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simplify finds_peak

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François Boulogne 2025-05-21 14:05:08 +02:00
parent 022966608a
commit 56aac01151
6 changed files with 66 additions and 88 deletions
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40
tests/test_basic.py
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@ -7,8 +7,7 @@ from optifik.analysis import thickness_from_fft
from optifik.analysis import thickness_from_minmax
from optifik.analysis import thickness_from_scheludko
from optifik.analysis import thickness_for_order0
from optifik.analysis import plot_xy
from optifik.analysis import Data_Smoothed
from optifik.analysis import smooth_intensities
from optifik.analysis import Prominence_from_fft
from optifik.analysis import finds_peak
from optifik.io import load_spectrum
@ -20,8 +19,8 @@ def test_FFT():
expected = 3524.51
spectrum_path = os.path.join(FOLDER, FILE_NAME)
raw_intensities = load_spectrum(spectrum_path)
smoothed_intensities, intensities, lambdas = Data_Smoothed(spectrum_path)
lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
smoothed_intensities = smooth_intensities(raw_intensities)
indice = 1.324188 + 3102.060378 / (lambdas**2)
thickness_FFT = thickness_from_fft(lambdas,
@ -37,8 +36,8 @@ def test_minmax_ransac():
expected = 1338.35
spectrum_path = os.path.join(FOLDER, FILE_NAME)
raw_intensities = load_spectrum(spectrum_path)
smoothed_intensities, intensities, lambdas = Data_Smoothed(spectrum_path)
lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
smoothed_intensities = smooth_intensities(raw_intensities)
indice = 1.324188 + 3102.060378 / (lambdas**2)
prominence = Prominence_from_fft(lambdas=lambdas,
@ -64,14 +63,15 @@ def test_scheludko_4peaks():
expected = 777.07
spectrum_path = os.path.join(FOLDER, FILE_NAME)
raw_intensities = load_spectrum(spectrum_path)
smoothed_intensities, intensities, lambdas = Data_Smoothed(spectrum_path)
lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
smoothed_intensities = smooth_intensities(raw_intensities)
indice = 1.324188 + 3102.060378 / (lambdas**2)
prominence = Prominence_from_fft(lambdas=lambdas, intensities=smoothed_intensities, refractive_index=indice, plot=False)
total_extrema, smoothed_intensities, raw_intensities, lambdas, peaks_min, peaks_max = finds_peak(spectrum_path,
min_peak_prominence=prominence)
total_extrema, peaks_min, peaks_max = finds_peak(lambdas, smoothed_intensities,
min_peak_prominence=prominence,
plot=False)
result = thickness_from_scheludko(lambdas, smoothed_intensities,
@ -89,15 +89,15 @@ def test_scheludko_2peaks():
expected = 495.69
spectrum_path = os.path.join(FOLDER, FILE_NAME)
raw_intensities = load_spectrum(spectrum_path)
smoothed_intensities, intensities, lambdas = Data_Smoothed(spectrum_path)
lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
smoothed_intensities = smooth_intensities(raw_intensities)
indice = 1.324188 + 3102.060378 / (lambdas**2)
prominence = 0.03
total_extrema, smoothed_intensities, raw_intensities, lambdas, peaks_min, peaks_max = finds_peak(spectrum_path,
min_peak_prominence=prominence)
total_extrema, peaks_min, peaks_max = finds_peak(lambdas, smoothed_intensities,
min_peak_prominence=prominence,
plot=False)
result = thickness_from_scheludko(lambdas, smoothed_intensities,
peaks_min, peaks_max,
@ -116,15 +116,15 @@ def test_order0():
expected = 115.33
spectrum_path = os.path.join(FOLDER, FILE_NAME)
raw_intensities = load_spectrum(spectrum_path)
smoothed_intensities, intensities, lambdas = Data_Smoothed(spectrum_path)
lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
smoothed_intensities = smooth_intensities(raw_intensities)
indice = 1.324188 + 3102.060378 / (lambdas**2)
prominence = 0.03
total_extrema, smoothed_intensities, raw_intensities, lambdas, peaks_min, peaks_max = finds_peak(spectrum_path,
min_peak_prominence=prominence)
total_extrema, peaks_min, peaks_max = finds_peak(lambdas, smoothed_intensities,
min_peak_prominence=prominence,
plot=False)
result = thickness_for_order0(lambdas, smoothed_intensities,
peaks_min, peaks_max,