bmtk.simulator.core.sonata_reader package
bmtk.simulator.core.sonata_reader.edge_adaptor module
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class bmtk.simulator.core.sonata_reader.edge_adaptor.EdgeAdaptor(network)[source]
Bases: object
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property batch_process
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classmethod create_adaptor(edge_group, network)[source]
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get_edge(sonata_node)[source]
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static patch_adaptor(adaptor, edge_group)[source]
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static preprocess_edge_types(network, edge_population)[source]
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class bmtk.simulator.core.sonata_reader.edge_adaptor.SonataBaseEdge(sonata_edge, edge_adaptor)[source]
Bases: object
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property delay
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property dynamics_params
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property edge_type_id
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property is_gap_junction
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property model_template
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property nsyns
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property preselected_targets
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property source_node_id
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property source_population
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syn_weight(src_node, trg_node)[source]
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property target_distance
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property target_node_id
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property target_population
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property target_sections
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property weight_function
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bmtk.simulator.core.sonata_reader.edge_adaptor.group_dynamics_params(self, node)[source]
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bmtk.simulator.core.sonata_reader.edge_adaptor.no_nsyns(self, edge)[source]
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bmtk.simulator.core.sonata_reader.edge_adaptor.nsyns(self, edge)[source]
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bmtk.simulator.core.sonata_reader.edge_adaptor.ret_none_function(self, edge)[source]
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bmtk.simulator.core.sonata_reader.edge_adaptor.syn_weight(self, edge, src_node, trg_node)[source]
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bmtk.simulator.core.sonata_reader.edge_adaptor.syn_weight_function(self, edge, src_node, trg_node)[source]
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bmtk.simulator.core.sonata_reader.edge_adaptor.types_dynamics_params(self, node)[source]
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bmtk.simulator.core.sonata_reader.edge_adaptor.weight_function(self, edge)[source]
bmtk.simulator.core.sonata_reader.network_reader module
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class bmtk.simulator.core.sonata_reader.network_reader.SonataEdges(edge_population, adaptor)[source]
Bases: EdgesReader
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get_edges()[source]
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get_source(node_id)[source]
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get_target(node_id)[source]
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initialize(network)[source]
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classmethod load(edges_h5, edge_types_csv, selected_populations=None, adaptor=<class 'bmtk.simulator.core.sonata_reader.edge_adaptor.EdgeAdaptor'>)[source]
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property name
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property source_nodes
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property target_nodes
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class bmtk.simulator.core.sonata_reader.network_reader.SonataNodes(sonata_node_population, prop_adaptor)[source]
Bases: NodesReader
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property adaptor
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filter(filter_conditons)[source]
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get_node(node_id)[source]
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get_nodes()[source]
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initialize(network)[source]
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classmethod load(nodes_h5, node_types_csv, gid_table=None, selected_nodes=None, adaptor=<class 'bmtk.simulator.core.sonata_reader.node_adaptor.NodeAdaptor'>)[source]
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n_nodes()[source]
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property name
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nodes_df(**params)[source]
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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]
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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
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class bmtk.simulator.core.sonata_reader.node_adaptor.NodeAdaptor(network)[source]
Bases: object
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COL_DYNAMICS_PARAM = 'dynamics_params'
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COL_GID = 'gid'
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COL_MODEL_PROCESSING = 'model_processing'
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COL_MODEL_TEMPLATE = 'model_template'
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COL_MODEL_TYPE = 'model_type'
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property batch_process
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classmethod create_adaptor(node_group, network)[source]
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get_node(sonata_node)[source]
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model_processing(node)[source]
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model_template(node)[source]
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model_type(node)[source]
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node_id(node)[source]
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classmethod patch_adaptor(adaptor, node_group, network)[source]
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static preprocess_node_types(network, node_population)[source]
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class bmtk.simulator.core.sonata_reader.node_adaptor.SonataBaseNode(node, prop_adaptor)[source]
Bases: object
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property dynamics_params
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property gid
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property model_processing
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property model_template
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property model_type
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property network
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property node_id
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property population
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property population_name
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bmtk.simulator.core.sonata_reader.node_adaptor.empty_list(self, node)[source]
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bmtk.simulator.core.sonata_reader.node_adaptor.group_dynamics_params(self, node)[source]
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bmtk.simulator.core.sonata_reader.node_adaptor.none_function(self, node)[source]
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bmtk.simulator.core.sonata_reader.node_adaptor.types_dynamics_params(self, node)[source]