paradigma 1.0.3__py3-none-any.whl → 1.1.0__py3-none-any.whl

paradigma/prepare_data.py

@@ -0,0 +1,409 @@
+"""
+Data preparation module for ParaDigMa toolbox.
+
+This module provides functions to prepare raw sensor data for analysis:
+- Unit conversion (m/s² to g, rad/s to deg/s)
+- Time column formatting
+- Column name standardization
+- Watch side orientation correction
+- Resampling to 100 Hz
+
+Based on data_preparation tutorial.
+"""
+
+import logging
+
+import pandas as pd
+
+from paradigma.constants import DataColumns, TimeUnit
+from paradigma.preprocessing import resample_data
+from paradigma.util import (
+    convert_units_accelerometer,
+    convert_units_gyroscope,
+    transform_time_array,
+)
+
+logger = logging.getLogger(__name__)
+
+
+def standardize_column_names(
+    df: pd.DataFrame,
+    column_mapping: dict[str, str] | None = None,
+) -> pd.DataFrame:
+    """
+    Standardize column names to ParaDigMa conventions.
+
+    Parameters
+    ----------
+    df : pd.DataFrame
+        Input DataFrame.
+    column_mapping : dict, optional
+        Custom column mapping.
+
+    Returns
+    -------
+    pd.DataFrame
+        DataFrame with standardized column names.
+    """
+    df = df.copy()
+
+    # Apply mapping for existing columns only
+    if column_mapping is None:
+        return df
+
+    existing_mapping = {k: v for k, v in column_mapping.items() if k in df.columns}
+    df = df.rename(columns=existing_mapping)
+
+    if existing_mapping:
+        logger.debug(f"Standardized columns: {existing_mapping}")
+    return df
+
+
+def convert_sensor_units(
+    df: pd.DataFrame,
+    accelerometer_units: str = "m/s^2",
+    gyroscope_units: str = "deg/s",
+) -> pd.DataFrame:
+    """
+    Convert sensor units to ParaDigMa expected format (g for acceleration,
+    deg/s for gyroscope).
+
+    Parameters
+    ----------
+    df : pd.DataFrame
+        Input DataFrame with sensor data.
+    accelerometer_units : str, default 'm/s^2'
+        Current units of accelerometer data.
+    gyroscope_units : str, default 'deg/s'
+        Current units of gyroscope data.
+
+    Returns
+    -------
+    pd.DataFrame
+        DataFrame with converted units.
+    """
+    df = df.copy()
+
+    # Convert accelerometer units
+    accelerometer_columns = [
+        col
+        for col in [
+            DataColumns.ACCELEROMETER_X,
+            DataColumns.ACCELEROMETER_Y,
+            DataColumns.ACCELEROMETER_Z,
+        ]
+        if col in df.columns
+    ]
+
+    if accelerometer_columns and accelerometer_units != "g":
+        logger.debug(f"Converting accelerometer units from {accelerometer_units} to g")
+        accelerometer_data = df[accelerometer_columns].values
+        df[accelerometer_columns] = convert_units_accelerometer(
+            data=accelerometer_data, units=accelerometer_units
+        )
+
+    # Convert gyroscope units
+    gyroscope_columns = [
+        col
+        for col in [
+            DataColumns.GYROSCOPE_X,
+            DataColumns.GYROSCOPE_Y,
+            DataColumns.GYROSCOPE_Z,
+        ]
+        if col in df.columns
+    ]
+
+    if gyroscope_columns and gyroscope_units != "deg/s":
+        logger.debug(f"Converting gyroscope units from {gyroscope_units} to deg/s")
+        gyroscope_data = df[gyroscope_columns].values
+        df[gyroscope_columns] = convert_units_gyroscope(
+            data=gyroscope_data, units=gyroscope_units
+        )
+
+    return df
+
+
+def prepare_time_column(
+    df: pd.DataFrame,
+    time_column: str = DataColumns.TIME,
+    input_unit_type: TimeUnit = TimeUnit.RELATIVE_S,
+    output_unit_type: TimeUnit = TimeUnit.RELATIVE_S,
+) -> pd.DataFrame:
+    """
+    Prepare time column to start from 0 seconds.
+
+    Parameters
+    ----------
+    df : pd.DataFrame
+        Input DataFrame.
+    time_column : str, default DataColumns.TIME
+        Name of time column.
+    input_unit_type : TimeUnit, default TimeUnit.RELATIVE_S
+        Input time unit type.
+    output_unit_type : TimeUnit, default TimeUnit.RELATIVE_S
+        Output time unit type.
+
+    Returns
+    -------
+    pd.DataFrame
+        DataFrame with prepared time column.
+    """
+    df = df.copy()
+
+    if time_column not in df.columns:
+        raise ValueError(f"Time column '{time_column}' not found in DataFrame")
+
+    logger.debug(f"Preparing time column: {input_unit_type} -> {output_unit_type}")
+
+    df[time_column] = transform_time_array(
+        time_array=df[time_column],
+        input_unit_type=input_unit_type,
+        output_unit_type=output_unit_type,
+    )
+
+    return df
+
+
+def correct_watch_orientation(
+    df: pd.DataFrame,
+    device_orientation: list[str] | None = None,
+    sensor: str = "both",
+) -> pd.DataFrame:
+    """
+    Apply custom device orientation mapping if provided.
+
+    Note: Watch-side inversion is handled separately during preprocessing
+    in the pipeline functions (preprocess_imu_data), not during data preparation.
+
+    Parameters
+    ----------
+    df : pd.DataFrame
+        Input DataFrame with sensor data
+    device_orientation : list of str, optional
+        Custom orientation correction multipliers for each axis.
+        Maps device axes to standard [x, y, z] orientation.
+    sensor: str, optional
+        Sensor to correct ('accelerometer', 'gyroscope', or 'both').
+
+    Returns
+    -------
+    pd.DataFrame
+        DataFrame with corrected device orientation (if custom mapping provided)
+    """
+    out = df.copy()
+
+    target_orientation = ["x", "y", "z"]
+    valid_axes = ["x", "-x", "y", "-y", "z", "-z"]
+
+    if sensor == "both":
+        sensors_to_correct = ["accelerometer", "gyroscope"]
+    elif sensor in ["accelerometer", "gyroscope"]:
+        sensors_to_correct = [sensor]
+    else:
+        raise ValueError("Sensor must be 'accelerometer', 'gyroscope', or 'both'")
+
+    if device_orientation is not None:
+        if any([axis not in valid_axes for axis in device_orientation]):
+            raise ValueError(
+                f"Invalid device_orientation values. Must be one of {valid_axes}"
+            )
+        if len(device_orientation) != 3:
+            raise ValueError("device_orientation must have exactly 3 elements")
+
+        if all([device_orientation[x] == target_orientation[x] for x in range(3)]):
+            logger.debug(
+                "Device orientation matches target orientation, "
+                "no correction applied"
+            )
+        else:
+            for sensor_type in sensors_to_correct:
+                for target_axis, mapping in zip(["x", "y", "z"], device_orientation):
+                    sign = -1 if mapping.startswith("-") else 1
+                    source_axis = mapping[-1]
+
+                    out[f"{sensor_type}_{target_axis}"] = (
+                        sign * df[f"{sensor_type}_{source_axis}"]
+                    )
+
+                    logger.debug(
+                        f"Applied custom orientation: {sensor_type} "
+                        f"{target_axis} mapped from {mapping}"
+                    )
+
+    return out
+
+
+def validate_prepared_data(df: pd.DataFrame) -> dict[str, bool | str]:
+    """
+    Validate that data is properly prepared for ParaDigMa analysis.
+
+    Parameters
+    ----------
+    df : pd.DataFrame
+        Prepared DataFrame
+
+    Returns
+    -------
+    dict
+        Validation results with checks and error messages
+    """
+    validation = {"valid": True, "errors": [], "warnings": []}
+
+    # Check required columns
+    if DataColumns.TIME not in df.columns:
+        validation["errors"].append(f"Missing required time column: {DataColumns.TIME}")
+
+    # Check for at least accelerometer or gyroscope data
+    accel_cols = [
+        DataColumns.ACCELEROMETER_X,
+        DataColumns.ACCELEROMETER_Y,
+        DataColumns.ACCELEROMETER_Z,
+    ]
+    gyro_cols = [
+        DataColumns.GYROSCOPE_X,
+        DataColumns.GYROSCOPE_Y,
+        DataColumns.GYROSCOPE_Z,
+    ]
+
+    has_accel = all(col in df.columns for col in accel_cols)
+    has_gyro = all(col in df.columns for col in gyro_cols)
+
+    if not has_accel and not has_gyro:
+        validation["errors"].append("Missing accelerometer and gyroscope data")
+    elif not has_accel:
+        validation["warnings"].append("Missing accelerometer data")
+    elif not has_gyro:
+        validation["warnings"].append("Missing gyroscope data")
+
+    # Check time column format
+    if DataColumns.TIME in df.columns:
+        if df[DataColumns.TIME].iloc[0] != 0:
+            validation["warnings"].append("Time column does not start at 0")
+
+        time_diff = df[DataColumns.TIME].diff().dropna()
+        if time_diff.std() / time_diff.mean() > 0.1:
+            validation["warnings"].append("Time column has irregular sampling")
+
+    # Check for NaN values
+    nan_columns = df.columns[df.isnull().any()].tolist()
+    if nan_columns:
+        validation["warnings"].append(f"Columns with NaN values: {nan_columns}")
+
+    # Check sampling frequency
+    if DataColumns.TIME in df.columns and len(df) > 1:
+        time_diff = df[DataColumns.TIME].diff().dropna()
+        current_dt = time_diff.median()
+        current_frequency = 1.0 / current_dt
+
+        if abs(current_frequency - 100.0) > 5.0:
+            validation["warnings"].append(
+                f"Sampling frequency {current_frequency:.2f} Hz differs from "
+                f"expected 100 Hz"
+            )
+
+    # Set overall validity
+    validation["valid"] = len(validation["errors"]) == 0
+
+    return validation
+
+
+def prepare_raw_data(
+    df: pd.DataFrame,
+    accelerometer_units: str = "m/s^2",
+    gyroscope_units: str = "deg/s",
+    time_input_unit: TimeUnit = TimeUnit.RELATIVE_S,
+    resampling_frequency: float = 100.0,
+    column_mapping: dict[str, str] | None = None,
+    device_orientation: dict[str, int] | None = None,
+    validate: bool = True,
+    auto_segment: bool = False,
+    max_segment_gap_s: float | None = None,
+    min_segment_length_s: float | None = None,
+) -> pd.DataFrame:
+    """
+    Complete data preparation pipeline for raw sensor data.
+
+    Parameters
+    ----------
+    df : pd.DataFrame
+        Raw sensor data
+    accelerometer_units : str, default 'm/s^2'
+        Current units of accelerometer data
+    gyroscope_units : str, default 'deg/s'
+        Current units of gyroscope data
+    time_input_unit : TimeUnit, default TimeUnit.RELATIVE_S
+        Input time unit type
+    resampling_frequency : float, default 100.0
+        Target sampling frequency in Hz
+    column_mapping : Dict[str, str], optional
+        Custom column name mapping
+    device_orientation : Dict[str, int], optional
+        Custom orientation correction
+    validate : bool, default True
+        Whether to validate the prepared data
+    auto_segment : bool, default False
+        If True, automatically split non-contiguous data into segments.
+        Adds 'data_segment_nr' column to output.
+    max_segment_gap_s : float, optional
+        Maximum gap (seconds) before starting new segment. Used when auto_segment=True.
+        Defaults to 1.5s.
+    min_segment_length_s : float, optional
+        Minimum segment length (seconds) to keep. Used when auto_segment=True.
+        Defaults to 1.5s.
+
+    Returns
+    -------
+    pd.DataFrame
+        Prepared data ready for ParaDigMa analysis. If auto_segment=True and multiple
+        segments found, includes 'data_segment_nr' column.
+    """
+    logger.info("Starting data preparation pipeline")
+
+    # Step 1: Standardize column names
+    logger.info("Step 1: Standardizing column names")
+    if column_mapping is None:
+        logger.debug("No column mapping provided, using default mapping")
+    else:
+        df = standardize_column_names(df, column_mapping)
+
+    # Step 2: Convert units
+    logger.info("Step 2: Converting sensor units")
+    df = convert_sensor_units(df, accelerometer_units, gyroscope_units)
+
+    # Step 3: Prepare time column
+    logger.info("Step 3: Preparing time column")
+    df = prepare_time_column(df, input_unit_type=time_input_unit)
+
+    # Step 4: Correct device orientation
+    logger.info("Step 4: Correcting device orientation")
+    df = correct_watch_orientation(df, device_orientation=device_orientation)
+
+    # Step 5: Resample to target frequency
+    logger.info(f"Step 5: Resampling to {resampling_frequency} Hz")
+    df = resample_data(
+        df,
+        resampling_frequency=resampling_frequency,
+        auto_segment=auto_segment,
+        max_segment_gap_s=max_segment_gap_s,
+        min_segment_length_s=min_segment_length_s,
+        verbose=1 if logger.level <= logging.INFO else 0,
+    )
+
+    # Step 6: Validate prepared data
+    if validate:
+        logger.info("Step 6: Validating prepared data")
+        validation = validate_prepared_data(df)
+
+        if validation["warnings"]:
+            for warning in validation["warnings"]:
+                logger.warning(warning)
+
+        if not validation["valid"]:
+            for error in validation["errors"]:
+                logger.error(error)
+            raise ValueError("Data preparation validation failed")
+
+    logger.info(
+        f"Data preparation completed: {df.shape[0]} rows, {df.shape[1]} columns"
+    )
+    return df