def setup_model_generation_helpers(self, neuron: ASTNeuron):
"""
Returns a namespace for Jinja2 neuron model documentation template.
:param neuron: a single neuron instance
:type neuron: ASTNeuron
:return: a map from name to functionality.
:rtype: dict
"""
converter = LatexReferenceConverter()
latex_expression_printer = LatexExpressionPrinter(converter)
namespace = dict()
namespace['now'] = datetime.datetime.utcnow()
namespace['neuron'] = neuron
namespace['neuronName'] = str(neuron.get_name())
namespace['printer'] = NestPrinter(latex_expression_printer)
namespace['assignments'] = NestAssignmentsHelper()
namespace['names'] = NestNamesConverter()
namespace['declarations'] = NestDeclarationsHelper()
namespace['utils'] = ASTUtils()
namespace['odeTransformer'] = OdeTransformer()
import textwrap
pre_comments_bak = neuron.pre_comments
neuron.pre_comments = []
namespace['neuron_source_code'] = textwrap.indent(
neuron.__str__(), " ")
neuron.pre_comments = pre_comments_bak
return namespace
def setup_index_generation_helpers(self, neurons: List[ASTNeuron]):
"""
Returns a namespace for Jinja2 neuron model index page template.
:param neurons: a list of neuron instances
:type neurons: List[ASTNeuron]
:return: a map from name to functionality.
:rtype: dict
"""
converter = LatexReferenceConverter()
latex_expression_printer = LatexExpressionPrinter(converter)
namespace = dict()
namespace['now'] = datetime.datetime.utcnow()
namespace['neurons'] = neurons
namespace['neuronNames'] = [
str(neuron.get_name()) for neuron in neurons
]
namespace['printer'] = NestPrinter(latex_expression_printer)
namespace['assignments'] = NestAssignmentsHelper()
namespace['names'] = NestNamesConverter()
namespace['declarations'] = NestDeclarationsHelper()
namespace['utils'] = ASTUtils()
namespace['odeTransformer'] = OdeTransformer()
return namespace
def setup_generation_helpers(neuron):
"""
Returns a standard namespace with often required functionality.
:param neuron: a single neuron instance
:type neuron: ASTNeuron
:return: a map from name to functionality.
:rtype: dict
"""
gsl_converter = GSLReferenceConverter()
gsl_printer = LegacyExpressionPrinter(gsl_converter)
# helper classes and objects
converter = NESTReferenceConverter(False)
legacy_pretty_printer = LegacyExpressionPrinter(converter)
namespace = dict()
namespace['neuronName'] = neuron.get_name()
namespace['neuron'] = neuron
namespace['moduleName'] = FrontendConfiguration.get_module_name()
namespace['printer'] = NestPrinter(legacy_pretty_printer)
namespace['assignments'] = NestAssignmentsHelper()
namespace['names'] = NestNamesConverter()
namespace['declarations'] = NestDeclarationsHelper()
namespace['utils'] = ASTUtils()
namespace['idemPrinter'] = LegacyExpressionPrinter()
namespace['outputEvent'] = namespace['printer'].print_output_event(neuron.get_body())
namespace['is_spike_input'] = ASTUtils.is_spike_input(neuron.get_body())
namespace['is_current_input'] = ASTUtils.is_current_input(neuron.get_body())
namespace['odeTransformer'] = OdeTransformer()
namespace['printerGSL'] = gsl_printer
namespace['now'] = datetime.datetime.utcnow()
define_solver_type(neuron, namespace)
return namespace
def setup_generation_helpers(self, neuron):
"""
Returns a standard namespace with often required functionality.
:param neuron: a single neuron instance
:type neuron: ASTNeuron
:return: a map from name to functionality.
:rtype: dict
"""
gsl_converter = GSLReferenceConverter()
gsl_printer = LegacyExpressionPrinter(gsl_converter)
# helper classes and objects
converter = NESTReferenceConverter(False)
legacy_pretty_printer = LegacyExpressionPrinter(converter)
namespace = dict()
namespace['neuronName'] = neuron.get_name()
namespace['neuron'] = neuron
namespace['moduleName'] = FrontendConfiguration.get_module_name()
namespace['printer'] = NestPrinter(legacy_pretty_printer)
namespace['assignments'] = NestAssignmentsHelper()
namespace['names'] = NestNamesConverter()
namespace['declarations'] = NestDeclarationsHelper()
namespace['utils'] = ASTUtils()
namespace['idemPrinter'] = LegacyExpressionPrinter()
namespace['outputEvent'] = namespace['printer'].print_output_event(neuron.get_body())
namespace['is_spike_input'] = ASTUtils.is_spike_input(neuron.get_body())
namespace['is_current_input'] = ASTUtils.is_current_input(neuron.get_body())
namespace['odeTransformer'] = OdeTransformer()
namespace['printerGSL'] = gsl_printer
namespace['now'] = datetime.datetime.utcnow()
namespace['tracing'] = FrontendConfiguration.is_dev
namespace['PredefinedUnits'] = pynestml.symbols.predefined_units.PredefinedUnits
namespace['UnitTypeSymbol'] = pynestml.symbols.unit_type_symbol.UnitTypeSymbol
rng_visitor = ASTRandomNumberGeneratorVisitor()
neuron.accept(rng_visitor)
namespace['norm_rng'] = rng_visitor._norm_rng_is_used
self.define_solver_type(neuron, namespace)
return namespace
def setup_generation_helpers(self, neuron: ASTNeuron) -> Dict:
"""
Returns a standard namespace with often required functionality.
:param neuron: a single neuron instance
:type neuron: ASTNeuron
:return: a map from name to functionality.
:rtype: dict
"""
gsl_converter = GSLReferenceConverter()
gsl_printer = UnitlessExpressionPrinter(gsl_converter)
# helper classes and objects
converter = NESTReferenceConverter(False)
unitless_pretty_printer = UnitlessExpressionPrinter(converter)
namespace = dict()
namespace['neuronName'] = neuron.get_name()
namespace['neuron'] = neuron
namespace['moduleName'] = FrontendConfiguration.get_module_name()
namespace['printer'] = NestPrinter(unitless_pretty_printer)
namespace['assignments'] = NestAssignmentsHelper()
namespace['names'] = NestNamesConverter()
namespace['declarations'] = NestDeclarationsHelper()
namespace['utils'] = ASTUtils()
namespace['idemPrinter'] = UnitlessExpressionPrinter()
namespace['outputEvent'] = namespace['printer'].print_output_event(
neuron.get_body())
namespace['is_spike_input'] = ASTUtils.is_spike_input(
neuron.get_body())
namespace['is_current_input'] = ASTUtils.is_current_input(
neuron.get_body())
namespace['odeTransformer'] = OdeTransformer()
namespace['printerGSL'] = gsl_printer
namespace['now'] = datetime.datetime.utcnow()
namespace['tracing'] = FrontendConfiguration.is_dev
namespace[
'PredefinedUnits'] = pynestml.symbols.predefined_units.PredefinedUnits
namespace[
'UnitTypeSymbol'] = pynestml.symbols.unit_type_symbol.UnitTypeSymbol
namespace['initial_values'] = {}
namespace['uses_analytic_solver'] = neuron.get_name() in self.analytic_solver.keys() \
and self.analytic_solver[neuron.get_name()] is not None
if namespace['uses_analytic_solver']:
namespace['analytic_state_variables'] = self.analytic_solver[
neuron.get_name()]["state_variables"]
namespace['analytic_variable_symbols'] = {
sym:
neuron.get_equations_block().get_scope().resolve_to_symbol(
sym, SymbolKind.VARIABLE)
for sym in namespace['analytic_state_variables']
}
namespace['update_expressions'] = {}
for sym, expr in self.analytic_solver[
neuron.get_name()]["initial_values"].items():
namespace['initial_values'][sym] = expr
for sym in namespace['analytic_state_variables']:
expr_str = self.analytic_solver[
neuron.get_name()]["update_expressions"][sym]
expr_ast = ModelParser.parse_expression(expr_str)
# pretend that update expressions are in "equations" block, which should always be present, as differential equations must have been defined to get here
expr_ast.update_scope(
neuron.get_equations_blocks().get_scope())
expr_ast.accept(ASTSymbolTableVisitor())
namespace['update_expressions'][sym] = expr_ast
namespace['propagators'] = self.analytic_solver[
neuron.get_name()]["propagators"]
namespace['uses_numeric_solver'] = neuron.get_name() in self.analytic_solver.keys() \
and self.numeric_solver[neuron.get_name()] is not None
if namespace['uses_numeric_solver']:
namespace['numeric_state_variables'] = self.numeric_solver[
neuron.get_name()]["state_variables"]
namespace['numeric_variable_symbols'] = {
sym:
neuron.get_equations_block().get_scope().resolve_to_symbol(
sym, SymbolKind.VARIABLE)
for sym in namespace['numeric_state_variables']
}
assert not any([
sym is None
for sym in namespace['numeric_variable_symbols'].values()
])
namespace['numeric_update_expressions'] = {}
for sym, expr in self.numeric_solver[
neuron.get_name()]["initial_values"].items():
namespace['initial_values'][sym] = expr
for sym in namespace['numeric_state_variables']:
expr_str = self.numeric_solver[
neuron.get_name()]["update_expressions"][sym]
expr_ast = ModelParser.parse_expression(expr_str)
# pretend that update expressions are in "equations" block, which should always be present, as differential equations must have been defined to get here
expr_ast.update_scope(
neuron.get_equations_blocks().get_scope())
expr_ast.accept(ASTSymbolTableVisitor())
namespace['numeric_update_expressions'][sym] = expr_ast
namespace['useGSL'] = namespace['uses_numeric_solver']
namespace['names'] = GSLNamesConverter()
converter = NESTReferenceConverter(True)
unitless_pretty_printer = UnitlessExpressionPrinter(converter)
namespace['printer'] = NestPrinter(unitless_pretty_printer)
namespace["spike_updates"] = neuron.spike_updates
rng_visitor = ASTRandomNumberGeneratorVisitor()
neuron.accept(rng_visitor)
namespace['norm_rng'] = rng_visitor._norm_rng_is_used
return namespace