"""
"""
from nineml.abstraction_layer import parse, writers, flattening
from nineml.abstraction_layer.testing_utils import (RecordValue,
TestableComponent,
std_pynn_simulation)
# Load the Component:
iz_file = '../../../../../../catalog/sample_xml_files/PostTF_izhikevich.xml'
iz = parse(iz_file)
# Write the component back out to XML
writers.XMLWriter.write(iz, 'TestOut_Iz.xml')
writers.DotWriter.write(iz, 'TestOut_Iz.dot')
writers.DotWriter.build('TestOut_Iz.dot')
# Simulate the Neuron:
records = [
RecordValue(what='V', tag='V', label='V'),
# RecordValue(what='U', tag='U', label='U'),
# RecordValue( what='regime', tag='Regime', label='Regime' ),
]
parameters = flattening.ComponentFlattener.flatten_namespace_dict({
'a':
0.02,
'b':
0.2,
'c':
# coba_syn.ports['Isyn'] -> leaky_iaf.ports['Isyn'] for multiple synapses (reduce port)
# Simulator attaches to SpikeInput and SpikeOutput ports for input and output.
# write to file object f if defined
c1 = leaky_iaf
try:
# This case is used in the test suite for examples.
c1.write(f)
except NameError:
import os
base = "gLIFid1"
c1.write(base + ".xml")
c2 = nineml.parse(base + ".xml")
assert c1 == c2
c1.to_dot(base + ".dot")
os.system("dot -Tpng %s -o %s" % (base + ".dot", base + ".png"))
c1 = coba_syn
# write to file object f if defined
try:
# This case is used in the test suite for examples.
c1.write(f)
except NameError:
import os
base = "exp_cond_id1"
import nineml.abstraction_layer as nineml
from brian import *
import brian.stdunits as units
import numpy
# Single Union hh model definition, which is Sequence and Event free.
hh = nineml.parse("hh.xml")
def component_to_native_brian(c):
assert len(c.regime_map) == 1, "brian supports 1 regime natively"
# back substitute aliases which need aliases
hh.backsub_aliases()
# substitute aliases in equations
hh.backsub_equations()
eqns = []
for e in hh.equations:
# this fudges brian's unit system
eqn = '%s = ( %s )/__time_factor__ : 1.' % (
e.lhs,
e.rhs,
)
eqns += [eqn]
return eqns
# have a look at what equations we got
eqns = component_to_native_brian(hh)
def get_Izh_FS_component():
"""
Load Fast spiking Izhikevich XML definition from file and parse into
Abstraction Layer of Python API.
"""
return al.parse('NineML_Izh_FS.xml')
# leaky_iaf.ports['V'] -> delta_syn.ports['V']
# delta_syn.ports['Isyn'] -> leaky_iaf.ports['Isyn'] for multiple synapses (reduce port)
# Simulator attaches to SpikeInput and SpikeOutput ports for input and output.
# write to file object f if defined
c1 = leaky_iaf
try:
# This case is used in the test suite for examples.
c1.write(f)
except NameError:
import os
base = "gLIFid1"
c1.write(base + ".xml")
c2 = nineml.parse(base + ".xml")
assert c1 == c2
c1.to_dot(base + ".dot")
os.system("dot -Tpng %s -o %s" % (base + ".dot", base + ".png"))
c1 = coba_syn
# write to file object f if defined
try:
# This case is used in the test suite for examples.
c1.write(f)
except NameError:
import os
base = "exp_cond_id1"
c1.write(base + ".xml")
import nineml.abstraction_layer as nineml
from brian import *
import brian.stdunits as units
import numpy
# Single Union hh model definition, which is Sequence and Event free.
hh = nineml.parse("hh.xml")
def component_to_native_brian(c):
assert len(c.regime_map)==1, "brian supports 1 regime natively"
# back substitute aliases which need aliases
hh.backsub_aliases()
# substitute aliases in equations
hh.backsub_equations()
eqns = []
for e in hh.equations:
# this fudges brian's unit system
eqn = '%s = ( %s )/__time_factor__ : 1.' % (e.lhs,e.rhs,)
eqns+=[eqn]
return eqns
# have a look at what equations we got
eqns = component_to_native_brian(hh)
for e in eqns:
print e
)]
analog_ports = [al.RecvPort("V"),
al.SendPort("Isyn = g(E-V)")]
coba_syn = al.ComponentClass("CoBaSynapse", regimes=regimes, analog_ports=analog_ports)
# User layer connects
# leaky_iaf.analog_ports['V'] -> coba_syn.analog_ports['V']
# coba_syn.analog_ports['Isyn'] -> leaky_iaf.analog_ports['Isyn'] for multiple synapses (reduce port)
# Simulator attaches to SpikeInput and SpikeOutput analog_ports for input and output.
# write to file object f if defined
c1 = coba_syn
try:
# This case is used in the test suite for examples.
c1.write(f)
except NameError:
import os
base = "leaky_iaf_ampa_analog_ports_events"
c1.write(base + ".xml")
c2 = al.parse(base + ".xml")
assert c1 == c2
c1.to_dot(base + ".dot")
os.system("dot -Tpng %s -o %s" % (base + ".dot", base + ".png"))
"""
"""
from nineml.abstraction_layer import parse, writers, flattening
from nineml.abstraction_layer.testing_utils import (RecordValue,
TestableComponent,
std_pynn_simulation)
# Load the Component:
iz_file = '../../../../../../catalog/sample_xml_files/PostTF_izhikevich.xml'
iz = parse(iz_file)
# Write the component back out to XML
writers.XMLWriter.write(iz, 'TestOut_Iz.xml')
writers.DotWriter.write(iz, 'TestOut_Iz.dot')
writers.DotWriter.build('TestOut_Iz.dot')
# Simulate the Neuron:
records = [
RecordValue(what='V', tag='V', label='V'),
# RecordValue(what='U', tag='U', label='U'),
# RecordValue( what='regime', tag='Regime', label='Regime' ),
]
parameters = flattening.ComponentFlattener.flatten_namespace_dict({
'a': 0.02,
'b': 0.2,
'c': -65,
'd': 8,
def get_Izh_FS_component():
"""
Load Fast spiking Izhikevich XML definition from file and parse into
Abstraction Layer of Python API.
"""
return al.parse('NineML_Izh_FS.xml')