ASTIM_batch.py
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	#!/usr/bin/env python
	# -- coding: utf-8 --
	# @Author: Theo Lemaire
	# @Date: 2017-02-13 18:16:09
	# @Email: theo.lemaire@epfl.ch
	# @Last Modified by: Theo Lemaire
	# @Last Modified time: 2017-08-28 14:18:21

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

	import os
	import logging
	import numpy as np
	from PointNICE.solvers import checkBatchLog, runAStimBatch
	from PointNICE.channels import *
	from PointNICE.utils import load_BLS_params
	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)

	# BLS parameters
	bls_params = load_BLS_params()

	# Geometry of BLS structure
	a = 32e-9 # in-plane radius (m)
	d = 0.0e-6 # embedding tissue thickness (m)
	geom = {"a": a, "d": d}

	# Channels mechanisms
	neurons = [CorticalLTS()]

	# Stimulation parameters
	stim_params = {
	'freqs': [3.5e5], # Hz
	'amps': [150e3], # Pa
	'durations': [50e-3], # s
	'PRFs': [1e2], # Hz
	'DFs': [0.5]
	}
	stim_params['offsets'] = [30e-3] * len(stim_params['durations']) # s

	# Select output directory
	try:
	(batch_dir, log_filepath) = checkBatchLog('A-STIM')
	except AssertionError as err:
	logger.error(err)
	quit()

	# Run A-STIM batch
	pkl_filepaths = runAStimBatch(batch_dir, log_filepath, neurons, bls_params, geom, stim_params)
	pkl_dir, _ = os.path.split(pkl_filepaths[0])

	# Plot resulting profiles
	plotBatch(pkl_dir, pkl_filepaths)