#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Copyright (C) 2012 Computational Neuroscience Group, NMBU.
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.
"""
import numpy as np
[docs]class PointProcess(object):
"""
Parent class of Synapse, StimIntElectrode. Created in order to import
and set some shared variables and extract Cartesian coordinates of segments
Parameters
----------
cell: obj
LFPy.Cell object
idx: int
index of segment
record_current: bool
Must be set to True for recording of pointprocess currents
record_potential: bool
Must be set to True for recording potential of pointprocess target idx
kwargs: pointprocess specific variables passed on to cell/neuron
See also
--------
Synapse
StimIntElectrode
"""
def __init__(
self,
cell,
idx,
record_current=False,
record_potential=False,
**kwargs):
self.idx = idx
self.record_current = record_current
self.record_potential = record_potential
self.kwargs = kwargs
self.update_pos(cell)
[docs] def update_pos(self, cell):
"""
Extract coordinates of point-process
"""
self.x = cell.x[self.idx].mean()
self.y = cell.y[self.idx].mean()
self.z = cell.z[self.idx].mean()
[docs]class Synapse(PointProcess):
"""
The synapse class, pointprocesses that spawn membrane currents.
See http://www.neuron.yale.edu/neuron/static/docs/help/neuron/neuron/\
mech.html#pointprocesses
for details, or corresponding mod-files.
This class is meant to be used with synaptic mechanisms, giving rise to
currents that will be part of the membrane currents at times governed
by the methods `set_spike_times` or `set_spike_times_w_netstim`.
Parameters
----------
cell: obj
`LFPy.Cell` or `LFPy.TemplateCell` instance to receive synapptic
input
idx: int
Cell index where the synaptic input arrives
syntype: str
Type of synapse, such as 'ExpSyn', 'Exp2Syn', 'AlphaSynapse'
record_current: bool
If True, record synapse to `<synapse>.i` in units of nA
**kwargs
Additional arguments to be passed on to
NEURON in `Cell.set_synapse`
Examples
--------
>>> import pylab as pl
>>> pl.interactive(1)
>>> import LFPy
>>> import os
>>> cellParameters = {
>>> 'morphology': os.path.join('examples', 'morphologies',
>>> 'L5_Mainen96_LFPy.hoc'),
>>> 'passive': True,
>>> 'tstop': 50,
>>> }
>>> cell = LFPy.Cell(**cellParameters)
>>> synapseParameters = {
>>> 'idx': cell.get_closest_idx(x=0, y=0, z=800),
>>> 'e': 0, # reversal potential
>>> 'syntype': 'ExpSyn', # synapse type
>>> 'tau': 2, # syn. time constant
>>> 'weight': 0.01, # syn. weight
>>> 'record_current': True # syn. current record
>>> }
>>> synapse = LFPy.Synapse(cell, **synapseParameters)
>>> synapse.set_spike_times(pl.array([10, 15, 20, 25]))
>>> cell.simulate()
>>> pl.subplot(211)
>>> pl.plot(cell.tvec, synapse.i)
>>> pl.title('Synapse current (nA)')
>>> pl.subplot(212)
>>> pl.plot(cell.tvec, cell.somav)
>>> pl.title('Somatic potential (mV)')
See also
--------
StimIntElectrode
"""
def __init__(self,
cell,
idx,
syntype,
record_current=False,
record_potential=False,
**kwargs):
super().__init__(cell=cell,
idx=idx,
record_current=record_current,
record_potential=record_potential,
**kwargs)
self.syntype = syntype
self.hocidx = int(cell.set_synapse(idx=idx, syntype=syntype,
record_current=record_current,
record_potential=record_potential,
**kwargs))
self._ns_index = int(cell._hoc_netstimlist.count()) - 1
cell.synapses.append(self)
cell.synidx.append(idx)
# needed by set_spike_times* methods:
self.cell = cell
def __del__(self):
"""Finalizer removing attributes which may contain hoc refs
"""
self.cell = None
[docs] def set_spike_times(self, sptimes=np.zeros(0)):
"""Set the spike times explicitly using numpy arrays
Parameters
----------
ndarray, dtype=float
Sequence of synapse activation times
"""
assert isinstance(sptimes, np.ndarray), \
'synapse activation times must be ndarray, not ({})'.format(
type(sptimes))
self.cell._sptimeslist[self._ns_index] = sptimes
[docs] def set_spike_times_w_netstim(self, noise=1., start=0., number=1E3,
interval=10., seed=1234.):
"""
Generate a train of pre-synaptic stimulus times by setting up the
neuron NetStim object associated with this synapse
Parameters
----------
noise: float in range [0, 1]
Fractional randomness, from deterministic to intervals that drawn
from negexp distribution (Poisson spiketimes).
start: float
ms, (most likely) start time of first spike
number: int
(average) number of spikes
interval: float
ms, (mean) time between spikes
seed: float
Random seed value
"""
self.cell._hoc_netstimlist[self._ns_index].noise = noise
self.cell._hoc_netstimlist[self._ns_index].start = start
self.cell._hoc_netstimlist[self._ns_index].number = number
self.cell._hoc_netstimlist[self._ns_index].interval = interval
self.cell._hoc_netstimlist[self._ns_index].seed(seed)
[docs] def collect_current(self, cell):
"""Collect synapse current. Sets ``<synapse>.i``
Parameters
----------
cell: LFPy.Cell like object
"""
try:
self.i = np.array(cell._hoc_synireclist.o(self.hocidx))
except BaseException:
raise Exception('cell.synireclist deleted from consequtive runs')
[docs] def collect_potential(self, cell):
"""Collect membrane potential of segment with synapse.
Sets ``<synapse>.v``
Parameters
----------
cell: LFPy.Cell like object
"""
try:
self.v = np.array(cell._hoc_synvreclist.o(self.hocidx))
except BaseException:
raise Exception('cell.synvreclist deleted from consequtive runs')
[docs]class StimIntElectrode(PointProcess):
"""Class for NEURON point processes representing electrode currents,
such as VClamp, SEClamp and ICLamp.
Membrane currents will no longer sum to zero if these mechanisms are used,
as the equivalent circuit is akin to a current input to the segment
from a far away extracellular location ("ground"), not immediately from
the surface to the inside of the segment as with transmembrane
currents.
Refer to NEURON documentation @ neuron.yale.edu for keyword arguments or
class documentation in Python issuing e.g.
help(neuron.h.VClamp)
Will insert pptype on cell-instance, pass the corresponding kwargs onto
cell.set_point_process.
Parameters
----------
cell: obj
`LFPy.Cell` or `LFPy.TemplateCell` instance to receive Stimulation
electrode input
idx: int
Cell segment index where the stimulation electrode is placed
pptype: str
Type of point process. Built-in examples: VClamp, SEClamp and ICLamp.
Defaults to 'SEClamp'.
record_current: bool
Decides if current is recorded
record_potential: bool
switch for recording the potential on postsynaptic segment index
**kwargs
Additional arguments to be passed on to
NEURON in `cell.set_point_process`
Examples
--------
>>> import pylab as pl
>>> pl.ion()
>>> import os
>>> import LFPy
>>> # define a list of different electrode implementations from NEURON
>>> pointprocesses = [
>>> {
>>> 'idx': 0,
>>> 'record_current': True,
>>> 'pptype': 'IClamp',
>>> 'amp': 1,
>>> 'dur': 20,
>>> 'delay': 10,
>>> },
>>> {
>>> 'idx': 0,
>>> 'record_current': True,
>>> 'pptype': 'VClamp',
>>> 'amp': [-70, 0, -70],
>>> 'dur': [10, 20, 10],
>>> },
>>> {
>>> 'idx': 0,
>>> 'record_current': True,
>>> 'pptype': 'SEClamp',
>>> 'dur1': 10,
>>> 'amp1': -70,
>>> 'dur2': 20,
>>> 'amp2': 0,
>>> 'dur3': 10,
>>> 'amp3': -70,
>>> },
>>> ]
>>> # create a cell instance for each electrode
>>> fix, axes = pl.subplots(2, 1, sharex=True)
>>> for pointprocess in pointprocesses:
>>> cell = LFPy.Cell(morphology=os.path.join('examples',
>>> 'morphologies',
>>> 'L5_Mainen96_LFPy.hoc'),
>>> passive=True)
>>> stimulus = LFPy.StimIntElectrode(cell, **pointprocess)
>>> cell.simulate()
>>> axes[0].plot(cell.tvec, stimulus.i, label=pointprocess['pptype'])
>>> axes[0].legend(loc='best')
>>> axes[0].set_title('Stimulus currents (nA)')
>>> axes[1].plot(cell.tvec, cell.somav, label=pointprocess['pptype'])
>>> axes[1].legend(loc='best')
>>> axes[1].set_title('Somatic potential (mV)')
See also
--------
Synapse
"""
def __init__(self, cell, idx, pptype='SEClamp',
record_current=False,
record_potential=False, **kwargs):
super().__init__(cell=cell, idx=idx,
record_current=record_current,
record_potential=record_potential)
self.pptype = pptype
self.hocidx = int(cell.set_point_process(
idx, pptype,
record_current=record_current,
record_potential=record_potential,
**kwargs))
cell.pointprocesses.append(self)
cell.pointprocess_idx.append(idx)
[docs] def collect_current(self, cell):
"""Fetch electrode current. Sets ``Sets ``<stimintelectrode>.i``
Parameters
----------
cell: LFPy.Cell like object
"""
self.i = np.array(cell._hoc_stimireclist.o(self.hocidx))
[docs] def collect_potential(self, cell):
"""Collect membrane potential of segment with PointProcess.
Sets ``<stimintelectrode>.v``
Parameters
----------
cell: LFPy.Cell like object
"""
self.v = np.array(cell._hoc_stimvreclist.o(self.hocidx))