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pymatgen.core.spectrum.html
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<!DOCTYPE html>
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<title>pymatgen.core.spectrum module — pymatgen 2019.5.1 documentation</title>
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<div class="section" id="module-pymatgen.core.spectrum">
<span id="pymatgen-core-spectrum-module"></span><h1>pymatgen.core.spectrum module<a class="headerlink" href="#module-pymatgen.core.spectrum" title="Permalink to this headline">¶</a></h1>
<dl class="class">
<dt id="pymatgen.core.spectrum.Spectrum">
<em class="property">class </em><code class="descname">Spectrum</code><span class="sig-paren">(</span><em>x</em>, <em>y</em>, <em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/core/spectrum.html#Spectrum"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.core.spectrum.Spectrum" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">monty.json.MSONable</span></code></p>
<p>Base class for any type of xas, essentially just x, y values. Examples
include XRD patterns, XANES, EXAFS, NMR, DOS, etc.</p>
<p>Implements basic tools like application of smearing, normalization, addition
multiplication, etc.</p>
<p>Subclasses should extend this object and ensure that super is called with
ALL args and kwargs. That ensures subsequent things like add and mult work
properly.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>x</strong> (<em>ndarray</em>) – A ndarray of N values.</p></li>
<li><p><strong>y</strong> (<em>ndarray</em>) – A ndarray of N x k values. The first dimension must be
the same as that of x. Each of the k values are interpreted as</p></li>
<li><p><strong>*args</strong> – All subclasses should provide args other than x and y
when calling super, e.g., super().__init__(
x, y, arg1, arg2, kwarg1=val1, ..). This guarantees the +, -, <a href="#id1"><span class="problematic" id="id2">*</span></a>,
etc. operators work properly.</p></li>
<li><p><strong>**kwargs</strong> – Same as that for *args.</p></li>
</ul>
</dd>
</dl>
<dl class="attribute">
<dt id="pymatgen.core.spectrum.Spectrum.XLABEL">
<code class="descname">XLABEL</code><em class="property"> = 'x'</em><a class="headerlink" href="#pymatgen.core.spectrum.Spectrum.XLABEL" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.core.spectrum.Spectrum.YLABEL">
<code class="descname">YLABEL</code><em class="property"> = 'y'</em><a class="headerlink" href="#pymatgen.core.spectrum.Spectrum.YLABEL" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="pymatgen.core.spectrum.Spectrum.copy">
<code class="descname">copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/core/spectrum.html#Spectrum.copy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.core.spectrum.Spectrum.copy" title="Permalink to this definition">¶</a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p>Copy of Spectrum object.</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.core.spectrum.Spectrum.get_interpolated_value">
<code class="descname">get_interpolated_value</code><span class="sig-paren">(</span><em>x</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/core/spectrum.html#Spectrum.get_interpolated_value"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.core.spectrum.Spectrum.get_interpolated_value" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns an interpolated y value for a particular x value.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>x</strong> – x value to return the y value for</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>Value of y at x</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.core.spectrum.Spectrum.normalize">
<code class="descname">normalize</code><span class="sig-paren">(</span><em>mode='max'</em>, <em>value=1</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/core/spectrum.html#Spectrum.normalize"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.core.spectrum.Spectrum.normalize" title="Permalink to this definition">¶</a></dt>
<dd><p>Normalize the spectrum with respect to the sum of intensity</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>mode</strong> (<em>str</em>) – Normalization mode. Supported modes are “max” (set the
max y value to value, e.g., in XRD patterns), “sum” (set the
sum of y to a value, i.e., like a probability density).</p></li>
<li><p><strong>value</strong> (<em>float</em>) – Value to normalize to. Defaults to 1.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.core.spectrum.Spectrum.smear">
<code class="descname">smear</code><span class="sig-paren">(</span><em>sigma</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/core/spectrum.html#Spectrum.smear"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.core.spectrum.Spectrum.smear" title="Permalink to this definition">¶</a></dt>
<dd><p>Apply Gaussian smearing to spectrum y value.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>sigma</strong> – Std dev for Gaussian smear function</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
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