def write_lems_file(lems_model, lems_file_name, validate=False):
lems_model.export_to_file(lems_file_name)
if validate:
from lems.base.util import validate_lems
validate_lems(lems_file_name)
def write_lems_file(lems_model, lems_file_name, validate=False):
lems_model.export_to_file(lems_file_name)
if validate:
from lems.base.util import validate_lems
validate_lems(lems_file_name)
def test_load_write_xml(self):
model = Model()
file_name = 'lems/test/hhcell_resaved2.xml'
model.import_from_file(file_name)
file_name2 = 'lems/test/hhcell_resaved3.xml'
model.export_to_file(file_name2)
print("----------------------------------------------")
print(open(file_name2,'r').read())
print("----------------------------------------------")
print("Written generated LEMS to %s"%file_name2)
from lems.base.util import validate_lems
validate_lems(file_name2)
ddt = src_svar.drift.replace('**', '^')
mass.dynamics.add(lems.StateVariable(name, 'none', name))
mass.dynamics.add(lems.TimeDerivative(name, '(%s)/MSEC'%ddt))
mass.add(lems.Exposure(name, 'none'))
''' On condition is not need on the model but NeuroML requires its definition -->
<OnCondition test="r .lt. 0">
<EventOut port="spike"/>
</OnCondition>'''
oc = lems.OnCondition(test='v .gt. 0')
oc.actions.append(lems.EventOut(port='spike'))
mass.dynamics.add(oc)
return model
if __name__ == '__main__':
import os
from lems.base.util import validate_lems
here = os.path.dirname(os.path.abspath(__file__))
for model in model_instances():
fname = os.path.join(here, model.name + '.lems.xml')
try:
build_lems_for_model(model).export_to_file(fname)
print('Successfully built %s'%fname)
validate_lems(fname)
except Exception as exc:
print('> Error converting %s: %s'%(fname,exc))
iaf1.add(lems.Parameter('reset', 'voltage'))
iaf1.add(lems.Parameter('refractoryPeriod', 'time'))
iaf1.add(lems.Parameter('capacitance', 'capacitance'))
iaf1.add(lems.Exposure('vexp', 'voltage'))
dp = lems.DerivedParameter('range', 'threshold - reset', 'voltage')
iaf1.add(dp)
iaf1.dynamics.add(lems.StateVariable('v','voltage', 'vexp'))
iaf1.dynamics.add(lems.DerivedVariable('v2',dimension='voltage', value='v*2'))
cdv = lems.ConditionalDerivedVariable('v_abs','voltage')
cdv.add(lems.Case('v .geq. 0','v'))
cdv.add(lems.Case('v .lt. 0','-1*v'))
iaf1.dynamics.add(cdv)
model.add(lems.Component('celltype_a', iaf1.name))
model.add(lems.Component('celltype_b', iaf1.name, threshold="20mV"))
fn = '/tmp/model.xml'
model.export_to_file(fn)
print("----------------------------------------------")
print(open(fn,'r').read())
print("----------------------------------------------")
print("Written generated LEMS to %s"%fn)
from lems.base.util import validate_lems
validate_lems(fn)
iaf1.add(lems.Parameter('reset', 'voltage'))
iaf1.add(lems.Parameter('refractoryPeriod', 'time'))
iaf1.add(lems.Parameter('capacitance', 'capacitance'))
iaf1.add(lems.Exposure('vexp', 'voltage'))
dp = lems.DerivedParameter('range', 'threshold - reset', 'voltage')
iaf1.add(dp)
iaf1.dynamics.add(lems.StateVariable('v','voltage', 'vexp'))
iaf1.dynamics.add(lems.DerivedVariable('v2',dimension='voltage', value='v*2'))
cdv = lems.ConditionalDerivedVariable('v_abs','voltage')
cdv.add(lems.Case('v .geq. 0','v'))
cdv.add(lems.Case('v .lt. 0','-1*v'))
iaf1.dynamics.add(cdv)
model.add(lems.Component('celltype_a', iaf1.name))
model.add(lems.Component('celltype_b', iaf1.name, threshold="20mV"))
fn = '/tmp/model.xml'
model.export_to_file(fn)
print("----------------------------------------------")
print(open(fn,'r').read())
print("----------------------------------------------")
print("Written generated LEMS to %s"%fn)
from lems.base.util import validate_lems
validate_lems(fn)
lorenz.dynamics.add(
lems.StateVariable(name="z", dimension="none", exposure="z"))
lorenz.dynamics.add(
lems.TimeDerivative(variable="x", value="( sigma * (y - x)) / sec"))
lorenz.dynamics.add(
lems.TimeDerivative(variable="y", value="( rho * x - y - x * z ) / sec"))
lorenz.dynamics.add(
lems.TimeDerivative(variable="z", value="( x * y - beta * z) / sec"))
onstart = lems.OnStart()
onstart.add(lems.StateAssignment(variable="x", value="x0"))
onstart.add(lems.StateAssignment(variable="y", value="y0"))
onstart.add(lems.StateAssignment(variable="z", value="z0"))
lorenz.dynamics.add(onstart)
model.add(
lems.Component(id_="lorenzCell",
type_=lorenz.name,
sigma="10",
beta="2.67",
rho="28",
x0="1.0",
y0="1.0",
z0="1.0"))
file_name = "LEMS_lorenz.xml"
model.export_to_file(file_name)
validate_lems(file_name)
