chemotools 0.0.27__py3-none-any.whl → 0.1.6__py3-none-any.whl

tests/test_functionality.py

@@ -1,616 +0,0 @@
-import numpy as np
-import pytest
-
-from chemotools.baseline import (
-    AirPls,
-    ArPls,
-    ConstantBaselineCorrection,
-    LinearCorrection,
-    NonNegative,
-    SubtractReference,
-)
-from chemotools.derivative import NorrisWilliams, SavitzkyGolay
-from chemotools.scale import MinMaxScaler, NormScaler, PointScaler
-from chemotools.scatter import (
-    ExtendedMultiplicativeScatterCorrection,
-    MultiplicativeScatterCorrection,
-    RobustNormalVariate,
-    StandardNormalVariate,
-)
-from chemotools.smooth import MeanFilter, MedianFilter, WhittakerSmooth
-from chemotools.variable_selection import RangeCut, SelectFeatures
-from tests.fixtures import (
-    spectrum,
-    spectrum_arpls,
-    reference_airpls,
-    reference_arpls,
-    reference_msc_mean,
-    reference_msc_median,
-    reference_sg_15_2,
-    reference_snv,
-    reference_whitakker,
-)
-
-
-def test_air_pls(spectrum, reference_airpls):
-    # Arrange
-    air_pls = AirPls()
-
-    # Act
-    spectrum_corrected = air_pls.fit_transform(spectrum)
-
-    # Assert
-    assert np.allclose(spectrum_corrected[0], reference_airpls[0], atol=1e-7)
-
-
-def test_ar_pls(spectrum_arpls, reference_arpls):
-    # Arrange
-    arpls = ArPls(1e2, 0.0001)
-    reference = np.array(spectrum_arpls) - np.array(reference_arpls)
-
-    # Act
-    spectrum_corrected = arpls.fit_transform(spectrum_arpls)
-
-    # Assert
-    assert np.allclose(spectrum_corrected[0], reference[0], atol=1e-4)
-
-
-def test_constant_baseline_correction():
-    # Arrange
-    spectrum = np.array([1, 1, 1, 1, 1, 1, 1, 2, 2, 1]).reshape(1, -1)
-    constant_baseline_correction = ConstantBaselineCorrection(start=7, end=8)
-
-    # Act
-    spectrum_corrected = constant_baseline_correction.fit_transform(spectrum)
-
-    # Assert
-    expected = np.array([-1, -1, -1, -1, -1, -1, -1, 0, 0, -1])
-    assert np.allclose(spectrum_corrected[0], expected, atol=1e-8)
-
-
-def test_constant_baseline_correction_with_wavenumbers():
-    # Arrange
-    spectrum = np.array([1, 1, 1, 1, 1, 1, 1, 2, 2, 1]).reshape(1, -1)
-    wavenumbers = np.array([2, 3, 4, 5, 6, 7, 8, 9, 10, 11])
-    constant_baseline_correction = ConstantBaselineCorrection(
-        start=9, end=10, wavenumbers=wavenumbers
-    )
-
-    # Act
-    spectrum_corrected = constant_baseline_correction.fit_transform(spectrum)
-
-    # Assert
-    expected = np.array([-1, -1, -1, -1, -1, -1, -1, 0, 0, -1])
-    assert np.allclose(spectrum_corrected[0], expected, atol=1e-8)
-
-
-def test_extended_baseline_correction():
-    # Arrange
-    spectrum = np.array([1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0]).reshape(
-        1, -1
-    )
-    reference = np.array([1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0])
-    emsc = ExtendedMultiplicativeScatterCorrection(reference=reference)
-
-    # Act
-    spectrum_emsc = emsc.fit_transform(spectrum)
-
-    # Assert
-    assert np.allclose(spectrum_emsc[0], reference, atol=1e-8)
-
-
-def test_extended_baseline_correction_with_weights():
-    # Arrange
-    spectrum = np.array([1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0]).reshape(
-        1, -1
-    )
-    reference = np.array([1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0])
-    weights = np.array([1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0])
-    emsc = ExtendedMultiplicativeScatterCorrection(reference=reference, weights=weights)
-
-    # Act
-    spectrum_emsc = emsc.fit_transform(spectrum)
-
-    # Assert
-    assert np.allclose(spectrum_emsc[0], reference, atol=1e-8)
-
-
-def test_extended_baseline_correction_with_wrong_reference():
-    # Arrange
-    spectrum = np.array([1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0]).reshape(
-        1, -1
-    )
-    reference = np.array([1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0])
-
-    # Act
-    emsc = ExtendedMultiplicativeScatterCorrection(reference=reference)
-
-    # Assert
-    with pytest.raises(ValueError):
-        emsc.fit_transform(spectrum)
-
-
-def test_extended_baseline_correction_with_wrong_weights():
-    # Arrange
-    spectrum = np.array([1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0]).reshape(
-        1, -1
-    )
-    weights = np.array([1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0])
-
-    # Act
-    emsc = ExtendedMultiplicativeScatterCorrection(weights=weights)
-
-    # Assert
-    with pytest.raises(ValueError):
-        emsc.fit_transform(spectrum)
-
-
-def test_extended_baseline_correction_with_noreference_no_median_no_mean():
-    # Arrange
-    emsc = ExtendedMultiplicativeScatterCorrection(use_mean=False)
-
-    # Act & Assert
-    with pytest.raises(ValueError):
-        emsc.fit_transform(spectrum)
-
-
-def test_extended_baseline_correction_through_msc(spectrum):
-    # EMSC of 0 order should be equivalient to MSC
-    # Arrange
-    msc = MultiplicativeScatterCorrection()
-    emsc = ExtendedMultiplicativeScatterCorrection(order=0)
-
-    # Act
-    spectrum_msc = msc.fit_transform(spectrum)
-    spectrum_emsc = emsc.fit_transform(spectrum)
-
-    # Assert
-    assert np.allclose(spectrum_emsc[0], spectrum_msc, atol=1e-8)
-
-
-def test_extended_baseline_correction_through_msc_median(spectrum):
-    # EMSC of 0 order should be equivalient to MSC
-    # Arrange
-    msc = MultiplicativeScatterCorrection(use_median=True)
-    emsc = ExtendedMultiplicativeScatterCorrection(order=0, use_median=True)
-
-    # Act
-    spectrum_msc = msc.fit_transform(spectrum)
-    spectrum_emsc = emsc.fit_transform(spectrum)
-
-    # Assert
-    assert np.allclose(spectrum_emsc[0], spectrum_msc, atol=1e-8)
-
-
-def test_l1_norm(spectrum):
-    # Arrange
-    norm = 1
-    l1_norm = NormScaler(l_norm=norm)
-    spectrum_norm = np.linalg.norm(spectrum[0], ord=norm)
-
-    # Act
-    spectrum_corrected = l1_norm.fit_transform(spectrum)
-
-    # Assert
-    assert np.allclose(spectrum_corrected[0], spectrum[0] / spectrum_norm, atol=1e-8)
-
-
-def test_l2_norm(spectrum):
-    # Arrange
-    norm = 2
-    l1_norm = NormScaler(l_norm=norm)
-    spectrum_norm = np.linalg.norm(spectrum[0], ord=norm)
-
-    # Act
-    spectrum_corrected = l1_norm.fit_transform(spectrum)
-
-    # Assert
-    assert np.allclose(spectrum_corrected[0], spectrum[0] / spectrum_norm, atol=1e-8)
-
-
-def test_linear_correction(spectrum):
-    # Arrange
-    linear_correction = LinearCorrection()
-
-    # Act
-    spectrum_corrected = linear_correction.fit_transform(spectrum)
-
-    # Assert
-    assert spectrum_corrected[0][0] == 0
-    assert spectrum_corrected[-1][0] == 0
-
-
-def test_max_norm(spectrum):
-    # Arrange
-    max_norm = MinMaxScaler(use_min=False)
-
-    # Act
-    spectrum_corrected = max_norm.fit_transform(spectrum)
-
-    # Assert
-    assert np.allclose(
-        spectrum_corrected[0], spectrum[0] / np.max(spectrum[0]), atol=1e-8
-    )
-
-
-def test_mean_filter():
-    # Arrange
-    array = np.array([[1.0, 2.0, 3.0, 4.0, 5.0]])
-    mean_filter = MeanFilter(window_size=2)
-
-    # Act
-    array_corrected = mean_filter.fit_transform(array)
-
-    # Assert
-    assert np.allclose(array_corrected[0], [1, 1.5, 2.5, 3.5, 4.5], atol=1e-8)
-
-
-def test_median_filter():
-    # Arrange
-    array = np.array([[1.0, 2.0, 30.0, 4.0, 5.0]])
-    mean_filter = MedianFilter(window_size=3)
-
-    # Act
-    array_corrected = mean_filter.fit_transform(array)
-
-    # Assert
-    assert np.allclose(array_corrected[0], [1, 2.0, 4.0, 5.0, 5.0], atol=1e-8)
-
-
-def test_min_norm(spectrum):
-    # Arrange
-    min_norm = MinMaxScaler()
-
-    # Act
-    spectrum_corrected = min_norm.fit_transform(spectrum)
-
-    # Assert
-    assert np.allclose(
-        spectrum_corrected[0],
-        (spectrum[0] - np.min(spectrum[0]))
-        / (np.max(spectrum[0]) - np.min(spectrum[0])),
-        atol=1e-8,
-    )
-
-
-def test_multiplicative_scatter_correction_mean(spectrum, reference_msc_mean):
-    # Arrange
-    msc = MultiplicativeScatterCorrection()
-
-    # Act
-    spectrum_corrected = msc.fit_transform(spectrum)
-
-    # Assert
-    assert np.allclose(spectrum_corrected[0], reference_msc_mean[0], atol=1e-8)
-
-
-def test_multiplicative_scatter_correction_with_reference(spectrum, reference_msc_mean):
-    # Arrange
-    msc = MultiplicativeScatterCorrection(reference=reference_msc_mean[0])
-
-    # Act
-    spectrum_corrected = msc.fit_transform(spectrum)
-
-    # Assert
-    assert np.allclose(spectrum_corrected[0], reference_msc_mean[0], atol=1e-8)
-
-
-def test_multiplicative_scatter_correction_median(spectrum, reference_msc_median):
-    # Arrange
-    msc = MultiplicativeScatterCorrection(use_median=True)
-
-    # Act
-    spectrum_corrected = msc.fit_transform(spectrum)
-
-    # Assert
-    assert np.allclose(spectrum_corrected[0], reference_msc_median[0], atol=1e-8)
-
-
-def test_multiplicative_scatter_correction_with_reference_median(
-    spectrum, reference_msc_median
-):
-    # Arrange
-    msc = MultiplicativeScatterCorrection(
-        reference=reference_msc_median[0], use_median=True
-    )
-
-    # Act
-    spectrum_corrected = msc.fit_transform(spectrum)
-
-    # Assert
-    assert np.allclose(spectrum_corrected[0], reference_msc_median[0], atol=1e-8)
-
-
-def test_multiplicative_scatter_correction_with_weights(spectrum, reference_msc_mean):
-    # Arrange
-    weights = np.ones(len(spectrum[0]))
-
-    msc = MultiplicativeScatterCorrection(weights=weights)
-
-    # Act
-    spectrum_corrected = msc.fit_transform(spectrum)
-
-    # Assert
-    assert np.allclose(spectrum_corrected[0], reference_msc_mean[0], atol=1e-8)
-
-
-def test_multiplicative_scatter_correction_with_wrong_weights(
-    spectrum, reference_msc_mean
-):
-    # Arrange
-    weights = np.ones(10)
-    msc = MultiplicativeScatterCorrection(weights=weights)
-
-    # Act & Assert
-    with pytest.raises(ValueError):
-        msc.fit_transform(spectrum)
-
-
-def test_multiplicative_scatter_correction_with_wrong_reference(spectrum):
-    # Arrange
-    reference = np.ones(10)
-    msc = MultiplicativeScatterCorrection(reference=reference)
-
-    # Act & Assert
-    with pytest.raises(ValueError):
-        msc.fit_transform(spectrum)
-
-
-def test_multiplicative_scatter_correction_no_mean_no_median_no_reference(spectrum):
-    # Arrange
-    reference = np.ones(10)
-    msc = MultiplicativeScatterCorrection(use_mean=False)
-
-    # Act & Assert
-    with pytest.raises(ValueError):
-        msc.fit_transform(spectrum)
-
-
-def test_non_negative_zeroes():
-    # Arrange
-    spectrum = np.array([[-1, 0, 1]])
-    non_negative = NonNegative(mode="zero")
-
-    # Act
-    spectrum_corrected = non_negative.fit_transform(spectrum)
-
-    # Assert
-    assert np.allclose(spectrum_corrected[0], [0, 0, 1], atol=1e-8)
-
-
-def test_non_negative_absolute():
-    # Arrange
-    spectrum = np.array([[-1, 0, 1]])
-    non_negative = NonNegative(mode="abs")
-
-    # Act
-    spectrum_corrected = non_negative.fit_transform(spectrum)
-
-    # Assert
-    assert np.allclose(spectrum_corrected[0], [1, 0, 1], atol=1e-8)
-
-
-def test_norris_williams_filter_1():
-    # Arrange
-    norris_williams_filter = NorrisWilliams()
-    array = np.ones((1, 10)).reshape(1, -1)
-
-    # Act
-    spectrum_corrected = norris_williams_filter.fit_transform(array)
-
-    # Assert
-    assert np.allclose(spectrum_corrected[0], np.zeros((1, 10)), atol=1e-2)
-
-
-def test_norris_williams_filter_2():
-    # Arrange
-    norris_williams_filter = NorrisWilliams(derivative_order=2)
-    array = np.ones((1, 10)).reshape(1, -1)
-
-    # Act
-    spectrum_corrected = norris_williams_filter.fit_transform(array)
-
-    # Assert
-    assert np.allclose(spectrum_corrected[0], np.zeros((1, 10)), atol=1e-2)
-
-
-def test_norris_williams_wrong_filter():
-    # Arrange
-    norris_williams_filter = NorrisWilliams(derivative_order=5)
-    array = np.ones((1, 10)).reshape(1, -1)
-
-    # Act & Assert
-
-    with pytest.raises(ValueError):
-        norris_williams_filter.fit_transform(array)
-
-
-def test_point_scaler(spectrum):
-    # Arrange
-    index_scaler = PointScaler(point=0)
-    reference_spectrum = [value / spectrum[0][0] for value in spectrum[0]]
-
-    # Act
-    spectrum_corrected = index_scaler.fit_transform(spectrum)
-
-    # Assert
-    assert np.allclose(spectrum_corrected[0], reference_spectrum, atol=1e-8)
-
-
-def test_point_scaler_with_wavenumbers():
-    # Arrange
-    wavenumbers = np.array([1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0])
-    spectrum = np.array([[10.0, 12.0, 14.0, 16.0, 14.0, 12.0, 10.0, 12.0, 14.0, 16.0]])
-
-    # Act
-    index_scaler = PointScaler(point=4, wavenumbers=wavenumbers)
-    spectrum_corrected = index_scaler.fit_transform(spectrum)
-
-    # Assert
-    assert np.allclose(spectrum_corrected[0], spectrum[0] / spectrum[0][3], atol=1e-8)
-
-
-def test_range_cut_by_index(spectrum):
-    # Arrange
-    range_cut = RangeCut(start=0, end=10)
-
-    # Act
-    spectrum_corrected = range_cut.fit_transform(spectrum)
-
-    # Assert
-    assert np.allclose(spectrum_corrected[0], spectrum[0][:10], atol=1e-8)
-
-
-def test_range_cut_by_wavenumber():
-    # Arrange
-    wavenumbers = np.array([1, 2, 3, 4, 5, 6, 7, 8, 9, 10])
-    spectrum = np.array([[10, 12, 14, 16, 14, 12, 10, 12, 14, 16]])
-    range_cut = RangeCut(start=2.5, end=7.9, wavenumbers=wavenumbers)
-
-    # Act
-    spectrum_corrected = range_cut.fit_transform(spectrum)
-
-    # Assert
-    assert np.allclose(spectrum_corrected[0], spectrum[0][1:7], atol=1e-8)
-
-
-def test_range_cut_by_wavenumber_2():
-    # Arrange
-    wavenumbers = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
-    spectrum = np.array([[10, 12, 14, 16, 14, 12, 10, 12, 14, 16]])
-    range_cut = RangeCut(start=2.5, end=7.9, wavenumbers=wavenumbers)
-
-    # Act
-    spectrum_corrected = range_cut.fit_transform(spectrum)
-
-    # Assert
-    assert np.allclose(spectrum_corrected[0], spectrum[0][1:7], atol=1e-8)
-
-
-def test_robust_normal_variate():
-    # Arrange
-    spectrum = np.array([2, 3.5, 5, 27, 8, 9]).reshape(1, -1)
-    reference = np.array([-2.5, -0.5, 1.5, 30.833333, 5.5, 6.83333333])
-    rnv = RobustNormalVariate()
-
-    # Act
-    spectrum_corrected = rnv.fit_transform(spectrum)
-
-    # Assert
-    assert np.allclose(spectrum_corrected[0], reference, atol=1e-8)
-
-
-def test_savizky_golay_filter_1(spectrum, reference_sg_15_2):
-    # Arrange
-    savitzky_golay_filter = SavitzkyGolay(
-        window_size=15, polynomial_order=2, derivate_order=1, mode="interp"
-    )
-
-    # Act
-    spectrum_corrected = savitzky_golay_filter.fit_transform(spectrum)
-
-    # Assert
-    assert np.allclose(spectrum_corrected[0], reference_sg_15_2[0], atol=1e-2)
-
-
-def test_saviszky_golay_filter_2():
-    # Arrange
-    savitzky_golay_filter = SavitzkyGolay(
-        window_size=3, polynomial_order=2, derivate_order=1, mode="interp"
-    )
-
-    array = np.ones((1, 10)).reshape(1, -1)
-
-    # Act
-    spectrum_corrected = savitzky_golay_filter.fit_transform(array)
-
-    # Assert
-    assert np.allclose(spectrum_corrected[0], np.zeros((1, 10)), atol=1e-2)
-
-
-def test_saviszky_golay_filter_3():
-    # Arrange
-    savitzky_golay_filter = SavitzkyGolay(
-        window_size=3, polynomial_order=2, derivate_order=1, mode="interp"
-    )
-
-    array = np.array([0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0]).reshape(1, -1)
-
-    # Act
-    spectrum_corrected = savitzky_golay_filter.fit_transform(array)
-
-    # Assert
-    assert np.allclose(spectrum_corrected[0], np.ones((1, 10)), atol=1e-2)
-
-
-def test_select_features():
-    # Arrange
-    spectrum = np.array([[1, 2, 3, 4, 5, 6, 7, 8, 9, 10]])
-    expected = np.array([[1, 2, 3, 8, 9, 10]])
-
-    # Act
-    select_features = SelectFeatures(features=np.array([0, 1, 2, 7, 8, 9]))
-    spectrum_corrected = select_features.fit_transform(spectrum)
-
-    # Assert
-    assert np.allclose(spectrum_corrected[0], expected, atol=1e-8)
-
-
-def test_select_features_with_wavenumbers():
-    # Arrange
-    wavenumbers = np.array([1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0])
-    spectrum = np.array([[1.0, 2.0, 3.0, 5.0, 8.0, 13.0, 21.0, 34.0, 55.0, 89.0]])
-    expected = np.array([[1.0, 2.0, 3.0, 34.0, 55.0, 89.0]])
-
-    # Act
-    select_features = SelectFeatures(
-        features=np.array([1, 2, 3, 8, 9, 10]), wavenumbers=wavenumbers
-    )
-    spectrum_corrected = select_features.fit_transform(spectrum)
-
-    # Assert
-    assert np.allclose(spectrum_corrected[0], expected, atol=1e-8)
-
-
-def test_standard_normal_variate(spectrum, reference_snv):
-    # Arrange
-    snv = StandardNormalVariate()
-
-    # Act
-    spectrum_corrected = snv.fit_transform(spectrum)
-
-    # Assert
-    assert np.allclose(spectrum_corrected[0], reference_snv[0], atol=1e-2)
-
-
-def test_subtract_reference(spectrum):
-    # Arrange
-    baseline = SubtractReference(reference=spectrum)
-
-    # Act
-    spectrum_corrected = baseline.fit_transform(spectrum)
-
-    # Assert
-    assert np.allclose(spectrum_corrected[0], np.zeros(len(spectrum)), atol=1e-8)
-
-
-def test_subtract_reference_without_reference(spectrum):
-    # Arrange
-    baseline = SubtractReference()
-
-    # Act
-    spectrum_corrected = baseline.fit_transform(spectrum)
-
-    # Assert
-    assert np.allclose(spectrum_corrected[0], spectrum, atol=1e-8)
-
-
-def test_whitakker_smooth(spectrum, reference_whitakker):
-    # Arrange
-    whitakker_smooth = WhittakerSmooth()
-
-    # Act
-    spectrum_corrected = whitakker_smooth.fit_transform(spectrum)
-
-    # Assert
-    assert np.allclose(spectrum_corrected[0], reference_whitakker[0], atol=1e-8)