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include peak detection in scheludko

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This commit is contained in:
François Boulogne 2025-05-21 14:43:20 +02:00
parent 56aac01151
commit ccd1f2c1f0
7 changed files with 100 additions and 82 deletions
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4
tests/test_SV1.py
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@ -29,10 +29,6 @@ def test_minmax(spectrum_path, expected):
indice = 1.324188 + 3102.060378 / (lambdas**2)
prominence = 0.02
total_extrema, peaks_min, peaks_max = finds_peak(lambdas, smoothed_intensities,
min_peak_prominence=prominence,
plot=False)
thickness_minmax = thickness_from_minmax(lambdas,
smoothed_intensities,
refractive_index=indice,

15
tests/test_SV2o5.py
View file

@ -6,7 +6,6 @@ import pytest
from optifik.scheludko import thickness_from_scheludko
from optifik.io import load_spectrum
from optifik.analysis import smooth_intensities
from optifik.analysis import finds_peak
import yaml
@ -22,22 +21,18 @@ def load():
@pytest.mark.parametrize("spectrum_path, expected", load())
def test_minmax(spectrum_path, expected):
def test_SV2o5(spectrum_path, expected):
lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
smoothed_intensities = smooth_intensities(raw_intensities)
refractive_index = 1.324188 + 3102.060378 / (lambdas**2)
prominence = 0.02
total_extrema, peaks_min, peaks_max = finds_peak(lambdas, smoothed_intensities,
min_peak_prominence=prominence,
plot=False)
thickness_scheludko = thickness_from_scheludko(lambdas,
smoothed_intensities,
peaks_min,
peaks_max,
refractive_index)
thickness_scheludko = thickness_from_scheludko(lambdas, smoothed_intensities,
refractive_index=refractive_index,
min_peak_prominence=prominence,
plot=False)
result = thickness_scheludko.thickness
assert_allclose(result, expected, rtol=1e-1)

26
tests/test_basic.py
View file

@ -3,13 +3,12 @@ import numpy as np
from numpy.testing import assert_allclose
import pytest
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.fft import thickness_from_fft
from optifik.minmax import thickness_from_minmax
from optifik.scheludko import thickness_from_scheludko
from optifik.scheludko import thickness_for_order0
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
@ -69,14 +68,10 @@ def test_scheludko_4peaks():
prominence = Prominence_from_fft(lambdas=lambdas, intensities=smoothed_intensities, refractive_index=indice, plot=False)
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,
refractive_index=indice,
min_peak_prominence=prominence,
plot=False)
assert_allclose(result.thickness, expected, rtol=1e-1)
@ -95,13 +90,9 @@ def test_scheludko_2peaks():
prominence = 0.03
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,
refractive_index=indice,
min_peak_prominence=prominence,
plot=False)
assert_allclose(result.thickness, expected, rtol=1e-1)
@ -122,13 +113,10 @@ def test_order0():
prominence = 0.03
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,
refractive_index=indice,
min_peak_prominence=prominence,
plot=False)
assert_allclose(result.thickness, expected, rtol=1e-1)