Source code for spynnaker.pyNN.models.populations.population_view

# Copyright (c) 2017-2019 The University of Manchester
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import logging
import neo
import numpy
from spinn_utilities.log import FormatAdapter
from pyNN import descriptions
from pyNN.random import NumpyRNG
from spinn_utilities.logger_utils import warn_once
from spinn_utilities.ranged.abstract_sized import AbstractSized
from .idmixin import IDMixin
from .population_base import PopulationBase

logger = FormatAdapter(logging.getLogger(__name__))


[docs]class PopulationView(PopulationBase): """ A view of a subset of neurons within a\ :py:class:`~spynnaker.pyNN.models.populations.Population`. In most ways, Populations and PopulationViews have the same behaviour, i.e., they can be recorded, connected with Projections, etc. It should be noted that any changes to neurons in a PopulationView will be reflected in the parent Population and *vice versa.* It is possible to have views of views. .. note:: Selector to Id is actually handled by :py:class:`~.AbstractSized`. """ __slots__ = [ "__annotations", "__indexes", "__label", "__mask", "__parent", "__population"] def __init__(self, parent, selector, label=None): """ :param parent: the population or view to make the view from :type parent: ~spynnaker.pyNN.models.populations.Population or ~spynnaker.pyNN.models.populations.PopulationView :param selector: a slice or numpy mask array. The mask array should either be a boolean array (ideally) of the same size as the parent, or an integer array containing cell indices, i.e. if `p.size == 5` then: :: PopulationView(p, array([False, False, True, False, True])) PopulationView(p, array([2, 4])) PopulationView(p, slice(2, 5, 2)) will all create the same view. :type selector: None or slice or int or list(bool) or list(int) or ~numpy.ndarray(bool) or ~numpy.ndarray(int) :param str label: A label for the view """ self.__parent = parent sized = AbstractSized(parent.size) ids = sized.selector_to_ids(selector, warn=True) if isinstance(parent, PopulationView): self.__population = parent.grandparent self.__indexes = parent.index_in_grandparent(ids) else: self.__population = parent self.__indexes = ids self.__mask = selector self.__label = label self.__annotations = dict() @property def size(self): """ The total number of neurons in the Population View. :rtype: int """ return len(self.__indexes) @property def label(self): """ A label for the Population View. :rtype: str """ return self.__label @property def celltype(self): """ The type of neurons making up the underlying Population. :rtype: AbstractPyNNModel """ return self.__population.celltype @property def initial_values(self): """ A dict containing the initial values of the state variables. :rtype: dict(str, ...) """ return self.__population._get_initial_values(selector=self.__indexes) @property def parent(self): """ A reference to the parent Population (that this is a view of). :rtype: ~spynnaker.pyNN.models.populations.Population """ return self.__parent @property def mask(self): """ The selector mask that was used to create this view. :rtype: None or slice or int or list(bool) or list(int) or ~numpy.ndarray(bool) or ~numpy.ndarray(int) """ return self.__mask @property def all_cells(self): """ An array containing the cell IDs of all neurons in the\ Population (all MPI nodes). :rtype: list(IDMixin) """ return [IDMixin(self.__population, idx) for idx in self.__indexes] @property def _indexes(self): return tuple(self.__indexes) @property def _vertex(self): return self.__population._vertex def __getitem__(self, index): """ Return either a single cell (ID object) from the Population,\ if index is an integer, or a subset of the cells\ (PopulationView object), if index is a slice or array. .. note:: ``__getitem__`` is called when using[] access, e.g. if ``p = Population(...)`` then ``p[2]`` is equivalent to ``p.__getitem__(2)``, and ``p[3:6]`` is equivalent to ``p.__getitem__(slice(3, 6))`` :rtype: ~.IDMixin or ~.PopulationView """ if isinstance(index, int): return IDMixin(self.__population, index) return PopulationView(self, index, label=self.label+"_" + str(index)) def __iter__(self): """ Iterator over cell IDs (on the local node). :rtype: iterable(~.IDMixin) """ for idx in self.__indexes: yield IDMixin(self, idx) def __len__(self): """ Return the total number of cells in the population (all nodes). :rtype: int """ return len(self.__indexes)
[docs] def all(self): """ Iterator over cell IDs (on all MPI nodes). :rtype: iterable(~.IDMixin) """ for idx in self.__indexes: yield IDMixin(self, idx)
[docs] def can_record(self, variable): """ Determine whether variable can be recorded from this population. :rtype: bool """ return self.__population.can_record(variable)
@property def conductance_based(self): """ Indicates whether the post-synaptic response is modelled as a\ change in conductance or a change in current. :rtype: bool """ return self.__population.conductance_based
[docs] def describe(self, template='populationview_default.txt', engine='default'): """ Returns a human-readable description of the population view. The output may be customized by specifying a different template together with an associated template engine (see pyNN.descriptions). If template is ``None``, then a dictionary containing the template context will be returned. :param str template: Template filename :param engine: Template substitution engine :type engine: str or ~pyNN.descriptions.TemplateEngine or None :rtype: str or dict """ context = {"label": self.label, "parent": self.parent.label, "mask": self.mask, "size": self.size} context.update(self.__annotations) return descriptions.render(engine, template, context)
[docs] def find_units(self, variable): """ Get the units of a variable .. warning:: No PyNN description of this method. :param str variable: The name of the variable :return: The units of the variable :rtype: str """ return self.__population.find_units(variable)
[docs] def get(self, parameter_names, gather=False, simplify=True): """ Get the values of the given parameters for every local cell in\ the population, or, if ``gather=True``,\ for all cells in the population. Values will be expressed in the standard PyNN units (i.e. millivolts, nanoamps, milliseconds, microsiemens, nanofarads, event per second). .. note:: SpiNNaker always gathers. :param parameter_names: :type parameter_names: str or list(str) :param bool gather: :param bool simplify: :rtype: iterable(float) """ if not gather: logger.warning("SpiNNaker only supports gather=True. We will run " "as if gather was set to True.") if simplify is not True: logger.warning("The simplify value is ignored if not set to true") return self.__population._get_by_selector( self.__indexes, parameter_names)
[docs] def get_data( self, variables='all', gather=True, clear=False, annotations=None): """ Return a Neo Block containing the data(spikes, state variables)\ recorded from the Population. :param variables: Either a single variable name or a list of variable names. Variables must have been previously recorded, otherwise an Exception will be raised. :type variables: str or list(str) :param bool gather: For parallel simulators, if gather is True, all data will be gathered to all nodes and the Neo Block will contain data from all nodes. Otherwise, the Neo Block will contain only data from the cells simulated on the local node. .. note:: SpiNNaker always gathers. :param bool clear: If True, recorded data will be deleted from the Population. :param annotations: annotations to put on the neo block :type annotations: dict(str, ...) :rtype: ~neo.core.Block :raises \ ~spinn_front_end_common.utilities.exceptions.ConfigurationException: If the variable or variables have not been previously set to record. """ if not gather: logger.warning("SpiNNaker only supports gather=True. We will run " "as if gather was set to True.") if annotations is not None: warn_once( logger, "Annotations parameter is not standard PyNN so may " "not be supported by all platforms.") return self.__population.get_data_by_indexes( variables, self.__indexes, clear=clear)
[docs] def get_spike_counts(self, gather=True): """ Returns a dict containing the number of spikes for each neuron. The dict keys are neuron IDs, not indices. .. note:: Implementation of this method is different to Population as the Populations uses PyNN 7 version of the ``get_spikes`` method which does not support indexes. :param bool gather: .. note:: SpiNNaker always gathers. :rtype: dict(int,int) """ if not gather: logger.warning( logger, "sPyNNaker only supports gather=True. We will run " "as if gather was set to True.") logger.info("get_spike_counts is inefficient as it just counts the " "results of get_datas('spikes')") neo_data = self.get_data("spikes") spiketrains = neo_data.segments[len(neo_data.segments) - 1].spiketrains return { idx: len(spiketrains[i]) for i, idx in enumerate(self.__indexes)}
@property def grandparent(self): """ Returns the parent Population at the root of the tree (since the\ immediate parent may itself be a PopulationView). The name "grandparent" is of course a little misleading, as it could be just the parent, or the great, great, great, ..., grandparent. :rtype: ~spynnaker.pyNN.models.populations.Population """ return self.__population
[docs] def id_to_index(self, id): # pylint: disable=redefined-builtin """ Given the ID(s) of cell(s) in the PopulationView, return its /\ their index / indices(order in the PopulationView). assert pv.id_to_index(pv[3]) == 3 :param id: :type id: int or list(int) :rtype: int or list(int) """ if isinstance(id, int): return self.__indexes.index(id) return [self.__indexes.index(idx) for idx in id]
[docs] def index_in_grandparent(self, indices): """ Given an array of indices, return the indices in the parent\ population at the root of the tree. :param list(int) indices: :rtype: list(int) """ return [self.__indexes[index] for index in indices]
[docs] def initialize(self, **initial_values): """ Set initial values of state variables, e.g. the membrane\ potential. Values passed to ``initialize()`` may be: * single numeric values (all neurons set to the same value), or * :py:class:`~pyNN.random.RandomDistribution` objects, or * lists / arrays of numbers of the same size as the population mapping functions, where a mapping function accepts a single argument (the cell index) and returns a single number. Values should be expressed in the standard PyNN units (i.e. millivolts, nanoamps, milliseconds, microsiemens, nanofarads, events per second). Examples:: p.initialize(v=-70.0) p.initialize(v=rand_distr, gsyn_exc=0.0) p.initialize(v=lambda i: -65 + i / 10.0) """ for variable, value in initial_values.items(): self.__population._initialize( variable, value, self.__indexes)
[docs] def record(self, variables, # pylint: disable=arguments-differ to_file=None, sampling_interval=None): """ Record the specified variable or variables for all cells in the\ Population or view. :param variables: either a single variable name, or a list of variable names, or ``all`` to record everything. For a given celltype class, celltype.recordable contains a list of variables that can be recorded for that celltype. :type variables: str or list(str) :param to_file: If specified, should be a Neo IO instance and :py:meth:`write_data` will be automatically called when `sim.end()` is called. :type to_file: ~neo.io or ~neo.rawio or str :param int sampling_interval: should be a value in milliseconds, and an integer multiple of the simulation timestep. """ self.__population._record( variables, to_file, sampling_interval, self.__indexes)
[docs] def sample(self, n, rng=None): """ Randomly sample `n` cells from the Population view, and return a\ new PopulationView object. :param int n: The number of cells to select :param ~pyNN.random.NumpyRNG rng: Random number generator :rtype: ~spynnaker.pyNN.models.populations.PopulationView """ if not rng: rng = NumpyRNG() indices = rng.permutation( numpy.arange(len(self), dtype=numpy.int))[0:n] return PopulationView( self, indices, label="Random sample size {} from {}".format(n, self.label))
[docs] def set(self, **parameters): """ Set one or more parameters for every cell in the population.\ Values passed to `set()` may be: * single values, * :py:class:`~pyNN.random.RandomDistribution` objects, or * lists / arrays of values of the same size as the population mapping functions, where a mapping function accepts a single argument (the cell index) and returns a single value. Here, a "single value" may be either a single number or a list / array of numbers (e.g. for spike times). Values should be expressed in the standard PyNN units (i.e. millivolts, nanoamps, milliseconds, microsiemens, nanofarads, event per second). Examples:: p.set(tau_m=20.0, v_rest=-65). p.set(spike_times=[0.3, 0.7, 0.9, 1.4]) p.set(cm=rand_distr, tau_m=lambda i: 10 + i / 10.0) """ for (parameter, value) in parameters.items(): self.__population.set_by_selector( selector=self.__indexes, parameter=parameter, value=value)
[docs] def write_data(self, io, variables='all', gather=True, clear=False, annotations=None): """ Write recorded data to file, using one of the file formats\ supported by Neo. :param io: a Neo IO instance or the name of a file to write :type io: neo.io.BaseIO or str :param variables: either a single variable name or a list of variable names. These must have been previously recorded, otherwise an Exception will be raised. :type variables: str or list(str) :param bool gather: For parallel simulators, if this is True, all data will be gathered to the master node and a single output file created there. Otherwise, a file will be written on each node, containing only data from the cells simulated on that node. .. note:: SpiNNaker always gathers. :param bool clear: If this is True, recorded data will be deleted from the Population. :param annotations: should be a dict containing simple data types such as numbers and strings. The contents will be written into the output data file as metadata. :type annotations: dict(str, ...) :raises \ ~spinn_front_end_common.utilities.exceptions.ConfigurationException: If the variable or variables have not been previously set to record. """ if not gather: logger.warning("SpiNNaker only supports gather=True. We will run " "as if gather was set to True.") data = self.__population.get_data_by_indexes( variables, self.__indexes, clear=clear) if isinstance(io, str): io = neo.get_io(io) # write the neo block to the file io.write(data)