API Documentation

API

• MiV Simulator
  • miv_simulator.cells
    • make_neurotree_hoc_cell()
    • make_hoc_cell()
    • make_input_cell()
    • make_section_graph()
    • BRKneuron
    • PRneuron
    • SCneuron
    • BiophysCell
    • get_distance_to_node()
    • connect_nodes()
    • import_morphology_from_hoc()
    • import_mech_dict_from_file()
    • reset_cable_by_node()
    • connect2target()
    • init_spike_detector()
    • update_biophysics_by_sec_type()
    • update_mechanism_by_node()
    • apply_mech_rules()
    • set_mech_param()
    • filter_nodes()
    • report_topology()
    • make_morph_graph()
    • load_biophys_cell_dicts()
    • init_biophysics()
    • correct_node_for_spines_g_pas()
    • correct_node_for_spines_cm()
    • correct_cell_for_spines_g_pas()
    • correct_cell_for_spines_cm()
    • make_biophys_cell()
    • make_BRK_cell()
    • make_PR_cell()
    • make_SC_cell()
    • register_cell()
    • is_cell_registered()
    • record_cell()
  • miv_simulator.connections
    • ConnectionProb
      • ConnectionProb.filter_by_distance()
      • ConnectionProb.get_prob()
    • choose_synapse_projection()
    • generate_synaptic_connections()
    • generate_uv_distance_connections()
  • miv_simulator.env
    • SynapseConfig
      • SynapseConfig.contacts
      • SynapseConfig.layers
      • SynapseConfig.mechanisms
      • SynapseConfig.proportions
      • SynapseConfig.sections
      • SynapseConfig.type
    • GapjunctionConfig
      • GapjunctionConfig.connection_bounds
      • GapjunctionConfig.connection_parameters
      • GapjunctionConfig.connection_probability
      • GapjunctionConfig.coupling_bounds
      • GapjunctionConfig.coupling_coefficients
      • GapjunctionConfig.coupling_parameters
      • GapjunctionConfig.sections
    • NetclampConfig
      • NetclampConfig.optimize_parameters
      • NetclampConfig.template_params
      • NetclampConfig.weight_generators
    • ArenaConfig
    • DomainConfig
    • StimulusConfig
    • Env
      • Env.parse_netclamp_config()
      • Env.parse_connection_config()
      • Env.parse_gapjunction_config()
      • Env.load_celltypes()
  • miv_simulator.lfp
    • interpxyz()
  • miv_simulator.lpt
    • lpt()
  • miv_simulator.network
    • ld_bal()
    • lpt_bal()
    • connect_cells()
    • find_gid_pop()
    • connect_cell_selection()
    • connect_gjs()
    • make_cells()
    • make_cell_selection()
    • make_input_cell_selection()
    • init_input_cells()
    • init()
    • shutdown()
    • run()
  • miv_simulator.plotting
    • save_figure()
    • plot_graph()
    • clean_axes()
    • plot_coordinates()
    • plot_spike_raster()
    • plot_spike_histogram()
    • plot_lfp()
    • plot_lfp_spectrogram()
    • plot_biophys_cell_tree()
    • plot_2D_rate_map()
    • plot_2D_histogram()
    • plot_intracellular_state()
    • plot_network_clamp()
    • plot_single_vertex_dist()
    • plot_spatial_spike_raster()
  • miv_simulator.spikedata
    • get_env_spike_dict()
    • read_spike_events()
    • make_spike_dict()
    • spike_density_estimate()
  • miv_simulator.statedata
  • miv_simulator.stgen
    • get_inhom_poisson_spike_times_by_thinning()
    • shotnoise_fromspikes()
  • miv_simulator.stimulus
    • PhaseModConfig
      • PhaseModConfig.frequency
      • PhaseModConfig.mod_depth
      • PhaseModConfig.phase_offset
      • PhaseModConfig.phase_pref
      • PhaseModConfig.phase_range
    • get_input_cell_config()
    • get_2D_arena_bounds()
    • get_2D_arena_extents()
    • get_2D_arena_spatial_mesh()
    • get_2D_arena_grid()
    • generate_linear_trajectory()
    • generate_input_spike_trains()
    • choose_input_selectivity_type()
    • generate_input_features()
    • bin_stimulus_features()
    • rate_maps_from_features()
    • arena_rate_maps_from_features()
    • oscillation_phase_mod_config()
    • global_oscillation_phase_shift()
    • global_oscillation_phase_pref()
    • global_oscillation_initial_phases()
    • stationary_phase_mod()
    • spatial_phase_mod()
  • miv_simulator.synapses
    • get_node_attribute()
    • synapse_seg_density()
    • synapse_seg_counts()
    • distribute_uniform_synapses()
    • distribute_poisson_synapses()
    • SynapseSource
    • SynapseAttributes
      • SynapseAttributes.init_syn_id_attrs_from_iter()
      • SynapseAttributes.init_syn_id_attrs()
      • SynapseAttributes.init_edge_attrs()
      • SynapseAttributes.init_edge_attrs_from_iter()
      • SynapseAttributes.add_pps()
      • SynapseAttributes.has_pps()
      • SynapseAttributes.get_pps()
      • SynapseAttributes.add_netcon()
      • SynapseAttributes.has_netcon()
      • SynapseAttributes.get_netcon()
      • SynapseAttributes.del_netcon()
      • SynapseAttributes.add_vecstim()
      • SynapseAttributes.has_vecstim()
      • SynapseAttributes.get_vecstim()
      • SynapseAttributes.has_mech_attrs()
      • SynapseAttributes.get_mech_attrs()
      • SynapseAttributes.add_mech_attrs()
      • SynapseAttributes.stash_mech_attrs()
      • SynapseAttributes.restore_mech_attrs()
      • SynapseAttributes.modify_mech_attrs()
      • SynapseAttributes.add_mech_attrs_from_iter()
      • SynapseAttributes.filter_synapses()
      • SynapseAttributes.partition_synapses_by_source()
      • SynapseAttributes.get_filtered_syn_ids()
      • SynapseAttributes.partition_syn_ids_by_source()
      • SynapseAttributes.del_syn_id_attr_dict()
    • insert_hoc_cell_syns()
    • insert_biophys_cell_syns()
    • config_biophys_cell_syns()
    • config_hoc_cell_syns()
    • config_syn()
    • syn_in_seg()
    • make_syn_mech()
    • make_shared_synapse_mech()
    • make_unique_synapse_mech()
    • get_syn_mech_param()
    • get_syn_filter_dict()
    • validate_syn_mech_param()
    • modify_syn_param()
    • update_syn_mech_by_sec_type()
    • update_syn_mech_param_by_sec_type()
    • apply_syn_mech_rules()
    • set_syn_mech_param()
    • init_syn_mech_attrs()
    • write_syn_spike_count()
  • miv_simulator.volume
    • network_volume()
    • make_network_volume()
• Simulator
  • miv_simulator.simulator.distribute_synapses
    • distribute_synapses()
  • miv_simulator.simulator.generate_connections
    • generate_connections()
  • miv_simulator.simulator.generate_network_architecture
    • generate_network_architecture()
  • miv_simulator.simulator.generate_synapse_forest
    • generate_synapse_forest()
  • miv_simulator.simulator.measure_distances
    • measure_distances()
• Geometry Modules
  • miv_simulator.geometry.alphavol
    • AlphaShape
      • AlphaShape.bounds
      • AlphaShape.points
      • AlphaShape.simplices
    • tri_graph()
    • angular_deviation()
    • feature_edges()
    • volumes()
    • circumcenters()
    • free_boundary()
    • alpha_shape()
  • miv_simulator.geometry.geometry
    • rotate2d()
    • rotate3d()
    • make_rotate3d()
    • transform_volume()
    • euclidean_distance()
    • get_volume_distances()
    • interp_soma_distances()
    • icp_transform()
  • miv_simulator.geometry.linear_volume
    • euclidean_distance()
    • cartesian_product()
  • miv_simulator.geometry.point_fit
    • PCA()
    • points_plane_fit()
  • miv_simulator.geometry.rbf_surface
    • euclidean_distance()
    • cartesian_product()
  • miv_simulator.geometry.rbf_volume
    • euclidean_distance()
    • cartesian_product()
• Clamps
  • miv_simulator.clamps.cell
    • init_biophys_cell()
    • measure_deflection()
    • fit_membrane_time_constant()
    • measure_time_constant()
  • miv_simulator.clamps.network
    • mpi_excepthook()
    • generate_weights()
    • init_inputs_from_spikes()
    • init_inputs_from_features()
    • init()
    • run()
    • run_with()
    • dist_ctrl()
    • dist_run()
    • show()
    • go()
    • optimize()
• Utilities
  • miv_simulator.utils.utils
    • AbstractEnv
    • ExprClosure
    • Promise
    • Context
      • Context.update()
    • EnumChoice
      • EnumChoice.convert()
    • IncludeLoader
      • IncludeLoader.include()
    • ExplicitDumper
    • write_to_yaml()
    • read_from_yaml()
    • print_param_dict_like_yaml()
    • yaml_convert_scalars()
    • list_index()
    • list_find()
    • list_find_all()
    • list_argsort()
    • viewvalues()
    • consecutive()
    • make_geometric_graph()
    • random_choice_w_replacement()
    • make_random_clusters()
    • random_clustered_shuffle()
    • NamedTupleWithDocstring()
    • partitionn()
    • generator_peek()
    • generator_ifempty()
    • ifempty()
    • compose_iter()
    • get_R2()
    • mvcorrcoef()
    • contiguous_ranges()
    • signal_power_spectrogram()
    • baks()
  • miv_simulator.utils.simtime
  • miv_simulator.utils.neuron
    • PRconfig
      • PRconfig.Ltotal
      • PRconfig.V_rest
      • PRconfig.V_threshold
      • PRconfig.cm_ratio
      • PRconfig.dend_d_Caconc
      • PRconfig.dend_g_pas
      • PRconfig.dend_gmax_Ca
      • PRconfig.dend_gmax_KAHP
      • PRconfig.dend_gmax_KCa
      • PRconfig.e_pas
      • PRconfig.gc
      • PRconfig.global_cm
      • PRconfig.global_diam
      • PRconfig.ic_constant
      • PRconfig.pp
      • PRconfig.soma_g_pas
      • PRconfig.soma_gmax_K
      • PRconfig.soma_gmax_Na
    • BRKconfig
      • BRKconfig.Ltotal
      • BRKconfig.V_rest
      • BRKconfig.V_threshold
      • BRKconfig.cm_ratio
      • BRKconfig.dend_alpha_Caconc
      • BRKconfig.dend_f_Caconc
      • BRKconfig.dend_g_pas
      • BRKconfig.dend_gmax_CaL
      • BRKconfig.dend_gmax_CaN
      • BRKconfig.dend_gmax_KCa
      • BRKconfig.dend_kCa_Caconc
      • BRKconfig.e_pas
      • BRKconfig.gc
      • BRKconfig.global_cm
      • BRKconfig.global_diam
      • BRKconfig.ic_constant
      • BRKconfig.pp
      • BRKconfig.soma_alpha_Caconc
      • BRKconfig.soma_f_Caconc
      • BRKconfig.soma_g_pas
      • BRKconfig.soma_gmax_CaN
      • BRKconfig.soma_gmax_K
      • BRKconfig.soma_gmax_KCa
      • BRKconfig.soma_gmax_Na
      • BRKconfig.soma_kCa_Caconc
    • HocCellInterface
      • HocCellInterface.ais
      • HocCellInterface.all
      • HocCellInterface.apical
      • HocCellInterface.axon
      • HocCellInterface.basal
      • HocCellInterface.hillock
      • HocCellInterface.is_art
      • HocCellInterface.is_reduced
      • HocCellInterface.sections
      • HocCellInterface.soma
      • HocCellInterface.state
    • lambda_f()
    • d_lambda_nseg()
    • reinit_diam()
    • init_nseg()
    • mknetcon()
    • mknetcon_vecstim()
    • load_cell_template()
    • find_template()
    • configure_hoc_env()
    • cx()
    • mkgap()
    • interplocs()
    • make_rec()
  • miv_simulator.utils.io
    • show_celltypes()
    • mkout()
    • spikeout()
    • recsout()
    • lfpout()
    • get_h5py_attr()
    • set_h5py_attr()
    • get_h5py_group()
    • write_cell_selection()
    • write_connection_selection()
    • write_input_cell_selection()
    • H5FileManager

Executables

• CLI Commands
  • Simulation Builder
  • Simulation Runner
  • Analysis scripts
  • Tools

Indices and tables

• Index

• Module Index

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