simplify finds_peak
This commit is contained in:
François Boulogne
parent
022966608a
commit
56aac01151
6 changed files with 66 additions and 88 deletions
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@ -4,9 +4,9 @@ from numpy.testing import assert_allclose
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import pytest
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from optifik.minmax import thickness_from_minmax
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from optifik.analysis import Data_Smoothed
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from optifik.analysis import finds_peak
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from optifik.io import load_spectrum
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from optifik.analysis import smooth_intensities
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from optifik.analysis import finds_peak
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import yaml
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@ -21,17 +21,17 @@ def load():
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return data
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@pytest.mark.parametrize("spectrum, expected", load())
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def test_minmax(spectrum, expected):
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raw_intensities = load_spectrum(spectrum)
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smoothed_intensities, intensities, lambdas = Data_Smoothed(spectrum)
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@pytest.mark.parametrize("spectrum_path, expected", load())
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def test_minmax(spectrum_path, expected):
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lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
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smoothed_intensities = smooth_intensities(raw_intensities)
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indice = 1.324188 + 3102.060378 / (lambdas**2)
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prominence = 0.02
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total_extrema, smoothed_intensities, raw_intensities, lambdas, peaks_min, peaks_max = finds_peak(spectrum,
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min_peak_prominence=prominence)
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total_extrema, peaks_min, peaks_max = finds_peak(lambdas, smoothed_intensities,
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min_peak_prominence=prominence,
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plot=False)
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thickness_minmax = thickness_from_minmax(lambdas,
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smoothed_intensities,
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@ -5,7 +5,7 @@ import pytest
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from optifik.scheludko import thickness_from_scheludko
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from optifik.io import load_spectrum
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from optifik.analysis import Data_Smoothed
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from optifik.analysis import smooth_intensities
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from optifik.analysis import finds_peak
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import yaml
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@ -21,17 +21,17 @@ def load():
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return data
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@pytest.mark.parametrize("spectrum, expected", load())
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def test_minmax(spectrum, expected):
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raw_intensities = load_spectrum(spectrum)
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smoothed_intensities, intensities, lambdas = Data_Smoothed(spectrum)
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@pytest.mark.parametrize("spectrum_path, expected", load())
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def test_minmax(spectrum_path, expected):
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lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
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smoothed_intensities = smooth_intensities(raw_intensities)
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refractive_index = 1.324188 + 3102.060378 / (lambdas**2)
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prominence = 0.02
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total_extrema, smoothed_intensities, raw_intensities, lambdas, peaks_min, peaks_max = finds_peak(spectrum,
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min_peak_prominence=prominence)
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total_extrema, peaks_min, peaks_max = finds_peak(lambdas, smoothed_intensities,
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min_peak_prominence=prominence,
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plot=False)
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thickness_scheludko = thickness_from_scheludko(lambdas,
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smoothed_intensities,
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@ -7,8 +7,7 @@ from optifik.analysis import thickness_from_fft
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from optifik.analysis import thickness_from_minmax
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from optifik.analysis import thickness_from_scheludko
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from optifik.analysis import thickness_for_order0
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from optifik.analysis import plot_xy
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from optifik.analysis import Data_Smoothed
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from optifik.analysis import smooth_intensities
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from optifik.analysis import Prominence_from_fft
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from optifik.analysis import finds_peak
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from optifik.io import load_spectrum
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@ -20,8 +19,8 @@ def test_FFT():
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expected = 3524.51
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spectrum_path = os.path.join(FOLDER, FILE_NAME)
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raw_intensities = load_spectrum(spectrum_path)
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smoothed_intensities, intensities, lambdas = Data_Smoothed(spectrum_path)
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lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
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smoothed_intensities = smooth_intensities(raw_intensities)
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indice = 1.324188 + 3102.060378 / (lambdas**2)
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thickness_FFT = thickness_from_fft(lambdas,
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@ -37,8 +36,8 @@ def test_minmax_ransac():
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expected = 1338.35
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spectrum_path = os.path.join(FOLDER, FILE_NAME)
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raw_intensities = load_spectrum(spectrum_path)
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smoothed_intensities, intensities, lambdas = Data_Smoothed(spectrum_path)
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lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
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smoothed_intensities = smooth_intensities(raw_intensities)
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indice = 1.324188 + 3102.060378 / (lambdas**2)
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prominence = Prominence_from_fft(lambdas=lambdas,
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@ -64,14 +63,15 @@ def test_scheludko_4peaks():
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expected = 777.07
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spectrum_path = os.path.join(FOLDER, FILE_NAME)
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raw_intensities = load_spectrum(spectrum_path)
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smoothed_intensities, intensities, lambdas = Data_Smoothed(spectrum_path)
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lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
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smoothed_intensities = smooth_intensities(raw_intensities)
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indice = 1.324188 + 3102.060378 / (lambdas**2)
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prominence = Prominence_from_fft(lambdas=lambdas, intensities=smoothed_intensities, refractive_index=indice, plot=False)
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total_extrema, smoothed_intensities, raw_intensities, lambdas, peaks_min, peaks_max = finds_peak(spectrum_path,
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min_peak_prominence=prominence)
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total_extrema, peaks_min, peaks_max = finds_peak(lambdas, smoothed_intensities,
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min_peak_prominence=prominence,
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plot=False)
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result = thickness_from_scheludko(lambdas, smoothed_intensities,
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@ -89,15 +89,15 @@ def test_scheludko_2peaks():
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expected = 495.69
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spectrum_path = os.path.join(FOLDER, FILE_NAME)
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raw_intensities = load_spectrum(spectrum_path)
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smoothed_intensities, intensities, lambdas = Data_Smoothed(spectrum_path)
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lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
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smoothed_intensities = smooth_intensities(raw_intensities)
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indice = 1.324188 + 3102.060378 / (lambdas**2)
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prominence = 0.03
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total_extrema, smoothed_intensities, raw_intensities, lambdas, peaks_min, peaks_max = finds_peak(spectrum_path,
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min_peak_prominence=prominence)
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total_extrema, peaks_min, peaks_max = finds_peak(lambdas, smoothed_intensities,
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min_peak_prominence=prominence,
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plot=False)
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result = thickness_from_scheludko(lambdas, smoothed_intensities,
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peaks_min, peaks_max,
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@ -116,15 +116,15 @@ def test_order0():
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expected = 115.33
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spectrum_path = os.path.join(FOLDER, FILE_NAME)
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raw_intensities = load_spectrum(spectrum_path)
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smoothed_intensities, intensities, lambdas = Data_Smoothed(spectrum_path)
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lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
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smoothed_intensities = smooth_intensities(raw_intensities)
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indice = 1.324188 + 3102.060378 / (lambdas**2)
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prominence = 0.03
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total_extrema, smoothed_intensities, raw_intensities, lambdas, peaks_min, peaks_max = finds_peak(spectrum_path,
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min_peak_prominence=prominence)
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total_extrema, peaks_min, peaks_max = finds_peak(lambdas, smoothed_intensities,
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min_peak_prominence=prominence,
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plot=False)
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result = thickness_for_order0(lambdas, smoothed_intensities,
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peaks_min, peaks_max,
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