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
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bmtk_simulator
¶
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examples_dir
¶
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target_simulator
¶
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class
bmtk.utils.sim_setup.
EnvBuilder
(base_dir='.', network_dir=None, components_dir=None, output_dir=None, node_sets_file=None)[source]¶ Bases:
object
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base_dir
¶
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bmtk_simulator
¶
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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, config_file='config.json', **run_args)[source]¶
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components_dir
¶
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examples_dir
¶
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network_dir
¶
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node_sets_file
¶
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output_dir
¶
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scripts_root
¶
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target_simulator
¶
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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
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bmtk_simulator
¶
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examples_dir
¶
-
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
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bmtk_simulator
¶
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examples_dir
¶
-
target_simulator
¶
-
-
class
bmtk.utils.sim_setup.
PopNetEnvBuilder
(base_dir='.', network_dir=None, components_dir=None, output_dir=None, node_sets_file=None)[source]¶ Bases:
bmtk.utils.sim_setup.EnvBuilder
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bmtk_simulator
¶
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examples_dir
¶
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target_simulator
¶
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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, config_file=None)[source]¶
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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, config_file='config.json')[source]¶
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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, config_file=None)[source]¶