pyneuroml.lems package#
- 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)#
pyneuroml.lems.LEMSSimulation module#
Helper class for generating LEMS xml files for simulations
- class pyneuroml.lems.LEMSSimulation.LEMSSimulation(sim_id: str, duration: float, dt: float, target: str = None, comment: str = '\n\n This LEMS file has been automatically generated using PyNeuroML v1.0.8 (libNeuroML v0.5.1)\n\n ', lems_file_generate_seed: Any = None, simulation_seed: int = 12345)#
Bases:
object
Helper class for creating LEMS Simulations for running NeuroML2 models.
- 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: str, column_id: str, quantity: str) None #
Add a column to the output file with id output_file_id
- Parameters:
output_file_id (str) – id of output file (must be created first using create_output_file)
column_id (str) – id of column to add
quantity (str) – quantity to add
- Returns:
None
- Raises:
ValueError – if provided output_file_id has not been created yet.
- add_line_to_display(display_id: str, line_id: str, quantity: str, scale: str = '1', color: str = None, timeScale: str = '1ms') None #
Add a new line to the display
- Parameters:
display_id (str) – id of display
line_id (str) – id of line
quantity – name of quantity being represented
scale (str) – scale of line
color (str) – color of line, randomly chosen if None
timeScale (str) – scale of time axis
- Returns:
None
- Raises:
ValueError – if provided display_id has not been created yet.
- add_selection_to_event_output_file(event_output_file_id: str, event_id: str, select: str, event_port: str) None #
Add a column to the event output file with id event_output_file_id.
- Parameters:
event_output_file_id (str) – id of output file (must be created first using create_output_file)
event_id (str) – id of event to add
select (str) – selection to add
event_port (str) – event port to add
- Returns:
None
- Raises:
ValueError – if provided event_output_file_id has not been created yet.
- assign_simulation_target(target: str) None #
Assign a simulation target.
- Parameters:
target (str) – id of target component
- Returns:
None
- create_display(id: str, title: str, ymin: str, ymax: str, timeScale: str = '1ms') None #
Create a new display
- Parameters:
id (str) – id of display
title (str) – title of display
ymin (str) – min y value of display
ymax (str) – max y value of display
timeScale (str) – time scale of display
- Returns:
None
- create_event_output_file(id, file_name, format='ID_TIME')#
Create a new output file for storing events recorded from simulations.
For storing other outputs (not events), please see create_output_file instead.
TODO: list what formats are available
- Parameters:
id (str) – id of output file
file_name (str) – name of output file
format (str) – format of file
- Returns:
None
- create_output_file(id: str, file_name: str)#
Create a new output file for storing values recorded for a simulation.
For storing events, such as spikes, please see create_event_output_file.
- Parameters:
id (str) – id of output file
file_name (str) – name of output file
- Returns:
None
- include_lems_file(lems_file_name: str, include_included: bool = True) None #
Include additional LEMS file in the simulation.
- Parameters:
lems_file_name (str) – name of LEMS file to include
include_included (bool) – toggle to include files included by provided LEMS file
- Returns:
None
- include_neuroml2_file(nml2_file_name: str, include_included: bool = True, relative_to_dir: str = '.') None #
Include additional NeuroML2 file.
This will only add the provided file if it has not already been included.
- Parameters:
nml2_file_name (str) – name of NeuroML2 file to include
include_included (bool) – toggle to include any files included in the provided file
relative_to_dir (str) – directory relative to which the provided nml2_file_name is being provided
- Returns:
None
- lems_info: dict[str, Any] = {}#
- my_random = <random.Random object>#
- save_to_file(file_name: str = None)#
Save LEMSSimulation to a file.
- Parameters:
file_name – name of file to store to. LEMS_<some id string>.xml is the suggested format. Leave empty to use LEMS_<sim_id>.xml :type file_name: str
- Returns:
name of file
- Return type:
str
- set_report_file(report_file_name: str) None #
Set a report file.
The report file is a short file saved after simulation with run time, simulator version etc.
- Parameters:
report_file_name (str) – name of report file
- Returns:
None
- to_xml() str #
Export simulation to XML.
- Returns:
XML representation
- Return type:
str