def generate_cases(subject_id, trials, bad_channels=[]):
'''
3x60
4x60
-> 12 * 60 = 720ms
-> 60ms overlap
'''
label_converter = LabelConverter()
data = []
labels = []
channel_meta = []
# trial_meta = [];
# trial_id = 0;
for stimulus, trial_data in trials.iteritems():
label = label_converter.get_stimulus_id(stimulus)
log.debug('processing {} with {} samples and label {}'.format(
stimulus, trial_data.shape, label))
channels = trial_data.transpose()
for i, channel in enumerate(channels):
channel_id = i + 1
if channel_id in bad_channels:
log.debug('skipping bad channel {}'.format(channel_id))
continue
# convert to float32
channel = np.asfarray(channel, dtype='float32')
data.append(channel)
labels.append(label)
# trial_meta.append([trial_id, stimulus]);
channel_meta.append(i)
# trial_id += 1;
data = np.vstack(data)
labels = np.vstack(labels)
# trial_meta = np.vstack(trial_meta);
channel_meta = np.vstack(channel_meta)
# subject_meta = np.vstack(subject_meta);
log.debug('generated {} data points and {} labels '.format(
data.shape, labels.shape))
# return data, labels, trial_meta, channel_meta;
return data, labels, channel_meta
def generate_cases(subject_id, trials, bad_channels=[]):
'''
3x60
4x60
-> 12 * 60 = 720ms
-> 60ms overlap
'''
label_converter = LabelConverter();
data = [];
labels = [];
channel_meta = [];
# trial_meta = [];
# trial_id = 0;
for stimulus, trial_data in trials.iteritems():
label = label_converter.get_stimulus_id(stimulus);
log.debug('processing {} with {} samples and label {}'.format(stimulus,trial_data.shape,label));
channels = trial_data.transpose();
for i, channel in enumerate(channels):
channel_id = i+1;
if channel_id in bad_channels:
log.debug('skipping bad channel {}'.format(channel_id));
continue;
# convert to float32
channel = np.asfarray(channel, dtype='float32');
data.append(channel);
labels.append(label);
# trial_meta.append([trial_id, stimulus]);
channel_meta.append(i);
# trial_id += 1;
data = np.vstack(data);
labels = np.vstack(labels);
# trial_meta = np.vstack(trial_meta);
channel_meta = np.vstack(channel_meta);
# subject_meta = np.vstack(subject_meta);
log.debug('generated {} data points and {} labels '.format(data.shape, labels.shape));
# return data, labels, trial_meta, channel_meta;
return data, labels, channel_meta;
def import_dataset(source_path, target_path):
# config = load_config(default_config='../train_sda.cfg');
# DATA_ROOT = source_path
# DATA_ROOT = config.eeg.get('dataset_root', './')
SAMPLE_RATE = 400 # in Hz
TRIAL_LENGTH = 32 # in sec
TRIAL_LENGTH += 4 # add 4s after end of presentation
TRIAL_SAMPLE_LENGTH = SAMPLE_RATE * TRIAL_LENGTH
log.info('using dataset at {}'.format(source_path))
'''
Note from Dan:
All subjects should have channels 15, 16, 17 and 18 removed [...]
If you want to make them truly identical, you could remove channel 19 from
the subjects with more channels, although this should be 'good' data.
'''
bad_channels = {}
bad_channels[1] = [5, 6, 15, 16, 17, 18, 20, 21]
bad_channels[2] = [7, 8, 15, 16, 17, 18, 20, 21]
bad_channels[3] = [5, 6, 15, 16, 17, 18, 20, 21]
bad_channels[4] = [7, 8, 15, 16, 17, 18, 20, 21]
bad_channels[5] = [7, 8, 15, 16, 17, 18, 20, 21]
bad_channels[6] = [7, 8, 9, 12, 15, 16, 17, 18]
bad_channels[7] = [5, 6, 12, 15, 16, 17, 18, 20]
bad_channels[8] = [7, 8, 15, 16, 17, 18, 20, 21]
bad_channels[9] = [5, 6, 12, 15, 16, 17, 18, 20]
bad_channels[10] = [5, 6, 15, 16, 17, 18, 20, 21]
bad_channels[11] = [5, 6, 15, 16, 17, 18, 20, 21]
bad_channels[12] = [5, 6, 15, 16, 17, 18, 20, 21]
bad_channels[13] = [5, 6, 12, 15, 16, 17, 18, 20]
label_converter = LabelConverter()
metadb_file = os.path.join(target_path, 'metadata_db.pklz')
metadb = {} # empty DB
with log_timing(log, 'generating datasets'):
for subject_id in xrange(1, 14):
search_path = os.path.join(source_path,
'Sub{0:03d}*'.format(subject_id))
sourcefile_path = glob.glob(search_path)
if sourcefile_path is None or len(sourcefile_path) == 0:
log.warn('nothing found at {}'.format(search_path))
continue
else:
sourcefile_path = sourcefile_path[0]
trials = split_session(sourcefile_path, TRIAL_SAMPLE_LENGTH)
for stimulus, trial_data in trials.iteritems():
stimulus_id = label_converter.get_stimulus_id(stimulus)
log.debug(
'processing {} with {} samples and stimulus_id {}'.format(
stimulus, trial_data.shape, stimulus_id))
channels = trial_data.transpose()
trial_data = []
channel_ids = []
for i, channel in enumerate(channels):
channel_id = i + 1
# filter bad channels
if channel_id in bad_channels[subject_id]:
log.debug('skipping bad channel {}'.format(channel_id))
continue
# convert to float32
channel = np.asfarray(channel, dtype='float32')
trial_data.append(channel)
channel_ids.append(channel_id)
trial_data = np.vstack(
trial_data).transpose() # fromat: (samples, channels)
log.debug('extracted {} from channels: {}'.format(
trial_data.shape, channel_ids))
label = label_converter.get_label(
stimulus_id, 'rhythm') # raw label, unsorted
label = label_converter.shuffle_classes[
label] # sorted label id
metadata = {
'subject':
subject_id,
'label':
label,
'meta_label':
label_converter.get_label(stimulus_id, 'rhythm_meta'),
'stimulus':
stimulus,
'stimulus_id':
stimulus_id,
'rhythm_type':
label_converter.get_label(stimulus_id, 'rhythm'),
'tempo':
label_converter.get_label(stimulus_id, 'tempo'),
'audio_file':
label_converter.get_label(stimulus_id, 'audio_file'),
'trial_no':
1,
'trial_type':
'perception',
'condition':
'n/a',
'channels':
channel_ids,
}
# save data
savepath = generate_filepath_from_metadata(metadata)
save(os.path.join(target_path, savepath),
(trial_data, metadata),
mkdirs=True)
# save metadata
metadb[savepath] = metadata
log.debug('imported {}={} as {}'.format(
label, metadata['meta_label'], savepath))
save(metadb_file, metadb, mkdirs=True)
log.info('import finished')
def import_dataset(source_path, target_path):
# config = load_config(default_config='../train_sda.cfg');
# DATA_ROOT = source_path
# DATA_ROOT = config.eeg.get('dataset_root', './')
SAMPLE_RATE = 400 # in Hz
TRIAL_LENGTH = 32 # in sec
TRIAL_LENGTH += 4 # add 4s after end of presentation
TRIAL_SAMPLE_LENGTH = SAMPLE_RATE * TRIAL_LENGTH
log.info('using dataset at {}'.format(source_path))
'''
Note from Dan:
All subjects should have channels 15, 16, 17 and 18 removed [...]
If you want to make them truly identical, you could remove channel 19 from
the subjects with more channels, although this should be 'good' data.
'''
bad_channels = {}
bad_channels[1] = [5, 6, 15, 16, 17, 18, 20, 21]
bad_channels[2] = [ 7, 8, 15, 16, 17, 18, 20, 21]
bad_channels[3] = [5, 6, 15, 16, 17, 18, 20, 21]
bad_channels[4] = [ 7, 8, 15, 16, 17, 18, 20, 21]
bad_channels[5] = [ 7, 8, 15, 16, 17, 18, 20, 21]
bad_channels[6] = [ 7, 8, 9, 12, 15, 16, 17, 18 ]
bad_channels[7] = [5, 6, 12, 15, 16, 17, 18, 20 ]
bad_channels[8] = [ 7, 8, 15, 16, 17, 18, 20, 21]
bad_channels[9] = [5, 6, 12, 15, 16, 17, 18, 20 ]
bad_channels[10] = [5, 6, 15, 16, 17, 18, 20, 21]
bad_channels[11] = [5, 6, 15, 16, 17, 18, 20, 21]
bad_channels[12] = [5, 6, 15, 16, 17, 18, 20, 21]
bad_channels[13] = [5, 6, 12, 15, 16, 17, 18, 20 ]
label_converter = LabelConverter()
metadb_file = os.path.join(target_path, 'metadata_db.pklz')
metadb = {} # empty DB
with log_timing(log, 'generating datasets'):
for subject_id in xrange(1,14):
search_path = os.path.join(source_path, 'Sub{0:03d}*'.format(subject_id))
sourcefile_path = glob.glob(search_path)
if sourcefile_path is None or len(sourcefile_path) == 0:
log.warn('nothing found at {}'.format(search_path))
continue
else:
sourcefile_path = sourcefile_path[0]
trials = split_session(sourcefile_path, TRIAL_SAMPLE_LENGTH)
for stimulus, trial_data in trials.iteritems():
stimulus_id = label_converter.get_stimulus_id(stimulus)
log.debug('processing {} with {} samples and stimulus_id {}'.
format(stimulus,trial_data.shape,stimulus_id))
channels = trial_data.transpose()
trial_data = []
channel_ids = []
for i, channel in enumerate(channels):
channel_id = i+1
# filter bad channels
if channel_id in bad_channels[subject_id]:
log.debug('skipping bad channel {}'.format(channel_id))
continue
# convert to float32
channel = np.asfarray(channel, dtype='float32')
trial_data.append(channel)
channel_ids.append(channel_id)
trial_data = np.vstack(trial_data).transpose() # fromat: (samples, channels)
log.debug('extracted {} from channels: {}'.format(trial_data.shape, channel_ids))
label = label_converter.get_label(stimulus_id, 'rhythm') # raw label, unsorted
label = label_converter.shuffle_classes[label] # sorted label id
metadata = {
'subject' : subject_id,
'label' : label,
'meta_label' : label_converter.get_label(stimulus_id, 'rhythm_meta'),
'stimulus' : stimulus,
'stimulus_id' : stimulus_id,
'rhythm_type' : label_converter.get_label(stimulus_id, 'rhythm'),
'tempo' : label_converter.get_label(stimulus_id, 'tempo'),
'audio_file' : label_converter.get_label(stimulus_id, 'audio_file'),
'trial_no' : 1,
'trial_type' : 'perception',
'condition' : 'n/a',
'channels' : channel_ids,
}
# save data
savepath = generate_filepath_from_metadata(metadata)
save(os.path.join(target_path, savepath), (trial_data, metadata), mkdirs=True)
# save metadata
metadb[savepath] = metadata
log.debug('imported {}={} as {}'.format(label, metadata['meta_label'], savepath))
save(metadb_file, metadb, mkdirs=True)
log.info('import finished')