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LEMSbrian.py
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LEMSbrian.py
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import lems.api as lems
from brian2 import *
from brian2.equations.equations import SingleEquation
from brian2.equations.codestrings import Expression
from lems.model.component import ComponentType,Component
class LEMSBrian:
def __init__(self, filepath):
self.component_list = self.get_components_from_file(filepath)
""" List of all the components in the file
@type: LEMSBrianComponent """
self.component_type_list = self.get_component_types_from_file(filepath)
""" List of all the component types in the file
@type: LEMSBrianComponentType """
def get_component_type(self, name):
a = self.component_list[name]
b = a.type
return self.component_type_list[b]
def get_model_from_file(self, filepath):
""" @type: lems.model.model.Model"""
m = lems.Model()
m.add_include_directory('/home/snigdha/neuroml_dev/NeuroML2/NeuroML2CoreTypes')
m.import_from_file(filepath)
return m
def get_components_from_file(self, filepath):
""" Imports the file as a model and returns its components """
mod = self.get_model_from_file(filepath)
comp = mod.components
compdict = {}
for c in comp:
c.__class__ = LEMSBrianComponent
compdict[c.id] = c
return compdict
def get_component_types_from_file(self, filepath):
""" Imports the file as a model and returns its component_types """
mod = self.get_model_from_file(filepath)
comptypes = mod.component_types
comptypedict = {}
for c in comptypes:
c.__class__ = LEMSBrianComponentType
comptypedict[c.name] = c
return comptypedict
class LEMSBrianComponent(Component):
def __init__(self, id_, type_, **params):
Component.__init__(self, id_, type_, **params)
class LEMSBrianComponentType(ComponentType):
def __init__(self, name):
ComponentType.__init__(self, name)
self.uf = None
def get_neurongroup(self, size):
""" Creates a NeuronGroup of the component with id component_name
@type: brian2.groups.neurongroup.NeuronGroup """
model = self.get_equations()
_threshold = self.get_threshold()
_reset = self.get_reset()
_refractory = self.get_refractory()
N = size
neuron_group = NeuronGroup(N, model, threshold = _threshold, reset = _reset, refractory = _refractory)
return neuron_group
def get_equations(self):
""" Returns the Equations of the component with id component_name
@type: brian2.equations.equations.Equations """
dyn = self.dynamics
tds = dyn.time_derivatives
eqs = []
_flags=[]
if(tds):
for t in tds:
ex = Expression(t.value)
self.get_refractory()
for i in self.uf:
if(self.uf==t):
_flags=['unless refractory']
s = SingleEquation('differential equation', t.variable, self.timederivative_dimension(t), 'float', ex, flags=_flags)
eqs.append(s)
rgs = dyn.regimes
for r in rgs:
rtds = r.time_derivatives
if(rtds):
for rtd in rtds:
ex = Expression(rtd.value)
self.get_refractory()
for i in self.uf :
if(i==rtd):
_flags=['unless refractory']
s = SingleEquation('differential equation', rtd.variable, self.timederivative_dimension(rtd), 'float', ex, flags=_flags)
eqs.append(s)
dvs = dyn.derived_variables
for d in dvs:
if(d.value):
ex = Expression(d.value)
s = SingleEquation('subexpression', d.name, self.getBrianSIUnits(d.dimension), 'float', ex)
eqs.append(s)
return Equations(eqs)
def timederivative_dimension(self, TimeDerivative):
""" Converts the TimeDerivative object into a string and return it
@type: str """
svs = self.dynamics.state_variables
d = None
for s in svs:
if(TimeDerivative.variable==s.name):
d = s.dimension
td_dim=self.getBrianSIUnits(d)
return td_dim
def getBrianSIUnits(self, dimension):
if(dimension=="voltage"): return volt;
if(dimension=="conductance"): return siemens;
if(dimension=="time"): return second;
if(dimension=="per_time"): return 1/second;
if(dimension=="capacitance"): return farad;
if(dimension=="current"): return amp;
if(dimension=="current"): return amp;
if(dimension=="volume"): return meter3;
if(dimension=="concentration"): return mmole;
def getUnitSymbol(self, dimension):
if(dimension=="voltage"): return "V";
if(dimension=="conductance"): return "S";
if(dimension=="time"): return "s";
if(dimension=="per_time"): return "1/s";
if(dimension=="capacitance"): return "F";
if(dimension=="current"): return "A";
if(dimension=="volume"): return "m";
if(dimension=="concentration"): return "mol";
def replace_operators(self, line):
line = line.replace(".gt." , ">")
line = line.replace(".lt." , "<")
line = line.replace(".leq." , "<=")
line = line.replace(".geq." , ">=")
line = line.replace(".eq." , "==")
line = line.replace(".neq." , "!=")
line = line.replace(".and." , "and")
line = line.replace(".or." , "or")
return line
def get_threshold(self):
""" returns the threshold conditions as a string if present otherwise, returns threshold=None
@type: str"""
rgs = self.dynamics.regimes
for r in rgs:
if(r.initial==True): main_regime = r
elif(r.initial==False): refractory_regime = r
roc = main_regime.event_handlers
threshcond = ""
for oc in roc:
if(type(oc) is lems.OnCondition):
threshcond = self.replace_operators(oc.test)
else: threshcond=None
return threshcond
def get_reset(self):
""" returns a multi string with the reset statements if present, otherwise returns reset=None
@type: str"""
resetcond = ""
# OnConditions in dynamics
dyn = self.dynamics
for ev in dyn.event_handlers:
if(type(ev) is lems.OnCondition):
for sa in ev.actions:
if(type(sa) is lems.StateAssignment):
resetcond+=sa.variable + " = " + sa.value + "\n"
rgs = self.dynamics.regimes
for r in rgs:
if(r.initial==True): main_regime = r
elif(r.initial==False): refractory_regime = r
# OnConditions in main regimes
roc = main_regime.event_handlers
for oc in roc:
if(type(oc) is lems.OnCondition):
for sa in oc.actions:
if(type(sa) is lems.StateAssignment):
resetcond+=sa.variable + " = " + sa.value + "\n"
# OnEntry in refractory regime
roe = refractory_regime.event_handlers
for oe in roe:
if(type(oe) is lems.OnEntry):
for sa in oe.actions:
if(type(sa) is lems.StateAssignment):
resetcond+=sa.variable + " = " + sa.value + "\n"
return resetcond
def get_refractory(self):
""" return the refractory conditions if present, otherwise returns refractory=None
@type: str"""
#OnCondition in refractory regime
rgs = self.dynamics.regimes
if len(rgs)>2 :
raise NotImplementedError("More than 2 regimes are not supported")
else :
refract = ""
for r in rgs:
if(r.initial==True): main_regime = r
elif(r.initial==False): refractory_regime = r
if(refractory_regime.time_derivatives):
for i in refractory_regime.time_derivatives:
if not (i.variable in main_regime.time_derivatives):
raise NotImplementedError
else:
self.uf=main_regime.time_derivatives
roc = refractory_regime.event_handlers
for oc in roc:
if(type(oc) is lems.OnCondition):
refract = "not(" + self.replace_operators(oc.test) + ")"
return refract
else:
refract = None
return refract