instantiate and execute network simulation

def simulate():
    '''instantiate and execute network simulation'''
    #separate model execution from parameters for safe import from other files
    nest.ResetKernel()

    '''
    Configuration of the simulation kernel by the previously defined time
    resolution used in the simulation. Setting "print_time" to True prints
    the already processed simulation time as well as its percentage of the
    total simulation time.
    '''

    nest.SetKernelStatus({"resolution": dt, "print_time": True,
                          "overwrite_files": True})
    
    print("Building network")
    
    
    '''
    Configuration of the model `iaf_psc_alpha` and `poisson_generator`
    using SetDefaults(). This function expects the model to be the
    inserted as a string and the parameter to be specified in a
    dictionary. All instances of theses models created after this point
    will have the properties specified in the dictionary by default.
    '''
    
    nest.SetDefaults("iaf_psc_alpha", neuron_params)
    nest.SetDefaults("poisson_generator",{"rate": p_rate})
    
    '''
    Creation of the nodes using `Create`. We store the returned handles in
    variables for later reference. Here the excitatory and inhibitory, as
    well as the poisson generator and two spike detectors. The spike
    detectors will later be used to record excitatory and inhibitory
    spikes.
    '''
    
    nodes_ex = nest.Create("iaf_psc_alpha",NE)
    nodes_in = nest.Create("iaf_psc_alpha",NI)
    noise    = nest.Create("poisson_generator")
    espikes  = nest.Create("spike_detector")
    ispikes  = nest.Create("spike_detector")
    
    print("first exc node: {}".format(nodes_ex[0]))
    print("first inh node: {}".format(nodes_in[0]))
    
    '''
    distribute membrane potentials
    '''
    nest.SetStatus(nodes_ex, "V_m",
                   random.rand(len(nodes_ex))*neuron_params["V_th"])
    nest.SetStatus(nodes_in, "V_m",
                   random.rand(len(nodes_in))*neuron_params["V_th"])
    
    '''
    Configuration of the spike detectors recording excitatory and
    inhibitory spikes using `SetStatus`, which expects a list of node
    handles and a list of parameter dictionaries. Setting the variable
    "to_file" to True ensures that the spikes will be recorded in a .gdf
    file starting with the string assigned to label. Setting "withtime"
    and "withgid" to True ensures that each spike is saved to file by
    stating the gid of the spiking neuron and the spike time in one line.
    '''
    
    nest.SetStatus(espikes,[{
                       "label": os.path.join(spike_output_path, label + "-EX"),
                       "withtime": True,
                       "withgid": True,
                       "to_file": True,
                       }])
    
    nest.SetStatus(ispikes,[{
                       "label": os.path.join(spike_output_path, label + "-IN"),
                       "withtime": True,
                       "withgid": True,
                       "to_file": True,}])
    
    print("Connecting devices")
    
    '''
    Definition of a synapse using `CopyModel`, which expects the model
    name of a pre-defined synapse, the name of the customary synapse and
    an optional parameter dictionary. The parameters defined in the
    dictionary will be the default parameter for the customary
    synapse. Here we define one synapse for the excitatory and one for the
    inhibitory connections giving the previously defined weights and equal
    delays.
    '''
    
    nest.CopyModel("static_synapse","excitatory",{"weight":J_ex, "delay":delay})
    nest.CopyModel("static_synapse","inhibitory",{"weight":J_in, "delay":delay})
    
    '''
    Connecting the previously defined poisson generator to the excitatory
    and inhibitory neurons using the excitatory synapse. Since the poisson
    generator is connected to all neurons in the population the default
    rule ('all_to_all') of Connect() is used. The synaptic properties are
    inserted via syn_spec which expects a dictionary when defining
    multiple variables or a string when simply using a pre-defined
    synapse.
    '''
    
    if Poisson:
      nest.Connect(noise,nodes_ex, 'all_to_all', "excitatory")
      nest.Connect(noise,nodes_in,'all_to_all', "excitatory")
    
    '''
    Connecting the first N_neurons nodes of the excitatory and inhibitory
    population to the associated spike detectors using excitatory
    synapses. Here the same shortcut for the specification of the synapse
    as defined above is used.
    '''
    
    nest.Connect(nodes_ex,espikes, 'all_to_all', "excitatory")
    nest.Connect(nodes_in,ispikes, 'all_to_all', "excitatory")
    
    print("Connecting network")
    
    print("Excitatory connections")
    
    '''
    Connecting the excitatory population to all neurons using the
    pre-defined excitatory synapse. Beforehand, the connection parameter
    are defined in a dictionary. Here we use the connection rule
    'fixed_indegree', which requires the definition of the indegree. Since
    the synapse specification is reduced to assigning the pre-defined
    excitatory synapse it suffices to insert a string.
    '''
    
    conn_params_ex = {'rule': 'fixed_indegree', 'indegree': CE}
    nest.Connect(nodes_ex, nodes_ex+nodes_in, conn_params_ex, "excitatory")
    
    print("Inhibitory connections")
    
    '''
    Connecting the inhibitory population to all neurons using the
    pre-defined inhibitory synapse. The connection parameter as well as
    the synapse paramtere are defined analogously to the connection from
    the excitatory population defined above.
    '''
    
    conn_params_in = {'rule': 'fixed_indegree', 'indegree': CI}
    nest.Connect(nodes_in, nodes_ex+nodes_in, conn_params_in, "inhibitory")
    
    
    '''
    Storage of the time point after the buildup of the network in a
    variable.
    '''
    
    endbuild=time.time()
    
    '''
    Simulation of the network.
    '''
    
    print("Simulating")
    
    nest.Simulate(simtime)
    
    '''
    Storage of the time point after the simulation of the network in a
    variable.
    '''
    
    endsimulate= time.time()
    
    '''
    Reading out the total number of spikes received from the spike
    detector connected to the excitatory population and the inhibitory
    population.
    '''
    
    events_ex = nest.GetStatus(espikes,"n_events")[0]
    events_in = nest.GetStatus(ispikes,"n_events")[0]
    
    '''
    Calculation of the average firing rate of the excitatory and the
    inhibitory neurons by dividing the total number of recorded spikes by
    the number of neurons recorded from and the simulation time. The
    multiplication by 1000.0 converts the unit 1/ms to 1/s=Hz.
    '''
    
    rate_ex   = events_ex/simtime*1000.0/N_neurons
    rate_in   = events_in/simtime*1000.0/N_neurons
    
    '''
    Reading out the number of connections established using the excitatory
    and inhibitory synapse model. The numbers are summed up resulting in
    the total number of synapses.
    '''
    
    num_synapses = nest.GetDefaults("excitatory")["num_connections"]+\
    nest.GetDefaults("inhibitory")["num_connections"]
    
    '''
    Establishing the time it took to build and simulate the network by
    taking the difference of the pre-defined time variables.
    '''
    
    build_time = endbuild-startbuild
    sim_time   = endsimulate-endbuild
    
    '''
    Printing the network properties, firing rates and building times.
    '''
    
    print("Brunel network simulation (Python)")
    print("Number of neurons : {0}".format(N_neurons))
    print("Number of synapses: {0}".format(num_synapses))
    print("       Exitatory  : {0}".format(int(CE * N_neurons) + N_neurons))
    print("       Inhibitory : {0}".format(int(CI * N_neurons)))
    print("Excitatory rate   : %.2f Hz" % rate_ex)
    print("Inhibitory rate   : %.2f Hz" % rate_in)
    print("Building time     : %.2f s" % build_time)
    print("Simulation time   : %.2f s" % sim_time)
    
    '''
    Plot a raster of the excitatory neurons and a histogram.
    '''
    
    if False:
        nest.raster_plot.from_device(espikes, hist=True)
        nest.raster_plot.from_device(ispikes, hist=True)
        nest.raster_plot.show()