def updateTicks(tickDtMap):
"""Try to assign dt values to ticks.
Parameters
----------
tickDtMap: dict
map from tick-no. to dt value. if it is empty, then default dt
values are assigned to the ticks.
"""
for tickNo, dt in tickDtMap.items():
if tickNo >= 0 and dt > 0.0:
_moose.setClock(tickNo, dt)
if all([(v == 0) for v in tickDtMap.values()]):
setDefaultDt()
def updateTicks(tickDtMap):
"""Try to assign dt values to ticks.
Parameters
----------
tickDtMap: dict
map from tick-no. to dt value. if it is empty, then default dt
values are assigned to the ticks.
"""
for tickNo, dt in tickDtMap.items():
if tickNo >= 0 and dt > 0.0:
_moose.setClock(tickNo, dt)
if all([(v == 0) for v in tickDtMap.values()]):
setDefaultDt()
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 setDefaultDt(elecdt=1e-5, chemdt=0.01, tabdt=1e-5, plotdt1=1.0, plotdt2=0.25e-3):
"""Setup the ticks with dt values.
Parameters
----------
elecdt: dt for ticks used in computing electrical biophysics, like
neuronal compartments, ion channels, synapses, etc.
chemdt: dt for chemical computations like enzymatic reactions.
tabdt: dt for lookup tables
plotdt1: dt for chemical kinetics plotting
plotdt2: dt for electrical simulations
"""
_moose.setClock(0, elecdt)
_moose.setClock(1, elecdt)
_moose.setClock(2, elecdt)
_moose.setClock(3, elecdt)
_moose.setClock(4, chemdt)
_moose.setClock(5, chemdt)
_moose.setClock(6, tabdt)
_moose.setClock(7, tabdt)
_moose.setClock(8, plotdt1) # kinetics sim
_moose.setClock(9, plotdt2) # electrical sim
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 setDefaultDt(elecdt=1e-5,
chemdt=0.01,
tabdt=1e-5,
plotdt1=1.0,
plotdt2=0.25e-3):
"""Setup the ticks with dt values.
Parameters
----------
elecdt: dt for ticks used in computing electrical biophysics, like
neuronal compartments, ion channels, synapses, etc.
chemdt: dt for chemical computations like enzymatic reactions.
tabdt: dt for lookup tables
plotdt1: dt for chemical kinetics plotting
plotdt2: dt for electrical simulations
"""
_moose.setClock(0, elecdt)
_moose.setClock(1, elecdt)
_moose.setClock(2, elecdt)
_moose.setClock(3, elecdt)
_moose.setClock(4, chemdt)
_moose.setClock(5, chemdt)
_moose.setClock(6, tabdt)
_moose.setClock(7, tabdt)
_moose.setClock(8, plotdt1) # kinetics sim
_moose.setClock(9, plotdt2) # electrical sim
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()