bmtk.simulator.pointnet package#

Subpackages#

Submodules#

bmtk.simulator.pointnet.config module#

class bmtk.simulator.pointnet.config.Config(dict_obj)[source]#

Bases: SimulationConfig

property io#
bmtk.simulator.pointnet.config.from_dict(config_file, validate=False)[source]#
bmtk.simulator.pointnet.config.from_json(config_file, validate=False)[source]#

bmtk.simulator.pointnet.gids module#

class bmtk.simulator.pointnet.gids.GidPool[source]#

Bases: object

add(name, node_id, gid)[source]#
add_gids(name, node_ids, gids)[source]#
add_nestids(name, node_ids, nest_ids)[source]#
create_pool(name)[source]#
get_gid(name, node_id)[source]#
get_gids(name, node_ids)[source]#
get_nestids(name, node_ids)[source]#
get_node_ids(nest_ids, with_populations=True)[source]#
get_pool_id(gid)[source]#
property gids#
property nestid2nodeid_df#
property populations#
class bmtk.simulator.pointnet.gids.PopulationID(node_id, population)#

Bases: tuple

node_id#

Alias for field number 0

population#

Alias for field number 1

bmtk.simulator.pointnet.gids.ids2list(nest_ids)#
bmtk.simulator.pointnet.gids.ids2list_nest2(nest_ids)[source]#
bmtk.simulator.pointnet.gids.ids2list_nest3(nest_ids)[source]#

bmtk.simulator.pointnet.glif_utils module#

bmtk.simulator.pointnet.glif_utils.convert_aibs2nest(model_template, dynamics_params)#
bmtk.simulator.pointnet.glif_utils.converter_builtin(model_template, dynamics_params)[source]#
bmtk.simulator.pointnet.glif_utils.converter_modules(model_template, dynamics_params)[source]#
bmtk.simulator.pointnet.glif_utils.lif_aibs_converter(config, tau_syn=[5.5, 8.5, 2.8, 5.8])[source]#
Parameters:

config

Returns:

bmtk.simulator.pointnet.glif_utils.lif_asc_aibs_converter(config, tau_syn=[5.5, 8.5, 2.8, 5.8])[source]#
Parameters:

config

Returns:

bmtk.simulator.pointnet.glif_utils.lif_asc_psc_aibs_converter(config, syn_tau=[5.5, 8.5, 2.8, 5.8])[source]#

Creates a nest glif_lif_asc_psc object

bmtk.simulator.pointnet.glif_utils.lif_psc_aibs_converter(config, syn_tau=[5.5, 8.5, 2.8, 5.8])[source]#

Creates a nest glif_lif_psc object

bmtk.simulator.pointnet.glif_utils.lif_r_aibs_converter(config)[source]#
Parameters:

config

Returns:

bmtk.simulator.pointnet.glif_utils.lif_r_asc_a_aibs_converter(config)[source]#

Creates a nest glif_lif_r_asc_a object

bmtk.simulator.pointnet.glif_utils.lif_r_asc_a_psc_aibs_converter(config, syn_tau=[5.5, 8.5, 2.8, 5.8])[source]#

Creates a nest glif_lif_r_asc_a_psc object

bmtk.simulator.pointnet.glif_utils.lif_r_asc_aibs_converter(config)[source]#

Creates a nest glif_lif_r_asc object

bmtk.simulator.pointnet.glif_utils.lif_r_asc_psc_aibs_converter(config, syn_tau=[5.5, 8.5, 2.8, 5.8])[source]#

Creates a nest glif_lif_r_asc_psc object

bmtk.simulator.pointnet.glif_utils.lif_r_psc_aibs_converter(config, syn_tau=[5.5, 8.5, 2.8, 5.8])[source]#

Creates a nest glif_lif_r_psc object

bmtk.simulator.pointnet.io_tools module#

Functions for logging, writing and reading from file.

class bmtk.simulator.pointnet.io_tools.NestIOUtils[source]#

Bases: IOUtils

barrier()[source]#

MPI Barrier call

quiet_simulator()[source]#

Turns off logging/messages of the native simulator

setup_output_dir(config_dir, log_file, overwrite=True)[source]#

bmtk.simulator.pointnet.nest_utils module#

bmtk.simulator.pointnet.nest_utils.get_version()[source]#

Trys to get NEST version major, minor, and patch (optional) of the current running version of nest. Will return as a list of ints [major, minor, patch], although patch may be None.

Returns:

[major, minor, patch] if able to parse version, None if fails. ‘patch’ may be None value.

bmtk.simulator.pointnet.pointnetwork module#

class bmtk.simulator.pointnet.pointnetwork.PointNetwork(**properties)[source]#

Bases: SimNetwork

add_nest_module(module_path)[source]#
add_spike_trains(spike_trains, node_set, sg_params={'precise_times': True}, t_offset=0.0)[source]#
add_weight_function(fnc, name=None, **kwargs)[source]#
build_nodes()[source]#
build_recurrent_edges(force_resolution=False)[source]#
find_edges(source_nodes=None, target_nodes=None)[source]#
get_node_id(population, node_id)[source]#
get_nodes_df(population)[source]#
get_weight_function(name)[source]#
property gid_map#
property gid_pool#
property py_function_caches#
set_default_weight_function(fnc)[source]#
bmtk.simulator.pointnet.pointnetwork.set_spikes(node_id, nest_obj, spike_trains, t_offset=0.0)#
bmtk.simulator.pointnet.pointnetwork.set_spikes_nest2(node_id, nest_obj, spike_trains, t_offset=0.0)[source]#
bmtk.simulator.pointnet.pointnetwork.set_spikes_nest3(node_id, nest_obj, spike_trains, t_offset=0.0)[source]#

bmtk.simulator.pointnet.pointsimulator module#

class bmtk.simulator.pointnet.pointsimulator.PointSimulator(graph, dt=0.001, overwrite=True, print_time=False, n_thread=1)[source]#

Bases: Simulator

add_mod(mod)[source]#
property dt#
classmethod from_config(configure, graph, n_thread=None)[source]#
get_spike_generator_params()[source]#
property gid_map#
property n_steps#
property net#
run(tstop=None)[source]#
set_spike_generator_params(**params)[source]#
simulation_time(units='ms')[source]#
property tstart#
property tstop#

bmtk.simulator.pointnet.property_map module#

class bmtk.simulator.pointnet.property_map.EdgePropertyMap(graph, source_population, target_population)[source]#

Bases: object

classmethod build_map(edge_group, biograph)[source]#
synaptic_model(edge)[source]#
synpatic_params(edge)[source]#
class bmtk.simulator.pointnet.property_map.NodePropertyMap(graph)[source]#

Bases: object

classmethod build_map(node_group, graph)[source]#
load_cell(node)[source]#
bmtk.simulator.pointnet.property_map.gid(self, node)[source]#
bmtk.simulator.pointnet.property_map.group_dynamics_params(self, node)[source]#
bmtk.simulator.pointnet.property_map.model_params(self, node)[source]#
bmtk.simulator.pointnet.property_map.model_params_batched(self, node_type_id)[source]#
bmtk.simulator.pointnet.property_map.model_type(self, node)[source]#
bmtk.simulator.pointnet.property_map.model_type_batched(self, node_type_id)[source]#
bmtk.simulator.pointnet.property_map.no_syns(self, edge)[source]#
bmtk.simulator.pointnet.property_map.node_id(self, node)[source]#
bmtk.simulator.pointnet.property_map.nsyns(self, edge)[source]#
bmtk.simulator.pointnet.property_map.syn_weight(self, edge)[source]#
bmtk.simulator.pointnet.property_map.types_dynamics_params(self, node)[source]#
bmtk.simulator.pointnet.property_map.weight_function(self, edge)[source]#

bmtk.simulator.pointnet.pyfunction_cache module#

bmtk.simulator.pointnet.sonata_adaptors module#

class bmtk.simulator.pointnet.sonata_adaptors.PointEdge(sonata_edge, edge_adaptor)[source]#

Bases: SonataBaseEdge

property nest_params#
property source_node_ids#
property target_node_ids#
class bmtk.simulator.pointnet.sonata_adaptors.PointEdgeAdaptor(network)[source]#

Bases: EdgeAdaptor

property batch_process#
get_batches(edge_group)[source]#
get_edge(sonata_node)[source]#
static patch_adaptor(adaptor, edge_group)[source]#
static preprocess_edge_types(network, edge_population)[source]#
synaptic_params(edge)[source]#
class bmtk.simulator.pointnet.sonata_adaptors.PointEdgeBatched(source_nids, target_nids, nest_params)[source]#

Bases: object

property nest_params#
property source_node_ids#
property target_node_ids#
class bmtk.simulator.pointnet.sonata_adaptors.PointNode(node, prop_adaptor)[source]#

Bases: SonataBaseNode

build()[source]#
property gids#
property n_nodes#
property nest_ids#
property nest_model#
property nest_params#
property node_ids#
class bmtk.simulator.pointnet.sonata_adaptors.PointNodeAdaptor(network)[source]#

Bases: NodeAdaptor

property batch_process#
get_batches(node_group)[source]#
get_node(sonata_node)[source]#
static patch_adaptor(adaptor, node_group, network)[source]#
static preprocess_node_types(network, node_population)[source]#
class bmtk.simulator.pointnet.sonata_adaptors.PointNodeBatched(node_ids, gids, node_types_table, node_type_id, grp_indices, node_group)[source]#

Bases: object

build()[source]#
property gids#
property model_name#
property model_schema#
property model_template#
property model_type#
property n_nodes#
property nest_ids#
property nest_model#
property nest_params#
property node_ids#
bmtk.simulator.pointnet.sonata_adaptors.all_null(node_group, column_name)[source]#

Helper function to determine if a column has any non-NULL values

bmtk.simulator.pointnet.sonata_adaptors.point_syn_weight(self, edge, src_node, trg_node)[source]#

bmtk.simulator.pointnet.utils module#

bmtk.simulator.pointnet.utils.gen_recurrent_csv(num, offset, csv_file)[source]#
bmtk.simulator.pointnet.utils.gen_recurrent_h5(num, offset, h5_file)[source]#
bmtk.simulator.pointnet.utils.load_conns(cnn_fn)[source]#

load information regarding connectivity from csv files

Parameters:
cnn_fn: json file name for connection information
Returns:
connection dictionary
bmtk.simulator.pointnet.utils.load_params(node_name, model_name)[source]#

load information regarding nodes and cell_models from csv files

Parameters:
node_name: json file name for node information
model_name: json file name for neuron model information
Returns:
node_info: 2d array of node info read out from the json file
mode_info: 2d array of model info read out from the json file
dict_coordinates: dictionary of coordinates. keyword is the node_id and entries are the x,y and z coordinates.
bmtk.simulator.pointnet.utils.read_LGN_activity(trial_num, file_name)[source]#
bmtk.simulator.pointnet.utils.read_conns(file_name)[source]#

Module contents#

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