paradigma 1.0.0__py3-none-any.whl → 1.0.2__py3-none-any.whl

paradigma/config.py

@@ -244,7 +244,7 @@ class TremorConfig(IMUConfig):
             }
 
         
-class HeartRateConfig(PPGConfig):
+class PulseRateConfig(PPGConfig):
     def __init__(self, sensor: str = 'ppg', min_window_length_s: int = 30) -> None:
         super().__init__()
 
@@ -265,14 +265,14 @@ class HeartRateConfig(PPGConfig):
         self.freq_bin_resolution = 0.05 # Hz
 
         # ---------------------
-        # Heart rate estimation
+        # Pulse rate estimation
         # ---------------------
         self.set_tfd_length(min_window_length_s)  # Set tfd length to default of 30 seconds
         self.threshold_sqa = 0.5
-        self.threshold_sqa_accelerometer = 0.13
+        self.threshold_sqa_accelerometer = 0.10
 
-        hr_est_length = 2
-        self.hr_est_samples = hr_est_length * self.sampling_frequency
+        pr_est_length = 2  # pulse rate estimation length in seconds
+        self.pr_est_samples = pr_est_length * self.sampling_frequency
 
         # Time-frequency distribution parameters
         self.kern_type = 'sep'
@@ -297,7 +297,7 @@ class HeartRateConfig(PPGConfig):
 
     def set_tfd_length(self, tfd_length: int):
         self.tfd_length = tfd_length
-        self.min_hr_samples = int(round(self.tfd_length * self.sampling_frequency))
+        self.min_pr_samples = int(round(self.tfd_length * self.sampling_frequency))
 
     def set_sensor(self, sensor):
         self.sensor = sensor 

paradigma/constants.py

@@ -58,8 +58,8 @@ class DataColumns():
     PRED_SQA_ACC_LABEL: str = "pred_sqa_acc_label"
     PRED_SQA: str = "pred_sqa"
 
-    # Constants for heart rate
-    HEART_RATE: str = "heart_rate"
+    # Constants for pulse rate
+    PULSE_RATE: str = "pulse_rate"
     
 @dataclass(frozen=True)
 class DataUnits():

paradigma/feature_extraction.py

@@ -7,7 +7,7 @@ from scipy.signal import find_peaks, windows
 from scipy.stats import kurtosis, skew
 from sklearn.decomposition import PCA
 
-from paradigma.config import HeartRateConfig
+from paradigma.config import PulseRateConfig
 
 
 def compute_statistics(data: np.ndarray, statistic: str, abs_stats: bool=False) -> np.ndarray:
@@ -353,7 +353,7 @@ def extract_frequency_peak(
 def compute_relative_power(
         freqs: np.ndarray, 
         psd: np.ndarray, 
-        config: HeartRateConfig
+        config: PulseRateConfig
     ) -> list:
     """
     Calculate relative power within the dominant frequency band in the physiological range (0.75 - 3 Hz).
@@ -364,11 +364,11 @@ def compute_relative_power(
         The frequency bins of the power spectral density.
     psd: np.ndarray
         The power spectral density of the signal.
-    config: HeartRateConfig
+    config: PulseRateConfig
         The configuration object containing the parameters for the feature extraction. The following
         attributes are used:
         - freq_band_physio: tuple
-            The frequency band for physiological heart rate (default: (0.75, 3)).
+            The frequency band for physiological pulse rate (default: (0.75, 3)).
         - bandwidth: float
             The bandwidth around the peak frequency to consider for relative power calculation (default: 0.5).
 

paradigma/pipelines/{heart_rate_pipeline.py → pulse_rate_pipeline.py}

@@ -10,14 +10,14 @@ from typing import List
 
 from paradigma.classification import ClassifierPackage
 from paradigma.constants import DataColumns
-from paradigma.config import HeartRateConfig
+from paradigma.config import PulseRateConfig
 from paradigma.feature_extraction import compute_statistics, compute_signal_to_noise_ratio, compute_auto_correlation, \
     compute_dominant_frequency, compute_relative_power, compute_spectral_entropy
-from paradigma.pipelines.heart_rate_utils import assign_sqa_label, extract_hr_segments, extract_hr_from_segment
+from paradigma.pipelines.pulse_rate_utils import assign_sqa_label, extract_pr_segments, extract_pr_from_segment
 from paradigma.segmenting import tabulate_windows, WindowedDataExtractor
-from paradigma.util import read_metadata, aggregate_parameter
+from paradigma.util import aggregate_parameter
 
-def extract_signal_quality_features(df_ppg: pd.DataFrame, df_acc: pd.DataFrame, ppg_config: HeartRateConfig, acc_config: HeartRateConfig) -> pd.DataFrame:
+def extract_signal_quality_features(df_ppg: pd.DataFrame, df_acc: pd.DataFrame, ppg_config: PulseRateConfig, acc_config: PulseRateConfig) -> pd.DataFrame:
     """	
     Extract signal quality features from the PPG signal.
     The features are extracted from the temporal and spectral domain of the PPG signal.
@@ -30,9 +30,9 @@ def extract_signal_quality_features(df_ppg: pd.DataFrame, df_acc: pd.DataFrame,
         The DataFrame containing the PPG signal.
     df_acc : pd.DataFrame
         The DataFrame containing the accelerometer signal.
-    ppg_config: HeartRateConfig
+    ppg_config: PulseRateConfig
         The configuration for the signal quality feature extraction of the PPG signal.
-    acc_config: HeartRateConfig
+    acc_config: PulseRateConfig
         The configuration for the signal quality feature extraction of the accelerometer signal.
 
     Returns
@@ -94,7 +94,7 @@ def extract_signal_quality_features(df_ppg: pd.DataFrame, df_acc: pd.DataFrame,
     return df_features
 
 
-def signal_quality_classification(df: pd.DataFrame, config: HeartRateConfig, full_path_to_classifier_package: str | Path) -> pd.DataFrame:
+def signal_quality_classification(df: pd.DataFrame, config: PulseRateConfig, full_path_to_classifier_package: str | Path) -> pd.DataFrame:
     """
     Classify the signal quality of the PPG signal using a logistic regression classifier. A probability close to 1 indicates a high-quality signal, while a probability close to 0 indicates a low-quality signal.
     The classifier is trained on features extracted from the PPG signal. The features are extracted using the extract_signal_quality_features function.
@@ -105,7 +105,7 @@ def signal_quality_classification(df: pd.DataFrame, config: HeartRateConfig, ful
     ----------
     df : pd.DataFrame
         The DataFrame containing the PPG features and the accelerometer feature for signal quality classification.
-    config : HeartRateConfig
+    config : PulseRateConfig
         The configuration for the signal quality classification.
     full_path_to_classifier_package : str | Path
         The path to the directory containing the classifier.
@@ -128,9 +128,9 @@ def signal_quality_classification(df: pd.DataFrame, config: HeartRateConfig, ful
     return df[[DataColumns.TIME, DataColumns.PRED_SQA_PROBA, DataColumns.PRED_SQA_ACC_LABEL]]  # Return only the relevant columns, namely the predicted probabilities for the PPG signal quality and the accelerometer label
 
 
-def estimate_heart_rate(df_sqa: pd.DataFrame, df_ppg_preprocessed: pd.DataFrame, config: HeartRateConfig) -> pd.DataFrame:  
+def estimate_pulse_rate(df_sqa: pd.DataFrame, df_ppg_preprocessed: pd.DataFrame, config: PulseRateConfig) -> pd.DataFrame:  
     """
-    Estimate the heart rate from the PPG signal using the time-frequency domain method.
+    Estimate the pulse rate from the PPG signal using the time-frequency domain method.
 
     Parameters
     ----------
@@ -138,13 +138,13 @@ def estimate_heart_rate(df_sqa: pd.DataFrame, df_ppg_preprocessed: pd.DataFrame,
         The DataFrame containing the signal quality assessment predictions.
     df_ppg_preprocessed : pd.DataFrame
         The DataFrame containing the preprocessed PPG signal.
-    config : HeartRateConfig
-        The configuration for the heart rate estimation.
+    config : PulseRateConfig
+        The configuration for the pulse rate estimation.
 
     Returns
     -------
-    df_hr : pd.DataFrame
-        The DataFrame containing the heart rate estimations.
+    df_pr : pd.DataFrame
+        The DataFrame containing the pulse rate estimations.
     """
 
     # Extract NumPy arrays for faster operations
@@ -156,13 +156,13 @@ def estimate_heart_rate(df_sqa: pd.DataFrame, df_ppg_preprocessed: pd.DataFrame,
     
     # Assign window-level probabilities to individual samples
     sqa_label = assign_sqa_label(ppg_post_prob, config, acc_label) # assigns a signal quality label to every individual data point
-    v_start_idx, v_end_idx = extract_hr_segments(sqa_label, config.min_hr_samples) # extracts heart rate segments based on the SQA label
+    v_start_idx, v_end_idx = extract_pr_segments(sqa_label, config.min_pr_samples) # extracts pulse rate segments based on the SQA label
     
-    v_hr_rel = np.array([])
-    t_hr_rel = np.array([])
+    v_pr_rel = np.array([])
+    t_pr_rel = np.array([])
 
-    edge_add = 2 * config.sampling_frequency  # Add 2s on both sides of the segment for HR estimation
-    step_size = config.hr_est_samples  # Step size for HR estimation
+    edge_add = 2 * config.sampling_frequency  # Add 2s on both sides of the segment for PR estimation
+    step_size = config.pr_est_samples  # Step size for PR estimation
 
     # Estimate the maximum size for preallocation
     valid_segments = (v_start_idx >= edge_add) & (v_end_idx <= len(ppg_preprocessed) - edge_add) # check if the segments are valid, e.g. not too close to the edges (2s)
@@ -171,55 +171,55 @@ def estimate_heart_rate(df_sqa: pd.DataFrame, df_ppg_preprocessed: pd.DataFrame,
     max_size = np.sum((valid_end_idx - valid_start_idx) // step_size) # maximum size for preallocation
   
     # Preallocate arrays
-    v_hr_rel = np.empty(max_size, dtype=float) 
-    t_hr_rel = np.empty(max_size, dtype=float)  
+    v_pr_rel = np.empty(max_size, dtype=float) 
+    t_pr_rel = np.empty(max_size, dtype=float)  
 
     # Track current position
-    hr_pos = 0
+    pr_pos = 0
 
     for start_idx, end_idx in zip(valid_start_idx, valid_end_idx):
         # Extract extended PPG segment
         extended_ppg_segment = ppg_preprocessed[start_idx - edge_add : end_idx + edge_add, ppg_idx]
 
-        # Estimate heart rate
-        hr_est = extract_hr_from_segment(
+        # Estimate pulse rate
+        pr_est = extract_pr_from_segment(
             extended_ppg_segment,
             config.tfd_length,
             config.sampling_frequency,
             config.kern_type,
             config.kern_params,
         )
-        n_hr = len(hr_est)  # Number of heart rate estimates
-        end_idx_time = n_hr * step_size + start_idx  # Calculate end index for time, different from end_idx since it is always a multiple of step_size, while end_idx is not
+        n_pr = len(pr_est)  # Number of pulse rate estimates
+        end_idx_time = n_pr * step_size + start_idx  # Calculate end index for time, different from end_idx since it is always a multiple of step_size, while end_idx is not
 
-        # Extract relative time for HR estimates
-        hr_time = ppg_preprocessed[start_idx : end_idx_time : step_size, time_idx]
+        # Extract relative time for PR estimates
+        pr_time = ppg_preprocessed[start_idx : end_idx_time : step_size, time_idx]
 
         # Insert into preallocated arrays
-        v_hr_rel[hr_pos:hr_pos + n_hr] = hr_est
-        t_hr_rel[hr_pos:hr_pos + n_hr] = hr_time
-        hr_pos += n_hr
+        v_pr_rel[pr_pos:pr_pos + n_pr] = pr_est
+        t_pr_rel[pr_pos:pr_pos + n_pr] = pr_time
+        pr_pos += n_pr
 
-    df_hr = pd.DataFrame({"time": t_hr_rel, "heart_rate": v_hr_rel})
+    df_pr = pd.DataFrame({"time": t_pr_rel, "pulse_rate": v_pr_rel})
 
-    return df_hr
+    return df_pr
 
 
-def aggregate_heart_rate(hr_values: np.ndarray, aggregates: List[str] = ['mode', '99p']) -> dict:
+def aggregate_pulse_rate(pr_values: np.ndarray, aggregates: List[str] = ['mode', '99p']) -> dict:
     """
-    Aggregate the heart rate estimates using the specified aggregation methods.
+    Aggregate the pulse rate estimates using the specified aggregation methods.
 
     Parameters
     ----------
-    hr_values : np.ndarray
-        The array containing the heart rate estimates
+    pr_values : np.ndarray
+        The array containing the pulse rate estimates
     aggregates : List[str]
-        The list of aggregation methods to be used for the heart 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'].
 
     Returns
     -------
     aggregated_results : dict
-        The dictionary containing the aggregated results of the heart rate estimates.
+        The dictionary containing the aggregated results of the pulse rate estimates.
     """
     # Initialize the dictionary for the aggregated results
     aggregated_results = {}
@@ -227,19 +227,19 @@ def aggregate_heart_rate(hr_values: np.ndarray, aggregates: List[str] = ['mode',
     # Initialize the dictionary for the aggregated results with the metadata
     aggregated_results = {
     'metadata': {
-        'nr_hr_est': len(hr_values)
+        'nr_pr_est': len(pr_values)
     },
-    'hr_aggregates': {}
+    'pr_aggregates': {}
 }
     for aggregate in aggregates:
-        aggregated_results['hr_aggregates'][f'{aggregate}_{DataColumns.HEART_RATE}'] = aggregate_parameter(hr_values, aggregate)
+        aggregated_results['pr_aggregates'][f'{aggregate}_{DataColumns.PULSE_RATE}'] = aggregate_parameter(pr_values, aggregate)
 
     return aggregated_results
 
 
 def extract_temporal_domain_features(
         ppg_windowed: np.ndarray, 
-        config: HeartRateConfig, 
+        config: PulseRateConfig, 
         quality_stats: List[str] = ['mean', 'std']
     ) -> pd.DataFrame:
     """
@@ -250,7 +250,7 @@ def extract_temporal_domain_features(
     ppg_windowed: np.ndarray
         The dataframe containing the windowed accelerometer signal
 
-    config: HeartRateConfig
+    config: PulseRateConfig
         The configuration object containing the parameters for the feature extraction
 
     quality_stats: list, optional
@@ -273,7 +273,7 @@ def extract_temporal_domain_features(
 
 def extract_spectral_domain_features(
         ppg_windowed: np.ndarray,
-        config: HeartRateConfig, 
+        config: PulseRateConfig, 
     ) -> pd.DataFrame:
     """
     Calculate the spectral features (dominant frequency, relative power, and spectral entropy)
@@ -285,7 +285,7 @@ def extract_spectral_domain_features(
     ppg_windowed: np.ndarray
         The dataframe containing the windowed ppg signal
 
-    config: HeartRateConfig
+    config: PulseRateConfig
         The configuration object containing the parameters for the feature extraction
 
     Returns
@@ -371,7 +371,7 @@ def extract_acc_power_feature(
 def extract_accelerometer_feature(
         acc_windowed: np.ndarray, 
         ppg_windowed: np.ndarray,
-        config: HeartRateConfig
+        config: PulseRateConfig
     ) -> pd.DataFrame:
     """
     Extract accelerometer features from the accelerometer signal in the PPG frequency range.
@@ -384,7 +384,7 @@ def extract_accelerometer_feature(
     ppg_windowed: np.ndarray
         The dataframe containing the corresponding windowed ppg signal
     
-    config: HeartRateConfig
+    config: PulseRateConfig
         The configuration object containing the parameters for the feature extraction
 
     Returns

paradigma/pipelines/{heart_rate_utils.py → pulse_rate_utils.py}

@@ -2,12 +2,12 @@ import numpy as np
 from scipy import signal
 from typing import Tuple
 
-from paradigma.config import HeartRateConfig
+from paradigma.config import PulseRateConfig
 
 
 def assign_sqa_label(
         ppg_prob: np.ndarray, 
-        config: HeartRateConfig, 
+        config: PulseRateConfig, 
         acc_label=None
     ) -> np.ndarray:
     """
@@ -17,7 +17,7 @@ def assign_sqa_label(
     ----------
     ppg_prob : np.ndarray
         The probabilities for PPG.
-    config : HeartRateConfig
+    config : PulseRateConfig
         The configuration parameters.
     acc_label : np.ndarray, optional
         The labels for the accelerometer.
@@ -61,23 +61,23 @@ def assign_sqa_label(
     return sqa_label
 
 
-def extract_hr_segments(sqa_label: np.ndarray, min_hr_samples: int) -> Tuple[np.ndarray, np.ndarray]:
+def extract_pr_segments(sqa_label: np.ndarray, min_pr_samples: int) -> Tuple[np.ndarray, np.ndarray]:
     """
-    Extracts heart rate segments based on the SQA label.
+    Extracts pulse rate segments based on the SQA label.
 
     Parameters
     ----------
     sqa_label : np.ndarray
         The signal quality assessment label.
-    min_hr_samples : int
-        The minimum number of samples required for a heart rate segment.
+    min_pr_samples : int
+        The minimum number of samples required for a pulse rate segment.
 
     Returns
     -------
     Tuple[v_start_idx_long, v_end_idx_long]
-        The start and end indices of the heart rate segments.
+        The start and end indices of the pulse rate segments.
     """
-    # Find the start and end indices of the heart rate segments
+    # Find the start and end indices of the pulse rate segments
     v_start_idx = np.where(np.diff(sqa_label.astype(int)) == 1)[0] + 1
     v_end_idx = np.where(np.diff(sqa_label.astype(int)) == -1)[0] + 1
 
@@ -88,13 +88,13 @@ def extract_hr_segments(sqa_label: np.ndarray, min_hr_samples: int) -> Tuple[np.
         v_end_idx = np.append(v_end_idx, len(sqa_label))
 
     # Check if the segments are long enough
-    v_start_idx_long = v_start_idx[(v_end_idx - v_start_idx) >= min_hr_samples]
-    v_end_idx_long = v_end_idx[(v_end_idx - v_start_idx) >= min_hr_samples]
+    v_start_idx_long = v_start_idx[(v_end_idx - v_start_idx) >= min_pr_samples]
+    v_end_idx_long = v_end_idx[(v_end_idx - v_start_idx) >= min_pr_samples]
 
     return v_start_idx_long, v_end_idx_long
 
 
-def extract_hr_from_segment(
+def extract_pr_from_segment(
         ppg: np.ndarray, 
         tfd_length: int, 
         fs: int, 
@@ -102,7 +102,7 @@ def extract_hr_from_segment(
         kern_params: dict
     ) -> np.ndarray:
     """
-    Extracts heart rate from the time-frequency distribution of the PPG signal.
+    Extracts pulse rate from the time-frequency distribution of the PPG signal.
 
     Parameters
     ----------
@@ -121,7 +121,7 @@ def extract_hr_from_segment(
     Returns
     -------
     np.ndarray
-        The estimated heart rate.
+        The estimated pulse rate.
     """
 
     # Constants to handle boundary effects
@@ -145,23 +145,23 @@ def extract_hr_from_segment(
             end_idx = len(ppg)
         ppg_segments.append(ppg[start_idx:end_idx])
 
-    hr_est_from_ppg = np.array([])
+    pr_est_from_ppg = np.array([])
     for segment in ppg_segments:
         # Calculate the time-frequency distribution
-        hr_tfd = extract_hr_with_tfd(segment, fs, kern_type, kern_params)
-        hr_est_from_ppg = np.concatenate((hr_est_from_ppg, hr_tfd)) 
+        pr_tfd = extract_pr_with_tfd(segment, fs, kern_type, kern_params)
+        pr_est_from_ppg = np.concatenate((pr_est_from_ppg, pr_tfd)) 
 
-    return hr_est_from_ppg
+    return pr_est_from_ppg
 
 
-def extract_hr_with_tfd(
+def extract_pr_with_tfd(
         ppg: np.ndarray, 
         fs: int, 
         kern_type: str, 
         kern_params: dict
     ) -> np.ndarray:
     """
-    Estimate heart rate (HR) from a PPG segment using a TFD method with optional 
+    Estimate pulse rate (PR) from a PPG segment using a TFD method with optional 
     moving average filtering.
 
     Parameters
@@ -177,8 +177,8 @@ def extract_hr_with_tfd(
 
     Returns
     -------
-    hr_smooth_tfd : np.ndarray
-        Estimated HR values (in beats per minute) for each 2-second segment of the PPG signal.
+    pr_smooth_tfd : np.ndarray
+        Estimated pr values (in beats per minute) for each 2-second segment of the PPG signal.
     """
     # Generate the TFD matrix using the specified kernel
     tfd_obj = TimeFreqDistr()
@@ -189,16 +189,16 @@ def extract_hr_with_tfd(
     time_axis = np.arange(num_time_samples) / fs
     freq_axis = np.linspace(0, 0.5, num_freq_bins) * fs
 
-    # Estimate HR by identifying the max frequency in the TFD
+    # Estimate pulse rate by identifying the max frequency in the TFD
     max_freq_indices = np.argmax(tfd, axis=0)
 
-    hr_smooth_tfd = np.array([])
+    pr_smooth_tfd = np.array([])
     for i in range(2, int(len(ppg) / fs) - 4 + 1, 2):  # Skip the first and last 2 seconds, add 1 to include the last segment
         relevant_indices = (time_axis >= i) & (time_axis < i + 2)
         avg_frequency = np.mean(freq_axis[max_freq_indices[relevant_indices]])
-        hr_smooth_tfd = np.concatenate((hr_smooth_tfd, [60 * avg_frequency]))  # Convert frequency to BPM
+        pr_smooth_tfd = np.concatenate((pr_smooth_tfd, [60 * avg_frequency]))  # Convert frequency to BPM
 
-    return hr_smooth_tfd
+    return pr_smooth_tfd
 
 
 class TimeFreqDistr:

paradigma/pipelines/tremor_pipeline.py

@@ -143,7 +143,6 @@ def detect_tremor(df: pd.DataFrame, config: TremorConfig, full_path_to_classifie
     
     return df
 
-
 def aggregate_tremor(df: pd.DataFrame, config: TremorConfig):
     """
     Quantifies the amount of tremor time and tremor power, aggregated over all windows in the input dataframe.
@@ -154,8 +153,8 @@ def aggregate_tremor(df: pd.DataFrame, config: TremorConfig):
     Parameters
     ----------
     df : pd.DataFrame
-        The input DataFrame containing extracted tremor features. The DataFrame must include
-        the necessary columns as specified in the classifier's feature names.
+        The input DataFrame containing the tremor predictions and computed tremor power.
+        The DataFrame must also contain a datatime column ('time_dt').
 
     config : TremorConfig
         Configuration object containing the percentile for aggregating tremor power.
@@ -251,6 +250,7 @@ def extract_spectral_domain_features(data: np.ndarray, config) -> pd.DataFrame:
     pd.DataFrame
         The feature dataframe containing the extracted spectral features, including 
         MFCCs, the frequency of the peak, the tremor power and below tremor power for each window.
+        
     """
 
     # Initialize a dictionary to hold the results

paradigma/testing.py

@@ -7,14 +7,14 @@ import tsdf
 from typing import List
 
 from paradigma.classification import ClassifierPackage
-from paradigma.config import IMUConfig, PPGConfig, GaitConfig, TremorConfig, HeartRateConfig
+from paradigma.config import IMUConfig, PPGConfig, GaitConfig, TremorConfig, PulseRateConfig
 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.heart_rate_pipeline import extract_signal_quality_features, signal_quality_classification, \
-    aggregate_heart_rate
+from paradigma.pipelines.pulse_rate_pipeline import extract_signal_quality_features, signal_quality_classification, \
+    aggregate_pulse_rate
 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
 
@@ -353,7 +353,7 @@ def aggregate_tremor_io(path_to_feature_input: str | Path, path_to_prediction_in
         json.dump(d_aggregates, json_file, indent=4)
 
 
-def extract_signal_quality_features_io(input_path: str | Path, output_path: str | Path, ppg_config: HeartRateConfig, acc_config: HeartRateConfig) -> 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.
 
@@ -363,9 +363,9 @@ def extract_signal_quality_features_io(input_path: str | Path, output_path: str
         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: HeartRateConfig
+    ppg_config: PulseRateConfig
         The configuration for the signal quality feature extraction of the ppg signal.
-    acc_config: HeartRateConfig
+    acc_config: PulseRateConfig
         The configuration for the signal quality feature extraction of the accelerometer signal.
 
     Returns
@@ -390,7 +390,7 @@ def extract_signal_quality_features_io(input_path: str | Path, output_path: str
     return df_windowed
 
 
-def signal_quality_classification_io(input_path: str | Path, output_path: str | Path, path_to_classifier_input: str | Path, config: HeartRateConfig) -> None:
+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)
@@ -399,32 +399,32 @@ def signal_quality_classification_io(input_path: str | Path, output_path: str |
     df_sqa = signal_quality_classification(df_windowed, config, path_to_classifier_input)
 
 
-def aggregate_heart_rate_io(
+def aggregate_pulse_rate_io(
         full_path_to_input: str | Path, 
         full_path_to_output: str | Path, 
         aggregates: List[str] = ['mode', '99p']
     ) -> None:
     """
-    Extract heart rate from the PPG signal and save the aggregated heart 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 heart rate estimates.
+        The path to the directory containing the pulse rate estimates.
     output_path : str | Path
-        The path to the directory where the aggregated heart 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 heart 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 heart rate estimates
+    # Load the pulse rate estimates
     with open(full_path_to_input, 'r') as f:
-        df_hr = json.load(f)
+        df_pr = json.load(f)
     
-    # Aggregate the heart rate estimates
-    hr_values = df_hr['heart_rate'].values
-    df_hr_aggregates = aggregate_heart_rate(hr_values, aggregates)
+    # Aggregate the pulse rate estimates
+    pr_values = df_pr['pulse_rate'].values
+    df_pr_aggregates = aggregate_pulse_rate(pr_values, aggregates)
 
-    # Save the aggregated heart rate estimates
+    # Save the aggregated pulse rate estimates
     with open(full_path_to_output, 'w') as json_file:
-        json.dump(df_hr_aggregates, json_file, indent=4)
+        json.dump(df_pr_aggregates, json_file, indent=4)

{paradigma-1.0.0.dist-info → paradigma-1.0.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: paradigma
-Version: 1.0.0
+Version: 1.0.2
 Summary: ParaDigMa - A toolbox for deriving Parkinson's disease Digital Markers from real-life wrist sensor data
 License: Apache-2.0
 Author: Erik Post
@@ -26,7 +26,7 @@ Description-Content-Type: text/markdown
 |:----:|----|
 | **Packages and Releases** | [![Latest release](https://img.shields.io/github/release/biomarkersparkinson/paradigma.svg)](https://github.com/biomarkersparkinson/paradigma/releases/latest) [![PyPI](https://img.shields.io/pypi/v/paradigma.svg)](https://pypi.python.org/pypi/paradigma/)  [![Static Badge](https://img.shields.io/badge/RSD-paradigma-lib)](https://research-software-directory.org/software/paradigma) |
 | **DOI** | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13838392.svg)](https://doi.org/10.5281/zenodo.13838392) |
-| **Build Status** | [![](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/) [![Build and test](https://github.com/biomarkersParkinson/paradigma/actions/workflows/build-and-test.yml/badge.svg)](https://github.com/biomarkersParkinson/paradigma/actions/workflows/build-and-test.yml) [![pages-build-deployment](https://github.com/biomarkersParkinson/paradigma/actions/workflows/pages/pages-build-deployment/badge.svg)](https://github.com/biomarkersParkinson/paradigma/actions/workflows/pages/pages-build-deployment) |
+| **Build Status** | [![](https://img.shields.io/badge/python-3.11+-blue.svg)](https://www.python.org/downloads/) [![Build and test](https://github.com/biomarkersParkinson/paradigma/actions/workflows/build-and-test.yml/badge.svg)](https://github.com/biomarkersParkinson/paradigma/actions/workflows/build-and-test.yml) [![pages-build-deployment](https://github.com/biomarkersParkinson/paradigma/actions/workflows/pages/pages-build-deployment/badge.svg)](https://github.com/biomarkersParkinson/paradigma/actions/workflows/pages/pages-build-deployment) |
 | **License** |  [![GitHub license](https://img.shields.io/github/license/biomarkersParkinson/paradigma)](https://github.com/biomarkersparkinson/paradigma/blob/main/LICENSE) |
 <!-- | **Fairness** |  [![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu) [![OpenSSF Best Practices](https://bestpractices.coreinfrastructure.org/projects/8083/badge)](https://www.bestpractices.dev/projects/8083) | --> 
 

{paradigma-1.0.0.dist-info → paradigma-1.0.2.dist-info}/RECORD

@@ -4,19 +4,19 @@ paradigma/assets/gait_filtering_clf_package.pkl,sha256=lAaLyhmXdV4X_drmYt0EM6wGw
 paradigma/assets/ppg_quality_clf_package.pkl,sha256=vUcM4v8gZwWAmDVK7E4UcHhVnhlEg27RSB71oPGloSc,1292
 paradigma/assets/tremor_detection_clf_package.pkl,sha256=S-KsK1EcUBJX6oGGBo8GqU0AhNZThA6Qe-cs0QPcWw4,1475
 paradigma/classification.py,sha256=sBJSePvwHZNPUQuLdx-pncfnDzMq-1naomsCxSJneWY,2921
-paradigma/config.py,sha256=72KkIEVV1v5dD9ZJDPI-mFNvorA8nBADEcA0A-jviHU,11163
-paradigma/constants.py,sha256=JlrD4Zx66g7myQALYAc4Gw_y6yW5EipZuvwj9_fjjpI,3543
-paradigma/feature_extraction.py,sha256=PAl9DgjTljxtifjPLpM1L_7xRs2fI6eUcybkaJ9kxAA,35323
+paradigma/config.py,sha256=hGmWpK1sjwjlmCn43bBa6DEWBTDZjRXlGANIp6X42mY,11206
+paradigma/constants.py,sha256=gR--OzxaZqS5nJnYlWLqnJ9xN05_GMNtd6ec3upsfms,3543
+paradigma/feature_extraction.py,sha256=zgu_fW1zpPvHxpgsPVpJILUiyWH44b9n1bGG7lV2HwE,35323
 paradigma/pipelines/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 paradigma/pipelines/gait_pipeline.py,sha256=ZhAc2RZbBX52SJ8hvSRjb5THM47WCfY50iEdImlszJM,26231
-paradigma/pipelines/heart_rate_pipeline.py,sha256=0-D9KcW9nwE5sgXsWHONkeKrsX6qZ5BYqjDttoffwL8,17726
-paradigma/pipelines/heart_rate_utils.py,sha256=aV2mTMWrFWHZD0KpHqy3IIC1onZykbppyp7_OUWxFTU,26764
-paradigma/pipelines/tremor_pipeline.py,sha256=ihe6QeTk4MT_tXBE8PUN5rWNh2r5n5HCC1k4xyJjtUw,14761
+paradigma/pipelines/pulse_rate_pipeline.py,sha256=aBDopwWvfabLCQM6De9PHNKKzL03xD_29jWcsElnjCw,17711
+paradigma/pipelines/pulse_rate_utils.py,sha256=rlXze04meLFlyPaxMBYhvz3_vu3SM77RF-7mLPegTm0,26772
+paradigma/pipelines/tremor_pipeline.py,sha256=qsKEV3QFPQ4bsTGdEX0nXHVMjVlBUpcEHbWEDcGsmVw,14758
 paradigma/preprocessing.py,sha256=OcrwiyNjZpw41IKCf9QRY75A-532kU4gSSSXjqWuTeE,14556
 paradigma/segmenting.py,sha256=hgT4dtg23eyvjUraEXCzX8u0kSRx4vArjQgF10r61P8,13909
-paradigma/testing.py,sha256=Ni68clfyHz_mQWBD8cDmls_uadd0rpKPq3-IKzolDZc,18547
+paradigma/testing.py,sha256=zWPBj7Q1Td6rgeMGoAWi6rIVLB8M6_FNUxlZSbpWqEM,18547
 paradigma/util.py,sha256=E1keTX7vMDowSUG1AGx3juUMIXD7znaGwuqWDfQTpXo,16424
-paradigma-1.0.0.dist-info/LICENSE,sha256=Lda8kIVC2kbmlSeYaUWwUwV75Q-q31idYvo18HUTfiw,9807
-paradigma-1.0.0.dist-info/METADATA,sha256=rnOYOPZkoDVOMF0z9dDLfEulaCspPPjmGWjDtBgUDPI,11654
-paradigma-1.0.0.dist-info/WHEEL,sha256=fGIA9gx4Qxk2KDKeNJCbOEwSrmLtjWCwzBz351GyrPQ,88
-paradigma-1.0.0.dist-info/RECORD,,
+paradigma-1.0.2.dist-info/LICENSE,sha256=Lda8kIVC2kbmlSeYaUWwUwV75Q-q31idYvo18HUTfiw,9807
+paradigma-1.0.2.dist-info/METADATA,sha256=XkUFT1LRgM2taKEqno1cZQl3c-KuCxJJd4kIUOckfE8,11654
+paradigma-1.0.2.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+paradigma-1.0.2.dist-info/RECORD,,

{paradigma-1.0.0.dist-info → paradigma-1.0.2.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.1.2
+Generator: poetry-core 2.1.3
 Root-Is-Purelib: true
 Tag: py3-none-any