def load_config(config):
if isinstance(config, string_types):
return ConfigDict.from_json(config)
elif isinstance(config, dict):
return ConfigDict.from_dict(config)
else:
raise Exception('Could not convert {} (type "{}") to json.'.format(config, type(config)))
def load_spikes_file(config_file=None, spikes_file=None):
if spikes_file is not None:
return SpikeTrains.load(spikes_file)
elif config_file is not None:
config = ConfigDict.from_json(config_file)
return SpikeTrains.load(config.spikes_file)
def from_config(cls, conf, **properties):
"""Generates a graph structure from a json config file or dictionary.
:param conf: name of json config file, or a dictionary with config parameters
:param properties: optional properties.
:return: A graph object of type cls
"""
network = cls(**properties)
# The simulation run script should create a config-dict since it's likely to vary based on the simulator engine,
# however in the case the user doesn't we will try a generic conversion from dict/json to ConfigDict
if isinstance(conf, ConfigDict):
config = conf
else:
try:
config = ConfigDict.load(conf)
except Exception as e:
network.io.log_exception('Could not convert {} (type "{}") to json.'.format(conf, type(conf)))
if not config.with_networks:
network.io.log_exception('Could not find any network files. Unable to build network.')
# TODO: These are simulator specific
network.spike_threshold = config.spike_threshold
network.dL = config.dL
# load components
for name, value in config.components.items():
network.add_component(name, value)
# load nodes
gid_map = config.gid_mappings
node_adaptor = network.get_node_adaptor('sonata')
for node_dict in config.nodes:
nodes = sonata_reader.load_nodes(node_dict['nodes_file'], node_dict['node_types_file'], gid_map,
adaptor=node_adaptor)
for node_pop in nodes:
network.add_nodes(node_pop)
# TODO: Raise a warning if more than one internal population and no gids (node_id collision)
# load edges
edge_adaptor = network.get_edge_adaptor('sonata')
for edge_dict in config.edges:
if not edge_dict.get('enabled', True):
continue
edges = sonata_reader.load_edges(edge_dict['edges_file'], edge_dict['edge_types_file'],
adaptor=edge_adaptor)
for edge_pop in edges:
network.add_edges(edge_pop)
# Add nodeset section
network.add_node_set('all', NodeSetAll(network))
for ns_name, ns_filter in config.node_sets.items():
network.add_node_set(ns_name, NodeSet(ns_filter, network))
return network
def load_reports(config_file):
cfg = ConfigDict.from_json(config_file)
reports = []
for report_name, report in cfg.reports.items():
if report['module'] not in ['membrane_report', 'multimeter_report']:
continue
report_file = report[
'file_name'] if 'file_name' in report else '{}.h5'.format(
report_name)
report_file = report_file if os.path.isabs(
report_file) else os.path.join(cfg.output_dir, report_file)
reports.append(CompartmentReport(report_file, 'r'))
return reports