chemotools 0.1.2__py3-none-any.whl → 0.1.3__py3-none-any.whl

chemotools/baseline/__init__.py

@@ -1,8 +1,8 @@
-from .air_pls import AirPls
-from .ar_pls import ArPls
-from .constant_baseline_correction import ConstantBaselineCorrection
-from .cubic_spline_correction import CubicSplineCorrection
-from .linear_correction import LinearCorrection
-from .non_negative import NonNegative
-from .polynomial_correction import PolynomialCorrection
-from .subtract_reference import SubtractReference
+from ._air_pls import AirPls
+from ._ar_pls import ArPls
+from ._constant_baseline_correction import ConstantBaselineCorrection
+from ._cubic_spline_correction import CubicSplineCorrection
+from ._linear_correction import LinearCorrection
+from ._non_negative import NonNegative
+from ._polynomial_correction import PolynomialCorrection
+from ._subtract_reference import SubtractReference

chemotools/baseline/{air_pls.py → _air_pls.py}

@@ -30,14 +30,6 @@ class AirPls(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
         The number of iterations used to calculate the baseline. Increasing the number of iterations can improve the
         accuracy of the baseline correction, but also increases the computation time.
 
-    Attributes
-    ----------
-    n_features_in_ : int
-        The number of features in the input data.
-
-    _is_fitted : bool
-        A flag indicating whether the estimator has been fitted to data.
-
     Methods
     -------
     fit(X, y=None)
@@ -85,13 +77,7 @@ class AirPls(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
             Returns the instance itself.
         """
         # Check that X is a 2D array and has only finite values
-        X = check_input(X)
-
-        # Set the number of features
-        self.n_features_in_ = X.shape[1]
-
-        # Set the fitted attribute to True
-        self._is_fitted = True
+        X = self._validate_data(X)
 
         return self
 
@@ -113,7 +99,7 @@ class AirPls(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
         """
 
         # Check that the estimator is fitted
-        check_is_fitted(self, "_is_fitted")
+        check_is_fitted(self, "n_features_in_")
 
         # Check that X is a 2D array and has only finite values
         X = check_input(X)

chemotools/baseline/{ar_pls.py → _ar_pls.py}

@@ -29,13 +29,6 @@ class ArPls(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     nr_iterations : int, optional (default=100)
         The maximum number of iterations for the weight updating scheme.
 
-    Attributes
-    ----------
-    n_features_in_ : int
-        The number of input features.
-
-    _is_fitted : bool
-        Whether the estimator has been fitted.
 
     Methods
     -------
@@ -86,13 +79,7 @@ class ArPls(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
         """
 
         # Check that X is a 2D array and has only finite values
-        X = check_input(X)
-
-        # Set the number of features
-        self.n_features_in_ = X.shape[1]
-
-        # Set the fitted attribute to True
-        self._is_fitted = True
+        X = self._validate_data(X)
 
         return self
 
@@ -114,7 +101,7 @@ class ArPls(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
         """
 
         # Check that the estimator is fitted
-        check_is_fitted(self, "_is_fitted")
+        check_is_fitted(self, "n_features_in_")
 
         # Check that X is a 2D array and has only finite values
         X = check_input(X)

chemotools/baseline/{constant_baseline_correction.py → _constant_baseline_correction.py}

@@ -30,12 +30,6 @@ class ConstantBaselineCorrection(OneToOneFeatureMixin, BaseEstimator, Transforme
     end_index_ : int
         The index of the end of the range. It is 1 if the wavenumbers are not provided.
 
-    n_features_in_ : int
-        The number of features in the input data.
-
-    _is_fitted : bool
-        Whether the transformer has been fitted to data.
-
     Methods
     -------
     fit(X, y=None)
@@ -46,7 +40,10 @@ class ConstantBaselineCorrection(OneToOneFeatureMixin, BaseEstimator, Transforme
     """
 
     def __init__(
-        self, start: int = 0, end: int = 1, wavenumbers: np.ndarray = None,
+        self,
+        start: int = 0,
+        end: int = 1,
+        wavenumbers: np.ndarray = None,
     ) -> None:
         self.start = start
         self.end = end
@@ -70,13 +67,7 @@ class ConstantBaselineCorrection(OneToOneFeatureMixin, BaseEstimator, Transforme
             The fitted transformer.
         """
         # Check that X is a 2D array and has only finite values
-        X = check_input(X)
-
-        # Set the number of features
-        self.n_features_in_ = X.shape[1]
-
-        # Set the fitted attribute to True
-        self._is_fitted = True
+        X = self._validate_data(X)
 
         # Set the start and end indices
         if self.wavenumbers is None:
@@ -109,7 +100,7 @@ class ConstantBaselineCorrection(OneToOneFeatureMixin, BaseEstimator, Transforme
             The transformed input data.
         """
         # Check that the estimator is fitted
-        check_is_fitted(self, "_is_fitted")
+        check_is_fitted(self, ["start_index_", "end_index_"])
 
         # Check that X is a 2D array and has only finite values
         X = check_input(X)

chemotools/baseline/{cubic_spline_correction.py → _cubic_spline_correction.py}

@@ -5,9 +5,10 @@ from sklearn.utils.validation import check_is_fitted
 
 from chemotools.utils.check_inputs import check_input
 
+
 class CubicSplineCorrection(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     """
-    A transformer that corrects a baseline by subtracting a cubic spline through the 
+    A transformer that corrects a baseline by subtracting a cubic spline through the
     points defined by the indices.
 
     Parameters
@@ -32,6 +33,7 @@ class CubicSplineCorrection(OneToOneFeatureMixin, BaseEstimator, TransformerMixi
         Transform the input data by subtracting the constant baseline value.
 
     """
+
     def __init__(self, indices: list = None) -> None:
         self.indices = indices
 
@@ -53,13 +55,7 @@ class CubicSplineCorrection(OneToOneFeatureMixin, BaseEstimator, TransformerMixi
             The fitted transformer.
         """
         # Check that X is a 2D array and has only finite values
-        X = check_input(X)
-
-        # Set the number of features
-        self.n_features_in_ = X.shape[1]
-
-        # Set the fitted attribute to True
-        self._is_fitted = True
+        X = self._validate_data(X)
 
         if self.indices is None:
             self.indices_ = [0, len(X[0]) - 1]
@@ -89,7 +85,7 @@ class CubicSplineCorrection(OneToOneFeatureMixin, BaseEstimator, TransformerMixi
             The transformed data.
         """
         # Check that the estimator is fitted
-        check_is_fitted(self, "_is_fitted")
+        check_is_fitted(self, "indices_")
 
         # Check that X is a 2D array and has only finite values
         X = check_input(X)
@@ -97,7 +93,9 @@ class CubicSplineCorrection(OneToOneFeatureMixin, BaseEstimator, TransformerMixi
 
         # 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 spline baseline correction
         for i, x in enumerate(X_):
@@ -106,7 +104,7 @@ class CubicSplineCorrection(OneToOneFeatureMixin, BaseEstimator, TransformerMixi
 
     def _spline_baseline_correct(self, x: np.ndarray) -> np.ndarray:
         indices = self.indices_
-        intensity = x[indices]  
+        intensity = x[indices]
         spl = CubicSpline(indices, intensity)
-        baseline = spl(range(len(x)))      
-        return x - baseline
+        baseline = spl(range(len(x)))
+        return x - baseline

chemotools/baseline/{linear_correction.py → _linear_correction.py}

@@ -10,17 +10,6 @@ class LinearCorrection(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     A transformer that corrects a baseline by subtracting a linear baseline through the
     initial and final points of the spectrum.
 
-    Parameters
-    ----------
-
-    Attributes
-    ----------
-    n_features_in_ : int
-        The number of features in the input data.
-
-    _is_fitted : bool
-        Whether the transformer has been fitted to data.
-
     Methods
     -------
     fit(X, y=None)
@@ -68,13 +57,7 @@ class LinearCorrection(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
             The fitted transformer.
         """
         # Check that X is a 2D array and has only finite values
-        X = check_input(X)
-
-        # Set the number of features
-        self.n_features_in_ = X.shape[1]
-
-        # Set the fitted attribute to True
-        self._is_fitted = True
+        X = self._validate_data(X)
 
         return self
 
@@ -99,7 +82,7 @@ class LinearCorrection(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
             The transformed data.
         """
         # Check that the estimator is fitted
-        check_is_fitted(self, "_is_fitted")
+        check_is_fitted(self, "n_features_in_")
 
         # Check that X is a 2D array and has only finite values
         X = check_input(X)

chemotools/baseline/{non_negative.py → _non_negative.py}

@@ -14,14 +14,6 @@ class NonNegative(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     mode : str, optional
         The mode to use for the non-negative values. Can be "zero" or "abs".
 
-    Attributes
-    ----------
-    n_features_in_ : int
-        The number of features in the input data.
-
-    _is_fitted : bool
-        Whether the transformer has been fitted to data.
-
     Methods
     -------
     fit(X, y=None)
@@ -52,13 +44,7 @@ class NonNegative(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
             The fitted transformer.
         """
         # Check that X is a 2D array and has only finite values
-        X = check_input(X)
-
-        # Set the number of features
-        self.n_features_in_ = X.shape[1]
-
-        # Set the fitted attribute to True
-        self._is_fitted = True
+        X = self._validate_data(X)
 
         return self
 
@@ -80,7 +66,7 @@ class NonNegative(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
             The transformed data.
         """
         # Check that the estimator is fitted
-        check_is_fitted(self, "_is_fitted")
+        check_is_fitted(self, "n_features_in_")
 
         # Check that X is a 2D array and has only finite values
         X = check_input(X)

chemotools/baseline/{polynomial_correction.py → _polynomial_correction.py}

@@ -4,9 +4,10 @@ from sklearn.utils.validation import check_is_fitted
 
 from chemotools.utils.check_inputs import check_input
 
+
 class PolynomialCorrection(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     """
-    A transformer that subtracts a polynomial baseline from the input data. The polynomial is 
+    A transformer that subtracts a polynomial baseline from the input data. The polynomial is
     fitted to the points in the spectrum specified by the indices parameter.
 
     Parameters
@@ -18,14 +19,6 @@ class PolynomialCorrection(OneToOneFeatureMixin, BaseEstimator, TransformerMixin
         The indices of the points in the spectrum to fit the polynomial to. Defaults to None,
         which fits the polynomial to all points in the spectrum (equivalent to detrend).
 
-    Attributes
-    ----------
-    n_features_in_ : int
-        The number of features in the input data.
-
-    _is_fitted : bool
-        Whether the transformer has been fitted to data.
-
     Methods
     -------
     fit(X, y=None)
@@ -37,6 +30,7 @@ class PolynomialCorrection(OneToOneFeatureMixin, BaseEstimator, TransformerMixin
     _baseline_correct_spectrum(x)
         Subtract the polynomial baseline from a single spectrum.
     """
+
     def __init__(self, order: int = 1, indices: list = None) -> None:
         self.order = order
         self.indices = indices
@@ -59,13 +53,7 @@ class PolynomialCorrection(OneToOneFeatureMixin, BaseEstimator, TransformerMixin
             The fitted transformer.
         """
         # Check that X is a 2D array and has only finite values
-        X = check_input(X)
-
-        # Set the number of features
-        self.n_features_in_ = X.shape[1]
-
-        # Set the fitted attribute to True
-        self._is_fitted = True
+        X = self._validate_data(X)
 
         if self.indices is None:
             self.indices_ = range(0, len(X[0]))
@@ -73,8 +61,8 @@ class PolynomialCorrection(OneToOneFeatureMixin, BaseEstimator, TransformerMixin
             self.indices_ = self.indices
 
         return self
-    
-    def transform(self, X: np.ndarray, y:int=0, copy:bool=True) -> np.ndarray:
+
+    def transform(self, X: np.ndarray, y: int = 0, copy: bool = True) -> np.ndarray:
         """
         Transform the input data by subtracting the polynomial baseline.
 
@@ -95,7 +83,7 @@ class PolynomialCorrection(OneToOneFeatureMixin, BaseEstimator, TransformerMixin
             The transformed data.
         """
         # Check that the estimator is fitted
-        check_is_fitted(self, "_is_fitted")
+        check_is_fitted(self, "indices_")
 
         # Check that X is a 2D array and has only finite values
         X = check_input(X)
@@ -103,13 +91,15 @@ class PolynomialCorrection(OneToOneFeatureMixin, 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 polynomial baseline correction
         for i, x in enumerate(X_):
             X_[i] = self._baseline_correct_spectrum(x)
         return X_.reshape(-1, 1) if X_.ndim == 1 else X_
-    
+
     def _baseline_correct_spectrum(self, x: np.ndarray) -> np.ndarray:
         """
         Subtract the polynomial baseline from a single spectrum.
@@ -126,5 +116,5 @@ class PolynomialCorrection(OneToOneFeatureMixin, BaseEstimator, TransformerMixin
         """
         intensity = x[self.indices_]
         poly = np.polyfit(self.indices_, intensity, self.order)
-        baseline = [np.polyval(poly, i) for i in range(0, len(x))]      
-        return x - baseline
+        baseline = [np.polyval(poly, i) for i in range(0, len(x))]
+        return x - baseline

chemotools/baseline/{subtract_reference.py → _subtract_reference.py}

@@ -15,14 +15,6 @@ class SubtractReference(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
         The reference spectrum to subtract from the input data. If None, the original spectrum
         is returned.
 
-    Attributes
-    ----------
-    n_features_in_ : int
-        The number of features in the input data.
-
-    _is_fitted : bool
-        Whether the transformer has been fitted to data.
-
     Methods
     -------
     fit(X, y=None)
@@ -34,6 +26,7 @@ class SubtractReference(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     _subtract_reference(x)
         Subtract the reference spectrum from a single spectrum.
     """
+
     def __init__(
         self,
         reference: np.ndarray = None,
@@ -58,20 +51,13 @@ class SubtractReference(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
             The fitted transformer.
         """
         # Check that X is a 2D array and has only finite values
-        X = check_input(X)
-
-        # Set the number of features
-        self.n_features_in_ = X.shape[1]
-
-        # Set the fitted attribute to True
-        self._is_fitted = True
+        X = self._validate_data(X)
 
         # Set the reference
-
         if self.reference is not None:
             self.reference_ = self.reference.copy()
             return self
-        
+
         return self
 
     def transform(self, X: np.ndarray, y=None) -> np.ndarray:
@@ -92,7 +78,7 @@ class SubtractReference(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
             The transformed data.
         """
         # Check that the estimator is fitted
-        check_is_fitted(self, "_is_fitted")
+        check_is_fitted(self, "n_features_in_")
 
         # Check that X is a 2D array and has only finite values
         X = check_input(X)
@@ -100,7 +86,9 @@ class SubtractReference(OneToOneFeatureMixin, 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]}"
+            )
 
         if self.reference is None:
             return X_.reshape(-1, 1) if X_.ndim == 1 else X_

chemotools/derivative/__init__.py

@@ -1,2 +1,2 @@
-from .norris_william import NorrisWilliams
-from .savitzky_golay import SavitzkyGolay
+from ._norris_william import NorrisWilliams
+from ._savitzky_golay import SavitzkyGolay

chemotools/derivative/{norris_william.py → _norris_william.py}

@@ -22,17 +22,9 @@ class NorrisWilliams(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
         The order of the derivative to calculate. Can be 1 or 2. Default is 1.
 
     mode : str, optional
-        The mode to use for the derivative calculation. Can be "nearest", "constant", 
+        The mode to use for the derivative calculation. Can be "nearest", "constant",
         "reflect", "wrap", "mirror" or "interp". Default is "nearest".
 
-    Attributes
-    ----------
-    n_features_in_ : int
-        The number of features in the input data.
-
-    _is_fitted : bool
-        Whether the transformer has been fitted to data.
-
     Methods
     -------
     fit(X, y=None)
@@ -41,6 +33,7 @@ class NorrisWilliams(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     transform(X, y=0, copy=True)
         Transform the input data by calculating the Norris-Williams derivative.
     """
+
     def __init__(
         self,
         window_size: int = 5,
@@ -71,13 +64,7 @@ class NorrisWilliams(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
             The fitted transformer.
         """
         # Check that X is a 2D array and has only finite values
-        X = check_input(X)
-
-        # Set the number of features
-        self.n_features_in_ = X.shape[1]
-
-        # Set the fitted attribute to True
-        self._is_fitted = True
+        X = self._validate_data(X)
 
         return self
 
@@ -99,7 +86,7 @@ class NorrisWilliams(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
             The transformed data.
         """
         # Check that the estimator is fitted
-        check_is_fitted(self, "_is_fitted")
+        check_is_fitted(self, "n_features_in_")
 
         # Check that X is a 2D array and has only finite values
         X = check_input(X)

chemotools/derivative/{savitzky_golay.py → _savitzky_golay.py}

@@ -27,14 +27,6 @@ class SavitzkyGolay(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
         The mode to use for the derivative calculation. Can be "nearest", "constant",
         "reflect", "wrap", "mirror" or "interp". Default is "nearest".
 
-    Attributes
-    ----------
-    n_features_in_ : int
-        The number of features in the input data.
-
-    _is_fitted : bool
-        Whether the transformer has been fitted to data.
-
     Methods
     -------
     fit(X, y=None)
@@ -74,13 +66,7 @@ class SavitzkyGolay(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
             The fitted transformer.
         """
         # Check that X is a 2D array and has only finite values
-        X = check_input(X)
-
-        # Set the number of features
-        self.n_features_in_ = X.shape[1]
-
-        # Set the fitted attribute to True
-        self._is_fitted = True
+        X = self._validate_data(X)
 
         return self
 
@@ -102,7 +88,7 @@ class SavitzkyGolay(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
             The transformed data.
         """
         # Check that the estimator is fitted
-        check_is_fitted(self, "_is_fitted")
+        check_is_fitted(self, "n_features_in_")
 
         # Check that X is a 2D array and has only finite values
         X = check_input(X)

chemotools/feature_selection/_index_selector.py

@@ -31,12 +31,6 @@ class IndexSelector(BaseEstimator, SelectorMixin):
     features_index_ : int
         The index of the features to select.
 
-    n_features_in_ : int
-        The number of features in the input data.
-
-    _is_fitted : bool
-        Whether the transformer has been fitted to data.
-
     Methods
     -------
     fit(X, y=None)
@@ -96,7 +90,7 @@ class IndexSelector(BaseEstimator, SelectorMixin):
 
         Returns
         -------
-        mask : ndarray of shape (n_features,)
+        mask : ndarray of shape (n_features_in_,)
             The mask indicating the selected features.
         """
         # Check that the estimator is fitted

chemotools/scale/__init__.py

@@ -1,3 +1,3 @@
-from .min_max_scaler import MinMaxScaler
-from .norm_scaler import NormScaler
-from .point_scaler import PointScaler
+from ._min_max_scaler import MinMaxScaler
+from ._norm_scaler import NormScaler
+from ._point_scaler import PointScaler

chemotools/scale/{min_max_scaler.py → _min_max_scaler.py}

@@ -8,23 +8,15 @@ from chemotools.utils.check_inputs import check_input
 class MinMaxScaler(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     """
     A transformer that scales the input data by subtracting the minimum and dividing by
-    the difference between the maximum and the minimum. When the use_min parameter is False, 
+    the difference between the maximum and the minimum. When the use_min parameter is False,
     the data is scaled by the maximum.
 
     Parameters
     ----------
     use_min : bool, default=True
-        The normalization to use. If True, the data is subtracted by the minimum and 
+        The normalization to use. If True, the data is subtracted by the minimum and
         scaled by the maximum. If False, the data is scaled by the maximum.
 
-    Attributes
-    ----------
-    n_features_in_ : int
-        The number of features in the input data.
-
-    _is_fitted : bool
-        Whether the transformer has been fitted to data.
-
     Methods
     -------
     fit(X, y=None)
@@ -55,13 +47,7 @@ class MinMaxScaler(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
             The fitted transformer.
         """
         # Check that X is a 2D array and has only finite values
-        X = check_input(X)
-
-        # Set the number of features
-        self.n_features_in_ = X.shape[1]
-
-        # Set the fitted attribute to True
-        self._is_fitted = True
+        X = self._validate_data(X)
 
         return self
 
@@ -83,7 +69,7 @@ class MinMaxScaler(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
             The transformed data.
         """
         # Check that the estimator is fitted
-        check_is_fitted(self, "_is_fitted")
+        check_is_fitted(self, "n_features_in_")
 
         # Check that X is a 2D array and has only finite values
         X = check_input(X)
@@ -97,8 +83,9 @@ class MinMaxScaler(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
 
         # Normalize the data by the maximum value
         if self.use_min:
-            X_ = (X_ - np.min(X_, axis=1, keepdims=True)) / (np.max(
-                X_, axis=1, keepdims=True) - np.min(X_, axis=1, keepdims=True))
+            X_ = (X_ - np.min(X_, axis=1, keepdims=True)) / (
+                np.max(X_, axis=1, keepdims=True) - np.min(X_, axis=1, keepdims=True)
+            )
 
         else:
             X_ = X_ / np.max(X_, axis=1, keepdims=True)

chemotools/scale/{norm_scaler.py → _norm_scaler.py}

@@ -12,15 +12,7 @@ class NormScaler(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     Parameters
     ----------
     l_norm : int, optional
-        The L-norm to use. Default is 2. 
-
-    Attributes
-    ----------
-    n_features_in_ : int
-        The number of features in the input data.
-
-    _is_fitted : bool
-        Whether the transformer has been fitted to data.
+        The L-norm to use. Default is 2.
 
     Methods
     -------
@@ -30,13 +22,14 @@ class NormScaler(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     transform(X, y=0, copy=True)
         Transform the input data by scaling by the L-norm.
     """
+
     def __init__(self, l_norm: int = 2):
         self.l_norm = l_norm
 
     def fit(self, X: np.ndarray, y=None) -> "NormScaler":
         """
         Fit the transformer to the input data.
-        
+
         Parameters
         ----------
         X : np.ndarray of shape (n_samples, n_features)
@@ -51,13 +44,7 @@ class NormScaler(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
             The fitted transformer.
         """
         # Check that X is a 2D array and has only finite values
-        X = check_input(X)
-
-        # Set the number of features
-        self.n_features_in_ = X.shape[1]
-
-        # Set the fitted attribute to True
-        self._is_fitted = True
+        X = self._validate_data(X)
 
         return self
 
@@ -79,7 +66,7 @@ class NormScaler(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
             The transformed data.
         """
         # Check that the estimator is fitted
-        check_is_fitted(self, "_is_fitted")
+        check_is_fitted(self, "n_features_in_")
 
         # Check that X is a 2D array and has only finite values
         X = check_input(X)

chemotools/scale/{point_scaler.py → _point_scaler.py}

@@ -7,12 +7,12 @@ from chemotools.utils.check_inputs import check_input
 
 class PointScaler(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     """
-    A transformer that scales the input data by the intensity value at a given point. 
+    A transformer that scales the input data by the intensity value at a given point.
     The point can be specified by an index or by a wavenumber.
 
     Parameters
     ----------
-    point : int, 
+    point : int,
         The point to scale the data by. It can be an index or a wavenumber.
 
     wavenumber : array-like, optional
@@ -25,12 +25,6 @@ class PointScaler(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     point_index_ : int
         The index of the point to scale the data by. It is 0 if the wavenumbers are not provided.
 
-    n_features_in_ : int
-        The number of features in the input data.
-
-    _is_fitted : bool
-        Whether the transformer has been fitted to data.
-
     Methods
     -------
     fit(X, y=None)
@@ -39,11 +33,11 @@ class PointScaler(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     transform(X, y=0, copy=True)
         Transform the input data by scaling by the value at a given Point.
     """
+
     def __init__(self, point: int = 0, wavenumbers: np.ndarray = None):
         self.point = point
         self.wavenumbers = wavenumbers
 
-
     def fit(self, X: np.ndarray, y=None) -> "PointScaler":
         """
         Fit the transformer to the input data.
@@ -62,13 +56,7 @@ class PointScaler(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
             The fitted transformer.
         """
         # Check that X is a 2D array and has only finite values
-        X = check_input(X)
-
-        # Set the number of features
-        self.n_features_in_ = X.shape[1]
-
-        # Set the fitted attribute to True
-        self._is_fitted = True
+        X = self._validate_data(X)
 
         # Set the point index
         if self.wavenumbers is None:
@@ -76,7 +64,6 @@ class PointScaler(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
         else:
             self.point_index_ = self._find_index(self.point)
 
-
         return self
 
     def transform(self, X: np.ndarray, y=None) -> np.ndarray:
@@ -97,7 +84,7 @@ class PointScaler(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
             The transformed data.
         """
         # Check that the estimator is fitted
-        check_is_fitted(self, "_is_fitted")
+        check_is_fitted(self, "point_index_")
 
         # Check that X is a 2D array and has only finite values
         X = check_input(X)
@@ -105,14 +92,16 @@ class PointScaler(OneToOneFeatureMixin, 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]}"
+            )
 
         # Scale the data by Point
         for i, x in enumerate(X_):
             X_[i] = x / x[self.point_index_]
-        
+
         return X_.reshape(-1, 1) if X_.ndim == 1 else X_
-    
+
     def _find_index(self, target: float) -> int:
         wavenumbers = np.array(self.wavenumbers)
-        return np.argmin(np.abs(wavenumbers - target))
+        return np.argmin(np.abs(wavenumbers - target))

chemotools/scatter/__init__.py

@@ -1,4 +1,4 @@
-from .extended_multiplicative_scatter_correction import ExtendedMultiplicativeScatterCorrection
-from .multiplicative_scatter_correction import MultiplicativeScatterCorrection
-from .robust_normal_variate import RobustNormalVariate
-from .standard_normal_variate import StandardNormalVariate
+from ._extended_multiplicative_scatter_correction import ExtendedMultiplicativeScatterCorrection
+from ._multiplicative_scatter_correction import MultiplicativeScatterCorrection
+from ._robust_normal_variate import RobustNormalVariate
+from ._standard_normal_variate import StandardNormalVariate

chemotools/scatter/{extended_multiplicative_scatter_correction.py → _extended_multiplicative_scatter_correction.py}

@@ -37,8 +37,6 @@ class ExtendedMultiplicativeScatterCorrection(
     ----------
     reference_ : np.ndarray
         The reference spectrum used for the correction.
-    n_features_in_ : int
-        The number of features in the training data.
 
     References
     ----------
@@ -82,13 +80,7 @@ class ExtendedMultiplicativeScatterCorrection(
             The fitted transformer.
         """
         # Check that X is a 2D array and has only finite values
-        X = check_input(X)
-
-        # Set the number of features
-        self.n_features_in_ = X.shape[1]
-
-        # Set the fitted attribute to True
-        self._is_fitted = True
+        X = self._validate_data(X)
 
         # Check that the length of the reference is the same as the number of features
         if self.reference is not None:
@@ -146,7 +138,7 @@ class ExtendedMultiplicativeScatterCorrection(
             The transformed data.
         """
         # Check that the estimator is fitted
-        check_is_fitted(self, "_is_fitted")
+        check_is_fitted(self, "n_features_in_")
 
         # Check that X is a 2D array and has only finite values
         X = check_input(X)

chemotools/scatter/{multiplicative_scatter_correction.py → _multiplicative_scatter_correction.py}

@@ -68,13 +68,7 @@ class MultiplicativeScatterCorrection(
             The fitted transformer.
         """
         # Check that X is a 2D array and has only finite values
-        X = check_input(X)
-
-        # Set the number of features
-        self.n_features_in_ = X.shape[1]
-
-        # Set the fitted attribute to True
-        self._is_fitted = True
+        X = self._validate_data(X)
 
         # Check that the length of the reference is the same as the number of features
         if self.reference is not None:
@@ -129,7 +123,7 @@ class MultiplicativeScatterCorrection(
             The transformed data.
         """
         # Check that the estimator is fitted
-        check_is_fitted(self, "_is_fitted")
+        check_is_fitted(self, "n_features_in_")
 
         # Check that X is a 2D array and has only finite values
         X = check_input(X)

chemotools/scatter/{robust_normal_variate.py → _robust_normal_variate.py}

@@ -15,14 +15,6 @@ class RobustNormalVariate(OneToOneFeatureMixin, BaseEstimator, TransformerMixin)
         The percentile to use for the robust normal variate. The value should be
         between 0 and 100. The default is 25.
 
-    Attributes
-    ----------
-    n_features_in_ : int
-        The number of features in the input data.
-
-    _is_fitted : bool
-        Whether the transformer has been fitted to data.
-
     Methods
     -------
     fit(X, y=None)
@@ -58,13 +50,7 @@ class RobustNormalVariate(OneToOneFeatureMixin, BaseEstimator, TransformerMixin)
             The fitted transformer.
         """
         # Check that X is a 2D array and has only finite values
-        X = check_input(X)
-
-        # Set the number of features
-        self.n_features_in_ = X.shape[1]
-
-        # Set the fitted attribute to True
-        self._is_fitted = True
+        X = self._validate_data(X)
 
         return self
 
@@ -86,7 +72,7 @@ class RobustNormalVariate(OneToOneFeatureMixin, BaseEstimator, TransformerMixin)
             The transformed data.
         """
         # Check that the estimator is fitted
-        check_is_fitted(self, "_is_fitted")
+        check_is_fitted(self, "n_features_in_")
 
         # Check that X is a 2D array and has only finite values
         X = check_input(X)

chemotools/scatter/{standard_normal_variate.py → _standard_normal_variate.py}

@@ -9,14 +9,6 @@ class StandardNormalVariate(OneToOneFeatureMixin, BaseEstimator, TransformerMixi
     """
     A transformer that calculates the standard normal variate of the input data.
 
-    Attributes
-    ----------
-    n_features_in_ : int
-        The number of features in the input data.
-
-    _is_fitted : bool
-        Whether the transformer has been fitted to data.
-
     Methods
     -------
     fit(X, y=None)
@@ -25,10 +17,11 @@ class StandardNormalVariate(OneToOneFeatureMixin, BaseEstimator, TransformerMixi
     transform(X, y=0, copy=True)
         Transform the input data by calculating the standard normal variate.
     """
+
     def fit(self, X: np.ndarray, y=None) -> "StandardNormalVariate":
         """
         Fit the transformer to the input data.
-        
+
         Parameters
         ----------
         X : np.ndarray of shape (n_samples, n_features)
@@ -43,13 +36,7 @@ class StandardNormalVariate(OneToOneFeatureMixin, BaseEstimator, TransformerMixi
             The fitted transformer.
         """
         # Check that X is a 2D array and has only finite values
-        X = check_input(X)
-
-        # Set the number of features
-        self.n_features_in_ = X.shape[1]
-
-        # Set the fitted attribute to True
-        self._is_fitted = True
+        X = self._validate_data(X)
 
         return self
 
@@ -71,7 +58,7 @@ class StandardNormalVariate(OneToOneFeatureMixin, BaseEstimator, TransformerMixi
             The transformed data.
         """
         # Check that the estimator is fitted
-        check_is_fitted(self, "_is_fitted")
+        check_is_fitted(self, "n_features_in_")
 
         # Check that X is a 2D array and has only finite values
         X = check_input(X)
@@ -79,7 +66,9 @@ class StandardNormalVariate(OneToOneFeatureMixin, BaseEstimator, TransformerMixi
 
         # 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 standard normal variate
         for i, x in enumerate(X_):
@@ -88,4 +77,4 @@ class StandardNormalVariate(OneToOneFeatureMixin, BaseEstimator, TransformerMixi
         return X_.reshape(-1, 1) if X_.ndim == 1 else X_
 
     def _calculate_standard_normal_variate(self, x) -> np.ndarray:
-        return (x - x.mean()) / x.std()
+        return (x - x.mean()) / x.std()

chemotools/smooth/__init__.py

@@ -1,4 +1,4 @@
-from .mean_filter import MeanFilter
-from .median_filter import MedianFilter
-from .savitzky_golay_filter import SavitzkyGolayFilter
-from .whittaker_smooth import WhittakerSmooth
+from ._mean_filter import MeanFilter
+from ._median_filter import MedianFilter
+from ._savitzky_golay_filter import SavitzkyGolayFilter
+from ._whittaker_smooth import WhittakerSmooth

chemotools/smooth/{mean_filter.py → _mean_filter.py}

@@ -14,19 +14,11 @@ class MeanFilter(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     ----------
     window_size : int, optional
         The size of the window to use for the mean filter. Must be odd. Default is 3.
-    
+
     mode : str, optional
         The mode to use for the mean filter. Can be "nearest", "constant", "reflect",
         "wrap", "mirror" or "interp". Default is "nearest".
 
-    Attributes
-    ----------
-    n_features_in_ : int
-        The number of features in the input data.
-
-    _is_fitted : bool
-        Whether the transformer has been fitted to data.
-
     Methods
     -------
     fit(X, y=None)
@@ -35,7 +27,8 @@ class MeanFilter(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     transform(X, y=0, copy=True)
         Transform the input data by calculating the mean filter.
     """
-    def __init__(self, window_size: int = 3, mode='nearest') -> None:
+
+    def __init__(self, window_size: int = 3, mode="nearest") -> None:
         self.window_size = window_size
         self.mode = mode
 
@@ -57,13 +50,7 @@ class MeanFilter(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
             The fitted transformer.
         """
         # Check that X is a 2D array and has only finite values
-        X = check_input(X)
-
-        # Set the number of features
-        self.n_features_in_ = X.shape[1]
-
-        # Set the fitted attribute to True
-        self._is_fitted = True
+        X = self._validate_data(X)
 
         return self
 
@@ -85,7 +72,7 @@ class MeanFilter(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
             The transformed data.
         """
         # Check that the estimator is fitted
-        check_is_fitted(self, "_is_fitted")
+        check_is_fitted(self, "n_features_in_")
 
         # Check that X is a 2D array and has only finite values
         X = check_input(X)

chemotools/smooth/{median_filter.py → _median_filter.py}

@@ -19,14 +19,6 @@ class MedianFilter(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
         The mode to use for the median filter. Can be "nearest", "constant", "reflect",
         "wrap", "mirror" or "interp". Default is "nearest".
 
-    Attributes
-    ----------
-    n_features_in_ : int
-        The number of features in the input data.
-
-    _is_fitted : bool
-        Whether the transformer has been fitted to data.
-
     Methods
     -------
     fit(X, y=None)
@@ -57,13 +49,7 @@ class MedianFilter(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
             The fitted transformer.
         """
         # Check that X is a 2D array and has only finite values
-        X = check_input(X)
-
-        # Set the number of features
-        self.n_features_in_ = X.shape[1]
-
-        # Set the fitted attribute to True
-        self._is_fitted = True
+        X = self._validate_data(X)
 
         return self
 
@@ -85,7 +71,7 @@ class MedianFilter(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
             The transformed data.
         """
         # Check that the estimator is fitted
-        check_is_fitted(self, "_is_fitted")
+        check_is_fitted(self, "n_features_in_")
 
         # Check that X is a 2D array and has only finite values
         X = check_input(X)

chemotools/smooth/{savitzky_golay_filter.py → _savitzky_golay_filter.py}

@@ -24,14 +24,6 @@ class SavitzkyGolayFilter(OneToOneFeatureMixin, BaseEstimator, TransformerMixin)
         The mode to use for the Savitzky-Golay filter. Can be "nearest", "constant",
         "reflect", "wrap", "mirror" or "interp". Default is "nearest".
 
-    Attributes
-    ----------
-    n_features_in_ : int
-        The number of features in the input data.
-
-    _is_fitted : bool
-        Whether the transformer has been fitted to data.
-
     Methods
     -------
     fit(X, y=None)
@@ -40,6 +32,7 @@ class SavitzkyGolayFilter(OneToOneFeatureMixin, BaseEstimator, TransformerMixin)
     transform(X, y=0, copy=True)
         Transform the input data by calculating the Savitzky-Golay filter.
     """
+
     def __init__(
         self, window_size: int = 3, polynomial_order: int = 1, mode: str = "nearest"
     ) -> None:
@@ -65,13 +58,7 @@ class SavitzkyGolayFilter(OneToOneFeatureMixin, BaseEstimator, TransformerMixin)
             The fitted transformer.
         """
         # Check that X is a 2D array and has only finite values
-        X = check_input(X)
-
-        # Set the number of features
-        self.n_features_in_ = X.shape[1]
-
-        # Set the fitted attribute to True
-        self._is_fitted = True
+        self._validate_data(X)
 
         return self
 
@@ -93,7 +80,7 @@ class SavitzkyGolayFilter(OneToOneFeatureMixin, BaseEstimator, TransformerMixin)
             The transformed data.
         """
         # Check that the estimator is fitted
-        check_is_fitted(self, "_is_fitted")
+        check_is_fitted(self, "n_features_in_")
 
         # Check that X is a 2D array and has only finite values
         X = check_input(X)

chemotools/smooth/{whittaker_smooth.py → _whittaker_smooth.py}

@@ -24,14 +24,6 @@ class WhittakerSmooth(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
     differences : int, optional
         The number of differences to use for the Whittaker smooth. Default is 1.
 
-    Attributes
-    ----------
-    n_features_in_ : int
-        The number of features in the input data.
-
-    _is_fitted : bool
-        Whether the transformer has been fitted to data.
-
     Methods
     -------
     fit(X, y=None)
@@ -66,13 +58,7 @@ class WhittakerSmooth(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
             The fitted transformer.
         """
         # Check that X is a 2D array and has only finite values
-        X = check_input(X)
-
-        # Set the number of features
-        self.n_features_in_ = X.shape[1]
-
-        # Set the fitted attribute to True
-        self._is_fitted = True
+        X = self._validate_data(X)
 
         return self
 
@@ -94,7 +80,7 @@ class WhittakerSmooth(OneToOneFeatureMixin, BaseEstimator, TransformerMixin):
             The transformed data.
         """
         # Check that the estimator is fitted
-        check_is_fitted(self, "_is_fitted")
+        check_is_fitted(self, "n_features_in_")
 
         # Check that X is a 2D array and has only finite values
         X = check_input(X)

{chemotools-0.1.2.dist-info → chemotools-0.1.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: chemotools
-Version: 0.1.2
+Version: 0.1.3
 Summary: Package to integrate chemometrics in scikit-learn pipelines
 Home-page: https://github.com/paucablop/chemotools
 Author: Pau Cabaneros Lopez

chemotools-0.1.3.dist-info/RECORD

@@ -0,0 +1,58 @@
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