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<!DOCTYPE html>
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<section id="module-diffpy.morph">
<span id="diffpy-morph-package"></span><h1>diffpy.morph package<a class="headerlink" href="#module-diffpy.morph" title="Link to this heading"></a></h1>
<p>Python package for manipulating and comparing PDF profiles.</p>
<section id="subpackages">
<h2>Subpackages<a class="headerlink" href="#subpackages" title="Link to this heading"></a></h2>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="diffpy.morph.morph_helpers.html">diffpy.morph.morph_helpers package</a></li>
<li class="toctree-l1"><a class="reference internal" href="diffpy.morph.morphs.html">diffpy.morph.morphs package</a></li>
</ul>
</div>
</section>
<section id="submodules">
<h2>Submodules<a class="headerlink" href="#submodules" title="Link to this heading"></a></h2>
<section id="module-diffpy.morph.plot">
<span id="diffpy-morph-plot-module"></span><h3>diffpy.morph.plot module<a class="headerlink" href="#module-diffpy.morph.plot" title="Link to this heading"></a></h3>
<p>Collection of plotting functions (originally specifically) for
PDFs.</p>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.plot.compare_funcs">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.plot.</span></span><span class="sig-name descname"><span class="pre">compare_funcs</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pairlist</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">labels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xmin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xmax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">show</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">maglim</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mag</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rw</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">legend</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">l_width</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.5</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/plot.html#compare_funcs"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.plot.compare_funcs" title="Link to this definition"></a></dt>
<dd><p>Plot two functions g(r) on top of each other and difference
curve.</p>
<p>The second function will be shown as blue circles below and the first as
a red line. The difference curve will be in green and offset for clarity.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>pairlist</strong> – Iterable of (r, gr) pairs to plot</p></li>
<li><p><strong>labels</strong> – Iterable of names for the pairs. If this is not the same length as
the pairlist, a legend will not be shown (default []).</p></li>
<li><p><strong>xmin</strong> – The minimum x-value to plot. If this is None (default), the lower
bound of the function is not altered.</p></li>
<li><p><strong>xmax</strong> – The maximum x-value to plot. If this is None (default), the upper
bound of the function is not altered.</p></li>
<li><p><strong>show</strong> – Show the plot (default True)</p></li>
<li><p><strong>maglim</strong> – Point after which to magnify the signal by mag. If None (default), no
magnification will take place.</p></li>
<li><p><strong>mag</strong> – Magnification factor (default 5)</p></li>
<li><p><strong>rw</strong> – Rw value to display on the plot, if any.</p></li>
<li><p><strong>legend</strong> – Display the legend (default True).</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.plot.plot_funcs">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.plot.</span></span><span class="sig-name descname"><span class="pre">plot_funcs</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pairlist</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">labels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">offset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'auto'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xmin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xmax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/plot.html#plot_funcs"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.plot.plot_funcs" title="Link to this definition"></a></dt>
<dd><p>Plots several functions f(x) on top of one another.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>pairlist</strong> – Iterable of (x, fx) pairs to plot.</p></li>
<li><p><strong>labels</strong> – Iterable of names for the pairs. If this is not the same length as
the pairlist, a legend will not be shown (default []).</p></li>
<li><p><strong>offset</strong> – Offset to place between plots. Functions will be sequentially shifted
in the y-direction by the offset. If offset is ‘auto’ (default), the
optimal offset will be determined automatically.</p></li>
<li><p><strong>xmin</strong> – The minimum r-value to plot. If this is None (default), the lower
bound of the function is not altered.</p></li>
<li><p><strong>xmax</strong> – The maximum r-value to plot. If this is None (default), the upper
bound of the function is not altered.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.plot.plot_param">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.plot.</span></span><span class="sig-name descname"><span class="pre">plot_param</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target_labels</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">param_list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">param_name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/plot.html#plot_param"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.plot.plot_param" title="Link to this definition"></a></dt>
<dd><p>Plot Rw values for multiple morphs.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>target_labels</strong> (<em>list</em>) – Names (or field if –sort-by given) of each file acting as target for
the morph.</p></li>
<li><p><strong>param_list</strong> (<em>list</em>) – Contains the values of some parameter corresponding to each file.</p></li>
<li><p><strong>param_name</strong> (<em>str</em>) – Name of the parameter.</p></li>
<li><p><strong>field</strong> (<em>list</em><em> or </em><em>None</em>) – When not None and entries in field are numerical, a line chart of Rw
versus field is made.
When None (default) or values are non-numerical, it plots a bar chart
of Rw values per file.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.plot.truncate_func">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.plot.</span></span><span class="sig-name descname"><span class="pre">truncate_func</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fx</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xmin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xmax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/plot.html#truncate_func"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.plot.truncate_func" title="Link to this definition"></a></dt>
<dd><p>Truncate a function f(x) to specified bounds.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>x</strong> – The x-values of the function f(x).</p></li>
<li><p><strong>fx</strong> – Function f(x) values at each x-value.</p></li>
<li><p><strong>xmin</strong> – The minimum x-value. If this is None (default), the lower bound of
the function is not altered.</p></li>
<li><p><strong>xmax</strong> – The maximum x-value. If this is None (default), the upper bound of
the function is not altered.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Returns the truncated x, fx.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>x, fx</p>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-diffpy.morph.morph_api">
<span id="diffpy-morph-morph-api-module"></span><h3>diffpy.morph.morph_api module<a class="headerlink" href="#module-diffpy.morph.morph_api" title="Link to this heading"></a></h3>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.morph_api.morph">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.morph_api.</span></span><span class="sig-name descname"><span class="pre">morph</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x_morph</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">y_morph</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">x_target</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">y_target</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xmin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xmax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xstep</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pearson</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">add_pearson</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fixed_operations</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">refine</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/morph_api.html#morph"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.morph_api.morph" title="Link to this definition"></a></dt>
<dd><p>Function to perform PDF morphing.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>x_morph</strong> (<em>numpy.array</em>) – An array of morphed x values, i.e., those will be manipulated by
morphing.</p></li>
<li><p><strong>y_morph</strong> (<em>numpy.array</em>) – An array of morphed y values, i.e., those will be manipulated by
morphing.</p></li>
<li><p><strong>x_target</strong> (<em>numpy.array</em>) – An array of target x values, i.e., those will be kept constant by
morphing.</p></li>
<li><p><strong>y_morph</strong> – An array of target y values, i.e., those will be kept constant by
morphing.</p></li>
<li><p><strong>xmin</strong> (<em>float</em><em>, </em><em>optional</em>) – A value to specify lower x-limit of morph operations.</p></li>
<li><p><strong>xmax</strong> (<em>float</em><em>, </em><em>optional</em>) – A value to specify upper x-limit of morph operations.</p></li>
<li><p><strong>xstep</strong> (<em>float</em><em>, </em><em>optional</em>) – A value to specify xstep of morph operations.</p></li>
<li><p><strong>pearson</strong> (<em>Bool</em><em>, </em><em>optional</em>) – <dl class="simple">
<dt>Option to include Pearson coefficient as a minimizing target</dt><dd><p>during morphing. Default to False.</p>
</dd>
</dl>
</p></li>
<li><p><strong>add_pearson</strong> (<em>Bool</em><em>, </em><em>optional</em>) – Option to include <strong>both</strong> Pearson coefficient and Rw as
minimizing targets during morphing. Default to False.</p></li>
<li><p><strong>fixed_operations</strong> (<em>list</em><em>, </em><em>optional</em>) – A list of string specifying operations will be keep fixed during
morphing. Default is None.</p></li>
<li><p><strong>refine</strong> (<em>bool</em><em>, </em><em>optional</em>) – Option to execute the minimization step in morphing. If False,
the morphing will be applied with parameter values specified in
<cite>morph_config</cite>. Default to True.</p></li>
<li><p><strong>verbose</strong> (<em>bool</em><em>, </em><em>optional</em>) – Option to print full result after morph. Default to False.</p></li>
<li><p><strong>kwargs</strong> (<em>dict</em><em>, </em><em>optional</em>) – <p>A dictionary with morph parameters as keys and initial
values of morph parameters as values. Currently supported morph
parparameters are:</p>
<blockquote>
<div><ul>
<li><p>’scale’</p></li>
<li><p>’stretch’</p></li>
<li><p>’smear’</p></li>
<li><p>’baselineslope’</p></li>
<li><p>’qdamp’</p></li>
<li><p>’squeeze’</p></li>
<li><p>’funcy’</p></li>
</ul>
</div></blockquote>
</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><p><strong>morph_rv_dict</strong> – A dictionary contains following key-value pairs:</p>
<ul class="simple">
<li><dl class="simple">
<dt>morph_chain: diffpy.morph.morphs.morphchain.MorphChain</dt><dd><p>The instance of processed morph chain.
Calling
<code class="docutils literal notranslate"><span class="pre">x_morph,</span> <span class="pre">y_morph,</span> <span class="pre">x_target,</span> <span class="pre">y_target</span> <span class="pre">=</span> <span class="pre">morph_chain.xyallout</span></code>
will conveniently return morphed data and reference data</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>morphed_cfg: dict</dt><dd><p>A dictionary of refined morphing parameters</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>rw: float</dt><dd><p>The agreement factor between morphed data and reference
data</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>pcc: float</dt><dd><dl class="simple">
<dt>The pearson correlation coefficient between morphed</dt><dd><p>data and referenced data</p>
</dd>
</dl>
</dd>
</dl>
</li>
</ul>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>dict</p>
</dd>
</dl>
<p class="rubric">Examples</p>
<p># morphing (x_morph, y_morph) pair to (x_target, y_target) pair with
scaling from diffpy.morph.morph_api import morph,
morph_default_config, plot_morph</p>
<p>morph_cfg = morph_default_config(scale=1.01)
morph_rv_dict = morph(x_morph, y_morph, x_target, y_target, <a href="#id1"><span class="problematic" id="id2">**</span></a>morph_cfg)</p>
<p># plot morhing result
plot_morph(morph_rv_dict[‘morph_chain’])</p>
<p># print morphing parameters, pearson correlation coefficient, Rw
print(morph_rv_dict[‘morphed_cfg’])
print(morph_rv_dict[‘pcc’])
print(morph_rv_dict[‘rw’])</p>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.morph_api.morph_default_config">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.morph_api.</span></span><span class="sig-name descname"><span class="pre">morph_default_config</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/morph_api.html#morph_default_config"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.morph_api.morph_default_config" title="Link to this definition"></a></dt>
<dd><p>Function to generate default morph configuration.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>kwargs</strong> – extra keyword arguments passed to the default morph config</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><strong>morph_default_config</strong> – A dictionary of morph configuration</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>dict</p>
</dd>
</dl>
<p class="rubric">Examples</p>
<p>morph_cfg = morph_default_config(scale=1.01)</p>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.morph_api.plot_morph">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.morph_api.</span></span><span class="sig-name descname"><span class="pre">plot_morph</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">chain</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/morph_api.html#plot_morph"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.morph_api.plot_morph" title="Link to this definition"></a></dt>
<dd><p>Plot the morphed PDF and the target PDF of a morphing operation.</p>
<p>Open a new figure unless a specific axis is provided for plotting.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>chain</strong> (<a class="reference internal" href="diffpy.morph.morphs.html#diffpy.morph.morphs.morphchain.MorphChain" title="diffpy.morph.morphs.morphchain.MorphChain"><em>diffpy.morph.morphs.morphchain.MorphChain</em></a>) – An instance of processed morph chain.</p></li>
<li><p><strong>ax</strong> (<em>matplotlib.axes.Axes</em><em>, </em><em>optional</em>) – An instance of Axes class to plot the morphing result.
If ax is None, instances of new Figure and Axes will be created.
Default to None.</p></li>
<li><p><strong>kwargs</strong> – Additional keyword arguments will be passed to <code class="docutils literal notranslate"><span class="pre">ax.plot(...**kwargs)</span></code></p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><strong>l_list</strong> – A list of <code class="docutils literal notranslate"><span class="pre">matplotlib.lines.Line2D</span></code> objects representing the
plotted data.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list</p>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-diffpy.morph.tools">
<span id="diffpy-morph-tools-module"></span><h3>diffpy.morph.tools module<a class="headerlink" href="#module-diffpy.morph.tools" title="Link to this heading"></a></h3>
<p>Tools used in morphs and morph chains.</p>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.tools.case_insensitive_dictionary_search">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.tools.</span></span><span class="sig-name descname"><span class="pre">case_insensitive_dictionary_search</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">key</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dictionary</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/tools.html#case_insensitive_dictionary_search"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.tools.case_insensitive_dictionary_search" title="Link to this definition"></a></dt>
<dd><p>Search for key in dictionary ignoring case.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>key</strong> (<em>str</em>)</p></li>
<li><p><strong>dictionary</strong> (<em>dict</em>)</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Corresponding value if key is in dictionary. None otherwise.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>value or None</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.tools.deserialize">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.tools.</span></span><span class="sig-name descname"><span class="pre">deserialize</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">serial_file</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/tools.html#deserialize"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.tools.deserialize" title="Link to this definition"></a></dt>
<dd><p>Call deserialize_data from diffpy.utils.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>serial_file</strong> – Name of file to deserialize.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Data read from serial file.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>dict</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.tools.estimateBaselineSlope">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.tools.</span></span><span class="sig-name descname"><span class="pre">estimateBaselineSlope</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">r</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gr</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rmin</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rmax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/tools.html#estimateBaselineSlope"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.tools.estimateBaselineSlope" title="Link to this definition"></a></dt>
<dd><p>Estimate the slope of the linear baseline of a PDF.</p>
<p>This fits a slope into the equation slope*r through the bottom of the PDF.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>r</strong> – The r-grid used for the PDF.</p></li>
<li><p><strong>gr</strong> – The PDF over the r-grid.</p></li>
<li><p><strong>rmin</strong> – The minimum r-value to consider. If this is None (default) is None,
then the minimum of r is used.</p></li>
<li><p><strong>rmax</strong> – The maximum r-value to consider. If this is None (default) is None,
then the maximum of r is used.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><strong>slope</strong> – The slope of baseline. If the PDF is scaled properly, this is equal
to -4*pi*rho0.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.tools.estimateScale">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.tools.</span></span><span class="sig-name descname"><span class="pre">estimateScale</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">y_morph_in</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">y_target_in</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/tools.html#estimateScale"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.tools.estimateScale" title="Link to this definition"></a></dt>
<dd><p>Set the scale that best matches the morph to the target.</p>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.tools.field_sort">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.tools.</span></span><span class="sig-name descname"><span class="pre">field_sort</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filepaths</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">field</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reverse</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">serfile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">get_field_values</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/tools.html#field_sort"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.tools.field_sort" title="Link to this definition"></a></dt>
<dd><p>Sort a list of files by a field stored in header information. All
files must contain this header information.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>filepaths</strong> – List of paths to files that we want to sort.</p></li>
<li><p><strong>field</strong> – The field we want to sort by. Not case-sensitive.</p></li>
<li><p><strong>reverse</strong> – Sort in reverse alphabetical/numerical order.</p></li>
<li><p><strong>serfile</strong> – Path to a serial file with field information for each file.</p></li>
<li><p><strong>get_field_values</strong> (<em>bool</em>) – Boolean indicating whether to also return a List of field values
(default False). This List of field values is parallel to the sorted
list of filepaths with items in the same position corresponding to
each other.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Sorted list of paths. When get_fv is true, also return an associated
field list.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.tools.getRw">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.tools.</span></span><span class="sig-name descname"><span class="pre">getRw</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">chain</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/tools.html#getRw"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.tools.getRw" title="Link to this definition"></a></dt>
<dd><p>Get Rw from the outputs of a morph or chain.</p>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.tools.get_pearson">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.tools.</span></span><span class="sig-name descname"><span class="pre">get_pearson</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">chain</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/tools.html#get_pearson"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.tools.get_pearson" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.tools.get_values_from_dictionary_collection">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.tools.</span></span><span class="sig-name descname"><span class="pre">get_values_from_dictionary_collection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dictionary_collection</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">iter</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_key</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/tools.html#get_values_from_dictionary_collection"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.tools.get_values_from_dictionary_collection" title="Link to this definition"></a></dt>
<dd><p>In an (iterable) collection of dictionaries, search for a target
key in each dictionary. Return a list of all found values
corresponding to that key.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>dictionary_collection</strong> (<em>iter</em>) – The collection of dictionaries to search through.</p></li>
<li><p><strong>target_key</strong> – The key to search for in each dictionary. For each dictionary in
dictionary_collection that has that key, the corresponding value is
appended to a List called values.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>The found values.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.tools.nn_value">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.tools.</span></span><span class="sig-name descname"><span class="pre">nn_value</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">val</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/tools.html#nn_value"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.tools.nn_value" title="Link to this definition"></a></dt>
<dd><p>Convenience function for ensuring certain non-negative inputs.</p>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.tools.readPDF">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.tools.</span></span><span class="sig-name descname"><span class="pre">readPDF</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fname</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/tools.html#readPDF"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.tools.readPDF" title="Link to this definition"></a></dt>
<dd><p>Reads an .gr file, loads r and G(r) vectors.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>fname</strong> – Name of the file we want to read.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Arrays read from data.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>r,gr</p>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-diffpy.morph.morphpy">
<span id="diffpy-morph-morphpy-module"></span><h3>diffpy.morph.morphpy module<a class="headerlink" href="#module-diffpy.morph.morphpy" title="Link to this heading"></a></h3>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.morphpy.get_args">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.morphpy.</span></span><span class="sig-name descname"><span class="pre">get_args</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parser</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">params</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/morphpy.html#get_args"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.morphpy.get_args" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.morphpy.morph">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.morphpy.</span></span><span class="sig-name descname"><span class="pre">morph</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">morph_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stretch</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">smear</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">plot</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/morphpy.html#morph"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.morphpy.morph" title="Link to this definition"></a></dt>
<dd><p>Run diffpy.morph at Python level.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>morph_file</strong> (<em>str</em><em> or </em><em>numpy.array</em>) – Path-like object to the file to be morphed.</p></li>
<li><p><strong>target_file</strong> (<em>str</em><em> or </em><em>numpy.array</em>) – Path-like object to the target file.</p></li>
<li><p><strong>scale</strong> (<em>float</em><em>, </em><em>optional</em>) – Initial guess for the scaling parameter.
Refinement is done only for parameter that are not None.</p></li>
<li><p><strong>stretch</strong> (<em>float</em><em>, </em><em>optional</em>) – Initial guess for the stretching parameter.</p></li>
<li><p><strong>smear</strong> (<em>float</em><em>, </em><em>optional</em>) – Initial guess for the smearing parameter.</p></li>
<li><p><strong>plot</strong> (<em>bool</em>) – Show a plot of the morphed and target functions as well as the
difference curve (default: False).</p></li>
<li><p><strong>kwargs</strong> (<em>str</em><em>, </em><em>float</em><em>, </em><em>list</em><em>, </em><em>tuple</em><em>, </em><em>bool</em>) – See the diffpy.morph website for full list of options.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><ul class="simple">
<li><p><strong>morph_info</strong> (<em>dict</em>) – Summary of morph parameters (e.g. scale, stretch, smear, rmin, rmax)
and results (e.g. Pearson, Rw).</p></li>
<li><p><strong>morph_table</strong> (<em>list</em>) – Function after morph where morph_table[:,0] is the abscissa and
morph_table[:,1] is the ordinate.</p></li>
</ul>
</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.morphpy.morph_arrays">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.morphpy.</span></span><span class="sig-name descname"><span class="pre">morph_arrays</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">morph_table</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_table</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stretch</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">smear</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">plot</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/morphpy.html#morph_arrays"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.morphpy.morph_arrays" title="Link to this definition"></a></dt>
<dd><p>Run diffpy.morph at Python level.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>morph_table</strong> (<em>numpy.array</em>) – Two-column array of (r, gr) for morphed function.</p></li>
<li><p><strong>target_table</strong> (<em>numpy.array</em>) – Two-column array of (r, gr) for target function.</p></li>
<li><p><strong>scale</strong> (<em>float</em><em>, </em><em>optional</em>) – Initial guess for the scaling parameter.
Refinement is done only for parameter that are not None.</p></li>
<li><p><strong>stretch</strong> (<em>float</em><em>, </em><em>optional</em>) – Initial guess for the stretching parameter.</p></li>
<li><p><strong>smear</strong> (<em>float</em><em>, </em><em>optional</em>) – Initial guess for the smearing parameter.</p></li>
<li><p><strong>plot</strong> (<em>bool</em>) – Show a plot of the morphed and target functions as well as the
difference curve (default: False).</p></li>
<li><p><strong>kwargs</strong> (<em>str</em><em>, </em><em>float</em><em>, </em><em>list</em><em>, </em><em>tuple</em><em>, </em><em>bool</em>) – See the diffpy.morph website for full list of options.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><ul class="simple">
<li><p><strong>morph_info</strong> (<em>dict</em>) – Summary of morph parameters (e.g. scale, stretch, smear, rmin, rmax)
and results (e.g. Pearson, Rw).</p></li>
<li><p><strong>morph_table</strong> (<em>list</em>) – Function after morph where morph_table[:,0] is the abscissa and
morph_table[:,1] is the ordinate.</p></li>
</ul>
</p>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-diffpy.morph.morph_io">
<span id="diffpy-morph-morph-io-module"></span><h3>diffpy.morph.morph_io module<a class="headerlink" href="#module-diffpy.morph.morph_io" title="Link to this heading"></a></h3>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.morph_io.build_morph_inputs_container">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.morph_io.</span></span><span class="sig-name descname"><span class="pre">build_morph_inputs_container</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">scale</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stretch</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">smear_pdf</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">smear</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">hshift</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vshift</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">squeeze</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/morph_io.html#build_morph_inputs_container"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.morph_io.build_morph_inputs_container" title="Link to this definition"></a></dt>
<dd><p>Helper function to extract input morphing parameters for CLI
morphs. Python morphs are handled separately.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>scale</strong> – opts.scale</p></li>
<li><p><strong>stretch</strong> – opts.stretch</p></li>
<li><p><strong>smear_pdf</strong> – opts.smear_pdf</p></li>
<li><p><strong>smear</strong> – opts.smear</p></li>
<li><p><strong>hshift</strong> – opts.hshift</p></li>
<li><p><strong>vshift</strong> – opts.vshift</p></li>
<li><p><strong>squeeze</strong> – opts.squeeze</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>The dictionary of input morphing parameters.
Only one of smear and smear_pdf is included
(takes smear_pdf over smear when both exist).
Does not include hshift if a degree zero
or above squeeze is used.
Does not include stretch if a degree one
or above squeeze is used.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>dict</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.morph_io.create_morphs_directory">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.morph_io.</span></span><span class="sig-name descname"><span class="pre">create_morphs_directory</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">save_directory</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/morph_io.html#create_morphs_directory"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.morph_io.create_morphs_directory" title="Link to this definition"></a></dt>
<dd><p>Create a directory for saving multiple morphed functions.</p>
<p>Takes in a user-given path to a directory save_directory and create a
subdirectory named Morphs. diffpy.morph will save all morphs into the
Morphs subdirectory while metadata about the morphs will be stored in
save_directory outside Morphs.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>save_directory</strong> – Path to a directory. diffpy.morph will save all generated files within
this directory.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>The absolute path to the Morph subdirectory.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>str</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.morph_io.custom_formatwarning">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.morph_io.</span></span><span class="sig-name descname"><span class="pre">custom_formatwarning</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">msg</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/morph_io.html#custom_formatwarning"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.morph_io.custom_formatwarning" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.morph_io.get_multisave_names">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.morph_io.</span></span><span class="sig-name descname"><span class="pre">get_multisave_names</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target_list</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">save_names_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mm</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/morph_io.html#get_multisave_names"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.morph_io.get_multisave_names" title="Link to this definition"></a></dt>
<dd><p>Create or import a dictionary that specifies names to save morphs
as. First attempt to import names from a specified file. If names
for certain morphs not found, use default naming scheme:
‘Morph_with_Target_<target file name>.cgr’.</p>
<p>Used when saving multiple morphs.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>target_list</strong> (<em>list</em>) – Target (or Morph if mm enabled) functions used for each morph.</p></li>
<li><p><strong>save_names_file</strong> – Name of file to import save names dictionary from (default None).</p></li>
<li><p><strong>mm</strong> (<em>bool</em>) – Rather than multiple targets, multiple morphs are being done.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>The names to save each morph as. Keys are the target function file
names used to produce that morph.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>dict</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.morph_io.handle_check_increase_warning">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.morph_io.</span></span><span class="sig-name descname"><span class="pre">handle_check_increase_warning</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">squeeze_morph</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/morph_io.html#handle_check_increase_warning"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.morph_io.handle_check_increase_warning" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.morph_io.handle_extrapolation_warnings">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.morph_io.</span></span><span class="sig-name descname"><span class="pre">handle_extrapolation_warnings</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">morph</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/morph_io.html#handle_extrapolation_warnings"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.morph_io.handle_extrapolation_warnings" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.morph_io.multiple_morph_output">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.morph_io.</span></span><span class="sig-name descname"><span class="pre">multiple_morph_output</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">morph_inputs</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">morph_results</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_files</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">field_list</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">save_directory</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">morph_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_directory</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stdout_flag</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mm</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/morph_io.html#multiple_morph_output"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.morph_io.multiple_morph_output" title="Link to this definition"></a></dt>
<dd><p>Helper function for printing details about a series of multiple
morphs. Handles both printing to terminal and printing to a file.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>morph_inputs</strong> (<em>dict</em>) – Input parameters given by the user.</p></li>
<li><p><strong>morph_results</strong> (<em>dict</em>) – Resulting data after morphing.</p></li>
<li><p><strong>target_files</strong> (<em>list</em>) – Files that acted as targets to morphs.</p></li>
<li><p><strong>save_directory</strong> – Name of directory to save morphs in.</p></li>
<li><p><strong>field</strong> – Name of field if data was sorted by a particular field.
Otherwise, leave blank.</p></li>
<li><p><strong>field_list</strong> (<em>list</em>) – List of field values for each target function.
Generated by diffpy.morph.tools.field_sort().</p></li>
<li><p><strong>morph_file</strong> – Name of the morphed function file.
Required to give summary data after saving to a directory.</p></li>
<li><p><strong>target_directory</strong> – Name of the directory containing the target function files.
Required to give summary data after saving to a directory.</p></li>
<li><p><strong>verbose</strong> (<em>bool</em>) – Print additional summary details when True (default False).</p></li>
<li><p><strong>stdout_flag</strong> (<em>bool</em>) – Print to terminal when True (default False).</p></li>
<li><p><strong>mm</strong> (<em>bool</em>) – Multiple morphs done with a single target rather than multiple
targets for a single morphed file. Swaps morph and target in the code.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.morph_io.single_morph_output">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.morph_io.</span></span><span class="sig-name descname"><span class="pre">single_morph_output</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">morph_inputs</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">morph_results</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">save_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">morph_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xy_out</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stdout_flag</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/morph_io.html#single_morph_output"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.morph_io.single_morph_output" title="Link to this definition"></a></dt>
<dd><p>Helper function for printing details about a single morph.
Handles both printing to terminal and printing to a file.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>morph_inputs</strong> (<em>dict</em>) – Parameters given by the user.</p></li>
<li><p><strong>morph_results</strong> (<em>dict</em>) – Resulting data after morphing.</p></li>
<li><p><strong>save_file</strong> – Name of file to print to. If None (default) print to terminal.</p></li>
<li><p><strong>morph_file</strong> – Name of the morphed function file. Required when printing to a
non-terminal file.</p></li>
<li><p><strong>xy_out</strong> (<em>param</em>) – List of the form [x_morph_out, y_morph_out]. x_morph_out is a List of
r values and y_morph_out is a List of gr values.</p></li>
<li><p><strong>verbose</strong> (<em>bool</em>) – Print additional details about the morph when True (default False).</p></li>
<li><p><strong>stdout_flag</strong> (<em>bool</em>) – Print to terminal when True (default False).</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.morph_io.tabulate_results">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.morph_io.</span></span><span class="sig-name descname"><span class="pre">tabulate_results</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">multiple_morph_results</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/morph_io.html#tabulate_results"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.morph_io.tabulate_results" title="Link to this definition"></a></dt>
<dd><p>Helper function to make a data table summarizing details about
the results of multiple morphs.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>multiple_morph_results</strong> – A collection of Dictionaries. Each Dictionary summarizes the
resultsof a single morph.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><strong>tabulated_results</strong> – Keys in tabulated_results are the table’s column names and each
corresponding value is a list of data for that column.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>dict</p>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-diffpy.morph.refine">
<span id="diffpy-morph-refine-module"></span><h3>diffpy.morph.refine module<a class="headerlink" href="#module-diffpy.morph.refine" title="Link to this heading"></a></h3>
<p>refine – Refine a morph or morph chain</p>
<dl class="py class">
<dt class="sig sig-object py" id="diffpy.morph.refine.Refiner">
<span class="property"><span class="k"><span class="pre">class</span></span><span class="w"> </span></span><span class="sig-prename descclassname"><span class="pre">diffpy.morph.refine.</span></span><span class="sig-name descname"><span class="pre">Refiner</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">chain</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">x_morph</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">y_morph</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">x_target</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">y_target</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tolerance</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1e-08</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/refine.html#Refiner"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.refine.Refiner" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>Class for refining a Morph or MorphChain.</p>
<p>This is provided to allow for custom residuals and refinement algorithms.</p>
<dl class="py attribute">
<dt class="sig sig-object py" id="diffpy.morph.refine.Refiner.chain">
<span class="sig-name descname"><span class="pre">chain</span></span><a class="headerlink" href="#diffpy.morph.refine.Refiner.chain" title="Link to this definition"></a></dt>
<dd><p>The Morph or MorphChain to refine.</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py">
<span class="sig-name descname"><span class="pre">x_morph,</span> <span class="pre">y_morph</span></span></dt>
<dd><p>Morphed arrays.</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py">
<span class="sig-name descname"><span class="pre">x_target,</span> <span class="pre">y_target</span></span></dt>
<dd><p>Target arrays.</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="diffpy.morph.refine.Refiner.pars">
<span class="sig-name descname"><span class="pre">pars</span></span><a class="headerlink" href="#diffpy.morph.refine.Refiner.pars" title="Link to this definition"></a></dt>
<dd><p>List of names of parameters to be refined.</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="diffpy.morph.refine.Refiner.residual">
<span class="sig-name descname"><span class="pre">residual</span></span><a class="headerlink" href="#diffpy.morph.refine.Refiner.residual" title="Link to this definition"></a></dt>
<dd><p>The residual function to optimize. Default _residual. Can be assigned
to other functions.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="diffpy.morph.refine.Refiner.refine">
<span class="sig-name descname"><span class="pre">refine</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kw</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/refine.html#Refiner.refine"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.refine.Refiner.refine" title="Link to this definition"></a></dt>
<dd><p>Refine the chain.</p>
<p>Additional arguments are used to specify which parameters are to be
refined.
If no arguments are passed, then all parameters will be refined.
Keywords pass initial values to the parameters, whether or not they
are refined.</p>
<p>This uses the leastsq algorithm from scipy.optimize.</p>
<p>This returns the final scalar residual value.
The parameters from the fit can be retrieved from the config
dictionary of the morph or morph chain.</p>
<dl class="field-list simple">
<dt class="field-odd">Raises<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>ValueError</strong> – Exception raised if a minimum cannot be found.</p></li>
<li><p><strong>ValueError</strong> – If the number of shared grid points between morphed function and
target function is smaller than the number of parameters.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</dd></dl>
</section>
<section id="module-diffpy.morph.morphapp">
<span id="diffpy-morph-morphapp-module"></span><h3>diffpy.morph.morphapp module<a class="headerlink" href="#module-diffpy.morph.morphapp" title="Link to this heading"></a></h3>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.morphapp.create_option_parser">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.morphapp.</span></span><span class="sig-name descname"><span class="pre">create_option_parser</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/morphapp.html#create_option_parser"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.morphapp.create_option_parser" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.morphapp.getPDFFromFile">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.morphapp.</span></span><span class="sig-name descname"><span class="pre">getPDFFromFile</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fn</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/morphapp.html#getPDFFromFile"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.morphapp.getPDFFromFile" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.morphapp.main">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.morphapp.</span></span><span class="sig-name descname"><span class="pre">main</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/morphapp.html#main"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.morphapp.main" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.morphapp.multiple_morphs">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.morphapp.</span></span><span class="sig-name descname"><span class="pre">multiple_morphs</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parser</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">opts</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pargs</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stdout_flag</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">python_wrap</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/morphapp.html#multiple_morphs"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.morphapp.multiple_morphs" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.morphapp.multiple_targets">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.morphapp.</span></span><span class="sig-name descname"><span class="pre">multiple_targets</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parser</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">opts</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pargs</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stdout_flag</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">python_wrap</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/morphapp.html#multiple_targets"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.morphapp.multiple_targets" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.morphapp.single_morph">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.morphapp.</span></span><span class="sig-name descname"><span class="pre">single_morph</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parser</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">opts</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pargs</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stdout_flag</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">python_wrap</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pymorphs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/morphapp.html#single_morph"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.morphapp.single_morph" title="Link to this definition"></a></dt>
<dd></dd></dl>
</section>
<section id="module-diffpy.morph.log">
<span id="diffpy-morph-log-module"></span><h3>diffpy.morph.log module<a class="headerlink" href="#module-diffpy.morph.log" title="Link to this heading"></a></h3>
<p>Configuration of loggers used in this package.</p>
<p>Logger instances:</p>
<p>plog – logger instance for normal operation</p>
<dl class="py function">
<dt class="sig sig-object py" id="diffpy.morph.log.set_verbosity">
<span class="sig-prename descclassname"><span class="pre">diffpy.morph.log.</span></span><span class="sig-name descname"><span class="pre">set_verbosity</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vb</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/diffpy/morph/log.html#set_verbosity"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#diffpy.morph.log.set_verbosity" title="Link to this definition"></a></dt>
<dd><p>Set verbosity of the diffpy.morph logger.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>vb</strong> – Integer or one of (‘debug’, ‘info’, ‘warning’, ‘error’) strings.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>No return value.</p>
</dd>
</dl>
</dd></dl>
</section>
</section>
</section>
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