def main(argv=None):
if argv is None:
argv = sys.argv[1:]
header = get_colored_header()
parser = argparse.ArgumentParser(
description=header, formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument('datafile', help='data file')
parser.add_argument('-e',
'--extension',
help='extension to consider for visualization',
default='')
if len(argv) == 0:
parser.print_help()
sys.exit()
args = parser.parse_args(argv)
filename = os.path.abspath(args.datafile)
extension = args.extension
params = CircusParser(filename)
if os.path.exists(params.logfile):
os.remove(params.logfile)
logger = init_logging(params.logfile)
logger = logging.getLogger(__name__)
data_file = params.get_data_file()
data_dtype = data_file.data_dtype
gain = data_file.gain
t_start = data_file.t_start
file_format = data_file.description
if file_format not in supported_by_matlab:
print_and_log([
"File format %s is not supported by MATLAB. Waveforms disabled" %
file_format
], 'info', logger)
if numpy.iterable(gain):
print_and_log(
['Multiple gains are not supported, using a default value of 1'],
'info', logger)
gain = 1
file_out_suff = params.get('data', 'file_out_suff')
if hasattr(data_file, 'data_offset'):
data_offset = data_file.data_offset
else:
data_offset = 0
probe = params.probe
if extension != '':
extension = '-' + extension
def generate_matlab_mapping(probe):
p = {}
positions = []
nodes = []
for key in probe['channel_groups'].keys():
p.update(probe['channel_groups'][key]['geometry'])
nodes += probe['channel_groups'][key]['channels']
positions += [
p[channel]
for channel in probe['channel_groups'][key]['channels']
]
idx = numpy.argsort(nodes)
positions = numpy.array(positions)[idx]
t = tempfile.NamedTemporaryFile().name + '.hdf5'
cfile = h5py.File(t, 'w')
to_write = {
'positions': positions / 10.,
'permutation': numpy.sort(nodes),
'nb_total': numpy.array([probe['total_nb_channels']])
}
write_datasets(cfile, to_write.keys(), to_write)
cfile.close()
return t
mapping = generate_matlab_mapping(probe)
if not params.getboolean('data', 'overwrite'):
filename = params.get('data', 'data_file_no_overwrite')
else:
filename = params.get('data', 'data_file')
apply_patch_for_similarities(params, extension)
gui_file = pkg_resources.resource_filename(
'circus', os.path.join('matlab_GUI', 'SortingGUI.m'))
# Change to the directory of the matlab file
os.chdir(os.path.abspath(os.path.dirname(gui_file)))
# Use quotation marks for string arguments
if file_format not in supported_by_matlab:
gui_params = [
params.rate,
os.path.abspath(file_out_suff),
'%s.mat' % extension, mapping, 2, t_start
]
is_string = [False, True, True, True, False]
else:
gui_params = [
params.rate,
os.path.abspath(file_out_suff),
'%s.mat' % extension, mapping, 2, t_start, data_dtype, data_offset,
gain, filename
]
is_string = [
False, True, True, True, False, False, True, False, False, True
]
arguments = ', '.join([
"'%s'" % arg if s else "%s" % arg
for arg, s in zip(gui_params, is_string)
])
matlab_command = 'SortingGUI(%s)' % arguments
print_and_log(["Launching the MATLAB GUI..."], 'info', logger)
print_and_log([matlab_command], 'debug', logger)
if params.getboolean('fitting', 'collect_all'):
print_and_log([
'You can not view the unfitted spikes with the MATLAB GUI',
'Please consider using phy if you really would like to see them'
], 'info', logger)
try:
sys.exit(
subprocess.call(
['matlab', '-nodesktop', '-nosplash', '-r', matlab_command]))
except Exception:
print_and_log(
["Something wrong with MATLAB. Try circus-gui-python instead?"],
'error', logger)
sys.exit(1)
def main(params, nb_cpu, nb_gpu, use_gpu, extension):
logger = init_logging(params.logfile)
logger = logging.getLogger('circus.converting')
data_file = params.data_file
file_out_suff = params.get('data', 'file_out_suff')
probe = params.probe
output_path = params.get('data', 'file_out_suff') + extension + '.GUI'
N_e = params.getint('data', 'N_e')
N_t = params.getint('detection', 'N_t')
erase_all = params.getboolean('converting', 'erase_all')
export_pcs = params.get('converting', 'export_pcs')
export_all = params.getboolean('converting', 'export_all')
sparse_export = params.getboolean('converting', 'sparse_export')
if export_all and not params.getboolean('fitting', 'collect_all'):
if comm.rank == 0:
print_and_log(['Export unfitted spikes only if [fitting] collect_all is True'], 'error', logger)
sys.exit(0)
def generate_mapping(probe):
p = {}
positions = []
nodes = []
for key in probe['channel_groups'].keys():
p.update(probe['channel_groups'][key]['geometry'])
nodes += probe['channel_groups'][key]['channels']
positions += [p[channel] for channel in probe['channel_groups'][key]['channels']]
idx = numpy.argsort(nodes)
positions = numpy.array(positions)[idx]
return positions
def get_max_loc_channel(params):
nodes, edges = get_nodes_and_edges(params)
max_loc_channel = 0
for key in edges.keys():
if len(edges[key]) > max_loc_channel:
max_loc_channel = len(edges[key])
return max_loc_channel
def write_results(path, params, extension):
result = io.get_results(params, extension)
spikes = numpy.zeros(0, dtype=numpy.uint64)
clusters = numpy.zeros(0, dtype=numpy.uint32)
amplitudes = numpy.zeros(0, dtype=numpy.double)
N_tm = len(result['spiketimes'])
for key in result['spiketimes'].keys():
temp_id = int(key.split('_')[-1])
data = result['spiketimes'].pop(key).astype(numpy.uint64)
spikes = numpy.concatenate((spikes, data))
data = result['amplitudes'].pop(key).astype(numpy.double)
amplitudes = numpy.concatenate((amplitudes, data[:, 0]))
clusters = numpy.concatenate((clusters, temp_id*numpy.ones(len(data), dtype=numpy.uint32)))
if export_all:
print_and_log(["Last %d templates are unfitted spikes on all electrodes" %N_e], 'info', logger)
garbage = io.load_data(params, 'garbage', extension)
for key in garbage['gspikes'].keys():
elec_id = int(key.split('_')[-1])
data = garbage['gspikes'].pop(key).astype(numpy.uint64)
spikes = numpy.concatenate((spikes, data))
amplitudes = numpy.concatenate((amplitudes, numpy.zeros(len(data))))
clusters = numpy.concatenate((clusters, (elec_id + N_tm)*numpy.ones(len(data), dtype=numpy.uint32)))
idx = numpy.argsort(spikes)
numpy.save(os.path.join(output_path, 'spike_templates'), clusters[idx])
numpy.save(os.path.join(output_path, 'spike_times'), spikes[idx])
numpy.save(os.path.join(output_path, 'amplitudes'), amplitudes[idx])
return
def write_templates(path, params, extension):
max_loc_channel = get_max_loc_channel(params)
templates = io.load_data(params, 'templates', extension)
N_tm = templates.shape[1]//2
if sparse_export:
n_channels_max = 0
for t in xrange(N_tm):
data = numpy.sum(numpy.sum(templates[:, t].toarray().reshape(N_e, N_t), 1) != 0)
if data > n_channels_max:
n_channels_max = data
else:
n_channels_max = N_e
if export_all:
to_write_sparse = numpy.zeros((N_tm + N_e, N_t, n_channels_max), dtype=numpy.float32)
mapping_sparse = -1 * numpy.ones((N_tm + N_e, n_channels_max), dtype=numpy.int32)
else:
to_write_sparse = numpy.zeros((N_tm, N_t, n_channels_max), dtype=numpy.float32)
mapping_sparse = -1 * numpy.ones((N_tm, n_channels_max), dtype=numpy.int32)
for t in xrange(N_tm):
tmp = templates[:, t].toarray().reshape(N_e, N_t).T
x, y = tmp.nonzero()
nb_loc = len(numpy.unique(y))
if sparse_export:
all_positions = numpy.zeros(y.max()+1, dtype=numpy.int32)
all_positions[numpy.unique(y)] = numpy.arange(nb_loc, dtype=numpy.int32)
pos = all_positions[y]
to_write_sparse[t, x, pos] = tmp[x, y]
mapping_sparse[t, numpy.arange(nb_loc)] = numpy.unique(y)
else:
pos = y
to_write_sparse[t, x, pos] = tmp[x, y]
if export_all:
for t in xrange(N_tm, N_tm + N_e):
mapping_sparse[t, 0] = t - N_tm
numpy.save(os.path.join(output_path, 'templates'), to_write_sparse)
if sparse_export:
numpy.save(os.path.join(output_path, 'template_ind'), mapping_sparse)
return N_tm
def write_pcs(path, params, extension, N_tm, mode=0):
spikes = numpy.load(os.path.join(output_path, 'spike_times.npy'))
labels = numpy.load(os.path.join(output_path, 'spike_templates.npy'))
max_loc_channel = get_max_loc_channel(params)
nb_features = params.getint('whitening', 'output_dim')
sign_peaks = params.get('detection', 'peaks')
nodes, edges = get_nodes_and_edges(params)
N_total = params.getint('data', 'N_total')
if export_all:
nb_templates = N_tm + N_e
else:
nb_templates = N_tm
pc_features_ind = numpy.zeros((nb_templates, max_loc_channel), dtype=numpy.int32)
clusters = io.load_data(params, 'clusters', extension)
best_elec = clusters['electrodes']
if export_all:
best_elec = numpy.concatenate((best_elec, numpy.arange(N_e)))
inv_nodes = numpy.zeros(N_total, dtype=numpy.int32)
inv_nodes[nodes] = numpy.argsort(nodes)
for count, elec in enumerate(best_elec):
nb_loc = len(edges[nodes[elec]])
pc_features_ind[count, numpy.arange(nb_loc)] = inv_nodes[edges[nodes[elec]]]
if sign_peaks in ['negative', 'both']:
basis_proj, basis_rec = io.load_data(params, 'basis')
elif sign_peaks in ['positive']:
basis_proj, basis_rec = io.load_data(params, 'basis-pos')
to_process = numpy.arange(comm.rank, nb_templates, comm.size)
all_offsets = numpy.zeros(nb_templates, dtype=numpy.int32)
for target in xrange(nb_templates):
if mode == 0:
all_offsets[target] = len(numpy.where(labels == target)[0])
elif mode == 1:
all_offsets[target] = min(500, len(numpy.where(labels == target)[0]))
all_paddings = numpy.concatenate(([0] , numpy.cumsum(all_offsets)))
total_pcs = numpy.sum(all_offsets)
pc_file = os.path.join(output_path, 'pc_features.npy')
pc_file_ids = os.path.join(output_path, 'pc_feature_spike_ids.npy')
from numpy.lib.format import open_memmap
if comm.rank == 0:
pc_features = open_memmap(pc_file, shape=(total_pcs, nb_features, max_loc_channel), dtype=numpy.float32, mode='w+')
if mode == 1:
pc_ids = open_memmap(pc_file_ids, shape=(total_pcs, ), dtype=numpy.int32, mode='w+')
comm.Barrier()
pc_features = open_memmap(pc_file, mode='r+')
if mode == 1:
pc_ids = open_memmap(pc_file_ids, mode='r+')
to_explore = xrange(comm.rank, nb_templates, comm.size)
if comm.rank == 0:
to_explore = get_tqdm_progressbar(to_explore)
all_idx = numpy.zeros(0, dtype=numpy.int32)
for gcount, target in enumerate(to_explore):
count = all_paddings[target]
if mode == 1:
idx = numpy.random.permutation(numpy.where(labels == target)[0])[:500]
pc_ids[count:count+len(idx)] = idx
elif mode == 0:
idx = numpy.where(labels == target)[0]
elec = best_elec[target]
indices = inv_nodes[edges[nodes[elec]]]
labels_i = target*numpy.ones(len(idx))
times_i = numpy.take(spikes, idx).astype(numpy.int64)
sub_data = io.get_stas(params, times_i, labels_i, elec, neighs=indices, nodes=nodes, auto_align=False)
pcs = numpy.dot(sub_data, basis_proj)
pcs = numpy.swapaxes(pcs, 1,2)
if mode == 0:
pc_features[idx, :, :len(indices)] = pcs
elif mode == 1:
pc_features[count:count+len(idx), :, :len(indices)] = pcs
comm.Barrier()
if comm.rank == 0:
numpy.save(os.path.join(output_path, 'pc_feature_ind'), pc_features_ind.astype(numpy.uint32)) #n_templates, n_loc_chan
do_export = True
if comm.rank == 0:
if os.path.exists(output_path):
if not erase_all:
do_export = query_yes_no(Fore.WHITE + "Export already made! Do you want to erase everything?", default=None)
if do_export:
if os.path.exists(os.path.abspath('.phy')):
shutil.rmtree(os.path.abspath('.phy'))
shutil.rmtree(output_path)
if do_export == True:
comm.bcast(numpy.array([1], dtype=numpy.int32), root=0)
elif do_export == False:
comm.bcast(numpy.array([0], dtype=numpy.int32), root=0)
else:
do_export = bool(comm.bcast(numpy.array([0], dtype=numpy.int32), root=0))
comm.Barrier()
if do_export:
if comm.rank == 0:
os.makedirs(output_path)
print_and_log(["Exporting data for the phy GUI with %d CPUs..." %nb_cpu], 'info', logger)
if params.getboolean('whitening', 'spatial'):
whitening_mat = io.load_data(params, 'spatial_whitening').astype(numpy.double)
numpy.save(os.path.join(output_path, 'whitening_mat'), whitening_mat)
numpy.save(os.path.join(output_path, 'whitening_mat_inv'), numpy.linalg.inv(whitening_mat))
else:
numpy.save(os.path.join(output_path, 'whitening_mat'), numpy.eye(N_e))
numpy.save(os.path.join(output_path, 'channel_positions'), generate_mapping(probe).astype(numpy.double))
nodes, edges = get_nodes_and_edges(params)
numpy.save(os.path.join(output_path, 'channel_map'), nodes.astype(numpy.int32))
write_results(output_path, params, extension)
N_tm = write_templates(output_path, params, extension)
apply_patch_for_similarities(params, extension)
template_file = h5py.File(file_out_suff + '.templates%s.hdf5' %extension, 'r', libver='earliest')
similarities = template_file.get('maxoverlap')[:]
template_file.close()
norm = N_e*N_t
if export_all:
to_write = numpy.zeros((N_tm + N_e, N_tm + N_e), dtype=numpy.single)
to_write[:N_tm, :N_tm] = (similarities[:N_tm, :N_tm]/norm).astype(numpy.single)
else:
to_write = (similarities[:N_tm, :N_tm]/norm).astype(numpy.single)
numpy.save(os.path.join(output_path, 'similar_templates'), to_write)
comm.bcast(numpy.array([N_tm], dtype=numpy.int32), root=0)
else:
N_tm = int(comm.bcast(numpy.array([0], dtype=numpy.int32), root=0))
comm.Barrier()
make_pcs = 2
if comm.rank == 0:
if export_pcs == 'prompt':
key = ''
while key not in ['a', 's', 'n']:
print(Fore.WHITE + "Do you want SpyKING CIRCUS to export PCs? (a)ll / (s)ome / (n)o")
key = raw_input('')
else:
key = export_pcs
if key == 'a':
make_pcs = 0
comm.bcast(numpy.array([0], dtype=numpy.int32), root=0)
elif key == 's':
make_pcs = 1
comm.bcast(numpy.array([1], dtype=numpy.int32), root=0)
elif key == 'n':
comm.bcast(numpy.array([2], dtype=numpy.int32), root=0)
if os.path.exists(os.path.join(output_path, 'pc_features.npy')):
os.remove(os.path.join(output_path, 'pc_features.npy'))
if os.path.exists(os.path.join(output_path, 'pc_feature_ind.npy')):
os.remove(os.path.join(output_path, 'pc_feature_ind.npy'))
else:
make_pcs = comm.bcast(numpy.array([0], dtype=numpy.int32), root=0)
make_pcs = make_pcs[0]
comm.Barrier()
if make_pcs < 2:
write_pcs(output_path, params, extension, N_tm, make_pcs)
def main(params, nb_cpu, nb_gpu, use_gpu, extension):
_ = init_logging(params.logfile)
logger = logging.getLogger('circus.converting')
data_file = params.data_file
file_out_suff = params.get('data', 'file_out_suff')
probe = params.probe
output_path = params.get('data', 'file_out_suff') + extension + '.GUI'
N_e = params.getint('data', 'N_e')
prelabelling = params.getboolean('converting', 'prelabelling')
N_t = params.getint('detection', 'N_t')
erase_all = params.getboolean('converting', 'erase_all')
export_pcs = params.get('converting', 'export_pcs')
export_all = params.getboolean('converting', 'export_all')
sparse_export = params.getboolean('converting', 'sparse_export')
rpv_threshold = params.getfloat('converting', 'rpv_threshold')
if export_all and not params.getboolean('fitting', 'collect_all'):
if comm.rank == 0:
print_and_log([
'Export unfitted spikes only if [fitting] collect_all is True'
], 'error', logger)
sys.exit(0)
def generate_mapping(probe):
p = {}
positions = []
nodes = []
shanks = []
for key in probe['channel_groups'].keys():
p.update(probe['channel_groups'][key]['geometry'])
nodes += probe['channel_groups'][key]['channels']
positions += [
p[channel]
for channel in probe['channel_groups'][key]['channels']
]
shanks += [key] * len(probe['channel_groups'][key]['channels'])
positions = numpy.array(positions)
shanks = numpy.array(shanks)
return positions, shanks
def get_max_loc_channel(params, extension):
if test_if_support(params, extension):
supports = io.load_data(params, 'supports', extension)
max_loc_channel = numpy.sum(supports, 1).max()
else:
nodes, edges = get_nodes_and_edges(params)
max_loc_channel = 0
for key in edges.keys():
if len(edges[key]) > max_loc_channel:
max_loc_channel = len(edges[key])
return max_loc_channel
def write_results(path, params, extension):
result = io.get_results(params, extension)
spikes = [numpy.zeros(0, dtype=numpy.uint64)]
clusters = [numpy.zeros(0, dtype=numpy.uint32)]
amplitudes = [numpy.zeros(0, dtype=numpy.double)]
N_tm = len(result['spiketimes'])
has_purity = test_if_purity(params, extension)
rpvs = []
if prelabelling:
labels = []
norms = io.load_data(params, 'norm-templates', extension)
norms = norms[:len(norms) // 2]
if has_purity:
purity = io.load_data(params, 'purity', extension)
for key in result['spiketimes'].keys():
temp_id = int(key.split('_')[-1])
myspikes = result['spiketimes'].pop(key).astype(numpy.uint64)
spikes.append(myspikes)
myamplitudes = result['amplitudes'].pop(key).astype(numpy.double)
amplitudes.append(myamplitudes[:, 0])
clusters.append(temp_id *
numpy.ones(len(myamplitudes), dtype=numpy.uint32))
rpv = get_rpv(myspikes, params.data_file.sampling_rate)
rpvs += [[temp_id, rpv]]
if prelabelling:
if has_purity:
if rpv <= rpv_threshold:
if purity[temp_id] > 0.75:
labels += [[temp_id, 'good']]
else:
if purity[temp_id] > 0.75:
labels += [[temp_id, 'mua']]
else:
labels += [[temp_id, 'noise']]
else:
median_amp = numpy.median(myamplitudes[:, 0])
std_amp = numpy.std(myamplitudes[:, 0])
if rpv <= rpv_threshold and numpy.abs(median_amp -
1) < 0.25:
labels += [[temp_id, 'good']]
else:
if median_amp < 0.5:
labels += [[temp_id, 'mua']]
elif norms[temp_id] < 0.1:
labels += [[temp_id, 'noise']]
if export_all:
print_and_log([
"Last %d templates are unfitted spikes on all electrodes" % N_e
], 'info', logger)
garbage = io.load_data(params, 'garbage', extension)
for key in garbage['gspikes'].keys():
elec_id = int(key.split('_')[-1])
data = garbage['gspikes'].pop(key).astype(numpy.uint64)
spikes.append(data)
amplitudes.append(numpy.ones(len(data)))
clusters.append((elec_id + N_tm) *
numpy.ones(len(data), dtype=numpy.uint32))
if prelabelling:
f = open(os.path.join(output_path, 'cluster_group.tsv'), 'w')
f.write('cluster_id\tgroup\n')
for l in labels:
f.write('%s\t%s\n' % (l[0], l[1]))
f.close()
# f = open(os.path.join(output_path, 'cluster_rpv.tsv'), 'w')
# f.write('cluster_id\trpv\n')
# for l in rpvs:
# f.write('%s\t%s\n' % (l[0], l[1]))
# f.close()
spikes = numpy.concatenate(spikes).astype(numpy.uint64)
amplitudes = numpy.concatenate(amplitudes).astype(numpy.double)
clusters = numpy.concatenate(clusters).astype(numpy.uint32)
idx = numpy.argsort(spikes)
numpy.save(os.path.join(output_path, 'spike_templates'), clusters[idx])
numpy.save(os.path.join(output_path, 'spike_times'), spikes[idx])
numpy.save(os.path.join(output_path, 'amplitudes'), amplitudes[idx])
return
def write_templates(path, params, extension):
max_loc_channel = get_max_loc_channel(params, extension)
templates = io.load_data(params, 'templates', extension)
N_tm = templates.shape[1] // 2
nodes, edges = get_nodes_and_edges(params)
if sparse_export:
n_channels_max = 0
for t in range(N_tm):
data = numpy.sum(
numpy.sum(templates[:, t].toarray().reshape(N_e, N_t), 1)
!= 0)
if data > n_channels_max:
n_channels_max = data
else:
n_channels_max = N_e
if export_all:
to_write_sparse = numpy.zeros((N_tm + N_e, N_t, n_channels_max),
dtype=numpy.float32)
mapping_sparse = -1 * numpy.ones(
(N_tm + N_e, n_channels_max), dtype=numpy.int32)
else:
to_write_sparse = numpy.zeros((N_tm, N_t, n_channels_max),
dtype=numpy.float32)
mapping_sparse = -1 * numpy.ones(
(N_tm, n_channels_max), dtype=numpy.int32)
has_purity = test_if_purity(params, extension)
if has_purity:
purity = io.load_data(params, 'purity', extension)
f = open(os.path.join(output_path, 'cluster_purity.tsv'), 'w')
f.write('cluster_id\tpurity\n')
for i in range(N_tm):
f.write('%d\t%g\n' % (i, purity[i]))
f.close()
for t in range(N_tm):
tmp = templates[:, t].toarray().reshape(N_e, N_t).T
x, y = tmp.nonzero()
nb_loc = len(numpy.unique(y))
if sparse_export:
all_positions = numpy.zeros(y.max() + 1, dtype=numpy.int32)
all_positions[numpy.unique(y)] = numpy.arange(
nb_loc, dtype=numpy.int32)
pos = all_positions[y]
to_write_sparse[t, x, pos] = tmp[x, y]
mapping_sparse[t, numpy.arange(nb_loc)] = numpy.unique(y)
else:
pos = y
to_write_sparse[t, x, pos] = tmp[x, y]
if export_all:
garbage = io.load_data(params, 'garbage', extension)
for t in range(N_tm, N_tm + N_e):
elec = t - N_tm
spikes = garbage['gspikes'].pop('elec_%d' % elec).astype(
numpy.uint64)
spikes = numpy.random.permutation(spikes)[:100]
mapping_sparse[t, 0] = t - N_tm
waveform = io.get_stas(params,
times_i=spikes,
labels_i=np.ones(len(spikes)),
src=elec,
neighs=[elec],
nodes=nodes,
mean_mode=True)
nb_loc = 1
if sparse_export:
to_write_sparse[t, :, 0] = waveform
else:
to_write_sparse[t, :, elec] = waveform
numpy.save(os.path.join(output_path, 'templates'), to_write_sparse)
if sparse_export:
numpy.save(os.path.join(output_path, 'template_ind'),
mapping_sparse)
return N_tm
def write_pcs(path, params, extension, N_tm, mode=0):
spikes = numpy.load(os.path.join(output_path, 'spike_times.npy'))
labels = numpy.load(os.path.join(output_path, 'spike_templates.npy'))
max_loc_channel = get_max_loc_channel(params, extension)
nb_features = params.getint('whitening', 'output_dim')
sign_peaks = params.get('detection', 'peaks')
nodes, edges = get_nodes_and_edges(params)
N_total = params.getint('data', 'N_total')
has_support = test_if_support(params, extension)
if has_support:
supports = io.load_data(params, 'supports', extension)
else:
inv_nodes = numpy.zeros(N_total, dtype=numpy.int32)
inv_nodes[nodes] = numpy.arange(len(nodes))
if export_all:
nb_templates = N_tm + N_e
else:
nb_templates = N_tm
pc_features_ind = numpy.zeros((nb_templates, max_loc_channel),
dtype=numpy.int32)
best_elec = io.load_data(params, 'electrodes', extension)
if export_all:
best_elec = numpy.concatenate((best_elec, numpy.arange(N_e)))
if has_support:
for count, support in enumerate(supports):
nb_loc = numpy.sum(support)
pc_features_ind[count, numpy.arange(nb_loc)] = numpy.where(
support == True)[0]
else:
for count, elec in enumerate(best_elec):
nb_loc = len(edges[nodes[elec]])
pc_features_ind[count, numpy.arange(nb_loc)] = inv_nodes[edges[
nodes[elec]]]
if sign_peaks in ['negative', 'both']:
basis_proj, basis_rec = io.load_data(params, 'basis')
elif sign_peaks in ['positive']:
basis_proj, basis_rec = io.load_data(params, 'basis-pos')
to_process = numpy.arange(comm.rank, nb_templates, comm.size)
all_offsets = numpy.zeros(nb_templates, dtype=numpy.int32)
for target in range(nb_templates):
if mode == 0:
all_offsets[target] = len(numpy.where(labels == target)[0])
elif mode == 1:
all_offsets[target] = min(
500, len(numpy.where(labels == target)[0]))
all_paddings = numpy.concatenate(([0], numpy.cumsum(all_offsets)))
total_pcs = numpy.sum(all_offsets)
pc_file = os.path.join(output_path, 'pc_features.npy')
pc_file_ids = os.path.join(output_path, 'pc_feature_spike_ids.npy')
from numpy.lib.format import open_memmap
if comm.rank == 0:
pc_features = open_memmap(pc_file,
shape=(total_pcs, nb_features,
max_loc_channel),
dtype=numpy.float32,
mode='w+')
if mode == 1:
pc_ids = open_memmap(pc_file_ids,
shape=(total_pcs, ),
dtype=numpy.int32,
mode='w+')
comm.Barrier()
pc_features = open_memmap(pc_file, mode='r+')
if mode == 1:
pc_ids = open_memmap(pc_file_ids, mode='r+')
to_explore = range(comm.rank, nb_templates, comm.size)
if comm.rank == 0:
to_explore = get_tqdm_progressbar(params, to_explore)
all_idx = numpy.zeros(0, dtype=numpy.int32)
for gcount, target in enumerate(to_explore):
count = all_paddings[target]
if mode == 1:
idx = numpy.random.permutation(
numpy.where(labels == target)[0])[:500]
pc_ids[count:count + len(idx)] = idx
elif mode == 0:
idx = numpy.where(labels == target)[0]
elec = best_elec[target]
if has_support:
indices = numpy.where(supports[target])[0]
else:
indices = inv_nodes[edges[nodes[elec]]]
labels_i = target * numpy.ones(len(idx))
times_i = numpy.take(spikes, idx).astype(numpy.int64)
sub_data = io.get_stas(params,
times_i,
labels_i,
elec,
neighs=indices,
nodes=nodes,
auto_align=False)
pcs = numpy.dot(sub_data, basis_proj)
pcs = numpy.swapaxes(pcs, 1, 2)
if mode == 0:
pc_features[idx, :, :len(indices)] = pcs
elif mode == 1:
pc_features[count:count + len(idx), :, :len(indices)] = pcs
comm.Barrier()
if comm.rank == 0:
numpy.save(os.path.join(output_path, 'pc_feature_ind'),
pc_features_ind.astype(
numpy.uint32)) # n_templates, n_loc_chan
do_export = True
if comm.rank == 0:
if os.path.exists(output_path):
if not erase_all:
do_export = query_yes_no(
Fore.WHITE +
"Export already made! Do you want to erase everything?",
default=None)
if do_export:
if os.path.exists(os.path.abspath('.phy')):
shutil.rmtree(os.path.abspath('.phy'))
shutil.rmtree(output_path)
if do_export:
comm.bcast(numpy.array([1], dtype=numpy.int32), root=0)
else:
comm.bcast(numpy.array([0], dtype=numpy.int32), root=0)
else:
do_export = bool(
comm.bcast(numpy.array([0], dtype=numpy.int32), root=0))
comm.Barrier()
if do_export:
apply_patch_for_similarities(params, extension)
if comm.rank == 0:
os.makedirs(output_path)
print_and_log(
["Exporting data for the phy GUI with %d CPUs..." % nb_cpu],
'info', logger)
if params.getboolean('whitening', 'spatial'):
whitening_mat = io.load_data(
params, 'spatial_whitening').astype(numpy.double)
numpy.save(os.path.join(output_path, 'whitening_mat'),
whitening_mat)
numpy.save(os.path.join(output_path, 'whitening_mat_inv'),
numpy.linalg.inv(whitening_mat))
else:
numpy.save(os.path.join(output_path, 'whitening_mat'),
numpy.eye(N_e))
positions, shanks = generate_mapping(probe)
numpy.save(os.path.join(output_path, 'channel_positions'),
positions.astype(numpy.double))
numpy.save(os.path.join(output_path, 'channel_shanks'),
shanks.astype(numpy.double))
nodes, edges = get_nodes_and_edges(params)
numpy.save(os.path.join(output_path, 'channel_map'),
nodes.astype(numpy.int32))
write_results(output_path, params, extension)
N_tm = write_templates(output_path, params, extension)
template_file = h5py.File(file_out_suff +
'.templates%s.hdf5' % extension,
'r',
libver='earliest')
similarities = template_file.get('maxoverlap')[:]
template_file.close()
norm = N_e * N_t
if export_all:
to_write = numpy.zeros((N_tm + N_e, N_tm + N_e),
dtype=numpy.single)
to_write[:N_tm, :N_tm] = (similarities[:N_tm, :N_tm] /
norm).astype(numpy.single)
else:
to_write = (similarities[:N_tm, :N_tm] / norm).astype(
numpy.single)
numpy.save(os.path.join(output_path, 'similar_templates'),
to_write)
comm.bcast(numpy.array([N_tm], dtype=numpy.int32), root=0)
else:
N_tm = int(comm.bcast(numpy.array([0], dtype=numpy.int32), root=0))
comm.Barrier()
make_pcs = 2
if comm.rank == 0:
if export_pcs == 'prompt':
key = ''
while key not in ['a', 's', 'n']:
print(
Fore.WHITE +
"Do you want SpyKING CIRCUS to export PCs? (a)ll / (s)ome / (n)o"
)
key = raw_input('')
else:
key = export_pcs
if key == 'a':
make_pcs = 0
comm.bcast(numpy.array([0], dtype=numpy.int32), root=0)
elif key == 's':
make_pcs = 1
comm.bcast(numpy.array([1], dtype=numpy.int32), root=0)
elif key == 'n':
comm.bcast(numpy.array([2], dtype=numpy.int32), root=0)
if os.path.exists(os.path.join(output_path,
'pc_features.npy')):
os.remove(os.path.join(output_path, 'pc_features.npy'))
if os.path.exists(
os.path.join(output_path, 'pc_feature_ind.npy')):
os.remove(os.path.join(output_path, 'pc_feature_ind.npy'))
else:
make_pcs = comm.bcast(numpy.array([0], dtype=numpy.int32), root=0)
make_pcs = make_pcs[0]
comm.Barrier()
if make_pcs < 2:
write_pcs(output_path, params, extension, N_tm, make_pcs)
supported_by_phy = ['raw_binary', 'mcs_raw_binary', 'mda']
file_format = data_file.description
gui_params = {}
if file_format in supported_by_phy:
if not params.getboolean('data', 'overwrite'):
gui_params['dat_path'] = r"%s" % params.get(
'data', 'data_file_no_overwrite')
else:
if params.get('data', 'stream_mode') == 'multi-files':
data_file = params.get_data_file(source=True,
has_been_created=False)
gui_params['dat_path'] = "["
for f in data_file.get_file_names():
gui_params['dat_path'] += 'r"%s", ' % f
gui_params['dat_path'] += "]"
else:
gui_params['dat_path'] = 'r"%s"' % params.get(
'data', 'data_file')
else:
gui_params['dat_path'] = 'giverandomname.dat'
gui_params['n_channels_dat'] = params.nb_channels
gui_params['n_features_per_channel'] = 5
gui_params['dtype'] = data_file.data_dtype
if 'data_offset' in data_file.params.keys():
gui_params['offset'] = data_file.data_offset
gui_params['sample_rate'] = params.rate
gui_params['dir_path'] = output_path
gui_params['hp_filtered'] = True
f = open(os.path.join(output_path, 'params.py'), 'w')
for key, value in gui_params.items():
if key in ['dir_path', 'dtype']:
f.write('%s = r"%s"\n' % (key, value))
else:
f.write("%s = %s\n" % (key, value))
f.close()
