gaitsetpy.dataset.physionet API documentation

# gaitsetpy.dataset.physionet

PhysioNet VGRF Dataset Loader. Maintainer: @aharshit123456

This file contains the PhysioNet VGRF dataset loader class that inherits from BaseDatasetLoader. The PhysioNet dataset contains vertical ground reaction force (VGRF) data from subjects with Parkinson's disease and healthy controls.

Dataset source: https://physionet.org/content/gaitpdb/1.0.0/

View Source

      1'''
      2PhysioNet VGRF Dataset Loader.
      3Maintainer: @aharshit123456
      4
      5This file contains the PhysioNet VGRF dataset loader class that inherits from BaseDatasetLoader.
      6The PhysioNet dataset contains vertical ground reaction force (VGRF) data from subjects with
      7Parkinson's disease and healthy controls.
      8
      9Dataset source: https://physionet.org/content/gaitpdb/1.0.0/
     10'''
     11
     12import os
     13import pandas as pd
     14import numpy as np
     15from typing import List, Dict, Tuple, Optional
     16from glob import glob
     17import requests
     18from tqdm import tqdm
     19import zipfile
     20from ..core.base_classes import BaseDatasetLoader
     21from .utils import sliding_window
     22
     23
     24class PhysioNetLoader(BaseDatasetLoader):
     25    """
     26    PhysioNet VGRF dataset loader class.
     27
     28    This class handles loading and processing of the PhysioNet Gait in Parkinson's Disease dataset.
     29    The dataset contains vertical ground reaction force (VGRF) data from subjects with Parkinson's
     30    disease and healthy controls.
     31    """
     32
     33    def __init__(self):
     34        super().__init__(
     35            name="physionet",
     36            description="PhysioNet Gait in Parkinson's Disease Dataset - Contains VGRF data from subjects with Parkinson's disease and healthy controls"
     37        )
     38        self.metadata = {
     39            'sensors': ['VGRF_L1', 'VGRF_L2', 'VGRF_L3', 'VGRF_L4', 'VGRF_L5', 'VGRF_L6', 'VGRF_L7', 'VGRF_L8',
     40                       'VGRF_R1', 'VGRF_R2', 'VGRF_R3', 'VGRF_R4', 'VGRF_R5', 'VGRF_R6', 'VGRF_R7', 'VGRF_R8'],
     41            'sampling_frequency': 100,  # 100 Hz sampling frequency
     42            'subjects': {
     43                'Co': 'Control subjects',
     44                'Pt': 'Parkinson\'s disease patients'
     45            },
     46            'window_size': 600,  # 6 seconds at 100 Hz
     47            'url': 'https://physionet.org/files/gaitpdb/1.0.0/'
     48        }
     49        self.labels = []
     50        self.subject_types = []
     51
     52    def _download_physionet_data(self, data_dir: str) -> str:
     53        """
     54        Download PhysioNet dataset if not already present.
     55
     56        Args:
     57            data_dir: Directory to store the dataset
     58
     59        Returns:
     60            Path to the downloaded/existing dataset directory
     61        """
     62        dataset_path = os.path.join(data_dir, "physionet_gaitpdb")
     63
     64        if os.path.exists(dataset_path) and len(os.listdir(dataset_path)) > 0:
     65            print(f"PhysioNet dataset already exists at: {dataset_path}")
     66            return dataset_path
     67
     68        os.makedirs(dataset_path, exist_ok=True)
     69
     70        # Download the dataset files
     71        base_url = "https://physionet.org/files/gaitpdb/1.0.0/"
     72
     73        # Get list of files (basic file names based on the reference)
     74        file_patterns = [
     75            # Control subjects - Ga prefix
     76            *[f"GaCo{i:02d}_{j:02d}.txt" for i in range(1, 18) for j in range(1, 3)],
     77            "GaCo22_01.txt", "GaCo22_10.txt",
     78
     79            # Parkinson's patients - Ga prefix
     80            *[f"GaPt{i:02d}_{j:02d}.txt" for i in range(3, 10) for j in range(1, 3)],
     81            *[f"GaPt{i:02d}_{j:02d}.txt" for i in range(12, 34) for j in range(1, 3)],
     82            *[f"GaPt{i:02d}_10.txt" for i in range(13, 34)],
     83
     84            # Control subjects - Ju prefix
     85            *[f"JuCo{i:02d}_01.txt" for i in range(1, 27)],
     86
     87            # Parkinson's patients - Ju prefix
     88            *[f"JuPt{i:02d}_{j:02d}.txt" for i in range(1, 30) for j in range(1, 8)],
     89
     90            # Control subjects - Si prefix
     91            *[f"SiCo{i:02d}_01.txt" for i in range(1, 31)],
     92
     93            # Parkinson's patients - Si prefix
     94            *[f"SiPt{i:02d}_01.txt" for i in range(2, 41)]
     95        ]
     96
     97        print(f"Downloading PhysioNet dataset to {dataset_path}")
     98        for filename in tqdm(file_patterns, desc="Downloading files"):
     99            file_url = base_url + filename
    100            file_path = os.path.join(dataset_path, filename)
    101
    102            if os.path.exists(file_path):
    103                continue
    104
    105            try:
    106                response = requests.get(file_url, stream=True)
    107                if response.status_code == 200:
    108                    with open(file_path, 'wb') as f:
    109                        for chunk in response.iter_content(chunk_size=8192):
    110                            f.write(chunk)
    111                else:
    112                    print(f"Could not download {filename} (status: {response.status_code})")
    113            except Exception as e:
    114                print(f"Error downloading {filename}: {e}")
    115
    116        return dataset_path
    117
    118    def load_data(self, data_dir: str, **kwargs) -> Tuple[List[pd.DataFrame], List[str]]:
    119        """
    120        Load PhysioNet VGRF dataset from the specified directory.
    121
    122        Args:
    123            data_dir: Directory to store/find the dataset
    124            **kwargs: Additional arguments (unused for PhysioNet)
    125
    126        Returns:
    127            Tuple of (data_list, names_list)
    128        """
    129        # Download dataset if needed
    130        dataset_path = self._download_physionet_data(data_dir)
    131
    132        physionet_data = []
    133        physionet_names = []
    134        self.labels = []
    135        self.subject_types = []
    136
    137        # Load all available files
    138        for filepath in sorted(glob(os.path.join(dataset_path, "Ga*.txt"))):
    139            filename = os.path.basename(filepath)
    140
    141            # Extract subject type from filename
    142            if 'Co' in filename:
    143                subject_type = 'Control'
    144                label = 'Co'
    145            elif 'Pt' in filename:
    146                subject_type = 'Patient'
    147                label = 'Pt'
    148            else:
    149                continue  # Skip files that don't match expected pattern
    150
    151            try:
    152                # Read the file - PhysioNet files are tab-delimited with variable columns
    153                # Column 0: time, Columns 1-16: VGRF sensors, additional columns may exist
    154                df = pd.read_csv(filepath, delimiter='\t', header=None)
    155
    156                # Handle variable number of columns
    157                n_cols = min(df.shape[1], 19)  # Limit to 19 columns max
    158                df = df.iloc[:, :n_cols]
    159
    160                # Create column names
    161                col_names = ['time']
    162                for i in range(1, n_cols):
    163                    if i <= 8:
    164                        col_names.append(f'VGRF_L{i}')
    165                    elif i <= 16:
    166                        col_names.append(f'VGRF_R{i-8}')
    167                    else:
    168                        col_names.append(f'sensor_{i}')
    169
    170                df.columns = col_names
    171
    172                # Set time as index
    173                df = df.set_index('time')
    174
    175                # Add subject metadata
    176                df['subject_type'] = subject_type
    177                df['label'] = label
    178
    179                physionet_data.append(df)
    180                physionet_names.append(filename)
    181                self.labels.append(label)
    182                self.subject_types.append(subject_type)
    183
    184            except Exception as e:
    185                print(f"Error loading {filename}: {e}")
    186                continue
    187
    188        # Store loaded data
    189        self.data = physionet_data
    190        self.names = physionet_names
    191
    192        print(f"Loaded {len(physionet_data)} PhysioNet files")
    193        print(f"Subject distribution: {dict(zip(*np.unique(self.subject_types, return_counts=True)))}")
    194
    195        return physionet_data, physionet_names
    196
    197    def create_sliding_windows(self, data: List[pd.DataFrame], names: List[str],
    198                             window_size: int = 600, step_size: int = 100) -> List[Dict]:
    199        """
    200        Create sliding windows from the PhysioNet dataset.
    201
    202        Args:
    203            data: List of DataFrames containing PhysioNet data
    204            names: List of names corresponding to the data
    205            window_size: Size of the sliding window (default: 600 for 6 seconds at 100Hz)
    206            step_size: Step size for the sliding window (default: 100)
    207
    208        Returns:
    209            List of dictionaries containing sliding windows for each DataFrame
    210        """
    211        windows_data = []
    212
    213        for idx, df in enumerate(data):
    214            # Remove metadata columns for windowing
    215            sensor_columns = [col for col in df.columns if col.startswith('VGRF_') or col.startswith('sensor_')]
    216            df_sensors = df[sensor_columns]
    217
    218            if df_sensors.empty or len(df_sensors) < window_size:
    219                continue
    220
    221            windows = []
    222
    223            # Create windows for each sensor
    224            for col in sensor_columns:
    225                try:
    226                    window_data = sliding_window(df_sensors[col].values, window_size, step_size)
    227                    windows.append({"name": col, "data": window_data})
    228                except Exception as e:
    229                    print(f"Error creating windows for {col} in {names[idx]}: {e}")
    230                    continue
    231
    232            if windows:
    233                windows_data.append({
    234                    "name": names[idx],
    235                    "windows": windows,
    236                    "metadata": {
    237                        "subject_type": df['subject_type'].iloc[0] if 'subject_type' in df.columns else 'Unknown',
    238                        "label": df['label'].iloc[0] if 'label' in df.columns else 'Unknown',
    239                        "window_size": window_size,
    240                        "step_size": step_size,
    241                        "num_windows": len(windows[0]["data"]) if windows else 0
    242                    }
    243                })
    244
    245        return windows_data
    246
    247    def get_supported_formats(self) -> List[str]:
    248        """
    249        Get list of supported file formats for PhysioNet dataset.
    250
    251        Returns:
    252            List of supported file extensions
    253        """
    254        return ['.txt']
    255
    256    def get_sensor_info(self) -> Dict[str, List[str]]:
    257        """
    258        Get information about sensors in the dataset.
    259
    260        Returns:
    261            Dictionary containing sensor information
    262        """
    263        return {
    264            'sensors': self.metadata['sensors'],
    265            'sampling_frequency': self.metadata['sampling_frequency'],
    266            'window_size': self.metadata['window_size']
    267        }
    268
    269    def get_subject_info(self) -> Dict[str, str]:
    270        """
    271        Get information about subjects in the dataset.
    272
    273        Returns:
    274            Dictionary containing subject information
    275        """
    276        return self.metadata['subjects']
    277
    278    def get_labels(self) -> List[str]:
    279        """
    280        Get labels for loaded data.
    281
    282        Returns:
    283            List of labels corresponding to loaded data
    284        """
    285        return self.labels
    286
    287    def filter_by_subject_type(self, subject_type: str) -> Tuple[List[pd.DataFrame], List[str]]:
    288        """
    289        Filter loaded data by subject type.
    290
    291        Args:
    292            subject_type: 'Control' or 'Patient'
    293
    294        Returns:
    295            Tuple of (filtered_data, filtered_names)
    296        """
    297        if not self.data:
    298            raise ValueError("No data loaded. Call load_data() first.")
    299
    300        filtered_data = []
    301        filtered_names = []
    302
    303        for i, df in enumerate(self.data):
    304            if df['subject_type'].iloc[0] == subject_type:
    305                filtered_data.append(df)
    306                filtered_names.append(self.names[i])
    307
    308        return filtered_data, filtered_names
    309
    310
    311# Legacy function for backward compatibility
    312def load_physionet_data(data_dir: str) -> Tuple[List[pd.DataFrame], List[str]]:
    313    """
    314    Legacy function to load PhysioNet data.
    315
    316    Args:
    317        data_dir: Directory containing the dataset
    318
    319    Returns:
    320        Tuple of (data_list, names_list)
    321    """
    322    loader = PhysioNetLoader()
    323    return loader.load_data(data_dir)
    324
    325
    326def create_physionet_windows(data: List[pd.DataFrame], names: List[str],
    327                           window_size: int = 600, step_size: int = 100) -> List[Dict]:
    328    """
    329    Legacy function to create sliding windows from PhysioNet data.
    330
    331    Args:
    332        data: List of DataFrames
    333        names: List of names
    334        window_size: Size of sliding window
    335        step_size: Step size for sliding window
    336
    337    Returns:
    338        List of sliding window dictionaries
    339    """
    340    loader = PhysioNetLoader()
    341    return loader.create_sliding_windows(data, names, window_size, step_size)

class PhysioNetLoader(gaitsetpy.core.base_classes.BaseDatasetLoader): View Source

     25class PhysioNetLoader(BaseDatasetLoader):
     26    """
     27    PhysioNet VGRF dataset loader class.
     28
     29    This class handles loading and processing of the PhysioNet Gait in Parkinson's Disease dataset.
     30    The dataset contains vertical ground reaction force (VGRF) data from subjects with Parkinson's
     31    disease and healthy controls.
     32    """
     33
     34    def __init__(self):
     35        super().__init__(
     36            name="physionet",
     37            description="PhysioNet Gait in Parkinson's Disease Dataset - Contains VGRF data from subjects with Parkinson's disease and healthy controls"
     38        )
     39        self.metadata = {
     40            'sensors': ['VGRF_L1', 'VGRF_L2', 'VGRF_L3', 'VGRF_L4', 'VGRF_L5', 'VGRF_L6', 'VGRF_L7', 'VGRF_L8',
     41                       'VGRF_R1', 'VGRF_R2', 'VGRF_R3', 'VGRF_R4', 'VGRF_R5', 'VGRF_R6', 'VGRF_R7', 'VGRF_R8'],
     42            'sampling_frequency': 100,  # 100 Hz sampling frequency
     43            'subjects': {
     44                'Co': 'Control subjects',
     45                'Pt': 'Parkinson\'s disease patients'
     46            },
     47            'window_size': 600,  # 6 seconds at 100 Hz
     48            'url': 'https://physionet.org/files/gaitpdb/1.0.0/'
     49        }
     50        self.labels = []
     51        self.subject_types = []
     52
     53    def _download_physionet_data(self, data_dir: str) -> str:
     54        """
     55        Download PhysioNet dataset if not already present.
     56
     57        Args:
     58            data_dir: Directory to store the dataset
     59
     60        Returns:
     61            Path to the downloaded/existing dataset directory
     62        """
     63        dataset_path = os.path.join(data_dir, "physionet_gaitpdb")
     64
     65        if os.path.exists(dataset_path) and len(os.listdir(dataset_path)) > 0:
     66            print(f"PhysioNet dataset already exists at: {dataset_path}")
     67            return dataset_path
     68
     69        os.makedirs(dataset_path, exist_ok=True)
     70
     71        # Download the dataset files
     72        base_url = "https://physionet.org/files/gaitpdb/1.0.0/"
     73
     74        # Get list of files (basic file names based on the reference)
     75        file_patterns = [
     76            # Control subjects - Ga prefix
     77            *[f"GaCo{i:02d}_{j:02d}.txt" for i in range(1, 18) for j in range(1, 3)],
     78            "GaCo22_01.txt", "GaCo22_10.txt",
     79
     80            # Parkinson's patients - Ga prefix
     81            *[f"GaPt{i:02d}_{j:02d}.txt" for i in range(3, 10) for j in range(1, 3)],
     82            *[f"GaPt{i:02d}_{j:02d}.txt" for i in range(12, 34) for j in range(1, 3)],
     83            *[f"GaPt{i:02d}_10.txt" for i in range(13, 34)],
     84
     85            # Control subjects - Ju prefix
     86            *[f"JuCo{i:02d}_01.txt" for i in range(1, 27)],
     87
     88            # Parkinson's patients - Ju prefix
     89            *[f"JuPt{i:02d}_{j:02d}.txt" for i in range(1, 30) for j in range(1, 8)],
     90
     91            # Control subjects - Si prefix
     92            *[f"SiCo{i:02d}_01.txt" for i in range(1, 31)],
     93
     94            # Parkinson's patients - Si prefix
     95            *[f"SiPt{i:02d}_01.txt" for i in range(2, 41)]
     96        ]
     97
     98        print(f"Downloading PhysioNet dataset to {dataset_path}")
     99        for filename in tqdm(file_patterns, desc="Downloading files"):
    100            file_url = base_url + filename
    101            file_path = os.path.join(dataset_path, filename)
    102
    103            if os.path.exists(file_path):
    104                continue
    105
    106            try:
    107                response = requests.get(file_url, stream=True)
    108                if response.status_code == 200:
    109                    with open(file_path, 'wb') as f:
    110                        for chunk in response.iter_content(chunk_size=8192):
    111                            f.write(chunk)
    112                else:
    113                    print(f"Could not download {filename} (status: {response.status_code})")
    114            except Exception as e:
    115                print(f"Error downloading {filename}: {e}")
    116
    117        return dataset_path
    118
    119    def load_data(self, data_dir: str, **kwargs) -> Tuple[List[pd.DataFrame], List[str]]:
    120        """
    121        Load PhysioNet VGRF dataset from the specified directory.
    122
    123        Args:
    124            data_dir: Directory to store/find the dataset
    125            **kwargs: Additional arguments (unused for PhysioNet)
    126
    127        Returns:
    128            Tuple of (data_list, names_list)
    129        """
    130        # Download dataset if needed
    131        dataset_path = self._download_physionet_data(data_dir)
    132
    133        physionet_data = []
    134        physionet_names = []
    135        self.labels = []
    136        self.subject_types = []
    137
    138        # Load all available files
    139        for filepath in sorted(glob(os.path.join(dataset_path, "Ga*.txt"))):
    140            filename = os.path.basename(filepath)
    141
    142            # Extract subject type from filename
    143            if 'Co' in filename:
    144                subject_type = 'Control'
    145                label = 'Co'
    146            elif 'Pt' in filename:
    147                subject_type = 'Patient'
    148                label = 'Pt'
    149            else:
    150                continue  # Skip files that don't match expected pattern
    151
    152            try:
    153                # Read the file - PhysioNet files are tab-delimited with variable columns
    154                # Column 0: time, Columns 1-16: VGRF sensors, additional columns may exist
    155                df = pd.read_csv(filepath, delimiter='\t', header=None)
    156
    157                # Handle variable number of columns
    158                n_cols = min(df.shape[1], 19)  # Limit to 19 columns max
    159                df = df.iloc[:, :n_cols]
    160
    161                # Create column names
    162                col_names = ['time']
    163                for i in range(1, n_cols):
    164                    if i <= 8:
    165                        col_names.append(f'VGRF_L{i}')
    166                    elif i <= 16:
    167                        col_names.append(f'VGRF_R{i-8}')
    168                    else:
    169                        col_names.append(f'sensor_{i}')
    170
    171                df.columns = col_names
    172
    173                # Set time as index
    174                df = df.set_index('time')
    175
    176                # Add subject metadata
    177                df['subject_type'] = subject_type
    178                df['label'] = label
    179
    180                physionet_data.append(df)
    181                physionet_names.append(filename)
    182                self.labels.append(label)
    183                self.subject_types.append(subject_type)
    184
    185            except Exception as e:
    186                print(f"Error loading {filename}: {e}")
    187                continue
    188
    189        # Store loaded data
    190        self.data = physionet_data
    191        self.names = physionet_names
    192
    193        print(f"Loaded {len(physionet_data)} PhysioNet files")
    194        print(f"Subject distribution: {dict(zip(*np.unique(self.subject_types, return_counts=True)))}")
    195
    196        return physionet_data, physionet_names
    197
    198    def create_sliding_windows(self, data: List[pd.DataFrame], names: List[str],
    199                             window_size: int = 600, step_size: int = 100) -> List[Dict]:
    200        """
    201        Create sliding windows from the PhysioNet dataset.
    202
    203        Args:
    204            data: List of DataFrames containing PhysioNet data
    205            names: List of names corresponding to the data
    206            window_size: Size of the sliding window (default: 600 for 6 seconds at 100Hz)
    207            step_size: Step size for the sliding window (default: 100)
    208
    209        Returns:
    210            List of dictionaries containing sliding windows for each DataFrame
    211        """
    212        windows_data = []
    213
    214        for idx, df in enumerate(data):
    215            # Remove metadata columns for windowing
    216            sensor_columns = [col for col in df.columns if col.startswith('VGRF_') or col.startswith('sensor_')]
    217            df_sensors = df[sensor_columns]
    218
    219            if df_sensors.empty or len(df_sensors) < window_size:
    220                continue
    221
    222            windows = []
    223
    224            # Create windows for each sensor
    225            for col in sensor_columns:
    226                try:
    227                    window_data = sliding_window(df_sensors[col].values, window_size, step_size)
    228                    windows.append({"name": col, "data": window_data})
    229                except Exception as e:
    230                    print(f"Error creating windows for {col} in {names[idx]}: {e}")
    231                    continue
    232
    233            if windows:
    234                windows_data.append({
    235                    "name": names[idx],
    236                    "windows": windows,
    237                    "metadata": {
    238                        "subject_type": df['subject_type'].iloc[0] if 'subject_type' in df.columns else 'Unknown',
    239                        "label": df['label'].iloc[0] if 'label' in df.columns else 'Unknown',
    240                        "window_size": window_size,
    241                        "step_size": step_size,
    242                        "num_windows": len(windows[0]["data"]) if windows else 0
    243                    }
    244                })
    245
    246        return windows_data
    247
    248    def get_supported_formats(self) -> List[str]:
    249        """
    250        Get list of supported file formats for PhysioNet dataset.
    251
    252        Returns:
    253            List of supported file extensions
    254        """
    255        return ['.txt']
    256
    257    def get_sensor_info(self) -> Dict[str, List[str]]:
    258        """
    259        Get information about sensors in the dataset.
    260
    261        Returns:
    262            Dictionary containing sensor information
    263        """
    264        return {
    265            'sensors': self.metadata['sensors'],
    266            'sampling_frequency': self.metadata['sampling_frequency'],
    267            'window_size': self.metadata['window_size']
    268        }
    269
    270    def get_subject_info(self) -> Dict[str, str]:
    271        """
    272        Get information about subjects in the dataset.
    273
    274        Returns:
    275            Dictionary containing subject information
    276        """
    277        return self.metadata['subjects']
    278
    279    def get_labels(self) -> List[str]:
    280        """
    281        Get labels for loaded data.
    282
    283        Returns:
    284            List of labels corresponding to loaded data
    285        """
    286        return self.labels
    287
    288    def filter_by_subject_type(self, subject_type: str) -> Tuple[List[pd.DataFrame], List[str]]:
    289        """
    290        Filter loaded data by subject type.
    291
    292        Args:
    293            subject_type: 'Control' or 'Patient'
    294
    295        Returns:
    296            Tuple of (filtered_data, filtered_names)
    297        """
    298        if not self.data:
    299            raise ValueError("No data loaded. Call load_data() first.")
    300
    301        filtered_data = []
    302        filtered_names = []
    303
    304        for i, df in enumerate(self.data):
    305            if df['subject_type'].iloc[0] == subject_type:
    306                filtered_data.append(df)
    307                filtered_names.append(self.names[i])
    308
    309        return filtered_data, filtered_names

PhysioNet VGRF dataset loader class.

This class handles loading and processing of the PhysioNet Gait in Parkinson's Disease dataset. The dataset contains vertical ground reaction force (VGRF) data from subjects with Parkinson's disease and healthy controls.

PhysioNetLoader() View Source

    34    def __init__(self):
    35        super().__init__(
    36            name="physionet",
    37            description="PhysioNet Gait in Parkinson's Disease Dataset - Contains VGRF data from subjects with Parkinson's disease and healthy controls"
    38        )
    39        self.metadata = {
    40            'sensors': ['VGRF_L1', 'VGRF_L2', 'VGRF_L3', 'VGRF_L4', 'VGRF_L5', 'VGRF_L6', 'VGRF_L7', 'VGRF_L8',
    41                       'VGRF_R1', 'VGRF_R2', 'VGRF_R3', 'VGRF_R4', 'VGRF_R5', 'VGRF_R6', 'VGRF_R7', 'VGRF_R8'],
    42            'sampling_frequency': 100,  # 100 Hz sampling frequency
    43            'subjects': {
    44                'Co': 'Control subjects',
    45                'Pt': 'Parkinson\'s disease patients'
    46            },
    47            'window_size': 600,  # 6 seconds at 100 Hz
    48            'url': 'https://physionet.org/files/gaitpdb/1.0.0/'
    49        }
    50        self.labels = []
    51        self.subject_types = []

Initialize the dataset loader.

Args: name: Name of the dataset description: Description of the dataset

metadata
labels
subject_types
def load_data( self, data_dir: str, **kwargs) -> Tuple[List[pandas.core.frame.DataFrame], List[str]]: View Source

    119    def load_data(self, data_dir: str, **kwargs) -> Tuple[List[pd.DataFrame], List[str]]:
    120        """
    121        Load PhysioNet VGRF dataset from the specified directory.
    122
    123        Args:
    124            data_dir: Directory to store/find the dataset
    125            **kwargs: Additional arguments (unused for PhysioNet)
    126
    127        Returns:
    128            Tuple of (data_list, names_list)
    129        """
    130        # Download dataset if needed
    131        dataset_path = self._download_physionet_data(data_dir)
    132
    133        physionet_data = []
    134        physionet_names = []
    135        self.labels = []
    136        self.subject_types = []
    137
    138        # Load all available files
    139        for filepath in sorted(glob(os.path.join(dataset_path, "Ga*.txt"))):
    140            filename = os.path.basename(filepath)
    141
    142            # Extract subject type from filename
    143            if 'Co' in filename:
    144                subject_type = 'Control'
    145                label = 'Co'
    146            elif 'Pt' in filename:
    147                subject_type = 'Patient'
    148                label = 'Pt'
    149            else:
    150                continue  # Skip files that don't match expected pattern
    151
    152            try:
    153                # Read the file - PhysioNet files are tab-delimited with variable columns
    154                # Column 0: time, Columns 1-16: VGRF sensors, additional columns may exist
    155                df = pd.read_csv(filepath, delimiter='\t', header=None)
    156
    157                # Handle variable number of columns
    158                n_cols = min(df.shape[1], 19)  # Limit to 19 columns max
    159                df = df.iloc[:, :n_cols]
    160
    161                # Create column names
    162                col_names = ['time']
    163                for i in range(1, n_cols):
    164                    if i <= 8:
    165                        col_names.append(f'VGRF_L{i}')
    166                    elif i <= 16:
    167                        col_names.append(f'VGRF_R{i-8}')
    168                    else:
    169                        col_names.append(f'sensor_{i}')
    170
    171                df.columns = col_names
    172
    173                # Set time as index
    174                df = df.set_index('time')
    175
    176                # Add subject metadata
    177                df['subject_type'] = subject_type
    178                df['label'] = label
    179
    180                physionet_data.append(df)
    181                physionet_names.append(filename)
    182                self.labels.append(label)
    183                self.subject_types.append(subject_type)
    184
    185            except Exception as e:
    186                print(f"Error loading {filename}: {e}")
    187                continue
    188
    189        # Store loaded data
    190        self.data = physionet_data
    191        self.names = physionet_names
    192
    193        print(f"Loaded {len(physionet_data)} PhysioNet files")
    194        print(f"Subject distribution: {dict(zip(*np.unique(self.subject_types, return_counts=True)))}")
    195
    196        return physionet_data, physionet_names

Load PhysioNet VGRF dataset from the specified directory.

Args: data_dir: Directory to store/find the dataset **kwargs: Additional arguments (unused for PhysioNet)

Returns: Tuple of (data_list, names_list)

def create_sliding_windows( self, data: List[pandas.core.frame.DataFrame], names: List[str], window_size: int = 600, step_size: int = 100) -> List[Dict]: View Source

    198    def create_sliding_windows(self, data: List[pd.DataFrame], names: List[str],
    199                             window_size: int = 600, step_size: int = 100) -> List[Dict]:
    200        """
    201        Create sliding windows from the PhysioNet dataset.
    202
    203        Args:
    204            data: List of DataFrames containing PhysioNet data
    205            names: List of names corresponding to the data
    206            window_size: Size of the sliding window (default: 600 for 6 seconds at 100Hz)
    207            step_size: Step size for the sliding window (default: 100)
    208
    209        Returns:
    210            List of dictionaries containing sliding windows for each DataFrame
    211        """
    212        windows_data = []
    213
    214        for idx, df in enumerate(data):
    215            # Remove metadata columns for windowing
    216            sensor_columns = [col for col in df.columns if col.startswith('VGRF_') or col.startswith('sensor_')]
    217            df_sensors = df[sensor_columns]
    218
    219            if df_sensors.empty or len(df_sensors) < window_size:
    220                continue
    221
    222            windows = []
    223
    224            # Create windows for each sensor
    225            for col in sensor_columns:
    226                try:
    227                    window_data = sliding_window(df_sensors[col].values, window_size, step_size)
    228                    windows.append({"name": col, "data": window_data})
    229                except Exception as e:
    230                    print(f"Error creating windows for {col} in {names[idx]}: {e}")
    231                    continue
    232
    233            if windows:
    234                windows_data.append({
    235                    "name": names[idx],
    236                    "windows": windows,
    237                    "metadata": {
    238                        "subject_type": df['subject_type'].iloc[0] if 'subject_type' in df.columns else 'Unknown',
    239                        "label": df['label'].iloc[0] if 'label' in df.columns else 'Unknown',
    240                        "window_size": window_size,
    241                        "step_size": step_size,
    242                        "num_windows": len(windows[0]["data"]) if windows else 0
    243                    }
    244                })
    245
    246        return windows_data

Create sliding windows from the PhysioNet dataset.

Args: data: List of DataFrames containing PhysioNet data names: List of names corresponding to the data window_size: Size of the sliding window (default: 600 for 6 seconds at 100Hz) step_size: Step size for the sliding window (default: 100)

Returns: List of dictionaries containing sliding windows for each DataFrame

def get_supported_formats(self) -> List[str]: View Source

    248    def get_supported_formats(self) -> List[str]:
    249        """
    250        Get list of supported file formats for PhysioNet dataset.
    251
    252        Returns:
    253            List of supported file extensions
    254        """
    255        return ['.txt']

Get list of supported file formats for PhysioNet dataset.

Returns: List of supported file extensions

def get_sensor_info(self) -> Dict[str, List[str]]: View Source

    257    def get_sensor_info(self) -> Dict[str, List[str]]:
    258        """
    259        Get information about sensors in the dataset.
    260
    261        Returns:
    262            Dictionary containing sensor information
    263        """
    264        return {
    265            'sensors': self.metadata['sensors'],
    266            'sampling_frequency': self.metadata['sampling_frequency'],
    267            'window_size': self.metadata['window_size']
    268        }

Get information about sensors in the dataset.

Returns: Dictionary containing sensor information

def get_subject_info(self) -> Dict[str, str]: View Source

    270    def get_subject_info(self) -> Dict[str, str]:
    271        """
    272        Get information about subjects in the dataset.
    273
    274        Returns:
    275            Dictionary containing subject information
    276        """
    277        return self.metadata['subjects']

Get information about subjects in the dataset.

Returns: Dictionary containing subject information

def get_labels(self) -> List[str]: View Source

    279    def get_labels(self) -> List[str]:
    280        """
    281        Get labels for loaded data.
    282
    283        Returns:
    284            List of labels corresponding to loaded data
    285        """
    286        return self.labels

Get labels for loaded data.

Returns: List of labels corresponding to loaded data

def filter_by_subject_type( self, subject_type: str) -> Tuple[List[pandas.core.frame.DataFrame], List[str]]: View Source

    288    def filter_by_subject_type(self, subject_type: str) -> Tuple[List[pd.DataFrame], List[str]]:
    289        """
    290        Filter loaded data by subject type.
    291
    292        Args:
    293            subject_type: 'Control' or 'Patient'
    294
    295        Returns:
    296            Tuple of (filtered_data, filtered_names)
    297        """
    298        if not self.data:
    299            raise ValueError("No data loaded. Call load_data() first.")
    300
    301        filtered_data = []
    302        filtered_names = []
    303
    304        for i, df in enumerate(self.data):
    305            if df['subject_type'].iloc[0] == subject_type:
    306                filtered_data.append(df)
    307                filtered_names.append(self.names[i])
    308
    309        return filtered_data, filtered_names

Filter loaded data by subject type.

Args: subject_type: 'Control' or 'Patient'

Returns: Tuple of (filtered_data, filtered_names)

##### Inherited Members

gaitsetpy.core.base_classes.BaseDatasetLoader
  name
  description
  data
  get_info

def load_physionet_data(data_dir: str) -> Tuple[List[pandas.core.frame.DataFrame], List[str]]: View Source

    313def load_physionet_data(data_dir: str) -> Tuple[List[pd.DataFrame], List[str]]:
    314    """
    315    Legacy function to load PhysioNet data.
    316
    317    Args:
    318        data_dir: Directory containing the dataset
    319
    320    Returns:
    321        Tuple of (data_list, names_list)
    322    """
    323    loader = PhysioNetLoader()
    324    return loader.load_data(data_dir)

Legacy function to load PhysioNet data.

Args: data_dir: Directory containing the dataset

Returns: Tuple of (data_list, names_list)

def create_physionet_windows( data: List[pandas.core.frame.DataFrame], names: List[str], window_size: int = 600, step_size: int = 100) -> List[Dict]: View Source

    327def create_physionet_windows(data: List[pd.DataFrame], names: List[str],
    328                           window_size: int = 600, step_size: int = 100) -> List[Dict]:
    329    """
    330    Legacy function to create sliding windows from PhysioNet data.
    331
    332    Args:
    333        data: List of DataFrames
    334        names: List of names
    335        window_size: Size of sliding window
    336        step_size: Step size for sliding window
    337
    338    Returns:
    339        List of sliding window dictionaries
    340    """
    341    loader = PhysioNetLoader()
    342    return loader.create_sliding_windows(data, names, window_size, step_size)

Legacy function to create sliding windows from PhysioNet data.

Args: data: List of DataFrames names: List of names window_size: Size of sliding window step_size: Step size for sliding window

Returns: List of sliding window dictionaries