batch_ESTIM.py
b8be2280d700master

batch_ESTIM.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: 2018-07-04 11:44:11

			""" Run batch electrical simulations of specific "point-neuron" models. """

			import sys
			import os
			import logging
			import numpy as np
			from PointNICE.utils import logger, InputError
			from PointNICE.solvers import setBatchDir, checkBatchLog, runEStimBatch
			from PointNICE.plt import plotBatch

			# Set logging level
			logger.setLevel(logging.INFO)

			# Neurons
			neurons = ['RS']

			# Stimulation parameters
			stim_params = {
			'amps': [10.0], # mA/m2
			'durations': [300e-3], # np.array([20, 40, 60, 80, 100, 150, 200, 250, 300]) * 1e-3, # s
			'PRFs': [1e2], # np.array([0.1, 0.2, 0.5, 1.0, 2.0, 5.0, 10.0]) * 1e3, # Hz
			'DCs': [0.9], # np.array([1, 2, 5, 10, 25, 50, 75, 100]) * 1e-2
			'offsets': [100e-3]
			}
			# stim_params['offsets'] = 350e-3 - stim_params['durations'] # s


			try:
			# Select output directory
			batch_dir = setBatchDir()
			log_filepath, _ = checkBatchLog(batch_dir, 'E-STIM')

			# Run E-STIM batch
			pkl_filepaths = runEStimBatch(batch_dir, log_filepath, neurons, stim_params)
			pkl_dir, _ = os.path.split(pkl_filepaths[0])

			# Plot resulting profiles
			yvars = {'Q_m': ['Qm']}
			plotBatch(pkl_dir, pkl_filepaths, yvars)

			except InputError as err:
			logger.error(err)
			sys.exit(1)