pyneuroml.lems package

Submodules

pyneuroml.lems.LEMSSimulation module

Helper class for generating LEMS xml files for simulations

class pyneuroml.lems.LEMSSimulation.LEMSSimulation(sim_id, duration, dt, target=None, comment='\n\n        This LEMS file has been automatically generated using PyNeuroML v0.5.13 (libNeuroML v0.2.55)\n\n    ', lems_file_generate_seed=None, simulation_seed=12345)

Bases: object

TEMPLATE_FILE = '/home/docs/checkouts/readthedocs.org/user_builds/pyneuroml/checkouts/development/pyneuroml/lems/LEMS_TEMPLATE.xml'
add_column_to_output_file(output_file_id, column_id, quantity)
add_line_to_display(display_id, line_id, quantity, scale=1, color=None, timeScale='1ms')
add_selection_to_event_output_file(event_output_file_id, event_id, select, event_port)
assign_simulation_target(target)
create_display(id, title, ymin, ymax, timeScale='1ms')
create_event_output_file(id, file_name, format='ID_TIME')
create_output_file(id, file_name)
include_lems_file(lems_file_name, include_included=True)
include_neuroml2_file(nml2_file_name, include_included=True, relative_to_dir='.')
lems_info = {}
my_random = <random.Random object>
save_to_file(file_name=None)
set_report_file(report_file_name)

short file saved after simulation with run time, simulator version etc.

to_xml()

Module contents

pyneuroml.lems.generate_lems_file_for_neuroml(sim_id, neuroml_file, target, duration, dt, lems_file_name, target_dir, nml_doc=None, include_extra_files=[], gen_plots_for_all_v=True, plot_all_segments=False, gen_plots_for_quantities={}, gen_plots_for_only_populations=[], gen_saves_for_all_v=True, save_all_segments=False, gen_saves_for_only_populations=[], gen_saves_for_quantities={}, gen_spike_saves_for_all_somas=False, gen_spike_saves_for_only_populations=[], gen_spike_saves_for_cells={}, spike_time_format='ID_TIME', copy_neuroml=True, report_file_name=None, lems_file_generate_seed=None, verbose=False, simulation_seed=12345)
pyneuroml.lems.get_pop_index(quantity)
pyneuroml.lems.safe_variable(quantity)