import logging
from . import env_builder
logger = logging.getLogger(__name__)
environment_builders = {
'bionet': env_builder.BioNetEnvBuilder,
'biophysical': env_builder.BioNetEnvBuilder,
'bio': env_builder.BioNetEnvBuilder,
'pointnet': env_builder.PointNetEnvBuilder,
'point': env_builder.PointNetEnvBuilder,
'filternet': env_builder.FilterNetEnvBuilder,
'filter': env_builder.FilterNetEnvBuilder,
'popnet': env_builder.PopNetEnvBuilder,
'pop': env_builder.PopNetEnvBuilder
}
[docs]def create_environment(simulator,
base_dir='.',
network_dir=None,
components_dir=None,
node_sets_file=None,
output_dir=None,
overwrite=False,
run_script=True,
config_file=None,
config_name=None,
split_configs=False,
network_filter=None,
report_vars=[],
report_nodes=None,
spikes_inputs=None,
rates_inputs=None,
clamp_reports=[],
current_clamp=None,
file_current_clamp=None,
se_voltage_clamp=None,
tstart=0.0,
tstop=1000.0,
dt=0.001,
dL=20.0,
spikes_threshold=-15.0,
nsteps_block=5000,
v_init=-80.0,
celsius=34.0,
compile_mechanisms=False,
use_relative_paths=True,
include_examples=False
):
"""
:param simulator:
:param base_dir:
:param network_dir:
:param components_dir:
:param node_sets_file:
:param output_dir:
:param overwrite:
:param run_script:
:param config_file:
:param config_name:
:param split_configs:
:param network_filter:
:param report_vars:
:param report_nodes:
:param spikes_inputs:
:param rates_inputs:
:param clamp_reports:
:param current_clamp:
:param file_current_clamp:
:param se_voltage_clamp:
:param tstart:
:param tstop:
:param dt:
:param dL:
:param spikes_threshold:
:param nstesp_block:
:param v_init:
:param celsius:
:param compile_mechanisms:
:param use_relative_paths:
:param include_examples:
"""
simulator_name = simulator.lower()
if simulator_name not in environment_builders.keys():
logging.error('Could not find bmtk simulator {}; available options: {}'.format(
simulator_name, list(environment_builders.keys())
))
build_cls = environment_builders[simulator_name]
env_builder = build_cls(
base_dir=base_dir,
network_dir=network_dir,
components_dir=components_dir,
output_dir=output_dir,
node_sets_file=node_sets_file
)
env_builder.build(
include_examples=include_examples,
use_relative_paths=use_relative_paths,
report_vars=report_vars,
report_nodes=report_nodes,
clamp_reports=clamp_reports,
current_clamp=current_clamp,
file_current_clamp=file_current_clamp,
se_voltage_clamp=se_voltage_clamp,
spikes_inputs=spikes_inputs,
rates_inputs=rates_inputs,
tstart=tstart,
tstop=tstop,
dt=dt,
dL=dL,
spikes_threshold=spikes_threshold,
nsteps_block=nsteps_block,
v_init=v_init,
celsius=celsius,
config_file=config_file,
overwrite_config=overwrite,
config_name=config_name,
split_configs=split_configs,
network_filter=network_filter,
run_script=run_script
)
if compile_mechanisms:
env_builder.compile_mechanisms()
