fr/tmp_optifik
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

upd API

Browse source
This commit is contained in:
François Boulogne 2025-06-20 13:35:19 +02:00
parent 12922f0f79
commit a9df27b7c7
13 changed files with 43 additions and 40 deletions
Download patch file Download diff file Expand all files Collapse all files

8
check.py
View file

@ -41,7 +41,7 @@ def minmax():
lambdas, intensities = io.load_spectrum(spectrum_file)
plot_spectrum(lambdas, intensities, title='Raw')
lambdas, intensities = io.load_spectrum(spectrum_file, lambda_min=450)
lambdas, intensities = io.load_spectrum(spectrum_file, wavelength_min=450)
plot_spectrum(lambdas, intensities, title='Raw, cropped')
smoothed_intensities = smooth_intensities(intensities)
@ -79,7 +79,7 @@ def play_order1():
lambdas, intensities = io.load_spectrum(spectrum_file)
plot_spectrum(lambdas, intensities, title='Raw')
lambdas, intensities = io.load_spectrum(spectrum_file, lambda_min=450)
lambdas, intensities = io.load_spectrum(spectrum_file, wavelength_min=450)
plot_spectrum(lambdas, intensities, title='Raw, cropped')
smoothed_intensities = smooth_intensities(intensities)
@ -129,7 +129,7 @@ def play_order0():
lambdas, intensities = io.load_spectrum(spectrum_file)
plot_spectrum(lambdas, intensities, title='Raw')
lambdas, intensities = io.load_spectrum(spectrum_file, lambda_min=450)
lambdas, intensities = io.load_spectrum(spectrum_file, wavelength_min=450)
plot_spectrum(lambdas, intensities, title='Raw, cropped')
@ -186,7 +186,7 @@ def check_SV1():
spectre_file = os.path.join(DATA_FOLDER, fn)
lambdas, raw_intensities = load_spectrum(spectre_file, lambda_min=450)
lambdas, raw_intensities = load_spectrum(spectre_file, wavelength_min=450)
##### Affichage du spectre lissé #####

14
optifik/io.py
View file

@ -2,8 +2,8 @@ import numpy as np
def load_spectrum(spectrum_path,
lambda_min=0,
lambda_max=np.inf,
wavelength_min=0,
wavelength_max=np.inf,
delimiter=','):
"""
Load a spectrum file.
@ -15,10 +15,10 @@ def load_spectrum(spectrum_path,
----------
spectrum_path : string
File path.
lambda_min : scalar, optional
Cut the data at this minimum wavelength in nm.
lambda_max : scalar, optional
Cut the data at this maximum wavelength in nm.
wavelength_min : scalar, optional
Cut the data at this minimum wavelength (included).
wavelength_max : scalar, optional
Cut the data at this maximum wavelength (included).
delimiter : string, optional
Delimiter between columns in the datafile.
@ -30,5 +30,5 @@ def load_spectrum(spectrum_path,
data = np.loadtxt(spectrum_path, delimiter=delimiter)
lambdas, intensities = np.column_stack(data)
mask = (lambdas > lambda_min) & (lambdas < lambda_max)
mask = (lambdas >= wavelength_min) & (lambdas <= wavelength_max)
return lambdas[mask], intensities[mask]

15
optifik/scheludko.py
View file

@ -288,14 +288,14 @@ def thickness_from_scheludko(wavelengths,
wavelengths_masked = wavelengths[mask]
r_index_masked = r_index[mask]
intensities_masked = intensities[mask]
intensities_I_min_masked = intensities_void[mask]
intensities_void_masked = intensities_void[mask]
interference_order = 0
thickness_values = _thicknesses_scheludko_at_order(wavelengths_masked,
intensities_masked,
interference_order,
r_index_masked,
Imin=intensities_I_min_masked)
intensities_void=intensities_void_masked)
elif interference_order > 0:
h_values = _thicknesses_scheludko_at_order(wavelengths_masked,
@ -312,8 +312,8 @@ def thickness_from_scheludko(wavelengths,
# Delta
if interference_order == 0:
num = intensities_masked - np.min(intensities_I_min_masked)
denom = np.max(intensities_masked) - np.min(intensities_I_min_masked)
num = intensities_masked - np.min(intensities_void_masked)
denom = np.max(intensities_masked) - np.min(intensities_void_masked)
else:
num = intensities_masked - np.min(intensities_masked)
denom = np.max(intensities_masked) - np.min(intensities_masked)
@ -340,7 +340,8 @@ def thickness_from_scheludko(wavelengths,
plt.figure()
plt.plot(wavelengths_masked, Delta_from_data,
'bo-', markersize=2, label=r'$\mathrm{{Smoothed}}\ \mathrm{{Data}}$')
'bo-', markersize=2,
label=r'$\mathrm{{Smoothed}}\ \mathrm{{Data}}$')
# Scheludko
label = rf'$\mathrm{{Scheludko}}\ (h = {np.mean(thickness_values):.1f} \pm {np.std(thickness_values):.1f}\ \mathrm{{nm}})$'
@ -348,7 +349,9 @@ def thickness_from_scheludko(wavelengths,
'go-', markersize=2, label=label)
# Fit
label = rf'$\mathrm{{Fit}}\ (h = {fitted_h:.1f}\pm {std_err:.1f} \ \mathrm{{nm}})$'
plt.plot(wavelengths_masked, Delta_values, 'ro-', markersize=2, label=label)
plt.plot(wavelengths_masked, Delta_values,
'ro-', markersize=2,
label=label)
plt.legend()
plt.ylabel(r'$\Delta$')

2
tests/test_SV1.py
View file

@ -23,7 +23,7 @@ def load():
@pytest.mark.parametrize("spectrum_path, expected", load())
def test_minmax(spectrum_path, expected):
lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
lambdas, raw_intensities = load_spectrum(spectrum_path, wavelength_min=450)
smoothed_intensities = smooth_intensities(raw_intensities)
assert_equal(len(lambdas), len(smoothed_intensities))

8
tests/test_SV2o0.py
View file

@ -24,10 +24,10 @@ def load(filename):
#@pytest.mark.skip('...')
@pytest.mark.parametrize("spectrum_path, expected", load('known_value.yaml'))
def test_SV2o0_small_tol(spectrum_path, expected):
lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
lambdas, raw_intensities = load_spectrum(spectrum_path, wavelength_min=450)
File_I_min = 'tests/spectre_trou/000043641.xy'
_, intensities_void = load_spectrum(File_I_min, lambda_min=450)
_, intensities_void = load_spectrum(File_I_min, wavelength_min=450)
smoothed_intensities = smooth_intensities(raw_intensities)
@ -54,10 +54,10 @@ def test_SV2o0_small_tol(spectrum_path, expected):
@pytest.mark.parametrize("spectrum_path, expected", load('known_value_large_tol.yaml'))
def test_SV2o0_large_tol(spectrum_path, expected):
lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
lambdas, raw_intensities = load_spectrum(spectrum_path, wavelength_min=450)
File_I_min = 'tests/spectre_trou/000043641.xy'
_, intensities_void = load_spectrum(File_I_min, lambda_min=450)
_, intensities_void = load_spectrum(File_I_min, wavelength_min=450)
smoothed_intensities = smooth_intensities(raw_intensities)

2
tests/test_SV2o1.py
View file

@ -24,7 +24,7 @@ def load():
#@pytest.mark.skip('...')
@pytest.mark.parametrize("spectrum_path, expected", load())
def test_SV2o1(spectrum_path, expected):
lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
lambdas, raw_intensities = load_spectrum(spectrum_path, wavelength_min=450)
smoothed_intensities = smooth_intensities(raw_intensities)
r_index = 1.324188 + 3102.060378 / (lambdas**2)

2
tests/test_SV2o2.py
View file

@ -23,7 +23,7 @@ def load():
@pytest.mark.parametrize("spectrum_path, expected", load())
def test_SV2o2(spectrum_path, expected):
lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
lambdas, raw_intensities = load_spectrum(spectrum_path, wavelength_min=450)
smoothed_intensities = smooth_intensities(raw_intensities)
r_index = 1.324188 + 3102.060378 / (lambdas**2)

2
tests/test_SV2o3.py
View file

@ -23,7 +23,7 @@ def load():
@pytest.mark.parametrize("spectrum_path, expected", load())
def test_SV2o3(spectrum_path, expected):
lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
lambdas, raw_intensities = load_spectrum(spectrum_path, wavelength_min=450)
smoothed_intensities = smooth_intensities(raw_intensities)
r_index = 1.324188 + 3102.060378 / (lambdas**2)

2
tests/test_SV2o4.py
View file

@ -23,7 +23,7 @@ def load():
@pytest.mark.parametrize("spectrum_path, expected", load())
def test_SV2o4(spectrum_path, expected):
lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
lambdas, raw_intensities = load_spectrum(spectrum_path, wavelength_min=450)
smoothed_intensities = smooth_intensities(raw_intensities)
r_index = 1.324188 + 3102.060378 / (lambdas**2)

2
tests/test_SV2o5.py
View file

@ -23,7 +23,7 @@ def load():
@pytest.mark.parametrize("spectrum_path, expected", load())
def test_SV2o5(spectrum_path, expected):
lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
lambdas, raw_intensities = load_spectrum(spectrum_path, wavelength_min=450)
smoothed_intensities = smooth_intensities(raw_intensities)
r_index = 1.324188 + 3102.060378 / (lambdas**2)

2
tests/test_fft.py
View file

@ -14,7 +14,7 @@ def test_FFT():
expected = 3524.51
spectrum_path = os.path.join(FOLDER, FILE_NAME)
lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
lambdas, raw_intensities = load_spectrum(spectrum_path, wavelength_min=450)
smoothed_intensities = smooth_intensities(raw_intensities)
r_index = 1.324188 + 3102.060378 / (lambdas**2)

4
tests/test_minmax.py
View file

@ -14,7 +14,7 @@ def test_minmax_ransac():
expected = 1338.35
spectrum_path = os.path.join(FOLDER, FILE_NAME)
lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
lambdas, raw_intensities = load_spectrum(spectrum_path, wavelength_min=450)
smoothed_intensities = smooth_intensities(raw_intensities)
r_index = 1.324188 + 3102.060378 / (lambdas**2)
@ -36,7 +36,7 @@ def test_minmax_linreg():
expected = 1338.35
spectrum_path = os.path.join(FOLDER, FILE_NAME)
lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
lambdas, raw_intensities = load_spectrum(spectrum_path, wavelength_min=450)
smoothed_intensities = smooth_intensities(raw_intensities)
r_index = 1.324188 + 3102.060378 / (lambdas**2)

8
tests/test_scheludko.py
View file

@ -17,7 +17,7 @@ def dataset1():
expected = 777.07
spectrum_path = os.path.join(FOLDER, FILE_NAME)
lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
lambdas, raw_intensities = load_spectrum(spectrum_path, wavelength_min=450)
smoothed_intensities = smooth_intensities(raw_intensities)
r_index = 1.324188 + 3102.060378 / (lambdas**2)
@ -97,7 +97,7 @@ def test_scheludko_2peaks():
expected = 495.69
spectrum_path = os.path.join(FOLDER, FILE_NAME)
lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
lambdas, raw_intensities = load_spectrum(spectrum_path, wavelength_min=450)
smoothed_intensities = smooth_intensities(raw_intensities)
r_index = 1.324188 + 3102.060378 / (lambdas**2)
@ -127,14 +127,14 @@ def test_order0():
expected = 115.33
spectrum_path = os.path.join(FOLDER, FILE_NAME)
lambdas, raw_intensities = load_spectrum(spectrum_path, lambda_min=450)
lambdas, raw_intensities = load_spectrum(spectrum_path, wavelength_min=450)
smoothed_intensities = smooth_intensities(raw_intensities)
r_index = 1.324188 + 3102.060378 / (lambdas**2)
prominence = 0.03
File_I_min = 'tests/spectre_trou/000043641.xy'
_, intensities_void = load_spectrum(File_I_min, lambda_min=450)
_, intensities_void = load_spectrum(File_I_min, wavelength_min=450)
w_start, w_stop = None, None