refactoring
This commit is contained in:
François Boulogne
parent
439104a17f
commit
12922f0f79
3 changed files with 87 additions and 37 deletions
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@ -9,10 +9,10 @@ from .analysis import finds_peak
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def _thicknesses_scheludko_at_order(wavelengths,
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intensities,
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interference_order,
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refractive_index,
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Imin=None):
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intensities,
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interference_order,
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refractive_index,
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intensities_void=None):
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"""
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Compute thicknesses vs wavelength for a given interference order.
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@ -26,25 +26,25 @@ def _thicknesses_scheludko_at_order(wavelengths,
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Interference order.
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refractive_index : array_like (or float)
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Refractive index.
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Imin : TYPE, optional
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DESCRIPTION. The default is None.
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intensities_void : array, optional
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Intensities of void.
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Returns
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-------
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thickness : TYPE
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DESCRIPTION.
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thicknesses : array
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"""
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if Imin is None:
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if intensities_void is None:
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Imin = np.min(intensities)
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else:
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Imin = intensities_void
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n = refractive_index
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m = interference_order
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I = (np.asarray(intensities) - Imin) / (np.max(intensities) - Imin)
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I_norm = (np.asarray(intensities) - Imin) / (np.max(intensities) - Imin)
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prefactor = wavelengths / (2 * np.pi * n)
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argument = np.sqrt(I / (1 + (1 - I) * (n**2 - 1)**2 / (4 * n**2)))
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argument = np.sqrt(I_norm / (1 + (1 - I_norm) * (n**2 - 1)**2 / (4 * n**2)))
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if m % 2 == 0:
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term1 = (m / 2) * np.pi
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@ -75,7 +75,6 @@ def _Delta(wavelengths, thickness, interference_order, refractive_index):
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-------
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ndarray
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Delta values.
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"""
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# ensure that the entries are numpy arrays
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@ -131,24 +130,51 @@ def get_default_start_stop_wavelengths(wavelengths,
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refractive_index,
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min_peak_prominence,
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plot=None):
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"""
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Returns the start and stop wavelength values of the last monotonic branch.
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Parameters
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----------
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wavelengths : array
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Wavelength values in nm.
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intensities : array
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Intensity values.
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refractive_index : scalar, optional
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Value of the refractive index of the medium.
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min_peak_prominence : scalar
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Required prominence of peaks.
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plot : bool, optional
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Display a curve, useful for checking or debuging. The default is None.
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Raises
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------
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RuntimeError
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if at least one maximum and one minimum are not detected.
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Returns
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-------
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wavelength_start : scalar
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wavelength_stop : scalar
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"""
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# idx_min idx max
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peaks_min, peaks_max = finds_peak(wavelengths, intensities,
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min_peak_prominence=min_peak_prominence,
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plot=plot)
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idx_peaks_min, idx_peaks_max = finds_peak(wavelengths, intensities,
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min_peak_prominence=min_peak_prominence,
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plot=plot)
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failure, message = False, ''
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if len(peaks_min) == 0:
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if len(idx_peaks_min) == 0:
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message += 'Failed to detect at least one minimum. '
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failure = True
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if len(peaks_max) == 0:
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if len(idx_peaks_max) == 0:
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message += 'Failed to detect at least one maximum. '
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failure = True
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if failure:
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raise RuntimeError(message)
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# Get the last oscillation peaks
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lambda_min = wavelengths[peaks_min[-1]]
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lambda_max = wavelengths[peaks_max[-1]]
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lambda_min = wavelengths[idx_peaks_min[-1]]
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lambda_max = wavelengths[idx_peaks_max[-1]]
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# Order them
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wavelength_start = min(lambda_min, lambda_max)
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@ -163,9 +189,10 @@ def thickness_from_scheludko(wavelengths,
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wavelength_start=None,
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wavelength_stop=None,
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interference_order=None,
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intensities_void=None,
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plot=None):
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"""
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Compute the film thickness based on Scheludko method.
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Parameters
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----------
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@ -175,13 +202,25 @@ def thickness_from_scheludko(wavelengths,
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Intensity values.
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refractive_index : scalar, optional
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Value of the refractive index of the medium.
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wavelength_start : scalar, optional
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Starting value of a monotonic branch.
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Mandatory if interference_order != 0.
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wavelength_start : scalar, optional
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Stoping value of a monotonic branch.
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Mandatory if interference_order != 0.
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interference_order : scalar, optional
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Interference order, zero or positive integer.
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If set to None, the value is guessed.
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intensities_void : array, optional
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Intensity in absence of a film.
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Mandatory if interference_order == 0.
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plot : bool, optional
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Display a curve, useful for checking or debuging. The default is None.
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Returns
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-------
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thickness : TYPE
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DESCRIPTION.
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results : Instance of `OptimizeResult` class.
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The attribute `thickness` gives the thickness value in nm.
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"""
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if plot:
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@ -196,7 +235,6 @@ def thickness_from_scheludko(wavelengths,
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r_index = refractive_index
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# Handle the interference order
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if interference_order is None:
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# A bit extreme...
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@ -208,7 +246,6 @@ def thickness_from_scheludko(wavelengths,
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r_index_masked = r_index[mask]
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intensities_masked = intensities[mask]
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min_difference = np.inf
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thickness_values = None
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@ -217,26 +254,25 @@ def thickness_from_scheludko(wavelengths,
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plt.ylabel(r'$h$ ($\mathrm{{nm}}$)')
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plt.xlabel(r'$\lambda$ ($ \mathrm{nm} $)')
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for m in range(0, max_tested_order+1):
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for _order in range(0, max_tested_order+1):
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h_values = _thicknesses_scheludko_at_order(wavelengths_masked,
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intensities_masked,
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m,
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_order,
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r_index_masked)
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difference = np.max(h_values) - np.min(h_values)
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print(f"h-difference for m={m}: {difference:.1f} nm")
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print(f"h-difference for m={_order}: {difference:.1f} nm")
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if difference < min_difference:
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min_difference = difference
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interference_order = m
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interference_order = _order
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thickness_values = h_values
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if plot:
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plt.plot(wavelengths_masked, h_values,'.', markersize=3, label=f"Épaisseur du film (Scheludko, m={m})")
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plt.plot(wavelengths_masked, h_values, '.',
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markersize=3, label=f"Order={_order}")
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elif interference_order == 0:
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File_I_min = 'tests/spectre_trou/000043641.xy'
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_, intensities_I_min = load_spectrum(File_I_min, lambda_min=450)
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min_peak_prominence = 0.02
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peaks_min, peaks_max = finds_peak(wavelengths, intensities,
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@ -252,7 +288,7 @@ def thickness_from_scheludko(wavelengths,
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wavelengths_masked = wavelengths[mask]
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r_index_masked = r_index[mask]
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intensities_masked = intensities[mask]
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intensities_I_min_masked =intensities_I_min[mask]
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intensities_I_min_masked = intensities_void[mask]
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interference_order = 0
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thickness_values = _thicknesses_scheludko_at_order(wavelengths_masked,
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@ -289,9 +325,9 @@ def thickness_from_scheludko(wavelengths,
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# Delta_from_data = (intensities_raw_masked -np.min(intensities_raw_masked))/(np.max(intensities_raw_masked) -np.min(intensities_raw_masked))
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DeltaScheludko = _Delta(wavelengths_masked,
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np.mean(thickness_values),
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interference_order,
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r_index_masked)
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np.mean(thickness_values),
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interference_order,
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r_index_masked)
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xdata = (wavelengths_masked, r_index_masked)
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