import datasets import numpy as np from pathlib import Path import torch import torch.nn.functional as F _DATASET_VERSION = datasets.Version("1.0.0") _N_EMBED = { "20x": 1, "10x": 4, "5x": 16, "2_5x": 64, "1_25x": 256, } _MAG_DICT = { "20x": 0, "10x": 1, "5x": 2, "2_5x": 3, "1_25x": 4, } _FIXED_SSL_FEATURE_DIM_1 = 1024 def get_ssl_feat_shape(mag_level, pool=False): first_dim = _N_EMBED[mag_level] h = int(np.sqrt(first_dim)) if pool: h = min(h, 8) return (_FIXED_SSL_FEATURE_DIM_1, h, h) def preprocess_features(feat_array): if len(feat_array.shape) == 1: feat_array = feat_array[:, None] mean = feat_array.mean(axis=0, keepdims=True) std = feat_array.std(axis=0, keepdims=True) feat_array = (feat_array - mean) / (std + 1e-8) return feat_array class MagnificationConfig(datasets.BuilderConfig): def __init__(self, mag_level=None, ssl_feat_shape_pooled=None, ssl_feat_shape_unpooled=None, data_dir=None, **kwargs): super(MagnificationConfig, self).__init__(**kwargs) self.mag_level = mag_level self.ssl_feat_shape_pooled = ssl_feat_shape_pooled self.ssl_feat_shape_unpooled = ssl_feat_shape_unpooled self.data_dir = data_dir class TCGADataset(datasets.GeneratorBasedBuilder): VERSION = _DATASET_VERSION BUILDER_CONFIGS = [] for mag_level_str in _MAG_DICT.keys(): builder_config_instance = MagnificationConfig( name=mag_level_str, version=_DATASET_VERSION, description=f"Dataset at {mag_level_str} mag", data_dir=mag_level_str, mag_level=mag_level_str, ssl_feat_shape_pooled=get_ssl_feat_shape(mag_level_str, pool=True), ssl_feat_shape_unpooled=get_ssl_feat_shape(mag_level_str, pool=False) ) BUILDER_CONFIGS.append(builder_config_instance) DEFAULT_CONFIG_NAME = "20x" def _info(self): return datasets.DatasetInfo( description=f"Dataset with images and SSL features. Configuration: {self.config.name}", features=datasets.Features( { "image": datasets.Image(), "ssl_feat": datasets.Array3D(shape=self.config.ssl_feat_shape_pooled, dtype="float32"), "ssl_feat_unpooled": datasets.Array3D(shape=self.config.ssl_feat_shape_unpooled, dtype="float32"), "mag": datasets.Value("int32"), } ), homepage="https://github.com/cvlab-stonybrook/ZoomLDM", ) def _split_generators(self, dl_manager): original_script_dir = Path(self.base_path) mag_folder_name = self.config.data_dir mag_data_abs_path = original_script_dir / "data" / mag_folder_name return [ datasets.SplitGenerator( name=datasets.Split.TRAIN, gen_kwargs={ "mag_folder_abs_path": mag_data_abs_path, "mag_level": self.config.mag_level, }, ), ] def _generate_examples(self, mag_folder_abs_path: Path, mag_level: str): idx = 0 for i in range(16): img_filename = f"{i}.jpg" feat_filename = f"{i}_ssl_feat.npy" img_path = mag_folder_abs_path / img_filename feat_path = mag_folder_abs_path / feat_filename ssl_feat_data = np.load(feat_path) ssl_feat_data = np.float32(ssl_feat_data) # Cast to float32 processed_feature = preprocess_features(ssl_feat_data) h = np.sqrt(processed_feature.shape[1]).astype(int) feat_array_unpooled = torch.tensor(processed_feature.reshape((-1, h, h))) if h > 8: shape = (8, 8) feat_array_pooled = F.adaptive_avg_pool2d(feat_array_unpooled, shape) else: feat_array_pooled = feat_array_unpooled yield idx, { "image": str(img_path), "ssl_feat": feat_array_pooled, "ssl_feat_unpooled": feat_array_unpooled, "mag": _MAG_DICT[mag_level], } idx += 1