ASTIM_batch.py
c61b8e3492f6master

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)