def create_raw_spike_signal(self, start, stop):
#signal=load:spikes()
if self.sd['params']['to_file']:
n_vp=my_nest.GetKernelStatus(['total_num_virtual_procs'])[0]
data_path=my_nest.GetKernelStatus(['data_path'])[0]
files=os.listdir(data_path)
file_names=[data_path+s for s in files
if s.split('-')[0]==self.sd['model']]
s, t = my_nest.get_spikes_from_file(file_names)
else:
s,t=my_nest.get_spikes_from_memory(self.sd['id'])
e = my_nest.GetStatus(self.sd['id'])[0]['events'] # get events
s = e['senders'] # get senders
t = e['times'] # get spike times
if comm.is_mpi_used():
s,t=my_nest.collect_spikes_mpi(s,t)
if stop:
s, t = s[t < stop], t[t < stop] # Cut out data
s, t = s[t >= start], t[t >= start] # Cut out data
signal = zip(s, t)
return signal
def create_raw_spike_signal(self, start, stop):
#signal=load:spikes()
if self.sd['params']['to_file']:
n_vp = my_nest.GetKernelStatus(['total_num_virtual_procs'])[0]
data_path = my_nest.GetKernelStatus(['data_path'])[0]
files = os.listdir(data_path)
file_names = [
data_path + s for s in files
if s.split('-')[0] == self.sd['model']
]
s, t = my_nest.get_spikes_from_file(file_names)
else:
s, t = my_nest.get_spikes_from_memory(self.sd['id'])
e = my_nest.GetStatus(self.sd['id'])[0]['events'] # get events
s = e['senders'] # get senders
t = e['times'] # get spike times
if comm.is_mpi_used():
s, t = my_nest.collect_spikes_mpi(s, t)
if stop:
s, t = s[t < stop], t[t < stop] # Cut out data
s, t = s[t >= start], t[t >= start] # Cut out data
signal = zip(s, t)
return signal
def save_fig(self, *args):
if comm.is_mpi_used():
with Barrier():
if comm.rank() == 0:
self._save_fig(*args)
else:
self._save_fig(*args)
def save_fig(self, *args):
if comm.is_mpi_used():
with Barrier():
if comm.rank()==0:
self._save_fig(*args)
else:
self._save_fig(*args)
def get_spikes_from_memory(sd_id):
e = GetStatus(sd_id)[0]['events'] # get events
s = e['senders'] # get senders
t = e['times'] # get spike times
if comm.is_mpi_used():
s, t = collect_spikes_mpi(s, t)
return s, t
def get_spikes_from_memory(sd_id):
e = GetStatus(sd_id)[0]['events'] # get events
s = e['senders'] # get senders
t = e['times'] # get spike times
if comm.is_mpi_used():
s,t=collect_spikes_mpi(s,t)
return s,t
def mkdir(*args, **kwargs):
'''
Arguments:
data - data to be pickled
fileName - full path or just file name
'''
if comm.is_mpi_used() and not kwargs.get('all_mpi', False):
_mkdir_mpi(*args)
else:
_mkdir(*args)
def mkdir(*args, **kwargs):
'''
Arguments:
data - data to be pickled
fileName - full path or just file name
'''
if comm.is_mpi_used() and not kwargs.get('all_mpi', False):
_mkdir_mpi(*args)
else:
_mkdir(*args)
def text_load(fileName, **kwargs):
'''
Arguments:
fileName - full path or just file name
'''
if comm.is_mpi_used() and not kwargs.get('all_mpi', False):
data = _text_load_mpi(fileName)
else:
data = _text_load(fileName)
return data
def text_save(text, fileName, **kwargs ):
'''
Arguments:
data - data to be pickled
fileName - full path or just file name
'''
mkdir('/'.join(fileName.split('/')[0:-1]))
if comm.is_mpi_used() and not kwargs.get('all_mpi', False):
_text_save_mpi(text, fileName)
else:
_text_save(text, fileName)
def text_save(text, fileName, **kwargs):
'''
Arguments:
data - data to be pickled
fileName - full path or just file name
'''
mkdir('/'.join(fileName.split('/')[0:-1]))
if comm.is_mpi_used() and not kwargs.get('all_mpi', False):
_text_save_mpi(text, fileName)
else:
_text_save(text, fileName)
def text_load(fileName, **kwargs):
'''
Arguments:
fileName - full path or just file name
'''
if comm.is_mpi_used()and not kwargs.get('all_mpi', False):
data=_text_load_mpi(fileName)
else:
data=_text_load(fileName)
return data
def pickle_save(data, fileName, file_extension='.pkl', **kwargs):
'''
Arguments:
data - data to be pickled
fileName - full path or just file name
'''
fileName = get_full_file_name(fileName, file_extension)
mkdir('/'.join(fileName.split('/')[0:-1]))
if comm.is_mpi_used() and not kwargs.get('all_mpi', False):
_pickle_save_mpi(data, fileName)
else:
_pickle_save(data, fileName)
def pickle_save(data, fileName, file_extension='.pkl', **kwargs):
'''
Arguments:
data - data to be pickled
fileName - full path or just file name
'''
fileName=get_full_file_name(fileName, file_extension)
mkdir('/'.join(fileName.split('/')[0:-1]))
if comm.is_mpi_used() and not kwargs.get('all_mpi', False):
_pickle_save_mpi(data, fileName)
else:
_pickle_save(data, fileName)
def pickle_load(fileName, file_extension='.pkl', **kwargs):
'''
Arguments:
fileName - full path or just file name
'''
# if 4<len(fileName) and fileName[-4:]!=file_extension:
# fileName=fileName+file_extension
# fileName=os.path.expanduser(fileName)
fileName = get_full_file_name(fileName, file_extension)
f = open(fileName, 'rb') # make sure file are read in binary mod
if comm.is_mpi_used() and not kwargs.get('all_mpi', False):
data = _pickle_load_mpi(f)
else:
data = pickle.load(f)
f.close()
return data
def pickle_load(fileName, file_extension='.pkl', **kwargs):
'''
Arguments:
fileName - full path or just file name
'''
# if 4<len(fileName) and fileName[-4:]!=file_extension:
# fileName=fileName+file_extension
# fileName=os.path.expanduser(fileName)
fileName=get_full_file_name(fileName, file_extension)
f=open(fileName, 'rb') # make sure file are read in binary mod
if comm.is_mpi_used()and not kwargs.get('all_mpi', False):
data=_pickle_load_mpi(f)
else:
data=pickle.load(f)
f.close()
return data
def Connect_speed(*args, **kwargs):
if comm.is_mpi_used():
_Connect_speed_mpi(*args, **kwargs)
else:
_Connect_speed(*args, **kwargs)
def Simulate(*args, **kwargs):
if comm.is_mpi_used():
_Simulate_mpi(*args, **kwargs)
else:
_Simulate(*args, **kwargs)
def Connect_DC(*args, **kwargs):
if comm.is_mpi_used():
_Connect_DC_mpi(*args, **kwargs)
else:
_Connect_DC(*args, **kwargs)
def Create(*args, **kwargs):
if comm.is_mpi_used():
return _Create_mpi(*args, **kwargs)
else:
return nest.Create(*args, **kwargs)
def get_spikes_from_file(file_names):
if comm.is_mpi_used():
return _get_spikes_from_file_mpi(file_names)
else:
return _get_spikes_from_file(file_names)
def Simulate(*args, **kwargs):
if comm.is_mpi_used():
_Simulate_mpi(*args, **kwargs)
else:
_Simulate(*args, **kwargs)
def delete_data(path, **kwargs):
if comm.is_mpi_used():
return _delete_data_mpi(path, **kwargs)
else:
return _delete_data(path, **kwargs)
def get_spikes_from_file(file_names):
if comm.is_mpi_used():
return _get_spikes_from_file_mpi(file_names)
else:
return _get_spikes_from_file(file_names)
def Connect_speed(*args, **kwargs):
if comm.is_mpi_used():
_Connect_speed_mpi(*args, **kwargs)
else:
_Connect_speed(*args, **kwargs)
def delete_data(path, **kwargs):
if comm.is_mpi_used():
return _delete_data_mpi(path, **kwargs)
else:
return _delete_data(path, **kwargs)
def Create(*args, **kwargs):
if comm.is_mpi_used():
return _Create_mpi(*args, **kwargs)
else:
return nest.Create(*args, **kwargs)
def garbage_collect(self):
if comm.is_mpi_used():
self._garbage_collect_mpi()
else:
self._garbage_collect()
def Connect_DC(*args, **kwargs):
if comm.is_mpi_used():
_Connect_DC_mpi(*args, **kwargs)
else:
_Connect_DC(*args, **kwargs)
def garbage_collect(self):
if comm.is_mpi_used():
self._garbage_collect_mpi()
else:
self._garbage_collect()