def save_nwb(output_path, v, sweep, sweeps_by_type):
'''Save a single voltage output result into an existing sweep in a NWB file.
This is intended to overwrite a recorded trace with a simulated voltage.
Parameters
----------
output_path : string
file name of a pre-existing NWB file.
v : numpy array
voltage
sweep : integer
which entry to overwrite in the file.
'''
output = NwbDataSet(output_path)
output.set_sweep(sweep, None, v)
sweep_by_type = {t: [ sweep ] for t, ss in sweeps_by_type.items() if sweep in ss }
sweep_features = extract_cell_features.extract_sweep_features(output,
sweep_by_type)
try:
spikes = sweep_features[sweep]['spikes']
spike_times = [ s['threshold_t'] for s in spikes ]
output.set_spike_times(sweep, spike_times)
except Exception, e:
logging.info("sweep %d has no sweep features. %s" % (sweep, e.message) )
def save_nwb(output_path, v, sweep, sweep_by_type= None):
'''Save a single voltage output result into an existing sweep in a NWB file.
This is intended to overwrite a recorded trace with a simulated voltage.
Parameters
----------
output_path : string
file name of a pre-existing NWB file.
v : numpy array
voltage
sweep : integer
which entry to overwrite in the file.
'''
output = NwbDataSet(output_path)
output.set_sweep(sweep, None, v)
if sweep_by_type is not None:
sweep_by_type = {t: [sweep]
for t, ss in sweeps_by_type.items() if sweep in ss}
sweep_features = extract_cell_features.extract_sweep_features(output,
sweep_by_type)
try:
spikes = sweep_features[sweep]['spikes']
spike_times = [s['threshold_t'] for s in spikes]
output.set_spike_times(sweep, spike_times)
except Exception as e:
logging.info("sweep %d has no sweep features. %s" % (sweep, e.args))
class Nwb1Appender(NwbAppender):
def __init__(self, nwb_file_name):
NwbAppender.__init__(self, nwb_file_name)
self.nwbfile = NwbDataSet(self.nwb_file_name)
def add_spike_times(self, sweep_spike_times):
for sweep_num, spike_times in sweep_spike_times.items():
self.nwbfile.set_spike_times(sweep_num, spike_times)
def write_sweep_response(file_name, sweep_number, response, spike_times):
''' Overwrite the response in a file. '''
logging.debug("writing sweep")
write_start_time = time.time()
ephds = NwbDataSet(file_name)
ephds.set_sweep(sweep_number, stimulus=None, response=response)
ephds.set_spike_times(sweep_number, spike_times)
logging.debug("write time %f" % (time.time() - write_start_time))
def write_sweep_response(file_name, sweep_number, response, spike_times):
''' Overwrite the response in a file. '''
logging.debug("writing sweep")
write_start_time = time.time()
ephds = NwbDataSet(file_name)
ephds.set_sweep(sweep_number, stimulus=None, response=response)
ephds.set_spike_times(sweep_number, spike_times)
logging.debug("write time %f" % (time.time() - write_start_time))
def prepare_nwb_output(nwb_stimulus_path, nwb_result_path):
"""Copy the stimulus file, zero out the recorded voltages and spike times.
Parameters
----------
nwb_stimulus_path : string
NWB file name
nwb_result_path : string
NWB file name
"""
copy(nwb_stimulus_path, nwb_result_path)
data_set = NwbDataSet(nwb_result_path)
data_set.fill_sweep_responses(0.0)
for sweep in data_set.get_sweep_numbers():
data_set.set_spike_times(sweep, [])
def prepare_nwb_output(nwb_stimulus_path, nwb_result_path):
'''Copy the stimulus file, zero out the recorded voltages and spike times.
Parameters
----------
nwb_stimulus_path : string
NWB file name
nwb_result_path : string
NWB file name
'''
output_dir = os.path.dirname(nwb_result_path)
if not os.path.exists(output_dir):
os.makedirs(output_dir)
copy(nwb_stimulus_path, nwb_result_path)
data_set = NwbDataSet(nwb_result_path)
data_set.fill_sweep_responses(0.0, extend_experiment=True)
for sweep in data_set.get_sweep_numbers():
data_set.set_spike_times(sweep, [])
def save_nwb(output_path, v, sweep):
'''Save a single voltage output result into an existing sweep in a NWB file.
This is intended to overwrite a recorded trace with a simulated voltage.
Parameters
----------
output_path : string
file name of a pre-existing NWB file.
v : numpy array
voltage
sweep : integer
which entry to overwrite in the file.
'''
output = NwbDataSet(output_path)
output.set_sweep(sweep, None, v)
sweep_features = extract_cell_features.extract_sweep_features(output_path,
[sweep])
spikes = sweep_features[sweep]['mean']['spikes']
spike_times = [ s['t'] for s in spikes ]
output.set_spike_times(sweep, spike_times)
def prepare_nwb_output(nwb_stimulus_path,
nwb_result_path):
'''Copy the stimulus file, zero out the recorded voltages and spike times.
Parameters
----------
nwb_stimulus_path : string
NWB file name
nwb_result_path : string
NWB file name
'''
output_dir = os.path.dirname(nwb_result_path)
if not os.path.exists(output_dir):
os.makedirs(output_dir)
copy(nwb_stimulus_path, nwb_result_path)
data_set = NwbDataSet(nwb_result_path)
data_set.fill_sweep_responses(0.0)
for sweep in data_set.get_sweep_numbers():
data_set.set_spike_times(sweep, [])
