def write(self, file, flatten=True):
"""Export this model to an XML file.
:params file: A filename or fileobject
:params flatten: Boolean specifying whether the component should be
flattened before saving
"""
from nineml.abstraction_layer.writers import XMLWriter
return XMLWriter.write(component=self, file=file, flatten=flatten)
def run(plot_and_show=True):
import sys
from os.path import abspath, realpath, join
import numpy
import nineml
root = abspath(join(realpath(nineml.__path__[0]), "../../.."))
sys.path.append(join(root, "lib9ml/python/examples/AL"))
sys.path.append(join(root, "code_generation/nmodl"))
sys.path.append(join(root, "code_generation/nest2"))
#from nineml.abstraction_layer.example_models import get_hierachical_iaf_3coba
from nineml.abstraction_layer.testing_utils import TestableComponent
from nineml.abstraction_layer.flattening import ComponentFlattener
import pyNN.neuron as sim
import pyNN.neuron.nineml as pyNNml
from pyNN.utility import init_logging
init_logging(None, debug=True)
sim.setup(timestep=0.1, min_delay=0.1)
#test_component = get_hierachical_iaf_3coba()
test_component = TestableComponent('hierachical_iaf_3coba')()
from nineml.abstraction_layer.writers import DotWriter
DotWriter.write(test_component, 'test1.dot')
from nineml.abstraction_layer.writers import XMLWriter
XMLWriter.write(test_component, 'iaf_3coba.xml')
celltype_cls = pyNNml.nineml_celltype_from_model(
name="iaf_3coba",
nineml_model=test_component,
synapse_components=[
pyNNml.CoBaSyn(namespace='AMPA', weight_connector='q'),
pyNNml.CoBaSyn(namespace='GABAa', weight_connector='q'),
pyNNml.CoBaSyn(namespace='GABAb', weight_connector='q'),
])
parameters = {
'iaf.cm': 1.0,
'iaf.gl': 50.0,
'iaf.taurefrac': 5.0,
'iaf.vrest': -65.0,
'iaf.vreset': -65.0,
'iaf.vthresh': -50.0,
'AMPA.tau': 2.0,
'GABAa.tau': 5.0,
'GABAb.tau': 50.0,
'AMPA.vrev': 0.0,
'GABAa.vrev': -70.0,
'GABAb.vrev': -95.0,
}
parameters = ComponentFlattener.flatten_namespace_dict(parameters)
cells = sim.Population(1, celltype_cls, parameters)
cells.initialize('iaf_V', parameters['iaf_vrest'])
cells.initialize('tspike', -1e99) # neuron not refractory at start
cells.initialize('regime', 1002) # temporary hack
input = sim.Population(3, sim.SpikeSourceArray)
numpy.random.seed(12345)
input[0].spike_times = numpy.add.accumulate(
numpy.random.exponential(1000.0 / 100.0, size=1000))
input[1].spike_times = numpy.add.accumulate(
numpy.random.exponential(1000.0 / 20.0, size=1000))
input[2].spike_times = numpy.add.accumulate(
numpy.random.exponential(1000.0 / 50.0, size=1000))
connector = sim.OneToOneConnector(weights=1.0, delays=0.5)
conn = [
sim.Projection(input[0:1], cells, connector, target='AMPA'),
sim.Projection(input[1:2], cells, connector, target='GABAa'),
sim.Projection(input[2:3], cells, connector, target='GABAb')
]
cells._record('iaf_V')
cells._record('AMPA_g')
cells._record('GABAa_g')
cells._record('GABAb_g')
cells.record()
sim.run(100.0)
cells.recorders['iaf_V'].write("Results/nineml_neuron.V",
filter=[cells[0]])
cells.recorders['AMPA_g'].write("Results/nineml_neuron.g_exc",
filter=[cells[0]])
cells.recorders['GABAa_g'].write("Results/nineml_neuron.g_gabaA",
filter=[cells[0]])
cells.recorders['GABAb_g'].write("Results/nineml_neuron.g_gagaB",
filter=[cells[0]])
t = cells.recorders['iaf_V'].get()[:, 1]
v = cells.recorders['iaf_V'].get()[:, 2]
gInhA = cells.recorders['GABAa_g'].get()[:, 2]
gInhB = cells.recorders['GABAb_g'].get()[:, 2]
gExc = cells.recorders['AMPA_g'].get()[:, 2]
if plot_and_show:
import pylab
pylab.subplot(211)
pylab.plot(t, v)
pylab.ylabel('voltage [mV]')
pylab.suptitle("AMPA, GABA_A, GABA_B")
pylab.subplot(212)
pylab.plot(t, gInhA, label='GABA_A')
pylab.plot(t, gInhB, label='GABA_B')
pylab.plot(t, gExc, label='AMPA')
pylab.ylabel('conductance [nS]')
pylab.xlabel('t [ms]')
pylab.legend()
pylab.show()
sim.end()
def run(plot_and_show=True):
import sys
from os.path import abspath, realpath, join
import numpy
import nineml
root = abspath(join(realpath(nineml.__path__[0]), "../../.."))
sys.path.append(join(root, "lib9ml/python/examples/AL"))
sys.path.append(join(root, "code_generation/nmodl"))
sys.path.append(join(root, "code_generation/nest2"))
#from nineml.abstraction_layer.example_models import get_hierachical_iaf_3coba
from nineml.abstraction_layer.testing_utils import TestableComponent
from nineml.abstraction_layer.flattening import ComponentFlattener
import pyNN.neuron as sim
import pyNN.neuron.nineml as pyNNml
from pyNN.utility import init_logging
init_logging(None, debug=True)
sim.setup(timestep=0.1, min_delay=0.1)
#test_component = get_hierachical_iaf_3coba()
test_component = TestableComponent('hierachical_iaf_3coba')()
from nineml.abstraction_layer.writers import DotWriter
DotWriter.write(test_component, 'test1.dot')
from nineml.abstraction_layer.writers import XMLWriter
XMLWriter.write(test_component, 'iaf_3coba.xml')
celltype_cls = pyNNml.nineml_celltype_from_model(
name = "iaf_3coba",
nineml_model = test_component,
synapse_components = [
pyNNml.CoBaSyn( namespace='AMPA', weight_connector='q' ),
pyNNml.CoBaSyn( namespace='GABAa', weight_connector='q' ),
pyNNml.CoBaSyn( namespace='GABAb', weight_connector='q' ),
]
)
parameters = {
'iaf.cm': 1.0,
'iaf.gl': 50.0,
'iaf.taurefrac': 5.0,
'iaf.vrest': -65.0,
'iaf.vreset': -65.0,
'iaf.vthresh': -50.0,
'AMPA.tau': 2.0,
'GABAa.tau': 5.0,
'GABAb.tau': 50.0,
'AMPA.vrev': 0.0,
'GABAa.vrev': -70.0,
'GABAb.vrev': -95.0,
}
parameters = ComponentFlattener.flatten_namespace_dict( parameters )
cells = sim.Population(1, celltype_cls, parameters)
cells.initialize('iaf_V', parameters['iaf_vrest'])
cells.initialize('tspike', -1e99) # neuron not refractory at start
cells.initialize('regime', 1002) # temporary hack
input = sim.Population(3, sim.SpikeSourceArray)
numpy.random.seed(12345)
input[0].spike_times = numpy.add.accumulate(numpy.random.exponential(1000.0/100.0, size=1000))
input[1].spike_times = numpy.add.accumulate(numpy.random.exponential(1000.0/20.0, size=1000))
input[2].spike_times = numpy.add.accumulate(numpy.random.exponential(1000.0/50.0, size=1000))
connector = sim.OneToOneConnector(weights=1.0, delays=0.5)
conn = [sim.Projection(input[0:1], cells, connector, target='AMPA'),
sim.Projection(input[1:2], cells, connector, target='GABAa'),
sim.Projection(input[2:3], cells, connector, target='GABAb')]
cells._record('iaf_V')
cells._record('AMPA_g')
cells._record('GABAa_g')
cells._record('GABAb_g')
cells.record()
sim.run(100.0)
cells.recorders['iaf_V'].write("Results/nineml_neuron.V", filter=[cells[0]])
cells.recorders['AMPA_g'].write("Results/nineml_neuron.g_exc", filter=[cells[0]])
cells.recorders['GABAa_g'].write("Results/nineml_neuron.g_gabaA", filter=[cells[0]])
cells.recorders['GABAb_g'].write("Results/nineml_neuron.g_gagaB", filter=[cells[0]])
t = cells.recorders['iaf_V'].get()[:,1]
v = cells.recorders['iaf_V'].get()[:,2]
gInhA = cells.recorders['GABAa_g'].get()[:,2]
gInhB = cells.recorders['GABAb_g'].get()[:,2]
gExc = cells.recorders['AMPA_g'].get()[:,2]
if plot_and_show:
import pylab
pylab.subplot(211)
pylab.plot(t,v)
pylab.ylabel('voltage [mV]')
pylab.suptitle("AMPA, GABA_A, GABA_B")
pylab.subplot(212)
pylab.plot(t,gInhA,label='GABA_A')
pylab.plot(t,gInhB, label='GABA_B')
pylab.plot(t,gExc, label='AMPA')
pylab.ylabel('conductance [nS]')
pylab.xlabel('t [ms]')
pylab.legend()
pylab.show()
sim.end()