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<section id="api-reference">
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<h1>API Reference<a class="headerlink" href="#api-reference" title="Link to this heading">¶</a></h1>
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<p>Below is the complete reference for Optifik’s public API.</p>
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<section id="module-optifik.io">
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<span id="io"></span><h2>io<a class="headerlink" href="#module-optifik.io" title="Link to this heading">¶</a></h2>
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<dl class="py function">
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<dt class="sig sig-object py" id="optifik.io.load_spectrum">
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<span class="sig-prename descclassname"><span class="pre">optifik.io.</span></span><span class="sig-name descname"><span class="pre">load_spectrum</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">spectrum_path</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">wavelength_min</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">wavelength_max</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">inf</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delimiter</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">','</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/optifik/io.html#load_spectrum"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#optifik.io.load_spectrum" title="Link to this definition">¶</a></dt>
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<dd><p>Load a spectrum file.</p>
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<p>TODO : describe expected format</p>
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<dl class="field-list simple">
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<dt class="field-odd">Parameters<span class="colon">:</span></dt>
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<dd class="field-odd"><dl class="simple">
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<dt><strong>spectrum_path</strong><span class="classifier">string</span></dt><dd><p>File path.</p>
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</dd>
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<dt><strong>wavelength_min</strong><span class="classifier">scalar, optional</span></dt><dd><p>Cut the data at this minimum wavelength (included).</p>
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</dd>
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<dt><strong>wavelength_max</strong><span class="classifier">scalar, optional</span></dt><dd><p>Cut the data at this maximum wavelength (included).</p>
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</dd>
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<dt><strong>delimiter</strong><span class="classifier">string, optional</span></dt><dd><p>Delimiter between columns in the datafile.</p>
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</dd>
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</dl>
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</dd>
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<dt class="field-even">Returns<span class="colon">:</span></dt>
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<dd class="field-even"><dl class="simple">
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<dt><strong>values</strong><span class="classifier">arrays</span></dt><dd><p>(lamdbas, intensities)</p>
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</dd>
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</dl>
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</dd>
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</dl>
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</dd></dl>
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</section>
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<section id="module-optifik.fft">
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<span id="fft"></span><h2>fft<a class="headerlink" href="#module-optifik.fft" title="Link to this heading">¶</a></h2>
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<dl class="py function">
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<dt class="sig sig-object py" id="optifik.fft.thickness_from_fft">
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<span class="sig-prename descclassname"><span class="pre">optifik.fft.</span></span><span class="sig-name descname"><span class="pre">thickness_from_fft</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">wavelengths</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intensities</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">refractive_index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_half_space</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">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/optifik/fft.html#thickness_from_fft"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#optifik.fft.thickness_from_fft" title="Link to this definition">¶</a></dt>
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<dd><p>Determine the tickness by Fast Fourier Transform.</p>
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<dl class="field-list">
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<dt class="field-odd">Parameters<span class="colon">:</span></dt>
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<dd class="field-odd"><dl class="simple">
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<dt><strong>wavelengths</strong><span class="classifier">array</span></dt><dd><p>Wavelength values in nm.</p>
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</dd>
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<dt><strong>intensities</strong><span class="classifier">array</span></dt><dd><p>Intensity values.</p>
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</dd>
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<dt><strong>refractive_index</strong><span class="classifier">scalar, optional</span></dt><dd><p>Value of the refractive index of the medium.</p>
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</dd>
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<dt><strong>num_half_space</strong><span class="classifier">scalar, optional</span></dt><dd><p>Number of points to compute FFT’s half space.
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If <cite>None</cite>, default corresponds to <cite>10*len(wavelengths)</cite>.</p>
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</dd>
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<dt><strong>plot</strong><span class="classifier">boolean, optional</span></dt><dd><p>Show plot of the transformed signal and the peak detection.</p>
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</dd>
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</dl>
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</dd>
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<dt class="field-even">Returns<span class="colon">:</span></dt>
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<dd class="field-even"><dl>
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<dt><strong>results</strong><span class="classifier">Instance of <cite>OptimizeResult</cite> class.</span></dt><dd><p>The attribute <cite>thickness</cite> gives the thickness value in nm.</p>
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</dd>
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</dl>
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</dd>
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</dl>
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</dd></dl>
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</section>
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<section id="module-optifik.minmax">
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<span id="minmax"></span><h2>minmax<a class="headerlink" href="#module-optifik.minmax" title="Link to this heading">¶</a></h2>
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<dl class="py function">
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<dt class="sig sig-object py" id="optifik.minmax.thickness_from_minmax">
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<span class="sig-prename descclassname"><span class="pre">optifik.minmax.</span></span><span class="sig-name descname"><span class="pre">thickness_from_minmax</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">wavelengths</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intensities</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">refractive_index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_peak_prominence</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_peak_distance</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'linreg'</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">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/optifik/minmax.html#thickness_from_minmax"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#optifik.minmax.thickness_from_minmax" title="Link to this definition">¶</a></dt>
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<dd><p>Return the thickness from a min-max detection.</p>
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<dl class="field-list">
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<dt class="field-odd">Parameters<span class="colon">:</span></dt>
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<dd class="field-odd"><dl class="simple">
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<dt><strong>wavelengths</strong><span class="classifier">array</span></dt><dd><p>Wavelength values in nm.</p>
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</dd>
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<dt><strong>intensities</strong><span class="classifier">array</span></dt><dd><p>Intensity values.</p>
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</dd>
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<dt><strong>refractive_index</strong><span class="classifier">scalar, optional</span></dt><dd><p>Value of the refractive index of the medium.</p>
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</dd>
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<dt><strong>min_peak_prominence</strong><span class="classifier">scalar, optional</span></dt><dd><p>Required prominence of peaks.</p>
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</dd>
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<dt><strong>min_peak_distance</strong><span class="classifier">scalar, optional</span></dt><dd><p>Minimum distance between peaks.</p>
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</dd>
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<dt><strong>method</strong><span class="classifier">string, optional</span></dt><dd><p>Either ‘linreg’ for linear regression or ‘ransac’
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for Randon Sampling Consensus.</p>
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</dd>
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<dt><strong>plot</strong><span class="classifier">boolean, optional</span></dt><dd><p>Show plots of peak detection and lin regression.</p>
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</dd>
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</dl>
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</dd>
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<dt class="field-even">Returns<span class="colon">:</span></dt>
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<dd class="field-even"><dl>
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<dt><strong>results</strong><span class="classifier">Instance of <cite>OptimizeResult</cite> class.</span></dt><dd><p>The attribute <cite>thickness</cite> gives the thickness value in nm.</p>
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</dd>
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</dl>
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</dd>
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</dl>
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<p class="rubric">Notes</p>
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<p>For more details about <cite>min_peak_prominence</cite> and <cite>min_peak_distance</cite>,
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see the documentation of <cite>scipy.signal.find_peaks</cite>. This function
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is used to find extrema.</p>
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</dd></dl>
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</section>
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<section id="module-optifik.scheludko">
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<span id="scheludko"></span><h2>scheludko<a class="headerlink" href="#module-optifik.scheludko" title="Link to this heading">¶</a></h2>
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<dl class="py function">
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<dt class="sig sig-object py" id="optifik.scheludko.get_default_start_stop_wavelengths">
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<span class="sig-prename descclassname"><span class="pre">optifik.scheludko.</span></span><span class="sig-name descname"><span class="pre">get_default_start_stop_wavelengths</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">wavelengths</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intensities</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">refractive_index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_peak_prominence</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">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/optifik/scheludko.html#get_default_start_stop_wavelengths"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#optifik.scheludko.get_default_start_stop_wavelengths" title="Link to this definition">¶</a></dt>
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<dd><p>Returns the start and stop wavelength values of the last monotonic branch.</p>
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<dl class="field-list simple">
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<dt class="field-odd">Parameters<span class="colon">:</span></dt>
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<dd class="field-odd"><dl class="simple">
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<dt><strong>wavelengths</strong><span class="classifier">array</span></dt><dd><p>Wavelength values in nm.</p>
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</dd>
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<dt><strong>intensities</strong><span class="classifier">array</span></dt><dd><p>Intensity values.</p>
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</dd>
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<dt><strong>refractive_index</strong><span class="classifier">scalar, optional</span></dt><dd><p>Value of the refractive index of the medium.</p>
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</dd>
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<dt><strong>min_peak_prominence</strong><span class="classifier">scalar</span></dt><dd><p>Required prominence of peaks.</p>
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</dd>
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<dt><strong>plot</strong><span class="classifier">bool, optional</span></dt><dd><p>Display a curve, useful for checking or debuging. The default is None.</p>
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</dd>
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</dl>
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</dd>
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<dt class="field-even">Returns<span class="colon">:</span></dt>
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<dd class="field-even"><dl class="simple">
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<dt><strong>wavelength_start</strong><span class="classifier">scalar</span></dt><dd></dd>
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<dt><strong>wavelength_stop</strong><span class="classifier">scalar</span></dt><dd></dd>
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</dl>
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</dd>
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<dt class="field-odd">Raises<span class="colon">:</span></dt>
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<dd class="field-odd"><dl class="simple">
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<dt>RuntimeError</dt><dd><p>if at least one maximum and one minimum are not detected.</p>
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</dd>
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</dl>
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</dd>
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</dl>
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</dd></dl>
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<dl class="py function">
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<dt class="sig sig-object py" id="optifik.scheludko.thickness_from_scheludko">
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<span class="sig-prename descclassname"><span class="pre">optifik.scheludko.</span></span><span class="sig-name descname"><span class="pre">thickness_from_scheludko</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">wavelengths</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intensities</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">refractive_index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">wavelength_start</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">wavelength_stop</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">interference_order</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">intensities_void</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">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/optifik/scheludko.html#thickness_from_scheludko"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#optifik.scheludko.thickness_from_scheludko" title="Link to this definition">¶</a></dt>
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<dd><p>Compute the film thickness based on Scheludko method.</p>
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<dl class="field-list">
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<dt class="field-odd">Parameters<span class="colon">:</span></dt>
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<dd class="field-odd"><dl class="simple">
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<dt><strong>wavelengths</strong><span class="classifier">array</span></dt><dd><p>Wavelength values in nm.</p>
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</dd>
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<dt><strong>intensities</strong><span class="classifier">array</span></dt><dd><p>Intensity values.</p>
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</dd>
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<dt><strong>refractive_index</strong><span class="classifier">scalar, optional</span></dt><dd><p>Value of the refractive index of the medium.</p>
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</dd>
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<dt><strong>wavelength_start</strong><span class="classifier">scalar, optional</span></dt><dd><p>Starting value of a monotonic branch.
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Mandatory if interference_order != 0.</p>
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</dd>
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<dt><strong>wavelength_stop</strong><span class="classifier">scalar, optional</span></dt><dd><p>Stoping value of a monotonic branch.
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Mandatory if interference_order != 0.</p>
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</dd>
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<dt><strong>interference_order</strong><span class="classifier">scalar, optional</span></dt><dd><p>Interference order, zero or positive integer.
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If set to None, the value is guessed.</p>
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</dd>
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<dt><strong>intensities_void</strong><span class="classifier">array, optional</span></dt><dd><p>Intensity in absence of a film.
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Mandatory if interference_order == 0.</p>
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</dd>
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<dt><strong>plot</strong><span class="classifier">bool, optional</span></dt><dd><p>Display a curve, useful for checking or debuging. The default is None.</p>
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</dd>
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</dl>
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</dd>
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<dt class="field-even">Returns<span class="colon">:</span></dt>
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<dd class="field-even"><dl>
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<dt><strong>results</strong><span class="classifier">Instance of <cite>OptimizeResult</cite> class.</span></dt><dd><p>The attribute <cite>thickness</cite> gives the thickness value in nm.</p>
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</dd>
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</dl>
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</dd>
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</dl>
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</dd></dl>
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</section>
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</section>
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<p class="caption" role="heading"><span class="caption-text">Documentation</span></p>
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<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
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<li class="toctree-l1 current"><a class="current reference internal" href="#">API Reference</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="#module-optifik.io">io</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#module-optifik.fft">fft</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#module-optifik.minmax">minmax</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#module-optifik.scheludko">scheludko</a></li>
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<h3>Related Topics</h3>
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<li><a href="index.html">Documentation overview</a><ul>
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