bmtk package

Subpackages

• bmtk.analyzer package
  • Submodules
  • bmtk.analyzer.cell_vars module
  • bmtk.analyzer.compartment module
    • plot_traces()
  • bmtk.analyzer.ecp module
    • plot_ecp()
  • bmtk.analyzer.edges module
  • bmtk.analyzer.firing_rates module
    • convert_rates()
    • firing_rates_equal()
    • plot_rates_popnet()
  • bmtk.analyzer.io_tools module
    • load_config()
  • bmtk.analyzer.spike_trains module
    • plot_raster()
    • plot_rates()
    • plot_rates_boxplot()
    • spike_statistics()
    • to_dataframe()
  • bmtk.analyzer.spikes_analyzer module
    • get_mean_firing_rates()
    • spike_files_equal()
    • spikes2dict()
    • spikes_equal_in_window()
  • bmtk.analyzer.spikes_loader module
    • load_spikes()
    • load_spikes_from_h5()
    • load_spikes_from_nwb()
    • load_spikes_from_txt()
  • bmtk.analyzer.utils module
    • listify()
  • Module contents
    • node_types_table()
    • nodes_table()
    • plot_calcium()
    • plot_calcium_hdf5()
    • plot_potential()
    • plot_potential_hdf5()
    • spikes_table()
• bmtk.builder package
  • Subpackages
    • bmtk.builder.auxi package
      • Submodules
      • bmtk.builder.auxi.edge_connectors module
      • bmtk.builder.auxi.node_params module
      • Module contents
    • bmtk.builder.bionet package
      • Submodules
      • bmtk.builder.bionet.swc_reader module
      • Module contents
    • bmtk.builder.edges_sorter package
      • Submodules
      • bmtk.builder.edges_sorter.memory_sorter module
      • bmtk.builder.edges_sorter.merge_sorter module
      • Module contents
    • bmtk.builder.network_adaptors package
      • Submodules
      • bmtk.builder.network_adaptors.dm_network module
      • bmtk.builder.network_adaptors.dm_network_orig module
      • bmtk.builder.network_adaptors.edge_props_table module
      • bmtk.builder.network_adaptors.edges_collator module
      • bmtk.builder.network_adaptors.network module
      • bmtk.builder.network_adaptors.nxnetwork module
      • Module contents
  • Submodules
  • bmtk.builder.builder_utils module
    • add_hdf5_attrs()
    • barrier()
    • build_time_uuid()
    • check_properties_across_ranks()
    • list_to_hash()
  • bmtk.builder.connection_map module
    • ConnectionMap
      • ConnectionMap.ParamsRules
      • ConnectionMap.add_properties()
      • ConnectionMap.connection_itr()
      • ConnectionMap.connector
      • ConnectionMap.connector_params
      • ConnectionMap.edge_type_id
      • ConnectionMap.edge_type_properties
      • ConnectionMap.iterator
      • ConnectionMap.max_connections()
      • ConnectionMap.params
      • ConnectionMap.properties_keys()
      • ConnectionMap.property_names
      • ConnectionMap.source_network_name
      • ConnectionMap.source_nodes
      • ConnectionMap.target_network_name
      • ConnectionMap.target_nodes
    • ListIterator
  • bmtk.builder.connector module
    • create()
    • register()
  • bmtk.builder.edge module
    • Edge
      • Edge.edge_type_id
      • Edge.edge_type_properties
      • Edge.source_gid
      • Edge.source_node_id
      • Edge.synaptic_properties
      • Edge.target_gid
      • Edge.target_node_id
  • bmtk.builder.functor_cache module
    • FunctorCache
      • FunctorCache.create()
      • FunctorCache.register()
  • bmtk.builder.id_generator module
    • IDGenerator
      • IDGenerator.get_ids()
      • IDGenerator.next()
      • IDGenerator.remove_id()
  • bmtk.builder.index_builders module
    • create_index_in_memory()
    • create_index_on_disk()
    • remove_index()
  • bmtk.builder.iterator module
    • IteratorCache
      • IteratorCache.create()
      • IteratorCache.register()
    • all_to_one_iterator()
    • all_to_one_list_iterator()
    • create()
    • lambda_iterator()
    • one_to_all_iterator()
    • one_to_all_list_iterator()
    • one_to_one_iterator()
    • one_to_one_list_iterator()
    • register()
  • bmtk.builder.network_builder module
    • BioNetBuilder
      • BioNetBuilder.add_edges()
      • BioNetBuilder.add_nodes()
    • NetworkBuilder
      • NetworkBuilder.add_edges()
      • NetworkBuilder.add_nodes()
      • NetworkBuilder.build()
      • NetworkBuilder.clear()
      • NetworkBuilder.edges()
      • NetworkBuilder.edges_built
      • NetworkBuilder.import_nodes()
      • NetworkBuilder.name
      • NetworkBuilder.nedges
      • NetworkBuilder.nnodes
      • NetworkBuilder.nodes()
      • NetworkBuilder.nodes_built
      • NetworkBuilder.save()
      • NetworkBuilder.save_edges()
      • NetworkBuilder.save_nodes()
    • PointNetBuilder
      • PointNetBuilder.add_edges()
      • PointNetBuilder.add_nodes()
    • PopNetBuilder
      • PopNetBuilder.add_edges()
      • PopNetBuilder.add_nodes()
  • bmtk.builder.networks module
  • bmtk.builder.node module
    • Node
      • Node.get()
      • Node.node_id
      • Node.node_type_id
      • Node.node_type_properties
      • Node.params
      • Node.params_hash
  • bmtk.builder.node_pool module
    • NodePool
      • NodePool.filter_str
      • NodePool.from_filter()
      • NodePool.network
      • NodePool.network_name
  • bmtk.builder.node_set module
    • NodeSet
      • NodeSet.N
      • NodeSet.build()
      • NodeSet.node_type_id
      • NodeSet.params_hash
      • NodeSet.params_keys
  • Module contents
• bmtk.simulator package
  • Subpackages
    • bmtk.simulator.bionet package
      • Subpackages
      • Submodules
      • bmtk.simulator.bionet.biocell module
      • bmtk.simulator.bionet.bionetwork module
      • bmtk.simulator.bionet.biosimulator module
      • bmtk.simulator.bionet.cell module
      • bmtk.simulator.bionet.config module
      • bmtk.simulator.bionet.gids module
      • bmtk.simulator.bionet.iclamp module
      • bmtk.simulator.bionet.io_tools module
      • bmtk.simulator.bionet.morphology module
      • bmtk.simulator.bionet.nml_reader module
      • bmtk.simulator.bionet.nrn module
      • bmtk.simulator.bionet.pointprocesscell module
      • bmtk.simulator.bionet.pointsomacell module
      • bmtk.simulator.bionet.pyfunction_cache module
      • bmtk.simulator.bionet.seclamp module
      • bmtk.simulator.bionet.sonata_adaptors module
      • bmtk.simulator.bionet.utils module
      • bmtk.simulator.bionet.virtualcell module
      • Module contents
    • bmtk.simulator.core package
      • Subpackages
      • Submodules
      • bmtk.simulator.core.edge_population module
      • bmtk.simulator.core.graph module
      • bmtk.simulator.core.io_tools module
      • bmtk.simulator.core.network_reader module
      • bmtk.simulator.core.node_population module
      • bmtk.simulator.core.node_sets module
      • bmtk.simulator.core.pyfunction_cache module
      • bmtk.simulator.core.simulation_config module
      • bmtk.simulator.core.simulation_config_validator module
      • bmtk.simulator.core.simulator module
      • bmtk.simulator.core.simulator_network module
      • Module contents
    • bmtk.simulator.filternet package
      • Subpackages
      • Submodules
      • bmtk.simulator.filternet.auditory_processing module
      • bmtk.simulator.filternet.cell module
      • bmtk.simulator.filternet.cell_models module
      • bmtk.simulator.filternet.config module
      • bmtk.simulator.filternet.filternetwork module
      • bmtk.simulator.filternet.filters module
      • bmtk.simulator.filternet.filtersimulator module
      • bmtk.simulator.filternet.io_tools module
      • bmtk.simulator.filternet.pyfunction_cache module
      • bmtk.simulator.filternet.sonata_adaptors module
      • bmtk.simulator.filternet.transfer_functions module
      • bmtk.simulator.filternet.utils module
      • Module contents
    • bmtk.simulator.pointnet package
      • Subpackages
      • Submodules
      • bmtk.simulator.pointnet.config module
      • bmtk.simulator.pointnet.gids module
      • bmtk.simulator.pointnet.glif_utils module
      • bmtk.simulator.pointnet.io_tools module
      • bmtk.simulator.pointnet.nest_utils module
      • bmtk.simulator.pointnet.pointnetwork module
      • bmtk.simulator.pointnet.pointsimulator module
      • bmtk.simulator.pointnet.property_map module
      • bmtk.simulator.pointnet.pyfunction_cache module
      • bmtk.simulator.pointnet.sonata_adaptors module
      • bmtk.simulator.pointnet.utils module
      • Module contents
    • bmtk.simulator.popnet package
      • Submodules
      • bmtk.simulator.popnet.config module
      • bmtk.simulator.popnet.popedge module
      • bmtk.simulator.popnet.popnetwork module
      • bmtk.simulator.popnet.popnode module
      • bmtk.simulator.popnet.popsimulator module
      • bmtk.simulator.popnet.sonata_adaptors module
      • bmtk.simulator.popnet.utils module
      • Module contents
    • bmtk.simulator.utils package
      • Submodules
      • bmtk.simulator.utils.simulation_inputs module
      • bmtk.simulator.utils.simulation_reports module
      • Module contents
  • Module contents
• bmtk.tests package
  • Subpackages
    • bmtk.tests.builder package
      • Subpackages
      • Submodules
      • bmtk.tests.builder.test_connection_map module
      • bmtk.tests.builder.test_connector module
      • bmtk.tests.builder.test_densenetwork module
      • bmtk.tests.builder.test_edge_iterator module
      • bmtk.tests.builder.test_edges_sorter module
      • bmtk.tests.builder.test_id_generator module
      • bmtk.tests.builder.test_index_builders module
      • bmtk.tests.builder.test_iterator module
      • bmtk.tests.builder.test_network module
      • bmtk.tests.builder.test_network_mpi module
      • bmtk.tests.builder.test_node_pool module
      • bmtk.tests.builder.test_node_set module
      • bmtk.tests.builder.test_save_network module
      • Module contents
    • bmtk.tests.simulator package
      • Subpackages
      • Module contents
    • bmtk.tests.utils package
      • Subpackages
      • Module contents
  • Module contents
• bmtk.utils package
  • Subpackages
    • bmtk.utils.compile_mechanisms package
      • Submodules
      • bmtk.utils.compile_mechanisms.compile_mechanisms module
      • Module contents
    • bmtk.utils.create_environment package
      • Submodules
      • bmtk.utils.create_environment.create_environment module
      • bmtk.utils.create_environment.env_builder module
      • Module contents
    • bmtk.utils.io package
      • Submodules
      • bmtk.utils.io.cell_vars module
      • bmtk.utils.io.firing_rates module
      • bmtk.utils.io.ioutils module
      • bmtk.utils.io.spike_trains module
      • Module contents
    • bmtk.utils.reports package
      • Subpackages
      • Submodules
      • bmtk.utils.reports.current_writer module
      • Module contents
    • bmtk.utils.sonata package
      • Subpackages
      • Submodules
      • bmtk.utils.sonata.column_property module
      • bmtk.utils.sonata.edge module
      • bmtk.utils.sonata.edge_stats module
      • bmtk.utils.sonata.file module
      • bmtk.utils.sonata.file_root module
      • bmtk.utils.sonata.group module
      • bmtk.utils.sonata.node module
      • bmtk.utils.sonata.population module
      • bmtk.utils.sonata.types_table module
      • bmtk.utils.sonata.utils module
      • Module contents
  • Submodules
  • bmtk.utils.hdf5_helper module
    • get_attribute_h5()
  • bmtk.utils.lazy_property module
    • lazy_property()
  • bmtk.utils.sim_setup module
    • BioNetEnvBuilder
      • BioNetEnvBuilder.bmtk_simulator
      • BioNetEnvBuilder.compile_mechanisms()
      • BioNetEnvBuilder.examples_dir
      • BioNetEnvBuilder.target_simulator
    • EnvBuilder
      • EnvBuilder.base_dir
      • EnvBuilder.bmtk_simulator
      • EnvBuilder.build()
      • EnvBuilder.components_dir
      • EnvBuilder.examples_dir
      • EnvBuilder.network_dir
      • EnvBuilder.node_sets_file
      • EnvBuilder.output_dir
      • EnvBuilder.scripts_root
      • EnvBuilder.target_simulator
    • FilterNetEnvBuilder
      • FilterNetEnvBuilder.bmtk_simulator
      • FilterNetEnvBuilder.examples_dir
      • FilterNetEnvBuilder.target_simulator
    • PointNetEnvBuilder
      • PointNetEnvBuilder.bmtk_simulator
      • PointNetEnvBuilder.examples_dir
      • PointNetEnvBuilder.target_simulator
    • PopNetEnvBuilder
      • PopNetEnvBuilder.bmtk_simulator
      • PopNetEnvBuilder.examples_dir
      • PopNetEnvBuilder.target_simulator
    • build_env_bionet()
    • build_env_filternet()
    • build_env_pointnet()
    • build_env_popnet()
  • Module contents

Module contents