def ingest_data(self, cache_dir, tf_dir, desired_frame_rate):
"""Reads the Jens data from mat files and ingest it to TFrecords.
Args:
cache_dir: Local copy of the original archive file from the Internet
tf_dir: Folder where tfrecord files are written out
desired_frame_rate: Desired frame rate after ingestion.
"""
mat_files_list = sorted(tf.io.gfile.glob(os.path.join(cache_dir,
'*.mat')))
eeg_dir = '.'
sound_dir = '.'
make_if_not_exists(tf_dir)
print('Ingesting %d files of Jens data.' % len(mat_files_list),
file=regression_data_print)
all_ingested_files = []
for sid, mat_file in enumerate(mat_files_list):
print('Ingesting %s' % mat_file,
file=regression_data_print)
tf_dir_subject = os.path.join(tf_dir,
'subject_{:02d}'.format(sid + 1))
mat_data = loadmat(mat_file)
mat_object = mat_data['data']
# Both framte rates should be 128Hz according to:
# https://zenodo.org/record/1158410/#.XvqtpZNKjVs
wav_fs = mat_object['fsample']
eeg_fs = mat_object['fsample']
trial_dict = {}
for trial_idx, trial in enumerate(mat_object['trial']):
eeg_signal = trial[:69, :].T
audio_signal = trial[69:70, :].T
p_eeg = preprocess.Preprocessor('eeg', eeg_fs, desired_frame_rate)
ds_eeg_signal = p_eeg.resample(eeg_signal)
p_audio = preprocess.Preprocessor('audio', wav_fs, desired_frame_rate)
ds_audio_signal = p_audio.resample(audio_signal)
eeg_dict = {'eeg_data': ds_eeg_signal}
audio_files_dict = {'intensity': ds_audio_signal}
trial_key = 'trial_{:02d}'.format(trial_idx + 1)
trial_dict[trial_key] = [
audio_files_dict,
ingest.MemoryBrainDataFile(eeg_dict, sr=desired_frame_rate)
]
logging.info('Audio and EEG data shapes: %s, %s',
''.join(str(audio_signal.shape)),
''.join(str(eeg_signal.shape)))
exp = ingest.BrainExperiment(
trial_dict, sound_dir, eeg_dir, frame_rate=desired_frame_rate)
exp.load_all_data(sound_dir, eeg_dir)
exp.z_score_all_data()
for trial in exp.iterate_trials():
trial.assemble_brain_data('eeg_data')
for k in trial.model_features:
logging.info('Trial # %s, audio shapes %s', str(k),
''.join(str(trial.model_features[k].shape)))
make_if_not_exists(tf_dir_subject)
all_ingested_files.extend(exp.write_all_data(tf_dir_subject))
write_summary(cache_dir, tf_dir, desired_frame_rate, all_ingested_files)
def ingest_data(self, cache_dir, tf_dir, desired_frame_rate):
"""Reads the Telluride4 data from mat file and ingest TFrecords.
Args:
cache_dir: Directory with the local copy of the original data
tf_dir: Where to store the TFRecord files.
desired_frame_rate: Desired frame rate after ingestion.
"""
mat_data = loadmat(os.path.join(cache_dir, 'Telluride2015.mat'))
mat_objects = mat_data['data']
eeg_signals = mat_objects['eeg']
audio_signals = mat_objects['wav']
logging.info('Audio and EEG data shapes: %s, %s',
''.join(str(audio_signals.shape)),
''.join(str(eeg_signals.shape)))
if audio_signals.shape[0] != 4: # Number of audio files.
raise ValueError('Incorrect shapes for audio_signals (%s)' %
audio_signals.shape)
if eeg_signals.shape[0] != 32: # Number of trials.
raise ValueError('Incorrect shapes for eeg_signals (%s)' %
eeg_signals.shape)
eeg_signals_count = eeg_signals.shape[0]
make_if_not_exists(tf_dir)
trial_dict = {}
all_ingested_files = []
for i in range(eeg_signals_count):
sound_dict = {
'intensity':
audio_signals[i % 4],
'ones':
np.ones(audio_signals[i % 4].shape,
dtype=audio_signals[i % 4].dtype)
}
eeg_dict = {'eeg_data': eeg_signals[i]}
trial_dict['trial_{:02d}'.format(i + 1)] = [
sound_dict, ingest.MemoryBrainDataFile(eeg_dict)
]
eeg_dir = '.'
sound_dir = '.'
exp = ingest.BrainExperiment(trial_dict,
sound_dir,
eeg_dir,
frame_rate=desired_frame_rate)
exp.load_all_data(sound_dir, eeg_dir)
exp.z_score_all_data()
for trial in exp.iterate_trials():
trial.assemble_brain_data('eeg_data')
for k in trial.model_features:
logging.info('Trial#, Audio shape: %s, %s', str(k),
''.join(str(trial.model_features[k].shape)))
make_if_not_exists(tf_dir)
all_ingested_files = exp.write_all_data(tf_dir)
write_summary(cache_dir, tf_dir, desired_frame_rate,
all_ingested_files)
def test_brain_memory_experiment2(self):
fs = 16000
audio_len = fs
audio_data = np.random.randn(audio_len)
frame_sr = 100
channel_one = np.arange(2 * frame_sr) # Use ints for easier debugging
channel_two = np.arange(2 * frame_sr) + 200
eeg_data = {'C1': channel_one, 'C2': channel_two}
df = ingest.MemoryBrainDataFile(eeg_data, frame_sr)
trial_two_name = 'trial_2'
experiment_dict = {
trial_two_name: [{
'audio_data': audio_data,
'audio_sr': fs
}, df],
}
experiment = ingest.BrainExperiment(experiment_dict,
self._test_dir,
self._test_dir,
frame_rate=frame_sr)
self.assertTrue(experiment)
experiment.load_all_data(self._test_dir, self._test_dir)
summary = experiment.summary()
self.assertIn('Found 1 trials', summary)
self.assertIn('Trial trial_2: 2 EEG channels with 2s of eeg data',
summary)
for trial in experiment.iterate_trials():
trial.compute_intensity()
trial.fix_eeg_offset(1.0)
trial.assemble_brain_data(list(eeg_data.keys()))
# Master copy of EEG data has moved from brain_data to audio_features dict
brain_data = trial.audio_features['eeg']
# Now the eeg size is shorter, due to fix_eeg_offset above.
self.assertEqual(brain_data.shape, (frame_sr, 2))
tmp_dir = '/tmp'
experiment.write_all_data(tmp_dir)
tf_file = os.path.join(tmp_dir, trial_two_name + '.tfrecords')
(count, error) = ingest.count_tfrecords(tf_file)
self.assertEqual(error, 0)
self.assertEqual(count, frame_sr)
file_data = ingest.read_tfrecords(tf_file)
print('Read in data and found keys:', list(file_data.keys()))
self.assertIn('eeg', file_data)
self.assertIn('loudness', file_data)
np.testing.assert_allclose(
file_data['eeg'],
np.hstack((np.reshape(channel_one[frame_sr:], (-1, 1)),
np.reshape(channel_two[frame_sr:], (-1, 1)))))
def test_brain_experiment(self):
df = ingest_brainvision.BvBrainDataFile('brainvision_test.vhdr')
sound_filename = 'subj01_1ksamples.wav'
trial_name = ingest.BrainExperiment.delete_suffix(sound_filename, '.wav')
trial_dict = {trial_name: [sound_filename, df]}
experiment = ingest.BrainExperiment(trial_dict,
self._test_data, self._test_data+'/meg')
experiment.load_all_data(self._test_data+'/meg', self._test_data)
summary = experiment.summary()
self.assertIn('Found 1 trials', summary)
self.assertIn('Trial subj01_1ksamples: 65 EEG channels with 0.01s of '
'eeg data', summary)
experiment.z_score_all_data()
def test_brain_memory_experiment(self):
fs = 16000
audio_len = 2 * fs
audio_data = np.random.randn(audio_len, 1)
frame_sr = 100
eeg_len = 2 * frame_sr
channel_one = np.arange(eeg_len) # Use ints for easier debugging
channel_two = np.arange(eeg_len) + 200
eeg_data = collections.OrderedDict(
(('C1', channel_one), ('C2', channel_two)))
df = ingest.MemoryBrainDataFile(eeg_data, frame_sr)
trial_two_name = 'trial_2'
experiment_dict = {
trial_two_name: [{
'audio_data': audio_data,
'audio_sr': fs
}, df],
}
experiment = ingest.BrainExperiment(experiment_dict,
self._test_dir,
self._test_dir,
frame_rate=frame_sr)
self.assertTrue(experiment)
experiment.load_all_data(self._test_dir, self._test_dir)
summary = experiment.summary()
self.assertIn('Found 1 trials', summary)
self.assertIn('Trial trial_2: 2 EEG channels with 2s of eeg data',
summary)
for trial in experiment.iterate_trials():
trial.assemble_brain_data(list(eeg_data.keys()))
# Master copy of EEG data has moved from brain_data to model_features dict
brain_data = trial.model_features['eeg']
self.assertEqual(brain_data.shape, (eeg_len, 2))
tmp_dir = flags.FLAGS.test_tmpdir or '/tmp'
all_ingested_files = experiment.write_all_data(tmp_dir)
self.assertLen(all_ingested_files, 1)
tf_file = os.path.join(tmp_dir, trial_two_name + '.tfrecords')
(_, error) = ingest.count_tfrecords(tf_file)
self.assertEqual(error, 0)
file_data = ingest.read_tfrecords(tf_file)
self.assertIn('eeg', file_data)
np.testing.assert_allclose(
file_data['eeg'],
np.hstack((np.reshape(channel_one[:eeg_len], (-1, 1)),
np.reshape(channel_two[:eeg_len], (-1, 1)))))
def test_brain_experiment(self):
one_data = np.arange(10) + 100
two_data = np.arange(10) + 200
channel_data = {'one': one_data, 'two': two_data}
test_sr = 4
df = ingest.MemoryBrainDataFile(channel_data, test_sr)
sound_filename = 'subj01_1ksamples.wav'
trial_name = ingest.BrainExperiment.delete_suffix(
sound_filename, '.wav')
trial_dict = {trial_name: [sound_filename, df]}
experiment = ingest.BrainExperiment(trial_dict, self._test_dir,
self._test_dir)
experiment.load_all_data(self._test_dir, self._test_dir)
summary = experiment.summary()
self.assertIn('Found 1 trials', summary)
self.assertIn(
'Trial subj01_1ksamples: 2 EEG channels with 2.5s of '
'eeg data', summary)
experiment.z_score_all_data()
def ingest_data(self, cache_dir, tf_dir, desired_frame_rate):
"""Reads the Jens data from mat files and ingest it to TFrecords.
Args:
cache_dir: Local copy of the original archive file from the Internet
tf_dir: Folder where tfrecord files are written out
desired_frame_rate: Desired frame rate after ingestion.
"""
eeg_dir = '.'
sound_dir = '.'
frame_rate = 512
make_if_not_exists(tf_dir)
# All subject directories from the cache directory
all_dirs = tf.io.gfile.listdir(cache_dir)
all_dirs_sub = sorted([f for f in all_dirs if f.startswith('sub-')])
print(
'Ingesting {} subject directories of Jens Hearing impaired data.'.
format(len(all_dirs_sub)))
for sid, subject_dir in enumerate(all_dirs_sub):
# There is a single EEG and events file per subject
eeg_file = os.path.join(
cache_dir, subject_dir,
'eeg/{}_task-selectiveattention_eeg.bdf'.format(subject_dir))
events_file = os.path.join(
cache_dir, subject_dir,
'eeg/{}_task-selectiveattention_events.tsv'.format(
subject_dir))
# Read in events file and load the start times of attended and
# unattended audio for all trials (48 trials, 32 with dual audio)
# Loading the events tsv file into a pandas Dataframe object:
# https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html
# - a tabular format. Each column in the table, accessed using a string
# key holds an array of objects of a fixed type. Keys are the column
# headers in the tsv file.
events_df = pd.read_csv(events_file, sep='\t')
# Subject 24 has events described in 2 parts hence the if case below
# which pulls the remaining data from the second file.
if sid == 23:
events_file_part = os.path.join(
cache_dir, subject_dir,
'eeg/{}_task-selectiveattention_run-2_events.tsv'.format(
subject_dir))
events_df_part = pd.read_csv(events_file_part, sep='\t')
events_df = pd.concat([events_df, events_df_part])
# Attended audio is called target and unattended audio called masker.
# target_onset and marker_onset events indicate the start of both of those
# audio streams. stim_file contains the filename storing the audio stream
# and sample indicates the EEG sample number at which the audio stream
# starts.
start_samples = events_df[events_df['trigger_type'] ==
'targetonset']['sample'].values
masker_df = events_df[events_df['trigger_type'] == 'maskeronset'][[
'sample', 'stim_file'
]]
# Get ids of experiments with masker audio from file names
masker_df['stim_file'] = masker_df['stim_file'].apply(
lambda x: int(x.split('/')[-1][1:-4]))
# Sanity check
if len(start_samples) != 48 or len(masker_df) != 32:
raise ValueError(
'Incorrect event counts for subject %s: %d/48 and %d/32' %
(subject_dir, len(start_samples), len(masker_df)))
# Load EEG file, which is in bdf format.
print('Reading in {}'.format(eeg_file))
f = pyedflib.EdfReader(eeg_file)
num_channels = f.signals_in_file
sigbufs = np.zeros((f.getNSamples()[0], num_channels))
for i in np.arange(num_channels):
sigbufs[:, i] = f.readSignal(i)
# Stuff for trials
tf_dir_subject = os.path.join(tf_dir,
'subject_{:02d}'.format(sid + 1))
trial_dict = {}
target_audio_signals = [] # List storing target audios
masker_audio_signals = [] # List storing masker audios
chopped_sigbufs = [
] # List storing chopped signals based on audio timing
all_ingested_files = []
for trial_idx in range(1, 49):
# Load the target audio file
target_audio_signal = loadmat(
os.path.join(
cache_dir,
'derivatives/stimuli/sub{:03d}/target/t{:03d}.mat'.
format(sid + 1, trial_idx)))['dat']['feat']
target_audio_signals.append(target_audio_signal)
# Load EEG portion based on audio start time
target_start_time = start_samples[trial_idx - 1]
current_chopped_signal = sigbufs[
target_start_time:target_start_time +
target_audio_signal.shape[0], :]
chopped_sigbufs.append(current_chopped_signal)
# Only trials having masker data will have start times. This is used to
# distinguish between trials having dual speaker data v/s ones having
# single speaker data.
masker_start_time = masker_df[masker_df['stim_file'] ==
trial_idx]['sample'].values
if masker_start_time:
# Masker is offset from target audio by jitter seconds
# Align accordingly
masker_audio_file = os.path.join(
cache_dir,
'derivatives/stimuli/sub{:03d}/masker/m{:03d}.mat'.
format(sid + 1, trial_idx))
masker_audio_signal = loadmat(
masker_audio_file)['dat']['feat']
start_time_diff = int(masker_start_time -
target_start_time)
masker_audio_signal = np.concatenate(
(np.zeros(start_time_diff),
masker_audio_signal[:-1 * start_time_diff]))
trial_key = 'trial_{:02d}_dual_speaker'.format(trial_idx)
else:
# Trials with single audio - dummy masked
masker_audio_signal = np.zeros_like(target_audio_signal)
trial_key = 'trial_{:02d}_single_speaker'.format(trial_idx)
masker_audio_signals.append(masker_audio_signal)
assert len(masker_audio_signal) == len(target_audio_signal)
eeg_dict = {'eeg_data': current_chopped_signal}
audio_files_dict = {
'attended_intensity': target_audio_signal,
'unattended_intensity': masker_audio_signal
}
trial_dict[trial_key] = [
audio_files_dict,
ingest.MemoryBrainDataFile(eeg_dict, sr=desired_frame_rate)
]
logging.info('Audio and EEG data shapes: %s, %s',
''.join(str(target_audio_signal.shape)),
''.join(str(current_chopped_signal.shape)))
chopped_sigbufs = np.vstack(chopped_sigbufs)
target_audio_signal_arr = np.hstack(target_audio_signals)
masker_audio_signal_arr = np.hstack(masker_audio_signals)
print('Raw EEG shape:{}'.format(sigbufs.shape))
print('Cut EEG shape:{}'.format(chopped_sigbufs.shape))
print('Target Audio shape: {}'.format(
target_audio_signal_arr.shape))
print('Masker audio shape: {}'.format(
masker_audio_signal_arr.shape))
exp = ingest.BrainExperiment(trial_dict,
sound_dir,
eeg_dir,
frame_rate=frame_rate)
exp.load_all_data(sound_dir, eeg_dir)
exp.z_score_all_data()
for trial in exp.iterate_trials():
trial.assemble_brain_data('eeg_data')
for k in trial.model_features:
logging.info('Trial # %s, audio shapes %s', str(k),
''.join(str(trial.model_features[k].shape)))
make_if_not_exists(tf_dir_subject)
exp.write_all_data(tf_dir_subject)
all_ingested_files = os.listdir(tf_dir_subject)
all_ingested_files = [
os.path.join(tf_dir_subject, f) for f in all_ingested_files
]
write_summary(cache_dir, tf_dir_subject, desired_frame_rate,
all_ingested_files)