def setUp(self):
'''Initialize storehouse
'''
self.compartments = _moose.wildcardFind('/##[TYPE=Compartment]')
self.tables = _moose.wildcardFind('/##[TYPE=Table]')
self.pulse_gens = _moose.wildcardFind('/##[TYPE=PulseGen]')
self.clocks = _moose.wildcardFind('/##[TYPE=Clock]')
self.nonZeroClockIds = None
def assignDefaultTicks(modelRoot='/model', dataRoot='/data', solver='hsolve'):
if isinstance(modelRoot, _moose.melement) or isinstance(
modelRoot, _moose.vec):
modelRoot = modelRoot.path
if isinstance(dataRoot, _moose.melement) or isinstance(
dataRoot, _moose.vec):
dataRoot = dataRoot.path
if solver != 'hsolve' or len(
_moose.wildcardFind('%s/##[ISA=HSolve]' % (modelRoot))) == 0:
_moose.useClock(0, '%s/##[ISA=Compartment]' % (modelRoot), 'init')
_moose.useClock(1, '%s/##[ISA=Compartment]' % (modelRoot), 'process')
_moose.useClock(2, '%s/##[ISA=HHChannel]' % (modelRoot), 'process')
# _moose.useClock(2, '%s/##[ISA=ChanBase]' % (modelRoot), 'process')
_moose.useClock(0, '%s/##[ISA=IzhikevichNrn]' % (modelRoot), 'process')
_moose.useClock(0, '%s/##[ISA=GapJunction]' % (modelRoot), 'process')
_moose.useClock(0, '%s/##[ISA=HSolve]' % (modelRoot), 'process')
_moose.useClock(1, '%s/##[ISA=LeakyIaF]' % (modelRoot), 'process')
_moose.useClock(1, '%s/##[ISA=IntFire]' % (modelRoot), 'process')
_moose.useClock(1, '%s/##[ISA=SpikeGen]' % (modelRoot), 'process')
_moose.useClock(1, '%s/##[ISA=PulseGen]' % (modelRoot), 'process')
_moose.useClock(1, '%s/##[ISA=StimulusTable]' % (modelRoot), 'process')
_moose.useClock(1, '%s/##[ISA=TimeTable]' % (modelRoot), 'process')
_moose.useClock(2, '%s/##[ISA=HHChannel2D]' % (modelRoot), 'process')
_moose.useClock(2, '%s/##[ISA=SynChan]' % (modelRoot), 'process')
_moose.useClock(2, '%s/##[ISA=MgBlock]' % (modelRoot), 'process')
_moose.useClock(3, '%s/##[ISA=CaConc]' % (modelRoot), 'process')
_moose.useClock(3, '%s/##[ISA=Func]' % (modelRoot), 'process')
# The voltage clamp circuit depends critically on the dt used for
# computing soma Vm and need to be on a clock with dt=elecdt.
_moose.useClock(0, '%s/##[ISA=DiffAmp]' % (modelRoot), 'process')
_moose.useClock(0, '%s/##[ISA=VClamp]' % (modelRoot), 'process')
_moose.useClock(0, '%s/##[ISA=PIDController]' % (modelRoot), 'process')
_moose.useClock(0, '%s/##[ISA=RC]' % (modelRoot), 'process')
# Special case for kinetics models
kinetics = _moose.wildcardFind('%s/##[FIELD(name)=kinetics]' % modelRoot)
if len(kinetics) > 0:
# Do nothing for kinetics models - until multiple scheduling issue is fixed.
_moose.useClock(4, '%s/##[ISA!=PoolBase]' % (kinetics[0].path),
'process')
_moose.useClock(5, '%s/##[ISA==PoolBase]' % (kinetics[0].path),
'process')
_moose.useClock(18, '%s/##[ISA=Table2]' % (dataRoot), 'process')
else:
# input() function is called in Table. process() which gets
# called at each timestep. When a message is connected
# explicitly to input() dest field, it is driven by the sender
# and process() adds garbage value to the vector. Hence not to
# be scheduled.
for tab in _moose.wildcardFind('%s/##[ISA=Table]' % (dataRoot)):
if len(tab.neighbors['input']) == 0:
_moose.useClock(9, tab.path, 'process')
def assignDefaultTicks(modelRoot='/model', dataRoot='/data', solver='hsolve'):
print 'assignDefaultTicks'
if isinstance(modelRoot, _moose.melement) or isinstance(modelRoot, _moose.vec):
modelRoot = modelRoot.path
if isinstance(dataRoot, _moose.melement) or isinstance(dataRoot, _moose.vec):
dataRoot = dataRoot.path
if solver != 'hsolve' or len(_moose.wildcardFind('%s/##[ISA=HSolve]' % (modelRoot))) == 0:
_moose.useClock(0, '%s/##[ISA=Compartment]' % (modelRoot), 'init')
_moose.useClock(1, '%s/##[ISA=Compartment]' % (modelRoot), 'process')
_moose.useClock(2, '%s/##[ISA=HHChannel]' % (modelRoot), 'process')
# _moose.useClock(2, '%s/##[ISA=ChanBase]' % (modelRoot), 'process')
_moose.useClock(0, '%s/##[ISA=IzhikevichNrn]' % (modelRoot), 'process')
_moose.useClock(0, '%s/##[ISA=GapJunction]' % (modelRoot), 'process')
_moose.useClock(0, '%s/##[ISA=HSolve]' % (modelRoot), 'process')
_moose.useClock(1, '%s/##[ISA=LeakyIaF]' % (modelRoot), 'process')
_moose.useClock(1, '%s/##[ISA=IntFire]' % (modelRoot), 'process')
_moose.useClock(1, '%s/##[ISA=SpikeGen]' % (modelRoot), 'process')
_moose.useClock(1, '%s/##[ISA=PulseGen]' % (modelRoot), 'process')
_moose.useClock(1, '%s/##[ISA=StimulusTable]' % (modelRoot), 'process')
_moose.useClock(1, '%s/##[ISA=TimeTable]' % (modelRoot), 'process')
_moose.useClock(2, '%s/##[ISA=HHChannel2D]' % (modelRoot), 'process')
_moose.useClock(2, '%s/##[ISA=SynChan]' % (modelRoot), 'process')
_moose.useClock(2, '%s/##[ISA=MgBlock]' % (modelRoot), 'process')
_moose.useClock(3, '%s/##[ISA=CaConc]' % (modelRoot), 'process')
_moose.useClock(3, '%s/##[ISA=Func]' % (modelRoot), 'process')
# The voltage clamp circuit depends critically on the dt used for
# computing soma Vm and need to be on a clock with dt=elecdt.
_moose.useClock(0, '%s/##[ISA=DiffAmp]' % (modelRoot), 'process')
_moose.useClock(0, '%s/##[ISA=VClamp]' % (modelRoot), 'process')
_moose.useClock(0, '%s/##[ISA=PIDController]' % (modelRoot), 'process')
_moose.useClock(0, '%s/##[ISA=RC]' % (modelRoot), 'process')
# Special case for kinetics models
kinetics = _moose.wildcardFind('%s/##[FIELD(name)=kinetics]' % modelRoot)
if len(kinetics) > 0:
# Do nothing for kinetics models - until multiple scheduling issue is fixed.
pass
# _moose.useClock(4, '%s/##[ISA!=PoolBase]' % (kinetics[0].path), 'process')
# _moose.useClock(5, '%s/##[ISA==PoolBase]' % (kinetics[0].path), 'process')
# _moose.useClock(8, '%s/##[ISA=Table]' % (dataRoot), 'process')
else:
# input() function is called in Table. process() which gets
# called at each timestep. When a message is connected
# explicitly to input() dest field, it is driven by the sender
# and process() adds garbage value to the vector. Hence not to
# be scheduled.
for tab in _moose.wildcardFind('%s/##[ISA=Table]' % (dataRoot)):
if len(tab.neighbors['input']) == 0:
_moose.useClock(9, tab.path, 'process')
def getMoosePaths(pat, isRoot=True):
''' Return a list of paths for a given pattern. '''
if type(pat) != str:
pat = pat.path
assert type(pat) == str
moose_paths = [x.path for x in _moose.wildcardFind(pat)]
return moose_paths
def getMoosePaths(pat, isRoot=True):
''' Return a list of paths for a given pattern. '''
if type(pat) != str:
pat = pat.path
assert type(pat) == str
moose_paths = [x.path for x in _moose.wildcardFind(pat)]
return moose_paths
def findAllBut(moose_wildcard, stringToExclude):
allValidObjects = _moose.wildcardFind(moose_wildcard)
refinedList = []
for validObject in allValidObjects:
if validObject.path.find(stringToExclude) == -1:
refinedList.append(validObject)
return refinedList
def findAllBut(moose_wildcard, stringToExclude):
allValidObjects = _moose.wildcardFind(moose_wildcard)
refinedList = []
for validObject in allValidObjects:
if validObject.path.find(stringToExclude) == -1:
refinedList.append(validObject)
return refinedList
def resetSim(simpaths, simdt, plotdt, simmethod='hsolve'):
""" For each of the MOOSE paths in simpaths, this sets the clocks and finally resets MOOSE.
If simmethod=='hsolve', it sets up hsolve-s for each Neuron under simpaths, and clocks for hsolve-s too. """
print 'Solver:', simmethod
_moose.setClock(INITCLOCK, simdt)
_moose.setClock(ELECCLOCK, simdt) # The hsolve and ee methods use clock 1
_moose.setClock(CHANCLOCK, simdt) # hsolve uses clock 2 for mg_block, nmdachan and others.
_moose.setClock(POOLCLOCK, simdt) # Ca/ion pools & funcs use clock 3
_moose.setClock(STIMCLOCK, simdt) # Ca/ion pools & funcs use clock 3
_moose.setClock(PLOTCLOCK, plotdt) # for tables
for simpath in simpaths:
## User can connect [qty]Out of an element to input of Table or
## requestOut of Table to get[qty] of the element.
## Scheduling the Table to a clock tick, will call process() of the Table
## which will send a requestOut and overwrite any value set by input(),
## thus adding garbage value to the vector. Hence schedule only if
## input message is not connected to the Table.
for table in _moose.wildcardFind(simpath+'/##[TYPE=Table]'):
if len(table.neighbors['input']) == 0:
_moose.useClock(PLOTCLOCK, table.path, 'process')
_moose.useClock(ELECCLOCK, simpath+'/##[TYPE=PulseGen]', 'process')
_moose.useClock(STIMCLOCK, simpath+'/##[TYPE=DiffAmp]', 'process')
_moose.useClock(STIMCLOCK, simpath+'/##[TYPE=VClamp]', 'process')
_moose.useClock(STIMCLOCK, simpath+'/##[TYPE=PIDController]', 'process')
_moose.useClock(STIMCLOCK, simpath+'/##[TYPE=RC]', 'process')
_moose.useClock(STIMCLOCK, simpath+'/##[TYPE=TimeTable]', 'process')
_moose.useClock(ELECCLOCK, simpath+'/##[TYPE=LeakyIaF]', 'process')
_moose.useClock(ELECCLOCK, simpath+'/##[TYPE=IntFire]', 'process')
_moose.useClock(ELECCLOCK, simpath+'/##[TYPE=IzhikevichNrn]', 'process')
_moose.useClock(ELECCLOCK, simpath+'/##[TYPE=SpikeGen]', 'process')
_moose.useClock(ELECCLOCK, simpath+'/##[TYPE=Interpol]', 'process')
_moose.useClock(ELECCLOCK, simpath+'/##[TYPE=Interpol2D]', 'process')
_moose.useClock(CHANCLOCK, simpath+'/##[TYPE=HHChannel2D]', 'process')
_moose.useClock(CHANCLOCK, simpath+'/##[TYPE=SynChan]', 'process')
## If simmethod is not hsolve, set clocks for the biophysics,
## else just put a clock on the hsolve:
## hsolve takes care of the clocks for the biophysics
if 'hsolve' not in simmethod.lower():
print 'Using exp euler'
_moose.useClock(INITCLOCK, simpath+'/##[TYPE=Compartment]', 'init')
_moose.useClock(ELECCLOCK, simpath+'/##[TYPE=Compartment]', 'process')
_moose.useClock(CHANCLOCK, simpath+'/##[TYPE=HHChannel]', 'process')
_moose.useClock(POOLCLOCK, simpath+'/##[TYPE=CaConc]', 'process')
_moose.useClock(POOLCLOCK, simpath+'/##[TYPE=Func]', 'process')
else: # use hsolve, one hsolve for each Neuron
print 'Using hsolve'
element = _moose.Neutral(simpath)
for childid in element.children:
childobj = _moose.Neutral(childid)
classname = childobj.className
if classname in ['Neuron']:
neuronpath = childobj.path
h = _moose.HSolve( neuronpath+'/solve' )
h.dt = simdt
h.target = neuronpath
_moose.useClock(INITCLOCK, h.path, 'process')
_moose.reinit()
def __init__(self, *args):
super(Backend, self).__init__()
self.args = args
self.compartments = []
self.pulseGens = []
self.tables = []
# A set of tuple of sourceCompartment.path and targetCompartment.path
self.connections = set()
self.clock = _moose.wildcardFind('/clock')[0]
def modelInfo(path = '/##', **kwargs):
"""Generate the list of all available moose-elements in model
"""
info("Couting elements in model under %s" % path)
msg = []
types = [ "Table", "Table2", "Compartment", "Pool", "BufPool", "Enz", "Reac" ]
for t in types:
paths = moose.wildcardFind("{}[TYPE={}]".format(path, t))
if len(paths) > 0:
msg.append("{:>20} : {}".format(t, len(paths)))
return "\n".join(msg)
def writeGraphviz(filename=None, pat='/##[TYPE=Compartment]'):
'''This is a generic function. It takes the the pattern, search for paths
and write a graphviz file.
'''
def fix(path):
'''Fix a given path so it can be written to a graphviz file'''
# If no [0] is at end of the path then append it.
global pathPat
if not pathPat.match(path):
path = path + '[0]'
return path
pathList = getMoosePaths(pat)
compList = _moose.wildcardFind(pat)
if not compList:
debug.dump("WARN"
, "No compartment found"
, frame = inspect.currentframe()
)
return None
dot = []
dot.append("digraph G {")
dot.append("\tconcentrate=true;")
for c in compList:
if c.neighbors['raxial']:
for n in c.neighbors['raxial']:
lhs = fix(c.path)
rhs = fix(n.path)
dot.append('\t"{}" -> "{}";'.format(lhs, rhs))
elif c.neighbors['axial']:
for n in c.neighbors['axial']:
lhs = fix(c.path)
rhs = fix(n.path)
dot.append('\t"{}" -> "{}" [dir=back];'.format(lhs, rhs))
else:
p = fix(c.path)
dot.append('\t"{}"'.format(p))
dot.append('}')
dot = '\n'.join(dot)
if not filename:
print(dot)
else:
with open(filename, 'w') as graphviz:
debug.dump("INFO"
, "Writing compartment topology to file {}".format(filename)
)
graphviz.write(dot)
return True
def writeGraphviz(filename=None, pat='/##[TYPE=Compartment]'):
'''This is a generic function. It takes the the pattern, search for paths
and write a graphviz file.
'''
def fix(path):
'''Fix a given path so it can be written to a graphviz file'''
# If no [0] is at end of the path then append it.
global pathPat
if not pathPat.match(path):
path = path + '[0]'
return path
pathList = getMoosePaths(pat)
compList = _moose.wildcardFind(pat)
if not compList:
debug.dump("WARN"
, "No compartment found"
, frame = inspect.currentframe()
)
dot = []
dot.append("digraph G {")
dot.append("\tconcentrate=true;")
for c in compList:
if c.neighbors['raxial']:
for n in c.neighbors['raxial']:
lhs = fix(c.path)
rhs = fix(n.path)
dot.append('\t"{}" -> "{}";'.format(lhs, rhs))
elif c.neighbors['axial']:
for n in c.neighbors['axial']:
lhs = fix(c.path)
rhs = fix(n.path)
dot.append('\t"{}" -> "{}" [dir=back];'.format(lhs, rhs))
else:
p = fix(c.path)
dot.append('\t"{}"'.format(p))
dot.append('}')
dot = '\n'.join(dot)
if not filename:
print(dot)
else:
with open(filename, 'w') as graphviz:
debug.dump("INFO"
, "Writing compartment topology to file {}".format(filename)
)
graphviz.write(dot)
return True
def autoposition(root):
"""Automatically set the positions of the endpoints of all the
compartments under `root`.
This keeps x and y constant and extends the positions in
z-direction only. This of course puts everything in a single line
but suffices for keeping electrical properties intact.
TODO: in future we may want to create the positions for nice
visual layout as well. My last attempt resulted in some
compartments overlapping in space.
"""
compartments = _moose.wildcardFind('%s/##[TYPE=Compartment]' % (root.path))
stack = [
compartment for compartment in map(_moose.element, compartments)
if len(compartment.neighbors['axial']) == 0
]
if len(stack) != 1:
raise Exception(
'There must be one and only one top level compartment. Found %d' %
(len(topcomp_list)))
ret = stack[0]
while len(stack) > 0:
comp = stack.pop()
parentlist = comp.neighbors['axial']
parent = None
if len(parentlist) > 0:
parent = parentlist[0]
comp.x0, comp.y0, comp.z0, = parent.x, parent.y, parent.z
else:
comp.x0, comp.y0, comp.z0, = (0, 0, 0)
if comp.length > 0:
comp.x, comp.y, comp.z, = comp.x0, comp.y0, comp.z0 + comp.length
else:
# for spherical compartments x0, y0, z0 are centre
# position nad x,y,z are on the surface
comp.x, comp.y, comp.z, = comp.x0, comp.y0, comp.z0 + comp.diameter / 2.0
# We take z == 0 as an indicator that this compartment has not
# been processed before - saves against inadvertent loops.
stack.extend([
childcomp
for childcomp in map(_moose.element, comp.neighbors['raxial'])
if childcomp.z == 0
])
return ret
def assignDefaultTicks(modelRoot="/model", dataRoot="/data"):
_moose.useClock(0, "%s/##[ISA=Compartment]" % (modelRoot), "init")
_moose.useClock(1, "%s/##[ISA=LeakyIaF]" % (modelRoot), "process")
_moose.useClock(1, "%s/##[ISA=IntFire]" % (modelRoot), "process")
_moose.useClock(1, "%s/##[ISA=Compartment]" % (modelRoot), "process")
_moose.useClock(1, "%s/##[ISA=PulseGen]" % (modelRoot), "process")
_moose.useClock(2, "%s/##[ISA=ChanBase]" % (modelRoot), "process")
_moose.useClock(2, "%s/##[ISA=MgBlock]" % (modelRoot), "process")
_moose.useClock(3, "%s/##[ISA=CaConc]" % (modelRoot), "process")
_moose.useClock(7, "%s/##[ISA=DiffAmp]" % (modelRoot), "process")
_moose.useClock(7, "%s/##[ISA=VClamp]" % (modelRoot), "process")
_moose.useClock(7, "%s/##[ISA=PIDController]" % (modelRoot), "process")
_moose.useClock(7, "%s/##[ISA=RC]" % (modelRoot), "process")
# Special case for kinetics models
kinetics = _moose.wildcardFind("%s/##[FIELD(name)=kinetics]" % modelRoot)
if len(kinetics) > 0:
_moose.useClock(4, "%s/##[ISA!=PoolBase]" % (kinetics[0].path), "process")
_moose.useClock(5, "%s/##[ISA==PoolBase]" % (kinetics[0].path), "process")
_moose.useClock(8, "%s/##[ISA=Table]" % (dataRoot), "process")
else:
_moose.useClock(9, "%s/##[ISA=Table]" % (dataRoot), "process")
def autoposition(root):
"""Automatically set the positions of the endpoints of all the
compartments under `root`.
This keeps x and y constant and extends the positions in
z-direction only. This of course puts everything in a single line
but suffices for keeping electrical properties intact.
TODO: in future we may want to create the positions for nice
visual layout as well. My last attempt resulted in some
compartments overlapping in space.
"""
compartments = _moose.wildcardFind("%s/##[TYPE=Compartment]" % (root.path))
stack = [
compartment for compartment in map(_moose.element, compartments) if len(compartment.neighbours["axial"]) == 0
]
if len(stack) != 1:
raise Exception("There must be one and only one top level compartment. Found %d" % (len(topcomp_list)))
ret = stack[0]
while len(stack) > 0:
comp = stack.pop()
parentlist = comp.neighbours["axial"]
parent = None
if len(parentlist) > 0:
parent = parentlist[0]
comp.x0, comp.y0, comp.z0, = parent.x, parent.y, parent.z
else:
comp.x0, comp.y0, comp.z0, = (0, 0, 0)
if comp.length > 0:
comp.x, comp.y, comp.z, = comp.x0, comp.y0, comp.z0 + comp.length
else:
# for spherical compartments x0, y0, z0 are centre
# position nad x,y,z are on the surface
comp.x, comp.y, comp.z, = comp.x0, comp.y0, comp.z0 + comp.diameter / 2.0
# We take z == 0 as an indicator that this compartment has not
# been processed before - saves against inadvertent loops.
stack.extend([childcomp for childcomp in map(_moose.element, comp.neighbours["raxial"]) if childcomp.z == 0])
return ret
def getComparments(self, **kwargs):
'''Get all compartments in moose '''
comps = _moose.wildcardFind('/##[TYPE=Compartment]')
self.compartments = comps
def getPulseGens(self, **kwargs):
""" Get all the pulse generators """
self.pulseGens = _moose.wildcardFind('/##[TYPE=PulseGen]')
def getTables(self, **kwargs):
""" Get all table we are recording from"""
self.tables = _moose.wildcardFind('/##[TYPE=Table]')
def resetSim(simpaths, simdt, plotdt, simmethod='hsolve'):
""" For each of the MOOSE paths in simpaths, this sets the clocks and finally resets MOOSE.
If simmethod=='hsolve', it sets up hsolve-s for each Neuron under simpaths, and clocks for hsolve-s too. """
print 'Solver:', simmethod
_moose.setClock(INITCLOCK, simdt)
_moose.setClock(ELECCLOCK, simdt) # The hsolve and ee methods use clock 1
_moose.setClock(
CHANCLOCK,
simdt) # hsolve uses clock 2 for mg_block, nmdachan and others.
_moose.setClock(POOLCLOCK, simdt) # Ca/ion pools & funcs use clock 3
_moose.setClock(STIMCLOCK, simdt) # Ca/ion pools & funcs use clock 3
_moose.setClock(PLOTCLOCK, plotdt) # for tables
for simpath in simpaths:
## User can connect [qty]Out of an element to input of Table or
## requestOut of Table to get[qty] of the element.
## Scheduling the Table to a clock tick, will call process() of the Table
## which will send a requestOut and overwrite any value set by input(),
## thus adding garbage value to the vector. Hence schedule only if
## input message is not connected to the Table.
for table in _moose.wildcardFind(simpath + '/##[TYPE=Table]'):
if len(table.neighbors['input']) == 0:
_moose.useClock(PLOTCLOCK, table.path, 'process')
_moose.useClock(ELECCLOCK, simpath + '/##[TYPE=PulseGen]', 'process')
_moose.useClock(STIMCLOCK, simpath + '/##[TYPE=DiffAmp]', 'process')
_moose.useClock(STIMCLOCK, simpath + '/##[TYPE=VClamp]', 'process')
_moose.useClock(STIMCLOCK, simpath + '/##[TYPE=PIDController]',
'process')
_moose.useClock(STIMCLOCK, simpath + '/##[TYPE=RC]', 'process')
_moose.useClock(STIMCLOCK, simpath + '/##[TYPE=TimeTable]', 'process')
_moose.useClock(ELECCLOCK, simpath + '/##[TYPE=LeakyIaF]', 'process')
_moose.useClock(ELECCLOCK, simpath + '/##[TYPE=IntFire]', 'process')
_moose.useClock(ELECCLOCK, simpath + '/##[TYPE=IzhikevichNrn]',
'process')
_moose.useClock(ELECCLOCK, simpath + '/##[TYPE=SpikeGen]', 'process')
_moose.useClock(ELECCLOCK, simpath + '/##[TYPE=Interpol]', 'process')
_moose.useClock(ELECCLOCK, simpath + '/##[TYPE=Interpol2D]', 'process')
_moose.useClock(CHANCLOCK, simpath + '/##[TYPE=HHChannel2D]',
'process')
_moose.useClock(CHANCLOCK, simpath + '/##[TYPE=SynChan]', 'process')
## If simmethod is not hsolve, set clocks for the biophysics,
## else just put a clock on the hsolve:
## hsolve takes care of the clocks for the biophysics
if 'hsolve' not in simmethod.lower():
print 'Using exp euler'
_moose.useClock(INITCLOCK, simpath + '/##[TYPE=Compartment]',
'init')
_moose.useClock(ELECCLOCK, simpath + '/##[TYPE=Compartment]',
'process')
_moose.useClock(CHANCLOCK, simpath + '/##[TYPE=HHChannel]',
'process')
_moose.useClock(POOLCLOCK, simpath + '/##[TYPE=CaConc]', 'process')
_moose.useClock(POOLCLOCK, simpath + '/##[TYPE=Func]', 'process')
else: # use hsolve, one hsolve for each Neuron
print 'Using hsolve'
element = _moose.Neutral(simpath)
for childid in element.children:
childobj = _moose.Neutral(childid)
classname = childobj.className
if classname in ['Neuron']:
neuronpath = childobj.path
h = _moose.HSolve(neuronpath + '/solve')
h.dt = simdt
h.target = neuronpath
_moose.useClock(INITCLOCK, h.path, 'process')
_moose.reinit()