def test_spykingcircus_extractor(self):
path1 = self.test_dir + '/sc'
se.SpykingCircusSortingExtractor.write_sorting(self.SX, path1)
SX_spy = se.SpykingCircusSortingExtractor(path1)
check_sorting_return_types(SX_spy)
check_sortings_equal(self.SX, SX_spy)
check_dumping(SX_spy)
def get_result_from_folder(output_folder):
sorting = se.SpykingCircusSortingExtractor(
folder_path=Path(output_folder) / 'recording')
return sorting
def spyking_circus(
recording,
output_folder=None, # Temporary working directory
probe_file=None,
file_name=None,
detect_sign=-1, # -1 - 1 - 0
adjacency_radius=100, # Channel neighborhood adjacency radius corresponding to geom file
spike_thresh=6, # Threshold for detection
template_width_ms=3, # Spyking circus parameter
filter=True,
merge_spikes=True,
n_cores=None,
electrode_dimensions=None,
whitening_max_elts=1000, # I believe it relates to subsampling and affects compute time
clustering_max_elts=10000, # I believe it relates to subsampling and affects compute time
):
try:
import circus
except ModuleNotFoundError:
raise ModuleNotFoundError(
"\nTo use Spyking-Circus, install spyking-circus: \n\n"
"\npip install spyking-circus"
"\nfor ubuntu install openmpi: "
"\nsudo apt install libopenmpi-dev"
"\nMore information on Spyking-Circus at: "
"\nhttps://spyking-circus.readthedocs.io/en/latest/")
source_dir = os.path.dirname(os.path.realpath(__file__))
if output_folder is None:
output_folder = 'spyking_circus'
else:
output_folder = join(output_folder, 'spyking_circus')
output_folder = os.path.abspath(output_folder)
if not os.path.isdir(output_folder):
os.makedirs(output_folder)
# save prb file:
if probe_file is None:
se.saveProbeFile(recording,
join(output_folder, 'probe.prb'),
format='spyking_circus',
radius=adjacency_radius,
dimensions=electrode_dimensions)
probe_file = join(output_folder, 'probe.prb')
# save binary file
if file_name is None:
file_name = 'recording'
elif file_name.endswith('.npy'):
file_name = file_name[file_name.find('.npy')]
np.save(join(output_folder, file_name),
recording.getTraces().astype('float32'))
if detect_sign < 0:
detect_sign = 'negative'
elif detect_sign > 0:
detect_sign = 'positive'
else:
detect_sign = 'both'
# set up spykingcircus config file
with open(join(source_dir, 'config_default.params'), 'r') as f:
circus_config = f.readlines()
if merge_spikes:
auto = 1e-5
else:
auto = 0
circus_config = ''.join(circus_config).format(
float(recording.getSamplingFrequency()), probe_file, template_width_ms,
spike_thresh, detect_sign, filter, whitening_max_elts,
clustering_max_elts, auto)
with open(join(output_folder, file_name + '.params'), 'w') as f:
f.writelines(circus_config)
print('Running spyking circus...')
t_start_proc = time.time()
if n_cores is None:
n_cores = np.maximum(1, int(os.cpu_count() / 2))
cmd = 'spyking-circus {} -c {} '.format(
join(output_folder, file_name + '.npy'), n_cores)
cmd_merge = 'spyking-circus {} -m merging -c {} '.format(
join(output_folder, file_name + '.npy'), n_cores)
# cmd_convert = 'spyking-circus {} -m converting'.format(join(output_folder, file_name+'.npy'))
print(cmd)
retcode = run_command_and_print_output(cmd)
if retcode != 0:
raise Exception('Spyking circus returned a non-zero exit code')
print(cmd_merge)
retcode = run_command_and_print_output(cmd_merge)
if retcode != 0:
raise Exception('Spyking circus merging returned a non-zero exit code')
processing_time = time.time() - t_start_proc
print('Elapsed time: ', processing_time)
sorting = se.SpykingCircusSortingExtractor(join(output_folder, file_name))
return sorting
def test_spykingcircus_extractor(self):
path1 = self.test_dir + '/firings_true'
se.SpykingCircusSortingExtractor.writeSorting(self.SX, path1)
SX_spy = se.SpykingCircusSortingExtractor(path1)
self._check_sorting_return_types(SX_spy)
self._check_sortings_equal(self.SX, SX_spy)
