include peak detection in scheludko
This commit is contained in:
François Boulogne
parent
56aac01151
commit
ccd1f2c1f0
7 changed files with 100 additions and 82 deletions
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@ -15,13 +15,23 @@ plt.rcParams.update({
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from .io import load_spectrum
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from .fft import *
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from .scheludko import *
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from .minmax import *
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def plot_spectrum(lambdas, intensities, title=''):
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plt.figure(figsize=(10, 6),dpi =600)
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plt.plot(lambdas, intensities, 'o-', markersize=2)
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plt.xlabel(r'$\lambda$ (nm)')
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plt.ylabel(r'$I^*$')
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plt.title(title)
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plt.tight_layout()
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plt.show()
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def plot_xy(file_path, plot=True):
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try:
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@ -62,40 +72,26 @@ def finds_peak(lambdas, intensities, min_peak_prominence, min_peak_distance=10,
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Distance minimale entre les pics.
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"""
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smoothed_intensities = intensities
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# Trouver les maxima et minima sur le signal lissé
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peaks_max, _ = find_peaks(smoothed_intensities, prominence=min_peak_prominence, distance=min_peak_distance)
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peaks_min, _ = find_peaks(-smoothed_intensities, prominence=min_peak_prominence, distance=min_peak_distance)
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peaks_max, _ = find_peaks(intensities, prominence=min_peak_prominence, distance=min_peak_distance)
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peaks_min, _ = find_peaks(-intensities, prominence=min_peak_prominence, distance=min_peak_distance)
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if plot:
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plt.figure(figsize=(10, 6),dpi =600)
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plt.plot(lambdas, smoothed_intensities, 'o-', markersize=2, label="Smoothed data")
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plt.plot(lambdas[peaks_max], smoothed_intensities[peaks_max], 'ro')
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plt.plot(lambdas[peaks_min], smoothed_intensities[peaks_min], 'ro')
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plt.plot(lambdas, intensities, 'o-', markersize=2, label="Smoothed data")
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plt.plot(lambdas[peaks_max], intensities[peaks_max], 'ro')
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plt.plot(lambdas[peaks_min], intensities[peaks_min], 'ro')
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plt.xlabel(r'$\lambda$ (nm)')
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plt.ylabel(r'$I^*$')
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plt.legend()
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plt.tight_layout()
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plt.show()
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# Nombre total d’extremums
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total_extrema = len(peaks_max) + len(peaks_min)
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if total_extrema >= 15:
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print('Number of extrema', total_extrema,'.')
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print('FFT method')
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if total_extrema <= 15 and total_extrema > 4:
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print('Number of extrema', total_extrema,'.')
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print('OOSpectro method')
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if total_extrema <= 4:
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print('Number of extrema', total_extrema,'.')
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print('Scheludko method')
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return total_extrema, peaks_min, peaks_max
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return peaks_min, peaks_max
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@ -3,10 +3,10 @@ import os.path
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from .analysis import *
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from .io import load_spectrum
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def auto(DATA_FOLDER, FILE_NAME, plot=None):
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def auto(spectrum_file, plot=None):
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spectre_file = os.path.join(DATA_FOLDER, FILE_NAME)
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spectre_file = spectrum_file
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##### Affichage du spectre brut et récupération des Intesités brutes#####
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@ -32,17 +32,20 @@ def auto(DATA_FOLDER, FILE_NAME, plot=None):
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prominence = 0.03
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##### Find Peak #####
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total_extrema, peaks_min, peaks_max = finds_peak(lambdas, smoothed_intensities,
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peaks_min, peaks_max = finds_peak(lambdas, smoothed_intensities,
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min_peak_prominence=prominence,
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plot=plot)
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plot=False)
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##### Epaisseur selon la methode #####
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#thickness_FFT = thickness_from_fft(lambdas,smoothed_intensities,refractive_index=1.33)
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total_extrema = len(peaks_max) + len(peaks_min)
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if total_extrema > 15 and total_extrema > 4:
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print('Apply method FFT')
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thickness_FFT = thickness_from_fft(lambdas,smoothed_intensities,
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thickness_FFT = thickness_from_fft(lambdas, smoothed_intensities,
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refractive_index=indice,
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plot=plot)
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thickness = thickness_FFT.thickness
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@ -51,7 +54,7 @@ def auto(DATA_FOLDER, FILE_NAME, plot=None):
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if total_extrema <= 15 and total_extrema > 4:
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print('Apply method minmax')
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thickness_minmax = thickness_from_minmax(lambdas,smoothed_intensities,
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thickness_minmax = thickness_from_minmax(lambdas, smoothed_intensities,
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refractive_index=indice,
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min_peak_prominence=prominence,
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plot=plot)
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@ -61,8 +64,8 @@ def auto(DATA_FOLDER, FILE_NAME, plot=None):
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if total_extrema <= 4 and total_extrema >= 2: #& 2peak minimum:
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print('Apply method Scheludko')
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thickness = thickness_from_scheludko(lambdas, smoothed_intensities,
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peaks_min, peaks_max,
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refractive_index=indice,
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min_peak_prominence=prominence,
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plot=plot)
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print(f'thickness: {thickness:.2f} nm')
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@ -70,8 +73,8 @@ def auto(DATA_FOLDER, FILE_NAME, plot=None):
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print('Apply method ordre0')
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thickness = thickness_for_order0(lambdas, smoothed_intensities,
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peaks_min, peaks_max,
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refractive_index=indice,
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min_peak_prominence=prominence,
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plot=plot)
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print(f'thickness: {thickness:.2f} nm')
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@ -1,6 +1,6 @@
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import numpy as np
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from .io import load_spectrum
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from scipy.optimize import curve_fit
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import matplotlib.pyplot as plt
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@ -12,8 +12,9 @@ plt.rcParams.update({
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'legend.fontsize': 23,
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})
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from .io import load_spectrum
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from .utils import OptimizeResult
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from .analysis import finds_peak
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def thickness_scheludko_at_order(wavelengths,
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intensity,
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@ -114,9 +115,8 @@ def Delta_fit(xdata, thickness, interference_order):
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def thickness_from_scheludko(lambdas,
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smoothed_intensities,
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peaks_min,
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peaks_max,
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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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@ -129,10 +129,6 @@ def thickness_from_scheludko(lambdas,
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DESCRIPTION.
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smoothed_intensities : TYPE
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DESCRIPTION.
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peaks_min : TYPE
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DESCRIPTION.
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peaks_max : TYPE
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DESCRIPTION.
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refractive_index : TYPE
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DESCRIPTION.
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plot : TYPE, optional
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@ -144,9 +140,13 @@ def thickness_from_scheludko(lambdas,
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DESCRIPTION.
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"""
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max_tested_order = 12
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r_index = refractive_index
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peaks_min, peaks_max = finds_peak(lambdas, smoothed_intensities,
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min_peak_prominence=min_peak_prominence,
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plot=False)
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lambda_min = lambdas[peaks_min[-1]]
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lambda_max = lambdas[peaks_max[-1]]
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@ -169,11 +169,12 @@ def thickness_from_scheludko(lambdas,
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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, 9):
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for m in range(0, max_tested_order+1):
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h_values = thickness_scheludko_at_order(lambdas_masked, intensities_masked, m, r_index_masked)
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if plot:
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plt.plot(lambdas_masked, h_values,'.', markersize =3, label=f"Épaisseur du film (Scheludko, m={m})")
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plt.plot(lambdas_masked, h_values,'.', markersize=3, label=f"Épaisseur du film (Scheludko, m={m})")
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ecart = np.max(h_values)-np.min(h_values)
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print(f"Écart pour m={m} : {ecart:.3f} nm")
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@ -213,15 +214,20 @@ def thickness_from_scheludko(lambdas,
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def thickness_for_order0(lambdas,
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smoothed_intensities,
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peaks_min,
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peaks_max,
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refractive_index,
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min_peak_prominence,
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plot=None):
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File_I_min = 'tests/spectre_trou/000043641.xy'
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r_index = refractive_index
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peaks_min, peaks_max = finds_peak(lambdas, smoothed_intensities,
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min_peak_prominence=min_peak_prominence,
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plot=False)
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lambdas_I_min, intensities_I_min = load_spectrum(File_I_min, lambda_min=450)
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