def plot_potential(cell_vars_h5=None,
config_file=None,
gids=None,
show_plot=True,
save=False):
if (cell_vars_h5 or config_file) is None:
raise Exception(
'Please specify a cell_vars hdf5 file or a simulation config.')
if cell_vars_h5 is not None:
plot_potential_hdf5(cell_vars_h5,
show_plot,
save_as='sim_potential.jpg' if save else None)
else:
# load the json file or object
if isinstance(config_file, basestring):
config = cfg.from_json(config_file)
elif isinstance(config_file, dict):
config = config_file
else:
raise Exception('Could not convert {} (type "{}") to json.'.format(
config_file, type(config_file)))
gid_list = gids or config['node_id_selections']['save_cell_vars']
for gid in gid_list:
save_as = '{}_v.jpg'.format(gid) if save else None
title = 'cell gid {}'.format(gid)
var_h5 = os.path.join(config['output']['cell_vars_dir'],
'{}.h5'.format(gid))
plot_potential_hdf5(var_h5, title, show_plot, save_as)
def test_load_simulator_config():
cfg_full_path = config_path('files/simulator_config.json')
config = cfg.from_json(cfg_full_path)
manifest = config['manifest']
assert ('run' in config)
assert (config['output']['log'] == os.path.join(manifest['$OUTPUT_DIR'],
'log.txt'))
def _get_config(config):
if isinstance(config, basestring):
return cfg.from_json(config)
elif isinstance(config, dict):
return config
else:
raise Exception('Could not convert {} (type "{}") to json.'.format(config, type(config)))
def test_load_parent_config():
"""Test a parent config file can pull in children configs"""
cfg_full_path = config_path('files/config.json')
config = cfg.from_json(cfg_full_path)
assert (config['config_path'] == cfg_full_path)
assert ('components' in config)
assert ('networks' in config)
assert ('run' in config)
def main(config_file):
configure = config.from_json(config_file)
graph = PopGraph.from_config(config_file,
network_format=TabularNetwork_AI,
property_schema=AIPropertySchema,
group_by='ei')
net = PopNetwork.from_config(configure, graph)
net.run()
def test_load_network_config():
cfg_full_path = config_path('files/circuit_config.json')
config = cfg.from_json(cfg_full_path)
manifest = config['manifest']
assert (config['config_path'] == cfg_full_path)
assert (config['components']['morphologies'] == os.path.join(
manifest['$COMPONENT_DIR'], 'morphologies'))
assert (config['networks']['node_files'][0]['nodes'] == os.path.join(
manifest['$NETWORK_DIR'], 'V1/v1_nodes.h5'))
def from_json(config_file, validate=True):
"""Converts a config file into a dictionary. Will resolve manifest variables, validate schema and input files, as
well as other behind-the-scenes actions required by bionet.
:param config_file: json file object or path to json configuration file
:param validate: will validate the config file against schemas/config_schema.json (Default True)
:return: config json file in dictionary format
"""
validator = bionet_validator if validate else None
return msdk_config.from_json(config_file, validator)
def plot_spikes_config(configure, group_key=None, exclude=[], save_as=None, show_plot=True):
if isinstance(configure, basestring):
conf = config.from_json(configure)
elif isinstance(configure, dict):
conf = configure
else:
raise Exception("configure variable must be either a json dictionary or json file name.")
cells_file_name = conf['internal']['nodes']
cell_models_file_name = conf['internal']['node_types']
spikes_file = conf['output']['spikes_ascii']
plot_spikes(cells_file_name, cell_models_file_name, spikes_file, group_key, exclude, save_as, show_plot)
def main(config_file):
configure = config.from_json(config_file)
graph = PopGraph.from_config(config_file, group_by='node_type_id')
#v1_pops = graph.get_populations('V1')
# print pop
print graph.get_populations('LGN')
pop0 = graph.get_population('LGN', 0)
#pop0.firing_rate = 12.2
net = PopNetwork.from_config(configure, graph)
net.run()
assert (firing_rates_equal('expected/spike_rates.txt', configure['output']['rates_file']))
def plot_spikes_config(configure, group_key=None, exclude=[], save_as=None, show_plot=True):
warnings.warn('Deprecated: Please use bmtk.analyzer.spike_trains.plot_raster instead.', DeprecationWarning)
if isinstance(configure, string_types):
conf = config.from_json(configure)
elif isinstance(configure, dict):
conf = configure
else:
raise Exception("configure variable must be either a json dictionary or json file name.")
cells_file_name = conf['internal']['nodes']
cell_models_file_name = conf['internal']['node_types']
spikes_file = conf['output']['spikes_ascii']
plot_spikes(cells_file_name, cell_models_file_name, spikes_file, group_key, exclude, save_as, show_plot)
def main(config_file):
configure = config.from_json(config_file)
graph = Graph(configure)
graph.add_weight_function(fn.wmax)
graph.add_weight_function(fn.gaussianLL)
net = nest_construction.Network(configure, graph)
net.run(configure['run']['duration'])
#assert(spike_files_equal(configure['output']['spikes_ascii'], 'expected/spikes.txt'))
#plot_spikes(configure, 'pop_name')
# Check all the output was created
"""
def from_json(config_file, validate=False):
return msdk_config.from_json(config_file)
import bmtk.simulator.utils.config as config
from bmtk.simulator.pointnet.graph import Graph
from bmtk.simulator.pointnet.network import Network
import weight_funcs as fn
configure = config.from_json('config.json')
graph = Graph(configure)
graph.add_weight_function(fn.wmax)
graph.add_weight_function(fn.gaussianLL)
net = Network(configure, graph)
net.run(configure['run']['duration'])
def main(config_file):
configure = config.from_json(config_file)
graph = PopGraph.from_config(config_file, group_by='node_type_id')
net = PopNetwork.from_config(configure, graph)
net.run()
