bmtk.utils package¶
Subpackages¶
- bmtk.utils.io package
- bmtk.utils.reports package
- Subpackages
- bmtk.utils.reports.compartment package
- bmtk.utils.reports.spike_trains package
- Submodules
- bmtk.utils.reports.spike_trains.core module
- bmtk.utils.reports.spike_trains.plotting module
- bmtk.utils.reports.spike_trains.spike_train_buffer module
- bmtk.utils.reports.spike_trains.spike_train_readers module
- bmtk.utils.reports.spike_trains.spike_trains module
- bmtk.utils.reports.spike_trains.spike_trains_api module
- bmtk.utils.reports.spike_trains.spikes_file_writers module
- bmtk.utils.reports.spike_trains.stats module
- Module contents
- Submodules
- bmtk.utils.reports.current_writer module
- Module contents
- Subpackages
- bmtk.utils.sonata package
- Subpackages
- Submodules
- bmtk.utils.sonata.column_property module
- bmtk.utils.sonata.edge module
- bmtk.utils.sonata.file module
- bmtk.utils.sonata.file_root module
- bmtk.utils.sonata.group module
- bmtk.utils.sonata.node module
- bmtk.utils.sonata.population module
- bmtk.utils.sonata.types_table module
- bmtk.utils.sonata.utils module
- Module contents
Submodules¶
bmtk.utils.hdf5_helper module¶
bmtk.utils.sim_setup module¶
- class bmtk.utils.sim_setup.BioNetEnvBuilder(base_dir='.', network_dir=None, components_dir=None, output_dir=None, node_sets_file=None)[source]¶
Bases:
bmtk.utils.sim_setup.EnvBuilder
- property bmtk_simulator¶
- property examples_dir¶
- property target_simulator¶
- class bmtk.utils.sim_setup.EnvBuilder(base_dir='.', network_dir=None, components_dir=None, output_dir=None, node_sets_file=None)[source]¶
Bases:
object
- property base_dir¶
- property bmtk_simulator¶
- build(include_examples=False, use_relative_paths=True, report_vars=[], report_nodes=None, clamp_reports=[], current_clamp=None, file_current_clamp=None, se_voltage_clamp=None, spikes_inputs=None, **run_args)[source]¶
- property components_dir¶
- property examples_dir¶
- property network_dir¶
- property node_sets_file¶
- property output_dir¶
- property scripts_root¶
- property target_simulator¶
- class bmtk.utils.sim_setup.FilterNetEnvBuilder(base_dir='.', network_dir=None, components_dir=None, output_dir=None, node_sets_file=None)[source]¶
Bases:
bmtk.utils.sim_setup.EnvBuilder
- property bmtk_simulator¶
- property examples_dir¶
- property target_simulator¶
- class bmtk.utils.sim_setup.PointNetEnvBuilder(base_dir='.', network_dir=None, components_dir=None, output_dir=None, node_sets_file=None)[source]¶
Bases:
bmtk.utils.sim_setup.EnvBuilder
- property bmtk_simulator¶
- property examples_dir¶
- property target_simulator¶
- bmtk.utils.sim_setup.build_env_bionet(base_dir='.', network_dir=None, components_dir=None, node_sets_file=None, include_examples=False, tstart=0.0, tstop=1000.0, dt=0.001, dL=20.0, spikes_threshold=- 15.0, nsteps_block=5000, v_init=- 80.0, celsius=34.0, report_vars=[], report_nodes=None, clamp_reports=[], current_clamp=None, file_current_clamp=None, se_voltage_clamp=None, spikes_inputs=None, compile_mechanisms=False, use_relative_paths=True)[source]¶
- bmtk.utils.sim_setup.build_env_filternet(base_dir='.', network_dir=None, components_dir=None, node_sets_file=None, include_examples=False, tstart=0.0, tstop=1000.0)[source]¶
- bmtk.utils.sim_setup.build_env_pointnet(base_dir='.', network_dir=None, components_dir=None, node_sets_file=None, include_examples=False, tstart=0.0, tstop=1000.0, dt=0.001, dL=20.0, spikes_threshold=- 15.0, nsteps_block=5000, v_init=- 80.0, celsius=34.0, report_vars=[], report_nodes=None, current_clamp=None, spikes_inputs=None, use_relative_paths=True)[source]¶