chemotools 0.0.17__tar.gz → 0.0.19__tar.gz

{chemotools-0.0.17 → chemotools-0.0.19}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: chemotools
-Version: 0.0.17
+Version: 0.0.19
 Summary: Package to integrate chemometrics in scikit-learn pipelines
 Home-page: https://github.com/paucablop/chemotools
 Author: Pau Cabaneros Lopez
@@ -13,10 +13,14 @@ Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 
+![chemotools](assets/images/logo_5.png)
+
+
 [![pypi](https://img.shields.io/pypi/v/chemotools)](https://pypi.org/project/chemotools)
 [![pypi](https://img.shields.io/pypi/pyversions/chemotools)](https://pypi.org/project/chemotools)
 [![pypi](https://img.shields.io/pypi/l/chemotools)](https://github.com/paucablop/chemotools/blob/main/LICENSE)
 [![codecov](https://codecov.io/github/paucablop/chemotools/branch/main/graph/badge.svg?token=D7JUJM89LN)](https://codecov.io/github/paucablop/chemotools)
+[![Downloads](https://static.pepy.tech/badge/chemotools)](https://pepy.tech/project/chemotools)
 
 # __chemotools__
 

{chemotools-0.0.17 → chemotools-0.0.19}/README.md

@@ -1,7 +1,11 @@
+![chemotools](assets/images/logo_5.png)
+
+
 [![pypi](https://img.shields.io/pypi/v/chemotools)](https://pypi.org/project/chemotools)
 [![pypi](https://img.shields.io/pypi/pyversions/chemotools)](https://pypi.org/project/chemotools)
 [![pypi](https://img.shields.io/pypi/l/chemotools)](https://github.com/paucablop/chemotools/blob/main/LICENSE)
 [![codecov](https://codecov.io/github/paucablop/chemotools/branch/main/graph/badge.svg?token=D7JUJM89LN)](https://codecov.io/github/paucablop/chemotools)
+[![Downloads](https://static.pepy.tech/badge/chemotools)](https://pepy.tech/project/chemotools)
 
 # __chemotools__
 

{chemotools-0.0.17 → chemotools-0.0.19}/chemotools/baseline/air_pls.py

@@ -1,13 +1,21 @@
 import logging
 import numpy as np
-from sklearn.base import BaseEstimator, TransformerMixin
+from scipy.sparse import csc_matrix, eye, diags
+from scipy.sparse.linalg import spsolve
+from sklearn.base import BaseEstimator, TransformerMixin, OneToOneFeatureMixin
 from sklearn.utils.validation import check_is_fitted
 
 from chemotools.utils.check_inputs import check_input
 
 logger = logging.getLogger(__name__)
 
-class AirPls(BaseEstimator, TransformerMixin):
+# This code is adapted from the following source:
+# Z.-M. Zhang, S. Chen, and Y.-Z. Liang,
+# Baseline correction using adaptive iteratively reweighted penalized least squares.
+# Analyst 135 (5), 1138-1146 (2010).P
+
+
+class AirPls(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     def __init__(
         self,
         nr_iterations: int = 15,
@@ -40,7 +48,9 @@ class AirPls(BaseEstimator, TransformerMixin):
 
         # Check that the number of features is the same as the fitted data
         if X_.shape[1] != self.n_features_in_:
-            raise ValueError(f"Expected {self.n_features_in_} features but got {X_.shape[1]}")
+            raise ValueError(
+                f"Expected {self.n_features_in_} features but got {X_.shape[1]}"
+            )
 
         # Calculate the air pls smooth
         for i, x in enumerate(X_):
@@ -49,15 +59,16 @@ class AirPls(BaseEstimator, TransformerMixin):
         return X_.reshape(-1, 1) if X_.ndim == 1 else X_
 
     def _calculate_whittaker_smooth(self, x, w):
-        x = np.asarray(x)
-        n = len(x)
-        D = np.diff(np.eye(n), self.polynomial_order)
+        X = np.matrix(x)
+        m = X.size
+        E = eye(m, format="csc")
         for i in range(self.polynomial_order):
-            W = np.diag(w) + 1e-8*np.eye(n)
-            Z = W + self.lam * np.dot(D, D.T)
-            z = np.linalg.solve(Z, w * x)
-            w = np.sqrt(np.maximum(z, 0))
-        return z
+            E = E[1:] - E[:-1]
+        W = diags(w, 0, shape=(m, m))
+        A = csc_matrix(W + (self.lam * E.T * E))
+        B = csc_matrix(W * X.T)
+        background = spsolve(A, B)
+        return np.array(background)
 
     def _calculate_air_pls(self, x):
         m = x.shape[0]
@@ -66,16 +77,16 @@ class AirPls(BaseEstimator, TransformerMixin):
         for i in range(1, self.nr_iterations):
             z = self._calculate_whittaker_smooth(x, w)
             d = x - z
-            dssn = np.abs(d[d<0].sum()) 
+            dssn = np.abs(d[d < 0].sum())
 
-            if dssn < 0.001 * np.abs(x).sum(): 
+            if dssn < 0.001 * np.abs(x).sum():
                 break
-                
+
             if i == self.nr_iterations - 1:
                 break
 
-            w[d>=0]=0
-            w[d<0] =  np.exp(i * np.abs(d[d < 0]) / dssn)
+            w[d >= 0] = 0
+            w[d < 0] = np.exp(i * np.abs(d[d < 0]) / dssn)
 
             negative_d = d[d < 0]
             if negative_d.size > 0:
@@ -84,5 +95,3 @@ class AirPls(BaseEstimator, TransformerMixin):
             w[-1] = w[0]
 
         return z
-
-

{chemotools-0.0.17 → chemotools-0.0.19}/chemotools/baseline/constant_baseline_correction.py

@@ -1,11 +1,11 @@
 import numpy as np
-from sklearn.base import BaseEstimator, TransformerMixin
+from sklearn.base import BaseEstimator, TransformerMixin, OneToOneFeatureMixin
 from sklearn.utils.validation import check_is_fitted
 
 from chemotools.utils.check_inputs import check_input
 
 
-class ConstantBaselineCorrection(BaseEstimator, TransformerMixin):
+class ConstantBaselineCorrection(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     def __init__(
         self, wavenumbers: np.ndarray = None, start: int = 0, end: int = 1
     ) -> None:

{chemotools-0.0.17 → chemotools-0.0.19}/chemotools/baseline/cubic_spline_correction.py

@@ -1,11 +1,11 @@
 import numpy as np
 from scipy.interpolate import CubicSpline
-from sklearn.base import BaseEstimator, TransformerMixin
+from sklearn.base import BaseEstimator, TransformerMixin, OneToOneFeatureMixin
 from sklearn.utils.validation import check_is_fitted
 
 from chemotools.utils.check_inputs import check_input
 
-class CubicSplineCorrection(BaseEstimator, TransformerMixin):
+class CubicSplineCorrection(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     def __init__(self, indices: np.ndarray = None) -> None:
         self.indices = indices
 

{chemotools-0.0.17 → chemotools-0.0.19}/chemotools/baseline/linear_correction.py

@@ -1,11 +1,11 @@
 import numpy as np
-from sklearn.base import BaseEstimator, TransformerMixin
+from sklearn.base import BaseEstimator, TransformerMixin, OneToOneFeatureMixin
 from sklearn.utils.validation import check_is_fitted
 
 from chemotools.utils.check_inputs import check_input
 
 
-class LinearCorrection(BaseEstimator, TransformerMixin):
+class LinearCorrection(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
 
     def _drift_correct_spectrum(self, x: np.ndarray) -> np.ndarray:
 

{chemotools-0.0.17 → chemotools-0.0.19}/chemotools/baseline/non_negative.py

@@ -1,12 +1,12 @@
 import numpy as np
-from sklearn.base import BaseEstimator, TransformerMixin
+from sklearn.base import BaseEstimator, TransformerMixin, OneToOneFeatureMixin
 from sklearn.utils.validation import check_is_fitted
 
 from chemotools.utils.check_inputs import check_input
 
 
 
-class NonNegative(BaseEstimator, TransformerMixin):
+class NonNegative(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     def __init__(self, mode: str = "zero"):
         self.mode = mode
 

{chemotools-0.0.17 → chemotools-0.0.19}/chemotools/baseline/polynomial_correction.py

@@ -1,10 +1,10 @@
 import numpy as np
-from sklearn.base import BaseEstimator, TransformerMixin
+from sklearn.base import BaseEstimator, TransformerMixin, OneToOneFeatureMixin
 from sklearn.utils.validation import check_is_fitted
 
 from chemotools.utils.check_inputs import check_input
 
-class PolynomialCorrection(BaseEstimator, TransformerMixin):
+class PolynomialCorrection(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     def __init__(self, order: int = 1, indices: list = None) -> None:
         self.order = order
         self.indices = indices

{chemotools-0.0.17 → chemotools-0.0.19}/chemotools/baseline/subtract_reference.py

@@ -1,11 +1,11 @@
 import numpy as np
-from sklearn.base import BaseEstimator, TransformerMixin
+from sklearn.base import BaseEstimator, TransformerMixin, OneToOneFeatureMixin
 from sklearn.utils.validation import check_is_fitted
 
 from chemotools.utils.check_inputs import check_input
 
 
-class SubtractReference(BaseEstimator, TransformerMixin):
+class SubtractReference(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     def __init__(
         self,
         reference: np.ndarray = None,

{chemotools-0.0.17 → chemotools-0.0.19}/chemotools/derivative/norris_william.py

@@ -1,12 +1,12 @@
 import numpy as np
 from scipy.ndimage import convolve1d
-from sklearn.base import BaseEstimator, TransformerMixin
+from sklearn.base import BaseEstimator, TransformerMixin, OneToOneFeatureMixin
 from sklearn.utils.validation import check_is_fitted
 
 from chemotools.utils.check_inputs import check_input
 
 
-class NorrisWilliams(BaseEstimator, TransformerMixin):
+class NorrisWilliams(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     def __init__(
         self,
         window_size: int = 5,

{chemotools-0.0.17 → chemotools-0.0.19}/chemotools/derivative/savitzky_golay.py

@@ -1,12 +1,12 @@
 import numpy as np
 from scipy.signal import savgol_filter
-from sklearn.base import BaseEstimator, TransformerMixin
+from sklearn.base import BaseEstimator, TransformerMixin, OneToOneFeatureMixin
 from sklearn.utils.validation import check_is_fitted
 
 from chemotools.utils.check_inputs import check_input
 
 
-class SavitzkyGolay(BaseEstimator, TransformerMixin):
+class SavitzkyGolay(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     def __init__(
         self, window_size: int = 3, polynomial_order: int = 1, derivate_order: int = 1, mode: str = "nearest"
     ) -> None:

{chemotools-0.0.17 → chemotools-0.0.19}/chemotools/scale/index_scaler.py

@@ -1,11 +1,11 @@
 import numpy as np
-from sklearn.base import BaseEstimator, TransformerMixin
+from sklearn.base import BaseEstimator, TransformerMixin, OneToOneFeatureMixin
 from sklearn.utils.validation import check_is_fitted
 
 from chemotools.utils.check_inputs import check_input
 
 
-class IndexScaler(BaseEstimator, TransformerMixin):
+class IndexScaler(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     def __init__(self, index: int = 0):
         self.index = index
 

{chemotools-0.0.17 → chemotools-0.0.19}/chemotools/scale/min_max_scaler.py

@@ -1,11 +1,11 @@
 import numpy as np
-from sklearn.base import BaseEstimator, TransformerMixin
+from sklearn.base import BaseEstimator, TransformerMixin, OneToOneFeatureMixin
 from sklearn.utils.validation import check_is_fitted
 
 from chemotools.utils.check_inputs import check_input
 
 
-class MinMaxScaler(BaseEstimator, TransformerMixin):
+class MinMaxScaler(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     def __init__(self, norm: str = 'max'):
         self.norm = norm
 

{chemotools-0.0.17 → chemotools-0.0.19}/chemotools/scale/norm_scaler.py

@@ -1,11 +1,11 @@
 import numpy as np
-from sklearn.base import BaseEstimator, TransformerMixin
+from sklearn.base import BaseEstimator, TransformerMixin, OneToOneFeatureMixin
 from sklearn.utils.validation import check_is_fitted
 
 from chemotools.utils.check_inputs import check_input
 
 
-class NormScaler(BaseEstimator, TransformerMixin):
+class NormScaler(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     def __init__(self, l_norm: int = 2):
         self.l_norm = l_norm
 

{chemotools-0.0.17 → chemotools-0.0.19}/chemotools/scatter/multiplicative_scatter_correction.py

@@ -1,11 +1,11 @@
 import numpy as np
-from sklearn.base import BaseEstimator, TransformerMixin
+from sklearn.base import BaseEstimator, TransformerMixin, OneToOneFeatureMixin
 from sklearn.utils.validation import check_is_fitted
 
 from chemotools.utils.check_inputs import check_input
 
 
-class MultiplicativeScatterCorrection(BaseEstimator, TransformerMixin):
+class MultiplicativeScatterCorrection(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     def __init__(
         self,
         reference: np.ndarray = None,

{chemotools-0.0.17 → chemotools-0.0.19}/chemotools/scatter/standard_normal_variate.py

@@ -1,11 +1,11 @@
 import numpy as np
-from sklearn.base import BaseEstimator, TransformerMixin
+from sklearn.base import BaseEstimator, TransformerMixin, OneToOneFeatureMixin
 from sklearn.utils.validation import check_is_fitted
 
 from chemotools.utils.check_inputs import check_input
 
 
-class StandardNormalVariate(BaseEstimator, TransformerMixin):
+class StandardNormalVariate(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     def fit(self, X: np.ndarray, y=None) -> "StandardNormalVariate":
         # Check that X is a 2D array and has only finite values
         X = check_input(X)

{chemotools-0.0.17 → chemotools-0.0.19}/chemotools/smooth/mean_filter.py

@@ -1,12 +1,12 @@
 import numpy as np
 from scipy.ndimage import uniform_filter1d
-from sklearn.base import BaseEstimator, TransformerMixin
+from sklearn.base import BaseEstimator, TransformerMixin, OneToOneFeatureMixin
 from sklearn.utils.validation import check_is_fitted
 
 from chemotools.utils.check_inputs import check_input
 
 
-class MeanFilter(BaseEstimator, TransformerMixin):
+class MeanFilter(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     def __init__(self, window_size: int = 3, mode='nearest') -> None:
         self.window_size = window_size
         self.mode = mode

{chemotools-0.0.17 → chemotools-0.0.19}/chemotools/smooth/median_filter.py

@@ -1,12 +1,12 @@
 import numpy as np
 from scipy.ndimage import median_filter
-from sklearn.base import BaseEstimator, TransformerMixin
+from sklearn.base import BaseEstimator, TransformerMixin, OneToOneFeatureMixin
 from sklearn.utils.validation import check_is_fitted
 
 from chemotools.utils.check_inputs import check_input
 
 
-class MedianFilter(BaseEstimator, TransformerMixin):
+class MedianFilter(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     def __init__(self, window_size: int = 3, mode: str = 'nearest') -> None:
         self.window_size = window_size
         self.mode = mode

{chemotools-0.0.17 → chemotools-0.0.19}/chemotools/smooth/savitzky_golay_filter.py

@@ -1,12 +1,12 @@
 import numpy as np
 from scipy.signal import savgol_filter
-from sklearn.base import BaseEstimator, TransformerMixin
+from sklearn.base import BaseEstimator, TransformerMixin, OneToOneFeatureMixin
 from sklearn.utils.validation import check_is_fitted
 
 from chemotools.utils.check_inputs import check_input
 
 
-class SavitzkyGolayFilter(BaseEstimator, TransformerMixin):
+class SavitzkyGolayFilter(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     def __init__(
         self, window_size: int = 3, polynomial_order: int = 1, mode: str = "nearest"
     ) -> None:

{chemotools-0.0.17 → chemotools-0.0.19}/chemotools/smooth/whittaker_smooth.py

@@ -1,11 +1,18 @@
 import numpy as np
-from sklearn.base import BaseEstimator, TransformerMixin
+from scipy.sparse import csc_matrix, eye, diags
+from scipy.sparse.linalg import spsolve
+from sklearn.base import BaseEstimator, TransformerMixin, OneToOneFeatureMixin
 from sklearn.utils.validation import check_is_fitted
 
 from chemotools.utils.check_inputs import check_input
 
+# This code is adapted from the following source:
+# Z.-M. Zhang, S. Chen, and Y.-Z. Liang, 
+# Baseline correction using adaptive iteratively reweighted penalized least squares. 
+# Analyst 135 (5), 1138-1146 (2010).
 
-class WhittakerSmooth(BaseEstimator, TransformerMixin):
+
+class WhittakerSmooth(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     def __init__(
         self,
         lam: float = 1e2,
@@ -36,22 +43,25 @@ class WhittakerSmooth(BaseEstimator, TransformerMixin):
 
         # Check that the number of features is the same as the fitted data
         if X_.shape[1] != self.n_features_in_:
-            raise ValueError(f"Expected {self.n_features_in_} features but got {X_.shape[1]}")
+            raise ValueError(
+                f"Expected {self.n_features_in_} features but got {X_.shape[1]}"
+            )
 
         # Calculate the whittaker smooth
         for i, x in enumerate(X_):
             X_[i] = self._calculate_whittaker_smooth(x)
-            
+
         return X_.reshape(-1, 1) if X_.ndim == 1 else X_
 
     def _calculate_whittaker_smooth(self, x):
-        x = np.asarray(x)
-        n = len(x)
-        D = np.diff(np.eye(n), self.differences)
-        w = np.ones(n)
-        for i in range(self.differences+1):
-            W = np.diag(w) + 1e-8*np.eye(n)
-            Z = W + self.lam * np.dot(D, D.T)
-            z = np.linalg.solve(Z, w * x)
-            w = np.sqrt(np.maximum(z, 0))
-        return z
+        X = np.matrix(x)
+        m = X.size
+        E = eye(m, format="csc")
+        w = np.ones(m)
+        for i in range(self.differences):
+            E = E[1:] - E[:-1]
+        W = diags(w, 0, shape=(m, m))
+        A = csc_matrix(W + (self.lam * E.T * E))
+        B = csc_matrix(W * X.T)
+        background = spsolve(A, B)
+        return np.array(background)

{chemotools-0.0.17 → chemotools-0.0.19}/chemotools/variable_selection/range_cut.py

@@ -1,11 +1,11 @@
 import numpy as np
-from sklearn.base import BaseEstimator, TransformerMixin
+from sklearn.base import BaseEstimator, TransformerMixin, OneToOneFeatureMixin
 from sklearn.utils.validation import check_is_fitted
 
 from chemotools.utils.check_inputs import check_input
 
 
-class RangeCut(BaseEstimator, TransformerMixin):
+class RangeCut(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     def __init__(
         self,
         wavenumbers: np.ndarray = None,

{chemotools-0.0.17 → chemotools-0.0.19}/chemotools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: chemotools
-Version: 0.0.17
+Version: 0.0.19
 Summary: Package to integrate chemometrics in scikit-learn pipelines
 Home-page: https://github.com/paucablop/chemotools
 Author: Pau Cabaneros Lopez
@@ -13,10 +13,14 @@ Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 
+![chemotools](assets/images/logo_5.png)
+
+
 [![pypi](https://img.shields.io/pypi/v/chemotools)](https://pypi.org/project/chemotools)
 [![pypi](https://img.shields.io/pypi/pyversions/chemotools)](https://pypi.org/project/chemotools)
 [![pypi](https://img.shields.io/pypi/l/chemotools)](https://github.com/paucablop/chemotools/blob/main/LICENSE)
 [![codecov](https://codecov.io/github/paucablop/chemotools/branch/main/graph/badge.svg?token=D7JUJM89LN)](https://codecov.io/github/paucablop/chemotools)
+[![Downloads](https://static.pepy.tech/badge/chemotools)](https://pepy.tech/project/chemotools)
 
 # __chemotools__
 

{chemotools-0.0.17 → chemotools-0.0.19}/tests/test_functionality.py

@@ -25,7 +25,7 @@ def test_air_pls(spectrum, reference_airpls):
     spectrum_corrected = air_pls.fit_transform(spectrum)
 
     # Assert
-    assert np.allclose(spectrum_corrected[0], reference_airpls[0], atol=1e-8)
+    assert np.allclose(spectrum_corrected[0], reference_airpls[0], atol=1e-7)
 
 def test_constant_baseline_correction():
     # Arrange
@@ -356,4 +356,4 @@ def test_whitakker_smooth(spectrum, reference_whitakker):
     spectrum_corrected = whitakker_smooth.fit_transform(spectrum)
 
     # Assert
-    assert np.allclose(spectrum_corrected[0], reference_whitakker[0], atol=1e-2)
+    assert np.allclose(spectrum_corrected[0], reference_whitakker[0], atol=1e-8)