def build_mod(cls, leak_chl, modfile_set):
base_writer = MM_ModFileWriterBase(suffix=leak_chl.get_neuron_suffix())
gbar_name = 'gLk'
e_rev_name = 'eLk'
g_scale_name = 'gScale'
gbar_units = NEURONChlWriterLeak.Units[gbar_name]
e_rev_units = NEURONChlWriterLeak.Units[e_rev_name]
# Parameters:
# {name: (value, unit, range)}
base_writer.parameters = {
gbar_name: (leak_chl.conductance.rescale(gbar_units).magnitude, (gbar_units), None),
e_rev_name: (leak_chl.reversalpotential.rescale(e_rev_units).magnitude, (e_rev_units), None),
g_scale_name: (1.0, None, None)
}
base_writer.currentequation = '(v-%s) * %s * %s' % (e_rev_name, gbar_name, g_scale_name)
base_writer.conductanceequation = '%s * %s' % (gbar_name, g_scale_name)
modtxt = base_writer.generate_modfile()
mod_file = ModFile(name=leak_chl.name, modtxt=modtxt)
modfile_set.append(mod_file)
def build_mod(cls, alphabeta_beta_chl, modfile_set):
gbar_name = 'gBar'
e_rev_name = 'eLk'
g_scale_name = 'gScale'
base_writer = MM_ModFileWriterBase(suffix=alphabeta_beta_chl.get_neuron_suffix())
# Naming Conventions:
state_tau = lambda s: '%stau' % s
state_inf = lambda s: '%sinf' % s
state_alpha = lambda s: '%s_alpha' % s
state_beta = lambda s: '%s_beta' % s
# State Equations and initial values:
for s in alphabeta_beta_chl.statevars:
base_writer.internalstates[s] = "%s" % state_inf(s) , "%s'=(%s-%s)/%s" % (s, state_inf(s), s, state_tau(s))
# Parameters:
# {name: (value, unit, range)}
base_writer.parameters = {
#gbar_name: (alphabeta_beta_chl.conductance.toval(ounit="S/cm2"), ("S/cm2"), None),
#e_rev_name: (alphabeta_beta_chl.reversalpotential.toval("mV"), ("mV"), None)
gbar_name: (alphabeta_beta_chl.conductance.rescale("S/cm2").magnitude, ("S/cm2"), None),
e_rev_name: (alphabeta_beta_chl.reversalpotential.rescale("mV").magnitude, ("mV"), None),
g_scale_name: (1.0, None, None)
}
# Rates:
# name : (locals, code), unit
for s in alphabeta_beta_chl.statevars:
base_writer.rates[state_alpha(s)] = (("", state_alpha(s) + "= StdAlphaBeta(%f, %f, %f, %f, %f, v)" % tuple(alphabeta_beta_chl.statevars[s][0]))), None
#base_writer.rates[state_beta(s)] = (("", state_beta(s) + "= StdBetaBeta(%f, %f, %f, %f, %f, %f, %f, %f, %f, %f, %f, v)" % tuple(alphabeta_beta_chl.statevars[s][1] + alphabeta_beta_chl.statevars[s][2] + [alphabeta_beta_chl.beta2threshold.toval(ounit="mV")]))), None
base_writer.rates[state_beta(s)] = (("", state_beta(s) + "= StdBetaBeta(%f, %f, %f, %f, %f, %f, %f, %f, %f, %f, %f, v)" % tuple(alphabeta_beta_chl.statevars[s][1] + alphabeta_beta_chl.statevars[s][2] + [alphabeta_beta_chl.beta2threshold.rescale("mV").magnitude]))), None
base_writer.rates[state_inf(s)] = (("", state_inf(s) + "= %s/(%s+%s)" % (state_alpha(s), state_alpha(s), state_beta(s))), None)
base_writer.rates[state_tau(s)] = (("", state_tau(s) + "= 1.0/(%s+%s)" % (state_alpha(s), state_beta(s))), "ms")
base_writer.ratecalcorder.extend([state_alpha(s), state_beta(s), state_inf(s), state_tau(s)])
base_writer.currentequation = "(v-%s) * %s * %s * %s" % (e_rev_name, gbar_name, alphabeta_beta_chl.eqn, g_scale_name)
base_writer.conductanceequation = "%s * %s * %s" % (gbar_name, alphabeta_beta_chl.eqn, g_scale_name)
#base_writer.currentequation = "(v-%s) * %s * %s" % (e_rev_name, gbar_name, alphabeta_beta_chl.eqn)
base_writer.functions = """
FUNCTION StdAlphaBeta(A, B, C, D, E, V){ StdAlphaBeta = (A + B*V) / (C + exp((D+V)/E)) }
FUNCTION StdBetaBeta(A, B, C, D, E, A2, B2, C2, D2, E2, beta2Threshold, V)
{
if(V < beta2Threshold)
{
StdBetaBeta = (A + B*V) / (C + exp((D+V)/E))
}
else
{
StdBetaBeta = (A2 + B2*V) / (C2 + exp((D2+V)/E2))
}
}
"""
txt = base_writer.generate_modfile()
mod_file = ModFile(name=alphabeta_beta_chl.name, modtxt=txt)
modfile_set.append(mod_file)
def build_mod(cls, alphabeta_beta_chl, modfile_set):
gbar_name = 'gBar'
e_rev_name = 'eLk'
g_scale_name = 'gScale'
base_writer = MM_ModFileWriterBase(suffix=alphabeta_beta_chl.get_neuron_suffix())
# Naming Conventions:
state_tau = lambda s: '%stau' % s
state_inf = lambda s: '%sinf' % s
state_alpha = lambda s: '%s_alpha' % s
state_beta = lambda s: '%s_beta' % s
# State Equations and initial values:
for s in alphabeta_beta_chl.statevars:
base_writer.internalstates[s] = "%s" % state_inf(s) , "%s'=(%s-%s)/%s" % (s, state_inf(s), s, state_tau(s))
# Parameters:
# {name: (value, unit, range)}
base_writer.parameters = {
#gbar_name: (alphabeta_beta_chl.conductance.toval(ounit="S/cm2"), ("S/cm2"), None),
#e_rev_name: (alphabeta_beta_chl.reversalpotential.toval("mV"), ("mV"), None)
gbar_name: (alphabeta_beta_chl.conductance.rescale("S/cm2").magnitude, ("S/cm2"), None),
e_rev_name: (alphabeta_beta_chl.reversalpotential.rescale("mV").magnitude, ("mV"), None),
g_scale_name: (1.0, None, None)
}
# Rates:
# name : (locals, code), unit
for s in alphabeta_beta_chl.statevars:
base_writer.rates[state_alpha(s)] = (("", state_alpha(s) + "= StdAlphaBeta(%f, %f, %f, %f, %f, v)" % tuple(alphabeta_beta_chl.statevars[s][0]))), None
#base_writer.rates[state_beta(s)] = (("", state_beta(s) + "= StdBetaBeta(%f, %f, %f, %f, %f, %f, %f, %f, %f, %f, %f, v)" % tuple(alphabeta_beta_chl.statevars[s][1] + alphabeta_beta_chl.statevars[s][2] + [alphabeta_beta_chl.beta2threshold.toval(ounit="mV")]))), None
base_writer.rates[state_beta(s)] = (("", state_beta(s) + "= StdBetaBeta(%f, %f, %f, %f, %f, %f, %f, %f, %f, %f, %f, v)" % tuple(alphabeta_beta_chl.statevars[s][1] + alphabeta_beta_chl.statevars[s][2] + [alphabeta_beta_chl.beta2threshold.rescale("mV").magnitude]))), None
base_writer.rates[state_inf(s)] = (("", state_inf(s) + "= %s/(%s+%s)" % (state_alpha(s), state_alpha(s), state_beta(s))), None)
base_writer.rates[state_tau(s)] = (("", state_tau(s) + "= 1.0/(%s+%s)" % (state_alpha(s), state_beta(s))), "ms")
base_writer.ratecalcorder.extend([state_alpha(s), state_beta(s), state_inf(s), state_tau(s)])
base_writer.currentequation = "(v-%s) * %s * %s * %s" % (e_rev_name, gbar_name, alphabeta_beta_chl.eqn, g_scale_name)
base_writer.conductanceequation = "%s * %s * %s" % (gbar_name, alphabeta_beta_chl.eqn, g_scale_name)
#base_writer.currentequation = "(v-%s) * %s * %s" % (e_rev_name, gbar_name, alphabeta_beta_chl.eqn)
base_writer.functions = """
FUNCTION StdAlphaBeta(A, B, C, D, E, V){ StdAlphaBeta = (A + B*V) / (C + exp((D+V)/E)) }
FUNCTION StdBetaBeta(A, B, C, D, E, A2, B2, C2, D2, E2, beta2Threshold, V)
{
if(V < beta2Threshold)
{
StdBetaBeta = (A + B*V) / (C + exp((D+V)/E))
}
else
{
StdBetaBeta = (A2 + B2*V) / (C2 + exp((D2+V)/E2))
}
}
"""
txt = base_writer.generate_modfile()
mod_file = ModFile(name=alphabeta_beta_chl.name, modtxt=txt)
modfile_set.append(mod_file)
def build_mod(cls, alphabeta_chl, modfile_set):
gbar_name = 'gBar'
e_rev_name = 'e_rev'
g_scale_name = 'gScale'
# gbarUnits = NEURONChlWriterAlphaBeta.Units[gbar_name]
# eRevUnits = NEURONChlWriterAlphaBeta.Units[e_rev_name]
base_writer = MM_ModFileWriterBase(suffix=alphabeta_chl.get_neuron_suffix())
# Naming Conventions:
state_tau = lambda s: '%stau' % s
state_inf = lambda s: '%sinf' % s
state_alpha = lambda s: '%s_alpha' % s
state_beta = lambda s: '%s_beta' % s
# State Equations and initial values:
for s in alphabeta_chl.statevars:
base_writer.internalstates[s] = "%s" % state_inf(s) , "%s'=(%s-%s)/%s" % (s, state_inf(s), s, state_tau(s))
# Parameters:
# {name: (value, unit, range)}
base_writer.parameters = {
gbar_name: (alphabeta_chl.conductance.rescale("S/cm2").magnitude, ("S/cm2"), None),
e_rev_name: (alphabeta_chl.reversalpotential.rescale("mV").magnitude, ("mV"), None),
g_scale_name: (1.0, None, None)
}
# Rates:
# name : (locals, code), unit
for s in alphabeta_chl.statevars:
base_writer.rates[state_alpha(s)] = (("", state_alpha(s) + "= StdAlphaBeta(%f, %f, %f, %f, %f, v)" % tuple(alphabeta_chl.statevars[s][0]))), None
base_writer.rates[state_beta(s)] = (("", state_beta(s) + "= StdAlphaBeta(%f, %f, %f, %f, %f, v)" % tuple(alphabeta_chl.statevars[s][1]))), None
base_writer.rates[state_inf(s)] = (("", state_inf(s) + "= %s/(%s+%s)" % (state_alpha(s), state_alpha(s), state_beta(s))), None)
base_writer.rates[state_tau(s)] = (("", state_tau(s) + "= 1.0/(%s+%s)" % (state_alpha(s), state_beta(s))), "ms")
base_writer.ratecalcorder.extend([state_alpha(s), state_beta(s), state_inf(s), state_tau(s)])
base_writer.currentequation = "(v-%s) * %s * %s * %s" % (e_rev_name, gbar_name, alphabeta_chl.eqn, g_scale_name)
base_writer.conductanceequation = "%s * %s * %s" % (gbar_name, alphabeta_chl.eqn, g_scale_name)
base_writer.functions = """FUNCTION StdAlphaBeta(A, B, C, D, E, V){ StdAlphaBeta = (A + B*V) / (C + exp((D+V)/E)) } """
txt = base_writer.generate_modfile()
mod_file = ModFile(name=alphabeta_chl.name, modtxt=txt, strict_modlunit=True)
modfile_set.append(mod_file)
def build_mod(cls, alphabeta_chl, modfile_set):
gbar_name = 'gBar'
e_rev_name = 'e_rev'
g_scale_name = 'gScale'
# gbarUnits = NEURONChlWriterAlphaBeta.Units[gbar_name]
# eRevUnits = NEURONChlWriterAlphaBeta.Units[e_rev_name]
base_writer = MM_ModFileWriterBase(
suffix=alphabeta_chl.get_neuron_suffix())
# Naming Conventions:
state_tau = lambda s: '%stau' % s
state_inf = lambda s: '%sinf' % s
state_alpha = lambda s: '%s_alpha' % s
state_beta = lambda s: '%s_beta' % s
# State Equations and initial values:
for s in alphabeta_chl.statevars:
base_writer.internalstates[s] = "%s" % state_inf(
s), "%s'=(%s-%s)/%s" % (s, state_inf(s), s, state_tau(s))
# Parameters:
# {name: (value, unit, range)}
base_writer.parameters = {
gbar_name: (alphabeta_chl.conductance.rescale("S/cm2").magnitude,
("S/cm2"), None),
e_rev_name:
(alphabeta_chl.reversalpotential.rescale("mV").magnitude, ("mV"),
None),
g_scale_name: (1.0, None, None)
}
# Rates:
# name : (locals, code), unit
for s in alphabeta_chl.statevars:
base_writer.rates[state_alpha(s)] = (
("", state_alpha(s) + "= StdAlphaBeta(%f, %f, %f, %f, %f, v)" %
tuple(alphabeta_chl.statevars[s][0]))), None
base_writer.rates[state_beta(s)] = (
("", state_beta(s) + "= StdAlphaBeta(%f, %f, %f, %f, %f, v)" %
tuple(alphabeta_chl.statevars[s][1]))), None
base_writer.rates[state_inf(s)] = (
("", state_inf(s) + "= %s/(%s+%s)" %
(state_alpha(s), state_alpha(s), state_beta(s))), None)
base_writer.rates[state_tau(s)] = (
("", state_tau(s) + "= 1.0/(%s+%s)" %
(state_alpha(s), state_beta(s))), "ms")
base_writer.ratecalcorder.extend(
[state_alpha(s),
state_beta(s),
state_inf(s),
state_tau(s)])
base_writer.currentequation = "(v-%s) * %s * %s * %s" % (
e_rev_name, gbar_name, alphabeta_chl.eqn, g_scale_name)
base_writer.conductanceequation = "%s * %s * %s" % (
gbar_name, alphabeta_chl.eqn, g_scale_name)
base_writer.functions = """FUNCTION StdAlphaBeta(A, B, C, D, E, V){ StdAlphaBeta = (A + B*V) / (C + exp((D+V)/E)) } """
txt = base_writer.generate_modfile()
mod_file = ModFile(name=alphabeta_chl.name, modtxt=txt)
modfile_set.append(mod_file)
def build_mod(cls, alphabeta_chl, modfile_set):
gbar_name = 'gBar'
e_rev_name = 'e_rev'
g_scale_name = 'gScale'
base_writer = \
MM_ModFileWriterBase(suffix=alphabeta_chl.get_neuron_suffix())
# Naming Conventions:
state_tau = lambda s: '%stau' % s
state_inf = lambda s: '%sinf' % s
# State Equations and initial values:
for s in alphabeta_chl.statevars_new:
base_writer.internalstates[s] = '%s' % state_inf(s), "%s'=(%s-%s)/%s" % (s, state_inf(s), s, state_tau(s))
# Parameters:
# {name: (value, unit, range)}
base_writer.parameters = {
gbar_name: (alphabeta_chl.conductance.rescale("S/cm2").magnitude, ("S/cm2"), None),
e_rev_name: (alphabeta_chl.reversalpotential.rescale("mV").magnitude, ("mV"), None),
g_scale_name: (1.0, None, None)
}
# Rates:
# name : (locals, code), unit
for s in alphabeta_chl.statevars_new:
base_writer.rates[state_inf(s)] = (('', state_inf(s) + "= %sInf(v)" % state_inf(s)), None)
base_writer.rates[state_tau(s)] = (('', state_tau(s) + "= %sTau(v)" % state_tau(s)), "ms")
base_writer.ratecalcorder.extend([state_inf(s), state_tau(s)])
base_writer.currentequation = '(v-%s) * %s * %s * %s' % (e_rev_name, gbar_name, alphabeta_chl.eqn, g_scale_name)
base_writer.conductanceequation = '%s * %s * %s' % (gbar_name, alphabeta_chl.eqn, g_scale_name)
base_writer.functions = """
VERBATIM
#include <gsl_wrapper.h>
ENDVERBATIM"""
def buildInterpolatorFunc(state, inftau, funcname):
if inftau == 'inf':
interp_str_x = ','.join(['%2.2f' % x for x in alphabeta_chl.statevars_new[s].V])
interp_str_y = ','.join(['%2.2f' % x for x in alphabeta_chl.statevars_new[s].inf])
elif inftau == 'tau':
interp_str_x = ','.join(['%2.2f' % x for x in alphabeta_chl.statevars_new[s].V])
interp_str_y = ','.join(['%2.2f' % x for x in alphabeta_chl.statevars_new[s].tau])
else:
assert False
variables = {'chlname':state_tau(s), 'nPts':len(alphabeta_chl.statevars_new[s].V), 'x0':interp_str_x, 'y0':interp_str_y, 'funcname':funcname }
f = """
FUNCTION %(funcname)s(V)
{
VERBATIM {
static void* pInterpolator = NULL;
if(!pInterpolator)
{
double x[%(nPts)s] = { %(x0)s };
double y[%(nPts)s] = { %(y0)s };
int nPts = %(nPts)d;
pInterpolator = makeIntWrapper(x, y, nPts);
}
_l%(funcname)s= interpolate2(_lV, pInterpolator);
}
ENDVERBATIM
}
\n\n""" % variables
return f
for s in alphabeta_chl.statevars_new:
base_writer.functions += buildInterpolatorFunc(state=s, inftau='inf', funcname='%sinfInf' % s)
base_writer.functions += buildInterpolatorFunc(state=s, inftau='tau', funcname='%stauTau' % s)
txt = base_writer.generate_modfile()
# TODO: Remove hard dependancy here
from morphforge.stdimports import RCMgr
additional_compile_flags = RCMgr.get('Neuron','additional_compile_flags') #"-I/home/michael/hw_to_come/morphforge/src/morphforgecontrib/simulation/neuron_gsl/cpp"
additional_link_flags = RCMgr.get('Neuron','additional_link_flags') # "-L/home/michael/hw_to_come/morphforge/src/morphforgecontrib/simulation/neuron_gsl/cpp -lgslwrapper -lgsl -lgslcblas"
mod_file = ModFile(name=alphabeta_chl.name, modtxt=txt, additional_compile_flags=additional_compile_flags, additional_link_flags=additional_link_flags)
modfile_set.append(mod_file)
def build_mod(cls, alphabeta_chl, modfile_set):
gbar_name = 'gBar'
e_rev_name = 'e_rev'
g_scale_name = 'gScale'
base_writer = \
MM_ModFileWriterBase(suffix=alphabeta_chl.get_neuron_suffix())
# Naming Conventions:
state_tau = lambda s: '%stau' % s
state_inf = lambda s: '%sinf' % s
# State Equations and initial values:
for s in alphabeta_chl.statevars_new:
base_writer.internalstates[s] = '%s' % state_inf(
s), "%s'=(%s-%s)/%s" % (s, state_inf(s), s, state_tau(s))
# Parameters:
# {name: (value, unit, range)}
base_writer.parameters = {
gbar_name: (alphabeta_chl.conductance.rescale("S/cm2").magnitude,
("S/cm2"), None),
e_rev_name:
(alphabeta_chl.reversalpotential.rescale("mV").magnitude, ("mV"),
None),
g_scale_name: (1.0, None, None)
}
# Rates:
# name : (locals, code), unit
for s in alphabeta_chl.statevars_new:
base_writer.rates[state_inf(s)] = (('', state_inf(s) +
"= %sInf(v)" % state_inf(s)),
None)
base_writer.rates[state_tau(s)] = (('', state_tau(s) +
"= %sTau(v)" % state_tau(s)),
"ms")
base_writer.ratecalcorder.extend([state_inf(s), state_tau(s)])
base_writer.currentequation = '(v-%s) * %s * %s * %s' % (
e_rev_name, gbar_name, alphabeta_chl.eqn, g_scale_name)
base_writer.conductanceequation = '%s * %s * %s' % (
gbar_name, alphabeta_chl.eqn, g_scale_name)
base_writer.functions = """
VERBATIM
#include <gsl_wrapper.h>
ENDVERBATIM"""
def buildInterpolatorFunc(state, inftau, funcname):
if inftau == 'inf':
interp_str_x = ','.join(
['%2.2f' % x for x in alphabeta_chl.statevars_new[s].V])
interp_str_y = ','.join(
['%2.2f' % x for x in alphabeta_chl.statevars_new[s].inf])
elif inftau == 'tau':
interp_str_x = ','.join(
['%2.2f' % x for x in alphabeta_chl.statevars_new[s].V])
interp_str_y = ','.join(
['%2.2f' % x for x in alphabeta_chl.statevars_new[s].tau])
else:
assert False
variables = {
'chlname': state_tau(s),
'nPts': len(alphabeta_chl.statevars_new[s].V),
'x0': interp_str_x,
'y0': interp_str_y,
'funcname': funcname
}
f = """
FUNCTION %(funcname)s(V)
{
VERBATIM {
static void* pInterpolator = NULL;
if(!pInterpolator)
{
double x[%(nPts)s] = { %(x0)s };
double y[%(nPts)s] = { %(y0)s };
int nPts = %(nPts)d;
pInterpolator = makeIntWrapper(x, y, nPts);
}
_l%(funcname)s= interpolate2(_lV, pInterpolator);
}
ENDVERBATIM
}
\n\n""" % variables
return f
for s in alphabeta_chl.statevars_new:
base_writer.functions += buildInterpolatorFunc(
state=s, inftau='inf', funcname='%sinfInf' % s)
base_writer.functions += buildInterpolatorFunc(
state=s, inftau='tau', funcname='%stauTau' % s)
txt = base_writer.generate_modfile()
# TODO: Remove hard dependancy here
additional_compile_flags = "-I/home/michael/hw_to_come/morphforge/src/morphforgecontrib/simulation/neuron_gsl/cpp"
additional_link_flags = "-L/home/michael/hw_to_come/morphforge/src/morphforgecontrib/simulation/neuron_gsl/cpp -lgslwrapper -lgsl -lgslcblas"
mod_file = ModFile(name=alphabeta_chl.name,
modtxt=txt,
additional_compile_flags=additional_compile_flags,
additional_link_flags=additional_link_flags)
modfile_set.append(mod_file)
