def build(self):
"""
Build the simulation components from the model.
@return: A runnable simulation object
@rtype: lems.sim.sim.Simulation
"""
self.sim = Simulation()
for component_id in self.model.default_runs:
if component_id not in self.model.context.components:
raise SimBuildError('Unable to find component \'{0}\' to run'\
.format(component_id))
component = self.model.context.components[component_id]
runnable = self.build_runnable(component)
self.sim.add_runnable(component.id, runnable)
return self.sim
def build(self):
"""
Build the simulation components from the model.
@return: A runnable simulation object
@rtype: lems.sim.sim.Simulation
"""
self.sim = Simulation()
for component_id in self.model.targets:
if component_id not in self.model.components:
raise SimBuildError("Unable to find target component '{0}'",
component_id)
component = self.model.fat_components[component_id]
runnable = self.build_runnable(component)
self.sim.add_runnable(runnable)
return self.sim
def build(self):
"""
Build the simulation components from the model.
@return: A runnable simulation object
@rtype: lems.sim.sim.Simulation
"""
self.sim = Simulation()
for component_id in self.model.default_runs:
if component_id not in self.model.context.components:
raise SimBuildError("Unable to find component '{0}' to run".format(component_id))
component = self.model.context.components[component_id]
runnable = self.build_runnable(component)
self.sim.add_runnable(component.id, runnable)
return self.sim
def build(self):
"""
Build the simulation components from the model.
@return: A runnable simulation object
@rtype: lems.sim.sim.Simulation
"""
self.sim = Simulation()
for component_id in self.model.targets:
if component_id not in self.model.components:
raise SimBuildError("Unable to find target component '{0}'",
component_id)
component = self.model.fat_components[component_id]
runnable = self.build_runnable(component)
self.sim.add_runnable(runnable)
return self.sim
class SimulationBuilder(LEMSBase):
"""
Simulation builder class.
"""
debug = False
def __init__(self, model):
"""
Constructor.
@param model: Model upon which the simulation is to be generated.
@type model: lems.model.model.Model
"""
self.model = model
""" Model to be used for constructing the simulation.
@type: lems.model.model.Model """
self.sim = None
""" Simulation built from the model.
@type: lems.sim.sim.Simulation """
self.current_record_target = None
self.current_data_output = None
def build(self):
"""
Build the simulation components from the model.
@return: A runnable simulation object
@rtype: lems.sim.sim.Simulation
"""
self.sim = Simulation()
for component_id in self.model.targets:
if component_id not in self.model.components:
raise SimBuildError("Unable to find target component '{0}'",
component_id)
component = self.model.fat_components[component_id]
runnable = self.build_runnable(component)
self.sim.add_runnable(runnable)
return self.sim
def build_runnable(self, component, parent = None, id_ = None):
"""
Build a runnable component from a component specification and add
it to the simulation.
@param component: Component specification
@type component: lems.model.component.FatComponent
@param parent: Parent runnable component.
@type parent: lems.sim.runnable.Runnable
@param id_: Optional id for therunnable. If it's not passed in,
the runnable will inherit the id of the component.
@raise SimBuildError: Raised when a component reference cannot be
resolved.
"""
if self.debug: print("++++++++ Calling build_runnable of %s with parent %s"%(component, parent))
if id_ == None:
runnable = Runnable(component.id, component, parent)
else:
runnable = Runnable(id_, component, parent)
simulation = component.simulation
record_target_backup = self.current_record_target
data_output_backup = self.current_data_output
do = None
for d in simulation.data_displays:
do = d
if do == None:
for d in simulation.data_writers:
do = d
if do != None:
self.current_data_output = do
for parameter in component.parameters:
runnable.add_instance_variable(parameter.name, parameter.numeric_value)
derived_parameter_code = []
derived_parameter_ordering = order_derived_parameters(component)
for dpn in derived_parameter_ordering:
derived_parameter = component.derived_parameters[dpn]
runnable.add_derived_variable(derived_parameter.name)
expression = self.build_expression_from_tree(runnable,
None,
derived_parameter.expression_tree)
derived_parameter_code += ['self.{0} = ({1})'.format(
derived_parameter.name,
expression)]
derived_parameter_code += ['self.{0}_shadow = ({1})'.format(
derived_parameter.name,
expression)]
suffix = ''
runnable.add_method('update_derived_parameters' + suffix, ['self'],
derived_parameter_code)
for constant in component.constants:
runnable.add_instance_variable(constant.name, constant.numeric_value)
for text in component.texts:
runnable.add_text_variable(text.name, text.value)
for link in component.links:
runnable.add_text_variable(link.name, link.value)
for ep in component.event_ports:
if ep.direction.lower() == 'in':
runnable.add_event_in_port(ep.name)
else:
runnable.add_event_out_port(ep.name)
dynamics = component.dynamics
self.add_dynamics_1(component, runnable, dynamics, dynamics)
for regime in dynamics.regimes:
self.add_dynamics_1(component, runnable, regime, dynamics)
if regime.initial:
runnable.current_regime = regime.name
rn = regime.name
if rn not in runnable.regimes:
runnable.add_regime(RunnableRegime(rn))
r = runnable.regimes[rn]
suffix = '_regime_' + rn
if runnable.__dict__.has_key('update_state_variables' + suffix):
r.update_state_variables = runnable.__dict__['update_state_variables' + suffix]
if runnable.__dict__.has_key('update_derived_variables' + suffix):
r.update_derived_variables = runnable.__dict__['update_derived_variables' + suffix]
if runnable.__dict__.has_key('run_startup_event_handlers' + suffix):
r.run_startup_event_handlers = runnable.__dict__['run_startup_event_handlers' + suffix]
if runnable.__dict__.has_key('run_preprocessing_event_handlers' + suffix):
r.run_preprocessing_event_handlers = runnable.__dict__['run_preprocessing_event_handlers' + suffix]
if runnable.__dict__.has_key('run_postprocessing_event_handlers' + suffix):
r.run_postprocessing_event_handlers = runnable.__dict__['run_postprocessing_event_handlers' + suffix]
self.process_simulation_specs(component, runnable, component.simulation)
for child in component.child_components:
child_runnable = self.build_runnable(child, runnable)
runnable.add_child(child.id, child_runnable)
for children in component.children:
#GG - These conditions need more debugging.
if children.type in child.types:
runnable.add_child_typeref(children.type, child_runnable)
if children.multiple:
if children.type in child.types:
runnable.add_child_to_group(children.name, child_runnable)
else:
if child_runnable.id == children.name:
runnable.add_child_typeref(children.name, child_runnable)
for attachment in component.attachments:
runnable.make_attachment(attachment.type, attachment.name)
self.build_structure(component, runnable, component.structure)
dynamics = component.dynamics
self.add_dynamics_2(component, runnable,
dynamics, dynamics)
for regime in dynamics.regimes:
self.add_dynamics_2(component, runnable, regime, dynamics)
if regime.name not in runnable.regimes:
runnable.add_regime(RunnableRegime(regime.name))
r = runnable.regimes[regime.name]
suffix = '_regime_' + regime.name
if runnable.__dict__.has_key('update_kinetic_scheme' + suffix):
r.update_kinetic_scheme = runnable.__dict__['update_kinetic_scheme' + suffix]
self.add_recording_behavior(component, runnable)
self.current_data_output = data_output_backup
self.current_record_target = record_target_backup
return runnable
def build_event_connections(self, component, runnable, structure):
"""
Adds event connections to a runnable component based on the structure
specifications in the component model.
@param component: Component model containing structure specifications.
@type component: lems.model.component.FatComponent
@param runnable: Runnable component to which structure is to be added.
@type runnable: lems.sim.runnable.Runnable
@param structure: The structure object to be used to add
structure code in the runnable component.
@type structure: lems.model.structure.Structure
"""
if self.debug: print("\n++++++++ Calling build_event_connections of %s with runnable %s, parent %s"%(component.id, runnable.id, runnable.parent))
# Process event connections
for ec in structure.event_connections:
if self.debug: print(ec.toxml())
source = runnable.parent.resolve_path(ec.from_)
target = runnable.parent.resolve_path(ec.to)
if ec.receiver:
receiver_template = self.build_runnable(ec.receiver,
target)
#receiver = copy.deepcopy(receiver_template)
receiver = receiver_template.copy()
receiver.id = "{0}__{1}__".format(component.id,
receiver_template.id)
if ec.receiver_container:
target.add_attachment(receiver, ec.receiver_container)
target.add_child(receiver_template.id, receiver)
target = receiver
else:
source = runnable.resolve_path(ec.from_)
target = runnable.resolve_path(ec.to)
source_port = ec.source_port
target_port = ec.target_port
if not source_port:
if len(source.event_out_ports) == 1:
source_port = source.event_out_ports[0]
else:
raise SimBuildError(("No source event port "
"uniquely identifiable"
" in '{0}'").format(source.id))
if not target_port:
if len(target.event_in_ports) == 1:
target_port = target.event_in_ports[0]
else:
raise SimBuildError(("No destination event port "
"uniquely identifiable "
"in '{0}'").format(target))
if self.debug: print("register_event_out_callback\n Source: %s, %s (port: %s) \n -> %s, %s (port: %s)"%(source, id(source), source_port, target, id(target), target_port))
source.register_event_out_callback(\
source_port, lambda: target.inc_event_in(target_port))
def build_structure(self, component, runnable, structure):
"""
Adds structure to a runnable component based on the structure
specifications in the component model.
@param component: Component model containing structure specifications.
@type component: lems.model.component.FatComponent
@param runnable: Runnable component to which structure is to be added.
@type runnable: lems.sim.runnable.Runnable
@param structure: The structure object to be used to add
structure code in the runnable component.
@type structure: lems.model.structure.Structure
"""
if self.debug: print("\n++++++++ Calling build_structure of %s with runnable %s, parent %s"%(component.id, runnable.id, runnable.parent))
# Process single-child instantiations
for ch in structure.child_instances:
child_runnable = self.build_runnable(ch.referenced_component, runnable)
runnable.add_child(child_runnable.id, child_runnable)
runnable.add_child_typeref(ch.component, child_runnable)
# Process multi-child instatiantions
for mi in structure.multi_instantiates:
template = self.build_runnable(mi.component,
runnable)
for i in range(mi.number):
#instance = copy.deepcopy(template)
instance = template.copy()
instance.id = "{0}__{1}__{2}".format(component.id,
template.id,
i)
runnable.array.append(instance)
# Process foreach statements
for fe in structure.for_eachs:
self.build_foreach(component, runnable, fe)
self.build_event_connections(component, runnable, structure)
def build_foreach(self, component, runnable, foreach, name_mappings = {}):
"""
Iterate over ForEach constructs and process nested elements.
@param component: Component model containing structure specifications.
@type component: lems.model.component.FatComponent
@param runnable: Runnable component to which structure is to be added.
@type runnable: lems.sim.runnable.Runnable
@param foreach: The ForEach structure object to be used to add
structure code in the runnable component.
@type foreach: lems.model.structure.ForEach
"""
if self.debug: print("\n++++++++ Calling build_foreach of %s with runnable %s, parent %s, name_mappings: %s"%(component.id, runnable.id, runnable.parent, name_mappings))
target_array = runnable.resolve_path(foreach.instances)
for target_runnable in target_array:
if self.debug: print("Applying contents of for_each to %s, as %s"%(target_runnable.id, foreach.as_))
name_mappings[foreach.as_] = target_runnable
# Process foreach statements
for fe2 in foreach.for_eachs:
#print fe2.toxml()
target_array2 = runnable.resolve_path(fe2.instances)
for target_runnable2 in target_array2:
name_mappings[fe2.as_] = target_runnable2
self.build_foreach(component, runnable, fe2, name_mappings)
# Process event connections
for ec in foreach.event_connections:
source = name_mappings[ec.from_]
target = name_mappings[ec.to]
source_port = ec.source_port
target_port = ec.target_port
if not source_port:
if len(source.event_out_ports) == 1:
source_port = source.event_out_ports[0]
else:
raise SimBuildError(("No source event port "
"uniquely identifiable"
" in '{0}'").format(source.id))
if not target_port:
if len(target.event_in_ports) == 1:
target_port = target.event_in_ports[0]
else:
raise SimBuildError(("No destination event port "
"uniquely identifiable "
"in '{0}'").format(target))
if self.debug: print("register_event_out_callback\n Source: %s, %s (port: %s) \n -> %s, %s (port: %s)"%(source, id(source), source_port, target, id(target), target_port))
source.register_event_out_callback(\
source_port, lambda: target.inc_event_in(target_port))
def add_dynamics_1(self, component, runnable, regime, dynamics):
"""
Adds dynamics to a runnable component based on the dynamics
specifications in the component model.
This method builds dynamics necessary for building child components.
@param component: Component model containing dynamics specifications.
@type component: lems.model.component.FatComponent
@param runnable: Runnable component to which dynamics is to be added.
@type runnable: lems.sim.runnable.Runnable
@param regime: The dynamics regime to be used to generate
dynamics code in the runnable component.
@type regime: lems.model.dynamics.Regime
@param dynamics: Shared dynamics specifications.
@type dynamics: lems.model.dynamics.Regime
@raise SimBuildError: Raised when a time derivative expression refers
to an undefined variable.
@raise SimBuildError: Raised when there are invalid time
specifications for the <Run> statement.
@raise SimBuildError: Raised when the component reference for <Run>
cannot be resolved.
"""
if isinstance(regime, Dynamics) or regime.name == '':
suffix = ''
else:
suffix = '_regime_' + regime.name
if isinstance(regime, Regime) and regime.initial:
runnable.new_regime = regime.name
# Process state variables
for sv in regime.state_variables:
runnable.add_instance_variable(sv.name, 0)
# Process time derivatives
time_step_code = []
for td in regime.time_derivatives:
if td.variable not in regime.state_variables and td.variable not in dynamics.state_variables:
raise SimBuildError(('Time derivative for undefined state '
'variable {0} in component {1}').format(td.variable, component.id))
exp = self.build_expression_from_tree(runnable,
regime,
td.expression_tree)
time_step_code += ['self.{0} += dt * ({1})'.format(td.variable,
exp)]
runnable.add_method('update_state_variables' + suffix, ['self', 'dt'],
time_step_code)
# Process derived variables
derived_variable_code = []
derived_variables_ordering = order_derived_variables(regime)
for dvn in derived_variables_ordering: #regime.derived_variables:
if dvn in dynamics.derived_variables:
dv = dynamics.derived_variables[dvn]
runnable.add_derived_variable(dv.name)
if dv.value:
derived_variable_code += ['self.{0} = ({1})'.format(
dv.name,
self.build_expression_from_tree(runnable,
regime,
dv.expression_tree))]
elif dv.select:
if dv.reduce:
derived_variable_code += self.build_reduce_code(dv.name,
dv.select,
dv.reduce)
else:
derived_variable_code += ['self.{0} = (self.{1})'.format(
dv.name,
dv.select.replace('/', '.'))]
else:
raise SimBuildError(('Inconsistent derived variable settings'
'for {0}').format(dvn))
elif dvn in dynamics.conditional_derived_variables:
dv = dynamics.conditional_derived_variables[dvn]
runnable.add_derived_variable(dv.name)
derived_variable_code += self.build_conditional_derived_var_code(runnable,
regime,
dv)
else:
raise SimBuildError("Unknown derived variable '{0}' in '{1}'",
dvn, runnable.id)
runnable.add_method('update_derived_variables' + suffix, ['self'],
derived_variable_code)
# Process event handlers
pre_event_handler_code = []
post_event_handler_code = []
startup_event_handler_code = []
on_entry_added = False
for eh in regime.event_handlers:
if isinstance(eh, OnStart):
startup_event_handler_code += self.build_event_handler(runnable,
regime,
eh)
elif isinstance(eh, OnCondition):
post_event_handler_code += self.build_event_handler(runnable,
regime,
eh)
else:
if isinstance(eh, OnEntry):
on_entry_added = True
pre_event_handler_code += self.build_event_handler(runnable,
regime,
eh)
if isinstance(regime, Regime) and not on_entry_added:
pre_event_handler_code += self.build_event_handler(runnable, regime, OnEntry())
runnable.add_method('run_startup_event_handlers' + suffix, ['self'],
startup_event_handler_code)
runnable.add_method('run_preprocessing_event_handlers' + suffix, ['self'],
pre_event_handler_code)
runnable.add_method('run_postprocessing_event_handlers' + suffix, ['self'],
post_event_handler_code)
def add_dynamics_2(self, component, runnable, regime, dynamics):
"""
Adds dynamics to a runnable component based on the dynamics
specifications in the component model.
This method builds dynamics dependent on child components.
@param component: Component model containing dynamics specifications.
@type component: lems.model.component.FatComponent
@param runnable: Runnable component to which dynamics is to be added.
@type runnable: lems.sim.runnable.Runnable
@param regime: The dynamics regime to be used to generate
dynamics code in the runnable component.
@type regime: lems.model.dynamics.Regime
@param dynamics: Shared dynamics specifications.
@type dynamics: lems.model.dynamics.Regime
@raise SimBuildError: Raised when a time derivative expression refers
to an undefined variable.
@raise SimBuildError: Raised when there are invalid time
specifications for the <Run> statement.
@raise SimBuildError: Raised when the component reference for <Run>
cannot be resolved.
"""
if isinstance(regime, Dynamics) or regime.name == '':
suffix = ''
else:
suffix = '_regime_' + regime.name
# Process kinetic schemes
ks_code = []
for ks in regime.kinetic_schemes:
raise NotImplementedError("KineticScheme element is not stable in PyLEMS yet, see https://github.com/LEMS/pylems/issues/15")
try:
###nodes = {node.id:node for node in runnable.__dict__[ks.nodes]}
nodes = {}
for node in runnable.__dict__[ks.nodes]:
nodes[node.id] = node
edges = runnable.__dict__[ks.edges]
for edge in edges:
from_ = edge.__dict__[ks.edge_source]
to = edge.__dict__[ks.edge_target]
ks_code += [('self.{0}.{2} += dt * (-self.{3}.{4} * self.{0}.{2}_shadow'
' + self.{3}.{5} * self.{1}.{2}_shadow)').format(
from_, to, ks.state_variable, edge.id,
ks.forward_rate, ks.reverse_rate)]
ks_code += [('self.{1}.{2} += dt * (self.{3}.{4} * self.{0}.{2}_shadow'
' - self.{3}.{5} * self.{1}.{2}_shadow)').format(
from_, to, ks.state_variable, edge.id,
ks.forward_rate, ks.reverse_rate)]
ks_code += ['sum = 0']
for node in nodes:
nodes[node].__dict__[ks.state_variable] = 1.0 / len(nodes)
nodes[node].__dict__[ks.state_variable + '_shadow'] = 1.0 / len(nodes)
ks_code += ['sum += self.{0}.{1}'.format(node, ks.state_variable)]
for node in nodes:
ks_code += ['self.{0}.{1} /= sum'.format(node, ks.state_variable)]
for node in nodes:
ks_code += [('self.{0}.{1}_shadow = '
'self.{0}.{1}').format(node,
ks.state_variable)]
except Exception as e:
raise SimBuildError(("Unable to construct kinetic scheme '{0}' "
"for component '{1}' - {2}").format(ks.name,
component.id,
str(e)))
runnable.add_method('update_kinetic_scheme' + suffix, ['self', 'dt'],
ks_code)
def process_simulation_specs(self, component, runnable, simulation):
"""
Process simulation-related aspects to a runnable component based on the
dynamics specifications in the component model.
@param component: Component model containing dynamics specifications.
@type component: lems.model.component.FatComponent
@param runnable: Runnable component to which dynamics is to be added.
@type runnable: lems.sim.runnable.Runnable
@param simulation: The simulation-related aspects to be implemented
in the runnable component.
@type simulation: lems.model.simulation.Simulation
@raise SimBuildError: Raised when a time derivative expression refers
to an undefined variable
@raise SimBuildError: Raised when there are invalid time
specifications for the <Run> statement.
@raise SimBuildError: Raised when the component reference for <Run>
cannot be resolved.
"""
# Process runs
for run in simulation.runs:
cid = run.component.id + '_' + component.id
target = self.build_runnable(run.component, runnable, cid)
self.sim.add_runnable(target)
self.current_record_target = target
target.configure_time(run.increment,
run.total)
def convert_op(self, op):
"""
Converts NeuroML arithmetic/logical operators to python equivalents.
@param op: NeuroML operator
@type op: string
@return: Python operator
@rtype: string
"""
if op == '.gt.':
return '>'
elif op == '.ge.' or op == '.geq.':
return '>='
elif op == '.lt.':
return '<'
elif op == '.le.':
return '<='
elif op == '.eq.':
return '=='
elif op == '.neq.':
return '!='
elif op == '.ne.': # .neq. is preferred!
return '!='
elif op == '^':
return '**'
elif op == '.and.':
return 'and'
elif op == '.or.':
return 'or'
else:
return op
def convert_func(self, func):
"""
Converts NeuroML arithmetic/logical functions to python equivalents.
@param func: NeuroML function
@type func: string
@return: Python operator
@rtype: string
"""
if func == 'ln':
return 'log'
if func == 'random':
return 'random.uniform'
else:
return func
def build_expression_from_tree(self, runnable, regime, tree_node):
"""
Recursively builds a Python expression from a parsed expression tree.
@param runnable: Runnable object to which this expression would be added.
@type runnable: lems.sim.runnable.Runnable
@param regime: Dynamics regime being built.
@type regime: lems.model.dynamics.Regime
@param tree_node: Root node for the tree from which the expression
is to be built.
@type tree_node: lems.parser.expr.ExprNode
@return: Generated Python expression.
@rtype: string
"""
component_type = self.model.component_types[runnable.component.type]
dynamics = component_type.dynamics
if tree_node.type == ExprNode.VALUE:
if tree_node.value[0].isalpha():
if tree_node.value == 't':
return 'self.time_completed'
elif tree_node.value in component_type.requirements:
var_prefix = 'self'
v = tree_node.value
r = runnable
while (v not in r.instance_variables and
v not in r.derived_variables):
var_prefix = '{0}.{1}'.format(var_prefix, 'parent')
r = r.parent
if r == None:
raise SimBuildError("Unable to resolve required "
"variable '{0}'".format(v))
return '{0}.{1}'.format(var_prefix, v)
elif (tree_node.value in dynamics.derived_variables or (regime is not None and tree_node.value in regime.derived_variables)):
return 'self.{0}'.format(tree_node.value)
else:
return 'self.{0}_shadow'.format(tree_node.value)
else:
return tree_node.value
elif tree_node.type == ExprNode.FUNC1:
pattern = '({0}({1}))'
func = self.convert_func(tree_node.func)
if 'random.uniform' in func:
pattern = '({0}(0,{1}))'
return pattern.format(\
func,
self.build_expression_from_tree(runnable,
regime,
tree_node.param))
else:
return '({0}) {1} ({2})'.format(\
self.build_expression_from_tree(runnable,
regime,
tree_node.left),
self.convert_op(tree_node.op),
self.build_expression_from_tree(runnable,
regime,
tree_node.right))
def build_event_handler(self, runnable, regime, event_handler):
"""
Build event handler code.
@param event_handler: Event handler object
@type event_handler: lems.model.dynamics.EventHandler
@return: Generated event handler code.
@rtype: list(string)
"""
if isinstance(event_handler, OnCondition):
return self.build_on_condition(runnable, regime, event_handler)
elif isinstance(event_handler, OnEvent):
return self.build_on_event(runnable, regime, event_handler)
elif isinstance(event_handler, OnStart):
return self.build_on_start(runnable, regime, event_handler)
elif isinstance(event_handler, OnEntry):
return self.build_on_entry(runnable, regime, event_handler)
else:
return []
def build_on_condition(self, runnable, regime, on_condition):
"""
Build OnCondition event handler code.
@param on_condition: OnCondition event handler object
@type on_condition: lems.model.dynamics.OnCondition
@return: Generated OnCondition code
@rtype: list(string)
"""
on_condition_code = []
on_condition_code += ['if {0}:'.format(\
self.build_expression_from_tree(runnable,
regime,
on_condition.expression_tree))]
for action in on_condition.actions:
code = self.build_action(runnable, regime, action)
for line in code:
on_condition_code += [' ' + line]
return on_condition_code
def build_on_event(self, runnable, regime, on_event):
"""
Build OnEvent event handler code.
@param on_event: OnEvent event handler object
@type on_event: lems.model.dynamics.OnEvent
@return: Generated OnEvent code
@rtype: list(string)
"""
on_event_code = []
if self.debug: on_event_code += ['print("Maybe handling something for %s ("+str(id(self))+")")'%(runnable.id),
'print("EICs ("+str(id(self))+"): "+str(self.event_in_counters))']
on_event_code += ['count = self.event_in_counters[\'{0}\']'.\
format(on_event.port),
'while count > 0:',
' print(" Handling event")' if self.debug else '',
' count -= 1']
for action in on_event.actions:
code = self.build_action(runnable, regime, action)
for line in code:
on_event_code += [' ' + line]
on_event_code += ['self.event_in_counters[\'{0}\'] = 0'.\
format(on_event.port),]
return on_event_code
def build_on_start(self, runnable, regime, on_start):
"""
Build OnStart start handler code.
@param on_start: OnStart start handler object
@type on_start: lems.model.dynamics.OnStart
@return: Generated OnStart code
@rtype: list(string)
"""
on_start_code = []
for action in on_start.actions:
code = self.build_action(runnable, regime, action)
for line in code:
on_start_code += [line]
return on_start_code
def build_on_entry(self, runnable, regime, on_entry):
"""
Build OnEntry start handler code.
@param on_entry: OnEntry start handler object
@type on_entry: lems.model.dynamics.OnEntry
@return: Generated OnEntry code
@rtype: list(string)
"""
on_entry_code = []
on_entry_code += ['if self.current_regime != self.last_regime:']
on_entry_code += [' self.last_regime = self.current_regime']
for action in on_entry.actions:
code = self.build_action(runnable, regime, action)
for line in code:
on_entry_code += [' ' + line]
return on_entry_code
def build_action(self, runnable, regime, action):
"""
Build event handler action code.
@param action: Event handler action object
@type action: lems.model.dynamics.Action
@return: Generated action code
@rtype: string
"""
if isinstance(action, StateAssignment):
return self.build_state_assignment(runnable, regime, action)
if isinstance(action, EventOut):
return self.build_event_out(action)
if isinstance(action, Transition):
return self.build_transition(action)
else:
return ['pass']
def build_state_assignment(self, runnable, regime, state_assignment):
"""
Build state assignment code.
@param state_assignment: State assignment object
@type state_assignment: lems.model.dynamics.StateAssignment
@return: Generated state assignment code
@rtype: string
"""
return ['self.{0} = {1}'.format(\
state_assignment.variable,
self.build_expression_from_tree(runnable,
regime,
state_assignment.expression_tree))]
def build_event_out(self, event_out):
"""
Build event out code.
@param event_out: event out object
@type event_out: lems.model.dynamics.EventOut
@return: Generated event out code
@rtype: string
"""
event_out_code = ['if "{0}" in self.event_out_callbacks:'.format(event_out.port),
' for c in self.event_out_callbacks[\'{0}\']:'.format(event_out.port),
' c()']
return event_out_code
def build_transition(self, transition):
"""
Build regime transition code.
@param transition: Transition object
@type transition: lems.model.dynamics.Transition
@return: Generated transition code
@rtype: string
"""
return ["self.new_regime = '{0}'".format(transition.regime)]
def build_reduce_code(self, result, select, reduce):
"""
Builds a reduce operation on the selected target range.
"""
select = select.replace('/', '.')
select = select.replace(' ', '')
if reduce == 'add':
reduce_op = '+'
acc_start = 0
else:
reduce_op = '*'
acc_start = 1
#bits = select.split('[*]')
bits = re.split('\[.*\]', select)
seps = re.findall('\[.*\]', select)
code = ['self.{0} = {1}'.format(result, acc_start)]
code += ['self.{0}_shadow = {1}'.format(result, acc_start)]
code += ['try:']
if len(bits) == 1:
target = select
code += [' self.{0} = self.{1}'.format(result, target)]
code += [' self.{0}_shadow = self.{1}'.format(result, target)]
elif len(bits) == 2:
sep = seps[0][1:-1]
if sep == '*':
array = bits[0]
ref = bits[1]
code += [' acc = {0}'.format(acc_start)]
code += [' for o in self.{0}:'.format(array)]
code += [' acc = acc {0} o{1}'.format(reduce_op, ref)]
code += [' self.{0} = acc'.format(result)]
code += [' self.{0}_shadow = acc'.format(result)]
else:
bits2 = sep.split('=')
if len(bits2) > 1:
array = bits[0]
ref = bits[1]
code += [' acc = {0}'.format(acc_start)]
code += [' for o in self.{0}:'.format(array)]
code += [' if o.{0} == {1}:'.format(bits2[0], bits2[1])]
code += [' acc = acc {0} o{1}'.format(reduce_op, ref)]
code += [' self.{0} = acc'.format(result)]
code += [' self.{0}_shadow = acc'.format(result)]
else:
raise SimbuildError("Invalid reduce target - '{0}'".format(select))
else:
raise SimbuildError("Invalid reduce target - '{0}'".format(select))
code += ['except:']
code += [' pass']
return code
def build_conditional_derived_var_code(self, runnable, regime, dv):
code = []
el = ''
for case in dv.cases:
if case.condition_expression_tree:
code += [el+'if {0}:'.format(self.build_expression_from_tree(runnable,
regime,
case.condition_expression_tree))]
el='el'
code += [' self.{0} = {1}'.format(dv.name, self.build_expression_from_tree(runnable,
regime,
case.value_expression_tree))]
for case in dv.cases:
if case.condition_expression_tree is None:
code += ['else: ']
code += [' self.{0} = {1}'.format(dv.name, self.build_expression_from_tree(runnable,
regime,
case.value_expression_tree))]
return code
def add_recording_behavior(self, component, runnable):
"""
Adds recording-related dynamics to a runnable component based on
the dynamics specifications in the component model.
@param component: Component model containing dynamics specifications.
@type component: lems.model.component.FatComponent runnable: Runnable component to which dynamics is to be added.
@type runnable: lems.sim.runnable.Runnable
@raise SimBuildError: Raised when a target for recording could not be
found.
"""
simulation = component.simulation
for rec in simulation.records:
rec.id = runnable.id
self.current_record_target.add_variable_recorder(self.current_data_output, rec)
class SimulationBuilder(LEMSBase):
"""
Simulation builder class.
"""
debug = False
def __init__(self, model):
"""
Constructor.
@param model: Model upon which the simulation is to be generated.
@type model: lems.model.model.Model
"""
self.model = model
""" Model to be used for constructing the simulation.
@type: lems.model.model.Model """
self.sim = None
""" Simulation built from the model.
@type: lems.sim.sim.Simulation """
self.current_record_target = None
self.current_data_output = None
def build(self):
"""
Build the simulation components from the model.
@return: A runnable simulation object
@rtype: lems.sim.sim.Simulation
"""
self.sim = Simulation()
for component_id in self.model.targets:
if component_id not in self.model.components:
raise SimBuildError("Unable to find target component '{0}'",
component_id)
component = self.model.fat_components[component_id]
runnable = self.build_runnable(component)
self.sim.add_runnable(runnable)
return self.sim
def build_runnable(self, component, parent = None, id_ = None):
"""
Build a runnable component from a component specification and add
it to the simulation.
@param component: Component specification
@type component: lems.model.component.FatComponent
@param parent: Parent runnable component.
@type parent: lems.sim.runnable.Runnable
@param id_: Optional id for therunnable. If it's not passed in,
the runnable will inherit the id of the component.
@raise SimBuildError: Raised when a component reference cannot be
resolved.
"""
if self.debug: print("++++++++ Calling build_runnable of %s with parent %s"%(component, parent))
if id_ == None:
runnable = Runnable(component.id, component, parent)
else:
runnable = Runnable(id_, component, parent)
simulation = component.simulation
record_target_backup = self.current_record_target
data_output_backup = self.current_data_output
do = None
for d in simulation.data_displays:
do = d
if do == None:
for d in simulation.data_writers:
do = d
if do != None:
self.current_data_output = do
for parameter in component.parameters:
runnable.add_instance_variable(parameter.name, parameter.numeric_value)
for property in component.properties:
print("\n\n*****************************************************************\n\n"+
" Property element is not stable in PyLEMS yet, see https://github.com/LEMS/pylems/issues/16\n\n"+
" Used in: %s\n\n"%property.toxml()+
"*****************************************************************\n\n\n")
runnable.add_instance_variable(property.name, property.default_value)
derived_parameter_code = []
derived_parameter_ordering = order_derived_parameters(component)
for dpn in derived_parameter_ordering:
derived_parameter = component.derived_parameters[dpn]
runnable.add_derived_variable(derived_parameter.name)
expression = self.build_expression_from_tree(runnable,
None,
derived_parameter.expression_tree)
derived_parameter_code += ['self.{0} = ({1})'.format(
derived_parameter.name,
expression)]
derived_parameter_code += ['self.{0}_shadow = ({1})'.format(
derived_parameter.name,
expression)]
suffix = ''
runnable.add_method('update_derived_parameters' + suffix, ['self'],
derived_parameter_code)
for constant in component.constants:
runnable.add_instance_variable(constant.name, constant.numeric_value)
for text in component.texts:
runnable.add_text_variable(text.name, text.value)
for link in component.links:
runnable.add_text_variable(link.name, link.value)
for ep in component.event_ports:
if ep.direction.lower() == 'in':
runnable.add_event_in_port(ep.name)
else:
runnable.add_event_out_port(ep.name)
dynamics = component.dynamics
self.add_dynamics_1(component, runnable, dynamics, dynamics)
for regime in dynamics.regimes:
self.add_dynamics_1(component, runnable, regime, dynamics)
if regime.initial:
runnable.current_regime = regime.name
rn = regime.name
if rn not in runnable.regimes:
runnable.add_regime(RunnableRegime(rn))
r = runnable.regimes[rn]
suffix = '_regime_' + rn
if runnable.__dict__.has_key('update_state_variables' + suffix):
r.update_state_variables = runnable.__dict__['update_state_variables' + suffix]
if runnable.__dict__.has_key('update_derived_variables' + suffix):
r.update_derived_variables = runnable.__dict__['update_derived_variables' + suffix]
if runnable.__dict__.has_key('run_startup_event_handlers' + suffix):
r.run_startup_event_handlers = runnable.__dict__['run_startup_event_handlers' + suffix]
if runnable.__dict__.has_key('run_preprocessing_event_handlers' + suffix):
r.run_preprocessing_event_handlers = runnable.__dict__['run_preprocessing_event_handlers' + suffix]
if runnable.__dict__.has_key('run_postprocessing_event_handlers' + suffix):
r.run_postprocessing_event_handlers = runnable.__dict__['run_postprocessing_event_handlers' + suffix]
self.process_simulation_specs(component, runnable, component.simulation)
for child in component.child_components:
child_runnable = self.build_runnable(child, runnable)
runnable.add_child(child.id, child_runnable)
for children in component.children:
#GG - These conditions need more debugging.
if children.type in child.types:
runnable.add_child_typeref(children.type, child_runnable)
if children.multiple:
if children.type in child.types:
runnable.add_child_to_group(children.name, child_runnable)
else:
if child_runnable.id == children.name:
runnable.add_child_typeref(children.name, child_runnable)
for attachment in component.attachments:
runnable.make_attachment(attachment.type, attachment.name)
self.build_structure(component, runnable, component.structure)
dynamics = component.dynamics
self.add_dynamics_2(component, runnable,
dynamics, dynamics)
for regime in dynamics.regimes:
self.add_dynamics_2(component, runnable, regime, dynamics)
if regime.name not in runnable.regimes:
runnable.add_regime(RunnableRegime(regime.name))
r = runnable.regimes[regime.name]
suffix = '_regime_' + regime.name
if runnable.__dict__.has_key('update_kinetic_scheme' + suffix):
r.update_kinetic_scheme = runnable.__dict__['update_kinetic_scheme' + suffix]
self.add_recording_behavior(component, runnable)
self.current_data_output = data_output_backup
self.current_record_target = record_target_backup
return runnable
def build_event_connections(self, component, runnable, structure):
"""
Adds event connections to a runnable component based on the structure
specifications in the component model.
@param component: Component model containing structure specifications.
@type component: lems.model.component.FatComponent
@param runnable: Runnable component to which structure is to be added.
@type runnable: lems.sim.runnable.Runnable
@param structure: The structure object to be used to add
structure code in the runnable component.
@type structure: lems.model.structure.Structure
"""
if self.debug: print("\n++++++++ Calling build_event_connections of %s with runnable %s, parent %s"%(component.id, runnable.id, runnable.parent))
# Process event connections
for ec in structure.event_connections:
if self.debug: print(ec.toxml())
source = runnable.parent.resolve_path(ec.from_)
target = runnable.parent.resolve_path(ec.to)
if ec.receiver:
receiver_template = self.build_runnable(ec.receiver,
target)
#receiver = copy.deepcopy(receiver_template)
receiver = receiver_template.copy()
receiver.id = "{0}__{1}__".format(component.id,
receiver_template.id)
if ec.receiver_container:
target.add_attachment(receiver, ec.receiver_container)
target.add_child(receiver_template.id, receiver)
target = receiver
else:
source = runnable.resolve_path(ec.from_)
target = runnable.resolve_path(ec.to)
source_port = ec.source_port
target_port = ec.target_port
if not source_port:
if len(source.event_out_ports) == 1:
source_port = source.event_out_ports[0]
else:
raise SimBuildError(("No source event port "
"uniquely identifiable"
" in '{0}'").format(source.id))
if not target_port:
if len(target.event_in_ports) == 1:
target_port = target.event_in_ports[0]
else:
raise SimBuildError(("No destination event port "
"uniquely identifiable "
"in '{0}'").format(target))
if self.debug: print("register_event_out_callback\n Source: %s, %s (port: %s) \n -> %s, %s (port: %s)"%(source, id(source), source_port, target, id(target), target_port))
source.register_event_out_callback(\
source_port, lambda: target.inc_event_in(target_port))
def build_structure(self, component, runnable, structure):
"""
Adds structure to a runnable component based on the structure
specifications in the component model.
@param component: Component model containing structure specifications.
@type component: lems.model.component.FatComponent
@param runnable: Runnable component to which structure is to be added.
@type runnable: lems.sim.runnable.Runnable
@param structure: The structure object to be used to add
structure code in the runnable component.
@type structure: lems.model.structure.Structure
"""
if self.debug: print("\n++++++++ Calling build_structure of %s with runnable %s, parent %s"%(component.id, runnable.id, runnable.parent))
# Process single-child instantiations
for ch in structure.child_instances:
child_runnable = self.build_runnable(ch.referenced_component, runnable)
runnable.add_child(child_runnable.id, child_runnable)
runnable.add_child_typeref(ch.component, child_runnable)
# Process multi-child instatiantions
for mi in structure.multi_instantiates:
template = self.build_runnable(mi.component,
runnable)
for i in range(mi.number):
#instance = copy.deepcopy(template)
instance = template.copy()
instance.id = "{0}__{1}__{2}".format(component.id,
template.id,
i)
runnable.array.append(instance)
# Process foreach statements
for fe in structure.for_eachs:
self.build_foreach(component, runnable, fe)
self.build_event_connections(component, runnable, structure)
def build_foreach(self, component, runnable, foreach, name_mappings = {}):
"""
Iterate over ForEach constructs and process nested elements.
@param component: Component model containing structure specifications.
@type component: lems.model.component.FatComponent
@param runnable: Runnable component to which structure is to be added.
@type runnable: lems.sim.runnable.Runnable
@param foreach: The ForEach structure object to be used to add
structure code in the runnable component.
@type foreach: lems.model.structure.ForEach
"""
if self.debug: print("\n++++++++ Calling build_foreach of %s with runnable %s, parent %s, name_mappings: %s"%(component.id, runnable.id, runnable.parent, name_mappings))
target_array = runnable.resolve_path(foreach.instances)
for target_runnable in target_array:
if self.debug: print("Applying contents of for_each to %s, as %s"%(target_runnable.id, foreach.as_))
name_mappings[foreach.as_] = target_runnable
# Process foreach statements
for fe2 in foreach.for_eachs:
#print fe2.toxml()
target_array2 = runnable.resolve_path(fe2.instances)
for target_runnable2 in target_array2:
name_mappings[fe2.as_] = target_runnable2
self.build_foreach(component, runnable, fe2, name_mappings)
# Process event connections
for ec in foreach.event_connections:
source = name_mappings[ec.from_]
target = name_mappings[ec.to]
source_port = ec.source_port
target_port = ec.target_port
if not source_port:
if len(source.event_out_ports) == 1:
source_port = source.event_out_ports[0]
else:
raise SimBuildError(("No source event port "
"uniquely identifiable"
" in '{0}'").format(source.id))
if not target_port:
if len(target.event_in_ports) == 1:
target_port = target.event_in_ports[0]
else:
raise SimBuildError(("No destination event port "
"uniquely identifiable "
"in '{0}'").format(target))
if self.debug: print("register_event_out_callback\n Source: %s, %s (port: %s) \n -> %s, %s (port: %s)"%(source, id(source), source_port, target, id(target), target_port))
source.register_event_out_callback(\
source_port, lambda: target.inc_event_in(target_port))
def add_dynamics_1(self, component, runnable, regime, dynamics):
"""
Adds dynamics to a runnable component based on the dynamics
specifications in the component model.
This method builds dynamics necessary for building child components.
@param component: Component model containing dynamics specifications.
@type component: lems.model.component.FatComponent
@param runnable: Runnable component to which dynamics is to be added.
@type runnable: lems.sim.runnable.Runnable
@param regime: The dynamics regime to be used to generate
dynamics code in the runnable component.
@type regime: lems.model.dynamics.Regime
@param dynamics: Shared dynamics specifications.
@type dynamics: lems.model.dynamics.Regime
@raise SimBuildError: Raised when a time derivative expression refers
to an undefined variable.
@raise SimBuildError: Raised when there are invalid time
specifications for the <Run> statement.
@raise SimBuildError: Raised when the component reference for <Run>
cannot be resolved.
"""
if isinstance(regime, Dynamics) or regime.name == '':
suffix = ''
else:
suffix = '_regime_' + regime.name
if isinstance(regime, Regime) and regime.initial:
runnable.new_regime = regime.name
# Process state variables
for sv in regime.state_variables:
runnable.add_instance_variable(sv.name, 0)
# Process time derivatives
time_step_code = []
for td in regime.time_derivatives:
if td.variable not in regime.state_variables and td.variable not in dynamics.state_variables:
raise SimBuildError(('Time derivative for undefined state '
'variable {0} in component {1}').format(td.variable, component.id))
exp = self.build_expression_from_tree(runnable,
regime,
td.expression_tree)
time_step_code += ['self.{0} += dt * ({1})'.format(td.variable,
exp)]
runnable.add_method('update_state_variables' + suffix, ['self', 'dt'],
time_step_code)
# Process derived variables
derived_variable_code = []
derived_variables_ordering = order_derived_variables(regime)
for dvn in derived_variables_ordering: #regime.derived_variables:
if dvn in dynamics.derived_variables:
dv = dynamics.derived_variables[dvn]
runnable.add_derived_variable(dv.name)
if dv.value:
derived_variable_code += ['self.{0} = ({1})'.format(
dv.name,
self.build_expression_from_tree(runnable,
regime,
dv.expression_tree))]
elif dv.select:
if dv.reduce:
derived_variable_code += self.build_reduce_code(dv.name,
dv.select,
dv.reduce)
else:
derived_variable_code += ['self.{0} = (self.{1})'.format(
dv.name,
dv.select.replace('/', '.'))]
else:
raise SimBuildError(('Inconsistent derived variable settings'
'for {0}').format(dvn))
elif dvn in dynamics.conditional_derived_variables:
dv = dynamics.conditional_derived_variables[dvn]
runnable.add_derived_variable(dv.name)
derived_variable_code += self.build_conditional_derived_var_code(runnable,
regime,
dv)
else:
raise SimBuildError("Unknown derived variable '{0}' in '{1}'",
dvn, runnable.id)
runnable.add_method('update_derived_variables' + suffix, ['self'],
derived_variable_code)
# Process event handlers
pre_event_handler_code = []
post_event_handler_code = []
startup_event_handler_code = []
on_entry_added = False
for eh in regime.event_handlers:
if isinstance(eh, OnStart):
startup_event_handler_code += self.build_event_handler(runnable,
regime,
eh)
elif isinstance(eh, OnCondition):
post_event_handler_code += self.build_event_handler(runnable,
regime,
eh)
else:
if isinstance(eh, OnEntry):
on_entry_added = True
pre_event_handler_code += self.build_event_handler(runnable,
regime,
eh)
if isinstance(regime, Regime) and not on_entry_added:
pre_event_handler_code += self.build_event_handler(runnable, regime, OnEntry())
runnable.add_method('run_startup_event_handlers' + suffix, ['self'],
startup_event_handler_code)
runnable.add_method('run_preprocessing_event_handlers' + suffix, ['self'],
pre_event_handler_code)
runnable.add_method('run_postprocessing_event_handlers' + suffix, ['self'],
post_event_handler_code)
def add_dynamics_2(self, component, runnable, regime, dynamics):
"""
Adds dynamics to a runnable component based on the dynamics
specifications in the component model.
This method builds dynamics dependent on child components.
@param component: Component model containing dynamics specifications.
@type component: lems.model.component.FatComponent
@param runnable: Runnable component to which dynamics is to be added.
@type runnable: lems.sim.runnable.Runnable
@param regime: The dynamics regime to be used to generate
dynamics code in the runnable component.
@type regime: lems.model.dynamics.Regime
@param dynamics: Shared dynamics specifications.
@type dynamics: lems.model.dynamics.Regime
@raise SimBuildError: Raised when a time derivative expression refers
to an undefined variable.
@raise SimBuildError: Raised when there are invalid time
specifications for the <Run> statement.
@raise SimBuildError: Raised when the component reference for <Run>
cannot be resolved.
"""
if isinstance(regime, Dynamics) or regime.name == '':
suffix = ''
else:
suffix = '_regime_' + regime.name
# Process kinetic schemes
ks_code = []
for ks in regime.kinetic_schemes:
raise NotImplementedError("KineticScheme element is not stable in PyLEMS yet, see https://github.com/LEMS/pylems/issues/15")
try:
###nodes = {node.id:node for node in runnable.__dict__[ks.nodes]}
nodes = {}
for node in runnable.__dict__[ks.nodes]:
nodes[node.id] = node
edges = runnable.__dict__[ks.edges]
for edge in edges:
from_ = edge.__dict__[ks.edge_source]
to = edge.__dict__[ks.edge_target]
ks_code += [('self.{0}.{2} += dt * (-self.{3}.{4} * self.{0}.{2}_shadow'
' + self.{3}.{5} * self.{1}.{2}_shadow)').format(
from_, to, ks.state_variable, edge.id,
ks.forward_rate, ks.reverse_rate)]
ks_code += [('self.{1}.{2} += dt * (self.{3}.{4} * self.{0}.{2}_shadow'
' - self.{3}.{5} * self.{1}.{2}_shadow)').format(
from_, to, ks.state_variable, edge.id,
ks.forward_rate, ks.reverse_rate)]
ks_code += ['sum = 0']
for node in nodes:
nodes[node].__dict__[ks.state_variable] = 1.0 / len(nodes)
nodes[node].__dict__[ks.state_variable + '_shadow'] = 1.0 / len(nodes)
ks_code += ['sum += self.{0}.{1}'.format(node, ks.state_variable)]
for node in nodes:
ks_code += ['self.{0}.{1} /= sum'.format(node, ks.state_variable)]
for node in nodes:
ks_code += [('self.{0}.{1}_shadow = '
'self.{0}.{1}').format(node,
ks.state_variable)]
except Exception as e:
raise SimBuildError(("Unable to construct kinetic scheme '{0}' "
"for component '{1}' - {2}").format(ks.name,
component.id,
str(e)))
runnable.add_method('update_kinetic_scheme' + suffix, ['self', 'dt'],
ks_code)
def process_simulation_specs(self, component, runnable, simulation):
"""
Process simulation-related aspects to a runnable component based on the
dynamics specifications in the component model.
@param component: Component model containing dynamics specifications.
@type component: lems.model.component.FatComponent
@param runnable: Runnable component to which dynamics is to be added.
@type runnable: lems.sim.runnable.Runnable
@param simulation: The simulation-related aspects to be implemented
in the runnable component.
@type simulation: lems.model.simulation.Simulation
@raise SimBuildError: Raised when a time derivative expression refers
to an undefined variable
@raise SimBuildError: Raised when there are invalid time
specifications for the <Run> statement.
@raise SimBuildError: Raised when the component reference for <Run>
cannot be resolved.
"""
# Process runs
for run in simulation.runs:
cid = run.component.id + '_' + component.id
target = self.build_runnable(run.component, runnable, cid)
self.sim.add_runnable(target)
self.current_record_target = target
target.configure_time(run.increment,
run.total)
def convert_op(self, op):
"""
Converts NeuroML arithmetic/logical operators to python equivalents.
@param op: NeuroML operator
@type op: string
@return: Python operator
@rtype: string
"""
if op == '.gt.':
return '>'
elif op == '.ge.' or op == '.geq.':
return '>='
elif op == '.lt.':
return '<'
elif op == '.le.':
return '<='
elif op == '.eq.':
return '=='
elif op == '.neq.':
return '!='
elif op == '.ne.': # .neq. is preferred!
return '!='
elif op == '^':
return '**'
elif op == '.and.':
return 'and'
elif op == '.or.':
return 'or'
else:
return op
def convert_func(self, func):
"""
Converts NeuroML arithmetic/logical functions to python equivalents.
@param func: NeuroML function
@type func: string
@return: Python operator
@rtype: string
"""
if func == 'ln':
return 'log'
elif func == 'random':
return 'random.uniform'
elif func == 'H':
def heaviside_step(x):
if x < 0: return 0
elif x > 0: return 1
else: return 0.5
return 'heaviside_step'
else:
return func
def build_expression_from_tree(self, runnable, regime, tree_node):
"""
Recursively builds a Python expression from a parsed expression tree.
@param runnable: Runnable object to which this expression would be added.
@type runnable: lems.sim.runnable.Runnable
@param regime: Dynamics regime being built.
@type regime: lems.model.dynamics.Regime
@param tree_node: Root node for the tree from which the expression
is to be built.
@type tree_node: lems.parser.expr.ExprNode
@return: Generated Python expression.
@rtype: string
"""
component_type = self.model.component_types[runnable.component.type]
dynamics = component_type.dynamics
if tree_node.type == ExprNode.VALUE:
if tree_node.value[0].isalpha():
if tree_node.value == 't':
return 'self.time_completed'
elif tree_node.value in component_type.requirements:
var_prefix = 'self'
v = tree_node.value
r = runnable
while (v not in r.instance_variables and
v not in r.derived_variables):
var_prefix = '{0}.{1}'.format(var_prefix, 'parent')
r = r.parent
if r == None:
raise SimBuildError("Unable to resolve required "
"variable '{0}'".format(v))
return '{0}.{1}'.format(var_prefix, v)
elif (tree_node.value in dynamics.derived_variables or (regime is not None and tree_node.value in regime.derived_variables)):
return 'self.{0}'.format(tree_node.value)
else:
return 'self.{0}_shadow'.format(tree_node.value)
else:
return tree_node.value
elif tree_node.type == ExprNode.FUNC1:
pattern = '({0}({1}))'
func = self.convert_func(tree_node.func)
if 'random.uniform' in func:
pattern = '({0}(0,{1}))'
return pattern.format(\
func,
self.build_expression_from_tree(runnable,
regime,
tree_node.param))
else:
return '({0}) {1} ({2})'.format(\
self.build_expression_from_tree(runnable,
regime,
tree_node.left),
self.convert_op(tree_node.op),
self.build_expression_from_tree(runnable,
regime,
tree_node.right))
def build_event_handler(self, runnable, regime, event_handler):
"""
Build event handler code.
@param event_handler: Event handler object
@type event_handler: lems.model.dynamics.EventHandler
@return: Generated event handler code.
@rtype: list(string)
"""
if isinstance(event_handler, OnCondition):
return self.build_on_condition(runnable, regime, event_handler)
elif isinstance(event_handler, OnEvent):
return self.build_on_event(runnable, regime, event_handler)
elif isinstance(event_handler, OnStart):
return self.build_on_start(runnable, regime, event_handler)
elif isinstance(event_handler, OnEntry):
return self.build_on_entry(runnable, regime, event_handler)
else:
return []
def build_on_condition(self, runnable, regime, on_condition):
"""
Build OnCondition event handler code.
@param on_condition: OnCondition event handler object
@type on_condition: lems.model.dynamics.OnCondition
@return: Generated OnCondition code
@rtype: list(string)
"""
on_condition_code = []
on_condition_code += ['if {0}:'.format(\
self.build_expression_from_tree(runnable,
regime,
on_condition.expression_tree))]
for action in on_condition.actions:
code = self.build_action(runnable, regime, action)
for line in code:
on_condition_code += [' ' + line]
return on_condition_code
def build_on_event(self, runnable, regime, on_event):
"""
Build OnEvent event handler code.
@param on_event: OnEvent event handler object
@type on_event: lems.model.dynamics.OnEvent
@return: Generated OnEvent code
@rtype: list(string)
"""
on_event_code = []
if self.debug: on_event_code += ['print("Maybe handling something for %s ("+str(id(self))+")")'%(runnable.id),
'print("EICs ("+str(id(self))+"): "+str(self.event_in_counters))']
on_event_code += ['count = self.event_in_counters[\'{0}\']'.\
format(on_event.port),
'while count > 0:',
' print(" Handling event")' if self.debug else '',
' count -= 1']
for action in on_event.actions:
code = self.build_action(runnable, regime, action)
for line in code:
on_event_code += [' ' + line]
on_event_code += ['self.event_in_counters[\'{0}\'] = 0'.\
format(on_event.port),]
return on_event_code
def build_on_start(self, runnable, regime, on_start):
"""
Build OnStart start handler code.
@param on_start: OnStart start handler object
@type on_start: lems.model.dynamics.OnStart
@return: Generated OnStart code
@rtype: list(string)
"""
on_start_code = []
for action in on_start.actions:
code = self.build_action(runnable, regime, action)
for line in code:
on_start_code += [line]
return on_start_code
def build_on_entry(self, runnable, regime, on_entry):
"""
Build OnEntry start handler code.
@param on_entry: OnEntry start handler object
@type on_entry: lems.model.dynamics.OnEntry
@return: Generated OnEntry code
@rtype: list(string)
"""
on_entry_code = []
on_entry_code += ['if self.current_regime != self.last_regime:']
on_entry_code += [' self.last_regime = self.current_regime']
for action in on_entry.actions:
code = self.build_action(runnable, regime, action)
for line in code:
on_entry_code += [' ' + line]
return on_entry_code
def build_action(self, runnable, regime, action):
"""
Build event handler action code.
@param action: Event handler action object
@type action: lems.model.dynamics.Action
@return: Generated action code
@rtype: string
"""
if isinstance(action, StateAssignment):
return self.build_state_assignment(runnable, regime, action)
if isinstance(action, EventOut):
return self.build_event_out(action)
if isinstance(action, Transition):
return self.build_transition(action)
else:
return ['pass']
def build_state_assignment(self, runnable, regime, state_assignment):
"""
Build state assignment code.
@param state_assignment: State assignment object
@type state_assignment: lems.model.dynamics.StateAssignment
@return: Generated state assignment code
@rtype: string
"""
return ['self.{0} = {1}'.format(\
state_assignment.variable,
self.build_expression_from_tree(runnable,
regime,
state_assignment.expression_tree))]
def build_event_out(self, event_out):
"""
Build event out code.
@param event_out: event out object
@type event_out: lems.model.dynamics.EventOut
@return: Generated event out code
@rtype: string
"""
event_out_code = ['if "{0}" in self.event_out_callbacks:'.format(event_out.port),
' for c in self.event_out_callbacks[\'{0}\']:'.format(event_out.port),
' c()']
return event_out_code
def build_transition(self, transition):
"""
Build regime transition code.
@param transition: Transition object
@type transition: lems.model.dynamics.Transition
@return: Generated transition code
@rtype: string
"""
return ["self.new_regime = '{0}'".format(transition.regime)]
def build_reduce_code(self, result, select, reduce):
"""
Builds a reduce operation on the selected target range.
"""
select = select.replace('/', '.')
select = select.replace(' ', '')
if reduce == 'add':
reduce_op = '+'
acc_start = 0
else:
reduce_op = '*'
acc_start = 1
#bits = select.split('[*]')
bits = re.split('\[.*\]', select)
seps = re.findall('\[.*\]', select)
code = ['self.{0} = {1}'.format(result, acc_start)]
code += ['self.{0}_shadow = {1}'.format(result, acc_start)]
code += ['try:']
if len(bits) == 1:
target = select
code += [' self.{0} = self.{1}'.format(result, target)]
code += [' self.{0}_shadow = self.{1}'.format(result, target)]
elif len(bits) == 2:
sep = seps[0][1:-1]
if sep == '*':
array = bits[0]
ref = bits[1]
code += [' acc = {0}'.format(acc_start)]
code += [' for o in self.{0}:'.format(array)]
code += [' acc = acc {0} o{1}'.format(reduce_op, ref)]
code += [' self.{0} = acc'.format(result)]
code += [' self.{0}_shadow = acc'.format(result)]
else:
bits2 = sep.split('=')
if len(bits2) > 1:
array = bits[0]
ref = bits[1]
code += [' acc = {0}'.format(acc_start)]
code += [' for o in self.{0}:'.format(array)]
code += [' if o.{0} == {1}:'.format(bits2[0], bits2[1])]
code += [' acc = acc {0} o{1}'.format(reduce_op, ref)]
code += [' self.{0} = acc'.format(result)]
code += [' self.{0}_shadow = acc'.format(result)]
else:
raise SimbuildError("Invalid reduce target - '{0}'".format(select))
else:
raise SimbuildError("Invalid reduce target - '{0}'".format(select))
code += ['except:']
code += [' pass']
return code
def build_conditional_derived_var_code(self, runnable, regime, dv):
code = []
el = ''
for case in dv.cases:
if case.condition_expression_tree:
code += [el+'if {0}:'.format(self.build_expression_from_tree(runnable,
regime,
case.condition_expression_tree))]
el='el'
code += [' self.{0} = {1}'.format(dv.name, self.build_expression_from_tree(runnable,
regime,
case.value_expression_tree))]
for case in dv.cases:
if case.condition_expression_tree is None:
code += ['else: ']
code += [' self.{0} = {1}'.format(dv.name, self.build_expression_from_tree(runnable,
regime,
case.value_expression_tree))]
return code
class SimulationBuilder(LEMSBase):
"""
Simulation builder class.
"""
def __init__(self, model):
"""
Constructor.
@param model: Model upon which the simulation is to be generated.
@type model: lems.model.model.Model
"""
self.model = model
""" Model to be used for constructing the simulation.
@type: lems.model.model.Model """
self.sim = None
""" Simulation built from the model.
@type: lems.sim.sim.Simulation """
self.current_record_target = None
def build(self):
"""
Build the simulation components from the model.
@return: A runnable simulation object
@rtype: lems.sim.sim.Simulation
"""
self.sim = Simulation()
for component_id in self.model.targets:
if component_id not in self.model.context.components:
raise SimBuildError('Unable to find component \'{0}\' to run'\
.format(component_id))
component = self.model.context.components[component_id]
runnable = self.build_runnable(component)
self.sim.add_runnable(runnable)
return self.sim
def build_runnable(self, component, parent = None, id_ = None):
"""
Build a runnable component from a component specification and add
it to the simulation.
@param component: Component specification
@type component: lems.model.component.Component
@param parent: Parent runnable component.
@type parent: lems.sim.runnable.Runnable
@param id_: Optional id for therunnable. If it's not passed in,
the runnable will inherit the id of the component.
@raise SimBuildError: Raised when a component reference cannot be
resolved.
"""
if id_ == None:
runnable = Runnable(component.id, component, parent)
else:
runnable = Runnable(id_, component, parent)
context = component.context
record_target_backup = self.current_record_target
for pn in context.parameters:
p = context.parameters[pn]
if p.numeric_value != None:
runnable.add_instance_variable(p.name, p.numeric_value)
elif p.dimension in ['__link__', '__text__']:
runnable.add_text_variable(p.name, p.value)
for port in context.event_in_ports:
runnable.add_event_in_port(port)
for port in context.event_out_ports:
runnable.add_event_out_port(port)
if context.selected_dynamics_profile:
dynamics = context.selected_dynamics_profile
self.add_dynamics_1(component, runnable,
dynamics.default_regime, dynamics.default_regime)
for rn in dynamics.regimes:
regime = dynamics.regimes[rn]
self.add_dynamics_1(component, runnable, regime, dynamics.default_regime)
if regime.initial:
runnable.current_regime = regime.name
if rn not in runnable.regimes:
runnable.add_regime(Regime(rn))
r = runnable.regimes[rn]
suffix = '_regime_' + rn
r.update_state_variables = runnable.__dict__['update_state_variables'
+ suffix]
r.update_derived_variables = runnable.__dict__['update_derived_variables'
+ suffix]
r.run_startup_event_handlers = runnable.__dict__['run_startup_event_handlers'
+ suffix]
r.run_preprocessing_event_handlers = runnable.__dict__['run_preprocessing_event_handlers'
+ suffix]
r.run_postprocessing_event_handlers = runnable.__dict__['run_postprocessing_event_handlers'
+ suffix]
else:
runnable.add_method('update_state_variables', ['self', 'dt'],
[])
runnable.add_method('update_derived_variables', ['self'],
[])
runnable.add_method('run_startup_event_handlers', ['self'],
[])
runnable.add_method('run_preprocessing_event_handlers', ['self'],
[])
runnable.add_method('run_postprocessing_event_handlers', ['self'],
[])
self.process_simulation_specs(component, runnable, context.simulation)
#for cn in context.components:
for cn in context.components_ordering:
child = context.components[cn]
child_runnable = self.build_runnable(child, runnable)
runnable.add_child(child.id, child_runnable)
for cdn in context.children_defs:
cdt = context.children_defs[cdn]
#if cdt == child.component_type:
if child.is_type(cdt):
runnable.add_child_to_group(cdn, child_runnable)
for type_ in context.attachments:
name = context.attachments[type_]
runnable.make_attachment(type_, name)
self.build_structure(component, runnable, context.structure)
if context.selected_dynamics_profile:
dynamics = context.selected_dynamics_profile
self.add_dynamics_2(component, runnable,
dynamics.default_regime, dynamics.default_regime)
for rn in dynamics.regimes:
regime = dynamics.regimes[rn]
self.add_dynamics_2(component, runnable, regime, dynamics.default_regime)
if rn not in runnable.regimes:
runnable.add_regime(Regime(rn))
r = runnable.regimes[rn]
suffix = '_regime_' + rn
r.update_kinetic_scheme = runnable.__dict__['update_kinetic_scheme'
+ suffix]
else:
runnable.add_method('update_kinetic_scheme', ['self', 'dt'],
[])
self.add_recording_behavior(component, runnable)
self.current_record_target = record_target_backup
return runnable
def build_structure(self, component, runnable, structure):
"""
Adds structure to a runnable component based on the structure
specifications in the component model.
@param component: Component model containing structure specifications.
@type component: lems.model.component.Component
@param runnable: Runnable component to which structure is to be added.
@type runnable: lems.sim.runnable.Runnable
@param structure: The structure object to be used to add
structure code in the runnable component.
@type structure: lems.model.structure.Structure
"""
context = component.context
# Process single-child instantiations
for c in structure.single_child_defs:
if c in context.component_refs:
cref = context.component_refs[c]
child = context.lookup_component(cref)
child_runnable = self.build_runnable(child, runnable)
runnable.add_child(c, child_runnable)
for cdn in context.children_defs:
cdt = context.children_defs[cdn]
if cdt == child.component_type:
runnable.add_child_to_group(cdn, child_runnable)
else:
raise SimBuildError('Unable to find component ref \'{0}\' '
'under \'{1}\''.format(\
c, runnable.id))
# Process multi-child instatiantions
for cparam in structure.multi_child_defs:
sparam = structure.multi_child_defs[cparam]
c1 = component
c2 = context.lookup_component(cparam)
template = self.build_runnable(context.lookup_component(cparam),
runnable)
for i in range(sparam):
instance = copy.deepcopy(template)
instance.id = "{0}__{1}__{2}".format(component.id,
template.id,
i)
runnable.array.append(instance)
# Process foreach statements
if structure.foreach:
self.build_foreach(component, runnable, structure)
# Process event connections
for event in structure.event_connections:
if True:
#try:
source_pathvar = structure.with_mappings[event.source_path]
target_pathvar = structure.with_mappings[event.target_path]
source_path = context.lookup_path_parameter(source_pathvar)
target_path = context.lookup_path_parameter(target_pathvar)
source = runnable.parent.resolve_path(source_path)
target = runnable.parent.resolve_path(target_path)
if event.receiver:
receiver_component = context.lookup_component_ref(event.receiver)
receiver_template = self.build_runnable(receiver_component,
target)
receiver = copy.deepcopy(receiver_template)
receiver.id = "{0}__{1}__".format(component.id,
receiver_template.id)
target.add_attachment(receiver)
target = receiver
source_port = context.lookup_text_parameter(event.source_port)
target_port = context.lookup_text_parameter(event.target_port)
if source_port == None:
if len(source.event_out_ports) == 1:
source_port = source.event_out_ports[0]
else:
raise SimBuildError(("No source event port "
"uniquely identifiable"
" in '{0}'").format(source.id))
if target_port == None:
if len(target.event_in_ports) == 1:
target_port = target.event_in_ports[0]
else:
raise SimBuildError(("No destination event port "
"uniquely identifiable "
"in '{0}'").format(target.id))
#except Exception as e:
#raise e
source.register_event_out_callback(\
source_port, lambda: target.inc_event_in(target_port))
def build_foreach(self, component, runnable, foreach, name_mappings = {}):
"""
Iterate over ForEach constructs and process nested elements.
@param component: Component model containing structure specifications.
@type component: lems.model.component.Component
@param runnable: Runnable component to which structure is to be added.
@type runnable: lems.sim.runnable.Runnable
@param foreach: The ForEach structure object to be used to add
structure code in the runnable component.
@type foreach: lems.model.structure.ForEach
"""
context = component.context
# Process foreach statements
for fe in foreach.foreach:
target_array = runnable.resolve_path(fe.target)
for target_runnable in target_array:
name_mappings[fe.name] = target_runnable
self.build_foreach(component, runnable, fe, name_mappings)
# Process event connections
for event in foreach.event_connections:
source = name_mappings[event.source_path]
target = name_mappings[event.target_path]
source_port = context.lookup_text_parameter(event.source_port)
target_port = context.lookup_text_parameter(event.target_port)
if source_port == None:
if len(source.event_out_ports) == 1:
source_port = source.event_out_ports[0]
else:
raise SimBuildError(("No source event port "
"uniquely identifiable"
" in '{0}'").format(source.id))
if target_port == None:
if len(target.event_in_ports) == 1:
target_port = target.event_in_ports[0]
else:
raise SimBuildError(("No destination event port uniquely"
"identifiable in '{0}'").format(target.id))
source.register_event_out_callback(\
source_port, lambda: target.inc_event_in(target_port))
def add_dynamics_1(self, component, runnable, regime, default_regime):
"""
Adds dynamics to a runnable component based on the dynamics
specifications in the component model.
This method builds dynamics necessary for building child components.
@param component: Component model containing dynamics specifications.
@type component: lems.model.component.Component
@param runnable: Runnable component to which dynamics is to be added.
@type runnable: lems.sim.runnable.Runnable
@param regime: The dynamics regime to be used to generate
dynamics code in the runnable component.
@type regime: lems.model.dynamics.Regime
@param default_regime: Shared dynamics specifications.
@type default_regime: lems.model.dynamics.Regime
@raise SimBuildError: Raised when a time derivative expression refers
to an undefined variable.
@raise SimBuildError: Raised when there are invalid time
specifications for the <Run> statement.
@raise SimBuildError: Raised when the component reference for <Run>
cannot be resolved.
"""
context = component.context
if regime.name == '':
suffix = ''
else:
suffix = '_regime_' + regime.name
if regime.initial:
runnable.new_regime = regime.name
# Process state variables
for svn in regime.state_variables:
sv = regime.state_variables[svn]
runnable.add_instance_variable(sv.name, 0)
# Process time derivatives
time_step_code = []
for tdn in regime.time_derivatives:
if tdn not in regime.state_variables and tdn not in default_regime.state_variables:
raise SimBuildError(('Time derivative for undefined state '
'variable {0}').format(tdn))
td = regime.time_derivatives[tdn]
exp = self.build_expression_from_tree(runnable,
context,
regime,
td.expression_tree)
time_step_code += ['self.{0} += dt * ({1})'.format(td.variable,
exp)]
runnable.add_method('update_state_variables' + suffix, ['self', 'dt'],
time_step_code)
# Process derived variables
derived_variable_code = []
derived_variables_ordering = order_derived_variables(regime)
for dvn in derived_variables_ordering: #regime.derived_variables:
dv = regime.derived_variables[dvn]
runnable.add_derived_variable(dv.name)
if dv.value:
derived_variable_code += ['self.{0} = ({1})'.format(
dv.name,
self.build_expression_from_tree(runnable,
context,
regime,
dv.expression_tree))]
elif dv.select:
if dv.reduce:
derived_variable_code += self.build_reduce_code(dv.name,
dv.select,
dv.reduce)
else:
derived_variable_code += ['self.{0} = (self.{1})'.format(
dv.name,
dv.select.replace('/', '.'))]
else:
raise SimBuildError(('Inconsistent derived variable settings'
'for {0}').format(dvn))
runnable.add_method('update_derived_variables' + suffix, ['self'],
derived_variable_code)
# Process event handlers
pre_event_handler_code = []
post_event_handler_code = []
startup_event_handler_code = []
for eh in regime.event_handlers:
if eh.type == EventHandler.ON_START:
startup_event_handler_code += self.build_event_handler(runnable,
context,
regime,
eh)
elif eh.type == EventHandler.ON_CONDITION:
post_event_handler_code += self.build_event_handler(runnable,
context,
regime,
eh)
else:
pre_event_handler_code += self.build_event_handler(runnable,
context,
regime,
eh)
runnable.add_method('run_startup_event_handlers' + suffix, ['self'],
startup_event_handler_code)
runnable.add_method('run_preprocessing_event_handlers' + suffix, ['self'],
pre_event_handler_code)
runnable.add_method('run_postprocessing_event_handlers' + suffix, ['self'],
post_event_handler_code)
def add_dynamics_2(self, component, runnable, regime, default_regime):
"""
Adds dynamics to a runnable component based on the dynamics
specifications in the component model.
This method builds dynamics dependent on child components.
@param component: Component model containing dynamics specifications.
@type component: lems.model.component.Component
@param runnable: Runnable component to which dynamics is to be added.
@type runnable: lems.sim.runnable.Runnable
@param regime: The dynamics regime to be used to generate
dynamics code in the runnable component.
@type regime: lems.model.dynamics.Regime
@param default_regime: Shared dynamics specifications.
@type default_regime: lems.model.dynamics.Regime
@raise SimBuildError: Raised when a time derivative expression refers
to an undefined variable.
@raise SimBuildError: Raised when there are invalid time
specifications for the <Run> statement.
@raise SimBuildError: Raised when the component reference for <Run>
cannot be resolved.
"""
context = component.context
if regime.name == '':
suffix = ''
else:
suffix = '_regime_' + regime.name
# Process kinetic schemes
ks_code = []
for ksn in regime.kinetic_schemes:
ks = regime.kinetic_schemes[ksn]
try:
nodes = {node.id:node for node in runnable.__dict__[ks.nodes]}
edges = runnable.__dict__[ks.edges]
for edge in edges:
from_ = edge.__dict__[ks.edge_source]
to = edge.__dict__[ks.edge_target]
ks_code += [('self.{0}.{2} += dt * (-self.{3}.{4} * self.{0}.{2}_shadow + '
'self.{3}.{5} * self.{1}.{2}_shadow)').format(
from_, to, ks.state_variable, edge.id, ks.forward_rate, ks.reverse_rate)]
ks_code += [('self.{1}.{2} += dt * (self.{3}.{4} * self.{0}.{2}_shadow - '
'self.{3}.{5} * self.{1}.{2}_shadow)').format(
from_, to, ks.state_variable, edge.id, ks.forward_rate, ks.reverse_rate)]
ks_code += ['sum = 0']
for node in nodes:
nodes[node].__dict__[ks.state_variable] = 1.0 / len(nodes)
nodes[node].__dict__[ks.state_variable + '_shadow'] = 1.0 / len(nodes)
ks_code += ['sum += self.{0}.{1}'.format(node, ks.state_variable)]
for node in nodes:
ks_code += ['self.{0}.{1} /= sum'.format(node, ks.state_variable)]
for node in nodes:
ks_code += ['self.{0}.{1}_shadow = self.{0}.{1}'.format(node, ks.state_variable)]
except Exception as e:
raise SimBuildError(("Unable to construct kinetic scheme '{0}' "
"for component '{1}' - {2}").format(ks.name, component.id, str(e)))
runnable.add_method('update_kinetic_scheme' + suffix, ['self', 'dt'],
ks_code)
def process_simulation_specs(self, component, runnable, simulation):
"""
Process simulation-related aspects to a runnable component based on the
dynamics specifications in the component model.
@param component: Component model containing dynamics specifications.
@type component: lems.model.component.Component
@param runnable: Runnable component to which dynamics is to be added.
@type runnable: lems.sim.runnable.Runnable
@param simulation: The simulation-related aspects to be implemented
in the runnable component.
@type simulation: lems.model.simulation.Simulation
@raise SimBuildError: Raised when a time derivative expression refers
to an undefined variable
@raise SimBuildError: Raised when there are invalid time
specifications for the <Run> statement.
@raise SimBuildError: Raised when the component reference for <Run>
cannot be resolved.
"""
context = component.context
# Process runs
for rn in simulation.runs:
run = simulation.runs[rn]
c = context.lookup_component_ref(run.component)
if c != None:
#cid = c.id
#if c.id in self.sim.runnables:
# idx = 2
# cid = c.id + '_' + str(idx)
# while cid in self.sim.runnables:
# idx = idx + 1
# cid = c.id + '_' + str(idx)
cid = c.id + '_' + component.id
target = self.build_runnable(c, runnable, cid)
self.sim.add_runnable(target)
self.current_record_target = target
time_step = context.lookup_parameter(run.increment)
time_total = context.lookup_parameter(run.total)
if time_step != None and time_total != None:
target.configure_time(time_step.numeric_value,
time_total.numeric_value)
else:
raise SimBuildError(('Invalid component reference {0} in '
'<Run>').format(c.id))
def convert_op(self, op):
"""
Converts NeuroML arithmetic/logical operators to python equivalents.
@param op: NeuroML operator
@type op: string
@return: Python operator
@rtype: string
"""
if op == '.gt.':
return '>'
elif op == '.ge.' or op == '.geq.':
return '>='
elif op == '.lt.':
return '<'
elif op == '.le.':
return '<='
elif op == '.eq.':
return '=='
elif op == '.ne.':
return '!='
elif op == '^':
return '**'
elif op == '.and.':
return 'and'
elif op == '.or.':
return 'or'
else:
return op
def build_expression_from_tree(self, runnable, context, regime, tree_node):
"""
Recursively builds a Python expression from a parsed expression tree.
@param runnable: Runnable object to which this expression would be added.
@type runnable: lems.sim.runnable.Runnable
@param context: Context from which variables are to be resolved.
@type context: lems.model.context.Context
@param regime: Dynamics regime being built.
@type regime: lems.model.dynamics.Regime
@param tree_node: Root node for the tree from which the expression
is to be built.
@type tree_node: lems.parser.expr.ExprNode
@return: Generated Python expression.
@rtype: string
"""
default_regime = context.selected_dynamics_profile.default_regime
if tree_node.type == ExprNode.VALUE:
if tree_node.value[0].isalpha():
if tree_node.value == 't':
return 'self.time_completed'
elif tree_node.value in context.requirements:
var_prefix = 'self'
v = tree_node.value
r = runnable
while (v not in r.instance_variables and
v not in r.derived_variables):
var_prefix = '{0}.{1}'.format(var_prefix, 'parent')
r = r.parent
if r == None:
raise SimBuildError("Unable to resolve required "
"variable '{0}'".format(v))
return '{0}.{1}'.format(var_prefix, v)
elif (tree_node.value in regime.derived_variables or
tree_node.value in default_regime.derived_variables):
return 'self.{0}'.format(tree_node.value)
else:
return 'self.{0}_shadow'.format(tree_node.value)
else:
return tree_node.value
elif tree_node.type == ExprNode.FUNC1:
return '({0}({1}))'.format(\
tree_node.func,
self.build_expression_from_tree(runnable,
context,
regime,
tree_node.param))
else:
return '({0}) {1} ({2})'.format(\
self.build_expression_from_tree(runnable,
context,
regime,
tree_node.left),
self.convert_op(tree_node.op),
self.build_expression_from_tree(runnable,
context,
regime,
tree_node.right))
def build_event_handler(self, runnable, context, regime, event_handler):
"""
Build event handler code.
@param event_handler: Event handler object
@type event_handler: lems.model.dynamics.EventHandler
@return: Generated event handler code.
@rtype: list(string)
"""
if event_handler.type == EventHandler.ON_CONDITION:
return self.build_on_condition(runnable, context, regime, event_handler)
elif event_handler.type == EventHandler.ON_EVENT:
return self.build_on_event(runnable, context, regime, event_handler)
elif event_handler.type == EventHandler.ON_START:
return self.build_on_start(runnable, context, regime, event_handler)
elif event_handler.type == EventHandler.ON_ENTRY:
return self.build_on_entry(runnable, context, regime, event_handler)
else:
return []
def build_on_condition(self, runnable, context, regime, on_condition):
"""
Build OnCondition event handler code.
@param on_condition: OnCondition event handler object
@type on_condition: lems.model.dynamics.OnCondition
@return: Generated OnCondition code
@rtype: list(string)
"""
on_condition_code = []
on_condition_code += ['if {0}:'.format(\
self.build_expression_from_tree(runnable,
context,
regime,
on_condition.expression_tree))]
for action in on_condition.actions:
code = self.build_action(runnable, context, regime, action)
for line in code:
on_condition_code += [' ' + line]
return on_condition_code
def build_on_event(self, runnable, context, regime, on_event):
"""
Build OnEvent event handler code.
@param on_event: OnEvent event handler object
@type on_event: lems.model.dynamics.OnEvent
@return: Generated OnEvent code
@rtype: list(string)
"""
on_event_code = []
on_event_code += ['count = self.event_in_counters[\'{0}\']'.\
format(on_event.port),
'while count > 0:',
' count -= 1']
for action in on_event.actions:
code = self.build_action(runnable, context, regime, action)
for line in code:
on_event_code += [' ' + line]
on_event_code += ['self.event_in_counters[\'{0}\'] = 0'.\
format(on_event.port),]
return on_event_code
def build_on_start(self, runnable, context, regime, on_start):
"""
Build OnStart start handler code.
@param on_start: OnStart start handler object
@type on_start: lems.model.dynamics.OnStart
@return: Generated OnStart code
@rtype: list(string)
"""
on_start_code = []
for action in on_start.actions:
code = self.build_action(runnable, context, regime, action)
for line in code:
on_start_code += [' ' + line]
return on_start_code
def build_on_entry(self, runnable, context, regime, on_entry):
"""
Build OnEntry start handler code.
@param on_start: OnStart start handler object
@type on_start: lems.model.dynamics.OnStart
@return: Generated OnStart code
@rtype: list(string)
"""
on_entry_code = []
on_entry_code += ['if self.current_regime != self.last_regime:']
on_entry_code += [' self.last_regime = self.current_regime']
for action in on_entry.actions:
code = self.build_action(runnable, context, regime, action)
for line in code:
on_entry_code += [' ' + line]
return on_entry_code
def build_action(self, runnable, context, regime, action):
"""
Build event handler action code.
@param action: Event handler action object
@type action: lems.model.dynamics.Action
@return: Generated action code
@rtype: string
"""
if action.type == Action.STATE_ASSIGNMENT:
return self.build_state_assignment(runnable, context, regime, action)
if action.type == Action.EVENT_OUT:
return self.build_event_out(action)
if action.type == Action.TRANSITION:
return self.build_transition(action)
else:
return ['pass']
def build_state_assignment(self, runnable, context, regime, state_assignment):
"""
Build state assignment code.
@param state_assignment: State assignment object
@type state_assignment: lems.model.dynamics.StateAssignment
@return: Generated state assignment code
@rtype: string
"""
return ['self.{0} = {1}'.format(\
state_assignment.variable,
self.build_expression_from_tree(runnable,
context,
regime,
state_assignment.expression_tree))]
def build_event_out(self, event_out):
"""
Build event out code.
@param event_out: event out object
@type event_out: lems.model.dynamics.EventOut
@return: Generated event out code
@rtype: string
"""
event_out_code = ['if "{0}" in self.event_out_callbacks:'.format(event_out.port),
' for c in self.event_out_callbacks[\'{0}\']:'.format(event_out.port),
' c()']
return event_out_code
def build_transition(self, transition):
"""
Build regime transition code.
@param transition: Transition object
@type transition: lems.model.dynamics.Transition
@return: Generated transition code
@rtype: string
"""
return ["self.new_regime = '{0}'".format(transition.regime)]
def build_reduce_code(self, result, select, reduce):
"""
Builds a reduce operation on the selected target range.
"""
select = select.replace('/', '.')
select = select.replace(' ', '')
if reduce == 'add':
reduce_op = '+'
acc_start = 0
else:
reduce_op = '*'
acc_start = 1
bits = select.split('[*]')
array = bits[0]
ref = bits[1]
code = ['acc = {0}'.format(acc_start)]
code += ['for o in self.{0}:'.format(array)]
code += [' acc = acc {0} o{1}'.format(reduce_op, ref)]
code += ['self.{0} = acc'.format(result)]
code += ['self.{0}_shadow = acc'.format(result)]
return code
def add_recording_behavior(self, component, runnable):
"""
Adds recording-related dynamics to a runnable component based on
the dynamics specifications in the component model.
@param component: Component model containing dynamics specifications.
@type component: lems.model.component.Component
@param runnable: Runnable component to which dynamics is to be added.
@type runnable: lems.sim.runnable.Runnable
@raise SimBuildError: Raised when a target for recording could not be
found.
"""
context = component.context
simulation = context.simulation
for rn in simulation.records:
rec = simulation.records[rn]
if self.current_record_target == None:
raise SimBuildError('No target available for '
'recording variables')
self.current_record_target.add_variable_recorder(rec)
class SimulationBuilder(LEMSBase):
"""
Simulation builder class.
"""
def __init__(self, model):
"""
Constructor.
@param model: Model upon which the simulation is to be generated.
@type model: lems.model.model.Model
"""
self.model = model
""" Model to be used for constructing the simulation.
@type: lems.model.model.Model """
self.sim = None
""" Simulation built from the model.
@type: lems.sim.sim.Simulation """
self.current_record_target = None
def build(self):
"""
Build the simulation components from the model.
@return: A runnable simulation object
@rtype: lems.sim.sim.Simulation
"""
self.sim = Simulation()
for component_id in self.model.default_runs:
if component_id not in self.model.context.components:
raise SimBuildError('Unable to find component \'{0}\' to run'\
.format(component_id))
component = self.model.context.components[component_id]
runnable = self.build_runnable(component)
self.sim.add_runnable(component.id, runnable)
return self.sim
def build_runnable(self, component, parent=None):
"""
Build a runnable component from a component specification and add
it to the simulation.
@param component: Component specification
@type component: lems.model.component.Component
@param parent: Parent runnable component.
@type parent: lems.sim.runnable.Runnable
@raise SimBuildError: Raised when a component reference cannot be
resolved.
"""
runnable = Runnable(component.id, parent)
context = component.context
record_target_backup = self.current_record_target
for pn in context.parameters:
p = context.parameters[pn]
if p.numeric_value:
runnable.add_instance_variable(p.name, p.numeric_value)
else:
pass
## if p.dimension == '__component_ref__':
## ref = context.parent.lookup_component(p.value)
## if ref == None:
## raise SimBuildError(('Unable to resolve component '
## 'reference {0}').\
## format(component_name))
## self.sim.add_runnable(ref.id, self.build_runnable(ref))
for port in context.event_in_ports:
runnable.add_event_in_port(port)
for port in context.event_out_ports:
runnable.add_event_out_port(port)
if context.selected_behavior_profile:
self.add_runnable_behavior(component, runnable,
context.selected_behavior_profile)
else:
runnable.add_method('update_state_variables', ['self', 'dt'], [])
runnable.add_method('run_preprocessing_event_handlers', ['self'],
[])
runnable.add_method('run_postprocessing_event_handlers', ['self'],
[])
for cn in context.components:
child = context.components[cn]
runnable.add_child(child.id, self.build_runnable(child, runnable))
self.build_structure(component, runnable, context.structure)
if context.selected_behavior_profile:
self.add_recording_behavior(component, runnable,
context.selected_behavior_profile)
self.current_record_target = record_target_backup
return runnable
def build_structure(self, component, runnable, structure):
"""
Adds structure to a runnable component based on the structure
specifications in the component model.
@param component: Component model containing structure specifications.
@type component: lems.model.component.Component
@param runnable: Runnable component to which structure is to be added.
@type runnable: lems.sim.runnable.Runnable
@param structure: The structure object to be used to add
structure code in the runnable component.
@type structure: lems.model.structure.Structure
"""
context = component.context
# Process single-child instantiations
# TBD
# Process multi-child instatiantions
for cparam in structure.multi_child_defs:
sparam = structure.multi_child_defs[cparam]
c1 = component
c2 = context.lookup_component(cparam)
template = self.build_runnable(context.lookup_component(cparam),
component)
for i in xrange(sparam):
instance = copy.deepcopy(template)
instance.id = "{0}#{1}#{2}".format(component.id, template.id,
i)
runnable.array.append(instance)
# Process event connections
for (from_component, from_port, to_component,
to_port) in structure.event_connections:
self.add_event_connection(runnable, from_component, from_port,
to_component, to_port)
def add_event_connection(self, runnable, from_component, from_port,
to_component, to_port):
if from_component in runnable.children:
from_ = runnable.children[from_component]
else:
raise SimBuildError('Unable to find component \'{0}\' '
'under \'{1}\''.format(\
from_component, runnable.id))
if to_component in runnable.children:
to = runnable.children[to_component]
else:
raise SimBuildError('Unable to find component \'{0}\' '
'under \'{1}\''.format(\
to_component, runnable.id))
from_.register_event_out_callback(\
from_port, lambda: to.inc_event_in(to_port))
def add_runnable_behavior(self, component, runnable, behavior_profile):
"""
Adds behavior to a runnable component based on the behavior
specifications in the component model.
@param component: Component model containing behavior specifications.
@type component: lems.model.component.Component
@param runnable: Runnable component to which behavior is to be added.
@type runnable: lems.sim.runnable.Runnable
@param behavior_profile: The behavior profile to be used to generate
behavior code in the runnable component.
@type behavior_profile: lems.model.behavior.Behavior
@raise SimBuildError: Raised when a time derivative expression refers
to an undefined variable.
@raise SimBuildError: Raised when there are invalid time
specifications for the <Run> statement.
@raise SimBuildError: Raised when the component reference for <Run>
cannot be resolved.
"""
context = component.context
regime = behavior_profile.default_regime
for svn in regime.state_variables:
sv = regime.state_variables[svn]
runnable.add_instance_variable(sv.name, 0)
time_step_code = []
for tdn in regime.time_derivatives:
if tdn not in regime.state_variables:
raise SimBuildError(('Time derivative for undefined state '
'variable {0}').format(tdn))
td = regime.time_derivatives[tdn]
time_step_code += ['self.{0} += dt * ({1})'.format(td.variable,
self.build_expression_from_tree(\
td.expression_tree))]
runnable.add_method('update_state_variables', ['self', 'dt'],
time_step_code)
pre_event_handler_code = []
post_event_handler_code = []
for eh in regime.event_handlers:
if eh.type == EventHandler.ON_CONDITION:
post_event_handler_code += self.build_event_handler(eh)
else:
pre_event_handler_code += self.build_event_handler(eh)
runnable.add_method('run_preprocessing_event_handlers', ['self'],
pre_event_handler_code)
runnable.add_method('run_postprocessing_event_handlers', ['self'],
post_event_handler_code)
for rn in regime.runs:
run = regime.runs[rn]
c = context.lookup_component_ref(run.component)
if c != None:
target = self.build_runnable(c, self)
self.sim.add_runnable(c.id, target)
self.current_record_target = target
time_step = context.lookup_parameter(run.increment)
time_total = context.lookup_parameter(run.total)
if time_step != None and time_total != None:
target.configure_time(time_step.numeric_value,
time_total.numeric_value)
else:
raise SimBuildError(('Invalid component reference {0} in '
'<Run>').format(c.id))
def convert_op(self, op):
"""
Converts NeuroML arithmetic/logical operators to python equivalents.
@param op: NeuroML operator
@type op: string
@return: Python operator
@rtype: string
"""
if op == '.gt.':
return '>'
elif op == '.ge.':
return '>='
elif op == '.lt.':
return '<'
elif op == '.le.':
return '<='
elif op == '.eq.':
return '=='
elif op == '.ne.':
return '!='
else:
return op
def build_expression_from_tree(self, tree_node):
"""
Recursively builds a Python expression from a parsed expression tree.
@param tree_node: Root node for the tree from which the expression
is to be built.
@type tree_node: lems.parser.expr.ExprNode
@return: Generated Python expression.
@rtype: string
"""
if tree_node.type == ExprNode.VALUE:
if tree_node.value[0].isalpha():
return 'self.{0}_shadow'.format(tree_node.value)
else:
return tree_node.value
else:
return '({0}) {1} ({2})'.format(\
self.build_expression_from_tree(tree_node.left),
self.convert_op(tree_node.op),
self.build_expression_from_tree(tree_node.right))
def build_event_handler(self, event_handler):
"""
Build event handler code.
@param event_handler: Event handler object
@type event_handler: lems.model.behavior.EventHandler
@return: Generated event handler code.
@rtype: list(string)
"""
if event_handler.type == EventHandler.ON_CONDITION:
return self.build_on_condition(event_handler)
elif event_handler.type == EventHandler.ON_EVENT:
return self.build_on_event(event_handler)
else:
return []
def build_on_condition(self, on_condition):
"""
Build OnCondition event handler code.
@param on_condition: OnCondition event handler object
@type on_condition: lems.model.behavior.OnCondition
@return: Generated OnCondition code
@rtype: list(string)
"""
on_condition_code = []
on_condition_code += ['if {0}:'.format(\
self.build_expression_from_tree(on_condition.expression_tree))]
for action in on_condition.actions:
on_condition_code += [' ' + self.build_action(action)]
return on_condition_code
def build_on_event(self, on_event):
"""
Build OnEvent event handler code.
@param on_event: OnEvent event handler object
@type on_event: lems.model.behavior.OnEvent
@return: Generated OnEvent code
@rtype: list(string)
"""
on_event_code = []
on_event_code += ['count = self.event_in_counters[\'{0}\']'.\
format(on_event.port),
'while count > 0:',
' count -= 1']
for action in on_event.actions:
on_event_code += [' ' + self.build_action(action)]
on_event_code += ['self.event_in_counters[\'{0}\'] = 0'.\
format(on_event.port),]
return on_event_code
def build_action(self, action):
"""
Build event handler action code.
@param action: Event handler action object
@type action: lems.model.behavior.Action
@return: Generated action code
@rtype: string
"""
if action.type == Action.STATE_ASSIGNMENT:
return self.build_state_assignment(action)
if action.type == Action.EVENT_OUT:
return self.build_event_out(action)
else:
return ''
def build_state_assignment(self, state_assignment):
"""
Build state assignment code.
@param state_assignment: State assignment object
@type state_assignment: lems.model.behavior.StateAssignment
@return: Generated state assignment code
@rtype: string
"""
return 'self.{0} = {1}'.format(\
state_assignment.variable,
self.build_expression_from_tree(state_assignment.expression_tree))
def build_event_out(self, event_out):
"""
Build event out code.
@param event_out: event out object
@type event_out: lems.model.behavior.StateAssignment
@return: Generated event out code
@rtype: string
"""
event_out_code = 'for c in self.event_out_callbacks[\'{0}\']: c()'.\
format(event_out.port)
return event_out_code
def add_recording_behavior(self, component, runnable, behavior_profile):
"""
Adds recording-related behavior to a runnable component based on
the behavior specifications in the component model.
@param component: Component model containing behavior specifications.
@type component: lems.model.component.Component
@param runnable: Runnable component to which behavior is to be added.
@type runnable: lems.sim.runnable.Runnable
@param behavior_profile: The behavior profile to be used to generate
behavior code in the runnable component.
@type behavior_profile: lems.model.behavior.Behavior
@raise SimBuildError: Raised when a target for recording could not be
found.
"""
context = component.context
regime = behavior_profile.default_regime
for rn in regime.records:
rec = regime.records[rn]
if self.current_record_target == None:
raise SimBuildError('No target available for '
'recording variables')
self.current_record_target.add_variable_recorder(rec.quantity)
class SimulationBuilder(LEMSBase):
"""
Simulation builder class.
"""
def __init__(self, model):
"""
Constructor.
@param model: Model upon which the simulation is to be generated.
@type model: lems.model.model.Model
"""
self.model = model
""" Model to be used for constructing the simulation.
@type: lems.model.model.Model """
self.sim = None
""" Simulation built from the model.
@type: lems.sim.sim.Simulation """
self.current_record_target = None
def build(self):
"""
Build the simulation components from the model.
@return: A runnable simulation object
@rtype: lems.sim.sim.Simulation
"""
self.sim = Simulation()
for component_id in self.model.default_runs:
if component_id not in self.model.context.components:
raise SimBuildError("Unable to find component '{0}' to run".format(component_id))
component = self.model.context.components[component_id]
runnable = self.build_runnable(component)
self.sim.add_runnable(component.id, runnable)
return self.sim
def build_runnable(self, component, parent=None):
"""
Build a runnable component from a component specification and add
it to the simulation.
@param component: Component specification
@type component: lems.model.component.Component
@param parent: Parent runnable component.
@type parent: lems.sim.runnable.Runnable
@raise SimBuildError: Raised when a component reference cannot be
resolved.
"""
runnable = Runnable(component.id, parent)
context = component.context
record_target_backup = self.current_record_target
for pn in context.parameters:
p = context.parameters[pn]
if p.numeric_value:
runnable.add_instance_variable(p.name, p.numeric_value)
else:
pass
## if p.dimension == '__component_ref__':
## ref = context.parent.lookup_component(p.value)
## if ref == None:
## raise SimBuildError(('Unable to resolve component '
## 'reference {0}').\
## format(component_name))
## self.sim.add_runnable(ref.id, self.build_runnable(ref))
for port in context.event_in_ports:
runnable.add_event_in_port(port)
for port in context.event_out_ports:
runnable.add_event_out_port(port)
if context.selected_behavior_profile:
self.add_runnable_behavior(component, runnable, context.selected_behavior_profile)
else:
runnable.add_method("update_state_variables", ["self", "dt"], [])
runnable.add_method("run_preprocessing_event_handlers", ["self"], [])
runnable.add_method("run_postprocessing_event_handlers", ["self"], [])
for cn in context.components:
child = context.components[cn]
runnable.add_child(child.id, self.build_runnable(child, runnable))
self.build_structure(component, runnable, context.structure)
if context.selected_behavior_profile:
self.add_recording_behavior(component, runnable, context.selected_behavior_profile)
self.current_record_target = record_target_backup
return runnable
def build_structure(self, component, runnable, structure):
"""
Adds structure to a runnable component based on the structure
specifications in the component model.
@param component: Component model containing structure specifications.
@type component: lems.model.component.Component
@param runnable: Runnable component to which structure is to be added.
@type runnable: lems.sim.runnable.Runnable
@param structure: The structure object to be used to add
structure code in the runnable component.
@type structure: lems.model.structure.Structure
"""
context = component.context
# Process single-child instantiations
# TBD
# Process multi-child instatiantions
for cparam in structure.multi_child_defs:
sparam = structure.multi_child_defs[cparam]
c1 = component
c2 = context.lookup_component(cparam)
template = self.build_runnable(context.lookup_component(cparam), component)
for i in xrange(sparam):
instance = copy.deepcopy(template)
instance.id = "{0}#{1}#{2}".format(component.id, template.id, i)
runnable.array.append(instance)
# Process event connections
for (from_component, from_port, to_component, to_port) in structure.event_connections:
self.add_event_connection(runnable, from_component, from_port, to_component, to_port)
def add_event_connection(self, runnable, from_component, from_port, to_component, to_port):
if from_component in runnable.children:
from_ = runnable.children[from_component]
else:
raise SimBuildError("Unable to find component '{0}' " "under '{1}'".format(from_component, runnable.id))
if to_component in runnable.children:
to = runnable.children[to_component]
else:
raise SimBuildError("Unable to find component '{0}' " "under '{1}'".format(to_component, runnable.id))
from_.register_event_out_callback(from_port, lambda: to.inc_event_in(to_port))
def add_runnable_behavior(self, component, runnable, behavior_profile):
"""
Adds behavior to a runnable component based on the behavior
specifications in the component model.
@param component: Component model containing behavior specifications.
@type component: lems.model.component.Component
@param runnable: Runnable component to which behavior is to be added.
@type runnable: lems.sim.runnable.Runnable
@param behavior_profile: The behavior profile to be used to generate
behavior code in the runnable component.
@type behavior_profile: lems.model.behavior.Behavior
@raise SimBuildError: Raised when a time derivative expression refers
to an undefined variable.
@raise SimBuildError: Raised when there are invalid time
specifications for the <Run> statement.
@raise SimBuildError: Raised when the component reference for <Run>
cannot be resolved.
"""
context = component.context
regime = behavior_profile.default_regime
for svn in regime.state_variables:
sv = regime.state_variables[svn]
runnable.add_instance_variable(sv.name, 0)
time_step_code = []
for tdn in regime.time_derivatives:
if tdn not in regime.state_variables:
raise SimBuildError(("Time derivative for undefined state " "variable {0}").format(tdn))
td = regime.time_derivatives[tdn]
time_step_code += [
"self.{0} += dt * ({1})".format(td.variable, self.build_expression_from_tree(td.expression_tree))
]
runnable.add_method("update_state_variables", ["self", "dt"], time_step_code)
pre_event_handler_code = []
post_event_handler_code = []
for eh in regime.event_handlers:
if eh.type == EventHandler.ON_CONDITION:
post_event_handler_code += self.build_event_handler(eh)
else:
pre_event_handler_code += self.build_event_handler(eh)
runnable.add_method("run_preprocessing_event_handlers", ["self"], pre_event_handler_code)
runnable.add_method("run_postprocessing_event_handlers", ["self"], post_event_handler_code)
for rn in regime.runs:
run = regime.runs[rn]
c = context.lookup_component_ref(run.component)
if c != None:
target = self.build_runnable(c, self)
self.sim.add_runnable(c.id, target)
self.current_record_target = target
time_step = context.lookup_parameter(run.increment)
time_total = context.lookup_parameter(run.total)
if time_step != None and time_total != None:
target.configure_time(time_step.numeric_value, time_total.numeric_value)
else:
raise SimBuildError(("Invalid component reference {0} in " "<Run>").format(c.id))
def convert_op(self, op):
"""
Converts NeuroML arithmetic/logical operators to python equivalents.
@param op: NeuroML operator
@type op: string
@return: Python operator
@rtype: string
"""
if op == ".gt.":
return ">"
elif op == ".ge.":
return ">="
elif op == ".lt.":
return "<"
elif op == ".le.":
return "<="
elif op == ".eq.":
return "=="
elif op == ".ne.":
return "!="
else:
return op
def build_expression_from_tree(self, tree_node):
"""
Recursively builds a Python expression from a parsed expression tree.
@param tree_node: Root node for the tree from which the expression
is to be built.
@type tree_node: lems.parser.expr.ExprNode
@return: Generated Python expression.
@rtype: string
"""
if tree_node.type == ExprNode.VALUE:
if tree_node.value[0].isalpha():
return "self.{0}_shadow".format(tree_node.value)
else:
return tree_node.value
else:
return "({0}) {1} ({2})".format(
self.build_expression_from_tree(tree_node.left),
self.convert_op(tree_node.op),
self.build_expression_from_tree(tree_node.right),
)
def build_event_handler(self, event_handler):
"""
Build event handler code.
@param event_handler: Event handler object
@type event_handler: lems.model.behavior.EventHandler
@return: Generated event handler code.
@rtype: list(string)
"""
if event_handler.type == EventHandler.ON_CONDITION:
return self.build_on_condition(event_handler)
elif event_handler.type == EventHandler.ON_EVENT:
return self.build_on_event(event_handler)
else:
return []
def build_on_condition(self, on_condition):
"""
Build OnCondition event handler code.
@param on_condition: OnCondition event handler object
@type on_condition: lems.model.behavior.OnCondition
@return: Generated OnCondition code
@rtype: list(string)
"""
on_condition_code = []
on_condition_code += ["if {0}:".format(self.build_expression_from_tree(on_condition.expression_tree))]
for action in on_condition.actions:
on_condition_code += [" " + self.build_action(action)]
return on_condition_code
def build_on_event(self, on_event):
"""
Build OnEvent event handler code.
@param on_event: OnEvent event handler object
@type on_event: lems.model.behavior.OnEvent
@return: Generated OnEvent code
@rtype: list(string)
"""
on_event_code = []
on_event_code += [
"count = self.event_in_counters['{0}']".format(on_event.port),
"while count > 0:",
" count -= 1",
]
for action in on_event.actions:
on_event_code += [" " + self.build_action(action)]
on_event_code += ["self.event_in_counters['{0}'] = 0".format(on_event.port)]
return on_event_code
def build_action(self, action):
"""
Build event handler action code.
@param action: Event handler action object
@type action: lems.model.behavior.Action
@return: Generated action code
@rtype: string
"""
if action.type == Action.STATE_ASSIGNMENT:
return self.build_state_assignment(action)
if action.type == Action.EVENT_OUT:
return self.build_event_out(action)
else:
return ""
def build_state_assignment(self, state_assignment):
"""
Build state assignment code.
@param state_assignment: State assignment object
@type state_assignment: lems.model.behavior.StateAssignment
@return: Generated state assignment code
@rtype: string
"""
return "self.{0} = {1}".format(
state_assignment.variable, self.build_expression_from_tree(state_assignment.expression_tree)
)
def build_event_out(self, event_out):
"""
Build event out code.
@param event_out: event out object
@type event_out: lems.model.behavior.StateAssignment
@return: Generated event out code
@rtype: string
"""
event_out_code = "for c in self.event_out_callbacks['{0}']: c()".format(event_out.port)
return event_out_code
def add_recording_behavior(self, component, runnable, behavior_profile):
"""
Adds recording-related behavior to a runnable component based on
the behavior specifications in the component model.
@param component: Component model containing behavior specifications.
@type component: lems.model.component.Component
@param runnable: Runnable component to which behavior is to be added.
@type runnable: lems.sim.runnable.Runnable
@param behavior_profile: The behavior profile to be used to generate
behavior code in the runnable component.
@type behavior_profile: lems.model.behavior.Behavior
@raise SimBuildError: Raised when a target for recording could not be
found.
"""
context = component.context
regime = behavior_profile.default_regime
for rn in regime.records:
rec = regime.records[rn]
if self.current_record_target == None:
raise SimBuildError("No target available for " "recording variables")
self.current_record_target.add_variable_recorder(rec.quantity)
