"""
The :mod:`chemotools.derivative._savitzky_golay` module implements the Savitzky-Golay
transformer to calculate the Savitzky-Golay derivative of spectral data.
"""
# Author: Pau Cabaneros
# License: MIT
from numbers import Integral
from typing import Literal
import numpy as np
from scipy.signal import savgol_filter
from sklearn.base import BaseEstimator, OneToOneFeatureMixin, TransformerMixin
from sklearn.utils._param_validation import Interval, StrOptions
from sklearn.utils.validation import check_is_fitted, validate_data
from chemotools._deprecation import (
DEPRECATED_PARAMETER,
deprecated_parameter_constraint,
resolve_renamed_parameter,
)
[docs]
class SavitzkyGolay(TransformerMixin, OneToOneFeatureMixin, BaseEstimator):
"""
A transformer that calculates the Savitzky-Golay derivative of the input data.
Parameters
----------
window_length : int, optional, default=3
The size of the window to use for the derivative
calculation. Must be odd. Default is 3.
polyorder : int, optional, default=1
The order of the polynomial to use for the derivative calculation. Must be less
than ``window_length``. Default is 1.
deriv : int, optional, default=1
The order of the derivative to calculate. Default is 1.
window_size : int, optional
Deprecated alias for ``window_length``.
polynomial_order : int, optional
Deprecated alias for ``polyorder``.
derivate_order : int, optional
Deprecated alias for ``deriv``.
mode : str, optional, default="nearest"
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.
References
----------
[1] Åsmund Rinnan, Frans van den Berg, Søren Balling Engelsen,
"Review of the most common pre-processing techniques for near-infrared spectra,"
TrAC Trends in Analytical Chemistry 28 (10) 1201-1222 (2009).
Examples
--------
>>> from chemotools.derivative import SavitzkyGolay
>>> from chemotools.datasets import load_fermentation_train
>>> # Load sample data
>>> X, _ = load_fermentation_train()
>>> # Instantiate the transformer
>>> transformer = SavitzkyGolay(window_length=3, polyorder=1)
SavitzkyGolay()
>>> transformer.fit(X)
>>> # Calculate Savitzky-Golay derivative
>>> X_corrected = transformer.transform(X)
"""
_parameter_constraints: dict = {
"window_length": [Interval(Integral, 3, None, closed="left")],
"polyorder": [Interval(Integral, 0, None, closed="left")],
"deriv": [Interval(Integral, 0, None, closed="left")],
"window_size": [
Interval(Integral, 3, None, closed="left"),
deprecated_parameter_constraint(),
],
"polynomial_order": [
Interval(Integral, 0, None, closed="left"),
deprecated_parameter_constraint(),
],
"derivate_order": [
Interval(Integral, 0, None, closed="left"),
deprecated_parameter_constraint(),
],
"mode": [StrOptions({"nearest", "constant", "wrap", "mirror", "interp"})],
}
def __init__(
self,
window_length: int = 3,
polyorder: int = 1,
deriv: int = 1,
mode: Literal["mirror", "constant", "nearest", "wrap", "interp"] = "nearest",
window_size=DEPRECATED_PARAMETER,
polynomial_order=DEPRECATED_PARAMETER,
derivate_order=DEPRECATED_PARAMETER,
) -> None:
self.window_length = window_length
self.polyorder = polyorder
self.deriv = deriv
self.window_size = window_size
self.polynomial_order = polynomial_order
self.derivate_order = derivate_order
self.mode = mode
[docs]
def fit(self, X: np.ndarray, y=None) -> "SavitzkyGolay":
"""
Fit the transformer to the input data.
Parameters
----------
X : np.ndarray of shape (n_samples, n_features)
The input data to fit the transformer to.
y : None
Ignored to align with API.
Returns
-------
self : SavitzkyGolay
The fitted transformer.
"""
# Check that X is a 2D array and has only finite values
X = validate_data(
self, X, y="no_validation", ensure_2d=True, reset=True, dtype=np.float64
)
self.window_length_ = resolve_renamed_parameter(
new_name="window_length",
new_value=self.window_length,
new_default=3,
old_name="window_size",
old_value=self.window_size,
)
self.polyorder_ = resolve_renamed_parameter(
new_name="polyorder",
new_value=self.polyorder,
new_default=1,
old_name="polynomial_order",
old_value=self.polynomial_order,
)
self.deriv_ = resolve_renamed_parameter(
new_name="deriv",
new_value=self.deriv,
new_default=1,
old_name="derivate_order",
old_value=self.derivate_order,
)
return self
