--- a +++ b/class_ecgdataset.py @@ -0,0 +1,109 @@ +import os +import torch +import numpy as np +from torch.utils.data import Dataset + +#---------------------------------------------------- +#----------storing-signals-implementation------------ +#---------------------------------------------------- + +class ECGDataset(Dataset): + def __init__(self, data_path, patient_ids, fs, n_windows, n_seconds, leads=None): + self.data_path = data_path + self.patient_ids = patient_ids + self.fs = fs + self.n_windows = n_windows + self.n_seconds = n_seconds + self.leads = leads + self.segments = [] + self.labels = [] + self.id_mapped = {pid: idx for idx, pid in enumerate(patient_ids)} + + # Precompute and store segments + for patient_id in self.patient_ids: + signal = self.load_signal(patient_id) + start_points = self.generate_starts(signal) + for start_point in start_points: + end_point = start_point + self.n_seconds * self.fs + segment = signal[:, start_point:end_point] + self.segments.append(segment) + self.labels.append(self.id_mapped[patient_id]) + + self.segments = np.array(self.segments) + self.labels = np.array(self.labels) + + def load_signal(self, patient_id): + signal_path = os.path.join(self.data_path, f"{patient_id}_signal.npy") + signal = np.load(signal_path) + signal = signal[:, :15*3600*self.fs] + if self.leads is not None: + signal = signal[self.leads, :] + return signal + + def generate_starts(self, signal): + max_start = signal.shape[1] - self.n_seconds * self.fs + all_starts = np.arange(0, max_start, self.n_seconds * self.fs) + chosen_starts = np.random.choice(all_starts, self.n_windows, replace=False) + return chosen_starts + + def __len__(self): + return len(self.segments) + + def __getitem__(self, index): + segment = self.segments[index] + label = self.labels[index] + return torch.tensor(segment, dtype=torch.float), torch.tensor(label, dtype=torch.long) + + + +#---------------------------------------------------- +#-------------on-the-go-implementation--------------- +#---------------------------------------------------- + +class ECGDataset_on_the_fly(Dataset): + def __init__(self, data_path, patient_ids, fs, n_windows, n_seconds, leads=None): + self.data_path = data_path + self.patient_ids = patient_ids + self.fs = fs + self.n_windows = n_windows + self.n_seconds = n_seconds + self.leads = leads + self.signal_cache = {} + self.id_mapped = {pid: idx for idx, pid in enumerate(patient_ids)} + self.segment_starts = {pid: self.generate_starts(pid) for pid in patient_ids} + + def load_signal(self, patient_id): + if patient_id not in self.signal_cache: + signal_path = os.path.join(self.data_path, f"{patient_id}_signal.npy") + signal = np.load(signal_path) + signal = signal[:, :15*3600*self.fs] + if self.leads is not None: + signal = signal[self.leads, :15*3600*self.fs] + self.signal_cache[patient_id] = signal + return self.signal_cache[patient_id] + + def generate_starts(self, patient_id): + signal = self.load_signal(patient_id) + max_start = signal.shape[1] - self.n_seconds * self.fs + # make a grid of points that are n_seconds apart + all_starts = np.arange(0, max_start, self.n_seconds * self.fs) + # and choose n_windows of them as our starting pts + chosen_starts = np.random.choice(all_starts, self.n_windows, replace=False) + return chosen_starts + + def __len__(self): + return len(self.patient_ids) * self.n_windows + + def __getitem__(self, index): + patient_index = index // self.n_windows + patient_id = self.patient_ids[patient_index] + window_index = index % self.n_windows + start_point = self.segment_starts[patient_id][window_index] + end_point = start_point + self.n_seconds * self.fs + + signal = self.load_signal(patient_id) + segment = signal[:, start_point:end_point] + label = self.id_mapped[patient_id] + + return torch.tensor(segment, dtype=torch.float), torch.tensor(label, dtype=torch.long) +