def __init__(self, name, parameters=(), aliases=(), constants=()):
self._name = validate_identifier(name)
BaseALObject.__init__(self)
DocumentLevelObject.__init__(self)
ContainerObject.__init__(self)
# Caches the dimension resolver so that it can be reused in subsequent
# calls
self._dimension_resolver = None
# Turn any strings in the parameter list into Parameters:
param_types = (basestring, Parameter)
param_td = filter_discrete_types(parameters, param_types)
params_from_strings = [Parameter(s) for s in param_td[basestring]]
parameters = param_td[Parameter] + params_from_strings
# Load the aliases as objects or strings:
aliases = normalise_parameter_as_list(aliases)
alias_td = filter_discrete_types(aliases, (basestring, Alias))
aliases_from_strs = [Alias.from_str(o) for o in alias_td[basestring]]
aliases = alias_td[Alias] + aliases_from_strs
constants = normalise_parameter_as_list(constants)
self.add(*parameters)
self.add(*aliases)
self.add(*constants)
def __init__(self, name, es, f, t):
AnnotatedNineMLObject.__init__(self)
ContainerObject.__init__(self)
self.name = name
self.add(*es)
self.f = f
self.t = t
def __init__(self, name, parameters=(), aliases=(), constants=()):
self._name = validate_identifier(name)
BaseALObject.__init__(self)
DocumentLevelObject.__init__(self)
ContainerObject.__init__(self)
# Caches the dimension resolver so that it can be reused in subsequent
# calls
self._dimension_resolver = None
# Turn any strings in the parameter list into Parameters:
param_types = (basestring, Parameter)
param_td = filter_discrete_types(parameters, param_types)
params_from_strings = [Parameter(s) for s in param_td[basestring]]
parameters = param_td[Parameter] + params_from_strings
# Load the aliases as objects or strings:
aliases = normalise_parameter_as_list(aliases)
alias_td = filter_discrete_types(aliases, (basestring, Alias))
aliases_from_strs = [Alias.from_str(o) for o in alias_td[basestring]]
aliases = alias_td[Alias] + aliases_from_strs
constants = normalise_parameter_as_list(constants)
self.add(*parameters)
self.add(*aliases)
self.add(*constants)
def __init__(self, name, es, f, t):
AnnotatedNineMLObject.__init__(self)
ContainerObject.__init__(self)
self.name = name
self.add(*es)
self.f = f
self.t = t
def __init__(self, name, definition, properties={}):
"""
Create a new component_class with the given name, definition and
properties, or create a prototype to another component_class that will
be resolved later.
"""
self._name = validate_identifier(name)
BaseULObject.__init__(self)
DocumentLevelObject.__init__(self)
ContainerObject.__init__(self)
if isinstance(definition, basestring):
if "#" in definition:
defn_url, name = definition.split("#")
else:
raise NineMLUsageError(
"Must provide name of class using '#' syntax when "
"providing definition as url string ('{}')".format(
definition))
definition = Definition(name=name, document=None, url=defn_url)
elif (isinstance(definition, ComponentClass)
or definition.nineml_type in ('Dynamics', 'MultiDynamics')):
definition = Definition(definition)
elif (isinstance(definition, Component) or definition.nineml_type
in ('DynamicsProperties', 'MultiDynamicsProperties')):
definition = Prototype(definition)
elif definition.nineml_type not in ('Definition', 'Prototype'):
raise ValueError("'definition' must be either a 'Definition', "
"'Prototype' element or url pointing to a "
"dynamics class")
self._definition = definition
if isinstance(properties, dict):
properties = (Property(name, qty)
for name, qty in properties.items())
self.add(*properties)
self.check_properties()
def __init__(self, name, a, bs, c, d, g):
ContainerObject.__init__(self)
self.name = name
DocumentLevelObject.__init__(self)
self.a = a
self.add(*bs)
self.c = c
self.d = d
self.g = g
def __init__(self, name, a, bs, c, d, g):
ContainerObject.__init__(self)
self.name = name
DocumentLevelObject.__init__(self)
self.a = a
self.add(*bs)
self.c = c
self.d = d
self.g = g
def __init__(self,
name,
pre,
post,
response,
delay,
connectivity=None,
connection_rule_properties=None,
plasticity=None,
port_connections=None,
analog_port_connections=None,
event_port_connections=None,
connectivity_class=Connectivity,
**kwargs):
"""
Create a new projection.
"""
self._name = validate_identifier(name)
BaseULObject.__init__(self)
ContainerObject.__init__(self)
DocumentLevelObject.__init__(self)
assert isinstance(name, basestring)
assert isinstance(delay, Quantity)
assert isinstance(pre, (Population, Selection))
assert isinstance(post, (Population, Selection))
assert isinstance(response, DynamicsProperties)
assert isinstance(plasticity, (DynamicsProperties, type(None)))
self._pre = pre
self._post = post
self._response = response
self._plasticity = plasticity
if connectivity is not None:
assert isinstance(connectivity, Connectivity)
if connection_rule_properties is not None:
raise NineMLUsageError(
"Cannot provide both connectivty and "
"connection_rule_properties as kwargs to projection class")
self._connectivity = connectivity
else:
self._connectivity = connectivity_class(connection_rule_properties,
pre.size, post.size,
**kwargs)
self._delay = delay
if port_connections is None:
port_connections = []
if analog_port_connections is None:
analog_port_connections = []
if event_port_connections is None:
event_port_connections = []
for port_connection in chain(port_connections, event_port_connections,
analog_port_connections):
if isinstance(port_connection, tuple):
port_connection = BasePortConnection.from_tuple(
port_connection, self)
port_connection.bind(self, to_roles=True)
self.add(port_connection)
def __init__(self, name, populations=[], projections=[], selections=[]):
# better would be *items, then sort by type, taking the name from the
# item
self._name = validate_identifier(name)
BaseULObject.__init__(self)
DocumentLevelObject.__init__(self)
ContainerObject.__init__(self)
self.add(*populations)
self.add(*projections)
self.add(*selections)
def __init__(self, *args, **kwargs):
BaseALObject.__init__(self)
ContainerObject.__init__(self)
valid_kwargs = ('name', 'transitions', 'on_events', 'on_conditions',
'time_derivatives', 'aliases')
for arg in kwargs:
if arg not in valid_kwargs:
err = 'Unexpected Arg: %s' % arg
raise NineMLUsageError(err)
name = kwargs.get('name', None)
if name is None:
self._name = 'default'
else:
self._name = validate_identifier(name)
validate_identifier(self._name)
# Get Time derivatives from args or kwargs
kw_tds = normalise_parameter_as_list(
kwargs.get('time_derivatives', None))
time_derivatives = list(args) + kw_tds
# Un-named arguments are time_derivatives:
time_derivatives = normalise_parameter_as_list(time_derivatives)
# time_derivatives.extend( args )
td_types = (basestring, TimeDerivative)
td_type_dict = filter_discrete_types(time_derivatives, td_types)
td_from_str = [TimeDerivative.from_str(o)
for o in td_type_dict[basestring]]
time_derivatives = td_type_dict[TimeDerivative] + td_from_str
# Check for double definitions:
td_dep_vars = [td.variable for td in time_derivatives]
assert_no_duplicates(
td_dep_vars,
("Multiple time derivatives found for the same state variable "
"in regime '{}' (found '{}')".format(
self.name,
"', '".join(td.variable for td in time_derivatives))))
self.add(*time_derivatives)
# We support passing in 'transitions', which is a list of both OnEvents
# and OnConditions as well as separate on_conditions and on_events.
transitions = normalise_parameter_as_list(
kwargs.get('transitions', None))
self.add(*transitions)
on_conditions = normalise_parameter_as_list(
kwargs.get('on_conditions', None))
self.add(*on_conditions)
on_events = normalise_parameter_as_list(
kwargs.get('on_events', None))
self.add(*on_events)
# Add regime specific aliases
aliases = normalise_parameter_as_list(kwargs.get('aliases', None))
self.add(*aliases)
def __init__(self, branches=None):
ContainerObject.__init__(self)
if isinstance(branches, OrderedDefaultListDict):
self._branches = branches
else:
self._branches = OrderedDefaultListDict()
if branches is not None:
for i, branch in enumerate(branches):
branch._abs_index = i
branch._rel_index = len(self._branches[(branch.name,
branch.ns)])
self._branches[(branch.name, branch.ns)].append(branch)
def __init__(self, name, dynamics_properties, synapse_propertiess=[],
connection_property_sets=[]):
# Initiate inherited base classes
BaseULObject.__init__(self)
DocumentLevelObject.__init__(self)
ContainerObject.__init__(self)
WithSynapsesProperties.__init__(self, name, dynamics_properties,
synapse_propertiess,
connection_property_sets)
# Create references to all dynamics member variables so that inherited
# MultiDynamicsProperties properties and methods can find them.
self._annotations = dynamics_properties._annotations
self._sub_components = dynamics_properties._sub_components
def __init__(self, name, dynamics_properties, port_connections=None,
analog_port_connections=None, event_port_connections=None):
super(SynapseProperties, self).__init__()
ContainerObject.__init__(self)
self._name = validate_identifier(name)
self._dynamics_properties = dynamics_properties.clone()
if port_connections is None:
port_connections = []
if analog_port_connections is None:
analog_port_connections = []
if event_port_connections is None:
event_port_connections = []
for port_conn in chain(port_connections, analog_port_connections,
event_port_connections):
self.add(port_conn.clone())
def __init__(self, name, dynamics_properties, synapses_properties=[],
connection_property_sets=[]):
WithSynapsesProperties.__init__(self, name, dynamics_properties,
synapses_properties,
connection_property_sets)
# Initiate inherited base classes
BaseULObject.__init__(self)
DocumentLevelObject.__init__(self, dynamics_properties.document)
ContainerObject.__init__(self)
# Create references to all dynamics member variables so that inherited
# DynamicsProperties properties and methods can find them.
self._annotations = dynamics_properties._annotations
self._properties = dynamics_properties._properties
self._initial_values = dynamics_properties._initial_values
self._initial_regime = dynamics_properties._initial_regime
def __init__(self,
name,
dynamics_properties,
synapse_propertiess=[],
connection_property_sets=[]):
# Initiate inherited base classes
BaseULObject.__init__(self)
DocumentLevelObject.__init__(self)
ContainerObject.__init__(self)
WithSynapsesProperties.__init__(self, name, dynamics_properties,
synapse_propertiess,
connection_property_sets)
# Create references to all dynamics member variables so that inherited
# MultiDynamicsProperties properties and methods can find them.
self._annotations = dynamics_properties._annotations
self._sub_components = dynamics_properties._sub_components
def __init__(self, name, pre, post, response, delay, connectivity=None,
connection_rule_properties=None,
plasticity=None, port_connections=None,
analog_port_connections=None, event_port_connections=None,
connectivity_class=Connectivity, **kwargs):
"""
Create a new projection.
"""
self._name = validate_identifier(name)
BaseULObject.__init__(self)
ContainerObject.__init__(self)
DocumentLevelObject.__init__(self)
assert isinstance(name, basestring)
assert isinstance(delay, Quantity)
assert isinstance(pre, (Population, Selection))
assert isinstance(post, (Population, Selection))
assert isinstance(response, DynamicsProperties)
assert isinstance(plasticity, (DynamicsProperties, type(None)))
self._pre = pre
self._post = post
self._response = response
self._plasticity = plasticity
if connectivity is not None:
assert isinstance(connectivity, Connectivity)
if connection_rule_properties is not None:
raise NineMLUsageError(
"Cannot provide both connectivty and "
"connection_rule_properties as kwargs to projection class")
self._connectivity = connectivity
else:
self._connectivity = connectivity_class(
connection_rule_properties, pre.size, post.size, **kwargs)
self._delay = delay
if port_connections is None:
port_connections = []
if analog_port_connections is None:
analog_port_connections = []
if event_port_connections is None:
event_port_connections = []
for port_connection in chain(port_connections,
event_port_connections,
analog_port_connections):
if isinstance(port_connection, tuple):
port_connection = BasePortConnection.from_tuple(
port_connection, self)
port_connection.bind(self, to_roles=True)
self.add(port_connection)
def __init__(self,
state_assignments=None,
output_events=None,
target_regime_name=None):
"""Abstract class representing a transition from one Regime to
another.
Transition objects are not created directly, but via the subclasses
OnEvent and OnCondition.
Parameters
----------
state_assignments: list(StateAssignment)
A list of the state-assignments performed
when this transition occurs. Objects in this list are either
`string` (e.g A = A+13) or StateAssignment objects.
output_events: list(OutputEvent)
A list of OutputEvent objects emitted when
this transition occurs.
target_regime_name: str | None
The name of the regime to go into after this
transition. `None` implies staying in the same regime. This has
to be specified as a string, not the object, because in general the
|Regime| object is not yet constructed. This is automatically
resolved by the Dynamics during construction.
"""
BaseALObject.__init__(self)
ContainerObject.__init__(self)
# Load state-assignment objects as strings or StateAssignment objects
state_assignments = state_assignments or []
sa_types = (basestring, StateAssignment)
sa_type_dict = filter_discrete_types(state_assignments, sa_types)
sa_from_str = [
StateAssignment.from_str(o) for o in sa_type_dict[basestring]
]
self.add(*(sa_type_dict[StateAssignment] + sa_from_str))
self.add(*normalise_parameter_as_list(output_events))
self._target_regime_name = (validate_identifier(target_regime_name) if
target_regime_name is not None else None)
self._target_regime = None
self._source_regime = None
def __init__(self, name, dynamics, synapses=[],
connection_parameter_sets=[]):
WithSynapses.__init__(self, name, dynamics, synapses,
connection_parameter_sets)
BaseALObject.__init__(self)
DocumentLevelObject.__init__(self, dynamics.document)
ContainerObject.__init__(self)
# Create references to all dynamics member variables so that inherited
# Dynamics properties and methods can find them.
self._annotations = dynamics._annotations
self._sub_components = dynamics._sub_components
self._analog_send_ports = dynamics._analog_send_ports
self._analog_receive_ports = dynamics._analog_receive_ports
self._analog_reduce_ports = dynamics._analog_reduce_ports
self._event_send_ports = dynamics._event_send_ports
self._event_receive_ports = dynamics._event_receive_ports
self._analog_port_connections = dynamics._analog_port_connections
self._event_port_connections = dynamics._event_port_connections
def __init__(self, state_assignments=None, output_events=None,
target_regime_name=None):
"""Abstract class representing a transition from one Regime to
another.
Transition objects are not created directly, but via the subclasses
OnEvent and OnCondition.
Parameters
----------
state_assignments: list(StateAssignment)
A list of the state-assignments performed
when this transition occurs. Objects in this list are either
`string` (e.g A = A+13) or StateAssignment objects.
output_events: list(OutputEvent)
A list of OutputEvent objects emitted when
this transition occurs.
target_regime_name: str | None
The name of the regime to go into after this
transition. `None` implies staying in the same regime. This has
to be specified as a string, not the object, because in general the
|Regime| object is not yet constructed. This is automatically
resolved by the Dynamics during construction.
"""
BaseALObject.__init__(self)
ContainerObject.__init__(self)
# Load state-assignment objects as strings or StateAssignment objects
state_assignments = state_assignments or []
sa_types = (basestring, StateAssignment)
sa_type_dict = filter_discrete_types(state_assignments, sa_types)
sa_from_str = [StateAssignment.from_str(o)
for o in sa_type_dict[basestring]]
self.add(*(sa_type_dict[StateAssignment] + sa_from_str))
self.add(*normalise_parameter_as_list(output_events))
self._target_regime_name = (
validate_identifier(target_regime_name)
if target_regime_name is not None else None)
self._target_regime = None
self._source_regime = None
def __init__(self,
name,
dynamics_properties,
port_connections=None,
analog_port_connections=None,
event_port_connections=None):
super(SynapseProperties, self).__init__()
ContainerObject.__init__(self)
self._name = validate_identifier(name)
self._dynamics_properties = dynamics_properties.clone()
if port_connections is None:
port_connections = []
if analog_port_connections is None:
analog_port_connections = []
if event_port_connections is None:
event_port_connections = []
for port_conn in chain(port_connections, analog_port_connections,
event_port_connections):
self.add(port_conn.clone())
def elements(self, local=False):
"""
Overrides the elements method in ContainerObject base class to allow
for "local" kwarg to only iterate the members that are declared in
this instance (i.e. not the prototype)
"""
if local:
return iter(self._properties.values())
else:
return ContainerObject.elements(self)
def elements(self, local=False):
"""
Overrides the elements method in ContainerObject base class to allow
for "local" kwarg to only iterate the members that are declared in
this instance (i.e. not the prototype)
"""
if local:
return iter(self._properties.values())
else:
return ContainerObject.elements(self)
def __init__(self, items, **kwargs):
BaseULObject.__init__(self, **kwargs)
ContainerObject.__init__(self, **kwargs)
items = list(items)
if all(isinstance(it, Item) for it in items):
indices = [it.index for it in items]
if min(indices) < 0 or max(indices) > len(indices):
raise NineMLUsageError(
"Indices are not contiguous, have duplicates, or don't "
"start from 0 ({})"
.format(', '.join(str(i) for i in indices)))
self.add(*items)
elif any(isinstance(it, Item) for it in items):
raise NineMLUsageError(
"Cannot mix Items and Populations/Selections in Concatenate "
"__init__ method ({})".format(', '.join(str(it)
for it in items)))
else:
self.add(*(Item(i, p) for i, p in enumerate(items)))
assert(self.num_items)
def __init__(self, name, definition, properties={}):
"""
Create a new component_class with the given name, definition and
properties, or create a prototype to another component_class that will
be resolved later.
"""
self._name = validate_identifier(name)
BaseULObject.__init__(self)
DocumentLevelObject.__init__(self)
ContainerObject.__init__(self)
if isinstance(definition, basestring):
if "#" in definition:
defn_url, name = definition.split("#")
else:
raise NineMLUsageError(
"Must provide name of class using '#' syntax when "
"providing definition as url string ('{}')"
.format(definition))
definition = Definition(
name=name,
document=None,
url=defn_url)
elif (isinstance(definition, ComponentClass) or
definition.nineml_type in ('Dynamics', 'MultiDynamics')):
definition = Definition(definition)
elif (isinstance(definition, Component) or
definition.nineml_type in ('DynamicsProperties',
'MultiDynamicsProperties')):
definition = Prototype(definition)
elif definition.nineml_type not in ('Definition', 'Prototype'):
raise ValueError("'definition' must be either a 'Definition', "
"'Prototype' element or url pointing to a "
"dynamics class")
self._definition = definition
if isinstance(properties, dict):
properties = (Property(name, qty)
for name, qty in properties.items())
self.add(*properties)
self.check_properties()
def __init__(self,
name,
dynamics,
synapses=[],
connection_parameter_sets=[]):
BaseALObject.__init__(self)
DocumentLevelObject.__init__(self)
ContainerObject.__init__(self)
WithSynapses.__init__(self, name, dynamics, synapses,
connection_parameter_sets)
# Create references to all dynamics member variables so that inherited
# Dynamics properties and methods can find them.
self._annotations = dynamics._annotations
self._sub_components = dynamics._sub_components
self._analog_send_port_exposures = dynamics._analog_send_port_exposures
self._analog_receive_port_exposures = (
dynamics._analog_receive_port_exposures)
self._analog_reduce_port_exposures = (
dynamics._analog_reduce_port_exposures)
self._event_send_port_exposures = dynamics._event_send_port_exposures
self._event_receive_port_exposures = (
dynamics._event_receive_port_exposures)
self._analog_port_connections = dynamics._analog_port_connections
self._event_port_connections = dynamics._event_port_connections
def __init__(self, port, properties):
super(ConnectionPropertySet, self).__init__()
ContainerObject.__init__(self)
self._port = validate_identifier(port)
for prop in properties:
self.add(prop.clone(as_class=Property))
def __init__(self, port, parameters):
super(ConnectionParameterSet, self).__init__()
ContainerObject.__init__(self)
self._port = validate_identifier(port)
for param in parameters:
self.add(param.clone(as_class=Parameter))
def __init__(self, port, parameters):
super(ConnectionParameterSet, self).__init__()
ContainerObject.__init__(self)
self._port = validate_identifier(port)
for param in parameters:
self.add(param.clone(as_class=Parameter))
def __init__(self, port, properties):
super(ConnectionPropertySet, self).__init__()
ContainerObject.__init__(self)
self._port = validate_identifier(port)
for prop in properties:
self.add(prop.clone(as_class=Property))