Simulation

Recurring Arguments
Name	Type	Description
output_path	`Path`	Path of the stored results.
iteration	`int`	Iteration count at which to obtain results.
element_path	`str`	Identifier which should be “cell_storage” or “voxel_storage”
threads	`int`	Number of threads to use simultaneously.
iteration	`int`	Iteration count at which to obtain results.

calculate_entropy(output_path, iteration) → ndarray

Obtain entropies for both species.

Parameters:

Returns:

Array containing entropy values for both species.

Return type:

np.ndarray

calculate_spatial_density(data, domain, weights=None)

Calculates the spatial entry given data for cells and domain.

Parameters:

data (pd.DataFrame) – DataFrame containing cellular properties.
domain (pd.DataFrame) – DataFrame containing domain properties.
weights (list) – List of weightings to use for calculating the entropy. Will be filled
provided. (automatically by the volume of the individual cells if not)

generate_cells(n_cells_1, n_cells_2, domain, randomness=0.0, pad=0.15, seed=0, homogenous=False): n_cells_1: int n_cells_2: int uniformity: float

Floating point number between 0.0 and 1.0

get_all_iterations(output_path, element_path='cell_storage')

Obtain a sorted list of all saved iteration counts.

Parameters:

output_path (Path) – Path of the stored results.
element_path (str) – Identifier which should be “cell_storage” or “voxel_storage”

Returns:

Sorted list of iteration counts.

Return type:

list[int]

get_elements_at_all_iterations(output_path: Path, element_path='cell_storage', threads=1)

Parameters:

output_path (Path) – Path of the stored results.
element_path (str) – Identifier which should be “cell_storage” or “voxel_storage”
threads (int) – Number of threads to use simultaneously.

Returns:

get_elements_at_iter(output_path: Path, iteration, element_path='cell_storage') → DataFrame

Helper function to obtain information about cells or the domain at a given iteration point.

Parameters:

output_path (Path) – Path of the stored results.
iteration (int) – Iteration count at which to obtain results.
element_path (str) – Identifier which should be “cell_storage” or “voxel_storage”

Returns:

DataFrame containing all information

Return type:

pd.DataFrame

get_last_output_path(name='pool_model', prefix='out') → Path

Returns the path of the last numerical result.

get_simulation_settings(output_path) → tuple[Any, Any, Any]

Obtain simulation settings for a given output path.

Parameters:: output_path (Path) – Path of the stored results.
Returns:: A tuple containing json results of the domain, initial cells and meta parameters.
Return type:: (Any, Any, Any)