convert_to_simularium_objects

convert_to_simularium_objects(series_key: str, simulation_type: str, categories: DataFrame, regions: list[str], frame_spec: tuple[int, int, int], box: tuple[int, int, int], ds: tuple[float, float, float], dt: float, colors: dict[str, str], group_size: int, url: str, jitter: float = 1.0) → str

Convert data to Simularium trajectory using mesh objects.

Parameters:

• series_key – Simulation series key.

• simulation_type ({'potts'}) – Simulation type.

• categories – Simulation data containing ID, FRAME, and CATEGORY.

• regions – List of regions.

• frame_spec – Specification for simulation ticks.

• box – Size of bounding box.

• ds – Spatial scaling in um/voxel.

• dt – Temporal scaling in hours/tick.

• colors – Map of category to colors.

• group_size – Number of objects in each mesh group.

• url – URL for mesh object files.

• jitter – Relative jitter applied to colors (set to 0 for exact colors).

Returns:

Simularium trajectory.

format_potts_for_objects(categories: DataFrame, frames: list[int], group_size: int, regions: list[str], length: int, width: int, height: int) → DataFrame

Format potts simulation data for object-based Simularium trajectory.

Parameters:

• categories – Simulation data containing ID, FRAME, and CATEGORY.

• frames – List of frames.

• group_size – Number of objects in each mesh group.

• regions – List of regions.

• length – Length of bounding box.

• width – Width of bounding box.

• height – Height of bounding box.

Returns:

Data formatted for trajectory.