334 lines
15 KiB
Python
334 lines
15 KiB
Python
import os
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import torch
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from torch.utils.data import Dataset
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import h5py
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import numpy as np
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from torch.nn.utils.rnn import pad_sequence
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import math
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class BrainToTextDataset(Dataset):
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'''
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Dataset for brain-to-text data
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Returns an entire batch of data instead of a single example
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'''
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def __init__(
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self,
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trial_indicies,
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n_batches,
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split = 'train',
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batch_size = 64,
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days_per_batch = 1,
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random_seed = -1,
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must_include_days = None,
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feature_subset = None
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):
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'''
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trial_indicies: (dict) - dictionary with day numbers as keys and lists of trial indices as values
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n_batches: (int) - number of random training batches to create
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split: (string) - string specifying if this is a train or test dataset
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batch_size: (int) - number of examples to include in batch returned from __getitem_()
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days_per_batch: (int) - how many unique days can exist in a batch; this is important for making sure that updates
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to individual day layers in the GRU are not excesively noisy. Validation data will always have 1 day per batch
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random_seed: (int) - seed to set for randomly assigning trials to a batch. If set to -1, trial assignment will be random
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must_include_days ([int]) - list of days that must be included in every batch
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feature_subset ([int]) - list of neural feature indicies that should be the only features included in the neural data
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'''
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# Set random seed for reproducibility
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if random_seed != -1:
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np.random.seed(random_seed)
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torch.manual_seed(random_seed)
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self.split = split
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# Ensure the split is valid
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if self.split not in ['train', 'test']:
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raise ValueError(f'split must be either "train" or "test". Received {self.split}')
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self.days_per_batch = days_per_batch
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self.batch_size = batch_size
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self.n_batches = n_batches
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self.days = {}
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self.n_trials = 0
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self.trial_indicies = trial_indicies
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self.n_days = len(trial_indicies.keys())
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self.feature_subset = feature_subset
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# Calculate total number of trials in the dataset
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for d in trial_indicies:
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self.n_trials += len(trial_indicies[d]['trials'])
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if must_include_days is not None and len(must_include_days) > days_per_batch:
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raise ValueError(f'must_include_days must be less than or equal to days_per_batch. Received {must_include_days} and days_per_batch {days_per_batch}')
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if must_include_days is not None and len(must_include_days) > self.n_days and split != 'train':
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raise ValueError(f'must_include_days is not valid for test data. Received {must_include_days} and but only {self.n_days} in the dataset')
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if must_include_days is not None:
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# Map must_include_days to correct indicies if they are negative
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for i, d in enumerate(must_include_days):
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if d < 0:
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must_include_days[i] = self.n_days + d
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self.must_include_days = must_include_days
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# Ensure that the days_per_batch is not greater than the number of days in the dataset. Raise error
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if self.split == 'train' and self.days_per_batch > self.n_days:
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raise ValueError(f'Requested days_per_batch: {days_per_batch} is greater than available days {self.n_days}.')
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if self.split == 'train':
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self.batch_index = self.create_batch_index_train()
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else:
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self.batch_index = self.create_batch_index_test()
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self.n_batches = len(self.batch_index.keys()) # The validation data has a fixed amount of data
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def __len__(self):
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'''
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How many batches are in this dataset.
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Because training data is sampled randomly, there is no fixed dataset length,
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however this method is required for DataLoader to work
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'''
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return self.n_batches
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def __getitem__(self, idx):
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'''
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Gets an entire batch of data from the dataset, not just a single item
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'''
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batch = {
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'input_features' : [],
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'seq_class_ids' : [],
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'n_time_steps' : [],
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'phone_seq_lens' : [],
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'day_indicies' : [],
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'transcriptions' : [],
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'block_nums' : [],
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'trial_nums' : [],
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}
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index = self.batch_index[idx]
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# Iterate through each day in the index
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for d in index.keys():
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# Open the hdf5 file for that day
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with h5py.File(self.trial_indicies[d]['session_path'], 'r') as f:
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# For each trial in the selected trials in that day
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for t in index[d]:
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try:
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g = f[f'trial_{t:04d}']
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# Remove features is neccessary
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input_features = torch.from_numpy(g['input_features'][:]) # neural data
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if self.feature_subset:
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input_features = input_features[:,self.feature_subset]
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batch['input_features'].append(input_features)
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batch['seq_class_ids'].append(torch.from_numpy(g['seq_class_ids'][:])) # phoneme labels
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batch['transcriptions'].append(torch.from_numpy(g['transcription'][:])) # character level transcriptions
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batch['n_time_steps'].append(g.attrs['n_time_steps']) # number of time steps in the trial - required since we are padding
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batch['phone_seq_lens'].append(g.attrs['seq_len']) # number of phonemes in the label - required since we are padding
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batch['day_indicies'].append(int(d)) # day index of each trial - required for the day specific layers
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batch['block_nums'].append(g.attrs['block_num'])
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batch['trial_nums'].append(g.attrs['trial_num'])
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except Exception as e:
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print(f'Error loading trial {t} from session {self.trial_indicies[d]["session_path"]}: {e}')
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continue
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# Pad data to form a cohesive batch
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batch['input_features'] = pad_sequence(batch['input_features'], batch_first = True, padding_value = 0)
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batch['seq_class_ids'] = pad_sequence(batch['seq_class_ids'], batch_first = True, padding_value = 0)
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batch['n_time_steps'] = torch.tensor(batch['n_time_steps'])
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batch['phone_seq_lens'] = torch.tensor(batch['phone_seq_lens'])
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batch['day_indicies'] = torch.tensor(batch['day_indicies'])
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batch['transcriptions'] = torch.stack(batch['transcriptions'])
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batch['block_nums'] = torch.tensor(batch['block_nums'])
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batch['trial_nums'] = torch.tensor(batch['trial_nums'])
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return batch
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def create_batch_index_train(self):
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'''
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Create an index that maps a batch_number to batch_size number of trials
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Each batch will have days_per_batch unique days of data, with the number of trials for each day evenly split between the days
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(or as even as possible if batch_size is not divisible by days_per_batch)
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'''
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batch_index = {}
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# Precompute the days that are not in must_include_days
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if self.must_include_days is not None:
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non_must_include_days = [d for d in self.trial_indicies.keys() if d not in self.must_include_days]
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for batch_idx in range(self.n_batches):
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batch = {}
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# Which days will be used for this batch. Picked randomly without replacement
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# TODO: In the future we may want to consider sampling days in proportion to the number of trials in each day
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# If must_include_days is not empty, we will use those days and then randomly sample the rest
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if self.must_include_days is not None and len(self.must_include_days) > 0:
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days = np.concatenate((self.must_include_days, np.random.choice(non_must_include_days, size = self.days_per_batch - len(self.must_include_days), replace = False)))
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# Otherwise we will select random days without replacement
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else:
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days = np.random.choice(list(self.trial_indicies.keys()), size = self.days_per_batch, replace = False)
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# How many trials will be sampled from each day
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num_trials = math.ceil(self.batch_size / self.days_per_batch) # Use ceiling to make sure we get at least batch_size trials
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for d in days:
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# Trials are sampled with replacement, so if a day has less than (self.batch_size / days_per_batch trials) trials, it won't be a problem
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trial_idxs = np.random.choice(self.trial_indicies[d]['trials'], size = num_trials, replace = True)
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batch[d] = trial_idxs
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# Remove extra trials
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extra_trials = (num_trials * len(days)) - self.batch_size
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# While we still have extra trials, remove the last trial from a random day
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while extra_trials > 0:
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d = np.random.choice(days)
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batch[d] = batch[d][:-1]
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extra_trials -= 1
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batch_index[batch_idx] = batch
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return batch_index
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def create_batch_index_test(self):
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'''
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Create an index that is all validation/testing data in batches of up to self.batch_size
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If a day does not have at least self.batch_size trials, then the batch size will be less than self.batch_size
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This index will ensures that every trial in the validation set is seen once and only once
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'''
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batch_index = {}
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batch_idx = 0
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for d in self.trial_indicies.keys():
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# Calculate how many batches we need for this day
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num_trials = len(self.trial_indicies[d]['trials'])
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num_batches = (num_trials + self.batch_size - 1) // self.batch_size
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# Create batches for this day
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for i in range(num_batches):
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start_idx = i * self.batch_size
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end_idx = min((i + 1) * self.batch_size, num_trials)
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# Get the trial indices for this batch
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batch_trials = self.trial_indicies[d]['trials'][start_idx:end_idx]
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# Add to batch_index
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batch_index[batch_idx] = {d : batch_trials}
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batch_idx += 1
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return batch_index
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def train_test_split_indicies(file_paths, test_percentage = 0.1, seed = -1, bad_trials_dict = None):
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'''
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Split data from file_paths into train and test splits
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Returns two dictionaries that detail which trials in each day will be a part of that split:
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Example:
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{
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0: trials[1,2,3], session_path: 'path'
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1: trials[2,5,6], session_path: 'path'
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}
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Args:
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file_paths (list): List of file paths to the hdf5 files containing the data
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test_percentage (float): Percentage of trials to use for testing. 0 will use all trials for training, 1 will use all trials for testing
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seed (int): Seed for reproducibility. If set to -1, the split will be random
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bad_trials_dict (dict): Dictionary of trials to exclude from the dataset. Formatted as:
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{
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'session_name_1': {block_num_1: [trial_nums], block_num_2: [trial_nums], ...},
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'session_name_2': {block_num_1: [trial_nums], block_num_2: [trial_nums], ...},
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...
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}
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'''
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# Set seed for reporoducibility
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if seed != -1:
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np.random.seed(seed)
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# Get trials in each day
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trials_per_day = {}
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for i, path in enumerate(file_paths):
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session = [s for s in path.split('/') if (s.startswith('t15.20') or s.startswith('t12.20'))][0]
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good_trial_indices = []
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if os.path.exists(path):
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with h5py.File(path, 'r') as f:
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num_trials = len(list(f.keys()))
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for t in range(num_trials):
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key = f'trial_{t:04d}'
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block_num = f[key].attrs['block_num']
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trial_num = f[key].attrs['trial_num']
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if (
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bad_trials_dict is not None
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and session in bad_trials_dict
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and str(block_num) in bad_trials_dict[session]
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and trial_num in bad_trials_dict[session][str(block_num)]
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):
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# print(f'Bad trial: {session}_{block_num}_{trial_num}')
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continue
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good_trial_indices.append(t)
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trials_per_day[i] = {'num_trials': len(good_trial_indices), 'trial_indices': good_trial_indices, 'session_path': path}
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# Pick test_percentage of trials from each day for testing and (1 - test_percentage) for training
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train_trials = {}
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test_trials = {}
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for day in trials_per_day.keys():
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num_trials = trials_per_day[day]['num_trials']
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# Generate all trial indices for this day (assuming 0-indexed)
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all_trial_indices = trials_per_day[day]['trial_indices']
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# If test_percentage is 0 or 1, we can just assign all trials to either train or test
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if test_percentage == 0:
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train_trials[day] = {'trials' : all_trial_indices, 'session_path' : trials_per_day[day]['session_path']}
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test_trials[day] = {'trials' : [], 'session_path' : trials_per_day[day]['session_path']}
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continue
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elif test_percentage == 1:
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train_trials[day] = {'trials' : [], 'session_path' : trials_per_day[day]['session_path']}
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test_trials[day] = {'trials' : all_trial_indices, 'session_path' : trials_per_day[day]['session_path']}
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continue
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else:
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# Calculate how many trials to use for testing
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num_test = max(1, int(num_trials * test_percentage))
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# Randomly select indices for testing
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test_indices = np.random.choice(all_trial_indices, size=num_test, replace=False).tolist()
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# Remaining indices go to training
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train_indices = [idx for idx in all_trial_indices if idx not in test_indices]
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# Store the split indices
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train_trials[day] = {'trials' : train_indices, 'session_path' : trials_per_day[day]['session_path']}
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test_trials[day] = {'trials' : test_indices, 'session_path' : trials_per_day[day]['session_path']}
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return train_trials, test_trials |