Python API reference

• multiscale_run package
  • Subpackages
  • Submodules
  • multiscale_run.bloodflow_manager module
    • MsrBloodflowManager
      • MsrBloodflowManager.get_boundary_flows()
      • MsrBloodflowManager.get_entry_nodes()
      • MsrBloodflowManager.get_flows()
      • MsrBloodflowManager.get_seg_points()
      • MsrBloodflowManager.get_vols()
      • MsrBloodflowManager.load_circuit()
      • MsrBloodflowManager.n_segs
      • MsrBloodflowManager.set_radii()
      • MsrBloodflowManager.update_static_flow()
  • multiscale_run.cli module
    • argument_parser()
    • check()
    • command()
    • compute()
    • edit_mod_files()
    • index()
    • init()
    • main()
    • post_processing()
    • stats()
  • multiscale_run.config module
    • MsrConfig
      • MsrConfig.bloodflow_dt
      • MsrConfig.check()
      • MsrConfig.compute_multiscale_run_ndts()
      • MsrConfig.conn_dt()
      • MsrConfig.conn_ndts()
      • MsrConfig.default()
      • MsrConfig.dt_info()
      • MsrConfig.is_bloodflow_active()
      • MsrConfig.is_conn_active()
      • MsrConfig.is_manager_active()
      • MsrConfig.is_metabolism_active()
      • MsrConfig.is_steps_active()
      • MsrConfig.items()
      • MsrConfig.manager_dt()
      • MsrConfig.manager_idts()
      • MsrConfig.manager_ndts()
      • MsrConfig.metabolism_dt
      • MsrConfig.multiscale_run_dt
      • MsrConfig.neurodamus_dt
      • MsrConfig.pretty_print_conn()
      • MsrConfig.steps_dt
      • MsrConfig.values()
    • MsrConfigException
    • MsrConfigSchemaError
    • NamedCircuit
      • NamedCircuit.config()
      • NamedCircuit.json()
  • multiscale_run.connection_manager module
    • MsrConnectionManager
      • MsrConnectionManager.bloodflow2metabolism_sync()
      • MsrConnectionManager.connect_bloodflow2steps()
      • MsrConnectionManager.connect_neurodamus2neurodamus()
      • MsrConnectionManager.connect_neurodamus2steps()
      • MsrConnectionManager.neurodamus2bloodflow_sync()
      • MsrConnectionManager.neurodamus2metabolism_sync()
      • MsrConnectionManager.neurodamus2steps_sync()
      • MsrConnectionManager.remove_gids()
      • MsrConnectionManager.steps2metabolism_sync()
      • MsrConnectionManager.sync()
  • multiscale_run.metabolism_manager module
    • MsrAbortSimulationException
    • MsrExcludeNeuronException
    • MsrMetabManagerException
    • MsrMetabolismManager
      • MsrMetabolismManager.alive_gids()
      • MsrMetabolismManager.check_inputs()
      • MsrMetabolismManager.errors
      • MsrMetabolismManager.get_error()
      • MsrMetabolismManager.get_parameters_idx()
      • MsrMetabolismManager.get_vm_idx()
      • MsrMetabolismManager.ndts
      • MsrMetabolismManager.ngids
      • MsrMetabolismManager.raw_gids
      • MsrMetabolismManager.reset_constants()
      • MsrMetabolismManager.reset_parameters()
      • MsrMetabolismManager.reset_u0()
      • MsrMetabolismManager.set_parameters_idxs()
      • MsrMetabolismManager.set_vm_idxs()
      • MsrMetabolismManager.solve()
  • multiscale_run.neurodamus_manager module
    • MsrNeurodamusManager
      • MsrNeurodamusManager.check_neuron_removal_status()
      • MsrNeurodamusManager.gen_secs()
      • MsrNeurodamusManager.gen_segs()
      • MsrNeurodamusManager.gen_to_be_removed_segs()
      • MsrNeurodamusManager.get_compartment_report_var()
      • MsrNeurodamusManager.get_nXsecMat()
      • MsrNeurodamusManager.get_nsecXnsegMat()
      • MsrNeurodamusManager.get_seg_points()
      • MsrNeurodamusManager.get_var()
      • MsrNeurodamusManager.get_vasc_radii()
      • MsrNeurodamusManager.get_vasculature_path()
      • MsrNeurodamusManager.gids()
      • MsrNeurodamusManager.set_managers()
      • MsrNeurodamusManager.set_var()
      • MsrNeurodamusManager.solve()
      • MsrNeurodamusManager.stats()
  • multiscale_run.preprocessor module
    • MsrMeshError
    • MsrPreprocessor
      • MsrPreprocessor.config
      • MsrPreprocessor.autogen_mesh()
      • MsrPreprocessor.autogen_node_sets()
      • MsrPreprocessor.check_mesh()
      • MsrPreprocessor.extract_information_from_circuit()
      • MsrPreprocessor.ntets
  • multiscale_run.reporter module
    • MsrReporter
      • MsrReporter.init_files()
      • MsrReporter.pick_config_reports_section()
      • MsrReporter.record()
    • MsrReporterException
  • multiscale_run.simulation module
    • MsrSimulation
      • MsrSimulation.compute()
      • MsrSimulation.finalize()
      • MsrSimulation.init()
      • MsrSimulation.init_metabolism()
      • MsrSimulation.init_multiscale_run()
      • MsrSimulation.init_neurodamus()
      • MsrSimulation.main()
      • MsrSimulation.stats()
      • MsrSimulation.sync()
      • MsrSimulation.warmup()
    • main()
  • multiscale_run.steps_manager module
    • MsrStepsManager
      • MsrStepsManager.add_curr_to_conc()
      • MsrStepsManager.bbox()
      • MsrStepsManager.check_pts_inside_mesh_bbox()
      • MsrStepsManager.get_nsegXtetMat()
      • MsrStepsManager.get_tetXbfSegMat()
      • MsrStepsManager.get_tetXtetInvMmat()
      • MsrStepsManager.get_tetXtetMat()
      • MsrStepsManager.get_tet_concs()
      • MsrStepsManager.get_tet_counts()
      • MsrStepsManager.get_tet_quantity()
      • MsrStepsManager.init_concentrations()
      • MsrStepsManager.init_mesh()
      • MsrStepsManager.init_sim()
  • multiscale_run.utils module
    • MsrException
    • PyExprEval
      • PyExprEval.simple_eval
    • append_suffix()
    • bbox()
    • cache_decorator()
    • check_value()
    • comm()
    • copy_symlinks()
    • delete_cols()
    • delete_rows()
    • describe_obj()
    • generate_cube_corners()
    • get_resolved_value()
    • get_subs_d()
    • get_var_name()
    • heavy_duty_MPI_Gather()
    • json_sanitize()
    • load_json()
    • log_stats()
    • logs_decorator()
    • merge_dicts()
    • mpi()
    • ppf()
    • print_once()
    • pushd()
    • pushtempd()
    • rank()
    • rank0()
    • rank_print()
    • remove_elems()
    • remove_path()
    • replace_values()
    • resolve_replaces()
    • size()
    • stats()
    • strtobool()
    • timesteps()
  • Module contents

Source

modules.rst