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refactoring

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This commit is contained in:
François Boulogne 2025-06-20 09:57:05 +02:00
parent c8868c3e63
commit 3debe82f0d
8 changed files with 202 additions and 106 deletions
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26
check.py
View file

@ -18,9 +18,10 @@ plt.rcParams.update({
})
def play_oder1():
def minmax():
##### Chemin du dossier contenant le spectre #####
from optifik.scheludko import thickness_from_scheludko
from optifik.scheludko import get_default_start_stop_wavelengths
DATA_FOLDER = os.path.abspath(os.path.join(os.path.curdir, 'tests', 'basic'))
@ -35,7 +36,7 @@ def play_oder1():
FILE_NAME = '000004310.xy' #TEST#
spectrum_file = os.path.join(DATA_FOLDER, FILE_NAME)
lambdas, intensities = io.load_spectrum(spectrum_file)
plot_spectrum(lambdas, intensities, title='Raw')
@ -51,12 +52,13 @@ def play_oder1():
peaks_min, peaks_max = finds_peak(lambdas, smoothed_intensities,
min_peak_prominence=prominence,
plot=True)
def play_order1():
##### Chemin du dossier contenant le spectre #####
from optifik.scheludko import thickness_from_scheludko
from optifik.scheludko import get_default_start_stop_wavelengths
DATA_FOLDER = os.path.abspath(os.path.join(os.path.curdir, 'tests', 'basic'))
@ -89,9 +91,19 @@ def play_order1():
min_peak_prominence=prominence,
plot=True)
result = thickness_from_scheludko(lambdas, smoothed_intensities,
w_start, w_stop = get_default_start_stop_wavelengths(lambdas,
smoothed_intensities,
refractive_index,
min_peak_prominence=prominence,
plot=True)
result = thickness_from_scheludko(lambdas,
smoothed_intensities,
refractive_index=refractive_index,
min_peak_prominence=prominence,
wavelength_start=w_start,
wavelength_stop=w_stop,
interference_order=None,
plot=True)
def play_order0():
@ -135,7 +147,7 @@ def play_order0():
min_peak_prominence=prominence,
plot=True)
def check_basic():
@ -219,4 +231,4 @@ if __name__ == '__main__':
#check_SV1()
#play()
play_order1()

125
optifik/scheludko.py
View file

@ -126,12 +126,43 @@ def _Delta_fit(xdata, thickness, interference_order):
return _Delta(lambdas, thickness, interference_order, r_index)
def get_default_start_stop_wavelengths(wavelengths,
intensities,
refractive_index,
min_peak_prominence,
plot=None):
# idx_min idx max
peaks_min, peaks_max = finds_peak(wavelengths, intensities,
min_peak_prominence=min_peak_prominence,
plot=plot)
failure, message = False, ''
if len(peaks_min) == 0:
message += 'Failed to detect at least one minimum. '
failure = True
if len(peaks_max) == 0:
message += 'Failed to detect at least one maximum. '
failure = True
if failure:
raise RuntimeError(message)
# Get the last oscillation peaks
lambda_min = wavelengths[peaks_min[-1]]
lambda_max = wavelengths[peaks_max[-1]]
# Order them
wavelength_start = min(lambda_min, lambda_max)
wavelength_stop = max(lambda_min, lambda_max)
return wavelength_start, wavelength_stop
def thickness_from_scheludko(wavelengths,
intensities,
refractive_index,
min_peak_prominence,
wavelength_start,
wavelength_stop,
interference_order=None,
plot=None):
"""
@ -160,69 +191,53 @@ def thickness_from_scheludko(wavelengths,
max_tested_order = 12
r_index = refractive_index
# idx_min idx max
peaks_min, peaks_max = finds_peak(wavelengths, intensities,
min_peak_prominence=min_peak_prominence,
plot=plot)
failure, message = False, ''
if len(peaks_min) == 0:
message += 'Failed to detect at least one minimum. '
failure = True
if len(peaks_max) == 0:
message += 'Failed to detect at least one maximum. '
failure = True
if failure:
raise RuntimeError(message)
# Get the last oscillation peaks
lambda_min = wavelengths[peaks_min[-1]]
lambda_max = wavelengths[peaks_max[-1]]
# Order them
lambda_start = min(lambda_min, lambda_max)
lambda_stop = max(lambda_min, lambda_max)
# Guess the order...
if interference_order is None:
# Guess the order...
# mask input data
mask = (wavelengths >= lambda_start) & (wavelengths <= lambda_stop)
wavelengths_masked = wavelengths[mask]
r_index_masked = r_index[mask]
intensities_masked = intensities[mask]
# mask input data
mask = (wavelengths >= wavelength_start) & (wavelengths <= wavelength_stop)
wavelengths_masked = wavelengths[mask]
r_index_masked = r_index[mask]
intensities_masked = intensities[mask]
min_difference = np.inf
best_m = None
best_h_values = None
if plot:
plt.figure()
plt.ylabel(r'$h$ ($\mathrm{{nm}}$)')
plt.xlabel(r'$\lambda$ ($ \mathrm{nm} $)')
for m in range(0, max_tested_order+1):
h_values = _thicknesses_scheludko_at_order(wavelengths_masked,
intensities_masked,
m, r_index_masked)
difference = np.max(h_values) - np.min(h_values)
print(f"h-difference for m={m}: {difference:.1f} nm")
if difference < min_difference:
min_difference = difference
best_m = m
best_h_values = h_values
min_difference = np.inf
best_m = None
best_h_values = None
if plot:
plt.plot(wavelengths_masked, h_values,'.', markersize=3, label=f"Épaisseur du film (Scheludko, m={m})")
plt.figure()
plt.ylabel(r'$h$ ($\mathrm{{nm}}$)')
plt.xlabel(r'$\lambda$ ($ \mathrm{nm} $)')
for m in range(0, max_tested_order+1):
h_values = _thicknesses_scheludko_at_order(wavelengths_masked,
intensities_masked,
m,
r_index_masked)
difference = np.max(h_values) - np.min(h_values)
print(f"h-difference for m={m}: {difference:.1f} nm")
if difference < min_difference:
min_difference = difference
best_m = m
best_h_values = h_values
if plot:
plt.plot(wavelengths_masked, h_values,'.', markersize=3, label=f"Épaisseur du film (Scheludko, m={m})")
else:
h_values = _thicknesses_scheludko_at_order(wavelengths_masked,
intensities_masked,
interference_order,
r_index_masked)
best_m = interference_order
best_h_values = h_values
print(f"Optimized: m={best_m}")
# Compute the thickness for the selected order

17
tests/test_SV2o1.py
View file

@ -4,6 +4,7 @@ from numpy.testing import assert_allclose
import pytest
from optifik.scheludko import thickness_from_scheludko
from optifik.scheludko import get_default_start_stop_wavelengths
from optifik.io import load_spectrum
from optifik.analysis import smooth_intensities
@ -26,13 +27,21 @@ def test_SV2o1(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)
r_index = 1.324188 + 3102.060378 / (lambdas**2)
prominence = 0.020
w_start, w_stop = get_default_start_stop_wavelengths(lambdas,
smoothed_intensities,
refractive_index=r_index,
min_peak_prominence=prominence,
plot=False)
result = thickness_from_scheludko(lambdas, smoothed_intensities,
refractive_index=refractive_index,
min_peak_prominence=prominence,
result = thickness_from_scheludko(lambdas,
smoothed_intensities,
refractive_index=r_index,
wavelength_start=w_start,
wavelength_stop=w_stop,
interference_order=None,
plot=False)
assert_allclose(result.thickness, expected, rtol=1e-1)

20
tests/test_SV2o2.py
View file

@ -4,6 +4,7 @@ from numpy.testing import assert_allclose
import pytest
from optifik.scheludko import thickness_from_scheludko
from optifik.scheludko import get_default_start_stop_wavelengths
from optifik.io import load_spectrum
from optifik.analysis import smooth_intensities
@ -25,14 +26,23 @@ def test_SV2o2(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)
r_index = 1.324188 + 3102.060378 / (lambdas**2)
prominence = 0.01
w_start, w_stop = get_default_start_stop_wavelengths(lambdas,
smoothed_intensities,
refractive_index=r_index,
min_peak_prominence=prominence,
plot=False)
thickness_scheludko = thickness_from_scheludko(lambdas,
smoothed_intensities,
refractive_index=r_index,
wavelength_start=w_start,
wavelength_stop=w_stop,
interference_order=None,
plot=False)
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)

20
tests/test_SV2o3.py
View file

@ -4,6 +4,7 @@ from numpy.testing import assert_allclose
import pytest
from optifik.scheludko import thickness_from_scheludko
from optifik.scheludko import get_default_start_stop_wavelengths
from optifik.io import load_spectrum
from optifik.analysis import smooth_intensities
@ -25,14 +26,23 @@ def test_SV2o3(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)
r_index = 1.324188 + 3102.060378 / (lambdas**2)
prominence = 0.02
w_start, w_stop = get_default_start_stop_wavelengths(lambdas,
smoothed_intensities,
refractive_index=r_index,
min_peak_prominence=prominence,
plot=False)
thickness_scheludko = thickness_from_scheludko(lambdas,
smoothed_intensities,
refractive_index=r_index,
wavelength_start=w_start,
wavelength_stop=w_stop,
interference_order=None,
plot=False)
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)

20
tests/test_SV2o4.py
View file

@ -4,6 +4,7 @@ from numpy.testing import assert_allclose
import pytest
from optifik.scheludko import thickness_from_scheludko
from optifik.scheludko import get_default_start_stop_wavelengths
from optifik.io import load_spectrum
from optifik.analysis import smooth_intensities
@ -25,14 +26,23 @@ def test_SV2o4(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)
r_index = 1.324188 + 3102.060378 / (lambdas**2)
prominence = 0.02
w_start, w_stop = get_default_start_stop_wavelengths(lambdas,
smoothed_intensities,
refractive_index=r_index,
min_peak_prominence=prominence,
plot=False)
thickness_scheludko = thickness_from_scheludko(lambdas,
smoothed_intensities,
refractive_index=r_index,
wavelength_start=w_start,
wavelength_stop=w_stop,
interference_order=None,
plot=False)
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)

21
tests/test_SV2o5.py
View file

@ -4,6 +4,7 @@ from numpy.testing import assert_allclose
import pytest
from optifik.scheludko import thickness_from_scheludko
from optifik.scheludko import get_default_start_stop_wavelengths
from optifik.io import load_spectrum
from optifik.analysis import smooth_intensities
@ -25,14 +26,24 @@ 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)
r_index = 1.324188 + 3102.060378 / (lambdas**2)
prominence = 0.02
w_start, w_stop = get_default_start_stop_wavelengths(lambdas,
smoothed_intensities,
refractive_index=r_index,
min_peak_prominence=prominence,
plot=False)
thickness_scheludko = thickness_from_scheludko(lambdas,
smoothed_intensities,
refractive_index=r_index,
wavelength_start=w_start,
wavelength_stop=w_stop,
interference_order=None,
plot=False)
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)

59
tests/test_basic.py
View file

@ -6,6 +6,7 @@ import pytest
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 get_default_start_stop_wavelengths
from optifik.scheludko import thickness_for_order0
from optifik.analysis import smooth_intensities
from optifik.io import load_spectrum
@ -19,15 +20,16 @@ def test_FFT():
spectrum_path = os.path.join(FOLDER, FILE_NAME)
lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
smoothed_intensities = smooth_intensities(raw_intensities)
indice = 1.324188 + 3102.060378 / (lambdas**2)
r_index = 1.324188 + 3102.060378 / (lambdas**2)
thickness_FFT = thickness_from_fft(lambdas,
smoothed_intensities,
refractive_index=indice)
refractive_index=r_index)
result = thickness_FFT.thickness
assert_allclose(result, expected, rtol=1e-1)
def test_minmax_ransac():
FOLDER = os.path.join('tests', 'basic')
FILE_NAME = '000004310.xy'
@ -36,13 +38,13 @@ def test_minmax_ransac():
spectrum_path = os.path.join(FOLDER, FILE_NAME)
lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
smoothed_intensities = smooth_intensities(raw_intensities)
indice = 1.324188 + 3102.060378 / (lambdas**2)
r_index = 1.324188 + 3102.060378 / (lambdas**2)
prominence = 0.02
result = thickness_from_minmax(lambdas,
smoothed_intensities,
refractive_index=indice,
refractive_index=r_index,
min_peak_prominence=prominence,
method='ransac',
plot=False)
@ -58,19 +60,29 @@ def test_scheludko_4peaks():
spectrum_path = os.path.join(FOLDER, FILE_NAME)
lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
smoothed_intensities = smooth_intensities(raw_intensities)
indice = 1.324188 + 3102.060378 / (lambdas**2)
r_index = 1.324188 + 3102.060378 / (lambdas**2)
prominence = 0.02
result = thickness_from_scheludko(lambdas, smoothed_intensities,
refractive_index=indice,
min_peak_prominence=prominence,
plot=False)
w_start, w_stop = get_default_start_stop_wavelengths(lambdas,
smoothed_intensities,
refractive_index=r_index,
min_peak_prominence=prominence,
plot=False)
result = thickness_from_scheludko(lambdas,
smoothed_intensities,
refractive_index=r_index,
wavelength_start=w_start,
wavelength_stop=w_stop,
interference_order=None,
plot=False)
assert_allclose(result.thickness, expected, rtol=1e-1)
def test_scheludko_2peaks():
FOLDER = os.path.join('tests', 'basic')
FILE_NAME = '000006544.xy'
@ -79,21 +91,28 @@ def test_scheludko_2peaks():
spectrum_path = os.path.join(FOLDER, FILE_NAME)
lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
smoothed_intensities = smooth_intensities(raw_intensities)
indice = 1.324188 + 3102.060378 / (lambdas**2)
r_index = 1.324188 + 3102.060378 / (lambdas**2)
prominence = 0.03
result = thickness_from_scheludko(lambdas, smoothed_intensities,
refractive_index=indice,
min_peak_prominence=prominence,
plot=False)
w_start, w_stop = get_default_start_stop_wavelengths(lambdas,
smoothed_intensities,
refractive_index=r_index,
min_peak_prominence=prominence,
plot=False)
result = thickness_from_scheludko(lambdas,
smoothed_intensities,
refractive_index=r_index,
wavelength_start=w_start,
wavelength_stop=w_stop,
interference_order=None,
plot=False)
assert_allclose(result.thickness, expected, rtol=1e-1)
def test_order0():
FOLDER = os.path.join('tests', 'basic')
FILE_NAME = '000018918.xy'
@ -102,13 +121,13 @@ def test_order0():
spectrum_path = os.path.join(FOLDER, FILE_NAME)
lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
smoothed_intensities = smooth_intensities(raw_intensities)
indice = 1.324188 + 3102.060378 / (lambdas**2)
r_index = 1.324188 + 3102.060378 / (lambdas**2)
prominence = 0.03
result = thickness_for_order0(lambdas, smoothed_intensities,
refractive_index=indice,
refractive_index=r_index,
min_peak_prominence=prominence,
plot=False)