67 lines
2.4 KiB
Python
67 lines
2.4 KiB
Python
import pytest
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import yaml
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from pathlib import Path
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import os.path
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import numpy as np
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from numpy.testing import assert_allclose
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from numpy.testing import assert_almost_equal
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from optifik.minmax import thickness_from_minmax
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from optifik.analysis import smooth_intensities
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from optifik.io import load_spectrum
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def load():
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test_data_dir = Path(__file__).parent.parent / 'data'
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FOLDER = test_data_dir / 'spectraLorene' / 'sample1'
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yaml_file = os.path.join(FOLDER, 'sample1.yaml')
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with open(yaml_file, "r") as yaml_file:
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thickness_dict = yaml.safe_load(yaml_file)
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#print(thickness_dict)
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data = [(os.path.join(FOLDER, fn), val) for fn, val in thickness_dict['known_thicknesses'].items()]
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return data
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def test_minmax_sample1():
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min_peak_prominence = 0.02
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min_peak_distance = 10
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skipped = ('011137.xy',
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'012426.xy',
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'012795.xy',
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'012979.xy',
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'011321.xy', #Insufficient number of data points
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)
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for path, expected in load():
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file = os.path.split(path)[-1]
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if file not in skipped:
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lambdas, raw_intensities = load_spectrum(path, wavelength_min=450)
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smoothed_intensities = smooth_intensities(raw_intensities)
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r_index = 1.33 #TODO
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prominence = 0.02
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distance = 10
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result = thickness_from_minmax(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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min_peak_distance=distance,
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method='ransac',
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plot=False)
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assert_allclose(result.thickness, expected, rtol=2.3e-1)
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#def test_fft_sample1():
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# for name, value in known_values.sample1['known_thicknesses'].items():
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# index = known_values.sample1['refractive_index']
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# # this method works only for large thicknesses
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# if value < 3000:
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# continue
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# path = os.path.join('spectra', name)
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# lambdas, intensities = io.load_spectrum(path, lambda_min=450)
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# result = thickness_from_fft(lambdas, intensities, refractive_index=index,)
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# error = 100 * np.abs(result.thickness - value) / value
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# assert(error < 5)
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