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.placement package
  • Box2D
    • Box2D.add()
    • Box2D.add_boundary()
    • Box2D.remove()
    • Box2D.step()
    • Box2D.verbose
  • Chipmunk
    • Chipmunk.add()
    • Chipmunk.add_boundary()
    • Chipmunk.clear()
    • Chipmunk.convergence_check_interval
    • Chipmunk.inner_step()
    • Chipmunk.look_back_threshold
    • Chipmunk.remove()
    • Chipmunk.step()
    • Chipmunk.verbose
  • PlacementSimulation
  • cellsium.simulation.placement.pybox2d module
    • Box2D
      • Box2D.add()
      • Box2D.add_boundary()
      • Box2D.remove()
      • Box2D.step()
      • Box2D.verbose
  • cellsium.simulation.placement.base module
    • NoPlacement
    • PhysicalPlacement
      • PhysicalPlacement.clear()
    • PlacementSimulation
    • PlacementSimulationSimplification
      • PlacementSimulationSimplification.default
      • PlacementSimulationSimplification.value
    • ensure_python()
  • cellsium.simulation.placement.pymunk module
    • Chipmunk
      • Chipmunk.add()
      • Chipmunk.add_boundary()
      • Chipmunk.clear()
      • Chipmunk.convergence_check_interval
      • Chipmunk.inner_step()
      • Chipmunk.look_back_threshold
      • Chipmunk.remove()
      • Chipmunk.step()
      • Chipmunk.verbose
    • ChipmunkPlacementRadius
      • ChipmunkPlacementRadius.default
      • ChipmunkPlacementRadius.value

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

step(timestep: float = 0.0) → Timestep

Advance the simulation by a timestep.

Parameters:

timestep – Time passed in seconds

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

property world: World

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

copy() → World

Creates a copy of thw World.

Returns:

Copy of the World

remove(cell: object) → None

Removes a cell from the world.

Parameters:

cell – Cell

Returns:

None