paradigma 1.0.4__py3-none-any.whl → 1.1.0__py3-none-any.whl

paradigma/__init__.py

@@ -1,6 +1,15 @@
+"""
+ParaDigMa: Parkinson Digital Biomarker Analysis Toolbox
+"""
+
 # read version from installed package
 from importlib.metadata import version
 
 __version__ = version("paradigma")
 
-__all__ = []
+# Import main pipeline functions for easy access
+from .orchestrator import run_paradigma
+
+__all__ = [
+    "run_paradigma",
+]

paradigma/classification.py

@@ -1,6 +1,6 @@
 import pickle
 from pathlib import Path
-from typing import Any, Optional
+from typing import Any
 
 import numpy as np
 from sklearn.base import BaseEstimator
@@ -10,9 +10,9 @@ from sklearn.preprocessing import StandardScaler
 class ClassifierPackage:
     def __init__(
         self,
-        classifier: Optional[BaseEstimator] = None,
-        threshold: Optional[float] = None,
-        scaler: Optional[Any] = None,
+        classifier: BaseEstimator | None = None,
+        threshold: float | None = None,
+        scaler: Any | None = None,
     ):
         """
         Initialize the ClassifierPackage with a classifier, threshold, and scaler.
@@ -30,13 +30,13 @@ class ClassifierPackage:
         self.threshold = threshold
         self.scaler = scaler
 
-    def transform_features(self, X) -> np.ndarray:
+    def transform_features(self, x) -> np.ndarray:
         """
         Transform the input features using the scaler.
 
         Parameters
         ----------
-        X : np.ndarray
+        x : np.ndarray
             The input features.
 
         Return
@@ -45,8 +45,8 @@ class ClassifierPackage:
             The transformed features.
         """
         if not self.scaler:
-            return X
-        return self.scaler.transform(X)
+            return x
+        return self.scaler.transform(x)
 
     def update_scaler(self, x_train: np.ndarray) -> None:
         """
@@ -60,13 +60,13 @@ class ClassifierPackage:
         scaler = StandardScaler()
         self.scaler = scaler.fit(x_train)
 
-    def predict_proba(self, X) -> float:
+    def predict_proba(self, x) -> float:
         """
         Make predictions using the classifier and apply the threshold.
 
         Parameters
         ----------
-        X : np.ndarray
+        x : np.ndarray
             The input features.
 
         Return
@@ -77,15 +77,15 @@ class ClassifierPackage:
         """
         if not self.classifier:
             raise ValueError("Classifier is not loaded.")
-        return self.classifier.predict_proba(X)[:, 1]
+        return self.classifier.predict_proba(x)[:, 1]
 
-    def predict(self, X) -> int:
+    def predict(self, x) -> int:
         """
         Make predictions using the classifier and apply the threshold.
 
         Parameters
         ----------
-        X : np.ndarray
+        x : np.ndarray
             The input features.
 
         Return
@@ -96,7 +96,7 @@ class ClassifierPackage:
         """
         if not self.classifier:
             raise ValueError("Classifier is not loaded.")
-        return int(self.predict_proba(X) >= self.threshold)
+        return int(self.predict_proba(x) >= self.threshold)
 
     def save(self, filepath: str | Path) -> None:
         """

paradigma/config.py

@@ -1,6 +1,5 @@
 import warnings
 from dataclasses import asdict
-from typing import Dict, List
 
 import numpy as np
 
@@ -19,7 +18,9 @@ class BaseConfig:
         self.set_filenames(sensor)
 
     def set_filenames(self, prefix: str) -> None:
-        """Sets the filenames based on the prefix. This method is duplicated from `gaits_analysis_config.py`.
+        """Sets the filenames based on the prefix.
+
+        This method is duplicated from `gaits_analysis_config.py`.
 
         Parameters
         ----------
@@ -51,12 +52,12 @@ class IMUConfig(BaseConfig):
 
         self.time_colname = self.column_mapping["TIME"]
 
-        self.accelerometer_colnames: List[str] = []
-        self.gyroscope_colnames: List[str] = []
-        self.gravity_colnames: List[str] = []
+        self.accelerometer_colnames: list[str] = []
+        self.gyroscope_colnames: list[str] = []
+        self.gravity_colnames: list[str] = []
 
-        self.d_channels_accelerometer: Dict[str, str] = {}
-        self.d_channels_gyroscope: Dict[str, str] = {}
+        self.d_channels_accelerometer: dict[str, str] = {}
+        self.d_channels_gyroscope: dict[str, str] = {}
 
         accel_keys = ["ACCELEROMETER_X", "ACCELEROMETER_Y", "ACCELEROMETER_Z"]
         grav_keys = [
@@ -83,7 +84,7 @@ class IMUConfig(BaseConfig):
                 c: self.rotation_units for c in self.gyroscope_colnames
             }
 
-        self.d_channels_imu: Dict[str, str] = {
+        self.d_channels_imu: dict[str, str] = {
             **self.d_channels_accelerometer,
             **self.d_channels_gyroscope,
         }
@@ -95,6 +96,10 @@ class IMUConfig(BaseConfig):
         self.upper_cutoff_frequency = 3.5
         self.filter_order = 4
 
+        # Segmentation parameters for handling non-contiguous data
+        self.max_segment_gap_s = 1.5
+        self.min_segment_length_s = 1.5
+
 
 class PPGConfig(BaseConfig):
 
@@ -150,7 +155,7 @@ class GaitConfig(IMUConfig):
         self.spectrum_high_frequency: int = int(self.sampling_frequency / 2)
 
         # Power in specified frequency bands
-        self.d_frequency_bandwidths: Dict[str, List[float]] = {
+        self.d_frequency_bandwidths: dict[str, list[float]] = {
             "power_below_gait": [0.2, 0.7],
             "power_gait": [0.7, 3.5],
             "power_tremor": [3.5, 8],
@@ -170,7 +175,7 @@ class GaitConfig(IMUConfig):
         # -----------------
         # TSDF data storage
         # -----------------
-        self.d_channels_values: Dict[str, str] = {
+        self.d_channels_values: dict[str, str] = {
             "accelerometer_std_norm": DataUnits.GRAVITY,
             "accelerometer_x_grav_mean": DataUnits.GRAVITY,
             "accelerometer_y_grav_mean": DataUnits.GRAVITY,
@@ -178,18 +183,18 @@ class GaitConfig(IMUConfig):
             "accelerometer_x_grav_std": DataUnits.GRAVITY,
             "accelerometer_y_grav_std": DataUnits.GRAVITY,
             "accelerometer_z_grav_std": DataUnits.GRAVITY,
-            "accelerometer_x_power_below_gait": DataUnits.POWER_SPECTRAL_DENSITY,
-            "accelerometer_y_power_below_gait": DataUnits.POWER_SPECTRAL_DENSITY,
-            "accelerometer_z_power_below_gait": DataUnits.POWER_SPECTRAL_DENSITY,
-            "accelerometer_x_power_gait": DataUnits.POWER_SPECTRAL_DENSITY,
-            "accelerometer_y_power_gait": DataUnits.POWER_SPECTRAL_DENSITY,
-            "accelerometer_z_power_gait": DataUnits.POWER_SPECTRAL_DENSITY,
-            "accelerometer_x_power_tremor": DataUnits.POWER_SPECTRAL_DENSITY,
-            "accelerometer_y_power_tremor": DataUnits.POWER_SPECTRAL_DENSITY,
-            "accelerometer_z_power_tremor": DataUnits.POWER_SPECTRAL_DENSITY,
-            "accelerometer_x_power_above_tremor": DataUnits.POWER_SPECTRAL_DENSITY,
-            "accelerometer_y_power_above_tremor": DataUnits.POWER_SPECTRAL_DENSITY,
-            "accelerometer_z_power_above_tremor": DataUnits.POWER_SPECTRAL_DENSITY,
+            "accelerometer_x_power_below_gait": DataUnits.POWER_SPECTRAL_DENSITY_ACC,
+            "accelerometer_y_power_below_gait": DataUnits.POWER_SPECTRAL_DENSITY_ACC,
+            "accelerometer_z_power_below_gait": DataUnits.POWER_SPECTRAL_DENSITY_ACC,
+            "accelerometer_x_power_gait": DataUnits.POWER_SPECTRAL_DENSITY_ACC,
+            "accelerometer_y_power_gait": DataUnits.POWER_SPECTRAL_DENSITY_ACC,
+            "accelerometer_z_power_gait": DataUnits.POWER_SPECTRAL_DENSITY_ACC,
+            "accelerometer_x_power_tremor": DataUnits.POWER_SPECTRAL_DENSITY_ACC,
+            "accelerometer_y_power_tremor": DataUnits.POWER_SPECTRAL_DENSITY_ACC,
+            "accelerometer_z_power_tremor": DataUnits.POWER_SPECTRAL_DENSITY_ACC,
+            "accelerometer_x_power_above_tremor": DataUnits.POWER_SPECTRAL_DENSITY_ACC,
+            "accelerometer_y_power_above_tremor": DataUnits.POWER_SPECTRAL_DENSITY_ACC,
+            "accelerometer_z_power_above_tremor": DataUnits.POWER_SPECTRAL_DENSITY_ACC,
             "accelerometer_x_dominant_frequency": DataUnits.FREQUENCY,
             "accelerometer_y_dominant_frequency": DataUnits.FREQUENCY,
             "accelerometer_z_dominant_frequency": DataUnits.FREQUENCY,
@@ -257,20 +262,23 @@ class TremorConfig(IMUConfig):
         # -----------
         # Aggregation
         # -----------
-        self.aggregates_tremor_power: List[str] = ["mode_binned", "median", "90p"]
+        self.aggregates_tremor_power: list[str] = ["mode_binned", "median", "90p"]
         self.evaluation_points_tremor_power: np.ndarray = np.linspace(0, 6, 301)
 
         # -----------------
         # TSDF data storage
         # -----------------
         if step == "features":
-            self.d_channels_values: Dict[str, str] = {}
+            self.d_channels_values: dict[str, str] = {}
             for mfcc_coef in range(1, self.n_coefficients_mfcc + 1):
-                self.d_channels_values[f"mfcc_{mfcc_coef}"] = "unitless"
+                self.d_channels_values[f"mfcc_{mfcc_coef}"] = DataUnits.NONE
+
+            self.d_channels_values[DataColumns.FREQ_PEAK] = DataUnits.FREQUENCY
+            self.d_channels_values[DataColumns.BELOW_TREMOR_POWER] = (
+                DataUnits.POWER_ROTATION
+            )
+            self.d_channels_values[DataColumns.TREMOR_POWER] = DataUnits.POWER_ROTATION
 
-            self.d_channels_values["freq_peak"] = "Hz"
-            self.d_channels_values["below_tremor_power"] = "(deg/s)^2"
-            self.d_channels_values["tremor_power"] = "(deg/s)^2"
         elif step == "classification":
             self.d_channels_values = {
                 DataColumns.PRED_TREMOR_PROBA: "probability",
@@ -299,7 +307,8 @@ class PulseRateConfig(PPGConfig):
             else:
                 self.imu_sampling_frequency = IMUConfig().sampling_frequency
                 warnings.warn(
-                    f"imu_sampling_frequency not provided, using default of {self.imu_sampling_frequency} Hz"
+                    f"imu_sampling_frequency not provided, using default "
+                    f"of {self.imu_sampling_frequency} Hz"
                 )
 
         # Windowing parameters

paradigma/constants.py

@@ -15,7 +15,9 @@ class DataColumns:
     GYROSCOPE_Z: str = "gyroscope_z"
     PPG: str = "green"
     TIME: str = "time"
-    SEGMENT_NR: str = "segment_nr"
+    GAIT_SEGMENT_NR: str = "gait_segment_nr"
+    SEGMENT_NR: str = "gait_segment_nr"  # Deprecated: Use GAIT_SEGMENT_NR instead
+    DATA_SEGMENT_NR: str = "data_segment_nr"
     SEGMENT_CAT: str = "segment_category"
 
     # Gait
@@ -37,6 +39,9 @@ class DataColumns:
     PRED_TREMOR_LOGREG: str = "pred_tremor_logreg"
     PRED_TREMOR_CHECKED: str = "pred_tremor_checked"
     PRED_ARM_AT_REST: str = "pred_arm_at_rest"
+    TREMOR_POWER: str = "tremor_power"
+    BELOW_TREMOR_POWER: str = "below_tremor_power"
+    FREQ_PEAK: str = "freq_peak"
 
     # Constants for PPG features
     VARIANCE: str = "variance"
@@ -78,9 +83,12 @@ class DataUnits:
     GRAVITY: str = "g"
     """ The acceleration due to gravity is in g. """
 
-    POWER_SPECTRAL_DENSITY: str = "g^2/Hz"
+    POWER_SPECTRAL_DENSITY_ACC: str = "g^2/Hz"
     """ The power spectral density is in g^2/Hz. """
 
+    POWER_ROTATION: str = "(deg/s)^2"
+    """ The power is in "(deg/s)^2. """
+
     FREQUENCY: str = "Hz"
     """ The frequency is in Hz. """