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R4670/sim/ESTIM_batch.py
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ESTIM_batch.py
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# -*- coding: utf-8 -*-
# @Author: Theo Lemaire
# @Date: 2017-08-24 11:55:07
# @Last Modified by: Theo Lemaire
# @Last Modified time: 2017-08-25 14:48:58
""" Run batch electrical simulations of specific "point-neuron" models. """
import os
import logging
from PointNICE.solvers import checkBatchLog, runEStimBatch
from PointNICE.channels import *
from PointNICE.plt import plotBatch
# Set logging options
logging.basicConfig(format='%(asctime)s %(message)s', datefmt='%d/%m/%Y %H:%M:%S:')
logger = logging.getLogger('PointNICE')
logger.setLevel(logging.DEBUG)
# Channels mechanisms
neurons = [LeechTouch()]
# Stimulation parameters
stim_params = {
'amps': [20.0], # mA/m2
'durations': [0.5], # s
'PRFs': [1e2], # Hz
'DFs': [1.0]
}
stim_params['offsets'] = [1.0] * len(stim_params['durations']) # s
# Select output directory
try:
(batch_dir, log_filepath) = checkBatchLog('E-STIM')
except AssertionError as err:
logger.error(err)
quit()
# Run E-STIM batch
pkl_filepaths = runEStimBatch(batch_dir, log_filepath, neurons, stim_params)
pkl_dir, _ = os.path.split(pkl_filepaths[0])
vars_RS_FS = {
'V_m': ['Vm'],
'i_{Na}\ kin.': ['m', 'h'],
'i_L\ kin.': ['n'],
'i_M\ kin.': ['p'],
'I': ['iNa', 'iK', 'iM', 'iL', 'iNet']
}
vars_LTS = {
'V_m': ['Vm'],
'i_{Na}\ kin.': ['m', 'h'],
'i_K\ kin.': ['n'],
'i_M\ kin.': ['p'],
'i_T\ kin.': ['s', 'u'],
'I': ['iNa', 'iK', 'iM', 'iT', 'iL', 'iNet']
}
vars_RE = {
'V_m': ['Vm'],
'i_{Na}\ kin.': ['m', 'h'],
'i_K\ kin.': ['n'],
'i_{TS}\ kin.': ['s', 'u'],
'I': ['iNa', 'iK', 'iTs', 'iL', 'iNet']
}
vars_TC = {
'V_m': ['Vm'],
'i_{Na}\ kin.': ['m', 'h'],
'i_K\ kin.': ['n'],
'i_{T}\ kin.': ['s', 'u'],
'i_{H}\ kin.': ['O', 'OL', 'O + 2OL'],
'I': ['iNa', 'iK', 'iT', 'iH', 'iKL', 'iL', 'iNet']
}
vars_LeechT = {
'V_m': ['Vm'],
'i_{Na}\ kin.': ['m', 'h'],
'i_K\ kin.': ['n'],
'i_{Ca}\ kin.': ['s'],
'pools': ['C_Na_arb', 'C_Na_arb_activation', 'C_Ca_arb', 'C_Ca_arb_activation'],
'I': ['iNa', 'iK', 'iCa', 'iKCa', 'iPumpNa', 'iL', 'iNet']
}
plotBatch(vars_LeechT, pkl_dir, pkl_filepaths, lw=2)
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