def expr_to_obj(s, name=None):
""" Construct nineml objects from expressions """
from util import StrToExpr
# import re
# Is our job already done?
if isinstance(s, (RegimeElement)):
return s
# strip surrounding whitespace
s = s.strip()
# Do we have a alias?
if StrToExpr.is_alias(s):
return StrToExpr.alias(s)
# re for an expression -> groups into lhs, op, rhs
p_eqn = re.compile(
r"(?P<lhs>[a-zA-Z_]+[a-zA-Z_0-9]*(/?[a-zA-Z_]+[a-zA-Z_0-9]*)?)\s*(?P<op>[+\-*/:]?=)\s*(?P<rhs>.*)")
m = p_eqn.match(s)
if not m:
raise ValueError, "Not a valid nineml expression: %s" % s
# get lhs, op, rhs
lhs, op, rhs = [m.group(x) for x in ['lhs', 'op', 'rhs']]
# do we have an TimeDerivative?
# re for lhs for TimeDerivative
p_ode_lhs = re.compile(r"(?:d)([a-zA-Z_]+[a-zA-Z_0-9]*)/(?:d)([a-zA-Z_]+[a-zA-Z_0-9]*)")
m = p_ode_lhs.match(lhs)
if m:
if op != "=":
raise ValueError, "TimeDerivative lhs, but op not '=' in %s" % s
dep_var = m.group(1)
indep_var = m.group(2)
return TimeDerivative(dep_var, indep_var, rhs, name=name)
# Do we have an Inplace op?
# if op in Inplace.op_name_map.keys():
# return Inplace(lhs,op,rhs, name = name)
# Do we have an assignment?
if op == "=":
return StateAssignment(lhs, rhs, name=name)
# If we get here, what do we have?
raise ValueError, "Cannot map expr '%s' to a nineml Expression" % s
def __init__(self, regimes=None, aliases=None, state_variables=None):
"""Dynamics object constructor
:param aliases: A list of aliases, which must be either |Alias|
objects or ``string``s.
:param regimes: A list containing at least one |Regime| object.
:param state_variables: An optional list of the state variables,
which can either be |StateVariable| objects or `string` s. If
provided, it must match the inferred state-variables from the
regimes; if it is not provided it will be inferred
automatically.
"""
aliases = nineml.utility.normalise_parameter_as_list(aliases)
regimes = nineml.utility.normalise_parameter_as_list(regimes)
state_variables = nineml.utility.normalise_parameter_as_list(state_variables)
# Load the aliases as objects or strings:
from nineml.utility import filter_discrete_types
alias_td = filter_discrete_types(aliases, (basestring, Alias))
aliases_from_strs = [StrToExpr.alias(o) for o in alias_td[basestring]]
aliases = alias_td[Alias] + aliases_from_strs
# Load the state variables as objects or strings:
sv_types = (basestring, StateVariable)
sv_td = filter_discrete_types(state_variables, sv_types)
sv_from_strings = [StateVariable(o) for o in sv_td[basestring]]
state_variables = sv_td[StateVariable] + sv_from_strings
self._regimes = regimes
self._aliases = aliases
self._state_variables = state_variables
def __init__(self, *args, **kwargs):
"""Regime constructor
:param name: The name of the constructor. If none, then a name will
be automatically generated.
:param time_derivatives: A list of time derivatives, as
either ``string``s (e.g 'dg/dt = g/gtau') or as |TimeDerivative|
objects.
:param transitions: A list containing either |OnEvent| or
|OnCondition| objects, which will automatically be sorted into
the appropriate classes automatically.
:param *args: Any non-keyword arguments will be treated as
time_derivatives.
"""
valid_kwargs = ('name', 'transitions', 'time_derivatives')
for arg in kwargs:
if not arg in valid_kwargs:
err = 'Unexpected Arg: %s' % arg
raise NineMLRuntimeError(err)
transitions = kwargs.get('transitions', None)
name = kwargs.get('name', None)
kw_tds = nineml.utility.normalise_parameter_as_list(kwargs.get('time_derivatives', None))
time_derivatives = list(args) + kw_tds
# Generate a name for unnamed regions:
self._name = name.strip() if name else Regime.get_next_name()
nineml.utility.ensure_valid_c_variable_name(self._name)
# Un-named arguments are time_derivatives:
time_derivatives = nineml.utility.normalise_parameter_as_list(time_derivatives)
# time_derivatives.extend( args )
td_types = (basestring, TimeDerivative)
td_type_dict = nineml.utility.filter_discrete_types(time_derivatives, td_types)
td_from_str = [StrToExpr.time_derivative(o) for o in td_type_dict[basestring]]
self._time_derivatives = td_type_dict[TimeDerivative] + td_from_str
# Check for double definitions:
td_dep_vars = [td.dependent_variable for td in self._time_derivatives]
nineml.utility.assert_no_duplicates(td_dep_vars)
# We support passing in 'transitions', which is a list of both OnEvents
# and OnConditions. So, lets filter this by type and add them
# appropriately:
transitions = nineml.utility.normalise_parameter_as_list(transitions)
f_dict = nineml.utility.filter_discrete_types(transitions, (OnEvent, OnCondition))
self._on_events = []
self._on_conditions = []
# Add all the OnEvents and OnConditions:
for event in f_dict[OnEvent]:
self.add_on_event(event)
for condition in f_dict[OnCondition]:
self.add_on_condition(condition)
def do_to_assignments_and_events(doList):
if not doList:
return [], []
# 'doList' is a list of strings, OutputEvents, and StateAssignments.
do_type_list = (OutputEvent, basestring, StateAssignment)
do_types = nineml.utility.filter_discrete_types(doList, do_type_list)
# Convert strings to StateAssignments:
sa_from_strs = [StrToExpr.state_assignment(s) for s in do_types[basestring]]
return do_types[StateAssignment] + sa_from_strs, do_types[OutputEvent]
def __init__(self, state_assignments=None, event_outputs=None,
target_regime_name=None):
"""Abstract class representing a transition from one |Regime| to
another.
|Transition| objects are not created directly, but via the subclasses
|OnEvent| and |OnCondition|.
:param state_assignments: A list of the state-assignments performed
when this transition occurs. Objects in this list are either
`string` (e.g A = A+13) or |StateAssignment| objects.
:param event_outputs: A list of |OutputEvent| objects emitted when
this transition occurs.
:param target_regime_name: The name of the regime to go into after this
transition. ``None`` implies staying in the same regime. This has
to be specified as a string, not the object, because in general the
|Regime| object is not yet constructed. This is automatically
resolved by the |ComponentClass| in
``_ResolveTransitionRegimeNames()`` during construction.
.. todo::
For more information about what happens at a regime transition, see
here: XXXXXXX
"""
if target_regime_name:
assert isinstance(target_regime_name, basestring)
# Load state-assignment objects as strings or StateAssignment objects
from nineml.utility import filter_discrete_types
state_assignments = state_assignments or []
sa_types = (basestring, StateAssignment)
sa_type_dict = filter_discrete_types(state_assignments, sa_types)
sa_from_str = [StrToExpr.state_assignment(o) for o in sa_type_dict[basestring]]
self._state_assignments = sa_type_dict[StateAssignment] + sa_from_str
self._event_outputs = event_outputs or []
self._target_regime_name = target_regime_name
self._source_regime_name = None
# Set later, once attached to a regime:
self._target_regime = None
self._source_regime = None