bmtk.simulator.pointnet.modules package¶
Submodules¶
bmtk.simulator.pointnet.modules.ecephys_module module¶
- class bmtk.simulator.pointnet.modules.ecephys_module.PointECEphysUnitsModule(name, **kwargs)[source]¶
Bases:
ECEphysUnitsModule
- bmtk.simulator.pointnet.modules.ecephys_module.set_spikes(node_id, nest_obj, spike_trains)¶
bmtk.simulator.pointnet.modules.iclamp module¶
bmtk.simulator.pointnet.modules.multimeter_reporter module¶
- class bmtk.simulator.pointnet.modules.multimeter_reporter.MultimeterMod(tmp_dir, file_name, variable_name, cells, tstart=None, tstop=None, interval=None, to_h5=True, delete_dat=True, **opt_params)[source]¶
Bases:
SimulatorMod
- bmtk.simulator.pointnet.modules.multimeter_reporter.create_multimeter(tstart, tstop, variable_name, label)¶
- bmtk.simulator.pointnet.modules.multimeter_reporter.create_multimeter_nest2(tstart, tstop, variable_name, label)[source]¶
- bmtk.simulator.pointnet.modules.multimeter_reporter.create_multimeter_nest3(tstart, tstop, variable_name, label)[source]¶
- bmtk.simulator.pointnet.modules.multimeter_reporter.read_dat(dat_file, variable_name)¶
bmtk.simulator.pointnet.modules.record_spikes module¶
- class bmtk.simulator.pointnet.modules.record_spikes.SpikesMod(tmp_dir, spikes_file_csv=None, spikes_file=None, spikes_file_nwb=None, spikes_sort_order=None, cache_to_disk=True, compression='gzip')[source]¶
Bases:
SimulatorMod
Module use for saving spikes
- bmtk.simulator.pointnet.modules.record_spikes.create_spike_detector(label)¶
- bmtk.simulator.pointnet.modules.record_spikes.read_spikes_file(spike_trains_writer, gid_map, label)¶
bmtk.simulator.pointnet.modules.sim_module module¶
- class bmtk.simulator.pointnet.modules.sim_module.SimulatorMod[source]¶
Bases:
object
Class for writing custom bionet functions that will be called during the simulation. To use overwrite one or more of the following methods in a subclass, and bionet will call the function at the appropiate time.
- To call during a simulation:
… sim = Simulation(…) mymod = MyModule(…) sim.add_mod(mymod) sim.run()
- block(sim, block_interval)[source]¶
This method is called once after every block of time, as specified by the configuration.
Unlike the step method which is called during every time-step, the block method will typically be called only a few times over the entire simulation. The block method is preferable for accessing and saving to the disk, summing up existing data, or similar functionality
- Parameters:
sim – Simulation object
block_interval – The time interval (tstep_start, tstep_end) for which the block is being called on.
- finalize(sim)[source]¶
Call once at the very end of the simulation.
- Parameters:
sim – Simulation object
- initialize(sim)[source]¶
Will be called once at the beginning of the simulation run, after the network and simulation parameters have all been finalized.
- Parameters:
sim – Simulation object
- preload(sim)[source]¶
Will be called once at the beginning of the simulation run before network is loaded
- Parameters:
sim – Simulation object
- step(sim, tstep)[source]¶
Called on every single time step (dt).
The step method is used for anything that should be recorded or changed continously. dt is determined during the setup, and the sim parameter can be used to access simulation, network and individual cell properties
- Parameters:
sim – Simulation object.
tstep – The decrete time-step
bmtk.simulator.pointnet.modules.spikes_inputs module¶
- class bmtk.simulator.pointnet.modules.spikes_inputs.SpikesInputsMod(name, input_type, module, **kwargs)[source]¶
Bases:
SimulatorMod
bmtk.simulator.pointnet.modules.weight_recorder module¶
- class bmtk.simulator.pointnet.modules.weight_recorder.WeightRecorder(name, nest_model, model_template, file_name, output_dir='.', **kwargs)[source]¶
Bases:
SimulatorMod