def run_neural_network(standardized_path, standardized_params, whiten_filter,
output_directory, if_file_exists, save_results):
"""Run neural network detection and autoencoder dimensionality reduction
Returns
-------
scores
Scores for all spikes
spike_index_clear
Spike indexes for clear spikes
spike_index_all
Spike indexes for all spikes
"""
logger = logging.getLogger(__name__)
CONFIG = read_config()
TMP_FOLDER = CONFIG.path_to_output_directory
# check if all scores, clear and collision spikes exist..
path_to_score = os.path.join(TMP_FOLDER, 'scores_clear.npy')
path_to_spike_index_clear = os.path.join(TMP_FOLDER,
'spike_index_clear.npy')
path_to_spike_index_all = os.path.join(TMP_FOLDER, 'spike_index_all.npy')
path_to_rotation = os.path.join(TMP_FOLDER, 'rotation.npy')
path_to_standardized = os.path.join(TMP_FOLDER, 'preprocess',
'standarized.bin')
paths = [path_to_score, path_to_spike_index_clear, path_to_spike_index_all]
exists = [os.path.exists(p) for p in paths]
if (if_file_exists == 'overwrite' or not any(exists)):
max_memory = (CONFIG.resources.max_memory_gpu
if GPU_ENABLED else CONFIG.resources.max_memory)
# make tensorflow tensors and neural net classes
detection_th = CONFIG.detect.neural_network_detector.threshold_spike
triage_th = CONFIG.detect.neural_network_triage.threshold_collision
detection_fname = CONFIG.detect.neural_network_detector.filename
ae_fname = CONFIG.detect.neural_network_autoencoder.filename
triage_fname = CONFIG.detect.neural_network_triage.filename
n_channels = CONFIG.recordings.n_channels
# open tensorflow for every chunk
NND = NeuralNetDetector.load(detection_fname, detection_th,
CONFIG.channel_index)
NNAE = AutoEncoder.load(ae_fname, input_tensor=NND.waveform_tf)
# run nn preprocess batch-wsie
neighbors = n_steps_neigh_channels(CONFIG.neigh_channels, 2)
# compute len of recording
filename_dat = os.path.join(CONFIG.data.root_folder,
CONFIG.data.recordings)
fp = np.memmap(filename_dat, dtype='int16', mode='r')
fp_len = fp.shape[0] / n_channels
# compute batch indexes
buffer_size = 200 # Cat: to set this in CONFIG file
sampling_rate = CONFIG.recordings.sampling_rate
#n_sec_chunk = CONFIG.resources.n_sec_chunk
# Cat: TODO: Set a different size chunk for clustering vs. detection
n_sec_chunk = 60
# take chunks
indexes = np.arange(0, fp_len, sampling_rate * n_sec_chunk)
# add last bit of recording if it's shorter
if indexes[-1] != fp_len:
indexes = np.hstack((indexes, fp_len))
idx_list = []
for k in range(len(indexes) - 1):
idx_list.append([
indexes[k], indexes[k + 1], buffer_size,
indexes[k + 1] - indexes[k] + buffer_size
])
idx_list = np.int64(np.vstack(idx_list))[:20]
#idx_list = idx_list
logger.info("# of chunks: %i", len(idx_list))
logger.info(idx_list)
# run tensorflow
processing_ctr = 0
#chunk_ctr = 0
# chunks to cycle over are 10 x as much as initial chosen data
total_processing = len(idx_list) * n_sec_chunk
# keep tensorflow open
# save iteratively
fname_detection = os.path.join(CONFIG.path_to_output_directory,
'detect')
if not os.path.exists(fname_detection):
os.mkdir(fname_detection)
# set tensorflow verbosity level
tf.logging.set_verbosity(tf.logging.ERROR)
# open etsnrflow session
with tf.Session() as sess:
#K.set_session(sess)
NND.restore(sess)
#triage = KerasModel(triage_fname,
# allow_longer_waveform_length=True,
# allow_more_channels=True)
# read chunks of data first:
# read chunk of raw standardized data
# Cat: TODO: don't save to lists, might want to use numpy arrays directl
#print (os.path.join(fname_detection,"detect_"+
# str(chunk_ctr).zfill(5)+'.npz'))
# loop over 10sec or 60 sec chunks
for chunk_ctr, idx in enumerate(idx_list):
if os.path.exists(
os.path.join(
fname_detection,
"detect_" + str(chunk_ctr).zfill(5) + '.npz')):
continue
# reset lists
spike_index_list = []
#idx_clean_list = []
energy_list = []
TC_list = []
offset_list = []
# load chunk of data
standardized_recording = binary_reader(idx, buffer_size,
path_to_standardized,
n_channels,
CONFIG.data.root_folder)
# run detection on smaller chunks of data, e.g. 1 sec
# Cat: TODO: add last bit at end in case short
indexes = np.arange(0, standardized_recording.shape[0],
sampling_rate)
# run tensorflow over 1sec chunks in general
for ctr, index in enumerate(indexes[:-1]):
# save absolute index of each subchunk
offset_list.append(idx[0] + indexes[ctr])
data_temp = standardized_recording[indexes[ctr]:indexes[ctr
+
1]]
# store size of recordings in case at end of dataset.
TC_list.append(data_temp.shape)
# run detect nn
res = NND.predict_recording(data_temp,
sess=sess,
output_names=('spike_index',
'waveform'))
spike_index, wfs = res
#idx_clean = (triage
# .predict_with_threshold(x=wfs,
# threshold=triage_th))
score = NNAE.predict(wfs, sess)
rot = NNAE.load_rotation(sess)
neighbors = n_steps_neigh_channels(CONFIG.neigh_channels,
2)
# idx_clean is the indexes of clear spikes in all_spikes
spike_index_list.append(spike_index)
#idx_clean_list.append(idx_clean)
# run AE nn; required for remove_axon function
# Cat: TODO: Do we really need this: can we get energy list faster?
#rot = NNAE.load_rotation()
energy_ = np.ptp(np.matmul(score[:, :, 0], rot.T), axis=1)
energy_list.append(energy_)
logger.info('processed chunk: %s/%s, # spikes: %s',
str(processing_ctr), str(total_processing),
spike_index.shape)
processing_ctr += 1
# save chunk of data in case crashes occur
np.savez(os.path.join(fname_detection,
"detect_" + str(chunk_ctr).zfill(5)),
spike_index_list=spike_index_list,
energy_list=energy_list,
TC_list=TC_list,
offset_list=offset_list)
# load all saved data;
spike_index_list = []
energy_list = []
TC_list = []
offset_list = []
for ctr, idx in enumerate(idx_list):
data = np.load(fname_detection + '/detect_' + str(ctr).zfill(5) +
'.npz')
spike_index_list.extend(data['spike_index_list'])
energy_list.extend(data['energy_list'])
TC_list.extend(data['TC_list'])
offset_list.extend(data['offset_list'])
# save all detected spikes pre axon_kill
spike_index_all_pre_deduplication = fix_indexes_firstbatch_3(
spike_index_list, offset_list, buffer_size, sampling_rate)
np.save(
os.path.join(TMP_FOLDER, 'spike_index_all_pre_deduplication.npy'),
spike_index_all_pre_deduplication)
# remove axons - compute axons to be killed
logger.info(' removing axons in parallel')
multi_procesing = 1
if CONFIG.resources.multi_processing:
keep = parmap.map(deduplicate,
list(
zip(spike_index_list, energy_list, TC_list,
np.arange(len(energy_list)))),
neighbors,
processes=CONFIG.resources.n_processors,
pm_pbar=True)
else:
keep = []
for k in range(len(energy_list)):
keep.append(
deduplicate(
(spike_index_list[k], energy_list[k], TC_list[k], k),
neighbors))
# Cat: TODO Note that we're killing spike_index_all as well.
# remove axons from clear spikes - keep only non-killed+clean events
spike_index_all_postkill = []
for k in range(len(spike_index_list)):
spike_index_all_postkill.append(spike_index_list[k][keep[k][0]])
logger.info(' fixing indexes from batching')
spike_index_all = fix_indexes_firstbatch_3(spike_index_all_postkill,
offset_list, buffer_size,
sampling_rate)
# get and clean all spikes
spikes_all = spike_index_all
#logger.info('Removing all indexes outside the allowed range to '
# 'draw a complete waveform...')
_n_observations = fp_len
spikes_all, _ = detect.remove_incomplete_waveforms(
spikes_all, CONFIG.spike_size + CONFIG.templates.max_shift,
_n_observations)
np.save(os.path.join(TMP_FOLDER, 'spike_index_all.npy'), spikes_all)
else:
spikes_all = np.load(os.path.join(TMP_FOLDER, 'spike_index_all.npy'))
return spikes_all
def test_splitting_in_batches_does_not_affect(path_to_config,
path_to_sample_pipeline_folder,
make_tmp_folder,
path_to_standardized_data):
yass.set_config(path_to_config, make_tmp_folder)
CONFIG = yass.read_config()
PATH_TO_DATA = path_to_standardized_data
with open(path.join(path_to_sample_pipeline_folder, 'preprocess',
'standardized.yaml')) as f:
PARAMS = yaml.load(f)
channel_index = make_channel_index(CONFIG.neigh_channels,
CONFIG.geom)
detection_th = CONFIG.detect.neural_network_detector.threshold_spike
triage_th = CONFIG.detect.neural_network_triage.threshold_collision
detection_fname = CONFIG.detect.neural_network_detector.filename
ae_fname = CONFIG.detect.neural_network_autoencoder.filename
triage_fname = CONFIG.detect.neural_network_triage.filename
# instantiate neural networks
NND = NeuralNetDetector.load(detection_fname, detection_th,
channel_index)
triage = KerasModel(triage_fname,
allow_longer_waveform_length=True,
allow_more_channels=True)
NNAE = AutoEncoder.load(ae_fname, input_tensor=NND.waveform_tf)
bp = BatchProcessor(PATH_TO_DATA, PARAMS['dtype'], PARAMS['n_channels'],
PARAMS['data_order'], '100KB',
buffer_size=CONFIG.spike_size)
out = ('spike_index', 'waveform')
fn = neuralnetwork.apply.fix_indexes_spike_index
# detector
with tf.Session() as sess:
# get values of above tensors
NND.restore(sess)
res = bp.multi_channel_apply(NND.predict_recording,
mode='memory',
sess=sess,
output_names=out,
cleanup_function=fn)
spike_index_new = np.concatenate([element[0] for element in res], axis=0)
wfs = np.concatenate([element[1] for element in res], axis=0)
idx_clean = triage.predict_with_threshold(wfs, triage_th)
score = NNAE.predict(wfs)
rot = NNAE.load_rotation()
neighbors = n_steps_neigh_channels(CONFIG.neigh_channels, 2)
(score_clear_new,
spike_index_clear_new) = post_processing(score,
spike_index_new,
idx_clean,
rot,
neighbors)
with tf.Session() as sess:
# get values of above tensors
NND.restore(sess)
res = bp.multi_channel_apply(NND.predict_recording,
mode='memory',
sess=sess,
output_names=('spike_index',
'waveform'),
cleanup_function=fn)
spike_index_batch, wfs = zip(*res)
spike_index_batch = np.concatenate(spike_index_batch, axis=0)
wfs = np.concatenate(wfs, axis=0)
idx_clean = triage.predict_with_threshold(x=wfs,
threshold=triage_th)
score = NNAE.predict(wfs)
rot = NNAE.load_rotation()
neighbors = n_steps_neigh_channels(CONFIG.neigh_channels, 2)
(score_clear_batch,
spike_index_clear_batch) = post_processing(score,
spike_index_batch,
idx_clean,
rot,
neighbors)