pangeo_fish.helpers.predict_positions

pangeo_fish.helpers.predict_positions#

pangeo_fish.helpers.predict_positions(*, ds: Dataset | None = None, target_root: str | None = None, storage_options: dict, chunks: dict, track_modes=['mean', 'mode'], additional_track_quantities=['speed', 'distance'], save=True, **kwargs)#

High-level helper function for predicting fish’s positions and generating the consequent trajectories. It futhermore saves the latter under states.zarr and trajectories.parq.

Warning

target_root must not end with “/”.

Parameters:

  • target_root (str) – Path to a folder that must contain a folder combined.zarr and the file parameters.json

  • storage_options (dict) – Additional information for xarray to open the .zarr array

  • chunks (dict) – Chunk size to load the xarray.Dataset combined.zarr

  • track_modes (list of str, default: [``”mean”, ``"mode"]) – Options for decoding trajectories.

  • additional_track_quantities (list of str, default: [``”speed”, ``"distance"]) – Additional quantities to compute from the decoded tracks.

  • save (bool, default: True) – Whether to save the states distribution and the trajectories.

Returns:

See also

pangeo_fish.hmm.estimator.EagerEstimator.decode