# Copyright (c) 2017-2019 The University of Manchester
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
from __future__ import division
import logging
from six import add_metaclass, itervalues
from spinn_utilities.abstract_base import (
AbstractBase, abstractmethod, abstractproperty)
from spinn_utilities.logger_utils import warn_once
logger = logging.getLogger(__name__)
def _we_dont_do_this_now(*args): # pylint: disable=unused-argument
# pragma: no cover
raise NotImplementedError("sPyNNaker8 does not currently do this")
def _this_is_wholly_deprecated(msg, *args): # pylint: disable=unused-argument
# pragma: no cover
raise NotImplementedError(msg)
[docs]@add_metaclass(AbstractBase)
class PopulationBase(object):
r""" Shared methods between :py:class:`Population`\ s and
:py:class:`PopulationView`\ s.
Mainly pass through and not implemented
"""
__slots__ = []
@property
def local_cells(self):
""" An array containing the cell IDs of those neurons in the\
Population that exist on the local MPI node.
:rtype: list(int)
"""
logger.warning("local calls do not really make sense on sPyNNaker so "
"local_cells just returns all_cells")
return self.all_cells
@abstractproperty
def all_cells(self):
""" An array containing the cell IDs of all neurons in the\
Population (all MPI nodes).
:rtype: list(int)
"""
def __add__(self, other):
""" A Population / PopulationView can be added to another\
Population, PopulationView or Assembly, returning an Assembly.
.. warning::
Currently unimplemented.
"""
# TODO: support assemblies
_we_dont_do_this_now(other) # pragma: no cover
[docs] def getSpikes(self, *args, **kwargs): # pylint: disable=unused-argument
"""
.. warning::
Deprecated. Use `get_data('spikes')` instead.
"""
logger.warning(
'getSpikes is deprecated. Call transfered to get_data("spikes") '
'without additional arguments')
return self.get_data("spikes")
[docs] @abstractmethod
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 this 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 this is True, recorded data will be deleted from the Population.
:param annotations: annotations to put on the neo block
:type annotations: None or dict(str, ...)
"""
[docs] def get_gsyn(self, *args, **kwargs): # pylint: disable=unused-argument
"""
.. warning::
Deprecated. Use `get_data(['gsyn_exc', 'gsyn_inh'])` instead.
"""
logger.warning(
'get_gsyn is deprecated. '
'Call transfered to get_data(["gsyn_exc", "gsyn_inh"]) '
'without additional arguments')
return self.get_data(['gsyn_exc', 'gsyn_inh'])
[docs] @abstractmethod
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.
:param bool gather:
For parallel simulators, if this 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.
:rtype: dict(int, int)
"""
[docs] def get_v(self, *args, **kwargs): # pylint: disable=unused-argument
"""
.. warning::
Deprecated. Use `get_data('v')` instead.
"""
logger.warning(
'getSpikes is deprecated. '
'Call transfered to get_data("v") without additional arguments')
return self.get_data("v")
[docs] def inject(self, current_source):
""" Connect a current source to all cells in the Population.
.. warning::
Currently unimplemented.
:param current_source:
:type current_source:
pyNN.neuron.standardmodels.electrodes.NeuronCurrentSource
"""
# TODO:
_we_dont_do_this_now(current_source) # pragma: no cover
[docs] def is_local(self,
id): # pylint: disable=unused-argument, redefined-builtin
""" Indicates whether the cell with the given ID exists on the\
local MPI node.
:rtype: bool
"""
logger.warning("local calls do not really make sense on sPyNNaker so "
"is_local always returns True")
return True
@property
def local_size(self):
""" Return the number of cells in the population on the local MPI node.
:rtype: int
"""
logger.warning("local calls do not really make sense on sPyNNaker so "
"is_local always returns size")
return len(self)
[docs] def meanSpikeCount(self, *args, **kwargs):
"""
.. warning::
Deprecated. Use `mean_spike_count()` instead.
"""
logger.warning(
'meanSpikeCount is deprecated. '
'Call transfered to mean_spike_count with additional arguements')
return self.mean_spike_count(*args, **kwargs)
[docs] def mean_spike_count(self, gather=True):
""" Returns the mean number of spikes per neuron.
:param bool gather:
For parallel simulators, if this 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.
:rtype: float
"""
if not gather:
warn_once(
logger, "sPyNNaker only supports gather=True. We will run "
"as if gather was set to True.")
counts = self.get_spike_counts()
return sum(itervalues(counts)) / len(counts)
[docs] def nearest(self, position):
""" Return the neuron closest to the specified position.
.. warning::
Currently unimplemented.
"""
# TODO: support neuron positions and spaces
_we_dont_do_this_now(position) # pragma: no cover
@property
def position_generator(self):
"""
.. note::
NO PyNN description of this method.
.. warning::
Currently unimplemented.
"""
# TODO: support neuron positions and spaces
_we_dont_do_this_now() # pragma: no cover
@property
def positions(self):
"""
.. note::
NO PyNN description of this method.
.. warning::
Currently unimplemented.
:rtype: ~numpy.ndarray(tuple(float, float, float))
"""
# TODO: support neuron positions and spaces
_we_dont_do_this_now() # pragma: no cover
[docs] @abstractmethod
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 a string for where to put a Neo instance
:type io: ~neo.io or ~neo.rawio or str
: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 this 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. This is pointless on
sPyNNaker.
.. note::
SpiNNaker always gathers.
:param bool clear:
clears the storage data if set to true after reading it back
:param annotations: annotations to put on the Neo block
:type annotations: None or dict(str, ...)
"""
# pylint: disable=too-many-arguments
[docs] def printSpikes(self, filename, gather=True):
"""
.. warning::
Deprecated. Use `write_data(file, 'spikes')` instead.
.. note::
Method signature is the PyNN0.7 one
"""
if not gather:
warn_once(
logger, "sPyNNaker only supports gather=True. We will run "
"as if gather was set to True.")
logger.warning(
'printSpikes is deprecated. '
'Call transfered to write_data(file, "spikes", gatherer) instead.')
self.write_data(filename, 'spikes', gather=True)
[docs] def print_gsyn(self, filename, gather=True):
"""
.. warning::
Deprecated. Use `write_data(file, ['gsyn_exc', 'gsyn_inh'])`\
instead.
.. note::
Method signature is the PyNN0.7 one
"""
if not gather:
warn_once(
logger, "sPyNNaker only supports gather=True. We will run "
"as if gather was set to True.")
logger.warning(
'print_gsyn is deprecated. Call transfered to '
'write_data(file, ["gsyn_exc", "gsyn_inh"], gatherer) instead.')
self.write_data(filename, ['gsyn_exc', 'gsyn_inh'], gather=True)
[docs] def print_v(self, filename, gather=True):
"""
.. warning::
Deprecated. Use `write_data(file, 'v')` instead.
.. note::
Method signature is the PyNN0.7 one
"""
if not gather:
warn_once(
logger, "sPyNNaker only supports gather=True. We will run "
"as if gather was set to True.")
logger.warning(
'print_v is deprecated. '
'Call transfered to write_data(file, "v", gatherer) instead.')
self.write_data(filename, 'v', gather=True)
[docs] def receptor_types(self):
"""
.. note::
NO PyNN description of this method.
.. warning::
Currently unimplemented.
"""
_we_dont_do_this_now() # pragma: no cover
[docs] @abstractmethod
def record(self, variables, 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. 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: a file to automatically record to (optional).
`write_data()` will be automatically called when `end()` is called.
:type to_file: ~neo.io or ~neo.rawio or str
:param int sampling_interval: a value in milliseconds, and an integer
multiple of the simulation timestep.
"""
[docs] def record_gsyn(self, sampling_interval=1, to_file=None):
"""
.. warning::
Deprecated. Use `record(['gsyn_exc', 'gsyn_inh'])` instead.
.. note::
Method signature is the PyNN 0.7 one
with the extra non-PyNN `sampling_interval` and `indexes`
"""
logger.warning(
'record_gsyn is deprecated. Call transfered to '
'record(["gsyn_exc", "gsyn_inh"], tofile) instead.')
return self.record(
['gsyn_exc', 'gsyn_inh'], to_file=to_file,
sampling_interval=sampling_interval)
[docs] def record_v(self, sampling_interval=1, to_file=None):
"""
.. warning::
Deprecated. Use `record('v')` instead.
.. note::
Method signature is the PyNN 0.7 one\
with the extra non-PyNN `sampling_interval` and `indexes`
"""
logger.warning('record_v is deprecated. '
'Call transfered to record(["v"], .....) instead.')
return self.record(
'v', to_file=to_file,
sampling_interval=sampling_interval)
[docs] def rset(self, *args, **kwargs):
"""
.. warning::
Deprecated. Use `set(parametername=rand_distr)` instead.
"""
_this_is_wholly_deprecated(
" Use set(parametername=rand_distr) instead.", args, kwargs)
[docs] def save_positions(self, file): # pylint: disable=redefined-builtin
""" Save positions to file. The output format is index x y z
.. warning::
Currently unimplemented.
"""
# TODO:
_we_dont_do_this_now(file) # pragma: no cover
@property
def structure(self):
""" The spatial structure of the parent Population.
.. warning::
Currently unimplemented.
:rtype: ~pyNN.space.BaseStructure
"""
# TODO: support neuron positions and spaces
_we_dont_do_this_now() # pragma: no cover
[docs] def tset(self, **kwargs):
"""
.. warning::
Deprecated. Use `set(parametername=value_array)` instead.
"""
_this_is_wholly_deprecated(
"Use set(parametername=value_array) instead.", kwargs)