def runSim():
f.pc.barrier()
timing('start', 'runTime')
if f.rank == 0:
print('\nRunning...')
runstart = time() # See how long the run takes
h.dt = f.cfg['dt'] # set time step
for key,val in f.cfg['hParams'].iteritems(): setattr(h, key, val) # set other h global vars (celsius, clamp_resist)
f.pc.set_maxstep(10)
mindelay = f.pc.allreduce(f.pc.set_maxstep(10), 2) # flag 2 returns minimum value
if f.rank==0 and f.cfg['verbose']: print 'Minimum delay (time-step for queue exchange) is ',mindelay
# reset all netstims so runs are always equivalent
for cell in f.net.cells:
for stim in cell.stims:
if 'hRandom' in stim:
stim['hRandom'].Random123(cell.gid, f.sim.id32('%d'%(stim['seed'])))
stim['hRandom'].negexp(1)
init()
f.pc.psolve(f.cfg['duration'])
if f.rank==0:
runtime = time()-runstart # See how long it took
print(' Done; run time = %0.2f s; real-time ratio: %0.2f.' % (runtime, f.cfg['duration']/1000/runtime))
f.pc.barrier() # Wait for all hosts to get to this point
timing('stop', 'runTime')
def go(self, sim_time=None):
"""
Launch a simulation of a given time
Parameters
----------
sim_time: an integer
the time in millisecond of the simulation
it replaces the self.sim_time if defined
Comments
--------
It seems that when multiple go method are done it does not
change the output vector.
"""
h.t = 0
#Start recording
self.set_recording()
h.dt = self.dt
self.cell.initialise()
init()
#while h.t < self.sim_time: #I was using this procedure before do not know which one is better
# h.fadvance()
if sim_time:
run(sim_time)
else:
run(self.sim_time)
def _sim_one(self, ps, rng):
"""
Run the simulation for one setting of parameters.
"""
# set parameters
h.IN.soma[0](0.5).g_pas = ps[0] # g_leak
h.IN.soma[0](0.5).gnabar_hh2 = ps[1] # gbar_Na
h.IN.soma[0](0.5).gkbar_hh2 = ps[2] # gbar_K
h.IN.soma[0](0.5).gkbar_im = ps[3] # gbar_M
h.IN.soma[0](0.5).e_pas = -ps[4] # E_leak
h.IN.soma[0](0.5).ena = ps[5] # E_Na
h.IN.soma[0](0.5).ek = -ps[6] # E_K
h.IN.soma[0](0.5).vtraub_hh2 = -ps[7] # V_T
h.IN.soma[0](0.5).kbetan1_hh2 = ps[8] # k_betan1
h.IN.soma[0](0.5).kbetan2_hh2 = ps[9] # k_betan2
h.taumax_im = ps[10] # tau_max
sigma = ps[11] # sigma
# set up current injection of noise
Iinj = rng.normal(0.5, sigma, np.array(h.t_vec).size)
Iinj_vec = h.Vector(Iinj)
Iinj_vec.play(h.El._ref_amp, h.t_vec)
# initialize and run
neuron.init()
h.finitialize(h.v_init)
neuron.run(h.tstop)
self.n_sims += 1
return np.array(h.v_vec)
def run_simulation(record_site, stim, simulation_time=5000, noise_amplitude=0):
rec_t, rec_v, rec_ca = record(record_site)
cvode = nrn.CVode()
if noise_amplitude == 0:
cvode.active(1)
nrn.finitialize(-60)
neuron.init()
neuron.run(simulation_time)
else:
cvode.active(0)
nrn.dt = 0.25
nrn.finitialize(-60)
neuron.init()
n_steps = int(np.ceil(simulation_time / nrn.dt)) + 1
noise = noise_amplitude * np.random.normal(size=n_steps) / np.sqrt(
nrn.dt)
# Add noise
i = 0
while nrn.t < simulation_time:
stim.amp = noise[i]
nrn.fadvance()
i += 1
return np.array(rec_t), np.array(rec_v), np.array(rec_ca)
def runSimWithIntervalFunc(interval, func):
f.pc.barrier()
timing('start', 'runTime')
if f.rank == 0:
print('\nRunning...')
runstart = time() # See how long the run takes
h.dt = f.cfg['dt']
f.pc.set_maxstep(10)
mindelay = f.pc.allreduce(f.pc.set_maxstep(10), 2) # flag 2 returns minimum value
if f.rank==0 and f.cfg['verbose']: print 'Minimum delay (time-step for queue exchange) is ',mindelay
# reset all netstims so runs are always equivalent
for cell in f.net.cells:
for stim in cell.stims:
stim['hRandom'].Random123(cell.gid, f.sim.id32('%d'%(f.cfg['seeds']['stim'])))
stim['hRandom'].negexp(1)
init()
#progUpdate = 1000 # update every second
while round(h.t) < f.cfg['duration']:
f.pc.psolve(min(f.cfg['duration'], h.t+interval))
#if f.cfg['verbose'] and (round(h.t) % progUpdate):
#print(' Sim time: %0.1f s (%d %%)' % (h.t/1e3, int(h.t/f.cfg['duration']*100)))
func(h.t) # function to be called at intervals
if f.rank==0:
runtime = time()-runstart # See how long it took
print(' Done; run time = %0.2f s; real-time ratio: %0.2f.' % (runtime, f.cfg['duration']/1000/runtime))
f.pc.barrier() # Wait for all hosts to get to this point
timing('stop', 'runTime')
def run(duration, anfs):
"""Run a simulation of spiral ganglion neurons.
This function takes care of proper acoustic and electric
initialization.
Parameters
----------
duration : float
Duration of the simulation in seconds.
anfs : list of sg.ANF objects
List of sg.ANF objects for initialization.
"""
for anf in anfs:
if anf.electrodes:
anf.einit()
neuron.init()
for anf in anfs:
if len(anf.vesicles) > 0:
anf.ainit()
neuron.run(duration * 1e3) # s -> ms
def initialize(self):
self.records = self.build_records(self.soma)
assign_hoc_globals(self.settings)
neuron.h.dt = self.dt
neuron.h.finitialize(self.settings['v_init'])
neuron.init()
def run(cmd):
global h, t, soma, ic, vc, syn, icRec, vcRec, vcrs
icRec.clear()
vcRec.clear()
dt = cmd['dt'] * 1e3 ## convert s -> ms
h.dt = dt
data = cmd['data']
mode = cmd['mode']
#print "data:", data.min(), data.max()
#times = h.Vector(np.linspace(h.t, h.t+len(data)*dt, len(data)))
#print "times:", times.min(), times.max()
if mode == 'ic':
#ic.delay = h.t
ic.delay = 0
vc.rs = 1e9
im = h.Vector(data * 1e9)
im.play(ic._ref_amp, dt)
elif mode == 'vc':
#vc.amp1 = data[0]
vc.rs = vcrs
ic.delay = 1e9
#vc.dur1 = h.t
vm = h.Vector(data * 1e3)
vm.play(vc._ref_amp1, dt)
syn.onset = 400. #ms
syn.tau = 1.5 # ms
syn.gmax = 0.04 # umho
syn.e = -7.0 # mV
#syn.i --- nA
else:
sys.stderr.write("Unknown mode '%s'" % sys.argv[1])
raise Exception("Unknown mode '%s'" % sys.argv[1])
#t2 = t + dt * (len(data)+2)
#print "run until:", t2
neuron.init()
h.finitialize(-65.)
tstop = (dt * len(data) + 2)
neuron.run(tstop) #dt * (len(data)+2))
#neuron.run(t2)
#t = t2
#print len(out), out
#out = np.array(out)[:len(data)]
if mode == 'ic':
out = np.array(icRec)[:len(data)] * 1e-3 + np.random.normal(
size=len(data), scale=0.3e-3)
elif mode == 'vc':
out = np.array(vcRec)[:len(data)] * 1e-9 + np.random.normal(
size=len(data), scale=3.e-12)
return out
def run(self, sim_time=None):
self.set_recording()
neuron.h.dt = self.dt
neuron.h.finitialize(self.cell.E)
neuron.init()
if sim_time:
neuron.run(sim_time)
else:
neuron.run(self.sim_time)
self.run_already = True
def go(self, sim_time=None):
self.set_recording()
neuron.h.dt = self.dt
neuron.h.finitialize(self.cell.E)
neuron.init()
if sim_time:
neuron.run(sim_time)
else:
neuron.run(self.sim_time)
self.go_already = True
def evaluate(self, p, sim, plt): """ gainbias drug manipulation """ if p.neuron_type != 'Bioneuron': # Scale the gains and biases self.wm.gain = sim.data[self.wm].gain * p.drug_gainbias[0] self.wm.bias = sim.data[self.wm].bias * p.drug_gainbias[1] # Set the solver of each connection out of wm to a ProxySolver. # This prevents the builder from calculating new optimal decoders # for the new gain/bias values, # which would effectively 'adapt' the network to the drug stimulation self.wm_recurrent.solver = ProxySolver( sim.model.params[self.wm_recurrent].weights) self.wm_to_decision.solver = ProxySolver( sim.model.params[self.wm_to_decision].weights) # Rebuild the network to affect the gain/bias change sim = nengo.Simulator(self.network, seed=p.seed, dt=p.dt) # , progress_bar=False else: # Apply the HCN channel opening/closing by manipulating g_HCN (gbar_ih in bahl.hoc) for nrn in sim.data[self.wm.neurons]: for seg in range(nrn.cell.apical.nseg): loc = 1.0 * seg / nrn.cell.apical.nseg # 0.0 to 1.0 nrn.cell.apical(loc).gbar_ih *= p.drug_biophysical for seg in range(nrn.cell.basal.nseg): loc = 1.0 * seg / nrn.cell.basal.nseg # 0.0 to 1.0 nrn.cell.basal(loc).gbar_ih *= p.drug_biophysical for seg in range(nrn.cell.tuft.nseg): loc = 1.0 * seg / nrn.cell.tuft.nseg # 0.0 to 1.0 nrn.cell.tuft(loc).gbar_ih *= p.drug_biophysical # nrn.cell.soma(0.5).gbar_nat *= p.drug_biophysical neuron.init() print 'Running Trial...' sim.run(p.t_cue+p.t_delay) if p.neuron_type == 'LIF': wm_data = sim.data[self.probe_wm] elif p.neuron_type == 'Bioneuron': lpf = nengo.Lowpass(p.tau_wm) act_bio = lpf.filt(sim.data[self.probe_spikes], dt=p.dt_sample) # wm_data = np.dot(act_bio, self.wm_recurrent.solver.decoders_bio) wm_data = np.dot(act_bio, self.d_readout) # cheaty way # oracle_solver = nengo.solvers.LstsqL2(reg=0.01) # decoders_bio_new = oracle_solver(self.act_bio, self.target)[0] # wm_data = np.dot(act_bio, decoders_bio_new) # wm_data = self.target # plot ideal value to make sure decoding has correct target return dict( time=np.arange(p.dt, p.t_cue+p.t_delay, p.dt_sample), wm=wm_data, output=sim.data[self.probe_output], spikes=sim.data[self.probe_spikes], encoder=sim.data[self.wm].encoders )
def __init__(self, spikes, connections):
self.spikes = spikes
self.connections = connections
self.reads = [spikes]
self.updates = []
self.sets = []
self.incs = []
neuron.init()
def __init__(self, spikes, connections):
self.spikes = spikes
self.connections = connections
self.reads = [spikes]
self.updates = []
self.sets = []
self.incs = []
neuron.init()
def run(self):
if self.verbose: print "Initializing Simulation"
self.set_stim()
neuron.h.dt = self.dt
neuron.h.celsius = 36
neuron.h.finitialize(-60)
neuron.h.load_file('parcom.hoc')
neuron.init()
if self.verbose: print "...Running Simulation"
neuron.run(self.sim_time)
if self.verbose: print "...Simulation Complete\n"
def __init__(self, neurons, J, output, voltage):
self.neurons = neurons
self.J = J
self.output = output
self.voltage = voltage
self.reads = [J]
self.sets = [output, voltage]
self.updates = []
self.incs = []
self.cells = [self.neurons.create() for i in range(len(self.J))]
neuron.init()
def __init__(self, neurons, J, output, voltage):
self.neurons = neurons
self.J = J
self.output = output
self.voltage = voltage
self.reads = [J]
self.sets = [output, voltage]
self.updates = []
self.incs = []
self.cells = [self.neurons.create() for i in range(self.J.shape[0])]
neuron.init()
def run(duration, objects=None):
if objects is not None:
for obj in objects:
obj.pre_init()
neuron.init()
if objects is not None:
for obj in objects:
obj.post_init()
neuron.run(duration * 1000)
def go(self, simTime=None):
self.set_recording()
self.h.celsius = self.T
print 'Temperature = %d' % int(self.h.celsius)
# self.h.dt = self.dt
self.cvode = self.h.CVode()
self.cvode.active()
self.h.finitialize(self.cell.E)
neuron.init()
if simTime:
neuron.run(simTime)
else:
neuron.run(self.simTime)
self.go_already = True
def run(cmd):
global t, soma, ic, vc, icRec, vcRec, vcrs
icRec.clear()
vcRec.clear()
dt = cmd['dt'] * 1e3 ## convert s -> ms
h.dt = dt
data = cmd['data']
mode = cmd['mode']
#print "data:", data.min(), data.max()
#times = h.Vector(np.linspace(h.t, h.t+len(data)*dt, len(data)))
#print "times:", times.min(), times.max()
if mode == 'ic':
#ic.delay = h.t
ic.delay = 0
vc.rs = 1e9
im = h.Vector(data * 1e9)
im.play(ic._ref_amp, dt)
elif mode == 'vc':
#vc.amp1 = data[0]
vc.rs = vcrs
ic.delay = 1e9
#vc.dur1 = h.t
vm = h.Vector(data * 1e3)
vm.play(vc._ref_amp1, dt)
else:
sys.stderr.write("Unknown mode '%s'" % sys.argv[1])
raise Exception("Unknown mode '%s'" % sys.argv[1])
#t2 = t + dt * (len(data)+2)
#print "run until:", t2
neuron.init()
#neuron.finitialize(-65)
neuron.run(dt * (len(data)+2))
#neuron.run(t2)
#t = t2
#print len(out), out
#out = np.array(out)[:len(data)]
if mode == 'ic':
out = np.array(icRec)[:len(data)] * 1e-3 + np.random.normal(size=len(data), scale=0.3e-3)
elif mode == 'vc':
out = np.array(vcRec)[:len(data)] * 1e-9 + np.random.normal(size=len(data), scale=3.e-12)
return out
def go(self, sim_time=None):
"""
Start the simulation once it's been intialized
"""
self.set_recording()
h.dt = self.dt
h.finitialize(self.v_init)
neuron.init()
if sim_time:
neuron.run(sim_time)
else:
neuron.run(self.sim_time)
self.go_already = True
def go(self, sim_time=None):
"""
Start the simulation once it's been intialized
"""
self.set_recording()
h.dt = self.dt
h.finitialize(self.v_init)
neuron.init()
if sim_time:
neuron.run(sim_time)
else:
neuron.run(self.sim_time)
self.go_already = True
def run_simulation(record_site):
"""
Runs the NEURON simulation
:param record_site: Where to record membrane potential from. Example: soma(0.5), where 0.5 means 'center',
0 would mean start, and 1 would mean at the end of the segment in question.
:return: Time and voltage numpy arrays
"""
rec_t = nrn.Vector()
rec_t.record(nrn._ref_t)
rec_v = nrn.Vector()
rec_v.record(record_site._ref_v)
neuron.h.dt = 2**-3
nrn.finitialize(-65)
neuron.init()
neuron.run(200)
return np.array(rec_t), np.array(rec_v)
def run_simulation(record_site):
"""
Runs the NEURON simulation
:param record_site: Where to record membrane potential from. Example: soma(0.5), where 0.5 means 'center',
0 would mean start, and 1 would mean at the end of the segment in question.
:return: Time and voltage numpy arrays
"""
rec_t = nrn.Vector()
rec_t.record(nrn._ref_t)
rec_v = nrn.Vector()
rec_v.record(record_site._ref_v)
neuron.h.dt = 2**-3
nrn.finitialize(-65)
neuron.init()
neuron.run(200)
return np.array(rec_t), np.array(rec_v)
def __init__(self, neurons, J, output, voltage, current=None):
self.neurons = neurons
self.J = J
self.output = output
self.voltage = voltage
args = [] if current is None else [current]
self.args = args
self.reads = [J]
self.sets = [output, voltage] + args
self.updates = []
self.incs = []
self.cells = [self.neurons.create() for i in range(self.J.shape[0])]
neuron.init()
def runSim():
f.pc.barrier()
timing('start', 'runTime')
if f.rank == 0:
print('\nRunning...')
runstart = time() # See how long the run takes
h.dt = f.cfg['dt']
f.pc.set_maxstep(10)
mindelay = f.pc.allreduce(f.pc.set_maxstep(10), 2) # flag 2 returns minimum value
if f.rank==0 and f.cfg['verbose']: print 'Minimum delay (time-step for queue exchange) is ',mindelay
init()
f.pc.psolve(f.cfg['duration'])
if f.rank==0:
runtime = time()-runstart # See how long it took
print(' Done; run time = %0.2f s; real-time ratio: %0.2f.' % (runtime, f.cfg['duration']/1000/runtime))
f.pc.barrier() # Wait for all hosts to get to this point
timing('stop', 'runTime')
def runSimWithIntervalFunc (interval, func):
from .. import sim
sim.pc.barrier()
sim.timing('start', 'runTime')
preRun()
init()
if sim.rank == 0: print('\nRunning...')
while round(h.t) < sim.cfg.duration:
sim.pc.psolve(min(sim.cfg.duration, h.t+interval))
func(h.t) # function to be called at intervals
sim.pc.barrier() # Wait for all hosts to get to this point
sim.timing('stop', 'runTime')
if sim.rank==0:
print((' Done; run time = %0.2f s; real-time ratio: %0.2f.' %
(sim.timingData['runTime'], sim.cfg.duration/1000/sim.timingData['runTime'])))
stim.dur = 3 # You can play with the NEURON-gui by typing # >>> from neuron import gui # For an overview (gui menu bar): Tools -> Model View -> 1 real cell -> root... # Record Time from NEURON (neuron.h._ref_t) rec_t = neuron.h.Vector() rec_t.record(neuron.h._ref_t) # Record Voltage from the center of the soma rec_v = neuron.h.Vector() rec_v.record(soma(0.5)._ref_v) neuron.h.finitialize(-60) neuron.init() neuron.run(5) # Plot the recordings with matplotlib # =================================== import matplotlib.pyplot as plt # get values from NEURON-vector format into Python format times = [] # Use list to add another trace later. voltages = [] times.append(list(rec_t)) # alternativ to `list(rec_t)`: `numpy.array(rec_t)` voltages.append(list(rec_v)) # check types by: # >>> type(rec_t) # >>> type(time[0])
def run(self, t=20, mode='batch'):
from neuron import h
import neuron
import numpy as np
h.celsius = 40.
h.dt = 0.0025
h.finitialize(-75)
neuron.init()
assert mode in {'batch', 'step'}
if mode == 'batch':
for p in self.populations:
assert p.record
print "run started"
neuron.run(t)
print "run ended"
imem = []
iloc = []
for p in self.populations:
for n in p.neurons:
imem_n, iloc_n = n.nodes_imem_loc()
imem.append(imem_n)
iloc.append(iloc_n)
for n in self.neurons:
imem_n, iloc_n = n.nodes_imem_loc()
imem.append(imem_n)
iloc.append(iloc_n)
print "calc potentials started"
for e in self.electrodes:
e.calc_fields(iloc, imem)
e.calc_csd(iloc, imem)
print "calc potentials ended"
if mode == 'step':
from time import time
counter = 0
interval = 1
t0 = time()
ti = h.t
print "starting stepwise run"
for p in self.populations:
assert not p.record
#TODO: stepwise initialisation
# do not record currents over time
imem = []
iloc = []
while h.t < t:
h.fadvance()
counter += 1.
if np.mod(counter, interval) == 0:
iloc = []
imem.append(np.array([[]]))
#rtfactor = (h.t - ti) * 1E-3 / (time() - t0)
#print 't = %.0f, realtime factor: %.3f' % (h.t, rtfactor)
t0 = time()
ti = h.t
for p in self.populations:
imem_n, iloc_n = p.nodes_imem_loc()
imem[-1] = np.append(imem[-1], imem_n)
iloc.append(iloc_n)
for n in self.neurons:
imem_n, iloc_n = n.nodes_imem_loc()
imem[-1] = np.append(imem[-1], imem_n)
iloc.append(iloc_n)
imem, iloc = np.vstack(imem), np.vstack(iloc)
for e in self.electrodes:
e.calc_fields(iloc, imem.T)
rec_v = h.Vector()
#rec_v.record(arms[0][9](0.5)._ref_v)
rec_v.record(muscle(0.5)._ref_v)
rec_ina = h.Vector()
rec_ina.record(muscle(0.5)._ref_ina)
rec_ik = h.Vector()
rec_ik.record(muscle(0.5)._ref_ik)
rec_ica = h.Vector()
rec_ica.record(muscle(0.5)._ref_ica)
h.dt = 0.05
h.finitialize(-70.0)
neuron.init()
sim_time = 500
if sim_time:
neuron.run(sim_time)
else:
neuron.run(sim_time)
x = np.array(rec_t)
y = np.array(rec_v)
plt.figure(1)
plt.subplot(411)
plt.plot(x, y)
na = np.array(rec_ina)
plt.subplot(412)
def run_simulation(soma, simulation_time=5000, noise_amplitude=0, dt=0.01):
"""
Runs the NEURON simulation.
Parameters
----------
record_site : neuron.Segment
Where to record membrane potential from. Example: soma(0.5), where 0.5
means 'center', 0 would mean start, and 1 would mean at the end of the
segment in question.
simulation_time : {float, int}, optional
Simulation time in ms. Default is 5000 ms.
noise_amplitude : float, optional
The amplitude of the noise added to the model, in nA. If 0, no noise is added.
Note that the model uses adaptive timesteps if there is no noise,
and fixed timesteps with dt=0.01 if there is noise. Default is 0.
dt : float, optional
Time step of the simulation. Only used when there is noise,
otherwise adaptive time steps is used. Default is 0.01.
Returns
-------
time : array
Time array for the simulation.
voltage : array
Voltage array for the simulation.
"""
rec_t, rec_v = record(soma(0.5))
cvode = nrn.CVode()
if noise_amplitude == 0:
cvode.active(1)
nrn.finitialize(-60)
neuron.init()
neuron.run(simulation_time)
else:
cvode.active(0)
noise_stim = insert_current_clamp(soma(0.5), duration=simulation_time)
nrn.dt = dt
nrn.finitialize(-60)
neuron.init()
n_steps = int(np.ceil(simulation_time / nrn.dt)) + 1
noise = noise_amplitude * np.random.normal(size=n_steps) / np.sqrt(
nrn.dt)
# Add noise
i = 0
while nrn.t < simulation_time:
noise_stim.amp = noise[i]
nrn.fadvance()
i += 1
return np.array(rec_t), np.array(rec_v)
def build_bias(model, bioensemble, biases, method, bias_gain=5e-5):
rng = np.random.RandomState(bioensemble.seed)
neurons_lif = 100
neurons_bio = bioensemble.n_neurons
tau = 0.01
lif = nengo.Ensemble(
neuron_type=nengo.LIF(),
dimensions=1,
n_neurons=neurons_lif,
seed=bioensemble.seed,
add_to_container=False)
model.seeds[lif] = bioensemble.seed # seeds normally set early in builder
model.build(lif) # add to the model
model.add_op(Copy(Signal(0), model.sig[lif]['in'], inc=True)) # connect input(t)=1
A = get_activities(model.params[lif], # grab tuning curve activities
lif,
model.params[lif].eval_points)
# Desired output function Y -- just repeat "bias" m times
Y = np.tile(biases, (A.shape[0], 1))
bias_decoders = nengo.solvers.LstsqL2()(A, Y)[0]
# initialize synaptic locations
syn_loc = get_synaptic_locations(
rng,
neurons_lif,
neurons_bio,
n_syn=1)
syn_weights = np.zeros((
neurons_bio,
neurons_lif,
syn_loc.shape[2]))
if method == 'weights':
for b in range(syn_weights.shape[0]):
syn_weights[b] = rng.uniform(np.max(biases), np.min(biases), size=syn_weights[b].shape)
if method == 'weights_fixed':
for b in range(syn_weights.shape[0]):
syn_weights[b] = bias_gain * biases[b]**5 * np.ones(syn_weights[b].shape)
# unit test that synapse and weight arrays are compatible shapes
if not syn_loc.shape[:-1] == bias_decoders.T.shape:
raise BuildError("Shape mismatch: syn_loc=%s, bias_decoders=%s"
% (syn_loc.shape[:-1], bias_decoders))
# add synapses to the bioneurons with weights = bias_decoders
neurons = model.params[bioensemble.neurons]
for j, bahl in enumerate(neurons):
assert isinstance(bahl, Bahl)
loc = syn_loc[j]
bahl.synapses[lif] = np.empty(
(loc.shape[0], loc.shape[1]), dtype=object)
for pre in range(loc.shape[0]):
for syn in range(loc.shape[1]):
# section = bahl.cell.tuft(loc[pre, syn])
section = bahl.cell.apical(loc[pre, syn])
# w_ij = np.dot(decoders[pre], gain * encoder)
if method == 'decode':
syn_weights[j, pre, syn] = bias_decoders[pre, j]
w_ij = syn_weights[j, pre, syn]
synapse = ExpSyn(section, w_ij, tau, loc[pre, syn])
bahl.synapses[lif][pre][syn] = synapse
neuron.init()
model.add_op(TransmitSpikes(
lif, bioensemble, None, neurons,
model.sig[lif]['out'], states=[model.time]))
def build_bioneurons(model, neuron_type, neurons):
ens = neurons.ensemble
bias_method = neuron_type.bias_method
# todo: generalize to new NEURON models specified by neuron_type
bioneurons = [Bahl() for _ in range(ens.n_neurons)]
# todo: call user-defined function that introduces variance into specific
# NEURON parameters in each bioneuron, to encourage heterogeneity
neuron.init()
model.sig[neurons]['voltage'] = Signal(
np.zeros(ens.n_neurons),
name='%s.voltage' % ens.label)
op = SimBioneuron(neuron_type=neuron_type,
neurons=bioneurons,
output=model.sig[neurons]['out'],
voltage=model.sig[neurons]['voltage'],
states=[model.time])
# Initialize encoders, gains, and biases according to some heuristics,
# unless the user has specified them already.
# Note: setting encoders/gains/biases in this way doesn't really
# respect the high-level ordering of the nengo build process.
# This can generate hard-to-track problems related to these attributes.
# However, setting them like 'neurons' are set below may not be possible
# because these attributes are used in more places in the build process.
rng = np.random.RandomState(seed=ens.seed)
if hasattr(ens, 'encoders') and ens.encoders is not None:
if not isinstance(ens.encoders, np.ndarray):
ens.encoders = nengo.dists.get_samples(ens.encoders, ens.n_neurons, ens.dimensions, rng)
else:
ens.encoders = gen_encoders(ens.n_neurons, ens.dimensions, ens.radius, rng)
if hasattr(ens, 'gain') and ens.gain is not None:
if not isinstance(ens.gain, np.ndarray):
ens.gain = nengo.dists.get_samples(ens.gain, ens.n_neurons, 1, rng)[:,0]
else:
ens.gain = gen_gains(ens.n_neurons, ens.dimensions, ens.radius, rng)
if hasattr(ens, 'bias') and ens.bias is not None:
if not isinstance(ens.bias, np.ndarray):
ens.bias = nengo.dists.get_samples(ens.bias, ens.n_neurons, 1, rng)[:,0]
else:
ens.bias = gen_bias(ens.n_neurons, ens.dimensions, ens.radius, rng, method=bias_method)
# if (hasattr(ens, 'encoders')
# and ens.encoders is not None
# and not isinstance(ens.encoders, np.ndarray)):
# ens.encoders = nengo.dists.get_samples(ens.encoders, ens.n_neurons, ens.dimensions, rng)
# else:
# ens.encoders = gen_encoders(
# ens.n_neurons,
# ens.dimensions,
# ens.radius,
# rng)
# if (hasattr(ens, 'gain')
# and ens.gain is not None
# and not isinstance(ens.gain, np.ndarray)):
# ens.gain = nengo.dists.get_samples(ens.gain, ens.n_neurons, 1, rng)[:,0]
# else:
# ens.gain = gen_gains(
# ens.n_neurons,
# ens.dimensions,
# ens.radius,
# rng)
# if (hasattr(ens, 'bias')
# and ens.bias is not None
# and not isinstance(ens.bias, np.ndarray)):
# ens.bias = nengo.dists.get_samples(ens.bias, ens.n_neurons, 1, rng)[:,0]
# else:
# ens.bias = gen_biases(
# ens.n_neurons,
# ens.dimensions,
# ens.radius,
# rng,
# method='decode')
model.add_op(op)
assert neurons not in model.params
model.params[neurons] = bioneurons
# Build a bias-emulating connection
build_bias(model, ens, ens.bias, method=bias_method)
def build_connection(model, conn):
"""
Method to build connections into bioensembles.
Calculates the optimal decoders for this conneciton as though
the presynaptic ensemble was connecting to a hypothetical LIF ensemble.
These decoders are used to calculate the synaptic weights
in init_connection().
Adds a transmit_spike operator for this connection to the model
"""
conn_pre = deref_objview(conn.pre)
conn_post = deref_objview(conn.post)
rng = np.random.RandomState(model.seeds[conn])
if isinstance(conn_pre, nengo.Ensemble) and \
isinstance(conn_pre.neuron_type, BahlNeuron):
# todo: generalize to custom online solvers
if not isinstance(conn.solver, NoSolver) and conn.syn_weights is None:
raise BuildError("Connections from bioneurons must provide a NoSolver or syn_weights"
" (got %s from %s to %s)" % (conn.solver, conn_pre, conn_post))
if (isinstance(conn_post, nengo.Ensemble) and \
isinstance(conn_post.neuron_type, BahlNeuron)):
if not isinstance(conn_pre, nengo.Ensemble) or \
'spikes' not in conn_pre.neuron_type.probeable:
raise BuildError("May only connect spiking neurons (pre=%s) to "
"bioneurons (post=%s)" % (conn_pre, conn_post))
"""
Given a parcicular connection, labeled by conn.pre,
Grab the initial decoders
Generate locations for synapses, then either
(a) Create synapses with weight equal to
w_ij=np.dot(d_i,alpha_j*e_j)/n_syn, where
- d_i is the initial decoder,
- e_j is the single bioneuron encoder
- alpha_j is the single bioneuron gain
- n_syn normalizes total input current for multiple-synapse conns
(b) Load synaptic weights from a prespecified matrix
Add synapses with those weights to bioneuron.synapses,
store this initial synaptic weight matrix in conn.weights = conn.syn_weights
Finally call neuron.init().
"""
if conn.syn_locs is None:
conn.syn_locs = get_synaptic_locations(
rng,
conn_pre.n_neurons,
conn_post.n_neurons,
conn.n_syn)
if conn.syn_weights is None:
use_syn_weights = False
conn.syn_weights = np.zeros((
conn_post.n_neurons,
conn_pre.n_neurons,
conn.syn_locs.shape[2]))
else:
use_syn_weights = True
conn.syn_weights = copy.copy(conn.syn_weights)
if conn.learning_node is not None and hasattr(conn.learning_node, 'syn_encoders'):
# initialize synaptic weights for EncoderNode learned connection
use_syn_weights = True
conn.syn_weights = np.array(conn.learning_node.update_weights())
# Grab decoders from the specified solver (usually nengo.solvers.NoSolver(d))
transform = full_transform(conn, slice_pre=False)
eval_points, decoders, solver_info = build_decoders(
model, conn, rng, transform)
# normalize the area under the ExpSyn curve to compensate for effect of tau
times = np.arange(0, 1.0, 0.001)
k_norm = np.linalg.norm(np.exp((-times/conn.tau_list[0])),1)
# todo: synaptic gains and encoders
# print conn, conn_post.gain, conn.post.encoders
neurons = model.params[conn_post.neurons] # set in build_bioneurons
for j, bahl in enumerate(neurons):
assert isinstance(bahl, Bahl)
loc = conn.syn_locs[j]
encoder = conn_post.encoders[j]
gain = conn_post.gain[j]
bahl.synapses[conn] = np.empty(
(loc.shape[0], loc.shape[1]), dtype=object)
for pre in range(loc.shape[0]):
for syn in range(loc.shape[1]):
if conn.sec == 'apical':
section = bahl.cell.apical(loc[pre, syn])
elif conn.sec == 'tuft':
section = bahl.cell.tuft(loc[pre, syn])
elif conn.sec == 'basal':
section = bahl.cell.basal(loc[pre, syn])
if use_syn_weights: # syn_weights already specified
w_ij = conn.syn_weights[j, pre, syn]
else: # syn_weights should be set by dec_pre and bio encoders/gain
w_ij = np.dot(decoders.T[pre], gain * encoder)
w_ij = w_ij / conn.n_syn / k_norm
conn.syn_weights[j, pre, syn] = w_ij
if conn.syn_type == 'ExpSyn':
tau = conn.tau_list[0]
synapse = ExpSyn(section, w_ij, tau, loc[pre, syn])
elif conn.syn_type == 'Exp2Syn':
assert len(conn.tau_list) == 2, 'Exp2Syn requires tau_rise, tau_fall'
tau1 = conn.tau_list[0]
tau2 = conn.tau_list[1]
synapse = Exp2Syn(section, w_ij, tau1, tau2, loc[pre, syn])
bahl.synapses[conn][pre][syn] = synapse
neuron.init()
model.add_op(TransmitSpikes(
conn, conn_post, conn.learning_node, neurons,
model.sig[conn_pre]['out'], states=[model.time]))
model.params[conn] = BuiltConnection(eval_points=eval_points,
solver_info=solver_info,
transform=transform,
weights=conn.syn_weights)
else: # normal connection
return nengo.builder.connection.build_connection(model, conn)
def simple_geo(props=None, retsoma=False):
# simulate stimulations, returns time, dend2_volt +/- soma_volt
P = set_props()
if props is None:
props=P
else:
for k in P.keys():
if k not in props:
props[k] = P[k]
for k in props.keys():
if k not in P.keys():
print("Don't know what the f**k %s is. Options are: " %k)
print(list(P.keys()))
# Creating the morphology
# soma (compartment: neuron.h.Section() )
soma = init_section(100, props['Ra'], 80, 10)
# dendrite0
dend_0 = init_section(200, props['Ra'], bound0)
# dendrite1, with taper
dend_1 = init_section(200, props['Ra'], bound0)
diams = np.linspace(bound0, bound1, dend_1.nseg)
rad = -1
for seg in dend_1:
rad = rad+1
seg.diam = diams[rad]
# dendrite2
dend_2 = init_section(200, props['Ra'], bound1)
dend_0.connect(soma, 1, 0) # connect soma(1) with dend_0(0)
dend_1.connect(dend_0, 1, 0) # connect dend_0(1) with dend_1(0)
dend_2.connect(dend_1, 1, 0) # connect dend_1(1) with dend_2(0)
# Implementing a current clamp electrode
# Locate the electrode at the center of the soma
stim = neuron.h.IClamp(soma(0.5))
# Setting recording paradigm
stim.delay = props['stim_delay']
stim.amp = props['stim_amp']
stim.dur = props['stim_dur']
# Setting passive parameters
for sec in neuron.h.allsec():
# Do with the present `sec`
sec.insert('pas')
sec.Ra = props['Ra']
# Do for each segment within `sec`:
for seg in sec:
# Do with the segment `seg`:
seg.pas.g = 0.01
seg.pas.e = -50
# Record Time from NEURON (neuron.h._ref_t)
rec_t = neuron.h.Vector()
rec_t.record(neuron.h._ref_t)
# Record Voltage from the center of the soma and the end of dend_2
rec_v = neuron.h.Vector()
rec_v.record(soma(0.5)._ref_v)
rec_2 = neuron.h.Vector()
rec_2.record(dend_2(1)._ref_v)
neuron.h.finitialize(-50)
neuron.init()
neuron.run(props['run_time'])
if retsoma==True:
return list(rec_t), list(rec_2), list(rec_v)
else:
return list(rec_t), list(rec_2)
def initAndRun(self, reset_V=-65):
nrn.h.finitialize(reset_V)
nrn.init()
nrn.run(self.tStop)