ALLEN INSTITUTE

# bmtk.tests.simulator.bionet package

## Submodules

## bmtk.tests.simulator.bionet.bionet_virtual_files module

class bmtk.tests.simulator.bionet.bionet_virtual_files.EdgeRow

  Bases: `object`

  property with_dynamics_params

class bmtk.tests.simulator.bionet.bionet_virtual_files.EdgesFile(target_nodes, source_nodes)

  Bases: `object`

  edges_itr(target_gid)
  load(edges_file, edge_types_file)
  property source_network

    Name of network containing the source gids

  property target_network

    Name of network containing the target gids

class bmtk.tests.simulator.bionet.bionet_virtual_files.NodeRow

  Bases: `object`

  property with_dynamics_params

class bmtk.tests.simulator.bionet.bionet_virtual_files.NodesFile(N)

  Bases: `object`

  get_node(gid, cache=False)
  property gids
  load(nodes_file, node_types_file)
  property name

    name of network containing these nodes

  next()
  property node_types_table
  property version

## bmtk.tests.simulator.bionet.conftest module

## bmtk.tests.simulator.bionet.set_cell_params module

bmtk.tests.simulator.bionet.set_cell_params.Biophys1(cell_prop)

  Set parameters for cells from the Allen Cell Types database Prior to setting parameters will replace the axon with the stub

bmtk.tests.simulator.bionet.set_cell_params.IntFire1(cell_prop)

  Set parameters for the IntFire1 cell models.

bmtk.tests.simulator.bionet.set_cell_params.fix_axon(hobj)

  Replace reconstructed axon with a stub

  Parameters:
    hobj: instance of a Biophysical template

      NEURON’s cell object

bmtk.tests.simulator.bionet.set_cell_params.set_params_peri(hobj, params_file_name)

  Set biophysical parameters for the cell

  Parameters:
    hobj: instance of a Biophysical template

      NEURON’s cell object

    params_file_name: string

      name of json file containing biophysical parameters for cell’s model which determine spiking behavior

## bmtk.tests.simulator.bionet.set_syn_params module

bmtk.tests.simulator.bionet.set_syn_params.exp2syn(syn_params, xs, secs)

  Create a list of exp2syn synapses

  Parameters:
    syn_params: dict

      parameters of a synapse

    xs: float

      normalized distance along the section

    secs: hoc object

      target section

  Returns:
    syns: synapse objects

## bmtk.tests.simulator.bionet.set_weights module

bmtk.tests.simulator.bionet.set_weights.gaussianLL(tar_prop, src_prop, con_prop)

bmtk.tests.simulator.bionet.set_weights.wmax(tar_prop, src_prop, con_prop)

## bmtk.tests.simulator.bionet.test_biograph module

bmtk.tests.simulator.bionet.test_biograph.test_add_edges()

bmtk.tests.simulator.bionet.test_biograph.test_add_nodes()

## bmtk.tests.simulator.bionet.test_gids module

bmtk.tests.simulator.bionet.test_gids.test_gid_pool()

## bmtk.tests.simulator.bionet.test_iclamp module

class bmtk.tests.simulator.bionet.test_iclamp.MockBioSimulator

  Bases: `object`

  get_cell_gid(_)
  get_node_set(_)
  gids()
  property local_gids

class bmtk.tests.simulator.bionet.test_iclamp.MockCell(swc_path='/build/bmtk-yBrUqs/bmtk-1.1.1+ds/bmtk/tests/simulator/bionet/components/morphology/rorb_480169178_morphology.swc')

  Bases: `object`

class bmtk.tests.simulator.bionet.test_iclamp.NRNPythonObj

  Bases: `object`

  post_fadvance()

bmtk.tests.simulator.bionet.test_iclamp.create_csv(amps, ts, amps_col='amps', ts_col='timestamps', sep=' ')

bmtk.tests.simulator.bionet.test_iclamp.run_sim(tstop, v_init)

bmtk.tests.simulator.bionet.test_iclamp.test_bad_input(input_type)

bmtk.tests.simulator.bionet.test_iclamp.test_iclamp_nwb()

bmtk.tests.simulator.bionet.test_iclamp.test_invalid_csv()

bmtk.tests.simulator.bionet.test_iclamp.test_invalid_onset()

bmtk.tests.simulator.bionet.test_iclamp.test_recalc_timestamps(ts, amps, expected_dt, expected_amps)

bmtk.tests.simulator.bionet.test_iclamp.test_sim_csv()

bmtk.tests.simulator.bionet.test_iclamp.test_sim_list()

bmtk.tests.simulator.bionet.test_iclamp.test_sim_scalar()

## bmtk.tests.simulator.bionet.test_morphology module

bmtk.tests.simulator.bionet.test_morphology.check_lazy_loading()

bmtk.tests.simulator.bionet.test_morphology.fix_axon_peri(hobj)

  Replace reconstructed axon with a stub

bmtk.tests.simulator.bionet.test_morphology.load_hobj()

bmtk.tests.simulator.bionet.test_morphology.test_base()

bmtk.tests.simulator.bionet.test_morphology.test_find_sections()

bmtk.tests.simulator.bionet.test_morphology.test_full()

bmtk.tests.simulator.bionet.test_morphology.test_get_swc_id()

bmtk.tests.simulator.bionet.test_morphology.test_get_target_segments()

bmtk.tests.simulator.bionet.test_morphology.test_move_and_rotate()

bmtk.tests.simulator.bionet.test_morphology.test_move_and_rotate_cached()

bmtk.tests.simulator.bionet.test_morphology.test_multicell()

bmtk.tests.simulator.bionet.test_morphology.test_remove_secs()

bmtk.tests.simulator.bionet.test_morphology.test_seg_props_cache()

## bmtk.tests.simulator.bionet.test_nrn module

bmtk.tests.simulator.bionet.test_nrn.test_cell_model()

bmtk.tests.simulator.bionet.test_nrn.test_cell_model_decorator()

bmtk.tests.simulator.bionet.test_nrn.test_load_py_modules()

bmtk.tests.simulator.bionet.test_nrn.test_synapse_model()

bmtk.tests.simulator.bionet.test_nrn.test_synapse_model_decorator()

bmtk.tests.simulator.bionet.test_nrn.test_weight()

bmtk.tests.simulator.bionet.test_nrn.test_weight_decorator()

## bmtk.tests.simulator.bionet.test_virtualcell module

class bmtk.tests.simulator.bionet.test_virtualcell.MockNode

  Bases: `object`

  node_id = 0

class bmtk.tests.simulator.bionet.test_virtualcell.MockSpikes(spike_times)

  Bases: `object`

  get_times(node_id)

class bmtk.tests.simulator.bionet.test_virtualcell.NRNPythonObj

  Bases: `object`

  post_fadvance()

bmtk.tests.simulator.bionet.test_virtualcell.test_spiketrain(spike_times)

bmtk.tests.simulator.bionet.test_virtualcell.test_spiketrains_negative(spike_times)

## Module contents