chemotools 0.0.22__py3-none-any.whl → 0.0.24__py3-none-any.whl

tests/test_functionality.py

@@ -1,4 +1,5 @@
 import numpy as np
+import pytest
 
 from chemotools.baseline import (
     AirPls,
@@ -10,7 +11,12 @@ from chemotools.baseline import (
 )
 from chemotools.derivative import NorrisWilliams, SavitzkyGolay
 from chemotools.scale import IndexScaler, MinMaxScaler, NormScaler
-from chemotools.scatter import MultiplicativeScatterCorrection, StandardNormalVariate
+from chemotools.scatter import (
+    ExtendedMultiplicativeScatterCorrection,
+    MultiplicativeScatterCorrection,
+    RobustNormalVariate,
+    StandardNormalVariate,
+)
 from chemotools.smooth import MeanFilter, MedianFilter, WhittakerSmooth
 from chemotools.variable_selection import RangeCut
 from tests.fixtures import (
@@ -78,6 +84,104 @@ def test_constant_baseline_correction_with_wavenumbers():
     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_index_scaler(spectrum):
     # Arrange
     index_scaler = IndexScaler(index=0)
@@ -190,7 +294,7 @@ def test_multiplicative_scatter_correction_mean(spectrum, reference_msc_mean):
 
 def test_multiplicative_scatter_correction_with_reference(spectrum, reference_msc_mean):
     # Arrange
-    msc = MultiplicativeScatterCorrection(reference=reference_msc_mean)
+    msc = MultiplicativeScatterCorrection(reference=reference_msc_mean[0])
 
     # Act
     spectrum_corrected = msc.fit_transform(spectrum)
@@ -214,9 +318,7 @@ def test_multiplicative_scatter_correction_with_reference_median(
     spectrum, reference_msc_median
 ):
     # Arrange
-    msc = MultiplicativeScatterCorrection(
-        reference=reference_msc_median, use_median=True
-    )
+    msc = MultiplicativeScatterCorrection(reference=reference_msc_median[0], use_median=True)
 
     # Act
     spectrum_corrected = msc.fit_transform(spectrum)
@@ -225,6 +327,49 @@ def test_multiplicative_scatter_correction_with_reference_median(
     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]])
@@ -273,6 +418,17 @@ def test_norris_williams_filter_2():
     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_range_cut_by_index(spectrum):
     # Arrange
     range_cut = RangeCut(start=0, end=10)
@@ -310,6 +466,19 @@ def test_range_cut_by_wavenumber_2():
     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(

tests/test_sklearn_compliance.py

@@ -12,7 +12,12 @@ from chemotools.baseline import (
 )
 from chemotools.derivative import NorrisWilliams, SavitzkyGolay
 from chemotools.scale import IndexScaler, MinMaxScaler, NormScaler
-from chemotools.scatter import MultiplicativeScatterCorrection, StandardNormalVariate
+from chemotools.scatter import (
+    ExtendedMultiplicativeScatterCorrection,
+    MultiplicativeScatterCorrection,
+    RobustNormalVariate,
+    StandardNormalVariate,
+)
 from chemotools.smooth import (
     MeanFilter,
     MedianFilter,
@@ -56,6 +61,13 @@ def test_compliance_cubic_spline_correction():
     check_estimator(transformer)
 
 
+# ExtendedMultiplicativeScatterCorrection
+def test_compliance_extended_multiplicative_scatter_correction():
+    # Arrange
+    transformer = ExtendedMultiplicativeScatterCorrection()
+    # Act & Assert
+    check_estimator(transformer) 
+
 # IndexScaler
 def test_compliance_index_scaler():
     # Arrange
@@ -176,6 +188,13 @@ def test_compliance_range_cut():
     check_estimator(transformer)
 
 
+# RobustNormalVariate
+def test_compliance_robust_normal_variate():
+    # Arrange
+    transformer = RobustNormalVariate()
+    # Act & Assert
+    check_estimator(transformer)
+
 # SubtractReference
 def test_compliance_subtract_reference():
     # Arrange