bmtk.tests.simulator.bionet package

Submodules

bmtk.tests.simulator.bionet.bionet_virtual_files module

class bmtk.tests.simulator.bionet.bionet_virtual_files.EdgeRow[source]

Bases: object

property with_dynamics_params
class bmtk.tests.simulator.bionet.bionet_virtual_files.EdgesFile(target_nodes, source_nodes)[source]

Bases: object

edges_itr(target_gid)[source]
load(edges_file, edge_types_file)[source]
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[source]

Bases: object

property with_dynamics_params
class bmtk.tests.simulator.bionet.bionet_virtual_files.NodesFile(N)[source]

Bases: object

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

name of network containing these nodes

next()[source]
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)[source]

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)[source]

Set parameters for the IntFire1 cell models.

bmtk.tests.simulator.bionet.set_cell_params.fix_axon(hobj)[source]

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)[source]

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)[source]

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

bmtk.tests.simulator.bionet.test_biograph module

bmtk.tests.simulator.bionet.test_biograph.test_add_edges()[source]
bmtk.tests.simulator.bionet.test_biograph.test_add_nodes()[source]

bmtk.tests.simulator.bionet.test_gids module

bmtk.tests.simulator.bionet.test_gids.test_gid_pool()[source]

bmtk.tests.simulator.bionet.test_iclamp module

class bmtk.tests.simulator.bionet.test_iclamp.MockBioSimulator[source]

Bases: object

get_cell_gid(_)[source]
get_node_set(_)[source]
gids()[source]
property local_gids
class bmtk.tests.simulator.bionet.test_iclamp.MockCell(swc_path='/build/reproducible-path/bmtk-1.1.1+ds/bmtk/tests/simulator/bionet/components/morphology/rorb_480169178_morphology.swc')[source]

Bases: object

class bmtk.tests.simulator.bionet.test_iclamp.NRNPythonObj[source]

Bases: object

post_fadvance()[source]
bmtk.tests.simulator.bionet.test_iclamp.create_csv(amps, ts, amps_col='amps', ts_col='timestamps', sep=' ')[source]
bmtk.tests.simulator.bionet.test_iclamp.run_sim(tstop, v_init)[source]
bmtk.tests.simulator.bionet.test_iclamp.test_bad_input(input_type)[source]
bmtk.tests.simulator.bionet.test_iclamp.test_iclamp_nwb()[source]
bmtk.tests.simulator.bionet.test_iclamp.test_invalid_csv()[source]
bmtk.tests.simulator.bionet.test_iclamp.test_invalid_onset()[source]
bmtk.tests.simulator.bionet.test_iclamp.test_recalc_timestamps(ts, amps, expected_dt, expected_amps)[source]
bmtk.tests.simulator.bionet.test_iclamp.test_sim_csv()[source]
bmtk.tests.simulator.bionet.test_iclamp.test_sim_list()[source]
bmtk.tests.simulator.bionet.test_iclamp.test_sim_scalar()[source]

bmtk.tests.simulator.bionet.test_morphology module

bmtk.tests.simulator.bionet.test_morphology.check_lazy_loading()[source]
bmtk.tests.simulator.bionet.test_morphology.fix_axon_peri(hobj)[source]

Replace reconstructed axon with a stub

bmtk.tests.simulator.bionet.test_morphology.load_hobj()[source]
bmtk.tests.simulator.bionet.test_morphology.test_base()[source]
bmtk.tests.simulator.bionet.test_morphology.test_find_sections()[source]
bmtk.tests.simulator.bionet.test_morphology.test_full()[source]
bmtk.tests.simulator.bionet.test_morphology.test_get_swc_id()[source]
bmtk.tests.simulator.bionet.test_morphology.test_get_target_segments()[source]
bmtk.tests.simulator.bionet.test_morphology.test_move_and_rotate()[source]
bmtk.tests.simulator.bionet.test_morphology.test_move_and_rotate_cached()[source]
bmtk.tests.simulator.bionet.test_morphology.test_multicell()[source]
bmtk.tests.simulator.bionet.test_morphology.test_remove_secs()[source]
bmtk.tests.simulator.bionet.test_morphology.test_seg_props_cache()[source]

bmtk.tests.simulator.bionet.test_nrn module

bmtk.tests.simulator.bionet.test_nrn.test_cell_model()[source]
bmtk.tests.simulator.bionet.test_nrn.test_cell_model_decorator()[source]
bmtk.tests.simulator.bionet.test_nrn.test_load_py_modules()[source]
bmtk.tests.simulator.bionet.test_nrn.test_synapse_model()[source]
bmtk.tests.simulator.bionet.test_nrn.test_synapse_model_decorator()[source]
bmtk.tests.simulator.bionet.test_nrn.test_weight()[source]
bmtk.tests.simulator.bionet.test_nrn.test_weight_decorator()[source]

bmtk.tests.simulator.bionet.test_virtualcell module

class bmtk.tests.simulator.bionet.test_virtualcell.MockNode[source]

Bases: object

node_id = 0
class bmtk.tests.simulator.bionet.test_virtualcell.MockSpikes(spike_times)[source]

Bases: object

get_times(node_id)[source]
class bmtk.tests.simulator.bionet.test_virtualcell.NRNPythonObj[source]

Bases: object

post_fadvance()[source]
bmtk.tests.simulator.bionet.test_virtualcell.test_spiketrain(spike_times)[source]
bmtk.tests.simulator.bionet.test_virtualcell.test_spiketrains_negative(spike_times)[source]

Module contents