def filter_file(data_file_in, data_file_out, do_filtering, do_remove_median, do_remove_ground):
"""
Performs a high-pass and low-pass Butterworth filter on the data file.
Parameters
----------
data_file_in :
data_file_out :
do_filtering : bool
do_remove_median : bool
do_remove_median : bool
"""
try:
cut_off = params.getfloat('filtering', 'cut_off', check=False)
cut_off = [cut_off, 0.95 * (params.rate / 2.0)] # Nyquist
except Exception:
cut_off = params.get('filtering', 'cut_off', check=False)
cut_off = cut_off.split(',')
try:
cut_off[0] = float(cut_off[0])
except Exception:
if comm.rank == 0:
print_and_log(['First value of cut off must be a valid number'], 'error', logger)
sys.exit(0)
cut_off[1] = cut_off[1].replace(' ', '')
if cut_off[1] == 'auto':
cut_off[1] = 0.95 * (params.rate / 2.0)
else:
try:
cut_off[1] = float(cut_off[1])
except Exception:
if comm.rank == 0:
print_and_log(['Second value of cut off must either auto, or a valid a number'], 'error', logger)
sys.exit(0)
chunk_size = detect_memory(params, filtering=True)
butter_order = params.getint('filtering', 'butter_order')
nb_chunks, _ = data_file_in.analyze(chunk_size)
b, a = signal.butter(butter_order, np.array(cut_off)/(params.rate/2.), 'pass')
all_chunks = numpy.arange(nb_chunks, dtype=numpy.int64)
to_process = all_chunks[comm.rank::comm.size]
loc_nb_chunks = len(to_process)
N_total = params.nb_channels
nb_shanks = len(params.probe['channel_groups'])
if nb_shanks > 1:
shank_channels = {}
for i in params.probe['channel_groups'].keys():
shank_channels[i] = numpy.array(params.probe['channel_groups'][i]['channels'], dtype=numpy.int32)
else:
channel_group = params.probe['channel_groups'].keys()[0]
process_all_channels = numpy.all(nodes == numpy.arange(N_total))
duration = int(0.1*params.rate)
if comm.rank == 0:
to_write = []
if do_filtering:
to_write += ["Filtering with a Butterworth filter (order %d) in [%g, %g] Hz" % (butter_order, cut_off[0], cut_off[1])]
if do_remove_median:
to_write += ["Median over all channels is subtracted to each channels"]
if do_remove_ground:
to_write += ["Channels %s are used as reference channels in respective shanks" % common_ground]
print_and_log(to_write, 'default', logger)
to_explore = range(comm.rank, nb_chunks, comm.size)
if comm.rank == 0:
to_explore = get_tqdm_progressbar(params, to_explore)
if data_file_in == data_file_out:
data_file_in.open(mode='r+')
else:
data_file_in.open(mode='r')
data_file_out.open(mode='r+')
for count, gidx in enumerate(to_explore):
is_first = data_file_in.is_first_chunk(gidx, nb_chunks)
is_last = data_file_in.is_last_chunk(gidx, nb_chunks)
if not (is_first and is_last):
if is_first:
padding = (0, duration)
elif is_last:
padding = (-duration, 0)
else:
padding = (-duration, duration)
else:
padding = (0, 0)
local_chunk, t_offset = data_file_in.get_data(gidx, chunk_size, padding)
len_chunk = len(local_chunk)
if do_filtering:
local_chunk = signal.filtfilt(b, a, local_chunk, axis=0)
local_chunk -= numpy.median(local_chunk, 0)
local_chunk = local_chunk[numpy.abs(padding[0]):len_chunk-numpy.abs(padding[1])]
if do_remove_median:
if nb_shanks == 1:
if not process_all_channels:
global_median = numpy.median(numpy.take(local_chunk, nodes, axis=1), 1)
else:
global_median = numpy.median(local_chunk, 1)
local_chunk -= global_median[:, numpy.newaxis]
else:
for i in params.probe['channel_groups'].keys():
global_median = numpy.median(numpy.take(local_chunk, shank_channels[i], axis=1), 1)
local_chunk[:, shank_channels[i]] -= global_median[:, numpy.newaxis]
if do_remove_ground:
if nb_shanks == 1:
ground = local_chunk[:, common_ground[channel_group]]
local_chunk -= ground[:, numpy.newaxis]
else:
for i in params.probe['channel_groups'].keys():
ground = local_chunk[:, common_ground[i]]
local_chunk[:, shank_channels[i]] -= ground[:, numpy.newaxis]
if data_file_in != data_file_out:
if data_file_in.is_stream:
g_offset = t_offset
else:
g_offset = t_offset - data_file_in.t_start
else:
g_offset = t_offset
data_file_out.set_data(g_offset, local_chunk)
sys.stderr.flush()
comm.Barrier()
def filter_file(data_file_in, data_file_out, do_filtering, do_remove_median, do_remove_ground):
"""
Performs a high-pass and low-pass Butterworth filter on the data file.
Parameters
----------
data_file_in :
data_file_out :
do_filtering : bool
do_remove_median : bool
do_remove_median : bool
"""
try:
cut_off = params.getfloat('filtering', 'cut_off', check=False)
cut_off = [cut_off, 0.95 * (params.rate / 2.0)] # Nyquist
except Exception:
cut_off = params.get('filtering', 'cut_off', check=False)
cut_off = cut_off.split(',')
try:
cut_off[0] = float(cut_off[0])
except Exception:
if comm.rank == 0:
print_and_log(['First value of cut off must be a valid number'], 'error', logger)
sys.exit(0)
cut_off[1] = cut_off[1].replace(' ', '')
if cut_off[1] == 'auto':
cut_off[1] = 0.95 * (params.rate / 2.0)
else:
try:
cut_off[1] = float(cut_off[1])
except Exception:
if comm.rank == 0:
print_and_log(['Second value of cut off must either auto, or a valid a number'], 'error', logger)
sys.exit(0)
chunk_size = detect_memory(params, filtering=True)
butter_order = params.getint('filtering', 'butter_order')
nb_chunks, _ = data_file_in.analyze(chunk_size)
b, a = signal.butter(butter_order, np.array(cut_off)/(params.rate/2.), 'pass')
all_chunks = numpy.arange(nb_chunks, dtype=numpy.int64)
to_process = all_chunks[comm.rank::comm.size]
loc_nb_chunks = len(to_process)
N_total = params.nb_channels
nb_shanks = len(params.probe['channel_groups'])
if nb_shanks > 1:
shank_channels = {}
for i in list(params.probe['channel_groups'].keys()):
shank_channels[i] = numpy.array(params.probe['channel_groups'][i]['channels'], dtype=numpy.int32)
else:
channel_group = list(params.probe['channel_groups'].keys())[0]
process_all_channels = numpy.all(nodes == numpy.arange(N_total))
duration = int(0.1*params.rate)
if comm.rank == 0:
to_write = []
if do_filtering:
to_write += ["Filtering with a Butterworth filter (order %d) in [%g, %g] Hz" % (butter_order, cut_off[0], cut_off[1])]
if do_remove_median:
to_write += ["Median over all channels is subtracted to each channels"]
if do_remove_ground:
to_write += ["Channels %s are used as reference channels in respective shanks" % common_ground]
print_and_log(to_write, 'default', logger)
to_explore = list(range(comm.rank, nb_chunks, comm.size))
if comm.rank == 0:
to_explore = get_tqdm_progressbar(params, to_explore)
if data_file_in == data_file_out:
data_file_in.open(mode='r+')
else:
data_file_in.open(mode='r')
data_file_out.open(mode='r+')
if flag_saturation:
comm.Barrier()
saturation_times = open(file_out_suff + '.times-%d.data' % comm.rank, 'wb')
saturation_channels = open(file_out_suff + '.channels-%d.data' % comm.rank, 'wb')
saturation_values = open(file_out_suff + '.values-%d.data' % comm.rank, 'wb')
if data_file_in.data_dtype in ['float32', numpy.float32, 'float64', numpy.float64]:
max_value = numpy.finfo(data_file_in.data_dtype).max
else:
max_value = numpy.iinfo(data_file_in.data_dtype).max - data_file_in.dtype_offset
saturation = sat_value * max_value
for count, gidx in enumerate(to_explore):
is_first = data_file_in.is_first_chunk(gidx, nb_chunks)
is_last = data_file_in.is_last_chunk(gidx, nb_chunks)
if not (is_first and is_last):
if is_first:
padding = (0, duration)
elif is_last:
padding = (-duration, 0)
else:
padding = (-duration, duration)
else:
padding = (0, 0)
local_chunk, t_offset = data_file_in.get_data(gidx, chunk_size, padding)
len_chunk = len(local_chunk)
if flag_saturation:
if sat_threshold == 'negative':
indices = numpy.where(local_chunk <= saturation * data_file_in.gain)
elif sat_threshold == 'positive':
indices = numpy.where(local_chunk >= saturation * data_file_in.gain)
elif sat_threshold == 'both':
indices = numpy.where(numpy.abs(local_chunk) >= saturation * data_file_in.gain)
if not process_all_channels:
to_keep = numpy.in1d(indices[1], nodes)
channels = inv_nodes[indices[1][to_keep]]
times = indices[0][to_keep]
else:
channels = indices[1]
times = indices[0]
to_keep = (times >= padding[0]) & (times < (len_chunk-numpy.abs(padding[1])))
sub_times = times[to_keep]
sub_channels = channels[to_keep]
saturation_times.write((sub_times + t_offset).astype(numpy.uint32).tostring())
saturation_channels.write(sub_channels.astype(numpy.uint32).tostring())
saturation_values.write(local_chunk[sub_times, sub_channels].tostring())
if do_filtering:
if not process_all_channels:
local_chunk[:, nodes] = signal.filtfilt(b, a, local_chunk[:, nodes], axis=0)
local_chunk[:, nodes] -= numpy.median(local_chunk[:, nodes], 0)
else:
local_chunk = signal.filtfilt(b, a, local_chunk, axis=0)
local_chunk -= numpy.median(local_chunk, 0)
if flag_saturation:
local_chunk[times, channels] = 0
local_chunk = local_chunk[numpy.abs(padding[0]):len_chunk-numpy.abs(padding[1])]
if do_remove_median:
if nb_shanks == 1:
if not process_all_channels:
global_median = numpy.median(numpy.take(local_chunk, nodes, axis=1), 1)
else:
global_median = numpy.median(local_chunk, 1)
local_chunk -= global_median[:, numpy.newaxis]
else:
for i in list(params.probe['channel_groups'].keys()):
global_median = numpy.median(numpy.take(local_chunk, shank_channels[i], axis=1), 1)
local_chunk[:, shank_channels[i]] -= global_median[:, numpy.newaxis]
if do_remove_ground:
if nb_shanks == 1:
ground = local_chunk[:, common_ground[channel_group]]
local_chunk -= ground[:, numpy.newaxis]
else:
for i in list(params.probe['channel_groups'].keys()):
ground = local_chunk[:, common_ground[i]]
local_chunk[:, shank_channels[i]] -= ground[:, numpy.newaxis]
if data_file_in != data_file_out:
if data_file_in.is_stream:
g_offset = t_offset
else:
g_offset = t_offset - data_file_in.t_start
else:
g_offset = t_offset
data_file_out.set_data(g_offset, local_chunk)
sys.stderr.flush()
comm.Barrier()
if flag_saturation:
saturation_times.flush()
os.fsync(saturation_times.fileno())
saturation_times.close()
saturation_values.flush()
os.fsync(saturation_values.fileno())
saturation_values.close()
saturation_channels.flush()
os.fsync(saturation_channels.fileno())
saturation_channels.close()
# We need to gather the results into a single file
if comm.rank == 0:
collect_saturation(comm.size, params, erase=True)
sys.stderr.flush()
comm.Barrier()
def main(params, nb_cpu, nb_gpu, use_gpu):
#################################################################
# params = detect_memory(params)
_ = init_logging(params.logfile)
SHARED_MEMORY = get_shared_memory_flag(params)
logger = logging.getLogger('circus.fitting')
data_file = params.data_file
n_e = params.getint('data', 'N_e')
n_total = params.nb_channels
n_t = params.getint('detection', 'N_t')
template_shift = params.getint('detection', 'template_shift')
# file_out = params.get('data', 'file_out')
file_out_suff = params.get('data', 'file_out_suff')
sign_peaks = params.get('detection', 'peaks')
matched_filter = params.getboolean('detection', 'matched-filter')
# spike_thresh = params.getfloat('detection', 'spike_thresh')
ratio_thresh = params.getfloat('fitting', 'ratio_thresh')
two_components = params.getboolean('fitting', 'two_components')
# spike_width = params.getfloat('detection', 'spike_width')
# dist_peaks = params.getint('detection', 'dist_peaks')
do_temporal_whitening = params.getboolean('whitening', 'temporal')
do_spatial_whitening = params.getboolean('whitening', 'spatial')
templates_normalization = params.getboolean('clustering', 'templates_normalization') # TODO test, switch, test!
chunk_size = detect_memory(params, fitting=True)
gpu_only = params.getboolean('fitting', 'gpu_only')
nodes, edges = get_nodes_and_edges(params)
tmp_limits = params.get('fitting', 'amp_limits').replace('(', '').replace(')', '').split(',')
tmp_limits = [float(v) for v in tmp_limits]
amp_auto = params.getboolean('fitting', 'amp_auto')
auto_nb_chances = params.getboolean('fitting', 'auto_nb_chances')
if auto_nb_chances:
nb_chances = io.load_data(params, 'nb_chances')
max_nb_chances = params.getint('fitting', 'max_nb_chances')
percent_nb_chances = params.getfloat('fitting', 'percent_nb_chances')
total_nb_chances = max(1, numpy.nanpercentile(nb_chances, percent_nb_chances))
total_nb_chances = min(total_nb_chances, max_nb_chances)
if comm.rank == 0:
print_and_log(['nb_chances set automatically to %g' %total_nb_chances], 'debug', logger)
else:
total_nb_chances = params.getfloat('fitting', 'nb_chances')
max_chunk = params.getfloat('fitting', 'max_chunk')
# noise_thr = params.getfloat('clustering', 'noise_thr')
collect_all = params.getboolean('fitting', 'collect_all')
min_second_component = params.getfloat('fitting', 'min_second_component')
debug = params.getboolean('fitting', 'debug')
ignore_dead_times = params.getboolean('triggers', 'ignore_times')
inv_nodes = numpy.zeros(n_total, dtype=numpy.int32)
inv_nodes[nodes] = numpy.arange(len(nodes))
data_file.open()
#################################################################
if use_gpu:
import cudamat as cmt
# # Need to properly handle multi GPU per MPI nodes?
if nb_gpu > nb_cpu:
gpu_id = int(comm.rank // nb_cpu)
else:
gpu_id = 0
cmt.cuda_set_device(gpu_id)
cmt.init()
cmt.cuda_sync_threads()
if SHARED_MEMORY:
templates, _ = io.load_data_memshared(params, 'templates', normalize=templates_normalization, transpose=True)
N_tm, x = templates.shape
else:
templates = io.load_data(params, 'templates')
x, N_tm = templates.shape
temp_2_shift = 2 * template_shift
temp_3_shift = 3 * template_shift
full_gpu = use_gpu and gpu_only
n_tm = N_tm // 2
n_scalar = n_e * n_t
temp_window = numpy.arange(-template_shift, template_shift + 1)
size_window = n_e * (2 * template_shift + 1)
if not amp_auto:
amp_limits = numpy.zeros((n_tm, 2))
amp_limits[:, 0] = tmp_limits[0]
amp_limits[:, 1] = tmp_limits[1]
else:
amp_limits = io.load_data(params, 'limits')
norm_templates = io.load_data(params, 'norm-templates')
if not templates_normalization:
norm_templates_2 = (norm_templates ** 2.0) * n_scalar
if not SHARED_MEMORY:
# Normalize templates (if necessary).
if templates_normalization:
for idx in range(templates.shape[1]):
myslice = numpy.arange(templates.indptr[idx], templates.indptr[idx+1])
templates.data[myslice] /= norm_templates[idx]
# Transpose templates.
templates = templates.T
waveform_neg = numpy.empty(0) # default assignment (for PyCharm code inspection)
matched_thresholds_neg = None # default assignment (for PyCharm code inspection)
waveform_pos = numpy.empty(0) # default assignment (for PyCharm code inspection)
matched_thresholds_pos = None # default assignment (for PyCharm code inspection)
if matched_filter:
if sign_peaks in ['negative', 'both']:
waveform_neg = io.load_data(params, 'waveform')[::-1]
waveform_neg /= (numpy.abs(numpy.sum(waveform_neg)) * len(waveform_neg))
matched_thresholds_neg = io.load_data(params, 'matched-thresholds')
if sign_peaks in ['positive', 'both']:
waveform_pos = io.load_data(params, 'waveform-pos')[::-1]
waveform_pos /= (numpy.abs(numpy.sum(waveform_pos)) * len(waveform_pos))
matched_thresholds_pos = io.load_data(params, 'matched-thresholds-pos')
if ignore_dead_times:
all_dead_times = get_dead_times(params)
else:
all_dead_times = None # default assignment (for PyCharm code inspection)
thresholds = io.get_accurate_thresholds(params, ratio_thresh)
neighbors = {}
if collect_all:
for i in range(0, n_tm):
tmp = templates[i, :].toarray().reshape(n_e, n_t)
if templates_normalization:
tmp = tmp * norm_templates[i]
neighbors[i] = numpy.where(numpy.sum(tmp, axis=1) != 0.0)[0]
if use_gpu:
templates = cmt.SparseCUDAMatrix(templates, copy_on_host=False)
info_string = ''
if comm.rank == 0:
if use_gpu:
info_string = "using %d GPUs" % comm.size
else:
info_string = "using %d CPUs" % comm.size
comm.Barrier()
c_overlap = io.get_overlaps(params, nb_cpu=nb_cpu, nb_gpu=nb_gpu, use_gpu=use_gpu)
over_shape = c_overlap.get('over_shape')[:]
n_over = int(numpy.sqrt(over_shape[0]))
s_over = over_shape[1]
# # If the number of overlaps is different from templates, we need to recompute them.
if n_over != N_tm:
if comm.rank == 0:
print_and_log(['Templates have been modified, recomputing the overlaps...'], 'default', logger)
c_overlap = io.get_overlaps(params, erase=True, nb_cpu=nb_cpu, nb_gpu=nb_gpu, use_gpu=use_gpu)
over_shape = c_overlap.get('over_shape')[:]
n_over = int(numpy.sqrt(over_shape[0]))
s_over = over_shape[1]
if SHARED_MEMORY:
c_overs, _ = io.load_data_memshared(params, 'overlaps')
else:
c_overs = io.load_data(params, 'overlaps')
comm.Barrier()
if n_tm == 0:
if comm.rank == 0:
print_and_log(["No templates present. Redo clustering?"], 'default', logger)
sys.exit(0)
if comm.rank == 0:
print_and_log(["Here comes the SpyKING CIRCUS %s and %d templates..." % (info_string, n_tm)], 'default', logger)
purge(file_out_suff, '.data')
if do_spatial_whitening:
spatial_whitening = io.load_data(params, 'spatial_whitening')
else:
spatial_whitening = None # default assignment (for PyCharm code inspection)
if do_temporal_whitening:
temporal_whitening = io.load_data(params, 'temporal_whitening')
else:
temporal_whitening = None # default assignment (for PyCharm code inspection)
if full_gpu:
try:
# If memory on the GPU is large enough, we load the overlaps onto it
for i in range(n_over):
c_overs[i] = cmt.SparseCUDAMatrix(c_overs[i], copy_on_host=False)
except Exception:
if comm.rank == 0:
print_and_log(["Not enough memory on GPUs: GPUs are used for projection only"], 'info', logger)
for i in range(n_over):
if i in c_overs:
del c_overs[i]
full_gpu = False
nb_chunks, last_chunk_len = data_file.analyze(chunk_size)
processed_chunks = int(min(nb_chunks, max_chunk))
comm.Barrier()
spiketimes_file = open(file_out_suff + '.spiketimes-%d.data' % comm.rank, 'wb')
comm.Barrier()
amplitudes_file = open(file_out_suff + '.amplitudes-%d.data' % comm.rank, 'wb')
comm.Barrier()
templates_file = open(file_out_suff + '.templates-%d.data' % comm.rank, 'wb')
comm.Barrier()
if collect_all:
garbage_times_file = open(file_out_suff + '.gspiketimes-%d.data' % comm.rank, 'wb')
comm.Barrier()
garbage_temp_file = open(file_out_suff + '.gtemplates-%d.data' % comm.rank, 'wb')
comm.Barrier()
else:
garbage_times_file = None # default assignment (for PyCharm code inspection)
garbage_temp_file = None # default assignment (for PyCharm code inspection)
if debug:
# Open debug files.
chunk_nbs_debug_file = open(file_out_suff + '.chunk_nbs_debug_%d.data' % comm.rank, mode='wb')
comm.Barrier()
iteration_nbs_debug_file = open(file_out_suff + '.iteration_nbs_debug_%d.data' % comm.rank, mode='wb')
comm.Barrier()
peak_nbs_debug_file = open(file_out_suff + '.peak_nbs_debug_%d.data' % comm.rank, mode='wb')
comm.Barrier()
peak_local_time_steps_debug_file = open(
file_out_suff + '.peak_local_time_steps_debug_%d.data' % comm.rank, mode='wb'
)
comm.Barrier()
peak_time_steps_debug_file = open(file_out_suff + '.peak_time_steps_debug_%d.data' % comm.rank, mode='wb')
comm.Barrier()
peak_scalar_products_debug_file = open(
file_out_suff + '.peak_scalar_products_debug_%d.data' % comm.rank, mode='wb'
)
comm.Barrier()
peak_solved_flags_debug_file = open(file_out_suff + '.peak_solved_flags_debug_%d.data' % comm.rank, mode='wb')
comm.Barrier()
template_nbs_debug_file = open(file_out_suff + '.template_nbs_debug_%d.data' % comm.rank, mode='wb')
comm.Barrier()
success_flags_debug_file = open(file_out_suff + '.success_flags_debug_%d.data' % comm.rank, mode='wb')
comm.Barrier()
else:
chunk_nbs_debug_file = None # default assignment (for PyCharm code inspection)
iteration_nbs_debug_file = None # default assignment (for PyCharm code inspection)
peak_nbs_debug_file = None # default assignment (for PyCharm code inspection)
peak_local_time_steps_debug_file = None # default assignment (for PyCharm code inspection)
peak_time_steps_debug_file = None # default assignment (for PyCharm code inspection)
peak_scalar_products_debug_file = None # default assignment (for PyCharm code inspection)
peak_solved_flags_debug_file = None # default assignment (for PyCharm code inspection)
template_nbs_debug_file = None # default assignment (for PyCharm code inspection)
success_flags_debug_file = None # default assignment (for PyCharm code inspection)
if use_gpu and do_spatial_whitening:
spatial_whitening = cmt.CUDAMatrix(spatial_whitening, copy_on_host=False)
last_chunk_size = 0
slice_indices = numpy.zeros(0, dtype=numpy.int32)
to_explore = range(comm.rank, processed_chunks, comm.size)
if comm.rank == 0:
to_explore = get_tqdm_progressbar(params, to_explore)
for gcount, gidx in enumerate(to_explore):
# print "Node", comm.rank, "is analyzing chunk", gidx, "/", nb_chunks, " ..."
# # We need to deal with the borders by taking chunks of size [0, chunck_size + template_shift].
is_first = data_file.is_first_chunk(gidx, nb_chunks)
is_last = data_file.is_last_chunk(gidx, nb_chunks)
if not (is_first and is_last):
if is_last:
padding = (-temp_3_shift, 0)
elif is_first:
padding = (0, temp_3_shift)
else:
padding = (-temp_3_shift, temp_3_shift)
else:
padding = (0, 0)
result = {
'spiketimes': [],
'amplitudes': [],
'templates': [],
}
result_debug = {
'chunk_nbs': [],
'iteration_nbs': [],
'peak_nbs': [],
'peak_local_time_steps': [],
'peak_time_steps': [],
'peak_scalar_products': [],
'peak_solved_flags': [],
'template_nbs': [],
'success_flags': [],
}
local_chunk, t_offset = data_file.get_data(gidx, chunk_size, padding, nodes=nodes)
len_chunk = len(local_chunk)
if do_spatial_whitening:
if use_gpu:
local_chunk = cmt.CUDAMatrix(local_chunk, copy_on_host=False)
local_chunk = local_chunk.dot(spatial_whitening).asarray()
else:
local_chunk = numpy.dot(local_chunk, spatial_whitening)
if do_temporal_whitening:
local_chunk = scipy.ndimage.filters.convolve1d(local_chunk, temporal_whitening, axis=0, mode='constant')
# Extracting peaks.
all_found_spikes = {}
if collect_all:
for i in range(n_e):
all_found_spikes[i] = []
local_peaktimes = [numpy.empty(0, dtype=numpy.uint32)]
if matched_filter:
if sign_peaks in ['positive', 'both']:
filter_chunk = scipy.ndimage.filters.convolve1d(local_chunk, waveform_pos, axis=0, mode='constant')
for i in range(n_e):
peaktimes = scipy.signal.find_peaks(filter_chunk[:, i], height=matched_thresholds_pos[i])[0]
local_peaktimes.append(peaktimes)
if collect_all:
all_found_spikes[i] += peaktimes.tolist()
if sign_peaks in ['negative', 'both']:
filter_chunk = scipy.ndimage.filters.convolve1d(local_chunk, waveform_neg, axis=0, mode='constant')
for i in range(n_e):
peaktimes = scipy.signal.find_peaks(filter_chunk[:, i], height=matched_thresholds_neg[i])[0]
local_peaktimes.append(peaktimes)
if collect_all:
all_found_spikes[i] += peaktimes.tolist()
local_peaktimes = numpy.concatenate(local_peaktimes)
else:
for i in range(n_e):
if sign_peaks == 'negative':
peaktimes = scipy.signal.find_peaks(-local_chunk[:, i], height=thresholds[i])[0]
elif sign_peaks == 'positive':
peaktimes = scipy.signal.find_peaks(local_chunk[:, i], height=thresholds[i])[0]
elif sign_peaks == 'both':
peaktimes = scipy.signal.find_peaks(numpy.abs(local_chunk[:, i]), height=thresholds[i])[0]
else:
raise ValueError("Unexpected value %s" % sign_peaks)
local_peaktimes.append(peaktimes)
if collect_all:
all_found_spikes[i] += peaktimes.tolist()
local_peaktimes = numpy.concatenate(local_peaktimes)
local_peaktimes = numpy.unique(local_peaktimes)
g_offset = t_offset + padding[0]
if ignore_dead_times:
dead_indices = numpy.searchsorted(all_dead_times, [t_offset, t_offset + chunk_size])
if dead_indices[0] != dead_indices[1]:
is_included = numpy.in1d(local_peaktimes + g_offset, all_dead_times[dead_indices[0]:dead_indices[1]])
local_peaktimes = local_peaktimes[~is_included]
local_peaktimes = numpy.sort(local_peaktimes)
else:
dead_indices = None # default assignment (for PyCharm code inspection)
# print "Removing the useless borders..."
local_borders = (template_shift, len_chunk - template_shift)
idx = (local_peaktimes >= local_borders[0]) & (local_peaktimes < local_borders[1])
local_peaktimes = numpy.compress(idx, local_peaktimes)
if collect_all:
for i in range(n_e):
all_found_spikes[i] = numpy.array(all_found_spikes[i], dtype=numpy.uint32)
if ignore_dead_times:
if dead_indices[0] != dead_indices[1]:
is_included = numpy.in1d(
all_found_spikes[i] + g_offset, all_dead_times[dead_indices[0]:dead_indices[1]]
)
all_found_spikes[i] = all_found_spikes[i][~is_included]
all_found_spikes[i] = numpy.sort(all_found_spikes[i])
idx = (all_found_spikes[i] >= local_borders[0]) & (all_found_spikes[i] < local_borders[1])
all_found_spikes[i] = numpy.compress(idx, all_found_spikes[i])
nb_local_peak_times = len(local_peaktimes)
if full_gpu:
# all_indices = cmt.CUDAMatrix(all_indices)
# tmp_gpu = cmt.CUDAMatrix(local_peaktimes.reshape((1, nb_local_peak_times)), copy_on_host=False)
_ = cmt.CUDAMatrix(local_peaktimes.reshape((1, nb_local_peak_times)), copy_on_host=False)
if nb_local_peak_times > 0:
# print "Computing the b (should full_gpu by putting all chunks on GPU if possible?)..."
if collect_all:
c_local_chunk = local_chunk.copy()
else:
c_local_chunk = None # default assignment (for PyCharm code inspection)
sub_mat = local_chunk[local_peaktimes[:, None] + temp_window]
sub_mat = sub_mat.transpose(2, 1, 0).reshape(size_window, nb_local_peak_times)
del local_chunk
if use_gpu:
sub_mat = cmt.CUDAMatrix(sub_mat, copy_on_host=False)
b = cmt.sparse_dot(templates, sub_mat)
else:
b = templates.dot(sub_mat)
del sub_mat
local_restriction = (t_offset, t_offset + chunk_size)
all_spikes = local_peaktimes + g_offset
# Because for GPU, slicing by columns is more efficient, we need to transpose b
# b = b.transpose()
if use_gpu and not full_gpu:
b = b.asarray()
failure = numpy.zeros(nb_local_peak_times, dtype=numpy.int32)
if full_gpu:
mask = numpy.zeros((2 * n_tm, nb_local_peak_times), dtype=numpy.float32)
mask[:n_tm, :] = 1
# data = cmt.empty(mask.shape)
_ = cmt.empty(mask.shape)
patch_gpu = b.shape[1] == 1
else:
patch_gpu = None
if collect_all:
c_all_times = numpy.zeros((len_chunk, n_e), dtype=numpy.bool)
c_min_times = numpy.maximum(numpy.arange(len_chunk) - template_shift, 0)
c_max_times = numpy.minimum(numpy.arange(len_chunk) + template_shift + 1, len_chunk)
for i in range(n_e):
c_all_times[all_found_spikes[i], i] = True
else:
c_all_times = None # default assignment (for PyCharm code inspection)
c_min_times = None # default assignment (for PyCharm code inspection)
c_max_times = None # default assignment (for PyCharm code inspection)
iteration_nb = 0
local_max = 0
numerous_argmax = False
nb_argmax = n_tm
best_indices = numpy.zeros(0, dtype=numpy.int32)
data = b[:n_tm, :]
flatten_data = data.ravel()
while numpy.mean(failure) < total_nb_chances:
# Is there a way to update sub_b * mask at the same time?
if full_gpu:
b_array = b.asarray()
else:
b_array = None
if numerous_argmax:
if len(best_indices) == 0:
best_indices = largest_indices(flatten_data, nb_argmax)
best_template_index, peak_index = numpy.unravel_index(best_indices[0], data.shape)
else:
best_template_index, peak_index = numpy.unravel_index(data.argmax(), data.shape)
peak_scalar_product = data[best_template_index, peak_index]
best_template2_index = best_template_index + n_tm
if templates_normalization:
if full_gpu:
best_amp = b_array[best_template_index, peak_index] / n_scalar
best_amp2 = b_array[best_template2_index, peak_index] / n_scalar
else:
best_amp = b[best_template_index, peak_index] / n_scalar
if two_components:
best_amp2 = b[best_template2_index, peak_index] / n_scalar
else:
best_amp2 = 0.0
best_amp_n = best_amp / norm_templates[best_template_index]
best_amp2_n = best_amp2 / norm_templates[best_template2_index]
else:
if full_gpu:
best_amp = b_array[best_template_index, peak_index]
best_amp = best_amp / norm_templates_2[best_template_index]
# TODO is `best_amp` value correct?
best_amp2 = b_array[best_template2_index, peak_index]
best_amp2 = best_amp2 / norm_templates_2[best_template2_index]
# TODO is `best_amp2` value correct?
else:
best_amp = b[best_template_index, peak_index]
best_amp = best_amp / norm_templates_2[best_template_index]
# TODO is `best_amp` value correct?
if two_components:
best_amp2 = b[best_template2_index, peak_index]
best_amp2 = best_amp2 / norm_templates_2[best_template2_index]
# TODO is `best_amp2` value correct?
else:
best_amp2 = 0.0
best_amp_n = best_amp
best_amp2_n = best_amp2
# Verify amplitude constraint.
a_min, a_max = amp_limits[best_template_index, :]
if (a_min <= best_amp_n) & (best_amp_n <= a_max):
# Keep the matching.
peak_time_step = local_peaktimes[peak_index]
peak_data = (local_peaktimes - peak_time_step).astype(np.int32)
is_neighbor = np.where(np.abs(peak_data) <= temp_2_shift)[0]
idx_neighbor = peak_data[is_neighbor] + temp_2_shift
nb_neighbors = len(is_neighbor)
indices = np.zeros((s_over, nb_neighbors), dtype=np.int32)
indices[idx_neighbor, np.arange(nb_neighbors)] = 1
if full_gpu:
indices = cmt.CUDAMatrix(indices, copy_on_host=False)
if patch_gpu:
b_lines = b.get_col_slice(0, b.shape[0])
else:
b_lines = b.get_col_slice(is_neighbor[0], is_neighbor[-1]+1)
tmp1 = cmt.sparse_dot(c_overs[best_template_index], indices, mult=-best_amp)
tmp2 = cmt.sparse_dot(c_overs[best_template2_index], indices, mult=-best_amp2)
b_lines.add(tmp1.add(tmp2))
del tmp1, tmp2
else:
tmp1 = c_overs[best_template_index].multiply(-best_amp)
if numpy.abs(best_amp2) > min_second_component:
tmp1 += c_overs[best_template2_index].multiply(-best_amp2)
b[:, is_neighbor] += tmp1.dot(indices)
numerous_argmax = False
# Add matching to the result.
t_spike = all_spikes[peak_index]
if (t_spike >= local_restriction[0]) and (t_spike < local_restriction[1]):
result['spiketimes'] += [t_spike]
result['amplitudes'] += [(best_amp_n, best_amp2_n)]
result['templates'] += [best_template_index]
# Mark current matching as tried.
b[best_template_index, peak_index] = -numpy.inf
# Save debug data.
if debug:
result_debug['chunk_nbs'] += [gidx]
result_debug['iteration_nbs'] += [iteration_nb]
result_debug['peak_nbs'] += [peak_index]
result_debug['peak_local_time_steps'] += [local_peaktimes[peak_index]]
result_debug['peak_time_steps'] += [all_spikes[peak_index]]
result_debug['peak_scalar_products'] += [peak_scalar_product]
result_debug['peak_solved_flags'] += [b[best_template_index, peak_index]]
result_debug['template_nbs'] += [best_template_index]
result_debug['success_flags'] += [True]
else:
# Reject the matching.
numerous_argmax = True
# Update failure counter of the peak.
failure[peak_index] += 1
# If the maximal number of failures is reached then mark peak as solved (i.e. not fitted).
if failure[peak_index] >= total_nb_chances:
# Mark all the matching associated to the current peak as tried.
b[:, peak_index] = -numpy.inf
index = numpy.arange(n_tm) * nb_local_peak_times + peak_index
else:
# Mark current matching as tried.
b[best_template_index, peak_index] = -numpy.inf
index = best_template_index * nb_local_peak_times + peak_index
if numerous_argmax:
best_indices = best_indices[~numpy.in1d(best_indices, index)]
# Save debug data.
if debug:
result_debug['chunk_nbs'] += [gidx]
result_debug['iteration_nbs'] += [iteration_nb]
result_debug['peak_nbs'] += [peak_index]
result_debug['peak_local_time_steps'] += [local_peaktimes[peak_index]]
result_debug['peak_time_steps'] += [all_spikes[peak_index]]
result_debug['peak_scalar_products'] += [peak_scalar_product]
result_debug['peak_solved_flags'] += [b[best_template_index, peak_index]]
result_debug['template_nbs'] += [best_template_index]
result_debug['success_flags'] += [False]
iteration_nb += 1
spikes_to_write = numpy.array(result['spiketimes'], dtype=numpy.uint32)
amplitudes_to_write = numpy.array(result['amplitudes'], dtype=numpy.float32)
templates_to_write = numpy.array(result['templates'], dtype=numpy.uint32)
spiketimes_file.write(spikes_to_write.tostring())
amplitudes_file.write(amplitudes_to_write.tostring())
templates_file.write(templates_to_write.tostring())
if collect_all:
for temp, spike in zip(templates_to_write, spikes_to_write - g_offset):
c_all_times[c_min_times[spike]:c_max_times[spike], neighbors[temp]] = False
gspikes = numpy.where(numpy.sum(c_all_times, 1) > 0)[0]
c_all_times = numpy.take(c_all_times, gspikes, axis=0)
c_local_chunk = numpy.take(c_local_chunk, gspikes, axis=0) * c_all_times
if sign_peaks == 'negative':
bestlecs = numpy.argmin(c_local_chunk, 1)
if matched_filter:
threshs = -matched_thresholds_neg[bestlecs]
else:
threshs = -thresholds[bestlecs]
idx = numpy.where(numpy.min(c_local_chunk, 1) < threshs)[0]
elif sign_peaks == 'positive':
bestlecs = numpy.argmax(c_local_chunk, 1)
if matched_filter:
threshs = matched_thresholds_pos[bestlecs]
else:
threshs = thresholds[bestlecs]
idx = numpy.where(numpy.max(c_local_chunk, 1) > threshs)[0]
elif sign_peaks == 'both':
c_local_chunk = numpy.abs(c_local_chunk)
bestlecs = numpy.argmax(c_local_chunk, 1)
if matched_filter:
threshs = numpy.minimum(matched_thresholds_neg[bestlecs], matched_thresholds_pos[bestlecs])
else:
threshs = thresholds[bestlecs]
idx = numpy.where(numpy.max(c_local_chunk, 1) > threshs)[0]
else:
raise ValueError("Unexpected value %s" % sign_peaks)
gspikes = numpy.take(gspikes, idx)
bestlecs = numpy.take(bestlecs, idx)
gspikes_to_write = numpy.array(gspikes + g_offset, dtype=numpy.uint32)
gtemplates_to_write = numpy.array(bestlecs, dtype=numpy.uint32)
garbage_times_file.write(gspikes_to_write.tostring())
garbage_temp_file.write(gtemplates_to_write.tostring())
if debug:
# Write debug data to debug files.
for field_label, field_dtype, field_file in [
('chunk_nbs', numpy.uint32, chunk_nbs_debug_file),
('iteration_nbs', numpy.uint32, iteration_nbs_debug_file),
('peak_nbs', numpy.uint32, peak_nbs_debug_file),
('peak_local_time_steps', numpy.uint32, peak_local_time_steps_debug_file),
('peak_time_steps', numpy.uint32, peak_time_steps_debug_file),
('peak_scalar_products', numpy.float32, peak_scalar_products_debug_file),
('peak_solved_flags', numpy.float32, peak_solved_flags_debug_file),
('template_nbs', numpy.uint32, template_nbs_debug_file),
('success_flags', numpy.bool, success_flags_debug_file),
]:
field_to_write = numpy.array(result_debug[field_label], dtype=field_dtype)
field_file.write(field_to_write.tostring())
if full_gpu:
del b, data
sys.stderr.flush()
spiketimes_file.flush()
os.fsync(spiketimes_file.fileno())
spiketimes_file.close()
amplitudes_file.flush()
os.fsync(amplitudes_file.fileno())
amplitudes_file.close()
templates_file.flush()
os.fsync(templates_file.fileno())
templates_file.close()
if collect_all:
garbage_temp_file.flush()
os.fsync(garbage_temp_file.fileno())
garbage_temp_file.close()
garbage_times_file.flush()
os.fsync(garbage_times_file.fileno())
garbage_times_file.close()
if debug:
# Close debug files.
for field_file in [
chunk_nbs_debug_file,
iteration_nbs_debug_file,
peak_nbs_debug_file,
peak_local_time_steps_debug_file,
peak_time_steps_debug_file,
peak_scalar_products_debug_file,
peak_solved_flags_debug_file,
template_nbs_debug_file,
success_flags_debug_file,
]:
field_file.flush()
os.fsync(field_file.fileno())
field_file.close()
comm.Barrier()
if comm.rank == 0:
io.collect_data(comm.size, params, erase=True)
data_file.close()
def main(params, nb_cpu, nb_gpu, use_gpu):
#################################################################
#params = detect_memory(params)
logger = init_logging(params.logfile)
SHARED_MEMORY = get_shared_memory_flag(params)
logger = logging.getLogger('circus.fitting')
data_file = params.data_file
N_e = params.getint('data', 'N_e')
N_total = params.nb_channels
N_t = params.getint('detection', 'N_t')
template_shift = params.getint('detection', 'template_shift')
file_out = params.get('data', 'file_out')
file_out_suff = params.get('data', 'file_out_suff')
sign_peaks = params.get('detection', 'peaks')
matched_filter = params.getboolean('detection', 'matched-filter')
spike_thresh = params.getfloat('detection', 'spike_thresh')
do_temporal_whitening = params.getboolean('whitening', 'temporal')
do_spatial_whitening = params.getboolean('whitening', 'spatial')
chunk_size = detect_memory(params, fitting=True)
gpu_only = params.getboolean('fitting', 'gpu_only')
nodes, edges = get_nodes_and_edges(params)
tmp_limits = params.get('fitting',
'amp_limits').replace('(',
'').replace(')',
'').split(',')
tmp_limits = map(float, tmp_limits)
amp_auto = params.getboolean('fitting', 'amp_auto')
nb_chances = params.getint('fitting', 'nb_chances')
max_chunk = params.getfloat('fitting', 'max_chunk')
noise_thr = params.getfloat('clustering', 'noise_thr')
collect_all = params.getboolean('fitting', 'collect_all')
ignore_dead_times = params.getboolean('triggers', 'ignore_times')
inv_nodes = numpy.zeros(N_total, dtype=numpy.int32)
inv_nodes[nodes] = numpy.arange(len(nodes))
data_file.open()
#################################################################
if use_gpu:
import cudamat as cmt
## Need to properly handle multi GPU per MPI nodes?
if nb_gpu > nb_cpu:
gpu_id = int(comm.rank // nb_cpu)
else:
gpu_id = 0
cmt.cuda_set_device(gpu_id)
cmt.init()
cmt.cuda_sync_threads()
if SHARED_MEMORY:
templates = io.load_data_memshared(params,
'templates',
normalize=True,
transpose=True)
N_tm, x = templates.shape
else:
templates = io.load_data(params, 'templates')
x, N_tm = templates.shape
temp_2_shift = 2 * template_shift
full_gpu = use_gpu and gpu_only
n_tm = N_tm // 2
n_scalar = N_e * N_t
temp_window = numpy.arange(-template_shift, template_shift + 1)
size_window = N_e * (2 * template_shift + 1)
if not amp_auto:
amp_limits = numpy.zeros((n_tm, 2))
amp_limits[:, 0] = tmp_limits[0]
amp_limits[:, 1] = tmp_limits[1]
else:
amp_limits = io.load_data(params, 'limits')
norm_templates = io.load_data(params, 'norm-templates')
if not SHARED_MEMORY:
for idx in xrange(templates.shape[1]):
myslice = numpy.arange(templates.indptr[idx],
templates.indptr[idx + 1])
templates.data[myslice] /= norm_templates[idx]
templates = templates.T
if matched_filter:
if sign_peaks in ['negative', 'both']:
waveform_neg = io.load_data(params, 'waveform')
waveform_neg /= (numpy.abs(numpy.sum(waveform_neg)) *
len(waveform_neg))
matched_tresholds_neg = io.load_data(params, 'matched-thresholds')
if sign_peaks in ['positive', 'both']:
waveform_pos = io.load_data(params, 'waveform-pos')
waveform_pos /= (numpy.abs(numpy.sum(waveform_pos)) *
len(waveform_pos))
matched_tresholds_pos = io.load_data(params,
'matched-thresholds-pos')
if ignore_dead_times:
all_dead_times = get_dead_times(params)
thresholds = io.load_data(params, 'thresholds')
if collect_all:
neighbors = {}
for i in xrange(n_tm):
tmp = templates[i, :].toarray().reshape(N_e,
N_t) * norm_templates[i]
neighbors[i] = numpy.where(numpy.sum(tmp, 1) != 0)[0]
if use_gpu:
templates = cmt.SparseCUDAMatrix(templates, copy_on_host=False)
info_string = ''
if comm.rank == 0:
if use_gpu:
info_string = "using %d GPUs" % (comm.size)
else:
info_string = "using %d CPUs" % (comm.size)
comm.Barrier()
c_overlap = io.get_overlaps(params,
nb_cpu=nb_cpu,
nb_gpu=nb_gpu,
use_gpu=use_gpu)
over_shape = c_overlap.get('over_shape')[:]
N_over = int(numpy.sqrt(over_shape[0]))
S_over = over_shape[1]
## If the number of overlaps is different from templates, we need to recompute them
if N_over != N_tm:
if comm.rank == 0:
print_and_log(
['Templates have been modified, recomputing the overlaps...'],
'default', logger)
c_overlap = io.get_overlaps(params,
erase=True,
nb_cpu=nb_cpu,
nb_gpu=nb_gpu,
use_gpu=use_gpu)
over_shape = c_overlap.get('over_shape')[:]
N_over = int(numpy.sqrt(over_shape[0]))
S_over = over_shape[1]
if SHARED_MEMORY:
c_overs = io.load_data_memshared(params, 'overlaps')
else:
c_overs = io.load_data(params, 'overlaps')
comm.Barrier()
if n_tm == 0:
if comm.rank == 0:
print_and_log(["No templates present. Redo clustering?"],
'default', logger)
sys.exit(0)
if comm.rank == 0:
print_and_log([
"Here comes the SpyKING CIRCUS %s and %d templates..." %
(info_string, n_tm)
], 'default', logger)
purge(file_out_suff, '.data')
if do_spatial_whitening:
spatial_whitening = io.load_data(params, 'spatial_whitening')
if do_temporal_whitening:
temporal_whitening = io.load_data(params, 'temporal_whitening')
if full_gpu:
try:
# If memory on the GPU is large enough, we load the overlaps onto it
for i in xrange(N_over):
c_overs[i] = cmt.SparseCUDAMatrix(c_overs[i],
copy_on_host=False)
except Exception:
if comm.rank == 0:
print_and_log([
"Not enough memory on GPUs: GPUs are used for projection only"
], 'info', logger)
for i in xrange(N_over):
if c_overs.has_key(i):
del c_overs[i]
full_gpu = False
nb_chunks, last_chunk_len = data_file.analyze(chunk_size)
processed_chunks = int(min(nb_chunks, max_chunk))
comm.Barrier()
spiketimes_file = open(file_out_suff + '.spiketimes-%d.data' % comm.rank,
'wb')
comm.Barrier()
amplitudes_file = open(file_out_suff + '.amplitudes-%d.data' % comm.rank,
'wb')
comm.Barrier()
templates_file = open(file_out_suff + '.templates-%d.data' % comm.rank,
'wb')
comm.Barrier()
if collect_all:
garbage_times_file = open(
file_out_suff + '.gspiketimes-%d.data' % comm.rank, 'wb')
comm.Barrier()
garbage_temp_file = open(
file_out_suff + '.gtemplates-%d.data' % comm.rank, 'wb')
comm.Barrier()
if use_gpu and do_spatial_whitening:
spatial_whitening = cmt.CUDAMatrix(spatial_whitening,
copy_on_host=False)
last_chunk_size = 0
to_explore = xrange(comm.rank, processed_chunks, comm.size)
if comm.rank == 0:
to_explore = get_tqdm_progressbar(to_explore)
for gcount, gidx in enumerate(to_explore):
#print "Node", comm.rank, "is analyzing chunk", gidx, "/", nb_chunks, " ..."
## We need to deal with the borders by taking chunks of size [0, chunck_size+template_shift]
is_first = data_file.is_first_chunk(gidx, nb_chunks)
is_last = data_file.is_last_chunk(gidx, nb_chunks)
if is_last:
padding = (-temp_2_shift, 0)
elif is_first:
padding = (0, temp_2_shift)
else:
padding = (-temp_2_shift, temp_2_shift)
result = {'spiketimes': [], 'amplitudes': [], 'templates': []}
local_chunk, t_offset = data_file.get_data(gidx,
chunk_size,
padding,
nodes=nodes)
len_chunk = len(local_chunk)
if do_spatial_whitening:
if use_gpu:
local_chunk = cmt.CUDAMatrix(local_chunk, copy_on_host=False)
local_chunk = local_chunk.dot(spatial_whitening).asarray()
else:
local_chunk = numpy.dot(local_chunk, spatial_whitening)
if do_temporal_whitening:
local_chunk = scipy.ndimage.filters.convolve1d(local_chunk,
temporal_whitening,
axis=0,
mode='constant')
#print "Extracting the peaks..."
if collect_all:
all_found_spikes = {}
for i in xrange(N_e):
all_found_spikes[i] = []
local_peaktimes = numpy.zeros(0, dtype=numpy.uint32)
if matched_filter:
if sign_peaks in ['positive', 'both']:
filter_chunk = scipy.ndimage.filters.convolve1d(
local_chunk, waveform_pos, axis=0, mode='constant')
for i in xrange(N_e):
peaktimes = algo.detect_peaks(filter_chunk[:, i],
matched_tresholds_pos[i])
local_peaktimes = numpy.concatenate(
(local_peaktimes, peaktimes))
if collect_all:
all_found_spikes[i] += peaktimes.tolist()
if sign_peaks in ['negative', 'both']:
filter_chunk = scipy.ndimage.filters.convolve1d(
local_chunk, waveform_neg, axis=0, mode='constant')
for i in xrange(N_e):
peaktimes = algo.detect_peaks(filter_chunk[:, i],
matched_tresholds_neg[i])
local_peaktimes = numpy.concatenate(
(local_peaktimes, peaktimes))
if collect_all:
all_found_spikes[i] += peaktimes.tolist()
else:
for i in xrange(N_e):
if sign_peaks == 'negative':
peaktimes = algo.detect_peaks(local_chunk[:, i],
thresholds[i],
valley=True)
elif sign_peaks == 'positive':
peaktimes = algo.detect_peaks(local_chunk[:, i],
thresholds[i],
valley=False)
elif sign_peaks == 'both':
peaktimes = algo.detect_peaks(numpy.abs(local_chunk[:, i]),
thresholds[i],
valley=False)
local_peaktimes = numpy.concatenate(
(local_peaktimes, peaktimes))
if collect_all:
all_found_spikes[i] += peaktimes.tolist()
local_peaktimes = numpy.unique(local_peaktimes)
g_offset = t_offset + padding[0]
if ignore_dead_times:
dead_indices = numpy.searchsorted(
all_dead_times, [t_offset, t_offset + chunk_size])
if dead_indices[0] != dead_indices[1]:
local_peaktimes = numpy.array(list(
set(local_peaktimes + g_offset).difference(
all_dead_times[dead_indices[0]:dead_indices[1]])),
dtype=numpy.uint32) - g_offset
local_peaktimes = numpy.sort(local_peaktimes)
#print "Removing the useless borders..."
local_borders = (template_shift, len_chunk - template_shift)
idx = (local_peaktimes >= local_borders[0]) & (local_peaktimes <
local_borders[1])
local_peaktimes = numpy.compress(idx, local_peaktimes)
if collect_all:
for i in xrange(N_e):
all_found_spikes[i] = numpy.array(all_found_spikes[i],
dtype=numpy.uint32)
if ignore_dead_times:
if dead_indices[0] != dead_indices[1]:
all_found_spikes[i] = numpy.array(
list(
set(all_found_spikes[i] + g_offset).difference(
all_dead_times[
dead_indices[0]:dead_indices[1]])),
dtype=numpy.uint32) - g_offset
all_found_spikes[i] = numpy.sort(all_found_spikes[i])
idx = (all_found_spikes[i] >= local_borders[0]) & (
all_found_spikes[i] < local_borders[1])
all_found_spikes[i] = numpy.compress(idx, all_found_spikes[i])
n_t = len(local_peaktimes)
if full_gpu:
# all_indices = cmt.CUDAMatrix(all_indices)
tmp_gpu = cmt.CUDAMatrix(local_peaktimes.reshape((1, n_t)),
copy_on_host=False)
if n_t > 0:
#print "Computing the b (should full_gpu by putting all chunks on GPU if possible?)..."
if collect_all:
c_local_chunk = local_chunk.copy()
local_chunk = local_chunk.T.ravel()
sub_mat = numpy.zeros((size_window, n_t), dtype=numpy.float32)
if len_chunk != last_chunk_size:
slice_indices = numpy.zeros(0, dtype=numpy.int32)
for idx in xrange(N_e):
slice_indices = numpy.concatenate(
(slice_indices, len_chunk * idx + temp_window))
last_chunk_size = len_chunk
for count, idx in enumerate(local_peaktimes):
sub_mat[:, count] = numpy.take(local_chunk,
slice_indices + idx)
del local_chunk
if use_gpu:
sub_mat = cmt.CUDAMatrix(sub_mat, copy_on_host=False)
b = cmt.sparse_dot(templates, sub_mat)
else:
b = templates.dot(sub_mat)
del sub_mat
local_restriction = (t_offset, t_offset + chunk_size)
all_spikes = local_peaktimes + g_offset
# Because for GPU, slicing by columns is more efficient, we need to transpose b
#b = b.transpose()
if use_gpu and not full_gpu:
b = b.asarray()
failure = numpy.zeros(n_t, dtype=numpy.int32)
if full_gpu:
mask = numpy.zeros((2 * n_tm, n_t), dtype=numpy.float32)
mask[:n_tm, :] = 1
data = cmt.empty(mask.shape)
patch_gpu = b.shape[1] == 1
else:
mask = numpy.ones((n_tm, n_t), dtype=numpy.float32)
sub_b = b[:n_tm, :]
if collect_all:
c_all_times = numpy.zeros((len_chunk, N_e), dtype=numpy.bool)
c_min_times = numpy.maximum(
numpy.arange(len_chunk) - template_shift, 0)
c_max_times = numpy.minimum(
numpy.arange(len_chunk) + template_shift + 1, len_chunk)
for i in xrange(N_e):
c_all_times[all_found_spikes[i], i] = True
while (numpy.mean(failure) < nb_chances):
if full_gpu:
gpu_mask = cmt.CUDAMatrix(mask, copy_on_host=False)
b.mult(gpu_mask, data)
tmp_mat = data.max(0)
argmax_bi = numpy.argsort(tmp_mat.asarray()[0, :])[::-1]
del tmp_mat
else:
data = sub_b * mask
argmax_bi = numpy.argsort(numpy.max(data, 0))[::-1]
for peak_index in argmax_bi:
if full_gpu:
b_array = b.asarray()
sub_b = b_array[:n_tm, :]
peak_scalar_products = np.take(sub_b, peak_index, axis=1)
best_template_index = np.argmax(peak_scalar_products,
axis=0)
best_template2_index = best_template_index + n_tm
if full_gpu:
best_amp = sub_b[best_template_index,
peak_index] / n_scalar
best_amp2 = b_array[best_template_index,
peak_index] / n_scalar
else:
best_amp = sub_b[best_template_index,
peak_index] / n_scalar
best_amp2 = b[best_template2_index,
peak_index] / n_scalar
best_amp_n = best_amp / norm_templates[best_template_index]
best_amp2_n = best_amp2 / norm_templates[
best_template2_index]
# Verify amplitude constraint.
a_min = amp_limits[best_template_index, 0]
a_max = amp_limits[best_template_index, 1]
if (a_min <= best_amp_n) & (best_amp_n <= a_max):
# Keep the matching.
peak_time_step = local_peaktimes[peak_index]
data = (local_peaktimes - peak_time_step).astype(
np.int32)
is_neighbor = np.where(np.abs(data) <= temp_2_shift)[0]
idx_neighbor = data[is_neighbor] + temp_2_shift
nb_neighbors = len(is_neighbor)
indices = np.zeros((S_over, nb_neighbors),
dtype=np.int32)
indices[idx_neighbor, np.arange(nb_neighbors)] = 1
if full_gpu:
indices = cmt.CUDAMatrix(indices,
copy_on_host=False)
if patch_gpu:
b_lines = b.get_col_slice(0, b.shape[0])
else:
b_lines = b.get_col_slice(
is_neighbor[0], is_neighbor[-1] + 1)
tmp1 = cmt.sparse_dot(c_overs[best_template_index],
indices,
mult=-best_amp[keep])
tmp2 = cmt.sparse_dot(
c_overs[best_template2_index],
indices,
mult=-best_amp2[keep])
b_lines.add(tmp1.add(tmp2))
del tmp1, tmp2
else:
tmp1 = c_overs[best_template_index].multiply(
-best_amp)
tmp2 = c_overs[best_template2_index].multiply(
-best_amp2)
b[:, is_neighbor] += (tmp1 + tmp2).dot(indices)
# Add matching to the result.
t_spike = all_spikes[peak_index]
if (t_spike >= local_restriction[0]) and (
t_spike < local_restriction[1]):
#print "Accept spikes", t_spike, local_restriction, type(t_spike), t_spike > local_restriction[0], t_spike < local_restriction[1]
result['spiketimes'] += [t_spike]
result['amplitudes'] += [(best_amp_n, best_amp2_n)]
result['templates'] += [best_template_index]
# Mark current matching as tried.
mask[best_template_index, peak_index] = 0
else:
# Reject the matching.
# Update failure counter of the peak.
failure[peak_index] += 1
# If the maximal number of failures is reached then mark peak as solved (i.e. not fitted).
if failure[peak_index] == nb_chances:
mask[:, peak_index] = 0
else:
mask[best_template_index, peak_index] = 0
spikes_to_write = numpy.array(result['spiketimes'],
dtype=numpy.uint32)
amplitudes_to_write = numpy.array(result['amplitudes'],
dtype=numpy.float32)
templates_to_write = numpy.array(result['templates'],
dtype=numpy.uint32)
spiketimes_file.write(spikes_to_write.tostring())
amplitudes_file.write(amplitudes_to_write.tostring())
templates_file.write(templates_to_write.tostring())
if collect_all:
for temp, spike in zip(templates_to_write,
spikes_to_write - g_offset):
c_all_times[c_min_times[spike]:c_max_times[spike],
neighbors[temp]] = False
gspikes = numpy.where(numpy.sum(c_all_times, 1) > 0)[0]
c_all_times = numpy.take(c_all_times, gspikes, axis=0)
c_local_chunk = numpy.take(c_local_chunk, gspikes,
axis=0) * c_all_times
if sign_peaks == 'negative':
bestlecs = numpy.argmin(c_local_chunk, 1)
if matched_filter:
threshs = -matched_tresholds_neg[bestlecs]
else:
threshs = -thresholds[bestlecs]
idx = numpy.where(numpy.min(c_local_chunk, 1) < threshs)[0]
elif sign_peaks == 'positive':
bestlecs = numpy.argmax(c_local_chunk, 1)
if matched_filter:
threshs = matched_tresholds_pos[bestlecs]
else:
threshs = thresholds[bestlecs]
idx = numpy.where(numpy.max(c_local_chunk, 1) > threshs)[0]
elif sign_peaks == 'both':
c_local_chunk = numpy.abs(c_local_chunk)
bestlecs = numpy.argmax(c_local_chunk, 1)
if matched_filter:
threshs = numpy.minimum(
matched_tresholds_neg[bestlecs],
matched_tresholds_pos[bestlecs])
else:
threshs = thresholds[bestlecs]
idx = numpy.where(numpy.max(c_local_chunk, 1) > threshs)[0]
gspikes = numpy.take(gspikes, idx)
bestlecs = numpy.take(bestlecs, idx)
gspikes_to_write = numpy.array(gspikes + g_offset,
dtype=numpy.uint32)
gtemplates_to_write = numpy.array(bestlecs, dtype=numpy.uint32)
garbage_times_file.write(gspikes_to_write.tostring())
garbage_temp_file.write(gtemplates_to_write.tostring())
if full_gpu:
del gpu_mask, b, data
sys.stderr.flush()
spiketimes_file.flush()
os.fsync(spiketimes_file.fileno())
spiketimes_file.close()
amplitudes_file.flush()
os.fsync(amplitudes_file.fileno())
amplitudes_file.close()
templates_file.flush()
os.fsync(templates_file.fileno())
templates_file.close()
if collect_all:
garbage_temp_file.flush()
os.fsync(garbage_temp_file.fileno())
garbage_temp_file.close()
garbage_times_file.flush()
os.fsync(garbage_times_file.fileno())
garbage_times_file.close()
comm.Barrier()
if comm.rank == 0:
io.collect_data(comm.size, params, erase=True)
data_file.close()
def main(params, nb_cpu, nb_gpu, use_gpu):
#################################################################
# params = detect_memory(params)
_ = init_logging(params.logfile)
SHARED_MEMORY = get_shared_memory_flag(params)
logger = logging.getLogger('circus.fitting')
data_file = params.data_file
N_e = params.getint('data', 'N_e')
N_total = params.nb_channels
N_t = params.getint('detection', 'N_t')
template_shift = params.getint('detection', 'template_shift')
file_out = params.get('data', 'file_out')
file_out_suff = params.get('data', 'file_out_suff')
sign_peaks = params.get('detection', 'peaks')
dist_peaks = params.getint('detection', 'dist_peaks')
matched_filter = params.getboolean('detection', 'matched-filter')
spike_thresh = params.getfloat('detection', 'spike_thresh')
spike_width = params.getfloat('detection', 'spike_width')
do_temporal_whitening = params.getboolean('whitening', 'temporal')
do_spatial_whitening = params.getboolean('whitening', 'spatial')
chunk_size = detect_memory(params)
gpu_only = params.getboolean('fitting', 'gpu_only')
nodes, edges = get_nodes_and_edges(params)
tmp_limits = params.get('fitting',
'amp_limits').replace('(',
'').replace(')',
'').split(',')
tmp_limits = map(float, tmp_limits)
amp_auto = params.getboolean('fitting', 'amp_auto')
nb_chances = params.getint('fitting', 'nb_chances')
max_chunk = params.getfloat('fitting', 'max_chunk')
noise_thr = params.getfloat('clustering', 'noise_thr')
collect_all = params.getboolean('fitting', 'collect_all')
ignore_dead_times = params.getboolean('triggers', 'ignore_times')
inv_nodes = numpy.zeros(N_total, dtype=numpy.int32)
inv_nodes[nodes] = numpy.arange(len(nodes))
data_file.open()
#################################################################
if use_gpu:
import cudamat as cmt
# # Need to properly handle multi GPU per MPI nodes?
if nb_gpu > nb_cpu:
gpu_id = int(comm.rank // nb_cpu)
else:
gpu_id = 0
cmt.cuda_set_device(gpu_id)
cmt.init()
cmt.cuda_sync_threads()
if matched_filter:
if sign_peaks in ['negative', 'both']:
waveform_neg = io.load_data(params, 'waveform')[::-1]
waveform_neg /= (numpy.abs(numpy.sum(waveform_neg)) *
len(waveform_neg))
matched_tresholds_neg = io.load_data(params, 'matched-thresholds')
if sign_peaks in ['positive', 'both']:
waveform_pos = io.load_data(params, 'waveform-pos')[::-1]
waveform_pos /= (numpy.abs(numpy.sum(waveform_pos)) *
len(waveform_pos))
matched_tresholds_pos = io.load_data(params,
'matched-thresholds-pos')
if ignore_dead_times:
all_dead_times = get_dead_times(params)
thresholds = io.load_data(params, 'thresholds')
comm.Barrier()
if comm.rank == 0:
print_and_log(["Extracting MUA activity..."], 'default', logger)
purge(file_out_suff, '.data')
if do_spatial_whitening:
spatial_whitening = io.load_data(params, 'spatial_whitening')
else:
spatial_whitening = None # default assignment (PyCharm code inspection)
if do_temporal_whitening:
temporal_whitening = io.load_data(params, 'temporal_whitening')
else:
temporal_whitening = None # default assignment (PyCharm code inspection)
nb_chunks, last_chunk_len = data_file.analyze(chunk_size)
processed_chunks = int(min(nb_chunks, max_chunk))
comm.Barrier()
spiketimes_file = open(file_out_suff + '.mua-%d.data' % comm.rank, 'wb')
comm.Barrier()
electrodes_file = open(file_out_suff + '.elec-%d.data' % comm.rank, 'wb')
comm.Barrier()
amplitudes_file = open(file_out_suff + '.amp-%d.data' % comm.rank, 'wb')
comm.Barrier()
if use_gpu and do_spatial_whitening:
spatial_whitening = cmt.CUDAMatrix(spatial_whitening,
copy_on_host=False)
to_explore = range(comm.rank, processed_chunks, comm.size)
if comm.rank == 0:
to_explore = get_tqdm_progressbar(to_explore)
for gcount, gidx in enumerate(to_explore):
# print "Node", comm.rank, "is analyzing chunk", gidx, "/", nb_chunks, " ..."
# # We need to deal with the borders by taking chunks of size [0, chunck_size + template_shift].
is_first = data_file.is_first_chunk(gidx, nb_chunks)
is_last = data_file.is_last_chunk(gidx, nb_chunks)
if is_last:
padding = (-dist_peaks, 0)
elif is_first:
padding = (0, dist_peaks)
else:
padding = (-dist_peaks, dist_peaks)
result = {'spiketimes': [], 'amplitudes': [], 'templates': []}
local_chunk, t_offset = data_file.get_data(gidx,
chunk_size,
padding,
nodes=nodes)
len_chunk = len(local_chunk)
if do_spatial_whitening:
if use_gpu:
local_chunk = cmt.CUDAMatrix(local_chunk, copy_on_host=False)
local_chunk = local_chunk.dot(spatial_whitening).asarray()
else:
local_chunk = numpy.dot(local_chunk, spatial_whitening)
if do_temporal_whitening:
local_chunk = scipy.ndimage.filters.convolve1d(local_chunk,
temporal_whitening,
axis=0,
mode='constant')
# print "Extracting the peaks..."
local_peaktimes = [numpy.zeros(0, dtype=numpy.uint32)]
local_elecs = [numpy.zeros(0, dtype=numpy.uint32)]
local_amps = [numpy.zeros(0, dtype=numpy.float32)]
if matched_filter:
if sign_peaks in ['positive', 'both']:
filter_chunk = scipy.ndimage.filters.convolve1d(
local_chunk, waveform_pos, axis=0, mode='constant')
for i in range(N_e):
peaktimes = scipy.signal.find_peaks(
filter_chunk[:, i],
height=matched_tresholds_pos[i],
width=spike_width,
distance=dist_peaks,
wlen=N_t)[0]
local_peaktimes.append(peaktimes)
local_elecs.append(
i * numpy.ones(len(peaktimes), dtype='uint32'))
local_amps.append(filter_chunk[peaktimes, i])
if sign_peaks in ['negative', 'both']:
filter_chunk = scipy.ndimage.filters.convolve1d(
local_chunk, waveform_neg, axis=0, mode='constant')
for i in range(N_e):
peaktimes = scipy.signal.find_peaks(
filter_chunk[:, i],
height=matched_tresholds_neg[i],
width=spike_width,
distance=dist_peaks,
wlen=N_t)[0]
local_peaktimes.append(peaktimes)
local_elecs.append(
i * numpy.ones(len(peaktimes), dtype='uint32'))
local_amps.append(filter_chunk[peaktimes, i])
else:
for i in range(N_e):
if sign_peaks == 'negative':
peaktimes = scipy.signal.find_peaks(-local_chunk[:, i],
height=thresholds[i],
width=spike_width,
distance=dist_peaks,
wlen=N_t)[0]
elif sign_peaks == 'positive':
peaktimes = scipy.signal.find_peaks(local_chunk[:, i],
height=thresholds[i],
width=spike_width,
distance=dist_peaks,
wlen=N_t)[0]
elif sign_peaks == 'both':
peaktimes = scipy.signal.find_peaks(numpy.abs(
local_chunk[:, i]),
height=thresholds[i],
width=spike_width,
distance=dist_peaks,
wlen=N_t)[0]
local_peaktimes.append(peaktimes)
local_elecs.append(i *
numpy.ones(len(peaktimes), dtype='uint32'))
local_amps.append(local_chunk[peaktimes, i])
local_peaktimes = numpy.concatenate(local_peaktimes)
local_elecs = numpy.concatenate(local_elecs)
local_amps = numpy.concatenate(local_amps)
g_offset = t_offset + padding[0]
if ignore_dead_times:
dead_indices = numpy.searchsorted(
all_dead_times, [t_offset, t_offset + chunk_size])
if dead_indices[0] != dead_indices[1]:
is_included = numpy.in1d(
local_peaktimes + g_offset,
all_dead_times[dead_indices[0]:dead_indices[1]])
local_peaktimes = local_peaktimes[~is_included]
local_elecs = local_elecs[~is_included]
local_amps = local_amps[~is_included]
# print "Removing the useless borders..."
local_borders = (dist_peaks, len_chunk - dist_peaks)
idx = (local_peaktimes >= local_borders[0]) & (local_peaktimes <
local_borders[1])
local_peaktimes = numpy.compress(idx, local_peaktimes) + g_offset
local_elecs = numpy.compress(idx, local_elecs)
local_amps = numpy.compress(idx, local_amps)
spiketimes_file.write(local_peaktimes.astype(numpy.uint32).tostring())
electrodes_file.write(local_elecs.tostring())
amplitudes_file.write(local_amps.tostring())
sys.stderr.flush()
spiketimes_file.flush()
os.fsync(spiketimes_file.fileno())
spiketimes_file.close()
electrodes_file.flush()
os.fsync(electrodes_file.fileno())
electrodes_file.close()
amplitudes_file.flush()
os.fsync(amplitudes_file.fileno())
amplitudes_file.close()
comm.Barrier()
if comm.rank == 0:
io.collect_mua(comm.size, params, erase=True)
data_file.close()
def filter_file(data_file_in, data_file_out, do_filtering,
do_remove_median, do_remove_ground):
"""
Performs a high-pass and low-pass Butterworth filter on the data file.
Parameters
----------
data_file_in :
data_file_out :
do_filtering : bool
do_remove_median : bool
do_remove_median : bool
"""
try:
cut_off = params.getfloat('filtering', 'cut_off', check=False)
cut_off = [cut_off, 0.95 * (params.rate / 2.)] # Nyquist
except Exception:
cut_off = params.get('filtering', 'cut_off', check=False)
cut_off = cut_off.split(',')
try:
cut_off[0] = float(cut_off[0])
except Exception:
if comm.rank == 0:
print_and_log(
['First value of cut off must be a valid number'],
'error', logger)
sys.exit(0)
cut_off[1] = cut_off[1].replace(' ', '')
if cut_off[1] == 'auto':
cut_off[1] = 0.95 * (params.rate / 2.)
else:
try:
cut_off[1] = float(cut_off[1])
except Exception:
if comm.rank == 0:
print_and_log([
'Second value of cut off must either auto, or a valid a number'
], 'error', logger)
sys.exit(0)
chunk_size = detect_memory(params, filtering=True)
butter_order = params.getint('filtering', 'butter_order')
nb_chunks, _ = data_file_in.analyze(chunk_size)
b, a = signal.butter(butter_order,
np.array(cut_off) / (params.rate / 2.), 'pass')
all_chunks = numpy.arange(nb_chunks, dtype=numpy.int64)
to_process = all_chunks[comm.rank::comm.size]
loc_nb_chunks = len(to_process)
N_total = params.nb_channels
process_all_channels = numpy.all(nodes == numpy.arange(N_total))
if comm.rank == 0:
to_write = []
if do_filtering:
to_write += [
"Filtering with a Butterworth filter (order %d) in [%g, %g] Hz"
% (butter_order, cut_off[0], cut_off[1])
]
if do_remove_median:
to_write += [
"Median over all channels is subtracted to each channels"
]
if do_remove_ground:
to_write += [
"Channel %s is used as a reference channel" % common_ground
]
print_and_log(to_write, 'default', logger)
to_explore = xrange(comm.rank, nb_chunks, comm.size)
data_file_in.open(mode='r+')
if comm.rank == 0:
to_explore = get_tqdm_progressbar(to_explore)
for count, gidx in enumerate(to_explore):
local_chunk, t_offset = data_file_in.get_data(gidx, chunk_size)
if do_filtering:
for i in nodes:
try:
local_chunk[:, i] = signal.filtfilt(
b, a, local_chunk[:, i])
except Exception:
pass
local_chunk[:, i] -= numpy.median(local_chunk[:, i])
if do_remove_median:
if not process_all_channels:
global_median = numpy.median(
numpy.take(local_chunk, nodes, axis=1), 1)
else:
global_median = numpy.median(local_chunk, 1)
for i in nodes:
local_chunk[:, i] -= global_median
if common_ground > -1:
for i in nodes:
local_chunk[:, i] -= local_chunk[:, common_ground]
if data_file_in != data_file_out and data_file_in.is_first_chunk(
gidx, nb_chunks):
if data_file_in.is_stream:
g_offset = t_offset - numpy.sum(
data_file_in.
_times[:data_file_in.
_get_streams_index_by_time(t_offset) + 1])
else:
g_offset = t_offset - data_file_in.t_start
else:
g_offset = t_offset
data_file_out.set_data(g_offset, local_chunk)
sys.stderr.flush()
comm.Barrier()
def main(params, nb_cpu, nb_gpu, use_gpu):
# Part 1: Whitening
numpy.random.seed(420)
# params = detect_memory(params)
_ = init_logging(params.logfile)
logger = logging.getLogger('circus.whitening')
#################################################################
data_file = params.data_file
N_e = params.getint('data', 'N_e')
hdf5_compress = params.getboolean('data', 'hdf5_compress')
N_total = params.nb_channels
N_t = params.getint('detection', 'N_t')
dist_peaks = params.getint('detection', 'dist_peaks')
template_shift = params.getint('detection', 'template_shift')
file_out_suff = params.get('data', 'file_out_suff')
spike_thresh = params.getfloat('detection', 'spike_thresh')
spike_width = params.getfloat('detection', 'spike_width')
matched_filter = params.getboolean('detection', 'matched-filter')
matched_thresh = params.getfloat('detection', 'matched_thresh')
fudge = params.getfloat('whitening', 'fudge')
sign_peaks = params.get('detection', 'peaks')
do_temporal_whitening = params.getboolean('whitening', 'temporal')
do_spatial_whitening = params.getboolean('whitening', 'spatial')
ignore_spikes = params.getboolean('whitening', 'ignore_spikes')
chunk_size = detect_memory(params, whitening=True)
plot_path = os.path.join(params.get('data', 'file_out_suff'), 'plots')
nodes, edges = get_nodes_and_edges(params)
safety_time = params.getint('whitening', 'safety_time')
safety_space = params.getboolean('whitening', 'safety_space')
sort_waveforms = params.getboolean('whitening', 'sort_waveforms')
nb_temp_white = min(max(20, comm.size), N_e)
max_silence_1 = int(20 * params.rate // comm.size)
max_silence_2 = 5000
inv_nodes = numpy.zeros(N_total, dtype=numpy.int32)
inv_nodes[nodes] = numpy.arange(len(nodes))
jitter_range = params.getint('detection', 'jitter_range')
template_shift_2 = template_shift + jitter_range
use_hanning = params.getboolean('detection', 'hanning')
rejection_threshold = params.getfloat('detection', 'rejection_threshold')
noise_window = params.getint('detection', 'noise_time')
data_file.open()
#################################################################
if use_hanning:
hanning_filter = numpy.hanning(N_t)
if comm.rank == 0:
print_and_log(
["Analyzing data to get whitening matrices and thresholds..."],
'default', logger)
nodes_indices = {}
for elec in numpy.arange(N_e):
nodes_indices[elec] = inv_nodes[edges[nodes[elec]]]
if use_gpu:
import cudamat as cmt
# # Need to properly handle multi GPU per MPI nodes?
if nb_gpu > nb_cpu:
gpu_id = int(comm.rank // nb_cpu)
else:
gpu_id = 0
cmt.cuda_set_device(gpu_id)
cmt.init()
cmt.cuda_sync_threads()
nb_chunks, last_chunk_len = data_file.analyze(chunk_size)
if nb_chunks < comm.size:
res = io.data_stats(params, show=False)
chunk_size = int(res * params.rate // comm.size)
if comm.rank == 0:
print_and_log(
["Too much cores, automatically resizing the data chunks"],
'debug', logger)
nb_chunks, last_chunk_len = data_file.analyze(chunk_size)
# I guess this is more relevant, to take signals from all over the recordings.
if nb_chunks > comm.size:
all_chunks = numpy.random.permutation(
numpy.arange(nb_chunks - 1, dtype=numpy.int32))
else:
all_chunks = numpy.random.permutation(
numpy.arange(nb_chunks, dtype=numpy.int32))
all_electrodes = numpy.random.permutation(N_e)
numpy.random.seed(comm.rank)
for gidx in [all_chunks[comm.rank]]:
# print "Node", comm.rank, "is analyzing chunk", gidx, "/", nb_chunks, " ..."
local_chunk, t_offset = data_file.get_data(gidx,
chunk_size,
nodes=nodes)
local_shape = len(local_chunk)
# print "Node", comm.rank, "computes the median absolute deviations in a random chunk"
thresholds = numpy.zeros(N_e, dtype=numpy.float32)
for i in range(N_e):
u = numpy.median(local_chunk[:, i], 0)
thresholds[i] = numpy.median(numpy.abs(local_chunk[:, i] - u), 0)
gdata = gather_array(thresholds, comm)
if comm.rank == 0:
gdata = gdata.reshape((comm.size, N_e))
thresholds = numpy.mean(gdata, 0)
bfile = h5py.File(file_out_suff + '.basis.hdf5',
'w',
libver='earliest')
io.write_datasets(bfile, ['thresholds'],
{'thresholds': thresholds},
compression=hdf5_compress)
bfile.close()
comm.Barrier()
thresholds = io.load_data(params, 'thresholds')
local_borders = (template_shift, local_shape - template_shift)
found_peaktimes = []
if ignore_spikes:
# Extracting the peaks.
local_peaktimes = [np.empty(0, dtype=numpy.uint32)]
for i in range(N_e):
peaktimes = scipy.signal.find_peaks(numpy.abs(local_chunk[:,
i]),
height=thresholds[i],
width=spike_width,
wlen=N_t)[0]
peaktimes = peaktimes.astype(numpy.uint32)
# print "Removing the useless borders..."
idx = (peaktimes >= local_borders[0]) & (peaktimes <
local_borders[1])
peaktimes = numpy.compress(idx, peaktimes)
found_peaktimes.append(peaktimes)
else:
for i in range(N_e):
found_peaktimes.append(numpy.zeros(0, dtype=numpy.uint32))
all_peaktimes = numpy.concatenate(found_peaktimes)
local_peaktimes = numpy.unique(all_peaktimes)
if len(local_peaktimes) > 0:
diff_times = local_peaktimes[-1] - local_peaktimes[0]
all_times = numpy.zeros((N_e, diff_times + 1), dtype=numpy.bool)
padded_peaks = (local_peaktimes - local_peaktimes[0]).astype(
numpy.int32)
min_times = numpy.maximum(padded_peaks - safety_time, 0)
max_times = numpy.minimum(padded_peaks + safety_time + 1,
diff_times + 1)
test_extremas = numpy.zeros((N_e, diff_times + 1),
dtype=numpy.bool)
for i in range(N_e):
test_extremas[i,
found_peaktimes[i] - local_peaktimes[0]] = True
argmax_peak = numpy.random.permutation(
numpy.arange(len(local_peaktimes)))
all_idx = numpy.take(local_peaktimes, argmax_peak)
# print "Selection of the peaks with spatio-temporal masks..."
for idx, peak in zip(argmax_peak, all_idx):
all_elecs = numpy.where(test_extremas[:, peak -
local_peaktimes[0]])[0]
data = local_chunk[peak, all_elecs]
elec = all_elecs[numpy.argmax(numpy.abs(data))]
indices = nodes_indices[elec]
if safety_space:
all_times[indices, min_times[idx]:max_times[idx]] = True
else:
all_times[elec, min_times[idx]:max_times[idx]] = True
else:
all_times = numpy.zeros((N_e, len(local_chunk)), dtype=numpy.bool)
if do_temporal_whitening:
local_res_temp = []
for elec in all_electrodes[numpy.arange(comm.rank, nb_temp_white,
comm.size)]:
res = numpy.zeros((0, N_t), dtype=numpy.float32)
scount = 0
indices = nodes_indices[elec]
all_times_elec = numpy.any(numpy.take(all_times, indices, axis=0),
0)
esubset = numpy.where(all_times_elec == False)[0]
bound = len(esubset) - N_t
while (scount < bound) and (len(res) < max_silence_2):
myslice = esubset[scount:scount + N_t]
if numpy.all((myslice - esubset[scount]) == numpy.arange(N_t)):
scount += N_t
res = numpy.vstack((res, local_chunk[myslice, elec]))
else:
scount += 1
if len(res) > 5:
local_res_temp += [numpy.cov(res.T)]
nb_elecs = numpy.array([len(local_res_temp)], dtype=numpy.float32)
local_res_temp = numpy.array(local_res_temp, dtype=numpy.float32)
if len(local_res_temp) == 0:
local_res_temp = numpy.zeros(0, dtype=numpy.float32)
else:
local_res_temp = numpy.sum(local_res_temp, 0)
all_res_temp = gather_array(local_res_temp.ravel(), comm, 0, 1)
all_elecs = gather_array(nb_elecs, comm, 0, 1)
if do_spatial_whitening:
local_res_spac = numpy.zeros((N_e, N_e), dtype=numpy.float32)
local_silences = []
for elec in numpy.arange(comm.rank, N_e, comm.size):
indices = nodes_indices[elec]
all_times_elec = numpy.any(numpy.take(all_times, indices, axis=0),
0)
esubset = numpy.where(all_times_elec == False)[0]
local_data = local_chunk[esubset][:, indices]
local_whitening = get_whitening_matrix(
local_data, fudge=fudge).astype(numpy.float32)
pos = numpy.where(elec == indices)[0]
local_res_spac[elec, indices] = local_whitening[pos]
local_silences += [len(esubset)]
all_res_spac = gather_array(local_res_spac.ravel(), comm, 0, 1)
all_silences = gather_array(
numpy.array(local_silences, dtype=numpy.int32), comm, 0, 1,
'uint32')
if comm.rank == 0:
to_write = {}
if do_temporal_whitening:
try:
nb_silences = numpy.sum(all_elecs > 0)
all_res_temp = all_res_temp.reshape((nb_silences, N_t**2))
except Exception:
print_and_log([
"No silent periods detected: something wrong with the parameters?"
], 'error', logger)
all_res_temp = numpy.sum(all_res_temp, 0)
all_res_temp = all_res_temp.reshape(
(N_t, N_t)) / numpy.sum(all_elecs)
temporal_whitening = get_whitening_matrix(
all_res_temp.astype(numpy.double),
fudge=1e-3)[template_shift].astype(numpy.float32)
temporal_whitening /= temporal_whitening.sum()
to_write['temporal'] = temporal_whitening
have_nans = numpy.sum(numpy.isnan(temporal_whitening))
if have_nans > 0:
temporal_whitening = numpy.zeros(N_t, dtype=numpy.float32)
temporal_whitening[N_t // 2] = 1
to_write['temporal'] = temporal_whitening
print_and_log(
["Disabling temporal whitening because of NaNs found"],
'info', logger)
if do_spatial_whitening:
all_res_spac = all_res_spac.reshape(comm.size, N_e, N_e)
spatial_whitening = numpy.sum(all_res_spac, 0)
to_write['spatial'] = spatial_whitening
if ignore_spikes:
print_and_log([
"Found %gs without spikes to compute the whitening matrix..."
% (numpy.mean(all_silences) / params.rate)
], 'default', logger)
else:
print_and_log([
"Found %gs to compute the whitening matrix..." %
(numpy.mean(all_silences) / params.rate)
], 'default', logger)
have_nans = numpy.sum(numpy.isnan(spatial_whitening))
if have_nans > 0:
spatial_whitening = numpy.eye(spatial_whitening.shape[0],
dtype=numpy.float32)
to_write['spatial'] = spatial_whitening
print_and_log(
["Disabling spatial whitening because of NaNs found"],
'info', logger)
bfile = h5py.File(file_out_suff + '.basis.hdf5',
'r+',
libver='earliest')
io.write_datasets(bfile,
list(to_write.keys()),
to_write,
compression=hdf5_compress)
bfile.close()
comm.Barrier()
if do_spatial_whitening or do_temporal_whitening:
if comm.rank == 0:
print_and_log(
["Because of whitening, need to recompute the thresholds..."],
'default', logger)
if do_spatial_whitening:
spatial_whitening = io.load_data(params, 'spatial_whitening')
if use_gpu:
spatial_whitening = cmt.CUDAMatrix(spatial_whitening,
copy_on_host=False)
if do_temporal_whitening:
temporal_whitening = io.load_data(params, 'temporal_whitening')
for gidx in [all_chunks[comm.rank]]:
local_chunk, t_offset = data_file.get_data(gidx,
chunk_size,
nodes=nodes)
local_shape = len(local_chunk)
if do_spatial_whitening:
if use_gpu:
local_chunk = cmt.CUDAMatrix(local_chunk,
copy_on_host=False)
local_chunk = local_chunk.dot(spatial_whitening).asarray()
else:
local_chunk = numpy.dot(local_chunk, spatial_whitening)
if do_temporal_whitening:
local_chunk = scipy.ndimage.filters.convolve1d(
local_chunk, temporal_whitening, axis=0, mode='constant')
thresholds = numpy.zeros(N_e, dtype=numpy.float32)
for i in range(N_e):
u = numpy.median(local_chunk[:, i], 0)
thresholds[i] = numpy.median(numpy.abs(local_chunk[:, i] - u),
0)
gdata = gather_array(thresholds, comm)
if comm.rank == 0:
gdata = gdata.reshape((comm.size, N_e))
thresholds = numpy.mean(gdata, 0)
bfile = h5py.File(file_out_suff + '.basis.hdf5',
'r+',
libver='earliest')
bfile.pop('thresholds')
io.write_datasets(bfile, ['thresholds'],
{'thresholds': thresholds},
compression=hdf5_compress)
bfile.close()
comm.Barrier()
# if comm.rank == 0:
# if not os.path.exists(plot_path):
# os.makedirs(plot_path)
# N_elec = min(int(numpy.sqrt(data_file.N_e)), 5)
# plot.view_fit(filename, t_start=0, t_stop=1, fit_on=False, square=True,
# n_elec=N_elec, save=[plot_path, 'electrodes'])
# Part 2: Basis
numpy.random.seed(422)
SHARED_MEMORY = get_shared_memory_flag(params)
#################################################################
file_out = params.get('data', 'file_out')
alignment = params.getboolean('detection', 'alignment')
over_factor = params.getint('detection', 'oversampling_factor')
nb_jitter = params.getint('detection', 'nb_jitter')
spike_thresh = params.getfloat('detection', 'spike_thresh')
nodes, edges = get_nodes_and_edges(params)
_, positions = get_nodes_and_positions(params)
do_temporal_whitening = params.getboolean('whitening', 'temporal')
do_spatial_whitening = params.getboolean('whitening', 'spatial')
use_barycenter = params.getboolean('detection', 'use_barycenter')
if matched_filter:
chunk_size = detect_memory(params, whitening=True)
else:
chunk_size = detect_memory(params)
safety_time = params.getint('whitening', 'safety_time')
max_elts_elec = params.getint('whitening', 'max_elts')
output_dim = params.getfloat('whitening', 'output_dim')
inv_nodes = numpy.zeros(N_total, dtype=numpy.int32)
inv_nodes[nodes] = numpy.arange(len(nodes))
smoothing_factor = params.getfloat('detection', 'smoothing_factor')
if sign_peaks == 'both':
max_elts_elec *= 2
nb_elts = int(
params.getfloat('whitening', 'nb_elts') * N_e * max_elts_elec)
weird_thresh = params.get('detection', 'weird_thresh')
if weird_thresh != '':
ignore_artefacts = True
weird_thresh = io.load_data(params, 'weird-thresholds')
else:
ignore_artefacts = False
ignore_dead_times = params.getboolean('triggers', 'ignore_times')
if ignore_dead_times:
if SHARED_MEMORY:
all_dead_times, mpi_memory_3 = get_dead_times(params)
else:
all_dead_times = get_dead_times(params)
data_file.open()
#################################################################
if comm.rank == 0:
print_and_log(["Searching spikes to construct the PCA basis..."],
'default', logger)
nb_chunks, last_chunk_len = data_file.analyze(chunk_size)
if nb_chunks < comm.size:
res = io.data_stats(params, show=False)
chunk_size = int(res * params.rate // comm.size)
if comm.rank == 0:
print_and_log(
["Too much cores, automatically resizing the data chunks"],
'debug', logger)
nb_chunks, last_chunk_len = data_file.analyze(chunk_size)
groups = {}
for i in range(N_e):
groups[i] = 0
# I guess this is more relevant, to take signals from all over the recordings
all_chunks = numpy.random.permutation(
numpy.arange(nb_chunks, dtype=numpy.int32))
max_elts_elec //= comm.size
nb_elts //= comm.size
elt_count_pos = 0
elt_count_neg = 0
if sign_peaks in ['positive', 'both']:
times_pos = numpy.zeros(nb_elts, dtype=numpy.int32)
electrodes_pos = numpy.zeros(nb_elts, dtype=numpy.int32)
extremum_pos = numpy.zeros(nb_elts, dtype=numpy.float32)
elts_pos = numpy.zeros((N_t, nb_elts), dtype=numpy.float32)
if sign_peaks in ['negative', 'both']:
times_neg = numpy.zeros(nb_elts, dtype=numpy.int32)
electrodes_neg = numpy.zeros(nb_elts, dtype=numpy.int32)
extremum_neg = numpy.zeros(nb_elts, dtype=numpy.float32)
elts_neg = numpy.zeros((N_t, nb_elts), dtype=numpy.float32)
thresholds = io.load_data(params, 'thresholds')
mads = io.load_data(params, 'mads')
stds = io.load_data(params, 'stds')
if alignment:
cdata = numpy.linspace(-jitter_range, +jitter_range, nb_jitter)
xdata = numpy.arange(-template_shift_2, template_shift_2 + 1)
xoff = len(cdata) / 2.0
snippet_duration = template_shift_2
m_size = 2 * template_shift_2 + 1
align_factor = m_size
local_factors = align_factor * ((smoothing_factor * mads)**2)
else:
snippet_duration = template_shift
xdata = numpy.arange(-template_shift, template_shift + 1)
if rejection_threshold > 0:
reject_noise = True
noise_levels = stds * (2 * noise_window + 1)
else:
reject_noise = False
to_explore = all_chunks[comm.rank::comm.size]
upper_bounds = max_elts_elec
if comm.rank == 0:
to_explore = get_tqdm_progressbar(params, to_explore)
for gcount, gidx in enumerate(to_explore):
if (elt_count_pos + elt_count_neg) < nb_elts:
# print "Node", comm.rank, "is analyzing chunk", gidx, "/", nb_chunks, " ..."
local_chunk, t_offset = data_file.get_data(gidx,
chunk_size,
nodes=nodes)
local_shape = len(local_chunk)
if do_spatial_whitening:
if use_gpu:
local_chunk = cmt.CUDAMatrix(local_chunk,
copy_on_host=False)
local_chunk = local_chunk.dot(spatial_whitening).asarray()
else:
local_chunk = numpy.dot(local_chunk, spatial_whitening)
if do_temporal_whitening:
local_chunk = scipy.ndimage.filters.convolve1d(
local_chunk, temporal_whitening, axis=0, mode='constant')
local_borders = (snippet_duration, local_shape - snippet_duration)
if ignore_dead_times:
dead_indices = numpy.searchsorted(
all_dead_times, [t_offset, t_offset + local_shape])
# Extracting the peaks.
all_peaktimes = [numpy.empty(0, dtype=numpy.uint32)]
found_peaktimes = []
found_peak_amplitudes = []
for i in range(N_e):
height = thresholds[i]
if sign_peaks == 'negative':
peaktimes = scipy.signal.find_peaks(-local_chunk[:, i],
height=height,
distance=dist_peaks)[0]
elif sign_peaks == 'positive':
peaktimes = scipy.signal.find_peaks(local_chunk[:, i],
height=height,
distance=dist_peaks)[0]
elif sign_peaks == 'both':
peaktimes = scipy.signal.find_peaks(numpy.abs(
local_chunk[:, i]),
height=height,
distance=dist_peaks)[0]
else:
peaktimes = numpy.empty(0, dtype=numpy.uint32)
if ignore_artefacts:
artetimes = scipy.signal.find_peaks(
numpy.abs(local_chunk[:,
i]), height=weird_thresh[i])[0]
to_keep = numpy.logical_not(
numpy.in1d(peaktimes, artetimes))
peaktimes = peaktimes[to_keep]
idx = (peaktimes >= local_borders[0]) & (peaktimes <
local_borders[1])
peaktimes = peaktimes[idx]
if ignore_dead_times:
if dead_indices[0] != dead_indices[1]:
is_included = numpy.in1d(
peaktimes + t_offset,
all_dead_times[dead_indices[0]:dead_indices[1]])
peaktimes = peaktimes[~is_included]
peaktimes = peaktimes.astype(numpy.uint32)
found_peaktimes.append(peaktimes)
peak_amplitudes = local_chunk[peaktimes, i]
found_peak_amplitudes.append(peak_amplitudes)
all_peaktimes = numpy.concatenate(
found_peaktimes) # i.e. concatenate once for efficiency
all_peak_amplitudes = numpy.concatenate(found_peak_amplitudes)
local_peaktimes, local_indices = numpy.unique(all_peaktimes,
return_inverse=True)
if len(local_peaktimes) > 0:
diff_times = (local_peaktimes[-1] - local_peaktimes[0]) + 1
all_times = numpy.zeros((N_e, diff_times), dtype=numpy.bool)
padded_peaks = (local_peaktimes - local_peaktimes[0]).astype(
numpy.int32)
min_times = numpy.maximum(padded_peaks - safety_time, 0)
max_times = numpy.minimum(padded_peaks + safety_time + 1,
diff_times + 1)
test_extremas = numpy.zeros((N_e, diff_times + 1),
dtype=numpy.bool)
for i in range(N_e):
test_extremas[i, found_peaktimes[i] -
local_peaktimes[0]] = True
# Consider the peaks by decreasing extremum.
if sort_waveforms:
order = numpy.argsort(-np.abs(all_peak_amplitudes))
all_idx = numpy.take(all_peaktimes, order)
argmax_peak = local_indices[order]
else:
n_times = len(all_peaktimes)
shuffling = numpy.random.permutation(numpy.arange(n_times))
all_idx = numpy.take(all_peaktimes, shuffling)
argmax_peak = local_indices[shuffling]
# print "Selection of the peaks with spatio-temporal masks..."
for midx, peak in zip(argmax_peak, all_idx):
if (elt_count_neg + elt_count_pos) == nb_elts:
break
all_elecs = numpy.where(
test_extremas[:, peak - local_peaktimes[0]])[0]
data = local_chunk[peak, all_elecs]
#target_area = test_extremas[:, min_times[midx]:max_times[midx]].sum(1)
#all_elecs = numpy.where(target_area)[0]
#data = local_chunk[peak, all_elecs]
if sign_peaks == 'negative':
if N_e > 1:
if use_barycenter:
weighed_position = data[:, numpy.
newaxis] * positions[
all_elecs]
barycenter = weighed_position.sum(
0) / data.sum()
elec = numpy.argmin(
numpy.linalg.norm(barycenter -
positions[all_elecs],
axis=1))
else:
elec = numpy.argmin(data)
else:
elec = 0
negative_peak = True
elif sign_peaks == 'positive':
if N_e > 1:
if use_barycenter:
weighed_position = data[:, numpy.
newaxis] * positions[
all_elecs]
barycenter = weighed_position.sum(
0) / data.sum()
elec = numpy.argmax(
numpy.linalg.norm(barycenter -
positions[all_elecs],
axis=1))
else:
elec = numpy.argmax(data)
else:
elec = 0
negative_peak = False
elif sign_peaks == 'both':
if N_e == 1:
if data < 0:
negative_peak = True
elif data > 0:
negative_peak = False
elec = 0
else:
if numpy.abs(numpy.max(data)) > numpy.abs(
numpy.min(data)):
elec = numpy.argmax(data)
negative_peak = False
else:
elec = numpy.argmin(data)
negative_peak = True
elec = all_elecs[elec]
if groups[elec] < upper_bounds:
indices = nodes_indices[elec]
myslice = all_times[indices,
min_times[midx]:max_times[midx]]
if not myslice.any():
sub_mat = local_chunk[peak -
snippet_duration:peak +
snippet_duration + 1, elec]
if reject_noise:
slice_window = sub_mat[
snippet_duration -
noise_window:snippet_duration +
noise_window + 1]
value = numpy.linalg.norm(
slice_window) / noise_levels[elec]
is_noise = value < rejection_threshold
else:
is_noise = False
if not is_noise:
extrema = sub_mat[snippet_duration]
if alignment:
smoothed = True
try:
f = scipy.interpolate.UnivariateSpline(
xdata,
sub_mat,
s=local_factors[elec],
k=3)
except Exception:
smoothed = False
f = scipy.interpolate.UnivariateSpline(
xdata, sub_mat, k=3, s=0)
if negative_peak:
rmin = (numpy.argmin(f(cdata)) -
xoff) / over_factor
else:
rmin = (numpy.argmax(f(cdata)) -
xoff) / over_factor
ddata = numpy.linspace(
rmin - template_shift,
rmin + template_shift, N_t)
if smoothed:
f = scipy.interpolate.UnivariateSpline(
xdata,
sub_mat,
s=local_factors[elec],
k=3)
else:
f = scipy.interpolate.UnivariateSpline(
xdata, sub_mat, s=0, k=3)
sub_mat = f(ddata).astype(numpy.float32)
if negative_peak:
times_neg[elt_count_neg] = peak + t_offset
electrodes_neg[elt_count_neg] = elec
extremum_neg[elt_count_neg] = extrema
elts_neg[:, elt_count_neg] = sub_mat
elt_count_neg += 1
else:
times_pos[elt_count_pos] = peak + t_offset
electrodes_pos[elt_count_pos] = elec
extremum_pos[elt_count_pos] = extrema
elts_pos[:, elt_count_pos] = sub_mat
elt_count_pos += 1
groups[elec] += 1
all_times[
indices,
min_times[midx]:max_times[midx]] = True
test_extremas[elec, peak -
local_peaktimes[0]] = False
sys.stderr.flush()
print_and_log([
"Node %d has collected %d waveforms" %
(comm.rank, elt_count_pos + elt_count_neg)
], 'debug', logger)
if sign_peaks in ['negative', 'both']:
times_neg = gather_array(times_neg[:elt_count_neg],
comm,
0,
1,
dtype='int32')
electrodes_neg = gather_array(electrodes_neg[:elt_count_neg],
comm,
0,
1,
dtype='int32')
extremum_neg = gather_array(extremum_neg[:elt_count_neg], comm, 0, 1)
gdata_neg = gather_array(elts_neg[:, :elt_count_neg].T, comm, 0, 1)
if sign_peaks in ['positive', 'both']:
times_pos = gather_array(times_pos[:elt_count_pos],
comm,
0,
1,
dtype='int32')
electrodes_pos = gather_array(electrodes_pos[:elt_count_pos],
comm,
0,
1,
dtype='int32')
extremum_pos = gather_array(extremum_pos[:elt_count_pos], comm, 0, 1)
gdata_pos = gather_array(elts_pos[:, :elt_count_pos].T, comm, 0, 1)
nb_waveforms = 0
if comm.rank == 0:
# DO PCA on elts and store the basis obtained.
if sign_peaks in ['negative', 'both']:
nb_waveforms += gdata_neg.shape[0]
if sign_peaks in ['positive', 'both']:
nb_waveforms += gdata_pos.shape[0]
nb_waveforms = all_gather_array(
numpy.array([nb_waveforms], dtype=numpy.float32), comm, 0)[0]
if comm.rank == 0:
print_and_log([
"Found %d waveforms over %d requested" %
(nb_waveforms, int(nb_elts * comm.size))
], 'default', logger)
if nb_waveforms == 0:
print_and_log(
['No waveforms found! Are the data properly loaded??'],
'error', logger)
if nb_waveforms == 0:
sys.exit(0)
if comm.rank == 0:
res = {}
pca = None
pca_pos = None
pca_neg = None
warning_n_t = False
if sign_peaks in ['negative', 'both']:
res['times'] = times_neg
res['electrodes'] = electrodes_neg
res['extremum'] = extremum_neg
if len(gdata_neg) > 0:
pca = PCA(output_dim)
if use_hanning:
pca.fit(gdata_neg * hanning_filter)
else:
pca.fit(gdata_neg)
res['proj'] = pca.components_.T.astype(numpy.float32)
pca_neg = numpy.sum(pca.explained_variance_ratio_)
else:
res['proj'] = numpy.identity(int(output_dim),
dtype=numpy.float32)
res['rec'] = res['proj'].T
res['waveform'] = numpy.median(gdata_neg, 0)
# dispersion = numpy.std(gdata_neg, 0) / numpy.median(stds)
# ratio = numpy.sum(dispersion > 1.1) / float(len(dispersion))
# if ratio < 0.25:
# print_and_log(["Time window N_t in [detection] seems too large!"], 'info', logger)
# warning_n_t = True
# elif ratio == 1:
# print_and_log(["Time window N_t in [detection] seems too small!"], 'info', logger)
# warning_n_t = True
idx = numpy.random.permutation(numpy.arange(
gdata_neg.shape[0]))[:2500]
res['waveforms'] = gdata_neg[idx, :]
if sign_peaks in ['positive', 'both']:
res['times_pos'] = times_pos
res['electrodes_pos'] = electrodes_pos
res['extremum_pos'] = extremum_pos
if len(gdata_pos) > 0:
pca = PCA(output_dim)
if use_hanning:
pca.fit(gdata_pos * hanning_filter)
else:
pca.fit(gdata_pos)
res['proj_pos'] = pca.components_.T.astype(numpy.float32)
pca_pos = numpy.sum(pca.explained_variance_ratio_)
else:
res['proj_pos'] = numpy.identity(int(output_dim),
dtype=numpy.float32)
res['rec_pos'] = res['proj_pos'].T
res['waveform_pos'] = numpy.median(gdata_pos, 0)
# dispersion = numpy.std(gdata_pos, 0) / numpy.median(stds)
# ratio = numpy.sum(dispersion > 1.1) / float(len(dispersion))
# if ratio < 0.25 and not warning_n_t:
# print_and_log(["Time window N_t in [detection] seems too large!"], 'info', logger)
# elif ratio == 1 and not warning_n_t:
# print_and_log(["Time window N_t in [detection] seems too small!"], 'info', logger)
idx = numpy.random.permutation(numpy.arange(
gdata_pos.shape[0]))[:2500]
res['waveforms_pos'] = gdata_pos[idx, :]
bfile = h5py.File(file_out_suff + '.basis.hdf5',
'r+',
libver='earliest')
io.write_datasets(bfile,
list(res.keys()),
res,
compression=hdf5_compress)
if sign_peaks == 'positive':
print_and_log([
"A basis with %s dimensions has been built" %
res['proj_pos'].shape[1]
], 'info', logger)
elif sign_peaks == 'negative':
print_and_log([
"A basis with %s dimensions has been built" %
res['proj'].shape[1]
], 'info', logger)
elif sign_peaks == 'both':
print_and_log([
"Two basis with %s dimensions has been built" %
res['proj'].shape[1]
], 'debug', logger)
if pca_pos is not None:
print_and_log([
"The percentage of variance explained is %s for positive spikes"
% pca_pos
], 'debug', logger)
if pca_neg is not None:
print_and_log([
"The percentage of variance explained is %s for negative spikes"
% pca_neg
], 'debug', logger)
bfile.close()
comm.Barrier()
if matched_filter:
if comm.rank == 0:
print_and_log([
"Because of matched filters, need to recompute the thresholds..."
], 'default', logger)
if do_spatial_whitening:
spatial_whitening = io.load_data(params, 'spatial_whitening')
if use_gpu:
spatial_whitening = cmt.CUDAMatrix(spatial_whitening,
copy_on_host=False)
if do_temporal_whitening:
temporal_whitening = io.load_data(params, 'temporal_whitening')
if sign_peaks in ['negative', 'both']:
waveform_neg = io.load_data(params, 'waveform')[::-1]
waveform_neg /= (numpy.abs(numpy.sum(waveform_neg)) *
len(waveform_neg))
if sign_peaks in ['positive', 'both']:
waveform_pos = io.load_data(params, 'waveform-pos')[::-1]
waveform_pos /= (numpy.abs(numpy.sum(waveform_pos)) *
len(waveform_pos))
for gidx in [all_chunks[comm.rank]]:
local_chunk, t_offset = data_file.get_data(gidx,
chunk_size,
nodes=nodes)
local_shape = len(local_chunk)
if do_spatial_whitening:
if use_gpu:
local_chunk = cmt.CUDAMatrix(local_chunk,
copy_on_host=False)
local_chunk = local_chunk.dot(spatial_whitening).asarray()
else:
local_chunk = numpy.dot(local_chunk, spatial_whitening)
if do_temporal_whitening:
local_chunk = scipy.ndimage.filters.convolve1d(
local_chunk, temporal_whitening, axis=0, mode='constant')
local_chunk /= thresholds
if sign_peaks in ['negative', 'both']:
tmp_chunk = scipy.ndimage.filters.convolve1d(local_chunk,
waveform_neg,
axis=0,
mode='constant')
thresholds = numpy.zeros(N_e, dtype=numpy.float32)
for i in range(N_e):
u = numpy.median(tmp_chunk[:, i], 0)
thresholds[i] = numpy.median(
numpy.abs(tmp_chunk[:, i] - u), 0)
gdata = gather_array(thresholds, comm)
if comm.rank == 0:
gdata = gdata.reshape((comm.size, N_e))
thresholds = numpy.mean(gdata, 0)
bfile = h5py.File(file_out_suff + '.basis.hdf5',
'r+',
libver='earliest')
io.write_datasets(bfile, ['matched_thresholds'],
{'matched_thresholds': thresholds},
compression=hdf5_compress)
bfile.close()
comm.Barrier()
if sign_peaks in ['positive', 'both']:
tmp_chunk = scipy.ndimage.filters.convolve1d(local_chunk,
waveform_pos,
axis=0,
mode='constant')
thresholds = numpy.zeros(N_e, dtype=numpy.float32)
for i in range(N_e):
u = numpy.median(tmp_chunk[:, i], 0)
thresholds[i] = numpy.median(
numpy.abs(tmp_chunk[:, i] - u), 0)
gdata = gather_array(thresholds, comm)
if comm.rank == 0:
gdata = gdata.reshape((comm.size, N_e))
thresholds = numpy.mean(gdata, 0)
bfile = h5py.File(file_out_suff + '.basis.hdf5',
'r+',
libver='earliest')
io.write_datasets(bfile, ['matched_thresholds_pos'],
{'matched_thresholds_pos': thresholds},
compression=hdf5_compress)
bfile.close()
comm.Barrier()
data_file.close()
if SHARED_MEMORY and ignore_dead_times:
mpi_memory_3.Free()
def main(params, nb_cpu, nb_gpu, use_gpu, file_name, benchmark, sim_same_elec):
"""
Useful tool to create synthetic datasets for benchmarking.
Arguments
---------
benchmark : {'fitting', 'clustering', 'synchrony', 'pca-validation', 'smart-search', 'drifts'}
"""
if sim_same_elec is None:
sim_same_elec = 0.8
_ = init_logging(params.logfile)
logger = logging.getLogger('circus.benchmarking')
numpy.random.seed(265)
file_name = os.path.abspath(file_name)
data_path = os.path.dirname(file_name)
data_suff, ext = os.path.splitext(os.path.basename(file_name))
file_out, ext = os.path.splitext(file_name)
if ext == '':
ext = '.dat'
file_name += ext
if ext != '.dat':
if comm.rank == 0:
print_and_log(
['Benchmarking produces raw files: select a .dat extension'],
'error', logger)
sys.exit(0)
if benchmark not in [
'fitting', 'clustering', 'synchrony', 'smart-search', 'drifts'
]:
if comm.rank == 0:
print_and_log([
'Benchmark need to be in [fitting, clustering, synchrony, smart-search, drifts]'
], 'error', logger)
sys.exit(0)
# The extension `.p` or `.pkl` or `.pickle` seems more appropriate than `.pic`.
# see: http://stackoverflow.com/questions/4530111/python-saving-objects-and-using-pickle-extension-of-filename
# see: https://wiki.python.org/moin/UsingPickle
def write_benchmark(filename,
benchmark,
cells,
rates,
amplitudes,
sampling,
probe,
trends=None):
"""Save benchmark parameters in a file to remember them."""
import cPickle
to_write = {'benchmark': benchmark}
to_write['cells'] = cells
to_write['rates'] = rates
to_write['probe'] = probe
to_write['amplitudes'] = amplitudes
to_write['sampling'] = sampling
if benchmark == 'drifts':
to_write['drifts'] = trends
cPickle.dump(to_write, open(filename + '.pic', 'w'))
# Retrieve some key parameters.
templates = io.load_data(params, 'templates')
N_tm = templates.shape[1] // 2
trends = None
# Normalize some variables.
if benchmark == 'fitting':
nb_insert = 25
n_cells = numpy.random.random_integers(0, N_tm - 1, nb_insert)
rate = nb_insert * [10]
amplitude = numpy.linspace(0.5, 5, nb_insert)
if benchmark == 'clustering':
n_point = 5
n_cells = numpy.random.random_integers(0, N_tm - 1, n_point**2)
x, y = numpy.mgrid[0:n_point, 0:n_point]
rate = numpy.linspace(0.5, 20, n_point)[x.flatten()]
amplitude = numpy.linspace(0.5, 5, n_point)[y.flatten()]
if benchmark == 'synchrony':
nb_insert = 5
corrcoef = 0.2
n_cells = nb_insert * [numpy.random.random_integers(0, N_tm - 1, 1)[0]]
rate = 10.0 / corrcoef
amplitude = 2
if benchmark == 'pca-validation':
nb_insert = 10
n_cells = numpy.random.random_integers(0, N_tm - 1, nb_insert)
rate_min = 0.5
rate_max = 20.0
rate = rate_min + (rate_max -
rate_min) * numpy.random.random_sample(nb_insert)
amplitude_min = 0.5
amplitude_max = 5.0
amplitude = amplitude_min + (amplitude_max - amplitude_min
) * numpy.random.random_sample(nb_insert)
if benchmark == 'smart-search':
nb_insert = 10
n_cells = nb_insert * [
numpy.random.random_integers(0, templates.shape[1] // 2 - 1, 1)[0]
]
rate = 1 + 5 * numpy.arange(nb_insert)
amplitude = 2
if benchmark == 'drifts':
n_point = 5
n_cells = numpy.random.random_integers(0, templates.shape[1] // 2 - 1,
n_point**2)
x, y = numpy.mgrid[0:n_point, 0:n_point]
rate = 5 * numpy.ones(n_point)[x.flatten()]
amplitude = numpy.linspace(0.5, 5, n_point)[y.flatten()]
trends = numpy.random.randn(n_point**2)
# Delete the output directory tree if this output directory exists.
if comm.rank == 0:
if os.path.exists(file_out):
shutil.rmtree(file_out)
# Check and normalize some variables.
if n_cells is None:
n_cells = 1
cells = [numpy.random.permutation(numpy.arange(n_cells))[0]]
elif not numpy.iterable(n_cells):
cells = [n_cells]
n_cells = 1
else:
cells = n_cells
n_cells = len(cells)
if numpy.iterable(rate):
assert len(rate) == len(
cells), "Should have the same number of rates and cells"
else:
rate = [rate] * len(cells)
if numpy.iterable(amplitude):
assert len(amplitude) == len(
cells), "Should have the same number of amplitudes and cells"
else:
amplitude = [amplitude] * len(cells)
# Retrieve some additional key parameters.
# params = detect_memory(params)
data_file = params.get_data_file(source=True)
N_e = params.getint('data', 'N_e')
N_total = params.nb_channels
hdf5_compress = params.getboolean('data', 'hdf5_compress')
nodes, edges = get_nodes_and_edges(params)
N_t = params.getint('detection', 'N_t')
inv_nodes = numpy.zeros(N_total, dtype=numpy.int32)
inv_nodes[nodes] = numpy.arange(len(nodes))
do_temporal_whitening = params.getboolean('whitening', 'temporal')
do_spatial_whitening = params.getboolean('whitening', 'spatial')
N_tm_init = templates.shape[1] // 2
thresholds = io.load_data(params, 'thresholds')
limits = io.load_data(params, 'limits')
best_elecs = io.load_data(params, 'electrodes')
norms = io.load_data(params, 'norm-templates')
# Create output directory if it does not exist.
if comm.rank == 0:
if not os.path.exists(file_out):
os.makedirs(file_out)
# Save benchmark parameters in a file to remember them.
if comm.rank == 0:
write_benchmark(file_out, benchmark, cells, rate, amplitude,
params.rate, params.get('data', 'mapping'), trends)
# Synchronize all the threads/processes.
comm.Barrier()
if do_spatial_whitening:
spatial_whitening = io.load_data(params, 'spatial_whitening')
else:
spatial_whitening = None # default assignment (PyCharm code inspection)
if do_temporal_whitening:
temporal_whitening = io.load_data(params, 'temporal_whitening')
else:
temporal_whitening = None # default assignment (PyCharm code inspection)
# Retrieve some additional key parameters.
chunk_size = detect_memory(params)
scalings = []
params.set('data', 'data_file', file_name)
data_file_out = params.get_data_file(is_empty=True)
data_file_out.allocate(shape=data_file.shape)
# Synchronize all the threads/processes.
comm.Barrier()
# For each wanted synthesized cell insert a generated template in the set of existing template.
for gcount, cell_id in enumerate(cells):
best_elec = best_elecs[cell_id]
indices = inv_nodes[edges[nodes[best_elec]]]
count = 0
new_indices = []
all_elecs = numpy.random.permutation(numpy.arange(N_e))
reference = templates[:, cell_id].toarray().reshape(N_e, N_t)
# Initialize the similarity (i.e. default value).
similarity = 1.0
# Find the first eligible template for the wanted synthesized cell.
while len(new_indices) != len(indices) or (similarity > sim_same_elec):
similarity = 0
if count == len(all_elecs):
if comm.rank == 0:
print_and_log([
"No electrode to move template %d (max similarity is %g)"
% (cell_id, similarity)
], 'error', logger)
sys.exit(0)
else:
# Get the next shuffled electrode.
n_elec = all_elecs[count]
if benchmark not in ['synchrony', 'smart-search']:
# Process if the shuffled electrode and the nearest electrode
# to the synthesized cell are not identical.
local_test = n_elec != best_elec
else:
# Process if the shuffled electrode and the nearest electrode
# to the synthesized cell are identical.
local_test = n_elec == best_elec
if local_test:
# Shuffle the neighboring electrodes without modifying
# the nearest electrode to the synthesized cell.
new_indices = inv_nodes[edges[nodes[n_elec]]]
idx = numpy.where(new_indices != best_elec)[0]
new_indices[idx] = numpy.random.permutation(
new_indices[idx])
if len(new_indices) == len(indices):
# Shuffle the templates on the neighboring electrodes.
new_temp = numpy.zeros(reference.shape,
dtype=numpy.float32)
new_temp[new_indices, :] = reference[indices, :]
# Compute the scaling factor which normalize the
# shuffled template.
gmin = new_temp.min()
data = numpy.where(new_temp == gmin)
scaling = -thresholds[data[0][0]] / gmin
for i in range(templates.shape[1] // 2):
match = templates[:, i].toarray().reshape(N_e, N_t)
d = numpy.corrcoef(match.flatten(),
scaling * new_temp.flatten())[0,
1]
if d > similarity:
similarity = d
else:
new_indices = []
# Go to the next shuffled electrode.
count += 1
# if comm.rank == 0:
# print "Template", cell_id, "is shuffled from electrode", best_elec, "to", n_elec, "(max similarity is %g)" %similarity
N_tm = templates.shape[1] // 2
to_insert = numpy.zeros(reference.shape, dtype=numpy.float32)
to_insert[new_indices] = scaling * amplitude[
gcount] * templates[:, cell_id].toarray().reshape(N_e,
N_t)[indices]
to_insert2 = numpy.zeros(reference.shape, dtype=numpy.float32)
to_insert2[new_indices] = scaling * amplitude[
gcount] * templates[:, cell_id + N_tm].toarray().reshape(
N_e, N_t)[indices]
# # Insert the selected template.
# Retrieve the number of existing templates in the dataset.
N_tm = templates.shape[1] // 2
# Generate the template of the synthesized cell from the selected
# template, the target amplitude and the rescaling (i.e. threshold of
# the target electrode).
to_insert = numpy.zeros(reference.shape, dtype=numpy.float32)
to_insert[new_indices] = scaling * amplitude[
gcount] * templates[:, cell_id].toarray().reshape(N_e,
N_t)[indices]
to_insert = to_insert.flatten()
to_insert2 = numpy.zeros(reference.shape, dtype=numpy.float32)
to_insert2[new_indices] = scaling * amplitude[
gcount] * templates[:, cell_id + N_tm].toarray().reshape(
N_e, N_t)[indices]
to_insert2 = to_insert2.flatten()
# Compute the norm of the generated template.
mynorm = numpy.sqrt(numpy.sum(to_insert**2) / (N_e * N_t))
mynorm2 = numpy.sqrt(numpy.sum(to_insert2**2) / (N_e * N_t))
# Insert the limits of the generated template.
limits = numpy.vstack((limits, limits[cell_id]))
# Insert the best electrode of the generated template.
best_elecs = numpy.concatenate((best_elecs, [n_elec]))
# Insert the norm of the generated template (i.e. central component and
# orthogonal component).
norms = numpy.insert(norms, N_tm, mynorm)
norms = numpy.insert(norms, 2 * N_tm + 1, mynorm2)
# Insert the scaling of the generated template.
scalings += [scaling]
# Retrieve the data about the existing templates.
templates = templates.tocoo()
xdata = templates.row
ydata = templates.col
zdata = templates.data
# Shift by one the orthogonal components of the existing templates.
idx = numpy.where(ydata >= N_tm)[0]
ydata[idx] += 1
# Insert the central component of the selected template.
dx = to_insert.nonzero()[0].astype(numpy.int32)
xdata = numpy.concatenate((xdata, dx))
ydata = numpy.concatenate(
(ydata, N_tm * numpy.ones(len(dx), dtype=numpy.int32)))
zdata = numpy.concatenate((zdata, to_insert[dx]))
# Insert the orthogonal component of the selected template.
dx = to_insert2.nonzero()[0].astype(numpy.int32)
xdata = numpy.concatenate((xdata, dx))
ydata = numpy.concatenate(
(ydata, (2 * N_tm + 1) * numpy.ones(len(dx), dtype=numpy.int32)))
zdata = numpy.concatenate((zdata, to_insert2[dx]))
# Reconstruct the matrix of templates.
templates = scipy.sparse.csc_matrix((zdata, (xdata, ydata)),
shape=(N_e * N_t, 2 * (N_tm + 1)))
# Remove all the expired data.
if benchmark == 'pca-validation':
# Remove all the expired data.
N_tm_init = 0
N_tm = templates.shape[1] / 2
limits = limits[N_tm - nb_insert:, :]
best_elecs = best_elecs[N_tm - nb_insert:]
norms = numpy.concatenate((norms[N_tm - nb_insert:N_tm],
norms[2 * N_tm - nb_insert:2 * N_tm]))
scalings = scalings
templates = templates.tocoo()
xdata = templates.row
ydata = templates.col
zdata = templates.data
idx_cen = numpy.logical_and(N_tm - nb_insert <= ydata, ydata < N_tm)
idx_cen = numpy.where(idx_cen)[0]
idx_ort = numpy.logical_and(2 * N_tm - nb_insert <= ydata,
ydata < 2 * N_tm)
idx_ort = numpy.where(idx_ort)[0]
ydata[idx_cen] = ydata[idx_cen] - (N_tm - nb_insert)
ydata[idx_ort] = ydata[idx_ort] - 2 * (N_tm - nb_insert)
idx = numpy.concatenate((idx_cen, idx_ort))
xdata = xdata[idx]
ydata = ydata[idx]
zdata = zdata[idx]
templates = scipy.sparse.csc_matrix((zdata, (xdata, ydata)),
shape=(N_e * N_t, 2 * nb_insert))
# Retrieve the information about the organisation of the chunks of data.
nb_chunks, last_chunk_len = data_file.analyze(chunk_size)
# Display informations about the generated benchmark.
if comm.rank == 0:
print_and_log([
"Generating benchmark data [%s] with %d cells" %
(benchmark, n_cells)
], 'info', logger)
purge(file_out, '.data')
template_shift = params.getint('detection', 'template_shift')
all_chunks = numpy.arange(nb_chunks)
to_process = all_chunks[numpy.arange(comm.rank, nb_chunks, comm.size)]
loc_nb_chunks = len(to_process)
numpy.random.seed(comm.rank)
to_explore = range(comm.rank, nb_chunks, comm.size)
# Initialize the progress bar about the generation of the benchmark.
if comm.rank == 0:
to_explore = get_tqdm_progressbar(to_explore)
# Open the file for collective I/O.
# g = myfile.Open(comm, file_name, MPI.MODE_RDWR)
# g.Set_view(data_offset, data_mpi, data_mpi)
data_file_out.open(mode='r+')
# Open the thread/process' files to collect the results.
spiketimes_filename = os.path.join(
file_out, data_suff + '.spiketimes-%d.data' % comm.rank)
spiketimes_file = open(spiketimes_filename, 'wb')
amplitude_filename = os.path.join(
file_out, data_suff + '.amplitudes-%d.data' % comm.rank)
amplitudes_file = open(amplitude_filename, 'wb')
templates_filename = os.path.join(
file_out, data_suff + '.templates-%d.data' % comm.rank)
templates_file = open(templates_filename, 'wb')
real_amps_filename = os.path.join(
file_out, data_suff + '.real_amps-%d.data' % comm.rank)
real_amps_file = open(real_amps_filename, 'wb')
voltages_filename = os.path.join(
file_out, data_suff + '.voltages-%d.data' % comm.rank)
voltages_file = open(voltages_filename, 'wb')
# For each chunk of data associate to the current thread/process generate
# the new chunk of data (i.e. with considering the added synthesized cells).
for count, gidx in enumerate(to_explore):
# if (last_chunk_len > 0) and (gidx == (nb_chunks - 1)):
# chunk_len = last_chunk_len
# chunk_size = last_chunk_len // N_total
result = {
'spiketimes': [],
'amplitudes': [],
'templates': [],
'real_amps': [],
'voltages': []
}
offset = gidx * chunk_size
local_chunk, t_offset = data_file.get_data(gidx,
chunk_size,
nodes=nodes)
if benchmark == 'pca-validation':
# Clear the current data chunk.
local_chunk = numpy.zeros(local_chunk.shape,
dtype=local_chunk.dtype)
# Handle whitening if necessary.
if do_spatial_whitening:
local_chunk = numpy.dot(local_chunk, spatial_whitening)
if do_temporal_whitening:
local_chunk = scipy.ndimage.filters.convolve1d(local_chunk,
temporal_whitening,
axis=0,
mode='constant')
if benchmark is 'synchrony':
# Generate some spike indices (i.e. times) at the given rate for
# 'synchrony' mode. Each synthesized cell will use a subset of this
# spike times.
mips = numpy.random.rand(chunk_size) < rate[0] / float(params.rate)
# For each synthesized cell generate its spike indices (i.e.times) and
# add them to the dataset.
for idx in range(len(cells)):
if benchmark is 'synchrony':
# Choose a subset of the spike indices generated before. The
# size of this subset is parameterized by the target correlation
# coefficients.
sidx = numpy.where(mips == True)[0]
spikes = numpy.zeros(chunk_size, dtype=numpy.bool)
spikes[sidx[numpy.random.rand(len(sidx)) < corrcoef]] = True
else:
# Generate some spike indices at the given rate.
spikes = numpy.random.rand(chunk_size) < rate[idx] / float(
params.rate)
if benchmark == 'drifts':
amplitudes = numpy.ones(len(spikes)) + trends[idx] * (
(spikes + offset) / (5 * 60 * float(params.rate)))
else:
amplitudes = numpy.ones(len(spikes))
# Padding with `False` to avoid the insertion of partial spikes at
# the edges of the signal.
spikes[:N_t] = False
spikes[-N_t:] = False
# Find the indices of the spike samples.
spikes = numpy.where(spikes)[0]
n_template = N_tm_init + idx
loc_template = templates[:, n_template].toarray().reshape(N_e, N_t)
first_flat = loc_template.T.flatten()
norm_flat = numpy.sum(first_flat**2)
# For each index (i.e. spike sample location) add the spike to the
# chunk of data.
refractory = int(5 * 1e-3 * params.rate)
t_last = -refractory
for scount, spike in enumerate(spikes):
if (spike - t_last) > refractory:
local_chunk[spike - template_shift:spike + template_shift +
1, :] += amplitudes[scount] * loc_template.T
amp = numpy.dot(
local_chunk[spike - template_shift:spike +
template_shift + 1, :].flatten(),
first_flat)
amp /= norm_flat
result['real_amps'] += [amp]
result['spiketimes'] += [spike + offset]
result['amplitudes'] += [(amplitudes[scount], 0)]
result['templates'] += [n_template]
result['voltages'] += [local_chunk[spike, best_elecs[idx]]]
t_last = spike
# Write the results into the thread/process' files.
spikes_to_write = numpy.array(result['spiketimes'], dtype=numpy.uint32)
amplitudes_to_write = numpy.array(result['amplitudes'],
dtype=numpy.float32)
templates_to_write = numpy.array(result['templates'],
dtype=numpy.int32)
real_amps_to_write = numpy.array(result['real_amps'],
dtype=numpy.float32)
voltages_to_write = numpy.array(result['voltages'],
dtype=numpy.float32)
spiketimes_file.write(spikes_to_write.tostring())
amplitudes_file.write(amplitudes_to_write.tostring())
templates_file.write(templates_to_write.tostring())
real_amps_file.write(real_amps_to_write.tostring())
voltages_file.write(voltages_to_write.tostring())
# print count, 'spikes inserted...'
# new_chunk = numpy.zeros((chunk_size, N_total), dtype=numpy.float32)
# new_chunk[:, nodes] = local_chunk
# Overwrite the new chunk of data using explicit offset.
# new_chunk = new_chunk.flatten()
# g.Write_at(gidx * chunk_len, new_chunk)
data_file_out.set_data(offset, local_chunk)
# Update the progress bar about the generation of the benchmark.
sys.stderr.flush()
# Close the thread/process' files.
spiketimes_file.flush()
os.fsync(spiketimes_file.fileno())
spiketimes_file.close()
amplitudes_file.flush()
os.fsync(amplitudes_file.fileno())
amplitudes_file.close()
templates_file.flush()
os.fsync(templates_file.fileno())
templates_file.close()
real_amps_file.flush()
os.fsync(real_amps_file.fileno())
real_amps_file.close()
voltages_file.flush()
os.fsync(voltages_file.fileno())
voltages_file.close()
# Close the file for collective I/O.
data_file_out.close()
data_file.close()
# Synchronize all the threads/processes.
comm.Barrier()
# # Eventually, perform all the administrative tasks (i.e. files and folders management).
file_params = file_out + '.params'
if comm.rank == 0:
# Create `injected` directory if it does not exist
result_path = os.path.join(file_out, 'injected')
if not os.path.exists(result_path):
os.makedirs(result_path)
# Copy initial configuration file from `<dataset1>.params` to `<dataset2>.params`.
shutil.copy2(
params.get('data', 'data_file_noext') + '.params', file_params)
new_params = CircusParser(file_name)
# Copy initial basis file from `<dataset1>/<dataset1>.basis.hdf5` to
# `<dataset2>/injected/<dataset2>.basis.hdf5.
shutil.copy2(
params.get('data', 'file_out') + '.basis.hdf5',
os.path.join(result_path, data_suff + '.basis.hdf5'))
# Save templates into `<dataset>/<dataset>.templates.hdf5`.
mydata = h5py.File(
os.path.join(file_out, data_suff + '.templates.hdf5'), 'w')
templates = templates.tocoo()
if hdf5_compress:
mydata.create_dataset('temp_x',
data=templates.row,
compression='gzip')
mydata.create_dataset('temp_y',
data=templates.col,
compression='gzip')
mydata.create_dataset('temp_data',
data=templates.data,
compression='gzip')
else:
mydata.create_dataset('temp_x', data=templates.row)
mydata.create_dataset('temp_y', data=templates.col)
mydata.create_dataset('temp_data', data=templates.data)
mydata.create_dataset('temp_shape',
data=numpy.array([N_e, N_t, templates.shape[1]],
dtype=numpy.int32))
mydata.create_dataset('limits', data=limits)
mydata.create_dataset('norms', data=norms)
mydata.close()
# Save electrodes into `<dataset>/<dataset>.clusters.hdf5`.
mydata = h5py.File(
os.path.join(file_out, data_suff + '.clusters.hdf5'), 'w')
mydata.create_dataset('electrodes', data=best_elecs)
mydata.close()
comm.Barrier()
if comm.rank == 0:
# Gather data from all threads/processes.
f_next, extension = os.path.splitext(file_name)
file_out_bis = os.path.join(f_next, os.path.basename(f_next))
# new_params.set('data', 'file_out', file_out_bis) # Output file without suffix
# new_params.set('data', 'file_out_suff', file_out_bis + params.get('data', 'suffix'))
new_params.get_data_file()
io.collect_data(comm.size,
new_params,
erase=True,
with_real_amps=True,
with_voltages=True,
benchmark=True)
# Change some flags in the configuration file.
new_params.write('whitening', 'temporal',
'False') # Disable temporal filtering
new_params.write('whitening', 'spatial',
'False') # Disable spatial filtering
new_params.write('data', 'data_dtype',
'float32') # Set type of the data to float32
new_params.write('data', 'dtype_offset',
'auto') # Set padding for data to auto
# Move results from `<dataset>/<dataset>.result.hdf5` to
# `<dataset>/injected/<dataset>.result.hdf5`.
shutil.move(os.path.join(file_out, data_suff + '.result.hdf5'),
os.path.join(result_path, data_suff + '.result.hdf5'))
# Save scalings into `<dataset>/injected/<dataset>.scalings.npy`.
numpy.save(os.path.join(result_path, data_suff + '.scalings'),
scalings)
file_name_noext, ext = os.path.splitext(file_name)
# Copy basis from `<dataset>/injected/<dataset>.basis.hdf5` to
# `<dataset>/<dataset>.basis.hdf5`.
shutil.copy2(os.path.join(result_path, data_suff + '.basis.hdf5'),
os.path.join(file_out, data_suff + '.basis.hdf5'))
if benchmark not in ['fitting', 'synchrony']:
# Copy templates from `<dataset>/<dataset>.templates.hdf5` to
# `<dataset>/injected/<dataset>.templates.hdf5`
shutil.move(
os.path.join(file_out, data_suff + '.templates.hdf5'),
os.path.join(result_path, data_suff + '.templates.hdf5'))
def main(params, nb_cpu, nb_gpu, use_gpu):
numpy.random.seed(426236)
# params = detect_memory(params)
parallel_hdf5 = get_parallel_hdf5_flag(params)
_ = init_logging(params.logfile)
logger = logging.getLogger('circus.extracting')
#################################################################
data_file = params.data_file
N_e = params.getint('data', 'N_e')
N_t = params.getint('detection', 'N_t')
N_total = params.nb_channels
template_shift = params.getint('detection', 'template_shift')
chunk_size = detect_memory(params)
file_out = params.get('data', 'file_out')
file_out_suff = params.get('data', 'file_out_suff')
do_temporal_whitening = params.getboolean('whitening', 'temporal')
do_spatial_whitening = params.getboolean('whitening', 'spatial')
nodes, edges = get_nodes_and_edges(params)
safety_time = params.getint('extracting', 'safety_time')
max_elts_temp = params.getint('extracting', 'max_elts')
output_dim = params.getfloat('extracting', 'output_dim')
noise_thr = params.getfloat('extracting', 'noise_thr')
hdf5_compress = params.getboolean('data', 'hdf5_compress')
blosc_compress = params.getboolean('data', 'blosc_compress')
tmp_limits = params.get('fitting',
'amp_limits').replace('(',
'').replace(')',
'').split(',')
amp_limits = map(float, tmp_limits)
elt_count = 0
inv_nodes = numpy.zeros(N_total, dtype=numpy.int32)
inv_nodes[nodes] = numpy.arange(len(nodes))
data_file.open()
#################################################################
if comm.rank == 0:
print_and_log(["Extracting templates from already found clusters..."],
'default', logger)
thresholds = io.load_data(params, 'thresholds')
basis_proj, basis_rec = io.load_data(params, 'basis')
clusters, spiketimes, N_clusters = io.load_data(params, 'spike-cluster')
inv_clusters = numpy.zeros(clusters.max() + 1, dtype=numpy.int32)
inv_clusters[numpy.unique(clusters)] = numpy.argsort(
numpy.unique(clusters))
if use_gpu:
import cudamat as cmt
# # Need to properly handle multi GPU per MPI nodes?
if nb_gpu > nb_cpu:
gpu_id = int(comm.rank // nb_cpu)
else:
gpu_id = 0
cmt.cuda_set_device(gpu_id)
cmt.init()
cmt.cuda_sync_threads()
if do_spatial_whitening:
spatial_whitening = io.load_data(params, 'spatial_whitening')
else:
spatial_whitening = None # default assignment (PyCharm code inspection)
if do_temporal_whitening:
temporal_whitening = io.load_data(params, 'temporal_whitening')
else:
temporal_whitening = None # default assignment (PyCharm code inspection)
if use_gpu and do_spatial_whitening:
spatial_whitening = cmt.CUDAMatrix(spatial_whitening,
copy_on_host=False)
result = {}
for i in range(N_clusters):
result['data_tmp_' + str(i)] = numpy.zeros(
(0, N_e * basis_proj.shape[1]), dtype=numpy.float32)
result['times_' + str(i)] = numpy.zeros(0, dtype=numpy.int32)
nb_chunks, last_chunk_len = data_file.analyze(chunk_size)
# I guess this is more relevant, to take signals from all over the recordings.
all_chunks = numpy.random.permutation(numpy.arange(nb_chunks))
nb_templates = numpy.sum(
comm.rank == numpy.mod(numpy.arange(N_clusters), comm.size))
nb_elts = max_elts_temp * nb_templates
to_explore = all_chunks
if comm.rank == 0:
to_explore = get_tqdm_progressbar(params, to_explore)
for gidx in all_chunks:
if elt_count < nb_elts:
# print "Node", comm.rank, "is analyzing chunk", gidx, "/", nb_chunks, " ..."
local_chunk, t_offset = data_file.get_data(gidx,
chunk_size,
nodes=nodes)
local_shape = len(local_chunk)
if do_spatial_whitening:
if use_gpu:
local_chunk = cmt.CUDAMatrix(local_chunk,
copy_on_host=False)
local_chunk = local_chunk.dot(spatial_whitening).asarray()
else:
local_chunk = numpy.dot(local_chunk, spatial_whitening)
if do_temporal_whitening:
local_chunk = scipy.ndimage.filters.convolve1d(
local_chunk, temporal_whitening, axis=0, mode='constant')
# print "Extracting the peaks..."
idx = numpy.where((spiketimes >= gidx * chunk_size)
& (spiketimes < (gidx + 1) * chunk_size))[0]
local_offset = t_offset
local_peaktimes = spiketimes[idx] - local_offset
# print "Removing the useless borders..."
local_borders = (template_shift, chunk_size - template_shift)
idx = (local_peaktimes >= local_borders[0]) & (local_peaktimes <
local_borders[1])
local_peaktimes = local_peaktimes[idx]
local_clusters = inv_clusters[clusters[idx]]
if len(local_peaktimes) > 0:
all_times = numpy.zeros(
(N_e, local_peaktimes[-1] - local_peaktimes[0] + 1),
dtype=numpy.bool)
min_times = numpy.maximum(
local_peaktimes - local_peaktimes[0] - safety_time, 0)
max_times = numpy.minimum(
local_peaktimes - local_peaktimes[0] + safety_time + 1,
local_peaktimes[-1] - local_peaktimes[0])
n_times = len(local_peaktimes)
argmax_peak = numpy.random.permutation(numpy.arange(n_times))
clusters_id = local_clusters[argmax_peak]
local_peaktimes = local_peaktimes[argmax_peak]
# print "Selection of the peaks with spatio-temporal masks..."
for idx in range(len(local_peaktimes)):
if elt_count == nb_elts:
break
temp = clusters_id[idx]
if numpy.mod(temp, comm.size) == comm.rank:
elec = numpy.argmin(local_chunk[local_peaktimes[idx]])
indices = inv_nodes[edges[nodes[elec]]]
myslice = all_times[indices,
min_times[idx]:max_times[idx]]
peak = local_peaktimes[idx]
if not myslice.any():
if len(result['data_tmp_' +
str(temp)]) < max_elts_temp:
elt_count += 1
sub_mat = local_chunk[peak -
template_shift:peak +
template_shift + 1, :]
sub_mat = numpy.dot(basis_rec, sub_mat)
nx, ny = sub_mat.shape
sub_mat = sub_mat.reshape((1, nx * ny))
result['data_tmp_' + str(temp)] = numpy.vstack(
(result['data_tmp_' + str(temp)], sub_mat))
to_add = numpy.array([peak + local_offset],
dtype=numpy.int32)
result['times_' +
str(temp)] = numpy.concatenate(
(result['times_' + str(temp)],
to_add))
all_times[indices,
min_times[idx]:max_times[idx]] = True
total_nb_elts = 0
for temp in range(N_clusters):
total_nb_elts += len(result['data_tmp_' + str(temp)])
gdata = gather_array(numpy.array([total_nb_elts], dtype=numpy.float32),
comm, 0)
if comm.rank == 0:
print_and_log([
"Found %d spikes over %d requested" %
(int(numpy.sum(gdata)), int(nb_elts))
], 'default', logger)
# print "Spikes extracted in", time.time() - t_start, "s"
comm.Barrier()
local_nb_clusters = 0
for temp in range(comm.rank, N_clusters, comm.size):
if len(result['data_tmp_' + str(temp)]) > 0:
local_nb_clusters += 1
# print total_nb_clusters, "found in", time.time() - t_start, "s"
gdata3 = gather_array(
numpy.array([local_nb_clusters], dtype=numpy.float32), comm, 0)
comm.Barrier()
if comm.rank == 0:
print_and_log(["Extracting the templates..."], 'default', logger)
total_nb_clusters = int(
comm.bcast(numpy.array([int(numpy.sum(gdata3))], dtype=numpy.int32),
root=0)[0])
offsets = numpy.zeros(comm.size, dtype=numpy.int32)
for i in range(comm.size - 1):
offsets[i + 1] = comm.bcast(numpy.array([local_nb_clusters],
dtype=numpy.int32),
root=i)
if parallel_hdf5:
node_pad = numpy.sum(offsets[:comm.rank + 1])
hfile = h5py.File(file_out_suff + '.templates.hdf5',
'w',
driver='mpio',
comm=comm,
libver='earliest')
norms = hfile.create_dataset('norms',
shape=(2 * total_nb_clusters, ),
dtype=numpy.float32,
chunks=True)
electrodes = hfile.create_dataset('electrodes',
shape=(total_nb_clusters, ),
dtype=numpy.int32,
chunks=True)
amps_lims = hfile.create_dataset('limits',
shape=(total_nb_clusters, 2),
dtype=numpy.float32,
chunks=True)
g_count = node_pad
g_offset = total_nb_clusters
else:
node_pad = 0
hfile = h5py.File(file_out_suff + '.templates-%d.hdf5' % comm.rank,
'w',
libver='earliest')
electrodes = hfile.create_dataset('electrodes',
shape=(local_nb_clusters, ),
dtype=numpy.int32,
chunks=True)
norms = hfile.create_dataset('norms',
shape=(2 * local_nb_clusters, ),
dtype=numpy.float32,
chunks=True)
amps_lims = hfile.create_dataset('limits',
shape=(local_nb_clusters, 2),
dtype=numpy.float32,
chunks=True)
g_count = 0
g_offset = local_nb_clusters
cfile = h5py.File(file_out_suff + '.clusters-%d.hdf5' % comm.rank,
'w',
libver='earliest')
count_templates = node_pad
temp_x = numpy.zeros(0, dtype=numpy.int32)
temp_y = numpy.zeros(0, dtype=numpy.int32)
temp_data = numpy.zeros(0, dtype=numpy.float32)
to_explore = range(comm.rank, N_clusters, comm.size)
if comm.rank == 0:
to_explore = get_tqdm_progressbar(params, to_explore)
for temp in to_explore:
n_data = len(result['data_tmp_' + str(temp)])
if n_data > 0:
data = result['data_tmp_' + str(temp)].reshape(
n_data, basis_proj.shape[1], N_e)
first_component = numpy.median(data, axis=0)
tmp_templates = numpy.dot(first_component.T, basis_rec)
electrodes[g_count] = indices[tmpidx[0][0]]
indices = inv_nodes[edges[nodes[electrodes[-1]]]]
templates = numpy.zeros((N_e, N_t), dtype=numpy.float32)
if shift > 0:
templates[indices, shift:] = tmp_templates[:, :-shift]
elif shift < 0:
templates[indices, :shift] = tmp_templates[:, -shift:]
else:
templates[indices, :] = tmp_templates
templates = templates.flatten()
dx = templates.nonzero()[0].astype(numpy.int32)
temp_x = numpy.concatenate((temp_x, dx))
temp_y = numpy.concatenate(
(temp_y,
count_templates * numpy.ones(len(dx), dtype=numpy.int32)))
temp_data = numpy.concatenate((temp_data, templates[dx]))
norms[g_count] = numpy.sqrt(
numpy.sum(templates.flatten()**2) / (N_e * N_t))
x, y, z = data.shape
data_flat = data.reshape(x, y * z)
first_flat = first_component.reshape(y * z, 1)
amplitudes = numpy.dot(data_flat, first_flat)
amplitudes /= numpy.sum(first_flat**2)
for i in range(x):
data_flat[i, :] -= amplitudes[i] * first_flat[:, 0]
variations = 10 * numpy.median(
numpy.abs(amplitudes - numpy.median(amplitudes)))
physical_limit = noise_thr * (
-thresholds[indices[tmpidx[0][0]]]) / tmp_templates.min()
amp_min = max(physical_limit,
numpy.median(amplitudes) - variations)
amp_max = min(amp_limits[1], numpy.median(amplitudes) + variations)
amps_lims[g_count] = [amp_min, amp_max]
if len(data_flat) > 1:
pca = PCA(1)
res_pca = pca.fit_transform(data_flat.astype(numpy.double))
second_component = pca.components_.T.astype(
numpy.float32).reshape(y, z)
else:
second_component = data_flat.reshape(y, z) / numpy.sum(
data_flat**2)
tmp_templates = numpy.dot(second_component.T, basis_rec)
offset = total_nb_clusters + count_templates
sub_templates = numpy.zeros((N_e, N_t), dtype=numpy.float32)
if shift > 0:
sub_templates[indices, shift:] = tmp_templates[:, :-shift]
elif shift < 0:
sub_templates[indices, :shift] = tmp_templates[:, -shift:]
else:
sub_templates[indices, :] = tmp_templates
sub_templates = sub_templates.flatten()
dx = sub_templates.nonzero()[0].astype(numpy.int32)
temp_x = numpy.concatenate((temp_x, dx))
temp_y = numpy.concatenate(
(temp_y, offset * numpy.ones(len(dx), dtype=numpy.int32)))
temp_data = numpy.concatenate((temp_data, sub_templates[dx]))
norms[g_count + g_offset] = numpy.sqrt(
numpy.sum(sub_templates.flatten()**2) / (N_e * N_t))
count_templates += 1
g_count += 1
io.write_datasets(cfile,
to_write,
result,
ielec,
compress=hdf5_compress)
# At the end we should have a templates variable to store.
cfile.close()
del result, templates, amps_lims
comm.Barrier()
# We need to gather the sparse arrays.
temp_x = gather_array(temp_x, comm, dtype='int32', compress=blosc_compress)
temp_y = gather_array(temp_y, comm, dtype='int32', compress=blosc_compress)
temp_data = gather_array(temp_data, comm, compress=blosc_compress)
if parallel_hdf5:
if comm.rank == 0:
rs = [
h5py.File(file_out_suff + '.clusters-%d.hdf5' % i,
'r',
libver='earliest') for i in range(comm.size)
]
cfile = h5py.File(file_out_suff + '.clusters.hdf5',
'w',
libver='earliest')
io.write_datasets(cfile, ['electrodes'],
{'electrodes': electrodes[:]},
compress=hdf5_compress)
for i in range(comm.size):
for j in range(i, N_e, comm.size):
io.write_datasets(cfile,
to_write,
rs[i],
j,
compress=hdf5_compress)
rs[i].close()
os.remove(file_out_suff + '.clusters-%d.hdf5' % i)
cfile.close()
hfile.close()
else:
hfile.close()
if comm.rank == 0:
ts = [
h5py.File(file_out_suff + '.templates-%d.hdf5' % i,
'r',
libver='earliest') for i in range(comm.size)
]
rs = [
h5py.File(file_out_suff + '.clusters-%d.hdf5' % i,
'r',
libver='earliest') for i in range(comm.size)
]
result = {}
hfile = h5py.File(file_out_suff + '.templates.hdf5',
'w',
libver='earliest')
cfile = h5py.File(file_out_suff + '.clusters.hdf5',
'w',
libver='earliest')
electrodes = hfile.create_dataset('electrodes',
shape=(total_nb_clusters, ),
dtype=numpy.int32,
chunks=True)
norms = hfile.create_dataset('norms',
shape=(2 * total_nb_clusters, ),
dtype=numpy.float32,
chunks=True)
amplitudes = hfile.create_dataset('limits',
shape=(total_nb_clusters, 2),
dtype=numpy.float32,
chunks=True)
count = 0
for i in range(comm.size):
loc_temp = ts[i].get('templates')
middle = loc_temp.shape[2] // 2
norms[count:count + middle] = loc_norms[:middle]
norms[n_clusters + count:n_clusters + count +
middle] = loc_norms[middle:]
electrodes[count:count + middle] = ts[i].get('electrodes')
amplitudes[count:count + middle] = ts[i].get('limits')
count += middle
for j in range(i, N_e, comm.size):
io.write_datasets(cfile,
to_write,
rs[i],
j,
compress=hdf5_compress)
ts[i].close()
rs[i].close()
os.remove(file_out_suff + '.templates-%d.hdf5' % i)
os.remove(file_out_suff + '.clusters-%d.hdf5' % i)
io.write_datasets(cfile, ['electrodes'],
{'electrodes': electrodes[:]},
compress=hdf5_compress)
hfile.close()
cfile.close()
if comm.rank == 0:
hfile = h5py.File(file_out_suff + '.templates.hdf5',
'r+',
libver='earliest')
hfile.create_dataset('temp_x', data=temp_x)
hfile.create_dataset('temp_y', data=temp_y)
hfile.create_dataset('temp_data', data=temp_data)
hfile.create_dataset('temp_shape',
data=numpy.array(
[N_e, N_t, 2 * total_nb_clusters],
dtype=numpy.int32))
hfile.close()
comm.Barrier()
if comm.rank == 0:
print_and_log(["Merging similar templates..."], 'default', logger)
merged1 = algo.merging_cc(params, parallel_hdf5)
comm.Barrier()
if remove_mixture:
if comm.rank == 0:
print_and_log(["Removing mixtures..."], 'default', logger)
merged2 = algo.delete_mixtures(params, parallel_hdf5)
else:
merged2 = [0, 0]
if comm.rank == 0:
lines = [
"Number of global merges : %d" % merged1[1],
"Number of mixtures removed : %d" % merged2[1],
]
print_and_log(lines, 'info', logger)
comm.Barrier()
io.get_overlaps(params, erase=True, parallel_hdf5=parallel_hdf5)
data_file.close()
def main(params, nb_cpu, nb_gpu, use_gpu):
# Part 1: Whitening
numpy.random.seed(420)
#params = detect_memory(params)
logger = init_logging(params.logfile)
logger = logging.getLogger('circus.whitening')
#################################################################
data_file = params.data_file
N_e = params.getint('data', 'N_e')
hdf5_compress = params.getboolean('data', 'hdf5_compress')
N_total = params.nb_channels
N_t = params.getint('detection', 'N_t')
dist_peaks = params.getint('detection', 'dist_peaks')
template_shift = params.getint('detection', 'template_shift')
file_out_suff = params.get('data', 'file_out_suff')
spike_thresh = params.getfloat('detection', 'spike_thresh')
spike_width = params.getfloat('detection', 'spike_width')
matched_filter = params.getboolean('detection', 'matched-filter')
matched_thresh = params.getfloat('detection', 'matched_thresh')
sign_peaks = params.get('detection', 'peaks')
do_temporal_whitening = params.getboolean('whitening', 'temporal')
do_spatial_whitening = params.getboolean('whitening', 'spatial')
chunk_size = detect_memory(params, whitening=True)
plot_path = os.path.join(params.get('data', 'file_out_suff'), 'plots')
nodes, edges = get_nodes_and_edges(params)
safety_time = params.getint('whitening', 'safety_time')
safety_space = params.getboolean('whitening', 'safety_space')
nb_temp_white = min(max(20, comm.size), N_e)
max_silence_1 = int(20 * params.rate // comm.size)
max_silence_2 = 5000
inv_nodes = numpy.zeros(N_total, dtype=numpy.int32)
inv_nodes[nodes] = numpy.arange(len(nodes))
jitter_range = params.getint('detection', 'jitter_range')
template_shift_2 = template_shift + jitter_range
use_hanning = params.getboolean('detection', 'hanning')
data_file.open()
#################################################################
if use_hanning:
hanning_filter = numpy.hanning(N_t)
if comm.rank == 0:
print_and_log(
["Analyzing data to get whitening matrices and thresholds..."],
'default', logger)
if use_gpu:
import cudamat as cmt
## Need to properly handle multi GPU per MPI nodes?
if nb_gpu > nb_cpu:
gpu_id = int(comm.rank // nb_cpu)
else:
gpu_id = 0
cmt.cuda_set_device(gpu_id)
cmt.init()
cmt.cuda_sync_threads()
nb_chunks, last_chunk_len = data_file.analyze(chunk_size)
if nb_chunks < comm.size:
res = io.data_stats(params, show=False)
chunk_size = int(res * params.rate // comm.size)
if comm.rank == 0:
print_and_log(
["Too much cores, automatically resizing the data chunks"],
'debug', logger)
nb_chunks, last_chunk_len = data_file.analyze(chunk_size)
# I guess this is more relevant, to take signals from all over the recordings
all_chunks = numpy.random.permutation(
numpy.arange(nb_chunks, dtype=numpy.int32))
all_electrodes = numpy.random.permutation(N_e)
for gidx in [all_chunks[comm.rank]]:
#print "Node", comm.rank, "is analyzing chunk", gidx, "/", nb_chunks, " ..."
local_chunk, t_offset = data_file.get_data(gidx,
chunk_size,
nodes=nodes)
local_shape = len(local_chunk)
#print "Node", comm.rank, "computes the median absolute deviations in a random chunk"
thresholds = numpy.zeros(N_e, dtype=numpy.float32)
for i in xrange(N_e):
u = numpy.median(local_chunk[:, i], 0)
thresholds[i] = numpy.median(numpy.abs(local_chunk[:, i] - u), 0)
gdata = gather_array(thresholds, comm)
if comm.rank == 0:
gdata = gdata.reshape((comm.size, N_e))
thresholds = numpy.mean(gdata, 0)
bfile = h5py.File(file_out_suff + '.basis.hdf5',
'w',
libver='earliest')
io.write_datasets(bfile, ['thresholds'],
{'thresholds': thresholds},
compression=hdf5_compress)
bfile.close()
comm.Barrier()
thresholds = io.load_data(params, 'thresholds')
#print "Extracting the peaks..."
local_peaktimes = numpy.zeros(0, dtype=numpy.uint32)
for i in xrange(N_e):
peaktimes = scipy.signal.find_peaks(numpy.abs(local_chunk[:, i]),
height=thresholds[i],
width=spike_width,
wlen=N_t)[0]
local_peaktimes = numpy.concatenate((local_peaktimes, peaktimes))
local_peaktimes = numpy.unique(local_peaktimes)
#print "Removing the useless borders..."
local_borders = (template_shift, local_shape - template_shift)
idx = (local_peaktimes >= local_borders[0]) & (local_peaktimes <
local_borders[1])
local_peaktimes = numpy.compress(idx, local_peaktimes)
if len(local_peaktimes) > 0:
diff_times = local_peaktimes[-1] - local_peaktimes[0]
all_times = numpy.zeros((N_e, diff_times + 1), dtype=numpy.bool)
min_times = numpy.maximum(
local_peaktimes - local_peaktimes[0] - safety_time, 0)
max_times = numpy.minimum(
local_peaktimes - local_peaktimes[0] + safety_time + 1,
diff_times)
argmax_peak = numpy.random.permutation(
numpy.arange(len(local_peaktimes)))
all_idx = numpy.take(local_peaktimes, argmax_peak)
#print "Selection of the peaks with spatio-temporal masks..."
for idx, peak in zip(argmax_peak, all_idx):
elec = numpy.argmax(numpy.abs(local_chunk[peak]))
indices = numpy.take(inv_nodes, edges[nodes[elec]])
if safety_space:
all_times[indices, min_times[idx]:max_times[idx]] = True
else:
all_times[elec, min_times[idx]:max_times[idx]] = True
else:
all_times = numpy.zeros((N_e, len(local_chunk)), dtype=numpy.bool)
if do_temporal_whitening:
local_res_temp = []
for elec in all_electrodes[numpy.arange(comm.rank, nb_temp_white,
comm.size)]:
res = numpy.zeros((0, N_t), dtype=numpy.float32)
scount = 0
indices = numpy.take(inv_nodes, edges[nodes[elec]])
all_times_elec = numpy.any(numpy.take(all_times, indices, axis=0),
0)
esubset = numpy.where(all_times_elec == False)[0]
bound = len(esubset) - N_t
while (scount < bound) and (len(res) < max_silence_2):
myslice = esubset[scount:scount + N_t]
if numpy.all((myslice - esubset[scount]) == numpy.arange(N_t)):
scount += N_t
res = numpy.vstack((res, local_chunk[myslice, elec]))
else:
scount += 1
if len(res) > 5:
local_res_temp += [numpy.cov(res.T)]
nb_elecs = numpy.array([len(local_res_temp)], dtype=numpy.float32)
local_res_temp = numpy.array(local_res_temp, dtype=numpy.float32)
if len(local_res_temp) == 0:
local_res_temp = numpy.zeros(0, dtype=numpy.float32)
else:
local_res_temp = numpy.sum(local_res_temp, 0)
all_res_temp = gather_array(local_res_temp.ravel(), comm, 0, 1)
all_elecs = gather_array(nb_elecs, comm, 0, 1)
if do_spatial_whitening:
local_res_spac = numpy.zeros((N_e, N_e), dtype=numpy.float32)
local_silences = []
for elec in numpy.arange(comm.rank, N_e, comm.size):
indices = numpy.take(inv_nodes, edges[nodes[elec]])
all_times_elec = numpy.any(numpy.take(all_times, indices, axis=0),
0)
esubset = numpy.where(all_times_elec == False)[0]
local_data = local_chunk[esubset][:, indices]
local_whitening = get_whitening_matrix(local_data).astype(
numpy.float32)
pos = numpy.where(elec == indices)[0]
local_res_spac[elec, indices] = local_whitening[pos]
local_silences += [len(esubset)]
all_res_spac = gather_array(local_res_spac.ravel(), comm, 0, 1)
all_silences = gather_array(
numpy.array(local_silences, dtype=numpy.int32), comm, 0, 1,
'uint32')
if comm.rank == 0:
to_write = {}
if do_temporal_whitening:
try:
nb_silences = numpy.sum(all_elecs > 0)
all_res_temp = all_res_temp.reshape((nb_silences, N_t**2))
except Exception:
print_and_log([
"No silent periods detected: something wrong with the parameters?"
], 'error', logger)
all_res_temp = numpy.sum(all_res_temp, 0)
all_res_temp = all_res_temp.reshape(
(N_t, N_t)) / numpy.sum(all_elecs)
temporal_whitening = get_whitening_matrix(
all_res_temp.astype(numpy.double),
fudge=1e-3)[template_shift].astype(numpy.float32)
temporal_whitening /= temporal_whitening.sum()
to_write['temporal'] = temporal_whitening
have_nans = numpy.sum(numpy.isnan(temporal_whitening))
if have_nans > 0:
temporal_whitening = numpy.zeros(N_t, dtype=numpy.float32)
temporal_whitening[N_t // 2] = 1
to_write['temporal'] = temporal_whitening
print_and_log(
["Disabling temporal whitening because of NaNs found"],
'info', logger)
if do_spatial_whitening:
all_res_spac = all_res_spac.reshape(comm.size, N_e, N_e)
spatial_whitening = numpy.sum(all_res_spac, 0)
to_write['spatial'] = spatial_whitening
print_and_log([
"Found %gs without spikes for whitening matrices..." %
(numpy.mean(all_silences) / params.rate)
], 'default', logger)
have_nans = numpy.sum(numpy.isnan(spatial_whitening))
if have_nans > 0:
spatial_whitening = numpy.eye(spatial_whitening.shape[0],
dtype=numpy.float32)
to_write['spatial'] = spatial_whitening
print_and_log(
["Disabling spatial whitening because of NaNs found"],
'info', logger)
bfile = h5py.File(file_out_suff + '.basis.hdf5',
'r+',
libver='earliest')
io.write_datasets(bfile,
to_write.keys(),
to_write,
compression=hdf5_compress)
bfile.close()
comm.Barrier()
if do_spatial_whitening or do_temporal_whitening:
if comm.rank == 0:
print_and_log(
["Because of whitening, need to recompute the thresholds..."],
'default', logger)
if do_spatial_whitening:
spatial_whitening = io.load_data(params, 'spatial_whitening')
if use_gpu:
spatial_whitening = cmt.CUDAMatrix(spatial_whitening,
copy_on_host=False)
if do_temporal_whitening:
temporal_whitening = io.load_data(params, 'temporal_whitening')
for gidx in [all_chunks[comm.rank]]:
local_chunk, t_offset = data_file.get_data(gidx,
chunk_size,
nodes=nodes)
local_shape = len(local_chunk)
if do_spatial_whitening:
if use_gpu:
local_chunk = cmt.CUDAMatrix(local_chunk,
copy_on_host=False)
local_chunk = local_chunk.dot(spatial_whitening).asarray()
else:
local_chunk = numpy.dot(local_chunk, spatial_whitening)
if do_temporal_whitening:
local_chunk = scipy.ndimage.filters.convolve1d(
local_chunk, temporal_whitening, axis=0, mode='constant')
thresholds = numpy.zeros(N_e, dtype=numpy.float32)
for i in xrange(N_e):
u = numpy.median(local_chunk[:, i], 0)
thresholds[i] = numpy.median(numpy.abs(local_chunk[:, i] - u),
0)
gdata = gather_array(thresholds, comm)
if comm.rank == 0:
gdata = gdata.reshape((comm.size, N_e))
thresholds = numpy.mean(gdata, 0)
bfile = h5py.File(file_out_suff + '.basis.hdf5',
'r+',
libver='earliest')
bfile.pop('thresholds')
io.write_datasets(bfile, ['thresholds'],
{'thresholds': thresholds},
compression=hdf5_compress)
bfile.close()
comm.Barrier()
#if comm.rank == 0:
#if not os.path.exists(plot_path):
# os.makedirs(plot_path)
#N_elec = min(int(numpy.sqrt(data_file.N_e)), 5)
#plot.view_fit(filename, t_start=0, t_stop=1, fit_on=False, square=True,
# n_elec=N_elec, save=[plot_path, 'electrodes'])
# Part 2: Basis
numpy.random.seed(422)
#################################################################
file_out = params.get('data', 'file_out')
alignment = params.getboolean('detection', 'alignment')
smoothing = params.getboolean('detection', 'smoothing')
isolation = params.getboolean('detection', 'isolation')
over_factor = params.getint('detection', 'oversampling_factor')
spike_thresh = params.getfloat('detection', 'spike_thresh')
nodes, edges = get_nodes_and_edges(params)
do_temporal_whitening = params.getboolean('whitening', 'temporal')
do_spatial_whitening = params.getboolean('whitening', 'spatial')
if matched_filter:
chunk_size = detect_memory(params, whitening=True)
else:
chunk_size = detect_memory(params)
safety_time = params.getint('whitening', 'safety_time')
max_elts_elec = params.getint('whitening', 'max_elts')
output_dim = params.getfloat('whitening', 'output_dim')
inv_nodes = numpy.zeros(N_total, dtype=numpy.int32)
inv_nodes[nodes] = numpy.arange(len(nodes))
smoothing_factor = params.getfloat(
'detection', 'smoothing_factor') * (1. / spike_thresh)**2
if sign_peaks == 'both':
max_elts_elec *= 2
nb_elts = int(
params.getfloat('whitening', 'nb_elts') * N_e * max_elts_elec)
ignore_dead_times = params.getboolean('triggers', 'ignore_times')
if ignore_dead_times:
all_dead_times = get_dead_times(params)
data_file.open()
#################################################################
if comm.rank == 0:
print_and_log(["Searching spikes to construct the PCA basis..."],
'default', logger)
nb_chunks, last_chunk_len = data_file.analyze(chunk_size)
if nb_chunks < comm.size:
res = io.data_stats(params, show=False)
chunk_size = int(res * params.rate // comm.size)
if comm.rank == 0:
print_and_log(
["Too much cores, automatically resizing the data chunks"],
'debug', logger)
nb_chunks, last_chunk_len = data_file.analyze(chunk_size)
groups = {}
for i in xrange(N_e):
groups[i] = 0
# I guess this is more relevant, to take signals from all over the recordings
all_chunks = numpy.random.permutation(
numpy.arange(nb_chunks, dtype=numpy.int32))
max_elts_elec //= comm.size
nb_elts //= comm.size
elt_count_pos = 0
elt_count_neg = 0
if sign_peaks in ['positive', 'both']:
elts_pos = numpy.zeros((N_t, nb_elts), dtype=numpy.float32)
if sign_peaks in ['negative', 'both']:
elts_neg = numpy.zeros((N_t, nb_elts), dtype=numpy.float32)
chunks_to_load = all_chunks[comm.rank::comm.size]
thresholds = io.load_data(params, 'thresholds')
mads = io.load_data(params, 'mads')
if alignment:
cdata = numpy.linspace(-jitter_range, jitter_range,
int(over_factor * 2 * jitter_range))
xdata = numpy.arange(-template_shift_2, template_shift_2 + 1)
xoff = len(cdata) / 2.
if isolation:
yoff = numpy.array(range(0, N_t // 4) + range(3 * N_t // 4, N_t))
to_explore = xrange(comm.rank, nb_chunks, comm.size)
if comm.rank == 0:
to_explore = get_tqdm_progressbar(to_explore)
for gcount, gidx in enumerate(to_explore):
gidx = all_chunks[gidx]
if ((elt_count_pos + elt_count_neg) < nb_elts):
#print "Node", comm.rank, "is analyzing chunk", gidx, "/", nb_chunks, " ..."
local_chunk, t_offset = data_file.get_data(gidx,
chunk_size,
nodes=nodes)
local_shape = len(local_chunk)
if do_spatial_whitening:
if use_gpu:
local_chunk = cmt.CUDAMatrix(local_chunk,
copy_on_host=False)
local_chunk = local_chunk.dot(spatial_whitening).asarray()
else:
local_chunk = numpy.dot(local_chunk, spatial_whitening)
if do_temporal_whitening:
local_chunk = scipy.ndimage.filters.convolve1d(
local_chunk, temporal_whitening, axis=0, mode='constant')
#print "Extracting the peaks..."
all_peaktimes = numpy.zeros(0, dtype=numpy.uint32)
all_extremas = numpy.zeros(0, dtype=numpy.uint32)
for i in xrange(N_e):
if sign_peaks == 'negative':
peaktimes = scipy.signal.find_peaks(-local_chunk[:, i],
height=thresholds[i],
width=spike_width,
distance=dist_peaks,
wlen=N_t)[0]
elif sign_peaks == 'positive':
peaktimes = scipy.signal.find_peaks(local_chunk[:, i],
height=thresholds[i],
width=spike_width,
wlen=N_t)[0]
elif sign_peaks == 'both':
peaktimes = scipy.signal.find_peaks(numpy.abs(
local_chunk[:, i]),
height=thresholds[i],
width=spike_width,
wlen=N_t)[0]
all_peaktimes = numpy.concatenate((all_peaktimes, peaktimes))
all_extremas = numpy.concatenate(
(all_extremas,
i * numpy.ones(len(peaktimes), dtype=numpy.uint32)))
#print "Removing the useless borders..."
if alignment:
local_borders = (template_shift_2,
local_shape - template_shift_2)
else:
local_borders = (template_shift, local_shape - template_shift)
idx = (all_peaktimes >= local_borders[0]) & (all_peaktimes <
local_borders[1])
all_peaktimes = numpy.compress(idx, all_peaktimes)
all_extremas = numpy.compress(idx, all_extremas)
local_peaktimes = numpy.unique(all_peaktimes)
if ignore_dead_times:
dead_indices = numpy.searchsorted(
all_dead_times, [t_offset, t_offset + local_shape])
if dead_indices[0] != dead_indices[1]:
is_included = numpy.in1d(
local_peaktimes + t_offset,
all_dead_times[dead_indices[0]:dead_indices[1]])
local_peaktimes = local_peaktimes[~is_included]
local_peaktimes = numpy.sort(local_peaktimes)
if len(local_peaktimes) > 0:
diff_times = local_peaktimes[-1] - local_peaktimes[0]
all_times = numpy.zeros((N_e, diff_times + 1),
dtype=numpy.bool)
min_times = numpy.maximum(
local_peaktimes - local_peaktimes[0] - safety_time, 0)
max_times = numpy.minimum(
local_peaktimes - local_peaktimes[0] + safety_time + 1,
diff_times)
n_times = len(local_peaktimes)
argmax_peak = numpy.random.permutation(numpy.arange(n_times))
all_idx = numpy.take(local_peaktimes, argmax_peak)
#print "Selection of the peaks with spatio-temporal masks..."
for midx, peak in zip(argmax_peak, all_idx):
if (elt_count_neg + elt_count_pos) == nb_elts:
break
if sign_peaks == 'negative':
elec = numpy.argmin(local_chunk[peak])
negative_peak = True
elif sign_peaks == 'positive':
elec = numpy.argmax(local_chunk[peak])
negative_peak = False
elif sign_peaks == 'both':
if N_e == 1:
if local_chunk[peak] < 0:
negative_peak = True
elif local_chunk[peak] > 0:
negative_peak = False
elec = 0
else:
if numpy.abs(numpy.max(
local_chunk[peak])) > numpy.abs(
numpy.min(local_chunk[peak])):
elec = numpy.argmax(local_chunk[peak])
negative_peak = False
else:
elec = numpy.argmin(local_chunk[peak])
negative_peak = True
indices = numpy.take(inv_nodes, edges[nodes[elec]])
myslice = all_times[indices,
min_times[midx]:max_times[midx]]
is_local_extrema = elec in all_extremas[all_peaktimes ==
peak]
if is_local_extrema and not myslice.any():
upper_bounds = max_elts_elec
if groups[elec] < upper_bounds:
if not alignment:
sub_mat = local_chunk[peak -
template_shift:peak +
template_shift + 1, elec]
elif alignment:
ydata = local_chunk[peak -
template_shift_2:peak +
template_shift_2 + 1, elec]
if smoothing:
factor = smoothing_factor * xdata.size
f = scipy.interpolate.UnivariateSpline(
xdata, ydata, s=factor, k=3)
else:
f = scipy.interpolate.UnivariateSpline(
xdata, ydata, k=3, s=0)
if negative_peak:
rmin = (numpy.argmin(f(cdata)) -
xoff) / over_factor
else:
rmin = (numpy.argmax(f(cdata)) -
xoff) / over_factor
ddata = numpy.linspace(rmin - template_shift,
rmin + template_shift,
N_t)
sub_mat = f(ddata).astype(numpy.float32)
if alignment:
if negative_peak:
if numpy.min(sub_mat) >= -thresholds[elec]:
to_accept = False
else:
if numpy.max(sub_mat) <= thresholds[elec]:
to_accept = False
if isolation:
to_accept = numpy.all(
numpy.max(numpy.abs(sub_mat[yoff])) <=
thresholds[elec])
else:
to_accept = True
if to_accept:
if negative_peak:
elts_neg[:, elt_count_neg] = sub_mat
else:
elts_pos[:, elt_count_pos] = sub_mat
if negative_peak:
elt_count_neg += 1
else:
elt_count_pos += 1
groups[elec] += 1
all_times[indices,
min_times[midx]:max_times[midx]] = True
sys.stderr.flush()
if isolation:
print_and_log([
"Node %d has collected %d isolated waveforms" %
(comm.rank, elt_count_pos + elt_count_neg)
], 'debug', logger)
else:
print_and_log([
"Node %d has collected %d waveforms" %
(comm.rank, elt_count_pos + elt_count_neg)
], 'debug', logger)
if sign_peaks in ['negative', 'both']:
gdata_neg = gather_array(elts_neg[:, :elt_count_neg].T, comm, 0, 1)
if sign_peaks in ['positive', 'both']:
gdata_pos = gather_array(elts_pos[:, :elt_count_pos].T, comm, 0, 1)
nb_waveforms = 0
if comm.rank == 0:
#DO PCA on elts and store the basis obtained.
if sign_peaks in ['negative', 'both']:
nb_waveforms += gdata_neg.shape[0]
if sign_peaks in ['positive', 'both']:
nb_waveforms += gdata_pos.shape[0]
nb_waveforms = all_gather_array(
numpy.array([nb_waveforms], dtype=numpy.float32), comm, 0)[0]
if comm.rank == 0:
if isolation:
print_and_log([
"Found %d isolated waveforms over %d requested" %
(nb_waveforms, int(nb_elts * comm.size))
], 'default', logger)
else:
print_and_log([
"Found %d waveforms over %d requested" %
(nb_waveforms, int(nb_elts * comm.size))
], 'default', logger)
if nb_waveforms == 0:
print_and_log(
['No waveforms found! Are the data properly loaded??'],
'error', logger)
if nb_waveforms == 0:
sys.exit(0)
if comm.rank == 0:
res = {}
pca = None
pca_pos = None
pca_neg = None
if sign_peaks in ['negative', 'both']:
if len(gdata_neg) > 0:
pca = PCA(output_dim)
if use_hanning:
pca.fit(gdata_neg * hanning_filter)
else:
pca.fit(gdata_neg)
res['proj'] = pca.components_.T.astype(numpy.float32)
pca_neg = numpy.sum(pca.explained_variance_ratio_)
else:
res['proj'] = numpy.identity(int(output_dim),
dtype=numpy.float32)
res['rec'] = res['proj'].T
res['waveform'] = numpy.median(gdata_neg, 0)
idx = numpy.random.permutation(numpy.arange(
gdata_neg.shape[0]))[:1000]
res['waveforms'] = gdata_neg[idx, :]
if sign_peaks in ['positive', 'both']:
if len(gdata_pos) > 0:
pca = PCA(output_dim)
if use_hanning:
pca.fit(gdata_pos * hanning_filter)
else:
pca.fit(gdata_pos)
res['proj_pos'] = pca.components_.T.astype(numpy.float32)
pca_pos = numpy.sum(pca.explained_variance_ratio_)
else:
res['proj_pos'] = numpy.identity(int(output_dim),
dtype=numpy.float32)
res['rec_pos'] = res['proj_pos'].T
res['waveform_pos'] = numpy.median(gdata_pos, 0)
idx = numpy.random.permutation(numpy.arange(
gdata_pos.shape[0]))[:1000]
res['waveforms_pos'] = gdata_pos[idx, :]
bfile = h5py.File(file_out_suff + '.basis.hdf5',
'r+',
libver='earliest')
io.write_datasets(bfile, res.keys(), res, compression=hdf5_compress)
if sign_peaks == 'positive':
print_and_log([
"A basis with %s dimensions has been built" %
res['proj_pos'].shape[1]
], 'info', logger)
elif sign_peaks == 'negative':
print_and_log([
"A basis with %s dimensions has been built" %
res['proj'].shape[1]
], 'info', logger)
elif sign_peaks == 'both':
print_and_log([
"Two basis with %s dimensions has been built" %
res['proj'].shape[1]
], 'debug', logger)
if pca_pos is not None:
print_and_log([
"The percentage of variance explained is %s for positive spikes"
% pca_pos
], 'debug', logger)
if pca_neg is not None:
print_and_log([
"The percentage of variance explained is %s for negative spikes"
% pca_neg
], 'debug', logger)
bfile.close()
comm.Barrier()
if matched_filter:
if comm.rank == 0:
print_and_log([
"Because of matched filters, need to recompute the thresholds..."
], 'default', logger)
if do_spatial_whitening:
spatial_whitening = io.load_data(params, 'spatial_whitening')
if use_gpu:
spatial_whitening = cmt.CUDAMatrix(spatial_whitening,
copy_on_host=False)
if do_temporal_whitening:
temporal_whitening = io.load_data(params, 'temporal_whitening')
if sign_peaks in ['negative', 'both']:
waveform_neg = io.load_data(params, 'waveform')[::-1]
waveform_neg /= (numpy.abs(numpy.sum(waveform_neg)) *
len(waveform_neg))
if sign_peaks in ['positive', 'both']:
waveform_pos = io.load_data(params, 'waveform-pos')[::-1]
waveform_pos /= (numpy.abs(numpy.sum(waveform_pos)) *
len(waveform_pos))
for gidx in [all_chunks[comm.rank]]:
local_chunk, t_offset = data_file.get_data(gidx,
chunk_size,
nodes=nodes)
local_shape = len(local_chunk)
if do_spatial_whitening:
if use_gpu:
local_chunk = cmt.CUDAMatrix(local_chunk,
copy_on_host=False)
local_chunk = local_chunk.dot(spatial_whitening).asarray()
else:
local_chunk = numpy.dot(local_chunk, spatial_whitening)
if do_temporal_whitening:
local_chunk = scipy.ndimage.filters.convolve1d(
local_chunk, temporal_whitening, axis=0, mode='constant')
local_chunk /= thresholds
if sign_peaks in ['negative', 'both']:
tmp_chunk = scipy.ndimage.filters.convolve1d(local_chunk,
waveform_neg,
axis=0,
mode='constant')
thresholds = numpy.zeros(N_e, dtype=numpy.float32)
for i in xrange(N_e):
u = numpy.median(tmp_chunk[:, i], 0)
thresholds[i] = numpy.median(
numpy.abs(tmp_chunk[:, i] - u), 0)
gdata = gather_array(thresholds, comm)
if comm.rank == 0:
gdata = gdata.reshape((comm.size, N_e))
thresholds = numpy.mean(gdata, 0)
bfile = h5py.File(file_out_suff + '.basis.hdf5',
'r+',
libver='earliest')
io.write_datasets(bfile, ['matched_thresholds'],
{'matched_thresholds': thresholds},
compression=hdf5_compress)
bfile.close()
comm.Barrier()
if sign_peaks in ['positive', 'both']:
tmp_chunk = scipy.ndimage.filters.convolve1d(local_chunk,
waveform_pos,
axis=0,
mode='constant')
thresholds = numpy.zeros(N_e, dtype=numpy.float32)
for i in xrange(N_e):
u = numpy.median(tmp_chunk[:, i], 0)
thresholds[i] = numpy.median(
numpy.abs(tmp_chunk[:, i] - u), 0)
gdata = gather_array(thresholds, comm)
if comm.rank == 0:
gdata = gdata.reshape((comm.size, N_e))
thresholds = numpy.mean(gdata, 0)
bfile = h5py.File(file_out_suff + '.basis.hdf5',
'r+',
libver='earliest')
io.write_datasets(bfile, ['matched_thresholds_pos'],
{'matched_thresholds_pos': thresholds},
compression=hdf5_compress)
bfile.close()
comm.Barrier()
data_file.close()
def main(params, nb_cpu, nb_gpu, use_gpu):
#################################################################
# params = detect_memory(params)
_ = init_logging(params.logfile)
SHARED_MEMORY = get_shared_memory_flag(params)
logger = logging.getLogger('circus.fitting')
data_file = params.data_file
n_e = params.getint('data', 'N_e')
n_total = params.nb_channels
n_t = params.getint('detection', 'N_t')
template_shift = params.getint('detection', 'template_shift')
# file_out = params.get('data', 'file_out')
file_out_suff = params.get('data', 'file_out_suff')
sign_peaks = params.get('detection', 'peaks')
matched_filter = params.getboolean('detection', 'matched-filter')
# spike_thresh = params.getfloat('detection', 'spike_thresh')
ratio_thresh = params.getfloat('fitting', 'ratio_thresh')
two_components = params.getboolean('fitting', 'two_components')
sparse_threshold = params.getfloat('fitting', 'sparse_thresh')
# spike_width = params.getfloat('detection', 'spike_width')
# dist_peaks = params.getint('detection', 'dist_peaks')
do_temporal_whitening = params.getboolean('whitening', 'temporal')
do_spatial_whitening = params.getboolean('whitening', 'spatial')
templates_normalization = params.getboolean('clustering', 'templates_normalization') # TODO test, switch, test!
chunk_size = detect_memory(params, fitting=True)
gpu_only = params.getboolean('fitting', 'gpu_only')
nodes, edges = get_nodes_and_edges(params)
tmp_limits = params.get('fitting', 'amp_limits').replace('(', '').replace(')', '').split(',')
tmp_limits = [float(v) for v in tmp_limits]
amp_auto = params.getboolean('fitting', 'amp_auto')
max_chunk = params.getfloat('fitting', 'max_chunk')
# noise_thr = params.getfloat('clustering', 'noise_thr')
collect_all = params.getboolean('fitting', 'collect_all')
min_second_component = params.getfloat('fitting', 'min_second_component')
debug = params.getboolean('fitting', 'debug')
ignore_dead_times = params.getboolean('triggers', 'ignore_times')
inv_nodes = numpy.zeros(n_total, dtype=numpy.int32)
inv_nodes[nodes] = numpy.arange(len(nodes))
data_file.open()
supports = io.load_data(params, 'supports')
low_channels_thr = params.getint('detection', 'low_channels_thr')
median_channels = numpy.median(numpy.sum(supports, 1))
fixed_amplitudes = params.getboolean('clustering', 'fixed_amplitudes')
weird_thresh = params.get('detection', 'weird_thresh')
if weird_thresh != '':
ignore_artefacts = True
weird_thresh = io.load_data(params, 'weird-thresholds')
else:
ignore_artefacts = False
if not fixed_amplitudes:
nb_amp_bins = params.getint('clustering', 'nb_amp_bins')
splits = np.linspace(0, params.data_file.duration, nb_amp_bins)
interpolated_times = np.zeros(len(splits) - 1, dtype=numpy.float32)
for count in range(0, len(splits) - 1):
interpolated_times[count] = (splits[count] + splits[count + 1])/2
interpolated_times = numpy.concatenate(([0], interpolated_times, [params.data_file.duration]))
nb_amp_times = len(splits) + 1
mse_error = params.getboolean('fitting', 'mse_error')
if mse_error:
stds = io.load_data(params, 'stds')
stds_norm = numpy.linalg.norm(stds)
# if median_channels < low_channels_thr:
# normalization = False
# if comm.rank == 0:
# print_and_log(['Templates defined on few channels (%g), turning off normalization' %median_channels], 'debug', logger)
#################################################################
if SHARED_MEMORY:
templates, mpi_memory_1 = io.load_data_memshared(params, 'templates', normalize=templates_normalization, transpose=True, sparse_threshold=sparse_threshold)
N_tm, x = templates.shape
is_sparse = not isinstance(templates, numpy.ndarray)
else:
templates = io.load_data(params, 'templates')
x, N_tm = templates.shape
if N_tm > 0:
sparsity = templates.nnz / (x * N_tm)
is_sparse = sparsity < sparse_threshold
else:
is_sparse = True
if not is_sparse:
if comm.rank == 0:
print_and_log(['Templates sparsity is low (%g): densified to speedup the algorithm' %sparsity], 'debug', logger)
templates = templates.toarray()
temp_2_shift = 2 * template_shift
temp_3_shift = 3 * template_shift
n_tm = N_tm // 2
n_scalar = n_e * n_t
temp_window = numpy.arange(-template_shift, template_shift + 1)
size_window = n_e * (2 * template_shift + 1)
if not amp_auto:
amp_limits = numpy.zeros((n_tm, 2))
amp_limits[:, 0] = tmp_limits[0]
amp_limits[:, 1] = tmp_limits[1]
else:
amp_limits = io.load_data(params, 'limits')
norm_templates = io.load_data(params, 'norm-templates')
sub_norm_templates = n_scalar * norm_templates[:n_tm]
if not templates_normalization:
norm_templates_2 = (norm_templates ** 2.0) * n_scalar
sub_norm_templates_2 = norm_templates_2[:n_tm]
if not SHARED_MEMORY:
# Normalize templates (if necessary).
if templates_normalization:
if is_sparse:
for idx in range(templates.shape[1]):
myslice = numpy.arange(templates.indptr[idx], templates.indptr[idx+1])
templates.data[myslice] /= norm_templates[idx]
else:
for idx in range(templates.shape[1]):
templates[:, idx] /= norm_templates[idx]
# Transpose templates.
templates = templates.T
maxoverlap = io.load_data(params, 'maxoverlap')/n_scalar
similar = np.where(maxoverlap > 0.5)
idx = similar[0] < similar[1]
similar = similar[0][idx], similar[1][idx]
nb_mixtures = len(similar[0])
waveform_neg = numpy.empty(0) # default assignment (for PyCharm code inspection)
matched_thresholds_neg = None # default assignment (for PyCharm code inspection)
waveform_pos = numpy.empty(0) # default assignment (for PyCharm code inspection)
matched_thresholds_pos = None # default assignment (for PyCharm code inspection)
if matched_filter:
if sign_peaks in ['negative', 'both']:
waveform_neg = io.load_data(params, 'waveform')[::-1]
waveform_neg /= (numpy.abs(numpy.sum(waveform_neg)) * len(waveform_neg))
matched_thresholds_neg = io.load_data(params, 'matched-thresholds')
if sign_peaks in ['positive', 'both']:
waveform_pos = io.load_data(params, 'waveform-pos')[::-1]
waveform_pos /= (numpy.abs(numpy.sum(waveform_pos)) * len(waveform_pos))
matched_thresholds_pos = io.load_data(params, 'matched-thresholds-pos')
if ignore_dead_times:
if SHARED_MEMORY:
all_dead_times, mpi_memory_3 = get_dead_times(params)
else:
all_dead_times = get_dead_times(params)
else:
all_dead_times = None # default assignment (for PyCharm code inspection)
thresholds = io.get_accurate_thresholds(params, ratio_thresh)
neighbors = {}
if collect_all:
is_sparse = not isinstance(templates, numpy.ndarray)
for i in range(0, n_tm):
if is_sparse:
tmp = templates[i, :].toarray().reshape(n_e, n_t)
else:
tmp = templates[i].reshape(n_e, n_t)
if templates_normalization:
tmp = tmp * norm_templates[i]
neighbors[i] = numpy.where(numpy.sum(tmp, axis=1) != 0.0)[0]
#N_tm, x = templates.shape
#sparsity_factor = templates.nnz / (N_tm * x)
#if sparsity_factor > sparse_threshold:
# if comm.rank == 0:
# print_and_log(['Templates are not sparse enough, we densify them for'], 'default', logger)
# templates = templates.toarray()
info_string = ''
if comm.rank == 0:
info_string = "using %d CPUs" % comm.size
comm.Barrier()
c_overlap = io.get_overlaps(params, nb_cpu=nb_cpu, nb_gpu=nb_gpu, use_gpu=use_gpu)
over_shape = c_overlap.get('over_shape')[:]
n_over = int(numpy.sqrt(over_shape[0]))
s_over = over_shape[1]
s_center = s_over // 2
# # If the number of overlaps is different from templates, we need to recompute them.
if n_over != N_tm:
if comm.rank == 0:
print_and_log(['Templates have been modified, recomputing the overlaps...'], 'default', logger)
c_overlap = io.get_overlaps(params, erase=True, nb_cpu=nb_cpu, nb_gpu=nb_gpu, use_gpu=use_gpu)
over_shape = c_overlap.get('over_shape')[:]
n_over = int(numpy.sqrt(over_shape[0]))
s_over = over_shape[1]
if SHARED_MEMORY:
c_overs, mpi_memory_2 = io.load_data_memshared(params, 'overlaps')
else:
c_overs = io.load_data(params, 'overlaps')
comm.Barrier()
if n_tm == 0:
if comm.rank == 0:
print_and_log(["No templates present. Redo clustering?"], 'default', logger)
sys.exit(0)
if comm.rank == 0:
print_and_log(["Here comes the SpyKING CIRCUS %s and %d templates..." % (info_string, n_tm)], 'default', logger)
purge(file_out_suff, '.data')
if do_spatial_whitening:
spatial_whitening = io.load_data(params, 'spatial_whitening')
else:
spatial_whitening = None # default assignment (for PyCharm code inspection)
if do_temporal_whitening:
temporal_whitening = io.load_data(params, 'temporal_whitening')
else:
temporal_whitening = None # default assignment (for PyCharm code inspection)
nb_chunks, last_chunk_len = data_file.analyze(chunk_size)
processed_chunks = int(min(nb_chunks, max_chunk))
comm.Barrier()
spiketimes_file = open(file_out_suff + '.spiketimes-%d.data' % comm.rank, 'wb')
comm.Barrier()
amplitudes_file = open(file_out_suff + '.amplitudes-%d.data' % comm.rank, 'wb')
comm.Barrier()
templates_file = open(file_out_suff + '.templates-%d.data' % comm.rank, 'wb')
comm.Barrier()
if ignore_artefacts:
comm.Barrier()
arte_spiketimes_file = open(file_out_suff + '.times-%d.sata' % comm.rank, 'wb')
comm.Barrier()
arte_electrodes_file = open(file_out_suff + '.elec-%d.sata' % comm.rank, 'wb')
comm.Barrier()
arte_amplitudes_file = open(file_out_suff + '.amp-%d.sata' % comm.rank, 'wb')
comm.Barrier()
if mse_error:
mse_file = open(file_out_suff + '.mses-%d.data' % comm.rank, 'wb')
comm.Barrier()
if collect_all:
garbage_times_file = open(file_out_suff + '.gspiketimes-%d.data' % comm.rank, 'wb')
comm.Barrier()
garbage_temp_file = open(file_out_suff + '.gtemplates-%d.data' % comm.rank, 'wb')
comm.Barrier()
else:
garbage_times_file = None # default assignment (for PyCharm code inspection)
garbage_temp_file = None # default assignment (for PyCharm code inspection)
if debug:
# Open debug files.
chunk_nbs_debug_file = open(file_out_suff + '.chunk_nbs_debug_%d.data' % comm.rank, mode='wb')
comm.Barrier()
iteration_nbs_debug_file = open(file_out_suff + '.iteration_nbs_debug_%d.data' % comm.rank, mode='wb')
comm.Barrier()
peak_nbs_debug_file = open(file_out_suff + '.peak_nbs_debug_%d.data' % comm.rank, mode='wb')
comm.Barrier()
peak_local_time_steps_debug_file = open(
file_out_suff + '.peak_local_time_steps_debug_%d.data' % comm.rank, mode='wb'
)
comm.Barrier()
peak_time_steps_debug_file = open(file_out_suff + '.peak_time_steps_debug_%d.data' % comm.rank, mode='wb')
comm.Barrier()
peak_scalar_products_debug_file = open(
file_out_suff + '.peak_scalar_products_debug_%d.data' % comm.rank, mode='wb'
)
comm.Barrier()
peak_solved_flags_debug_file = open(file_out_suff + '.peak_solved_flags_debug_%d.data' % comm.rank, mode='wb')
comm.Barrier()
template_nbs_debug_file = open(file_out_suff + '.template_nbs_debug_%d.data' % comm.rank, mode='wb')
comm.Barrier()
success_flags_debug_file = open(file_out_suff + '.success_flags_debug_%d.data' % comm.rank, mode='wb')
comm.Barrier()
else:
chunk_nbs_debug_file = None # default assignment (for PyCharm code inspection)
iteration_nbs_debug_file = None # default assignment (for PyCharm code inspection)
peak_nbs_debug_file = None # default assignment (for PyCharm code inspection)
peak_local_time_steps_debug_file = None # default assignment (for PyCharm code inspection)
peak_time_steps_debug_file = None # default assignment (for PyCharm code inspection)
peak_scalar_products_debug_file = None # default assignment (for PyCharm code inspection)
peak_solved_flags_debug_file = None # default assignment (for PyCharm code inspection)
template_nbs_debug_file = None # default assignment (for PyCharm code inspection)
success_flags_debug_file = None # default assignment (for PyCharm code inspection)
last_chunk_size = 0
slice_indices = numpy.zeros(0, dtype=numpy.int32)
to_explore = list(range(comm.rank, processed_chunks, comm.size))
if comm.rank == 0:
to_explore = get_tqdm_progressbar(params, to_explore)
if fixed_amplitudes:
min_scalar_products = amp_limits[:,0][:, numpy.newaxis]
max_scalar_products = amp_limits[:,1][:, numpy.newaxis]
if templates_normalization:
min_sps = min_scalar_products * sub_norm_templates[:, numpy.newaxis]
max_sps = max_scalar_products * sub_norm_templates[:, numpy.newaxis]
else:
min_sps = min_scalar_products * sub_norm_templates_2[:, numpy.newaxis]
max_sps = max_scalar_products * sub_norm_templates_2[:, numpy.newaxis]
for gcount, gidx in enumerate(to_explore):
# print "Node", comm.rank, "is analyzing chunk", gidx, "/", nb_chunks, " ..."
# # We need to deal with the borders by taking chunks of size [0, chunck_size + template_shift].
is_first = data_file.is_first_chunk(gidx, nb_chunks)
is_last = data_file.is_last_chunk(gidx, nb_chunks)
if not (is_first and is_last):
if is_last:
padding = (-temp_3_shift, 0)
elif is_first:
padding = (0, temp_3_shift)
else:
padding = (-temp_3_shift, temp_3_shift)
else:
padding = (0, 0)
result = {
'spiketimes': [],
'amplitudes': [],
'templates': [],
}
if mse_error:
mse_fit = {
'spiketimes': [],
'amplitudes': [],
'templates': [],
}
result_debug = {
'chunk_nbs': [],
'iteration_nbs': [],
'peak_nbs': [],
'peak_local_time_steps': [],
'peak_time_steps': [],
'peak_scalar_products': [],
'peak_solved_flags': [],
'template_nbs': [],
'success_flags': [],
}
local_chunk, t_offset = data_file.get_data(gidx, chunk_size, padding, nodes=nodes)
len_chunk = len(local_chunk)
if is_last:
my_chunk_size = last_chunk_size
else:
my_chunk_size = chunk_size
if do_spatial_whitening:
local_chunk = numpy.dot(local_chunk, spatial_whitening)
if do_temporal_whitening:
local_chunk = scipy.ndimage.filters.convolve1d(local_chunk, temporal_whitening, axis=0, mode='constant')
# Extracting peaks.
all_found_spikes = {}
if collect_all:
for i in range(n_e):
all_found_spikes[i] = []
local_peaktimes = [numpy.empty(0, dtype=numpy.uint32)]
if ignore_artefacts:
artefacts_peaktimes = [numpy.zeros(0, dtype=numpy.uint32)]
artefacts_elecs = [numpy.zeros(0, dtype=numpy.uint32)]
artefacts_amps = [numpy.zeros(0, dtype=numpy.float32)]
if matched_filter:
if sign_peaks in ['positive', 'both']:
filter_chunk = scipy.ndimage.filters.convolve1d(local_chunk, waveform_pos, axis=0, mode='constant')
for i in range(n_e):
peaktimes = scipy.signal.find_peaks(filter_chunk[:, i], height=matched_thresholds_pos[i])[0]
if ignore_artefacts:
artetimes = scipy.signal.find_peaks(numpy.abs(filter_chunk[:, i]), height=weird_thresh[i])[0]
to_keep = numpy.logical_not(numpy.in1d(peaktimes, artetimes))
peaktimes = peaktimes[to_keep]
artefacts_peaktimes.append(artetimes)
artefacts_elecs.append(i*numpy.ones(len(artetimes), dtype='uint32'))
artefacts_amps.append(local_chunk[artetimes, i])
local_peaktimes.append(peaktimes)
if collect_all:
all_found_spikes[i] += peaktimes.tolist()
if sign_peaks in ['negative', 'both']:
filter_chunk = scipy.ndimage.filters.convolve1d(local_chunk, waveform_neg, axis=0, mode='constant')
for i in range(n_e):
peaktimes = scipy.signal.find_peaks(filter_chunk[:, i], height=matched_thresholds_neg[i])[0]
if ignore_artefacts:
artetimes = scipy.signal.find_peaks(numpy.abs(filter_chunk[:, i]), height=weird_thresh[i])[0]
to_keep = numpy.logical_not(numpy.in1d(peaktimes, artetimes))
peaktimes = peaktimes[to_keep]
artefacts_peaktimes.append(artetimes)
artefacts_elecs.append(i*numpy.ones(len(artetimes), dtype='uint32'))
artefacts_amps.append(local_chunk[artetimes, i])
local_peaktimes.append(peaktimes)
if collect_all:
all_found_spikes[i] += peaktimes.tolist()
local_peaktimes = numpy.concatenate(local_peaktimes)
if ignore_artefacts:
artefacts_peaktimes = numpy.concatenate(artefacts_peaktimes)
artefacts_elecs = numpy.concatenate(artefacts_elecs)
artefacts_amps = numpy.concatenate(artefacts_amps)
else:
for i in range(n_e):
if sign_peaks == 'negative':
peaktimes = scipy.signal.find_peaks(-local_chunk[:, i], height=thresholds[i])[0]
elif sign_peaks == 'positive':
peaktimes = scipy.signal.find_peaks(local_chunk[:, i], height=thresholds[i])[0]
elif sign_peaks == 'both':
peaktimes = scipy.signal.find_peaks(numpy.abs(local_chunk[:, i]), height=thresholds[i])[0]
else:
raise ValueError("Unexpected value %s" % sign_peaks)
if ignore_artefacts:
artetimes = scipy.signal.find_peaks(numpy.abs(local_chunk[:, i]), height=weird_thresh[i])[0]
to_keep = numpy.logical_not(numpy.in1d(peaktimes, artetimes))
peaktimes = peaktimes[to_keep]
artefacts_peaktimes.append(artetimes)
artefacts_elecs.append(i*numpy.ones(len(artetimes), dtype='uint32'))
artefacts_amps.append(local_chunk[artetimes, i])
local_peaktimes.append(peaktimes)
if collect_all:
all_found_spikes[i] += peaktimes.tolist()
local_peaktimes = numpy.concatenate(local_peaktimes)
if ignore_artefacts:
artefacts_peaktimes = numpy.concatenate(artefacts_peaktimes)
artefacts_elecs = numpy.concatenate(artefacts_elecs)
artefacts_amps = numpy.concatenate(artefacts_amps)
local_peaktimes = numpy.unique(local_peaktimes)
g_offset = t_offset + padding[0]
if ignore_dead_times:
dead_indices = numpy.searchsorted(all_dead_times, [t_offset, t_offset + my_chunk_size])
if dead_indices[0] != dead_indices[1]:
is_included = numpy.in1d(local_peaktimes + g_offset, all_dead_times[dead_indices[0]:dead_indices[1]])
local_peaktimes = local_peaktimes[~is_included]
if ignore_artefacts:
is_included = numpy.in1d(artefacts_peaktimes + g_offset, all_dead_times[dead_indices[0]:dead_indices[1]])
artefacts_peaktimes = artefacts_peaktimes[~is_included]
artefacts_elecs = artefacts_elecs[~is_included]
artefacts_amps = artefacts_amps[~is_included]
local_peaktimes = numpy.sort(local_peaktimes)
else:
dead_indices = None # default assignment (for PyCharm code inspection)
# print "Removing the useless borders..."
local_borders = (template_shift, len_chunk - template_shift)
idx = (local_peaktimes >= local_borders[0]) & (local_peaktimes < local_borders[1])
local_peaktimes = numpy.compress(idx, local_peaktimes)
if ignore_artefacts:
artefacts_peaktimes = artefacts_peaktimes + g_offset
idx = (artefacts_peaktimes >= t_offset) & (artefacts_peaktimes < t_offset + my_chunk_size)
artefacts_peaktimes = numpy.compress(idx, artefacts_peaktimes)
artefacts_elecs = numpy.compress(idx, artefacts_elecs)
artefacts_amps = numpy.compress(idx, artefacts_amps)
if collect_all:
for i in range(n_e):
all_found_spikes[i] = numpy.array(all_found_spikes[i], dtype=numpy.uint32)
if ignore_dead_times:
if dead_indices[0] != dead_indices[1]:
is_included = numpy.in1d(
all_found_spikes[i] + g_offset, all_dead_times[dead_indices[0]:dead_indices[1]]
)
all_found_spikes[i] = all_found_spikes[i][~is_included]
all_found_spikes[i] = numpy.sort(all_found_spikes[i])
idx = (all_found_spikes[i] >= local_borders[0]) & (all_found_spikes[i] < local_borders[1])
all_found_spikes[i] = numpy.compress(idx, all_found_spikes[i])
nb_local_peak_times = len(local_peaktimes)
if nb_local_peak_times > 0:
# print "Computing the b (should full_gpu by putting all chunks on GPU if possible?)..."
if collect_all or mse_error:
c_local_chunk = local_chunk.copy()
else:
c_local_chunk = None # default assignment (for PyCharm code inspection)
sub_mat = local_chunk[local_peaktimes[:, None] + temp_window]
sub_mat = sub_mat.transpose(2, 1, 0).reshape(size_window, nb_local_peak_times)
del local_chunk
b = templates.dot(sub_mat)
del sub_mat
local_restriction = (t_offset, t_offset + my_chunk_size)
all_spikes = local_peaktimes + g_offset
if collect_all:
c_all_times = numpy.zeros((len_chunk, n_e), dtype=numpy.bool)
c_min_times = numpy.maximum(numpy.arange(len_chunk) - template_shift, 0)
c_max_times = numpy.minimum(numpy.arange(len_chunk) + template_shift + 1, len_chunk)
for i in range(n_e):
c_all_times[all_found_spikes[i], i] = True
else:
c_all_times = None # default assignment (for PyCharm code inspection)
c_min_times = None # default assignment (for PyCharm code inspection)
c_max_times = None # default assignment (for PyCharm code inspection)
iteration_nb = 0
data = b[:n_tm, :]
if not fixed_amplitudes:
amp_index = numpy.searchsorted(splits, local_restriction[0], 'right')
scaling = 1/(splits[amp_index] - splits[amp_index - 1])
min_scalar_products = amp_limits[:, amp_index, 0] + (amp_limits[:, amp_index, 0] - amp_limits[:, amp_index+1, 0])*scaling
max_scalar_products = amp_limits[:, amp_index, 1] + (amp_limits[:, amp_index, 1] - amp_limits[:, amp_index+1, 0])*scaling
min_scalar_products = min_scalar_products[:, numpy.newaxis]
max_scalar_products = max_scalar_products[:, numpy.newaxis]
if templates_normalization:
min_sps = min_scalar_products * sub_norm_templates[:, numpy.newaxis]
max_sps = max_scalar_products * sub_norm_templates[:, numpy.newaxis]
else:
min_sps = min_scalar_products * sub_norm_templates_2[:, numpy.newaxis]
max_sps = max_scalar_products * sub_norm_templates_2[:, numpy.newaxis]
while True:
is_valid = (data > min_sps)*(data < max_sps)
valid_indices = numpy.where(is_valid)
if len(valid_indices[0]) == 0:
break
best_amplitude_idx = data[is_valid].argmax()
best_template_index, peak_index = valid_indices[0][best_amplitude_idx], valid_indices[1][best_amplitude_idx]
peak_scalar_product = data[is_valid][best_amplitude_idx]
best_template2_index = best_template_index + n_tm
if templates_normalization:
best_amp = b[best_template_index, peak_index] / n_scalar
best_amp_n = best_amp / norm_templates[best_template_index]
if two_components:
best_amp2 = b[best_template2_index, peak_index] / n_scalar
best_amp2_n = best_amp2 / norm_templates[best_template2_index]
else:
best_amp2 = 0
best_amp2_n = 0
else:
best_amp = b[best_template_index, peak_index] / norm_templates_2[best_template_index]
best_amp_n = best_amp
if two_components:
best_amp2 = b[best_template2_index, peak_index] / norm_templates_2[best_template2_index]
best_amp2_n = best_amp2
else:
best_amp2 = 0
best_amp2_n = 0
peak_time_step = local_peaktimes[peak_index]
peak_data = (local_peaktimes - peak_time_step).astype(np.int32)
is_neighbor = np.abs(peak_data) <= temp_2_shift
idx_neighbor = peak_data[is_neighbor] + temp_2_shift
tmp1 = c_overs[best_template_index].multiply(-best_amp)
if numpy.abs(best_amp2_n) > min_second_component:
tmp1 += c_overs[best_template2_index].multiply(-best_amp2)
to_add = tmp1.toarray()[:, idx_neighbor]
b[:, is_neighbor] += to_add
b[best_template_index, peak_index] = -numpy.inf
# Add matching to the result.
t_spike = all_spikes[peak_index]
if (t_spike >= local_restriction[0]) and (t_spike < local_restriction[1]):
result['spiketimes'] += [t_spike]
result['amplitudes'] += [(best_amp_n, best_amp2_n)]
result['templates'] += [best_template_index]
elif mse_error:
mse_fit['spiketimes'] += [t_spike]
mse_fit['amplitudes'] += [(best_amp_n, best_amp2_n)]
mse_fit['templates'] += [best_template_index]
# Save debug data.
if debug:
result_debug['chunk_nbs'] += [gidx]
result_debug['iteration_nbs'] += [iteration_nb]
result_debug['peak_nbs'] += [peak_index]
result_debug['peak_local_time_steps'] += [local_peaktimes[peak_index]]
result_debug['peak_time_steps'] += [all_spikes[peak_index]]
result_debug['peak_scalar_products'] += [peak_scalar_product]
result_debug['peak_solved_flags'] += [b[best_template_index, peak_index]]
result_debug['template_nbs'] += [best_template_index]
result_debug['success_flags'] += [True]
iteration_nb += 1
spikes_to_write = numpy.array(result['spiketimes'], dtype=numpy.uint32)
amplitudes_to_write = numpy.array(result['amplitudes'], dtype=numpy.float32)
templates_to_write = numpy.array(result['templates'], dtype=numpy.uint32)
spiketimes_file.write(spikes_to_write.tostring())
amplitudes_file.write(amplitudes_to_write.tostring())
templates_file.write(templates_to_write.tostring())
if ignore_artefacts:
arte_spiketimes_file.write(artefacts_peaktimes.astype(numpy.uint32).tostring())
arte_electrodes_file.write(artefacts_elecs.tostring())
arte_amplitudes_file.write(artefacts_amps.tostring())
if mse_error:
curve = numpy.zeros((len_chunk, n_e), dtype=numpy.float32)
for spike, temp_id, amplitude in zip(result['spiketimes'], result['templates'], result['amplitudes']):
spike = spike - t_offset - padding[0]
if is_sparse:
tmp1 = templates[temp_id].toarray().reshape(n_e, n_t)
tmp2 = templates[temp_id + n_tm].toarray().reshape(n_e, n_t)
else:
tmp1 = templates[temp_id].reshape(n_e, n_t)
tmp2 = templates[temp_id + n_tm].reshape(n_e, n_t)
curve[spike - template_shift:spike + template_shift + 1, :] += (amplitude[0] * tmp1 + amplitude[1] * tmp2).T
for spike, temp_id, amplitude in zip(mse_fit['spiketimes'], mse_fit['templates'], mse_fit['amplitudes']):
spike = spike - t_offset + padding[0]
if is_sparse:
tmp1 = templates[temp_id].toarray().reshape(n_e, n_t)
tmp2 = templates[temp_id + n_tm].toarray().reshape(n_e, n_t)
else:
tmp1 = templates[temp_id].reshape(n_e, n_t)
tmp2 = templates[temp_id + n_tm].reshape(n_e, n_t)
try:
curve[int(spike) - template_shift:int(spike) + template_shift + 1, :] += (amplitude[0] * tmp1 + amplitude[1] * tmp2).T
except Exception:
pass
mse = numpy.linalg.norm((curve - c_local_chunk)[-padding[0]:-padding[1]])
nb_points = len(curve) - (padding[1] - padding[0])
mse_ratio = mse/(numpy.sqrt(nb_points)*stds_norm)
mse_to_write = numpy.array([g_offset, mse_ratio], dtype=numpy.float32)
mse_file.write(mse_to_write.tostring())
if collect_all:
for temp, spike in zip(templates_to_write, spikes_to_write - g_offset):
c_all_times[c_min_times[spike]:c_max_times[spike], neighbors[temp]] = False
gspikes = numpy.where(numpy.sum(c_all_times, 1) > 0)[0]
c_all_times = numpy.take(c_all_times, gspikes, axis=0)
c_local_chunk = numpy.take(c_local_chunk, gspikes, axis=0) * c_all_times
if sign_peaks == 'negative':
bestlecs = numpy.argmin(c_local_chunk, 1)
if matched_filter:
threshs = -matched_thresholds_neg[bestlecs]
else:
threshs = -thresholds[bestlecs]
idx = numpy.where(numpy.min(c_local_chunk, 1) < threshs)[0]
elif sign_peaks == 'positive':
bestlecs = numpy.argmax(c_local_chunk, 1)
if matched_filter:
threshs = matched_thresholds_pos[bestlecs]
else:
threshs = thresholds[bestlecs]
idx = numpy.where(numpy.max(c_local_chunk, 1) > threshs)[0]
elif sign_peaks == 'both':
c_local_chunk = numpy.abs(c_local_chunk)
bestlecs = numpy.argmax(c_local_chunk, 1)
if matched_filter:
threshs = numpy.minimum(matched_thresholds_neg[bestlecs], matched_thresholds_pos[bestlecs])
else:
threshs = thresholds[bestlecs]
idx = numpy.where(numpy.max(c_local_chunk, 1) > threshs)[0]
else:
raise ValueError("Unexpected value %s" % sign_peaks)
gspikes = numpy.take(gspikes, idx)
bestlecs = numpy.take(bestlecs, idx)
gspikes_to_write = numpy.array(gspikes + g_offset, dtype=numpy.uint32)
gtemplates_to_write = numpy.array(bestlecs, dtype=numpy.uint32)
garbage_times_file.write(gspikes_to_write.tostring())
garbage_temp_file.write(gtemplates_to_write.tostring())
if debug:
# Write debug data to debug files.
for field_label, field_dtype, field_file in [
('chunk_nbs', numpy.uint32, chunk_nbs_debug_file),
('iteration_nbs', numpy.uint32, iteration_nbs_debug_file),
('peak_nbs', numpy.uint32, peak_nbs_debug_file),
('peak_local_time_steps', numpy.uint32, peak_local_time_steps_debug_file),
('peak_time_steps', numpy.uint32, peak_time_steps_debug_file),
('peak_scalar_products', numpy.float32, peak_scalar_products_debug_file),
('peak_solved_flags', numpy.float32, peak_solved_flags_debug_file),
('template_nbs', numpy.uint32, template_nbs_debug_file),
('success_flags', numpy.bool, success_flags_debug_file),
]:
field_to_write = numpy.array(result_debug[field_label], dtype=field_dtype)
field_file.write(field_to_write.tostring())
sys.stderr.flush()
spiketimes_file.flush()
os.fsync(spiketimes_file.fileno())
spiketimes_file.close()
amplitudes_file.flush()
os.fsync(amplitudes_file.fileno())
amplitudes_file.close()
templates_file.flush()
os.fsync(templates_file.fileno())
templates_file.close()
if collect_all:
garbage_temp_file.flush()
os.fsync(garbage_temp_file.fileno())
garbage_temp_file.close()
garbage_times_file.flush()
os.fsync(garbage_times_file.fileno())
garbage_times_file.close()
if mse_error:
mse_file.flush()
os.fsync(mse_file.fileno())
mse_file.close()
if ignore_artefacts:
arte_spiketimes_file.flush()
os.fsync(arte_spiketimes_file.fileno())
arte_spiketimes_file.close()
arte_electrodes_file.flush()
os.fsync(arte_electrodes_file.fileno())
arte_electrodes_file.close()
arte_amplitudes_file.flush()
os.fsync(arte_amplitudes_file.fileno())
arte_amplitudes_file.close()
if debug:
# Close debug files.
for field_file in [
chunk_nbs_debug_file,
iteration_nbs_debug_file,
peak_nbs_debug_file,
peak_local_time_steps_debug_file,
peak_time_steps_debug_file,
peak_scalar_products_debug_file,
peak_solved_flags_debug_file,
template_nbs_debug_file,
success_flags_debug_file,
]:
field_file.flush()
os.fsync(field_file.fileno())
field_file.close()
comm.Barrier()
if SHARED_MEMORY:
for memory in mpi_memory_1 + mpi_memory_2:
memory.Free()
if ignore_dead_times:
mpi_memory_3.Free()
if comm.rank == 0:
io.collect_data(comm.size, params, erase=True)
if ignore_artefacts:
io.collect_artefacts(comm.size, params, erase=True)
data_file.close()
