def __init__(self):
"""
Constructor.
"""
self.withs = Map()
""" Map of With statements.
@type: Map(str -> lems.model.structure.With) """
self.tunnels = Map()
""" Map of tunnel statements.
@type: Map(str -> lems.model.structure.Tunnel) """
self.event_connections = list()
""" List of event connections.
@type: list(lems.model.structure.EventConnection) """
self.child_instances = list()
""" List of child instantations.
@type: list(lems.model.structure.ChildInstance) """
self.multi_instantiates = list()
""" List of child multi-instantiations.
@type: list(lems.model.structure.MultiInstantiate) """
self.for_eachs = list()
""" List of for each specs.
def __init__(self):
"""
Constructor.
See instance variable documentation for more details on parameters.
"""
self.parent_behavioral = None
""" Parent behavioral object.
@type: lems.model.dynamics.Behavioral """
self.state_variables = Map()
""" Map of state variables in this behavior regime.
@type: dict(str -> lems.model.dynamics.StateVariable """
self.derived_variables = Map()
""" Map of derived variables in this behavior regime.
@type: dict(str -> lems.model.dynamics.DerivedVariable """
self.conditional_derived_variables = Map()
""" Map of conditional derived variables in this behavior regime.
@type: dict(str -> lems.model.dynamics.ConditionalDerivedVariable """
self.time_derivatives = Map()
""" Map of time derivatives in this behavior regime.
@type: dict(str -> lems.model.dynamics.TimeDerivative) """
self.event_handlers = list()
""" List of event handlers in this behavior regime.
@type: list(lems.model.dynamics.EventHandler) """
self.kinetic_schemes = Map()
""" Map of kinetic schemes in this behavior regime.
def __init__(self, include_includes=True, fail_on_missing_includes=True):
"""
Constructor.
"""
self.targets = list()
""" List of targets to be run on startup.
@type: list(str) """
self.includes = Map()
""" Dictionary of includes defined in the model.
@type: dict(str -> lems.model.fundamental.Include """
self.dimensions = Map()
""" Dictionary of dimensions defined in the model.
@type: dict(str -> lems.model.fundamental.Dimension """
self.units = Map()
""" Map of units defined in the model.
@type: dict(str -> lems.model.fundamental.Unit """
self.component_types = Map()
""" Map of component types defined in the model.
@type: dict(str -> lems.model.component.ComponentType) """
self.components = Map()
""" Map of root components defined in the model.
@type: dict(str -> lems.model.component.Component) """
self.fat_components = Map()
""" Map of root fattened components defined in the model.
@type: dict(str -> lems.model.component.FatComponent) """
self.constants = Map()
""" Map of constants in this component type.
@type: dict(str -> lems.model.component.Constant) """
self.include_directories = []
""" List of include directories to search for included LEMS files.
@type: list(str) """
self.included_files = []
""" List of files already included.
@type: list(str) """
self.description = None
""" Short description of contents of LEMS file
@type: str """
self.include_includes = include_includes
""" Whether to include LEMS definitions in <Include> elements
@type: boolean """
self.fail_on_missing_includes = fail_on_missing_includes
""" Whether to raise an Exception when a file in an <Include> element is not found
def __init__(self, include_includes=True, fail_on_missing_includes=True):
"""
Constructor.
"""
self.targets = list()
""" List of targets to be run on startup.
@type: list(str) """
self.includes = Map()
""" Dictionary of includes defined in the model.
@type: dict(str -> lems.model.fundamental.Include """
self.dimensions = Map()
""" Dictionary of dimensions defined in the model.
@type: dict(str -> lems.model.fundamental.Dimension """
self.units = Map()
""" Map of units defined in the model.
@type: dict(str -> lems.model.fundamental.Unit """
self.component_types = Map()
""" Map of component types defined in the model.
@type: dict(str -> lems.model.component.ComponentType) """
self.components = Map()
""" Map of root components defined in the model.
@type: dict(str -> lems.model.component.Component) """
self.fat_components = Map()
""" Map of root fattened components defined in the model.
@type: dict(str -> lems.model.component.FatComponent) """
self.constants = Map()
""" Map of constants in this component type.
@type: dict(str -> lems.model.component.Constant) """
self.include_directories = []
""" List of include directories to search for included LEMS files.
@type: list(str) """
self.included_files = []
""" List of files already included.
@type: list(str) """
self.description = None
""" Short description of contents of LEMS file
@type: str """
self.include_includes = include_includes
""" Whether to include LEMS definitions in <Include> elements
@type: boolean """
self.fail_on_missing_includes = fail_on_missing_includes
""" Whether to raise an Exception when a file in an <Include> element is not found
def __init__(self):
"""
Constructor.
"""
Behavioral.__init__(self)
self.regimes = Map()
""" Map of behavior regimes.
def __init__(self):
"""
Constructor.
"""
self.runs = Map()
""" Map of runs in this dynamics regime.
@type: Map(string -> lems.model.simulation.Run) """
self.records = Map()
""" Map of recorded variables in this dynamics regime.
@type: Map(string -> lems.model.simulation.Record """
self.data_displays = Map()
""" Map of data displays mapping titles to regions.
@type: Map(string -> string) """
self.data_writers = Map()
""" Map of recorded variables to data writers.
class Model(LEMSBase):
"""
Stores a model.
"""
logging.basicConfig(level=logging.INFO)
target_lems_version = '0.7.3'
branch = 'development'
schema_location = 'https://raw.githubusercontent.com/LEMS/LEMS/{0}/Schemas/LEMS/LEMS_v{1}.xsd'.format(branch, target_lems_version)
#schema_location = '/home/padraig/LEMS/Schemas/LEMS/LEMS_v%s.xsd'%target_lems_version
debug = False
def __init__(self, include_includes=True, fail_on_missing_includes=True):
"""
Constructor.
"""
self.targets = list()
""" List of targets to be run on startup.
@type: list(str) """
self.includes = Map()
""" Dictionary of includes defined in the model.
@type: dict(str -> lems.model.fundamental.Include """
self.dimensions = Map()
""" Dictionary of dimensions defined in the model.
@type: dict(str -> lems.model.fundamental.Dimension """
self.units = Map()
""" Map of units defined in the model.
@type: dict(str -> lems.model.fundamental.Unit """
self.component_types = Map()
""" Map of component types defined in the model.
@type: dict(str -> lems.model.component.ComponentType) """
self.components = Map()
""" Map of root components defined in the model.
@type: dict(str -> lems.model.component.Component) """
self.fat_components = Map()
""" Map of root fattened components defined in the model.
@type: dict(str -> lems.model.component.FatComponent) """
self.constants = Map()
""" Map of constants in this component type.
@type: dict(str -> lems.model.component.Constant) """
self.include_directories = []
""" List of include directories to search for included LEMS files.
@type: list(str) """
self.included_files = []
""" List of files already included.
@type: list(str) """
self.description = None
""" Short description of contents of LEMS file
@type: str """
self.include_includes = include_includes
""" Whether to include LEMS definitions in <Include> elements
@type: boolean """
self.fail_on_missing_includes = fail_on_missing_includes
""" Whether to raise an Exception when a file in an <Include> element is not found
@type: boolean """
def add_target(self, target):
"""
Adds a simulation target to the model.
@param target: Name of the component to be added as a
simulation target.
@type target: str
"""
self.targets.append(target)
def add_include(self, include):
"""
Adds an include to the model.
@param include: Include to be added.
@type include: lems.model.fundamental.Include
"""
self.includes[include.file] = include
def add_dimension(self, dimension):
"""
Adds a dimension to the model.
@param dimension: Dimension to be added.
@type dimension: lems.model.fundamental.Dimension
"""
self.dimensions[dimension.name] = dimension
def add_unit(self, unit):
"""
Adds a unit to the model.
@param unit: Unit to be added.
@type unit: lems.model.fundamental.Unit
"""
self.units[unit.symbol] = unit
def add_component_type(self, component_type):
"""
Adds a component type to the model.
@param component_type: Component type to be added.
@type component_type: lems.model.fundamental.ComponentType
"""
name = component_type.name
# To handle colons in names in LEMS
if ':' in name:
name = name.replace(':', '_')
component_type.name = name
self.component_types[name] = component_type
def add_component(self, component):
"""
Adds a component to the model.
@param component: Component to be added.
@type component: lems.model.fundamental.Component
"""
self.components[component.id] = component
def add_fat_component(self, fat_component):
"""
Adds a fattened component to the model.
@param fat_component: Fattened component to be added.
@type fat_component: lems.model.fundamental.Fat_component
"""
self.fat_components[fat_component.id] = fat_component
def add_constant(self, constant):
"""
Adds a paramter to the model.
@param constant: Constant to be added.
@type constant: lems.model.component.Constant
"""
self.constants[constant.name] = constant
def add(self, child):
"""
Adds a typed child object to the model.
@param child: Child object to be added.
"""
if isinstance(child, Include):
self.add_include(child)
elif isinstance(child, Dimension):
self.add_dimension(child)
elif isinstance(child, Unit):
self.add_unit(child)
elif isinstance(child, ComponentType):
self.add_component_type(child)
elif isinstance(child, Component):
self.add_component(child)
elif isinstance(child, FatComponent):
self.add_fat_component(child)
elif isinstance(child, Constant):
self.add_constant(child)
else:
raise ModelError('Unsupported child element')
def add_include_directory(self, path):
"""
Adds a directory to the include file search path.
@param path: Directory to be added.
@type path: str
"""
self.include_directories.append(path)
def include_file(self, path, include_dirs = []):
"""
Includes a file into the current model.
@param path: Path to the file to be included.
@type path: str
@param include_dirs: Optional alternate include search path.
@type include_dirs: list(str)
"""
if self.include_includes:
if self.debug: print("------------------ Including a file: %s"%path)
inc_dirs = include_dirs if include_dirs else self.include_dirs
parser = LEMSFileParser(self, inc_dirs, self.include_includes)
if os.access(path, os.F_OK):
if not path in self.included_files:
parser.parse(open(path).read())
self.included_files.append(path)
return
else:
if self.debug: print("Already included: %s"%path)
return
else:
for inc_dir in inc_dirs:
new_path = (inc_dir + '/' + path)
if os.access(new_path, os.F_OK):
if not new_path in self.included_files:
parser.parse(open(new_path).read())
self.included_files.append(new_path)
return
else:
if self.debug: print("Already included: %s"%path)
return
msg = 'Unable to open ' + path
if self.fail_on_missing_includes:
raise Exception(msg)
elif self.debug:
print(msg)
def import_from_file(self, filepath):
"""
Import a model from a file.
@param filepath: File to be imported.
@type filepath: str
"""
inc_dirs = self.include_directories[:]
inc_dirs.append(dirname(filepath))
parser = LEMSFileParser(self, inc_dirs, self.include_includes)
with open(filepath) as f:
parser.parse(f.read())
def export_to_dom(self):
"""
Exports this model to a DOM.
"""
namespaces = 'xmlns="http://www.neuroml.org/lems/%s" ' + \
'xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" ' + \
'xsi:schemaLocation="http://www.neuroml.org/lems/%s %s"'
namespaces = namespaces%(self.target_lems_version,self.target_lems_version,self.schema_location)
xmlstr = '<Lems %s>'%namespaces
for include in self.includes:
xmlstr += include.toxml()
for target in self.targets:
xmlstr += '<Target component="{0}"/>'.format(target)
for dimension in self.dimensions:
xmlstr += dimension.toxml()
for unit in self.units:
xmlstr += unit.toxml()
for constant in self.constants:
xmlstr += constant.toxml()
for component_type in self.component_types:
xmlstr += component_type.toxml()
for component in self.components:
xmlstr += component.toxml()
xmlstr += '</Lems>'
xmldom = minidom.parseString(xmlstr)
return xmldom
def export_to_file(self, filepath, level_prefix = ' '):
"""
Exports this model to a file.
@param filepath: File to be exported to.
@type filepath: str
"""
xmldom = self.export_to_dom()
xmlstr = xmldom.toprettyxml(level_prefix, '\n',)
f = open(filepath, 'w')
f.write(xmlstr)
f.close()
def resolve(self):
"""
Resolves references in this model.
"""
model = self.copy()
for ct in model.component_types:
model.resolve_component_type(ct)
for c in model.components:
if c.id not in model.fat_components:
model.add(model.fatten_component(c))
for c in ct.constants:
c2 = c.copy()
c2.numeric_value = model.get_numeric_value(c2.value, c2.dimension)
model.add(c2)
return model
def resolve_component_type(self, component_type):
"""
Resolves references in the specified component type.
@param component_type: Component type to be resolved.
@type component_type: lems.model.component.ComponentType
"""
# Resolve component type from base types if present.
if component_type.extends:
try:
base_ct = self.component_types[component_type.extends]
except:
raise ModelError("Component type '{0}' trying to extend unknown component type '{1}'",
component_type.name, component_type.extends)
self.resolve_component_type(base_ct)
self.merge_component_types(component_type, base_ct)
component_type.types = set.union(component_type.types, base_ct.types)
component_type.extends = None
def merge_component_types(self, ct, base_ct):
"""
Merge various maps in the given component type from a base
component type.
@param ct: Component type to be resolved.
@type ct: lems.model.component.ComponentType
@param base_ct: Component type to be resolved.
@type base_ct: lems.model.component.ComponentType
"""
#merge_maps(ct.parameters, base_ct.parameters)
for parameter in base_ct.parameters:
if parameter.name in ct.parameters:
p = ct.parameters[parameter.name]
basep = base_ct.parameters[parameter.name]
if p.fixed:
p.value = p.fixed_value
p.dimension = basep.dimension
else:
ct.parameters[parameter.name] = base_ct.parameters[parameter.name]
merge_maps(ct.properties, base_ct.properties)
merge_maps(ct.derived_parameters, base_ct.derived_parameters)
merge_maps(ct.index_parameters, base_ct.index_parameters)
merge_maps(ct.constants, base_ct.constants)
merge_maps(ct.exposures, base_ct.exposures)
merge_maps(ct.requirements, base_ct.requirements)
merge_maps(ct.component_requirements, base_ct.component_requirements)
merge_maps(ct.instance_requirements, base_ct.instance_requirements)
merge_maps(ct.children, base_ct.children)
merge_maps(ct.texts, base_ct.texts)
merge_maps(ct.links, base_ct.links)
merge_maps(ct.paths, base_ct.paths)
merge_maps(ct.event_ports, base_ct.event_ports)
merge_maps(ct.component_references, base_ct.component_references)
merge_maps(ct.attachments, base_ct.attachments)
merge_maps(ct.dynamics.state_variables, base_ct.dynamics.state_variables)
merge_maps(ct.dynamics.derived_variables, base_ct.dynamics.derived_variables)
merge_maps(ct.dynamics.conditional_derived_variables, base_ct.dynamics.conditional_derived_variables)
merge_maps(ct.dynamics.time_derivatives, base_ct.dynamics.time_derivatives)
#merge_lists(ct.dynamics.event_handlers, base_ct.dynamics.event_handlers)
merge_maps(ct.dynamics.kinetic_schemes, base_ct.dynamics.kinetic_schemes)
merge_lists(ct.structure.event_connections, base_ct.structure.event_connections)
merge_lists(ct.structure.child_instances, base_ct.structure.child_instances)
merge_lists(ct.structure.multi_instantiates, base_ct.structure.multi_instantiates)
merge_maps(ct.simulation.runs, base_ct.simulation.runs)
merge_maps(ct.simulation.records, base_ct.simulation.records)
merge_maps(ct.simulation.event_records, base_ct.simulation.event_records)
merge_maps(ct.simulation.data_displays, base_ct.simulation.data_displays)
merge_maps(ct.simulation.data_writers, base_ct.simulation.data_writers)
merge_maps(ct.simulation.event_writers, base_ct.simulation.event_writers)
def fatten_component(self, c):
"""
Fatten a component but resolving all references into the corresponding component type.
@param c: Lean component to be fattened.
@type c: lems.model.component.Component
@return: Fattened component.
@rtype: lems.model.component.FatComponent
"""
if self.debug: print("Fattening %s"%c.id)
try:
ct = self.component_types[c.type]
except:
raise ModelError("Unable to resolve type '{0}' for component '{1}'; existing: {2}",
c.type, c.id, self.component_types.keys())
fc = FatComponent(c.id, c.type)
if c.parent_id: fc.set_parent_id(c.parent_id)
### Resolve parameters
for parameter in ct.parameters:
if self.debug: print("Checking: %s"%parameter)
if parameter.name in c.parameters:
p = parameter.copy()
p.value = c.parameters[parameter.name]
p.numeric_value = self.get_numeric_value(p.value, p.dimension)
fc.add_parameter(p)
elif parameter.fixed:
p = parameter.copy()
p.numeric_value = self.get_numeric_value(p.value, p.dimension)
fc.add_parameter(p)
else:
raise ModelError("Parameter '{0}' not initialized for component '{1}'",
parameter.name, c.id)
### Resolve properties
for property in ct.properties:
property2 = property.copy()
fc.add(property2)
### Resolve derived_parameters
for derived_parameter in ct.derived_parameters:
derived_parameter2 = derived_parameter.copy()
fc.add(derived_parameter2)
### Resolve derived_parameters
for index_parameter in ct.index_parameters:
raise ModelError("IndexParameter not yet implemented in PyLEMS!")
index_parameter2 = index_parameter.copy()
fc.add(index_parameter2)
### Resolve constants
for constant in ct.constants:
constant2 = constant.copy()
constant2.numeric_value = self.get_numeric_value(constant2.value, constant2.dimension)
fc.add(constant2)
### Resolve texts
for text in ct.texts:
t = text.copy()
t.value = c.parameters[text.name] if text.name in c.parameters else ''
fc.add(t)
### Resolve texts
for link in ct.links:
if link.name in c.parameters:
l = link.copy()
l.value = c.parameters[link.name]
fc.add(l)
else:
raise ModelError("Link parameter '{0}' not initialized for component '{1}'",
link.name, c.id)
### Resolve paths
for path in ct.paths:
if path.name in c.parameters:
p = path.copy()
p.value = c.parameters[path.name]
fc.add(p)
else:
raise ModelError("Path parameter '{0}' not initialized for component '{1}'",
path.name, c.id)
if len(ct.component_requirements)>0:
raise ModelError("ComponentRequirement not yet implemented in PyLEMS!")
if len(ct.instance_requirements)>0:
raise ModelError("InstanceRequirement not yet implemented in PyLEMS!")
### Resolve component references.
for cref in ct.component_references:
if cref.local:
raise ModelError("Attribute local on ComponentReference not yet implemented in PyLEMS!")
if cref.name in c.parameters:
cref2 = cref.copy()
cid = c.parameters[cref.name]
if cid not in self.fat_components:
self.add(self.fatten_component(self.components[cid]))
cref2.referenced_component = self.fat_components[cid]
fc.add(cref2)
else:
raise ModelError("Component reference '{0}' not initialized for component '{1}'",
cref.name, c.id)
merge_maps(fc.exposures, ct.exposures)
merge_maps(fc.requirements, ct.requirements)
merge_maps(fc.component_requirements, ct.component_requirements)
merge_maps(fc.instance_requirements, ct.instance_requirements)
merge_maps(fc.children, ct.children)
merge_maps(fc.texts, ct.texts)
merge_maps(fc.links, ct.links)
merge_maps(fc.paths, ct.paths)
merge_maps(fc.event_ports, ct.event_ports)
merge_maps(fc.attachments, ct.attachments)
fc.dynamics = ct.dynamics.copy()
if len(fc.dynamics.regimes) != 0:
fc.dynamics.clear()
self.resolve_structure(fc, ct)
self.resolve_simulation(fc, ct)
fc.types = ct.types
### Resolve children
for child in c.children:
fc.add(self.fatten_component(child))
return fc
def get_parent_component(self, fc):
"""
TODO: Replace with more efficient way to do this...
"""
if self.debug: print("Looking for parent of %s (%s)"%(fc.id, fc.parent_id))
parent_comp = None
for comp in self.components.values():
if self.debug: print(" - Checking "+comp.id)
for child in comp.children:
if parent_comp == None:
if child.id == fc.id and comp.id == fc.parent_id:
if self.debug: print("1) It is "+comp.id)
parent_comp = comp
else:
for child2 in child.children:
if self.debug: print(" - Checking child: %s, %s"%(child.id,child2.id))
if parent_comp == None and child2.id == fc.id and child.id == fc.parent_id:
if self.debug: print("2) It is "+child.id)
parent_comp = child
break
else:
if self.debug: print("No..." )
return parent_comp
def resolve_structure(self, fc, ct):
"""
Resolve structure specifications.
"""
if self.debug: print("++++++++ Resolving structure of (%s) with %s"%(fc, ct))
for w in ct.structure.withs:
try:
if w.instance == 'parent' or w.instance == 'this':
w2 = With(w.instance, w.as_)
else:
w2 = With(fc.paths[w.instance].value,
w.as_)
except:
raise ModelError("Unable to resolve With parameters for "
"'{0}' in component '{1}'",
w.as_, fc.id)
fc.structure.add(w2)
if len(ct.structure.tunnels) > 0:
raise ModelError("Tunnel is not yet supported in PyLEMS!");
for fe in ct.structure.for_eachs:
fc.structure.add_for_each(fe)
for ev in ct.structure.event_connections:
try:
from_inst = fc.structure.withs[ev.from_].instance
to_inst = fc.structure.withs[ev.to].instance
if self.debug: print("EC..: "+from_inst+" to "+to_inst+ " in "+str(fc.paths))
if len(fc.texts) > 0 or len(fc.paths) > 0:
source_port = fc.texts[ev.source_port].value if ev.source_port and len(ev.source_port)>0 and ev.source_port in fc.texts else None
target_port = fc.texts[ev.target_port].value if ev.target_port and len(ev.target_port)>0 and ev.target_port in fc.texts else None
if self.debug: print("sp: %s"%source_port)
if self.debug: print("tp: %s"%target_port)
receiver = None
# TODO: Get more efficient way to find parent comp
if '../' in ev.receiver:
receiver_id = None
parent_attr = ev.receiver[3:]
if self.debug: print("Finding %s in the parent of: %s (%i)"%(parent_attr, fc, id(fc)))
for comp in self.components.values():
if self.debug: print(" - Checking %s (%i)" %(comp.id,id(comp)))
for child in comp.children:
if self.debug: print(" - Checking %s (%i)" %(child.id,id(child)))
for child2 in child.children:
if child2.id == fc.id and child2.type == fc.type and child.id == fc.parent_id:
if self.debug: print(" - Got it?: %s (%i), child: %s"%(child.id, id(child), child2))
receiver_id = child.parameters[parent_attr]
if self.debug: print("Got it: "+receiver_id)
break
if receiver_id is not None:
for comp in self.fat_components:
if comp.id == receiver_id:
receiver = comp
if self.debug: print("receiver is: %s"%receiver)
if self.debug: print("rec1: %s"%receiver)
if not receiver:
receiver = fc.component_references[ev.receiver].referenced_component if ev.receiver else None
receiver_container = fc.texts[ev.receiver_container].value if (fc.texts and ev.receiver_container) else ''
if self.debug: print("rec2: %s"%receiver)
if len(receiver_container)==0:
# TODO: remove this hard coded check!
receiver_container = 'synapses'
else:
#if from_inst == 'parent':
#par = fc.component_references[ev.receiver]
if self.debug:
print("+++++++++++++++++++")
print(ev.toxml())
print(ev.source_port)
print(fc)
source_port = ev.source_port
target_port = ev.target_port
receiver = None
receiver_container = None
ev2 = EventConnection(from_inst,
to_inst,
source_port,
target_port,
receiver,
receiver_container)
if self.debug:
print("Created EC: "+ev2.toxml())
print(receiver)
print(receiver_container)
except:
logging.exception("Something awful happened!")
raise ModelError("Unable to resolve event connection parameters in component '{0}'",fc)
fc.structure.add(ev2)
for ch in ct.structure.child_instances:
try:
if self.debug: print(ch.toxml())
if '../' in ch.component:
parent = self.get_parent_component(fc)
if self.debug: print("Parent: %s"%parent)
comp_ref = ch.component[3:]
if self.debug: print("comp_ref: %s"%comp_ref)
comp_id = parent.parameters[comp_ref]
comp = self.fat_components[comp_id]
ch2 = ChildInstance(ch.component, comp)
else:
ref_comp = fc.component_references[ch.component].referenced_component
ch2 = ChildInstance(ch.component, ref_comp)
except Exception as e:
if self.debug: print(e)
raise ModelError("Unable to resolve child instance parameters for "
"'{0}' in component '{1}'",
ch.component, fc.id)
fc.structure.add(ch2)
for mi in ct.structure.multi_instantiates:
try:
if mi.component:
mi2 = MultiInstantiate(component=fc.component_references[mi.component].referenced_component,
number=int(fc.parameters[mi.number].numeric_value))
else:
mi2 = MultiInstantiate(component_type=fc.component_references[mi.component_type].referenced_component,
number=int(fc.parameters[mi.number].numeric_value))
except:
raise ModelError("Unable to resolve multi-instantiate parameters for "
"'{0}' in component '{1}'",
mi.component, fc)
fc.structure.add(mi2)
def resolve_simulation(self, fc, ct):
"""
Resolve simulation specifications.
"""
for run in ct.simulation.runs:
try:
run2 = Run(fc.component_references[run.component].referenced_component,
run.variable,
fc.parameters[run.increment].numeric_value,
fc.parameters[run.total].numeric_value)
except:
raise ModelError("Unable to resolve simulation run parameters in component '{0}'",
fc.id)
fc.simulation.add(run2)
for record in ct.simulation.records:
try:
record2 = Record(fc.paths[record.quantity].value,
fc.parameters[record.scale].numeric_value if record.scale else 1,
fc.texts[record.color].value if record.color else '#000000')
except:
raise ModelError("Unable to resolve simulation record parameters in component '{0}'",
fc.id)
fc.simulation.add(record2)
for event_record in ct.simulation.event_records:
try:
event_record2 = EventRecord(fc.paths[event_record.quantity].value,
fc.texts[event_record.eventPort].value)
except:
raise ModelError("Unable to resolve simulation event_record parameters in component '{0}'",
fc.id)
fc.simulation.add(event_record2)
for dd in ct.simulation.data_displays:
try:
dd2 = DataDisplay(fc.texts[dd.title].value,
'')
if 'timeScale' in fc.parameters:
dd2.timeScale = fc.parameters['timeScale'].numeric_value
except:
raise ModelError("Unable to resolve simulation display parameters in component '{0}'",
fc.id)
fc.simulation.add(dd2)
for dw in ct.simulation.data_writers:
try:
path = '.'
if fc.texts[dw.path] and fc.texts[dw.path].value:
path = fc.texts[dw.path].value
dw2 = DataWriter(path,
fc.texts[dw.file_name].value)
except:
raise ModelError("Unable to resolve simulation writer parameters in component '{0}'",
fc.id)
fc.simulation.add(dw2)
for ew in ct.simulation.event_writers:
try:
path = '.'
if fc.texts[ew.path] and fc.texts[ew.path].value:
path = fc.texts[ew.path].value
ew2 = EventWriter(path,
fc.texts[ew.file_name].value,
fc.texts[ew.format].value)
except:
raise ModelError("Unable to resolve simulation writer parameters in component '{0}'",
fc.id)
fc.simulation.add(ew2)
def get_numeric_value(self, value_str, dimension = None):
"""
Get the numeric value for a parameter value specification.
@param value_str: Value string
@type value_str: str
@param dimension: Dimension of the value
@type dimension: str
"""
n = None
i = len(value_str)
while n is None:
try:
part = value_str[0:i]
nn = float(part)
n = nn
s = value_str[i:]
except ValueError:
i = i-1
number = n
sym = s
numeric_value = None
if sym == '':
numeric_value = number
else:
if sym in self.units:
unit = self.units[sym]
if dimension:
if dimension != unit.dimension and dimension != '*':
raise SimBuildError("Unit symbol '{0}' cannot "
"be used for dimension '{1}'",
sym, dimension)
else:
dimension = unit.dimension
numeric_value = (number * (10 ** unit.power) * unit.scale) + unit.offset
else:
raise SimBuildError("Unknown unit symbol '{0}'. Known: {1}",
sym, self.units)
#print("Have converted %s to value: %s, dimension %s"%(value_str, numeric_value, dimension))
return numeric_value
class Model(LEMSBase):
"""
Stores a model.
"""
target_lems_version = '0.7.3'
branch = 'development'
schema_location = 'https://raw.github.com/LEMS/LEMS/{0}/Schemas/LEMS/LEMS_v{1}.xsd'.format(
branch, target_lems_version)
#schema_location = '/home/padraig/LEMS/Schemas/LEMS/LEMS_v%s.xsd'%target_lems_version
debug = False
def __init__(self, include_includes='True'):
"""
Constructor.
"""
self.targets = list()
""" List of targets to be run on startup.
@type: list(str) """
self.dimensions = Map()
""" Dictionary of dimensions defined in the model.
@type: dict(str -> lems.model.fundamental.Dimension """
self.units = Map()
""" Map of units defined in the model.
@type: dict(str -> lems.model.fundamental.Unit """
self.component_types = Map()
""" Map of component types defined in the model.
@type: dict(str -> lems.model.component.ComponentType) """
self.components = Map()
""" Map of root components defined in the model.
@type: dict(str -> lems.model.component.Component) """
self.fat_components = Map()
""" Map of root fattened components defined in the model.
@type: dict(str -> lems.model.component.FatComponent) """
self.constants = Map()
""" Map of constants in this component type.
@type: dict(str -> lems.model.component.Constant) """
self.include_directories = []
""" List of include directories to search for included LEMS files.
@type: list(str) """
self.included_files = []
""" List of files already included.
@type: list(str) """
self.description = None
""" Short description of contents of LEMS file
@type: str """
self.include_includes = include_includes
""" Whether to include LEMS definitions in <Include> elements
@type: boolean """
def add_target(self, target):
"""
Adds a simulation target to the model.
@param target: Name of the component to be added as a
simulation target.
@type target: str
"""
self.targets.append(target)
def add_dimension(self, dimension):
"""
Adds a dimension to the model.
@param dimension: Dimension to be added.
@type dimension: lems.model.fundamental.Dimension
"""
self.dimensions[dimension.name] = dimension
def add_unit(self, unit):
"""
Adds a unit to the model.
@param unit: Unit to be added.
@type unit: lems.model.fundamental.Unit
"""
self.units[unit.symbol] = unit
def add_component_type(self, component_type):
"""
Adds a component type to the model.
@param component_type: Component type to be added.
@type component_type: lems.model.fundamental.ComponentType
"""
self.component_types[component_type.name] = component_type
def add_component(self, component):
"""
Adds a component to the model.
@param component: Component to be added.
@type component: lems.model.fundamental.Component
"""
self.components[component.id] = component
def add_fat_component(self, fat_component):
"""
Adds a fattened component to the model.
@param fat_component: Fattened component to be added.
@type fat_component: lems.model.fundamental.Fat_component
"""
self.fat_components[fat_component.id] = fat_component
def add_constant(self, constant):
"""
Adds a paramter to the model.
@param constant: Constant to be added.
@type constant: lems.model.component.Constant
"""
self.constants[constant.name] = constant
def add(self, child):
"""
Adds a typed child object to the model.
@param child: Child object to be added.
"""
if isinstance(child, Dimension):
self.add_dimension(child)
elif isinstance(child, Unit):
self.add_unit(child)
elif isinstance(child, ComponentType):
self.add_component_type(child)
elif isinstance(child, Component):
self.add_component(child)
elif isinstance(child, FatComponent):
self.add_fat_component(child)
elif isinstance(child, Constant):
self.add_constant(child)
else:
raise ModelError('Unsupported child element')
def add_include_directory(self, path):
"""
Adds a directory to the include file search path.
@param path: Directory to be added.
@type path: str
"""
self.include_directories.append(path)
def include_file(self, path, include_dirs=[]):
"""
Includes a file into the current model.
@param path: Path to the file to be included.
@type path: str
@param include_dirs: Optional alternate include search path.
@type include_dirs: list(str)
"""
if self.include_includes:
if self.debug:
print(
"------------------ Including a file: %s"
% path)
inc_dirs = include_dirs if include_dirs else self.include_dirs
parser = LEMSFileParser(self, inc_dirs, self.include_includes)
if os.access(path, os.F_OK):
if not path in self.included_files:
parser.parse(open(path).read())
self.included_files.append(path)
return
else:
if self.debug: print("Already included: %s" % path)
return
else:
for inc_dir in inc_dirs:
new_path = (inc_dir + '/' + path)
if os.access(new_path, os.F_OK):
if not new_path in self.included_files:
parser.parse(open(new_path).read())
self.included_files.append(new_path)
return
else:
if self.debug: print("Already included: %s" % path)
return
raise Exception('Unable to open ' + path)
def import_from_file(self, filepath):
"""
Import a model from a file.
@param filepath: File to be imported.
@type filepath: str
"""
inc_dirs = self.include_directories[:]
inc_dirs.append(dirname(filepath))
parser = LEMSFileParser(self, inc_dirs, self.include_includes)
with open(filepath) as f:
parser.parse(f.read())
def export_to_file(self, filepath, level_prefix=' '):
"""
Exports this model to a file.
@param filepath: File to be exported to.
@type filepath: str
"""
namespaces = 'xmlns="http://www.neuroml.org/lems/%s" ' + \
'xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" ' + \
'xsi:schemaLocation="http://www.neuroml.org/lems/%s %s"'
namespaces = namespaces % (self.target_lems_version,
self.target_lems_version,
self.schema_location)
xmlstr = '<Lems %s>' % namespaces
for target in self.targets:
xmlstr += '<Target component="{0}"/>'.format(target)
for dimension in self.dimensions:
xmlstr += dimension.toxml()
for unit in self.units:
xmlstr += unit.toxml()
for constant in self.constants:
xmlstr += constant.toxml()
for component_type in self.component_types:
xmlstr += component_type.toxml()
for component in self.components:
xmlstr += component.toxml()
xmlstr += '</Lems>'
xmlstr = minidom.parseString(xmlstr).toprettyxml(
level_prefix,
'\n',
)
with open(filepath, 'w') as f:
f.write(xmlstr)
def resolve(self):
"""
Resolves references in this model.
"""
model = self.copy()
for ct in model.component_types:
model.resolve_component_type(ct)
for c in model.components:
if c.id not in model.fat_components:
model.add(model.fatten_component(c))
for c in ct.constants:
c2 = c.copy()
c2.numeric_value = model.get_numeric_value(c2.value, c2.dimension)
model.add(c2)
return model
def resolve_component_type(self, component_type):
"""
Resolves references in the specified component type.
@param component_type: Component type to be resolved.
@type component_type: lems.model.component.ComponentType
"""
# Resolve component type from base types if present.
if component_type.extends:
try:
base_ct = self.component_types[component_type.extends]
except:
raise ModelError(
"Component type '{0}' trying to extend unknown component type '{1}'",
component_type.name, component_type.extends)
self.resolve_component_type(base_ct)
self.merge_component_types(component_type, base_ct)
component_type.types = set.union(component_type.types,
base_ct.types)
component_type.extends = None
def merge_component_types(self, ct, base_ct):
"""
Merge various maps in the given component type from a base
component type.
@param ct: Component type to be resolved.
@type ct: lems.model.component.ComponentType
@param base_ct: Component type to be resolved.
@type base_ct: lems.model.component.ComponentType
"""
#merge_maps(ct.parameters, base_ct.parameters)
for parameter in base_ct.parameters:
if parameter.name in ct.parameters:
p = ct.parameters[parameter.name]
basep = base_ct.parameters[parameter.name]
if p.fixed:
p.value = p.fixed_value
p.dimension = basep.dimension
else:
ct.parameters[parameter.name] = base_ct.parameters[
parameter.name]
merge_maps(ct.derived_parameters, base_ct.derived_parameters)
merge_maps(ct.constants, base_ct.constants)
merge_maps(ct.exposures, base_ct.exposures)
merge_maps(ct.requirements, base_ct.requirements)
merge_maps(ct.children, base_ct.children)
merge_maps(ct.texts, base_ct.texts)
merge_maps(ct.links, base_ct.links)
merge_maps(ct.paths, base_ct.paths)
merge_maps(ct.event_ports, base_ct.event_ports)
merge_maps(ct.component_references, base_ct.component_references)
merge_maps(ct.attachments, base_ct.attachments)
merge_maps(ct.dynamics.state_variables,
base_ct.dynamics.state_variables)
merge_maps(ct.dynamics.derived_variables,
base_ct.dynamics.derived_variables)
merge_maps(ct.dynamics.conditional_derived_variables,
base_ct.dynamics.conditional_derived_variables)
merge_maps(ct.dynamics.time_derivatives,
base_ct.dynamics.time_derivatives)
#merge_lists(ct.dynamics.event_handlers, base_ct.dynamics.event_handlers)
merge_maps(ct.dynamics.kinetic_schemes,
base_ct.dynamics.kinetic_schemes)
merge_lists(ct.structure.event_connections,
base_ct.structure.event_connections)
merge_lists(ct.structure.child_instances,
base_ct.structure.child_instances)
merge_lists(ct.structure.multi_instantiates,
base_ct.structure.multi_instantiates)
merge_maps(ct.simulation.runs, base_ct.simulation.runs)
merge_maps(ct.simulation.records, base_ct.simulation.records)
merge_maps(ct.simulation.data_displays,
base_ct.simulation.data_displays)
merge_maps(ct.simulation.data_writers, base_ct.simulation.data_writers)
def fatten_component(self, c):
"""
Fatten a component but resolving all references into the corresponding component type.
@param c: Lean component to be fattened.
@type c: lems.model.component.Component
@return: Fattened component.
@rtype: lems.model.component.FatComponent
"""
if self.debug: print("Fattening %s" % c.id)
try:
ct = self.component_types[c.type]
except:
raise ModelError(
"Unable to resolve type '{0}' for component '{1}'; existing: {2}",
c.type, c.id, self.component_types.keys())
fc = FatComponent(c.id, c.type)
if c.parent_id: fc.set_parent_id(c.parent_id)
### Resolve parameters
for parameter in ct.parameters:
if parameter.name in c.parameters:
p = parameter.copy()
p.value = c.parameters[parameter.name]
p.numeric_value = self.get_numeric_value(p.value, p.dimension)
fc.add_parameter(p)
elif parameter.fixed:
p = parameter.copy()
p.numeric_value = self.get_numeric_value(p.value, p.dimension)
fc.add_parameter(p)
else:
raise ModelError(
"Parameter '{0}' not initialized for component '{1}'",
parameter.name, c.id)
### Resolve derived_parameters
for derived_parameter in ct.derived_parameters:
derived_parameter2 = derived_parameter.copy()
#derived_parameter2.numeric_value = self.get_numeric_value(constant2.value, constant2.dimension)
fc.add(derived_parameter2)
### Resolve constants
for constant in ct.constants:
constant2 = constant.copy()
constant2.numeric_value = self.get_numeric_value(
constant2.value, constant2.dimension)
fc.add(constant2)
### Resolve texts
for text in ct.texts:
t = text.copy()
t.value = c.parameters[
text.name] if text.name in c.parameters else ''
fc.add(t)
### Resolve texts
for link in ct.links:
if link.name in c.parameters:
l = link.copy()
l.value = c.parameters[link.name]
fc.add(l)
else:
raise ModelError(
"Link parameter '{0}' not initialized for component '{1}'",
link.name, c.id)
### Resolve paths
for path in ct.paths:
if path.name in c.parameters:
p = path.copy()
p.value = c.parameters[path.name]
fc.add(p)
else:
raise ModelError(
"Path parameter '{0}' not initialized for component '{1}'",
path.name, c.id)
### Resolve component references.
for cref in ct.component_references:
if cref.name in c.parameters:
cref2 = cref.copy()
cid = c.parameters[cref.name]
if cid not in self.fat_components:
self.add(self.fatten_component(self.components[cid]))
cref2.referenced_component = self.fat_components[cid]
fc.add(cref2)
else:
raise ModelError(
"Component reference '{0}' not initialized for component '{1}'",
cref.name, c.id)
merge_maps(fc.exposures, ct.exposures)
merge_maps(fc.requirements, ct.requirements)
merge_maps(fc.children, ct.children)
merge_maps(fc.texts, ct.texts)
merge_maps(fc.links, ct.links)
merge_maps(fc.paths, ct.paths)
merge_maps(fc.event_ports, ct.event_ports)
merge_maps(fc.attachments, ct.attachments)
fc.dynamics = ct.dynamics.copy()
if len(fc.dynamics.regimes) != 0:
fc.dynamics.clear()
self.resolve_structure(fc, ct)
self.resolve_simulation(fc, ct)
fc.types = ct.types
### Resolve children
for child in c.children:
fc.add(self.fatten_component(child))
return fc
def get_parent_component(self, fc):
"""
TODO: Replace with more efficient way to do this...
"""
if self.debug:
print("Looking for parent of %s (%s)" % (fc.id, fc.parent_id))
parent_comp = None
for comp in self.components.values():
if self.debug: print(" - Checking " + comp.id)
for child in comp.children:
if parent_comp == None:
if child.id == fc.id and comp.id == fc.parent_id:
if self.debug: print("1) It is " + comp.id)
parent_comp = comp
else:
for child2 in child.children:
if self.debug:
print(" - Checking child: %s, %s" %
(child.id, child2.id))
if parent_comp == None and child2.id == fc.id and child.id == fc.parent_id:
if self.debug: print("2) It is " + child.id)
parent_comp = child
break
else:
if self.debug: print("No...")
return parent_comp
def resolve_structure(self, fc, ct):
"""
Resolve structure specifications.
"""
if self.debug:
print("++++++++ Resolving structure of (%s) with %s" % (fc, ct))
for w in ct.structure.withs:
try:
if w.instance == 'parent' or w.instance == 'this':
w2 = With(w.instance, w.as_)
else:
w2 = With(fc.paths[w.instance].value, w.as_)
except:
raise ModelError(
"Unable to resolve With parameters for "
"'{0}' in component '{1}'", w.as_, fc.id)
fc.structure.add(w2)
for fe in ct.structure.for_eachs:
fc.structure.add_for_each(fe)
for ev in ct.structure.event_connections:
try:
from_inst = fc.structure.withs[ev.from_].instance
to_inst = fc.structure.withs[ev.to].instance
if self.debug:
print("EC..: " + from_inst + " to " + to_inst + " in " +
str(fc.paths))
if len(fc.texts) > 0 or len(fc.paths) > 0:
source_port = fc.texts[
ev.source_port].value if ev.source_port and len(
ev.source_port
) > 0 and ev.source_port in fc.texts else None
target_port = fc.texts[
ev.target_port].value if ev.target_port and len(
ev.target_port
) > 0 and ev.target_port in fc.texts else None
if self.debug: print("sp: %s" % source_port)
if self.debug: print("tp: %s" % target_port)
receiver = None
# TODO: Get more efficient way to find parent comp
if '../' in ev.receiver:
receiver_id = None
parent_attr = ev.receiver[3:]
if self.debug:
print("Finding %s in the parent of: %s (%i)" %
(parent_attr, fc, id(fc)))
for comp in self.components.values():
if self.debug:
print(" - Checking %s (%i)" %
(comp.id, id(comp)))
for child in comp.children:
if self.debug:
print(" - Checking %s (%i)" %
(child.id, id(child)))
for child2 in child.children:
if child2.id == fc.id and child2.type == fc.type and child.id == fc.parent_id:
if self.debug:
print(
" - Got it?: %s (%i), child: %s"
%
(child.id, id(child), child2))
receiver_id = child.parameters[
parent_attr]
if self.debug:
print("Got it: " + receiver_id)
break
if receiver_id is not None:
for comp in self.fat_components:
if comp.id == receiver_id:
receiver = comp
if self.debug:
print("receiver is: %s" % receiver)
if self.debug: print("rec1: %s" % receiver)
if not receiver:
receiver = fc.component_references[
ev.
receiver].referenced_component if ev.receiver else None
receiver_container = fc.texts[
ev.receiver_container].value if (
fc.texts and ev.receiver_container) else ''
if self.debug: print("rec2: %s" % receiver)
if len(receiver_container) == 0:
# TODO: remove this hard coded check!
receiver_container = 'synapses'
else:
#if from_inst == 'parent':
#par = fc.component_references[ev.receiver]
if self.debug:
print("+++++++++++++++++++")
print(ev.toxml())
print(ev.source_port)
print(fc)
source_port = ev.source_port
target_port = ev.target_port
receiver = None
receiver_container = None
ev2 = EventConnection(from_inst, to_inst, source_port,
target_port, receiver,
receiver_container)
if self.debug:
print("Created EC: " + ev2.toxml())
print(receiver)
print(receiver_container)
except:
logging.exception("Something awful happened!")
raise ModelError(
"Unable to resolve event connection parameters in component '{0}'",
fc)
fc.structure.add(ev2)
for ch in ct.structure.child_instances:
try:
if self.debug: print(ch.toxml())
if '../' in ch.component:
parent = self.get_parent_component(fc)
if self.debug: print("Parent: %s" % parent)
comp_ref = ch.component[3:]
if self.debug: print("comp_ref: %s" % comp_ref)
comp_id = parent.parameters[comp_ref]
comp = self.fat_components[comp_id]
ch2 = ChildInstance(ch.component, comp)
else:
ref_comp = fc.component_references[
ch.component].referenced_component
ch2 = ChildInstance(ch.component, ref_comp)
except Exception as e:
if self.debug: print(e)
raise ModelError(
"Unable to resolve child instance parameters for "
"'{0}' in component '{1}'", ch.component, fc.id)
fc.structure.add(ch2)
for mi in ct.structure.multi_instantiates:
try:
mi2 = MultiInstantiate(
fc.component_references[mi.component].referenced_component,
int(fc.parameters[mi.number].numeric_value))
except:
raise ModelError(
"Unable to resolve multi-instantiate parameters for "
"'{0}' in component '{1}'", mi.component, fc)
fc.structure.add(mi2)
def resolve_simulation(self, fc, ct):
"""
Resolve simulation specifications.
"""
for run in ct.simulation.runs:
try:
run2 = Run(
fc.component_references[
run.component].referenced_component, run.variable,
fc.parameters[run.increment].numeric_value,
fc.parameters[run.total].numeric_value)
except:
raise ModelError(
"Unable to resolve simulation run parameters in component '{0}'",
fc.id)
fc.simulation.add(run2)
for record in ct.simulation.records:
try:
record2 = Record(
fc.paths[record.quantity].value,
fc.parameters[record.scale].numeric_value
if record.scale else 1, fc.texts[record.color].value
if record.color else '#000000')
except:
raise ModelError(
"Unable to resolve simulation record parameters in component '{0}'",
fc.id)
fc.simulation.add(record2)
for dd in ct.simulation.data_displays:
try:
dd2 = DataDisplay(fc.texts[dd.title].value, '')
if 'timeScale' in fc.parameters:
dd2.timeScale = fc.parameters['timeScale'].numeric_value
except:
raise ModelError(
"Unable to resolve simulation display parameters in component '{0}'",
fc.id)
fc.simulation.add(dd2)
for dw in ct.simulation.data_writers:
try:
path = '.'
if fc.texts[dw.path] and fc.texts[dw.path].value:
path = fc.texts[dw.path].value
dw2 = DataWriter(path, fc.texts[dw.file_name].value)
except:
raise ModelError(
"Unable to resolve simulation writer parameters in component '{0}'",
fc.id)
fc.simulation.add(dw2)
def get_numeric_value(self, value_str, dimension=None):
"""
Get the numeric value for a parameter value specification.
@param value_str: Value string
@type value_str: str
@param dimension: Dimension of the value
@type dimension: str
"""
n = None
i = len(value_str)
while n is None:
try:
part = value_str[0:i]
nn = float(part)
n = nn
s = value_str[i:]
except ValueError:
i = i - 1
number = n
sym = s
numeric_value = None
if sym == '':
numeric_value = number
else:
if sym in self.units:
unit = self.units[sym]
if dimension:
if dimension != unit.dimension and dimension != '*':
raise SimBuildError(
"Unit symbol '{0}' cannot "
"be used for dimension '{1}'", sym, dimension)
else:
dimension = unit.dimension
numeric_value = (number *
(10**unit.power) * unit.scale) + unit.offset
else:
raise SimBuildError("Unknown unit symbol '{0}'. Known: {1}",
sym, self.units)
#print("Have converted %s to value: %s, dimension %s"%(value_str, numeric_value, dimension))
return numeric_value
def clear(self):
"""
Clear behavioral entities.
"""
self.time_derivatives = Map()
def __init__(self):
"""
Constructor.
See instance variable documentation for more details on parameters.
"""
self.parameters = Map()
""" Map of parameters in this component type.
@type: Map(str -> lems.model.component.Parameter) """
self.properties = Map()
""" Map of properties in this component type.
@type: Map(str -> lems.model.component.Property) """
self.derived_parameters = Map()
""" Map of derived_parameters in this component type.
@type: Map(str -> lems.model.component.Parameter) """
self.index_parameters = Map()
""" Map of index_parameters in this component type.
@type: Map(str -> lems.model.component.IndexParameter) """
self.constants = Map()
""" Map of constants in this component type.
@type: Map(str -> lems.model.component.Constant) """
self.exposures = Map()
""" Map of exposures in this component type.
@type: Map(str -> lems.model.component.Exposure) """
self.requirements = Map()
""" Map of requirements.
@type: Map(str -> lems.model.component.Requirement) """
self.component_requirements = Map()
""" Map of component requirements.
@type: Map(str -> lems.model.component.ComponentRequirement) """
self.instance_requirements = Map()
""" Map of instance requirements.
@type: Map(str -> lems.model.component.InstanceRequirement) """
self.children = Map()
""" Map of children.
@type: Map(str -> lems.model.component.Children) """
self.texts = Map()
""" Map of text entries.
@type: Map(str -> lems.model.component.Text) """
self.links = Map()
""" Map of links.
@type: Map(str -> lems.model.component.Link) """
self.paths = Map()
""" Map of path entries.
@type: Map(str -> lems.model.component.Path) """
self.event_ports = Map()
""" Map of event ports.
@type: Map(str -> lems.model.component.EventPort """
self.component_references = Map()
""" Map of component references.
@type: Map(str -> lems.model.component.ComponentReference) """
self.attachments = Map()
""" Map of attachment type specifications.
@type: Map(str -> lems.model.component.Attachments) """
self.dynamics = Dynamics()
""" Behavioural dynamics object.
@type: lems.model.dynamics.Dynamics """
self.structure = Structure()
""" Structural properties object.
@type: lems.model.structure.Structure """
self.simulation = Simulation()
""" Simulation attributes.
@type: lems.model.simulation.Simulation """
self.types = set()
""" Set of compatible component types.
