def test_klusta_extractor(self):
path1 = self.test_dir + '/firings_true.kwik'
se.KlustaSortingExtractor.write_sorting(self.SX, path1)
SX_kl = se.KlustaSortingExtractor(path1)
self._check_sorting_return_types(SX_kl)
self._check_sortings_equal(self.SX, SX_kl)
def get_result_from_folder(output_folder):
sorting = se.KlustaSortingExtractor(output_folder / 'recording.kwik')
return sorting
def _klusta(
recording, # The recording extractor
output_folder=None,
probe_file=None,
file_name=None,
adjacency_radius=None,
threshold_strong_std_factor=5,
threshold_weak_std_factor=2,
detect_sign=-1,
extract_s_before=16,
extract_s_after=32,
n_features_per_channel=3,
pca_n_waveforms_max=10000,
num_starting_clusters=50):
try:
import klusta
import klustakwik2
except ModuleNotFoundError:
raise ModuleNotFoundError(
"\nTo use Klusta, install klusta and klustakwik2: \n\n"
"\npip install klusta klustakwik\n"
"\nMore information on klusta at: "
"\nhttps://github.com/kwikteam/phy"
"\nhttps://github.com/kwikteam/klusta")
source_dir = Path(__file__).parent
if output_folder is None:
output_folder = Path('klusta')
else:
output_folder = Path(output_folder)
if not output_folder.is_dir():
output_folder.mkdir()
# save prb file:
if probe_file is None:
probe_file = output_folder / 'probe.prb'
se.saveProbeFile(recording,
probe_file,
format='klusta',
radius=adjacency_radius)
# save binary file
if file_name is None:
file_name = Path('recording')
elif file_name.suffix == '.dat':
file_name = file_name.stem
se.writeBinaryDatFormat(recording, output_folder / file_name)
if detect_sign < 0:
detect_sign = 'negative'
elif detect_sign > 0:
detect_sign = 'positive'
else:
detect_sign = 'both'
# set up klusta config file
with (source_dir / 'config_default.prm').open('r') as f:
klusta_config = f.readlines()
klusta_config = ''.join(klusta_config).format(
output_folder / file_name, probe_file,
float(recording.getSamplingFrequency()), recording.getNumChannels(),
"'float32'", threshold_strong_std_factor, threshold_weak_std_factor,
"'" + detect_sign + "'", extract_s_before, extract_s_after,
n_features_per_channel, pca_n_waveforms_max, num_starting_clusters)
with (output_folder / 'config.prm').open('w') as f:
f.writelines(klusta_config)
print('Running Klusta')
cmd = 'klusta {} --overwrite'.format(output_folder / 'config.prm')
print(cmd)
_call_command(cmd)
if not (output_folder / (file_name.name + '.kwik')).is_file():
raise Exception('Klusta did not run successfully')
sorting = se.KlustaSortingExtractor(output_folder /
(file_name.name + '.kwik'))
return sorting
def get_result_from_folder(output_folder):
sorting = se.KlustaSortingExtractor(
file_or_folder_path=Path(output_folder) / 'recording.kwik')
return sorting
def klusta(
recording, # The recording extractor
output_folder=None,
probe_file=None,
file_name=None,
threshold_strong_std_factor=5,
threshold_weak_std_factor=2,
detect_spikes='negative',
extract_s_before=16,
extract_s_after=32,
n_features_per_channel=3,
pca_n_waveforms_max=10000,
num_starting_clusters=50):
try:
import klusta
import klustakwik2
except ModuleNotFoundError:
raise ModuleNotFoundError(
"\nTo use Klusta, install klusta and klustakwik2: \n\n"
"\npip install klusta klustakwik\n"
"\nMore information on klusta at: "
"\nhttps://github.com/kwikteam/phy"
"\nhttps://github.com/kwikteam/klusta")
source_dir = os.path.dirname(os.path.realpath(__file__))
if output_folder is None:
output_folder = 'klusta'
else:
output_folder = join(output_folder, 'klusta')
if not os.path.isdir(output_folder):
os.makedirs(output_folder)
# save prb file:
if probe_file is None:
si.saveProbeFile(recording,
join(output_folder, 'probe.prb'),
format='klusta')
probe_file = join(output_folder, 'probe.prb')
# save binary file
if file_name is None:
file_name = 'recording'
elif file_name.endswith('.dat'):
file_name = file_name[file_name.find('.dat')]
si.writeBinaryDatFormat(recording, join(output_folder, file_name))
# set up klusta config file
with open(join(source_dir, 'config_default.prm'), 'r') as f:
klusta_config = f.readlines()
klusta_config = ''.join(klusta_config).format(
join(output_folder, file_name), probe_file,
float(recording.getSamplingFrequency()), recording.getNumChannels(),
"'float32'", threshold_strong_std_factor, threshold_weak_std_factor,
"'" + detect_spikes + "'", extract_s_before, extract_s_after,
n_features_per_channel, pca_n_waveforms_max, num_starting_clusters)
with open(join(output_folder, 'config.prm'), 'w') as f:
f.writelines(klusta_config)
print('Running Klusta')
t_start_proc = time.time()
cmd = 'klusta {} --overwrite'.format(join(output_folder, 'config.prm'))
print(cmd)
retcode = run_command_and_print_output(cmd)
if retcode != 0:
raise Exception('Klusta returned a non-zero exit code')
print('Elapsed time: ', time.time() - t_start_proc)
sorting = si.KlustaSortingExtractor(
join(output_folder, file_name + '.kwik'))
return sorting