Source code for brian2.monitors.statemonitor

from import Sequence
import numbers

import numpy as np

from brian2.core.variables import (Variables, Subexpression, get_dtype)
from import Group, CodeRunner
from brian2.utils.logger import get_logger
from brian2.units.fundamentalunits import Unit, Quantity
from brian2.units.allunits import second

__all__ = ['StateMonitor']

logger = get_logger(__name__)

[docs]class StateMonitorView(object): def __init__(self, monitor, item): self.monitor = monitor self.item = item self.indices = self._calc_indices(item) self._group_attribute_access_active = True def __getattr__(self, item): # We do this because __setattr__ and __getattr__ are not active until # _group_attribute_access_active attribute is set, and if it is set, # then __getattr__ will not be called. Therefore, if getattr is called # with this name, it is because it hasn't been set yet and so this # method should raise an AttributeError to agree that it hasn't been # called yet. if item == '_group_attribute_access_active': raise AttributeError if not hasattr(self, '_group_attribute_access_active'): raise AttributeError mon = self.monitor if item == 't': return Quantity(mon.variables['t'].get_value(), dim=second.dim) elif item == 't_': return mon.variables['t'].get_value() elif item in mon.record_variables: dims = mon.variables[item].dim return Quantity(mon.variables[item].get_value().T[self.indices], dim=dims, copy=True) elif item.endswith('_') and item[:-1] in mon.record_variables: return mon.variables[item[:-1]].get_value().T[self.indices].copy() else: raise AttributeError('Unknown attribute %s' % item) def _calc_indices(self, item): ''' Convert the neuron indices to indices into the stored values. For example, if neurons [0, 5, 10] have been recorded, [5, 10] is converted to [1, 2]. ''' dtype = get_dtype(item) # scalar value if np.issubdtype(dtype, np.signedinteger) and not isinstance(item, np.ndarray): indices = np.nonzero(self.monitor.record == item)[0] if len(indices) == 0: raise IndexError('Index number %d has not been recorded' % item) return indices[0] if self.monitor.record_all: return item indices = [] for index in item: if index in self.monitor.record: indices.append(np.nonzero(self.monitor.record == index)[0][0]) else: raise IndexError('Index number %d has not been recorded' % index) return np.array(indices) def __repr__(self): description = '<{classname}, giving access to elements {elements} recorded by {monitor}>' return description.format(classname=self.__class__.__name__, elements=repr(self.item),
[docs]class StateMonitor(Group, CodeRunner): ''' Record values of state variables during a run To extract recorded values after a run, use the ``t`` attribute for the array of times at which values were recorded, and variable name attribute for the values. The values will have shape ``(len(indices), len(t))``, where ``indices`` are the array indices which were recorded. When indexing the `StateMonitor` directly, the returned object can be used to get the recorded values for the specified indices, i.e. the indexing semantic refers to the indices in ``source``, not to the relative indices of the recorded values. For example, when recording only neurons with even numbers, `mon[[0, 2]].v` will return the values for neurons 0 and 2, whereas `mon.v[[0, 2]]` will return the values for the first and third *recorded* neurons, i.e. for neurons 0 and 4. Parameters ---------- source : `Group` Which object to record values from. variables : str, sequence of str, True Which variables to record, or ``True`` to record all variables (note that this may use a great deal of memory). record : bool, sequence of ints Which indices to record, nothing is recorded for ``False``, everything is recorded for ``True`` (warning: may use a great deal of memory), or a specified subset of indices. dt : `Quantity`, optional The time step to be used for the monitor. 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 clock of the `source` will be used. when : str, optional At which point during a time step the values should be recorded. Defaults to ``'start'``. 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 object, otherwise will use ``'statemonitor_0'``, etc. codeobj_class : `CodeObject`, optional The `CodeObject` class to create. Examples -------- Record all variables, first 5 indices:: eqs = """ dV/dt = (2-V)/(10*ms) : 1 """ threshold = 'V>1' reset = 'V = 0' G = NeuronGroup(100, eqs, threshold=threshold, reset=reset) G.V = rand(len(G)) M = StateMonitor(G, True, record=range(5)) run(100*ms) plot(M.t, M.V.T) show() Notes ----- Since this monitor by default records in the ``'start'`` time slot, recordings of the membrane potential in integrate-and-fire models may look unexpected: the recorded membrane potential trace will never be above threshold in an integrate-and-fire model, because the reset statement will have been applied already. Set the ``when`` keyword to a different value if this is not what you want. Note that ``record=True`` only works in runtime mode for synaptic variables. This is because the actual array of indices has to be calculated and this is not possible in standalone mode, where the synapses have not been created yet at this stage. Consider using an explicit array of indices instead, i.e. something like ``record=np.arange(n_synapses)``. ''' invalidates_magic_network = False add_to_magic_network = True def __init__(self, source, variables, record, dt=None, clock=None, when='start', order=0, name='statemonitor*', codeobj_class=None): self.source = source # Make the monitor use the explicitly defined namespace of its source # group (if it exists) self.namespace = getattr(source, 'namespace', None) self.codeobj_class = codeobj_class # run by default on source clock at the end if dt is None and clock is None: clock = source.clock # variables should always be a list of strings if variables is True: variables = source.equations.names elif isinstance(variables, str): variables = [variables] #: The variables to record self.record_variables = variables # record should always be an array of ints self.record_all = False if hasattr(record, '_indices'): # The ._indices method always returns absolute indices # If the source is already a subgroup of another group, we therefore # have to shift the indices to become relative to the subgroup record = record._indices() - getattr(source, '_offset', 0) if record is True: self.record_all = True try: record = np.arange(len(source), dtype=np.int32) except NotImplementedError: # In standalone mode, this is not possible for synaptic # variables because the number of synapses is not defined yet raise NotImplementedError(('Cannot determine the actual ' 'indices to record for record=True. ' 'This can occur for example in ' 'standalone mode when trying to ' 'record a synaptic variable. ' 'Consider providing an explicit ' 'array of indices for the record ' 'argument.')) elif record is False: record = np.array([], dtype=np.int32) elif isinstance(record, numbers.Number): record = np.array([record], dtype=np.int32) else: record = np.asarray(record, dtype=np.int32) #: The array of recorded indices self.record = record self.n_indices = len(record) # Some dummy code so that code generation takes care of the indexing # and subexpressions code = ['_to_record_%s = _source_%s' % (v, v) for v in variables] code = '\n'.join(code) CodeRunner.__init__(self, group=self, template='statemonitor', code=code, name=name, clock=clock, dt=dt, when=when, order=order, check_units=False) self.add_dependency(source) # Setup variables self.variables = Variables(self) self.variables.add_dynamic_array('t', size=0, dimensions=second.dim, constant=False, dtype=self._clock.variables['t'].dtype) self.variables.add_array('N', dtype=np.int32, size=1, scalar=True, read_only=True) self.variables.add_array('_indices', size=len(self.record), dtype=self.record.dtype, constant=True, read_only=True, values=self.record) self.variables.create_clock_variables(self._clock, prefix='_clock_') for varname in variables: var = source.variables[varname] if var.scalar and len(self.record) > 1: logger.warn(('Variable %s is a shared variable but it will be ' 'recorded once for every target.' % varname), once=True) index = source.variables.indices[varname] self.variables.add_reference('_source_%s' % varname, source, varname, index=index) if not index in ('_idx', '0') and index not in variables: self.variables.add_reference(index, source) self.variables.add_dynamic_array(varname, size=(0, len(self.record)), resize_along_first=True, dimensions=var.dim, dtype=var.dtype, constant=False, read_only=True) for varname in variables: var = self.source.variables[varname] self.variables.add_auxiliary_variable('_to_record_' + varname, dimensions=var.dim, dtype=var.dtype, scalar=var.scalar) self.recorded_variables = dict([(varname, self.variables[varname]) for varname in variables]) recorded_names = [varname for varname in variables] self.needed_variables = recorded_names self.template_kwds = {'_recorded_variables': self.recorded_variables} self.written_readonly_vars = {self.variables[varname] for varname in self.record_variables} self._enable_group_attributes()
[docs] def resize(self, new_size): self.variables['N'].set_value(new_size) self.variables['t'].resize(new_size) for var in self.recorded_variables.values(): var.resize((new_size, self.n_indices))
[docs] def reinit(self): raise NotImplementedError()
def __getitem__(self, item): dtype = get_dtype(item) if np.issubdtype(dtype, np.signedinteger): return StateMonitorView(self, item) elif isinstance(item, Sequence): index_array = np.array(item) if not np.issubdtype(index_array.dtype, np.signedinteger): raise TypeError('Index has to be an integer or a sequence ' 'of integers') return StateMonitorView(self, item) elif hasattr(item, '_indices'): # objects that support the indexing interface will return absolute # indices but here we need relative ones # TODO: How to we prevent the use of completely unrelated objects here? source_offset = getattr(self.source, '_offset', 0) return StateMonitorView(self, item._indices() - source_offset) else: raise TypeError('Cannot use object of type %s as an index' % type(item)) def __getattr__(self, item): # We do this because __setattr__ and __getattr__ are not active until # _group_attribute_access_active attribute is set, and if it is set, # then __getattr__ will not be called. Therefore, if getattr is called # with this name, it is because it hasn't been set yet and so this # method should raise an AttributeError to agree that it hasn't been # called yet. if item == '_group_attribute_access_active': raise AttributeError if not hasattr(self, '_group_attribute_access_active'): raise AttributeError if item in self.record_variables: var_dim = self.variables[item].dim return Quantity(self.variables[item].get_value().T, dim=var_dim, copy=True) elif item.endswith('_') and item[:-1] in self.record_variables: return self.variables[item[:-1]].get_value().T else: return Group.__getattr__(self, item) def __repr__(self): description = '<{classname}, recording {variables} from {source}>' return description.format(classname=self.__class__.__name__, variables=repr(self.record_variables),
[docs] def record_single_timestep(self): ''' Records a single time step. Useful for recording the values at the end of the simulation -- otherwise a `StateMonitor` will not record the last simulated values since its ``when`` attribute defaults to ``'start'``, i.e. the last recording is at the *beginning* of the last time step. Notes ----- This function will only work if the `StateMonitor` has been already run, but a run with a length of ``0*ms`` does suffice. Examples -------- >>> from brian2 import * >>> G = NeuronGroup(1, 'dv/dt = -v/(5*ms) : 1') >>> G.v = 1 >>> mon = StateMonitor(G, 'v', record=True) >>> run(0.5*ms) >>> print(np.array_str(mon.v[:], precision=3)) [[ 1. 0.98 0.961 0.942 0.923]] >>> print(mon.t[:]) [ 0. 100. 200. 300. 400.] us >>> print(np.array_str(G.v[:], precision=3)) # last value had not been recorded [ 0.905] >>> mon.record_single_timestep() >>> print(mon.t[:]) [ 0. 100. 200. 300. 400. 500.] us >>> print(np.array_str(mon.v[:], precision=3)) [[ 1. 0.98 0.961 0.942 0.923 0.905]] ''' if self.codeobj is None: raise TypeError('Can only record a single time step after the ' 'network has been run once.') self.codeobj()