cellsium.simulation package
Simulation package contains the simulation/simulator-related classes.
- class cellsium.simulation.BaseSimulator
Bases:
object
- add(cell: object) None
Add a cell to the simulation.
- Parameters
cell – Cell
- Returns
None
- add_boundary(coordinates: ndarray) None
Add a boundary to the simulation.
- Parameters
coordinates – Coordinates of the boundary
- Returns
None
- clear() None
Clear the (world of the) simulation.
- Returns
None
- remove(cell) None
Remove a cell from the simulation.
- Parameters
cell – Cell
- Returns
None
- step(timestep: float) None
Advance the simulation by a timestep.
- Parameters
timestep – Time passed in seconds
- Returns
None
cellsium.simulation.simulator module
Simulator base classes.
- class cellsium.simulation.simulator.Simulation
Bases:
object
Simulation represents the simulation state at a certain timepoint, i.e. a World and a time.
- class cellsium.simulation.simulator.Simulator
Bases:
BaseSimulator
Simulator class, a class serving as interface to World and sub-simulators (such as physical placement), as well as the caller of each cells step function.
- add(cell: object) None
Add a cell to the simulation.
- Parameters
cell – Cell
- Returns
None
- add_boundary(coordinates: ndarray) None
Add a boundary to the simulation.
- Parameters
coordinates – Coordinates of the boundary
- Returns
None
- clear() None
Clear the (world of the) simulation.
- Returns
None
- remove(cell: object) None
Remove a cell from the simulation.
- Parameters
cell – Cell
- Returns
None
- class cellsium.simulation.simulator.Timestep(timestep: float, simulation: Simulation, simulator: Simulator)
Bases:
object
Timestep is an auxiliary class combining a certain timepoint, simulation and simulator.
- property hours: float
The hours passed within this timestep.
- Returns
Hours
- simulation
- simulator
- property time: float
Total simulation time passed in seconds.
- Returns
Seconds
- property time_hours: float
Total simulation time passed in hours.
- Returns
Hours
- timestep
- class cellsium.simulation.simulator.World
Bases:
object
The World class contains the cells and, if present, the boundaries.
- add(cell: object) None
Adds a cell to the World.
- Parameters
cell – Cell
- Returns
None
- add_boundary(coordinates: ndarray) None
Add a boundary to the simulation.
- Parameters
coordinates – Coordinates of the boundary.
- Returns
None
- clear() None
Resets the World.
- Returns
None
- commit() None
Commits a step. Cells to be added, and cells to be removed, will only be applied once commit is called.
- Returns
None
- remove(cell: object) None
Removes a cell from the world.
- Parameters
cell – Cell
- Returns
None