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<h1>Source code for optifik.fft</h1><div class="highlight"><pre>
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<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>
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<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>
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<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>
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<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>
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<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>
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<div class="viewcode-block" id="thickness_from_fft">
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<a class="viewcode-back" href="../../api_reference.html#optifik.fft.thickness_from_fft">[docs]</a>
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<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>
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<span class="n">refractive_index</span><span class="p">,</span>
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<span class="n">num_half_space</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
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<span class="n">plot</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
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<span class="w"> </span><span class="sd">"""</span>
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<span class="sd"> Determine the tickness by Fast Fourier Transform.</span>
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<span class="sd"> Parameters</span>
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<span class="sd"> ----------</span>
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<span class="sd"> wavelengths : array</span>
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<span class="sd"> Wavelength values in nm.</span>
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<span class="sd"> intensities : array</span>
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<span class="sd"> Intensity values.</span>
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<span class="sd"> refractive_index : scalar, optional</span>
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<span class="sd"> Value of the refractive index of the medium.</span>
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<span class="sd"> num_half_space : scalar, optional</span>
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<span class="sd"> Number of points to compute FFT's half space.</span>
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<span class="sd"> If `None`, default corresponds to `10*len(wavelengths)`.</span>
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<span class="sd"> plot : boolean, optional</span>
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<span class="sd"> Show plot of the transformed signal and the peak detection.</span>
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<span class="sd"> Returns</span>
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<span class="sd"> -------</span>
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<span class="sd"> results : Instance of `OptimizeResult` class.</span>
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<span class="sd"> The attribute `thickness` gives the thickness value in nm.</span>
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<span class="sd"> """</span>
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<span class="k">if</span> <span class="n">plot</span><span class="p">:</span>
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<span class="n">setup_matplotlib</span><span class="p">()</span>
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<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>
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<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>
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<span class="c1"># FFT requires evenly spaced data.</span>
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<span class="c1"># So, we interpolate the signal.</span>
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<span class="c1"># Interpolate to get a linear increase of 1 / wavelengths.</span>
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<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>
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<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>
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<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>
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<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>
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<span class="mi">2</span><span class="o">*</span><span class="n">num_half_space</span><span class="p">)</span>
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<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>
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<span class="c1"># Perform FFT</span>
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<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>
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<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>
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<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>
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<span class="c1"># The FFT is symetrical over [0:N] and [N:2N].</span>
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<span class="c1"># Keep over [N:2N], ie for positive freq.</span>
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<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>
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<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>
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<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>
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<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>
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<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>
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<span class="k">if</span> <span class="n">plot</span><span class="p">:</span>
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<span class="n">plt</span><span class="o">.</span><span class="n">figure</span><span class="p">()</span>
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<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>
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<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">'o'</span><span class="p">)</span>
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<span class="n">plt</span><span class="o">.</span><span class="n">xlabel</span><span class="p">(</span><span class="s1">'Frequency'</span><span class="p">)</span>
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<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">'FFT($I^*$)'</span><span class="p">)</span>
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<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">'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">'</span><span class="p">)</span>
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<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>
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</pre></div>
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<h1>Source code for optifik.io</h1><div class="highlight"><pre>
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<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>
|
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|
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<div class="viewcode-block" id="load_spectrum">
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<a class="viewcode-back" href="../../api_reference.html#optifik.io.load_spectrum">[docs]</a>
|
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<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">','</span><span class="p">):</span>
|
||||
<span class="w"> </span><span class="sd">"""</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"> """</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">>=</span> <span class="n">wavelength_min</span><span class="p">)</span> <span class="o">&</span> <span class="p">(</span><span class="n">lambdas</span> <span class="o"><=</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>
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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">'linreg'</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">"""</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 'linreg' for linear regression or 'ransac'</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"> """</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"><</span> <span class="mi">2</span><span class="p">:</span>
|
||||
<span class="c1"># Can'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">'ransac'</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">'extremum n°'</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">'$n$($\lambda$) / $\lambda$'</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">'xb'</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">'Inliers'</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">'+r'</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">'Outliers'</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">'-g'</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="s1">'Fit'</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">'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'</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">'linreg'</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">'extremum n°'</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">'$n$($\lambda$) / $\lambda$'</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">'s'</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="s1">'Extrema'</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">'Fit'</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">'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'</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">'Wrong method'</span><span class="p">)</span></div>
|
||||
|
||||
</pre></div>
|
||||
|
||||
</div>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
<div class="sphinxsidebar" role="navigation" aria-label="Main">
|
||||
<div class="sphinxsidebarwrapper">
|
||||
<h1 class="logo"><a href="../../index.html">optifik</a></h1>
|
||||
|
||||
|
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|
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||||
|
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|
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<search id="searchbox" style="display: none" role="search">
|
||||
<div class="searchformwrapper">
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||||
<form class="search" action="../../search.html" method="get">
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<input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false" placeholder="Search"/>
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<script>document.getElementById('searchbox').style.display = "block"</script><h3>Navigation</h3>
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<p class="caption" role="heading"><span class="caption-text">Documentation</span></p>
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<li class="toctree-l1"><a class="reference internal" href="../../installation.html">Installation</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="../../api_reference.html">API Reference</a></li>
|
||||
<li class="toctree-l1"><a class="reference internal" href="../../examples.html">Examples</a></li>
|
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</ul>
|
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<div class="relations">
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<h3>Related Topics</h3>
|
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<ul>
|
||||
<li><a href="../../index.html">Documentation overview</a><ul>
|
||||
<li><a href="../index.html">Module code</a><ul>
|
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|
||||
</ul></li>
|
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|
||||
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|
||||
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|
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|
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|
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|
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|
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|
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</div>
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</div>
|
||||
<div class="clearer"></div>
|
||||
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|
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<div class="footer">
|
||||
©2025, F. Boulogne et al..
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471
docs/_build/html/_modules/optifik/scheludko.html
vendored
Normal file
471
docs/_build/html/_modules/optifik/scheludko.html
vendored
Normal file
|
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@ -0,0 +1,471 @@
|
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<!DOCTYPE html>
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<html lang="en" data-content_root="../../">
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<title>optifik.scheludko — optifik documentation</title>
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<div class="document">
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<div class="body" role="main">
|
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|
||||
<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">"""</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"> """</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">"""</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"> """</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">"""</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"> """</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">"""</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"> """</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">''</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">'Failed to detect at least one minimum. '</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">'Failed to detect at least one maximum. '</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">"""</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"> """</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">></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">'wavelength_start and wavelength_stop must be passed for interference_order != 0.'</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">></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">'wavelength_start and wavelength_stop are swapped.'</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">>=</span> <span class="n">wavelength_start</span><span class="p">)</span> <span class="o">&</span> <span class="p">(</span><span class="n">wavelengths</span> <span class="o"><=</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">'$h$ ($\mathrm{{nm}}$)'</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">'$\lambda$ ($ \mathrm</span><span class="si">{nm}</span><span class="s1"> $)'</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">"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"</span><span class="p">)</span>
|
||||
|
||||
<span class="k">if</span> <span class="n">difference</span> <span class="o"><</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">'.'</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">"Order=</span><span class="si">{</span><span class="n">_order</span><span class="si">}</span><span class="s2">"</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">'Failed to detect a single maximum peak.'</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">>=</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">></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">'interference_order must be >= 0.'</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">'bo-'</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">'$\mathrm{{Smoothed}}\ \mathrm{{Data}}$'</span><span class="p">)</span>
|
||||
|
||||
<span class="c1"># Scheludko</span>
|
||||
<span class="n">label</span> <span class="o">=</span> <span class="sa">rf</span><span class="s1">'$\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">)$'</span>
|
||||
<span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">wavelengths_masked</span><span class="p">,</span> <span class="n">DeltaScheludko</span><span class="p">,</span>
|
||||
<span class="s1">'go-'</span><span class="p">,</span> <span class="n">markersize</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="n">label</span><span class="p">)</span>
|
||||
<span class="c1"># Fit</span>
|
||||
<span class="n">label</span> <span class="o">=</span> <span class="sa">rf</span><span class="s1">'$\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">)$'</span>
|
||||
<span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">wavelengths_masked</span><span class="p">,</span> <span class="n">Delta_values</span><span class="p">,</span>
|
||||
<span class="s1">'ro-'</span><span class="p">,</span> <span class="n">markersize</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span>
|
||||
<span class="n">label</span><span class="o">=</span><span class="n">label</span><span class="p">)</span>
|
||||
|
||||
<span class="n">plt</span><span class="o">.</span><span class="n">legend</span><span class="p">()</span>
|
||||
<span class="n">plt</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="sa">r</span><span class="s1">'$\Delta$'</span><span class="p">)</span>
|
||||
<span class="n">plt</span><span class="o">.</span><span class="n">xlabel</span><span class="p">(</span><span class="sa">r</span><span class="s1">'$\lambda$ ($ \mathrm</span><span class="si">{nm}</span><span class="s1"> $)'</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>
|
||||
|
||||
</div>
|
||||
|
||||
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|
||||
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|
||||
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||||
<div class="sphinxsidebarwrapper">
|
||||
<h1 class="logo"><a href="../../index.html">optifik</a></h1>
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||||
|
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|
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<search id="searchbox" style="display: none" role="search">
|
||||
<div class="searchformwrapper">
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||||
<form class="search" action="../../search.html" method="get">
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||||
<input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false" placeholder="Search"/>
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||||
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||||
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|
||||
<ul>
|
||||
<li class="toctree-l1"><a class="reference internal" href="../../installation.html">Installation</a></li>
|
||||
<li class="toctree-l1"><a class="reference internal" href="../../api_reference.html">API Reference</a></li>
|
||||
<li class="toctree-l1"><a class="reference internal" href="../../examples.html">Examples</a></li>
|
||||
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|
||||
|
||||
<div class="relations">
|
||||
<h3>Related Topics</h3>
|
||||
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|
||||
<li><a href="../../index.html">Documentation overview</a><ul>
|
||||
<li><a href="../index.html">Module code</a><ul>
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
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|
||||
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|
||||
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|
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