ASTIM_lookups.py
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ASTIM_lookups.py
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			#!/usr/bin/env python
			# -- coding: utf-8 --
			# @Author: Theo Lemaire
			# @Date: 2017-06-02 17:50:10
			# @Email: theo.lemaire@epfl.ch
			# @Last Modified by: Theo Lemaire
			# @Last Modified time: 2017-08-28 14:18:17

			""" Create lookup tables for different acoustic frequencies. """

			import logging
			import numpy as np

			import PointNICE
			from PointNICE.utils import load_BLS_params
			from PointNICE.channels import *

			# 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
			params = load_BLS_params()

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

			# Channel mechanisms
			neurons = [ThalamoCortical()]

			# Stimulation parameters
			freqs = [690e3] # Hz
			amps = np.logspace(np.log10(0.1), np.log10(600), num=50) * 1e3 # Pa
			amps = np.insert(amps, 0, 0.0) # adding amplitude 0

			logger.info('Starting batch lookup creation')

			for ch_mech in neurons:
			# Create a SolverUS instance (with dummy frequency parameter)
			solver = PointNICE.SolverUS(geom, params, ch_mech, 0.0)
			charges = np.arange(np.round(ch_mech.Vm0 - 10.0), 50.0 + 1.0, 1.0) * 1e-5 # C/m2

			# Create lookups for each frequency
			for Fdrive in freqs:
			solver.createLookup(ch_mech, Fdrive, amps, charges)

			logger.info('Lookup tables successfully created')