parameters.py
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
# Memory Stimulation and Phase-Amplitude Coupling
# Copyright 2021 Nikolaos Vardlakis & Nicolas P. Rougier
# Released under the BSD 3-clauses license
# -----------------------------------------------------------------------------
import os
import json
import time
import subprocess
from numpy import pi
# Constants
noise_exc = 10e-06
noise_inh = 1e-06
# Default parameters
_data = {
"seed_val" : 42, # Reproducibility
# areas, tables 3.1-3.3, pages 45-48, Aussel
"areas": {
"EC" : {
"E" : {
"N" : int(10e3),
"type" : "PyCAN",
"noise" : noise_exc # Volts
},
"I" : {
"N" : int(1e3),
"type" : "Inh",
"noise" : noise_inh
}
},
"DG" : {
"E" : {
"N" : int(10e3),
"type" : "Py",
"noise" : noise_exc
},
"I" : {
"N" : int(0.1e3),
"type" : "Inh",
"noise" : noise_inh
}
},
"CA3" : {
"E" : {
"N" : int(1e3),
"type" : "PyCAN",
"noise" : noise_exc
},
"I" : {
"N" : int(0.1e3),
"type" : "Inh",
"noise" : noise_inh
}
},
"CA1" : {
"E" : {
"N" : int(10e3),
"type" : "PyCAN",
"noise" : noise_exc
},
"I" : {
"N" : int(1e3),
"type" : "Inh",
"noise" : noise_inh
}
}
},
# Kuramoto oscillator parameters
"Kuramoto" : {
"N" : 250,
"f0" : 6.,
"sigma" : 0.5, # normal std
"kN" : 15,
"gain_reset" : 4.0,
"gain_rhythm" : 1.0, # nA
"offset" : -0*pi/2
},
# connectivity parameters
"connectivity" : {
"intra" : { # intra-area conn. probabilities per area |
"EC" : [[0., 0.37], [0.54, 0.]], # [[E-E, E-I], [I-E, I-I]]
"DG" : [[0., 0.06], [0.14, 0.]],
"CA3" : [[0.56, 0.75], [0.75, 0.]],
"CA1" : [[0., 0.28], [0.3, 0.7]]
},
"inter" : { # inter-area conn. probabilities
"p_tri" : 0.45, # tri: [DG->CA3, CA3->CA1, CA1->EC] Aussel, pages 49,59
"p_mono" : 0.2 # mono: [EC->CA3, EC->CA1]
}
},
# synapses
# "synapses" : {
# "gmax_e" : 60., # pSiemens
# "gmax_i" : 600.
# },
# stimulation parameters
"stimulation" : {
"target" : "CA1", # target area [EC | DG | CA3 | CA1]
"coordinates" : (5.0, -8., 7.5), # point electrode coordinates (x,y,z) [mm]
"sigma" : 0.33, # conductivity of homogeneous conductive medium [S/m]
"duration" : 3., # [sec]
"dt" : .1e-3, # [sec]
"onset" : 1.615, # [sec]
"I" : [10.], # stimulation amplitude [nA]
"pulse_width" : [1.e-3], # width (in time) of pulse ON phase [sec]
"stim_freq" : 5, # stimulation frequency [Hz]
"pulse_freq" : 100, # pulse frequency, determines ON duration [Hz]
"nr_of_trains" : 1, # number of pulse trains
"nr_of_pulses" : 1, # number of pulses per train
"ipi" : .1e-3 # inter-pulse interval [sec]
},
# simulation parameters
"simulation" : {
"duration" : 3.0, # second
"dt" : .1e-3, # second
"debugging" : False
},
# git stuff
"timestamp" : None,
"git_branch" : None,
"git_hash" : None,
"git_short_hash" : None
}
def is_git_repo():
""" Return whether current directory is a git directory """
if subprocess.call(["git", "branch"],
stderr=subprocess.STDOUT, stdout=open(os.devnull, 'w')) != 0:
return False
return True
def get_git_revision_hash():
""" Get current git hash """
if is_git_repo():
answer = subprocess.check_output(
['git', 'rev-parse', 'HEAD'])
return answer.decode("utf8").strip("\n")
return "None"
def get_git_revision_short_hash():
""" Get current git short hash """
if is_git_repo():
answer = subprocess.check_output(
['git', 'rev-parse', '--short', 'HEAD'])
return answer.decode("utf8").strip("\n")
return "None"
def get_git_revision_branch():
""" Get current git branch """
if is_git_repo():
answer = subprocess.check_output(
['git', 'rev-parse', '--abbrev-ref', 'HEAD'])
return answer.decode("utf8").strip("\n")
return "None"
def default():
""" Get default parameters """
_data["timestamp"] = time.ctime()
_data["git_branch"] = get_git_revision_branch()
_data["git_hash"] = get_git_revision_hash()
_data["git_short_hash"] = get_git_revision_short_hash()
return _data
def save(filename, data=None):
""" Save parameters into a json file """
if data is None:
data = { name : eval(name) for name in _data.keys()
if name not in ["timestamp", "git_branch", "git_hash"] }
data["timestamp"] = time.ctime()
data["git_branch"] = get_git_revision_branch()
data["git_hash"] = get_git_revision_hash()
data["git_short_hash"] = get_git_revision_short_hash()
with open(filename, "w") as outfile:
json.dump(data, outfile, indent=4, sort_keys=False)
def load(filename):
""" Load parameters from a json file """
with open(filename) as infile:
data = json.load(infile)
return data
def dump(data):
if not _data["timestamp"]:
_data["timestamp"] = time.ctime()
if not _data["git_branch"]:
_data["git_branch"] = get_git_revision_branch()
if not _data["git_hash"]:
_data["git_hash"] = get_git_revision_hash()
_data["git_short_hash"] = get_git_revision_short_hash()
for key, value in data.items():
print(f"{key:15s} : {value}")
# -----------------------------------------------------------------------------
if __name__ == "__main__":
import argparse
parser = argparse.ArgumentParser(
description='Generate parameters file using JSON format')
parser.add_argument('parameters_file',
default='default',
type=str, nargs='?',
help='Parameters file (json format)')
args = parser.parse_args()
filename = "./configs/{0}.json".format(args.parameters_file)
print('Saving file "{0}"'.format(filename))
save(filename, _data)
print('..:: Unit Testing ::..')
print('----------------------------------')
data = load(filename)
dump(data)
print('----------------------------------')
locals().update(data)
print('Saving file "{0}"'.format(filename))
save(filename)
