examples/l5pc/l5pc_evaluator.py
"""Run simple cell optimisation"""
"""
Copyright (c) 2016-2020, 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 l5pc_model # NOQA
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_protocols(do_replace_axon=True, sim='nrn'):
"""Define protocols"""
protocol_definitions = load_protocols()
return create_protocols(protocol_definitions, do_replace_axon, sim=sim)
def load_protocols():
return json.load(
open(
os.path.join(
config_dir,
'protocols.json')))
def create_protocols(protocol_definitions, do_replace_axon=None, sim='nrn'):
protocols = {}
if sim == 'nrn':
soma_loc = ephys.locations.NrnSeclistCompLocation(
name='soma',
seclist_name='somatic',
sec_index=0,
comp_x=0.5)
elif sim == 'arb':
soma_loc = ephys.locations.ArbBranchRelLocation(
name='soma',
branch=0,
pos=0.5)
else:
raise ValueError('Simulator must be either nrn or arb, not %s' % sim)
for protocol_name, protocol_definition in protocol_definitions.items():
# By default include somatic recording
somav_recording = ephys.recordings.CompRecording(
name='%s.soma.v' %
protocol_name,
location=soma_loc,
variable='v')
recordings = [somav_recording]
if 'extra_recordings' in protocol_definition:
for recording_definition in protocol_definition['extra_recordings']:
if recording_definition['type'] == 'somadistance':
if sim == 'nrn':
location = ephys.locations.NrnSomaDistanceCompLocation(
name=recording_definition['name'],
soma_distance=recording_definition['somadistance'],
seclist_name=recording_definition['seclist_name'])
else:
# L5PC has disconnected topology
location = ephys.locations.ArbLocsetLocation(
name=recording_definition['name'],
locset='(restrict (distal-translate (proximal %s) %s) (proximal-interval (distal (branch %s))))' %
(ephys.morphologies.ArbFileMorphology.region_labels[recording_definition['seclist_name']].ref,
recording_definition['somadistance'],
recording_definition['arbor_branch_index_with_replaced_axon'] if do_replace_axon else
recording_definition['arbor_branch_index']))
var = recording_definition['var']
recording = ephys.recordings.CompRecording(
name='%s.%s.%s' % (protocol_name, location.name, var),
location=location,
variable=recording_definition['var'])
recordings.append(recording)
else:
raise Exception(
'Recording type %s not supported' %
recording_definition['type'])
stimuli = []
for stimulus_definition in protocol_definition['stimuli']:
stimuli.append(ephys.stimuli.NrnSquarePulse(
step_amplitude=stimulus_definition['amp'],
step_delay=stimulus_definition['delay'],
step_duration=stimulus_definition['duration'],
location=soma_loc,
total_duration=stimulus_definition['totduration']))
if sim == 'nrn':
protocols[protocol_name] = ephys.protocols.SweepProtocol(
protocol_name,
stimuli,
recordings)
else:
protocols[protocol_name] = ephys.protocols.ArbSweepProtocol(
protocol_name,
stimuli,
recordings)
return protocols
def define_fitness_calculator(protocols):
"""Define fitness calculator"""
feature_definitions = json.load(
open(
os.path.join(
config_dir,
'features.json')))
# TODO: add bAP stimulus
objectives = []
for protocol_name, locations in feature_definitions.items():
for location, features in locations.items():
for efel_feature_name, meanstd in features.items():
feature_name = '%s.%s.%s' % (
protocol_name, location, efel_feature_name)
recording_names = {'': '%s.%s.v' % (protocol_name, location)}
stimulus = protocols[protocol_name].stimuli[0]
stim_start = stimulus.step_delay
if location == 'soma':
threshold = -20
elif 'dend' in location:
threshold = -55
if protocol_name == 'bAP':
stim_end = stimulus.total_duration
else:
stim_end = stimulus.step_delay + stimulus.step_duration
feature = ephys.efeatures.eFELFeature(
feature_name,
efel_feature_name=efel_feature_name,
recording_names=recording_names,
stim_start=stim_start,
stim_end=stim_end,
exp_mean=meanstd[0],
exp_std=meanstd[1],
threshold=threshold)
objective = ephys.objectives.SingletonObjective(
feature_name,
feature)
objectives.append(objective)
fitcalc = ephys.objectivescalculators.ObjectivesCalculator(objectives)
return fitcalc
def create(do_replace_axon=True, sim='nrn'):
"""Setup"""
l5pc_cell = l5pc_model.create(do_replace_axon=do_replace_axon)
fitness_protocols = define_protocols(
do_replace_axon=do_replace_axon, sim=sim)
fitness_calculator = define_fitness_calculator(fitness_protocols)
param_names = [param.name
for param in l5pc_cell.params.values()
if not param.frozen]
if sim == 'nrn':
simulator = ephys.simulators.NrnSimulator()
elif sim == 'arb':
simulator = ephys.simulators.ArbSimulator()
if do_replace_axon:
nrn_sim = ephys.simulators.NrnSimulator()
l5pc_cell.instantiate_morphology_3d(nrn_sim)
else:
raise ValueError('Simulator must be either \'nrn\' or \'arb\'.')
return ephys.evaluators.CellEvaluator(
cell_model=l5pc_cell,
param_names=param_names,
fitness_protocols=fitness_protocols,
fitness_calculator=fitness_calculator,
sim=simulator)