def gaussian_model_par(self, types=['C_m'], std_rel=0.1, sead=None):
'''
GaussianModelPar(self, types=['C_m'], std_rel=0.1, sead=None)
Make model parameters gaussian distributed
'''
#! Used identical sead.
if sead:
random.seed(sead)
for par in types:
for node in self.ids:
# OBS Does not work when GetStatus is taken on all nodes. Simulation
# hang. Need to reproduce this on the side and post on my_nest forum.
# sta=my_nest.GetStatus([nodes[0]])[0]
# If node type is proxynode then do nothing. The node is then a
# a shadow node for mpi process as I understand it.
nodetype = my_nest.GetStatus([node])[0]['model']
if nodetype != 'proxynode':
val = my_nest.GetStatus([node], par)[0]
rand = numpy.abs(random.gauss(val, std_rel * val))
if par in ['V_t', 'V_r']: rand = -rand
my_nest.SetStatus([node], {par: rand})
def voltage_response(self, currents, times, start, sim_time, id):
scg = my_nest.Create('step_current_generator', n=1)
my_nest.SetStatus(scg, {
'amplitude_times': times,
'amplitude_values': currents
})
rec = my_nest.GetStatus([id])[0]['receptor_types']
my_nest.Connect(scg, [id], params={'receptor_type': rec['CURR']})
my_nest.MySimulate(sim_time)
self.get_signal('v', 'V_m', start=start, stop=sim_time)
self.get_signal('s') #, start=start, stop=sim_time)
self.signals['V_m'].my_set_spike_peak(15,
spkSignal=self.signals['spikes'])
voltage = self.signals['V_m'][id].signal
times = numpy.arange(0,
len(voltage) * self.mm['params']['interval'],
self.mm['params']['interval'])
if len(times) != len(voltage):
raise Exception('The vectors has to be the same length')
return times, voltage
def model_par_randomize(self):
'''
Example:
self.randomization={ 'C_m':{'active':True,
'gaussian':{'sigma':0.2*C_m, 'my':C_m}}}
'''
pyrngs = self.set_random_states_nest()
for p, val in self.rand.iteritems():
if not val['active']:
continue
local_nodes = []
# st=my_nest.GetStatus(self.ids, ['local', 'gloabal_id', 'vp'])
for _id in self.ids:
ni = my_nest.GetStatus([_id])[0]
if ni['local']:
local_nodes.append((ni['global_id'], ni['vp']))
# local_nodes=[(ni['global_id'], ni['vp'])
# for ni in st if ni['local']]
for gid, vp in local_nodes:
val_rand = numpy.round(get_random_number(pyrngs, vp, val), 2)
# print val_rand
my_nest.SetStatus([gid], {p: val_rand})
def __init__(self, name, **kwargs):
'''
Constructor
Arguments:
ids provide ids if nodes already created
model my_nest model type, can be a list
n number of model to create, can be a list
params common parameters for model to be set
mm_dt multimeter recording precision
sname file basename
spath Path to save file at
sd boolean, True if spikes should me recorded
mm boolean, True if mulitmeter should record
'''
model = kwargs.get('model', 'iaf_neuron')
n = kwargs.get('n', 1)
params = kwargs.get('params', {})
ids = kwargs.get('ids', my_nest.Create(model, n, params))
self._ids = slice(ids[0], ids[-1], 1)
self.local_ids = []
for _id in self.ids:
if my_nest.GetStatus([_id], 'local'):
self.local_ids.append(_id)
self.model = model
self.name = name
self.n = n
self.sets = kwargs.get('sets', [misc.my_slice(0, n, 1)])
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 get_model_par(self, type='C_m'):
'''
Retrieve one or several parameter values from all nodes
'''
model_par = [my_nest.GetStatus([node], type)[0] for node in self.ids]
return model_par
def find_connections(self):
'''
FindConnections(self)
Find connections for each node in layer
'''
# Clear
self.connections = {}
for node in self.ids:
self.connections[str(node)] = [
target for target in my_nest.GetStatus(
my_nest.FindConnections([node]), 'target')
if target not in self.sd + self.mm
]
def get_conn_par(self, type='delay'):
'''
Get all connections parameter values for type
'''
conn_par = {}
if not self.connections: self.Find_connections()
for source, targets in self.connections.iteritems():
conn_par[source] = [
my_nest.GetStatus(
my_nest.FindConnections([int(source)], [target]),
'delay')[0] for target in targets
]
return conn_par
def gaussian_conn_par(self, type='delay', std_rel=0.1, sead=None):
'''
GaussianConnPar(self, type='delay', std_rel=0.1, sead=None)
Make connection parameters gaussian distributed
'''
#! Used identical sead.
if sead:
random.seed(sead)
if not self.connections:
self.find_connections()
for source, targets in self.connections.iteritems():
for target in targets:
conn = my_nest.FindConnections([int(source)], [target])
val = my_nest.GetStatus(conn, type)[0]
my_nest.SetStatus(
conn,
params={type: numpy.abs(random.gauss(val, std_rel * val))})
def mean_weights(self):
'''
Return a dictionary with mean_weights for each synapse type with mean weight
and receptor type
'''
print 'Calculating mean weights', self.models
syn_dict = {} # container weights per synapse type
rev_rt = {} # receptor type number dictionary
rt_nb = [] # receptor type numbers
for source in self.ids: # retrieve all weights per synapse type
for conn in my_nest.GetStatus(my_nest.FindConnections([source])):
st = conn['synapse_type']
if syn_dict.has_key(st):
syn_dict[st]['weights'].append(conn['weight'])
else:
syn_dict[st] = {}
syn_dict[st]['weights'] = [conn['weight']]
syn_dict[st]['receptor_type'] = {
st: my_nest.GetDefaults(st)['receptor_type']
}
mw = {} # container mean weights per synapse type
for key, val in syn_dict.iteritems():
if len(val['weights']) > 0:
syn_dict[key]['mean_weight'] = sum(val['weights']) / len(
val['weights']) # calculate mean weight
syn_dict[key]['weights'] = numpy.array(
syn_dict[key]['weights'])
syn_dict[key]['nb_conn'] = len(val['weights'])
else:
syn_dict[key]['mean_weight'] = 0
syn_dict[key]['nb_conn'] = 0
return syn_dict
def save_group(self):
'''
Not complete
'''
group = {}
group["connections"] = self.connections
group["models"] = self.models
group["ids"] = self.ids
group["recordables"] = self.recordables
group["receptor_types"] = self.receptor_types
group["sname"] = self.sname
group["GID"] = str(my_nest.GetStatus(self.sd)[0]['global_id'])
group["mm_dt"] = self.mm_dt
output = open(
self.spath + '/' + self.sname + '-' + str(my_nest.Rank()) + '.' +
'pickle', 'w')
# Pickle dictionary
pickle.dump(group, output)
output.close()
def set_spike_times(self,
rates=[],
times=[],
t_stop=None,
ids=None,
seed=None,
idx=None):
df = my_nest.GetDefaults(self.model)
if ids is None and (not idx is None):
tmp_ids = numpy.array(self.ids)
ids = list(tmp_ids[idx])
if ids is None:
ids = self.ids
#print df.keys()
#print df['model']
# Spike generator
if 'spike_generator' == df['model']:
for id in ids:
seed = random_integers(0, 10**5)
spikeTimes = misc.inh_poisson_spikes(rates,
times,
t_stop=t_stop,
n_rep=1,
seed=seed)
if any(spikeTimes):
rs = my_nest.GetKernelStatus('resolution')
n_dec = int(-numpy.log10(rs))
spikeTimes = numpy.round(spikeTimes, n_dec)
my_nest.SetStatus([id], params={'spike_times': spikeTimes})
# MIP
elif 'mip_generator' == df['model']:
c = df['p_copy']
seed = random_integers(0, 10**6)
new_ids = []
t_starts = times
t_stops = times[1:] + [t_stop]
for id in ids:
i = 0
for r, start, stop in rates, t_starts, t_stops:
r_mother = r / c
params = {
'rate': r_mother,
'start': start,
'stop': stop,
'p_copy': c,
'mother_seed': seed
}
if i == 0:
nest.SetStatus(id, params)
else:
new_id = my_nest.Create('mip_generator', 1, params)
new_ids.append(new_id)
self.ids.append(new_ids)
# Poisson generator
elif 'poisson_generator' == df['model']:
t_starts = times
t_stops = list(times[1:]) + list([t_stop])
for i in range(len(ids)):
id = ids[i]
model = my_nest.GetStatus([id], 'model')[0]
if model == 'parrot_neuron':
j = 1
else:
ids[i] = my_nest.Create('parrot_neuron')[0]
my_nest.Connect([id], [ids[i]])
#self.ids_mul_visited[id]=True
j = 0
for r, start, stop in zip(rates, t_starts, t_stops):
params = {'rate': r, 'start': start, 'stop': stop}
if j == 0:
#print my_nest.GetStatus([id])
my_nest.SetStatus([id], params)
else:
if params['rate'] != 0:
#print params
new_id = my_nest.Create('poisson_generator', 1,
params)
#self.ids_mul[ids[i]].append(new_id[0])
my_nest.Connect(new_id, [ids[i]])
j += 1
if not idx is None:
tmp_ids = numpy.array(self.ids)
tmp_ids[idx] = list(ids)
self.ids = list(tmp_ids)
else:
self.ids = list(ids)
self.local_ids = list(self.ids) # Nedd to put on locals also
def __init__(self,
model='iaf_neuron',
n=1,
params={},
mm_dt=1.0,
sname='',
spath='',
sname_nb=0,
sd=False,
sd_params={},
mm=False,
record_from=[],
ids=[]):
'''
Constructor
Arguments:
ids provide ids if nodes already created
model my_nest model type, can be a list
n number of model to create, can be a list
params common parameters for model to be set
mm_dt multimeter recording precision
sname file basename
spath Path to save file at
sd boolean, True if spikes should me recorded
mm boolean, True if mulitmeter should record
'''
self.connections = {
} # Set after network has been built with FindConnections
self.ids = []
self.local_ids = []
self.mm = [] # Id of multimeter
self.mm_dt = 0 # Recording interval multimeter
self.model = model
self.params = []
self.record_from = []
self.receptor_types = {}
self.recordables = {}
self.sd = [] # Id of spike detector
self.sd_params = sd_params
self.sname_nb = sname_nb # number for sname string
self.sname = '' # Specific file basename
self.spath = '' # Path to save file at
self.signals = {
} # dictionary with signals for current, conductance, voltage or spikes
if not self.sname:
self.sname = model + '-' + str(sname_nb) + '-'
else:
self.sname = self.snam + '-' + str(sname_nb) + '-'
# If no spath is provided current path plus data_tmp is set to
# spath.
if spath is '':
self.spath = os.getcwd() + '/output_tmp'
else:
self.spath = spath
# Create save dir if it do not exist
try:
msg = os.system('mkdir ' + self.spath + ' 2>/dev/null')
except:
pass
if ids:
self.ids = ids
else:
self.ids = my_nest.Create(model, n, params) # Create models
# Get local ids on this processor. Necessary to have for mpi run.
for id in self.ids:
nodetype = my_nest.GetStatus([id])[0]['model']
if nodetype != 'proxynode':
self.local_ids.append(id)
self.params = my_nest.GetStatus(self.ids)
# Pick out recordables and receptor types using first model.
try:
self.recordables = my_nest.GetDefaults(model)['recordables']
except:
pass
try:
self.receptor_types = my_nest.GetDefaults(model)['receptor_types']
except:
pass
if self.recordables:
if any(record_from):
self.record_from = record_from
else:
self.record_from = self.recordables
# Add spike detector
if sd:
self.sd = my_nest.Create("spike_detector")
self.sd_params.update({"withgid": True})
my_nest.SetStatus(self.sd, self.sd_params)
my_nest.ConvergentConnect(self.ids, self.sd)
# Record with multimeter from first neuron
if mm:
self.mm = my_nest.Create("multimeter")
self.mm_dt = mm_dt # Recording interval
my_nest.SetStatus(self.mm, {
'interval': self.mm_dt,
'record_from': self.record_from
})
my_nest.DivergentConnect(self.mm, self.ids)
def IV_I_clamp(self, I_vec, id=None, tStim=2000):
'''
Assure no simulations has been run before this (reset kernel).
Function that creates I-V by injecting hyperpolarizing currents
and then measuring steady-state membrane (current clamp). Each
trace is preceded and followed by 1/5 of the simulation time
of no stimulation
Inputs:
I_vec - step currents to inject
id - id of neuron to use for calculating I-F relation
tStim - lenght of each step current stimulation in ms
Returns:
I_vec - current for each voltage
vSteadyState - steady state voltage
Examples:
>> n = my_nest.Create('izhik_cond_exp')
>> sc = [ float( x ) for x in range( -300, 100, 50 ) ]
>> tr_t, tr_v, v_ss = IV_I_clamp( id = n, tSim = 500,
I_vec = sc ):
'''
vSteadyState = []
if not id: id = self.ids[0]
if isinstance(id, int): id = [id]
tAcum = 1 # accumulated simulation time, step_current_generator
# recuires it to start at t>0
scg = my_nest.Create('step_current_generator')
rec = my_nest.GetStatus(id)[0]['receptor_types']
my_nest.Connect(scg, id, params={'receptor_type': rec['CURR']})
ampTimes = []
ampValues = []
for I_e in I_vec:
ampTimes.extend([float(tAcum)])
ampValues.extend([float(I_e)])
tAcum += tStim
my_nest.SetStatus(scg,
params={
'amplitude_times': ampTimes,
'amplitude_values': ampValues
})
my_nest.Simulate(tAcum)
self.get_signal('v', 'V_m', stop=tAcum) # retrieve signal
self.get_signal('s')
if 0 < self.signals['spikes'].mean_rate():
print 'hej'
tAcum = 1
for I_e in I_vec:
if 0 >= self.signals['spikes'].mean_rate(tAcum + 10,
tAcum + tStim):
signal = self.signals['V_m'].my_time_slice(
tAcum + 10, tAcum + tStim)
vSteadyState.append(signal[1].signal[-1])
tAcum += tStim
I_vec = I_vec[0:len(vSteadyState)]
return I_vec, vSteadyState
def IF(self, I_vec, id=None, tStim=None):
'''
Function that creates I-F curve
Inputs:
id - id of neuron to use for calculating
I-F relation
tStim - lenght of each step current injection
in miliseconds
I_vec - step currents to inject
Returns:
fIsi - first interspike interval
mIsi - mean interspike interval
Examples:
>> n = nest.Create('izhik_cond_exp')
>> sc = [ float( x ) for x in range( 10, 270, 50 ) ]
>> f_isi, m_isi, l_isi = IF_curve( id = n, sim_time = 500, I_vec = sc ):
'''
if not id: id = self.ids[0]
if isinstance(id, int): id = [id]
fIsi, mIsi, lIsi = [], [], [] # first, mean and last isi
if not tStim: tStim = 500.0
tAcum = 0
I_e0 = my_nest.GetStatus(id)[0]['I_e'] # Retrieve neuron base current
isi_list = []
for I_e in I_vec:
my_nest.SetStatus(id, params={'I_e': float(I_e + I_e0)})
my_nest.SetStatus(id, params={'V_m': float(-61)})
#my_nest.SetStatus( id, params = { 'w': float(0) } )
my_nest.SetStatus(id, params={'u': float(0)})
simulate = True
tStart = tAcum
while simulate:
my_nest.Simulate(tStim)
tAcum += tStim
self.get_signal('s', start=tStart, stop=tAcum)
signal = self.signals['spikes'].time_slice(tStart, tAcum)
if signal.mean_rate() > 0.1 or tAcum > 20000:
simulate = False
isi = signal.isi()[0]
if not any(isi): isi = [1000000.]
fIsi.append(isi[0]) # retrieve first isi
mIsi.append(numpy.mean(isi)) # retrieve mean isi
if len(isi) > 100: lIsi.append(isi[-1])
else: lIsi.append(isi[-1]) # retrieve last isi
isi_list.append(numpy.array(isi))
fIsi = numpy.array(fIsi)
mIsi = numpy.array(mIsi)
lIsi = numpy.array(lIsi)
I_vec = numpy.array(I_vec)
return I_vec, fIsi, mIsi, lIsi
def _create_signal_object(self,
dataType,
recordable='spikes',
start=None,
stop=None):
'''
-_create_signal_object(self, self, dataType, recordable='times', stop=None )
Creates NeuroTool signal object for the recordable simulation data.
Arguments:
dataType type of data. 's' or 'spikes' for spike data,
'g' for conductance data, 'c' for current data and
'v' for voltage data
recordable Need to be supplied for conductance, current and
voltage data. It is the name of my_nest recorded data with
multimeter, e.g. V_m, I_GABAA_1, g_NMDA.
stop end of signal in ms
About files in nest
[model|label]-gid-vp.[dat|gdf]
The first part is the name of the model (e.g. voltmeter or spike_detector) or,
if set, the label of the recording device. The second part is the global id
(GID) of the recording device. The third part is the id of the virtual process
the recorder is assigned to, counted from 0. The extension is gdf for spike
files and dat for analog recordings. The label and file_extension of a
recording device can be set like any other parameter of a node using SetStatus.
'''
ids = self.local_ids # Eacj processor has its set of ids
# Spike data
if dataType in ['s', 'spikes']:
signal = self.create_raw_spike_signal(start, stop) # create signal
# Mulitmeter data, conductance, current or voltage data
elif dataType in ['g', 'c', 'v']:
mm_dt = self.mm['params']['interval']
e = my_nest.GetStatus(self.mm['id'])[0]['events'] # get events
v = e[recordable] # get analog value
s = e['senders'] # get senders
t = e['times'] # get spike times
#import pylab
#pylab.plot(e['V_m'][e['senders'] ==12])
#pylab.show()
if start != None and stop != None:
s = s[(t > start) * (t < stop)]
v = v[(t > start) * (t < stop)]
t = t[(t > start) * (t < stop)]
#start, stop=t[0], t[-1]
if stop:
s, v = s[t <= stop], v[t <= stop] # Cut out data
start = stop - len(s) / len(ids) * float(mm_dt)
else:
start = t[0] # start time for NeuroTools
# start, stop=t[0]-mm_dt/2, t[-1]+mm_dt/2
signal = zip(s, v) # create signal
#abs(self.t_stop-self.t_start - self.dt * len(self.signal)) > 0.1*self.dt
if dataType in ['s', 'spikes']:
signal = MySpikeList(signal, ids, start, stop)
if dataType in ['g']:
signal = MyConductanceList(signal, ids, mm_dt, start, stop)
if dataType in ['c']:
signal = MyCurrentList(signal, ids, mm_dt, start, stop)
if dataType in ['v']:
signal = MyVmList(signal, ids, mm_dt, start, stop)
return signal
def _create_signal_object(self,
dataType,
recordable='spikes',
start=None,
stop=None):
'''
-_create_signal_object(self, self, dataType, recordable='times', stop=None )
Creates NeuroTool signal object for the recordable simulation data.
Arguments:
dataType type of data. 's' or 'spikes' for spike data,
'g' for conductance data, 'c' for current data and
'v' for voltage data
recordable Need to be supplied for conductance, current and
voltage data. It is the name of my_nest recorded data with
multimeter, e.g. V_m, I_GABAA_1, g_NMDA.
stop end of signal in ms
'''
# Short cuts
ids = self.local_ids # Eacj processor has its set of ids
mm_dt = self.mm_dt
spath = self.spath
sname = self.sname
# File to save to
extension = '-' + recordable + '-' + str(my_nest.Rank()) + '.dat'
fileName = spath + '/' + sname + extension
# Spike data
if dataType in ['s', 'spikes']:
e = my_nest.GetStatus(self.sd)[0]['events'] # get events
s = e['senders'] # get senders
t = e['times'] # get spike times
if stop: s, t = s[t < stop], t[t < stop] # Cut out data
signal = zip(s, t) # create signal
# Mulitmeter data, conductance, current or voltage data
elif dataType in ['g', 'c', 'v']:
e = my_nest.GetStatus(self.mm)[0]['events'] # get events
v = e[recordable] # get analog value
s = e['senders'] # get senders
t = e['times'] # get spike times
if stop:
s, v = s[t < stop], v[t < stop] # Cut out data
start = stop - len(s) / len(ids) * float(mm_dt)
else:
start = t[0] # start time for NeuroTools
signal = zip(s, v) # create signal
if dataType in ['s', 'spikes']:
list = MySpikeList(signal, ids, start, stop)
if dataType in ['g']:
list = MyConductanceList(signal, ids, mm_dt, start, stop)
if dataType in ['c']:
list = MyCurrentList(signal, ids, mm_dt, start, stop)
if dataType in ['v']: list = MyVmList(signal, ids, mm_dt, start, stop)
return list