#!/usr/bin/env python
"""Python script to run cell model"""
"""
/* Copyright (c) 2015 EPFL-BBP, All rights reserved.
THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
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BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN
IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
This work is licensed under a
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
To view a copy of this license, visit
http://creativecommons.org/licenses/by-nc-sa/4.0/legalcode or send a letter to
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"""
"""
* @file run.py
* @brief Run simulation using pyneuron
* @author Werner Van Geit @ BBP
* @date 2015
"""
# pylint: disable=C0325, W0212, F0401, W0612, F0401
import os
import neuron
import numpy
import sys
def create_cell(add_synapses=True):
"""Create the cell model"""
# Load morphology
neuron.h.load_file("morphology.hoc")
# Load biophysics
neuron.h.load_file("biophysics.hoc")
# Load main cell template
neuron.h.load_file("template.hoc")
# Instantiate the cell from the template
print("Loading cell bNAC219_L1_NGCDA_b030a58a66")
cell = neuron.h.bNAC219_L1_NGCDA_b030a58a66(1 if add_synapses else 0)
return cell
def create_stimuli(cell, step_number):
"""Create the stimuli"""
print('Attaching stimulus electrodes')
stimuli = []
step_amp = [0] * 3
with open('current_amps.dat', 'r') as current_amps_file:
first_line = current_amps_file.read().split('\n')[0].strip()
hyp_amp, step_amp[0], step_amp[1], step_amp[2] = first_line.split(' ')
iclamp = neuron.h.IClamp(0.5, sec=cell.soma[0])
iclamp.delay = 700
iclamp.dur = 2000
iclamp.amp = float(step_amp[step_number - 1])
print('Setting up step current clamp: '
'amp=%f nA, delay=%f ms, duration=%f ms' %
(iclamp.amp, iclamp.delay, iclamp.dur))
stimuli.append(iclamp)
hyp_iclamp = neuron.h.IClamp(0.5, sec=cell.soma[0])
hyp_iclamp.delay = 0
hyp_iclamp.dur = 3000
hyp_iclamp.amp = float(hyp_amp)
print('Setting up hypamp current clamp: '
'amp=%f nA, delay=%f ms, duration=%f ms' %
(hyp_iclamp.amp, hyp_iclamp.delay, hyp_iclamp.dur))
stimuli.append(hyp_iclamp)
return stimuli
def create_recordings(cell):
"""Create the recordings"""
print('Attaching recording electrodes')
recordings = {}
recordings['time'] = neuron.h.Vector()
recordings['soma(0.5)'] = neuron.h.Vector()
recordings['time'].record(neuron.h._ref_t, 0.1)
recordings['soma(0.5)'].record(cell.soma[0](0.5)._ref_v, 0.1)
return recordings
def run_step(step_number, plot_traces=None):
"""Run step current simulation with index step_number"""
cell = create_cell(add_synapses=False)
stimuli = create_stimuli(cell, step_number)
recordings = create_recordings(cell)
# Overriding default 30s simulation,
print('Setting simulation time to 3s for the step currents')
neuron.h.tstop = 3000
print('Disabling variable timestep integration')
neuron.h.cvode_active(0)
print('Running for %f ms' % neuron.h.tstop)
neuron.h.run()
time = numpy.array(recordings['time'])
soma_voltage = numpy.array(recordings['soma(0.5)'])
recordings_dir = 'python_recordings'
soma_voltage_filename = os.path.join(
recordings_dir,
'soma_voltage_step%d.dat' % step_number)
numpy.savetxt(
soma_voltage_filename,
numpy.transpose(
numpy.vstack((
time,
soma_voltage))))
print('Soma voltage for step %d saved to: %s'
% (step_number, soma_voltage_filename))
if plot_traces:
import pylab
pylab.figure()
pylab.plot(recordings['time'], recordings['soma(0.5)'])
pylab.xlabel('time (ms)')
pylab.ylabel('Vm (mV)')
pylab.gcf().canvas.set_window_title('Step %d' % step_number)
def init_simulation():
"""Initialise simulation environment"""
neuron.h.load_file("stdrun.hoc")
neuron.h.load_file("import3d.hoc")
print('Loading constants')
neuron.h.load_file('constants.hoc')
def main(plot_traces=True):
"""Main"""
# Import matplotlib to plot the traces
if plot_traces:
import matplotlib
matplotlib.rcParams['path.simplify'] = False
init_simulation()
for step_number in range(1, 4):
run_step(step_number, plot_traces=plot_traces)
if plot_traces:
import pylab
pylab.show()
if __name__ == '__main__':
if len(sys.argv) == 1:
main(plot_traces=True)
elif len(sys.argv) == 2 and sys.argv[1] == '--no-plots':
main(plot_traces=False)
else:
raise Exception(
"Script only accepts one argument: --no-plots, not %s" %
str(sys.argv))