simulation.readdy.loader

Class for loading and shaping ReaDDy trajectories.

Classes

ReaddyLoader

Load and shape data from a ReaDDy trajectory.

class ReaddyLoader

Load and shape data from a ReaDDy trajectory.

Trajectory is loaded from the simulation output h5 file of the .dat pickle file. If a .dat pickle location and key are provided, the loaded trajectory is saved to the given location for faster reloads.

__init__(h5_file_path: str, min_time_ix: int = 0, max_time_ix: int = -1, time_inc: int = 1, timestep: float = 100.0, pickle_location: str | None = None, pickle_key: str | None = None)

h5_file_path: str

Path to the ReaDDy .h5 file or .dat pickle file.

min_time_ix: int

First time index to include.

max_time_ix: int

Last time index to include.

time_inc: int

Include every time_inc timestep.

timestep: float

Real time for each simulation timestep.

pickle_location: str | None

Location to save pickle file (AWS S3 bucket or local path).

pickle_key: str | None

Name of pickle file (AWS S3 bucket or local path).

readdy_trajectory() → readdy.Trajectory

Lazy load the ReaDDy trajectory object.

Note that loading ReaDDy trajectories requires a path to a local file. Loading currently does not support S3 locations.

Returns:

The ReaDDy trajectory object.

trajectory() → list[FrameData]

Lazy load the shaped trajectory.

Returns:

The trajectory of data shaped for analysis.