152 lines
5.6 KiB
Python
152 lines
5.6 KiB
Python
import pytest
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from pathlib import Path
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import numpy as np
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from numpy.testing import assert_allclose
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from optifik.scheludko import thickness_from_scheludko
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from optifik.scheludko import get_default_start_stop_wavelengths
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from optifik.analysis import smooth_intensities
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from optifik.io import load_spectrum
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@pytest.fixture
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def test_data_dir():
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return Path(__file__).parent.parent / 'data'
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@pytest.fixture
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def dataset1(test_data_dir):
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spectrum_path = test_data_dir / 'basic' / '000005253.xy'
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expected = 777.07
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lambdas, raw_intensities = load_spectrum(spectrum_path, wavelength_min=450)
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smoothed_intensities = smooth_intensities(raw_intensities)
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r_index = 1.324188 + 3102.060378 / (lambdas**2)
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return {
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"expected": expected,
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"lambdas": lambdas,
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"smoothed_intensities": smoothed_intensities,
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"r_index": r_index,
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}
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def test_interference_order_positive(dataset1):
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expected = dataset1['expected']
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lambdas = dataset1['lambdas']
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smoothed_intensities = dataset1['smoothed_intensities']
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r_index = dataset1['r_index']
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prominence = 0.02
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w_start, w_stop = 300, 500
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with pytest.raises(ValueError):
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result = thickness_from_scheludko(lambdas,
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smoothed_intensities,
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refractive_index=r_index,
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wavelength_start=w_start,
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wavelength_stop=w_stop,
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interference_order=-1,
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plot=False)
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def test_start_stop_swapped(dataset1):
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expected = dataset1['expected']
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lambdas = dataset1['lambdas']
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smoothed_intensities = dataset1['smoothed_intensities']
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r_index = dataset1['r_index']
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prominence = 0.02
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w_start, w_stop = 500, 300
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with pytest.raises(ValueError):
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result = thickness_from_scheludko(lambdas,
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smoothed_intensities,
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refractive_index=r_index,
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wavelength_start=w_start,
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wavelength_stop=w_stop,
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interference_order=None,
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plot=False)
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def test_scheludko_4peaks(dataset1):
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expected = dataset1['expected']
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lambdas = dataset1['lambdas']
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smoothed_intensities = dataset1['smoothed_intensities']
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r_index = dataset1['r_index']
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prominence = 0.02
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w_start, w_stop = get_default_start_stop_wavelengths(lambdas,
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smoothed_intensities,
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refractive_index=r_index,
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min_peak_prominence=prominence,
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plot=False)
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result = thickness_from_scheludko(lambdas,
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smoothed_intensities,
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refractive_index=r_index,
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wavelength_start=w_start,
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wavelength_stop=w_stop,
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interference_order=None,
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plot=False)
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assert_allclose(result.thickness, expected, rtol=1e-1)
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def test_scheludko_2peaks(test_data_dir):
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spectrum_path = test_data_dir / 'basic' / '000006544.xy'
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expected = 495.69
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lambdas, raw_intensities = load_spectrum(spectrum_path, wavelength_min=450)
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smoothed_intensities = smooth_intensities(raw_intensities)
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r_index = 1.324188 + 3102.060378 / (lambdas**2)
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prominence = 0.03
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w_start, w_stop = get_default_start_stop_wavelengths(lambdas,
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smoothed_intensities,
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refractive_index=r_index,
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min_peak_prominence=prominence,
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plot=False)
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result = thickness_from_scheludko(lambdas,
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smoothed_intensities,
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refractive_index=r_index,
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wavelength_start=w_start,
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wavelength_stop=w_stop,
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interference_order=None,
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plot=False)
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assert_allclose(result.thickness, expected, rtol=1e-1)
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def test_order0(test_data_dir):
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spectrum_path = test_data_dir / 'basic' / '000018918.xy'
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expected = 115.33
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lambdas, raw_intensities = load_spectrum(spectrum_path, wavelength_min=450)
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smoothed_intensities = smooth_intensities(raw_intensities)
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r_index = 1.324188 + 3102.060378 / (lambdas**2)
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prominence = 0.03
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File_I_min = test_data_dir / 'basic' / 'void.xy'
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_, intensities_void = load_spectrum(File_I_min, wavelength_min=450)
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w_start, w_stop = None, None
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result = thickness_from_scheludko(lambdas,
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smoothed_intensities,
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refractive_index=r_index,
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wavelength_start=w_start,
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wavelength_stop=w_stop,
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interference_order=0,
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intensities_void=intensities_void,
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plot=False)
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assert_allclose(result.thickness, expected, rtol=1e-1)
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