def assignTicks(tickTargetMap):
"""
Assign ticks to target elements.
Parameters
----------
tickTargetMap:
Map from tick no. to target path and method. The path can be wildcard expression also.
"""
if len(tickTargetMap) == 0:
assignDefaultTicks()
for tickNo, target in tickTargetMap.items():
if not isinstance(target, basestring):
if len(target) == 1:
_moose.useClock(tickNo, target[0], 'process')
elif len(target) == 2:
_moose.useClock(tickNo, target[0], target[1])
else:
_moose.useClock(tickNo, target, 'process')
def assignTicks(tickTargetMap):
"""
Assign ticks to target elements.
Parameters
----------
tickTargetMap:
Map from tick no. to target path and method. The path can be wildcard expression also.
"""
if len(tickTargetMap) == 0:
assignDefaultTicks()
for tickNo, target in tickTargetMap.items():
if not isinstance(target, basestring):
if len(target) == 1:
_moose.useClock(tickNo, target[0], 'process')
elif len(target) == 2:
_moose.useClock(tickNo, target[0], target[1])
else:
_moose.useClock(tickNo, target, 'process')
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 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 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 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 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 use clock 3
_moose.setClock(STIMCLOCK, simdt) # Ca/ion pools use clock 3
_moose.setClock(PLOTCLOCK, plotdt) # for tables
for simpath in simpaths:
_moose.useClock(PLOTCLOCK, simpath + "/##[TYPE=Table]", "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(ELECCLOCK, simpath + "/##[TYPE=LeakyIaF]", "process")
_moose.useClock(ELECCLOCK, simpath + "/##[TYPE=IntFire]", "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")
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.class_
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 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")