organoid_tracker.imaging.list_io module

Often, multiple experiments are used together for a certain analysis. You can save the path to where these experiments are stored in an autlist file. This module contains functions to save and load Used to load multiple experiments (with images) at once.

organoid_tracker.imaging.list_io.count_experiments_in_list_file(open_files_list_file: str) → int

Counts the number of experiments in the given file. Used as a quick way to get that number, instead of loading everything.

organoid_tracker.imaging.list_io.load_experiment_list_file(open_files_list_file: str, *, load_images: bool = True, min_time_point: int = - 100000000, max_time_point: int = 100000000) → Iterable[Experiment]

Loads all the listed files in the given file..

organoid_tracker.imaging.list_io.save_experiment_list_file(experiments: List[Experiment], json_file_name: str, *, tracking_files_folder: Optional[str] = None, append_to_file: bool = False) → None

Saves references to the given experiments to a file.

If a folder has been specified for tracking_files_folder, the experiments will be saved to that folder.

Otherwise, the file will reference the current location where the tracking files are stored, taken from experiment.last_save_file. This method does not check for unsaved changes in the experiments. Raises ValueError if the experiment contains positions or splines, but no value for experiment.last_save_file. For an interactive version where the user is prompted to save unsaved changes, see action.to_experiment_list_file_structure(…).

When saving many experiments at once, it can become expensive to keep them all in memory. In that case, you can save them one by one to the list file, by setting append_to_file=True. For the first iteration though, make sure that the file does not exist yet or that you set append_to_file=False, otherwise the old file will keep on growing.