def sort(algorithm: str,
recording_path: str,
sorting_out: str = None,
params: dict = None,
container: str = 'default',
git_annex_mode=True,
use_singularity: bool = False,
job_timeout: float = 3600) -> str:
from spikeforest2 import sorters
HITHER_USE_SINGULARITY = os.getenv('HITHER_USE_SINGULARITY')
if HITHER_USE_SINGULARITY is None:
HITHER_USE_SINGULARITY = False
print('HITHER_USE_SINGULARITY: ' + HITHER_USE_SINGULARITY)
if not hasattr(sorters, algorithm):
raise Exception('Sorter not found: {}'.format(algorithm))
sorter = getattr(sorters, algorithm)
if algorithm in [
'kilosort2', 'kilosort', 'ironclust', 'tridesclous', 'jrclust'
]:
gpu = True
else:
gpu = False
if not sorting_out:
sorting_out = hither.File()
if not recording_path.startswith(
'sha1dir://') or not recording_path.startswith('sha1://'):
if os.path.isfile(recording_path):
recording_path = ka.store_file(recording_path)
elif os.path.isdir(recording_path):
recording_path = ka.store_dir(recording_path,
git_annex_mode=git_annex_mode)
if params is None:
params = dict()
params_hither = dict(gpu=gpu, container=container)
if job_timeout is not None:
params_hither['job_timeout'] = job_timeout
with hither.config(**params_hither):
result = sorter.run(recording_path=recording_path,
sorting_out=sorting_out,
**params)
print('SORTING')
print('==============================================')
return ka.store_file(result.outputs.sorting_out._path,
basename='firings.mda')
# def set_params(sorter, params_file):
# params = {}
# names_float = ['detection_thresh']
# with open(params_file, 'r') as myfile:
# for line in myfile:
# name, var = line.partition("=")[::2]
# name = name.strip()
# params[name.strip()] = var
# sorter.set_params(**params)
def patch_recording_geom(recording, geom_fname):
print(f'PATCHING geom for recording: {recording["name"]}')
geom_info = ka.get_file_info(geom_fname)
x = recording['directory']
y = ka.store_dir(x).replace('sha1dir://', 'sha1://')
obj = ka.load_object(y)
obj['files']['geom.csv'] = dict(size=geom_info['size'],
sha1=geom_info['sha1'])
x2 = ka.store_object(obj)
recording['directory'] = 'sha1dir://' + ka.get_file_hash(x2) + '.patched'
def register_study(*,
path_from,
path_to,
studySetName,
studyName,
to='default_readwrite'):
list_rec = [
str(f) for f in os.listdir(path_from)
if os.path.isdir(os.path.join(path_from, f))
]
print('# files: {}'.format(len(list_rec)))
study_obj = dict(name=studyName, studySetName=studySetName, recordings=[])
mkdir_(path_to)
for rec1 in list_rec:
print(f'Uploading {rec1}')
path_rec1 = os.path.join(path_from, rec1)
register_groundtruth(recdir=path_rec1,
output_fname=os.path.join(
path_to, rec1 + '.firings_true.json'),
label=rec1)
rec = MdaRecordingExtractor(recording_directory=path_rec1)
sorting = MdaSortingExtractor(firings_file=path_rec1 +
'/firings_true.mda',
samplerate=rec.get_sampling_frequency())
recording_obj = dict(
name=rec1,
studyName=studyName,
studySetName=studySetName,
directory=ka.store_dir(path_rec1),
firingsTrue=ka.store_file(os.path.join(path_to, rec1 +
'.firings_true.json'),
basename='firings_true.json'),
sampleRateHz=rec.get_sampling_frequency(),
numChannels=len(rec.get_channel_ids()),
durationSec=rec.get_num_frames() / rec.get_sampling_frequency(),
numTrueUnits=len(sorting.get_unit_ids()),
spikeSign=-1 # TODO: get this from params.json
)
study_obj['recordings'].append(recording_obj)
# update .json files
register_recording(recdir=path_rec1,
output_fname=os.path.join(path_to, rec1 + '.json'),
label=rec1)
study_obj['self_reference'] = ka.store_object(study_obj)
with open(os.path.join(path_to, studyName + '.json'), 'w') as f:
json.dump(study_obj, f, indent=4)
return study_obj
if os.path.isdir(os.path.join(path_from, f))
]
print('# files: {}'.format(len(list_rec)))
study_obj = dict(name=study_name, studySetName=studyset_name, recordings=[])
for rec1 in list_rec:
print(f'Uploading {rec1}')
path_rec1 = os.path.join(path_from, rec1)
rec = MdaRecordingExtractor(recording_directory=path_rec1)
sorting = MdaSortingExtractor(firings_file=path_rec1 + '/firings_true.mda',
samplerate=rec.get_sampling_frequency())
recording_obj = dict(
name=rec1,
studyName=study_name,
studySetName=studyset_name,
directory=ka.store_dir(path_rec1),
firingsTrue=ka.store_file(os.path.join(path_to,
rec1 + '.firings_true.json'),
basename='firings_true.json'),
sampleRateHz=rec.get_sampling_frequency(),
numChannels=len(rec.get_channel_ids()),
durationSec=rec.get_num_frames() / rec.get_sampling_frequency(),
numTrueUnits=len(sorting.get_unit_ids()),
spikeSign=-1 # TODO: get this from params.json
)
study_obj['recordings'].append(recording_obj)
study_obj['self_reference'] = ka.store_object(study_obj)
with open(os.path.join(path_to, study_name + '.json'), 'w') as f:
json.dump(study_obj, f, indent=4)