bmtk.simulator.pointnet package

Submodules

bmtk.simulator.pointnet.config module

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

Bases: bmtk.simulator.core.simulation_config.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_pool_id(gid)[source]
property gids
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.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: bmtk.simulator.core.io_tools.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.pointnetwork module

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

Bases: bmtk.simulator.core.simulator_network.SimNetwork

add_spike_trains(spike_trains, node_set, sg_params={'precise_times': True})[source]
add_weight_function(fnc, name=None, **kwargs)[source]
build_nodes()[source]
build_recurrent_edges()[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.pointsimulator module

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

Bases: bmtk.simulator.core.simulator.Simulator

add_mod(mod)[source]
add_step_currents(amp_times, amp_values, node_set, input_name)[source]
property dt
classmethod from_config(configure, graph)[source]
get_spike_generator_params()[source]
property gid_map
property n_steps
property net
run(tstop=None)[source]
set_spike_generator_params(**params)[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.pyfunction_cache.add_cell_model(func, directive, model_type, overwrite=True)[source]
bmtk.simulator.pointnet.pyfunction_cache.add_cell_processor(func, name=None, overwrite=True)[source]
bmtk.simulator.pointnet.pyfunction_cache.add_synapse_model(func, name=None, overwrite=True)[source]
bmtk.simulator.pointnet.pyfunction_cache.add_weight_function(func, name=None, overwrite=True)[source]
bmtk.simulator.pointnet.pyfunction_cache.cell_model(*wargs, **wkwargs)[source]

A decorator for registering NEURON cell loader functions.

bmtk.simulator.pointnet.pyfunction_cache.load_py_modules(cell_models=None, syn_models=None, syn_weights=None)[source]
bmtk.simulator.pointnet.pyfunction_cache.synapse_model(*wargs, **wkwargs)[source]

A decorator for registering NEURON synapse loader functions.

bmtk.simulator.pointnet.pyfunction_cache.synaptic_weight(*wargs, **wkwargs)[source]

A decorator for registering a function as a synaptic weight function. To use either:

@synaptic_weight
def weight_function():
    ...

or:

@synaptic_weight(name='name_in_edge_types')
def weight_function():
    ...

Once the decorator has been attached and imported the functions will automatically be added to py_modules.

bmtk.simulator.pointnet.sonata_adaptors module

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

Bases: bmtk.simulator.core.sonata_reader.edge_adaptor.SonataBaseEdge

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

Bases: bmtk.simulator.core.sonata_reader.edge_adaptor.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: bmtk.simulator.core.sonata_reader.node_adaptor.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: bmtk.simulator.core.sonata_reader.node_adaptor.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)[source]

Bases: object

build()[source]
property gids
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