bmtk.simulator.bionet.modules package¶
Submodules¶
bmtk.simulator.bionet.modules.ecp module¶
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class
bmtk.simulator.bionet.modules.ecp.
EcpMod
(tmp_dir, file_name, electrode_positions, contributions_dir=None, cells=None, variable_name='v', electrode_channels=None, cell_bounds=None)[source]¶ Bases:
bmtk.simulator.bionet.modules.sim_module.SimulatorMod
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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 simular functionality
Parameters: - sim – Simulation object
- block_interval – The time interval (tstep_start, tstep_end) for which the block is being called on.
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finalize
(sim)[source]¶ Call once at the very end of the simulation.
Parameters: sim – Simulation object
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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
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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
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bmtk.simulator.bionet.modules.record_cellvars module¶
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class
bmtk.simulator.bionet.modules.record_cellvars.
MembraneReport
(tmp_dir, file_name, variable_name, cells=None, gids=None, sections='all', buffer_data=True, transform={}, **kwargs)[source]¶ Bases:
bmtk.simulator.bionet.modules.sim_module.SimulatorMod
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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 simular 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
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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
-
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
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class
bmtk.simulator.bionet.modules.record_cellvars.
SomaReport
(tmp_dir, file_name, variable_name, cells, sections='soma', buffer_data=True, transform={}, **kwargs)[source]¶ Bases:
bmtk.simulator.bionet.modules.record_cellvars.MembraneReport
Special case for when only needing to save the soma variable
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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
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step
(sim, tstep, rel_time=0.0)[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
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bmtk.simulator.bionet.modules.record_clamp module¶
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class
bmtk.simulator.bionet.modules.record_clamp.
ClampReport
(tmp_dir, file_name, variable_name, buffer_data=True, **kwargs)[source]¶ Bases:
bmtk.simulator.bionet.modules.sim_module.SimulatorMod
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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 simular 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
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initialize
(sim, clamps)[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
-
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
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variable
¶
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bmtk.simulator.bionet.modules.record_netcons module¶
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class
bmtk.simulator.bionet.modules.record_netcons.
NetconReport
(tmp_dir, file_name, variable_name, cells, sections='all', syn_type='Exp2Syn', buffer_data=True, transform={})[source]¶ Bases:
bmtk.simulator.bionet.modules.sim_module.SimulatorMod
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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 simular 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
-
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
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bmtk.simulator.bionet.modules.record_spikes module¶
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class
bmtk.simulator.bionet.modules.record_spikes.
SpikesMod
(tmp_dir, spikes_file_csv=None, spikes_file=None, spikes_file_nwb=None, cache_to_disk=True, spikes_sort_order=None, mode='a')[source]¶ Bases:
bmtk.simulator.bionet.modules.sim_module.SimulatorMod
Module use for saving spikes
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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 simular functionality
Parameters: - sim – Simulation object
- block_interval – The time interval (tstep_start, tstep_end) for which the block is being called on.
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bmtk.simulator.bionet.modules.save_synapses module¶
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class
bmtk.simulator.bionet.modules.save_synapses.
ConnectionWriter
(network_dir)[source]¶ Bases:
object
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class
bmtk.simulator.bionet.modules.save_synapses.
H5Merger
(network_dir, grp_keys)[source]¶ Bases:
object
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class
bmtk.simulator.bionet.modules.save_synapses.
SaveSynapses
(network_dir, single_file=False, **params)[source]¶ Bases:
bmtk.simulator.bionet.modules.sim_module.SimulatorMod
bmtk.simulator.bionet.modules.sim_module module¶
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class
bmtk.simulator.bionet.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()
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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 simular 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
-
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.bionet.modules.xstim module¶
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class
bmtk.simulator.bionet.modules.xstim.
StimXElectrode
(positions_file, waveform, mesh_files_dir, dt)[source]¶ Bases:
object
Extracellular Stimulating electrode
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class
bmtk.simulator.bionet.modules.xstim.
XStimMod
(positions_file, waveform, mesh_files_dir=None, cells=None, set_nrn_mechanisms=True, node_set=None)[source]¶ Bases:
bmtk.simulator.bionet.modules.sim_module.SimulatorMod
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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
-
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
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bmtk.simulator.bionet.modules.xstim_waveforms module¶
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class
bmtk.simulator.bionet.modules.xstim_waveforms.
BaseWaveform
[source]¶ Bases:
object
Abstraction of waveform class to ensure calculate method is implemented
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class
bmtk.simulator.bionet.modules.xstim_waveforms.
BaseWaveformType
(waveform_config)[source]¶ Bases:
object
Specific waveform type
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class
bmtk.simulator.bionet.modules.xstim_waveforms.
ComplexWaveform
(el_collection)[source]¶ Bases:
bmtk.simulator.bionet.modules.xstim_waveforms.BaseWaveform
Superposition of simple waveforms
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class
bmtk.simulator.bionet.modules.xstim_waveforms.
WaveformCustom
(waveform_file)[source]¶ Bases:
bmtk.simulator.bionet.modules.xstim_waveforms.BaseWaveform
Custom waveform defined by csv file
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class
bmtk.simulator.bionet.modules.xstim_waveforms.
WaveformTypeDC
(waveform_config)[source]¶ Bases:
bmtk.simulator.bionet.modules.xstim_waveforms.BaseWaveformType
,bmtk.simulator.bionet.modules.xstim_waveforms.BaseWaveform
DC (step) waveform
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class
bmtk.simulator.bionet.modules.xstim_waveforms.
WaveformTypeSin
(waveform_config)[source]¶ Bases:
bmtk.simulator.bionet.modules.xstim_waveforms.BaseWaveformType
,bmtk.simulator.bionet.modules.xstim_waveforms.BaseWaveform
Sinusoidal waveform