metrics.analysis.simulation module

class Simulation(simulation_file: str)[source]

Bases: object

Container for simulated tumor object data.

file: Path and file name for the simulation file.

path: Directory to the folder of simulation file.

key: File name without extension or seed.

seed: Seed of the simulation.

extension: Extension of the simulation file.

timepoints: Time point(s) (in days) in the simulation file.

max_radius: Maximum radius of the simulation.

static get_feature_list() → List[metrics.feature.feature.Feature][source]

Return a list of valid Feature objects.

Returns: List of Feature objects.

static get_feature_object(feature_name: str) → Union[metrics.feature.continuous_feature.ContinuousFeature, metrics.feature.discrete_feature.DiscreteFeature][source]

Return feature object valid for statistics calculation.

Parameters: feature_name – Name of feature.
Returns: Feature object.

static get_szudzik_pair(u: int, v: int) → float[source]

Convert positions with positive or negative UV coordinates into a coordinate ID with signed Szudzik pairing function. A pairing function on a set associates each pair of numbers with a unique number through mathematical functions.

Parameters

u – U coordinate of the position.
v – V coordinate of the position.

Returns

The unique ID of the position coordinate.

load_simulation(suffix: str = '') → dict[source]

Load simulation file into memory.

Parameters: suffix – Suffix of the file.
Returns: Loaded simulation file.

parse_config() → None[source]: Parse out attributes from loaded simulation file.

parse_file() → None[source]: Parse out attributes from file name.

parse_timepoint(timepoint: float) → pandas.core.frame.DataFrame[source]

Parse data from simulation.

Parameters: timepoint – Time point to parse simulation.
Returns: Dataframe with simulation data.