def _connect(self):
'''Connect populations.'''
sigma = self._params['sigma']
cutoff = self._max_dist
self._cs = csa.cset(
csa.cross([0], xrange(self._N - 1)) *
(csa.random * (csa.gaussian(sigma, cutoff) * self._d)), 1.0, 1.0)
def _connect(self):
'''Connect populations.'''
g1 = self._geometryFunction(self._ls)
g2 = self._geometryFunction(self._lt)
d = csa.euclidMetric2d(g1, g2)
sigma = self._params['sigma']
cutoff = self._max_dist
cs = csa.cset(
csa.cross([0], xrange(self._N - 1)) *
(csa.random * (csa.gaussian(sigma, cutoff) * d)), 1.0, 1.0)
nest.CGConnect(
nest.GetLeaves(self._ls)[0],
nest.GetLeaves(self._lt)[0], cs, {
'weight': 0,
'delay': 1
})
def csa_topology_example():
# layers have 20x20 neurons and extent 1 x 1
pop1 = topo.CreateLayer({'elements': 'iaf_neuron',
'rows': 20, 'columns': 20})
pop2 = topo.CreateLayer({'elements': 'iaf_neuron',
'rows': 20, 'columns': 20})
# create CSA-style geometry functions and metric
g1 = geometryFunction(pop1)
g2 = geometryFunction(pop2)
d = csa.euclidMetric2d(g1, g2)
# Gaussian connectivity profile, sigma = 0.2, cutoff at 0.5
cs = csa.cset(csa.random * (csa.gaussian(0.2, 0.5) * d), 10000.0, 1.0)
# create connections
nest.CGConnect(pop1, pop2, cs, {"weight": 0, "delay": 1})
# show targets of center neuron
topo.PlotTargets(topo.FindCenterElement(pop1), pop2)
})
"""
For each layer, we create a CSA-style geometry function and a CSA
metric based on them.
"""
g1 = geometryFunction(pop1)
g2 = geometryFunction(pop2)
d = csa.euclidMetric2d(g1, g2)
"""
The connection set ``cs`` describes a Gaussian connectivity profile
with sigma = 0.2 and cutoff at 0.5, and two values (10000.0 and 1.0)
used as weight and delay, respectively.
"""
cs = csa.cset(csa.random * (csa.gaussian(0.2, 0.5) * d), 10000.0, 1.0)
"""
We can now connect the populations using the `CGConnect` function.
It takes the IDs of pre- and postsynaptic neurons (``pop1`` and
``pop2``), the connection set (``cs``) and a dictionary that maps
the parameters weight and delay to positions in the value set
associated with the connection set.
"""
# This is a work-around until NEST 3.0 is released. It will issue a deprecation
# warning.
pop1_gids = nest.GetLeaves(pop1)[0]
pop2_gids = nest.GetLeaves(pop2)[0]
nest.CGConnect(pop1_gids, pop2_gids, cs, {"weight": 0, "delay": 1})
"""
"""
For each layer, we create a CSA-style geometry function and a CSA
metric based on them.
"""
g1 = geometryFunction(pop1)
g2 = geometryFunction(pop2)
d = csa.euclidMetric2d(g1, g2)
"""
The connection set ``cs`` describes a Gaussian connectivity profile
with sigma = 0.2 and cutoff at 0.5, and two values (10000.0 and 1.0)
used as weight and delay, respectively.
"""
cs = csa.cset(csa.random * (csa.gaussian(0.2, 0.5) * d), 10000.0, 1.0)
"""
We can now connect the populations using the `CGConnect` function.
It takes the IDs of pre- and postsynaptic neurons (``pop1`` and
``pop2``), the connection set (``cs``) and a dictionary that maps
the parameters weight and delay to positions in the value set
associated with the connection set.
"""
# This is a work-around until NEST 3.0 is released. It will issue a deprecation
# warning.
pop1_gids = nest.GetLeaves(pop1)[0]
pop2_gids = nest.GetLeaves(pop2)[0]
nest.CGConnect(pop1_gids, pop2_gids, cs, {"weight": 0, "delay": 1})
print "Process with rank %d running on %s" % (node, socket.gethostname())
rng = NumpyRNG(seed=seed, parallel_safe=True)
print "[%d] Creating populations" % node
n_spikes = int(2*tstop*input_rate/1000.0)
spike_times = numpy.add.accumulate(rng.next(n_spikes, 'exponential',
[1000.0/input_rate], mask_local=False))
input_population = Population(10, SpikeSourceArray, {'spike_times': spike_times }, label="input")
output_population = Population(10, IF_curr_exp, cell_params, label="output")
g=csa.grid2d(3)
d=csa.euclidMetric2d(g,g)
connector = CSAConnector(csa.cset(csa.random(0.5), csa.gaussian(0.1,1.0)*d, 1.0))
projection = Projection(input_population, output_population, connector, rng=rng)
file_stem = "Results/simpleRandomNetwork_np%d_%s" % (num_processes(), simulator_name)
projection.saveConnections('%s.conn' % file_stem)
output_population.record_v()
print "[%d] Running simulation" % node
run(tstop)
print "[%d] Writing Vm to disk" % node
output_population.print_v('%s.v' % file_stem)
print "[%d] Finishing" % node
