def check_properties(self):
# First check the names
properties = set(self.property_names)
parameters = set(self.component_class.parameter_names)
msg = []
diff_a = properties.difference(parameters)
diff_b = parameters.difference(properties)
if diff_a:
msg.append("User properties of '{}' (url:{}) contain the "
"following parameters that are not present in the "
"definition of '{}' (url:{}): {}\n\n".format(
self.name, self.url, self.component_class.name,
self.component_class.url, ",".join(diff_a)))
if diff_b:
msg.append("Definition of '{}' (url:{}) contains the following "
"parameters that are not present in the user properties"
" of '{}' (url:{}): {}".format(
self.component_class.name, self.component_class.url,
self.name, self.url, ",".join(diff_b)))
if msg:
# need a more specific type of Exception
raise NineMLUsageError(". ".join(msg))
# Check dimensions match
for param in self.component_class.parameters:
prop_units = self.property(param.name).units
prop_dimension = prop_units.dimension
param_dimension = param.dimension
if prop_dimension != param_dimension:
raise NineMLUsageError(
"Dimensions for '{}' property, {}, in '{}' don't match "
"that of its definition in '{}', {}.".format(
param.name, prop_dimension, self.name,
self.component_class.name, param_dimension))
def nineml_expression(**kwargs):
if isinstance(self.rhs,
(bool, int, float, BooleanTrue, BooleanFalse)):
val = self.rhs
else:
if self.rhs.is_Boolean:
try:
val = self.rhs.subs(kwargs)
except Exception:
raise NineMLUsageError(
"Incorrect arguments provided to expression ('{}')"
": '{}'\n".format(
"', '".join(self.rhs_symbol_names),
"', '".join(list(kwargs.keys()))))
else:
try:
val = self.rhs.evalf(subs=kwargs)
except Exception:
raise NineMLUsageError(
"Incorrect arguments provided to expression '{}'"
": '{}' (expected '{}')\n".format(
self.rhs, "', '".join(list(kwargs.keys())),
"', '".join(self.rhs_symbol_names)))
try:
val = float(val)
except TypeError:
try:
locals_dict = deepcopy(kwargs)
locals_dict.update(str_to_npfunc_map)
val = eval(str(val), {}, locals_dict)
except Exception:
raise NineMLUsageError(
"Could not evaluate expression: {}".format(
self.rhs_str))
return val
def __init__(self, target=None, name=None, url=None, document=None):
super(BaseReference, self).__init__()
if target is not None:
assert isinstance(target, DocumentLevelObject)
self._target = target
if name is not None or url is not None or document is not None:
raise NineMLUsageError(
"'name', 'url' and 'document' kwargs cannot be used in "
"conjunction with 'target'")
else:
assert name is not None
document_url = document.url if document is not None else None
if url is not None and url != document_url:
if url.startswith('.'):
if document_url is None:
raise NineMLUsageError(
"Must supply a document with a non-None URL that "
"is being referenced from if definition is a "
"relative URL string, '{}'".format(url))
relative_to = os.path.dirname(document.url)
else:
relative_to = None
if (relative_to is not None and os.path.realpath(
os.path.join(relative_to, url)) == document_url):
remote_doc = document
else:
remote_doc = nineml.read(url, relative_to=relative_to)
else:
remote_doc = document
self._target = remote_doc[name]
def __init__(self, lhs, rhs, assign_to_reserved=False):
ExpressionWithLHS.__init__(self, rhs)
if not is_single_symbol(lhs):
err = 'Expecting a single symbol on the LHS; got: %s' % lhs
raise NineMLUsageError(err)
if not assign_to_reserved and not is_valid_lhs_target(lhs):
err = 'Invalid LHS target: %s' % lhs
raise NineMLUsageError(err)
self._name = validate_identifier(lhs)
def _check_ports(self):
if not isinstance(self.send_port, EventSendPort):
raise NineMLUsageError(
"Send port '{}' must be an EventSendPort to be connected with"
" an EventPortConnection".format(self.send_port.name))
if not isinstance(self.receive_port, EventReceivePort):
raise NineMLUsageError(
"Send port '{}' must be an EventSendPort to be connected with"
" an EventPortConnection".format(self.receive_port.name))
def from_tuple(cls, tple, container):
# FIXME: Needs comments to explain what is going on and better
# exception messages
sender, send_port, receiver, receive_port = tple
init_kwargs = {}
try:
sender_dynamicss = getattr(container, sender).component_classes
init_kwargs['sender_role'] = sender
except AttributeError:
try:
sender_dynamicss = [container[sender].component_class]
init_kwargs['sender_name'] = sender
except (TypeError, KeyError) as e:
raise NineMLUsageError(
"Did not find sender {} '{}' in '{}' container".format(
'name' if isinstance(e, KeyError) else 'role',
receiver, container.name))
try:
getattr(container, receiver).component_classes
init_kwargs['receiver_role'] = receiver
except AttributeError:
try:
container[receiver].component_class
init_kwargs['receiver_name'] = receiver
except (TypeError, KeyError) as e:
raise NineMLUsageError(
"Did not find receiver {} '{}' in '{}' container".format(
'name' if isinstance(e, KeyError) else 'role',
receiver, container.name))
port_type = None
for dyn in sender_dynamicss:
pt = dyn.port(send_port).nineml_type
if port_type is None:
port_type = pt
elif port_type != pt:
raise NineMLUsageError(
"Mismatching port types for '{}' port in populations in "
"Selection '{}'".format(send_port, container.name))
if port_type in ('AnalogSendPort', 'AnalogSendPortExposure'):
port_connection = AnalogPortConnection(
receive_port_name=receive_port,
send_port_name=send_port,
**init_kwargs)
elif port_type in ('EventSendPort', 'EventSendPortExposure'):
port_connection = EventPortConnection(
receive_port_name=receive_port,
send_port_name=send_port,
**init_kwargs)
else:
assert False, "'{}' should be a send port not '{}'".format(
send_port, port_type)
return port_connection
def add(self, nineml_obj, clone=True, cloner=None, **kwargs):
"""
Adds a cloned version of the element to the document, setting the
document reference (and the corresponding url) of clones to the
document.
Parameters
----------
nineml_obj : DocumentLevelObject
A document level object to add to the document
clone : bool
Whether to clone the element before adding it to the document
clone_definitions : str
Whether to clone definitions of user layer objects
kwargs : dict
Keyword arguments passed to the clone method
"""
if not isinstance(nineml_obj, DocumentLevelObject):
raise NineMLUsageError(
"Cannot add {} element to document as it is not a \"document"
"-level\" object".format(nineml_obj))
if nineml_obj.name in self:
# Ignore if the element is already added (this can happen
# implictly when writing other elements that refer to this element)
if nineml_obj is not self[nineml_obj.name]:
if nineml_obj == self[nineml_obj.name]:
nineml_obj = self[nineml_obj.name]
else:
nineml_obj.find_mismatch(self[nineml_obj.name])
raise NineMLNameError(
"Could not add '{}' as a different object with that "
"name already exists in the document '{}':\n{}"
.format(nineml_obj.name, self.url,
nineml_obj.find_mismatch(
self[nineml_obj.name])))
elif nineml_obj.document is not None and not clone:
raise NineMLUsageError(
"Attempting to add the same object '{}' {} to document"
" '{}' document when it is already in another "
"document, '{}' and 'clone' kwarg is False"
.format(nineml_obj.name, nineml_obj.nineml_type,
self.url, nineml_obj.document.url))
else:
if clone:
if cloner is None:
cloner = Cloner(**kwargs)
nineml_obj = cloner.clone(nineml_obj, **kwargs)
AddToDocumentVisitor(self).visit(nineml_obj, **kwargs)
return nineml_obj
def __init__(self, rule_properties, source_size,
destination_size, **kwargs): # @UnusedVariable
if (rule_properties.lib_type == 'OneToOne' and
source_size != destination_size):
raise NineMLUsageError(
"Cannot connect to populations of different sizes "
"({} and {}) with OneToOne connection rule"
.format(source_size, destination_size))
if not isinstance(rule_properties, ConnectionRuleProperties):
raise NineMLUsageError(
"'rule_properties' argument ({}) must be a "
"ConnectcionRuleProperties instance".format(rule_properties))
self._rule_properties = rule_properties
self._source_size = source_size
self._destination_size = destination_size
def substitute(self, expr):
"""
Substitute alias symbols in expression with equivalent expression
of inputs, constants and reserved identifiers
Parameters
----------
nineml_obj : Expression
An expression object to substitute alias symbols in
"""
if expr.temporary:
raise NineMLUsageError(
"Attempting to substitute aliases using temporary object "
"{}({})".format(type(expr).__name__, expr))
assert isinstance(expr, Expression)
try:
rhs = self.cache[expr.id]
except KeyError:
for sym in list(expr.rhs_symbols):
# Substitute all alias symbols with their RHS expresssions
if str(sym) in self.component_class.alias_names:
alias = self.get_alias(str(sym))
expr.subs(sym, self.substitute(alias))
self.cache[expr.id] = rhs = expr.rhs
return rhs
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, source, destination, source_port,
destination_port, delay, connectivity=None,
connection_rule_properties=None,
connectivity_class=Connectivity):
self._name = validate_identifier(name)
BaseULObject.__init__(self)
DocumentLevelObject.__init__(self)
self._source = source
self._destination = destination
self._source_port = source_port
self._destination_port = destination_port
if connectivity is not None:
assert isinstance(connectivity, BaseConnectivity)
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:
connectivity = connectivity_class(
connection_rule_properties, source.size, destination.size)
self._connectivity = connectivity
self._delay = delay
if isinstance(source_port, Port):
self._check_ports(source_port, destination_port)
def __init__(self, name, dimension=None, operator='+'):
if operator not in list(self._operator_map.keys()):
err = ("%s('%s')" + "specified undefined operator: '%s'") %\
(self.__class__.__name__, name, str(operator))
raise NineMLUsageError(err)
super(AnalogReducePort, self).__init__(name, dimension)
self._operator = str(operator)
def __getitem__(self, index):
if self.value.is_array():
return self._value.values[index] * self.units
elif self.value.is_single():
return self._value.value * self.units
else:
raise NineMLUsageError("Cannot get item from random distribution")
def from_sympy(self, expr):
if expr == 1:
return dimensionless
elif not isinstance(expr, sympy.Basic):
raise NineMLUsageError(
"Cannot convert '{}' dimension, must be 1 or sympy expression".
format(expr))
powers = {}
stack = [expr]
while stack:
expr = stack.pop()
if isinstance(expr, sympy.Mul):
stack.extend(expr.args)
elif isinstance(expr, sympy.Pow):
powers[str(expr.args[0])] = expr.args[1]
else:
powers[str(expr)] = 1
name_num = []
name_den = []
for sym, p in powers.items():
name = self.dimension_names[next(
i for i, s in enumerate(self.dimension_symbols) if s == sym)]
if abs(p) > 1:
name += str(abs(p))
if p > 0:
name_num.append(name)
else:
name_den.append(name)
name = '_'.join(name_num)
if name_den:
if name:
name += '_'
name += 'per_' + '_'.join(name_den)
return Dimension(name, **powers)
def check_initial_values(self):
for var in self.definition.component_class.state_variables:
try:
initial_value = self.initial_value(var.name)
except KeyError:
raise NineMLUsageError(
"Initial value not specified for {}".format(var.name))
initial_units = initial_value.units
initial_dimension = initial_units.dimension
var_dimension = var.dimension
if initial_dimension != var_dimension:
raise NineMLUsageError(
"Dimensions for '{}' initial value, {}, in '{}' don't "
"match that of its definition in '{}', {}.".format(
var.name, initial_dimension, self.name,
self.component_class.name, var_dimension))
def from_str(cls, alias_string):
"""Creates an Alias object from a string"""
if not cls.is_alias_str(alias_string):
errmsg = "Invalid Alias: %s" % alias_string
raise NineMLUsageError(errmsg)
lhs, rhs = alias_string.split(':=')
return Alias(name=lhs.strip(), rhs=rhs.strip())
def __init__(self, component_class, **kwargs): # @UnusedVariable
BaseDynamicsVisitor.__init__(self)
self.sv_declared = []
self.time_derivatives_used = []
self.visit(component_class)
for td in self.time_derivatives_used:
if td not in self.sv_declared:
raise NineMLUsageError(
"StateVariable '{}' not declared".format(td))
def __pow__(self, power):
"self ** expr"
if self.offset != 0:
raise NineMLUsageError(
"Can't raise units to power with nonzero offsets ({})".format(
self))
return Unit(Dimension.make_name([self.name], power=power),
dimension=(self.dimension**power),
power=(self.power * power))
def __init__(self, component_class, **kwargs): # @UnusedVariable
BaseDynamicsVisitor.__init__(self)
self.sv_declared = []
self.state_assignments_lhs = []
self.visit(component_class)
for sa in self.state_assignments_lhs:
if sa not in self.sv_declared:
raise NineMLUsageError(
"Not Assigning to state-variable: {}".format(sa))
def check_conflicting_symbol(self, symbol):
symbol = symbol.lower()
if symbol in self.symbols:
raise NineMLUsageError(
"Found duplication of '{}' symbol in {} "
"(Note that symbols must be case-insensitively unique despite "
"being case-sensitive in general)".format(
symbol, self.component_class))
self.symbols.append(symbol)
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 _check_ports(self):
if not isinstance(self.send_port, AnalogSendPort):
raise NineMLUsageError(
"Send port '{}' must be an AnalogSendPort to be connected with"
" an AnalogPortConnection".format(self.send_port.name))
if not isinstance(self.receive_port,
(AnalogReceivePort, AnalogReducePort)):
raise NineMLUsageError(
"Send port '{}' must be an AnalogSendPort to be connected with"
" an AnalogPortConnection".format(self.receive_port.name))
if self.send_port.dimension != self.receive_port.dimension:
raise NineMLDimensionError(
"Dimensions do not match in analog port connection: sender "
"port"
" '{}' has dimensions of '{}' and receive port '{}' has"
" dimensions of '{}'".format(self.send_port.name,
self.send_port.dimension,
self.receive_port.name,
self.receive_port.dimension))
def check_conflicting_dimension(self, dimension):
try:
if dimension != self.dimensions[dimension.name]:
err = ("Duplication of dimension name '{}' for differing "
"dimensions ('{}', '{}')".format(
dimension.name, dimension,
self.dimensions[dimension.name]))
raise NineMLUsageError(err)
except KeyError:
self.dimensions[dimension.name] = dimension
def __init__(self, component_class, **kwargs): # @UnusedVariable
super(EventPortsDynamicsValidator, self).__init__()
# Mapping component_class to list of events/eventports at that
# component_class
self.event_send_ports = {}
self.event_receive_ports = {}
self.output_events = []
self.input_events = []
# Visit all elements of the component class
self.visit(component_class)
# Check that each output event has a corresponding event_port with a
# send mode:
for output_event in self.output_events:
if output_event not in self.event_send_ports:
raise NineMLUsageError(
"Can't find port definition matching OutputEvent: {}"
.format(output_event))
# Check that each input event has a corresponding event_port with a
# recv/reduce mode:
for input_event in self.input_events:
if input_event not in self.event_receive_ports:
raise NineMLUsageError(
"Can't find port definition matching input event: {}"
.format(input_event))
# Check that each EventSendPort emits at least one output event
for port_name in list(self.event_send_ports.keys()):
if port_name not in self.output_events:
raise NineMLUsageError(
"Unable to find events generated for '{}' in '{}'"
.format(port_name, component_class.name))
# Check that each Event port emits/recieves at least one
for port_name in list(self.event_receive_ports.keys()):
if port_name not in self.input_events:
raise NineMLUsageError(
"Unable to find event transitions triggered by '{}' in "
"'{}'".format(port_name, component_class.name))
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, *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 default_action(self, obj, **kwargs): # @UnusedVariable
if obj.id in self.ids:
raise NineMLUsageError(
"ID of {} {} ({}) already seen [{}]".format(
type(obj).__name__, obj, obj.id, self.context_str()))
if self.print_all:
print('{}: {}, {} [{}]'.format(obj.id, type(obj).__name__, obj,
self.context_str()))
self.ids.append(obj.id)
if obj.temporary:
self.temp_mem_address.add(id(obj))
def __mul__(self, other):
"self * other"
try:
if (self.offset != 0 or other.offset != 0):
raise NineMLUsageError(
"Can't multiply units with nonzero offsets ({} and {})".
format(self, other))
return Unit(Dimension.make_name([self.name, other.name]),
dimension=self.dimension * other.dimension,
power=(self.power + other.power))
except AttributeError:
return Quantity(other, self)
def get_alias(self, name):
alias = None
for context in reversed(self.contexts):
try:
alias = context.parent.alias(name)
break
except (NineMLNameError, AttributeError):
continue
if alias is None:
raise NineMLUsageError("Did not find alias '{}' in any "
"context".format(name))
return alias
def __init__(self, component_class, **kwargs): # @UnusedVariable
super(OutputAnalogPortsDynamicsValidator, self).__init__()
self.output_analogports = []
self.available_symbols = []
self.component_class = component_class
self.visit(component_class)
for ap in self.output_analogports:
if ap not in self.available_symbols:
raise NineMLUsageError(
"Unable to find an Alias or State variable for "
"analog-port '{}' (available '{}')"
.format(ap, "', '".join(self.available_symbols)))