deepof.arena_utils.get_arenas

deepof.arena_utils.get_arenas(coordinates: deepof_project | deepof_coordinates, arena: str, arena_dims: int, number_of_rois: int, segmentation_model_path: str, video_path: str, videos: list | None = None, test: bool = False, roi_dicts: dict | None = None, arena_params: dict | None = None, edit_tag: str = '', scales: dict | None = None)

Extract arena parameters from a project or coordinates object.

Parameters:

  • coordinates (coordinates) – Coordinates object.

  • tables (table_dict) – TableDict object containing tracklets per animal.

  • arena (str) – Arena type (must be either “polygonal-manual”, “circular-manual”, “polygonal-autodetect”, or “circular-autodetect”).

  • arena_dims (int) – Arena dimensions.

  • number_of_rois (int) – number of behavior rois,

  • segmentation_model_path (str) – Path to segmentation model used for automatic arena detection.

  • video_path (str) – Path to folder with videos.

  • videos (dict) – Dictionary of videos to extract arena parameters from. Defaults to None (all videos are used).

  • debug (bool) – If True, a frame per video with the detected arena is saved. Defaults to False.

  • edit_tag (str) – optional affix for arena or roi name to prevent overwriting of existing images.

  • test (bool) – If True, the function is run in test mode. This means that instead of waiting for user-inputs fixed artifical user-inputs are used. Defaults to False.

Returns:

Dictionary of scaling information. Each scales object consists of:

  • x position of the center of arena in mm

  • y position of the center of the arena in mm

  • diameter of the arena (when circular) or length of first edge in pixels

  • diameter of the arena (when circular) or length of first edge in mm

arena_params (dict): Dictionary of arena parameters. Each arena parameter object consists of:

(when circular) - x position of the center of arena in pixel - y position of the center of the arena in pixel - x axis radii of the arena in pixel - y axis radii of the arena in pixel - angle of the elipse (when polygonal) - x and y positions of the polygon vertices in pixel

video_resolution (dict): Dictionary of video resolutions. Each video resolution object consists of:

  • height of the video in pixel

  • width of the video in pixel

Return type:

scales (dict)