def initialize_refractory(self, refractory):
if isinstance(refractory, float):
refractory = refractory * ones(self.N)
self.refractory_arr = gpuarray.to_gpu(
array(rint(refractory / self.dt), dtype=int32))
self.next_allowed_spiketime_arr = gpuarray.to_gpu(
-ones(self.N, dtype=int32))
def run(self, **param_values):
delays = param_values.pop('delays', zeros(self.neurons))
# print self.refractory,self.max_refractory
if self.max_refractory is not None:
refractory = param_values.pop('refractory', zeros(self.neurons))
else:
refractory = self.refractory*ones(self.neurons)
tau_metric = param_values.pop('tau_metric', zeros(self.neurons))
self.update_neurongroup(**param_values)
# repeat spike delays and refractory to take slices into account
delays = kron(delays, ones(self.slices))
refractory = kron(refractory, ones(self.slices))
tau_metric = kron(tau_metric, ones(self.slices))
# TODO: add here parameters to criterion_params if a criterion must use some parameters
criterion_params = dict(delays=delays)
if self.criterion.__class__.__name__ == 'Brette':
criterion_params['tau_metric'] = tau_metric
self.update_neurongroup(**param_values)
self.initialize_criterion(**criterion_params)
if self.use_gpu:
# Reinitializes the simulation object
self.mf.reinit_vars(self.criterion_object,
self.inputs_inline, self.inputs_offset,
self.spikes_inline, self.spikes_offset,
self.traces_inline, self.traces_offset,
delays, refractory
)
# LAUNCHES the simulation on the GPU
self.mf.launch(self.sliced_duration, self.stepsize)
# Synchronize the GPU values with a call to gpuarray.get()
self.criterion_object.update_gpu_values()
else:
# set the refractory period
if self.max_refractory is not None:
self.group.refractory = refractory
# Launch the simulation on the CPU
self.group.clock.reinit()
net = Network(self.group, self.criterion_object)
if self.statemonitor_var is not None:
self.statemonitors = []
for state in self.statemonitor_var:
monitor = StateMonitor(self.group, state, record=True)
self.statemonitors.append(monitor)
net.add(monitor)
net.run(self.sliced_duration)
sliced_values = self.criterion_object.get_values()
combined_values = self.combine_sliced_values(sliced_values)
values = self.criterion_object.normalize(combined_values)
return values
def initialize(self, delta, coincidence_count_algorithm):
self.algorithm = coincidence_count_algorithm
self.delta = int(rint(delta / self.dt))
self.spike_count = zeros(self.N, dtype='int')
self.coincidences = zeros(self.N, dtype='int')
self.spiketime_index = self.spikes_offset
self.last_spike_time = array(rint(self.spikes_inline[self.spiketime_index] / self.dt), dtype=int)
self.next_spike_time = array(rint(self.spikes_inline[self.spiketime_index + 1] / self.dt), dtype=int)
# First target spikes (needed for the computation of
# the target train firing rates)
# self.first_target_spike = zeros(self.N)
self.last_spike_allowed = ones(self.N, dtype='bool')
self.next_spike_allowed = ones(self.N, dtype='bool')
def transform_traces(self, traces):
# from standard structure to inline structure
K, T = traces.shape
traces_inline = traces.flatten()
traces_offset = array(kron(arange(K), T * ones(self.subpopsize)),
dtype=int)
return traces_inline, traces_offset
def evaluate(self, **param_values):
"""
Use fitparams['delays'] to take delays into account
Use fitparams['refractory'] to take refractory into account
"""
delays = param_values.pop('delays', zeros(self.neurons))
refractory = param_values.pop('refractory', zeros(self.neurons))
tau_metric = param_values.pop('tau_metric', zeros(self.neurons))
# repeat spike delays and refractory to take slices into account
delays = kron(delays, ones(self.slices))
refractory = kron(refractory, ones(self.slices))
tau_metric = kron(tau_metric, ones(self.slices))
self.update_neurongroup(**param_values)
if self.criterion.__class__.__name__ == 'Brette':
self.initialize_criterion(delays,tau_metric)
else:
self.initialize_criterion(delays)
if self.use_gpu:
pass
#########
# TODO
#########
# # Reinitializes the simulation object
# self.mf.reinit_vars(self.input, self.I_offset, self.spiketimes, self.spiketimes_offset, delays, refractory)
# # LAUNCHES the simulation on the GPU
# self.mf.launch(self.duration, self.stepsize)
# coincidence_count = self.mf.coincidence_count
# spike_count = self.mf.spike_count
else:
# set the refractory period
if self.max_refractory is not None:
self.group.refractory = refractory
# Launch the simulation on the CPU
self.group.clock.reinit()
net = Network(self.group, self.criterion_object)
net.run(self.duration)
sliced_values = self.criterion_object.get_values()
combined_values = self.combine_sliced_values(sliced_values)
values = self.criterion_object.normalize(combined_values)
return values
def initialize_cuda_variables(self):
"""
Initialize GPU variables to pass to the kernel
"""
self.spike_count_gpu = gpuarray.to_gpu(zeros(self.N, dtype=int32))
self.coincidences_gpu = gpuarray.to_gpu(zeros(self.N, dtype=int32))
if self.algorithm == 'exclusive':
self.last_spike_allowed_arr = gpuarray.to_gpu(zeros(self.N, dtype=bool))
self.next_spike_allowed_arr = gpuarray.to_gpu(ones(self.N, dtype=bool))
def initialize(self, delta, coincidence_count_algorithm):
self.algorithm = coincidence_count_algorithm
self.delta = int(rint(delta / self.dt))
self.spike_count = zeros(self.N, dtype='int')
self.coincidences = zeros(self.N, dtype='int')
self.spiketime_index = self.spikes_offset
self.last_spike_time = array(rint(
self.spikes_inline[self.spiketime_index] / self.dt),
dtype=int)
self.next_spike_time = array(rint(
self.spikes_inline[self.spiketime_index + 1] / self.dt),
dtype=int)
# First target spikes (needed for the computation of
# the target train firing rates)
# self.first_target_spike = zeros(self.N)
self.last_spike_allowed = ones(self.N, dtype='bool')
self.next_spike_allowed = ones(self.N, dtype='bool')
def initialize_cuda_variables(self):
"""
Initialize GPU variables to pass to the kernel
"""
self.spike_count_gpu = gpuarray.to_gpu(zeros(self.N, dtype=int32))
self.coincidences_gpu = gpuarray.to_gpu(zeros(self.N, dtype=int32))
if self.algorithm == 'exclusive':
self.last_spike_allowed_arr = gpuarray.to_gpu(
zeros(self.N, dtype=bool))
self.next_spike_allowed_arr = gpuarray.to_gpu(
ones(self.N, dtype=bool))
def update_neurongroup(self, **param_values):
"""
Inject fitting parameters into the NeuronGroup
"""
# Sets the parameter values in the NeuronGroup object
self.group.reinit()
for param, value in param_values.iteritems():
self.group.state(param)[:] = kron(value, ones(self.slices)) # kron param_values if slicing
# Reinitializes the model variables
if self.initial_values is not None:
for param, value in self.initial_values.iteritems():
self.group.state(param)[:] = value
def initialize_refractory(self, refractory):
if isinstance(refractory, float):
refractory = refractory*ones(self.N)
self.refractory_arr = gpuarray.to_gpu(array(rint(refractory / self.dt), dtype=int32))
self.next_allowed_spiketime_arr = gpuarray.to_gpu(-ones(self.N, dtype=int32))
def transform_traces(self, traces):
# from standard structure to inline structure
K, T = traces.shape
traces_inline = traces.flatten()
traces_offset = array(kron(arange(K), T*ones(self.subpopsize)), dtype=int)
return traces_inline, traces_offset
def initialize(self,tau_metric):
self.delay_range =max(self.delays)- min(self.delays)#delay range
self.min_delay = abs(min(self.delays))#minimum of possible delay
self.corr_vector=zeros(self.N)
self.norm_pop = zeros(self.N)
self.norm_target = zeros(self.N)
self.nbr_neurons_group = self.N/self.K
eqs="""
tau:second
dv/dt=(-v)/tau: volt
"""
# network to convolve target spikes with the kernel
self.input_target=SpikeGeneratorGroup(self.K,self.spikes,clock=self.group.clock)
self.kernel_target=NeuronGroup(self.N,model=eqs,clock=self.group.clock)
self.C_target = DelayConnection(self.input_target, self.kernel_target, 'v', structure='sparse', max_delay=self.min_delay)
self.kernel_target.tau=tau_metric
for igroup in xrange(self.K):
self.C_target.W[igroup,igroup*self.nbr_neurons_group:(1+igroup)*self.nbr_neurons_group] = ones(self.nbr_neurons_group)
self.C_target.delay[igroup,igroup*self.nbr_neurons_group:(1+igroup)*self.nbr_neurons_group] = self.min_delay * ones(self.nbr_neurons_group)
# network to convolve population spikes with the kernel
self.kernel_population=NeuronGroup(self.N,model=eqs,clock=self.group.clock)
self.C_population = DelayConnection(self.group, self.kernel_population, 'v', structure='sparse', max_delay=self.delay_range)
for iN in xrange(self.N):
self.C_population.delay[iN,iN] = diagflat(self.min_delay + self.delays[iN])
self.C_population.connect_one_to_one(self.group,self.kernel_population)
self.kernel_population.tau=tau_metric
self.spikecount = SpikeCounter(self.group)
self.contained_objects = [self.kernel_population,self.C_population,self.spikecount,self.input_target,self.C_target,self.kernel_target]