cellsium.cli package

CLI package, home to the individual entry points

cellsium.cli.Cell

alias of SizerCell

class cellsium.cli.SizerCell(**kwargs)

Bases: PlacedCell, SizerCell

Cell.

class cellsium.cli.TimerCell(**kwargs)

Bases: PlacedCell, TimerCell

Cell.

cellsium.cli.add_output_prefix(output_name: str, output: Output) → str

Adds an prefix to an output filename.

Parameters:

• output_name – Output name

• output – Output object

Returns:

Name

cellsium.cli.initialize_cells(simulator: Simulator, count: int = 1, cell_type: Optional[PlacedCell] = None, sequence: Optional[Any] = None) → Simulator

Initialize cells and add them to a simulator.

Parameters:

• simulator – Simulator to add cells to.

• count – Count of cells to generate

• cell_type – cell type to use

• sequence – Random number sequence to use

Returns:

Simulator

cellsium.cli.initialize_simulator() → Simulator

Constructor helper for a simulator.

Returns:

Simulator instance

• cellsium.cli.render package
  • subcommand_argparser()
  • subcommand_main()
• cellsium.cli.simulate package
  • BoundariesFile
    • BoundariesFile.default
    • BoundariesFile.value
  • BoundariesScaleFactor
    • BoundariesScaleFactor.default
    • BoundariesScaleFactor.value
  • SimulationDuration
    • SimulationDuration.default
    • SimulationDuration.value
  • SimulationOutputFirstState
    • SimulationOutputFirstState.default
    • SimulationOutputFirstState.value
  • SimulationOutputInterval
    • SimulationOutputInterval.default
    • SimulationOutputInterval.value
  • SimulationTimestep
    • SimulationTimestep.default
    • SimulationTimestep.value
  • add_boundaries_from_dxf()
  • add_boundaries_from_tunables()
  • compose()
  • initialize_output_times_from_tunables()
  • measure_duration()
  • perform_outputs()
  • perform_simulation()
  • prepare_output_name()
  • subcommand_main()
• cellsium.cli.training package
  • TrainingCellCount
    • TrainingCellCount.default
    • TrainingCellCount.value
  • TrainingDataCount
    • TrainingDataCount.default
    • TrainingDataCount.value
  • TrainingImageHeight
    • TrainingImageHeight.default
    • TrainingImageHeight.value
  • TrainingImageWidth
    • TrainingImageWidth.default
    • TrainingImageWidth.value
  • subcommand_main()

cellsium.cli.cli module

CLI entrypoint.

cellsium.cli.cli.load_class_from_module(module_class: str, default_class_name: str) → type

cellsium.cli.cli.main(args: Optional[Iterable[str]] = None) → Optional[int]

Main entrypoint of the script, will redirect to various sub-scripts.

Parameters:

args – arguments, if not specified will be taken from sys.argv

Returns:

The return code of the individual subcommand

cellsium.cli.cli.parse_arguments_and_init(args: Iterable[str], parser_callback: Optional[Callable[[ArgumentParser], None]] = None) → Namespace

Basic setup (i.e. logging) and argument parsing.

Parameters:

• args – Arguments

• parser_callback – Additional callback to configure the argument parser

Returns:

Parsed arguments