span><span class="n">imagefile</span><span class="p">,</span><span class="n">fp</span><span class="p">,</span><span class="n">G2frame</span><span class="p">)</span>
     446            <span class="k">except</span> <span class="n">rd</span><span class="o">.</span><span class="n">ImportException</span> <span class="k">as</span> <span class="n">detail</span><span class="p">:</span>
     447                <span class="n">rd</span><span class="o">.</span><span class="n">errors</span> <span class="o">+=</span> <span class="s">&quot;</span><span class="se">\n</span><span class="s">  Read exception: &quot;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">detail</span><span class="p">)</span>
     448            <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">detail</span><span class="p">:</span>
     449                <span class="kn">import</span> <span class="nn">traceback</span>
     450                <span class="n">rd</span><span class="o">.</span><span class="n">errors</span> <span class="o">+=</span> <span class="s">&quot;</span><span class="se">\n</span><span class="s">  Unhandled read exception: &quot;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">detail</span><span class="p">)</span>
     451                <span class="n">rd</span><span class="o">.</span><span class="n">errors</span> <span class="o">+=</span> <span class="s">&quot;</span><span class="se">\n</span><span class="s">  Traceback info:</span><span class="se">\n</span><span class="s">&quot;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">traceback</span><span class="o">.</span><span class="n">format_exc</span><span class="p">())</span>
     452        <span class="k">if</span> <span class="n">flag</span><span class="p">:</span> <span class="c"># this read succeeded</span>
     453            <span class="k">if</span> <span class="n">rd</span><span class="o">.</span><span class="n">Image</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
     454                <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">&#39;No image read. Strange!&#39;</span><span class="p">)</span>
     455            <span class="k">if</span> <span class="n">GSASIIpath</span><span class="o">.</span><span class="n">GetConfigValue</span><span class="p">(</span><span class="s">&#39;Transpose&#39;</span><span class="p">):</span>
     456                <span class="k">print</span> <span class="s">&#39;Transposing Image!&#39;</span>
     457                <span class="n">rd</span><span class="o">.</span><span class="n">Image</span> <span class="o">=</span> <span class="n">rd</span><span class="o">.</span><span class="n">Image</span><span class="o">.</span><span class="n">T</span>
     458            <span class="c">#rd.readfilename = imagefile</span>
     459            <span class="k">if</span> <span class="n">imageOnly</span><span class="p">:</span>
     460                <span class="k">return</span> <span class="n">rd</span><span class="o">.</span><span class="n">Image</span>
     461            <span class="k">else</span><span class="p">:</span>
     462                <span class="k">return</span> <span class="n">rd</span><span class="o">.</span><span class="n">Comments</span><span class="p">,</span><span class="n">rd</span><span class="o">.</span><span class="n">Data</span><span class="p">,</span><span class="n">rd</span><span class="o">.</span><span class="n">Npix</span><span class="p">,</span><span class="n">rd</span><span class="o">.</span><span class="n">Image</span>
     463    <span class="k">else</span><span class="p">:</span>
     464        <span class="k">print</span><span class="p">(</span><span class="s">&#39;Error reading file &#39;</span><span class="o">+</span><span class="n">filename</span><span class="p">)</span>
     465        <span class="k">print</span><span class="p">(</span><span class="s">&#39;Error messages(s)</span><span class="se">\n</span><span class="s">&#39;</span><span class="o">+</span><span class="n">errorReport</span><span class="p">)</span>
     466        <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>
    398467    </div>
    399468<div class="viewcode-block" id="GetImageData"><a class="viewcode-back" href="../GSASIIGUIr.html#GSASIIIO.GetImageData">[docs]</a><span class="k">def</span> <span class="nf">GetImageData</span><span class="p">(</span><span class="n">G2frame</span><span class="p">,</span><span class="n">imagefile</span><span class="p">,</span><span class="n">imageOnly</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
     
    412481
    413482<span class="sd">    &#39;&#39;&#39;</span>
     483    <span class="k">if</span> <span class="n">GSASIIpath</span><span class="o">.</span><span class="n">GetConfigValue</span><span class="p">(</span><span class="s">&#39;debug&#39;</span><span class="p">):</span>  <span class="c"># test out using replacement routine</span>
     484        <span class="k">return</span> <span class="n">ReadImageData</span><span class="p">(</span><span class="n">G2frame</span><span class="p">,</span><span class="n">imagefile</span><span class="p">,</span><span class="n">imageOnly</span><span class="p">)</span>
     485   
    414486    <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>
    415487    <span class="n">Comments</span> <span class="o">=</span> <span class="p">[]</span>
     
    453525    <span class="k">if</span> <span class="n">imageOnly</span><span class="p">:</span>
    454526        <span class="k">if</span> <span class="n">TRANSP</span><span class="p">:</span>
     527            <span class="k">print</span> <span class="s">&#39;Transposing Image!&#39;</span>
    455528            <span class="k">return</span> <span class="n">Image</span><span class="o">.</span><span class="n">T</span>
    456529        <span class="k">else</span><span class="p">:</span>
     
    458531    <span class="k">else</span><span class="p">:</span>
    459532        <span class="k">if</span> <span class="n">TRANSP</span><span class="p">:</span>
     533            <span class="k">print</span> <span class="s">&#39;Transposing Image!&#39;</span>
    460534            <span class="k">return</span> <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">T</span>
    461535        <span class="k">else</span><span class="p">:</span>
     
    569643    <span class="k">else</span><span class="p">:</span>
    570644        <span class="k">return</span> <span class="n">head</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>
    571    
    572         </div>
     645    </div>
    573646<div class="viewcode-block" id="GetGEsumData"><a class="viewcode-back" href="../GSASIIGUIr.html#GSASIIIO.GetGEsumData">[docs]</a><span class="k">def</span> <span class="nf">GetGEsumData</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span><span class="n">imageOnly</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
    574647    <span class="s">&#39;Read SUM file as produced at 1-ID from G.E. images&#39;</span>
     
    20022075        <span class="bp">self</span><span class="o">.</span><span class="n">numbanks</span> <span class="o">=</span> <span class="mi">1</span>
    20032076        <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>
     2077
     2078<span class="c">######################################################################</span></div></div>
     2079<div class="viewcode-block" id="ImportImage"><a class="viewcode-back" href="../GSASIIGUIr.html#GSASIIIO.ImportImage">[docs]</a><span class="k">class</span> <span class="nc">ImportImage</span><span class="p">(</span><span class="n">ImportBaseclass</span><span class="p">):</span>
     2080    <span class="sd">&#39;&#39;&#39;Defines a base class for the reading of images</span>
     2081
     2082<span class="sd">    Structure factors are read with a call to :meth:`GSASII.GSASII.OnImportImage`</span>
     2083<span class="sd">    which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`, which calls</span>
     2084<span class="sd">    methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and</span>
     2085<span class="sd">    :meth:`Reader`.</span>
     2086
     2087<span class="sd">    See :ref:`Writing a Import Routine&lt;Import_Routines&gt;`</span>
     2088<span class="sd">    for an explanation on how to use import classes in general. The specifics </span>
     2089<span class="sd">    for reading an image requires that the ``Reader()`` routine in the import</span>
     2090<span class="sd">    class need to do only a few things:...</span>
     2091<span class="sd">    </span>
     2092<span class="sd">    (should load :attr:`RefDict` item ``&#39;RefList&#39;`` with the reflection list,</span>
     2093<span class="sd">    (and set :attr:`Parameters` with the instrument parameters</span>
     2094<span class="sd">    (initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).</span>
     2095<span class="sd">    &#39;&#39;&#39;</span>
     2096    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">formatName</span><span class="p">,</span><span class="n">longFormatName</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span><span class="n">extensionlist</span><span class="o">=</span><span class="p">[],</span>
     2097        <span class="n">strictExtension</span><span class="o">=</span><span class="bp">False</span><span class="p">,):</span>
     2098        <span class="n">ImportBaseclass</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">formatName</span><span class="p">,</span><span class="n">longFormatName</span><span class="p">,</span>
     2099            <span class="n">extensionlist</span><span class="p">,</span><span class="n">strictExtension</span><span class="p">)</span>
     2100        <span class="bp">self</span><span class="o">.</span><span class="n">InitParameters</span><span class="p">()</span>
     2101       
     2102<div class="viewcode-block" id="ImportImage.ReInitialize"><a class="viewcode-back" href="../GSASIIGUIr.html#GSASIIIO.ImportImage.ReInitialize">[docs]</a>    <span class="k">def</span> <span class="nf">ReInitialize</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
     2103        <span class="s">&#39;Reinitialize the Reader to initial settings -- not used at present&#39;</span>
     2104        <span class="n">ImportBaseclass</span><span class="o">.</span><span class="n">ReInitialize</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
     2105        <span class="bp">self</span><span class="o">.</span><span class="n">InitParameters</span><span class="p">()</span>
     2106        </div>
     2107<div class="viewcode-block" id="ImportImage.InitParameters"><a class="viewcode-back" href="../GSASIIGUIr.html#GSASIIIO.ImportImage.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>
     2108        <span class="s">&#39;initialize the instrument parameters structure&#39;</span>
     2109        <span class="bp">self</span><span class="o">.</span><span class="n">Comments</span> <span class="o">=</span> <span class="p">[</span><span class="s">&#39;No comments&#39;</span><span class="p">]</span>
     2110        <span class="bp">self</span><span class="o">.</span><span class="n">Data</span> <span class="o">=</span> <span class="p">{}</span>
     2111        <span class="bp">self</span><span class="o">.</span><span class="n">Npix</span> <span class="o">=</span> <span class="mi">0</span>
     2112        <span class="bp">self</span><span class="o">.</span><span class="n">Image</span> <span class="o">=</span> <span class="bp">None</span>
     2113
    20042114<span class="c">######################################################################</span></div></div>
    20052115<div class="viewcode-block" id="ExportBaseclass"><a class="viewcode-back" href="../GSASIIGUIr.html#GSASIIIO.ExportBaseclass">[docs]</a><span class="k">class</span> <span class="nc">ExportBaseclass</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
  • sphinxdocs/build/html/_modules/GSASIIgrid.html

    r1998 r2010  
    5252<span class="c">#GSASIIgrid - data display routines</span>
    5353<span class="c">########### SVN repository information ###################</span>
    54 <span class="c"># $Date: 2015-10-08 19:02:13 -0500 (Thu, 08 Oct 2015) $</span>
     54<span class="c"># $Date: 2015-10-10 21:59:34 -0500 (Sat, 10 Oct 2015) $</span>
    5555<span class="c"># $Author: toby $</span>
    56 <span class="c"># $Revision: 1994 $</span>
     56<span class="c"># $Revision: 1998 $</span>
    5757<span class="c"># $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/GSASIIgrid.py $</span>
    58 <span class="c"># $Id: GSASIIgrid.py 1994 2015-10-09 00:02:13Z toby $</span>
     58<span class="c"># $Id: GSASIIgrid.py 1998 2015-10-11 02:59:34Z toby $</span>
    5959<span class="c">########### SVN repository information ###################</span>
    6060<span class="sd">&#39;&#39;&#39;</span>
     
    7777<span class="kn">import</span> <span class="nn">scipy.optimize</span> <span class="kn">as</span> <span class="nn">so</span>
    7878<span class="kn">import</span> <span class="nn">GSASIIpath</span>
    79 <span class="n">GSASIIpath</span><span class="o">.</span><span class="n">SetVersionNumber</span><span class="p">(</span><span class="s">&quot;$Revision: 1994 $&quot;</span><span class="p">)</span>
     79<span class="n">GSASIIpath</span><span class="o">.</span><span class="n">SetVersionNumber</span><span class="p">(</span><span class="s">&quot;$Revision: 1998 $&quot;</span><span class="p">)</span>
    8080<span class="kn">import</span> <span class="nn">GSASIImath</span> <span class="kn">as</span> <span class="nn">G2mth</span>
    8181<span class="kn">import</span> <span class="nn">GSASIIIO</span> <span class="kn">as</span> <span class="nn">G2IO</span>
  • sphinxdocs/build/html/_modules/GSASIIlattice.html

    r1998 r2010  
    7474<span class="sd">&#39;&#39;&#39;</span>
    7575<span class="c">########### SVN repository information ###################</span>
    76 <span class="c"># $Date: 2015-07-24 14:55:09 -0500 (Fri, 24 Jul 2015) $</span>
     76<span class="c"># $Date: 2015-10-12 09:12:45 -0500 (Mon, 12 Oct 2015) $</span>
    7777<span class="c"># $Author: vondreele $</span>
    78 <span class="c"># $Revision: 1947 $</span>
     78<span class="c"># $Revision: 1999 $</span>
    7979<span class="c"># $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/GSASIIlattice.py $</span>
    80 <span class="c"># $Id: GSASIIlattice.py 1947 2015-07-24 19:55:09Z vondreele $</span>
     80<span class="c"># $Id: GSASIIlattice.py 1999 2015-10-12 14:12:45Z vondreele $</span>
    8181<span class="c">########### SVN repository information ###################</span>
    8282<span class="kn">import</span> <span class="nn">math</span>
     
    8686<span class="kn">import</span> <span class="nn">GSASIImath</span> <span class="kn">as</span> <span class="nn">G2mth</span>
    8787<span class="kn">import</span> <span class="nn">GSASIIspc</span> <span class="kn">as</span> <span class="nn">G2spc</span>
    88 <span class="n">GSASIIpath</span><span class="o">.</span><span class="n">SetVersionNumber</span><span class="p">(</span><span class="s">&quot;$Revision: 1947 $&quot;</span><span class="p">)</span>
     88<span class="n">GSASIIpath</span><span class="o">.</span><span class="n">SetVersionNumber</span><span class="p">(</span><span class="s">&quot;$Revision: 1999 $&quot;</span><span class="p">)</span>
    8989<span class="c"># trig functions in degrees</span>
    9090<span class="n">sind</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">x</span><span class="o">*</span><span class="n">np</span><span class="o">.</span><span class="n">pi</span><span class="o">/</span><span class="mf">180.</span><span class="p">)</span>
     
    323323<span class="sd">    &quot;&quot;&quot;</span>
    324324    <span class="n">U</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span>
    325         <span class="p">[</span><span class="n">U6</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>  <span class="n">U6</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span>  <span class="n">U6</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span><span class="o">/</span><span class="mf">2.</span><span class="p">],</span>
    326         <span class="p">[</span><span class="n">U6</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span>  <span class="n">U6</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>  <span class="n">U6</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span><span class="o">/</span><span class="mf">2.</span><span class="p">],</span>
    327         <span class="p">[</span><span class="n">U6</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span>  <span class="n">U6</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span>  <span class="n">U6</span><span class="p">[</span><span class="mi">2</span><span class="p">]]])</span>
     325        <span class="p">[</span><span class="n">U6</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>  <span class="n">U6</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span>  <span class="n">U6</span><span class="p">[</span><span class="mi">4</span><span class="p">]],</span>
     326        <span class="p">[</span><span class="n">U6</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span>  <span class="n">U6</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>  <span class="n">U6</span><span class="p">[</span><span class="mi">5</span><span class="p">]],</span>
     327        <span class="p">[</span><span class="n">U6</span><span class="p">[</span><span class="mi">4</span><span class="p">],</span>  <span class="n">U6</span><span class="p">[</span><span class="mi">5</span><span class="p">],</span>  <span class="n">U6</span><span class="p">[</span><span class="mi">2</span><span class="p">]]])</span>
    328328    <span class="k">return</span> <span class="n">U</span>
    329329</div>
     
    332332<span class="sd">    NB: there is a non numpy version in GSASIIspc: Uij2U</span>
    333333<span class="sd">    &quot;&quot;&quot;</span>
    334     <span class="n">U6</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">U</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span><span class="n">U</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span><span class="n">U</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="mi">2</span><span class="p">],</span><span class="n">U</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="o">*</span><span class="mf">2.</span><span class="p">,</span><span class="n">U</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">2</span><span class="p">]</span><span class="o">*</span><span class="mf">2.</span><span class="p">,</span><span class="n">U</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="mi">2</span><span class="p">]</span><span class="o">*</span><span class="mf">2.</span><span class="p">])</span>
     334    <span class="n">U6</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">U</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span><span class="n">U</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span><span class="n">U</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="mi">2</span><span class="p">],</span><span class="n">U</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="n">U</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">2</span><span class="p">],</span><span class="n">U</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="mi">2</span><span class="p">]])</span>
    335335    <span class="k">return</span> <span class="n">U6</span>
    336336</div>
  • sphinxdocs/build/html/_modules/GSASIIstrMath.html

    r1998 r2010  
    5555<span class="sd">&#39;&#39;&#39;</span>
    5656<span class="c">########### SVN repository information ###################</span>
    57 <span class="c"># $Date: 2015-10-09 14:57:18 -0500 (Fri, 09 Oct 2015) $</span>
     57<span class="c"># $Date: 2015-10-12 13:00:08 -0500 (Mon, 12 Oct 2015) $</span>
    5858<span class="c"># $Author: vondreele $</span>
    59 <span class="c"># $Revision: 1996 $</span>
     59<span class="c"># $Revision: 2000 $</span>
    6060<span class="c"># $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/GSASIIstrMath.py $</span>
    61 <span class="c"># $Id: GSASIIstrMath.py 1996 2015-10-09 19:57:18Z vondreele $</span>
     61<span class="c"># $Id: GSASIIstrMath.py 2000 2015-10-12 18:00:08Z vondreele $</span>
    6262<span class="c">########### SVN repository information ###################</span>
    6363<span class="kn">import</span> <span class="nn">time</span>
     
    6969<span class="kn">import</span> <span class="nn">scipy.stats</span> <span class="kn">as</span> <span class="nn">st</span>
    7070<span class="kn">import</span> <span class="nn">GSASIIpath</span>
    71 <span class="n">GSASIIpath</span><span class="o">.</span><span class="n">SetVersionNumber</span><span class="p">(</span><span class="s">&quot;$Revision: 1996 $&quot;</span><span class="p">)</span>
     71<span class="n">GSASIIpath</span><span class="o">.</span><span class="n">SetVersionNumber</span><span class="p">(</span><span class="s">&quot;$Revision: 2000 $&quot;</span><span class="p">)</span>
    7272<span class="kn">import</span> <span class="nn">GSASIIElem</span> <span class="kn">as</span> <span class="nn">G2el</span>
    7373<span class="kn">import</span> <span class="nn">GSASIIlattice</span> <span class="kn">as</span> <span class="nn">G2lat</span>
     
    804804        <span class="k">else</span><span class="p">:</span>
    805805            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">TwinLaw</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
    806                 <span class="n">refl</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">9</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">fas</span><span class="p">[:,:,</span><span class="mi">0</span><span class="p">],</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span><span class="o">**</span><span class="mi">2</span><span class="o">+</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">fbs</span><span class="p">[:,:,</span><span class="mi">0</span><span class="p">],</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span><span class="o">**</span><span class="mi">2</span>   <span class="c">#FcT from primary twin element</span>
     806                <span class="n">refl</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">9</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">fas</span><span class="p">[:,:,</span><span class="mi">0</span><span class="p">]</span><span class="o">**</span><span class="mi">2</span><span class="p">,</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span><span class="o">+</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">fbs</span><span class="p">[:,:,</span><span class="mi">0</span><span class="p">]</span><span class="o">**</span><span class="mi">2</span><span class="p">,</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>   <span class="c">#FcT from primary twin element</span>
    807807                <span class="n">refl</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">7</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">TwinFr</span><span class="o">*</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">TwMask</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">,:,:]</span><span class="o">*</span><span class="n">fas</span><span class="p">,</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span><span class="o">**</span><span class="mi">2</span><span class="p">,</span><span class="n">axis</span><span class="o">=-</span><span class="mi">1</span><span class="p">)</span><span class="o">+</span>   \
    808808                    <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">TwinFr</span><span class="o">*</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">TwMask</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">,:,:]</span><span class="o">*</span><span class="n">fbs</span><span class="p">,</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span><span class="o">**</span><span class="mi">2</span><span class="p">,</span><span class="n">axis</span><span class="o">=-</span><span class="mi">1</span><span class="p">)</span>                        <span class="c">#Fc sum over twins</span>
    809809                <span class="n">refl</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">10</span><span class="p">]</span> <span class="o">=</span> <span class="n">atan2d</span><span class="p">(</span><span class="n">fbs</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span><span class="n">fas</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>  <span class="c">#ignore f&#39; &amp; f&quot;</span>
    810810            <span class="k">else</span><span class="p">:</span>
    811                 <span class="n">refl</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">9</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">fas</span><span class="p">,</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span><span class="o">**</span><span class="mi">2</span><span class="o">+</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">fbs</span><span class="p">,</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span><span class="o">**</span><span class="mi">2</span>
     811                <span class="n">refl</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">9</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">fas</span><span class="o">**</span><span class="mi">2</span><span class="p">,</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span><span class="o">+</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">fbs</span><span class="o">**</span><span class="mi">2</span><span class="p">,</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
    812812                <span class="n">refl</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">7</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="n">refl</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">9</span><span class="p">])</span>               
    813813                <span class="n">refl</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">10</span><span class="p">]</span> <span class="o">=</span> <span class="n">atan2d</span><span class="p">(</span><span class="n">fbs</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span><span class="n">fas</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>  <span class="c">#ignore f&#39; &amp; f&quot;</span>
     
    899899        <span class="n">fot</span> <span class="o">=</span> <span class="p">(</span><span class="n">FF</span><span class="o">+</span><span class="n">FP</span><span class="o">-</span><span class="n">Bab</span><span class="p">)</span><span class="o">*</span><span class="n">Tcorr</span>
    900900        <span class="n">fotp</span> <span class="o">=</span> <span class="n">FPP</span><span class="o">*</span><span class="n">Tcorr</span>       
    901         <span class="n">fa</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">FF</span><span class="o">+</span><span class="n">FP</span><span class="p">)</span><span class="o">.</span><span class="n">T</span><span class="o">-</span><span class="n">Bab</span><span class="p">)</span><span class="o">.</span><span class="n">T</span><span class="o">*</span><span class="n">cosp</span><span class="o">*</span><span class="n">Tcorr</span><span class="p">,</span><span class="o">-</span><span class="n">Flack</span><span class="o">*</span><span class="n">FPP</span><span class="o">*</span><span class="n">sinp</span><span class="o">*</span><span class="n">Tcorr</span><span class="p">])</span> <span class="c"># array(2,nTwin,nEqv,nAtoms)</span>
     901        <span class="n">fa</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">FF</span><span class="o">+</span><span class="n">FP</span><span class="p">)</span><span class="o">.</span><span class="n">T</span><span class="o">-</span><span class="n">Bab</span><span class="p">)</span><span class="o">.</span><span class="n">T</span><span class="o">*</span><span class="n">cosp</span><span class="o">*</span><span class="n">Tcorr</span><span class="p">,</span><span class="o">-</span><span class="n">Flack</span><span class="o">*</span><span class="n">FPP</span><span class="o">*</span><span class="n">sinp</span><span class="o">*</span><span class="n">Tcorr</span><span class="p">])</span>
    902902        <span class="n">fb</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">FF</span><span class="o">+</span><span class="n">FP</span><span class="p">)</span><span class="o">.</span><span class="n">T</span><span class="o">-</span><span class="n">Bab</span><span class="p">)</span><span class="o">.</span><span class="n">T</span><span class="o">*</span><span class="n">sinp</span><span class="o">*</span><span class="n">Tcorr</span><span class="p">,</span><span class="n">Flack</span><span class="o">*</span><span class="n">FPP</span><span class="o">*</span><span class="n">cosp</span><span class="o">*</span><span class="n">Tcorr</span><span class="p">])</span>
    903903        <span class="n">fas</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">fa</span><span class="p">,</span><span class="n">axis</span><span class="o">=-</span><span class="mi">1</span><span class="p">),</span><span class="n">axis</span><span class="o">=-</span><span class="mi">1</span><span class="p">)</span>      <span class="c">#real sum over atoms &amp; unique hkl array(2,nTwins)</span>
     
    948948                <span class="mf">2.</span><span class="o">*</span><span class="p">(</span><span class="n">fbs</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdua</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdua</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
    949949        <span class="k">else</span><span class="p">:</span>
    950             <span class="n">SA</span> <span class="o">=</span> <span class="n">fas</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">-</span><span class="n">fbs</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
     950            <span class="n">SA</span> <span class="o">=</span> <span class="n">fas</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
    951951            <span class="n">SB</span> <span class="o">=</span> <span class="n">fbs</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fas</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
    952952            <span class="k">if</span> <span class="n">nTwin</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
    953                 <span class="n">dFdfr</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mf">2.</span><span class="o">*</span><span class="n">TwMask</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">SA</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="p">(</span><span class="n">dfadfr</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">+</span><span class="n">dfbdfr</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">it</span><span class="p">])</span><span class="o">*</span><span class="n">Mdata</span><span class="o">/</span><span class="nb">len</span><span class="p">(</span><span class="n">Uniq</span><span class="p">[</span><span class="n">it</span><span class="p">])</span><span class="o">+</span> \
    954                     <span class="mf">2.</span><span class="o">*</span><span class="n">TwMask</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">SB</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="p">(</span><span class="n">dfbdfr</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">+</span><span class="n">dfadfr</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">it</span><span class="p">])</span><span class="o">*</span><span class="n">Mdata</span><span class="o">/</span><span class="nb">len</span><span class="p">(</span><span class="n">Uniq</span><span class="p">[</span><span class="n">it</span><span class="p">])</span> <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">nTwin</span><span class="p">)]</span>
    955                 <span class="n">dFdx</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mf">2.</span><span class="o">*</span><span class="n">TwMask</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">SA</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="p">(</span><span class="n">dfadx</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">dfbdx</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">1</span><span class="p">])</span><span class="o">+</span><span class="mf">2.</span><span class="o">*</span><span class="n">TwMask</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">SB</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="p">(</span><span class="n">dfbdx</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">dfadx</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">1</span><span class="p">])</span> <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">nTwin</span><span class="p">)]</span>
    956                 <span class="n">dFdui</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mf">2.</span><span class="o">*</span><span class="n">TwMask</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">SA</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="p">(</span><span class="n">dfadui</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">+</span><span class="n">dfbdui</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">it</span><span class="p">])</span><span class="o">+</span><span class="mf">2.</span><span class="o">*</span><span class="n">TwMask</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">SB</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="p">(</span><span class="n">dfbdui</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">+</span><span class="n">dfadui</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">it</span><span class="p">])</span> <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">nTwin</span><span class="p">)]</span>
    957                 <span class="n">dFdua</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mf">2.</span><span class="o">*</span><span class="n">TwMask</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">SA</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="p">(</span><span class="n">dfadua</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">dfbdua</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">1</span><span class="p">])</span><span class="o">+</span><span class="mf">2.</span><span class="o">*</span><span class="n">TwMask</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">SB</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="p">(</span><span class="n">dfbdua</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">dfadua</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">1</span><span class="p">])</span> <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">nTwin</span><span class="p">)]</span>
     953                <span class="n">dFdfr</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mf">2.</span><span class="o">*</span><span class="n">TwMask</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="p">(</span><span class="n">fas</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfadfr</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">+</span><span class="n">fas</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfadfr</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdfr</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdfr</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">it</span><span class="p">])</span><span class="o">*</span><span class="n">Mdata</span><span class="o">/</span><span class="nb">len</span><span class="p">(</span><span class="n">Uniq</span><span class="p">[</span><span class="n">it</span><span class="p">])</span> <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">nTwin</span><span class="p">)]</span>
     954                <span class="n">dFdx</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mf">2.</span><span class="o">*</span><span class="n">TwMask</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="p">(</span><span class="n">fas</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfadx</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fas</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfadx</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdx</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdx</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">1</span><span class="p">])</span> <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">nTwin</span><span class="p">)]</span>
     955                <span class="n">dFdui</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mf">2.</span><span class="o">*</span><span class="n">TwMask</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="p">(</span><span class="n">fas</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfadui</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fas</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfadui</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdui</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdui</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">1</span><span class="p">])</span> <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">nTwin</span><span class="p">)]</span>
     956                <span class="n">dFdua</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mf">2.</span><span class="o">*</span><span class="n">TwMask</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="p">(</span><span class="n">fas</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfadua</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fas</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfadua</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdua</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdua</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">1</span><span class="p">])</span> <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">nTwin</span><span class="p">)]</span>
    958957                <span class="n">dFdtw</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">TwMask</span><span class="o">*</span><span class="n">fas</span><span class="p">,</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span><span class="o">**</span><span class="mi">2</span><span class="o">+</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">TwMask</span><span class="o">*</span><span class="n">fbs</span><span class="p">,</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span><span class="o">**</span><span class="mi">2</span>
    959958               
    960959            <span class="k">else</span><span class="p">:</span>   <span class="c">#these are good for no twin single crystals</span>
    961                 <span class="n">dFdfr</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="n">SA</span><span class="o">*</span><span class="p">(</span><span class="n">dfadfr</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">dfbdfr</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span><span class="o">*</span><span class="n">Mdata</span><span class="o">/</span><span class="nb">len</span><span class="p">(</span><span class="n">Uniq</span><span class="p">)</span><span class="o">+</span> \
    962                     <span class="mf">2.</span><span class="o">*</span><span class="n">SB</span><span class="o">*</span><span class="p">(</span><span class="n">dfbdfr</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">dfadfr</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span><span class="o">*</span><span class="n">Mdata</span><span class="o">/</span><span class="nb">len</span><span class="p">(</span><span class="n">Uniq</span><span class="p">)</span> <span class="c">#array(nRef,nAtom)</span>
    963                 <span class="n">dFdx</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="n">SA</span><span class="o">*</span><span class="p">(</span><span class="n">dfadx</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">dfbdx</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span><span class="o">+</span><span class="mf">2.</span><span class="o">*</span><span class="n">SB</span><span class="o">*</span><span class="p">(</span><span class="n">dfbdx</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">dfadx</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>    <span class="c">#array(nRef,nAtom,3)</span>
    964                 <span class="n">dFdui</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="n">SA</span><span class="o">*</span><span class="p">(</span><span class="n">dfadui</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">dfbdui</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span><span class="o">+</span><span class="mf">2.</span><span class="o">*</span><span class="n">SB</span><span class="o">*</span><span class="p">(</span><span class="n">dfbdui</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">dfadui</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>   <span class="c">#array(nRef,nAtom)</span>
    965                 <span class="n">dFdua</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="n">SA</span><span class="o">*</span><span class="p">(</span><span class="n">dfadua</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">dfbdua</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span><span class="o">+</span><span class="mf">2.</span><span class="o">*</span><span class="n">SB</span><span class="o">*</span><span class="p">(</span><span class="n">dfbdua</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">dfadua</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>    <span class="c">#array(nRef,nAtom,6)</span>
     960                <span class="n">dFdfr</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="p">(</span><span class="n">fas</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">*</span><span class="n">dfadfr</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fas</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">*</span><span class="n">dfadfr</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdfr</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdfr</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span><span class="o">*</span><span class="n">Mdata</span><span class="o">/</span><span class="nb">len</span><span class="p">(</span><span class="n">Uniq</span><span class="p">)</span>
     961                <span class="n">dFdx</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="p">(</span><span class="n">fas</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">*</span><span class="n">dfadx</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fas</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">*</span><span class="n">dfadx</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdx</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdx</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
     962                <span class="n">dFdui</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="p">(</span><span class="n">fas</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">*</span><span class="n">dfadui</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fas</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">*</span><span class="n">dfadui</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdui</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdui</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
     963                <span class="n">dFdua</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="p">(</span><span class="n">fas</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">*</span><span class="n">dfadua</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fas</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">*</span><span class="n">dfadua</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdua</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdua</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
    966964                <span class="n">dFdfl</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">SA</span><span class="o">*</span><span class="n">dfadfl</span><span class="o">-</span><span class="n">SB</span><span class="o">*</span><span class="n">dfbdfl</span>  <span class="c">#array(nRef,)</span>
    967965        <span class="n">dFdbab</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="n">fas</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">*</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">dfadba</span><span class="o">*</span><span class="n">dBabdA</span><span class="p">),</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="o">-</span><span class="n">dfadba</span><span class="o">*</span><span class="n">parmDict</span><span class="p">[</span><span class="n">phfx</span><span class="o">+</span><span class="s">&#39;BabA&#39;</span><span class="p">]</span><span class="o">*</span><span class="n">SQfactor</span><span class="o">*</span><span class="n">dBabdA</span><span class="p">)])</span><span class="o">.</span><span class="n">T</span><span class="o">+</span> \
     
    980978            <span class="n">dFdvDict</span><span class="p">[</span><span class="n">pfx</span><span class="o">+</span><span class="s">&#39;AU22:&#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">dFdua</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">i</span><span class="p">]</span><span class="o">*</span><span class="n">TwinFr</span><span class="p">[:,</span><span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">],</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
    981979            <span class="n">dFdvDict</span><span class="p">[</span><span class="n">pfx</span><span class="o">+</span><span class="s">&#39;AU33:&#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">dFdua</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="n">i</span><span class="p">]</span><span class="o">*</span><span class="n">TwinFr</span><span class="p">[:,</span><span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">],</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
    982             <span class="n">dFdvDict</span><span class="p">[</span><span class="n">pfx</span><span class="o">+</span><span class="s">&#39;AU12:&#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="mf">0.5</span><span class="o">*</span><span class="n">dFdua</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">3</span><span class="p">][</span><span class="n">i</span><span class="p">]</span><span class="o">*</span><span class="n">TwinFr</span><span class="p">[:,</span><span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">],</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
    983             <span class="n">dFdvDict</span><span class="p">[</span><span class="n">pfx</span><span class="o">+</span><span class="s">&#39;AU13:&#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="mf">0.5</span><span class="o">*</span><span class="n">dFdua</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">4</span><span class="p">][</span><span class="n">i</span><span class="p">]</span><span class="o">*</span><span class="n">TwinFr</span><span class="p">[:,</span><span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">],</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
    984             <span class="n">dFdvDict</span><span class="p">[</span><span class="n">pfx</span><span class="o">+</span><span class="s">&#39;AU23:&#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="mf">0.5</span><span class="o">*</span><span class="n">dFdua</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">5</span><span class="p">][</span><span class="n">i</span><span class="p">]</span><span class="o">*</span><span class="n">TwinFr</span><span class="p">[:,</span><span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">],</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
     980            <span class="n">dFdvDict</span><span class="p">[</span><span class="n">pfx</span><span class="o">+</span><span class="s">&#39;AU12:&#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">dFdua</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">3</span><span class="p">][</span><span class="n">i</span><span class="p">]</span><span class="o">*</span><span class="n">TwinFr</span><span class="p">[:,</span><span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">],</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
     981            <span class="n">dFdvDict</span><span class="p">[</span><span class="n">pfx</span><span class="o">+</span><span class="s">&#39;AU13:&#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">dFdua</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">4</span><span class="p">][</span><span class="n">i</span><span class="p">]</span><span class="o">*</span><span class="n">TwinFr</span><span class="p">[:,</span><span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">],</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
     982            <span class="n">dFdvDict</span><span class="p">[</span><span class="n">pfx</span><span class="o">+</span><span class="s">&#39;AU23:&#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">dFdua</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">5</span><span class="p">][</span><span class="n">i</span><span class="p">]</span><span class="o">*</span><span class="n">TwinFr</span><span class="p">[:,</span><span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">],</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
    985983    <span class="k">else</span><span class="p">:</span>
    986984        <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">Mdata</span><span class="p">)):</span>
     
    993991            <span class="n">dFdvDict</span><span class="p">[</span><span class="n">pfx</span><span class="o">+</span><span class="s">&#39;AU22:&#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span> <span class="o">=</span> <span class="n">dFdua</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">i</span><span class="p">]</span>
    994992            <span class="n">dFdvDict</span><span class="p">[</span><span class="n">pfx</span><span class="o">+</span><span class="s">&#39;AU33:&#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span> <span class="o">=</span> <span class="n">dFdua</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="n">i</span><span class="p">]</span>
    995             <span class="n">dFdvDict</span><span class="p">[</span><span class="n">pfx</span><span class="o">+</span><span class="s">&#39;AU12:&#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span> <span class="o">=</span> <span class="mf">0.5</span><span class="o">*</span><span class="n">dFdua</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">3</span><span class="p">][</span><span class="n">i</span><span class="p">]</span>
    996             <span class="n">dFdvDict</span><span class="p">[</span><span class="n">pfx</span><span class="o">+</span><span class="s">&#39;AU13:&#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span> <span class="o">=</span> <span class="mf">0.5</span><span class="o">*</span><span class="n">dFdua</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">4</span><span class="p">][</span><span class="n">i</span><span class="p">]</span>
    997             <span class="n">dFdvDict</span><span class="p">[</span><span class="n">pfx</span><span class="o">+</span><span class="s">&#39;AU23:&#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span> <span class="o">=</span> <span class="mf">0.5</span><span class="o">*</span><span class="n">dFdua</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">5</span><span class="p">][</span><span class="n">i</span><span class="p">]</span>
     993            <span class="n">dFdvDict</span><span class="p">[</span><span class="n">pfx</span><span class="o">+</span><span class="s">&#39;AU12:&#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="n">dFdua</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">3</span><span class="p">][</span><span class="n">i</span><span class="p">]</span>
     994            <span class="n">dFdvDict</span><span class="p">[</span><span class="n">pfx</span><span class="o">+</span><span class="s">&#39;AU13:&#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="n">dFdua</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">4</span><span class="p">][</span><span class="n">i</span><span class="p">]</span>
     995            <span class="n">dFdvDict</span><span class="p">[</span><span class="n">pfx</span><span class="o">+</span><span class="s">&#39;AU23:&#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="n">dFdua</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">5</span><span class="p">][</span><span class="n">i</span><span class="p">]</span>
    998996        <span class="n">dFdvDict</span><span class="p">[</span><span class="n">phfx</span><span class="o">+</span><span class="s">&#39;Flack&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mf">4.</span><span class="o">*</span><span class="n">dFdfl</span><span class="o">.</span><span class="n">T</span>
    999997    <span class="n">dFdvDict</span><span class="p">[</span><span class="n">phfx</span><span class="o">+</span><span class="s">&#39;BabA&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">dFdbab</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
     
    11251123        <span class="k">else</span><span class="p">:</span>
    11261124            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">TwinLaw</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
    1127                 <span class="n">refl</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">10</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">fas</span><span class="p">[:,:,</span><span class="mi">0</span><span class="p">],</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span><span class="o">**</span><span class="mi">2</span><span class="o">+</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">fbs</span><span class="p">[:,:,</span><span class="mi">0</span><span class="p">],</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span><span class="o">**</span><span class="mi">2</span>   <span class="c">#FcT from primary twin element</span>
     1125                <span class="n">refl</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">10</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">fas</span><span class="p">[:,:,</span><span class="mi">0</span><span class="p">]</span><span class="o">**</span><span class="mi">2</span><span class="p">,</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span><span class="o">+</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">fbs</span><span class="p">[:,:,</span><span class="mi">0</span><span class="p">]</span><span class="o">**</span><span class="mi">2</span><span class="p">,</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>   <span class="c">#FcT from primary twin element</span>
    11281126                <span class="n">refl</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">8</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">TwinFr</span><span class="o">*</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">TwMask</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">,:,:]</span><span class="o">*</span><span class="n">fas</span><span class="p">,</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span><span class="o">**</span><span class="mi">2</span><span class="p">,</span><span class="n">axis</span><span class="o">=-</span><span class="mi">1</span><span class="p">)</span><span class="o">+</span>   \
    11291127                    <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">TwinFr</span><span class="o">*</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">TwMask</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">,:,:]</span><span class="o">*</span><span class="n">fbs</span><span class="p">,</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span><span class="o">**</span><span class="mi">2</span><span class="p">,</span><span class="n">axis</span><span class="o">=-</span><span class="mi">1</span><span class="p">)</span>                        <span class="c">#Fc sum over twins</span>
    11301128                <span class="n">refl</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">11</span><span class="p">]</span> <span class="o">=</span> <span class="n">atan2d</span><span class="p">(</span><span class="n">fbs</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span><span class="n">fas</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>  <span class="c">#ignore f&#39; &amp; f&quot;</span>
    11311129            <span class="k">else</span><span class="p">:</span>
    1132                 <span class="n">refl</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">10</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">fas</span><span class="p">,</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span><span class="o">**</span><span class="mi">2</span><span class="o">+</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">fbs</span><span class="p">,</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span><span class="o">**</span><span class="mi">2</span>
     1130                <span class="n">refl</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">10</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">fas</span><span class="o">**</span><span class="mi">2</span><span class="p">,</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span><span class="o">+</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">fbs</span><span class="o">**</span><span class="mi">2</span><span class="p">,</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
    11331131                <span class="n">refl</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">8</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="n">refl</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">10</span><span class="p">])</span>               
    11341132                <span class="n">refl</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">11</span><span class="p">]</span> <span class="o">=</span> <span class="n">atan2d</span><span class="p">(</span><span class="n">fbs</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span><span class="n">fas</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>  <span class="c">#ignore f&#39; &amp; f&quot;</span>
     
    13031301            <span class="n">SB</span> <span class="o">=</span> <span class="n">fbs</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fas</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
    13041302            <span class="k">if</span> <span class="n">nTwin</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
    1305                 <span class="n">dFdfr</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mf">2.</span><span class="o">*</span><span class="n">TwMask</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">SA</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="p">(</span><span class="n">dfadfr</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">+</span><span class="n">dfbdfr</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">it</span><span class="p">])</span><span class="o">*</span><span class="n">Mdata</span><span class="o">/</span><span class="nb">len</span><span class="p">(</span><span class="n">Uniq</span><span class="p">[</span><span class="n">it</span><span class="p">])</span><span class="o">+</span> \
    1306                     <span class="mf">2.</span><span class="o">*</span><span class="n">TwMask</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">SB</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="p">(</span><span class="n">dfbdfr</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">+</span><span class="n">dfadfr</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">it</span><span class="p">])</span><span class="o">*</span><span class="n">Mdata</span><span class="o">/</span><span class="nb">len</span><span class="p">(</span><span class="n">Uniq</span><span class="p">[</span><span class="n">it</span><span class="p">])</span> <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">nTwin</span><span class="p">)]</span>
    1307                 <span class="n">dFdx</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mf">2.</span><span class="o">*</span><span class="n">TwMask</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">SA</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="p">(</span><span class="n">dfadx</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">dfbdx</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">1</span><span class="p">])</span><span class="o">+</span><span class="mf">2.</span><span class="o">*</span><span class="n">TwMask</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">SB</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="p">(</span><span class="n">dfbdx</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">dfadx</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">1</span><span class="p">])</span> <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">nTwin</span><span class="p">)]</span>
    1308                 <span class="n">dFdui</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mf">2.</span><span class="o">*</span><span class="n">TwMask</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">SA</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="p">(</span><span class="n">dfadui</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">+</span><span class="n">dfbdui</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">it</span><span class="p">])</span><span class="o">+</span><span class="mf">2.</span><span class="o">*</span><span class="n">TwMask</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">SB</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="p">(</span><span class="n">dfbdui</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">+</span><span class="n">dfadui</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">it</span><span class="p">])</span> <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">nTwin</span><span class="p">)]</span>
    1309                 <span class="n">dFdua</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mf">2.</span><span class="o">*</span><span class="n">TwMask</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">SA</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="p">(</span><span class="n">dfadua</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">dfbdua</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">1</span><span class="p">])</span><span class="o">+</span><span class="mf">2.</span><span class="o">*</span><span class="n">TwMask</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">SB</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="p">(</span><span class="n">dfbdua</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">dfadua</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">1</span><span class="p">])</span> <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">nTwin</span><span class="p">)]</span>
     1303                <span class="n">dFdfr</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mf">2.</span><span class="o">*</span><span class="n">TwMask</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="p">(</span><span class="n">fas</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfadfr</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">+</span><span class="n">fas</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfadfr</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdfr</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdfr</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">it</span><span class="p">])</span><span class="o">*</span><span class="n">Mdata</span><span class="o">/</span><span class="nb">len</span><span class="p">(</span><span class="n">Uniq</span><span class="p">[</span><span class="n">it</span><span class="p">])</span> <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">nTwin</span><span class="p">)]</span>
     1304                <span class="n">dFdx</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mf">2.</span><span class="o">*</span><span class="n">TwMask</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="p">(</span><span class="n">fas</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfadx</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fas</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfadx</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdx</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdx</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">1</span><span class="p">])</span> <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">nTwin</span><span class="p">)]</span>
     1305                <span class="n">dFdui</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mf">2.</span><span class="o">*</span><span class="n">TwMask</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="p">(</span><span class="n">fas</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfadui</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fas</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfadui</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdui</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdui</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">1</span><span class="p">])</span> <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">nTwin</span><span class="p">)]</span>
     1306                <span class="n">dFdua</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mf">2.</span><span class="o">*</span><span class="n">TwMask</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="p">(</span><span class="n">fas</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfadua</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fas</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfadua</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdua</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdua</span><span class="p">[</span><span class="n">it</span><span class="p">][</span><span class="mi">1</span><span class="p">])</span> <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">nTwin</span><span class="p">)]</span>
     1307                <span class="n">dFdGx</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mf">2.</span><span class="o">*</span><span class="n">TwMask</span><span class="p">[</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="p">(</span><span class="n">fas</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfadGx</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fas</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfadGx</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdGx</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">it</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdGx</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <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">nTwin</span><span class="p">)]</span>
    13101308                <span class="n">dFdtw</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">TwMask</span><span class="o">*</span><span class="n">fas</span><span class="p">,</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span><span class="o">**</span><span class="mi">2</span><span class="o">+</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">TwMask</span><span class="o">*</span><span class="n">fbs</span><span class="p">,</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span><span class="o">**</span><span class="mi">2</span>
    13111309               
    13121310            <span class="k">else</span><span class="p">:</span>   <span class="c">#these are good for no twin single crystals</span>
    1313                 <span class="n">dFdfr</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="n">SA</span><span class="o">*</span><span class="p">(</span><span class="n">dfadfr</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">dfbdfr</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span><span class="o">*</span><span class="n">Mdata</span><span class="o">/</span><span class="nb">len</span><span class="p">(</span><span class="n">Uniq</span><span class="p">)</span><span class="o">+</span> \
    1314                     <span class="mf">2.</span><span class="o">*</span><span class="n">SB</span><span class="o">*</span><span class="p">(</span><span class="n">dfbdfr</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">dfadfr</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span><span class="o">*</span><span class="n">Mdata</span><span class="o">/</span><span class="nb">len</span><span class="p">(</span><span class="n">Uniq</span><span class="p">)</span> <span class="c">#array(nRef,nAtom)</span>
    1315                 <span class="n">dFdx</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="n">SA</span><span class="o">*</span><span class="p">(</span><span class="n">dfadx</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">dfbdx</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span><span class="o">+</span><span class="mf">2.</span><span class="o">*</span><span class="n">SB</span><span class="o">*</span><span class="p">(</span><span class="n">dfbdx</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">dfadx</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>    <span class="c">#array(nRef,nAtom,3)</span>
    1316                 <span class="n">dFdui</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="n">SA</span><span class="o">*</span><span class="p">(</span><span class="n">dfadui</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">dfbdui</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span><span class="o">+</span><span class="mf">2.</span><span class="o">*</span><span class="n">SB</span><span class="o">*</span><span class="p">(</span><span class="n">dfbdui</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">dfadui</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>   <span class="c">#array(nRef,nAtom)</span>
    1317                 <span class="n">dFdua</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="n">SA</span><span class="o">*</span><span class="p">(</span><span class="n">dfadua</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">dfbdua</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span><span class="o">+</span><span class="mf">2.</span><span class="o">*</span><span class="n">SB</span><span class="o">*</span><span class="p">(</span><span class="n">dfbdua</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">dfadua</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>    <span class="c">#array(nRef,nAtom,6)</span>
     1311                <span class="n">dFdfr</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="p">(</span><span class="n">fas</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">*</span><span class="n">dfadfr</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fas</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">*</span><span class="n">dfadfr</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdfr</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdfr</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span><span class="o">*</span><span class="n">Mdata</span><span class="o">/</span><span class="nb">len</span><span class="p">(</span><span class="n">Uniq</span><span class="p">)</span> <span class="c">#array(nRef,nAtom)</span>
     1312                <span class="n">dFdx</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="p">(</span><span class="n">fas</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">*</span><span class="n">dfadx</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdx</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdx</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fas</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">*</span><span class="n">dfadx</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>    <span class="c">#array(nRef,nAtom,3)</span>
     1313                <span class="n">dFdui</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="p">(</span><span class="n">fas</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">*</span><span class="n">dfadui</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdui</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdui</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fas</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">*</span><span class="n">dfadui</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>   <span class="c">#array(nRef,nAtom)</span>
     1314                <span class="n">dFdua</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="p">(</span><span class="n">fas</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">*</span><span class="n">dfadua</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdua</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdua</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fas</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">*</span><span class="n">dfadua</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>    <span class="c">#array(nRef,nAtom,6)</span>
    13181315                <span class="n">dFdfl</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">SA</span><span class="o">*</span><span class="n">dfadfl</span><span class="o">-</span><span class="n">SB</span><span class="o">*</span><span class="n">dfbdfl</span>                  <span class="c">#array(nRef,)</span>
    1319                 <span class="n">dFdGx</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="n">SA</span><span class="o">*</span><span class="p">(</span><span class="n">dfadGx</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">dfbdGx</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span><span class="o">+</span><span class="mf">2.</span><span class="o">*</span><span class="n">SB</span><span class="o">*</span><span class="p">(</span><span class="n">dfadGx</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">+</span><span class="n">dfbdGx</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>      <span class="c">#array(nRef,natom,nwave,6)</span>
     1316                <span class="n">dFdGx</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="p">(</span><span class="n">fas</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">*</span><span class="n">dfadGx</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fas</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">*</span><span class="n">dfadGx</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdGx</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">fbs</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">*</span><span class="n">dfbdGx</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>      <span class="c">#array(nRef,natom,nwave,6)</span>
    13201317        <span class="n">dFdbab</span><span class="p">[</span><span class="n">iref</span><span class="p">]</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="n">fas</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">*</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">dfadba</span><span class="o">*</span><span class="n">dBabdA</span><span class="p">),</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="o">-</span><span class="n">dfadba</span><span class="o">*</span><span class="n">parmDict</span><span class="p">[</span><span class="n">phfx</span><span class="o">+</span><span class="s">&#39;BabA&#39;</span><span class="p">]</span><span class="o">*</span><span class="n">SQfactor</span><span class="o">*</span><span class="n">dBabdA</span><span class="p">)])</span><span class="o">.</span><span class="n">T</span><span class="o">+</span> \
    13211318            <span class="mf">2.</span><span class="o">*</span><span class="n">fbs</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">*</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">dfbdba</span><span class="o">*</span><span class="n">dBabdA</span><span class="p">),</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="o">-</span><span class="n">dfbdba</span><span class="o">*</span><span class="n">parmDict</span><span class="p">[</span><span class="n">phfx</span><span class="o">+</span><span class="s">&#39;BabA&#39;</span><span class="p">]</span><span class="o">*</span><span class="n">SQfactor</span><span class="o">*</span><span class="n">dBabdA</span><span class="p">)])</span><span class="o">.</span><span class="n">T</span>
     
    13301327        <span class="n">dFdvDict</span><span class="p">[</span><span class="n">pfx</span><span class="o">+</span><span class="s">&#39;AU22:&#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span> <span class="o">=</span> <span class="n">dFdua</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">i</span><span class="p">]</span>
    13311328        <span class="n">dFdvDict</span><span class="p">[</span><span class="n">pfx</span><span class="o">+</span><span class="s">&#39;AU33:&#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span> <span class="o">=</span> <span class="n">dFdua</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="n">i</span><span class="p">]</span>
    1332         <span class="n">dFdvDict</span><span class="p">[</span><span class="n">pfx</span><span class="o">+</span><span class="s">&#39;AU12:&#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span> <span class="o">=</span> <span class="o">.</span><span class="mi">5</span><span class="o">*</span><span class="n">dFdua</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">3</span><span class="p">][</span><span class="n">i</span><span class="p">]</span>
    1333         <span class="n">dFdvDict</span><span class="p">[</span><span class="n">pfx</span><span class="o">+</span><span class="s">&#39;AU13:&#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span> <span class="o">=</span> <span class="o">.</span><span class="mi">5</span><span class="o">*</span><span class="n">dFdua</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">4</span><span class="p">][</span><span class="n">i</span><span class="p">]</span>
    1334         <span class="n">dFdvDict</span><span class="p">[</span><span class="n">pfx</span><span class="o">+</span><span class="s">&#39;AU23:&#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span> <span class="o">=</span> <span class="o">.</span><span class="mi">5</span><span class="o">*</span><span class="n">dFdua</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">5</span><span class="p">][</span><span class="n">i</span><span class="p">]</span>
     1329        <span class="n">dFdvDict</span><span class="p">[</span><span class="n">pfx</span><span class="o">+</span><span class="s">&#39;AU12:&#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="n">dFdua</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">3</span><span class="p">][</span><span class="n">i</span><span class="p">]</span>
     1330        <span class="n">dFdvDict</span><span class="p">[</span><span class="n">pfx</span><span class="o">+</span><span class="s">&#39;AU13:&#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="n">dFdua</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">4</span><span class="p">][</span><span class="n">i</span><span class="p">]</span>
     1331        <span class="n">dFdvDict</span><span class="p">[</span><span class="n">pfx</span><span class="o">+</span><span class="s">&#39;AU23:&#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span> <span class="o">=</span> <span class="mf">2.</span><span class="o">*</span><span class="n">dFdua</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">5</span><span class="p">][</span><span class="n">i</span><span class="p">]</span>
    13351332        <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">XSSdata</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]):</span>
    13361333            <span class="n">dFdvDict</span><span class="p">[</span><span class="n">pfx</span><span class="o">+</span><span class="s">&#39;Xsin:&#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)</span><span class="o">+</span><span class="s">&#39;:&#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">j</span><span class="p">)]</span> <span class="o">=</span> <span class="n">dFdGx</span><span class="o">.</span><span class="n">T</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">j</span><span class="p">][</span><span class="n">i</span><span class="p">]</span>
  • sphinxdocs/build/html/_modules/config_example.html

    r1998 r2010  
    9393<span class="sd">&#39;&#39;&#39;</span>
    9494
     95<span class="n">Transpose</span> <span class="o">=</span> <span class="bp">False</span>
     96<span class="s">&#39;Set to True to cause images to be Transposed when read (for code development)&#39;</span>
     97
    9598<span class="n">Enable_logging</span> <span class="o">=</span> <span class="bp">False</span>
    9699<span class="s">&#39;Set to True to enable use of command logging (under development.)&#39;</span>
  • sphinxdocs/build/html/_modules/index.html

    r1709 r2010  
    4848  <h1>All modules for which code is available</h1>
    4949<ul><li><a href="G2export_CIF.html">G2export_CIF</a></li>
     50<li><a href="G2export_FIT2D.html">G2export_FIT2D</a></li>
    5051<li><a href="G2export_PDB.html">G2export_PDB</a></li>
    5152<li><a href="G2export_csv.html">G2export_csv</a></li>
     
    5556<li><a href="G2export_pwdr.html">G2export_pwdr</a></li>
    5657<li><a href="G2export_shelx.html">G2export_shelx</a></li>
     58<li><a href="G2img_1TIF.html">G2img_1TIF</a></li>
    5759<li><a href="G2phase.html">G2phase</a></li>
    5860<li><a href="G2phase_CIF.html">G2phase_CIF</a></li>
  • sphinxdocs/build/html/exports.html

    r1998 r2010  
    6161(&#8216;project&#8217;, &#8216;phase&#8217;, &#8216;single&#8217;, &#8216;powder&#8217;, &#8216;image&#8217;, &#8216;map&#8217; or (someday)
    6262&#8216;pdf&#8217;) and of <tt class="docutils literal"><span class="pre">self.multiple</span></tt>
    63 determines if only a single phase, data set, etc. can be exported at a time (when False) or more than one can be selected.</p>
     63determines if only a single phase, data set, etc. can be exported at a
     64time (when False) or more than one can be selected.</p>
     65<p>Powder export routines may optionally define a <tt class="docutils literal"><span class="pre">Writer()</span></tt>
     66method that accepts the histogram tree name as well as a file name to
     67be written. This allows <tt class="xref py py-func docutils literal"><span class="pre">ExportPowder()</span></tt> to use the exporter
     68independent of the GUI.</p>
    6469<span class="target" id="module-G2export_examples"></span><div class="section" id="module-g2export-examples-examples">
    6570<h2><em>Module G2export_examples: Examples</em><a class="headerlink" href="#module-g2export-examples-examples" title="Permalink to this headline">¶</a></h2>
     
    840845
    841846</div>
     847<span class="target" id="module-G2export_FIT2D"></span><div class="section" id="module-g2export-fit2d-fit2d-chi-export">
     848<h2><em>Module G2export_FIT2D: Fit2D &#8220;Chi&#8221; export</em><a class="headerlink" href="#module-g2export-fit2d-fit2d-chi-export" title="Permalink to this headline">¶</a></h2>
     849<p>Code to create .chi (Fit2D like) files for GSAS-II powder data export</p>
     850<dl class="class">
     851<dt id="G2export_FIT2D.ExportPowderCSV">
     852<em class="property">class </em><tt class="descclassname">G2export_FIT2D.</tt><tt class="descname">ExportPowderCSV</tt><big>(</big><em>G2frame</em><big>)</big><a class="reference internal" href="_modules/G2export_FIT2D.html#ExportPowderCSV"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#G2export_FIT2D.ExportPowderCSV" title="Permalink to this definition">¶</a></dt>
     853<dd><p>Used to create a csv file for a powder data set</p>
     854<table class="docutils field-list" frame="void" rules="none">
     855<col class="field-name" />
     856<col class="field-body" />
     857<tbody valign="top">
     858<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>G2frame</strong> (<em>wx.Frame</em>) &#8211; reference to main GSAS-II frame</td>
     859</tr>
     860</tbody>
     861</table>
     862<dl class="method">
     863<dt id="G2export_FIT2D.ExportPowderCSV.Exporter">
     864<tt class="descname">Exporter</tt><big>(</big><em>event=None</em><big>)</big><a class="reference internal" href="_modules/G2export_FIT2D.html#ExportPowderCSV.Exporter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#G2export_FIT2D.ExportPowderCSV.Exporter" title="Permalink to this definition">¶</a></dt>
     865<dd><p>Export a set of powder data as a Fit2D .chi file</p>
     866</dd></dl>
     867
     868</dd></dl>
     869
     870</div>
    842871</div>
    843872
     
    862891<li><a class="reference internal" href="#module-g2export-cif-cif-exports"><em>Module G2export_CIF: CIF Exports</em></a></li>
    863892<li><a class="reference internal" href="#module-g2export-pwdr-export-powder-input-files"><em>Module G2export_pwdr: Export powder input files</em></a></li>
     893<li><a class="reference internal" href="#module-g2export-fit2d-fit2d-chi-export"><em>Module G2export_FIT2D: Fit2D &#8220;Chi&#8221; export</em></a></li>
    864894</ul>
    865895</li>
  • sphinxdocs/build/html/genindex.html

    r1998 r2010  
    534534
    535535     
    536   <dt><a href="imports.html#G2phase.EXP_ReaderClass.ContentsValidator">ContentsValidator() (G2phase.EXP_ReaderClass method)</a>
     536  <dt><a href="imports.html#G2img_1TIF.TIF_ReaderClass.ContentsValidator">ContentsValidator() (G2img_1TIF.TIF_ReaderClass method)</a>
    537537  </dt>
    538538
    539539      <dd><dl>
     540       
     541  <dt><a href="imports.html#G2phase.EXP_ReaderClass.ContentsValidator">(G2phase.EXP_ReaderClass method)</a>
     542  </dt>
     543
    540544       
    541545  <dt><a href="imports.html#G2phase.JANA_ReaderClass.ContentsValidator">(G2phase.JANA_ReaderClass method)</a>
     
    10161020      <dd><dl>
    10171021       
     1022  <dt><a href="exports.html#G2export_FIT2D.ExportPowderCSV.Exporter">(G2export_FIT2D.ExportPowderCSV method)</a>
     1023  </dt>
     1024
     1025       
    10181026  <dt><a href="exports.html#G2export_PDB.ExportPhaseCartXYZ.Exporter">(G2export_PDB.ExportPhaseCartXYZ method)</a>
    10191027  </dt>
     
    11381146  </dt>
    11391147
     1148      <dd><dl>
     1149       
     1150  <dt><a href="exports.html#G2export_FIT2D.ExportPowderCSV">(class in G2export_FIT2D)</a>
     1151  </dt>
     1152
     1153      </dl></dd>
    11401154     
    11411155  <dt><a href="exports.html#G2export_pwdr.ExportPowderFXYE">ExportPowderFXYE (class in G2export_pwdr)</a>
     
    14091423
    14101424     
     1425  <dt><a href="exports.html#module-G2export_FIT2D">G2export_FIT2D (module)</a>
     1426  </dt>
     1427
     1428     
    14111429  <dt><a href="exports.html#module-G2export_image">G2export_image (module)</a>
    14121430  </dt>
     
    14371455
    14381456     
     1457  <dt><a href="imports.html#module-G2img_1TIF">G2img_1TIF (module)</a>
     1458  </dt>
     1459
     1460     
     1461  <dt><a href="imports.html#module-G2img_ADSC">G2img_ADSC (module)</a>
     1462  </dt>
     1463
     1464     
     1465  <dt><a href="imports.html#module-G2img_CheMin">G2img_CheMin (module)</a>
     1466  </dt>
     1467
     1468     
     1469  <dt><a href="imports.html#module-G2img_EDF">G2img_EDF (module)</a>
     1470  </dt>
     1471
     1472     
     1473  <dt><a href="imports.html#module-G2img_GE">G2img_GE (module)</a>
     1474  </dt>
     1475
     1476     
     1477  <dt><a href="imports.html#module-G2img_MAR">G2img_MAR (module)</a>
     1478  </dt>
     1479
     1480     
     1481  <dt><a href="imports.html#module-G2img_Rigaku">G2img_Rigaku (module)</a>
     1482  </dt>
     1483
     1484     
     1485  <dt><a href="imports.html#module-G2img_SumG2">G2img_SumG2 (module)</a>
     1486  </dt>
     1487
     1488     
    14391489  <dt><a href="GSASIIGUIr.html#GSASIIctrls.G2LoggedButton">G2LoggedButton (class in GSASIIctrls)</a>
    14401490  </dt>
     
    19261976     
    19271977  <dt><a href="GSASIIGUIr.html#GSASIIctrls.GetItemOrder">GetItemOrder() (in module GSASIIctrls)</a>
    1928   </dt>
    1929 
    1930      
    1931   <dt><a href="GSASIIutil.html#GSASIIlattice.GetKcl">GetKcl() (in module GSASIIlattice)</a>
    1932   </dt>
    1933 
    1934      
    1935   <dt><a href="GSASIIutil.html#GSASIIlattice.GetKclKsl">GetKclKsl() (in module GSASIIlattice)</a>
    1936   </dt>
    1937 
    1938      
    1939   <dt><a href="GSASIIutil.html#GSASIIspc.GetKNsym">GetKNsym() (in module GSASIIspc)</a>
    1940   </dt>
    1941 
    1942      
    1943   <dt><a href="GSASIIutil.html#GSASIIlattice.GetKsl">GetKsl() (in module GSASIIlattice)</a>
    1944   </dt>
    1945 
    1946      
    1947   <dt><a href="GSASIIutil.html#GSASIIElem.GetMagFormFacCoeff">GetMagFormFacCoeff() (in module GSASIIElem)</a>
    19481978  </dt>
    19491979
    19501980  </dl></td>
    19511981  <td style="width: 33%" valign="top"><dl>
     1982     
     1983  <dt><a href="GSASIIutil.html#GSASIIlattice.GetKcl">GetKcl() (in module GSASIIlattice)</a>
     1984  </dt>
     1985
     1986     
     1987  <dt><a href="GSASIIutil.html#GSASIIlattice.GetKclKsl">GetKclKsl() (in module GSASIIlattice)</a>
     1988  </dt>
     1989
     1990     
     1991  <dt><a href="GSASIIutil.html#GSASIIspc.GetKNsym">GetKNsym() (in module GSASIIspc)</a>
     1992  </dt>
     1993
     1994     
     1995  <dt><a href="GSASIIutil.html#GSASIIlattice.GetKsl">GetKsl() (in module GSASIIlattice)</a>
     1996  </dt>
     1997
     1998     
     1999  <dt><a href="GSASIIutil.html#GSASIIElem.GetMagFormFacCoeff">GetMagFormFacCoeff() (in module GSASIIElem)</a>
     2000  </dt>
     2001
    19522002     
    19532003  <dt><a href="GSASIIGUIr.html#GSASIIIO.GetMAR345Data">GetMAR345Data() (in module GSASIIIO)</a>
     
    26172667
    26182668     
     2669  <dt><a href="GSASIIGUIr.html#GSASIIIO.ImportImage">ImportImage (class in GSASIIIO)</a>
     2670  </dt>
     2671
     2672     
    26192673  <dt><a href="GSASIIGUIr.html#GSASIIIO.ImportPhase">ImportPhase (class in GSASIIIO)</a>
    26202674  </dt>
     
    26592713
    26602714     
    2661   <dt><a href="GSASIIGUIr.html#GSASIIIO.ImportStructFactor.InitParameters">InitParameters() (GSASIIIO.ImportStructFactor method)</a>
    2662   </dt>
    2663 
     2715  <dt><a href="GSASIIGUIr.html#GSASIIIO.ImportImage.InitParameters">InitParameters() (GSASIIIO.ImportImage method)</a>
     2716  </dt>
     2717
     2718      <dd><dl>
     2719       
     2720  <dt><a href="GSASIIGUIr.html#GSASIIIO.ImportStructFactor.InitParameters">(GSASIIIO.ImportStructFactor method)</a>
     2721  </dt>
     2722
     2723      </dl></dd>
    26642724     
    26652725  <dt><a href="GSASIImapvars.html#GSASIImapvars.InitVars">InitVars() (in module GSASIImapvars)</a>
     
    27792839
    27802840     
     2841  <dt><a href="GSASIIGUIr.html#GSASIIIO.LoadImage">LoadImage() (in module GSASIIIO)</a>
     2842  </dt>
     2843
     2844     
    27812845  <dt><a href="GSASIIGUIr.html#GSASIIIO.ExportBaseclass.loadParmDict">loadParmDict() (GSASIIIO.ExportBaseclass method)</a>
    27822846  </dt>
     
    32193283
    32203284     
     3285  <dt><a href="GSASII.html#GSASII.GSASII.OnImportImage">OnImportImage() (GSASII.GSASII method)</a>
     3286  </dt>
     3287
     3288     
    32213289  <dt><a href="GSASII.html#GSASII.GSASII.OnImportPhase">OnImportPhase() (GSASII.GSASII method)</a>
    32223290  </dt>
     
    35483616  </dt>
    35493617
     3618     
     3619  <dt><a href="GSASIIplot.html#GSASIIplot.PlotPeakWidths">PlotPeakWidths() (in module GSASIIplot)</a>
     3620  </dt>
     3621
    35503622  </dl></td>
    35513623  <td style="width: 33%" valign="top"><dl>
    35523624     
    3553   <dt><a href="GSASIIplot.html#GSASIIplot.PlotPeakWidths">PlotPeakWidths() (in module GSASIIplot)</a>
    3554   </dt>
    3555 
    3556      
    35573625  <dt><a href="GSASIIplot.html#GSASIIplot.PlotPowderLines">PlotPowderLines() (in module GSASIIplot)</a>
    35583626  </dt>
     
    36363704     
    36373705  <dt><a href="GSASIIGUIr.html#GSASIIgrid.DataFrame.PrefillDataMenu">PrefillDataMenu() (GSASIIgrid.DataFrame method)</a>
     3706  </dt>
     3707
     3708     
     3709  <dt><a href="GSASII.html#GSASII.GSASII.PreviewFile">PreviewFile() (GSASII.GSASII method)</a>
    36383710  </dt>
    36393711
     
    37493821
    37503822     
    3751   <dt><a href="imports.html#G2phase.EXP_ReaderClass.Reader">Reader() (G2phase.EXP_ReaderClass method)</a>
     3823  <dt><a href="imports.html#G2img_1TIF.TIF_ReaderClass.Reader">Reader() (G2img_1TIF.TIF_ReaderClass method)</a>
    37523824  </dt>
    37533825
    37543826      <dd><dl>
    37553827       
     3828  <dt><a href="imports.html#G2phase.EXP_ReaderClass.Reader">(G2phase.EXP_ReaderClass method)</a>
     3829  </dt>
     3830
     3831       
    37563832  <dt><a href="imports.html#G2phase.JANA_ReaderClass.Reader">(G2phase.JANA_ReaderClass method)</a>
    37573833  </dt>
     
    38163892     
    38173893  <dt><a href="imports.html#G2phase.EXP_ReaderClass.ReadEXPPhase">ReadEXPPhase() (G2phase.EXP_ReaderClass method)</a>
     3894  </dt>
     3895
     3896     
     3897  <dt><a href="GSASIIGUIr.html#GSASIIIO.ReadImageData">ReadImageData() (in module GSASIIIO)</a>
    38183898  </dt>
    38193899
     
    38733953
    38743954      <dd><dl>
     3955       
     3956  <dt><a href="GSASIIGUIr.html#GSASIIIO.ImportImage.ReInitialize">(GSASIIIO.ImportImage method)</a>
     3957  </dt>
     3958
    38753959       
    38763960  <dt><a href="GSASIIGUIr.html#GSASIIIO.ImportPowderData.ReInitialize">(GSASIIIO.ImportPowderData method)</a>
     
    46384722  </dt>
    46394723
     4724     
     4725  <dt><a href="GSASIIutil.html#gltext.Text.text">text (gltext.Text attribute)</a>
     4726  </dt>
     4727
     4728      <dd><dl>
     4729       
     4730  <dt><a href="GSASIIutil.html#gltext.TextElement.text">(gltext.TextElement attribute)</a>
     4731  </dt>
     4732
     4733      </dl></dd>
    46404734  </dl></td>
    46414735  <td style="width: 33%" valign="top"><dl>
    46424736     
    4643   <dt><a href="GSASIIutil.html#gltext.Text.text">text (gltext.Text attribute)</a>
     4737  <dt><a href="GSASIIutil.html#gltext.Text.text_element">text_element (gltext.Text attribute)</a>
     4738  </dt>
     4739
     4740     
     4741  <dt><a href="GSASIIutil.html#gltext.TextElement">TextElement (class in gltext)</a>
     4742  </dt>
     4743
     4744     
     4745  <dt><a href="GSASIIutil.html#gltext.Text.texture">texture (gltext.Text attribute)</a>
    46444746  </dt>
    46454747
    46464748      <dd><dl>
    46474749       
    4648   <dt><a href="GSASIIutil.html#gltext.TextElement.text">(gltext.TextElement attribute)</a>
     4750  <dt><a href="GSASIIutil.html#gltext.TextElement.texture">(gltext.TextElement attribute)</a>
    46494751  </dt>
    46504752
    46514753      </dl></dd>
    46524754     
    4653   <dt><a href="GSASIIutil.html#gltext.Text.text_element">text_element (gltext.Text attribute)</a>
    4654   </dt>
    4655 
    4656      
    4657   <dt><a href="GSASIIutil.html#gltext.TextElement">TextElement (class in gltext)</a>
    4658   </dt>
    4659 
    4660      
    4661   <dt><a href="GSASIIutil.html#gltext.Text.texture">texture (gltext.Text attribute)</a>
     4755  <dt><a href="GSASIIutil.html#gltext.Text.texture_size">texture_size (gltext.Text attribute)</a>
    46624756  </dt>
    46634757
    46644758      <dd><dl>
    46654759       
    4666   <dt><a href="GSASIIutil.html#gltext.TextElement.texture">(gltext.TextElement attribute)</a>
     4760  <dt><a href="GSASIIutil.html#gltext.TextElement.texture_size">(gltext.TextElement attribute)</a>
    46674761  </dt>
    46684762
    46694763      </dl></dd>
    46704764     
    4671   <dt><a href="GSASIIutil.html#gltext.Text.texture_size">texture_size (gltext.Text attribute)</a>
     4765  <dt><a href="GSASIIutil.html#GSASIIlattice.textureIndex">textureIndex() (in module GSASIIlattice)</a>
     4766  </dt>
     4767
     4768     
     4769  <dt><a href="imports.html#G2img_1TIF.TIF_ReaderClass">TIF_ReaderClass (class in G2img_1TIF)</a>
     4770  </dt>
     4771
     4772     
     4773  <dt><a href="GSASIImath.html#GSASIImath.TLS2Uij">TLS2Uij() (in module GSASIImath)</a>
     4774  </dt>
     4775
     4776     
     4777  <dt><a href="GSASIIutil.html#GSASIIlattice.TOF2dsp">TOF2dsp() (in module GSASIIlattice)</a>
     4778  </dt>
     4779
     4780     
     4781  <dt><a href="GSASIIGUIr.html#GSASIIctrls.ASCIIValidator.TransferFromWindow">TransferFromWindow() (GSASIIctrls.ASCIIValidator method)</a>
    46724782  </dt>
    46734783
    46744784      <dd><dl>
    46754785       
    4676   <dt><a href="GSASIIutil.html#gltext.TextElement.texture_size">(gltext.TextElement attribute)</a>
     4786  <dt><a href="GSASIIGUIr.html#GSASIIctrls.NumberValidator.TransferFromWindow">(GSASIIctrls.NumberValidator method)</a>
    46774787  </dt>
    46784788
    46794789      </dl></dd>
    46804790     
    4681   <dt><a href="GSASIIutil.html#GSASIIlattice.textureIndex">textureIndex() (in module GSASIIlattice)</a>
    4682   </dt>
    4683 
    4684      
    4685   <dt><a href="GSASIImath.html#GSASIImath.TLS2Uij">TLS2Uij() (in module GSASIImath)</a>
    4686   </dt>
    4687 
    4688      
    4689   <dt><a href="GSASIIutil.html#GSASIIlattice.TOF2dsp">TOF2dsp() (in module GSASIIlattice)</a>
    4690   </dt>
    4691 
    4692      
    4693   <dt><a href="GSASIIGUIr.html#GSASIIctrls.ASCIIValidator.TransferFromWindow">TransferFromWindow() (GSASIIctrls.ASCIIValidator method)</a>
     4791  <dt><a href="GSASIIGUIr.html#GSASIIctrls.ASCIIValidator.TransferToWindow">TransferToWindow() (GSASIIctrls.ASCIIValidator method)</a>
    46944792  </dt>
    46954793
    46964794      <dd><dl>
    46974795       
    4698   <dt><a href="GSASIIGUIr.html#GSASIIctrls.NumberValidator.TransferFromWindow">(GSASIIctrls.NumberValidator method)</a>
     4796  <dt><a href="GSASIIGUIr.html#GSASIIctrls.NumberValidator.TransferToWindow">(GSASIIctrls.NumberValidator method)</a>
    46994797  </dt>
    47004798
    47014799      </dl></dd>
    47024800     
    4703   <dt><a href="GSASIIGUIr.html#GSASIIctrls.ASCIIValidator.TransferToWindow">TransferToWindow() (GSASIIctrls.ASCIIValidator method)</a>
    4704   </dt>
    4705 
    4706       <dd><dl>
    4707        
    4708   <dt><a href="GSASIIGUIr.html#GSASIIctrls.NumberValidator.TransferToWindow">(GSASIIctrls.NumberValidator method)</a>
    4709   </dt>
    4710 
    4711       </dl></dd>
    4712      
    47134801  <dt><a href="GSASIIpwd.html#GSASIIpwd.Transmission">Transmission() (in module GSASIIpwd)</a>
     4802  </dt>
     4803
     4804     
     4805  <dt><a href="GSASIIutil.html#config_example.Transpose">Transpose (in module config_example)</a>
    47144806  </dt>
    47154807
  • sphinxdocs/build/html/imports.html

    r1998 r2010  
    342342<a class="reference internal" href="GSASIIGUIr.html#GSASIIIO.ImportPowderData" title="GSASIIIO.ImportPowderData"><tt class="xref py py-class docutils literal"><span class="pre">GSASIIIO.ImportPowderData</span></tt></a>.
    343343They must be found in files named <cite>G2pwd*.py</cite> that are in the Python path
    344 and the class must override the <tt class="docutils literal"><span class="pre">__init__</span></tt> method and add a <tt class="docutils literal"><span class="pre">Reader</span></tt> method.
    345 The distributed routines are:</p>
     344and the class must override the <tt class="docutils literal"><span class="pre">__init__</span></tt> method and add a
     345<tt class="docutils literal"><span class="pre">Reader</span></tt> method.</p>
     346<p>The distributed routines are:</p>
    346347<span class="target" id="module-G2pwd_GPX"></span><div class="section" id="module-g2pwd-gpx-gsas-ii-projects">
    347348<h3><em>Module G2pwd_GPX: GSAS-II projects</em><a class="headerlink" href="#module-g2pwd-gpx-gsas-ii-projects" title="Permalink to this headline">¶</a></h3>
     
    679680</dd></dl>
    680681
     682</div>
     683</div>
     684<div class="section" id="image-import-routines">
     685<h2>Image Import Routines<a class="headerlink" href="#image-import-routines" title="Permalink to this headline">¶</a></h2>
     686<p>Image import routines are classes derived from
     687, <a class="reference internal" href="GSASIIGUIr.html#GSASIIIO.ImportImage" title="GSASIIIO.ImportImage"><tt class="xref py py-class docutils literal"><span class="pre">GSASIIIO.ImportImage</span></tt></a>.
     688They must be found in files named <cite>G2img*.py</cite> that are in the Python path
     689and the class must override the <tt class="docutils literal"><span class="pre">__init__</span></tt> method and add a <tt class="docutils literal"><span class="pre">Reader</span></tt> method.
     690The distributed routines are:</p>
     691<span class="target" id="module-G2img_ADSC"></span><div class="section" id="module-g2img-adsc-img-image-file">
     692<h3><em>Module G2img_ADSC: .img image file</em><a class="headerlink" href="#module-g2img-adsc-img-image-file" title="Permalink to this headline">¶</a></h3>
     693<p>Routine to read an ADSC .img file</p>
     694</div>
     695<span class="target" id="module-G2img_EDF"></span><div class="section" id="module-g2img-edf-edf-image-file">
     696<h3><em>Module G2img_EDF: .edf image file</em><a class="headerlink" href="#module-g2img-edf-edf-image-file" title="Permalink to this headline">¶</a></h3>
     697<p>Routine to read a Read European detector data edf file</p>
     698</div>
     699<span class="target" id="module-G2img_SumG2"></span><div class="section" id="module-g2img-g2-python-pickled-image">
     700<h3><em>Module G2img_G2: Python pickled image</em><a class="headerlink" href="#module-g2img-g2-python-pickled-image" title="Permalink to this headline">¶</a></h3>
     701<p>Routine to read an image that has been pickled in Python. Images
     702in this format are created by the &#8220;Sum image data&#8221; command.</p>
     703</div>
     704<span class="target" id="module-G2img_GE"></span><div class="section" id="module-g2img-ge-summed-ge-image-file">
     705<h3><em>Module G2img_GE: summed GE image file</em><a class="headerlink" href="#module-g2img-ge-summed-ge-image-file" title="Permalink to this headline">¶</a></h3>
     706<p>Routine to read a summed GE image from APS Sector 1</p>
     707</div>
     708<span class="target" id="module-G2img_MAR"></span><div class="section" id="module-g2img-mar-mar-image-files">
     709<h3><em>Module G2img_MAR: MAR image files</em><a class="headerlink" href="#module-g2img-mar-mar-image-files" title="Permalink to this headline">¶</a></h3>
     710<p>Routine to read several MAR formats, .mar3450,.mar2300,.mar2560</p>
     711</div>
     712<span class="target" id="module-G2img_Rigaku"></span><div class="section" id="module-g2img-rigaku-stl-image-file">
     713<h3><em>Module G2img_Rigaku: .stl image file</em><a class="headerlink" href="#module-g2img-rigaku-stl-image-file" title="Permalink to this headline">¶</a></h3>
     714<p>Routine to read a Rigaku R-Axis IV image file</p>
     715</div>
     716<span class="target" id="module-G2img_1TIF"></span><div class="section" id="module-g2img-tif-tif-image-file">
     717<h3><em>Module G2img_TIF: .tif image file</em><a class="headerlink" href="#module-g2img-tif-tif-image-file" title="Permalink to this headline">¶</a></h3>
     718<p>Routine to read an image in Tagged-image file (TIF) format as well as a variety
     719of slightly incorrect pseudo-TIF formats used at instruments around the world.</p>
     720<dl class="class">
     721<dt id="G2img_1TIF.TIF_ReaderClass">
     722<em class="property">class </em><tt class="descclassname">G2img_1TIF.</tt><tt class="descname">TIF_ReaderClass</tt><a class="reference internal" href="_modules/G2img_1TIF.html#TIF_ReaderClass"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#G2img_1TIF.TIF_ReaderClass" title="Permalink to this definition">¶</a></dt>
     723<dd><p>Routine to read an image in Tagged-image file (TIF) format as well as a variety
     724of slightly incorrect pseudo-TIF formats</p>
     725<dl class="method">
     726<dt id="G2img_1TIF.TIF_ReaderClass.ContentsValidator">
     727<tt class="descname">ContentsValidator</tt><big>(</big><em>filepointer</em><big>)</big><a class="reference internal" href="_modules/G2img_1TIF.html#TIF_ReaderClass.ContentsValidator"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#G2img_1TIF.TIF_ReaderClass.ContentsValidator" title="Permalink to this definition">¶</a></dt>
     728<dd><p>Does the header match the required TIF header?</p>
     729</dd></dl>
     730
     731<dl class="method">
     732<dt id="G2img_1TIF.TIF_ReaderClass.Reader">
     733<tt class="descname">Reader</tt><big>(</big><em>filename</em>, <em>filepointer</em>, <em>ParentFrame=None</em>, <em>**unused</em><big>)</big><a class="reference internal" href="_modules/G2img_1TIF.html#TIF_ReaderClass.Reader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#G2img_1TIF.TIF_ReaderClass.Reader" title="Permalink to this definition">¶</a></dt>
     734<dd><p>Read the TIF file using Bob&#8217;s routine</p>
     735</dd></dl>
     736
     737</dd></dl>
     738
     739</div>
     740<span class="target" id="module-G2img_CheMin"></span><div class="section" id="module-g2img-png-png-image-file">
     741<h3><em>Module G2img_png: png image file</em><a class="headerlink" href="#module-g2img-png-png-image-file" title="Permalink to this headline">¶</a></h3>
     742<p>Routine to read an image in .png (Portable Network Graphics) format.
     743For now, the only known use of this is with converted CheMin tif files
     744so default parameters are that machine.</p>
    681745</div>
    682746</div>
     
    732796<li><a class="reference internal" href="#small-angle-scattering-data-import-routines">Small Angle Scattering Data Import Routines</a><ul>
    733797<li><a class="reference internal" href="#module-g2sad-xye-read-small-angle-data"><em>Module G2sad_xye: read small angle data</em></a></li>
     798</ul>
     799</li>
     800<li><a class="reference internal" href="#image-import-routines">Image Import Routines</a><ul>
     801<li><a class="reference internal" href="#module-g2img-adsc-img-image-file"><em>Module G2img_ADSC: .img image file</em></a></li>
     802<li><a class="reference internal" href="#module-g2img-edf-edf-image-file"><em>Module G2img_EDF: .edf image file</em></a></li>
     803<li><a class="reference internal" href="#module-g2img-g2-python-pickled-image"><em>Module G2img_G2: Python pickled image</em></a></li>
     804<li><a class="reference internal" href="#module-g2img-ge-summed-ge-image-file"><em>Module G2img_GE: summed GE image file</em></a></li>
     805<li><a class="reference internal" href="#module-g2img-mar-mar-image-files"><em>Module G2img_MAR: MAR image files</em></a></li>
     806<li><a class="reference internal" href="#module-g2img-rigaku-stl-image-file"><em>Module G2img_Rigaku: .stl image file</em></a></li>
     807<li><a class="reference internal" href="#module-g2img-tif-tif-image-file"><em>Module G2img_TIF: .tif image file</em></a></li>
     808<li><a class="reference internal" href="#module-g2img-png-png-image-file"><em>Module G2img_png: png image file</em></a></li>
    734809</ul>
    735810</li>
  • sphinxdocs/build/html/index.html

    r1998 r2010  
    146146<li class="toctree-l2"><a class="reference internal" href="exports.html#module-g2export-cif-cif-exports"><em>Module G2export_CIF: CIF Exports</em></a></li>
    147147<li class="toctree-l2"><a class="reference internal" href="exports.html#module-g2export-pwdr-export-powder-input-files"><em>Module G2export_pwdr: Export powder input files</em></a></li>
     148<li class="toctree-l2"><a class="reference internal" href="exports.html#module-g2export-fit2d-fit2d-chi-export"><em>Module G2export_FIT2D: Fit2D &#8220;Chi&#8221; export</em></a></li>
    148149</ul>
    149150</li>
     
    186187<li class="toctree-l2"><a class="reference internal" href="imports.html#small-angle-scattering-data-import-routines">Small Angle Scattering Data Import Routines</a><ul>
    187188<li class="toctree-l3"><a class="reference internal" href="imports.html#module-g2sad-xye-read-small-angle-data"><em>Module G2sad_xye: read small angle data</em></a></li>
     189</ul>
     190</li>
     191<li class="toctree-l2"><a class="reference internal" href="imports.html#image-import-routines">Image Import Routines</a><ul>
     192<li class="toctree-l3"><a class="reference internal" href="imports.html#module-g2img-adsc-img-image-file"><em>Module G2img_ADSC: .img image file</em></a></li>
     193<li class="toctree-l3"><a class="reference internal" href="imports.html#module-g2img-edf-edf-image-file"><em>Module G2img_EDF: .edf image file</em></a></li>
     194<li class="toctree-l3"><a class="reference internal" href="imports.html#module-g2img-g2-python-pickled-image"><em>Module G2img_G2: Python pickled image</em></a></li>
     195<li class="toctree-l3"><a class="reference internal" href="imports.html#module-g2img-ge-summed-ge-image-file"><em>Module G2img_GE: summed GE image file</em></a></li>
     196<li class="toctree-l3"><a class="reference internal" href="imports.html#module-g2img-mar-mar-image-files"><em>Module G2img_MAR: MAR image files</em></a></li>
     197<li class="toctree-l3"><a class="reference internal" href="imports.html#module-g2img-rigaku-stl-image-file"><em>Module G2img_Rigaku: .stl image file</em></a></li>
     198<li class="toctree-l3"><a class="reference internal" href="imports.html#module-g2img-tif-tif-image-file"><em>Module G2img_TIF: .tif image file</em></a></li>
     199<li class="toctree-l3"><a class="reference internal" href="imports.html#module-g2img-png-png-image-file"><em>Module G2img_png: png image file</em></a></li>
    188200</ul>
    189201</li>
  • sphinxdocs/build/html/py-modindex.html

    r1709 r2010  
    135135       <td></td>
    136136       <td>
     137       <a href="exports.html#module-G2export_FIT2D"><tt class="xref">G2export_FIT2D</tt></a></td><td>
     138       <em>Export powder data in Fit2D (.chi) format</em></td></tr>
     139     <tr>
     140       <td></td>
     141       <td>
    137142       <a href="exports.html#module-G2export_image"><tt class="xref">G2export_image</tt></a></td><td>
    138143       <em>Exports images</em></td></tr>
     
    157162       <a href="exports.html#module-G2export_shelx"><tt class="xref">G2export_shelx</tt></a></td><td>
    158163       <em>Export a phase in Shelx format</em></td></tr>
     164     <tr>
     165       <td></td>
     166       <td>
     167       <a href="imports.html#module-G2img_1TIF"><tt class="xref">G2img_1TIF</tt></a></td><td>
     168       <em></em></td></tr>
     169     <tr>
     170       <td></td>
     171       <td>
     172       <a href="imports.html#module-G2img_ADSC"><tt class="xref">G2img_ADSC</tt></a></td><td>
     173       <em></em></td></tr>
     174     <tr>
     175       <td></td>
     176       <td>
     177       <a href="imports.html#module-G2img_CheMin"><tt class="xref">G2img_CheMin</tt></a></td><td>
     178       <em></em></td></tr>
     179     <tr>
     180       <td></td>
     181       <td>
     182       <a href="imports.html#module-G2img_EDF"><tt class="xref">G2img_EDF</tt></a></td><td>
     183       <em></em></td></tr>
     184     <tr>
     185       <td></td>
     186       <td>
     187       <a href="imports.html#module-G2img_GE"><tt class="xref">G2img_GE</tt></a></td><td>
     188       <em></em></td></tr>
     189     <tr>
     190       <td></td>
     191       <td>
     192       <a href="imports.html#module-G2img_MAR"><tt class="xref">G2img_MAR</tt></a></td><td>
     193       <em></em></td></tr>
     194     <tr>
     195       <td></td>
     196       <td>
     197       <a href="imports.html#module-G2img_Rigaku"><tt class="xref">G2img_Rigaku</tt></a></td><td>
     198       <em></em></td></tr>
     199     <tr>
     200       <td></td>
     201       <td>
     202       <a href="imports.html#module-G2img_SumG2"><tt class="xref">G2img_SumG2</tt></a></td><td>
     203       <em></em></td></tr>
    159204     <tr>
    160205       <td></td>
  • sphinxdocs/build/html/searchindex.js

    r1998 r2010  
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