Refactor individual dataset creation for improved I/O efficiency and add logging for error handling

model_training_nnn_tpu/dataset_tf.py

@@ -3,6 +3,8 @@ import tensorflow as tf
 import h5py
 import numpy as np
 import math
+import logging
+from itertools import groupby
 from typing import Dict, List, Tuple, Optional, Any
 from scipy.ndimage import gaussian_filter1d
 
@@ -430,35 +432,65 @@ class BrainToTextDatasetTF:
 
     def create_individual_dataset(self) -> tf.data.Dataset:
         """
-        Create tf.data.Dataset that yields individual examples for TPU-optimized batching
+        Create tf.data.Dataset that yields individual examples with I/O optimization.
 
-        This method creates individual examples instead of pre-batched data,
-        allowing TensorFlow's padded_batch to handle fixed-shape batching for TPU.
+        This generator is refactored to group trial loading by session file,
+        drastically reducing the number of file open/close operations from
+        N_trials to N_sessions, which is ideal for slow disk I/O.
         """
 
         def individual_example_generator():
-            """Generator that yields individual trial examples"""
-            for batch_idx in range(self.n_batches):
-                batch_index = self.batch_indices[batch_idx]
+            """Generator that groups reads by file to minimize disk I/O."""
 
-                # Process each trial in the batch individually
+            # 1. 创建一个所有试验的扁平列表: [(day, trial), (day, trial), ...]
+            all_trials_to_load = []
+            # 注意：这里的迭代顺序决定了大致的读取顺序
+            # _create_batch_index_train 已经为我们随机化了批次
+            for batch_idx in sorted(self.batch_indices.keys()):
+                batch_index = self.batch_indices[batch_idx]
                 for day in batch_index.keys():
                     for trial in batch_index[day]:
-                        trial_data = self._load_trial_data(day, trial)
+                        all_trials_to_load.append((day, trial))
+
+            # 2. 按 'day' (即按文件) 对试验列表进行分组
+            # key=lambda x: x[0] 表示使用元组的第一个元素 (day) 作为分组键
+            for day, group in groupby(sorted(all_trials_to_load, key=lambda x: x[0]), key=lambda x: x[0]):
+
+                session_path = self.trial_indices[day]['session_path']
+
+                # 3. 为每个分组（每个文件）只打开一次 HDF5 文件
+                try:
+                    with h5py.File(session_path, 'r') as f:
+                        # 4. 在文件打开的状态下，读取这个文件中需要的所有试验
+                        for current_day, current_trial in group:
+                            try:
+                                # 直接从打开的文件句柄 'f' 中读取，而不是调用旧的加载函数
+                                g = f[f'trial_{current_trial:04d}']
+
+                                input_features = g['input_features'][:]
+                                if self.feature_subset:
+                                    input_features = input_features[:, self.feature_subset]
 
-                        # Yield individual example with all required fields
                                 example = {
-                            'input_features': trial_data['input_features'].astype(np.float32),
-                            'seq_class_ids': trial_data['seq_class_ids'].astype(np.int32),
-                            'n_time_steps': np.int32(trial_data['n_time_steps']),
-                            'phone_seq_lens': np.int32(trial_data['phone_seq_lens']),
-                            'day_indices': np.int32(trial_data['day_index']),
-                            'transcriptions': trial_data['transcription'].astype(np.int32),
-                            'block_nums': np.int32(trial_data['block_num']),
-                            'trial_nums': np.int32(trial_data['trial_num'])
+                                    'input_features': input_features.astype(np.float32),
+                                    'seq_class_ids': g['seq_class_ids'][:].astype(np.int32),
+                                    'n_time_steps': np.int32(g.attrs['n_time_steps']),
+                                    'phone_seq_lens': np.int32(g.attrs['seq_len']),
+                                    'day_indices': np.int32(current_day),
+                                    'transcriptions': g['transcription'][:].astype(np.int32),
+                                    'block_nums': np.int32(g.attrs['block_num']),
+                                    'trial_nums': np.int32(g.attrs['trial_num'])
                                 }
                                 yield example
 
+                            except KeyError:
+                                logging.warning(f"Trial {current_trial} not found in file {session_path}. Skipping.")
+                                continue
+
+                except (IOError, FileNotFoundError) as e:
+                    logging.error(f"Could not open or read HDF5 file: {session_path}. Error: {e}. Skipping all trials for this day.")
+                    continue
+
         # Define output signature for individual examples
         output_signature = {
             'input_features': tf.TensorSpec(shape=(None, None), dtype=tf.float32),
@@ -479,8 +511,8 @@ class BrainToTextDatasetTF:
 
         # Shuffle individual examples if training (more effective than batch-level shuffle)
         if self.split == 'train':
-            # Use a reasonable shuffle buffer - not too large to avoid memory issues
-            shuffle_buffer = min(1000, self.n_trials)
+            # 可以适当增大buffer，因为现在I/O更高效了
+            shuffle_buffer = min(2048, self.n_trials)
             dataset = dataset.shuffle(buffer_size=shuffle_buffer)
 
         return dataset
@@ -727,7 +759,8 @@ def train_test_split_indices(file_paths: List[str],
 # Utility functions for TPU-optimized data pipeline
 def create_input_fn(dataset_tf: BrainToTextDatasetTF,
                    transform_args: Dict[str, Any],
-                   training: bool = True) -> tf.data.Dataset:
+                   training: bool = True,
+                   cache_path: Optional[str] = None) -> tf.data.Dataset:
     """
     Create input function for TPU training with fixed-shape batching and data augmentation
 
@@ -735,14 +768,32 @@ def create_input_fn(dataset_tf: BrainToTextDatasetTF,
         dataset_tf: BrainToTextDatasetTF instance
         transform_args: Data transformation configuration
         training: Whether this is for training (applies augmentations)
+        cache_path: Optional path for disk caching to improve I/O performance
 
     Returns:
         tf.data.Dataset ready for TPU training with fixed shapes
     """
 
-    # Create individual example dataset instead of pre-batched dataset
+    # Create individual example dataset with file-grouping I/O optimization
     dataset = dataset_tf.create_individual_dataset()
 
+    # ========================= I/O OPTIMIZATION SOLUTION =========================
+    # 在数据加载之后、随机操作（如数据增强）之前进行缓存
+    if training:
+        # 对于训练，缓存到磁盘文件或内存
+        if cache_path:
+            dataset = dataset.cache(cache_path)
+            print(f"🗃️ Dataset caching enabled: {cache_path}")
+            print("⚠️ First epoch will be slow while building cache, subsequent epochs will be much faster")
+        else:
+            # 如果内存足够大，可以缓存到内存，速度更快
+            # 但对于大型数据集，推荐使用文件缓存
+            dataset = dataset.cache()
+            print("🗃️ Dataset caching enabled: in-memory cache")
+            print("⚠️ First epoch will be slow while building cache, subsequent epochs will be much faster")
+    # (对于验证集通常不需要缓存，因为它只运行一次)
+    # ================================================================
+
     def apply_transforms(example):
         """Apply data transformations to individual examples"""
         features = example['input_features']
@@ -762,7 +813,7 @@ def create_input_fn(dataset_tf: BrainToTextDatasetTF,
 
         return example
 
-    # Apply transformations to individual examples
+    # 在缓存之后应用随机的数据增强，确保每个epoch的增强都不同
     dataset = dataset.map(
         apply_transforms,
         num_parallel_calls=tf.data.AUTOTUNE