Datatypes

This module contains storage solutions for information about cellular history and their relations.

Cellular History and Relations
Method	Description
`CellContainer.get_cells()`	All simulation snapshots
`CellContainer.get_cells_at_iteration()`	Simulation snapshot at iteration
`CellContainer.get_cell_history()`	History of one particular cell
`CellContainer.get_all_identifiers()`	Get all identifiers of all cells
`CellContainer.get_all_identifiers_unsorted()`	Get all identifiers (unsorted)
`CellContainer.get_parent_map()`	Maps a cell to its parent.
`CellContainer.get_child_map()`	Maps each cell to its children.
`CellContainer.get_parent()`	Get parent of a cell
`CellContainer.get_children()`	Get all children of a cell
`CellContainer.cells_are_siblings()`	Check if two cells have the same parent

class CellContainer(all_cells)

Bases: object

Manages all information resulting from an executed simulation

cell_identifier_to_counter(identifier): Get the CellIdentifier associated to the given counter. Used in cr_mech_coli.imaging techniques.

cells_are_siblings(ident1, ident2): Determines if two cells share a common parent

counter_to_cell_identifier(counter)

Obtains the cell corresponding to the given counter of this simulation Used in cr_mech_coli.imaging techniques.

Parameters:: counter (int) – Counter of some cell
Returns:: The unique identifier associated with this counter
Return type:: CellIdentifier

get_all_identifiers(): Returns all CellIdentifier used in the simulation sorted in order.

get_all_identifiers_unsorted(): Identical to CellContainer.get_all_identifiers() but returns unsorted list.

get_all_iterations(): Obtain all iterations as a sorted list.

get_cell_from_color(color)

Obtains the cell which had been assigned this color

Parameters:: color (tuple[int, int, int]) – A tuple (or list) with 3 8bit values
Returns:: The identifier of the cell
Return type:: CellIdentifier | None

get_cell_history(identifier)

Load the history of a single cell

Parameters:: identifier (CellIdentifier) – The identifier of the cell in question
Returns:: A dictionary with all timespoints and the cells confiruation at this time-point. Also returns the parent CellIdentifier if present.
Return type:: tuple[dict[int, PyObject], CellIdentifier | None]

get_cells()

Get all cells at all iterations

Returns:: A dictionary containing all cells with their identifiers, values and possible parent identifiers for every iteration.
Return type:: dict[int, dict[CellIdentifier, tuple[PyObject, CellIdentifier | None]]

get_cells_at_iteration(iteration)

Get cells at a specific iteration.

Parameters:

iteration (int) – Positive integer of simulation step iteration.

Returns:

A dictionary mapping identifiers to the cell and its possible parent.

Return type:

cells (dict)

Raises:

SimulationError – Generic error related to cellular_raza
if any of the internal methods returns an error. –

get_child_map(): A dictionary mapping each cell to its children

get_children(identifier)

Obtains all children of a given cell

Parameters:: identifier (CellIdentifier) – The cells unique identifier
Returns:: All children of the given cell
Return type:: list[CellIdentifier]

get_color(identifier)

Obtains the color assigned to the cell

Parameters:: identifier (CellIdentifier) – The cells unique identifier
Returns:: The assigned color
Return type:: tuple[int, int, int] | None

get_parent(identifier)

Obtains the parent identifier of a cell if it had a parent.

Parameters:: identifier (CellIdentifier) – The cells unique identifier
Returns:: The parents identifier or None
Return type:: CellIdentifier | None

get_parent_map(): A dictionary mapping each cell to its parent

cell_to_color: Maps each cell to its color

cells: Contains snapshots of all cells at each saved step

child_map: Maps each cell to its children

color_to_cell: Maps each color back to its cell

parent_map: Maps each cell to its parent if existent

class CellIdentifier(voxel_plain_index, counter)

Bases: object

Unique identifier which is given to every cell in the simulation

The identifier is comprised of the [VoxelPlainIndex] in which the cell was first spawned. This can be due to initial setup or due to other methods such as division in a cell cycle. The second parameter is a counter which is unique for each voxel. This ensures that each cell obtains a unique identifier over the course of the simulation.

copy(): Returns an identical clone of the identifier