Source code for brian2.groups.neurongroup

'''
This model defines the `NeuronGroup`, the core of most simulations.
'''
import collections
import numbers
import string

import numpy as np
import sympy
from pyparsing import Word

from brian2.codegen.translation import analyse_identifiers
from brian2.core.preferences import prefs
from brian2.core.spikesource import SpikeSource
from brian2.core.variables import (Variables, LinkedVariable,
                                   DynamicArrayVariable, Subexpression)
from brian2.equations.equations import (Equations, DIFFERENTIAL_EQUATION,
                                        SUBEXPRESSION, PARAMETER,
                                        check_subexpressions,
                                        extract_constant_subexpressions)
from brian2.equations.refractory import add_refractoriness
from brian2.parsing.expressions import (parse_expression_dimensions,
                                        is_boolean_expression)
from brian2.stateupdaters.base import StateUpdateMethod
from brian2.units.allunits import second
from brian2.units.fundamentalunits import (Quantity, Unit, DIMENSIONLESS,
                                           have_same_dimensions,
                                           DimensionMismatchError,
                                           fail_for_dimension_mismatch)
from brian2.utils.logger import get_logger
from brian2.utils.stringtools import get_identifiers
from .group import Group, CodeRunner, get_dtype
from .subgroup import Subgroup

__all__ = ['NeuronGroup']

logger = get_logger(__name__)


IDENTIFIER = Word(string.ascii_letters + '_',
                  string.ascii_letters + string.digits + '_').setResultsName('identifier')

def _valid_event_name(event_name):
    '''
    Helper function to check whether a name is a valid name for an event.

    Parameters
    ----------
    event_name : str
        The name to check

    Returns
    -------
    is_valid : bool
        Whether the given name is valid
    '''
    parse_result = list(IDENTIFIER.scanString(event_name))

    # parse_result[0][0][0] refers to the matched string -- this should be the
    # full identifier, if not it is an illegal identifier like "3foo" which only
    # matched on "foo"
    return len(parse_result) == 1 and parse_result[0][0][0] == event_name

def _guess_membrane_potential(equations):
    '''
    Little helper function to guess which variable represents the membrane
    potential. This follows the same logic as in Brian1 but is only used to
    give a suggestion in the error message when a Brian1-style syntax is used
    for threshold or reset.
    '''
    if len(equations) == 1:
        return equations.keys()[0]
    for name, eq in equations.iteritems():
        if name in ['V', 'v', 'Vm', 'vm']:
            return name

    # nothing found
    return None


# Note that we do not register this function with
# Equations.register_identifier_check, because we do not want this check to
# apply unconditionally to all equation objects ("x_post = ... : ... (summed)"
# needs to be allowed)
[docs]def check_identifier_pre_post(identifier): 'Do not allow names ending in ``_pre`` or ``_post`` to avoid confusion.' if identifier.endswith('_pre') or identifier.endswith('_post'): raise ValueError('"%s" cannot be used as a variable name, the "_pre" ' 'and "_post" suffixes are used to refer to pre- and ' 'post-synaptic variables in synapses.' % identifier)
[docs]def to_start_stop(item, N): ''' Helper function to transform a single number, a slice or an array of contiguous indices to a start and stop value. This is used to allow for some flexibility in the syntax of specifying subgroups in `.NeuronGroup` and `.SpatialNeuron`. Parameters ---------- item : slice, int or sequence The slice, index, or sequence of indices to use. Note that a sequence of indices has to be a sorted ascending sequence of subsequent integers. N : int The total number of elements in the group. Returns ------- start : int The start value of the slice. stop : int The stop value of the slice. Examples -------- >>> from brian2.groups.neurongroup import to_start_stop >>> to_start_stop(slice(3, 6), 10) (3, 6) >>> to_start_stop(slice(3, None), 10) (3, 10) >>> to_start_stop(5, 10) (5, 6) >>> to_start_stop([3, 4, 5], 10) (3, 6) >>> to_start_stop([3, 5, 7], 10) Traceback (most recent call last): ... IndexError: Subgroups can only be constructed using contiguous indices. ''' if isinstance(item, slice): start, stop, step = item.indices(N) elif isinstance(item, numbers.Integral): start = item stop = item + 1 step = 1 elif (isinstance(item, (collections.Sequence, np.ndarray)) and not isinstance(item, basestring)): if not (len(item) > 0 and np.all(np.diff(item) == 1)): raise IndexError('Subgroups can only be constructed using ' 'contiguous indices.') if not np.issubdtype(np.asarray(item).dtype, np.integer): raise TypeError('Subgroups can only be constructed using integer ' 'values.') start = int(item[0]) stop = int(item[-1]) + 1 step = 1 else: raise TypeError('Subgroups can only be constructed using slicing ' 'syntax, a single index, or an array of contiguous ' 'indices.') if step != 1: raise IndexError('Subgroups have to be contiguous') if start >= stop: raise IndexError('Illegal start/end values for subgroup, %d>=%d' % (start, stop)) if start >= N: raise IndexError('Illegal start value for subgroup, %d>=%d' % (start, N)) if stop > N: raise IndexError('Illegal stop value for subgroup, %d>%d' % (stop, N)) if start < 0: raise IndexError('Indices have to be positive.') return start, stop
[docs]class StateUpdater(CodeRunner): ''' The `CodeRunner` that updates the state variables of a `NeuronGroup` at every timestep. ''' def __init__(self, group, method, method_options=None): self.method_choice = method self.method_options = method_options CodeRunner.__init__(self, group, 'stateupdate', code='', # will be set in update_abstract_code clock=group.clock, when='groups', order=group.order, name=group.name + '_stateupdater*', check_units=False, generate_empty_code=False) def _get_refractory_code(self, run_namespace): ref = self.group._refractory if ref is False: # No refractoriness abstract_code = '' elif isinstance(ref, Quantity): fail_for_dimension_mismatch(ref, second, ('Refractory period has to ' 'be specified in units ' 'of seconds but got ' '{value}'), value=ref) if prefs.legacy.refractory_timing: abstract_code = 'not_refractory = (t - lastspike) > %f\n' % ref else: abstract_code = 'not_refractory = timestep(t - lastspike, dt) >= timestep(%f, dt)\n' % ref else: identifiers = get_identifiers(ref) variables = self.group.resolve_all(identifiers, run_namespace, user_identifiers=identifiers) dims = parse_expression_dimensions(str(ref), variables) if dims is second.dim: if prefs.legacy.refractory_timing: abstract_code = '(t - lastspike) > %s\n' % ref else: abstract_code = 'not_refractory = timestep(t - lastspike, dt) >= timestep(%s, dt)\n' % ref elif dims is DIMENSIONLESS: if not is_boolean_expression(str(ref), variables): raise TypeError(('Refractory expression is dimensionless ' 'but not a boolean value. It needs to ' 'either evaluate to a timespan or to a ' 'boolean value.')) # boolean condition # we have to be a bit careful here, we can't just use the given # condition as it is, because we only want to *leave* # refractoriness, based on the condition abstract_code = 'not_refractory = not_refractory or not (%s)\n' % ref else: raise TypeError(('Refractory expression has to evaluate to a ' 'timespan or a boolean value, expression' '"%s" has units %s instead') % (ref, dims)) return abstract_code
[docs] def update_abstract_code(self, run_namespace): # Update the not_refractory variable for the refractory period mechanism self.abstract_code = self._get_refractory_code(run_namespace=run_namespace) # Get the names used in the refractory code _, used_known, unknown = analyse_identifiers(self.abstract_code, self.group.variables, recursive=True) # Get all names used in the equations (and always get "dt") names = self.group.equations.names external_names = self.group.equations.identifiers | {'dt'} variables = self.group.resolve_all(used_known | unknown | names | external_names, run_namespace, # we don't need to raise any warnings # for the user here, warnings will # be raised in create_runner_codeobj user_identifiers=set()) if len(self.group.equations.diff_eq_names) > 0: stateupdate_output = StateUpdateMethod.apply_stateupdater(self.group.equations, variables, self.method_choice, method_options=self.method_options, group_name=self.group.name) if isinstance(stateupdate_output, basestring): self.abstract_code += stateupdate_output else: # Note that the reason to send self along with this method is so the StateUpdater # can be modified! i.e. in GSL StateUpdateMethod a custom CodeObject gets added # to the StateUpdater together with some auxiliary information self.abstract_code += stateupdate_output(self) user_code = '\n'.join(['{var} = {expr}'.format(var=var, expr=expr) for var, expr in self.group.equations.get_substituted_expressions(variables)]) self.user_code = user_code
[docs]class SubexpressionUpdater(CodeRunner): ''' The `CodeRunner` that updates the state variables storing the values of subexpressions that have been marked as "constant over dt". ''' def __init__(self, group, subexpressions, when='before_start'): code_lines = [] for subexpr in subexpressions.ordered: code_lines.append('{} = {}'.format(subexpr.varname, subexpr.expr)) code = '\n'.join(code_lines) CodeRunner.__init__(self, group, 'stateupdate', code=code, # will be set in update_abstract_code clock=group.clock, when=when, order=group.order, name=group.name + '_subexpression_update*')
[docs]class Thresholder(CodeRunner): ''' The `CodeRunner` that applies the threshold condition to the state variables of a `NeuronGroup` at every timestep and sets its ``spikes`` and ``refractory_until`` attributes. ''' def __init__(self, group, when='thresholds', event='spike'): self.event = event if group._refractory is False or event != 'spike': template_kwds = {'_uses_refractory': False} needed_variables = [] else: template_kwds = {'_uses_refractory': True} needed_variables=['t', 'not_refractory', 'lastspike'] # Since this now works for general events not only spikes, we have to # pass the information about which variable to use to the template, # it can not longer simply refer to "_spikespace" eventspace_name = '_{}space'.format(event) template_kwds['eventspace_variable'] = group.variables[eventspace_name] needed_variables.append(eventspace_name) self.variables = Variables(self) self.variables.add_auxiliary_variable('_cond', dtype=np.bool) CodeRunner.__init__(self, group, 'threshold', code='', # will be set in update_abstract_code clock=group.clock, when=when, order=group.order, name=group.name+'_thresholder*', needed_variables=needed_variables, template_kwds=template_kwds)
[docs] def update_abstract_code(self, run_namespace): code = self.group.events[self.event] # Raise a useful error message when the user used a Brian1 syntax if not isinstance(code, basestring): if isinstance(code, Quantity): t = 'a quantity' else: t = '%s' % type(code) error_msg = 'Threshold condition has to be a string, not %s.' % t if self.event == 'spike': try: vm_var = _guess_membrane_potential(self.group.equations) except AttributeError: # not a group with equations... vm_var = None if vm_var is not None: error_msg += " Probably you intended to use '%s > ...'?" % vm_var raise TypeError(error_msg) self.user_code = '_cond = ' + code identifiers = get_identifiers(code) variables = self.group.resolve_all(identifiers, run_namespace, user_identifiers=identifiers) if not is_boolean_expression(code, variables): raise TypeError(('Threshold condition "%s" is not a boolean ' 'expression') % code) if self.group._refractory is False or self.event != 'spike': self.abstract_code = '_cond = %s' % code else: self.abstract_code = '_cond = (%s) and not_refractory' % code
[docs]class Resetter(CodeRunner): ''' The `CodeRunner` that applies the reset statement(s) to the state variables of neurons that have spiked in this timestep. ''' def __init__(self, group, when='resets', order=None, event='spike'): self.event = event # Since this now works for general events not only spikes, we have to # pass the information about which variable to use to the template, # it can not longer simply refer to "_spikespace" eventspace_name = '_{}space'.format(event) template_kwds = {'eventspace_variable': group.variables[eventspace_name]} needed_variables= [eventspace_name] order = order if order is not None else group.order CodeRunner.__init__(self, group, 'reset', code='', # will be set in update_abstract_code clock=group.clock, when=when, order=order, name=group.name + '_resetter*', override_conditional_write=['not_refractory'], needed_variables=needed_variables, template_kwds=template_kwds)
[docs] def update_abstract_code(self, run_namespace): code = self.group.event_codes[self.event] # Raise a useful error message when the user used a Brian1 syntax if not isinstance(code, basestring): if isinstance(code, Quantity): t = 'a quantity' else: t = '%s' % type(code) error_msg = 'Reset statement has to be a string, not %s.' % t if self.event == 'spike': vm_var = _guess_membrane_potential(self.group.equations) if vm_var is not None: error_msg += " Probably you intended to use '%s = ...'?" % vm_var raise TypeError(error_msg) self.abstract_code = code
[docs]class NeuronGroup(Group, SpikeSource): ''' A group of neurons. Parameters ---------- N : int Number of neurons in the group. model : (str, `Equations`) The differential equations defining the group method : (str, function), optional The numerical integration method. Either a string with the name of a registered method (e.g. "euler") or a function that receives an `Equations` object and returns the corresponding abstract code. If no method is specified, a suitable method will be chosen automatically. threshold : str, optional The condition which produces spikes. Should be a single line boolean expression. reset : str, optional The (possibly multi-line) string with the code to execute on reset. refractory : {str, `Quantity`}, optional Either the length of the refractory period (e.g. ``2*ms``), a string expression that evaluates to the length of the refractory period after each spike (e.g. ``'(1 + rand())*ms'``), or a string expression evaluating to a boolean value, given the condition under which the neuron stays refractory after a spike (e.g. ``'v > -20*mV'``) events : dict, optional User-defined events in addition to the "spike" event defined by the ``threshold``. Has to be a mapping of strings (the event name) to strings (the condition) that will be checked. namespace: dict, optional A dictionary mapping identifier names to objects. If not given, the namespace will be filled in at the time of the call of `Network.run`, with either the values from the ``namespace`` argument of the `Network.run` method or from the local context, if no such argument is given. dtype : (`dtype`, `dict`), optional The `numpy.dtype` that will be used to store the values, or a dictionary specifying the type for variable names. If a value is not provided for a variable (or no value is provided at all), the preference setting `core.default_float_dtype` is used. codeobj_class : class, optional The `CodeObject` class to run code with. dt : `Quantity`, optional The time step to be used for the simulation. Cannot be combined with the `clock` argument. clock : `Clock`, optional The update clock to be used. If neither a clock, nor the `dt` argument is specified, the `defaultclock` will be used. order : int, optional The priority of of this group for operations occurring at the same time step and in the same scheduling slot. Defaults to 0. name : str, optional A unique name for the group, otherwise use ``neurongroup_0``, etc. Notes ----- `NeuronGroup` contains a `StateUpdater`, `Thresholder` and `Resetter`, and these are run at the 'groups', 'thresholds' and 'resets' slots (i.e. the values of their `when` attribute take these values). The `order` attribute will be passed down to the contained objects but can be set individually by setting the `order` attribute of the `state_updater`, `thresholder` and `resetter` attributes, respectively. ''' add_to_magic_network = True def __init__(self, N, model, method=('exact', 'euler', 'heun'), method_options=None, threshold=None, reset=None, refractory=False, events=None, namespace=None, dtype=None, dt=None, clock=None, order=0, name='neurongroup*', codeobj_class=None): Group.__init__(self, dt=dt, clock=clock, when='start', order=order, name=name) if dtype is None: dtype = {} if isinstance(dtype, collections.MutableMapping): dtype['lastspike'] = self._clock.variables['t'].dtype self.codeobj_class = codeobj_class try: self._N = N = int(N) except ValueError: if isinstance(N, str): raise TypeError("First NeuronGroup argument should be size, not equations.") raise if N < 1: raise ValueError("NeuronGroup size should be at least 1, was " + str(N)) self.start = 0 self.stop = self._N ##### Prepare and validate equations if isinstance(model, basestring): model = Equations(model) if not isinstance(model, Equations): raise TypeError(('model has to be a string or an Equations ' 'object, is "%s" instead.') % type(model)) # Check flags model.check_flags({DIFFERENTIAL_EQUATION: ('unless refractory',), PARAMETER: ('constant', 'shared', 'linked'), SUBEXPRESSION: ('shared', 'constant over dt')}) # add refractoriness #: The original equations as specified by the user (i.e. without #: the multiplied `int(not_refractory)` term for equations marked as #: `(unless refractory)`) self.user_equations = model if refractory is not False: model = add_refractoriness(model) uses_refractoriness = len(model) and any( ['unless refractory' in eq.flags for eq in model.itervalues() if eq.type == DIFFERENTIAL_EQUATION]) # Separate subexpressions depending whether they are considered to be # constant over a time step or not model, constant_over_dt = extract_constant_subexpressions(model) self.equations = model self._linked_variables = set() logger.diagnostic("Creating NeuronGroup of size {self._N}, " "equations {self.equations}.".format(self=self)) if namespace is None: namespace = {} #: The group-specific namespace self.namespace = namespace # All of the following will be created in before_run #: The refractory condition or timespan self._refractory = refractory if uses_refractoriness and refractory is False: logger.warn('Model equations use the "unless refractory" flag but ' 'no refractory keyword was given.', 'no_refractory') #: The state update method selected by the user self.method_choice = method if events is None: events = {} if threshold is not None: if 'spike' in events: raise ValueError(("The NeuronGroup defines both a threshold " "and a 'spike' event")) events['spike'] = threshold # Setup variables # Since we have to create _spikespace and possibly other "eventspace" # variables, we pass the supported events self._create_variables(dtype, events=events.keys()) #: Events supported by this group self.events = events #: Code that is triggered on events (e.g. reset) self.event_codes = {} #: Checks the spike threshold (or abitrary user-defined events) self.thresholder = {} #: Reset neurons which have spiked (or perform arbitrary actions for #: user-defined events) self.resetter = {} for event_name in events.iterkeys(): if not isinstance(event_name, basestring): raise TypeError(('Keys in the "events" dictionary have to be ' 'strings, not type %s.') % type(event_name)) if not _valid_event_name(event_name): raise TypeError(("The name '%s' cannot be used as an event " "name.") % event_name) # By default, user-defined events are checked after the threshold when = 'thresholds' if event_name == 'spike' else 'after_thresholds' # creating a Thresholder will take care of checking the validity # of the condition thresholder = Thresholder(self, event=event_name, when=when) self.thresholder[event_name] = thresholder self.contained_objects.append(thresholder) if reset is not None: self.run_on_event('spike', reset, when='resets') #: Performs numerical integration step self.state_updater = StateUpdater(self, method, method_options) self.contained_objects.append(self.state_updater) #: Update the "constant over a time step" subexpressions self.subexpression_updater = None if len(constant_over_dt): self.subexpression_updater = SubexpressionUpdater(self, constant_over_dt) self.contained_objects.append(self.subexpression_updater) if refractory is not False: # Set the refractoriness information self.variables['lastspike'].set_value(-1e4*second) self.variables['not_refractory'].set_value(True) # Activate name attribute access self._enable_group_attributes() @property def spikes(self): ''' The spikes returned by the most recent thresholding operation. ''' # Note that we have to directly access the ArrayVariable object here # instead of using the Group mechanism by accessing self._spikespace # Using the latter would cut _spikespace to the length of the group spikespace = self.variables['_spikespace'].get_value() return spikespace[:spikespace[-1]]
[docs] def state(self, name, use_units=True, level=0): try: return Group.state(self, name, use_units=use_units, level=level+1) except KeyError as ex: if name in self._linked_variables: raise TypeError(('Link target for variable %s has not been ' 'set.') % name) else: raise ex
[docs] def run_on_event(self, event, code, when='after_resets', order=None): ''' Run code triggered by a custom-defined event (see `NeuronGroup` documentation for the specification of events).The created `Resetter` object will be automatically added to the group, it therefore does not need to be added to the network manually. However, a reference to the object will be returned, which can be used to later remove it from the group or to set it to inactive. Parameters ---------- event : str The name of the event that should trigger the code code : str The code that should be executed when : str, optional The scheduling slot that should be used to execute the code. Defaults to `'after_resets'`. order : int, optional The order for operations in the same scheduling slot. Defaults to the order of the `NeuronGroup`. Returns ------- obj : `Resetter` A reference to the object that will be run. ''' if event not in self.events: error_message = "Unknown event '%s'." % event if event == 'spike': error_message += ' Did you forget to define a threshold?' raise ValueError(error_message) if event in self.resetter: raise ValueError(("Cannot add code for event '%s', code for this " "event has already been added.") % event) self.event_codes[event] = code resetter = Resetter(self, when=when, order=order, event=event) self.resetter[event] = resetter self.contained_objects.append(resetter) return resetter
[docs] def set_event_schedule(self, event, when='after_thresholds', order=None): ''' Change the scheduling slot for checking the condition of an event. Parameters ---------- event : str The name of the event for which the scheduling should be changed when : str, optional The scheduling slot that should be used to check the condition. Defaults to `'after_thresholds'`. order : int, optional The order for operations in the same scheduling slot. Defaults to the order of the `NeuronGroup`. ''' if event not in self.thresholder: raise ValueError("Unknown event '%s'." % event) order = order if order is not None else self.order self.thresholder[event].when = when self.thresholder[event].order = order
def __setattr__(self, key, value): # attribute access is switched off until this attribute is created by # _enable_group_attributes if not hasattr(self, '_group_attribute_access_active') or key in self.__dict__: object.__setattr__(self, key, value) elif key in self._linked_variables: if not isinstance(value, LinkedVariable): raise ValueError(('Cannot set a linked variable directly, link ' 'it to another variable using "linked_var".')) linked_var = value.variable if isinstance(linked_var, DynamicArrayVariable): raise NotImplementedError(('Linking to variable %s is not ' 'supported, can only link to ' 'state variables of fixed ' 'size.') % linked_var.name) eq = self.equations[key] if eq.dim is not linked_var.dim: raise DimensionMismatchError(('Unit of variable %s does not ' 'match its link target %s') % (key, linked_var.name)) if not isinstance(linked_var, Subexpression): var_length = len(linked_var) else: var_length = len(linked_var.owner) if value.index is not None: try: index_array = np.asarray(value.index) if not np.issubsctype(index_array.dtype, np.int): raise TypeError() except TypeError: raise TypeError(('The index for a linked variable has ' 'to be an integer array')) size = len(index_array) source_index = value.group.variables.indices[value.name] if source_index not in ('_idx', '0'): # we are indexing into an already indexed variable, # calculate the indexing into the target variable index_array = value.group.variables[source_index].get_value()[index_array] if not index_array.ndim == 1 or size != len(self): raise TypeError(('Index array for linked variable %s ' 'has to be a one-dimensional array of ' 'length %d, but has shape ' '%s') % (key, len(self), str(index_array.shape))) if min(index_array) < 0 or max(index_array) >= var_length: raise ValueError('Index array for linked variable %s ' 'contains values outside of the valid ' 'range [0, %d[' % (key, var_length)) self.variables.add_array('_%s_indices' % key, size=size, dtype=index_array.dtype, constant=True, read_only=True, values=index_array) index = '_%s_indices' % key else: if linked_var.scalar or (var_length == 1 and self._N != 1): index = '0' else: index = value.group.variables.indices[value.name] if index == '_idx': target_length = var_length else: target_length = len(value.group.variables[index]) # we need a name for the index that does not clash with # other names and a reference to the index new_index = '_' + value.name + '_index_' + index self.variables.add_reference(new_index, value.group, index) index = new_index if len(self) != target_length: raise ValueError(('Cannot link variable %s to %s, the size of ' 'the target group does not match ' '(%d != %d). You can provide an indexing ' 'scheme with the "index" keyword to link ' 'groups with different sizes') % (key, linked_var.name, len(self), target_length)) self.variables.add_reference(key, value.group, value.name, index=index) log_msg = ('Setting {target}.{targetvar} as a link to ' '{source}.{sourcevar}').format(target=self.name, targetvar=key, source=value.variable.owner.name, sourcevar=value.variable.name) if index is not None: log_msg += '(using "{index}" as index variable)'.format(index=index) logger.diagnostic(log_msg) else: if isinstance(value, LinkedVariable): raise TypeError(('Cannot link variable %s, it has to be marked ' 'as a linked variable with "(linked)" in the ' 'model equations.') % key) else: Group.__setattr__(self, key, value, level=1) def __getitem__(self, item): start, stop = to_start_stop(item, self._N) return Subgroup(self, start, stop) def _create_variables(self, user_dtype, events): ''' Create the variables dictionary for this `NeuronGroup`, containing entries for the equation variables and some standard entries. ''' self.variables = Variables(self) self.variables.add_constant('N', self._N) # Standard variables always present for event in events: self.variables.add_array('_{}space'.format(event), size=self._N+1, dtype=np.int32, constant=False) # Add the special variable "i" which can be used to refer to the neuron index self.variables.add_arange('i', size=self._N, constant=True, read_only=True) # Add the clock variables self.variables.create_clock_variables(self._clock) for eq in self.equations.itervalues(): dtype = get_dtype(eq, user_dtype) check_identifier_pre_post(eq.varname) if eq.type in (DIFFERENTIAL_EQUATION, PARAMETER): if 'linked' in eq.flags: # 'linked' cannot be combined with other flags if not len(eq.flags) == 1: raise SyntaxError(('The "linked" flag cannot be ' 'combined with other flags')) self._linked_variables.add(eq.varname) else: constant = 'constant' in eq.flags shared = 'shared' in eq.flags size = 1 if shared else self._N self.variables.add_array(eq.varname, size=size, dimensions=eq.dim, dtype=dtype, constant=constant, scalar=shared) elif eq.type == SUBEXPRESSION: self.variables.add_subexpression(eq.varname, dimensions=eq.dim, expr=str(eq.expr), dtype=dtype, scalar='shared' in eq.flags) else: raise AssertionError('Unknown type of equation: ' + eq.eq_type) # Add the conditional-write attribute for variables with the # "unless refractory" flag if self._refractory is not False: for eq in self.equations.itervalues(): if (eq.type == DIFFERENTIAL_EQUATION and 'unless refractory' in eq.flags): not_refractory_var = self.variables['not_refractory'] var = self.variables[eq.varname] var.set_conditional_write(not_refractory_var) # Stochastic variables for xi in self.equations.stochastic_variables: self.variables.add_auxiliary_variable(xi, dimensions=(second ** -0.5).dim) # Check scalar subexpressions for eq in self.equations.itervalues(): if eq.type == SUBEXPRESSION and 'shared' in eq.flags: var = self.variables[eq.varname] for identifier in var.identifiers: if identifier in self.variables: if not self.variables[identifier].scalar: raise SyntaxError(('Shared subexpression %s refers ' 'to non-shared variable %s.') % (eq.varname, identifier))
[docs] def before_run(self, run_namespace=None): # Check units self.equations.check_units(self, run_namespace=run_namespace) # Check that subexpressions that refer to stateful functions are labeled # as "constant over dt" check_subexpressions(self, self.equations, run_namespace) super(NeuronGroup, self).before_run(run_namespace=run_namespace)
def _repr_html_(self): text = [r'NeuronGroup "%s" with %d neurons.<br>' % (self.name, self._N)] text.append(r'<b>Model:</b><nr>') text.append(sympy.latex(self.equations)) def add_event_to_text(event): if event=='spike': event_header = 'Spiking behaviour' event_condition = 'Threshold condition' event_code = 'Reset statement(s)' else: event_header = 'Event "%s"' % event event_condition = 'Event condition' event_code = 'Executed statement(s)' condition = self.events[event] text.append(r'<b>%s:</b><ul style="list-style-type: none; margin-top: 0px;">' % event_header) text.append(r'<li><i>%s: </i>' % event_condition) text.append('<code>%s</code></li>' % str(condition)) statements = self.event_codes.get(event, None) if statements is not None: text.append(r'<li><i>%s:</i>' % event_code) if '\n' in str(statements): text.append('</br>') text.append(r'<code>%s</code></li>' % str(statements)) text.append('</ul>') if 'spike' in self.events: add_event_to_text('spike') for event in self.events: if event!='spike': add_event_to_text(event) return '\n'.join(text)