class OptCvodeChasteModel(CvodeChasteModel):
""" Holds information specific for the Cvode Optimised model type. Builds on Cvode 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 _print_jacobian(self):
with self._lookup_tables.method_being_printed(
'EvaluateAnalyticJacobian'):
return super()._print_jacobian()
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_derivative_equations(self, derivative_equations):
""" Format derivative equations for chaste output"""
with self._lookup_tables.method_being_printed('EvaluateYDerivatives'):
return super()._format_derivative_equations(derivative_equations)
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()
def test_nested_method_printed_for(s_model):
lut = LookupTables(s_model)
lut.calc_lookup_tables(s_model.equations)
printer = ChastePrinter(lookup_table_function=lut.print_lut_expr)
output = ""
for eq in s_model.equations:
with lut.method_being_printed('outer_method'):
with lut.method_being_printed('innter_method'):
output += printer.doprint(eq.rhs)
assert '_lt_0_row[0]' in output
params_for_printing = lut.print_lookup_parameters(printer)
assert len(params_for_printing) == 1
assert sorted(params_for_printing[0].keys()) == \
['lookup_epxrs', 'mTableMaxs', 'mTableMins', 'mTableSteps', 'metadata_tag', 'table_used_in_methods', 'var']
assert params_for_printing[0]['metadata_tag'] == 'membrane_voltage'
assert params_for_printing[0]['metadata_tag'] == 'membrane_voltage'
assert params_for_printing[0]['mTableMins'] == -250.0
assert params_for_printing[0]['mTableMaxs'] == 550.0
assert params_for_printing[0]['mTableSteps'] == 0.001
assert params_for_printing[0]['table_used_in_methods'] == set({'outer_method'})
assert params_for_printing[0]['var'] == 'cell$V'
expected = open(os.path.join(TESTS_FOLDER, 'test_lookup_tables_nested_method_printed_for.txt'), 'r').read()
assert str(params_for_printing[0]['lookup_epxrs']) == expected, str(params_for_printing[0]['lookup_epxrs'])
def test_no_method_printed_for(s_model):
lut = LookupTables(s_model)
lut.calc_lookup_tables(s_model.equations)
printer = ChastePrinter(lookup_table_function=lut.print_lut_expr)
output = ""
for eq in s_model.equations:
output += printer.doprint(eq)
assert '_lt_0_row[0]' not in output
# We can't use an external text files here since the data contains sets
# printing these would make the test dependant on their order
params_for_printing = lut.print_lookup_parameters(printer)
assert len(params_for_printing) == 1
assert sorted(params_for_printing[0].keys()) == \
['lookup_epxrs', 'mTableMaxs', 'mTableMins', 'mTableSteps', 'metadata_tag', 'table_used_in_methods', 'var']
assert params_for_printing[0]['metadata_tag'] == 'membrane_voltage'
assert params_for_printing[0]['metadata_tag'] == 'membrane_voltage'
assert params_for_printing[0]['mTableMins'] == -250.0
assert params_for_printing[0]['mTableMaxs'] == 550.0
assert params_for_printing[0]['mTableSteps'] == 0.001
assert params_for_printing[0]['table_used_in_methods'] == set()
assert params_for_printing[0]['var'] == 'cell$V'
expected = open(os.path.join(TESTS_FOLDER, 'test_lookup_tables_no_method_printed_for.txt'), 'r').read()
assert str(params_for_printing[0]['lookup_epxrs']) == expected, str(params_for_printing[0]['lookup_epxrs'])
def test_no_print_after_table(s_model):
lut = LookupTables(s_model)
printer = ChastePrinter(lookup_table_function=lut.print_lut_expr)
assert lut.print_lookup_parameters(printer) == []
with pytest.raises(ValueError, match="Cannot print lookup expression after main table has been printed"):
for eq in s_model.equations:
printer.doprint(eq)
def test_change_lookup_table(be_model):
lut = LookupTables(be_model, lookup_params=[['membrane_voltage', -25.0001, 54.9999, 0.01],
['cytosolic_calcium_concentration', 0.0, 50.0, 0.01],
['unknown_tag', 0.0, 50.0, 0.01]])
lut.calc_lookup_tables(be_model.equations)
printer = ChastePrinter(lookup_table_function=lut.print_lut_expr)
output = ""
for eq in be_model.equations:
with lut.method_being_printed('template_method'):
output += printer.doprint(eq.rhs)
assert '_lt_0_row[0]' in output
assert '_lt_1_row[0]' in output
assert '_lt_2_row[0]' not in output
params_for_printing = lut.print_lookup_parameters(printer)
assert len(params_for_printing) == 2
assert all([sorted(p.keys()) ==
['lookup_epxrs', 'mTableMaxs', 'mTableMins', 'mTableSteps', 'metadata_tag',
'table_used_in_methods', 'var'] for p in params_for_printing])
assert params_for_printing[0]['metadata_tag'] == 'membrane_voltage'
assert params_for_printing[0]['mTableMins'] == -25.0001
assert params_for_printing[0]['mTableMaxs'] == 54.9999
assert params_for_printing[0]['mTableSteps'] == 0.01
assert params_for_printing[0]['table_used_in_methods'] == set({'template_method'})
assert params_for_printing[0]['var'] == 'membrane$V'
expected = open(os.path.join(TESTS_FOLDER, 'test_lookup_tables_change_lookup_table.txt'), 'r').read()
assert str(params_for_printing[0]['lookup_epxrs']) == expected, str(params_for_printing[0]['lookup_epxrs'])
assert params_for_printing[1]['metadata_tag'] == 'cytosolic_calcium_concentration'
assert params_for_printing[1]['mTableMins'] == 0.0
assert params_for_printing[1]['mTableMaxs'] == 50.0
assert params_for_printing[1]['mTableSteps'] == 0.01
assert params_for_printing[1]['table_used_in_methods'] == set({'template_method'})
assert params_for_printing[1]['var'] == 'slow_inward_current$Cai'
assert str(params_for_printing[1]['lookup_epxrs']) \
== "[['-82.3 - 13.0287 * log(0.001 * slow_inward_current$Cai)', False]]"
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_derivative_equation(self, eq, modifiers_with_defining_eqs):
""" Format an individual derivative equation"""
formatted_eq = None
if isinstance(eq.lhs, Derivative
) and eq.lhs.args[0] is self._model.membrane_voltage_var:
formatted_eq = super().format_derivative_equation(
eq, modifiers_with_defining_eqs)
elif eq in self._derivative_eqs_excl_voltage: # Indicate use of lookup table
with self._lookup_tables.method_being_printed(
'ComputeOneStepExceptVoltage'):
formatted_eq = super().format_derivative_equation(
eq, modifiers_with_defining_eqs)
if eq in self._derivative_eqs_voltage: # Indicate use of lookup table
with self._lookup_tables.method_being_printed(
'UpdateTransmembranePotential'):
formatted_eq = super().format_derivative_equation(
eq, modifiers_with_defining_eqs)
assert formatted_eq is not None, (
'Derivative equation should be dvdt or in _derivative_eqs_voltage '
'or in _derivative_eqs_excl_voltage')
return formatted_eq
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()
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)
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'])
class BackwardEulerOptModel(BackwardEulerModel):
""" Holds information specific for the Optimised Backward Euler 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._update_formatted_deriv_eq()
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 _pre_print_hook(self):
""" Retreives out linear and non-linear derivatives and the relevant jacobian for it.
And calculates lookup tables for the jacobian."""
super()._pre_print_hook()
# calculate lookup tables for the jacobians created by the Backward Euler
self._lookup_tables.calc_lookup_tables(
(Eq(lhs, rhs) for lhs, rhs in self._jacobian_equations))
def _update_formatted_deriv_eq(self):
"""Update derivatibve equation information for lookup table printing"""
for eq in self._vars_for_template['y_derivative_equations']:
if not eq['linear']:
with self._lookup_tables.method_being_printed(
'ComputeResidual'):
eq['rhs'] = self._printer.doprint(eq['sympy_rhs'])
if eq['in_membrane_voltage']:
with self._lookup_tables.method_being_printed(
'UpdateTransmembranePotential'):
eq['rhs'] = self._printer.doprint(eq['sympy_rhs'])
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_derivative_equations(self, derivative_equations):
""" Format derivative equations for chaste output"""
with self._lookup_tables.method_being_printed('EvaluateYDerivatives'):
return super()._format_derivative_equations(derivative_equations)
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()
def format_linear_deriv_eqs(self, linear_deriv_eqs):
""" Format linear derivative equations beloning, to update what belongs were"""
with self._lookup_tables.method_being_printed(
'ComputeOneStepExceptVoltage'):
return super().format_linear_deriv_eqs(linear_deriv_eqs)
def format_jacobian(self):
"""Format the jacobian to update what belongs were"""
with self._lookup_tables.method_being_printed('ComputeJacobian'):
return super().format_jacobian()
class RushLarsenOptModel(RushLarsenModel):
""" Holds template and information specific for the RushLarsen 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_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_derivative_equations(self, derivative_equations):
""" Format derivative equations for chaste output"""
with self._lookup_tables.method_being_printed('EvaluateYDerivatives'):
return super()._format_derivative_equations(derivative_equations)
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()
def _get_formatted_alpha_beta(self):
"""Gets the information for r_alpha_or_tau, r_beta_or_inf in the c++ output and formatted equations
Rearranges in the form (inf-x)/tau
"""
with self._lookup_tables.method_being_printed('EvaluateEquations'):
return super()._get_formatted_alpha_beta()
def format_deriv_eqs_EvaluateEquations(self, deriv_eqs_EvaluateEquations):
""" Format derivative equations beloning to EvaluateEquations, to update what equation belongs were"""
voltage_eqs = set(
get_equations_for(self._model, [
d for d in self._model.y_derivatives
if d.args[0] is self._model.membrane_voltage_var
]))
other_eqs = set(
get_equations_for(self._model, [
d for d in self._model.y_derivatives
if d.args[0] is not self._model.membrane_voltage_var
]))
voltage_eqs -= set(other_eqs)
self._derivative_eqs_voltage |= voltage_eqs
return super().format_deriv_eqs_EvaluateEquations(
deriv_eqs_EvaluateEquations)