ASTIM_titration_batch.py
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ASTIM_titration_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: 2017-08-22 17:15:29

			""" Run batch parameter titrations of the NICE model. """

			import logging
			import numpy as np
			from PointNICE.solvers import runTitrationBatch
			from PointNICE.channels import *
			from PointNICE.utils import LoadParams, CheckBatchLog

			# 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 = LoadParams()

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

			# Channels mechanisms
			neurons = [CorticalRS()]

			# Stimulation parameters
			stim_params = {
			'freqs': [3.5e5], # Hz
			# 'amps': [100e3], # Pa
			'durations': [50e-3], # s
			'PRFs': [1e2], # Hz
			'DFs': [1.0]
			}

			# Select output directory
			try:
			(batch_dir, log_filepath) = CheckBatchLog('elec')
			except AssertionError as err:
			logger.error(err)
			quit()

			# Run titration batch
			runTitrationBatch(batch_dir, log_filepath, neurons, bls_params, geom, stim_params)