def make_multiinstantiate(self, special_properties, name, parameters):
"""
Adds ComponentType with MultiInstantiate in order to make
a population of neurons.
Parameters
----------
special_properties : dict
all variables to be defined in MultiInstantiate
name : str
MultiInstantiate component name
parameters : dict
all extra parameters needed
"""
PARAM_SUBSCRIPT = "_p"
self._model_namespace["ct_populationname"] = name+"Multi"
multi_ct = lems.ComponentType(self._model_namespace["ct_populationname"], extends=BASE_POPULATION)
structure = lems.Structure()
multi_ins = lems.MultiInstantiate(component_type=name,
number="N")
param_dict = {}
# number of neruons
multi_ct.add(lems.Parameter(name="N", dimension="none"))
# other parameters
for sp in special_properties:
if special_properties[sp] is None:
multi_ct.add(lems.Parameter(name=sp+PARAM_SUBSCRIPT, dimension=self._all_params_unit[sp]))
multi_ins.add(lems.Assign(property=sp, value=sp+PARAM_SUBSCRIPT))
param_dict[sp] = parameters[sp]
else:
# multi_ct.add(lems.Parameter(name=sp, dimension=self._all_params_unit[sp]))
# check if there are some units in equations
equation = special_properties[sp]
# add spaces around brackets to prevent mismatching
equation = re.sub("\(", " ( ", equation)
equation = re.sub("\)", " ) ", equation)
for i in get_identifiers(equation):
# iterator is a special case
if i == "i":
regexp_noletter = "[^a-zA-Z0-9]"
equation = re.sub("{re}i{re}".format(re=regexp_noletter),
" {} ".format(INDEX), equation)
# here it's assumed that we don't use Netwton in neuron models
elif i in name_to_unit and i != "N":
const_i = i+'const'
multi_ct.add(lems.Constant(name=const_i, symbol=const_i,
dimension=self._all_params_unit[sp], value="1"+i))
equation = re.sub(i, const_i, equation)
multi_ins.add(lems.Assign(property=sp, value=equation))
structure.add(multi_ins)
multi_ct.structure = structure
self._model.add(multi_ct)
param_dict = dict([(k+"_p", v) for k, v in param_dict.items()])
param_dict["N"] = self._nr_of_neurons
self._model_namespace["populationname"] = self._model_namespace["ct_populationname"] + "pop"
self._model_namespace["networkname"] = self._model_namespace["ct_populationname"] + "Net"
self.add_population(self._model_namespace["networkname"],
self._model_namespace["populationname"],
self._model_namespace["ct_populationname"],
**param_dict)
def _determine_parameters(self, paramdict):
"""
Iterator giving `lems.Parameter` for every parameter from *paramdict*.
"""
for var in paramdict:
if is_dimensionless(paramdict[var]):
self._all_params_unit[var] = "none"
yield lems.Parameter(var, "none")
else:
dim = _determine_dimension(paramdict[var])
self._all_params_unit[var] = dim
yield lems.Parameter(var, dim)
def build_lems_for_model(src):
model = lems.Model()
model.add(lems.Dimension('time', t=1))
# model.add(lems.Dimension('au'))
# primary element of the model is a mass model component
mass = lems.ComponentType(src.name, extends="baseCellMembPot")
model.add(mass)
######### Adding v is required to ease mapping to NEURON...
mass.dynamics.add(lems.StateVariable(name="v", dimension="voltage", exposure="v"))
mass.add(lems.Attachments(name="synapses",type_="basePointCurrentDL"))
for input in src.input:
mass.dynamics.add(lems.DerivedVariable(name=input,
dimension='none',
exposure=input,
select='synapses[*]/I',
reduce='add'))
mass.add(lems.Exposure(input, 'none'))
for key, val in src.const.items():
mass.add(lems.Parameter(key, 'none')) # TODO units
mass.add(lems.Constant(name="MSEC", dimension="time", value="1ms"))
mass.add(lems.Constant(name="PI", dimension="none", value="3.14159265359"))
states = []
der_vars = []
# for key in src.param:
# mass.add(lems.Parameter(key, 'au')) # TODO units
for key, val in src.auxex:
val = val.replace('**', '^')
mass.dynamics.add(lems.DerivedVariable(key, value=val))
for key in src.obsrv:
name_dv = key.replace('(','_').replace(')','').replace(' - ','_min_')
mass.dynamics.add(lems.DerivedVariable(name_dv, value=key, exposure=name_dv))
mass.add(lems.Exposure(name_dv, 'none'))
for src_svar in src.state_space:
name = src_svar.name
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
import lems.api as lems
model = lems.Model()
model.add(lems.Dimension('voltage', m=1, l=3, t=-3, i=-1))
model.add(lems.Dimension('time', t=1))
model.add(lems.Dimension('capacitance', m=-1, l=-2, t=4, i=2))
model.add(lems.Unit('milliVolt', 'mV', 'voltage', -3))
model.add(lems.Unit('milliSecond', 'ms', 'time', -3))
model.add(lems.Unit('microFarad', 'uF', 'capacitance', -12))
iaf1 = lems.ComponentType('iaf1')
model.add(iaf1)
iaf1.add(lems.Parameter('threshold', 'voltage'))
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.Dimension(name="time", t=1))
model.add(lems.Unit(name="second", symbol="s", dimension="time", power=1))
model.add(
lems.Unit(name="milli second", symbol="ms", dimension="time", power=-3))
lorenz = lems.ComponentType(
name="lorenz1963",
description=
"The Lorenz system is a simplified model for atomspheric convection, derived from the Navier Stokes equations"
)
model.add(lorenz)
lorenz.add(
lems.Parameter(name="sigma",
dimension="none",
description="Prandtl Number"))
lorenz.add(
lems.Parameter(name="beta",
dimension="none",
description="Also named b elsewhere"))
lorenz.add(
lems.Parameter(
name="rho",
dimension="none",
description="Related to the Rayleigh number, also named r elsewhere"))
lorenz.add(lems.Parameter(name="x0", dimension="none"))
lorenz.add(lems.Parameter(name="y0", dimension="none"))
lorenz.add(lems.Parameter(name="z0", dimension="none"))
def mdf_to_neuroml(graph, save_to=None, format=None, run_duration_sec=2):
print("Converting graph: %s to NeuroML" % (graph.id))
net = neuromllite.Network(id=graph.id)
net.notes = "NeuroMLlite export of {} graph: {}".format(
format if format else "MDF",
graph.id,
)
model = lems.Model()
lems_definitions = "%s_lems_definitions.xml" % graph.id
for node in graph.nodes:
print(" Node: %s" % node.id)
node_comp_type = "%s__definition" % node.id
node_comp = "%s__instance" % node.id
# Create the ComponentType which defines behaviour of the general class
ct = lems.ComponentType(node_comp_type, extends="baseCellMembPotDL")
ct.add(lems.Attachments("only_input_port", "basePointCurrentDL"))
ct.dynamics.add(
lems.DerivedVariable(name="V",
dimension="none",
value="0",
exposure="V"))
model.add(ct)
# Define the Component - an instance of the ComponentType
comp = lems.Component(node_comp, node_comp_type)
model.add(comp)
cell = neuromllite.Cell(id=node_comp,
lems_source_file=lems_definitions)
net.cells.append(cell)
pop = neuromllite.Population(
id=node.id,
size=1,
component=cell.id,
properties={
"color": "0.2 0.2 0.2",
"radius": 3
},
)
net.populations.append(pop)
if len(node.input_ports) > 1:
raise Exception(
"Currently only max 1 input port supported in NeuroML...")
for ip in node.input_ports:
ct.add(lems.Exposure(ip.id, "none"))
ct.dynamics.add(
lems.DerivedVariable(
name=ip.id,
dimension="none",
select="only_input_port[*]/I",
reduce="add",
exposure=ip.id,
))
on_start = None
for p in node.parameters:
print("Converting %s" % p)
if p.value is not None:
try:
v_num = float(p.value)
ct.add(lems.Parameter(p.id, "none"))
comp.parameters[p.id] = v_num
print(comp.parameters[p.id])
except Exception as e:
ct.add(lems.Exposure(p.id, "none"))
dv = lems.DerivedVariable(
name=p.id,
dimension="none",
value="%s" % (p.value),
exposure=p.id,
)
ct.dynamics.add(dv)
elif p.function is not None:
ct.add(lems.Exposure(p.id, "none"))
func_info = mdf_functions[p.function]
expr = func_info["expression_string"]
expr2 = substitute_args(expr, p.args)
for arg in p.args:
expr += ";{}={}".format(arg, p.args[arg])
dv = lems.DerivedVariable(name=p.id,
dimension="none",
value="%s" % (expr2),
exposure=p.id)
ct.dynamics.add(dv)
else:
ct.add(lems.Exposure(p.id, "none"))
ct.dynamics.add(
lems.StateVariable(name=p.id,
dimension="none",
exposure=p.id))
if p.default_initial_value:
if on_start is None:
on_start = lems.OnStart()
ct.dynamics.add(on_start)
sa = lems.StateAssignment(
variable=p.id,
value=str(evaluate_expr(p.default_initial_value)))
on_start.actions.append(sa)
if p.time_derivative:
td = lems.TimeDerivative(variable=p.id,
value=p.time_derivative)
ct.dynamics.add(td)
if len(node.output_ports) > 1:
raise Exception(
"Currently only max 1 output port supported in NeuroML...")
for op in node.output_ports:
ct.add(lems.Exposure(op.id, "none"))
ct.dynamics.add(
lems.DerivedVariable(name=op.id,
dimension="none",
value=op.value,
exposure=op.id))
only_output_port = "only_output_port"
ct.add(lems.Exposure(only_output_port, "none"))
ct.dynamics.add(
lems.DerivedVariable(
name=only_output_port,
dimension="none",
value=op.id,
exposure=only_output_port,
))
if len(graph.edges) > 0:
model.add(
lems.Include(
os.path.join(os.path.dirname(__file__),
"syn_definitions.xml")))
rsDL = neuromllite.Synapse(id="rsDL",
lems_source_file=lems_definitions)
net.synapses.append(rsDL)
# syn_id = 'silentSyn'
# silentSynDL = neuromllite.Synapse(id=syn_id, lems_source_file=lems_definitions)
for edge in graph.edges:
print(f" Edge: {edge.id} connects {edge.sender} to {edge.receiver}")
ssyn_id = "silentSyn_proj_%s" % edge.id
ssyn_id = "silentSyn_proj_%s" % edge.id
# ssyn_id = 'silentSynX'
silentDLin = neuromllite.Synapse(id=ssyn_id,
lems_source_file=lems_definitions)
model.add(lems.Component(ssyn_id, "silentRateSynapseDL"))
net.synapses.append(silentDLin)
net.projections.append(
neuromllite.Projection(
id="proj_%s" % edge.id,
presynaptic=edge.sender,
postsynaptic=edge.receiver,
synapse=rsDL.id,
pre_synapse=silentDLin.id,
type="continuousProjection",
weight=1,
random_connectivity=neuromllite.RandomConnectivity(
probability=1),
))
# Much more todo...
model.export_to_file(lems_definitions)
print("Nml net: %s" % net)
if save_to:
new_file = net.to_json_file(save_to)
print("Saved NML to: %s" % save_to)
################################################################################
### Build Simulation object & save as JSON
simtime = 1000 * run_duration_sec
dt = 0.1
sim = neuromllite.Simulation(
id="Sim%s" % net.id,
network=new_file,
duration=simtime,
dt=dt,
seed=123,
recordVariables={"OUTPUT": {
"all": "*"
}},
)
recordVariables = {}
for node in graph.nodes:
for ip in node.input_ports:
if not ip.id in recordVariables:
recordVariables[ip.id] = {}
recordVariables[ip.id][node.id] = 0
for p in node.parameters:
if p.is_stateful():
if not p.id in recordVariables:
recordVariables[p.id] = {}
recordVariables[p.id][node.id] = 0
for op in node.output_ports:
if not op.id in recordVariables:
recordVariables[op.id] = {}
recordVariables[op.id][node.id] = 0
sim.recordVariables = recordVariables
if save_to:
sf = sim.to_json_file()
print("Saved Simulation to: %s" % sf)
return net, sim
