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)[source]

Bases: object

batch_process
classmethod create_adaptor(edge_group, network)[source]
get_edge(sonata_node)[source]
static patch_adaptor(adaptor, edge_group)[source]
static preprocess_edge_types(network, edge_population)[source]
class bmtk.simulator.core.sonata_reader.edge_adaptor.SonataBaseEdge(sonata_edge, edge_adaptor)[source]

Bases: object

delay
dynamics_params
edge_type_id
is_gap_junction
model_template
nsyns
preselected_targets
source_node_id
source_population
syn_weight(src_node, trg_node)[source]
target_distance
target_node_id
target_population
target_sections
weight_function
bmtk.simulator.core.sonata_reader.edge_adaptor.group_dynamics_params(self, node)[source]
bmtk.simulator.core.sonata_reader.edge_adaptor.no_nsyns(self, edge)[source]
bmtk.simulator.core.sonata_reader.edge_adaptor.nsyns(self, edge)[source]
bmtk.simulator.core.sonata_reader.edge_adaptor.ret_none_function(self, edge)[source]
bmtk.simulator.core.sonata_reader.edge_adaptor.syn_weight(self, edge, src_node, trg_node)[source]
bmtk.simulator.core.sonata_reader.edge_adaptor.syn_weight_function(self, edge, src_node, trg_node)[source]
bmtk.simulator.core.sonata_reader.edge_adaptor.types_dynamics_params(self, node)[source]
bmtk.simulator.core.sonata_reader.edge_adaptor.weight_function(self, edge)[source]

bmtk.simulator.core.sonata_reader.network_reader module

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

Bases: bmtk.simulator.core.network_reader.EdgesReader

get_edges()[source]
get_source(node_id)[source]
get_target(node_id)[source]
initialize(network)[source]
classmethod load(edges_h5, edge_types_csv, selected_populations=None, adaptor=<class 'bmtk.simulator.core.sonata_reader.edge_adaptor.EdgeAdaptor'>)[source]
name
source_nodes
target_nodes
class bmtk.simulator.core.sonata_reader.network_reader.SonataNodes(sonata_node_population, prop_adaptor)[source]

Bases: bmtk.simulator.core.network_reader.NodesReader

adaptor
filter(filter_conditons)[source]
get_node(node_id)[source]
get_nodes()[source]
initialize(network)[source]
classmethod load(nodes_h5, node_types_csv, gid_table=None, selected_nodes=None, adaptor=<class 'bmtk.simulator.core.sonata_reader.node_adaptor.NodeAdaptor'>)[source]
n_nodes()[source]
name
nodes_df(**params)[source]
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'>)[source]
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'>)[source]

bmtk.simulator.core.sonata_reader.node_adaptor module

class bmtk.simulator.core.sonata_reader.node_adaptor.NodeAdaptor(network)[source]

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'
batch_process
classmethod create_adaptor(node_group, network)[source]
get_node(sonata_node)[source]
model_processing(node)[source]
model_template(node)[source]
model_type(node)[source]
node_id(node)[source]
classmethod patch_adaptor(adaptor, node_group, network)[source]
static preprocess_node_types(network, node_population)[source]
class bmtk.simulator.core.sonata_reader.node_adaptor.SonataBaseNode(node, prop_adaptor)[source]

Bases: object

dynamics_params
gid
model_processing
model_template
model_type
network
node_id
population
population_name
bmtk.simulator.core.sonata_reader.node_adaptor.empty_list(self, node)[source]
bmtk.simulator.core.sonata_reader.node_adaptor.group_dynamics_params(self, node)[source]
bmtk.simulator.core.sonata_reader.node_adaptor.none_function(self, node)[source]
bmtk.simulator.core.sonata_reader.node_adaptor.types_dynamics_params(self, node)[source]

Module contents