136 lines
5 KiB
Python
136 lines
5 KiB
Python
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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import pytest
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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 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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def test_FFT():
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FOLDER = os.path.join('tests', 'basic')
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FILE_NAME = '003582.xy'
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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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indice = 1.324188 + 3102.060378 / (lambdas**2)
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thickness_FFT = thickness_from_fft(lambdas,
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smoothed_intensities,
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refractive_index=indice)
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result = thickness_FFT.thickness
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assert_allclose(result, expected, rtol=1e-1)
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def test_minmax_ransac():
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FOLDER = os.path.join('tests', 'basic')
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FILE_NAME = '000004310.xy'
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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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indice = 1.324188 + 3102.060378 / (lambdas**2)
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prominence = Prominence_from_fft(lambdas=lambdas,
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intensities=smoothed_intensities,
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refractive_index=indice,
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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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refractive_index=indice,
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min_peak_prominence=prominence,
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method='ransac',
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plot=False)
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result = thickness_minmax.thickness
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assert_allclose(result, expected, rtol=1e-1)
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def test_scheludko_4peaks():
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FOLDER = os.path.join('tests', 'basic')
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FILE_NAME = '000005253.xy'
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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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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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result = thickness_from_scheludko(lambdas, smoothed_intensities,
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peaks_min, peaks_max,
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refractive_index=indice,
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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():
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FOLDER = os.path.join('tests', 'basic')
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FILE_NAME = '000006544.xy'
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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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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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result = thickness_from_scheludko(lambdas, smoothed_intensities,
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peaks_min, peaks_max,
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refractive_index=indice,
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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():
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FOLDER = os.path.join('tests', 'basic')
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FILE_NAME = '000018918.xy'
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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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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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result = thickness_for_order0(lambdas, smoothed_intensities,
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peaks_min, peaks_max,
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refractive_index=indice,
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plot=False)
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assert_allclose(result.thickness, expected, rtol=1e-1)
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