cellsium.simulation.placement package

Placement simulation package, contains the placement simulators.

class cellsium.simulation.placement.Box2D(*args, **kwargs)

Bases: PhysicalPlacement, PlacementSimulation

add(cell: PlacedCell) → 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

remove(cell: PlacedCell) → 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

verbose: bool = False

class cellsium.simulation.placement.Chipmunk(*args, **kwargs)

Bases: PhysicalPlacement, PlacementSimulation, Default

add(cell: PlacedCell) → 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

convergence_check_interval: int = 15

inner_step(time_step: float = 0.1, iterations: int = 9999, converge: bool = True, epsilon: float = 0.1) → float

look_back_threshold: int = 5

remove(cell: PlacedCell) → 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

verbose: bool = False

class cellsium.simulation.placement.PlacementSimulation(*args, **kwargs): Bases: BaseSimulator, Selectable

cellsium.simulation.placement.pybox2d module

Placement simulation using Box2D physics engine.

class cellsium.simulation.placement.pybox2d.Box2D(*args, **kwargs)

Bases: PhysicalPlacement, PlacementSimulation

add(cell: PlacedCell) → 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

remove(cell: PlacedCell) → 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

verbose: bool = False

cellsium.simulation.placement.base module

class cellsium.simulation.placement.base.NoPlacement(*args, **kwargs): Bases: PlacementSimulation

class cellsium.simulation.placement.base.PhysicalPlacement(*args, **kwargs)

Bases: PlacementSimulation, Virtual

clear() → None

Clear the (world of the) simulation.

Returns:: None

class cellsium.simulation.placement.base.PlacementSimulation(*args, **kwargs): Bases: BaseSimulator, Selectable

class cellsium.simulation.placement.base.PlacementSimulationSimplification(*args, **kwargs)

Bases: Tunable

How much the placement should be simplified, 0: use the normal shapes, 1: use simplified shapes, 2: use many-circle approximations

default: int = 0

value = 0

cellsium.simulation.placement.base.ensure_python(value: Any) → Any

cellsium.simulation.placement.pymunk module

Placement simulation using Pymunk physics engine.

class cellsium.simulation.placement.pymunk.Chipmunk(*args, **kwargs)

Bases: PhysicalPlacement, PlacementSimulation, Default

add(cell: PlacedCell) → 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

convergence_check_interval: int = 15

inner_step(time_step: float = 0.1, iterations: int = 9999, converge: bool = True, epsilon: float = 0.1) → float

look_back_threshold: int = 5

remove(cell: PlacedCell) → 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

verbose: bool = False

class cellsium.simulation.placement.pymunk.ChipmunkPlacementRadius(*args, **kwargs)

Bases: Tunable

Chipmunk placement radius, additional radius objects will have around them

default: float = 0.05

value = 0.05