def _handle_input(self, domain, time, M_i, M_e, cell_models,
stimulus=None, applied_current=None):
# Check input and store attributes
msg = "Expecting domain to be a Mesh instance, not %r" % domain
assert isinstance(domain, Mesh), msg
self._domain = domain
msg = "Expecting time to be a Constant instance, not %r." % time
assert isinstance(time, Constant) or time is None, msg
self._time = time
self._intracellular_conductivity = M_i
self._extracellular_conductivity = M_e
# Handle cell_models
self._cell_models = handle_markerwise(cell_models, CardiacCellModel)
if isinstance(self._cell_models, Markerwise):
msg = "Different cell_models are currently not supported."
error(msg)
# Handle stimulus
self._stimulus = handle_markerwise(stimulus, GenericFunction)
# Handle applied current
ac = applied_current
self._applied_current = handle_markerwise(ac, GenericFunction)
def handle_markerwise(g, classtype):
# Handle stimulus
if (g is None \
or isinstance(g, classtype) \
or isinstance(g, Markerwise) \
or isinstance(g, object)): ## HAHAHA
return g
else:
msg = "Expecting stimulus to be a %s or Markerwise, not %r " \
% (str(classtype), g)
error(msg)
def set_initial_conditions(self, **init):
"Update initial_conditions in model"
for init_name, init_value in init.items():
if init_name not in self._initial_conditions:
error("'%s' is not a parameter in %s" %(init_name, self))
if not isinstance(init_value, (float, int, GenericFunction)):
error("'%s' is not a scalar or a GenericFunction" % init_name)
if isinstance(init_value, GenericFunction) and \
init_value.value_size() != 1:
error("expected the value_size of '%s' to be 1" % init_name)
self._initial_conditions[init_name] = init_value
def set_parameters(self, **params):
"Update parameters in model"
for param_name, param_value in params.items():
if param_name not in self._parameters:
error("'%s' is not a parameter in %s" %(param_name, self))
if not isinstance(param_value, (float, int, GenericFunction)):
error("'%s' is not a scalar or a GenericFunction" % param_name)
if isinstance(param_value, GenericFunction) and \
param_value.value_size() != 1:
error("expected the value_size of '%s' to be 1" % param_name)
self._parameters[param_name] = param_value
def I(self, v, s, time=None, index=None):
if index is None:
error("(Domain) index must be specified for multi cell models")
# Extract which cell model index (given by index in incoming tuple)
k = self._key_to_cell_model[index]
return self._cell_models[k].I(v, s, time)
def num_states(self):
"""Return number of state variables (in addition to the
membrane potential)."""
error("Must overload num_states")
def I(self, v, s, time=None):
"Return the ionic current."
error("Must define I = I(v, s)")
def F(self, v, s, time=None):
"Return right-hand side for state variable evolution."
error("Must define F = F(v, s)")
