def test_coba_synapse():
nineml_component = TestableComponent('coba_synapse')()
if not nineml_component:
raise RuntimeError('Cannot load NineML component')
timeHorizon = 1
reportingInterval = 0.001
parameters = {
'CobaSyn.q': 4.0E-9,
'CobaSyn.tau': 0.005,
'CobaSyn.vrev': 0.0
}
initial_conditions = {
'CobaSyn.g': 1E-8,
}
analog_ports_expressions = {'CobaSyn.V': -0.050}
event_ports_expressions = {
'CobaSyn.spikeinput':
'' #'0.05, 0.10, 0.20, 0.30, 0.40, 0.50, 0.60, 0.70, 0.80, 0.90'
}
active_regimes = {'CobaSyn': 'cobadefaultregime'}
variables_to_report = {'CobaSyn.I': True}
inspector = nineml_component_inspector()
inspector.inspect(nineml_component,
timeHorizon=timeHorizon,
reportingInterval=reportingInterval,
parameters=parameters,
initial_conditions=initial_conditions,
active_regimes=active_regimes,
analog_ports_expressions=analog_ports_expressions,
event_ports_expressions=event_ports_expressions,
variables_to_report=variables_to_report)
results = inspector.showQtGUI()
return results, inspector
def test_iaf():
nineml_component = TestableComponent('iaf')()
if not nineml_component:
raise RuntimeError('Cannot load NineML component')
timeHorizon = 1
reportingInterval = 0.001
parameters = {
'iaf.cm': 0.2E-9,
'iaf.gl': 1E-8,
'iaf.taurefrac': 0.001,
'iaf.vreset': -0.060,
'iaf.vrest': -0.060,
'iaf.vthresh': -0.040
}
initial_conditions = {'iaf.V': -0.050, 'iaf.tspike': -1.0}
analog_ports_expressions = {'iaf.ISyn': 0.0}
event_ports_expressions = {}
active_regimes = {'iaf': 'subthresholdregime'}
variables_to_report = {'iaf.V': True}
inspector = nineml_component_inspector()
inspector.inspect(nineml_component,
timeHorizon=timeHorizon,
reportingInterval=reportingInterval,
parameters=parameters,
initial_conditions=initial_conditions,
active_regimes=active_regimes,
analog_ports_expressions=analog_ports_expressions,
event_ports_expressions=event_ports_expressions,
variables_to_report=variables_to_report)
results = inspector.showQtGUI()
return results, inspector
def test_Izhikevich():
nineml_component = TestableComponent('izhikevich')()
if not nineml_component:
raise RuntimeError('Cannot load NineML component')
timeHorizon = 1
reportingInterval = 0.001
parameters = {
"Izhikevich.a": 0.02,
"Izhikevich.b": 0.2,
"Izhikevich.c": -0.05,
"Izhikevich.d": 2.0,
"Izhikevich.theta": 0.03
}
initial_conditions = {"Izhikevich.U": 0.0, "Izhikevich.V": -0.07}
analog_ports_expressions = {"Izhikevich.Isyn": "0.1"}
event_ports_expressions = {}
active_regimes = {}
variables_to_report = {'Izhikevich.U': True, 'Izhikevich.V': True}
inspector = nineml_component_inspector()
inspector.inspect(nineml_component,
timeHorizon=timeHorizon,
reportingInterval=reportingInterval,
parameters=parameters,
initial_conditions=initial_conditions,
active_regimes=active_regimes,
analog_ports_expressions=analog_ports_expressions,
event_ports_expressions=event_ports_expressions,
variables_to_report=variables_to_report)
results = inspector.showQtGUI()
return results, inspector
def main(src=None):
build_dir = 'build/'
output_dir = 'output/'
print 'Clearing output directory: %s' % output_dir
clear_and_recreate_dir(output_dir)
# single_file_mode = os.path.isfile(src)
if src:
print ' Testing Component: %s' % src
src_files = [src]
else:
print ' Testing all Components.'
src_files = TestableComponent.list_available()
# src_files = glob.glob( src + '/*.py')
for src_file in src_files:
# Clear the build-dir
clear_and_recreate_dir(build_dir)
clear_and_recreate_dir('nineml_mechanisms')
# Load the file:
print ' -- Loading from file: %s' % src_file
t = TestableComponent(src_file)
# Run some tests:
TestXMLWriteReadWrite.test(t, build_dir=build_dir)
TestWriteDot.test(t, build_dir=build_dir)
if t.has_metadata():
if t.metadata.is_neuron_model:
test_write_mod(t)
if src:
flg = 'supports_test_pynn_neuron_std'
if t.metadata.__dict__.get(flg, False):
test_pynn_neuron_std(t)
# Save all the output files:
shutil.move(build_dir, output_dir)
shutil.move(os.path.join(output_dir, build_dir),
os.path.join(output_dir, src_file.replace('.py', '')))
print ' Everything Ran Fine'
print ' -------------------'
def test_other(component_name):
nineml_component = TestableComponent(component_name)()
if not nineml_component:
raise RuntimeError(
'Cannot load NineML component {0}'.format(component_name))
inspector = nineml_component_inspector()
inspector.inspect(nineml_component)
results = inspector.showQtGUI()
return results, inspector
def test_hierachical_iaf_1coba():
nineml_component = TestableComponent('hierachical_iaf_1coba')()
if not nineml_component:
raise RuntimeError('Cannot load NineML component')
timeHorizon = 1.0
reportingInterval = 0.001
initial_conditions = {
"iaf_1coba.iaf.tspike": -1.0,
"iaf_1coba.iaf.V": -0.060,
"iaf_1coba.cobaExcit.g": 0.0
}
parameters = {
"iaf_1coba.iaf.gl": 1E-8,
"iaf_1coba.iaf.vreset": -0.060,
"iaf_1coba.iaf.taurefrac": 0.001,
"iaf_1coba.iaf.vthresh": -0.040,
"iaf_1coba.iaf.vrest": -0.060,
"iaf_1coba.iaf.cm": 0.2E-9,
"iaf_1coba.cobaExcit.vrev": 0.0,
"iaf_1coba.cobaExcit.q": 4.0E-9,
"iaf_1coba.cobaExcit.tau": 0.005
}
variables_to_report = {
"iaf_1coba.cobaExcit.I": True,
"iaf_1coba.iaf.V": True
}
event_ports_expressions = {
"iaf_1coba.cobaExcit.spikeinput":
"0.05, 0.10, 0.20, 0.30, 0.40, 0.50, 0.60, 0.70, 0.80, 0.90"
}
active_regimes = {
"iaf_1coba.cobaExcit": "cobadefaultregime",
"iaf_1coba.iaf": "subthresholdregime"
}
analog_ports_expressions = {}
inspector = nineml_component_inspector()
inspector.inspect(nineml_component,
timeHorizon=timeHorizon,
reportingInterval=reportingInterval,
parameters=parameters,
initial_conditions=initial_conditions,
active_regimes=active_regimes,
analog_ports_expressions=analog_ports_expressions,
event_ports_expressions=event_ports_expressions,
variables_to_report=variables_to_report)
results = inspector.showQtGUI()
return results, inspector
"""
#import nineml.abstraction_layer as nineml
#import os
from nineml.abstraction_layer.testing_utils import TestableComponent
from nineml.abstraction_layer.flattening import flatten
#from nineml.abstraction_layer.flattening import ComponentFlattener
from nineml.abstraction_layer.component_modifiers import ComponentModifier
from nineml.utility import LocationMgr
#from nineml.abstraction_layer.visitors import RenameSymbol
LocationMgr.StdAppendToPath()
comp_data = TestableComponent('nestequivalent_iaf_cond_exp')
# Build the component:
component = comp_data()
component = flatten(component)
component.backsub_all()
ComponentModifier.close_all_reduce_ports(component=component)
# Copy the descriptive strings:
component.short_description = comp_data.metadata.short_description
component.long_description = comp_data.metadata.long_description
# Get the initial regime. If this component comes from an flattened component,
# then we should look up the new regime from the locations in the old
# components, hence the nedd for this code:
initial_regime = comp_data.metadata.initial_regime
.format(outdir, texFile))
res = os.system(
'/usr/bin/pdflatex -interaction=nonstopmode -output-directory {0} {1}'
.format(outdir, texFile))
else:
res = os.system(
'/usr/bin/pdflatex -interaction=nonstopmode {0}'.format(texFile))
res = os.system(
'/usr/bin/pdflatex -interaction=nonstopmode {0}'.format(texFile))
return res
def showFile(pdf):
if os.name == 'nt':
os.filestart(pdf)
elif os.name == 'posix':
os.system('/usr/bin/xdg-open ' + pdf)
if __name__ == "__main__":
component = 'hierachical_iaf_1coba'
tex = component + '.tex'
pdf = component + '.pdf'
nineml_component = TestableComponent(component)()
inspector = nineml_component_inspector()
inspector.inspect(nineml_component)
createLatexReport(inspector, [], 'nineml-tex-template.tex', tex)
res = createPDF(tex)
showFile(pdf)
"iaf_1coba.cobaExcit.I": True,
"iaf_1coba.iaf.V": True
}
spike_times = [str(t) for t in numpy.arange(0, 0.20, 0.005)]
#print(spike_times)
event_ports_expressions = {
"iaf_1coba.cobaExcit.spikeinput": '' #', '.join(spike_times)
}
active_regimes = {
"iaf_1coba.cobaExcit": "cobadefaultregime",
"iaf_1coba.iaf": "subthresholdregime"
}
analog_ports_expressions = {}
# Load the Component:
nineml_comp = TestableComponent('hierachical_iaf_1coba')()
if not nineml_comp:
raise RuntimeError('Cannot load NineML component')
# Create Log, Solver, DataReporter and Simulation object
log = daeBaseLog()
daesolver = daeIDAS()
#from daetools.solvers import pySuperLU as superlu
#lasolver = superlu.daeCreateSuperLUSolver()
#daesolver.SetLASolver(lasolver)
model = nineml_daetools_bridge(nineml_comp.name, nineml_comp, None, '')
simulation = nineml_daetools_simulation(
model,
timeHorizon=timeHorizon,
"""
Example of using a cell type defined in 9ML with pyNN.neuron
"""
#from std_pynn_simulation import std_pynn_simulation, RecordValue
from nineml.abstraction_layer.testing_utils import TestableComponent
from nineml.abstraction_layer.testing_utils import std_pynn_simulation, RecordValue
test_component = TestableComponent('hierachical_iaf_2coba')()
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,
'cobaExcit.tau': 2.0,
'cobaInhib.tau': 5.0,
'cobaExcit.vrev': 0.0,
'cobaInhib.vrev': -70.0,
}
initial_values = {
'iaf_V': parameters['iaf.vrest'],
'tspike': -1e99,
'regime': 1002,
}
synapse_components = [
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 test_generator():
testable_components = [TestableComponent(source_file)
for source_file in TestableComponent.list_available()]
nrn_components = [tc() for tc in testable_components] # if (tc.has_metadata() and tc.metadata.is_neuron_model)]
for tc in nrn_components:
yield write_and_compile_nmodl, tc
#import pyNN.neuron.nineml as pyNNml
import pyNN.nest as sim
import pyNN.nest.nineml as pyNNml
from pyNN.nest import simulator
from pyNN import common, recording
common.simulator = simulator
recording.simulator = simulator
from pyNN.utility import init_logging
init_logging(None, debug=True)
sim.setup(timestep=0.01, min_delay=0.1)
#testModel = get_hierachical_iaf_3coba()
testModel = TestableComponent('hierachical_iaf_3coba')
celltype_cls = pyNNml.nineml_celltype_from_model(
name="iaf_3coba",
nineml_model=testModel,
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,
"""
"""
from nineml.abstraction_layer.testing_utils import RecordValue, TestableComponent
from nineml.abstraction_layer import ComponentClass, flattening, writers
from nineml.abstraction_layer.testing_utils import std_pynn_simulation
# Load the Component:
coba1_base = TestableComponent('hierachical_iaf_1coba')
coba1 = coba1_base()
# Write the component back out to XML
writers.XMLWriter.write(coba1, 'TestOut_Coba1.xml')
writers.DotWriter.write(coba1, 'TestOut_Coba1.dot')
writers.DotWriter.build('TestOut_Coba1.dot')
# Simulate the Neuron:
records = [
RecordValue(what='iaf_V', tag='V', label='V'),
RecordValue(what='regime', tag='Regime', label='Regime'),
]
parameters = flattening.ComponentFlattener.flatten_namespace_dict({
'cobaExcit_tau':
5.0,
'cobaExcit_vrev':
0,
'iaf_cm':
1,
'iaf_gl':
def test_other(component_name):
nineml_component = TestableComponent(component_name)()
if not nineml_component:
raise RuntimeError('Cannot load NineML component {0}'.format(component_name))
inspector = nineml_component_inspector()
inspector.inspect(nineml_component)
results = inspector.showQtGUI()
return results, inspector
if __name__ == "__main__":
tests_data = []
tmpFolder = tempfile.gettempdir()
app = QtGui.QApplication(sys.argv)
components = sorted(TestableComponent.list_available())
component_name, ok = QtGui.QInputDialog.getItem(None, "nineml_desktop_app", "Select the testable component name", components, 0, False)
if not ok:
exit(0)
component_name = str(component_name)
if(component_name == 'iaf'):
results, inspector = test_iaf()
elif(component_name == 'coba_synapse'):
results, inspector = test_coba_synapse()
elif(component_name == 'hierachical_iaf_1coba'):
results, inspector = test_hierachical_iaf_1coba()
else:
results, inspector = test_other(component_name)
if results:
if not nineml_component:
raise RuntimeError(
'Cannot load NineML component {0}'.format(component_name))
inspector = nineml_component_inspector()
inspector.inspect(nineml_component)
results = inspector.showQtGUI()
return results, inspector
if __name__ == "__main__":
tests_data = []
tmpFolder = tempfile.gettempdir()
app = QtGui.QApplication(sys.argv)
components = sorted(TestableComponent.list_available())
component_name, ok = QtGui.QInputDialog.getItem(
None, "nineml_desktop_app", "Select the testable component name",
components, 0, False)
if not ok:
exit(0)
component_name = str(component_name)
if (component_name == 'iaf'):
results, inspector = test_iaf()
elif (component_name == 'coba_synapse'):
results, inspector = test_coba_synapse()
elif (component_name == 'hierachical_iaf_1coba'):
results, inspector = test_hierachical_iaf_1coba()
else:
results, inspector = test_other(component_name)