def is_vectorized_assignment(cls, assignment):
"""
Indicates whether the handed over assignment is vectorized, i.e., an assignment of vectors.
:param assignment: a single assignment.
:type assignment: ASTAssignment
:return: True if vectorized, otherwise False.
:rtype: bool
"""
from pynestml.symbols.symbol import SymbolKind
assert isinstance(assignment, ASTAssignment), \
'(PyNestML.CodeGeneration.Assignments) No or wrong type of assignment provided (%s)!' % type(assignment)
symbol = assignment.get_scope().resolve_to_symbol(assignment.get_variable().get_complete_name(),
SymbolKind.VARIABLE)
if symbol is not None:
if symbol.has_vector_parameter():
return True
else:
# otherwise we have to check if one of the variables used in the rhs is a vector
for var in assignment.get_expression().get_variables():
symbol = var.get_scope().resolve_to_symbol(var.get_complete_name(), SymbolKind.VARIABLE)
if symbol is not None and symbol.has_vector_parameter():
return True
return False
else:
Logger.log_message(message='No symbol could be resolved!', log_level=LoggingLevel.ERROR)
return False
def is_vectorized_assignment(cls, assignment):
"""
Indicates whether the handed over assignment is vectorized, i.e., an assignment of vectors.
:param assignment: a single assignment.
:type assignment: ASTAssignment
:return: True if vectorized, otherwise False.
:rtype: bool
"""
from pynestml.symbols.symbol import SymbolKind
assert isinstance(assignment, ASTAssignment), \
'(PyNestML.CodeGeneration.Assignments) No or wrong type of assignment provided (%s)!' % type(assignment)
symbol = assignment.get_scope().resolve_to_symbol(
assignment.get_variable().get_complete_name(), SymbolKind.VARIABLE)
if symbol is not None:
if symbol.has_vector_parameter():
return True
else:
# otherwise we have to check if one of the variables used in the rhs is a vector
for var in assignment.get_expression().get_variables():
symbol = var.get_scope().resolve_to_symbol(
var.get_complete_name(), SymbolKind.VARIABLE)
if symbol is not None and symbol.has_vector_parameter():
return True
return False
else:
Logger.log_message(message='No symbol could be resolved!',
log_level=LoggingLevel.ERROR)
return False
def visit_simple_expression(self, node):
"""
Visits a single variable as contained in a simple expression and derives its type.
:param node: a single simple expression
:type node: ASTSimpleExpression
"""
assert isinstance(node, ASTSimpleExpression), \
'(PyNestML.Visitor.VariableVisitor) No or wrong type of simple expression provided (%s)!' % type(node)
assert (node.get_scope() is not None), \
'(PyNestML.Visitor.VariableVisitor) No scope found, run symboltable creator!'
scope = node.get_scope()
var_name = node.get_variable().get_name()
var_resolve = scope.resolve_to_symbol(var_name, SymbolKind.VARIABLE)
# update the type of the variable according to its symbol type.
if var_resolve is not None:
node.type = var_resolve.get_type_symbol()
node.type.referenced_object = node
else:
# check if var_name is actually a type literal (e.g. "mV")
var_resolve = scope.resolve_to_symbol(var_name, SymbolKind.TYPE)
if var_resolve is not None:
node.type = var_resolve
node.type.referenced_object = node
else:
message = 'Variable ' + str(node) + ' could not be resolved!'
Logger.log_message(code=MessageCode.SYMBOL_NOT_RESOLVED,
error_position=node.get_source_position(),
message=message, log_level=LoggingLevel.ERROR)
node.type = ErrorTypeSymbol()
return
def visit_expression(self, node):
"""
Visits an expression which uses a binary logic operator and updates the type.
:param node: a single expression.
:type node: ast_expression
"""
lhs_type = node.get_lhs().type
rhs_type = node.get_rhs().type
lhs_type.referenced_object = node.get_lhs()
rhs_type.referenced_object = node.get_rhs()
if isinstance(lhs_type, BooleanTypeSymbol) and isinstance(rhs_type, BooleanTypeSymbol):
node.type = PredefinedTypes.get_boolean_type()
else:
if isinstance(lhs_type, BooleanTypeSymbol):
offending_type = lhs_type
else:
offending_type = rhs_type
code, message = Messages.get_type_different_from_expected(BooleanTypeSymbol(), offending_type)
Logger.log_message(code=code, message=message,
error_position=lhs_type.referenced_object.get_source_position(),
log_level=LoggingLevel.ERROR)
node.type = ErrorTypeSymbol()
return
def generate_module_code(self, neurons):
# type: (list(ASTNeuron)) -> None
"""
Generates code that is necessary to integrate neuron models into the NEST infrastructure.
:param neurons: a list of neurons
:type neurons: list(ASTNeuron)
"""
namespace = {'neurons': neurons,
'moduleName': FrontendConfiguration.get_module_name(),
'now': datetime.datetime.utcnow()}
if not os.path.exists(FrontendConfiguration.get_target_path()):
os.makedirs(FrontendConfiguration.get_target_path())
with open(str(os.path.join(FrontendConfiguration.get_target_path(),
FrontendConfiguration.get_module_name())) + '.h', 'w+') as f:
f.write(str(self._template_module_header.render(namespace)))
with open(str(os.path.join(FrontendConfiguration.get_target_path(),
FrontendConfiguration.get_module_name())) + '.cpp', 'w+') as f:
f.write(str(self._template_module_class.render(namespace)))
with open(str(os.path.join(FrontendConfiguration.get_target_path(),
'CMakeLists')) + '.txt', 'w+') as f:
f.write(str(self._template_cmakelists.render(namespace)))
if not os.path.isdir(os.path.realpath(os.path.join(FrontendConfiguration.get_target_path(), 'sli'))):
os.makedirs(os.path.realpath(os.path.join(FrontendConfiguration.get_target_path(), 'sli')))
with open(str(os.path.join(FrontendConfiguration.get_target_path(), 'sli',
FrontendConfiguration.get_module_name() + "-init")) + '.sli', 'w+') as f:
f.write(str(self._template_sli_init.render(namespace)))
code, message = Messages.get_module_generated(FrontendConfiguration.get_target_path())
Logger.log_message(None, code, message, None, LoggingLevel.INFO)
def check_simple_delta(_expr=None):
if _expr.is_function_call() and _expr.get_function_call().get_name(
) == "delta":
deltafunc = _expr.get_function_call()
parent = neuron.get_parent(_expr)
# check the argument
if not (len(deltafunc.get_args()) == 1 and
type(deltafunc.get_args()[0]) is ASTSimpleExpression
and deltafunc.get_args()[0].get_variable() is not None
and deltafunc.get_args()[0].get_variable().name
== "t"):
code, message = Messages.delta_function_one_arg(deltafunc)
Logger.log_message(
code=code,
message=message,
error_position=_expr.get_source_position(),
log_level=LoggingLevel.ERROR)
if type(parent) is not ASTKernel:
code, message = Messages.delta_function_cannot_be_mixed()
Logger.log_message(
code=code,
message=message,
error_position=_expr.get_source_position(),
log_level=LoggingLevel.ERROR)
def ode_toolbox_analysis(self, neuron: ASTNeuron,
kernel_buffers: Mapping[ASTKernel, ASTInputPort]):
"""
Prepare data for ODE-toolbox input format, invoke ODE-toolbox analysis via its API, and return the output.
"""
assert isinstance(
neuron.get_equations_blocks(),
ASTEquationsBlock), "only one equation block should be present"
equations_block = neuron.get_equations_block()
if len(equations_block.get_kernels()) == 0 and len(
equations_block.get_ode_equations()) == 0:
# no equations defined -> no changes to the neuron
return None, None
code, message = Messages.get_neuron_analyzed(neuron.get_name())
Logger.log_message(neuron, code, message, neuron.get_source_position(),
LoggingLevel.INFO)
parameters_block = neuron.get_parameter_blocks()
odetoolbox_indict = self.transform_ode_and_kernels_to_json(
neuron, parameters_block, kernel_buffers)
odetoolbox_indict["options"] = {}
odetoolbox_indict["options"]["output_timestep_symbol"] = "__h"
solver_result = analysis(
odetoolbox_indict,
disable_stiffness_check=True,
debug=FrontendConfiguration.logging_level == "DEBUG")
analytic_solver = None
analytic_solvers = [
x for x in solver_result if x["solver"] == "analytical"
]
assert len(
analytic_solvers
) <= 1, "More than one analytic solver not presently supported"
if len(analytic_solvers) > 0:
analytic_solver = analytic_solvers[0]
# if numeric solver is required, generate a stepping function that includes each state variable
numeric_solver = None
numeric_solvers = [
x for x in solver_result if x["solver"].startswith("numeric")
]
if numeric_solvers:
solver_result = analysis(
odetoolbox_indict,
disable_stiffness_check=True,
disable_analytic_solver=True,
debug=FrontendConfiguration.logging_level == "DEBUG")
numeric_solvers = [
x for x in solver_result if x["solver"].startswith("numeric")
]
assert len(
numeric_solvers
) <= 1, "More than one numeric solver not presently supported"
if len(numeric_solvers) > 0:
numeric_solver = numeric_solvers[0]
return analytic_solver, numeric_solver
def visit_assignment(self, node):
symbol = node.get_scope().resolve_to_symbol(node.get_variable().get_complete_name(),
SymbolKind.VARIABLE)
if symbol is None:
code, message = Messages.get_variable_not_defined(node.get_variable().get_complete_name())
Logger.log_message(code=code, message=message, error_position=node.get_source_position(),
log_level=LoggingLevel.ERROR, neuron=self.neuron)
def add_ode_to_variable(ode_equation):
"""
Resolves to the corresponding symbol and updates the corresponding ode-declaration. In the case that
:param ode_equation: a single ode-equation
:type ode_equation: ast_ode_equation
"""
# the definition of a differential equations is defined by stating the derivation, thus derive the actual order
diff_order = ode_equation.get_lhs().get_differential_order() - 1
# we check if the corresponding symbol already exists, e.g. V_m' has already been declared
existing_symbol = (ode_equation.get_scope().resolve_to_symbol(
ode_equation.get_lhs().get_name() + '\'' * diff_order,
SymbolKind.VARIABLE))
if existing_symbol is not None:
existing_symbol.set_ode_definition(ode_equation.get_rhs())
# todo added on merge
ode_equation.get_scope().update_variable_symbol(existing_symbol)
code, message = Messages.get_ode_updated(
ode_equation.get_lhs().get_name_of_lhs())
Logger.log_message(error_position=existing_symbol.
get_referenced_object().get_source_position(),
code=code,
message=message,
log_level=LoggingLevel.INFO)
else:
code, message = Messages.get_no_variable_found(
ode_equation.get_lhs().get_name_of_lhs())
Logger.log_message(code=code,
message=message,
error_position=ode_equation.get_source_position(),
log_level=LoggingLevel.ERROR)
return
def visit_simple_expression(self, node):
"""
Visits a single variable as contained in a simple expression and derives its type.
:param node: a single simple expression
:type node: ASTSimpleExpression
"""
assert isinstance(node, ASTSimpleExpression), \
'(PyNestML.Visitor.VariableVisitor) No or wrong type of simple expression provided (%s)!' % type(node)
assert (node.get_scope() is not None), \
'(PyNestML.Visitor.VariableVisitor) No scope found, run symboltable creator!'
scope = node.get_scope()
var_name = node.get_variable().get_name()
var_resolve = scope.resolve_to_symbol(var_name, SymbolKind.VARIABLE)
# update the type of the variable according to its symbol type.
if var_resolve is not None:
node.type = var_resolve.get_type_symbol()
node.type.referenced_object = node
else:
message = 'Variable ' + str(node) + ' could not be resolved!'
Logger.log_message(code=MessageCode.SYMBOL_NOT_RESOLVED,
error_position=node.get_source_position(),
message=message,
log_level=LoggingLevel.ERROR)
node.type = ErrorTypeSymbol()
return
def handle_input_path(cls, path):
if path is None or path == '':
# check if the mandatory path arg has been handed over, just terminate
raise InvalidPathException('No input path specified.')
cls.paths_to_compilation_units = list()
if os.path.isabs(path):
cls.provided_path = path
else:
# a relative path, reconstruct it. get the parent dir where models, pynestml etc. is located
pynestml_dir = os.getcwd()
cls.provided_path = os.path.join(pynestml_dir, path)
if os.path.isfile(cls.provided_path):
cls.paths_to_compilation_units.append(cls.provided_path)
elif os.path.isdir(cls.provided_path):
for filename in os.listdir(cls.provided_path):
if filename.endswith('.nestml'):
cls.paths_to_compilation_units.append(
os.path.join(cls.provided_path, filename))
else:
# input_path should be either a file or a directory
code, message = Messages.get_input_path_not_found(
path=cls.provided_path)
Logger.log_message(code=code,
message=message,
log_level=LoggingLevel.ERROR)
raise Exception(message)
def add_ode_to_variable(ode_equation):
"""
Resolves to the corresponding symbol and updates the corresponding ode-declaration.
:param ode_equation: a single ode-equation
:type ode_equation: ast_ode_equation
"""
for diff_order in range(ode_equation.get_lhs().get_differential_order()):
var_name = ode_equation.get_lhs().get_name() + "'" * diff_order
existing_symbol = ode_equation.get_scope().resolve_to_symbol(
var_name, SymbolKind.VARIABLE)
if existing_symbol is None:
code, message = Messages.get_no_variable_found(
ode_equation.get_lhs().get_name_of_lhs())
Logger.log_message(
code=code,
message=message,
error_position=ode_equation.get_source_position(),
log_level=LoggingLevel.ERROR)
return
existing_symbol.set_ode_or_kernel(ode_equation)
ode_equation.get_scope().update_variable_symbol(existing_symbol)
code, message = Messages.get_ode_updated(
ode_equation.get_lhs().get_name_of_lhs())
Logger.log_message(error_position=existing_symbol.
get_referenced_object().get_source_position(),
code=code,
message=message,
log_level=LoggingLevel.INFO)
def analyse_neuron(self, neuron):
# type: (ASTNeuron) -> None
"""
Analyse and transform a single neuron.
:param neuron: a single neuron.
"""
code, message = Messages.get_start_processing_neuron(neuron.get_name())
Logger.log_message(neuron, code, message, neuron.get_source_position(), LoggingLevel.INFO)
# make normalization
# apply spikes to buffers
# get rid of convolve, store them and apply then at the end
equations_block = neuron.get_equations_block()
shape_to_buffers = {}
if neuron.get_equations_block() is not None:
# extract function names and corresponding incoming buffers
convolve_calls = OdeTransformer.get_sum_function_calls(equations_block)
for convolve in convolve_calls:
shape_to_buffers[str(convolve.get_args()[0])] = str(convolve.get_args()[1])
OdeTransformer.refactor_convolve_call(neuron.get_equations_block())
self.make_functions_self_contained(equations_block.get_ode_functions())
self.replace_functions_through_defining_expressions(equations_block.get_ode_equations(),
equations_block.get_ode_functions())
# transform everything into gsl processable (e.g. no functional shapes) or exact form.
self.transform_shapes_and_odes(neuron, shape_to_buffers)
self.apply_spikes_from_buffers(neuron, shape_to_buffers)
# update the symbol table
symbol_table_visitor = ASTSymbolTableVisitor()
symbol_table_visitor.after_ast_rewrite_ = True # ODE block might have been removed entirely: suppress warnings
neuron.accept(symbol_table_visitor)
def convert_name_reference(self,
ast_variable: ASTVariable,
prefix: str = ''):
"""
Converts a single name reference to a gsl processable format.
:param ast_variable: a single variable
:type ast_variable: ASTVariable
:return: a gsl processable format of the variable
:rtype: str
"""
variable_name = NestNamesConverter.convert_to_cpp_name(
ast_variable.get_name())
if variable_name == PredefinedVariables.E_CONSTANT:
return 'numerics::e'
symbol = ast_variable.get_scope().resolve_to_symbol(
ast_variable.get_complete_name(), SymbolKind.VARIABLE)
if symbol is None:
# test if variable name can be resolved to a type
if PredefinedUnits.is_unit(ast_variable.get_complete_name()):
return str(
UnitConverter.get_factor(
PredefinedUnits.get_unit(
ast_variable.get_complete_name()).get_unit()))
code, message = Messages.get_could_not_resolve(variable_name)
Logger.log_message(
log_level=LoggingLevel.ERROR,
code=code,
message=message,
error_position=ast_variable.get_source_position())
return ''
if symbol.is_init_values():
return GSLNamesConverter.name(symbol)
if symbol.is_buffer():
if isinstance(symbol.get_type_symbol(), UnitTypeSymbol):
units_conversion_factor = UnitConverter.get_factor(
symbol.get_type_symbol().unit.unit)
else:
units_conversion_factor = 1
s = ""
if not units_conversion_factor == 1:
s += "(" + str(units_conversion_factor) + " * "
s += prefix + 'B_.' + NestNamesConverter.buffer_value(symbol)
if symbol.has_vector_parameter():
s += '[i]'
if not units_conversion_factor == 1:
s += ")"
return s
if symbol.is_local() or symbol.is_function:
return variable_name
if symbol.has_vector_parameter():
return prefix + 'get_' + variable_name + '()[i]'
return prefix + 'get_' + variable_name + '()'
def endvisit_assignment(self, node):
scope = node.get_scope()
var_name = node.get_variable().get_name()
_expr = node.get_expression()
var_symbol = scope.resolve_to_symbol(var_name, SymbolKind.VARIABLE)
_equals = var_symbol.get_type_symbol().equals(_expr.type) \
or var_symbol.get_type_symbol().differs_only_in_magnitude(_expr.type)
message = 'line ' + str(_expr.get_source_position()) + ' : LHS = ' + \
var_symbol.get_type_symbol().get_symbol_name() + \
' RHS = ' + _expr.type.get_symbol_name() + \
' Equal ? ' + str(_equals)
if isinstance(_expr.type, UnitTypeSymbol):
message += " Neuroscience Factor: " + \
str(UnitConverter().get_factor(_expr.type.astropy_unit))
Logger.log_message(error_position=node.get_source_position(), code=MessageCode.TYPE_MISMATCH,
message=message, log_level=LoggingLevel.INFO)
if _equals is False:
Logger.log_message(message="Type mismatch in test!",
code=MessageCode.TYPE_MISMATCH,
error_position=node.get_source_position(),
log_level=LoggingLevel.ERROR)
return
def visit_expression(self, node):
"""
Visits a single expression containing a plus or minus operator and updates its type.
:param node: a single expression
:type node: ast_expression
"""
lhs_type = node.get_lhs().type
rhs_type = node.get_rhs().type
arith_op = node.get_binary_operator()
lhs_type.referenced_object = node.get_lhs()
rhs_type.referenced_object = node.get_rhs()
node.type = ErrorTypeSymbol()
if arith_op.is_plus_op:
node.type = lhs_type + rhs_type
elif arith_op.is_minus_op:
node.type = lhs_type - rhs_type
if isinstance(node.type, ErrorTypeSymbol):
code, message = Messages.get_binary_operation_type_could_not_be_derived(
lhs=str(node.get_lhs()),
operator=str(arith_op),
rhs=str(node.get_rhs()),
lhs_type=str(lhs_type.print_nestml_type()),
rhs_type=str(rhs_type.print_nestml_type()))
Logger.log_message(code=code,
message=message,
error_position=node.get_source_position(),
log_level=LoggingLevel.ERROR)
def move_decls(cls, var_name, from_block, to_block, var_name_suffix, block_type: BlockType, mode="move", scope=None) -> List[ASTDeclaration]:
from pynestml.codegeneration.ast_transformers import ASTTransformers
from pynestml.visitors.ast_symbol_table_visitor import ASTSymbolTableVisitor
assert mode in ["move", "copy"]
if not from_block \
or not to_block:
return []
decls = ASTTransformers.get_declarations_from_block(var_name, from_block)
if var_name.endswith(var_name_suffix):
decls.extend(ASTTransformers.get_declarations_from_block(var_name.removesuffix(var_name_suffix), from_block))
if decls:
Logger.log_message(None, -1, "Moving definition of " + var_name + " from synapse to neuron",
None, LoggingLevel.INFO)
for decl in decls:
if mode == "move":
from_block.declarations.remove(decl)
if mode == "copy":
decl = decl.clone()
assert len(decl.get_variables()) <= 1
if not decl.get_variables()[0].name.endswith(var_name_suffix):
ASTUtils.add_suffix_to_decl_lhs(decl, suffix=var_name_suffix)
to_block.get_declarations().append(decl)
decl.update_scope(to_block.get_scope())
ast_symbol_table_visitor = ASTSymbolTableVisitor()
ast_symbol_table_visitor.block_type_stack.push(block_type)
decl.accept(ast_symbol_table_visitor)
ast_symbol_table_visitor.block_type_stack.pop()
return decls
def analyse_and_generate_neuron(neuron):
# type: (ASTNeuron) -> None
"""
Analysis a single neuron, solves it and generates the corresponding code.
:param neuron: a single neuron.
"""
code, message = Messages.get_start_processing_neuron(neuron.get_name())
Logger.log_message(neuron, code, message, neuron.get_source_position(), LoggingLevel.INFO)
# make normalization
# apply spikes to buffers
# get rid of convolve, store them and apply then at the end
equations_block = neuron.get_equations_block()
shape_to_buffers = {}
if neuron.get_equations_block() is not None:
# extract function names and corresponding incoming buffers
convolve_calls = OdeTransformer.get_sum_function_calls(equations_block)
for convolve in convolve_calls:
shape_to_buffers[str(convolve.get_args()[0])] = str(convolve.get_args()[1])
OdeTransformer.refactor_convolve_call(neuron.get_equations_block())
make_functions_self_contained(equations_block.get_ode_functions())
replace_functions_through_defining_expressions(equations_block.get_ode_equations(),
equations_block.get_ode_functions())
# transform everything into gsl processable (e.g. no functional shapes) or exact form.
transform_shapes_and_odes(neuron, shape_to_buffers)
# update the symbol table
neuron.accept(ASTSymbolTableVisitor())
generate_nest_code(neuron)
# now store the transformed model
store_transformed_model(neuron)
# at that point all shapes are transformed into the ODE form and spikes can be applied
code, message = Messages.get_code_generated(neuron.get_name(), FrontendConfiguration.get_target_path())
Logger.log_message(neuron, code, message, neuron.get_source_position(), LoggingLevel.INFO)
def visit_variable(self, node):
"""
Visits each shape and checks if it is used correctly.
:param node: a single node.
:type node: AST_
"""
for shapeName in self.__shapes:
# in order to allow shadowing by local scopes, we first check if the element has been declared locally
symbol = node.get_scope().resolve_to_symbol(shapeName, SymbolKind.VARIABLE)
# if it is not a shape just continue
if symbol is None:
code, message = Messages.get_no_variable_found(shapeName)
Logger.log_message(neuron=self.__neuron_node, code=code, message=message, log_level=LoggingLevel.ERROR)
continue
if not symbol.is_shape():
continue
if node.get_complete_name() == shapeName:
parent = self.__neuron_node.get_parent(node)
if parent is not None:
if isinstance(parent, ASTOdeShape):
continue
grandparent = self.__neuron_node.get_parent(parent)
if grandparent is not None and isinstance(grandparent, ASTFunctionCall):
grandparent_func_name = grandparent.get_name()
if grandparent_func_name == 'curr_sum' or grandparent_func_name == 'cond_sum' or \
grandparent_func_name == 'convolve':
continue
code, message = Messages.get_shape_outside_convolve(shapeName)
Logger.log_message(error_position=node.get_source_position(),
code=code, message=message,
log_level=LoggingLevel.ERROR)
return
def check_co_co(cls, _neuron=None):
"""
Checks the coco for the handed over neuron.
:param _neuron: a single neuron instance.
:type _neuron: ASTNeuron
"""
assert (_neuron is not None and isinstance(_neuron, ASTNeuron)), \
'(PyNestML.CoCo.FunctionCallsConsistent) No or wrong type of neuron provided (%s)!' % type(_neuron)
cls.__neuronName = _neuron.get_name()
for userDefinedFunction in _neuron.get_functions():
cls.processed_function = userDefinedFunction
symbol = userDefinedFunction.get_scope().resolve_to_symbol(userDefinedFunction.get_name(),
SymbolKind.FUNCTION)
# first ensure that the block contains at least one statement
if symbol is not None and len(userDefinedFunction.get_block().get_stmts()) > 0:
# now check that the last statement is a return
cls.__check_return_recursively(symbol.get_return_type(),
userDefinedFunction.get_block().get_stmts(), False)
# now if it does not have a statement, but uses a return type, it is an error
elif symbol is not None and userDefinedFunction.has_return_type() and \
not symbol.get_return_type().equals(PredefinedTypes.get_void_type()):
code, message = Messages.get_no_return()
Logger.log_message(node=_neuron, code=code, message=message,
error_position=userDefinedFunction.get_source_position(),
log_level=LoggingLevel.ERROR)
return
def binary_operation_not_defined_error(self, _operator, _other):
from pynestml.symbols.error_type_symbol import ErrorTypeSymbol
result = ErrorTypeSymbol()
code, message = Messages.get_binary_operation_not_defined(lhs=self, operator=_operator, rhs=_other)
Logger.log_message(code=code, message=message, error_position=self.referenced_object.get_source_position(),
log_level=LoggingLevel.ERROR)
return result
def visit_variable(self, node: ASTNode):
"""
Visits each kernel and checks if it is used correctly.
:param node: a single node.
"""
for kernelName in self.__kernels:
# in order to allow shadowing by local scopes, we first check if the element has been declared locally
symbol = node.get_scope().resolve_to_symbol(
kernelName, SymbolKind.VARIABLE)
# if it is not a kernel just continue
if symbol is None:
continue
if not symbol.is_kernel():
continue
if node.get_complete_name() == kernelName:
parent = self.__neuron_node.get_parent(node)
if parent is not None:
if isinstance(parent, ASTKernel):
continue
grandparent = self.__neuron_node.get_parent(parent)
if grandparent is not None and isinstance(
grandparent, ASTFunctionCall):
grandparent_func_name = grandparent.get_name()
if grandparent_func_name == 'convolve':
continue
code, message = Messages.get_kernel_outside_convolve(
kernelName)
Logger.log_message(code=code,
message=message,
log_level=LoggingLevel.ERROR,
error_position=node.get_source_position())
def add_ode_shape_to_variable(ode_shape):
"""
Adds the shape as the defining equation.
:param ode_shape: a single shape object.
:type ode_shape: ast_ode_shape
"""
if ode_shape.get_variable().get_differential_order() == 0:
# we only update those which define an ode
return
# we check if the corresponding symbol already exists, e.g. V_m' has already been declared
existing_symbol = ode_shape.get_scope().resolve_to_symbol(
ode_shape.get_variable().get_name_of_lhs(), SymbolKind.VARIABLE)
if existing_symbol is not None:
existing_symbol.set_ode_definition(ode_shape.get_expression())
existing_symbol.set_variable_type(VariableType.SHAPE)
ode_shape.get_scope().update_variable_symbol(existing_symbol)
code, message = Messages.get_ode_updated(
ode_shape.get_variable().get_name_of_lhs())
Logger.log_message(error_position=existing_symbol.
get_referenced_object().get_source_position(),
code=code,
message=message,
log_level=LoggingLevel.INFO)
else:
code, message = Messages.get_no_variable_found(
ode_shape.get_variable().get_name_of_lhs())
Logger.log_message(code=code,
message=message,
error_position=ode_shape.get_source_position(),
log_level=LoggingLevel.ERROR)
return
def visit_while_stmt(self, node):
"""
Visits a single while stmt and checks that its condition is of boolean type.
:param node: a single while stmt
:type node: ASTWhileStmt
"""
if node.get_source_position().equals(
ASTSourceLocation.get_added_source_position()):
# no type checks are executed for added nodes, since we assume correctness
return
cond_type = node.get_condition().type
if isinstance(cond_type, ErrorTypeSymbol):
code, message = Messages.get_type_could_not_be_derived(
node.get_condition())
Logger.log_message(
code=code,
message=message,
error_position=node.get_condition().get_source_position(),
log_level=LoggingLevel.ERROR)
elif not cond_type.equals(PredefinedTypes.get_boolean_type()):
code, message = Messages.get_type_different_from_expected(
PredefinedTypes.get_boolean_type(), cond_type)
Logger.log_message(
code=code,
message=message,
error_position=node.get_condition().get_source_position(),
log_level=LoggingLevel.ERROR)
return
def generate_nest_module_code(neurons):
# type: (list(ASTNeuron)) -> None
"""
Generates code that is necessary to integrate neuron models into the NEST infrastructure.
:param neurons: a list of neurons
:type neurons: list(ASTNeuron)
"""
namespace = {'neurons': neurons, 'moduleName': FrontendConfiguration.get_module_name(),
'now': datetime.datetime.utcnow()}
if not os.path.exists(FrontendConfiguration.get_target_path()):
os.makedirs(FrontendConfiguration.get_target_path())
with open(str(os.path.join(FrontendConfiguration.get_target_path(),
FrontendConfiguration.get_module_name())) + '.h', 'w+') as f:
f.write(str(template_module_header.render(namespace)))
with open(str(os.path.join(FrontendConfiguration.get_target_path(),
FrontendConfiguration.get_module_name())) + '.cpp', 'w+') as f:
f.write(str(template_module_class.render(namespace)))
with open(str(os.path.join(FrontendConfiguration.get_target_path(),
'CMakeLists')) + '.txt', 'w+') as f:
f.write(str(template_cmakelists.render(namespace)))
if not os.path.isdir(os.path.realpath(os.path.join(FrontendConfiguration.get_target_path(), 'sli'))):
os.makedirs(os.path.realpath(os.path.join(FrontendConfiguration.get_target_path(), 'sli')))
with open(str(os.path.join(FrontendConfiguration.get_target_path(), 'sli',
FrontendConfiguration.get_module_name() + "-init")) + '.sli', 'w+') as f:
f.write(str(template_sli_init.render(namespace)))
code, message = Messages.get_module_generated(FrontendConfiguration.get_target_path())
Logger.log_message(None, code, message, None, LoggingLevel.INFO)
def endvisit_assignment(self, node):
scope = node.get_scope()
var_name = node.get_variable().get_name()
_expr = node.get_expression()
var_symbol = scope.resolve_to_symbol(var_name, SymbolKind.VARIABLE)
_equals = var_symbol.get_type_symbol().equals(_expr.type)
message = 'line ' + str(_expr.get_source_position()) + ' : LHS = ' + \
var_symbol.get_type_symbol().get_symbol_name() + \
' RHS = ' + _expr.type.get_symbol_name() + \
' Equal ? ' + str(_equals)
if isinstance(_expr.type, UnitTypeSymbol):
message += " Neuroscience Factor: " + \
str(UnitConverter().get_factor(_expr.type.astropy_unit))
Logger.log_message(error_position=node.get_source_position(), code=MessageCode.TYPE_MISMATCH,
message=message, log_level=LoggingLevel.INFO)
if _equals is False:
Logger.log_message(message="Type mismatch in test!",
code=MessageCode.TYPE_MISMATCH,
error_position=node.get_source_position(),
log_level=LoggingLevel.ERROR)
return
def visit_declaration(self, node):
"""
Checks the coco for a declaration.
:param node: a single declaration.
:type node: ASTDeclaration
"""
assert isinstance(node, ASTDeclaration)
if node.has_invariant():
invariant_type = node.get_invariant().type
if invariant_type is None or isinstance(invariant_type,
ErrorTypeSymbol):
code, message = Messages.get_type_could_not_be_derived(
str(node.get_invariant()))
Logger.log_message(
error_position=node.get_invariant().get_source_position(),
code=code,
message=message,
log_level=LoggingLevel.ERROR)
elif not invariant_type.equals(PredefinedTypes.get_boolean_type()):
code, message = Messages.get_type_different_from_expected(
PredefinedTypes.get_boolean_type(), invariant_type)
Logger.log_message(
error_position=node.get_invariant().get_source_position(),
code=code,
message=message,
log_level=LoggingLevel.ERROR)
return
def visit_declaration(self, node):
"""
Checks the coco.
:param node: a single declaration.
:type node: ast_declaration
"""
if node.has_expression():
variables = node.get_expression().get_variables()
for variable in variables:
if variable is not None:
symbol = node.get_scope().resolve_to_symbol(
variable.get_complete_name(), SymbolKind.VARIABLE)
if symbol is not None and symbol.has_vector_parameter(
) and not node.has_size_parameter():
code, message = Messages.get_vector_in_non_vector(
vector=symbol.get_symbol_name(),
non_vector=list(var.get_complete_name()
for var in node.get_variables()))
Logger.log_message(
error_position=node.get_source_position(),
code=code,
message=message,
log_level=LoggingLevel.ERROR)
return
def visit_simple_expression(self, node):
"""
Visits a single function call as stored in a simple expression and checks to see whether any calls are made to generate a random number. If so, set a flag so that the necessary initialisers can be called at the right time in the generated code.
"""
assert isinstance(node, ASTSimpleExpression), \
'(PyNestML.Visitor.FunctionCallVisitor) No or wrong type of simple expression provided (%s)!' % tuple(node)
assert (node.get_scope() is not None), \
"(PyNestML.Visitor.FunctionCallVisitor) No scope found, run symboltable creator!"
scope = node.get_scope()
if node.get_function_call() is None:
return
function_name = node.get_function_call().get_name()
method_symbol = scope.resolve_to_symbol(function_name, SymbolKind.FUNCTION)
# check if this function exists
if method_symbol is None:
code, message = Messages.get_could_not_resolve(function_name)
Logger.log_message(code=code, message=message, error_position=node.get_source_position(),
log_level=LoggingLevel.ERROR)
node.type = ErrorTypeSymbol()
return
if function_name == PredefinedFunctions.RANDOM_NORMAL:
self._norm_rng_is_used = True
return
def try_to_recover_or_error(_lhs_type_symbol, _rhs_type_symbol,
_containing_expression):
if _rhs_type_symbol.is_castable_to(_lhs_type_symbol):
if isinstance(_lhs_type_symbol, UnitTypeSymbol) \
and isinstance(_rhs_type_symbol, UnitTypeSymbol):
conversion_factor = UnitTypeSymbol.get_conversion_factor(
_lhs_type_symbol.astropy_unit,
_rhs_type_symbol.astropy_unit)
if not conversion_factor == 1.:
# the units are mutually convertible, but require a factor unequal to 1 (e.g. mV and A*Ohm)
TypeCaster.do_magnitude_conversion_rhs_to_lhs(
_rhs_type_symbol, _lhs_type_symbol,
_containing_expression)
# the units are mutually convertible (e.g. V and A*Ohm)
code, message = Messages.get_implicit_cast_rhs_to_lhs(
_rhs_type_symbol.print_symbol(),
_lhs_type_symbol.print_symbol())
Logger.log_message(
error_position=_containing_expression.get_source_position(),
code=code,
message=message,
log_level=LoggingLevel.INFO)
else:
code, message = Messages.get_type_different_from_expected(
_lhs_type_symbol, _rhs_type_symbol)
Logger.log_message(
error_position=_containing_expression.get_source_position(),
code=code,
message=message,
log_level=LoggingLevel.ERROR)
def visit_assignment(self, node):
symbol = node.get_scope().resolve_to_symbol(node.get_variable().get_complete_name(),
SymbolKind.VARIABLE)
if symbol is None:
code, message = Messages.get_variable_not_defined(node.get_variable().get_complete_name())
Logger.log_message(code=code, message=message, error_position=node.get_source_position(),
log_level=LoggingLevel.ERROR, node=self.neuron)
def convert_name_reference(self, variable):
"""
Converts a single variable to nest processable format.
:param variable: a single variable.
:type variable: ASTVariable
:return: a nest processable format.
:rtype: str
"""
from pynestml.codegeneration.nest_printer import NestPrinter
assert (variable is not None and isinstance(variable, ASTVariable)), \
'(PyNestML.CodeGeneration.NestReferenceConverter) No or wrong type of uses-gsl provided (%s)!' % type(
variable)
variable_name = NestNamesConverter.convert_to_cpp_name(
variable.get_complete_name())
if variable_name == PredefinedVariables.E_CONSTANT:
return 'numerics::e'
else:
symbol = variable.get_scope().resolve_to_symbol(
variable_name, SymbolKind.VARIABLE)
if symbol is None:
# test if variable name can be resolved to a type
if PredefinedUnits.is_unit(variable.get_complete_name()):
return str(
UnitConverter.get_factor(
PredefinedUnits.get_unit(
variable.get_complete_name()).get_unit()))
code, message = Messages.get_could_not_resolve(variable_name)
Logger.log_message(
log_level=LoggingLevel.ERROR,
code=code,
message=message,
error_position=variable.get_source_position())
return ''
else:
if symbol.is_local():
return variable_name + (
'[i]' if symbol.has_vector_parameter() else '')
elif symbol.is_buffer():
return NestPrinter.print_origin(symbol) + NestNamesConverter.buffer_value(symbol) \
+ ('[i]' if symbol.has_vector_parameter() else '')
else:
if symbol.is_function:
return 'get_' + variable_name + '()' + (
'[i]' if symbol.has_vector_parameter() else '')
else:
if symbol.is_init_values():
temp = NestPrinter.print_origin(symbol)
if self.uses_gsl:
temp += GSLNamesConverter.name(symbol)
else:
temp += NestNamesConverter.name(symbol)
temp += ('[i]'
if symbol.has_vector_parameter() else '')
return temp
else:
return NestPrinter.print_origin(symbol) + \
NestNamesConverter.name(symbol) + \
('[i]' if symbol.has_vector_parameter() else '')
def visit_neuron(self, node):
"""
Private method: Used to visit a single neuron and create the corresponding global as well as local scopes.
:return: a single neuron.
:rtype: ast_neuron
"""
# set current processed neuron
Logger.set_current_neuron(node)
code, message = Messages.get_start_building_symbol_table()
Logger.log_message(neuron=node, code=code, error_position=node.get_source_position(),
message=message, log_level=LoggingLevel.INFO)
# before starting the work on the neuron, make everything which was implicit explicit
# but if we have a model without an equations block, just skip this step
if node.get_equations_blocks() is not None:
make_implicit_odes_explicit(node.get_equations_blocks())
scope = Scope(scope_type=ScopeType.GLOBAL, source_position=node.get_source_position())
node.update_scope(scope)
node.get_body().update_scope(scope)
# now first, we add all predefined elements to the scope
variables = PredefinedVariables.get_variables()
functions = PredefinedFunctions.get_function_symbols()
types = PredefinedTypes.get_types()
for symbol in variables.keys():
node.get_scope().add_symbol(variables[symbol])
for symbol in functions.keys():
node.get_scope().add_symbol(functions[symbol])
for symbol in types.keys():
node.get_scope().add_symbol(types[symbol])
def check_co_co(cls, _neuron=None):
"""
Checks the coco for the handed over neuron.
:param _neuron: a single neuron instance.
:type _neuron: ASTNeuron
"""
assert (_neuron is not None and isinstance(_neuron, ASTNeuron)), \
'(PyNestML.CoCo.FunctionCallsConsistent) No or wrong type of neuron provided (%s)!' % type(_neuron)
cls.__neuronName = _neuron.get_name()
for userDefinedFunction in _neuron.get_functions():
cls.processed_function = userDefinedFunction
symbol = userDefinedFunction.get_scope().resolve_to_symbol(userDefinedFunction.get_name(),
SymbolKind.FUNCTION)
# first ensure that the block contains at least one statement
if symbol is not None and len(userDefinedFunction.get_block().get_stmts()) > 0:
# now check that the last statement is a return
cls.__check_return_recursively(symbol.get_return_type(),
userDefinedFunction.get_block().get_stmts(), False)
# now if it does not have a statement, but uses a return type, it is an error
elif symbol is not None and userDefinedFunction.has_return_type() and \
not symbol.get_return_type().equals(PredefinedTypes.get_void_type()):
code, message = Messages.get_no_return()
Logger.log_message(neuron=_neuron, code=code, message=message,
error_position=userDefinedFunction.get_source_position(),
log_level=LoggingLevel.ERROR)
return
def visit_input_line(self, node):
"""
Checks the coco on the current node.
:param node: a single input line.
:type node: ast_input_line
"""
if node.is_spike():
if node.has_input_types() and len(node.get_input_types()) > 1:
inh = 0
ext = 0
for typ in node.get_input_types():
if typ.is_excitatory:
ext += 1
if typ.is_inhibitory:
inh += 1
if inh > 1:
code, message = Messages.get_multiple_keywords(
'inhibitory')
Logger.log_message(
error_position=node.get_source_position(),
code=code,
message=message,
log_level=LoggingLevel.ERROR)
if ext > 1:
code, message = Messages.get_multiple_keywords(
'excitatory')
Logger.log_message(
error_position=node.get_source_position(),
code=code,
message=message,
log_level=LoggingLevel.ERROR)
return
def visit_neuron(self, node):
"""
Private method: Used to visit a single neuron and create the corresponding global as well as local scopes.
:return: a single neuron.
:rtype: ast_neuron
"""
# set current processed neuron
Logger.set_current_node(node)
code, message = Messages.get_start_building_symbol_table()
Logger.log_message(node=node,
code=code,
error_position=node.get_source_position(),
message=message,
log_level=LoggingLevel.INFO)
scope = Scope(scope_type=ScopeType.GLOBAL,
source_position=node.get_source_position())
node.update_scope(scope)
node.get_body().update_scope(scope)
# now first, we add all predefined elements to the scope
variables = PredefinedVariables.get_variables()
functions = PredefinedFunctions.get_function_symbols()
types = PredefinedTypes.get_types()
for symbol in variables.keys():
node.get_scope().add_symbol(variables[symbol])
for symbol in functions.keys():
node.get_scope().add_symbol(functions[symbol])
for symbol in types.keys():
node.get_scope().add_symbol(types[symbol])
def visit_expression(self, node):
"""
Visits an expression which uses a binary logic operator and updates the type.
:param node: a single expression.
:type node: ast_expression
"""
lhs_type = node.get_lhs().type
rhs_type = node.get_rhs().type
lhs_type.referenced_object = node.get_lhs()
rhs_type.referenced_object = node.get_rhs()
if isinstance(lhs_type, BooleanTypeSymbol) and isinstance(
rhs_type, BooleanTypeSymbol):
node.type = PredefinedTypes.get_boolean_type()
else:
if isinstance(lhs_type, BooleanTypeSymbol):
offending_type = lhs_type
else:
offending_type = rhs_type
code, message = Messages.get_type_different_from_expected(
BooleanTypeSymbol(), offending_type)
Logger.log_message(code=code,
message=message,
error_position=lhs_type.referenced_object.
get_source_position(),
log_level=LoggingLevel.ERROR)
node.type = ErrorTypeSymbol()
return
def add_kernel_to_variable(kernel):
"""
Adds the kernel as the defining equation.
If the definition of the kernel is e.g. `g'' = ...` then variable symbols `g` and `g'` will have their kernel definition and variable type set.
:param kernel: a single kernel object.
:type kernel: ASTKernel
"""
if len(kernel.get_variables()) == 1 \
and kernel.get_variables()[0].get_differential_order() == 0:
# we only update those which define an ODE; skip "direct function of time" specifications
return
for var, expr in zip(kernel.get_variables(), kernel.get_expressions()):
for diff_order in range(var.get_differential_order()):
var_name = var.get_name() + "'" * diff_order
existing_symbol = kernel.get_scope().resolve_to_symbol(
var_name, SymbolKind.VARIABLE)
if existing_symbol is None:
code, message = Messages.get_no_variable_found(
var.get_name_of_lhs())
Logger.log_message(code=code,
message=message,
error_position=kernel.get_source_position(),
log_level=LoggingLevel.ERROR)
return
existing_symbol.set_ode_or_kernel(expr)
existing_symbol.set_variable_type(VariableType.KERNEL)
kernel.get_scope().update_variable_symbol(existing_symbol)
def visit_neuron(self, node):
"""
Private method: Used to visit a single neuron and create the corresponding global as well as local scopes.
:return: a single neuron.
:rtype: ast_neuron
"""
# set current processed neuron
Logger.set_current_neuron(node)
code, message = Messages.get_start_building_symbol_table()
Logger.log_message(neuron=node,
code=code,
error_position=node.get_source_position(),
message=message,
log_level=LoggingLevel.INFO)
# before starting the work on the neuron, make everything which was implicit explicit
# but if we have a model without an equations block, just skip this step
if node.get_equations_blocks() is not None:
make_implicit_odes_explicit(node.get_equations_blocks())
scope = Scope(scope_type=ScopeType.GLOBAL,
source_position=node.get_source_position())
node.update_scope(scope)
node.get_body().update_scope(scope)
# now first, we add all predefined elements to the scope
variables = PredefinedVariables.get_variables()
functions = PredefinedFunctions.get_function_symbols()
types = PredefinedTypes.get_types()
for symbol in variables.keys():
node.get_scope().add_symbol(variables[symbol])
for symbol in functions.keys():
node.get_scope().add_symbol(functions[symbol])
for symbol in types.keys():
node.get_scope().add_symbol(types[symbol])
def visit_simple_expression(self, node):
"""
Visits a single function call
:param node: a simple expression
"""
assert isinstance(node, ASTSimpleExpression), \
'(PyNestML.Visitor.FunctionCallVisitor) No or wrong type of simple expression provided (%s)!' % tuple(node)
assert (node.get_scope() is not None), \
"(PyNestML.Visitor.FunctionCallVisitor) No scope found, run symboltable creator!"
if node.get_function_call() is None:
return
function_name = node.get_function_call().get_name()
if function_name == PredefinedFunctions.TIME_RESOLUTION:
_node = node
while _node:
_node = self.neuron.get_parent(_node)
if isinstance(_node, ASTEquationsBlock) \
or isinstance(_node, ASTFunction):
code, message = Messages.get_could_not_resolve(
function_name)
Logger.log_message(
code=code,
message=message,
error_position=node.get_source_position(),
log_level=LoggingLevel.ERROR)
def analyse_neuron(self, neuron):
# type: (ASTNeuron) -> None
"""
Analyse and transform a single neuron.
:param neuron: a single neuron.
"""
code, message = Messages.get_start_processing_neuron(neuron.get_name())
Logger.log_message(neuron, code, message, neuron.get_source_position(),
LoggingLevel.INFO)
# make normalization
# apply spikes to buffers
# get rid of convolve, store them and apply then at the end
equations_block = neuron.get_equations_block()
shape_to_buffers = {}
if neuron.get_equations_block() is not None:
# extract function names and corresponding incoming buffers
convolve_calls = OdeTransformer.get_sum_function_calls(
equations_block)
for convolve in convolve_calls:
shape_to_buffers[str(convolve.get_args()[0])] = str(
convolve.get_args()[1])
OdeTransformer.refactor_convolve_call(neuron.get_equations_block())
self.make_functions_self_contained(
equations_block.get_ode_functions())
self.replace_functions_through_defining_expressions(
equations_block.get_ode_equations(),
equations_block.get_ode_functions())
# transform everything into gsl processable (e.g. no functional shapes) or exact form.
self.transform_shapes_and_odes(neuron, shape_to_buffers)
self.apply_spikes_from_buffers(neuron, shape_to_buffers)
# update the symbol table
symbol_table_visitor = ASTSymbolTableVisitor()
symbol_table_visitor.after_ast_rewrite_ = True # ODE block might have been removed entirely: suppress warnings
neuron.accept(symbol_table_visitor)
def visit_assignment(self, node):
symbol = node.get_scope().resolve_to_symbol(node.get_variable().get_name(), SymbolKind.VARIABLE)
if symbol is not None and (symbol.block_type == BlockType.INPUT_BUFFER_SPIKE or
symbol.block_type == BlockType.INPUT_BUFFER_CURRENT):
code, message = Messages.get_value_assigned_to_buffer(node.get_variable().get_complete_name())
Logger.log_message(code=code, message=message,
error_position=node.get_source_position(),
log_level=LoggingLevel.ERROR)
return
def visit_unit_type(self, node):
"""
Check if the coco applies,
:param node: a single unit type object.
:type node: ast_unit_type
"""
if node.is_div and isinstance(node.lhs, int) and node.lhs != 1:
code, message = Messages.get_wrong_numerator(str(node))
Logger.log_message(code=code, message=message, error_position=node.get_source_position(),
log_level=LoggingLevel.ERROR)
def visit_ode_equation(self, node):
"""
Checks the coco.
:param node: A single ode equation.
:type node: ast_ode_equation
"""
if node.get_lhs().get_differential_order() == 0:
code, message = Messages.get_order_not_declared(node.get_lhs().get_name())
Logger.log_message(error_position=node.get_source_position(), code=code,
message=message, log_level=LoggingLevel.ERROR)
def handle_target(cls, target):
if target is None or target.upper() == "NONE":
target = "" # make sure `target` is always a string
if target not in CodeGenerator.get_known_targets():
code, message = Messages.get_unknown_target(target)
Logger.log_message(None, code, message, None, LoggingLevel.ERROR)
raise InvalidTargetException()
cls.target = target
def register_type(cls, symbol):
"""
Registers a new type into the system.
:param: a single type symbol.
:type: UnitTypeSymbol
"""
if not symbol.is_primitive() and symbol.unit.get_name() not in cls.name2type.keys():
cls.name2type[symbol.unit.get_name()] = symbol
code, message = Messages.get_new_type_registered(symbol.unit.get_name())
Logger.log_message(code=code, message=message, log_level=LoggingLevel.INFO)
return
def visit_declaration(self, node):
"""
Checks if the coco applies.
:param node: a single declaration.
:type node: ASTDeclaration.
"""
if node.is_function and not node.has_expression():
code, message = Messages.get_no_rhs(node.get_variables()[0].get_name())
Logger.log_message(error_position=node.get_source_position(), log_level=LoggingLevel.ERROR,
code=code, message=message)
return
def visit_declaration(self, node):
"""
Checks the coco.
:param node: a single declaration.
:type node: ast_declaration
"""
if node.is_function and len(node.get_variables()) > 1:
code, message = Messages.get_several_lhs(list((var.get_name() for var in node.get_variables())))
Logger.log_message(error_position=node.get_source_position(),
log_level=LoggingLevel.ERROR,
code=code, message=message)
return
def analyse_transform_neurons(self, neurons):
# type: (list(ASTNeuron)) -> None
"""
Analyse and transform a list of neurons.
:param neurons: a list of neurons.
"""
for neuron in neurons:
code, message = Messages.get_analysing_transforming_neuron(neuron.get_name())
Logger.log_message(None, code, message, None, LoggingLevel.INFO)
self.analyse_neuron(neuron)
# now store the transformed model
self.store_transformed_model(neuron)
def visit_ode_equation(self, node):
"""
Ensures the coco.
:param node: a single equation object.
:type node: ast_ode_equation
"""
symbol = node.get_scope().resolve_to_symbol(node.get_lhs().get_name_of_lhs(), SymbolKind.VARIABLE)
if symbol is not None and not symbol.is_init_values():
code, message = Messages.get_equation_var_not_in_init_values_block(node.get_lhs().get_name_of_lhs())
Logger.log_message(code=code, message=message,
error_position=node.get_source_position(),
log_level=LoggingLevel.ERROR)
return
def check_co_co(cls, node):
"""
Ensures the coco for the handed over neuron.
:param node: a single neuron instance.
:type node: ast_neuron
"""
for func in node.get_functions():
if func.get_name() in cls.nest_name_space:
code, message = Messages.get_nest_collision(func.get_name())
Logger.log_message(error_position=func.get_source_position(),
code=code, message=message,
log_level=LoggingLevel.ERROR)
return
def visit_assignment(self, node):
"""
Checks the coco on the current node.
:param node: a single node.
:type node: ast_assignment
"""
symbol = node.get_scope().resolve_to_symbol(node.get_variable().get_name(), SymbolKind.VARIABLE)
if (symbol is not None and symbol.block_type == BlockType.PARAMETERS and
node.get_scope().get_scope_type() != ScopeType.GLOBAL):
code, message = Messages.get_assignment_not_allowed(node.get_variable().get_complete_name())
Logger.log_message(error_position=node.get_source_position(),
code=code, message=message,
log_level=LoggingLevel.ERROR)
return
def get_unit(cls, name):
"""
Returns a single UnitType if the corresponding unit has been predefined.
:param name: the name of a unit
:type name: str
:return: a single UnitType object, or None
:rtype: UnitType
"""
if name in cls.name2unit.keys():
return cls.name2unit[name]
else:
code, message = Messages.get_unit_does_not_exist(name)
Logger.log_message(code=code, message=message, log_level=LoggingLevel.ERROR)
return None
def visit_input_line(self, node):
"""
Private method: Used to visit a single input line, create the corresponding symbol and update the scope.
:param node: a single input line.
:type node: ast_input_line
"""
if node.is_spike() and node.has_datatype():
node.get_datatype().update_scope(node.get_scope())
elif node.is_spike():
code, message = Messages.get_buffer_type_not_defined(node.get_name())
Logger.log_message(code=code, message=message, error_position=node.get_source_position(),
log_level=LoggingLevel.WARNING)
for inputType in node.get_input_types():
inputType.update_scope(node.get_scope())
def visit_simple_expression(self, node):
"""
Visits a single function call as stored in a simple expression and derives the correct type of all its
parameters. :param node: a simple expression :type node: ASTSimpleExpression :rtype void
"""
assert isinstance(node, ASTSimpleExpression), \
'(PyNestML.Visitor.FunctionCallVisitor) No or wrong type of simple expression provided (%s)!' % tuple(node)
assert (node.get_scope() is not None), \
"(PyNestML.Visitor.FunctionCallVisitor) No scope found, run symboltable creator!"
scope = node.get_scope()
function_name = node.get_function_call().get_name()
method_symbol = scope.resolve_to_symbol(function_name, SymbolKind.FUNCTION)
# check if this function exists
if method_symbol is None:
code, message = Messages.get_could_not_resolve(function_name)
Logger.log_message(code=code, message=message, error_position=node.get_source_position(),
log_level=LoggingLevel.ERROR)
node.type = ErrorTypeSymbol()
return
return_type = method_symbol.get_return_type()
return_type.referenced_object = node
# convolve symbol does not have a return type set.
# returns whatever type the second parameter is.
if function_name == PredefinedFunctions.CONVOLVE:
# Deviations from the assumptions made here are handled in the convolveCoco
buffer_parameter = node.get_function_call().get_args()[1]
if buffer_parameter.get_variable() is not None:
buffer_name = buffer_parameter.get_variable().get_name()
buffer_symbol_resolve = scope.resolve_to_symbol(buffer_name, SymbolKind.VARIABLE)
if buffer_symbol_resolve is not None:
node.type = buffer_symbol_resolve.get_type_symbol()
return
# getting here means there is an error with the parameters to convolve
code, message = Messages.get_convolve_needs_buffer_parameter()
Logger.log_message(code=code, message=message, error_position=node.get_source_position(),
log_level=LoggingLevel.ERROR)
node.type = ErrorTypeSymbol()
return
if isinstance(method_symbol.get_return_type(), VoidTypeSymbol):
# todo by KP: the error message is not used here, @ptraeder fix this
# error_msg = ErrorStrings.message_void_function_on_rhs(self, function_name, node.get_source_position())
node.type = ErrorTypeSymbol()
return
# if nothing special is handled, just get the expression type from the return type of the function
node.type = return_type
def do_magnitude_conversion_rhs_to_lhs(_rhs_type_symbol, _lhs_type_symbol, _containing_expression):
"""
determine conversion factor from rhs to lhs, register it with the relevant expression, drop warning
"""
_containing_expression.set_implicit_conversion_factor(
UnitTypeSymbol.get_conversion_factor(_lhs_type_symbol.astropy_unit,
_rhs_type_symbol.astropy_unit))
_containing_expression.type = _lhs_type_symbol
code, message = Messages.get_implicit_magnitude_conversion(_lhs_type_symbol, _rhs_type_symbol,
_containing_expression.get_implicit_conversion_factor())
Logger.log_message(code=code, message=message,
error_position=_containing_expression.get_source_position(),
log_level=LoggingLevel.WARNING)
def convert_name_reference(self, variable):
"""
Converts a single variable to nest processable format.
:param variable: a single variable.
:type variable: ASTVariable
:return: a nest processable format.
:rtype: str
"""
from pynestml.codegeneration.nest_printer import NestPrinter
assert (variable is not None and isinstance(variable, ASTVariable)), \
'(PyNestML.CodeGeneration.NestReferenceConverter) No or wrong type of uses-gsl provided (%s)!' % type(
variable)
variable_name = NestNamesConverter.convert_to_cpp_name(variable.get_complete_name())
if PredefinedUnits.is_unit(variable.get_complete_name()):
return str(
UnitConverter.get_factor(PredefinedUnits.get_unit(variable.get_complete_name()).get_unit()))
if variable_name == PredefinedVariables.E_CONSTANT:
return 'numerics::e'
else:
symbol = variable.get_scope().resolve_to_symbol(variable_name, SymbolKind.VARIABLE)
if symbol is None:
# this should actually not happen, but an error message is better than an exception
code, message = Messages.get_could_not_resolve(variable_name)
Logger.log_message(log_level=LoggingLevel.ERROR, code=code, message=message,
error_position=variable.get_source_position())
return ''
else:
if symbol.is_local():
return variable_name + ('[i]' if symbol.has_vector_parameter() else '')
elif symbol.is_buffer():
return NestPrinter.print_origin(symbol) + NestNamesConverter.buffer_value(symbol) \
+ ('[i]' if symbol.has_vector_parameter() else '')
else:
if symbol.is_function:
return 'get_' + variable_name + '()' + ('[i]' if symbol.has_vector_parameter() else '')
else:
if symbol.is_init_values():
temp = NestPrinter.print_origin(symbol)
if self.uses_gsl:
temp += GSLNamesConverter.name(symbol)
else:
temp += NestNamesConverter.name(symbol)
temp += ('[i]' if symbol.has_vector_parameter() else '')
return temp
else:
return NestPrinter.print_origin(symbol) + \
NestNamesConverter.name(symbol) + \
('[i]' if symbol.has_vector_parameter() else '')
def visit_expression(self, node):
"""
Visits a single rhs but does not execute any steps besides printing a message. This
visitor indicates that no functionality has been implemented for this type of nodes.
:param node: a single rhs
:type node: ast_expression or ast_simple_expression
"""
error_msg = ErrorStrings.message_no_semantics(self, str(node), node.get_source_position())
node.type = ErrorTypeSymbol()
# just warn though
Logger.log_message(message=error_msg,
code=MessageCode.NO_SEMANTICS,
error_position=node.get_source_position(),
log_level=LoggingLevel.WARNING)
return
def visit_function_call(self, node):
"""
Checks the coco on the current function call.
:param node: a single function call.
:type node: ast_function_call
"""
f_name = node.get_name()
if f_name == PredefinedFunctions.CURR_SUM or \
f_name == PredefinedFunctions.COND_SUM or f_name == PredefinedFunctions.CONVOLVE:
for arg in node.get_args():
if not isinstance(arg, ASTSimpleExpression) or not arg.is_variable():
code, message = Messages.get_not_a_variable(str(arg))
Logger.log_message(code=code, message=message,
error_position=arg.get_source_position(), log_level=LoggingLevel.ERROR)
return
def visit_input_line(self, node):
"""
Checks the coco on the current node.
:param node: a single input line node.
:type node: ast_input_line
"""
if node.is_spike() and not node.has_datatype():
code, message = Messages.get_data_type_not_specified(node.get_name())
Logger.log_message(error_position=node.get_source_position(), log_level=LoggingLevel.ERROR,
code=code, message=message)
if node.is_current() and node.has_datatype():
code, message = Messages.get_not_type_allowed(node.get_name())
Logger.log_message(error_position=str(node.get_source_position()),
code=code, message=message,
log_level=LoggingLevel.ERROR)
return