simulation.cytosim.post_processing

Methods for processing Cytosim simulations.

Module Attributes

COLUMN_NAMES	Parsed tidy data column names.
COLUMN_DTYPES	Parsed tidy data column data types.
CYTOSIM_SCALE_FACTOR	Default Cytosim position scaling factor.
CYTOSIM_RIGIDITY	Default Cytosim rigidity.

Functions

parse_cytosim_simulation_curvature_data(data)	Parse Cytosim fiber segment curvature data into tidy data format.
parse_cytosim_simulation_data(bucket, ...)	Parse Cytosim simulation data for select conditions and seeds.

COLUMN_NAMES: list[str] = ['fiber_id', 'xpos', 'ypos', 'zpos', 'xforce', 'yforce', 'zforce', 'segment_curvature', 'time', 'fiber_point']

Parsed tidy data column names.

COLUMN_DTYPES: dict[str, type[float] | type[int]] = {'fiber_id': <class 'int'>, 'fiber_point': <class 'int'>, 'segment_curvature': <class 'float'>, 'time': <class 'float'>, 'xforce': <class 'float'>, 'xpos': <class 'float'>, 'yforce': <class 'float'>, 'ypos': <class 'float'>, 'zforce': <class 'float'>, 'zpos': <class 'float'>}

Parsed tidy data column data types.

CYTOSIM_SCALE_FACTOR: int = 1000

Default Cytosim position scaling factor.

CYTOSIM_RIGIDITY: float = 0.041

Default Cytosim rigidity.

parse_cytosim_simulation_data(bucket: str, series_name: str, condition_keys: list[str], random_seeds: list[int]) → None

Parse Cytosim simulation data for select conditions and seeds.

Parameters:

• bucket – Name of S3 bucket for input and output files.

• series_name – Name of simulation series.

• condition_keys – List of condition keys.

• random_seeds – Random seeds for simulations.

parse_cytosim_simulation_curvature_data(data: str, rigidity: float = 0.041, scale_factor: int = 1000) → DataFrame

Parse Cytosim fiber segment curvature data into tidy data format.

Parameters:

• data – Output data from Cytosim report fiber:segment_energy.

• rigidity – Fiber rigidity used to calculate segment energy.

• scale_factor – Scaling factor for fiber points.

Returns:

Data for individual fiber points.