def _connect(self):
'''Connect populations.'''
finite_set = csa.cross(xrange(self._N_s), xrange(self._N_t))
if self._fan == 'in':
self._cs = csa.cset(csa.random(fanIn=self._C) * finite_set)
else:
self._cs = csa.cset(csa.random(fanOut=self._C) * finite_set)
def _connect(self):
'''Connect populations.'''
finite_set = csa.cross(xrange(self._N_s), xrange(self._N_t))
if self._fan == 'in':
cs = csa.cset(csa.random(fanIn=self._C) * finite_set)
else:
cs = csa.cset(csa.random(fanOut=self._C) * finite_set)
nest.CGConnect(self._source_pop, self._target_pop, csa.cset(cs))
def test_CSA_OneToOne_subnet_1d(self):
"""One-to-one connectivity with 1-dim subnets"""
nest.ResetKernel()
n = 4 # number of neurons
pop0 = nest.LayoutNetwork("iaf_neuron", [n])
pop1 = nest.LayoutNetwork("iaf_neuron", [n])
cg = csa.cset(csa.oneToOne)
nest.CGConnect(pop0, pop1, cg)
sources = nest.GetLeaves(pop0)[0]
targets = nest.GetLeaves(pop1)[0]
for i in range(n):
conns = nest.GetStatus(nest.FindConnections([sources[i]]),
'target')
self.assertEqual(len(conns), 1)
self.assertEqual(conns[0], targets[i])
conns = nest.GetStatus(nest.FindConnections([targets[i]]),
'target')
self.assertEqual(len(conns), 0)
def test_CSA_cgnext(self):
"""cgnext"""
nest.ResetKernel()
w = 10000.0
d = 1.0
cs = csa.cset(csa.oneToOne, w, d)
nest.sli_push(cs)
nest.sli_run('dup')
nest.sli_push(numpy.array([0, 1, 2, 3]))
nest.sli_push(numpy.array([0, 1, 2, 3]))
nest.sli_run('cgsetmask')
nest.sli_run('dup')
nest.sli_run('cgstart')
for i in range(4):
nest.sli_run('dup')
nest.sli_run('cgnext')
self.assertEqual(nest.sli_pop(), True)
self.assertEqual(nest.sli_pop(), d)
self.assertEqual(nest.sli_pop(), w)
self.assertEqual(nest.sli_pop(), i)
self.assertEqual(nest.sli_pop(), i)
nest.sli_run('cgnext')
self.assertEqual(nest.sli_pop(), False)
def test_CSA_OneToOne_params(self):
"""One-to-one connectivity using CGConnect with paramters"""
nest.ResetKernel()
n_neurons = 4
weight = 10000.0
delay = 2.0
sources = nest.Create("iaf_psc_alpha", n_neurons)
targets = nest.Create("iaf_psc_alpha", n_neurons)
# Create a connection set with values for weight and delay
cs = csa.cset(csa.oneToOne, weight, delay)
# Connect sources and targets using the connection set cs and
# a parameter map mapping weight to position 0 in the value
# set and delay to position 1
nest.CGConnect(sources, targets, cs, {"weight": 0, "delay": 1})
for i in range(n_neurons):
# We expect all connections from sources to have the
# correct targets, weights and delays
conns = nest.GetStatus(nest.GetConnections(sources[i]))
self.assertEqual(len(conns), 1)
self.assertEqual(conns[0]["target"], targets[i].get('global_id'))
self.assertEqual(conns[0]["weight"], weight)
self.assertEqual(conns[0]["delay"], delay)
# We expect the targets to have no connections at all
conns = nest.GetStatus(nest.GetConnections(targets[i]))
self.assertEqual(len(conns), 0)
def test_CSA_OneToOne_tuples(self):
"""One-to-one connectivity using CGConnect with id tuples"""
nest.ResetKernel()
n_neurons = 4
sources = nest.Create("iaf_psc_alpha", n_neurons)
targets = nest.Create("iaf_psc_alpha", n_neurons)
# Create a plain connection set
cg = csa.cset(csa.oneToOne)
# Connect sources and targets using the connection set
# cs. This will internally call the variant of CGConnect that
# takes lists
nest.CGConnect(sources, targets, cg)
for i in range(n_neurons):
# We expect all connections from sources to have the
# correct targets
conns = nest.GetStatus(nest.GetConnections([sources[i]]))
self.assertEqual(len(conns), 1)
self.assertEqual(conns[0]["target"], targets[i])
# We expect the targets to have no connections at all
conns = nest.GetStatus(nest.GetConnections([targets[i]]))
self.assertEqual(len(conns), 0)
def test_CSA_cgnext(self):
"""cgnext"""
nest.ResetKernel()
w = 10000.0
d = 1.0
cs = csa.cset(csa.oneToOne, w, d)
nest.sli_push(cs)
nest.sli_run('dup')
nest.sli_push(numpy.array([0, 1, 2, 3]))
nest.sli_push(numpy.array([0, 1, 2, 3]))
nest.sli_run('cgsetmask')
nest.sli_run('dup')
nest.sli_run('cgstart')
for i in range(4):
nest.sli_run('dup')
nest.sli_run('cgnext')
self.assertEqual(nest.sli_pop(), True)
self.assertEqual(nest.sli_pop(), d)
self.assertEqual(nest.sli_pop(), w)
self.assertEqual(nest.sli_pop(), i)
self.assertEqual(nest.sli_pop(), i)
nest.sli_run('cgnext')
self.assertEqual(nest.sli_pop(), False)
def test_CSA_OneToOne_params(self):
"""One-to-one connectivity using CGConnect with paramters"""
nest.ResetKernel()
n_neurons = 4
weight = 10000.0
delay = 2.0
sources = nest.Create("iaf_psc_alpha", n_neurons)
targets = nest.Create("iaf_psc_alpha", n_neurons)
# Create a connection set with values for weight and delay
cs = csa.cset(csa.oneToOne, weight, delay)
# Connect sources and targets using the connection set cs and
# a parameter map mapping weight to position 0 in the value
# set and delay to position 1
nest.CGConnect(sources, targets, cs, {"weight": 0, "delay": 1})
for i in range(n_neurons):
# We expect all connections from sources to have the
# correct targets, weights and delays
conns = nest.GetStatus(nest.GetConnections([sources[i]]))
self.assertEqual(len(conns), 1)
self.assertEqual(conns[0]["target"], targets[i])
self.assertEqual(conns[0]["weight"], weight)
self.assertEqual(conns[0]["delay"], delay)
# We expect the targets to have no connections at all
conns = nest.GetStatus(nest.GetConnections([targets[i]]))
self.assertEqual(len(conns), 0)
def test_Conngen_OneToOne_params(self):
"""One-to-one connectivity using conngen Connect with parameters"""
nest.ResetKernel()
n_neurons = 4
weight = 10000.0
delay = 2.0
sources = nest.Create("iaf_psc_alpha", n_neurons)
targets = nest.Create("iaf_psc_alpha", n_neurons)
# Create a connection set with values for weight and delay
cg = csa.cset(csa.oneToOne, weight, delay)
# Connect sources and targets using the connection set cs and
# a parameter map mapping weight to position 0 in the value
# set and delay to position 1
params_map = {"weight": 0, "delay": 1}
connspec = {"rule": "conngen", "cg": cg, "params_map": params_map}
nest.Connect(sources, targets, connspec)
for i in range(n_neurons):
# We expect all connections from sources to have the
# correct targets, weights and delays
conns = nest.GetConnections(sources[i])
self.assertEqual(len(conns), 1)
self.assertEqual(conns.target, targets[i].get('global_id'))
self.assertEqual(conns.weight, weight)
self.assertEqual(conns.delay, delay)
# We expect the targets to have no connections at all
conns = nest.GetConnections(targets[i])
self.assertEqual(len(conns), 0)
def test_Conngen_error_weight_and_delay_in_synspec_and_conngen(self):
"""
Error handling for conflicting weight/delay in conngen Connect
"""
nest.ResetKernel()
cg = csa.cset(csa.oneToOne, 10000.0, 2.0)
params_map = {"weight": 0, "delay": 1}
connspec = {"rule": "conngen", "cg": cg, "params_map": params_map}
synspec_w = {'weight': 10.0}
synspec_d = {'delay': 10.0}
synspec_wd = {'weight': 10.0, 'delay': 10.0}
n_neurons = 4
pop = nest.Create("iaf_psc_alpha", n_neurons)
self.assertRaisesRegex(nest.kernel.NESTError, "BadProperty",
nest.Connect, pop, pop, connspec, synspec_w)
self.assertRaisesRegex(nest.kernel.NESTError, "BadProperty",
nest.Connect, pop, pop, connspec, synspec_d)
self.assertRaisesRegex(nest.kernel.NESTError, "BadProperty",
nest.Connect, pop, pop, connspec, synspec_wd)
def test_CSA_OneToOne_intvectors(self):
"""One-to-one connectivity using CGConnect with id intvectors"""
nest.ResetKernel()
n_neurons = 4
sources = nest.Create("iaf_psc_alpha", n_neurons)
targets = nest.Create("iaf_psc_alpha", n_neurons)
# Create a plain connection set
cg = csa.cset(csa.oneToOne)
# Connect sources and targets (both converted to NumPy arrays)
# using the connection set cs. This will internally call the
# variant of CGConnect that takes intvector instead of lists
nest.CGConnect(numpy.array(sources), numpy.array(targets), cg)
for i in range(n_neurons):
# We expect all connections from sources to have the
# correct targets
conns = nest.GetStatus(nest.GetConnections(sources[i]))
self.assertEqual(len(conns), 1)
self.assertEqual(conns[0]["target"], targets[i].get('global_id'))
# We expect the targets to have no connections at all
conns = nest.GetStatus(nest.GetConnections(targets[i]))
self.assertEqual(len(conns), 0)
def csa_example():
cs = csa.cset(csa.random(0.1), 10000.0, 1.0)
pop1 = nest.LayoutNetwork("iaf_neuron", [16])
pop2 = nest.LayoutNetwork("iaf_neuron", [16])
nest.PrintNetwork(10)
nest.CGConnect(pop1, pop2, cs, {"weight": 0, "delay": 1})
pg = nest.Create("poisson_generator", params={"rate": 80000.0})
nest.DivergentConnect(pg, nest.GetLeaves(pop1)[0], 1.2, 1.0)
vm_params = {"record_to": ["memory"], "withgid": True,
"withtime": True, "interval": 0.1}
vm = nest.Create("voltmeter", params=vm_params)
nest.DivergentConnect(vm, nest.GetLeaves(pop2)[0])
nest.Simulate(50.0)
from nest import visualization
allnodes = pg + nest.GetLeaves(pop1)[0] + nest.GetLeaves(pop2)[0] + vm
visualization.plot_network(allnodes, "test_csa.png")
if havePIL:
im = Image.open("test_csa.png")
im.show()
from nest import voltage_trace
voltage_trace.from_device(vm)
def test_CSA_OneToOne_params(self):
"""One-to-one connectivity"""
nest.ResetKernel()
n = 4 # number of neurons
pop0 = nest.LayoutNetwork("iaf_neuron", [n])
pop1 = nest.LayoutNetwork("iaf_neuron", [n])
cs = csa.cset(csa.oneToOne, 10000.0, 1.0)
nest.CGConnect(pop0, pop1, cs, {"weight": 0, "delay": 1})
sources = nest.GetLeaves(pop0)[0]
targets = nest.GetLeaves(pop1)[0]
for i in xrange(n):
conns = nest.GetStatus(nest.FindConnections([sources[i]]),
'target')
self.assertEqual(len(conns), 1)
self.assertEqual(conns[0], targets[i])
conns = nest.GetStatus(nest.FindConnections([targets[i]]),
'target')
self.assertEqual(len(conns), 0)
def test_CSA_cgnext(self):
"""cgnext"""
nest.ResetKernel()
w = 10000.0
d = 1.0
cs = csa.cset(csa.oneToOne, w, d)
kernel.pushsli(cs)
kernel.runsli('dup')
kernel.pushsli(numpy.array([0, 1, 2, 3]))
kernel.pushsli(numpy.array([0, 1, 2, 3]))
kernel.runsli('cgsetmask_cg_a_a')
kernel.runsli('dup')
kernel.runsli('cgstart')
for i in xrange(4):
kernel.runsli('dup')
kernel.runsli('cgnext')
self.assertEqual(kernel.popsli(), True)
self.assertEqual(kernel.popsli(), d)
self.assertEqual(kernel.popsli(), w)
self.assertEqual(kernel.popsli(), i)
self.assertEqual(kernel.popsli(), i)
kernel.runsli('cgnext')
self.assertEqual(kernel.popsli(), False)
def csa_example():
cs = csa.cset(csa.random(0.1), 10000.0, 1.0)
pop1 = nest.LayoutNetwork("iaf_neuron", [16])
pop2 = nest.LayoutNetwork("iaf_neuron", [16])
nest.PrintNetwork(10)
nest.CGConnect(pop1, pop2, cs, {"weight": 0, "delay": 1})
pg = nest.Create("poisson_generator", params={"rate": 80000.0})
nest.DivergentConnect(pg, nest.GetLeaves(pop1)[0], 1.2, 1.0)
vm_params = {
"record_to": ["memory"],
"withgid": True,
"withtime": True,
"interval": 0.1
}
vm = nest.Create("voltmeter", params=vm_params)
nest.DivergentConnect(vm, nest.GetLeaves(pop2)[0])
nest.Simulate(50.0)
from nest import visualization
allnodes = pg + nest.GetLeaves(pop1)[0] + nest.GetLeaves(pop2)[0] + vm
visualization.plot_network(allnodes, "test_csa.png")
if havePIL:
im = Image.open("test_csa.png")
im.show()
from nest import voltage_trace
voltage_trace.from_device(vm)
def test_CSA_OneToOne_subnet_1d(self):
"""One-to-one connectivity with 1-dim subnets"""
nest.ResetKernel()
n = 4 # number of neurons
pop0 = nest.LayoutNetwork("iaf_neuron", [n])
pop1 = nest.LayoutNetwork("iaf_neuron", [n])
cg = csa.cset(csa.oneToOne)
nest.CGConnect(pop0, pop1, cg)
sources = nest.GetLeaves(pop0)[0]
targets = nest.GetLeaves(pop1)[0]
for i in range(n):
conns = nest.GetStatus(
nest.FindConnections([sources[i]]), 'target')
self.assertEqual(len(conns), 1)
self.assertEqual(conns[0], targets[i])
conns = nest.GetStatus(
nest.FindConnections([targets[i]]), 'target')
self.assertEqual(len(conns), 0)
def test_Conngen_OneToOne_synmodel(self):
"""One-to-one connectivity using conngen Connect and synapse_model"""
nest.ResetKernel()
n_neurons = 4
synmodel = "stdp_synapse"
tau_plus = 10.0
sources = nest.Create("iaf_psc_alpha", n_neurons)
targets = nest.Create("iaf_psc_alpha", n_neurons)
# Create a plain connection set
cg = csa.cset(csa.oneToOne)
# Connect with a non-standard synapse model
connspec = {"rule": "conngen", "cg": cg}
synspec = {'synapse_model': synmodel, "tau_plus": tau_plus}
nest.Connect(sources, targets, connspec, synspec)
for i in range(n_neurons):
# We expect all connections to have the correct targets
# and the non-standard synapse model set
conns = nest.GetConnections(sources[i])
self.assertEqual(len(conns), 1)
self.assertEqual(conns.target, targets[i].get('global_id'))
self.assertEqual(conns.synapse_model, synmodel)
self.assertEqual(conns.tau_plus, tau_plus)
# We expect the targets to have no connections at all
conns = nest.GetConnections(targets[i])
self.assertEqual(len(conns), 0)
def test_CSA_OneToOne_synmodel(self):
"""One-to-one connectivity using CGConnect with synmodel"""
nest.ResetKernel()
n_neurons = 4
synmodel = "stdp_synapse"
sources = nest.Create("iaf_psc_alpha", n_neurons)
targets = nest.Create("iaf_psc_alpha", n_neurons)
# Create a plain connection set
cs = csa.cset(csa.oneToOne)
# Connect with a non-standard synapse model
nest.CGConnect(sources, targets, cs, model=synmodel)
for i in range(n_neurons):
# We expect all connections to have the correct targets
# and the non-standard synapse model set
conns = nest.GetStatus(nest.GetConnections([sources[i]]))
self.assertEqual(len(conns), 1)
self.assertEqual(conns[0]["target"], targets[i])
self.assertEqual(conns[0]["synapse_model"], synmodel)
# We expect the targets to have no connections at all
conns = nest.GetStatus(nest.GetConnections([targets[i]]))
self.assertEqual(len(conns), 0)
def test_CSA_OneToOne_tuples(self):
"""One-to-one connectivity using CGConnect with id tuples"""
nest.ResetKernel()
n_neurons = 4
sources = nest.Create("iaf_psc_alpha", n_neurons)
targets = nest.Create("iaf_psc_alpha", n_neurons)
# Create a plain connection set
cg = csa.cset(csa.oneToOne)
# Connect sources and targets using the connection set
# cs. This will internally call the variant of CGConnect that
# takes lists
nest.CGConnect(sources, targets, cg)
for i in range(n_neurons):
# We expect all connections from sources to have the
# correct targets
conns = nest.GetStatus(nest.GetConnections(sources[i]))
self.assertEqual(len(conns), 1)
self.assertEqual(conns[0]["target"], targets[i].get('global_id'))
# We expect the targets to have no connections at all
conns = nest.GetStatus(nest.GetConnections(targets[i]))
self.assertEqual(len(conns), 0)
def test_CSA_OneToOne_params(self):
"""One-to-one connectivity"""
nest.ResetKernel()
n = 4 # number of neurons
pop0 = nest.LayoutNetwork("iaf_neuron", [n])
pop1 = nest.LayoutNetwork("iaf_neuron", [n])
cs = csa.cset(csa.oneToOne, 10000.0, 1.0)
nest.CGConnect(pop0, pop1, cs, {"weight": 0, "delay": 1})
sources = nest.GetLeaves(pop0)[0]
targets = nest.GetLeaves(pop1)[0]
for i in range(n):
conns = nest.GetStatus(
nest.FindConnections([sources[i]]), 'target')
self.assertEqual(len(conns), 1)
self.assertEqual(conns[0], targets[i])
conns = nest.GetStatus(
nest.FindConnections([targets[i]]), 'target')
self.assertEqual(len(conns), 0)
def test_CSA_OneToOne_synmodel(self):
"""One-to-one connectivity using CGConnect with synmodel"""
nest.ResetKernel()
n_neurons = 4
synmodel = "stdp_synapse"
sources = nest.Create("iaf_psc_alpha", n_neurons)
targets = nest.Create("iaf_psc_alpha", n_neurons)
# Create a plain connection set
cs = csa.cset(csa.oneToOne)
# Connect with a non-standard synapse model
nest.CGConnect(sources, targets, cs, model=synmodel)
for i in range(n_neurons):
# We expect all connections to have the correct targets
# and the non-standard synapse model set
conns = nest.GetStatus(nest.GetConnections(sources[i]))
self.assertEqual(len(conns), 1)
self.assertEqual(conns[0]["target"], targets[i].get('global_id'))
self.assertEqual(conns[0]["synapse_model"], synmodel)
# We expect the targets to have no connections at all
conns = nest.GetStatus(nest.GetConnections(targets[i]))
self.assertEqual(len(conns), 0)
def test_CSA_OneToOne_intvectors(self):
"""One-to-one connectivity using CGConnect with id intvectors"""
nest.ResetKernel()
n_neurons = 4
sources = nest.Create("iaf_psc_alpha", n_neurons)
targets = nest.Create("iaf_psc_alpha", n_neurons)
# Create a plain connection set
cg = csa.cset(csa.oneToOne)
# Connect sources and targets (both converted to NumPy arrays)
# using the connection set cs. This will internally call the
# variant of CGConnect that takes intvector instead of lists
nest.CGConnect(numpy.array(sources), numpy.array(targets), cg)
for i in range(n_neurons):
# We expect all connections from sources to have the
# correct targets
conns = nest.GetStatus(nest.GetConnections([sources[i]]))
self.assertEqual(len(conns), 1)
self.assertEqual(conns[0]["target"], targets[i])
# We expect the targets to have no connections at all
conns = nest.GetStatus(nest.GetConnections([targets[i]]))
self.assertEqual(len(conns), 0)
def test_CSA_cgnext(self):
"""cgnext"""
nest.ResetKernel()
w = 10000.0
d = 1.0
cs = csa.cset(csa.oneToOne, w, d)
kernel.pushsli(cs)
kernel.runsli('dup')
kernel.pushsli(numpy.array([0,1,2,3]))
kernel.pushsli(numpy.array([0,1,2,3]))
kernel.runsli('cgsetmask_cg_a_a')
kernel.runsli('dup')
kernel.runsli('cgstart')
for i in xrange(4):
kernel.runsli('dup')
kernel.runsli('cgnext')
self.assertEqual(kernel.popsli(), True)
self.assertEqual(kernel.popsli(), d)
self.assertEqual(kernel.popsli(), w)
self.assertEqual(kernel.popsli(), i)
self.assertEqual(kernel.popsli(), i)
kernel.runsli('cgnext')
self.assertEqual(kernel.popsli(), False)
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 test_CSA_OneToOne_subnet_nd(self):
"""One-to-one connectivity with n-dim subnets"""
nest.ResetKernel()
n = 2 # number of neurons per dimension
pop0 = nest.LayoutNetwork("iaf_neuron", [n, n])
pop1 = nest.LayoutNetwork("iaf_neuron", [n, n])
cg = csa.cset(csa.oneToOne)
self.assertRaisesRegex(nest.NESTError, "BadProperty", nest.CGConnect, pop0, pop1, cg)
def test_CSA_OneToOne_subnet_nd(self):
"""One-to-one connectivity with n-dim subnets"""
nest.ResetKernel()
n = 2 # number of neurons per dimension
pop0 = nest.LayoutNetwork("iaf_neuron", [n, n])
pop1 = nest.LayoutNetwork("iaf_neuron", [n, n])
cg = csa.cset(csa.oneToOne)
self.assertRaisesRegex(nest.NESTError, "BadProperty", nest.CGConnect,
pop0, pop1, cg)
def test_CSA_error_unknown_nodes(self):
"""Error handling of CGConnect in case of unknown nodes"""
nest.ResetKernel()
# Create a plain connection set
cs = csa.cset(csa.oneToOne)
nonnodes = [1, 2, 3]
# We expect CGConnect to fail with an UnknownNode exception if
# unknown nodes are given
self.assertRaisesRegex(nest.NESTError, "UnknownNode",
nest.CGConnect, nonnodes, nonnodes, cs)
def test_CSA_error_unknown_nodes(self):
"""Error handling of CGConnect in case of unknown nodes"""
nest.ResetKernel()
# Create a plain connection set
cs = csa.cset(csa.oneToOne)
nonnodes = [1, 2, 3]
# We expect CGConnect to fail with an UnknownNode exception if
# unknown nodes are given
self.assertRaisesRegex(nest.kernel.NESTError, "UnknownNode",
nest.CGConnect, nonnodes, nonnodes, cs)
def test_Conngen_error_collocated_synapses(self):
"""
Error handling for collocated synapses in conngen Connect
"""
nest.ResetKernel()
# Create a plain connection set
cg = csa.cset(csa.oneToOne)
connspec = {"rule": "conngen", "cg": cg}
synspec = nest.CollocatedSynapses({'weight': -2.}, {'weight': 2.})
pop = nest.Create('iaf_psc_alpha', 3)
self.assertRaisesRegex(nest.kernel.NESTError, "BadProperty",
nest.Connect, pop, pop, connspec, synspec)
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 test_Conngen_error_unknown_synapse(self):
"""
Error handling for unknown synapse model in conngen Connect
"""
nest.ResetKernel()
# Create a plain connection set
cg = csa.cset(csa.oneToOne)
connspec = {"rule": "conngen", "cg": cg}
synspec = {'synapse_model': "fantasy_synapse"}
n_neurons = 4
pop = nest.Create("iaf_psc_alpha", n_neurons)
self.assertRaisesRegex(nest.kernel.NESTError, "UnknownSynapseType",
nest.Connect, pop, pop, connspec, synspec)
def test_CSA_error_unknown_synapse(self):
"""Error handling of CGConnect in case of unknown synapse model"""
nest.ResetKernel()
# Create a plain connection set
cs = csa.cset(csa.oneToOne)
n_neurons = 4
sources = nest.Create("iaf_psc_alpha", n_neurons)
targets = nest.Create("iaf_psc_alpha", n_neurons)
# We expect CGConnect to fail with an UnknownSynapseType
# exception if an unknown synapse model is given
self.assertRaisesRegex(nest.NESTError, "UnknownSynapseType",
nest.CGConnect, sources, targets, cs,
model="nonexistent_synapse")
def csa_example():
cs = csa.cset(csa.random(0.1), 10000.0, 1.0)
# This does not work yet, as the implementation does not yet
# support nested subnets.
#
#pop1 = nest.LayoutNetwork("iaf_neuron", [4,4])
#pop2 = nest.LayoutNetwork("iaf_neuron", [4,4])
pop1 = nest.LayoutNetwork("iaf_neuron", [16])
pop2 = nest.LayoutNetwork("iaf_neuron", [16])
nest.PrintNetwork(10)
nest.CGConnect(pop1, pop2, cs, {"weight": 0, "delay": 1})
pg = nest.Create("poisson_generator", params={"rate": 80000.0})
nest.DivergentConnect(pg, nest.GetLeaves(pop1)[0], 1.2, 1.0)
vm = nest.Create("voltmeter",
params={
"record_to": ["memory"],
"withgid": True,
"withtime": True,
"interval": 0.1
})
nest.DivergentConnect(vm, nest.GetLeaves(pop2)[0])
nest.Simulate(50.0)
# Not yet supported in NEST
#from nest import visualization
#allnodes = [pg, nest.GetLeaves(pop1)[0], nest.GetLeaves(pop2)[0], vm]
#visualization.plot_network(allnodes, "test_csa.png", "png", plot_modelnames=True
#if havePIL:
# im = Image.open("test_csa.png")
# im.show()
from nest import voltage_trace
voltage_trace.from_device(vm)
def test_CSA_OneToOne_idrange(self):
"""One-to-one connectivity with id ranges"""
nest.ResetKernel()
n = 4 # number of neurons
sources = nest.Create("iaf_neuron", n)
targets = nest.Create("iaf_neuron", n)
cg = csa.cset(csa.oneToOne)
nest.CGConnect (sources, targets, cg)
for i in range(n):
conns = nest.GetStatus(nest.FindConnections([sources[i]]), 'target')
self.assertEqual(len(conns), 1)
self.assertEqual(conns[0], targets[i])
conns = nest.GetStatus(nest.FindConnections([targets[i]]), 'target')
self.assertEqual(len(conns), 0)
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)
def test_CSA_OneToOne_idrange(self):
"""One-to-one connectivity with id ranges"""
nest.ResetKernel()
n = 4 # number of neurons
sources = nest.Create("iaf_neuron", n)
targets = nest.Create("iaf_neuron", n)
cg = csa.cset(csa.oneToOne)
nest.CGConnect(sources, targets, cg)
for i in range(n):
conns = nest.GetStatus(nest.FindConnections([sources[i]]),
'target')
self.assertEqual(len(conns), 1)
self.assertEqual(conns[0], targets[i])
conns = nest.GetStatus(nest.FindConnections([targets[i]]),
'target')
self.assertEqual(len(conns), 0)
def csa_example():
cs = csa.cset(csa.random(0.1), 10000.0, 1.0)
# This does not work yet, as the implementation does not yet
# support nested subnets.
#
# pop1 = nest.LayoutNetwork("iaf_neuron", [4,4])
# pop2 = nest.LayoutNetwork("iaf_neuron", [4,4])
pop1 = nest.LayoutNetwork("iaf_neuron", [16])
pop2 = nest.LayoutNetwork("iaf_neuron", [16])
nest.PrintNetwork(10)
nest.CGConnect(pop1, pop2, cs, {"weight": 0, "delay": 1})
pg = nest.Create("poisson_generator", params={"rate": 80000.0})
nest.DivergentConnect(pg, nest.GetLeaves(pop1)[0], 1.2, 1.0)
vm = nest.Create("voltmeter", params={"record_to": ["memory"], "withgid": True, "withtime": True, "interval": 0.1})
nest.DivergentConnect(vm, nest.GetLeaves(pop2)[0])
nest.Simulate(50.0)
# Not yet supported in NEST
# from nest import visualization
# allnodes = [pg, nest.GetLeaves(pop1)[0], nest.GetLeaves(pop2)[0], vm]
# visualization.plot_network(allnodes, "test_csa.png", "png", plot_modelnames=True
# if havePIL:
# im = Image.open("test_csa.png")
# im.show()
from nest import voltage_trace
voltage_trace.from_device(vm)
import csa
haveCSA = True
except ImportError:
print("This example requires CSA to be installed in order to run.\n"
+ "Please make sure you compiled NEST using --with-libneurosim=PATH\n"
+ "and CSA and libneurosim are available from PYTHONPATH.")
import sys
sys.exit()
"""
To set up the connectivity, We create a ``random`` connection set
with a probability of 0.1 and two associated values (10000.0 and 1.0)
used as weight and delay, respectively.
"""
cs = csa.cset(csa.random(0.1), 10000.0, 1.0)
"""
Using the `Create` command from PyNEST, we create the neurons of
the pre- and postsynaptic populations, each of which containing 16
neurons.
"""
pre = nest.Create("iaf_neuron", 16)
post = nest.Create("iaf_neuron", 16)
"""
We can now connect the populations using the `CGConnect` function.
It takes the IDs of pre- and postsynaptic neurons (``pre`` and
``post``), the connection set (``cs``) and a dictionary that maps
the parameters weight and delay to positions in the value set
})
"""
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})
"""
exc_cells = all_cells[:n_exc]
inh_cells = all_cells[n_exc:]
if benchmark == "COBA":
ext_stim = Population(20, SpikeSourcePoisson, {'rate' : rate, 'duration' : stim_dur}, label="expoisson")
rconn = 0.01
ext_conn = FixedProbabilityConnector(rconn, weights=0.1)
print "%s Initialising membrane potential to random values..." % node_id
rng = NumpyRNG(seed=rngseed, parallel_safe=parallel_safe)
uniformDistr = RandomDistribution('uniform', [v_reset,v_thresh], rng=rng)
all_cells.initialize('v', uniformDistr)
print "%s Connecting populations..." % node_id
#exc_conn = FixedProbabilityConnector(pconn, weights=w_exc, delays=delay)
#inh_conn = FixedProbabilityConnector(pconn, weights=w_inh, delays=delay)
exc_conn = CSAConnector(csa.cset (csa.random (pconn), w_exc, delay))
inh_conn = CSAConnector(csa.cset (csa.random (pconn), w_inh, delay))
connections={}
connections['exc'] = Projection(exc_cells, all_cells, exc_conn, target='excitatory', rng=rng)
connections['inh'] = Projection(inh_cells, all_cells, inh_conn, target='inhibitory', rng=rng)
if (benchmark == "COBA"):
connections['ext'] = Projection(ext_stim, all_cells, ext_conn, target='excitatory')
# === Setup recording ==========================================================
print "%s Setting up recording..." % node_id
all_cells.record()
vrecord_list = [exc_cells[0],exc_cells[1]]
exc_cells.record_v(vrecord_list)
buildCPUTime = timer.diff()
import csa
haveCSA = True
except ImportError:
print(
"This example requires CSA to be installed in order to run.\n" +
"Please make sure you compiled NEST using --with-libneurosim=PATH\n" +
"and CSA and libneurosim are available from PYTHONPATH.")
import sys
sys.exit()
"""
To set up the connectivity, We create a ``random`` connection set
with a probability of 0.1 and two associated values (10000.0 and 1.0)
used as weight and delay, respectively.
"""
cs = csa.cset(csa.random(0.1), 10000.0, 1.0)
"""
Using the `Create` command from PyNEST, we create the neurons of
the pre- and postsynaptic populations, each of which containing 16
neurons.
"""
pre = nest.Create("iaf_neuron", 16)
post = nest.Create("iaf_neuron", 16)
"""
We can now connect the populations using the `CGConnect` function.
It takes the IDs of pre- and postsynaptic neurons (``pre`` and
``post``), 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.
"""
ext_conn = sim.FixedProbabilityConnector(rconn)
ext_syn = sim.StaticSynapse(weight=0.1)
print("%s Initialising membrane potential to random values..." % node_id)
rng = NumpyRNG(seed=rngseed, parallel_safe=parallel_safe)
uniformDistr = RandomDistribution('uniform', low=v_reset, high=v_thresh, rng=rng)
if options.use_views:
all_cells.initialize(v=uniformDistr)
else:
exc_cells.initialize(v=uniformDistr)
inh_cells.initialize(v=uniformDistr)
print("%s Connecting populations..." % node_id)
progress_bar = ProgressBar(width=20)
if options.use_csa:
connector = CSAConnector(csa.cset(csa.random(pconn)))
else:
connector = sim.FixedProbabilityConnector(pconn, rng=rng, callback=progress_bar)
exc_syn = sim.StaticSynapse(weight=w_exc, delay=delay)
inh_syn = sim.StaticSynapse(weight=w_inh, delay=delay)
connections = {}
if options.use_views or options.use_assembly:
connections['exc'] = sim.Projection(exc_cells, all_cells, connector, exc_syn, receptor_type='excitatory')
connections['inh'] = sim.Projection(inh_cells, all_cells, connector, inh_syn, receptor_type='inhibitory')
if (options.benchmark == "COBA"):
connections['ext'] = sim.Projection(ext_stim, all_cells, ext_conn, ext_syn, receptor_type='excitatory')
else:
connections['e2e'] = sim.Projection(exc_cells, exc_cells, connector, exc_syn, receptor_type='excitatory')
connections['e2i'] = sim.Projection(exc_cells, inh_cells, connector, exc_syn, receptor_type='excitatory')
connections['i2e'] = sim.Projection(inh_cells, exc_cells, connector, inh_syn, receptor_type='inhibitory')
"""
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})
def _connect(self):
'''Connect populations.'''
finite_set = csa.cross(xrange(self._N_s), xrange(self._N_t))
cs = csa.cset(csa.random(p=self._p) * finite_set)
nest.CGConnect(self._source_pop, self._target_pop, csa.cset(cs))
print("%s Initialising membrane potential to random values..." % node_id)
rng = NumpyRNG(seed=rngseed, parallel_safe=parallel_safe)
uniformDistr = RandomDistribution('uniform',
low=v_reset,
high=v_thresh,
rng=rng)
if options.use_views:
all_cells.initialize(v=uniformDistr)
else:
exc_cells.initialize(v=uniformDistr)
inh_cells.initialize(v=uniformDistr)
print("%s Connecting populations..." % node_id)
progress_bar = ProgressBar(width=20)
if options.use_csa:
connector = sim.CSAConnector(csa.cset(csa.random(pconn)))
else:
connector = sim.FixedProbabilityConnector(pconn,
rng=rng,
callback=progress_bar)
exc_syn = sim.StaticSynapse(weight=w_exc, delay=delay)
inh_syn = sim.StaticSynapse(weight=w_inh, delay=delay)
connections = {}
if options.use_views or options.use_assembly:
connections['exc'] = sim.Projection(exc_cells,
all_cells,
connector,
exc_syn,
receptor_type='excitatory')
connections['inh'] = sim.Projection(inh_cells,
def _connect(self):
'''Connect populations.'''
finite_set = csa.cross(xrange(self._N_s), xrange(self._N_t))
self._cs = csa.cset(csa.random(p=self._p) * finite_set)
'rate': rate,
'duration': stim_dur
},
label="expoisson")
rconn = 0.01
ext_conn = FixedProbabilityConnector(rconn, weights=0.1)
print "%s Initialising membrane potential to random values..." % node_id
rng = NumpyRNG(seed=rngseed, parallel_safe=parallel_safe)
uniformDistr = RandomDistribution('uniform', [v_reset, v_thresh], rng=rng)
all_cells.initialize('v', uniformDistr)
print "%s Connecting populations..." % node_id
#exc_conn = FixedProbabilityConnector(pconn, weights=w_exc, delays=delay)
#inh_conn = FixedProbabilityConnector(pconn, weights=w_inh, delays=delay)
exc_conn = CSAConnector(csa.cset(csa.random(pconn), w_exc, delay))
inh_conn = CSAConnector(csa.cset(csa.random(pconn), w_inh, delay))
connections = {}
connections['exc'] = Projection(exc_cells,
all_cells,
exc_conn,
target='excitatory',
rng=rng)
connections['inh'] = Projection(inh_cells,
all_cells,
inh_conn,
target='inhibitory',
rng=rng)
if (benchmark == "COBA"):
connections['ext'] = Projection(ext_stim,
ext_stim = Population(20, SpikeSourcePoisson(rate=rate, duration=stim_dur), label="expoisson")
rconn = 0.01
ext_conn = FixedProbabilityConnector(rconn)
syn = StaticSynapse(weight=0.1)
print "%s Initialising membrane potential to random values..." % node_id
rng = NumpyRNG(seed=rngseed, parallel_safe=parallel_safe)
uniformDistr = RandomDistribution('uniform', low=v_reset, high=v_thresh, rng=rng)
all_cells.initialize(v=uniformDistr)
print "%s Connecting populations..." % node_id
#exc_conn = FixedProbabilityConnector(pconn, weights=w_exc, delays=delay)
#inh_conn = FixedProbabilityConnector(pconn, weights=w_inh, delays=delay)
exc_syn = StaticSynapse(weight=w_exc, delay=delay)
inh_syn = StaticSynapse(weight=w_inh, delay=delay)
exc_conn = CSAConnector(csa.cset (csa.random (pconn)))
inh_conn = CSAConnector(csa.cset (csa.random (pconn)))
connections={}
connections['exc'] = Projection(exc_cells, all_cells, exc_conn, exc_syn, receptor_type='excitatory')
connections['inh'] = Projection(inh_cells, all_cells, inh_conn, inh_syn, receptor_type='inhibitory')
if (benchmark == "COBA"):
connections['ext'] = Projection(ext_stim, all_cells, ext_conn, syn, receptor_type='excitatory')
# === Setup recording ==========================================================
print "%s Setting up recording..." % node_id
all_cells.record('spikes')
exc_cells[0:2].record('v')
buildCPUTime = timer.diff()
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