bmtk.simulator.core.sonata_reader package

Submodules

bmtk.simulator.core.sonata_reader.edge_adaptor module

class bmtk.simulator.core.sonata_reader.edge_adaptor.EdgeAdaptor(network)

Bases: object

property batch_process

classmethod create_adaptor(edge_group, network)

get_edge(sonata_node)

static patch_adaptor(adaptor, edge_group)

static preprocess_edge_types(network, edge_population)

class bmtk.simulator.core.sonata_reader.edge_adaptor.SonataBaseEdge(sonata_edge, edge_adaptor)

Bases: object

property delay

property dynamics_params

property edge_type_id

property is_gap_junction

property model_template

property nsyns

property preselected_targets

property source_node_id

property source_population

syn_weight(src_node, trg_node)

property target_distance

property target_node_id

property target_population

property target_sections

property weight_function

bmtk.simulator.core.sonata_reader.edge_adaptor.group_dynamics_params(self, node)

bmtk.simulator.core.sonata_reader.edge_adaptor.no_nsyns(self, edge)

bmtk.simulator.core.sonata_reader.edge_adaptor.nsyns(self, edge)

bmtk.simulator.core.sonata_reader.edge_adaptor.ret_none_function(self, edge)

bmtk.simulator.core.sonata_reader.edge_adaptor.syn_weight(self, edge, src_node, trg_node)

bmtk.simulator.core.sonata_reader.edge_adaptor.syn_weight_function(self, edge, src_node, trg_node)

bmtk.simulator.core.sonata_reader.edge_adaptor.types_dynamics_params(self, node)

bmtk.simulator.core.sonata_reader.edge_adaptor.weight_function(self, edge)

bmtk.simulator.core.sonata_reader.network_reader module

class bmtk.simulator.core.sonata_reader.network_reader.SonataEdges(edge_population, adaptor)

Bases: EdgesReader

get_edges()

get_source(node_id)

get_target(node_id)

initialize(network)

classmethod load(edges_h5, edge_types_csv, selected_populations=None, adaptor=<class 'bmtk.simulator.core.sonata_reader.edge_adaptor.EdgeAdaptor'>)

property name

property source_nodes

property target_nodes

class bmtk.simulator.core.sonata_reader.network_reader.SonataNodes(sonata_node_population, prop_adaptor)

Bases: NodesReader

property adaptor

filter(filter_conditons)

get_node(node_id)

get_nodes()

initialize(network)

classmethod load(nodes_h5, node_types_csv, gid_table=None, selected_nodes=None, adaptor=<class 'bmtk.simulator.core.sonata_reader.node_adaptor.NodeAdaptor'>)

n_nodes()

property name

nodes_df(**params)

bmtk.simulator.core.sonata_reader.network_reader.load_edges(edges_h5, edge_types_csv, selected_populations=None, adaptor=<class 'bmtk.simulator.core.sonata_reader.edge_adaptor.EdgeAdaptor'>)

bmtk.simulator.core.sonata_reader.network_reader.load_nodes(nodes_h5, node_types_csv, gid_table=None, selected_nodes=None, adaptor=<class 'bmtk.simulator.core.sonata_reader.node_adaptor.NodeAdaptor'>)

bmtk.simulator.core.sonata_reader.node_adaptor module

class bmtk.simulator.core.sonata_reader.node_adaptor.NodeAdaptor(network)

Bases: object

COL_DYNAMICS_PARAM = 'dynamics_params'

COL_GID = 'gid'

COL_MODEL_PROCESSING = 'model_processing'

COL_MODEL_TEMPLATE = 'model_template'

COL_MODEL_TYPE = 'model_type'

property batch_process

classmethod create_adaptor(node_group, network)

get_node(sonata_node)

model_processing(node)

model_template(node)

model_type(node)

node_id(node)

classmethod patch_adaptor(adaptor, node_group, network)

static preprocess_node_types(network, node_population)

class bmtk.simulator.core.sonata_reader.node_adaptor.SonataBaseNode(node, prop_adaptor)

Bases: object

property dynamics_params

property gid

property model_processing

property model_template

property model_type

property network

property node_id

property population

property population_name

bmtk.simulator.core.sonata_reader.node_adaptor.empty_list(self, node)

bmtk.simulator.core.sonata_reader.node_adaptor.group_dynamics_params(self, node)

bmtk.simulator.core.sonata_reader.node_adaptor.none_function(self, node)

bmtk.simulator.core.sonata_reader.node_adaptor.types_dynamics_params(self, node)

Module contents