def test_load_save_probes(self):
SX = se.loadProbeFile(self.RX, 'tests/probe_test.prb')
# print(SX.getChannelPropertyNames())
assert 'location' in SX.getChannelPropertyNames()
assert 'group' in SX.getChannelPropertyNames()
positions = [SX.getChannelProperty(chan, 'location') for chan in range(self.RX.getNumChannels())]
# save in csv
se.saveProbeFile(SX, Path(self.test_dir) / 'geom.csv')
# load csv locations
SX_load = se.loadProbeFile(SX, Path(self.test_dir) / 'geom.csv')
position_loaded = [SX_load.getChannelProperty(chan, 'location') for chan in range(SX_load.getNumChannels())]
self.assertTrue(np.allclose(positions[10], position_loaded[10]))
def yass_helper(
recording,
output_folder=None, # Temporary working directory
probe_file=None,
file_name=None,
detect_sign=-1, # -1 - 1 - 0
template_width_ms=1, # yass parameter
filter=True,
adjacency_radius=100):
source_dir = os.path.dirname(os.path.realpath(__file__))
# make output dir
if output_folder is None:
output_folder = 'yass'
else:
output_folder = join(output_folder, 'yass')
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:
probe_file = join_abspath_(output_folder, 'probe.npy')
se.saveProbeFile(recording, probe_file, format='yass')
# save binary file
if file_name is None:
file_name = 'raw.bin'
bin_file = join_abspath_(output_folder, file_name)
# print('bin_file:{}'.format(bin_file))
writeRecording_(recording=recording, save_path=bin_file,
fReversePolarity=(detect_sign > 0), dtype=np.float32, scale_factor=1)
#print('bin_file exists? {}'.format(os.path.exists(bin_file)))
# set up yass config file
print(source_dir)
with open(join(source_dir, 'config_default.yaml'), 'r') as f:
yass_config = f.read()
# get the order
# root_folder, recordings, geometry, dtype, sampling_rate, n_channels, spatial_radius, spike_size_ms, filter
n_channels = recording.getNumChannels()
sampling_rate = recording.getSamplingFrequency()
# print('sampling_rate={}'.format(sampling_rate))
yaml_file = join(output_folder, file_name + '.yaml')
yass_config = yass_config.format(
output_folder, bin_file, probe_file, 'single', int(sampling_rate), n_channels, adjacency_radius, template_width_ms, filter)
with open(yaml_file, 'w') as f:
f.write(yass_config)
with open(yaml_file) as ff:
print('YASS CONFIG:')
print(ff.read())
print('Running yass...')
t_start_proc = time.time()
yass_path = '/usr/local/bin'
num_cores_str = ''
# cmd = 'python2 {}/yass {} {} '.format(
# yass_path, join(output_folder, file_name+'.yaml'), num_cores_str)
cmd = 'yass {}'.format(join(output_folder, file_name+'.yaml'))
retcode = run_command_and_print_output(cmd)
if retcode != 0:
raise Exception('yass returned a non-zero exit code')
# retcode = run_command_and_print_output(cmd_merge)
# if retcode != 0:
# raise Exception('yass merging returned a non-zero exit code')
processing_time = time.time() - t_start_proc
print('Elapsed time: ', processing_time)
sorting = yassSortingExtractor(join_abspath_(output_folder, 'tmp'))
return sorting, yaml_file
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 _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 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