import numpy as np import torch import torch.nn.functional as F from torch.utils.data import Dataset, DataLoader class SpatialSEAAD_Dataset(Dataset): def __init__(self, X, y_class, y_subclass, y_supertype, batch_donor, spatial_coords, cps, confidence, meta_info): self.X = torch.from_numpy(X).float() self.y_class = torch.from_numpy(y_class).long() self.y_subclass = torch.from_numpy(y_subclass).long() self.y_supertype = torch.from_numpy(y_supertype).long() self.batch_donor = torch.from_numpy(batch_donor).long() self.spatial_coords = torch.from_numpy(spatial_coords).float() self.cps = torch.from_numpy(cps).float() self.confidence = torch.from_numpy(confidence).float() self.num_c = meta_info.item().get('num_class') self.num_sc = meta_info.item().get('num_subclass') self.num_st = meta_info.item().get('num_supertype') # Per-donor z-score normalized spatial coords (scaled to ~gene expression range) self.spatial_zscore = self._zscore_spatial_per_donor( spatial_coords, batch_donor, scale=2.0) @staticmethod def _zscore_spatial_per_donor(spatial, batch_donor, scale=2.0): """Z-score normalize spatial coords per donor, then scale.""" spatial_norm = np.zeros_like(spatial, dtype=np.float32) for d in np.unique(batch_donor): mask = batch_donor == d s = spatial[mask] mean = s.mean(axis=0) std = s.std(axis=0) + 1e-8 spatial_norm[mask] = (s - mean) / std * scale return torch.from_numpy(spatial_norm).float() def __len__(self): return self.X.shape[0] def __getitem__(self, idx): return { 'X': self.X[idx], 'spatial': self.spatial_coords[idx], 'spatial_zscore': self.spatial_zscore[idx], 'batch_id': self.batch_donor[idx], 'y_class': self.y_class[idx], 'y_subclass': self.y_subclass[idx], 'y_supertype': self.y_supertype[idx], 'cps': self.cps[idx], 'confidence': self.confidence[idx] } def build_dataloaders(npz_path, batch_size=256, seed=42, num_workers=8): data = np.load(npz_path, allow_pickle=True) # 提取所有特征 X_all, y_c_all, y_sc_all, y_st_all = data['X'], data['y_class'], data['y_subclass'], data['y_supertype'] batch_all, spatial_all = data['batch_donor'], data['spatial'] cps_all, confidence_all = data['cps'], data['y_supertype_confidence'] meta_info = data['meta'] unique_donors = np.unique(batch_all) np.random.seed(seed) np.random.shuffle(unique_donors) test_donors = unique_donors[:6] val_donors = unique_donors[6:9] train_donors = unique_donors[9:] mask_train = np.isin(batch_all, train_donors) mask_val = np.isin(batch_all, val_donors) mask_test = np.isin(batch_all, test_donors) train_dataset = SpatialSEAAD_Dataset( X_all[mask_train], y_c_all[mask_train], y_sc_all[mask_train], y_st_all[mask_train], batch_all[mask_train], spatial_all[mask_train], cps_all[mask_train], confidence_all[mask_train], meta_info ) val_dataset = SpatialSEAAD_Dataset( X_all[mask_val], y_c_all[mask_val], y_sc_all[mask_val], y_st_all[mask_val], batch_all[mask_val], spatial_all[mask_val], cps_all[mask_val], confidence_all[mask_val], meta_info ) test_dataset = SpatialSEAAD_Dataset( X_all[mask_test], y_c_all[mask_test], y_sc_all[mask_test], y_st_all[mask_test], batch_all[mask_test], spatial_all[mask_test], cps_all[mask_test], confidence_all[mask_test], meta_info ) train_loader = DataLoader(train_dataset, batch_size=batch_size, shuffle=True, drop_last=True, num_workers=num_workers) val_loader = DataLoader(val_dataset, batch_size=batch_size, shuffle=True, num_workers=num_workers) test_loader = DataLoader(test_dataset, batch_size=batch_size, shuffle=False, num_workers=num_workers) return train_loader, val_loader, test_loader