def connect(self,
sender,
send_port_name,
receive_port_name,
delay=0.0 * un.ms,
properties=None):
"""
Connects a port of the cell to a matching port on the 'other' cell
Parameters
----------
sender : pype9.simulator.neuron.cells.Cell
The sending cell to connect the from
send_port_name : str
Name of the port in the sending cell to connect to
receive_port_name : str
Name of the receive port in the current cell to connect from
delay : nineml.Quantity (time)
The delay of the connection
properties : list(nineml.Property)
The connection properties of the event port
"""
send_port = sender.component_class.send_port(send_port_name)
receive_port = self.component_class.receive_port(receive_port_name)
delay = float(delay.in_units(un.ms))
if properties is None:
properties = []
if send_port.communicates != receive_port.communicates:
raise Pype9UsageError(
"Cannot connect {} send port, '{}', to {} receive port, '{}'".
format(send_port.communicates, send_port_name,
receive_port.communicates, receive_port_name))
if receive_port.communicates == 'event':
if len(list(self.component_class.event_receive_ports)) > 1:
raise Pype9Unsupported9MLException(
"Multiple event receive ports ('{}') are not currently "
"supported".format("', '".join([
p.name
for p in self.component_class.event_receive_ports
])))
netcon = h.NetCon(sender._hoc, self._hoc, sec=self._sec)
if delay:
netcon.delay = delay
self._check_connection_properties(receive_port_name, properties)
if len(properties) > 1:
raise Pype9Unsupported9MLException(
"Cannot handle more than one connection property per port")
elif properties:
netcon.weight[0] = self.unit_handler.scale_value(
properties[0].quantity)
self._input_auxs.append(netcon)
elif receive_port.communicates == 'analog':
raise Pype9UsageError(
"Cannot individually 'connect' analog ports. Simulate the "
"sending cell in a separate simulation then play the analog "
"signal in the port")
else:
raise Pype9UsageError(
"Unrecognised port communication '{}'".format(
receive_port.communicates))
def _prepare(self, **kwargs):
"Reset the simulation and prepare it for creating new cells/networks"
if self._min_delay is None:
if self.num_threads() == 1:
min_delay = self.device_delay
else:
raise Pype9UsageError(
"Min delay needs to be set for NEST simulator if using "
"more than one thread")
else:
min_delay = self._min_delay
if self._max_delay is None:
if self.num_threads() == 1:
max_delay = self.DEFAULT_MAX_DELAY
else:
raise Pype9UsageError(
"Max delay needs to be set for NEST simulator if using "
"more than one thread")
else:
max_delay = self._max_delay
pyNN_setup(timestep=float(self.dt.in_units(un.ms)),
min_delay=float(min_delay.in_units(un.ms)),
max_delay=float(max_delay.in_units(un.ms)),
grng_seed=self.global_seed,
rng_seeds=self.all_dynamics_seeds,
**kwargs)
def parse_units(unit_str):
# TODO: Should donate this function to the nineml.units module
try:
unit_expr = sympy.sympify(unit_str)
except:
raise Pype9UsageError(
"Unit expression '{}' is not a valid expression".format(unit_str))
try:
return _parse_subexpr(unit_expr)
except Pype9UnitStrError:
raise Pype9UsageError(
"Unit expression '{}' contains operators other than "
"multiplication and division".format(unit_str))
def register_cell(self, cell):
if cell.code_generator != self.code_generator:
raise Pype9UsageError(
"Equivlent code generators must be provided to both the "
"CellMetaClass and Simulation objects ({} and {})".format(
cell.code_generator, self.code_generator))
self._registered_cells.append(cell)
def register_array(self, array):
cell_code_gen = array.celltype.model.code_generator
if cell_code_gen != self.code_generator:
raise Pype9UsageError(
"Equivlent code generators must be provided to both the "
"Network and Simulation objects ({} and {})".format(
cell_code_gen, self.code_generator))
self._registered_arrays.append(array)
def _check_units(self, varname, val, dimension, allow_none=False):
if not (val is None and allow_none):
try:
assert val.units.dimension == dimension
except (AssertionError, AttributeError):
raise Pype9UsageError(
"Provided value to {} ({}) is not a valid '{}' "
"quantity".format(varname, val, dimension.name))
def play(self, port_name, signal, properties=[]):
"""
Injects current into the segment
Parameters
----------
port_name : str
The name of the receive port to play the signal into
signal : neo.AnalogSignal (current) | neo.SpikeTrain
Signal to play into the port
properties : list(nineml.Property)
The connection properties of the event port
"""
ext_is = self.build_component_class.annotations.get(
(BUILD_TRANS, PYPE9_NS), EXTERNAL_CURRENTS).split(',')
port = self.component_class.port(port_name)
if isinstance(port, EventPort):
if len(list(self.component_class.event_receive_ports)) > 1:
raise Pype9Unsupported9MLException(
"Multiple event receive ports ('{}') are not currently "
"supported".format("', '".join([
p.name
for p in self.component_class.event_receive_ports
])))
if signal.t_start < 1.0:
raise Pype9UsageError(
"Signal must start at or after 1 ms to handle delay in "
"neuron ({})".format(signal.t_start))
times = numpy.asarray(signal.times.rescale(pq.ms)) - 1.0
vstim = h.VecStim()
vstim_times = h.Vector(times)
vstim.play(vstim_times)
vstim_con = h.NetCon(vstim, self._hoc, sec=self._sec)
self._check_connection_properties(port_name, properties)
if len(properties) > 1:
raise NotImplementedError(
"Cannot handle more than one connection property per port")
elif properties:
vstim_con.weight[0] = self.unit_handler.scale_value(
properties[0].quantity)
self._inputs['vstim'] = vstim
self._input_auxs.extend((vstim_times, vstim_con))
else:
if port_name not in ext_is:
raise Pype9Unsupported9MLException(
"Can only play into external current ports ('{}'), not "
"'{}' port.".format("', '".join(ext_is), port_name))
iclamp = h.IClamp(0.5, sec=self._sec)
iclamp.delay = 0.0
iclamp.dur = 1e12
iclamp.amp = 0.0
iclamp_amps = h.Vector(pq.Quantity(signal, 'nA'))
iclamp_times = h.Vector(signal.times.rescale(pq.ms))
iclamp_amps.play(iclamp._ref_amp, iclamp_times)
self._inputs['iclamp'] = iclamp
self._input_auxs.extend((iclamp_amps, iclamp_times))
def activate(self):
if self.__class__._active is not None:
raise Pype9UsageError(
"Cannot enter context of multiple {} simulations at the same "
"time".format(self.__class__.name))
self._set_seeds()
self._running = False
self._prepare()
self._registered_cells = []
self._registered_arrays = []
self.__class__._active = self
def _get(self, varname):
varname = self._escaped_name(varname)
try:
return getattr(self._hoc, varname)
except AttributeError:
try:
return getattr(self._sec, varname)
except AttributeError:
raise Pype9UsageError(
"'{}' doesn't have an attribute '{}'".format(
self.name, varname))
def __init__(self,
dt,
t_start=0.0 * un.s,
seed=None,
properties_seed=None,
min_delay=1 * un.ms,
max_delay=10 * un.ms,
code_generator=None,
build_base_dir=None,
**options):
self._check_units('dt', dt, un.time)
self._check_units('t_start', dt, un.time)
self._check_units('min_delay', dt, un.time, allow_none=True)
self._check_units('max_delay', dt, un.time, allow_none=True)
self._dt = dt
self._t_start = t_start
self._t = t_start
self._min_delay = min_delay if min_delay > dt else dt
self._max_delay = max_delay if max_delay > dt else dt
self._options = options
self._registered_cells = None
self._registered_arrays = None
if seed is not None and (seed < 0 or seed > self.max_seed):
raise Pype9UsageError(
"Provided seed {} is out of range, must be between (0 and {})".
format(seed, self.max_seed))
self._base_seed = seed
if properties_seed is not None and (properties_seed < 0 or
properties_seed > self.max_seed):
raise Pype9UsageError(
"Provided structure seed {} is out of range, must be between "
"(0 and {})".format(seed, self.max_seed))
self._base_properties_seed = properties_seed
if code_generator is None:
code_generator = self.CodeGenerator(base_dir=build_base_dir)
elif build_base_dir is not None:
raise Pype9UsageError(
"Cannot provide both code generator and 'build_base_dir' "
"options to Simulation __init__")
self._code_generator = code_generator
def _trim_analog_signal(self, signal, t_start, interval):
sim_start = self.unit_handler.to_pq_quantity(self._t_start)
offset = (t_start - sim_start)
if offset > 0.0 * pq.s:
offset_index = offset / interval
if round(offset_index) != offset_index:
raise Pype9UsageError(
"Difference between recording start time ({}) needs to"
"and simulation start time ({}) must be an integer "
"multiple of the sampling interval ({})".format(
t_start, sim_start, interval))
signal = signal[int(offset_index):]
return signal
def _parse_subexpr(expr):
"""parse_units helper function"""
try:
return standard_units[str(expr)]
except KeyError:
if isinstance(expr, sympy.Symbol):
raise Pype9UsageError("Unrecognised unit '{}'".format(expr))
elif isinstance(expr, (sympy.Mul, sympy.Pow)):
op = operator.mul if isinstance(expr, sympy.Mul) else operator.pow
return reduce(op, (_parse_subexpr(a) for a in expr.args))
elif isinstance(expr, sympy.Integer):
return int(expr)
else:
raise Pype9UnitStrError
def set_regime(self, regime):
if regime not in self.component_class.regime_names:
raise Pype9UsageError(
"'{}' is not a name of a regime in '{} cells "
"(regimes are '{}')".format(
regime, self.name,
"', '".join(self.component_class.regime_names)))
try:
# If regime is an integer (as it will be when passed from PyNN)
index = int(regime)
except ValueError:
# If the regime is the regime name
index = self.regime_index(regime)
super(Cell, self).__setattr__('_regime_index', index)
self._set_regime()
def run(argv):
import neo
from pype9.exceptions import Pype9UsageError
args = argparser().parse_args(argv)
if args.hide:
import matplotlib # @IgnorePep8
matplotlib.use('Agg') # Set to use Agg so DISPLAY is not required
from pype9.plot import plot # @IgnorePep8
segments = neo.PickleIO(args.filename).read()
if len(segments) > 1:
raise Pype9UsageError(
"Expected only a single recording segment in file '{}', found {}."
.format(args.filename, len(segments)))
seg = segments[0]
plot(seg, dims=args.dims, show=not args.hide, resolution=args.resolution,
save=args.save)
def _get_port_details(self, port_name):
"""
Return the communication type of the corresponding port and its fully
qualified name in the cell-synapse namespace (e.g. the 'spike_output'
port in the cell namespace will be 'spike_output__cell')
Parameters
----------
port_name : str
Name of the port or state variable
Returns
-------
communicates : str
Either 'event' or 'analog' depending on the type of port port_name
corresponds to
record_name : str
Name of the port fully qualified in the joint cell-synapse
namespace
"""
# TODO: Need to add a check that the port was recorded
component_class = self.celltype.model.component_class
port = None
for name in (port_name, port_name + '__cell'):
try:
port = component_class.send_port(name)
except NineMLNameError:
try:
port = component_class.state_variable(name)
except NineMLNameError:
pass
if port is None:
raise Pype9UsageError(
"Unknown port or state-variable '{}' for '{}' "
"component array (available '{}').".format(
port_name, self.name, "', '".join(chain(
component_class.send_port_names,
component_class.sub_component(
'cell').send_port_names))))
if isinstance(port, StateVariable):
communicates = 'analog'
else:
communicates = port.communicates
return communicates, port.name
def play(self, port_name, signal, properties=[]):
"""
Injects current into the segment
Parameters
----------
port_name : str
The name of the receive port to play the signal into
signal : neo.AnalogSignal (current) | neo.SpikeTrain
Signal to play into the port
properties : list(nineml.Property)
The connection properties of the event port
"""
port = self.component_class.receive_port(port_name)
if port.nineml_type in ('EventReceivePort',
'EventReceivePortExposure'):
# Shift the signal times to account for the minimum delay and
# match the NEURON implementation
spike_times = (numpy.asarray(signal.rescale(pq.ms)) -
self.device_delay_ms)
if any(spike_times <= 0.0):
raise Pype9UsageError(
"Some spike times are less than device delay and so "
"can't be played into cell ({})".format(
', '.join(spike_times < self.device_delay_ms)))
self._inputs[port_name] = nest.Create(
'spike_generator', 1, {'spike_times': list(spike_times)})
syn_spec = {
'receptor_type': self._receive_ports[port_name],
'delay': self.device_delay_ms
}
self._check_connection_properties(port_name, properties)
if len(properties) > 1:
raise NotImplementedError(
"Cannot handle more than one connection property per port")
elif properties:
syn_spec['weight'] = self.unit_handler.scale_value(
properties[0].quantity)
nest.Connect(self._inputs[port_name],
self._cell,
syn_spec=syn_spec)
elif port.nineml_type in ('AnalogReceivePort', 'AnalogReducePort',
'AnalogReceivePortExposure',
'AnalogReducePortExposure'):
# Signals are played into NEST cells include a delay (set to be the
# minimum), which is is subtracted from the start of the signal so
# that the effect of the signal aligns with other simulators
t_start = (float(signal.t_start.rescale(pq.ms)) -
self.device_delay_ms)
if t_start <= 0.0:
raise Pype9UsageError(
"Start time of signal played into port '{}' ({}) must "
"be greater than device delay ({})".format(
port_name, signal.t_start, self.device_delay))
step_current_params = {
'amplitude_values':
list(numpy.ravel(pq.Quantity(signal, 'pA'))),
'amplitude_times':
list(
numpy.ravel(numpy.asarray(signal.times.rescale(pq.ms))) -
self.device_delay_ms),
'start':
t_start,
'stop':
float(signal.t_stop.rescale(pq.ms))
}
self._inputs[port_name] = nest.Create('step_current_generator', 1,
step_current_params)
nest.Connect(self._inputs[port_name],
self._cell,
syn_spec={
"receptor_type": self._receive_ports[port_name],
'delay': self.device_delay_ms
})
else:
raise Pype9UsageError(
"Unrecognised port type '{}' to play signal into".format(port))
def get_v_threshold(self, dynamics_properties, port_name):
"""
Returns the voltage threshold at which an event is emitted from the
given event port
Parameters
----------
component_class : nineml.Dynamics
The component class of the cell to find the v-threshold for
port_name : str
Name of the event send port to threshold
"""
comp_class = (
dynamics_properties.component_class._dynamics.substitute_aliases())
transitions = OuputEventTransitionsFinder(
comp_class, comp_class.event_send_port(port_name)).transitions
assert transitions
try:
triggers = set(t.trigger for t in transitions)
except AttributeError:
raise Pype9UsageError(
"Cannot get threshold for event port '{}' in {} as it is "
"emitted from at least OnEvent transition ({})".format(
port_name, comp_class,
', '.join(str(t) for t in transitions)))
if len(triggers) > 1:
raise Pype9UsageError(
"Cannot get threshold for event port '{}' in {} as it is the "
"condition from at least OnEvent transition ({})".format(
port_name, comp_class, ', '.join(transitions)))
expr = next(iter(triggers)).rhs
v = sympy.Symbol(
self.component_class.annotations.get((BUILD_TRANS, PYPE9_NS),
MEMBRANE_VOLTAGE))
if v not in expr.free_symbols:
raise Pype9UsageError(
"Trigger expression for '{}' port in {} is not an expression "
"of membrane voltage '{}'".format(port_name, comp_class, v))
solution = None
if isinstance(expr, (sympy.StrictGreaterThan, sympy.StrictLessThan)):
# Get the equation for the transition between true and false
equality = sympy.Eq(*expr.args)
solutions = sympy.solvers.solve(equality, v)
if len(solutions) == 1:
solution = solutions[0]
if solution is None:
raise Pype9UsageError(
"Cannot solve threshold equation for trigger expression '{}' "
"for '{}' (to find condition where spikes are emitted from "
"'{}' event send port) in {} as it is not a simple inequality".
format(expr, v, port_name, comp_class))
values = {}
for sym in solution.free_symbols:
sym_str = str(sym)
try:
prop = dynamics_properties.property(sym_str)
except NineMLNameError:
try:
prop = comp_class.constant(sym_str)
except NineMLNameError:
raise Pype9UsageError(
"Cannot calculated fixed value for voltage threshold "
"as it contains reference to {}".format(
comp_class.element(sym_str)))
values[sym] = self.unit_handler.scale_value(prop.quantity)
threshold = solution.subs(values)
return float(threshold)
def __init__(self, *args, **kwargs):
self._in_array = kwargs.pop('_in_array', False)
# Flag to determine whether the cell has been initialized or not
# (it makes a difference to how the state of the cell is updated,
# either saved until the 'initialze' method is called or directly
# set to the state)
sim = self.Simulation.active()
self._t_start = sim.t_start
self._t_stop = None
if self.in_array:
for k, v in kwargs.items():
self._set(k, v) # Values should be in the right units.
self._regime_index = None
else:
# These position arguments are a little more complex to retrieve
# due to Python 2's restriction of **kwargs only following
# *args.
# Get prototype argument
if len(args) >= 1:
prototype = args[0]
if 'prototype_' in kwargs:
raise Pype9UsageError(
"Cannot provide prototype as (1st) argument ({}) and "
"keyword arg ({})".format(prototype,
kwargs['prototype_']))
else:
prototype = kwargs.pop('prototype_', self.component_class)
# Get regime argument
if len(args) >= 2:
regime = args[1]
if 'regime_' in kwargs:
raise Pype9UsageError(
"Cannot provide regime as (2nd) argument ({}) and "
"keyword arg ({})".format(regime, kwargs['regime_']))
else:
try:
regime = kwargs.pop('regime_')
except KeyError:
regime = None
if regime is None:
if self.component_class.num_regimes == 1:
regime = next(self.component_class.regime_names)
else:
raise Pype9UsageError(
"Need to specify initial regime using 'regime_' "
"keyword arg for component class with multiple "
"regimes ('{}')".format(
self.component_class.regime_names))
if len(args) > 2:
raise Pype9UsageError(
"Only two non-keyword arguments ('prototype_' and "
"'regime_' permitted in Cell __init__ (provided: {})"
.format(', '.join(args)))
self.set_regime(regime)
properties = []
initial_values = []
for name, qty in kwargs.items():
if isinstance(qty, pq.Quantity):
qty = self.unit_handler.from_pq_quantity(qty)
if name in self.component_class.state_variable_names:
initial_values.append(nineml.Initial(name, qty))
else:
properties.append(nineml.Property(name, qty))
self._nineml = nineml.DynamicsProperties(
name=self.name + '_properties',
definition=prototype,
properties=properties, initial_values=initial_values,
check_initial_values=True)
# Set up references from parameter names to internal variables and
# set parameters
for p in chain(self.properties, self.initial_values):
qty = p.quantity
if qty.value.nineml_type != 'SingleValue':
raise Pype9UsageError(
"Only SingleValue quantities can be used to initiate "
"individual cell classes ({})".format(p))
self._set(p.name, float(self.unit_handler.scale_value(qty)))
sim.register_cell(self)
def write(self, file, **kwargs): # @ReservedAssignment
if self.in_array:
raise Pype9UsageError(
"Can only write cell properties when they are not in an "
"array")
self._nineml.write(file, **kwargs)
def run(argv):
"""
Runs the simulation script from the provided arguments
"""
import nineml
from pype9.exceptions import Pype9UsageError
import neo.io
args = argparser().parse_args(argv)
time = args.time * un.ms
timestep = args.timestep * un.ms
if args.simulator == 'neuron':
from pype9.simulate.neuron import Network, CellMetaClass, Simulation # @UnusedImport @IgnorePep8
elif args.simulator == 'nest':
from pype9.simulate.nest import Network, CellMetaClass, Simulation # @Reimport @IgnorePep8
else:
assert False
if not args.record:
raise Pype9UsageError(
"No recorders set, please specify at least one with the '--record'"
" option")
min_delay = (float(args.min_delay[0]) * parse_units(args.min_delay[1])
if args.min_delay is not None else 1.0 * un.ms)
device_delay = (float(args.device_delay[0]) *
parse_units(args.device_delay[1])
if args.device_delay is not None else None)
# Parse record specs
record_specs = []
for rec in args.record:
if len(rec) == 4:
rec_t_start = pq.Quantity(float(rec[2]), rec[3])
elif len(rec) == 2:
rec_t_start = None
else:
raise Pype9UsageError(
"Record options can be passed either have 2 or 4 (provided {})"
": PORT/STATE-VARIABLE FILENAME [T_START T_START_UNITS]")
record_specs.append(RecordSpec(rec[0], rec[1], rec_t_start))
# Check for clashing record paths
record_paths = [r.fname for r in record_specs]
for pth in record_paths:
if record_paths.count(pth) > 1:
raise Pype9UsageError(
"Duplicate record paths '{}' given to separate '--record' "
"options".format(pth))
# For convenience
model = args.model
if isinstance(model, nineml.Network) and not model.num_projections:
raise Pype9UsageError(
"Provided network model '{}' (may have been implicitly created "
"from complete document) does not contain any projections".format(
model))
if isinstance(model, nineml.Network):
with Simulation(dt=timestep,
seed=args.seed,
properties_seed=args.properties_seed,
device_delay=device_delay,
**model.delay_limits()) as sim:
# Construct the network
logger.info("Constructing network")
network = Network(model,
build_mode=args.build_mode,
build_base_dir=args.build_dir)
logger.info("Finished constructing the '{}' network".format(
model.name))
for rspec in record_specs:
pop_name, port_name = rspec.port.split('.')
network.component_array(pop_name).record(port_name)
logger.info("Running the simulation")
sim.run(time)
logger.info("Writing recorded data to file")
for rspec in record_specs:
pop_name, port_name = rspec.port.split('.')
pop = network.component_array(pop_name)
neo.PickleIO(rspec.fname).write(
pop.recording(port_name, t_start=rspec.t_start))
else:
assert isinstance(model, (nineml.DynamicsProperties, nineml.Dynamics))
# Override properties passed as options
if args.prop:
props_dict = dict((parm, float(val) * parse_units(unts))
for parm, val, unts in args.prop)
props = nineml.DynamicsProperties(model.name + '_props', model,
props_dict)
component_class = model
elif isinstance(model, nineml.DynamicsProperties):
props = model
component_class = model.component_class
else:
raise Pype9UsageError(
"Specified model {} is not a dynamics properties object and "
"no properties supplied to simulate command via --prop option".
format(model))
# Get the initial state
init_state = dict((sv, float(val) * parse_units(units))
for sv, val, units in args.init_value)
# Get the init_regime
init_regime = args.init_regime
if init_regime is None:
if component_class.num_regimes == 1:
# If there is only one regime it doesn't need to be specified
init_regime = next(component_class.regimes).name
else:
raise Pype9UsageError(
"Need to specify initial regime as dynamics has more than "
"one '{}'".format("', '".join(
r.name for r in component_class.regimes)))
# FIXME: A bit of a hack until better detection of input currents is
# implemented in neuron code gen.
external_currents = []
for port_name, _ in args.play:
if component_class.port(port_name).dimension == un.current:
external_currents.append(port_name)
# Build cell class
Cell = CellMetaClass(component_class,
build_mode=args.build_mode,
external_currents=external_currents,
build_version=args.build_version,
build_base_dir=args.build_dir)
record_regime = False
with Simulation(dt=timestep,
seed=args.seed,
min_delay=min_delay,
device_delay=device_delay,
build_base_dir=args.build_dir) as sim:
# Create cell
cell = Cell(props, regime_=init_regime, **init_state)
# Play inputs
for port_name, fname in args.play:
port = component_class.receive_port(port_name)
seg = neo.io.PickleIO(filename=fname).read()[0]
if port.communicates == 'event':
signal = seg.spiketrains[0]
else:
signal = seg.analogsignals[0]
logger.info("Playing signal (t_start: {}, t_stop: {}, dt: {}) "
"into port '{}".format(signal.t_start,
signal.t_stop,
signal.sampling_period,
port_name))
# Input is an event train or analog signal
cell.play(port_name, signal)
# Set up recorders
for rspec in record_specs:
if (component_class.num_regimes > 1 and component_class.port(
rspec.port).communicates == 'analog'):
record_regime = True
cell.record(rspec.port, t_start=rspec.t_start)
if record_regime:
cell.record_regime()
# Run simulation
sim.run(time)
# Collect data into Neo Segments
fnames = set(r.fname for r in record_specs)
data_segs = {}
for fname in fnames:
data_segs[fname] = neo.Segment(
description="Simulation of '{}' cell".format(model.name))
for rspec in record_specs:
data = cell.recording(rspec.port, t_start=rspec.t_start)
if isinstance(data, neo.AnalogSignal):
data_segs[rspec.fname].analogsignals.append(data)
else:
data_segs[rspec.fname].spiketrains.append(data)
if record_regime:
data_segs[rspec.fname].epochs.append(cell.regime_epochs())
# Write data to file
for fname, data_seg in data_segs.items():
neo.io.PickleIO(fname).write(data_seg)
logger.info("Finished simulation of '{}' for {}".format(model.name, time))
def properties_rng(self):
if self._properties_rng is None:
raise Pype9UsageError(
"Can only access rng inside simulation context")
return self._properties_rng
def connect(self,
sender,
send_port_name,
receive_port_name,
delay=None,
properties=None):
"""
Connects a port of the cell to a matching port on the 'other' cell
Parameters
----------
sender : pype9.simulator.nest.cells.Cell
The sending cell to connect the from
send_port_name : str
Name of the port in the sending cell to connect to
receive_port_name : str
Name of the receive port in the current cell to connect from
delay : nineml.Quantity (time)
The delay of the connection
properties : list(nineml.Property)
The connection properties of the event port
"""
if delay is None:
delay = self.device_delay
if properties is None:
properties = []
delay = float(delay.in_units(un.ms))
send_port = sender.component_class.send_port(send_port_name)
receive_port = self.component_class.receive_port(receive_port_name)
if send_port.communicates != receive_port.communicates:
raise Pype9UsageError(
"Cannot connect {} send port, '{}', to {} receive port, '{}'".
format(send_port.communicates, send_port_name,
receive_port.communicates, receive_port_name))
if receive_port.communicates == 'event':
if self.component_class.num_event_send_ports > 1:
raise Pype9Unsupported9MLException(
"Cannot currently differentiate between multiple event "
"send ports in NEST implementation ('{}')".format(
"', '".join(
self.component_class.event_send_port_names)))
syn_spec = {
'receptor_type': self._receive_ports[receive_port_name],
'delay': delay
}
if len(properties) > 1:
raise Pype9Unsupported9MLException(
"Cannot handle more than one connection property per port")
elif properties:
self._check_connection_properties(receive_port_name,
properties)
syn_spec['weight'] = self.unit_handler.scale_value(
properties[0].quantity)
nest.Connect(sender._cell, self._cell, syn_spec=syn_spec)
elif receive_port.communicates == 'analog':
raise Pype9UsageError(
"Cannot individually 'connect' analog ports. Simulate the "
"sending cell in a separate simulation then play the analog "
"signal in the port")
else:
raise Pype9UsageError(
"Unrecognised port communication '{}'".format(
receive_port.communicates))