"""Analyse scores"""
"""
Copyright (c) 2018, EPFL/Blue Brain Project
This file is part of BluePyMM <https://github.com/BlueBrain/BluePyMM>
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, C0325, W0640
# pylama: ignore=E402
import os
from bluepymm import tools
from . import sqlite_io, reporting, megate_output
from . import process_megate_config as proc_config
[docs]
def select_combos(conf_filename, n_processes):
"""Parse conf file and run select combos"""
# Parse configuration file
conf_dict = tools.load_json(conf_filename)
select_combos_from_conf(conf_dict, n_processes)
[docs]
def select_combos_from_conf(conf_dict, n_processes=None):
"""Compare scores of me-combinations to thresholds, select successful
combinations, and write results out to file.
Args:
conf_filename: filename of configuration (.json file)
n_processes: integer number of processes, `None` will use all of them
"""
scores_db_filename = conf_dict['scores_db']
pdf_filename = conf_dict['pdf_filename']
output_dir = conf_dict['output_dir']
print('Reading configuration files')
# read skip features
to_skip_patterns, to_skip_features = \
proc_config.read_to_skip_features(
conf_dict)
# read megate thresholds
megate_patterns, megate_thresholds = \
proc_config.read_megate_thresholds(
conf_dict)
select_perc_best = conf_dict.get('select_perc_best', None)
print('Reading tables from sqlite')
# read score tables
scores, score_values = sqlite_io.read_and_process_sqlite_score_tables(
scores_db_filename)
print('Checking if all combos have run')
tools.check_all_combos_have_run(scores, scores_db_filename)
print('Start creation of ext_neurondb')
# create final database and write report
ext_neurondb = \
reporting.create_final_db_and_write_report(
pdf_filename,
to_skip_features,
to_skip_patterns,
megate_thresholds,
megate_patterns,
conf_dict.get('skip_repaired_exemplar', False),
conf_dict.get('check_opt_scores', True),
scores, score_values,
conf_dict.get('plot_emodels_per_morphology', False),
output_dir,
select_perc_best,
n_processes=n_processes)
print('Wrote pdf to %s' % os.path.abspath(pdf_filename))
# write output files
compliant = conf_dict.get('make_names_neuron_compliant', False)
extneurondb_path, mecombo_emodel_path = \
megate_output.save_megate_results(
ext_neurondb,
output_dir,
sort_key='combo_name',
make_names_neuron_compliant=compliant)
emodels_hoc_path = conf_dict['emodels_hoc_dir']
megate_output.write_mecomboreleasejson(
output_dir,
emodels_hoc_path,
extneurondb_path,
mecombo_emodel_path)
[docs]
def add_parser(action):
"""Add parser"""
parser = action.add_parser('select',
help='Select feasible me-combinations')
parser.add_argument('conf_filename')
parser.add_argument('--n_processes', help='number of processes',
type=int)