.gitignore

@@ -1,10 +0,0 @@
-__pycache__
-.backups
-optifik.egg-info
-*.bak
-*.pyc
-.ipynb_checkpoints
-.venv
-build/
-_build/
-dist/

.venv

@@ -0,0 +1 @@
+victor

CHANGELOG.md

@@ -1,4 +0,0 @@
-
-# x.x.x
-
-First version

ProminenceFunction.txt

@@ -0,0 +1,83 @@
+def Prominence_from_fft(lambdas, intensities, refractive_index, num_half_space=None, plot=True):
+    if num_half_space is None:
+        num_half_space = len(lambdas)
+
+    # # # 1. Spectre original
+    # if plot:
+    #     plt.figure(figsize=(10, 6), dpi=150)
+    #     plt.plot(1/lambdas, intensities, label='Spectre original')
+    #     plt.xlabel('1/Longueur d\'onde (nm-1)')
+    #     plt.ylabel('Intensité')
+    #     plt.legend()
+    #     plt.show()
+
+
+    # 2. Conversion lambda → k = n(λ) / λ
+    k_vals = refractive_index / lambdas
+    f_interp = interp1d(k_vals, intensities, kind='linear', fill_value="extrapolate")
+
+    # 3. Axe k uniforme + interpolation
+    k_linspace = np.linspace(k_vals[0], k_vals[-1], 2 * num_half_space)
+    intensities_k = f_interp(k_linspace)
+
+    # 4. FFT
+    delta_k = (k_vals[-1] - k_vals[0]) / (2 * num_half_space)
+    fft_vals = fft(intensities_k)
+    freqs = fftfreq(2 * num_half_space, delta_k)
+
+    # 5. Pic FFT
+    freqs_pos = freqs[freqs > 0]
+    abs_fft_pos = np.abs(fft_vals[freqs > 0])
+    idx_max = np.argmax(abs_fft_pos)
+    F_max = freqs_pos[idx_max]
+
+    if plot:
+        plt.figure(figsize=(10, 6), dpi=150)
+        plt.plot(freqs_pos, abs_fft_pos, label='|FFT|')
+        plt.axvline(F_max, color='r', linestyle='--', label='Pic principal')
+        plt.xlabel('Distance optique [nm]')
+        plt.ylabel(r'FFT($I^*$)')
+        plt.xscale('log')
+        plt.yscale('log')
+        plt.legend()
+        plt.show()
+
+    # 6. Filtrage (garde hautes fréquences)
+    cutoff_HF =  2*F_max
+    
+    mask_HF = np.abs(freqs) >= cutoff_HF
+    fft_filtered_HF = np.zeros_like(fft_vals, dtype=complex)
+    fft_filtered_HF[mask_HF] = fft_vals[mask_HF]
+    
+    # 7. Filtrage (garde basses fréquences)
+    cutoff_BF =  10*F_max
+    mask_BF = np.abs(freqs) <= cutoff_BF
+    fft_filtered_BF = np.zeros_like(fft_vals, dtype=complex)
+    fft_filtered_BF[mask_BF] = fft_vals[mask_BF]
+    
+    
+    # 8. Reconstruction
+    signal_filtered_HF = np.real(ifft(fft_filtered_HF))
+    signal_filtered_BF = np.real(ifft(fft_filtered_BF))
+    lambda_reconstructed = np.interp(k_linspace, k_vals[::-1], lambdas[::-1])
+
+    # Masque dans la plage [550, 700] nm
+    mask_Cam_Sensitivity = (lambda_reconstructed >= 550) & (lambda_reconstructed <= 700)
+    
+    # 9. Affichage reconstruction
+    if plot:
+        plt.figure(figsize=(10, 6), dpi=150)
+        plt.plot(lambda_reconstructed, intensities_k, '--', label='Original interpolé')
+        plt.plot(lambda_reconstructed, signal_filtered_HF,'--',color='gray')
+
+        plt.plot(lambda_reconstructed[mask_Cam_Sensitivity], signal_filtered_HF[mask_Cam_Sensitivity],color='orange', label='Spectre filtré HF')
+        plt.plot(lambda_reconstructed, signal_filtered_BF, label='Spectre filtré BF')
+
+        plt.xlabel('Longueur d\'onde (nm)')
+        plt.ylabel('Intensité')
+        plt.legend()
+        plt.show()
+
+    max_amplitude = np.max(np.abs(signal_filtered_HF[mask_Cam_Sensitivity]))
+    
+    return max_amplitude,signal_filtered_BF,lambda_reconstructed

README.md

@@ -1,56 +0,0 @@
-# Optifik
-
-TODO: write a paragraph here...
-
-
-This library replaces oospectro.
-
-
-## Installation
-
-The use of pip must be limited to virtualenv
-
-
-* From PyPI
-```
-pip install optifik
-```
-
-* From tarball
-```
-pip install /path/to/optifik-0.1.0.tar.gz
-```
-
-* From the source code
-```
-pip install .
-```
-
-
-## For contributors
-
-* Install an editable version
-```
-pip install -e .
-```
-
-* Install dev tools
-```
-pip install -e ".[dev]"
-```
-
-* Install doc tools
-```
-pip install -e ".[docs]"
-```
-
-* Build the doc
-```
-cd docs
-make html
-```
-
-## Licence
-
-The source code is released under the GNU General Public License v3.0.
-See LICENSE for details.

RELEASE.md

@@ -1,32 +0,0 @@
-
-# Step by step release process
-
-
-* Write changelog
-
-* Push version
-
-```
-bumpver update --major	# MAJOR (breaking changes)	1.0.0 → 2.0.0
-bumpver update --minor	# MINOR (nouvelles fonctionnalités)	1.0.0 → 1.1.0
-bumpver update --patch	# PATCH (correctifs)	1.0.0 → 1.0.1
-bumpver update --pre alpha	# Version alpha (1.0.0a1)	1.0.0 → 1.0.0a1
-bumpver update --pre beta	# Version beta (1.0.0b1)	1.0.0 → 1.0.0b1
-bumpver update --pre rc  # Version release candidate (1.0.0rc1)	1.0.0 → 1.0.0rc1
-```
-
-
-* Build
-```
-python -m build
-```
-
-* Check
-```
-twine check dist/*
-```
-
-* Push to pipy
-```
-twine upload dist/*
-```

TODO.txt

@@ -1,9 +0,0 @@
-# Matplotlib
-
-* nom de fonction à introduire
-* Unités
-*  * en \star
-
-
-
-

_modules/index.html

@@ -0,0 +1,104 @@
+<!DOCTYPE html>
+
+<html lang="en" data-content_root="../">
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>Overview: module code &#8212; optifik  documentation</title>
+    <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=5ecbeea2" />
+    <link rel="stylesheet" type="text/css" href="../_static/basic.css?v=b08954a9" />
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+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          
+
+          <div class="body" role="main">
+            
+  <h1>All modules for which code is available</h1>
+<ul><li><a href="optifik/fft.html">optifik.fft</a></li>
+<li><a href="optifik/io.html">optifik.io</a></li>
+<li><a href="optifik/minmax.html">optifik.minmax</a></li>
+<li><a href="optifik/scheludko.html">optifik.scheludko</a></li>
+</ul>
+
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+    </div>
+</search>
+<script>document.getElementById('searchbox').style.display = "block"</script><h3>Navigation</h3>
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+<li class="toctree-l1"><a class="reference internal" href="../examples.html">Examples</a></li>
+</ul>
+
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+  <li><a href="../index.html">Documentation overview</a><ul>
+  </ul></li>
+</ul>
+</div>
+
+
+
+
+
+
+
+
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="footer">
+      &#169;2025, F. Boulogne et al..
+      
+      |
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+    
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+</html>

_modules/optifik/fft.html

@@ -0,0 +1,184 @@
+<!DOCTYPE html>
+
+<html lang="en" data-content_root="../../">
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>optifik.fft &#8212; optifik  documentation</title>
+    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=5ecbeea2" />
+    <link rel="stylesheet" type="text/css" href="../../_static/basic.css?v=b08954a9" />
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+  
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+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          
+
+          <div class="body" role="main">
+            
+  <h1>Source code for optifik.fft</h1><div class="highlight"><pre>
+<span></span><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">scipy.interpolate</span><span class="w"> </span><span class="kn">import</span> <span class="n">interp1d</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">scipy.fftpack</span><span class="w"> </span><span class="kn">import</span> <span class="n">fft</span><span class="p">,</span> <span class="n">ifft</span><span class="p">,</span> <span class="n">fftfreq</span>
+
+
+<span class="kn">import</span><span class="w"> </span><span class="nn">matplotlib.pyplot</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">plt</span>
+
+<span class="kn">from</span><span class="w"> </span><span class="nn">.utils</span><span class="w"> </span><span class="kn">import</span> <span class="n">OptimizeResult</span><span class="p">,</span> <span class="n">setup_matplotlib</span>
+
+
+
+<div class="viewcode-block" id="thickness_from_fft">
+<a class="viewcode-back" href="../../api_reference.html#optifik.fft.thickness_from_fft">[docs]</a>
+<span class="k">def</span><span class="w"> </span><span class="nf">thickness_from_fft</span><span class="p">(</span><span class="n">wavelengths</span><span class="p">,</span> <span class="n">intensities</span><span class="p">,</span>
+                       <span class="n">refractive_index</span><span class="p">,</span>
+                       <span class="n">num_half_space</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+                       <span class="n">plot</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Determine the tickness by Fast Fourier Transform.</span>
+
+<span class="sd">    Parameters</span>
+<span class="sd">    ----------</span>
+<span class="sd">    wavelengths : array</span>
+<span class="sd">        Wavelength values in nm.</span>
+<span class="sd">    intensities : array</span>
+<span class="sd">        Intensity values.</span>
+<span class="sd">    refractive_index : scalar, optional</span>
+<span class="sd">        Value of the refractive index of the medium.</span>
+<span class="sd">    num_half_space : scalar, optional</span>
+<span class="sd">        Number of points to compute FFT&#39;s half space.</span>
+<span class="sd">        If `None`, default corresponds to `10*len(wavelengths)`.</span>
+<span class="sd">    plot : boolean, optional</span>
+<span class="sd">        Show plot of the transformed signal and the peak detection.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">    -------</span>
+<span class="sd">    results : Instance of `OptimizeResult` class.</span>
+<span class="sd">        The attribute `thickness` gives the thickness value in nm.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">if</span> <span class="n">plot</span><span class="p">:</span>
+        <span class="n">setup_matplotlib</span><span class="p">()</span>
+
+    <span class="k">if</span> <span class="n">num_half_space</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+        <span class="n">num_half_space</span> <span class="o">=</span> <span class="mi">10</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">wavelengths</span><span class="p">)</span>
+
+    <span class="c1"># FFT requires evenly spaced data.</span>
+    <span class="c1"># So, we interpolate the signal.</span>
+    <span class="c1"># Interpolate to get a linear increase of 1 / wavelengths.</span>
+    <span class="n">inverse_wavelengths_times_n</span> <span class="o">=</span> <span class="n">refractive_index</span> <span class="o">/</span> <span class="n">wavelengths</span>
+    <span class="n">f</span> <span class="o">=</span> <span class="n">interp1d</span><span class="p">(</span><span class="n">inverse_wavelengths_times_n</span><span class="p">,</span> <span class="n">intensities</span><span class="p">)</span>
+
+    <span class="n">inverse_wavelengths_linspace</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="n">inverse_wavelengths_times_n</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                                           <span class="n">inverse_wavelengths_times_n</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span>
+                                           <span class="mi">2</span><span class="o">*</span><span class="n">num_half_space</span><span class="p">)</span>
+    <span class="n">intensities_linspace</span> <span class="o">=</span> <span class="n">f</span><span class="p">(</span><span class="n">inverse_wavelengths_linspace</span><span class="p">)</span>
+
+
+    <span class="c1"># Perform FFT</span>
+    <span class="n">density</span> <span class="o">=</span> <span class="p">(</span><span class="n">inverse_wavelengths_times_n</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">-</span><span class="n">inverse_wavelengths_times_n</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">/</span> <span class="p">(</span><span class="mi">2</span><span class="o">*</span><span class="n">num_half_space</span><span class="p">)</span>
+    <span class="n">inverse_wavelengths_fft</span> <span class="o">=</span> <span class="n">fftfreq</span><span class="p">(</span><span class="mi">2</span><span class="o">*</span><span class="n">num_half_space</span><span class="p">,</span> <span class="n">density</span><span class="p">)</span>
+    <span class="n">intensities_fft</span> <span class="o">=</span> <span class="n">fft</span><span class="p">(</span><span class="n">intensities_linspace</span><span class="p">)</span>
+
+    <span class="c1"># The FFT is symetrical over [0:N] and [N:2N].</span>
+    <span class="c1"># Keep over [N:2N], ie for positive freq.</span>
+    <span class="n">intensities_fft</span> <span class="o">=</span> <span class="n">intensities_fft</span><span class="p">[</span><span class="n">num_half_space</span><span class="p">:</span><span class="mi">2</span><span class="o">*</span><span class="n">num_half_space</span><span class="p">]</span>
+    <span class="n">inverse_wavelengths_fft</span> <span class="o">=</span> <span class="n">inverse_wavelengths_fft</span><span class="p">[</span><span class="n">num_half_space</span><span class="p">:</span><span class="mi">2</span><span class="o">*</span><span class="n">num_half_space</span><span class="p">]</span>
+
+    <span class="n">idx_max_fft</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">argmax</span><span class="p">(</span><span class="nb">abs</span><span class="p">(</span><span class="n">intensities_fft</span><span class="p">))</span>
+    <span class="n">freq_max</span> <span class="o">=</span> <span class="n">inverse_wavelengths_fft</span><span class="p">[</span><span class="n">idx_max_fft</span><span class="p">]</span>
+
+    <span class="n">thickness_fft</span> <span class="o">=</span> <span class="n">freq_max</span> <span class="o">/</span> <span class="mf">2.</span>
+
+    <span class="k">if</span> <span class="n">plot</span><span class="p">:</span>
+        <span class="n">plt</span><span class="o">.</span><span class="n">figure</span><span class="p">()</span>
+        <span class="n">plt</span><span class="o">.</span><span class="n">loglog</span><span class="p">(</span><span class="n">inverse_wavelengths_fft</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="n">intensities_fft</span><span class="p">))</span>
+        <span class="n">plt</span><span class="o">.</span><span class="n">loglog</span><span class="p">(</span><span class="n">freq_max</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="n">intensities_fft</span><span class="p">[</span><span class="n">idx_max_fft</span><span class="p">]),</span> <span class="s1">&#39;o&#39;</span><span class="p">)</span>
+        <span class="n">plt</span><span class="o">.</span><span class="n">xlabel</span><span class="p">(</span><span class="s1">&#39;Frequency&#39;</span><span class="p">)</span>
+        <span class="n">plt</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;FFT($I^*$)&#39;</span><span class="p">)</span>
+        <span class="n">plt</span><span class="o">.</span><span class="n">title</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;Thickness=</span><span class="si">{</span><span class="n">thickness_fft</span><span class="si">:</span><span class="s1">.2f</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">OptimizeResult</span><span class="p">(</span><span class="n">thickness</span><span class="o">=</span><span class="n">thickness_fft</span><span class="p">,)</span></div>
+
+</pre></div>
+
+          </div>
+          
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="Main">
+        <div class="sphinxsidebarwrapper">
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+<ul>
+  <li><a href="../../index.html">Documentation overview</a><ul>
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+  </ul></li>
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_modules/optifik/io.html

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+<!DOCTYPE html>
+
+<html lang="en" data-content_root="../../">
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>optifik.io &#8212; optifik  documentation</title>
+    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=5ecbeea2" />
+    <link rel="stylesheet" type="text/css" href="../../_static/basic.css?v=b08954a9" />
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+          
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+            
+  <h1>Source code for optifik.io</h1><div class="highlight"><pre>
+<span></span><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
+
+
+<div class="viewcode-block" id="load_spectrum">
+<a class="viewcode-back" href="../../api_reference.html#optifik.io.load_spectrum">[docs]</a>
+<span class="k">def</span><span class="w"> </span><span class="nf">load_spectrum</span><span class="p">(</span><span class="n">spectrum_path</span><span class="p">,</span>
+                  <span class="n">wavelength_min</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span>
+                  <span class="n">wavelength_max</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">inf</span><span class="p">,</span>
+                  <span class="n">delimiter</span><span class="o">=</span><span class="s1">&#39;,&#39;</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Load a spectrum file.</span>
+
+
+<span class="sd">    TODO : describe expected format</span>
+
+<span class="sd">    Parameters</span>
+<span class="sd">    ----------</span>
+<span class="sd">    spectrum_path : string</span>
+<span class="sd">        File path.</span>
+<span class="sd">    wavelength_min : scalar, optional</span>
+<span class="sd">        Cut the data at this minimum wavelength (included).</span>
+<span class="sd">    wavelength_max : scalar, optional</span>
+<span class="sd">        Cut the data at this maximum wavelength (included).</span>
+<span class="sd">    delimiter : string, optional</span>
+<span class="sd">        Delimiter between columns in the datafile.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">    -------</span>
+<span class="sd">    values : arrays</span>
+<span class="sd">        (lamdbas, intensities)</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="n">data</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">loadtxt</span><span class="p">(</span><span class="n">spectrum_path</span><span class="p">,</span> <span class="n">delimiter</span><span class="o">=</span><span class="n">delimiter</span><span class="p">)</span>
+    <span class="n">lambdas</span><span class="p">,</span> <span class="n">intensities</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">column_stack</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
+
+    <span class="n">mask</span> <span class="o">=</span> <span class="p">(</span><span class="n">lambdas</span> <span class="o">&gt;=</span> <span class="n">wavelength_min</span><span class="p">)</span> <span class="o">&amp;</span> <span class="p">(</span><span class="n">lambdas</span> <span class="o">&lt;=</span> <span class="n">wavelength_max</span><span class="p">)</span>
+    <span class="k">return</span> <span class="n">lambdas</span><span class="p">[</span><span class="n">mask</span><span class="p">],</span> <span class="n">intensities</span><span class="p">[</span><span class="n">mask</span><span class="p">]</span></div>
+
+</pre></div>
+
+          </div>
+          
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+      <div class="sphinxsidebar" role="navigation" aria-label="Main">
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+<script>document.getElementById('searchbox').style.display = "block"</script><h3>Navigation</h3>
+<p class="caption" role="heading"><span class="caption-text">Documentation</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../../installation.html">Installation</a></li>
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+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+  <li><a href="../../index.html">Documentation overview</a><ul>
+  <li><a href="../index.html">Module code</a><ul>
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+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="footer">
+      &#169;2025, F. Boulogne et al..
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_modules/optifik/minmax.html

@@ -0,0 +1,258 @@
+<!DOCTYPE html>
+
+<html lang="en" data-content_root="../../">
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>optifik.minmax &#8212; optifik  documentation</title>
+    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=5ecbeea2" />
+    <link rel="stylesheet" type="text/css" href="../../_static/basic.css?v=b08954a9" />
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+            
+  <h1>Source code for optifik.minmax</h1><div class="highlight"><pre>
+<span></span><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
+
+<span class="kn">from</span><span class="w"> </span><span class="nn">scipy</span><span class="w"> </span><span class="kn">import</span> <span class="n">stats</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">skimage.measure</span><span class="w"> </span><span class="kn">import</span> <span class="n">ransac</span><span class="p">,</span> <span class="n">LineModelND</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">scipy.signal</span><span class="w"> </span><span class="kn">import</span> <span class="n">find_peaks</span>
+
+<span class="kn">import</span><span class="w"> </span><span class="nn">matplotlib.pyplot</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">plt</span>
+
+<span class="kn">from</span><span class="w"> </span><span class="nn">.utils</span><span class="w"> </span><span class="kn">import</span> <span class="n">OptimizeResult</span><span class="p">,</span> <span class="n">setup_matplotlib</span>
+
+
+<div class="viewcode-block" id="thickness_from_minmax">
+<a class="viewcode-back" href="../../api_reference.html#optifik.minmax.thickness_from_minmax">[docs]</a>
+<span class="k">def</span><span class="w"> </span><span class="nf">thickness_from_minmax</span><span class="p">(</span><span class="n">wavelengths</span><span class="p">,</span>
+                          <span class="n">intensities</span><span class="p">,</span>
+                          <span class="n">refractive_index</span><span class="p">,</span>
+                          <span class="n">min_peak_prominence</span><span class="p">,</span>
+                          <span class="n">min_peak_distance</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span>
+                          <span class="n">method</span><span class="o">=</span><span class="s1">&#39;linreg&#39;</span><span class="p">,</span>
+                          <span class="n">plot</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Return the thickness from a min-max detection.</span>
+
+<span class="sd">    Parameters</span>
+<span class="sd">    ----------</span>
+<span class="sd">    wavelengths : array</span>
+<span class="sd">        Wavelength values in nm.</span>
+<span class="sd">    intensities : array</span>
+<span class="sd">        Intensity values.</span>
+<span class="sd">    refractive_index : scalar, optional</span>
+<span class="sd">        Value of the refractive index of the medium.</span>
+<span class="sd">    min_peak_prominence : scalar, optional</span>
+<span class="sd">        Required prominence of peaks.</span>
+<span class="sd">    min_peak_distance : scalar, optional</span>
+<span class="sd">        Minimum distance between peaks.</span>
+<span class="sd">    method : string, optional</span>
+<span class="sd">        Either &#39;linreg&#39; for linear regression or &#39;ransac&#39;</span>
+<span class="sd">        for Randon Sampling Consensus.</span>
+<span class="sd">    plot : boolean, optional</span>
+<span class="sd">        Show plots of peak detection and lin regression.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">    -------</span>
+<span class="sd">    results : Instance of `OptimizeResult` class.</span>
+<span class="sd">        The attribute `thickness` gives the thickness value in nm.</span>
+
+<span class="sd">    Notes</span>
+<span class="sd">    -----</span>
+<span class="sd">    For more details about `min_peak_prominence` and `min_peak_distance`,</span>
+<span class="sd">    see the documentation of `scipy.signal.find_peaks`. This function</span>
+<span class="sd">    is used to find extrema.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">if</span> <span class="n">plot</span><span class="p">:</span>
+        <span class="n">setup_matplotlib</span><span class="p">()</span>
+
+    <span class="n">peaks_max</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="n">find_peaks</span><span class="p">(</span><span class="n">intensities</span><span class="p">,</span> <span class="n">prominence</span><span class="o">=</span><span class="n">min_peak_prominence</span><span class="p">,</span> <span class="n">distance</span><span class="o">=</span><span class="n">min_peak_distance</span><span class="p">)</span>
+    <span class="n">peaks_min</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="n">find_peaks</span><span class="p">(</span><span class="o">-</span><span class="n">intensities</span><span class="p">,</span> <span class="n">prominence</span><span class="o">=</span><span class="n">min_peak_prominence</span><span class="p">,</span> <span class="n">distance</span><span class="o">=</span><span class="n">min_peak_distance</span><span class="p">)</span>
+    <span class="n">peaks</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">concatenate</span><span class="p">((</span><span class="n">peaks_min</span><span class="p">,</span> <span class="n">peaks_max</span><span class="p">))</span>
+    <span class="n">peaks</span><span class="o">.</span><span class="n">sort</span><span class="p">()</span>
+
+    <span class="n">k_values</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">peaks</span><span class="p">))</span>
+
+    <span class="k">if</span> <span class="n">k_values</span><span class="o">.</span><span class="n">size</span> <span class="o">&lt;</span> <span class="mi">2</span><span class="p">:</span>
+        <span class="c1"># Can&#39;t fit if less than two points.</span>
+        <span class="k">return</span> <span class="n">OptimizeResult</span><span class="p">(</span><span class="n">thickness</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">nan</span><span class="p">)</span>
+
+
+    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">refractive_index</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span>
+        <span class="c1">#refractive_index = refractive_index[peaks][::-1]</span>
+        <span class="n">n_over_lambda</span> <span class="o">=</span> <span class="n">refractive_index</span><span class="p">[</span><span class="n">peaks</span><span class="p">][::</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">/</span> <span class="n">wavelengths</span><span class="p">[</span><span class="n">peaks</span><span class="p">][::</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+    <span class="k">else</span><span class="p">:</span>
+        <span class="n">n_over_lambda</span> <span class="o">=</span> <span class="n">refractive_index</span> <span class="o">/</span> <span class="n">wavelengths</span><span class="p">[</span><span class="n">peaks</span><span class="p">][::</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+
+    <span class="k">if</span> <span class="n">method</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s1">&#39;ransac&#39;</span><span class="p">:</span>
+        <span class="n">residual_threshold</span> <span class="o">=</span> <span class="mf">4e-5</span>
+        <span class="n">min_samples</span> <span class="o">=</span> <span class="mi">2</span>
+        <span class="c1"># Scikit-image</span>
+        <span class="n">data</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">column_stack</span><span class="p">([</span><span class="n">k_values</span><span class="p">,</span> <span class="n">n_over_lambda</span><span class="p">])</span>
+        <span class="n">model_robust</span><span class="p">,</span> <span class="n">inliers</span> <span class="o">=</span> <span class="n">ransac</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">LineModelND</span><span class="p">,</span>
+                                       <span class="n">min_samples</span><span class="o">=</span><span class="n">min_samples</span><span class="p">,</span>
+                                       <span class="n">residual_threshold</span><span class="o">=</span><span class="n">residual_threshold</span><span class="p">,</span>
+                                       <span class="n">max_trials</span><span class="o">=</span><span class="mi">100</span><span class="p">)</span>
+        <span class="n">slope</span> <span class="o">=</span> <span class="n">model_robust</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span>
+        <span class="n">thickness_minmax</span> <span class="o">=</span> <span class="mi">1</span> <span class="o">/</span> <span class="n">slope</span> <span class="o">/</span>  <span class="mi">4</span>
+
+        <span class="c1"># Scikit-learn</span>
+        <span class="c1">#X, y = k_values.reshape(-1, 1), 1/wavelengths[peaks][::-1]</span>
+
+        <span class="c1">## Fit line using all data</span>
+        <span class="c1">#lr = linear_model.LinearRegression()</span>
+        <span class="c1">#lr.fit(X, y)</span>
+
+        <span class="c1">#slransac = linear_model.RANSACRegressor(min_samples=min_samples,</span>
+        <span class="c1">#                                        residual_threshold=residual_threshold)</span>
+        <span class="c1">#slransac.fit(X, y)</span>
+        <span class="c1">#inlier_mask = slransac.inlier_mask_</span>
+        <span class="c1">#outlier_mask = np.logical_not(inlier_mask)</span>
+
+        <span class="c1">## Predict data of estimated models</span>
+        <span class="c1">#line_X = np.arange(X.min(), X.max())[:, np.newaxis]</span>
+        <span class="c1">#line_y = lr.predict(line_X)</span>
+        <span class="c1">#line_y_ransac = slransac.predict(line_X)</span>
+
+        <span class="c1">#slope = slransac.estimator_.coef_[0]</span>
+
+        <span class="k">if</span> <span class="n">plot</span><span class="p">:</span>
+            <span class="n">fig</span><span class="p">,</span> <span class="n">ax</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplots</span><span class="p">()</span>
+
+            <span class="n">ax</span><span class="o">.</span><span class="n">set_xlabel</span><span class="p">(</span><span class="s1">&#39;extremum n°&#39;</span><span class="p">)</span>
+            <span class="n">ax</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="s1">&#39;$n$($\lambda$) / $\lambda$&#39;</span><span class="p">)</span>
+            <span class="n">ax</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">inliers</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="n">data</span><span class="p">[</span><span class="n">inliers</span><span class="p">,</span> <span class="mi">1</span><span class="p">],</span> <span class="s1">&#39;xb&#39;</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mf">0.6</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="s1">&#39;Inliers&#39;</span><span class="p">)</span>
+            <span class="n">ax</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="o">~</span><span class="n">inliers</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="n">data</span><span class="p">[</span><span class="o">~</span><span class="n">inliers</span><span class="p">,</span> <span class="mi">1</span><span class="p">],</span> <span class="s1">&#39;+r&#39;</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mf">0.6</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="s1">&#39;Outliers&#39;</span><span class="p">)</span>
+            <span class="n">ax</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">k_values</span><span class="p">,</span> <span class="n">model_robust</span><span class="o">.</span><span class="n">predict_y</span><span class="p">(</span><span class="n">k_values</span><span class="p">),</span> <span class="s1">&#39;-g&#39;</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="s1">&#39;Fit&#39;</span><span class="p">)</span>
+
+            <span class="n">ax</span><span class="o">.</span><span class="n">legend</span><span class="p">()</span>
+            <span class="n">ax</span><span class="o">.</span><span class="n">set_title</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;Thickness = </span><span class="si">{</span><span class="n">thickness_minmax</span><span class="si">:</span><span class="s1">.2f</span><span class="si">}</span><span class="s1"> nm&#39;</span><span class="p">)</span>
+            <span class="kn">import</span><span class="w"> </span><span class="nn">inspect</span>
+            <span class="n">plt</span><span class="o">.</span><span class="n">title</span><span class="p">(</span><span class="n">inspect</span><span class="o">.</span><span class="n">currentframe</span><span class="p">()</span><span class="o">.</span><span class="n">f_code</span><span class="o">.</span><span class="n">co_name</span><span class="p">)</span>
+            <span class="n">plt</span><span class="o">.</span><span class="n">tight_layout</span><span class="p">()</span>
+            <span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
+
+        <span class="k">return</span> <span class="n">OptimizeResult</span><span class="p">(</span><span class="n">thickness</span><span class="o">=</span><span class="n">thickness_minmax</span><span class="p">,</span>
+                              <span class="n">num_inliers</span><span class="o">=</span><span class="n">inliers</span><span class="o">.</span><span class="n">sum</span><span class="p">(),</span>
+                              <span class="n">num_outliers</span><span class="o">=</span><span class="p">(</span><span class="o">~</span><span class="n">inliers</span><span class="p">)</span><span class="o">.</span><span class="n">sum</span><span class="p">(),</span>
+                              <span class="n">peaks_max</span><span class="o">=</span><span class="n">peaks_max</span><span class="p">,</span>
+                              <span class="n">peaks_min</span><span class="o">=</span><span class="n">peaks_min</span><span class="p">)</span>
+
+    <span class="k">elif</span> <span class="n">method</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s1">&#39;linreg&#39;</span><span class="p">:</span>
+        <span class="n">slope</span><span class="p">,</span> <span class="n">intercept</span><span class="p">,</span> <span class="n">r_value</span><span class="p">,</span> <span class="n">p_value</span><span class="p">,</span> <span class="n">std_err</span> <span class="o">=</span> <span class="n">stats</span><span class="o">.</span><span class="n">linregress</span><span class="p">(</span><span class="n">k_values</span><span class="p">,</span> <span class="n">n_over_lambda</span><span class="p">)</span>
+        <span class="c1">#mean_n = np.mean(refractive_index)</span>
+        <span class="n">thickness_minmax</span> <span class="o">=</span> <span class="mi">1</span> <span class="o">/</span> <span class="n">slope</span> <span class="o">/</span> <span class="mi">4</span>
+
+        <span class="k">if</span> <span class="n">plot</span><span class="p">:</span>
+            <span class="n">fig</span><span class="p">,</span> <span class="n">ax</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplots</span><span class="p">()</span>
+
+            <span class="n">ax</span><span class="o">.</span><span class="n">set_xlabel</span><span class="p">(</span><span class="s1">&#39;extremum n°&#39;</span><span class="p">)</span>
+            <span class="n">ax</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="s1">&#39;$n$($\lambda$) / $\lambda$&#39;</span><span class="p">)</span>
+            <span class="n">ax</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">k_values</span><span class="p">,</span> <span class="n">n_over_lambda</span><span class="p">,</span> <span class="s1">&#39;s&#39;</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="s1">&#39;Extrema&#39;</span><span class="p">)</span>
+            <span class="n">ax</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">k_values</span><span class="p">,</span> <span class="n">intercept</span> <span class="o">+</span> <span class="n">k_values</span> <span class="o">*</span> <span class="n">slope</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="s1">&#39;Fit&#39;</span><span class="p">)</span>
+
+            <span class="n">ax</span><span class="o">.</span><span class="n">legend</span><span class="p">()</span>
+            <span class="n">ax</span><span class="o">.</span><span class="n">set_title</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;Thickness = </span><span class="si">{</span><span class="n">thickness_minmax</span><span class="si">:</span><span class="s1">.2f</span><span class="si">}</span><span class="s1"> nm&#39;</span><span class="p">)</span>
+            <span class="kn">import</span><span class="w"> </span><span class="nn">inspect</span>
+            <span class="n">plt</span><span class="o">.</span><span class="n">title</span><span class="p">(</span><span class="n">inspect</span><span class="o">.</span><span class="n">currentframe</span><span class="p">()</span><span class="o">.</span><span class="n">f_code</span><span class="o">.</span><span class="n">co_name</span><span class="p">)</span>
+            <span class="n">plt</span><span class="o">.</span><span class="n">tight_layout</span><span class="p">()</span>
+            <span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
+
+        <span class="k">return</span> <span class="n">OptimizeResult</span><span class="p">(</span><span class="n">thickness</span><span class="o">=</span><span class="n">thickness_minmax</span><span class="p">,</span>
+                              <span class="n">peaks_max</span><span class="o">=</span><span class="n">peaks_max</span><span class="p">,</span>
+                              <span class="n">peaks_min</span><span class="o">=</span><span class="n">peaks_min</span><span class="p">,</span>
+                              <span class="n">stderr</span><span class="o">=</span><span class="n">std_err</span><span class="p">)</span>
+
+    <span class="k">else</span><span class="p">:</span>
+        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">&#39;Wrong method&#39;</span><span class="p">)</span></div>
+
+</pre></div>
+
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_modules/optifik/scheludko.html

@@ -0,0 +1,471 @@
+<!DOCTYPE html>
+
+<html lang="en" data-content_root="../../">
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>optifik.scheludko &#8212; optifik  documentation</title>
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+          <div class="body" role="main">
+            
+  <h1>Source code for optifik.scheludko</h1><div class="highlight"><pre>
+<span></span><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">scipy.optimize</span><span class="w"> </span><span class="kn">import</span> <span class="n">curve_fit</span>
+
+<span class="kn">import</span><span class="w"> </span><span class="nn">matplotlib.pyplot</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">plt</span>
+
+<span class="kn">from</span><span class="w"> </span><span class="nn">.io</span><span class="w"> </span><span class="kn">import</span> <span class="n">load_spectrum</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.utils</span><span class="w"> </span><span class="kn">import</span> <span class="n">OptimizeResult</span><span class="p">,</span> <span class="n">setup_matplotlib</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">.analysis</span><span class="w"> </span><span class="kn">import</span> <span class="n">finds_peak</span>
+
+
+<span class="k">def</span><span class="w"> </span><span class="nf">_thicknesses_scheludko_at_order</span><span class="p">(</span><span class="n">wavelengths</span><span class="p">,</span>
+                                    <span class="n">intensities</span><span class="p">,</span>
+                                    <span class="n">interference_order</span><span class="p">,</span>
+                                    <span class="n">refractive_index</span><span class="p">,</span>
+                                    <span class="n">intensities_void</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Compute thicknesses vs wavelength for a given interference order.</span>
+
+<span class="sd">    Parameters</span>
+<span class="sd">    ----------</span>
+<span class="sd">    wavelengths : array</span>
+<span class="sd">        Wavelength values in nm.</span>
+<span class="sd">    intensities : array</span>
+<span class="sd">        Intensity values.</span>
+<span class="sd">    interference_order : int</span>
+<span class="sd">        Interference order.</span>
+<span class="sd">    refractive_index : array_like (or float)</span>
+<span class="sd">        Refractive index.</span>
+<span class="sd">    intensities_void : array, optional</span>
+<span class="sd">        Intensities of void.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">    -------</span>
+<span class="sd">    thicknesses : array</span>
+
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">if</span> <span class="n">intensities_void</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+        <span class="n">Imin</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">intensities</span><span class="p">)</span>
+    <span class="k">else</span><span class="p">:</span>
+        <span class="n">Imin</span> <span class="o">=</span> <span class="n">intensities_void</span>
+
+    <span class="n">n</span> <span class="o">=</span> <span class="n">refractive_index</span>
+    <span class="n">m</span> <span class="o">=</span> <span class="n">interference_order</span>
+    <span class="n">I_norm</span> <span class="o">=</span> <span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">intensities</span><span class="p">)</span> <span class="o">-</span> <span class="n">Imin</span><span class="p">)</span> <span class="o">/</span> <span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">intensities</span><span class="p">)</span> <span class="o">-</span> <span class="n">Imin</span><span class="p">)</span>
+
+    <span class="n">prefactor</span> <span class="o">=</span> <span class="n">wavelengths</span> <span class="o">/</span> <span class="p">(</span><span class="mi">2</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">pi</span> <span class="o">*</span> <span class="n">n</span><span class="p">)</span>
+    <span class="n">argument</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">I_norm</span> <span class="o">/</span> <span class="p">(</span><span class="mi">1</span> <span class="o">+</span> <span class="p">(</span><span class="mi">1</span> <span class="o">-</span> <span class="n">I_norm</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">n</span><span class="o">**</span><span class="mi">2</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span><span class="o">**</span><span class="mi">2</span> <span class="o">/</span> <span class="p">(</span><span class="mi">4</span> <span class="o">*</span> <span class="n">n</span><span class="o">**</span><span class="mi">2</span><span class="p">)))</span>
+
+    <span class="k">if</span> <span class="n">m</span> <span class="o">%</span> <span class="mi">2</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+        <span class="n">term1</span> <span class="o">=</span> <span class="p">(</span><span class="n">m</span> <span class="o">/</span> <span class="mi">2</span><span class="p">)</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">pi</span>
+    <span class="k">else</span><span class="p">:</span>
+        <span class="n">term1</span> <span class="o">=</span> <span class="p">((</span><span class="n">m</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span> <span class="o">/</span> <span class="mi">2</span><span class="p">)</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">pi</span>
+
+    <span class="n">term2</span> <span class="o">=</span> <span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span><span class="o">**</span><span class="n">m</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">arcsin</span><span class="p">(</span><span class="n">argument</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">prefactor</span> <span class="o">*</span> <span class="p">(</span><span class="n">term1</span> <span class="o">+</span> <span class="n">term2</span><span class="p">)</span>
+
+
+<span class="k">def</span><span class="w"> </span><span class="nf">_Delta</span><span class="p">(</span><span class="n">wavelengths</span><span class="p">,</span> <span class="n">thickness</span><span class="p">,</span> <span class="n">interference_order</span><span class="p">,</span> <span class="n">refractive_index</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Compute the Delta values.</span>
+
+<span class="sd">    Parameters</span>
+<span class="sd">    ----------</span>
+<span class="sd">    wavelengths : array</span>
+<span class="sd">        Wavelength values in nm.</span>
+<span class="sd">    thickness : array_like (or float)</span>
+<span class="sd">        Film thickness.</span>
+<span class="sd">    interference_order : int</span>
+<span class="sd">        Interference order.</span>
+<span class="sd">    refractive_index : array_like (or float)</span>
+<span class="sd">        Refractive index.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">    -------</span>
+<span class="sd">    ndarray</span>
+<span class="sd">        Delta values.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="c1"># ensure that the entries are numpy arrays</span>
+    <span class="n">wavelengths</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">wavelengths</span><span class="p">)</span>
+    <span class="n">h</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">thickness</span><span class="p">)</span>
+    <span class="n">n</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">refractive_index</span><span class="p">)</span>
+    <span class="n">m</span> <span class="o">=</span> <span class="n">interference_order</span>
+
+    <span class="c1"># Calculation of p as a function of the parity of m</span>
+    <span class="k">if</span> <span class="n">m</span> <span class="o">%</span> <span class="mi">2</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+        <span class="n">p</span> <span class="o">=</span> <span class="n">m</span> <span class="o">/</span> <span class="mi">2</span>
+    <span class="k">else</span><span class="p">:</span>
+        <span class="n">p</span> <span class="o">=</span> <span class="p">(</span><span class="n">m</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> <span class="o">/</span> <span class="mi">2</span>
+
+    <span class="c1"># Calculation of alpha</span>
+    <span class="n">alpha</span> <span class="o">=</span> <span class="p">((</span><span class="n">n</span><span class="o">**</span><span class="mi">2</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span><span class="o">**</span><span class="mi">2</span><span class="p">)</span> <span class="o">/</span> <span class="p">(</span><span class="mi">4</span> <span class="o">*</span> <span class="n">n</span><span class="o">**</span><span class="mi">2</span><span class="p">)</span>
+
+    <span class="c1"># Argument of sinus</span>
+    <span class="n">angle</span> <span class="o">=</span> <span class="p">(</span><span class="mi">2</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">pi</span> <span class="o">*</span> <span class="n">n</span> <span class="o">*</span> <span class="n">h</span> <span class="o">/</span> <span class="n">wavelengths</span><span class="p">)</span> <span class="o">-</span> <span class="n">p</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">pi</span>
+
+    <span class="c1"># A = sin²(argument)</span>
+    <span class="n">A</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">angle</span><span class="p">)</span><span class="o">**</span><span class="mi">2</span>
+
+    <span class="c1"># Final calcuation of Delta</span>
+    <span class="k">return</span> <span class="p">(</span><span class="n">A</span> <span class="o">*</span> <span class="p">(</span><span class="mi">1</span> <span class="o">+</span> <span class="n">alpha</span><span class="p">))</span> <span class="o">/</span> <span class="p">(</span><span class="mi">1</span> <span class="o">+</span> <span class="n">A</span> <span class="o">*</span> <span class="n">alpha</span><span class="p">)</span>
+
+
+<span class="k">def</span><span class="w"> </span><span class="nf">_Delta_fit</span><span class="p">(</span><span class="n">xdata</span><span class="p">,</span> <span class="n">thickness</span><span class="p">,</span> <span class="n">interference_order</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Wrapper on Delta() for curve_fit.</span>
+
+<span class="sd">    Parameters</span>
+<span class="sd">    ----------</span>
+<span class="sd">    xdata : tuple</span>
+<span class="sd">        (wavelengths, refractive_index)</span>
+<span class="sd">    thickness : array_like (or float)</span>
+<span class="sd">        Film thickness.</span>
+<span class="sd">    interference_order : int</span>
+<span class="sd">        Interference order.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">    -------</span>
+<span class="sd">    ndarray</span>
+<span class="sd">        Delta values.</span>
+
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="n">lambdas</span><span class="p">,</span> <span class="n">r_index</span> <span class="o">=</span> <span class="n">xdata</span>
+    <span class="k">return</span> <span class="n">_Delta</span><span class="p">(</span><span class="n">lambdas</span><span class="p">,</span> <span class="n">thickness</span><span class="p">,</span> <span class="n">interference_order</span><span class="p">,</span> <span class="n">r_index</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="get_default_start_stop_wavelengths">
+<a class="viewcode-back" href="../../api_reference.html#optifik.scheludko.get_default_start_stop_wavelengths">[docs]</a>
+<span class="k">def</span><span class="w"> </span><span class="nf">get_default_start_stop_wavelengths</span><span class="p">(</span><span class="n">wavelengths</span><span class="p">,</span>
+                                       <span class="n">intensities</span><span class="p">,</span>
+                                       <span class="n">refractive_index</span><span class="p">,</span>
+                                       <span class="n">min_peak_prominence</span><span class="p">,</span>
+                                       <span class="n">plot</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Returns the start and stop wavelength values of the last monotonic branch.</span>
+
+<span class="sd">    Parameters</span>
+<span class="sd">    ----------</span>
+<span class="sd">    wavelengths : array</span>
+<span class="sd">        Wavelength values in nm.</span>
+<span class="sd">    intensities : array</span>
+<span class="sd">        Intensity values.</span>
+<span class="sd">    refractive_index : scalar, optional</span>
+<span class="sd">        Value of the refractive index of the medium.</span>
+<span class="sd">    min_peak_prominence : scalar</span>
+<span class="sd">        Required prominence of peaks.</span>
+<span class="sd">    plot : bool, optional</span>
+<span class="sd">        Display a curve, useful for checking or debuging. The default is None.</span>
+
+
+<span class="sd">    Raises</span>
+<span class="sd">    ------</span>
+<span class="sd">    RuntimeError</span>
+<span class="sd">        if at least one maximum and one minimum are not detected.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">    -------</span>
+<span class="sd">    wavelength_start : scalar</span>
+<span class="sd">    wavelength_stop : scalar</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="c1"># idx_min idx max</span>
+    <span class="n">idx_peaks_min</span><span class="p">,</span> <span class="n">idx_peaks_max</span> <span class="o">=</span> <span class="n">finds_peak</span><span class="p">(</span><span class="n">wavelengths</span><span class="p">,</span> <span class="n">intensities</span><span class="p">,</span>
+                                              <span class="n">min_peak_prominence</span><span class="o">=</span><span class="n">min_peak_prominence</span><span class="p">,</span>
+                                              <span class="n">plot</span><span class="o">=</span><span class="n">plot</span><span class="p">)</span>
+
+    <span class="n">failure</span><span class="p">,</span> <span class="n">message</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="s1">&#39;&#39;</span>
+    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">idx_peaks_min</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+        <span class="n">message</span> <span class="o">+=</span> <span class="s1">&#39;Failed to detect at least one minimum. &#39;</span>
+        <span class="n">failure</span> <span class="o">=</span> <span class="kc">True</span>
+    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">idx_peaks_max</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+        <span class="n">message</span> <span class="o">+=</span> <span class="s1">&#39;Failed to detect at least one maximum. &#39;</span>
+        <span class="n">failure</span> <span class="o">=</span> <span class="kc">True</span>
+    <span class="k">if</span> <span class="n">failure</span><span class="p">:</span>
+        <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="n">message</span><span class="p">)</span>
+
+    <span class="c1"># Get the last oscillation peaks</span>
+    <span class="n">lambda_min</span> <span class="o">=</span> <span class="n">wavelengths</span><span class="p">[</span><span class="n">idx_peaks_min</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]]</span>
+    <span class="n">lambda_max</span> <span class="o">=</span> <span class="n">wavelengths</span><span class="p">[</span><span class="n">idx_peaks_max</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]]</span>
+
+    <span class="c1"># Order them</span>
+    <span class="n">wavelength_start</span> <span class="o">=</span> <span class="nb">min</span><span class="p">(</span><span class="n">lambda_min</span><span class="p">,</span> <span class="n">lambda_max</span><span class="p">)</span>
+    <span class="n">wavelength_stop</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="n">lambda_min</span><span class="p">,</span> <span class="n">lambda_max</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">wavelength_start</span><span class="p">,</span> <span class="n">wavelength_stop</span></div>
+
+
+
+<div class="viewcode-block" id="thickness_from_scheludko">
+<a class="viewcode-back" href="../../api_reference.html#optifik.scheludko.thickness_from_scheludko">[docs]</a>
+<span class="k">def</span><span class="w"> </span><span class="nf">thickness_from_scheludko</span><span class="p">(</span><span class="n">wavelengths</span><span class="p">,</span>
+                             <span class="n">intensities</span><span class="p">,</span>
+                             <span class="n">refractive_index</span><span class="p">,</span>
+                             <span class="n">wavelength_start</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+                             <span class="n">wavelength_stop</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+                             <span class="n">interference_order</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+                             <span class="n">intensities_void</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+                             <span class="n">plot</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Compute the film thickness based on Scheludko method.</span>
+
+<span class="sd">    Parameters</span>
+<span class="sd">    ----------</span>
+<span class="sd">    wavelengths : array</span>
+<span class="sd">        Wavelength values in nm.</span>
+<span class="sd">    intensities : array</span>
+<span class="sd">        Intensity values.</span>
+<span class="sd">    refractive_index : scalar, optional</span>
+<span class="sd">        Value of the refractive index of the medium.</span>
+<span class="sd">    wavelength_start : scalar, optional</span>
+<span class="sd">        Starting value of a monotonic branch.</span>
+<span class="sd">        Mandatory if interference_order != 0.</span>
+<span class="sd">    wavelength_stop : scalar, optional</span>
+<span class="sd">        Stoping value of a monotonic branch.</span>
+<span class="sd">        Mandatory if interference_order != 0.</span>
+<span class="sd">    interference_order : scalar, optional</span>
+<span class="sd">        Interference order, zero or positive integer.</span>
+<span class="sd">        If set to None, the value is guessed.</span>
+<span class="sd">    intensities_void : array, optional</span>
+<span class="sd">        Intensity in absence of a film.</span>
+<span class="sd">        Mandatory if interference_order == 0.</span>
+<span class="sd">    plot : bool, optional</span>
+<span class="sd">        Display a curve, useful for checking or debuging. The default is None.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">    -------</span>
+<span class="sd">    results : Instance of `OptimizeResult` class.</span>
+<span class="sd">        The attribute `thickness` gives the thickness value in nm.</span>
+
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">if</span> <span class="n">plot</span><span class="p">:</span>
+        <span class="n">setup_matplotlib</span><span class="p">()</span>
+
+    <span class="k">if</span> <span class="n">interference_order</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">interference_order</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
+        <span class="k">if</span> <span class="n">wavelength_stop</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">wavelength_start</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">&#39;wavelength_start and wavelength_stop must be passed for interference_order != 0.&#39;</span><span class="p">)</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="k">if</span> <span class="n">wavelength_start</span> <span class="o">&gt;</span> <span class="n">wavelength_stop</span><span class="p">:</span>
+                <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">&#39;wavelength_start and wavelength_stop are swapped.&#39;</span><span class="p">)</span>
+
+    <span class="n">r_index</span> <span class="o">=</span> <span class="n">refractive_index</span>
+
+    <span class="c1"># Handle the interference order</span>
+    <span class="k">if</span> <span class="n">interference_order</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+        <span class="c1"># A bit extreme...</span>
+        <span class="n">max_tested_order</span> <span class="o">=</span> <span class="mi">12</span>
+
+        <span class="c1"># mask input data</span>
+        <span class="n">mask</span> <span class="o">=</span> <span class="p">(</span><span class="n">wavelengths</span> <span class="o">&gt;=</span> <span class="n">wavelength_start</span><span class="p">)</span> <span class="o">&amp;</span> <span class="p">(</span><span class="n">wavelengths</span> <span class="o">&lt;=</span> <span class="n">wavelength_stop</span><span class="p">)</span>
+        <span class="n">wavelengths_masked</span> <span class="o">=</span> <span class="n">wavelengths</span><span class="p">[</span><span class="n">mask</span><span class="p">]</span>
+        <span class="n">r_index_masked</span> <span class="o">=</span> <span class="n">r_index</span><span class="p">[</span><span class="n">mask</span><span class="p">]</span>
+        <span class="n">intensities_masked</span> <span class="o">=</span> <span class="n">intensities</span><span class="p">[</span><span class="n">mask</span><span class="p">]</span>
+
+        <span class="n">min_difference</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">inf</span>
+        <span class="n">thickness_values</span> <span class="o">=</span> <span class="kc">None</span>
+
+        <span class="k">if</span> <span class="n">plot</span><span class="p">:</span>
+            <span class="n">plt</span><span class="o">.</span><span class="n">figure</span><span class="p">()</span>
+            <span class="n">plt</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;$h$ ($\mathrm{{nm}}$)&#39;</span><span class="p">)</span>
+            <span class="n">plt</span><span class="o">.</span><span class="n">xlabel</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;$\lambda$ ($ \mathrm</span><span class="si">{nm}</span><span class="s1"> $)&#39;</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">_order</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">max_tested_order</span><span class="o">+</span><span class="mi">1</span><span class="p">):</span>
+            <span class="n">h_values</span> <span class="o">=</span> <span class="n">_thicknesses_scheludko_at_order</span><span class="p">(</span><span class="n">wavelengths_masked</span><span class="p">,</span>
+                                                       <span class="n">intensities_masked</span><span class="p">,</span>
+                                                       <span class="n">_order</span><span class="p">,</span>
+                                                       <span class="n">r_index_masked</span><span class="p">)</span>
+
+            <span class="n">difference</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">h_values</span><span class="p">)</span> <span class="o">-</span> <span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">h_values</span><span class="p">)</span>
+
+            <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;h-difference for m=</span><span class="si">{</span><span class="n">_order</span><span class="si">}</span><span class="s2">: </span><span class="si">{</span><span class="n">difference</span><span class="si">:</span><span class="s2">.1f</span><span class="si">}</span><span class="s2"> nm&quot;</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">difference</span> <span class="o">&lt;</span> <span class="n">min_difference</span><span class="p">:</span>
+                <span class="n">min_difference</span> <span class="o">=</span> <span class="n">difference</span>
+                <span class="n">interference_order</span> <span class="o">=</span> <span class="n">_order</span>
+                <span class="n">thickness_values</span> <span class="o">=</span> <span class="n">h_values</span>
+
+            <span class="k">if</span> <span class="n">plot</span><span class="p">:</span>
+                <span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">wavelengths_masked</span><span class="p">,</span> <span class="n">h_values</span><span class="p">,</span> <span class="s1">&#39;.&#39;</span><span class="p">,</span>
+                         <span class="n">markersize</span><span class="o">=</span><span class="mi">3</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;Order=</span><span class="si">{</span><span class="n">_order</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+    <span class="k">elif</span> <span class="n">interference_order</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+
+        <span class="n">min_peak_prominence</span> <span class="o">=</span> <span class="mf">0.02</span>
+        <span class="n">peaks_min</span><span class="p">,</span> <span class="n">peaks_max</span> <span class="o">=</span> <span class="n">finds_peak</span><span class="p">(</span><span class="n">wavelengths</span><span class="p">,</span> <span class="n">intensities</span><span class="p">,</span>
+                                          <span class="n">min_peak_prominence</span><span class="o">=</span><span class="n">min_peak_prominence</span><span class="p">,</span>
+                                          <span class="n">plot</span><span class="o">=</span><span class="n">plot</span><span class="p">)</span>
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">peaks_max</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">1</span><span class="p">:</span>
+            <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s1">&#39;Failed to detect a single maximum peak.&#39;</span><span class="p">)</span>
+
+        <span class="n">lambda_unique</span> <span class="o">=</span> <span class="n">wavelengths</span><span class="p">[</span><span class="n">peaks_max</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span>
+
+        <span class="c1"># keep rhs from the maximum</span>
+        <span class="n">mask</span> <span class="o">=</span> <span class="n">wavelengths</span> <span class="o">&gt;=</span> <span class="n">lambda_unique</span>
+        <span class="n">wavelengths_masked</span> <span class="o">=</span> <span class="n">wavelengths</span><span class="p">[</span><span class="n">mask</span><span class="p">]</span>
+        <span class="n">r_index_masked</span> <span class="o">=</span> <span class="n">r_index</span><span class="p">[</span><span class="n">mask</span><span class="p">]</span>
+        <span class="n">intensities_masked</span> <span class="o">=</span> <span class="n">intensities</span><span class="p">[</span><span class="n">mask</span><span class="p">]</span>
+        <span class="n">intensities_void_masked</span> <span class="o">=</span> <span class="n">intensities_void</span><span class="p">[</span><span class="n">mask</span><span class="p">]</span>
+
+        <span class="n">interference_order</span> <span class="o">=</span> <span class="mi">0</span>
+        <span class="n">thickness_values</span> <span class="o">=</span> <span class="n">_thicknesses_scheludko_at_order</span><span class="p">(</span><span class="n">wavelengths_masked</span><span class="p">,</span>
+                                                     <span class="n">intensities_masked</span><span class="p">,</span>
+                                                     <span class="n">interference_order</span><span class="p">,</span>
+                                                     <span class="n">r_index_masked</span><span class="p">,</span>
+                                                     <span class="n">intensities_void</span><span class="o">=</span><span class="n">intensities_void_masked</span><span class="p">)</span>
+
+    <span class="k">elif</span> <span class="n">interference_order</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
+        <span class="n">h_values</span> <span class="o">=</span> <span class="n">_thicknesses_scheludko_at_order</span><span class="p">(</span><span class="n">wavelengths_masked</span><span class="p">,</span>
+                                                   <span class="n">intensities_masked</span><span class="p">,</span>
+                                                   <span class="n">interference_order</span><span class="p">,</span>
+                                                   <span class="n">r_index_masked</span><span class="p">)</span>
+        <span class="n">thickness_values</span> <span class="o">=</span> <span class="n">h_values</span>
+    <span class="k">else</span><span class="p">:</span>
+        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">&#39;interference_order must be &gt;= 0.&#39;</span><span class="p">)</span>
+
+
+
+    <span class="c1"># Compute the thickness for the selected order</span>
+
+    <span class="c1"># Delta</span>
+    <span class="k">if</span> <span class="n">interference_order</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+        <span class="n">num</span> <span class="o">=</span> <span class="n">intensities_masked</span> <span class="o">-</span> <span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">intensities_void_masked</span><span class="p">)</span>
+        <span class="n">denom</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">intensities_masked</span><span class="p">)</span> <span class="o">-</span> <span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">intensities_void_masked</span><span class="p">)</span>
+    <span class="k">else</span><span class="p">:</span>
+        <span class="n">num</span> <span class="o">=</span> <span class="n">intensities_masked</span> <span class="o">-</span> <span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">intensities_masked</span><span class="p">)</span>
+        <span class="n">denom</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">intensities_masked</span><span class="p">)</span> <span class="o">-</span> <span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">intensities_masked</span><span class="p">)</span>
+    <span class="n">Delta_from_data</span> <span class="o">=</span> <span class="n">num</span> <span class="o">/</span> <span class="n">denom</span>
+
+
+
+    <span class="c1"># Delta_from_data = (intensities_masked -np.min(intensities_masked))/(np.max(intensities_masked) -np.min(intensities_masked))</span>
+    <span class="c1"># Delta_from_data = (intensities_raw_masked -np.min(intensities_raw_masked))/(np.max(intensities_raw_masked) -np.min(intensities_raw_masked))</span>
+
+    <span class="n">DeltaScheludko</span> <span class="o">=</span> <span class="n">_Delta</span><span class="p">(</span><span class="n">wavelengths_masked</span><span class="p">,</span>
+                            <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">thickness_values</span><span class="p">),</span>
+                            <span class="n">interference_order</span><span class="p">,</span>
+                            <span class="n">r_index_masked</span><span class="p">)</span>
+
+
+    <span class="n">xdata</span> <span class="o">=</span> <span class="p">(</span><span class="n">wavelengths_masked</span><span class="p">,</span> <span class="n">r_index_masked</span><span class="p">)</span>
+    <span class="n">popt</span><span class="p">,</span> <span class="n">pcov</span> <span class="o">=</span> <span class="n">curve_fit</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">,</span> <span class="n">h</span><span class="p">:</span> <span class="n">_Delta_fit</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">h</span><span class="p">,</span> <span class="n">interference_order</span><span class="p">),</span> <span class="n">xdata</span><span class="p">,</span> <span class="n">Delta_from_data</span><span class="p">,</span> <span class="n">p0</span><span class="o">=</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">thickness_values</span><span class="p">)])</span>
+    <span class="n">fitted_h</span> <span class="o">=</span> <span class="n">popt</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+    <span class="n">std_err</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">pcov</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">])</span>
+
+    <span class="k">if</span> <span class="n">plot</span><span class="p">:</span>
+        <span class="n">Delta_values</span> <span class="o">=</span> <span class="n">_Delta</span><span class="p">(</span><span class="n">wavelengths_masked</span><span class="p">,</span> <span class="n">fitted_h</span><span class="p">,</span> <span class="n">interference_order</span><span class="p">,</span> <span class="n">r_index_masked</span><span class="p">)</span>
+
+        <span class="n">plt</span><span class="o">.</span><span class="n">figure</span><span class="p">()</span>
+        <span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">wavelengths_masked</span><span class="p">,</span> <span class="n">Delta_from_data</span><span class="p">,</span>
+                 <span class="s1">&#39;bo-&#39;</span><span class="p">,</span> <span class="n">markersize</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span>
+                 <span class="n">label</span><span class="o">=</span><span class="sa">r</span><span class="s1">&#39;$\mathrm{{Smoothed}}\ \mathrm{{Data}}$&#39;</span><span class="p">)</span>
+
+        <span class="c1"># Scheludko</span>
+        <span class="n">label</span> <span class="o">=</span> <span class="sa">rf</span><span class="s1">&#39;$\mathrm</span><span class="se">{{</span><span class="s1">Scheludko</span><span class="se">}}</span><span class="s1">\ (h = </span><span class="si">{</span><span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">thickness_values</span><span class="p">)</span><span class="si">:</span><span class="s1">.1f</span><span class="si">}</span><span class="s1"> \pm </span><span class="si">{</span><span class="n">np</span><span class="o">.</span><span class="n">std</span><span class="p">(</span><span class="n">thickness_values</span><span class="p">)</span><span class="si">:</span><span class="s1">.1f</span><span class="si">}</span><span class="s1">\ \mathrm</span><span class="se">{{</span><span class="s1">nm</span><span class="se">}}</span><span class="s1">)$&#39;</span>
+        <span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">wavelengths_masked</span><span class="p">,</span> <span class="n">DeltaScheludko</span><span class="p">,</span>
+                 <span class="s1">&#39;go-&#39;</span><span class="p">,</span> <span class="n">markersize</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="n">label</span><span class="p">)</span>
+        <span class="c1"># Fit</span>
+        <span class="n">label</span> <span class="o">=</span> <span class="sa">rf</span><span class="s1">&#39;$\mathrm</span><span class="se">{{</span><span class="s1">Fit</span><span class="se">}}</span><span class="s1">\ (h = </span><span class="si">{</span><span class="n">fitted_h</span><span class="si">:</span><span class="s1">.1f</span><span class="si">}</span><span class="s1">\pm </span><span class="si">{</span><span class="n">std_err</span><span class="si">:</span><span class="s1">.1f</span><span class="si">}</span><span class="s1"> \ \mathrm</span><span class="se">{{</span><span class="s1">nm</span><span class="se">}}</span><span class="s1">)$&#39;</span>
+        <span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">wavelengths_masked</span><span class="p">,</span>  <span class="n">Delta_values</span><span class="p">,</span>
+                 <span class="s1">&#39;ro-&#39;</span><span class="p">,</span> <span class="n">markersize</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span>
+                 <span class="n">label</span><span class="o">=</span><span class="n">label</span><span class="p">)</span>
+
+        <span class="n">plt</span><span class="o">.</span><span class="n">legend</span><span class="p">()</span>
+        <span class="n">plt</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;$\Delta$&#39;</span><span class="p">)</span>
+        <span class="n">plt</span><span class="o">.</span><span class="n">xlabel</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;$\lambda$ ($ \mathrm</span><span class="si">{nm}</span><span class="s1"> $)&#39;</span><span class="p">)</span>
+        <span class="kn">import</span><span class="w"> </span><span class="nn">inspect</span>
+        <span class="n">plt</span><span class="o">.</span><span class="n">title</span><span class="p">(</span><span class="n">inspect</span><span class="o">.</span><span class="n">currentframe</span><span class="p">()</span><span class="o">.</span><span class="n">f_code</span><span class="o">.</span><span class="n">co_name</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">OptimizeResult</span><span class="p">(</span><span class="n">thickness</span><span class="o">=</span><span class="n">fitted_h</span><span class="p">,</span> <span class="n">stderr</span><span class="o">=</span><span class="n">std_err</span><span class="p">)</span></div>
+
+
+</pre></div>
+
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+       /* Matches the 30px from the "ul, ol" selector above */
+        margin-left: 30px;
+    }
+}
+
+
+/* misc. */
+
+.revsys-inline {
+    display: none!important;
+}
+
+/* Hide ugly table cell borders in ..bibliography:: directive output */
+table.docutils.citation, table.docutils.citation td, table.docutils.citation th {
+  border: none;
+  /* Below needed in some edge cases; if not applied, bottom shadows appear */
+  -moz-box-shadow: none;
+  -webkit-box-shadow: none;
+  box-shadow: none;
+}
+
+
+/* relbar */
+
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+    line-height: 30px;
+    width: 100%;
+    font-size: 0.9rem;
+}
+
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+    border-bottom: 1px solid #EEE;
+    margin-bottom: 20px;
+}
+
+.related.bottom {
+    border-top: 1px solid #EEE;
+}
+
+.related ul {
+    padding: 0;
+    margin: 0;
+    list-style: none;
+}
+
+.related li {
+    display: inline;
+}
+
+nav#rellinks {
+    float: right;
+}
+
+nav#rellinks li+li:before {
+    content: "|";
+}
+
+nav#breadcrumbs li+li:before {
+    content: "\00BB";
+}
+
+/* Hide certain items when printing */
+@media print {
+    div.related {
+        display: none;
+    }
+}
+
+img.github  {
+    position: absolute;
+    top: 0;
+    border: 0;
+    right: 0;
+}

_static/basic.css

@@ -0,0 +1,906 @@
+/*
+ * Sphinx stylesheet -- basic theme.
+ */
+
+/* -- main layout ----------------------------------------------------------- */
+
+div.clearer {
+    clear: both;
+}
+
+div.section::after {
+    display: block;
+    content: '';
+    clear: left;
+}
+
+/* -- relbar ---------------------------------------------------------------- */
+
+div.related {
+    width: 100%;
+    font-size: 90%;
+}
+
+div.related h3 {
+    display: none;
+}
+
+div.related ul {
+    margin: 0;
+    padding: 0 0 0 10px;
+    list-style: none;
+}
+
+div.related li {
+    display: inline;
+}
+
+div.related li.right {
+    float: right;
+    margin-right: 5px;
+}
+
+/* -- sidebar --------------------------------------------------------------- */
+
+div.sphinxsidebarwrapper {
+    padding: 10px 5px 0 10px;
+}
+
+div.sphinxsidebar {
+    float: left;
+    width: 230px;
+    margin-left: -100%;
+    font-size: 90%;
+    word-wrap: break-word;
+    overflow-wrap : break-word;
+}
+
+div.sphinxsidebar ul {
+    list-style: none;
+}
+
+div.sphinxsidebar ul ul,
+div.sphinxsidebar ul.want-points {
+    margin-left: 20px;
+    list-style: square;
+}
+
+div.sphinxsidebar ul ul {
+    margin-top: 0;
+    margin-bottom: 0;
+}
+
+div.sphinxsidebar form {
+    margin-top: 10px;
+}
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+div.sphinxsidebar input {
+    border: 1px solid #98dbcc;
+    font-family: sans-serif;
+    font-size: 1em;
+}
+
+div.sphinxsidebar #searchbox form.search {
+    overflow: hidden;
+}
+
+div.sphinxsidebar #searchbox input[type="text"] {
+    float: left;
+    width: 80%;
+    padding: 0.25em;
+    box-sizing: border-box;
+}
+
+div.sphinxsidebar #searchbox input[type="submit"] {
+    float: left;
+    width: 20%;
+    border-left: none;
+    padding: 0.25em;
+    box-sizing: border-box;
+}
+
+
+img {
+    border: 0;
+    max-width: 100%;
+}
+
+/* -- search page ----------------------------------------------------------- */
+
+ul.search {
+    margin-top: 10px;
+}
+
+ul.search li {
+    padding: 5px 0;
+}
+
+ul.search li a {
+    font-weight: bold;
+}
+
+ul.search li p.context {
+    color: #888;
+    margin: 2px 0 0 30px;
+    text-align: left;
+}
+
+ul.keywordmatches li.goodmatch a {
+    font-weight: bold;
+}
+
+/* -- index page ------------------------------------------------------------ */
+
+table.contentstable {
+    width: 90%;
+    margin-left: auto;
+    margin-right: auto;
+}
+
+table.contentstable p.biglink {
+    line-height: 150%;
+}
+
+a.biglink {
+    font-size: 1.3em;
+}
+
+span.linkdescr {
+    font-style: italic;
+    padding-top: 5px;
+    font-size: 90%;
+}
+
+/* -- general index --------------------------------------------------------- */
+
+table.indextable {
+    width: 100%;
+}
+
+table.indextable td {
+    text-align: left;
+    vertical-align: top;
+}
+
+table.indextable ul {
+    margin-top: 0;
+    margin-bottom: 0;
+    list-style-type: none;
+}
+
+table.indextable > tbody > tr > td > ul {
+    padding-left: 0em;
+}
+
+table.indextable tr.pcap {
+    height: 10px;
+}
+
+table.indextable tr.cap {
+    margin-top: 10px;
+    background-color: #f2f2f2;
+}
+
+img.toggler {
+    margin-right: 3px;
+    margin-top: 3px;
+    cursor: pointer;
+}
+
+div.modindex-jumpbox {
+    border-top: 1px solid #ddd;
+    border-bottom: 1px solid #ddd;
+    margin: 1em 0 1em 0;
+    padding: 0.4em;
+}
+
+div.genindex-jumpbox {
+    border-top: 1px solid #ddd;
+    border-bottom: 1px solid #ddd;
+    margin: 1em 0 1em 0;
+    padding: 0.4em;
+}
+
+/* -- domain module index --------------------------------------------------- */
+
+table.modindextable td {
+    padding: 2px;
+    border-collapse: collapse;
+}
+
+/* -- general body styles --------------------------------------------------- */
+
+div.body {
+    min-width: inherit;
+    max-width: 800px;
+}
+
+div.body p, div.body dd, div.body li, div.body blockquote {
+    -moz-hyphens: auto;
+    -ms-hyphens: auto;
+    -webkit-hyphens: auto;
+    hyphens: auto;
+}
+
+a.headerlink {
+    visibility: hidden;
+}
+
+a:visited {
+    color: #551A8B;
+}
+
+h1:hover > a.headerlink,
+h2:hover > a.headerlink,
+h3:hover > a.headerlink,
+h4:hover > a.headerlink,
+h5:hover > a.headerlink,
+h6:hover > a.headerlink,
+dt:hover > a.headerlink,
+caption:hover > a.headerlink,
+p.caption:hover > a.headerlink,
+div.code-block-caption:hover > a.headerlink {
+    visibility: visible;
+}
+
+div.body p.caption {
+    text-align: inherit;
+}
+
+div.body td {
+    text-align: left;
+}
+
+.first {
+    margin-top: 0 !important;
+}
+
+p.rubric {
+    margin-top: 30px;
+    font-weight: bold;
+}
+
+img.align-left, figure.align-left, .figure.align-left, object.align-left {
+    clear: left;
+    float: left;
+    margin-right: 1em;
+}
+
+img.align-right, figure.align-right, .figure.align-right, object.align-right {
+    clear: right;
+    float: right;
+    margin-left: 1em;
+}
+
+img.align-center, figure.align-center, .figure.align-center, object.align-center {
+  display: block;
+  margin-left: auto;
+  margin-right: auto;
+}
+
+img.align-default, figure.align-default, .figure.align-default {
+  display: block;
+  margin-left: auto;
+  margin-right: auto;
+}
+
+.align-left {
+    text-align: left;
+}
+
+.align-center {
+    text-align: center;
+}
+
+.align-default {
+    text-align: center;
+}
+
+.align-right {
+    text-align: right;
+}
+
+/* -- sidebars -------------------------------------------------------------- */
+
+div.sidebar,
+aside.sidebar {
+    margin: 0 0 0.5em 1em;
+    border: 1px solid #ddb;
+    padding: 7px;
+    background-color: #ffe;
+    width: 40%;
+    float: right;
+    clear: right;
+    overflow-x: auto;
+}
+
+p.sidebar-title {
+    font-weight: bold;
+}
+
+nav.contents,
+aside.topic,
+div.admonition, div.topic, blockquote {
+    clear: left;
+}
+
+/* -- topics ---------------------------------------------------------------- */
+
+nav.contents,
+aside.topic,
+div.topic {
+    border: 1px solid #ccc;
+    padding: 7px;
+    margin: 10px 0 10px 0;
+}
+
+p.topic-title {
+    font-size: 1.1em;
+    font-weight: bold;
+    margin-top: 10px;
+}
+
+/* -- admonitions ----------------------------------------------------------- */
+
+div.admonition {
+    margin-top: 10px;
+    margin-bottom: 10px;
+    padding: 7px;
+}
+
+div.admonition dt {
+    font-weight: bold;
+}
+
+p.admonition-title {
+    margin: 0px 10px 5px 0px;
+    font-weight: bold;
+}
+
+div.body p.centered {
+    text-align: center;
+    margin-top: 25px;
+}
+
+/* -- content of sidebars/topics/admonitions -------------------------------- */
+
+div.sidebar > :last-child,
+aside.sidebar > :last-child,
+nav.contents > :last-child,
+aside.topic > :last-child,
+div.topic > :last-child,
+div.admonition > :last-child {
+    margin-bottom: 0;
+}
+
+div.sidebar::after,
+aside.sidebar::after,
+nav.contents::after,
+aside.topic::after,
+div.topic::after,
+div.admonition::after,
+blockquote::after {
+    display: block;
+    content: '';
+    clear: both;
+}
+
+/* -- tables ---------------------------------------------------------------- */
+
+table.docutils {
+    margin-top: 10px;
+    margin-bottom: 10px;
+    border: 0;
+    border-collapse: collapse;
+}
+
+table.align-center {
+    margin-left: auto;
+    margin-right: auto;
+}
+
+table.align-default {
+    margin-left: auto;
+    margin-right: auto;
+}
+
+table caption span.caption-number {
+    font-style: italic;
+}
+
+table caption span.caption-text {
+}
+
+table.docutils td, table.docutils th {
+    padding: 1px 8px 1px 5px;
+    border-top: 0;
+    border-left: 0;
+    border-right: 0;
+    border-bottom: 1px solid #aaa;
+}
+
+th {
+    text-align: left;
+    padding-right: 5px;
+}
+
+table.citation {
+    border-left: solid 1px gray;
+    margin-left: 1px;
+}
+
+table.citation td {
+    border-bottom: none;
+}
+
+th > :first-child,
+td > :first-child {
+    margin-top: 0px;
+}
+
+th > :last-child,
+td > :last-child {
+    margin-bottom: 0px;
+}
+
+/* -- figures --------------------------------------------------------------- */
+
+div.figure, figure {
+    margin: 0.5em;
+    padding: 0.5em;
+}
+
+div.figure p.caption, figcaption {
+    padding: 0.3em;
+}
+
+div.figure p.caption span.caption-number,
+figcaption span.caption-number {
+    font-style: italic;
+}
+
+div.figure p.caption span.caption-text,
+figcaption span.caption-text {
+}
+
+/* -- field list styles ----------------------------------------------------- */
+
+table.field-list td, table.field-list th {
+    border: 0 !important;
+}
+
+.field-list ul {
+    margin: 0;
+    padding-left: 1em;
+}
+
+.field-list p {
+    margin: 0;
+}
+
+.field-name {
+    -moz-hyphens: manual;
+    -ms-hyphens: manual;
+    -webkit-hyphens: manual;
+    hyphens: manual;
+}
+
+/* -- hlist styles ---------------------------------------------------------- */
+
+table.hlist {
+    margin: 1em 0;
+}
+
+table.hlist td {
+    vertical-align: top;
+}
+
+/* -- object description styles --------------------------------------------- */
+
+.sig {
+	font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace;
+}
+
+.sig-name, code.descname {
+    background-color: transparent;
+    font-weight: bold;
+}
+
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+	font-size: 1.1em;
+}
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+    font-size: 1.2em;
+}
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+    background-color: transparent;
+}
+
+.optional {
+    font-size: 1.3em;
+}
+
+.sig-paren {
+    font-size: larger;
+}
+
+.sig-param.n {
+	font-style: italic;
+}
+
+/* C++ specific styling */
+
+.sig-inline.c-texpr,
+.sig-inline.cpp-texpr {
+	font-family: unset;
+}
+
+.sig.c   .k, .sig.c   .kt,
+.sig.cpp .k, .sig.cpp .kt {
+	color: #0033B3;
+}
+
+.sig.c   .m,
+.sig.cpp .m {
+	color: #1750EB;
+}
+
+.sig.c   .s, .sig.c   .sc,
+.sig.cpp .s, .sig.cpp .sc {
+	color: #067D17;
+}
+
+
+/* -- other body styles ----------------------------------------------------- */
+
+ol.arabic {
+    list-style: decimal;
+}
+
+ol.loweralpha {
+    list-style: lower-alpha;
+}
+
+ol.upperalpha {
+    list-style: upper-alpha;
+}
+
+ol.lowerroman {
+    list-style: lower-roman;
+}
+
+ol.upperroman {
+    list-style: upper-roman;
+}
+
+:not(li) > ol > li:first-child > :first-child,
+:not(li) > ul > li:first-child > :first-child {
+    margin-top: 0px;
+}
+
+:not(li) > ol > li:last-child > :last-child,
+:not(li) > ul > li:last-child > :last-child {
+    margin-bottom: 0px;
+}
+
+ol.simple ol p,
+ol.simple ul p,
+ul.simple ol p,
+ul.simple ul p {
+    margin-top: 0;
+}
+
+ol.simple > li:not(:first-child) > p,
+ul.simple > li:not(:first-child) > p {
+    margin-top: 0;
+}
+
+ol.simple p,
+ul.simple p {
+    margin-bottom: 0;
+}
+
+aside.footnote > span,
+div.citation > span {
+    float: left;
+}
+aside.footnote > span:last-of-type,
+div.citation > span:last-of-type {
+  padding-right: 0.5em;
+}
+aside.footnote > p {
+  margin-left: 2em;
+}
+div.citation > p {
+  margin-left: 4em;
+}
+aside.footnote > p:last-of-type,
+div.citation > p:last-of-type {
+    margin-bottom: 0em;
+}
+aside.footnote > p:last-of-type:after,
+div.citation > p:last-of-type:after {
+    content: "";
+    clear: both;
+}
+
+dl.field-list {
+    display: grid;
+    grid-template-columns: fit-content(30%) auto;
+}
+
+dl.field-list > dt {
+    font-weight: bold;
+    word-break: break-word;
+    padding-left: 0.5em;
+    padding-right: 5px;
+}
+
+dl.field-list > dd {
+    padding-left: 0.5em;
+    margin-top: 0em;
+    margin-left: 0em;
+    margin-bottom: 0em;
+}
+
+dl {
+    margin-bottom: 15px;
+}
+
+dd > :first-child {
+    margin-top: 0px;
+}
+
+dd ul, dd table {
+    margin-bottom: 10px;
+}
+
+dd {
+    margin-top: 3px;
+    margin-bottom: 10px;
+    margin-left: 30px;
+}
+
+.sig dd {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
+.sig dl {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
+dl > dd:last-child,
+dl > dd:last-child > :last-child {
+    margin-bottom: 0;
+}
+
+dt:target, span.highlighted {
+    background-color: #fbe54e;
+}
+
+rect.highlighted {
+    fill: #fbe54e;
+}
+
+dl.glossary dt {
+    font-weight: bold;
+    font-size: 1.1em;
+}
+
+.versionmodified {
+    font-style: italic;
+}
+
+.system-message {
+    background-color: #fda;
+    padding: 5px;
+    border: 3px solid red;
+}
+
+.footnote:target  {
+    background-color: #ffa;
+}
+
+.line-block {
+    display: block;
+    margin-top: 1em;
+    margin-bottom: 1em;
+}
+
+.line-block .line-block {
+    margin-top: 0;
+    margin-bottom: 0;
+    margin-left: 1.5em;
+}
+
+.guilabel, .menuselection {
+    font-family: sans-serif;
+}
+
+.accelerator {
+    text-decoration: underline;
+}
+
+.classifier {
+    font-style: oblique;
+}
+
+.classifier:before {
+    font-style: normal;
+    margin: 0 0.5em;
+    content: ":";
+    display: inline-block;
+}
+
+abbr, acronym {
+    border-bottom: dotted 1px;
+    cursor: help;
+}
+
+/* -- code displays --------------------------------------------------------- */
+
+pre {
+    overflow: auto;
+    overflow-y: hidden;  /* fixes display issues on Chrome browsers */
+}
+
+pre, div[class*="highlight-"] {
+    clear: both;
+}
+
+span.pre {
+    -moz-hyphens: none;
+    -ms-hyphens: none;
+    -webkit-hyphens: none;
+    hyphens: none;
+    white-space: nowrap;
+}
+
+div[class*="highlight-"] {
+    margin: 1em 0;
+}
+
+td.linenos pre {
+    border: 0;
+    background-color: transparent;
+    color: #aaa;
+}
+
+table.highlighttable {
+    display: block;
+}
+
+table.highlighttable tbody {
+    display: block;
+}
+
+table.highlighttable tr {
+    display: flex;
+}
+
+table.highlighttable td {
+    margin: 0;
+    padding: 0;
+}
+
+table.highlighttable td.linenos {
+    padding-right: 0.5em;
+}
+
+table.highlighttable td.code {
+    flex: 1;
+    overflow: hidden;
+}
+
+.highlight .hll {
+    display: block;
+}
+
+div.highlight pre,
+table.highlighttable pre {
+    margin: 0;
+}
+
+div.code-block-caption + div {
+    margin-top: 0;
+}
+
+div.code-block-caption {
+    margin-top: 1em;
+    padding: 2px 5px;
+    font-size: small;
+}
+
+div.code-block-caption code {
+    background-color: transparent;
+}
+
+table.highlighttable td.linenos,
+span.linenos,
+div.highlight span.gp {  /* gp: Generic.Prompt */
+  user-select: none;
+  -webkit-user-select: text; /* Safari fallback only */
+  -webkit-user-select: none; /* Chrome/Safari */
+  -moz-user-select: none; /* Firefox */
+  -ms-user-select: none; /* IE10+ */
+}
+
+div.code-block-caption span.caption-number {
+    padding: 0.1em 0.3em;
+    font-style: italic;
+}
+
+div.code-block-caption span.caption-text {
+}
+
+div.literal-block-wrapper {
+    margin: 1em 0;
+}
+
+code.xref, a code {
+    background-color: transparent;
+    font-weight: bold;
+}
+
+h1 code, h2 code, h3 code, h4 code, h5 code, h6 code {
+    background-color: transparent;
+}
+
+.viewcode-link {
+    float: right;
+}
+
+.viewcode-back {
+    float: right;
+    font-family: sans-serif;
+}
+
+div.viewcode-block:target {
+    margin: -1px -10px;
+    padding: 0 10px;
+}
+
+/* -- math display ---------------------------------------------------------- */
+
+img.math {
+    vertical-align: middle;
+}
+
+div.body div.math p {
+    text-align: center;
+}
+
+span.eqno {
+    float: right;
+}
+
+span.eqno a.headerlink {
+    position: absolute;
+    z-index: 1;
+}
+
+div.math:hover a.headerlink {
+    visibility: visible;
+}
+
+/* -- printout stylesheet --------------------------------------------------- */
+
+@media print {
+    div.document,
+    div.documentwrapper,
+    div.bodywrapper {
+        margin: 0 !important;
+        width: 100%;
+    }
+
+    div.sphinxsidebar,
+    div.related,
+    div.footer,
+    #top-link {
+        display: none;
+    }
+}

_static/custom.css

@@ -0,0 +1 @@
+/* This file intentionally left blank. */

_static/doctools.js

@@ -0,0 +1,149 @@
+/*
+ * Base JavaScript utilities for all Sphinx HTML documentation.
+ */
+"use strict";
+
+const BLACKLISTED_KEY_CONTROL_ELEMENTS = new Set([
+  "TEXTAREA",
+  "INPUT",
+  "SELECT",
+  "BUTTON",
+]);
+
+const _ready = (callback) => {
+  if (document.readyState !== "loading") {
+    callback();
+  } else {
+    document.addEventListener("DOMContentLoaded", callback);
+  }
+};
+
+/**
+ * Small JavaScript module for the documentation.
+ */
+const Documentation = {
+  init: () => {
+    Documentation.initDomainIndexTable();
+    Documentation.initOnKeyListeners();
+  },
+
+  /**
+   * i18n support
+   */
+  TRANSLATIONS: {},
+  PLURAL_EXPR: (n) => (n === 1 ? 0 : 1),
+  LOCALE: "unknown",
+
+  // gettext and ngettext don't access this so that the functions
+  // can safely bound to a different name (_ = Documentation.gettext)
+  gettext: (string) => {
+    const translated = Documentation.TRANSLATIONS[string];
+    switch (typeof translated) {
+      case "undefined":
+        return string; // no translation
+      case "string":
+        return translated; // translation exists
+      default:
+        return translated[0]; // (singular, plural) translation tuple exists
+    }
+  },
+
+  ngettext: (singular, plural, n) => {
+    const translated = Documentation.TRANSLATIONS[singular];
+    if (typeof translated !== "undefined")
+      return translated[Documentation.PLURAL_EXPR(n)];
+    return n === 1 ? singular : plural;
+  },
+
+  addTranslations: (catalog) => {
+    Object.assign(Documentation.TRANSLATIONS, catalog.messages);
+    Documentation.PLURAL_EXPR = new Function(
+      "n",
+      `return (${catalog.plural_expr})`
+    );
+    Documentation.LOCALE = catalog.locale;
+  },
+
+  /**
+   * helper function to focus on search bar
+   */
+  focusSearchBar: () => {
+    document.querySelectorAll("input[name=q]")[0]?.focus();
+  },
+
+  /**
+   * Initialise the domain index toggle buttons
+   */
+  initDomainIndexTable: () => {
+    const toggler = (el) => {
+      const idNumber = el.id.substr(7);
+      const toggledRows = document.querySelectorAll(`tr.cg-${idNumber}`);
+      if (el.src.substr(-9) === "minus.png") {
+        el.src = `${el.src.substr(0, el.src.length - 9)}plus.png`;
+        toggledRows.forEach((el) => (el.style.display = "none"));
+      } else {
+        el.src = `${el.src.substr(0, el.src.length - 8)}minus.png`;
+        toggledRows.forEach((el) => (el.style.display = ""));
+      }
+    };
+
+    const togglerElements = document.querySelectorAll("img.toggler");
+    togglerElements.forEach((el) =>
+      el.addEventListener("click", (event) => toggler(event.currentTarget))
+    );
+    togglerElements.forEach((el) => (el.style.display = ""));
+    if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) togglerElements.forEach(toggler);
+  },
+
+  initOnKeyListeners: () => {
+    // only install a listener if it is really needed
+    if (
+      !DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS &&
+      !DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS
+    )
+      return;
+
+    document.addEventListener("keydown", (event) => {
+      // bail for input elements
+      if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return;
+      // bail with special keys
+      if (event.altKey || event.ctrlKey || event.metaKey) return;
+
+      if (!event.shiftKey) {
+        switch (event.key) {
+          case "ArrowLeft":
+            if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break;
+
+            const prevLink = document.querySelector('link[rel="prev"]');
+            if (prevLink && prevLink.href) {
+              window.location.href = prevLink.href;
+              event.preventDefault();
+            }
+            break;
+          case "ArrowRight":
+            if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break;
+
+            const nextLink = document.querySelector('link[rel="next"]');
+            if (nextLink && nextLink.href) {
+              window.location.href = nextLink.href;
+              event.preventDefault();
+            }
+            break;
+        }
+      }
+
+      // some keyboard layouts may need Shift to get /
+      switch (event.key) {
+        case "/":
+          if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break;
+          Documentation.focusSearchBar();
+          event.preventDefault();
+      }
+    });
+  },
+};
+
+// quick alias for translations
+const _ = Documentation.gettext;
+
+_ready(Documentation.init);

_static/documentation_options.js

@@ -0,0 +1,13 @@
+const DOCUMENTATION_OPTIONS = {
+    VERSION: '',
+    LANGUAGE: 'en',
+    COLLAPSE_INDEX: false,
+    BUILDER: 'html',
+    FILE_SUFFIX: '.html',
+    LINK_SUFFIX: '.html',
+    HAS_SOURCE: true,
+    SOURCELINK_SUFFIX: '.txt',
+    NAVIGATION_WITH_KEYS: false,
+    SHOW_SEARCH_SUMMARY: true,
+    ENABLE_SEARCH_SHORTCUTS: true,
+};

_static/github-banner.svg

@@ -0,0 +1,5 @@
+<svg xmlns="http://www.w3.org/2000/svg" width="80" height="80" viewBox="0 0 250 250" fill="#fff">
+    <path d="M0 0l115 115h15l12 27 108 108V0z" fill="#151513"/>
+    <path d="M128 109c-15-9-9-19-9-19 3-7 2-11 2-11-1-7 3-2 3-2 4 5 2 11 2 11-3 10 5 15 9 16"/>
+    <path d="M115 115s4 2 5 0l14-14c3-2 6-3 8-3-8-11-15-24 2-41 5-5 10-7 16-7 1-2 3-7 12-11 0 0 5 3 7 16 4 2 8 5 12 9s7 8 9 12c14 3 17 7 17 7-4 8-9 11-11 11 0 6-2 11-7 16-16 16-30 10-41 2 0 3-1 7-5 11l-12 11c-1 1 1 5 1 5z"/>
+</svg>

_static/language_data.js

@@ -0,0 +1,192 @@
+/*
+ * This script contains the language-specific data used by searchtools.js,
+ * namely the list of stopwords, stemmer, scorer and splitter.
+ */
+
+var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"];
+
+
+/* Non-minified version is copied as a separate JS file, if available */
+
+/**
+ * Porter Stemmer
+ */
+var Stemmer = function() {
+
+  var step2list = {
+    ational: 'ate',
+    tional: 'tion',
+    enci: 'ence',
+    anci: 'ance',
+    izer: 'ize',
+    bli: 'ble',
+    alli: 'al',
+    entli: 'ent',
+    eli: 'e',
+    ousli: 'ous',
+    ization: 'ize',
+    ation: 'ate',
+    ator: 'ate',
+    alism: 'al',
+    iveness: 'ive',
+    fulness: 'ful',
+    ousness: 'ous',
+    aliti: 'al',
+    iviti: 'ive',
+    biliti: 'ble',
+    logi: 'log'
+  };
+
+  var step3list = {
+    icate: 'ic',
+    ative: '',
+    alize: 'al',
+    iciti: 'ic',
+    ical: 'ic',
+    ful: '',
+    ness: ''
+  };
+
+  var c = "[^aeiou]";          // consonant
+  var v = "[aeiouy]";          // vowel
+  var C = c + "[^aeiouy]*";    // consonant sequence
+  var V = v + "[aeiou]*";      // vowel sequence
+
+  var mgr0 = "^(" + C + ")?" + V + C;                      // [C]VC... is m>0
+  var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$";    // [C]VC[V] is m=1
+  var mgr1 = "^(" + C + ")?" + V + C + V + C;              // [C]VCVC... is m>1
+  var s_v   = "^(" + C + ")?" + v;                         // vowel in stem
+
+  this.stemWord = function (w) {
+    var stem;
+    var suffix;
+    var firstch;
+    var origword = w;
+
+    if (w.length < 3)
+      return w;
+
+    var re;
+    var re2;
+    var re3;
+    var re4;
+
+    firstch = w.substr(0,1);
+    if (firstch == "y")
+      w = firstch.toUpperCase() + w.substr(1);
+
+    // Step 1a
+    re = /^(.+?)(ss|i)es$/;
+    re2 = /^(.+?)([^s])s$/;
+
+    if (re.test(w))
+      w = w.replace(re,"$1$2");
+    else if (re2.test(w))
+      w = w.replace(re2,"$1$2");
+
+    // Step 1b
+    re = /^(.+?)eed$/;
+    re2 = /^(.+?)(ed|ing)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      re = new RegExp(mgr0);
+      if (re.test(fp[1])) {
+        re = /.$/;
+        w = w.replace(re,"");
+      }
+    }
+    else if (re2.test(w)) {
+      var fp = re2.exec(w);
+      stem = fp[1];
+      re2 = new RegExp(s_v);
+      if (re2.test(stem)) {
+        w = stem;
+        re2 = /(at|bl|iz)$/;
+        re3 = new RegExp("([^aeiouylsz])\\1$");
+        re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+        if (re2.test(w))
+          w = w + "e";
+        else if (re3.test(w)) {
+          re = /.$/;
+          w = w.replace(re,"");
+        }
+        else if (re4.test(w))
+          w = w + "e";
+      }
+    }
+
+    // Step 1c
+    re = /^(.+?)y$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(s_v);
+      if (re.test(stem))
+        w = stem + "i";
+    }
+
+    // Step 2
+    re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      suffix = fp[2];
+      re = new RegExp(mgr0);
+      if (re.test(stem))
+        w = stem + step2list[suffix];
+    }
+
+    // Step 3
+    re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      suffix = fp[2];
+      re = new RegExp(mgr0);
+      if (re.test(stem))
+        w = stem + step3list[suffix];
+    }
+
+    // Step 4
+    re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
+    re2 = /^(.+?)(s|t)(ion)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(mgr1);
+      if (re.test(stem))
+        w = stem;
+    }
+    else if (re2.test(w)) {
+      var fp = re2.exec(w);
+      stem = fp[1] + fp[2];
+      re2 = new RegExp(mgr1);
+      if (re2.test(stem))
+        w = stem;
+    }
+
+    // Step 5
+    re = /^(.+?)e$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(mgr1);
+      re2 = new RegExp(meq1);
+      re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+      if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
+        w = stem;
+    }
+    re = /ll$/;
+    re2 = new RegExp(mgr1);
+    if (re.test(w) && re2.test(w)) {
+      re = /.$/;
+      w = w.replace(re,"");
+    }
+
+    // and turn initial Y back to y
+    if (firstch == "y")
+      w = firstch.toLowerCase() + w.substr(1);
+    return w;
+  }
+}
+

_static/pygments.css

@@ -0,0 +1,84 @@
+pre { line-height: 125%; }
+td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }
+span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }
+td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
+span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
+.highlight .hll { background-color: #ffffcc }
+.highlight { background: #f8f8f8; }
+.highlight .c { color: #8F5902; font-style: italic } /* Comment */
+.highlight .err { color: #A40000; border: 1px solid #EF2929 } /* Error */
+.highlight .g { color: #000 } /* Generic */
+.highlight .k { color: #004461; font-weight: bold } /* Keyword */
+.highlight .l { color: #000 } /* Literal */
+.highlight .n { color: #000 } /* Name */
+.highlight .o { color: #582800 } /* Operator */
+.highlight .x { color: #000 } /* Other */
+.highlight .p { color: #000; font-weight: bold } /* Punctuation */
+.highlight .ch { color: #8F5902; font-style: italic } /* Comment.Hashbang */
+.highlight .cm { color: #8F5902; font-style: italic } /* Comment.Multiline */
+.highlight .cp { color: #8F5902 } /* Comment.Preproc */
+.highlight .cpf { color: #8F5902; font-style: italic } /* Comment.PreprocFile */
+.highlight .c1 { color: #8F5902; font-style: italic } /* Comment.Single */
+.highlight .cs { color: #8F5902; font-style: italic } /* Comment.Special */
+.highlight .gd { color: #A40000 } /* Generic.Deleted */
+.highlight .ge { color: #000; font-style: italic } /* Generic.Emph */
+.highlight .ges { color: #000 } /* Generic.EmphStrong */
+.highlight .gr { color: #EF2929 } /* Generic.Error */
+.highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
+.highlight .gi { color: #00A000 } /* Generic.Inserted */
+.highlight .go { color: #888 } /* Generic.Output */
+.highlight .gp { color: #745334 } /* Generic.Prompt */
+.highlight .gs { color: #000; font-weight: bold } /* Generic.Strong */
+.highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */
+.highlight .gt { color: #A40000; font-weight: bold } /* Generic.Traceback */
+.highlight .kc { color: #004461; font-weight: bold } /* Keyword.Constant */
+.highlight .kd { color: #004461; font-weight: bold } /* Keyword.Declaration */
+.highlight .kn { color: #004461; font-weight: bold } /* Keyword.Namespace */
+.highlight .kp { color: #004461; font-weight: bold } /* Keyword.Pseudo */
+.highlight .kr { color: #004461; font-weight: bold } /* Keyword.Reserved */
+.highlight .kt { color: #004461; font-weight: bold } /* Keyword.Type */
+.highlight .ld { color: #000 } /* Literal.Date */
+.highlight .m { color: #900 } /* Literal.Number */
+.highlight .s { color: #4E9A06 } /* Literal.String */
+.highlight .na { color: #C4A000 } /* Name.Attribute */
+.highlight .nb { color: #004461 } /* Name.Builtin */
+.highlight .nc { color: #000 } /* Name.Class */
+.highlight .no { color: #000 } /* Name.Constant */
+.highlight .nd { color: #888 } /* Name.Decorator */
+.highlight .ni { color: #CE5C00 } /* Name.Entity */
+.highlight .ne { color: #C00; font-weight: bold } /* Name.Exception */
+.highlight .nf { color: #000 } /* Name.Function */
+.highlight .nl { color: #F57900 } /* Name.Label */
+.highlight .nn { color: #000 } /* Name.Namespace */
+.highlight .nx { color: #000 } /* Name.Other */
+.highlight .py { color: #000 } /* Name.Property */
+.highlight .nt { color: #004461; font-weight: bold } /* Name.Tag */
+.highlight .nv { color: #000 } /* Name.Variable */
+.highlight .ow { color: #004461; font-weight: bold } /* Operator.Word */
+.highlight .pm { color: #000; font-weight: bold } /* Punctuation.Marker */
+.highlight .w { color: #F8F8F8 } /* Text.Whitespace */
+.highlight .mb { color: #900 } /* Literal.Number.Bin */
+.highlight .mf { color: #900 } /* Literal.Number.Float */
+.highlight .mh { color: #900 } /* Literal.Number.Hex */
+.highlight .mi { color: #900 } /* Literal.Number.Integer */
+.highlight .mo { color: #900 } /* Literal.Number.Oct */
+.highlight .sa { color: #4E9A06 } /* Literal.String.Affix */
+.highlight .sb { color: #4E9A06 } /* Literal.String.Backtick */
+.highlight .sc { color: #4E9A06 } /* Literal.String.Char */
+.highlight .dl { color: #4E9A06 } /* Literal.String.Delimiter */
+.highlight .sd { color: #8F5902; font-style: italic } /* Literal.String.Doc */
+.highlight .s2 { color: #4E9A06 } /* Literal.String.Double */
+.highlight .se { color: #4E9A06 } /* Literal.String.Escape */
+.highlight .sh { color: #4E9A06 } /* Literal.String.Heredoc */
+.highlight .si { color: #4E9A06 } /* Literal.String.Interpol */
+.highlight .sx { color: #4E9A06 } /* Literal.String.Other */
+.highlight .sr { color: #4E9A06 } /* Literal.String.Regex */
+.highlight .s1 { color: #4E9A06 } /* Literal.String.Single */
+.highlight .ss { color: #4E9A06 } /* Literal.String.Symbol */
+.highlight .bp { color: #3465A4 } /* Name.Builtin.Pseudo */
+.highlight .fm { color: #000 } /* Name.Function.Magic */
+.highlight .vc { color: #000 } /* Name.Variable.Class */
+.highlight .vg { color: #000 } /* Name.Variable.Global */
+.highlight .vi { color: #000 } /* Name.Variable.Instance */
+.highlight .vm { color: #000 } /* Name.Variable.Magic */
+.highlight .il { color: #900 } /* Literal.Number.Integer.Long */

_static/searchtools.js

@@ -0,0 +1,635 @@
+/*
+ * Sphinx JavaScript utilities for the full-text search.
+ */
+"use strict";
+
+/**
+ * Simple result scoring code.
+ */
+if (typeof Scorer === "undefined") {
+  var Scorer = {
+    // Implement the following function to further tweak the score for each result
+    // The function takes a result array [docname, title, anchor, descr, score, filename]
+    // and returns the new score.
+    /*
+    score: result => {
+      const [docname, title, anchor, descr, score, filename, kind] = result
+      return score
+    },
+    */
+
+    // query matches the full name of an object
+    objNameMatch: 11,
+    // or matches in the last dotted part of the object name
+    objPartialMatch: 6,
+    // Additive scores depending on the priority of the object
+    objPrio: {
+      0: 15, // used to be importantResults
+      1: 5, // used to be objectResults
+      2: -5, // used to be unimportantResults
+    },
+    //  Used when the priority is not in the mapping.
+    objPrioDefault: 0,
+
+    // query found in title
+    title: 15,
+    partialTitle: 7,
+    // query found in terms
+    term: 5,
+    partialTerm: 2,
+  };
+}
+
+// Global search result kind enum, used by themes to style search results.
+class SearchResultKind {
+    static get index() { return  "index"; }
+    static get object() { return "object"; }
+    static get text() { return "text"; }
+    static get title() { return "title"; }
+}
+
+const _removeChildren = (element) => {
+  while (element && element.lastChild) element.removeChild(element.lastChild);
+};
+
+/**
+ * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping
+ */
+const _escapeRegExp = (string) =>
+  string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string
+
+const _displayItem = (item, searchTerms, highlightTerms) => {
+  const docBuilder = DOCUMENTATION_OPTIONS.BUILDER;
+  const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX;
+  const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX;
+  const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY;
+  const contentRoot = document.documentElement.dataset.content_root;
+
+  const [docName, title, anchor, descr, score, _filename, kind] = item;
+
+  let listItem = document.createElement("li");
+  // Add a class representing the item's type:
+  // can be used by a theme's CSS selector for styling
+  // See SearchResultKind for the class names.
+  listItem.classList.add(`kind-${kind}`);
+  let requestUrl;
+  let linkUrl;
+  if (docBuilder === "dirhtml") {
+    // dirhtml builder
+    let dirname = docName + "/";
+    if (dirname.match(/\/index\/$/))
+      dirname = dirname.substring(0, dirname.length - 6);
+    else if (dirname === "index/") dirname = "";
+    requestUrl = contentRoot + dirname;
+    linkUrl = requestUrl;
+  } else {
+    // normal html builders
+    requestUrl = contentRoot + docName + docFileSuffix;
+    linkUrl = docName + docLinkSuffix;
+  }
+  let linkEl = listItem.appendChild(document.createElement("a"));
+  linkEl.href = linkUrl + anchor;
+  linkEl.dataset.score = score;
+  linkEl.innerHTML = title;
+  if (descr) {
+    listItem.appendChild(document.createElement("span")).innerHTML =
+      " (" + descr + ")";
+    // highlight search terms in the description
+    if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
+      highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
+  }
+  else if (showSearchSummary)
+    fetch(requestUrl)
+      .then((responseData) => responseData.text())
+      .then((data) => {
+        if (data)
+          listItem.appendChild(
+            Search.makeSearchSummary(data, searchTerms, anchor)
+          );
+        // highlight search terms in the summary
+        if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
+          highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
+      });
+  Search.output.appendChild(listItem);
+};
+const _finishSearch = (resultCount) => {
+  Search.stopPulse();
+  Search.title.innerText = _("Search Results");
+  if (!resultCount)
+    Search.status.innerText = Documentation.gettext(
+      "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories."
+    );
+  else
+    Search.status.innerText = Documentation.ngettext(
+      "Search finished, found one page matching the search query.",
+      "Search finished, found ${resultCount} pages matching the search query.",
+      resultCount,
+    ).replace('${resultCount}', resultCount);
+};
+const _displayNextItem = (
+  results,
+  resultCount,
+  searchTerms,
+  highlightTerms,
+) => {
+  // results left, load the summary and display it
+  // this is intended to be dynamic (don't sub resultsCount)
+  if (results.length) {
+    _displayItem(results.pop(), searchTerms, highlightTerms);
+    setTimeout(
+      () => _displayNextItem(results, resultCount, searchTerms, highlightTerms),
+      5
+    );
+  }
+  // search finished, update title and status message
+  else _finishSearch(resultCount);
+};
+// Helper function used by query() to order search results.
+// Each input is an array of [docname, title, anchor, descr, score, filename, kind].
+// Order the results by score (in opposite order of appearance, since the
+// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically.
+const _orderResultsByScoreThenName = (a, b) => {
+  const leftScore = a[4];
+  const rightScore = b[4];
+  if (leftScore === rightScore) {
+    // same score: sort alphabetically
+    const leftTitle = a[1].toLowerCase();
+    const rightTitle = b[1].toLowerCase();
+    if (leftTitle === rightTitle) return 0;
+    return leftTitle > rightTitle ? -1 : 1; // inverted is intentional
+  }
+  return leftScore > rightScore ? 1 : -1;
+};
+
+/**
+ * Default splitQuery function. Can be overridden in ``sphinx.search`` with a
+ * custom function per language.
+ *
+ * The regular expression works by splitting the string on consecutive characters
+ * that are not Unicode letters, numbers, underscores, or emoji characters.
+ * This is the same as ``\W+`` in Python, preserving the surrogate pair area.
+ */
+if (typeof splitQuery === "undefined") {
+  var splitQuery = (query) => query
+      .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu)
+      .filter(term => term)  // remove remaining empty strings
+}
+
+/**
+ * Search Module
+ */
+const Search = {
+  _index: null,
+  _queued_query: null,
+  _pulse_status: -1,
+
+  htmlToText: (htmlString, anchor) => {
+    const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html');
+    for (const removalQuery of [".headerlink", "script", "style"]) {
+      htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() });
+    }
+    if (anchor) {
+      const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`);
+      if (anchorContent) return anchorContent.textContent;
+
+      console.warn(
+        `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.`
+      );
+    }
+
+    // if anchor not specified or not found, fall back to main content
+    const docContent = htmlElement.querySelector('[role="main"]');
+    if (docContent) return docContent.textContent;
+
+    console.warn(
+      "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template."
+    );
+    return "";
+  },
+
+  init: () => {
+    const query = new URLSearchParams(window.location.search).get("q");
+    document
+      .querySelectorAll('input[name="q"]')
+      .forEach((el) => (el.value = query));
+    if (query) Search.performSearch(query);
+  },
+
+  loadIndex: (url) =>
+    (document.body.appendChild(document.createElement("script")).src = url),
+
+  setIndex: (index) => {
+    Search._index = index;
+    if (Search._queued_query !== null) {
+      const query = Search._queued_query;
+      Search._queued_query = null;
+      Search.query(query);
+    }
+  },
+
+  hasIndex: () => Search._index !== null,
+
+  deferQuery: (query) => (Search._queued_query = query),
+
+  stopPulse: () => (Search._pulse_status = -1),
+
+  startPulse: () => {
+    if (Search._pulse_status >= 0) return;
+
+    const pulse = () => {
+      Search._pulse_status = (Search._pulse_status + 1) % 4;
+      Search.dots.innerText = ".".repeat(Search._pulse_status);
+      if (Search._pulse_status >= 0) window.setTimeout(pulse, 500);
+    };
+    pulse();
+  },
+
+  /**
+   * perform a search for something (or wait until index is loaded)
+   */
+  performSearch: (query) => {
+    // create the required interface elements
+    const searchText = document.createElement("h2");
+    searchText.textContent = _("Searching");
+    const searchSummary = document.createElement("p");
+    searchSummary.classList.add("search-summary");
+    searchSummary.innerText = "";
+    const searchList = document.createElement("ul");
+    searchList.setAttribute("role", "list");
+    searchList.classList.add("search");
+
+    const out = document.getElementById("search-results");
+    Search.title = out.appendChild(searchText);
+    Search.dots = Search.title.appendChild(document.createElement("span"));
+    Search.status = out.appendChild(searchSummary);
+    Search.output = out.appendChild(searchList);
+
+    const searchProgress = document.getElementById("search-progress");
+    // Some themes don't use the search progress node
+    if (searchProgress) {
+      searchProgress.innerText = _("Preparing search...");
+    }
+    Search.startPulse();
+
+    // index already loaded, the browser was quick!
+    if (Search.hasIndex()) Search.query(query);
+    else Search.deferQuery(query);
+  },
+
+  _parseQuery: (query) => {
+    // stem the search terms and add them to the correct list
+    const stemmer = new Stemmer();
+    const searchTerms = new Set();
+    const excludedTerms = new Set();
+    const highlightTerms = new Set();
+    const objectTerms = new Set(splitQuery(query.toLowerCase().trim()));
+    splitQuery(query.trim()).forEach((queryTerm) => {
+      const queryTermLower = queryTerm.toLowerCase();
+
+      // maybe skip this "word"
+      // stopwords array is from language_data.js
+      if (
+        stopwords.indexOf(queryTermLower) !== -1 ||
+        queryTerm.match(/^\d+$/)
+      )
+        return;
+
+      // stem the word
+      let word = stemmer.stemWord(queryTermLower);
+      // select the correct list
+      if (word[0] === "-") excludedTerms.add(word.substr(1));
+      else {
+        searchTerms.add(word);
+        highlightTerms.add(queryTermLower);
+      }
+    });
+
+    if (SPHINX_HIGHLIGHT_ENABLED) {  // set in sphinx_highlight.js
+      localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" "))
+    }
+
+    // console.debug("SEARCH: searching for:");
+    // console.info("required: ", [...searchTerms]);
+    // console.info("excluded: ", [...excludedTerms]);
+
+    return [query, searchTerms, excludedTerms, highlightTerms, objectTerms];
+  },
+
+  /**
+   * execute search (requires search index to be loaded)
+   */
+  _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => {
+    const filenames = Search._index.filenames;
+    const docNames = Search._index.docnames;
+    const titles = Search._index.titles;
+    const allTitles = Search._index.alltitles;
+    const indexEntries = Search._index.indexentries;
+
+    // Collect multiple result groups to be sorted separately and then ordered.
+    // Each is an array of [docname, title, anchor, descr, score, filename, kind].
+    const normalResults = [];
+    const nonMainIndexResults = [];
+
+    _removeChildren(document.getElementById("search-progress"));
+
+    const queryLower = query.toLowerCase().trim();
+    for (const [title, foundTitles] of Object.entries(allTitles)) {
+      if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) {
+        for (const [file, id] of foundTitles) {
+          const score = Math.round(Scorer.title * queryLower.length / title.length);
+          const boost = titles[file] === title ? 1 : 0;  // add a boost for document titles
+          normalResults.push([
+            docNames[file],
+            titles[file] !== title ? `${titles[file]} > ${title}` : title,
+            id !== null ? "#" + id : "",
+            null,
+            score + boost,
+            filenames[file],
+            SearchResultKind.title,
+          ]);
+        }
+      }
+    }
+
+    // search for explicit entries in index directives
+    for (const [entry, foundEntries] of Object.entries(indexEntries)) {
+      if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) {
+        for (const [file, id, isMain] of foundEntries) {
+          const score = Math.round(100 * queryLower.length / entry.length);
+          const result = [
+            docNames[file],
+            titles[file],
+            id ? "#" + id : "",
+            null,
+            score,
+            filenames[file],
+            SearchResultKind.index,
+          ];
+          if (isMain) {
+            normalResults.push(result);
+          } else {
+            nonMainIndexResults.push(result);
+          }
+        }
+      }
+    }
+
+    // lookup as object
+    objectTerms.forEach((term) =>
+      normalResults.push(...Search.performObjectSearch(term, objectTerms))
+    );
+
+    // lookup as search terms in fulltext
+    normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms));
+
+    // let the scorer override scores with a custom scoring function
+    if (Scorer.score) {
+      normalResults.forEach((item) => (item[4] = Scorer.score(item)));
+      nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item)));
+    }
+
+    // Sort each group of results by score and then alphabetically by name.
+    normalResults.sort(_orderResultsByScoreThenName);
+    nonMainIndexResults.sort(_orderResultsByScoreThenName);
+
+    // Combine the result groups in (reverse) order.
+    // Non-main index entries are typically arbitrary cross-references,
+    // so display them after other results.
+    let results = [...nonMainIndexResults, ...normalResults];
+
+    // remove duplicate search results
+    // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept
+    let seen = new Set();
+    results = results.reverse().reduce((acc, result) => {
+      let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(',');
+      if (!seen.has(resultStr)) {
+        acc.push(result);
+        seen.add(resultStr);
+      }
+      return acc;
+    }, []);
+
+    return results.reverse();
+  },
+
+  query: (query) => {
+    const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query);
+    const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms);
+
+    // for debugging
+    //Search.lastresults = results.slice();  // a copy
+    // console.info("search results:", Search.lastresults);
+
+    // print the results
+    _displayNextItem(results, results.length, searchTerms, highlightTerms);
+  },
+
+  /**
+   * search for object names
+   */
+  performObjectSearch: (object, objectTerms) => {
+    const filenames = Search._index.filenames;
+    const docNames = Search._index.docnames;
+    const objects = Search._index.objects;
+    const objNames = Search._index.objnames;
+    const titles = Search._index.titles;
+
+    const results = [];
+
+    const objectSearchCallback = (prefix, match) => {
+      const name = match[4]
+      const fullname = (prefix ? prefix + "." : "") + name;
+      const fullnameLower = fullname.toLowerCase();
+      if (fullnameLower.indexOf(object) < 0) return;
+
+      let score = 0;
+      const parts = fullnameLower.split(".");
+
+      // check for different match types: exact matches of full name or
+      // "last name" (i.e. last dotted part)
+      if (fullnameLower === object || parts.slice(-1)[0] === object)
+        score += Scorer.objNameMatch;
+      else if (parts.slice(-1)[0].indexOf(object) > -1)
+        score += Scorer.objPartialMatch; // matches in last name
+
+      const objName = objNames[match[1]][2];
+      const title = titles[match[0]];
+
+      // If more than one term searched for, we require other words to be
+      // found in the name/title/description
+      const otherTerms = new Set(objectTerms);
+      otherTerms.delete(object);
+      if (otherTerms.size > 0) {
+        const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase();
+        if (
+          [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0)
+        )
+          return;
+      }
+
+      let anchor = match[3];
+      if (anchor === "") anchor = fullname;
+      else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname;
+
+      const descr = objName + _(", in ") + title;
+
+      // add custom score for some objects according to scorer
+      if (Scorer.objPrio.hasOwnProperty(match[2]))
+        score += Scorer.objPrio[match[2]];
+      else score += Scorer.objPrioDefault;
+
+      results.push([
+        docNames[match[0]],
+        fullname,
+        "#" + anchor,
+        descr,
+        score,
+        filenames[match[0]],
+        SearchResultKind.object,
+      ]);
+    };
+    Object.keys(objects).forEach((prefix) =>
+      objects[prefix].forEach((array) =>
+        objectSearchCallback(prefix, array)
+      )
+    );
+    return results;
+  },
+
+  /**
+   * search for full-text terms in the index
+   */
+  performTermsSearch: (searchTerms, excludedTerms) => {
+    // prepare search
+    const terms = Search._index.terms;
+    const titleTerms = Search._index.titleterms;
+    const filenames = Search._index.filenames;
+    const docNames = Search._index.docnames;
+    const titles = Search._index.titles;
+
+    const scoreMap = new Map();
+    const fileMap = new Map();
+
+    // perform the search on the required terms
+    searchTerms.forEach((word) => {
+      const files = [];
+      // find documents, if any, containing the query word in their text/title term indices
+      // use Object.hasOwnProperty to avoid mismatching against prototype properties
+      const arr = [
+        { files: terms.hasOwnProperty(word) ? terms[word] : undefined, score: Scorer.term },
+        { files: titleTerms.hasOwnProperty(word) ? titleTerms[word] : undefined, score: Scorer.title },
+      ];
+      // add support for partial matches
+      if (word.length > 2) {
+        const escapedWord = _escapeRegExp(word);
+        if (!terms.hasOwnProperty(word)) {
+          Object.keys(terms).forEach((term) => {
+            if (term.match(escapedWord))
+              arr.push({ files: terms[term], score: Scorer.partialTerm });
+          });
+        }
+        if (!titleTerms.hasOwnProperty(word)) {
+          Object.keys(titleTerms).forEach((term) => {
+            if (term.match(escapedWord))
+              arr.push({ files: titleTerms[term], score: Scorer.partialTitle });
+          });
+        }
+      }
+
+      // no match but word was a required one
+      if (arr.every((record) => record.files === undefined)) return;
+
+      // found search word in contents
+      arr.forEach((record) => {
+        if (record.files === undefined) return;
+
+        let recordFiles = record.files;
+        if (recordFiles.length === undefined) recordFiles = [recordFiles];
+        files.push(...recordFiles);
+
+        // set score for the word in each file
+        recordFiles.forEach((file) => {
+          if (!scoreMap.has(file)) scoreMap.set(file, new Map());
+          const fileScores = scoreMap.get(file);
+          fileScores.set(word, record.score);
+        });
+      });
+
+      // create the mapping
+      files.forEach((file) => {
+        if (!fileMap.has(file)) fileMap.set(file, [word]);
+        else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word);
+      });
+    });
+
+    // now check if the files don't contain excluded terms
+    const results = [];
+    for (const [file, wordList] of fileMap) {
+      // check if all requirements are matched
+
+      // as search terms with length < 3 are discarded
+      const filteredTermCount = [...searchTerms].filter(
+        (term) => term.length > 2
+      ).length;
+      if (
+        wordList.length !== searchTerms.size &&
+        wordList.length !== filteredTermCount
+      )
+        continue;
+
+      // ensure that none of the excluded terms is in the search result
+      if (
+        [...excludedTerms].some(
+          (term) =>
+            terms[term] === file ||
+            titleTerms[term] === file ||
+            (terms[term] || []).includes(file) ||
+            (titleTerms[term] || []).includes(file)
+        )
+      )
+        break;
+
+      // select one (max) score for the file.
+      const score = Math.max(...wordList.map((w) => scoreMap.get(file).get(w)));
+      // add result to the result list
+      results.push([
+        docNames[file],
+        titles[file],
+        "",
+        null,
+        score,
+        filenames[file],
+        SearchResultKind.text,
+      ]);
+    }
+    return results;
+  },
+
+  /**
+   * helper function to return a node containing the
+   * search summary for a given text. keywords is a list
+   * of stemmed words.
+   */
+  makeSearchSummary: (htmlText, keywords, anchor) => {
+    const text = Search.htmlToText(htmlText, anchor);
+    if (text === "") return null;
+
+    const textLower = text.toLowerCase();
+    const actualStartPosition = [...keywords]
+      .map((k) => textLower.indexOf(k.toLowerCase()))
+      .filter((i) => i > -1)
+      .slice(-1)[0];
+    const startWithContext = Math.max(actualStartPosition - 120, 0);
+
+    const top = startWithContext === 0 ? "" : "...";
+    const tail = startWithContext + 240 < text.length ? "..." : "";
+
+    let summary = document.createElement("p");
+    summary.classList.add("context");
+    summary.textContent = top + text.substr(startWithContext, 240).trim() + tail;
+
+    return summary;
+  },
+};
+
+_ready(Search.init);

_static/sphinx_highlight.js

@@ -0,0 +1,154 @@
+/* Highlighting utilities for Sphinx HTML documentation. */
+"use strict";
+
+const SPHINX_HIGHLIGHT_ENABLED = true
+
+/**
+ * highlight a given string on a node by wrapping it in
+ * span elements with the given class name.
+ */
+const _highlight = (node, addItems, text, className) => {
+  if (node.nodeType === Node.TEXT_NODE) {
+    const val = node.nodeValue;
+    const parent = node.parentNode;
+    const pos = val.toLowerCase().indexOf(text);
+    if (
+      pos >= 0 &&
+      !parent.classList.contains(className) &&
+      !parent.classList.contains("nohighlight")
+    ) {
+      let span;
+
+      const closestNode = parent.closest("body, svg, foreignObject");
+      const isInSVG = closestNode && closestNode.matches("svg");
+      if (isInSVG) {
+        span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
+      } else {
+        span = document.createElement("span");
+        span.classList.add(className);
+      }
+
+      span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+      const rest = document.createTextNode(val.substr(pos + text.length));
+      parent.insertBefore(
+        span,
+        parent.insertBefore(
+          rest,
+          node.nextSibling
+        )
+      );
+      node.nodeValue = val.substr(0, pos);
+      /* There may be more occurrences of search term in this node. So call this
+       * function recursively on the remaining fragment.
+       */
+      _highlight(rest, addItems, text, className);
+
+      if (isInSVG) {
+        const rect = document.createElementNS(
+          "http://www.w3.org/2000/svg",
+          "rect"
+        );
+        const bbox = parent.getBBox();
+        rect.x.baseVal.value = bbox.x;
+        rect.y.baseVal.value = bbox.y;
+        rect.width.baseVal.value = bbox.width;
+        rect.height.baseVal.value = bbox.height;
+        rect.setAttribute("class", className);
+        addItems.push({ parent: parent, target: rect });
+      }
+    }
+  } else if (node.matches && !node.matches("button, select, textarea")) {
+    node.childNodes.forEach((el) => _highlight(el, addItems, text, className));
+  }
+};
+const _highlightText = (thisNode, text, className) => {
+  let addItems = [];
+  _highlight(thisNode, addItems, text, className);
+  addItems.forEach((obj) =>
+    obj.parent.insertAdjacentElement("beforebegin", obj.target)
+  );
+};
+
+/**
+ * Small JavaScript module for the documentation.
+ */
+const SphinxHighlight = {
+
+  /**
+   * highlight the search words provided in localstorage in the text
+   */
+  highlightSearchWords: () => {
+    if (!SPHINX_HIGHLIGHT_ENABLED) return;  // bail if no highlight
+
+    // get and clear terms from localstorage
+    const url = new URL(window.location);
+    const highlight =
+        localStorage.getItem("sphinx_highlight_terms")
+        || url.searchParams.get("highlight")
+        || "";
+    localStorage.removeItem("sphinx_highlight_terms")
+    url.searchParams.delete("highlight");
+    window.history.replaceState({}, "", url);
+
+    // get individual terms from highlight string
+    const terms = highlight.toLowerCase().split(/\s+/).filter(x => x);
+    if (terms.length === 0) return; // nothing to do
+
+    // There should never be more than one element matching "div.body"
+    const divBody = document.querySelectorAll("div.body");
+    const body = divBody.length ? divBody[0] : document.querySelector("body");
+    window.setTimeout(() => {
+      terms.forEach((term) => _highlightText(body, term, "highlighted"));
+    }, 10);
+
+    const searchBox = document.getElementById("searchbox");
+    if (searchBox === null) return;
+    searchBox.appendChild(
+      document
+        .createRange()
+        .createContextualFragment(
+          '<p class="highlight-link">' +
+            '<a href="javascript:SphinxHighlight.hideSearchWords()">' +
+            _("Hide Search Matches") +
+            "</a></p>"
+        )
+    );
+  },
+
+  /**
+   * helper function to hide the search marks again
+   */
+  hideSearchWords: () => {
+    document
+      .querySelectorAll("#searchbox .highlight-link")
+      .forEach((el) => el.remove());
+    document
+      .querySelectorAll("span.highlighted")
+      .forEach((el) => el.classList.remove("highlighted"));
+    localStorage.removeItem("sphinx_highlight_terms")
+  },
+
+  initEscapeListener: () => {
+    // only install a listener if it is really needed
+    if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return;
+
+    document.addEventListener("keydown", (event) => {
+      // bail for input elements
+      if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return;
+      // bail with special keys
+      if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return;
+      if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) {
+        SphinxHighlight.hideSearchWords();
+        event.preventDefault();
+      }
+    });
+  },
+};
+
+_ready(() => {
+  /* Do not call highlightSearchWords() when we are on the search page.
+   * It will highlight words from the *previous* search query.
+   */
+  if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords();
+  SphinxHighlight.initEscapeListener();
+});

api_reference.html

@@ -0,0 +1,294 @@
+<!DOCTYPE html>
+
+<html lang="en" data-content_root="./">
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
+
+    <title>API Reference &#8212; optifik  documentation</title>
+    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=5ecbeea2" />
+    <link rel="stylesheet" type="text/css" href="_static/basic.css?v=b08954a9" />
+    <link rel="stylesheet" type="text/css" href="_static/alabaster.css?v=27fed22d" />
+    <script src="_static/documentation_options.js?v=5929fcd5"></script>
+    <script src="_static/doctools.js?v=9bcbadda"></script>
+    <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+    <link rel="index" title="Index" href="genindex.html" />
+    <link rel="search" title="Search" href="search.html" />
+    <link rel="next" title="Examples" href="examples.html" />
+    <link rel="prev" title="Installation" href="installation.html" />
+   
+  <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+  
+
+  
+  
+
+  </head><body>
+  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          
+
+          <div class="body" role="main">
+            
+  <section id="api-reference">
+<h1>API Reference<a class="headerlink" href="#api-reference" title="Link to this heading">¶</a></h1>
+<p>Below is the complete reference for Optifik’s public API.</p>
+<section id="module-optifik.io">
+<span id="io"></span><h2>io<a class="headerlink" href="#module-optifik.io" title="Link to this heading">¶</a></h2>
+<dl class="py function">
+<dt class="sig sig-object py" id="optifik.io.load_spectrum">
+<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>
+<dd><p>Load a spectrum file.</p>
+<p>TODO : describe expected format</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><dl class="simple">
+<dt><strong>spectrum_path</strong><span class="classifier">string</span></dt><dd><p>File path.</p>
+</dd>
+<dt><strong>wavelength_min</strong><span class="classifier">scalar, optional</span></dt><dd><p>Cut the data at this minimum wavelength (included).</p>
+</dd>
+<dt><strong>wavelength_max</strong><span class="classifier">scalar, optional</span></dt><dd><p>Cut the data at this maximum wavelength (included).</p>
+</dd>
+<dt><strong>delimiter</strong><span class="classifier">string, optional</span></dt><dd><p>Delimiter between columns in the datafile.</p>
+</dd>
+</dl>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><dl class="simple">
+<dt><strong>values</strong><span class="classifier">arrays</span></dt><dd><p>(lamdbas, intensities)</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+</section>
+<section id="module-optifik.fft">
+<span id="fft"></span><h2>fft<a class="headerlink" href="#module-optifik.fft" title="Link to this heading">¶</a></h2>
+<dl class="py function">
+<dt class="sig sig-object py" id="optifik.fft.thickness_from_fft">
+<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>
+<dd><p>Determine the tickness by Fast Fourier Transform.</p>
+<dl class="field-list">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><dl class="simple">
+<dt><strong>wavelengths</strong><span class="classifier">array</span></dt><dd><p>Wavelength values in nm.</p>
+</dd>
+<dt><strong>intensities</strong><span class="classifier">array</span></dt><dd><p>Intensity values.</p>
+</dd>
+<dt><strong>refractive_index</strong><span class="classifier">scalar, optional</span></dt><dd><p>Value of the refractive index of the medium.</p>
+</dd>
+<dt><strong>num_half_space</strong><span class="classifier">scalar, optional</span></dt><dd><p>Number of points to compute FFT’s half space.
+If <cite>None</cite>, default corresponds to <cite>10*len(wavelengths)</cite>.</p>
+</dd>
+<dt><strong>plot</strong><span class="classifier">boolean, optional</span></dt><dd><p>Show plot of the transformed signal and the peak detection.</p>
+</dd>
+</dl>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><dl>
+<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>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+</section>
+<section id="module-optifik.minmax">
+<span id="minmax"></span><h2>minmax<a class="headerlink" href="#module-optifik.minmax" title="Link to this heading">¶</a></h2>
+<dl class="py function">
+<dt class="sig sig-object py" id="optifik.minmax.thickness_from_minmax">
+<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>
+<dd><p>Return the thickness from a min-max detection.</p>
+<dl class="field-list">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><dl class="simple">
+<dt><strong>wavelengths</strong><span class="classifier">array</span></dt><dd><p>Wavelength values in nm.</p>
+</dd>
+<dt><strong>intensities</strong><span class="classifier">array</span></dt><dd><p>Intensity values.</p>
+</dd>
+<dt><strong>refractive_index</strong><span class="classifier">scalar, optional</span></dt><dd><p>Value of the refractive index of the medium.</p>
+</dd>
+<dt><strong>min_peak_prominence</strong><span class="classifier">scalar, optional</span></dt><dd><p>Required prominence of peaks.</p>
+</dd>
+<dt><strong>min_peak_distance</strong><span class="classifier">scalar, optional</span></dt><dd><p>Minimum distance between peaks.</p>
+</dd>
+<dt><strong>method</strong><span class="classifier">string, optional</span></dt><dd><p>Either ‘linreg’ for linear regression or ‘ransac’
+for Randon Sampling Consensus.</p>
+</dd>
+<dt><strong>plot</strong><span class="classifier">boolean, optional</span></dt><dd><p>Show plots of peak detection and lin regression.</p>
+</dd>
+</dl>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><dl>
+<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>
+</dd>
+</dl>
+</dd>
+</dl>
+<p class="rubric">Notes</p>
+<p>For more details about <cite>min_peak_prominence</cite> and <cite>min_peak_distance</cite>,
+see the documentation of <cite>scipy.signal.find_peaks</cite>. This function
+is used to find extrema.</p>
+</dd></dl>
+
+</section>
+<section id="module-optifik.scheludko">
+<span id="scheludko"></span><h2>scheludko<a class="headerlink" href="#module-optifik.scheludko" title="Link to this heading">¶</a></h2>
+<dl class="py function">
+<dt class="sig sig-object py" id="optifik.scheludko.get_default_start_stop_wavelengths">
+<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>
+<dd><p>Returns the start and stop wavelength values of the last monotonic branch.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><dl class="simple">
+<dt><strong>wavelengths</strong><span class="classifier">array</span></dt><dd><p>Wavelength values in nm.</p>
+</dd>
+<dt><strong>intensities</strong><span class="classifier">array</span></dt><dd><p>Intensity values.</p>
+</dd>
+<dt><strong>refractive_index</strong><span class="classifier">scalar, optional</span></dt><dd><p>Value of the refractive index of the medium.</p>
+</dd>
+<dt><strong>min_peak_prominence</strong><span class="classifier">scalar</span></dt><dd><p>Required prominence of peaks.</p>
+</dd>
+<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>
+</dd>
+</dl>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><dl class="simple">
+<dt><strong>wavelength_start</strong><span class="classifier">scalar</span></dt><dd></dd>
+<dt><strong>wavelength_stop</strong><span class="classifier">scalar</span></dt><dd></dd>
+</dl>
+</dd>
+<dt class="field-odd">Raises<span class="colon">:</span></dt>
+<dd class="field-odd"><dl class="simple">
+<dt>RuntimeError</dt><dd><p>if at least one maximum and one minimum are not detected.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="optifik.scheludko.thickness_from_scheludko">
+<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>
+<dd><p>Compute the film thickness based on Scheludko method.</p>
+<dl class="field-list">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><dl class="simple">
+<dt><strong>wavelengths</strong><span class="classifier">array</span></dt><dd><p>Wavelength values in nm.</p>
+</dd>
+<dt><strong>intensities</strong><span class="classifier">array</span></dt><dd><p>Intensity values.</p>
+</dd>
+<dt><strong>refractive_index</strong><span class="classifier">scalar, optional</span></dt><dd><p>Value of the refractive index of the medium.</p>
+</dd>
+<dt><strong>wavelength_start</strong><span class="classifier">scalar, optional</span></dt><dd><p>Starting value of a monotonic branch.
+Mandatory if interference_order != 0.</p>
+</dd>
+<dt><strong>wavelength_stop</strong><span class="classifier">scalar, optional</span></dt><dd><p>Stoping value of a monotonic branch.
+Mandatory if interference_order != 0.</p>
+</dd>
+<dt><strong>interference_order</strong><span class="classifier">scalar, optional</span></dt><dd><p>Interference order, zero or positive integer.
+If set to None, the value is guessed.</p>
+</dd>
+<dt><strong>intensities_void</strong><span class="classifier">array, optional</span></dt><dd><p>Intensity in absence of a film.
+Mandatory if interference_order == 0.</p>
+</dd>
+<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>
+</dd>
+</dl>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><dl>
+<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>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+</section>
+</section>
+
+
+          </div>
+          
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="Main">
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+<h1 class="logo"><a href="index.html">optifik</a></h1>
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+<search id="searchbox" style="display: none" role="search">
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+<script>document.getElementById('searchbox').style.display = "block"</script><h3>Navigation</h3>
+<p class="caption" role="heading"><span class="caption-text">Documentation</span></p>
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+<li class="toctree-l1 current"><a class="current reference internal" href="#">API Reference</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#module-optifik.io">io</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#module-optifik.fft">fft</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#module-optifik.minmax">minmax</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#module-optifik.scheludko">scheludko</a></li>
+</ul>
+</li>
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+</ul>
+
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+  <li><a href="index.html">Documentation overview</a><ul>
+      <li>Previous: <a href="installation.html" title="previous chapter">Installation</a></li>
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check.py

@@ -1,234 +0,0 @@
-
-
-import os
-import matplotlib.pyplot as plt
-
-
-
-
-from optifik.analysis import *
-from optifik import io
-
-plt.rc('text', usetex=True)
-plt.rcParams.update({
-    'axes.labelsize': 26,
-    'xtick.labelsize': 32,
-    'ytick.labelsize': 32,
-    'legend.fontsize': 23,
-})
-
-
-def minmax():
-    ##### Chemin du dossier contenant le spectre #####
-    from optifik.scheludko import thickness_from_scheludko
-    from optifik.scheludko import get_default_start_stop_wavelengths
-
-    DATA_FOLDER = os.path.abspath(os.path.join(os.path.curdir, 'tests', 'basic'))
-
-    #SAVE_FOLDER = DATA_FOLDER
-
-    # FILE_NAME = '003582.xy' #FFT Exemple -> FFT 3524.51
-    # FILE_NAME = '000004310.xy' #OOspectro Exemple -> minmax 1338.35
-    # FILE_NAME = '000005253.xy'#Scheludko 4 pics Exemple -> scheludko ²
-    # FILE_NAME = '000006544.xy'#Scheludko 2 pics Exemple -> ombre ## Diviser prominence FFT par 2
-    # FILE_NAME = '000018918.xy' #Scheludko 1 pic max Exemple -> ombre ## Diviser prominence FFT par 2
-
-    FILE_NAME = '000004310.xy' #TEST#
-    spectrum_file = os.path.join(DATA_FOLDER, FILE_NAME)
-
-
-
-    lambdas, intensities = io.load_spectrum(spectrum_file)
-    plot_spectrum(lambdas, intensities, title='Raw')
-
-    lambdas, intensities = io.load_spectrum(spectrum_file, wavelength_min=450)
-    plot_spectrum(lambdas, intensities, title='Raw, cropped')
-
-    smoothed_intensities = smooth_intensities(intensities)
-    plot_spectrum(lambdas, smoothed_intensities, title='Smoothed')
-
-    refractive_index =  1.324188 + 3102.060378 / (lambdas**2)
-    prominence = 0.025
-    peaks_min, peaks_max = finds_peak(lambdas, smoothed_intensities,
-                                                     min_peak_prominence=prominence,
-                                                     plot=True)
-
-
-
-def play_order1():
-    ##### Chemin du dossier contenant le spectre #####
-    from optifik.scheludko import thickness_from_scheludko
-    from optifik.scheludko import get_default_start_stop_wavelengths
-
-    DATA_FOLDER = os.path.abspath(os.path.join(os.path.curdir, 'tests', 'basic'))
-
-    #SAVE_FOLDER = DATA_FOLDER
-
-    # FILE_NAME = '003582.xy' #FFT Exemple -> FFT 3524.51
-    # FILE_NAME = '000004310.xy' #OOspectro Exemple -> minmax 1338.35
-    # FILE_NAME = '000005253.xy'#Scheludko 4 pics Exemple -> scheludko ²
-    # FILE_NAME = '000006544.xy'#Scheludko 2 pics Exemple -> ombre ## Diviser prominence FFT par 2
-    # FILE_NAME = '000018918.xy' #Scheludko 1 pic max Exemple -> ombre ## Diviser prominence FFT par 2
-
-    FILE_NAME = '000004310.xy' #TEST#
-    spectrum_file = os.path.join(DATA_FOLDER, FILE_NAME)
-
-
-    spectrum_file = 'tests/spectraVictor2/order5/T5817.xy' #TEST#
-
-    lambdas, intensities = io.load_spectrum(spectrum_file)
-    plot_spectrum(lambdas, intensities, title='Raw')
-
-    lambdas, intensities = io.load_spectrum(spectrum_file, wavelength_min=450)
-    plot_spectrum(lambdas, intensities, title='Raw, cropped')
-
-    smoothed_intensities = smooth_intensities(intensities)
-    plot_spectrum(lambdas, smoothed_intensities, title='Smoothed')
-
-    refractive_index =  1.324188 + 3102.060378 / (lambdas**2)
-    prominence = 0.025
-    peaks_min, peaks_max = finds_peak(lambdas, smoothed_intensities,
-                                                     min_peak_prominence=prominence,
-                                                     plot=True)
-
-    w_start, w_stop = get_default_start_stop_wavelengths(lambdas,
-                                                         smoothed_intensities,
-                                                         refractive_index,
-                                                         min_peak_prominence=prominence,
-                                                         plot=True)
-
-
-    result = thickness_from_scheludko(lambdas,
-                                      smoothed_intensities,
-                                      refractive_index=refractive_index,
-                                      wavelength_start=w_start,
-                                      wavelength_stop=w_stop,
-                                      interference_order=None,
-                                      plot=True)
-
-def play_order0():
-    ##### Chemin du dossier contenant le spectre #####
-    from optifik.scheludko import thickness_for_order0
-
-    DATA_FOLDER = os.path.abspath(os.path.join(os.path.curdir, 'tests', 'basic'))
-
-    #SAVE_FOLDER = DATA_FOLDER
-
-    # FILE_NAME = '003582.xy' #FFT Exemple -> FFT 3524.51
-    # FILE_NAME = '000004310.xy' #OOspectro Exemple -> minmax 1338.35
-    # FILE_NAME = '000005253.xy'#Scheludko 4 pics Exemple -> scheludko ²
-    # FILE_NAME = '000006544.xy'#Scheludko 2 pics Exemple -> ombre ## Diviser prominence FFT par 2
-    # FILE_NAME = '000018918.xy' #Scheludko 1 pic max Exemple -> ombre ## Diviser prominence FFT par 2
-
-    FILE_NAME = '000004310.xy' #TEST#
-    spectrum_file = os.path.join(DATA_FOLDER, FILE_NAME)
-
-
-    spectrum_file = 'tests/spectraVictor2/order0/T16053.xy' #TEST#
-
-    lambdas, intensities = io.load_spectrum(spectrum_file)
-    plot_spectrum(lambdas, intensities, title='Raw')
-
-    lambdas, intensities = io.load_spectrum(spectrum_file, wavelength_min=450)
-    plot_spectrum(lambdas, intensities, title='Raw, cropped')
-
-
-    smoothed_intensities = smooth_intensities(intensities)
-    plot_spectrum(lambdas, smoothed_intensities, title='Smoothed')
-
-    refractive_index =  1.324188 + 3102.060378 / (lambdas**2)
-    prominence = .02
-    peaks_min, peaks_max = finds_peak(lambdas, smoothed_intensities,
-                                                     min_peak_prominence=prominence,
-                                                     plot=True)
-
-    result = thickness_for_order0(lambdas, smoothed_intensities,
-                                      refractive_index=refractive_index,
-                                      min_peak_prominence=prominence,
-                                      plot=True)
-
-
-
-def check_basic():
-
-    ##### Chemin du dossier contenant le spectre #####
-
-    DATA_FOLDER = os.path.abspath(os.path.join(os.path.curdir, 'tests', 'basic'))
-
-    #SAVE_FOLDER = DATA_FOLDER
-
-    # FILE_NAME = '003582.xy' #FFT Exemple -> FFT 3524.51
-    # FILE_NAME = '000004310.xy' #OOspectro Exemple -> minmax 1338.35
-    # FILE_NAME = '000005253.xy'#Scheludko 4 pics Exemple -> scheludko ²
-    # FILE_NAME = '000006544.xy'#Scheludko 2 pics Exemple -> ombre ## Diviser prominence FFT par 2
-    # FILE_NAME = '000018918.xy' #Scheludko 1 pic max Exemple -> ombre ## Diviser prominence FFT par 2
-
-    FILE_NAME = '000004310.xy' #TEST#
-
-    spectrum_file = os.path.join(DATA_FOLDER, FILE_NAME)
-    auto(spectrum_file, plot=False)
-
-
-def check_SV1():
-
-
-    DATA_FOLDER = os.path.join('tests', 'spectraVictor1')
-
-    import yaml
-
-    yaml_file = os.path.join(DATA_FOLDER, 'known_value.yaml')
-    with open(yaml_file, "r") as yaml_file:
-        thickness_dict = yaml.safe_load(yaml_file)
-
-
-    for fn, val in thickness_dict.items():
-        #auto(DATA_FOLDER, fn)
-
-        spectre_file = os.path.join(DATA_FOLDER, fn)
-
-        lambdas, raw_intensities = load_spectrum(spectre_file, wavelength_min=450)
-
-        ##### Affichage du spectre lissé #####
-
-        #smoothed_intensities, intensities, lambdas = Data_Smoothed(spectre_file)
-
-        smoothed_intensities = smooth_intensities(raw_intensities)
-
-
-#        smoothed_intensities, intensities, lambdas = Data_Smoothed(spectre_file)
-
-        ##### Indice Optique en fonction de Lambda #####
-
-        indice =  1.324188 + 3102.060378 / (lambdas**2)
-
-        prominence = 0.02
-
-        ##### Find Peak #####
-
-        peaks_min, peaks_max = finds_peak(lambdas, smoothed_intensities,
-                                                     min_peak_prominence=prominence,
-                                                     plot=False)
-
-        result = thickness_from_minmax(lambdas,
-                                                 smoothed_intensities,
-                                                 refractive_index=indice,
-                                                 min_peak_prominence=prominence)
-        print(f'thickness: {result.thickness:.2f} nm')
-
-
-        print(f'expected: {val}')
-        print('#-' * 10)
-
-
-
-
-if __name__ == '__main__':
-
-    from optifik.utils import is_latex_installed
-    print(is_latex_installed())
-
-    #check_basic()
-    #check_SV1()
-    #play()
-    play_order1()
-

data/basic/003582.xy

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