Source code for chaste_codegen.generalised_rush_larsen_1_opt_model
from sympy import Derivative
from chaste_codegen._lookup_tables import DEFAULT_LOOKUP_PARAMETERS, LookupTables
from chaste_codegen._partial_eval import partial_eval
from chaste_codegen.generalised_rush_larsen_1_model import GeneralisedRushLarsenFirstOrderModel
[docs]class GeneralisedRushLarsenFirstOrderModelOpt(GeneralisedRushLarsenFirstOrderModel):
""" Holds template and information specific for the GeneralisedRushLarsenOpt model type"""
def __init__(self, model, file_name, **kwargs):
self._lookup_tables = LookupTables(model, lookup_params=kwargs.get('lookup_table', DEFAULT_LOOKUP_PARAMETERS))
super().__init__(model, file_name, **kwargs)
self._vars_for_template['model_type'] += 'Opt'
self._vars_for_template['lookup_parameters'] = self._lookup_tables.print_lookup_parameters(self._printer)
def _get_stimulus(self):
""" Get the partially evaluated stimulus currents in the model"""
return_stim_eqs = super()._get_stimulus()
return partial_eval(return_stim_eqs, self._model.stimulus_params | self._model.modifiable_parameters)
def _get_extended_ionic_vars(self):
""" Get the partially evaluated equations defining the ionic derivatives and all dependant equations"""
extended_ionic_vars = partial_eval(super()._get_extended_ionic_vars(), self._model.ionic_vars)
self._lookup_tables.calc_lookup_tables(extended_ionic_vars)
return extended_ionic_vars
def _get_derivative_equations(self):
""" Get partially evaluated equations defining the derivatives including V (self._model.membrane_voltage_var)"""
derivative_equations = partial_eval(super()._get_derivative_equations(), self._model.y_derivatives)
self._lookup_tables.calc_lookup_tables(derivative_equations)
return derivative_equations
def _add_printers(self):
""" Initialises Printers for outputting chaste code. """
super()._add_printers(lookup_table_function=self._lookup_tables.print_lut_expr)
def _format_ionic_vars(self):
""" Format equations and dependant equations ionic derivatives"""
with self._lookup_tables.method_being_printed('GetIIonic'):
return super()._format_ionic_vars()
def _format_derived_quant_eqs(self):
""" Format equations for derived quantities based on current settings"""
with self._lookup_tables.method_being_printed('ComputeDerivedQuantities'):
return super()._format_derived_quant_eqs()
[docs] def eq_in_evaluate_y_derivative(self, eq, used_equations):
"""Indicate if the lhs of equation eq appears in used_equations"""
super().eq_in_evaluate_y_derivative(eq, used_equations)
if eq['in_evaluate_y_derivative'][-1]:
# Reprint to indicate use of lookup table
with self._lookup_tables.method_being_printed('ComputeOneStepExceptVoltage' +
str(len(eq['in_evaluate_y_derivative']) - 1)):
modifiers_with_defining_eqs = \
set((eq.lhs for eq in self._derivative_equations)) | self._model.state_vars
eq['rhs'] = self._print_rhs_with_modifiers(eq['sympy_lhs'], eq['sympy_rhs'],
modifiers_with_defining_eqs)
[docs] def eq_in_evaluate_partial_derivative(self, eq, used_jacobian_vars):
"""Indicate if the lhs of equation eq appears in used_jacobian_vars"""
super().eq_in_evaluate_partial_derivative(eq, used_jacobian_vars)
if eq['in_evaluate_partial_derivative'][-1]:
# Reprint to indicate use of lookup table
with self._lookup_tables.method_being_printed('EvaluatePartialDerivative' +
str(len(eq['in_evaluate_partial_derivative']) - 1)):
eq['rhs'] = self._printer.doprint(eq['sympy_rhs'])