commit 82eff060570e69744e0246d8da21c2a1e09da3b5 Author: François Boulogne Date: Wed Jun 25 12:16:11 2025 +0200 doc diff --git a/.venv b/.venv new file mode 100644 index 0000000..dcb9c5b --- /dev/null +++ b/.venv @@ -0,0 +1 @@ +victor diff --git a/ProminenceFunction.txt b/ProminenceFunction.txt new file mode 100644 index 0000000..0aba478 --- /dev/null +++ b/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 diff --git a/_modules/index.html b/_modules/index.html new file mode 100644 index 0000000..e0b7285 --- /dev/null +++ b/_modules/index.html @@ -0,0 +1,104 @@ + + + + + + + Overview: module code — optifik documentation + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +

All modules for which code is available

+ + +
+ +
+
+ +
+
+
+ ©2025, F. Boulogne et al.. + + | + Powered by Sphinx 8.2.3 + & Alabaster 1.0.0 + +
+ + + + + + \ No newline at end of file diff --git a/_modules/optifik/fft.html b/_modules/optifik/fft.html new file mode 100644 index 0000000..b29e00c --- /dev/null +++ b/_modules/optifik/fft.html @@ -0,0 +1,184 @@ + + + + + + + optifik.fft — optifik documentation + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +

Source code for optifik.fft

+import numpy as np
+from scipy.interpolate import interp1d
+from scipy.fftpack import fft, ifft, fftfreq
+
+
+import matplotlib.pyplot as plt
+
+from .utils import OptimizeResult, setup_matplotlib
+
+
+
+

+[docs]
+def thickness_from_fft(wavelengths, intensities,
+                       refractive_index,
+                       num_half_space=None,
+                       plot=None):
+    """
+    Determine the tickness by Fast Fourier Transform.
+
+    Parameters
+    ----------
+    wavelengths : array
+        Wavelength values in nm.
+    intensities : array
+        Intensity values.
+    refractive_index : scalar, optional
+        Value of the refractive index of the medium.
+    num_half_space : scalar, optional
+        Number of points to compute FFT's half space.
+        If `None`, default corresponds to `10*len(wavelengths)`.
+    plot : boolean, optional
+        Show plot of the transformed signal and the peak detection.
+
+    Returns
+    -------
+    results : Instance of `OptimizeResult` class.
+        The attribute `thickness` gives the thickness value in nm.
+    """
+    if plot:
+        setup_matplotlib()
+
+    if num_half_space is None:
+        num_half_space = 10 * len(wavelengths)
+
+    # FFT requires evenly spaced data.
+    # So, we interpolate the signal.
+    # Interpolate to get a linear increase of 1 / wavelengths.
+    inverse_wavelengths_times_n = refractive_index / wavelengths
+    f = interp1d(inverse_wavelengths_times_n, intensities)
+
+    inverse_wavelengths_linspace = np.linspace(inverse_wavelengths_times_n[0],
+                                           inverse_wavelengths_times_n[-1],
+                                           2*num_half_space)
+    intensities_linspace = f(inverse_wavelengths_linspace)
+
+
+    # Perform FFT
+    density = (inverse_wavelengths_times_n[-1]-inverse_wavelengths_times_n[0]) / (2*num_half_space)
+    inverse_wavelengths_fft = fftfreq(2*num_half_space, density)
+    intensities_fft = fft(intensities_linspace)
+
+    # The FFT is symetrical over [0:N] and [N:2N].
+    # Keep over [N:2N], ie for positive freq.
+    intensities_fft = intensities_fft[num_half_space:2*num_half_space]
+    inverse_wavelengths_fft = inverse_wavelengths_fft[num_half_space:2*num_half_space]
+
+    idx_max_fft = np.argmax(abs(intensities_fft))
+    freq_max = inverse_wavelengths_fft[idx_max_fft]
+
+    thickness_fft = freq_max / 2.
+
+    if plot:
+        plt.figure()
+        plt.loglog(inverse_wavelengths_fft, np.abs(intensities_fft))
+        plt.loglog(freq_max, np.abs(intensities_fft[idx_max_fft]), 'o')
+        plt.xlabel('Frequency')
+        plt.ylabel(r'FFT($I^*$)')
+        plt.title(f'Thickness={thickness_fft:.2f}')
+
+    return OptimizeResult(thickness=thickness_fft,)

+
+
+ +
+ +
+
+ +
+
+
+ ©2025, F. Boulogne et al.. + + | + Powered by Sphinx 8.2.3 + & Alabaster 1.0.0 + +
+ + + + + + \ No newline at end of file diff --git a/_modules/optifik/io.html b/_modules/optifik/io.html new file mode 100644 index 0000000..6121250 --- /dev/null +++ b/_modules/optifik/io.html @@ -0,0 +1,139 @@ + + + + + + + optifik.io — optifik documentation + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +

Source code for optifik.io

+import numpy as np
+
+
+

+[docs]
+def load_spectrum(spectrum_path,
+                  wavelength_min=0,
+                  wavelength_max=np.inf,
+                  delimiter=','):
+    """
+    Load a spectrum file.
+
+
+    TODO : describe expected format
+
+    Parameters
+    ----------
+    spectrum_path : string
+        File path.
+    wavelength_min : scalar, optional
+        Cut the data at this minimum wavelength (included).
+    wavelength_max : scalar, optional
+        Cut the data at this maximum wavelength (included).
+    delimiter : string, optional
+        Delimiter between columns in the datafile.
+
+    Returns
+    -------
+    values : arrays
+        (lamdbas, intensities)
+    """
+    data = np.loadtxt(spectrum_path, delimiter=delimiter)
+    lambdas, intensities = np.column_stack(data)
+
+    mask = (lambdas >= wavelength_min) & (lambdas <= wavelength_max)
+    return lambdas[mask], intensities[mask]

+
+
+ +
+ +
+
+ +
+
+
+ ©2025, F. Boulogne et al.. + + | + Powered by Sphinx 8.2.3 + & Alabaster 1.0.0 + +
+ + + + + + \ No newline at end of file diff --git a/_modules/optifik/minmax.html b/_modules/optifik/minmax.html new file mode 100644 index 0000000..e661880 --- /dev/null +++ b/_modules/optifik/minmax.html @@ -0,0 +1,258 @@ + + + + + + + optifik.minmax — optifik documentation + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +

Source code for optifik.minmax

+import numpy as np
+
+from scipy import stats
+from skimage.measure import ransac, LineModelND
+from scipy.signal import find_peaks
+
+import matplotlib.pyplot as plt
+
+from .utils import OptimizeResult, setup_matplotlib
+
+
+

+[docs]
+def thickness_from_minmax(wavelengths,
+                          intensities,
+                          refractive_index,
+                          min_peak_prominence,
+                          min_peak_distance=10,
+                          method='linreg',
+                          plot=None):
+
+    """
+    Return the thickness from a min-max detection.
+
+    Parameters
+    ----------
+    wavelengths : array
+        Wavelength values in nm.
+    intensities : array
+        Intensity values.
+    refractive_index : scalar, optional
+        Value of the refractive index of the medium.
+    min_peak_prominence : scalar, optional
+        Required prominence of peaks.
+    min_peak_distance : scalar, optional
+        Minimum distance between peaks.
+    method : string, optional
+        Either 'linreg' for linear regression or 'ransac'
+        for Randon Sampling Consensus.
+    plot : boolean, optional
+        Show plots of peak detection and lin regression.
+
+    Returns
+    -------
+    results : Instance of `OptimizeResult` class.
+        The attribute `thickness` gives the thickness value in nm.
+
+    Notes
+    -----
+    For more details about `min_peak_prominence` and `min_peak_distance`,
+    see the documentation of `scipy.signal.find_peaks`. This function
+    is used to find extrema.
+    """
+    if plot:
+        setup_matplotlib()
+
+    peaks_max, _ = find_peaks(intensities, prominence=min_peak_prominence, distance=min_peak_distance)
+    peaks_min, _ = find_peaks(-intensities, prominence=min_peak_prominence, distance=min_peak_distance)
+    peaks = np.concatenate((peaks_min, peaks_max))
+    peaks.sort()
+
+    k_values = np.arange(len(peaks))
+
+    if k_values.size < 2:
+        # Can't fit if less than two points.
+        return OptimizeResult(thickness=np.nan)
+
+
+    if isinstance(refractive_index, np.ndarray):
+        #refractive_index = refractive_index[peaks][::-1]
+        n_over_lambda = refractive_index[peaks][::-1] / wavelengths[peaks][::-1]
+    else:
+        n_over_lambda = refractive_index / wavelengths[peaks][::-1]
+
+    if method.lower() == 'ransac':
+        residual_threshold = 4e-5
+        min_samples = 2
+        # Scikit-image
+        data = np.column_stack([k_values, n_over_lambda])
+        model_robust, inliers = ransac(data, LineModelND,
+                                       min_samples=min_samples,
+                                       residual_threshold=residual_threshold,
+                                       max_trials=100)
+        slope = model_robust.params[1][1]
+        thickness_minmax = 1 / slope /  4
+
+        # Scikit-learn
+        #X, y = k_values.reshape(-1, 1), 1/wavelengths[peaks][::-1]
+
+        ## Fit line using all data
+        #lr = linear_model.LinearRegression()
+        #lr.fit(X, y)
+
+        #slransac = linear_model.RANSACRegressor(min_samples=min_samples,
+        #                                        residual_threshold=residual_threshold)
+        #slransac.fit(X, y)
+        #inlier_mask = slransac.inlier_mask_
+        #outlier_mask = np.logical_not(inlier_mask)
+
+        ## Predict data of estimated models
+        #line_X = np.arange(X.min(), X.max())[:, np.newaxis]
+        #line_y = lr.predict(line_X)
+        #line_y_ransac = slransac.predict(line_X)
+
+        #slope = slransac.estimator_.coef_[0]
+
+        if plot:
+            fig, ax = plt.subplots()
+
+            ax.set_xlabel('extremum n°')
+            ax.set_ylabel('$n$($\lambda$) / $\lambda$')
+            ax.plot(data[inliers, 0], data[inliers, 1], 'xb', alpha=0.6, label='Inliers')
+            ax.plot(data[~inliers, 0], data[~inliers, 1], '+r', alpha=0.6, label='Outliers')
+            ax.plot(k_values, model_robust.predict_y(k_values), '-g', label='Fit')
+
+            ax.legend()
+            ax.set_title(f'Thickness = {thickness_minmax:.2f} nm')
+            import inspect
+            plt.title(inspect.currentframe().f_code.co_name)
+            plt.tight_layout()
+            plt.show()
+
+        return OptimizeResult(thickness=thickness_minmax,
+                              num_inliers=inliers.sum(),
+                              num_outliers=(~inliers).sum(),
+                              peaks_max=peaks_max,
+                              peaks_min=peaks_min)
+
+    elif method.lower() == 'linreg':
+        slope, intercept, r_value, p_value, std_err = stats.linregress(k_values, n_over_lambda)
+        #mean_n = np.mean(refractive_index)
+        thickness_minmax = 1 / slope / 4
+
+        if plot:
+            fig, ax = plt.subplots()
+
+            ax.set_xlabel('extremum n°')
+            ax.set_ylabel('$n$($\lambda$) / $\lambda$')
+            ax.plot(k_values, n_over_lambda, 's', label='Extrema')
+            ax.plot(k_values, intercept + k_values * slope, label='Fit')
+
+            ax.legend()
+            ax.set_title(f'Thickness = {thickness_minmax:.2f} nm')
+            import inspect
+            plt.title(inspect.currentframe().f_code.co_name)
+            plt.tight_layout()
+            plt.show()
+
+        return OptimizeResult(thickness=thickness_minmax,
+                              peaks_max=peaks_max,
+                              peaks_min=peaks_min,
+                              stderr=std_err)
+
+    else:
+        raise ValueError('Wrong method')

+
+
+ +
+ +
+
+ +
+
+
+ ©2025, F. Boulogne et al.. + + | + Powered by Sphinx 8.2.3 + & Alabaster 1.0.0 + +
+ + + + + + \ No newline at end of file diff --git a/_modules/optifik/scheludko.html b/_modules/optifik/scheludko.html new file mode 100644 index 0000000..8adf74f --- /dev/null +++ b/_modules/optifik/scheludko.html @@ -0,0 +1,471 @@ + + + + + + + optifik.scheludko — optifik documentation + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +

Source code for optifik.scheludko

+import numpy as np
+from scipy.optimize import curve_fit
+
+import matplotlib.pyplot as plt
+
+from .io import load_spectrum
+from .utils import OptimizeResult, setup_matplotlib
+from .analysis import finds_peak
+
+
+def _thicknesses_scheludko_at_order(wavelengths,
+                                    intensities,
+                                    interference_order,
+                                    refractive_index,
+                                    intensities_void=None):
+    """
+    Compute thicknesses vs wavelength for a given interference order.
+
+    Parameters
+    ----------
+    wavelengths : array
+        Wavelength values in nm.
+    intensities : array
+        Intensity values.
+    interference_order : int
+        Interference order.
+    refractive_index : array_like (or float)
+        Refractive index.
+    intensities_void : array, optional
+        Intensities of void.
+
+    Returns
+    -------
+    thicknesses : array
+
+    """
+    if intensities_void is None:
+        Imin = np.min(intensities)
+    else:
+        Imin = intensities_void
+
+    n = refractive_index
+    m = interference_order
+    I_norm = (np.asarray(intensities) - Imin) / (np.max(intensities) - Imin)
+
+    prefactor = wavelengths / (2 * np.pi * n)
+    argument = np.sqrt(I_norm / (1 + (1 - I_norm) * (n**2 - 1)**2 / (4 * n**2)))
+
+    if m % 2 == 0:
+        term1 = (m / 2) * np.pi
+    else:
+        term1 = ((m+1) / 2) * np.pi
+
+    term2 = (-1)**m * np.arcsin(argument)
+
+    return prefactor * (term1 + term2)
+
+
+def _Delta(wavelengths, thickness, interference_order, refractive_index):
+    """
+    Compute the Delta values.
+
+    Parameters
+    ----------
+    wavelengths : array
+        Wavelength values in nm.
+    thickness : array_like (or float)
+        Film thickness.
+    interference_order : int
+        Interference order.
+    refractive_index : array_like (or float)
+        Refractive index.
+
+    Returns
+    -------
+    ndarray
+        Delta values.
+    """
+
+    # ensure that the entries are numpy arrays
+    wavelengths = np.asarray(wavelengths)
+    h = np.asarray(thickness)
+    n = np.asarray(refractive_index)
+    m = interference_order
+
+    # Calculation of p as a function of the parity of m
+    if m % 2 == 0:
+        p = m / 2
+    else:
+        p = (m + 1) / 2
+
+    # Calculation of alpha
+    alpha = ((n**2 - 1)**2) / (4 * n**2)
+
+    # Argument of sinus
+    angle = (2 * np.pi * n * h / wavelengths) - p * np.pi
+
+    # A = sin²(argument)
+    A = np.sin(angle)**2
+
+    # Final calcuation of Delta
+    return (A * (1 + alpha)) / (1 + A * alpha)
+
+
+def _Delta_fit(xdata, thickness, interference_order):
+    """
+    Wrapper on Delta() for curve_fit.
+
+    Parameters
+    ----------
+    xdata : tuple
+        (wavelengths, refractive_index)
+    thickness : array_like (or float)
+        Film thickness.
+    interference_order : int
+        Interference order.
+
+    Returns
+    -------
+    ndarray
+        Delta values.
+
+    """
+    lambdas, r_index = xdata
+    return _Delta(lambdas, thickness, interference_order, r_index)
+
+
+

+[docs]
+def get_default_start_stop_wavelengths(wavelengths,
+                                       intensities,
+                                       refractive_index,
+                                       min_peak_prominence,
+                                       plot=None):
+    """
+    Returns the start and stop wavelength values of the last monotonic branch.
+
+    Parameters
+    ----------
+    wavelengths : array
+        Wavelength values in nm.
+    intensities : array
+        Intensity values.
+    refractive_index : scalar, optional
+        Value of the refractive index of the medium.
+    min_peak_prominence : scalar
+        Required prominence of peaks.
+    plot : bool, optional
+        Display a curve, useful for checking or debuging. The default is None.
+
+
+    Raises
+    ------
+    RuntimeError
+        if at least one maximum and one minimum are not detected.
+
+    Returns
+    -------
+    wavelength_start : scalar
+    wavelength_stop : scalar
+    """
+    # idx_min idx max
+    idx_peaks_min, idx_peaks_max = finds_peak(wavelengths, intensities,
+                                              min_peak_prominence=min_peak_prominence,
+                                              plot=plot)
+
+    failure, message = False, ''
+    if len(idx_peaks_min) == 0:
+        message += 'Failed to detect at least one minimum. '
+        failure = True
+    if len(idx_peaks_max) == 0:
+        message += 'Failed to detect at least one maximum. '
+        failure = True
+    if failure:
+        raise RuntimeError(message)
+
+    # Get the last oscillation peaks
+    lambda_min = wavelengths[idx_peaks_min[-1]]
+    lambda_max = wavelengths[idx_peaks_max[-1]]
+
+    # Order them
+    wavelength_start = min(lambda_min, lambda_max)
+    wavelength_stop = max(lambda_min, lambda_max)
+
+    return wavelength_start, wavelength_stop

+
+
+
+

+[docs]
+def thickness_from_scheludko(wavelengths,
+                             intensities,
+                             refractive_index,
+                             wavelength_start=None,
+                             wavelength_stop=None,
+                             interference_order=None,
+                             intensities_void=None,
+                             plot=None):
+    """
+    Compute the film thickness based on Scheludko method.
+
+    Parameters
+    ----------
+    wavelengths : array
+        Wavelength values in nm.
+    intensities : array
+        Intensity values.
+    refractive_index : scalar, optional
+        Value of the refractive index of the medium.
+    wavelength_start : scalar, optional
+        Starting value of a monotonic branch.
+        Mandatory if interference_order != 0.
+    wavelength_stop : scalar, optional
+        Stoping value of a monotonic branch.
+        Mandatory if interference_order != 0.
+    interference_order : scalar, optional
+        Interference order, zero or positive integer.
+        If set to None, the value is guessed.
+    intensities_void : array, optional
+        Intensity in absence of a film.
+        Mandatory if interference_order == 0.
+    plot : bool, optional
+        Display a curve, useful for checking or debuging. The default is None.
+
+    Returns
+    -------
+    results : Instance of `OptimizeResult` class.
+        The attribute `thickness` gives the thickness value in nm.
+
+    """
+    if plot:
+        setup_matplotlib()
+
+    if interference_order is None or interference_order > 0:
+        if wavelength_stop is None or wavelength_start is None:
+            raise ValueError('wavelength_start and wavelength_stop must be passed for interference_order != 0.')
+        else:
+            if wavelength_start > wavelength_stop:
+                raise ValueError('wavelength_start and wavelength_stop are swapped.')
+
+    r_index = refractive_index
+
+    # Handle the interference order
+    if interference_order is None:
+        # A bit extreme...
+        max_tested_order = 12
+
+        # mask input data
+        mask = (wavelengths >= wavelength_start) & (wavelengths <= wavelength_stop)
+        wavelengths_masked = wavelengths[mask]
+        r_index_masked = r_index[mask]
+        intensities_masked = intensities[mask]
+
+        min_difference = np.inf
+        thickness_values = None
+
+        if plot:
+            plt.figure()
+            plt.ylabel(r'$h$ ($\mathrm{{nm}}$)')
+            plt.xlabel(r'$\lambda$ ($ \mathrm{nm} $)')
+
+        for _order in range(0, max_tested_order+1):
+            h_values = _thicknesses_scheludko_at_order(wavelengths_masked,
+                                                       intensities_masked,
+                                                       _order,
+                                                       r_index_masked)
+
+            difference = np.max(h_values) - np.min(h_values)
+
+            print(f"h-difference for m={_order}: {difference:.1f} nm")
+
+            if difference < min_difference:
+                min_difference = difference
+                interference_order = _order
+                thickness_values = h_values
+
+            if plot:
+                plt.plot(wavelengths_masked, h_values, '.',
+                         markersize=3, label=f"Order={_order}")
+    elif interference_order == 0:
+
+        min_peak_prominence = 0.02
+        peaks_min, peaks_max = finds_peak(wavelengths, intensities,
+                                          min_peak_prominence=min_peak_prominence,
+                                          plot=plot)
+        if len(peaks_max) != 1:
+            raise RuntimeError('Failed to detect a single maximum peak.')
+
+        lambda_unique = wavelengths[peaks_max[0]]
+
+        # keep rhs from the maximum
+        mask = wavelengths >= lambda_unique
+        wavelengths_masked = wavelengths[mask]
+        r_index_masked = r_index[mask]
+        intensities_masked = intensities[mask]
+        intensities_void_masked = intensities_void[mask]
+
+        interference_order = 0
+        thickness_values = _thicknesses_scheludko_at_order(wavelengths_masked,
+                                                     intensities_masked,
+                                                     interference_order,
+                                                     r_index_masked,
+                                                     intensities_void=intensities_void_masked)
+
+    elif interference_order > 0:
+        h_values = _thicknesses_scheludko_at_order(wavelengths_masked,
+                                                   intensities_masked,
+                                                   interference_order,
+                                                   r_index_masked)
+        thickness_values = h_values
+    else:
+        raise ValueError('interference_order must be >= 0.')
+
+
+
+    # Compute the thickness for the selected order
+
+    # Delta
+    if interference_order == 0:
+        num = intensities_masked - np.min(intensities_void_masked)
+        denom = np.max(intensities_masked) - np.min(intensities_void_masked)
+    else:
+        num = intensities_masked - np.min(intensities_masked)
+        denom = np.max(intensities_masked) - np.min(intensities_masked)
+    Delta_from_data = num / denom
+
+
+
+    # Delta_from_data = (intensities_masked -np.min(intensities_masked))/(np.max(intensities_masked) -np.min(intensities_masked))
+    # Delta_from_data = (intensities_raw_masked -np.min(intensities_raw_masked))/(np.max(intensities_raw_masked) -np.min(intensities_raw_masked))
+
+    DeltaScheludko = _Delta(wavelengths_masked,
+                            np.mean(thickness_values),
+                            interference_order,
+                            r_index_masked)
+
+
+    xdata = (wavelengths_masked, r_index_masked)
+    popt, pcov = curve_fit(lambda x, h: _Delta_fit(x, h, interference_order), xdata, Delta_from_data, p0=[np.mean(thickness_values)])
+    fitted_h = popt[0]
+    std_err = np.sqrt(pcov[0][0])
+
+    if plot:
+        Delta_values = _Delta(wavelengths_masked, fitted_h, interference_order, r_index_masked)
+
+        plt.figure()
+        plt.plot(wavelengths_masked, Delta_from_data,
+                 'bo-', markersize=2,
+                 label=r'$\mathrm{{Smoothed}}\ \mathrm{{Data}}$')
+
+        # Scheludko
+        label = rf'$\mathrm{{Scheludko}}\ (h = {np.mean(thickness_values):.1f} \pm {np.std(thickness_values):.1f}\ \mathrm{{nm}})$'
+        plt.plot(wavelengths_masked, DeltaScheludko,
+                 'go-', markersize=2, label=label)
+        # Fit
+        label = rf'$\mathrm{{Fit}}\ (h = {fitted_h:.1f}\pm {std_err:.1f} \ \mathrm{{nm}})$'
+        plt.plot(wavelengths_masked,  Delta_values,
+                 'ro-', markersize=2,
+                 label=label)
+
+        plt.legend()
+        plt.ylabel(r'$\Delta$')
+        plt.xlabel(r'$\lambda$ ($ \mathrm{nm} $)')
+        import inspect
+        plt.title(inspect.currentframe().f_code.co_name)
+
+    return OptimizeResult(thickness=fitted_h, stderr=std_err)

+
+
+
+ +
+ +
+
+ +
+
+
+ ©2025, F. Boulogne et al.. + + | + Powered by Sphinx 8.2.3 + & Alabaster 1.0.0 + +
+ + + + + + \ No newline at end of file diff --git a/_sources/api_reference.rst.txt b/_sources/api_reference.rst.txt new file mode 100644 index 0000000..4535a57 --- /dev/null +++ b/_sources/api_reference.rst.txt @@ -0,0 +1,35 @@ +API Reference +============= + +Below is the complete reference for Optifik's public API. + + + +io +-- +.. automodule:: optifik.io + :members: + :undoc-members: + :show-inheritance: + +fft +--- +.. automodule:: optifik.fft + :members: + :undoc-members: + :show-inheritance: + +minmax +------ +.. automodule:: optifik.minmax + :members: + :undoc-members: + :show-inheritance: + +scheludko +--------- +.. automodule:: optifik.scheludko + :members: + :undoc-members: + :show-inheritance: + diff --git a/_sources/examples.rst.txt b/_sources/examples.rst.txt new file mode 100644 index 0000000..735e8c7 --- /dev/null +++ b/_sources/examples.rst.txt @@ -0,0 +1,34 @@ +Examples +======== + +Basic Optimization +------------------ + +Here's a simple example using Optifik to solve a quadratic function. + +.. code-block:: python + + from optifik import minimize + + def quadratic(x): + return (x - 3) ** 2 + + result = minimize(quadratic, x0=0) + print(result) + +Constrained Optimization +------------------------ + +.. code-block:: python + + from optifik import minimize + + def objective(x): + return x[0] ** 2 + x[1] ** 2 + + def constraint(x): + return x[0] + x[1] - 1 + + result = minimize(objective, x0=[0, 0], constraints=[constraint]) + print(result) + diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt new file mode 100644 index 0000000..d9ef27d --- /dev/null +++ b/_sources/index.rst.txt @@ -0,0 +1,24 @@ +Optifik Documentation +===================== + +Welcome to the documentation for **Optifik**, a Python library for + + +Contents +-------- + +.. toctree:: + :maxdepth: 2 + :caption: Documentation + + installation + api_reference + examples + +Indices and tables +------------------ + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` + diff --git a/_sources/installation.rst.txt b/_sources/installation.rst.txt new file mode 100644 index 0000000..a0e132e --- /dev/null +++ b/_sources/installation.rst.txt @@ -0,0 +1,28 @@ +Installation +============ + +You can install Optifik using `pip`: + +.. code-block:: bash + + pip install optifik + +Alternatively, you can install it from source: + +.. code-block:: bash + + git clone https://github.com/yourusername/optifik.git + cd optifik + pip install -e . + +Requirements +------------ + +- Python >= 3.8 +- NumPy >= 1.21 + +Optional for extended functionality: + +- SciPy +- Matplotlib + diff --git a/_static/alabaster.css b/_static/alabaster.css new file mode 100644 index 0000000..7e75bf8 --- /dev/null +++ b/_static/alabaster.css @@ -0,0 +1,663 @@ +/* -- page layout ----------------------------------------------------------- */ + +body { + font-family: Georgia, serif; 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+} + +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; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + 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; + } +} \ No newline at end of file diff --git a/_static/custom.css b/_static/custom.css new file mode 100644 index 0000000..2a924f1 --- /dev/null +++ b/_static/custom.css @@ -0,0 +1 @@ +/* This file intentionally left blank. */ diff --git a/_static/doctools.js b/_static/doctools.js new file mode 100644 index 0000000..0398ebb --- /dev/null +++ b/_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); diff --git a/_static/documentation_options.js b/_static/documentation_options.js new file mode 100644 index 0000000..7e4c114 --- /dev/null +++ b/_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, +}; \ No newline at end of file diff --git a/_static/file.png b/_static/file.png new file mode 100644 index 0000000..a858a41 Binary files /dev/null and b/_static/file.png differ diff --git a/_static/github-banner.svg b/_static/github-banner.svg new file mode 100644 index 0000000..c47d9dc --- /dev/null +++ b/_static/github-banner.svg @@ -0,0 +1,5 @@ + + + + + diff --git a/_static/language_data.js b/_static/language_data.js new file mode 100644 index 0000000..c7fe6c6 --- /dev/null +++ b/_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; + } +} + diff --git a/_static/minus.png b/_static/minus.png new file mode 100644 index 0000000..d96755f Binary files /dev/null and b/_static/minus.png differ diff --git a/_static/plus.png b/_static/plus.png new file mode 100644 index 0000000..7107cec Binary files /dev/null and b/_static/plus.png differ diff --git a/_static/pygments.css b/_static/pygments.css new file mode 100644 index 0000000..9392ddc --- /dev/null +++ b/_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; 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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 */ \ No newline at end of file diff --git a/_static/searchtools.js b/_static/searchtools.js new file mode 100644 index 0000000..91f4be5 --- /dev/null +++ b/_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); diff --git a/_static/sphinx_highlight.js b/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/_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( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * 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(); +}); diff --git a/api_reference.html b/api_reference.html new file mode 100644 index 0000000..13216fe --- /dev/null +++ b/api_reference.html @@ -0,0 +1,294 @@ + + + + + + + + API Reference — optifik documentation + + + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +
+

API Reference

+

Below is the complete reference for Optifik’s public API.

+
+

io

+
+
+optifik.io.load_spectrum(spectrum_path, wavelength_min=0, wavelength_max=inf, delimiter=',')[source]
+

Load a spectrum file.

+

TODO : describe expected format

+
+
Parameters:
+
+
spectrum_pathstring

File path.

+
+
wavelength_minscalar, optional

Cut the data at this minimum wavelength (included).

+
+
wavelength_maxscalar, optional

Cut the data at this maximum wavelength (included).

+
+
delimiterstring, optional

Delimiter between columns in the datafile.

+
+
+
+
Returns:
+
+
valuesarrays

(lamdbas, intensities)

+
+
+
+
+
+ +
+
+

fft

+
+
+optifik.fft.thickness_from_fft(wavelengths, intensities, refractive_index, num_half_space=None, plot=None)[source]
+

Determine the tickness by Fast Fourier Transform.

+
+
Parameters:
+
+
wavelengthsarray

Wavelength values in nm.

+
+
intensitiesarray

Intensity values.

+
+
refractive_indexscalar, optional

Value of the refractive index of the medium.

+
+
num_half_spacescalar, optional

Number of points to compute FFT’s half space. +If None, default corresponds to 10*len(wavelengths).

+
+
plotboolean, optional

Show plot of the transformed signal and the peak detection.

+
+
+
+
Returns:
+
+
resultsInstance of OptimizeResult class.

The attribute thickness gives the thickness value in nm.

+
+
+
+
+
+ +
+
+

minmax

+
+
+optifik.minmax.thickness_from_minmax(wavelengths, intensities, refractive_index, min_peak_prominence, min_peak_distance=10, method='linreg', plot=None)[source]
+

Return the thickness from a min-max detection.

+
+
Parameters:
+
+
wavelengthsarray

Wavelength values in nm.

+
+
intensitiesarray

Intensity values.

+
+
refractive_indexscalar, optional

Value of the refractive index of the medium.

+
+
min_peak_prominencescalar, optional

Required prominence of peaks.

+
+
min_peak_distancescalar, optional

Minimum distance between peaks.

+
+
methodstring, optional

Either ‘linreg’ for linear regression or ‘ransac’ +for Randon Sampling Consensus.

+
+
plotboolean, optional

Show plots of peak detection and lin regression.

+
+
+
+
Returns:
+
+
resultsInstance of OptimizeResult class.

The attribute thickness gives the thickness value in nm.

+
+
+
+
+

Notes

+

For more details about min_peak_prominence and min_peak_distance, +see the documentation of scipy.signal.find_peaks. This function +is used to find extrema.

+
+ +
+
+

scheludko

+
+
+optifik.scheludko.get_default_start_stop_wavelengths(wavelengths, intensities, refractive_index, min_peak_prominence, plot=None)[source]
+

Returns the start and stop wavelength values of the last monotonic branch.

+
+
Parameters:
+
+
wavelengthsarray

Wavelength values in nm.

+
+
intensitiesarray

Intensity values.

+
+
refractive_indexscalar, optional

Value of the refractive index of the medium.

+
+
min_peak_prominencescalar

Required prominence of peaks.

+
+
plotbool, optional

Display a curve, useful for checking or debuging. The default is None.

+
+
+
+
Returns:
+
+
wavelength_startscalar
+
wavelength_stopscalar
+
+
+
Raises:
+
+
RuntimeError

if at least one maximum and one minimum are not detected.

+
+
+
+
+
+ +
+
+optifik.scheludko.thickness_from_scheludko(wavelengths, intensities, refractive_index, wavelength_start=None, wavelength_stop=None, interference_order=None, intensities_void=None, plot=None)[source]
+

Compute the film thickness based on Scheludko method.

+
+
Parameters:
+
+
wavelengthsarray

Wavelength values in nm.

+
+
intensitiesarray

Intensity values.

+
+
refractive_indexscalar, optional

Value of the refractive index of the medium.

+
+
wavelength_startscalar, optional

Starting value of a monotonic branch. +Mandatory if interference_order != 0.

+
+
wavelength_stopscalar, optional

Stoping value of a monotonic branch. +Mandatory if interference_order != 0.

+
+
interference_orderscalar, optional

Interference order, zero or positive integer. +If set to None, the value is guessed.

+
+
intensities_voidarray, optional

Intensity in absence of a film. +Mandatory if interference_order == 0.

+
+
plotbool, optional

Display a curve, useful for checking or debuging. The default is None.

+
+
+
+
Returns:
+
+
resultsInstance of OptimizeResult class.

The attribute thickness gives the thickness value in nm.

+
+
+
+
+
+ +
+
+ + +
+ +
+
+ +
+
+
+ ©2025, F. Boulogne et al.. + + | + Powered by Sphinx 8.2.3 + & Alabaster 1.0.0 + + | + Page source +
+ + + + + + \ No newline at end of file diff --git a/data/spectraManue/.backups/known_values.py b/data/spectraManue/.backups/known_values.py new file mode 100644 index 0000000..436a154 --- /dev/null +++ b/data/spectraManue/.backups/known_values.py @@ -0,0 +1,52 @@ +from collections import OrderedDict + +# Data obtained by Lorene Champougny +known_thicknesses = OrderedDict({ + 'sample1/003582.xy' : 3521, + 'sample1/003766.xy' : 3430, + 'sample1/003952.xy' : 3494, + 'sample1/004136.xy' : 3485, + 'sample1/004320.xy' : 3410, + 'sample1/004504.xy' : 3280, + 'sample1/004689.xy' : 3111, + 'sample1/004872.xy' : 2878, + 'sample1/005057.xy' : 2629, + 'sample1/005241.xy' : 2411, + 'sample1/005426.xy' : 2287, + 'sample1/005610.xy' : 2180, + 'sample1/005794.xy' : 2110, + 'sample1/005978.xy' : 2033, + 'sample1/006163.xy' : 1958, + 'sample1/006347.xy' : 1889, + 'sample1/006528.xy' : 1789, + 'sample1/006715.xy' : 1703, + 'sample1/006900.xy' : 1629, + 'sample1/007084.xy' : 1549, + 'sample1/007268.xy' : 1459, + 'sample1/008188.xy' : 1054, + 'sample1/008373.xy' : 1016, + 'sample1/008557.xy' : 999, + 'sample1/008742.xy' : 982, + 'sample1/008926.xy' : 973, + 'sample1/009111.xy' : 958, + 'sample1/009294.xy' : 940, + 'sample1/009479.xy' : 915, + 'sample1/009848.xy' : 833, + 'sample1/010032.xy' : 804, + 'sample1/010215.xy' : 778, + 'sample1/010399.xy' : 744, + 'sample1/010581.xy' : 717, + 'sample1/010768.xy' : 697, + 'sample1/010953.xy' : 668, + 'sample1/011137.xy' : 643, + 'sample1/011321.xy' : 618, + 'sample1/011505.xy' : 593, + 'sample1/011688.xy' : 572, + 'sample1/011873.xy' : 559, + 'sample1/012058.xy' : 535, + 'sample1/012242.xy' : 509, + 'sample1/012426.xy' : 485, + 'sample1/012610.xy' : 456, + 'sample1/012795.xy' : 432, + 'sample1/012979.xy' : 418, + }) diff --git a/data/spectraManue/__pycache__/known_values.cpython-313.pyc b/data/spectraManue/__pycache__/known_values.cpython-313.pyc new file mode 100644 index 0000000..c540564 Binary files /dev/null and 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When it is not found, a full rebuild will be done. +config: 2564f2e9aab3ad84ebb1853bea9a5155 +tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/_build/html/.buildinfo.bak b/docs/_build/html/.buildinfo.bak new file mode 100644 index 0000000..80d809d --- /dev/null +++ b/docs/_build/html/.buildinfo.bak @@ -0,0 +1,4 @@ +# Sphinx build info version 1 +# This file records the configuration used when building these files. When it is not found, a full rebuild will be done. +config: 9a8159084d6bd6134d2065fde4a6ca63 +tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/_build/html/_modules/index.html b/docs/_build/html/_modules/index.html new file mode 100644 index 0000000..e0b7285 --- /dev/null +++ b/docs/_build/html/_modules/index.html @@ -0,0 +1,104 @@ + + + + + + + Overview: module code — optifik documentation + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +

All modules for which code is available

+ + +
+ +
+
+ +
+
+
+ ©2025, F. Boulogne et al.. + + | + Powered by Sphinx 8.2.3 + & Alabaster 1.0.0 + +
+ + + + + + \ No newline at end of file diff --git a/docs/_build/html/_modules/optifik/fft.html b/docs/_build/html/_modules/optifik/fft.html new file mode 100644 index 0000000..b29e00c --- /dev/null +++ b/docs/_build/html/_modules/optifik/fft.html @@ -0,0 +1,184 @@ + + + + + + + optifik.fft — optifik documentation + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +

Source code for optifik.fft

+import numpy as np
+from scipy.interpolate import interp1d
+from scipy.fftpack import fft, ifft, fftfreq
+
+
+import matplotlib.pyplot as plt
+
+from .utils import OptimizeResult, setup_matplotlib
+
+
+
+

+[docs]
+def thickness_from_fft(wavelengths, intensities,
+                       refractive_index,
+                       num_half_space=None,
+                       plot=None):
+    """
+    Determine the tickness by Fast Fourier Transform.
+
+    Parameters
+    ----------
+    wavelengths : array
+        Wavelength values in nm.
+    intensities : array
+        Intensity values.
+    refractive_index : scalar, optional
+        Value of the refractive index of the medium.
+    num_half_space : scalar, optional
+        Number of points to compute FFT's half space.
+        If `None`, default corresponds to `10*len(wavelengths)`.
+    plot : boolean, optional
+        Show plot of the transformed signal and the peak detection.
+
+    Returns
+    -------
+    results : Instance of `OptimizeResult` class.
+        The attribute `thickness` gives the thickness value in nm.
+    """
+    if plot:
+        setup_matplotlib()
+
+    if num_half_space is None:
+        num_half_space = 10 * len(wavelengths)
+
+    # FFT requires evenly spaced data.
+    # So, we interpolate the signal.
+    # Interpolate to get a linear increase of 1 / wavelengths.
+    inverse_wavelengths_times_n = refractive_index / wavelengths
+    f = interp1d(inverse_wavelengths_times_n, intensities)
+
+    inverse_wavelengths_linspace = np.linspace(inverse_wavelengths_times_n[0],
+                                           inverse_wavelengths_times_n[-1],
+                                           2*num_half_space)
+    intensities_linspace = f(inverse_wavelengths_linspace)
+
+
+    # Perform FFT
+    density = (inverse_wavelengths_times_n[-1]-inverse_wavelengths_times_n[0]) / (2*num_half_space)
+    inverse_wavelengths_fft = fftfreq(2*num_half_space, density)
+    intensities_fft = fft(intensities_linspace)
+
+    # The FFT is symetrical over [0:N] and [N:2N].
+    # Keep over [N:2N], ie for positive freq.
+    intensities_fft = intensities_fft[num_half_space:2*num_half_space]
+    inverse_wavelengths_fft = inverse_wavelengths_fft[num_half_space:2*num_half_space]
+
+    idx_max_fft = np.argmax(abs(intensities_fft))
+    freq_max = inverse_wavelengths_fft[idx_max_fft]
+
+    thickness_fft = freq_max / 2.
+
+    if plot:
+        plt.figure()
+        plt.loglog(inverse_wavelengths_fft, np.abs(intensities_fft))
+        plt.loglog(freq_max, np.abs(intensities_fft[idx_max_fft]), 'o')
+        plt.xlabel('Frequency')
+        plt.ylabel(r'FFT($I^*$)')
+        plt.title(f'Thickness={thickness_fft:.2f}')
+
+    return OptimizeResult(thickness=thickness_fft,)

+
+
+ +
+ +
+
+ +
+
+
+ ©2025, F. Boulogne et al.. + + | + Powered by Sphinx 8.2.3 + & Alabaster 1.0.0 + +
+ + + + + + \ No newline at end of file diff --git a/docs/_build/html/_modules/optifik/io.html b/docs/_build/html/_modules/optifik/io.html new file mode 100644 index 0000000..6121250 --- /dev/null +++ b/docs/_build/html/_modules/optifik/io.html @@ -0,0 +1,139 @@ + + + + + + + optifik.io — optifik documentation + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +

Source code for optifik.io

+import numpy as np
+
+
+

+[docs]
+def load_spectrum(spectrum_path,
+                  wavelength_min=0,
+                  wavelength_max=np.inf,
+                  delimiter=','):
+    """
+    Load a spectrum file.
+
+
+    TODO : describe expected format
+
+    Parameters
+    ----------
+    spectrum_path : string
+        File path.
+    wavelength_min : scalar, optional
+        Cut the data at this minimum wavelength (included).
+    wavelength_max : scalar, optional
+        Cut the data at this maximum wavelength (included).
+    delimiter : string, optional
+        Delimiter between columns in the datafile.
+
+    Returns
+    -------
+    values : arrays
+        (lamdbas, intensities)
+    """
+    data = np.loadtxt(spectrum_path, delimiter=delimiter)
+    lambdas, intensities = np.column_stack(data)
+
+    mask = (lambdas >= wavelength_min) & (lambdas <= wavelength_max)
+    return lambdas[mask], intensities[mask]

+
+
+ +
+ +
+
+ +
+
+
+ ©2025, F. Boulogne et al.. + + | + Powered by Sphinx 8.2.3 + & Alabaster 1.0.0 + +
+ + + + + + \ No newline at end of file diff --git a/docs/_build/html/_modules/optifik/minmax.html b/docs/_build/html/_modules/optifik/minmax.html new file mode 100644 index 0000000..e661880 --- /dev/null +++ b/docs/_build/html/_modules/optifik/minmax.html @@ -0,0 +1,258 @@ + + + + + + + optifik.minmax — optifik documentation + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +

Source code for optifik.minmax

+import numpy as np
+
+from scipy import stats
+from skimage.measure import ransac, LineModelND
+from scipy.signal import find_peaks
+
+import matplotlib.pyplot as plt
+
+from .utils import OptimizeResult, setup_matplotlib
+
+
+

+[docs]
+def thickness_from_minmax(wavelengths,
+                          intensities,
+                          refractive_index,
+                          min_peak_prominence,
+                          min_peak_distance=10,
+                          method='linreg',
+                          plot=None):
+
+    """
+    Return the thickness from a min-max detection.
+
+    Parameters
+    ----------
+    wavelengths : array
+        Wavelength values in nm.
+    intensities : array
+        Intensity values.
+    refractive_index : scalar, optional
+        Value of the refractive index of the medium.
+    min_peak_prominence : scalar, optional
+        Required prominence of peaks.
+    min_peak_distance : scalar, optional
+        Minimum distance between peaks.
+    method : string, optional
+        Either 'linreg' for linear regression or 'ransac'
+        for Randon Sampling Consensus.
+    plot : boolean, optional
+        Show plots of peak detection and lin regression.
+
+    Returns
+    -------
+    results : Instance of `OptimizeResult` class.
+        The attribute `thickness` gives the thickness value in nm.
+
+    Notes
+    -----
+    For more details about `min_peak_prominence` and `min_peak_distance`,
+    see the documentation of `scipy.signal.find_peaks`. This function
+    is used to find extrema.
+    """
+    if plot:
+        setup_matplotlib()
+
+    peaks_max, _ = find_peaks(intensities, prominence=min_peak_prominence, distance=min_peak_distance)
+    peaks_min, _ = find_peaks(-intensities, prominence=min_peak_prominence, distance=min_peak_distance)
+    peaks = np.concatenate((peaks_min, peaks_max))
+    peaks.sort()
+
+    k_values = np.arange(len(peaks))
+
+    if k_values.size < 2:
+        # Can't fit if less than two points.
+        return OptimizeResult(thickness=np.nan)
+
+
+    if isinstance(refractive_index, np.ndarray):
+        #refractive_index = refractive_index[peaks][::-1]
+        n_over_lambda = refractive_index[peaks][::-1] / wavelengths[peaks][::-1]
+    else:
+        n_over_lambda = refractive_index / wavelengths[peaks][::-1]
+
+    if method.lower() == 'ransac':
+        residual_threshold = 4e-5
+        min_samples = 2
+        # Scikit-image
+        data = np.column_stack([k_values, n_over_lambda])
+        model_robust, inliers = ransac(data, LineModelND,
+                                       min_samples=min_samples,
+                                       residual_threshold=residual_threshold,
+                                       max_trials=100)
+        slope = model_robust.params[1][1]
+        thickness_minmax = 1 / slope /  4
+
+        # Scikit-learn
+        #X, y = k_values.reshape(-1, 1), 1/wavelengths[peaks][::-1]
+
+        ## Fit line using all data
+        #lr = linear_model.LinearRegression()
+        #lr.fit(X, y)
+
+        #slransac = linear_model.RANSACRegressor(min_samples=min_samples,
+        #                                        residual_threshold=residual_threshold)
+        #slransac.fit(X, y)
+        #inlier_mask = slransac.inlier_mask_
+        #outlier_mask = np.logical_not(inlier_mask)
+
+        ## Predict data of estimated models
+        #line_X = np.arange(X.min(), X.max())[:, np.newaxis]
+        #line_y = lr.predict(line_X)
+        #line_y_ransac = slransac.predict(line_X)
+
+        #slope = slransac.estimator_.coef_[0]
+
+        if plot:
+            fig, ax = plt.subplots()
+
+            ax.set_xlabel('extremum n°')
+            ax.set_ylabel('$n$($\lambda$) / $\lambda$')
+            ax.plot(data[inliers, 0], data[inliers, 1], 'xb', alpha=0.6, label='Inliers')
+            ax.plot(data[~inliers, 0], data[~inliers, 1], '+r', alpha=0.6, label='Outliers')
+            ax.plot(k_values, model_robust.predict_y(k_values), '-g', label='Fit')
+
+            ax.legend()
+            ax.set_title(f'Thickness = {thickness_minmax:.2f} nm')
+            import inspect
+            plt.title(inspect.currentframe().f_code.co_name)
+            plt.tight_layout()
+            plt.show()
+
+        return OptimizeResult(thickness=thickness_minmax,
+                              num_inliers=inliers.sum(),
+                              num_outliers=(~inliers).sum(),
+                              peaks_max=peaks_max,
+                              peaks_min=peaks_min)
+
+    elif method.lower() == 'linreg':
+        slope, intercept, r_value, p_value, std_err = stats.linregress(k_values, n_over_lambda)
+        #mean_n = np.mean(refractive_index)
+        thickness_minmax = 1 / slope / 4
+
+        if plot:
+            fig, ax = plt.subplots()
+
+            ax.set_xlabel('extremum n°')
+            ax.set_ylabel('$n$($\lambda$) / $\lambda$')
+            ax.plot(k_values, n_over_lambda, 's', label='Extrema')
+            ax.plot(k_values, intercept + k_values * slope, label='Fit')
+
+            ax.legend()
+            ax.set_title(f'Thickness = {thickness_minmax:.2f} nm')
+            import inspect
+            plt.title(inspect.currentframe().f_code.co_name)
+            plt.tight_layout()
+            plt.show()
+
+        return OptimizeResult(thickness=thickness_minmax,
+                              peaks_max=peaks_max,
+                              peaks_min=peaks_min,
+                              stderr=std_err)
+
+    else:
+        raise ValueError('Wrong method')

+
+
+ +
+ +
+
+ +
+
+
+ ©2025, F. Boulogne et al.. + + | + Powered by Sphinx 8.2.3 + & Alabaster 1.0.0 + +
+ + + + + + \ No newline at end of file diff --git a/docs/_build/html/_modules/optifik/scheludko.html b/docs/_build/html/_modules/optifik/scheludko.html new file mode 100644 index 0000000..8adf74f --- /dev/null +++ b/docs/_build/html/_modules/optifik/scheludko.html @@ -0,0 +1,471 @@ + + + + + + + optifik.scheludko — optifik documentation + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +

Source code for optifik.scheludko

+import numpy as np
+from scipy.optimize import curve_fit
+
+import matplotlib.pyplot as plt
+
+from .io import load_spectrum
+from .utils import OptimizeResult, setup_matplotlib
+from .analysis import finds_peak
+
+
+def _thicknesses_scheludko_at_order(wavelengths,
+                                    intensities,
+                                    interference_order,
+                                    refractive_index,
+                                    intensities_void=None):
+    """
+    Compute thicknesses vs wavelength for a given interference order.
+
+    Parameters
+    ----------
+    wavelengths : array
+        Wavelength values in nm.
+    intensities : array
+        Intensity values.
+    interference_order : int
+        Interference order.
+    refractive_index : array_like (or float)
+        Refractive index.
+    intensities_void : array, optional
+        Intensities of void.
+
+    Returns
+    -------
+    thicknesses : array
+
+    """
+    if intensities_void is None:
+        Imin = np.min(intensities)
+    else:
+        Imin = intensities_void
+
+    n = refractive_index
+    m = interference_order
+    I_norm = (np.asarray(intensities) - Imin) / (np.max(intensities) - Imin)
+
+    prefactor = wavelengths / (2 * np.pi * n)
+    argument = np.sqrt(I_norm / (1 + (1 - I_norm) * (n**2 - 1)**2 / (4 * n**2)))
+
+    if m % 2 == 0:
+        term1 = (m / 2) * np.pi
+    else:
+        term1 = ((m+1) / 2) * np.pi
+
+    term2 = (-1)**m * np.arcsin(argument)
+
+    return prefactor * (term1 + term2)
+
+
+def _Delta(wavelengths, thickness, interference_order, refractive_index):
+    """
+    Compute the Delta values.
+
+    Parameters
+    ----------
+    wavelengths : array
+        Wavelength values in nm.
+    thickness : array_like (or float)
+        Film thickness.
+    interference_order : int
+        Interference order.
+    refractive_index : array_like (or float)
+        Refractive index.
+
+    Returns
+    -------
+    ndarray
+        Delta values.
+    """
+
+    # ensure that the entries are numpy arrays
+    wavelengths = np.asarray(wavelengths)
+    h = np.asarray(thickness)
+    n = np.asarray(refractive_index)
+    m = interference_order
+
+    # Calculation of p as a function of the parity of m
+    if m % 2 == 0:
+        p = m / 2
+    else:
+        p = (m + 1) / 2
+
+    # Calculation of alpha
+    alpha = ((n**2 - 1)**2) / (4 * n**2)
+
+    # Argument of sinus
+    angle = (2 * np.pi * n * h / wavelengths) - p * np.pi
+
+    # A = sin²(argument)
+    A = np.sin(angle)**2
+
+    # Final calcuation of Delta
+    return (A * (1 + alpha)) / (1 + A * alpha)
+
+
+def _Delta_fit(xdata, thickness, interference_order):
+    """
+    Wrapper on Delta() for curve_fit.
+
+    Parameters
+    ----------
+    xdata : tuple
+        (wavelengths, refractive_index)
+    thickness : array_like (or float)
+        Film thickness.
+    interference_order : int
+        Interference order.
+
+    Returns
+    -------
+    ndarray
+        Delta values.
+
+    """
+    lambdas, r_index = xdata
+    return _Delta(lambdas, thickness, interference_order, r_index)
+
+
+

+[docs]
+def get_default_start_stop_wavelengths(wavelengths,
+                                       intensities,
+                                       refractive_index,
+                                       min_peak_prominence,
+                                       plot=None):
+    """
+    Returns the start and stop wavelength values of the last monotonic branch.
+
+    Parameters
+    ----------
+    wavelengths : array
+        Wavelength values in nm.
+    intensities : array
+        Intensity values.
+    refractive_index : scalar, optional
+        Value of the refractive index of the medium.
+    min_peak_prominence : scalar
+        Required prominence of peaks.
+    plot : bool, optional
+        Display a curve, useful for checking or debuging. The default is None.
+
+
+    Raises
+    ------
+    RuntimeError
+        if at least one maximum and one minimum are not detected.
+
+    Returns
+    -------
+    wavelength_start : scalar
+    wavelength_stop : scalar
+    """
+    # idx_min idx max
+    idx_peaks_min, idx_peaks_max = finds_peak(wavelengths, intensities,
+                                              min_peak_prominence=min_peak_prominence,
+                                              plot=plot)
+
+    failure, message = False, ''
+    if len(idx_peaks_min) == 0:
+        message += 'Failed to detect at least one minimum. '
+        failure = True
+    if len(idx_peaks_max) == 0:
+        message += 'Failed to detect at least one maximum. '
+        failure = True
+    if failure:
+        raise RuntimeError(message)
+
+    # Get the last oscillation peaks
+    lambda_min = wavelengths[idx_peaks_min[-1]]
+    lambda_max = wavelengths[idx_peaks_max[-1]]
+
+    # Order them
+    wavelength_start = min(lambda_min, lambda_max)
+    wavelength_stop = max(lambda_min, lambda_max)
+
+    return wavelength_start, wavelength_stop

+
+
+
+

+[docs]
+def thickness_from_scheludko(wavelengths,
+                             intensities,
+                             refractive_index,
+                             wavelength_start=None,
+                             wavelength_stop=None,
+                             interference_order=None,
+                             intensities_void=None,
+                             plot=None):
+    """
+    Compute the film thickness based on Scheludko method.
+
+    Parameters
+    ----------
+    wavelengths : array
+        Wavelength values in nm.
+    intensities : array
+        Intensity values.
+    refractive_index : scalar, optional
+        Value of the refractive index of the medium.
+    wavelength_start : scalar, optional
+        Starting value of a monotonic branch.
+        Mandatory if interference_order != 0.
+    wavelength_stop : scalar, optional
+        Stoping value of a monotonic branch.
+        Mandatory if interference_order != 0.
+    interference_order : scalar, optional
+        Interference order, zero or positive integer.
+        If set to None, the value is guessed.
+    intensities_void : array, optional
+        Intensity in absence of a film.
+        Mandatory if interference_order == 0.
+    plot : bool, optional
+        Display a curve, useful for checking or debuging. The default is None.
+
+    Returns
+    -------
+    results : Instance of `OptimizeResult` class.
+        The attribute `thickness` gives the thickness value in nm.
+
+    """
+    if plot:
+        setup_matplotlib()
+
+    if interference_order is None or interference_order > 0:
+        if wavelength_stop is None or wavelength_start is None:
+            raise ValueError('wavelength_start and wavelength_stop must be passed for interference_order != 0.')
+        else:
+            if wavelength_start > wavelength_stop:
+                raise ValueError('wavelength_start and wavelength_stop are swapped.')
+
+    r_index = refractive_index
+
+    # Handle the interference order
+    if interference_order is None:
+        # A bit extreme...
+        max_tested_order = 12
+
+        # mask input data
+        mask = (wavelengths >= wavelength_start) & (wavelengths <= wavelength_stop)
+        wavelengths_masked = wavelengths[mask]
+        r_index_masked = r_index[mask]
+        intensities_masked = intensities[mask]
+
+        min_difference = np.inf
+        thickness_values = None
+
+        if plot:
+            plt.figure()
+            plt.ylabel(r'$h$ ($\mathrm{{nm}}$)')
+            plt.xlabel(r'$\lambda$ ($ \mathrm{nm} $)')
+
+        for _order in range(0, max_tested_order+1):
+            h_values = _thicknesses_scheludko_at_order(wavelengths_masked,
+                                                       intensities_masked,
+                                                       _order,
+                                                       r_index_masked)
+
+            difference = np.max(h_values) - np.min(h_values)
+
+            print(f"h-difference for m={_order}: {difference:.1f} nm")
+
+            if difference < min_difference:
+                min_difference = difference
+                interference_order = _order
+                thickness_values = h_values
+
+            if plot:
+                plt.plot(wavelengths_masked, h_values, '.',
+                         markersize=3, label=f"Order={_order}")
+    elif interference_order == 0:
+
+        min_peak_prominence = 0.02
+        peaks_min, peaks_max = finds_peak(wavelengths, intensities,
+                                          min_peak_prominence=min_peak_prominence,
+                                          plot=plot)
+        if len(peaks_max) != 1:
+            raise RuntimeError('Failed to detect a single maximum peak.')
+
+        lambda_unique = wavelengths[peaks_max[0]]
+
+        # keep rhs from the maximum
+        mask = wavelengths >= lambda_unique
+        wavelengths_masked = wavelengths[mask]
+        r_index_masked = r_index[mask]
+        intensities_masked = intensities[mask]
+        intensities_void_masked = intensities_void[mask]
+
+        interference_order = 0
+        thickness_values = _thicknesses_scheludko_at_order(wavelengths_masked,
+                                                     intensities_masked,
+                                                     interference_order,
+                                                     r_index_masked,
+                                                     intensities_void=intensities_void_masked)
+
+    elif interference_order > 0:
+        h_values = _thicknesses_scheludko_at_order(wavelengths_masked,
+                                                   intensities_masked,
+                                                   interference_order,
+                                                   r_index_masked)
+        thickness_values = h_values
+    else:
+        raise ValueError('interference_order must be >= 0.')
+
+
+
+    # Compute the thickness for the selected order
+
+    # Delta
+    if interference_order == 0:
+        num = intensities_masked - np.min(intensities_void_masked)
+        denom = np.max(intensities_masked) - np.min(intensities_void_masked)
+    else:
+        num = intensities_masked - np.min(intensities_masked)
+        denom = np.max(intensities_masked) - np.min(intensities_masked)
+    Delta_from_data = num / denom
+
+
+
+    # Delta_from_data = (intensities_masked -np.min(intensities_masked))/(np.max(intensities_masked) -np.min(intensities_masked))
+    # Delta_from_data = (intensities_raw_masked -np.min(intensities_raw_masked))/(np.max(intensities_raw_masked) -np.min(intensities_raw_masked))
+
+    DeltaScheludko = _Delta(wavelengths_masked,
+                            np.mean(thickness_values),
+                            interference_order,
+                            r_index_masked)
+
+
+    xdata = (wavelengths_masked, r_index_masked)
+    popt, pcov = curve_fit(lambda x, h: _Delta_fit(x, h, interference_order), xdata, Delta_from_data, p0=[np.mean(thickness_values)])
+    fitted_h = popt[0]
+    std_err = np.sqrt(pcov[0][0])
+
+    if plot:
+        Delta_values = _Delta(wavelengths_masked, fitted_h, interference_order, r_index_masked)
+
+        plt.figure()
+        plt.plot(wavelengths_masked, Delta_from_data,
+                 'bo-', markersize=2,
+                 label=r'$\mathrm{{Smoothed}}\ \mathrm{{Data}}$')
+
+        # Scheludko
+        label = rf'$\mathrm{{Scheludko}}\ (h = {np.mean(thickness_values):.1f} \pm {np.std(thickness_values):.1f}\ \mathrm{{nm}})$'
+        plt.plot(wavelengths_masked, DeltaScheludko,
+                 'go-', markersize=2, label=label)
+        # Fit
+        label = rf'$\mathrm{{Fit}}\ (h = {fitted_h:.1f}\pm {std_err:.1f} \ \mathrm{{nm}})$'
+        plt.plot(wavelengths_masked,  Delta_values,
+                 'ro-', markersize=2,
+                 label=label)
+
+        plt.legend()
+        plt.ylabel(r'$\Delta$')
+        plt.xlabel(r'$\lambda$ ($ \mathrm{nm} $)')
+        import inspect
+        plt.title(inspect.currentframe().f_code.co_name)
+
+    return OptimizeResult(thickness=fitted_h, stderr=std_err)

+
+
+
+ +
+ +
+
+ +
+
+
+ ©2025, F. Boulogne et al.. + + | + Powered by Sphinx 8.2.3 + & Alabaster 1.0.0 + +
+ + + + + + \ No newline at end of file diff --git a/docs/_build/html/_sources/api_reference.rst.txt b/docs/_build/html/_sources/api_reference.rst.txt new file mode 100644 index 0000000..4535a57 --- /dev/null +++ b/docs/_build/html/_sources/api_reference.rst.txt @@ -0,0 +1,35 @@ +API Reference +============= + +Below is the complete reference for Optifik's public API. + + + +io +-- +.. automodule:: optifik.io + :members: + :undoc-members: + :show-inheritance: + +fft +--- +.. automodule:: optifik.fft + :members: + :undoc-members: + :show-inheritance: + +minmax +------ +.. automodule:: optifik.minmax + :members: + :undoc-members: + :show-inheritance: + +scheludko +--------- +.. automodule:: optifik.scheludko + :members: + :undoc-members: + :show-inheritance: + diff --git a/docs/_build/html/_sources/examples.rst.txt b/docs/_build/html/_sources/examples.rst.txt new file mode 100644 index 0000000..735e8c7 --- /dev/null +++ b/docs/_build/html/_sources/examples.rst.txt @@ -0,0 +1,34 @@ +Examples +======== + +Basic Optimization +------------------ + +Here's a simple example using Optifik to solve a quadratic function. + +.. code-block:: python + + from optifik import minimize + + def quadratic(x): + return (x - 3) ** 2 + + result = minimize(quadratic, x0=0) + print(result) + +Constrained Optimization +------------------------ + +.. code-block:: python + + from optifik import minimize + + def objective(x): + return x[0] ** 2 + x[1] ** 2 + + def constraint(x): + return x[0] + x[1] - 1 + + result = minimize(objective, x0=[0, 0], constraints=[constraint]) + print(result) + diff --git a/docs/_build/html/_sources/index.rst.txt b/docs/_build/html/_sources/index.rst.txt new file mode 100644 index 0000000..d9ef27d --- /dev/null +++ b/docs/_build/html/_sources/index.rst.txt @@ -0,0 +1,24 @@ +Optifik Documentation +===================== + +Welcome to the documentation for **Optifik**, a Python library for + + +Contents +-------- + +.. toctree:: + :maxdepth: 2 + :caption: Documentation + + installation + api_reference + examples + +Indices and tables +------------------ + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` + diff --git a/docs/_build/html/_sources/installation.rst.txt b/docs/_build/html/_sources/installation.rst.txt new file mode 100644 index 0000000..a0e132e --- /dev/null +++ b/docs/_build/html/_sources/installation.rst.txt @@ -0,0 +1,28 @@ +Installation +============ + +You can install Optifik using `pip`: + +.. code-block:: bash + + pip install optifik + +Alternatively, you can install it from source: + +.. code-block:: bash + + git clone https://github.com/yourusername/optifik.git + cd optifik + pip install -e . + +Requirements +------------ + +- Python >= 3.8 +- NumPy >= 1.21 + +Optional for extended functionality: + +- SciPy +- Matplotlib + diff --git a/docs/_build/html/_static/alabaster.css b/docs/_build/html/_static/alabaster.css new file mode 100644 index 0000000..7e75bf8 --- /dev/null +++ b/docs/_build/html/_static/alabaster.css @@ -0,0 +1,663 @@ +/* -- page layout ----------------------------------------------------------- */ + +body { + font-family: Georgia, serif; 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+ 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; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + 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; + } +} \ No newline at end of file diff --git a/docs/_build/html/_static/custom.css b/docs/_build/html/_static/custom.css new file mode 100644 index 0000000..2a924f1 --- /dev/null +++ b/docs/_build/html/_static/custom.css @@ -0,0 +1 @@ +/* This file intentionally left blank. */ diff --git a/docs/_build/html/_static/doctools.js b/docs/_build/html/_static/doctools.js new file mode 100644 index 0000000..0398ebb --- /dev/null +++ b/docs/_build/html/_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); diff --git a/docs/_build/html/_static/documentation_options.js b/docs/_build/html/_static/documentation_options.js new file mode 100644 index 0000000..7e4c114 --- /dev/null +++ b/docs/_build/html/_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, +}; \ No newline at end of file diff --git a/docs/_build/html/_static/file.png b/docs/_build/html/_static/file.png new file mode 100644 index 0000000..a858a41 Binary files /dev/null and b/docs/_build/html/_static/file.png differ diff --git a/docs/_build/html/_static/github-banner.svg b/docs/_build/html/_static/github-banner.svg new file mode 100644 index 0000000..c47d9dc --- /dev/null +++ b/docs/_build/html/_static/github-banner.svg @@ -0,0 +1,5 @@ + + + + + diff --git a/docs/_build/html/_static/language_data.js b/docs/_build/html/_static/language_data.js new file mode 100644 index 0000000..c7fe6c6 --- /dev/null +++ b/docs/_build/html/_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; + } +} + diff --git a/docs/_build/html/_static/minus.png b/docs/_build/html/_static/minus.png new file mode 100644 index 0000000..d96755f Binary files /dev/null and b/docs/_build/html/_static/minus.png differ diff --git a/docs/_build/html/_static/plus.png b/docs/_build/html/_static/plus.png new file mode 100644 index 0000000..7107cec Binary files /dev/null and b/docs/_build/html/_static/plus.png differ diff --git a/docs/_build/html/_static/pygments.css b/docs/_build/html/_static/pygments.css new file mode 100644 index 0000000..9392ddc --- /dev/null +++ b/docs/_build/html/_static/pygments.css @@ -0,0 +1,84 @@ +pre { line-height: 125%; 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+ +/** + * 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); diff --git a/docs/_build/html/_static/sphinx_highlight.js b/docs/_build/html/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/docs/_build/html/_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( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * 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(); +}); diff --git a/docs/_build/html/api_reference.html b/docs/_build/html/api_reference.html new file mode 100644 index 0000000..13216fe --- /dev/null +++ b/docs/_build/html/api_reference.html @@ -0,0 +1,294 @@ + + + + + + + + API Reference — optifik documentation + + + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +
+

API Reference

+

Below is the complete reference for Optifik’s public API.

+
+

io

+
+
+optifik.io.load_spectrum(spectrum_path, wavelength_min=0, wavelength_max=inf, delimiter=',')[source]
+

Load a spectrum file.

+

TODO : describe expected format

+
+
Parameters:
+
+
spectrum_pathstring

File path.

+
+
wavelength_minscalar, optional

Cut the data at this minimum wavelength (included).

+
+
wavelength_maxscalar, optional

Cut the data at this maximum wavelength (included).

+
+
delimiterstring, optional

Delimiter between columns in the datafile.

+
+
+
+
Returns:
+
+
valuesarrays

(lamdbas, intensities)

+
+
+
+
+
+ +
+
+

fft

+
+
+optifik.fft.thickness_from_fft(wavelengths, intensities, refractive_index, num_half_space=None, plot=None)[source]
+

Determine the tickness by Fast Fourier Transform.

+
+
Parameters:
+
+
wavelengthsarray

Wavelength values in nm.

+
+
intensitiesarray

Intensity values.

+
+
refractive_indexscalar, optional

Value of the refractive index of the medium.

+
+
num_half_spacescalar, optional

Number of points to compute FFT’s half space. +If None, default corresponds to 10*len(wavelengths).

+
+
plotboolean, optional

Show plot of the transformed signal and the peak detection.

+
+
+
+
Returns:
+
+
resultsInstance of OptimizeResult class.

The attribute thickness gives the thickness value in nm.

+
+
+
+
+
+ +
+
+

minmax

+
+
+optifik.minmax.thickness_from_minmax(wavelengths, intensities, refractive_index, min_peak_prominence, min_peak_distance=10, method='linreg', plot=None)[source]
+

Return the thickness from a min-max detection.

+
+
Parameters:
+
+
wavelengthsarray

Wavelength values in nm.

+
+
intensitiesarray

Intensity values.

+
+
refractive_indexscalar, optional

Value of the refractive index of the medium.

+
+
min_peak_prominencescalar, optional

Required prominence of peaks.

+
+
min_peak_distancescalar, optional

Minimum distance between peaks.

+
+
methodstring, optional

Either ‘linreg’ for linear regression or ‘ransac’ +for Randon Sampling Consensus.

+
+
plotboolean, optional

Show plots of peak detection and lin regression.

+
+
+
+
Returns:
+
+
resultsInstance of OptimizeResult class.

The attribute thickness gives the thickness value in nm.

+
+
+
+
+

Notes

+

For more details about min_peak_prominence and min_peak_distance, +see the documentation of scipy.signal.find_peaks. This function +is used to find extrema.

+
+ +
+
+

scheludko

+
+
+optifik.scheludko.get_default_start_stop_wavelengths(wavelengths, intensities, refractive_index, min_peak_prominence, plot=None)[source]
+

Returns the start and stop wavelength values of the last monotonic branch.

+
+
Parameters:
+
+
wavelengthsarray

Wavelength values in nm.

+
+
intensitiesarray

Intensity values.

+
+
refractive_indexscalar, optional

Value of the refractive index of the medium.

+
+
min_peak_prominencescalar

Required prominence of peaks.

+
+
plotbool, optional

Display a curve, useful for checking or debuging. The default is None.

+
+
+
+
Returns:
+
+
wavelength_startscalar
+
wavelength_stopscalar
+
+
+
Raises:
+
+
RuntimeError

if at least one maximum and one minimum are not detected.

+
+
+
+
+
+ +
+
+optifik.scheludko.thickness_from_scheludko(wavelengths, intensities, refractive_index, wavelength_start=None, wavelength_stop=None, interference_order=None, intensities_void=None, plot=None)[source]
+

Compute the film thickness based on Scheludko method.

+
+
Parameters:
+
+
wavelengthsarray

Wavelength values in nm.

+
+
intensitiesarray

Intensity values.

+
+
refractive_indexscalar, optional

Value of the refractive index of the medium.

+
+
wavelength_startscalar, optional

Starting value of a monotonic branch. +Mandatory if interference_order != 0.

+
+
wavelength_stopscalar, optional

Stoping value of a monotonic branch. +Mandatory if interference_order != 0.

+
+
interference_orderscalar, optional

Interference order, zero or positive integer. +If set to None, the value is guessed.

+
+
intensities_voidarray, optional

Intensity in absence of a film. +Mandatory if interference_order == 0.

+
+
plotbool, optional

Display a curve, useful for checking or debuging. The default is None.

+
+
+
+
Returns:
+
+
resultsInstance of OptimizeResult class.

The attribute thickness gives the thickness value in nm.

+
+
+
+
+
+ +
+
+ + +
+ +
+
+ +
+
+
+ ©2025, F. Boulogne et al.. + + | + Powered by Sphinx 8.2.3 + & Alabaster 1.0.0 + + | + Page source +
+ + + + + + \ No newline at end of file diff --git a/docs/_build/html/examples.html b/docs/_build/html/examples.html new file mode 100644 index 0000000..ca5effb --- /dev/null +++ b/docs/_build/html/examples.html @@ -0,0 +1,140 @@ + + + + + + + + Examples — optifik documentation + + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +
+

Examples

+
+

Basic Optimization

+

Here’s a simple example using Optifik to solve a quadratic function.

+
from optifik import minimize
+
+def quadratic(x):
+    return (x - 3) ** 2
+
+result = minimize(quadratic, x0=0)
+print(result)
+
+
+
+
+

Constrained Optimization

+
from optifik import minimize
+
+def objective(x):
+    return x[0] ** 2 + x[1] ** 2
+
+def constraint(x):
+    return x[0] + x[1] - 1
+
+result = minimize(objective, x0=[0, 0], constraints=[constraint])
+print(result)
+
+
+
+
+ + +
+ +
+
+ +
+
+
+ ©2025, F. Boulogne et al.. + + | + Powered by Sphinx 8.2.3 + & Alabaster 1.0.0 + + | + Page source +
+ + + + + + \ No newline at end of file diff --git a/docs/_build/html/genindex.html b/docs/_build/html/genindex.html new file mode 100644 index 0000000..2fbfb10 --- /dev/null +++ b/docs/_build/html/genindex.html @@ -0,0 +1,195 @@ + + + + + + + Index — optifik documentation + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ + +

Index

+ +
+ G + | L + | M + | O + | T + +
+

G

+ + +
+ +

L

+ + +
+ +

M

+ + +
+ +

O

+ + + +
    +
  • + optifik.fft + +
    • +
  • + optifik.io + +
    • +
    +
  • + optifik.minmax + +
    • +
  • + optifik.scheludko + +
    • +
+ +

T

+ + + +
+ + + +
+ +
+
+ +
+
+
+ ©2025, F. Boulogne et al.. + + | + Powered by Sphinx 8.2.3 + & Alabaster 1.0.0 + +
+ + + + + + \ No newline at end of file diff --git a/docs/_build/html/index.html b/docs/_build/html/index.html new file mode 100644 index 0000000..36a3765 --- /dev/null +++ b/docs/_build/html/index.html @@ -0,0 +1,141 @@ + + + + + + + + Optifik Documentation — optifik documentation + + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +
+

Optifik Documentation

+

Welcome to the documentation for Optifik, a Python library for

+
+

Contents

+
+

Documentation

+ +
+
+
+

Indices and tables

+ +
+
+ + +
+ +
+
+ +
+
+
+ ©2025, F. Boulogne et al.. + + | + Powered by Sphinx 8.2.3 + & Alabaster 1.0.0 + + | + Page source +
+ + + + + + \ No newline at end of file diff --git a/docs/_build/html/installation.html b/docs/_build/html/installation.html new file mode 100644 index 0000000..f8235b9 --- /dev/null +++ b/docs/_build/html/installation.html @@ -0,0 +1,135 @@ + + + + + + + + Installation — optifik documentation + + + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +
+

Installation

+

You can install Optifik using pip:

+
pip install optifik
+
+
+

Alternatively, you can install it from source:

+
git clone https://github.com/yourusername/optifik.git
+cd optifik
+pip install -e .
+
+
+
+

Requirements

+
    +

  • Python >= 3.8

    • +

  • NumPy >= 1.21

    • +
+

Optional for extended functionality:

+
    +

  • SciPy

    • +

  • Matplotlib

    • +
+
+
+ + +
+ +
+
+ +
+
+
+ ©2025, F. Boulogne et al.. + + | + Powered by Sphinx 8.2.3 + & Alabaster 1.0.0 + + | + Page source +
+ + + + + + \ No newline at end of file diff --git a/docs/_build/html/objects.inv b/docs/_build/html/objects.inv new file mode 100644 index 0000000..d7e2df7 Binary files /dev/null and b/docs/_build/html/objects.inv differ diff --git a/docs/_build/html/py-modindex.html b/docs/_build/html/py-modindex.html new file mode 100644 index 0000000..f274dbd --- /dev/null +++ b/docs/_build/html/py-modindex.html @@ -0,0 +1,140 @@ + + + + + + + Python Module Index — optifik documentation + + + + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ + +

Python Module Index

+ +
+ o +
+ + + + + + + + + + + + + + + + + + + +
 
+ o
+ optifik +
    + optifik.fft +
    + optifik.io +
    + optifik.minmax +
    + optifik.scheludko +
+ + +
+ +
+
+ +
+
+
+ ©2025, F. Boulogne et al.. + + | + Powered by Sphinx 8.2.3 + & Alabaster 1.0.0 + +
+ + + + + + \ No newline at end of file diff --git a/docs/_build/html/search.html b/docs/_build/html/search.html new file mode 100644 index 0000000..70179d7 --- /dev/null +++ b/docs/_build/html/search.html @@ -0,0 +1,123 @@ + + + + + + + Search — optifik documentation + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +

Search

+ + + + +

+ Searching for multiple words only shows matches that contain + all words. +

+ + +
+ + + +
+ + +
+ + +
+ +
+
+ +
+
+
+ ©2025, F. Boulogne et al.. + + | + Powered by Sphinx 8.2.3 + & Alabaster 1.0.0 + +
+ + + + + + \ No newline at end of file diff --git a/docs/_build/html/searchindex.js b/docs/_build/html/searchindex.js new file mode 100644 index 0000000..507f4a8 --- /dev/null +++ b/docs/_build/html/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({"alltitles":{"API Reference":[[0,null]],"Basic Optimization":[[1,"basic-optimization"]],"Constrained Optimization":[[1,"constrained-optimization"]],"Contents":[[2,"contents"]],"Documentation":[[2,null]],"Examples":[[1,null]],"Indices and tables":[[2,"indices-and-tables"]],"Installation":[[3,null]],"Optifik 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Reference","Examples","Optifik Documentation","Installation"],"titleterms":{"api":0,"basic":1,"constrain":1,"content":2,"document":2,"exampl":1,"fft":0,"indic":2,"instal":3,"io":0,"minmax":0,"optifik":2,"optim":1,"refer":0,"requir":3,"scheludko":0,"tabl":2}}) \ No newline at end of file diff --git a/examples.html b/examples.html new file mode 100644 index 0000000..ca5effb --- /dev/null +++ b/examples.html @@ -0,0 +1,140 @@ + + + + + + + + Examples — optifik documentation + + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +
+

Examples

+
+

Basic Optimization

+

Here’s a simple example using Optifik to solve a quadratic function.

+
from optifik import minimize
+
+def quadratic(x):
+    return (x - 3) ** 2
+
+result = minimize(quadratic, x0=0)
+print(result)
+
+
+
+
+

Constrained Optimization

+
from optifik import minimize
+
+def objective(x):
+    return x[0] ** 2 + x[1] ** 2
+
+def constraint(x):
+    return x[0] + x[1] - 1
+
+result = minimize(objective, x0=[0, 0], constraints=[constraint])
+print(result)
+
+
+
+
+ + +
+ +
+
+ +
+
+
+ ©2025, F. Boulogne et al.. + + | + Powered by Sphinx 8.2.3 + & Alabaster 1.0.0 + + | + Page source +
+ + + + + + \ No newline at end of file diff --git a/genindex.html b/genindex.html new file mode 100644 index 0000000..2fbfb10 --- /dev/null +++ b/genindex.html @@ -0,0 +1,195 @@ + + + + + + + Index — optifik documentation + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ + +

Index

+ +
+ G + | L + | M + | O + | T + +
+

G

+ + +
+ +

L

+ + +
+ +

M

+ + +
+ +

O

+ + + +
    +
  • + optifik.fft + +
    • +
  • + optifik.io + +
    • +
    +
  • + optifik.minmax + +
    • +
  • + optifik.scheludko + +
    • +
+ +

T

+ + + +
+ + + +
+ +
+
+ +
+
+
+ ©2025, F. Boulogne et al.. + + | + Powered by Sphinx 8.2.3 + & Alabaster 1.0.0 + +
+ + + + + + \ No newline at end of file diff --git a/index.html b/index.html new file mode 100644 index 0000000..36a3765 --- /dev/null +++ b/index.html @@ -0,0 +1,141 @@ + + + + + + + + Optifik Documentation — optifik documentation + + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +
+

Optifik Documentation

+

Welcome to the documentation for Optifik, a Python library for

+
+

Contents

+
+

Documentation

+ +
+
+
+

Indices and tables

+ +
+
+ + +
+ +
+
+ +
+
+
+ ©2025, F. Boulogne et al.. + + | + Powered by Sphinx 8.2.3 + & Alabaster 1.0.0 + + | + Page source +
+ + + + + + \ No newline at end of file diff --git a/installation.html b/installation.html new file mode 100644 index 0000000..f8235b9 --- /dev/null +++ b/installation.html @@ -0,0 +1,135 @@ + + + + + + + + Installation — optifik documentation + + + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +
+

Installation

+

You can install Optifik using pip:

+
pip install optifik
+
+
+

Alternatively, you can install it from source:

+
git clone https://github.com/yourusername/optifik.git
+cd optifik
+pip install -e .
+
+
+
+

Requirements

+
    +

  • Python >= 3.8

    • +

  • NumPy >= 1.21

    • +
+

Optional for extended functionality:

+
    +

  • SciPy

    • +

  • Matplotlib

    • +
+
+
+ + +
+ +
+
+ +
+
+
+ ©2025, F. Boulogne et al.. + + | + Powered by Sphinx 8.2.3 + & Alabaster 1.0.0 + + | + Page source +
+ + + + + + \ No newline at end of file diff --git a/objects.inv b/objects.inv new file mode 100644 index 0000000..d7e2df7 Binary files /dev/null and b/objects.inv differ diff --git a/optifik.egg-info/PKG-INFO b/optifik.egg-info/PKG-INFO new file mode 100644 index 0000000..1f7b65b --- /dev/null +++ b/optifik.egg-info/PKG-INFO @@ -0,0 +1,28 @@ +Metadata-Version: 2.4 +Name: optifik +Version: 0.1.0 +Summary: Compute film thickness from interferometry +Author-email: François Boulogne , Victor Ziapkoff +License-Expression: GPL-3.0-or-later +Project-URL: Homepage, https://github.com/votrecompte/votreprojet +Project-URL: Documentation, https://github.com/votrecompte/votreprojet#readme +Project-URL: Repository, https://github.com/sciunto-org/optifik +Project-URL: Issues, https://github.com/sciunto-org/optifik/issues +Requires-Python: >=3.8 +Description-Content-Type: text/markdown +Requires-Dist: numpy>=1.10.0 +Requires-Dist: scipy>=1.1.0 +Requires-Dist: matplotlib>=1.3.1 +Provides-Extra: dev 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