/usr/share/pyshared/pyNN/brian/electrodes.py is in python-pynn 0.7.4-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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Current source classes for the brian module.
Classes:
DCSource -- a single pulse of current of constant amplitude.
StepCurrentSource -- a step-wise time-varying current.
:copyright: Copyright 2006-2011 by the PyNN team, see AUTHORS.
:license: CeCILL, see LICENSE for details.
$Id: electrodes.py 1117 2012-04-02 16:06:20Z apdavison $
"""
from brian import ms, nA, network_operation
import simulator
import numpy
current_sources = []
@network_operation(when='start')
def update_currents():
global current_sources
for current_source in current_sources:
current_source._update_current()
class CurrentSource(object):
"""Base class for a source of current to be injected into a neuron."""
def __init__(self):
global current_sources
self.cell_list = []
current_sources.append(self)
def inject_into(self, cell_list):
"""Inject this current source into some cells."""
for cell in cell_list:
if not cell.celltype.injectable:
raise TypeError("Can't inject current into a spike source.")
self.cell_list.extend(cell_list)
class StepCurrentSource(CurrentSource):
"""A step-wise time-varying current source."""
def __init__(self, times, amplitudes):
"""Construct the current source.
Arguments:
times -- list/array of times at which the injected current changes.
amplitudes -- list/array of current amplitudes to be injected at the
times specified in `times`.
The injected current will be zero up until the first time in `times`. The
current will continue at the final value in `amplitudes` until the end
of the simulation.
"""
CurrentSource.__init__(self)
assert len(times) == len(amplitudes), "times and amplitudes must be the same size (len(times)=%d, len(amplitudes)=%d" % (len(times), len(amplitudes))
self.times = times
self.amplitudes = numpy.array(amplitudes) * nA
self.i = 0
self.running = True
def _update_current(self):
"""
Check whether the current amplitude needs updating, and then do so if
needed.
This is called at every timestep.
"""
if self.running and simulator.state.t >= self.times[self.i]: #*ms:
for cell in self.cell_list:
index = cell.parent.id_to_index(cell)
cell.parent_group.i_inj[index] = self.amplitudes[self.i]
self.i += 1
if self.i >= len(self.times):
self.running = False
class DCSource(StepCurrentSource):
"""Source producing a single pulse of current of constant amplitude."""
def __init__(self, amplitude=1.0, start=0.0, stop=None):
"""Construct the current source.
Arguments:
start -- onset time of pulse in ms
stop -- end of pulse in ms
amplitude -- pulse amplitude in nA
"""
self.start = start
self.stop = stop
self.amplitude = amplitude
times = [0.0, start, (stop or 1e99)]
amplitudes = [0.0, amplitude, 0.0]
StepCurrentSource.__init__(self, times, amplitudes)
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