"""Run simple cell optimisation"""

"""

Copyright (c) 2016, EPFL/Blue Brain Project

This file is part of BluePyOpt <https://github.com/BlueBrain/BluePyOpt>

This library is free software; you can redistribute it and/or modify it under

the terms of the GNU Lesser General Public License version 3.0 as published

by the Free Software Foundation.

This library is distributed in the hope that it will be useful, but WITHOUT

ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS

FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more

details.

You should have received a copy of the GNU Lesser General Public License

along with this library; if not, write to the Free Software Foundation, Inc.,

51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.

"""

# pylint: disable=R0914

import os

import json

import bluepyopt.ephys as ephys

script_dir = os.path.dirname(__file__)

config_dir = os.path.join(script_dir, 'config')

# TODO store definition dicts in json

# TODO rename 'score' into 'objective'

# TODO add functionality to read settings of every object from config format

def define_mechanisms():

"""Define mechanisms"""

mech_definitions = json.load(

open(

os.path.join(

config_dir,

'mechanisms.json')))

mechanisms = []

for sectionlist, channels in mech_definitions.iteritems():

seclist_loc = ephys.locations.NrnSeclistLocation(

sectionlist,

seclist_name=sectionlist)

for channel in channels:

mechanisms.append(ephys.mechanisms.NrnMODMechanism(

name='%s.%s' % (channel, sectionlist),

mod_path=None,

prefix=channel,

locations=[seclist_loc],

preloaded=True))

return mechanisms

def define_parameters():

"""Define parameters"""

param_configs = json.load(open(os.path.join(config_dir, 'parameters.json')))

parameters = []

for param_config in param_configs:

if 'value' in param_config:

frozen = True

value = param_config['value']

bounds = None

elif 'bounds':

frozen = False

bounds = param_config['bounds']

value = None

else:

raise Exception(

'Parameter config has to have bounds or value: %s'

% param_config)

if param_config['type'] == 'global':

parameters.append(

ephys.parameters.NrnGlobalParameter(

name=param_config['param_name'],

param_name=param_config['param_name'],

frozen=frozen,

bounds=bounds,

value=value))

elif param_config['type'] in ['section', 'range']:

if param_config['dist_type'] == 'uniform':

scaler = ephys.parameterscalers.NrnSegmentLinearScaler()

elif param_config['dist_type'] == 'exp':

scaler = ephys.parameterscalers.NrnSegmentSomaDistanceScaler(

distribution=param_config['dist'])

seclist_loc = ephys.locations.NrnSeclistLocation(

param_config['sectionlist'],

seclist_name=param_config['sectionlist'])

name = '%s.%s' % (param_config['param_name'],

param_config['sectionlist'])

if param_config['type'] == 'section':

parameters.append(

ephys.parameters.NrnSectionParameter(

name=name,

param_name=param_config['param_name'],

value_scaler=scaler,

value=value,

frozen=frozen,

bounds=bounds,

locations=[seclist_loc]))

elif param_config['type'] == 'range':

parameters.append(

ephys.parameters.NrnRangeParameter(

name=name,

param_name=param_config['param_name'],

value_scaler=scaler,

value=value,

frozen=frozen,

bounds=bounds,

locations=[seclist_loc]))

else:

raise Exception(

'Param config type has to be global, section or range: %s' %

param_config)

return parameters

# def define_morphology():

# """Define morphology"""

# return ephys.morphologies.NrnFileMorphology(

# os.path.join(

# script_dir,

# 'morphology/C060114A7.asc'),

# do_replace_axon=True)

def create():

"""Create cell model"""

cell = ephys.models.CellModel(

'abi_cell',

morph=define_morphology(),

mechs=define_mechanisms(),

params=define_parameters())

return cell