def spykingcircus(recording_path,
sorting_out,
detect_sign=-1,
adjacency_radius=200,
detect_threshold=6,
template_width_ms=3,
filter=True,
merge_spikes=True,
auto_merge=0.75,
whitening_max_elts=1000,
clustering_max_elts=10000):
import spiketoolkit as st
import spikesorters as ss
from spikeforest2_utils import AutoRecordingExtractor, AutoSortingExtractor
recording = AutoRecordingExtractor(dict(path=recording_path),
download=True)
# Sorting
print('Sorting...')
sorter = ss.SpykingcircusSorter(recording=recording,
output_folder='/tmp/tmp_spykingcircus_' +
_random_string(8),
delete_output_folder=True)
num_workers = os.environ.get('NUM_WORKERS', None)
if not num_workers: num_workers = '1'
num_workers = int(num_workers)
sorter.set_params(detect_sign=detect_sign,
adjacency_radius=adjacency_radius,
detect_threshold=detect_threshold,
template_width_ms=template_width_ms,
filter=filter,
merge_spikes=merge_spikes,
auto_merge=auto_merge,
num_workers=num_workers,
whitening_max_elts=whitening_max_elts,
clustering_max_elts=clustering_max_elts)
timer = sorter.run()
print('#SF-SORTER-RUNTIME#{:.3f}#'.format(timer))
sorting = sorter.get_result()
AutoSortingExtractor.write_sorting(sorting=sorting, save_path=sorting_out)
def spykingcircus_wrapper1(recording_object: dict,
detect_sign=-1,
adjacency_radius=100,
detect_threshold=6,
template_width_ms=3,
filter=True,
merge_spikes=True,
auto_merge=0.75,
whitening_max_elts=1000,
clustering_max_elts=10000) -> dict:
import sortingview as sv
import spikesorters as ss
recording = sv.LabboxEphysRecordingExtractor(recording_object)
# Sorting
with kc.TemporaryDirectory(prefix='tmp_spykingcircus') as tmpdir:
sorter = ss.SpykingcircusSorter(recording=recording,
output_folder=f'{tmpdir}/working',
delete_output_folder=True)
num_workers = 1
sorter.set_params(detect_sign=detect_sign,
adjacency_radius=adjacency_radius,
detect_threshold=detect_threshold,
template_width_ms=template_width_ms,
filter=filter,
merge_spikes=merge_spikes,
auto_merge=auto_merge,
num_workers=num_workers,
whitening_max_elts=whitening_max_elts,
clustering_max_elts=clustering_max_elts)
timer = sorter.run()
print('#SF-SORTER-RUNTIME#{:.3f}#'.format(timer))
sorting = sorter.get_result()
return sv.LabboxEphysSortingExtractor.store_sorting(
sorting=sorting).object()
def run(self):
import spikesorters as sorters
print('SpyKING CIRCUS......')
recording = SFMdaRecordingExtractor(self.recording_dir)
code = ''.join(
random.choice(string.ascii_uppercase) for x in range(10))
tmpdir = os.environ.get('TEMPDIR', '/tmp') + '/spyking-circus-' + code
num_workers = int(os.environ.get('NUM_WORKERS', '1'))
sorter = sorters.SpykingcircusSorter(recording=recording,
output_folder=tmpdir,
verbose=True,
delete_output_folder=True)
sorter.set_params(
detect_sign=self.detect_sign,
adjacency_radius=self.adjacency_radius,
detect_threshold=self.detect_threshold,
template_width_ms=self.template_width_ms,
filter=self.filter,
merge_spikes=True,
auto_merge=0.5,
num_workers=num_workers,
electrode_dimensions=None,
whitening_max_elts=self.whitening_max_elts,
clustering_max_elts=self.clustering_max_elts,
)
timer = sorter.run()
print('#SF-SORTER-RUNTIME#{:.3f}#'.format(timer))
sorting = sorter.get_result()
SFMdaSortingExtractor.write_sorting(sorting=sorting,
save_path=self.firings_out)
def spykingcircus(recording, sorting_out):
import spiketoolkit as st
import spikesorters as ss
from spikeforest2_utils import AutoRecordingExtractor, AutoSortingExtractor
import kachery as ka
# TODO: need to think about how to deal with this
ka.set_config(fr='default_readonly')
recording = AutoRecordingExtractor(dict(path=recording), download=True)
# Sorting
print('Sorting...')
sorter = ss.SpykingcircusSorter(recording=recording,
output_folder='/tmp/tmp_spykingcircus_' +
_random_string(8),
delete_output_folder=True)
sorter.set_params()
timer = sorter.run()
print('#SF-SORTER-RUNTIME#{:.3f}#'.format(timer))
sorting = sorter.get_result()
AutoSortingExtractor.write_sorting(sorting=sorting, save_path=sorting_out)