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

paradigma/testing.py

@@ -1,55 +1,101 @@
 import json
-import numpy as np
 import os
-import pandas as pd
 from pathlib import Path
+
+import numpy as np
+import pandas as pd
 import tsdf
-from typing import List
 
 from paradigma.classification import ClassifierPackage
-from paradigma.config import IMUConfig, PPGConfig, GaitConfig, TremorConfig, PulseRateConfig
+from paradigma.config import (
+    GaitConfig,
+    IMUConfig,
+    PPGConfig,
+    PulseRateConfig,
+    TremorConfig,
+)
 from paradigma.constants import DataColumns, TimeUnit
-from paradigma.pipelines.gait_pipeline import extract_gait_features, detect_gait, \
-    extract_arm_activity_features, filter_gait
-from paradigma.pipelines.tremor_pipeline import extract_tremor_features, detect_tremor, \
-    aggregate_tremor
-from paradigma.pipelines.pulse_rate_pipeline import extract_signal_quality_features, signal_quality_classification, \
-    aggregate_pulse_rate
+from paradigma.pipelines.gait_pipeline import (
+    detect_gait,
+    extract_arm_activity_features,
+    extract_gait_features,
+    filter_gait,
+)
+from paradigma.pipelines.pulse_rate_pipeline import (
+    aggregate_pulse_rate,
+    extract_signal_quality_features,
+)
+from paradigma.pipelines.tremor_pipeline import (
+    aggregate_tremor,
+    detect_tremor,
+    extract_tremor_features,
+)
 from paradigma.preprocessing import preprocess_imu_data, preprocess_ppg_data
-from paradigma.util import read_metadata, write_df_data, get_end_iso8601, merge_predictions_with_timestamps
-
-
-def preprocess_imu_data_io(path_to_input: str | Path, path_to_output: str | Path, 
-                           config: IMUConfig, sensor: str, watch_side: str) -> None:
+from paradigma.util import (
+    get_end_iso8601,
+    merge_predictions_with_timestamps,
+    read_metadata,
+    write_df_data,
+)
+
+
+def preprocess_imu_data_io(
+    path_to_input: str | Path,
+    path_to_output: str | Path,
+    config: IMUConfig,
+    sensor: str,
+    watch_side: str,
+) -> None:
     # Load data
-    metadata_time, metadata_values = read_metadata(str(path_to_input), str(config.meta_filename),
-                                                    str(config.time_filename), str(config.values_filename))
-    df = tsdf.load_dataframe_from_binaries([metadata_time, metadata_values], tsdf.constants.ConcatenationType.columns)
+    metadata_time, metadata_values = read_metadata(
+        str(path_to_input),
+        str(config.meta_filename),
+        str(config.time_filename),
+        str(config.values_filename),
+    )
+    df = tsdf.load_dataframe_from_binaries(
+        [metadata_time, metadata_values], tsdf.constants.ConcatenationType.columns
+    )
 
     # Preprocess data
     df = preprocess_imu_data(df=df, config=config, sensor=sensor, watch_side=watch_side)
 
     # Store data
-    for sensor, units in zip(['accelerometer', 'gyroscope'], ['g', config.rotation_units]):
+    for sensor, units in zip(
+        ["accelerometer", "gyroscope"], ["g", config.rotation_units]
+    ):
         if any(sensor in col for col in df.columns):
             df_sensor = df[[DataColumns.TIME] + [x for x in df.columns if sensor in x]]
 
             metadata_values.channels = [x for x in df.columns if sensor in x]
-            metadata_values.units = list(np.repeat(units, len(metadata_values.channels)))
+            metadata_values.units = list(
+                np.repeat(units, len(metadata_values.channels))
+            )
             metadata_values.scale_factors = []
-            metadata_values.file_name = f'{sensor}_values.bin'
+            metadata_values.file_name = f"{sensor}_values.bin"
 
-            metadata_time.file_name = f'{sensor}_time.bin'
+            metadata_time.file_name = f"{sensor}_time.bin"
             metadata_time.units = [TimeUnit.RELATIVE_S]
 
-            write_df_data(metadata_time, metadata_values, path_to_output, f'{sensor}_meta.json', df_sensor)
-
-
-def preprocess_ppg_data_io(path_to_input_ppg: str | Path, path_to_input_imu: str | Path,
-                           output_path: str | Path, ppg_config: PPGConfig, 
-                           imu_config: IMUConfig) -> None:
-    """	
-    Preprocess PPG and IMU data by resampling, filtering, and aligning the data segments.
+            write_df_data(
+                metadata_time,
+                metadata_values,
+                path_to_output,
+                f"{sensor}_meta.json",
+                df_sensor,
+            )
+
+
+def preprocess_ppg_data_io(
+    path_to_input_ppg: str | Path,
+    path_to_input_imu: str | Path,
+    output_path: str | Path,
+    ppg_config: PPGConfig,
+    imu_config: IMUConfig,
+) -> None:
+    """
+    Preprocess PPG and IMU data by resampling, filtering, and aligning the
+    data segments.
 
     Parameters
     ----------
@@ -67,176 +113,234 @@ def preprocess_ppg_data_io(path_to_input_ppg: str | Path, path_to_input_imu: str
     Returns
     -------
     None
-    """ 
+    """
 
     # Load PPG data
-        # Load data
-    metadata_time_ppg, metadata_values_ppg = read_metadata(path_to_input_ppg, ppg_config.meta_filename,
-                                                    ppg_config.time_filename, ppg_config.values_filename)
-    df_ppg = tsdf.load_dataframe_from_binaries([metadata_time_ppg, metadata_values_ppg], tsdf.constants.ConcatenationType.columns)
+    # Load data
+    metadata_time_ppg, metadata_values_ppg = read_metadata(
+        path_to_input_ppg,
+        ppg_config.meta_filename,
+        ppg_config.time_filename,
+        ppg_config.values_filename,
+    )
+    df_ppg = tsdf.load_dataframe_from_binaries(
+        [metadata_time_ppg, metadata_values_ppg],
+        tsdf.constants.ConcatenationType.columns,
+    )
 
     # Load IMU data
-    metadata_time_imu, metadata_values_imu = read_metadata(path_to_input_imu, imu_config.meta_filename,
-                                                    imu_config.time_filename, imu_config.values_filename)
-    df_imu = tsdf.load_dataframe_from_binaries([metadata_time_imu, metadata_values_imu], tsdf.constants.ConcatenationType.columns)
+    metadata_time_imu, metadata_values_imu = read_metadata(
+        path_to_input_imu,
+        imu_config.meta_filename,
+        imu_config.time_filename,
+        imu_config.values_filename,
+    )
+    df_imu = tsdf.load_dataframe_from_binaries(
+        [metadata_time_imu, metadata_values_imu],
+        tsdf.constants.ConcatenationType.columns,
+    )
 
     # Drop the gyroscope columns from the IMU data
-    cols_to_drop = df_imu.filter(regex='^gyroscope_').columns
-    df_acc = df_imu.drop(cols_to_drop, axis=1)
+    colnames_to_drop = df_imu.filter(regex="^gyroscope_").columns
+    df_acc = df_imu.drop(colnames_to_drop, axis=1)
 
     # Preprocess data
     df_ppg_proc, df_acc_proc = preprocess_ppg_data(
-        df_ppg=df_ppg, 
-        df_acc=df_acc, 
-        ppg_config=ppg_config, 
+        df_ppg=df_ppg,
+        df_acc=df_acc,
+        ppg_config=ppg_config,
         imu_config=imu_config,
         start_time_ppg=metadata_time_ppg.start_iso8601,
-        start_time_imu=metadata_time_imu.start_iso8601
+        start_time_imu=metadata_time_imu.start_iso8601,
     )
 
     # Store data
     metadata_values_imu.channels = list(imu_config.d_channels_accelerometer.keys())
     metadata_values_imu.units = list(imu_config.d_channels_accelerometer.values())
-    metadata_values_imu.file_name = 'accelerometer_values.bin'
+    metadata_values_imu.file_name = "accelerometer_values.bin"
     metadata_time_imu.units = [TimeUnit.ABSOLUTE_MS]
-    metadata_time_imu.file_name = 'accelerometer_time.bin'
-    write_df_data(metadata_time_imu, metadata_values_imu, output_path, 'accelerometer_meta.json', df_acc_proc)
+    metadata_time_imu.file_name = "accelerometer_time.bin"
+    write_df_data(
+        metadata_time_imu,
+        metadata_values_imu,
+        output_path,
+        "accelerometer_meta.json",
+        df_acc_proc,
+    )
 
     metadata_values_ppg.channels = list(ppg_config.d_channels_ppg.keys())
     metadata_values_ppg.units = list(ppg_config.d_channels_ppg.values())
-    metadata_values_ppg.file_name = 'PPG_values.bin'
+    metadata_values_ppg.file_name = "PPG_values.bin"
     metadata_time_ppg.units = [TimeUnit.ABSOLUTE_MS]
-    metadata_time_ppg.file_name = 'PPG_time.bin'
-    write_df_data(metadata_time_ppg, metadata_values_ppg, output_path, 'PPG_meta.json', df_ppg_proc)
+    metadata_time_ppg.file_name = "PPG_time.bin"
+    write_df_data(
+        metadata_time_ppg,
+        metadata_values_ppg,
+        output_path,
+        "PPG_meta.json",
+        df_ppg_proc,
+    )
 
 
 def extract_gait_features_io(
-        config: GaitConfig,
-        path_to_input: str | Path, 
-        path_to_output: str | Path
-    ) -> None:
+    config: GaitConfig, path_to_input: str | Path, path_to_output: str | Path
+) -> None:
     # Load data
-    metadata_time, metadata_values = read_metadata(path_to_input, config.meta_filename, config.time_filename, config.values_filename)
-    df = tsdf.load_dataframe_from_binaries([metadata_time, metadata_values], tsdf.constants.ConcatenationType.columns)
+    metadata_time, metadata_values = read_metadata(
+        path_to_input,
+        config.meta_filename,
+        config.time_filename,
+        config.values_filename,
+    )
+    df = tsdf.load_dataframe_from_binaries(
+        [metadata_time, metadata_values], tsdf.constants.ConcatenationType.columns
+    )
 
     # Extract gait features
     df_features = extract_gait_features(df=df, config=config)
 
     # Store data
-    end_iso8601 = get_end_iso8601(start_iso8601=metadata_time.start_iso8601,
-                                  window_length_seconds=int(df_features[DataColumns.TIME][-1:].values[0] + config.window_length_s))
+    end_iso8601 = get_end_iso8601(
+        start_iso8601=metadata_time.start_iso8601,
+        window_length_seconds=int(
+            df_features[DataColumns.TIME][-1:].values[0] + config.window_length_s
+        ),
+    )
 
-    metadata_values.file_name = 'gait_values.bin'
-    metadata_time.file_name = 'gait_time.bin'
+    metadata_values.file_name = "gait_values.bin"
+    metadata_time.file_name = "gait_time.bin"
     metadata_values.end_iso8601 = end_iso8601
     metadata_time.end_iso8601 = end_iso8601
-    
+
     metadata_values.channels = list(config.d_channels_values.keys())
     metadata_values.units = list(config.d_channels_values.values())
 
     metadata_time.channels = [DataColumns.TIME]
     metadata_time.units = [TimeUnit.RELATIVE_S]
 
-    write_df_data(metadata_time, metadata_values, path_to_output, 'gait_meta.json', df_features)
+    write_df_data(
+        metadata_time, metadata_values, path_to_output, "gait_meta.json", df_features
+    )
 
 
 def detect_gait_io(
-        config: GaitConfig, 
-        path_to_input: str | Path, 
-        path_to_output: str | Path, 
-        full_path_to_classifier_package: str | Path, 
-    ) -> None:
-    
+    config: GaitConfig,
+    path_to_input: str | Path,
+    path_to_output: str | Path,
+    full_path_to_classifier_package: str | Path,
+) -> None:
+
     # Load the data
-    config.set_filenames('gait')
+    config.set_filenames("gait")
 
-    metadata_time, metadata_values = read_metadata(path_to_input, config.meta_filename, config.time_filename, config.values_filename)
-    df = tsdf.load_dataframe_from_binaries([metadata_time, metadata_values], tsdf.constants.ConcatenationType.columns)
+    metadata_time, metadata_values = read_metadata(
+        path_to_input,
+        config.meta_filename,
+        config.time_filename,
+        config.values_filename,
+    )
+    df = tsdf.load_dataframe_from_binaries(
+        [metadata_time, metadata_values], tsdf.constants.ConcatenationType.columns
+    )
 
     clf_package = ClassifierPackage.load(full_path_to_classifier_package)
 
-    df[DataColumns.PRED_GAIT_PROBA] = detect_gait(
-        df=df, 
-        clf_package=clf_package
-    )
+    df[DataColumns.PRED_GAIT_PROBA] = detect_gait(df=df, clf_package=clf_package)
 
     # Prepare the metadata
-    metadata_values.file_name = 'gait_values.bin'
-    metadata_time.file_name = 'gait_time.bin'
+    metadata_values.file_name = "gait_values.bin"
+    metadata_time.file_name = "gait_time.bin"
 
     metadata_values.channels = [DataColumns.PRED_GAIT_PROBA]
-    metadata_values.units = ['probability']
+    metadata_values.units = ["probability"]
 
     metadata_time.channels = [DataColumns.TIME]
     metadata_time.units = [TimeUnit.RELATIVE_S]
 
-    write_df_data(metadata_time, metadata_values, path_to_output, 'gait_meta.json', df)
+    write_df_data(metadata_time, metadata_values, path_to_output, "gait_meta.json", df)
 
 
 def extract_arm_activity_features_io(
-        config: GaitConfig, 
-        path_to_timestamp_input: str | Path, 
-        path_to_prediction_input: str | Path, 
-        full_path_to_classifier_package: str | Path, 
-        path_to_output: str | Path
-    ) -> None:
+    config: GaitConfig,
+    path_to_timestamp_input: str | Path,
+    path_to_prediction_input: str | Path,
+    full_path_to_classifier_package: str | Path,
+    path_to_output: str | Path,
+) -> None:
     # Load accelerometer and gyroscope data
     dfs = []
-    for sensor in ['accelerometer', 'gyroscope']:
+    for sensor in ["accelerometer", "gyroscope"]:
         config.set_sensor(sensor)
-        meta_ts_filename = f'{sensor}_meta.json'
-        values_ts_filename = f'{sensor}_values.bin'
-        time_ts_filename = f'{sensor}_time.bin'
+        meta_ts_filename = f"{sensor}_meta.json"
+        values_ts_filename = f"{sensor}_values.bin"
+        time_ts_filename = f"{sensor}_time.bin"
 
-        metadata_ts_dict = tsdf.load_metadata_from_path(os.path.join(path_to_timestamp_input, meta_ts_filename))
+        metadata_ts_dict = tsdf.load_metadata_from_path(
+            os.path.join(path_to_timestamp_input, meta_ts_filename)
+        )
         metadata_ts_time = metadata_ts_dict[time_ts_filename]
         metadata_ts_values = metadata_ts_dict[values_ts_filename]
-        dfs.append(tsdf.load_dataframe_from_binaries([metadata_ts_time, metadata_ts_values], tsdf.constants.ConcatenationType.columns))
+        dfs.append(
+            tsdf.load_dataframe_from_binaries(
+                [metadata_ts_time, metadata_ts_values],
+                tsdf.constants.ConcatenationType.columns,
+            )
+        )
 
     df_ts = pd.merge(dfs[0], dfs[1], on=DataColumns.TIME)
 
     # Load gait predictions
-    meta_pred_filename = 'gait_meta.json'
-    values_pred_filename = 'gait_values.bin'
-    time_pred_filename = 'gait_time.bin'
+    meta_pred_filename = "gait_meta.json"
+    values_pred_filename = "gait_values.bin"
+    time_pred_filename = "gait_time.bin"
 
-    metadata_pred_dict = tsdf.load_metadata_from_path(os.path.join(path_to_prediction_input, meta_pred_filename))
+    metadata_pred_dict = tsdf.load_metadata_from_path(
+        os.path.join(path_to_prediction_input, meta_pred_filename)
+    )
     metadata_pred_time = metadata_pred_dict[time_pred_filename]
     metadata_pred_values = metadata_pred_dict[values_pred_filename]
 
-    df_pred_gait = tsdf.load_dataframe_from_binaries([metadata_pred_time, metadata_pred_values], tsdf.constants.ConcatenationType.columns)
+    df_pred_gait = tsdf.load_dataframe_from_binaries(
+        [metadata_pred_time, metadata_pred_values],
+        tsdf.constants.ConcatenationType.columns,
+    )
 
     clf_package = ClassifierPackage.load(full_path_to_classifier_package)
 
-    gait_preprocessing_config = GaitConfig(step='gait')
+    gait_preprocessing_config = GaitConfig(step="gait")
 
     df = merge_predictions_with_timestamps(
-        df_ts=df_ts, 
-        df_predictions=df_pred_gait, 
+        df_ts=df_ts,
+        df_predictions=df_pred_gait,
         pred_proba_colname=DataColumns.PRED_GAIT_PROBA,
         window_length_s=gait_preprocessing_config.window_length_s,
-        fs=gait_preprocessing_config.sampling_frequency
+        fs=gait_preprocessing_config.sampling_frequency,
     )
 
     # Add a column for predicted gait based on a fitted threshold
-    df[DataColumns.PRED_GAIT] = (df[DataColumns.PRED_GAIT_PROBA] >= clf_package.threshold).astype(int)
+    df[DataColumns.PRED_GAIT] = (
+        df[DataColumns.PRED_GAIT_PROBA] >= clf_package.threshold
+    ).astype(int)
 
     # Filter the DataFrame to only include predicted gait (1)
-    df = df.loc[df[DataColumns.PRED_GAIT]==1].reset_index(drop=True)
+    df = df.loc[df[DataColumns.PRED_GAIT] == 1].reset_index(drop=True)
 
     # Extract arm activity features
-    config = GaitConfig(step='arm_activity')
+    config = GaitConfig(step="arm_activity")
     df_features = extract_arm_activity_features(
-        df=df, 
+        df=df,
         config=config,
     )
 
-    end_iso8601 = get_end_iso8601(metadata_ts_values.start_iso8601, df_features[DataColumns.TIME][-1:].values[0] + config.window_length_s)
+    end_iso8601 = get_end_iso8601(
+        metadata_ts_values.start_iso8601,
+        df_features[DataColumns.TIME][-1:].values[0] + config.window_length_s,
+    )
 
     metadata_ts_values.end_iso8601 = end_iso8601
-    metadata_ts_values.file_name = 'arm_activity_values.bin'
+    metadata_ts_values.file_name = "arm_activity_values.bin"
     metadata_ts_time.end_iso8601 = end_iso8601
-    metadata_ts_time.file_name = 'arm_activity_time.bin'
+    metadata_ts_time.file_name = "arm_activity_time.bin"
 
     metadata_ts_values.channels = list(config.d_channels_values.keys())
     metadata_ts_values.units = list(config.d_channels_values.values())
@@ -244,103 +348,154 @@ def extract_arm_activity_features_io(
     metadata_ts_time.channels = [DataColumns.TIME]
     metadata_ts_time.units = [TimeUnit.RELATIVE_S]
 
-    write_df_data(metadata_ts_time, metadata_ts_values, path_to_output, 'arm_activity_meta.json', df_features)
+    write_df_data(
+        metadata_ts_time,
+        metadata_ts_values,
+        path_to_output,
+        "arm_activity_meta.json",
+        df_features,
+    )
 
 
 def filter_gait_io(
-        config: GaitConfig, 
-        path_to_input: str | Path, 
-        path_to_output: str | Path, 
-        full_path_to_classifier_package: str | Path, 
-    ) -> None:
+    config: GaitConfig,
+    path_to_input: str | Path,
+    path_to_output: str | Path,
+    full_path_to_classifier_package: str | Path,
+) -> None:
     # Load the data
-    config.set_filenames('arm_activity')
+    config.set_filenames("arm_activity")
 
-    metadata_time, metadata_values = read_metadata(path_to_input, config.meta_filename, config.time_filename, config.values_filename)
-    df = tsdf.load_dataframe_from_binaries([metadata_time, metadata_values], tsdf.constants.ConcatenationType.columns)
+    metadata_time, metadata_values = read_metadata(
+        path_to_input,
+        config.meta_filename,
+        config.time_filename,
+        config.values_filename,
+    )
+    df = tsdf.load_dataframe_from_binaries(
+        [metadata_time, metadata_values], tsdf.constants.ConcatenationType.columns
+    )
 
     clf_package = ClassifierPackage.load(filepath=full_path_to_classifier_package)
 
     df[DataColumns.PRED_NO_OTHER_ARM_ACTIVITY_PROBA] = filter_gait(
-        df=df, 
-        clf_package=clf_package
+        df=df, clf_package=clf_package
     )
 
     # Prepare the metadata
-    metadata_values.file_name = 'arm_activity_values.bin'
-    metadata_time.file_name = 'arm_activity_time.bin'
+    metadata_values.file_name = "arm_activity_values.bin"
+    metadata_time.file_name = "arm_activity_time.bin"
 
     metadata_values.channels = [DataColumns.PRED_NO_OTHER_ARM_ACTIVITY_PROBA]
-    metadata_values.units = ['probability']
+    metadata_values.units = ["probability"]
 
     metadata_time.channels = [DataColumns.TIME]
     metadata_time.units = [TimeUnit.RELATIVE_S]
 
-    write_df_data(metadata_time, metadata_values, path_to_output, 'arm_activity_meta.json', df)
+    write_df_data(
+        metadata_time, metadata_values, path_to_output, "arm_activity_meta.json", df
+    )
 
 
-def extract_tremor_features_io(input_path: str | Path, output_path: str | Path, config: TremorConfig) -> None:
+def extract_tremor_features_io(
+    input_path: str | Path, output_path: str | Path, config: TremorConfig
+) -> None:
     # Load data
-    metadata_time, metadata_values = read_metadata(input_path, config.meta_filename, config.time_filename, config.values_filename)
-    df = tsdf.load_dataframe_from_binaries([metadata_time, metadata_values], tsdf.constants.ConcatenationType.columns)
+    metadata_time, metadata_values = read_metadata(
+        input_path, config.meta_filename, config.time_filename, config.values_filename
+    )
+    df = tsdf.load_dataframe_from_binaries(
+        [metadata_time, metadata_values], tsdf.constants.ConcatenationType.columns
+    )
 
     # Extract tremor features
     df_windowed = extract_tremor_features(df, config)
 
     # Store data
-    end_iso8601 = get_end_iso8601(start_iso8601=metadata_time.start_iso8601,
-                                  window_length_seconds=int(df_windowed[DataColumns.TIME][-1:].values[0] + config.window_length_s))
+    end_iso8601 = get_end_iso8601(
+        start_iso8601=metadata_time.start_iso8601,
+        window_length_seconds=int(
+            df_windowed[DataColumns.TIME][-1:].values[0] + config.window_length_s
+        ),
+    )
 
     metadata_values.end_iso8601 = end_iso8601
-    metadata_values.file_name = 'tremor_values.bin'
+    metadata_values.file_name = "tremor_values.bin"
     metadata_time.end_iso8601 = end_iso8601
-    metadata_time.file_name = 'tremor_time.bin'
+    metadata_time.file_name = "tremor_time.bin"
 
     metadata_values.channels = list(config.d_channels_values.keys())
     metadata_values.units = list(config.d_channels_values.values())
 
     metadata_time.channels = [DataColumns.TIME]
-    metadata_time.units = ['relative_time_ms']
+    metadata_time.units = ["relative_time_ms"]
+
+    write_df_data(
+        metadata_time, metadata_values, output_path, "tremor_meta.json", df_windowed
+    )
 
-    write_df_data(metadata_time, metadata_values, output_path, 'tremor_meta.json', df_windowed)
 
+def detect_tremor_io(
+    input_path: str | Path,
+    output_path: str | Path,
+    path_to_classifier_input: str | Path,
+    config: TremorConfig,
+) -> None:
 
-def detect_tremor_io(input_path: str | Path, output_path: str | Path, path_to_classifier_input: str | Path, config: TremorConfig) -> None:
-    
     # Load the data
-    config.set_filenames('tremor')
+    config.set_filenames("tremor")
 
-    metadata_time, metadata_values = read_metadata(input_path, config.meta_filename, config.time_filename, config.values_filename)
-    df = tsdf.load_dataframe_from_binaries([metadata_time, metadata_values], tsdf.constants.ConcatenationType.columns)
+    metadata_time, metadata_values = read_metadata(
+        input_path, config.meta_filename, config.time_filename, config.values_filename
+    )
+    df = tsdf.load_dataframe_from_binaries(
+        [metadata_time, metadata_values], tsdf.constants.ConcatenationType.columns
+    )
 
     df = detect_tremor(df, config, path_to_classifier_input)
 
     # Prepare the metadata
-    metadata_values.file_name = 'tremor_values.bin'
-    metadata_time.file_name = 'tremor_time.bin'
+    metadata_values.file_name = "tremor_values.bin"
+    metadata_time.file_name = "tremor_time.bin"
 
     metadata_values.channels = list(config.d_channels_values.keys())
     metadata_values.units = list(config.d_channels_values.values())
 
     metadata_time.channels = [DataColumns.TIME]
-    metadata_time.units = ['relative_time_ms']
+    metadata_time.units = ["relative_time_ms"]
+
+    write_df_data(metadata_time, metadata_values, output_path, "tremor_meta.json", df)
 
-    write_df_data(metadata_time, metadata_values, output_path, 'tremor_meta.json', df)
 
+def aggregate_tremor_io(
+    path_to_feature_input: str | Path,
+    path_to_prediction_input: str | Path,
+    output_path: str | Path,
+    config: TremorConfig,
+) -> None:
 
-def aggregate_tremor_io(path_to_feature_input: str | Path, path_to_prediction_input: str | Path, output_path: str | Path, config: TremorConfig) -> None:
-    
     # Load the features & predictions
-    metadata_time, metadata_values = read_metadata(path_to_feature_input, config.meta_filename, config.time_filename, config.values_filename)
-    df_features = tsdf.load_dataframe_from_binaries([metadata_time, metadata_values], tsdf.constants.ConcatenationType.columns)
+    metadata_time, metadata_values = read_metadata(
+        path_to_feature_input,
+        config.meta_filename,
+        config.time_filename,
+        config.values_filename,
+    )
+    df_features = tsdf.load_dataframe_from_binaries(
+        [metadata_time, metadata_values], tsdf.constants.ConcatenationType.columns
+    )
 
-    metadata_dict = tsdf.load_metadata_from_path(path_to_prediction_input / config.meta_filename)
+    metadata_dict = tsdf.load_metadata_from_path(
+        path_to_prediction_input / config.meta_filename
+    )
     metadata_time = metadata_dict[config.time_filename]
     metadata_values = metadata_dict[config.values_filename]
-    df_predictions = tsdf.load_dataframe_from_binaries([metadata_time, metadata_values], tsdf.constants.ConcatenationType.columns)
+    df_predictions = tsdf.load_dataframe_from_binaries(
+        [metadata_time, metadata_values], tsdf.constants.ConcatenationType.columns
+    )
 
     # Subset features
-    df_features = df_features[['tremor_power', 'below_tremor_power']]
+    df_features = df_features[["tremor_power", "below_tremor_power"]]
 
     # Concatenate predictions and tremor power
     df = pd.concat([df_predictions, df_features], axis=1)
@@ -349,82 +504,119 @@ def aggregate_tremor_io(path_to_feature_input: str | Path, path_to_prediction_in
     d_aggregates = aggregate_tremor(df, config)
 
     # Save output
-    with open(output_path / "tremor_aggregates.json", 'w') as json_file:
+    with open(output_path / "tremor_aggregates.json", "w") as json_file:
         json.dump(d_aggregates, json_file, indent=4)
 
 
-def extract_signal_quality_features_io(input_path: str | Path, output_path: str | Path, ppg_config: PulseRateConfig, acc_config: PulseRateConfig) -> pd.DataFrame:
+def extract_signal_quality_features_io(
+    input_path: str | Path,
+    output_path: str | Path,
+    ppg_config: PulseRateConfig,
+    acc_config: PulseRateConfig,
+) -> pd.DataFrame:
     """
     Extract signal quality features from the PPG signal and save them to a file.
 
     Parameters
     ----------
     input_path : str | Path
-        The path to the directory containing the preprocessed PPG and accelerometer data.
+        The path to the directory containing the preprocessed PPG and
+        accelerometer data.
     output_path : str | Path
         The path to the directory where the extracted features will be saved.
     ppg_config: PulseRateConfig
         The configuration for the signal quality feature extraction of the ppg signal.
     acc_config: PulseRateConfig
-        The configuration for the signal quality feature extraction of the accelerometer signal.
+        The configuration for the signal quality feature extraction of the
+        accelerometer signal.
 
     Returns
     -------
     df_windowed : pd.DataFrame
         The DataFrame containing the extracted signal quality features.
 
-    """	
+    """
     # Load PPG data
-    metadata_time, metadata_values = read_metadata(input_path, ppg_config.meta_filename, ppg_config.time_filename, ppg_config.values_filename)
-    df_ppg = tsdf.load_dataframe_from_binaries([metadata_time, metadata_values], tsdf.constants.ConcatenationType.columns)
-    
+    metadata_time, metadata_values = read_metadata(
+        input_path,
+        ppg_config.meta_filename,
+        ppg_config.time_filename,
+        ppg_config.values_filename,
+    )
+    df_ppg = tsdf.load_dataframe_from_binaries(
+        [metadata_time, metadata_values], tsdf.constants.ConcatenationType.columns
+    )
+
     # Load IMU data
-    metadata_time, metadata_values = read_metadata(input_path, acc_config.meta_filename, acc_config.time_filename, acc_config.values_filename)
-    df_acc = tsdf.load_dataframe_from_binaries([metadata_time, metadata_values], tsdf.constants.ConcatenationType.columns)
+    metadata_time, metadata_values = read_metadata(
+        input_path,
+        acc_config.meta_filename,
+        acc_config.time_filename,
+        acc_config.values_filename,
+    )
+    df_acc = tsdf.load_dataframe_from_binaries(
+        [metadata_time, metadata_values], tsdf.constants.ConcatenationType.columns
+    )
 
     # Extract signal quality features
-    df_windowed = extract_signal_quality_features(df_ppg, df_acc, ppg_config, acc_config)
-    
+    df_windowed = extract_signal_quality_features(
+        df_ppg, df_acc, ppg_config, acc_config
+    )
+
     # Save the extracted features
-    #TO BE ADDED
+    # TO BE ADDED
     return df_windowed
 
 
-def signal_quality_classification_io(input_path: str | Path, output_path: str | Path, path_to_classifier_input: str | Path, config: PulseRateConfig) -> None:
-    
-    # Load the data
-    metadata_time, metadata_values = read_metadata(input_path, config.meta_filename, config.time_filename, config.values_filename)
-    df_windowed = tsdf.load_dataframe_from_binaries([metadata_time, metadata_values], tsdf.constants.ConcatenationType.columns)
+# def signal_quality_classification_io(
+#     input_path: str | Path,
+#     output_path: str | Path,
+#     path_to_classifier_input: str | Path,
+#     config: PulseRateConfig,
+# ) -> None:
+
+#     # Load the data
+#     metadata_time, metadata_values = read_metadata(
+#         input_path, config.meta_filename, config.time_filename, config.values_filename
+#     )
+#     df_windowed = tsdf.load_dataframe_from_binaries(
+#         [metadata_time, metadata_values], tsdf.constants.ConcatenationType.columns
+#     )
 
-    df_sqa = signal_quality_classification(df_windowed, config, path_to_classifier_input)
+#     df_sqa = signal_quality_classification(
+#         df_windowed, config, path_to_classifier_input
+#     )
 
 
 def aggregate_pulse_rate_io(
-        full_path_to_input: str | Path, 
-        full_path_to_output: str | Path, 
-        aggregates: List[str] = ['mode', '99p']
-    ) -> None:
+    full_path_to_input: str | Path,
+    full_path_to_output: str | Path,
+    aggregates: list[str] = ["mode", "99p"],
+) -> None:
     """
-    Extract pulse rate from the PPG signal and save the aggregated pulse rate estimates to a file.
+    Extract pulse rate from the PPG signal and save the aggregated pulse rate
+    estimates to a file.
 
     Parameters
     ----------
     input_path : str | Path
         The path to the directory containing the pulse rate estimates.
     output_path : str | Path
-        The path to the directory where the aggregated pulse rate estimates will be saved.
+        The path to the directory where the aggregated pulse rate estimates
+        will be saved.
     aggregates : List[str]
-        The list of aggregation methods to be used for the pulse rate estimates. The default is ['mode', '99p'].
+        The list of aggregation methods to be used for the pulse rate
+        estimates. The default is ['mode', '99p'].
     """
 
     # Load the pulse rate estimates
-    with open(full_path_to_input, 'r') as f:
+    with open(full_path_to_input) as f:
         df_pr = json.load(f)
-    
+
     # Aggregate the pulse rate estimates
-    pr_values = df_pr['pulse_rate'].values
+    pr_values = df_pr["pulse_rate"].values
     df_pr_aggregates = aggregate_pulse_rate(pr_values, aggregates)
 
     # Save the aggregated pulse rate estimates
-    with open(full_path_to_output, 'w') as json_file:
-        json.dump(df_pr_aggregates, json_file, indent=4)
+    with open(full_path_to_output, "w") as json_file:
+        json.dump(df_pr_aggregates, json_file, indent=4)