def run_simulation(sim,Params):
print "Running Network"
timer = Timer()
timer.reset()
sim.run(Params['run_time'])
simCPUtime = timer.elapsedTime()
print "Simulation Time: %s" % str(simCPUtime)
def run_simulation(sim, params):
print "Running Network ..."
timer = Timer()
timer.reset()
sim.run(params['run_time'])
simCPUtime = timer.elapsedTime()
print "... The simulation took %s ms to run." % str(simCPUtime)
def run(self, params, verbose=True):
tmpdir = tempfile.mkdtemp()
timer = Timer()
timer.start() # start timer on construction
# === Build the network ========================================================
if verbose: print "Setting up simulation"
sim.setup(timestep=params.simulation.dt,
max_delay=params.simulation.syn_delay,
debug=False)
N = params.N
#dc_generator
current_source = sim.DCSource(amplitude=params.snr,
start=params.simulation.simtime / 4,
stop=params.simulation.simtime / 4 * 3)
# internal noise model (NEST specific)
noise = sim.Population(N, 'noise_generator', {
'mean': 0.,
'std': params.noise_std
})
# target population
output = sim.Population(N, sim.IF_cond_exp)
# initialize membrane potential
numpy.random.seed(params.simulation.kernelseed)
V_rest, V_spike = -70., -53.
output.tset('v_init',
V_rest + numpy.random.rand(N, ) * (V_spike - V_rest))
# Connecting the network
conn = sim.OneToOneConnector(weights=params.weight)
sim.Projection(noise, output, conn)
for cell in output:
cell.inject(current_source)
output.record()
# reads out time used for building
buildCPUTime = timer.elapsedTime()
# === Run simulation ===========================================================
if verbose: print "Running simulation"
timer.reset() # start timer on construction
sim.run(params.simulation.simtime)
simCPUTime = timer.elapsedTime()
timer.reset() # start timer on construction
output_filename = os.path.join(tmpdir, 'output.gdf')
#print output_filename
output.printSpikes(output_filename) #
output_DATA = load_spikelist(output_filename,
N,
t_start=0.0,
t_stop=params.simulation.simtime)
writeCPUTime = timer.elapsedTime()
if verbose:
print "\nFiber Network Simulation:"
print "Number of Neurons : ", N
print "Mean Output rate : ", output_DATA.mean_rate(
), "Hz during ", params.simulation.simtime, "ms"
print("Build time : %g s" % buildCPUTime)
print("Simulation time : %g s" % simCPUTime)
print("Writing time : %g s" % writeCPUTime)
os.remove(output_filename)
os.rmdir(tmpdir)
return output_DATA
def run(self,params, verbose =True):
tmpdir = tempfile.mkdtemp()
timer = Timer()
timer.start() # start timer on construction
# === Build the network ========================================================
if verbose: print "Setting up simulation"
sim.setup(timestep=params.simulation.dt,max_delay=params.simulation.syn_delay, debug=False)
N = params.N
#dc_generator
current_source = sim.DCSource( amplitude= params.snr,
start=params.simulation.simtime/4,
stop=params.simulation.simtime/4*3)
# internal noise model (NEST specific)
noise = sim.Population(N,'noise_generator',{'mean':0.,'std':params.noise_std})
# target population
output = sim.Population(N , sim.IF_cond_exp)
# initialize membrane potential
numpy.random.seed(params.simulation.kernelseed)
V_rest, V_spike = -70., -53.
output.tset('v_init',V_rest + numpy.random.rand(N,)* (V_spike -V_rest))
# Connecting the network
conn = sim.OneToOneConnector(weights = params.weight)
sim.Projection(noise, output, conn)
for cell in output:
cell.inject(current_source)
output.record()
# reads out time used for building
buildCPUTime= timer.elapsedTime()
# === Run simulation ===========================================================
if verbose: print "Running simulation"
timer.reset() # start timer on construction
sim.run(params.simulation.simtime)
simCPUTime = timer.elapsedTime()
timer.reset() # start timer on construction
output_filename = os.path.join(tmpdir,'output.gdf')
#print output_filename
output.printSpikes(output_filename)#
output_DATA = load_spikelist(output_filename,N,
t_start=0.0, t_stop=params.simulation.simtime)
writeCPUTime = timer.elapsedTime()
if verbose:
print "\nFiber Network Simulation:"
print "Number of Neurons : ", N
print "Mean Output rate : ", output_DATA.mean_rate(), "Hz during ",params.simulation.simtime, "ms"
print("Build time : %g s" % buildCPUTime)
print("Simulation time : %g s" % simCPUTime)
print("Writing time : %g s" % writeCPUTime)
os.remove(output_filename)
os.rmdir(tmpdir)
return output_DATA
def run(self, params, verbose=True):
"""
params are the parameters to use
"""
tmpdir = tempfile.mkdtemp()
myTimer = Timer()
# === Build the network ========================================================
if verbose: print "Setting up simulation"
myTimer.start() # start timer on construction
sim.setup(timestep=params['dt'], max_delay=params['syn_delay'])
N = params['N']
#dc_generator
phr_ON = sim.Population((N, ), 'dc_generator')
phr_OFF = sim.Population((N, ), 'dc_generator')
for factor, phr in [(-params['snr'], phr_OFF),
(params['snr'], phr_ON)]:
phr.tset('amplitude', params['amplitude'] * factor)
phr.set({
'start': params['simtime'] / 4,
'stop': params['simtime'] / 4 * 3
})
# internal noise model (see benchmark_noise)
noise_ON = sim.Population((N, ), 'noise_generator', {
'mean': 0.,
'std': params['noise_std']
})
noise_OFF = sim.Population((N, ), 'noise_generator', {
'mean': 0.,
'std': params['noise_std']
})
# target ON and OFF populations (what about a tridimensional Population?)
out_ON = sim.Population(
(N, ), sim.IF_curr_alpha
) #'IF_cond_alpha) #iaf_sfa_neuron')# EIF_cond_alpha_isfa_ista, IF_cond_exp_gsfa_grr,sim.IF_cond_alpha)#'iaf_sfa_neuron',params['parameters_gc'])#'iaf_cond_neuron')# IF_cond_alpha) #
out_OFF = sim.Population(
(N, ), sim.IF_curr_alpha
) #'IF_cond_alpha) #IF_curr_alpha)#'iaf_sfa_neuron')#sim.IF_curr_alpha)#,params['parameters_gc'])
# initialize membrane potential TODO: and conductances?
from pyNN.random import RandomDistribution, NumpyRNG
rng = NumpyRNG(seed=params['kernelseed'])
vinit_distr = RandomDistribution(distribution='uniform',
parameters=[-70, -55],
rng=rng)
for out_ in [out_ON, out_OFF]:
out_.randomInit(vinit_distr)
retina_proj_ON = sim.Projection(phr_ON, out_ON,
sim.OneToOneConnector())
retina_proj_ON.setWeights(params['weight'])
# TODO fix setWeight, add setDelays to 10 ms (relative to stimulus onset)
retina_proj_OFF = sim.Projection(phr_OFF, out_OFF,
sim.OneToOneConnector())
retina_proj_OFF.setWeights(params['weight'])
noise_proj_ON = sim.Projection(noise_ON, out_ON,
sim.OneToOneConnector())
noise_proj_ON.setWeights(params['weight'])
noise_proj_OFF = sim.Projection(
noise_OFF, out_OFF, sim.OneToOneConnector(
)) # implication if ON and OFF have the same noise input?
noise_proj_OFF.setWeights(params['weight'])
out_ON.record()
out_OFF.record()
# reads out time used for building
buildCPUTime = myTimer.elapsedTime()
# === Run simulation ===========================================================
if verbose: print "Running simulation"
myTimer.reset() # start timer on construction
sim.run(params['simtime'])
simCPUTime = myTimer.elapsedTime()
myTimer.reset() # start timer on construction
# TODO LUP use something like "for pop in [phr, out]" ?
out_ON_filename = os.path.join(tmpdir, 'out_on.gdf')
out_OFF_filename = os.path.join(tmpdir, 'out_off.gdf')
out_ON.printSpikes(out_ON_filename) #
out_OFF.printSpikes(out_OFF_filename) #
# TODO LUP get out_ON_DATA on a 2D grid independantly of out_ON.cell.astype(int)
out_ON_DATA = load_spikelist(out_ON_filename,
range(N),
t_start=0.0,
t_stop=params['simtime'])
out_OFF_DATA = load_spikelist(out_OFF_filename,
range(N),
t_start=0.0,
t_stop=params['simtime'])
out = {
'out_ON_DATA': out_ON_DATA,
'out_OFF_DATA': out_OFF_DATA
} #,'out_ON_pos':out_ON}
# cleans up
os.remove(out_ON_filename)
os.remove(out_OFF_filename)
os.rmdir(tmpdir)
writeCPUTime = myTimer.elapsedTime()
if verbose:
print "\nRetina Network Simulation:"
print(params['description'])
print "Number of Neurons : ", N
print "Output rate (ON) : ", out_ON_DATA.mean_rate(
), "Hz/neuron in ", params['simtime'], "ms"
print "Output rate (OFF) : ", out_OFF_DATA.mean_rate(
), "Hz/neuron in ", params['simtime'], "ms"
print("Build time : %g s" % buildCPUTime)
print("Simulation time : %g s" % simCPUTime)
print("Writing time : %g s" % writeCPUTime)
return out
def run(self, params, verbose=True):
"""
params are the parameters to use
"""
tmpdir = tempfile.mkdtemp()
myTimer = Timer()
# === Build the network ========================================================
if verbose:
print "Setting up simulation"
myTimer.start() # start timer on construction
sim.setup(timestep=params["dt"], max_delay=params["syn_delay"])
N = params["N"]
# dc_generator
phr_ON = sim.Population((N,), "dc_generator")
phr_OFF = sim.Population((N,), "dc_generator")
for factor, phr in [(-params["snr"], phr_OFF), (params["snr"], phr_ON)]:
phr.tset("amplitude", params["amplitude"] * factor)
phr.set({"start": params["simtime"] / 4, "stop": params["simtime"] / 4 * 3})
# internal noise model (see benchmark_noise)
noise_ON = sim.Population((N,), "noise_generator", {"mean": 0.0, "std": params["noise_std"]})
noise_OFF = sim.Population((N,), "noise_generator", {"mean": 0.0, "std": params["noise_std"]})
# target ON and OFF populations (what about a tridimensional Population?)
out_ON = sim.Population(
(N,), sim.IF_curr_alpha
) #'IF_cond_alpha) #iaf_sfa_neuron')# EIF_cond_alpha_isfa_ista, IF_cond_exp_gsfa_grr,sim.IF_cond_alpha)#'iaf_sfa_neuron',params['parameters_gc'])#'iaf_cond_neuron')# IF_cond_alpha) #
out_OFF = sim.Population(
(N,), sim.IF_curr_alpha
) #'IF_cond_alpha) #IF_curr_alpha)#'iaf_sfa_neuron')#sim.IF_curr_alpha)#,params['parameters_gc'])
# initialize membrane potential TODO: and conductances?
from pyNN.random import RandomDistribution, NumpyRNG
rng = NumpyRNG(seed=params["kernelseed"])
vinit_distr = RandomDistribution(distribution="uniform", parameters=[-70, -55], rng=rng)
for out_ in [out_ON, out_OFF]:
out_.randomInit(vinit_distr)
retina_proj_ON = sim.Projection(phr_ON, out_ON, sim.OneToOneConnector())
retina_proj_ON.setWeights(params["weight"])
# TODO fix setWeight, add setDelays to 10 ms (relative to stimulus onset)
retina_proj_OFF = sim.Projection(phr_OFF, out_OFF, sim.OneToOneConnector())
retina_proj_OFF.setWeights(params["weight"])
noise_proj_ON = sim.Projection(noise_ON, out_ON, sim.OneToOneConnector())
noise_proj_ON.setWeights(params["weight"])
noise_proj_OFF = sim.Projection(
noise_OFF, out_OFF, sim.OneToOneConnector()
) # implication if ON and OFF have the same noise input?
noise_proj_OFF.setWeights(params["weight"])
out_ON.record()
out_OFF.record()
# reads out time used for building
buildCPUTime = myTimer.elapsedTime()
# === Run simulation ===========================================================
if verbose:
print "Running simulation"
myTimer.reset() # start timer on construction
sim.run(params["simtime"])
simCPUTime = myTimer.elapsedTime()
myTimer.reset() # start timer on construction
# TODO LUP use something like "for pop in [phr, out]" ?
out_ON_filename = os.path.join(tmpdir, "out_on.gdf")
out_OFF_filename = os.path.join(tmpdir, "out_off.gdf")
out_ON.printSpikes(out_ON_filename) #
out_OFF.printSpikes(out_OFF_filename) #
# TODO LUP get out_ON_DATA on a 2D grid independantly of out_ON.cell.astype(int)
out_ON_DATA = load_spikelist(out_ON_filename, range(N), t_start=0.0, t_stop=params["simtime"])
out_OFF_DATA = load_spikelist(out_OFF_filename, range(N), t_start=0.0, t_stop=params["simtime"])
out = {"out_ON_DATA": out_ON_DATA, "out_OFF_DATA": out_OFF_DATA} # ,'out_ON_pos':out_ON}
# cleans up
os.remove(out_ON_filename)
os.remove(out_OFF_filename)
os.rmdir(tmpdir)
writeCPUTime = myTimer.elapsedTime()
if verbose:
print "\nRetina Network Simulation:"
print (params["description"])
print "Number of Neurons : ", N
print "Output rate (ON) : ", out_ON_DATA.mean_rate(), "Hz/neuron in ", params["simtime"], "ms"
print "Output rate (OFF) : ", out_OFF_DATA.mean_rate(), "Hz/neuron in ", params["simtime"], "ms"
print ("Build time : %g s" % buildCPUTime)
print ("Simulation time : %g s" % simCPUTime)
print ("Writing time : %g s" % writeCPUTime)
return out
shutil.copy('./'+opts.param_file, opts.data_folder+ str(run)+'/'+opts.param_file+'_'+str(comb)+'.py')
if not opts.analysis:
already_computed = 0
for pop in params['Populations'].keys():
if os.path.exists(opts.data_folder + str(run) +'/'+pop+str(comb)+'.pkl'):
already_computed = already_computed + 1
if already_computed > 0:
print "already computed"
else:
Populations = h.build_network(sim,params)
h.record_data(params, Populations)
h.perform_injections(params, Populations)
print "Running Network"
timer = Timer()
timer.reset()
interval = 10
sim.run(params['run_time'], callbacks = SetInput(Populations, interval, params['dt']))
simCPUtime = timer.elapsedTime()
print "Simulation Time: %s" % str(simCPUtime)
h.save_data(Populations, opts.data_folder + str(run), str(comb))
sim.end()
else :
if search:
already_computed = 0
for pop in params['Populations'].keys():
if os.path.exists(opts.data_folder + str(run) +'/'+pop+str(comb)+'.png'):
already_computed = already_computed + 1
if already_computed > len(params['Populations']) - 1:
print "already analysed"
else:
delays=None),
target='excitatory',
rng=rng)
# Recording
#pyB.record_v(10)
#inhB.record_v(10)
py.record()
inh.record()
pyB.record()
inhB.record()
#
print "Running Network"
timer = Timer()
timer.reset()
run(run_time)
simCPUtime = timer.elapsedTime()
print "Simulation Time: %s" % str(simCPUtime)
#os.chdir('Insert Data Directory Here')
#pyB.print_v('pyB_v.dat')
#inhB.print_v('inhB_v.dat')
py.printSpikes('py.dat')
inh.printSpikes('inh.dat')
pyB.printSpikes('pyB.dat')
inhB.printSpikes('inhB.dat')
#py_py.saveConnections('py_py.conn')
def run_simulation(run):
info = {}
# run combinations
for i,comb in enumerate(combinations):
print "param combination",i, "trial",run
print "current set:",comb
# replacement
for ckey,val in comb.iteritems():
keys = ckey.split('.') # get list from dotted string
replace(params,keys,val)
# save parameters in the data_folder
if not os.path.exists(opts.data_folder+str(run)):
os.makedirs(opts.data_folder+str(run))
shutil.copy('./'+opts.param_file, opts.data_folder + str(run)+'/'+opts.param_file+'_'+str(comb)+'.py')
if not opts.analysis: #run simulation
# run simulation if it hasn't already been ran for these parameters
already_computed = 0
for pop in params['Populations'].keys():
if os.path.exists(opts.data_folder + str(run) +'/'+pop+str(comb)+'.pkl'):
already_computed = already_computed + 1
if already_computed > 0:
print "already computed"
else:
Populations = h.build_network(sim,params)
h.record_data(params, Populations)
h.perform_injections(params, Populations)
print "Running Network"
timer = Timer()
timer.reset()
inject_spikes = partial(inject_spikes_pop,Populations = Populations)
sim.run(params['run_time'], [inject_spikes])
simCPUtime = timer.elapsedTime()
print "Simulation Time: %s" % str(simCPUtime)
h.save_data(Populations, opts.data_folder + str(run), str(comb))
sim.end()
else : #do analysis
if search: #then compute the csv needed for the search maps
already_analysed = 0 #analyse only those that haven't already been analysed
for pop in params['Populations'].keys():
if os.path.exists(opts.data_folder + str(run) +'/'+pop+str(comb)+'.png'):
already_analysed = already_analysed + 1
if already_analysed >= len(params['Populations'])-1 :
print "already analysed"
else:
ratio,fqcy,psd,freq, fqcy_ratio = h.analyse(params, opts.data_folder + str(run), str(comb), opts.remove)
#save computed values in csv files
gen = (pop for pop in params['Populations'].keys() if pop != 'ext')
for pop in gen:
if i == 0:
with open(opts.data_folder+ str(run)+'/map-'+pop+'.csv', 'wb') as csvfile:
mywriter = csv.writer(csvfile)
mywriter.writerow( ['#'+str(testParams[1])+ ':' +str(search[testParams[1]]) ] )
mywriter.writerow( ['#'+str(testParams[0])+ ':' +str(search[testParams[0]]) ] )
with open(opts.data_folder+ str(run)+'/psdmap-'+pop+'.csv', 'wb') as csvfile:
mywriter = csv.writer(csvfile)
mywriter.writerow( ['#'+str(testParams[1])+ ':' +str(search[testParams[1]]) ] )
mywriter.writerow( ['#'+str(testParams[0])+ ':' +str(search[testParams[0]]) ] )
if pop in freq:
mywriter.writerow(freq[pop])
info[pop] = []
if pop in ratio and pop in fqcy:
info[pop].append([ratio[pop],fqcy[pop],fqcy_ratio[pop]])
if (i+1)%len(search[testParams[1]]) == 0:
with open(opts.data_folder+str(run)+'/map-'+pop+'.csv', 'a') as csvfile:
mywriter = csv.writer(csvfile)
mywriter.writerow(info[pop])
info[pop] = []
if pop in psd:
with open(opts.data_folder+str(run)+'/psdmap-'+pop+'.csv', 'a') as csvfile:
mywriter = csv.writer(csvfile)
mywriter.writerow(psd[pop])
else:
h.analyse(params, opts.data_folder+str(run), str(comb), opts.remove)