# encoding: utf-8
"""
Machinery for implementation of "standard models", i.e. neuron and synapse models
that are available in multiple simulators:
Functions:
build_translations()
Classes:
StandardModelType
StandardCellType
ModelNotAvailable
STDPWeightDependence
STDPTimingDependence
:copyright: Copyright 2006-2016 by the PyNN team, see AUTHORS.
:license: CeCILL, see LICENSE for details.
"""
from pyNN import errors, models
from pyNN.parameters import ParameterSpace
import numpy
from pyNN.core import is_listlike, itervalues
from copy import deepcopy
import neo
import quantities as pq
# ==============================================================================
# Standard cells
# ==============================================================================
def build_translations(*translation_list):
"""
Build a translation dictionary from a list of translations/transformations.
"""
translations = {}
for item in translation_list:
assert 2 <= len(item) <= 4, "Translation tuples must have between 2 and 4 items. Actual content: %s" % str(item)
pynn_name = item[0]
sim_name = item[1]
if len(item) == 2: # no transformation
f = pynn_name
g = sim_name
elif len(item) == 3: # simple multiplicative factor
scale_factor = item[2]
f = "float(%g)*%s" % (scale_factor, pynn_name)
g = "%s/float(%g)" % (sim_name, scale_factor)
elif len(item) == 4: # more complex transformation
f = item[2]
g = item[3]
translations[pynn_name] = {'translated_name': sim_name,
'forward_transform': f,
'reverse_transform': g}
return translations
class StandardModelType(models.BaseModelType):
"""Base class for standardized cell model and synapse model classes."""
translations = {}
extra_parameters = {}
@property
def native_parameters(self):
"""
A :class:`ParameterSpace` containing parameter names and values
translated from the standard PyNN names and units to simulator-specific
("native") names and units.
"""
return self.translate(self.parameter_space)
def translate(self, parameters, copy=True):
"""Translate standardized model parameters to simulator-specific parameters."""
if copy:
_parameters = deepcopy(parameters)
else:
_parameters = parameters
cls = self.__class__
if parameters.schema != self.get_schema():
raise Exception("Schemas do not match: %s != %s" % (parameters.schema, self.get_schema())) # should replace this with a PyNN-specific exception type
native_parameters = {}
for name in parameters.keys():
D = self.translations[name]
pname = D['translated_name']
if callable(D['forward_transform']):
pval = D['forward_transform'](**_parameters)
else:
try:
pval = eval(D['forward_transform'], globals(), _parameters)
except NameError as errmsg:
raise NameError("Problem translating '%s' in %s. Transform: '%s'. Parameters: %s. %s"
% (pname, cls.__name__, D['forward_transform'], parameters, errmsg))
except ZeroDivisionError:
raise
#pval = 1e30 # this is about the highest value hoc can deal with
native_parameters[pname] = pval
return ParameterSpace(native_parameters, schema=None, shape=parameters.shape)
def reverse_translate(self, native_parameters):
"""Translate simulator-specific model parameters to standardized parameters."""
cls = self.__class__
standard_parameters = {}
for name, D in self.translations.items():
tname = D['translated_name']
if tname in native_parameters.keys():
if callable(D['reverse_transform']):
standard_parameters[name] = D['reverse_transform'](**native_parameters)
else:
try:
standard_parameters[name] = eval(D['reverse_transform'], {}, native_parameters)
except NameError as errmsg:
raise NameError("Problem translating '%s' in %s. Transform: '%s'. Parameters: %s. %s"
% (name, cls.__name__, D['reverse_transform'], native_parameters, errmsg))
return ParameterSpace(standard_parameters, schema=self.get_schema(), shape=native_parameters.shape)
def simple_parameters(self):
"""Return a list of parameters for which there is a one-to-one
correspondance between standard and native parameter values."""
return [name for name in self.translations if self.translations[name]['forward_transform'] == name]
def scaled_parameters(self):
"""Return a list of parameters for which there is a unit change between
standard and native parameter values."""
def scaling(trans):
return (not callable(trans)) and ("float" in trans)
return [name for name in self.translations if scaling(self.translations[name]['forward_transform'])]
def computed_parameters(self):
"""Return a list of parameters whose values must be computed from
more than one other parameter."""
return [name for name in self.translations if name not in self.simple_parameters() + self.scaled_parameters()]
def get_native_names(self, *names):
"""
Return a list of native parameter names for a given model.
"""
if names:
translations = (self.translations[name] for name in names)
else: # return all names
translations = itervalues(self.translations)
return [D['translated_name'] for D in translations]
[docs]class StandardCellType(StandardModelType, models.BaseCellType):
"""Base class for standardized cell model classes."""
recordable = ['spikes', 'v', 'gsyn']
receptor_types = ('excitatory', 'inhibitory')
always_local = False # override for NEST spike sources
class StandardCurrentSource(StandardModelType, models.BaseCurrentSource):
"""Base class for standardized current source model classes."""
def inject_into(self, cells):
"""
Inject the current from this source into the supplied group of cells.
`cells` may be a :class:`Population`, :class:`PopulationView`,
:class:`Assembly` or a list of :class:`ID` objects.
"""
raise NotImplementedError("Should be redefined in the local simulator electrodes")
def __getattr__(self, name):
if name == "set":
errmsg = "For current sources, set values using the parameter name directly, " \
"e.g. source.amplitude = 0.5, or use 'set_parameters()' " \
"e.g. source.set_parameters(amplitude=0.5)"
raise AttributeError(errmsg)
try:
val = self.__getattribute__(name)
except AttributeError:
try:
val = self.get_parameters()[name]
except KeyError:
raise errors.NonExistentParameterError(name,
self.__class__.__name__,
self.get_parameter_names())
return val
def __setattr__(self, name, value):
if self.has_parameter(name):
self.set_parameters(**{name: value})
else:
object.__setattr__(self, name, value)
def set_parameters(self, copy=True, **parameters):
"""
Set current source parameters, given as a sequence of parameter=value arguments.
"""
# if some of the parameters are computed from the values of other
# parameters, need to get and translate all parameters
computed_parameters = self.computed_parameters()
have_computed_parameters = numpy.any([p_name in computed_parameters
for p_name in parameters])
if have_computed_parameters:
all_parameters = self.get_parameters()
all_parameters.update(parameters)
parameters = all_parameters
else:
parameters = ParameterSpace(parameters, self.get_schema(), (1,))
parameters = self.translate(parameters, copy=copy)
self.set_native_parameters(parameters)
def get_parameters(self):
"""Return a dict of all current source parameters."""
parameters = self.get_native_parameters()
parameters = self.reverse_translate(parameters)
return parameters
def set_native_parameters(self, parameters):
raise NotImplementedError
def get_native_parameters(self):
raise NotImplementedError
def _round_timestamp(self, value, resolution):
# todo: consider using decimals module, since rounding of floating point numbers is so horrible
return numpy.rint(value/resolution) * resolution
def get_data(self):
"""Return the recorded current as a Neo signal object"""
t_arr, i_arr = self._get_data()
intervals = numpy.diff(t_arr)
if intervals.size > 0 and intervals.max() - intervals.min() < 1e-9:
signal = neo.AnalogSignal(i_arr, units="nA", t_start=t_arr[0] * pq.ms,
sampling_period=intervals[0] * pq.ms)
else:
signal = neo.IrregularlySampledSignal(t_arr, i_arr, units="nA", time_units="ms")
return signal
class ModelNotAvailable(object):
"""Not available for this simulator."""
def __init__(self, *args, **kwargs):
raise NotImplementedError("The %s model is not available for this simulator." % self.__class__.__name__)
# ==============================================================================
# Synapse Dynamics classes
# ==============================================================================
def check_weights(weights, projection):
# if projection.post is an Assembly, some components might have cond-synapses, others curr, so need a more sophisticated check here
synapse_sign = projection.receptor_type
is_conductance = projection.post.conductance_based
if isinstance(weights, numpy.ndarray):
all_negative = (weights <= 0).all()
all_positive = (weights >= 0).all()
if not (all_negative or all_positive):
raise errors.ConnectionError("Weights must be either all positive or all negative")
elif numpy.isreal(weights):
all_positive = weights >= 0
all_negative = weights < 0
else:
raise errors.ConnectionError("Weights must be a number or an array of numbers.")
if is_conductance or synapse_sign == 'excitatory':
if not all_positive:
raise errors.ConnectionError("Weights must be positive for conductance-based and/or excitatory synapses")
elif is_conductance is False and synapse_sign == 'inhibitory':
if not all_negative:
raise errors.ConnectionError("Weights must be negative for current-based, inhibitory synapses")
else: # This should never happen.
raise Exception("Can't check weight, conductance status unknown.")
def check_delays(delays, projection):
min_delay = projection._simulator.state.min_delay
max_delay = projection._simulator.state.max_delay
if isinstance(delays, numpy.ndarray):
below_max = (delays <= max_delay).all()
above_min = (delays >= min_delay).all()
in_range = below_max and above_min
elif numpy.isreal(delays):
in_range = min_delay <= delays <= max_delay
else:
raise errors.ConnectionError("Delays must be a number or an array of numbers.")
if not in_range:
raise errors.ConnectionError("Delay (%s) is out of range [%s, %s]" % (delays, min_delay, max_delay))
[docs]class StandardSynapseType(StandardModelType, models.BaseSynapseType):
parameter_checks = {
'weight': check_weights,
'delay': check_delays
}
[docs] def get_schema(self):
"""
Returns the model schema: i.e. a mapping of parameter names to allowed
parameter types.
"""
base_schema = dict((name, type(value))
for name, value in self.default_parameters.items())
base_schema['delay'] = float # delay has default value None, meaning "use the minimum delay", so we have to correct the auto-generated schema
return base_schema
[docs]class STDPWeightDependence(StandardModelType):
"""Base class for models of STDP weight dependence."""
def __init__(self, **parameters):
StandardModelType.__init__(self, **parameters)
[docs]class STDPTimingDependence(StandardModelType):
"""Base class for models of STDP timing dependence (triplets, etc)"""
def __init__(self, **parameters):
StandardModelType.__init__(self, **parameters)
