Source code for pyNN.neuron

# encoding: utf-8
"""
nrnpython implementation of the PyNN API.

:copyright: Copyright 2006-2020 by the PyNN team, see AUTHORS.
:license: CeCILL, see LICENSE for details.

"""

import warnings
try:
    from mpi4py import MPI
except ImportError:
    warnings.warn("mpi4py not available")
from pyNN.random import NumpyRNG, GSLRNG
from pyNN import common, core, space, __doc__
from pyNN.common.control import DEFAULT_MAX_DELAY, DEFAULT_TIMESTEP, DEFAULT_MIN_DELAY
from pyNN.standardmodels import StandardCellType
from pyNN.recording import get_io
from pyNN.space import Space
from pyNN.neuron import simulator
from pyNN.neuron.random import NativeRNG
from pyNN.neuron.standardmodels.cells import *
from pyNN.neuron.connectors import *
from pyNN.neuron.standardmodels.synapses import *
from pyNN.neuron.standardmodels.electrodes import *
from pyNN.neuron.populations import Population, PopulationView, Assembly
from pyNN.neuron.projections import Projection
from pyNN.neuron.cells import NativeCellType, IntFire1, IntFire2, IntFire4
try:
    from . import nineml
except ImportError:
    pass  # nineml is an optional dependency

import logging
logger = logging.getLogger("PyNN")

# ==============================================================================
#   Utility functions
# ==============================================================================


[docs]def list_standard_models(): """Return a list of all the StandardCellType classes available for this simulator.""" return [obj.__name__ for obj in globals().values() if (isinstance(obj, type) and issubclass(obj, StandardCellType) and obj is not StandardCellType)]
# ============================================================================== # Functions for simulation set-up and control # ==============================================================================
[docs]def setup(timestep=DEFAULT_TIMESTEP, min_delay=DEFAULT_MIN_DELAY, **extra_params): """ Should be called at the very beginning of a script. `extra_params` contains any keyword arguments that are required by a given simulator but not by others. NEURON specific extra_params: use_cvode - use the NEURON cvode solver. Defaults to False. Optional cvode Parameters: -> rtol - specify relative error tolerance -> atol - specify absolute error tolerance native_rng_baseseed - added to MPI.rank to form seed for SpikeSourcePoisson, etc. default_maxstep - TODO returns: MPI rank """ common.setup(timestep, min_delay, **extra_params) simulator.initializer.clear() simulator.state.clear() simulator.state.dt = timestep simulator.state.min_delay = min_delay simulator.state.max_delay = extra_params.get('max_delay', DEFAULT_MAX_DELAY) if 'use_cvode' in extra_params: simulator.state.cvode.active(int(extra_params['use_cvode'])) if 'rtol' in extra_params: simulator.state.cvode.rtol(float(extra_params['rtol'])) if 'atol' in extra_params: simulator.state.cvode.atol(float(extra_params['atol'])) if 'native_rng_baseseed' in extra_params: simulator.state.native_rng_baseseed = int(extra_params['native_rng_baseseed']) if 'default_maxstep' in extra_params: simulator.state.default_maxstep = float(extra_params['default_maxstep']) return rank()
[docs]def end(compatible_output=True): """Do any necessary cleaning up before exiting.""" for (population, variables, filename) in simulator.state.write_on_end: io = get_io(filename) population.write_data(io, variables) simulator.state.write_on_end = []
#simulator.state.finalize() run, run_until = common.build_run(simulator) run_for = run reset = common.build_reset(simulator) initialize = common.initialize # ============================================================================== # Functions returning information about the simulation state # ============================================================================== get_current_time, get_time_step, get_min_delay, get_max_delay, \ num_processes, rank = common.build_state_queries(simulator) # ============================================================================== # Low-level API for creating, connecting and recording from individual neurons # ============================================================================== create = common.build_create(Population) connect = common.build_connect(Projection, FixedProbabilityConnector, StaticSynapse) set = common.set record = common.build_record(simulator) record_v = lambda source, filename: record(['v'], source, filename) record_gsyn = lambda source, filename: record(['gsyn_exc', 'gsyn_inh'], source, filename) # ==============================================================================